bioRxiv Channel: Johns Hopkins University https://biorxiv.org This feed contains articles for bioRxiv Channel "Johns Hopkins University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Functional normalization of 450k methylation array data improves replication in large cancer studies ]]> https://biorxiv.org/content/10.1101/002956v1?rss=1 Jean-Philippe Fortin Aurelie Labbe Mathieu Lemire Brent W. Zanke Thomas J. Hudson Elana J. Fertig Celia M.T. Greenwood Kasper D. Hansen 2014-02-23 doi:10.1101/002956 Cold Spring Harbor Laboratory Press 2014-02-23 <![CDATA[ Flexible analysis of transcriptome assemblies with Ballgown ]]> https://biorxiv.org/content/10.1101/003665v1?rss=1 Alyssa C Frazee Geo Pertea Andrew E Jaffe Ben Langmead Steven L Salzberg Jeffrey T Leek 2014-03-30 doi:10.1101/003665 Cold Spring Harbor Laboratory Press 2014-03-30 <![CDATA[ The Evolution of Power and the Divergence of Cooperative Norms ]]> https://biorxiv.org/content/10.1101/004416v1?rss=1 Michael D Makowsky Paul E Smaldino 2014-04-24 doi:10.1101/004416 Cold Spring Harbor Laboratory Press 2014-04-24 <![CDATA[ Lighter: fast and memory-efficient error correction without counting ]]> https://biorxiv.org/content/10.1101/005579v1?rss=1 Li Song Liliana Florea Ben Langmead 2014-05-27 doi:10.1101/005579 Cold Spring Harbor Laboratory Press 2014-05-27 <![CDATA[ Polyester: simulating RNA-seq datasets with differential transcript expression ]]> https://biorxiv.org/content/10.1101/006015v1?rss=1 Alyssa C Frazee Andrew E Jaffe Ben Langmead Jeffrey Leek 2014-06-06 doi:10.1101/006015 Cold Spring Harbor Laboratory Press 2014-06-06 <![CDATA[ Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space ]]> https://biorxiv.org/content/10.1101/007641v1?rss=1 >> ]]> Richard Wilton Tamas Budavari Ben Langmead Sarah J Wheelan Steven Salzberg Alex Szalay 2014-08-01 doi:10.1101/007641 Cold Spring Harbor Laboratory Press 2014-08-01 <![CDATA[ HiFive: a tool suite for easy and efficient HiC and 5C data analysis ]]> https://biorxiv.org/content/10.1101/009951v1?rss=1 Michael EG Sauria Jennifer E Phillips-Cremins Victor G Corces James Taylor 2014-10-03 doi:10.1101/009951 Cold Spring Harbor Laboratory Press 2014-10-03 <![CDATA[ Sharing and specificity of co-expression networks across 35 human tissues ]]> https://biorxiv.org/content/10.1101/010843v1?rss=1 Emma Pierson GTEx Consortium Daphne Koller Alexis Battle Sara Mostafavi 2014-10-29 doi:10.1101/010843 Cold Spring Harbor Laboratory Press 2014-10-29 <![CDATA[ Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes ]]> https://biorxiv.org/content/10.1101/010884v1?rss=1 Dmitri Pervouchine Sarah Djebali Alessandra Breschi Carrie A Davis Pablo Prieto Barja Alex Dobin Andrea Tanzer Julien Lagarde Chris Zaleski Lei-Hoon See Meagan Fastuca Jorg Drenkow Huaien Wang Giovanni Bussotti Baikang Pei Suganthi Balasubramanian Jean Monlong Arif Harmanci Mark Gerstein Michael A Beer Cedric Notredame Roderic Guigo Thomas R Gingeras 2014-10-30 doi:10.1101/010884 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ Genome-wide comparative analysis reveals human- mouse regulatory landscape and evolution ]]> https://biorxiv.org/content/10.1101/010926v1?rss=1 Olgert Denas Richard Sandstrom Yong Cheng Kathryn Beal Javier Herrero Ross Hardison James Taylor 2014-10-30 doi:10.1101/010926 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ CLASS: Accurate and Efficient Splice Variant Annotation from RNA-seq Reads ]]> https://biorxiv.org/content/10.1101/011718v1?rss=1 Li Song Sarven Sabunciyan Liliana D Florea 2014-11-20 doi:10.1101/011718 Cold Spring Harbor Laboratory Press 2014-11-20 <![CDATA[ SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing ]]> https://biorxiv.org/content/10.1101/011833v1?rss=1 Noushin Niknafs Violeta Beleva Guthrie Daniel Q Naiman Rachel Karchin 2014-11-26 doi:10.1101/011833 Cold Spring Harbor Laboratory Press 2014-11-26 <![CDATA[ HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts ]]> https://biorxiv.org/content/10.1101/012591v1?rss=1 Daehwan Kim Ben Langmead Steven Salzberg 2014-12-12 doi:10.1101/012591 Cold Spring Harbor Laboratory Press 2014-12-12 <![CDATA[ Different DNA repair pathways are required following excision and integration of the DNA cut &amp; paste transposon piggyBat in Saccharomyces cerevisiae. ]]> https://biorxiv.org/content/10.1101/015289v1?rss=1 Weifeng She Courtney Busch Cambouris Nancy L. Craig 2015-02-17 doi:10.1101/015289 Cold Spring Harbor Laboratory Press 2015-02-17 <![CDATA[ Flexible expressed region analysis for RNA-seq with derfinder ]]> https://biorxiv.org/content/10.1101/015370v1?rss=1 Leonardo Collado Torres Abhinav Nellore Alyssa C Frazee Christopher Wilks Michael I Love Ben Langmead Rafael A Irizarry Jeffrey Leek Andrew E Jaffe 2015-02-19 doi:10.1101/015370 Cold Spring Harbor Laboratory Press 2015-02-19 <![CDATA[ Spatial model predicts dispersal and cell turnover cause reduced intra-tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/016824v1?rss=1 Bartlomiej Waclaw Ivana Bozic Meredith E Pittman Ralph H Hruban Bert Vogelstein Martin A Nowak 2015-03-20 doi:10.1101/016824 Cold Spring Harbor Laboratory Press 2015-03-20 <![CDATA[ Choosing subsamples for sequencing studies by minimizing the average distance to the closest leaf ]]> https://biorxiv.org/content/10.1101/017822v1?rss=1 Jonathan T. L. Kang Peng Zhang Sebastian Zöllner Noah A. Rosenberg 2015-04-09 doi:10.1101/017822 Cold Spring Harbor Laboratory Press 2015-04-09 <![CDATA[ Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq ]]> https://biorxiv.org/content/10.1101/018085v1?rss=1 Ben Busby Allissa Dillman Claire L. Simpson Ian Fingerman Sijung Yun David M. Kristensen Lisa Federer Naisha Shah Matthew C. LaFave Laura Jimenez-Barron Manusha Pande Wen Luo Brendan Miller Cem Mayden Dhruva Chandramohan Kipper Fletez-Brant Paul W. Bible Sergej Nowoshilow Alfred Chan Eric JC Galvez Jeremy Chignell Joseph N. Paulson Manoj Kandpal Suhyeon Yoon Esther Asaki Abhinav Nellore Adam Stine Robert Sanders Jesse Becker Matt Lesko Mordechai Abzug Eugene Yaschenko 2015-04-16 doi:10.1101/018085 Cold Spring Harbor Laboratory Press 2015-04-16 <![CDATA[ Big city, small world: Density, contact rates, and transmission of dengue across Pakistan. ]]> https://biorxiv.org/content/10.1101/018481v1?rss=1 Moritz U. G. Kraemer T. Alex Perkins Derek A.T. Cummings Rubeena Zakar Simon I. Hay David L. Smith Robert C. Reiner 2015-04-27 doi:10.1101/018481 Cold Spring Harbor Laboratory Press 2015-04-27 <![CDATA[ Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns ]]> https://biorxiv.org/content/10.1101/018648v1?rss=1 Tychele Turner Christopher Douville Dewey Kim Peter D Stenson David N Cooper Aravinda Chakravarti Rachel Karchin 2015-04-27 doi:10.1101/018648 Cold Spring Harbor Laboratory Press 2015-04-27 <![CDATA[ Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1 ]]> https://biorxiv.org/content/10.1101/018911v1?rss=1 Daniel I S Rosenbloom Oliver Elliott Alison L Hill Timothy J Henrich Janet M Siliciano Robert F Siliciano 2015-05-03 doi:10.1101/018911 Cold Spring Harbor Laboratory Press 2015-05-03 <![CDATA[ Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data ]]> https://biorxiv.org/content/10.1101/019000v1?rss=1 Jean-Philippe Fortin Kasper D Hansen 2015-05-06 doi:10.1101/019000 Cold Spring Harbor Laboratory Press 2015-05-06 <![CDATA[ Rail-RNA: Scalable analysis of RNA-seq splicing and coverage ]]> https://biorxiv.org/content/10.1101/019067v1?rss=1 Abhinav Nellore Leonardo Collado-Torres Andrew E Jaffe José Alquicira-Hernández Jacob Pritt James Morton Jeffrey T Leek Ben Langmead 2015-05-07 doi:10.1101/019067 Cold Spring Harbor Laboratory Press 2015-05-07 <![CDATA[ PIK3CA Mutational Analysis in Formalin-Fixed, Paraffin-Embedded Archival Tissues of Urothelial Carcinoma of Urinary Bladder ]]> https://biorxiv.org/content/10.1101/020263v1?rss=1 Alcides Chaux Julie S. Cohen Luciana Schultz Roula Albadine Sana Jadallah Kathleen M. Murphy Diana Teheri Mark P. Schoenberg George J. Netto 2015-06-01 doi:10.1101/020263 Cold Spring Harbor Laboratory Press 2015-06-01 <![CDATA[ Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis ]]> https://biorxiv.org/content/10.1101/025346v1?rss=1 David Ellison Andrew Mugler Matthew Brennan Sung Hoon Lee Robert Huebner Eliah Shamir Laura A Woo Joseph Kim Patrick Amar Ilya Nemenman Andrew J Ewald Andre Levchenko 2015-08-23 doi:10.1101/025346 Cold Spring Harbor Laboratory Press 2015-08-23 <![CDATA[ Allele-specific expression reveals interactions between genetic variation and environment ]]> https://biorxiv.org/content/10.1101/025874v1?rss=1 David A Knowles Joe R Davis Anil Raj Xiaowei Zhu James B Potash Myrna M Weissman Jianxin Shi Douglas F Levinson Sara Mostafavi Stephen B Montgomery Alexis Battle 2015-09-01 doi:10.1101/025874 Cold Spring Harbor Laboratory Press 2015-09-01 <![CDATA[ Crucial Roles of the Arp2/3 Complex during Mammalian Corticogenesis ]]> https://biorxiv.org/content/10.1101/026161v1?rss=1 Pei-Shan Wang Fu-Sheng Chou Fengli Guo Praveen Suraneni Sheng Xia Sree Ramachandran Rong Li 2015-09-06 doi:10.1101/026161 Cold Spring Harbor Laboratory Press 2015-09-06 <![CDATA[ Nanopore sequencing detects structural variants in cancer ]]> https://biorxiv.org/content/10.1101/028290v1?rss=1 Alexis L. Norris Rachael E. Workman Yunfan Fan James R. Eshleman Winston Timp 2015-10-04 doi:10.1101/028290 Cold Spring Harbor Laboratory Press 2015-10-04 <![CDATA[ Transcriptome Analysis of Cortical Tissue Reveals Shared Sets of Down-Regulated Genes in Autism and Schizophrenia ]]> https://biorxiv.org/content/10.1101/029132v1?rss=1 Shannon E Ellis Rebecca Panitch Andrew West Dan E Arking 2015-10-14 doi:10.1101/029132 Cold Spring Harbor Laboratory Press 2015-10-14 <![CDATA[ Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community ]]> https://biorxiv.org/content/10.1101/029934v1?rss=1 Alexander Crits-Christoph Diego R Gelsinger Bing Ma Jacek Wierzchos Jacques Ravel Alfonso Davila M. Cristina Casero Jocelyne DiRuggiero 2015-10-26 doi:10.1101/029934 Cold Spring Harbor Laboratory Press 2015-10-26 <![CDATA[ Stochastic Models for Population Dynamics ]]> https://biorxiv.org/content/10.1101/031237v1?rss=1 Sean Sun 2015-12-03 doi:10.1101/031237 Cold Spring Harbor Laboratory Press 2015-12-03 <![CDATA[ Nanopore Sequencing in Microgravity ]]> https://biorxiv.org/content/10.1101/032342v1?rss=1 Alexa B.R. McIntyre Lindsay Rizzardi Angela M Yu Gail L. Rosen Noah Alexander Douglas J. Botkin Kristen K. John Sarah L. Castro-Wallace Aaron S. Burton Andrew Feinberg Christopher E. Mason 2015-12-10 doi:10.1101/032342 Cold Spring Harbor Laboratory Press 2015-12-10 <![CDATA[ Phylogenetic and functional substrate specificity for endolithic microbial communities in hyper-arid environments ]]> https://biorxiv.org/content/10.1101/033340v1?rss=1 Alexander Crits-Christoph Courtney K Robinson Bing Ma Jacques Ravel Jacek Wierzchos Carmen Ascaso Octavio Artieda Virginia Souza-Egipsy M. Cristina Casero Jocelyne DiRuggiero 2015-12-01 doi:10.1101/033340 Cold Spring Harbor Laboratory Press 2015-12-01 <![CDATA[ Multiscale Modeling of Cancer ]]> https://biorxiv.org/content/10.1101/033977v1?rss=1 Kerri-Ann Norton Meghan M McCabe Pryor Aleksander S Popel 2015-12-08 doi:10.1101/033977 Cold Spring Harbor Laboratory Press 2015-12-08 <![CDATA[ Winners curse correction and variable thresholding improve performance of polygenic risk modeling based on summary-level data from genome-wide association studies ]]> https://biorxiv.org/content/10.1101/034082v1?rss=1 Jianxin Shi JuHyun Park Jubao Duan Sonja Berndt Winton Moy William Wheeler Xing Hua Debra Silverman Montserrat Garcia-Closas Chao Agnes Hsiung Jonine D. Figueroa Victoria K. Cortessis Nuria Malats Margaret R. Karagas Paolo Vineis I-Shou Chang Dongxin Lin Baosen Zhou Adeline Seow Keitaro Matsuo Yun-Chul Hong Neil E. Caporaso Brian Wolpin Eric Jacobs Gloria Petersen Donghui Li Harvey Risch Alan R. Sanders Li Hsu Robert E. Schoen Hermann Brenner Rachael Stolzenberg-Solomon Pablo Gejman Qing Lan Nathaniel Rothman Laufey T. Amundadottir Alison P. Klein Maria Teresa Landi Douglas F. Levinson Stephen 2016-01-10 doi:10.1101/034082 Cold Spring Harbor Laboratory Press 2016-01-10 <![CDATA[ A protein truncating R179X variant in RNF186 confers protection against ulcerative colitis ]]> https://biorxiv.org/content/10.1101/035105v1?rss=1 Manuel A Rivas Daniel Graham Patrick Sulem Christine Stevens Nicole Desch Philippe Goyette Daniel Gudbjartsson Ingileif Jonsdottir Unnur Thorsteinsdottir Frauke Degenhardt Soren Mucha Mitja I Kurki Dalin Li Mauro D'Amato Vito Annese Severine Vermeire Rinse Weersma Jonas Halfvarsson Paulina Paavola-Sakki Maarit Lappalainen Monkol Lek Beryl Cummings Taru Tukianen Talin Haritunians Leena Halme Lotta Koskinen Ashwin Ananthakrishnan Yang Luo Graham A Heap Marijn Visschedijk NIDDK IBD Genetics Consortium UK IBD Genetics Consortium Daniel G MacArthur Benjamin M Neale Tariq Ahmad Carl A Anderson Steve 2015-12-23 doi:10.1101/035105 Cold Spring Harbor Laboratory Press 2015-12-23 <![CDATA[ Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce ]]> https://biorxiv.org/content/10.1101/035287v1?rss=1 Abhinav Nellore Christopher Wilks Kasper D Hansen Jeffrey T Leek Ben Langmead 2015-12-24 doi:10.1101/035287 Cold Spring Harbor Laboratory Press 2015-12-24 <![CDATA[ Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression ]]> https://biorxiv.org/content/10.1101/035808v1?rss=1 Weiqiang Zhou Ben Sherwood Zhicheng Ji Fang Du Jiawei Bai Hongkai Ji 2016-01-01 doi:10.1101/035808 Cold Spring Harbor Laboratory Press 2016-01-01 <![CDATA[ Global Prediction of Chromatin Accessibility Using RNA-seq from Small Number of Cells ]]> https://biorxiv.org/content/10.1101/035816v1?rss=1 Weiqiang Zhou Zhicheng Ji Hongkai Ji 2016-01-01 doi:10.1101/035816 Cold Spring Harbor Laboratory Press 2016-01-01 <![CDATA[ Real-time predictions of reservoir size and rebound time during antiretroviral therapy interruption trials for HIV ]]> https://biorxiv.org/content/10.1101/038091v1?rss=1 Alison L Hill Daniel Scholes Rosenbloom Edward Goldstein Emily Hanhauser Daniel R Kuritzkes Robert F Siliciano Timothy J Henrich 2016-01-28 doi:10.1101/038091 Cold Spring Harbor Laboratory Press 2016-01-28 <![CDATA[ Human splicing diversity across the Sequence Read Archive ]]> https://biorxiv.org/content/10.1101/038224v1?rss=1 Abhinav Nellore Andrew E Jaffe Jean-Philippe Fortin José Alquicira-Hernández Leonardo Collado-Torres Siruo Wang Robert A Phillips Nishika Karbhari Kasper D Hansen Ben Langmead Jeffrey T Leek 2016-01-29 doi:10.1101/038224 Cold Spring Harbor Laboratory Press 2016-01-29 <![CDATA[ Information-dependent Enrichment Analysis Reveals Time-dependent Transcriptional Regulation of the Estrogen Pathway of Toxicity ]]> https://biorxiv.org/content/10.1101/038570v1?rss=1 Salil N. Pendse Alexandra Maertens Michael Rosenberg Dipanwita Roy Rick A. Fasani Marguerite M. Vantangoli Samantha J. Madnick Kim Boekelheide Albert J. Fornace James D. Yager Thomas Hartung Melvin E. Andersen Patrick D. McMullen 2016-02-04 doi:10.1101/038570 Cold Spring Harbor Laboratory Press 2016-02-04 <![CDATA[ Next-generation sequencing in neuropathological diagnosis of infections of the nervous system ]]> https://biorxiv.org/content/10.1101/039222v1?rss=1 Steven L. Salzberg Florian Breitwieser Anupama Kumar Haiping Hao Peter Burger Fausto J. Rodriguez Michael Lim Alfredo Quinones-Hinojosa Gary L. Gallia Jeffrey A. Tornheim Michael T. Melia Cynthia L. Sears Carlos A. Pardo 2016-02-09 doi:10.1101/039222 Cold Spring Harbor Laboratory Press 2016-02-09 <![CDATA[ Evaluation of Techniques for Performing Cellular Isolation and Preservation during Microgravity Conditions ]]> https://biorxiv.org/content/10.1101/040014v1?rss=1 Lindsay F Rizzardi Hawley Kunz Kathleen Rubins Alexander Chouker Heather Quiriarte Clarence Sams Brian Crucian Andrew P Feinberg 2016-02-19 doi:10.1101/040014 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects ]]> https://biorxiv.org/content/10.1101/040493v1?rss=1 Christian Marshall Daniel Howrigan Daniele Merico Bhooma Thiruvahindrapuram Wenting Wu Douglas Greer Daniel Antaki Aniket Shetty Peter Holmans Dalila Pinto Madhusudan Gujral William Brandler Dheeraj Malholtra Zhouzhi Wang Karin Fuentes Fajarado Stephan Ripke Ingrid Agartz Esben Agerbo Margot Albus Madeline Alexander Farooq Amin Joshua Atkins Silviu Bacanu Richard Belliveau Sarah Bergen Marcelo Bertalan Elizabeth Bevilacqua Tim Bigdeli Donald Black Richard Bruggeman Nancy Buccola Randy Buckner Brendan Bulik-Sullivan William Byerley Wiepke Cahn Guiqing Cai Murray Cairns Dominique Campion Rita Ca 2016-02-23 doi:10.1101/040493 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Boiler: Lossy compression of RNA-seq alignments using coverage vectors ]]> https://biorxiv.org/content/10.1101/040634v1?rss=1 Jacob Pritt Ben Langmead 2016-02-22 doi:10.1101/040634 Cold Spring Harbor Laboratory Press 2016-02-22 <![CDATA[ A Powerful Procedure for Pathway-based Meta-Analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations ]]> https://biorxiv.org/content/10.1101/041244v1?rss=1 Han Zhang William Wheeler Paula L Hyland Yifan Yang Jianxin Shi Nilanjan Chatterjee Kai Yu 2016-02-24 doi:10.1101/041244 Cold Spring Harbor Laboratory Press 2016-02-24 <![CDATA[ Regulating telomere length from the inside out: The replication fork model ]]> https://biorxiv.org/content/10.1101/041772v1?rss=1 Carol W Greider 2016-02-29 doi:10.1101/041772 Cold Spring Harbor Laboratory Press 2016-02-29 <![CDATA[ Times to Key Events in the Course of Zika Infection and their Implications for Surveillance: A Systematic Review and Pooled Analysis ]]> https://biorxiv.org/content/10.1101/041913v1?rss=1 Justin Lessler Cassandra T. Ott Andrea C. Carcelen Jacob M. Konikoff Joe Williamson Qifang Bi Nicholas G. Reich Derek A. T. Cummings Lauren M. Kucirka Lelia H. Chaisson 2016-03-02 doi:10.1101/041913 Cold Spring Harbor Laboratory Press 2016-03-02 <![CDATA[ Structural basis for acyl group discrimination by human Gcn5L2 ]]> https://biorxiv.org/content/10.1101/043364v1?rss=1 Alison E. Ringel Cynthia Wolberger 2016-03-11 doi:10.1101/043364 Cold Spring Harbor Laboratory Press 2016-03-11 <![CDATA[ Computational Pan-Genomics: Status, Promises and Challenges ]]> https://biorxiv.org/content/10.1101/043430v1?rss=1 Tobias Marschall Manja Marz Thomas Abeel Louis Dijkstra Bas E Dutilh Ali Ghaffaari Paul Kersey Wigard Kloosterman Veli Makinen Adam Novak Benedict Paten David Porubsky Eric RIVALS Can Alkan Jasmijn Baaijens Paul I. W. de Bakker Valentina Boeva Raoul J.P. Bonnal Francesca Chiaromonte Rayan Chikhi Francesca D. Ciccarelli Robin Cijvat Erwin Datema Cornelia M. Van Duijn Evan E. Eichler Corinna Ernst Eleazar Eskin Erik Garrison Mohammed El-Kebir Gunnar W. Klau Jan O Korbel Eric-Wubbo Lameijer Ben Langmead Marcel Martin Paul Medvedev John C. Mu Pieter Neerincx Klaasjan Ouwens Pierre Peterlongo Pisan 2016-03-12 doi:10.1101/043430 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/044412v1?rss=1 9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ~2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, p = 5.87x10-9; odds ratio = 1.12) and markers within ERBB2 (rs2517959, p = 4.53x10-9; odds ratio = 1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS. ]]> Liping Hou Sarah E Bergen Nirmala Akula Jie Song Christina M Hultman Mikael Landen Mazda Adli Martin Alda Raffaella Ardau Barbara Arias Jean-Michel Aubry Lena Backlund Judith A Badner Thomas B Barrett Michael Bauer Bernhard T Baune Frank Bellivier Antonio Benabarre Susanne Bengesser Wade H Berrettini Abesh Kumar Bhattacharjee Joanna M Biernacka Armin Birner Cinnamon S Bloss Clara Brichant-Petitjean Elise T Bui William Byerley Pablo Cervantes Caterina Chillotti Sven Cichon Francesc Colom William Coryell David W Craig Cristiana Cruceanu Piotr M Czerski Tony Davis Alexandre Dayer Franziska Degenh 2016-03-22 doi:10.1101/044412 Cold Spring Harbor Laboratory Press 2016-03-22 <![CDATA[ Assemblytics: a web analytics tool for the detection of assembly-based variants ]]> https://biorxiv.org/content/10.1101/044925v1?rss=1 Maria Nattestad Michael C Schatz 2016-03-20 doi:10.1101/044925 Cold Spring Harbor Laboratory Press 2016-03-20 <![CDATA[ Gene cloning and construction of prokaryotic and plant expression vectors of RICIN-A-Chain/PAP-S1 fusion protein and its inhibition of protein synthesis ]]> https://biorxiv.org/content/10.1101/046060v1?rss=1 Yasser S. Hassan Sherry L. Ogg 2016-03-28 doi:10.1101/046060 Cold Spring Harbor Laboratory Press 2016-03-28 <![CDATA[ Synthetic miR-16-5p does not act as a reverse transcriptase co-factor to enhance detection of small RNA ]]> https://biorxiv.org/content/10.1101/047001v1?rss=1 Melissa A McAlexander Kenneth W Witwer 2016-04-04 doi:10.1101/047001 Cold Spring Harbor Laboratory Press 2016-04-04 <![CDATA[ Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer ]]> https://biorxiv.org/content/10.1101/047142v1?rss=1 Jared T Simpson Rachael Workman Philip C Zuzarte Matei David Lewis Jonathan Dursi Winston Timp 2016-04-04 doi:10.1101/047142 Cold Spring Harbor Laboratory Press 2016-04-04 <![CDATA[ Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe. ]]> https://biorxiv.org/content/10.1101/047266v1?rss=1 Daniel Charlton Jeffares Clemency Jolly Mimoza Hoti Doug Speed Charalampos Rallis Liam Shaw Francois Balloux Christophe Dessimoz Jurg Bahler Fritz Sedlazeck 2016-04-13 doi:10.1101/047266 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Reconstructing phylogenies of metastatic cancers ]]> https://biorxiv.org/content/10.1101/048157v1?rss=1 Johannes G Reiter Alvin P Makohon-Moore Jeffrey M Gerold Ivana Bozic Krishnendu Chatterjee Christine A Iacobuzio-Donahue Bert Vogelstein Martin A Nowak 2016-04-11 doi:10.1101/048157 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Scalable Production of Human Erythrocytes from Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/050021v1?rss=1 98% purity when using a 1-litre spinner flask for suspension culture. Erythrocytes generated from our system can reach a mature stage with red blood cell (RBC) characteristics of enucleation, {beta}-globin protein expression and oxygen-binding ability. The entire process is xeno-free and clinically compliant, allowing future mass production of hiPSC-derived RBCs for transfusion medicine purposes. ]]> Ying Wang Yongxing Gao Chaoxie He Zhaohui Ye Sharon Gerecht Linzhao Cheng 2016-04-23 doi:10.1101/050021 Cold Spring Harbor Laboratory Press 2016-04-23 <![CDATA[ Recombineering in C. elegans: genome editing using in vivo assembly of linear DNAs ]]> https://biorxiv.org/content/10.1101/050815v1?rss=1 Alexandre Paix Helen Schmidt Geraldine Seydoux 2016-04-28 doi:10.1101/050815 Cold Spring Harbor Laboratory Press 2016-04-28 <![CDATA[ Bracken: Estimating species abundance in metagenomics data ]]> https://biorxiv.org/content/10.1101/051813v1?rss=1 Jennifer Lu Florian P Breitwieser Peter Thielen Steven L Salzberg 2016-05-05 doi:10.1101/051813 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Figure-ground organization in visual cortex for natural scenes ]]> https://biorxiv.org/content/10.1101/053488v1?rss=1 Jonathan R. Williford Rüdiger von der Heydt 2016-05-15 doi:10.1101/053488 Cold Spring Harbor Laboratory Press 2016-05-15 <![CDATA[ Synthesizer: Expediting synthesis studies from context-free data with natural language processing ]]> https://biorxiv.org/content/10.1101/053629v1?rss=1 Lisa Gandy Jordan Gumm Benjamin Fertig Michael J Kennish Sameer Chavan Ann Thessen Luigi Marchionni Xiaoxan Xia Shambhavi Shankrit Elana J Fertig 2016-05-16 doi:10.1101/053629 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ Parvalbumin interneuron dysfunction in a thalamus - prefrontal cortex circuit in Disc1 deficiency mice ]]> https://biorxiv.org/content/10.1101/054759v1?rss=1 Kristen Delevich Hanna Jaaro-Peled Mario Penzo Akira Sawa Bo Li 2016-05-21 doi:10.1101/054759 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ Centrifuge: rapid and sensitive classification of metagenomic sequences ]]> https://biorxiv.org/content/10.1101/054965v1?rss=1 Daehwan Kim Li Song Florian P Breitwieser Steven L Salzberg 2016-05-24 doi:10.1101/054965 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ The impact of structural variation on human gene expression ]]> https://biorxiv.org/content/10.1101/055962v1?rss=1 Colby Chiang Alexandra J Scott Joe R Davis Emily K Tsang Xin Li Yungil Kim Farhan N Damani Liron Ganel GTEx Consortium Stephen B Montgomery Alexis Battle Donald F Conrad Ira M Hall 2016-06-09 doi:10.1101/055962 Cold Spring Harbor Laboratory Press 2016-06-09 <![CDATA[ Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing ]]> https://biorxiv.org/content/10.1101/056887v1?rss=1 Chen-Shan Chin Paul Peluso Fritz J. Sedlazeck Maria Nattestad Gregory T. Concepcion Alicia Clum Christopher Dunn Ronan O'Malley Rosa Figueroa-Balderas Abraham Morales-Cruz Grant R. Cramer Massimo Delledonne Chongyuan Luo Joseph R. Ecker Dario Cantu David R. Rank Michael C. Schatz 2016-06-03 doi:10.1101/056887 Cold Spring Harbor Laboratory Press 2016-06-03 <![CDATA[ Post-selection Inference Following Aggregate Level Hypothesis Testing in Large Scale Genomic Data ]]> https://biorxiv.org/content/10.1101/058404v1?rss=1 Ruth Heller Nilanjan Chatterjee Abba Krieger Jianxin Shi 2016-06-11 doi:10.1101/058404 Cold Spring Harbor Laboratory Press 2016-06-11 <![CDATA[ “Gap Hunting” to identify multimodal distributions of DNA methylation ]]> https://biorxiv.org/content/10.1101/059659v1?rss=1 Shan V. Andrews Christine Ladd-Acosta Andrew P. Feinberg Kasper D. Hansen M. Daniele Fallin 2016-06-18 doi:10.1101/059659 Cold Spring Harbor Laboratory Press 2016-06-18 <![CDATA[ Potential energy landscapes reveal the information-theoretic nature of the epigenome ]]> https://biorxiv.org/content/10.1101/059766v1?rss=1 Garrett Jenkinson Elisabet Pujadas John Goutsias Andrew P Feinberg 2016-06-18 doi:10.1101/059766 Cold Spring Harbor Laboratory Press 2016-06-18 <![CDATA[ Evaluating the Evaluation of Cancer Driver Genes ]]> https://biorxiv.org/content/10.1101/060426v1?rss=1 Collin Tokheim Nickolas Papadopoulis Kenneth W Kinzler Bert Vogelstein Rachel Karchin 2016-06-23 doi:10.1101/060426 Cold Spring Harbor Laboratory Press 2016-06-23 <![CDATA[ Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies ]]> https://biorxiv.org/content/10.1101/062075v1?rss=1 Minsun Song Bill Wheeler Neil Caporaso Maria Teressa Landi Nilanjan Chatterjee 2016-07-04 doi:10.1101/062075 Cold Spring Harbor Laboratory Press 2016-07-04 <![CDATA[ Rare copy number variants in NRXN1 and CNTN6 increase risk for Tourette syndrome ]]> https://biorxiv.org/content/10.1101/062471v1?rss=1 Alden Y Huang Dongmei Yu Lea K Davis Jae-Hoon Sul Fotis Tsetsos Vasily Ramensky Ivette Zelaya Eliana Marisa Ramos Lisa Osiecki Jason A Chen Lauren M McGrath Cornelia Illmann Paul Sandor Cathy L Barr Marco Grados Harvey S Singer Markus M Noethen Johannes Hebebrand Robert A King Yves Dion Guy Rouleau Cathy L Budman Christel Depienne Yulia Worbe Andreas Hartmann Kirsten R Muller-Vahl Manfred Stuhrmann Harald Aschauer Mara Stamenkovic Monika Schloegelhofer Anastasios Konstantinidis Gholson L Lyon William M McMahon Csaba Barta Zsanett Tarnok Peter Nagy James R Batterson Renata Rizzo Danielle C Cath 2016-07-08 doi:10.1101/062471 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver ]]> https://biorxiv.org/content/10.1101/062588v1?rss=1 Xin Li Yun Liu Tal Salz Kasper D Hansen Andrew P Feinberg 2016-07-10 doi:10.1101/062588 Cold Spring Harbor Laboratory Press 2016-07-10 <![CDATA[ ADPriboDB: The Database of ADP-ribosylated Proteins ]]> https://biorxiv.org/content/10.1101/063768v1?rss=1 Christina Vivelo Ricky Wat Charul Agrawal Hui Yi Tee Anthony Leung 2016-07-13 doi:10.1101/063768 Cold Spring Harbor Laboratory Press 2016-07-13 <![CDATA[ Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm ]]> https://biorxiv.org/content/10.1101/066100v1?rss=1 Aleksey V Zimin Daniela Puiu Ming-Cheng Luo Tingting Zhu Sergey Koren James A. Yorke Jan Dvorak Steven Salzberg 2016-07-26 doi:10.1101/066100 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ recount: A large-scale resource of analysis-ready RNA-seq expression data ]]> https://biorxiv.org/content/10.1101/068478v1?rss=1 Leonardo Collado-Torres Abhinav Nellore Kai Kammers Shannon E Ellis Margaret A Taub Kasper D Hansen Andrew E Jaffe Ben Langmead Jeffrey Leek 2016-08-08 doi:10.1101/068478 Cold Spring Harbor Laboratory Press 2016-08-08 <![CDATA[ Exaggerated CpH Methylation in the Autism-Affected Brain ]]> https://biorxiv.org/content/10.1101/069120v1?rss=1 Shannon E Ellis Simone Gupta Anna Moes Andrew B West Dan E Arking 2016-08-11 doi:10.1101/069120 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Modeling and docking antibody structures with Rosetta ]]> https://biorxiv.org/content/10.1101/069930v1?rss=1 Brian D. Weitzner Jeliazko Jeliazkov Sergey Lyskov Nicholas A Marze Daisuke Kuroda Rahel Frick Naireeta Biswas Jeffrey J Gray 2016-08-16 doi:10.1101/069930 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Molecular signatures associated with ZIKV exposure in human cortical neural progenitors ]]> https://biorxiv.org/content/10.1101/071183v1?rss=1 Feiran Zhang Christy Hammack Sarah Ogden Yichen Cheng Emily Lee Zhexing Wen Xuyu Qian Ha Nam Nguyen Yujing Li Bing Yao Miao Xu Tianlei Xu Li Chen Zhiqin Wang Hao Feng Wei-Kai Huang Ki-jun Yoon Chao Shan Pei-Yong Shi Luxoiu Huang Zhaohui Qin Kimberly Christian Mingjiang Xu Menghang Xia Wei Zheng Hao Wu Hongjun Song Hengli Tang Guo-li Ming Peng Jin 2016-08-23 doi:10.1101/071183 Cold Spring Harbor Laboratory Press 2016-08-23 <![CDATA[ A framework for RNA quality correction in differential expression analysis ]]> https://biorxiv.org/content/10.1101/074245v1?rss=1 3x) across two large independent postmortem human brain studies of schizophrenia. Finally, we explored public datasets to demonstrate potential RNA quality confounding when comparing expression levels of different brain regions and diagnostic groups beyond schizophrenia. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from the human brain. ]]> Andrew E Jaffe Ran Tao Alexis Norris Marc Kealhofer Abhinav Nellore Yankai Jia Thomas Hyde Joel Kleinman Richard Straub Jeffrey T Leek Daniel Weinberger 2016-09-09 doi:10.1101/074245 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Distant regulatory effects of genetic variation in multiple human tissues ]]> https://biorxiv.org/content/10.1101/074419v1?rss=1 Brian Jo Yuan He Benjamin J Strober Princy Parsana Francois Aguet Andrew A Brown Stephane E Castel Eric R Gamazon Ariel Gewirtz Genna Gliner Buhm Han Amy Z He Eun Yong Kang Ian C McDowell Xiao Li Pejman Mohammadi Christine B Peterson Gerald Quon Ashis Saha Ayellet V Segre Jae Hoon Sul Timothy J Sullivan Kristin G Ardlie Christopher D Brown Donald F Conrad Nancy J Cox Emmanouil T Dermitzakis Eleazar Eskin Manolis Kellis Tuuli Lappalainen Chiara Sabatti GTEx Consortium Barbara E Engelhardt Alexis Battle 2016-09-09 doi:10.1101/074419 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ The impact of rare variation on gene expression across tissues ]]> https://biorxiv.org/content/10.1101/074443v1?rss=1 Xin Li Yungil Kim Emily K. Tsang Joe R. Davis Farhan N. Damani Colby Chiang Zachary Zappala Benjamin J. Strober Alexandra J. Scott Andrea Ganna Jason Merker GTEx Consortium Ira M. Hall Alexis Battle Stephen B. Montgomery 2016-09-09 doi:10.1101/074443 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Local genetic effects on gene expression across 44 human tissues ]]> https://biorxiv.org/content/10.1101/074450v1?rss=1 Francois Aguet Andrew A Brown Stephane Castel Joe R Davis Pejman Mohammadi Ayellet V Segre Zachary Zappala Nathan S Abell Laure Fresard Eric R Gamazon Ellen Gelfand Machael J Gloudemans Yuan He Farhad Hormozdiari Xiao Li Xin Li Boxiang Liu Diego Garrido-Martin Halit Ongen John J Palowitch YoSon Park Christine B Peterson Gerald Quon Stephan Ripke Andrey A Shabalin Tyler C Shimko Benjamin J Strober Timothy J Sullivan Nicole A Teran Emily K Tsang Hailei Zhang Yi-Hui Zhou Alexis Battle Carlos D Bustamonte Nancy J Cox Barbara E Engelhardt Eleazar Eskin Gad Getz Manolis Kellis Gen Li Daniel G MacArt 2016-09-09 doi:10.1101/074450 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry ]]> https://biorxiv.org/content/10.1101/074567v1?rss=1 Ben C Collins Christie L Hunter Yansheng Liu Birgit Schilling George Rosenberger Rosenberger Samuel L Bader Daniel W Chan Bradford W Gibson Anne-Claude Gingras Jason M Held Mio Hirayama-Kurogi Guixue Hou Christoph Krisp Krisp Brett Larsen Liang Lin Siqi Liu Mark P Molloy Robert L Moritz Sumio Ohtsuki Ralph Schlapbach Nathalie Selevsek Stefani N Thomas Shin-Cheng Tzeng Hui Zhang Ruedi Aebersold 2016-09-14 doi:10.1101/074567 Cold Spring Harbor Laboratory Press 2016-09-14 <![CDATA[ Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter ]]> https://biorxiv.org/content/10.1101/075457v1?rss=1 Björn Grüning Eric Rasche Boris Rebolledo Jaramillo Carl Eberhard Torsten Houwaart John Chilton Nathan Coraor Rolf Backofen James Taylor Anton Nekrutenko 2016-09-16 doi:10.1101/075457 Cold Spring Harbor Laboratory Press 2016-09-16 <![CDATA[ GenomeScope: Fast reference-free genome profiling from short reads ]]> https://biorxiv.org/content/10.1101/075978v1?rss=1 Gregory W Vurture Fritz J Sedlazeck Maria Nattestad Charles J. Underwood Han Fang James Gurtowski Michael Schatz 2016-09-19 doi:10.1101/075978 Cold Spring Harbor Laboratory Press 2016-09-19 <![CDATA[ Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data ]]> https://biorxiv.org/content/10.1101/076620v1?rss=1 Nicolas Borisov Maria Suntsova Andrew Garazha Ksenia Lezhnina Olga Kovalchuk Alexander Aliper Elena Ilnitskaya Maxim Sorokin Mihkail Korzinkin Vyacheslav Saenko Yury Saenko Dmitry G. Sokov Nurshat M. Gaifullin Kirill Kashintsev Valery Shirokorad Irina Shabalina Alex Zhavoronkov Bhubaneswar Mishra Charles R. Cantor Anton Buzdin 2016-09-21 doi:10.1101/076620 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Choice of reference genome can introduce massive bias in bisulfite sequencing data ]]> https://biorxiv.org/content/10.1101/076844v1?rss=1 Phillip Wulfridge Ben Langmead Andrew P Feinberg Kasper Hansen 2016-09-22 doi:10.1101/076844 Cold Spring Harbor Laboratory Press 2016-09-22 <![CDATA[ Insights into the genetic epidemiology of Crohn’s and rare diseases in the Ashkenazi Jewish population ]]> https://biorxiv.org/content/10.1101/077180v1?rss=1 C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohns disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically evaluate whether strong acting rare alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohns disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are strongly enriched in AJ, including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC to pinpoint genetic variation that contributes to variable disease predisposition across populations. ]]> Manuel Antonio Rivas Jukka Koskela Hailiang Huang Christine Stevens Brandon E Avila Talin Haritunians Benjamin Neale Mitja Kurki Andrea Ganna Daniel Graham Benjamin Glaser Inga Peter Gil Atzmon Nir Barzilai Adam Levine Elena Schiff Nikolas Pontikos Ben Weisburd Konrad J Karczewski Eric Minikel Britt-Sabina Petersen Laurent Beaugerie Philippe Seksik Jacques Cosnes Stefan Schreiber Bernd Bokemeyer Johannes Bethge NIDDK IBD Genetics consortium T2D-GENES consortium Graham Heap Tariq Ahmad Vincent Plagnol Anthony W Segal Stephan Targan Dan Turner Paivi Saavalainen Martti Farkkila Kimmo Kontula Matt 2016-09-25 doi:10.1101/077180 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis ]]> https://biorxiv.org/content/10.1101/077610v1?rss=1 Xinxing Yang Zhixin Lyu Amanda Miguel Ryan McQuillen Kerwyn Kerwyn Casey Huang Jie Xiao 2016-09-26 doi:10.1101/077610 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ Comparing multi- and single-sample variant calls to improve variant call sets from deep coverage whole-genome sequencing data ]]> https://biorxiv.org/content/10.1101/078642v1?rss=1 Suyash S. Shringarpure Rasika A. Mathias Ryan D Hernandez Timothy D. O'Connor Zachary A. Szpiech Raul Torres Francisco M. De La Vega Carlos D. Bustamante Kathleen C. Barnes Margaret A. Taub on behalf of the CAAPA consortium 2016-09-30 doi:10.1101/078642 Cold Spring Harbor Laboratory Press 2016-09-30 <![CDATA[ Co-expression networks reveal the tissue-specific regulation of transcription and splicing ]]> https://biorxiv.org/content/10.1101/078741v1?rss=1 Ashis Saha Yungil Kim Ariel D. H. Gewirtz Brian Jo Chuan Gao Ian C McDowell GTEx Consortium Barbara E Engelhardt Alexis Battle 2016-10-02 doi:10.1101/078741 Cold Spring Harbor Laboratory Press 2016-10-02 <![CDATA[ BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods ]]> https://biorxiv.org/content/10.1101/079145v1?rss=1 Krzysztof J. Gorgolewski Fidel Alfaro-Almagro Tibor Auer Pierre Bellec Mihai Capota Mallar Chakravarty Nathan W. Churchill R. Cameron Craddock Gabriel Devenyi Anders Eklund Oscar Esteban Guillaume Flandin Satrajit Ghosh J. Swaroop Guntupalli Mark Jenkinson Anisha Keshavan Gregory Kiar Pradeep Reddy Raamana David Raffelt Christopher J. Steele Pierre-Olivier Quirion Robert E. Smith Stephen Strother Gael Varoquaux Tal Yarkoni Yida Wang Russell Poldrack 2016-10-04 doi:10.1101/079145 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Recovery of hand function after stroke: separable systems for finger strength and control ]]> https://biorxiv.org/content/10.1101/079269v1?rss=1 Jing Xu Naveed Ejaz Benjamin Hertler Meret Branscheidt Mario Widmer Andreia V Faria Michelle Harran Juan C Cortes Nathan Kim Pablo A Celnik Tomoko Kitago Andreas Luft John W Krakauer Jörn Diedrichsen 2016-10-04 doi:10.1101/079269 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Development of a modular automated system for maintenance and differentiation of adherent human pluripotent stem cells. ]]> https://biorxiv.org/content/10.1101/079335v1?rss=1 Duncan E Crombie Maciej Daniszewski Helena H Liang Tejal Kulkarni Fan Li Grace E Lidgerwood Alison Conquest Damian Hernandez Sandy S Hung Katherine P Gill Elisabeth De Smit Lisa S Kearns Linda Clarke Valentin M Sluch Xitiz Chamling Donald J Zack Raymond CB Wong Alex Hewitt Alice Pebay 2016-10-05 doi:10.1101/079335 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ Representations of Subjective Effort Cost ]]> https://biorxiv.org/content/10.1101/079467v1?rss=1 Patrick S Hogan Cary D Frydman Joseph K Galaro Vikram S Chib 2016-10-06 doi:10.1101/079467 Cold Spring Harbor Laboratory Press 2016-10-06 <![CDATA[ iCARE: An R Package to Build and Apply Absolute Risk Models ]]> https://biorxiv.org/content/10.1101/079954v1?rss=1 Paige Maas William Wheeler Mark Brook David Check Montserrat Garcia-Closas Nilanjan Chatterjee 2016-10-12 doi:10.1101/079954 Cold Spring Harbor Laboratory Press 2016-10-12 <![CDATA[ The Chd1 chromatin remodeler shifts hexasomes unidirectionally ]]> https://biorxiv.org/content/10.1101/080010v1?rss=1 Robert F Levendosky Anton Sabantsev Sebastian Deindl Gregory D Bowman 2016-10-09 doi:10.1101/080010 Cold Spring Harbor Laboratory Press 2016-10-09 <![CDATA[ Temporal order of Alzheimer’s disease-related cognitive marker changes in BLSA and WRAP longitudinal studies ]]> https://biorxiv.org/content/10.1101/081174v1?rss=1 Bilgel, M. Koscik, R. L. An, Y. Prince, J. L. Resnick, S. M. Johnson, S. C. Jedynak, B. M. 2016-10-14 doi:10.1101/081174 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ Serum extracellular vesicle depletion processes affect release and infectivity of HIV-1 in culture ]]> https://biorxiv.org/content/10.1101/081687v1?rss=1 Liao, Z. Muth, D. C. Eitan, E. Travers, M. Lehrmann, E. Witwer, K. W. 2016-12-08 doi:10.1101/081687 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Ribbon: Visualizing complex genome alignments and structural variation ]]> https://biorxiv.org/content/10.1101/082123v1?rss=1 Nattestad, M. Chin, C.-S. Schatz, M. C. 2016-10-20 doi:10.1101/082123 Cold Spring Harbor Laboratory Press 2016-10-20 <![CDATA[ PatternMarkers and Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS) for data-driven detection of novel biomarkers via whole transcriptome Non-negative matrix factorization (NMF) ]]> https://biorxiv.org/content/10.1101/083717v1?rss=1 Stein-O'Brien, G. Carey, J. Lee, W.-s. Considine, M. Favorov, A. Flam, E. Guo, T. Li, L. Marchionni, L. Sherman, T. Gaykalova, D. McKay, R. Ochs, M. Colantuoni, C. Fertig, E. 2016-10-26 doi:10.1101/083717 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Dual origins of measured phase-amplitude coupling reveal distinct neural mechanisms underlying episodic memory in the human cortex ]]> https://biorxiv.org/content/10.1101/084194v1?rss=1 Vaz, A. P. Yaffe, R. B. Wittig, J. H. Inati, S. K. Zaghloul, K. A. 2016-10-28 doi:10.1101/084194 Cold Spring Harbor Laboratory Press 2016-10-28 <![CDATA[ Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification ]]> https://biorxiv.org/content/10.1101/084715v1?rss=1 Breitwieser, F. P. Salzberg, S. L. 2016-10-31 doi:10.1101/084715 Cold Spring Harbor Laboratory Press 2016-10-31 <![CDATA[ Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP ]]> https://biorxiv.org/content/10.1101/086579v1?rss=1 Koehler Leman, J. Lyskov, S. Bonneau, R. 2016-11-10 doi:10.1101/086579 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Systematic integration of biomedical knowledge prioritizes drugs for repurposing ]]> https://biorxiv.org/content/10.1101/087619v1?rss=1 Himmelstein, D. S. Lizee, A. Hessler, C. Brueggeman, L. Chen, S. L. Hadley, D. Green, A. Khankhanian, P. Baranzini, S. E. 2016-11-14 doi:10.1101/087619 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ SplitThreader: Exploration and analysis of rearrangements in cancer genomes ]]> https://biorxiv.org/content/10.1101/087981v1?rss=1 Nattestad, M. Alford, M. C. Sedlazeck, F. J. Schatz, M. C. 2016-11-15 doi:10.1101/087981 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ Heat-stable preservation of protein expression systems for portable therapeutics production ]]> https://biorxiv.org/content/10.1101/089664v1?rss=1 Karig, D. Bessling, S. Thielen, P. Zhang, S. Wolfe, J. 2016-11-26 doi:10.1101/089664 Cold Spring Harbor Laboratory Press 2016-11-26 <![CDATA[ Genetic determinants of chromatin accessibility and gene regulation in T cell activation across human individuals ]]> https://biorxiv.org/content/10.1101/090241v1?rss=1 Cheng, C. S. Gate, R. E. Aiden, A. P. Siba, A. Tabaka, M. Lituiev, D. Machol, I. Subramaniam, M. Shammim, M. Hougen, K. L. Wortman, I. Huang, S.-C. Durand, N. C. Feng, T. De Jager, P. L. Chang, H. Y. Lieberman Aiden, E. Benoist, C. Beer, M. A. Ye, C. J. Regev, A. 2016-12-02 doi:10.1101/090241 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Tuning the course of evolution on the biophysical fitness landscape of an RNA virus ]]> https://biorxiv.org/content/10.1101/090258v1?rss=1 Rotem, A. Serohijos, A. Chang, C. Wolfe, J. Fischer, A. Mehoke, T. Zhang, H. Tao, Y. Ung, L. Choi, J.-M. Kolawole, A. Koehler, S. Wu, S. Thielen, P. Cui, N. Demirev, P. Giacobbi, N. Julian, T. Schwab, K. Lin, J. Smith, T. Pipas, J. Wobus, C. Feldman, A. Weitz, D. Shakhnovich, E. 2016-11-28 doi:10.1101/090258 Cold Spring Harbor Laboratory Press 2016-11-28 <![CDATA[ MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data ]]> https://biorxiv.org/content/10.1101/090456v1?rss=1 Friedman, S. H. Anderson, A. R. A. Bortz, D. M. Fletcher, A. G. Frieboes, H. B. Ghaffarizadeh, A. Grimes, D. R. Hawkins-Daarud, A. Hoehme, S. Juarez, E. F. Kesselman, C. Merks, R. Mumenthaler, S. M. Newton, P. K. Norton, K.-A. Rawat, R. Rockne, R. C. Ruderman, D. Scott, J. Sindi, S. S. Sparks, J. L. Swanson, K. Agus, D. B. Macklin, P. 2016-11-30 doi:10.1101/090456 Cold Spring Harbor Laboratory Press 2016-11-30 <![CDATA[ The NCA-1 ion channel functions downstream of Gq and Rho to regulate locomotion in C. elegans ]]> https://biorxiv.org/content/10.1101/090514v1?rss=1 Topalidou, I. Chen, P.-A. Cooper, K. Watanabe, S. Jorgensen, E. M. Ailion, M. 2016-11-30 doi:10.1101/090514 Cold Spring Harbor Laboratory Press 2016-11-30 <![CDATA[ MultiCellDS: a standard and a community for sharing multicellular data ]]> https://biorxiv.org/content/10.1101/090696v1?rss=1 Friedman, S. H. Anderson, A. R. A. Bortz, D. M. Fletcher, A. G. Frieboes, H. B. Ghaffarizadeh, A. Grimes, D. R. Hawkins-Daarud, A. Hoehme, S. Juarez, E. F. Kesselman, C. Merks, R. M. H. Mumenthaler, S. M. Newton, P. K. Norton, K.-A. Rawat, R. Rockne, R. C. Ruderman, D. Scott, J. Sindi, S. S. Sparks, J. L. Swanson, K. Agus, D. B. Macklin, P. 2016-12-09 doi:10.1101/090696 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ A Bayesian Heteroscedastic GLM with Application to fMRI Data with Motion Spikes ]]> https://biorxiv.org/content/10.1101/091066v1?rss=1 Eklund, A. Lindquist, M. A. Villani, M. 2016-12-02 doi:10.1101/091066 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/091330v1?rss=1 Andrews, S. V. Ellis, S. E. Bakulski, K. M. Sheppard, B. Croen, L. A. Hertz-Picciotto, I. Newschaffer, C. J. Feinberg, A. P. Arking, D. E. Ladd-Acosta, C. Fallin, M. D. 2016-12-05 doi:10.1101/091330 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ Splice Expression Variation Analysis (SEVA) for Differential Gene Isoform Usage in Cancer ]]> https://biorxiv.org/content/10.1101/091637v1?rss=1 Afsari, B. Guo, T. Considine, M. Florea, L. Kelly, D. Flam, E. Ha, P. Geman, D. Ochs, M. F. Califano, J. A. Gaykalova, D. A. Favorov, A. V. Fertig, E. J. 2016-12-05 doi:10.1101/091637 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ Analysis of copy number variants on chromosome 21 in Down syndrome-associated congenital heart defects ]]> https://biorxiv.org/content/10.1101/093583v1?rss=1 Rambo-Martin, B. L. Mulle, J. G. Cutler, D. J. Bean, L. J. H. Rosser, T. C. Dooley, K. J. Cua, C. Capone, G. Maslen, C. L. Reeves, R. H. Sherman, S. L. Zwick, M. E. 2016-12-28 doi:10.1101/093583 Cold Spring Harbor Laboratory Press 2016-12-28 <![CDATA[ grID: A CRISPR-Cas9 guide RNA Database and Resource for Genome-Editing ]]> https://biorxiv.org/content/10.1101/097352v1?rss=1 Jaskula-Ranga, V. Zack, D. J. 2016-12-30 doi:10.1101/097352 Cold Spring Harbor Laboratory Press 2016-12-30 <![CDATA[ Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples ]]> https://biorxiv.org/content/10.1101/097881v1?rss=1 Wilks, C. Gaddipati, P. Nellore, A. Langmead, B. 2017-01-09 doi:10.1101/097881 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway ]]> https://biorxiv.org/content/10.1101/100545v1?rss=1 de Jonge, R. Ebert, M. K. Huitt-Roehl, C. R. Pal, P. Suttle, J. C. Neubauer, J. D. Jurick, W. M. Secor, G. A. Thomma, B. P. Van de Peer, Y. Townsend, C. A. Bolton, M. D. 2017-01-15 doi:10.1101/100545 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Simplified Power Calculations for Aggregate-level Association Tests Provide Insights to Challenges for Rare Variant Association Studies ]]> https://biorxiv.org/content/10.1101/100891v1?rss=1 Derkach, A. Zhang, H. Chatterjee, N. 2017-01-16 doi:10.1101/100891 Cold Spring Harbor Laboratory Press 2017-01-16 <![CDATA[ LRSim: a Linked Reads Simulator generating insights for better genome partitioning ]]> https://biorxiv.org/content/10.1101/103549v1?rss=1 Luo, R. Sedlazeck, F. J. Darby, C. A. Kelly, S. M. Schatz, M. C. 2017-01-26 doi:10.1101/103549 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ A tandem simulation framework for predicting mapping quality ]]> https://biorxiv.org/content/10.1101/103952v1?rss=1 Langmead, B. 2017-01-30 doi:10.1101/103952 Cold Spring Harbor Laboratory Press 2017-01-30 <![CDATA[ The Rosetta all-atom energy function for macromolecular modeling and design ]]> https://biorxiv.org/content/10.1101/106054v1?rss=1 Alford, R. F. Leaver-Fay, A. Jeliazkov, J. R. O'Meara, M. J. DiMaio, F. P. Park, H. Shapovalov, M. V. Renfrew, P. D. Mulligan, V. K. Kappel, K. Labonte, J. W. Pacella, M. S. Bonneau, R. Bradley, P. Dunbrack, R. L. Das, R. Baker, D. Kuhlman, B. Kortemme, T. Gray, J. J. 2017-02-07 doi:10.1101/106054 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ TOWARDS A GLOBAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES ]]> https://biorxiv.org/content/10.1101/110825v1?rss=1 Anderson, W. Apweiler, R. Bateman, A. Bauer, G. A. Berman, H. Blake, J. A. Blomberg, N. Burley, S. K. Cochrane, G. Di Francesco, V. Donohue, T. Durinx, C. Game, A. Green, E. Gojobori, T. Goodhand, P. Hamosh, A. Hermjakob, H. Kanehisa, M. Kiley, R. McEntyre, J. McKibbin, R. Miyano, S. Pauly, B. Perrimon, N. Ragan, M. A. Richards, G. Teo, Y.-Y. Westerfield, M. Westhof, E. Lasko, P. F. 2017-02-23 doi:10.1101/110825 Cold Spring Harbor Laboratory Press 2017-02-23 <![CDATA[ Novel blood pressure locus and gene discovery using GWAS and expression datasets from blood and the kidney ]]> https://biorxiv.org/content/10.1101/110833v1?rss=1 International Consortium for Blood Pressure GWAS, Ehret, G. Wain, L. 2017-02-22 doi:10.1101/110833 Cold Spring Harbor Laboratory Press 2017-02-22 <![CDATA[ Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource ]]> https://biorxiv.org/content/10.1101/111039v1?rss=1 Strande, N. T. Riggs, E. R. Buchanan, A. H. Ceyhan-Birsoy, O. Dwight, S. T. Dwight, S. S. Goldstein, J. L. Ghosh, R. Seifert, B. A. Sneddon, T. P. Wright, M. W. Milko, L. V. Giovanni, M. A. Murray, M. F. O'Daniel, J. M. Ramos, E. M. Santani, A. B. Scott, A. F. Cherry, J. M. Plon, S. E. Rehm, H. L. Martin, C. L. Berg, J. S. 2017-02-22 doi:10.1101/111039 Cold Spring Harbor Laboratory Press 2017-02-22 <![CDATA[ 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model ]]> https://biorxiv.org/content/10.1101/111393v1?rss=1 Luo, R. Schatz, M. C. Salzberg, S. 2017-02-24 doi:10.1101/111393 Cold Spring Harbor Laboratory Press 2017-02-24 <![CDATA[ BRD4 inhibitors block telomere elongation ]]> https://biorxiv.org/content/10.1101/112169v1?rss=1 Wang, S. Pike, A. Lee, S. Connelly, C. Greider, C. W. 2017-02-27 doi:10.1101/112169 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ Varying Effects of Common Tuberculosis Drugs on Enhancing Clofazimine Activity in vitro ]]> https://biorxiv.org/content/10.1101/112573v1?rss=1 Zhang, S. Shi, W. Feng, J. Zhang, W. Zhang, Y. 2017-03-05 doi:10.1101/112573 Cold Spring Harbor Laboratory Press 2017-03-05 <![CDATA[ Activity of Sulfa Drugs and Their Combinations against Stationary Phase B. burgdorferi in vitro ]]> https://biorxiv.org/content/10.1101/112607v1?rss=1 Feng, J. ZHANG, S. Shi, W. ZHANG, Y. 2017-03-03 doi:10.1101/112607 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Genome-wide association study of asthma in individuals of African ancestry reveals novel asthma susceptibility loci ]]> https://biorxiv.org/content/10.1101/112953v1?rss=1 Daya, M. Rafaels, N. Chavan, S. Johnston, H. R. Shetty, A. Gignoux, C. R. Boorgula, M. P. Campbell, M. Maul, P. Maul, T. Vergara, C. Levin, A. M. Wojcik, G. Torgerson, D. G. Ortega, V. E. Doumatey, A. Araujo, M. I. Avila, P. C. Bleecker, E. Bustamante, C. Caraballo, L. Dunston, G. M. Faruque, M. U. Ferguson, T. Figueiredo, C. Ford, J. G. Gourraud, P.-A. Hansel, N. N. Hernandez, R. D. Herrera-Paz, E. F. Kenny, E. E. Knight-Madden, J. Kumar, R. Lange, L. A. Lange, E. M. Lizee, A. Mayorga, A. Meyers, D. Nicolae, D. L. O'Connor, T. D. Oliveira, R. R. Olopad 2017-03-02 doi:10.1101/112953 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Identification of drug candidates that enhance pyrazinamide activity from a clinical drug library ]]> https://biorxiv.org/content/10.1101/113704v1?rss=1 Niu, H. Ma, C. Cui, P. Shi, W. Zhang, S. Feng, J. Sullivan, D. Zhu, B. Zhang, W. Zhang, Y. 2017-03-04 doi:10.1101/113704 Cold Spring Harbor Laboratory Press 2017-03-04 <![CDATA[ Association between Mitochondrial DNA Copy Number and Sudden Cardiac Death: Findings from the Atherosclerosis Risk in Communities Study (ARIC) ]]> https://biorxiv.org/content/10.1101/113878v1?rss=1 Zhang, Y. Guallar, E. Ashar, F. Longchamps, R. Castellani, C. Lane, J. Grove, M. Coresh, J. Sotoodehnia, N. Ilkhanoff, L. Boerwinkle, E. Pankratz, N. Arking, D. 2017-03-06 doi:10.1101/113878 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis ]]> https://biorxiv.org/content/10.1101/114025v1?rss=1 Kagohara, L. Stein-O'Brien, G. Kelley, D. Flam, E. Wick, H. Danilova, L. Easwaran, H. Favorov, A. Qian, J. Gaykalova, D. Fertig, E. 2017-03-08 doi:10.1101/114025 Cold Spring Harbor Laboratory Press 2017-03-08 <![CDATA[ Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/114116v1?rss=1 Zhang, S. Chen, J. Cui, P. Shi, W. Zhang, W. Zhnag, Y. 2017-03-05 doi:10.1101/114116 Cold Spring Harbor Laboratory Press 2017-03-05 <![CDATA[ ES cell derived neural progenitors improves visual functions in retinal ganglion cells - depleted mouse models ]]> https://biorxiv.org/content/10.1101/114678v1?rss=1 Mundackal Sivaraman, D. Vazhanthodi Abdul, R. Schmidt, T. Soundararajan, L. Hattar, S. James, J. 2017-03-08 doi:10.1101/114678 Cold Spring Harbor Laboratory Press 2017-03-08 <![CDATA[ Identification of a Novel Gene argJ involved in Arginine Biosynthesis Critical for Persister Formation in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/114827v1?rss=1 Yee, R. Cui, P. Xu, T. Shi, W. Feng, J. Zhang, W. Zhang, Y. 2017-03-07 doi:10.1101/114827 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors. ]]> https://biorxiv.org/content/10.1101/116442v1?rss=1 Venkataraman, A. Yang, K. Irrizary, J. Mackiewicz, M. Mita, P. Kuang, Z. Xue, L. Ghosh, D. Liu, S. Ramos, P. Hu, S. Bayron, D. Keegan, S. Saul, R. Colantonio, S. Zhang, H. Pauli Behn, F. Song, G. Albino, E. Asencio, L. Ramos, L. Lugo, L. Morell, G. Rivera, J. Ruiz, K. Almodovar, R. Nazario, L. Murphy, K. Vargas, I. Rivera-Pacheco, Z. Rosa, C. Vargas, M. McDade, J. Clark, B. Yoo, S. Khambadkone, S. de Melo, J. Stevanovic, M. Jiang, L. Li, Y. Yap, W. Jones, B. Tandon, A. Campbell, E. Anderson, S. Myers, R. Boeke, J. Fenyo, D. Whiteley, G. Bader, J 2017-03-14 doi:10.1101/116442 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ Bio-Docklets: Virtualization Containers for Single-Step Execution of NGS Pipelines. ]]> https://biorxiv.org/content/10.1101/116962v1?rss=1 Kim, B. Ali, T. A. Lijeron, C. Afgan, E. Krampis, K. 2017-03-15 doi:10.1101/116962 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris ]]> https://biorxiv.org/content/10.1101/117218v1?rss=1 Workman, R. E. Myrka, A. M. Tseng, E. Wong, G. W. Welch, K. C. Timp, W. 2017-03-15 doi:10.1101/117218 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers ]]> https://biorxiv.org/content/10.1101/117572v1?rss=1 Nakamura, H. Lee, A. A. Afshar, A. S. Watanabe, S. Rho, E. Razavi, S. Suarez, A. Lin, Y.-C. Tanigawa, M. Huang, B. DeRose, R. Bobb, D. Hong, W. Gabelli, S. B. Goutsias, J. Inoue, T. 2017-03-16 doi:10.1101/117572 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X ]]> https://biorxiv.org/content/10.1101/119495v1?rss=1 Migeon, B. R. Beer, M. A. Bjornsson, H. T. 2017-03-22 doi:10.1101/119495 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ Neuronal brain region-specific DNA methylation andchromatin accessibility are associated with neuropsychiatric disease heritability ]]> https://biorxiv.org/content/10.1101/120386v1?rss=1 10-fold enrichment of explained heritability associated with addictive behavior, as well as schizophrenia- and neuroticism-associated regions, suggesting that common psychiatric illness is mediated through brain region-specific epigenetic marks. ]]> Rizzardi, L. Hickey, P. Rodriguez, V. Tryggvadottir, R. Callahan, C. Idrizi, A. Hansen, K. Feinberg, A. P. 2017-03-24 doi:10.1101/120386 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Towards the human cellular microRNAome ]]> https://biorxiv.org/content/10.1101/120394v1?rss=1 McCall, M. N. Kim, M.-S. Adil, M. Patil, A. H. Lu, Y. Mitchell, C. J. Leal-Rojas, P. Xu, J. Kumar, M. Dawson, V. L. Dawson, T. M. Baras, A. S. Rosenberg, A. Z. Arking, D. E. Burns, K. H. Pandey, A. Halushka, M. 2017-03-24 doi:10.1101/120394 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Alternative miRNAs: Human Sequences Misidentified As Plant miRNAs In Plant Studies And In Human Plasma ]]> https://biorxiv.org/content/10.1101/120634v1?rss=1 Witwer, K. W. 2017-03-25 doi:10.1101/120634 Cold Spring Harbor Laboratory Press 2017-03-25 <![CDATA[ Chromosome Conformation Paints Reveal The Role Of Lamina Association In Genome Organization And Regulation ]]> https://biorxiv.org/content/10.1101/122226v1?rss=1 Luperchio, T. R. Sauria, M. E. Wong, X. Gaillard, M.-C. Tsang, P. Pekrun, K. Ach, R. A. Yamada, N. A. Taylor, J. Reddy, K. 2017-03-30 doi:10.1101/122226 Cold Spring Harbor Laboratory Press 2017-03-30 <![CDATA[ FtsEX-Mediated Regulation Of Inner Membrane Fusion And Cell Separation Reveals Morphogenetic Plasticity In Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/124214v1?rss=1 Meier, E. L. Yao, Q. Daitch, A. K. Jensen, G. J. Goley, E. D. 2017-04-04 doi:10.1101/124214 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML ]]> https://biorxiv.org/content/10.1101/124263v1?rss=1 Gore, L. Triche, T. J. Farrar, J. E. Wai, D. Legendre, C. Gooden, G. C. Liang, W. S. Carpten, J. Lee, D. W. Alvaro, F. Macy, M. E. Arndt, C. Barnette, P. Cooper, T. Martin, L. Narendran, A. Pollard, J. Meshinchi, S. Boklan, J. Arceci, R. J. Salhia, B. 2017-06-14 doi:10.1101/124263 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ Developmental And Genetic Regulation Of The Human Cortex Transcriptome In Schizophrenia ]]> https://biorxiv.org/content/10.1101/124321v1?rss=1 Jaffe, A. E. Straub, R. E. Shin, J. H. Tao, R. Gao, Y. Collado Torres, L. Kam-Thong, T. Xi, H. S. Quan, J. Chen, Q. Colantuoni, C. Ulrich, B. Maher, B. J. Deep-Soboslay, A. The BrainSeq Consortium, Cross, A. Brandon, N. J. Leek, J. T. Hyde, T. M. Kleinman, J. E. Weinberger, D. R. 2017-04-05 doi:10.1101/124321 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Sympathetic Nerve Activity Promotes Cardiomyocyte Cell-Cycle Arrest And Binucleation ]]> https://biorxiv.org/content/10.1101/124347v1?rss=1 Chen, L. Payumo, A. Y. Hirose, K. Bigley, R. B. Lovas, J. Kuruvilla, R. Huang, G. N. 2017-04-05 doi:10.1101/124347 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Disruption of perineuronal nets increases the frequency of sharp wave ripples ]]> https://biorxiv.org/content/10.1101/124677v1?rss=1 Sun, Z. Bozzelli, P. L. Caccavano, A. Allen, M. Balmuth, J. Vicini, S. Wu, J.-Y. Conant, K. 2017-04-06 doi:10.1101/124677 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Comparison Of NMR And Crystal Structures Of Membrane Proteins And Computational Refinement To Improve Model Quality ]]> https://biorxiv.org/content/10.1101/127142v1?rss=1 Koehler Leman, J. D'Avino, A. R. Bhatnagar, Y. D. Gray, J. J. 2017-04-13 doi:10.1101/127142 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Estimating Autoantibody Signatures To Detect Autoimmune Disease Patient Subsets ]]> https://biorxiv.org/content/10.1101/128199v1?rss=1 Wu, Z. Casciola-Rosen, L. Shah, A. A. Rosen, A. Zeger, S. L. 2017-04-18 doi:10.1101/128199 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Improved de novo Genome Assembly: Synthetic long read sequencing combined with optical mapping produce a high quality mammalian genome at relatively low cost ]]> https://biorxiv.org/content/10.1101/128348v1?rss=1 Mohr, D. W. Naguib, A. Weisenfeld, N. Kumar, V. Shah, P. Church, D. M. Jaffe, D. Scott, A. F. 2017-04-18 doi:10.1101/128348 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection ]]> https://biorxiv.org/content/10.1101/128975v1?rss=1 Huang, H. Duggal, P. Thio, C. Latanich, R. Goedert, J. Mangia, A. Cox, A. Kirk, G. Mehta, S. Blankson, J. Aneja, J. Alric, L. Donfield, S. Cramp, M. Khakoo, S. Tobler, L. Busch, M. Alexander, G. Rosen, H. Edlin, B. Lauer, G. Thomas, D. Daly, M. Chung, R. Kim, A. 2017-04-20 doi:10.1101/128975 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Finger recruitment patterns during mirror movements suggest two systems for hand recovery after stroke ]]> https://biorxiv.org/content/10.1101/129510v1?rss=1 Ejaz, N. Xu, J. Branscheidt, M. Hertler, B. Schambra, H. Widmer, M. Faria, A. V. Harran, M. Cortes, J. C. Kim, N. Kitago, T. Celnik, P. A. Luft, A. Krakauer, J. W. Diedrichsen, J. 2017-04-22 doi:10.1101/129510 Cold Spring Harbor Laboratory Press 2017-04-22 <![CDATA[ mTORC1-mediated inhibition of 4EBP1 is essential for Hedgehog (HH) signaling and can be targeted to suppress HH-driven medulloblastoma ]]> https://biorxiv.org/content/10.1101/130872v1?rss=1 Wu, C.-C. Hou, S. Orr, B. A. Youn, Y. H. Roth, F. Eberhart, C. G. Han, Y.-G. 2017-04-25 doi:10.1101/130872 Cold Spring Harbor Laboratory Press 2017-04-25 <![CDATA[ High Activity Of Selective Essential Oils Against Stationary Phase Borrelia burgdorferi As A Persister Model ]]> https://biorxiv.org/content/10.1101/130898v1?rss=1 Feng, J. Zhang, S. Shi, W. Zubcevik, N. Miklossy, J. Zhang, Y. 2017-05-17 doi:10.1101/130898 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Long-Lasting Contribution Of Dopamine In The Nucleus Accumbens Core, But Not Dorsal Lateral Striatum, To Sign-Tracking ]]> https://biorxiv.org/content/10.1101/132977v1?rss=1 Fraser, K. M. Janak, P. H. 2017-05-01 doi:10.1101/132977 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Role of Membrane-tension Gated Ca Flux in Cell Mechanosensation ]]> https://biorxiv.org/content/10.1101/134395v1?rss=1 He, L. Tao, J. Si, F. Wu, Y. Wu, T. Prasath, V. Wirtz, D. Sun, S. X. 2017-05-04 doi:10.1101/134395 Cold Spring Harbor Laboratory Press 2017-05-04 <![CDATA[ Whole-Brain Serial-Section Electron Microscopy In Larval Zebrafish ]]> https://biorxiv.org/content/10.1101/134882v1?rss=1 Hildebrand, D. G. C. Cicconet, M. Torres, R. M. Choi, W. Quan, T. M. Moon, J. Wetzel, A. W. Champion, A. S. Graham, B. J. Randlett, O. Plummer, G. S. Portugues, R. Bianco, I. H. Saalfeld, S. Baden, A. D. Lillaney, K. Burns, R. Vogelstein, J. T. Schier, A. F. Lee, W.-C. A. Jeong, W.-K. Lichtman, J. W. Engert, F. 2017-05-07 doi:10.1101/134882 Cold Spring Harbor Laboratory Press 2017-05-07 <![CDATA[ Untangling The Gene-Epigenome Networks: Timing Of Epigenetic Regulation Of Gene Expression In Acquired Cetuximab Resistance ]]> https://biorxiv.org/content/10.1101/136564v1?rss=1 Stein-O'Brien, G. Kagohara, L. T. Li, S. Thakar, M. Ranaweera, R. Ozawa, H. Cheng, H. Considine, M. Favorov, A. Danilova, L. Califano, J. Izumchenko, E. Gaykalova, D. A. Chung, C. H. Fertig, E. J. 2017-05-10 doi:10.1101/136564 Cold Spring Harbor Laboratory Press 2017-05-10 <![CDATA[ Ionic Current Correlations Are Ubiquitous Across Phyla ]]> https://biorxiv.org/content/10.1101/137133v1?rss=1 Tran, T. Unal, C. T. Zaborszky, L. Rotstein, H. G. Kirkwood, A. Golowasch, J. P. 2017-05-12 doi:10.1101/137133 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Molecular Mechanisms Of Human Papillomavirus-Related Carcinogenesis In Head And Neck Cancer ]]> https://biorxiv.org/content/10.1101/137653v1?rss=1 Faraji, F. Zaidi, M. Fakhry, C. Gaykalova, D. A. 2017-05-16 doi:10.1101/137653 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Expression Of Pokeweed Antiviral Protein Isoform S1 (PAP-S1) And Of Ricin-A-Chain/PAP-S1 Novel Fusion Protein (RTA/PAP-S1) In Escherichia coli And Their Comparative Inhibition Of Protein Synthesis In Vitro ]]> https://biorxiv.org/content/10.1101/137919v1?rss=1 Hassan, Y. Ogg, S. 2017-05-14 doi:10.1101/137919 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ The Cerebellum Does More Than Sensory-Prediction-Error-Based Learning In Sensorimotor Adaptation Tasks ]]> https://biorxiv.org/content/10.1101/139337v1?rss=1 Butcher, P. A. Ivry, R. Kuo, S.-H. Rydz, D. Krakauer, J. W. Taylor, J. A. 2017-05-17 doi:10.1101/139337 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ A CRISPR-Based Yeast Two-Hybrid System For Investigating RNA-Protein Interactions ]]> https://biorxiv.org/content/10.1101/139600v1?rss=1 Hass, E. P. Zappulla, D. C. 2017-05-19 doi:10.1101/139600 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ Re-Evaluating Evolution In The HIV Reservoir ]]> https://biorxiv.org/content/10.1101/140731v1?rss=1 Rosenbloom, D. I. S. Hill, A. L. Laskey, S. B. Siliciano, R. F. 2017-05-22 doi:10.1101/140731 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ A Complete Electron Microscopy Volume Of The Brain Of Adult Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/140905v1?rss=1 Zheng, Z. Lauritzen, J. S. Perlman, E. Robinson, C. G. Nichols, M. Milkie, D. Torrens, O. Price, J. Fisher, C. B. Sharifi, N. Calle-Schuler, S. A. Kmecova, L. Ali, I. J. Karsh, B. Trautman, E. T. Bogovic, J. Hanslovsky, P. Jefferis, G. S. X. E. Kazhdan, M. Khairy, K. Saalfeld, S. Fetter, R. D. Bock, D. D. 2017-05-22 doi:10.1101/140905 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Advancing A Science For Sustaining Health: Establishing A Model Health District in Madagascar ]]> https://biorxiv.org/content/10.1101/141549v1?rss=1 Bonds, M. Garchitorena, A. Cordier, L. Miller, A. C. McCarty, M. Andriamihaja, B. Ratsirarson, J. Randrianambinina, A. Rabeza, V. R. Finnegan, K. Gillespie, T. Wright, P. C. Farmer, P. E. Loyd, T. Murray, M. B. Herrnstein, R. M. Herrnstein, J. PIVOT Impact Team, Gikic, D. Ouenzar, M. A. Hall, L. Rich, M. L. 2017-05-30 doi:10.1101/141549 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ The Complete Connectome Of A Learning And Memory Center In An Insect Brain ]]> https://biorxiv.org/content/10.1101/141762v1?rss=1 Eichler, K. Litwin-Kumar, A. Li, F. Park, Y. Andrade, I. Schneider-Mizell, C. M. Saumweber, T. Huser, A. Eschbach, C. Gerber, B. Fetter, R. D. Truman, J. W. Priebe, C. E. Abbott, L. F. Thum, A. S. Zlatic, M. Cardona, A. 2017-05-24 doi:10.1101/141762 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility ]]> https://biorxiv.org/content/10.1101/143933v1?rss=1 - International Multiple Sclerosis Genetics Consorti, Patsopoulos, N. Baranzini, S. E. Santaniello, A. Shoostari, P. Cotsapas, C. Wong, G. Beecham, A. H. James, T. Replogle, J. Vlachos, I. McCabe, C. Pers, T. Brandes, A. White, C. Keenan, B. Cimpean, M. Winn, P. Panteliadis, I.-P. Robbins, A. Andlauer, T. F. M. Zarzycki, O. Dubois, B. Goris, A. Bach Sondergaard, H. Sellebjerg, F. Soelberg Sorensen, P. Ullum, H. Wegner Thoerner, L. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Berthele, A. Biberacher, V. B 2017-07-13 doi:10.1101/143933 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Temporal and spatial variation among single dopaminergic neuron transcriptomes informs cellular phenotype diversity and Parkinson’s Disease gene prioritization ]]> https://biorxiv.org/content/10.1101/148049v1?rss=1 Hook, P. McClymont, S. A. Cannon, G. H. Law, W. D. Goff, L. A. McCallion, A. S. 2017-06-09 doi:10.1101/148049 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Fluctuations of fMRI activation patterns reveal theta-band dynamics of visual object priming ]]> https://biorxiv.org/content/10.1101/148635v1?rss=1 Guo, B. Lu, Z. Goold, J. E. Luo, H. Meng, M. 2017-06-12 doi:10.1101/148635 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays: Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank ]]> https://biorxiv.org/content/10.1101/150219v1?rss=1 Nelson, S. C. Romm, J. M. Doheny, K. F. Pugh, E. W. Laurie, C. C. 2017-06-14 doi:10.1101/150219 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ MIMoSA: A Method for Inter-Modal Segmentation Analysis ]]> https://biorxiv.org/content/10.1101/150284v1?rss=1 Valcarcel, A. Linn, K. Vandekar, S. Satterthwaite, T. Calabresi, P. Pham, D. Shinohara, R. 2017-06-15 doi:10.1101/150284 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature Sensitive Mutants via Molecular Inversion Probes ]]> https://biorxiv.org/content/10.1101/150862v1?rss=1 Mok, C. Au, V. Thompson, O. Edgley, M. Gevirtzman, L. Yochem, J. Lowry, J. Memar, N. Wallenfang, M. Rasoloson, D. Bowerman, B. Schnabel, R. Seydoux, G. Moerman, D. G. Waterston, R. H. 2017-06-22 doi:10.1101/150862 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Dynamic interhemispheric coordination in face processing ]]> https://biorxiv.org/content/10.1101/151076v1?rss=1 Lu, Z. Guo, B. Meng, M. 2017-06-16 doi:10.1101/151076 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Sex differences in gene regulation in the dorsal root ganglion after nerve injury ]]> https://biorxiv.org/content/10.1101/152652v1?rss=1 Stephens, K. E. Zhou, W. Ji, Z. He, S. Ji, H. Guan, Y. Taverna, S. D. 2017-06-20 doi:10.1101/152652 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library ]]> https://biorxiv.org/content/10.1101/152777v1?rss=1 Hulse-Kemp, A. M. Maheshwari, S. Stoffel, K. Hill, T. A. Jaffe, D. Williams, S. Weisenfeld, N. Ramakrishnan, S. Kumar, V. Shah, P. Schatz, M. C. Church, D. M. Van Deynze, A. 2017-06-20 doi:10.1101/152777 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Natural variation in stochastic photoreceptor specification and color preference in Drosophila ]]> https://biorxiv.org/content/10.1101/153445v1?rss=1 Anderson, C. Reiss, I. Zhou, C. Cho, A. Siddiqi, H. Mormann, B. Avelis, C. M. Bergland, A. Roberts, E. Taylor, J. Vasiliauskas, D. Johnston, R. J. 2017-06-21 doi:10.1101/153445 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Prediction of peptide binding to MHC Class I proteins in the age of deep learning ]]> https://biorxiv.org/content/10.1101/154757v1?rss=1 Bhattacharya, R. Tokheim, C. Sivakumar, A. Guthrie, V. B. Anagnostou, V. Velculescu, V. E. Karchin, R. 2017-06-23 doi:10.1101/154757 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Spectrin is a mechanoresponsive protein shaping the architecture of intercellular invasion ]]> https://biorxiv.org/content/10.1101/154831v1?rss=1 Duan, R. Kim, J. H. Shilagardi, K. Schiffhauer, E. Son, S. Lee, D. Li, S. Thomas, C. Luo, T. Fletcher, D. A. Robinson, D. N. Chen, E. H. 2017-06-23 doi:10.1101/154831 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution ]]> https://biorxiv.org/content/10.1101/156588v1?rss=1 Fang, H. Huang, Y.-F. Radhakrishnan, A. Siepel, A. Lyon, G. J. Schatz, M. C. 2017-06-27 doi:10.1101/156588 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Variation in neuronal activity state, axonal projection target, and position principally define the transcriptional identity of individual neocortical projection neurons. ]]> https://biorxiv.org/content/10.1101/157149v1?rss=1 Chevee, M. A. Robertson, J. D. Cannon, G. H. Brown, S. P. Goff, L. A. 2017-06-28 doi:10.1101/157149 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Dissection of purified LINE-1 reveals distinct nuclear and cytoplasmic intermediates ]]> https://biorxiv.org/content/10.1101/157818v1?rss=1 Molloy, K. R. Taylor, M. S. Altukhov, I. Mita, P. Jiang, H. Adney, E. M. Wudzinska, A. Ischenko, D. Burns, K. H. Fenyo, D. Chait, B. T. Alexeev, D. Rout, M. P. Boeke, J. LaCava, J. 2017-06-30 doi:10.1101/157818 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum ]]> https://biorxiv.org/content/10.1101/159111v1?rss=1 Zimin, A. V. Puiu, D. Hall, R. Kingan, S. Salzberg, S. L. 2017-07-03 doi:10.1101/159111 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ In vivo calcium imaging visualizes peripheral neuron sensitization in murine osteoarthritis ]]> https://biorxiv.org/content/10.1101/160416v1?rss=1 Miller, R. Kim, Y. S. Tran, P. B. Dong, X. Miller, R. J. Malfait, A.-M. 2017-07-06 doi:10.1101/160416 Cold Spring Harbor Laboratory Press 2017-07-06 <![CDATA[ Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks ]]> https://biorxiv.org/content/10.1101/161109v1?rss=1 Paix, A. Folkmann, A. Goldman, D. H. Kulaga, H. Grzelak, M. Rasoloson, D. Paidemarry, S. Green, R. Reed, R. Seydoux, G. 2017-07-09 doi:10.1101/161109 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers ]]> https://biorxiv.org/content/10.1101/161356v1?rss=1 Yuan, Y. Ju, Y. S. Kim, Y. Li, J. Wang, Y. Yang, Y. Martincorena, I. Creighton, C. Weinstein, J. N. Xu, Y. Han, L. Kim, H.-L. Nakagawa, H. Park, K. Campbell, P. J. Liang, H. - PCAWG Network, 2017-07-09 doi:10.1101/161356 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ CRAVAT 4: Cancer-Related Analysis of Variants Toolkit ]]> https://biorxiv.org/content/10.1101/162859v1?rss=1 Masica, D. Douville, C. Tokheim, C. Bhattacharya, R. Kim, R. Moad, K. Ryan, M. C. Karchin, R. 2017-07-12 doi:10.1101/162859 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Specification of the germline by Nanos-dependent down-regulation of the somatic synMuvB transcription factor LIN-15B ]]> https://biorxiv.org/content/10.1101/163642v1?rss=1 Lee, C.-Y. S. Lu, T. Seydoux, G. 2017-07-14 doi:10.1101/163642 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ Cytosolic proteins can exploit membrane localization to trigger functional assembly ]]> https://biorxiv.org/content/10.1101/164152v1?rss=1 Yogurtcu, O. N. Johnson, M. E. 2017-07-15 doi:10.1101/164152 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ Causal role of beta oscillations in time estimation ]]> https://biorxiv.org/content/10.1101/165233v1?rss=1 Wiener, M. Parikh, A. Krakow, A. Coslett, H. B. 2017-07-19 doi:10.1101/165233 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ Unexpected Properties of Short Genomic Tandem Repeats ]]> https://biorxiv.org/content/10.1101/165308v1?rss=1 3). That is, the observed frequency of repeats of this length in the human genome is higher than expected by chance based on the frequency of shorter repeats.nnWe have hypothesized that this pattern may be a general property of genomic DNA. If true, this could have implications with regard to the dynamics of repeat expansion generally. To test this hypothesis, we have analyzed the genomic sequences of a broad range of eukaryotic organisms as well as several complete human genomes and obtained a number of thought provoking results. We establish that this unexpected elevation in frequency of 3n - 1 long repeats is statistically significant. We also expanded this analysis to different classes of genomic regions and tandem repeats of length four and five. The specific pattern was found in 13 of the 20 organisms analyzed, including all chordate and insect genomes tested. The bias pattern, however, was not confined to a single branch of the evolutionary tree. For some genomes, such as Drosophila melanogaster, the repeat bias surprisingly was also identified in exons. The pattern is present in both small and large genomes. A similar pattern was also found in tetranucleotide and pentanucleotide repeats in the human genome. Another surprising property was identified for the flanking GC content for triplet repeats of length 3n. These findings indicate a puzzling new genomic phenomenon with possible evolutionary and disease-related implications. ]]> Glotova, I. Molla, M. Delcher, A. L. Kasif, S. 2017-07-18 doi:10.1101/165308 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Serial dependence transfers between perceptual objects ]]> https://biorxiv.org/content/10.1101/165399v1?rss=1 Huffman, G. Pratt, J. Honey, C. J. 2017-07-19 doi:10.1101/165399 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ Repositioning the Sm-binding site in S. cerevisiae telomerase RNA reveals RNP organizational flexibility and Sm-directed 3′-end formation ]]> https://biorxiv.org/content/10.1101/167361v1?rss=1 Hass, E. P. Zappulla, D. C. 2017-07-22 doi:10.1101/167361 Cold Spring Harbor Laboratory Press 2017-07-22 <![CDATA[ Temporal expression divergence of network modules ]]> https://biorxiv.org/content/10.1101/167734v1?rss=1 Park, Y. Kang, T.-H. Friedmann, T. Bader, J. 2017-07-24 doi:10.1101/167734 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ A GAL80 collection to nullify transgenes in Drosophila olfactory sensory neurons ]]> https://biorxiv.org/content/10.1101/168468v1?rss=1 Eliason, J. Afify, A. Potter, C. Matsumura, I. 2017-07-26 doi:10.1101/168468 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Experience-dependent translational state defined by cell type-specific ribosome profiling ]]> https://biorxiv.org/content/10.1101/169425v1?rss=1 Eacker, S. M. Crawford, K. Brichta, L. Riessland, M. Ingolia, N. T. Greengard, P. Dawson, T. M. Dawson, V. L. 2017-07-28 doi:10.1101/169425 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Accurate detection of complex structural variations using single molecule sequencing ]]> https://biorxiv.org/content/10.1101/169557v1?rss=1 Sedlazeck, F. J. Rescheneder, P. Smolka, M. Fang, H. Nattestad, M. von Haeseler, A. Schatz, M. 2017-07-28 doi:10.1101/169557 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ The intrinsically disordered C-terminal linker of FtsZ regulates protofilament dynamics and superstructure in vitro ]]> https://biorxiv.org/content/10.1101/171280v1?rss=1 Sundararajan, K. Goley, E. D. 2017-08-01 doi:10.1101/171280 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue ]]> https://biorxiv.org/content/10.1101/171397v1?rss=1 Yu, J. Boyle, P. M. Klimas, A. Williams, J. C. Trayanova, N. A. Entcheva, E. 2017-08-02 doi:10.1101/171397 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans) ]]> https://biorxiv.org/content/10.1101/171975v1?rss=1 Luo, R. Zimin, A. Workman, R. Fan, Y. Pertea, G. Grossman, N. Wear, M. Jia, B. Miller, H. Casadevall, A. Timp, W. Zhang, S. Salzberg, S. 2017-08-03 doi:10.1101/171975 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide ]]> https://biorxiv.org/content/10.1101/173831v1?rss=1 Satizabal, C. L. Adams, H. H. H. Hibar, D. P. White, C. C. Stein, J. L. Scholz, M. Sargurupremraj, M. Jahanshad, N. Smith, A. V. Bis, J. C. Jian, X. Luciano, M. Hofer, E. Teumer, A. van der Lee, S. J. Yang, J. Yanek, L. R. Lee, T. V. Li, S. Hu, Y. Koh, J. Y. Eicher, J. D. Desrivieres, S. Arias-Vasquez, A. Chauhan, G. Athanasiu, L. Renteria, M. E. Kim, S. Hohn, D. Armstrong, N. J. Chen, Q. Holmes, A. J. den Braber, A. Kloszewska, I. Andersson, M. Espeseth, T. Grimm, O. Abramovic, L. Alhusaini, S. Milaneschi, Y. Papmeyer, M. Axelsson, T. Ehrlich, S. Roi 2017-08-28 doi:10.1101/173831 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Suppression and facilitation of human neural responses ]]> https://biorxiv.org/content/10.1101/174466v1?rss=1 Schallmo, M.-P. Kale, A. M. Millin, R. Flevaris, A. V. Brkanac, Z. Edden, R. A. E. Bernier, R. A. Murray, S. 2017-08-10 doi:10.1101/174466 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line ]]> https://biorxiv.org/content/10.1101/174938v1?rss=1 Nattestad, M. Goodwin, S. Ng, K. Baslan, T. Sedlazeck, F. J. Rescheneder, P. Garvin, T. Fang, H. Gurtowski, J. Hutton, E. Tseng, E. Chin, C.-S. Beck, T. Sundaravadanam, Y. Kramer, M. Antoniou, E. McPherson, J. D. Hicks, J. McCombie, W. R. Schatz, M. C. 2017-08-10 doi:10.1101/174938 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World ]]> https://biorxiv.org/content/10.1101/175067v1?rss=1 20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. Fatty acid desaturase (FADS) 1 and 2 catalyze the rate-limiting steps in the biosynthesis of LC-PUFAs. The FADS region contains two haplotypes; ancestral and derived, where the derived haplotypes are associated with more efficient LC-PUFA biosynthesis and is nearly fixed in Africa. In addition, Native American populations appear to be nearly fixed for the lesser efficient ancestral haplotype, which could be a public health problem due to associated low LC-PUFA levels, while Eurasia is polymorphic. This haplotype frequency distribution is suggestive of archaic re-introduction of the ancestral haplotype to non-African populations or ancient polymorphism with differential selection patterns across the globe. Therefore, we tested the FADS region for archaic introgression or ancient polymorphism. We specifically addressed the genetic architecture of the FADS region in Native American populations to better understand this potential public health impact.nnResultsWe confirmed Native American ancestry is nearly fixed for the ancestral haplotype and is under positive selection. The ancestral haplotype frequency is also correlated to Siberian populations geographic location further suggesting the ancestral haplotype s role in cold weather adaptation and leading to the high haplotype frequency within Native American populations. We also find that the Neanderthal is more closely related to the derived haplotypes while the Denisovan clusters closer to the ancestral haplotypes. In addition, the derived haplotypes have a time to the most recent common ancestor of 688,474 years ago which is within the range of the modern-archaic hominin divergence.nnConclusionsThese results support an ancient polymorphism forming in the FADS gene region with differential selection pressures acting on the derived and ancestral haplotypes due to the old age of the derived haplotypes and the ancestral haplotype being under positive selection in Native American ancestry populations. Further, the near fixation of the less efficient ancestral haplotype in Native American ancestry suggests the need for future studies to explore the potential health risk of associated low LC-PUFA levels in Native American ancestry populations. ]]> Harris, D. N. Ruczinski, I. Yanek, L. R. Becker, L. C. Becker, D. M. Guio, H. Cui, T. Chilton, F. H. Mathias, R. A. O'Connor, T. 2017-08-10 doi:10.1101/175067 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits and implications for the future ]]> https://biorxiv.org/content/10.1101/175406v1?rss=1 Zhang, Y. Qi, G. Park, J.-H. Chatterjee, N. 2017-08-11 doi:10.1101/175406 Cold Spring Harbor Laboratory Press 2017-08-11 <![CDATA[ GPU-accelerated alignment of bisulfite-treated short-read sequences ]]> https://biorxiv.org/content/10.1101/175729v1?rss=1 Wilton, R. Li, X. Feinberg, A. P. Szalay, A. S. 2017-08-25 doi:10.1101/175729 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Ninety-nine independent genetic loci influencing general cognitive function include genes associated with brain health and structure (N = 280,360) ]]> https://biorxiv.org/content/10.1101/176511v1?rss=1 Davies, G. Lam, M. Harris, S. E. Trampush, J. Luciano, M. Hill, W. D. Hagenaars, S. P. Ritchie, S. J. Marioni, R. E. Fawns-Ritchie, C. Liewald, D. C. Okely, J. Ahola-Olli, A. Barnes, C. L. K. Bertram, L. Bis, J. C. Burdick, K. E. Christoforou, A. DeRosse, P. Djurovic, S. Espeseth, T. Giakoumaki, S. Giddaluru, S. Gustavson, D. E. Hayward, C. Hofer, E. Ikram, M. A. Karlsson, R. Knowles, E. Lahti, J. Leber, M. Li, S. Mather, K. A. Melle, I. Morris, D. Oldmeadow, C. Palviainen, T. Payton, A. Pazoki, R. Petrovic, K. Reynolds, C. A. Sargurupremraj, M. Scholz 2017-08-17 doi:10.1101/176511 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Transient Reduction of DNA Methylation at the Onset of Meiosis in Male Mice ]]> https://biorxiv.org/content/10.1101/177535v1?rss=1 Gaysinskaya, V. Miller, B. F. van der Heijden, G. W. Hansen, K. D. Bortvin, A. 2017-08-17 doi:10.1101/177535 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours ]]> https://biorxiv.org/content/10.1101/179705v1?rss=1 Rodriguez-Martin, B. Alvarez, E. G. Baez-Ortega, A. Demeulemeester, J. Ju, Y. S. Zamora, J. Detering, H. Li, Y. Contino, G. Dentro, S. C. Bruzos, A. L. Dueso-Barroso, A. Ardeljan, D. Tojo, M. Roberts, N. D. Blanco, M. G. Edwards, P. A. W. Weischenfeldt, J. Santamarina, M. Puiggros, M. Chong, Z. Chen, K. Lee, E. A. Wala, J. A. Raine, K. Butler, A. Waszak, S. M. Navarro, F. C. P. Schumacher, S. E. Monlong, J. Maura, F. Bolli, N. Bourque, G. Gerstein, M. Park, P. J. Berroukhim, R. Torrents, D. Korbel, J. O. Martincorena, I. Fitzgerald, R. C. Van Loo, P. Ka 2017-08-24 doi:10.1101/179705 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation ]]> https://biorxiv.org/content/10.1101/181057v1?rss=1 0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired individual samples ranged from r=0.66 to r=0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (5 sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P=0.86), and estimated cell counts were highly correlated between paired samples (r=0.99).nnConclusionsDifferences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared. ]]> Dou, J. Schmidt, R. J. Benke, K. S. Newschaffer, C. Hertz-Picciotto, I. Croen, L. A. Iosif, A.-M. LaSalle, J. Fallin, M. D. Bakulski, K. 2017-08-31 doi:10.1101/181057 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility ]]> https://biorxiv.org/content/10.1101/182576v1?rss=1 Grotjahn, D. A. Chowdhury, S. Xu, Y. McKenney, R. J. Schroer, T. Lander, G. 2017-08-31 doi:10.1101/182576 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Applying the auxin-inducible degradation (AID) system for rapid protein depletion in mammalian cells ]]> https://biorxiv.org/content/10.1101/182840v1?rss=1 Lambrus, B. G. Moyer, T. C. Holland, A. 2017-08-31 doi:10.1101/182840 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression ]]> https://biorxiv.org/content/10.1101/182972v1?rss=1 Doganay, S. Lee, M. Y. Baum, A. Peh, J. Hwang, S.-Y. Yoo, J.-Y. Hergenrother, P. J. Garcia-Sastre, A. Myong, S. Ha, T. 2017-08-31 doi:10.1101/182972 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina. ]]> https://biorxiv.org/content/10.1101/183285v1?rss=1 de Melo, J. Venkataraman, A. Zibetti, C. Clark, B. S. Blackshaw, S. 2017-09-01 doi:10.1101/183285 Cold Spring Harbor Laboratory Press 2017-09-01 <![CDATA[ A predictive model of rats’ calorie intake as a function of diet energy density ]]> https://biorxiv.org/content/10.1101/184085v1?rss=1 Beheshti, R. Treesukosol, Y. Igusa, T. Moran, T. H. 2017-09-04 doi:10.1101/184085 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence ]]> https://biorxiv.org/content/10.1101/184853v1?rss=1 Savage, J. E. Jansen, P. R. Stringer, S. Watanabe, K. Bryois, J. de Leeuw, C. A. Nagel, M. Awasthi, S. Barr, P. B. Coleman, J. R. I. Grasby, K. L. Hammerschlag, A. R. Kaminski, J. Karlsson, R. Krapohl, E. Lam, M. Nygaard, M. Reynolds, C. A. Trampush, J. W. Young, H. Zabaneh, D. Hägg, S. Hansell, N. K. Karlsson, I. K. Linnarsson, S. Montgomery, G. W. Munoz-Manchado, A. B. Quinlan, E. B. Schumann, G. Skene, N. Webb, B. T. White, T. Arking, D. E. Attix, D. K. Avramopoulos, D. Bilder, R. M. Bitsios, P. Burdick, K. E. Cannon, T. D. Chiba-Falek, O. Chr 2017-09-06 doi:10.1101/184853 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Instantiation of incentive value and movement invigoration by distinct midbrain dopamine circuits ]]> https://biorxiv.org/content/10.1101/186502v1?rss=1 Saunders, B. Richard, J. Margolis, E. Janak, P. 2017-09-10 doi:10.1101/186502 Cold Spring Harbor Laboratory Press 2017-09-10 <![CDATA[ Genetic Diversity Turns a New PAGE in Our Understanding of Complex Traits ]]> https://biorxiv.org/content/10.1101/188094v1?rss=1 Wojcik, G. Graff, M. Nishimura, K. K. Tao, R. Haessler, J. Gignoux, C. R. Highland, H. M. Patel, Y. M. Sorokin, E. P. Avery, C. L. Belbin, G. M. Bien, S. A. Cheng, I. Hodonsky, C. J. Huckins, L. M. Jeff, J. Justice, A. E. Kocarnik, J. M. Lim, U. Lin, B. M. Lu, Y. Nelson, S. C. Park, S.-S. L. Preuss, M. H. Richard, M. A. Schurmann, C. Setiawan, V. W. Vahi, K. Vishnu, A. Verbanck, M. Walker, R. Young, K. L. Zubair, N. Ambite, J. L. Boerwinkle, E. Bottinger, E. Bustamante, C. D. Caberto, C. Conomos, M. P. Deelman, E. Do, R. Doheny, K. Fernandez-Rhodes, L. 2017-09-15 doi:10.1101/188094 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ A Comprehensive Cloud Framework for Accurate and Reliable Human Connectome Estimation and Meganalysis ]]> https://biorxiv.org/content/10.1101/188706v1?rss=1 Kiar, G. Bridgeford, E. Chandrashekhar, V. Mhembere, D. Burns, R. Gray Roncal, W. Vogelstein, J. 2017-09-14 doi:10.1101/188706 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Measuring the reproducibility and quality of Hi-C data ]]> https://biorxiv.org/content/10.1101/188755v1?rss=1 Yardimci, G. Ozadam, H. Sauria, M. E. G. Ursu, O. Yan, K.-K. Yang, T. Chakraborty, A. Kaul, A. Lajoie, B. R. Song, F. Zhan, Y. Ay, F. Gerstein, M. Kundaje, A. Li, Q. Taylor, J. Yue, F. Dekker, J. Noble, W. S. 2017-09-14 doi:10.1101/188755 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Harnessing the adaptive potential of mechanoresponsive proteins to overwhelm pancreatic cancer dissemination and invasion ]]> https://biorxiv.org/content/10.1101/190553v1?rss=1 Surcel, A. Schiffhauer, E. S. Thomas, D. Zhu, Q. DiNapoli, K. Herbig, M. Otto, O. Guck, J. Jaffee, E. Iglesias, P. Anders, R. Robinson, D. 2017-09-19 doi:10.1101/190553 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Single Cell RNA Sequencing of stem cell-derived retinal ganglion cells. ]]> https://biorxiv.org/content/10.1101/191395v1?rss=1 Daniszewski, M. Senabouth, A. Nguyen, Q. Crombie, D. E. Lukowski, S. W. Kulkarni, T. Zack, D. J. Pebay, A. Powell, J. E. Hewitt, A. 2017-09-22 doi:10.1101/191395 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Clofazimine targets essential nucleoid associated protein, mycobacterial integration host factor (mIHF), in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/192161v1?rss=1 Shi, W. Zhang, S. Feng, J. Cui, P. Zhang, W. Zhang, Y. 2017-09-21 doi:10.1101/192161 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis ]]> https://biorxiv.org/content/10.1101/192724v1?rss=1 Singh, D. Wang, Y. Mallon, J. Yang, O. Fei, J. Poddar, A. Ceylan, D. Bailey, S. Ha, T. 2017-09-22 doi:10.1101/192724 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Learning naturalistic temporal structure in the posterior medial network ]]> https://biorxiv.org/content/10.1101/196287v1?rss=1 Aly, M. Chen, J. Turk-Browne, N. B. Hasson, U. 2017-10-01 doi:10.1101/196287 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ A unified web platform for network-based analyses of genomic data ]]> https://biorxiv.org/content/10.1101/196303v1?rss=1 Li, T. Kim, A. Mercer, J. Rosenbluh, J. Horn, H. Greenfeld, L. An, D. Zimmer, A. Liberzon, A. Bistline, J. Natoli, T. Li, Y. Tsherniak, A. Narayan, R. Subramanian, A. Liefeld, T. Wong, B. Thompson, D. Calvo, S. Carr, S. Boehm, J. Jaffe, J. Mesirov, J. Hacohen, N. Regev, A. Lage, K. 2017-10-02 doi:10.1101/196303 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Linear models enable powerful differential activity analysis in massively parallel reporter assays ]]> https://biorxiv.org/content/10.1101/196394v1?rss=1 Myint, L. Avramopoulos, D. G. Goff, L. A. Hansen, K. 2017-09-30 doi:10.1101/196394 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Brief targeted memory reactivation during the awake state enhances memory stability and benefits the weakest memories ]]> https://biorxiv.org/content/10.1101/196436v1?rss=1 Tambini, A. Berners-Lee, A. Davachi, L. 2017-09-30 doi:10.1101/196436 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Enter the matrix: Interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data ]]> https://biorxiv.org/content/10.1101/196915v1?rss=1 Stein-O'Brien, G. L. Arora, R. Culhane, A. C. Favorov, A. Greene, C. Goff, L. A. Li, Y. Ngom, A. Ochs, M. F. Xu, Y. Fertig, E. 2017-10-02 doi:10.1101/196915 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ A Feed-forward Relay between Bicoid and Orthodenticle Regulates the Timing ofEmbryonic Patterning in Drosophila ]]> https://biorxiv.org/content/10.1101/198036v1?rss=1 Datta, R. Ling, J. Kurland, J. Ren, X. Zhe, X. Yucel, G. Moore, J. Shokri, L. Baker, I. Bishop, T. Struffi, P. Levina, R. Bulyk, M. Johnston, R. Small, S. 2017-10-03 doi:10.1101/198036 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ ZMPSTE24 Missense Mutations that Cause Progeroid Diseases Decrease Prelamin A Cleavage Activity, Protein Stability, or Both ]]> https://biorxiv.org/content/10.1101/198069v1?rss=1 Spear, E. Hsu, E.-T. Nie, L. Carpenter, E. P. Hrycyna, C. Michaelis, S. 2017-10-04 doi:10.1101/198069 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Genetic analysis of over one million people identifies 535 novel loci for blood pressure. ]]> https://biorxiv.org/content/10.1101/198234v1?rss=1 Evangelou, E. Warren, H. R. Mosen-Ansorena, D. Mifsud, B. Pazoki, R. Gao, H. Ntritsos, G. Dimou, N. Cabrera, C. P. Karaman, I. Ng, F. L. Evangelou, M. Witkowska, K. Tzanis, E. Hellwege, J. N. Giri, A. Velez Edwards, D. R. Sun, Y. V. Cho, K. Gaziano, J. M. Wilson, P. W. F. Tsao, P. S. Kovesdy, C. P. Esko, T. Magi, R. Milani, L. Almgren, P. Boutin, T. Debette, S. Ding, J. Giulianini, F. Holliday, E. G. Jackson, A. U. Li-Gao, R. Lin, W.-Y. Luan, J. Mangino, M. Oldmeadow, C. Prins, B. Qian, Y. Sargurupremraj, M. Shah, N. Surendran, P. Theriault, S. Verwe 2017-10-11 doi:10.1101/198234 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Glutathione S-transferases: unexpected roles in astrocyte activation and astrocyte-microglia communication during brain inflammation ]]> https://biorxiv.org/content/10.1101/199612v1?rss=1 Kano, S.-i. Choi, E. Y. Dohi, E. Rose, I. V. L. Chang, D. J. Wilson, A. M. Lo, B. D. Imai, T. Sawa, A. 2017-10-07 doi:10.1101/199612 Cold Spring Harbor Laboratory Press 2017-10-07 <![CDATA[ Practical computational reproducibility in the life sciences ]]> https://biorxiv.org/content/10.1101/200683v1?rss=1 Grüning, B. Chilton, J. Köster, J. Dale, R. Goecks, J. Backofen, R. Nekrutenko, A. Taylor, J. 2017-10-10 doi:10.1101/200683 Cold Spring Harbor Laboratory Press 2017-10-10 <![CDATA[ Skill Acquisition and Habit Formation as Distinct Effects of Practice ]]> https://biorxiv.org/content/10.1101/201095v1?rss=1 Hardwick, R. M. Forrence, A. D. Krakauer, J. W. Haith, A. M. 2017-10-14 doi:10.1101/201095 Cold Spring Harbor Laboratory Press 2017-10-14 <![CDATA[ Chr21 protein-protein interactions: enrichment in products involved in intellectual disabilities, autism and Late Onset Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2019.12.11.872606v1?rss=1 Viard, J. Loe-Mie, Y. Khelfaoui, M. Daudin, R. Plancon, C. Boland, A. Tejedor, F. Huganir, R. Kim, E. Kinoshita, M. Liu, G. Haucke, V. Moncion, T. Yu, E. Hindie, V. Blehaut, H. Mircher, C. Herault, Y. Deleuze, J.-F. Rain, J.-C. Simonneau, M. Lepagnol-Bestel, A.-M. 2019-12-12 doi:10.1101/2019.12.11.872606 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Phase of Firing Coding of Learning Variables across Prefrontal Cortex, Anterior Cingulate Cortex and Striatum during Feature Learning ]]> https://biorxiv.org/content/10.1101/2019.12.12.874859v1?rss=1 Voloh, B. Oemisch, M. Womelsdorf, T. 2019-12-13 doi:10.1101/2019.12.12.874859 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Fatty acid synthesis in satellite glial cell promotes regenerative growth in sensory neurons ]]> https://biorxiv.org/content/10.1101/2019.12.13.874669v1?rss=1 Avraham, O. Deng, P.-Y. Jones, S. Kuruvilla, R. Semenkovich, C. F. Klyachko, V. A. Cavalli, V. 2019-12-13 doi:10.1101/2019.12.13.874669 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ PULL-PUSH NEUROMODULATION OF CORTICAL PLASTICITY ENABLES RAPID BI-DIRECTIONAL SHIFTS IN OCULAR DOMINANCE ]]> https://biorxiv.org/content/10.1101/2019.12.13.875849v1?rss=1 Hong, S. huang, S. Severin, D. kirkwood, a. 2019-12-13 doi:10.1101/2019.12.13.875849 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies ]]> https://biorxiv.org/content/10.1101/2019.12.17.864991v1?rss=1 Zimin, A. V. Salzberg, S. 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Baxter, E. Van Doren, M. 2019-12-18 doi:10.1101/2019.12.17.880070 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ A clinically and genomically annotated nerve sheath tumor biospecimen repository. ]]> https://biorxiv.org/content/10.1101/2019.12.19.871897v1?rss=1 Pollard, K. Banerjee, J. Doan, X. Wang, J. Guo, X. Allaway, R. J. Langmead, S. Slobogean, B. Meyer, C. Loeb, D. Morris, C. Belzberg, A. Blakeley, J. O. Rodriguez, F. Guinney, J. Gosline, S. J. Pratilas, C. A. 2019-12-19 doi:10.1101/2019.12.19.871897 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ An in situ atlas of mitochondrial DNA in mammalian tissues reveals high content in stem/progenitor cells ]]> https://biorxiv.org/content/10.1101/2019.12.19.876144v1?rss=1 Chen, J. Zheng, Q. Peiffer, L. B. Hicks, J. L. Haffner, M. C. Rosenberg, A. Z. Levi, M. Wang, X. X. Ozbek, B. Yegnasubramanian, S. De Marzo, A. M. 2019-12-19 doi:10.1101/2019.12.19.876144 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Loss of function variants in PCYT1A causing spondylometaphyseal dysplasia with cone/rod dystrophy have broad consequences on lipid metabolism, chondrocyte differentiation, and lipid droplet formation. ]]> https://biorxiv.org/content/10.1101/2019.12.19.882191v1?rss=1 Jurgens, J. Chen, S. Sobreira, N. Robbins, S. Franca Anzmann, A. Dastgheyb, R. Khuder, S. S. Hoover-Fong, J. Woods, C. Collins, F. Christodoulou, J. Lopes Yamamoto, G. Romeo Bertola, D. Baratela, W. A. R. Curie, S. D. Haughey, N. Cornell, R. B. Valle, D. 2019-12-19 doi:10.1101/2019.12.19.882191 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Protein Docking and Steered Molecular Dynamics Reveal Alternative Regulatory Sites on the SERCA Calcium Transporter ]]> https://biorxiv.org/content/10.1101/2019.12.19.883355v1?rss=1 Alford, R. F. Smolin, N. Young, H. S. Gray, J. J. Robia, S. L. 2019-12-20 doi:10.1101/2019.12.19.883355 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Categorical signaling of the strongest stimulus by an inhibitory midbrain nucleus ]]> https://biorxiv.org/content/10.1101/2019.12.19.883702v1?rss=1 Schryver, H. M. Straka, M. Mysore, S. P. 2019-12-20 doi:10.1101/2019.12.19.883702 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Vargas: heuristic-free alignment for assessing linear and graph read aligners ]]> https://biorxiv.org/content/10.1101/2019.12.20.884676v1?rss=1 Darby, C. A. Gaddipati, R. Schatz, M. C. Langmead, B. 2019-12-21 doi:10.1101/2019.12.20.884676 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Real-time monitoring of cotranscriptional riboswitch folding and switching ]]> https://biorxiv.org/content/10.1101/2019.12.20.885053v1?rss=1 Hua, B. Jones, C. P. Mitra, J. Murray, P. J. Rosenthal, R. FerreDAmare, A. R. Ha, T. 2019-12-22 doi:10.1101/2019.12.20.885053 Cold Spring Harbor Laboratory Press 2019-12-22 <![CDATA[ The protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study ]]> https://biorxiv.org/content/10.1101/2019.12.20.885384v1?rss=1 Milne, S. Li, X. Hernandez Cordero, A. I. Yang, C. X. Cho, M. H. Beaty, T. H. Ruczinski, I. Hansel, N. N. Bosse, Y. Brandsma, C.-A. Sin, D. D. Obeidat, M. 2019-12-21 doi:10.1101/2019.12.20.885384 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Quantifiable In Vivo Imaging Biomarkers of Retinal Regeneration by Photoreceptor Cell Transplantation ]]> https://biorxiv.org/content/10.1101/2019.12.21.884973v1?rss=1 Liu, Y. V. Sodhi, S. Xue, G. Teng, D. Agakishiev, D. McNally, M. M. Harris-Bookman, S. McBride, C. Konar, G. Singh, M. 2019-12-23 doi:10.1101/2019.12.21.884973 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ TrkB agonists prevent post-ischemic BDNF-TrkB mediated emergence of refractory neonatal seizures in CD-1 pups. ]]> https://biorxiv.org/content/10.1101/2019.12.23.887190v1?rss=1 Kipnis, P. A. Sullivan, B. J. Carter, B. M. Kadam, S. D. 2019-12-23 doi:10.1101/2019.12.23.887190 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Neural circuit mechanism for generating categorical representations ]]> https://biorxiv.org/content/10.1101/2019.12.24.887810v1?rss=1 Mahajan, N. R. Mysore, S. P. 2019-12-24 doi:10.1101/2019.12.24.887810 Cold Spring Harbor Laboratory Press 2019-12-24 <![CDATA[ Disrupted neural synchrony mediates the relationship between white matter integrity and cognitive performance in older adults. ]]> https://biorxiv.org/content/10.1101/2019.12.29.890228v1?rss=1 Hinault, T. T. Kraut, M. Bakker, A. Dagher, A. Courtney, S. 2019-12-30 doi:10.1101/2019.12.29.890228 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Calcium induced calcium release in proximity to hair cell BK channels revealed by PKA activation ]]> https://biorxiv.org/content/10.1101/2019.12.30.890558v1?rss=1 Bai, J. Xue, N. Lawal, O. Nyati, A. Santos-Sacchi, J. Navaratnam, D. S. 2019-12-30 doi:10.1101/2019.12.30.890558 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Single molecule tracking reveals the role of transitory dynamics of nucleoid-associated protein HU in organizing the bacterial chromosome ]]> https://biorxiv.org/content/10.1101/2019.12.31.725226v1?rss=1 Bettridge, K. Verma, S. Weng, X. Adhya, S. Xiao, J. 2019-12-31 doi:10.1101/2019.12.31.725226 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ The immediate early gene Arc is not required for hippocampal long-term potentiation. ]]> https://biorxiv.org/content/10.1101/2020.01.03.893305v1?rss=1 Kyrke-Smith, M. Volk, L. J. Cooke, S. F. Bear, M. F. Huganir, R. L. Shepherd, J. D. 2020-01-03 doi:10.1101/2020.01.03.893305 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ What matters to patients?: a timely question for Value Based Care ]]> https://biorxiv.org/content/10.1101/2020.01.03.893826v1?rss=1 Hirpa, M. Woreta, T. Addis, H. Kebede, S. 2020-01-06 doi:10.1101/2020.01.03.893826 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism ]]> https://biorxiv.org/content/10.1101/2020.01.06.894287v1?rss=1 Starostik, M. R. Sosina, O. A. McCoy, R. C. 2020-01-07 doi:10.1101/2020.01.06.894287 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Role of DNA Methylation in Persister Formation in Uropathogenic E. coli ]]> https://biorxiv.org/content/10.1101/2020.01.07.897686v1?rss=1 Xu, Y. Liu, S. Zhang, W. Zhang, Y. 2020-01-08 doi:10.1101/2020.01.07.897686 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Inhibition of the polyamine synthesis enzyme ornithine decarboxylase sensitizes triple-negative breast cancer cells to cytotoxic chemotherapy ]]> https://biorxiv.org/content/10.1101/2020.01.08.899492v1?rss=1 Geck, R. C. Foley, J. R. Murray Stewart, T. R. Asara, J. M. Casero, R. A. Toker, A. 2020-01-09 doi:10.1101/2020.01.08.899492 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit ]]> https://biorxiv.org/content/10.1101/2020.01.10.902312v1?rss=1 Tenner, B. Getz, M. Ross, B. Ohadi, D. Bohrer, C. H. Greenwald, E. Mehta, S. Xiao, J. Rangamani, P. Zhang, J. 2020-01-11 doi:10.1101/2020.01.10.902312 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Complement and coagulation cascades are potentially involved in dopaminergic neurodegeneration in alpha-synuclein-based mouse models of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2020.01.11.900886v1?rss=1 Ma, S.-X. Kim, D. Xiong, Y. Kwon, S.-H. Brahmachari, S. Kim, S. Kam, T.-I. Nirujogi, R. S. Kwon, S. H. Dawson, V. L. Dawson, T. M. Pandey, A. Na, C. H. Ko, H. S. 2020-01-13 doi:10.1101/2020.01.11.900886 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Integrative analysis identifies candidate tumor microenvironment and intracellular signaling pathways that define tumor heterogeneity in NF1 ]]> https://biorxiv.org/content/10.1101/2020.01.13.904771v1?rss=1 Banerjee, J. Allaway, R. J. Taroni, J. N. Baker, A. Zhang, X. Moon, C. I. Blakeley, J. O. Guinney, J. Hirbe, A. Greene, C. S. Gosline, S. J. 2020-01-14 doi:10.1101/2020.01.13.904771 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Recent fluctuations in Mexican American genomes have altered the genetic architecture of biomedical traits ]]> https://biorxiv.org/content/10.1101/2020.01.13.905141v1?rss=1 Spear, M. L. Diaz-Papkovich, A. Ziv, E. Gravel, S. Torgerson, D. G. Hernandez, R. 2020-01-14 doi:10.1101/2020.01.13.905141 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Quantifying Epithelial Plasticity as a Platform to Reverse Epithelial Injury ]]> https://biorxiv.org/content/10.1101/2020.01.14.906008v1?rss=1 Nishida, K. Ghosh, B. Chandrala, L. Mahmud, S. Chen, S. Khosla, A. A. Katz, J. Sidhaye, V. K. 2020-01-15 doi:10.1101/2020.01.14.906008 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ De novo learning versus adaptation of continuous control in a manual tracking task ]]> https://biorxiv.org/content/10.1101/2020.01.15.906545v1?rss=1 Yang, C. S. Cowan, N. J. Haith, A. M. 2020-01-16 doi:10.1101/2020.01.15.906545 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ A Whole-Brain Regression Method to Identify Individual and Group Variations in Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2020.01.16.909580v1?rss=1 Zhao, Y. Caffo, B. S. Wang, B. Li, C.-s. R. Luo, X. 2020-01-17 doi:10.1101/2020.01.16.909580 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Splicing of the SynGAP Carboxyl-Terminus Enables Isoform-Specific Tuning of NMDA Receptor Signaling Linked to Cognitive Function ]]> https://biorxiv.org/content/10.1101/2020.01.18.911487v1?rss=1 Kilinc, M. Creson, T. K. Rojas, C. Maity, S. Le, A. A. Lauterborn, J. Wilkinson, B. Hartel, N. Graham, N. A. Reich, A. Gou, G. Araki, Y. Bayes, A. Coba, M. P. Lynch, G. Miller, C. A. Rumbaugh, G. 2020-01-19 doi:10.1101/2020.01.18.911487 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ Strategies for cellular deconvolution in human brain RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2020.01.19.910976v1?rss=1 Sosina, O. A. Tran, M. N. Maynard, K. Tao, R. Taub, M. A. Martinowich, K. Semick, S. A. Weinberger, D. Quach, B. C. Hyde, T. M. Hancock, D. B. Kleinman, J. E. Leek, J. T. Jaffe, A. E. 2020-01-20 doi:10.1101/2020.01.19.910976 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Prenylation of axonally translated proteins controls NGF-dependent axon growth ]]> https://biorxiv.org/content/10.1101/2020.01.21.914606v1?rss=1 Scott-Solomon, E. Kuruvilla, R. 2020-01-22 doi:10.1101/2020.01.21.914606 Cold Spring Harbor Laboratory Press 2020-01-22 <![CDATA[ Implicit adaptation is driven by direct policy updates rather than forward-model-based learning ]]> https://biorxiv.org/content/10.1101/2020.01.22.914473v1?rss=1 Hadjiosif, A. M. Krakauer, J. W. Haith, A. M. 2020-01-23 doi:10.1101/2020.01.22.914473 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Proteogenomic single cell analysis of skeletal muscle myocytes ]]> https://biorxiv.org/content/10.1101/2020.01.23.916791v1?rss=1 Fomchenko, K. M. Verma, R. X. Kannan, S. Lin, B. L. Yang, X. Nieuwenhuis, T. O. Patil, A. H. Fox-Talbot, K. McCall, M. N. Kwon, C. Kass, D. A. Rosenberg, A. Z. Halushka, M. K. 2020-01-24 doi:10.1101/2020.01.23.916791 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Bayesian copy number detection and association in large-scale studies ]]> https://biorxiv.org/content/10.1101/2020.01.24.918672v1?rss=1 Cristiano, S. McKean, D. Carey, J. Bracci, P. Brennan, P. Chou, M. Du, M. Gallinger, S. Goggins, M. G. Hassan, M. Hung, R. Kurtz, R. Li, D. Lu, L. Neale, R. Olson, S. Petersen, G. Rabe, K. Fu, J. Risch, H. Rosner, G. Ruczinski, I. Klein, A. P. Scharpf, R. B. 2020-01-25 doi:10.1101/2020.01.24.918672 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Human stem cell derived sensory neurons are positioned to support varicella zoster virus latency ]]> https://biorxiv.org/content/10.1101/2020.01.24.919290v1?rss=1 Sadaoka, T. Rajbhandari, L. Shukla, P. Jagdish, B. Lee, H. Lee, G. Venkatesan, A. 2020-01-25 doi:10.1101/2020.01.24.919290 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank ]]> https://biorxiv.org/content/10.1101/2020.01.26.920173v1?rss=1 Steinegger, M. Salzberg, S. L. 2020-01-26 doi:10.1101/2020.01.26.920173 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ A mediation analysis of schizophrenia variants: Risk alleles may affect a gene's expression differently from how the expression affects risk ]]> https://biorxiv.org/content/10.1101/2020.01.27.904680v1?rss=1 Peng, X. Bader, J. S. Avramopoulos, D. 2020-01-27 doi:10.1101/2020.01.27.904680 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ SynGAP splice isoforms differentially regulate synaptic plasticity and dendritic development ]]> https://biorxiv.org/content/10.1101/2020.01.28.922013v1?rss=1 Araki, Y. Hong, I. Gamache, T. R. Ju, S. Collado-Torres, L. Shin, J. H. Huganir, R. L. 2020-01-28 doi:10.1101/2020.01.28.922013 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ The γ-herpesviral TATA box binding protein directly interacts with RNA Polymerase II to direct late gene transcription ]]> https://biorxiv.org/content/10.1101/2020.01.28.922526v1?rss=1 Castaneda, A. F. Didychuk, A. L. Louder, R. K. McCollum, C. O. Davis, Z. H. Nogales, E. Glaunsinger, B. 2020-01-29 doi:10.1101/2020.01.28.922526 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Effects of catechol-O-methyltransferase inhibition on effort-related choice behavior in male mice ]]> https://biorxiv.org/content/10.1101/2020.01.28.924142v1?rss=1 DeBrosse, A. Wheeler, A. M. Barrow, J. C. Carr, G. V. 2020-01-29 doi:10.1101/2020.01.28.924142 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Pervasive promoter hypermethylation of silenced TERT alleles in human cancers ]]> https://biorxiv.org/content/10.1101/2020.01.29.925552v1?rss=1 Esopi, D. Graham, M. K. Brosnan-Cashman, J. A. Meyers, J. Vaghasia, A. Gupta, A. Kumar, B. Haffner, M. C. Heaphy, C. M. De Marzo, A. M. Meeker, A. K. Nelson, W. Wheelan, S. J. Yegnasubramanian, S. 2020-01-30 doi:10.1101/2020.01.29.925552 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Sapling: Accelerating Suffix Array Queries with Learned Data Models ]]> https://biorxiv.org/content/10.1101/2020.01.29.925768v1?rss=1 Kirsche, M. Das, A. Schatz, M. 2020-01-30 doi:10.1101/2020.01.29.925768 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Electrostatic effects in proteins are governed by pH-redistribution of the conformational ensemble ]]> https://biorxiv.org/content/10.1101/2020.02.02.931253v1?rss=1 Kougentakis, C. M. Majumdar, A. Garcia-Moreno E., B. 2020-02-03 doi:10.1101/2020.02.02.931253 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Tumor susceptibility gene-101 regulates glucocorticoid receptor through disorder-mediated allostery ]]> https://biorxiv.org/content/10.1101/2020.02.02.931485v1?rss=1 White, J. T. Rives, J. Tharp, M. E. Wrabl, J. O. Thompson, E. B. Hilser, V. J. 2020-02-03 doi:10.1101/2020.02.02.931485 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED ]]> https://biorxiv.org/content/10.1101/2020.02.03.931923v1?rss=1 Kovaka, S. Fan, Y. Ni, B. Timp, W. Schatz, M. C. 2020-02-03 doi:10.1101/2020.02.03.931923 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ The properties of buried ion pairs are governed by the propensity of proteins to reorganize ]]> https://biorxiv.org/content/10.1101/2020.02.03.932012v1?rss=1 Kougentakis, C. M. Skerritt, L. Majumdar, A. Schlessman, J. L. Garcia-Moreno E., B. 2020-02-04 doi:10.1101/2020.02.03.932012 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Common variation at the LRRK2 locus is associated with survival in the primary tauopathy progressive supranuclear palsy ]]> https://biorxiv.org/content/10.1101/2020.02.04.932335v1?rss=1 Jabbari, E. Tan, M. M. X. Reynolds, R. H. Mok, K. Y. Ferrari, R. Murphy, D. P. Valentino, R. R. Ross, O. A. Dickson, D. W. Al-Sarraj, S. Gentleman, S. M. Allinson, K. S. J. Jaunmuktane, Z. Holton, J. L. Revesz, T. Warner, T. T. Lees, A. J. Cookson, M. R. Gibbs, J. R. Ding, J. Chia, R. Traynor, B. J. Scholz, S. W. Pantelyat, A. Viollet, C. Dalgard, C. L. Pletnikova, O. Troncoso, J. C. Boxer, A. L. Respondek, G. Hoglinger, G. U. Burn, D. J. Pavese, N. Gerhard, A. Kobylecki, C. Leigh, P. N. Church, A. Hu, M. T. M. Rowe, J. B. Ryten, M. Hardy, J. Shoai, M. 2020-02-04 doi:10.1101/2020.02.04.932335 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53 ]]> https://biorxiv.org/content/10.1101/2020.02.04.933192v1?rss=1 Moosmueller, C. Tralie, C. J. Kooshkbaghi, M. Belkhatir, Z. Pouryahya, M. Reyes, J. Deasy, J. O. Tannenbaum, A. R. Kevrekidis, I. G. 2020-02-04 doi:10.1101/2020.02.04.933192 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Ribosome Profiling in Archaea Reveals Leaderless Translation, Novel Translational Initiation Sites, and Ribosome Pausing at Single Codon Resolution ]]> https://biorxiv.org/content/10.1101/2020.02.04.934349v1?rss=1 Gelsinger, D. R. Dallon, E. Reddy, R. Mohammad, F. Buskirk, A. R. DiRuggiero, J. 2020-02-04 doi:10.1101/2020.02.04.934349 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Identifying Nootropic Drug Targets via Large-Scale Cognitive GWAS and Transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.02.06.934752v1?rss=1 Lam, M. Chen, C.-Y. Yan, X. Hill, D. W. Trampush, J. Yu, J. Knowles, E. Davies, G. Stahl, E. Huckins, L. Liewald, D. C. Djurovic, S. Melle, I. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. J. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Hartmann, A. M. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Koltai, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. C. Avramopoulos, D. Hatzimanolis, A. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, T 2020-02-06 doi:10.1101/2020.02.06.934752 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ PGC1/PPAR Drive Cardiomyocyte Maturation through Regulation of Yap1 and SF3B2 ]]> https://biorxiv.org/content/10.1101/2020.02.06.937797v1?rss=1 Murphy, S. Miyamoto, M. Kervadec, A. Kannan, S. Tampakakis, E. Kambhampati, S. Lin, B. L. Paek, S. Andersen, P. Lee, D.-I. Zhu, R. An, S. S. Kass, D. A. Uosaki, H. Colas, A. R. Kwon, C. 2020-02-07 doi:10.1101/2020.02.06.937797 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures ]]> https://biorxiv.org/content/10.1101/2020.02.09.940254v1?rss=1 Ruffolo, J. A. Guerra, C. Mahajan, S. P. Sulam, J. Gray, J. J. 2020-02-10 doi:10.1101/2020.02.09.940254 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Influence of species and processing parameters on recovery and content of brain tissue-derived extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2020.02.10.940999v1?rss=1 Huang, Y. Cheng, L. Turchinovich, A. Mahairaki, V. Troncoso, J. C. Pletnikov, O. Haughey, N. J. Vella, L. J. Hill, A. Zheng, L. Witwer, K. W. 2020-02-12 doi:10.1101/2020.02.10.940999 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Telacebec for ultra-short treatment of Buruli ulcer in a mouse model ]]> https://biorxiv.org/content/10.1101/2020.02.10.943175v1?rss=1 Almeida, D. Converse, P. J. Omansen, T. F. TYAGI, S. Tasneen, R. kim, J. Nuermberger, E. 2020-02-12 doi:10.1101/2020.02.10.943175 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Excessive O-GlcNAcylation causes heart failure and sudden death ]]> https://biorxiv.org/content/10.1101/2020.02.11.943910v1?rss=1 Umapathi, P. Banerjee, P. Zachara, N. E. Abrol, N. Wang, Q. Mesubi, O. O. Luczak, E. D. Wu, Y. Granger, J. M. Wei, A.-C. Reyes Gaido, O. E. Florea, L. D. Talbot, C. C. Hart, G. W. Anderson, M. E. 2020-02-12 doi:10.1101/2020.02.11.943910 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Osprey: Open-Source Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data ]]> https://biorxiv.org/content/10.1101/2020.02.12.944207v1?rss=1 Oeltzschner, G. Zoellner, H. J. Hui, S. C. N. Mikkelsen, M. Saleh, M. G. Tapper, S. Edden, R. A. E. 2020-02-12 doi:10.1101/2020.02.12.944207 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Co-expression analysis is biased by a mean-correlation relationship ]]> https://biorxiv.org/content/10.1101/2020.02.13.944777v1?rss=1 Wang, Y. Hicks, S. C. Hansen, K. D. 2020-02-13 doi:10.1101/2020.02.13.944777 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Efficient immune cell genome engineering with improved CRISPR editing tools ]]> https://biorxiv.org/content/10.1101/2020.02.13.947002v1?rss=1 Chan, W. Gottschalk, R. A. Yao, Y. Pomerantz, J. Germain, R. N. 2020-02-14 doi:10.1101/2020.02.13.947002 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction ]]> https://biorxiv.org/content/10.1101/2020.02.13.947119v1?rss=1 Wu, C. Ranjan, A. Nguyen, V. Q. Liu, S. Wisniewski, J. Kim, J. M. Tang, X. Mizuguchi, G. Elalaoui, E. Jou, V. Nickels, T. J. English, B. P. Zheng, Q. Luk, E. Lavis, L. D. Lionnet, T. 2020-02-13 doi:10.1101/2020.02.13.947119 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Mitochondrial CaMKII causes metabolic reprogramming, energetic insufficiency, and dilated cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2020.02.13.947564v1?rss=1 Luczak, E. D. Wu, Y. Granger, J. M. Joiner, M.-l. A. Wilson, N. R. Gupta, A. Umapathi, P. Murphy, K. R. Reyes Gaido, O. E. Sabet, A. Corradini, E. Wang, Y. Heck, A. J. Wei, A.-C. Weiss, R. G. Anderson, M. E. 2020-02-14 doi:10.1101/2020.02.13.947564 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ G4C2 repeat RNA mediates the disassembly of the nuclear pore complex in C9orf72 ALS/FTD ]]> https://biorxiv.org/content/10.1101/2020.02.13.947721v1?rss=1 Rothstein, J. D. Coyne, A. N. Hayes, L. Zaepfel, B. L. Fitchman, B. Salzberg, Y. Bowen, K. Trost, H. Rigo, F. Harel, A. Svendsen, C. N. Sareen, D. 2020-02-14 doi:10.1101/2020.02.13.947721 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Maternal antibodies to gliadin and autism spectrum disorders in offspring - A population-based case-control study in Sweden ]]> https://biorxiv.org/content/10.1101/2020.02.13.948620v1?rss=1 Gardner, R. M. Samuelsson, I. Severance, E. G. Sjoqvist, H. Yolken, R. H. Dalman, C. Karlsson, H. 2020-02-14 doi:10.1101/2020.02.13.948620 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Increased mTOR activity and metabolic efficiency in mouse and human cells containing the African-centric tumor-predisposing p53 variant Pro47Ser ]]> https://biorxiv.org/content/10.1101/2020.02.14.946269v1?rss=1 Gnanapradeepan, K. Basu, S. Barnoud, T. Leu, J. I.-J. Good, M. Lee, J. V. Quinn, W. J. Kung, C.-P. Ahima, R. S. Baur, J. A. Wellen, K. E. Liu, Q. Schug, Z. T. George, D. L. Murphy, M. E. 2020-02-15 doi:10.1101/2020.02.14.946269 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Promoter CpG density is predictive of downstream gene loss-of-function intolerance ]]> https://biorxiv.org/content/10.1101/2020.02.15.936351v1?rss=1 Boukas, L. Bjornsson, H. T. Hansen, K. D. 2020-02-16 doi:10.1101/2020.02.15.936351 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ Proteomic and phosphoproteomic analysis identifies novel liver-related signaling in retinal pigment epithelial cells during epithelial-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2020.02.17.953315v1?rss=1 Mertz, J. L. Sripathi, S. R. Yang, X. Chen, L. Esumi, N. Zhang, H. Zack, D. J. 2020-02-18 doi:10.1101/2020.02.17.953315 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Comparison of three glycoproteomic methods for the analysis of CHO cells treated with 1,3,4-O-Bu3ManNAc ]]> https://biorxiv.org/content/10.1101/2020.02.18.954198v1?rss=1 Mertz, J. L. Sun, S. Yin, B. Betenbaugh, M. J. Yarema, K. J. Zhang, H. 2020-02-19 doi:10.1101/2020.02.18.954198 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ O-GlcNAcylation and oxidation contribute to atrial fibrillation in diabetes by activating CaMKII ]]> https://biorxiv.org/content/10.1101/2020.02.18.954909v1?rss=1 Mesubi, O. O. Rokita, A. G. Abrol, N. Wu, Y. Chen, B. Wang, Q. Granger, J. M. Luczak, E. D. Banerjee, P. S. Maier, L. S. Wehrens, X. H. Pomerantz, J. L. Song, L.-S. Ahima, R. S. Zachara, N. E. Hart, G. W. Anderson, M. E. 2020-02-19 doi:10.1101/2020.02.18.954909 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Multiple timescales of neural dynamics and integration of task-relevant signals across cortex ]]> https://biorxiv.org/content/10.1101/2020.02.18.955427v1?rss=1 Spitmaan, M. M. Seo, H. Lee, D. Soltani, A. 2020-02-19 doi:10.1101/2020.02.18.955427 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms in the 2014-15 influenza season ]]> https://biorxiv.org/content/10.1101/2020.02.20.956979v1?rss=1 Blumenkrantz, D. Mehoke, T. Hardick, J. Shaw-Saliba, K. Liu, H. Powell, H. Macias, E. Evans, J. Lewis, M. Medina, R. Sauer, L. M. Dugas, A. DuVal, A. Lane, A. P. Gaydos, C. Rothman, R. Thielen, P. Pekosz, A. 2020-02-21 doi:10.1101/2020.02.20.956979 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Human Influenza A Virus H1N1pdm Full-length Genome Sequencing in USA and Taiwan in 2015-16 Flu Season and Disease Correlation ]]> https://biorxiv.org/content/10.1101/2020.02.20.957068v1?rss=1 Liu, H. Gong, Y.-N. Shaw-Saliba, K. Mehoke, T. Evans, J. Liu, Z.-Y. Lewis, M. Sauer, L. Thielen, P. Rothman, R. Chen, K.-F. Pekosz, A. 2020-02-21 doi:10.1101/2020.02.20.957068 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Neuraminidase antigenic drift of influenza A virus H3N2 clade 3c.2a viruses alters virus replication, enzymatic activity and inhibitory antibody binding ]]> https://biorxiv.org/content/10.1101/2020.02.20.957399v1?rss=1 Powell, H. Pekosz, A. 2020-02-20 doi:10.1101/2020.02.20.957399 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Visual psychophysics and limits of visual discrimination performance in freely behaving mice ]]> https://biorxiv.org/content/10.1101/2020.02.20.958652v1?rss=1 You, W.-K. Mysore, S. P. 2020-02-24 doi:10.1101/2020.02.20.958652 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Genetic loci associated with prevalent and incident myocardial infarction and coronary heart disease in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium ]]> https://biorxiv.org/content/10.1101/2020.02.21.959312v1?rss=1 Hahn, J. Fu, Y.-P. Brown, M. R. Bis, J. C. de Vries, P. S. Feitosa, M. F. Yanek, L. R. Weiss, S. Giulianini, F. Smith, A. V. Guo, X. Bartz, T. M. Becker, D. M. Becker, L. C. Boerwinkle, E. Brody, J. A. Chen, Y.-D. I. Franco, O. H. Grove, M. Harris, T. B. Hofman, A. Hwang, S.-J. Kral, B. G. Launer, L. J. Markus, M. R. P. Rice, K. M. Rich, S. S. Ridker, P. M. Rivadeneira, F. Rotter, J. I. Sotoodehnia, N. Taylor, K. D. Uitterlinden, A. G. Völker, U. Völzke, H. Yao, J. Chasman, D. I. Dörr, M. Gudnason, V. Mathias, R. A. Post, W. Psaty, B. M. Dehghan, A. 2020-02-21 doi:10.1101/2020.02.21.959312 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Structural and functional characterization of the Spo11 core complex ]]> https://biorxiv.org/content/10.1101/2020.02.21.960211v1?rss=1 Claeys Bouuaert, C. Tischfield, S. E. Pu, S. Mimitou, E. P. Arias-Palomo, E. Berger, J. M. Keeney, S. 2020-02-24 doi:10.1101/2020.02.21.960211 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis ]]> https://biorxiv.org/content/10.1101/2020.02.25.964197v1?rss=1 Fan, H. Atiya, H. Wang, Y. Pisanic, T. Wang, J. Shih, I.-M. Foy, K. Frisbie, L. Chandler, C. Shen, H. Coffman, L. G. 2020-02-26 doi:10.1101/2020.02.25.964197 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor ]]> https://biorxiv.org/content/10.1101/2020.02.26.963322v1?rss=1 Vornhagen, J. Bassis, C. Ramakrishnan, S. Hein, R. Mason, S. Bergman, Y. Sunshine, N. Fan, Y. Timp, W. Schatz, M. C. Young, V. B. Simner, P. J. Bachman, M. A. 2020-02-27 doi:10.1101/2020.02.26.963322 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Reducing monocarboxylate transporter MCT1 worsens experimental diabetic peripheral neuropathy ]]> https://biorxiv.org/content/10.1101/2020.02.26.965152v1?rss=1 Jha, M. K. Ament, X. H. Yang, F. Liu, Y. Polydefkis, M. Pellerin, L. Morrison, B. M. 2020-02-27 doi:10.1101/2020.02.26.965152 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Glucose-mediated expansion of a gut commensal bacterium promotes Plasmodium infection through alkalizing mosquito midgut ]]> https://biorxiv.org/content/10.1101/2020.02.27.967315v1?rss=1 Wang, M. An, Y. Dong, S. Feng, Y. Gao, L. Wang, P. Dimopoulus, G. Tang, H. Wang, J. 2020-02-27 doi:10.1101/2020.02.27.967315 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ SkewIT: Skew Index Test for detecting mis-assembled bacterial genomes ]]> https://biorxiv.org/content/10.1101/2020.02.27.968214v1?rss=1 Lu, J. Salzberg, S. 2020-02-27 doi:10.1101/2020.02.27.968214 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Intestinal Bacteria Maintain Adult Enteric Nervous System and Nitrinergic Neurons via Toll-like Receptor 2-induced Neurogenesis in Mice ]]> https://biorxiv.org/content/10.1101/2020.03.01.968727v1?rss=1 Yarandi, S. Kulkarni, S. Saha, M. Sylvia, K. Sears, C. Pasricha, P. J. 2020-03-02 doi:10.1101/2020.03.01.968727 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Visualizing synaptic plasticity in vivo by large-scale imaging of endogenous AMPA receptors ]]> https://biorxiv.org/content/10.1101/2020.03.01.972216v1?rss=1 Graves, A. R. Roth, R. Tan, H. Zhu, Q. Bygrave, A. Lopez-Ortega, E. Spiegel, A. Hong, I. Johnson, R. Vogelstein, J. Tward, D. Miller, M. Huganir, R. L. 2020-03-02 doi:10.1101/2020.03.01.972216 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ A Numerical Representation and Classification of Codons to Investigate Codon Alternation Patterns during Genetic Mutations on Disease Pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.03.02.971036v1?rss=1 Sengupta, A. Pal Choudhury, P. Chakraborty, S. Roy, S. Das, J. K. Mallick, D. Jana, S. S. 2020-03-03 doi:10.1101/2020.03.02.971036 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Reducing reference bias using multiple population reference genomes ]]> https://biorxiv.org/content/10.1101/2020.03.03.975219v1?rss=1 Chen, N.-C. Solomon, B. Mun, T. Iyer, S. Langmead, B. 2020-03-04 doi:10.1101/2020.03.03.975219 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ An Integrated Systems Biology Approach Identifies the Proteasome as a Critical Host Machinery for ZIKV and DENV Replication ]]> https://biorxiv.org/content/10.1101/2020.03.04.976548v1?rss=1 Song, G. Lee, E. M. Pan, J. Xu, M. Rho, H.-S. Cheng, Y. Whitt, N. Yang, S. Kouznetsova, J. Klumpp-Thomas, C. Michael, S. Moore, C. Yoon, K.-J. Christian, K. Simeonov, A. Huang, W. Xia, M. Huang, R. Lal-Nag, M. Tang, H. Zheng, W. Qian, J. Song, H. Ming, G.-l. Zhu, H. 2020-03-05 doi:10.1101/2020.03.04.976548 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ The anti-tubercular activity of simvastatin is mediated by cholesterol-dependent regulation of autophagy via the AMPK-mTORC1-TFEB axis ]]> https://biorxiv.org/content/10.1101/2020.03.04.977579v1?rss=1 Bruiners, N. Dutta, N. K. Guerrini, V. Salamon, H. Yamaguchi, K. Karakousis, P. Gennaro, M. L. 2020-03-05 doi:10.1101/2020.03.04.977579 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ The architecture of brain co-expression reveals the brain-wide basis of disease susceptibility ]]> https://biorxiv.org/content/10.1101/2020.03.05.965749v1?rss=1 Hartl, C. L. Ramaswami, G. Pembroke, W. Saha, A. Parsana, P. Muller, S. Pintacuda, G. Lage, K. Battle, A. Geschwind, D. H. 2020-03-05 doi:10.1101/2020.03.05.965749 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Role of Specialized mSWI/SNF Complexes in Prostate Cancer Lineage Plasticity ]]> https://biorxiv.org/content/10.1101/2020.03.06.949131v1?rss=1 Cyrta, J. Augspach, A. de Filippo, M. R. Prandi, D. Thienger, P. Benelli, M. Cooley, V. Bareja, R. Wilkes, D. Chae, S.-S. Cavaliere, P. Dephoure, N. Uldry, A.-C. Lagache, S. B. Cohen, S. Jaquet, M. Brandt, L. P. Alshalalfa, M. Sboner, A. Feng, F. Wang, S. Beltran, H. Lotan, T. Spahn, M. Kruithof-de Julio, M. Chen, Y. Ballman, K. V. Demichelis, F. Piscuoglio, S. Rubin, M. 2020-03-08 doi:10.1101/2020.03.06.949131 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.03.08.980383v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@1d7fd4borg.highwire.dtl.DTLVardef@136563borg.highwire.dtl.DTLVardef@57641dorg.highwire.dtl.DTLVardef@16de9a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jenkins, C. Orsburn, B. 2020-03-10 doi:10.1101/2020.03.08.980383 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ X-chromosome dosage compensation dynamics in human early embryos ]]> https://biorxiv.org/content/10.1101/2020.03.08.982694v1?rss=1 Fan, G. Zeng, Q. Feng, Y. Hu, Y. An, Q. Li, T. Qin, L.-J. Xue, Z. Huang, K. Liu, J.-y. 2020-03-09 doi:10.1101/2020.03.08.982694 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Remyelination alters the pattern of myelin in the cerebral cortex ]]> https://biorxiv.org/content/10.1101/2020.03.09.983569v1?rss=1 Orthmann-Murphy, J. Call, C. L. Molina-Castro, G. C. Hsieh, Y. C. Rasband, M. N. Calabresi, P. A. Bergles, D. E. 2020-03-13 doi:10.1101/2020.03.09.983569 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Massively parallel encapsulation of single cells with structured microparticles and secretion-based flow sorting ]]> https://biorxiv.org/content/10.1101/2020.03.09.984245v1?rss=1 1,000,000 events in less than an hour. The reported microparticles can be easily stored, and distributed as a consumable reagent amongst researchers, democratizing access to high-throughput functional cell screening. ]]> de Rutte, J. Dimatteo, R. van Zee, M. Damoiseaux, R. Di Carlo, D. 2020-03-11 doi:10.1101/2020.03.09.984245 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Object representations in the human brain reflect the co-occurrence statistics of vision and language ]]> https://biorxiv.org/content/10.1101/2020.03.09.984625v1?rss=1 Bonner, M. F. Epstein, R. A. 2020-03-11 doi:10.1101/2020.03.09.984625 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Deficient uracil base excision repair leads to persistent dUMP in HIV proviruses during infection of monocytes and macrophages ]]> https://biorxiv.org/content/10.1101/2020.03.10.985283v1?rss=1 Meshesha, M. Esadze, A. Cui, J. Churgulia, N. Sahu, S. K. Stivers, J. T. 2020-03-17 doi:10.1101/2020.03.10.985283 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Inhibition of KDM1A activity restores adult neurogenesis and improves hippocampal memory in a mouse model of Kabuki syndrome ]]> https://biorxiv.org/content/10.1101/2020.03.11.986976v1?rss=1 Zhang, L. Pilarowski, G. O. Pich, E. M. Nakatani, A. Dunlop, J. Baba, R. Matsuda, S. Daini, M. Hattori, Y. Matsumoto, S. Ito, M. Kimura, H. Bjornsson, H. T. 2020-03-11 doi:10.1101/2020.03.11.986976 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Maternal cannabis vapor exposure causes long-term alterations in emotional reactivity, social behavior, and behavioral flexibility in offspring. ]]> https://biorxiv.org/content/10.1101/2020.03.12.989210v1?rss=1 Weimar, H. V. Wright, H. R. Warrick, C. R. Brown, A. M. Lugo, J. M. Freels, T. G. McLaughlin, R. J. 2020-03-13 doi:10.1101/2020.03.12.989210 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ A Clock-Driven Neural Network Critical for Arousal ]]> https://biorxiv.org/content/10.1101/2020.03.12.989921v1?rss=1 500 million years of evolution and define a clock-regulated neural network critical for arousal. ]]> Bell, B. J. Liu, Q. Kim, D. W. Lee, S. S. Liu, Q. Blum, I. D. Wang, A. Bedont, J. L. Chang, A. Issa, H. Cohen, J. Y. Blackshaw, S. Wu, M. N. 2020-03-14 doi:10.1101/2020.03.12.989921 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Parallel social information processing circuits are differentially impacted in autism ]]> https://biorxiv.org/content/10.1101/2020.03.13.990549v1?rss=1 Lewis, E. M. Stein-O'Brien, G. Patino, A. Nardou, R. Grossman, C. D. Brown, M. Bangamwabo, B. Ndiaye, N. Giovinazzo, D. Dardani, I. Jiang, C. Goff, L. Dolen, G. 2020-03-14 doi:10.1101/2020.03.13.990549 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Distinct neural mechanisms construct classical versus extraclassical inhibitory surrounds in an inhibitory nucleus in the midbrain attention network ]]> https://biorxiv.org/content/10.1101/2020.03.13.990952v1?rss=1 Schryver, H. M. Lim, J. X. Mysore, S. P. 2020-03-15 doi:10.1101/2020.03.13.990952 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Connexin 43 hemichannels mediate spatial and temporal disease spread in ALS ]]> https://biorxiv.org/content/10.1101/2020.03.14.990747v1?rss=1 Almad, A. A. Taga, A. Joseph, J. Welsh, C. Patankar, A. Gross, S. K. Richard, J.-P. Pokharel, A. Lillo, M. Dastgheyb, R. Eggan, K. Haughey, N. Contreras, J. E. Maragakis, N. J. 2020-03-15 doi:10.1101/2020.03.14.990747 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Efferent Synaptic Transmission at the Vestibular Type II Hair Cell Synapse ]]> https://biorxiv.org/content/10.1101/2020.03.14.992180v1?rss=1 Yu, Z. Mcintosh, J. M. Sadeghi, S. G. Glowatzki, E. 2020-03-16 doi:10.1101/2020.03.14.992180 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Rational design and implementation of a chemically inducible hetero-trimerization system ]]> https://biorxiv.org/content/10.1101/2020.03.16.994277v1?rss=1 Wu, H. D. Kikuchi, M. Dagliyan, O. Aragaki, A. K. Nakamura, H. Dokholyan, N. V. Umehara, T. Inoue, T. 2020-03-18 doi:10.1101/2020.03.16.994277 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Stability and detection of nucleic acid from viruses and hosts in mosquito blood meals ]]> https://biorxiv.org/content/10.1101/2020.03.17.995126v1?rss=1 Reddy, M. R. Drummond, C. Gebhardt, M. E. Saenz Robles, M. T. Carpi, G. Hoyer, I. Pastusiak, A. Norris, D. E. Pipas, J. M. Jackson, E. K. 2020-03-17 doi:10.1101/2020.03.17.995126 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ The giant sequoia genome and proliferation of disease resistance genes ]]> https://biorxiv.org/content/10.1101/2020.03.17.995944v1?rss=1 Scott, A. D. Zimin, A. Puiu, D. Workman, R. Britton, M. Zaman, S. Caballero, M. Read, A. C. Bogdanove, A. J. Burns, E. Wegrzyn, J. L. Timp, W. Salzberg, S. L. Neale, D. B. 2020-03-19 doi:10.1101/2020.03.17.995944 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Assembly and Annotation of an Ashkenazi Human Reference Genome ]]> https://biorxiv.org/content/10.1101/2020.03.18.997395v1?rss=1 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. 40 of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. 11 genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes. ]]> Shumate, A. Zimin, A. V. Sherman, R. M. Puiu, D. Wagner, J. M. Olson, N. D. Pertea, M. Salit, M. L. Zook, J. M. Salzberg, S. L. 2020-03-18 doi:10.1101/2020.03.18.997395 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR-T cell testing ]]> https://biorxiv.org/content/10.1101/2020.03.19.999110v1?rss=1 Jacob, F. P. Ming, G.-l. Song, H. 2020-03-20 doi:10.1101/2020.03.19.999110 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain ]]> https://biorxiv.org/content/10.1101/2020.03.22.002618v1?rss=1 Tward, D. J. Li, X. Huo, B. Lee, B. C. Miller, M. Mitra, P. P. 2020-03-23 doi:10.1101/2020.03.22.002618 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Integrative Epigenomic and Transcriptomic Analysis Reveals Robust Metabolic Switching in the Brain During Intermittent Fasting ]]> https://biorxiv.org/content/10.1101/2020.03.22.002725v1?rss=1 Ng, G. Y.-Q. Sheng, D. P. L. K. Kang, S.-W. Fann, D. Y.-W. Kim, J. Alli-Shaik, A. Cho, Y.-S. Han, J. Sul, J.-H. Karamyan, V. Okun, E. Dheen, T. Hande, M. P. Vemuganti, R. Mallilankaraman, K. Kennedy, B. K. Drummond, G. R. Sobey, C. G. Gunaratne, J. Mattson, M. P. Foo, R. S.-Y. Jo, D.-G. Arumugam, T. 2020-03-25 doi:10.1101/2020.03.22.002725 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Dynamic Sex Chromosome Expression in Drosophila Male Germ Cells ]]> https://biorxiv.org/content/10.1101/2020.03.23.000356v1?rss=1 Mahadevaraju, S. Fear, J. M. Akeju, M. Galletta, B. J. Pinheiro, M. M. Avelino, C. C. Cabral-de-Mello, D. C. Conlon, K. Dell'Orso, S. Demere, Z. Mansuria, K. Mendonca, C. A. Palacios-Gimenez, O. M. Ross, E. Savery, M. Yu, K. Smith, H. E. Sartorelli, V. Rusan, N. M. Vibranovski, M. D. Matunis, E. Oliver, B. 2020-03-23 doi:10.1101/2020.03.23.000356 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Spontaneous recovery and the multiple timescales of human motor memory ]]> https://biorxiv.org/content/10.1101/2020.03.24.006023v1?rss=1 Orozco, S. P. Albert, S. T. Shadmehr, R. 2020-03-26 doi:10.1101/2020.03.24.006023 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ mir-21 is associated with inactive low molecular weight Argonaute complexes in thyroid cancer cell lines ]]> https://biorxiv.org/content/10.1101/2020.03.24.006072v1?rss=1 Powell, B. H. Turchinovich, A. Wang, Y. Liao, Z. Aasif Dar, M. La Rocca, G. Umanah, G. E. Zeiger, M. A. Umbricht, C. B. Witwer, K. W. 2020-03-25 doi:10.1101/2020.03.24.006072 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Large-scale Phenotypic Drug Screen Identifies Neuroprotectants in Zebrafish and Mouse Models of Retinitis Pigmentosa ]]> https://biorxiv.org/content/10.1101/2020.03.26.010009v1?rss=1 Zhang, L. Chen, C. Fu, J. Lilley, B. Berlinicke, C. Hansen, B. Ding, D. Wang, G. Wang, T. Daniel, D. Ye, Y. Saxena, M. T. Hall, K. R. Sharrock, A. V. Brandon, C. Shim, J. S. Hanes, J. Ji, H. Liu, J. O. Qian, J. Ackerley, D. F. Rohrer, B. Zack, D. Mumm, J. S. 2020-03-28 doi:10.1101/2020.03.26.010009 Cold Spring Harbor Laboratory Press 2020-03-28 <![CDATA[ Ultrafast and accurate 16S microbial community analysis using Kraken 2 ]]> https://biorxiv.org/content/10.1101/2020.03.27.012047v1?rss=1 Lu, J. Salzberg, S. 2020-03-29 doi:10.1101/2020.03.27.012047 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Evaluating the transcriptional fidelity of cancer models ]]> https://biorxiv.org/content/10.1101/2020.03.27.012757v1?rss=1 Peng, D. Gleyzer, R. Tai, W.-H. Kumar, P. Bian, Q. Issacs, B. Lummertz da Rocha, E. Cai, S. DiNapoli, K. Cahan, P. 2020-03-29 doi:10.1101/2020.03.27.012757 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ The E3/E4 ubiquitin conjugation factor UBE4B interacts with and ubiquitinates the HTLV-1 Tax oncoprotein to promote NF-kB activation ]]> https://biorxiv.org/content/10.1101/2020.03.30.016253v1?rss=1 Harhaj, E. W. Mohanty, S. Han, T. Choi, Y. B. Lavorgna, A. Zhang, J. 2020-03-30 doi:10.1101/2020.03.30.016253 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ ActuAtor, a molecular tool for generating force in living cells: Controlled deformation of intracellular structures ]]> https://biorxiv.org/content/10.1101/2020.03.30.016360v1?rss=1 Nakamura, H. Rho, E. Deng, D. Razavi, S. Matsubayshi, H. T. Inoue, T. 2020-03-31 doi:10.1101/2020.03.30.016360 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Nuclease-mediated depletion biases in ribosome footprint profiling libraries ]]> https://biorxiv.org/content/10.1101/2020.03.30.017061v1?rss=1 Zinshteyn, B. Wangen, J. R. Hua, B. Green, R. 2020-04-01 doi:10.1101/2020.03.30.017061 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Risperidone-induced changes in DNA methylation from peripheral blood in first-episode schizophrenia parallel neuroimaging and cognitive phenotype ]]> https://biorxiv.org/content/10.1101/2020.03.31.018283v1?rss=1 Hu, M. Xia, Y. Zong, X. Sweeney, J. A. Bishop, J. R. Giase, G. Li, B. Rubin, L. H. Chen, X. Wang, Y. Kunney, L. Li, Z. He, Y. Liu, C. Chen, C. Chen, X. Tang, J. 2020-04-02 doi:10.1101/2020.03.31.018283 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ EXPRESSION OF Mycobacterium tuberculosis RpsA IN Mycobacterium smegmatis INCREASES SUSCEPTIBILITY TO PYRAZINAMIDE ]]> https://biorxiv.org/content/10.1101/2020.03.31.018390v1?rss=1 7500 {micro}g/mL respectively). ]]> Antiparra, R. A. Santos, M. Toledo, A. K. Gilman, R. H. Kirwan, D. E. Sheen, P. Zimic, M. 2020-03-31 doi:10.1101/2020.03.31.018390 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice ]]> https://biorxiv.org/content/10.1101/2020.03.31.018556v1?rss=1 Rajeshkumar, N. V. Yabuuchi, S. Pai, S. G. Maitra, A. Hidalgo, M. Dang, C. V. 2020-04-04 doi:10.1101/2020.03.31.018556 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C ]]> https://biorxiv.org/content/10.1101/2020.03.31.019380v1?rss=1 Smith, B. Pekosz, A. 2020-04-01 doi:10.1101/2020.03.31.019380 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Coding de novo mutations identified by WGS reveal novel orofacial cleft genes ]]> https://biorxiv.org/content/10.1101/2020.04.01.019927v1?rss=1 Bishop, M. Diaz Perez, K. Sun, M. Ho, S. Chopra, P. Mukhopadhyay, N. Hetmanski, J. Taub, M. Moreno-Uribe, L. Valencia-Ramirez, L. C. Restrepo Muneton, C. Wehby, G. Hecht, J. Deleyiannis, F. Weinberg, S. Wu-Chou, Y. H. Chen, P. Brand, H. Epstein, M. Ruczinski, I. Murray, J. Beaty, T. Feingold, E. Lipinski, R. Cutler, D. Marazita, M. Leslie, E. 2020-04-02 doi:10.1101/2020.04.01.019927 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ People can learn new walking patterns without walking ]]> https://biorxiv.org/content/10.1101/2020.04.02.021949v1?rss=1 Song, C. N. Stenum, J. Leech, K. A. Keller, C. Roemmich, R. T. 2020-04-03 doi:10.1101/2020.04.02.021949 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy ]]> https://biorxiv.org/content/10.1101/2020.04.02.022368v1?rss=1 O'Brien, E. S. Fuglestad, B. Lessen, H. J. Stetz, M. A. Lin, D. W. Marques, B. S. Gupta, K. Fleming, K. G. Wand, A. J. 2020-04-03 doi:10.1101/2020.04.02.022368 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Transcriptomic entropy quantifies cardiomyocyte maturation at single cell level ]]> https://biorxiv.org/content/10.1101/2020.04.02.022632v1?rss=1 Kannan, S. Farid, M. Lin, B. L. Miyamoto, M. Kwon, C. 2020-04-03 doi:10.1101/2020.04.02.022632 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Automatic subtyping of individuals with Primary Progressive Aphasia ]]> https://biorxiv.org/content/10.1101/2020.04.04.025593v1?rss=1 Themistocleous, C. Ficek, B. Webster, K. den Ouden, D.-B. Hillis, A. E. Tsapkini, K. 2020-04-05 doi:10.1101/2020.04.04.025593 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Punishment history biases corticothalamic responses to motivationally-significant stimuli ]]> https://biorxiv.org/content/10.1101/2020.04.06.027888v1?rss=1 Lucantonio, F. Su, Z. Chang, A. J. Bari, B. A. Cohen, J. Y. 2020-04-07 doi:10.1101/2020.04.06.027888 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Store Independent Ca2+ Entry Regulates the DNA Damage Response in Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/2020.04.06.027946v1?rss=1 Makena, M. R. Ko, M. Mekile, A. X. Dang, D. K. Warrington, J. M. Buckhaults, P. J. Talbot, C. Rao, R. 2020-04-07 doi:10.1101/2020.04.06.027946 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes ]]> https://biorxiv.org/content/10.1101/2020.04.06.028746v1?rss=1 Alonge, M. Shumate, A. Puiu, D. Zimin, A. Salzberg, S. L. 2020-04-07 doi:10.1101/2020.04.06.028746 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif ]]> https://biorxiv.org/content/10.1101/2020.04.09.033522v1?rss=1 Navratil, V. Lionnard, L. Longhi, S. Combet, C. Aouacheria, A. 2020-04-10 doi:10.1101/2020.04.09.033522 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ A Powerful Method for Pleiotropic Analysis under Composite Null Hypothesis Identifies Novel Shared Loci Between Type 2 Diabetes and Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2020.04.11.037630v1?rss=1 Ray, D. Chatterjee, N. 2020-04-13 doi:10.1101/2020.04.11.037630 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Relevance of enriched expression of SARS-CoV-2 binding receptor ACE2 in gastrointestinal tissue with pathogenesis of digestive symptoms, diabetes-associated mortality, and disease recurrence in COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.04.14.040204v1?rss=1 Etiologically Elusive Disorders Research Network (EEDRN), Kumar, A. Faiq, M. A. Pareek, V. Raza, K. Narayan, R. K. Prasoon, P. Kumar, P. Kulandhasamy, M. Kumari, C. Kant, K. Singh, H. N. Qadri, R. Pandey, S. N. Kumar, S. 2020-04-15 doi:10.1101/2020.04.14.040204 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms ]]> https://biorxiv.org/content/10.1101/2020.04.15.030874v1?rss=1 Macedonia, M. C. Drewes, J. L. Markham, N. O. Simmons, A. J. Roland, J. T. Vega, P. N. Scurrah, C. R. Coffey, R. J. Shrubsole, M. J. Sears, C. L. Lau, K. S. 2020-04-17 doi:10.1101/2020.04.15.030874 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Cholinergic modulation of membrane properties of calyx terminals in the vestibular periphery ]]> https://biorxiv.org/content/10.1101/2020.04.15.041491v1?rss=1 Ramakrishna, Y. Manca, M. Sadeghi, S. G. 2020-04-17 doi:10.1101/2020.04.15.041491 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ TOWARD A CONNECTIVITY GRADIENT-BASED FRAMEWORK FOR REPRODUCIBLE BIOMARKER DISCOVERY ]]> https://biorxiv.org/content/10.1101/2020.04.15.043315v1?rss=1 Hong, S.-J. Xu, T. Nikolaidis, A. Smallwood, J. Margulies, D. S. Bernhardt, B. Vogelstein, J. Milham, M. 2020-04-17 doi:10.1101/2020.04.15.043315 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms ]]> https://biorxiv.org/content/10.1101/2020.04.16.044214v1?rss=1 Yee, R. Breitwieser, F. P. Hao, S. Opene, B. N. A. Workman, R. E. Tamma, P. D. Dien Bard, J. Timp, W. Simner, P. J. 2020-04-18 doi:10.1101/2020.04.16.044214 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ KIF13A mediates the activity-dependent transport of ESCRT-0 proteins in axons ]]> https://biorxiv.org/content/10.1101/2020.04.16.044818v1?rss=1 Birdsall, V. Imoto, Y. Waites, C. Watanabe, S. 2020-04-18 doi:10.1101/2020.04.16.044818 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ The aggregate effect of implementation strength of family planning programs on modern contraceptive use at the health systems level in rural Malawi ]]> https://biorxiv.org/content/10.1101/2020.04.17.046524v1?rss=1 Pattnaik, A. Mohan, D. Tsui, A. Chipokosa, S. Katengeza, H. Ndawala, J. Marx, M. 2020-04-17 doi:10.1101/2020.04.17.046524 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Combining In Vivo Corneal Confocal Microscopy with Deep Learning-based Analysis Reveals Sensory Nerve Fiber Loss in Acute SIV Infection ]]> https://biorxiv.org/content/10.1101/2020.04.19.048926v1?rss=1 McCarron, M. E. Weinberg, R. L. Izzi, J. M. Queen, S. E. Misra, S. L. Russakoff, D. B. Oakley, J. Mankowski, J. 2020-04-20 doi:10.1101/2020.04.19.048926 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Neural markers of vulnerability to anxiety outcomes following traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2020.04.20.051649v1?rss=1 Popovitz, J. M. B. Mysore, S. P. Adwanikar, H. 2020-04-23 doi:10.1101/2020.04.20.051649 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Redesigned Reporter Gene for Improved Proton Exchange-based Molecular MRI Contrast ]]> https://biorxiv.org/content/10.1101/2020.04.21.053157v1?rss=1 Perlman, O. Ito, H. Gilad, A. A. McMahon, M. T. Chiocca, E. A. Nakashima, H. Farrar, C. T. 2020-04-23 doi:10.1101/2020.04.21.053157 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Social Stress Alters Immune Response and Results in Higher Viral Load During Acute SIV Infection in a Pigtailed Macaque Model of HIV ]]> https://biorxiv.org/content/10.1101/2020.04.21.054130v1?rss=1 Guerrero-Martin, S. M. Rubin, L. H. Mcgee, K. M. Shirk, E. N. Queen, S. E. Li, M. Bullock, B. Carlson, B. W. Adams, R. J. Gama, L. Graham, D. Zink, C. Clements, J. E. Mankowski, J. L. Metcalf Pate, K. A. 2020-04-23 doi:10.1101/2020.04.21.054130 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Microglia-targeted dendrimer-2PMPA therapy robustly inhibits GCPII and improves cognition in a mouse model of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2020.04.22.055228v1?rss=1 Hollinger, K. R. Sharma, A. Tallon, C. Lovell, L. Thomas, A. G. Zhu, X. Kambhampati, S. P. Liaw, K. Sharma, R. Rojas, C. Rais, R. Kannan, S. Kannan, R. M. Slusher, B. 2020-04-24 doi:10.1101/2020.04.22.055228 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Engineering highly multivalent sperm-binding IgG antibodies for potent non-hormonal female contraception ]]> https://biorxiv.org/content/10.1101/2020.04.22.055301v1?rss=1 99.9%) reduction of progressively motile sperm in the sheep vagina using 33 micrograms of the 10 Fab HM-IgG. HM-IgGs produce at comparable yields and possess identical thermal stability to the parent IgG, with greater homogeneity. HM-IgGs represent not only promising biologics for non-hormonal contraception but also a promising platform for generating potent agglutinating mAb for diverse medical applications. ]]> Shrestha, B. Schaefer, A. Saada, J. Yong, Z. Jacobs, T. M. Chavez, E. C. Omsted, S. S. Vincent, K. Moench, T. R. Lai, S. K. 2020-04-24 doi:10.1101/2020.04.22.055301 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Modular output circuits of the fastigial nucleus mediate diverse motor and nonmotor functions of the cerebellar vermis ]]> https://biorxiv.org/content/10.1101/2020.04.23.047100v1?rss=1 Fujita, H. Kodama, T. du Lac, S. 2020-04-25 doi:10.1101/2020.04.23.047100 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Fussing about fission: defining variety among mainstream and exotic apicomplexan cell division modes ]]> https://biorxiv.org/content/10.1101/2020.04.23.056333v1?rss=1 Gubbels, M.-J. Keroack, C. D. Dangoudoubiyam, S. Worliczek, H. L. Paul, A. S. Bauwens, C. Elsworth, B. Engelberg, K. Howe, D. K. Coppens, I. Duraisingh, M. T. 2020-04-24 doi:10.1101/2020.04.23.056333 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Ligand-independent EGFR oligomers do not rely on the active state asymmetric kinase dimer ]]> https://biorxiv.org/content/10.1101/2020.04.24.056077v1?rss=1 Byrne, P. O. Hristova, K. Leahy, D. J. 2020-04-25 doi:10.1101/2020.04.24.056077 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Tumor-infiltrating nerves create an electro-physiologically active microenvironment and contribute to treatment resistance ]]> https://biorxiv.org/content/10.1101/2020.04.24.058594v1?rss=1 Kovacs, A. Vermeer, D. W. Madeo, M. Vermeer, S. J. Williamson, C. S. Rickel, A. Stamp, J. Lucido, C. T. Cain, J. Bell, M. Morgan, M. Yoon, J.-Y. Mitchell, M. A. Tulina, N. Stuckelberger, S. Budina, A. Orman, D. Jung, E. Schwartz, L. E. Eichwald, T. Hong, Z. Weimer, J. Hooper, J. E. Godwin, A. K. Talbot, S. Drapkin, R. Vermeer, P. D. 2020-04-25 doi:10.1101/2020.04.24.058594 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Efficient Representations of Tumor Diversity with Paired DNA-RNA Anomalies ]]> https://biorxiv.org/content/10.1101/2020.04.24.060129v1?rss=1 Ke, Q. Dinalankara, W. Younes, L. Marchionni, L. Geman, D. 2020-04-25 doi:10.1101/2020.04.24.060129 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The Role of Rif1 in telomere length regulation is separable from its role in origin firing ]]> https://biorxiv.org/content/10.1101/2020.04.24.060491v1?rss=1 Shubin, C. B. Greider, C. W. 2020-04-25 doi:10.1101/2020.04.24.060491 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Recombinant BCG overexpressing a STING agonist elicits trained immunity and improved antitumor efficacy in non-muscle invasive bladder ]]> https://biorxiv.org/content/10.1101/2020.04.25.061531v1?rss=1 Singh, A. K. K. Praharaj, M. Lombardo, K. A. Yoshida, T. Matoso, A. Baras, A. S. Zhao, L. Prasad, P. Powell, J. D. Kates, M. McConkey, D. Bivalacqua, T. J. Bishai, W. 2020-04-25 doi:10.1101/2020.04.25.061531 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Toward Minimally Invasive Therapeutic Ultrasound: Ultrasound-guided Ablation in Neuro-oncology ]]> https://biorxiv.org/content/10.1101/2020.04.25.061788v1?rss=1 Belzberg, M. Mahapatra, S. Chavez, F. Morrison, K. Xiong, K. T. Gamo, N. J. Restaino, S. Iyer, R. R. Groves, M. Thakor, N. Theodore, N. Luciano, M. G. Brem, H. Cohen, A. R. Manbachi, A. 2020-04-27 doi:10.1101/2020.04.25.061788 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated bacterial genome segregation ]]> https://biorxiv.org/content/10.1101/2020.04.26.062497v1?rss=1 Hu, L. Rech, J. Bouet, J.-Y. Liu, J. 2020-04-26 doi:10.1101/2020.04.26.062497 Cold Spring Harbor Laboratory Press 2020-04-26 <![CDATA[ Identification of essential genes and fluconazole resistance genes in Candida glabrata by profiling of Hermes transposon insertions. ]]> https://biorxiv.org/content/10.1101/2020.04.27.064048v1?rss=1 Gale, A. N. Sakhawala, R. M. Levitan, A. Sharan, R. Berman, J. Timp, W. Cunningham, K. W. 2020-04-29 doi:10.1101/2020.04.27.064048 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ De novo mutation in ancestral generations evolves haplotypes contributing to disease ]]> https://biorxiv.org/content/10.1101/2020.04.27.064824v1?rss=1 2.64 Mb) runs of homozygosity (ROH) regions (p-value=2.09e-18). We show that long-sized ROHs are more likely to be formed on recently configured haplotypes enriched for rare homozygous deleterious variants in the TK-affected compared to TK-unaffected individuals (p-value= 3.35e-11). Analysis of genotype-phenotype correlations reveals that genes with rare homozygous deleterious variants in long-sized ROHs provide the most comprehensive set of molecular diagnoses for the observed disease traits with a systematic quantitative analysis of HPO (Human Phenotype Ontology) terms. ConclusionOur findings support the notion that novel rare variants on newly configured haplotypes arising within the recent past generations of a family or clan contribute significantly to recessive disease traits in the TK population. ]]> Coban Akdemir, Z. Song, X. Pehlivan, D. Karaca, E. Bayram, Y. Gambin, T. L. Jhangiani, S. muzny, d. m. Lewis, R. Baylor Hopkins Center for Mendelian Genomics, Liu, P. Boerwinkle, E. Hamosh, A. Gibbs, R. A. Sutton, R. Sobreira, N. Carvalho, C. M. B. Posey, J. Shaw, C. A. Valle, D. Lupski, J. R. 2020-04-28 doi:10.1101/2020.04.27.064824 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Field-deployable molecular diagnostic platform for arbovirus and Wolbachia detection in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2020.04.28.066514v1?rss=1 Rutkowski, N. N. Dong, Y. Dimopoulos, G. 2020-04-29 doi:10.1101/2020.04.28.066514 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ The SecA motor generates mechanical force during protein translocation ]]> https://biorxiv.org/content/10.1101/2020.04.29.066415v1?rss=1 Gupta, R. Toptygin, D. Kaiser, C. M. 2020-04-29 doi:10.1101/2020.04.29.066415 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Modern Machine Learning: Partition & Vote ]]> https://biorxiv.org/content/10.1101/2020.04.29.068460v1?rss=1 Priebe, C. E. Vogelstein, J. Engert, F. White, C. M. 2020-04-30 doi:10.1101/2020.04.29.068460 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Synthesis runs counter to the directional folding pathway of a nascent protein domain ]]> https://biorxiv.org/content/10.1101/2020.04.29.068593v1?rss=1 Chen, X. Rajasekaran, N. Liu, K. Kaiser, C. M. 2020-04-30 doi:10.1101/2020.04.29.068593 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Fractional re-distribution among cell motility states during ageing ]]> https://biorxiv.org/content/10.1101/2020.04.29.069286v1?rss=1 Phillip, J. M. Zamponi, N. Phillip, M. P. Daya, J. McGovern, S. Williams, W. Tschudi, K. Jayatilaka, H. Wu, P.-H. Walston, J. Wirtz, D. 2020-05-01 doi:10.1101/2020.04.29.069286 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Leveraging Tools from Autonomous Navigation for Rapid, Robust Neuron Connectivity ]]> https://biorxiv.org/content/10.1101/2020.04.30.070755v1?rss=1 Drenkow, N. Joyce, J. Matelsky, J. Larabi, R. Heiko, J. Kleissas, D. Wester, B. Johnson, E. C. Gray-Roncal, W. R. 2020-05-02 doi:10.1101/2020.04.30.070755 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Conservative and liberal attitudes drive polarized neural responses to political content ]]> https://biorxiv.org/content/10.1101/2020.04.30.071084v1?rss=1 Leong, Y. C. Chen, J. Willer, R. Zaki, J. 2020-05-02 doi:10.1101/2020.04.30.071084 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Release sites are positioned to activate NMDA receptors ]]> https://biorxiv.org/content/10.1101/2020.05.01.072157v1?rss=1 Li, S. Raychaudhuri, S. Lee, S. A. Wang, J. Kusick, G. F. Prater, C. Syed, S. Falahati, H. Ramos, R. Bartol, T. M. Hosy, E. Watanabe, S. 2020-05-02 doi:10.1101/2020.05.01.072157 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Decreased investigatory head scanning during exploration in learning-impaired, aged rats ]]> https://biorxiv.org/content/10.1101/2020.05.01.072249v1?rss=1 Rao, G. Lee, H. Gallagher, M. Knierim, J. J. 2020-05-02 doi:10.1101/2020.05.01.072249 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Reference genome for the highly transformable Setaria viridis cultivar ME034V ]]> https://biorxiv.org/content/10.1101/2020.05.02.073684v1?rss=1 300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis cultivars. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community. ]]> Thielen, P. M. Pendelton, A. L. Player, R. A. Bowden, K. V. Lawton, T. J. Wisecaver, J. H. 2020-05-03 doi:10.1101/2020.05.02.073684 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes ]]> https://biorxiv.org/content/10.1101/2020.05.02.074096v1?rss=1 Sedlazeck, F. J. Yu, B. Mansfield, A. J. Chen, H. Krasheninina, O. Tin, A. Qi, Q. Zarate, S. Traynelis, J. Menon, V. BCM HGSC Sequencing Lab, Hu, J. doddapaneni, h. v. Metcalf, G. Coresh, J. Kaplan, R. muzny, d. m. Jun, G. Gibbs, R. A. Salerno, W. Boerwinkle, E. 2020-05-03 doi:10.1101/2020.05.02.074096 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules ]]> https://biorxiv.org/content/10.1101/2020.05.02.074336v1?rss=1 Kelly, M. L. Chu, C.-C. Shi, H. Ganser, L. R. Bogerd, H. P. Huynh, K. Hou, Y. Cullen, B. R. Al-Hashimi, H. M. 2020-05-03 doi:10.1101/2020.05.02.074336 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ The Notch Ligand Jagged1 is Required for the Formation, Maintenance, and Survival of Hensen Cells in the Mouse Cochlea ]]> https://biorxiv.org/content/10.1101/2020.05.04.076448v1?rss=1 Chrysostomou, E. Zhou, L. Darcy, Y. L. Graves, K. A. Doetzlhofer, A. Cox, B. C. 2020-05-05 doi:10.1101/2020.05.04.076448 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ IDENTIFICATION AND CHARACTERIZATION OF A LARGE SOURCE OF PRIMARY MESENCHYMAL STEM CELLS TIGHTLY ADHERED TO BONE SURFACES OF HUMAN VERTEBRAL BODY MARROW CAVITIES ]]> https://biorxiv.org/content/10.1101/2020.05.04.076950v1?rss=1 Johnstone, B. H. Miller, H. M. Beck, M. R. Gu, D. Thirumala, S. LaFontaine, M. Brandacher, G. Woods, e. J. 2020-05-05 doi:10.1101/2020.05.04.076950 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ UPREGULATION OF SUPEROXIDE DISMUTASE 2 BY ASTROCYTES IN THE SIV/MACAQUE MODEL OF HIV-ASSOCIATED NEUROLOGIC DISEASE ]]> https://biorxiv.org/content/10.1101/2020.05.05.078691v1?rss=1 Sullivan, M. N. Brill, S. A. Mangus, L. M. Jeong, Y. J. Solis, C. V. Knight, A. C. Colantuoni, C. Keceli, G. Paolocci, N. Queen, S. E. Mankowski, J. L. 2020-05-06 doi:10.1101/2020.05.05.078691 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ A novel platform to accelerate antimicrobial susceptibility testing in Neisseria gonorrhoeae using RNA signatures ]]> https://biorxiv.org/content/10.1101/2020.05.05.078808v1?rss=1 M.Hashemi, M. Ram-Mohan, N. Gessner, N. R. Carroll, K. C. Wang, T.-H. Yang, S. 2020-05-06 doi:10.1101/2020.05.05.078808 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Systemic immune dysfunction in cancer patients driven by IL6 and IL8 induction of an inhibitory receptor module in peripheral CD8+ T cells ]]> https://biorxiv.org/content/10.1101/2020.05.06.081471v1?rss=1 Somasundaram, A. Cillo, A. R. Lampenfeld, C. Oliveri, L. Velez, M. A. Joyce, S. Calderon, M. J. Dadey, R. Rajasundaram, D. Normolle, D. P. Watkins, S. C. Herman, J. G. Kirkwood, J. M. Lipson, E. J. Ferris, R. L. Bruno, T. C. Vignali, D. A. A. 2020-05-08 doi:10.1101/2020.05.06.081471 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Impact of Concatenating fMRI Data on Reliability for Functional Connectomics ]]> https://biorxiv.org/content/10.1101/2020.05.06.081679v1?rss=1 Cho, J. W. Korchmaros, A. Vogelstein, J. T. Milham, M. Xu, T. 2020-05-08 doi:10.1101/2020.05.06.081679 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Elevated ACE2 expression in the olfactory neuroepithelium: implications for anosmia and upper respiratory SARS-CoV-2 entry and replication ]]> https://biorxiv.org/content/10.1101/2020.05.08.084996v1?rss=1 Chen, M. Shen, W. Rowan, N. Kulaga, H. Hillel, A. Ramanathan, M. Lane, A. P. 2020-05-09 doi:10.1101/2020.05.08.084996 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Hypothermia is a characteristic of the fungal kingdom ]]> https://biorxiv.org/content/10.1101/2020.05.09.085969v1?rss=1 Cordero, R. J. Casadevall, A. 2020-05-09 doi:10.1101/2020.05.09.085969 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.05.09.086165v1?rss=1 Zhou, L. Xu, Z. Castiglione, G. M. Soiberman, U. S. Eberhart, C. G. Duh, E. J. 2020-05-09 doi:10.1101/2020.05.09.086165 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Synthetic Maturation of Multilineage Human Liver Organoids via Genetically Guided Engineering ]]> https://biorxiv.org/content/10.1101/2020.05.10.087445v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@6ec32aorg.highwire.dtl.DTLVardef@1cf2eeforg.highwire.dtl.DTLVardef@1128748org.highwire.dtl.DTLVardef@16fb5a7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Velazquez, J. J. LeGraw, R. Moghadam, F. Tan, Y. Kilbourne, J. Hislop, J. Liu, S. Cats, D. Chuva de Sousa Lopes, S. M. Plaisier, C. Cahan, P. Kiani, S. Ebrahimkhani, M. R. 2020-05-10 doi:10.1101/2020.05.10.087445 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Protease Activity Profiling Via Programmable Phage Display ]]> https://biorxiv.org/content/10.1101/2020.05.11.089607v1?rss=1 Roman-Melendez, G. Venkataraman, T. Monaco, D. Larman, H. B. 2020-05-13 doi:10.1101/2020.05.11.089607 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence ]]> https://biorxiv.org/content/10.1101/2020.05.12.091397v1?rss=1 Nguyen, T. T. Abdelrazek, M. Nguyen, D. T. Aryal, S. Nguyen, D. T. Khatami, A. 2020-05-13 doi:10.1101/2020.05.12.091397 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Resolution of subcomponents of synaptic release from post-synaptic currents in rat hair-cell/auditory-nerve fiber dendrites ]]> https://biorxiv.org/content/10.1101/2020.05.13.070920v1?rss=1 Young, E. D. Wu, J. S. Niwa, M. Glowatzki, E. 2020-05-15 doi:10.1101/2020.05.13.070920 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Preventive efficacy of a tenofovir alafenamide fumarate nanofluidic implant in SHIV-challenged nonhuman primates ]]> https://biorxiv.org/content/10.1101/2020.05.13.091694v1?rss=1 Pons-Faudoa, F. P. Sizovs, A. Shelton, K. A. Momin, Z. Bushman, L. R. Chua, C. Y. X. Nichols, J. E. Hawkins, T. Rooney, J. F. Marzinke, M. A. Kimata, J. T. Anderson, P. L. Nehete, P. N. Arduino, R. C. Ferrari, M. Sastry, K. J. Grattoni, A. 2020-05-17 doi:10.1101/2020.05.13.091694 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Establishing a transcriptome-based drug discovery paradigm for neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2020.05.13.093468v1?rss=1 Dhindsa, R. S. Zoghbi, A. W. Krizay, D. K. Vasavda, C. Goldstein, D. B. 2020-05-15 doi:10.1101/2020.05.13.093468 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ A new paradigm for Prelamin A proteolytic processing by ZMPSTE24: the upstream SY^LL cleavage occurs first and there is no CaaX processing by ZMPSTE24 ]]> https://biorxiv.org/content/10.1101/2020.05.13.093849v1?rss=1 Nie, L. Spear, E. Babatz, T. D. Quigley, A. Dong, Y. Y. Chu, A. Rotty, B. Chalk, R. Mukhopadhyay, S. M. M. Burgess-Brown, N. A. Pike, A. C. W. Young, S. G. Michaelis, S. Carpenter, E. P. 2020-05-13 doi:10.1101/2020.05.13.093849 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ A rapid, point of care red blood cell agglutination assay for detecting antibodies against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.05.13.094490v1?rss=1 Kruse, R. L. Huang, Y. Smetana, H. Gehrie, E. A. Amukele, T. K. Tobian, A. A. Mostafa, H. H. Wang, Z. Z. 2020-05-14 doi:10.1101/2020.05.13.094490 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ A Chemical-genetics and Nanoparticle Enabled Approach for in vivo Protein Kinase Analysis ]]> https://biorxiv.org/content/10.1101/2020.05.13.094573v1?rss=1 500 protein kinases, and regulates up to 30% of the proteome. Kinase study is currently hindered by a lack of in vivo analysis approaches due to two factors: our inability to distinguish the kinase reaction of interest from those of other kinases in live cells and the cell impermeability of the ATP analogs. Herein, we tackled this issue by combining the widely used chemical genetic method developed by Dr. Kevan Shokat and colleagues with nanoparticle-mediated intracellular delivery of the ATP analog. The critical AKT1 protein kinase, which has been successfully studied with the method, was used as our initial prototype. Briefly, enlargement of the ATP binding pocket, by mutating the gate-keeper Methionine residue to a Glycine, prompted the mutant AKT1 to preferentially use the bulky ATP analog N6-Benzyl-ATP-{gamma}-S (A*TP{gamma}S) and, thus, differentiating AKT1-catalyzed and other phosphorylation events. The lipid/calcium/phosphate (LCP) nanoparticle was used for efficient intracellular delivery of A*TP{gamma}S, overcoming the cell impermeability issue. The mutant, but not wild-type, AKT1 used the delivered A*TP{gamma}S for autophosphorylation and phosphorylating its substrates in live cells. Thus, an in vivo protein kinase analysis method has been developed. The strategy should be widely applicable to other protein kinases. ]]> Chen, F. Liu, Q. Hilliard, T. Wang, T. Liang, H. Gao, W. Huang, L. Wang, D. 2020-05-15 doi:10.1101/2020.05.13.094573 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Expression changes in immune and epigenetic gene pathways associated with nutritional metabolites in maternal blood from pregnancies resulting in autism and atypical neurodevelopment ]]> https://biorxiv.org/content/10.1101/2020.05.14.096586v1?rss=1 Zhu, Y. Mordaunt, C. E. Durbin-Johnson, B. P. Caudill, M. A. Malysheva, O. V. Miller, J. W. Green, R. James, S. J. Melnyk, S. B. Fallin, M. D. Hertz-Picciotto, I. Schmidt, R. J. LaSalle, J. M. 2020-05-16 doi:10.1101/2020.05.14.096586 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ AFTERHYPERPOLARIZATION AMPLITUDE IN CA1 PYRAMIDAL CELLS OF AGED LONG-EVANS RATS CHARACTERIZED FOR INDIVIDUAL DIFFERENCES ]]> https://biorxiv.org/content/10.1101/2020.05.15.098376v1?rss=1 kirkwood, a. Severin, D. Gallagher, M. 2020-05-16 doi:10.1101/2020.05.15.098376 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ intern: Integrated Toolkit for Extensible and Reproducible Neuroscience ]]> https://biorxiv.org/content/10.1101/2020.05.15.098707v1?rss=1 Matelsky, J. K. Rodriguez, L. Xenes, D. Gion, T. Hider, R. Wester, B. Gray-Roncal, W. 2020-05-16 doi:10.1101/2020.05.15.098707 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Guiding and interpreting brain network classification with transcriptional data ]]> https://biorxiv.org/content/10.1101/2020.05.15.099028v1?rss=1 Li, M. Kessler, D. Arroyo, J. Freytag, S. Bahlo, M. Levina, E. Yang, J. Y. H. 2020-05-16 doi:10.1101/2020.05.15.099028 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Adenine Nucleotide Translocase regulates the airway epithelium, mitochondrial metabolism and ciliary function ]]> https://biorxiv.org/content/10.1101/2020.05.18.101378v1?rss=1 Kliment, C. Nguyen, J. M. K. Kaltreider, M. J. Lu, Y.-W. Claypool, S. M. Radder, J. E. Sciurba, F. C. Zhang, Y. Gregory, A. D. Iglesias, P. A. Sidhaye, V. K. Robinson, D. N. 2020-05-19 doi:10.1101/2020.05.18.101378 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Population coding in the cerebellum and its implications for learning from error ]]> https://biorxiv.org/content/10.1101/2020.05.18.102376v1?rss=1 Shadmehr, R. 2020-05-20 doi:10.1101/2020.05.18.102376 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Network reconstruction for trans acting genetic loci using multi-omics data and prior information ]]> https://biorxiv.org/content/10.1101/2020.05.19.101592v1?rss=1 Hawe, J. S. Saha, A. Waldenberger, M. Kunze, S. Wahl, S. Mueller-Nurasyid, M. Prokisch, H. Grallert, H. Herder, C. Peters, A. Strauch, K. Theis, F. J. Gieger, C. Chambers, J. Battle, A. Heinig, M. 2020-05-21 doi:10.1101/2020.05.19.101592 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Selective role of the translin/trax RNase complex in hippocampal synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2020.05.19.105189v1?rss=1 Park, A. J. Shetty, M. S. Baraban, J. M. Abel, T. 2020-05-20 doi:10.1101/2020.05.19.105189 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ A redesigned TetR-aptamer system to control gene expression in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2020.05.19.105411v1?rss=1 Rajaram, K. Liu, H. B. Prigge, S. T. 2020-05-20 doi:10.1101/2020.05.19.105411 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ In vivo CRISPR screening identifies Fli1 as a transcriptional safeguard that restrains effector CD8 T cell differentiation during infection and cancer ]]> https://biorxiv.org/content/10.1101/2020.05.20.087379v1?rss=1 Chen, Z. Arai, E. Khan, O. Zhang, Z. Ngiow, S. F. He, Y. Huang, H. Manne, S. Cao, Z. Baxter, A. E. Cai, Z. Freilich, E. Ali, M. A. Giles, J. R. Wu, J. E. Greenplate, A. R. Kurachi, M. Nzingha, K. Ekshyyan, V. Wen, Z. Speck, N. A. Battle, A. Berger, S. L. Wherry, E. J. Shi, J. 2020-05-20 doi:10.1101/2020.05.20.087379 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Glyphosate Inhibits Melanization and Increases Insect Susceptibility to Infection ]]> https://biorxiv.org/content/10.1101/2020.05.20.105353v1?rss=1 Smith, D. F. Q. Camacho, E. Thakur, R. Barron, A. J. Broderick, N. A. Casadevall, A. 2020-05-20 doi:10.1101/2020.05.20.105353 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Electro-acupuncture alleviates METH withdrawal-induced spatial memory deficits by restoring astrocyte-derived glutamate uptake in dCA1 ]]> https://biorxiv.org/content/10.1101/2020.05.20.106153v1?rss=1 Shi, P. Li, Z. Xu, X. Nie, J. Liu, D. Cai, Q. Zhao, Y. Guan, Y. Ge, F. Guan, X. 2020-05-22 doi:10.1101/2020.05.20.106153 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons. ]]> https://biorxiv.org/content/10.1101/2020.05.21.106963v1?rss=1 Kim, D. W. Liu, K. Wang, Z. Q. Zhang, Y. S. Bathini, A. Brown, M. P. Lin, S. H. Washington, P. W. Sun, C. Lindtner, S. Lee, B. Wang, H. Shimogori, T. Rubenstein, J. L. R. Blackshaw, S. 2020-05-25 doi:10.1101/2020.05.21.106963 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ MitoWave: Spatiotemporal analysis of mitochondrial membrane potential fluctuations during ischemia-reperfusion ]]> https://biorxiv.org/content/10.1101/2020.05.21.108670v1?rss=1 O'Rourke, B. Ashok, D. 2020-05-23 doi:10.1101/2020.05.21.108670 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ NTR 2.0: a rationally-engineered prodrug converting enzyme with substantially enhanced efficacy for targeted cell ablation ]]> https://biorxiv.org/content/10.1101/2020.05.22.111427v1?rss=1 Sharrock, A. v. Mulligan, T. S. Hall, K. R. Williams, E. M. White, D. T. Zhang, L. Matthews, F. Nimmagadda, S. Washington, S. Le, K. Meir-Levi, D. Cox, O. L. Saxena, M. T. Calof, A. Lopez-Burks, M. E. Lander, A. D. Ding, D. Ji, H. Ackerley, D. F. Mumm, J. S. 2020-05-24 doi:10.1101/2020.05.22.111427 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ A three-dimensional thalamocortical dataset for characterizing brain heterogeneity ]]> https://biorxiv.org/content/10.1101/2020.05.22.111617v1?rss=1 Prasad, J. A. Balwani, A. H. Johnson, E. C. Miano, J. D. Sampathkumar, V. de Andrade, V. Fezza, K. Du, M. Vescovi, R. Jacobsen, C. Kording, K. P. Gürsoy, D. Gray-Roncal, W. Kasthuri, N. Dyer, E. L. 2020-05-25 doi:10.1101/2020.05.22.111617 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues ]]> https://biorxiv.org/content/10.1101/2020.05.23.111310v1?rss=1 Cao, X. Zhang, Y. Payer, L. M. Lords, H. Steranka, J. P. Burns, K. H. Xing, J. 2020-05-25 doi:10.1101/2020.05.23.111310 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Modeling Human Peripheral Myelin Fully from Pluripotent Stem Cells and Immune-mediated Neuropathy In Vitro using ZIKA Virus ]]> https://biorxiv.org/content/10.1101/2020.05.23.112748v1?rss=1 Mirakhori, F. Xu, Z. Qin, C.-F. 2020-05-23 doi:10.1101/2020.05.23.112748 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Computer code comprehension shares neural resources with formal logical inference in the fronto-parietal network ]]> https://biorxiv.org/content/10.1101/2020.05.24.096180v1?rss=1 Liu, Y.-F. Kim, J. Wilson, C. Bedny, M. 2020-05-25 doi:10.1101/2020.05.24.096180 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Characterization of mWake expression in the murine brain ]]> https://biorxiv.org/content/10.1101/2020.05.25.114363v1?rss=1 Bell, B. J. Wang, A. A. Kim, D. W. Blackshaw, S. Wu, M. N. 2020-05-25 doi:10.1101/2020.05.25.114363 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Robustification of RosettaAntibody and Rosetta SnugDock ]]> https://biorxiv.org/content/10.1101/2020.05.26.116210v1?rss=1 Jeliazkov, J. R. Frick, R. Zhou, J. Gray, J. J. 2020-05-26 doi:10.1101/2020.05.26.116210 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Atoh7-independent specification of retinal ganglion cell identity ]]> https://biorxiv.org/content/10.1101/2020.05.27.116954v1?rss=1 Brodie-Kommit, J. Hattar, S. Clark, B. S. Shi, Q. Shiau, F. Kim, D. W. Langel, J. Sheely, C. Schmidt, T. M. Glaser, T. Badea, T. Zhao, H. Singer, J. H. Blackshaw, S. 2020-05-28 doi:10.1101/2020.05.27.116954 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ mbkmeans: fast clustering for single cell data using mini-batch k-means ]]> https://biorxiv.org/content/10.1101/2020.05.27.119438v1?rss=1 Hicks, S. C. Liu, R. Ni, Y. Purdom, E. Risso, D. 2020-05-27 doi:10.1101/2020.05.27.119438 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ -SATA: A MATLAB based toolbox to estimate Current Density generated by Transcranial Direct Current Stimulation in an Individual Brain ]]> https://biorxiv.org/content/10.1101/2020.05.28.120774v1?rss=1 Kashyap, R. Bhattacharjee, S. Arumugam, R. Oishi, K. Desmond, J. E. Chen, S. A. 2020-05-30 doi:10.1101/2020.05.28.120774 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ GalaxyCloudRunner: enhancing scalable computing for Galaxy ]]> https://biorxiv.org/content/10.1101/2020.05.28.121772v1?rss=1 Goonasekera, N. Mahmoud, A. Chilton, J. Afgan, E. 2020-05-30 doi:10.1101/2020.05.28.121772 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Rules of Contact Inhibition of Locomotion for Cells on Suspended Nanofibers ]]> https://biorxiv.org/content/10.1101/2020.05.28.122218v1?rss=1 Singh, J. Camley, B. A. Nain, A. S. 2020-05-29 doi:10.1101/2020.05.28.122218 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Dynamic regulation of translation quality control associated with ribosome stalling ]]> https://biorxiv.org/content/10.1101/2020.05.29.121954v1?rss=1 Goldman, D. H. Livingston, N. M. Movsik, J. Wu, B. Green, R. 2020-05-30 doi:10.1101/2020.05.29.121954 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Conserved Roles for Receptor Tyrosine Kinase Extracellular Regions in Regulating Receptor and Pathway Activity ]]> https://biorxiv.org/content/10.1101/2020.05.29.122135v1?rss=1 Gonzalez-Magaldi, M. McCabe, J. M. Cartwright, H. N. Sun, N. Leahy, D. J. 2020-05-31 doi:10.1101/2020.05.29.122135 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure ]]> https://biorxiv.org/content/10.1101/2020.05.29.123505v1?rss=1 Wang, H. Noordam, R. Cade, B. E. Schwander, K. Winkler, T. W. Lee, J. Sung, Y. J. Bentley, A. R. Manning, A. K. Aschard, H. Kilpelainen, T. O. Ilkov, M. Brown, M. R. Horimoto, A. R. Richard, M. Bartz, T. M. Vojinovic, D. Lim, E. Nierenberg, J. L. Liu, Y. Chitrala, K. Rankinen, T. Musani, S. K. Franceschini, N. Rauramaa, R. Alver, M. Zee, P. Harris, S. E. van der Most, P. J. Nolte, I. M. Munroe, P. B. Palmer, N. D. Kuhnel, B. Weiss, S. Wen, W. Hall, K. A. Lyytikainen, L.-P. O'Connell, J. R. Eiriksdottir, G. Launer, L. J. de Vries, P. S. Arking, D. Chen, 2020-05-31 doi:10.1101/2020.05.29.123505 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Obesity phenotypes are preserved in intestinal stem cell enteroids from morbidly obese patients ]]> https://biorxiv.org/content/10.1101/2020.05.29.123737v1?rss=1 Hasan, N. Johnson, K. Yin, J. Baetz, N. Sherman, V. Blutt, S. Estes, M. K. Kumbhari, V. Zachos, N. Kovbasnjuk, O. 2020-05-31 doi:10.1101/2020.05.29.123737 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ LIN28B controls the regenerative capacity of neonatal murine auditory supporting cells through activation of mTOR signaling ]]> https://biorxiv.org/content/10.1101/2020.05.31.126193v1?rss=1 Li, X. Doetzlhofer, A. 2020-05-31 doi:10.1101/2020.05.31.126193 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Direct detection of RNA modifications and structure using single molecule nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2020.05.31.126763v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1d13067org.highwire.dtl.DTLVardef@c0d0aaorg.highwire.dtl.DTLVardef@c362eeorg.highwire.dtl.DTLVardef@193ffdb_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Stephenson, W. Razaghi, R. Busan, S. Weeks, K. M. Timp, W. Smibert, P. 2020-06-01 doi:10.1101/2020.05.31.126763 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Optogenetic currents in myofibroblasts acutely alter electrophysiology and conduction of co-cultured cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.06.02.124529v1?rss=1 Kostecki, G. Shi, Y. Chen, C. S. Reich, D. H. Entcheva, E. Tung, L. 2020-06-03 doi:10.1101/2020.06.02.124529 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping ]]> https://biorxiv.org/content/10.1101/2020.06.03.130591v1?rss=1 Credle, J. J. Robinson, M. Gunn, J. Monaco, D. Sie, B. Tchir, A. L. Hardick, J. Zheng, X. Shaw-Saliba, K. Rothman, R. Eshleman, S. Pekosz, A. Hansen, K. Mostafa, H. Steinegger, M. Larman, H. B. 2020-06-03 doi:10.1101/2020.06.03.130591 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Locus coeruleus spiking differently correlates with somatosensory cortex activity and pupil diameter ]]> https://biorxiv.org/content/10.1101/2020.06.04.134676v1?rss=1 Yang, H. Bari, B. A. Cohen, J. Y. O'Connor, D. H. 2020-06-04 doi:10.1101/2020.06.04.134676 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Hippocampal and striatal responses during motor learning are modulated byprefrontal cortex stimulation ]]> https://biorxiv.org/content/10.1101/2020.06.05.136531v1?rss=1 Gann, M. A. King, B. R. Dolfen, N. Veldman, M. P. Chan, K. L. Puts, N. A. J. Edden, R. A. E. Davare, M. Swinnen, S. P. Mantini, D. Robertson, E. M. Albouy, G. 2020-06-06 doi:10.1101/2020.06.05.136531 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Comparison of algorithms for linear-combination modelling of short-echo-time magnetic resonance spectra ]]> https://biorxiv.org/content/10.1101/2020.06.05.136796v1?rss=1 Zollner, H. J. Povazan, M. Hui, S. Tapper, S. Edden, R. A. Oeltzschner, G. 2020-06-07 doi:10.1101/2020.06.05.136796 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework ]]> https://biorxiv.org/content/10.1101/2020.06.06.137570v1?rss=1 Tekman, M. Batut, B. Ostrovsky, A. Antoniewski, C. Clements, D. Ramirez, F. Etherington, G. J. Hotz, H.-R. Scholtalbers, J. Manning, J. R. Bellenger, L. Doyle, M. A. Heydarian, M. Huang, N. Soranzo, N. Moreno, P. Papatheodorou, I. Nekrutenko, A. Taylor, J. Blankenberg, D. Backofen, R. Grüning, B. 2020-06-08 doi:10.1101/2020.06.06.137570 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Multiple, independent, common variants overlapping known and putative gut enhancers at RET, SEMA3 and NRG1 underlie Hirschsprung disease risk in European ancestry subjects ]]> https://biorxiv.org/content/10.1101/2020.06.07.138719v1?rss=1 25- fold. ConclusionGene regulatory networks in HSCR-relevant cell types quantify the total burden of risk alleles through sensing reduced gene expression of multiple genes on disease. ]]> Kapoor, A. Nandakumar, P. Auer, D. Sosa, M. Ross, H. Bollinger, J. Yan, J. Berrios, C. The Hirschsprung Disease Research Collaborative (HDRC), Chakravarti, A. 2020-06-08 doi:10.1101/2020.06.07.138719 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ The long non-coding RNA lnc-HLX-2-7 is oncogenic in group 3 medulloblastomas ]]> https://biorxiv.org/content/10.1101/2020.06.08.140251v1?rss=1 KATSUSHIMA, K. Lee, B. Kunhiraman, H. Zhong, C. Murath, R. Ying, J. Liu, B. Garancher, A. Gonzalez-Gomez, I. Stapleton, S. Vibhakar, R. Bettegowda, C. Wechsler-Reya, R. J. Jallo, G. Raabe, E. Eberhart, C. G. Perera, R. J. 2020-06-09 doi:10.1101/2020.06.08.140251 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Connectome subgraph isomorphisms and graph queries with DotMotif ]]> https://biorxiv.org/content/10.1101/2020.06.08.140533v1?rss=1 Matelsky, J. K. Reilly, E. P. Johnson, E. C. Wester, B. A. Gray-Roncal, W. 2020-06-09 doi:10.1101/2020.06.08.140533 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Aging interacts with tumor biology to produce major changes in the immune tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2020.06.08.140764v1?rss=1 Erbe, R. Wang, Z. Zaidi, N. Topper, M. Baylin, S. Jaffee, E. Easwaran, H. Fertig, E. J. 2020-06-08 doi:10.1101/2020.06.08.140764 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Mendelian randomization identifies folliculin expression as a mediator of diabetic retinopathy. ]]> https://biorxiv.org/content/10.1101/2020.06.09.143164v1?rss=1 Skol, A. D. Jung, S. C. Sokovic, A. M. Chen, S. Fazal, S. Sosina, O. Borkar, P. P. Lin, A. Sverdlov, M. Cao, D. Swaroop, A. Bebu, I. DCCT/EDIC Study Group, Stranger, B. Grassi, M. A. 2020-06-11 doi:10.1101/2020.06.09.143164 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Preserved efficacy and reduced toxicity with intermittent linezolid dosing in combination with bedaquiline and pretomanid in a murine TB model ]]> https://biorxiv.org/content/10.1101/2020.06.10.145334v1?rss=1 Bigelow, K. M. Tasneen, R. Chang, Y. S. Dooley, K. E. Nuermberger, E. 2020-06-12 doi:10.1101/2020.06.10.145334 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris. ]]> https://biorxiv.org/content/10.1101/2020.06.12.148619v1?rss=1 Ali, R. S. Dick, M. F. Muhammad, S. Sarver, D. Wong, G. W. Welch, K. 2020-06-13 doi:10.1101/2020.06.12.148619 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Evaluation of Field Sampling Techniques for Environmental Microbial Exposure: Assessing Efficacy and Feasibility ]]> https://biorxiv.org/content/10.1101/2020.06.14.150722v1?rss=1 Dalton, K. R. Spicer, K. Ludwig, S. Clemons-Erby, D. Green, T. Rule, A. M. Koehler, K. McCormack, M. C. Davis, M. F. 2020-06-15 doi:10.1101/2020.06.14.150722 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Immune Selection Pressure Contributes to Pancreatic Cancer Immune Evasion ]]> https://biorxiv.org/content/10.1101/2020.06.15.151274v1?rss=1 Ajina, R. Zuo, A. Wang, S. Moussa, M. Cooper, C. J. Shen, Y. Johnson, Q. R. Parks, J. M. Smith, J. C. Catalfamo, M. Fertig, E. J. Jablonski, S. A. Weiner, L. M. 2020-06-15 doi:10.1101/2020.06.15.151274 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Cortical microinfarcts potentiate recurrent ischemic injury through NLRP3-dependent trained immunity ]]> https://biorxiv.org/content/10.1101/2020.06.17.157289v1?rss=1 Feng, Y. Wu, T. Feng, Y. Liang, F. Li, G. Li, Y. Guan, Y. Liu, S. Zhang, Y. Xu, G. Zhong, P. 2020-06-18 doi:10.1101/2020.06.17.157289 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program ]]> https://biorxiv.org/content/10.1101/2020.06.18.146423v1?rss=1 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants from up to 17 TOPMed studies per phenotype. We discuss the challenges faced in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include (1) the code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify or extend these harmonizations to additional studies; and (2) results of labeling thousands of phenotype variables with controlled vocabulary terms. ]]> Stilp, A. M. Emery, L. S. Broome, J. G. Buth, E. J. Khan, A. T. Laurie, C. A. Wang, F. F. Wong, Q. Chen, D. D'Augustine, C. M. Heard-Costa, N. L. Hohensee, C. R. Johnson, W. C. Juarez, L. D. Liu, J. Mutalik, K. M. Raffield, L. M. Wiggins, K. L. de Vries, P. S. Kelly, T. N. Kooperberg, C. Natarajan, P. Peloso, G. M. Peyser, P. A. Reiner, A. P. Arnett, D. K. Aslibekyan, S. Barnes, K. C. Bielak, L. F. Bis, J. C. Cade, B. E. Chen, M.-H. Correa, A. Cupples, L. A. de Andrade, M. Ellinor, P. T. Fornage, M. Franceschini, N. Gan, W. Ganesh, S. K. Graffelman, J. 2020-06-20 doi:10.1101/2020.06.18.146423 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ The mitochondrial carrier SFXN1 is critical for Complex III integrity and cellular metabolism ]]> https://biorxiv.org/content/10.1101/2020.06.18.157495v1?rss=1 Acoba, M. G. Alpergin, E. S. S. Renuse, S. Fernandez-del-Rio, L. Lu, Y.-W. Clarke, C. F. Pandey, A. Wolfgang, M. J. Claypool, S. M. 2020-06-19 doi:10.1101/2020.06.18.157495 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease ]]> https://biorxiv.org/content/10.1101/2020.06.18.159459v1?rss=1 Chatterjee, S. Karasaki, K. M. Kapoor, A. Chakravarti, A. 2020-06-18 doi:10.1101/2020.06.18.159459 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Neuronal Classification from Network Connectivity via Adjacency Spectral Embedding ]]> https://biorxiv.org/content/10.1101/2020.06.18.160259v1?rss=1 Mehta, K. Goldin, R. F. Marchette, D. Vogelstein, J. T. Priebe, C. E. Ascoli, G. A. 2020-06-20 doi:10.1101/2020.06.18.160259 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Modelling the effects of lymph node swelling on T-cell response ]]> https://biorxiv.org/content/10.1101/2020.06.19.161232v1?rss=1 Johnson, S. C. Frattolin, J. Edgar, L. T. Jafarnejad, M. Moore, J. E. 2020-06-19 doi:10.1101/2020.06.19.161232 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope ]]> https://biorxiv.org/content/10.1101/2020.06.20.160499v1?rss=1 Sidhom, J.-W. Baras, A. S. 2020-06-20 doi:10.1101/2020.06.20.160499 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins ]]> https://biorxiv.org/content/10.1101/2020.06.20.163253v1?rss=1 Singh, N. Reyes-Ordonez, A. Compagnone, M. A. Moreno Castillo, J. F. Leslie, B. J. Ha, T. Chen, J. 2020-06-21 doi:10.1101/2020.06.20.163253 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Puromycin reactivity does not accurately localize translation at the subcellular level ]]> https://biorxiv.org/content/10.1101/2020.06.22.165217v1?rss=1 Enam, S. U. Zinshteyn, B. Goldman, D. H. Cassani, M. Livingston, N. M. Seydoux, G. Green, R. 2020-06-23 doi:10.1101/2020.06.22.165217 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries ]]> https://biorxiv.org/content/10.1101/2020.06.23.167759v1?rss=1 Kwong, A. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Blackwell, T. W. TOPMed Analysis Working Group, LeFaive, J. de Andrade, M. Barnard, J. Barnes, K. C. Blangero, J. Boerwinkle, E. Burchard, E. G. Cade, B. E. Chasman, D. Chen, H. Conomos, M. Cupples, L. A. Ellinor, P. T. Eng, C. Gao, Y. Guo, X. Irvin, M. R. Kelly, T. Kim, W. Kooperberg, C. Lubitz, S. A. Mak, A. C. Y. Manichaikul, A. W. Mathias, R. A. Montasser, M. E. Montgomery, C. G. Musani, S. Palmer, N. D. Peloso, G. Qiao, D. Reiner, A. P. Roden, D. M. Shoemaker, M. B. Smith, J. A 2020-06-24 doi:10.1101/2020.06.23.167759 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Hypomyelination leads to alterations in inhibitory function and parvalbumin-positive neuron density in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.06.23.167833v1?rss=1 Meng, X. Borges, B. C. Long, P. Kanold, P. O. Corfas, G. 2020-06-24 doi:10.1101/2020.06.23.167833 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Diverse scientific benchmarks for implicit membrane energy functions ]]> https://biorxiv.org/content/10.1101/2020.06.23.168021v1?rss=1 Alford, R. F. Gray, J. J. 2020-06-24 doi:10.1101/2020.06.23.168021 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Liftoff: an accurate gene annotation mapping tool ]]> https://biorxiv.org/content/10.1101/2020.06.24.169680v1?rss=1 99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.4% of human protein-coding genes to a chimpanzee genome assembly with 98.7% sequence identity. AvailabilityThe source code for Liftoff is available at https://github.com/agshumate/Liftoff ]]> Shumate, A. Salzberg, S. 2020-06-26 doi:10.1101/2020.06.24.169680 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2 ]]> https://biorxiv.org/content/10.1101/2020.06.25.171371v1?rss=1 Mahajan, S. P. Srinivasan, Y. Labonte, J. W. DeLisa, M. P. Gray, J. J. 2020-06-27 doi:10.1101/2020.06.25.171371 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS ]]> https://biorxiv.org/content/10.1101/2020.06.26.173021v1?rss=1 Cunningham, K. M. Zhang, K. Ruan, K. Maulding, K. Senturk, M. Grima, J. Sung, H. Zuo, Z. Song, H. Rothstein, J. D. Bellen, H. J. Lloyd, T. 2020-06-26 doi:10.1101/2020.06.26.173021 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions ]]> https://biorxiv.org/content/10.1101/2020.06.27.175224v1?rss=1 Marold, J. Sforza, K. Geiger-Schuller, K. Aksel, T. Klein, S. Petersen, M. Poliakova-Georgantas, E. Barrick, D. 2020-06-28 doi:10.1101/2020.06.27.175224 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ High-resolution mapping of glycoprotein structure-activity relationships by shotgun scanning glycomutagenesis ]]> https://biorxiv.org/content/10.1101/2020.06.28.176198v1?rss=1 Li, M. Zheng, X. Shanker, S. Jaroentomeechai, T. Kocer, I. Byrne, J. Cox, E. C. Labonte, J. W. Gray, J. J. DeLisa, M. P. 2020-06-29 doi:10.1101/2020.06.28.176198 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Stochastic Analysis Probes the Role of the Chaperone Hfq in E. coli Sugar Shock Response ]]> https://biorxiv.org/content/10.1101/2020.06.30.178566v1?rss=1 Bianchi, D. M. Brier, T. A. Poddar, A. Azam, M. S. Vanderpool, C. K. Ha, T. Luthey-Schulten, Z. 2020-07-01 doi:10.1101/2020.06.30.178566 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ eEF3 promotes late stages of tRNA translocation on the ribosome ]]> https://biorxiv.org/content/10.1101/2020.07.01.182105v1?rss=1 Ranjan, N. Pochopien, A. A. Wu, C. C.-C. Beckert, B. Blanchet, S. Green, R. Rodnina, M. V. Wilson, D. N. 2020-07-01 doi:10.1101/2020.07.01.182105 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Loop extrusion model predicts CTCF interaction specificity ]]> https://biorxiv.org/content/10.1101/2020.07.02.185389v1?rss=1 Xi, W. Beer, M. A. 2020-07-03 doi:10.1101/2020.07.02.185389 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights ]]> https://biorxiv.org/content/10.1101/2020.07.02.185595v1?rss=1 Johnson, M. E. Chen, A. Faeder, J. Henning, P. Moraru, I. I. Meier-Schellersheim, M. Murphy, R. F. Prustel, T. Theriot, J. A. Uhrmacher, A. 2020-07-04 doi:10.1101/2020.07.02.185595 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Evoked pain intensity representation is distributed across brain systems: A multistudy mega-analysis ]]> https://biorxiv.org/content/10.1101/2020.07.04.182873v1?rss=1 20% more of individual subject pain ratings than the best elementary region). Full brain models showed no predictive advantage over multi-system models. These findings quantify the extent that representation of evoked pain experience is distributed across multiple cortical and subcortical systems, show that pain representation is not circumscribed by any elementary region or conical network, and provide a blueprint for identifying the spatial scale of information in other domains. Significance StatementWe define modular, multisystem and global views of brain function, use multivariate fMRI decoding to characterize pain representations at each level, and provide evidence for a multisystem representation of evoked pain. We further show that local views necessarily exclude important components of pain representation, while a global full brain representation is superfluous, even though both are viable frameworks for representing pain. These findings quantitatively juxtapose and reconcile divergent conclusions from evoked pain studies within a generalized neuroscientific framework, and provide a blueprint for investigating representational architecture for diverse brain processes. ]]> Petre, B. Kragel, P. A. Atlas, L. Y. Geuter, S. Jepma, M. Koban, L. Krishnan, A. Lopez-Sola, M. Roy, M. Woo, C.-W. Wager, T. D. 2020-07-04 doi:10.1101/2020.07.04.182873 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Publicly available hiPSC lines with extreme polygenic risk scores for modeling schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.07.04.185348v1?rss=1 Rehbach, K. Zhang, H. Das, D. Sara Abdollahi, S. Prorok, T. Ghosh, S. Weintraub, S. Genovese, G. Powell, S. Lund, A. Akbarian, S. Eggan, K. McCarroll, S. A. Duan, J. Avramopoulos, D. Brennand, K. J. 2020-07-04 doi:10.1101/2020.07.04.185348 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Purifying selection acts on germline methylation to modify the CpG mutation rate at promoters ]]> https://biorxiv.org/content/10.1101/2020.07.04.187880v1?rss=1 Boukas, L. Bjornsson, H. T. Hansen, K. D. 2020-07-04 doi:10.1101/2020.07.04.187880 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Astroglial Calcium Signaling Encodes Sleep Need in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.04.187906v1?rss=1 Blum, I. D. Keles, M. F. Baz, E.-S. Han, E. Park, K. Luu, S. Issa, H. Brown, M. Ho, M. C. W. Tabuchi, M. Liu, S. Wu, M. 2020-07-05 doi:10.1101/2020.07.04.187906 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2020.07.04.187989v1?rss=1 Zhou, T. Tsybovsky, Y. Olia, A. S. Gorman, J. Rapp, M. A. Cerutti, G. Katsamba, P. S. Nazzari, A. Schon, A. Wang, P. D. Bimela, J. Shi, W. Teng, I.-T. Zhang, B. Boyington, J. C. Chuang, G.-Y. Sampson, J. M. Sastry, M. Stephens, T. Stuckey, J. Wang, S. Friesner, R. A. Ho, D. D. Mascola, J. R. Shapiro, L. Kwong, P. D. 2020-07-04 doi:10.1101/2020.07.04.187989 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture ]]> https://biorxiv.org/content/10.1101/2020.07.06.185066v1?rss=1 Chia, R. Sabir, M. S. Bandres-Ciga, S. Saez-Atienzar, S. Reynolds, R. H. Gustavsson, E. Walton, R. L. Ahmed, S. Viollet, C. Ding, J. Makarious, M. B. Diez-Fairen, M. Portley, M. K. Shah, Z. Abramzon, Y. Hernandez, D. G. Blauwendraat, C. Stone, D. J. Eicher, J. Parkkinen, L. Ansorge, O. Clark, L. Honig, L. S. Marder, K. Lemstra, A. St. George-Hyslop, P. Londos, E. Morgan, K. Lashley, T. Warner, T. T. Jaunmuktane, Z. Galasko, D. Santana, I. Tienari, P. Myllykangas, L. Oinas, M. Cairns, N. J. Morris, J. C. Halliday, G. M. Van Deerlin, V. M. Trojanowski, J. 2020-07-06 doi:10.1101/2020.07.06.185066 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Neutrophil extracellular traps impair regeneration ]]> https://biorxiv.org/content/10.1101/2020.07.06.189910v1?rss=1 Garza, L. Wier, E. 2020-07-06 doi:10.1101/2020.07.06.189910 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Tau forms oligomeric complexes on microtubules that are distinct from pathological oligomers in disease ]]> https://biorxiv.org/content/10.1101/2020.07.07.192146v1?rss=1 Gyparaki, M. T. Arab, A. Sorokina, E. M. Santiago-Ruiz, A. N. Bohrer, C. H. Xiao, J. Lakadamyali, M. 2020-07-08 doi:10.1101/2020.07.07.192146 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Knockout of Cyp26a1 and Cyp26b1 during post-natal life causes reduced lifespan, dermatitis, splenomegaly and systemic inflammation in mice ]]> https://biorxiv.org/content/10.1101/2020.07.09.196170v1?rss=1 Jessica M Snyder Guo Zhong Cathryn Hogarth Weize Huang Traci Topping Jeffrey LaFrance Laura Palau Lindsay C Czuba Michael Griswold Gabriel Ghiaur Nina Isoherranen 2020-07-09 doi:10.1101/2020.07.09.196170 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ ACE2-expressing endothelial cells in aging mouse brain ]]> https://biorxiv.org/content/10.1101/2020.07.11.198770v1?rss=1 SU Bin Lim Valina L. Dawson Ted M. Dawson Sung-Ung Kang 2020-07-11 doi:10.1101/2020.07.11.198770 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Solid-state NMR spectroscopy identifies three classes of lipids in C. neoformans melanized cell walls and whole fungal cells ]]> https://biorxiv.org/content/10.1101/2020.07.13.200741v1?rss=1 Chrissian, C. Camacho, E. Kelly, J. E. Wang, H. Casadevall, A. Stark, R. E. 2020-07-13 doi:10.1101/2020.07.13.200741 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Structural engraftment and topographic spacing of transplanted human stem cell-derived retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2020.07.14.196055v1?rss=1 Zhang, K. Y. Tuffy, C. Mertz, J. L. Quillen, S. Wechsler, L. Quigley, H. A. Zack, D. J. Johnson, T. V. 2020-07-16 doi:10.1101/2020.07.14.196055 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Development of a genetically-encoded oxytocin sensor ]]> https://biorxiv.org/content/10.1101/2020.07.14.202598v1?rss=1 Mignocchi, N. L. Kruessel, S. Jung, K. Lee, D. Kwon, H.-B. 2020-07-14 doi:10.1101/2020.07.14.202598 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Multiscale label-free volumetric holographic histopathology of thick-tissue slides with subcellular resolution ]]> https://biorxiv.org/content/10.1101/2020.07.15.205633v1?rss=1 View larger version (98K): org.highwire.dtl.DTLVardef@dcf15corg.highwire.dtl.DTLVardef@16a05d3org.highwire.dtl.DTLVardef@1a48860org.highwire.dtl.DTLVardef@f57430_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hugonnet, H. Kim, Y. W. Lee, M. Shin, S. Hruban, R. H. Hong, S.-M. Park, Y. 2020-07-16 doi:10.1101/2020.07.15.205633 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Prevalence of Hepatitis B Virus (HBV) Basal Core Promoter/Precore region molecular variants among HIV/HBV co-infected and HBV mono-infected patients in Ile-Ife, Nigeria ]]> https://biorxiv.org/content/10.1101/2020.07.16.206151v1?rss=1 Osasona, O. G. Boudarene, L. Adewale-Fasoro, O. George, U. Oguzie, J. Ariyo, O. E. Olumade, T. J. Adeniyi, A. Adewumi, M. O. Adeniji, A. J. 2020-07-16 doi:10.1101/2020.07.16.206151 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Keratin 17 regulates nuclear morphology and chromatin organization ]]> https://biorxiv.org/content/10.1101/2020.07.16.206730v1?rss=1 Jacob, J. T. Nair, R. R. Poll, B. G. Pineda, C. M. Hobbs, R. P. Matunis, M. J. Coulombe, P. A. 2020-07-16 doi:10.1101/2020.07.16.206730 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Lack of redundancy between electrophysiological measures of long-range neuronal communication ]]> https://biorxiv.org/content/10.1101/2020.07.16.207001v1?rss=1 Strahnen, D. Kapanaiah, S. K. T. Bygrave, A. M. Kaetzel, D. 2020-07-17 doi:10.1101/2020.07.16.207001 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease ]]> https://biorxiv.org/content/10.1101/2020.07.17.209023v1?rss=1 Yang, S. Y. Castellani, C. A. Longchamps, R. J. Pillalamarri, V. K. O'Rourke, B. Guallar, E. Arking, D. E. 2020-07-18 doi:10.1101/2020.07.17.209023 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Signal Peptide of HIV-1 Envelope Functions to Modulate Glycosylation Impacting Exposure of V1V2 Epitopes ]]> https://biorxiv.org/content/10.1101/2020.07.21.212183v1?rss=1 Upadhyay, C. Feyznezhad, R. Cao, L. Chan, K.-W. Liu, K. Yang, W. Zhang, H. Yolitz, J. Arthos, J. Nadas, A. Kong, X.-P. Zolla-Pazner, S. Hioe, C. E. 2020-07-21 doi:10.1101/2020.07.21.212183 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Kv1.2 contributes to pattern separation by regulating the hippocampal CA3 neuronal ensemble size ]]> https://biorxiv.org/content/10.1101/2020.07.21.213538v1?rss=1 Eom, K. Lee, H. R. Hyun, J. H. Ryu, H.-H. Lee, Y.-S. Lee, I. Ho, W.-K. Lee, S.-H. 2020-07-21 doi:10.1101/2020.07.21.213538 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ The frailty syndrome as an emergent state of parallel dysregulation in multiple physiological systems ]]> https://biorxiv.org/content/10.1101/2020.07.22.214718v1?rss=1 Ghachem, A. Fried, L. P. Legault, V. Bandeen-Roche, K. Presse, N. Cohen, A. A. 2020-07-23 doi:10.1101/2020.07.22.214718 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Differential Mast Cell Phenotypes in Benign versus Cancer Tissues and Prostate Cancer Oncologic Outcomes ]]> https://biorxiv.org/content/10.1101/2020.07.23.216408v1?rss=1 Hempel Sullivan, H. Maynard, J. P. Heaphy, C. M. Lu, J. De Marzo, A. M. Lotan, T. L. Joshu, C. E. Sfanos, K. S. 2020-07-24 doi:10.1101/2020.07.23.216408 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ A Feedback Mechanism Regulates Odorant Receptor Expression in the Malaria Mosquito, Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/2020.07.23.218586v1?rss=1 Maguire, S. E. Afify, A. Goff, L. Potter, C. J. 2020-07-24 doi:10.1101/2020.07.23.218586 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ The trajectory of cortical GABA levels across thelifespan: An individual participant datameta-analysis of edited MRS studies ]]> https://biorxiv.org/content/10.1101/2020.07.23.218792v1?rss=1 Porges, E. C. Jensen, G. Foster, B. Edden, R. A. E. Puts, N. A. J. 2020-07-24 doi:10.1101/2020.07.23.218792 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Benchmarking challenging small variants with linked and long reads ]]> https://biorxiv.org/content/10.1101/2020.07.24.212712v1?rss=1 Wagner, J. Olson, N. D. Harris, L. Khan, Z. Farek, J. Mahmoud, M. Stankovic, A. Kovacevic, V. Wenger, A. M. Rowell, W. J. Xiao, C. Yoo, B. Miller, N. Rosenfeld, J. A. Ni, B. Zarate, S. Kirsche, M. Aganezov, S. Schatz, M. Narzisi, G. Byrska-Bishop, M. Clarke, W. Evani, U. S. Markello, C. Shafin, K. Zhou, X. Sidow, A. Bansal, V. Martinez Barrio, A. Fiddes, I. T. Fungtammasan, A. Chin, C.-S. Sedlazeck, F. J. Carroll, A. Salit, M. Zook, J. M. Genome in a Bottle Consortium, 2020-07-25 doi:10.1101/2020.07.24.212712 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Effects of individual base-pairs on in vivo target search and destruction kinetics of small RNA ]]> https://biorxiv.org/content/10.1101/2020.07.24.215095v1?rss=1 Poddar, A. Azam, M. S. Kayikcioglu, T. Bobrovskyy, M. Zhang, J. Ma, X. Labhsetwar, P. Fei, J. Singh, D. Luthey-Schulten, Z. Vanderpool, C. K. Ha, T. 2020-07-26 doi:10.1101/2020.07.24.215095 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Domino: reconstructing intercellular signaling dynamics with transcription factor activation in model biomaterial environments ]]> https://biorxiv.org/content/10.1101/2020.07.24.218537v1?rss=1 Cherry, C. Cahan, P. Garmire, L. X. Elisseeff, J. H. 2020-07-25 doi:10.1101/2020.07.24.218537 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Two-dimensional video-based analysis of human gait using pose estimation ]]> https://biorxiv.org/content/10.1101/2020.07.24.218776v1?rss=1 Stenum, J. Rossi, C. Roemmich, R. T. 2020-07-26 doi:10.1101/2020.07.24.218776 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Structure and function of a novel osmoregulated periplasmic fiber-forming high-molecular-weight carbohydrate of Myxococcus xanthus ]]> https://biorxiv.org/content/10.1101/2020.07.26.208595v1?rss=1 Agrawal, S. Heiss, C. Zuckerman, D. M. So, J. M. T. Semeijn, K. Naran, R. Azadi, P. Hoiczyk, E. 2020-07-26 doi:10.1101/2020.07.26.208595 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling ]]> https://biorxiv.org/content/10.1101/2020.07.27.223321v1?rss=1 Sugino, K. Miyares, R. L. Espinosa-Medina, I. Chen, H.-M. Potter, C. J. Lee, T. 2020-07-29 doi:10.1101/2020.07.27.223321 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Larger organ size caused by obesity is a mechanism for higher cancer risk. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223529v1?rss=1 Grant, H. Zhang, Y. Li, L. Wang, Y. Kawamoto, S. Penisson, S. Fouladi, D. F. Shayesteh, S. Blanco, A. Ghandili, S. Zinreich, E. Graves, J. S. Park, S. Kern, S. Hooper, J. Yuille, A. L. Fishman, E. K. Chu, L. Tomasetti, C. 2020-07-29 doi:10.1101/2020.07.27.223529 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Low-cost 3D-printed inverted microscope to detect Mycobacterium tuberculosis in a MODS culture ]]> https://biorxiv.org/content/10.1101/2020.07.27.223701v1?rss=1 Salguedo, M. I. Zarate, G. W. Gilman, R. Comina, G. Coronel, J. Sheen, P. Zimic, M. 2020-07-27 doi:10.1101/2020.07.27.223701 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Oncogenic gene fusions in non-neoplastic precursors as evidence that bacterial infection initiates prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.07.27.224154v1?rss=1 Shrestha, E. Coulter, J. Guzman, W. Ozbek, B. Mummert, L. Ernst, S. Maynard, J. Meeker, A. Heaphy, C. Haffner, M. De Marzo, A. M. Sfanos, K. S. 2020-07-28 doi:10.1101/2020.07.27.224154 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Comparative Analysis of Human Coronaviruses Focusing on Nucleotide Variability and Synonymous Codon Usage Pattern ]]> https://biorxiv.org/content/10.1101/2020.07.28.224386v1?rss=1 Das, J. Roy, S. 2020-07-28 doi:10.1101/2020.07.28.224386 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism ]]> https://biorxiv.org/content/10.1101/2020.07.28.225151v1?rss=1 Jacob, F. Pather, S. Huang, W.-K. Wong, S. Z. H. Zhou, H. Zhang, F. Cubitt, B. Chen, C. Z. Xu, M. Pradhan, M. Zhang, D. Y. Zheng, W. Bang, A. G. Song, H. de la Torre, J. C. Ming, G.-l. 2020-07-28 doi:10.1101/2020.07.28.225151 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.07.29.226217v1?rss=1 Das, J. Chakrobarty, S. Roy, S. 2020-07-29 doi:10.1101/2020.07.29.226217 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy ]]> https://biorxiv.org/content/10.1101/2020.07.31.231613v1?rss=1 Cheng, S. Fu, S. Kim, Y. M. Song, W. Li, Y. Xue, Y. Yi, J. Tian, L. 2020-08-02 doi:10.1101/2020.07.31.231613 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Time-resolved expression analysis comparing two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative regulatory networks. ]]> https://biorxiv.org/content/10.1101/2020.08.04.236299v1?rss=1 Walker, S. L. Wang, G. Emmerich, K. B. Wang, F. White, D. T. Saxena, M. T. Teng, Y. Qian, J. Mumm, J. S. 2020-08-05 doi:10.1101/2020.08.04.236299 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Characterization of extracellular vesicles and artificial nanoparticles with four orthogonal single-particle analysis platforms ]]> https://biorxiv.org/content/10.1101/2020.08.04.237156v1?rss=1 Mallick, E. R. Arab, T. Huang, Y. Dong, L. Liao, Z. Zhao, Z. Smith, B. Haughey, N. J. Pienta, K. J. Slusher, B. S. Tarwater, P. M. Tosar, J. P. Zivkovic, A. M. Vreeland, W. N. Paulaitis, M. E. Witwer, K. W. 2020-08-05 doi:10.1101/2020.08.04.237156 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Transcriptome Analysis of Human Induced Excitatory Neurons Supports a Strong Effect of Clozapine on Cholesterol Biosynthesis ]]> https://biorxiv.org/content/10.1101/2020.08.05.238212v1?rss=1 Das, D. Peng, X. Lam, A.-T. Bader, J. S. Avramopoulos, D. 2020-08-06 doi:10.1101/2020.08.05.238212 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Dendrimer-targeted immunosuppression of microglia reactivity super-accelerates photoreceptor regeneration in the zebrafish retina ]]> https://biorxiv.org/content/10.1101/2020.08.05.238352v1?rss=1 Emmerich, K. B. White, D. T. Kambhamptati, S. P. Lee, G. Y. Fu, T.-M. Sahoo, A. Betzig, E. Kannan, R. M. Mumm, J. S. Saxena, M. T. 2020-08-06 doi:10.1101/2020.08.05.238352 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ IL-4 receptor targeting as an effective immunotherapy against triple-negative breast cancer ]]> https://biorxiv.org/content/10.1101/2020.08.05.238824v1?rss=1 Parveen, S. Siddharth, S. Cheung, L. S. Kumar, A. Murphy, J. R. Sharma, D. Bishai, W. R. 2020-08-06 doi:10.1101/2020.08.05.238824 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Single amino acid mutations effect Zika virus replication in vitro and virulence in vivo ]]> https://biorxiv.org/content/10.1101/2020.08.06.239392v1?rss=1 Collette, N. K. Lao, V. K. Weilhammer, D. Zingg, B. Cohen, S. K. Hwang, M. K. Coffey, L. Grady, S. Zemla, A. K. Borucki, M. K. 2020-08-06 doi:10.1101/2020.08.06.239392 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.08.06.240200v1?rss=1 Choi, C. P. Tay, R. J. Starostik, M. R. Feng, S. Moresco, J. J. Montgomery, B. E. Xu, E. Hammond, M. A. Schatz, M. C. Montgomery, T. A. Yates, J. R. Jacobsen, S. E. Kim, J. K. 2020-08-06 doi:10.1101/2020.08.06.240200 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ SVCollector: Optimized sample selection for cost-efficient long-read population sequencing ]]> https://biorxiv.org/content/10.1101/2020.08.06.240390v1?rss=1 Ranallo-Benavidez, T. R. Lemmon, Z. H. Soyk, S. Aganezov, S. Salerno, W. J. McCoy, R. C. Lippman, Z. B. Schatz, M. C. Sedlazeck, F. J. 2020-08-06 doi:10.1101/2020.08.06.240390 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Human muscle stem cells are refractory to aging ]]> https://biorxiv.org/content/10.1101/2020.08.07.238477v1?rss=1 Novak, J. S. Mazala, D. Nearing, M. Habib, N. F. Dickson, T. Ioffe, O. B. Harris, B. T. Fidelia-Lambert, M. N. Rossi, C. T. Ashley Hill, D. Wagner, K. R. Hoffman, E. P. Partridge, T. A. 2020-08-07 doi:10.1101/2020.08.07.238477 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence ]]> https://biorxiv.org/content/10.1101/2020.08.07.241190v1?rss=1 Fu, M. S. Liporagi-Lopes, L. C. dos Santos Junior, S. R. Tenor, J. Perfect, J. R. Cuomo, C. Casadevall, A. 2020-08-07 doi:10.1101/2020.08.07.241190 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ The female-specific VC neurons are mechanically activated, feed-forward motor neurons that facilitate serotonin-induced egg laying in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.08.11.246942v1?rss=1 Kopchock, R. J. Ravi, B. Bode, A. Collins, K. M. 2020-08-12 doi:10.1101/2020.08.11.246942 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Midkine in chick and mouse retinas: neuroprotection, glial reactivity and the formation of Müller glia-derived progenitor cells ]]> https://biorxiv.org/content/10.1101/2020.08.12.248245v1?rss=1 Campbell, W. A. Fritsch-Kelleher, A. Palazzo, I. Hoang, T. Blackshaw, S. Fischer, A. J. 2020-08-12 doi:10.1101/2020.08.12.248245 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Capturing in situ Virus-Host Range and Interaction Dynamics through Gene Fusion with epicPCR ]]> https://biorxiv.org/content/10.1101/2020.08.14.250803v1?rss=1 Sakowski, E. G. Arora-Williams, K. Tian, F. Zayed, A. Zablocki, O. Sullivan, M. B. Preheim, S. P. 2020-08-14 doi:10.1101/2020.08.14.250803 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Asymmetric histone inheritance regulates stem cell fate in Drosophila midgut ]]> https://biorxiv.org/content/10.1101/2020.08.15.252403v1?rss=1 Zion, E. Chen, X. 2020-08-15 doi:10.1101/2020.08.15.252403 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Cleavage Site Specificity for Processing of Farnesylated Prelamin A by the Zinc Metalloprotease ZMPSTE24 ]]> https://biorxiv.org/content/10.1101/2020.08.17.254532v1?rss=1 Babatz, T. D. Spear, E. D. Xu, W. Sun, O. L. Nie, L. Carpenter, E. P. Michaelis, S. 2020-08-17 doi:10.1101/2020.08.17.254532 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Measuring DNA mechanics on the genome scale ]]> https://biorxiv.org/content/10.1101/2020.08.17.255042v1?rss=1 Basu, A. Bobrovnikov, D. G. Qureshi, Z. Kayikcioglu, T. Ngo, T. T. Ranjan, A. Eustermann, S. Cieza, B. Hejna, M. Rube, T. H. Hopfner, K.-P. Wolberger, C. Song, J. S. Ha, T. 2020-08-18 doi:10.1101/2020.08.17.255042 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Characterization of histone inheritance patterns in the Drosophila female germline ]]> https://biorxiv.org/content/10.1101/2020.08.18.255455v1?rss=1 Chen, X. Kahney, E. W. Sohn, L. Viets-Layng, K. Johnston, R. 2020-08-19 doi:10.1101/2020.08.18.255455 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Botanical Medicines with Activity against Stationary Phase Bartonella henselae ]]> https://biorxiv.org/content/10.1101/2020.08.19.256768v1?rss=1 Zhang, Y. Ma, X. Leone, J. Schweig, S. 2020-08-23 doi:10.1101/2020.08.19.256768 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ N6-methyladenine DNA demethylase ALKBH1 regulates mammalian axon regeneration ]]> https://biorxiv.org/content/10.1101/2020.08.19.258038v1?rss=1 Li, Q. Qian, C. Feng, H. Lin, T. Huang, Y. Zhou, F.-Q. 2020-08-20 doi:10.1101/2020.08.19.258038 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ CD300lf conditional knockout mouse reveals strain-specific cellular tropism for murine norovirus ]]> https://biorxiv.org/content/10.1101/2020.08.19.258467v1?rss=1 Graziano, V. R. Alfajaro, M. M. Schmitz, C. Filler, R. B. Strine, M. S. Wei, J. Hsieh, L. L. Baldridge, M. T. Nice, T. J. Lee, S. Orchard, R. C. Wilen, C. B. 2020-08-21 doi:10.1101/2020.08.19.258467 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Deciphering the mechanical code of genome and epigenome ]]> https://biorxiv.org/content/10.1101/2020.08.22.262352v1?rss=1 Basu, A. Bobrovnikov, D. G. Cieza, B. Qureshi, Z. Ha, T. 2020-08-24 doi:10.1101/2020.08.22.262352 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Light-emitting diode-based transcranial photoacoustic measurement of sagittal sinus oxyhemoglobin saturation in hypoxic neonatal piglets ]]> https://biorxiv.org/content/10.1101/2020.08.22.262451v1?rss=1 20 frame averaging), graded hypoxia was successfully identified in neonatal piglets in vivo with less than 10.0 % of root mean squared error (RMSE). This preclinical study suggests the feasibility of a rapid, cost-effective, and safe LED-trPA monitoring of perinatal hypoxia-ischemia and prompt interventions for clinical use. ]]> Kang, J. Koehler, R. C. Adams, S. Graham, E. M. Boctor, E. M. 2020-08-24 doi:10.1101/2020.08.22.262451 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ The Japan Monkey Centre Primates Brain Imaging Repository of high-resolution postmortem magnetic resonance imaging: the second phase of the archive of digital records ]]> https://biorxiv.org/content/10.1101/2020.08.23.263517v1?rss=1 Sakai, T. Hata, J. Shintaku, Y. Ohta, H. Sogabe, K. Mori, S. Okano, H. J. Hamada, Y. Hirabayashi, T. Minamimoto, T. Sadato, N. Okano, H. Oishi, K. 2020-08-24 doi:10.1101/2020.08.23.263517 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Neural crest-derived neurons are replaced by a newly identified mesodermal lineage in the post-natal and aging enteric nervous system ]]> https://biorxiv.org/content/10.1101/2020.08.25.262832v1?rss=1 Kulkarni, S. Saha, M. Becker, L. S. Wang, Z. Liu, G. Leser, J. Kumar, M. Bakhshi, S. Anderson, M. J. Lewandoski, M. Slosberg, J. Nagaraj, S. Vincent, E. Goff, L. Pasricha, P. J. 2020-08-25 doi:10.1101/2020.08.25.262832 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Longitudinal changes in brain metabolites in healthy subjects and patients with first episode psychosis (FEP): a 7-Tesla MRS study ]]> https://biorxiv.org/content/10.1101/2020.08.25.267419v1?rss=1 Wang, M. Barker, P. B. Cascella, N. Coughlin, J. M. Nestadt, G. Nucifora, F. C. Sedlak, T. W. Kelly, A. Younes, L. Geman, D. Sawa, A. Yang, K. 2020-08-26 doi:10.1101/2020.08.25.267419 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Imaging meningeal inflammation in CNS autoimmunity identifies a therapeutic role for BTK inhibition ]]> https://biorxiv.org/content/10.1101/2020.08.26.268250v1?rss=1 Bhargava, P. Kim, S. Reyes, A. A. Grenningloh, R. Boshcert, U. Absinta, M. Pardo-Villamizar, C. Van Zijl, P. Zhang, J. Calabresi, P. 2020-08-27 doi:10.1101/2020.08.26.268250 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ A Phased Canis lupus familiaris Labrador Retriever Reference Genome Utilizing High Molecular Weight DNA Extraction Methods and High Resolution Sequencing Technologies ]]> https://biorxiv.org/content/10.1101/2020.08.26.269076v1?rss=1 Player, R. A. Forsyth, E. R. Verratti, K. J. Mohr, D. W. Scott, A. F. Bradburne, C. E. 2020-08-27 doi:10.1101/2020.08.26.269076 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ SynapsEM: computer-assisted synapse morphometry ]]> https://biorxiv.org/content/10.1101/2020.08.28.271882v1?rss=1 Watanabe, S. Davis, M. W. Kusick, G. F. Iwasa, J. Jorgensen, E. M. 2020-08-29 doi:10.1101/2020.08.28.271882 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration ]]> https://biorxiv.org/content/10.1101/2020.08.28.272039v1?rss=1 Orvis, J. Gottfried, B. Kancherla, J. Adkins, R. S. Song, Y. Dror, A. A. Olley, D. Rose, K. Chrysostomou, E. Kelley, M. C. Milon, B. Matern, M. S. Azaiez, H. Herb, B. Colantuoni, C. Carter, R. L. Ament, S. A. Kelley, M. W. White, O. Bravo, H. C. Mahurkar, A. Hertzano, R. 2020-08-31 doi:10.1101/2020.08.28.272039 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Non-Refoldability is Pervasive Across the E. coli Proteome ]]> https://biorxiv.org/content/10.1101/2020.08.28.273110v1?rss=1 To, P. Whitehead, B. Tarbox, H. E. Fried, S. D. 2020-08-29 doi:10.1101/2020.08.28.273110 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ De novo genome assembly of the Tobacco Hornworm moth (Manduca sexta) ]]> https://biorxiv.org/content/10.1101/2020.08.29.270983v1?rss=1 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism. ]]> Gershman, A. Romer, T. G. Fan, Y. Razaghi, R. Smith, W. A. Timp, W. 2020-08-31 doi:10.1101/2020.08.29.270983 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Heterogeneity of age-related neural hyperactivity along the CA3 transverse axis ]]> https://biorxiv.org/content/10.1101/2020.08.31.275156v1?rss=1 Lee, H. Wang, Z. Zeger, S. L. Gallagher, M. Knierim, J. J. 2020-09-01 doi:10.1101/2020.08.31.275156 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration ]]> https://biorxiv.org/content/10.1101/2020.08.31.276733v1?rss=1 Cooper, R. E. Mangus, L. M. Lynch, J. Schonvisky, K. Wright, J. McLimans, C. J. Wong, H. T. Chen See, J. R. Lamendella, R. Mankowski, J. L. 2020-09-01 doi:10.1101/2020.08.31.276733 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Meaningful Effects in the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/2020.09.01.276451v1?rss=1 Dick, A. S. Watts, A. L. Heeringa, S. G. Lopez, D. A. Bartsch, H. Fan, C. C. Palmer, C. E. Reuter, C. Marshall, A. T. Haist, F. Hawes, S. Nichols, T. Barch, D. M. Jernigan, T. L. Garavan, H. Grant, S. Pariyadath, V. Hoffman, E. Neale, M. Paulus, M. P. Sher, K. Thompson, W. 2020-09-01 doi:10.1101/2020.09.01.276451 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Water Controls Membrane Protein Stability ]]> https://biorxiv.org/content/10.1101/2020.09.01.277897v1?rss=1 Marx, D. C. Fleming, K. G. 2020-09-01 doi:10.1101/2020.09.01.277897 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Defining Substrate Requirements for Cleavage of Farnesylated Prelamin A by the Integral Membrane Zinc Metalloprotease ZMPSTE24 ]]> https://biorxiv.org/content/10.1101/2020.09.02.279661v1?rss=1 Wood, K. M. Spear, E. D. Mossberg, O. W. Odinammadu, K. O. Xu, W. Michaelis, S. 2020-09-03 doi:10.1101/2020.09.02.279661 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Host-cell interactions and innate immune response to an enteric pathogen in a human intestinal enteroid-neutrophil co-culture ]]> https://biorxiv.org/content/10.1101/2020.09.03.281535v1?rss=1 Lemme-Dumit, J. M. Doucet, M. Zachos, N. Pasetti, M. F. 2020-09-04 doi:10.1101/2020.09.03.281535 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Polygenic Risk Scores for Kidney Function to the Circulating Proteome, and Incident Kidney Diseases: the Atherosclerosis Risk in Communities Study ]]> https://biorxiv.org/content/10.1101/2020.09.05.284265v1?rss=1 Yu, Z. Jin, J. Tin, A. Kottgen, A. Yu, B. Chen, J. Surapaneni, A. Zhou, L. Ballantyne, C. M. Hoogeveen, R. C. Arking, D. E. Chatterjee, N. Grams, M. E. Coresh, J. 2020-09-08 doi:10.1101/2020.09.05.284265 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Balrog: A universal protein model for prokaryotic gene prediction ]]> https://biorxiv.org/content/10.1101/2020.09.06.285304v1?rss=1 Sommer, M. J. Salzberg, S. L. 2020-09-08 doi:10.1101/2020.09.06.285304 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Feasibility of Integrating Canine Olfaction with Chemical and Microbial Profiling of Urine to Detect Lethal Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2020.09.09.288258v1?rss=1 Guest, C. Harris, R. Sfanos, K. S. Shrestha, E. Partin, A. W. Trock, B. Mangold, L. Bader, R. Kozak, A. Mclean, S. Simons, J. Soule, H. Johnson, T. Lee, W.-Y. Gao, Q. Aziz, S. Stathatou, P. Thaler, S. Foster, S. Mershin, A. 2020-09-10 doi:10.1101/2020.09.09.288258 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus ]]> https://biorxiv.org/content/10.1101/2020.09.09.290502v1?rss=1 Scheben, A. Mendivil Ramos, O. Kramer, M. Goodwin, S. Oppenheim, S. J. Becker, D. J. Schatz, M. C. Simmons, N. B. Siepel, A. McCombie, W. R. 2020-09-09 doi:10.1101/2020.09.09.290502 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Supraphysiological testosterone induces ferroptosis and activates NF-kappaB mediated immune pathways in prostate cancer through nucleophagy ]]> https://biorxiv.org/content/10.1101/2020.09.10.286252v1?rss=1 Mendonca, J. Kumar, R. Owoyemi, O. Boyapati, K. Thomas, N. Kanacharoen, S. Coffey, M. Topiwala, D. Gomes, C. Ozbek, B. Jones, T. Rosen, M. Dong, L. Wiens, S. Brennen, W. N. Isaacs, J. De Marzo, A. M. Markowski, M. Antonarakis, E. S. Qian, D. Pienta, K. Pardoll, D. Carducci, M. Denmeade, S. Kachhap, S. 2020-09-10 doi:10.1101/2020.09.10.286252 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ DETECTION OF INCIPIENT PANCREATIC CANCER WITH NOVEL TUMOR-SPECIFIC ANTIBODIES IN MOUSE MODELS ]]> https://biorxiv.org/content/10.1101/2020.09.10.292193v1?rss=1 Oni, T. E. Bautista, C. Merrill, J. R. Goos, J. A. C. M. Rivera, K. D. Miyabayashi, K. Biffi, G. Garcia, L. Plenker, D. Patel, H. Elyada, E. Samaritano, M. Yu, K. H. Pappin, D. J. Goggins, M. G. Hruban, R. H. Lewis, J. S. Yeh, J. T. Tuveson, D. A. 2020-09-10 doi:10.1101/2020.09.10.292193 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Induction of AmpC-mediated-βlactam resistance requires a single lytic transglycosylase in Agrobacterium tumefaciens ]]> https://biorxiv.org/content/10.1101/2020.09.10.292490v1?rss=1 Figueroa-Cuilan, W. Howell, M. Richards, C. Randich, A. Yadav, A. K. Cava, F. Brown, P. J. B. 2020-09-12 doi:10.1101/2020.09.10.292490 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Mutations in fbiD(Rv2983) as a novel determinant of resistance to pretomanid and delamanid in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.09.10.292508v1?rss=1 Rifat, D. Li, S.-Y. Ioerger, T. R. Shah, K. Lanoix, J.-P. Lee, J. Bashiri, G. Sacchettini, J. C. Nuermberger, E. 2020-09-11 doi:10.1101/2020.09.10.292508 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Expression of varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency ]]> https://biorxiv.org/content/10.1101/2020.09.11.294280v1?rss=1 Ouwendijk, W. J. D. Depledge, D. P. Rajbhandari, L. Rovis, T. R. Jonjic, S. Breuer, J. Venkatesan, A. Verjans, G. M. G. M. Sadaoka, T. 2020-09-11 doi:10.1101/2020.09.11.294280 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Designed PKC-targeting bryostatin analogs modulate innate immunity and neuroinflammation ]]> https://biorxiv.org/content/10.1101/2020.09.12.294918v1?rss=1 Abramson, E. Hardman, C. Shimizu, A. Hwang, S. Hester, L. D. Snyder, S. H. Wender, P. A. Kim, P. M. Kornberg, M. D. 2020-09-12 doi:10.1101/2020.09.12.294918 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity ]]> https://biorxiv.org/content/10.1101/2020.09.13.276923v1?rss=1 Inde, Z. Yapp, C. Joshi, G. N. Spetz, J. Fraser, C. Deskin, B. Ghelfi, E. Sodhi, C. Hackam, D. Kobzik, L. Croker, B. Brownfield, D. Jia, H. Sarosiek, K. A. 2020-09-13 doi:10.1101/2020.09.13.276923 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ A chemiluminescent protease probe for rapid, sensitive, and inexpensive detection of live Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.09.14.296772v1?rss=1 Babin, B. M. Fernandez-Cuervo, G. Sheng, J. Green, O. Ordonez, A. A. Turner, M. L. Keller, L. J. Jain, S. K. Shabat, D. Bogyo, M. 2020-09-14 doi:10.1101/2020.09.14.296772 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Targeting ischemia-induced KCC2 hypofunction rescues refractory neonatal seizures and mitigates epileptogenesis in a mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.15.298596v1?rss=1 Sullivan, B. J. Kipnis, P. A. Carter, B. M. Kadam, S. D. 2020-09-15 doi:10.1101/2020.09.15.298596 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Msp1/ATAD1 restores mitochondrial function in Zellweger Spectrum Disease ]]> https://biorxiv.org/content/10.1101/2020.09.19.303826v1?rss=1 Nuebel, E. Morgan, J. T. Fogarty, S. Winter, J. M. Lettlova, S. Berg, J. A. Chen, Y.-C. Kidwell, C. U. Maschek, J. A. Clowers, K. J. Argyriou, C. Chen, L. Wittig, I. Cox, J. E. Roh-Johnson, M. Braverman, N. Steinberg, S. J. Gygi, S. P. Rutter, J. 2020-09-19 doi:10.1101/2020.09.19.303826 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie ]]> https://biorxiv.org/content/10.1101/2020.09.21.300913v1?rss=1 Varabyou, A. Pockrandt, C. Salzberg, S. L. Pertea, M. 2020-09-21 doi:10.1101/2020.09.21.300913 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ A causal study of bumetanide on a marker of excitatory-inhibitory balance in the human brain ]]> https://biorxiv.org/content/10.1101/2020.09.22.304279v1?rss=1 Botch, T. L. Spiegel, A. Ricciardi, C. Robertson, C. E. 2020-09-23 doi:10.1101/2020.09.22.304279 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Germline DNA replication shapes the recombination landscape in mammals ]]> https://biorxiv.org/content/10.1101/2020.09.23.308874v1?rss=1 Pratto, F. Brick, K. Cheng, G. Lam, K.-W. G. Cloutier, J. M. Dahiya, D. Wellard, S. R. Jordan, P. W. Camerini-Otero, R. D. 2020-09-23 doi:10.1101/2020.09.23.308874 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Coarse Raman and optical diffraction tomographic imaging enable label-free phenotyping of isogenic breast cancer cells of varying metastatic potential ]]> https://biorxiv.org/content/10.1101/2020.09.23.309138v1?rss=1 Paidi, S. K. Shah, V. Raj, P. Glunde, K. Pandey, R. Barman, I. 2020-09-24 doi:10.1101/2020.09.23.309138 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome ]]> https://biorxiv.org/content/10.1101/2020.09.23.310227v1?rss=1 Reinhardt, J. A. Baker, R. H. Zimin, A. V. Ladias, C. Paczolt, K. Werren, J. Hayashi, C. Wilkinson, G. S. 2020-09-23 doi:10.1101/2020.09.23.310227 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ A phospho-regulated ensemble signal motif of α-TAT1 drives dynamic microtubule acetylation ]]> https://biorxiv.org/content/10.1101/2020.09.23.310235v1?rss=1 Inoue, T. Deb Roy, A. Gross, E. Pillai, G. Seetharaman, S. Etienne-Manneville, S. 2020-09-23 doi:10.1101/2020.09.23.310235 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins ]]> https://biorxiv.org/content/10.1101/2020.09.24.298851v1?rss=1 Ayyappan, V. Wat, R. Barber, C. Vivelo, C. Gauch, K. Visanpattanasin, P. Cook, G. Sazeides, C. Leung, A. K. L. 2020-09-25 doi:10.1101/2020.09.24.298851 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Widespread methylation quantitative trait loci and their role in schizophrenia risk ]]> https://biorxiv.org/content/10.1101/2020.09.24.311878v1?rss=1 Perzel Mandell, K. A. Eagles, N. J. Wilton, R. Price, A. J. Semick, S. A. Collado-Torres, L. Tao, R. Han, S. Szalay, A. S. Hyde, T. M. Kleinman, J. E. Weinberger, D. R. Jaffe, A. E. 2020-09-24 doi:10.1101/2020.09.24.311878 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Detecting and phasing minor single-nucleotide variants from long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2020.09.25.314252v1?rss=1 Feng, Z. Clemente, J. Wong, B. Schadt, E. 2020-09-27 doi:10.1101/2020.09.25.314252 Cold Spring Harbor Laboratory Press 2020-09-27 <![CDATA[ Regulation of retinal neurogenesis by somatostatin signaling. ]]> https://biorxiv.org/content/10.1101/2020.09.26.314104v1?rss=1 Weir, K. Kim, D. W. Blackshaw, S. 2020-09-26 doi:10.1101/2020.09.26.314104 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Synthetic auxotrophy remains stable after continuous evolution and in co-culture with mammalian cells ]]> https://biorxiv.org/content/10.1101/2020.09.27.315804v1?rss=1 Kunjapur, A. M. Napolitano, M. G. Hysolli, E. Noguera, K. Appleton, E. M. Schubert, M. G. Jones, M. A. Iyer, S. Mandell, D. J. Church, G. M. 2020-09-28 doi:10.1101/2020.09.27.315804 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Interpreting blood GLUcose data with R package iglu ]]> https://biorxiv.org/content/10.1101/2020.09.28.310482v1?rss=1 Broll, S. Urbanek, J. Buchanan, D. Chun, E. Muschelli, J. Punjabi, N. Gaynanova, I. 2020-09-29 doi:10.1101/2020.09.28.310482 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Leptin receptor expression in the dorsomedial hypothalamus stimulates breathing during NREM sleep in db/db mice ]]> https://biorxiv.org/content/10.1101/2020.09.29.318758v1?rss=1 Pho, H. Berger, S. Freire, C. Kim, L. Shin, M.-k. Streeter, S. Hosamane, N. Cabassa, M. Anokye-Danso, F. Dergacheva, O. Amorim, M. Fleury-Curado, T. Jun, J. Schwartz, A. Ahima, R. Mendelowitz, D. Polotsky, V. 2020-10-01 doi:10.1101/2020.09.29.318758 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2020.09.29.319756v1?rss=1 Sun, C. Wang, H. Ma, Q. Chen, C. Yue, J. Li, B. Zhang, X. 2020-10-01 doi:10.1101/2020.09.29.319756 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions ]]> https://biorxiv.org/content/10.1101/2020.09.30.320150v1?rss=1 Masonbrink, R. Alt, D. Bayles, D. O. Boggiatto, P. Edwards, W. Tatum, F. Williams, J. Wilson-Welder, J. Zimin, A. Severin, A. Olsen, S. 2020-09-30 doi:10.1101/2020.09.30.320150 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Applying Machine Learning to Increase Efficiency and Accuracy of Meta-Analytic Review ]]> https://biorxiv.org/content/10.1101/2020.10.06.314245v1?rss=1 Gorelik, A. J. Gorelik, M. G. Ridout, K. K. Nimarko, A. F. Peisch, V. Kuramkote, S. R. Low, M. Pan, T. Singh, S. Nrusimha, A. Singh, M. K. 2020-10-08 doi:10.1101/2020.10.06.314245 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Antinociceptive, hypothermic, and appetitive effects of vaped and injected Δ9-tetrahydrocannabinol (THC) in rats: exposure and dose-effect comparisons by strain and sex ]]> https://biorxiv.org/content/10.1101/2020.10.06.327312v1?rss=1 Moore, C. F. Davis, C. M. Harvey, E. L. Taffe, M. A. Weerts, E. M. 2020-10-08 doi:10.1101/2020.10.06.327312 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Phase-locking of resting-state brain networks with the gastric basal electrical rhythm ]]> https://biorxiv.org/content/10.1101/2020.10.06.328054v1?rss=1 Choe, A. S. Tang, B. Smith, K. R. Honari, H. Lindquist, M. A. Caffo, B. S. Pekar, J. J. 2020-10-07 doi:10.1101/2020.10.06.328054 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Optimal Adaptive Electrode Selection to Maximize Simultaneously Recorded Neuron Yield ]]> https://biorxiv.org/content/10.1101/2020.10.06.328526v1?rss=1 Choi, J. Kumar, K. Khazali, M. Wingel, K. Choudhury, M. Charles, A. Pesaran, B. 2020-10-08 doi:10.1101/2020.10.06.328526 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Single-Cell Transcriptomic Analysis Reveals Molecular Diversity of Human Oligodendrocyte Progenitor Cells ]]> https://biorxiv.org/content/10.1101/2020.10.07.328971v1?rss=1 Chamling, X. Kallman, A. Berlinicke, C. Devkota, P. Mertz, J. L. Chang, C. Kaushik, A. Chen, L. Calabresi, P. Mao, H.-Q. Wang, J. T.-H. Zack, D. 2020-10-08 doi:10.1101/2020.10.07.328971 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Single-nucleus transcriptome analysis reveals cell type-specific molecular signatures across reward circuitry in the human brain ]]> https://biorxiv.org/content/10.1101/2020.10.07.329839v1?rss=1 Tran, M. N. Maynard, K. R. Spangler, A. Collado Torres, L. Sadashivaiah, V. Tippani, M. Barry, B. K. Hancock, D. B. Hicks, S. C. Kleinman, J. E. Hyde, T. M. Martinowich, K. Jaffe, A. E. 2020-10-08 doi:10.1101/2020.10.07.329839 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Extracting Brain Disease-Related Connectome Subgraphs by Adaptive Dense Subgraph Discovery ]]> https://biorxiv.org/content/10.1101/2020.10.07.330027v1?rss=1 Wu, Q. Huang, X. Culbreth, A. Waltz, J. Hong, L. E. Chen, S. 2020-10-09 doi:10.1101/2020.10.07.330027 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Sequence evaluation and comparative analysis of novel assays for intact proviral HIV-1 DNA ]]> https://biorxiv.org/content/10.1101/2020.10.07.330787v1?rss=1 Gaebler, C. Falcinelli, S. D. Stoffel, E. Read, J. Murtagh, R. Oliveira, T. Ramos, V. Lorenzi, J. C. Kirchherr, J. L. James, K. S. Allard, B. Baker, C. Kuruc, J. D. Caskey, M. Archin, N. Siliciano, R. F. Margolis, D. M. Nussenzweig, M. C. 2020-10-09 doi:10.1101/2020.10.07.330787 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Aging alters the mediating effect of endogenous GABA on the interaction between functional connectivity and motor-state transitions. ]]> https://biorxiv.org/content/10.1101/2020.10.08.331637v1?rss=1 Heise, K.-F. Rueda Delgado, L. M. Chalavi, S. King, B. R. Santos Monteiro, T. Edden, R. A. E. Mantini, D. Swinnen, S. P. 2020-10-09 doi:10.1101/2020.10.08.331637 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Transcriptional landscape of PTEN loss in primary prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.10.08.332049v1?rss=1 Imada, E. L. Sanchez, D. F. Dinalankara, W. Vidotto, T. Ebot, E. M. Tyekucheva, S. Franco, G. R. Mucci, L. Loda, M. Schaeffer, E. M. Lotan, T. Marchionni, L. 2020-10-09 doi:10.1101/2020.10.08.332049 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Expanding the Galaxy's reference data ]]> https://biorxiv.org/content/10.1101/2020.10.09.327114v1?rss=1 VijayKrishna, N. Joshi, J. Coraor, N. Hillman-Jackson, J. Bouvier, D. van den Beek, M. Eguinoa, I. Coppens, F. Golitsynskiy, S. Stolarczyk, M. Sheffield, N. C. Gladman, S. Cuccuru, G. Grüning, B. Soranzo, N. Rasche, H. Langhorst, B. W. Bernt, M. Fornika, D. de Lima Morais, D. A. Barrette, M. van Heusden, P. Petrillo, M. Puertas-Gallardo, A. Patak, A. Hotz, H.-R. Blankenberg, D. 2020-10-10 doi:10.1101/2020.10.09.327114 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Age-related differences in network structure and dynamic synchrony of cognitive control ]]> https://biorxiv.org/content/10.1101/2020.10.09.333567v1?rss=1 Hinault, T. T. Mijalkov, M. Pereira, J. Volpe, G. Bakker, A. Courtney, S. M. 2020-10-10 doi:10.1101/2020.10.09.333567 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Coronin-1 is necessary for enteric pathogen-induced transcytosis across human ileal enteroid monolayers expressing M cells ]]> https://biorxiv.org/content/10.1101/2020.10.12.305565v1?rss=1 Staab, J. F. Doucet, M. Latanich, R. Lee, S. Estes, M. K. Kaper, J. B. Zachos, N. 2020-10-16 doi:10.1101/2020.10.12.305565 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Temperature and species-dependent regulation of browning in retrobulbar fat. ]]> https://biorxiv.org/content/10.1101/2020.10.12.333807v1?rss=1 Rajaii, F. Kim, D. W. Pan, J. Mahoney, N. R. Eberhardt, C. G. Qian, J. Blackshaw, S. 2020-10-12 doi:10.1101/2020.10.12.333807 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea ]]> https://biorxiv.org/content/10.1101/2020.10.12.336255v1?rss=1 Gelsinger, D. R. Reddy, R. Whittington, K. Debic, S. DiRuggiero, J. 2020-10-12 doi:10.1101/2020.10.12.336255 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Scale-invariant time registration of 24-hour accelerometric rest-activity profiles and its application to human chronotypes ]]> https://biorxiv.org/content/10.1101/2020.10.13.337550v1?rss=1 McDonnell, E. I. Zipunnikov, V. Schrack, J. A. Goldsmith, J. Wrobel, J. 2020-10-14 doi:10.1101/2020.10.13.337550 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Isoform-specific roles of the Drosophila filamin-type protein Jitterbug (Jbug) during development ]]> https://biorxiv.org/content/10.1101/2020.10.13.337626v1?rss=1 Chung, S. Le, T. P. Vishwakarma, V. Cheng, Y. L. Andrew, D. J. 2020-10-14 doi:10.1101/2020.10.13.337626 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Obesity alters Ace2 and Tmprss2 expression in lung, trachea, and esophagus in a sex-dependent manner: Implications for COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.10.13.337907v1?rss=1 Sarver, D. C. Wong, G. W. 2020-10-14 doi:10.1101/2020.10.13.337907 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ In Vivo Brain Glutathione is Higher in Older Age and Correlates with Mobility ]]> https://biorxiv.org/content/10.1101/2020.10.14.339507v1?rss=1 Hupfeld, K. E. Hyatt, H. W. Alvarez Jerez, P. Mikkelsen, M. Hass, C. J. Edden, R. A. E. Seidler, R. D. Porges, E. C. 2020-10-14 doi:10.1101/2020.10.14.339507 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Differential in vitro activity of individual drugs and bedaquiline-rifabutin combinations against actively multiplying and nutrient-starved Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2020.10.14.340422v1?rss=1 Lee, J. Ammerman, N. C. Agarwal, A. Naji, M. Li, S.-Y. Nuermberger, E. 2020-10-15 doi:10.1101/2020.10.14.340422 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Coordination of RNA and protein condensation by the P granule protein MEG-3 ]]> https://biorxiv.org/content/10.1101/2020.10.15.340570v1?rss=1 Schmidt, H. Putnam, A. Rasoloson, D. Seydoux, G. 2020-10-15 doi:10.1101/2020.10.15.340570 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Inflight head stabilization associated with wingbeat cycle and sonar emissions in the Egyptian fruit bat. ]]> https://biorxiv.org/content/10.1101/2020.10.15.341545v1?rss=1 Rossborough, J. Salles, A. Stidsholt, L. Madsen, P. Moss, C. Hoffman, L. 2020-10-16 doi:10.1101/2020.10.15.341545 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Chronic exposure of ErbB TKIs inhibits DRA expression and activity through an ERK/Elk-1/CREB/AP-1 dependent pathway ]]> https://biorxiv.org/content/10.1101/2020.10.16.342139v1?rss=1 Yang, H. Lin, R.-X. Sarker, R. Donowitz, M. 2020-10-16 doi:10.1101/2020.10.16.342139 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis ]]> https://biorxiv.org/content/10.1101/2020.10.17.343020v1?rss=1 Abante, J. Goutsias, J. 2020-10-17 doi:10.1101/2020.10.17.343020 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Urine single cell RNA-sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures in immune cells and podocytes ]]> https://biorxiv.org/content/10.1101/2020.10.18.343285v1?rss=1 Latt, K. Z. Heymann, J. Jessee, J. H. Rosenberg, A. Z. Berthier, C. C. Eddy, S. Yoshida, T. Zhao, Y. Chen, V. Nelson, G. W. Cam, M. Kumar, P. Mehta, M. Kelly, M. C. Kretzler, M. The Nephrotic Syndrome Study Network (NEPTUNE), The Accelerating Medicines Partnership in RA and SLE (AMP RA/SLE) consortium, Winkler, C. A. Kopp, J. B. 2020-10-19 doi:10.1101/2020.10.18.343285 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ De novo design of transmembrane beta-barrels ]]> https://biorxiv.org/content/10.1101/2020.10.22.346965v1?rss=1 Vorobieva, A. A. White, P. Liang, B. Horne, J. E. Bera, A. K. Chow, C. M. Gerben, S. R. Marx, S. Kang, A. Stiving, A. Q. Harvey, S. R. Marx, D. C. Khan, N. Fleming, K. G. Wysocki, V. H. Brockwell, D. J. Tamm, L. K. Radford, S. E. Baker, D. 2020-10-23 doi:10.1101/2020.10.22.346965 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase ]]> https://biorxiv.org/content/10.1101/2020.10.22.351288v1?rss=1 Levine, Z. G. Potter, S. C. Joiner, C. M. Fei, G. Q. Nabet, B. Sonnett, M. Zachara, N. E. Paulo, J. A. Walker, S. 2020-10-22 doi:10.1101/2020.10.22.351288 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Chemoprophylaxis vaccination with a Plasmodium liver stage autophagy mutant affords enhanced and long-lasting protection ]]> https://biorxiv.org/content/10.1101/2020.10.23.352799v1?rss=1 Coppens, I. Sahu, T. Gehrke, E. Flores Garcia, Y. Mlambo, G. Romano, J. 2020-10-24 doi:10.1101/2020.10.23.352799 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ nearBynding: A flexible pipeline characterizing protein binding to local RNA structure ]]> https://biorxiv.org/content/10.1101/2020.10.24.352591v1?rss=1 Busa, V. F. Favorov, A. V. Fertig, E. J. Leung, A. 2020-10-25 doi:10.1101/2020.10.24.352591 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Serotonin neurons modulate learning rate through uncertainty ]]> https://biorxiv.org/content/10.1101/2020.10.24.353508v1?rss=1 Grossman, C. D. Bari, B. A. Cohen, J. Y. 2020-10-24 doi:10.1101/2020.10.24.353508 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Allantoin induces pruritus by activating MrgprD in chronic kidney disease ]]> https://biorxiv.org/content/10.1101/2020.10.26.354654v1?rss=1 Tang, Z. yang, y. sun, y. guan, d. chen, d. wang, d. liu, t. sheng, m. tao, j. shi, j. zhu, c. Yu, G. Dong, X. 2020-10-26 doi:10.1101/2020.10.26.354654 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Comprehensive and scalable quantification of splicing differences with MntJULiP ]]> https://biorxiv.org/content/10.1101/2020.10.26.355941v1?rss=1 Yang, G. Sabunciyan, S. Florea, L. D. 2020-10-27 doi:10.1101/2020.10.26.355941 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ THE INFLUENCE OF PRE-SUPPLEMENTARY MOTOR AREA TARGETED HIGH-DEFINITION TRANSCRANIAL DIRECT CURRENT STIMULATION ON INHIBITORY CONTROL ]]> https://biorxiv.org/content/10.1101/2020.10.27.358242v1?rss=1 DeLaRosa, B. Spence, J. Motes, M. To, W. Vanneste, S. Hart, J. Kraut, M. 2020-10-28 doi:10.1101/2020.10.27.358242 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ The highly evolvable nature of the antibiotic efflux protein TolC limits use of phages and bacterial toxins as antibacterial agents ]]> https://biorxiv.org/content/10.1101/2020.10.28.332486v1?rss=1 Tamer, Y. T. Gaszek, I. Rodrigues, M. Coskun, F. S. Farid, M. Koh, A. Y. Russ, W. Toprak, E. 2020-10-28 doi:10.1101/2020.10.28.332486 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes ]]> https://biorxiv.org/content/10.1101/2020.10.29.357400v1?rss=1 Walker, T. Quek, S. Jeffries, C. L. Bandibabone, J. Dhokiya, V. Bamou, R. Kristan, M. Messenger, L. A. Gidley, A. Hornett, E. A. Anderson, E. R. Cansado-Utrilla, C. Hegde, S. Bantuzeko, C. Stevenson, J. C. Lobo, N. F. Wagstaff, S. Nkondjio, C. A. Heinz, E. Hughes, G. 2020-10-29 doi:10.1101/2020.10.29.357400 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis ]]> https://biorxiv.org/content/10.1101/2020.10.29.361196v1?rss=1 Duan, D. Hanson, M. Holland, D. O. Johnson, M. E. 2020-10-29 doi:10.1101/2020.10.29.361196 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Molecular mechanisms of LC3-associated phagocytosis in the macrophage response to Paracoccidioides spp. ]]> https://biorxiv.org/content/10.1101/2020.10.30.362681v1?rss=1 Oliveira, G. P. d. Sousa, H. R. d. Gorgonha, K. C. d. M. Borges, T. K. d. S. Rangel, K. T. Fabricant, S. Gustavo, F. C. K. Albuquerque, L. F. F. Rossi, A. Hurtado, F. A. Paes, H. C. Casadevall, A. Silva-Pereira, I. Albuquerque, P. Felipe, M. S. S. Nicola, A. M. 2020-10-31 doi:10.1101/2020.10.30.362681 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ HP1 proteins compact DNA into mechanically and positionally stable phase separated domains ]]> https://biorxiv.org/content/10.1101/2020.10.30.362772v1?rss=1 Keenen, M. M. Brown, D. Brennan, L. D. Renger, R. Khoo, H. Carlson, C. R. Huang, B. Grill, S. W. Narlikar, G. J. Redding, S. 2020-10-31 doi:10.1101/2020.10.30.362772 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients ]]> https://biorxiv.org/content/10.1101/2020.11.01.362269v1?rss=1 The NeuroLINCS Consortium, Ornelas, L. Gomez, E. Panther, L. Frank, A. Lei, S. Mandefro, B. Banuelos, M. G. Shelley, B. Kaye, J. A. Lima, L. Wyman, S. Lim, R. G. Wu, J. Stocksdale, J. Casale, M. Dardov, V. Matlock, A. Venkatraman, V. Holewenski, R. Milani, P. Adam, M. Wassie, B. T. Cheng, A. Coyne, A. N. Daigle, J. G. Li, J. Yang, S. Cox, V. Wilhelm, M. Lloyd, T. E. Hayes, L. Pham, J. Escalante-Chong, R. Lenail, A. Sachs, K. Patel-Murray, N. L. Ramamoorthy, D. Thompson, T. G. NYGC ALS Consortium, Finkbeiner, S. Fraenkel, E. Rothstein, J. D. Sareen 2020-11-01 doi:10.1101/2020.11.01.362269 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Epigenetic regulation of epithelial dectin-1 through an IL-33-STAT3 axis in allergic disease ]]> https://biorxiv.org/content/10.1101/2020.11.01.364067v1?rss=1 Yong, H. M. Gour, N. Sharma, D. Khalil, S. M. Lane, A. P. Lajoie, S. 2020-11-01 doi:10.1101/2020.11.01.364067 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Control of neurogenic competence in mammalian hypothalamic tanycytes. ]]> https://biorxiv.org/content/10.1101/2020.11.02.359992v1?rss=1 Yoo, S. Kim, J. Lyu, P. Hoang, T. Ma, A. Trinh, V. Dai, W. Jiang, L. Leavey, P. Won, J.-K. Park, S.-H. Qian, J. Brown, S. P. Blackshaw, S. 2020-11-02 doi:10.1101/2020.11.02.359992 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Reaction-Diffusion Model of Cortical Atrophy Spread during Early Stages of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2020.11.02.362855v1?rss=1 Kulason, S. Miller, M. Trouve, A. 2020-11-03 doi:10.1101/2020.11.02.362855 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Adipose Triglyceride Lipase is needed for homeostatic control of Sterol Element-Binding Protein-1c driven hepatic lipogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.02.363440v1?rss=1 Wieser, B. I. Pena de la Sancha, P. Schauer, S. Reicher, H. Sattler, W. Breinbauer, R. Schweiger, M. Espenshade, P. J. Zechner, R. Hoefler, G. Vesely, P. W. 2020-11-02 doi:10.1101/2020.11.02.363440 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Synergistic Coding of Human Odorants in the Mosquito Brain ]]> https://biorxiv.org/content/10.1101/2020.11.02.365916v1?rss=1 Shankar, S. Tauxe, G. M. Spikol, E. D. Li, M. Akbari, O. S. Giraldo, D. McMeniman, C. J. 2020-11-04 doi:10.1101/2020.11.02.365916 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Multi-compartment tumor organoids ]]> https://biorxiv.org/content/10.1101/2020.11.03.367334v1?rss=1 Lee, M.-H. Rahmanto, Y. S. Russo, G. C. Wu, P.-h. Gilkes, D. Kiemen, A. Miyamoto, T. Yu, Y. Habibi, M. Shih, I.-M. Wang, T.-L. Wirtz, D. 2020-11-04 doi:10.1101/2020.11.03.367334 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Comparative molecular and immunoregulatory analysis of extracellular vesicles from Candida albicans and Candida auris. ]]> https://biorxiv.org/content/10.1101/2020.11.04.368472v1?rss=1 Zamith-Miranda, D. Heyman, H. M. Couvillion, S. P. Cordero, R. J. B. Rodrigues, M. Nimrichter, L. Casadevall, A. Amatuzzi, R. Alves, L. R. Nakayasu, E. S. Nosanchuk, J. D. 2020-11-04 doi:10.1101/2020.11.04.368472 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates ]]> https://biorxiv.org/content/10.1101/2020.11.04.368597v1?rss=1 Klein, A. Solinski, H. J. Malewicz, N. Ieong, H. F.-h. Shimada, S. Hartke, T. V. Wooten, M. Wu, G. Hoon, M. A. LaMotte, R. H. Ringkamp, M. 2020-11-04 doi:10.1101/2020.11.04.368597 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ E-cadherin promotes cell hyper-proliferation in breast cancer ]]> https://biorxiv.org/content/10.1101/2020.11.04.368746v1?rss=1 Russo, G. C. Karl, M. N. Clark, D. Cui, J. Carney, R. Su, B. Starich, B. A. Lih, T.-S. Zhang, Q. Wu, P.-h. Lee, M.-H. Leong, H. S. Zhang, H. Wirtz, D. 2020-11-04 doi:10.1101/2020.11.04.368746 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ PDE1 inhibition modulates Cav1.2 channel to stimulate cardiomyocyte contraction ]]> https://biorxiv.org/content/10.1101/2020.11.05.368852v1?rss=1 Muller, G. K. Song, J. Jani, V. Wu, Y. Anderson, M. E. Kass, D. A. 2020-11-05 doi:10.1101/2020.11.05.368852 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination ]]> https://biorxiv.org/content/10.1101/2020.11.06.371419v1?rss=1 Tsai, S.-J. Guo, C. Atai, N. A. Gould, S. J. 2020-11-06 doi:10.1101/2020.11.06.371419 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Widespread Polymodal Chemosensory Receptor Expression in <em>Drosophila</em> Olfactory Neurons ]]> https://biorxiv.org/content/10.1101/2020.11.07.355651v1?rss=1 Task, D. Lin, C.-C. Afify, A. Li, H. Vulpe, A. Menuz, K. Potter, C. J. 2020-11-08 doi:10.1101/2020.11.07.355651 Drosophila Olfactory Neurons]]> Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Retardation of folding rates of substrate proteins in the nanocage of GroEL ]]> https://biorxiv.org/content/10.1101/2020.11.08.373423v1?rss=1 Koculi, E. Thirumalai, D. 2020-11-09 doi:10.1101/2020.11.08.373423 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Leveraging the Mendelian Disorders of the Epigenetic Machinery to Systematically Map Functional Epigenetic Variation ]]> https://biorxiv.org/content/10.1101/2020.11.08.373456v1?rss=1 Luperchio, T. R. Boukas, L. Zhang, L. Pilarowski, G. O. Jiang, J. Kalinousky, A. Hansen, K. D. Bjornsson, H. T. 2020-11-08 doi:10.1101/2020.11.08.373456 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Evaluation of the Abbott ARCHITECT HIV Ag/Ab Combo Assay for Determining Recent HIV-1 Infection ]]> https://biorxiv.org/content/10.1101/2020.11.09.374017v1?rss=1 Curtis, K. A. Rudolph, D. L. Yi, P. Delaney, K. Anastos, K. DeHovitz, J. Kassaye, S. Hanson, C. French, A. Golub, E. Adimora, A. Ofotokun, I. Bolivar, H. Kempf, M.-C. Peters, P. J. Switzer, W. M. 2020-11-09 doi:10.1101/2020.11.09.374017 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Building blocks of protein structures - Physics meets Biology ]]> https://biorxiv.org/content/10.1101/2020.11.10.375105v1?rss=1 Skrbic, T. Maritan, A. Giacometti, A. Rose, G. D. Banavar, J. R. 2020-11-11 doi:10.1101/2020.11.10.375105 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ LongTron: Automated Analysis of Long Read Spliced Alignment Accuracy ]]> https://biorxiv.org/content/10.1101/2020.11.10.376871v1?rss=1 Wilks, C. Schatz, M. C. 2020-11-11 doi:10.1101/2020.11.10.376871 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Epigenetic Modulation of SPCA2 Reverses Epithelial to Mesenchymal Transition in Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/2020.11.12.379685v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@13b2565org.highwire.dtl.DTLVardef@14317forg.highwire.dtl.DTLVardef@1bdbd34org.highwire.dtl.DTLVardef@1d0bd83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Makena, M. R. Ko, M. Dang, D. K. Rao, R. 2020-11-12 doi:10.1101/2020.11.12.379685 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Primate anterior insular cortex represents economic decision variables postulated by Prospect theory ]]> https://biorxiv.org/content/10.1101/2020.11.12.380758v1?rss=1 Yang, Y.-P. Li, X. Stuphorn, V. 2020-11-15 doi:10.1101/2020.11.12.380758 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ GABAergic signaling promotes early-life seizures in epileptic SYNGAP1+/- mice ]]> https://biorxiv.org/content/10.1101/2020.11.14.381749v1?rss=1 Sullivan, B. J. Kipnis, P. A. Ammanuel, S. G. Kadam, S. D. 2020-11-15 doi:10.1101/2020.11.14.381749 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Hydrogel-coating improves the in-vivo stability of electrochemical aptamer-based biosensors ]]> https://biorxiv.org/content/10.1101/2020.11.15.383992v1?rss=1 Li, S. Dai, J. Zhu, M. Arroyo-Curras, N. Li, H. Wang, Y. Wang, Q. Lou, X. Kippin, T. E. Wang, S. Plaxco, K. W. Li, H. Xia, F. 2020-11-17 doi:10.1101/2020.11.15.383992 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Adding software to package management systems can increase their citation by 280% ]]> https://biorxiv.org/content/10.1101/2020.11.16.385211v1?rss=1 Jalili, V. Clements, D. Gruning, B. Blankenberg, D. Goecks, J. 2020-11-17 doi:10.1101/2020.11.16.385211 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ HTT silencing delays onset and slows progression of Huntington disease like phenotype: Monitoring with a novel neurovascular biomarker ]]> https://biorxiv.org/content/10.1101/2020.11.17.386631v1?rss=1 Liu, H. Zhang, C. Xu, J. Jin, J. Cheng, l. Wu, Q. Wei, Z. Liu, P. Lu, H. van Zijl, P. Ross, C. A. Hua, J. Duan, W. 2020-11-19 doi:10.1101/2020.11.17.386631 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Human methylome variation across Infinium 450K data on the Gene Expression Omnibus ]]> https://biorxiv.org/content/10.1101/2020.11.17.387548v1?rss=1 Maden, S. K. Thompson, R. F. Hansen, K. D. Nellore, A. 2020-11-19 doi:10.1101/2020.11.17.387548 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Comparative efficacy of the novel diarylquinoline TBAJ-587 and bedaquiline against a resistant Rv0678 mutant in a mouse model of tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.11.17.387977v1?rss=1 Xu, J. Converse, P. J. Upton, A. Mdluli, K. Fotouhi, N. Nuermberger, E. 2020-11-18 doi:10.1101/2020.11.17.387977 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ A short course of Tofacitinib sustains the immunoregulatory effect of CTLA4-Ig in presence of inflammatory cytokines and promotes long-term survival of murine cardiac allografts ]]> https://biorxiv.org/content/10.1101/2020.11.18.388595v1?rss=1 Iglesias, M. Khalifian, S. Oh, B. C. Zhang, Y. Miller, D. Beck, S. Brandacher, G. Raimondi, G. 2020-11-20 doi:10.1101/2020.11.18.388595 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Age-related Changes in Memory for Object and Position-In-Context ]]> https://biorxiv.org/content/10.1101/2020.11.22.393355v1?rss=1 Tran, T. T. Tobin, K. E. Block, S. H. Puliyadi, V. Gallagher, M. Bakker, A. 2020-11-22 doi:10.1101/2020.11.22.393355 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ The contribution of object size, manipulability, and stability on neural responses to inanimate objects ]]> https://biorxiv.org/content/10.1101/2020.11.22.393397v1?rss=1 Magri, C. Konkle, T. Caramazza, A. 2020-11-22 doi:10.1101/2020.11.22.393397 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Peptide Ancestry Informative Markers in Uterine Neoplasms from Women of European, African and Asian Ancestry ]]> https://biorxiv.org/content/10.1101/2020.11.23.380337v1?rss=1 260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms. ]]> Bateman, N. W. Tarney, C. Abulez, T. Hood, B. L. Conrads, K. Zhou, M. Soltis, A. R. Teng, P.-i. Jackson, A. Tian, C. Dalgard, C. Wilkerson, M. Kessler, M. Shriver, C. D. Hu, H. Cote, M. Parker, G. J. Segars, J. Al-Hendy, A. Risinger, J. Darcy, K. Casablanca, Y. George, M. L. Conrads, T. P. O'Connor, T. D. 2020-11-23 doi:10.1101/2020.11.23.380337 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Cocaine receptor identified as BASP1 ]]> https://biorxiv.org/content/10.1101/2020.11.23.392787v1?rss=1 Harraz, M. M. Malla, A. P. Semenza, E. R. Shishikura, M. Hwang, Y. Kang, I. G. Song, Y. J. Snowman, A. M. Cortes, P. Snyder, S. H. 2020-11-23 doi:10.1101/2020.11.23.392787 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ find-tfbs: a tool to identify functional non-coding variants associated with complex human traits using open chromatin maps and phased whole-genome sequences ]]> https://biorxiv.org/content/10.1101/2020.11.23.394296v1?rss=1 2000 associations at P<1x10-9, implicating specific blood cell-types, transcription factors and causal genes. The vast majority of these associations are captured by variants identified in large genome-wide association studies (GWAS) for blood-cell traits. find-tfbs is computationally efficient and robust, allowing for the rapid identification of non-coding variants associated with multiple human phenotypes in very large sample size. Availabilityhttps://github.com/Helkafen/find-tfbs and https://github.com/Helkafen/find-tfbs-demo Contactssebastian.meric.de.bellefon@umontreal.ca and guillaume.lettre@umontreal.ca Supplementary informationSupplementary data are available. ]]> Meric de Bellefon, S. Thibord, F. Auer, P. L. Blangero, J. Coban-Akdemir, Z. H. Floyd, J. S. Fornage, M. Johnsen, J. M. Lange, L. A. Lewis, J. P. Mathias, R. A. McHugh, C. P. Moon, J.-Y. Reiner, A. P. Stilp, A. M. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Lettre, G. 2020-11-23 doi:10.1101/2020.11.23.394296 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Differences in functional connectivity distribution after transcranial direct-current stimulation: a connectivity density point of view ]]> https://biorxiv.org/content/10.1101/2020.11.23.395160v1?rss=1 Tang, B. Zhao, Y. Venkataraman, A. Tsapkini, K. Lindquist, M. Pekar, J. J. Caffo, B. S. 2020-11-24 doi:10.1101/2020.11.23.395160 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Rif1 regulates telomere length through conserved HEAT repeats ]]> https://biorxiv.org/content/10.1101/2020.11.24.394866v1?rss=1 Shubin, C. B. Mayangsari, R. Swett, A. D. Greider, C. W. 2020-11-24 doi:10.1101/2020.11.24.394866 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Sleep is required for odor exposure to consolidate memory and remodel olfactory synapses. ]]> https://biorxiv.org/content/10.1101/2020.11.24.395228v1?rss=1 Munoz-Lobato, F. Benedetti, K. L. Farah, F. Chandra, R. Bokka, A. Brueggemann, C. Saifuddin, F. M. Nordquist, S. K. Li, J. Chang, E. Varshney, A. Jiminez, V. Andersen, K. E. Baradwaj, A. Miller, J. M. Dunn, R. L. Tsujimoto, B. Duong, A. Tran, A. Churgin, M. Fang-Yen, C. Bremer, M. Kato, S. VanHoven, M. L'Etoile, N. 2020-11-25 doi:10.1101/2020.11.24.395228 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ COUNTEN an AI-driven tool for rapid, and objective structural analyses of the Enteric Nervous System ]]> https://biorxiv.org/content/10.1101/2020.11.24.396408v1?rss=1 Kobayashi, Y. Bukowski, A. Das, S. Espenel, C. Gomez-Frittelli, J. Wagle, N. Bakhshi, S. Saha, M. Kaltschmidt, J. A. Venkataraman, A. Kulkarni, S. 2020-11-25 doi:10.1101/2020.11.24.396408 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Regulating enzymatic reactions in Escherichia coli utilizing light-responsive cellular compartments based on liquid-liquid phase separation ]]> https://biorxiv.org/content/10.1101/2020.11.26.395616v1?rss=1 Huang, Z. Sun, L. Lu, G. Liu, H. Zhai, Z. Feng, S. Gao, J. Chen, C. Qing, C. Fang, M. Chen, B. Fu, J. Wang, X. Chen, G.-Q. 2020-11-29 doi:10.1101/2020.11.26.395616 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite ]]> https://biorxiv.org/content/10.1101/2020.11.27.399857v1?rss=1 Lin, M.-J. Lin, Y.-C. Chen, N.-C. Luo, A. C.-L. Lai, S.-K. Hsu, C.-L. Hsu, J. S. Chen, C.-Y. Yang, W.-S. Chen, P.-L. 2020-11-27 doi:10.1101/2020.11.27.399857 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Unveiling functions of the visual cortex using task-specific deep neural networks ]]> https://biorxiv.org/content/10.1101/2020.11.27.401380v1?rss=1 Dwivedi, K. Bonner, M. F. Cichy, R. M. Roig, G. 2020-11-27 doi:10.1101/2020.11.27.401380 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Transient neuronal suppression for exploitation of new sensory evidence ]]> https://biorxiv.org/content/10.1101/2020.11.29.403089v1?rss=1 Shinn, M. Lee, D. Murray, J. D. Seo, H. 2020-11-30 doi:10.1101/2020.11.29.403089 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Adaptation with correlated noise predicts negative interval correlations in neuronal spike trains ]]> https://biorxiv.org/content/10.1101/2020.11.30.403725v1?rss=1 Sidhu, R. S. Johnson, E. C. Jones, D. L. Ratnam, R. 2020-11-30 doi:10.1101/2020.11.30.403725 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivo ]]> https://biorxiv.org/content/10.1101/2020.12.01.402651v1?rss=1 Simonetti, F. R. Zhang, H. Soroosh, G. P. Duan, J. Rhodehouse, K. Hill, A. L. Beg, S. A. McCormick, K. Raymond, H. Nobles, C. L. Everett, J. Kwon, K. J. White, J. A. Lai, J. Margolick, J. B. Hoh, R. Deeks, S. G. Bushman, F. D. Siliciano, J. D. Siliciano, R. F. 2020-12-01 doi:10.1101/2020.12.01.402651 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Biliverdin reductase bridges focal adhesion kinase to Src to modulate synaptic signaling ]]> https://biorxiv.org/content/10.1101/2020.12.01.405720v1?rss=1 Vasavda, C. Semenza, E. R. Liew, J. Kothari, R. Dhindsa, R. S. Shanmukha, S. Ricco, C. Tokhunts, R. Snowman, A. M. Albacarys, L. K. Paul, B. D. Snyder, S. H. 2020-12-02 doi:10.1101/2020.12.01.405720 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Competition between parallel sensorimotor learning systems ]]> https://biorxiv.org/content/10.1101/2020.12.01.406777v1?rss=1 Albert, S. T. Jang, J. Haith, A. M. Lerner, G. Della-Maggiore, V. Krakauer, J. W. Shadmehr, R. 2020-12-02 doi:10.1101/2020.12.01.406777 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ NMDAR-independent acetylcholine, serotonin, and norepinephrine mediated modulation of synaptic eligibility traces into LTD in mice visual cortex ]]> https://biorxiv.org/content/10.1101/2020.12.02.408948v1?rss=1 Khan, S. 2020-12-03 doi:10.1101/2020.12.02.408948 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Functional maps of the primate cortex revealed by through-skull wide-field optical imaging ]]> https://biorxiv.org/content/10.1101/2020.12.05.413047v1?rss=1 Song, X. Guo, Y. Li, H. Chen, C. Schmidt, Z. Wang, X. 2020-12-06 doi:10.1101/2020.12.05.413047 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Dendritic signal integration in Drosophila Mushroom Body Output Neuron (MBON) essential for learning and memory ]]> https://biorxiv.org/content/10.1101/2020.12.06.413500v1?rss=1 Hafez, O. Escribano, B. Ziegler, R. Hirtz, J. J. Niebur, E. Pielage, J. 2020-12-07 doi:10.1101/2020.12.06.413500 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia ]]> https://biorxiv.org/content/10.1101/2020.12.06.413930v1?rss=1 Chen, C. Yu, W. Alikarami, F. Qiu, Q. Chen, C.-h. Flournoy, J. Gao, P. Uzun, Y. Fang, L. Yu, Y. Zhu, Q. Wang, K. Libbrecht, C. Felmeister, A. Rozich, I. Ding, Y.-y. Hunger, S. P. Wu, H. Brown, P. A. Guest, E. M. Barrett, D. M. Bernt, K. M. Tan, K. 2020-12-07 doi:10.1101/2020.12.06.413930 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Overt visual attention and value computation in complex risky choice ]]> https://biorxiv.org/content/10.1101/2020.12.08.416313v1?rss=1 Fan, X. Elsey, J. Wyngaard, A. Yang, Y.-P. Sampson, A. Emeric, E. E. Glickman, M. Usher, M. Levy, D. Stuphorn, V. Niebur, E. 2020-12-09 doi:10.1101/2020.12.08.416313 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ In situ characterization of the 3D microanatomy of the pancreas and pancreatic cancer at single cell resolution ]]> https://biorxiv.org/content/10.1101/2020.12.08.416909v1?rss=1 Kiemen, A. L. Braxton, A. M. Grahn, M. P. Han, K. S. Mahesh Babu, J. Reichel, R. Amoa, F. Hong, S.-M. Cornish, T. C. Thompson, E. D. Wood, L. D. Hruban, R. H. Wu, P.-H. Wirtz, D. 2020-12-09 doi:10.1101/2020.12.08.416909 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike ]]> https://biorxiv.org/content/10.1101/2020.12.08.417022v1?rss=1 Guo, C. Tsai, S. J. Ai, Y. Li, M. Pekosz, A. Cox, A. Atai, N. Gould, S. 2020-12-09 doi:10.1101/2020.12.08.417022 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Differential expression levels of Sox9 in early neocortical radial glial cells regulate the decision between stem cell maintenance and differentiation ]]> https://biorxiv.org/content/10.1101/2020.12.09.417931v1?rss=1 Fabra-Beser, J. Alves Medeiros de Araujo, J. Coelho, D. M. Goff, L. Mueller, U. Gil-Sanz, C. 2020-12-09 doi:10.1101/2020.12.09.417931 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Thermodynamics and free energy landscape of BAR-domain dimerization from molecular simulations ]]> https://biorxiv.org/content/10.1101/2020.12.09.418020v1?rss=1 Jhaveri, A. Maisuria, D. Varga, M. J. Mohammadyani, D. Johnson, M. E. 2020-12-09 doi:10.1101/2020.12.09.418020 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors ]]> https://biorxiv.org/content/10.1101/2020.12.10.416495v1?rss=1 Sam, P. Calzada, E. Acoba, M. G. Zhao, T. Watanabe, Y. Nejatfard, A. Trinidad, J. Shutt, T. Neal, S. E. Claypool, S. M. 2020-12-11 doi:10.1101/2020.12.10.416495 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Effective host-directed therapy for tuberculosis by targeted depletion of myeloid-derived suppressor cells using a diphtheria toxin-based fusion protein ]]> https://biorxiv.org/content/10.1101/2020.12.10.420224v1?rss=1 Parveen, S. Lun, S. Urbanowski, M. E. Cardin, M. Murphy, J. R. Bishai, W. R. 2020-12-10 doi:10.1101/2020.12.10.420224 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Highly multiplexed imaging of biosensors in live cells ]]> https://biorxiv.org/content/10.1101/2020.12.11.419655v1?rss=1 Yang, J.-M. Chi, W.-Y. Liang, J. Iglesias, P. A. Huang, C.-H. 2020-12-11 doi:10.1101/2020.12.11.419655 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response ]]> https://biorxiv.org/content/10.1101/2020.12.14.422616v1?rss=1 Mishra, H. K. Ying, N. M. Luis, A. Wei, H. Nguyen, M. Nakhla, T. Vandenburgh, S. Alda, M. Berrettini, W. H. Brennand, K. J. Calabrese, J. R. Coryell, W. H. Frye, M. A. Gage, F. H. Gershon, E. S. McInnis, M. G. Nievergelt, C. M. Nurnberger, J. I. Shilling, P. D. Oedegaard, K. J. Zandi, P. P. The Pharmacogenomics of Bipolar Disorder Study, Kelsoe, J. R. Welsh, D. K. McCarthy, M. J. 2020-12-15 doi:10.1101/2020.12.14.422616 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs ]]> https://biorxiv.org/content/10.1101/2020.12.14.422680v1?rss=1 Nguyen, T. Phan, K. L. Kreitler, D. E. Andrews, L. C. Gabelli, S. B. Kozakov, D. Jakoncic, J. Sweet, R. M. Soares, A. Bernstein, H. J. 2020-12-14 doi:10.1101/2020.12.14.422680 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Interplay between intraocular and intracranial pressure effects on the optic nerve head in vivo ]]> https://biorxiv.org/content/10.1101/2020.12.14.422760v1?rss=1 Zhu, Z. Waxman, S. Wang, B. Wallace, J. Schmitt, S. E. Tyler-Kabara, E. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2020-12-15 doi:10.1101/2020.12.14.422760 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Deep Learning Identification of Stiffness Markers in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2020.12.17.423077v1?rss=1 Sneider, A. Kim, J. H. Kiemen, A. Wu, P.-H. Habibi, M. White, M. Phillip, J. M. Gu, L. Wirtz, D. 2020-12-17 doi:10.1101/2020.12.17.423077 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ Megadepth: efficient coverage quantification for BigWigs and BAMs ]]> https://biorxiv.org/content/10.1101/2020.12.17.423317v1?rss=1 Wilks, C. Ahmed, O. Baker, D. N. Zhang, D. Collado-Torres, L. Langmead, B. 2020-12-18 doi:10.1101/2020.12.17.423317 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Loss of PI3-kinase activity of inositol polyphosphate multikinase impairs PDK1-mediated AKT activation, cell migration, and intestinal homeostasis ]]> https://biorxiv.org/content/10.1101/2020.12.18.423145v1?rss=1 Guha, P. Snyder, S. Reilly, L. Mishra, S. Abramson, E. Sei, Y. Wank, S. A. Semenza, E. Donowitz, M. 2020-12-18 doi:10.1101/2020.12.18.423145 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Functional tagging of endogenous proteins and rapid selection of cell pools (Rapid generation of endogenously tagged piwi in ovarian somatic sheath cells.) ]]> https://biorxiv.org/content/10.1101/2020.12.18.423517v1?rss=1 Marlin Andrews, C. Konstantinidou, P. Genzor, P. Stoyko, D. Elchert, A. R. Benner, L. Sobti, S. Katz, E. Y. Meng, Q. Haase, A. D. 2020-12-20 doi:10.1101/2020.12.18.423517 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Activation of MrgprA3 and MrgprC11 on bladder-innervating afferents induces peripheral and central hypersensitivity to bladder distension ]]> https://biorxiv.org/content/10.1101/2020.12.18.423548v1?rss=1 Grundy, L. Caldwell, A. Garcia Caraballo, S. Grundy, D. Spencer, N. Dong, X. Castro, J. Harrington, A. M. Brierley, S. 2020-12-20 doi:10.1101/2020.12.18.423548 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes ]]> https://biorxiv.org/content/10.1101/2020.12.22.423783v1?rss=1 170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels. ]]> Hindy, G. Dornbos, P. Chaffin, M. D. Liu, D. J. Wang, M. X. Aguilar-Salinas, C. A. Antonacci-Fulton, L. Ardissino, D. Arnett, D. K. Aslibekyan, S. Atzmon, G. Ballantyne, C. M. Barajas-Olmos, F. Barzilai, N. Becker, L. C. Bielak, L. F. Bis, J. C. Blangero, J. Boerwinkle, E. Bonnycastle, L. L. Bottinger, E. Bowden, D. W. Bown, M. J. Brody, J. A. Broome, J. G. Burtt, N. P. Cade, B. E. Centeno-Cruz, F. Chan, E. Chang, Y.-C. Chen, Y.-D. I. Cheng, C.-Y. Choi, W. J. Chowdhury, R. Contreras-Cubas, C. Cordova, E. J. Correa, A. Cupples, L. A. Curran, J. E. Danesh, 2020-12-23 doi:10.1101/2020.12.22.423783 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ 15-PGDH as a Negative Regulator of Age-Related Organ Fitness ]]> https://biorxiv.org/content/10.1101/2020.12.22.424017v1?rss=1 Ho, W. J. Smith, J. N. P. Park, Y. S. Hadiono, M. Christo, K. F. Jogasuria, A. Zhang, Y. Broncano, A. V. Kasturi, L. Dawson, D. M. Gerson, S. L. Markowitz, S. D. Desai, A. B. 2020-12-22 doi:10.1101/2020.12.22.424017 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ PARprolink: a photoaffinity probe for identifying poly(ADP-ribose)-binding proteins ]]> https://biorxiv.org/content/10.1101/2020.12.28.424596v1?rss=1 Dasovich, M. Beckett, M. Q. Bailey, S. Ong, S.-E. Greenberg, M. Leung, A. 2020-12-28 doi:10.1101/2020.12.28.424596 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ High resolution copy number inference in cancer using short-molecule nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2020.12.28.424602v1?rss=1 Baslan, T. Kovaka, S. Sedlazeck, F. J. Zhang, Y. Wappel, R. Lowe, S. J. Goodwin, S. Schatz, M. C. 2020-12-29 doi:10.1101/2020.12.28.424602 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ A persistent invasive phenotype in post-hypoxic tumor cells is revealed by novel fate-mapping and computational modeling ]]> https://biorxiv.org/content/10.1101/2020.12.30.424757v1?rss=1 Rocha, H. L. Godet, I. Kurtoglu, F. Metzcar, J. Konstantinopoulos, K. Bhoyar, S. Gilkes, D. M. Macklin, P. 2021-01-01 doi:10.1101/2020.12.30.424757 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Spatio-Temporal Coordination Of Transcription Preinitiation Complex Assembly In Live Cells ]]> https://biorxiv.org/content/10.1101/2020.12.30.424853v1?rss=1 Wu, C. Nguyen, V. Q. Ranjan, A. Liu, S. Tang, X. Ling, Y. H. Wisniewski, J. Mizuguchi, G. Li, K. Y. Jou, V. Zheng, Q. Lavis, L. Lionnet, T. 2020-12-30 doi:10.1101/2020.12.30.424853 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ All-or-none disconnection of pyramidal inputs onto parvalbumin-positive interneurons gates ocular dominance plasticity ]]> https://biorxiv.org/content/10.1101/2020.12.30.424871v1?rss=1 Severin, D. Hong, S. Z. Roh, S.-E. Zhou, J. Bridi, M. C. D. Murase, S. Robertson, S. Haberman, R. Huganir, R. Gallaghe, M. Quinlan, E. M. Worley, P. kirkwood, a. 2021-01-01 doi:10.1101/2020.12.30.424871 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Pyruvate oxidase as a key determinant of pneumococcal viability during transcytosis across the blood-brain barrier endothelium ]]> https://biorxiv.org/content/10.1101/2020.12.31.424967v1?rss=1 Anil, A. Parthasarathy, A. Madhavan, S. Kim, K. S. Banerjee, A. 2021-01-02 doi:10.1101/2020.12.31.424967 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Machine Learning to Summarize and Provide Context for Sleep and Eating Schedules. ]]> https://biorxiv.org/content/10.1101/2020.12.31.424983v1?rss=1 Chen, T. Chen, Y. Gao, J. Gao, P. Moon, J. H. Ren, J. Zhu, R. Song, S. Clark, J. M. Bennett, W. Lehman, H. Budavari, T. Woolf, T. 2021-01-04 doi:10.1101/2020.12.31.424983 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Human brain region-specific variably methylated regions (VMRs) are enriched for heritability of distinct neuropsychiatric traits ]]> https://biorxiv.org/content/10.1101/2021.01.02.425010v1?rss=1 Rizzardi, L. F. Hickey, P. F. Idrizi, A. Tryggvadottir, R. Callahan, C. M. Stephens, K. E. Taverna, S. D. Zhang, H. Ramazanoglu, S. GTEx Consortium, Hansen, K. D. Feinberg, A. P. 2021-01-02 doi:10.1101/2021.01.02.425010 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ The ancient cardioprotective mechanisms of ACE2 bestow SARS-CoV-2 with a wide host range ]]> https://biorxiv.org/content/10.1101/2021.01.03.425115v1?rss=1 Castiglione, G. M. Zhou, L. Xu, Z. Neiman, Z. Hung, C.-F. Duh, E. J. 2021-01-04 doi:10.1101/2021.01.03.425115 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Barth syndrome cellular models have dysregulated respiratory chain complex I and mitochondrial quality control due to abnormal cardiolipin ]]> https://biorxiv.org/content/10.1101/2021.01.06.425502v1?rss=1 Franca Anzmann, A. Sniezek, O. Pado, A. Busa, V. F. Vaz, F. M. Kreimer, S. Cole, N. R. Le, A. Kirsch, B. Claypool, S. M. Vernon, H. 2021-01-08 doi:10.1101/2021.01.06.425502 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Improving variant calling using population data and deep learning ]]> https://biorxiv.org/content/10.1101/2021.01.06.425550v1?rss=1 Chen, N.-C. Kolesnikov, A. Goel, S. Yun, T. Chang, P.-C. Carroll, A. 2021-01-07 doi:10.1101/2021.01.06.425550 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ In vivo deciduous dental eruption in LuiKotale bonobos and Gombe chimpanzees ]]> https://biorxiv.org/content/10.1101/2021.01.06.425588v1?rss=1 Lee, S. M. Sutherland, L. J. Fruth, B. Murray, C. M. Lonsdorf, E. V. Arbenz-Smith, K. Augusto, R. Brogan, S. Canington, S. L. Lee, K. C. McGrath, K. McFarlin, S. C. Hohmann, G. 2021-01-08 doi:10.1101/2021.01.06.425588 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Determining pathogenicity of variants of uncertain significance and identification of a founder variant in the epilepsy-associated gene, SZT2 ]]> https://biorxiv.org/content/10.1101/2021.01.06.425612v1?rss=1 Calhoun, J. D. Aziz, M. C. Happ, H. C. Gunti, J. Gleason, C. Mohamed, N. Zeng, K. Hiller, M. Bryant, E. Mithal, D. Bellinski, I. Kinsley, L. Grimmel, M. Schwaibold, E. M. Smith-Hicks, C. Chassevent, A. Scala, M. Accogli, A. Torella, A. Striano, P. Capra, V. Bird, L. M. Ben-Sahra, I. Ekhilevich, N. Hershkovitz, T. Weiss, K. Millichap, J. Gerard, E. E. Carvill, G. L. 2021-01-07 doi:10.1101/2021.01.06.425612 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Resolving the molecular fingerprint of the distal carboxy tail in modulating CaV1 calcium dependent inactivation ]]> https://biorxiv.org/content/10.1101/2021.01.06.425618v1?rss=1 Sang, L. Vieira, D. C. O. Yue, D. T. Ben-Johny, M. Dick, I. E. 2021-01-06 doi:10.1101/2021.01.06.425618 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Neuron-type specificity of dorsal raphe projections to ventral tegmental area ]]> https://biorxiv.org/content/10.1101/2021.01.06.425641v1?rss=1 Chang, A. J. Wang, L. Lucantonio, F. Adams, M. Lemire, A. Dudman, J. T. Cohen, J. Y. 2021-01-07 doi:10.1101/2021.01.06.425641 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Online learning for orientation estimation during translation in an insect ring attractor network ]]> https://biorxiv.org/content/10.1101/2021.01.07.425323v1?rss=1 Robinson, B. S. Norman-Tenazas, R. Cervantes, M. Symonette, D. Johnson, E. C. Joyce, J. Rivlin, P. K. Hwang, G. Zhang, K. Gray-Roncal, W. R. 2021-01-07 doi:10.1101/2021.01.07.425323 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Selective enhancement of neural coding in V1 underlies fine discrimination learning in tree shrew. ]]> https://biorxiv.org/content/10.1101/2021.01.10.426145v1?rss=1 Schumacher, J. W. McCann, M. K. Maximov, K. J. Fitzpatrick, D. 2021-01-10 doi:10.1101/2021.01.10.426145 Cold Spring Harbor Laboratory Press 2021-01-10 <![CDATA[ Comparative genomic analysis and characterization of Staphylococcus sp. AOAB, isolated from a notoriously invasive Mnemiopsis leidyi gut revealed multiple antibiotic resistance determinants ]]> https://biorxiv.org/content/10.1101/2021.01.11.426108v1?rss=1 Mariita, R. M. Hossain, M. J. Moss, A. G. 2021-01-11 doi:10.1101/2021.01.11.426108 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Low oxygen arrests Babesia duncani schizonts and leads to increased drug susceptibilities in hamster erythrocytes ]]> https://biorxiv.org/content/10.1101/2021.01.11.426147v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@6414b2org.highwire.dtl.DTLVardef@8ad845org.highwire.dtl.DTLVardef@17cd3bcorg.highwire.dtl.DTLVardef@30f1f2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe in vitro growth of B. duncani requires high level oxygen and the culture condition of 5% CO2 ambient air is optimal C_LIO_LILow level oxygen results B. duncani in low growth rate and high schizont ratio in vitro C_LIO_LICompared with 5% CO2 ambient air, in vitro drug susceptibilities of B. duncani can be significantly increased when cultured in microaerobic condition C_LI ]]> Zhang, Y. Manzo, H. A. Zhang, Y. 2021-01-12 doi:10.1101/2021.01.11.426147 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Modifying TIMER, a slow-folding DsRed derivative, for optimal use in quickly-dividing bacteria ]]> https://biorxiv.org/content/10.1101/2021.01.12.426338v1?rss=1 Patel, P. O'Hara, B. J. Aunins, E. Davis, K. M. 2021-01-12 doi:10.1101/2021.01.12.426338 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Biomaterials direct functional B cell response in a material specific manner ]]> https://biorxiv.org/content/10.1101/2021.01.12.426347v1?rss=1 Moore, E. Maestas, D. R. Cherry, C. C. Garcia, J. A. Comeau, H. Y. Davenport Huyer, L. Blosser, R. L. Rosson, G. D. Elisseeff, J. H. 2021-01-13 doi:10.1101/2021.01.12.426347 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2021.01.13.426413v1?rss=1 Cui Zhou, D. Jayasinghe, R. G. Herndon, J. M. Storrs, E. Mo, C.-K. Wu, Y. Fulton, R. S. Wyczalkowski, M. A. Fronick, C. C. Fulton, L. A. Thammavong, L. Sato, K. Zhu, H. Sun, H. Wang, L.-B. Li, Y. Zuo, C. McMichael, J. F. Davies, S. R. Appelbaum, E. L. Robbins, K. J. Chasnoff, S. E. Yang, X. Liu, R. Reeb, A. N. Wendl, M. C. Oh, C. Serasanambati, M. Lal, P. Varghese, R. Mashl, J. R. Ponce, J. Terekhanova, N. V. Naser Al Deen, N. Yao, L. Wang, F. Chen, L. Schnaubelt, M. Puram, S. V. Kim, A. H. Song, S.-K. Shoghi, K. I. Ju, T. Hawkins, W. G. Chen, K. Ch 2021-01-14 doi:10.1101/2021.01.13.426413 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ The cost of correcting for error during sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2021.01.13.426535v1?rss=1 Sedaghat-Nejad, E. Shadmehr, R. 2021-01-15 doi:10.1101/2021.01.13.426535 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Proprotein Convertase Subtilisin/kexin Type 9 Links Inflammation to Vascular Endothelial Cell Dysfunction ]]> https://biorxiv.org/content/10.1101/2021.01.15.426820v1?rss=1 Leucker, T. M. Amat-Codina, N. Chelko, S. Gerstenblith, G. 2021-01-17 doi:10.1101/2021.01.15.426820 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Anterior insula-associated social novelty recognition: orchestrated regulation by a local retinoic acid cascade and oxytocin signaling ]]> https://biorxiv.org/content/10.1101/2021.01.15.426848v1?rss=1 Kim, S.-H. An, K. Namkung, H. Rannals, M. D. Moore, J. R. Cash-Padgett, T. Mihaljevic, M. Saha, S. Oh, L. S. Kondo, M. A. Yang, K. Maher, B. J. Niwa, M. Sawa, A. 2021-01-15 doi:10.1101/2021.01.15.426848 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline ]]> https://biorxiv.org/content/10.1101/2021.01.18.427129v1?rss=1 Patil, A. H. Halushka, M. K. 2021-01-19 doi:10.1101/2021.01.18.427129 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ CRISPR Del/Rei: A simple, flexible and efficient pipeline for scarless genome editing ]]> https://biorxiv.org/content/10.1101/2021.01.18.427163v1?rss=1 Wahbeh, M. H. Feuer, K. L. Abdollahi, S. Yovo, C. Rabie, E. Lam, A.-T. Young, L. Avramopoulos, D. 2021-01-18 doi:10.1101/2021.01.18.427163 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Myocardial BDNF regulates cardiac bioenergetics through the transcription factor Yin Yang 1 ]]> https://biorxiv.org/content/10.1101/2021.01.19.427213v1?rss=1 Yang, X. Zhang, M. Zimmerman, R. J. Wang, Q. Wei, A.-c. Zhu, G. Bedja, D. Jiang, H. Shiva, S. S. Scott, I. O'Rourke, B. Kass, D. A. Paolocci, N. Feng, N. 2021-01-21 doi:10.1101/2021.01.19.427213 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Personalized Perturbation Profiles Reveal Concordance between Autism Blood Transcriptome Datasets ]]> https://biorxiv.org/content/10.1101/2021.01.25.427953v1?rss=1 Laird, J. Maertens, A. 2021-01-25 doi:10.1101/2021.01.25.427953 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Reagent-free Raman and quantitative phase imaging offer a unique morpho-molecular platform for recognition of malignancy and stages of B-cell acute lymphoblastic leukemia ]]> https://biorxiv.org/content/10.1101/2021.01.25.428006v1?rss=1 Paidi, S. K. Raj, P. Bordett, R. Zhang, C. Karandikar, S. H. Pandey, R. Barman, I. 2021-01-27 doi:10.1101/2021.01.25.428006 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Genome-wide analysis of mitochondrial DNA copy number reveals multiple loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation ]]> https://biorxiv.org/content/10.1101/2021.01.25.428086v1?rss=1 Longchamps, R. J. Yang, S. Y. Castellani, C. A. Shi, W. Lane, J. Grove, M. L. Bartz, T. M. Sarnowski, C. Burrows, K. Guyatt, A. L. Gaunt, T. R. Kacprowski, T. Yang, J. De, P. L. Yu, L. CHARGE Aging and Longevity Group, Bergman, A. Xia, R. Fornage, M. Feitosa, M. F. Wojczynski, M. K. Kraja, A. T. Province, M. A. Amin, N. Rivadeneira, F. Tiemeier, H. Uitterlinden, A. G. Broer, L. Van, J. Van, C. Raffield, L. M. Lange, L. Rich, S. S. Lemaitre, R. N. Goodarzi, M. O. Sitlani, C. M. Mak, A. C. Bennett, D. A. Rodriguez, S. Murabito, J. M. Lunetta, K. L. Soto 2021-01-28 doi:10.1101/2021.01.25.428086 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ tTARGIT AAVs: A sensitive and flexible method to manipulate intersectional neuronal populations ]]> https://biorxiv.org/content/10.1101/2021.01.26.428259v1?rss=1 Sabatini, P. Wang, J. Rupp, A. C. Affinati, A. H. Flak, J. N. Li, C. Olson, D. Myers, M. 2021-01-27 doi:10.1101/2021.01.26.428259 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Local adaptation and archaic introgression shape global diversity at human structural variant loci ]]> https://biorxiv.org/content/10.1101/2021.01.26.428314v1?rss=1 Yan, S. M. Sherman, R. M. Taylor, D. J. Nair, D. R. Bortvin, A. N. Schatz, M. C. McCoy, R. C. 2021-01-26 doi:10.1101/2021.01.26.428314 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ CloudReg: Automatic Terabyte-Scale Cross-Modal Brain Volume Registration ]]> https://biorxiv.org/content/10.1101/2021.01.26.428355v1?rss=1 Chandrashekhar, V. Tward, D. J. Crowley, D. G. Crow, A. K. Wright, M. A. Hsueh, B. Y. Gore, F. Machado, T. A. Branch, A. Rosenblum, J. S. Deisseroth, K. Vogelstein, J. T. 2021-01-27 doi:10.1101/2021.01.26.428355 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain ]]> https://biorxiv.org/content/10.1101/2021.01.27.427793v1?rss=1 Stephens, K. E. Zhou, W. Renfro, Z. Ji, Z. Ji, H. Guan, Y. Taverna, S. D. 2021-01-28 doi:10.1101/2021.01.27.427793 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ AAV-Txnip prolongs cone survival and vision in mouse models of retinitis pigmentosa ]]> https://biorxiv.org/content/10.1101/2021.01.27.428411v1?rss=1 20 million people worldwide. Loss of daylight vision typically occurs due to the dysfunction/loss of cone photoreceptors, the cell type that initiates our color and high acuity vision. Currently, there is no effective treatment for RP, other than gene therapy for a limited number of specific disease genes. To develop a gene-agnostic therapy, we screened {approx}20 genes for their ability to prolong cone photoreceptor survival in vivo. Here, we report an adeno-associated virus (AAV) vector expressing Txnip, which prolongs the survival of cone photoreceptors and improves visual acuity in RP mouse models. A Txnip allele, C247S, which blocks the association of Txnip with thioredoxin, provides an even greater benefit. Additionally, the rescue effect of Txnip depends on lactate dehydrogenase b (Ldhb), and correlates with the presence of healthier mitochondria, suggesting that Txnip saves RP cones by enhancing their lactate catabolism. ]]> Xue, Y. Wang, S. K. Rana, P. West, E. R. Hong, C. M. Feng, H. Wu, D. M. Cepko, C. L. 2021-01-27 doi:10.1101/2021.01.27.428411 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Genome and transcriptome of a pathogenic yeast, Candida nivariensis ]]> https://biorxiv.org/content/10.1101/2021.01.27.428461v1?rss=1 Fan, Y. Gale, A. Timp, W. 2021-01-27 doi:10.1101/2021.01.27.428461 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Altered cleavage of Caspase-1 in hepatocytes limits control of malaria in the liver ]]> https://biorxiv.org/content/10.1101/2021.01.28.427517v1?rss=1 Marques-da-Silva, C. Poudel, B. Baptista, R. P. Peissig, K. Hancox, L. S. Shiau, J. C. Pewe, L. Shears, M. J. Kanneganti, T.-D. Sinnis, P. Kyle, D. E. Gurung, P. Harty, J. T. Kurup, S. P. 2021-01-28 doi:10.1101/2021.01.28.427517 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ The Similarity Structure of Real-World Memories ]]> https://biorxiv.org/content/10.1101/2021.01.28.428278v1?rss=1 Tomita, T. M. Barense, M. D. Honey, C. J. 2021-01-30 doi:10.1101/2021.01.28.428278 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Allosteric Regulation of the EphA2 Receptor Intracellular Region by Serine/Threonine Kinases ]]> https://biorxiv.org/content/10.1101/2021.01.28.428700v1?rss=1 Lechtenberg, B. C. Gehring, M. P. Light, T. P. Matsumoto, M. W. Hristova, K. Pasquale, E. B. 2021-01-29 doi:10.1101/2021.01.28.428700 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity. ]]> https://biorxiv.org/content/10.1101/2021.01.29.428708v1?rss=1 Sidiropoulos, D. N. Rafie, C. Christmas, B. J. Davis-Marcisak, E. F. Sharma, G. Bigelow, E. Gupta, A. Yegnasubramanian, S. Stearns, V. Connolly, R. M. Gaykalova, D. A. Kagohara, L. T. Jaffee, E. M. Fertig, E. J. Roussos-Torres, E. T. 2021-01-30 doi:10.1101/2021.01.29.428708 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Speed limits of protein assembly with reversible membrane localization ]]> https://biorxiv.org/content/10.1101/2021.01.29.428888v1?rss=1 Mishra, B. Johnson, M. E. 2021-01-29 doi:10.1101/2021.01.29.428888 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Cardiac progenitors auto-regulate second heart field cell fate via Wnt secretion ]]> https://biorxiv.org/content/10.1101/2021.01.31.428968v1?rss=1 Miyamoto, M. Kannan, S. Uosaki, H. Kakani, T. Murphy, S. Andersen, P. Kwon, C. 2021-01-31 doi:10.1101/2021.01.31.428968 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2021.01.31.428969v1?rss=1 Kannan, S. Miyamoto, M. Lin, B. L. Kwon, C. 2021-01-31 doi:10.1101/2021.01.31.428969 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Genomic Considerations for FHIR; eMERGE Implementation Lessons ]]> https://biorxiv.org/content/10.1101/2021.01.31.429037v1?rss=1 Murugan, M. Babb, L. J. Taylor, C. O. Rasmussen, L. V. Freimuth, R. R. Venner, E. Yan, F. Yi, V. Granite, S. J. Zouk, H. Aronson, S. J. Power, K. Fedotov, A. Crosslin, D. R. Fasel, D. Jarvik, G. P. Hakonarson, H. Bangash, H. Kullo, I. J. Connolly, J. J. Nestor, J. G. Caraballo, P. J. Wei, W. Wiley, K. Rehm, H. L. Gibbs, R. A. 2021-02-01 doi:10.1101/2021.01.31.429037 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Video-based quantification of human movement frequency using pose estimation ]]> https://biorxiv.org/content/10.1101/2021.02.01.429161v1?rss=1 Cornman, H. L. Stenum, J. Roemmich, R. T. 2021-02-02 doi:10.1101/2021.02.01.429161 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Increased energy expenditure and protection from diet-induced obesity in mice lacking the cGMP-specific phosphodiesterase, PDE9 ]]> https://biorxiv.org/content/10.1101/2021.02.02.429406v1?rss=1 Ceddia, R. P. Liu, D. Shi, F. Mishra, S. Kass, D. A. Collins, S. 2021-02-02 doi:10.1101/2021.02.02.429406 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Colonic epithelial adaptation to EGFR-independent growth induces induces chromosomal instability and is accelerated by prior injury ]]> https://biorxiv.org/content/10.1101/2021.02.02.429426v1?rss=1 Chen, T. Zeineldin, M. Johnson, B. Dong, Y. Narkar, A. Li, T. Zhu, J. Li, R. Larman, T. 2021-02-02 doi:10.1101/2021.02.02.429426 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ PDE9 Inhibition Activates PPARa to Stimulate Mitochondrial Fat Metabolism and Reduce Cardiometabolic Syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.02.429442v1?rss=1 Mishra, S. Hahn, V. Sadagopan, N. Dunkerly-Eyring, B. Rodriguez, S. Sarver, D. C. Ceddia, R. P. Murphy, S. Knutsdottir, H. Jani, V. Ashok, D. Oeing, C. U. O'Rourke, B. Sharma, K. Gangoiti, J. Sears, D. D. Wong, G. W. Collins, S. Kass, D. A. 2021-02-02 doi:10.1101/2021.02.02.429442 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration ]]> https://biorxiv.org/content/10.1101/2021.02.03.429622v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@d6d9e5org.highwire.dtl.DTLVardef@17b6790org.highwire.dtl.DTLVardef@cc581eorg.highwire.dtl.DTLVardef@1ad2129_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fitzgerald, A. A. Marcisak, E. F. Nasir, A. Glasgow, E. Jablonski, S. Van der Veken, P. Pearson, G. Fertig, E. J. Mace, E. M. Weiner, L. M. 2021-02-03 doi:10.1101/2021.02.03.429622 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ LevioSAM: Fast lift-over of alternate reference alignments ]]> https://biorxiv.org/content/10.1101/2021.02.05.429867v1?rss=1 Mun, T. Chen, N.-C. Langmead, B. 2021-02-05 doi:10.1101/2021.02.05.429867 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Mendelian Randomization Analysis Using Multiple Biomarkers of an Underlying Common Exposure ]]> https://biorxiv.org/content/10.1101/2021.02.05.429979v1?rss=1 Jin, J. Qi, G. Yu, Z. Chatterjee, N. 2021-02-07 doi:10.1101/2021.02.05.429979 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Force-dependent activation of actin elongation factor mDia1 protects the cytoskeleton from mechanical damage and facilitates stress fiber repair. ]]> https://biorxiv.org/content/10.1101/2021.02.08.430278v1?rss=1 Valencia, F. R. Sandoval, E. Liu, J. Plotnikov, S. V. 2021-02-08 doi:10.1101/2021.02.08.430278 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Structure of the human SAGA coactivator complex ]]> https://biorxiv.org/content/10.1101/2021.02.08.430339v1?rss=1 Nogales, E. Herbst, D. Esbin, M. Louder, R. K. Dugast-Darzacq, C. Dailey, G. Fang, Q. Darzacq, X. Tjian, R. 2021-02-08 doi:10.1101/2021.02.08.430339 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Reversible blood-brain barrier opening utilizing the membrane active peptide melittin in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2021.02.09.430012v1?rss=1 Linville, R. M. Komin, A. Lan, X. DeStefano, J. G. Chu, C. Liu, G. Walczak, P. Hristova, K. Searson, P. C. 2021-02-10 doi:10.1101/2021.02.09.430012 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Synaptotagmin 7 is enriched at the plasma membrane to promote vesicle docking and control synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2021.02.09.430404v1?rss=1 Vevea, J. D. Kusick, G. F. Chen, E. Courtney, K. C. Watanabe, S. Chapman, E. R. 2021-02-09 doi:10.1101/2021.02.09.430404 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Beyond massive univariate tests: Covariance regression reveals complex patterns of functional connectivity related to attention-deficit/hyperactivity disorder, age, sex, and response control ]]> https://biorxiv.org/content/10.1101/2021.02.09.430522v1?rss=1 Zhao, Y. Nebel, M. B. Caffo, B. S. Mostofsky, S. H. Rosch, K. S. 2021-02-12 doi:10.1101/2021.02.09.430522 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Mitochondrial Fission Regulates Transcription of Ribosomal Protein Genes in Embryonic Hearts ]]> https://biorxiv.org/content/10.1101/2021.02.10.430627v1?rss=1 Zhao, Q. Yan, S. Lu, J. Parker, D. J. Wu, H. Sun, Q. Crossman, D. Liu, S. Wang, Q. Sesaki, H. Mitra, K. Liu, K. Jiao, K. 2021-02-11 doi:10.1101/2021.02.10.430627 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitors ]]> https://biorxiv.org/content/10.1101/2021.02.10.430690v1?rss=1 Zhou, J. Flores-Bellver, M. Pan, J. Benito-Martin, A. Shi, C. Onwumere, O. Mighty, J. Qian, J. Zhong, X. Hogue, T. Amponsah-Antwi, B. Einbond, L. Gharbaran, R. Wu, H. Chen, B.-J. Zheng, Z. Tchaikovskaya, T. Zhang, X. Peinado, H. Canto-Soler, V. Redenti, S. 2021-02-11 doi:10.1101/2021.02.10.430690 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Dual mTORC1/mTORC2 inhibition as a Host-Directed Therapeutic Target in Pathologically Distinct Mouse Models of Tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.02.10.430715v1?rss=1 Tasneen, R. Mortensen, D. S. Converse, P. J. Urbanowski, M. E. Upton, A. Fotouhi, N. Nuermberger, E. Hawryluk, N. 2021-02-12 doi:10.1101/2021.02.10.430715 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Automated in vivo tracking of cortical oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2021.02.12.430879v1?rss=1 Xu, Y. K. T. Call, C. L. Sulam, J. Bergles, D. E. 2021-02-15 doi:10.1101/2021.02.12.430879 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Revealing the Physiological Origin of Event-Related Potentials using Electrocorticography in Humans ]]> https://biorxiv.org/content/10.1101/2021.02.12.430921v1?rss=1 Cho, H. Schalk, G. Adamek, M. Moheimanian, L. Coon, W. G. Jun, S. C. Wolpaw, J. R. Brunner, P. 2021-02-16 doi:10.1101/2021.02.12.430921 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Epigenetic modulation in the pathogenesis and treatment of inherited aortic aneurysm conditions ]]> https://biorxiv.org/content/10.1101/2021.02.12.431010v1?rss=1 Kang, B. E. Bagirzadeh, R. Bedja, D. Doyle, J. J. MacFarlane, E. G. Dietz, H. C. 2021-02-14 doi:10.1101/2021.02.12.431010 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Synthesis, Physiochemical and Biological evaluation of Inclusion Complex of Benzyl Isothiocyanate encapsulated in cyclodextrins for triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/2021.02.14.430873v1?rss=1 Uppal, S. Kumar, R. Kaur, K. Sareen, S. Bhatia, A. Mehta, S. K. 2021-02-15 doi:10.1101/2021.02.14.430873 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Corollary discharge prevents signal distortion and enhances sensing during locomotion ]]> https://biorxiv.org/content/10.1101/2021.02.15.431323v1?rss=1 Skandalis, D. A. Lunsford, E. T. Liao, J. 2021-02-17 doi:10.1101/2021.02.15.431323 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Dynamin is primed at endocytic sites for ultrafast endocytosis ]]> https://biorxiv.org/content/10.1101/2021.02.15.431332v1?rss=1 Imoto, Y. Raychaudhuri, S. Fenske, P. Sandoval, E. Itoh, K. Blumrich, E.-M. Mamer, L. Zarebidaki, F. Sohl-Kielczynski, B. Trimbuch, T. Nayak, S. Iwasa, J. H. Jorgensen, E. M. Cousin, M. A. Rosenmund, C. A. Watanabe, S. 2021-02-16 doi:10.1101/2021.02.15.431332 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ 3D stochastic simulation of chemoattractant-mediated excitability in cells ]]> https://biorxiv.org/content/10.1101/2021.02.17.431608v1?rss=1 Biswas, D. Devreotes, P. N. Iglesias, P. A. 2021-02-17 doi:10.1101/2021.02.17.431608 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Human breast milk enhances intestinal mucosal barrier function and innate immunity in a pediatric human enteroid model ]]> https://biorxiv.org/content/10.1101/2021.02.17.431653v1?rss=1 Noel, G. In, J. Lemme-Dumit, J. M. DeVine, L. R. Cole, R. N. Guerrerio, A. L. Kovbasnjuk, O. Pasetti, M. F. 2021-02-18 doi:10.1101/2021.02.17.431653 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Remyelination restores myelin content on distinct neuronal subtypes in the cerebral cortex ]]> https://biorxiv.org/content/10.1101/2021.02.17.431685v1?rss=1 Call, C. L. Bergles, D. E. 2021-02-18 doi:10.1101/2021.02.17.431685 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Finding Druggable Sites in Proteins using TACTICS ]]> https://biorxiv.org/content/10.1101/2021.02.21.432120v1?rss=1 Evans, D. J. Yovanno, R. A. Rahman, S. Cao, D. W. Beckett, M. Q. Patel, M. H. Bandak, A. F. Lau, A. Y. 2021-02-21 doi:10.1101/2021.02.21.432120 Cold Spring Harbor Laboratory Press 2021-02-21 <![CDATA[ Estimating DNA methylation potential energy landscapes from nanopore sequencing data ]]> https://biorxiv.org/content/10.1101/2021.02.22.431480v1?rss=1 Abante, J. Kambhampati, S. Feinberg, A. P. Goutsias, J. 2021-02-22 doi:10.1101/2021.02.22.431480 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Draft metagenomes of endolithic cyanobacteria and co-habitants from hyper-arid deserts ]]> https://biorxiv.org/content/10.1101/2021.02.23.432541v1?rss=1 Murray, B. Dailey, M. Ertekin, E. DiRuggiero, J. 2021-02-23 doi:10.1101/2021.02.23.432541 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Genetic determinants of intrinsic antibiotic tolerance in Mycobacterium avium ]]> https://biorxiv.org/content/10.1101/2021.02.23.432616v1?rss=1 Matern, W. M. Parker, H. Danchik, C. Hoover, L. Bader, J. Karakousis, P. C. 2021-02-24 doi:10.1101/2021.02.23.432616 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ A simple and robust method for automating analysis of naïve and regenerating peripheral nerves ]]> https://biorxiv.org/content/10.1101/2021.02.25.432836v1?rss=1 Wong, A. L. Hricz, N. Malapati, H. von Guionneau, N. Wong, M. J. Harris, T. Boudreau, M. Cohen-Adad, J. Tuffaha, S. 2021-02-25 doi:10.1101/2021.02.25.432836 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Periodic synchronization of dengue epidemics in Thailand: the roles played by temperature and immunity ]]> https://biorxiv.org/content/10.1101/2021.03.01.433325v1?rss=1 Garcia-Carreras, B. Yang, B. Grabowski, M. K. Sheppard, L. W. Huang, A. T. Salje, H. Clapham, H. E. Iamsirithaworn, S. Doung-Ngern, P. Lessler, J. Cummings, D. A. T. 2021-03-01 doi:10.1101/2021.03.01.433325 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo ]]> https://biorxiv.org/content/10.1101/2021.03.01.433447v1?rss=1 Smith, J. J. Xiao, Y. Pars, N. Martinez, M. A. Q. Moore, F. E. Q. Palmisano, N. J. Kohrman, A. Q. Delos Reyes, M. C. Adikes, R. C. Medwig-Kinney, T. N. N. Liu, S. Bracht, S. Zhang, W. Wen, K. Kratsios, P. Matus, D. Q. 2021-03-02 doi:10.1101/2021.03.01.433447 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly ]]> https://biorxiv.org/content/10.1101/2021.03.02.432977v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@a3c55aorg.highwire.dtl.DTLVardef@1f1c840org.highwire.dtl.DTLVardef@920bc7org.highwire.dtl.DTLVardef@43633e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Credle, J. J. Gunn, J. Sangkhapreecha, P. Monaco, D. R. Zheng, X. A. Tsai, H.-J. Wilbon, A. Morgenlander, W. R. Dong, Y. Jayaraman, S. Tosi, L. Parekkadan, B. Baer, A. N. Roederer, M. Bloch, E. M. Tobian, A. A. R. Zyskind, I. Silverberg, J. I. Rosenberg, A. Z. Cox, A. L. Lloyd, T. Mammen, A. L. Larman, H. B. 2021-03-03 doi:10.1101/2021.03.02.432977 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/2021.03.03.433798v1?rss=1 Hippen, A. A. Falco, M. M. Weber, L. M. Erkan, E. P. Zhang, K. Doherty, J. A. Vähärautio, A. Greene, C. S. Hicks, S. C. 2021-03-03 doi:10.1101/2021.03.03.433798 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex ]]> https://biorxiv.org/content/10.1101/2021.03.04.433962v1?rss=1 Ramnauth, A. D. Maynard, K. Kardian, A. S. Phan, B. N. Tippani, M. Rajpurohit, S. Hobbs, J. W. Page, S. C. Jaffe, A. E. Martinowich, K. 2021-03-04 doi:10.1101/2021.03.04.433962 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Multiomics Analyses Reveal Dynamic Bioenergetic Pathways and Functional Remodeling of the Heart During Intermittent Fasting ]]> https://biorxiv.org/content/10.1101/2021.03.04.433999v1?rss=1 Arumugam, T. V. Alli-Shaik, A. Liehn, E. A. Selvaraji, S. Poh, L. Rajeev, V. Kim, J. Swa, H. L. F. Hao, D. T. Z. Ratttanasopa, C. Fann, D. Y.-W. Mayan, D. C. Ng, G. Y.-Q. Baik, S.-H. Mallilankaraman, K. Gelderblom, M. Drummond, G. R. Sobey, C. G. Kennedy, B. K. Jo, D.-G. Singaraja, R. R. Mattson, M. P. Gunaratne, J. 2021-03-05 doi:10.1101/2021.03.04.433999 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Nrf2 Regulates β-cell Mass by Suppressing Cell Death and Promoting Proliferation ]]> https://biorxiv.org/content/10.1101/2021.03.05.434145v1?rss=1 Baumel-Alterzon, S. Katz, L. S. Brill, G. Jean-Pierre, C. Li, Y. Biswal, S. Garcia-Ocana, A. Scott, D. K. 2021-03-06 doi:10.1101/2021.03.05.434145 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ BCOR and BCORL1 mutations disrupt PRC1.1 repressive function in leukemia by unlinking the RING-PCGF1 enzymatic core from target genes ]]> https://biorxiv.org/content/10.1101/2021.03.08.433705v1?rss=1 Schaefer, E. J. Wang, W. C. Meyer, C. A. Cejas, P. Gearhart, M. D. Adelman, E. R. Fares, I. Apffel, A. Lim, K. Xie, Y. Gibson, C. J. Schenone, M. Murdock, H. M. Wang, E. S. Gondek, L. P. Carroll, M. P. Vedula, R. S. Winer, E. S. Garcia, J. S. Stone, R. M. Luskin, M. R. Carr, S. A. Long, H. W. Bardwell, V. J. Figueroa, M. E. Lindsley, R. C. 2021-03-08 doi:10.1101/2021.03.08.433705 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Estimating Ectopic Beat Probability with Simplified Statistical Models that Account for Experimental Uncertainty ]]> https://biorxiv.org/content/10.1101/2021.03.08.434403v1?rss=1 Jin, Q. Greenstein, J. L. Winlsow, R. L. 2021-03-09 doi:10.1101/2021.03.08.434403 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ A viral genome packaging ring-ATPase is a flexibly coordinated pentamer ]]> https://biorxiv.org/content/10.1101/2021.03.08.434477v1?rss=1 Dai, L. Singh, D. Lu, S. Kottadiel, V. Vafabakhsh, R. Mahalingam, M. Chemla, Y. R. Ha, T. Rao, V. B. 2021-03-09 doi:10.1101/2021.03.08.434477 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Differential condensation of sister chromatids coordinates with Cdc6 to ensure distinct cell cycle progression in Drosophila male germline stem cell lineage ]]> https://biorxiv.org/content/10.1101/2021.03.08.434490v1?rss=1 Chen, X. Ranjan, R. Snedeker, J. Wooten, M. Chu, C. Bracer, S. Mouton, T. 2021-03-09 doi:10.1101/2021.03.08.434490 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Sex, age, tissue, and disease patterns of matrisome expression in GTEx transcriptome data ]]> https://biorxiv.org/content/10.1101/2021.03.09.434609v1?rss=1 Nieuwenhuis, T. O. Rosenberg, A. Z. McCall, M. N. Halushka, M. K. 2021-03-10 doi:10.1101/2021.03.09.434609 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples ]]> https://biorxiv.org/content/10.1101/2021.03.09.434660v1?rss=1 Nadel, B. Oliva, M. Shou, B. L. Mitchell, K. Ma, F. Montoya, D. J. Mouton, A. Kim-Hellmuth, S. Stranger, B. Pellegrini, M. Mangul, S. 2021-03-10 doi:10.1101/2021.03.09.434660 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools ]]> https://biorxiv.org/content/10.1101/2021.03.10.434297v1?rss=1 Pockrandt, C. Steinegger, M. Salzberg, S. 2021-03-11 doi:10.1101/2021.03.10.434297 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Face processing of social cognition in patients with first episode psychosis: Its deficits and association with the right subcallosal anterior cingulate cortex ]]> https://biorxiv.org/content/10.1101/2021.03.12.435039v1?rss=1 Narita, Z. Kuga, H. Piancharoen, P. Faria, A. Mihaljevic, M. Longo, L. Etyemez, S. Namkung, H. Coughlin, J. Nestadt, G. Nucifora, F. Sedlak, T. Schaub, R. Crawford, J. Schretlen, D. Ishizuka, K. Miyata, J. Yang, K. Sawa, A. 2021-03-12 doi:10.1101/2021.03.12.435039 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of Glycopeptide Data ]]> https://biorxiv.org/content/10.1101/2021.03.14.435332v1?rss=1 Kawahara, R. Alagesan, K. Bern, M. Cao, W. Chalkley, R. J. Cheng, K. Choo, M. S. Edwards, N. Goldman, R. Hoffmann, M. Hu, Y. Huang, Y. Kim, J. Y. Kletter, D. Liquet-Weiland, B. Liu, M. Mechref, Y. Meng, B. Neelamegham, S. Nguyen-Khuong, T. Nilsson, J. Pap, A. Park, G. W. Parker, B. L. Pegg, C. L. Penninger, J. M. Phung, T. K. Pioch, M. Rapp, E. Sakalli, E. Sanda, M. Shulz, B. L. Scott, N. E. Sofronov, G. Stadlmann, J. Vakhrushev, S. Y. Woo, C. M. Wu, H.-Y. Yang, P. Ying, W. Zhang, H. Zhang, Y. Zhao, J. Zaia, J. Haslam, S. M. Palmisano, G. Yoo, J. S 2021-03-15 doi:10.1101/2021.03.14.435332 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Modeling the three-way feedback between cellular contractility, actin polymerization, and adhesion turnover resolves the contradictory effects of RhoA and Rac1 on endothelial junction dynamics ]]> https://biorxiv.org/content/10.1101/2021.03.15.435512v1?rss=1 McEvoy, E. Sneh, T. Moeendarbary, E. Marino, G. E. Chen, X. Escribano, J. Spill, F. Garcia-Aznar, J. M. Weeraratna, A. T. Svitkina, T. M. Kamm, R. D. Shenoy, V. B. 2021-03-16 doi:10.1101/2021.03.15.435512 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Large Bi-Ethnic Study of Plasma Proteome Leads to Comprehensive Mapping of cis-pQTL and Models for Proteome-wide Association Studies ]]> https://biorxiv.org/content/10.1101/2021.03.15.435533v1?rss=1 Zhang, J. Dutta, D. Köttgen, A. Tin, A. Schlosser, P. Grams, M. E. Harvey, B. Yu, B. Boerwinkle, E. Coresh, J. Chatterjee, N. 2021-03-16 doi:10.1101/2021.03.15.435533 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ P-sort: an open-source software for cerebellar neurophysiology ]]> https://biorxiv.org/content/10.1101/2021.03.16.435644v1?rss=1 Sedaghat-Nejad, E. Fakharian, M. A. Pi, J. Hage, P. Kojima, Y. Soetedjo, R. Ohmae, S. Medina, J. F. Shadmehr, R. 2021-03-17 doi:10.1101/2021.03.16.435644 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy ]]> https://biorxiv.org/content/10.1101/2021.03.17.435706v1?rss=1 Guerler, A. Baker, D. van den Beek, M. Bouvier, D. Coraor, N. Schatz, M. C. Nekrutenko, A. 2021-03-19 doi:10.1101/2021.03.17.435706 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ CHRONIC INFLAMMATION IN ULCERATIVE COLITIS CAUSES LONG TERM CHANGES IN GOBLETCELL FUNCTION ]]> https://biorxiv.org/content/10.1101/2021.03.17.435871v1?rss=1 Singh, V. Johnson, K. Yin, J. Lee, S. Lin, R.-X. Yu, H. In, J. Abel, J. F. Zachos, N. 2021-03-19 doi:10.1101/2021.03.17.435871 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Brain Water as a Function of Age and Weight in Normal Rats ]]> https://biorxiv.org/content/10.1101/2021.03.18.436025v1?rss=1 Gottschalk, A. Scafidi, S. Toung, T. 2021-03-18 doi:10.1101/2021.03.18.436025 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Sex-specific transcript diversity is regulated by a maternal pioneer factor in early Drosophila embryos ]]> https://biorxiv.org/content/10.1101/2021.03.18.436074v1?rss=1 Ray, M. Conard, A. M. Urban, J. Larschan, E. 2021-03-19 doi:10.1101/2021.03.18.436074 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Explicit and implicit depth-cue integration: evidence of systematic biases with real objects ]]> https://biorxiv.org/content/10.1101/2021.03.19.436171v1?rss=1 Campagnoli, C. Hung, B. Domini, F. 2021-03-22 doi:10.1101/2021.03.19.436171 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Two-stage Linked Component Analysis for Joint Decomposition of Multiple Biologically Related Data Sets ]]> https://biorxiv.org/content/10.1101/2021.03.22.435728v1?rss=1 Chen, H. Caffo, B. Stein-O'Brien, G. Liu, J. Langmead, B. Colantuoni, C. Xiao, L. 2021-03-22 doi:10.1101/2021.03.22.435728 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Pan-genomic Matching Statistics for Targeted Nanopore Sequencing ]]> https://biorxiv.org/content/10.1101/2021.03.23.436610v1?rss=1 Ahmed, O. Rossi, M. Kovaka, S. Schatz, M. Gagie, T. Boucher, C. Langmead, B. 2021-03-23 doi:10.1101/2021.03.23.436610 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ minicore: Fast scRNA-seq clustering with various distance measures ]]> https://biorxiv.org/content/10.1101/2021.03.24.436859v1?rss=1 Baker, D. N. Dyjack, N. Braverman, V. Hicks, S. C. Langmead, B. 2021-03-25 doi:10.1101/2021.03.24.436859 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Base editing using CRISPR/Cas9 in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.03.24.436868v1?rss=1 T (or G>A) mutations at targeted sites. Here, we test base editing in Drosophila by expressing a transgenic Drosophila base editor (DBE2, based on the mammalian BE2) which consists of a fusion protein of cytidine deaminase, dCas9, and uracil glycosylase inhibitor. We utilized transgenic lines expressing gRNAs along with pan-tissue expression of the Drosophila Base Editor (Actin5C-DBE2) and found high rates of base editing at multiple targeted loci in the 20 bp target sequence. Highest rates of conversion of C>T were found in positions 3-9 of the gRNA targeted site, with conversion reaching nearly 100% of targeted DNA is somatic tissues. The simultaneous use of two gRNA targeting a genomic region spaced [~]50 bps apart led to mutations between the two gRNA targets, implicating a method to broaden the available sites accessible to targeting. These results indicate base editing is efficient in Drosophila, and could be used to induce point mutations at select loci. ]]> Marr, E. Potter, C. J. 2021-03-25 doi:10.1101/2021.03.24.436868 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Antiviral Antibody Epitope Selection is a Heritable Trait ]]> https://biorxiv.org/content/10.1101/2021.03.25.436790v1?rss=1 Venkataraman, T. Valencia, C. Mangino, M. Morgenlander, W. Clipman, S. J. Liechti, T. Valencia, A. Christofidou, P. Spector, T. D. Roederer, M. Duggal, P. Larman, H. B. 2021-03-26 doi:10.1101/2021.03.25.436790 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Neural circuitry for maternal oxytocin release induced by infant cries ]]> https://biorxiv.org/content/10.1101/2021.03.25.436883v1?rss=1 Valtcheva, S. Issa, H. A. Martin, K. A. Jung, K. Kwon, H.-B. Froemke, R. C. 2021-03-25 doi:10.1101/2021.03.25.436883 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Cannabinoid signaling promotes the reprogramming of Muller glia into proliferating progenitor cells. ]]> https://biorxiv.org/content/10.1101/2021.03.25.436969v1?rss=1 Campbell, W. Blum, S. Reske, A. Hoang, T. Blackshaw, S. Fischer, A. 2021-03-25 doi:10.1101/2021.03.25.436969 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring ]]> https://biorxiv.org/content/10.1101/2021.03.25.437046v1?rss=1 Maier, W. Bray, S. van den Beek, M. Bouvier, D. Coraor, N. Miladi, M. Singh, B. Rambla De Argila, J. Baker, D. Roach, N. Gladman, S. Coppens, F. Martin, D. Lonie, A. Gruning, B. Kosakovsky Pond, S. Nekrutenko, A. 2021-03-25 doi:10.1101/2021.03.25.437046 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses ]]> https://biorxiv.org/content/10.1101/2021.03.25.437060v1?rss=1 Ordonez, A. A. Bullen, C. K. Villabona-Rueda, A. F. Thompson, E. A. Turner, M. L. Davis, S. L. Komm, O. Powell, J. D. D'Alessio, F. R. Yolken, R. H. Jain, S. K. Jones-Brando, L. 2021-03-25 doi:10.1101/2021.03.25.437060 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling ]]> https://biorxiv.org/content/10.1101/2021.03.26.437132v1?rss=1 Light, T. L. Brun, D. Guardado-Calvo, P. Pederzoli, R. Haouz, A. Neipel, F. Rey, F. A. Hristova, K. Backovic, M. 2021-03-28 doi:10.1101/2021.03.26.437132 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Little evidence that Eurasian jays (Garrulus glandarius) protect their caches by responding to cues about a conspecific's desire and visual perspective ]]> https://biorxiv.org/content/10.1101/2021.03.26.437226v1?rss=1 Amodio, P. Farrar, B. G. Krupenye, C. Ostojic, L. Clayton, N. S. 2021-03-29 doi:10.1101/2021.03.26.437226 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Functional selectivity for naturalistic social interaction perception in the human superior temporal sulcus ]]> https://biorxiv.org/content/10.1101/2021.03.26.437258v1?rss=1 Lee Masson, H. Isik, L. 2021-03-26 doi:10.1101/2021.03.26.437258 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Temporal regulation of green and red cone specification in human retinas and retinal organoids ]]> https://biorxiv.org/content/10.1101/2021.03.30.437763v1?rss=1 Hadyniak, S. E. Eldred, K. C. Brenerman, B. Hussey, K. A. McCoy, R. C. Sauria, M. E. G. Kuchenbecker, J. A. Neitz, M. Neitz, J. Taylor, J. Johnston, R. J. 2021-03-31 doi:10.1101/2021.03.30.437763 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Predicting skeletal stature using ancient DNA ]]> https://biorxiv.org/content/10.1101/2021.03.31.437877v1?rss=1 Cox, S. L. Moots, H. Stock, J. T. Shbat, A. Bitarello, B. D. Haak, W. Rosenstock, E. Ruff, C. B. Mathieson, I. 2021-03-31 doi:10.1101/2021.03.31.437877 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Three Dimensions of Association Link Migraine Symptoms and Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2021.03.31.437905v1?rss=1 Krimmel, S. R. DeSouza, D. D. Keaser, M. L. Sanjanwala, B. M. Cowan, R. P. Lindquist, M. A. Haythornthwaite, J. Seminowicz, D. A. 2021-04-01 doi:10.1101/2021.03.31.437905 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Dorsomedial striatal activity tracks completion of behavioral sequences ]]> https://biorxiv.org/content/10.1101/2021.04.01.437899v1?rss=1 Vandaele, Y. Ottenheimer, D. J. Janak, P. H. 2021-04-02 doi:10.1101/2021.04.01.437899 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Naturalistic audio-movies reveal common spatial organization across "visual" cortices of different blind individuals ]]> https://biorxiv.org/content/10.1101/2021.04.01.438106v1?rss=1 Musz, E. Loiotile, R. E. Chen, J. Bedny, M. 2021-04-01 doi:10.1101/2021.04.01.438106 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Mechanisms that ensure speed and fidelity in eukaryotic translation termination ]]> https://biorxiv.org/content/10.1101/2021.04.01.438116v1?rss=1 Lawson, M. R. Lessen, L. N. Wang, J. Prabhakar, A. Corsepius, N. C. Green, R. Puglisi, J. D. 2021-04-02 doi:10.1101/2021.04.01.438116 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Is it that simple? Linear mapping models in cognitive neuroscience ]]> https://biorxiv.org/content/10.1101/2021.04.02.438248v1?rss=1 Ivanova, A. A. Schrimpf, M. Anzellotti, S. Zaslavsky, N. Fedorenko, E. Isik, L. 2021-04-04 doi:10.1101/2021.04.02.438248 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Sex differences in lung imaging and SARS-CoV-2 antibody responses in a COVID-19 golden Syrian hamster model ]]> https://biorxiv.org/content/10.1101/2021.04.02.438292v1?rss=1 Dhakal, S. Ruiz-Bedoya, C. A. Zhou, R. Creisher, P. Villano, J. Littlefield, K. Castillo, J. Marinho, P. Jedlicka, A. Ordonez, A. Majewska, N. Betenbaugh, M. Flavahan, K. Mueller, A. Looney, M. Quijada, D. Mota, F. Beck, S. E. Brockhurst, J. K. Braxton, A. Castell, N. D'Alessio, F. Metcalf Pate, K. A. Karakousis, P. C. Mankowski, J. L. Pekosz, A. Jain, S. K. Klein, S. L. 2021-04-04 doi:10.1101/2021.04.02.438292 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Unveiling the neural correlates of habit in the dorsal striatum ]]> https://biorxiv.org/content/10.1101/2021.04.03.438314v1?rss=1 Vandaele, Y. Janak, P. H. 2021-04-04 doi:10.1101/2021.04.03.438314 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks ]]> https://biorxiv.org/content/10.1101/2021.04.04.438423v1?rss=1 Koehler Leman, J. Lyskov, S. Lewis, S. Adolf-Bryfogle, J. Alford, R. F. Barlow, K. Ben-Aharon, Z. Farrell, D. Fell, J. Hansen, W. A. Harmalkar, A. Jeliazkov, J. Krys, J. D. Kuenze, G. Ljubetic, A. Loshbaugh, A. L. Maguire, J. Moretti, R. Mulligan, V. K. Nguyen, P. T. OConchuir, S. Roy Burman, S. S. Smith, S. T. Teets, F. Tiemann, J. K. Watkins, A. Woods, H. Yachnin, B. J. Bahl, C. D. Bailey-Kellogg, C. Baker, D. Das, R. DiMaio, F. Khare, S. D. Kortemme, T. Labonte, J. W. Lindorff-Larsen, K. Meiler, J. Schief, W. Schueler-Furman, O. Siegel, J. Stein, A. 2021-04-05 doi:10.1101/2021.04.04.438423 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Universal prediction of cell cycle position using transfer learning ]]> https://biorxiv.org/content/10.1101/2021.04.06.438463v1?rss=1 Zheng, S. C. Stein-O'Brien, G. Augustin, J. J. Slosberg, J. Carosso, G. A. Winer, B. Shin, G. Bjornsson, H. T. Goff, L. A. Hansen, K. D. 2021-04-06 doi:10.1101/2021.04.06.438463 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Co-opting propelling and perturbing appendages facilitates strenuous ground self-righting ]]> https://biorxiv.org/content/10.1101/2021.04.06.438657v1?rss=1 Othayoth, R. Xuan, Q. Li, C. 2021-04-08 doi:10.1101/2021.04.06.438657 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ APOE ε4 allele advances the age-dependent decline of amyloid β clearance in the human cortex ]]> https://biorxiv.org/content/10.1101/2021.04.07.438832v1?rss=1 Saito, A. Kageyama, Y. Pletnikova, O. Rudow, G. L. An, Y. Irie, Y. Kita, A. Miki, K. Li, L. Southall, P. Irie, K. Troncoso, J. C. 2021-04-08 doi:10.1101/2021.04.07.438832 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors. ]]> https://biorxiv.org/content/10.1101/2021.04.09.438683v1?rss=1 View larger version (73K): org.highwire.dtl.DTLVardef@18ac4c2org.highwire.dtl.DTLVardef@17bb90aorg.highwire.dtl.DTLVardef@1b17cceorg.highwire.dtl.DTLVardef@178e769_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kim, D. W. Place, E. Chinnaiya, K. Manning, E. Sun, C. Dai, W. Ohyama, K. Burbridge, S. Placzek, M. Blackshaw, S. 2021-04-09 doi:10.1101/2021.04.09.438683 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Loss of TDP-43 function and rimmed vacuoles persist after T cell depletion in a xenograft model of sporadic inclusion body myositis ]]> https://biorxiv.org/content/10.1101/2021.04.09.439185v1?rss=1 Britson, K. A. Ling, J. P. Braunstein, K. E. Montagne, J. M. Kastenschmidt, J. M. Wilson, A. Ikenaga, C. Tsao, W. Pinal-Fernandez, I. Russel, K. A. Reed, N. Wagner, K. R. Ostrow, L. W. Corse, A. M. Mammen, A. L. Villalta, S. A. Larman, H. B. Wong, P. C. Lloyd, T. E. 2021-04-11 doi:10.1101/2021.04.09.439185 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ High-quality genome and methylomes illustrate features underlying evolutionary success of oaks ]]> https://biorxiv.org/content/10.1101/2021.04.09.439191v1?rss=1 Sork, V. L. Cokus, S. Fitz-Gibbon, S. T. Zimin, A. V. Puiu, D. Garcia, J. A. Gugger, P. F. Henriquez, C. L. Zhen, Y. Lohmueller, K. E. Pellegrini, M. Salzberg, S. L. 2021-04-11 doi:10.1101/2021.04.09.439191 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Human Fronto-Striatal Connectivity is Organized into Discrete Functional Subnetworks ]]> https://biorxiv.org/content/10.1101/2021.04.12.439415v1?rss=1 Gordon, E. M. Laumann, T. O. Marek, S. Newbold, D. J. Hampton, J. M. Seider, N. A. Montez, D. F. Nielsen, A. M. Van, A. N. Zheng, A. Miller, R. Siegel, J. S. Kay, B. P. Snyder, A. Z. Greene, D. J. Schlaggar, B. L. Petersen, S. Nelson, S. M. Dosenbach, N. 2021-04-12 doi:10.1101/2021.04.12.439415 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ TAZ/TEAD complex regulates TGF-β1-mediated fibrosis in iPSC-derived renal organoids ]]> https://biorxiv.org/content/10.1101/2021.04.15.440011v1?rss=1 Yang, X. Delsante, M. Deneshpajouhnejad, P. Fenaroli, P. Mandell, K. P. Wang, X. Takahashi, S. Halushka, M. K. Kopp, J. B. Levi, M. Rosenberg, A. Z. 2021-04-16 doi:10.1101/2021.04.15.440011 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Post mortem mapping of connectional anatomy for the validation of diffusion MRI ]]> https://biorxiv.org/content/10.1101/2021.04.16.440223v1?rss=1 Yendiki, A. Aggarwal, M. Axer, M. Howard, A. F. van Cappellen van Walsum, A.-M. Haber, S. N. 2021-04-19 doi:10.1101/2021.04.16.440223 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Surface residues and non-additive interactions stabilize a consensus homeodomain protein ]]> https://biorxiv.org/content/10.1101/2021.04.19.440332v1?rss=1 Sternke, M. Tripp, K. W. Barrick, D. 2021-04-20 doi:10.1101/2021.04.19.440332 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Development of Small Molecule Inhibitors Targeting PBX1 Transcription Signaling as a Novel Cancer Therapeutic Strategy ]]> https://biorxiv.org/content/10.1101/2021.04.19.440460v1?rss=1 Wang, T.-L. Shih, I.-M. Shen, Y.-A. Jung, J. Shimberg, G. D. Hsu, F.-C. Rahmanto, Y. S. Gaillard, S. L. Hong, J. Bosch, J. Chuang, C.-M. 2021-04-19 doi:10.1101/2021.04.19.440460 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Accurate assignment of disease liability to genetic variants using only population data ]]> https://biorxiv.org/content/10.1101/2021.04.19.440463v1?rss=1 Collaco, J. M. Raraigh, K. S. Betz, J. F. Aksit, M. A. Blau, N. Brown, J. Dietz, H. C. MacCarrick, G. Nogee, L. M. Sheridan, M. B. Vernon, H. Beaty, T. H. Louis, T. A. Cutting, G. 2021-04-19 doi:10.1101/2021.04.19.440463 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ The SARS CoV-1 3a protein disrupts Golgi complex morphology and cargo trafficking ]]> https://biorxiv.org/content/10.1101/2021.04.19.440492v1?rss=1 Gonzales, R. R. Machamer, C. E. 2021-04-19 doi:10.1101/2021.04.19.440492 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins ]]> https://biorxiv.org/content/10.1101/2021.04.19.440502v1?rss=1 Guo, S.-K. Sodt, A. J. Johnson, M. E. 2021-04-20 doi:10.1101/2021.04.19.440502 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Hierarchical Computational Anatomy: Unifying the Molecular to Tissue Continuum via Measure Representations of the Brain ]]> https://biorxiv.org/content/10.1101/2021.04.19.440540v1?rss=1 Miller, M. I. Tward, D. J. Trouve, A. 2021-04-19 doi:10.1101/2021.04.19.440540 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Highly task-specific and distributed neural connectivity in working memory revealed by single-trial decoding in mice and humans ]]> https://biorxiv.org/content/10.1101/2021.04.20.440621v1?rss=1 Strahnen, D. Kapanaiah, S. K. T. Bygrave, A. M. Liss, B. Bannerman, D. M. Akam, T. Grewe, B. F. Johnson, E. L. Kätzel, D. 2021-04-21 doi:10.1101/2021.04.20.440621 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Post-weaning social isolation modulates reward-seeking behavior in a sex-specific manner in mice ]]> https://biorxiv.org/content/10.1101/2021.04.20.440665v1?rss=1 Noback, M. Barrow, J. C. Carr, G. V. 2021-04-20 doi:10.1101/2021.04.20.440665 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Novel neuroanatomical integration and scaling define avian brain shape evolution and development ]]> https://biorxiv.org/content/10.1101/2021.04.20.440700v1?rss=1 Watanabe, A. Balanoff, A. M. Gignac, P. M. Gold, M. E. L. Norell, M. A. 2021-04-21 doi:10.1101/2021.04.20.440700 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin ]]> https://biorxiv.org/content/10.1101/2021.04.21.440742v1?rss=1 Kim, J. M. Visanpattanasin, P. Jou, V. Liu, S. Tang, X. Zheng, Q. Li, K. Y. Snedeker, J. Lavis, L. D. Lionnet, T. Wu, C. 2021-04-21 doi:10.1101/2021.04.21.440742 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Host regulator PARP1 contributes to sex differences and immune responses in a mouse model of tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.04.21.440820v1?rss=1 Krug, S. Ordonez, A. A. Klunk, M. Kang, B. G. Jain, S. K. Dawson, T. M. Dawson, V. L. Bishai, W. 2021-04-22 doi:10.1101/2021.04.21.440820 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) ]]> https://biorxiv.org/content/10.1101/2021.04.22.436044v1?rss=1 Schatz, M. C. Philippakis, A. A. Afgan, E. Banks, E. Carey, V. J. Carroll, R. J. Culotti, A. Ellrott, K. Goecks, J. Grossman, R. L. Hall, I. Hansen, K. D. Lawson, J. Leek, J. T. O'Donnell Luria, A. Mosher, S. Morgan, M. Nekrutenko, A. O'Connor, B. D. Osborn, K. Paten, B. Patterson, C. Tan, F. J. Overby Taylor, C. Vessio, J. Waldron, L. D. Wang, T. Wuichet, K. AnVIL Team, 2021-04-23 doi:10.1101/2021.04.22.436044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Developmental Alcohol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain ]]> https://biorxiv.org/content/10.1101/2021.04.22.440913v1?rss=1 Mokashi, S. S. Shankar, V. MacPherson, R. A. Hannah, R. C. Mackay, T. F. C. Anholt, R. R. H. 2021-04-22 doi:10.1101/2021.04.22.440913 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ A continuum membrane model predicts curvature sensing by helix insertion ]]> https://biorxiv.org/content/10.1101/2021.04.22.440963v1?rss=1 Fu, Y. Zeno, W. Stachowiak, J. Johnson, M. E. 2021-04-23 doi:10.1101/2021.04.22.440963 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Citrullination of a phage displayed human peptidome library reveals the fine specificities of rheumatoid arthritis-associated autoantibodies ]]> https://biorxiv.org/content/10.1101/2021.04.22.441021v1?rss=1 Roman-Melendez, G. D. Monaco, D. R. Montagne, J. M. Quizon, R. S. Konig, M. F. Astatke, M. Darrah, E. Larman, H. B. 2021-04-23 doi:10.1101/2021.04.22.441021 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ MG53 preserves neuromuscular junction integrity and alleviates ALS disease progression ]]> https://biorxiv.org/content/10.1101/2021.04.22.441038v1?rss=1 Yi, J. Li, A. Li, X. Park, K. H. Zhou, X. Yi, F. Xiao, Y. Yoon, D. Tan, T. Ostrow, L. W. Ma, J. Zhou, J. 2021-04-23 doi:10.1101/2021.04.22.441038 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ An N-terminal Fusion Allele to Study Melanin Concentrating Hormone Receptor 1 ]]> https://biorxiv.org/content/10.1101/2021.04.23.440964v1?rss=1 Jasso, K. R. Kamba, T. K. Zimmerman, A. D. Bansal, R. Engle, S. Everett, T. Wu, C.-H. Kulaga, H. Reed, R. Berbari, N. F. McIntyre, J. C. 2021-04-24 doi:10.1101/2021.04.23.440964 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.04.23.441024v1?rss=1 McDonald, J. T. Enguita, F. J. Taylor, D. Bowen, R. A. Griffin, R. J. Priebe, W. Emmett, M. R. McGrath, M. Sajadi, M. Harris, A. D. Clement, J. Dybas, J. M. Aykin-Burns, N. Guarnieri, J. W. Singh, L. N. Grabham, P. Baylin, S. Yousey, A. Pearson, A. N. Corry, P. M. Saravia-Butler, A. Aunins, T. R. Nagpal, P. Meydan, C. Foox, J. Mozsary, C. Cerqueira, B. Zaksas, V. Singh, U. Wurtele, E. S. Costes, S. V. Galeano, D. Paccanaro, A. Meinig, S. L. Hagan, R. S. Bowman, N. M. UNC COVID-19 Pathobiology Consortium, Wolfgang, M. C. Altinok, S. Sapoval, N. Treangen 2021-04-23 doi:10.1101/2021.04.23.441024 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Altered Cortical Activation Associated with Mirror Overflow Driven by Non-Dominant Hand Movement in Attention-Deficit/Hyperactivity Disorder ]]> https://biorxiv.org/content/10.1101/2021.04.23.441107v1?rss=1 Luo, Y. Chen, C. Adamek, J. Crocetti, D. Mostofsky, S. Ewen, J. 2021-04-23 doi:10.1101/2021.04.23.441107 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis ]]> https://biorxiv.org/content/10.1101/2021.04.24.441277v1?rss=1 Li, X. Gordon, P. J. Gaynes, J. A. Fuller, A. W. Ringuette, R. Santiago, C. P. Wallace, V. A. Blackshaw, S. Li, P. LEVINE, E. M. 2021-04-26 doi:10.1101/2021.04.24.441277 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Narratives as Networks: Predicting Memory from the Structure of Naturalistic Events ]]> https://biorxiv.org/content/10.1101/2021.04.24.441287v1?rss=1 Lee, H. Chen, J. 2021-04-24 doi:10.1101/2021.04.24.441287 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Bacterial chaperone protein Hfq facilitates the annealing of sponge RNAs to small regulatory RNAs ]]> https://biorxiv.org/content/10.1101/2021.04.25.441314v1?rss=1 Malecka, E. M. Sobanska, D. Olejniczak, M. 2021-04-26 doi:10.1101/2021.04.25.441314 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Dysregulation of NRSF/REST via EHMT1 is association with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/2021.04.26.441439v1?rss=1 Alsaqati, M. Davis, B. A. Wood, J. Jones, M. Jones, L. Petter, O. Isles, A. R. Linden, D. van den Bree, M. B. Owen, M. Hall, J. Harwood, A. J. 2021-04-26 doi:10.1101/2021.04.26.441439 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ PodoCount: A robust, fully automated whole-slide podocyte quantification tool ]]> https://biorxiv.org/content/10.1101/2021.04.27.441689v1?rss=1 Santo, B. A. Govind, D. Daneshpajouhnejad, P. Yang, X. Wang, X. X. Myakala, K. Jones, B. A. Levi, M. Kopp, J. B. Niedernhofer, L. J. Manthey, D. Moon, K. C. Han, S. S. Rosenberg, A. Z. Sarder, P. 2021-04-28 doi:10.1101/2021.04.27.441689 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ SARS-COV-2 induced Diarrhea is inflammatory, Ca2+ Dependent and involves activation of calcium activated Cl channels ]]> https://biorxiv.org/content/10.1101/2021.04.27.441695v1?rss=1 >basolateral media of polarized enteroids 48 h after exposure. This is the first demonstration of basolateral appearance of live virus after apical exposure. High vRNA concentration was detected in cell lysates and in the apical and basolateral media up to 5 days after exposure. 2) Two days after viral exposure, cytokine measurements of media showed significantly increased levels of IL-6, IL-8 and MCP-1. 3) Two days after viral exposure, mRNA levels of ACE2, NHE3 and DRA were reduced but there was no change in mRNA of CFTR. NHE3 protein was also decreased. 4) Live viral studies were mimicked by some studies with VLP exposure for 48 h. VLPs with Spike-D614G bound to the enteroid apical surface and was taken up; this resulted in decreased mRNA levels of ACE2, NHE3, DRA and CFTR. 4) VLP effects were determined on active anion secretion measured with the Ussing chamber/voltage clamp technique. S-D614G acutely exposed to apical surface of human ileal enteroids did not alter the short-circuit current (Isc). However, VLPS-D614G exposure to enteroids that were pretreated for [~]24 h with IL-6 plus IL-8 induced a concentration dependent increase in Isc indicating stimulated anion secretion, that was delayed in onset by [~]8 min. The anion secretion was inhibited by apical exposure to a specific calcium activated Cl channel (CaCC) inhibitor (AO1) but not by a specific CFTR inhibitor (BP027); was inhibited by basolateral exposure to the K channel inhibit clortimazole; and was prevented by pretreatment with the calcium buffer BAPTA-AM. 5) The calcium dependence of the VLP-induced increase in Isc was studied in Caco-2/BBe cells stably expressing the genetically encoded Ca2+ sensor GCaMP6s. 24 h pretreatment with IL-6/IL-8 did not alter intracellular Ca2+. However, in IL-6/IL-8 pretreated cells, VLP S-D614G caused appearance of Ca2+waves and an overall increase in intracellular Ca2+ with a delay of [~]10 min after VLP addition. We conclude that the diarrhea of COVID-19 appears to an example of a calcium dependent inflammatory diarrhea that involves both acutely stimulated Ca2+ dependent anion secretion (stimulated Isc) that involves CaCC and likely inhibition of neutral NaCl absorption (decreased NHE3 protein and mRNA and decreased DRA mRNA). ]]> Donowitz, M. Tse, C.-M. Dokladny, K. Rawat, M. Hurwitz, I. Ye, C. Kell, A. Lin, R. Lee, S. Guo, C. G. Tsai, S. J. Cox, A. Gould, S. In, J. Bradfute, S. B. Zachos, N. Kovbasnjuk, O. 2021-04-28 doi:10.1101/2021.04.27.441695 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Sequence-based correction of barcode bias in massively parallel reporter assays ]]> https://biorxiv.org/content/10.1101/2021.04.29.442047v1?rss=1 Lee, D. Kapoor, A. Lee, C. Mudgett, M. Beer, M. A. Chakravarti, A. 2021-04-30 doi:10.1101/2021.04.29.442047 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Germline Sex Determination regulates sex-specific signaling between germline stem cells and their niche ]]> https://biorxiv.org/content/10.1101/2021.04.30.442141v1?rss=1 Bhaskar, P. K. Southard, S. Baxter, K. Van Doren, M. 2021-04-30 doi:10.1101/2021.04.30.442141 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ A Novel In Situ Activity Assay for Lysyl Oxidases ]]> https://biorxiv.org/content/10.1101/2021.04.30.442175v1?rss=1 Wang, H. Poe, A. Pak, L. Jandu, S. Nandakumar, K. Steppan, J. Loser, R. Santhanam, L. 2021-04-30 doi:10.1101/2021.04.30.442175 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Aplp1 and the Aplp1-Lag3 Complex facilitates transmission of pathologic alpha-synuclein ]]> https://biorxiv.org/content/10.1101/2021.05.01.442157v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1d746bforg.highwire.dtl.DTLVardef@65acb2org.highwire.dtl.DTLVardef@12cf2f0org.highwire.dtl.DTLVardef@19d6e_HPS_FORMAT_FIGEXP M_FIG Aplp1 and the Aplp1-Lag3 complex facilitates transmission of pathologic -synuclein. Aplp1 is a receptor that drives pathologic -syn transmission, and genetic depletion of Aplp1 can significantly reduce the -synuclein pathogenesis. Aplp1 and Lag3 forms an Aplp1-Lag3 complex that accounts for substantial binding of pathologic -syn to cortical neurons. Together Aplp1 and Lag3 play a major role in pathologic -syn internalization, transmission and toxicity. Double knockout of Aplp1 and Lag3 and or a Lag3 antibody that disrupts the Aplp1 and Lag3 complex almost completely blocks -syn PFF-induced neurodegeneration. C_FIG ]]> Mao, X. Gu, H. Kim, D. Kimura, Y. Wang, N. Xu, E. Chen, C. Zhang, S. Jia, C. Liu, Y. Bian, H. Karuppagounder, S. Jia, L. Ke, X. Chang, M. Lee, A. Yang, J. Rastegar, C. Sriparna, M. Ge, P. Brahmachari, S. Kim, S. Zhang, S. Shimoda, Y. Saar, M. Workman, C. Vignali, D. Muller, U. Liu, C. Ko, H. Dawson, V. Dawson, T. 2021-05-01 doi:10.1101/2021.05.01.442157 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ A multimodal study of a first episode psychosis cohort: potential markers of antipsychotic treatment resistance ]]> https://biorxiv.org/content/10.1101/2021.05.03.442450v1?rss=1 Yang, K. Longo, L. Narita, Z. Cascella, N. Nucifora, F. C. Coughlin, J. M. Nestadt, G. Sedlak, T. W. Mihaljevic, M. Wang, M. Kenkare, A. Nagpal, A. Sethi, M. Kelly, A. Di Carlo, P. Kamath, V. Faria, A. Barker, P. B. Sawa, A. 2021-05-04 doi:10.1101/2021.05.03.442450 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Digital 3D Brain MRI Arterial Territories Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.03.442478v1?rss=1 Liu, C.-F. Hsu, J. Xu, X. Kim, N. G. Sheppard, S. Meier, E. Miller, M. Hillis, A. E. Faria, A. V. 2021-05-04 doi:10.1101/2021.05.03.442478 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Genetic Basis of Variation in Ubiquitin-Proteasome System Activity ]]> https://biorxiv.org/content/10.1101/2021.05.05.442832v1?rss=1 Collins, M. A. Mekonnen, G. Albert, F. W. 2021-05-06 doi:10.1101/2021.05.05.442832 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Reinforcement learning modeling reveals a reward-history-dependent strategy underlying reversal learning in squirrel monkeys ]]> https://biorxiv.org/content/10.1101/2021.05.05.442852v1?rss=1 Bari, B. A. Moerke, M. J. Jedema, H. P. Effinger, D. P. Cohen, J. Y. Bradberry, C. W. 2021-05-06 doi:10.1101/2021.05.05.442852 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Analysis of melanotic Plasmodium spp. capsules in mosquitoes reveal eumelanin-pheomelanin composition and identify AgMesh as a modulator of parasite infection ]]> https://biorxiv.org/content/10.1101/2021.05.07.443077v1?rss=1 Camacho, E. Dong, Y. Anglero-Rodriguez, Y. Smith, D. Jacomini, R. S. Dimopoulos, G. Casadevall, A. 2021-05-08 doi:10.1101/2021.05.07.443077 Cold Spring Harbor Laboratory Press 2021-05-08 <![CDATA[ RNA toxicity and perturbation of rRNA processing in spinocerebellar ataxia type 2 ]]> https://biorxiv.org/content/10.1101/2021.05.07.443200v1?rss=1 Li, P. P. Moulick, R. Feng, H. Sun, X. Arbez, N. Jin, J. Marque, L. O. Hedglen, E. Chan, H. Y. E. Ross, C. A. Pulst, S. M. Margolis, R. L. Woodson, S. Rudnicki, D. D. 2021-05-09 doi:10.1101/2021.05.07.443200 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Integrative Wireless Device for Remote Continuous Blood Biomarker Monitoring ]]> https://biorxiv.org/content/10.1101/2021.05.07.443203v1?rss=1 Phan, D.-T. 2021-05-09 doi:10.1101/2021.05.07.443203 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Edaravone activates the GDNF/RET neurotrophic signaling pathway and protects mRNA-induced motor neurons from iPS cells. ]]> https://biorxiv.org/content/10.1101/2021.05.09.443325v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@cd0bc9org.highwire.dtl.DTLVardef@1c0c0b6org.highwire.dtl.DTLVardef@1ac0952org.highwire.dtl.DTLVardef@1980f5b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, Q. Feng, Y. Xue, Y. Zhan, X. Fu, Y. Gui, G. Richard, J.-P. Taga, A. Mao, X. Maragakis, N. J. Ying, M. 2021-05-10 doi:10.1101/2021.05.09.443325 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ General Finite-Element Framework of the Virtual Fields Method in Nonlinear Elasticity ]]> https://biorxiv.org/content/10.1101/2021.05.10.443225v1?rss=1 Mei, Y. Liu, J. Guo, X. Zimmerman, B. Nguyen, T. D. Avril, S. 2021-05-10 doi:10.1101/2021.05.10.443225 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Orc6 at replication fork enables efficient mismatch repair ]]> https://biorxiv.org/content/10.1101/2021.05.10.443400v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@bfdaa8org.highwire.dtl.DTLVardef@1ac791dorg.highwire.dtl.DTLVardef@436d1corg.highwire.dtl.DTLVardef@b07689_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHuman Orc6 is dispensable for G1 licensing, but required for S-phase progression C_LIO_LIHuman Orc6 at the replication fork is an accessory factor for MMR complex C_LIO_LIDepletion of hOrc6 sensitizes cells to DNA damage and impairs ATR activation C_LIO_LIHuman Orc6 regulates MMR complex assembly and activity C_LI ]]> Lin, Y.-C. Chakraborty, A. Liu, D. Mitra, J. Kadyrova, L. Hsu, R. Arif, M. Adusumilli, S. Ha, T. Kadyrov, F. Prasanth, K. V. Prasanth, S. G. 2021-05-10 doi:10.1101/2021.05.10.443400 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Cannabinoid tetrad effects of oral Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) in male and female rats: sex, dose-effects and time course evaluations ]]> https://biorxiv.org/content/10.1101/2021.05.11.443601v1?rss=1 7 hours). CBD modestly increased mechanical pain sensitivity and produced sex-dependent effects on body temperature and locomotor activity. Conclusions Oral THC and CBD produced long lasting effects, that differed in magnitude and time course when compared with other routes of administration. Examination of cannabinoid effects administered via different routes of administration, species, and in both males and females is critical to enhance translation. ]]> Moore, C. F. Weerts, E. M. 2021-05-13 doi:10.1101/2021.05.11.443601 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Colicin-mediated transport of DNA through the iron transporter FepA ]]> https://biorxiv.org/content/10.1101/2021.05.11.443673v1?rss=1 Cohen-Khait, R. Harmalkar, A. Pham, P. Webby, M. N. Housden, N. G. Elliston, E. Hopper, J. T. Mohammed, S. Robinson, C. V. Gray, J. J. Kleanthous, C. 2021-05-11 doi:10.1101/2021.05.11.443673 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ NMNAT promotes glioma growth through regulating post-translational modifications of p53 to inhibit apoptosis ]]> https://biorxiv.org/content/10.1101/2021.05.12.443736v1?rss=1 Zhai, R. G. Liu, J. Zhu, Y. Tao, X. Ruan, K. Wang, H. 2021-05-13 doi:10.1101/2021.05.12.443736 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ The repeat region of the circumsporozoite protein is an elastic linear spring with a functional role in Plasmodium sporozoite motility ]]> https://biorxiv.org/content/10.1101/2021.05.12.443759v1?rss=1 Balaban, A. Kanatani, S. Mitra, J. Gregory, J. Vartak, N. Sinnis-Bourozikas, A. Frischknecht, F. Ha, T. Sinnis, P. 2021-05-12 doi:10.1101/2021.05.12.443759 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ The Origin of Bladder Cancer from Mucosal Field Effects ]]> https://biorxiv.org/content/10.1101/2021.05.12.443785v1?rss=1 Bondaruk, J. Jaksik, R. Wang, Z. Cogdell, D. Lee, S. Chen, Y. Dinh, K. N. Majewski, T. Zhang, L. Cao, S. Yao, H. Weinstein, J. N. Navai, N. Dinney, C. Gao, J. Theodorescu, D. Logothetis, C. Guo, C. C. Wang, W. McConkey, D. J. Wei, P. Kimmel, M. Czerniak, B. 2021-05-14 doi:10.1101/2021.05.12.443785 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis ]]> https://biorxiv.org/content/10.1101/2021.05.12.443930v1?rss=1 Aumiller, K. Stevens, E. Scheffler, R. Guvener, Z. T. Tung, E. Grimaldo, A. B. Carlson, H. K. Deutschbauer, A. M. Taga, M. E. Marco, M. L. Ludington, W. B. 2021-05-14 doi:10.1101/2021.05.12.443930 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Transcriptomic profiling of human orbital fat and differentiating orbital fibroblasts ]]> https://biorxiv.org/content/10.1101/2021.05.13.443857v1?rss=1 Kim, D. W. Taneja, K. Hoang, T. Santiago, C. P. McCulley, T. J. Merbs, S. L. Mahoney, N. R. Blackshaw, S. Rajaii, F. 2021-05-15 doi:10.1101/2021.05.13.443857 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Potent macrocycle inhibitors of the human SAGA deubiquitinating module ]]> https://biorxiv.org/content/10.1101/2021.05.13.444038v1?rss=1 Morgan, M. T. Ikenoue, T. Suga, H. Wolberger, C. 2021-05-14 doi:10.1101/2021.05.13.444038 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ "How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.05.17.443632v1?rss=1 Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Farina, S. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffman, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. E. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. Su 2021-05-17 doi:10.1101/2021.05.17.443632 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ HLA Gene Expression Mediates Tumor Immunogenicity and Escape ]]> https://biorxiv.org/content/10.1101/2021.05.17.444511v1?rss=1 Gong, X. Karchin, R. 2021-05-18 doi:10.1101/2021.05.17.444511 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Haplotype-aware inference of human chromosome abnormalities ]]> https://biorxiv.org/content/10.1101/2021.05.18.444721v1?rss=1 Ariad, D. Yan, S. M. Victor, A. R. Barnes, F. L. Zouves, C. G. Viotti, M. McCoy, R. C. 2021-05-20 doi:10.1101/2021.05.18.444721 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Protein detection in blood with single-molecule imaging ]]> https://biorxiv.org/content/10.1101/2021.05.19.444873v1?rss=1 Mao, C.-P. Wang, S.-C. Su, Y.-P. Tseng, S.-H. He, L. Wu, A. Xiao, J. Roden, R. Hung, C.-F. 2021-05-20 doi:10.1101/2021.05.19.444873 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Novel entropy-based metrics for predicting choice behavior based on local response to reward ]]> https://biorxiv.org/content/10.1101/2021.05.20.445009v1?rss=1 Trepka, E. Spitmaan, M. Bari, B. A. Costa, V. D. Cohen, J. Y. Soltani, A. 2021-05-21 doi:10.1101/2021.05.20.445009 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ The proportional recovery rule redux: Arguments for its biological and predictive relevance ]]> https://biorxiv.org/content/10.1101/2021.05.20.445022v1?rss=1 Goldsmith, J. Kitago, T. Garcia de la Garza, A. Kundert, R. Luft, A. Stinear, C. M. Byblow, W. D. Kwakkel, G. Krakauer, J. W. 2021-05-21 doi:10.1101/2021.05.20.445022 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ recount3: summaries and queries for large-scale RNA-seq expression and splicing ]]> https://biorxiv.org/content/10.1101/2021.05.21.445138v1?rss=1 Wilks, C. Zheng, S. C. Chen, F. Y. Charles, R. Solomon, B. Ling, J. P. Imada, E. L. Zhang, D. Joseph, L. Leek, J. T. Jaffe, A. E. Nellore, A. Collado-Torres, L. Hansen, K. D. Langmead, B. 2021-05-23 doi:10.1101/2021.05.21.445138 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Distinct movement patterns generate stages of spider web-building ]]> https://biorxiv.org/content/10.1101/2021.05.24.444987v1?rss=1 Corver, A. Wilkerson, N. Miller, J. Gordus, A. G. 2021-05-25 doi:10.1101/2021.05.24.444987 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Neurotrophin signaling is modulated by specific transmembrane domain interactions ]]> https://biorxiv.org/content/10.1101/2021.05.24.445441v1?rss=1 Franco, M. L. Nadezhdin, K. D. Light, T. P. Goncharuk, S. A. Soler-Lopez, A. Ahmed, F. Mineev, K. S. Hristova, K. Arseniev, A. S. Vilar, M. 2021-05-26 doi:10.1101/2021.05.24.445441 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging ]]> https://biorxiv.org/content/10.1101/2021.05.24.445514v1?rss=1 Charles, A. S. Cermak, N. Affan, R. Scott, B. Schiller, J. Mishne, G. 2021-05-25 doi:10.1101/2021.05.24.445514 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Biological Constraints Can Improve Prediction inPrecision Oncology ]]> https://biorxiv.org/content/10.1101/2021.05.25.445604v1?rss=1 Omar, M. Mulder, L. Coady, T. Zanettini, C. Imada, E. L. Dinalankara, W. Younes, L. Geman, D. Marchionni, L. 2021-05-27 doi:10.1101/2021.05.25.445604 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Diversity of satellite glia in sympathetic and sensory ganglia ]]> https://biorxiv.org/content/10.1101/2021.05.25.445647v1?rss=1 Mapps, A. Thomsen, M. Boehm, E. Zhao, H. Hattar, S. Kuruvilla, R. 2021-05-25 doi:10.1101/2021.05.25.445647 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Epigenetic Patterns in a Complete Human Genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.443420v1?rss=1 Gershman, A. Sauria, M. E. G. Hook, P. W. Hoyt, S. Razaghi, R. Koren, S. Altemose, N. Caldas, G. V. Vollger, M. R. Logsdon, G. Rhie, A. Eichler, E. Schatz, M. O'Neill, R. J. Phillippy, A. M. Miga, K. H. Timp, W. 2021-05-27 doi:10.1101/2021.05.26.443420 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Segmental duplications and their variation in a complete human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445678v1?rss=1 Vollger, M. R. Guitart, X. Dishuck, P. C. Mercuri, L. Harvey, W. T. Gershman, A. Diekhans, M. Sulovari, A. Munson, K. M. Lewis, A. M. Hoekzema, K. Porubsky, D. Li, R. Nurk, S. Koren, S. Miga, K. H. Phillippy, A. M. Timp, W. Ventura, M. Eichler, E. E. 2021-05-26 doi:10.1101/2021.05.26.445678 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ The complete sequence of a human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1 Nurk, S. Koren, S. Rhie, A. Rautiainen, M. Bzikadze, A. V. Mikheenko, A. Vollger, M. R. Altemose, N. Uralsky, L. Gershman, A. Aganezov, S. Hoyt, S. J. Diekhans, M. Logsdon, G. A. Alonge, M. Antonarakis, S. E. Borchers, M. Bouffard, G. G. Brooks, S. Y. Caldas, G. V. Cheng, H. Chin, C.-S. Chow, W. de Lima, L. G. Dishuck, P. C. Durbin, R. Dvorkina, T. Fiddes, I. T. Formenti, G. Fulton, R. S. Fungtammasan, A. Garrison, E. Grady, P. G. S. Graves-Lindsay, T. A. Hall, I. M. Hansen, N. F. Hartley, G. A. Haukness, M. Howe, K. Hunkapiller, M. W. Jain, C. Jain, M. 2021-05-27 doi:10.1101/2021.05.26.445798 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Comparison of linear combination modeling strategies for GABA-edited MRS at 3T ]]> https://biorxiv.org/content/10.1101/2021.05.26.445817v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@129ce60org.highwire.dtl.DTLVardef@1ac3797org.highwire.dtl.DTLVardef@1759d69org.highwire.dtl.DTLVardef@b190a3_HPS_FORMAT_FIGEXP M_FIG C_FIG 102 strategies to model GABA-edited MRS with linear combination modeling were evaluated to quantify GABA and GABA+ in Osprey. Significantly different GABA and GABA+ estimates were found when a well-parameterized macro-molecule at 3 ppm was included. The findings suggest that linear combination modeling needs to be adapted for quantification of GABA-edited MRS. ]]> Zöllner, H. J. Tapper, S. Hui, S. C. N. Barker, P. B. Edden, R. A. E. Oeltzschner, G. 2021-05-26 doi:10.1101/2021.05.26.445817 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Somatic reversion impacts MDS/AML evolution in the short telomere syndromes ]]> https://biorxiv.org/content/10.1101/2021.05.26.445858v1?rss=1 Schratz, K. E. Gayasinskaya, V. Cosner, Z. L. DeBoy, E. A. Xiang, Z. Kasch-Semenza, L. Florea, L. D. Shah, P. D. Armanios, M. 2021-05-27 doi:10.1101/2021.05.26.445858 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Jasmine: Population-scale structural variant comparison and analysis ]]> https://biorxiv.org/content/10.1101/2021.05.27.445886v1?rss=1 Kirsche, M. Prabhu, G. Sherman, R. Ni, B. Aganezov, S. Schatz, M. C. 2021-05-28 doi:10.1101/2021.05.27.445886 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Successful IL-12 cancer immunotherapy requires NK cell-derived CCL5 for anti-tumor DC-T cell crosstalk ]]> https://biorxiv.org/content/10.1101/2021.05.27.445981v1?rss=1 Kirchhammer, N. Trefny, M. P. Natoli, M. Bruecher, D. Smith, S. N. Werner, F. Koch, V. Schreiner, D. Bartoszek, E. Buchi, M. Schmid, M. Breu, D. Hartmann, K. P. Zaytseva, P. Thommen, D. S. Laubli, H. Stanczak, M. A. Kashyap, A. Plueckthun, A. Zippelius, A. 2021-05-27 doi:10.1101/2021.05.27.445981 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Antibody structure prediction using interpretable deep learning ]]> https://biorxiv.org/content/10.1101/2021.05.27.445982v1?rss=1 Ruffolo, J. A. Sulam, J. Gray, J. J. 2021-05-27 doi:10.1101/2021.05.27.445982 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression ]]> https://biorxiv.org/content/10.1101/2021.05.27.446073v1?rss=1 Masuda, I. Hwang, J.-Y. Christian, T. Maharjan, S. Mohammad, F. Gamper, H. Buskirk, A. Hou, Y.-M. 2021-05-28 doi:10.1101/2021.05.27.446073 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A Biologically Interpretable Graph Convolutional Network to Link Genetic Risk Pathways and Neuroimaging Phenotypes of Disease ]]> https://biorxiv.org/content/10.1101/2021.05.28.446066v1?rss=1 Ghosal, S. Pergola, G. Chen, Q. Goldman, A. Ulrich, W. Weinberger, D. R. Venkataraman, A. 2021-05-30 doi:10.1101/2021.05.28.446066 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Oligodendrocyte precursor cells prune axons in the mouse neocortex ]]> https://biorxiv.org/content/10.1101/2021.05.29.446047v1?rss=1 Buchanan, J. Elabaddy, L. Collman, F. Jorstad, N. L. Bakken, T. E. Ott, C. Glatzer, J. Bleckert, A. A. Bodor, A. L. Brittan, D. Bumbarger, D. J. Mahalingam, G. Seshamani, S. Schneider-Mizell, C. M. Takeno, M. M. Torres, R. Yin, W. Hodge, R. D. Castro, M. Dorkenwald, S. Ih, D. Jordan, C. S. Kemnitz, N. Lee, K. Lu, R. Macrina, T. Mu, S. Popovych, S. Silversmith, W. M. Tartavull, I. Turner, N. L. Wilson, A. M. Wong, W. Wu, J. Zlateski, A. Zung, J. Lippincott-Schwartz, J. Lein, E. S. Seung, H. S. Bergles, D. E. Reid, R. C. Macarico da Costa, N. 2021-05-29 doi:10.1101/2021.05.29.446047 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ The genetic and epigenetic landscape of the Arabidopsis centromeres ]]> https://biorxiv.org/content/10.1101/2021.05.30.446350v1?rss=1 Naish, M. R. Alonge, M. Wlodzimierz, P. Tock, A. J. Abramson, B. W. Lambing, C. A. Kuo, P. Yelina, N. Hartwick, N. Colt, K. Kakutani, T. Martienssen, R. A. Bousios, A. Michael, T. P. Schatz, M. C. Henderson, I. R. 2021-05-30 doi:10.1101/2021.05.30.446350 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Spatial and temporal autocorrelation weave human brain networks ]]> https://biorxiv.org/content/10.1101/2021.06.01.446561v1?rss=1 Shinn, M. Hu, A. Turner, L. Noble, S. Achard, S. Anticevic, A. Scheinost, D. Constable, R. T. Lee, D. Bullmore, E. T. Murray, J. D. 2021-06-01 doi:10.1101/2021.06.01.446561 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ The Rab11-Family Interacting Proteins reveal selective interaction of mammalian recycling endosomes with the Toxoplasma parasitophorous vacuole in a Rab11- and Arf6-dependent manner ]]> https://biorxiv.org/content/10.1101/2021.06.01.446625v1?rss=1 Hartman, E. J. Romano, J. D. Coppens, I. 2021-06-01 doi:10.1101/2021.06.01.446625 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Raman spectroscopy reveals phenotype switches in breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2021.06.02.446487v1?rss=1 Paidi, S. K. Troncoso, J. R. Harper, M. G. Liu, Z. Nguyen, K. G. Ravindranathan, S. Ivers, J. D. Zaharoff, D. A. Rajaram, N. Barman, I. 2021-06-02 doi:10.1101/2021.06.02.446487 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Rapid Biomarker Screening of Alzheimer's Disease by Machine Learning and Graphene-Assisted Raman Spectroscopy ]]> https://biorxiv.org/content/10.1101/2021.06.03.446929v1?rss=1 Wang, Z. Ye, J. Ding, L. Granzier-Nakajima, T. Sharma, S. Biase, I. Terrones, M. Choi, S. H. Ran, C. Tanzi, R. E. Huang, S. Zhang, C. M. Huang, S. 2021-06-03 doi:10.1101/2021.06.03.446929 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation ]]> https://biorxiv.org/content/10.1101/2021.06.03.446970v1?rss=1 Elorbany, R. Popp, J. M. Rhodes, K. Strober, B. J. Barr, K. Qi, G. Gilad, Y. M. Battle, A. 2021-06-03 doi:10.1101/2021.06.03.446970 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ P2X4 Purinergic Receptors as a Therapeutic Target in Aggressive Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2021.06.04.446195v1?rss=1 Maynard, J. P. Lu, J. Vidal, I. Hicks, J. Mummert, L. Ali, T. Kempski, R. Carter, A. M. Sosa, R. Peiffer, L. B. Joshu, C. E. Lotan, T. L. De Marzo, A. M. Sfanos, K. S. 2021-06-06 doi:10.1101/2021.06.04.446195 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes ]]> https://biorxiv.org/content/10.1101/2021.06.07.444885v1?rss=1 Wagner, J. Olson, N. D. Harris, L. McDaniel, J. Cheng, H. Fungtammasan, A. Hwang, Y.-C. Gupta, R. Wenger, A. M. Rowell, W. J. Khan, Z. M. Farek, J. Zhu, Y. Pisupati, A. Mahmoud, M. Xiao, C. Yoo, B. Sahraeian, S. M. E. Miller, D. E. Jaspez, D. Lorenzo-Salazar, J. M. Munoz-Barrera, A. Rubio-Rodriguez, L. A. Flores, C. Narzisi, G. Evani, U. S. Clarke, W. E. Lee, J. Mason, C. E. Lincoln, S. E. Miga, K. H. Ebbert, M. T. Shumate, A. Li, H. Chin, C.-S. Zook, J. M. Sedlazeck, F. J. 2021-06-07 doi:10.1101/2021.06.07.444885 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2021.06.07.447263v1?rss=1 Sholes, S. L. Karimian, K. Gershman, A. Kelly, T. J. Timp, W. Greider, C. W. 2021-06-07 doi:10.1101/2021.06.07.447263 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Cortical waves mediate the cellular response to electric fields ]]> https://biorxiv.org/content/10.1101/2021.06.08.447600v1?rss=1 Yang, Q. Miao, Y. Campanello, L. J. Hourwitz, M. J. Bull, A. L. Devreotes, P. N. Fourkas, J. T. Losert, W. 2021-06-08 doi:10.1101/2021.06.08.447600 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Integrative Epigenomic and High-Throughput Functional Enhancer Profiling Reveals Determinants of Enhancer Heterogeneity in Gastric Cancer ]]> https://biorxiv.org/content/10.1101/2021.06.09.447637v1?rss=1 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. Specifically, we identified cancer-relevant genes (e.g. ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4 as a master trans-acting factor associated with GC enhancer heterogeneity. ConclusionsOur study indicates that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, and provides insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity. ]]> Sheng, T. Ho, S. W. T. Ooi, W. F. Xu, C. Xing, M. Padmanabhan, N. Huang, K. K. Ma, L. Ray, M. Guo, Y. A. Leng, S. N. Anene-Nzelu, C. G. Chang, M. M. Razavi-Mohseni, M. Beer, M. Foo, R. Tan, A. L. K. Ong, X. Jacobsen Skanderup, A. White, K. P. Jha, S. Tan, P. 2021-06-10 doi:10.1101/2021.06.09.447637 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Hepatocyte androgen receptor in females mediates androgen-induced hepatocellular glucose mishandling and systemic insulin resistance ]]> https://biorxiv.org/content/10.1101/2021.06.09.447759v1?rss=1 Andrisse, S. Feng, M. Wang, Z. Awe, O. Yu, L. Zhang, H. Bi, S. Wang, H. Li, L. Joseph, S. Heller, N. Mauvais-Jarvis, F. Wong, G. W. Segars, J. Wolfe, A. Divall, S. Ahima, R. Wu, S. 2021-06-09 doi:10.1101/2021.06.09.447759 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Pervasive fold switching in a ubiquitous protein superfamily ]]> https://biorxiv.org/content/10.1101/2021.06.10.447921v1?rss=1 58,000 non-redundant proteins support this assumption, though it has recently been challenged by [~]100 fold-switching proteins2. These "metamorphic3" proteins, though ostensibly rare, raise the question of how many uncharacterized proteins have shapeshifting-rather than fixed-secondary structures. To address this question, we developed a comparative sequence-based approach that predicts fold-switching proteins from differences in secondary structure propensity. We applied this approach to the universally conserved NusG transcription factor family of [~]15,000 proteins, one of which has a 50-residue regulatory subunit experimentally shown to switch between -helical and {beta}-sheet folds4. Our approach predicted that 25% of the sequences in this family undergo similar -helix {rightleftharpoons} {beta}-sheet transitions, a frequency two orders of magnitude larger than previously observed. Our predictions evade state-of-the-art computational methods but were confirmed experimentally by circular dichroism and nuclear magnetic resonance spectroscopy for all 10 assiduously chosen dissimilar variants. These results suggest that fold switching is a pervasive mechanism of transcriptional regulation in all kingdoms of life and imply that numerous uncharacterized proteins may also switch folds. ]]> Porter, L. Kim, A. K. Looger, L. L. Majumdar, A. Starich, M. R. 2021-06-11 doi:10.1101/2021.06.10.447921 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ A reference-quality, fully annotated genome from a Puerto Rican individual ]]> https://biorxiv.org/content/10.1101/2021.06.10.447952v1?rss=1 Zimin, A. V. Shumate, A. Shinder, I. Heinz, J. Puiu, D. Pertea, M. Salzberg, S. L. 2021-06-11 doi:10.1101/2021.06.10.447952 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Age-related increases in reaction time result from slower preparation, not delayed initiation ]]> https://biorxiv.org/content/10.1101/2021.06.12.448183v1?rss=1 Hardwick, R. M. Forrence, A. D. Costello, M. G. Zachowski, K. Haith, A. M. 2021-06-14 doi:10.1101/2021.06.12.448183 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors ]]> https://biorxiv.org/content/10.1101/2021.06.12.448194v1?rss=1 Zheng, L. Wood, L. Karchin, R. Scharpf, R. B. 2021-06-13 doi:10.1101/2021.06.12.448194 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ A novel and accurate full-length HTT mouse model for Huntington's disease ]]> https://biorxiv.org/content/10.1101/2021.06.14.448318v1?rss=1 Li, C. Zheng, S. Shenoy, S. A. Liu, W. Dai, Y. Liu, Y. Hou, Z. Mori, S. Duan, W. 2021-06-14 doi:10.1101/2021.06.14.448318 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Regulome-wide association study identifies enhancer properties associated with risk for schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.06.14.448418v1?rss=1 Casella, A. M. Colantuoni, C. Ament, S. A. 2021-06-15 doi:10.1101/2021.06.14.448418 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Reference-free cell-type deconvolution of pixel-resolution spatially resolved transcriptomics data ]]> https://biorxiv.org/content/10.1101/2021.06.15.448381v1?rss=1 Miller, B. F. Atta, L. Sahoo, A. Huang, F. Fan, J. 2021-06-16 doi:10.1101/2021.06.15.448381 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types ]]> https://biorxiv.org/content/10.1101/2021.06.16.448714v1?rss=1 Rhodes, K. Barr, K. A. Popp, J. M. Strober, B. J. Battle, A. Gilad, Y. 2021-06-16 doi:10.1101/2021.06.16.448714 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Incorporation of data from multiple hypervariable regions when analyzing bacterial 16S rRNA sequencing data ]]> https://biorxiv.org/content/10.1101/2021.06.17.448728v1?rss=1 Jones, C. B. White, J. R. Ernst, S. E. Sfanos, K. S. Peiffer, L. B. 2021-06-17 doi:10.1101/2021.06.17.448728 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Distinct Processing of Sensory Prediction Error and Task Error during Motor Learning ]]> https://biorxiv.org/content/10.1101/2021.06.20.449180v1?rss=1 Tsay, J. Haith, A. Ivry, R. B. Kim, H. E. 2021-06-20 doi:10.1101/2021.06.20.449180 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Inhibiting adenine synthesis attenuates glioblastoma cell stemness and temozolomide resistance ]]> https://biorxiv.org/content/10.1101/2021.06.21.449341v1?rss=1 Singh, S. X. Yang, R. Roso, K. Hansen, L. J. Du, C. Chen, L. H. Greer, P. K. Pirozzi, C. J. He, Y. 2021-06-22 doi:10.1101/2021.06.21.449341 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Pickering stabilization of a dynamic intracellular emulsion ]]> https://biorxiv.org/content/10.1101/2021.06.22.449249v1?rss=1 Folkmann, A. W. Putnam, A. A. Lee, C. F. Seydoux, G. 2021-06-22 doi:10.1101/2021.06.22.449249 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Norepinephrine Potentiates and Serotonin Depresses Visual Cortical Responses by Transforming Eligibility Traces ]]> https://biorxiv.org/content/10.1101/2021.06.22.449441v1?rss=1 Hong, S. Z. Mesik, L. Grossman, C. D. Cohen, J. Y. Lee, B. Lee, H.-K. Hell, J. W. kirkwood, a. 2021-06-22 doi:10.1101/2021.06.22.449441 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Impact of dose, duration and host immune status on ultrashort telacebec treatment in a mouse model of Buruli ulcer ]]> https://biorxiv.org/content/10.1101/2021.06.22.449541v1?rss=1 Converse, P. J. Almeida, D. Komm, O. Nuermberger, E. 2021-06-23 doi:10.1101/2021.06.22.449541 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Ultrashort treatment with telacebec alone and with companion drugs in immunocompetent and immunosuppressed mouse footpad models of Buruli ulcer ]]> https://biorxiv.org/content/10.1101/2021.06.22.449542v1?rss=1 Converse, P. J. Komm, O. Almeida, D. Omansen, T. F. Nuermberger, E. 2021-06-23 doi:10.1101/2021.06.22.449542 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Aliquoting of isobaric labeling reagents for low concentration and single cell proteomics samples ]]> https://biorxiv.org/content/10.1101/2021.06.23.449560v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@18cd7eeorg.highwire.dtl.DTLVardef@1b48065org.highwire.dtl.DTLVardef@159761forg.highwire.dtl.DTLVardef@5a0896_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yuan, Y. Orsburn, B. C. 2021-06-23 doi:10.1101/2021.06.23.449560 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Flexible encoding of objects and space in single cells of the dentate gyrus ]]> https://biorxiv.org/content/10.1101/2021.06.25.449795v1?rss=1 GoodSmith, D. Kim, S. H. Puliyadi, V. Ming, G.-l. Song, H. Knierim, J. J. Christian, K. M. 2021-06-25 doi:10.1101/2021.06.25.449795 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Progression and Resolution of SARS-1 CoV-2 Infection in Golden Syrian Hamsters ]]> https://biorxiv.org/content/10.1101/2021.06.25.449918v1?rss=1 Mulka, K. Beck, S. Solis, C. Johanson, A. Queen, S. McCarron, M. Richardson, M. Zhou, R. Marinho, P. Jedlicka, A. Guerrero-Martin, S. Shirk, E. Braxton, A. Brockhurst, J. Creisher, P. Dhakal, S. Brayton, C. Veenhuis, R. Metcalf Pate, K. Karakousis, P. Klein, S. L. Tarwater, P. Pekosz, A. Villano, J. Jain, S. K. Mankowski, J. 2021-06-26 doi:10.1101/2021.06.25.449918 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ A bacterial extracellular vesicle-based intranasal vaccine against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.06.28.450181v1?rss=1 Jiang, L. Driedonks, T. Lowman, M. Jong, W. S. van den Berg van Saparoea, H. B. Dhakal, S. Zhou, R. Caputo, C. Littlefield, K. Sitaris, I. Chen, M. W. Lima, G. Gololobova, O. Smith, B. Lane, A. P. Klein, S. L. Pekosz, A. Brayton, C. F. Luirink, J. Villano, J. S. Witwer, K. W. 2021-06-28 doi:10.1101/2021.06.28.450181 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Conserved Transcription Factors Control Chromatin Accessibility and Gene Expression to Maintain Cell Fate Stability and Restrict Reprogramming of Differentiated Cells ]]> https://biorxiv.org/content/10.1101/2021.06.28.450261v1?rss=1 Missinato, M. A. Murphy, S. A. Lynott, M. Kervadec, A. Yu, M. S. Chang, Y.-L. Kannan, S. Loreti, M. Lee, C. Amatya, P. Tanaka, H. Huang, C.-T. Puri, P. L. Kwon, C. Adams, P. D. Qian, L. Sacco, A. Andersen, P. Colas, A. R. 2021-06-29 doi:10.1101/2021.06.28.450261 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Genome-wide association study and functional validation implicates JADE1 in tauopathy ]]> https://biorxiv.org/content/10.1101/2021.06.30.450599v1?rss=1 Farrell, K. Kim, S. Han, N. Iida, M. A. Gonzalez, E. Otero-Garcia, M. Walker, J. Richardson, T. Renton, A. E. Andrews, S. J. Fulton-Howard, B. Humphrey, J. Vialle, R. A. Bowles, K. R. Whitney, K. Dangoor, D. K. Marcora, E. Hefti, M. M. Casella, A. Bhangale, T. Hunkapiller, J. Ayalon, G. Graham, R. Cherry, J. D. Cortes, E. Borukov, V. McKee, A. C. Stein, T. D. Vonsattel, J. P. Teich, A. F. Gearing, M. Glass, J. Troncoso, J. C. Frosch, M. P. Hyman, B. T. Dickson, D. W. Murray, M. E. Attems, J. Flanagan, M. E. Mao, Q. Mesulam, M. M. Weintraub, S. Woltjer, 2021-07-01 doi:10.1101/2021.06.30.450599 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Proximity-dependent biotinylation to elucidate the interactome of TNK2 non-receptor tyrosine kinase ]]> https://biorxiv.org/content/10.1101/2021.06.30.450607v1?rss=1 Tahir, R. Madugundu, A. K. Udainiya, S. Cutler, J. A. Renuse, S. Wang, L. Pearson, N. A. Mitchell, C. Mahajan, N. Pandey, A. Wu, X. 2021-07-01 doi:10.1101/2021.06.30.450607 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71 ]]> https://biorxiv.org/content/10.1101/2021.06.30.450637v1?rss=1 Wirick, M. J. Cale, A. R. Smith, I. T. Alessi, A. F. Starostik, M. R. Cuko, L. Lalk, K. Schmidt, M. N. Olson, B. S. Salomon, P. M. Santos, A. Schmitter-Sanchez, A. Galagali, H. Ranke, K. J. Wolbert, P. A. Knoblock, M. L. Kim, J. K. Karp, X. 2021-07-01 doi:10.1101/2021.06.30.450637 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies ]]> https://biorxiv.org/content/10.1101/2021.07.02.450803v1?rss=1 Mc Cartney, A. M. Shafin, K. Alonge, M. Bzikadze, A. V. Formenti, G. Fungtammasan, A. Howe, K. Jain, C. Koren, S. Logsdon, G. A. Miga, K. H. Mikheenko, A. Paten, B. Shumate, A. Soto, D. C. Sovic, I. Wood, J. M. Zook, J. M. Phillippy, A. M. Rhie, A. 2021-07-02 doi:10.1101/2021.07.02.450803 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Betacoronavirus-specific alternate splicing ]]> https://biorxiv.org/content/10.1101/2021.07.02.450920v1?rss=1 Karlebach, G. Aronow, B. J. Baylin, S. J. Butler, D. Foox, J. Levy, S. Meydan, C. Mozsary, C. Saravia-Butler, A. M. Taylor, D. M. Wurtele, E. Mason, C. Beheshti, A. Robinson, P. N. 2021-07-02 doi:10.1101/2021.07.02.450920 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Accurately positioning functional residues with robotics-inspired computational protein design ]]> https://biorxiv.org/content/10.1101/2021.07.02.450934v1?rss=1 Krivacic, C. Kundert, K. Pan, X. Pache, R. A. Liu, L. O Conchuir, S. Jeliazkov, J. R. Gray, J. J. Thompson, M. C. Fraser, J. S. Kortemme, T. 2021-07-03 doi:10.1101/2021.07.02.450934 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER. ]]> https://biorxiv.org/content/10.1101/2021.07.04.450352v1?rss=1 Haffner, M. C. Bhamidipati, A. Tsai, H. K. Esopi, D. M. Vaghasia, A. M. Low, J.-Y. Patel, R. A. Guner, G. Pham, M.-T. Castagna, N. Hicks, J. Wyhs, N. Aebersold, R. De Marzo, A. M. Nelson, W. G. Guo, T. Yegnasubramanian, S. 2021-07-05 doi:10.1101/2021.07.04.450352 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly ]]> https://biorxiv.org/content/10.1101/2021.07.04.451050v1?rss=1 250 distinct cell types across all tissues. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution. ]]> Li, H. Janssens, J. De Waegeneer, M. Kolluru, S. S. Davie, K. Gardeux, V. Sealens, W. David, F. Brbic, M. Leskovec, J. McLaughlin, C. Xie, Q. Jones, R. Brueckner, K. Shim, J. Tattikota, S. G. Schnorrer, F. Rust, K. Nystul, T. Carvalho-Santos, Z. Ribeiro, C. Pal, S. Przytycka, T. M. Allen, A. Goodwin, S. Berry, C. Fuller, M. T. White-Cooper, H. Matunis, E. DiNardo, S. Galenza, A. O'Brien, L. E. Dow, J. A. T. FCA Consortium, Jasper, H. Oliver, B. Perrimon, N. Deplancke, B. Quake, S. Luo, L. Aerts, S. 2021-07-05 doi:10.1101/2021.07.04.451050 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ D-cysteine is an endogenous regulator of neural progenitor cell dynamics in the mammalian brain ]]> https://biorxiv.org/content/10.1101/2021.07.05.451211v1?rss=1 Semenza, E. R. Harraz, M. M. Abramson, E. Malla, A. P. Vasavda, C. Gadalla, M. M. Kornberg, M. D. Snyder, S. H. Roychaudhuri, R. 2021-07-06 doi:10.1101/2021.07.05.451211 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Daily oscillation of the excitation/inhibition ratio is disrupted in two mouse models of autism ]]> https://biorxiv.org/content/10.1101/2021.07.05.451213v1?rss=1 Bridi, M. Luo, N. Kim, G. O'Ferrall, C. Oatel, R. Bertrand, S. Kannan, S. Kirkwood, A. 2021-07-06 doi:10.1101/2021.07.05.451213 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ MONI: A Pangenomics Index for Finding MEMs ]]> https://biorxiv.org/content/10.1101/2021.07.06.451246v1?rss=1 Rossi, M. Oliva, M. Langmead, B. Gagie, T. Boucher, C. 2021-07-07 doi:10.1101/2021.07.06.451246 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Myeloid-to-mesenchymal NGF-p75 signaling coordinates skeletal cell migration during repair ]]> https://biorxiv.org/content/10.1101/2021.07.07.451468v1?rss=1 Xu, J. Li, Z. Tower, R. J. Negri, S. Wang, Y. Meyers, C. A. Sono, T. Qin, Q. Lu, A. McCarthy, E. F. Clemens, T. L. James, A. W. 2021-07-07 doi:10.1101/2021.07.07.451468 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Transcranial photoacoustic characterization of neurovascular physiology during early-stage photothrombotic stroke in neonatal piglets in vivo ]]> https://biorxiv.org/content/10.1101/2021.07.08.451613v1?rss=1 Kang, J. Liu, X. Cao, S. Zeiler, S. R. Graham, E. M. Boctor, E. M. Koehler, R. C. 2021-07-09 doi:10.1101/2021.07.08.451613 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2 ]]> https://biorxiv.org/content/10.1101/2021.07.09.451812v1?rss=1 Prevost, J. Richard, J. Gasser, R. Ding, S. Fage, C. Anand, S. P. Adam, D. Gupta Vergara, N. Tauzin, A. Benlarbi, M. Gong, S. Y. Goyette, G. Prive, A. Moreira, S. Charest, H. Roger, M. Mothes, W. Pazgier, M. Brochiero, E. Boivin, G. Abrams, C. F. Schon, A. Finzi, A. 2021-07-09 doi:10.1101/2021.07.09.451812 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Enhanced chemotaxis through spatially-regulated absolute concentration robustness ]]> https://biorxiv.org/content/10.1101/2021.07.10.451673v1?rss=1 Biswas, D. Bhattacharya, S. Iglesias, P. A. 2021-07-11 doi:10.1101/2021.07.10.451673 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Structural basis for carbapenam C-alkylation by TokK, a B12-dependent radical SAM enzyme ]]> https://biorxiv.org/content/10.1101/2021.07.10.451909v1?rss=1 Knox, H. Sinner, E. Townsend, C. Boal, A. Booker, S. 2021-07-11 doi:10.1101/2021.07.10.451909 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Circuit motifs and graph properties of connectome development in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.11.451911v1?rss=1 Matelsky, J. K. Norman-Tenazas, R. Davenport, F. Reilly, E. P. Gray-Roncal, W. R. 2021-07-12 doi:10.1101/2021.07.11.451911 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Glby, is a PBP with β-lactamase activity and is required for in vivo viability of M. abscessus ]]> https://biorxiv.org/content/10.1101/2021.07.11.451952v1?rss=1 Lamichhane, G. Galanis, C. Maggioncalda, E. C. Kumar, G. 2021-07-11 doi:10.1101/2021.07.11.451952 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ From telomere to telomere: the transcriptional and epigenetic state of human repeat elements ]]> https://biorxiv.org/content/10.1101/2021.07.12.451456v1?rss=1 Hoyt, S. J. Storer, J. M. Hartley, G. A. Grady, P. G. S. Gershman, A. de Lima, L. G. Limouse, C. Halabian, R. Wojenski, L. Rodriguez, M. Altemose, N. Core, L. Gerton, J. L. Makalowski, W. Olson, D. Rosen, J. Smit, A. F. A. Straight, A. F. Vollger, M. R. Wheeler, T. Schatz, M. Eichler, E. Phillippy, A. M. Timp, W. Miga, K. H. O'Neill, R. J. 2021-07-12 doi:10.1101/2021.07.12.451456 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Pparα and fatty acid oxidation coordinate hepatic transcriptional architecture ]]> https://biorxiv.org/content/10.1101/2021.07.12.451949v1?rss=1 Cavagnini, K. S. Wolfgang, M. J. 2021-07-12 doi:10.1101/2021.07.12.451949 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Complete genomic and epigenetic maps of human centromeres ]]> https://biorxiv.org/content/10.1101/2021.07.12.452052v1?rss=1 Altemose, N. Logsdon, G. Bzikadze, A. V. Sidhwani, P. Langley, S. A. Caldas, G. V. Hoyt, S. J. Uralsky, L. Ryabov, F. D. Shew, C. Sauria, M. E. G. Borchers, M. Gershman, A. Mikheenko, A. Shepelev, V. A. Dvorkina, T. Kunyavskaya, O. Vollger, M. R. Rhie, A. McCartney, A. M. Asri, M. Lorig-Roach, R. Shafin, K. Aganezov, S. Olson, D. Gomes de Lima, L. Potapova, T. Hartley, G. A. Haukness, M. Kerpedjiev, P. Gusev, F. Tigyi, K. Brooks, S. Y. Young, A. Nurk, S. Koren, S. Salama, S. Paten, B. Rogaev, E. I. Streets, A. M. Karpen, G. H. Dernburg, A. Sullivan, B. 2021-07-13 doi:10.1101/2021.07.12.452052 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ A complete reference genome improves analysis of human genetic variation ]]> https://biorxiv.org/content/10.1101/2021.07.12.452063v1?rss=1 Aganezov, S. Yan, S. M. Soto, D. C. Kirsche, M. Zarate, S. Avdeyev, P. Taylor, D. J. Shafin, K. Shumate, A. Xiao, C. Wagner, J. McDaniel, J. Olson, N. D. Sauria, M. E. G. Vollger, M. R. Rhie, A. Meredith, M. Martin, S. Lee, J. Koren, S. Rosenfeld, J. Paten, B. Layer, R. Chin, C.-S. Sedlazeck, F. J. Hansen, N. F. Miller, D. E. Phillippy, A. M. Miga, K. H. McCoy, R. C. Dennis, M. Y. Zook, J. M. Schatz, M. C. 2021-07-13 doi:10.1101/2021.07.12.452063 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing ]]> https://biorxiv.org/content/10.1101/2021.07.13.451380v1?rss=1 Dahn, H. A. Mountcastle, J. Balacco, J. Winkler, S. Bista, I. Schmitt, A. D. Vinnere Pettersson, O. Formenti, G. Oliver, K. Smith, M. Tan, W. Kraus, A. Mac, S. Komoroske, L. M. Lama, T. Crawford, A. J. Murphy, R. W. Brown, S. Scott, A. F. Morin, P. A. Jarvis, E. D. Fedrigo, O. 2021-07-14 doi:10.1101/2021.07.13.451380 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Single Serine on TSC2 Exerts Biased Control over mTORC1 Activation by ERK1/2 but Not Akt ]]> https://biorxiv.org/content/10.1101/2021.07.13.452249v1?rss=1 Dunkerly-Eyring, B. L. Pinilla-Vera, M. McKoy, D. Mishra, S. Grajeda Martinez, M. I. Oeing, C. U. Ranek, M. J. Kass, D. A. 2021-07-14 doi:10.1101/2021.07.13.452249 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis ]]> https://biorxiv.org/content/10.1101/2021.07.14.452380v1?rss=1 Bhan, N. J. Castinado, A. Glaser, J. I. Kalhor, R. K. Strutz, J. Boyden, E. Church, G. Kording, K. P. Tyo, K. 2021-07-14 doi:10.1101/2021.07.14.452380 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria ]]> https://biorxiv.org/content/10.1101/2021.07.15.452266v1?rss=1 Pudlo, N. A. Urs, K. Crawford, R. Pirani, A. Atherly, T. Jimenez, R. Terrapon, N. Henrissat, B. Peterson, D. A. Ziemer, C. Snitkin, E. S. Martens, E. 2021-07-15 doi:10.1101/2021.07.15.452266 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Classification of Free-Living Body Posture with ECG Patch Accelerometers: Application to the Multicenter AIDS Cohort Study ]]> https://biorxiv.org/content/10.1101/2021.07.16.452654v1?rss=1 Etzkorn, L. H. Heravi, A. S. Wu, K. C. Post, W. S. Urbanek, J. K. Crainiceanu, C. 2021-07-16 doi:10.1101/2021.07.16.452654 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Knockout of E-cadherin in adult mouse epithelium results in emphysema and airway disease ]]> https://biorxiv.org/content/10.1101/2021.07.18.452342v1?rss=1 Ghosh, B. Loube, J. Thapa, S. Capodanno, E. Mahmud, S. Girgis, M. Chen, S. Nishida, K. Ying, L. Swaby, C. Wally, A. Bhowmik, D. R. Zaykaner, M. E. Mitzner, W. Sidhaye, V. K. 2021-07-18 doi:10.1101/2021.07.18.452342 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Cardiac-generated sympathetic stress alters heart-brain communication, reduces EEG-theta activity, and increases locomotor behavior ]]> https://biorxiv.org/content/10.1101/2021.07.19.452502v1?rss=1 Agrimi, J. Menicucci, D. Laurino, M. Mackey, C. Hasnain, L. Dodaballapur, S. McDevit, R. A. Hoover, D. B. Gemignani, A. Paolocci, N. Lakatta, E. G. 2021-07-20 doi:10.1101/2021.07.19.452502 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus ]]> https://biorxiv.org/content/10.1101/2021.07.20.453090v1?rss=1 Herb, B. Glover, H. J. Bhaduri, A. Casella, A. M. Bale, T. L. Kriegstein, A. Doege, C. Ament, S. A. 2021-07-20 doi:10.1101/2021.07.20.453090 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Widespread germline genetic heterogeneity of human ribosomal RNA genes ]]> https://biorxiv.org/content/10.1101/2021.07.21.453267v1?rss=1 Fan, W. Eklund, E. Sherman, R. M. Liu, H. Pitts, S. Ford, B. NV, R. Laiho, M. 2021-07-25 doi:10.1101/2021.07.21.453267 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Effects of reward history on decision-making and movement vigor ]]> https://biorxiv.org/content/10.1101/2021.07.22.453376v1?rss=1 Sukumar, S. Shadmehr, R. Ahmed, A. A. 2021-07-23 doi:10.1101/2021.07.22.453376 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Functional connectomics spanning multiple areas of mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2021.07.28.454025v1?rss=1 MICrONs Consortium, Bodor, A. L. Halageri, A. Sterling, A. Tolias, A. S. Ramos, A. Nehoran, B. Silverman, B. Celii, B. Smith, C. L. Schneider-Mizell, C. M. Jordan, C. Xu, C. Papadopoulos, C. Gamlin, C. Kapner, D. Bumbarger, D. J. Brittain, D. Yatsenko, D. Walker, E. Y. Miranda, E. Froudarakis, E. Mitchell, E. Cobos, E. Sinz, F. H. Ye, F. Collman, F. Mahalingam, G. Williams, G. Seung, H. S. Bae, J. A. Reimer, J. Hebditch, J. Gager, J. Wu, J. Buchanan, J. Kuehner, K. Li, K. Lee, K. Willie, K. Elabbady, L. Baptiste, M. Castro, M. A. Takeno, M. Moore, 2021-07-29 doi:10.1101/2021.07.28.454025 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Pharmacokinetics and biodistribution of extracellular vesicles administered intravenously and intranasally to Macaca nemestrina ]]> https://biorxiv.org/content/10.1101/2021.07.28.454192v1?rss=1 Driedonks, T. Jiang, L. Carlson, B. Han, Z. Liu, G. Queen, S. E. Shirk, E. N. Gololobova, O. Nyberg, L. Lima, G. Schonvisky, K. Stover, M. Guerrero-Martin, S. Richardson, M. R. Smith, B. Lai, C. P. Izzi, J. M. Hutchinson, E. K. Pate, K. A. Witwer, K. W. 2021-07-29 doi:10.1101/2021.07.28.454192 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Keratin 19 interacts with GSK3β to regulate its nuclear accumulation and degradation of cyclin D3 ]]> https://biorxiv.org/content/10.1101/2021.07.28.454205v1?rss=1 Sharma, P. Tiufekchiev, S. Lising, V. Chung, S. W. Suk, J. S. Chung, B. M. 2021-07-28 doi:10.1101/2021.07.28.454205 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ TREM2 interacts with TDP-43 and mediates microglial neuroprotection against TDP-43-related neurodegeneration ]]> https://biorxiv.org/content/10.1101/2021.07.28.454242v1?rss=1 Xie, M. Liu, Y. U. Zhao, S. Zhang, L. Bosco, D. B. Pang, Y.-P. Zhong, J. Sheth, U. Martens, Y. A. Zhao, N. Liu, C.-C. Zhuang, Y. Wang, L. Dickson, D. W. Mattson, M. P. Bu, G. Wu, L.-J. 2021-07-29 doi:10.1101/2021.07.28.454242 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ The META tool optimizes metagenomic analyses across sequencing platforms and classifiers. ]]> https://biorxiv.org/content/10.1101/2021.07.29.454031v1?rss=1 Player, R. A. Aguinaldo, A. M. Merritt, B. B. Maszkiewicz, L. N. Adeyemo, O. E. Forsyth, E. R. Verratti, K. J. Chee, B. W. Grady, S. L. Bradburne, C. E. 2021-07-29 doi:10.1101/2021.07.29.454031 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ The role of the atypical chemokine receptor CCRL2 in myelodysplastic syndrome and secondary acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2021.07.29.454394v1?rss=1 KARANTANOS, T. Teodorescu, P. Perkins, B. Christodolou, I. Esteb, C. Varadhan, R. Helmenstine, E. Rajkhowa, T. Paun, B. Bonifant, C. Dalton, W. B. Gondek, L. P. Moliterno, A. R. Levis, M. J. Ghiaur, G. Jones, R. J. 2021-07-30 doi:10.1101/2021.07.29.454394 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina. ]]> https://biorxiv.org/content/10.1101/2021.07.31.454200v1?rss=1 Lyu, P. Hoang, T. Santiago, C. P. Thomas, E. Timms, A. Appel, H. Gimmen, M. Le, N. Jiang, L. Kim, D. W. Chen, S. Espinoza, D. Tegler, A. Weir, K. Clark, B. Cherry, T. M. Qian, J. Blackshaw, S. 2021-08-02 doi:10.1101/2021.07.31.454200 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk. ]]> https://biorxiv.org/content/10.1101/2021.07.31.454254v1?rss=1 Thomas, E. D. Timms, A. E. Giles, S. Harkins-Perry, S. Lyu, P. Hoang, T. Qian, J. Jackson, V. Bahlo, M. Blackshaw, S. Friedlander, M. Eade, K. Cherry, T. J. 2021-08-02 doi:10.1101/2021.07.31.454254 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ The CHK-2 antagonizing phosphatase PPM-1.D regulates meiotic entry via catalytic and non-catalytic activities ]]> https://biorxiv.org/content/10.1101/2021.08.02.453806v1?rss=1 Baudrimont, A. Paouneskou, D. Mohammad, A. Lichtenberger, R. Blundon, J. Kim, Y. Hartl, M. Falk, S. Schedl, T. Jantsch, V. 2021-08-02 doi:10.1101/2021.08.02.453806 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Gene-dependent yeast cell death pathway requires AP-3 vesicle trafficking leading to vacuole membrane permeabilization ]]> https://biorxiv.org/content/10.1101/2021.08.02.454728v1?rss=1 Stolp, Z. D. Kulkarni, M. Liu, Y. Zhu, C. Jalisi, A. Lin, S. Casadevall, A. Cunningham, K. W. Pineda, F. J. Teng, X. Hardwick, J. M. 2021-08-03 doi:10.1101/2021.08.02.454728 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Dynamic Cognitive States Predict Individual Variability in Behavior and Modulate with EEG Functional Connectivity during Working Memory ]]> https://biorxiv.org/content/10.1101/2021.08.02.454757v1?rss=1 Beauchene, C. Hinault, T. T. Sarma, S. Courtney, S. 2021-08-04 doi:10.1101/2021.08.02.454757 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Transcriptome Profiles of Anopheles gambiae Harboring Natural Low-Level Plasmodium Infection Reveal Adaptive Advantages for the Mosquito ]]> https://biorxiv.org/content/10.1101/2021.08.02.454766v1?rss=1 Carr, A. L. Rinker, D. Dong, Y. Dimopoulos, G. Zwiebel, L. 2021-08-02 doi:10.1101/2021.08.02.454766 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Genetic screens identify connections between ribosome recycling and nonsense mediated decay ]]> https://biorxiv.org/content/10.1101/2021.08.03.454884v1?rss=1 D'Orazio, K. N. Lessen, L. N. Veltri, A. J. Neiman, Z. Pacheco, M. E. Loll-Krippleber, R. Brown, G. W. Green, R. 2021-08-03 doi:10.1101/2021.08.03.454884 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Cross-organ transcriptomic comparison reveals universal factors during maturation ]]> https://biorxiv.org/content/10.1101/2021.08.03.454962v1?rss=1 Kambhampati, S. Murphy, S. A. Uosaki, H. Kwon, C. 2021-08-04 doi:10.1101/2021.08.03.454962 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ VistoSeg: a MATLAB pipeline to process, analyze and visualize high resolution histology images for Visium spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2021.08.04.452489v1?rss=1 Tippani, M. Divecha, H. R. Catallini, J. L. Weber, L. M. Spangler, A. Jaffe, A. E. Hicks, S. C. Martinowich, K. Collado-Torres, L. Page, S. C. Maynard, K. R. 2021-08-06 doi:10.1101/2021.08.04.452489 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ The lesser Pacific striped octopus, Octopus chierchiae: an emerging laboratory model for the study of octopuses ]]> https://biorxiv.org/content/10.1101/2021.08.04.455148v1?rss=1 Grearson, A. G. Dugan, A. Sakmar, T. Dolen, G. Gire, D. H. Sivitilli, D. M. Niell, C. Caldwell, R. L. Wang, Z. Y. Grasse, B. 2021-08-06 doi:10.1101/2021.08.04.455148 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Large field-of-view incoherent volumetric imaging in living human retina by confocal oblique scanning laser ophthalmoscopy ]]> https://biorxiv.org/content/10.1101/2021.08.05.455286v1?rss=1 20{degrees} viewing angle within only 5 seconds. The depth resolution is [~]45 microns in vivo. We demonstrated label-free incoherent contrast by CoSLO, revealing unique features in the retina. CoSLO will be an important technique for clinical care of retinal conditions and fundamental vision science, by offering unique volumetric incoherent contrasts. ]]> Shao, W. Yi, J. 2021-08-06 doi:10.1101/2021.08.05.455286 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs ]]> https://biorxiv.org/content/10.1101/2021.08.06.455336v1?rss=1 Cook, A. L. Wyhs, N. Sur, S. B. Ptak, B. Popoli, M. Dobbyn, L. Papadopoulos, T. Bettegowda, C. Papadopoulos, N. Vogelstein, B. Zhou, S. Kinzler, K. W. 2021-08-08 doi:10.1101/2021.08.06.455336 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Modeling bottlenecks, modularity, and context-dependency in behavioral control ]]> https://biorxiv.org/content/10.1101/2021.08.06.455452v1?rss=1 Nande, A. Dubinkina, V. Ravasio, R. Zhang, G. Berman, G. J. 2021-08-08 doi:10.1101/2021.08.06.455452 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ In vitro activity of bedaquiline and imipenem against actively growing, nutrient-starved, and intracellular Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2021.08.06.455495v1?rss=1 Martins, O. Ammerman, N. Lee, J. Kaushik, A. Dooley, K. E. Nuermberger, E. 2021-08-09 doi:10.1101/2021.08.06.455495 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole Genome Sequencing ]]> https://biorxiv.org/content/10.1101/2021.08.09.455584v1?rss=1 Pham, M.-T. N. Gupta, H. Gupta, A. Vaghasia, A. Skaist, A. Garrison, M. A. Coulter, J. B. Haffner, M. C. Wheelan, S. J. Isaacs, W. Nelson, W. Yegnasubramanian, S. 2021-08-10 doi:10.1101/2021.08.09.455584 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Noncanonical Notch signals have opposing roles during cardiac development ]]> https://biorxiv.org/content/10.1101/2021.08.09.455692v1?rss=1 Miyamoto, M. Andersen, P. Sulistio, E. Liu, X. Murphy, S. Kannan, S. Nam, L. Miyamoto, W. Tampakakis, E. Hibino, N. Uosaki, H. Kwon, C. 2021-08-09 doi:10.1101/2021.08.09.455692 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria ]]> https://biorxiv.org/content/10.1101/2021.08.11.455919v1?rss=1 Wang, L. T. Hurlburt, N. K. Schon, A. Flynn, B. J. Pereira, L. S. Dillon, M. Flores-Garcia, Y. Bonilla, B. Zavala, F. Idris, A. H. Francica, J. R. Pancera, M. Seder, R. A. 2021-08-11 doi:10.1101/2021.08.11.455919 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ cDNA-detector: Detection and removal of cDNA contamination in DNA sequencing libraries ]]> https://biorxiv.org/content/10.1101/2021.08.11.455962v1?rss=1 Qi, M. Nayar, U. Ludwig, L. Wagle, N. Rheinbay, E. 2021-08-12 doi:10.1101/2021.08.11.455962 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Association between Neighborhood Socioeconomic Status and Executive System Activation in Youth ]]> https://biorxiv.org/content/10.1101/2021.08.12.454903v1?rss=1 Murtha, K. A. Larsen, B. Pines, A. R. Parkes, L. M. Moore, T. M. Adebimpe, A. Alexander-Bloch, A. Calkins, M. E. Davila, D. G. Lindquist, M. A. Mackey, A. P. Roalf, D. R. Scott, J. C. Wolf, D. H. Gur, R. C. Gur, R. E. Barzilay, R. A. Satterthwaite, T. D. 2021-08-17 doi:10.1101/2021.08.12.454903 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Two parallel sRNA amplification cycles contribute to RNAi inheritance in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.08.13.456232v1?rss=1 Ouyang, J. P. T. Zhang, W. Seydoux, G. 2021-08-13 doi:10.1101/2021.08.13.456232 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Ribosome collisions in bacteria promote ribosome rescue by triggering mRNA cleavage by SmrB ]]> https://biorxiv.org/content/10.1101/2021.08.16.456513v1?rss=1 Saito, K. Kratzat, H. Campbell, A. Buschauer, R. Burroughs, A. M. Berninghausen, O. Aravind, L. Beckmann, R. Green, R. Buskirk, A. R. 2021-08-16 doi:10.1101/2021.08.16.456513 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ A user-friendly tool for cloud-based whole slide image segmentation, with examples from renal histopathology ]]> https://biorxiv.org/content/10.1101/2021.08.16.456524v1?rss=1 Lutnick, B. R. Manthey, D. Becker, J. U. Ginley, B. Moos, K. Zuckerman, J. E. Rodrigues, L. Gallan, A. J. Barisoni, L. Alpers, C. E. Wang, X. Myakala, K. Jones, B. A. Levi, M. Kopp, J. B. Yoshida, T. Han, S. S. Jain, S. Rosenberg, A. Z. Jen, K. Y. Sarder, P. Kidney Precision Medicine Project, 2021-08-17 doi:10.1101/2021.08.16.456524 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Age-related Immune-Stromal Networks Inhibit Response to Regenerative Immunotherapies ]]> https://biorxiv.org/content/10.1101/2021.08.17.456641v1?rss=1 Han, J. Cherry, C. Ruta, A. Maestas, D. R. Mejias, J. C. Nguyen, H. H. Fertig, E. J. Housseau, F. Ganguly, S. Moore, E. Tam, A. J. Pardoll, D. M. Elisseeff, J. H. 2021-08-18 doi:10.1101/2021.08.17.456641 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and non-functional ]]> https://biorxiv.org/content/10.1101/2021.08.18.456613v1?rss=1 Nissley, D. A. Jiang, Y. Trovato, F. Sitarik, I. Narayan, K. O'Brien, E. P. 2021-08-18 doi:10.1101/2021.08.18.456613 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ How synonymous mutations alter enzyme structure andfunction over long time scales ]]> https://biorxiv.org/content/10.1101/2021.08.18.456802v1?rss=1 Jiang, Y. Neti, S. S. Pradhan, P. Booker, S. J. O'Brien, E. P. 2021-08-18 doi:10.1101/2021.08.18.456802 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ The DNA sensors AIM2 and IFI16 are NET-binding SLE autoantigens ]]> https://biorxiv.org/content/10.1101/2021.08.19.456941v1?rss=1 Antiochos, B. Fenaroli, P. Rosenberg, A. Baer, A. Sohn, J. Li, J. Petri, M. Goldman, D. W. Mecoli, C. Casciola-Rosen, L. Rosen, A. 2021-08-19 doi:10.1101/2021.08.19.456941 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Fatty acid-binding proteins and fatty acid synthase influence glial reactivity and promote the formation of Müller glia-derived progenitor cells in the avian retina ]]> https://biorxiv.org/content/10.1101/2021.08.19.456977v1?rss=1 Campbell, W. A. Tangeman, A. El-Hodiri, H. Hawthorn, E. Hathoot, M. Hoang, T. Blackshaw, S. Fischer, A. J. 2021-08-19 doi:10.1101/2021.08.19.456977 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Optimized Data-Independent Acquisition Approach for Proteomic Analysis at Single-Cell Level ]]> https://biorxiv.org/content/10.1101/2021.08.19.457000v1?rss=1 Wang, Y. Lih, T.-S. M. Chen, L. Xu, Y. Kuczler, M. D. Cao, L. Pienta, K. J. Amend, S. R. Zhang, H. 2021-08-20 doi:10.1101/2021.08.19.457000 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Role of miR-181c in Diet-Induced Obesity Through Regulation of Lipid Synthesis in Liver ]]> https://biorxiv.org/content/10.1101/2021.08.20.457144v1?rss=1 Akiyoshi, K. Boersma, G. J. Johnson, M. D. Velasquez, F. C. Dunkerly-Eyring, B. OBrien, S. Yamaguchi, A. Steenbergen, C. Tamashiro, K. L. K. Das, S. 2021-08-20 doi:10.1101/2021.08.20.457144 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Upstrap for estimating power and sample size in complex models ]]> https://biorxiv.org/content/10.1101/2021.08.21.457220v1?rss=1 Karas, M. Crainiceanu, C. 2021-08-23 doi:10.1101/2021.08.21.457220 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Yersinia pseudotuberculosis YopE prevents uptake by M cells and instigates M cell extrusion in human ileal enteroid-derived monolayers. ]]> https://biorxiv.org/content/10.1101/2021.08.23.457340v1?rss=1 Fasciano, A. C. Dasanayake, G. S. Estes, M. K. Zachos, N. C. Breault, D. T. Isberg, R. R. Tan, S. Mecsas, J. 2021-08-23 doi:10.1101/2021.08.23.457340 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ FtsN activates septal cell wall synthesis by forming a processive complex with the septum-specific peptidoglycan synthase in E. coli ]]> https://biorxiv.org/content/10.1101/2021.08.23.457437v1?rss=1 Lyu, Z. Yahashiri, A. Yang, X. McCausland, J. W. Kaus, G. M. McQuillen, R. Weiss, D. S. Xiao, J. 2021-08-24 doi:10.1101/2021.08.23.457437 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export ]]> https://biorxiv.org/content/10.1101/2021.08.24.457459v1?rss=1 Duan, L. Zaepfel, B. Aksenova, V. Dasso, M. Rothstein, J. Kalab, P. Hayes, L. R. 2021-08-24 doi:10.1101/2021.08.24.457459 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Reading Modality Modifies Reading Network: Insights from Neural basis of Braille in Proficient Blind Readers ]]> https://biorxiv.org/content/10.1101/2021.08.24.457544v1?rss=1 Tian, M. Saccone, E. J. Kim, J. S. Kanjlia, S. Bedny, M. 2021-08-25 doi:10.1101/2021.08.24.457544 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Cell competition between wild-type and JAK2V617F mutant cells prevents disease relapse after stem cell transplantation in a murine model of myeloproliferative neoplasm ]]> https://biorxiv.org/content/10.1101/2021.08.24.457589v1?rss=1 Zhang, H. Castiglione, M. Zheng, L. Zhan, H. 2021-08-26 doi:10.1101/2021.08.24.457589 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The cyclin Cln1 controls polyploid titan cell formation following a stress-induced G2 arrest in Cryptococcus ]]> https://biorxiv.org/content/10.1101/2021.08.24.457603v1?rss=1 Altamirano, S. Li, Z. Fu, M. S. Ding, M. Fulton, S. R. Yoder, J. M. Tran, V. Nielsen, K. 2021-08-25 doi:10.1101/2021.08.24.457603 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ The indoleamine 2,3 dioxygenase pathway drives intratumoral B cell maintenance. ]]> https://biorxiv.org/content/10.1101/2021.08.25.456776v1?rss=1 Johnson, B. A. Aragaki, A. K. Williams, D. M. Rogers, O. Mountain, J. Luo, L. Zhang, W. Xian, L. Feng, M. Chia, L. Dordai, D. Hahn, N. M. Desiderio, S. Johnson, T. S. McConkey, D. J. Resar, L. M. S. 2021-08-27 doi:10.1101/2021.08.25.456776 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Identifying Gene-wise Differences in Latent Space Projections Across Cell Types and Species in Single Cell Data using scProject ]]> https://biorxiv.org/content/10.1101/2021.08.25.457650v1?rss=1 Baraban, A. Clark, B. S. Slosberg, J. Fertig, E. J. Goff, L. A. Stein-O'Brien, G. 2021-08-27 doi:10.1101/2021.08.25.457650 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ A novel multifunctional role for Hsp70 in binding post-translational modifications on clients ]]> https://biorxiv.org/content/10.1101/2021.08.25.457671v1?rss=1 Nitika, Zheng, B. Ruan, L. Kline, J. Sikora, J. Torres, M. T. Wang, Y. Takakuwa, J. Huguet, R. Klemm, C. Segarra, V. A. Winters, M. Pryciak, P. Thorpe, P. H. Tatebayashi, K. Li, R. Fornelli, L. Truman, A. 2021-08-25 doi:10.1101/2021.08.25.457671 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Cryptococcus neoformans melanization incorporates multiple catecholamines to produce polytypic melanin ]]> https://biorxiv.org/content/10.1101/2021.08.26.457838v1?rss=1 Baker, R. P. Chrissian, C. Stark, R. E. Casadevall, A. 2021-08-27 doi:10.1101/2021.08.26.457838 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ The Macromolecular MR Spectrum in Healthy Aging ]]> https://biorxiv.org/content/10.1101/2021.08.27.457961v1?rss=1 0.004). No differences were observed between sex groups. The voxels were segmented as 80 {+/-} 4% white matter, 18 {+/-} 4% gray matter, and 2 {+/-} 1% CSF for CSO and 28 {+/-} 4% white matter, 61 {+/-} 4% gray matter and 11 {+/-} 1% CSF for PCC. WM and GM showed a significant (p < 0.05) negative linear association with age in the WM-predominant CSO (R = -0.29) and GM-predominant PCC regions (R = -0.57) respectively while CSF increased significantly with age in both regions. ConclusionOur findings indicate that the MM spectrum is stable across a large age range and between sexes, suggesting a pre-defined MM basis function can be used for linear combination modeling of metabolite data from different age and sex groups. HighlightsO_LIA large publicly available MM-aging dataset is presented. C_LIO_LIMacromolecule signals do not change with age between 20 and 70. C_LIO_LIThere is no sex difference for macromolecule integrals. C_LI ]]> Hui, S. Gong, T. Zoellner, H. J. Song, Y. Murali-Manohar, S. Oeltzschner, G. Mikkelsen, M. Tapper, S. Chen, Y. Saleh, M. Porges, E. C. Chen, W. Wang, G. Edden, R. A. E. 2021-08-28 doi:10.1101/2021.08.27.457961 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood-brain barrier microvessels ]]> https://biorxiv.org/content/10.1101/2021.08.27.457975v1?rss=1 Linville, R. M. Sklar, M. B. Grifno, G. N. Nerenberg, R. F. Zhou, J. Ye, R. DeStefano, J. G. Guo, Z. Jha, R. Jamieson, J. J. Zhao, N. Searson, P. C. 2021-08-28 doi:10.1101/2021.08.27.457975 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification ]]> https://biorxiv.org/content/10.1101/2021.08.27.457982v1?rss=1 Voortman, L. Anderson, C. Urban, E. Yuan, M. Tran, S. Neuhaus-Follini, A. Derrick, J. Gregor, T. Johnston, R. J. 2021-08-28 doi:10.1101/2021.08.27.457982 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Frontal cortex activity underlying the production of diverse vocal signals during social communication in marmoset monkeys ]]> https://biorxiv.org/content/10.1101/2021.08.30.458300v1?rss=1 Zhao, L. Wang, X. 2021-08-31 doi:10.1101/2021.08.30.458300 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Stimulus degradation impairs performance in a rodent continuous performance test ]]> https://biorxiv.org/content/10.1101/2021.08.31.458320v1?rss=1 DeBrosse, A. C. Li, Y. Wiseman, R. Ross, R. Garrison, S. Hallock, H. L. Barrow, J. C. Martinowich, K. Carr, G. V. 2021-09-01 doi:10.1101/2021.08.31.458320 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ A terrain treadmill to study small animal locomotion through large obstacles ]]> https://biorxiv.org/content/10.1101/2021.08.31.458392v1?rss=1 Othayoth, R. Strebel, B. Han, Y. Francois, E. Li, C. 2021-09-01 doi:10.1101/2021.08.31.458392 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Sequential Transmission of Task-Relevant Information in Cortical Neuronal Networks ]]> https://biorxiv.org/content/10.1101/2021.08.31.458395v1?rss=1 Francis, N. Mukherjee, S. Kocillari, L. Panzeri, S. Babadi, B. Kanold, P. O. 2021-09-01 doi:10.1101/2021.08.31.458395 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Robust designation of meiotic crossover sites by CDK-2 through phosphorylation of the MutSγ complex ]]> https://biorxiv.org/content/10.1101/2021.08.31.458431v1?rss=1 Haversat, J. Woglar, A. Klatt, K. Akerib, C. C. Roberts, V. Salazar, C. C. Chen, S.-Y. Arur, S. Villeneuve, A. M. Kim, Y. 2021-09-01 doi:10.1101/2021.08.31.458431 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Prolonged tonic pain in healthy humans enhances functional connectivity of descending pain modulation networks involving the amygdala, periaqueductal gray and parabrachial nucleus to cortical sensory-discriminative areas ]]> https://biorxiv.org/content/10.1101/2021.08.31.458440v1?rss=1 pain d=0.25). sgACC-PAG FC became positively related to pain intensity (R=0.38; t=2.81; p=0.007). Right PBN-PAG FC during pain-free rest positively correlated with subsequently experienced pain (R=0.44; t=3.43; p=0.001). During tonic pain, FC of this connection was abolished (paired t=-3.17; p=0.0026). During pain-free rest, FC between left AMYG and right superior parietal lobule and caudate nucleus were positively correlated with subsequent pain. During tonic pain, FC between left AMYG and right inferior temporal and superior frontal gyri negatively correlated with pain. Subsequent pain positively correlated with right AMYG FC and right claustrum; left and right primary visual cortex; right middle temporal gyrus and right temporo-occipitoparietal junction. Finally, subsequent pain positively correlated with PAG FC and left cerebellum, left dorsolateral prefrontal, right posterior cingulate cortex and paracentral lobule, inferior parietal lobule, medial precuneus and PBN. ConclusionWe demonstrate 1) tonic pain weakly disrupts of sgACC-PAG FC; 2) sgACC-PAG tonic pain FC positively correlates with pain; 3) right PBN-PAG FC predicts subsequent pain and is abolished during tonic pain. Finally, we reveal PAG- and right AMYG-anchored networks which predict intensity of tonic pain. Our findings suggest specific connectivity patterns within the DPMN at rest predict experienced pain and are modulated by tonic pain. These nodes and their functional modulation may reveal new therapeutic targets for neuromodulation and biomarkers to guide interventions. HighlightsO_LIParabrachial-periaqueductal gray (PAG) functional connectivity (FC) predicts pain C_LIO_LISubgenual anterior cingulate cortex-PAG FC correlates with pain during tonic pain C_LIO_LIPAG- and amydalocortical networks at rest predict tonic pain intensity C_LIO_LIResting FC of PAG supports cortical targets of neuromodulation to control pain C_LI ]]> Meeker, T. J. Schmid, A.-C. Keaser, M. L. Khan, S. A. Gullapalli, R. P. Dorsey, S. G. Greenspan, J. D. Seminowicz, D. A. 2021-09-02 doi:10.1101/2021.08.31.458440 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model ]]> https://biorxiv.org/content/10.1101/2021.09.01.458491v1?rss=1 Wu, Y. Janmey, P. Sun, S. X. 2021-09-01 doi:10.1101/2021.09.01.458491 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning ]]> https://biorxiv.org/content/10.1101/2021.09.01.458493v1?rss=1 Mizusaki, B. E. P. Li, S. S. Y. Costa, R. P. Sjöström, J. 2021-09-01 doi:10.1101/2021.09.01.458493 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Wide-Angle, Monocular Head Tracking using Passive Markers ]]> https://biorxiv.org/content/10.1101/2021.09.01.458583v1?rss=1 Vagvolgyi, B. P. Jayakumar, R. P. Madhav, M. S. Knierim, J. J. Cowan, N. 2021-09-03 doi:10.1101/2021.09.01.458583 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Batch Effects are Causal Effects: Applications in Human Connectomics ]]> https://biorxiv.org/content/10.1101/2021.09.03.458920v1?rss=1 Bridgeford, E. W. Powell, M. Kiar, G. Lawrence, R. Caffo, B. Milham, M. Vogelstein, J. T. 2021-09-06 doi:10.1101/2021.09.03.458920 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Allosteric cooperation in β-lactam binding to a non-classical transpeptidase ]]> https://biorxiv.org/content/10.1101/2021.09.06.459080v1?rss=1 Ahmad, N. Kachhap, S. Chauhan, V. Juneja, P. Sharma, K. Bullen, C. K. Borowski, T. Bishai, W. R. Lamichhane, G. Kumar, P. 2021-09-06 doi:10.1101/2021.09.06.459080 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ A generalized cortical activity pattern at internally-generated mental context boundaries during unguided narrative recall ]]> https://biorxiv.org/content/10.1101/2021.09.07.459300v1?rss=1 Lee, H. Chen, J. 2021-09-08 doi:10.1101/2021.09.07.459300 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses ]]> https://biorxiv.org/content/10.1101/2021.09.08.459480v1?rss=1 He, W.-t. Musharrafieh, R. Song, G. Dueker, K. Callaghan, S. Yong, P. Beutler, N. Torres, J. L. Volk, R. M. Zhou, P. Yuan, M. Liu, H. Anzanello, F. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Wilson, I. A. Ward, A. B. Rogers, T. Burton, D. R. Andrabi, R. 2021-09-08 doi:10.1101/2021.09.08.459480 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ The language network supports both lexical access and sentence generation during language production ]]> https://biorxiv.org/content/10.1101/2021.09.10.459596v1?rss=1 Hu, J. Small, H. Kean, H. Takahashi, A. Zekelman, L. Kleinman, D. Ryan, E. Ferreira, V. Fedorenko, E. 2021-09-11 doi:10.1101/2021.09.10.459596 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ N-myc Downstream Regulated Gene 1 (NDRG1) functions as a molecular switch for cellular adaptation to hypoxia ]]> https://biorxiv.org/content/10.1101/2021.09.10.459675v1?rss=1 Park, J. S. Gabel, A. M. Kang, L. Canales, B. Kassir, P. Osei-Ntansah, A. Tran, N. D. Viswanathan, S. Lee, Y.-S. Brewster, R. 2021-09-10 doi:10.1101/2021.09.10.459675 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ A transcriptome atlas of the mouse iris at single cell resolution defines cell types and the genomic response to pupil dilation ]]> https://biorxiv.org/content/10.1101/2021.09.10.459739v1?rss=1 Nathans, J. 2021-09-11 doi:10.1101/2021.09.10.459739 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ iCn3D: from Web-based 3D Viewer to Structure Analysis Tool in Batch Mode ]]> https://biorxiv.org/content/10.1101/2021.09.10.459868v1?rss=1 Wang, J. Youkharibache, P. Marchler-Bauer, A. Lanczycki, C. Zhang, D. Lu, S. Madej, T. Marchler, G. H. Cheng, T. Chong, L. C. Zhao, S. Yang, K. Lin, J. Cheng, Z. Dunn, R. Malkaram, S. A. Tai, C.-H. Enoma, D. Busby, B. Johnson, N. Tabaro, F. Song, G. Ge, Y. 2021-09-11 doi:10.1101/2021.09.10.459868 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Hobotnica: exploring molecular signature quality ]]> https://biorxiv.org/content/10.1101/2021.09.12.459931v1?rss=1 Stupnikov, A. Sizykh, A. Favorov, A. Afsari, B. Wheelan, S. J. Marchionni, L. Medvedeva, Y. A. 2021-09-15 doi:10.1101/2021.09.12.459931 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants ]]> https://biorxiv.org/content/10.1101/2021.09.12.459978v1?rss=1 Yang, T.-J. Yu, P.-Y. Chang, Y.-C. Chang, N.-E. Tsai, Y.-X. Liang, K.-H. Draczkowski, P. Lin, B. Wang, Y.-S. Chien, Y.-C. Khoo, K.-H. Wu, H.-C. Hsu, S.-T. D. 2021-09-13 doi:10.1101/2021.09.12.459978 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Elevated levels of active Transforming Growth Factor β1 in the subchondral bone relate spatially to cartilage loss and impaired bone quality in human knee osteoarthritis ]]> https://biorxiv.org/content/10.1101/2021.09.13.459432v1?rss=1 Muratovic, D. Findlay, D. Quarrington, R. Cao, X. Solomon, B. Atkins, G. J. Kuliwaba, J. 2021-09-13 doi:10.1101/2021.09.13.459432 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Random Forest Factorization Reveals Latent Structure in Single Cell RNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/2021.09.13.460168v1?rss=1 Brenerman, B. M. Shapiro, B. Schatz, M. Battle, A. 2021-09-14 doi:10.1101/2021.09.13.460168 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Model-Based Meta-Analysis of Relapsing Mouse Model Studies from the Critical Path to Tuberculosis Drug Regimens Initiative Database ]]> https://biorxiv.org/content/10.1101/2021.09.13.460195v1?rss=1 Berg, A. Clary, J. Hanna, D. Nuermberger, E. Lenaerts, A. Ammerman, N. Ramey, M. E. Hartley, D. Hermann, D. 2021-09-15 doi:10.1101/2021.09.13.460195 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Naturalistic stimuli reveal a critical period in visual cortex development: Evidence from adult-onset blindness ]]> https://biorxiv.org/content/10.1101/2021.09.14.460305v1?rss=1 18 years-of-age, AB, n=14) and sighted (n=22) individuals. Participants listened to auditory excerpts from movies; a spoken narrative; and matched meaningless auditory stimuli (i.e., shuffled sentences, backwards speech) during fMRI scanning. These rich naturalistic stimuli made it possible to simultaneous engage a broad range of cognitive domains. We correlated the voxel-wise timecourses of different participants within each group. For all groups, all stimulus conditions induced synchrony in auditory cortex and for all groups only the narrative stimuli synchronized responses in higher-cognitive fronto-parietal and temporal regions. Inter-subject synchrony in visual cortices was high in the CB group for the movie and narrative stimuli but not for meaningless auditory controls. In contrast, visual cortex synchrony was equally low among AB and sighted blindfolded participants. Even many years of blindness in adulthood fail to enable responses to naturalistic auditory information in visual cortices of people who had sight as children. These findings suggest that cross-modal responses in visual cortex of people born blind reflect the plasticity of developing visual cortex during a sensitive period. ]]> Musz, E. Loiotile, R. E. Chen, J. Cusack, R. Bedny, M. 2021-09-15 doi:10.1101/2021.09.14.460305 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Proximal CA3 is the primary locus of age-related pattern separation deficits in rats ]]> https://biorxiv.org/content/10.1101/2021.09.14.460329v1?rss=1 Lee, H. Tilekeratne, A. Lukish, N. Wang, Z. Zeger, S. Gallagher, M. Knierim, J. J. 2021-09-16 doi:10.1101/2021.09.14.460329 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes ]]> https://biorxiv.org/content/10.1101/2021.09.15.460475v1?rss=1 Hunt, M. Letcher, B. Malone, K. M. Nguyen, G. Hall, M. B. Colquhoun, R. M. Lima, L. Schatz, M. Ramakrishnan, S. The CRyPTIC Consortium, Iqbal, Z. 2021-09-15 doi:10.1101/2021.09.15.460475 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Synchronous spiking of cerebellar Purkinje cells during control of movements ]]> https://biorxiv.org/content/10.1101/2021.09.16.460700v1?rss=1 Sedaghat-Nejad, E. Pi, J. Hage, P. Fakharian, M. A. Shadmehr, R. 2021-09-19 doi:10.1101/2021.09.16.460700 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies ]]> https://biorxiv.org/content/10.1101/2021.09.16.460702v1?rss=1 Ray, D. Vergara, C. I. Taub, M. I. Wojcik, G. L. Ladd-Acosta, C. Beaty, T. H. Duggal, P. 2021-09-20 doi:10.1101/2021.09.16.460702 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Two common and distinct forms of variation in human functional brain networks ]]> https://biorxiv.org/content/10.1101/2021.09.17.460799v1?rss=1 Dworetsky, A. Seitzman, B. A. Adeyemo, B. Smith, D. M. Petersen, S. E. Gratton, C. 2021-09-18 doi:10.1101/2021.09.17.460799 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Directing multicellular organization by varying the aspect ratio of soft hydrogel microwells ]]> https://biorxiv.org/content/10.1101/2021.09.17.460849v1?rss=1 Pahapale, G. J. Tao, J. Nikolic, M. Gao, S. Scarcelli, G. Sun, S. Romer, L. H. Gracias, D. H. 2021-09-20 doi:10.1101/2021.09.17.460849 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Anti-Bat Ultrasound Production in Moths is Globally and Phylogenetically Widespread ]]> https://biorxiv.org/content/10.1101/2021.09.20.460855v1?rss=1 Barber, J. R. Plotkin, D. Rubin, J. J. Homziak, N. T. Leavell, B. C. Houlihan, P. Miner, K. A. Breinholt, J. W. Quirk-Royal, B. Padron, P. S. Nunez, M. Kawahara, A. Y. 2021-09-22 doi:10.1101/2021.09.20.460855 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Progenitor-intrinsic Metabolic Sensing Promotes Hematopoietic Homeostasis ]]> https://biorxiv.org/content/10.1101/2021.09.20.461098v1?rss=1 Pizzato, H. A. Wang, Y. Wolfgang, M. Finck, B. Patti, G. J. Bhattacharya, D. 2021-09-20 doi:10.1101/2021.09.20.461098 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Methodological considerations in analyzing synchronization of resting-state brain networks with the intrinsic electrical rhythm of the stomach: Advantages of weighted phase-locking ]]> https://biorxiv.org/content/10.1101/2021.09.20.461120v1?rss=1 Choe, A. S. Tang, B. Smith, K. Honari, H. Lindquist, M. A. Caffo, B. S. Pekar, J. J. 2021-09-21 doi:10.1101/2021.09.20.461120 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ What is unique about the human eye? Comparative image analysis on the external eye morphology of human and nonhuman great apes ]]> https://biorxiv.org/content/10.1101/2021.09.21.461196v1?rss=1 Kano, F. Furuichi, T. Hashimoto, C. Krupenye, C. Leinwand, J. G. Hopper, L. M. Martin, C. F. Otsuka, R. Tajima, T. 2021-09-21 doi:10.1101/2021.09.21.461196 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal-macrophage interaction ]]> https://biorxiv.org/content/10.1101/2021.09.21.461206v1?rss=1 Jung, E. H. Park, Y.-D. Dragotakes, Q. Ramirez, L. S. Smith, D. F. Dziedzic, A. Williamson, P. R. Jedlicka, A. Casadevall, A. Coelho, C. 2021-09-21 doi:10.1101/2021.09.21.461206 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Neural signatures of compression in the retelling of past events ]]> https://biorxiv.org/content/10.1101/2021.09.21.461232v1?rss=1 Musz, E. Chen, J. 2021-09-24 doi:10.1101/2021.09.21.461232 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ How Our Cells Become Our Selves: The Cellular Phylodynamic Biology of Growth and Development ]]> https://biorxiv.org/content/10.1101/2021.09.22.461268v1?rss=1 Chodrow, P. Su, J. Lee, D. Ahmed, T. He, N. De Man, R. Tiwari, A. Mannherz, W. Citi, L. DiCorpo, D. Michaelson, J. S. 2021-09-24 doi:10.1101/2021.09.22.461268 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Improved antibody structure prediction by deep learning of side chain conformations ]]> https://biorxiv.org/content/10.1101/2021.09.22.461349v1?rss=1 Akpinaroglu, D. Ruffolo, J. A. Mahajan, S. P. Gray, J. J. 2021-09-22 doi:10.1101/2021.09.22.461349 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Engineering CAR-NK cells to secrete IL15 sustains their anti-AML functionality, but is associated with systemic toxicities ]]> https://biorxiv.org/content/10.1101/2021.09.23.461509v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@4d09eaorg.highwire.dtl.DTLVardef@1c61411org.highwire.dtl.DTLVardef@14f8097org.highwire.dtl.DTLVardef@8375ac_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefSecretion of IL15 from anti-CD123.2B4.CD3{zeta} CAR-NK cells enhances their activation and killing potential against Acute Myelogenous Leukemia, but carries the risk of severe systemic toxicity. ]]> Christodoulou, I. Ho, W. J. Marple, A. Ravich, J. W. Tam, A. Rahnama, R. Fearnow, A. Rietberg, C. Yanik, S. Solomou, E. E. Varadhan, R. Koldobskiy, M. A. Bonifant, C. L. 2021-09-24 doi:10.1101/2021.09.23.461509 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Satellite glia are essential modulators of sympathetic neuron survival, activity, and autonomic function ]]> https://biorxiv.org/content/10.1101/2021.09.23.461591v1?rss=1 Mapps, A. Boehm, E. Beier, C. Keenan, W. T. Langel, J. Liu, M. Hattar, S. Zhao, H. Tampakakis, E. Kuruvilla, R. 2021-09-23 doi:10.1101/2021.09.23.461591 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ UCHL1 inhibited by A1 astrocytes facilitates aggregates clearance to promote neural stem cells activation after spinal cord injury ]]> https://biorxiv.org/content/10.1101/2021.09.23.461600v1?rss=1 Ding, L. Chu, W. Xia, Y. Li, T. Shi, M. Zhou, F.-Q. Deng, Y. 2021-09-24 doi:10.1101/2021.09.23.461600 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Myofibril orientation as a metric for characterizing heart disease ]]> https://biorxiv.org/content/10.1101/2021.09.24.461697v1?rss=1 Ma, W. Gong, H. Jani, V. Landim-Vieira, M. Papadaki, M. Pinto, J. Aslam, M. I. Cammarato, A. Irving, T. 2021-09-25 doi:10.1101/2021.09.24.461697 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Tuning in scene-preferring cortex for mid-level visual features gives rise to selectivity across multiple levels of stimulus complexity ]]> https://biorxiv.org/content/10.1101/2021.09.24.461733v1?rss=1 Li, S. P. D. Bonner, M. F. 2021-09-25 doi:10.1101/2021.09.24.461733 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design ]]> https://biorxiv.org/content/10.1101/2021.09.27.462000v1?rss=1 Adolf-Bryfogle, J. Labonte, J. W. Kraft, J. C. Shapavolov, M. Raemisch, S. Lutteke, T. Dimaio, F. Bahl, C. D. Pallesen, J. King, N. P. Gray, J. J. Kulp, D. W. Schief, W. R. 2021-09-27 doi:10.1101/2021.09.27.462000 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ The DarTG toxin-antitoxin system provides phage defense by ADP-ribosylating viral DNA ]]> https://biorxiv.org/content/10.1101/2021.09.27.462013v1?rss=1 LeRoux, M. Srikant, S. Littlehale, M. L. Teodoro, G. Doron, S. Badiee, M. Leung, A. Sorek, R. Laub, M. T. 2021-09-27 doi:10.1101/2021.09.27.462013 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Direct quantification of ligand-induced lipid and protein microdomains with distinctive signaling properties ]]> https://biorxiv.org/content/10.1101/2021.09.28.462247v1?rss=1 Wirth, D. Paul, M. Pasquale, E. B. Hristova, K. 2021-09-30 doi:10.1101/2021.09.28.462247 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ A Pre-Processing Pipeline to Quantify, Visualize andReduce Technical Variation in Protein Microarray ]]> https://biorxiv.org/content/10.1101/2021.09.29.461966v1?rss=1 Berube, S. Kobayashi, T. Wesolowski, A. Norris, D. E. Ruczinski, I. Moss, W. J. Louis, T. A. 2021-10-01 doi:10.1101/2021.09.29.461966 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A gut commensal niche regulates stable association of a multispecies microbiota ]]> https://biorxiv.org/content/10.1101/2021.09.30.462663v1?rss=1 Dodge, R. Jones, E. W. Zhu, H. Obadia, B. Martinez, D. J. Wang, C. Aranda-Diaz, A. Aumiller, K. Liu, Z. Voltolini, M. Brodie, E. L. Huang, K. C. Carlson, J. M. Sivak, D. A. Spradling, A. C. Ludington, W. B. 2021-09-30 doi:10.1101/2021.09.30.462663 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors ]]> https://biorxiv.org/content/10.1101/2021.10.01.462481v1?rss=1 Angkeow, J. W. Monaco, D. R. Chen, A. Venkataraman, T. Jayaraman, S. Valencia, C. Sie, B. M. Liechti, T. Farhadi, P. N. Funez-dePagnier, G. Sherman-Baust, C. A. Wong, M. Q. Sears, C. L. Simner, P. J. Round, J. L. Duggal, P. Laserson, U. Steiner, T. S. Sen, R. Lloyd, T. E. Roederer, M. Mammen, A. L. Longman, R. S. Rider, L. G. Larman, H. B. 2021-10-02 doi:10.1101/2021.10.01.462481 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Mechanical Compression Creates a Quiescent Muscle Stem Cell Niche ]]> https://biorxiv.org/content/10.1101/2021.10.02.462865v1?rss=1 Tao, J. Choudhury, M. I. Maity, D. Kim, T. Sun, S. Fan, C.-M. 2021-10-02 doi:10.1101/2021.10.02.462865 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Cockroaches adjust body and appendages to traverse cluttered large obstacles ]]> https://biorxiv.org/content/10.1101/2021.10.02.462900v1?rss=1 Wang, Y. Othayoth, R. Li, C. 2021-10-04 doi:10.1101/2021.10.02.462900 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ The first transchromosomic rat model with human chromosome 21 shows robust Down syndrome features ]]> https://biorxiv.org/content/10.1101/2021.10.03.462958v1?rss=1 93% of its protein coding genes. RNA-Seq of neonatal forebrains demonstrates that TcHSA21rat not only expresses HSA21 genes but also has an imbalance in global gene expression. Using EGFP as a marker for trisomic cells, flow cytometry analyses of peripheral blood cells from 361 adult TcHSA21rat animals show that 81% of animals retain HSA21 in >80% of cells, the criterion for a "Down syndrome karyotype" in people. TcHSA21rat exhibits learning and memory deficits and shows increased anxiety and hyperactivity. TcHSA21rat recapitulates well-characterized DS brain morphology, including smaller brain volume and reduced cerebellar size. In addition, the rat model shows reduced cerebellar foliation, a prominent feature of DS that is not observed in DS mouse models. Moreover, TcHSA21rat exhibits anomalies in craniofacial morphology, heart development, husbandry, and stature. TcHSA21rat is a robust DS animal model that can facilitate DS basic research and provide a unique tool for preclinical validation to accelerate DS drug development. ]]> Kazuki, Y. Gao, F. J. Yamakawa, M. Hirabayashi, M. Kazuki, K. Kajitani, N. Miyagawa-Tomita, S. Abe, S. Sanbo, M. Hara, H. Kuniishi, H. Ichisaka, S. Hata, Y. Koshima, M. Takayama, H. Takehara, S. Nakayama, Y. Hiratsuka, M. Iida, Y. Matsukura, S. Noda, N. Li, Y. Moyer, A. J. Cheng, B. Singh, N. Richtsmeier, J. T. Oshimura, M. Reeves, R. H. 2021-10-04 doi:10.1101/2021.10.03.462958 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Ptbp1 deletion does not induce glia-to-neuron conversion in adult mouse retina and brain. ]]> https://biorxiv.org/content/10.1101/2021.10.04.462784v1?rss=1 Blackshaw, S. Hoang, T. Kim, D. W. Appel, H. Pannullo, N. Ozawa, M. Zheng, S. Yu, M. Peachey, N. Kim, J. 2021-10-05 doi:10.1101/2021.10.04.462784 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ NFkB-signaling suppresses Müller glia-mediated neuron regeneration in the mammalian retina ]]> https://biorxiv.org/content/10.1101/2021.10.05.463152v1?rss=1 Palazzo, I. Todd, L. Hoang, T. V. Reh, T. A. Blackshaw, S. Fischer, A. J. 2021-10-07 doi:10.1101/2021.10.05.463152 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Silencing XIST on the future active X: Searching human and bovine preimplantation embryos for the repressor ]]> https://biorxiv.org/content/10.1101/2021.10.05.463256v1?rss=1 Aksit, M. A. Roelen, B. A. Yu, B. Migeon, B. R. 2021-10-07 doi:10.1101/2021.10.05.463256 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Global Dynamics as Communication Sensors in Peptide Synthetase Cyclization Domains. ]]> https://biorxiv.org/content/10.1101/2021.10.06.461881v1?rss=1 Mishra, S. H. Kancherla, A. K. Marincin, K. A. Bouvignies, G. Nerli, S. Sgourakis, N. Dowling, D. P. Frueh, D. P. 2021-10-07 doi:10.1101/2021.10.06.461881 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ High-throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain ]]> https://biorxiv.org/content/10.1101/2021.10.07.463234v1?rss=1 Dasovich, M. A. Zhou, J. Thomas, A. G. Goodman, J. A. McPherson, R. L. Jayabalan, A. K. Busa, V. F. Cheng, S.-J. Murphy, B. Redinger, K. R. Tsukamoto, T. Slusher, B. S. Bosch, J. Wei, J. Leung, A. 2021-10-07 doi:10.1101/2021.10.07.463234 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ scatterHatch: an R/Bioconductor package for colorblind accessible visualization of single-cell data ]]> https://biorxiv.org/content/10.1101/2021.10.07.463279v1?rss=1 Guha, T. Fertig, E. Deshpande, A. 2021-10-07 doi:10.1101/2021.10.07.463279 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ The Endosomal pH Regulator NHE9 is a Driver of Stemness in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.10.07.463493v1?rss=1 Ko, M. Makena, M. R. Schiapparelli, P. V. Suarez Meade, P. Mekile, A. X. Lal, B. Lopez-Bertoni, H. Laterra, J. Quinones-Hinojosa, A. Rao, R. 2021-10-07 doi:10.1101/2021.10.07.463493 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Non-invasive Imaging of Sense of Smell by Tracking the Voltage-Gated Sodium Channel NaV1.7 ]]> https://biorxiv.org/content/10.1101/2021.10.07.463532v1?rss=1 Adilbay, D. Gonzales, J. Demetrio de Souza Franca, P. Roberts, S. Patel, S. Viray, T. Chow, C. Y. King, G. F. Jain, S. K. Ordonez, A. A. Caroll, L. S. Pillarsetty, N. Reiner, T. 2021-10-08 doi:10.1101/2021.10.07.463532 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Learning from the physical consequences of our actions improves motor memory ]]> https://biorxiv.org/content/10.1101/2021.10.07.463541v1?rss=1 Bakkum, A. Marigold, D. S. 2021-10-09 doi:10.1101/2021.10.07.463541 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Human pluripotent stem cell-derived photoreceptors switch from cell autonomous axon extension to non-cell autonomous process pulling during synaptic marker redistribution. ]]> https://biorxiv.org/content/10.1101/2021.10.10.463810v1?rss=1 Rempel, S. K. Welch, M. J. Ludwig, A. L. Phillips, M. J. Kancherla, Y. Zack, D. Gamm, D. M. Gomez, T. M. 2021-10-10 doi:10.1101/2021.10.10.463810 Cold Spring Harbor Laboratory Press 2021-10-10 <![CDATA[ Whole genome sequence analysis of blood lipid levels in >66,000 individuals ]]> https://biorxiv.org/content/10.1101/2021.10.11.463514v1?rss=1 Selvaraj, M. S. Li, X. Li, Z. Pampana, A. Zhang, D. Y. Park, J. Aslibekyan, S. Bis, J. C. Brody, J. A. Cade, B. E. Chuang, L.-M. Chung, R.-H. Curran, J. E. de las Fuentes, L. de Vries, P. S. Duggirala, R. Freedman, B. I. Graff, M. Guo, X. Heard-Costa, N. Hidalgo, B. Hwu, C.-M. Irvin, M. R. Kelly, T. N. Kral, B. G. Lange, L. Li, X. Lisa, M. Lubitz, S. A. Manichaikul, A. W. Michael, P. Montasser, M. E. Morrison, A. C. Naseri, T. O'Connell, J. R. Palmer, N. D. Peyser, P. A. Reupena, M. S. Smith, J. A. Sun, X. Taylor, K. D. Tracy, R. P. Tsai, M. Y. Wang, 2021-10-12 doi:10.1101/2021.10.11.463514 66,000 individuals]]> Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Rare instances of non-random dropout with the monochrome multiplex qPCR assay for mitochondrial DNA copy number ]]> https://biorxiv.org/content/10.1101/2021.10.11.463983v1?rss=1 3 standard deviations below the sample mean, which corresponds to roughly 1% of assayed individuals (Figure 1). After examining whole genome sequencing data, this seems to be due to specific polymorphisms within the D-loop primer region, at positions MT 338, 340, 452, 457, 458, 460, 461, 466, and 467. All individuals with a variant in at least one of these positions have non-concordant mtDNA-CN measurements. Meanwhile, variants observed at other positions within the primer region do not appear to cause dropout. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/463983v1_fig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@134ca51org.highwire.dtl.DTLVardef@ce9196org.highwire.dtl.DTLVardef@1b82af6org.highwire.dtl.DTLVardef@c9701_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Discrepancy between the monochrome multiplex qPCR mtDNA-CN and the whole genome sequencing mtDNA-CN for 1,732 distinct individuals. Data are centered at 0 and scaled so that the standard deviation = 1. The dotted red line represents 3 standard deviations beneath the sample mean. Individuals in the U, L1, L4, and T haplogroups have a disproportionately higher risk of discordant measures between the two assays. C_FIG ]]> Yang, S. Y. Newcomb, C. E. Battle, S. L. Hsieh, A. Y. Chapman, H. L. Cote, H. C. Arking, D. E. 2021-10-11 doi:10.1101/2021.10.11.463983 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Tagging active neurons by soma-targeted Cal-Light ]]> https://biorxiv.org/content/10.1101/2021.10.13.464095v1?rss=1 Hyun, J. H. Nagahama, K. Namkung, H. Mignocchi, N. Hannan, P. Kruessel, S. Kwak, C. McElroy, A. Liu, B. Cui, M. Lee, S. Lee, D. Huganir, R. L. Sawa, A. Kwon, H. 2021-10-14 doi:10.1101/2021.10.13.464095 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Early life stress-induced vulnerability to postpartum mental disturbance: prolonged dysregulation of the HPA axis and behavior ]]> https://biorxiv.org/content/10.1101/2021.10.13.464258v1?rss=1 Niwa, M. Lockhart, S. Wood, D. J. Yang, K. Kin, K. Wand, G. S. Kano, S.-i. Payne, J. L. Sawa, A. 2021-10-13 doi:10.1101/2021.10.13.464258 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Regulation of Liver Regeneration by hepatocyte O-GlcNAcylation in mice ]]> https://biorxiv.org/content/10.1101/2021.10.14.464401v1?rss=1 Robarts, D. R. McGreal, S. R. Umbaugh, D. S. Parkes, W. S. Kotulkar, M. Abernathy, S. Lee, N. Jaeschke, H. Gunewardena, S. Whelan, S. A. Hanover, J. A. Zachara, N. E. Slawson, C. Apte, U. 2021-10-14 doi:10.1101/2021.10.14.464401 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Brain functional connectome defines a transdiagnostic dimension associated with cognition and psychopathology in youth ]]> https://biorxiv.org/content/10.1101/2021.10.14.464403v1?rss=1 Xiao, X. Hammond, C. J. Salmeron, B. J. Gu, H. Zhai, T. Nguyen, H. Lu, H. Ross, T. J. Yang, Y. 2021-10-16 doi:10.1101/2021.10.14.464403 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Alpha cell dysfunction in early type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.10.15.464545v1?rss=1 Doliba, N. Rozo, A. Roman, J. Qin, W. Traum, D. Gao, L. Liu, J. Manduchi, E. Liu, C. Golson, M. Vahedi, G. Naji, A. Matschinsky, F. Atkinson, M. Powers, A. Brissova, M. Kaestner, K. H. Stoffers, D. 2021-10-16 doi:10.1101/2021.10.15.464545 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Source-sink connectivity: a novel resting-state EEG marker of the epileptogenic zone ]]> https://biorxiv.org/content/10.1101/2021.10.15.464594v1?rss=1 Gunnarsdottir, K. M. Li, A. Smith, R. J. Kang, J.-Y. Crone, N. Korzeniewska, A. Rouse, A. G. Cameron, N. Cajigas, I. Inati, S. Zaghloul, K. A. Boerwinkle, V. Wyckoff, S. Barot, N. Elarjani, T. Bicchi, M. M. Gonzalez-Martinez, J. Sarma, S. V. 2021-10-18 doi:10.1101/2021.10.15.464594 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity ]]> https://biorxiv.org/content/10.1101/2021.10.15.464608v1?rss=1 Liu, H. Ling, W. Hua, X. Moon, J.-Y. Williams-Nguyen, J. S. Zhan, X. Plantinga, A. M. Zhao, N. Zhang, A. Knight, R. Qi, Q. Burk, R. D. Kaplan, R. C. Wu, M. C. 2021-10-16 doi:10.1101/2021.10.15.464608 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Amyloid-beta and tau pathologies are both necessary to induce novel stage-specific microglia subtypes during Alzheimer's disease progression. ]]> https://biorxiv.org/content/10.1101/2021.10.16.464454v1?rss=1 Kim, D. W. Tu, K. Wei, A. Lau, A. Gonzalez-Gil, A. Cao, T. Braunstein, K. Ling, J. P. Troncoso, J. C. Wong, P. C. Blackshaw, S. Schnaar, R. L. Li, T. 2021-10-16 doi:10.1101/2021.10.16.464454 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ The ASCC2 CUE domain contacts adjacent ubiquitins to recognize K63-linked polyubiquitin ]]> https://biorxiv.org/content/10.1101/2021.10.17.464694v1?rss=1 Lombardi, P. M. Haile, S. Rusanov, T. Rodell, R. Anoh, R. Baer, J. G. Burke, K. A. Gray, L. N. Hacker, A. R. Kebreau, K. R. Ngandu, C. K. Orland, H. A. Osei-Asante, E. Schmelyun, D. P. Shorb, D. E. Syed, S. H. Veilleux, J. M. Majumdar, A. Mosammaparast, N. Wolberger, C. 2021-10-17 doi:10.1101/2021.10.17.464694 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Sculpting rupture-free nuclear shapes in fibrous environments ]]> https://biorxiv.org/content/10.1101/2021.10.19.465049v1?rss=1 Jana, A. Tran, A. Gill, A. Kapania, R. Konstantopoulos, K. Nain, A. 2021-10-20 doi:10.1101/2021.10.19.465049 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ The miR-124-AMPAR pathway connects polygenic risks with behavioral changes shared between schizophrenia and bipolar disorder ]]> https://biorxiv.org/content/10.1101/2021.10.19.465053v1?rss=1 Namkung, H. Yukitake, H. Fukudome, D. Lee, B. J. Ursin, G. Lam, S. Kannan, S. Saito, A. Niwa, M. Sharma, K. Zandi, P. Jaaro-Peled, H. Ishizuka, K. Chatterjee, N. Huganir, R. Sawa, A. 2021-10-20 doi:10.1101/2021.10.19.465053 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ De novo motor learning of a bimanual control task over multiple days of practice ]]> https://biorxiv.org/content/10.1101/2021.10.21.465196v1?rss=1 Haith, A. M. Yang, C. S. Pakpoor, J. Kita, K. 2021-10-22 doi:10.1101/2021.10.21.465196 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Effect of reversible osmotic stress on live cell plasma membranes, probed via Laurdan general polarization measurements ]]> https://biorxiv.org/content/10.1101/2021.10.21.465302v1?rss=1 Zapata-Mercado, E. Hristova, K. 2021-10-22 doi:10.1101/2021.10.21.465302 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ The SAMBA tool uses long reads to improve the contiguity of genome assemblies ]]> https://biorxiv.org/content/10.1101/2021.10.21.465348v1?rss=1 Zimin, A. V. Salzberg, S. V. 2021-10-22 doi:10.1101/2021.10.21.465348 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Kinetic principles underlying pioneer function of GAGA transcription factor in live cells ]]> https://biorxiv.org/content/10.1101/2021.10.21.465351v1?rss=1 Wu, C. Tang, X. Li, T. Liu, S. Wisniewski, J. Zheng, Q. Lavis, L. Rong, Y. 2021-10-23 doi:10.1101/2021.10.21.465351 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Coordinated DNA and Histone Dynamics Drive Accurate Histone H2A.Z Exchange ]]> https://biorxiv.org/content/10.1101/2021.10.22.465479v1?rss=1 Poyton, M. F. Feng, X. A. Ranjan, A. Lei, Q. Wang, F. Zarb, J. S. Louder, R. K. Park, G. Jo, M. H. Ye, Z. Liu, S. Ha, T. Wu, C. 2021-10-23 doi:10.1101/2021.10.22.465479 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Social-affective features drive human representations of observed actions ]]> https://biorxiv.org/content/10.1101/2021.10.25.465740v1?rss=1 Dima, D. C. Tomita, T. M. Honey, C. J. Isik, L. 2021-10-26 doi:10.1101/2021.10.25.465740 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ The Wernicke conundrum revisited: evidence from connectome-based lesion-symptom mapping in post-stroke aphasia ]]> https://biorxiv.org/content/10.1101/2021.10.25.465746v1?rss=1 Matchin, W. den Ouden, D.-B. Hickok, G. Hillis, A. E. Bonilha, L. Fridriksson, J. 2021-10-26 doi:10.1101/2021.10.25.465746 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Distinct Representations of Body and Head motion are Dynamically Encoded by Purkinje cell Populations in the Macaque Cerebellum ]]> https://biorxiv.org/content/10.1101/2021.10.25.465748v1?rss=1 Zobeiri, O. A. Cullen, K. E. 2021-10-26 doi:10.1101/2021.10.25.465748 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia ]]> https://biorxiv.org/content/10.1101/2021.10.25.465813v1?rss=1 De La Torre, A. Sekhwal, M. K. Puiu, D. Salzberg, S. Scott, A. D. Allen, B. Neale, D. B. Chin, A. Buckley, T. N. 2021-10-26 doi:10.1101/2021.10.25.465813 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Experience-induced remodeling of the hippocampal post-synaptic proteome and phosphoproteome ]]> https://biorxiv.org/content/10.1101/2021.10.26.465788v1?rss=1 Heo, S. L. Kang, T. Bygrave, A. M. Larsen, M. R. Huganir, R. L. 2021-10-28 doi:10.1101/2021.10.26.465788 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ The Ribb-osome: Ribbon boosts ribosomal protein gene expression to coordinate organ form and function ]]> https://biorxiv.org/content/10.1101/2021.10.27.466115v1?rss=1 Loganathan, R. Levings, D. C. Kim, J. H. Wells, M. B. Chiu, H. Wu, Y. Slattery, M. Andrew, D. J. 2021-10-28 doi:10.1101/2021.10.27.466115 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Computational Fontan Analysis: Preserving accuracy while expediting workflow ]]> https://biorxiv.org/content/10.1101/2021.10.28.466272v1?rss=1 Liu, X. Aslan, S. Kim, B. Warburton, L. Jackson, D. Muhuri, A. Subramanian, A. Mass, P. Cleveland, V. Loke, Y.-H. Hibino, N. Olivieri, L. Krieger, A. 2021-10-29 doi:10.1101/2021.10.28.466272 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Development and Validation of Subject-Specific 3D Human Head Models Based on a Nonlinear Visco-Hyperelastic Constitutive Framework ]]> https://biorxiv.org/content/10.1101/2021.10.28.466370v1?rss=1 Upadhyay, K. Alshareef, A. Knutsen, A. K. Johnson, C. L. Carass, A. Bayly, P. V. Ramesh, K. T. 2021-11-01 doi:10.1101/2021.10.28.466370 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Modeling the efficacy of CRISPR gene drive for schistosomiasis control ]]> https://biorxiv.org/content/10.1101/2021.10.29.466423v1?rss=1 Grewelle, R. E. Perez-Saez, J. Tycko, J. Namigai, E. K. Rickards, C. G. De Leo, G. A. 2021-10-29 doi:10.1101/2021.10.29.466423 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Dysconnectivity between auditory-cognitive network associated with auditory GABA and glutamate levels in presbycusis patients ]]> https://biorxiv.org/content/10.1101/2021.10.31.466279v1?rss=1 Li, N. Ma, W. Ren, F. Li, X. Li, F. Zong, W. Wu, L. Dai, Z. Hui, S. C. N. Edden, R. A. E. Li, M. Gao, F. 2021-11-03 doi:10.1101/2021.10.31.466279 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ A simple tool extends TIMSTOF compatibility with historic data processing tools and enables ion mobility-enhanced spectral libraries ]]> https://biorxiv.org/content/10.1101/2021.10.31.466659v1?rss=1 Orsburn, B. C. 2021-10-31 doi:10.1101/2021.10.31.466659 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ A low-resource reliable pipeline to democratize multi-modal connectome estimation and analysis ]]> https://biorxiv.org/content/10.1101/2021.11.01.466686v1?rss=1 Lawrence, R. Loftus, A. Kiar, G. Bridgeford, E. Consortium for Reliability and Reproducibility, Chandrashekhar, V. Mhembere, D. Ryman, S. Zuo, X.-N. Margulies, D. Craddock, R. C. Priebe, C. E. Jung, R. Calhoun, V. D. Caffo, B. Burns, R. Milham, M. P. Vogelstein, J. 2021-11-03 doi:10.1101/2021.11.01.466686 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Dense granule protein, GRA64 interacts with host cell ESCRT proteins during Toxoplasma gondii infection ]]> https://biorxiv.org/content/10.1101/2021.11.02.467042v1?rss=1 Mayoral, J. Guevara, R. B. Rivera-Cuevas, Y. Tu, V. Tomita, T. Romano, J. D. Gunther-Cummins, L. Sidoli, S. Coppens, I. Carruthers, V. B. Weiss, L. M. 2021-11-03 doi:10.1101/2021.11.02.467042 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Sketching and sampling approaches for fast and accurate long read classification ]]> https://biorxiv.org/content/10.1101/2021.11.04.467374v1?rss=1 Das, A. Schatz, M. C. 2021-11-05 doi:10.1101/2021.11.04.467374 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies ]]> https://biorxiv.org/content/10.1101/2021.11.05.467531v1?rss=1 Li, Z. Li, X. Zhou, H. Gaynor, S. M. Selvaraj, M. S. Arapoglou, T. Quick, C. Liu, Y. Chen, H. Sun, R. Dey, R. Arnett, D. K. Bielak, L. F. Bis, J. C. Blackwell, T. Blangero, J. Boerwinkle, E. Bowden, D. W. Brody, J. A. Cade, B. E. Conomos, M. Correa, A. Cupples, L. A. Curran, J. E. de Vries, P. S. Duggirala, R. Freedman, B. I. Goring, H. H. H. Guo, X. Kalyani, R. R. Kooperberg, C. Kral, B. G. Lange, L. A. Manichaikul, A. W. Martin, L. W. Mitchell, B. D. Montasser, M. Morrison, A. Naseri, T. O'Connell, J. R. Palmer, N. D. Peyser, P. A. Psaty, B. M. Raff 2021-11-08 doi:10.1101/2021.11.05.467531 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ NIfTI-MRS: A standard format for magnetic resonance spectroscopic data ]]> https://biorxiv.org/content/10.1101/2021.11.09.467912v1?rss=1 Clarke, W. T. Mikkelsen, M. Oeltzschner, G. Bell, T. Shamaei, A. Soher, B. J. Emir, U. E. Wilson, M. 2021-11-11 doi:10.1101/2021.11.09.467912 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Photochemical pre-bleaching of formalin-fixed archival prostate tissues significantly reduces autofluorescence to facilitate multiplex immunofluorescence staining ]]> https://biorxiv.org/content/10.1101/2021.11.09.467916v1?rss=1 Meeker, A. K. Heaphy, C. M. Davis, C. M. Roy, S. Platz, E. A. 2021-11-11 doi:10.1101/2021.11.09.467916 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43 ]]> https://biorxiv.org/content/10.1101/2021.11.09.467933v1?rss=1 Heo, D. Ling, J. P. Molina-Castro, G. C. Langseth, A. J. Waisman, A. Nave, K.-A. Moebius, W. Wong, P. C. Bergles, D. E. 2021-11-09 doi:10.1101/2021.11.09.467933 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ DNA Self-Assembled Plasmonic Nanodiamonds for Biological Sensing ]]> https://biorxiv.org/content/10.1101/2021.11.09.467982v1?rss=1 Liang, L. Zheng, P. Jia, S. Ray, K. Chen, Y. Barman, I. 2021-11-11 doi:10.1101/2021.11.09.467982 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Persistent CAD activity in memory CD8+ T cells supports rRNA synthesis and ribosomal biogenesis required at rechallenge ]]> https://biorxiv.org/content/10.1101/2021.11.10.468070v1?rss=1 Claiborne, M. Sengupta, S. Zhao, L. Arwood, M. L. Sun, I.-M. Wen, J. Thompson, E. A. Mitchell-Flack, M. Laiho, M. Powell, J. D. 2021-11-11 doi:10.1101/2021.11.10.468070 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice ]]> https://biorxiv.org/content/10.1101/2021.11.11.465186v1?rss=1 Wang, Y. Shiladardi, K. Hsu, T. Odinammadu, K. O. Maruyama, T. Wu, W. Lin, C.-S. Damoci, C. B. Spear, E. D. Shin, J.-Y. Hsu, W. Michaelis, S. Worman, H. J. 2021-11-12 doi:10.1101/2021.11.11.465186 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ HA and M2 sequences alter the replication of 2013-16 H1 Live Attenuated Influenza Vaccine Infection in Human Nasal Epithelial Cell cultures ]]> https://biorxiv.org/content/10.1101/2021.11.11.468304v1?rss=1 Resnick, J. D. Canaday, L. M. Liu, H. Powell, H. McCoy, A. M. Nguyen, D. Pekosz, A. 2021-11-12 doi:10.1101/2021.11.11.468304 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Cryptococcus neoformans capsule regrowth experiments reveal dynamics of enlargement and architecture ]]> https://biorxiv.org/content/10.1101/2021.11.15.468433v1?rss=1 Wear, M. P. Jacobs, E. Wang, S. McConnell, S. Bowen, A. Strother, C. Cordero, R. J. Casadevall, A. 2021-11-15 doi:10.1101/2021.11.15.468433 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Comparison of seven modelling algorithms for GABA-edited 1H-MRS ]]> https://biorxiv.org/content/10.1101/2021.11.15.468534v1?rss=1 Craven, A. R. Bhattacharyya, P. K. Clarke, W. T. Dydak, U. Edden, R. A. E. Ersland, L. Mandal, P. K. Mikkelsen, M. Murdoch, J. B. Near, J. Rideaux, R. Shukla, D. Wang, M. Wilson, M. Zöllner, H. Hugdahl, K. Oeltzschner, G. 2021-11-19 doi:10.1101/2021.11.15.468534 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ WebSeq: A Genomic Data Analytics Platform for Monogenic Disease Discovery ]]> https://biorxiv.org/content/10.1101/2021.11.16.460500v1?rss=1 Agarwal, M. Ghimire, K. Cogan, J. D. Undiagnosed Disease Network, Markle, J. 2021-11-19 doi:10.1101/2021.11.16.460500 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ A Predictive Energy Landscape Model of MetamorphicProtein Conformational Specificity ]]> https://biorxiv.org/content/10.1101/2021.11.16.468851v1?rss=1 Wrabl, J. O. Voortman-Sheetz, K. Hilser, V. J. 2021-11-16 doi:10.1101/2021.11.16.468851 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Identification of shared bacterial strains in the vaginal microbiota of reproductive-age mothers and daughters using genome-resolved metagenomics ]]> https://biorxiv.org/content/10.1101/2021.11.16.468914v1?rss=1 France, M. T. Brown, S. E. rompalo, a. m. Brotman, R. M. Ravel, J. 2021-11-17 doi:10.1101/2021.11.16.468914 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Senescent stroma induces nuclear deformations in cancer cells via the inhibition of RhoA/ROCK/myosin II-based cytoskeletal tension ]]> https://biorxiv.org/content/10.1101/2021.11.17.468902v1?rss=1 Aifuwa, I. Phillip, J. M. Kim, B. Luperchio, T. Jimenez, A. Perestrelo, T. Lee, S.-H. Longe, N. Reddy, K. Ha, T. Wirtz, D. 2021-11-18 doi:10.1101/2021.11.17.468902 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Hidden temporal structure of the ongoing task impacts detection strategy and is reflected in pupillary dynamics ]]> https://biorxiv.org/content/10.1101/2021.11.17.469021v1?rss=1 Lawlor, J. Zagala, A. Jamali, S. Boubenec, Y. 2021-11-19 doi:10.1101/2021.11.17.469021 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Systems medicine dissection of chromosome 1q amplification reveals oncogenic regulatory circuits and informs targeted therapy in cancer ]]> https://biorxiv.org/content/10.1101/2021.11.17.469031v1?rss=1 Trasanidis, N. Katsarou, A. Ponnusamy, K. Shen, Y.-A. Kostopoulos, I. V. Bergonia, B. Keren, K. Reema, P. Xiao, X. Szydlo, R. M. Sabbattini, P. M. Roberts, I. A. Auner, H. W. Naresh, K. N. Chaidos, A. Wang, T.-L. Magnani, L. Caputo, V. S. Karadimitris, A. 2021-11-19 doi:10.1101/2021.11.17.469031 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Eliminating fibroblast activation protein-α expressing cells by photoimmunotheranostics ]]> https://biorxiv.org/content/10.1101/2021.11.18.469110v1?rss=1 Jin, J. Barnett, J. D. Krishnamachary, B. Mironchik, Y. Luo, C. K. Kobayashi, H. Bhujwalla, Z. M. 2021-11-19 doi:10.1101/2021.11.18.469110 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing ]]> https://biorxiv.org/content/10.1101/2021.11.18.469135v1?rss=1 Alonge, M. Lebeigle, L. Kirsche, M. Aganezov, S. Wang, X. Lippman, Z. B. Schatz, M. C. Soyk, S. 2021-11-19 doi:10.1101/2021.11.18.469135 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Strict adherence to Mendel's First Law across a large sample of human sperm genomes ]]> https://biorxiv.org/content/10.1101/2021.11.19.469261v1?rss=1 Carioscia, S. A. Weaver, K. J. Bortvin, A. N. Ariad, D. Bell, A. D. McCoy, R. C. 2021-11-20 doi:10.1101/2021.11.19.469261 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding ]]> https://biorxiv.org/content/10.1101/2021.11.19.469335v1?rss=1 Taglauer, E. S. Wachman, E. M. Juttukonda, L. Klouda, T. Kim, J. Wang, Q. Ishiyama, A. Hackam, D. J. Yuan, K. Jia, H. 2021-11-22 doi:10.1101/2021.11.19.469335 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Systematic Interrogation of Protein Refolding Under Cellular-Like Conditions ]]> https://biorxiv.org/content/10.1101/2021.11.20.469408v1?rss=1 To, P. Lee, S. O. Xia, Y. Devlin, T. Fleming, K. G. Fried, S. D. 2021-11-21 doi:10.1101/2021.11.20.469408 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ IReNA: integrated regulatory network analysis of single-cell transcriptomes ]]> https://biorxiv.org/content/10.1101/2021.11.22.469628v1?rss=1 jiang, j. Blackshaw, S. Qian, J. Wang, J. 2021-11-23 doi:10.1101/2021.11.22.469628 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines ]]> https://biorxiv.org/content/10.1101/2021.11.24.469906v1?rss=1 Wang, L. Kainulainen, M. H. Jiang, N. Di, H. Bonenfant, G. Mills, L. Currier, M. Shrivastava-Ranjan, P. Calderon, B. M. Sheth, M. Mann, B. R. Hossain, J. Lin, X. Lester, S. Pusch, E. Jones, J. Cui, D. Chatterjee, P. Jenks, H. M. Morantz, E. Larson, G. Hatta, M. Harcourt, J. Tamin, A. Lin, Y. Tao, Y. Zhao, K. Lacek, K. Burroughs, A. Wong, T. Tong, S. Barnes, J. R. Tenforde, M. W. Self, W. H. Shapiro, N. I. Exline, M. C. Files, D. C. Gibbs, K. W. Hager, D. N. Patel, M. Laufer Halpin, A. S. McMullan, L. K. Lee, J. S. Spiropoulou, C. F. Thornburg, N. J. 2021-11-30 doi:10.1101/2021.11.24.469906 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ MK2 Expression Promotes Non-Small Cell Lung Cancer Cell Death and Predicts Survival ]]> https://biorxiv.org/content/10.1101/2021.11.30.470656v1?rss=1 Del Rosario, O. Suresh, K. Kallem, M. Singh, G. Shah, A. Xin, Y. Philip, N. D'Alessio, F. Srivastava, M. Bera, A. Shimoda, L. Merchant, M. Rane, M. Machamer, C. Mock, J. Hagan, R. Kolb, T. Damarla, M. 2021-12-01 doi:10.1101/2021.11.30.470656 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Black-box testing in motor sequence learning ]]> https://biorxiv.org/content/10.1101/2021.12.01.470563v1?rss=1 Maceira-Elvira, P. Timmermann, J. E. Popa, T. Schmid, A.-C. Krakauer, J. W. Morishita, T. Wessel, M. J. Hummel, F. C. 2021-12-01 doi:10.1101/2021.12.01.470563 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Moving Beyond Processing and Analysis-Related Variation in Neuroscience ]]> https://biorxiv.org/content/10.1101/2021.12.01.470790v1?rss=1 Li, X. Ai, L. Giavasis, S. Jin, H. Feczko, E. Xu, T. Clucas, J. Franco, A. Heinsfeld, A. S. Adebimpe, A. Vogelstein, J. T. Yan, C.-G. Esteban, O. Poldrack, R. A. Craddock, C. Fair, D. Satterthwaite, T. Kiar, G. Milham, M. P. 2021-12-03 doi:10.1101/2021.12.01.470790 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Distinct ribosome states trigger diverse mRNA quality control pathways ]]> https://biorxiv.org/content/10.1101/2021.12.01.470814v1?rss=1 Veltri, A. J. D'Orazio, K. N. Lessen, L. N. Loll-Krippleber, R. Brown, G. W. Green, R. 2021-12-01 doi:10.1101/2021.12.01.470814 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Pupillary dynamics of optimal effort ]]> https://biorxiv.org/content/10.1101/2021.12.02.470970v1?rss=1 Sayali, C. Heling, E. Cools, R. 2021-12-03 doi:10.1101/2021.12.02.470970 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ NAD metabolism modulates mitochondrial function and inflammation and prevents progression of diabetic kidney disease ]]> https://biorxiv.org/content/10.1101/2021.12.05.471273v1?rss=1 Myakala, K. Wang, X. Jones, B. A. Hirschey, M. D. Yang, X. Rosenberg, A. Z. Ginley, B. Sarder, P. Brodsky, L. Jang, Y. Na, C. H. Chi, Y. Zhang, X. Guha, U. Lewien, P. Wu, C. Bansal, S. Ma, J. Cheema, A. Panov, J. Levi, M. 2021-12-07 doi:10.1101/2021.12.05.471273 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Neuron-like function of the nephron central command ]]> https://biorxiv.org/content/10.1101/2021.12.06.471478v1?rss=1 Gyarmati, G. Shroff, U. N. Riquier-Brison, A. Stocker, S. D. Izuhara, A. Deepak, S. Chen, Y. Biemesderfer, D. James, A. Minichiello, L. Zlokovic, B. V. Peti-Peterdi, J. 2021-12-07 doi:10.1101/2021.12.06.471478 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Attentive deep learning-based tumor-only somatic mutation classifier achieves high accuracy agnostic of tissue type and capture kit. ]]> https://biorxiv.org/content/10.1101/2021.12.07.471513v1?rss=1 McLaughlin, R. T. Asthana, M. Di Meo, M. Ceccarelli, M. Jacob, H. J. Masica, D. L. 2021-12-09 doi:10.1101/2021.12.07.471513 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Induced fit with replica exchange improves protein complex structure prediction ]]> https://biorxiv.org/content/10.1101/2021.12.08.471786v1?rss=1 0.4) on targets that exhibit significant conformational change upon binding. To overcome limitations in capturing backbone motions, we developed a new, aggressive sampling method that incorporates temperature replica exchange Monte Carlo (T-REMC) and conformational sampling techniques within docking protocols in Rosetta. Our method, ReplicaDock 2.0, mimics induced-fit mechanism of protein binding to sample backbone motions across putative interface residues on-the-fly, thereby recapitulating binding-partner induced conformational changes. Furthermore, ReplicaDock 2.0 clocks in at 150-500 CPU hours per target (protein-size dependent); a runtime that is significantly faster than Molecular Dynamics based approaches. For a benchmark set of 88 proteins with moderate to high flexibility (unbound-to-bound iRMSD over 1.2 [A]), ReplicaDock 2.0 successfully docks 61% of moderately flexible complexes and 35% of highly flexible complexes. Additionally, we demonstrate that by biasing backbone sampling particularly towards residues comprising flexible loops or hinge domains, highly flexible targets can be predicted to under 2 [A] accuracy. This indicates that additional gains are possible when mobile protein segments are known. Significance StatementProteins bind each other in a highly specific and regulated manner, and these associated dynamics of binding are intimately linked to their function. Conventional techniques of structure determination such as cryo-EM, X-ray crystallography and NMR are time-consuming and arduous. Using a temperature-replica exchange Monte Carlo approach that mimics the kinetic mechanism of "induced fit" binding, we improved prediction of protein complex structures, particularly for targets that exhibit considerable conformational changes upon binding (Interface root mean square deviation (unbound-bound) > 1.2 [A]. Capturing these binding-induced conformational changes in proteins can aid us in better understanding biological mechanisms and suggest intervention strategies for disease mechanisms. ]]> Harmalkar, A. Mahajan, S. P. Gray, J. J. 2021-12-10 doi:10.1101/2021.12.08.471786 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Development and validation of inducible protein degradation and quantitative phosphoproteomics to identify kinase-substrate relationships. ]]> https://biorxiv.org/content/10.1101/2021.12.08.471812v1?rss=1 Hards, R. Howarth, C. L. Wiredu, K. LaCroix, I. Mercado del Valle, J. C. Adamo, M. E. Holland, A. J. Kettenbach, A. Gerber, S. A. 2021-12-10 doi:10.1101/2021.12.08.471812 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Improved Transcriptome Assembly Using a Hybrid of Long and Short Reads with StringTie ]]> https://biorxiv.org/content/10.1101/2021.12.08.471868v1?rss=1 Shumate, A. Wong, B. Pertea, G. Pertea, M. 2021-12-10 doi:10.1101/2021.12.08.471868 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ No evidence of paralogous loci or new bona fide microRNAs in telomere to telomere (T2T) genomic data ]]> https://biorxiv.org/content/10.1101/2021.12.09.471935v1?rss=1 4,000 primary cell samples to the new T2T sequence. Based on sequence and structure, no bona fide miRNAs were identified. Ninety-seven miRNAs of questionable authenticity (frequently known repeat elements) were identified from the miRBase dataset across the newly described regions of the human genome. These 97 represent only 51 miRNA families due to paralogy of highly similar miRNAs such as 24 members of the hsa-mir-548 family. Altogether, this data strongly supports our having identified widely expressed bona fide miRNAs in the human genome and move us further toward the completion of human miRNA discovery. ]]> Patil, A. H. Halushka, M. K. Fromm, B. K. 2021-12-13 doi:10.1101/2021.12.09.471935 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Clonal hematopoiesis is driven by aberrant activation of TCL1A ]]> https://biorxiv.org/content/10.1101/2021.12.10.471810v1?rss=1 Weinstock, J. S. Gopakumar, J. Burugula, B. B. Uddin, M. M. Jahn, N. Belk, J. A. Daniel, B. Ly, N. Mack, T. M. Laurie, C. A. Broome, J. G. Taylor, K. D. Guo, X. Sinner, M. F. von Falkenhausen, A. S. Kaab, S. Shuldiner, A. R. O'Connell, J. R. Lewis, J. P. Boerwinkle, E. Barnes, K. C. Chami, N. Kenny, E. E. Loos, R. J. F. Fornage, M. Hou, L. Lloyd-Jones, D. M. Redline, S. Cade, B. E. Psaty, B. M. Bis, J. C. Brody, J. A. Silverman, E. K. Yun, J. H. Qiao, D. Palmer, N. D. Freedman, B. I. Bowden, D. W. Cho, M. H. DeMeo, D. L. Vasan, R. S. Johnson, A. D. Mat 2021-12-13 doi:10.1101/2021.12.10.471810 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Neuroimaging signature associated with symptom exacerbation in early-stage psychosis ]]> https://biorxiv.org/content/10.1101/2021.12.10.472143v1?rss=1 Mihaljevic, M. Nagpal, A. Etyemez, S. Narita, Z. Ross, A. Schaub, R. Cascella, N. Nucifora, F. C. Coughlin, J. M. Nestadt, G. Sedlak, T. W. Calhoun, V. Faria, A. Yang, K. Sawa, A. 2021-12-14 doi:10.1101/2021.12.10.472143 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Spatially distributed computation in cortical circuits ]]> https://biorxiv.org/content/10.1101/2021.12.13.472322v1?rss=1 Gepshtein, S. Pawar, A. Kwon, S. Savelev, S. Albright, T. D. 2021-12-14 doi:10.1101/2021.12.13.472322 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ Generative Language Modeling for Antibody Design ]]> https://biorxiv.org/content/10.1101/2021.12.13.472419v1?rss=1 Shuai, R. W. Ruffolo, J. A. Gray, J. J. 2021-12-14 doi:10.1101/2021.12.13.472419 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ A reference induced pluripotent stem cell line for large-scale collaborative studies ]]> https://biorxiv.org/content/10.1101/2021.12.15.472643v1?rss=1 View larger version (84K): org.highwire.dtl.DTLVardef@cef106org.highwire.dtl.DTLVardef@31d5d8org.highwire.dtl.DTLVardef@1ce6d8corg.highwire.dtl.DTLVardef@17a19d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pantazis, C. B. Yang, A. Lara, E. McDonough, J. A. Blauwendraat, C. Peng, L. Oguro, H. Zou, J. Sebesta, D. Pratt, G. Cross, E. Blockwick, J. Buxton, P. Kinner-Bibeau, L. Medura, C. Tompkins, C. Hughes, S. Santiana, M. Faghri, F. Nalls, M. A. Vitale, D. Qi, Y. A. Ramos, D. M. Anderson, K. Stadler, J. Narayan, P. Papademetriou, J. Reilly, L. Nelson, M. P. Aggarwal, S. Rosen, L. U. Kirwan, P. Pisupati, V. Coon, S. L. Scholz, S. W. Coccia, E. Sarrafha, L. Ahfeldt, T. Funes, S. Bosco, D. A. Beccari, M. S. Cleveland, D. W. Zanellati, M. C. Basundra, R. Des 2021-12-17 doi:10.1101/2021.12.15.472643 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ The neural cell adhesion molecule NrCAM regulates development of hypothalamic tanycytes ]]> https://biorxiv.org/content/10.1101/2021.12.15.472761v1?rss=1 Moore, A. Chinnaiya, K. Kim, D. W. Brown, S. Stewart, I. Robins, S. Dowsett, G. Muir, C. Travaglio, M. Lewis, J. E. Ebling, F. Blackshaw, S. Furley, A. Placzek, M. 2021-12-16 doi:10.1101/2021.12.15.472761 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a new mode of engaging poly(ADP-ribose) ]]> https://biorxiv.org/content/10.1101/2021.12.15.472832v1?rss=1 Kuttiyatveetil, J. R. A. Soufari, H. Dasovich, M. Uribe, I. R. Cheng, S.-J. Leung, A. Pascal, J. M. 2021-12-16 doi:10.1101/2021.12.15.472832 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ LY6S, a New Interferon-Inducible Human Member of the Ly6a-Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance ]]> https://biorxiv.org/content/10.1101/2021.12.16.472998v1?rss=1 Shmerling, M. Chalik, M. Smorodinsky, N. I. Meeker, A. Roy, S. Sagi-Assif, O. Meshel, T. Danilevsky, A. Shomron, N. Levinger, S. Nishry, B. Baruchi, D. Shargorodsky, A. Ziv, R. Sarusi-Portuguez, A. Lahav, M. Ehrlich, M. Braschi, B. Bruford, E. Witz, I. P. Wreschner, D. H. 2021-12-17 doi:10.1101/2021.12.16.472998 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Notch inhibition promotes regeneration and immunosuppression supports cone survival in a zebrafish model of inherited retinal dystrophy ]]> https://biorxiv.org/content/10.1101/2021.12.19.473212v1?rss=1 Fogerty, J. Song, P. Boyd, P. Grabinski, S. Hoang, T. Reich, A. Cianciolo, L. Blackshaw, S. Mumm, J. S. Hyde, D. Perkins, B. 2021-12-21 doi:10.1101/2021.12.19.473212 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Gene regulation network inference using k-nearest neighbor-based mutual information estimation- Revisiting an old DREAM ]]> https://biorxiv.org/content/10.1101/2021.12.20.473242v1?rss=1 Shachaf, L. I. Roberts, E. Cahan, P. Xiao, J. 2021-12-21 doi:10.1101/2021.12.20.473242 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Δ9-tetrahydrocannabinol (THC) vapor exposure produces conditioned rewarding effects in male and female rats ]]> https://biorxiv.org/content/10.1101/2021.12.20.473475v1?rss=1 Moore, C. F. Davis, C. M. Weerts, E. M. 2021-12-21 doi:10.1101/2021.12.20.473475 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients ]]> https://biorxiv.org/content/10.1101/2021.12.20.473535v1?rss=1 Sun, Q. Liu, W. Rosen, J. D. Huang, L. Pace, R. G. Dang, H. Gallins, P. J. Blue, E. E. Ling, H. Corvol, H. Strug, L. Bamshad, M. J. Gibson, R. L. Pugh, E. W. Blackman, S. M. Cutting, G. O'Neal, W. K. Zhou, Y.-H. Wright, F. A. Knowles, M. R. The Cystic Fibrosis Genome Project (CFGP) Consortium, Wen, J. Li, Y. 2021-12-21 doi:10.1101/2021.12.20.473535 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Proprioceptive Re-alignment drives Implicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2021.12.21.473747v1?rss=1 Tsay, J. S. Kim, H. E. Haith, A. M. Ivry, R. B. 2021-12-23 doi:10.1101/2021.12.21.473747 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ The African mosquito-borne diseasosome: Geographical patterns and range expansion ]]> https://biorxiv.org/content/10.1101/2021.12.21.473756v1?rss=1 25 countries, the typical ranges of both mosquitoes and MBPs are surprisingly small. The striking similarity in diversity and especially in range distributions of mosquitoes and MBPs suggest that most MBPs are transmitted by one or few narrow-range mosquito vectors. Exceptionally widespread mosquito species (e.g., Ae. aegypti, Cx. quinquefasciatus, and 10 Anopheles species) feed preferentially on people and domestic animals, and nearly half are windborne migrants. Likewise, exceptionally widespread MBPs are transmitted between people or domestic animals and are vectored by one or more of the aforementioned widespread mosquitoes. Our results suggest that few MBPs have undergone a dramatic range expansion, after adapting to people or domestic animals as well as to exceptionally-widespread mosquitoes. During the intermediate phase of range expansion, MBPs extend their vector and vertebrate host ranges with a concomitant gradual increase in geographical range. Because range size may serve as a marker of the phase of range expansion, ranking the African MBPs according to range, we identified several MBPs that pose elevated risk for disease emergence (e.g., Wesselsbron virus). Taken together, our database, approach, and results can help improve MBD surveillance and lead to a better understanding of disease emergence. This knowledge has the potential to improve capacity to prevent and mitigate new and emerging MBD threats. ]]> Lehmann, T. Kouam, C. Woo, J. Diallo, M. Wilkerson, R. Linton, Y.-M. 2021-12-23 doi:10.1101/2021.12.21.473756 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Bionized nanoferrite particles alter the course of experimental Cryptococcus neoformans pneumonia ]]> https://biorxiv.org/content/10.1101/2021.12.21.473767v1?rss=1 Liporagi Lopes, L. C. Korangath, P. dos Santos Junior, S. R. Gabrielson, K. L. Ivkov, R. Casadevall, A. 2021-12-24 doi:10.1101/2021.12.21.473767 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Combination of Mycobacterium tuberculosis RS ratio and CFU improves the ability of murine efficacy experiments to distinguish between drug treatments ]]> https://biorxiv.org/content/10.1101/2021.12.21.473768v1?rss=1 Dide-Agossou, C. Bauman, A. A. Ramey, M. E. Rossmassler, K. Al Mubarak, R. Pauly, S. Voskuil, M. I. Garcia?Cremades, M. Savic, R. M. Nahid, P. Moore, C. M. Tasneen, R. Nuermburger, E. Robertson, G. T. Walter, N. D. 2021-12-24 doi:10.1101/2021.12.21.473768 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Novel regimens of bedaquiline-pyrazinamide combined with moxifloxacin, rifabutin, delamanid and/or OPC-167832 in murine tuberculosis models ]]> https://biorxiv.org/content/10.1101/2021.12.21.473769v1?rss=1 Nuermberger, E. Tasneen, R. Garcia, A. Converse, P. J. Zimmerman, M. D. Dartois, V. A. Kurbatova, E. V. Vernon, A. Carr, W. Stout, J. E. Dooley, K. E. 2021-12-23 doi:10.1101/2021.12.21.473769 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation. ]]> https://biorxiv.org/content/10.1101/2021.12.26.472655v1?rss=1 Taglauer, E. Dhole, Y. Boateng, J. Snyder-Cappione, J. E. Parker, S. E. Clarke, K. Juttukonda, L. Devera, J. Hunnewell, J. Barnett, E. Jia, H. Yarrington, C. Sabharwal, V. Wachman, E. 2021-12-28 doi:10.1101/2021.12.26.472655 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Prenatal immune stress induces a prolonged blunting of microglia activation that impacts striatal connectivity ]]> https://biorxiv.org/content/10.1101/2021.12.27.473694v1?rss=1 Hayes, L. N. An, K. Carloni, E. Li, F. Vincent, E. Paranjpe, M. Dolen, G. Goff, L. A. Ramos, A. Kano, S.-i. Sawa, A. 2021-12-28 doi:10.1101/2021.12.27.473694 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Importance of linear combination modeling for quantification of Glutathione and GABA levels using Hadamard-edited MRS ]]> https://biorxiv.org/content/10.1101/2021.12.28.474256v1?rss=1 Song, Y. Zollner, H. J. Hui, S. C. N. Oeltzschner, G. Prisciandaro, J. J. Edden, R. A. E. 2021-12-28 doi:10.1101/2021.12.28.474256 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Ret loss-of-function decreases enteric neural crest progenitor proliferation and restricts developmental fate potential during enteric nervous system development ]]> https://biorxiv.org/content/10.1101/2021.12.28.474390v1?rss=1 Vincent, E. Chatterjee, S. Cannon, G. H. Auer, D. Ross, H. Chakravarti, A. Goff, L. A. 2021-12-29 doi:10.1101/2021.12.28.474390 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Differences in running performance of single- and group-housed mice ]]> https://biorxiv.org/content/10.1101/2021.12.29.474296v1?rss=1 Plenz, U. T. Kanold, P. O. 2021-12-30 doi:10.1101/2021.12.29.474296 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ A spatial stochastic model reveals the role of supercoiling in transcription regulation ]]> https://biorxiv.org/content/10.1101/2021.12.29.474406v1?rss=1 Geng, Y. Bohrer, C. H. Yehya, N. Hendrix, H. Shachaf, L. Liu, J. Xiao, J. Roberts, E. 2021-12-29 doi:10.1101/2021.12.29.474406 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Normal Reproductive function in male mice lacking pituitary kisspeptin receptor. ]]> https://biorxiv.org/content/10.1101/2021.12.30.474587v1?rss=1 Ma, Y. Awe, O. Radovick, S. Yang, X. Divall, S. Wolfe, A. Wu, S. 2022-01-01 doi:10.1101/2021.12.30.474587 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Adjunctive inhibition of the integrated stress response pathway accelerates bacterial clearance in a mouse model of tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.12.31.474642v1?rss=1 Krug, S. Prasad, P. Xiao, S. Lun, S. Ruiz-Bedoya, C. A. Klunk, M. Ordonez, A. A. Jain, S. K. Srikrishna, G. Kramnik, I. Bishai, W. 2022-01-02 doi:10.1101/2021.12.31.474642 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Nested spatial and temporal modeling of environmental conditions associated with genetic markers of Vibrio parahaemolyticus in Washington state Pacific oysters ]]> https://biorxiv.org/content/10.1101/2022.01.03.471994v1?rss=1 27 ppt). There was also a positive relationship between tissue temperature and tdh, but only above 20{degrees}C. The tdh:tlh ratio displayed analogous inverted non-linear relationships as tlh. The non-linear associations found between the genetic targets and environmental measures demonstrate the complex habitat suitability of V. parahaemolyticus. Additional associations with both spatial and temporal variables also suggest there are influential unmeasured environmental conditions that could further explain bacterium variability. Overall, these findings confirm previous ecological risk factors for vibriosis in Washington State, while also identifying new associations between lagged temporal effects and pathogenic markers of V. parahaemolyticus. ]]> Fries, B. Davis, B. J. K. Corrigan, A. E. DePaola, A. Curriero, F. C. 2022-01-04 doi:10.1101/2022.01.03.471994 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Missense variants causing Wiedemann-Steiner syndrome preferentially occur in the KMT2A-CXXC domain and are accurately classified using AlphaFold2 ]]> https://biorxiv.org/content/10.1101/2022.01.03.474770v1?rss=1 Reynisdottir, T. Anderson, K. Boukas, L. Bjornsson, H. 2022-01-03 doi:10.1101/2022.01.03.474770 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences ]]> https://biorxiv.org/content/10.1101/2022.01.03.474815v1?rss=1 Hess, R. A. Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. C. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffmann, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. J 2022-01-05 doi:10.1101/2022.01.03.474815 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Encoding of speech in convolutional layers and the brain stem based on language experience ]]> https://biorxiv.org/content/10.1101/2022.01.03.474864v1?rss=1 Begus, G. Zhou, A. Zhao, C. 2022-01-04 doi:10.1101/2022.01.03.474864 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons of Pirt-EGFPf mice in neuropathic pain condition ]]> https://biorxiv.org/content/10.1101/2022.01.06.475187v1?rss=1 Zhang, C. Hu, M.-W. He, S. Wang, X. Cao, X. Zhou, F. Qian, J. Guan, Y. 2022-01-06 doi:10.1101/2022.01.06.475187 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Bias in FGFR1 signaling in response to FGF4, FGF8, and FGF9 ]]> https://biorxiv.org/content/10.1101/2022.01.06.475273v1?rss=1 Karl, K. A. Hristova, K. Krejci, P. Del Piccolo, N. 2022-01-06 doi:10.1101/2022.01.06.475273 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories ]]> https://biorxiv.org/content/10.1101/2022.01.10.475373v1?rss=1 Bentley, B. P. Carrasco-Valenzuela, T. Ramos, E. K. S. Pawar, H. Arantes, L. S. Alexander, A. Banerjee, S. M. Masterson, P. Kuhlwilm, M. Pippel, M. Mountcastle, J. Haase, B. Silva, M. U. Formenti, G. Howe, K. Chow, W. Tracey, A. Sims, Y. Pelan, S. Wood, J. Perrault, J. R. Stewart, K. Benson, S. Levy, Y. Todd, E. V. Shaffer, H. B. Scott, P. Henen, B. T. Murphy, R. W. Mohr, D. W. Scott, A. F. Gemmell, N. Suh, A. Winkler, S. Thibaud-Nissen, F. Nery, M. F. Marques-Bonet, T. Antunes, A. Tikochinski, Y. Dutton, P. H. Fedrigo, O. Myers, E. W. Jarvis, E. Mazz 2022-01-12 doi:10.1101/2022.01.10.475373 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Activated MST2 kinase is free of kinetic regulation ]]> https://biorxiv.org/content/10.1101/2022.01.13.476221v1?rss=1 Koehler, T. J. Tran, T. Kavran, J. M. 2022-01-14 doi:10.1101/2022.01.13.476221 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Metabolic switching and cell wall remodelling of Mycobacterium tuberculosis during bone tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.01.13.476285v1?rss=1 2; p-value [≤]0.05) in human bone TB specimens. Overall, the mycobacteria displayed a hypo-metabolic state with significant (p[≤]0.05) downregulation of major pathways involved in translational machinery, cellular and protein metabolism and response to hypoxia. However, significant enrichment (p [≤]0.05) of amino-sugar metabolic processes, membrane glycolipid biosynthesis, amino acid biosynthesis (serine, glycine, arginine and cysteine) and accumulation of mycolyl-arabinogalactan-peptidoglycan complex suggests possible mycobacterial survival strategies within the bone lesions by strengthening its cell wall and cellular integrity. Data were also screened for M.tb virulence proteins using Virulent Pred and VICM Pred tools, which revealed five genes (Rv1046c, Rv1230c, DppD, PE_PGRS26 and PE_PGRS43) with a possible role in the pathogenesis of bone TB. Next, an osteoblast cell line model for bone TB was developed allowing for significant intracellular multiplication of M.tb. Interestingly, three virulence genes (Rv1046c, DppD and PE_PGRS26) identified from human bone TB microarray data were also found to be overexpressed by intracellular M. tuberculosis in osteoblast cell lines. Overall, these data demonstrate that M. tuberculosis alters its transcriptome as an adaptive strategy to survive in the host and establish infection in bone. Additionally, the in vitro osteoblast model we describe may facilitate our understanding of the pathogenesis of bone TB. Author SummaryMusculoskeletal tuberculosis is the third most common manifestation of extra-pulmonary tuberculosis and massive bone destruction along with vertebral discs are one of the hallmarks of this disease. Mycobacterium tuberculosis, the causative agent, has the tremendous potential to adapt itself to different host environments due to its ability to alter the expression of genes/proteins belonging to different pathways. This study shows that the mycobacterial infection in bone is driven by the increased expression of genes belonging to cell wall remodelling and DNA damage repair pathways important for its survival. Further data analysis showed that some of these genes are coding for proteins possessing virulence potential that may be essential for survival of M. tuberculosis under such hostile environment of bone. We also developed an in vitro model of bone tuberculosis using an osteoblast cell line and validated the expression of these virulence factors. Identification of such virulence factors in the bone environment by M. tuberculosis may aid to identify new therapeutic targets for bone TB. Further, development of cell line model for bone TB is important to understand some unknown facets of this disease. ]]> Kaur, K. Sharma, S. Abhishek, S. Kaur, P. Saini, U. C. Dhillon, M. S. Karakousis, P. C. Verma, I. 2022-01-15 doi:10.1101/2022.01.13.476285 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Functional variability in adhesion and flocculation of yeast megasatellite genes ]]> https://biorxiv.org/content/10.1101/2022.01.14.476295v1?rss=1 Saguez, C. Viterbo, D. Descorps-Declere, S. Cormack, B. P. Dujon, B. Richard, G.-F. 2022-01-17 doi:10.1101/2022.01.14.476295 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Fam49b dampens TCR signal strength to regulate survival of positively selected thymocytes ]]> https://biorxiv.org/content/10.1101/2022.01.18.476719v1?rss=1 Park, C.-S. Guan, J. Rhee, P. Gonzalez, F. Coscoy, L. Robey, E. A. Shastri, N. Sadegh-Nasseri, S. 2022-01-18 doi:10.1101/2022.01.18.476719 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ High-Throughput Screening for Myelination Promoting Compounds Using Human Stem Cell-derived Oligodendrocyte Progenitor Cells Identifies Novel Targets ]]> https://biorxiv.org/content/10.1101/2022.01.18.476755v1?rss=1 Li, W. Berlinicke, C. Huang, Y. Fang, W. Chen, C. Takaesu, F. Chang, X. Duan, Y. Chang, C. Mao, H.-Q. Sheng, G. Giera, S. Dodge, J. C. Ji, H. Madden, S. L. Zack, D. J. Chamling, X. 2022-01-20 doi:10.1101/2022.01.18.476755 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Nucleosome topology and DNA sequence modulate the engagement of pioneer factors SOX2 and OCT4 ]]> https://biorxiv.org/content/10.1101/2022.01.18.476780v1?rss=1 Malaga Gadea, F. C. Nikolova, E. N. 2022-01-21 doi:10.1101/2022.01.18.476780 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Stabilization of E-cadherin adhesions by COX-2/GSK3β signaling is a targetable pathway in metastatic breast cancer ]]> https://biorxiv.org/content/10.1101/2022.01.18.476813v1?rss=1 Balamurugan, K. Sehareen, S. Sharan, S. Krishnamurthy, S. Tang, W. McKennett, L. Padmanaba, V. Czarra, K. T. Ewald, A. J. Ambs, S. Ueno, N. T. Poria, D. K. Sterneck, E. 2022-01-21 doi:10.1101/2022.01.18.476813 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Massively parallel genomic perturbations with multi-target CRISPR reveal new insights on Cas9 activity and DNA damage responses at endogenous sites ]]> https://biorxiv.org/content/10.1101/2022.01.18.476836v1?rss=1 Zou, R. S. Marin-Gonzalez, A. Liu, Y. Liu, H. B. Shen, L. Dveirin, R. Luo, J. X. J. Kalhor, R. Ha, T. 2022-01-20 doi:10.1101/2022.01.18.476836 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Pathogen Detection in RNA-Seq Data with Pathonoia ]]> https://biorxiv.org/content/10.1101/2022.01.19.476681v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@16775f2org.highwire.dtl.DTLVardef@17099f4org.highwire.dtl.DTLVardef@18b8dfeorg.highwire.dtl.DTLVardef@117498b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liebhoff, A.-M. Menden, K. Laschtowitz, A. Franke, A. Schramm, C. Bonn, S. 2022-01-21 doi:10.1101/2022.01.19.476681 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Hedgehog regulation of epithelial cell state and morphogenesis in the larynx ]]> https://biorxiv.org/content/10.1101/2022.01.19.476887v1?rss=1 Ramachandran, J. Zhou, W. Bardenhagen, A. E. Nasr, T. Zorn, A. M. Ji, H. Vokes, S. A. 2022-01-20 doi:10.1101/2022.01.19.476887 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Detecting Antibody Reactivities in Phage ImmunoPrecipitation Sequencing Data ]]> https://biorxiv.org/content/10.1101/2022.01.19.476926v1?rss=1 Chen, A. Kammers, K. Larman, H. B. Scharpf, R. B. Ruczinski, I. 2022-01-21 doi:10.1101/2022.01.19.476926 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ NELL-1 regulates the matrisome to alter osteosarcoma disease progression ]]> https://biorxiv.org/content/10.1101/2022.01.21.477245v1?rss=1 Qin, Q. Gomez-Salazar, M. Tower, R. J. Chang, L. Morris, C. D. McCarthy, E. F. Ting, K. Zhang, X. James, A. W. 2022-01-23 doi:10.1101/2022.01.21.477245 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ RNA-Targeting CRISPR/Cas13d System Eliminates Disease-Related Phenotypes in Pre-clinical Models of Huntington's Disease. ]]> https://biorxiv.org/content/10.1101/2022.01.23.477417v1?rss=1 Morelli, K. H. Wu, Q. Gosztyla, M. L. Liu, H. Zhang, C. Chen, J. Marina, R. Lee, K. Jones, K. L. Duan, W. Yeo, G. W. 2022-01-24 doi:10.1101/2022.01.23.477417 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA ]]> https://biorxiv.org/content/10.1101/2022.01.24.477290v1?rss=1 Carcamo, C. C. Poyton, M. F. Ranjan, A. Park, G. Louder, R. K. Dzu, T. Wu, C. Ha, T. 2022-01-26 doi:10.1101/2022.01.24.477290 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ BOLD cofluctuation 'events' are predicted from static functional connectivity ]]> https://biorxiv.org/content/10.1101/2022.01.24.477543v1?rss=1 50% of BOLD timepoints show high modularity and similarity to time- averaged FC C_LIO_LIStationary null models identified events with similar behavior to real data C_LIO_LIEvents may not be a transient driver of static FC, but rather an expected outcome of it. C_LI ]]> Ladwig, Z. Seitzman, B. A. Dworetsky, A. Yu, Y. Adeyemo, B. Smith, D. M. Petersen, S. E. Gratton, C. 2022-01-27 doi:10.1101/2022.01.24.477543 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ PD-L1 blockade restores CAR T cell activity through IFNγ-regulation of CD163+ macrophages ]]> https://biorxiv.org/content/10.1101/2022.01.25.477150v1?rss=1 Yamaguchi, Y. Gibson, J. Ou, K. Ng, R. H. Jonsson, V. D. Zarif, J. C. Lee, P. P. Wang, X. Martinez, C. Dorff, T. B. Forman, S. J. Priceman, S. J. 2022-01-28 doi:10.1101/2022.01.25.477150 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Multiple Ciliary Localization Signals Control INPP5E Ciliary Targeting ]]> https://biorxiv.org/content/10.1101/2022.01.25.477585v1?rss=1 Cilleros-Rodriguez, D. Martin-Morales, R. Barbeito, P. Deb Roy, A. Loukil, A. Sierra-Rodero, B. Herranz, G. Pampliega, O. Redrejo-Rodriguez, M. Goetz, S. C. Izquierdo, M. Inoue, T. Garcia-Gonzalo, F. R. 2022-01-26 doi:10.1101/2022.01.25.477585 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Design and Characterization of Lipid Nanocarriers for Oral Delivery of Immunotherapeutic Peptides ]]> https://biorxiv.org/content/10.1101/2022.01.27.478027v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@1d18054org.highwire.dtl.DTLVardef@14038ddorg.highwire.dtl.DTLVardef@1555abdorg.highwire.dtl.DTLVardef@b83a42_HPS_FORMAT_FIGEXP M_FIG The development of nanostructured lipid carriers containing a nominal antigen (insulin peptide) for oral delivery consists on (1) nanoparticle formulation using a statistical method, (2) in-vitro studies to assess cellular toxicity and uptake and T cell activation, and (3) in-vivo studies to assess bio-distribution. C_FIG ]]> Calderon Colon, X. Zhang, Y. Tiburzi, O. Wang, J. Raimondi, G. Patrone, J. 2022-01-28 doi:10.1101/2022.01.27.478027 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Cross-modality supervised image restoration enables nanoscale tracking of synaptic plasticity in living mice ]]> https://biorxiv.org/content/10.1101/2022.01.27.478042v1?rss=1 Xu, Y. K. T. Graves, A. R. Coste, G. I. Huganir, R. L. Bergles, D. E. Charles, A. S. Sulam, J. 2022-01-28 doi:10.1101/2022.01.27.478042 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ A Guide for Quantifying and Optimizing Measurement Reliability for the Study of Individual Differences ]]> https://biorxiv.org/content/10.1101/2022.01.27.478100v1?rss=1 Xu, T. Cho, J. Kiar, G. Bridgeford, E. W. Vogelstein, J. T. Milham, M. P. 2022-01-28 doi:10.1101/2022.01.27.478100 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Neural correlates of perceived emotions in human insula and amygdala ]]> https://biorxiv.org/content/10.1101/2022.01.29.477631v1?rss=1 Zhang, Y. Zhou, W. Huang, J. Hong, B. Wang, X. 2022-01-31 doi:10.1101/2022.01.29.477631 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Neuronal membrane proteasomes homeostatically regulate neural circuit activity in vivo and are required for learning-induced behavioral plasticity ]]> https://biorxiv.org/content/10.1101/2022.01.29.478314v1?rss=1 He, H.-y. Ramachandran, K. McLain, N. Faulkner, R. Ahsan, A. Bera, R. Margolis, S. S. Cline, H. T. 2022-01-30 doi:10.1101/2022.01.29.478314 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Chronic brain functional ultrasound imaging in freely moving rodents performing cognitive tasks ]]> https://biorxiv.org/content/10.1101/2022.01.29.478327v1?rss=1 El Hady, A. Takahashi, D. Y. Sun, R. Boyd-Meredith, T. Zhang, Y. Charles, A. Brody, C. 2022-01-31 doi:10.1101/2022.01.29.478327 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ mTOR-regulated Mitochondrial Metabolism Limits Mycobacterium-induced Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2022.01.30.478369v1?rss=1 Pagan, A. J. Lee, L. J. Edwards-Hicks, J. Moens, C. B. Tobin, D. M. Busch-Nentwich, E. M. Pearce, E. L. Ramakrishnan, L. 2022-01-30 doi:10.1101/2022.01.30.478369 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Inside-out tracking and projection mapping for robot-assisted transcranial magnetic stimulation ]]> https://biorxiv.org/content/10.1101/2022.01.30.478399v1?rss=1 Liu, Y. Liu, S. Sefati, S. Tian, J. Kheradmand, A. Armand, M. 2022-02-01 doi:10.1101/2022.01.30.478399 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Single-cell atlas of epithelial and stromal cell heterogeneity by lobe and strain in the mouse prostate ]]> https://biorxiv.org/content/10.1101/2022.01.31.478481v1?rss=1 Graham, M. K. Chikarmane, R. Wang, R. Vaghasia, A. M. Gupta, A. Zheng, Q. Wodu, B. P. Pan, X. Castagna, N. Liu, J. Meyers, J. Skaist, A. Wheelan, S. J. Simons, B. W. Bieberich, C. Nelson, W. DeWeese, T. L. De Marzo, A. M. Yegnasubramanian, S. 2022-01-31 doi:10.1101/2022.01.31.478481 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ A Mouse Model with Complete Penetrance for Atrioventricular Septal Defect/Complete AV Canal ]]> https://biorxiv.org/content/10.1101/2022.02.03.478994v1?rss=1 Li, Y. Andersen, P. Liu, X. Moyer, A. J. Kwon, C. Reeves, R. H. 2022-02-03 doi:10.1101/2022.02.03.478994 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ A scalable and unbiased discordance metric with H+ ]]> https://biorxiv.org/content/10.1101/2022.02.03.479015v1?rss=1 Dyjack, N. Baker, D. N. Braverman, V. Langmead, B. Hicks, S. C. 2022-02-05 doi:10.1101/2022.02.03.479015 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Therapeutic vulnerability to ATR inhibition in concurrent NF1 and ATRX-deficient high-grade solid tumors ]]> https://biorxiv.org/content/10.1101/2022.02.03.479021v1?rss=1 Yuan, M. Eberhart, C. G. Pratilas, C. A. Blakeley, J. O. Davis, C. Stojanova, M. Reilly, K. Meeker, A. K. Heaphy, C. M. Rodriguez, F. J. 2022-02-03 doi:10.1101/2022.02.03.479021 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ LRLoop: Feedback loops as a design principle of cell-cell communication ]]> https://biorxiv.org/content/10.1101/2022.02.04.479174v1?rss=1 Xin, Y. Lyu, P. Jiang, J. Zhou, F. Wang, J. Blackshaw, S. Qian, J. 2022-02-08 doi:10.1101/2022.02.04.479174 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ GSK2556286 is a novel antitubercular drug candidate effective in vivo with the potential to shorten tuberculosis treatment ]]> https://biorxiv.org/content/10.1101/2022.02.04.479214v1?rss=1 Nuermberger, E. Martinez, M. S. Sanz, O. Urones, B. Esquivias, J. Soni, H. Tasneen, R. Tyagi, S. Li, S.-Y. Converse, P. J. Boshoff, H. I. Robertson, G. T. Besra, G. Abrahams, K. A. Upton, A. Mdluli, K. Boyle, G. W. Turner, S. Fotouhi, N. Cammack, N. C. Siles, J. M. Alonso, M. Excribano, J. Lelievre, J. Perez-Herran, E. M. Bates, R. H. Maher-Edwards, G. X. Barros-Aguirre, D. Ballell, L. Jimenez, E. N. 2022-02-06 doi:10.1101/2022.02.04.479214 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ Rtt105 configurationally staples RPA and blocks facilitated exchange and interactions with RPA-interacting proteins ]]> https://biorxiv.org/content/10.1101/2022.02.05.479199v1?rss=1 Kuppa, S. Deveryshetty, J. Chadda, R. Mattice, J. Pokhrel, N. Kaushik, V. Patterson, A. Dhingra, N. Pangeni, S. Sadauskas, M. K. Shiekh, S. Balci, H. Ha, T. Zhao, X. Bothner, B. Antony, E. 2022-02-05 doi:10.1101/2022.02.05.479199 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ InfoMuNet: Information-theory-based Functional Muscle Network Tracks Sensorimotor Integration Post-stroke ]]> https://biorxiv.org/content/10.1101/2022.02.10.479324v1?rss=1 90% of the subjects conformed with the improvement resulting from this sensory exposure. InfoMuNet also shows high sensitivity to tactile, kinesthetic, and visual input alterations at the subject level, highlighting the potential use in precision rehabilitation interventions. ]]> O'Keeffe, R. Shirazi, S. Y. Bilaloglu, S. Jahed, S. Bighamian, R. Raghavan, P. Atashzar, S. F. 2022-02-10 doi:10.1101/2022.02.10.479324 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution. ]]> https://biorxiv.org/content/10.1101/2022.02.10.479955v1?rss=1 Laszlo, A. H. Craig, J. M. Gavrilov, M. Tippana, R. Nova, I. C. Huang, J. R. Kim, H. C. Abell, S. J. deCampos-Stairiker, M. Mount, J. W. Bowman, J. L. Baker, K. S. Higinbotham, H. Bobrovnikov, D. Ha, T. Gundlach, J. H. 2022-02-11 doi:10.1101/2022.02.10.479955 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Single Cell Proteomics Using a Trapped Ion Mobility Time-of-Flight Mass Spectrometer Provides Insight into the Post-translational Modification Landscape of Individual Human Cells ]]> https://biorxiv.org/content/10.1101/2022.02.12.480144v1?rss=1 Orsburn, B. C. Yuan, Y. Bumpus, N. N. 2022-02-12 doi:10.1101/2022.02.12.480144 Cold Spring Harbor Laboratory Press 2022-02-12 <![CDATA[ Enhanced Sodium Channel Inactivation by Temperature and FHF2 Deficiency Blocks Heat Nociception ]]> https://biorxiv.org/content/10.1101/2022.02.12.480202v1?rss=1 Marra, C. Hartke, T. Ringkamp, M. Goldfarb, M. 2022-02-13 doi:10.1101/2022.02.12.480202 Cold Spring Harbor Laboratory Press 2022-02-13 <![CDATA[ Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcoding ]]> https://biorxiv.org/content/10.1101/2022.02.13.480215v1?rss=1 Fang, W. Bell, C. M. Sapirstein, A. Asami, S. Leeper, K. Zack, D. J. Ji, H. Kalhor, R. 2022-02-14 doi:10.1101/2022.02.13.480215 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ The exchange rates of amide and arginine guanidinium CEST in the mouse brain ]]> https://biorxiv.org/content/10.1101/2022.02.14.480399v1?rss=1 Wang, K. Sui, R. Chen, L. Li, Y. Xu, J. 2022-02-16 doi:10.1101/2022.02.14.480399 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ The calcium channel Orai1 is required for osteoblast development: studies in a chimeric mouse with variable in vivo Runx-cre deletion of Orai-1 ]]> https://biorxiv.org/content/10.1101/2022.02.14.480443v1?rss=1 Robinson, L. J. Soboloff, J. Tourkova, I. L. Larrouture, Q. C. Papachristou, D. J. Gross, S. Hooper, R. Samakai, E. Worley, P. F. Tuckermann, J. Witt, M. R. Blair, H. C. 2022-02-14 doi:10.1101/2022.02.14.480443 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ A Bayesian Hierarchical Model for Signal Extraction from Protein Microarrays ]]> https://biorxiv.org/content/10.1101/2022.02.16.480698v1?rss=1 Berube, S. Kobayashi, T. Norris, D. E. Ruczinski, I. Moss, W. J. Wesolowski, A. Louis, T. A. 2022-02-19 doi:10.1101/2022.02.16.480698 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ A Random Forest Classifier Uses Antibody Responses to Plasmodium Antigens to Reveal Candidate Biomarkers of the Intensity and Timing of Past Exposure to Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.02.16.480705v1?rss=1 Berube, S. Kobayashi, T. Norris, D. E. Ruczinski, I. Moss, W. J. Wesolowski, A. Louis, T. A. 2022-02-17 doi:10.1101/2022.02.16.480705 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Oligodendrocytes form paranodal bridges that generate chains of myelin sheaths vulnerable to degeneration with age ]]> https://biorxiv.org/content/10.1101/2022.02.16.480718v1?rss=1 Call, C. L. Neely, S. A. Early, J. J. James, O. G. Zoupi, L. Williams, A. C. Chandran, S. Lyons, D. A. Bergles, D. E. 2022-02-17 doi:10.1101/2022.02.16.480718 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Using Mathematical Modeling to Distinguish Intrinsic and Acquired Targeted Therapeutic Resistance in Head and Neck Cancer ]]> https://biorxiv.org/content/10.1101/2022.02.18.481078v1?rss=1 Cardenas, S. D. Reznik, C. J. Ranaweera, R. Song, F. Chung, C. H. Fertig, E. J. Gevertz, J. L. 2022-02-18 doi:10.1101/2022.02.18.481078 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2022.02.19.481089v1?rss=1 Guarnieri, J. W. Dybas, J. M. Fazelinia, H. Kim, M. S. Frere, J. Zhang, Y. Albrecht, Y. S. Murdock, D. G. Angelin, A. Singh, L. N. Weiss, S. L. Best, S. M. Lott, M. T. Cope, H. Zaksas, V. Saravia-Butler, A. Meydan, C. Foox, J. Mozsary, C. Kidane, Y. H. Priebe, W. Emmett, M. Meller, R. Singh, U. Bram, Y. tenOever, B. R. Heise, M. T. Moorman, N. J. Madden, E. A. Taft-Benz, S. A. Anderson, E. J. Sanders, W. A. Dickmander, R. J. Baxter, V. K. Baylin, S. Wurtele, E. Moraes-vieira, P. Taylor, D. Mason, C. Schisler, J. C. Schwartz, R. E. Beheshti, A. Wallace, 2022-02-22 doi:10.1101/2022.02.19.481089 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Neuromuscular embodiment of feedback control elements in Drosophila flight ]]> https://biorxiv.org/content/10.1101/2022.02.22.481344v1?rss=1 Whitehead, S. C. Leone, S. Lindsay, T. Meiselman, M. R. Cowan, N. Dickinson, M. H. Yapici, N. Stern, D. Shirangi, T. Cohen, I. 2022-02-24 doi:10.1101/2022.02.22.481344 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Systematic Elucidation and Pharmacological Targeting of Tumor-Infiltrating Regulatory T Cell Master Regulators ]]> https://biorxiv.org/content/10.1101/2022.02.22.481404v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1cca60borg.highwire.dtl.DTLVardef@a93ce6org.highwire.dtl.DTLVardef@dd2aa2org.highwire.dtl.DTLVardef@1a2c98_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Obradovic, A. Ager, C. Turunen, M. Nirschl, T. Khosravi-Maharlooei, M. Jackson, C. Yegnasubramanian, V. DeMarzo, A. Kochel, C. Allaf, M. Bivalacqua, T. Lim, M. Karan, C. Drake, C. Califano, A. 2022-02-23 doi:10.1101/2022.02.22.481404 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome ]]> https://biorxiv.org/content/10.1101/2022.02.22.481460v1?rss=1 Fields, P. D. Waneka, G. Naish, M. Schatz, M. C. Henderson, I. R. Sloan, D. B. 2022-02-22 doi:10.1101/2022.02.22.481460 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Diagnostic Ion Data Analysis Reduction (DIDAR) allows rapid quality control analysis and filtering of multiplexed single cell proteomics data ]]> https://biorxiv.org/content/10.1101/2022.02.22.481489v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@1380a32org.highwire.dtl.DTLVardef@258660org.highwire.dtl.DTLVardef@199411eorg.highwire.dtl.DTLVardef@824aa1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jenkins, C. J. Orsburn, B. C. 2022-02-24 doi:10.1101/2022.02.22.481489 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation ]]> https://biorxiv.org/content/10.1101/2022.02.23.480720v1?rss=1 Vandiver, A. R. Pielstick, B. Gilpatrick, T. Hoang, A. Vernon, H. Wanagat, J. Timp, W. 2022-02-24 doi:10.1101/2022.02.23.480720 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Toxoplasma gondii-s basal complex: the other apicomplexan business end is multifunctional ]]> https://biorxiv.org/content/10.1101/2022.02.23.481603v1?rss=1 Gubbels, M.-J. Ferguson, D. J. Saha, S. Romano, J. D. Chavan, S. Primo, V. A. Michaud, C. Coppens, I. Engelberg, K. 2022-02-24 doi:10.1101/2022.02.23.481603 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Resident T cells orchestrate adipose tissue remodeling in a site peripheral to infection ]]> https://biorxiv.org/content/10.1101/2022.02.24.481701v1?rss=1 Kabat, A. M. Hackl, A. Sanin, D. E. Zeis, P. Grzes, K. M. Baixauli, F. Kyle, R. Caputa, G. Edwards-Hicks, J. Villa, M. Rana, N. Curtis, J. D. Castoldi, A. Cupovic, J. Dreesen, L. Sibilia, M. Pospisilik, J. A. Urban, J. F. Grün, D. Pearce, E. L. Pearce, E. J. 2022-02-26 doi:10.1101/2022.02.24.481701 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization ]]> https://biorxiv.org/content/10.1101/2022.02.24.481835v1?rss=1 Narang, S. Evensen, N. Saliba, J. Pierro, J. Loh, M. L. Brown, P. A. Mulder, H. Shao, Y. Easton, J. Ma, X. Tsirigos, A. Carroll, W. L. 2022-02-25 doi:10.1101/2022.02.24.481835 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ PSMA-bearing extracellular vesicles secreted from prostate cancer convert the microenvironment to a tumor-supporting, pro-angiogenic state. ]]> https://biorxiv.org/content/10.1101/2022.02.25.482024v1?rss=1 Machado, C. M. Skubal, M. Haedicke, K. Pittela, F. S. Stater, E. P. Larney, B. M. Silva, T. L. A. O. Costa, E. T. Masotti, C. Otake, A. H. Andrade, L. N. S. Junqueira, M. S. Hsu, H.-T. Das, S. Pratt, E. C. Romin, Y. Fan, N. Todorova, K. M. Pomper, M. Grimm, J. 2022-02-26 doi:10.1101/2022.02.25.482024 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Enabling spatiotemporal regulation within biomaterials using DNA reaction- diffusion waveguides ]]> https://biorxiv.org/content/10.1101/2022.02.26.482105v1?rss=1 Dorsey, P. J. Scalise, D. Schulman, R. 2022-02-28 doi:10.1101/2022.02.26.482105 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV-2 nsp3 Macrodomain ]]> https://biorxiv.org/content/10.1101/2022.02.27.482176v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@167aceorg.highwire.dtl.DTLVardef@1d88c47org.highwire.dtl.DTLVardef@1e1b34borg.highwire.dtl.DTLVardef@c2321a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sherrill, L. M. Joya, E. E. Walker, A. Roy, A. Alhammad, Y. M. Atobatele, M. Wazir, S. Abbas, G. Keane, P. Zhuo, J. Leung, A. Johnson, D. K. Lehtio, L. Fehr, A. Ferraris, D. V. 2022-02-28 doi:10.1101/2022.02.27.482176 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ A Single Multipurpose FSH-Blocking Therapeutic for Osteoporosis and Obesity ]]> https://biorxiv.org/content/10.1101/2022.02.28.482279v1?rss=1 Gera, S. Kuo, T.-C. Korkmaz, F. Sant, D. DeMambro, V. Gumerova, A. A. Sudha, K. Padilla, A. Prevot, G. Munitz, J. Teunissen, A. van Leent, M. M. T. Post, T. G. J. M. Fernandes, J. C. Netto, J. Sultana, F. Shelly, E. Kumar, P. Cullen, L. Chatterjee, J. Miyashita, S. Kannangara, H. Bhongade, M. Ievleva, K. Muradova, V. Batista, R. Robinson, C. Macdonald, A. Babunovic, S. Saxena, M. Meseck, M. Caminis, J. Iqbal, J. New, M. I. Ryu, V. Kim, S.-M. Cao, J. Zaidi, N. Fayad, Z. A. Lizneva, D. J. Rosen, C. Yuen, T. Zaidi, M. 2022-03-02 doi:10.1101/2022.02.28.482279 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.02.28.482334v1?rss=1 Vesuna, F. Akhrymuk, I. Smith, A. Winnard, P. T. Lin, S.-C. Scharpf, R. Kehn-Hall, K. Raman, V. 2022-03-01 doi:10.1101/2022.02.28.482334 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Psilocybin induces spatially constrained alterations in thalamic functional organization and connectivity ]]> https://biorxiv.org/content/10.1101/2022.02.28.482395v1?rss=1 Gaddis, A. Lidstone, D. E. Nebel, M. B. Griffiths, R. R. Mostofsky, S. H. Meija, A. Barrett, F. S. 2022-03-02 doi:10.1101/2022.02.28.482395 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening ]]> https://biorxiv.org/content/10.1101/2022.03.01.482536v1?rss=1 Roy, A. Alhammad, Y. M. McDonald, P. Johnson, D. K. Zhuo, J. Wazir, S. Ferraris, D. V. Lehtiö, L. Leung, A. Fehr, A. R. 2022-03-02 doi:10.1101/2022.03.01.482536 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Developmentally programmed epigenome regulates cellular plasticity at the parental-to-zygote transition ]]> https://biorxiv.org/content/10.1101/2022.03.01.482564v1?rss=1 Gleason, R. J. Semancik, C. S. Lakshminarayanan, G. Chen, X. 2022-03-04 doi:10.1101/2022.03.01.482564 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Cell-specific regulation of gene expression using splicing-dependent frameshifting. ]]> https://biorxiv.org/content/10.1101/2022.03.02.481623v1?rss=1 Ling, J. Bygrave, A. Santiago, C. Carmen, R. Trinh, V. Yu, M. Li, Y. Han, J. Taneja, K. Liu, Y. Dongmo, R. Babola, T. Parker, P. Jiang, L. Leavey, P. Smith, J. Vistein, R. Gimmen, M. Dubner, B. Teodorescu, P. KARANTANOS, T. Ghiaur, G. Kanold, P. Bergles, D. E. Langmead, B. Sun, S. Nielsen, K. Peachey, N. Singh, M. Dalton, W. Rajaii, F. Huganir, R. L. Blackshaw, S. 2022-03-02 doi:10.1101/2022.03.02.481623 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ The mitochondrion of Plasmodium falciparum generates essential acetyl-CoA for protein acetylation ]]> https://biorxiv.org/content/10.1101/2022.03.02.482627v1?rss=1 Nair, S. C. Munro, J. T. Mann, A. Llinas, M. Prigge, S. T. 2022-03-02 doi:10.1101/2022.03.02.482627 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Combining transgenesis with paratransgenesis to fight malaria ]]> https://biorxiv.org/content/10.1101/2022.03.02.482642v1?rss=1 Huang, W. Vega-Rodriguez, J. Kizito, C. Cha, S.-J. Jacobs-Lorena, M. 2022-03-02 doi:10.1101/2022.03.02.482642 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Transcytosis-mediated anterograde transport of TrkA receptors is necessary for sympathetic neuron development and function ]]> https://biorxiv.org/content/10.1101/2022.03.03.482877v1?rss=1 Connor, B. Yamashita, N. Kuruvilla, R. 2022-03-04 doi:10.1101/2022.03.03.482877 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease ]]> https://biorxiv.org/content/10.1101/2022.03.04.479488v1?rss=1 Zhou, P. Song, G. He, W.-t. Beutler, N. Tse, L. V. Martinez, D. R. Schafer, A. Anzanello, F. Yong, P. Peng, L. Dueker, K. Musharrafieh, R. Callaghan, S. Capozzola, T. Yuan, M. Liu, H. Limbo, O. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Nemazee, D. Jardine, J. G. Wilson, I. A. Safonova, Y. Rogers, T. Baric, R. S. Gralinski, L. E. Burton, D. R. Andrabi, R. 2022-03-07 doi:10.1101/2022.03.04.479488 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ The ion permeability of DNA nanotube channels ]]> https://biorxiv.org/content/10.1101/2022.03.04.482952v1?rss=1 Dhanasekar, N. N. Li, Y. Schulman, R. 2022-03-04 doi:10.1101/2022.03.04.482952 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Lyophilization induces alterations in cryptococcal exopolysaccharide resulting in reduced antibody binding ]]> https://biorxiv.org/content/10.1101/2022.03.04.483041v1?rss=1 Wear, M. P. Hargett, A. A. Kelly, J. E. McConnell, S. A. Crawford, C. Freedberg, D. I. Stark, R. E. E. Casadevall, A. 2022-03-05 doi:10.1101/2022.03.04.483041 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Protein Optimization Evolving Tool (POET) based on Genetic Programming ]]> https://biorxiv.org/content/10.1101/2022.03.05.483103v1?rss=1 Bricco, A. R. Miralavy, I. Bo, S. Perlman, O. Farrar, C. T. McMahon,, M. T. Banzhaf, W. Gilad, A. 2022-03-06 doi:10.1101/2022.03.05.483103 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Automated assembly of high-quality diploid human reference genomes ]]> https://biorxiv.org/content/10.1101/2022.03.06.483034v1?rss=1 Jarvis, E. D. Formenti, G. Rhie, A. Guarracino, A. Yang, C. Wood, J. Tracey, A. Thibaud-Nissen, F. Vollger, M. R. Porubsky, D. Cheng, H. Asri, M. Logsdon, G. A. Carnevali, P. Chaisson, M. Chin, C.-S. Cody, S. Collins, J. Ebert, P. Escalona, M. Fedrigo, O. Fulton, R. S. Fulton, L. L. Garg, S. Ghurye, J. Green, E. Hall, I. M. Harvey, W. H. Hasenfeld, P. Hastie, A. Haukness, M. Jain, M. Kirsche, M. Kolmogorov, M. Korbel, J. O. Koren, S. Korlach, J. Lee, J. Li, D. Lindsay, T. Lucas, J. Luo, F. Marschall, T. McDaniel, J. Nie, F. Olsen, H. E. Olson, N. 2022-03-06 doi:10.1101/2022.03.06.483034 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ LanA (Language Atlas): A probabilistic atlas for the language network based on fMRI data from >800 individuals ]]> https://biorxiv.org/content/10.1101/2022.03.06.483177v1?rss=1 Lipkin, B. Tuckute, G. Affourtit, J. Small, H. Mineroff, Z. Kean, H. Jouravlev, O. Rakocevic, L. Pritchett, B. Siegelman, M. Hoeflin, C. Pongos, A. Blank, I. Shruhl, M. K. Ivanova, A. Shannon, S. Sathe, A. Hoffmann, M. Nieto-Castanon, A. Fedorenko, E. 2022-03-07 doi:10.1101/2022.03.06.483177 800 individuals]]> Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Excitatory and inhibitory D-serine binding to the NMDA receptor ]]> https://biorxiv.org/content/10.1101/2022.03.07.483247v1?rss=1 Yovanno, R. A. Chou, T. H. Brantley, S. J. Furukawa, H. Lau, A. Y. 2022-03-08 doi:10.1101/2022.03.07.483247 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Non-literal language processing is jointly supported by the language and Theory of Mind networks: Evidence from a novel meta-analytic fMRI approach ]]> https://biorxiv.org/content/10.1101/2022.03.08.481056v1?rss=1 Hauptman, M. Blank, I. Fedorenko, E. 2022-03-10 doi:10.1101/2022.03.08.481056 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ The vigor paradox: saccade velocity during deliberation encodes utility of effortful actions ]]> https://biorxiv.org/content/10.1101/2022.03.09.483677v1?rss=1 Korbisch, C. C. Apuan, D. Shadmehr, R. Ahmed, A. A. 2022-03-11 doi:10.1101/2022.03.09.483677 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ IPMK modulates insulin-mediated suppression of hepatic glucose production ]]> https://biorxiv.org/content/10.1101/2022.03.10.483655v1?rss=1 Jung, I.-R. Anokye-Danso, F. Jin, S. Ahima, R. S. Kim, S. F. 2022-03-10 doi:10.1101/2022.03.10.483655 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Assembly and phylogeographic analysis of novel Taenia solium mitochondrial genomes reveal further differentiation between and within Asian and African-American genotypes ]]> https://biorxiv.org/content/10.1101/2022.03.10.483888v1?rss=1 Jimenez-Avalos, G. Soto Obando, A. Solis, M. Gilman, R. H. Cama, V. Garcia, H. H. Sheen, P. Requena, D. Zimic, M. 2022-03-11 doi:10.1101/2022.03.10.483888 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Dimensionality reduction of calcium-imaged neuronal population activity ]]> https://biorxiv.org/content/10.1101/2022.03.11.480682v1?rss=1 Koh, T. H. Bishop, W. E. Kawashima, T. Jeon, B. B. Srinivasan, R. Kuhlman, S. J. Ahrens, M. B. Chase, S. M. Yu, B. M. 2022-03-14 doi:10.1101/2022.03.11.480682 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events ]]> https://biorxiv.org/content/10.1101/2022.03.14.484207v1?rss=1 Allen, G. Weiss, B. Panasenko, O. O. Huch, S. Villanyi, Z. Albert, B. Dilg, D. Zagatti, M. Schaughency, P. Liao, S. Corden, J. Polte, C. Shore, D. Ignatova, Z. Pelechano, V. Collart, M. A. 2022-03-14 doi:10.1101/2022.03.14.484207 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Unleashing alternative polyadenylation analyses with REPAC ]]> https://biorxiv.org/content/10.1101/2022.03.14.484280v1?rss=1 Imada, E. L. Wilks, C. Langmead, B. Marchionni, L. 2022-03-16 doi:10.1101/2022.03.14.484280 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Dynamic single-cell RNA sequencing reveals BCG vaccination curtails SARS-CoV-2 induced disease severity and lung inflammation ]]> https://biorxiv.org/content/10.1101/2022.03.15.484018v1?rss=1 Singh, A. K. Wang, R. Lombardo, K. A. Praharaj, M. Bullen, C. K. Um, P. Davis, S. Komm, O. Illei, P. B. Ordonez, A. A. Bahr, M. Huang, J. Gupta, A. Psoter, K. J. Jain, S. K. Bivalacqua, T. J. Yegnasubramanian, S. Bishai, W. 2022-03-15 doi:10.1101/2022.03.15.484018 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ -Labeled PARP-1 PET Imaging of PSMA Targeted Alpha Particle Radiotherapy Response ]]> https://biorxiv.org/content/10.1101/2022.03.16.484613v1?rss=1 Zhang, H. Abou, D. Villmer, A. Benabdallah, N. Jiang, W. Ulmert, D. Carlin, S. Rogers, B. E. Turtle, N. F. McDevitt, M. Baumann, B. Simons, B. W. Zhou, D. Thorek, D. L. 2022-03-18 doi:10.1101/2022.03.16.484613 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Projective LDDMM: Spatially Reconstructing a Story of Rostrally-Dominant Tau in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.03.16.484623v1?rss=1 Stouffer, K. Witter, M. Chen, C. Xu, E. Albert, M. Mori, S. Troncoso, J. Tward, D. J. Miller, M. 2022-03-18 doi:10.1101/2022.03.16.484623 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Interface resistance of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2022.03.16.484641v1?rss=1 Zhang, Y. Pyo, A. G. T. Jiang, Y. Brangwynne, C. P. Stone, H. A. Wingreen, N. S. 2022-03-18 doi:10.1101/2022.03.16.484641 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria ]]> https://biorxiv.org/content/10.1101/2022.03.17.484479v1?rss=1 Pejaver, V. Byrne, A. B. Feng, B.-J. Pagel, K. A. Mooney, S. D. Karchin, R. O'Donnell-Luria, A. Harrison, S. M. Tavtigian, S. V. Greenblatt, M. S. Biesecker, L. G. Radivojac, P. Brenner, S. E. ClinGen Sequence Variant Interpretation Working Group, 2022-03-19 doi:10.1101/2022.03.17.484479 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Studies of a siderophore-producing cyclization domain: A refined proposal of substrate binding ]]> https://biorxiv.org/content/10.1101/2022.03.18.483834v1?rss=1 Gnann, A. D. Xia, Y. Soule, J. Barthelemy, C. Mawani, J. S. Nzikoba Musoke, S. Castellano, B. M. Brignole, E. J. Frueh, D. Dowling, D. P. 2022-03-19 doi:10.1101/2022.03.18.483834 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Accurate Protein Domain Structure Annotation with DomainMapper ]]> https://biorxiv.org/content/10.1101/2022.03.19.484986v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@1900be8org.highwire.dtl.DTLVardef@1fdae2borg.highwire.dtl.DTLVardef@1b5bd5corg.highwire.dtl.DTLVardef@a31d56_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Manriquez-Sandoval, E. Fried, S. D. 2022-03-20 doi:10.1101/2022.03.19.484986 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ HDAC6 inhibitor ACY-1083 shows lung epithelial protective features in COPD ]]> https://biorxiv.org/content/10.1101/2022.03.21.485098v1?rss=1 Horndahl, J. Svärd, R. Berntsson, P. Wingren, C. Li, J. Abdillahi, S. M. Ghosh, B. Capodanno, E. Chan, J. Ripa, L. Astrand, A. Sidhaye, V. K. Collins, M. 2022-03-21 doi:10.1101/2022.03.21.485098 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2022.03.21.485199v1?rss=1 Ravi, A. Gainor, J. F. Arniella, M. B. Holton, M. Freeman, S. S. Stewart, C. Leshchiner, I. Kim, J. Akiyama, Y. Griffin, A. T. Vokes, N. I. Sakhi, M. Kamesan, V. Rizvi, H. Ricciuti, B. Forde, P. M. Anagnostou, V. Reiss, J. W. Gibbons, D. L. Pennell, N. A. Velcheti, V. Digumarthy, S. R. Mino-Kenudson, M. Califano, A. Heymach, J. V. Herbst, R. S. Brahmer, J. R. Schalper, K. A. Velculescu, V. E. Henick, B. S. Rizvi, N. Janne, P. A. Awad, M. M. Chow, A. Greenbaum, B. D. Luksza, M. Shaw, A. T. Wolchok, J. Hacohen, N. Getz, G. Hellmann, M. D. 2022-03-23 doi:10.1101/2022.03.21.485199 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Multi-finger Receptive Field Properties in Primary Somatosensory Cortex: A Revised Account of the Spatio-Temporal Integration Functions of Area 3b ]]> https://biorxiv.org/content/10.1101/2022.03.21.485210v1?rss=1 Trzcinski, N. K. Hsiao, S. S. Connor, C. E. Gomez-Ramirez, M. 2022-03-23 doi:10.1101/2022.03.21.485210 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Genomic insights into metabolic flux in ruby-throated hummingbirds ]]> https://biorxiv.org/content/10.1101/2022.03.21.485221v1?rss=1 Gershman, A. Hauck, Q. Dick, M. Jamison, J. M. Tassia, M. Agirrezabala, X. Muhammad, S. Ali, R. Workman, R. E. Valle, M. Wong, G. W. Welch, K. C. Timp, W. 2022-03-21 doi:10.1101/2022.03.21.485221 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies ]]> https://biorxiv.org/content/10.1101/2022.03.22.485297v1?rss=1 Cherry, C. Andorko, J. I. Krishnan, K. Mejias, J. C. Nguyen, H. H. Stivers, K. B. Gray-Gaillard, E. F. Ruta, A. Hamada, N. Hamada, M. Sturmlechner, I. Trewartha, S. Michel, J. H. Huyer, L. D. Wolf, M. T. Tam, A. Pena, A. N. Le Saux, C. J. Fertig, E. J. Baker, D. J. Housseau, F. van Deursen, J. M. Pardoll, D. M. Elisseeff, J. H. 2022-03-25 doi:10.1101/2022.03.22.485297 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ MRSCloud: a Cloud-based MR Spectroscopy Tool for Basis Set Simulation ]]> https://biorxiv.org/content/10.1101/2022.03.22.485310v1?rss=1 Hui, S. C. N. Saleh, M. Zoellner, H. J. Oeltzschner, G. Fan, H. Li, Y. Song, Y. Jiang, H. Near, J. Lu, H. Mori, S. Edden, R. 2022-03-25 doi:10.1101/2022.03.22.485310 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Novel Methods for Multi-ancestry Polygenic Prediction and their Evaluations in 3.7 Million Individuals of Diverse Ancestry ]]> https://biorxiv.org/content/10.1101/2022.03.24.485519v1?rss=1 Zhang, H. Zhan, J. Jin, J. Ahearn, T. U. Yu, Z. O'Connell, J. Jiang, Y. Chen, T. 23andMe Research Team, Garcia-Closas, M. Lin, X. Koelsch, B. L. Chatterjee, N. 2022-03-27 doi:10.1101/2022.03.24.485519 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert ]]> https://biorxiv.org/content/10.1101/2022.03.24.485700v1?rss=1 Perez-Fernandez, C. Wilburn, P. Davila, A. DiRuggiero, J. 2022-03-24 doi:10.1101/2022.03.24.485700 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Peripheral blood T-cell deficiency and hyperinflammatory monocyte responses associate with MAC lung disease ]]> https://biorxiv.org/content/10.1101/2022.03.25.485768v1?rss=1 Lindestam Arlehamn, C. S. Benson, B. Kuan, R. Dill-McFarland, K. A. Peterson, G. J. Paul, S. Nguyen, F. K. Gilman, R. H. Saito, M. Taplitz, R. Arentz, M. Goss, C. H. Aitken, M. L. Horne, D. J. Shah, J. A. Sette, A. Hawn, T. R. 2022-03-27 doi:10.1101/2022.03.25.485768 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ The Human Motoneuron Expression Signature is Defined by ALS-Related Genes ]]> https://biorxiv.org/content/10.1101/2022.03.25.485808v1?rss=1 Yadav, A. Matson, K. J. E. Li, L. Hua, I. Gaur, P. Alkaslasi, M. R. Hasan, S. Galuta, A. Dedek, A. Ameri, S. Parnell, J. Alshardan, M. M. Ququmji, F. A. Alhamad, S. M. Wang, A. P. Poulen, G. Lonjon, N. Vachiery-Lahaye, F. Nalls, M. A. Nalls, M. A. Qi, Y. A. Hildebrand, M. E. Mery, P.-F. Bourinet, E. Bauchet, L. Tsai, E. C. Ward, M. E. Le Pichon, C. Menon, V. Levine, A. 2022-03-28 doi:10.1101/2022.03.25.485808 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Mutational Changes and Enhanced Cell Migration during Transformation of Breast Non-tumorigenic Cells to Tumorigenic Cells ]]> https://biorxiv.org/content/10.1101/2022.03.27.485986v1?rss=1 Lee, S. H. T. Kim, J. Y. Kim, P. Su, C.-Y. Ahn, E. H. 2022-03-28 doi:10.1101/2022.03.27.485986 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Intracellular Energy Controls Dynamics of Stress-induced Ribonucleoprotein Granules ]]> https://biorxiv.org/content/10.1101/2022.03.28.486002v1?rss=1 Wang, T. Tian, X. Jang, Y. Huang, P. Na, C. H. Wang, J. 2022-03-28 doi:10.1101/2022.03.28.486002 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Comprehensive profiling of antibody responses to the human anellome using programmable phage display ]]> https://biorxiv.org/content/10.1101/2022.03.28.486145v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@132dfforg.highwire.dtl.DTLVardef@130c47dorg.highwire.dtl.DTLVardef@b3fc97org.highwire.dtl.DTLVardef@8c49f9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Venkataraman, T. Swaminathan, H. Arze, C. Jacobo, S. M. Bhattacharyya, A. David, T. Nawandar, D. Delagrave, S. Mani, V. Yozwiak, N. L. Larman, H. B. 2022-03-29 doi:10.1101/2022.03.28.486145 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Mesoscopic oblique plane microscopy (Meso-OPM) - enabling large-scale 4D isotropic cellular resolution imaging with a diffractive light sheet ]]> https://biorxiv.org/content/10.1101/2022.03.29.486239v1?rss=1 Shao, W. Chang, M. Emmerich, K. Kanold, P. O. Mumm, J. S. Yi, J. 2022-03-30 doi:10.1101/2022.03.29.486239 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ OTTERS: A powerful TWAS framework leveraging summary-level reference data ]]> https://biorxiv.org/content/10.1101/2022.03.30.486451v1?rss=1 Dai, Q. Zhou, G. Zhao, H. Vosa, U. Franke, L. Battle, A. Teumer, A. Lehtimaki, T. Raitakari, O. Esko, T. eQTLGen Consortium, Epstein, M. P. Yang, J. 2022-04-01 doi:10.1101/2022.03.30.486451 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Screening the Pathogen Box Compounds for Activity Against Plasmodium falciparum Sporozoite Motility ]]> https://biorxiv.org/content/10.1101/2022.03.30.486498v1?rss=1 kanatani, S. Elahi, R. Kanchanabhogin, S. Vartek, N. Tripathi, A. Prigge, S. Sinnis, P. 2022-03-31 doi:10.1101/2022.03.30.486498 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of "genetic purging" ]]> https://biorxiv.org/content/10.1101/2022.03.31.486393v1?rss=1 Mohr, D. W. Gaughran, S. J. Paschall, J. Naguib, A. Pang, A. W. C. Dudchenko, O. Aiden, E. L. Church, D. M. Scott, A. F. 2022-03-31 doi:10.1101/2022.03.31.486393 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ On the relationship between Pathogenic Potential and Infective Inoculum ]]> https://biorxiv.org/content/10.1101/2022.03.31.486506v1?rss=1 Smith, D. F. Q. Casadevall, A. 2022-03-31 doi:10.1101/2022.03.31.486506 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Oncogene-induced matrix reorganization controls CD8+ T cell function in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.03.31.486627v1?rss=1 Pruitt, H. C. Fuller, A. M. Song, H. Liu, Y. DeVine, A. Katti, R. S. Devalaraja, S. Ciotti, G. E. Gonzalez, M. Williams, E. F. Murazzi, I. Skuli, N. Hakonarson, H. Weber, K. Haldar, M. Fraietta, J. A. Gerecht, S. Eisinger-Mathason, T. S. K. 2022-03-31 doi:10.1101/2022.03.31.486627 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome ]]> https://biorxiv.org/content/10.1101/2022.04.04.486905v1?rss=1 Hoffmann, N. Rahman, S. Worden, E. J. Smith, M. L. Namitz, K. E. Knutson, B. Cosgrove, M. S. Wolberger, C. 2022-04-04 doi:10.1101/2022.04.04.486905 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ The influence of stereopsis on visual saliency in a proto-object based model of selective attention ]]> https://biorxiv.org/content/10.1101/2022.04.04.486976v1?rss=1 Uejima, T. Mancinelli, E. Niebur, E. Etienne-Cummings, R. 2022-04-05 doi:10.1101/2022.04.04.486976 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Engineering functional membrane-membrane interface by InterSpy ]]> https://biorxiv.org/content/10.1101/2022.04.04.487023v1?rss=1 Moghimianavval, H. Patel, C. Mohapatra, S. Hwang, S.-W. Kayikcioglu, T. Bashirzadeh, Y. Liu, A. P. Ha, T. 2022-04-04 doi:10.1101/2022.04.04.487023 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation, and ssDNA binding kinetics ]]> https://biorxiv.org/content/10.1101/2022.04.05.486416v1?rss=1 Orris, B. Huynh, K. W. Ammirati, M. Han, S. Bolanos, B. Carmody, J. Petroski, M. D. Bosbach, B. Shields, D. J. Stivers, J. T. 2022-04-06 doi:10.1101/2022.04.05.486416 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut ]]> https://biorxiv.org/content/10.1101/2022.04.05.487115v1?rss=1 Mohammed, M. Dziedziech, A. Sekar, V. Ernest, M. Alves E Silva, T. L. Balan, B. Emami, S. N. Biryukova, I. Friedlander, M. R. Jex, A. Jacobs-Lorena, M. Henriksson, J. Vega-Rodriguez, J. Ankarklev, J. 2022-04-05 doi:10.1101/2022.04.05.487115 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Ectopic insert-dependent neuronal expression of GFAP promoter-driven AAV constructs in adult mouse retina. ]]> https://biorxiv.org/content/10.1101/2022.04.06.487191v1?rss=1 Le, N. Appel, H. Pannullo, N. Hoang, T. Blackshaw, S. 2022-04-09 doi:10.1101/2022.04.06.487191 Cold Spring Harbor Laboratory Press 2022-04-09 <![CDATA[ Genetically defined nucleus incertus neurons differ in connectivity and function ]]> https://biorxiv.org/content/10.1101/2022.04.07.487414v1?rss=1 Spikol, E. D. Cheng, J. Macurak, M. Subedi, A. Halpern, M. E. 2022-04-10 doi:10.1101/2022.04.07.487414 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Structural insights into sodium/iodide symporter (NIS) substrate binding and specificity ]]> https://biorxiv.org/content/10.1101/2022.04.07.487502v1?rss=1 Ravera, S. Nicola, J. P. Salazar de Simone, G. Sigworth, F. J. Karakas, E. Amzel, L. M. Bianchet, M. A. Carrasco, N. 2022-04-08 doi:10.1101/2022.04.07.487502 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ In Silico Improvement of Highly Protective Anti-Malarial Antibodies ]]> https://biorxiv.org/content/10.1101/2022.04.08.487687v1?rss=1 Mateo, M. Tripathi, P. Da Silva Pereira, L. Kiyuka, P. Liu, T. Zhang, B. Yang, Y. Bonilla, B. G. Dillon, M. Lee, M. Shen, C.-H. Schon, A. Kratochvil, S. Batista, F. D. Idris, A. H. Seder, R. A. Kwong, P. D. Rawi, R. 2022-04-09 doi:10.1101/2022.04.08.487687 Cold Spring Harbor Laboratory Press 2022-04-09 <![CDATA[ Manipulating the 3D organization of the largest synthetic yeast chromosome ]]> https://biorxiv.org/content/10.1101/2022.04.09.487066v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@18bf586org.highwire.dtl.DTLVardef@1a471d5org.highwire.dtl.DTLVardef@12d7690org.highwire.dtl.DTLVardef@1c32510_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDe novo synthesis of the largest eukaryotic chromosome, synIV C_LIO_LISynIV shows similar 3D structure to wild-type IV, despite thousands of changes made to it C_LIO_LI"Inside-out" repositioning of synIV in nucleus shows minor transcriptional changes C_LIO_LIMultipoint tethering synIV to inner nuclear membrane represses transcription of whole chromosome C_LI ]]> Zhang, W. Stefanita, L. L. Yamashita, H. Shen, M. J. Mitchell, L. A. Kurasawa, H. Haase, M. A. B. Sun, X. Jiang, Q. Lauer, S. L. McCulloch, L. H. Zhao, Y. Ichikawa, D. Easo, N. Lin, S. J. Fanfani, V. Camellato, B. R. Zhu, Y. Cai, J. Xu, Z. Sacasa, M. Accardo, R. Ahn, J. Y. Annadanam, S. Brammer Basta, L. A. Bello, N. Cai, L. Cerritos, S. Cornwell, M. D'Amato, A. Hacker, M. Hersey, K. Kennedy, E. Kianercy, A. Kim, D. Lim, H. S. McCutcheon, G. McGirr, K. Meaney, N. Meyer, L. Moyer, A. Nimer, M. Sabbatini, C. Scheifele, L. Shores, L. Silvestrone, C. S 2022-04-10 doi:10.1101/2022.04.09.487066 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Toxoplasma scavenges mammalian host organelles through usurpation of host ESCRT-III and Vps4 ]]> https://biorxiv.org/content/10.1101/2022.04.11.487923v1?rss=1 Coppens, I. Romano, J. D. Mayoral, J. A. Guevara, R. Rivera-Cuevas, Y. Carruthers, V. B. Weiss, L. M. 2022-04-11 doi:10.1101/2022.04.11.487923 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2022.04.12.487379v1?rss=1 Chen, M. Pekosz, A. Villano, J. Shen, W. Zhou, R. Kulaga, H. Li, Z. Beck, S. E. Witwer, K. W. Mankowski, J. Ramanathan, M. Rowan, N. Lane, A. 2022-04-12 doi:10.1101/2022.04.12.487379 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Human and murine Cryptococcus neoformans infection selects for common genomic changes in an environmental isolate. ]]> https://biorxiv.org/content/10.1101/2022.04.12.487930v1?rss=1 Sephton-Clark, P. McConnell, S. A. Grossman, N. Baker, R. Dragotakes, Q. Fan, Y. Fu, M. S. Gerbig, G. Greengo, S. Hardwick, J. M. Kulkarni, M. Levitz, S. M. Nosanchuk, J. D. Shoham, S. Smith, D. Stempinski, P. Wear, M. Cuomo, C. A. Casadevall, A. 2022-04-12 doi:10.1101/2022.04.12.487930 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ EstG is a novel esterase required for cell envelope integrity ]]> https://biorxiv.org/content/10.1101/2022.04.12.488081v1?rss=1 Daitch, A. K. Orsburn, B. C. Chen, Z. Alvarez, L. Eberhard, C. D. Sundararajan, K. Zeinert, R. Kreitler, D. F. Jakoncic, J. Chien, P. Cava, F. Gabelli, S. B. Bumpus, N. N. Goley, E. D. 2022-04-12 doi:10.1101/2022.04.12.488081 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ In macrophages fatty acid oxidation spares glutamate for use in diverse metabolic pathways required for alternative activation ]]> https://biorxiv.org/content/10.1101/2022.04.13.487890v1?rss=1 van Teijlingen Bakker, N. Flachsmann, L. Carrizo, G. E. Sanin, D. E. Lawless, S. Castoldi, A. Monteiro, L. Kabat, A. M. Matsushita, M. Haessler, F. Patterson, A. Klein Geltink, R. O'Sullivan, D. Pearce, E. L. Pearce, E. J. 2022-04-13 doi:10.1101/2022.04.13.487890 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Lossless end-to-end transport of small molecules through micron-length DNA nanochannels ]]> https://biorxiv.org/content/10.1101/2022.04.13.488239v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@fec963org.highwire.dtl.DTLVardef@157bb83org.highwire.dtl.DTLVardef@d7a274org.highwire.dtl.DTLVardef@ea961c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, Y. Maffeo, C. Joshi, H. Aksimentiev, A. Menard, B. Schulman, R. 2022-04-14 doi:10.1101/2022.04.13.488239 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Metastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation ]]> https://biorxiv.org/content/10.1101/2022.04.17.488591v1?rss=1 Kaur, A. Kiani, K. Fingerman, D. Dunagin, M. C. Li, J. Dardani, I. Sanford, E. M. Pemberton, J. Goyal, Y. Weeraratna, A. T. Herlyn, M. Raj, A. 2022-04-18 doi:10.1101/2022.04.17.488591 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Nucleosome sliding by the Chd1 chromatin remodeler relies on theintegrity of the DNA duplex ]]> https://biorxiv.org/content/10.1101/2022.04.19.488687v1?rss=1 Park, S. Ha, T. Bowman, G. 2022-04-19 doi:10.1101/2022.04.19.488687 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ An intranasal stringent response vaccine targeting dendritic cells as a novel adjunctive therapy against tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.04.19.488816v1?rss=1 Karanika, S. Gordy, J. Neupane, P. KARANTANOS, T. Castillo, J. Quijada, D. Comstock, K. Sandhu, A. Hui, Y. Ayeh, S. Tasneen, R. Krug, S. Danchik, C. Wang, T. Schill, C. Markham, R. t. Karakousis, P. 2022-04-19 doi:10.1101/2022.04.19.488816 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via epigenetic regulation of key regenerative pathways ]]> https://biorxiv.org/content/10.1101/2022.04.19.488817v1?rss=1 Wang, X.-W. Yang, S.-G. Hu, M.-W. Wang, R.-Y. Zhang, C. Kosanam, A. R. Ochuba, A. J. Jiang, J.-J. Luo, X. Qian, J. Liu, C.-M. Zhou, F.-Q. 2022-04-19 doi:10.1101/2022.04.19.488817 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies ]]> https://biorxiv.org/content/10.1101/2022.04.20.488972v1?rss=1 Ruffolo, J. A. Chu, L.-S. Mahajan, S. P. Gray, J. J. 2022-04-21 doi:10.1101/2022.04.20.488972 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Synaptotagmin 7 docks synaptic vesicles for Doc2α-triggered asynchronous neurotransmitter release ]]> https://biorxiv.org/content/10.1101/2022.04.21.489101v1?rss=1 Wu, Z. Kusick, G. F. Raychaudhuri, S. Itoh, K. Chapman, E. R. Watanabe, S. 2022-04-21 doi:10.1101/2022.04.21.489101 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Projective LDDMM: Mapping Molecular Digital Pathology with Tissue MRI ]]> https://biorxiv.org/content/10.1101/2022.04.22.489163v1?rss=1 Stouffer, K. Witter, M. Tward, D. J. Miller, M. I. 2022-04-24 doi:10.1101/2022.04.22.489163 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ Simple within-stride changes in treadmill speed can drive selective changes in human gait symmetry ]]> https://biorxiv.org/content/10.1101/2022.04.22.489204v1?rss=1 Browne, M. G. Stenum, J. Padmanabhan, P. Roemmich, R. T. 2022-04-22 doi:10.1101/2022.04.22.489204 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ The language network reliably 'tracks' naturalistic meaningful non-verbal stimuli ]]> https://biorxiv.org/content/10.1101/2022.04.24.489316v1?rss=1 Sueoka, Y. Paunov, A. Ivanova, A. Blank, I. A. Fedorenko, E. 2022-04-25 doi:10.1101/2022.04.24.489316 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Pseudomonas aeruginosa Elicits Sustained IL-1β Upregulation in Alveolar Macrophages from Lung Transplant Recipients ]]> https://biorxiv.org/content/10.1101/2022.04.26.489590v1?rss=1 Britton, N. Rueda, A. V. Whiteside, S. A. Mathew, J. Kelley, M. Agbor-Enoh, S. McDyer, J. Christie, J. D. Collman, R. G. Cox, A. Shah, P. D'Alessio, F. 2022-04-26 doi:10.1101/2022.04.26.489590 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Age-related changes of deep-brain neurophysiological activity ]]> https://biorxiv.org/content/10.1101/2022.04.27.489652v1?rss=1 Hinault, T. T. Baillet, S. T. Courtney, S. 2022-04-28 doi:10.1101/2022.04.27.489652 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Improved sequence mapping using a complete reference genome and lift-over ]]> https://biorxiv.org/content/10.1101/2022.04.27.489683v1?rss=1 Chen, N.-C. Paulin, L. F. Sedlazeck, F. J. Koren, S. Phillippy, A. M. Langmead, B. 2022-04-28 doi:10.1101/2022.04.27.489683 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ The lateral habenula mediates the association of a conditioned stimulus with the absence of an appetitive unconditioned stimulus ]]> https://biorxiv.org/content/10.1101/2022.04.27.489815v1?rss=1 Kim, D.-H. Jin, I.-B. Kim, N.-H. Jeon, Y.-J. Choi, B.-R. Gallagher, M. Han, J.-S. 2022-04-29 doi:10.1101/2022.04.27.489815 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ C-Jun N-terminal Kinase Promotes Stress Granule Assembly and Neurodegeneration in C9orf72-mediated ALS and FTD ]]> https://biorxiv.org/content/10.1101/2022.04.28.489917v1?rss=1 TG, S. Chase, K. J. Liu, F. Lloyd, T. E. Rossoll, W. Zhang, K. 2022-04-29 doi:10.1101/2022.04.28.489917 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Control becomes habitual early on when learning a novel motor skill ]]> https://biorxiv.org/content/10.1101/2022.04.28.489941v1?rss=1 Yang, C. S. Cowan, N. J. Haith, A. M. 2022-04-28 doi:10.1101/2022.04.28.489941 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Ex vivo to in vivo model of malignant peripheral nerve sheath tumors for precision oncology ]]> https://biorxiv.org/content/10.1101/2022.04.29.490078v1?rss=1 Bhatia^, H. Larsson^, A. T. Calizo^, A. Pollard, K. Zhang, X. Conniff, E. Tibbitts, J. F. Osum, S. H. Williams, K. B. Crampton, A. L. Jubenville, T. Schefer, D. Yang, K. Lyu, Y. Bade, J. Pino, J. C. Gosline, S. J. Pratilas, C. A. Largaespada, D. A. Wood, D. K. Hirbe, A. C. 2022-05-02 doi:10.1101/2022.04.29.490078 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains ]]> https://biorxiv.org/content/10.1101/2022.05.01.489089v1?rss=1 Kos, J. T. Safonova, Y. Shields, K. M. Silver, C. A. Lees, W. D. Collins, A. M. Watson, C. T. 2022-05-01 doi:10.1101/2022.05.01.489089 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Light-dependent modulation of protein localization and function in living bacteria cells ]]> https://biorxiv.org/content/10.1101/2022.05.01.490209v1?rss=1 McQuillen, R. Yang, X. Bohrer, C. H. McCausland, J. Xiao, J. 2022-05-01 doi:10.1101/2022.05.01.490209 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Microbial metabolite butyrate-prodrug polymeric micelles promote gut health and treat food allergies ]]> https://biorxiv.org/content/10.1101/2022.05.01.490224v1?rss=1 Wang, R. Cao, S. Bashir, M. E. H. Hesser, L. A. Su, Y. Hong, S. M. C. Thompson, A. Culleen, E. Sabados, M. Dylla, N. P. Campbell, E. Alshaikh, A. A. Shim, H.-N. Wu, H. Bao, R. Wilson, D. S. Nagler, C. R. Hubbell, J. A. 2022-05-01 doi:10.1101/2022.05.01.490224 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Helminth egg derivatives as pro-regenerative immunotherapies ]]> https://biorxiv.org/content/10.1101/2022.05.02.490277v1?rss=1 Maestas, D. R. Chung, L. Han, J. Wang, X. Sommerfeld, S. D. Moore, E. Hieu Nguyen, H. Mejias, J. C. Pena, A. N. Zhang, H. Hooks, J. S. T. Chin, A. F. Andorko, J. I. Berlicke, C. Krishnan, K. Choi, Y. Anderson, A. E. Mahatme, R. Mejia, C. Eric, M. Woo, J. Ganguly, S. Zack, D. J. Housseau, F. Pardoll, D. M. Elisseeff, J. H. 2022-05-04 doi:10.1101/2022.05.02.490277 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Hypereosinophilia causes progressive cardiac pathologies in mice ]]> https://biorxiv.org/content/10.1101/2022.05.04.490445v1?rss=1 Diny, N. L. Wood, M. K. Won, T. Talor, M. V. Lukban, C. Bedja, D. Wang, N. Talbot, C. C. Lin, B. L. Cihakova, D. 2022-05-05 doi:10.1101/2022.05.04.490445 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Contributions and synaptic basis of diverse cortical neuron responses to task performance ]]> https://biorxiv.org/content/10.1101/2022.05.04.490676v1?rss=1 Insanally, M. N. Albanna, B. F. Toth, J. DePasquale, B. Fadaei, S. Gupta, T. Kuchibhotla, K. Rajan, K. Froemke, R. C. 2022-05-05 doi:10.1101/2022.05.04.490676 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine ]]> https://biorxiv.org/content/10.1101/2022.05.04.490709v1?rss=1 Venkatesh, D. Anderson, T. K. Kimble, J. B. Chang, J. Lopes, S. Souza, C. K. Pekosz, A. Shaw-Saliba, K. Rothman, R. E. Chen, K.-F. Lewis, N. Vincent, A. L. 2022-05-05 doi:10.1101/2022.05.04.490709 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ A parallel channel of state-dependent sensory signaling from the cholinergic basal forebrain to the auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.05.05.490613v1?rss=1 Zhu, F. Elnozahy, S. E. Lawlor, J. Kuchibhotla, K. V. 2022-05-05 doi:10.1101/2022.05.05.490613 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Inter-scanner brain MRI volumetric biases persist even in a harmonized multi-subject study of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2022.05.05.490645v1?rss=1 50% of the variation for most estimated volumes. This expanded to > 75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intra-scanner differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact. ConclusionDifferences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating inter-scanner differences show promise in reducing biases in multi-center studies of MS. ]]> Clark, K. A. O'Donnell, C. M. Elliott, M. A. Tauhid, S. Dewey, B. E. Chu, R. Khalil, S. Nair, G. Sati, P. DuVal, A. Pellegrini, N. Bar-Or, A. Markowitz, C. Schindler, M. K. Zurawski, J. Calabresi, P. A. Reich, D. S. Bakshi, R. Shinohara, R. T. The North American Imaging in Multiple Sclerosis Cooperative, 2022-05-05 doi:10.1101/2022.05.05.490645 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Senescent Preosteoclast Secretome Promotes Metabolic Syndrome Associated Osteoarthritis through Cyclooxygenase 2 ]]> https://biorxiv.org/content/10.1101/2022.05.05.490792v1?rss=1 Wan, M. Su, W. Liu, G. Mohajer, B. Wang, J. Shen, A. Zhang, W. Liu, B. Guermazi, A. Gao, P. Cao, X. Demehri, S. 2022-05-05 doi:10.1101/2022.05.05.490792 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Hierarchical cue control of drug seeking in the face of cost ]]> https://biorxiv.org/content/10.1101/2022.05.05.490799v1?rss=1 Collins, V. Bornhoft, K. N. Wolff, A. Sinha, S. Saunders, B. T. 2022-05-05 doi:10.1101/2022.05.05.490799 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Autonomous untethered microinjectors for gastrointestinal delivery of insulin ]]> https://biorxiv.org/content/10.1101/2022.05.05.490821v1?rss=1 Ghosh, A. Liu, W. Li, L. Pahapale, G. Choi, S. Y. Xu, L. Huang, Q. Selaru, F. M. Gracias, D. 2022-05-05 doi:10.1101/2022.05.05.490821 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Reinstatement of Pavlovian responses to alcohol cues by stress ]]> https://biorxiv.org/content/10.1101/2022.05.06.490952v1?rss=1 Armstrong, A. Rosenthal, H. Stout, N. Richard, J. M. 2022-05-08 doi:10.1101/2022.05.06.490952 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Adipokine C1q/Tumor necrosis factor-related protein 3 (CTRP3) Attenuates Intestinal Inflammation via Histone Deacetylase Sirtuin 1 (SIRT1)/NF-κB Signaling ]]> https://biorxiv.org/content/10.1101/2022.05.08.491034v1?rss=1 Yu, H. Zhang, Z. Li, G. Feng, Y. Xian, L. Bakhsh, F. J. Xu, D. Xu, C. Vong, T. Wu, B. Selaru, F. M. Wan, F. Wong, G. W. Donowitz, M. 2022-05-08 doi:10.1101/2022.05.08.491034 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Spatiotemporal atlas of the fetal brain depicts cortical developmental gradient in Chinese population ]]> https://biorxiv.org/content/10.1101/2022.05.09.491258v1?rss=1 Xu, X. Sun, C. Sun, J. Shi, W. Shen, Y. Zhao, R. Luo, W. Li, M. Wang, G. Wu, D. 2022-05-10 doi:10.1101/2022.05.09.491258 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Novel tumorigenic FOXM1-PTAFR-PTAF axis revealed by multi-omic profiling in TP53/CDKN2A-double knockout human gastroesophageal junction organoid model ]]> https://biorxiv.org/content/10.1101/2022.05.10.491356v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@18dcb8dorg.highwire.dtl.DTLVardef@2ec0d6org.highwire.dtl.DTLVardef@17622b8org.highwire.dtl.DTLVardef@e184bc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhao, H. Cheng, Y. Kalra, A. Ma, K. Zheng, Y. Ziman, B. Tressler, C. Glunde, K. Shin, E. J. Ngamruengphong, S. Khashab, M. Singh, V. Anders, R. A. Jit, S. Wyhs, N. Chen, W. Li, X. Lin, D.-c. Meltzer, S. J. 2022-05-11 doi:10.1101/2022.05.10.491356 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ A spatial map of antennal-expressed olfactory ionotropic receptors in the malaria mosquito ]]> https://biorxiv.org/content/10.1101/2022.05.11.491386v1?rss=1 Raji, J. R. Potter, C. J. 2022-05-12 doi:10.1101/2022.05.11.491386 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ APOE Expression and Secretion are Modulated by Copper-Dependent and -Independent Mitochondrial Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.05.11.491499v1?rss=1 Wynne, M. E. Ogunbona, O. Lane, A. R. Gokhale, A. Zlatic, S. A. Xu, C. Wen, Z. Duong, D. Ivanova, A. Orlund, E. A. Seyfried, N. T. Crocker, A. Shanbhag, V. Petris, M. Senoo, N. Kandasamy, S. Claypool, S. M. Wingo, A. P. Wingo, T. S. Levey, A. Werner, E. Faundez, V. 2022-05-11 doi:10.1101/2022.05.11.491499 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Evidence for a common mechanism supporting invigoration of action selection and action execution ]]> https://biorxiv.org/content/10.1101/2022.05.12.491560v1?rss=1 Kita, K. Du, Y. Haith, A. M. 2022-05-13 doi:10.1101/2022.05.12.491560 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Polo-like kinase-1 Inhibitors and the Antiandrogen Abiraterone Synergistically Disrupt Mitosis and Kill Cancer Cells of Disparate Origin Independently of Androgen Receptor Signaling ]]> https://biorxiv.org/content/10.1101/2022.05.12.491633v1?rss=1 Patterson, J. C. Varkaris, A. Croucher, P. J. P. Ridinger, M. Darlymple, S. Nouri, M. Xie, F. Varmeh, S. Jonas, O. Whitman, M. A. Chen, S. Rashed, S. Makusha, L. Luo, J. Isaacs, J. T. Erlander, M. G. Einstein, D. J. Balk, S. P. Yaffe, M. B. 2022-05-13 doi:10.1101/2022.05.12.491633 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Transretinal migration of astrocytes and brain/spinal cord-like cells arising from transplanted human retinal organoids. ]]> https://biorxiv.org/content/10.1101/2022.05.12.491655v1?rss=1 Liu, Y. Santiago, C. Sogunro, A. Konar, G. K. Hu, M.-W. McNally, M. M. Lu, Y. Li, Z. Agakishiev, D. Hadyniak, S. Hussey, K. Creamer, T. J. Orzolek, L. D. Teng, D. Qian, J. Jiang, Z. Johnston, R. J. Blackshaw, S. Singh, M. S. 2022-05-13 doi:10.1101/2022.05.12.491655 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Picking winners in cell-cell collisions: wetting, speed, and contact ]]> https://biorxiv.org/content/10.1101/2022.05.13.491710v1?rss=1 Zadeh, P. Camley, B. A. 2022-05-14 doi:10.1101/2022.05.13.491710 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ TGFβ treatment alters the scleral fibroblast migratory response to cyclic strain in an ERK-dependent manner ]]> https://biorxiv.org/content/10.1101/2022.05.14.491950v1?rss=1 Mozzer, A. Pitha, I. 2022-05-14 doi:10.1101/2022.05.14.491950 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ A curated human cellular microRNAome based on 196 primary cell types ]]> https://biorxiv.org/content/10.1101/2022.05.16.492160v1?rss=1 Patil, A. H. Baran, A. Brehm, Z. McCall, M. N. Halushka, M. K. 2022-05-17 doi:10.1101/2022.05.16.492160 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Primary cilia regulate Meibomian glands development and dimensions without impairing the lipid composition of the meibum ]]> https://biorxiv.org/content/10.1101/2022.05.16.492188v1?rss=1 Portal, C. Lin, Y. Rastogi, V. Peterson, C. Foster, J. Wilkerson, A. Butovich, I. A. Iomini, C. 2022-05-17 doi:10.1101/2022.05.16.492188 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Serine Racemase is a Cysteine Racemase and Physiologic Down Regulator of Insulin Promoter Methylation ]]> https://biorxiv.org/content/10.1101/2022.05.17.492243v1?rss=1 Roychaudhuri, R. Gadalla, M. M. Albacarys, L. West, T. Saavedra, H. Amzel, L. M. Snyder, S. H. 2022-05-17 doi:10.1101/2022.05.17.492243 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Considerations for Deconvolution: A Case Study with GTEx Coronary Artery Tissues ]]> https://biorxiv.org/content/10.1101/2022.05.17.492324v1?rss=1 Brehm, Z. P. Sherina, V. Rosenberg, A. Z. Halushka, M. K. McCall, M. N. 2022-05-19 doi:10.1101/2022.05.17.492324 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Jak2V617F Reversible Activation Shows an Essential Requirement for Jak2V617F in Myeloproliferative Neoplasms ]]> https://biorxiv.org/content/10.1101/2022.05.18.492332v1?rss=1 Dunbar, A. Bowman, R. L. Park, Y. Izzo, F. Myers, R. M. Karzai, A. Jun Kim, W. Fernandez Maestre, I. Waarts, M. R. Nazir, A. Xiao, W. Brodsky, M. Farina, M. Cai, L. Cai, S. F. Wang, B. An, W. Yang, J. L. Mowla, S. Eisman, S. E. Mishra, T. Houston, R. Guzzardi, E. Martinez Benitez, A. R. Viny, A. Koche, R. Landau, D. A. Levine, R. L. 2022-05-18 doi:10.1101/2022.05.18.492332 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ The TERT promoter is polycomb-repressed in neuroblastoma cells with long telomeres ]]> https://biorxiv.org/content/10.1101/2022.05.18.492493v1?rss=1 Graham, M. K. Xu, B. Davis, C. Meeker, A. K. Heaphy, C. M. Yegnasubramanian, S. Dyer, M. A. Zeineldin, M. 2022-05-20 doi:10.1101/2022.05.18.492493 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Pangenomic genotyping with the marker array ]]> https://biorxiv.org/content/10.1101/2022.05.19.492566v1?rss=1 Mun, T. Vaddadi, N. S. K. Langmead, B. 2022-05-20 doi:10.1101/2022.05.19.492566 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Spatiotemporal dynamics of membrane surface charge regulates cell polarity and migration ]]> https://biorxiv.org/content/10.1101/2022.05.19.492577v1?rss=1 Banerjee, T. Biswas, D. Pal, D. S. Miao, Y. Iglesias, P. A. Devreotes, P. N. 2022-05-20 doi:10.1101/2022.05.19.492577 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Bisected graph matching improves automated pairing of bilaterally homologous neurons from connectomes ]]> https://biorxiv.org/content/10.1101/2022.05.19.492713v1?rss=1 Pedigo, B. D. Winding, M. Priebe, C. E. Vogelstein, J. T. 2022-05-20 doi:10.1101/2022.05.19.492713 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Overexpression screen of chromosome 21 genes reveals modulators of Sonic hedgehog signaling relevant to Down syndrome ]]> https://biorxiv.org/content/10.1101/2022.05.19.492735v1?rss=1 Moyer, A. J. Fernandez, F. X. Li, Y. Klinedinst, D. K. Florea, L. D. Kazuki, Y. Oshimura, M. Reeves, R. H. 2022-05-19 doi:10.1101/2022.05.19.492735 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Periostin+ stromal cells guide lymphovascular invasion by cancer cells ]]> https://biorxiv.org/content/10.1101/2022.05.19.492742v1?rss=1 Null, J. L. Kim, D. J. McCann, J. V. Kumar, P. Edatt, L. Pecot, C. V. Dudley, A. C. 2022-05-20 doi:10.1101/2022.05.19.492742 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ A Remarkable Adaptive Paradigm Of Heart Performance And Protection Emerges In Response To The Constitutive Challenge Of Marked Cardiac-Specific Overexpression Of Adenylyl Cyclase Type 8 ]]> https://biorxiv.org/content/10.1101/2022.05.20.491883v1?rss=1 Tarasov, K. V. Chakir, K. Riordon, D. R. Lyashkov, A. E. Ahmet, I. Perino, M. G. Silvester, A. J. Zhang, J. Wang, M. Lukyanenko, Y. O. Qu, J.-H. Barrera, M. C.-R. Juhaszova, M. Tarasova, Y. S. Ziman, B. Telljohann, R. Kumar, V. Ranek, M. Lammons, J. Beshkov, R. deCabo, R. Jun, S. Keceli, G. Gupta, A. Yang, D. Aon, M. A. Adamo, L. Morrell, C. H. Otu, W. Carroll, C. Chambers, S. Paolocci, N. Huynh, T. Pacak, K. Weiss, R. Field, L. Sollott, S. S. Lakatta, E. G. 2022-05-20 doi:10.1101/2022.05.20.491883 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Quantification and statistical modeling of Chromium-based single-nucleus RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/2022.05.20.492835v1?rss=1 Kuo, A. Hansen, K. D. Hicks, S. C. 2022-05-20 doi:10.1101/2022.05.20.492835 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Unique Effects of Sedatives, Dissociatives, Psychedelics, Stimulants, and Cannabinoids on Episodic Memory: A Review and Reanalysis of Acute Drug Effects on Recollection, Familiarity, and Metamemory ]]> https://biorxiv.org/content/10.1101/2022.05.20.492842v1?rss=1 Doss, M. Samaha, J. Barrett, F. S. Griffiths, R. de Wit, H. Gallo, D. Koen, J. 2022-05-24 doi:10.1101/2022.05.20.492842 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ The SARS-CoV-2 spike protein binds and modulates estrogen receptors ]]> https://biorxiv.org/content/10.1101/2022.05.21.492920v1?rss=1 9,000 human proteins and found significant S-host protein interactions, including one between S and human estrogen receptor alpha (ER). After confirming this interaction in a secondary assay, we used bioinformatics, supercomputing, and experimental assays to identify a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit and an S-ER binding mode. In cultured cells, S DNA transfection increased ER cytoplasmic accumulation, and S treatment induced ER-dependent biological effects and ACE2 expression. Noninvasive multimodal PET/CT imaging in SARS-CoV-2-infected hamsters using [18F]fluoroestradiol (FES) localized lung pathology with increased ER lung levels. Postmortem experiments in lung tissues from SARS-CoV-2-infected hamsters and humans confirmed an increase in cytoplasmic ER expression and its colocalization with S protein in alveolar macrophages. These findings describe the discovery and characterization of a novel S-ER interaction, imply a role for S as an NRC, and are poised to advance knowledge of SARS-CoV-2 biology, COVID-19 pathology, and mechanisms of sex differences in the pathology of infectious disease. ]]> Solis, O. Beccari, A. R. Iaconis, D. Talarico, C. Ruiz-Bedoya, C. A. Nwachukwu, J. C. Cimini, A. Castelli, V. Bertini, R. Montopoli, M. Cocetta, V. Borocci, S. Prandi, I. G. Flavahan, K. Bahr, M. Napiorkowski, A. Chillemi, G. Ooka, M. Yang, X. Zhang, S. Xia, M. Zheng, W. Bonaventura, J. Pomper, M. G. Hooper, J. E. Morales, M. Rosenberg, A. Z. Nettles, K. W. Jain, S. K. Allegretti, M. Michaelides, M. 2022-05-23 doi:10.1101/2022.05.21.492920 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Identification of Potent CD43+ Effector CD8+ T cells Elicited After Transplantation ]]> https://biorxiv.org/content/10.1101/2022.05.21.492934v1?rss=1 Cohen, G. Kallarakal, M. Ibukun, F. I. Krummey, S. 2022-05-22 doi:10.1101/2022.05.21.492934 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ Cardiac-Gated Spectroscopic Photoacoustic Imaging for Ablation-Induced Necrotic Lesion Visualization: In Vivo Demonstration in a Beating Heart ]]> https://biorxiv.org/content/10.1101/2022.05.23.492682v1?rss=1 Gao, S. Ashikaga, H. Suzuki, M. Mansi, T. Kim, Y.-H. Ghesu, F.-C. Kang, J. Boctor, E. M. Halperin, H. R. Zhang, H. K. 2022-05-24 doi:10.1101/2022.05.23.492682 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry ]]> https://biorxiv.org/content/10.1101/2022.05.23.493136v1?rss=1 Sarni, S. H. Roca, J. Du, C. Jia, M. Li, H. Damjanovic, A. Małecka, E. Wysocki, V. Woodson, S. A. 2022-05-23 doi:10.1101/2022.05.23.493136 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Adaptation of cyanobacteria to the endolithic light spectrum in hyper-arid deserts ]]> https://biorxiv.org/content/10.1101/2022.05.24.493334v1?rss=1 Murray, B. Ertekin, E. Dailey, M. Soulier, N. T. Shen, G. Bryant, D. A. Perez-Fernandez, C. DiRuggiero, J. 2022-05-25 doi:10.1101/2022.05.24.493334 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Variation in glutamate and GABA genes and their association with brain structure and chemistry in autism ]]> https://biorxiv.org/content/10.1101/2022.05.25.493390v1?rss=1 Naaijen, J. Arenella, M. Zoellner, H. J. Puts, N. Lythgoe, D. J. Brandeis, D. Durston, S. Poelmans, G. Ruisch, I. H. Buitelaar, J. K. 2022-05-25 doi:10.1101/2022.05.25.493390 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ PACeR: a bioinformatic pipeline for the analysis of chimeric RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.05.25.493487v1?rss=1 Mills, W. T. Jaffe, A. E. Meffert, M. K. 2022-05-29 doi:10.1101/2022.05.25.493487 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ ALDH9A1 Deficiency as a Source of Endogenous DNA Damage that Requires Repair by the Fanconi Anemia Pathway ]]> https://biorxiv.org/content/10.1101/2022.05.26.493623v1?rss=1 Jung, M. Ilyashov, I. Park, Y. Donovan, F. X. Ramanagoudr Bhojappa, R. Keahi, D. Durmaz, J. A. Choijilsuren, H. B. Goldfarb, A. Stein, M. Kim, J. White, R. R. Sridhar, S. Noonan, R. Wiley, T. Carroll, T. S. Lach, F. P. Auerbach, A. D. Miranda, I. Chandrasekharappa, S. C. Smogorzewska, A. 2022-05-27 doi:10.1101/2022.05.26.493623 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ sMAP: An interactive microarray data analysis tool for early-stage researchers ]]> https://biorxiv.org/content/10.1101/2022.05.27.492984v1?rss=1 Bharti, S. Krishnan, N. Veyssi, A. Momeni, M. Raj, S. 2022-05-29 doi:10.1101/2022.05.27.492984 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ On How, and Why, and When, We Grow Old ]]> https://biorxiv.org/content/10.1101/2022.05.29.493895v1?rss=1 Citti, L. Su, J. Michaelson, J. S. 2022-06-02 doi:10.1101/2022.05.29.493895 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Engineered human cytokine/antibody fusion proteins expand regulatory T cells and confer autoimmune disease protection ]]> https://biorxiv.org/content/10.1101/2022.05.29.493918v1?rss=1 VanDyke, D. Iglesias, M. Tomala, J. Young, A. Smith, J. Perry, J. A. Gebara, E. Cross, A. R. Cheung, L. S. Dykema, A. G. Orcutt-Jahns, B. T. Henclova, T. Golias, J. Balolong, J. Tomasovic, L. M. Funda, D. Meyer, A. S. Pardoll, D. M. Hester, J. Issa, F. Hunter, C. A. Anderson, M. S. Bluestone, J. A. Raimondi, G. Spangler, J. B. 2022-05-29 doi:10.1101/2022.05.29.493918 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ The Value of Zero-filling in In Vivo MRS ]]> https://biorxiv.org/content/10.1101/2022.05.31.494144v1?rss=1 Murali-Manohar, S. Oeltzschner, G. Barker, P. B. Edden, R. A. E. 2022-06-01 doi:10.1101/2022.05.31.494144 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Multiple Cullin-Associated E3 Ligases Regulate Cyclin D1 Protein Stability ]]> https://biorxiv.org/content/10.1101/2022.05.31.494151v1?rss=1 Lu, K. Zhang, M. Xiao, G. Tong, L. Chen, D. 2022-06-01 doi:10.1101/2022.05.31.494151 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Mitochondrial function determines severity but not risk of amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2022.05.31.494229v1?rss=1 Harvey, C. Weinreich, M. Zhang, S. Hop, P. J. Zwamborn, R. A. van Eijk, K. R. Julian, T. H. Moll, T. Iacoangeli, A. R. Al-Khleifat, A. Quinn, J. P. Pfaff, A. L. Koks, S. Poulton, J. Battle, S. L. Arking, D. Snyder, M. Project MinE ALS Sequencing Consortium, Veldink, J. Kenna, K. P. Shaw, P. J. Cooper-Knock, J. 2022-06-01 doi:10.1101/2022.05.31.494229 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Achieving single nucleotide sensitivity in direct hybridization genome imaging ]]> https://biorxiv.org/content/10.1101/2022.05.31.494230v1?rss=1 Wang, Y. Cottle, W. T. Wang, H. Gavrilov, M. Zou, R. S. Bailey, S. Ha, T. 2022-06-01 doi:10.1101/2022.05.31.494230 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Greater breadth of vaccine-induced immunity in females than males is mediated by increased antibody diversity in germinal center B cells ]]> https://biorxiv.org/content/10.1101/2022.05.31.494237v1?rss=1 Ursin, R. L. Dhakal, S. Liu, H. Jayaraman, S. Park, H.-S. Powell, H. R. Sherer, M. L. Littlefield, K. E. Fink, A. L. Ma, Z. Mueller, A. L. Chen, A. P. Woldetsadik, Y. A. Gearhart, P. J. Larman, H. B. Maul, R. W. Pekosz, A. Klein, S. L. 2022-06-01 doi:10.1101/2022.05.31.494237 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Inter-regional delays fluctuate in the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2022.06.01.494224v1?rss=1 Moon, J.-Y. Muesch, K. Schroeder, C. Valiante, T. Honey, C. 2022-06-03 doi:10.1101/2022.06.01.494224 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Leveraging place field repetition to understand positional versus nonpositional inputs to hippocampal field CA1 ]]> https://biorxiv.org/content/10.1101/2022.06.01.494227v1?rss=1 Hockeimer, W. Lai, R.-Y. Natrajan, M. Snider, W. Knierim, J. J. 2022-06-02 doi:10.1101/2022.06.01.494227 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Scalable graph analysis tools for the connectomics community ]]> https://biorxiv.org/content/10.1101/2022.06.01.494307v1?rss=1 Matelsky, J. K. Johnson, E. C. Wester, B. Gray-Roncal, W. R. 2022-06-02 doi:10.1101/2022.06.01.494307 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.06.01.494337v1?rss=1 Sessions, D. T. Kim, K.-B. Kashatus, J. A. Churchill, N. Park, K.-S. Mayo, M. W. Sesaki, H. Kashatus, D. F. 2022-06-01 doi:10.1101/2022.06.01.494337 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Metagenomic classification with KrakenUniq on low-memory computers ]]> https://biorxiv.org/content/10.1101/2022.06.01.494344v1?rss=1 Pockrandt, C. Zimin, A. V. Salzberg, S. L. 2022-06-02 doi:10.1101/2022.06.01.494344 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Dynamin forms liquid-like condensates at synapses to support ultrafast endocytosis ]]> https://biorxiv.org/content/10.1101/2022.06.01.494432v1?rss=1 Imoto, Y. Ma, Y. Itoh, K. Blumrich, E.-M. Matsubayashi, H. T. Liu, J. Wu, B. Cousin, M. A. Ha, T. Inoue, T. Watanabe, S. 2022-06-03 doi:10.1101/2022.06.01.494432 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces ]]> https://biorxiv.org/content/10.1101/2022.06.02.490672v1?rss=1 Deshpande, A. Loth, M. Sidiropoulos, D. N. Zhang, S. Yuan, L. Bell, A. Zhu, Q. Ho, W. J. Santa-Maria, C. A. Gilkes, D. M. Williams, S. Uytingco, C. Chew, J. Hartnett, A. Bent, Z. Favorov, A. V. Popel, A. S. Yarchoan, M. Zheng, L. Jaffee, E. M. Anders, R. Danilova, L. Stein-O'Brien, G. Kagohara, L. T. Fertig, E. J. 2022-06-02 doi:10.1101/2022.06.02.490672 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Advances in non-invasive tracking of wave-type electric fish in natural and laboratory settings ]]> https://biorxiv.org/content/10.1101/2022.06.02.494479v1?rss=1 Raab, T. Jayakumar, R. P. Madhav, M. Henninger, J. Cowan, N. Benda, J. 2022-06-03 doi:10.1101/2022.06.02.494479 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Galaxy Training: A Powerful Framework for Teaching! ]]> https://biorxiv.org/content/10.1101/2022.06.02.494505v1?rss=1 Hiltemann, S. Rasche, H. Gladman, S. Hotz, H.-R. Lariviere, D. Blankenberg, D. Jagtap, P. D. Wollmann, T. Bretaudeau, A. Goue, N. Griffin, T. J. Royaux, C. Le Bras, Y. Mehta, S. Syme, A. E. Coppens, F. Droesbeke, B. Soranzo, N. Bacon, W. Psomopoulos, F. E. Gallardo-Alba, C. Davis, J. Föll, M. C. Fahrner, M. Doyle, M. A. Serrano-Solano, B. Fouilloux, A. C. van Heusden, P. Maier, W. Clements, D. Heyl, F. Grüning, B. A. Batut, B. Galaxy Training Network, 2022-06-03 doi:10.1101/2022.06.02.494505 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC ]]> https://biorxiv.org/content/10.1101/2022.06.03.494617v1?rss=1 Liu, S. Li, L. Zhang, F. van Sambeek, B. Appleton, E. Ng, A. H. M. Khoshakhlagh, P. Chen, Y. Garcia-Corral, M. Wu, C.-T. Huang, J. Y. Tan, Y. Chao, G. Aach, J. Tam, J. Lim, E. T. Raychaudhuri, S. Church, G. 2022-06-03 doi:10.1101/2022.06.03.494617 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Genome-Wide Large-Scale Multi-Trait Analysis Characterizes Global Patterns of Pleiotropy and Unique Trait-Specific Variants ]]> https://biorxiv.org/content/10.1101/2022.06.03.494686v1?rss=1 Qi, G. Chhetri, S. B. Ray, D. Dutta, D. Battle, A. Bhattacharjee, S. Chatterjee, N. 2022-06-03 doi:10.1101/2022.06.03.494686 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features ]]> https://biorxiv.org/content/10.1101/2022.06.03.494724v1?rss=1 Harmalkar, A. Rao, R. M. Honer, J. Deisting, W. Anlahr, J. Hoenig, A. Czwikla, J. Sienz-Widmann, E. Rau, D. Rice, A. Riley, T. P. Li, D. Catterall, H. B. Tinberg, C. E. Gray, J. J. Wei, K. Y. 2022-06-04 doi:10.1101/2022.06.03.494724 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Proteome-wide microarray-based screening of PAR-binding proteins ]]> https://biorxiv.org/content/10.1101/2022.06.06.494829v1?rss=1 Kang, B. G. Kang, S.-U. Kim, J. J. Kwon, J.-S. Gagne, J.-P. Lee, S. Y. Kim, S. Sangwon, K. L. Ha, S. Jeong, J. S. Lee, Y.-I. Zhu, H. Kim, D. Poirier, G. G. Kang, H. C. Dawson, V. L. Dawson, T. M. 2022-06-06 doi:10.1101/2022.06.06.494829 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Amygdalar and ERC Rostral Atrophy and Tau Pathology Reconstruction in Preclinical Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.06.06.494859v1?rss=1 Stouffer, K. Chen, C. Kulason, S. Xu, E. Witter, M. Ceritoglu, C. Albert, M. Mori, S. Troncoso, J. Tward, D. J. Miller, M. I. 2022-06-08 doi:10.1101/2022.06.06.494859 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ PLK4 drives centriole amplification and apical surface area expansion in multiciliated cells ]]> https://biorxiv.org/content/10.1101/2022.06.06.494981v1?rss=1 LoMastro, G. M. Drown, C. G. Maryniak, A. L. Jewett, C. E. Strong, M. A. Holland, A. J. 2022-06-07 doi:10.1101/2022.06.06.494981 Cold Spring Harbor Laboratory Press 2022-06-07 <![CDATA[ Hallucinating structure-conditioned antibody libraries for target-specific binders ]]> https://biorxiv.org/content/10.1101/2022.06.06.494991v1?rss=1 Mahajan, S. P. Ruffolo, J. A. Frick, R. Gray, J. J. 2022-06-06 doi:10.1101/2022.06.06.494991 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Plasticity of transmembrane helix interactions in EphA2 dimers and oligomers ]]> https://biorxiv.org/content/10.1101/2022.06.06.495010v1?rss=1 Wirth, D. Ozdemir, E. Wimley, W. C. Pasquale, E. B. Hristova, K. 2022-06-06 doi:10.1101/2022.06.06.495010 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ The efficacy of EphA2 tyrosine phosphorylation increases with EphA2 oligomer size ]]> https://biorxiv.org/content/10.1101/2022.06.07.495003v1?rss=1 Zapata-Mercado, E. Biener, G. McKenzie, D. Wimley, W. C. Pasquale, E. B. Raicu, V. Hristova, K. 2022-06-09 doi:10.1101/2022.06.07.495003 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Neurometabolic timecourse of healthy aging ]]> https://biorxiv.org/content/10.1101/2022.06.08.495050v1?rss=1 0.25). Levels of sI were significantly higher in the PCC in female subjects (p<0.001) than in male subjects. There was a significant positive correlation between linewidth and age. ConclusionThe results indicated age correlations for tCho, tCr, sI, and mI in CSO and for tCr, tCho and GABA in PCC, while no age-related changes were found for NAA, tNAA, GSH, Glu or Glx. Our results provide a normative foundation for future work investigating the neurometabolic time course of healthy aging using MRS. HighlightsO_LIA large structured cross-sectional cohort of neurometabolic aging dataset is presented; C_LIO_LIAge correlations were observed for tCho, tCr, sI, and mI in CSO and for tCr, tCho and GABA in PCC; C_LIO_LINo age correlations were found for NAA, tNAA, GSH, Glu or Glx in either region. C_LI ]]> Gong, T. Hui, S. C. N. Zollner, H. J. Britton, M. Song, Y. Chen, Y. Gudmundson, A. T. Hupfeld, K. E. Murali-Manohar, S. Porges, E. Oeltzschner, G. Chen, W. Wang, G. Edden, R. A. E. 2022-06-10 doi:10.1101/2022.06.08.495050 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Subtype-specific single β1 integrin mechanics for activation, mechanotransduction and cytoskeleton remodeling ]]> https://biorxiv.org/content/10.1101/2022.06.08.495291v1?rss=1 54-pN) via myosin II. Conformational activation of both integrins occurs below 12-pN, suggesting that post-activation subtype-specific cytoskeletal remodeling imposes the higher threshold for spreading on RGD substrates. Multiple layers of single integrin mechanics for activation, mechanotransduction and cytoskeleton remodeling revealed here may underlie subtype-dependence of diverse processes such as somite formation and durotaxis. ]]> Jo, M. H. Li, J. Jaumouille, V. Hao, Y. Coppola, J. Yan, J. Waterman, C. M. Springer, T. A. Ha, T. 2022-06-09 doi:10.1101/2022.06.08.495291 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Highly accurate isoform identification for the human transcriptome ]]> https://biorxiv.org/content/10.1101/2022.06.08.495354v1?rss=1 Sommer, M. J. Cha, S. Varabyou, A. Rincon, N. Park, S. Minkin, I. Pertea, M. Steinegger, M. Salzberg, S. 2022-06-09 doi:10.1101/2022.06.08.495354 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Loss of the protein disrupted in schizophrenia 1 (DISC1) impairs cardiac resistance against ischemia. ]]> https://biorxiv.org/content/10.1101/2022.06.09.494639v1?rss=1 Gurdeep Marwahra, G. Pinho, M. J. Slagsvold, K. H. Wahba, A. Rosbjorgen, R. E. Enguita, F. J. Yang, K. Ishizuka, K. Casas, C. A. A. Pettersen, K. Bjorkoy, G. Sawa, A. Hoydal, M. A. 2022-06-10 doi:10.1101/2022.06.09.494639 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Image Downsampling Expedited Adaptive Least-squares (IDEAL) fitting improves intravoxel incoherent motion (IVIM) analysis in the human kidney ]]> https://biorxiv.org/content/10.1101/2022.06.09.495469v1?rss=1 Stabinska, J. Zollner, H. J. Thiel, T. A. Wittsack, H.-J. Ljimani, A. 2022-06-11 doi:10.1101/2022.06.09.495469 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Serine Racemase mediates Subventricular Zone Neurogenesis via Fatty acid Metabolism. ]]> https://biorxiv.org/content/10.1101/2022.06.09.495488v1?rss=1 Roychaudhuri, R. Atashi, H. Snyder, S. 2022-06-09 doi:10.1101/2022.06.09.495488 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Nanotopography modulates intracellular excitable systems through cytoskeleton actuation ]]> https://biorxiv.org/content/10.1101/2022.06.09.495528v1?rss=1 Yang, Q. Miao, Y. Banerjee, P. Hourwitz, M. J. Hu, M. Qing, Q. Iglesias, P. A. Devreotes, P. N. Fourkas, J. T. Losert, W. 2022-06-10 doi:10.1101/2022.06.09.495528 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Inclusion of a GaAs detector model in the Photon Counting Toolkit software for the study of breast imaging systems ]]> https://biorxiv.org/content/10.1101/2022.06.10.495610v1?rss=1 Ghammraoui, B. Taguchi, K. Glick, S. J. 2022-06-10 doi:10.1101/2022.06.10.495610 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis ]]> https://biorxiv.org/content/10.1101/2022.06.12.495801v1?rss=1 Jing, H. Ogunmowo, T. Raychaudhuri, S. Kusick, G. F. Imoto, Y. Li, S. Itoh, K. Chapman, E. R. Ha, T. Watanabe, S. Liu, J. 2022-06-12 doi:10.1101/2022.06.12.495801 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Closed-loop control and recalibration of place cells by optic flow ]]> https://biorxiv.org/content/10.1101/2022.06.12.495823v1?rss=1 Madhav, M. S. Jayakumar, R. P. Li, B. Y. Savelli, F. Knierim, J. J. Cowan, N. J. 2022-06-15 doi:10.1101/2022.06.12.495823 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Comparative immune responses to Mycobacterium tuberculosis in people with latent infection or sterilizing protection ]]> https://biorxiv.org/content/10.1101/2022.06.13.495865v1?rss=1 Jalbert, E. Liu, C. Mave, V. Lang, N. Kagal, A. Valvi, C. Paradkar, M. Gupte, N. Lokhande, R. Bharadwaj, R. Kulkarni, V. Gupta, A. Weinberg, A. 2022-06-15 doi:10.1101/2022.06.13.495865 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus ]]> https://biorxiv.org/content/10.1101/2022.06.14.495972v1?rss=1 Miller, J. Zimin, A. Gordus, A. G. 2022-06-16 doi:10.1101/2022.06.14.495972 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability ]]> https://biorxiv.org/content/10.1101/2022.06.14.495995v1?rss=1 Makarov, M. Rocha, A. C. S. Krystufek, R. Cherepashuk, I. Dzmitruk, V. Charnavets, T. Faustino, A. M. Lebl, M. Fujishima, K. Fried, S. D. Hlouchova, K. 2022-06-16 doi:10.1101/2022.06.14.495995 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ The Impact of Storage Condition and Duration on Function of Native and Cargo-Loaded Mesenchymal Stromal Cell Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2022.06.14.496108v1?rss=1 Levy, D. Jeyaram, A. Born, L. J. Chang, K.-H. Nourmohammadi Abadchi, S. Ting Wei Hsu, A. Solomon, T. Aranda, A. Stewart, S. He, X. Harmon, J. W. Jay, S. M. 2022-06-17 doi:10.1101/2022.06.14.496108 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ JASPER: a fast genome polishing tool that improves accuracy and creates population-specific reference genomes ]]> https://biorxiv.org/content/10.1101/2022.06.14.496115v1?rss=1 Guo, A. Salzberg, S. Zimin, A. V. 2022-06-16 doi:10.1101/2022.06.14.496115 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Daily administration of low-dose daunorubicin or doxorubicin inhibits hypoxia-inducible factor 1 and tumor vascularization ]]> https://biorxiv.org/content/10.1101/2022.06.15.492526v1?rss=1 Yang, Y. Chen, D. Z. Rey, S. Liu, J. O. Semenza, G. L. 2022-06-17 doi:10.1101/2022.06.15.492526 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Insights for disease modeling from single cell transcriptomics of iPSC-derived neurons and astrocytes across differentiation time and co-culture ]]> https://biorxiv.org/content/10.1101/2022.06.15.495952v1?rss=1 Das, D. Sonthalia, S. Stein-O'Brien, G. G. Wahbeh, M. Feuer, K. Colantuoni, C. Machairaki, V. Avramopoulos, D. 2022-06-16 doi:10.1101/2022.06.15.495952 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Dermal nerve growth factor is increased in prurigo nodularis compared to atopic dermatitis ]]> https://biorxiv.org/content/10.1101/2022.06.15.496275v1?rss=1 Deng, J. Parthasarathy, V. Bordeaux, Z. Marani, M. Lee, K. Trinh, C. Sutaria, N. Cornman, H. Kambala, A. Pritchard, T. Chen, S. Oladipo, O. O. Kwatra, M. M. Alphonse, M. A. Kwatra, S. G. 2022-06-17 doi:10.1101/2022.06.15.496275 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Mechanotransductive feedback control of endothelial cell motility and vascular morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.15.496293v1?rss=1 Mason, D. E. Goeckel, M. Vega, S. L. Wu, P.-H. Johnson, D. Heo, S.-J. Wirtz, D. Burdick, J. A. Wood, L. Chow, B. Y. Stratman, A. N. Boerckel, J. D. 2022-06-16 doi:10.1101/2022.06.15.496293 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Sex-specific age-related changes in excitatory and inhibitory intra-cortical circuits in mouse primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.06.15.496332v1?rss=1 Xue, B. Kao, J. P.-Y. Kanold, P. O. 2022-06-17 doi:10.1101/2022.06.15.496332 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Constitutive Inhibition of Transient Receptor Potential CanonicalType 6 (TRPC6) by O-GlcNAcylation at Threonine-221 ]]> https://biorxiv.org/content/10.1101/2022.06.15.496344v1?rss=1 Kass, D. A. Mishra, S. Ma, J. Sasaki, M. Farinelli, F. Page, R. C. Ranek, M. J. Zachara, N. 2022-06-15 doi:10.1101/2022.06.15.496344 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Pumping the brakes on RNA velocity -- understanding and interpreting RNA velocity estimates ]]> https://biorxiv.org/content/10.1101/2022.06.19.494717v1?rss=1 Zheng, S. C. Stein-O'Brien, G. Boukas, L. Goff, L. A. Hansen, K. D. 2022-06-20 doi:10.1101/2022.06.19.494717 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Location-Specific Facilitation in Marmoset Auditory Cortex ]]> https://biorxiv.org/content/10.1101/2022.06.19.496736v1?rss=1 Chen, C. Xu, S. Wang, Y. Wang, X. 2022-06-20 doi:10.1101/2022.06.19.496736 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ ztf-16 is a novel heterochronic modulator that opposes adult cell fate in dauer and continuous life histories in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.06.20.496913v1?rss=1 Hansen, M. A. Dahal, A. Bernstein, T. A. Kohtz, C. Ali, S. Daul, A. L. Montoye, E. A. Panzade, G. P. Alessi, A. F. Flibotte, S. Vargas, M. L. Bourgeois, J. Brown, C. J. Kim, J. K. Rougvie, A. E. Zinovyeva, A. Karp, X. 2022-06-22 doi:10.1101/2022.06.20.496913 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.06.21.497047v1?rss=1 Farjo, M. Koelle, K. Martin, M. A. Gibson, L. L. Walden, K. K. Rendon, G. Fields, C. J. Alnaji, F. Gallagher, N. Luo, C. H. Mostafa, H. H. Manabe, Y. C. Pekosz, A. Smith, R. L. McManus, D. D. Brooke, C. B. 2022-06-22 doi:10.1101/2022.06.21.497047 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ MrgprA3-expressing pruriceptors drive pruritogen-induced alloknesis through mechanosensitive Piezo2 channel ]]> https://biorxiv.org/content/10.1101/2022.06.22.497257v1?rss=1 Lu, P. Zhao, Y. Xie, Z. Dong, X. Wu, G. Kim, B. Feng, J. Hu, H. 2022-06-26 doi:10.1101/2022.06.22.497257 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Expression Microdissection for use in qPCR based analysis of miRNA in a single cell type ]]> https://biorxiv.org/content/10.1101/2022.06.24.497524v1?rss=1 Jenike, A. E. Bunkelman, B. Perzel Mandell, K. A. Oduor, C. Chin, D. Mair, D. Jenike, K. M. Kim, D.-H. Bailey, J. A. Rafailovich, M. H. Rosenberg, A. Z. Halushka, M. K. 2022-06-28 doi:10.1101/2022.06.24.497524 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Enrichment of breast cancer stem cells following cytotoxic chemotherapy is mediated by hypoxia-inducible factors ]]> https://biorxiv.org/content/10.1101/2022.06.27.497729v1?rss=1 Samanta, D. Gilkes, D. M. Xiang, L. Chaturvedi, P. Semenza, G. L. 2022-06-30 doi:10.1101/2022.06.27.497729 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Ancient midbrain inhibitory neurons control selective spatial attention ]]> https://biorxiv.org/content/10.1101/2022.06.27.497794v1?rss=1 Kothari, N. B. You, W.-K. Banerjee, A. Zhang, Q. Mysore, S. P. 2022-06-28 doi:10.1101/2022.06.27.497794 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Action inhibition revisited: Stopping is not faster than going ]]> https://biorxiv.org/content/10.1101/2022.06.29.497798v1?rss=1 Du, Y. Forrence, A. D. Metcalf, D. M. Haith, A. M. 2022-07-03 doi:10.1101/2022.06.29.497798 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Developmental spontaneous activity promotes sensory domains, frequency tuning and proper gain in central auditory circuits ]]> https://biorxiv.org/content/10.1101/2022.06.30.498184v1?rss=1 Kersbergen, C. J. Babola, T. A. Rock, J. Bergles, D. E. 2022-07-03 doi:10.1101/2022.06.30.498184 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos ]]> https://biorxiv.org/content/10.1101/2022.07.03.498614v1?rss=1 McCoy, R. C. Summers, M. C. McCollin, A. Ottolini, C. S. Ahuja, K. Handyside, A. H. 2022-07-03 doi:10.1101/2022.07.03.498614 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ On the automaticity of visual statistical learning ]]> https://biorxiv.org/content/10.1101/2022.07.04.498716v1?rss=1 Himberger, K. D. Finn, A. S. Honey, C. J. 2022-07-06 doi:10.1101/2022.07.04.498716 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Antibody repertoire gene usage is explained by common genetic variants in the immunoglobulin heavy chain locus ]]> https://biorxiv.org/content/10.1101/2022.07.04.498729v1?rss=1 Rodriguez, O. L. Safonova, Y. Silver, C. A. Shields, K. Gibson, W. S. Kos, J. T. Tieri, D. Ke, H. Jackson, K. J. L. Boyd, S. D. Smith, M. Marasco, W. Watson, C. T. 2022-07-04 doi:10.1101/2022.07.04.498729 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Restoration of PITPNA in Type 2 diabetic human islets reverses pancreatic beta-cell dysfunction ]]> https://biorxiv.org/content/10.1101/2022.07.06.498991v1?rss=1 Yeh, Y.-T. Sona, C. Yan, X. Pathak, A. McDermott, M. I. Xie, Z. Liu, L. Arunagiri, A. Wang, Y. Cazenave-Gassiot, A. Ghosh, A. von Meyenn, F. Kumarasamy, S. Najjar, S. M. Jia, S. Wenk, M. R. Traynor-Kaplan, A. Arvan, P. Barg, S. Bankaitis, V. Poy, M. N. 2022-07-06 doi:10.1101/2022.07.06.498991 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Cohort-mean measured macromolecules lead to more robust linear-combination modeling than subject-specific or parameterized ones ]]> https://biorxiv.org/content/10.1101/2022.07.07.499181v1?rss=1 0.6). The lowest relative model residuals and AIC values were found for the cohort-mean measured MM. Metabolite-age associations were consistently found for two major singlet signals (tCr, tCho) for all MM strategies, however, findings for highly J-coupled metabolites it was depended on the MM strategy. A variance partition analysis indicated that up to 44% of the total variance was related to the choice of MM strategy. Additionally, the variance partition analysis reproduced the metabolite-age association for tCr and tCho found in the simpler correlation analysis. In summary, the inclusion of a single high-SNR MM basis function (cohort-mean) leads to more robust metabolite estimation (lower model residuals and AIC values) compared to MM strategies with more degrees of freedom (Gaussian parametrization) or subject-specific MM information. Integration of multiple LCM analyses into a single statistical model potentially improves the robustness in the detection of underlying effects (e.g. metabolite vs age), reduces algorithm-based bias, and estimates algorithm-related variance. ]]> Zöllner, H. J. Davies-Jenkins, C. W. Murali-Manohar, S. Gong, T. Song, Y. Hui, S. C. N. Chen, W. Wang, G. Edden, R. A. E. Oeltzschner, G. 2022-07-10 doi:10.1101/2022.07.07.499181 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering ]]> https://biorxiv.org/content/10.1101/2022.07.07.499188v1?rss=1 Razaghi, R. Hook, P. W. Ou, S. Schatz, M. Hansen, K. D. Jain, M. Timp, W. 2022-07-08 doi:10.1101/2022.07.07.499188 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ An RNA binding protein, RNP1A, works with Contractility Kit proteins to facilitate macropinocytosis ]]> https://biorxiv.org/content/10.1101/2022.07.08.499268v1?rss=1 Liu, Y. Leng, J. Nguyen, L. T. Robinson, D. N. 2022-07-08 doi:10.1101/2022.07.08.499268 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS ]]> https://biorxiv.org/content/10.1101/2022.07.09.499398v1?rss=1 Johnson, J. A. I. Tsang, A. Mitchell, J. T. Davis-Marcisak, E. F. Sherman, T. Liefeld, T. Loth, M. Goff, L. Zimmerman, J. Kinny-Köster, B. Jaffee, E. Tamayo, P. Mesirov, J. Reich, M. Fertig, E. J. Stein-O'Brien, G. L. 2022-07-11 doi:10.1101/2022.07.09.499398 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Dynamics of Borrelia Burgdorferi Invasion and Intravasation in a Tissue Engineered Dermal Microvessel Model ]]> https://biorxiv.org/content/10.1101/2022.07.10.499449v1?rss=1 Guo, Z. Zhao, N. Chung, T. D. Singh, A. Pandey, I. Wang, L. Gu, X. Ademola, A. Linville, R. M. Pal, U. Dumler, J. S. Searson, P. C. 2022-07-10 doi:10.1101/2022.07.10.499449 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Impact of gradient scheme and shimming on out-of-voxel echo artifacts in edited MRS ]]> https://biorxiv.org/content/10.1101/2022.07.10.499491v1?rss=1 Song, y. Zöllner, H. J. Hui, S. C. N. Hupfeld, K. Oeltzschner, G. Edden, R. A. E. 2022-07-10 doi:10.1101/2022.07.10.499491 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Homeostatic responses to hypoxia by the carotid body and adrenal medulla are based on mutual antagonism between HIF-1α and HIF-2α ]]> https://biorxiv.org/content/10.1101/2022.07.11.499380v1?rss=1 Yuan, G. Peng, Y.-J. Reddy, V. D. Makarenko, V. Nanduri, J. Khan, S. A. Garcia, J. A. Kumar, G. K. Semenza, G. L. Prabhakar, N. R. 2022-07-11 doi:10.1101/2022.07.11.499380 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ DNA-Stimulated Liquid-Liquid Phase Separation by Eukaryotic Topoisomerase II Modulates Catalytic Function ]]> https://biorxiv.org/content/10.1101/2022.07.11.499568v1?rss=1 Jeong, J. Lee, J. H. Carcamo, C. C. Parker, M. W. Berger, J. M. 2022-07-11 doi:10.1101/2022.07.11.499568 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Signaling the agency of an erroneous outcome via synchronization of spikes in the cerebellum ]]> https://biorxiv.org/content/10.1101/2022.07.11.499614v1?rss=1 Pi, J. S. Sedaghat-Nejad, E. Fakharian, M. A. Hage, P. Shadmehr, R. 2022-07-13 doi:10.1101/2022.07.11.499614 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Activating and repressing gene expression between chromosomes during stochastic fate specification ]]> https://biorxiv.org/content/10.1101/2022.07.11.499628v1?rss=1 Urban, E. A. Chernoff, C. Viets-Layng, K. Han, J. Anderson, C. Konzman, D. Johnston, R. J. 2022-07-12 doi:10.1101/2022.07.11.499628 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ In search of a brain microbiome: A machine learning search pipeline for electron microscopy images of brain tissue ]]> https://biorxiv.org/content/10.1101/2022.07.12.499807v1?rss=1 Matelsky, J. K. Shih, C. Hijazi, K. Johnson, E. C. 2022-07-14 doi:10.1101/2022.07.12.499807 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ High-performing neural network models of visual cortex benefit from high latent dimensionality ]]> https://biorxiv.org/content/10.1101/2022.07.13.499969v1?rss=1 Elmoznino, E. Bonner, M. F. 2022-07-13 doi:10.1101/2022.07.13.499969 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Inflammatory Signaling and Fibroblast-Cancer Cell Interactions Transfer from a Harmonized Human Single-cell RNA Sequencing Atlas of Pancreatic Ductal Adenocarcinoma to Organoid Co-Culture ]]> https://biorxiv.org/content/10.1101/2022.07.14.500096v1?rss=1 Kinny-Koster, B. Guinn, S. Tandurella, J. A. Mitchell, J. T. Sidiropoulos, D. N. Loth, M. Lyman, M. R. Pucsek, A. B. Seppala, T. T. Cherry, C. Suri, R. Zlomke, H. He, J. Wolfgang, C. L. Yu, J. Zheng, L. Ryan, D. P. Ting, D. T. Kimmelman, A. Gupta, A. Danilova, L. Elisseef, J. Wood, L. D. Stein-O'Brien, G. Kagohara, L. T. Burkhart, R. A. Jaffee, E. M. Fertig, E. J. Zimmerman, J. W. 2022-07-16 doi:10.1101/2022.07.14.500096 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Molecular recording of calcium signaling via calcium-dependent protein proximity labeling ]]> https://biorxiv.org/content/10.1101/2022.07.14.500122v1?rss=1 Kim, J. W. Yong, A. J. H. Dawson, T. M. Dawson, V. L. Jan, Y.-N. Ingolia, N. T. 2022-07-14 doi:10.1101/2022.07.14.500122 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Melanization of Candida auris is Associated with Alteration of Extracellular pH ]]> https://biorxiv.org/content/10.1101/2022.07.14.500134v1?rss=1 Smith, D. F. Q. Mudrak, N. J. Zamith-Miranda, D. Honorato, L. Nimrichter, L. Smith, B. Gerfen, G. J. Nosanchuk, J. D. Casadevall, A. 2022-07-15 doi:10.1101/2022.07.14.500134 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand ]]> https://biorxiv.org/content/10.1101/2022.07.15.500197v1?rss=1 Blount, B. A. Lu, X. Driessen, M. R. M. Jovicevic, D. Sanchez, M. I. Ciurkot, K. Zhao, Y. Lauer, S. McKiernan, R. M. Gowers, G.-O. F. Sweeney, F. Fanfani, V. Lobzaev, E. Palacios-Flores, K. Walker, R. Hesketh, A. Oliver, S. G. Cai, Y. Stracquadanio, G. Mitchell, L. A. Bader, J. S. Boeke, J. D. Ellis, T. 2022-07-16 doi:10.1101/2022.07.15.500197 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Mixed selectivity coding of content-temporal detail by dorsomedial posterior parietal neurons ]]> https://biorxiv.org/content/10.1101/2022.07.16.500237v1?rss=1 Wang, L. Zhou, X. Yang, J. Zeng, F. Zuo, S. Kusunoki, M. Wang, H. Zhou, Y.-d. Chen, A. Kwok, S. C. 2022-07-18 doi:10.1101/2022.07.16.500237 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Spatial transcriptomics of FFPE pancreatic intraepithelial neoplasias reveals cellular and molecular alterations of progression to pancreatic ductal carcinoma ]]> https://biorxiv.org/content/10.1101/2022.07.16.500312v1?rss=1 Bell, A. T. F. Mitchell, J. T. Kiemen, A. L. Fujikura, K. Fedor, H. Gambichler, B. Deshpande, A. Wu, P.-H. Sidiropoulos, D. N. Erbe, R. Stern, J. Chan, R. Williams, S. Chell, J. M. Zimmerman, J. W. Wirtz, D. Jaffee, E. M. Wood, L. D. Fertig, E. J. Kagohara, L. T. 2022-07-18 doi:10.1101/2022.07.16.500312 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Neuromorphic Model of Hippocampus Place cells using an Oscillatory Interference Technique for Hardware Implementation ]]> https://biorxiv.org/content/10.1101/2022.07.18.500440v1?rss=1 Chen, Z. Nasrallah, A. Alemohammad, M. Furuta, M. Eitienne-Cummings, R. 2022-07-19 doi:10.1101/2022.07.18.500440 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ S100a9 Attenuates Inflammation during Repeated Social Defeat Stress ]]> https://biorxiv.org/content/10.1101/2022.07.18.500493v1?rss=1 Moshfegh, C. M. Elkhatib, S. K. Watson, G. F. Drake, J. Taylor, Z. N. Reed, E. C. Lauten, T. H. Clopp, A. J. Vladimirov, V. I. Case, A. J. 2022-07-20 doi:10.1101/2022.07.18.500493 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ NeuVue: A Framework and Workflows for High-Throughput Electron Microscopy Connectomics Proofreading ]]> https://biorxiv.org/content/10.1101/2022.07.18.500521v1?rss=1 Xenes, D. Kitchell, L. M. Rivlin, P. K. Brodsky, R. Gooden, H. Joyce, J. Luna, D. Norman-Tenazas, R. Ramsden, D. Romero, K. Rose, V. Villafane-Delgado, M. Gray-Roncal, W. Wester, B. 2022-07-20 doi:10.1101/2022.07.18.500521 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ A New Class of Protein Misfolding is Observed in All-atom Folding Simulations ]]> https://biorxiv.org/content/10.1101/2022.07.19.500586v1?rss=1 Vu, Q. V. Jiang, Y. Sitarik, I. Li, M. S. O'Brien, E. P. 2022-07-20 doi:10.1101/2022.07.19.500586 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Temporal interference current stimulation in peripheral nerves ]]> https://biorxiv.org/content/10.1101/2022.07.20.500811v1?rss=1 Budde, R. B. Williams, M. T. Irazoqui, P. 2022-07-21 doi:10.1101/2022.07.20.500811 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry ]]> https://biorxiv.org/content/10.1101/2022.07.21.501021v1?rss=1 Lu, P. Oetjen, K. A. Bender, D. E. Ruzinova, M. B. Fisher, D. A. Shim, K. G. Pachynski, R. K. Brennen, W. N. Oh, S. Link, D. C. Thorek, D. L. 2022-07-22 doi:10.1101/2022.07.21.501021 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements ]]> https://biorxiv.org/content/10.1101/2022.07.22.501046v1?rss=1 Williams, T. C. Kroukamp, H. Xu, X. Wightman, E. L. I. Llorente, B. Borneman, A. R. Carpenter, A. C. Van Wyk, N. Espinosa, M. I. Daniel, E. L. Walker, R. S. K. Cai, Y. Nevalainen, H. K. M. Curach, N. C. Deveson, I. W. Mercer, T. R. Johnson, D. L. Mitchell, L. A. Bader, J. S. Stracquadanio, G. Boeke, J. D. Goold, H. D. Pretorius, I. S. Paulsen, I. T. 2022-07-23 doi:10.1101/2022.07.22.501046 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Suboptimal phenotypic reliability impedes reproducible human neuroscience ]]> https://biorxiv.org/content/10.1101/2022.07.22.501193v1?rss=1 Nikolaidis, A. Chen, A. A. He, X. Shinohara, R. Vogelstein, J. Milham, M. Shou, H. 2022-07-23 doi:10.1101/2022.07.22.501193 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Fully Desktop Fabricated Flexible Graphene Electrocorticography (ECoG) Arrays ]]> https://biorxiv.org/content/10.1101/2022.07.25.501414v1?rss=1 Hu, J. Hossain, R. F. Navabi, Z. S. Tillery, A. Laroque, M. Donaldson, P. D. Swisher, S. L. Kodandaramaiah, S. B. 2022-07-27 doi:10.1101/2022.07.25.501414 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ naRNA is a canonical neutrophil extracellular trap (NET) component and novel inflammation-amplifying composite DAMP ]]> https://biorxiv.org/content/10.1101/2022.07.26.499571v1?rss=1 View larger version (94K): org.highwire.dtl.DTLVardef@11b866org.highwire.dtl.DTLVardef@16139ceorg.highwire.dtl.DTLVardef@1a2905org.highwire.dtl.DTLVardef@17b0e7e_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with biorender.com ]]> Bork, F. Greve, C. L. Youn, C. Chen, S. Wang, Y. Nasri, M. Focken, J. Scheurer, J. Engels, P. Dubbelaar, M. Hipp, K. Schittek, B. Bugl, S. Loeffler, M. W. Skokowa, J. Archer, N. E. Weber, A. N. 2022-07-27 doi:10.1101/2022.07.26.499571 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes ]]> https://biorxiv.org/content/10.1101/2022.07.26.501581v1?rss=1 Raz, A. A. Vida, G. S. Stern, S. R. Mahadevaraju, S. Fingerhut, J. M. Viveiros, J. M. Pal, S. Grey, J. R. Grace, M. R. Berry, C. W. Li, H. Janssens, J. Saelens, W. Shao, Z. Hun, C. Yamashita, Y. M. Przytycka, T. M. Oliver, B. Brill, J. A. Krause, H. M. Matunis, E. L. White-Cooper, H. DiNardo, S. Fuller, M. T. 2022-07-27 doi:10.1101/2022.07.26.501581 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ MISPEL: A deep learning approach for harmonizingmulti-scanner matched neuroimaging data ]]> https://biorxiv.org/content/10.1101/2022.07.27.501786v1?rss=1 Torbati, M. E. Minhas, D. S. Laymon, C. M. Maillard, P. Wilson, J. D. Chen, C.-L. Crainiceanu, C. M. DeCarli, C. S. Hwang, S. J. Tudorascu, D. L. 2022-07-29 doi:10.1101/2022.07.27.501786 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Novel Smartphone Based Free Flap Monitoring Tool Using Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.07.28.501864v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@e0ac8aorg.highwire.dtl.DTLVardef@5fc495org.highwire.dtl.DTLVardef@1632f1dorg.highwire.dtl.DTLVardef@aa24e9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Sample depictions of frame from the video and corresponding cropped regions of a control region, the contralateral hand (leftmost image of hand), and hand undergoing occlusion (rightmost image of hand). C_FIG ]]> Provenzano, D. Chandawarkar, A. Caterson, E. 2022-08-01 doi:10.1101/2022.07.28.501864 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Basolateral amygdala and orbitofrontal cortex, but not dorsal hippocampus, are necessary for the control of reward-seeking by occasion setters ]]> https://biorxiv.org/content/10.1101/2022.07.28.501885v1?rss=1 Fraser, K. M. Janak, P. H. 2022-08-01 doi:10.1101/2022.07.28.501885 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome ]]> https://biorxiv.org/content/10.1101/2022.07.29.502011v1?rss=1 He, J. Alonge, M. Ramakrishnan, S. Benoit, M. Soyk, S. Reem, N. Hendelman, A. Van Eck, J. Schatz, M. Lippman, Z. 2022-07-30 doi:10.1101/2022.07.29.502011 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ A comprehensive single-cell breast tumor atlas defines cancer epithelial and immune cell heterogeneity and interactions predicting anti-PD-1 therapy response ]]> https://biorxiv.org/content/10.1101/2022.08.01.501918v1?rss=1 Xu, L. Saunders, K. N. Knutsdottir, H. Chen, K. Maues, J. Hodgdon, C. Roussos-Torres, E. T. Reddy, S. Xu, L. Chan, I. S. 2022-08-03 doi:10.1101/2022.08.01.501918 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ 3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources ]]> https://biorxiv.org/content/10.1101/2022.08.01.501973v1?rss=1 Varadi, M. Nair, S. S. Sillitoe, I. Tauriello, G. Anyango, S. Bienert, S. Borges, C. Deshpande, M. Green, T. Hatos, A. Hegedus, T. Hekkelman, M. L. Joosten, R. Jumper, J. Laydon, A. Molodenskiy, D. Piovesan, D. Salladini, E. Salzberg, S. L. Sommer, M. J. Steinegger, M. Suhajda, E. Svergun, D. Tenorio-Ku, L. Tosatto, S. Tunyasuvunakool, K. Waterhouse, A. M. Zidek, A. Hassabis, D. Schwede, T. Orengo, C. Velankar, S. 2022-08-03 doi:10.1101/2022.08.01.501973 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Next-generation large-scale binary protein interaction network for Drosophila ]]> https://biorxiv.org/content/10.1101/2022.08.02.502359v1?rss=1 10,000 Drosophila proteins, resulting in the FlyBi dataset of 8,723 PPIs among 2,939 proteins. As part of this effort, we tested subsets of our data and data from previous PPI datasets using an orthogonal assay, which allowed us to normalize data quality across datasets. Next, we integrated our FlyBi data with previous PPI data, resulting in an expanded, high-confidence binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6,511 proteins. These data are accessible through the Molecular Interaction Search Tool (MIST) and other databases. To assess the utility of the PPI resource, we used novel interactions from the FlyBi dataset to generate an autophagy interaction network that we validated in vivo using two different autophagy-related assays. We found that deformed wings (dwg) encodes a protein that is both a regulator and a target of autophagy. Altogether, the resources generated in this project provide a strong foundation for building high-confidence new hypotheses regarding protein networks and function. ]]> Tang, H.-W. Spirohn, K. Hu, Y. Hao, T. Kovacs, I. A. Gao, Y. Binari, R. Yang-Zhou, D. Wan, K. H. Bader, J. S. Balcha, D. Bian, W. Booth, B. W. Cote, A. G. De Rouck, S. Desbuleux, A. Kim, D.-K. Knapp, J. J. Lee, W. X. Lemmens, I. Li, C. Li, M. Li, R. Lim, H. Luck, K. Markey, D. Pollis, C. Rangarajan, S. Rodiger, J. Schlabach, S. Shen, Y. TeeKing, B. Roth, F. P. Tavernier, J. Calderwood, M. Hill, D. E. Celniker, S. E. Vidal, M. Perrimon, N. Mohr, S. 2022-08-03 doi:10.1101/2022.08.02.502359 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline granule that regulates maternal RNAs ]]> https://biorxiv.org/content/10.1101/2022.08.02.502436v1?rss=1 Pozmanter, C. Kelly, S. Curnutte, H. Van Doren, M. 2022-08-03 doi:10.1101/2022.08.02.502436 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Design Principles for Inflammasome Inhibition by Pyrin-Only-Proteins ]]> https://biorxiv.org/content/10.1101/2022.08.02.502519v1?rss=1 Mazanek, Z. Wu, S. Belotte, G. Zhou, J. J. Stallings, C. M. Garg, A. Lueck, J. Sohn, J. 2022-08-02 doi:10.1101/2022.08.02.502519 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Pla2g12b is Essential for Expansion of Nascent Lipoprotein Particles ]]> https://biorxiv.org/content/10.1101/2022.08.02.502564v1?rss=1 Thierer, J. H. Foresti, O. Yadav, P. K. Wilson, M. H. Moll, T. Shen, M.-C. Busch-Nentwich, E. Morash, M. Mohlke, K. Rawls, J. F. Malhotra, V. Hussain, M. M. Farber, S. A. 2022-08-03 doi:10.1101/2022.08.02.502564 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins ]]> https://biorxiv.org/content/10.1101/2022.08.03.502619v1?rss=1 Agam, G. Gebhardt, C. Popara, M. Maechtel, R. Folz, J. Ambrose, B. Chamachi, N. Chung, S. Y. Craggs, T. D. de Boer, M. Grohmann, D. Ha, T. Hartmann, A. Hendrix, J. Hirschfeld, V. Huebner, C. G. Hugel, T. Kammerer, D. Kang, H. S. Kapanidis, A. Krainer, G. Kramm, K. Lemke, E. Lerner, E. Margeat, E. Martens, K. Michaelis, J. Mitra, J. Munoz, G. G. M. Quast, R. Robb, N. Sattler, M. Schlierf, M. Schneider, J. Schroeder, T. Sefer, A. Tan, P. S. Thurn, J. Tinnefeld, P. van Noort, J. Weiss, S. Wendler, N. Barth, A. Seidel, C. A. M. Lamb, D. C. Cordes, T. 2022-08-05 doi:10.1101/2022.08.03.502619 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Characterization of a Novel Hyper-Variable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3) ]]> https://biorxiv.org/content/10.1101/2022.08.03.502653v1?rss=1 Apsley, A. T. Domico, E. R. Verbiest, M. A. Brogan, C. A. Buck, E. R. Burich, A. J. Cardone, K. M. Stone, W. J. Anisimova, M. Vandenbergh, D. J. 2022-08-05 doi:10.1101/2022.08.03.502653 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Vibrio cholerae alkalizes its environment via citrate metabolism to inhibit enteric growth ]]> https://biorxiv.org/content/10.1101/2022.08.04.502819v1?rss=1 Kostiuk, B. Becker, M. E. Churaman, C. N. Black, J. J. Payne, S. M. Pukatzki, S. Koestler, B. J. 2022-08-04 doi:10.1101/2022.08.04.502819 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Transcriptomic forecasting with neural ODEs ]]> https://biorxiv.org/content/10.1101/2022.08.04.502825v1?rss=1 Erbe, R. Stein-O'Brien, G. Fertig, E. J. 2022-08-05 doi:10.1101/2022.08.04.502825 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Object representation in a gravitational reference frame ]]> https://biorxiv.org/content/10.1101/2022.08.06.503060v1?rss=1 Emonds, A. M. Srinath, R. Nielsen, K. J. Connor, C. E. 2022-08-07 doi:10.1101/2022.08.06.503060 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual ]]> https://biorxiv.org/content/10.1101/2022.08.08.503226v1?rss=1 Chao, K.-H. Zimin, A. V. Pertea, M. Salzberg, S. L. 2022-08-11 doi:10.1101/2022.08.08.503226 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Phosphorylation at Ser65 modulates ubiquitin conformational dynamics ]]> https://biorxiv.org/content/10.1101/2022.08.09.502833v1?rss=1 Yovanno, R. A. Yu, A. Wied, T. J. Lau, A. Y. 2022-08-11 doi:10.1101/2022.08.09.502833 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Role of human HSPE1 for OPA1 processing independent of HSPD1 ]]> https://biorxiv.org/content/10.1101/2022.08.11.503680v1?rss=1 Sesaki, H. Iijima, M. Murata, D. Yeung, N. 2022-08-11 doi:10.1101/2022.08.11.503680 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Sound localization acuity of the common marmoset (Callithrix jacchus) ]]> https://biorxiv.org/content/10.1101/2022.08.13.503849v1?rss=1 Remington, E. Chen, C. Wang, X. 2022-08-16 doi:10.1101/2022.08.13.503849 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ From Prediction to Action: Dissociable Roles of Ventral Tegmental Area and Substantia Nigra Dopamine Neurons in Instrumental Reinforcement ]]> https://biorxiv.org/content/10.1101/2022.08.15.501890v1?rss=1 Fraser, K. M. Pribut, H. J. Janak, P. H. Keiflin, R. 2022-08-15 doi:10.1101/2022.08.15.501890 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Internal states as a source of subject-dependent movement variability and their representation by large-scale networks ]]> https://biorxiv.org/content/10.1101/2022.08.16.504130v1?rss=1 Breault, M. S. Sacre, P. Fitzgerald, Z. B. Gale, J. T. Cullen, K. E. Gonzalez-Martinez, J. A. Sarma, S. V. 2022-08-17 doi:10.1101/2022.08.16.504130 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Perpendicular Shear Stresses Drive Transmural Helical Remodeling in Engineered Human Ventricular Models ]]> https://biorxiv.org/content/10.1101/2022.08.18.504345v1?rss=1 Williams, N. P. Beussman, K. M. Foster, J. R. Rhodehamel, M. Williams, C. A. Tsui, J. H. Smith, A. S. T. Mack, D. L. Murry, C. E. Sniadecki, N. J. Kim, D.-H. 2022-08-19 doi:10.1101/2022.08.18.504345 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Transport of Antibody into the Skin is Only Partially Dependent Upon the Neonatal Fc-Receptor ]]> https://biorxiv.org/content/10.1101/2022.08.19.504586v1?rss=1 Nasir, G. Sinnis, P. 2022-08-20 doi:10.1101/2022.08.19.504586 Cold Spring Harbor Laboratory Press 2022-08-20 <![CDATA[ Diversity, composition, altitude, and seasonality of high-altitude windborne migrating mosquitoes in the Sahel: Implications for disease transmission ]]> https://biorxiv.org/content/10.1101/2022.08.19.504620v1?rss=1 Yaro, A. S. Linton, Y.-M. Diallo, M. Sanogo, Z. L. Samake, D. Ousman, Y. Kouam, C. Krajacich, B. J. Faiman, R. Bamou, R. Woo, J. Chapman, J. Reynolds, D. R. Lehmann, T. 2022-08-20 doi:10.1101/2022.08.19.504620 Cold Spring Harbor Laboratory Press 2022-08-20 <![CDATA[ Multiple mechanisms prevent ectopic condensation of FG nucleoporins in the cytoplasm ]]> https://biorxiv.org/content/10.1101/2022.08.22.504855v1?rss=1 Thomas, L. Askjaer, P. Seydoux, G. 2022-08-22 doi:10.1101/2022.08.22.504855 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Genome-wide analysis of Structural Variants in Parkinson's Disease using Short-Read Sequencing data ]]> https://biorxiv.org/content/10.1101/2022.08.22.504867v1?rss=1 Billingsley, K. J. Ding, J. jerez, p. a. illarionova, a. Makarious, M. B. moore, a. vitale, d. reed, x. Hernandez, D. Torkamani, A. Ryten, M. Hardy, J. Chia, R. Scholz, S. W. Traynor, B. Dalgard, C. L. ehrlich, d. Tanaka, T. Ferrucci, L. Beach, T. Serrano, G. E. Quinn, J. Bubb, V. Collins, R. L. Zhao, X. Walker, M. Pierce-Hoffman, E. Brand, H. Talkowski, M. Casey, B. Cookson, M. R. Markham, A. Nalls, M. A. Mahmoud, M. Sedlazeck, F. Blauwendraat, C. Gibbs, R. Singleton, A. 2022-08-22 doi:10.1101/2022.08.22.504867 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self ]]> https://biorxiv.org/content/10.1101/2022.08.23.504566v1?rss=1 Geiger, K. Manoharan, M. Coombs, R. Park, C.-s. Lee, A. Shastri, N. Robey, E. Coscoy, L. 2022-08-23 doi:10.1101/2022.08.23.504566 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Norepinephrine enhances oligodendrocyte precursor cell calcium dynamics in the cerebral cortex during arousal ]]> https://biorxiv.org/content/10.1101/2022.08.25.505119v1?rss=1 Lu, T.-Y. Hanumaihgari, P. Hsu, E. T. Agarwal, A. Bergles, D. E. 2022-08-25 doi:10.1101/2022.08.25.505119 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Circadian Gene Expression in Mouse Renal Proximal Tubule ]]> https://biorxiv.org/content/10.1101/2022.08.26.505418v1?rss=1 Bingham, M. A. Neijman, K. Kikuchi, H. Jung, H. J. Poll, B. G. Raghuram, V. Park, E. Yang, C.-R. Chou, C.-L. Chen, L. Leipziger, J. Knepper, M. A. Dona, M. 2022-08-26 doi:10.1101/2022.08.26.505418 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ CNTNAP4 signaling regulates osteosarcoma disease progression ]]> https://biorxiv.org/content/10.1101/2022.08.26.505419v1?rss=1 James, A. Qin, Q. Ramesh, S. Gomez-Salazar, M. Zhong, L. Cherief, M. Pratapneni, A. Morris, C. D. McCarthy, E. F. Zhang, X. 2022-08-27 doi:10.1101/2022.08.26.505419 Cold Spring Harbor Laboratory Press 2022-08-27 <![CDATA[ Early Signaling Events in Renal Compensatory Hypertrophy Revealed by Multi-Omics ]]> https://biorxiv.org/content/10.1101/2022.08.29.505304v1?rss=1 Kikuchi, H. Chou, C.-L. Yang, C.-R. Chen, L. Jung, H. J. Limbutara, K. Carter, B. Knepper, M. A. 2022-08-30 doi:10.1101/2022.08.29.505304 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Deep Neural Networks Predict MHC-I Epitope Presentation and Transfer Learn Neoepitope Immunogenicity ]]> https://biorxiv.org/content/10.1101/2022.08.29.505690v1?rss=1 Albert, B. A. Yang, Y. Shao, X. M. Singh, D. Smith, K. N. Anagnostou, V. Karchin, R. 2022-08-29 doi:10.1101/2022.08.29.505690 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Molecular mechanism underlying desensitization of the proton-activated chloride channel PAC ]]> https://biorxiv.org/content/10.1101/2022.08.30.505880v1?rss=1 Osei-Owusu, J. Ruan, Z. Matasic, D. S. Lu, W. Qiu, Z. 2022-08-30 doi:10.1101/2022.08.30.505880 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Therapeutic Potential of Blocking GAPDH Nitrosylation with CGP3466b in Experimental Autoimmune Encephalomyelitis ]]> https://biorxiv.org/content/10.1101/2022.08.31.505712v1?rss=1 Godfrey, W. H. Hwang, S. Gharibani, P. Abramson, E. Kornberg, M. D. 2022-09-03 doi:10.1101/2022.08.31.505712 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ A Camera-Assisted Pathology Microscope to Capture the Lost Data in Clinical Glass Slide Diagnosis ]]> https://biorxiv.org/content/10.1101/2022.08.31.506042v1?rss=1 Ashman, K. Cooper, M. S. Zhuge, H. Fox, S. E. Epstein, J. I. Wenk, C. Summa, B. Brown, J. Q. 2022-09-03 doi:10.1101/2022.08.31.506042 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues ]]> https://biorxiv.org/content/10.1101/2022.08.31.506054v1?rss=1 Martinez Villegas, L. E. Radl, J. Dimopoulos, G. Short, S. M. 2022-08-31 doi:10.1101/2022.08.31.506054 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids ]]> https://biorxiv.org/content/10.1101/2022.08.31.506125v1?rss=1 Costa, B. Li Calzi, M. Castellano, M. Blanco, V. Cuevasanta, E. Litvan, I. Ivanov, P. Witwer, K. Cayota, A. Tosar, J. P. 2022-09-02 doi:10.1101/2022.08.31.506125 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast ]]> https://biorxiv.org/content/10.1101/2022.09.01.506252v1?rss=1 Shen, Y. Gao, F. Wang, Y. Wang, Y. Zheng, J. Gong, J. Zhang, J. Luo, Z.-Q. Schindler, D. Deng, Y. Ding, W. Lin, T. Swidah, R. Zhao, H. Jiang, S. Chen, S. Chen, T. Wang, Y. Luo, Y. Mitchell, L. A. Bader, J. Zhang, G. Shen, X. Wang, J. Fu, X. Dai, J. Boeke, J. D. Yang, H. D. Xu, X. Cai, Y. 2022-09-02 doi:10.1101/2022.09.01.506252 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Melaninization Reduces Cryptococcus neoformans Susceptibility to Mechanical Stress ]]> https://biorxiv.org/content/10.1101/2022.09.01.506291v1?rss=1 Mattoon, E. R. Cordero, R. J. Casadevall, A. 2022-09-02 doi:10.1101/2022.09.01.506291 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Canonical and Replicable Multi-Scale Intrinsic Connectivity Networks in 100k+ Resting-State fMRI Datasets ]]> https://biorxiv.org/content/10.1101/2022.09.03.506487v1?rss=1 Iraji, A. Fu, Z. Faghiri, A. Duda, M. Chen, J. Rachakonda, S. DeRamus, T. P. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Bustillo, J. R. Yang, K. Ishizuka, K. Sawa, A. Hutchison, K. Osuch, E. A. Theberge, J. Abbott, C. Mueller, B. A. Zhi, D. Zhuo, C. Liu, S. Xu, Y. Salman, M. Liu, J. Du, Y. SUI, J. Adali, T. Calhoun, V. 2022-09-05 doi:10.1101/2022.09.03.506487 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Roles of the distinct N-terminal amino acid between H3 and H3.3 in Drosophila male germline stem cell lineage ]]> https://biorxiv.org/content/10.1101/2022.09.03.506490v1?rss=1 Chandrasekhara, C. Ranjan, R. Urban, J. A. Ku, W. L. Snedeker, J. Zhao, K. Chen, X. 2022-09-04 doi:10.1101/2022.09.03.506490 Cold Spring Harbor Laboratory Press 2022-09-04 <![CDATA[ Longitudinal characterization of circulating extracellular vesicles and small RNA during simian immunodeficiency virus infection and antiretroviral therapy ]]> https://biorxiv.org/content/10.1101/2022.09.04.506571v1?rss=1 Huang, Y. Liao, Z. Dang, P. Queen, S. Abreu, C. M. Zheng, L. Witwer, K. W. 2022-09-05 doi:10.1101/2022.09.04.506571 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Global remapping in granule cells and mossy cells of the mouse dentate gyrus ]]> https://biorxiv.org/content/10.1101/2022.09.06.506812v1?rss=1 Kim, S. H. GoodSmith, D. Temme, S. J. Moriya, F. Ming, G.-l. Christian, K. Song, H. Knierim, J. J. 2022-09-08 doi:10.1101/2022.09.06.506812 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ GRAS-1 is a conserved novel regulator of early meiotic chromosome dynamics in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.09.06.506874v1?rss=1 Martinez-Garcia, M. Robles, P. Skinner, M. W. Baran, K. A. Nadarajan, S. Shin, N. Silva-Garcia, C. G. Saito, T. T. Beese-Sims, S. Castaner, A. Pacheco, S. Martinez-Perez, E. Jordan, P. W. Colaiacovo, M. P. 2022-09-07 doi:10.1101/2022.09.06.506874 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Topical GZ21T inhibits the growth of actinic keratoses in a UVB induced model of skin carcinogenesis ]]> https://biorxiv.org/content/10.1101/2022.09.07.506864v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@1254e6corg.highwire.dtl.DTLVardef@3fd190org.highwire.dtl.DTLVardef@1d75eb5org.highwire.dtl.DTLVardef@8afc97_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bordeaux, Z. A. Choi, J. Braun, G. Davis, C. Marani, M. Lee, K. Samuel, C. Adams, J. Windom, R. Kambala, A. Cornman, H. Reddy, S. V. Pollizzi, A. LU, W. Oladipo, O. O. Alphonse, M. P. West, C. E. Kwatra, S. G. Kwatra, M. M. 2022-09-07 doi:10.1101/2022.09.07.506864 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Platform-Agnostic CellNet (PACNet) enables cross-study meta-analysis of cell fate engineering protocols ]]> https://biorxiv.org/content/10.1101/2022.09.07.506886v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@e4e985org.highwire.dtl.DTLVardef@9f485borg.highwire.dtl.DTLVardef@1475d0borg.highwire.dtl.DTLVardef@2d8c31_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lo, E. K. Velazquez, J. Peng, D. Kwon, C. Ebrahimkhani, M. Cahan, P. 2022-09-08 doi:10.1101/2022.09.07.506886 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Functional MRS studies of GABA and Glutamate/Glx: a systematic review and meta-analysis ]]> https://biorxiv.org/content/10.1101/2022.09.07.506899v1?rss=1 Pasanta, D. He, J. L. Ford, T. C. Oeltzschner, G. Lythgoe, D. Puts, N. A. 2022-09-08 doi:10.1101/2022.09.07.506899 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ The functional impact of rare variation across the regulatory cascade ]]> https://biorxiv.org/content/10.1101/2022.09.07.507008v1?rss=1 Li, T. Ferraro, N. Strober, B. J. Aguet, F. Kasela, S. Arvanitis, M. Ni, B. van de Wiel, L. Hershberg, E. Ardlie, K. Arking, D. E. Beer, R. L. Brody, J. Blackwell, T. W. Clish, C. Gabriel, S. Gerszten, R. Guo, X. Gupta, N. Johnson, W. C. Lappalainen, T. Lin, H. J. Liu, Y. Nickerson, D. A. Papanicolaou, G. Pritchard, J. K. Qasba, P. Shojaie, A. Smith, J. Sotoodehnia, N. Taylor, K. D. Tracy, R. P. Van den Berg, D. Wheeler, M. Rich, S. S. Rotter, J. I. Battle, A. J. Montgomery, S. B. 2022-09-09 doi:10.1101/2022.09.07.507008 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ SPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests ]]> https://biorxiv.org/content/10.1101/2022.09.08.506805v1?rss=1 Ahmed, O. Rossi, M. Gagie, T. Boucher, C. Langmead, B. 2022-09-11 doi:10.1101/2022.09.08.506805 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Activity of EGFR transmembrane region variants indicates specific transmembrane dimers are not required for EGFR activity ]]> https://biorxiv.org/content/10.1101/2022.09.08.507182v1?rss=1 Bartzoka, F. Gonzalez-Magaldi, M. Byrne, P. O. Callery, N. I. Hristova, K. Leahy, D. J. 2022-09-08 doi:10.1101/2022.09.08.507182 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Identification of regulatory elements in primary sensory neurons involved in neuropathic pain ]]> https://biorxiv.org/content/10.1101/2022.09.09.507328v1?rss=1 Stephens, K. E. Moore, C. Vinson, D. A. White, B. E. Renfro, Z. Zhou, W. E. Ji, Z. Ji, H. Zhu, H. Guan, Y. Taverna, S. 2022-09-10 doi:10.1101/2022.09.09.507328 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Co-targeting BCL-XL and MCL-1 with DT2216 and AZD8055 synergistically inhibits small-cell lung cancer growth without causing on-target toxicities in mice ]]> https://biorxiv.org/content/10.1101/2022.09.12.507616v1?rss=1 KHAN, S. Kellish, P. Connis, N. Thummuri, D. Wiegand, J. Zhang, P. Zhang, X. Budamagunta, V. Hua, N. Yang, Y. De, U. Jin, L. Zhang, W. Zheng, G. Hromas, R. Hann, C. Zajac-Kaye, M. Kaye, F. J. Zhou, D. 2022-09-14 doi:10.1101/2022.09.12.507616 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Drosophila Males Use 5'-to-3' Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides ]]> https://biorxiv.org/content/10.1101/2022.09.12.507655v1?rss=1 Venkei, Z. G. Gainetdinov, I. Starostik, M. Choi, C. Chen, P. Balsara, C. Whitfield, T. Bell, G. W. Feng, S. Jacobsen, S. E. Aravin, A. Kim, J. K. Zamore, P. Yamashita, Y. M. 2022-09-13 doi:10.1101/2022.09.12.507655 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Polymer physics of structural evolution in synthetic yeast chromosomes ]]> https://biorxiv.org/content/10.1101/2022.09.14.507906v1?rss=1 Stracquadanio, G. Yang, K. Boeke, J. D. Koszul, R. Bader, J. S. 2022-09-14 doi:10.1101/2022.09.14.507906 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Molecular determinants of Karyopherin-β2 chaperone and disaggregation activity ]]> https://biorxiv.org/content/10.1101/2022.09.14.508025v1?rss=1 Fare, C. Rhine, K. Lam, A. Myong, S. Shorter, J. 2022-09-15 doi:10.1101/2022.09.14.508025 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Cells in the Polyaneuploid Cancer Cell (PACC) state have increased metastatic potential ]]> https://biorxiv.org/content/10.1101/2022.09.16.508155v1?rss=1 Mallin, M. M. Kim, N. Choudhury, M. I. Lee, S. J. An, S. S. Sun, S. X. Konstantopoulos, K. Pienta, K. J. Amend, S. R. 2022-09-19 doi:10.1101/2022.09.16.508155 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ The cingulo-opercular network is composed of two distinct sub-systems ]]> https://biorxiv.org/content/10.1101/2022.09.16.508254v1?rss=1 Gratton, C. Dworetsky, A. Adeyemo, B. Seitzman, B. A. Smith, D. M. Petersen, S. E. Neta, M. 2022-09-18 doi:10.1101/2022.09.16.508254 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions ]]> https://biorxiv.org/content/10.1101/2022.09.16.508329v1?rss=1 WEN, J. Yang, Z. Nasrallah, I. Cui, Y. Erus, G. Srinivasan, D. Abdulkadir, A. Mamourian, E. Hwang, G. Singh, A. Bergman, M. Bao, J. Varol, E. Zhou, Z. Boquet-Pujadas, A. Chen, J. Toga, A. W. Saykin, A. J. Hohman, T. Thompson, P. Villeneuve, S. Gollub, R. Sotiras, A. Wittfeld, K. Grabe, H. Tosun, D. Bilgel, M. An, Y. Marcus, D. LaMontagne, P. J. Heckbert, S. Austin, T. Launer, L. Espeland, M. Masters, C. Maruff, P. Fripp, J. Johnson, S. C. Morris, j. Albert, M. Nick, R. Resnick, S. M. Ferrucci, L. Fan, Y. Mohamad, H. Wolk, D. Shen, L. Shou, H. Dav 2022-09-19 doi:10.1101/2022.09.16.508329 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Nuclear morphology and functional characteristics that enable survival of cells in the polyaneuploid cancer cell state following cytotoxic chemotherapy ]]> https://biorxiv.org/content/10.1101/2022.09.19.508515v1?rss=1 Kim, C.-J. Gonye, A. L. Truskowski, K. Lee, C.-F. Pienta, K. J. Amend, S. R. 2022-09-19 doi:10.1101/2022.09.19.508515 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Proteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo ]]> https://biorxiv.org/content/10.1101/2022.09.20.508727v1?rss=1 View larger version (68K): org.highwire.dtl.DTLVardef@1952331org.highwire.dtl.DTLVardef@3988a0org.highwire.dtl.DTLVardef@138fbfcorg.highwire.dtl.DTLVardef@279569_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Faustino, A. M. Sharma, P. Yadav, D. Fried, S. D. 2022-09-20 doi:10.1101/2022.09.20.508727 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Cellular and molecular dynamics in the lungs of neonatal and juvenile mice in response to E. coli ]]> https://biorxiv.org/content/10.1101/2022.09.21.508849v1?rss=1 McGrath-Morrow, S. A. Venezia, J. Ndeh, R. Singer, B. D. Cimbro, R. Soloski, M. Scott, A. L. 2022-09-21 doi:10.1101/2022.09.21.508849 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Shape-shifting microgel automata controlled by DNA sequence instructions ]]> https://biorxiv.org/content/10.1101/2022.09.21.508918v1?rss=1 Shi, R. Chen, K.-L. Fern, J. Deng, S. Liu, Y. Scalise, D. Huang, Q. Cowan, N. Gracias, D. Schulman, R. 2022-09-22 doi:10.1101/2022.09.21.508918 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Profiling emergent behaviors from single-cell motility ]]> https://biorxiv.org/content/10.1101/2022.09.21.508955v1?rss=1 Maity, D. Kamat, P. Zamponi, N. Jayatilaka, H. Giri, A. Du, W. Johnston, A. Starich, B. Karl, M. Agrawal, A. Riley, D. Venturitti, L. Melnick, A. Cerchietti, L. Walston, J. Phillip, J. M. 2022-09-22 doi:10.1101/2022.09.21.508955 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation ]]> https://biorxiv.org/content/10.1101/2022.09.22.508219v1?rss=1 Ma, W. You, S. Regnier, M. McCammon, J. A. 2022-09-23 doi:10.1101/2022.09.22.508219 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ A data-driven investigation of human action representations ]]> https://biorxiv.org/content/10.1101/2022.09.22.509054v1?rss=1 Dima, D. C. Hebart, M. N. Isik, L. 2022-09-23 doi:10.1101/2022.09.22.509054 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Neuronal pentraxin Nptx2 regulates complement activity in the brain ]]> https://biorxiv.org/content/10.1101/2022.09.22.509106v1?rss=1 Zhou, J. Wade, S. D. Graykowski, D. Xiao, M.-F. Zhao, B. Giannini, L. A. Hanson, J. E. van Swieten, J. C. Sheng, M. Worley, P. F. Dejanovic, B. 2022-09-23 doi:10.1101/2022.09.22.509106 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Marginal Zone B cells are Necessary for the Formation of Anti-Donor IgG After Allogeneic Sensitization ]]> https://biorxiv.org/content/10.1101/2022.09.23.509210v1?rss=1 Kallarakal, M. A. Cohen, G. Ibukun, F. I. Krummey, S. 2022-09-26 doi:10.1101/2022.09.23.509210 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Multiplatform Modeling of Atrial Fibrillation Identifies Phospholamban as Central Regulator of Cardiac Rhythm ]]> https://biorxiv.org/content/10.1101/2022.09.23.509238v1?rss=1 33 million people worldwide. Although AF is often developed secondary to cardiovascular diseases, endocrine disorders, or lifestyle factors, recent GWAS studies have identified >200 genetic variants that substantially contribute to AF risk. However, it is currently not known how these genetic predispositions contribute to the initiation and/or maintenance of AF-associated phenotypes. In this context, one major barrier to progress is the lack of experimental systems enabling to rapidly explore the function of large cohort of genes on rhythm parameters in models with human atrial relevance. To address these modeling challenges, we have developed a new multi-model platform enabling 1) high-throughput characterization of the role of AF-associated genes on action potential duration and rhythm parameters at the cellular level, using human iPSC-derived atrial-like cardiomyocytes (ACMs), and at the whole organ level, using the Drosophila heart model, and 2) validation of the physiological relevance of our experimental results using computational models of heterogenous human adult atrial myocytes (HAMs) and tissue. As proof of concept, we screened a cohort of 20 AF-associated genes and identified Phospholamban (PLN) loss of function as a top conserved hit that significantly shortens action potential duration in ACMs, HAMs and fly cardiomyocytes. Remarkably, while PLN knock-down (KD) was not sufficient to induce arrhythmia phenotypes, addition of environmental stressors (i.e fibroblasts, {beta}-adrenergic stimulation) to the model systems, led to the robust generation of irregular beat to beat intervals, delayed after depolarizations, and triggered action potentials, as compared to controls. Finally, to delineate the mechanism underlying PLN KD-dependent arrhythmia, we used a logistic regression approach in HAM populations, and predicted that PLN functionally interacts with both NCX (loss of function) and L-type calcium channels (gain of function) to mediate these arrhythmic phenotypes. Consistent with our predictions, co-KD of PLN and NCX in ACMs and flies, led to increased arrhythmic events, while treatment of ACMs with L-type calcium channel inhibitor, verapamil, reverted these phenotypes. In summary, these results collectively demonstrate that our integrated multi-model system approach was successful in identifying and characterizing conserved roles (i.e regulation of Ca2+ homeostasis) for AF-associated genes and phenotypes, and thus paves the way for the discovery and molecular delineation of new gene regulatory networks controlling atrial rhythm with application to AF. ]]> Colas, A. Ocorr, K. Grandi, E. Andersen, P. Kannan, S. Spiering, S. Yu, M. Ni, H. Kezos, J. Kervadec, A. 2022-09-26 doi:10.1101/2022.09.23.509238 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Olfactory neuronal cells: biopsied surrogates for neurons in the brain ]]> https://biorxiv.org/content/10.1101/2022.09.23.509290v1?rss=1 Yang, K. Ishizuka, K. Narita, Z. Lema, Y. Y. Zhang, S. Duan, J. Younes, L. Geman, D. Lane, A. P. Sawa, A. 2022-09-24 doi:10.1101/2022.09.23.509290 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ Diversity, Equity, and Inclusion in the Melanoma Research Community ]]> https://biorxiv.org/content/10.1101/2022.09.24.509278v1?rss=1 Portuallo, M. E. Lu, D. Y. Alicea, G. M. Bolling, J. Lee, R. McQuade, J. Warner, A. B. Davies, M. Weeraratna, A. Villanueva, J. Rebecca, V. W. 2022-09-28 doi:10.1101/2022.09.24.509278 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Novel Biosensor Identifies Ruxolitinib as a Potent and Cardioprotective CaMKII Inhibitor ]]> https://biorxiv.org/content/10.1101/2022.09.24.509320v1?rss=1 Reyes Gaido, O. E. Granger, J. M. Nkashama, L. J. Lin, B. L. Long, A. Mesubi, O. O. Schole, K. L. Terrillion, C. E. Liu, J. O. Luczak, E. D. Anderson, M. E. 2022-09-24 doi:10.1101/2022.09.24.509320 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ From Correlation to Communication: disentangling hidden factors from functional connectivity changes ]]> https://biorxiv.org/content/10.1101/2022.09.25.509384v1?rss=1 Yu, Y. Gratton, C. Smith, D. M. 2022-09-27 doi:10.1101/2022.09.25.509384 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Feasibility Analyses and Experimental Confirmation of Dove Prism Based Dual-fiberscope Rotary Joint ]]> https://biorxiv.org/content/10.1101/2022.09.25.509388v1?rss=1 Liu, Y. Park, H.-C. Zhang, H. Li, X. 2022-09-27 doi:10.1101/2022.09.25.509388 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Antiretroviral Therapy Does Not Restore Brain Lipids During SIV Infection: Regional Analysis of Metabolic Homeostasis and Depletion ]]> https://biorxiv.org/content/10.1101/2022.09.26.508302v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@598d53org.highwire.dtl.DTLVardef@14d5cf1org.highwire.dtl.DTLVardef@10f6c9org.highwire.dtl.DTLVardef@1ba1aab_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> White, C. J. Gausepohl, A. M. Seneviratne, H. K. Bumpus, N. N. Williams, D. W. 2022-09-27 doi:10.1101/2022.09.26.508302 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Concurrent measurement of perfusion parameters related to small blood and lymphatic vessels in the human brain using dynamic dual-spin-echo perfusion (DDSEP) MRI ]]> https://biorxiv.org/content/10.1101/2022.09.26.509366v1?rss=1 Cao, D. Sun, Y. Su, P. Pillai, J. J. Qiao, Y. Lu, H. Van Zijl, P. C. M. Knutsson, L. Hua, J. 2022-09-27 doi:10.1101/2022.09.26.509366 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3 ]]> https://biorxiv.org/content/10.1101/2022.09.26.509529v1?rss=1 Schindewolf, C. Lokugamage, K. Vu, M. Johnson, B. A. Scharton, D. Plante, J. A. Kalveram, B. K. Crocquet-Valdes, P. A. Sotcheff, S. L. Jaworski, E. Alvarado, R. E. Debbink, K. Daugherty, M. D. Weaver, S. Routh, A. L. Walker, D. H. Plante, K. S. Menachery, V. D. 2022-09-26 doi:10.1101/2022.09.26.509529 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Perturbation variance suppresses error sensitivity in the implicit learning system ]]> https://biorxiv.org/content/10.1101/2022.09.26.509572v1?rss=1 Albert, S. T. Shadmehr, R. 2022-09-27 doi:10.1101/2022.09.26.509572 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2022.09.27.509669v1?rss=1 Harrington, E. P. Catenacci, R. B. Smith, M. D. Heo, D. Miller, C. E. Meyers, K. R. Glatzer, J. Bergles, D. E. Calabresi, P. A. 2022-09-28 doi:10.1101/2022.09.27.509669 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Cardiac muscle-restricted partial loss of Nos1ap expression has limited impact on electro- and echo-cardiographic features ]]> https://biorxiv.org/content/10.1101/2022.09.27.509782v1?rss=1 Smith, A. Auer, D. Johnson, M. Sanchez, E. Ross, H. Ward, C. Chakravarti, A. Kapoor, A. 2022-09-28 doi:10.1101/2022.09.27.509782 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ More than half of the variance in in-vivo 1H-MRS metabolite estimates is common to all metabolites ]]> https://biorxiv.org/content/10.1101/2022.09.29.510115v1?rss=1 Prisciandaro, J. J. Zöllner, H. J. Murali-Manohar, S. Oeltzschner, G. Edden, R. A. E. 2022-09-30 doi:10.1101/2022.09.29.510115 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia ]]> https://biorxiv.org/content/10.1101/2022.09.30.510315v1?rss=1 Michki, N. S. Ndeh, R. Helmin, K. A. Singer, B. D. McGrath-Morrow, S. A. 2022-10-01 doi:10.1101/2022.09.30.510315 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells ]]> https://biorxiv.org/content/10.1101/2022.09.30.510412v1?rss=1 Sarabipour, S. Kinghorn, K. Quigley, K. M. Kovacs-Kasa, A. Annex, B. H. Bautch, V. L. Mac Gabhann, F. 2022-10-01 doi:10.1101/2022.09.30.510412 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Mechanisms of adjustments to different types of uncertainty in the reward environment across mice and monkeys ]]> https://biorxiv.org/content/10.1101/2022.10.01.510477v1?rss=1 Hyung Woo, J. Aguirre, C. G. Bari, B. A. Tsutsui, K.-I. Grabenhorst, F. Cohen, J. Y. Schultz, W. Izquierdo, A. Soltani, A. 2022-10-04 doi:10.1101/2022.10.01.510477 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Enhanced mTORC1 signaling and Protein Synthesis in Parkinson Disease Pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.10.03.510455v1?rss=1 Khan, M. R. Yin, X. Kang, S.-u. Mitra, J. Wang, H. Brahmachari, S. Karuppagounder, S. S. Kimura, Y. Jhaldiyal, A. Kim, H. H. Gu, H. Chen, R. Redding-Ochoa, J. Troncoso, J. Ha, T. Dawson, V. L. Dawson, T. M. 2022-10-06 doi:10.1101/2022.10.03.510455 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast ]]> https://biorxiv.org/content/10.1101/2022.10.03.510608v1?rss=1 Schindler, D. Walker, R. S. K. Jiang, S. Brooks, A. N. Wang, Y. Mueller, C. A. Cockram, C. Luo, Y. Garcia, A. Schraivogel, D. Mozziconacci, J. Blount, B. A. Cai, J. Ogunlana, L. Liu, W. Joensson, K. Abramczyk, D. Garcia-Ruiz, E. Turowski, T. W. Swidah, R. Ellis, T. Antequera, F. Shen, Y. Nieduszynski, C. A. Koszul, R. Dai, J. Steinmetz, L. M. Boeke, J. D. Cai, Y. 2022-10-03 doi:10.1101/2022.10.03.510608 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ A shared neural code for social interaction encoding and memory in the human superior temporal sulcus ]]> https://biorxiv.org/content/10.1101/2022.10.03.510639v1?rss=1 Lee Masson, H. Chen, J. Isik, L. 2022-10-04 doi:10.1101/2022.10.03.510639 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Second-generation dual-channel visible light optical coherence tomography enables wide-field, full-range, and shot-noise limited retinal imaging ]]> https://biorxiv.org/content/10.1101/2022.10.05.511048v1?rss=1 60{degrees} wide-field imaging over large retinal curvature at peripheral retina and optic nerve head, as well as high-definition imaging at ultrahigh 1.3 um depth resolution (water). The dual-channel design includes a conventional near infrared (NIR) channel, compatible with Doppler OCT and OCT angiography (OCTA). The comprehensive structure-function measurement by 2nd-Gen VIS-OCT system is a significant advance towards broader adaptation of VIS-OCT in clinical applications. ]]> Wang, J. Nolen, S. Song, W. Shao, W. Yi, W. Yi, J. 2022-10-07 doi:10.1101/2022.10.05.511048 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Inhibition of the proton-activated chloride channel PAC by PIP2 ]]> https://biorxiv.org/content/10.1101/2022.10.06.511171v1?rss=1 Mihaljevic, L. Zheng, R. Osei-Owusu, J. Lü, W. Qiu, Z. 2022-10-07 doi:10.1101/2022.10.06.511171 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects ]]> https://biorxiv.org/content/10.1101/2022.10.06.511215v1?rss=1 Qi, G. Strober, B. J. Popp, J. M. Ji, H. Battle, A. 2022-10-06 doi:10.1101/2022.10.06.511215 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI ]]> https://biorxiv.org/content/10.1101/2022.10.06.511219v1?rss=1 Sun, Q. Rowland, B. T. Chen, J. Mikhaylova, A. V. Avery, C. Peters, U. Lundin, J. Matise, T. Buyske, S. Tao, R. Mathias, R. A. Reiner, A. P. Auer, P. L. Cox, N. J. Kooperberg, C. Thornton, T. Raffield, L. M. Li, Y. 2022-10-08 doi:10.1101/2022.10.06.511219 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Pantr2, a trans-acting lncRNA, modulates the differentiation potential of neural progenitors in vivo ]]> https://biorxiv.org/content/10.1101/2022.10.07.511381v1?rss=1 Augustin, J. J. Takayangi, S. Hoang, T. Winer, B. Blackshaw, S. Goff, L. A. 2022-10-08 doi:10.1101/2022.10.07.511381 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Differences in activity and stability drive transposable element variation in tropical and temperate maize. ]]> https://biorxiv.org/content/10.1101/2022.10.09.511471v1?rss=1 Ou, S. Collins, T. Qiu, Y. Seetharam, A. S. Menard, C. C. Manchanda, N. Gent, J. I. Schatz, M. C. Anderson, S. N. Hufford, M. B. Hirsch, C. N. 2022-10-09 doi:10.1101/2022.10.09.511471 Cold Spring Harbor Laboratory Press 2022-10-09 <![CDATA[ A machine learning based approach towards high-dimensional mediation analysis ]]> https://biorxiv.org/content/10.1101/2022.10.10.511329v1?rss=1 Nath, T. Caffo, B. Wager, T. Lindquist, M. 2022-10-11 doi:10.1101/2022.10.10.511329 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ The Children's Brain Tumor Network (CBTN) - Accelerating Research in Pediatric Central Nervous System Tumors through Collaboration and Open Science ]]> https://biorxiv.org/content/10.1101/2022.10.14.511975v1?rss=1 5,000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors. ]]> Lilly, J. V. Rokita, J. L. Mason, J. L. Patton, T. Stefankiewiz, S. Higgins, D. Trooskin, G. Larouci, C. A. Arya, K. Appert, E. Heath, A. P. Zhu, Y. Brown, M. A. Zhang, B. Farrow, B. K. Robins, S. Morgan, A. M. Nguyen, T. Q. Frenkel, E. Lehmann, K. Drake, E. Sullivan, C. Plisiewicz, A. Coleman, N. Patterson, L. Koptyra, M. Helili, Z. Van Kuren, N. Young, N. M. Kim, M. C. Friedman, C. Lubneuski, A. Blackden, C. Williams, M. Baubet, V. Tauhid, L. Galanaugh, J. Boucher, K. Ijaz, H. Cole, K. A. Choudhari, N. Santi, M. Moulder, R. W. Waller, J. Rife, W. 2022-10-18 doi:10.1101/2022.10.14.511975 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Filtering Microbial Populations with a Magnetic Field ]]> https://biorxiv.org/content/10.1101/2022.10.14.512298v1?rss=1 Nazareth, M. Kilinc, E. Deamer, D. W. 2022-10-15 doi:10.1101/2022.10.14.512298 Cold Spring Harbor Laboratory Press 2022-10-15 <![CDATA[ WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs ]]> https://biorxiv.org/content/10.1101/2022.10.15.512390v1?rss=1 Chao, K.-H. Chen, P.-W. Seshia, S. A. Langmead, B. 2022-10-18 doi:10.1101/2022.10.15.512390 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing ]]> https://biorxiv.org/content/10.1101/2022.10.16.512384v1?rss=1 Baker, D. N. Langmead, B. 2022-10-20 doi:10.1101/2022.10.16.512384 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements ]]> https://biorxiv.org/content/10.1101/2022.10.17.512624v1?rss=1 Sarabipour, S. Burgess, S. J. Niemi, N. M. Smith, C. T. Bisson Filho, A. W. Ibrahim, A. Clark, K. 2022-10-19 doi:10.1101/2022.10.17.512624 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Surface phenotyping and quantitative proteomics reveal differentially enriched proteins of brain-derived extracellular vesicles in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2022.10.17.512628v1?rss=1 Arab, T. Huang, Y. Nagaraj, R. Gizzie, E. Redding-Ochoa, J. Troncoso, J. C. Pletnikova, O. Boronina, T. Cole, R. N. Mahairaki, V. Routenberg, D. A. Witwer, K. W. 2022-10-18 doi:10.1101/2022.10.17.512628 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ MLL1 regulates cytokine-driven cell migration and metastasis ]]> https://biorxiv.org/content/10.1101/2022.10.18.512715v1?rss=1 Nair, P. R. Danilova, L. Gomez-de-Mariscal, E. Kim, D. Fan, R. Munoz-Barrutia, A. Fertig, E. J. Wirtz, D. 2022-10-19 doi:10.1101/2022.10.18.512715 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ A developmental program that regulates mammalian organ size offsets evolutionary distance ]]> https://biorxiv.org/content/10.1101/2022.10.19.512107v1?rss=1 Shimamura, Y. Tanaka, J. Kakiuchi, M. Sarmah, H. Miura, A. Hwang, Y. Sawada, A. Ninish, Z. Yamada, K. Cai, J. J. Mori, M. 2022-10-21 doi:10.1101/2022.10.19.512107 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Revisiting Macromolecular Hydration with HullRadSAS ]]> https://biorxiv.org/content/10.1101/2022.10.20.513022v1?rss=1 Fleming, P. J. Correia, J. J. Fleming, K. G. 2022-10-21 doi:10.1101/2022.10.20.513022 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Survivin Regulates Intracellular Stiffness and Extracellular Matrix Production in Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2022.10.24.513582v1?rss=1 Krajnik, A. Nimmer, E. Sullivan, A. Joseph, B. A. Heo, Y. Krug, A. Kolega, J. Heo, S.-J. Lee, K. Weil, B. R. Kim, D.-H. Bae, Y. 2022-10-24 doi:10.1101/2022.10.24.513582 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Genes vary greatly in their propensity for collateral fitness effects of mutations ]]> https://biorxiv.org/content/10.1101/2022.10.24.513589v1?rss=1 Mehlhoff, J. D. Ostermeier, M. 2022-10-25 doi:10.1101/2022.10.24.513589 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Adding meaning to memories: How parietal cortex combines semantic content with episodic experience ]]> https://biorxiv.org/content/10.1101/2022.10.25.513263v1?rss=1 Lee, H. Keene, P. A. Sweigart, S. C. Hutchinson, J. B. Kuhl, B. A. 2022-10-27 doi:10.1101/2022.10.25.513263 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide ]]> https://biorxiv.org/content/10.1101/2022.10.26.513573v1?rss=1 BICCN Data Ecosytem Collaboration, Hawrylycz, M. J. Martone, M. E. Hof, P. R. Lein, E. S. Regev, A. Ascoli, G. A. A. Bjaalie, J. G. Dong, H.-W. Ghosh, S. S. Gillis, J. Hertzano, R. Haynor, D. R. Kim, Y. Liu, Y. Miller, J. A. Mitra, P. P. Mukamel, E. Osumi-Sutherland, D. Peng, H. Ray, P. L. Sanchez, R. Ropelewski, A. Scheuermann, R. H. Tan, S. Z. K. Tickle, T. Tilgner, H. Varghese, M. Wester, B. White, O. Aevermann, B. Allemang, D. Ament, S. Athey, T. L. Baker, P. M. Baker, C. Baker, K. S. Bandrowski, A. Bishwakarma, P. Carr, A. Chen, M. Choudhury, R. 2022-10-30 doi:10.1101/2022.10.26.513573 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Direct activation of the Ras-Akt network mediates polarity and organizes protrusions in human neutrophil migration ]]> https://biorxiv.org/content/10.1101/2022.10.27.513966v1?rss=1 Pal, D. S. Banerjee, T. Lin, Y. Borleis, J. Devreotes, P. N. 2022-10-28 doi:10.1101/2022.10.27.513966 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ An exploratory study of a simple approach for evaluating drug solubility in milk related vehicles ]]> https://biorxiv.org/content/10.1101/2022.10.27.514033v1?rss=1 Li, S. Gabriel, J. J. Martinez, M. N. Longstaff, D. G. Coffey, M. J. Zhao, F. 2022-10-27 doi:10.1101/2022.10.27.514033 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Palmitoylation regulates neuropilin-2 localization and function in cortical neurons and conveys specificity to semaphorin signaling via palmitoyl acyltransferases ]]> https://biorxiv.org/content/10.1101/2022.10.28.514228v1?rss=1 Koropouli, E. Wang, Q. Mejias-Estevez, R. Hand, R. Wang, T. Ginty, D. D. Kolodkin, A. L. 2022-10-28 doi:10.1101/2022.10.28.514228 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics ]]> https://biorxiv.org/content/10.1101/2022.10.29.514358v1?rss=1 Van Wieren, A. Durrant, J. Majumdar, S. 2022-10-30 doi:10.1101/2022.10.29.514358 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+ ]]> https://biorxiv.org/content/10.1101/2022.10.29.514376v1?rss=1 Zou, R. S. Liu, Y. Reyes Gaido, O. E. Konig, M. F. Mog, B. J. Shen, L. L. Aviles-Vazquez, F. Marin-Gonzalez, A. Ha, T. 2022-10-30 doi:10.1101/2022.10.29.514376 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ In-vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2022.10.31.514397v1?rss=1 DeBerardinis, R. J. Kaushik, A. Burroughs, L. K. Tarangelo, A. Ragavan, M. Wu, C.-Y. Li, X. Ahumada, K. Tcheuyap, V. T. Saatchi, F. Do, Q. Yong, C. Rosales, T. Stevens, C. Rao, A. D. Faubert, B. Pachnis, P. Zacharias, L. G. Vu, H. Cai, F. Mathews, T. P. Slusher, B. S. P. Kapur, P. Sun, X. Merritt, M. Brugarolas, J. Zhang, Y. Chiang, J.-C. Genovese, G. 2022-11-01 doi:10.1101/2022.10.31.514397 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ The Plasmodium falciparum apicoplast cysteine desulfurase provides sulfur for both iron sulfur cluster assembly and tRNA modification ]]> https://biorxiv.org/content/10.1101/2022.10.31.514511v1?rss=1 Prigge, S. T. Swift, R. P. Elahi, R. Rajaram, K. Liu, H. B. 2022-11-01 doi:10.1101/2022.10.31.514511 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Generation of Unfolded Outer Membrane Protein Ensembles Targeted by Hydrodynamic Properties ]]> https://biorxiv.org/content/10.1101/2022.10.31.514552v1?rss=1 Devlin, T. Fleming, P. J. Loza, N. Fleming, K. G. 2022-11-01 doi:10.1101/2022.10.31.514552 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ The Transcription Factor Foxi1 Promotes Expression of V-ATPase and Gpr116 in M-1 cells ]]> https://biorxiv.org/content/10.1101/2022.10.31.514579v1?rss=1 Kui, M. Pluznick, J. L. Zaidman, N. 2022-11-01 doi:10.1101/2022.10.31.514579 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Cell lineage predicts neural connectivity beyond cell type ]]> https://biorxiv.org/content/10.1101/2022.11.01.514680v1?rss=1 Matelsky, J. K. Wester, B. Kording, K. P. 2022-11-01 doi:10.1101/2022.11.01.514680 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Fitness and functional landscapes of the E. coli RNase III gene rnc ]]> https://biorxiv.org/content/10.1101/2022.11.01.514689v1?rss=1 Weeks, R. Ostermeier, M. 2022-11-02 doi:10.1101/2022.11.01.514689 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ FkpA Enhances Membrane Protein Folding using an Extensive Interaction Surface ]]> https://biorxiv.org/content/10.1101/2022.11.01.514694v1?rss=1 Devlin, T. Marx, D. C. Roskopf, M. A. Bubb, Q. R. Plummer, A. M. Fleming, K. G. 2022-11-02 doi:10.1101/2022.11.01.514694 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Preservation of prehearing spontaneous activityenables early auditory system development in deaf mice ]]> https://biorxiv.org/content/10.1101/2022.11.01.514787v1?rss=1 Kersbergen, C. J. Babola, T. A. Kanold, P. O. Bergles, D. E. 2022-11-01 doi:10.1101/2022.11.01.514787 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Phase-separating pyrenoid proteins form complexes in the dilute phase ]]> https://biorxiv.org/content/10.1101/2022.11.01.514800v1?rss=1 He, G. GrandPre, T. Wilson, H. Zhang, Y. Jonikas, M. C. Wingreen, N. S. Wang, Q. 2022-11-03 doi:10.1101/2022.11.01.514800 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Gene model correction for PVRIG in single cell and bulk sequencing data enables accurate detection and study of its functional relevance ]]> https://biorxiv.org/content/10.1101/2022.11.02.514879v1?rss=1 Nemzer, S. Sabath, N. Wool, A. Alteber, Z. Ando, H. Nickles-Fader, A. Wang, T.-L. Shih, I.-M. Pardoll, D. M. Ganguly, S. Turpaz, Y. Levine, Z. Granit, R. Z. 2022-11-03 doi:10.1101/2022.11.02.514879 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Continuous automated MRS data analysis workflow for applied studies ]]> https://biorxiv.org/content/10.1101/2022.11.03.515056v1?rss=1 Zoellner, H. J. Davies-Jenkins, C. W. Lee, E. G. Hendrickson, T. J. Edden, R. A. Gudmundson, A. T. Oeltzschner, G. 2022-11-07 doi:10.1101/2022.11.03.515056 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Facemap: a framework for modeling neural activity based on orofacial tracking ]]> https://biorxiv.org/content/10.1101/2022.11.03.515121v1?rss=1 Syeda, A. Zhong, L. Tung, R. Long, W. Pachitariu, M. Stringer, C. 2022-11-04 doi:10.1101/2022.11.03.515121 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Integration of cell wall synthesis activation and chromosome segregation during cell division in Caulobacter ]]> https://biorxiv.org/content/10.1101/2022.11.05.515301v1?rss=1 Mahone, C. R. Yang, X. McCausland, J. W. Payne, I. P. Xiao, J. Goley, E. D. 2022-11-05 doi:10.1101/2022.11.05.515301 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ XIST ribonucleoproteins promote female sex-biased autoimmunity ]]> https://biorxiv.org/content/10.1101/2022.11.05.515306v1?rss=1 Dou, D. R. Zhao, Y. Belk, J. A. Casey, K. M. Chen, D. C. Li, R. Yu, B. Abe, B. T. Kraft, K. Hellstrom, C. Sjoberg, R. Chang, S. E. Feng, A. Goldman, D. W. Shah, A. A. Petri, M. Wigley, F. M. Chung, L. S. Fiorentino, D. F. Lundberg, E. K. Wutz, A. Utz, P. J. Chang, H. 2022-11-05 doi:10.1101/2022.11.05.515306 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ The Cousa objective: a long working distance air objective for multiphoton imaging in vivo ]]> https://biorxiv.org/content/10.1101/2022.11.06.515343v1?rss=1 4 mm2 field-of-view with submicron lateral resolution, and is compatible with commonly used multiphoton imaging systems. We share the full optical prescription, and report performance including in vivo 2-photon and 3-photon imaging in a range of species and preparations. ]]> Yu, C.-H. Yu, Y. Adsit, L. M. Chang, J. T. Barchini, J. Moberly, A. H. Benisty, H. Kim, J. Ricci, A. J. Fitzpatrick, D. Cardin, J. A. Higley, M. Smith, G. B. Nielsen, K. J. Smith, I. T. Smith, S. L. 2022-11-06 doi:10.1101/2022.11.06.515343 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Modular cell type organization of cortical areas revealed by in situ sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.06.515380v1?rss=1 Chen, X. Fischer, S. Zhang, A. Gillis, J. Zador, A. 2022-11-06 doi:10.1101/2022.11.06.515380 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.07.515222v1?rss=1 Auer, P. L. Jakubek, Y. A. Zhou, Y. Stilp, A. M. Bacon, J. Wong, J. Mitchell, B. Lewis, J. Boerwinkle, E. Loos, R. J. F. Preuss, M. Barnes, K. Pankratz, N. Fornage, M. Redline, S. Psaty, B. M. Bis, J. C. Silverman, E. Cho, M. Yun, J. Ramachandran, V. Mathias, R. A. Taub, M. Peyser, P. A. Smith, J. A. Kardia, S. Arnett, D. North, K. E. Raffield, L. M. Carson, A. Doyle, M. Rich, S. Rotter, J. Guo, X. Cox, N. Mack, T. Chasman, D. Machiela, M. Ozcan, Z. Conomos, M. Li, Y. Desai, P. Bick, A. Reiner, A. P. Scheet, P. 2022-11-08 doi:10.1101/2022.11.07.515222 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Structured Joint Decomposition (SJD) identifies conserved molecular dynamics across collections of biologically related multi-omics data matrices ]]> https://biorxiv.org/content/10.1101/2022.11.07.515489v1?rss=1 Chen, H. Liu, J. Sonthalia, S. Stein-OBrien, G. Xiao, L. Caffo, B. Colantuoni, C. 2022-11-08 doi:10.1101/2022.11.07.515489 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of retinal detachment-related proliferative vitreoretinopathy. ]]> https://biorxiv.org/content/10.1101/2022.11.07.515504v1?rss=1 Santiago, C. P. Gimmen, M. Y. Lu, Y. McNally, M. M. Duncan, L. H. Creamer, T. Orzolek, L. Blackshaw, S. Singh, M. 2022-11-08 doi:10.1101/2022.11.07.515504 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Potassium regulates axon-oligodendrocyte signaling and metabolic coupling in white matter ]]> https://biorxiv.org/content/10.1101/2022.11.08.515614v1?rss=1 Looser, Z. J. Ravotto, L. Jung, R. B. Werner, H. B. Ruhwedel, T. Moebius, W. Bergles, D. E. Barros, L. F. Nave, K.-A. Weber, B. Saab, A. S. 2022-11-09 doi:10.1101/2022.11.08.515614 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Neural signatures of reading-related orthographic processing in braille ]]> https://biorxiv.org/content/10.1101/2022.11.09.515790v1?rss=1 Liu, Y.-F. Rapp, B. Bedny, M. 2022-11-09 doi:10.1101/2022.11.09.515790 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Integration of exogenous and endogenous co-stimulatory signals by CAR-Tregs ]]> https://biorxiv.org/content/10.1101/2022.11.10.516049v1?rss=1 Rosado-Sanchez, I. Haque, M. Salim, K. Speck, M. Fung, V. Boardman, D. Mojibian, M. Raimondi, G. Levings, M. K. 2022-11-10 doi:10.1101/2022.11.10.516049 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Exploration of mechanisms of drug resistance by polyaneuploid cancer cells in a microfluidic device and patient tissues ]]> https://biorxiv.org/content/10.1101/2022.11.14.515727v1?rss=1 Lim, W. Hwang, I. Zhang, J. Chen, Z. Jeonghun, J. Koo, B.-K. Kim, S. Lee, J. E. Pienta, K. j. Amend, S. R. Austin, R. H. Ahn, J.-Y. Park, S. 2022-11-16 doi:10.1101/2022.11.14.515727 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Rate of neuronal turnover in the healthy adult murine myenteric ganglia varies with ganglia size ]]> https://biorxiv.org/content/10.1101/2022.11.14.516462v1?rss=1 Gorecki, A. M. Singh, A. Zhang, C. Gurumurthy, R. Kulkarni, S. 2022-11-14 doi:10.1101/2022.11.14.516462 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Application of a Latent Trait Modeling Method for Missing Data Across Datasets: Guidance on Appropriate Factor Structure ]]> https://biorxiv.org/content/10.1101/2022.11.14.516488v1?rss=1 bartlett, c. Gorham, T. J. Knapp, E. A. Kress, A. M. Klamer, B. Buyske, S. Lau, B. Petrill, S. A. 2022-11-16 doi:10.1101/2022.11.14.516488 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Tumor proliferation and invasion are coupled through cell-extracellular matrix friction ]]> https://biorxiv.org/content/10.1101/2022.11.15.516548v1?rss=1 Crawford, A. J. Gomez-Cruz, C. Russo, G. C. Huang, W. Bhorkar, I. Munoz-Barrutia, A. Wirtz, D. Garcia-Gonzalez, D. 2022-11-15 doi:10.1101/2022.11.15.516548 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ An evolutionarily conserved olfactory receptor is required for sex differences in blood pressure ]]> https://biorxiv.org/content/10.1101/2022.11.16.516677v1?rss=1 Xu, J. Choi, R. Gupta, K. Warren, H. R. Santhanam, L. Pluznick, J. L. 2022-11-17 doi:10.1101/2022.11.16.516677 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Amplicon sequencing reveals complex infection in infants congenitally infected with Trypanosoma cruzi and informs the dynamics of parasite transmission ]]> https://biorxiv.org/content/10.1101/2022.11.16.516746v1?rss=1 Hakim, J. M. Waltmann, A. Tinajeros, F. Kharabora, O. Malaga Machaca, E. Calderon, M. Menduina, M. d. C. Wang, J. Rueda, D. Zimic, M. Verastegui, M. Juliano, J. J. Gilman, R. H. Mugnier, M. R. Bowman, N. M. Chagas working group, 2022-11-16 doi:10.1101/2022.11.16.516746 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Using Attention-based Deep Learning to Predict ERG:TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images ]]> https://biorxiv.org/content/10.1101/2022.11.18.517111v1?rss=1 Omar, M. Xu, Z. Rand, S. B. Mohammad, M. Salles, D. C. Schaeffer, E. M. Robinson, B. D. Lotan, T. L. Loda, M. Marchionni, L. 2022-11-20 doi:10.1101/2022.11.18.517111 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ DPYSL2/CRMP2 isoform B knockout in human iPSC-derived glutamatergic neurons confirms its role in mTOR signaling and neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2022.11.19.517191v1?rss=1 Feuer, K. L. Peng, X. Yovo, C. Avramopoulos, D. 2022-11-19 doi:10.1101/2022.11.19.517191 Cold Spring Harbor Laboratory Press 2022-11-19 <![CDATA[ Defects in the HIV immature lattice support essential lattice remodeling within budded virions ]]> https://biorxiv.org/content/10.1101/2022.11.21.517392v1?rss=1 Guo, S.-K. Saha, I. Saffarian, S. Johnson, M. E. 2022-11-21 doi:10.1101/2022.11.21.517392 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Dependence of Nucleosome Mechanical Stability on DNA Mismatches and Histone Variants ]]> https://biorxiv.org/content/10.1101/2022.11.21.517409v1?rss=1 Ngo, T. T. M. Wang, F. Liu, B. Basu, A. Wu, C. Ha, T. 2022-11-21 doi:10.1101/2022.11.21.517409 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Neurogenetic identification of mosquito sensory neurons ]]> https://biorxiv.org/content/10.1101/2022.11.22.517370v1?rss=1 GFP and Orco>GFP mosquitoes, we predict the extent of neurons expressing Ionotropic Receptors or other chemosensory receptors. This work introduces a valuable genetic tool for the functional analysis of Anopheles mosquito neurobiology and initiates characterization of the sensory neurons that guide mosquito behavior. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/517370v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1ebbf69org.highwire.dtl.DTLVardef@63bcd2org.highwire.dtl.DTLVardef@1bab0org.highwire.dtl.DTLVardef@18799a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Konopka, J. K. Task, D. Poinapen, D. Potter, C. J. 2022-11-22 doi:10.1101/2022.11.22.517370 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ miR-210 expression is strongly hypoxia-induced in anaplastic thyroid cancer cell lines and is associated with extracellular vesicles & Argonaute-2 ]]> https://biorxiv.org/content/10.1101/2022.11.23.515840v1?rss=1 Powell, B. H. Turchinovich, A. Wang, Y. Gololobova, O. Buschmann, D. Zeiger, M. A. Umbricht, C. B. Witwer, K. W. 2022-11-24 doi:10.1101/2022.11.23.515840 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Direct observation of the evolution of cell-type specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells ]]> https://biorxiv.org/content/10.1101/2022.11.23.517662v1?rss=1 Jenike, A. E. Jenike, K. M. Peterson, K. J. Fromm, B. Halushka, M. K. 2022-11-24 doi:10.1101/2022.11.23.517662 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Poly ADP-Ribose Signaling is Dysregulated in Huntington Disease Patients ]]> https://biorxiv.org/content/10.1101/2022.11.23.517669v1?rss=1 Maiuri, T. Bazan, C. B. Harding, R. J. Begeja, N. Kam, T.-I. Byrne, L. M. Rodrigues, F. B. Warner, M. M. Neuman, K. Mansoor, M. Badiee, M. Dasovich, M. Leung, A. K. Andres, S. N. Wild, E. J. Dawson, T. M. Dawson, V. L. Arrowsmith, C. H. Truant, R. 2022-11-24 doi:10.1101/2022.11.23.517669 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Simultaneous Noise Reduction and Layer Segmentation for Visible Light Optical Coherence Tomography in Human Retina ]]> https://biorxiv.org/content/10.1101/2022.11.25.518000v1?rss=1 Ye, T. Wang, J. Yi, J. 2022-11-27 doi:10.1101/2022.11.25.518000 Cold Spring Harbor Laboratory Press 2022-11-27 <![CDATA[ Independence and interaction between the control of moving and holding still in post-stroke arm paresis ]]> https://biorxiv.org/content/10.1101/2022.11.26.517884v1?rss=1 Hadjiosif, A. M. Kita, K. Albert, S. T. Scheidt, R. A. Shadmehr, R. Krakauer, J. W. 2022-11-27 doi:10.1101/2022.11.26.517884 Cold Spring Harbor Laboratory Press 2022-11-27 <![CDATA[ Astrocyte MCT1 expression does not contribute to the axonal degenerative phenotype observed with ubiquitous MCT1 depletion. ]]> https://biorxiv.org/content/10.1101/2022.11.27.518094v1?rss=1 Phillips, T. Thompson, E. G. Vijayakumar, B. G. Kent, E. R. Millar, S. J. Vidensky, S. Farah, M. H. Rothstein, J. D. 2022-11-28 doi:10.1101/2022.11.27.518094 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism ]]> https://biorxiv.org/content/10.1101/2022.11.27.518129v1?rss=1 Britton, B. M. Yovanno, R. A. Costa, S. F. McCausland, J. Lau, A. Y. Xiao, J. Hensel, Z. 2022-11-28 doi:10.1101/2022.11.27.518129 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ The connectome of an insect brain ]]> https://biorxiv.org/content/10.1101/2022.11.28.516756v1?rss=1 Winding, M. Pedigo, B. D. Barnes, C. L. Patsolic, H. G. Park, Y. Kazimiers, T. Fushiki, A. Andrade, I. V. Li, F. Valdes-Aleman, J. Khandelwal, A. Randel, N. Barsotti, E. Correia, A. Fetter, R. D. Hartenstein, V. Priebe, C. E. Vogelstein, J. T. Cardona, A. Zlatic, M. 2022-11-28 doi:10.1101/2022.11.28.516756 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Generative network modeling reveals quantitative definitions of bilateral symmetry exhibited by a whole insect brain connectome ]]> https://biorxiv.org/content/10.1101/2022.11.28.518219v1?rss=1 Pedigo, B. D. Powell, M. Bridgeford, E. W. Winding, M. Priebe, C. E. Vogelstein, J. T. 2022-11-28 doi:10.1101/2022.11.28.518219 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Automated head-fixation training system with high levels of animal participation in psychoacoustic tasks ]]> https://biorxiv.org/content/10.1101/2022.11.29.518279v1?rss=1 Liu, J. Maximov, K. Kanold, P. O. 2022-12-01 doi:10.1101/2022.11.29.518279 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Signaling Node at TSC2 S1365 Potently Regulates T-Cell Differentiation and Improves Adoptive Cellular Cancer Therapy ]]> https://biorxiv.org/content/10.1101/2022.11.30.518569v1?rss=1 Kass, D. A. Powell, J. D. Patel, C. Dong, Y. Dunkerly-Eyring, B. L. Wen, J. Ranek, M. J. Bartle, L. M. Henderson, D. B. Sagart, J. 2022-12-02 doi:10.1101/2022.11.30.518569 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ The complete sequence of a human Y chromosome ]]> https://biorxiv.org/content/10.1101/2022.12.01.518724v1?rss=1 Rhie, A. Nurk, S. Cechova, M. Hoyt, S. J. Taylor, D. J. Altemose, N. Hook, P. W. Koren, S. Rautiainen, M. Alexandrov, I. A. Allen, J. Asri, M. Bzikadze, A. V. Chen, N.-C. Chin, C.-S. Diekhans, M. Flicek, P. Formenti, G. Fungtammasan, A. Garcia Giron, C. Garrison, E. Gershman, A. Gerton, J. Grady, P. G. Guarracino, A. Haggerty, L. Halabian, R. Hansen, N. F. Harris, R. Hartley, G. A. Harvey, W. T. Haukness, M. Heinz, J. Hourlier, T. Hubley, R. M. Hunt, S. E. Hwang, S. Jain, M. Kesharwani, R. K. Lewis, A. P. Li, H. Logsdon, G. A. Lucas, J. K. Makalowski, 2022-12-01 doi:10.1101/2022.12.01.518724 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ GluN2B-containing NMDA receptors are required for potentiation and depression of responses in ocular dominance plasticity ]]> https://biorxiv.org/content/10.1101/2022.12.01.518760v1?rss=1 Bridi, M. Hong, S. Z. Severin, D. kirkwood, a. 2022-12-01 doi:10.1101/2022.12.01.518760 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Mycobacterium tuberculosis disease associates with higher HIV-1-specific antibody responses ]]> https://biorxiv.org/content/10.1101/2022.12.02.518812v1?rss=1 Adeoye, B. Nakiyingi, L. Moreau, Y. Nankya, E. Olson, A. J. Zhang, M. Jacobson, K. R. Gupta, A. Manabe, Y. Hosseinipour, M. C. Kumwenda, J. Sagar, M. 2022-12-02 doi:10.1101/2022.12.02.518812 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ SLC26A3 (DRA) is stimulated in a synergistic, intracellular Ca2+ dependent manner by cAMP AND ATP in intestinal epithelial cells ]]> https://biorxiv.org/content/10.1101/2022.12.02.518884v1?rss=1 Sarker, R. Lin, R.-X. Singh, V. Donowitz, M. Tse, C. M. 2022-12-03 doi:10.1101/2022.12.02.518884 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Intrusion of pathological synergies does not explain impaired 3D arm movements in subacute stroke ]]> https://biorxiv.org/content/10.1101/2022.12.03.518692v1?rss=1 Avni, I. Arac, A. Binyamin-Netser, R. Kramer, S. Krakauer, J. Shmuelof, L. 2022-12-03 doi:10.1101/2022.12.03.518692 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging ]]> https://biorxiv.org/content/10.1101/2022.12.05.519134v1?rss=1 Vandiver, A. Hoang, A. Herbst, A. Lee, C. C. Aiken, J. McKenzie, D. Timp, W. Wanagat, J. 2022-12-05 doi:10.1101/2022.12.05.519134 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ RNA conformational propensities determine cellular activity ]]> https://biorxiv.org/content/10.1101/2022.12.05.519207v1?rss=1 Kelly, M. L. Roy, R. Geng, A. Ganser, L. R. Manghrani, A. Cullen, B. R. Schulze-Gahmen, U. Herschlag, D. Al-Hashimi, H. M. 2022-12-07 doi:10.1101/2022.12.05.519207 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Sniper2L, a high-fidelity Cas9 variant with high activity ]]> https://biorxiv.org/content/10.1101/2022.12.05.519240v1?rss=1 Kim, Y.-h. Kim, N. Okafor, I. Choi, S. Min, S. Lee, J. Choi, K. Choi, J. Harihar, V. Kim, Y. Kim, J.-S. Lee, J. K. Ha, T. Kim, H. H. 2022-12-06 doi:10.1101/2022.12.05.519240 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Poverty shapes the transcriptome of immune cells ]]> https://biorxiv.org/content/10.1101/2022.12.06.517536v1?rss=1 Arnold, N. S. Resztak, J. Alazizi, A. Hooten, N. N. Evans, M. K. Odera-Marah, V. Dluzen, D. F. Pique-Regi, R. Luca, F. 2022-12-07 doi:10.1101/2022.12.06.517536 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ The effect of random and systematic visual stimulation on entrained infraslow quasi-periodic global waves in human brain activity ]]> https://biorxiv.org/content/10.1101/2022.12.06.519337v1?rss=1 Xu, N. Smith, D. M. Jeno, G. Seeburger, D. T. Schumacher, E. H. Keilholz, S. D. 2022-12-07 doi:10.1101/2022.12.06.519337 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice ]]> https://biorxiv.org/content/10.1101/2022.12.07.519501v1?rss=1 Deshpande, R. A. Marin-Gonzalez, A. Ha, T. Paull, T. T. 2022-12-07 doi:10.1101/2022.12.07.519501 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Commensal Microbiota Regulate Renal Gene Expression ]]> https://biorxiv.org/content/10.1101/2022.12.08.519662v1?rss=1 Moore, B. N. Pluznick, J. L. 2022-12-11 doi:10.1101/2022.12.08.519662 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Two types of locus coeruleus norepinephrine neurons drive reinforcement learning ]]> https://biorxiv.org/content/10.1101/2022.12.08.519670v1?rss=1 Su, Z. Cohen, J. Y. 2022-12-09 doi:10.1101/2022.12.08.519670 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Vimo: Visual Analysis of Neuronal Connectivity Motifs ]]> https://biorxiv.org/content/10.1101/2022.12.09.519772v1?rss=1 Troidl, J. Warchol, S. Choi, J. Matelsky, J. Dhanysai, N. Wang, X. Wester, B. Wei, D. Lichtman, J. W. Pfister, H. Beyer, J. 2022-12-11 doi:10.1101/2022.12.09.519772 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Daily and cell type-specific membrane capacitance changes in mouse cortical neurons ]]> https://biorxiv.org/content/10.1101/2022.12.09.519806v1?rss=1 Severin, D. Shirley, S. Kirkwood, A. Golowasch, J. 2022-12-11 doi:10.1101/2022.12.09.519806 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Transcriptomic profiling reveals distinct subsets of immune checkpoint inhibitor-induced myositis ]]> https://biorxiv.org/content/10.1101/2022.12.12.520136v1?rss=1 Pinal-Fernandez, I. Quintana, A. Milisenda, J. Casal-Dominguez, M. Munoz-Braceras, S. Derfoul, A. Torres-Ruiz, J. Pak, K. Del Orso, S. Naz, F. Gutierrez-Cruz, G. Milone, M. Shelly, S. Duque-Jaimez, Y. Tobias-Baraja, E. Matas-Garcia, A. Garrabou, G. Padrosa, J. Ros, J. Trallero-Araguas, E. Walitt, B. Christopher-Stine, L. Lloyd, T. E. Zhao, C. Swift, S. Rajan, A. Grau, J. M. Selva-O'Callaghan, A. Liewluck, T. Mammen, A. L. 2022-12-14 doi:10.1101/2022.12.12.520136 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Interactive auditory task reveals complex sensory-action integration in mouse primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.12.12.520155v1?rss=1 Liu, J. Kanold, P. O. 2022-12-13 doi:10.1101/2022.12.12.520155 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Internal limiting membrane disruption facilitates engraftment of transplanted human stem cell derived retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2022.12.13.519327v1?rss=1 Aguzzi, E. A. Zhang, K. Y. Nagalingam, A. Quillen, S. Hariharakumar, S. Chetla, N. Madhoun, S. Edwards, M. M. Quigley, H. Zack, D. J. Johnson, T. V. 2022-12-13 doi:10.1101/2022.12.13.519327 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response ]]> https://biorxiv.org/content/10.1101/2022.12.13.520329v1?rss=1 73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment naive non-small cell lung cancers (NSCLC) with single cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Notably, one subset selectively expresses high levels of OX40 and GITR, whose engangement by cognate ligand mediated proliferative programs and NF-kB activation, as well as multiple genes involved in Treg suppression, in particular LAG3. Functionally, the OX40hiGITRhi subset in the most highly suppressive ex vivo and Treg expression of OX40, GITR and LAG3, correlated with resistance to PD-1 blockade. Surprisingly, in the murine tumor model, we found that virtually all TIL-Treg expressing T cell receptors that are specific for TAA fully develop a distinct Th1-like signature over a two-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFN{gamma} and certain pro-inflammatory granzymes. Application of a gene score from the murine TAA-specific Th1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1 responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally-defined subsets with potentially opposing effects on ICB-induced anti-tumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to anti-tumor responses. One-Sentence SummaryWe define 10 subsets of lung cancer-infiltrating regulatory T cells, one of which is highly suppressive and enriched in anti-PD-1 non-responders and the other is Th1-like and is enriched in PD-1 responders. ]]> Dykema, A. G. Zhang, J. Zhang, B. Cheung, L. S. Zeng, Z. Cherry, C. M. Li, T. Caushi, J. X. Nishimoto, M. Connor, S. Ji, Z. Munoz, A. J. Hou, W. Zhan, W. Singh, D. Rashid, R. Mitchell-Flack, M. Bom, S. Tam, A. Wang, Y. Sawosik, C. A. Tirado, L. E. Tomasovic, L. M. VanDyke, D. Spangler, J. B. Anagnostou, V. Yang, S. Spicer, J. Rayes, R. Taube, J. M. Brahmer, J. R. Forde, P. M. Yegnasubramanian, S. Ji, H. Pardoll, D. M. Smith, K. N. 2022-12-15 doi:10.1101/2022.12.13.520329 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Analyzing patterns in tyrosine sulfation in naive antibody repertoires ]]> https://biorxiv.org/content/10.1101/2022.12.13.520330v1?rss=1 Pospelova, M. Safonova, Y. 2022-12-15 doi:10.1101/2022.12.13.520330 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Chaotic signatures in host-microbe interactions ]]> https://biorxiv.org/content/10.1101/2022.12.14.520402v1?rss=1 Sella, Y. Broderick, N. A. Stouffer, K. McEwan, D. L. Ausubel, F. M. Casadevall, A. Bergman, A. 2022-12-14 doi:10.1101/2022.12.14.520402 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Cellular and Fibrillar Collagen Analyses in an Animal Model of Retinal Detachment-Related Proliferative Vitreoretinopathy Reveals a Defined Transition to Chronic Fibrosis ]]> https://biorxiv.org/content/10.1101/2022.12.14.520462v1?rss=1 Peterson, C. Santiago, C. P. Lu, Y. Price, A. McNally, M. M. Schubert, W. Blackshaw, S. Eberhart, C. G. Singh, M. S. 2022-12-16 doi:10.1101/2022.12.14.520462 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Multi-modal multi-resolution atlas of the human neonatal cerebral cortex based on microstructural similarity ]]> https://biorxiv.org/content/10.1101/2022.12.14.520508v1?rss=1 Li, M. Xu, X. Cao, Z. Chen, R. Zhao, R. Zhao, Z. Dang, X. Oishi, K. Wu, D. 2022-12-15 doi:10.1101/2022.12.14.520508 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Wolbachia endosymbionts manipulate GSC self-renewal and differentiation to enhance host fertility ]]> https://biorxiv.org/content/10.1101/2022.12.15.520626v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@151904corg.highwire.dtl.DTLVardef@1d86e41org.highwire.dtl.DTLVardef@2e768eorg.highwire.dtl.DTLVardef@697109_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights[bullet] The wMel strain of Wolbachia restores fertility in females and males deficient for the essential translational regulator meiotic-P26 [bullet]Mei-P26s germline maintenance and oocyte cyst differentiation functions are genetically rescued by wMel infection [bullet]Perturbed pMad, Sxl, Bam, and Orb protein expression are mitigated by wMel infection [bullet]wMel infection elevates lifetime egg lay and hatch rates in OreR flies [bullet]Ovary transcriptomes reveal wMel infection restores or offsets changes in gene expression induced by the loss of functional mei-P26 Significance StatementWolbachia bacterial symbionts are being harnessed as biological control agents through the use of their costly manipulations to host fertility. Here, we reveal that the wMel strain can have a beneficial impact on fruit fly development in both mutant and wild-type flies. This phenotype is essential to the long-term use of these bacteria for host population control. ]]> Russell, S. L. Castillo, J. R. Sullivan, W. T. 2022-12-17 doi:10.1101/2022.12.15.520626 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ Quantifying constraint in human mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2022.12.16.520778v1?rss=1 Lake, N. J. Liu, W. Battle, S. L. Laricchia, K. M. Tiao, G. Compton, A. G. Cowie, S. Christodoulou, J. Thorburn, D. R. Zhao, H. Arking, D. E. Sunyaev, S. R. Lek, M. 2022-12-19 doi:10.1101/2022.12.16.520778 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ A refined characterization of large-scale genomic differences in the first complete human genome ]]> https://biorxiv.org/content/10.1101/2022.12.17.520860v1?rss=1 Yang, X. Wang, X. Zou, Y. Zhang, S. Xia, M. Vollger, M. R. Chen, N.-C. Taylor, D. J. Harvey, W. T. Logsdon, G. A. Meng, D. Shi, J. McCoy, R. C. Schatz, M. C. Li, W. Eichler, E. E. Lu, Q. Mao, Y. 2022-12-19 doi:10.1101/2022.12.17.520860 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells ]]> https://biorxiv.org/content/10.1101/2022.12.19.520435v1?rss=1 Busa, V. F. Ando, Y. Aigner, S. Yee, B. A. Yeo, G. W. Leung, A. K. L. 2022-12-19 doi:10.1101/2022.12.19.520435 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ HIGHLY PHAGOCYTIC LIPID-ASSOCIATED MACROPHAGES (LAMs) ARE INCREASED IN COLONIC LAMINA PROPRIA IN OBESITY ]]> https://biorxiv.org/content/10.1101/2022.12.20.521239v1?rss=1 Castoldi, A. Sanin, D. E. Bakker, N. v. T. Aguiar, C. F. Monteiro, L. d. B. Rana, N. Grzes, K. M. Kabat, A. M. Curtis, J. Cameron, A. M. Caputa, G. de Souza, T. A. Souto, F. O. Buescher, J. M. Hicks, J. E. Pearce, E. L. Pearce, E. J. Camara, N. O. S. 2022-12-20 doi:10.1101/2022.12.20.521239 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Multi-center integrated analysis of non-coding CRISPR screens ]]> https://biorxiv.org/content/10.1101/2022.12.21.520137v1?rss=1 Yao, D. Tycko, J. Oh, W. Bounds, L. R. Gosai, S. J. Lataniotis, L. Mackay-Smith, A. Doughty, B. R. Gabdank, I. Schmidt, H. Youngworth, I. Andreeva, K. Ren, X. Barrera, A. Luo, Y. Siklenka, K. Yardimci, G. G. The ENCODE4 Consortium, Tewhey, R. Kundaje, A. Greenleaf, W. J. Sabeti, P. C. Leslie, C. Pritykin, Y. Moore, J. E. Beer, M. A. Gersbach, C. Reddy, T. E. Shen, Y. Engreitz, J. M. Bassik, M. C. Reilly, S. K. 2022-12-22 doi:10.1101/2022.12.21.520137 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure ]]> https://biorxiv.org/content/10.1101/2022.12.21.521274v1?rss=1 Varabyou, A. Sommer, M. J. Erdogdu, B. Shinder, I. Minkin, I. Chao, K.-H. Park, S. Heinz, J. Pockrandt, C. Shumate, A. Rincon, N. Puiu, D. Steinegger, M. Salzberg, S. L. Pertea, M. 2022-12-22 doi:10.1101/2022.12.21.521274 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ DNA methylation entropy is associated with DNA sequence featuresand developmental epigenetic divergence ]]> https://biorxiv.org/content/10.1101/2022.12.21.521278v1?rss=1 Fang, Y. Ji, Z. Zhou, W. Abante, J. Koldobskiy, M. Ji, H. Feinberg, A. P. 2022-12-21 doi:10.1101/2022.12.21.521278 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulateslipid-dependent channel activity ]]> https://biorxiv.org/content/10.1101/2022.12.21.521430v1?rss=1 Goretzki, B. Wiedemann, C. McCray, B. A. Schaefer, S. L. Jansen, J. Tebbe, F. Mitrovic, S.-A. Noeth, J. Donohue, J. Jeffries, C. M. Steinchen, W. Stengel, F. Sumner, C. J. Hummer, G. Hellmich, U. A. 2022-12-22 doi:10.1101/2022.12.21.521430 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Legionella pneumophila inhibits type I interferon signaling to avoid cell-intrinsic host cell defense. ]]> https://biorxiv.org/content/10.1101/2022.12.21.521455v1?rss=1 Allen, C. N. S. Banks, D. A. Shuster, M. Vogel, S. N. O'Connor, T. J. Briken, V. 2022-12-22 doi:10.1101/2022.12.21.521455 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Migration and division in cell monolayers on substrates with topological defect ]]> https://biorxiv.org/content/10.1101/2022.12.22.521493v1?rss=1 Kaiyrbekov, K. Endresen, K. Sullivan, K. Chen, Y. Zheng, Z. Serra, F. Camley, B. A. 2022-12-22 doi:10.1101/2022.12.22.521493 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Air-Liquid-Interface Reorganizes Membrane Lipid and Enhance Recruitment of Slc26a3 to Lipid-Rich Domains in Human Colon ]]> https://biorxiv.org/content/10.1101/2022.12.22.521645v1?rss=1 2 m compared to cells grown as submerged cultures. ASMase inhibitor, desipramine disrupted CRPs and reduced the ALI-induced increase in DRA expression in the apical membrane. Exposing normal human colonoid monolayers to ALI increased the ASMase activity and enhanced differentiation of colonoids along with enhancing basal and forskolin-stimulated DRA activity. ConclusionsALI increases DRA activity and expression by increasing ASMase activity and platform formation in Caco-2/BBe cells and by enhancing the differentiation of normal human colonoids. SynopsisAir-liquid interface (ALI) enhances total and brush border DRA expression and activity in Caco-2/BBe cells and human colonoids by causing differentiation of enterocytes and acid sphingomyelinase-dependent enhanced retention of DRA in ceramide-rich platform-like structures at the plasma membrane. ]]> Tse, C. M. Rong, Y. Zhang, Z. Lin, R. Sarker, R. Donowitz, M. Singh, V. 2022-12-22 doi:10.1101/2022.12.22.521645 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models ]]> https://biorxiv.org/content/10.1101/2022.12.22.521678v1?rss=1 Strober, B. J. Tayeb, K. Popp, J. Qi, G. Gordon, M. G. Perez, R. Ye, C. J. Battle, A. 2022-12-23 doi:10.1101/2022.12.22.521678 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Superinfection plays an important role in the acquisition of complex Plasmodium falciparum infections among female Anopheles mosquitoes ]]> https://biorxiv.org/content/10.1101/2022.12.23.521802v1?rss=1 Berube, S. Freedman, B. Menya, D. Kipkoech, J. Abel, L. Lapp, Z. Taylor, S. M. O'Meara, W. P. Obala, A. A. Wesolowski, A. 2022-12-27 doi:10.1101/2022.12.23.521802 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Host MOSPD2 enrichment at the parasitophorous vacuole membrane varies between Toxoplasma strains and involves complex interactions ]]> https://biorxiv.org/content/10.1101/2022.12.23.521848v1?rss=1 Ferrel, A. Romano, J. D. Panas, M. W. Coppens, I. Boothroyd, J. C. 2022-12-24 doi:10.1101/2022.12.23.521848 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ A semi-field system for quantifying Anopheles gambiae attraction to human scent ]]> https://biorxiv.org/content/10.1101/2022.12.25.521702v1?rss=1 Giraldo, D. Rankin-Turner, S. Corver, A. Tauxe, G. M. Gao, A. L. Jackson, D. M. Simubali, L. Book, C. Stevenson, J. C. Thuma, P. E. Gordus, A. Mburu, M. M. Simulundu, E. McMeniman, C. J. 2022-12-26 doi:10.1101/2022.12.25.521702 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ Quantitative analysis of morphogenesis and growth dynamics in an obligate intracellular bacterium ]]> https://biorxiv.org/content/10.1101/2022.12.26.521939v1?rss=1 Figueroa-Cuilan, W. M. Irazoki, O. Feeley, M. Smith, E. Nguyen, T. Cava, F. Goley, E. D. 2022-12-27 doi:10.1101/2022.12.26.521939 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs. ]]> https://biorxiv.org/content/10.1101/2022.12.27.522023v1?rss=1 Driedonks, T. Nyberg, L. Conte, A. Ma, Z. Pekosz, A. Duban, E. Sültmann, H. Turchinovich, A. Witwer, K. 2022-12-27 doi:10.1101/2022.12.27.522023 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Astroglial mediation of fast-acting antidepressant effect in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.12.29.522099v1?rss=1 Duque, M. Chen, A. B. Narayan, S. Olson, D. E. Fishman, M. C. Engert, F. Ahrens, M. B. 2022-12-29 doi:10.1101/2022.12.29.522099 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ The SAGA HAT module is tethered by its SWIRM domain and modulates activity of the SAGA DUB module ]]> https://biorxiv.org/content/10.1101/2022.12.29.522244v1?rss=1 Haile, S. T. Rahman, S. Orsburn, B. Bumpus, N. N. Wolberger, C. 2022-12-29 doi:10.1101/2022.12.29.522244 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Differential Roles of positive and negative supercoiling in compacting the E. coli genome ]]> https://biorxiv.org/content/10.1101/2022.12.30.522362v1?rss=1 Fu, Z. Guo, M. S. Zhou, W. Xiao, J. 2022-12-31 doi:10.1101/2022.12.30.522362 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85beta/AP-2-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/2022.12.31.522383v1?rss=1 Matsubayashi, H. T. Mountain, J. Yao, T. Peterson, A. F. Deb Roy, A. Inoue, T. 2023-01-02 doi:10.1101/2022.12.31.522383 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ A dynamic partitioning mechanism polarizes membrane protein distribution ]]> https://biorxiv.org/content/10.1101/2023.01.03.522496v1?rss=1 Banerjee, T. Matsuoka, S. Biswas, D. Miao, Y. Pal, D. S. Kamimura, Y. Ueda, M. Devreotes, P. N. Iglesias, P. A. 2023-01-03 doi:10.1101/2023.01.03.522496 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis ]]> https://biorxiv.org/content/10.1101/2023.01.03.522637v1?rss=1 DeRollo, R. E. Cazarin, J. Ahmad Shahidan, S. N. A. B. Burchett, J. B. Mwangi, D. Krishnaiah, S. Hsieh, A. L. Walton, Z. E. Brooks, R. Mello, S. S. Weljie, A. M. Dang, C. V. Altman, B. J. 2023-01-03 doi:10.1101/2023.01.03.522637 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Dimensional Reduction for Single Molecule Imaging of DNA and Nucleosome Condensation by Polyamines, HP1α and Ki-67 ]]> https://biorxiv.org/content/10.1101/2023.01.04.522433v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1ed0cc9org.highwire.dtl.DTLVardef@1e26b5dorg.highwire.dtl.DTLVardef@1f6e73corg.highwire.dtl.DTLVardef@c7227b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Benning, N. A. Kaestel-Hansen, J. Rashid, F. Park, S. Urteaga, R. M. Liao, T.-W. Hao, J. Berger, J. M. Hatzakis, N. S. Ha, T. 2023-01-04 doi:10.1101/2023.01.04.522433 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Metabolite T1 relaxation times differ across the adult lifespan ]]> https://biorxiv.org/content/10.1101/2023.01.06.522927v1?rss=1 Murali-Manohar, S. Gudmundson, A. T. Hupfeld, K. E. Zöllner, H. J. Hui, S. C. N. Song, Y. Davies-Jenkins, C. W. Gong, T. Wang, G. Oeltzschner, G. Edden, R. A. E. 2023-01-08 doi:10.1101/2023.01.06.522927 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Massively parallel single molecule tracking of sequence-dependent DNA mismatch repair in vivo ]]> https://biorxiv.org/content/10.1101/2023.01.08.523062v1?rss=1 Kayikcioglu, T. Zarb, J. S. Lin, C.-T. Mohapatra, S. London, J. A. Hansen, K. D. Rishel, R. Ha, T. 2023-01-08 doi:10.1101/2023.01.08.523062 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants ]]> https://biorxiv.org/content/10.1101/2023.01.08.523127v1?rss=1 Jiang, N. Wang, L. Hatta, M. Feng, C. Currier, M. Lin, X. Hossain, J. Cui, D. Mann, B. R. Kovacs, N. A. Wang, W. Atteberry, G. Wilson, M. Chau, R. Lacek, K. A. Paden, C. R. Hassell, N. Rambo-Martin, B. Barnes, J. R. Kondor, R. J. Self, W. H. Rhoads, J. P. Baughman, A. Chappell, J. D. Shapiro, N. I. Gibbs, K. W. Hager, D. N. Lauring, A. S. Surie, D. McMorrow, M. L. Thornburg, N. J. Wentworth, D. E. Zhou, B. 2023-01-09 doi:10.1101/2023.01.08.523127 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ ATP-releasing SWELL1 channel in spinal microglia contributes to neuropathic pain ]]> https://biorxiv.org/content/10.1101/2023.01.08.523161v1?rss=1 Chu, J. Qiu, Z. Yang, J. Zhou, Y. Chen, J. Chen, K. Zhang, C. Cheng, H. Koylass, N. Liu, J. O. Guan, Y. 2023-01-08 doi:10.1101/2023.01.08.523161 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Mapping multidimensional content representations to neural and behavioral expressions of episodic memory ]]> https://biorxiv.org/content/10.1101/2023.01.09.523096v1?rss=1 Wang, Y. Lee, H. Kuhl, B. A. 2023-01-09 doi:10.1101/2023.01.09.523096 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Major trends and environmental correlates of spatiotemporal shifts in the distribution of genes compared to a biogeochemical model simulation in the Chesapeake Bay ]]> https://biorxiv.org/content/10.1101/2023.01.09.523340v1?rss=1 Preheim, S. P. Morris, S. Zhang, Y. Holder, C. Arora-Williams, K. Gensbigler, P. Hinton, A. Jin, R. Pradal, M.-A. Gnanadesikan, A. 2023-01-10 doi:10.1101/2023.01.09.523340 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Deconfounded Dimension Reduction via Partial Embeddings ]]> https://biorxiv.org/content/10.1101/2023.01.10.523448v1?rss=1 Chen, A. A. Clark, K. Dewey, B. DuVal, A. Pellegrini, N. Nair, G. Jalkh, Y. Khalil, S. Zurawski, J. Calabresi, P. Reich, D. Bakshi, R. Shou, H. Shinohara, R. T. 2023-01-11 doi:10.1101/2023.01.10.523448 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence ]]> https://biorxiv.org/content/10.1101/2023.01.10.523481v1?rss=1 Zhang, S. Yuan, L. Danilova, L. Mo, G. Zhu, Q. Deshpande, A. Bell, A. T. F. Elisseeff, J. Popel, A. S. Anders, R. A. Jaffee, E. M. Yarchoan, M. Fertig, E. J. Kagohara, L. T. 2023-01-12 doi:10.1101/2023.01.10.523481 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Next-generation diarylquinolines improve sterilizing activity of regimens with pretomanid and the novel oxazolidinone TBI-223 in a mouse tuberculosis model ]]> https://biorxiv.org/content/10.1101/2023.01.10.523519v1?rss=1 Li, S.-Y. Converse, P. J. Betoudji, F. Lee, J. Mdluli, K. Upton, A. Fotouhi, N. Nuermberger, E. 2023-01-11 doi:10.1101/2023.01.10.523519 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Organisms employ a mode-switching strategy for solving the explore-vs-exploit problem ]]> https://biorxiv.org/content/10.1101/2023.01.11.523566v1?rss=1 Biswas, D. Lamperski, A. Yang, Y. Hoffman, K. Guckenheimer, J. Fortune, E. S. Cowan, N. J. 2023-01-11 doi:10.1101/2023.01.11.523566 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Bacterial meningitis in the early postnatal mouse studied at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2023.01.11.523597v1?rss=1 Wang, J. Rattner, A. Nathans, J. 2023-01-11 doi:10.1101/2023.01.11.523597 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ FOXM1 acts sexually dimorphically to regulate functional β-cell mass ]]> https://biorxiv.org/content/10.1101/2023.01.12.523673v1?rss=1 Peng, G. Mosleh, E. Yuhas, A. Katada, K. Cherry, C. Golson, M. L. 2023-01-12 doi:10.1101/2023.01.12.523673 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ MARCH5-dependent NLRP3 ubiquitination is an essential step for NEK7 docking on the mitochondria ]]> https://biorxiv.org/content/10.1101/2023.01.12.523764v1?rss=1 Park, Y.-J. Dodantenna, N. Kim, T.-H. Lee, H.-S. Yoo, Y.-S. Lee, E.-S. Lee, J.-H. Kwon, M.-H. Kang, H. C. Lee, J.-S. Cho, H. 2023-01-12 doi:10.1101/2023.01.12.523764 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation ]]> https://biorxiv.org/content/10.1101/2023.01.12.523790v1?rss=1 Kolmogorov, M. Billingsley, K. J. Mastoras, M. Meredith, M. Monlong, J. Lorig-Roach, R. Asri, M. Alvarez Jerez, P. Malik, L. Dewan, R. Reed, X. Genner, R. M. Daida, K. Behera, S. Shafin, K. Pesout, T. Prabakaran, J. Carnevali, P. North American Brain Expression Consortium (NABEC), Yang, J. Rhie, A. Scholz, S. W. Traynor, B. J. Miga, K. H. Jain, M. Timp, W. Phillippy, A. M. Chaisson, M. Sedlazeck, F. J. Blauwendraat, C. Paten, B. 2023-01-15 doi:10.1101/2023.01.12.523790 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Reactivation of the progenitor gene Trim71 enhances the mitotic and hair cell-forming potential of cochlear supporting cells ]]> https://biorxiv.org/content/10.1101/2023.01.12.523802v1?rss=1 Li, X.-J. Morgan, C. Nadar-Ponniah, P. T. Kolanus, W. Doetzlhofer, A. 2023-01-13 doi:10.1101/2023.01.12.523802 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Microbiome derived acidity protects against microbial invasion in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.01.12.523836v1?rss=1 Barron, A. J. Lesperance, D. N. A. Doucette, J. Calle, S. Broderick, N. A. 2023-01-12 doi:10.1101/2023.01.12.523836 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Pathogenesis of Breakthrough Infections with SARS-CoV-2 Variants in Syrian Hamsters ]]> https://biorxiv.org/content/10.1101/2023.01.12.523876v1?rss=1 Plunkard, J. Mulka, K. Zhou, R. Tarwater, P. Zhong, W. Lowman, M. Wong, A. Pekosz, A. Villano, J. 2023-01-13 doi:10.1101/2023.01.12.523876 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Genome-wide CRISPR screen reveals genetic modifiers of Ca2+-mediated cell death ]]> https://biorxiv.org/content/10.1101/2023.01.13.523980v1?rss=1 Reyes Gaido, O. E. Schole, K. L. Anderson, M. E. Luczak, E. D. 2023-01-14 doi:10.1101/2023.01.13.523980 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Cuticular profiling of insecticide resistant Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2023.01.13.523989v1?rss=1 Jacobs, E. Chrissian, C. Rankin-Turner, S. Wear, M. Camacho, E. Scott, J. G. Broderick, N. A. McMeniman, C. J. Stark, R. E. Casadevall, A. 2023-01-13 doi:10.1101/2023.01.13.523989 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ The role of intestine in metabolic dysregulation in murine Wilson disease ]]> https://biorxiv.org/content/10.1101/2023.01.13.524009v1?rss=1 Sarode, G. V. Mazi, T. A. Neier, K. E. Shibata, N. M. Jospin, G. Harder, N. H. O. Heffern, M. Sharma, A. K. More, S. Dave, M. Schroeder, S. M. Wang, L. LaSalle, J. M. Svetlana, L. Medici, V. 2023-01-15 doi:10.1101/2023.01.13.524009 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming ]]> https://biorxiv.org/content/10.1101/2023.01.16.524187v1?rss=1 Antunes, A. V. Shahinas, M. Swale, C. Farhat, D. C. Ramakrishnan, C. Bruley, C. Cannella, D. Corrao, C. Coute, Y. Hehl, A. B. Bougdour, A. Coppens, I. Hakimi, M.-a. 2023-01-17 doi:10.1101/2023.01.16.524187 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ VAP spatially stabilizes dendritic mitochondria to locally fuel synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2023.01.16.524245v1?rss=1 Bapat, O. Purimetla, T. Kruessel, S. Thum, C. Rupprecht, F. Shah, M. Langer, J. D. Rangaraju, V. 2023-01-18 doi:10.1101/2023.01.16.524245 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ RepairSwitch: simultaneous functional assessment of homologous recombination and end joining DNA repair pathways in living cells ]]> https://biorxiv.org/content/10.1101/2023.01.17.524235v1?rss=1 Steinberg, R. C. Liu, J. Vaghasia, A. M. Giovinazzo, H. Pham, M.-T. N. Tselenchuk, D. Chikarmane, R. Haffner, M. C. Nelson, W. G. Yegnasubramanian, S. 2023-01-17 doi:10.1101/2023.01.17.524235 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Genomic Landscape of Patients with Germline RUNX1 Variants and Familial Platelet Disorder with Myeloid Malignancies in a Natural History Study ]]> https://biorxiv.org/content/10.1101/2023.01.17.524290v1?rss=1 Yu, K. Deuitch, N. Merguerian, M. Cunningham, L. Davis, J. Bresciani, E. Diemer, J. Andrews, E. Young, A. Donovan, F. Sood, R. Craft, K. Chong, S. Chandrasekharappa, S. Mullikin, J. C. Liu, P. P. 2023-01-17 doi:10.1101/2023.01.17.524290 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Hierarchical Deviant Processing in Auditory Cortex of Awake Mice ]]> https://biorxiv.org/content/10.1101/2023.01.18.524413v1?rss=1 Luo, D. Liu, J. Auksztulewicz, R. Yip, T. K.-W. Kanold, P. O. Schnupp, J. W. H. 2023-01-20 doi:10.1101/2023.01.18.524413 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Informing generative replay for continual learning with long-term memory formation in the fruit fly ]]> https://biorxiv.org/content/10.1101/2023.01.18.524467v1?rss=1 Robinson, B. S. Joyce, J. Norman-Tenazas, R. Vallabha, G. K. Johnson, E. C. 2023-01-20 doi:10.1101/2023.01.18.524467 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ sLASER and PRESS Perform Similarly at Revealing Metabolite-Age Correlations ]]> https://biorxiv.org/content/10.1101/2023.01.18.524597v1?rss=1 Hui, S. C. N. Gong, T. Zoellner, H. J. Hupfeld, K. E. Gudmundson, A. Murali-Manohar, S. Davies-Jenkins, C. Song, Y. Chen, Y. Oeltzschner, G. Wang, G. Edden, R. A. E. 2023-01-20 doi:10.1101/2023.01.18.524597 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Translational predictions of phase 2a first-in patient efficacy studies for antituberculosis drugs ]]> https://biorxiv.org/content/10.1101/2023.01.18.524608v1?rss=1 Savic, R. M. Goh, J. J. N. Ernest, J. P. Strydom, N. Wang, Q. van Wijk, R. C. Zhang, N. Deitchman, A. Nuermberger, E. 2023-01-20 doi:10.1101/2023.01.18.524608 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ ARPC5 deficiency leads to severe early onset systemic inflammation and early mortality ]]> https://biorxiv.org/content/10.1101/2023.01.19.524688v1?rss=1 Sindram, E. Caballero-Oteyza, A. Cogata, N. Huang, S. C. M. Alizadeh, Z. Gamez-Diaz, L. Fazlollahi, M. R. Peng, X. Grimbacher, B. Way, M. Proietti, M. 2023-01-21 doi:10.1101/2023.01.19.524688 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Gesture profiles distinguish primary progressive aphasia variants ]]> https://biorxiv.org/content/10.1101/2023.01.19.524719v1?rss=1 Dresang, H. C. Williamson, R. Kim, H. Hillis, A. E. Buxbaum, L. J. 2023-01-19 doi:10.1101/2023.01.19.524719 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Dasatinib Resensitizes MAPK Inhibitor Efficacy in Standard-of-Care Relapsed Melanomas ]]> https://biorxiv.org/content/10.1101/2023.01.20.524923v1?rss=1 Rebecca, V. W. Xiao, M. Kossenkov, A. Godok, T. Brown, G. S. Fingerman, D. Alicea, G. M. Wei, M. Ji, H. Bravo, J. Chen, Y. Fane, M. E. Villanueva, J. Nathanson, K. L. Liu, Q. Gopal, Y. N. V. Daies, M. A. Herlyn, M. 2023-01-21 doi:10.1101/2023.01.20.524923 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Impact of acquisition and modeling parameters on test-retest reproducibility of edited GABA+ ]]> https://biorxiv.org/content/10.1101/2023.01.20.524952v1?rss=1 Hupfeld, K. E. Zollner, H. J. Hui, S. C. N. Song, Y. Murali Manohar, S. Yedavalli, V. Oeltzschner, G. Prisciandaro, J. J. Edden, R. A. E. 2023-01-21 doi:10.1101/2023.01.20.524952 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ A fluid biomarker reveals loss of TDP-43 splicing repression in pre-symptomatic ALS ]]> https://biorxiv.org/content/10.1101/2023.01.23.525202v1?rss=1 Irwin, K. E. Jasin, P. Braunstein, K. E. Sinha, I. Bowden, K. D. Moghekar, A. Oh, E. S. Raitcheva, D. Bartlett, D. Berry, J. D. Traynor, B. Ling, J. P. Wong, P. C. 2023-01-24 doi:10.1101/2023.01.23.525202 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Utility of long-read sequencing for All of Us ]]> https://biorxiv.org/content/10.1101/2023.01.23.525236v1?rss=1 Mahmoud, M. Huang, Y. Garimella, K. Audano, P. A. Wan, W. Prasad, N. Handsaker, R. E. Hall, S. Pionzio, A. Schatz, M. C. Talkowski, M. E. Eichler, E. E. Levy, S. E. Sedlazeck, F. J. 2023-01-24 doi:10.1101/2023.01.23.525236 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.01.23.525270v1?rss=1 Boyd, R. J. McClymont, S. A. Barrientos, N. B. Hook, P. W. Law, W. D. Rose, R. J. Waite, E. L. Avramopoulos, D. McCallion, A. S. 2023-01-24 doi:10.1101/2023.01.23.525270 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Epidermal SIRT1 and BDNF modulate mechanical allodynia in mouse models of diabetic neuropathy ]]> https://biorxiv.org/content/10.1101/2023.01.24.523981v1?rss=1 O'Brien, J. Niehaus, P. Remark, J. Salimian, M. Kevas, Y. Rubin, S. Kristian, T. Chandrasekeran, K. Lu, C. P.-J. Russell, J. Ho, C.-Y. 2023-01-25 doi:10.1101/2023.01.24.523981 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Reinforcement Learning Is Impaired in the Sub-acute Post-stroke Period ]]> https://biorxiv.org/content/10.1101/2023.01.25.525408v1?rss=1 Branscheidt, M. Hadjiosif, A. M. Anaya, M. A. Keller, J. Widmer, M. Runnalls, K. D. Luft, A. R. Bastian, A. J. Krakauer, J. W. M. Celnik, P. 2023-01-25 doi:10.1101/2023.01.25.525408 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Structural variation across 138,134 samples in the TOPMed consortium ]]> https://biorxiv.org/content/10.1101/2023.01.25.525428v1?rss=1 90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression. ]]> Jun, G. English, A. C. Metcalf, G. A. Yang, J. Chaisson, M. J. Pankratz, N. Menon, V. K. Salerno, W. J. Krasheninina, O. Smith, A. V. Lane, J. A. Blackwell, T. Kang, H. M. Salvi, S. Meng, Q. Shen, H. Pasham, D. Bhamidipati, S. Kottapalli, K. Arnett, D. K. Ashley-Koch, A. Auer, P. L. Beutel, K. M. Bis, J. C. Blangero, J. Bowden, D. W. Brody, J. A. Cade, B. E. Chen, Y.-D. I. Cho, M. H. Curran, J. E. Fornage, M. Freedman, B. I. Fingerlin, T. Gelb, B. D. Hou, L. Hung, Y.-J. Kane, J. P. Kaplan, R. Kim, W. Loos, R. J. F. Marcus,, G. M. Mathias, R. A. McGarv 2023-01-26 doi:10.1101/2023.01.25.525428 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker ]]> https://biorxiv.org/content/10.1101/2023.01.25.525462v1?rss=1 Taylor, M. S. Connie, W. Fridy, P. C. Senussi, Y. Cheng, W.-C. Heaps, J. Mori, K. Cohen, L. Molloy, K. R. Chait, B. T. Goggins, M. Bhan, I. Franses, J. W. Yang, X. Taplin, M.-E. Wang, X. Christiani, D. C. Johnson, B. E. Meyerson, M. Uppaluri, R. Egloff, A. M. Denault, E. N. Spring, L. M. Wang, T.-L. Shih, I.-M. Jung, E. Arora, K. S. Zukerberg, L. R. Yilmaz, O. H. Chi, G. Norden, B. L. Song, Y. Nieman, L. Parikh, A. R. Strickland, M. Mustelin, T. Eng, G. Yilmaz, O. H. Matulonis, U. A. Skates, S. J. Rueda, B. R. Drapkin, R. Klempner, S. J. Deshpande, V. 2023-01-25 doi:10.1101/2023.01.25.525462 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Scientific civility and academic performance ]]> https://biorxiv.org/content/10.1101/2023.01.26.525747v1?rss=1 Camacho, E. Dragotakes, Q. Hartshorn, I. Casadevall, A. Buccino, D. L. 2023-01-27 doi:10.1101/2023.01.26.525747 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ A defined clathrin-mediated trafficking pathway regulates sFLT1/VEGFR1 secretion from endothelial cells ]]> https://biorxiv.org/content/10.1101/2023.01.27.525517v1?rss=1 Kinghorn, K. Gill, A. Marvin, A. Li, R. Quigley, K. le Noble, F. Mac Gabhann, F. Bautch, V. L. 2023-01-28 doi:10.1101/2023.01.27.525517 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions ]]> https://biorxiv.org/content/10.1101/2023.01.27.525553v1?rss=1 Braxton, A. M. Kiemen, A. L. Grahn, M. P. Forjaz, A. Babu, J. M. Zheng, L. Jiang, L. Cheng, H. Song, Q. Reichel, R. Graham, S. Damanakis, A. I. Fischer, C. G. Mou, S. Metz, C. Granger, J. Liu, X.-D. Bachmann, N. Almagro-Perez, C. Jiang, A. C. Yoo, J. Kim, B. Du, S. Foster, E. Hsu, J. Y. Rivera, P. A. Chu, L. C. Liu, F. Niknafs, N. Fishman, E. Yuille, A. Roberts, N. J. Thompson, E. D. Scharpf, R. B. Cornish, T. C. Jiao, Y. Karchin, R. Hruban, R. H. Wu, P.-H. Wirtz, D. Wood, L. D. 2023-01-28 doi:10.1101/2023.01.27.525553 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Downfield Proton MRSI with whole-brain coverage at 3T ]]> https://biorxiv.org/content/10.1101/2023.01.27.525726v1?rss=1 Ozdemir, I. Ganji, S. Gillen, J. Etyemez, S. Povazan, M. Barker, P. B. 2023-01-27 doi:10.1101/2023.01.27.525726 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Can a Fish Learn to Ride a Bicycle? Sensorimotor Adaptation to Destabilizing Dynamics in Weakly Electric Fish ]]> https://biorxiv.org/content/10.1101/2023.01.27.525956v1?rss=1 Yang, Y. Yared, D. G. Cowan, N. J. 2023-01-30 doi:10.1101/2023.01.27.525956 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Cleo: a testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optogenetics ]]> https://biorxiv.org/content/10.1101/2023.01.27.525963v1?rss=1 Johnsen, K. A. Cruzado, N. A. Willats, A. A. Rozell, C. J. 2023-01-28 doi:10.1101/2023.01.27.525963 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Foveolar cone subtype patterning in human retinal organoids ]]> https://biorxiv.org/content/10.1101/2023.01.28.526051v1?rss=1 Hussey, K. Eldred, K. Reh, T. A. Johnston, R. J. 2023-01-29 doi:10.1101/2023.01.28.526051 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Single-cell RNA sequencing reveals dysregulated fibroblast subclusters in prurigo nodularis ]]> https://biorxiv.org/content/10.1101/2023.01.29.526050v1?rss=1 Patel, J. R. Joel, M. Z. Lee, K. K. Kambala, A. Cornman, H. Oladipo, O. Taylor, M. Deng, J. Parthasarathy, V. Cravero, K. Marani, M. Zhao, R. Sankararam, S. Li, R. Pritchard, T. Rebecca, V. Kwatra, M. M. Dong, X. Kang, S. Kwatra, S. G. 2023-01-31 doi:10.1101/2023.01.29.526050 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Molecular and cellular mechanisms by which cardiac sympathetic denervation prevents heart failure and sudden cardiac arrest ]]> https://biorxiv.org/content/10.1101/2023.01.29.526082v1?rss=1 DeMazumder, D. Joshi, P. O'Rourke, B. Estes, S. Dey, S. 2023-01-31 doi:10.1101/2023.01.29.526082 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ In vivo Modulation of Intraocular and Intracranial Pressures Causes Nonlinear and Non-monotonic Deformations of the Lamina Cribrosa and Scleral Canal ]]> https://biorxiv.org/content/10.1101/2023.01.29.526113v1?rss=1 Zhu, Z. Waxman, S. Wang, B. Wallace, J. Schmitt, S. E. Tyler-Kabara, E. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2023-01-31 doi:10.1101/2023.01.29.526113 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Hypermetabolism in mice carrying a near complete human chromosome 21 ]]> https://biorxiv.org/content/10.1101/2023.01.30.526183v1?rss=1 Sarver, D. C. Xu, C. Rodriguez, S. Aja, S. Jaffe, A. E. Gao, F. J. Delannoy, M. Periasamy, M. Kazuki, Y. Oshimura, M. Reeves, R. H. Wong, G. W. 2023-01-31 doi:10.1101/2023.01.30.526183 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ AGAP1-associated endolysosomal trafficking abnormalities link gene-environment interactions in a neurodevelopmental disorder with incomplete penetrance ]]> https://biorxiv.org/content/10.1101/2023.01.31.526497v1?rss=1 Lewis, S. A. Bakhtiari, S. Forstrom, J. Bayat, A. Billan, F. Le Guyader, G. Alkhunaiz, E. Vernon, H. Padilla-Lopez, S. R. Kruer, M. C. 2023-02-02 doi:10.1101/2023.01.31.526497 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ SATB2 loss in inflammatory bowel disease-associated small intestinal metaplasia of the distal colon ]]> https://biorxiv.org/content/10.1101/2023.02.01.526729v1?rss=1 Zeineldin, M. Larman, T. C. 2023-02-03 doi:10.1101/2023.02.01.526729 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon restoration of RB function in malignant peripheral nerve sheath tumors ]]> https://biorxiv.org/content/10.1101/2023.02.02.526674v1?rss=1 Wang, J. Calizo, A. Zhang, L. Pino, J. C. Lyu, Y. Pollard, K. Zhang, X. Larsson, A. T. Conniff, E. Llosa, N. Wood, D. K. Largaespada, D. A. Moody, S. E. Gosline, S. J. Hirbe, A. C. Pratilas, C. A. 2023-02-03 doi:10.1101/2023.02.02.526674 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ DandD: efficient measurement of sequence growth and similarity ]]> https://biorxiv.org/content/10.1101/2023.02.02.526837v1?rss=1 Bonnie, J. K. Ahmed, O. Langmead, B. 2023-02-03 doi:10.1101/2023.02.02.526837 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Experience-Dependent Plasticity in Nucleus Laminaris of the Barn Owl ]]> https://biorxiv.org/content/10.1101/2023.02.02.526884v1?rss=1 Carr, C. E. Wang, T. Kraemer, I. Kuokkanen, P. T. Capshaw, G. Ashida, G. Kempter, R. Koeppl, C. 2023-02-03 doi:10.1101/2023.02.02.526884 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Auditory memory of complex sounds in sparsely distributed, highly correlated neurons in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.02.02.526903v1?rss=1 Kang, H. Kanold, P. O. 2023-02-03 doi:10.1101/2023.02.02.526903 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Experiment-based Computational Model Predicts that IL-6 Trans-Signaling Plays a Dominant Role in IL-6 mediated signaling in Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2023.02.03.526721v1?rss=1 Song, M. Wang, Y. Annex, B. H. Popel, A. S. 2023-02-03 doi:10.1101/2023.02.03.526721 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ BAF chromatin complexes do not mediate GLI transcriptional repression of Hedgehog target genes ]]> https://biorxiv.org/content/10.1101/2023.02.03.527038v1?rss=1 Ramachandran, J. Chen, W. Lex, R. K. Windsor, K. Lee, H. Wang, T. Zhou, W. Ji, H. Vokes, S. A. 2023-02-08 doi:10.1101/2023.02.03.527038 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Effort cost of harvest affects decisions and movement vigor of marmosets during foraging ]]> https://biorxiv.org/content/10.1101/2023.02.04.527146v1?rss=1 Hage, P. Jang, I. K. Looi, V. Fakharian, M. A. Orozco, S. P. Sedaghat-Nejad, E. Pi, J. Shadmehr, R. 2023-02-04 doi:10.1101/2023.02.04.527146 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Targeting sterol regulatory element binding proteins (SREBPs) activation lowers intraocular pressure by halting its mechanosensing function in the trabecular meshwork ]]> https://biorxiv.org/content/10.1101/2023.02.05.527136v1?rss=1 Wang, T. Soundararajan, A. Rabinowitz, J. Jaiswal, A. Osborne, T. Pattabiraman, P. P. 2023-02-05 doi:10.1101/2023.02.05.527136 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Pramipexole restores behavioral inhibition in highly impulsive rats through a paradoxical modulation of frontostriatal networks ]]> https://biorxiv.org/content/10.1101/2023.02.05.527198v1?rss=1 Magnard, R. Fouyssac, M. Vachez, Y. M. Cheng, Y. Dufourd, T. Carcenac, C. Boulet, s. Janak, P. H. Savasta, M. Belin, D. Carnicella, S. 2023-02-05 doi:10.1101/2023.02.05.527198 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation ]]> https://biorxiv.org/content/10.1101/2023.02.06.527353v1?rss=1 84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants. ]]> van Loggerenberg, W. Sowlati-Hashjin, S. Weile, J. Hamilton, R. Chawla, A. Gebbia, M. Kishore, N. Fresard, L. Mustajoki, S. Pischik, E. Di Pierro, E. Barbaro, M. Floderus, Y. Schmitt, C. Gouya, L. Colavin, A. Nussbaum, R. Friesema, E. C. H. Kauppinen, R. To-Figueras, J. Aarsand, A. K. Desnick, R. J. Garton, M. Roth, F. P. 2023-02-06 doi:10.1101/2023.02.06.527353 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing ]]> https://biorxiv.org/content/10.1101/2023.02.07.527484v1?rss=1 Gilpatrick, T. Wang, J. Z. Weiss, D. Norris, A. L. Eshleman, J. R. Timp, W. 2023-02-07 doi:10.1101/2023.02.07.527484 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Differential regulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) receptor tetramerization by auxiliary subunits ]]> https://biorxiv.org/content/10.1101/2023.02.07.527516v1?rss=1 Certain, N. Gan, Q. Bennett, J. Hsieh, H. Wollmuth, L. 2023-02-08 doi:10.1101/2023.02.07.527516 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Transmissibility of clinically relevant atovaquone-resistant Plasmodium falciparum by anopheline mosquitoes ]]> https://biorxiv.org/content/10.1101/2023.02.07.527535v1?rss=1 Balta, V. A. Stiffler, D. Sayeed, A. Tripathi, A. K. Elahi, R. Mlambo, G. Bakshi, R. P. Dziedzic, A. G. Jedlicka, A. E. Nenortas, E. Romero-Rodriguez, K. Canonizado, M. A. Mann, A. Owen, A. Sullivan, D. J. Prigge, S. T. Sinnis, P. Shapiro, T. A. 2023-02-07 doi:10.1101/2023.02.07.527535 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly ]]> https://biorxiv.org/content/10.1101/2023.02.08.527704v1?rss=1 Qian, Y. Evans, D. Mishra, B. Fu, Y. Liu, Z. Guo, S.-K. Johnson, M. E. 2023-02-08 doi:10.1101/2023.02.08.527704 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ In vivo proton MR Spectroscopy of the healthy and diseased human brain ]]> https://biorxiv.org/content/10.1101/2023.02.10.528046v1?rss=1 Gudmundson, A. T. Koo, A. Virovka, A. Amirault, A. L. Soo, M. Cho, J. H. Murali-Manohar, S. Oeltzschner, G. T. Edden, R. A. Barker, P. B. Stark, C. E. 2023-02-12 doi:10.1101/2023.02.10.528046 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Immature neurons in the primate amygdala: changes with early development and disrupted early environment ]]> https://biorxiv.org/content/10.1101/2023.02.10.528076v1?rss=1 McHale-Matthews, A. C. DeCampo, D. M. Love, T. Cameron, J. L. Fudge, J. L. 2023-02-12 doi:10.1101/2023.02.10.528076 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Quantification of ligand and mutation-induced bias in EGFR phosphorylation in direct response to ligand binding ]]> https://biorxiv.org/content/10.1101/2023.02.13.528340v1?rss=1 Wirth, D. Ozdemir, E. Hristova, K. 2023-02-13 doi:10.1101/2023.02.13.528340 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ A hyper-quiescent chromatin state formed during aging is reversed by regeneration ]]> https://biorxiv.org/content/10.1101/2023.02.14.528512v1?rss=1 Yang, N. Occean, J. R. Melters, D. P. Shi, C. Wang, L. Stransky, S. Doyle, M. E. Cui, C.-Y. Delannoy, M. Fan, J. Slama, E. Egan, J. M. De, S. Cunningham, S. C. Cabo, R. d. Sidoli, S. Dalal, Y. Sen, P. 2023-02-15 doi:10.1101/2023.02.14.528512 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Joint Modeling of Gene-Environment Correlations and Interactions using Polygenic Risk Scores in Case-Control Studies ]]> https://biorxiv.org/content/10.1101/2023.02.14.528572v1?rss=1 Wang, Z. Shi, W. Carroll, R. J. Chatterjee, N. 2023-02-15 doi:10.1101/2023.02.14.528572 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Disentangled deep generative models reveal coding principles of the human face processing network ]]> https://biorxiv.org/content/10.1101/2023.02.15.528489v1?rss=1 Soulos, P. Isik, L. 2023-02-15 doi:10.1101/2023.02.15.528489 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Amygdala AVPR1A mediates susceptibility to chronic social isolation in females ]]> https://biorxiv.org/content/10.1101/2023.02.15.528679v1?rss=1 Francois, M. Delgado, I. C. Lafond, A. Lewis, E. Kuromaru, M. Hassouna, R. Deng, S. Thaker, V. V. Dolen, G. Zeltser, L. M. 2023-02-15 doi:10.1101/2023.02.15.528679 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Prospectively predicting BPaMZ Phase IIb outcomes using a translational preclinical mouse to human platform ]]> https://biorxiv.org/content/10.1101/2023.02.16.528876v1?rss=1 Wang, Q. Goh, J. J. N. Zhang, N. Nuermberger, E. Savic, R. M. 2023-02-16 doi:10.1101/2023.02.16.528876 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ The Essential Role of O-GlcNAcylation in Hepatic Differentiation ]]> https://biorxiv.org/content/10.1101/2023.02.16.528884v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@aed343org.highwire.dtl.DTLVardef@1b00966org.highwire.dtl.DTLVardef@391ef9org.highwire.dtl.DTLVardef@206d8c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISingle-Cell RNA-sequencing reveals loss of metabolic liver zonation in O-GlcNAcylation deficient livers. C_LIO_LILoss of O-GlcNAcylation promoted DEN-Induced HCC. C_LIO_LIIncrease of hepatic O-GlcNAcylation prevented HCC progression. C_LI ]]> Robarts, D. R. Kotulkar, M. Paine-Cabrera, D. Venneman, K. K. Hanover, J. A. Zachara, N. E. Slawson, C. Apte, U. 2023-02-17 doi:10.1101/2023.02.16.528884 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Paraburkholderia bonniea symbiont strain identity impacts amoeba host fitness and rate of horizontal transmission ]]> https://biorxiv.org/content/10.1101/2023.02.16.528903v1?rss=1 Noh, S. Larson, E. R. Covitz, R. M. Chen, A. Mazumder, P. R. Hamilton, M. C. Dettmann, R. A. 2023-02-17 doi:10.1101/2023.02.16.528903 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression ]]> https://biorxiv.org/content/10.1101/2023.02.20.529259v1?rss=1 Chen, J. Zheng, Q. Hicks, J. L. Trabzonlu, L. Ozbek, B. Jones, T. Vaghasia, A. Larman, T. C. Wang, R. Markowski, M. C. Denmeade, S. R. Pienta, K. J. Hruban, R. H. Antonaraskis, E. S. Gupta, A. Dang, C. V. Yegnasubramanian, S. De Marzo, A. M. 2023-02-21 doi:10.1101/2023.02.20.529259 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Mechanisms of Nuclear Pore Complex disassembly by the mitotic Polo-Like Kinase 1 (PLK-1) in C. elegans embryos ]]> https://biorxiv.org/content/10.1101/2023.02.21.528438v1?rss=1 Nkombo Nkoula, S. Velez-Aguilera, G. Ossareh-Nazari, B. Van Hove, L. Ayuso, C. Legros, V. Chevreux, G. Thomas, L. Seydoux, G. Askjaer, P. PINTARD, L. 2023-02-22 doi:10.1101/2023.02.21.528438 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Myomatrix arrays for high-definition muscle recording ]]> https://biorxiv.org/content/10.1101/2023.02.21.529200v1?rss=1 Chung, B. Zia, M. Thomas, K. Michaels, J. A. Jacob, A. Pack, A. Williams, M. Nagapudi, K. Teng, L. H. Arrambide, E. Ouellette, L. Oey, N. Gibbs, R. Anschutz, P. Lu, J. Wu, Y. Kashefi, M. Oya, T. Kersten, R. Mosberger, A. C. O`Connell, S. Wang, R. Marques, H. G. P. Mendes, A. R. Lenschow, C. Kondakath, G. Kim, J. J. Olson, W. Quinn, K. Perkins, P. Gatto, G. Thanawalla, A. R. Coltman, S. K. Kim, T. Smith, T. S. Binder-Markey, B. Zaback, M. Thompson, C. K. Giszter, S. Person, A. Goulding, M. Azim, E. Thakor, N. O`Connor, D. Trimmer, B. Q. Lima, S. Car 2023-02-22 doi:10.1101/2023.02.21.529200 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Investigating racial disparities in carcinomas through TCGA transcriptomic and proteomic database ]]> https://biorxiv.org/content/10.1101/2023.02.21.529336v1?rss=1 Lei, B. Jiang, X. Saxena, A. 2023-02-22 doi:10.1101/2023.02.21.529336 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Experimental Glaucoma and Optic Nerve Crush ]]> https://biorxiv.org/content/10.1101/2023.02.21.529410v1?rss=1 Keuthan, C. J. Schaub, J. Wei, M. Fang, W. Quillen, S. Kimball, E. Johnson, T. V. Ji, H. Zack, D. J. Quigley, H. A. 2023-02-21 doi:10.1101/2023.02.21.529410 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Early retinal deprivation crossmodally alters nascent subplate circuits and activity in the auditory cortex during the precritical period ]]> https://biorxiv.org/content/10.1101/2023.02.21.529453v1?rss=1 Mukherjee, D. Xue, B. Chen, C.-T. Chang, M. Kao, J. P.-Y. Kanold, P. O. 2023-02-21 doi:10.1101/2023.02.21.529453 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants ]]> https://biorxiv.org/content/10.1101/2023.02.22.529542v1?rss=1 Pinto, B. J. O'Connor, B. Schatz, M. Zarate, S. Wilson, M. A. 2023-02-22 doi:10.1101/2023.02.22.529542 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis ]]> https://biorxiv.org/content/10.1101/2023.02.23.529702v1?rss=1 Ahmadi, A. R. Song, G. Gao, T. Ma, J. Han, X. Hu, M.-W. Cameron, A. Wesson, R. N. Philosophe, B. Ottmann, S. King, E. Gurakar, A. Qi, L. Peiffer, B. Burdick, J. Anders, R. Zhou, Z. Feng, D. Lu, H. Chen, C.-S. Qian, J. Gao, B. Zhu, H. Sun, Z. 2023-02-23 doi:10.1101/2023.02.23.529702 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Glutamine metabolism inhibition has dual immunomodulatory and antibacterial activities against Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2023.02.23.529704v1?rss=1 Parveen, S. Shen, J. Lun, S. Zhao, L. Koleske, B. Leone, R. D. Rais, R. Powell, J. D. Murphy, J. R. Slusher, B. S. Bishai, W. R. 2023-02-23 doi:10.1101/2023.02.23.529704 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ A mechanistic simulation of molecular cell states over time ]]> https://biorxiv.org/content/10.1101/2023.02.23.529720v1?rss=1 Erbe, R. Stein-O'Brien, G. Fertig, E. J. 2023-02-23 doi:10.1101/2023.02.23.529720 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Reconstructing the pressure field around a swimming fish using a physics-informed neural network ]]> https://biorxiv.org/content/10.1101/2023.02.27.530217v1?rss=1 Calicchia, M. A. Mittal, R. Seo, J.-H. Ni, R. 2023-02-28 doi:10.1101/2023.02.27.530217 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes ]]> https://biorxiv.org/content/10.1101/2023.02.28.530429v1?rss=1 Athey, T. Wright, M. Pavlovic, M. Chandrashekhar, V. Deisseroth, K. Miller, M. Vogelstein, J. 2023-03-01 doi:10.1101/2023.02.28.530429 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Primary lung fibroblasts respond to IL-33, IL-13, and IL-17A by secreting factors that activate macrophages ]]> https://biorxiv.org/content/10.1101/2023.02.28.530495v1?rss=1 Venezia, J. Gour, N. Loube, J. Mitzner, W. Scott, A. L. 2023-03-01 doi:10.1101/2023.02.28.530495 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Brain-wide neural activity underlying memory-guided movement ]]> https://biorxiv.org/content/10.1101/2023.03.01.530520v1?rss=1 Chen, S. Liu, Y. Wang, Z. Colonell, J. Liu, L. D. Hou, H. Tien, N.-W. Wang, T. Harris, T. Druckmann, S. Li, N. Svoboda, K. 2023-03-02 doi:10.1101/2023.03.01.530520 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Commensal Bacteria Maintain a Qa-1b-restricted Unconventional CD8+ T Population in Gut Epithelium ]]> https://biorxiv.org/content/10.1101/2023.03.01.530600v1?rss=1 Guan, J. Manoharan Valerio, M. Peske, J. D. Park, C. Robey, E. A. Sadegh-Nasseri, S. Shastri, N. 2023-03-02 doi:10.1101/2023.03.01.530600 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Farnesoid X receptor agonism prevents neutrophil extracellular traps via reduced sphingosine-1-phosphate in chronic kidney disease ]]> https://biorxiv.org/content/10.1101/2023.03.01.530697v1?rss=1 Jones, B. A. Myakala, K. Guha, M. Davidson, S. Adapa, S. Lopez Santiago, I. Schaffer, I. Yue, Y. Allegood, J. Cowart, L. A. Wang, X. X. Rosenberg, A. Z. Levi, M. 2023-03-02 doi:10.1101/2023.03.01.530697 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Conformational entropy of intrinsically disordered proteins bars intruders from biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2023.03.03.531005v1?rss=1 Grigorev, V. Wingreen, N. S. Zhang, Y. 2023-03-04 doi:10.1101/2023.03.03.531005 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ Convergent Evolution of A-Lineage (Clade 19B) SARS-CoV-2 Spike Sequences with B-Lineage Variants of Concern Affects Virus Replication in a Temperature-Dependent Manner on Human Nasal Epithelial Cell Cultures ]]> https://biorxiv.org/content/10.1101/2023.03.03.531067v1?rss=1 Yoon, S. Anaya, E. U. Sachithanandham, J. Pinsky, B. A. Sullivan, D. J. Mostafa, H. H. Pekosz, A. 2023-03-06 doi:10.1101/2023.03.03.531067 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Functional profiling of the Toxoplasma genome during acute mouse infection ]]> https://biorxiv.org/content/10.1101/2023.03.05.531216v1?rss=1 Giuliano, C. J. Wei, K. J. Harling, F. M. Waldman, B. S. Farringer, M. A. Boydston, E. A. Lan, T. C. T. Thomas, R. W. Herneisen, A. L. Sanderlin, A. G. Coppens, I. Dvorin, J. D. Lourido, S. 2023-03-06 doi:10.1101/2023.03.05.531216 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Operant training for highly palatable food alters translating mRNA in nucleus accumbens D2 neurons and reveals a modulatory role of Neurochondrin ]]> https://biorxiv.org/content/10.1101/2023.03.07.531496v1?rss=1 Montalban, E. Giralt, A. Taing, L. Nakamura, Y. Pelosi, A. Brown, M. de Pins, B. Valjent, E. Martin, M. Nairn, A. C. Greengard, P. Flajolet, M. Herve, D. Gambardella, N. Roussarie, J.-P. Girault, J.-A. 2023-03-09 doi:10.1101/2023.03.07.531496 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions ]]> https://biorxiv.org/content/10.1101/2023.03.07.531569v1?rss=1 Luo, R. Yan, J. Oh, J. W. Xi, W. Shigaki, D. Wong, W. Cho, H. Murphy, D. Cutler, R. Rosen, B. P. Pulecio, J. Yang, D. Glenn, R. Chen, T. Li, Q. V. Vierbuchen, T. Sidoli, S. Apostolou, E. Huangfu, D. Beer, M. A. 2023-03-09 doi:10.1101/2023.03.07.531569 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level ]]> https://biorxiv.org/content/10.1101/2023.03.08.531827v1?rss=1 Liao, T.-W. Huang, L. Wilson, T. J. Ganser, L. Lilley, D. M. J. Ha, T. 2023-03-11 doi:10.1101/2023.03.08.531827 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors ]]> https://biorxiv.org/content/10.1101/2023.03.09.530832v1?rss=1 Heiser, C. N. Simmons, A. J. Revetta, F. McKinley, E. T. Ramirez-Solano, M. A. Wang, J. Shao, J. Ayers, G. D. Wang, Y. Glass, S. E. Kaur, H. Rolong, A. Chen, B. Vega, P. N. Drewes, J. L. Saleh, N. Vandekar, S. Jones, A. L. Washington, M. K. Roland, J. T. Sears, C. L. Liu, Q. Shrubsole, M. J. Coffey, R. J. Lau, K. S. 2023-03-12 doi:10.1101/2023.03.09.530832 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Serotonin in the orbitofrontal cortex enhances cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2023.03.09.531880v1?rss=1 Hyun, J. H. Hannan, P. Iwamoto, H. Blakely, R. Kwon, H.-B. 2023-03-09 doi:10.1101/2023.03.09.531880 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Dimerization and autophosphorylation of the MST family of kinases are controlled by the same set of residues ]]> https://biorxiv.org/content/10.1101/2023.03.09.531926v1?rss=1 Kavran, J. M. Weingartner, K. A. Tran, T. Tripp, K. W. 2023-03-09 doi:10.1101/2023.03.09.531926 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Patterns of unwanted biological and technical expression variation across 49 human tissues ]]> https://biorxiv.org/content/10.1101/2023.03.09.531935v1?rss=1 Nieuwenhuis, T. O. Giles, H. H. McCall, M. N. Halushka, M. K. 2023-03-12 doi:10.1101/2023.03.09.531935 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Right Ventricular Sarcomere Contractile Depression and the Role of Thick Filament Activation in Human Heart Failure with Pulmonary Hypertension ]]> https://biorxiv.org/content/10.1101/2023.03.09.531988v1?rss=1 Jani, V. Aslam, M. I. Fenwick, A. J. Ma, W. Gong, H. Milburn, G. Nissen, D. Cubero Salazar, I. M. Hanselman, O. Mukherjee, M. Halushka, M. K. Margulies, K. B. Campbell, K. Irving, T. C. Kass, D. A. Hsu, S. 2023-03-12 doi:10.1101/2023.03.09.531988 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ An adaptive behavioral control motif mediated by cortical axo-axonic inhibition ]]> https://biorxiv.org/content/10.1101/2023.03.10.531767v1?rss=1 Jung, K. Chang, M. Steinecke, A. Burke, B. Choi, Y. Yasuhiro, O. Fitzpatrick, D. Taniguchi, H. Kwon, H.-B. 2023-03-11 doi:10.1101/2023.03.10.531767 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding ]]> https://biorxiv.org/content/10.1101/2023.03.11.531013v1?rss=1 Badiee, M. Kenet, A. L. Ganser, L. R. Paul, T. Myong, S. Leung, A. K. 2023-03-13 doi:10.1101/2023.03.11.531013 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ B12-dependent virioplankton demonstrate interseasonal dynamics and associate with a diversity of pelagic bacterioplankton ]]> https://biorxiv.org/content/10.1101/2023.03.13.532061v1?rss=1 Wu, L.-Y. Piedade, G. J. Moore, R. M. Harrison, A. O. Martins, A. M. Bidle, K. D. Polson, S. W. Sakowski, E. Nissimov, J. I. Dums, J. T. Ferrell, B. D. Wommack, K. E. 2023-03-14 doi:10.1101/2023.03.13.532061 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Prostaglandin E2 controls the metabolic adaptation of T cells to the intestinal microenvironment ]]> https://biorxiv.org/content/10.1101/2023.03.13.532431v1?rss=1 Villa, M. Sanin, D. E. Apostolova, P. Corrado, M. Kabat, A. M. Cristinzio, C. Regina, A. Carrizo, G. Rana, N. Stanczak, M. A. Baixauli, F. Grzes, K. M. Cupovic, J. Solagna, F. Hackl, A. Globig, A.-M. Haessler, F. Puleston, D. J. Kelly, B. Cabezas-Wallscheid, N. Hasselblatt, P. Bengsch, B. Zeiser, R. Sagar, Buescher, J. M. Pearce, E. J. Pearce, E. L. 2023-03-15 doi:10.1101/2023.03.13.532431 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level ]]> https://biorxiv.org/content/10.1101/2023.03.14.531382v1?rss=1 Canner, S. W. Shanker, S. Gray, J. J. 2023-03-15 doi:10.1101/2023.03.14.531382 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ NEURD: A mesh decomposition framework forautomated proofreading and morphologicalanalysis of neuronal EM reconstructions ]]> https://biorxiv.org/content/10.1101/2023.03.14.532674v1?rss=1 Celii, B. Papadopoulos, S. Ding, Z. Fahey, P. G. Wang, E. Papadopoulos, C. Kunin, A. Patel, S. Bae, J. A. Bodor, A. L. Brittain, D. Buchanan, J. Bumbarger, D. J. Castro, M. A. Cobos, E. Dorkenwald, S. Elabbady, L. Halageri, A. Jia, Z. Jordan, C. Kapner, D. Kemnitz, N. Kinn, S. Lee, K. Li, K. Lu, R. Macrina, T. Mahalingam, G. Mitchell, E. Mondal, S. S. Mu, S. Nehoran, B. Popovych, S. Schneider-Mizell, C. M. Silversmith, W. Takeno, M. Torres, R. Turner, N. L. Wong, W. Wu, J. Yu, S.-c. Yin, W. Xenes, D. Kitchell, L. M. Rivlin, P. K. Rose, V. A. Bishop 2023-03-15 doi:10.1101/2023.03.14.532674 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing ]]> https://biorxiv.org/content/10.1101/2023.03.15.532749v1?rss=1 Yoon, J.-H. Min, K.-W. Jo, M. H. Song, M. Ko, S. Lee, J. W. Shim, M. J. Kim, K. Park, H. B. Ha, S. Mun, H. Polash, A. Hafner, M. Cho, J.-H. Kim, D.-S. Hohng, S. Kang, S.-U. 2023-03-15 doi:10.1101/2023.03.15.532749 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations ]]> https://biorxiv.org/content/10.1101/2023.03.18.532837v1?rss=1 Zhao, S. Mekbib, K. Y. van der Ent, M. A. Allington, G. Prendergast, A. Chau, J. E. Smith, H. Shohfi, J. Ocken, J. Duran, D. Furey, C. G. Le, H. T. Duy, P. Q. Reeves, B. C. Zhang, J. Nelson-Williams, C. Chen, D. Li, B. Nottoli, T. Bai, S. Rolle, M. Zeng, X. Dong, W. Fu, P.-Y. Wang, Y.-C. Mane, S. Piwowarczyk, P. Fehnel, K. P. See, A. P. Iskandar, B. J. Aagaard-Kienitz, B. Kundishora, A. J. DeSpenza, T. Greenberg, A. B. W. Kidanemariam, S. M. Prendergast, A. Johnston, J. M. Jackson, E. Storm, P. B. Lang, S.-S. Butler, W. E. Carter, B. S. Chapman, P. St 2023-03-22 doi:10.1101/2023.03.18.532837 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Evolutionary Insights Into Felidae Iris Color Through Ancestral State Reconstruction ]]> https://biorxiv.org/content/10.1101/2023.03.20.533527v1?rss=1 Tabin, J. A. Chiasson, K. A. 2023-03-23 doi:10.1101/2023.03.20.533527 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Hepatobiliary manganese homeostasis is dynamic in the setting of illness in mice ]]> https://biorxiv.org/content/10.1101/2023.03.22.533688v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@a1db9aorg.highwire.dtl.DTLVardef@588af9org.highwire.dtl.DTLVardef@10be4b0org.highwire.dtl.DTLVardef@1d2eebc_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com ]]> Sunuwar, L. Tomar, V. Wildeman, A. Culotta, V. Melia, J. M. 2023-03-24 doi:10.1101/2023.03.22.533688 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Latent transcriptional programs reveal histology-encoded tumor features spanning tissue origins ]]> https://biorxiv.org/content/10.1101/2023.03.22.533810v1?rss=1 Hieromnimon, H. M. Dolezal, J. Doytcheva, K. Howard, F. M. Kochanny, S. Zhang, Z. Grossman, R. L. Tanager, K. Wang, C. Kather, J. N. Izumchenko, E. Cipriani, N. A. Fertig, E. J. Pearson, A. T. Riesenfeld, S. J. 2023-03-24 doi:10.1101/2023.03.22.533810 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage ]]> https://biorxiv.org/content/10.1101/2023.03.23.533704v1?rss=1 Varabyou, A. Erdogdu, B. Salzberg, S. L. Pertea, M. 2023-03-25 doi:10.1101/2023.03.23.533704 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ PARP inhibition and pharmacological ascorbate demonstrate synergy in castration-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.03.23.533944v1?rss=1 Gordon, N. Gallagher, P. T. Neupane, N. P. Mandigo, A. C. McCann, J. K. Dylgjeri, E. Vasilevskaya, I. McNair, C. Paller, C. J. Kelly, W. K. Knudsen, K. E. Shafi, A. A. Schiewer, M. J. 2023-03-23 doi:10.1101/2023.03.23.533944 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Adverse outcomes in SARS-CoV-2 infected pregnant mice are gestational age-dependent and resolve with antiviral treatment ]]> https://biorxiv.org/content/10.1101/2023.03.23.533961v1?rss=1 Creisher, P. S. Perry, J. L. Zhong, W. Lei, J. Mulka, K. R. Ryan, H. Zhou, R. Akin, E. H. Liu, A. Mitzner, W. Burd, I. Pekosz, A. Klein, S. L. 2023-03-23 doi:10.1101/2023.03.23.533961 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Analysis of single cells treated with the KRASG12D inhibitor MRTX 1133 reveals new challenges for the emerging field of single cell proteomics ]]> https://biorxiv.org/content/10.1101/2023.03.23.533981v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@87cbdorg.highwire.dtl.DTLVardef@1356aaborg.highwire.dtl.DTLVardef@1ee3a9dorg.highwire.dtl.DTLVardef@14a4fc0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Orsburn, B. 2023-03-23 doi:10.1101/2023.03.23.533981 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ MIDAS: a fast and simple simulator for realistic microbiome data ]]> https://biorxiv.org/content/10.1101/2023.03.23.533996v1?rss=1 He, M. Satten, G. Zhao, N. 2023-03-25 doi:10.1101/2023.03.23.533996 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Glycopolymer-conjugated antigens as an inverse vaccine platform prevent anaphylaxis in a pre-clinical model of food allergy ]]> https://biorxiv.org/content/10.1101/2023.03.23.534004v1?rss=1 Cao, S. Maulloo, C. D. Raczy, M. M. Sabados, M. Slezak, A. J. Nguyen, M. Solanki, A. Wallace, R. P. Shim, H.-N. Wilson, D. S. Hubbell, J. A. 2023-03-25 doi:10.1101/2023.03.23.534004 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ BEATRICE: Bayesian Fine-mapping from Summary Datausing Deep Variational Inference ]]> https://biorxiv.org/content/10.1101/2023.03.24.534116v1?rss=1 Ghosal, S. Schatz, M. Venkataraman, A. 2023-03-25 doi:10.1101/2023.03.24.534116 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening ]]> https://biorxiv.org/content/10.1101/2023.03.24.534183v1?rss=1 Rich, M. H. Sharrock, A. V. Mulligan, T. S. Matthews, F. Brown, A. S. Lee-Harwood, H. R. Williams, E. M. Copp, J. N. Little, R. F. Francis, J. J. Horvat, C. N. Stevenson, L. J. Owen, J. G. Saxena, M. T. Mumm, J. S. Ackerley, D. F. 2023-03-25 doi:10.1101/2023.03.24.534183 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.03.26.534192v1?rss=1 Jackson, C. Cherry, C. Bom, S. Dykema, A. Thompson, E. Zheng, M. Ji, Z. Hou, W. Li, R. Zhang, H. Choi, J. Rodriguez, F. Weingart, J. Yegnasubramanian, S. Lim, M. Bettegowda, C. Powell, J. Eliesseff, J. Ji, H. Pardoll, D. 2023-03-27 doi:10.1101/2023.03.26.534192 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores ]]> https://biorxiv.org/content/10.1101/2023.03.27.534346v1?rss=1 Burigotto, M. Vigorito, V. Mattivi, A. Gliech, C. Ghetti, S. Bisio, A. Lolli, G. Holland, A. J. Fava, L. L. 2023-03-27 doi:10.1101/2023.03.27.534346 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Mechanism of histone H2B monoubiquitination by Bre1 ]]> https://biorxiv.org/content/10.1101/2023.03.27.534461v1?rss=1 Zhao, F. Hicks, C. Wolberger, C. 2023-03-29 doi:10.1101/2023.03.27.534461 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Genetic and environmental contributions to ancestry differences in gene expression in the human brain ]]> https://biorxiv.org/content/10.1101/2023.03.28.534458v1?rss=1 Benjamin, K. J. Chen, Q. Eagles, N. J. Huuki-Myers, L. A. Collado-Torres, L. Stolz, J. M. Shin, J. H. Paquola, A. C. Hyde, T. M. Kleinman, J. E. Jaffe, A. E. Han, S. Weinberger, D. R. 2023-03-30 doi:10.1101/2023.03.28.534458 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming ]]> https://biorxiv.org/content/10.1101/2023.03.28.534622v1?rss=1 Stouffer, K. M. Trouve, A. Younes, L. Kunst, M. Ng, L. Zeng, H. Anant, M. Fan, J. Kim, Y. Miller, M. I. 2023-03-29 doi:10.1101/2023.03.28.534622 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Metabolic regulation of misfolded protein import into mitochondria ]]> https://biorxiv.org/content/10.1101/2023.03.29.534670v1?rss=1 Wang, Y. Ruan, L. Zhu, J. Zhang, X. Chang, A. Tomaszewski, A. Li, R. 2023-03-29 doi:10.1101/2023.03.29.534670 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Difluoromethylornithine rebalances aberrant polyamine ratios in Snyder-Robinson syndrome: mechanism of action and therapeutic potential ]]> https://biorxiv.org/content/10.1101/2023.03.30.534977v1?rss=1 Stewart, T. R. M. Foley, J. R. Holbert, C. E. Khomutov, M. A. Rastkari, N. Tao, X. Khomutov, A. R. Zhai, R. G. Casero, R. A. 2023-03-30 doi:10.1101/2023.03.30.534977 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Human Connectomes Are Heritable ]]> https://biorxiv.org/content/10.1101/2023.04.02.532875v1?rss=1 Chung, J. Bridgeford, E. W. Powell, M. Vogelstein, J. T. 2023-04-03 doi:10.1101/2023.04.02.532875 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes ]]> https://biorxiv.org/content/10.1101/2023.04.02.535219v1?rss=1 Xiang, G. He, X. Giardine, B. M. Weaver, K. J. Taylor, D. J. McCoy, R. C. Jansen, C. Keller, C. A. Wixom, A. Q. Cockburn, A. Miller, A. Qi, Q. He, Y. Li, Y. Lichtenberg, J. Heuston, E. F. Anderson, S. M. Luan, J. Vermunt, M. W. Yue, F. Sauria, M. E. G. Schatz, M. C. Taylor, J. Gottgens, B. Hughes, J. R. Higgs, D. R. Weiss, M. J. Cheng, Y. Blobel, G. A. Bodine, D. Zhang, Y. Li, Q. Mahony, S. Hardison, R. C. 2023-04-04 doi:10.1101/2023.04.02.535219 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Bidirectional transcription at the PPP2R2B gene locus in spinocerebellar ataxia type 12 ]]> https://biorxiv.org/content/10.1101/2023.04.02.535298v1?rss=1 Zhou, C. Liu, H. B. Bakhsh, F. J. Wu, B. Ying, M. Margolis, R. L. Li, P. P. 2023-04-03 doi:10.1101/2023.04.02.535298 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Human Surfactant Protein A Alleviates SARS-CoV-2 Infectivity in Human Lung Epithelial Cells ]]> https://biorxiv.org/content/10.1101/2023.04.03.535215v1?rss=1 Jacob, I. B. Gemmiti, A. Xiong, W. Reynolds, E. Nicholas, B. Thangamani, S. Jia, H. Wang, G. 2023-04-03 doi:10.1101/2023.04.03.535215 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Mechanism of delayed cell death following simultaneous CRISPR-Cas9 targeting in pancreatic cancers ]]> https://biorxiv.org/content/10.1101/2023.04.03.535384v1?rss=1 90% tumor growth inhibition by targeting 9 sites with cancer-specific single-guide RNAs (sgRNAs). Through both bioinformatics and cytogenetics analyses, we found that CRISPR-Cas9-induced DSBs triggered ongoing chromosomal rearrangements, with 87% of structural variants not directly produced from the initial CRISPR-Cas9-induced DSBs, and chromosomal instability (CIN) peaking before cell death. By comparing the cytotoxicity of CRISPR-Cas9- to radiation-induced DSBs, we demonstrate that the number of DSBs required to achieve equitoxic effects was [~]3 times higher for radiation than CRISPR-Cas9. Finally, we show that PC cells that had survived CRISPR-Cas9 targeting retained susceptibility to subsequent CRISPR-Cas9-induced DSBs at different genomic sites with >87% growth inhibition. Together, our data support the therapeutic potential of CRISPR-Cas9 as an anti-cancer strategy. ]]> Teh, S. S. K. Halper-Stromberg, E. Morsberger, L. Bennett, A. Bowland, K. Skaist, A. Cai, F. Liang, H. Hruban, R. H. Roberts, N. J. Scharpf, R. B. Zou, Y. S. Eshleman, J. R. 2023-04-05 doi:10.1101/2023.04.03.535384 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Interrogation of dynamic glucose-enhanced MRI and fluorescence-based imaging reveals a perturbed glymphatic network in Huntington disease ]]> https://biorxiv.org/content/10.1101/2023.04.03.535397v1?rss=1 Duan, W. 2023-04-03 doi:10.1101/2023.04.03.535397 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Fluorescence lifetime analysis of smFRET with contribution of PIFE on donor and acceptor ]]> https://biorxiv.org/content/10.1101/2023.04.03.535482v1?rss=1 Jazani, S. Ha, T. 2023-04-06 doi:10.1101/2023.04.03.535482 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Chromogenic detection of telomere lengths in situ aids the identification of precancerous lesions in the prostate ]]> https://biorxiv.org/content/10.1101/2023.04.04.535575v1?rss=1 Ertunc, O. Smearman, E. Zheng, Q. Hicks, J. L. Brosnan-Cashman, J. A. Jones, T. Gomes-Alexandre, C. Trabzonlu, L. Meeker, A. K. De Marzo, A. M. Heaphy, C. M. 2023-04-06 doi:10.1101/2023.04.04.535575 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ A supervised data-driven spatial filter denoising method for acoustic-induced artifacts in intracranial electrophysiological recordings ]]> https://biorxiv.org/content/10.1101/2023.04.05.535577v1?rss=1 Peterson, V. Vissani, M. Luo, S. Rabbani, Q. Crone, N. E. Bush, A. Richardson, M. 2023-04-06 doi:10.1101/2023.04.05.535577 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Detailed Social Network Interactions and Gut Microbiome Strain-Sharing Within Isolated Honduras Villages ]]> https://biorxiv.org/content/10.1101/2023.04.06.535875v1?rss=1 Pullman, J. Beghini, F. Alexander, M. Vishnempet Shridhar, S. Prinster, D. Brito, I. L. Christakis, N. A. 2023-04-07 doi:10.1101/2023.04.06.535875 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ CellCover Defines Conserved Cell Types and Temporal Progression in scRNA-seq Data across Mammalian Neocortical Development ]]> https://biorxiv.org/content/10.1101/2023.04.06.535943v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@893301org.highwire.dtl.DTLVardef@173a6baorg.highwire.dtl.DTLVardef@1c70e7eorg.highwire.dtl.DTLVardef@1888ab3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ji, L. Wang, A. Sonthalia, S. Naiman, D. Q. Younes, L. Colantuoni, C. Geman, D. 2023-04-07 doi:10.1101/2023.04.06.535943 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Determining the Statistical Significance of the Difference Between Arbitrary Curves: A Spreadsheet Approach ]]> https://biorxiv.org/content/10.1101/2023.04.06.535947v1?rss=1 Wimley, W. C. Hristova, K. 2023-04-08 doi:10.1101/2023.04.06.535947 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Transcriptional Regulation of the P-bodies Associated Psoriasis Candidate Gene CCHCR1 ]]> https://biorxiv.org/content/10.1101/2023.04.08.535951v1?rss=1 Ling, Y. H. Chen, Y. Y. Leung, K. N. Chan, K. M. Liu, W. K. 2023-04-08 doi:10.1101/2023.04.08.535951 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Alignment of spatial transcriptomics data using diffeomorphic metric mapping ]]> https://biorxiv.org/content/10.1101/2023.04.11.534630v1?rss=1 Clifton, K. Anant, M. Aimiuwu, O. K. Kebschull, J. M. Miller, M. I. Tward, D. Fan, J. 2023-04-12 doi:10.1101/2023.04.11.534630 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ ME-Bayes SL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups ]]> https://biorxiv.org/content/10.1101/2023.04.12.536510v1?rss=1 Jin, J. Zhan, J. Zhang, J. Zhao, R. O'Connell, J. Jiang, Y. 23andMe Research Team, Buyske, S. Gignoux, C. R. Haiman, C. A. Kenny, E. Kooperberg, C. North, K. E. Koelsch, B. L. Wojcik, G. L. Zhang, H. Chatterjee, N. 2023-04-13 doi:10.1101/2023.04.12.536510 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Identification of differentially recognized T cell epitopes in the spectrum of Mtb infection ]]> https://biorxiv.org/content/10.1101/2023.04.12.536550v1?rss=1 Panda, S. Morgan, J. Cheng, C. Saito, M. Gilman, R. H. Ciobanu, N. Crudu, V. Catanzaro, D. G. Catanzaro, A. Rodwell, T. Perera, J. S. Chathuranga, T. Gunasena, B. DeSilva, A. D. Peters, B. Sette, A. Lindestam Arlehamn, C. S. 2023-04-13 doi:10.1101/2023.04.12.536550 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/2023.04.12.536593v1?rss=1 Matern, W. M. Harris, H. T. Danchik, C. McDonald, M. Patel, G. Srivastava, A. Ioerger, T. R. Bader, J. Karakousis, P. C. 2023-04-12 doi:10.1101/2023.04.12.536593 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Using dynamic oral dosing of rifapentine and rifabutin to simulate exposure profiles of long-acting formulations in a mouse model of tuberculosis preventive therapy ]]> https://biorxiv.org/content/10.1101/2023.04.12.536604v1?rss=1 Chang, Y. S. Li, S.-Y. Pertinez, H. Betoudji, F. Lee, J. Rannard, S. Owen, A. Nuermberger, E. Ammerman, N. C. 2023-04-12 doi:10.1101/2023.04.12.536604 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Somatic protospacer adjacent motifs are numerous and selectively targetable in cancers ]]> https://biorxiv.org/content/10.1101/2023.04.15.537042v1?rss=1 80% selective cell death of two targeted pancreatic cancer cell lines in co-cultures using 4-9 sgRNAs, targeting noncoding regions, designed from the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs through WGS. Statement of significanceThis study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy. It requires just a few targets to induce double strand breaks for significant cytotoxicity. Our findings markedly expand the repertoire of targetable mutations in cancers and support genetically targeting other adult solid tumor types. ]]> Teh, S. S. K. Bowland, K. Bennett, A. Halper-Stromberg, E. Skaist, A. Pallavajjala, A. Tang, J. Cai, F. Macoretta, A. Liang, H. Wheelan, S. Lin, M.-T. Hruban, R. H. Scharpf, R. B. Roberts, N. J. Eshleman, J. R. 2023-04-17 doi:10.1101/2023.04.15.537042 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Complex spikes perturb movements, revealing the sensorimotor map of Purkinje cells ]]> https://biorxiv.org/content/10.1101/2023.04.16.537034v1?rss=1 Muller, S. Z. Pi, J. S. Hage, P. Fakharian, M. A. Sedaghat-Nejad, E. Shadmehr, R. 2023-04-16 doi:10.1101/2023.04.16.537034 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ Nucleus accumbens and dorsal medial striatal dopamine and neural activity are essential for action sequence performance ]]> https://biorxiv.org/content/10.1101/2023.04.17.537212v1?rss=1 Fraser, K. M. Chen, B. J. Janak, P. H. 2023-04-17 doi:10.1101/2023.04.17.537212 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma ]]> https://biorxiv.org/content/10.1101/2023.04.17.537256v1?rss=1 Duchatel, R. J. Jackson, E. R. Parackal, S. G. Sun, C. Daniel, P. Mannan, A. Findlay, I. J. Staudt, D. Germon, Z. P. Laternser, S. Kiltschewskij, D. Kearney, P. S. Jamaluddin, M. F. B. Douglas, A. M. Beitaki, T. Perrson, M. Manning, E. E. Murray, H. C. Verrills, N. M. Skerrett-Byrne, D. A. Nixon, B. Hua, S. Valdes Mora, F. Tsoli, M. Ziegler, D. S. Cairns, M. J. Raabe, E. H. Vitanza, N. A. Koschmann, C. Alvaro, F. Dayas, C. V. Tinkle, C. Eisenstat, D. Firestein, R. Mueller, S. Nazarian, J. Cain, J. Dun, M. D. 2023-04-17 doi:10.1101/2023.04.17.537256 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Electrophysiological correlates of attention in the locus coeruleus - anterior cingulate cortex circuit during the rodent continuous performance test ]]> https://biorxiv.org/content/10.1101/2023.04.19.537406v1?rss=1 Hallock, H. L. Adiraju, S. Miranda-Barrientos, J. McInerney, J. M. Oh, S. DeBrosse, A. C. Li, Y. Carr, G. Martinowich, K. 2023-04-20 doi:10.1101/2023.04.19.537406 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex ]]> https://biorxiv.org/content/10.1101/2023.04.20.537710v1?rss=1 Kwon, S. H. Parthiban, S. Tippani, M. Divecha, H. R. Eagles, N. J. Lobana, J. S. Williams, S. R. Mark, M. Bharadwaj, R. A. Kleinman, J. E. Hyde, T. M. Page, S. C. Hicks, S. C. Martinowich, K. Maynard, K. R. Collado-Torres, L. 2023-04-20 doi:10.1101/2023.04.20.537710 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Stitching flexible electronics into the brain ]]> https://biorxiv.org/content/10.1101/2023.04.20.537740v1?rss=1 86%. In-vivo histological images at each site of probes, implanted by stitching using either glass capillary or ultrathin metal insertion needles exhibit seamless tissue-probe interfaces with negligible chronic immune response. In addition, electrophysiology studies demonstrated the ability to track single neuron activities at every injection site with chronic stability over at least one month. Notably, the measured spike amplitudes and signal-to-noise ratios at different implantation sites showed no statistically significant differences. Multi-site stitching implantation of flexible electronics in the brain opens up new opportunities for both fundamental neuroscience research and electrotherapeutic applications. ]]> Lee, J. M. Lin, D. Pyo, Y.-W. Kim, H.-R. Park, H.-G. Lieber, C. M. 2023-04-21 doi:10.1101/2023.04.20.537740 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ XIAP-mediated targeting of endolysosomes to stressed mitochondria occurs in a switch-like, global manner and results in autophagy-independent, sub-organelle level mitochondrial degradation ]]> https://biorxiv.org/content/10.1101/2023.04.23.538008v1?rss=1 Wang, T. S. Coppens, I. Brady, N. R. Hamacher-Brady, A. 2023-04-24 doi:10.1101/2023.04.23.538008 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics ]]> https://biorxiv.org/content/10.1101/2023.04.24.538053v1?rss=1 SHAO, B. Yan, J. Zhang, J. Buskirk, A. 2023-04-28 doi:10.1101/2023.04.24.538053 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Precision pharmacological reversal of genotype-specific diet-induced metabolic syndrome in mice informed by transcriptional regulation ]]> https://biorxiv.org/content/10.1101/2023.04.25.538156v1?rss=1 Wulfridge, P. Davidovich, A. Salvador, A. C. Manno, G. C. Tryggvadottir, R. Idrizi, A. Huda, M. N. Bennett, B. J. Adams, L. G. Hansen, K. D. Threadgill, D. W. Feinberg, A. P. 2023-04-28 doi:10.1101/2023.04.25.538156 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition ]]> https://biorxiv.org/content/10.1101/2023.04.25.538191v1?rss=1 Wang, H. Arulraj, T. Kimko, H. Popel, A. S. 2023-04-28 doi:10.1101/2023.04.25.538191 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ IPMK modulates FFA-induced insulin resistance in primary mouse hepatocytes ]]> https://biorxiv.org/content/10.1101/2023.04.26.538310v1?rss=1 Jung, I.-R. Ahima, R. S. Kim, S. F. 2023-04-26 doi:10.1101/2023.04.26.538310 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies ]]> https://biorxiv.org/content/10.1101/2023.04.26.538452v1?rss=1 Blake, L. A. Liu, Y. Inoue, T. Wu, B. 2023-04-26 doi:10.1101/2023.04.26.538452 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift ]]> https://biorxiv.org/content/10.1101/2023.04.26.538488v1?rss=1 Song, G. Yuan, M. Liu, H. Capozzola, T. Lin, R. N. Torres, J. L. He, W.-t. Musharrafieh, R. Dueker, K. Zhou, P. Callaghan, S. Mishra, N. Yong, P. Anzanello, F. Avillion, G. Vo, A. L. Li, X. Makhdoomi, M. Feng, Z. Zhu, X. Peng, L. Nemazee, D. Safonova, Y. Briney, B. Ward, A. B. Burton, D. R. Wilson, I. A. Andrabi, R. 2023-04-27 doi:10.1101/2023.04.26.538488 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice ]]> https://biorxiv.org/content/10.1101/2023.05.03.539199v1?rss=1 Shaku, M. T. Um, P. Ocius, K. Apostolos, A. Pires, M. Bishai, W. Kana, B. 2023-05-04 doi:10.1101/2023.05.03.539199 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Lactate transporter MCT1 in hepatic stellate cells promotes fibrotic collagen expression in nonalcoholic steatohepatitis ]]> https://biorxiv.org/content/10.1101/2023.05.03.539244v1?rss=1 Min, K. Yenilmez, B. Kelly, M. Echeverria, D. Elleby, M. Lifshitz, L. M. Raymond, N. Tsagkaraki, E. Harney, S. M. DiMarzio, C. McHugh, N. Bramato, B. Morrison, B. Rothstein, J. D. Khvorova, A. Czech, M. P. 2023-05-03 doi:10.1101/2023.05.03.539244 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ Endothelial cells signaling and patterning under hypoxia: a mechanistic computational model ]]> https://biorxiv.org/content/10.1101/2023.05.03.539270v1?rss=1 Oliveira, R. H. d. M. Annex, B. H. Popel, A. S. 2023-05-05 doi:10.1101/2023.05.03.539270 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Engineered cytokine/antibody fusion proteins improve delivery of IL-2 to pro-inflammatory cells and promote antitumor activity ]]> https://biorxiv.org/content/10.1101/2023.05.03.539272v1?rss=1 Leonard, E. K. Tomala, J. Leff, M. I. Lin, J.-X. Lin, P. Porter, M. J. Johansen, E. R. Thompson, L. Cao, S. D. Henclova, T. Huliciak, M. Vanek, O. Kovar, M. Leonard, W. J. Spangler, J. B. 2023-05-04 doi:10.1101/2023.05.03.539272 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ VERY LONG-CHAIN ACYL-CoA SYNTHETASE-3 (ACSVL3) PROMOTES THE MALIGNANT GROWTH BEHAVIOR OF U87 GLIOMA CELLS VIA CHANGES IN CELL CYCLE WITHOUT AFFECTING APOPTOSIS ]]> https://biorxiv.org/content/10.1101/2023.05.04.539403v1?rss=1 Yang, H. Shi, X. Kolar, E. A. Clay, E. M. Xia, S. Pei, Z. Watkins, P. A. 2023-05-04 doi:10.1101/2023.05.04.539403 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ PiE: An open source pipeline for home cage behavioral analysis. ]]> https://biorxiv.org/content/10.1101/2023.05.05.539097v1?rss=1 Benedict, J. Cudmore, R. H. 2023-05-07 doi:10.1101/2023.05.05.539097 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant ]]> https://biorxiv.org/content/10.1101/2023.05.05.539595v1?rss=1 Senoo, N. Chinthapalli, D. K. Baile, M. G. Golla, V. K. Saha, B. Ogunbona, O. B. Saba, J. A. Munteanu, T. Valdez, Y. Whited, K. Chorev, D. Alder, N. May, E. R. Robinson, C. V. Claypool, S. M. 2023-05-06 doi:10.1101/2023.05.05.539595 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ B. subtilis MutS2 splits stalled ribosomesinto subunits without mRNA cleavage ]]> https://biorxiv.org/content/10.1101/2023.05.05.539626v1?rss=1 Park, E. Mackens-Kiani, T. Berhane, R. Esser, H. Erdenebat, C. Burroughs, A. M. Berninghausen, O. Aravind, L. Beckmann, R. Green, R. Buskirk, A. R. 2023-05-06 doi:10.1101/2023.05.05.539626 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ Insights from a survey of mentorship experiences by graduate and postdoctoral researchers ]]> https://biorxiv.org/content/10.1101/2023.05.05.539640v1?rss=1 Sarabipour, S. Niemi, N. M. Burgess, S. J. Smith, C. T. Bisson Filho, A. W. Ibrahim, A. Clark, K. 2023-05-08 doi:10.1101/2023.05.05.539640 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles ]]> https://biorxiv.org/content/10.1101/2023.05.06.539665v1?rss=1 Huang, Y. Arab, T. Russell, A. E. Mallick, E. R. Nagaraj, R. Gizzie, E. Redding, J. Troncoso, J. C. Pletnikova, O. Turchinovich, A. Routenberg, D. A. Witwer, K. W. 2023-05-08 doi:10.1101/2023.05.06.539665 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Apposed networks of interacting TCRs and BCRs exhibiting mosaicked CDR3 sequences made of fixed junctional motifs ]]> https://biorxiv.org/content/10.1101/2023.05.06.539704v1?rss=1 Ahmed, R. Majety, N. Chan, K. C. Giwa, A. Heinemann, J. Zhang, H. Margolick, J. Al-Hallaf, R. Paul, P. Bell, D. R. Song, Y. Lee, S. Zhou, R. Wolfe, R. M. Donner, T. Jie, C. Hamad, A. R. A. 2023-05-08 doi:10.1101/2023.05.06.539704 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ RaMALDI: enabling simultaneous Raman and MALDI imaging of the same tissue section ]]> https://biorxiv.org/content/10.1101/2023.05.07.539107v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1829ccaorg.highwire.dtl.DTLVardef@3d018org.highwire.dtl.DTLVardef@531015org.highwire.dtl.DTLVardef@144f1a3_HPS_FORMAT_FIGEXP M_FIG C_FIG We demonstrate for the first time RaMALDI imaging, a streamlined, integrated multimodal imaging workflow of Raman spectroscopy imaging (RSI) and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI), which is performed on a single sample and uses one sample preparation protocol. RaMALDI imaging of various tissues effectively integrates molecular information acquired from both RSI and MALDI MSI of the same sample. ]]> Yang, E. Kim, J. H. Tressler, C. M. Shen, X. E. Brown, D. R. Johnson, C. C. Barman, I. Glunde, K. 2023-05-07 doi:10.1101/2023.05.07.539107 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Redefining Pleiotropic Drug Resistance in a Pathogenic Yeast: Pdr1 Functions as a Sensor of Cellular Stresses in Candida glabrata ]]> https://biorxiv.org/content/10.1101/2023.05.07.539747v1?rss=1 Gale, A. N. Pavesic, M. W. Nickels, T. J. Xu, Z. Cormack, B. P. Cunningham, K. W. 2023-05-09 doi:10.1101/2023.05.07.539747 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ The spatiotemporal richness of hummingbird wing deformations ]]> https://biorxiv.org/content/10.1101/2023.05.08.539717v1?rss=1 95% of typical stroke cycle wing shape variation and were broadly correlated with specific conventional descriptors like wing twist and area. Moreover, shape variables decomposed wing deformations into pairs of in- and out-of-plane components at integer multiples of the stroke frequency. This property allowed us to identify spatiotemporal deformation profiles characteristic of hoverfeeding with experimentally imposed kinematic constraints, including through shape variables explaining <10% of typical shape variation. Hoverfeeding in front of a visual barrier restricted stroke amplitude and elicited increased stroke frequencies together with in- and out-of-plane deformations throughout the stroke cycle. Lifting submaximal loads increased stroke amplitudes at similar stroke frequencies together with prominent in-plane deformations during the upstroke and pronation. Our study highlights how spatially and temporally distinct changes in wing shape can contribute to agile fluidic locomotion. SummaryHummingbirds exhibit complex wing deformations throughout the stroke cycle, and the timing and origin of these deformations differs between hoverfeeding behaviours. ]]> Skandalis, D. A. Baliga, V. B. Goller, B. Altshuler, D. L. 2023-05-10 doi:10.1101/2023.05.08.539717 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ The AGNOSTIC MRS Benchmark Dataset: Deep Learning for Out-of-voxel Artifacts ]]> https://biorxiv.org/content/10.1101/2023.05.08.539813v1?rss=1 Gudmundson, A. T. Davies-Jenkins, C. W. Ozdemir, I. Murali-Manohar, S. Zollner, H. J. Song, Y. Hupfeld, K. E. Schnitzler, A. Oeltzschner, G. Stark, C. E. L. Edden, R. A. E. 2023-05-08 doi:10.1101/2023.05.08.539813 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Ischemia/Reperfusion Injury and Oxidative Stress Impair Cardiac Desmin Proteostasis ]]> https://biorxiv.org/content/10.1101/2023.05.09.540017v1?rss=1 Li, Z. Jun, S. Singh, K. K. Calhoun, P. J. Keceli, G. Patel, K. Kadioglu, H. Paolocci, N. Agnetti, G. 2023-05-09 doi:10.1101/2023.05.09.540017 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ A GALLIUM-68-LABELED PEPTIDE RADIOTRACER FOR CD38-TARGETED IMAGING IN MULTIPLE MYELOMA WITH PET ]]> https://biorxiv.org/content/10.1101/2023.05.09.540036v1?rss=1 Sharma, A. K. Gupta, K. Mishra, A. Lofland, G. Marsh, I. Kumar, D. Ghiaur, G. Imus, P. Hobbs, R. F. Gocke, C. Nimmagadda, S. 2023-05-12 doi:10.1101/2023.05.09.540036 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ EASTR: Correcting systematic alignment errors in multi-exon genes ]]> https://biorxiv.org/content/10.1101/2023.05.10.540179v1?rss=1 Shinder, I. Hu, R. Ji, H. J. Chao, K.-H. Pertea, M. 2023-05-12 doi:10.1101/2023.05.10.540179 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ SMYD5 is a novel epigenetic gatekeeper of the mild hypothermia response ]]> https://biorxiv.org/content/10.1101/2023.05.11.540170v1?rss=1 Rafnsdottir, S. Jang, K. Halldorsdottir, S. T. Tomasdottir, A. Vinod, M. Moller, K. Reynisdottir, T. Atladottir, L. H. Allison, K. E. He, J. Zhang, L. Northington, F. J. Chavez-Valdez, R. Anderson, K. J. Bjornsson, H. 2023-05-14 doi:10.1101/2023.05.11.540170 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Elevated nuclear TDP-43 induces constitutive exon skipping ]]> https://biorxiv.org/content/10.1101/2023.05.11.540291v1?rss=1 Carmen-Orozco, R. P. Tsao, W. Ye, Y. Sinha, I. R. Chang, K. Trinh, V. Chung, W. Bowden, K. D. Troncoso, J. C. Blackshaw, S. Hayes, L. R. Sun, S. Wong, P. C. Ling, J. P. 2023-05-12 doi:10.1101/2023.05.11.540291 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Rapid processing of observed touch through social perceptual brain regions: an EEG-fMRI fusion study ]]> https://biorxiv.org/content/10.1101/2023.05.11.540376v1?rss=1 Lee Masson, H. Isik, L. 2023-05-12 doi:10.1101/2023.05.11.540376 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Multi-site identification and generalization of clusters of walking impairment in individuals with chronic stroke ]]> https://biorxiv.org/content/10.1101/2023.05.11.540385v1?rss=1 Sanchez, N. Schweighofer, N. Mulroy, S. Roemmich, R. T. Kesar, T. M. Torres-Oviedo, G. Fisher, B. E. Finley, J. Winstein, C. J. 2023-05-12 doi:10.1101/2023.05.11.540385 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ An ex vivo model of interactions between extracellular vesicles and peripheral mononuclear blood cells in whole blood ]]> https://biorxiv.org/content/10.1101/2023.05.11.540421v1?rss=1 Rodriguez, B. V. Wen, Y. Shirk, E. N. Vazquez, S. Gololobova, O. Maxwell, A. Plunkard, J. Castell, N. V. Carlson, B. Queen, S. E. Izzi, J. M. Driedonks, T. A. P. Witwer, K. W. 2023-05-14 doi:10.1101/2023.05.11.540421 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Thioflavin T In-gel Stain to Study Protein Misfolding in Frozen Tissue Specimens ]]> https://biorxiv.org/content/10.1101/2023.05.12.540528v1?rss=1 Oldam, J. Tchernyshyov, I. Van Eyk, J. Troncoso, J. Glabe, C. G. Agnetti, G. 2023-05-12 doi:10.1101/2023.05.12.540528 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Hierarchical gradient of timescales in the mammalian forebrain ]]> https://biorxiv.org/content/10.1101/2023.05.12.540610v1?rss=1 Song, M. Shin, E. J. Seo, H. Soltani, A. Steinmetz, N. A. Lee, D. Jung, M. W. Paik, S.-B. 2023-05-13 doi:10.1101/2023.05.12.540610 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ The role of structural vs cellular remodeling in arrhythmogenesis: personalized computer models of atrial fibrillation. ]]> https://biorxiv.org/content/10.1101/2023.05.13.540632v1?rss=1 Pikunov, A. V. Syunyaev, R. A. Ali, R. Prakosa, A. Boyle, P. M. Steckmeister, V. Kutschka, I. Rytkin, E. Voigt, N. Trayanova, N. Efimov, I. R. 2023-05-14 doi:10.1101/2023.05.13.540632 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Skp1 proteins are structural components of the synaptonemal complex in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.05.13.540652v1?rss=1 Blundon, J. Cesar, B. Bae, J. W. Cavka, I. Haversat, J. Ries, J. Koehler, S. Kim, Y. 2023-05-14 doi:10.1101/2023.05.13.540652 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Optimal reaching subject to computational and physical constraints reveals structure of the sensorimotor control system ]]> https://biorxiv.org/content/10.1101/2023.05.14.540714v1?rss=1 Greene, P. Bastian, A. Schieber, M. H. Sarma, S. V. 2023-05-14 doi:10.1101/2023.05.14.540714 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Synergistic activity of IL-2 mutein with tolerogenic ImmTOR nanoparticles leads to massive expansion of antigen-specific Tregs and protection against autoimmune disease ]]> https://biorxiv.org/content/10.1101/2023.05.15.540840v1?rss=1 Kishimoto, T. K. Fournier, M. Michaud, A. Rizzo, G. Roy, C. Capela, T. Nukolova, N. Li, N. Doyle, L. Fu, F.-n. VanDyke, D. Traber, P. G. Spangler, J. B. Leung, S. S. Ilyinskii, P. O. 2023-05-16 doi:10.1101/2023.05.15.540840 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity ]]> https://biorxiv.org/content/10.1101/2023.05.15.540865v1?rss=1 Reese, F. Williams, B. Balderrama-Gutierrez, G. Wyman, D. Celik, M. H. Rebboah, E. Rezaie, N. Trout, D. Razavi-Mohseni, M. Jiang, Y. Borsari, B. Morabito, S. Liang, H. Y. McGill, C. J. Rahmanian, S. Sakr, J. Jiang, S. Zeng, W. Carvalho, K. Weimer, A. K. Dionne, L. A. McShane, A. Bedi, K. Elhajjajy, S. I. Upchurch, S. Jou, J. Youngworth, I. Gabdank, I. Sud, P. Jolanki, O. Strattan, J. S. Kagda, M. S. Snyder, M. P. Hitz, B. C. Moore, J. E. Weng, Z. Bennett, D. Reinholdt, L. Ljungman, M. Beer, M. A. Gerstein, M. B. Pachter, L. Guigo, R. Wold, B. J. Mort 2023-05-16 doi:10.1101/2023.05.15.540865 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Utility of FRET in studies of membrane protein oligomerization: the concept of the effective dissociation constant ]]> https://biorxiv.org/content/10.1101/2023.05.16.540587v1?rss=1 McKenzie, D. M. Wirth, D. Pogorelov, T. V. Hristova, K. 2023-05-16 doi:10.1101/2023.05.16.540587 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Pathological Tau transmission initiated by binding lymphocyte-activation gene 3 ]]> https://biorxiv.org/content/10.1101/2023.05.16.541015v1?rss=1 Chen, C. Kumbhar, R. R. Wang, H. Yang, X. Gadhave, K. Rastegar, C. Kimura, Y. Behensky, A. Katakam, S. Jeong, D. Wang, L. Wang, A. Chen, R. Zhang, S. Jin, L. Workman, C. J. Vignali, D. A. A. Pletinkova, O. Nauen, D. W. Wong, P. C. Troncoso, J. Ying, M. Dawson, V. L. Dawson, T. Mao, X. 2023-05-17 doi:10.1101/2023.05.16.541015 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Xylazine co-self-administration suppresses fentanyl consumption during self-administration and induces a unique sex-specific withdrawal syndrome that is not altered by naloxone in rats ]]> https://biorxiv.org/content/10.1101/2023.05.17.541158v1?rss=1 Khatri, S. N. Sadek, S. Kendrick, P. T. Bondy, E. O. Hong, M. Pauss, S. Luo, D. Prisinzano, T. Dunn, K. E. Marusich, J. A. Beckmann, J. Hinds, T. Gipson, C. D. 2023-05-17 doi:10.1101/2023.05.17.541158 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Particulate matter composition drives differential molecular and morphological responses in lung epithelial cells ]]> https://biorxiv.org/content/10.1101/2023.05.17.541204v1?rss=1 Engels, S. M. Kamat, P. Pafilis, G. S. Li, Y. Agrawal, A. Haller, D. J. Phillip, J. M. Contreras, L. M. 2023-05-20 doi:10.1101/2023.05.17.541204 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Multicore fiber optic imaging reveals that astrocyte calcium activity in the cerebral cortex is modulated by internal motivational state ]]> https://biorxiv.org/content/10.1101/2023.05.18.541390v1?rss=1 Gau, Y.-T. A. Hsu, E. Cha, J. Pak, R. W. Looger, L. L. Kang, J. U. Bergles, D. E. 2023-05-18 doi:10.1101/2023.05.18.541390 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Model-X knockoffs reveal data-dependent limits on regulatory network identification ]]> https://biorxiv.org/content/10.1101/2023.05.23.541948v1?rss=1 Kernfeld, E. M. Keener, R. M. Cahan, P. Battle, A. 2023-05-24 doi:10.1101/2023.05.23.541948 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers ]]> https://biorxiv.org/content/10.1101/2023.05.24.541452v1?rss=1 Lee, G. Wong, C. Cho, A. West, J. J. Crawford, A. J. Russo, G. C. Si, B. R. Kim, J. Hoffner, L. Jang, C. Jung, M. Leone, R. D. Konstantopoulos, K. Ewald, A. J. Wirtz, D. Jeong, S. 2023-05-24 doi:10.1101/2023.05.24.541452 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories ]]> https://biorxiv.org/content/10.1101/2023.05.24.542054v1?rss=1 Wuestefeld, A. Baumeister, H. Adams, J. N. de Flores, R. Hodgetts, C. Mazloum-Farzaghi, N. Olsen, R. K. Puliyadi, V. Tran, T. T. Bakker, A. Canada, K. L. Dalton, M. A. Daugherty, A. M. La Joie, R. Wang, L. Bedard, M. Buendia, E. Denning, A. Irwin, D. J. Ittyerah, R. Lee, E. B. Lim, S. Iniguez de Onzono Martin, M. M. Munoz Lopez, M. Schuck, T. Trotman, W. Vela, A. Yushkevich, P. Amunts, K. Augustinack, J. C. Ding, S.-L. Insausti, R. Kedo, O. Berron, D. Wisse, L. E. M. 2023-05-24 doi:10.1101/2023.05.24.542054 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Mouse models of SYNGAP1-related intellectual disability ]]> https://biorxiv.org/content/10.1101/2023.05.25.542312v1?rss=1 A. While reduction in Syngap1 mRNA varies from 30-50% depending on the specific mutation, both models show [~]50% reduction in Syngap1 protein, have deficits in synaptic plasticity, and recapitulate key features of SRID including hyperactivity and impaired working memory. These data suggest that half the amount of SYNGAP1 protein is key to the pathogenesis of SRID. These results provide a resource to study SRID and establish a framework for the development of therapeutic strategies for this disorder. Significance StatementSYNGAP1 is a protein enriched at excitatory synapses in the brain that is an important regulator of synapse structure and function. SYNGAP1 mutations cause SYNGAP1-related intellectual disability (SRID), a neurodevelopmental disorder with cognitive impairment, social deficits, seizures, and sleep disturbances. To explore how SYNGAP1 mutations found in humans lead to disease, we generated the first knock-in mouse models with causal SRID variants: one with a frameshift mutation and a second with an intronic mutation that creates a cryptic splice acceptor site. Both models show decreased Syngap1 mRNA and Syngap1 protein and recapitulate key features of SRID including hyperactivity and impaired working memory. These results provide a resource to study SRID and establish a framework for the development of therapeutic strategies. HighlightsO_LITwo mouse models with SYNGAP1-related intellectual disability (SRID) mutations found in humans were generated: one with a frameshift mutation that results in a premature stop codon and the other with an intronic mutation resulting in a cryptic splice acceptor site and premature stop codon. C_LIO_LIBoth SRID mouse models show 35[~]50% reduction in mRNA and [~]50% reduction in Syngap1 protein. C_LIO_LIBoth SRID mouse models display deficits in synaptic plasticity and behavioral phenotypes found in people. C_LIO_LIRNA-seq confirmed cryptic splice acceptor activity in one SRID mouse model and revealed broad transcriptional changes also identified in Syngap1+/- mice. C_LIO_LINovel SRID mouse models generated here provide a resource and establish a framework for development of future therapeutic intervention. C_LI ]]> Araki, Y. Gerber, E. E. Rajkovich, K. E. Hong, I. Johnson, R. C. Lee, H.-K. Kirkwood, A. Huganir, R. L. 2023-05-25 doi:10.1101/2023.05.25.542312 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Single-cell transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states associated with senescence ]]> https://biorxiv.org/content/10.1101/2023.05.25.542370v1?rss=1 Walter, L. D. Orton, J. L. Fong, E. H. H. Maymi, V. I. Rudd, B. R. Elisseeff, J. H. Cosgrove, B. D. 2023-05-26 doi:10.1101/2023.05.25.542370 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors ]]> https://biorxiv.org/content/10.1101/2023.05.26.542165v1?rss=1 Palmer, T. Kessler, M. D. Shao, X. M. Balan, A. Yarchoan, M. Zaidi, N. Lopez-Vidal, T. Y. Saeed, A. Gore, J. Azad, N. Favorov, A. V. Anagnostou, V. Karchin, R. Gaykalova, D. Danilova, L. Fertig, E. J. 2023-05-26 doi:10.1101/2023.05.26.542165 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Syntenin and CD63 Promote Exosome Biogenesis from the Plasma Membrane by Blocking Cargo Endocytosis ]]> https://biorxiv.org/content/10.1101/2023.05.26.542409v1?rss=1 Ai, Y. Guo, C. Garcia-Contreras, M. Sanchez, L. S. Saftics, A. Shodubi, O. Raghunandan, S. Xu, J. Tsai, S.-J. Dong, Y. Li, R. Jovanovic-Talisman, T. Gould, S. 2023-05-27 doi:10.1101/2023.05.26.542409 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Cholecystokinin is the follicle-stimulating hormone (FSH)-releasing hormone ]]> https://biorxiv.org/content/10.1101/2023.05.26.542428v1?rss=1 Uehara, S. K. Nishiike, Y. Maeda, K. Karigo, T. Kuraku, S. Okubo, K. Kanda, S. 2023-05-26 doi:10.1101/2023.05.26.542428 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ GPI-anchored Gas1 protein regulates cytosolic proteostasis in yeast ]]> https://biorxiv.org/content/10.1101/2023.05.26.542479v1?rss=1 Wang, Y. Ruan, L. Li, R. 2023-05-27 doi:10.1101/2023.05.26.542479 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling ]]> https://biorxiv.org/content/10.1101/2023.05.26.542511v1?rss=1 Tague, N. Andreani, V. Fan, Y. Timp, W. Dunlop, M. 2023-05-26 doi:10.1101/2023.05.26.542511 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels ]]> https://biorxiv.org/content/10.1101/2023.05.26.542533v1?rss=1 Giese, A. P. J. Weng, W.-H. Kindt, K. S. Chang, V. H. H. Montgomery, J. S. Ratzan, E. M. Beirl, A. J. Aponte Rivera, R. Lotthammer, J. M. Walujkar, S. Foster, M. P. Zobeiri, O. A. Holt, J. R. Riazuddin, S. Cullen, K. E. Sotomayor, M. Ahmed, Z. M. 2023-05-30 doi:10.1101/2023.05.26.542533 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ FluoMALDI microscopy: matrix co-crystallization simultaneously enhances fluorescence and MALDI imaging ]]> https://biorxiv.org/content/10.1101/2023.05.27.542340v1?rss=1 Yang, E. Shen, X. E. West-Foyle, H. Brown, D. R. Johnson, C. C. Kim, J. H. Roker, L. A. Tressler, C. M. Barman, I. Kuo, S. C. Glunde, K. 2023-05-27 doi:10.1101/2023.05.27.542340 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Neuronal Tau Pathology Worsens Late Phase White Matter Degeneration After Traumatic Brain Injury in Transgenic Mice ]]> https://biorxiv.org/content/10.1101/2023.05.27.542567v1?rss=1 Yu, F. Iacono, D. Perl, D. P. Lai, C. Gill, J. Le, T. Q. Lee, P. Sukumar, G. Armstrong, R. C. 2023-05-30 doi:10.1101/2023.05.27.542567 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Toward single cell tattoos: Biotransfer printing of lithographic gold nanopatterns on live cells ]]> https://biorxiv.org/content/10.1101/2023.05.28.542285v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@16f6e1corg.highwire.dtl.DTLVardef@a60bacorg.highwire.dtl.DTLVardef@1485d06org.highwire.dtl.DTLVardef@1d365c9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kwok, K. S. Zuo, Y. Choi, S. J. Pahapale, G. J. Gu, L. Gracias, D. H. 2023-05-28 doi:10.1101/2023.05.28.542285 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Exomap1 mouse: a transgenic model for in vivo studies of exosome biology ]]> https://biorxiv.org/content/10.1101/2023.05.29.542707v1?rss=1 5 nm in size. Taken together, these results establish the exomap1 mouse as a useful tool for in vivo studies of exosome biology, and for mapping cell type-specific contributions to biofluid exosome populations. In addition, our data confirm that CD81 is a highly-specific marker for exosomes and is not enriched in the larger microvesicle class of EVs. ]]> Fordjour, F. K. Abuelreich, S. Hong, X. Chatterjee, E. Lallai, V. Ng, M. Saftics, A. Deng, F. Carnel-Amar, N. Wakimoto, H. Shimizu, K. Anh Phu, T. Vu, N. K. Geiger, P. C. Raffai, R. L. Fowler, C. D. Shimizu, K. Das, S. Christenson, L. K. Jovanovic-Talisman, T. Gould, S. 2023-05-29 doi:10.1101/2023.05.29.542707 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation ]]> https://biorxiv.org/content/10.1101/2023.05.29.542732v1?rss=1 Posey, A. E. Bagheri, M. Ross, K. A. Lanum, E. N. Khan, M. A. Jennings, C. M. Harwig, M. C. Kennedy, N. W. Hilser, V. J. Harden, J. L. Hill, R. B. 2023-05-29 doi:10.1101/2023.05.29.542732 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Boosting Single-Cell RNA Sequencing Analysis with Simple Neural Attention ]]> https://biorxiv.org/content/10.1101/2023.05.29.542760v1?rss=1 Davalos, O. A. Heydari, A. A. Fertig, E. J. Sindi, S. Hoyer, K. K. 2023-06-01 doi:10.1101/2023.05.29.542760 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Angiogenic Steroids Induce Pathologic Scarring in a Preclinical Swine Model Via Dysfunctional Extracellular Matrix Deposition. ]]> https://biorxiv.org/content/10.1101/2023.05.29.542765v1?rss=1 Reiche, E. Keller, P. R. Soares, V. Schuster, C. R. Mroueh, J. Mroueh, V. Tan, Y. Kim, S. Y. Billaud, M. Newell-Fugate, A. E. Lian, C. G. O'Brien-Coon, D. 2023-06-01 doi:10.1101/2023.05.29.542765 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ An Open-Source Tool for Automated Human-Level Circling Behavior Detection ]]> https://biorxiv.org/content/10.1101/2023.05.30.540066v1?rss=1 90% accuracy in discriminating videos of wild type mice from videos of mutants. As using this technique requires no experience writing or modifying code, it also provides a convenient, noninvasive, quantitative tool for analyzing circling mouse models. Additionally, as our approach was agnostic to the underlying behavior, these results support the feasibility of algorithmically detecting specific, research-relevant behaviors using readily-interpretable parameters tuned on the basis of human consensus. ]]> Stanley, O. R. Swaminathan, A. Wojahn, E. Ahmed, Z. M. Cullen, K. E. 2023-05-30 doi:10.1101/2023.05.30.540066 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Poly(ADP-ribose) mediates bioenergetic defects and redox imbalance in neurons following oxygen and glucose deprivation ]]> https://biorxiv.org/content/10.1101/2023.05.30.542910v1?rss=1 Hossain, M. I. Lee, J. H. Gagne, J.-P. Khan, J. Poirier, G. G. Dawson, V. L. Dawson, T. M. Anadrabi, S. A. 2023-05-31 doi:10.1101/2023.05.30.542910 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Zoledronic acid improves bone quality and muscle function in a high bone turnover state ]]> https://biorxiv.org/content/10.1101/2023.06.01.543305v1?rss=1 Trivedi, T. Manaa, M. John, S. Reiken, S. Murthy, S. Pagnotti, G. M. Dole, N. S. She, Y. Suresh, S. Hain, B. A. Regan, J. Ofer, R. Wright, L. Robling, A. Cao, X. Alliston, T. Marks, A. R. Waning, D. L. Mohammad, K. S. Guise, T. A. 2023-06-05 doi:10.1101/2023.06.01.543305 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.06.02.542933v1?rss=1 Fryer, E. Guha, S. Rogel-Hernandez, L. E. Logan-Garbisch, T. Farah, H. N. Molhoff, I. Rezaei, E. Nekimken, A. L. Xu, A. Fechner, S. Druckman, S. Clandinin, T. R. Rhee, S. Y. Goodman, M. B. 2023-06-03 doi:10.1101/2023.06.02.542933 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Conjunctive vector coding and place coding in hippocampus share a common directional signal ]]> https://biorxiv.org/content/10.1101/2023.06.02.543340v1?rss=1 Zhou, Y.-Q. Puliyadi, V. Chen, X. Lee, J. L. Zhang, L.-Y. Knierim, J. J. 2023-06-06 doi:10.1101/2023.06.02.543340 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Spatial Transcriptomics of Meningeal Inflammation Reveals Variable Penetrance of Inflammatory Gene Signatures into Adjacent Brain Parenchyma ]]> https://biorxiv.org/content/10.1101/2023.06.02.543421v1?rss=1 Gadani, S. Singh, S. Kim, S. Calabresi, P. Smith, M. Bhargava, P. 2023-06-06 doi:10.1101/2023.06.02.543421 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity ]]> https://biorxiv.org/content/10.1101/2023.06.02.543449v1?rss=1 Mout, R. Bretherton, R. C. Decarreau, J. Lee, S. Edman, N. I. Ahlrichs, M. Hsia, Y. Sahtoe, D. D. Ueda, G. Gregorio, N. Sharma, A. Schulman, R. DeForest, C. A. Baker, D. 2023-06-03 doi:10.1101/2023.06.02.543449 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Mesostriatal dopamine is sensitive to specific cue-reward contingencies ]]> https://biorxiv.org/content/10.1101/2023.06.05.543690v1?rss=1 Garr, E. Cheng, Y. Jeong, H. Brooke, S. Castell, L. Bal, A. Magnard, R. Namboodiri, V. M. K. Janak, P. H. 2023-06-05 doi:10.1101/2023.06.05.543690 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Precision-engineered biomimetics: the human fallopian tube ]]> https://biorxiv.org/content/10.1101/2023.06.06.543923v1?rss=1 Crawford, A. J. Forjaz, A. Bhorkar, I. Roy, T. Schell, D. Queiroga, V. Ren, K. Kramer, D. Bons, J. Huang, W. Russo, G. C. Lee, M.-H. Schilling, B. Wu, P.-H. Shih, I.-M. Wang, T.-L. Kiemen, A. Wirtz, D. 2023-06-07 doi:10.1101/2023.06.06.543923 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Aberrant landscapes of maternal meiotic crossoverscontribute to aneuploidies in human embryos ]]> https://biorxiv.org/content/10.1101/2023.06.07.543910v1?rss=1 Ariad, D. Madjunkova, S. Madjunkov, M. Chen, S. Abramov, R. Librach, C. McCoy, R. C. 2023-06-09 doi:10.1101/2023.06.07.543910 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Peripheral direct current for suppression of physiologically evoked nociceptive responses at the spinal cord ]]> https://biorxiv.org/content/10.1101/2023.06.07.544048v1?rss=1 Su, T. F. Hamilton, J. D. Guo, Y. Potas, J. R. Shivdasani, M. N. Moalem-Taylor, G. Fridman, G. Y. Aplin, F. P. 2023-06-11 doi:10.1101/2023.06.07.544048 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets ]]> https://biorxiv.org/content/10.1101/2023.06.08.544045v1?rss=1 Koldobskiy, M. A. Camacho, O. Reddy, P. Izpisua Belmonte, J. C. Feinberg, A. P. 2023-06-09 doi:10.1101/2023.06.08.544045 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Formation of Müller glia-derived progenitor cells in retinas depleted of microglia ]]> https://biorxiv.org/content/10.1101/2023.06.08.544205v1?rss=1 El-Hodiri, H. Bentley, J. R. Reske, A. G. Palazzo, I. Campbell, W. A. Halloy, N. R. Fischer, A. J. 2023-06-09 doi:10.1101/2023.06.08.544205 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ Select EZH2 inhibitors enhance the viral mimicry effects of DNMT inhibition through a mechanism involving calcium-calcineurin-NFAT signaling ]]> https://biorxiv.org/content/10.1101/2023.06.09.544393v1?rss=1 Chomiak, A. A. Tiedemann, R. Liu, Y. Kong, X. Cui, Y. Thurlow, K. Cornett, E. M. Topper, M. J. Baylin, S. Rothbart, S. B. 2023-06-11 doi:10.1101/2023.06.09.544393 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Roadmap for Canonical and Extended Endocannabinoid System Receptors in Peripheral Organs of Preclinical Animal Models ]]> https://biorxiv.org/content/10.1101/2023.06.10.544455v1?rss=1 Rosado-Franco, J. J. Ellison, A. L. White, C. J. Price, A. S. Moore, C. F. Williams, R. E. Fridman, L. B. Weerts, E. M. Williams, D. W. 2023-06-10 doi:10.1101/2023.06.10.544455 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Excitatory neurons derived from human induced Pluripotent Stem Cells show transcriptomic differences in Alzheimers patients from controls ]]> https://biorxiv.org/content/10.1101/2023.06.10.544465v1?rss=1 Sagar, R. Azoidis, I. Zivko, C. Xydia, A. Oh, E. Rosenberg, P. B. Lyketsos, C. G. Mahairaki, V. Avramopoulos, D. 2023-06-10 doi:10.1101/2023.06.10.544465 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ RNA Helicase DDX3 Regulates RAD51 Localization and DNA Damage Repair in Ewing Sarcoma ]]> https://biorxiv.org/content/10.1101/2023.06.10.544474v1?rss=1 Randolph, M. E. Afifi, M. Gorthi, A. Weil, R. Wilky, B. A. Weinreb, J. Ciero, P. ter Hoeve, N. van Diest, P. J. Raman, V. Bishop, A. J. Loeb, D. M. 2023-06-10 doi:10.1101/2023.06.10.544474 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid ]]> https://biorxiv.org/content/10.1101/2023.06.11.544494v1?rss=1 GrandPre, T. Zhang, Y. Pyo, A. G. T. Weiner, B. Li, J.-L. Jonikas, M. C. Wingreen, N. S. 2023-06-11 doi:10.1101/2023.06.11.544494 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Targeting Ras signaling excitability in cancer cells through combined inhibition of FAK and PI3K ]]> https://biorxiv.org/content/10.1101/2023.06.12.544386v1?rss=1 Chen, C.-C. Wang, S. Yang, J.-M. Huang, C.-H. 2023-06-13 doi:10.1101/2023.06.12.544386 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers ]]> https://biorxiv.org/content/10.1101/2023.06.13.544671v1?rss=1 Kim, J. M. Carcamo, C. C. Jazani, S. Xie, Z. Feng, X. A. Poyton, M. F. Holland, K. L. Grimm, J. B. Lavis, L. D. Ha, T. Wu, C. 2023-06-13 doi:10.1101/2023.06.13.544671 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Development of an in situ cell-type specific proteome analysis method using antibody-mediated biotinylation ]]> https://biorxiv.org/content/10.1101/2023.06.13.544682v1?rss=1 Ryu, T. Kim, S.-Y. Thuraisamy, T. Jang, Y. Na, C. H. 2023-06-14 doi:10.1101/2023.06.13.544682 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Spatially clustered neurons encode vocalization categories in the bat midbrain ]]> https://biorxiv.org/content/10.1101/2023.06.14.545029v1?rss=1 Lawlor, J. Wohlgemuth, M. Moss, C. F. Kuchibhotla, K. V. 2023-06-14 doi:10.1101/2023.06.14.545029 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies ]]> https://biorxiv.org/content/10.1101/2023.06.15.544806v1?rss=1 Orris, B. Sung, M. W. Bhat, S. Xu, Y. Huynh, K. W. Han, S. Johnson, D. C. Bosbach, B. Shields, D. J. Stivers, J. T. 2023-06-15 doi:10.1101/2023.06.15.544806 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Injectable ventral spinal stimulator evokes programmable and biomimetic hindlimb motion ]]> https://biorxiv.org/content/10.1101/2023.06.15.545178v1?rss=1 LIN, D. Lee, J. M. Wang, C. Park, H.-G. Lieber, C. M. 2023-06-15 doi:10.1101/2023.06.15.545178 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Histone H1.2 Dependent Translocation of Poly (ADP-ribose) Initiates Parthanatos ]]> https://biorxiv.org/content/10.1101/2023.06.18.545460v1?rss=1 Fang, J. Kang, B. G. Kam, T.-I. Behensky, A. Rines, J. Kang, H. C. Dawson, V. L. Dawson, T. 2023-06-18 doi:10.1101/2023.06.18.545460 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Contezolid can replace linezolid in a novel combination with bedaquiline and pretomanid in a murine model of tuberculosis ]]> https://biorxiv.org/content/10.1101/2023.06.18.545492v1?rss=1 Almeida, D. V. Li, S.-Y. Lee, J. Hafkin, B. Mdluli, K. Fotouhi, N. Nuermberger, E. 2023-06-19 doi:10.1101/2023.06.18.545492 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Ets1 and IL17RA cooperate to regulate autoimmune responses as well as skin immunity to Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.06.19.545307v1?rss=1 Battaglia, M. C. Sunshine, A. Luo, W. Jin, R. Stith, A. Lindemann, M. Miller, L. S. Sinha, S. Wohlfert, E. Garrett-Sinha, L. A. 2023-06-20 doi:10.1101/2023.06.19.545307 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Measuring stimulus-related redundant and synergistic functional connectivity with single cell resolution in auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.06.19.545531v1?rss=1 Kocillari, L. Celotto, M. Francis, N. A. Mukherjee, S. Babadi, B. Kanold, P. O. Panzeri, S. 2023-06-21 doi:10.1101/2023.06.19.545531 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Frequency modulation increases the specificity of time-resolved connectivity: A resting-state fMRI study ]]> https://biorxiv.org/content/10.1101/2023.06.20.545786v1?rss=1 Faghiri, A. Yang, K. Ishizuka, K. Sawa, A. Adali, T. Calhoun, V. 2023-06-21 doi:10.1101/2023.06.20.545786 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Tiny Earth CURE improves student persistence in science ]]> https://biorxiv.org/content/10.1101/2023.06.21.543782v1?rss=1 Miller, S. Aldana, C. C. Du, W. Lee, H. Maldonado, N. Sandoval, P. Vong, J. Young, G. Handelsman, J. Broderick, N. A. Hernandez, P. R. Estrada, M. 2023-06-23 doi:10.1101/2023.06.21.543782 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Drebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons ]]> https://biorxiv.org/content/10.1101/2023.06.21.545958v1?rss=1 Dorskind, J. M. Sudarsanam, S. Hand, R. A. Ziak, J. Amoah-Dankwah, M. Guzman-Clavel, L. Soto-Vargas, J. L. Kolodkin, A. L. 2023-06-21 doi:10.1101/2023.06.21.545958 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Collagen type VI regulates TGFβ bioavailability in skeletal muscle ]]> https://biorxiv.org/content/10.1101/2023.06.22.545964v1?rss=1 Mohassel, P. Rooney, J. Zou, Y. Johnson, K. Norato, G. Hearn, H. Nalls, M. A. Yun, P. Ogata, T. Silverstein, S. Sleboda, D. Roberts, T. J. Rifkin, D. B. Bonnemann, C. G. 2023-06-24 doi:10.1101/2023.06.22.545964 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Modeling wild type and mutant p53 in telomerase-immortalized human cells ]]> https://biorxiv.org/content/10.1101/2023.06.22.546141v1?rss=1 Miciak, J. J. Bunz, F. 2023-06-25 doi:10.1101/2023.06.22.546141 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PINK1-deficient Human Dopamine Neurons ]]> https://biorxiv.org/content/10.1101/2023.06.23.546087v1?rss=1 Wang, H. Chen, R. Xiao, L. Kumar, M. Acevedo-Cintron, J. Siuda, J. Koziorowski, D. Wszolek, Z. K. Dawson, V. L. Dawson, T. 2023-06-26 doi:10.1101/2023.06.23.546087 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition ]]> https://biorxiv.org/content/10.1101/2023.06.23.546270v1?rss=1 Gao, C. W. Lin, W. Riddle, R. C. Kushwaha, P. Boukas, L. Bjornsson, H. T. Hansen, K. D. Fahrner, J. A. 2023-06-26 doi:10.1101/2023.06.23.546270 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer ]]> https://biorxiv.org/content/10.1101/2023.06.23.546338v1?rss=1 Murray, J. C. Sivapalan, L. Hummelink, K. Balan, A. White, J. R. Niknafs, N. Rhymee, L. Pereira, G. Rao, N. Phallen, J. Leal, A. Bartlett, D. L. Marrone, K. A. Naidoo, J. Levy, B. Rosner, S. Hann, C. L. Scott, S. C. Feliciano, J. Lam, V. K. Ettinger, D. S. Li, Q. K. Illei, P. B. Monkhorst, K. Zaidi, A. H. Scharpf, R. B. Brahmer, J. R. Velculescu, V. E. Forde, P. M. Anagnostou, V. 2023-06-26 doi:10.1101/2023.06.23.546338 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Intrarenal myeloid subsets associated with kidney injury are comparable in mice and patients with lupus nephritis ]]> https://biorxiv.org/content/10.1101/2023.06.24.546409v1?rss=1 Hoover, P. Lieb, D. J. Kang, J. Li, S. Peters, M. Raparia, C. Arazi, A. Eisenhaure, T. Gurajala, S. S. Xiao, Q. Mishra, R. Spurrell, M. Menon, R. Kretzler, M. Chen, J. Nieman, L. Sonny, A. Demeke, D. Hodgin, J. Guthridge, J. Fava, A. Clancy, R. Putterman, C. Izmirly, P. Belmont, H. M. Kalunian, K. Kamen, D. Wofsy, D. Buyon, J. James, J. A. Petri, M. Diamond, B. Raychaudhuri, S. The Kidney Precision Medicine Project, The Accelerating Medicines Partnership: RA/SLE network, Hacohen, N. Davidson, A. 2023-06-25 doi:10.1101/2023.06.24.546409 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates ]]> https://biorxiv.org/content/10.1101/2023.06.25.546465v1?rss=1 To, P. Bhagwat, A. M. Tarbox, H. E. Ecer, A. Wendorff, H. Jamieson, Z. Trcek, T. Fried, S. D. 2023-06-25 doi:10.1101/2023.06.25.546465 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Implicit model to capture electrostatic features of membrane environment. ]]> https://biorxiv.org/content/10.1101/2023.06.26.546486v1?rss=1 Samanta, R. Gray, J. J. 2023-06-27 doi:10.1101/2023.06.26.546486 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ G2C4 targeting antisense oligonucleotides potently mitigate TDP-43 dysfunction in C9orf72 ALS/FTD human neurons ]]> https://biorxiv.org/content/10.1101/2023.06.26.546581v1?rss=1 Rothstein, J. D. Baskerville, V. Rapuri, S. Mehlhop, E. Jafar-nejad, P. Rigo, F. Bennett, F. Mizielinska, S. Isaacs, A. Coyne, A. N. 2023-06-26 doi:10.1101/2023.06.26.546581 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy ]]> https://biorxiv.org/content/10.1101/2023.06.27.546748v1?rss=1 Zhang, J. Newman, J. Wang, Z. Qian, Y. Guo, W. Chen, Z. S. Linghu, C. Etienne-Cummings, R. Fossum, E. Boyden, E. Wilson, M. A. 2023-06-29 doi:10.1101/2023.06.27.546748 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy ]]> https://biorxiv.org/content/10.1101/2023.06.28.546576v1?rss=1 Lariviere, D. Abueg, L. Brajuka, N. Gallardo-Alba, C. Gruning, B. Ko, B. J. Ostrovsky, A. Palmada-Flores, M. Pickett, B. D. Rabbani, K. Balacco, J. R. Chaisson, M. Cheng, H. Collins, J. Denisova, A. Fedrigo, O. Gallo, G. R. Giani, A. M. Gooder, G. M. Jain, N. Johnson, C. Kim, H. Lee, C. Marques-Bonet, T. O'Toole, B. Rhie, A. Secomandi, S. Sozzoni, M. Tilley, T. Uliano-Silva, M. van den Beek, M. Waterhouse, R. M. Phillippy, A. M. Jarvis, E. D. Schatz, M. Nekrutenko, A. Formenti, G. 2023-06-30 doi:10.1101/2023.06.28.546576 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Encoding and context-dependent control of reward consumption within the central nucleus of the amygdala ]]> https://biorxiv.org/content/10.1101/2023.06.28.546936v1?rss=1 Fraser, K. M. Kim, T. H. Castro, M. Drieu, C. Padovan-Hernandez, Y. Chen, B. J. Pat, F. Ottenheimer, D. J. Janak, P. H. 2023-06-30 doi:10.1101/2023.06.28.546936 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Sex peptide receptor is not required for refractoriness to remating or induction of egg laying in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2023.06.28.546954v1?rss=1 Amaro, I. A. Wohl, M. P. Pitcher, S. Alfonso-Parra, C. Avila, F. W. Paige, A. S. Helinski, M. Duvall, L. B. Harrington, L. C. Wolfner, M. F. McMeniman, C. J. 2023-06-30 doi:10.1101/2023.06.28.546954 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins ]]> https://biorxiv.org/content/10.1101/2023.06.29.547063v1?rss=1 Nixon, C. Lim, S. A. Sternke, M. Barrick, D. Harms, M. J. Marqusee, S. 2023-07-01 doi:10.1101/2023.06.29.547063 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ TrkB-dependent regulation of molecular signaling across septal cell types ]]> https://biorxiv.org/content/10.1101/2023.06.29.547069v1?rss=1 Rodriguez, L. A. Tran, M. N. Garcia-Flores, R. Pattie, E. A. Kim, S.-H. Shin, J. H. Lee, Y. K. Divecha, H. R. Montoya, C. Jaffe, A. E. Torres, L. C. Page, S. C. Martinowich, K. C. 2023-07-01 doi:10.1101/2023.06.29.547069 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer ]]> https://biorxiv.org/content/10.1101/2023.06.29.547134v1?rss=1 Chu, L.-S. Ruffolo, J. A. Harmalkar, A. Gray, J. J. 2023-07-01 doi:10.1101/2023.06.29.547134 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ The leptin receptor has no role in delta-cell control of beta-cell function in the mouse ]]> https://biorxiv.org/content/10.1101/2023.06.30.547271v1?rss=1 Zhang, J. Katada, K. Mosleh, E. Peng, G. Golson, M. L. 2023-07-01 doi:10.1101/2023.06.30.547271 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Small extracellular vesicles promote stiffness-mediated metastasis ]]> https://biorxiv.org/content/10.1101/2023.07.01.545937v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1be1dbdorg.highwire.dtl.DTLVardef@928710org.highwire.dtl.DTLVardef@1e14e9borg.highwire.dtl.DTLVardef@efdb7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sneider, A. Liu, Y. Starich, B. Du, W. Marar, C. Faqih, N. Ciotti, G. E. Kim, J. H. Krishnan, S. Ibrahim, S. Igboko, M. Locke, A. Lewis, D. M. Hong, H. Karl, M. Vij, R. Russo, G. C. Nair, P. R. Gomez-de-Mariscal, E. Habibi, M. Munoz-Barrutia, A. Gu, L. Eisinger-Mathason, T. S. K. Wirtz, D. 2023-07-02 doi:10.1101/2023.07.01.545937 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ VTA dopamine neurons drive spatiotemporally heterogeneous striatal dopamine signals during learning ]]> https://biorxiv.org/content/10.1101/2023.07.01.547331v1?rss=1 Engel, L. Wolff, A. R. Blake, M. Collins, V. L. Sinha, S. Saunders, B. T. 2023-07-02 doi:10.1101/2023.07.01.547331 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Revealing abrupt transitions from goal-directed to habitual behavior ]]> https://biorxiv.org/content/10.1101/2023.07.05.547783v1?rss=1 Moore, S. Wang, Z. Zhu, Z. Sun, R. Lee, A. Charles, A. Kuchibhotla, K. V. 2023-07-07 doi:10.1101/2023.07.05.547783 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ ABDS: tool suite for analyzing biologically diverse samples ]]> https://biorxiv.org/content/10.1101/2023.07.05.547797v1?rss=1 Du, D. Bhardwaj, S. Parker, S. J. Cheng, Z. Zhang, Z. Lu, Y. Van Eyk, J. E. Yu, G. Clarke, R. Herrington, D. M. Wang, Y. 2023-07-05 doi:10.1101/2023.07.05.547797 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Polygenic Risk Score Associates with Atherosclerotic Plaque Characteristics at Autopsy ]]> https://biorxiv.org/content/10.1101/2023.07.05.547891v1?rss=1 Cornelissen, A. Gadhoke, N. Ryan, K. A. Hodonsky, C. J. Mitchell, R. N. Bihlmeyer, N. A. Duong, T. Chen, Z. Dikongue, A. Sakamoto, A. Sato, Y. Kawakami, R. Mori, M. Kawai, K. Fernandez, R. Ghosh, S. K. B. Braumann, R. Abebe, B. Kutys, R. Kutyna, M. D. Romero, M. E. Kolodgie, F. Miller, C. L. Hong, C. C. Grove, M. L. Brody, J. A. Sotoodehnia, N. Arking, D. E. Schunkert, H. Mitchell, B. D. Guo, L. Virmani, R. Finn, A. V. 2023-07-09 doi:10.1101/2023.07.05.547891 Cold Spring Harbor Laboratory Press 2023-07-09 <![CDATA[ In Vitro Modulator Responsiveness of 655 CFTR Variants Found in People With CF ]]> https://biorxiv.org/content/10.1101/2023.07.07.548159v1?rss=1 Bihler, H. Sivachenko, A. Millen, L. Bhatt, P. Thakerar Patel, A. Chin, J. Bailey, V. Musisi, I. LaPan, A. Allaire, N. E. Conte, J. Simon, N. R. Magaret, A. S. Raraigh, K. S. Cutting, G. R. Skach, W. R. Bridges, R. J. Thomas, P. J. Mense, M. 2023-07-11 doi:10.1101/2023.07.07.548159 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Phase-Amplitude Coupling Detection and Analysis of Human 2-Dimensional Neural Cultures in Multi-well Microelectrode Array in Vitro ]]> https://biorxiv.org/content/10.1101/2023.07.08.548227v1?rss=1 Salimpour, Y. Anderson, W. S. Dastgheyb, R. Liu, S. Ming, G.-L. Song, H. Maragakis, N. J. Habela, C. W. 2023-07-10 doi:10.1101/2023.07.08.548227 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Detecting differential transcript usage in complex diseases with SPIT ]]> https://biorxiv.org/content/10.1101/2023.07.10.548289v1?rss=1 Erdogdu, B. Varabyou, A. Hicks, S. C. Salzberg, S. L. Pertea, M. 2023-07-10 doi:10.1101/2023.07.10.548289 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes ]]> https://biorxiv.org/content/10.1101/2023.07.12.548702v1?rss=1 Keener, R. Chhetri, S. B. Connelly, C. J. Taub, M. A. Conomos, M. P. Weinstock, J. S. Ni, B. Strober, B. J. Aslibekyan, S. Auer, P. L. Barwick, L. Becker, L. C. Blangero, J. Bleecker, E. R. Brody, J. A. Cade, B. E. Celedon, J. C. Chang, Y.-C. Cupples, L. A. Custer, B. Freedman, B. I. Gladwin, M. T. Heckbert, S. R. Hou, L. Irvin, M. R. Isasi, C. R. Johnsen, J. M. Kenny, E. E. Kooperberg, C. Minster, R. L. Nekhai, S. Pankratz, N. Peyser, P. A. Rotter, J. I. Taylor, K. D. Telen, M. J. Wu, B. Yanek, L. R. Yang, I. V. Albert, C. Arnett, D. K. Ashley-Koch, A. 2023-07-14 doi:10.1101/2023.07.12.548702 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ A microfluidic strategy to capture antigen-specific high affinity B cells ]]> https://biorxiv.org/content/10.1101/2023.07.12.548739v1?rss=1 Alhassan, A. M. Shirure, V. S. Luo, J. Nguyen, B. B. Rollins, Z. A. Shergill, B. S. Zhu, X. Baumgarth, N. George, S. C. 2023-07-14 doi:10.1101/2023.07.12.548739 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Insight into the structural hierarchy of the protease cascade that regulates the mosquito melanization response ]]> https://biorxiv.org/content/10.1101/2023.07.13.548954v1?rss=1 Saab, S. A. Zhang, X. Morejon, B. Michel, K. Osta, M. A. 2023-07-15 doi:10.1101/2023.07.13.548954 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ GAGA Factor Overcomes 1D Diffusion Barrier by 3D Diffusion in Search of Nucleosomal Targets ]]> https://biorxiv.org/content/10.1101/2023.07.14.549009v1?rss=1 Feng, X. A. Ness, K. M. Liu, C. Ahmed, I. Bowman, G. D. Ha, T. Wu, C. 2023-07-15 doi:10.1101/2023.07.14.549009 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2023.07.14.549118v1?rss=1 Qian, C. Xin, Y. Qi, C. Wang, H. Dong, B. C. Zack, D. Blackshaw, S. Hattar, S. Zhou, F. Qian, J. 2023-07-17 doi:10.1101/2023.07.14.549118 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Brain aromatase dynamics reflect parental experience and behaviour in male mice ]]> https://biorxiv.org/content/10.1101/2023.07.15.549144v1?rss=1 Duarte-Guterman, P. Skandalis, D. A. Merkl, A. Geissler, D. B. Ehret, G. 2023-07-18 doi:10.1101/2023.07.15.549144 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Spatial IMIX: A Mixture Model Approach to Spatially Correlated Multi-Omics Data Integration ]]> https://biorxiv.org/content/10.1101/2023.07.15.549148v1?rss=1 Wang, Z. Czerniak, B. Wei, P. 2023-07-17 doi:10.1101/2023.07.15.549148 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Contextual protein encodings from equivariant graph transformers ]]> https://biorxiv.org/content/10.1101/2023.07.15.549154v1?rss=1 Mahajan, S. P. Ruffolo, J. A. Gray, J. J. 2023-07-17 doi:10.1101/2023.07.15.549154 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes ]]> https://biorxiv.org/content/10.1101/2023.07.16.548274v1?rss=1 Lee, C. Y. Riffle, D. Xiong, Y. Momtaz, N. Hwang, A. Duan, Z. Zhang, J. 2023-07-18 doi:10.1101/2023.07.16.548274 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription ]]> https://biorxiv.org/content/10.1101/2023.07.18.549494v1?rss=1 LaMarca, E. A. Saito, A. Plaza-Jennings, A. Hellmich, A. Fernando, M. B. Javidfar, B. Espeso-Gil, S. Estill, M. Liao, W. Townsley, K. Florio, A. Ethridge, J. E. Do, C. Tycko, B. Shen, L. Kamiya, A. Tsankova, N. M. Brennand, K. J. Akbarian, S. 2023-07-18 doi:10.1101/2023.07.18.549494 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ The HCM-Linked Mutation Arg92Leu in TNNT2 Allosterically Alters the cTnC-cTnI Interface and Disrupts the PKA-mediated Regulation of Myofilament Relaxation ]]> https://biorxiv.org/content/10.1101/2023.07.18.549569v1?rss=1 Lynn, M. L. Jimenez, J. Castillo, R. L. Klass, M. M. Vasquez, C. Baldo, A. P. Gibson, C. Murphy, A. M. Tardiff, J. C. 2023-07-19 doi:10.1101/2023.07.18.549569 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Calcium-permeable AMPA receptors govern PV neuron feature selectivity ]]> https://biorxiv.org/content/10.1101/2023.07.20.549908v1?rss=1 Hong, I. Kim, J. Hainmueller, T. Kim, D. W. Johnson, R. C. Park, S. H. Limjunyawong, N. Yang, Z. Cheon, D. Hwang, T. Agarwal, A. Cholvin, T. Krienen, F. M. McCarroll, S. A. Dong, X. Leopold, D. A. Blackshaw, S. Bergles, D. E. Bartos, M. Brown, S. P. Huganir, R. L. 2023-07-20 doi:10.1101/2023.07.20.549908 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Membrane mechanics dictate axonal morphology and function ]]> https://biorxiv.org/content/10.1101/2023.07.20.549958v1?rss=1 Griswold, J. M. Bonilla-Quintana, M. Pepper, R. Lee, C. T. Raychaudhuri, S. Ma, S. Gan, Q. Syed, S. Zhu, C. Bell, M. Suga, M. Yamaguchi, Y. Chereau, R. Nagerl, V. Knott, G. W. Rangamani, P. Watanabe, S. 2023-07-21 doi:10.1101/2023.07.20.549958 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Targeting pioneer transcription factor Ascl1 to promote optic nerve regeneration ]]> https://biorxiv.org/content/10.1101/2023.07.20.549959v1?rss=1 Dong, B. Luo, X. Qi, C. Qian, J. Qian, C. Zhou, F.-Q. 2023-07-23 doi:10.1101/2023.07.20.549959 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Exuberant de novo dendritic spine growth in mature neurons ]]> https://biorxiv.org/content/10.1101/2023.07.21.550095v1?rss=1 Kruessel, S. Deb, I. Son, S. Ewall, G. Chang, M. Lee, H.-K. Heo, W. D. Kwon, H.-B. 2023-07-25 doi:10.1101/2023.07.21.550095 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Assessing the effect of antibody responses on viral rebound dynamics in postnatally SHIV-infected infant Rhesus macaques ]]> https://biorxiv.org/content/10.1101/2023.07.22.550159v1?rss=1 Mainou, E. Berendam, S. J. Obregon-Perko, V. Uffman, E. A. Phan, C. T. Shaw, G. M. Bar, K. J. Conway, J. M. Chan, C. Chahroudi, A. M. McCarthy, J. Permar, S. R. Silvestri, G. Siliciano, R. F. Silicano, J. Fouda, G. J. Fray, E. J. Kumar, M. R. 2023-07-22 doi:10.1101/2023.07.22.550159 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ ME3BP-7 is a targeted cytotoxic agent that rapidly kills pancreatic cancer cells expressing high levels of monocarboxylate transporter MCT1 ]]> https://biorxiv.org/content/10.1101/2023.07.23.550207v1?rss=1 Rincon-Torroella, J. Dal Molin, M. Mog, B. Han, G. Watson, E. Wyhs, N. Ishiyama, S. Ahmedna, T. Minn, I. Azad, N. S. Bettegowda, C. Papadopoulos, N. Kinzler, K. W. Zhou, S. Vogelstein, B. Gabrielson, K. L. Sur, S. 2023-07-25 doi:10.1101/2023.07.23.550207 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Microglial cannabinoid receptor type1 mediates social memory deficits produced by adolescent THC exposure and 16p11.2 duplication ]]> https://biorxiv.org/content/10.1101/2023.07.24.550212v1?rss=1 Hasegawa, Y. Kim, J. Ursini, G. Jouroukhin, Y. Zhu, X. Miyahara, Y. Xiong, F. Madireddy, S. Obayashi, M. Lutz, B. Sawa, A. Brown, S. P. Pletnikov, M. V. Kamiya, A. 2023-07-26 doi:10.1101/2023.07.24.550212 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Protein Assembly Modulation: A New Approach to ALS Therapeutics ]]> https://biorxiv.org/content/10.1101/2023.07.24.550252v1?rss=1 Yu, S. F. Paulvannan, K. Solas, D. Lingappa, A. F. Moreira, A. R. Sahu, S. Michon, M. Goldsmith, D. DeYarman, N. Mallesh, S. Prasad, M. D. Maios, C. Ruan, K. Tomassy, G. S. Jensen, E. McGuirk, E. Bader, V. Meuller-Schiffmann, A. Reed, J. C. Lingappa, J. R. Asundi, V. Hong, S. Jacobsen, S. Ostrow, L. Lloyd, T. Parker, A. E. Staats, K. A. Ichida, J. Dodge, J. Dey, D. Korth, C. Selvarajah, S. Lingappa, V. R. Rosenfeld, J. 2023-07-26 doi:10.1101/2023.07.24.550252 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ CellSNAP: A fast, accurate algorithm for 3D cell segmentation in quantitative phase imaging ]]> https://biorxiv.org/content/10.1101/2023.07.24.550376v1?rss=1 Raj, P. Paidi, S. Conway, L. Chatterjee, A. Barman, I. 2023-07-26 doi:10.1101/2023.07.24.550376 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Sympathetic NPY controls glucose homeostasis, cold tolerance, and cardiovascular functions in mice ]]> https://biorxiv.org/content/10.1101/2023.07.24.550381v1?rss=1 Kumari, R. Pascalau, R. Wang, H. Bajpayi, S. Yurgel, M. Quansah, K. Hattar, S. Tampakakis, E. Kuruvilla, R. 2023-07-26 doi:10.1101/2023.07.24.550381 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Polyamine transport inhibition and cisplatin synergistically enhance tumor control through oxidative stress in murine head and neck cancer models ]]> https://biorxiv.org/content/10.1101/2023.07.25.550524v1?rss=1 Yassin-Kassab, A. Wang, N. Foley, J. R. Murray Stewart, T. R. Burns, M. R. Casero, R. A. Harbison, R. A. Duvvuri, U. 2023-07-27 doi:10.1101/2023.07.25.550524 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Human Plasma Proteomic Profile of Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.07.25.550557v1?rss=1 Yu, Z. Vromman, A. Nguyen, N. Q. H. Vellarikkal, S. K. Uddin, M. M. Niroula, A. Griffin, G. Honigberg, M. C. Lin, A. E. Gibson, C. J. Katz, D. H. Tahir, U. Haidermota, S. Ganesh, S. Antoine, T. Weinstock, J. Austin, T. R. Vasan, R. S. peloso, G. M. Hornsby, W. Ganz, P. Manson, J. E. Haring, B. Kooperberg, C. L. Reiner, A. P. Bis, J. C. Psaty, B. M. Min, Y.-I. Correa, A. Lange, L. A. Post, W. Rotter, J. I. Rich, S. S. Wilson, J. G. Ebert, B. L. Yu, B. Ballantyne, C. M. Coresh, J. Sankaran, V. G. Bick, A. G. Jaiswal, S. Libby, P. Gerszten, R. E. NHLBI T 2023-07-27 doi:10.1101/2023.07.25.550557 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Systematic assessment of long-read RNA-seq methods for transcript identification and quantification ]]> https://biorxiv.org/content/10.1101/2023.07.25.550582v1?rss=1 Pardo-Palacios, F. J. Wang, D. Reese, F. Diekhans, M. Carbonell-Sala, S. Williams, B. Loveland, J. E. De Maria, M. Adams, M. S. Balderrama-Gutierrez, G. Behera, A. K. Gonzalez, J. M. Hunt, T. Lagarde, J. Liang, C. E. Li, H. Meade, M. J. Amador, D. A. M. Prjibelski, A. D. Birol, I. Bostan, H. Brooks, A. M. Celik, M. H. Chen, Y. Du, M. R. M. Felton, C. Goke, J. Hafezqorani, S. Herwig, R. Kawaji, H. Lee, J. Li, J.-L. Lienhard, M. Mikheenko, A. Mulligan, D. Nip, K. M. Pertea, M. Ritchie, M. E. Sim, A. D. Tang, A. D. Wan, Y. K. Wang, C. Wong, B. Y. Yang, C 2023-07-27 doi:10.1101/2023.07.25.550582 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Transcriptomic Effects of Low-Dose Inorganic Arsenic Exposure on Murine Bone Marrow-Derived Macrophages. ]]> https://biorxiv.org/content/10.1101/2023.07.26.550543v1?rss=1 Illingworth, E. J. Maertens, A. Sille, F. C. M. 2023-07-27 doi:10.1101/2023.07.26.550543 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ CAVE: Connectome Annotation Versioning Engine ]]> https://biorxiv.org/content/10.1101/2023.07.26.550598v1?rss=1 Dorkenwald, S. Schneider-Mizell, C. M. Brittain, D. Halageri, A. Jordan, C. Kemnitz, N. Castro, M. A. Silversmith, W. Maitin-Shephard, J. Troidl, J. Pfister, H. Gillet, V. Xenes, D. Bae, J. A. Bodor, A. L. Buchanan, J. Bumbarger, D. J. Elabbady, L. Jia, Z. Kapner, D. Kinn, S. Lee, K. Li, K. Lu, R. Macrina, T. Mahalingam, G. Mitchell, E. Mondal, S. S. Mu, S. Nehoran, B. Popovych, S. Takeno, M. Torres, R. Turner, N. L. Wong, W. Wu, J. Yin, W. Yu, S.-c. Reid, R. C. da Costa, N. M. Seung, H. S. Collman, F. 2023-07-28 doi:10.1101/2023.07.26.550598 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ The influence of polarized membrane ion carriers and extracellular electrical/pH gradients on cell ionic homeostasis and locomotion ]]> https://biorxiv.org/content/10.1101/2023.07.26.550658v1?rss=1 Li, Y. Sun, S. 2023-07-27 doi:10.1101/2023.07.26.550658 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Splam: a deep-learning-based splice site predictor that improves spliced alignments ]]> https://biorxiv.org/content/10.1101/2023.07.27.550754v1?rss=1 Chao, K.-H. Mao, A. Salzberg, S. L. Pertea, M. 2023-07-29 doi:10.1101/2023.07.27.550754 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Mechano-induced homotypic patterned domain formation by monocytes ]]> https://biorxiv.org/content/10.1101/2023.07.27.550819v1?rss=1 Du, W. Zhu, J. Wu, Y. Kiemen, A. Sun, S. Wirtz, D. 2023-07-28 doi:10.1101/2023.07.27.550819 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Whole genome assembly of a hybrid Trypanosoma cruzi strain assembled with nanopore sequencing alone ]]> https://biorxiv.org/content/10.1101/2023.07.27.550875v1?rss=1 Hakim, J. M. Guarnizo, S. A. G. Machaca, E. M. Gilman, R. H. Mugnier, M. R. 2023-07-27 doi:10.1101/2023.07.27.550875 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Enhanced microglial dynamics and paucity of tau seeding in the amyloid plaque microenvironment contributes to cognitive resilience in Alzheimer 's disease ]]> https://biorxiv.org/content/10.1101/2023.07.27.550884v1?rss=1 Jury-Garfe, N. You, Y. Martinez, P. Redding-Ochoa, J. Karahan, H. Johnson, T. S. Zhang, J. Kim, J. Troncoso, J. C. Lasagna-Reeves, C. A. 2023-07-28 doi:10.1101/2023.07.27.550884 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Major data analysis errors invalidate cancer microbiome findings ]]> https://biorxiv.org/content/10.1101/2023.07.28.550993v1?rss=1 Gihawi, A. Ge, Y. Lu, J. Puiu, D. Xu, A. Cooper, C. S. Brewer, D. S. Pertea, M. Salzberg, S. 2023-07-31 doi:10.1101/2023.07.28.550993 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ A systematic comparison of computational methods for expression forecasting ]]> https://biorxiv.org/content/10.1101/2023.07.28.551039v1?rss=1 Kernfeld, E. M. Yang, Y. Weinstock, J. S. Battle, A. Cahan, P. M. 2023-07-31 doi:10.1101/2023.07.28.551039 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Cocaine Regulates Antiretroviral Therapy CNS Access Through Pregnane-X Receptor-Mediated Drug Transporter and Metabolizing Enzyme Modulation at the Blood Brain Barrier ]]> https://biorxiv.org/content/10.1101/2023.07.28.551042v1?rss=1 Fridman, L. B. Knerler, S. Price, A.-S. Colon Ortiz, R. Mercado, A. Wilkins, H. Flores, B. R. Orsburn, B. Williams, D. 2023-07-29 doi:10.1101/2023.07.28.551042 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Reliable protein-protein docking with AlphaFold, Rosetta and replica-exchange ]]> https://biorxiv.org/content/10.1101/2023.07.28.551063v1?rss=1 Harmalkar, A. Lyskov, S. Gray, J. J. 2023-07-29 doi:10.1101/2023.07.28.551063 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ The Endosomal pH Regulator NHE6 is Required for Insulin-Stimulated Glucose Uptake in Adipocytes ]]> https://biorxiv.org/content/10.1101/2023.07.30.551163v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@f6fc88org.highwire.dtl.DTLVardef@13d7faforg.highwire.dtl.DTLVardef@89d577org.highwire.dtl.DTLVardef@11da50a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mekile, A. X. Makena, M. R. Gupta, R. White, C. J. Bowman, R. W. Patnayak, R. L. Lorenzo, D. N. Rao, R. 2023-07-30 doi:10.1101/2023.07.30.551163 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn ]]> https://biorxiv.org/content/10.1101/2023.07.30.551179v1?rss=1 Liebhoff, A.-M. Venkataraman, T. Morgenlander, W. R. Na, M. Kula, T. Waugh, K. Morrison, C. Rewers, M. Longman, R. Round, J. Elledge, S. Ruczinski, I. Langmead, B. Larman, H. B. 2023-07-31 doi:10.1101/2023.07.30.551179 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Immunometabolic cues recompose and reprogram the microenvironment around biomaterials ]]> https://biorxiv.org/content/10.1101/2023.07.30.551180v1?rss=1 Maduka, C. V. Schmitter-Sanchez, A. D. Makela, A. V. Ural, E. Stivers, K. B. Pope, H. Kuhnert, M. M. Habeeb, O. M. Tundo, A. Alhaj, M. Kiselev, A. Chen, S. Olive, A. J. Hankenson, K. D. D. Narayan, R. Park, S. Elisseeff, J. H. Contag, C. H. 2023-07-31 doi:10.1101/2023.07.30.551180 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Combined, yet Separate: cocktails of carriers (not drugs) for α-particle therapy of solid tumors expressing moderate-to-low levels of targetable markers ]]> https://biorxiv.org/content/10.1101/2023.07.31.551152v1?rss=1 Nair, R. Prasad, A. Bhatavdekar, O. Sarkar, A. Gabrielson, K. L. Sofou, S. 2023-08-02 doi:10.1101/2023.07.31.551152 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets ]]> https://biorxiv.org/content/10.1101/2023.07.31.551302v1?rss=1 Ling, Y. H. Ye, J. Yu, C. Liang, C. Park, G. Corden, J. Wu, C. 2023-08-02 doi:10.1101/2023.07.31.551302 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Growth media affects susceptibility of air-lifted human nasal epithelial cell cultures to SARS-CoV2, but not Influenza A, virus infection. ]]> https://biorxiv.org/content/10.1101/2023.07.31.551381v1?rss=1 Resnick, J. D. Wilson, J. L. Anaya, E. U. Conte, A. Li, M. Zhong, W. Beer, M. Pekosz, A. 2023-08-02 doi:10.1101/2023.07.31.551381 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice ]]> https://biorxiv.org/content/10.1101/2023.08.01.551456v1?rss=1 Boukas, L. Luperchio, T. R. Razi, A. Hansen, K. D. Bjornsson, H. T. 2023-08-03 doi:10.1101/2023.08.01.551456 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Acetic acid is a superior acidifier for sub-nanogram and single cell proteomic studies ]]> https://biorxiv.org/content/10.1101/2023.08.01.551522v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@89a781org.highwire.dtl.DTLVardef@1540fa9org.highwire.dtl.DTLVardef@1d0260eorg.highwire.dtl.DTLVardef@727fcf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Orsburn, B. C. 2023-08-02 doi:10.1101/2023.08.01.551522 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes ]]> https://biorxiv.org/content/10.1101/2023.08.01.551528v1?rss=1 Zhang, X. Das, T. Kalab, P. Hayes, L. R. 2023-08-02 doi:10.1101/2023.08.01.551528 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Anopheles gambiae mosGILT regulates innate immune genes and zpg expression ]]> https://biorxiv.org/content/10.1101/2023.08.01.551536v1?rss=1 Arora, G. Tang, X. Cui, Y. Yang, J. Chuang, Y.-M. Joshi, J. Sajid, A. Dong, Y. Cresswell, P. Dimopoulos, G. Fikrig, E. 2023-08-02 doi:10.1101/2023.08.01.551536 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Tmem263 deletion disrupts the GH/IGF-1 axis and causes dwarfism and impairs skeletal acquisition ]]> https://biorxiv.org/content/10.1101/2023.08.02.551694v1?rss=1 Sarver, D. C. Garcia-Diaz, J. Riddle, R. C. Wong, G. W. 2023-08-03 doi:10.1101/2023.08.02.551694 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ A semi-automated method for quantifying optokinetic reflex tracking acuity ]]> https://biorxiv.org/content/10.1101/2023.08.03.551461v1?rss=1 Kiraly, J. K. Harris, S. C. Al-Khindi, T. Dunn, F. Kolodkin, A. L. 2023-08-06 doi:10.1101/2023.08.03.551461 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Multi-day Neuron Tracking in High Density Electrophysiology Recordings using EMD ]]> https://biorxiv.org/content/10.1101/2023.08.03.551724v1?rss=1 Harris, T. D. Yuan, A. X. Colonell, J. I. Lebedeva, A. Charles, A. 2023-08-05 doi:10.1101/2023.08.03.551724 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ A unifying computational account of temporal context effects in language across the human cortex ]]> https://biorxiv.org/content/10.1101/2023.08.03.551886v1?rss=1 Vo, V. A. Jain, S. Beckage, N. Chien, H.-Y. S. Obinwa, C. Huth, A. G. 2023-08-04 doi:10.1101/2023.08.03.551886 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ MEK inhibition enhances the antitumor effect of radiation therapy in NF1-deficient glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.08.04.552061v1?rss=1 Ioannou, M. Lalwani, K. Ayanlaja, A. A. Chinnasamy, V. Pratilas, C. A. Schreck, K. C. 2023-08-06 doi:10.1101/2023.08.04.552061 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ SynGAP regulates synaptic plasticity and cognition independent of its catalytic activity ]]> https://biorxiv.org/content/10.1101/2023.08.06.552111v1?rss=1 Araki, Y. Rajkovich, K. E. Gerber, E. E. Gamache, T. R. Johnson, R. C. Tran, T. H. Liu, B. Hong, I. Kirkwood, A. Huganir, R. L. 2023-08-06 doi:10.1101/2023.08.06.552111 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention ]]> https://biorxiv.org/content/10.1101/2023.08.06.552215v1?rss=1 dos Passos, P. M. Hemamali, E. H. Mamede, L. D. Hayes, L. R. Ayala, Y. M. 2023-08-07 doi:10.1101/2023.08.06.552215 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation ]]> https://biorxiv.org/content/10.1101/2023.08.07.552254v1?rss=1 Cheng, K. C. L. Frost, J. M. Sanchez-Luque, F. J. Garcia-Canadas, M. Taylor, D. Yang, W. R. Irayanar, B. Sampath, S. Patani, H. Agger, K. Helin, K. Ficz, G. Burns, K. H. Ewing, A. D. Garcia-Perez, J. L. Branco, M. R. 2023-08-07 doi:10.1101/2023.08.07.552254 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ The AKT2/SIRT5/TFEB pathway as a potential therapeutic target in atrophic AMD ]]> https://biorxiv.org/content/10.1101/2023.08.08.552343v1?rss=1 Ghosh, S. Sharma, R. Bammidi, S. Koontz, V. Nemani, M. Yazdankhah, M. Kedziora, K. M. Wallace, C. T. Yu-Wei, C. Franks, J. Bose, D. Rajasundaram, D. Hose, S. Sahel, J.-A. Puertollano, R. Finkel, T. Zigler, J. S. Sergeev, Y. Watkins, S. C. Goetzman, E. S. Flores-Bellver, M. Kaarniranta, K. Sodhi, A. Bharti, K. Handa, J. T. Sinha, D. 2023-08-09 doi:10.1101/2023.08.08.552343 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ In vivo Mapping of Cellular Resolution Neuropathology in Brain Ischemia by Diffusion MRI ]]> https://biorxiv.org/content/10.1101/2023.08.08.552374v1?rss=1 Wu, D. Turnbill, V. Lee, H.-H. Wang, X. Ba, R. Walczak, P. Martin, L. J. Fieremans, E. Novikov, D. S. Northington, F. J. Zhang, J. 2023-08-10 doi:10.1101/2023.08.08.552374 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. ]]> https://biorxiv.org/content/10.1101/2023.08.08.552451v1?rss=1 Lyu, P. Iribarne, M. Serjanov, D. Zhai, Y. Hoang, T. Campbell, L. Boyd, P. Palazzo, I. Nagashima, M. Silva, N. J. Hitchcock, P. Qian, J. Hyde, D. Blackshaw, S. 2023-08-08 doi:10.1101/2023.08.08.552451 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ The Dynamic Response of Human Lungs Due to Underwater Shock Wave Exposure ]]> https://biorxiv.org/content/10.1101/2023.08.08.552452v1?rss=1 Bar-Kochba, E. Iwaskiw, A. S. Dunn, J. M. Ott, K. A. Harrigan, T. P. Demetropoulos, C. K. 2023-08-12 doi:10.1101/2023.08.08.552452 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Plasma Glycomic Markers of Accelerated Biological Aging During Chronic HIV Infection ]]> https://biorxiv.org/content/10.1101/2023.08.09.551369v1?rss=1 Giron, L. B. Liu, Q. Adeniji, O. S. Yin, X. Kannan, T. Ding, J. Lu, D. Y. Langan, S. Zhang, J. Azevedo, J. L. L. C. Hanna, D. B. Ofotokun, I. Lazar, J. Fischl, M. A. Haberlen, S. Macatangay, B. Adimora, A. A. Jamieson, B. D. Rinaldo, C. Merenstein, D. Roan, N. R. Kutsch, O. Gange, S. Wolinsky, S. Witt, M. Post, W. S. Kossenkov, A. Landay, A. Frank, I. Tien, P. C. Gross, R. Brown, T. T. Mohsen, M. A. 2023-08-10 doi:10.1101/2023.08.09.551369 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ The heme oxygenase-1 metalloporphyrin inhibitor stannsoporfin enhances the bactericidal activity of a novel regimen for multidrug-resistant tuberculosis in a murine model ]]> https://biorxiv.org/content/10.1101/2023.08.09.552716v1?rss=1 Ruelas Castillo, J. Neupane, P. Karanika, S. Krug, S. Quijada, D. Garcia, A. Ayeh, S. Costa, D. L. Sher, A. Fotouhi, N. Serbina, N. Karakousis, P. C. 2023-08-09 doi:10.1101/2023.08.09.552716 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Plug-and-play protein biosensors using aptamer-regulated in vitro transcription ]]> https://biorxiv.org/content/10.1101/2023.08.10.552680v1?rss=1 Lee, H. Xie, T. Yu, X. Schaffter, S. W. Schulman, R. 2023-08-14 doi:10.1101/2023.08.10.552680 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Sphingolipid metabolism is spatially regulated in the developing embryo by SOXE genes ]]> https://biorxiv.org/content/10.1101/2023.08.10.552770v1?rss=1 Piacentino, M. L. Fasse, A. J. Camacho-Avila, A. Grabylnikov, I. Bronner, M. E. 2023-08-11 doi:10.1101/2023.08.10.552770 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial ]]> https://biorxiv.org/content/10.1101/2023.08.11.553000v1?rss=1 Zhang, S. Deshpande, A. Verma, B. K. Wang, H. Mi, H. Yuan, L. Ho, W. J. Jaffee, E. M. Zhu, Q. Anders, R. A. Yarchoan, M. Kagohara, L. T. Fertig, E. J. Popel, A. S. 2023-08-15 doi:10.1101/2023.08.11.553000 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Cerebellar damage impairs long-term but not short-term sensorimotor memory ]]> https://biorxiv.org/content/10.1101/2023.08.11.553008v1?rss=1 25 sec). This dissociation uncovers a new role for the cerebellum as a gateway for the formation of long-term but not short-term sensorimotor memories, mirroring the role of the medial temporal lobe for declarative memories. It thus reveals the existence of distinct neural substrates for short-term and long-term sensorimotor memory, and it explains both newly-identified trial-to-trial differences and long-standing study-to-study differences in the effects of cerebellar damage on sensorimotor learning ability. Significance StatementA key discovery about the neural underpinnings of memory, made more than half a century ago, is that long-term, but not short-term, memory formation depends on neural structures in the brains medial temporal lobe (MTL). However, this dichotomy holds only for declarative memories - memories for explicit facts such as names and dates - as long-term procedural memories - memories for implicit knowledge such as sensorimotor skills - are largely unaffected even with substantial MTL damage. Here we demonstrate that the formation of long-term, but not short-term, sensorimotor memory depends on a neural structure known as the cerebellum, and we show that this finding explains the variability previously reported in the extent to which cerebellar damage affects sensorimotor learning. ]]> Hadjiosif, A. M. Gibo, T. L. Smith, M. A. 2023-08-12 doi:10.1101/2023.08.11.553008 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Reduced brain glutathione levels during normal aging are associated with visuospatial memory ]]> https://biorxiv.org/content/10.1101/2023.08.13.553100v1?rss=1 Hu, X. Pan, K. Zhao, M. Lv, J. Wang, J. Zhang, X. Liu, Y. Song, y. Gudmundson, A. T. Edden, R. A. E. Ren, F. Zhang, T. gao, f. 2023-08-15 doi:10.1101/2023.08.13.553100 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Protective concentric cardiac proteostasis adaptations to chronic cAMP-stress at young ages wanes in advanced age leading to accelerated cardiac aging ]]> https://biorxiv.org/content/10.1101/2023.08.13.553128v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@73ff64org.highwire.dtl.DTLVardef@1842158org.highwire.dtl.DTLVardef@1a92684org.highwire.dtl.DTLVardef@1fe596_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Perino, M. G. Calvo-Rubio Barrera, M. Agnetti, G. Ranek, M. Riordon, D. Morrell, C. Chakir, K. Qu, J. Tarasov, K. Lakatta, E. 2023-08-14 doi:10.1101/2023.08.13.553128 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ H2-O deficiency promotes regulatory T cell differentiation and CD4 hyperactivity ]]> https://biorxiv.org/content/10.1101/2023.08.14.553240v1?rss=1 Welsh, R. A. Song, N. Park, C.-s. Peske, J. D. Sadegh-Nasseri, S. 2023-08-16 doi:10.1101/2023.08.14.553240 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Crowdsourcing and phylogenetic modelling reveal parrot tool use is not rare ]]> https://biorxiv.org/content/10.1101/2023.08.14.553302v1?rss=1 Bastos, A. P. Claessens, S. Nelson, X. J. Welch, D. Atkinson, Q. D. Taylor, A. H. 2023-08-14 doi:10.1101/2023.08.14.553302 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Shining Light on Osteoarthritis: Spatially Offset Raman Spectroscopy as a Window into Cartilage Health ]]> https://biorxiv.org/content/10.1101/2023.08.14.553328v1?rss=1 Raj, P. Wu, L. Almeida, C. Conway, L. Tanwar, S. Middendorf, J. Barman, I. 2023-08-16 doi:10.1101/2023.08.14.553328 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Sigmoni: classification of nanopore signal with a compressed pangenome index ]]> https://biorxiv.org/content/10.1101/2023.08.15.553308v1?rss=1 Shivakumar, V. S. Ahmed, O. Y. Kovaka, S. Zakeri, M. Langmead, B. 2023-08-17 doi:10.1101/2023.08.15.553308 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Dopamine Release Plateau and Outcome Signals in Dorsal Striatum Contrast with Classic Reinforcement Learning Formulations ]]> https://biorxiv.org/content/10.1101/2023.08.15.553421v1?rss=1 Kim, M. J. Gibson, D. J. Hu, D. Mahar, A. Schofield, C. J. Sompolpong, P. Yoshida, T. Tran, K. T. Graybiel, A. M. 2023-08-17 doi:10.1101/2023.08.15.553421 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ A neurogenetic toolkit to decode Anopheles gambiae olfaction ]]> https://biorxiv.org/content/10.1101/2023.08.16.553590v1?rss=1 Giraldo, D. Hammond, A. M. Wu, J. Feole, B. Al-Saloum, N. McMeniman, C. J. 2023-08-17 doi:10.1101/2023.08.16.553590 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Trigeminal innervation and tactile responses in mouse tongue ]]> https://biorxiv.org/content/10.1101/2023.08.17.553449v1?rss=1 Zhang, L. Nagel, M. Olson, W. P. Chesler, A. T. O'Connor, D. H. 2023-08-19 doi:10.1101/2023.08.17.553449 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling ]]> https://biorxiv.org/content/10.1101/2023.08.19.553321v1?rss=1 Huang, B. Abedi, M. Ahn, G. Coventry, B. Sappington, I. Wang, R. Schlichthaerle, T. Zhang, J. Z. Wang, Y. Goreshnik, I. Chiu, C. W. Chazin-Gray, A. Chan, S. Gerben, S. Murray, A. Wang, S. O'Neill, J. Yeh, R. Misquith, A. Wolf, A. Tomasovic, L. M. Piraner, D. I. Gonzalez, M. J. D. Bennett, N. R. Venkatesh, P. Ahlrichs, M. Dobbins, C. Yang, W. Wang, X. Vafeados, D. Mout, R. Shivaei, S. Cao, L. Carter, L. Stewart, L. Spangler, J. B. Bernardes, G. J. L. Roybal, K. T. Greisen, P. J. Li, X. Bertozzi, C. Baker, D. 2023-08-21 doi:10.1101/2023.08.19.553321 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Rule-based modulation of a sensorimotor transformation across cortical areas ]]> https://biorxiv.org/content/10.1101/2023.08.21.554194v1?rss=1 Chang, Y.-T. Finkel, E. A. Xu, D. O'Connor, D. H. 2023-08-22 doi:10.1101/2023.08.21.554194 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Intersectin and Endophilin condensates prime synaptic vesicles for release site replenishment ]]> https://biorxiv.org/content/10.1101/2023.08.22.554276v1?rss=1 Ogunmowo, T. Hoffmann, C. Pepper, R. Wang, H. Gowrisankaran, S. Ho, A. Raychaudhuri, S. Cooper, B. H. Milosevic, I. Milovanovic, D. Watanabe, S. 2023-08-23 doi:10.1101/2023.08.22.554276 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Neural specialization for 'visual' concepts emerges in the absence of vision ]]> https://biorxiv.org/content/10.1101/2023.08.23.552701v1?rss=1 Hauptman, M. Elli, G. Pant, R. Bedny, M. 2023-08-24 doi:10.1101/2023.08.23.552701 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings ]]> https://biorxiv.org/content/10.1101/2023.08.23.554527v1?rss=1 Ye, Z. Shelton, A. M. Shaker, J. R. Boussard, J. M. Colonell, J. Minavi, S. Chen, S. Windolf, C. Hurwitz, C. Namima, T. Pedraja, F. Weiss, S. Raducanu, B. Ness, T. Einevoll, G. T. Laurent, G. Sawtell, N. B. Bair, W. Pasupathy, A. Mora-Lopez, C. Dutta, B. Paninski, L. Siegle, J. H. Koch, C. Olsen, S. r. Harris, T. D. Steinmetz, N. A. 2023-08-24 doi:10.1101/2023.08.23.554527 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Nitric Oxide modulates spontaneous Ca2+ release and ventricular arrhythmias during β adrenergic signalling through S-nitrosylation of Calcium/Calmodulin dependent kinase II ]]> https://biorxiv.org/content/10.1101/2023.08.23.554546v1?rss=1 Power, A. S. Asamudo, E. Worthington, L. P. Alim, C. C. Parackal, R. Wallace, R. S. Ebenebe, O. V. Heller Brown, J. Kohr, M. J. Bers, D. M. Erickson, J. 2023-08-25 doi:10.1101/2023.08.23.554546 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity. ]]> https://biorxiv.org/content/10.1101/2023.08.24.554647v1?rss=1 Stevenson, D. W. Ramakrishnan, S. Alves, C. d. S. Coelho, L. A. Kramer, M. Goodwin, S. Ramos, O. M. Eshel, G. Sondervan, V. M. Frangos, S. Zumajo-Cardona, C. Jenike, K. Ou, S. Wang, X. Lee, Y. P. Loke, S. Rossetto, M. McPherson, H. Nigris, S. Moschin, S. Little, D. P. Katari, M. S. Varala, K. Kolokotronis, S.-O. Ambrose, B. Croft, L. J. Coruzzi, G. M. Schatz, M. McCombie, W. R. Martienssen, R. A. 2023-08-24 doi:10.1101/2023.08.24.554647 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Time-Resolved Cryo-EM Specimen Preparation with Single Millisecond Precision ]]> https://biorxiv.org/content/10.1101/2023.08.24.554704v1?rss=1 Montano Romero, A. Bonin, C. Twomey, E. C. 2023-08-24 doi:10.1101/2023.08.24.554704 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Effort cost of reaching prompts vigor reduction in older adults ]]> https://biorxiv.org/content/10.1101/2023.08.28.555022v1?rss=1 Summerside, E. M. Courter, R. J. Shadmehr, R. Ahmed, A. A. 2023-08-29 doi:10.1101/2023.08.28.555022 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination ]]> https://biorxiv.org/content/10.1101/2023.08.28.555084v1?rss=1 Gharibani, P. Abramson, E. Shanmukha, S. Smith, M. D. Godfrey, W. H. Lee, J. J. Hu, J. Baydyuk, M. Dorion, M.-F. Deng, X. Guo, Y. Hwang, S. Huang, J. K. Calabresi, P. A. Kornberg, M. D. Kim, P. M. 2023-08-29 doi:10.1101/2023.08.28.555084 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Tumor-Specific CD8+ T Cells from the Bone Marrow Resist Exhaustion and Exhibit Increased Persistence in Tumor-Bearing Hosts as Compared to Tumor Infiltrating Lymphocytes ]]> https://biorxiv.org/content/10.1101/2023.08.28.555119v1?rss=1 Zawidzka, E. M. Biavati, L. Thomas, A. Zanettini, C. L. Marchionni, L. Leone, R. Borrello, I. 2023-08-29 doi:10.1101/2023.08.28.555119 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ OpgH is an essential regulator of Caulobacter morphology ]]> https://biorxiv.org/content/10.1101/2023.08.28.555136v1?rss=1 Daitch, A. K. Goley, E. D. 2023-08-28 doi:10.1101/2023.08.28.555136 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ A subclass of evening cells promotes the switch from arousal to sleep at dusk ]]> https://biorxiv.org/content/10.1101/2023.08.28.555147v1?rss=1 Brown, M. P. Verma, S. Palmer, I. Zuniga, A. G. Rosensweig, C. Keles, M. F. Wu, M. N. 2023-08-29 doi:10.1101/2023.08.28.555147 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ SCP Viz - A universal graphical user interface for single protein analysis in single cell proteomics datasets ]]> https://biorxiv.org/content/10.1101/2023.08.29.555397v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1c9d1d5org.highwire.dtl.DTLVardef@eefcfeorg.highwire.dtl.DTLVardef@23c098org.highwire.dtl.DTLVardef@1394161_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Warshanna, A. Orsburn, B. 2023-08-29 doi:10.1101/2023.08.29.555397 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Loss of finger control complexity and intrusion of flexor biases are dissociable in finger individuation impairment after stroke ]]> https://biorxiv.org/content/10.1101/2023.08.29.555444v1?rss=1 Xu, J. Ma, T. Kumar, S. Olds, K. Brown, J. Carducci, J. Forrence, A. Krakauer, J. W. 2023-08-31 doi:10.1101/2023.08.29.555444 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Discovering optimal kinetic pathways for self-assembly using automatic differentiation ]]> https://biorxiv.org/content/10.1101/2023.08.30.555551v1?rss=1 Jhaveri, A. Loggia, S. Qian, Y. Johnson, M. E. 2023-09-01 doi:10.1101/2023.08.30.555551 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Gene count normalization in single-cell imaging-based spatially resolved transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.08.30.555624v1?rss=1 Atta, L. Clifton, K. Anant, M. Fan, J. 2023-09-01 doi:10.1101/2023.08.30.555624 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Ras-mediated homeostatic control of front-back signaling dictates cell polarity ]]> https://biorxiv.org/content/10.1101/2023.08.30.555648v1?rss=1 Lin, Y. Pal, D. S. Banerjee, P. Banerjee, T. Qin, G. Deng, Y. Borleis, J. Iglesias, P. A. Devreotes, P. 2023-09-01 doi:10.1101/2023.08.30.555648 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Electrostatic modulation of signaling at cell membrane: Waveform- and time-dependent electric control of ERK dynamics ]]> https://biorxiv.org/content/10.1101/2023.08.31.555453v1?rss=1 Hu, M. Li, H. Zhu, K. Guo, L. Zhao, M. Zhan, H. Devreotes, P. Qing, Q. 2023-09-03 doi:10.1101/2023.08.31.555453 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ A Toxoplasma gondii putative arginine transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation ]]> https://biorxiv.org/content/10.1101/2023.08.31.555807v1?rss=1 Piro, F. Masci, S. Kannan, G. Focaia, R. Schultz, T. L. Carruthers, V. B. Di Cristina, M. 2023-09-01 doi:10.1101/2023.08.31.555807 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Cytoskeletal activation of NHE1 regulates cell volume and DNA methylation ]]> https://biorxiv.org/content/10.1101/2023.08.31.555808v1?rss=1 Ni, Q. Ge, Z. Li, Y. Shatkin, G. Fu, J. Bera, K. Yang, Y. Wang, Y. Sen, A. Wu, Y. Vasconcelosi, A. C. N. Feinberg, A. P. Konstantopoulos, K. Sun, S. X. 2023-09-03 doi:10.1101/2023.08.31.555808 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states ]]> https://biorxiv.org/content/10.1101/2023.08.31.555823v1?rss=1 Balasubramanian, R. Kizhatil, K. Li, T. Tolman, N. Bhandari, A. Clark, G. Bupp-Chickering, V. Zhou, S. Peregrin, J. Simon, M. Montgomery, C. Qian, J. John, S. 2023-09-03 doi:10.1101/2023.08.31.555823 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ AP profiling resolves co-translational folding pathway and chaperone interactions in vivo ]]> https://biorxiv.org/content/10.1101/2023.09.01.555749v1?rss=1 Chen, X. Kaiser, C. 2023-09-01 doi:10.1101/2023.09.01.555749 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Galvanic vs. Pulsatile Effects on Decision-Making Networks: Reshaping the Neural Activation Landscape ]]> https://biorxiv.org/content/10.1101/2023.09.01.555903v1?rss=1 1s), has re-emerged as an alternative to pulsatile stimulation. In this paper, we use a winner-take-all decision-making cortical network model to investigate differences between pulsatile and galvanic stimulation in the context of a perceptual decision-making task. Based on previous work, we hypothesized that galvanic stimulation would produce more spatiotemporally distributed, network-sensitive neural responses, while pulsatile stimulation would produce highly synchronized activation of a limited group of neurons. Our results in-silico support these hypotheses for low-amplitude galvanic stimulation but deviate when galvanic amplitudes are large enough to directly activate or block nearby neurons. We conclude that with careful parametrization, galvanic stimulation could overcome some limitations of pulsatile stimulation to deliver more naturalistic firing patterns in the group of targeted neurons. ]]> Adkisson, P. W. Steinhardt, C. R. Fridman, G. Y. 2023-09-05 doi:10.1101/2023.09.01.555903 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ HCN channels sense temperature and determine heart rate responses to heat ]]> https://biorxiv.org/content/10.1101/2023.09.02.556046v1?rss=1 Wu, Y. Wang, Q. Granger, J. Reyes Gaido, O. E. Aguilar, E. N. Ludwig, A. Moroni, A. Bianchet, M. A. Anderson, M. E. 2023-09-03 doi:10.1101/2023.09.02.556046 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains ]]> https://biorxiv.org/content/10.1101/2023.09.04.555754v1?rss=1 Guo, L. Mann, J. R. Mauna, J. C. Copley, K. E. Wang, H. Rubien, J. D. Odeh, H. M. Lin, J. Lee, B. L. Ganser, L. Robinson, E. Kim, K. M. Murthy, A. C. Paul, T. Portz, B. Gleixner, A. M. Diaz, Z. Carey, J. L. Smirnov, A. Padilla, G. Lavorando, E. Espy, C. Shang, Y. Huang, E. J. Chesi, A. Fawzi, N. L. Myong, S. Donnelly, C. J. Shorter, J. 2023-09-04 doi:10.1101/2023.09.04.555754 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Hopanoid lipids promote soybean-Bradyrhizobium symbiosis ]]> https://biorxiv.org/content/10.1101/2023.09.04.556284v1?rss=1 Pan, H. Shim, A. Lubin, M. B. Belin, B. J. 2023-09-05 doi:10.1101/2023.09.04.556284 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Enriched Single-Nucleus RNA-Sequencing reveals unique attributes of distal convoluted tubule cells ]]> https://biorxiv.org/content/10.1101/2023.09.05.555810v1?rss=1 Su, X.-T. Reyes, J. V. Lackey, A. E. Maeoka, Y. Cornelius, R. J. McCormick, J. A. Yang, C.-L. Jung, H. J. Welling, P. A. Nelson, J. W. Ellison, D. H. 2023-09-06 doi:10.1101/2023.09.05.555810 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Convergent alterations in the tumor microenvironment of MYC-driven human and murine prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.09.07.553268v1?rss=1 Graham, M. K. Wang, R. Chikarmane, R. Wodu, B. Vaghasia, A. Gupta, A. Zheng, Q. Hicks, J. Sysa-Shah, P. Pan, X. Castagna, N. Liu, J. Meyers, J. Skaist, A. Zhang, Y. Schuebel, K. Simons, B. Bieberich, C. J. Nelson, W. Lupold, S. E. DeWeese, T. L. De Marzo, A. M. Yegnasubramanian, S. 2023-09-08 doi:10.1101/2023.09.07.553268 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Subchronic exposure to ambient PM2.5 impairs novelty recognition and spatial memory ]]> https://biorxiv.org/content/10.1101/2023.09.07.556582v1?rss=1 Kim, S.-H. Das, D. Sille, F. C. M. Ramachandran, G. Biswal, S. 2023-09-12 doi:10.1101/2023.09.07.556582 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ "Surviving and Thriving": Evidence for Cortical GABA Stabilization in Cognitively-Intact Oldest-Old Adults ]]> https://biorxiv.org/content/10.1101/2023.09.08.556410v1?rss=1 Britton, M. K. Jensen, G. Edden, R. A. Puts, N. A. Nolin, S. A. Merritt, S. S. Rezaei, R. F. Forbes, M. Johnson, K. J. Bharadwaj, P. Franchetti, M. K. Raichlen, D. A. Jessup, C. J. Hishaw, G. A. Van Etten, E. J. Gudmundson, A. T. Murali-Manohar, S. Cowart, H. Trouard, T. P. Geldmacher, D. S. Wadley, V. G. Alperin, N. Levin, B. E. Rundek, T. Visscher, K. M. Woods, A. J. Alexander, G. E. Cohen, R. A. Porges, E. C. 2023-09-09 doi:10.1101/2023.09.08.556410 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Intrinsic and extrinsic factors regulate FtsZ function in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2023.09.08.556907v1?rss=1 Barrows, J. M. Anderson, A. S. Talavera-Figueroa, B. K. Goley, E. D. 2023-09-10 doi:10.1101/2023.09.08.556907 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium ]]> https://biorxiv.org/content/10.1101/2023.09.10.555215v1?rss=1 Jiang, M.-Z. Gaynor, S. M. Li, X. Van Buren, E. Stilp, A. Buth, E. Wang, F. F. Manansala, R. Gogarten, S. M. Li, Z. Polfus, L. M. Salimi, S. Bis, J. C. Pankratz, N. Yanek, L. R. Durda, P. Tracy, R. P. Rich, S. S. Rotter, J. I. Mitchell, B. D. Lewis, J. P. Psaty, B. M. Pratte, K. A. Silverman, E. K. Kaplan, R. C. Avery, C. North, K. Mathias, R. A. Faraday, N. Lin, H. Wang, B. Carson, A. P. Norwood, A. F. Gibbs, R. A. Kooperberg, C. Lundin, J. Peters, U. Dupuis, J. Hou, L. Fornage, M. Benjamin, E. J. Reiner, A. P. Bowler, R. P. Lin, X. Auer, P. L. Raf 2023-09-12 doi:10.1101/2023.09.10.555215 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Disease related changes in ATAC-Seq of more than 450 iPSC-derived motor neuron lines from ALS patients and controls ]]> https://biorxiv.org/content/10.1101/2023.09.11.557005v1?rss=1 Tsitkov, S. Valentine, K. Kozareva, V. Donde, A. Frank, A. Lei, S. Answer ALS Consortium, Van Eyk, J. Finkbeiner, S. Rothstein, J. Thompson, L. Sareen, D. Svendsen, C. N. Fraenkel, E. 2023-09-13 doi:10.1101/2023.09.11.557005 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Regulation of interferon signaling by transposon exonization ]]> https://biorxiv.org/content/10.1101/2023.09.11.557241v1?rss=1 Pasquesi, G. I. M. Allen, H. Ivancevic, A. Barbachano-Guerrero, A. Joyner, O. Guo, K. Simpson, D. M. Gapin, K. Horton, I. Nguyen, L. Yang, Q. Warren, C. J. Florea, L. D. Bitler, B. G. Santiago, M. L. Sawyer, S. L. Chuong, E. B. 2023-09-15 doi:10.1101/2023.09.11.557241 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ DBT is a metabolic switch for maintenance of proteostasis under proteasomal impairment ]]> https://biorxiv.org/content/10.1101/2023.09.12.556394v1?rss=1 Hwang, R.-D. Lu, Y. Tang, Q. Periz, G. Park, G. Li, X. Liu, Y. Zhang, T. Wang, J. 2023-09-13 doi:10.1101/2023.09.12.556394 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ X chromosome encoded histone demethylase UTX regulates mammalian axon regeneration via microRNA-124 ]]> https://biorxiv.org/content/10.1101/2023.09.12.557354v1?rss=1 Yang, S.-G. Wang, X.-W. Li, C.-P. Huang, T. Li, Q. Zhao, L. Qian, C. Saijilafu, Qian, J. Liu, C.-M. Zhou, F.-Q. 2023-09-13 doi:10.1101/2023.09.12.557354 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Rat Wetness Response: Sensory Cues, Behavior & Fur-based Drying ]]> https://biorxiv.org/content/10.1101/2023.09.13.557175v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@ea8b80org.highwire.dtl.DTLVardef@6ca3d9org.highwire.dtl.DTLVardef@78fccdorg.highwire.dtl.DTLVardef@11d0c83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Triumph Attah, A. Negron-Moreno, P. Amigo-Duran, M. Zhang, L. Kenngott, M. Brecht, M. Clemens, A. M. 2023-09-13 doi:10.1101/2023.09.13.557175 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Measuring, visualizing and diagnosing reference bias with biastools ]]> https://biorxiv.org/content/10.1101/2023.09.13.557552v1?rss=1 Lin, M.-J. Iyer, S. Chen, N.-C. Langmead, B. 2023-09-16 doi:10.1101/2023.09.13.557552 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Secreted footprints let cells switch between confined, oscillatory, and exploratory migration ]]> https://biorxiv.org/content/10.1101/2023.09.14.557437v1?rss=1 Ipina, E. P. D'Alessandro, J. Ladoux, B. Camley, B. A. 2023-09-16 doi:10.1101/2023.09.14.557437 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Linking Gba1 E326K mutation to microglia activation and mild age-dependent dopaminergic Neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.09.14.557673v1?rss=1 Kweon, S. H. Ryu, H. G. Park, H. Lee, S. Kim, N. Kwon, S.-H. Ma, S. Kim, S. Ko, H. S. 2023-09-14 doi:10.1101/2023.09.14.557673 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ A novel approach to increase glial cell populations in brain microphysiological systems ]]> https://biorxiv.org/content/10.1101/2023.09.14.557775v1?rss=1 Pantoja, I. E. M. Ding, L. Leite, P. E. C. Marques, S. A. Din, D. M. A. Romero, J. C. Zack, D. J. Chamling, X. Smirnova, L. 2023-09-15 doi:10.1101/2023.09.14.557775 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Diverse Plant-Parasitic Nematodes are Selectively Killed by Oxadiazole Thioether Pro-Nematicides ]]> https://biorxiv.org/content/10.1101/2023.09.14.557801v1?rss=1 Knox, J. Burns, A. R. Cooke, B. Cammalleri, S. R. Kitner, M. Ching, J. Castelli, J. M. P. Puumala, E. Snider, J. Koury, E. Collins, J. B. Andersen, E. C. Stagljar, I. Cowen, L. Lautens, M. Zasada, I. Roy, P. 2023-09-17 doi:10.1101/2023.09.14.557801 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Unravelling Paralog-Specific Notch Signaling through Ternary Complex Stability and Transcriptional Activation Measurements Using Chimeric Receptors ]]> https://biorxiv.org/content/10.1101/2023.09.15.557970v1?rss=1 Ramsey, K. M. Barrick, D. 2023-09-17 doi:10.1101/2023.09.15.557970 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease ]]> https://biorxiv.org/content/10.1101/2023.09.17.557749v1?rss=1 Weinstock, J. S. Arce, M. M. Freimer, J. W. Ota, M. Marson, A. Battle, A. Pritchard, J. K. 2023-09-17 doi:10.1101/2023.09.17.557749 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Digitize your Biology! Modeling multicellular systems through interpretable cell behavior ]]> https://biorxiv.org/content/10.1101/2023.09.17.557982v1?rss=1 Johnson, J. A. I. Stein-O'Brien, G. L. Booth, M. Heiland, R. Kurtoglu, F. Bergman, D. Bucher, E. Deshpande, A. Forjaz, A. Getz, M. Godet, I. Lyman, M. Metzcar, J. Mitchell, J. Raddatz, A. Rocha, H. L. Solorzano, J. Sundus, A. Wang, Y. Gilkes, D. M. Kagohara, L. T. Kiemen, A. L. Thompson, E. D. Wirtz, D. Wu, P.-H. Zaidi, N. Zheng, L. Zimmerman, J. W. Jaffee, E. M. Chang, Y. H. Coussens, L. Gray, J. Heiser, L. M. Fertig, E. J. Macklin, P. 2023-09-17 doi:10.1101/2023.09.17.557982 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Motivation upregulates the adaptive response in sensorimotor learning ]]> https://biorxiv.org/content/10.1101/2023.09.17.558102v1?rss=1 Khatib, S. Chib, V. S. Mawase, F. 2023-09-17 doi:10.1101/2023.09.17.558102 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Context-dependent hyperactivity in syngap1a and syngap1b zebrafish autism models. ]]> https://biorxiv.org/content/10.1101/2023.09.20.557316v1?rss=1 Sumathipala, S. H. Khan, S. Kozol, R. A. Araki, Y. Syed, S. Huganir, R. L. Dallman, J. 2023-09-21 doi:10.1101/2023.09.20.557316 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Dopamine and schizophrenia from bench to bedside: Discovery of a striatal co-expression risk gene set that predicts in vivo measures of striatal function. ]]> https://biorxiv.org/content/10.1101/2023.09.20.558594v1?rss=1 Sportelli, L. Eisenberg, D. P. Passiatore, R. D'Ambrosio, E. Antonucci, L. A. Chen, Q. Czarapata, J. Goldman, A. L. Gregory, M. Griffiths, K. Hyde, T. M. Kleinman, J. E. Pardinas, A. F. Parihar, M. Popolizio, T. Rampino, A. Shin, J. H. Veronese, M. Ulrich, W. S. Zink, C. F. Bertolino, A. Howes, O. D. Berman, K. F. Weinberger, D. Pergola, G. 2023-09-21 doi:10.1101/2023.09.20.558594 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis ]]> https://biorxiv.org/content/10.1101/2023.09.21.558797v1?rss=1 Imoto, Y. Xue, J. Luo, L. Raychaudhuri, S. Itoh, K. Craft, G. E. Kwan, A. H. Mackay, J. Ha, T. Watanabe, S. Robinson, P. J. 2023-09-21 doi:10.1101/2023.09.21.558797 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Placebo treatment affects brain systems related to affective and cognitive processes, but not nociceptive pain ]]> https://biorxiv.org/content/10.1101/2023.09.21.558825v1?rss=1 Botvinik-Nezer, R. Petre, B. Ceko, M. Lindquist, M. A. Friedman, N. P. Wager, T. D. 2023-09-22 doi:10.1101/2023.09.21.558825 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ B cells occupy a unique, dynamic, biological niche within the human myocardium ]]> https://biorxiv.org/content/10.1101/2023.09.21.558902v1?rss=1 Bermea, K. C. Duque, C. Cohen, C. D. Bhalodia, A. Rousseau, S. Lovell, J. Zita, M. D. Mugnier, M. C. Adamo, L. 2023-09-23 doi:10.1101/2023.09.21.558902 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Continuous motor skills as flexible control policies: a video game study ]]> https://biorxiv.org/content/10.1101/2023.09.21.558913v1?rss=1 Huberdeau, D. M. Haith, A. M. Krakauer, J. W. 2023-09-22 doi:10.1101/2023.09.21.558913 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Light affects the prefrontal cortex via intrinsically photosensitive retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2023.09.22.556752v1?rss=1 Lazzerini Ospri, L. Zhan, J. Thomsen, M. Wang, H. Messanvi, F. du Hoffmann, J. Cravedi, K. Chudasama, Y. Zhao, H. Hattar, S. Komal, R. 2023-09-25 doi:10.1101/2023.09.22.556752 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Neural stem cells protect the integrity of blood-brain barrier via the p38, JNK and ERK1/2 pathways following intracerebral hemorrhage in rats ]]> https://biorxiv.org/content/10.1101/2023.09.22.558889v1?rss=1 Sun, J. yang, x. Kim, T. J. Kim, Y.-J. Wei, Z. Han, L. Carmichael, A. Stanciu, N. Ko, S.-B. Nan, G. Yoon, B.-W. 2023-09-22 doi:10.1101/2023.09.22.558889 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Synthetic control of actin polymerization and symmetry breaking in activeprotocells ]]> https://biorxiv.org/content/10.1101/2023.09.22.559060v1?rss=1 Razavi, S. Wong, F. Abubaker-Sharif, B. Matsubayashi, H. T. Nakamura, H. Sandoval, E. Robinson, D. N. Chen, B. Liu, J. Iglesias, P. A. Inoue, T. 2023-09-23 doi:10.1101/2023.09.22.559060 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Male violence disrupts estrogen receptor β signaling in the female hippocampus ]]> https://biorxiv.org/content/10.1101/2023.09.23.559092v1?rss=1 Agrimi, J. Bernardele, L. Sbaiti, N. Canato, M. Marchionni, I. Oeing, C. U. Vignoli, B. Canossa, M. Kaludercic, N. Lodovichi, C. Dal Maschio, M. Paolocci, N. 2023-09-23 doi:10.1101/2023.09.23.559092 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells ]]> https://biorxiv.org/content/10.1101/2023.09.23.559117v1?rss=1 Johnson, B. A. Liu, A. Z. Bi, T. Dong, Y. Li, T. Zhou, D. Narkar, A. Wu, Y. Sun, S. Larman, T. C. Zhu, J. Li, R. 2023-09-24 doi:10.1101/2023.09.23.559117 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Automatic learning mechanisms for flexible human locomotion. ]]> https://biorxiv.org/content/10.1101/2023.09.25.559267v1?rss=1 Rossi, C. Leech, K. Roemmich, R. T. Bastian, A. J. 2023-09-25 doi:10.1101/2023.09.25.559267 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata ]]> https://biorxiv.org/content/10.1101/2023.09.25.559325v1?rss=1 Pavesic, M. W. Gale, A. N. Nickels, T. J. Harrington, A. A. Bussey, M. Cunningham, K. W. 2023-09-25 doi:10.1101/2023.09.25.559325 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Tenofovir Activation is Diminished in the Brain and Liver of Creatine Kinase Brain-Type Knockout Mice ]]> https://biorxiv.org/content/10.1101/2023.09.25.559370v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1f8d26aorg.highwire.dtl.DTLVardef@be3d8corg.highwire.dtl.DTLVardef@1bab6d0org.highwire.dtl.DTLVardef@1381293_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Eberhard, C. D. Mosher, E. P. Bumpus, N. N. Orsburn, B. C. 2023-09-26 doi:10.1101/2023.09.25.559370 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Sleep and circadian rhythm disruption by NPTX2 loss of function ]]> https://biorxiv.org/content/10.1101/2023.09.26.559408v1?rss=1 Roh, S.-E. Xiao, M. Delgado, A. Kwak, C. Savonenko, A. Bakker, A. Kwon, H.-B. Worley, P. 2023-09-27 doi:10.1101/2023.09.26.559408 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Sensorimotor Integration Supporting Perception Requires Syngap1 Expression in Cortex ]]> https://biorxiv.org/content/10.1101/2023.09.27.559787v1?rss=1 Vaissiere, T. Michaelson, S. Creson, T. Goins, J. Fürth, D. Balazsfi, D. Rojas, C. Golovin, R. Meletis, K. Miller, C. O'Connor, D. H. Rumbaugh, G. 2023-09-27 doi:10.1101/2023.09.27.559787 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Brain Glutathione and GABA+ levels in autistic children ]]> https://biorxiv.org/content/10.1101/2023.09.28.559718v1?rss=1 Song, Y. Hupfeld, K. E. Davies-Jenkins, C. W. Zöllner, H. J. Murali-Manohar, S. Abdul-Nashirudeen, M. Crocetti, D. Yedavalli, V. Oeltzschner, G. Alessi, N. Batschelett, M. A. Puts, N. A. J. Mostofsky, S. H. Edden, R. A. E. 2023-09-29 doi:10.1101/2023.09.28.559718 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ An autophagy adaptor TRIAD3A promotes tau fibrillation by phase separation ]]> https://biorxiv.org/content/10.1101/2023.09.28.559893v1?rss=1 Zhou, J. Chuang, Y. a. Redding-Ochoa, J. Platero, A. Barrett, A. Troncoso, J. Worley, P. Zhang, W. 2023-09-29 doi:10.1101/2023.09.28.559893 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Prenatal Arsenite Exposure Alters Maternal Cardiac Remodeling During Late Pregnancy ]]> https://biorxiv.org/content/10.1101/2023.09.28.559986v1?rss=1 Taube, N. Kabir, R. Ebenebe, O. V. Garbus, H. Alam El Din, S.-M. Illingworth, E. Fitch, M. Wang, N. Kohr, M. J. 2023-09-29 doi:10.1101/2023.09.28.559986 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling ]]> https://biorxiv.org/content/10.1101/2023.09.28.560060v1?rss=1 Dong, Y. Johns, B. A. Ruan, L. Zeineldin, M. Liu, A. Raychaudhuri, S. Chiu, I. Zhu, J. Smith, B. Zhao, N. Searson, P. Watanabe, S. Donowitz, M. Larman, T. C. Li, R. 2023-09-29 doi:10.1101/2023.09.28.560060 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry ]]> https://biorxiv.org/content/10.1101/2023.09.30.560331v1?rss=1 Ratcliff, J. Merritt, B. Gooden, H. Siegers, J. Srikanth, A. Yann, S. Kol, S. Sin, S. Tok, S. Karlsson, E. A. Thielen, P. M. 2023-10-02 doi:10.1101/2023.09.30.560331 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Arrested Agonist Paradigm For Selective Radiosensitization of Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.10.01.560227v1?rss=1 Coulter, J. B. Haffner, M. Zhang, Y. Zhou, H. Pham, M.-T. N. Chen, J. Chikarmane, R. Mishra, A. Mehl, M. S. Kazibwe, S. Choi, K. Archey, A. Valluri, S. Lupold, S. E. Song, D. De Marzo, A. M. Nelson, W. G. DeWeese, T. L. Yegnasubramanian, S. 2023-10-02 doi:10.1101/2023.10.01.560227 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Controlling pericellular oxygen tension in cell culture reveals distinct breast cancer responses to low oxygen tensions ]]> https://biorxiv.org/content/10.1101/2023.10.02.560369v1?rss=1 Rogers, Z. J. Colombani, T. C. Khan, S. Bhatt, K. Nukovic, A. Zhou, G. Woolston, B. M. Taylor, C. T. Gilkes, D. M. Slavov, N. Bencherif, S. A. 2023-10-03 doi:10.1101/2023.10.02.560369 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Immunologic changes are detectable in the peripheral blood transcriptome of clinically asymptomatic Chagas cardiomyopathy patients ]]> https://biorxiv.org/content/10.1101/2023.10.03.560680v1?rss=1 Duque, C. So, J. Castro-Sesquen, Y. E. DeToy, K. Guarnizo, S. A. G. Jahanbakhsh, F. Machaca, E. M. Miranda-Schaeubinger, M. Chakravarti, I. Cooper, V. Schmidt, M. E. Luigi, A. Marcus, R. Talaat, K. R. Gilman, R. H. Mugnier, M. R. Chagas working group, 2023-10-05 doi:10.1101/2023.10.03.560680 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Chromatinization Modulates Topoisomerase II Processivity ]]> https://biorxiv.org/content/10.1101/2023.10.03.560726v1?rss=1 6000 turns. We further discovered that topo II could relax supercoiled DNA prior to plectoneme formation, but with a [~]100-fold reduction in processivity; strikingly, the relaxation rate in this regime decreased with diminishing torsion in a manner consistent with the capture of transient DNA loops by topo II. Chromatinization preserved the high processivity of the enzyme under high torsional stress. Interestingly, topo II was still highly processive ([~] 1000 turns) even under low torsional stress, consistent with the predisposition of chromatin to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function, capable of enhancing function even under low torsional stress. ]]> Lee, J. Wu, M. Inman, J. Singh, G. Park, S. h. Lee, J. H. Fulbright, R. M. Hong, Y. Jeong, J. D. Berger, J. M. Wang, M. D. 2023-10-04 doi:10.1101/2023.10.03.560726 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Characterizing cell-type spatial relationships across length scales in spatially resolved omics data ]]> https://biorxiv.org/content/10.1101/2023.10.05.560733v1?rss=1 dos Santos Peixoto, R. Miller, B. F. Brusko, M. A. Atta, L. Anant, M. Atkinson, M. A. Brusko, T. M. Wasserfall, C. H. Fan, J. 2023-10-06 doi:10.1101/2023.10.05.560733 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ The developmental trajectory of 1H-MRS brain metabolites from childhood to adulthood. ]]> https://biorxiv.org/content/10.1101/2023.10.05.560892v1?rss=1 Thomson, A. Hwa, H. Pasanta, D. Hopwood, B. Powell, H. Lawrence, R. Gracia-Tabuenca, Z. Arichi, T. Edden, R. Chai, X. J. Puts, N. 2023-10-06 doi:10.1101/2023.10.05.560892 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ A murine model of Trypanosoma brucei-induced myocarditis and cardiac dysfunction ]]> https://biorxiv.org/content/10.1101/2023.10.05.560950v1?rss=1 Crilly, N. Zita, M. D. Beaver, A. Sysa-Shah, P. Gabrielson, K. Adamo, L. Mugnier, M. 2023-10-05 doi:10.1101/2023.10.05.560950 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Calcium Sulfate Microparticle Size Modification for Improved Alginate Hydrogel Fabrication and Its Application in 3D Cell Culture ]]> https://biorxiv.org/content/10.1101/2023.10.05.560969v1?rss=1 Kim, J. H. Iyer, S. Tessman, C. Lakshman, S. Kang, H. Gu, L. 2023-10-07 doi:10.1101/2023.10.05.560969 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ High-resolution label-free transcranial imaging of in vivo neural activity via interferometric measurement of tissue deformation ]]> https://biorxiv.org/content/10.1101/2023.10.05.561052v1?rss=1 Lefebvre, A. T. Rodriguez, C. L. Bar-Kochba, E. Steiner, N. E. Mirski, M. Blodgett, D. W. 2023-10-08 doi:10.1101/2023.10.05.561052 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Biomarker discovery in progressive supranuclear palsy from human cerebrospinal fluid using mass spectrometry-based proteomics ]]> https://biorxiv.org/content/10.1101/2023.10.05.561075v1?rss=1 Jang, Y. Oh, S. Hall, A. J. Zhang, Z. Tropea, T. F. Chen-Plotkin, A. Rosenthal, L. S. Dawson, T. M. Na, C.-H. Pantelyat, A. Y. 2023-10-07 doi:10.1101/2023.10.05.561075 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia ]]> https://biorxiv.org/content/10.1101/2023.10.05.561081v1?rss=1 Michki, N. S. Singer, B. D. Perez, J. V. Thomas, A. J. Natale, V. Helmin, K. A. Wright, J. Cheng, L. Young, L. R. Lederman, H. M. McGrath-Morrow, S. A. 2023-10-07 doi:10.1101/2023.10.05.561081 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Auditory Hair Cells and Spiral Ganglion Neurons Regenerate Synapses with Refined Release Properties In Vitro ]]> https://biorxiv.org/content/10.1101/2023.10.05.561095v1?rss=1 VINCENT, P. F. Y. Young, E. D. Edge, A. Glowatzki, E. 2023-10-07 doi:10.1101/2023.10.05.561095 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals ]]> https://biorxiv.org/content/10.1101/2023.10.06.561128v1?rss=1 Oh, J. W. Beer, M. A. 2023-10-06 doi:10.1101/2023.10.06.561128 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Merging-limited coarsening governs long-term stability of nanoscale condensates ]]> https://biorxiv.org/content/10.1101/2023.10.06.561146v1?rss=1 Chen, F. Zhang, Y. Shum, H. C. 2023-10-09 doi:10.1101/2023.10.06.561146 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Sliding windows analysis can undo the effects of preprocessing when applied to fMRI data ]]> https://biorxiv.org/content/10.1101/2023.10.06.561221v1?rss=1 Lindquist, M. A. 2023-10-09 doi:10.1101/2023.10.06.561221 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Design of a low-cost photomodulator for in vivo photoactivation of a mGluR5 inhibitor ]]> https://biorxiv.org/content/10.1101/2023.10.07.561310v1?rss=1 Ajieren, H. Fox, A. Biggs, E. Albors, G. Llebaria, A. Irazoqui, P. 2023-10-10 doi:10.1101/2023.10.07.561310 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES ]]> https://biorxiv.org/content/10.1101/2023.10.08.561395v1?rss=1 Guarnieri, J. W. Topper, M. Beigel, K. Haltoom, J. A. Chadburn, A. Frere, J. An, J. Cope, H. Borczuk, A. Sinha, S. Lim, C. Kim, J. Park, J. Meydan, C. Foox, J. Mozsary, C. Bram, Y. Richard, S. Epsi, N. Agan, B. Chenoweth, J. Simons, M. Tribble, D. Burgess, T. Dalgard, C. L. Heise, M. T. Moorman, N. Baxter, V. Madden, E. A. Taft-Benz, S. Anderson, E. Sanders, W. A. Dickmander, R. J. Widjaja, G. A. Janssen, K. Lie, T. Murdock, D. G. Angelin, A. Albrecht, Y. E. S. Olali, A. Dybas, J. M. Priebe, W. Emmett, M. R. Best, S. Johnson, M. K. Trovao, N. S. Cl 2023-10-09 doi:10.1101/2023.10.08.561395 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Multiparameter flow cytometric detection and analysis of rare cells in in vivo models of cancer metastasis ]]> https://biorxiv.org/content/10.1101/2023.10.12.562110v1?rss=1 Mallin, M. M. Pienta, K. J. Amend, S. R. 2023-10-16 doi:10.1101/2023.10.12.562110 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ PARP10 is Critical for Stress Granule Initiation ]]> https://biorxiv.org/content/10.1101/2023.10.13.562236v1?rss=1 Jayabalan, A. k. Bhambhani, K. Leung, A. 2023-10-14 doi:10.1101/2023.10.13.562236 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Growth retardation in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1 ]]> https://biorxiv.org/content/10.1101/2023.10.15.562327v1?rss=1 Gao, C. W. Lin, W.-Y. Riddle, R. C. Chopra, S. Boukas, L. Hansen, K. D. Bjornsson, H. T. Fahrner, J. A. 2023-10-16 doi:10.1101/2023.10.15.562327 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2023.10.16.562104v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@859572org.highwire.dtl.DTLVardef@169ed2org.highwire.dtl.DTLVardef@11510f0org.highwire.dtl.DTLVardef@b39a4_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LSTHighlightsC_LSTO_LIIn patients with hepatocellular carcinoma (HCC), tertiary lymphoid structures (TLS) are induced by neoadjuvant immunotherapy and are associated with favorable clinical outcomes. C_LIO_LITLS within the same tumor demonstrate extensive sharing of expanded granzyme K and granzyme B-expressing CD8+ T effector memory clonotypes, but the B cell repertoires of individual TLS are almost wholly distinct, consistent with independent germinal center reactions. C_LIO_LIWithin areas of viable tumor, mature TLS are characterized by high expression of CD21 and CD23, BCL6+ germinal center B cells, and close interactions between DCLAMP+ mature dendritic cells and CXCR5-CXCR3+ CD4 T peripheral helper cells within a T cell zone adjacent to the B cell follicle. C_LIO_LIWithin areas of tumor regression, an involuted TLS morphology is identified that is notable for dissolution of the B cell germinal center, retention of the T cell zone, and increased T cell memory. C_LI ]]> Shu, D. H. Ho, W. J. Kagohara, L. T. Girgis, A. Shin, S. M. Danilova, L. Lee, J. W. Sidiropoulos, D. N. Mitchell, S. Munjal, K. Howe, K. Bendinelli, K. J. Qi, H. Mo, G. Montagne, J. Leatherman, J. M. Lopez-Vidal, T. Y. Zhu, Q. Huff, A. L. Yuan, X. Hernandez, A. Coyne, E. M. Zaidi, N. Zabransky, D. J. Engle, L. L. Ogurtsova, A. Baretti, M. Laheru, D. Durham, J. N. Wang, H. Anders, R. Jaffee, E. M. Fertig, E. J. Yarchoan, M. 2023-10-19 doi:10.1101/2023.10.16.562104 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Data-driven motif discovery in biological neural networks ]]> https://biorxiv.org/content/10.1101/2023.10.16.562590v1?rss=1 Matelsky, J. K. Robinette, M. R. Wester, B. Gray-Roncal, W. R. Johnson, E. C. Reilly, E. P. 2023-10-17 doi:10.1101/2023.10.16.562590 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Accelerated Aging after Traumatic Brain Injury: an ENIGMA Multi-Cohort Mega-Analysis ]]> https://biorxiv.org/content/10.1101/2023.10.16.562638v1?rss=1 Dennis, E. L. Vervoordt, S. Adamson, M. M. Amiri, H. Bigler, E. Caeyenberghs, K. Cole, J. H. Dams-O'Connor, K. Deutscher, E. M. Dobryakova, E. Genova, H. M. Grafman, J. H. Haberg, A. K. Hellstrom, T. Irimia, A. Koliatsos, V. E. Lindsey, H. M. Livny, A. Menon, D. K. Merkley, T. L. Mohamed, A. Z. Mondello, S. Monti, M. M. Newcombe, V. F. Newsome, M. R. Ponsford, J. Smevik, H. Spitz, G. Westlye, L. T. Zafonte, R. Thompson, P. M. Wilde, E. A. Olsen, A. Hillary, F. G. 2023-10-17 doi:10.1101/2023.10.16.562638 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development ]]> https://biorxiv.org/content/10.1101/2023.10.17.562742v1?rss=1 Honnell, V. Sweeney, S. Norrie, J. Ramirez, C. Xu, B. Teubner, B. Lee, A. Y. Bell, C. Dyer, M. A. 2023-10-17 doi:10.1101/2023.10.17.562742 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ The structural OFF and ON states of myosin can be decoupled from the biochemical super-relaxed and disordered-relaxed states. ]]> https://biorxiv.org/content/10.1101/2023.10.18.562891v1?rss=1 Ma, W. Jani, V. Song, T. Gao, C. Gong, H. Sadayappan, S. Kass, D. A. Irving, T. 2023-10-20 doi:10.1101/2023.10.18.562891 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein ]]> https://biorxiv.org/content/10.1101/2023.10.19.563042v1?rss=1 Shinkai, Y. Ding, Y. Matsui, T. Devitt, G. Akiyama, M. Shen, T.-L. Nishida, M. Ida, T. Akaike, T. Mahajan, S. Fukuto, J. M. Shigeta, Y. Kumagai, Y. 2023-10-19 doi:10.1101/2023.10.19.563042 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Flap endonuclease 1 repairs DNA-protein crosslinks via ADP-ribosylation ]]> https://biorxiv.org/content/10.1101/2023.10.19.563118v1?rss=1 Sun, Y. Jenkins, L. M. El Touny, L. H. Jo, U. Yang, X. Maity, T. K. Uribe, I. Saha, S. Takeda, S. Leung, A. K. L. Cheng, K. Pommier, Y. 2023-10-19 doi:10.1101/2023.10.19.563118 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ A Novel Semi-automated Proofreading and Mesh Error Detection Pipeline for Neuron Extension ]]> https://biorxiv.org/content/10.1101/2023.10.20.563359v1?rss=1 Joyce, J. Chalavadi, R. Chan, J. Tanna, S. Xenes, D. Kitchell, L. Kuo, N. Rose, V. Bishop, C. Rivlin, P. Villafane-Delgado, M. Wester, B. 2023-10-23 doi:10.1101/2023.10.20.563359 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Preventing NK cell activation in the damaged liver induced by cabozantinib/PD-1 blockade increases survival in hepatocellular carcinoma models ]]> https://biorxiv.org/content/10.1101/2023.10.20.563378v1?rss=1 Morita, S. Kikuchi, H. Birch, G. Matsui, A. Morita, A. Kobayashi, T. Ruan, Z. Huang, P. Hernandez, A. Coyne, E. M. Shin, S. M. Yarchoan, M. Kenudson, M. M. Romee, R. Ho, W. J. Duda, D. G. 2023-10-23 doi:10.1101/2023.10.20.563378 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Genotype prediction of 336,463 samples from public expression data ]]> https://biorxiv.org/content/10.1101/2023.10.21.562237v1?rss=1 Razi, A. Lo, C. C. Wang, S. Leek, J. T. Hansen, K. D. 2023-10-22 doi:10.1101/2023.10.21.562237 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ Regulating the proinflammatory response to implanted composite biomaterials comprising polylactide and hydroxyapatite by targeting immunometabolism ]]> https://biorxiv.org/content/10.1101/2023.10.21.563447v1?rss=1 Maduka, C. V. Makela, A. V. Ural, E. Stivers, K. B. Kuhnert, M. M. Tundo, A. Alhaj, M. Hoque Apu, E. Ashammakhi, N. Hankenson, K. D. Narayan, R. Elisseeff, J. H. Contag, C. H. 2023-10-25 doi:10.1101/2023.10.21.563447 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Hyperbolic graph embedding of MEG brain networks to study brain alterations in individuals with subjective cognitive decline ]]> https://biorxiv.org/content/10.1101/2023.10.23.563643v1?rss=1 Baker, C. Mendez, I. S. Smith, G. Marsh, E. B. Funke, M. Mosher, J. C. Maestu, F. Xu, M. Pantazis, D. 2023-10-25 doi:10.1101/2023.10.23.563643 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ PhysiCell Studio: a graphical tool to make agent-based modeling more accessible ]]> https://biorxiv.org/content/10.1101/2023.10.24.563727v1?rss=1 Heiland, R. Bergman, D. R. Lyons, B. Cass, J. L. Rocha, H. Ruscone, M. Noël, V. Macklin, P. 2023-10-27 doi:10.1101/2023.10.24.563727 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming ]]> https://biorxiv.org/content/10.1101/2023.10.24.563862v1?rss=1 Thielman, N. Funes, V. Davuluri, S. lbanez, H. Sun, W.-C. Fu, J. Li, K. Muth, S. Pan, X. Fujiwara, K. Thomas, D. Henderson, M. Teh, S. S. Zhu, Q. Thompson, E. Jaffee, E. M. Kolodkin, A. Meng, F. Zheng, L. 2023-10-27 doi:10.1101/2023.10.24.563862 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ LOXL2 inhibition ameliorates pulmonary artery remodeling in pulmonary hypertension ]]> https://biorxiv.org/content/10.1101/2023.10.24.563874v1?rss=1 Steppan, J. Wang, H. Nandakumar, K. Poe, A. Pak, L. Brady, T. Gadkari, M. Berkowitz, D. E. Shimoda, L. A. Santhanam, L. 2023-10-28 doi:10.1101/2023.10.24.563874 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations ]]> https://biorxiv.org/content/10.1101/2023.10.25.564012v1?rss=1 Wang, T. Coshic, K. Badiee, M. Aksimentiev, A. Pollack, L. Leung, A. 2023-10-27 doi:10.1101/2023.10.25.564012 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Transcriptomic network analysis of brain and bone reveals shared molecular mechanisms underlyingAlzheimer's Disease and related dementias and Osteoporosis ]]> https://biorxiv.org/content/10.1101/2023.10.26.559969v1?rss=1 Nagarajan, A. Laird, J. Ugochukwu, O. Reppe, S. Gautvik, K. Ross, R. D. Bennett, D. A. Rosen, C. J. Kiel, D. P. Higginbotham, L. A. Seyfried, N. Lary, C. W. 2023-10-28 doi:10.1101/2023.10.26.559969 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Senescence of endplate osteoclasts induces sensory innervation and spinal pain ]]> https://biorxiv.org/content/10.1101/2023.10.26.564218v1?rss=1 Pan, D. Benkato, K. G. Han, X. Zheng, J. Kumar, V. Wan, M. Zheng, J. Cao, X. 2023-10-26 doi:10.1101/2023.10.26.564218 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Robust reprogramming of glia into neurons by inhibition of Notch signaling and NFI factors in adult mammalian retina. ]]> https://biorxiv.org/content/10.1101/2023.10.29.560483v1?rss=1 Le, N. Vu, T.-D. Pulya, R. Kim, Y. Blackshaw, S. Hoang, T. 2023-11-01 doi:10.1101/2023.10.29.560483 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Adolescent social anxiety is associated with diminished discrimination of anticipated threat and safety ]]> https://biorxiv.org/content/10.1101/2023.10.30.564701v1?rss=1 Hur, J. Tillman, R. M. Kim, H. C. Didier, P. Anderson, A. S. Islam, S. Stockbridge, M. D. De Los Reyes, A. DeYoung, K. A. Smith, J. F. Shackman, A. J. 2023-11-02 doi:10.1101/2023.10.30.564701 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Deep Phenotyping of Sleep in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.10.30.564733v1?rss=1 Keles, M. F. Sapcı, A. O. B. Brody, C. Palmer, I. Le, C. Tastan, O. Keles, S. Wu, M. 2023-11-02 doi:10.1101/2023.10.30.564733 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies ]]> https://biorxiv.org/content/10.1101/2023.10.30.564764v1?rss=1 Li, X. Chen, H. Selvaraj, M. S. Van Buren, E. Zhou, H. Wang, Y. Sun, R. McCaw, Z. R. Yu, Z. Arnett, D. K. Bis, J. C. Blangero, J. Boerwinkle, E. Bowden, D. W. Brody, J. A. Cade, B. E. Carson, A. P. Carlson, J. C. Chami, N. Chen, Y.-D. I. Curran, J. E. de Vries, P. S. Fornage, M. Franceschini, N. Freedman, B. I. Gu, C. Heard-Costa, N. L. He, J. Hou, L. Hung, Y.-J. Irvin, M. R. Kaplan, R. C. Kardia, S. L. R. Kelly, T. Konigsberg, I. Kooperberg, C. Kral, B. G. Li, C. Loos, R. J. F. Mahaney, M. C. Martin, L. W. Mathias, R. A. Minster, R. L. Mitchell, B. D 2023-11-02 doi:10.1101/2023.10.30.564764 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Decoding Heterogenous Single-cell Perturbation Responses ]]> https://biorxiv.org/content/10.1101/2023.10.30.564796v1?rss=1 Song, B. Liu, D. Dai, W. McMyn, N. Wang, Q. Yang, D. Krejci, A. Vasilyev, A. Untermoser, N. Loregger, A. Song, D. Williams, B. Rosen, B. Cheng, X. Chao, L. Kale, H. Zhang, H. Diao, Y. Bürckstümmer, T. Siliciano, J. M. Li, J. J. Siliciano, R. Huangfu, D. Li, W. 2023-11-02 doi:10.1101/2023.10.30.564796 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Decreased fucosylation impacts epithelial integrity and increases risk for COPD. ]]> https://biorxiv.org/content/10.1101/2023.10.31.564805v1?rss=1 Swaby, C. Yeung-Luk, B. Thapa, S. Nishida, K. Wally, A. Ghosh, B. Niederkofler, A. Luk, S. Girgis, M. Keller, A. Cortez, C. Ramaswamy, S. Wilmsen, K. Bouche, L. Dell, A. Drummond, M. B. Putcha, N. Haslam, S. M. Mathias, R. Hansel, N. N. Sheng, J. Sidhaye, V. K. 2023-11-02 doi:10.1101/2023.10.31.564805 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Pathological claustrum activity drives aberrant cognitive network processing in human chronic pain ]]> https://biorxiv.org/content/10.1101/2023.11.01.564054v1?rss=1 Stewart, B. W. Keaser, M. L. Lee, H. Margerison, S. M. Cormie, M. A. Moayedi, M. Lindquist, M. Chen, S. Mathur, B. N. Seminowicz, D. A. 2023-11-02 doi:10.1101/2023.11.01.564054 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Neuropeptide Signaling Is Required To Implement A Line Attractor Encoding A Persistent Internal Behavioral State ]]> https://biorxiv.org/content/10.1101/2023.11.01.565073v1?rss=1 Mountoufaris, G. Nair, A. Yang, B. Kim, D.-W. Anderson, D. J. 2023-11-02 doi:10.1101/2023.11.01.565073 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Loss of CTRP10 results in female obesity with preserved metabolic health ]]> https://biorxiv.org/content/10.1101/2023.11.01.565163v1?rss=1 Chen, F. Sarver, D. C. Saqib, M. Velez, L. M. Aja, S. Seldin, M. M. Wong, G. W. 2023-11-04 doi:10.1101/2023.11.01.565163 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Simultaneous multi-transient linear-combination modeling of MRS data improves uncertainty estimation ]]> https://biorxiv.org/content/10.1101/2023.11.01.565164v1?rss=1 Zollner, H. J. Davies-Jenkins, C. B. Simicic, D. B. Tal, A. Sulam, J. Oeltzschner, G. 2023-11-04 doi:10.1101/2023.11.01.565164 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Engineering the microstructure and spatial bioactivity of MAP scaffolds in vitro instructs neovascularization in vivo ]]> https://biorxiv.org/content/10.1101/2023.11.01.565182v1?rss=1 Anderson, A. R. Caston, E. L. P. Riley, L. Nguyen, L. Ntekoumes, D. Gerecht, S. Segura, T. 2023-11-01 doi:10.1101/2023.11.01.565182 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins ]]> https://biorxiv.org/content/10.1101/2023.11.01.565189v1?rss=1 Saba, J. A. Huang, Z. Schole, K. L. Ye, X. Bhatt, S. D. Li, Y. Timp, W. Cheng, J. Green, R. 2023-11-02 doi:10.1101/2023.11.01.565189 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Transcriptional Control of Neocortical Size and Microcephaly ]]> https://biorxiv.org/content/10.1101/2023.11.02.565322v1?rss=1 Barao, S. Xu, Y. Vistein, R. Goff, L. Nielsen, K. Bae, B.-I. Smith, R. S. Walsh, C. A. Stein O Brien, G. Muller, U. 2023-11-02 doi:10.1101/2023.11.02.565322 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2023.11.03.565539v1?rss=1 Sambaturu, N. Fray, E. J. Wu, F. Zitzmann, C. Simonetti, F. R. Barouch, D. H. Siliciano, J. D. Siliciano, R. F. Ribeiro, R. M. Perelson, A. S. Molina-Paris, C. Leitner, T. 2023-11-03 doi:10.1101/2023.11.03.565539 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Transcriptomics and chromatin accessibility in multiple African population samples ]]> https://biorxiv.org/content/10.1101/2023.11.04.564839v1?rss=1 DeGorter, M. K. Goddard, P. C. Karakoc, E. Kundu, S. Yan, S. M. Nachun, D. C. Abell, N. Aguirre, M. Carstensen, T. Chen, Z. Durrant, M. G. Dwaracherla, V. Feng, K. Gloudemans, M. J. Hunter, N. Sathya Moorthy, M. P. Pomilla, C. Rodrigues, K. B. Smith, C. J. Smith, K. S. Ungar, R. A. Balliu, B. Fellay, J. Flicek, P. McLaren, P. J. Henn, B. M. McCoy, R. C. Sugden, L. A. Kundaje, A. Sandhu, M. S. Gurdasani, D. Montgomery, S. B. 2023-11-06 doi:10.1101/2023.11.04.564839 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Movi: a fast and cache-efficient full-text pangenome index ]]> https://biorxiv.org/content/10.1101/2023.11.04.565615v1?rss=1 Zakeri, M. Brown, N. K. Ahmed, O. Y. Gagie, T. Langmead, B. 2023-11-05 doi:10.1101/2023.11.04.565615 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Sources of gene expression variation in a globally diverse cohort ]]> https://biorxiv.org/content/10.1101/2023.11.04.565639v1?rss=1 15,000 putatively causal eQTLs and >16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1310 eQTLs and 1657 sQTLs that are largely private to previously underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations and that apparent "population-specific" effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands understanding of gene expression diversity across human populations and provides an inclusive resource for studying the evolution and function of human genomes. ]]> Taylor, D. J. Chhetri, S. B. Biddanda, A. Tassia, M. G. Battle, A. McCoy, R. C. 2023-11-05 doi:10.1101/2023.11.04.565639 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Contexts facilitate dynamic value encoding in the mesolimbic dopamine system ]]> https://biorxiv.org/content/10.1101/2023.11.05.565687v1?rss=1 Fraser, K. M. Collins, V. L. Wolff, A. R. Ottenheimer, D. J. Bornhoft, K. N. Pat, F. Chen, B. J. Janak, P. H. Saunders, B. T. 2023-11-05 doi:10.1101/2023.11.05.565687 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Hypermetabolic state is associated with circadian rhythm disruption in mouse and human cancer cells ]]> https://biorxiv.org/content/10.1101/2023.11.08.566310v1?rss=1 Iascone, D. M. Zhang, X. Bafford, P. Mesaros, C. Sela, Y. Hofbauer, S. Zhang, S. L. Cook, K. Pivarshev, P. Stanger, B. Anderson, S. A. Dang, C. V. Sehgal, A. 2023-11-13 doi:10.1101/2023.11.08.566310 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ An encyclopedia of enhancer-gene regulatory interactions in the human genome ]]> https://biorxiv.org/content/10.1101/2023.11.09.563812v1?rss=1 13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 element-gene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancer-promoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics. ]]> Gschwind, A. R. Mualim, K. S. Karbalayghareh, A. Sheth, M. U. Dey, K. K. Jagoda, E. Nurtdinov, R. N. Xi, W. Tan, A. S. Jones, H. Ma, X. R. Yao, D. Nasser, J. Avsec, Z. James, B. T. Shamim, M. S. Durand, N. C. Rao, S. S. P. Mahajan, R. Doughty, B. R. Andreeva, K. Ulirsch, J. C. Fan, K. Perez, E. M. Nguyen, T. C. Kelley, D. R. Finucane, H. K. Moore, J. E. Weng, Z. Kellis, M. Bassik, M. C. Price, A. L. Beer, M. A. Guigo, R. Stamatoyannopoulos, J. A. Aiden, E. L. Greenleaf, W. J. Leslie, C. S. Steinmetz, L. M. Kundaje, A. Engreitz, J. M. 2023-11-13 doi:10.1101/2023.11.09.563812 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Lipid metabolism drives allele-specific early-stage hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.11.10.564562v1?rss=1 O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/564562v1_ufig2.gif" ALT="Figure 1"> O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/564562v1_ufig3.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@195b1d7org.highwire.dtl.DTLVardef@cead88org.highwire.dtl.DTLVardef@e2bf35org.highwire.dtl.DTLVardef@776765_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Vaniya, A. Karlstaedt, A. Ates Gulkok, D. Thottakara, T. Liu, Y. Fan, S. Eades, H. Fukunaga, R. Vernon, H. J. Fiehn, O. Abraham, M. R. 2023-11-15 doi:10.1101/2023.11.10.564562 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury ]]> https://biorxiv.org/content/10.1101/2023.11.10.566497v1?rss=1 Ghag, R. Kaushal, M. Nwanne, G. Knoten, A. Kiryluk, K. Rosenberg, A. Menez, S. Bagnasco, S. M. Sperati, C. J. Atta, M. G. Gaut, J. P. Williams, J. C. El-Achkar, T. M. Arend, L. J. Parikh, C. R. Jain, S. 2023-11-12 doi:10.1101/2023.11.10.566497 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput ]]> https://biorxiv.org/content/10.1101/2023.11.11.566649v1?rss=1 Kennedy, P. H. Deh Sheikh, A. A. Balakar, M. Jones, A. C. Olive, M. E. Hedge, M. Matias, M. I. Pirete, N. Burt, R. Levy, J. Little, T. Hogan, P. G. Liu, D. R. Doench, J. G. Newton, A. C. Gottschalk, R. A. de Boer, C. Alarcon, S. Newby, G. Myers, S. A. 2023-11-14 doi:10.1101/2023.11.11.566649 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers and engulfment by microglia ]]> https://biorxiv.org/content/10.1101/2023.11.13.564824v1?rss=1 Francis, V. Liddle, C. Camacho, E. Kulkarni, M. Junior, S. R. Harvey, J. A. Ballou, E. R. Thompson, D. D. Hardwick, J. M. Casadevall, A. Witton, J. Coelho, C. 2023-11-13 doi:10.1101/2023.11.13.564824 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification ]]> https://biorxiv.org/content/10.1101/2023.11.15.567129v1?rss=1 Song, L. Langmead, B. 2023-11-17 doi:10.1101/2023.11.15.567129 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Time-restricted feeding ameliorates MCDD-induced steatohepatitis in mice ]]> https://biorxiv.org/content/10.1101/2023.11.15.567214v1?rss=1 Jung, I.-R. Ahima, R. S. Kim, S. F. 2023-11-17 doi:10.1101/2023.11.15.567214 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ The MYC axis in advanced prostate cancer is impacted through concurrent targeting of ERβ and AR using a novel ERβ-selective ligand alongside Enzalutamide ]]> https://biorxiv.org/content/10.1101/2023.11.15.567282v1?rss=1 Gray, J. S. Wani, S. A. Hussain, S. Huang, P. Nayak, D. Long, M. D. Yates, C. Clinton, S. K. Bennett, C. E. Coss, C. C. Campbell, M. J. 2023-11-17 doi:10.1101/2023.11.15.567282 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A genome sequence for the threatened whitebark pine ]]> https://biorxiv.org/content/10.1101/2023.11.16.567420v1?rss=1 Neale, D. B. Zimin, A. V. Meltzer, A. Bhattarai, A. Amee, M. Figueroa Corona, L. Allen, B. J. Puiu, D. Wright, J. De La Torre, A. R. McGuire, P. E. Timp, W. Salzberg, S. L. Wegrzyn, J. L. 2023-11-17 doi:10.1101/2023.11.16.567420 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Semaphorin 6A in Retinal Ganglion Cells Regulates Functional Specialization of the Inner Retina ]]> https://biorxiv.org/content/10.1101/2023.11.18.567662v1?rss=1 James, R. E. Hamilton, N. R. Huffman, L. N. Pasterkamp, J. Goff, L. A. Kolodkin, A. L. 2023-11-18 doi:10.1101/2023.11.18.567662 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ An integrated method for single cell proteomics with simultaneous measurements of intracellular drug concentration implicates new mechanisms for adaptation to KRASG12D inhibitors ]]> https://biorxiv.org/content/10.1101/2023.11.18.567669v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@11e5cfborg.highwire.dtl.DTLVardef@6a7dfborg.highwire.dtl.DTLVardef@1751923org.highwire.dtl.DTLVardef@c573a3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Orsburn, B. 2023-11-18 doi:10.1101/2023.11.18.567669 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height ]]> https://biorxiv.org/content/10.1101/2023.11.19.566520v1?rss=1 Hawkes, G. Beaumont, R. N. Li, Z. Mandla, R. Li, X. Albert, C. M. Arnett, D. K. Ashley-Koch, A. E. Ashrani, A. A. Barnes, K. C. Boerwinkle, E. Brody, J. A. Carson, A. P. Chami, N. Chen, Y.-D. I. Chung, M. K. Curran, J. E. Darbar, D. Ellinor, P. T. Fornage, M. Gordeuk, V. R. Guo, X. He, J. Hwu, C.-M. Kalyani, R. R. Kaplan, R. Kardia, S. L. R. Kooperberg, C. Loos, R. J. F. Lubitz, S. A. Minster, R. L. Mitchell, B. D. Murabito, J. M. Palmer, N. D. Psaty, B. M. Redline, S. Shoemaker, M. B. Silverman, E. K. Telen, M. J. Weiss, S. T. Yanek, L. R. Zhou, H. NH 2023-11-20 doi:10.1101/2023.11.19.566520 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.11.20.567573v1?rss=1 Miles, J. Lozano, G. L. Rajendhran, J. Stabb, E. V. Handelsman, J. Broderick, N. A. 2023-11-21 doi:10.1101/2023.11.20.567573 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation ]]> https://biorxiv.org/content/10.1101/2023.11.20.567792v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@dac365org.highwire.dtl.DTLVardef@522ecaorg.highwire.dtl.DTLVardef@17ddb38org.highwire.dtl.DTLVardef@1c371b0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO (i) ChAMP is added to fix and permeabilized cells, where it binds (ii) any antibody, and upon the addition of SAM, methylates nearby GpC sites, to be detected by sequencing (iii-iv). C_FIG ]]> Thatavarty, A. Sagy, N. Erdos, M. R. Lee, I. Simpson, J. T. Timp, W. Collins, F. S. Bar, D. Z. 2023-11-20 doi:10.1101/2023.11.20.567792 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Fish Playpens: Method for raising individual juvenile zebrafish on a recirculating system for studies requiring repeated measures ]]> https://biorxiv.org/content/10.1101/2023.11.20.567840v1?rss=1 Moll, T. O. C. Farber, S. A. 2023-11-21 doi:10.1101/2023.11.20.567840 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Molecular regulation of retinal regeneration is context specific ]]> https://biorxiv.org/content/10.1101/2023.11.20.567904v1?rss=1 Emmerich, K. Hageter, J. Hoang, T. Lyu, P. Sharrock, A. V. Ceisel, A. Thierer, J. Chunawala, Z. Nimmagadda, S. Palazzo, I. Matthews, F. Zhang, L. White, D. T. Rodriguez, C. Graziano, G. Marcos, P. May, A. Mulligan, T. Reibman, B. Saxena, M. T. Ackerley, D. F. Qian, J. Blackshaw, S. Horstick, E. Mumm, J. S. 2023-11-21 doi:10.1101/2023.11.20.567904 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Alpha9alpha10 knockout mice show altered physiological and behavioral responses to signals in masking noise ]]> https://biorxiv.org/content/10.1101/2023.11.21.567909v1?rss=1 Mondul, J. Burke, K. Morley, B. Lauer, A. 2023-11-21 doi:10.1101/2023.11.21.567909 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Multidimensional neural representations of social features during movie viewing ]]> https://biorxiv.org/content/10.1101/2023.11.22.568258v1?rss=1 Lee Masson, H. Chang, L. Isik, L. 2023-11-22 doi:10.1101/2023.11.22.568258 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Preventing evolutionary rescue in cancer ]]> https://biorxiv.org/content/10.1101/2023.11.22.568336v1?rss=1 Patil, S. Viossat, Y. Noble, R. J. 2023-11-22 doi:10.1101/2023.11.22.568336 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Molecular Regulation of Invasive Protrusion Formation at the Mammalian Fusogenic Synapse ]]> https://biorxiv.org/content/10.1101/2023.11.27.568897v1?rss=1 Lu, Y. Walji, T. Ravaux, B. Pandey, P. Li, B. Lam, K. H. Zhang, R. Goldhamer, D. J. Li, R. Schmidtke, D. W. Pan, D. Chen, E. H. 2023-11-27 doi:10.1101/2023.11.27.568897 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ In-bore MRI-compatible Transrectal Ultrasound and Photoacoustic Imaging ]]> https://biorxiv.org/content/10.1101/2023.11.27.568947v1?rss=1 Murakami, R. Wang, Y. Lesniak, W. Tsumura, R. Tang, Y. Tsunoi, Y. Nycz, C. J. Pomper, M. G. Fischer, G. S. Zhang, H. K. 2023-11-28 doi:10.1101/2023.11.27.568947 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Expression and fusogenic activity of SARS CoV-2 Spike protein displayed in the HSV-1 Virion. ]]> https://biorxiv.org/content/10.1101/2023.11.28.568860v1?rss=1 Desai, P. J. 2023-11-28 doi:10.1101/2023.11.28.568860 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A (Sub)field Guide to Quality Control in Hippocampal Subfield Segmentation on High-resolution T2-weighted MRI ]]> https://biorxiv.org/content/10.1101/2023.11.29.568895v1?rss=1 Canada, K. L. Mazloum-Farzaghi, N. Radman, G. Adams, J. N. Bakker, A. Baumeister, H. Berron, D. Bocchetta, M. Carr, V. Dalton, M. A. de Flores, R. Keresztes, A. LaJoie, R. Mueller, S. Raz, N. Santini, T. Shaw, T. Stark, C. E. L. Tran, T. T. Wang, L. Wisse, L. Wuestefeld, A. Yushkevich, P. A. Olsen, R. Daugherty, A. 2023-12-01 doi:10.1101/2023.11.29.568895 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Identification of conserved gene expression programs activated in multiple modes of torpor across vertebrate clades. ]]> https://biorxiv.org/content/10.1101/2023.11.29.569284v1?rss=1 Weir, K. Blackshaw, S. Vega, N. Busa, V. Sajdak, B. Kallestad, L. Merriman, D. Palczewski, K. Carroll, J. 2023-12-01 doi:10.1101/2023.11.29.569284 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Paradoxical mTORC1-Dependent microRNA-mediated Translation Repression in the Nucleus Accumbens of Mice Consuming Alcohol Attenuates Glycolysis ]]> https://biorxiv.org/content/10.1101/2023.11.29.569312v1?rss=1 Ehinger, Y. Laguesse, S. Phamluong, K. Salvi, A. Hoisington, Z. W. Soneja, D. Sei, Y. J. Nakamura, K. Ron, D. 2023-12-01 doi:10.1101/2023.11.29.569312 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Minimizing Reference Bias with an Impute-First Approach ]]> https://biorxiv.org/content/10.1101/2023.11.30.568362v1?rss=1 Vaddadi, N. S. K. Mun, T. Langmead, B. 2023-12-02 doi:10.1101/2023.11.30.568362 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569198v1?rss=1 100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species. ]]> Makova, K. D. Pickett, B. D. Harris, R. S. Hartley, G. A. Cechova, M. Pal, K. Nurk, S. Yoo, D. Li, Q. Hebbar, P. McGrath, B. C. Antonacci, F. Aubel, M. Biddanda, A. Borchers, M. Bornberg, E. Bouffard, G. G. Brooks, S. Y. Carbone, L. Carrel, L. Carroll, A. Chang, P.-C. Chin, C.-S. Cook, D. E. Craig, S. J. C. de Gennaro, L. Diekhans, M. Dutra, A. Garcia, G. H. Grady, P. G. S. Green, R. E. Haddad, D. Hallast, P. Harvey, W. T. Hickey, G. Hillis, D. A. Hoyt, S. J. Jeong, H. Kamali, K. Pond, S. L. K. LaPolice, T. M. Lee, C. Lewis, A. P. Loh, Y.-H. E. Maste 2023-12-01 doi:10.1101/2023.11.30.569198 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Plasmacytoid dendritic cells (pDCs) display surface but not membrane-bound IgE across a broad range of total serum IgE levels ]]> https://biorxiv.org/content/10.1101/2023.11.30.569292v1?rss=1 Chen, J. MacGlashan, D. McCormack, A. Schroeder, J. Tversky, J. 2023-12-02 doi:10.1101/2023.11.30.569292 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Quality assessment of splice site annotation based on conservation across multiple species ]]> https://biorxiv.org/content/10.1101/2023.12.01.569581v1?rss=1 View larger version (10K): org.highwire.dtl.DTLVardef@4c1e31org.highwire.dtl.DTLVardef@1525b89org.highwire.dtl.DTLVardef@1f7a3f3org.highwire.dtl.DTLVardef@12cdff2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Minkin, I. Salzberg, S. 2023-12-02 doi:10.1101/2023.12.01.569581 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Power-law growth models explain incidences and sizes of pancreatic cancer precursor lesions and confirm spatial genomic findings ]]> https://biorxiv.org/content/10.1101/2023.12.01.569633v1?rss=1 1,000 PanIN and found that lesion size is distributed according to a power law with a fitted exponent of -1.7 over > 3 orders of magnitude. Our data also suggest that PanIN growth is not very sensitive to the pancreatic microenvironment or an individuals age, family history, and lifestyle, and is rather shaped by general growth behavior. We analyze several models of PanIN growth and fit the predicted size distributions to the observed data. The best fitting models suggest that both intraductal spread of PanIN lesions and fusing of multiple lesions into large, highly branched structures drive PanIN growth patterns. This work lays the groundwork for future mathematical modeling efforts integrating PanIN incidence, morphology, genomic, and transcriptomic features to understand pancreas tumorigenesis, and demonstrates the utility of combining experimental measurement of human tissues with dynamic modeling for understanding cancer tumorigenesis. ]]> Kiemen, A. L. Wu, P. Braxton, A. M. Cornish, T. C. Hruban, R. H. Wood, L. D. Wirtz, D. Zwicker, D. 2023-12-04 doi:10.1101/2023.12.01.569633 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe ]]> https://biorxiv.org/content/10.1101/2023.12.04.569947v1?rss=1 Manriquez-Sandoval, E. Brewer, J. Lule, G. Lopez, S. Fried, S. D. 2023-12-05 doi:10.1101/2023.12.04.569947 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Three-dimensional assessments are necessary to determine the true spatial tissue composition of diseased tissues ]]> https://biorxiv.org/content/10.1101/2023.12.04.569986v1?rss=1 Forjaz, A. Vaz, E. Romero, V. M. Joshi, S. Braxton, A. M. Jiang, A. C. Fujikura, K. Cornish, T. Hong, S.-M. Hruban, R. H. Wu, P.-H. Wood, L. D. Kiemen, A. L. Wirtz, D. 2023-12-06 doi:10.1101/2023.12.04.569986 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Cue-Invariant Geometric Structure of the Population Codes in Macaque V1 and V2 ]]> https://biorxiv.org/content/10.1101/2023.12.05.570110v1?rss=1 Massot, C. Zhang, X. Wang, Z. Rockwell, H. Papandreou, G. Yuille, A. Lee, T.-S. 2023-12-07 doi:10.1101/2023.12.05.570110 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy ]]> https://biorxiv.org/content/10.1101/2023.12.06.570168v1?rss=1 Hickey, J. W. Agmon, E. Horowitz, N. Lamore, M. Sunwoo, J. B. Covert, M. Nolan, G. P. 2023-12-08 doi:10.1101/2023.12.06.570168 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ The Role of Attention in Multi Attribute Decision Making ]]> https://biorxiv.org/content/10.1101/2023.12.06.570439v1?rss=1 Sampson, A. L. Yang, Y.-P. Usher, M. Levy, D. Niebur, E. Stuphorn, V. 2023-12-08 doi:10.1101/2023.12.06.570439 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Machine Learning Elucidates Design Features of Plasmid DNA Lipid Nanoparticles for Cell Type-Preferential Transfection ]]> https://biorxiv.org/content/10.1101/2023.12.07.570602v1?rss=1 Cheng, L. Zhu, Y. Ma, J. Aggarwal, A. Toh, W. H. Shin, C. Sangpachatanaruk, W. Weng, G. Kumar, R. Mao, H.-Q. 2023-12-08 doi:10.1101/2023.12.07.570602 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures ]]> https://biorxiv.org/content/10.1101/2023.12.07.570622v1?rss=1 Dequiedt, L. Forjaz, A. Lo, J. O. McCarty, O. J. Wu, P.-H. Rosenberg, A. Wirtz, D. Kiemen, A. L. 2023-12-08 doi:10.1101/2023.12.07.570622 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Category-based attention facilitates memory search ]]> https://biorxiv.org/content/10.1101/2023.12.08.570779v1?rss=1 Shang, L. Yeh, L.-C. Zhao, Y. Wiegand, I. Peelen, M. V. 2023-12-09 doi:10.1101/2023.12.08.570779 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions ]]> https://biorxiv.org/content/10.1101/2023.12.09.570606v1?rss=1 Pangeni, S. Biswas, G. Kaushik, V. Kuppa, S. Yang, O. Lin, C.-T. Mishra, G. Levy, Y. Antony, E. Ha, T. 2023-12-10 doi:10.1101/2023.12.09.570606 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Alpha-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinsons disease ]]> https://biorxiv.org/content/10.1101/2023.12.11.571045v1?rss=1 Geibl, F. F. Henrich, M. T. Xie, Z. Zampese, E. Tkatch, T. Wokosin, D. L. Nasiri, E. Grotmann, C. A. Dawson, V. L. Dawson, T. M. Chandel, N. S. Oertel, W. H. Surmeier, D. J. 2023-12-11 doi:10.1101/2023.12.11.571045 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Cross-species Myocardial Proteomics For Animal Models of Cardiometabolic Heart Failure With Preserved Ejection Fraction ]]> https://biorxiv.org/content/10.1101/2023.12.11.571180v1?rss=1 Guo, A. Yoo, E. J. 2023-12-12 doi:10.1101/2023.12.11.571180 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Highly variable molecular signatures of TDP-43 loss of function are associated with nuclear pore complex injury in a population study of sporadic ALS patient iPSNs ]]> https://biorxiv.org/content/10.1101/2023.12.12.571299v1?rss=1 150 control, C9orf72 ALS/FTD, and sALS patients to examine molecular signatures of TDP-43 dysfunction. This data set defines a time dependent and variable profile of individual molecular hallmarks of TDP-43 loss of function within and amongst individual patient lines. Importantly, nearly identical changes are observed in postmortem CNS tissues obtained from a subset of patients whose iPSNs were examined. Notably, these studies provide evidence that induction of nuclear pore complex (NPC) injury via reduction of the transmembrane Nup POM121 in wildtype iPSNs is sufficient to phenocopy disease associated signatured of TDP-43 loss of function thereby directly linking NPC integrity to TDP-43 loss of function. Therapeutically, we demonstrate that the expression of all mRNA species associated with TDP-43 loss of function can be restored in sALS iPSNs via two independent methods to repair NPC injury. Collectively, this data 1) represents a substantial resource for the community to examine TDP-43 loss of function events in authentic sALS patient iPSNs, 2) demonstrates that patient derived iPSNs can accurately reflect actual TDP-43 associated alterations in patient brain, and 3) that targeting NPC injury events can be preclinically and reliably accomplished in an iPSN based platform of a sporadic disease. ]]> Rothstein, J. D. Warlick, C. Coyne, A. N. 2023-12-13 doi:10.1101/2023.12.12.571299 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ A software tool for at-home measurement of sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2023.12.12.571359v1?rss=1 Jang, J. Shadmehr, R. Albert, S. T. 2023-12-13 doi:10.1101/2023.12.12.571359 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ Targeting LOXL2 Improves Arterial Stiffness and Function in Angiotensin II-induced Hypertension in Males but not Females ]]> https://biorxiv.org/content/10.1101/2023.12.13.571541v1?rss=1 Santhanam, L. Wang, H. Yus, M. M. Brady, T. Choi, R. Nandakumar, K. Smith, L. Jang, R. Wodu, B. P. Almodiel, D. Stoddart, L. Kim, D.-H. Steppan, J. 2023-12-14 doi:10.1101/2023.12.13.571541 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Improved bladder cancer antitumor efficacy with a recombinant BCG that releases a STING agonist ]]> https://biorxiv.org/content/10.1101/2023.12.15.571740v1?rss=1 Um, P. K. Praharaj, M. Lombardo, K. A. Yoshida, T. Matoso, A. Baras, A. S. Zhao, L. Srikrishna, G. Huang, J. Prasad, P. Kates, M. McConkey, D. Pardoll, D. M. Bishai, W. R. Bivalacqua, T. J. 2023-12-15 doi:10.1101/2023.12.15.571740 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors ]]> https://biorxiv.org/content/10.1101/2023.12.18.570445v1?rss=1 Ray, C. M. Yang, H. Spangler, J. B. Mac Gabhann, F. 2023-12-19 doi:10.1101/2023.12.18.570445 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ A Functional Schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. ]]> https://biorxiv.org/content/10.1101/2023.12.18.570831v1?rss=1 200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes; yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated 4 isogenic clones homozygous for the risk allele and 5 clones homozygous for the non-risk allele into neural precursor cells. Employing RNA-seq, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at FDR <0.05 and 259 genes at FDR <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk. ]]> Wahbeh, M. H. Boyd, R. J. Yovo, C. Rike, B. McCallion, A. S. Avramopoulos, D. 2023-12-19 doi:10.1101/2023.12.18.570831 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Spatial and Compositional Biomarkers in Tumor Microenvironment Predicts Clinical Outcomes in Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2023.12.18.572234v1?rss=1 Mi, H. Varadhan, R. Cimino-Mathews, A. M. Emens, L. A. Santa-Maria, C. A. Popel, A. S. 2023-12-20 doi:10.1101/2023.12.18.572234 Cold Spring Harbor Laboratory Press 2023-12-20 <![CDATA[ Temporal recording of mammalian development and precancer ]]> https://biorxiv.org/content/10.1101/2023.12.18.572260v1?rss=1 Islam, M. Yang, Y. Simmons, A. J. Shah, V. M. Pavan, M. K. Xu, Y. Tasneem, N. Chen, Z. Trinh, L. T. Molina, P. Ramirez-Solano, M. A. Sadien, I. Dou, J. Chen, K. Magnuson, M. A. Rathmell, J. Macara, I. G. Winton, D. J. Liu, Q. Zafar, H. Kalhor, R. Church, G. M. Shrubsole, M. J. Coffey, R. J. Lau, K. 2023-12-19 doi:10.1101/2023.12.18.572260 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Enhancement of antibody thermostability and affinity by computational design in the absence of antigen ]]> https://biorxiv.org/content/10.1101/2023.12.19.572421v1?rss=1 Hutchinson, M. Ruffolo, J. A. Haskins, N. Iannotti, M. Vozza, G. Pham, T. Mehzabeen, N. Shandilya, H. Rickert, K. Croasdale-Wood, R. Damschroder, M. Fu, Y. Dippel, A. Gray, J. J. Kaplan, G. 2023-12-19 doi:10.1101/2023.12.19.572421 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter ]]> https://biorxiv.org/content/10.1101/2023.12.20.572625v1?rss=1 Smith, E. L. Panis, G. Woldemeskel, S. A. Viollier, P. H. Chien, P. Goley, E. D. 2023-12-21 doi:10.1101/2023.12.20.572625 Cold Spring Harbor Laboratory Press 2023-12-21 <![CDATA[ Human telomere length is chromosome specific and conserved across individuals ]]> https://biorxiv.org/content/10.1101/2023.12.21.572870v1?rss=1 Greider, C. W. Karimian, K. Groot, A. Huso, V. Kahidi, R. Tan, K.-T. Sholes, S. Keener, R. W. McDyer, J. F. Alder, J. K. Li, H. K. Rechtsteiner, A. 2023-12-22 doi:10.1101/2023.12.21.572870 Cold Spring Harbor Laboratory Press 2023-12-22 <![CDATA[ Steroid signaling controls sex-specific development in an invertebrate ]]> https://biorxiv.org/content/10.1101/2023.12.22.573099v1?rss=1 Grmai, L. Jimenez, E. Baxter, K. Van Doren, M. 2023-12-23 doi:10.1101/2023.12.22.573099 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Decoding contextual influences on auditory perception from primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.12.24.573229v1?rss=1 Englitz, B. Akram, S. Elhilali, M. Shamma, S. 2023-12-24 doi:10.1101/2023.12.24.573229 Cold Spring Harbor Laboratory Press 2023-12-24 <![CDATA[ Chitinase 3-like-1 (CHI3L1) Inhibits Innate Anti-Tumor and Tissue Remodeling ImmuneResponses by Regulating CD47-SIRPα and CD24-Siglec10-Mediated Phagocytosis ]]> https://biorxiv.org/content/10.1101/2023.12.27.573478v1?rss=1 Ma, B. Kamle, S. Lee, C.-M. Lee, J. H. Yee, D. Zhu, Z. Silverman, E. K. DeMeo, D. Choi, A. M. K. Lee, C. G. Elias, J. A. 2023-12-28 doi:10.1101/2023.12.27.573478 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity ]]> https://biorxiv.org/content/10.1101/2023.12.28.573507v1?rss=1 Kimura, H. Lahouel, K. Tomasetti, C. Roberts, N. J. 2023-12-28 doi:10.1101/2023.12.28.573507 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape ]]> https://biorxiv.org/content/10.1101/2023.12.28.573594v1?rss=1 Cook, A. L. Sur, S. Dobbyn, L. Watson, E. Cohen, J. D. Ptak, B. Lee, B. S. Paul, S. Hsiue, E. Popoli, M. Vogelstein, B. Papadopoulos, N. Bettegowda, C. Gabrielson, K. Zhou, S. Kinzler, K. W. Wyhs, N. 2023-12-29 doi:10.1101/2023.12.28.573594 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Basolateral amygdala population coding of a cued reward seeking state depends on orbitofrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.12.31.573789v1?rss=1 Ottenheimer, D. J. Vitale, K. R. Ambroggi, F. Janak, P. H. Saunders, B. T. 2024-01-01 doi:10.1101/2023.12.31.573789 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ A food color based colorimetric assay for Cryptococcus neoformans laccase activity ]]> https://biorxiv.org/content/10.1101/2024.01.01.573823v1?rss=1 Ramirez, L. R. S. Dragotakes, Q. Casadevall, A. 2024-01-01 doi:10.1101/2024.01.01.573823 Cold Spring Harbor Laboratory Press 2024-01-01 <![CDATA[ MntJULiP and Jutils: Differential splicing analysis of RNA-seq data with covariates ]]> https://biorxiv.org/content/10.1101/2024.01.01.573825v1?rss=1 Lui, W. W. Yang, G. Florea, L. 2024-01-02 doi:10.1101/2024.01.01.573825 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ Novel metagenomics analysis suggests a Vibrio species is associated with stony coral tissue loss disease ]]> https://biorxiv.org/content/10.1101/2024.01.02.573916v1?rss=1 Heinz, J. M. Sommer, M. Rosales, S. M. Lu, J. Huebner, L. K. Salzberg, S. L. 2024-01-03 doi:10.1101/2024.01.02.573916 Cold Spring Harbor Laboratory Press 2024-01-03 <![CDATA[ Progressive heterogeneity of enlarged and irregularly shaped apicoplasts in P. falciparum persister blood stages after drug treatment ]]> https://biorxiv.org/content/10.1101/2024.01.03.574077v1?rss=1 Micchelli, C. Percopo, C. Traver, M. Brzostowski, J. Amin, S. N. Prigge, S. T. Sa, J. M. Wellems, T. 2024-01-04 doi:10.1101/2024.01.03.574077 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ Predicting Alu exonization in the human genome with a deep learning model ]]> https://biorxiv.org/content/10.1101/2024.01.03.574099v1?rss=1 He, Z. Chen, O. Phillips, N. Pasquesi, G. I. M. Sabunciyan, S. Florea, L. D. 2024-01-04 doi:10.1101/2024.01.03.574099 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ Air pollution drives macrophage senescence through a phagolysosome-15-lipoxygenase pathway ]]> https://biorxiv.org/content/10.1101/2024.01.04.574228v1?rss=1 Thomas, S. A. Yong, H. M. Rule, A. M. Gour, N. Lajoie, S. 2024-01-04 doi:10.1101/2024.01.04.574228 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ Antigen-display exosomes provide adjuvant-free protection against SARS-CoV-2 disease at nanogram levels of spike protein ]]> https://biorxiv.org/content/10.1101/2024.01.04.574272v1?rss=1 Guo, C. Sachithanandham, J. Zhong, W. Craney, M. Villano, J. Pekosz, A. Gould, S. 2024-01-05 doi:10.1101/2024.01.04.574272 Cold Spring Harbor Laboratory Press 2024-01-05 <![CDATA[ Innate Immune Activation and Mitochondrial ROS Invoke Persistent Cardiac Conduction System Dysfunction after COVID-19 ]]> https://biorxiv.org/content/10.1101/2024.01.05.574280v1?rss=1 Ashok, D. Liu, T. Criscione, J. Prakash, M. Kim, B. Chow, J. Craney, M. Papanicolaou, K. Sidor, A. Foster, D. B. Pekosz, A. Villano, J. Kim, D.-H. O'Rourke, B. 2024-01-08 doi:10.1101/2024.01.05.574280 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Stable Individual Differences from Dynamic Patterns of Function: Brain Network Flexibility Predicts Openness/Intellect and Intelligence ]]> https://biorxiv.org/content/10.1101/2024.01.05.574386v1?rss=1 Sassenberg, T. A. Safron, A. DeYoung, C. G. 2024-01-06 doi:10.1101/2024.01.05.574386 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ Single cell proteomics by mass spectrometry reveals deep epigenetic insight and new targets of a class specific histone deacetylase inhibitor ]]> https://biorxiv.org/content/10.1101/2024.01.05.574437v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@89811corg.highwire.dtl.DTLVardef@17b7971org.highwire.dtl.DTLVardef@16221deorg.highwire.dtl.DTLVardef@19d9968_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Orsburn, B. 2024-01-06 doi:10.1101/2024.01.05.574437 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ EEG responses to rapidly unfolding stochastic sounds reflect precision tracking ]]> https://biorxiv.org/content/10.1101/2024.01.08.574691v1?rss=1 Zhao, S. Skirritt-Davis, B. Elhilali, M. Dick, F. Chait, M. 2024-01-08 doi:10.1101/2024.01.08.574691 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Late consolidation of rRNA structure during co-transcriptional assembly in E. coli by time-resolved DMS footprinting ]]> https://biorxiv.org/content/10.1101/2024.01.10.574868v1?rss=1 Hao, Y. Hulscher, R. M. Zinshteyn, B. Woodson, S. 2024-01-10 doi:10.1101/2024.01.10.574868 Cold Spring Harbor Laboratory Press 2024-01-10 <![CDATA[ Recurrent connections enable point attractor dynamics and dimensionality reduction in a connectome-constrained model of the insect learning center ]]> https://biorxiv.org/content/10.1101/2024.01.10.574960v1?rss=1 Joyce, J. Norman-Tenazas, R. Rivlin, P. Hwang, G. M. Western, I. Zhang, K. Gray-Roncal, W. Robinson, B. 2024-01-11 doi:10.1101/2024.01.10.574960 Cold Spring Harbor Laboratory Press 2024-01-11 <![CDATA[ A comprehensive stroke risk assessment by combining atrial computational fluid dynamics simulations and functional patient data ]]> https://biorxiv.org/content/10.1101/2024.01.11.575156v1?rss=1 Zingaro, A. Ahmad, Z. Kholmovski, E. Sakata, K. Dede', L. Morris, A. K. Quarteroni, A. Trayanova, N. A. 2024-01-15 doi:10.1101/2024.01.11.575156 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ A dynamic subpopulation of CRISPR-Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage ]]> https://biorxiv.org/content/10.1101/2024.01.11.575229v1?rss=1 Stoltzfus, M. J. Workman, R. E. Keith, N. C. Modell, J. W. 2024-01-11 doi:10.1101/2024.01.11.575229 Cold Spring Harbor Laboratory Press 2024-01-11 <![CDATA[ The lateral habenula integrates age and experience to promote social transitions in developing rats ]]> https://biorxiv.org/content/10.1101/2024.01.12.575446v1?rss=1 Cobb-Lewis, D. E. George, A. Hu, S. Packard, K. Song, M. Nguyen-Lopez, O. Tesone, E. I. Rowden, J. Wang, J. Opendak, M. 2024-01-14 doi:10.1101/2024.01.12.575446 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ FLAb: Benchmarking deep learning methods for antibody fitness prediction ]]> https://biorxiv.org/content/10.1101/2024.01.13.575504v1?rss=1 Chungyoun, M. Ruffolo, J. A. Gray, J. J. 2024-01-15 doi:10.1101/2024.01.13.575504 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis ]]> https://biorxiv.org/content/10.1101/2024.01.14.575609v1?rss=1 Horisberger, A. Griffith, A. Keegan, J. Arazi, A. Pulford, J. Murzin, E. Howard, K. Hancock, B. Fava, A. Sasaki, T. Ghosh, T. Inamo, J. Beuschel, R. Cao, Y. Preisinger, K. Gutierrez-Arcelus, M. Eisenhaure, T. M. Guthridge, J. Hoover, P. J. Dall'Era, M. Wofsy, D. Kamen, D. L. Kalunian, K. C. Furie, R. Belmont, M. Izmirly, P. Clancy, R. Hildeman, D. Woodle, E. S. Apruzzese, W. McMahon, M. A. Grossman, J. Barnas, J. L. Payan-Schober, F. Ishimori, M. Weisman, M. Kretzler, M. Berthier, C. C. Hodgin, J. B. Demeke, D. S. Putterman, C. Accelerating Medicines Pa 2024-01-16 doi:10.1101/2024.01.14.575609 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Transposon-mediated genic rearrangements underlie variation in small RNA pathways ]]> https://biorxiv.org/content/10.1101/2024.01.15.575659v1?rss=1 Zhang, G. Felix, M.-A. Andersen, E. C. 2024-01-15 doi:10.1101/2024.01.15.575659 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Predicting how lipid composition controls protein curvature sensing with a continuum bilayer membrane model ]]> https://biorxiv.org/content/10.1101/2024.01.15.575755v1?rss=1 Fu, Y. Johnson, D. Beaven, A. Sodt, A. J. Zeno, W. F. Johnson, M. E. 2024-01-17 doi:10.1101/2024.01.15.575755 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ Biochemical and Structural Characterization of Fapy·dG Replication by Human DNA Polymerase β ]]> https://biorxiv.org/content/10.1101/2024.01.15.575758v1?rss=1 Gao, S. Oden, P. N. Ryan, B. J. Yang, H. Freudenthal, B. D. Greenberg, M. M. 2024-01-16 doi:10.1101/2024.01.15.575758 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Neuronal polyunsaturated fatty acids are protective in FTD/ALS ]]> https://biorxiv.org/content/10.1101/2024.01.16.575677v1?rss=1 Giblin, A. Cammack, A. J. Blomberg, N. Mikheenko, A. Carcole, M. Coneys, R. Zhou, L. Mohammed, Y. Olivier-Jimenez, D. Atilano, M. L. Niccoli, T. Coyne, A. N. van der Kant, R. Lashley, T. Giera, M. Partridge, L. Isaacs, A. M. 2024-01-17 doi:10.1101/2024.01.16.575677 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ ProteinMPNN Recovers Complex Sequence Properties of Transmembrane β-Barrels ]]> https://biorxiv.org/content/10.1101/2024.01.16.575764v1?rss=1 Dolorfino, M. D. Vorobieva, A. A. 2024-01-17 doi:10.1101/2024.01.16.575764 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2024.01.17.576106v1?rss=1 Mandl, A. Jasmine, S. Krueger, T. E. G. Kumar, R. Coleman, I. M. Dalrymple, S. L. Antony, L. Rosen, D. M. Jing, Y. Hanratty, B. Patel, R. A. Low, J.-Y. Dias, J. Celatka, C. A. Tapper, A. E. Kleppe, M. Kanayama, M. Speranzini, V. Wang, Y. Luo, J. Corey, E. Sena, L. A. Casero, R. A. Lotan, T. Trock, B. J. Kachhap, S. K. Denmeade, S. R. Carducci, M. A. Mattevi, A. Haffner, M. C. Nelson, P. S. Rienhoff, H. H. Isaacs, J. T. Brennen, W. N. 2024-01-22 doi:10.1101/2024.01.17.576106 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ OPA1 protects intervertebral disc and knee joint health in aged mice by maintaining the structure and metabolic functions of mitochondria ]]> https://biorxiv.org/content/10.1101/2024.01.17.576115v1?rss=1 Madhu, V. Hernandez-Meadows, M. Coleman, A. Sao, K. Inguito, K. Haslam, O. Boneski, P. K. Sesaki, H. Collins, J. A. Risbud, M. V. 2024-01-20 doi:10.1101/2024.01.17.576115 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Geometric changes in the nucleoids of Deinococcus radiodurans reveal involvement of new proteins in recovery from ionizing radiation. ]]> https://biorxiv.org/content/10.1101/2024.01.17.576117v1?rss=1 Cordova, A. Niese, B. Sweet, P. Kamat, P. Phillip, J. M. Gordon, V. Contreras, L. M. 2024-01-20 doi:10.1101/2024.01.17.576117 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Collective movement of schooling fish reduces locomotor cost in turbulence ]]> https://biorxiv.org/content/10.1101/2024.01.18.576168v1?rss=1 zhang, y. Ko, H. Calicchia, M. A. Ni, R. Lauder, G. 2024-01-22 doi:10.1101/2024.01.18.576168 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Self-Supervised Transformer Model Training for a Sleep-EEG Foundation Model ]]> https://biorxiv.org/content/10.1101/2024.01.18.576245v1?rss=1 Ogg, M. Coon, W. G. 2024-01-20 doi:10.1101/2024.01.18.576245 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Laying the Foundation: Modern Transformers for Gold-Standard Sleep Analysis ]]> https://biorxiv.org/content/10.1101/2024.01.18.576246v1?rss=1 Coon, W. G. Ogg, M. 2024-01-20 doi:10.1101/2024.01.18.576246 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation ]]> https://biorxiv.org/content/10.1101/2024.01.20.575817v1?rss=1 Chin Sang, C. Moore, G. Tereshchenko, M. Nosella, M. L. Zhang, H. Alderson, T. R. Dasovich, M. Leung, A. Finkelstein, I. J. Forman-Kay, J. D. Lee, H. O. 2024-01-22 doi:10.1101/2024.01.20.575817 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Aggregation of recount3 RNA-seq data improves the inference of consensus and tissue-specific gene co-expression networks. ]]> https://biorxiv.org/content/10.1101/2024.01.20.576447v1?rss=1 Battle, A. Ravichandran, P. Parsana, P. Keener, R. Hansen, K. 2024-01-22 doi:10.1101/2024.01.20.576447 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Genomic features of NF1-associated peripheral nerve sheath tumors: a cohort analysis from the Johns Hopkins NF1 biospecimen repository ]]> https://biorxiv.org/content/10.1101/2024.01.23.576977v1?rss=1 Banerjee, J. Lyu, Y. Makri, S. C. Scott, A. J. Zhang, L. Calizo, A. Pollard, K. Yang, K. Gross, J. M. Wang, J. Romo, C. G. Allaway, R. J. Blakeley, J. O. Hirbe, A. C. Pratilas, C. A. 2024-01-26 doi:10.1101/2024.01.23.576977 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Mimicking the breast metastatic microenvironment: characterization of a novel syngeneic model of HER2+ breast cancer ]]> https://biorxiv.org/content/10.1101/2024.01.25.577282v1?rss=1 Baugh, A. G. Gonzalez, E. Narumi, V. H. Kreger, J. Liu, Y. Rafie, C. Castanon, S. Jang, J. Kagohara, L. T. Anastasiadou, D. P. Leatherman, J. Armstrong, T. D. Chan, I. Karagiannis, G. S. Jaffee, E. M. MacLean, A. Roussos Torres, E. T. 2024-01-30 doi:10.1101/2024.01.25.577282 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ Paraoxonase-like APMAP maintains endoplasmic reticulum-associated lipid and lipoprotein homeostasis ]]> https://biorxiv.org/content/10.1101/2024.01.26.577049v1?rss=1 Paul, B. Merta, H. Ugrankar-Banerjee, R. Hensley, M. Tran, S. Dias do Vale, G. McDonald, J. G. Farber, S. A. Henne, W. M. 2024-01-28 doi:10.1101/2024.01.26.577049 Cold Spring Harbor Laboratory Press 2024-01-28 <![CDATA[ Islands of genomic stability in the face of genetically unstable metastatic cancer ]]> https://biorxiv.org/content/10.1101/2024.01.26.577508v1?rss=1 Bowland, K. Lai, J. Skaist, A. Zhang, Y. Teh, S. S. K. Roberts, N. J. Thompson, E. Wheelan, S. J. Hruban, R. H. Karchin, R. Iacobuzio-Donahue, C. A. Eshleman, J. R. 2024-01-29 doi:10.1101/2024.01.26.577508 Cold Spring Harbor Laboratory Press 2024-01-29 <![CDATA[ Self-organizing glycolytic waves fuel cell migration and cancer progression ]]> https://biorxiv.org/content/10.1101/2024.01.28.577603v1?rss=1 Zhan, H. Pal, D. S. Borleis, J. Janetopoulos, C. Huang, C.-H. Devreotes, P. N. 2024-01-28 doi:10.1101/2024.01.28.577603 Cold Spring Harbor Laboratory Press 2024-01-28 <![CDATA[ Plasmodium RON11 triggers biogenesis of the merozoite rhoptry pair and is essential for erythrocyte invasion ]]> https://biorxiv.org/content/10.1101/2024.01.29.577654v1?rss=1 Anaguano, D. Adewale Fasoro, O. Vick, G. S. Blauwkamp, J. A. Yanik, S. Fierro, M. A. Absalon, S. SRINIVASAN, P. Muralidharan, V. 2024-01-31 doi:10.1101/2024.01.29.577654 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ Mitochondrial DNA copy number reduction via in vitro TFAM knockout remodels the nuclear epigenome and transcriptome ]]> https://biorxiv.org/content/10.1101/2024.01.29.577835v1?rss=1 Nguyen, J. Win, P. W. Nagano, T. S. Shin, E. H. Newcomb, C. Arking, D. E. Castellani, C. A. 2024-01-31 doi:10.1101/2024.01.29.577835 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ FtsZ-mediated spatial-temporal control over septal cell wall synthesis ]]> https://biorxiv.org/content/10.1101/2024.01.29.577872v1?rss=1 Hu, L. Perez, A. Nesterova, T. Lyu, Z. Yahashiri, A. Weiss, D. S. Xiao, J. Liu, J. 2024-01-31 doi:10.1101/2024.01.29.577872 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ Targeting PD-L1 in solid cancer with myeloid cells expressing a CAR-like immune receptor ]]> https://biorxiv.org/content/10.1101/2024.01.29.577873v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@1657eborg.highwire.dtl.DTLVardef@e61ae3org.highwire.dtl.DTLVardef@ef3df4org.highwire.dtl.DTLVardef@cc90ea_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefWe described here an adoptive cell therapy approach employing PD-L1-specific CAR-like immune receptor (CARIR) modified myeloid cells as a potential immune cell therapy strategy for treating PD-L1+ solid cancer. O_LICARIR expression directed human THP-1 macrophages to recognize PD-L1+ target cells, which led to an upregulation of co-stimulatory molecule CD86 and production of proinflammatory cytokines TNF- and IL-1{beta}. C_LIO_LICARIR expression in human THP-1 macrophages had increased % phagocytosis and killing against PD-L1+ tumor cells in vitro. C_LIO_LIAdoptive transfer of CARIR transduced myeloid cells in immunocompetent syngeneic mice with established aggressive 4T1 tumor significantly slowed tumor growth and prolonged survival. C_LI ]]> Chen, K. M. Grun, D. Gautier, B. Venkatesha, S. Maddox, M. Zhang, A.-H. Andersen, P. 2024-02-01 doi:10.1101/2024.01.29.577873 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ A Novel Therapeutic Approach using CXCR3 Blockade to Treat Immune Checkpoint Inhibitor-mediated Myocarditis ]]> https://biorxiv.org/content/10.1101/2024.01.30.576279v1?rss=1 Huang, Y. V. Lee, D. Sun, Y. Chou, H. Xu, B. Lin, Z. Branche, C. Bayer, A. L. Waliany, S. Neal, J. Wakelee, H. Witteles, R. Nguyen, P. Graves, E. E. Alcaide, P. Berry, G. J. Wu, S. M. Zhu, H. 2024-02-02 doi:10.1101/2024.01.30.576279 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ FGF2 promotes the expansion of parietal mesothelial progenitor pools and inhibits BMP4-mediated smooth muscle cell differentiation ]]> https://biorxiv.org/content/10.1101/2024.01.31.577512v1?rss=1 Hwang, Y. Shimamura, Y. Tanaka, J. Miura, A. Sawada, A. SARMAH, H. Shimizu, D. Kondo, Y. Ninish, Z. Yamada, K. Mori, M. 2024-02-02 doi:10.1101/2024.01.31.577512 Cold Spring Harbor Laboratory Press 2024-02-02 <![CDATA[ Multiplexing of temporal and spatial information in the lateral entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2024.01.31.578307v1?rss=1 Wang, C. Lee, H. Rao, G. Knierim, J. J. 2024-02-01 doi:10.1101/2024.01.31.578307 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ Counter-regulation of RNA stability by UPF1 and TDP43 ]]> https://biorxiv.org/content/10.1101/2024.01.31.578310v1?rss=1 Gomez, N. Hsieh, C. Li, X. Dykstra, M. Waksmacki, J. Altheim, C. Bechar, Y. Klim, J. Zaepful, B. Rothstein, J. Tank, E. M. Barmada, S. J. 2024-02-04 doi:10.1101/2024.01.31.578310 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Quantifying the fitness effects of resistance alleles with and without anthelmintic selection pressure using Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.02.01.578300v1?rss=1 Shaver, A. O. Miller, I. R. Schaye, E. S. Moya, N. D. Collins, J. B. Wit, J. Blanco, A. H. Shao, F. M. Andersen, E. J. Khan, S. A. Paredes, G. Andersen, E. C. 2024-02-06 doi:10.1101/2024.02.01.578300 Cold Spring Harbor Laboratory Press 2024-02-06 <![CDATA[ DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements ]]> https://biorxiv.org/content/10.1101/2024.02.01.578352v1?rss=1 Ferreira DaSilva, L. Senan, S. Patel, Z. M. Reddy, A. J. Gabbita, S. Nussbaum, Z. Cordova, C. M. V. Wenteler, A. Weber, N. Tunjic, T. M. Khan, T. A. Li, Z. Smith, C. R. Bejan, M. Louis, L. K. Cornejo, P. Connell, W. Wong, E. S. Meuleman, W. Pinello, L. 2024-02-01 doi:10.1101/2024.02.01.578352 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ Neural substrates underlying the expectation of rewards resulting from effortful exertion ]]> https://biorxiv.org/content/10.1101/2024.02.01.578411v1?rss=1 Kim, A. Chib, V. S. 2024-02-04 doi:10.1101/2024.02.01.578411 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis ]]> https://biorxiv.org/content/10.1101/2024.02.01.578436v1?rss=1 Aihara, G. Clifton, K. Chen, M. Atta, L. Miller, B. F. Fan, J. 2024-02-05 doi:10.1101/2024.02.01.578436 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ TPPB modulates PKC activity to attenuate neuroinflammation and ameliorate experimental multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2024.02.02.578637v1?rss=1 Shanmukha, S. Godfrey, W. H. Gharibani, P. Lee, J. J. Guo, Y. Deng, X. Wender, P. A. Kornberg, M. D. Kim, P. M. 2024-02-07 doi:10.1101/2024.02.02.578637 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Large-Scale Functional Connectome Fingerprinting for Generalization and Transfer Learning in Neuroimaging ]]> https://biorxiv.org/content/10.1101/2024.02.02.578642v1?rss=1 Ogg, M. Kitchell, L. 2024-02-04 doi:10.1101/2024.02.02.578642 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies ]]> https://biorxiv.org/content/10.1101/2024.02.02.578662v1?rss=1 Yao, J. Yu, J. Caffo, B. Page, S. C. Martinowich, K. Hicks, S. C. 2024-02-04 doi:10.1101/2024.02.02.578662 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Semi-synthetic glycoconjugate vaccine candidate against Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2024.02.02.578725v1?rss=1 Crawford, C. J. Liporagi-Lopes, L. Coelho, C. Santos Junior, S. R. Nicola, A. M. Wear, M. P. Oscarson, S. Casadevall, A. 2024-02-03 doi:10.1101/2024.02.02.578725 Cold Spring Harbor Laboratory Press 2024-02-03 <![CDATA[ SREBP-dependent regulation of lipid homeostasis is required for progression and growth of pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.02.04.578802v1?rss=1 Ishida, C. T. Myers, S. L. Shao, W. McGuire, M. R. Liu, C. Kubota, C. S. Ewachiw, T. E. Mukhopadhyay, D. Ke, S. Wang, H. Rasheed, Z. A. Anders, R. A. Espenshade, P. J. 2024-02-08 doi:10.1101/2024.02.04.578802 Cold Spring Harbor Laboratory Press 2024-02-08 <![CDATA[ Transport activity regulates mitochondrial bioenergetics and biogenesis in renal tubules ]]> https://biorxiv.org/content/10.1101/2024.02.04.578838v1?rss=1 Cheng, C.-J. Nizar, J. M. Dai, D.-F. Huang, C.-L. 2024-02-08 doi:10.1101/2024.02.04.578838 Cold Spring Harbor Laboratory Press 2024-02-08 <![CDATA[ Host response during unresolved urinary tract infection alters mammary tissue homeostasis through collagen deposition and TIMP1 ]]> https://biorxiv.org/content/10.1101/2024.02.05.578977v1?rss=1 Henry, S. Lewis, S. M. Cyrill, S. L. Callaway, M. K. Chatterjee, D. Somasundara, A. V. H. Jones, G. He, X. Y. Caligiuri, G. Ciccone, M. F. Diaz, I. A. Biswas, A. Hernandez, E. Ha, T. Wilkinson, J. E. EGEBLAD, M. Tuveson, D. Dos Santos, C. O. 2024-02-06 doi:10.1101/2024.02.05.578977 Cold Spring Harbor Laboratory Press 2024-02-06 <![CDATA[ A TBX5-dependent compartment boundary patterns the cardiac interventricular septum ]]> https://biorxiv.org/content/10.1101/2024.02.05.578995v1?rss=1 Kathiriya, I. S. Dominguez, M. H. Rao, K. S. Muncie-Vasic, J. M. Devine, W. P. Hu, K. M. Hota, S. K. Garay, B. I. Quintero, D. Goyal, P. Matthews, M. N. Thomas, R. Sukonnik, T. Miguel-Perez, D. Winchester, S. Brower, E. F. Forjaz, A. Wu, P.-H. Wirtz, D. Kiemen, A. L. Bruneau, B. G. 2024-02-05 doi:10.1101/2024.02.05.578995 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ Substrate stiffness modulates the emergence and magnitude of senescence phenotypes ]]> https://biorxiv.org/content/10.1101/2024.02.06.579151v1?rss=1 Starich, B. Yang, F. Tanrioven, D. Kung, H.-C. Baek, J. Nair, P. R. Kamat, P. Macaluso, N. Eoh, J. Han, K. S. Gu, L. Sun, S. Wu, P.-H. Wirtz, D. Phillip, J. M. 2024-02-07 doi:10.1101/2024.02.06.579151 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Neural basis of self-control ]]> https://biorxiv.org/content/10.1101/2024.02.07.578652v1?rss=1 Lee, K. E. Elsey, J. Hwang, J. Emeric, E. Stuphorn, V. 2024-02-08 doi:10.1101/2024.02.07.578652 Cold Spring Harbor Laboratory Press 2024-02-08 <![CDATA[ Microtubule-dependent orchestration of centriole amplification in brain multiciliated cells ]]> https://biorxiv.org/content/10.1101/2024.02.09.579615v1?rss=1 Boudjema, A.-R. Balague, R. Jewett, C. E. LoMastro, G. M. Mercy, O. Al Jord, A. Faucourt, M. Schaeffer, A. Nous, C. Delgehyr, N. Holland, A. J. Spassky, N. Meunier, A. 2024-02-12 doi:10.1101/2024.02.09.579615 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ The lateral habenula is required for maternal behavior in the mouse dam ]]> https://biorxiv.org/content/10.1101/2024.02.12.577842v1?rss=1 Benedict, J. Cudmore, R. H. Linden, D. J. Oden, D. Spruell, A. 2024-02-13 doi:10.1101/2024.02.12.577842 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ Continuous Bump Attractor Networks Require Explicit Error Coding for Gain Recalibration ]]> https://biorxiv.org/content/10.1101/2024.02.12.579874v1?rss=1 Secer, G. Knierim, J. J. Cowan, N. J. 2024-02-12 doi:10.1101/2024.02.12.579874 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ CRM1 regulates androgen receptor stability and impacts DNA repair pathways in prostate cancer, independent of the androgen receptor. ]]> https://biorxiv.org/content/10.1101/2024.02.13.579966v1?rss=1 Kumar, R. Mendonca, J. Shetty, A. Yang, Y. Owoyemi, O. Wilson, L. C. Boyapati, K. Topiwala, D. Thomas, N. Nguyen, H. Luo, J. Paller, C. J. Denmeade, S. R. Carducci, M. A. Kachhap, S. K. 2024-02-16 doi:10.1101/2024.02.13.579966 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Complementary Cytoskeletal Feedback Loops Control Signal Transduction Excitability and Cell Polarity ]]> https://biorxiv.org/content/10.1101/2024.02.13.580131v1?rss=1 Kuhn, J. A. Banerjee, P. Haye, A. Robinson, D. N. Iglesias, P. A. Devreotes, P. N. 2024-02-13 doi:10.1101/2024.02.13.580131 Cold Spring Harbor Laboratory Press 2024-02-13 <![CDATA[ UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation ]]> https://biorxiv.org/content/10.1101/2024.02.13.580169v1?rss=1 Tiedemann, R. Hrit, J. Du, Q. Wiseman, A. K. Eden, H. E. Dickson, B. M. Kong, X. Chomiak, A. Vaughan, R. M. Hebert, J. M. David, Y. Zhou, W. M. Baylin, S. Jones, P. A. Clark, S. Rothbart, S. B. 2024-02-16 doi:10.1101/2024.02.13.580169 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Exact centriole counts are critical for B cell development but not function ]]> https://biorxiv.org/content/10.1101/2024.02.14.580240v1?rss=1 Schapfl, M. A. LoMastro, G. M. Braun, V. Z. Hirai, M. Levine, M. S. Kiermaier, E. Labi, V. Holland, A. J. Villunger, A. 2024-02-15 doi:10.1101/2024.02.14.580240 Cold Spring Harbor Laboratory Press 2024-02-15 <![CDATA[ The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation ]]> https://biorxiv.org/content/10.1101/2024.02.14.580277v1?rss=1 Vidaurre, V. Song, A. Li, T. Ku, W. L. Zhao, K. Qian, J. Chen, X. 2024-02-14 doi:10.1101/2024.02.14.580277 Cold Spring Harbor Laboratory Press 2024-02-14 <![CDATA[ Integrated Short-TE and Hadamard-edited Multi-Sequence (ISTHMUS) for Advanced MRS ]]> https://biorxiv.org/content/10.1101/2024.02.15.580516v1?rss=1 Hui, S. C. N. Murali-Manohar, S. Zollner, H. J. Hupfeld, K. E. Davies-Jenkins, C. W. Gudmundson, A. T. Song, Y. Yedavalli, V. Wisnowski, J. L. Gagoski, B. Oeltzschner, G. Edden, R. A. E. 2024-02-20 doi:10.1101/2024.02.15.580516 Cold Spring Harbor Laboratory Press 2024-02-20 <![CDATA[ A Neural Network Approach to Identify Left-Right Orientation of Anatomical Brain MRI ]]> https://biorxiv.org/content/10.1101/2024.02.15.580574v1?rss=1 Nishimaki, K. Iyatomi, H. Oishi, K. 2024-02-20 doi:10.1101/2024.02.15.580574 Cold Spring Harbor Laboratory Press 2024-02-20 <![CDATA[ Pathologic α-Synuclein-NOD2 Interaction and RIPK2 Activation Drives Microglia-Induced Neuroinflammation in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.02.19.580982v1?rss=1 View larger version (74K): org.highwire.dtl.DTLVardef@10c010aorg.highwire.dtl.DTLVardef@1183b23org.highwire.dtl.DTLVardef@1d289dborg.highwire.dtl.DTLVardef@158b6ef_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefPathological -Synuclein (-Syn) binds to the microglial NOD2 protein, which in turn triggers NOD2/RIPK2 complex and RIPK2 phosphorylation/ubiquitination. This process activates the NF-kB/MAPK pathways, ultimately leading to neurotoxic reactive astrocyte-induced dopaminergic neurodegeneration. Depletion of RIPK2 (RIPK2 KO) or NOD2 (NOD2) protects dopamine neurons in a mouse model of Parkinsons disease (PD). These findings provide insights into -Syn-driven neuroinflammation and offer potential therapeutic strategies for PD. HighlightsNOD2/RIPK2 signaling is identified as a crucial regulator of neuroinflammation in PD. NOD2/RIPK2 signaling is highly active in microglia in human PD brains and -Syn PFF mouse models. Pathological -Syn binds to NOD2, triggering self-oligomerization and RIPK2 complex formation, leading to MAPK and NF-kB activation Genetic depletion of NOD2 or RIPK2 reduces neuroinflammation and protects dopamine neurons by blocking the formation of neurotoxic reactive astrocytes. ]]> Ko, H. Dawson, T. M. Seo, B. A. Kwon, S.-H. Kim, D. Kim, H.-B. Ma, S.-X. Gadhave, K. Burgess, N. Mao, X. Rosenthal, L. S. Redding-Ochoa, J. Troncoso, J. C. Lee, S. Dawson, V. L. 2024-02-25 doi:10.1101/2024.02.19.580982 Cold Spring Harbor Laboratory Press 2024-02-25 <![CDATA[ Causal Discovery Analysis Reveals Insights into Psychosis Proneness, Brain Function, and Environmental Factors among Young Individuals ]]> https://biorxiv.org/content/10.1101/2024.02.19.581044v1?rss=1 Sahin-Ilikoglu, T. Ma, S. Kummerfeld, E. Rawls, E. Tan, H. Y. Toulopoulou, T. 2024-02-22 doi:10.1101/2024.02.19.581044 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Voice patches in the marmoset auditory cortex revealed by wide-field calcium imaging ]]> https://biorxiv.org/content/10.1101/2024.02.19.581089v1?rss=1 Zhang, Y. Song, X. Guo, Y. Chen, C. Osmanski, M. S. Wang, X. 2024-02-22 doi:10.1101/2024.02.19.581089 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Rejuvenating silicon probes for acute electrophysiology ]]> https://biorxiv.org/content/10.1101/2024.02.20.581222v1?rss=1 Shoup, A. Porwal, N. Fakharian, M. A. Hage, P. Orozco, S. P. Shadmehr, R. 2024-02-23 doi:10.1101/2024.02.20.581222 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH ]]> https://biorxiv.org/content/10.1101/2024.02.21.581401v1?rss=1 Troyer, Z. Gololobova, O. Koppula, A. Liao, Z. Horns, F. Elowitz, M. B. Tosar, J. P. Batish, M. Witwer, K. W. 2024-02-22 doi:10.1101/2024.02.21.581401 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Development of novel tools for dissection of central versus peripheral dopamine D2-like receptor signaling in dysglycemia ]]> https://biorxiv.org/content/10.1101/2024.02.21.581451v1?rss=1 Bonifazi, A. Ellenberger, M. Farino, Z. J. Aslanoglou, D. Rais, R. Pereira, S. Mantilla-Rivas, J. O. Boateng, C. A. Eshleman, A. J. Janowsky, A. Hahn, M. K. Schwartz, G. J. Slusher, B. S. Freyberg, Z. 2024-02-23 doi:10.1101/2024.02.21.581451 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time ]]> https://biorxiv.org/content/10.1101/2024.02.21.581474v1?rss=1 Satterlee, J. W. Alonso, D. Gramazio, P. Jenike, K. M. He, J. Arrones, A. Villanueva, G. Plazas, M. Ramakrishnan, S. Benoit, M. Gentile, I. Hendelman, A. Shohat, H. Fitzgerald, B. Robitaille, G. M. Green, Y. Swartwood, K. Passalacqua, M. J. Gagnon, E. Hilgenhof, R. Huggins, T. D. Eizenga, G. C. Gur, A. Rutten, T. Stein, N. Yao, S. Bellot, C. Bendahmane, M. Frary, A. Knapp, S. Sarkinen, T. Gillis, J. Van Eck, J. Schatz, M. C. Eshed, Y. Prohens, J. Vilanova, S. Lippman, Z. B. 2024-02-22 doi:10.1101/2024.02.21.581474 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch ]]> https://biorxiv.org/content/10.1101/2024.02.22.581437v1?rss=1 Hicks, C. W. Rahman, S. Gloor, S. L. Fields, J. K. Husby, N. L. Vaidya, A. Maier, K. E. Morgan, M. Keogh, M.-C. Wolberger, C. 2024-02-22 doi:10.1101/2024.02.22.581437 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. ]]> https://biorxiv.org/content/10.1101/2024.02.22.581585v1?rss=1 Cahn, J. Regulski, M. Lynn, J. Ernst, E. de Santis Alves, C. Ramakrishnan, S. Chougule, K. Wei, S. Lu, Z. Xu, X. Drenkow, J. Kramer, M. Seetharam, A. Hufford, M. B. McCombie, W. R. Ware, D. Jackson, D. Schatz, M. C. Gingeras, T. R. Martienssen, R. A. 2024-02-23 doi:10.1101/2024.02.22.581585 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Nicotinamide riboside activates renal metabolism and protects the kidney in a model of Alport syndrome ]]> https://biorxiv.org/content/10.1101/2024.02.26.580911v1?rss=1 Jones, B. A. Gisch, D. L. Myakala, K. Sadiq, A. Cheng, Y.-H. Taranenko, E. Panov, J. Korolowicz, K. Wang, X. Rosenberg, A. Z. Jain, S. Eadon, M. T. Levi, M. 2024-02-29 doi:10.1101/2024.02.26.580911 Cold Spring Harbor Laboratory Press 2024-02-29 <![CDATA[ Cognate Antigen Engagement Induces HIV-1 Expression In CD4+ T Cells From People On Long-Term ART ]]> https://biorxiv.org/content/10.1101/2024.02.27.582096v1?rss=1 Moskovjlevic, M. Dragoni, F. Board, N. L. Wu, F. Lai, J. Zhang, H. White, J. R. Ho, R. Lynn, K. Tebas, P. Mounzer, K. Deeks, S. G. Montaner, L. J. Siliciano, J. D. Simonetti, F. R. Siliciano, R. F. 2024-03-01 doi:10.1101/2024.02.27.582096 Cold Spring Harbor Laboratory Press 2024-03-01 <![CDATA[ Linewidth-related bias in modelled concentration estimates from GABA-edited 1H-MRS ]]> https://biorxiv.org/content/10.1101/2024.02.27.582249v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@612fbaorg.highwire.dtl.DTLVardef@8462aforg.highwire.dtl.DTLVardef@16af040org.highwire.dtl.DTLVardef@1c3141f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG To assess the degree to which aspects of linewidth, lineshape and SNR may confound GABA+ estimates, a collection of in-vivo datasets were quantified with six modelling algorithms, with linebroadening and SNR varied experimentally. Most algorithms showed a strong association between GABA+ estimate and Lorentzian linebroadening (2-5% decrease per Hz), with weaker effects for Gaussian broadening. This indicates a potentially significant confound in cases of differing relaxation parameters between groups or experimental conditions. ]]> Craven, A. R. Bell, T. K. Ersland, L. Harris, A. D. Hugdahl, K. Oeltzschner, G. 2024-02-28 doi:10.1101/2024.02.27.582249 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ A Lung Cancer Mouse Model Database ]]> https://biorxiv.org/content/10.1101/2024.02.28.582577v1?rss=1 Cai, L. Gao, Y. DeBerardinis, R. J. Chen, T. Winslow, M. M. Xiao, G. Rudin, C. Oliver, T. G. Minna, J. D. Xie, Y. 2024-02-29 doi:10.1101/2024.02.28.582577 Cold Spring Harbor Laboratory Press 2024-02-29 <![CDATA[ Analysis of justification for and gender bias in author order among those contributing equally ]]> https://biorxiv.org/content/10.1101/2024.03.01.582955v1?rss=1 Mattoon, E. R. Miles, M. Casadevall, A. Broderick, N. A. 2024-03-04 doi:10.1101/2024.03.01.582955 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ Thermal Characterization and Preclinical Validation of an Accessible, Carbon Dioxide-Based Cryotherapy System ]]> https://biorxiv.org/content/10.1101/2024.03.01.582967v1?rss=1 Hu, Y. Gordon, N. Ogg, K. Kraitchman, D. L. Durr, N. J. Surtees, B. 2024-03-04 doi:10.1101/2024.03.01.582967 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ Molecular Signatures of Normal Pressure Hydrocephalus: A Large-scale Proteomic Analysis of Cerebrospinal Fluid ]]> https://biorxiv.org/content/10.1101/2024.03.01.583014v1?rss=1 Kamalian, A. Shirzadeh Barough, S. Ho, S. G. Albert, M. Luciano, M. G. Yasar, S. Moghekar, A. 2024-03-04 doi:10.1101/2024.03.01.583014 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2024.03.03.583159v1?rss=1 Takada, H. Paternoga, H. Fujiwara, K. Nakamoto, J. A. Park, E. N. Dimitrova-Paternoga, L. Beckert, B. Saarma, M. Tenson, T. Buskirk, A. Atkinson, G. C. Chiba, S. Wilson, D. N. Hauryliuk, V. 2024-03-04 doi:10.1101/2024.03.03.583159 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ Hyaluronidase impacts exposures of long-acting injectable paliperidone palmitate in rodent models ]]> https://biorxiv.org/content/10.1101/2024.03.03.583160v1?rss=1 Pertinez, H. Kaushik, A. Curley, P. Arshad, U. El-Khateeb, E. Li, S.-Y. Tasneen, R. Sharp, J. Kijak, E. Herriott, J. Neary, M. Noe, M. Flexner, C. Nuermberger, E. Owen, A. Ammerman, N. C. 2024-03-06 doi:10.1101/2024.03.03.583160 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Integrated stress response associated with dark microglia promotes microglial lipogenesis and contributes to neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.03.04.582965v1?rss=1 Flury, A. Aljayousi, L. Aziz, S. Park, H.-J. Khakpour, M. Sandberg, C. Ibanez, F. G. Braniff, O. Deme, P. McGrath, J. D. Ngo, T. Mechler, J. Ramirez, D. M. Avnon-Klein, D. Murray, J. W. Liu, J. Haughey, N. J. Werneburg, S. Tremblay, M.-E. Ayata, P. 2024-03-08 doi:10.1101/2024.03.04.582965 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Chronic infection alters pathogen virulence, microbiome composition, and fly physiology across generations. ]]> https://biorxiv.org/content/10.1101/2024.03.04.583275v1?rss=1 Maya-Maldonado, K. Broderick, N. A. 2024-03-05 doi:10.1101/2024.03.04.583275 Cold Spring Harbor Laboratory Press 2024-03-05 <![CDATA[ Sarm1 is not necessary for activation of neuron-intrinsic growth programs yet required for the Schwann cell repair response and peripheral nerve regeneration. ]]> https://biorxiv.org/content/10.1101/2024.03.04.583374v1?rss=1 Schmitd, L. B. Hafner, H. Ward, A. Adib, E. A. Biscola, N. P. Kohen, R. Patel, M. Williamson, R. E. Desai, E. Bennett, J. Saxman, G. Athaiya, M. Wilborn, D. Shumpert, J. Zhao, X.-F. Kawaguchi, R. Geschwind, D. H. Hoke, A. Shrager, P. Collins, C. A. Havton, L. A. Kalinski, A. L. Giger, R. J. 2024-03-08 doi:10.1101/2024.03.04.583374 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment ]]> https://biorxiv.org/content/10.1101/2024.03.05.583511v1?rss=1 Kovaka, S. Hook, P. W. Jenike, K. M. Shivakumar, V. Morina, L. B. Razaghi, R. Timp, W. Schatz, M. C. 2024-03-11 doi:10.1101/2024.03.05.583511 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ The Molecular Basis for Hydrodynamic Properties of PEGylated Human Serum Albumin ]]> https://biorxiv.org/content/10.1101/2024.03.05.583576v1?rss=1 Fleming, P. Correia, J. J. Fleming, K. G. 2024-03-11 doi:10.1101/2024.03.05.583576 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Centriole structural integrity defects are a crucial feature of Hydrolethalus Syndrome ]]> https://biorxiv.org/content/10.1101/2024.03.06.583733v1?rss=1 Curinha, A. Huang, Z. Anglen, T. Strong, M. A. Gliech, C. R. Jewett, C. E. Friskes, A. Holland, A. J. 2024-03-06 doi:10.1101/2024.03.06.583733 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Pharmacological inhibition of macrophage triglyceride biosynthesis pathways does not improve Mycobacterium tuberculosis control in infected mice ]]> https://biorxiv.org/content/10.1101/2024.03.06.583745v1?rss=1 Castillo, J. R. Guerrini, V. Quijada, D. Karanika, S. Neupane, P. Harris, H. Garcia, A. Shenkoya, B. Yilma, A. Bailey, H. Khan, R. Gopalakrishnan, M. Gennaro, M. L. Karakousis, P. C. 2024-03-11 doi:10.1101/2024.03.06.583745 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness ]]> https://biorxiv.org/content/10.1101/2024.03.06.583771v1?rss=1 Liu, N. Qiang, W. Jordan, P. Marko, J. F. Qiao, H. 2024-03-11 doi:10.1101/2024.03.06.583771 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Comparing Automated Subcortical Volume Estimation Methods; Amygdala Volumes Estimated by FSL and FreeSurfer Have Poor Consistency ]]> https://biorxiv.org/content/10.1101/2024.03.07.583900v1?rss=1 Sadil, P. Lindquist, M. A. 2024-03-10 doi:10.1101/2024.03.07.583900 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping ]]> https://biorxiv.org/content/10.1101/2024.03.07.583909v1?rss=1 Joshi, S. Forjaz, A. Sang Han, K. Shen, Y. Xenes, D. Matelsky, J. Wester, B. Munoz-Barrutia, A. Kiemen, A. L. Wu, P.-H. Wirtz, D. 2024-03-10 doi:10.1101/2024.03.07.583909 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ In vitro and in vivo validation of cwlM and pbpB essentiality for viability and resistance to imipenem in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2024.03.08.584109v1?rss=1 Nuermberger, E. L. Lee, J. I. Li, S.-Y. Rifat, D. Kurepina, N. Chen, L. Kreiswirth, B. N. 2024-03-09 doi:10.1101/2024.03.08.584109 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Direct inhibitors of InhA with efficacy similar or superior to isoniazid in novel drug regimens for tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.03.08.584126v1?rss=1 Encinas, L. Li, S.-Y. Rullas-Trincado, J. Tasneen, R. TYAGI, S. Soni, H. garcia-perez, a. Lee, J. Gonzalez del Rio, R. De Mercado, J. Sousa, V. Sosi?, I. Gobec, S. Mendoza-Losana, A. Converse, P. J. Mdluli, K. Fotouhi, N. BARROS-AGUIRRE, D. Nuermberger, E. L. 2024-03-14 doi:10.1101/2024.03.08.584126 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ The carrier proteome limit should be reassessed for each mass analyzer architecture ]]> https://biorxiv.org/content/10.1101/2024.03.08.584130v1?rss=1 Orsburn, B. 2024-03-12 doi:10.1101/2024.03.08.584130 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ An Amygdalar Oscillator Coordinates Cellular and Behavioral Rhythms ]]> https://biorxiv.org/content/10.1101/2024.03.08.584151v1?rss=1 Liu, Q. Xiong, J. Kim, D. W. Lee, S. S. Bell, B. J. Alexandre, C. Blackshaw, S. Latremoliere, A. Wu, M. N. 2024-03-13 doi:10.1101/2024.03.08.584151 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Deepening biomedical research training: Community-Building Wellness Workshops for Post-Baccalaureate Research Education Program (PREP) Trainees ]]> https://biorxiv.org/content/10.1101/2024.03.10.584300v1?rss=1 Cole, D. Eneim, A. S. White, C. J. Eddings, C. R. Beckett, M. Q. Clark, V. Jeffery, J. Wimalasena, V. K. Figueroa, A. Rosado-Franco, J. J. Alhariri, R. Powell, B. H. Washington, P. W. Christensen, L. N. Wilson, K. L. Kavran, J. M. 2024-03-13 doi:10.1101/2024.03.10.584300 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level and its Application in HIV ]]> https://biorxiv.org/content/10.1101/2024.03.10.584315v1?rss=1 He, M. Zhao, N. 2024-03-13 doi:10.1101/2024.03.10.584315 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Chronic Ethanol Exposure Produces Persistent Impairment in Cognitive Flexibility and Decision Signals in the Striatum ]]> https://biorxiv.org/content/10.1101/2024.03.10.584332v1?rss=1 Cheng, Y. Magnard, R. Langdon, A. Lee, D. Janak, P. H. 2024-03-12 doi:10.1101/2024.03.10.584332 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Rejuvenation of aged oocyte through exposure to young follicular microenvironment ]]> https://biorxiv.org/content/10.1101/2024.03.11.584343v1?rss=1 Wang, H. Huang, Z. Lee, Y. Song, X. Shen, X. Shu, C. Wu, L. H. Pakkiri, L. S. Lim, P. L. Zhang, X. Drum, C. L. Zhu, J. Li, R. 2024-03-13 doi:10.1101/2024.03.11.584343 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Modulation of GABAAreceptor trafficking by WWC2 reveals class-specific mechanisms of synapse regulation by WWC family proteins ]]> https://biorxiv.org/content/10.1101/2024.03.11.584487v1?rss=1 Dunham, T. L. Wilkerson, J. R. Johnson, R. C. Huganir, R. L. Volk, L. J. 2024-03-12 doi:10.1101/2024.03.11.584487 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Cervical collagen network porosity assessed by SHG endomicroscopy distinguishes preterm and normal pregnancy - a pilot study ]]> https://biorxiv.org/content/10.1101/2024.03.12.584664v1?rss=1 Liang, W. Liu, Y. Guan, H. Sakulsaengprapha, V. Luby-Phelps, K. Mahendroo, M. Li, X. 2024-03-14 doi:10.1101/2024.03.12.584664 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Adoptive Transfer of CD49a+ Tissue Resident memory cells reverses pulmonary fibrosis in mice. ]]> https://biorxiv.org/content/10.1101/2024.03.13.584814v1?rss=1 Collins, S. L. Chan-Li, Y. Shenderov, K. Nelson, A. M. Loube, J. M. Mitzner, W. A. Powell, J. D. Horton, M. R. Gillich, A. 2024-03-14 doi:10.1101/2024.03.13.584814 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Applying 3D correlative structured illumination microscopy and X-ray tomography to characterise herpes simplex virus-1 morphogenesis ]]> https://biorxiv.org/content/10.1101/2024.03.13.584906v1?rss=1 pUL21 > VP16 > pUL16 > pUS3) according to the levels of attenuation observed for each virus. Correlative imaging also revealed the roles of five viral proteins in cytoplasmic envelopment. VP16 was found to be important in capsid delivery to envelopment compartments, while cytoplasmic clusters of virus particles plus features of stalled envelopment not previously described were observed in the absence of pUL11, pUL51, gK, and gE. Finally, this 3D imaging approach was used to capture different assembly stages during cytoplasmic envelopment and to determine that envelopment occurs by particle budding rather than wrapping. The findings demonstrate that tomographic 3D correlative imaging is an emerging technology that sheds new light on viral protein functions and virion morphogenesis. ImportanceTo date, the characterisation of HSV-1 mutants in the study of virus assembly has been limited to transmission electron microscopy (TEM) without the addition of correlative light microscopy to identify fluorescently labelled viral proteins. In addition, only a small number of mutants are typically used in each study. Herein, a comparative analysis of nine HSV-1 mutants lacking specific structural proteins was performed using correlative fluorescence microscopy and X-ray tomography for the first time, revealing the relative roles of each viral protein in virus assembly. pUL11, pUL51, gK, and gE were shown to have important roles in cytoplasmic envelopment, with the loss of their functions leading to various stalled cytoplasmic envelopment phenotypes involving polarised arrays of capsids at one side of cytoplasmic vesicles that to our knowledge have never been seen with TEM. This correlative imaging approach enabled the study of cytoplasmic envelopment in 3D, revealing an envelopment mechanism driven by capsid budding rather than membrane wrapping. Further cryoSIM experiments revealed that pUL16 and pUL21 are important in nuclear egress of HSV-1 and that VP16 promotes nuclear egress and delivery of capsids to cytoplasmic envelopment compartments. By providing novel and comparative insights into the roles of different viral proteins in various stages of HSV-1 assembly, these findings highlight the utility of correlative cryo-fluorescence plus cryo-soft-X-ray tomography for probing trajectories of intracellular pathogen assembly. ]]> Nahas, K. L. Connor, V. Wijesinghe, K. J. Barrow, H. G. Dobbie, I. M. Harkiolaki, M. Graham, S. C. Crump, C. M. 2024-03-13 doi:10.1101/2024.03.13.584906 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Pavlovian cue-evoked alcohol seeking is disrupted by ventral pallidal inhibition ]]> https://biorxiv.org/content/10.1101/2024.03.14.585064v1?rss=1 Richard, J. M. Armstrong, A. Newell, B. Muruganandan, P. Janak, P. H. Saunders, B. T. 2024-03-14 doi:10.1101/2024.03.14.585064 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Epidemiological, Serological, and Virological Analysis of an Outbreak of Elephant Hemorrhagic Disease in Switzerland ]]> https://biorxiv.org/content/10.1101/2024.03.14.585086v1?rss=1 Ackermann, M. Kubacki, J. Heaggans-Ebbeson, S. Hayward, G. S. Lechmann, J. 2024-03-15 doi:10.1101/2024.03.14.585086 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Tobacco Smoke Exposure is Characterized by a Distinct Nasal Rhinotype in a Pediatric Population ]]> https://biorxiv.org/content/10.1101/2024.03.15.585112v1?rss=1 Monaco, H. Elaiho, C. Liu, B. Chan, T. Cantor, A. Collaco, J. M. McGrath-Morrow, S. Wilson, K. Clemente, J. C. 2024-03-18 doi:10.1101/2024.03.15.585112 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ Mapping the breast tumor microenvironment: proximity analysis reveals spatial relationships between macrophage subtypes and metastasis-initiating cancer cells ]]> https://biorxiv.org/content/10.1101/2024.03.15.585195v1?rss=1 Grasset, E. M. Desphande, A. Lee, J. W. Cho, Y. Shin, S. M. Coyne, E. M. Hernandez, A. Yuan, X. Cimino-Matthews, A. Ewald, A. J. Ho, W. J. 2024-03-17 doi:10.1101/2024.03.15.585195 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Gapless assembly of complete human and plant chromosomes using only nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2024.03.15.585294v1?rss=1 Koren, S. Bao, Z. Guarracino, A. Ou, S. Goodwin, S. Jenike, K. M. Lucas, J. McNulty, B. Park, J. Rautianinen, M. Rhie, A. Roelofs, D. Schneiders, H. Vrijenhoek, I. Nijbroek, K. Ware, D. Schatz, M. C. Garrison, E. Huang, S. McCombie, W. R. Miga, K. H. Wittenberg, A. H. J. Phillippy, A. M. 2024-03-17 doi:10.1101/2024.03.15.585294 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations ]]> https://biorxiv.org/content/10.1101/2024.03.17.585370v1?rss=1 Fernandez, E. C. Tomassoni, L. Zhang, X. Wang, J. Obradovic, A. Laise, P. Griffin, A. T. Vlahos, L. Minns, H. E. Morales, D. V. Simmons, C. Gallitto, M. Wei, H.-J. Martins, T. J. Becker, P. S. Crawford, J. R. Tzaridis, T. Wechsler-Reya, R. J. Garvin, J. Gartrell, R. D. Szalontay, L. Zacharoulis, S. Wu, C.-C. Zhang, Z. Califano, A. Pavisic, J. 2024-03-17 doi:10.1101/2024.03.17.585370 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Light-gated Integrator for Highlighting Kinase Activity in Living Cells ]]> https://biorxiv.org/content/10.1101/2024.03.18.585554v1?rss=1 Lin, W. Phatarphekar, A. Zhong, Y. Liu, L. Kwon, H.-B. Gerwick, W. H. Wang, Y. Mehta, S. Zhang, J. 2024-03-20 doi:10.1101/2024.03.18.585554 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Transformer Model Generated Bacteriophage Genomes are Compositionally Distinct from Natural Sequences ]]> https://biorxiv.org/content/10.1101/2024.03.19.585716v1?rss=1 Ratcliff, J. D. 2024-03-22 doi:10.1101/2024.03.19.585716 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology ]]> https://biorxiv.org/content/10.1101/2024.03.21.586102v1?rss=1 Mimar, S. Paul, A. S. Lucarelli, N. Boarder, S. Naglah, A. Barisoni, L. Hodgin, J. Rosenberg, A. Clapp, W. Sarder, P. 2024-03-26 doi:10.1101/2024.03.21.586102 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Engineered Flt3L Drives Tolerogenic State to Attenuate Anti-drug Antibody Responses ]]> https://biorxiv.org/content/10.1101/2024.03.21.586168v1?rss=1 Alpar, A. T. Wallace, R. P. Refvik, K. C. Gomes, S. Solanki, A. Gray, L. T. Slezak, A. J. Lauterbach, A. L. Hesser, L. A. Cao, S. Medellin, J. E. G. Robinson, L. G. Hubbell, J. A. 2024-03-27 doi:10.1101/2024.03.21.586168 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Upstream open reading frames may contain hundreds of novel human exons ]]> https://biorxiv.org/content/10.1101/2024.03.22.586333v1?rss=1 Ji, H. J. Salzberg, S. 2024-03-23 doi:10.1101/2024.03.22.586333 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Switching between newly learned motor skills ]]> https://biorxiv.org/content/10.1101/2024.03.22.586357v1?rss=1 Kita, K. Du, Y. Haith, A. M. 2024-03-27 doi:10.1101/2024.03.22.586357 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Global coral genomic vulnerability explains recent reef losses ]]> https://biorxiv.org/content/10.1101/2024.03.25.586253v1?rss=1 Selmoni, O. Cleves, P. A. Exposito-Alonso, M. 2024-03-25 doi:10.1101/2024.03.25.586253 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Senolytic therapy preserves blood-brain barrier integrity and promotes microglia homeostasis in a tauopathy model ]]> https://biorxiv.org/content/10.1101/2024.03.25.586662v1?rss=1 Yao, M. Wei, Z. Nielsen, J. S. Kakazu, A. Ouyang, Y. Li, R. Chu, T. Scafidi, S. Lu, H. Aggarwal, M. Duan, W. 2024-03-29 doi:10.1101/2024.03.25.586662 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function ]]> https://biorxiv.org/content/10.1101/2024.03.26.586740v1?rss=1 Ono, K. Jarysta, A. Hughes, N. Jukic, A. Chang, V. H. H. Deans, M. R. Eatock, R. A. Cullen, K. E. Kindt, K. S. Tarchini, B. 2024-03-29 doi:10.1101/2024.03.26.586740 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age ]]> https://biorxiv.org/content/10.1101/2024.03.26.586781v1?rss=1 Sarver, D. C. Saqib, M. Chen, F. Wong, G. W. 2024-03-29 doi:10.1101/2024.03.26.586781 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Model-based frequency-and-phase correction of 1H MRS data with 2D linear-combination modeling. ]]> https://biorxiv.org/content/10.1101/2024.03.26.586804v1?rss=1 Simicic, D. Zöllner, H. J. Davies-Jenkins, C. W. Hupfeld, K. E. Edden, R. A. E. Oeltzschner, G. 2024-03-29 doi:10.1101/2024.03.26.586804 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ KAT6A deficiency impairs cognitive functions through suppressing RSPO2/Wnt signaling in hippocampal CA3 ]]> https://biorxiv.org/content/10.1101/2024.03.26.586861v1?rss=1 Liu, Y. Fan, M. Yang, J. Mihaljevic, L. Chen, K. H. Ye, Y. Sun, S. Qiu, Z. 2024-03-29 doi:10.1101/2024.03.26.586861 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ A 3D in vitro assay to study combined immune cell infiltration and cytotoxicity ]]> https://biorxiv.org/content/10.1101/2024.03.27.586980v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@6a161dorg.highwire.dtl.DTLVardef@d1e5d3org.highwire.dtl.DTLVardef@47b87corg.highwire.dtl.DTLVardef@a0e051_HPS_FORMAT_FIGEXP M_FIG The 3D combined infiltration/cytotoxicity assay captures three important steps of immune cell infiltration into the solid tumor microenvironment: (1) circulating immune cells extravasate and invade the stromal matrix, (2) immune cells migrate through the stromal matrix to reach the tumor core, and (3) immune cells that successfully navigate the stroma must cross a basement membrane boundary secreted by the cancer cells to contact and kill the cancer cells within a solid tumor. C_FIG ]]> Crawford, A. J. Johnston, A. Du, W. Hanna, E. A. Schell, D. Wan, Z. Chen, T.-H. Wu, F. Ren, K. Lim, Y. Nair, P. R. Wirtz, D. 2024-03-28 doi:10.1101/2024.03.27.586980 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Outer membrane vesicles can contribute to cellulose degradation in Teredinibacter turnerae, a cultivable intracellular endosymbiont of shipworms ]]> https://biorxiv.org/content/10.1101/2024.03.27.587001v1?rss=1 Gasser, M. T. Liu, A. Altamia, M. A. Bresinger, B. Brewer, S. L. Flatau, R. Hancock, E. Preheim, S. P. Filone, C. M. Distel, D. L. 2024-03-27 doi:10.1101/2024.03.27.587001 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage ]]> https://biorxiv.org/content/10.1101/2024.03.27.587041v1?rss=1 Boerner, K. Blood, P. D. Silverstein, J. C. Ruffalo, M. Teichmann, S. A. Pryhuber, G. Misra, R. S. Purkerson, J. M. Fan, J. Hickey, J. W. Molla, G. Xu, C. Zhang, Y. Weber, G. M. Jain, Y. Qaurooni, D. Kong, Y. Bueckle, A. Herr, B. W. 2024-04-02 doi:10.1101/2024.03.27.587041 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Development and Application of Decontamination Methods for the Re-Use of Laboratory Grade Plastic Pipette Tips ]]> https://biorxiv.org/content/10.1101/2024.03.27.587071v1?rss=1 Lee, S. H. Kastor, W. Fu, X. Soni, V. Keidar, M. Donohue, M. Wood, S. Karunasena, E. 2024-03-29 doi:10.1101/2024.03.27.587071 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ TraitProtNet: Deciphering the Genome for Trait Prediction with Interpretable Deep Learning ]]> https://biorxiv.org/content/10.1101/2024.03.28.587180v1?rss=1 Wang, S. 2024-03-31 doi:10.1101/2024.03.28.587180 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ 3D Imaging Reveals Changes in the Neurovascular Architecture of the Murine Calvarium with Aging ]]> https://biorxiv.org/content/10.1101/2024.03.28.587299v1?rss=1 Horenberg, A. Ren, Y. Rindone, A. Pathak, A. Grayson, W. 2024-04-01 doi:10.1101/2024.03.28.587299 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Foraging Under Uncertainty Follows the Marginal Value Theorem with Bayesian Updating of Environment Representations ]]> https://biorxiv.org/content/10.1101/2024.03.30.587253v1?rss=1 Webb, J. Steffan, P. Hayden, B. Y. Lee, D. Kemere, C. McGinley, M. 2024-03-31 doi:10.1101/2024.03.30.587253 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine ]]> https://biorxiv.org/content/10.1101/2024.04.01.587658v1?rss=1 He, Y. Barisoni, L. Rosenberg, A. Z. Robinson, P. Diehl, A. D. Chen, Y. Phuong, J. P. Hansen, J. Herr, B. W. Borner, K. Schaub, J. Bonevich, N. Arnous, G. Boddapati, S. Zheng, J. Alakwaa, F. Sarder, P. Duncan, W. D. Liang, C. Valerius, M. T. Jain, S. Iyengar, R. Himmelfarb, J. Kretzler, M. Kidney Precision Medicine Project, 2024-04-02 doi:10.1101/2024.04.01.587658 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Seeding competent TDP-43 persists in human patient and mouse muscle ]]> https://biorxiv.org/content/10.1101/2024.04.03.587918v1?rss=1 Lynch, E. M. Pittman, S. Daw, J. Ikenaga, C. Chen, S. Dhavale, D. D. Jackrel, M. E. Ayala, Y. M. Kotzbauer, P. Ly, C. V. Pestronk, A. Lloyd, T. E. Weihl, C. C. 2024-04-04 doi:10.1101/2024.04.03.587918 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ The microanatomy of human skin in aging ]]> https://biorxiv.org/content/10.1101/2024.04.03.588011v1?rss=1 Han, K. S. Sander, I. B. Kumer, J. Resnick, E. P. Booth, C. Starich, B. Walston, J. Kiemen, A. L. Reddy, S. Joshu, C. Sunshine, J. Wirtz, D. Wu, P.-H. 2024-04-05 doi:10.1101/2024.04.03.588011 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Tonotopic organization of auditory cortex in awake marmosets revealed by multi-modal wide-field optical imaging ]]> https://biorxiv.org/content/10.1101/2024.04.05.588237v1?rss=1 Song, X. Guo, Y. Chen, C. Lee, J. H. Wang, X. 2024-04-10 doi:10.1101/2024.04.05.588237 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain ]]> https://biorxiv.org/content/10.1101/2024.04.06.588331v1?rss=1 Patel, K. D. Oliver, R. A. Lichstrahl, M. S. Li, R. Townsend, C. A. Gulick, A. M. 2024-04-06 doi:10.1101/2024.04.06.588331 Cold Spring Harbor Laboratory Press 2024-04-06 <![CDATA[ An inferotemporal coding strategy robust to partial object occlusion ]]> https://biorxiv.org/content/10.1101/2024.04.09.588746v1?rss=1 80% correct over a period of weeks, after which AIT neurons showed clear learning effects, with increased selectivity for multi-part configurations within the trained alphabet shapes. But these neurons were not exclusively tuned for unique letters based on training, since their responsiveness generalized to different, non-trained shapes containing the same configurations. This multi-part configuration coding limit in AIT is not maximally sparse, but it could explain the robustness of primate vision to partial object occlusion, which is common in the natural world and problematic for computer vision. Multi-part configurations are highly diagnostic of identity, and neural signals for various partial object structures can provide different but equally sufficient evidence for whole object identity across most occlusion conditions. ]]> Cheng, A. Sokol, S. Connor, C. 2024-04-13 doi:10.1101/2024.04.09.588746 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ The relationship between event boundary strength and pattern shifts across the cortical hierarchy during naturalistic movie-viewing ]]> https://biorxiv.org/content/10.1101/2024.04.10.588931v1?rss=1 Lee, Y. Chen, J. 2024-04-14 doi:10.1101/2024.04.10.588931 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Distinguishing microgliosis and tau deposition in the mouse brain using paramagnetic and diamagnetic susceptibility source separation ]]> https://biorxiv.org/content/10.1101/2024.04.11.588962v1?rss=1 Joshi, J. Yao, M. Kakazu, A. Ouyang, Y. Duan, W. Aggarwal, M. 2024-04-15 doi:10.1101/2024.04.11.588962 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Quantitative tests of albendazole resistance in beta-tubulin mutants ]]> https://biorxiv.org/content/10.1101/2024.04.11.589070v1?rss=1 Collins, J. Stone, S. Koury, E. Paredes, A. Shao, F. Lovato, C. Chen, M. Shi, R. Li, A. Candal, I. Al Moutaa, K. Moya, N. Andersen, E. C. 2024-04-13 doi:10.1101/2024.04.11.589070 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ A dual-receptor model of serotonergic psychedelics: therapeutic insights from simulated cortical dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.12.589282v1?rss=1 Juliani, A. Chelu, V. Graesser, L. Safron, A. 2024-04-15 doi:10.1101/2024.04.12.589282 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner ]]> https://biorxiv.org/content/10.1101/2024.04.13.589356v1?rss=1 Ji, H. J. Pertea, M. 2024-04-16 doi:10.1101/2024.04.13.589356 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity ]]> https://biorxiv.org/content/10.1101/2024.04.14.589442v1?rss=1 Wu, Y. Song, Y. Soto, J. Hoffman, T. Zhang, A. Han, X. Fang, Z. Eoh, J. Gu, L. Gu, Z. Li, S. 2024-04-17 doi:10.1101/2024.04.14.589442 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Modeling of HIV-1 prophylactic efficacy and toxicity with islatravir shows non-superiority for oral dosing, but promise as a subdermal implant ]]> https://biorxiv.org/content/10.1101/2024.04.15.589489v1?rss=1 90% protection, while not being suitable for post-exposure prophylaxis. ]]> Kim, H.-y. Zhang, L. Hendrix, C. W. Haberer, J. E. von Kleist, M. 2024-04-19 doi:10.1101/2024.04.15.589489 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Conservation of neuron-astrocyte coordinated activity among sensory processing centers of the developing brain ]]> https://biorxiv.org/content/10.1101/2024.04.15.589519v1?rss=1 Kellner, V. Parker, P. Mi, X. Yu, G. Saher, G. Bergles, D. E. 2024-04-15 doi:10.1101/2024.04.15.589519 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ ModDotPlot - Rapid and interactive visualization of complex repeats ]]> https://biorxiv.org/content/10.1101/2024.04.15.589623v1?rss=1 Sweeten, A. P. Schatz, M. C. Phillippy, A. M. 2024-04-19 doi:10.1101/2024.04.15.589623 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ An optogenetic assay for the dauer decision in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.04.15.589657v1?rss=1 Parker, A. Mullins, J. Corver, A. Miller, A. Mosley, I. Gordus, A. G. 2024-04-17 doi:10.1101/2024.04.15.589657 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species ]]> https://biorxiv.org/content/10.1101/2024.04.16.589693v1?rss=1 Murray, C. S. Karram, M. Bass, D. J. Doceti, M. Becker, D. Nunez, J. C. B. Ratan, A. Bergland, A. O. 2024-04-20 doi:10.1101/2024.04.16.589693 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ GPnotebook: A pan-cancer glycoproteomic database and toolkit for analysis of protein glycosylation changes associated with cancer phenotypes ]]> https://biorxiv.org/content/10.1101/2024.04.18.589619v1?rss=1 Zhang, H. Hu, Y. 2024-04-19 doi:10.1101/2024.04.18.589619 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Cell-TIMP: Cellular Trajectory Inference based on Morphological Parameter ]]> https://biorxiv.org/content/10.1101/2024.04.18.590109v1?rss=1 Raj, P. Gupta, H. Anantha, P. Barman, I. 2024-04-22 doi:10.1101/2024.04.18.590109 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.19.590229v1?rss=1 Gutierrez-Garcia, K. Aumiller, K. Dodge, R. Obadia, B. Deng, A. Agrawal, S. Yuan, X. Wolff, R. Garud, N. Ludington, W. B. 2024-04-19 doi:10.1101/2024.04.19.590229 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Transcriptomic Profiling of Thyroid Eye Disease Orbital Fat Demonstrates Differences in Adipogenicity and IGF-1R Pathway ]]> https://biorxiv.org/content/10.1101/2024.04.19.590238v1?rss=1 Kim, D. W. Kim, S. Han, J. Belday, K. Li, E. Mahoney, N. Blackshaw, S. Rajaii, F. 2024-04-21 doi:10.1101/2024.04.19.590238 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Bi-level Graph Learning Unveils Prognosis-Relevant Tumor Microenvironment Patterns from Breast Multiplexed Digital Pathology ]]> https://biorxiv.org/content/10.1101/2024.04.22.590118v1?rss=1 Wang, Z. Santa-Maria, C. A. Popel, A. S. Sulam, J. 2024-04-26 doi:10.1101/2024.04.22.590118 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Gut-Initiated Alpha Synuclein Fibrils Drive Parkinson's Disease Phenotypes: Temporal Mapping of non-Motor Symptoms and REM Sleep Behavior Disorder ]]> https://biorxiv.org/content/10.1101/2024.04.22.590542v1?rss=1 Dautan, D. Paslawski, W. Montejo, S. Doyon, D. Marangiu, R. Kaplitt, M. G. Chen, R. Dawson, V. L. Zhang, X. Dawson, T. M. Svenningsson, P. 2024-04-26 doi:10.1101/2024.04.22.590542 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Ribonuclease activity undermines immune sensing of naked extracellular RNA ]]> https://biorxiv.org/content/10.1101/2024.04.23.590771v1?rss=1 Castellano, M. Blanco, V. Li Calzi, M. Costa, B. Witwer, K. Hill, M. Cayota, A. Segovia, M. Tosar, J. P. 2024-04-23 doi:10.1101/2024.04.23.590771 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.04.26.590643v1?rss=1 Nelson, E. D. Tippani, M. Ramnauth, A. D. Divecha, H. R. Miller, R. A. Eagles, N. J. Pattie, E. A. Kwon, S. H. Bach, S. V. Kaipa, U. M. Yao, J. Kleinman, J. E. Collado-Torres, L. Han, S. Maynard, K. R. Hyde, T. M. Martinowich, K. Page, S. C. Hicks, S. C. 2024-04-28 doi:10.1101/2024.04.26.590643 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin ]]> https://biorxiv.org/content/10.1101/2024.04.26.591383v1?rss=1 Snedeker, J. Davis, B. E. M. Ranjan, R. Wooten, M. I. Blundon, J. Chen, X. 2024-04-29 doi:10.1101/2024.04.26.591383 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Stem cell models of TAFAZZIN deficiency reveal novel tissue-specific pathologies in Barth Syndrome ]]> https://biorxiv.org/content/10.1101/2024.04.28.591534v1?rss=1 Carney, O. S. Harris, K. W. Wohlfarter, Y. Lee, K. Butschek, G. Anzmann, A. Claypool, S. M. Hamacher-Brady, A. Keller, M. A. Vernon, H. J. 2024-04-29 doi:10.1101/2024.04.28.591534 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Comparison of Different Approaches to Single Cell RNA Sequencing of Cancer Associated Fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.04.29.591011v1?rss=1 Kung, H.-C. Loycano, M. Zheng, L. Chen, S. Y. Zimmerman, J. W. 2024-05-01 doi:10.1101/2024.04.29.591011 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Neurocognitive Mechanism of Radiologists Perceptual Errors: Results of Preliminary Studies ]]> https://biorxiv.org/content/10.1101/2024.04.29.591746v1?rss=1 Bruno, M. A. Krupinski, E. A. Bunce, S. F. Baird, G. Mills, C. Karunanayaka, P. Egeth, H. Chang, R. Cottrill, R. Jump, S. Sathian, K. Mosher, T. J. 2024-05-02 doi:10.1101/2024.04.29.591746 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Double training reveals an interval-invariant subsecond temporal structure in the brain ]]> https://biorxiv.org/content/10.1101/2024.04.30.591981v1?rss=1 Guan, S.-C. Xiong, Y.-Z. Yu, C. 2024-05-01 doi:10.1101/2024.04.30.591981 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures ]]> https://biorxiv.org/content/10.1101/2024.05.02.592174v1?rss=1 Popp, J. M. Rhodes, K. Jangi, R. Li, M. Barr, K. A. Tayeb, K. Battle, A. Gilad, Y. 2024-05-03 doi:10.1101/2024.05.02.592174 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Discovering Intron Gain Events in Humans through Large-Scale Evolutionary Comparisons ]]> https://biorxiv.org/content/10.1101/2024.05.02.592247v1?rss=1 Hoh, C. Salzberg, S. 2024-05-04 doi:10.1101/2024.05.02.592247 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Tn-seq of the Candida glabrata reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin ]]> https://biorxiv.org/content/10.1101/2024.05.02.592251v1?rss=1 Cunningham, K. W. Nickels, T. J. Gale, A. N. Harrington, A. A. Timp, W. 2024-05-03 doi:10.1101/2024.05.02.592251 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Dark exposure reduces high-frequency hearing loss in C57BL/6J mice ]]> https://biorxiv.org/content/10.1101/2024.05.02.592252v1?rss=1 Jendrichovsky, P. Lee, H.-K. Kanold, P. O. 2024-05-03 doi:10.1101/2024.05.02.592252 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ In vivo CRISPR screening identifies geranylgeranyl diphosphate as a pancreatic cancer tumor growth dependency ]]> https://biorxiv.org/content/10.1101/2024.05.03.592368v1?rss=1 Kubota, C. S. Myers, S. L. Seppala, T. T. Burkhart, R. A. Espenshade, P. S. 2024-05-05 doi:10.1101/2024.05.03.592368 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Mitochondrial Oxidative Phosphorylation Capacity in Skeletal Muscle Measured by Ultrafast Z-Spectroscopy (UFZ) MRI at 3T ]]> https://biorxiv.org/content/10.1101/2024.05.05.592570v1?rss=1 Ju, L. Schar, M. Wang, K. Li, A. M. Wu, Y. Samuel, T. J. Ganji, S. van Zijl, P. C. M. Yadav, N. N. Weiss, R. G. Xu, J. 2024-05-05 doi:10.1101/2024.05.05.592570 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity ]]> https://biorxiv.org/content/10.1101/2024.05.06.591758v1?rss=1 Badurdeen, D. S. Li, Z. Lee, J.-H. Ma, T. Bhagwate, A. V. Latanich, R. Dogiparthi, A. Ordog, T. Kovbasnjuk, O. Kumbhari, V. Foulke-Abel, J. 2024-05-09 doi:10.1101/2024.05.06.591758 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Resiliency to Alzheimer's disease neuropathology can be distinguished from dementia using cortical astrogliosis imaging ]]> https://biorxiv.org/content/10.1101/2024.05.06.592719v1?rss=1 Barsoum, S. Latimer, C. S. Nolan, A. Barrett, A. Chang, K. Troncoso, J. Keene, C. D. Benjamini, D. 2024-05-08 doi:10.1101/2024.05.06.592719 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred C. elegans mutation accumulation lines ]]> https://biorxiv.org/content/10.1101/2024.05.08.593038v1?rss=1 Crombie, T. A. Rajaei, M. Saxena, A. S. Johnson, L. M. Saber, S. Tanny, R. E. Ponciano, J. M. Andersen, E. C. Zhou, J. Baer, C. F. 2024-05-10 doi:10.1101/2024.05.08.593038 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ B cell-mediated antigen presentation promotes adverse cardiac remodeling in chronic heart failure ]]> https://biorxiv.org/content/10.1101/2024.05.08.593153v1?rss=1 Lovell, J. P. Duque, C. Rousseau, S. Bhalodia, A. Bermea, K. Cohen, C. D. Adamo, L. 2024-05-11 doi:10.1101/2024.05.08.593153 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Molecular Myelin Dysfunction in the Most Common Inherited Peripheral Neuropathies - CMT1A and HNPP ]]> https://biorxiv.org/content/10.1101/2024.05.10.592618v1?rss=1 Moss, K. R. Gutierrez, D. Mi, R. Cetinkaya-Fisgin, A. Hoke, A. 2024-05-10 doi:10.1101/2024.05.10.592618 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Oncogenic signaling in the adult Drosophila prostate-like accessory gland leads to activation of a conserved pro-tumorigenic program, in the absence of proliferation. ]]> https://biorxiv.org/content/10.1101/2024.05.10.593549v1?rss=1 Church, S. J. Pulianmackal, A. J. Dixon, J. A. Loftus, L. V. Amend, S. R. Pienta, K. Cackowski, F. C. Buttitta, L. A. 2024-05-12 doi:10.1101/2024.05.10.593549 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Convolutional architectures are cortex-aligned de novo ]]> https://biorxiv.org/content/10.1101/2024.05.10.593623v1?rss=1 Kazemian, A. Elmoznino, E. Bonner, M. F. 2024-05-14 doi:10.1101/2024.05.10.593623 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.05.10.593637v1?rss=1 Phillip, J. M. Kamat, P. Macaluso, N. Min, C. Li, Y. Agrawal, A. Winston, A. Pan, L. Starich, B. M. Stewert, T. Wu, P.-H. Fan, J. Walston, J. 2024-05-14 doi:10.1101/2024.05.10.593637 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Naturalistic acute pain states decoded from neural and facial dynamics ]]> https://biorxiv.org/content/10.1101/2024.05.10.593652v1?rss=1 Huang, Y. Gopal, J. Kakusa, B. Li, A. Huang, W. Wang, J. B. Persad, A. Ramayya, A. Parvizi, J. Buch, V. P. Keller, C. 2024-05-12 doi:10.1101/2024.05.10.593652 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Video-Language Models as Flexible Social and Physical Reasoners ]]> https://biorxiv.org/content/10.1101/2024.05.11.593700v1?rss=1 Fleury, D. 2024-05-14 doi:10.1101/2024.05.11.593700 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Post-translation digital data encoding into the genomes of mammalian cell populations ]]> https://biorxiv.org/content/10.1101/2024.05.12.591851v1?rss=1 Callisto, A. Strutz, J. Leeper, K. Kalhor, R. Church, G. Tyo, K. Bhan, N. 2024-05-12 doi:10.1101/2024.05.12.591851 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ FtsN coordinates septal peptidoglycan synthesis and degradation through self-interaction of SPOR in E. coli ]]> https://biorxiv.org/content/10.1101/2024.05.13.594014v1?rss=1 Lyu, Z. Yang, X. Yahashiri, A. Ha, S. McCausland, J. W. Britton, B. M. Weiss, D. S. Xiao, J. 2024-05-13 doi:10.1101/2024.05.13.594014 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ PSAURON: a tool for assessing protein annotation across a broad range of species ]]> https://biorxiv.org/content/10.1101/2024.05.15.594385v1?rss=1 Sommer, M. J. Zimin, A. V. Salzberg, S. L. 2024-05-18 doi:10.1101/2024.05.15.594385 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Combining DNA and protein alignments to improve genome annotation with LiftOn ]]> https://biorxiv.org/content/10.1101/2024.05.16.593026v1?rss=1 Chao, K.-H. Heinz, J. M. Hoh, C. Mao, A. Pertea, M. Salzberg, S. 2024-05-17 doi:10.1101/2024.05.16.593026 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ TRIM52 is a primate-specific player in the DNA repair process under tight proteolytic control by a triad of giant E3 ligases ]]> https://biorxiv.org/content/10.1101/2024.05.16.594269v1?rss=1 Shulkina, A. Hacker, K. Ehrmann, J. F. Budroni, V. Mandlbauer, A. Bock, J. Grabarczyk, D. B. Cochella, L. Clausen, T. Versteeg, G. A. 2024-05-16 doi:10.1101/2024.05.16.594269 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Sensitivity to visual features in inattentional blindness ]]> https://biorxiv.org/content/10.1101/2024.05.18.593967v1?rss=1 Nartker, M. Firestone, C. Egeth, H. Phillips, I. 2024-05-20 doi:10.1101/2024.05.18.593967 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ SARS-CoV-2 variants from long-term, persistently infected immunocompromised patients have altered syncytia formation, temperature-dependent replication, and serum neutralizing antibody escape ]]> https://biorxiv.org/content/10.1101/2024.05.18.594818v1?rss=1 Wouters, C. Sachithanandham, J. Akin, E. Pieterse, L. Fall, A. Truong, T. T. Bard, J. D. Yee, R. Sullivan, D. J. Mostafa, H. H. Pekosz, A. 2024-05-20 doi:10.1101/2024.05.18.594818 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1-mediated cell-intrinsic resistance ]]> https://biorxiv.org/content/10.1101/2024.05.19.594134v1?rss=1 Liu, J. He, Q.-L. Zhou, J. Chikarmane, R. Hauk, G. Rachakonda, A. Vaghasia, A. M. Castagna, N. Steinberg, R. C. Pham, M.-T. Anders, N. M. Wanjiku, T. M. Nuhn, P. Shim, J. S. Giovinazzo, H. Esopi, D. M. Kim, K. Coulter, J. Wang, R. Zhou, J. Rudek, M. A. Berger, J. M. Liu, J. O. Nelson, W. G. Yegnasubramanian, S. 2024-05-21 doi:10.1101/2024.05.19.594134 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Cell-Driven Fluid Dynamics: A Physical Model of Active Systemic Circulation ]]> https://biorxiv.org/content/10.1101/2024.05.19.594862v1?rss=1 Wu, Y. Benson, M. Sun, S. 2024-05-21 doi:10.1101/2024.05.19.594862 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Human birth tissue products as a regenerative medicine to inhibit post-surgical pain through multi-modal action ]]> https://biorxiv.org/content/10.1101/2024.05.19.594874v1?rss=1 Zhang, C. Huang, Q. Ford, N. C. Limjunyawong, N. Lin, Q. Yang, F. Cui, X. Uniyal, A. Liu, J. Mahabole, M. He, H. Wang, X. Duff, I. Wang, Y. Wan, J. Zhu, G. Raja, S. N. Jia, H. Yang, D. Dong, X. Tseng, S. He, S. Guan, Y. 2024-05-20 doi:10.1101/2024.05.19.594874 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ The buoyancy of cryptococcal cells and its implications for transport and persistence of Cryptococcus in aqueous environments ]]> https://biorxiv.org/content/10.1101/2024.05.20.595024v1?rss=1 Jimenez, I. A. Stempinski, P. R. Dragotakes, Q. Greengo, S. D. Sanchez Ramirez, L. R. Casadevall, A. 2024-05-21 doi:10.1101/2024.05.20.595024 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ MEM-based pangenome indexing for k-mer queries ]]> https://biorxiv.org/content/10.1101/2024.05.20.595044v1?rss=1 Hwang, S. Brown, N. K. Ahmed, O. Y. Jenike, K. M. Kovaka, S. Schatz, M. C. Langmead, B. 2024-05-22 doi:10.1101/2024.05.20.595044 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Comparative Analysis of Within-Host Dynamics of Acute Infection and Viral Rebound Dynamics in Postnatally SHIV-Infected ART-Treated Infant Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2024.05.21.595130v1?rss=1 Mainou, E. Berendam, S. Obregon-Perko, V. Uffman, E. Phan, C. Shaw, G. M. Bar, K. Kumar, M. Fray, E. Siliciano, R. F. Siliciano, J. Silvestri, G. Permar, S. R. Fouda, G. McCarthy, J. Chahroudi, A. Chan, C. Conway, J. M. 2024-05-23 doi:10.1101/2024.05.21.595130 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Enhanced dynamic covalent chemistry for the controlled release of small molecules and biologics from a nanofibrous peptide hydrogel platform ]]> https://biorxiv.org/content/10.1101/2024.05.21.595134v1?rss=1 Pogostin, B. H. Wu, S. X. Swierczynski, M. J. Pennington, C. Li, S.-Y. Vohidova, D. Seeley, E. H. Agrawal, A. Tang, C. Cabler, J. Dey, A. Veiseh, O. Nuermberger, E. L. Ball, Z. T. Hartgerink, J. D. McHugh, K. J. 2024-05-23 doi:10.1101/2024.05.21.595134 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Temporal-Coherence Induces Binding in Responses to Sound Sequences in Ferret Auditory Cortex ]]> https://biorxiv.org/content/10.1101/2024.05.21.595170v1?rss=1 Lu, K. Dutta, K. Elhilali, M. Shamma, S. 2024-05-22 doi:10.1101/2024.05.21.595170 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Temporal Coherence Shapes Cortical Responses to Speech Mixtures in a Ferret Cocktail Party ]]> https://biorxiv.org/content/10.1101/2024.05.21.595171v1?rss=1 Joshi, N. Ng, Y. Thakkkar, K. Duque, D. Yin, P. Fritz, J. Elhilali, M. Shamma, S. 2024-05-22 doi:10.1101/2024.05.21.595171 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Virtual patient analysis identifies strategies to improve the performance of predictive biomarkers for PD-1 blockade ]]> https://biorxiv.org/content/10.1101/2024.05.21.595235v1?rss=1 Arulraj, T. Wang, H. Deshpande, A. Varadhan, R. Emens, L. A. Jaffee, E. M. Fertig, E. J. Santa-Maria, C. A. Popel, A. S. 2024-05-21 doi:10.1101/2024.05.21.595235 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Haspin kinase binds to a nucleosomal DNA supergroove ]]> https://biorxiv.org/content/10.1101/2024.05.21.595243v1?rss=1 Hicks, C. W. Gliech, C. R. Zhang, X. Rahman, S. Vasquez, S. Holland, A. J. Wolberger, C. 2024-05-23 doi:10.1101/2024.05.21.595243 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling ]]> https://biorxiv.org/content/10.1101/2024.05.22.595309v1?rss=1 Evans, D. J. Sheraz, S. Lau, A. Y. 2024-05-22 doi:10.1101/2024.05.22.595309 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Investigating Subpopulation Dynamics in Clonal CHO-K1 Cells with Single-Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2024.05.22.595338v1?rss=1 Morina, L. B. Cao, H. C. Chen, A. Kumar, S. McFarland, K. S. Majewska, N. I. Betenbaugh, M. Timp, W. 2024-05-24 doi:10.1101/2024.05.22.595338 Cold Spring Harbor Laboratory Press 2024-05-24 <![CDATA[ Effects of age on responses of principal cells of the mouse anteroventral cochlear nucleus in quiet and noise ]]> https://biorxiv.org/content/10.1101/2024.05.22.595362v1?rss=1 Postolache, M. Graham, C. J. C. Burke, K. Lauer, A. M. Xu-Friedman, M. A. 2024-05-22 doi:10.1101/2024.05.22.595362 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Mesendodermal cells fail to contribute to heart formation following blastocyst injection ]]> https://biorxiv.org/content/10.1101/2024.05.22.595392v1?rss=1 Li, B. Kwon, C. 2024-05-23 doi:10.1101/2024.05.22.595392 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Interferon-Induced PARP14-Mediated ADP-Ribosylation in p62 Bodies Requires an Active Ubiquitin-Proteasome System ]]> https://biorxiv.org/content/10.1101/2024.05.22.595402v1?rss=1 Raja, R. Biswas, B. Abraham, R. Liu, H. Chang, C.-Y. Vu, H. Leung, A. K. L. 2024-05-24 doi:10.1101/2024.05.22.595402 Cold Spring Harbor Laboratory Press 2024-05-24 <![CDATA[ Contribute to balance, wire in accordance: Emergence of backpropagation from a simple, bio-plausible neuroplasticity rule ]]> https://biorxiv.org/content/10.1101/2024.05.22.595438v1?rss=1 Fan, X. Mysore, S. P. 2024-05-23 doi:10.1101/2024.05.22.595438 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Natural killer cells associate with epithelial cells in the pancreatic ductal adenocarcinoma tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.05.23.593868v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@17df874org.highwire.dtl.DTLVardef@142c809org.highwire.dtl.DTLVardef@15af4a7org.highwire.dtl.DTLVardef@74183a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Malchiodi, Z. X. Suter, R. K. Deshpande, A. Peran, I. Harris, B. T. Duttargi, A. Chien, M.-J. Hariharan, S. Wetherill, L. Jablonski, S. A. Ho, W. J. Fertig, E. J. Weiner, L. M. 2024-05-28 doi:10.1101/2024.05.23.593868 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project ]]> https://biorxiv.org/content/10.1101/2024.05.24.595788v1?rss=1 Ge, Y. Lu, J. Revsine, M. Puiu, D. Salzberg, S. L. 2024-05-29 doi:10.1101/2024.05.24.595788 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Cliffy: robust 16S rRNA classification based on a compressed LCA index ]]> https://biorxiv.org/content/10.1101/2024.05.25.595899v1?rss=1 Ahmed, O. Y. Boucher, C. Langmead, B. 2024-05-30 doi:10.1101/2024.05.25.595899 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Deep Learning Detection of Subtle Torsional Eye Movements: Preliminary Results ]]> https://biorxiv.org/content/10.1101/2024.05.26.595236v1?rss=1 Mukunda, K. N. Ye, T. Luo, Y. Zoitou, A. Kwon, K. E. Singh, R. Woo, J. Sivakumar, N. Greenstein, J. L. Taylor, C. O. Kheradmand, A. Green, K. E. 2024-05-26 doi:10.1101/2024.05.26.595236 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides ]]> https://biorxiv.org/content/10.1101/2024.05.27.595990v1?rss=1 Hsiao, M.-H. Miao, Y. Liu, Z. Schutze, K. Limjunyawong, N. Chien, D. C.-C. Monteiro, W. D. Chu, L.-S. Morgenlander, W. Jayaraman, S. Jang, S.-e. Gray, J. J. Zhu, H. Dong, X. Steinegger, M. Larman, H. B. 2024-05-27 doi:10.1101/2024.05.27.595990 Cold Spring Harbor Laboratory Press 2024-05-27 <![CDATA[ ApoE ϵ4-dependent alteration of CXCR3+CD127+ CD4+ T cells is associated with elevated plasma neurofilament light chain in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.05.28.596276v1?rss=1 Hu, D. Chen, M. Li, X. Daley, S. Han, Y. Hemberg, M. Weiner, H. L. Xia, W. 2024-06-02 doi:10.1101/2024.05.28.596276 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Directly Measuring Atherogenic Lipoprotein Kinetics in Zebrafish with the Photoconvertible LipoTimer Reporter ]]> https://biorxiv.org/content/10.1101/2024.05.29.596423v1?rss=1 Moll, T. O. C. Klemek, M. L. Farber, S. A. 2024-05-31 doi:10.1101/2024.05.29.596423 Cold Spring Harbor Laboratory Press 2024-05-31 <![CDATA[ Complement Biosensors Identify a Classical Pathway Stimulus in Complement-Mediated Hemolytic Uremic Syndrome ]]> https://biorxiv.org/content/10.1101/2024.05.29.596475v1?rss=1 Cole, M. A. Ranjan, N. Gerber, G. F. Pan, X.-Z. Flores-Guerrero, D. Chaturvedi, S. Sperati, C. J. McCrae, K. Brodsky, R. A. 2024-06-02 doi:10.1101/2024.05.29.596475 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ From Molecules to Behavior: Linking Brain Biochemistry in the Dorsal Anterior Cingulate Cortex to 'Anxiety to Eat' Responses in Anorexia Nervosa ]]> https://biorxiv.org/content/10.1101/2024.05.29.596476v1?rss=1 Song, y. Guo, S. H. Davies-Jenkins, C. W. Guarda, A. Edden, R. A. E. Smith, K. R. 2024-05-30 doi:10.1101/2024.05.29.596476 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ The Cell Division Protein FzlA Performs a Conserved Function in Diverse Alphaproteobacteria ]]> https://biorxiv.org/content/10.1101/2024.05.29.596507v1?rss=1 Payne, I. P. Aubry, B. Barrows, J. M. Brown, P. J. B. Goley, E. D. 2024-05-29 doi:10.1101/2024.05.29.596507 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages ]]> https://biorxiv.org/content/10.1101/2024.05.30.596468v1?rss=1 Jaroenlak, P. McCarty, K. L. Xia, B. Lam, C. Zwack, E. E. Yanai, I. Bhabha, G. Ekiert, D. C. 2024-05-30 doi:10.1101/2024.05.30.596468 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Late sporogonic stages of Plasmodium parasites are susceptible to the melanization response in Anopheles gambiae mosquitoes ]]> https://biorxiv.org/content/10.1101/2024.05.31.596773v1?rss=1 Zeineddine, S. Jaber, S. Saab, S. A. Nakhleh, J. Dimopoulos, G. Osta, M. A. 2024-06-01 doi:10.1101/2024.05.31.596773 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Stick-slip unfolding favors self-association of expanded HTT mRNA ]]> https://biorxiv.org/content/10.1101/2024.05.31.596809v1?rss=1 O'Brien, B. M. Moulick, R. Jimenez Avalos, G. Rajasekaran, N. Kaiser, C. M. Woodson, S. 2024-06-03 doi:10.1101/2024.05.31.596809 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ OneSC: A computational platform for recapitulating cell state transitions ]]> https://biorxiv.org/content/10.1101/2024.05.31.596831v1?rss=1 Peng, D. Cahan, P. 2024-06-03 doi:10.1101/2024.05.31.596831 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development ]]> https://biorxiv.org/content/10.1101/2024.05.31.596852v1?rss=1 Tian, S. Nguyen, H. Ye, Z. Rouskin, S. Thirumalai, D. Trcek, T. 2024-06-01 doi:10.1101/2024.05.31.596852 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Decomposed Linear Dynamical Systems (dLDS) modelsreveal context-dependent dynamic connectivity in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.05.31.596903v1?rss=1 Yezerets, E. Mudrik, N. Charles, A. 2024-06-01 doi:10.1101/2024.05.31.596903 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Assessing the impact of autologous neutralizing antibodies on rebound dynamics in postnatally SHIV-infected ART-treated infant Rhesus macaques ]]> https://biorxiv.org/content/10.1101/2024.06.01.596971v1?rss=1 Mainou, E. Berendam, S. Obregon-Perko, V. Uffman, E. Phan, C. Shaw, G. Bar, K. Kumar, M. Fray, E. Siliciano, J. Siliciano, R. Silvestri, G. Permar, S. Fouda, G. McCarthy, J. Chan, C. Conway, J. M. 2024-06-03 doi:10.1101/2024.06.01.596971 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ CTPS1 inhibition synergizes with replication stress signaling inhibition in MYC-amplified Group 3 medulloblastoma ]]> https://biorxiv.org/content/10.1101/2024.06.03.597242v1?rss=1 Hathaway, M. R. Gadek, K. E. Jagana, H. L. Terrones, I. C. Hemenway, J. M. Miyaki, A. Rajendran, A. Meechan, M. Elena-Sanchez, L. Vitanza, N. A. Slusher, B. S. Pattwell, S. S. Evans, M. K. 2024-06-04 doi:10.1101/2024.06.03.597242 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Impact of Parental Time-Restricted Feeding on Offspring Metabolic Phenotypic Traits ]]> https://biorxiv.org/content/10.1101/2024.06.04.597276v1?rss=1 Fan, Y. Peng, X. Tabassum, N. I. Cheng, X. Selvaraji, S. Tran, V. Hughes, T. H. G. Wickramasinghe, B. Jamal, A. Dinh, Q. N. Gelderblom, M. Drummond, G. R. Sobey, C. G. Penman, J. Johns, T. G. Vemuganti, R. Gunaratne, J. Mattson, M. P. Jo, D.-G. Jelinic, M. Arumugam, T. V. 2024-06-06 doi:10.1101/2024.06.04.597276 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ The AID2 system offers a potent tool for rapid, reversible, or sustained degradation of essential proteins in live mice ]]> https://biorxiv.org/content/10.1101/2024.06.04.597287v1?rss=1 Sladky, V. C. Strong, M. A. Tapias-Gomez, D. Jewett, C. E. Drown, C. G. Scott, P. M. Holland, A. J. 2024-06-05 doi:10.1101/2024.06.04.597287 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ Mapping Somatosensory Afferent Circuitry to Bone Identifies Neurotrophic Signals Required for Fracture Healing ]]> https://biorxiv.org/content/10.1101/2024.06.06.597786v1?rss=1 Xu, M. Thottappillil, N. Cherief, M. Li, Z. Zhu, M. Xing, X. Gomez-Salazar, M. Mwirigi, J. M. Sankaranarayanan, I. Tavares-Ferreira, D. Zhang, C. Wang, X.-W. Archer, M. Guan, Y. Tower, R. J. Cahan, P. Price, T. J. Clemens, T. L. James, A. W. 2024-06-07 doi:10.1101/2024.06.06.597786 Cold Spring Harbor Laboratory Press 2024-06-07 <![CDATA[ The MICOS Complex Regulates Mitochondrial Structure and Oxidative Stress During Age-Dependent Structural Deficits in the Kidney ]]> https://biorxiv.org/content/10.1101/2024.06.09.598108v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@1a868f0org.highwire.dtl.DTLVardef@1817bfborg.highwire.dtl.DTLVardef@1f2a1a3org.highwire.dtl.DTLVardef@520692_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Vue, Z. Prasad, P. Le, H. Neikirk, K. Harris, C. Garza-Lopez, E. Wang, E. Murphy, A. Jenkins, B. Vang, L. Scudese, E. Shao, B. Kadam, A. Shao, J. Marshall, A. G. Crabtree, A. Kirk, B. Koh, A. Wilson, G. Oliver, A. Rodman, T. Kabugi, K. Koh, H.-J. Smith, Q. Zaganjor, E. Wanjalla, C. N. Dash, C. Evans, C. Phillips, M. A. Hubert, D. Ajijola, O. Whiteside, A. Koo, Y. D. Kinder, A. Demirci, M. Albritton, C. F. Wandira, N. Jamison, S. Ahmed, T. Saleem, M. Tomar, D. Williams, C. R. Sweetwyne, M. T. Murray, S. A. Cooper, A. Kirabo, A. Jadiya, P. Quintana, 2024-06-10 doi:10.1101/2024.06.09.598108 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Monocytes Mobilized by Gut Neurons Remodel the Enteric Nervous System ]]> https://biorxiv.org/content/10.1101/2024.06.09.598124v1?rss=1 Kurapati, S. Shin, C. Szabo, K. Liu, Y. Ashraf, A. Koscso, B. Dash, C. Navarro, L. Saha, M. Nagaraj, S. Wang, W. Zhu, J. Shulzhenko, N. Baer, C. Srinivasan, S. Kulkarni, S. Pasricha, P. Peters, L. Bogunovic, M. 2024-06-10 doi:10.1101/2024.06.09.598124 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Improving the reliability of T2 measurement in magnetic resonance imaging ]]> https://biorxiv.org/content/10.1101/2024.06.09.598128v1?rss=1 Yang, X. 2024-06-10 doi:10.1101/2024.06.09.598128 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ An expanded metabolic pathway for androgen production by host-associated bacteria ]]> https://biorxiv.org/content/10.1101/2024.06.09.598130v1?rss=1 Wang, T. Ahmad, S. Cruz-Lebron, A. Ernst, S. E. Caicedo, K. Y. O. Jeong, Y. Binion, B. Mbuvi, P. Dutta, D. Fernandez-Materan, F. V. Breister, A. M. Lee, J. W. Kang, J. D. Harris, S. C. Ikegawa, S. Gaskins, H. R. Erdman, J. W. Yang, G. Cann, I. Daniel, S. L. Hylemon, P. B. Anantharaman, K. Bernardi, R. C. Alves, J. M. P. Sfanos, K. S. Irudayaraj, J. Ridlon, J. M. 2024-06-09 doi:10.1101/2024.06.09.598130 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ ATP Citrate Lyase Supports Cardiac Function and NAD+/NADH Balance And Is Depressed in Human Heart Failure ]]> https://biorxiv.org/content/10.1101/2024.06.09.598152v1?rss=1 Meddeb, M. Koleini, N. Jun, S. Keykhaei, M. Farshidfar, F. Zhao, L. Kwon, S. Lin, B. Keceli, G. Paolocci, N. Hahn, V. Sharma, K. Pearce, E. L. Kass, D. A. 2024-06-10 doi:10.1101/2024.06.09.598152 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Rapid emergence of latent knowledge in the sensory cortex drives learning ]]> https://biorxiv.org/content/10.1101/2024.06.10.597946v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@951aadorg.highwire.dtl.DTLVardef@10a6bbforg.highwire.dtl.DTLVardef@127e8eeorg.highwire.dtl.DTLVardef@12d84ba_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Auditory cortex silencing impairs sound-guided learning and performance during learning.a, Head-fixed mice were trained on an auditory go/no-go task with 3 -spaced pure tones. H: hit, M: miss, FA: false alarm, CR: correct reject. b, Every day during training, task knowledge is probed by omitting reinforcement for 20 trials. c, Two distinct learning trajectories are revealed: a fast acquisition of task contingencies (measured in probe trials; green) and a slower knowledge expression (measured in reinforced trials; black). d, Probabilistic optogenetic silencing of the auditory cortex over learning. e, Testing conditions. f, Accuracy in reinforced light-on trials (two-way ANOVA, p < 10-8). g, Action rate in reinforced light-on trials (HIT, p = 0.07; FA, p < 10-33). See also Supplementary Figure 4. h, Accuracy in probe light-off trials (two-way ANOVA, p < 10-4). i, Tone response index in S+ trials (see Methods; two-way ANOVA, p < 10-101). Black and gray lines are individual mice and dots indicate change points (see Methods). j, Maximal difference between hit and FA rates in probe light-off trials over the first 6 days (t-test, p < 10-3). k, Hit lick latency in probe light-off trials (median {+/-} s.e.median; Wilcoxon test, p = 0.007). l, Accuracy in reinforced light-off trials (two-way ANOVA, p < 10-8). m, Action rate in reinforced light-off trials (two-way ANOVA, HIT: p = 0.57, FA: p < 10-8). n, Accuracy in reinforced light-off trials with inter-subject alignment to the day where probe accuracy[≥] 0.65 (green triangle) (two-way ANOVA, p < 10-5). Supplementary Figure 3a-c. o, Comparison of light-off versus light-on trials to measure auditory cortex silencing effect on on-line performance. p, Session density plot of accuracy in reinforced light-on against light-off. Top, control; bottom, PV-ChR2. See also Supplementary Figure 3d-g. q, Within subject accuracy difference in reinforced light-on and light-off trials, aligned to the day where FA rate < 0.3 in reinforced light-off (two-way ANOVA, p < 10-15). r, Within subject accuracy difference in reinforced light-on and light-off when silencing started at expert level (n = 4; t-test, p = 0.58). See also Supplementary Figure 6. mean {+/-} s.e.m.; *p < 0.05; **p < 0.01; ***p < 0.001, n.s.: not significant. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=38 SRC="FIGDIR/small/597946v1_figs1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@164efbdorg.highwire.dtl.DTLVardef@1b784e2org.highwire.dtl.DTLVardef@1754599org.highwire.dtl.DTLVardef@2c7b07_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 1.C_FLOATNO Stimulus decoding in the auditory cortex is at ceiling from Day 1 of learning. a, Stimulus decoding is at ceiling on Day 1 and remains high throughout learning (example mouse) Only the cells tracked across all days were used to decode tone identity. b, Stimulus decoding is at ceiling on day 1 and remains high throughout passive exposure over 15 days (example mouse). c, Average decoding accuracy for all Learning mice (n = 5). d, Average decoding accuracy for all Passive mice (n = 3). e, Evolution of tone decoding accuracy in the tone-evoked window across days for Learning and Passive mice compared to chance level (trial shuffle, see Methods). C_FIG O_FIG O_LINKSMALLFIG WIDTH=125 HEIGHT=200 SRC="FIGDIR/small/597946v1_figs4.gif" ALT="Figure 4"> View larger version (42K): org.highwire.dtl.DTLVardef@4114f7org.highwire.dtl.DTLVardef@c76c77org.highwire.dtl.DTLVardef@a20971org.highwire.dtl.DTLVardef@19dc17_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 4.C_FLOATNO Effect of AC full trial silencing on lick patterns a, Example control (top) and ChR2 (bottom) mice accuracy in probe light-off, reinforced light-off and reinforced light-on trials across day. Dashed rectangle indicates day where licks in b are extracted from. b, Lick raster plots from day 4 from the example mouse from A in probe light-off (left), reinforced light-off (middle) and reinforced light-on (right) trials, split into target (black, left) and foil (red, right) trials. Green and red dots indicates correct and incorrect trials, respectively. Note the difference in discrimination in all contexts between control and PV-ChR2 mice. c, Average lick probability across training days for control (n = 8) and ChR2 (n = 8) mice in response to target (vertical green line) and foil (vertical red line) tones, in reinforced light-off (black) and light-on (blue) trials. d, Insets showing faster lick latencies (red arrow heads) in response to both tones and higher lick probability in response to the foil (incorrect licking) in reinforced light-on compared to light-off in ChR2 mice (right). Light has no effect on lick structure in control mice (left). e, Lick latencies (top) and lick rate (bottom) in response to target (HIT trials; left) and foil (false alarm (FA) trials; right) tones in reinforced light-off trials (HIT lick latencies, Days: F (20, 256) = 8.2738, p < 10-17, Groups: F (1, 256) = 8.1568, p = 0.0046, Days*Groups: F (20, 256) = 0.9176, p = 0.56; FA Lick latencies, Days: F (20, 190) = 2.2393, p = 0.0027, Groups: F (1, 190) = 1.8422, p = 0.18, Days*Group: F (20, 190) = 1.5563, p = 0.067; HIT lick rate, Days: F (20, 256) = 4.3619, p < 10-8, Groups: F (1, 256) = 2.9549, p = 0.087, Days*Groups: F (20, 256) = 0.2927, p = 0.99; FA lick rate, Days: F (20, 190) = 4.04477, p < 10-6, Groups: F (1, 190) = 7.4070, p = 0.0071, Days*Groups: F (20, 190) = 1.1944, p = 0.26). f, Lick latencies (top) and lick rate (bottom) in response to target (HIT trials; left) and foil (false alarm (FA) trials; right) tones in reinforced light-on trials (HIT lick latencies, Days: F (20, 256) = 10.5303, p < 10-22, Groups: F (1, 256) = 11.2328, p < 10-3, Days*Groups: F (20, 256) = 0.6211, p = 0.90; FA Lick latencies, Days: F (20, 254) = 3.9111, p < 10-6, Groups: F (1, 254) = 450.4358, p < 10-57, Days*Group: F (20, 254) = 2.1947, p = 0.0029; HIT lick rate, Days: F (20, 256) = 2.6372, p < 10-3, Groups: F (1, 256) = 3.7748, p = 0.0531, Days*Groups: F (20, 256) = 0.4520, p = 0.98; FA lick rate, Days: F (20, 254) = 6.4469, p < 10-13, Groups: F (1, 254) = 301.2679, p < 10-44, Days*Groups: F (20, 254) = 0.6326, p = 0.89). g, Lick latencies (left) and lick rate (right) in response to target (HIT) and foil (FA) tones in probe light-off trials (HIT lick latencies, Days: F (5, 83) = 6.4522, p < 10-4, Groups: F (1, 83) = 11.7734, p < 10-3, Days*Groups: F (5, 83) = 0.2878, p = 0.92; FA Lick latencies, Days: F (5, 58) = 2.9217, p = 0.020, Groups: F (1, 58) = 0.9337, p = 0.338, Days*Group: F (5, 58) = 2.1909, p = 0.068; HIT lick rate, Days: F (5, 83) = 2.0103, p = 0.086, Groups: F (1, 83) = 5.9422, p = 0.017, Days*Groups: F (5, 83) = 0.5721, p = 0.72; FA lick rate, Days: F (5, 58) = 5.6386, p < 10-3, Groups: F (1, 58) = 0.0192, p = 0.89, Days*Groups: F (5, 58) = 1.6182, p = 0.17). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/597946v1_figs3.gif" ALT="Figure 3"> View larger version (23K): org.highwire.dtl.DTLVardef@1c07f99org.highwire.dtl.DTLVardef@f919c8org.highwire.dtl.DTLVardef@bd263org.highwire.dtl.DTLVardef@217412_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 3.C_FLOATNO AC full trial silencing impairs expression and on-line performance a, Assessment of the impact of AC full trial silencing over learning on Expression by controlling for the delay in Acquisition. b, Cumulative distribution function (CDF) of mice as function of the day to reach an accuracy[≥] 0.65 in probe trials. c, Cumulative distribution function (CDF) of mice as function of the relative number of days to reach accuracy (acc.) criteria of >0.7 (left), >0.8 (middle), and >0.9 (right) in reinforced light-off trials after reaching an accuracy[≥] 0.65 in probe trials. Black and dark gray vertical lines correspond to when CDF was reach for acc.>0.7 and >0.8, respectively. d, Comparing action rate and accuracy between reinforced light-off versus reinforced light-on trials to assess the impact of AC silencing on on-line performance. e, Hit (solid line) and FA (dashed line) of an example control mouse (top) and an example PV-ChR2 mouse (bottom) in reinforced light-off (black) and reinforced light-on (blue) trials across learning. f, Averaged action rate in reinforced light-off (black) and reinforced light-on (blue) trials per day for control (top) and PV-ChR2 (bottom) groups. g, Accuracy in light-on reinforced trials from the day when FA<0.3 in light-off reinforced trials. Note how PV-ChR2 mice (gray lines) increase accuracy (positive slopes) with light-on, showing that performance impairment fades away. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=43 SRC="FIGDIR/small/597946v1_figs6.gif" ALT="Figure 6"> View larger version (14K): org.highwire.dtl.DTLVardef@4b4bdcorg.highwire.dtl.DTLVardef@1617149org.highwire.dtl.DTLVardef@547fb7org.highwire.dtl.DTLVardef@18ce33e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 6.C_FLOATNO AC full trial silencing at expert level a, Probabilistic optogenetic silencing of the auditory cortex at expert level. Silencing starts once stable performance is reached. b, Accuracy in probe light-off (green), reinforced light-off (black) and reinforced light-on (blue) trials. Silencing is performed from day 19 to 23. c, Accuracy in reinforced light-off and light-on trials (paired t-test, p = 0.602). C_FIG The auditory cortex is the default pathway for sound-guided learningLesion studies have suggested that the AC may not be essential to learn or execute cue-guided tasks with simple sensory stimuli12-15. However, permanent lesions cannot determine whether the AC is normally used for, or causally produces16, learning in an intact brain. To address this, we exploited a transient silencing approach to prevent the recruitment of alternative pathways15,17-20 while also using a probabilistic design to allow assessment of learning as distinct from performance by measuring behavior on non-silenced trials, thereby avoiding direct effects of silencing on performance. We examined the impact of bilateral cortical silencing of the AC throughout learning (Fig. 1a). We probabilistically silenced the AC on 90% of reinforced trials throughout learning ( light-on reinforced, Fig. 1d), leaving 10% of reinforced ( light-off reinforced) and 100% of probe trials ( light-off probe) with intact AC activity. Silenced trials were pseudo-randomly sequenced and equally split between S+ and S-. Silencing was achieved by shining blue light bilaterally through cranial windows implanted above the AC of double transgenic mice (n=8) expressing channel rhodopsin (ChR2) in parvalbumin (PV) interneurons14,21 (Fig. 1d). We confirmed that the excitatory network was effectively silenced using this approach by combining two-photon calcium imaging of excitatory neurons and full-field optogenetic stimulation in PV-ChR2 mice (Supplementary Figure 2). Control mice (n=8) received the same light stimulation but did not express ChR2. This experimental design allowed us to assay the impact of cortical silencing on performance (control vs PV-ChR2 performance on light-on reinforced trials) versus acquisition learning (control vs PV-ChR2 performance on light-off probe trials) and expression learning (control vs PV-ChR2 performance on light-off reinforced trials) (Fig. 1e). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/597946v1_figs2.gif" ALT="Figure 2"> View larger version (61K): org.highwire.dtl.DTLVardef@9b2f88org.highwire.dtl.DTLVardef@4d8c14org.highwire.dtl.DTLVardef@127aa8borg.highwire.dtl.DTLVardef@12daa04_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 2.C_FLOATNO Activating PV+ neurons in the auditory cortex robustly suppresses stimulus-evoked activity of excitatory neurons. a, PV-ChR2 mice (n = 2) were injected with AAV-CaMKII-GCaMP6f to allow simultaneous one-photon excitation of PV cells and two-photon recordings of pyramidal cell population. b, Schematic of simultaneous widefield optogenetics and two-photon imaging. c, Optogenetic activation was locked to frame acquisition. d, Trial-averaged{Delta} F/F aligned to tone onset (black vertical line) of an example neuron at different intensity of LED power (blue scale). Yellow rectangle indicates period of light delivery. mean {+/-} s.e.m. e, Effect of optogenetic silencing as a function of LED power (n = 454 neurons; Friedman test, p [~] 0).{Delta} F/F at powers 0-0.26 mW/mm2 are all significantly different from{Delta} F/F at powers 0.84-3.15 mW/mm2 (post hoc comparisons with Tukey-Kramer test, ***p < 0.001). Black line is the logistic fit. median {+/-} s.e.median. f, Immunostaining of PV-ChR2 mice auditory cortex showing ChR2 expression in PV cells (PV+ and ChR2+ colocalization). g, Post-task imaging of a representative control (top) and a representative test (PV-ChR2, bottom) mouse used in AC silencing experiments. Note that no fluorescence below the dura is detected in control mice. C_FIG We first compared performance in light-on reinforced trials between PV-ChR2 and control mice (Fig. 1e) and observed a large performance impairment in PV-ChR2 mice (Fig. 1f,g). To address whether this performance reduction was accompanied by an impairment in rapid learning, we compared performance in PV-ChR2 and control animals in light-off probe trials (Fig. 1e,h-k) when the AC was not silenced and knowledge acquisition can be accurately measured7. Accuracy was lower during probe trials in PV-ChR2 mice (Fig. 1h), with delayed S+-response learning (Fig. 1i), lower discrimination (Fig. 1j), and longer lick latency on hit trials (Fig. 1k). Rapid acquisition of task knowledge was therefore impaired in PV-ChR2 mice. Accuracy was also lower in reinforced light-off trials in PV-ChR2 mice (Fig. 1l,m). This remained true even after controlling for their slower task acquisition (Figs.1n, Supplementary Figure 3a-c). These impairments were also apparent in response latency and response vigor (Supplementary Figure 4). Together, these results suggest that the AC is the default pathway for sound-guided reward learning, even when not needed for perceptual sharpening. The auditory cortex is used during learning but becomes dispensable at expert levelsWe next sought to understand the contribution of AC activity for the expression of the learned behavior as animals transitioned to expert performance. Transient inactivation of auditory cortex in expert animals has led to conflicting results, with some reports showing degradation of sound-guided behavior14,17,22,23 and others not14,24,25. We exploited our probabilistic silencing strategy and compared performance in light-on (AC silenced) versus light-off (AC functional) reinforced trials within subjects (Fig. 1o). Performance on these two trial types was similar at early periods of training, as performance was poor overall (Fig. 1p). As training progressed, performance remained poor on light-on trials but improved on light-off trials (Fig. 1p), demonstrating that the AC is used for task performance at early and intermediate time-point during learning. Surprisingly, this deficit in performance on light-on trials gradually waned (Fig. 1p,q), suggesting that while the AC was used during learning, it became dispensable once the mice had mastered the task. These results could be explained by three alternative explanations. First, the optogenetic manipulation per se may not be interfering with a task-relevant process but instead could be distracting the animal, necessitating more time to increase performance in light-on trials. We reasoned that bilateral silencing of another cortical region that is nominally unrelated to the task would serve as an important control. We bilaterally silenced the visual cortex throughout learning in PV-ChR2 mice and found no evidence of performance impairment in light-on trials (Supplementary Figure 5), demonstrating that the performance impairment was specific to AC silencing. Second, it is possible that AC silencing altered tone perception, increasing task difficulty at the perceptual level in light-on trials. Third, the reduction of impairment during light-on trials could be driven by a reduction of the silencing effect with time due, for example, to brain damage induced by repeated silencing. To address the second and third possibilities, we trained a separate cohort of PV-ChR2 mice without daily inactivation and, instead, inactivated the AC only after they reached expert performance (see Methods). We observed no impact from AC silencing (Figs.1r, Supplementary Figure 6)14. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/597946v1_figs5.gif" ALT="Figure 5"> View larger version (28K): org.highwire.dtl.DTLVardef@f501baorg.highwire.dtl.DTLVardef@1449653org.highwire.dtl.DTLVardef@1e923cborg.highwire.dtl.DTLVardef@12d042e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 5.C_FLOATNO Silencing of the visual cortex does not impair performance throughout learning a, Silencing of the visual cortex in 90% of the reinforced trials throughout learning (n = 8 PV-ChR2 mice). b, Comparison of reinforced light-off versus light-on trials shows no deficit when silencing the VC demonstrating the specificity of the effects of AC silencing. c, Accuracy in reinforced light-off and light-on trials across days (two-way repeated measures ANOVA, Group: F (1, 140) = 0.5093, p = 0.50). d, Accuracy in reinforced light-off and light-on trials (n = 168 sessions; Wilcoxon signed rank, p = 0.41). e, Difference in accuracy in reinforced light-on versus light-off trials per session. f, Difference in accuracy in reinforced light-on versus light-off trials across days in visual cortex PV-ChR2 mice (dashed line) versus auditory cortex control mice (solid line) (two-way ANOVA, Days: F (20, 271) = 1.5547, p = 0.06, Groups: F (1, 271) = 2.3072, p = 0.13, Days*Groups: F (20, 271) = 1.1540, p = 0.2950). C_FIG Altogether, these results show that the AC is engaged during learning but is dispensable at expert levels, potentially tutoring subcortical structures that take over once the associations are learned. Unsupervised discovery of learning-related dynamics by low-rank tensor decompositionWe next sought to understand the nature and dynamics of auditory cortical activity underlying learning and performance. To do so, we performed longitudinal, two-photon calcium imaging of thousands of excitatory neurons in mice learning the auditory go/no-go task (n = 5). A separate group of water-restricted mice was passively exposed to two pure tones over the same duration but with no association with reinforcement (n = 3, see Methods; Supplementary Figure 7). This design allowed us to use the passive network as a base-case model to isolate learning-related neural dynamics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/597946v1_figs7.gif" ALT="Figure 7"> View larger version (17K): org.highwire.dtl.DTLVardef@6d72deorg.highwire.dtl.DTLVardef@1906cd7org.highwire.dtl.DTLVardef@d99914org.highwire.dtl.DTLVardef@1d1311b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 7.C_FLOATNO Experimental design and timeline of imaging experiments. a, After surgery, animals underwent a 10-day recovery period after which water restriction started. Tonotopic mapping (tuning curve session) of the auditory cortex took place 5 days later under the two-photon microscope, followed by two days of lick training under the two-photon microscope. These two sessions also allowed for habituation to head fixation and context. Behavior sessions started the following day for 15 or 16 days, after which tonotopic mapping sessions took place at day +1, +7 and +15 post learning. b, One behavioral session consisted of three blocks of 80 or 100 trials, and a baseline session (no tone presented). Two groups of mice were imaged under the two-photon microscope: the Passive group (top; n = 3) was presented with two pure tones but was never rewarded (lick tube out), and the Learning group (n = 5) was rewarded (3{micro}l water drop) if licking in the response window after the S+ tone. Two probe blocks of 10 trials each were introduced in two of the three reinforced blocks. c, Trial structure. After a no-lick period of 1s, a 100-ms tone was played, followed by a 200-ms dead period and a[≤] 2.5s response period. The length of the delay period was of 2s after a miss (M, no lick after S+) or a correct reject (CR, no lick after S-), 4s after a hit (H, lick after S+) and 7s after a false alarm (FA, lick after S-). C_FIG We expressed the genetically encoded calcium indicator GCaMP6f under the CaMKII pro-moter, targeting AC layer 2/3 pyramidal neurons. We imaged two planes[~] 50{micro}m apart (Fig. 2a), allowing us to record simultaneously hundreds of neurons per animal (n=7,137 neurons in 8 mice). All mice were passively presented with a series of pure tones (4 to 64kHz, quarter-octave spaced) to characterize auditory tuning properties within the local area of expression. We computed single-neuron tuning curves and then constructed a best frequency map confirming the location in the AC (Fig. 2b). For each mouse, we chose two stimuli that were similarly represented in the recorded population and were 3/4 octaves apart (Fig. 2c). We used a custom head-fixation system that allowed for kinematic registration and tracked the activity of the same neurons across weeks, including pre- and post-learning tuning curve sessions (n = 4, 643 neurons in 8 mice, see Methods; Fig. 2d-g). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/597946v1_fig2.gif" ALT="Figure 2"> View larger version (85K): org.highwire.dtl.DTLVardef@ef252borg.highwire.dtl.DTLVardef@716b28org.highwire.dtl.DTLVardef@321266org.highwire.dtl.DTLVardef@155e6a3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Low-rank tensor decomposition reveals learning-related network dynamics. a, Multi-plane, longitudinal two-photon calcium imaging of layer 2/3 excitatory network in the auditory cortex during learning (n = 5 mice) or passive exposure (n = 3 mice; see Methods). b, Tonotopic organization of the field of view of one example mouse before learning (left). Cells are colored according to their best frequency and tone-evoked responses of example cells circled in black to 17 pure tones ranging from 4 to 64 kHz are displayed on the right. c, Tone-evoked activity (top) and proportion of responsive cells (bottom) to pure tones. S+ and S- (filled and unfilled triangles, respectively) are chosen for training in the task based on their equal representation in the field of view in b. d, Six example cells tracked everyday across weeks. e, Two planes recorded in one example mouse. Cells are colored according to the number of days tracked among the 19 recording sessions in this mouse. f, Distribution of number of tracked days per cells in e. g, Cumulative distribution of tracked cells according to the percentage of recording sessions. Data for mouse in e is the light blue line. h, Calcium data is arranged by neurons x time within trial (-1 to +4s relative to tone onset, vertical line) x trials over time x trial outcomes. i, Activity from all Learning and Passive cells are concatenated together to create a fourth-order tensor (megamouse; left). In the 3rd, across trials dimension, data is aligned across mice according to learning phases: Acquisition (performance increases in probe trials), Expression (performance increases in reinforced trials), and Expert (high, stable performance in reinforced trials; see Methods and Supplementary Figure 8). j, Megamouse tensor decomposition identifies six neuronal dynamics (numbered; see Methods) that are characterized by a set of four factors: Neuron, Within trial, Across trial, and Outcome (see also Supplementary Figure 10). k, Projection of the tensor decomposition output onto principal subspace. WNr, WW r and WAr indicate neuronal, within trial and across trial weights for a component r, respectively. l, t-distributed stochastic neighbor embedding (t-SNE) projections of neuronal weights. Each dot represents a cell, colored according to the neuronal dynamic it contributed in the most. Bars (right) display the proportion of learning and passive cells among the highest contributors for each dynamic. Dynamics 1 and 2 are driven by the passive network (burgundy), while Dynamics 3 to 6 are driven by the learning network (blue). m, In the passive network, the highest contributing cells in Dynamic 1 define cell ensemble 1, and highest contributing cells in Dynamic 2 define cell ensemble 2. Similarly, in the learning network, cell ensembles 3 to 6 are constituted of the highest contributing cells to Dynamics 3 to 6, respectively. n, Absolute weights of cell ensembles across the six identified dynamics. Neurons can participate in more than one dynamic. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/597946v1_figs8.gif" ALT="Figure 8"> View larger version (42K): org.highwire.dtl.DTLVardef@990420org.highwire.dtl.DTLVardef@1ddf61corg.highwire.dtl.DTLVardef@148c3e4org.highwire.dtl.DTLVardef@34ef05_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 8.C_FLOATNO Inter-subject performance alignment for megamouse tensor. a, Accuracy in probe and reinforced contexts across days of all Learning mice. b, Action rate in reinforced context across days of all Learning mice. c, Action rate in probe context across days of all Learning mice. Please note that we fixed the probe performance at the maximum discrimination that was followed by a decrease in hit rate do to extinction. d, After the alignment procedure, action rate from the megamouse (all learning mice pooled) in reinforced context across learning phases. e, Megamouse accuracy in reinforced context across learning phases. f, Accuracy difference between the start and the end of the three learning phases in probe (green) and reinforced (black) contexts. Acquisition is characterized by an increase of accuracy in probe trials (paired t-test, p = 5.47.10-4) but not in reinforced trials (paired t-test, p = 0.07), Expression corresponds to an increase of accuracy in reinforced trials (paired t-test, p = 0.008) and Expert is when accuracy in reinforced trials is high and stable (paired t-test, p = 0.27). C_FIG O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/597946v1_figs10.gif" ALT="Figure 10"> View larger version (36K): org.highwire.dtl.DTLVardef@1383264org.highwire.dtl.DTLVardef@747519org.highwire.dtl.DTLVardef@1b3d529org.highwire.dtl.DTLVardef@16f8e2f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 10.C_FLOATNO Low-rank tensor decomposition. a, Similarity score as a function of model components. Each dot shows the similarity of a single optimization run compared to the best-fit model within each category. b, Model reconstruction error as a function of the number of components, where each dot corresponds to a different optimization run. c, Neuronal contribution (Learning vs Passive cells) per components (binomial proportion tests, all p < 0.001). d, Positive and negative neuronal weights across components in cell population recorded in learning mice (Learning) or in passive mice (Passive) (Wilcoxon tests). e, Positive and negative neuronal weights across components and individual mice. f, t-SNE of neuronal weights. Note how Learning and Passive cell populations are largely non-overlapping. g, Projection of neuronal x within trial weights of Learning and Passive network activity into principal component space. h, Projection of neuronal x within trial x trial outcome weights of Learning and Passive network activity into principal component space. i, Projection of neuronal x within trial x across trials x trial outcome (H/M and CR only) weights of Learning and Passive network activity into principal component space. C_FIG From this high-dimensional dataset, we sought to identify single neurons and neuronal ensembles carrying learning-related information, resolve stimulus and non-stimulus related activity within a given trial, identify changes in representation across trials, and determine outcome-specific dynamics. To do so, we organized our data into a 4-dimensional array containing neurons x time in trial x trials across learning x trial outcome (Fig. 2h). To identify shared and distinct variability in neuronal populations recorded in passive mice (n = 2, 339, passive network) and in learning mice (n = 2, 304, learning network), we created a megamouse by combining data from all mice and aligning neural activity to learning phase (n=4,643 neurons, see Methods; Fig. 2i; Supplementary Figure 8). We then used low-rank tensor decomposition to allow unsupervised identification of demixed, low-dimensional neural dynamics across multiple (> 2) dimensions26,27 (Supplementary Figure 9 and Supplementary Figure 10a,b; see Methods). The tensor decomposition revealed six neuronal dynamics, each characterized by the four factors of the original tensor (see Methods; Figs.2j, Supplementary Figure 10c,d, Supplementary Figure 11d). These six dynamics represented independent computations performed by the auditory cortical networks. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/597946v1_figs9.gif" ALT="Figure 9"> View larger version (18K): org.highwire.dtl.DTLVardef@dfedf2org.highwire.dtl.DTLVardef@17eb071org.highwire.dtl.DTLVardef@7205f4org.highwire.dtl.DTLVardef@1e4d76d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 9.C_FLOATNO Tensor representation of neural data. a, Data are organized into a fourth-order tensor with dimensions NxWxAxO. Tensor decom-position approximates the data as a sum of outer products of four vectors. Each outer product contains a neuron factor (green rectangles), within trial factor (pink rectangles), across trial factor (blue rectangles) and outcome factor (purple rectangles). Each set of low-dimensional factors (i.e. component) describes the activity of group of neurons within and across trials according to trial outcomes. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/597946v1_figs11.gif" ALT="Figure 11"> View larger version (22K): org.highwire.dtl.DTLVardef@fb3b34org.highwire.dtl.DTLVardef@1ec029corg.highwire.dtl.DTLVardef@19f8a32org.highwire.dtl.DTLVardef@129f839_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 11.C_FLOATNO Defining unique cell ensembles based on neuronal weights. a, Neuronal weights in the four components. Each neuron is attributed to a given dynamic according to its highest absolute weights, i.e. highest contribution. As a result, each dynamic is attributed to a unique cell ensemble (gray rectangles). b, Neuronal weights distribution before (raw, black) and after unique contribution attribution (gray). c, Learning and Passive cell proportion among components after unique attribution (binomial proportion tests). d, Learning and Passive cell proportion among components and given neuronal weight sign after unique attribution. In other words, proportion of cells from Learning and Passive networks describing the tensor-revealed neuronal dynamics (binomial proportion tests). ***p < 0.001, n.s.: not significant. C_FIG Projecting the product of the decomposition into principal component subspace showed that learning and passive networks exhibit almost orthogonal dynamics (Fig. 2k; Supplementary Figure 10f,g) and that the neural dynamics of different trial types evolved further apart in the learning network than in the passive network (Supplementary Figure 10h,i). Importantly, we ensured that the identified dynamics were not driven by isolated mice (Supplementary Figure 10e). Therefore, decomposition of the megamouse tensor discovered distinct dynamics exhibited by passive versus learning networks. For further analyses, we attributed each dynamic to individual neurons based on the neurons maximum weight ( unique participation; Fig. 2l; see Methods and Supplementary Figure 11). This allowed us to map the six dynamics onto six distinct cell ensembles, i.e. groups of neurons maximally encoding a particular network-specific dynamic (Fig. 2m and Supplementary Figure 11d). It is important to note that individual neurons (and corresponding ensembles) could exhibit mixed selectivity for the six dynamics, which allows an individual neurons to contribute to multiple, independent computations (Fig. 2n). Learning counteracts tone-evoked habituation by maintaining stimulus selectivity in distinct cell populationsA prevailing view in sensory systems holds that sensory cortices subserve associative learning through plasticity of the cue representation5,28-36. This model posits that individual neurons (via changes in sensory tuning) and neural populations (via cortical map expansion) enhance the representation of behaviorally relevant cues for use by downstream regions37-39. These studies, however, measure neural tuning and map expansion outside of the task context in a pre and post learning design and infer that plasticity of cue representations reflects the mechanistic role of the sensory cortex. To assess this model, we initially focused on the cell ensembles that exhibited classical stimulus-evoked activity (Fig. 2j), namely cell ensembles 1-4. We observed a prominent signature of stimulus-evoked habituation over hundreds to thousands of trials. This habituation dominated activity in passive networks, as seen in cell ensembles 1 and 2 which represented[~] 77% (1, 803/2, 339) of all passive cells (Fig. 3a,d). These neurons exhibited stimulus-evoked activation (cell ensemble 1) or suppression (cell ensemble 2), both of which decreased in amplitude over time (Fig. 3b-c,e-f). These cell ensembles were not stimulus selective and displayed the same dynamic in both stimulus 1 (S1) and stimulus 2 (S2) trials (Fig. 3b,e). These ensembles thus reflected the broad-based suppression of non-selective neurons after long-term repeated presentation of the same sounds. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/597946v1_fig3.gif" ALT="Figure 3"> View larger version (53K): org.highwire.dtl.DTLVardef@678173org.highwire.dtl.DTLVardef@163d156org.highwire.dtl.DTLVardef@447847org.highwire.dtl.DTLVardef@1349c3a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Learning counteracts tone-evoked habituation by maintaining stimulus selectivity in distinct populations. a, Representation of cell ensemble 1 in the Passive network. b, Average activity of cell ensemble 1 in S1 (black) and S2 (gray) trials across time in 80-trial blocks. Black triangles indicate tone onset, gray lines delimit averaged trial blocks. Black dashed lines separate time phases indicated by light to dark gray rectangles at the top: early, middle and late (see Methods). c, Cell ensemble 1 tone-evoked calcium responses across time phases for S1 and S2 trials combined (Friedman test, p = 1.26.10-291). d, Representation of cell ensemble 2 in the Passive network. e, Average activity of cell ensemble 2 in S1 and S2 trials across time. f, Cell ensemble 2 tone-evoked calcium responses across time phases for S1 and S2 trials combined (Friedman test, p = 7.32.10-121). g, Representation of cell ensemble 3 in the Learning network. h, Average activity of cell ensemble 3 in hit (green) and CR (yellow) trials across learning in 80-trial blocks. Black triangles indicate tone onset, gray lines delimit averaged trial blocks. Black dashed lines separate learning phases indicated by colored rectangles at the top: Acquisition, Expression and Expert (see Methods). i, Representation of cell ensemble 4 in the Learning network. j, Average activity of cell ensemble 4 in hit and CR trials across learning. k, Response index (response probability over learning; see Methods) of cell ensembles 1 and 2 (red) vs cell ensembles 3 and 4 (blue) (Wilcoxon test, p = 1.23.10-30). l, Selectivity index (see Methods) of cell ensembles 1 and 2 (red) vs cell ensembles 3 and 4 (blue) (Wilcoxon test, p = 1.37.10-94). m, Pre (top raw) and post (bottom raw) learning tonotopic maps (left), after spatial binning (middle) and restricted to surface with S+ (filled triangle) and S- (open triangle) best frequency (right) of one example mouse. n, Change in surface representation of S+ and S- pre- vs post-task learning (Learning) or pre- vs post-passive exposure (Passive) (binomial proportion tests). o, Pre vs post-learning change in percentage of neurons responsive to S+ and S-(binomial proportion tests). p, Pre vs post-learning change in tone-evoked responses of pre-task S+ and S- responsive neurons (KW test, p = 2.77.10-5). q, Pre- vs post-learning comparison of local best frequency differences in tonotopic maps. r, Distribution of local differences (from difference maps in q) in Learning versus Passive. median {+/-} s.e.median; *p < 0.05; **p < 0.01; ***p < 0.001, n.s.: not significant. C_FIG Stimulus-evoked responses in learning networks were observed in cell ensembles 3 and 4 (Fig. 3g-j). This includes a high selectivity for the S- (cell ensemble 3) or S+ (cell ensemble 4) cues (Fig. 3g-j). Cell ensemble 3 consisted of 19% of the Learning cell population (Fig. 3g), and displayed a slight habituation but mainly a strong preference for the S- throughout learning (Fig. 3h), while cell ensemble 4 (12% of total learning cells; Fig. 3j) exhibited S+ selectivity throughout learning (Fig. 3j). Cell ensembles 3 and 4 were more tone responsive and tone selective than cell ensembles 1 and 2 (Fig. 3k,l). Stimulus-evoked activity analyses across days of all recorded neurons (n = 7, 137) also support these results (Supplementary Figure 12, Supplementary Figure 13). Therefore, learning counteracted tone-evoked habituation by maintaining distinct ensembles that encoded either the S+ or S- selectively. O_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/597946v1_figs12.gif" ALT="Figure 12"> View larger version (69K): org.highwire.dtl.DTLVardef@fcbe19org.highwire.dtl.DTLVardef@1247daaorg.highwire.dtl.DTLVardef@b654b2org.highwire.dtl.DTLVardef@729d91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 12.C_FLOATNO Evolution of tone-evoked responses across days. a, Tone-evoked responses to S+ and S- in Learning mice across days for all cells recorded. b, Tone-evoked responses to S1 and S2 in Passive mice across days for all cells recorded. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=33 SRC="FIGDIR/small/597946v1_figs13.gif" ALT="Figure 13"> View larger version (10K): org.highwire.dtl.DTLVardef@c6a200org.highwire.dtl.DTLVardef@b5b179org.highwire.dtl.DTLVardef@96ad75org.highwire.dtl.DTLVardef@5604a2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 13.C_FLOATNO Learning counteracts tone-evoked habituation. a, Proportion of tone-responsive cells across days among Passive and Learning cells. b, Averaged proportion of tone-responsive cells in Passive and Learning networks (mean {+/-} s.e.m.; t-test, p = 3.89.10-5). c, Proportion of tone-responsive cells in days 1-5 versus days 11-15 in Learning and Passive networks (mean {+/-} s.e.m.; two-way ANOVA, Time x Group, p = 1.73.10-7). d, Proportion of cells responsive to S+ and S- in Learning network and S1, S2 or S1 or S2 (S) in Passive network. e, Averaged proportion of cells responsive to S+, S- or S (mean {+/-} s.e.m.; ANOVA, p = 1.93.10-6). C_FIG Learning was not associated with cortical map expansionTo directly test representational expansion and tuning shifts, we conducted a series of analyses focusing on stimulus-evoked responses before (pre-task) and after (post-task) learning, akin to classical measures of tuning and tonotopy. We computed the change in surface area occupied by S+ and S- preferring cells in tuning curve sessions, outside the task (Fig. 3m). Surprisingly, we observed no increase in the map-level representation of the S+ or S- after learning, and instead, observed a modest decrease (Fig. 3m-n). In addition to the best frequency representation, the fraction of neurons responding to the S+ and S- decreased (Fig. 3o) and the response amplitude of neurons that were initially tuned to the S+ and S- was lower after learning (Fig. 3p). Interestingly, while we observed no increase in representation to the S+ and S-, learning networks favored the representation of frequencies in between S+ and S-, but not higher or lower as seen in passive networks (Fig. 3n). Finally, using our passive networks as a base-case comparison, we calculated the local changes in the tonotopic map structure (Fig. 3q). Learning networks were surprisingly stable and exhibited less local changes than passive networks (Fig. 3r). These pre- vs post-learning changes in responsiveness and tonotopy thus mirrored the responsiveness observed online during learning (in dynamics 1 and 2) in a stable, tracked network (n=4,643 neurons, Fig. 3a-l), as well as when we include all neurons from each session (n=7,137 neurons) (Supplementary Figure 13). Altogether, our results suggest that cortical map expansion and changes in single-neuron tuning are unlikely to be the substrate for associative learning40,41. Tone-restricted silencing only partially impairs learning and performanceWe next sought to understand the extent to which the maintenance of stimulus-selectivity by learning networks was important to learning and performing the task. We performed daily bilateral silencing of AC during stimulus presentation throughout learning (Supplementary Figure 14a). Tone-restricted AC silencing impaired task performance throughout learning (Supplementary Figure 14b-e), task acquisition (Supplementary Figure 14f-i), and online performance during learning, with gradual fading of the effect at expert performance (Supplementary Figure 14n-q). Accuracy and action rate were not affected in reinforced light-off trials (Supplementary Figure 14j-k), but PV-ChR2 mice lick more and faster to the S- (Supplementary Figure 14l-m), suggesting that tone-restricted AC silencing also impaired expression, but to a lesser extent than full-trial silencing. Altogether, these results showed that information carried by the AC network in the tone-evoked window is used during learning. Interestingly, tone-restricted silencing impacted learning less than full trial silencing across nearly all measures (Fig. 1, Supplementary Figure 14), suggesting that activity after the tone-evoked window was critical for rapid contingency acquisition and performance during learning. O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/597946v1_figs14.gif" ALT="Figure 14"> View larger version (51K): org.highwire.dtl.DTLVardef@14a2aedorg.highwire.dtl.DTLVardef@486bd0org.highwire.dtl.DTLVardef@9e6054org.highwire.dtl.DTLVardef@1c64aea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 14.C_FLOATNO AC silencing restricted to sound presentation impairs audiomotor learning and on-line performance during learning. a, Probabilistic optogenetic silencing of the auditory cortex during learning. Light-on periods were restricted to sound presentation only (see Methods). b, Accuracy in reinforced light-on trials (two-way ANOVA, Days: F (17, 86) = 5.4950, p < 10-7; Groups: F (1, 86) = 50.5343, p < 10-9; Days*Groups: F (17, 86) = 0.70700, p = 0.79). c, Action rate in reinforced light-on trials (HIT, two-way ANOVAs, HIT, Days: F (17, 86)10.68010, p < 10-14; Groups: F (1, 86) = 0.0200, p = 0.89; Days*Groups: F (17, 86) = 1.0647, p = 0.40; FA, Days: F (17, 86) = 2.7330, p = 0.0012; Groups: F (1, 86) = 41.5010, p < 10-8; Days*Groups: F (17, 86) = 0.7255, p = 0.77). d, False alarm lick rate in reinforced light-on trials (two-way ANOVA, Days: F (17, 86) = 0.8663, p = 0.6140; Groups: F (1, 86) = 89.3004, p < 10-14; Days*Groups: F (17, 86) = 3.2285, p < 10-3). e, False alarm lick latency in reinforced light-on trials (two-way ANOVA, Days: F (17, 86) = 2.0216, p = 0.018; Groups: F (1, 86) = 251.7387, p < 10-26; Days*Groups: F (17, 86) = 4.8600, p < 10-6). f, Accuracy in probe light-off trials (two-way ANOVA, Days: F (5, 30) = 8.3041, p < 10-4; Groups: F (1, 30) = 4.7288, p = 0.038; Days*Groups: F (5, 30) = 0.7288, p = 0.619). g, Action rate in probe light-off trials (two-way ANOVAs, HIT, Days: F (5, 30) = 5.4632, p = 0.0011; Groups: F (1, 30) = 6.3510, p = 0.017; Days*Groups: F (5, 30) = 1.2158, p = 0.33; FA, Days: F (5, 30) = 5.5019, p = 0.0010; Groups: F (1, 30) = 0, p = 1; Days*Groups: F (5, 30) = 1.1320, p = 0.37). h, HIT lick latency in probe light-off trials (two-way ANOVA, Days: F (5, 29) = 6.0308, p < 10-3; Groups: F (1, 29) = 10.3058, p = 0.0032; Days*Groups: F (5, 29) = 0.1542, p = 0.98). i, Maximal difference between hit and false alarm rates in probe light-off trials over the first 6 days (t-test, p = 0.40). j,Accuracy in reinforced light-off trials (two-way ANOVA, Days: F (17, 86) = 8.3579, p < 10-11; Groups: F (1, 86) = 1.6832, p = 0.20; Days*Groups: F (17, 86) = 0.2356, p = 1). k, Action rate in reinforced light-off trials (two-way ANOVAs, HIT, Days: F (17, 86) = 11.1314, p < 10-14; Groups: F (1, 86) = 2.1423, p = 0.15; Days*Groups: F (17, 86) = 0.9107, p = 0.56; FA, Days: F (17, 86) = 4.2760, p < 10-5; Groups: F (1, 86) = 0.5043, p = 0.48; Days*Groups: F (17, 86) = 0.3026, p = 1). l, FA lick latency in reinforced light-off trials (two-way ANOVA, Days: F (17, 78) = 1.7364, p = 0.053; Groups: F (1, 78) = 9.0848, p = 0.0035; Days*Groups: F (17, 78) = 1.3749, p = 0.17). m, FA lick rate in reinforced light-off trials (two-way ANOVA, Days: F (17, 78) = 0.7983, p = 0.69; Groups: F (1, 78) = 13.4564, p < 10-3; Days*Groups: F (17, 78) = 1.4494, p = 0.14). n, Comparison of light-off versus light-on trials to measure auditory cortex silencing effect on on-line performance. o, Session density plot of accuracy in reinforced light-on against light-off. Top, control; bottom, PV-ChR2. p, Accuracy in light-on reinforced trials from day where FA< 0.3 in light-off reinforced trials. Note the general trend for ChR2 mice (gray lines) to increase accuracy (positive slopes), i.e. performance impairment fades away. q, Within subject difference between accuracy in reinforced light-on and light-off aligned to the day where false alarm rate < 0.3 in reinforced light-off. C_FIG Rapid emergence of reward prediction activity in the auditory cortexThe sensory cortex is widely considered to be specialized for perception by interpreting complex sensory objects42,43 or adjusting representations of behaviorally-relevant stimuli2,33,37,44,45. Recent evidence, however, suggests that sensory cortical neurons directly encode non-sensory variables such as movement46-49, reward timing50-53, expectation54,55, and context23,45,56-63. Conjoint representations of sensory and non-sensory variables in the same network could further hone perception or, alternatively, subserve more integrative associative processes. Inspection of the within-trial dynamics of learning-driven cell ensembles 5 and 6 suggested that these neurons exhibited non-canonical activity in the form of a signal that occurred late in the trial, delayed from the tone-evoked response (Fig. 2j). This late-in-trial signal increased over learning and was trial type selective (Fig. 2j). We next sought to further explore the encoding properties of these two cell ensembles. Cell ensemble 5 (n = 155 cells from the learning network), exhibited late-in-trial activity on hit trials (licking to the S+) that increased with learning (Fig. 4a). This delayed activity was not apparent on correct S-trials (correct reject, CR), where neurons exhibited classical stimulus-evoked response that habituated over learning (Fig. 4b). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/597946v1_fig4.gif" ALT="Figure 4"> View larger version (76K): org.highwire.dtl.DTLVardef@16050bdorg.highwire.dtl.DTLVardef@54ba70org.highwire.dtl.DTLVardef@9c1355org.highwire.dtl.DTLVardef@b96c3b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Rapid emergence of reward prediction encoding drives learning. a, Heat map of cell ensemble 5 activity (n = 155 cells) across learning phases (delimited by horizontal white dashed lines) in hit trials (20-trial blocks). White trace represents the average trial trace. Inserts (right) show average activity at time indicated by black triangles. Colored rectangles indicate learning phases: Acquisition (green), Expression (black) and Expert (blue). b, Heat map of cell ensemble 5 activity across learning phases (delimited by horizontal white dashed lines) in CR trials (20-trial blocks). c, Heat map of the activity of a fraction of cells from cell ensemble 5 (n = 20 cells) from one example mouse across consecutive S+ trials. Black dots indicate licks. Trial outcome is represented on the right (green circle: hit; blue stars: miss). d, Cell ensemble 5 activity in hit vs miss trials (time and number matched, see Methods and Supplementary Figure 15a). e, Area under the curve (AUC) quantification of data in gray rectangle in d (Wilcoxon signed rank test, p = 6.78.10-21). f, Procedure of reinforced and probe hit trial (H) matching. g, Average cell ensemble 5 activity in reinforced hit trials immediately before (black) or after (gray) probe hit trials (green). h, AUC quantification of data in h (Friedman test, p = 0.3071). i, Lick PSTHs in reinforced hit trials immediately before (black) or after (gray) probe hit trials (green). j, Quantification of number of licks in 1-s window post-tone (KW test, p = 3.18.10-56). k, Average activity of cell ensemble 5 over the first five blocks of 40-reinforced hit trials in learning. l, Late peak activity in HIT trials across learning phases of cell ensemble 5 (green) and low weighted cells (null, black). m, Procedure of reinforced and probe FA trial (fa) matching (top) and corresponding local accuracy quantification (bottom; see Methods; repeated measures ANOVA, p = 3.16.10-4). n, Average cell ensemble 5 activity in FA trials in the probe, non-reinforced context (orange). AUC late-in-trial (gray rectangle) compared to zero (Wilcoxon signed rank test, p = 1.46.10-8). o, Average activity of cell ensemble 5 (n = 51 cells) from one example mouse in FA trials in the reinforced context (n = 423) after classification based on the detection of a reward prediction signal. Bottom, average activity of FA trials with (RP+, n = 101) or without (RP-, n = 322) reward prediction signal, and activity during FA trials in the probe context (n = 19 trials, orange) reflecting knowledge errors (see also Supplementary Figure 16). p, Heat map of the activity of a fraction of cells from cell ensemble 5 (n = 51 cells) from the same example mouse in o across consecutive FA trials in the reinforced context. Identification of a RP signal is represented by a black dot (right). q, Distribution of RP+ and RP- FA trials over learning in learning mice (binomial proportion tests, Acquisition, p = 1.65.10-7, Expression, p = 3.32.10-10, Expert, p = 0.22). r, Trial-specific closed-loop optogenetic AC inactivation over learning. s, Performance index (left, see Methods; two-way ANOVA, p = 2.11.10-21) and hit lick latency (right; two-way ANOVA, p = 0.013) in probe context in post-hit silencing experiments. t, Performance index (left, see Methods; two-way ANOVA, p = 6.36.10-5) and hit lick latency (right; two-way ANOVA, p = 0.008) in probe context in post-FA silencing experiments. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/597946v1_figs15.gif" ALT="Figure 15"> View larger version (26K): org.highwire.dtl.DTLVardef@170c926org.highwire.dtl.DTLVardef@1a60375org.highwire.dtl.DTLVardef@2cfc4corg.highwire.dtl.DTLVardef@168027e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 15.C_FLOATNO Emergence of reward prediction signal. a, Procedure of hit and miss trial matching. b, Heat map of members of cell ensemble 5 (n = 105) activity aligned to lick bout onset outside task events in day 1 of training. Lick PSTH is represented above. c, Quantification of z-scored calcium activity 1s pre- vs 1s post-lick bout onset (Wilcoxon test, p = 0.11). d, Average cell ensemble 5 activity in reinforced hit (green) and FA (orange) trials over Expression phase. e, Lick PSTHs aligned to tone onset of FA trials in Expression and hit trials in probe context. f, Cell ensemble 5 activity over the first 300 hit trials (20-trial blocks). Only significant activity (and higher than null population, see Methods) is represented. Note the emergence of a stable late-on-trial signal after 40 hit trials onwards. g, Quantification of Fig. 4l, i.e. evolution of late-in-trial signal of cell ensemble 5 across learning, taking first and last two 40-hit trial blocks (KW test, p = 1.05.10-23). *p < 0.05, **p < 0.01, ***p < 0.001, n.s.: not significant. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/597946v1_figs16.gif" ALT="Figure 16"> View larger version (26K): org.highwire.dtl.DTLVardef@17bc3d8org.highwire.dtl.DTLVardef@76c09forg.highwire.dtl.DTLVardef@601c80org.highwire.dtl.DTLVardef@1ef45da_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 16.C_FLOATNO Reward prediction signal on error trials. a, Classification of hit versus CR trials in the reinforced context from the AUC post-tone of a fraction of cell ensemble 5 (n = 51) recorded in the example mouse showed in Fig. 4p,q. Right: posterior probability of being part of CR class. b, Proportion of RP+ and RP- FA trials from the example mouse showed in Fig. 4o,p. c, No difference in lick latency was observed between RP+ and RP- FA trials (Wilcoxon test, p = 0.83). d, AUC quantification of RP+, RP- and probe FA trials (KW, p = 9.76.10-28). e, Proportion of RP+ among all FA trials and misclassification rate in each learning mice. *p < 0.05, **p < 0.01, ***p < 0.001, n.s.: not significant. C_FIG To understand the nature of the late-in-trial activity, we exploited our multiple trial types to disambiguate the contribution of sensory, motor, and reward signals. To assess whether the late-in-trial signal was a delayed form of sensory activity, we compared activity in hit trials to activity in trials where the same stimulus was presented but the mice did not lick and did not get rewarded (miss trials, Figs.1a and 4c-e). To ensure an appropriate comparison between hit and miss trials, we generated a balanced set of trials that were matched in number (given that miss trials were less frequent) and occurred within the same time period (given that the signal amplitude evolved with learning) (Supplementary Figure 15a). Cell ensemble 5 did not exhibit late-in-trial activity on miss trials (Fig. 4c-e), discarding the possibility that it reflected a delayed sensory response. We then asked whether this activity reflected reward consumption. We compared cell ensemble activity during hit trials in the reinforced context to the activity during hit trials in the probe context (Fig. 4f), where the mice expected reward and thus correctly licked to the S+ but the reward was omitted (Fig. 1b). We matched the number of trials between reinforced and probe contexts and controlled for within-session and across-session changes by comparing probe hit trials to reinforced hit trials immediately before and after the probe block (Fig. 4f). Strikingly, late-in-trial activity was preserved in probe trials (Fig. 4g,h), indicating that it did not reflect reward consumption. Finally, although movement has been reported to decrease auditory cortical activity46,64-66, we sought to understand the degree to which this late-in-trial signal could be driven by licking itself. To do this, we first exploited probe hit trials where the lick rate was strongly reduced compared to reinforced hit trials (Fig. 4i,j). We observed no difference in the late-in-trial neural signal and could thus conclude that the signal was not due to ongoing licking (Fig. 4i,j). Second, we tested the possibility that this late-in-trial signal was driven by the initiation of a lick bout as compared to the ongoing licking activity. We isolated spontaneous lick bouts in between training blocks and observed that the cell ensemble was not lick-responsive (Supplementary Figure 15b,c). In addition, if lick initiation drove this activity, we would also expect to see it on false alarm trials (incorrect licking to the S-). For this analysis, we focused on false alarms that occurred after task acquisition, as these errors are unlikely to be errors due to imperfect task knowledge. We observed no systematic late-in-trial activity on these trials (Supplementary Figure 15d) even though the licking pattern in false alarm trials was similar to that during probe hit trials (Supplementary Figure 15e). Taken together, the late-in-trial activity did not reflect stimulus, reward consumption, licking, nor lick initiation. Instead, these results showed that cell ensemble 5 encoded the higher-order process of reward prediction (RP). We next sought to identify the precise moment when a contingency is formed by identifying the trials when this reward prediction signal emerged. Initially, these neurons exhibited classical tone-evoked responses but then abruptly and within only 40 hit trials, developed a robust reward prediction activity (Fig. 4k, Supplementary Figure 15f). This reward prediction signal continued to develop over Acquisition, strengthened during Expression, and then surprisingly receded at Expert level when learning is nominally complete (Fig. 4a,l, Supplementary Figure 15g). This longitudinal temporal dynamic mirrored our optogenetic results which demonstrates that the AC is the default pathway for learning but then becomes dispensable at expert levels. Altogether, these results show that a reward prediction signal rapidly emerges at the timescale of Acquisition in auditory cortical networks. Revealing the underlying cognitive drivers of errorsIdentifying the cognitive drivers of errors is particularly challenging during learning 4. Errors during learning are typically considered mistakes while discriminative contingencies (task knowledge) are still forming. However, errors arise not only from knowledge-related mistakes (for which animals incorrectly expect reward), but also from factors such as impulsivity, disengagement, and exploration (for which animals do not expect reward). While detailed behavioral inspection has been a promising route to uncover the nature of errors11, an alternative approach is to use neural activity itself. Given our findings of reward prediction encoding on correct trials, we hypothesized that the same signal would be present when animals make knowledge-related errors, when animals incorrectly expected rewards on S- trials. To address this, we first focused on the occasional false alarms (FA) that occurred during probe trials, as they reflected errors of task knowledge (Fig. 4m)7. Strikingly, we observed a robust reward prediction activity in these trials (Fig. 4n), strongly suggesting that animals were indeed expecting reward. We next reasoned that such knowledge errors should be present not only on probe trials, but also in a subset of reinforced trials, interspersed with non-knowledge errors. We classified individual FA trials in the reinforced context based on the presence of a reward prediction signal (see Methods; Supplementary Figure 16a). We identified a significant proportion of trials that exhibited robust reward prediction activity, but also many that did not (Fig. 4o, Supplementary Figure 16b). The reward prediction signal was identical to that observed in probe trials (Fig. 4o, Supplementary Figure 16d), providing further confidence that these were indeed knowledge errors. These data suggest that we could isolate knowledge errors using neural data, which was not possible from behavioral inspection alone (Supplementary Figure 16c). Interestingly, we found that knowledge errors were interspersed with errors that did not elicit reward prediction activity (Fig. 4p). Finally, we hypothesized that knowledge errors should predominantly occur during the Acquisition phase of behavior, when animals are still learning the discriminative contingencies. We computed the fraction of RP+ (knowledge-related errors) and RP-(non-knowledge errors) over time and found that RP+ errors peaked during the Acquisition phase of learning, and rar ]]> Drieu, C. Zhu, Z. Wang, Z. Fuller, K. Wang, A. Elnozahy, S. Kuchibhotla, K. 2024-06-10 doi:10.1101/2024.06.10.597946 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ A mechanism for telomere-specific telomere length regulation ]]> https://biorxiv.org/content/10.1101/2024.06.12.598646v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1c3bb52org.highwire.dtl.DTLVardef@13f338forg.highwire.dtl.DTLVardef@51f91aorg.highwire.dtl.DTLVardef@1b95ac0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Teplitz, G. M. Pasquier, E. Bonnell, E. De Laurentiis, E. Bartle, L. Lucier, J.-F. Sholes, S. Greider, C. W. Wellinger, R. J. 2024-06-12 doi:10.1101/2024.06.12.598646 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ T cell responsiveness to IL-10 defines the immunomodulatory effect of costimulation blockade via anti-CD154 and impacts transplant survival ]]> https://biorxiv.org/content/10.1101/2024.06.12.598652v1?rss=1 Iglesias, M. Bibicheff, D. Komin, A. Chicco, M. Guinn, S. Foley, B. Raimondi, G. 2024-06-14 doi:10.1101/2024.06.12.598652 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Transcriptomics and proteomics of projection neurons in a circuit linking hippocampus with dorsolateral prefrontal cortex in human brain ]]> https://biorxiv.org/content/10.1101/2024.06.12.598714v1?rss=1 90% accuracy) and proteomic data (>97% accuracy) compared with gene-level expression data (<70% in bulk). Patients with SCZ show hippocampal-specific differential protein phosphorylation. SCZ risk co-expression gene-sets that replicate across transcript and protein networks are enriched for transmembrane transporters in the DLPFC and CA1 and postsynaptic processes in the SUB. We demonstrate a strong directional connectivity effect of SCZ risk in that excitatory synaptic genes in CA1 unidirectionally predict gene expression in SUB. Finally, parallel CA1 snRNA-seq results suggest that in SCZ excitatory efferents in CA1 are affected by interactions with glia and by downregulation of inhibitory neuropeptide inputs. Our study proposes molecular mechanisms by which hippocampal communication, previously associated with SCZ at the macroscopic level, may be altered at the inter-field and interregional circuit level. ]]> Bharadwaj, R. A. Borcuk, C. Kikidis, G. C. Sportelli, L. Bertolino, A. Cole, R. N. DeVine, L. Kleinman, J. E. Maher, B. Sripathy, S. R. Mallepalli, V. Parihar, M. Shin, J. Lee, Y. Montoya, C. Deep-Soboslay, A. Hyde, T. M. Weinberger, D. R. Pergola, G. 2024-06-13 doi:10.1101/2024.06.12.598714 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Proteogenomic Reprogramming to a Functional Human Totipotent Stem Cell State via a PARP-DUX4 Regulatory Axis ]]> https://biorxiv.org/content/10.1101/2024.06.14.598510v1?rss=1 Zimmerlin, L. Angarita, A. Park, T. S. Evans-Moses, R. Thomas, J. Yan, S. Uribe, I. Vegas, I. Kochendoerfer, C. Buys, W. Leung, A. Zambidis, E. T. 2024-06-15 doi:10.1101/2024.06.14.598510 Cold Spring Harbor Laboratory Press 2024-06-15 <![CDATA[ Polyamine Depletion by D, L-alpha-difluoromethylornithine Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis ]]> https://biorxiv.org/content/10.1101/2024.06.14.599064v1?rss=1 Offenbacher, R. Jackson, K. Hayashi, M. Zhang, J. Peng, D. Tan, Y. Stewart, T. M. Ciero, P. Foley, J. R. Casero, R. A. Cahan, P. Loeb, D. M. 2024-06-17 doi:10.1101/2024.06.14.599064 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ The value of initiating a pursuit in temporal decision-making ]]> https://biorxiv.org/content/10.1101/2024.06.16.599189v1?rss=1 Sutlief, E. Walters, C. Marton, T. Hussain Shuler, M. G. 2024-06-16 doi:10.1101/2024.06.16.599189 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Molecular patterns and mechanisms of tumorigenesis in HPV-associated and HPV-independent sinonasal squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2024.06.17.598514v1?rss=1 Zamuner, F. T. Gunti, S. Starrett, G. J. Faraji, F. Toni, T. Saraswathula, A. Vu, K. Gupta, A. Zhang, Y. Faden, D. Bryan, M. E. Guo, T. Rowan, N. R. Ramanathan, M. Lane, A. P. Fakhry, C. Gallia, G. L. Allen, C. T. Rooper, L. R. London, N. R. 2024-06-18 doi:10.1101/2024.06.17.598514 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ A Multi-Omics Approach to Defining Target Organ Injury in Youth with Primary Hypertension ]]> https://biorxiv.org/content/10.1101/2024.06.17.599125v1?rss=1 Ananthamohan, K. Brady, T. M. Arif, M. Daniels, S. Falkner, B. Ferguson, M. Flynn, J. T. Hanevold, C. Hooper, S. R. Ingelfinger, J. Lande, M. Martin, L. J. Meyers, K. E. Mitsnefes, M. Rosner, B. Samuels, J. A. Kuffel, G. Zilliox, M. J. Becker, R. C. Urbina, E. M. Sadayappan, S. 2024-06-18 doi:10.1101/2024.06.17.599125 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ Rapid rebalancing of co-tuned ensemble activity in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2024.06.17.599418v1?rss=1 Kang, H. Babola, T. Kanold, P. O. 2024-06-18 doi:10.1101/2024.06.17.599418 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ Cell type-specific expression of angiotensin receptors in the human lung with implications for health, aging, and chronic disease ]]> https://biorxiv.org/content/10.1101/2024.06.17.599425v1?rss=1 Benjamin, K. J. M. Sauler, M. Poonyagariyagorn, H. Neptune, E. R. 2024-06-22 doi:10.1101/2024.06.17.599425 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Nanopore Decoding with Speed and Versatility for Data Storage ]]> https://biorxiv.org/content/10.1101/2024.06.18.599582v1?rss=1 Volkel, K. Hook, P. W. Keung, A. J. Timp, W. Tuck, J. M. 2024-06-18 doi:10.1101/2024.06.18.599582 Cold Spring Harbor Laboratory Press 2024-06-18 <![CDATA[ 3D in-situ characterization reveals the instability-induced auxetic behavior of collagen scaffolds for tissue engineering ]]> https://biorxiv.org/content/10.1101/2024.06.18.599620v1?rss=1 Chen, E. Kim, B. Bouklas, N. Bonassar, L. J. Gaitanaros, S. 2024-06-22 doi:10.1101/2024.06.18.599620 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Cortical inhibitory parvalbumin interneurons exhibit metabolic specializations coordinated by PGC-1α that are lost in rodents and humans after traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2024.06.19.599637v1?rss=1 Quinones, S. Wang, J. Kim, E. Bottom-Tanzer, S. Armbruster, M. Macedo, J. Hawkinson, T. Ribas, R. Singh, P. K. Wu, L. Cantrell, A. R. Kumar, P. George, J. Tai, A. Whalen, M. McConnell, M. Sun, R. C. Gentry, M. S. Dulla, C. G. 2024-06-23 doi:10.1101/2024.06.19.599637 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Epigenomic programming of peripheral monocytes determines their transcriptional response to the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.06.19.599675v1?rss=1 Kiss, M. Halasz, L. Hadadi, E. Berger, W. K. Tzerpos, P. Poliska, S. Kancheva, D. Debraekeleer, A. Brughmans, J. Elkrim, Y. Martens, L. Saeys, Y. Daniel, B. Czimmerer, Z. Laoui, D. Nagy, L. Van Ginderachter, J. A. 2024-06-23 doi:10.1101/2024.06.19.599675 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Metabolite T2 relaxation times decrease across the adult lifespan in a large multi-site cohort ]]> https://biorxiv.org/content/10.1101/2024.06.19.599719v1?rss=1 Hupfeld, K. E. Murali-Manohar, S. Zollner, H. J. Song, Y. Davies-Jenkins, C. W. Gudmundson, A. T. Simicic, D. Simegn, G. Carter, E. E. Hui, S. C. Yedavalli, V. Oeltzschner, G. Porges, E. C. Edden, R. A. 2024-06-24 doi:10.1101/2024.06.19.599719 Cold Spring Harbor Laboratory Press 2024-06-24 <![CDATA[ Glia-enriched stem-cell 3D model of the human brain mimics the glial-immune neurodegenerative phenotypes of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2024.06.20.597748v1?rss=1 Fagiani, F. Pedrini, E. Taverna, S. Brambilla, E. Murtaj, V. Podini, P. Ruffini, F. Butti, E. Braccia, C. Andolfo, A. Magliozzi, R. Smirnova, L. Kuhlmann, T. Quattrini, A. Calabresi, P. A. Reich, D. S. Martino, G. Panina-Bordignon, P. Absinta, M. 2024-06-24 doi:10.1101/2024.06.20.597748 Cold Spring Harbor Laboratory Press 2024-06-24 <![CDATA[ TrkA+ sensory neurons regulate osteosarcoma proliferation and vascularization to promote disease progression ]]> https://biorxiv.org/content/10.1101/2024.06.20.599869v1?rss=1 James, A. W. Qin, Q. Ramesh, S. Li, Z. Zhong, L. Cherief, M. Archer, M. Xing, X. Thottappillil, N. Gomez-Salazar, M. Zhu, M. Chang, L. Uniyal, A. Mazhar, K. Mittal, M. McCarthy, E. F. Morris, C. D. Levi, B. Guan, Y. Clemens, T. L. Price, T. J. 2024-06-25 doi:10.1101/2024.06.20.599869 Cold Spring Harbor Laboratory Press 2024-06-25 <![CDATA[ Cell wall melanin impedes growth of the Cryptococcus neoformans polysaccharide capsule by sequestering calcium ]]> https://biorxiv.org/content/10.1101/2024.06.20.599928v1?rss=1 Baker, R. P. Liu, A. Z. Casadevall, A. 2024-06-20 doi:10.1101/2024.06.20.599928 Cold Spring Harbor Laboratory Press 2024-06-20 <![CDATA[ A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks ]]> https://biorxiv.org/content/10.1101/2024.06.21.599974v1?rss=1 Jung, H. Amini, M. Hunt, B. J. Murphy, E. I. Sadil, P. Halchenko, Y. O. Petre, B. Miao, Z. Kragel, P. A. Han, X. Heilicher, M. O. Sun, M. Collins, O. G. Lindquist, M. A. Wager, T. D. 2024-06-26 doi:10.1101/2024.06.21.599974 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Myo-optogenetics: optogenetic stimulation and electrical recording in skeletal muscles ]]> https://biorxiv.org/content/10.1101/2024.06.21.600113v1?rss=1 Kim, J. J. Wyche, I. S. Olson, W. Lu, J. Bakir, M. S. Sober, S. J. O'Connor, D. H. 2024-06-25 doi:10.1101/2024.06.21.600113 Cold Spring Harbor Laboratory Press 2024-06-25 <![CDATA[ VERICIGUAT RESCUES cGMP PRODUCTION IN HUMAN AORTIC VASCULAR SMOOTH MUSCLE CELLS AND AUGMENTS VASORELAXATION IN AORTIC RINGS EXPOSED TO HIGH GLUCOSE ]]> https://biorxiv.org/content/10.1101/2024.06.21.600154v1?rss=1 Polhemus, D. J. Almodiel, D. Harb, T. Ziogos, E. Amat-Alarcon, N. Ranek, M. Santhanam, L. Gerstenblith, G. Leucker, T. M. 2024-06-22 doi:10.1101/2024.06.21.600154 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during cell growth arrest. ]]> https://biorxiv.org/content/10.1101/2024.06.22.600200v1?rss=1 Neri, F. Zheng, S. Watson, M. Desprez, P. Y. Gerencser, A. Campisi, J. Wirtz, D. Wu, P.-H. Schilling, B. 2024-06-26 doi:10.1101/2024.06.22.600200 Cold Spring Harbor Laboratory Press 2024-06-26 <![CDATA[ Phosphoglycerate mutase regulates Treg differentiation through control of serine synthesis and one-carbon metabolism ]]> https://biorxiv.org/content/10.1101/2024.06.23.600101v1?rss=1 Godfrey, W. H. Cho, K. Deng, X. Ambati, C. S. R. Putluri, V. Kamal, A. H. M. Putluri, N. Kornberg, M. D. 2024-06-28 doi:10.1101/2024.06.23.600101 Cold Spring Harbor Laboratory Press 2024-06-28 <![CDATA[ Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis ]]> https://biorxiv.org/content/10.1101/2024.06.23.600305v1?rss=1 Zhuang, X. Wang, Q. Joost, S. Ferrena, A. Humphreys, D. T. LI, Z. Blum, M. Bastl, K. Ding, S. Landais, Y. Zhan, Y. Zhao, Y. Chaligne, R. Lee, J.-H. Carrasco, S. E. Bhanot, U. K. Koche, R. P. Bott, M. J. Katajisto, P. Soto-Feliciano, Y. M. Pisanic, T. R. Thomas, T. Zheng, D. Wong, E. Tammela, T. 2024-06-28 doi:10.1101/2024.06.23.600305 Cold Spring Harbor Laboratory Press 2024-06-28 <![CDATA[ Depletion of TDP-43 exacerbates tauopathy-dependent brain atrophy by sensitizing vulnerable neurons to caspase 3-mediated endoproteolysis of tau in a mouse model of Multiple Etiology Dementia ]]> https://biorxiv.org/content/10.1101/2024.06.26.600814v1?rss=1 Baghel, M. S. Burns, G. D. Tsapatsis, M. Peethambaran Mallika, A. Cruz, A. L. F. Cao, T. Chen, X. K. Rosa, I. D. L. Marx, S. R. Ye, Y. Sun, S. Li, T. Wong, P. C. 2024-06-29 doi:10.1101/2024.06.26.600814 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Loss of asgr1a leads to the secretion of excess dietary cholesterol in zebrafish ]]> https://biorxiv.org/content/10.1101/2024.06.26.600848v1?rss=1 Moll, T. O. C. Derrick, J. T. Sweeney, D. W. Shin, J. Farber, S. A. 2024-06-29 doi:10.1101/2024.06.26.600848 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Lineage-dependence of the neuroblastoma surfaceome defines tumor cell state-dependent and independent immunotherapeutic targets ]]> https://biorxiv.org/content/10.1101/2024.06.27.600865v1?rss=1 Kendsersky, N. M. Odrobina, M. Mabe, N. W. Farrel, A. Grossmann, L. Tsang, M. Wolpaw, A. J. Zammarchi, F. van Berkel, P. H. Dang, C. V. Mosse, Y. P. Stegmaier, K. Maris, J. 2024-07-02 doi:10.1101/2024.06.27.600865 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Contribution of telacebec to novel drug regimens in a murine tuberculosis model ]]> https://biorxiv.org/content/10.1101/2024.06.27.601059v1?rss=1 Komm, O. D. Tyagi, S. Garcia, A. Almeida, D. V. Chang, Y. S. Li, S.-Y. Castillo, J. R. Converse, P. J. Black, T. Fotouhi, N. Nuermberger, E. L. 2024-06-27 doi:10.1101/2024.06.27.601059 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Confinement, jamming, and adhesion in cancer cells dissociating from a collectively invading strand ]]> https://biorxiv.org/content/10.1101/2024.06.28.601053v1?rss=1 Wang, W. Law, R. A. Perez Ipina, E. Konstantopoulos, K. Camley, B. A. 2024-06-29 doi:10.1101/2024.06.28.601053 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Aberrant N-glycosylation is a therapeutic target in carriers of a common and highly pleiotropic mutation in the manganese transporter ZIP8 ]]> https://biorxiv.org/content/10.1101/2024.06.28.601207v1?rss=1 Tomar, V. Kang, J. Lin, R. Brant, S. R. Lazarev, M. Tressler, C. Glunde, K. Zachara, N. Melia, J. M. 2024-07-02 doi:10.1101/2024.06.28.601207 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Multi-sample non-negative spatial factorization ]]> https://biorxiv.org/content/10.1101/2024.07.01.599554v1?rss=1 Wang, Y. Woyshner, K. Sriworarat, C. Stein-O'Brien, G. Goff, L. A. Hansen, K. D. 2024-07-01 doi:10.1101/2024.07.01.599554 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ Opto-Myomatrix: μLED integrated microelectrode arrays for optogenetic activation and electrical recording in muscle tissue ]]> https://biorxiv.org/content/10.1101/2024.07.01.601601v1?rss=1 Lu, J. Zia, M. Baig, D. A. Yan, G. Kim, J. J. Nagapudi, K. Anschutz, P. Oh, S. O'Connor, D. H. Sober, S. J. Bakir, M. S. 2024-07-04 doi:10.1101/2024.07.01.601601 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Cytosolic N6AMT1-dependent translation supports mitochondrial RNA processing ]]> https://biorxiv.org/content/10.1101/2024.07.02.601698v1?rss=1 Foged, M. M. Recazens, E. Chollet, S. Lisci, M. Allen, G. E. Zinshteyn, B. Boutguetait, D. Munch, C. A. Mootha, V. K. Jourdain, A. A. 2024-07-02 doi:10.1101/2024.07.02.601698 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Biochemical implementation of acceleration sensing and PIDA control ]]> https://biorxiv.org/content/10.1101/2024.07.02.601775v1?rss=1 Alexis, E. Espinel-Rios, S. Kevrekidis, I. G. Avalos, J. L. 2024-07-02 doi:10.1101/2024.07.02.601775 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Memantine Inhibits Calcium-Permeable AMPA Receptors ]]> https://biorxiv.org/content/10.1101/2024.07.02.601784v1?rss=1 Carrillo, E. Montano Romero, A. Gonzalez, C. U. Turcu, A. L. Chen, S.-R. Chen, H. Pan, H.-L. Vazquez, S. Twomey, E. C. Jayaraman, V. 2024-07-04 doi:10.1101/2024.07.02.601784 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ A scene with an invisible wall - navigational experience shapes visual scene representation ]]> https://biorxiv.org/content/10.1101/2024.07.03.601933v1?rss=1 Li, S. P. D. Shao, J. Lu, Z. McCloskey, M. Park, S. 2024-07-05 doi:10.1101/2024.07.03.601933 Cold Spring Harbor Laboratory Press 2024-07-05 <![CDATA[ EM-Compressor: Electron Microscopy Image Compression in Connectomics with Variational Autoencoders ]]> https://biorxiv.org/content/10.1101/2024.07.07.601368v1?rss=1 Li, Y. Park, C. F. Xenes, D. Bishop, C. Berger, D. R. Samuel, A. D. T. Wester, B. Lichtman, J. W. Pfister, H. Li, W. Meirovitch, Y. 2024-07-08 doi:10.1101/2024.07.07.601368 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct expression patterns and potential markers of progression ]]> https://biorxiv.org/content/10.1101/2024.07.07.602385v1?rss=1 Wang, Y. Lih, T.-S. M. Lee, J. W. Ohtsuka, T. Hozaka, Y. Mino-Kenudson, M. Adsay, N. V. Luchini, C. Scarpa, A. Maker, A. V. Kim, G. E. Paulino, J. Chen, L. Jiao, L. Sun, Z. Goodman, D. Pfluger, M. J. Roberts, N. J. Matthaei, H. Wood, L. D. Furukawa, T. Zhang, H. Hruban, R. H. 2024-07-07 doi:10.1101/2024.07.07.602385 Cold Spring Harbor Laboratory Press 2024-07-07 <![CDATA[ Hippocampal-prefrontal communication subspaces align with behavioral and network patterns in a spatial memory task ]]> https://biorxiv.org/content/10.1101/2024.07.08.601617v1?rss=1 Young, R. A. Shin, J. D. Guo, Z. Jadhav, S. P. 2024-07-11 doi:10.1101/2024.07.08.601617 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries ]]> https://biorxiv.org/content/10.1101/2024.07.08.602478v1?rss=1 Ling, Y. H. Liang, C. Wang, S. Wu, C. 2024-07-11 doi:10.1101/2024.07.08.602478 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Age-dependent predictors of effective reinforcement motor learning across childhood ]]> https://biorxiv.org/content/10.1101/2024.07.09.602665v1?rss=1 Hill, N. M. Tripp, H. M. Wolpert, D. M. Malone, L. A. J Bastian, A. 2024-07-09 doi:10.1101/2024.07.09.602665 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology ]]> https://biorxiv.org/content/10.1101/2024.07.09.602778v1?rss=1 Border, S. Melo Ferreira, R. Lucarelli, N. Kumar, S. Paul, A. Manthey, D. Barisoni, L. Strekalova, Y. Ray, J. Cheng, Y.-H. Rosenberg, A. Z. Tomaszewski, J. E. Mimar, S. Hodgin, J. B. HuBMAP consortium, El-Achkar, T. M. Jain, S. Eadon, M. T. Sarder, P. 2024-07-14 doi:10.1101/2024.07.09.602778 Cold Spring Harbor Laboratory Press 2024-07-14 <![CDATA[ Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta ]]> https://biorxiv.org/content/10.1101/2024.07.09.602802v1?rss=1 2.2 [A]). In a local docking scenario, i.e. with membrane protein partners starting {approx}10 [A] apart embedded in the membrane in their unbound conformations, Rosetta-MPDock successfully predicts the correct interface (success defined as achieving 3 near-native structures in the 5 top-ranked models) for 67% moderately flexible targets and 60% of the highly flexible targets, a substantial improvement from the existing membrane protein docking methods. Further, by integrating AlphaFold2-multimer for structure determination and using Rosetta-MPDock for docking and refinement, we demonstrate improved success rates over the benchmark targets from 64% to 73%. Rosetta-MPDock advances the capabilities for membrane protein complex structure prediction and modeling to tackle key biological questions and elucidate functional mechanisms in the membrane environment. The benchmark set and the code is available for public use at github.com/Graylab/MPDock. ]]> Samnata, R. Harmalkar, A. Prathima, P. Gray, J. J. 2024-07-13 doi:10.1101/2024.07.09.602802 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Inferring illness causes recruits the animacy semantic network ]]> https://biorxiv.org/content/10.1101/2024.07.10.602983v1?rss=1 Hauptman, M. Bedny, M. 2024-07-13 doi:10.1101/2024.07.10.602983 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Cells in the Polyaneuploid Cancer Cell State are Pro-Metastatic ]]> https://biorxiv.org/content/10.1101/2024.07.12.603285v1?rss=1 Mallin, M. M. Rolle, L. T. A. Schmidt, M. J. Priyadarsini Nair, S. Zurita, A. J. Kuhn, P. Hicks, J. Pienta, K. J. Amend, S. R. 2024-07-16 doi:10.1101/2024.07.12.603285 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Local keratinocyte-nociceptor interactions enhance obesity-mediated small fiber neuropathy via NGF-TrkA-PI3K signaling axis ]]> https://biorxiv.org/content/10.1101/2024.07.12.603316v1?rss=1 Koui, Y. Song, S. Dong, X. Mukouyama, Y.-S. 2024-07-16 doi:10.1101/2024.07.12.603316 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites ]]> https://biorxiv.org/content/10.1101/2024.07.13.603322v1?rss=1 Usmani, M. Coudray, N. Riggi, M. Raghu, R. Ramchandani, H. Bobe, D. Kopylov, M. Zhong, E. D. Iwasa, J. H. Ekiert, D. C. Bhabha, G. 2024-07-13 doi:10.1101/2024.07.13.603322 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Resistance to age-related hearing loss in the echolocating big brown bat (Eptesicus fuscus) ]]> https://biorxiv.org/content/10.1101/2024.07.15.603592v1?rss=1 Capshaw, G. Diebold, C. A. Adams, D. M. Rayner, J. Wilkinson, G. S. Moss, C. F. Lauer, A. M. 2024-07-18 doi:10.1101/2024.07.15.603592 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ The Neurobiology of Cognitive Fatigue and Its Influence on Effort-Based Choice ]]> https://biorxiv.org/content/10.1101/2024.07.15.603598v1?rss=1 Steward, G. E. Chib, V. S. 2024-07-18 doi:10.1101/2024.07.15.603598 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.07.16.603739v1?rss=1 Du, W. Zhou, B. Forjaz, A. Shin, S. M. Wu, F. Crawford, A. J. Nair, P. R. Johnston, A. C. West-Foyle, H. Tang, A. Kim, D. Fan, R. Kiemen, A. L. Wu, P.-H. Phillip, J. M. Ho, W. J. Sanin, D. E. Wirtz, D. 2024-07-18 doi:10.1101/2024.07.16.603739 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells ]]> https://biorxiv.org/content/10.1101/2024.07.18.604156v1?rss=1 Ran, R. Trapecar, M. Brubaker, D. 2024-07-19 doi:10.1101/2024.07.18.604156 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Cell cycle expression heterogeneity predicts degree of differentiation ]]> https://biorxiv.org/content/10.1101/2024.07.19.604184v1?rss=1 Noller, K. Cahan, P. 2024-07-22 doi:10.1101/2024.07.19.604184 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome ]]> https://biorxiv.org/content/10.1101/2024.07.19.604339v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1b913caorg.highwire.dtl.DTLVardef@1c23ce3org.highwire.dtl.DTLVardef@12b8a25org.highwire.dtl.DTLVardef@17a9a4e_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Reynisdottir, T. Anderson, K. J. Brinn, A. Franklin, K. Ouyang, J. Snorradottir, A. O. Lutz, C. M. Zuberi, A. R. DeLeon, V. B. Bjornsson, H. T. 2024-07-23 doi:10.1101/2024.07.19.604339 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads ]]> https://biorxiv.org/content/10.1101/2024.07.20.604421v1?rss=1 Lin, M.-J. Langmead, B. Safonova, Y. 2024-07-23 doi:10.1101/2024.07.20.604421 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Host-derived CEACAM-laden vesicles engage enterotoxigenic E. coli for elimination and toxin neutralization. ]]> https://biorxiv.org/content/10.1101/2024.07.24.604983v1?rss=1 Sheikh, A. Ganguli, D. Vickers, T. J. Singer, B. Foulke-Abel, J. Akhtar, M. Khatoon, N. Setu, B. Basu, S. Maier, N. Beatty, W. Chakraborty, S. Bhuiyan, T. R. Qadri, F. Donowitz, M. Fleckenstein, J. M. 2024-07-24 doi:10.1101/2024.07.24.604983 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Control of tongue movements by the Purkinje cells of the cerebellum ]]> https://biorxiv.org/content/10.1101/2024.07.25.604757v1?rss=1 Hage, P. Fakharian, M. A. Shoup, A. M. Pi, J. S. Sedaghat-Nejad, E. Orozco, S. P. Jang, I. K. Looi, V. Arginteanu, T. Shadmehr, R. 2024-07-25 doi:10.1101/2024.07.25.604757 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Protein surface chemistry encodes an adaptive resistance to desiccation ]]> https://biorxiv.org/content/10.1101/2024.07.28.604841v1?rss=1 Romero-Perez, P. S. Moran, H. M. Horani, A. Truong, A. Manriquez-Sandoval, E. Ramirez, J. F. Martinez, A. Golub, E. Hunter, K. Lotthammer, J. M. Emenecker, R. J. Boothby, T. C. Holehouse, A. S. Fried, S. D. Sukenik, S. 2024-07-29 doi:10.1101/2024.07.28.604841 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ IPMK Deficiency Reduces Skeletal Muscle Oxidative Metabolism and Exercise Capacity ]]> https://biorxiv.org/content/10.1101/2024.07.28.605526v1?rss=1 Lee, J.-H. Jung, I.-R. Tu-Sekine, B. Jin, S. Anokye-Danso, F. Ahima, R. S. Kim, S. F. 2024-07-29 doi:10.1101/2024.07.28.605526 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Arc controls organ architecture through modulation of Crb and MyoII ]]> https://biorxiv.org/content/10.1101/2024.07.29.605562v1?rss=1 Kim, J. H. Maruyama, R. Kim, K. Vertrees, D. Paul, P. Britson, K. A. Andrew, D. J. 2024-07-29 doi:10.1101/2024.07.29.605562 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Structures of H2A.Z-associated human chromatin remodelers SRCAP and TIP60 reveal divergent mechanisms of chromatin engagement ]]> https://biorxiv.org/content/10.1101/2024.07.30.605802v1?rss=1 Park, G. Patel, A. B. Wu, C. Louder, R. K. 2024-07-30 doi:10.1101/2024.07.30.605802 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Closing the genome of Teredinibacter turnerae T7902 by long-read nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2024.07.30.605897v1?rss=1 Gasser, M. T. Liu, A. Flatau, R. Altamia, M. A. Filone, C. M. Distel, D. L. 2024-07-30 doi:10.1101/2024.07.30.605897 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Drug Metabolism and Transport Capacity of Endothelial Cells, Pericytes, and Astrocytes: Implications for CNS Drug Disposition ]]> https://biorxiv.org/content/10.1101/2024.08.01.606165v1?rss=1 Wilkins, H. N. Knerler, S. A. Warshanna, A. Ortiz, R. C. Haas, K. Orsburn, B. C. Williams, D. W. 2024-08-05 doi:10.1101/2024.08.01.606165 Cold Spring Harbor Laboratory Press 2024-08-05 <![CDATA[ The estrous cycle modulates hippocampal spine dynamics, dendritic processing, and spatial coding ]]> https://biorxiv.org/content/10.1101/2024.08.02.606418v1?rss=1 Wolcott, N. S. Redman, W. T. Karpinska, M. Jacobs, E. G. Goard, M. J. 2024-08-03 doi:10.1101/2024.08.02.606418 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ 3D histology reveals that immune response to pancreatic precancers is heterogeneous and depends on global pancreas structure ]]> https://biorxiv.org/content/10.1101/2024.08.03.606493v1?rss=1 Kiemen, A. L. Almagro Perez, C. Matos Romero, V. Forjaz, A. Braxton, A. M. Dequiedt, L. Parksong, J. Cannon, C. D. Yuan, X. Shin, S. M. Mahesh Babu, J. Thompson, E. D. Cornish, T. C. Ho, W. J. Wood, L. D. Wu, P. Munoz-Barrutia, A. Hruban, R. H. Wirtz, D. 2024-08-06 doi:10.1101/2024.08.03.606493 Cold Spring Harbor Laboratory Press 2024-08-06 <![CDATA[ Transcranial real-time in vivo recording of electrophysiological neural activity in the rodent brain with near-infrared photoacoustic voltage-sensitive dye imaging ]]> https://biorxiv.org/content/10.1101/202408v1?rss=1 Kang, J. Zhang, H. K. Kadam, S. D. Julie, F. Valentine, H. Kang, J. U. Rahmim, A. Gjedde, A. Loew, L. M. Wong, D. F. Boctor, E. M. 2017-10-16 doi:10.1101/202408 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Addressing confounding artifacts in reconstruction of gene co-expression networks ]]> https://biorxiv.org/content/10.1101/202903v1?rss=1 Parsana, P. Ruberman, C. Jaffe, A. E. Schatz, M. C. Battle, A. Leek, J. T. 2017-10-13 doi:10.1101/202903 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Non-invasive detection of upper tract urothelial carcinomas through the analysis of driver gene mutations and aneuploidy in urine ]]> https://biorxiv.org/content/10.1101/203968v1?rss=1 Springer, S. U. Chen, C.-H. Li, L. Douville, C. Wang, Y. Cohen, J. Afsari, B. Danilova, L. Silliman, N. Schaeffer, J. Ptak, J. Dobbyn, L. Papoli, M. Kinde, I. Huang, C.-Y. Shun, C.-T. Karchin, R. Netto, G. J. Turesky, R. J. Yun, B. H. Rosenquist, T. A. Hruban, R. H. Pu, Y.-S. Grollman, A. P. Tomasetti, C. Papadopoulos, N. Kinzler, K. W. Vogelstein, B. Dickman, K. G. 2017-10-16 doi:10.1101/203968 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Non-invasive detection of bladder cancer through the analysis of driver gene mutations and aneuploidy ]]> https://biorxiv.org/content/10.1101/203976v1?rss=1 Springer, S. U. Rodriguez Pena, M. D. C. Li, L. Douville, C. Wang, Y. Cohen, J. Taheri, D. Silliman, N. Schaeffer, J. Ptak, J. Dobbyn, L. Papoli, M. Kinde, I. Afsari, B. Tregnago, A. C. Bezerra, S. M. VandenBussche, C. Fujita, K. Ertoy, D. Cunha, I. W. Yu, L. Schoenberg, M. Bivalacqua, T. J. Dickman, K. G. Grollman, A. P. Diaz, L. A. Karchin, R. Hruban, R. H. Tomasetti, C. Papadopoulos, N. Kinzler, K. W. Vogelstein, B. Netto, G. J. 2017-10-16 doi:10.1101/203976 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data ]]> https://biorxiv.org/content/10.1101/204438v1?rss=1 Sauria, M. E. Taylor, J. 2017-10-17 doi:10.1101/204438 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Organizing principles of pulvino-cortical connectivity in humans ]]> https://biorxiv.org/content/10.1101/205039v1?rss=1 Arcaro, M. Pinsk, M. Chen, J. Kastner, S. 2017-10-18 doi:10.1101/205039 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Scaling read aligners to hundreds of threads on general-purpose processors ]]> https://biorxiv.org/content/10.1101/205328v1?rss=1 Langmead, B. Wilks, C. Antonescu, V. Charles, R. 2017-10-24 doi:10.1101/205328 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 ]]> https://biorxiv.org/content/10.1101/205575v1?rss=1 Singh, D. Mallon, J. Poddar, A. Wang, Y. Tipanna, R. Yang, O. Bailey, S. Ha, T. 2017-10-18 doi:10.1101/205575 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis ]]> https://biorxiv.org/content/10.1101/205674v1?rss=1 Holland, D. O. Johnson, M. E. 2017-10-18 doi:10.1101/205674 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ An olfactogenetic approach identifies olfactory neurons and brain centers directing negative oviposition decisions in Drosophila. ]]> https://biorxiv.org/content/10.1101/206342v1?rss=1 Chin, S. G. Maguire, S. E. Huoviala, P. Jefferis, G. S. X. E. Potter, C. J. 2017-10-20 doi:10.1101/206342 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ OGT (O-GlcNAc Transferase) selectively modifies multiple residues unique to lamin A ]]> https://biorxiv.org/content/10.1101/206458v1?rss=1 12 diseases, termed laminopathies. Lamins A and C are identical for their first 566 residues. However, they form distinct filaments in vivo with apparently distinct roles. We report that lamin A is O-GlcNAc modified in human hepatoma (Huh7) cells and in mouse liver. In vitro assays with purified OGT enzyme showed robust O-GlcNAcylation of recombinant mature lamin A tails (residues 385-646), with no detectable modification of lamin B1, lamin C, or progerin ({Delta}50) tails. Using mass spectrometry, we identified 11 O-GlcNAc sites in a sweet spot unique to lamin A, with up to seven sugars per peptide. Most sites were unpredicted by current algorithms. Double-mutant (S612A/T643A) lamin A tails were still robustly O-GlcNAc-modified at seven sites. By contrast, O-GlcNAcylation was undetectable on tails bearing deletion {Delta}50, which causes Hutchinson-Gilford progeria syndrome, and greatly reduced by deletion {Delta}35, suggesting this region is required for substrate recognition or modification by OGT in vitro. These results suggest OGT, an essential protein and master regulator, regulates partners or function(s) unique to lamin A that are lost in progeria. ]]> Simon, D. N. Wriston, A. Fan, Q. Shabanowitz, J. Florwick, A. Dharmaraj, T. Peterson, S. B. Gruenbaum, Y. Carlson, C. R. Gronning-Wang, L. M. Hunt, D. F. Wilson, K. L. 2017-10-26 doi:10.1101/206458 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Elucidating relations between fMRI, ECoG and EEG through a common natural stimulus ]]> https://biorxiv.org/content/10.1101/207456v1?rss=1 Haufe, S. DeGuzman, P. Henin, S. Arcaro, M. Honey, C. J. Hasson, U. Parra, L. C. 2017-10-22 doi:10.1101/207456 Cold Spring Harbor Laboratory Press 2017-10-22 <![CDATA[ Computational discovery of tissue morphology biomarkers in very long-term survivors with pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/207969v1?rss=1 10 years. Deciphering underlying reasons behind prolonged survival could potentially provide new opportunities to treat PDAC; however, no genomic, transcriptomic, proteomic, or clinical signatures have been found to robustly separate this subset of patients. Digital pathology, in combination with machine learning, provides an opportunity to computationally search for tissue morphology patterns associated with disease outcomes. Here, we developed a computational framework to analyze whole-slide images (WSI) of PDAC patient tissue and identify tissue-morphology signatures for very long term surviving patients. Our results indicate that less tissue morphology heterogeneity is significantly linked to better patient survival and that the extra-tumoral space encodes prognostic information for survival. Based on information from morphological heterogeneity in the tumor and its adjacent area, we established a machine learning model with an AUC of 0.94. Our analysis workflow highlighted a quantitative visual-based tissue phenotype analysis that also allows direct interaction with pathology. This study demonstrates a pathway to accelerate the discovery of undetermined tissue morphology associated with pathogenesis states and prognosis and diagnosis of patients by utilizing new computational approaches. ]]> Sarnecki, J. S. Wood, L. D. Wolfgang, C. L. Hruban, R. H. Maitra, A. Wirtz, D. Wu, P.-H. 2017-10-25 doi:10.1101/207969 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ 3D cell nuclear morphology: microscopy imaging dataset and voxel-based morphometry classification results ]]> https://biorxiv.org/content/10.1101/208207v1?rss=1 Kalinin, A. A. Allyn-Feuer, A. Ade, A. Fon, G.-V. Meixner, W. Dilworth, D. de Wet, J. R. Higgins, G. A. Zheng, G. Creekmore, A. Wiley, J. W. Verdone, J. E. Veltri, R. W. Pienta, K. J. Coffey, D. S. Athey, B. D. Dinov, I. D. 2017-10-25 doi:10.1101/208207 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Germline determinants of the somatic mutation landscape in 2,642 cancer genomes ]]> https://biorxiv.org/content/10.1101/208330v1?rss=1 T mutagenesis at CpG dinucleotides, a ubiquitous mutational process acting across tissues. Analysis of somatic structural variation exposed complex rearrangement patterns, involving cycles of templated insertions and tandem duplications, in BRCA1-deficient tumours. Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer types. We further inferred over a hundred polymorphic L1/LINE elements with somatic retrotransposition activity in cancer. Our study highlights the major impact of rare and common germline variants on mutational landscapes in cancer. ]]> Waszak, S. M. Tiao, G. Zhu, B. Rausch, T. Muyas, F. Rodriguez-Martin, B. Rabionet, R. Yakneen, S. Escaramis, G. Li, Y. Saini, N. Roberts, S. A. Demidov, G. M. Pitkanen, E. Delaneau, O. Heredia-Genestar, J. M. Weischenfeldt, J. Shringarpure, S. S. Chen, J. Nakagawa, H. Alexandrov, L. B. Drechsel, O. Dursi, L. J. Segre, A. V. Garrison, E. Erkek, S. Habermann, N. Urban, L. Khurana, E. Cafferkey, A. Hayashi, S. Imoto, S. Aaltonen, L. A. Alvarez, E. G. Baez-Ortega, A. Bailey, M. Bosio, M. Bruzos, A. L. Buchhalter, I. Bustamante, C. D. Calabrese, C. DiBiase, 2017-11-01 doi:10.1101/208330 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Listeria monocytogenes virulence factors are secreted in biologically active Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/210906v1?rss=1 Coelho, C. Brown, L. Maryam, M. Burnet, M. C. Kyle, J. E. Heyman, H. M. Prados-Rosales, R. Lauvau, G. Nakayasu, E. S. Brady, N. R. Brady, A. Coppens, I. Casadevall, A. 2017-10-29 doi:10.1101/210906 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Spatial theta cells in competitive burst synchronization networks: Reference frames from phase codes ]]> https://biorxiv.org/content/10.1101/211458v1?rss=1 Monaco, J. D. Blair, H. T. Zhang, K. 2017-10-30 doi:10.1101/211458 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Lamins organize the global three-dimensional genome from the nuclear periphery ]]> https://biorxiv.org/content/10.1101/211656v1?rss=1 Zheng, X. Hu, J. Yue, S. Kristiani, L. Kim, M. Sauria, M. Taylor, J. Kim, Y. Zheng, Y. 2017-10-31 doi:10.1101/211656 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ An automated statistical technique for counting distinct multiple sclerosis lesions can recover aspects of lesion history and provide relevant disease information ]]> https://biorxiv.org/content/10.1101/212860v1?rss=1 .40). Reliability was determined using 14 scans of a clinically stable subject acquired at 7 sites, and variability of lesion count was equivalent to that of lesion load. Accounting for lesion load and age, lesion count was negatively associated (t58 = -2.73, p < .01) with the Expanded Disability Status Scale (EDSS). Average lesion size had a higher association with EDSS (r =.35, p < .01) than lesion load (r = .10, p > .40) or lesion count (r = -.12, p > .30) alone.nnConclusionThese findings demonstrate that it is possible to recover important aspects of the natural history of lesion formation without longitudinal data, and suggest that lesion size provides complementary information about disease.nnGrant SupportThe project described was supported in part by the NIH grants R01 NS085211, R21 NS093349, and R01 NS094456 from the National Institute of Neurological Disorders and Stroke (NINDS). The study was also supported by the Intramural Research Program of NINDS and the Race to Erase MS Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. ]]> Dworkin, J. D. Linn, K. A. Oguz, I. Fleishman, G. M. Bakshi, R. Nair, G. Calabresi, P. A. Henry, R. G. Oh, J. Papinutto, N. Pelletier, D. Rooney, W. Stern, W. Sicotte, N. L. Reich, D. S. Shinohara, R. T. 2017-11-01 doi:10.1101/212860 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ TCGA-Assembler 2: Software Pipeline for Retrieval and Processing of TCGA/CPTAC Data ]]> https://biorxiv.org/content/10.1101/214320v1?rss=1 Wei, L. Jin, Z. Yang, S. Xu, Y. Zhu, Y. Ji, Y. 2017-11-05 doi:10.1101/214320 Cold Spring Harbor Laboratory Press 2017-11-05 <![CDATA[ Spatio-temporal elasticity patterns in extracellular matrix during Hydra morphogenesis ]]> https://biorxiv.org/content/10.1101/214718v1?rss=1 Veschgini, M. Petersen, H. O. Abuillan, W. Rossetti, F. F. Özbek, S. Burghammer, M. Holstein, T. W. Tanaka, M. 2017-11-06 doi:10.1101/214718 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ A substrate for modular, extensible data-visualization ]]> https://biorxiv.org/content/10.1101/217349v1?rss=1 Matelsky, J. K. Downs, J. Wester, B. Gray Roncal, W. 2017-11-10 doi:10.1101/217349 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ The Block Object Storage Service (bossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery ]]> https://biorxiv.org/content/10.1101/217745v1?rss=1 Kleissas, D. Hider, R. Pryor, D. Gion, T. Manavalan, P. Matelsky, J. Baden, A. Lillaney, K. Burns, R. D'Angelo, D. Gray Roncal, W. Wester, B. 2017-11-10 doi:10.1101/217745 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ Heritability Informed Power Optimization (HIPO) Leads to Enhanced Detection of Genetic Associations Across Multiple Traits ]]> https://biorxiv.org/content/10.1101/218404v1?rss=1 Qi, G. Chatterjee, N. 2017-11-12 doi:10.1101/218404 Cold Spring Harbor Laboratory Press 2017-11-12 <![CDATA[ Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert ]]> https://biorxiv.org/content/10.1101/218446v1?rss=1 Meslier, V. Casero, M. C. Dailey, M. Wierzchos, J. Ascaso, C. Artieda, O. DiRuggiero, J. 2017-11-13 doi:10.1101/218446 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ BayCount: A Bayesian Decomposition Method for Inferring Tumor Heterogeneity using RNA-Seq Counts ]]> https://biorxiv.org/content/10.1101/218511v1?rss=1 Xie, F. Zhou, M. Xu, Y. 2017-11-13 doi:10.1101/218511 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Transcriptional landscape and regulatory roles of small non-coding RNAs in the oxidative stress response of the haloarchaeon Haloferax volcanii ]]> https://biorxiv.org/content/10.1101/218552v1?rss=1 Gelsinger, D. R. DiRuggiero, J. 2017-11-13 doi:10.1101/218552 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Co-expression patterns define epigenetic regulators associated with neurological dysfunction ]]> https://biorxiv.org/content/10.1101/219097v1?rss=1 Boukas, L. Havrilla, J. M. Quinlan, A. R. Bjornsson, H. T. Hansen, K. D. 2018-05-07 doi:10.1101/219097 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ What are the most influencing factors in reconstructing a reliable transcriptome assembly? ]]> https://biorxiv.org/content/10.1101/220269v1?rss=1 Ghaffari, N. Abante, J. Singh, R. Blood, P. D. Pipes, L. Mason, C. Johnson, C. D. 2017-11-16 doi:10.1101/220269 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS ]]> https://biorxiv.org/content/10.1101/221978v1?rss=1 Bobrovskyy, M. Frandsen, J. Zhang, J. Poddar, A. Azam, M. S. Henkin, T. M. Ha, T. Vanderpool, C. K. 2017-11-19 doi:10.1101/221978 Cold Spring Harbor Laboratory Press 2017-11-19 <![CDATA[ Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets ]]> https://biorxiv.org/content/10.1101/223511v1?rss=1 Marze, N. A. Roy Burman, S. S. Sheffler, W. Gray, J. J. 2017-11-22 doi:10.1101/223511 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Proof of concept continuous event logging in living cells ]]> https://biorxiv.org/content/10.1101/225151v1?rss=1 Shur, A. Murray, R. M. 2017-11-25 doi:10.1101/225151 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ Community-driven data analysis training for biology ]]> https://biorxiv.org/content/10.1101/225680v1?rss=1 Batut, B. Hiltemann, S. Bagnacani, A. Baker, D. Bhardwaj, V. Blank, C. Bretaudeau, A. Gueguen, L. Cech, M. Chilton, J. Clements, D. Doppelt-Azeroual, O. Erxleben, A. Freeberg, M. Gladman, S. Hoogstrate, Y. Hotz, H.-R. Houwaart, T. Jagtap, P. Lariviere, D. Le Corguille, G. Manke, T. Mareuil, F. Ramirez, F. Ryan, D. Sigloch, F. Soranzo, N. Wolff, J. Videm, P. Wolfien, M. Wubuli, A. Yusuf, D. Backofen, R. Nekrutenko, A. Grüning, B. 2017-11-29 doi:10.1101/225680 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Diagnostic utility of telomere length measurement in a hospital setting ]]> https://biorxiv.org/content/10.1101/225797v1?rss=1 Alder, J. K. Hanumanthu, V. S. Strong, M. A. DeZern, A. E. Stanley, S. E. Takemoto, C. M. Danilova, L. Applegate, C. D. Bolton, S. G. Mohr, D. W. Brodsky, R. A. Casella, J. F. Greider, C. W. Jackson, J. B. Armanios, M. 2017-12-06 doi:10.1101/225797 Cold Spring Harbor Laboratory Press 2017-12-06 <![CDATA[ Practice induces a qualitative change in the memory representation for visuomotor learning ]]> https://biorxiv.org/content/10.1101/226415v1?rss=1 Huberdeau, D. M. Krakauer, J. W. Haith, A. M. 2017-11-28 doi:10.1101/226415 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ An open resource for nonhuman primate imaging ]]> https://biorxiv.org/content/10.1101/227462v1?rss=1 Milham, M. Ai, L. Koo, B. Xu, T. Balezeau, F. Baxter, M. G. Croxson, P. L. Damatac, C. G. Harel, N. Freiwald, W. Griffiths, T. D. Everling, S. Jung, B. Kastner, S. Leopold, D. A. Mars, R. B. Menon, R. S. Messinger, A. Morrison, J. H. Nacef, J. Nagy, J. Rios, M. O. Petkov, C. I. Pinsk, M. Poirier, C. Rajimehr, R. Rushworth, M. F. Russ, B. E. Schmid, M. Schwiedrzik, C. M. Sallet, J. Seidlitz, J. Ungerleider, L. Thiele, A. Tsao, D. Yacoub, E. Ye, F. Zarco, W. Margulies, D. S. Schroeder, C. E. 2017-11-30 doi:10.1101/227462 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Testing Equality of Curves After Covariate Adjustment ]]> https://biorxiv.org/content/10.1101/228148v1?rss=1 Pal Choudhury, P. Kundu, P. Xue, Q.-L. Westbrook, R. Crainiceanu, C. 2017-12-04 doi:10.1101/228148 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Spontaneous Pre-encoding Activation of Neural Patterns Predicts Memory ‎ ]]> https://biorxiv.org/content/10.1101/229401v1?rss=1 Sadeh, T. Chen, J. Goshen-Gottstein, Y. Moscovitch, M. 2017-12-05 doi:10.1101/229401 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification ]]> https://biorxiv.org/content/10.1101/230417v1?rss=1 Jeliazkov, J. R. Sljoka, A. Kuroda, D. Tsuchimura, N. Katoh, N. Tsumoto, K. Gray, J. J. 2017-12-08 doi:10.1101/230417 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Examination of the Shared Genetic Basis of Anorexia Nervosa and Obsessive-Compulsive Disorder ]]> https://biorxiv.org/content/10.1101/231076v1?rss=1 Yilmaz, Z. Halvorsen, M. Bryois, J. Yu, D. Eating Disorders Working Group of the PGC, Tourette Syndrome/OCD Working Group of the PGC, Thornton, L. M. Zerwas, S. Micali, N. Moessner, R. Burton, C. L. Zai, G. Erdman, L. Kas, M. J. Arnold, P. D. Davis, L. K. Knowles, J. A. Breen, G. Scharf, J. M. Nestadt, G. Mathews, C. A. Bulik, C. M. Mattheisen, M. Crowley, J. J. 2017-12-08 doi:10.1101/231076 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Phasic Activation of Ventral Tegmental, but not Substantia Nigra, Dopamine Neurons Promotes Model-Based Pavlovian Reward Learning ]]> https://biorxiv.org/content/10.1101/232678v1?rss=1 Keiflin, R. Pribut, H. J. Shah, N. B. Janak, P. H. 2017-12-13 doi:10.1101/232678 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Reanalysis of global proteomic and phosphoproteomic data identified a large number of glycopeptides ]]> https://biorxiv.org/content/10.1101/233247v1?rss=1 Hu, Y. Shah, P. Clark, D. J. Ao, M. Zhang, H. 2017-12-13 doi:10.1101/233247 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Neural network control of focal position during time-lapse microscopy of cells ]]> https://biorxiv.org/content/10.1101/233940v1?rss=1 Wei, L. Roberts, E. 2017-12-13 doi:10.1101/233940 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ A Comprehensive Evaluation of the Genetic Architecture of Sudden Cardiac Arrest ]]> https://biorxiv.org/content/10.1101/235234v1?rss=1 Ashar, F. N. Mitchell, R. N. Albert, C. M. Newton-Cheh, C. Brody, J. A. Muller-Nurasyid, M. Moes, A. Meitinger, T. Mak, A. Huikuri, H. Junttila, M. J. Goyette, P. Pulit, S. L. Pazoki, R. Tanck, M. W. Blom, M. T. Zhao, X. Hauvlinna, A. S. Jabbari, R. Glinge, C. Tragante, V. Escher, S. A. Chakravarti, A. Ehret, G. Coresh, J. Li, M. Prineas, R. J. Franco, O. H. Kwok, P.-Y. Lumley, T. Dumas, F. McKnight, B. Rotter, J. I. Lemaitre, R. N. Heckbert, S. R. O'Donnell, C. J. Hwang, S.-J. Tardif, J.-C. Kortelainen, M.-L. VanDenburgh, M. Uitterlinden, A. G. Hofman, 2017-12-16 doi:10.1101/235234 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Anomalous Diffusion as a Descriptive Model of Cell Migration ]]> https://biorxiv.org/content/10.1101/236356v1?rss=1 Luzhanskey, I. D. MacMunn, J. P. Cohen, J. D. Barney, L. E. Jansen, L. E. Schwartz, A. D. Peyton, S. 2017-12-18 doi:10.1101/236356 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. ]]> https://biorxiv.org/content/10.1101/236737v1?rss=1 Newman, E. A. Wan, J. Wang, J. Qian, J. Blackshaw, S. 2017-12-19 doi:10.1101/236737 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Active site alanine substitutions can convert deubiquitinating enzymes into avid ubiquitin-binding domains ]]> https://biorxiv.org/content/10.1101/238154v1?rss=1 Morrow, M. Morgan, M. Clerici, M. Growkova, K. Yan, M. Komander, D. Simicek, M. Sixma, T. Wolberger, C. 2017-12-22 doi:10.1101/238154 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells. ]]> https://biorxiv.org/content/10.1101/238279v1?rss=1 Blackshaw, S. Zibetti, C. Liu, S. Wan, J. Qian, J. 2017-12-21 doi:10.1101/238279 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Catching up to a fast-moving target: Evaluation of a health system strengthening intervention in rural Rwanda 2005-2010 using data from repeated cross-sectional surveys ]]> https://biorxiv.org/content/10.1101/238543v1?rss=1 Thomson, D. Amoroso, C. Atwood, S. Bonds, M. H. Rwabukwisi, F. C. Drobac, P. Finnegan, K. E. Farmer, D. B. Farmer, P. E. Habinshuti, A. Hirschhorn, L. R. Manzi, A. Niyigena, P. Rich, M. L. Stulac, S. Murray, M. Binagwaho, A. 2017-12-22 doi:10.1101/238543 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Genome-wide association meta-analysis of PR interval identifies 47 novel loci associated with atrial and atrioventricular electrical activity ]]> https://biorxiv.org/content/10.1101/241489v1?rss=1 van Setten, J. Brody, J. A. Jamshidi, Y. Swenson, B. R. Butler, A. M. Campbell, H. Del Greco, F. M. Evans, D. S. Gibson, Q. Gudbjartsson, D. F. Kerr, K. F. Krijthe, B. P. Lyytikainen, L.-P. Muller, C. Muller-Nurasyid, M. Nolte, I. M. Padmanabhan, S. Ritchie, M. D. Robino, A. Smith, A. V. Steri, M. Tanaka, T. Teumer, A. Trompet, S. Ulivi, S. Verweij, N. Yin, X. Arnar, D. O. Asselbergs, F. W. Bader, J. S. Barnard, J. Bis, J. Blankenberg, S. Boerwinkle, E. Bradford, Y. Buckley, B. M. Chung, M. K. Crawford, D. den Hoed, M. Denny, J. Dominiczak, A. F. Ehret, 2018-01-17 doi:10.1101/241489 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Asymmetric histone incorporation during DNA replication in Drosophila male germline stem cells ]]> https://biorxiv.org/content/10.1101/242768v1?rss=1 Wooten, M. Nizami, Z. Yang, X. Snedeker, J. Ranjan, R. Kim, J. M. Urban, E. Tran, V. Buss, J. Gall, J. Xiao, J. Chen, X. 2018-01-04 doi:10.1101/242768 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ The Amyloid Clearance Defect in ApoE4 Astrocytes is Corrected by Epigenetic Restoration of NHE6 ]]> https://biorxiv.org/content/10.1101/243097v1?rss=1 Prasad, H. Rao, R. 2018-01-04 doi:10.1101/243097 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Combinatorial neural inhibition for stimulus selection across space ]]> https://biorxiv.org/content/10.1101/243279v1?rss=1 Mahajan, N. R. Mysore, S. P. 2018-03-26 doi:10.1101/243279 Cold Spring Harbor Laboratory Press 2018-03-26 <![CDATA[ Genotype Imputation Performance of Three Reference Panels Using African Ancestry Individuals ]]> https://biorxiv.org/content/10.1101/245035v1?rss=1 0.5) and for rare, low frequency, and common variants. When merging the results of the three panels the total number of imputed variants was 62M-63M with 20M overlapping variants imputed by all three panels, and a range of 5 to 15M unique variants imputed exclusively with one of the three panels. For overlapping variants, imputation quality was highest for HRC, followed by 1000G, then CAAPA, and improved as the minor allele frequency increased. The 1000G, HRC and CAAPA participants of African ancestry provided high performance and accuracy for imputation of African American admixed individuals, increasing the total number of variants with high quality available for subsequent analyses. These three panels are complementary and would benefit from the development of an integrated African reference panel, including data from multiple sources and populations. ]]> Vergara, C. Parker, M. M. Franco, L. Cho, M. H. Valencia-Duarte, A. V. Beaty, T. H. Duggal, P. 2018-01-08 doi:10.1101/245035 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ PET Brain imaging of α7-nAChR with ASEM Reproducibility, occupancy, receptor density, and changes in schizophrenia ]]> https://biorxiv.org/content/10.1101/245118v1?rss=1 90%) (variability [≤] 7%) of [18F]ASEM volume of distribution (VO_SCPLOWTC_SCPLOW) estimates in healthy volunteers. Repeated sessions of PET in five healthy subjects included baseline and effect of inhibition after oral administration of 150 mg DMXB-A. From reduction of binding potentials, we estimated the dose-dependent occupancy of 7-nAChR by DMXB-A at 17-49% for plasma concentrations at 60-200 nM DMXB-A. In agreement with evidence post-mortem, 7-nAChR density (Bmax) averaged 0.67-0.82 nM and inhibitor affinity constant (KO_SCPLOWIC_SCPLOW) averaged 170-385 nM. Median VO_SCPLOWTC_SCPLOW in a feasibility study of six patients with schizophrenia was lower than in healthy volunteers in cingulate cortex, frontal cortex, and hippocampus. Mann-Whitney test identified cingulate cortex and hippocampus as regions with significantly lower median VO_SCPLOWTC_SCPLOW in patients than in healthy volunteers when a single outlier patient was excluded from analysis (P = 0.02, corrected for multiple comparisons). ]]> Wong, D. F. Kuwabara, H. Horti, A. G. Roberts, J. Nandi, A. Cascella, N. Brasic, J. R. Weerts, E. Kitzmiller, K. Phan, J. A. Gapasin, L. Sawa, A. Valentine, H. Wand, G. George, N. McDonald, M. Kem, W. Freedman, R. Gjedde, A. 2018-01-08 doi:10.1101/245118 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Coronavirus S protein-induced fusion is blocked prior to hemifusion by Abl kinase inhibitors ]]> https://biorxiv.org/content/10.1101/246991v1?rss=1 Sisk, J. Frieman, M. B. Machamer, C. E. 2018-01-12 doi:10.1101/246991 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ RNA-seq transcript quantification from reduced-representation data in recount2 ]]> https://biorxiv.org/content/10.1101/247346v1?rss=1 Fu, J. Kammers, K. Nellore, A. Collado-Torres, L. Leek, J. T. Taub, M. A. 2018-01-12 doi:10.1101/247346 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Using Network Analysis to Localize the Epileptogenic Zone from Invasive EEG Recordings in Intractable Focal Epilepsy ]]> https://biorxiv.org/content/10.1101/247387v1?rss=1 Li, A. Chennuri, B. Subramanian, S. Yaffe, R. Gliske, S. Stacey, W. Norton, R. Jordan, A. Zaghloul, K. A. Inati, S. K. Agrawal, S. Haagensen, J. Hopp, J. Atallah, C. Johnson, E. Crone, N. Anderson, W. S. Fitzgerald, Z. Bulacio, J. Gale, J. T. Sarma, S. V. Gonzalez-Martinez, J. 2018-01-16 doi:10.1101/247387 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ Impact of Human Behavioral Papers at Journal of Neuroscience ]]> https://biorxiv.org/content/10.1101/248526v1?rss=1 Herzfeld, D. J. Shadmehr, R. 2018-01-16 doi:10.1101/248526 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ Mutations in efflux pump Rv1258c (Tap) cause resistance to pyrazinamide and other drugs in M. tuberculosis ]]> https://biorxiv.org/content/10.1101/249102v1?rss=1 Zhang, Y. Liu, J. Zhang, S. Cassell, G. Maslov, D. Hao, X. Shur, K. Bekker, O. Danilenko, V. Shi, W. 2018-01-17 doi:10.1101/249102 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Identification of novel mutations in LprG (rv1411c), rv0521, rv3630, rv0010c, ppsC, cyp128 associated with pyrazinoic acid/pyrazinamide resistance in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/249201v1?rss=1 Zhang, Y. Shi, W. Chen, J. Zhang, S. Zhang, W. 2018-01-17 doi:10.1101/249201 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ Imaging neural activity in the ventral nerve cord of behaving adult Drosophila ]]> https://biorxiv.org/content/10.1101/250118v1?rss=1 Chen, C.-L. Hermans, L. Viswanathan, M. C. Fortun, D. Unser, M. Cammarato, A. Dickinson, M. H. Ramdya, P. 2018-01-22 doi:10.1101/250118 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior ]]> https://biorxiv.org/content/10.1101/250332v1?rss=1 Maynard, K. R. Hobbs, J. W. Phan, B. N. Gupta, A. Rajpurohit, S. Williams, C. Rajpurohit, N. Shin, J. H. Jaffe, A. E. Martinowich, K. 2018-01-19 doi:10.1101/250332 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ miRge 2.0: An updated tool to comprehensively analyze microRNA sequencing data ]]> https://biorxiv.org/content/10.1101/250779v1?rss=1 Lu, Y. Baras, A. S. Halushka, M. K. 2018-01-19 doi:10.1101/250779 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer ]]> https://biorxiv.org/content/10.1101/251090v1?rss=1 Kumar, B. Rosenberg, A. Z. Choi, S. M. Fox-Talbot, K. De Marzo, A. M. Nonn, L. Brennen, W. N. Marchionni, L. Halushka, M. K. Lupold, S. E. 2018-01-20 doi:10.1101/251090 Cold Spring Harbor Laboratory Press 2018-01-20 <![CDATA[ A conserved mechanism for regulation of endo-lysosomal pH by histone deacetylases ]]> https://biorxiv.org/content/10.1101/252122v1?rss=1 Rao, R. Prasad, H. 2018-01-22 doi:10.1101/252122 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Detection of de novo copy number deletions from targeted sequencing of trios ]]> https://biorxiv.org/content/10.1101/252833v1?rss=1 Fu, J. M. Leslie, E. J. Scott, A. F. Murray, J. C. Marazita, M. L. Beaty, T. H. Scharpf, R. B. Ruczinski, I. 2018-01-24 doi:10.1101/252833 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Automatic error control during forward flux sampling of rare events in master equation models ]]> https://biorxiv.org/content/10.1101/254896v1?rss=1 Klein, M. C. Roberts, E. 2018-01-27 doi:10.1101/254896 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ Type-I interferons inhibit interleukin-10 signaling and favor type 1 diabetes development in NOD mice ]]> https://biorxiv.org/content/10.1101/258525v1?rss=1 Iglesias, M. Arun, A. Chicco, M. Lam, B. Talbot, C. Ivanova, V. Lee, W. P. A. Brandacher, G. Raimondi, G. 2018-02-01 doi:10.1101/258525 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach ]]> https://biorxiv.org/content/10.1101/260869v1?rss=1 Chen, X. Shi, X. Hilakivi-Clarke, L. Clarke, R. Wang, T.-L. Xuan, J. 2018-02-07 doi:10.1101/260869 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Removing Contaminants from Metagenomic Databases ]]> https://biorxiv.org/content/10.1101/261859v1?rss=1 Lu, J. Salzberg, S. 2018-02-08 doi:10.1101/261859 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ The upstrap ]]> https://biorxiv.org/content/10.1101/262436v1?rss=1 Crainiceanu, C. 2018-02-15 doi:10.1101/262436 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ High-Speed Imaging of Paw Withdrawal Reflex to Objectively Assess Pain State in Mice ]]> https://biorxiv.org/content/10.1101/263400v1?rss=1 Abdus-Saboor, I. Fried, N. T. Lay, M. Dong, P. Burdge, J. Lu, M. Ma, M. Dong, X. Long, D. Luo, W. 2018-02-12 doi:10.1101/263400 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Real-time fine aerosol exposures in taconite mining operations ]]> https://biorxiv.org/content/10.1101/263442v1?rss=1 Huynh, T. Ramachandran, G. Quick, H. Hwang, J. Raynor, P. C. Alexander, B. H. Mandel, J. H. 2018-02-13 doi:10.1101/263442 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186-5p as a potential retroviral restriction factor in macrophages ]]> https://biorxiv.org/content/10.1101/263947v1?rss=1 Zhao, Z. Muth, D. C. Mulka, K. Powell, B. H. Hancock, G. V. Liao, Z. Metcalf Pate, K. A. Witwer, K. W. 2018-02-11 doi:10.1101/263947 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ Combinatorial library of biodegradable polyesters enables delivery of plasmid DNA to polarized human RPE monolayers for retinal gene therapy ]]> https://biorxiv.org/content/10.1101/264390v1?rss=1 Mishra, B. Wilson, D. R. Sripathi, S. R. Suprenant, M. P. Rui, Y. Wahlin, K. J. Berlinicke, C. Green, J. J. Zack, D. J. 2018-02-13 doi:10.1101/264390 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ A widespread decrease of chromatin accessibility in age-related macular degeneration ]]> https://biorxiv.org/content/10.1101/264564v1?rss=1 Wang, J. Zibetti, C. Shang, P. Sripathi, S. R. Zhang, P. Cano, M. Hoang, T. Ji, H. Merbs, S. L. Zack, D. J. Handa, J. T. Sinha, D. Blackshaw, S. Qian, J. Xia, S. 2018-02-13 doi:10.1101/264564 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Axon Guidance Signaling Modulates Epithelial to Mesenchymal Transition in Stem Cell-Derived Retinal Pigment Epithelium ]]> https://biorxiv.org/content/10.1101/264705v1?rss=1 Sripathi, S. R. Liu, M. M. Hu, M.-W. Wan, J. Cheng, J. Duan, Y. Mertz, J. Wahlin, K. Maruotti, J. Berlinicke, C. A. Qian, J. Zack, D. J. 2018-02-13 doi:10.1101/264705 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer ]]> https://biorxiv.org/content/10.1101/266197v1?rss=1 Kim, D. Paggi, J. M. Salzberg, S. 2018-02-15 doi:10.1101/266197 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Constriction rate modulation can drive cell size control and homeostasis in C. crescentus ]]> https://biorxiv.org/content/10.1101/266817v1?rss=1 Manley, S. Lambert, A. Vanhecke, A. Archetti, A. Holden, S. Schaber, F. Pincus, Z. Laub, M. T. Goley, E. D. 2018-02-16 doi:10.1101/266817 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ Phosphatidylethanolamine produced in the inner mitochondrial membrane is essential for yeast cytochrome bc1 complex function ]]> https://biorxiv.org/content/10.1101/269233v1?rss=1 Calzada, E. Claypool, S. 2018-02-21 doi:10.1101/269233 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Survey of human chromosome 21 gene expression effects on early development in Danio rerio ]]> https://biorxiv.org/content/10.1101/269944v1?rss=1 Edie, S. Zaghloul, N. A. Leitch, C. C. Klinedinst, D. K. Lebron, J. Thole, J. F. McCallion, A. S. Katsanis, N. Reeves, R. H. 2018-02-22 doi:10.1101/269944 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ Household Transmission Study of Cryptosporidiosis in Bangladesh ]]> https://biorxiv.org/content/10.1101/269985v1?rss=1 Korpe, P. S. Gilchrist, C. Burkey, C. Ahmed, E. Madan, V. Castillo, R. Ahmed, S. Arju, T. Alam, M. Kabir, M. Petri, W. A. Haque, R. Faruque, A. S. G. Duggal, P. 2018-02-23 doi:10.1101/269985 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ The fungal ligand chitin directly binds and signals inflammation dependent on oligomer size and TLR2 ]]> https://biorxiv.org/content/10.1101/270405v1?rss=1 Fuchs, K. Cardona Gloria, Y. Wolz, O.-O. Herster, F. Sharma, L. Dillen, C. Täumer, C. Dickhöfer, S. Bittner, Z. Dang, T.-M. Singh, A. Haischer, D. Schlöffel, M. A. Koymans, K. J. Sanmuganantham, T. Krach, M. Schilling, N. A. Frauhammer, F. Miller, L. Nürnberger, T. LeibundGut-Landmann, S. Gust, A. A. Macek, B. Frank, M. Gouttefangeas, C. Dela-Cruz, C. S. Hartl, D. Weber, A. 2018-02-23 doi:10.1101/270405 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Regulation of midgut cell proliferation impacts Aedes aegypti susceptibility to dengue virus ]]> https://biorxiv.org/content/10.1101/271288v1?rss=1 Taracena, M. L. Bottino-Rojas, V. Talyuli, O. A. C. Walter-Nuno, A. B. Oliveira, J. H. M. Anglero-Rodriguez, Y. I. Wells, M. B. Dimopoulos, G. Oliveira, P. L. Paiva-Silva, G. O. 2018-02-24 doi:10.1101/271288 Cold Spring Harbor Laboratory Press 2018-02-24 <![CDATA[ On variational solutions for whole brain serial-section histology using the computational anatomy random orbit model ]]> https://biorxiv.org/content/10.1101/271692v1?rss=1 Lee, B. C. Tward, D. J. Mitra, P. P. Miller, M. 2018-02-25 doi:10.1101/271692 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Activated BAX/BAK enable mitochondrial inner membrane permeabilisation and mtDNA release during cell death ]]> https://biorxiv.org/content/10.1101/272104v1?rss=1 Riley, J. Quarato, G. Lopez, J. O'Prey, J. Pearson, M. Chapman, J. Sesaki, H. Carlin, L. Passos, J. Wheeler, A. Oberst, A. Ryan, K. Tait, S. 2018-02-26 doi:10.1101/272104 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Discovering patterns of pleiotropy in genome-wide association studies ]]> https://biorxiv.org/content/10.1101/273540v1?rss=1 Zhan, J. Arking, D. E. Bader, J. S. 2018-02-28 doi:10.1101/273540 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Recruitment of Two Dyneins to an mRNA-Dependent Bicaudal D Transport Complex ]]> https://biorxiv.org/content/10.1101/273755v1?rss=1 Sladewski, T. E. Billington, N. Ali, M. Y. Bookwalter, C. S. Lu, H. Krementsova, E. B. Schroer, T. A. Trybus, K. M. 2018-02-28 doi:10.1101/273755 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ miRNAs in platelet-poor blood plasma and purified RNA are highly stable: a confirmatory study ]]> https://biorxiv.org/content/10.1101/273797v1?rss=1 Muth, D. C. Powell, B. H. Zhao, Z. Witwer, K. W. 2018-03-01 doi:10.1101/273797 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Transition from actin-driven to water-driven cell migration depends on external hydraulic resistance ]]> https://biorxiv.org/content/10.1101/275123v1?rss=1 Li, Y. Sun, S. X. 2018-03-08 doi:10.1101/275123 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Electromechanics and Volume Dynamics in Non-excitable Tissue Cells ]]> https://biorxiv.org/content/10.1101/275339v1?rss=1 Yellin, F. Li, Y. Sreenivasan, V. K. A. Farrell, B. Johny, M. Yu, D. Sun, S. X. 2018-03-08 doi:10.1101/275339 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ crsra: A package for Cleaning and Analyzing Coursera Research Export Data ]]> https://biorxiv.org/content/10.1101/275537v1?rss=1 Hadavand, A. Leek, J. 2018-03-05 doi:10.1101/275537 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ miR-21-5p and miR-30a-5p are identical in human and bovine, have similar isomiR distribution, and cannot be used to identify xenomiR uptake from cow milk ]]> https://biorxiv.org/content/10.1101/275834v1?rss=1 Fromm, B. Tosar, J. P. Yu, L. Halushka, M. K. Witwer, K. W. 2018-03-05 doi:10.1101/275834 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Identification of novel mutations associated with clofazimine resistance in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/276022v1?rss=1 Chen, Y. Chen, J. Zhang, S. Zhang, W. Zhang, W. Zhu, M. Zhang, Y. 2018-03-04 doi:10.1101/276022 Cold Spring Harbor Laboratory Press 2018-03-04 <![CDATA[ Accelerometry data in health research: challenges and opportunities. Review and examples ]]> https://biorxiv.org/content/10.1101/276154v1?rss=1 Karas, M. Bai, J. Straczkiewicz, M. Harezlak, J. Glynn, N. W. Harris, T. Zipunnikov, V. Crainiceanu, C. Urbanek, J. K. 2018-03-05 doi:10.1101/276154 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Focal optogenetic suppression in macaque area MT biases direction discrimination and choice confidence, but only transiently ]]> https://biorxiv.org/content/10.1101/277251v1?rss=1 Fetsch, C. R. Odean, N. N. Jeurissen, D. El-Shamayleh, Y. Horwitz, G. D. Shadlen, M. N. 2018-03-06 doi:10.1101/277251 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Arsenite exposure inhibits histone acetyltransferase p300 for attenuating H3K27ac at enhancers in low-dose exposed mouse embryonic fibroblast cells ]]> https://biorxiv.org/content/10.1101/278424v1?rss=1 Zhu, Y. Li, Y. Lou, D. Gao, Y. Yu, J. Kong, D. Zhang, Q. Jia, Y. Zhang, H. Wang, Z. 2018-03-14 doi:10.1101/278424 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Species- and C-terminal linker-dependent variations in the dynamic behavior of FtsZ on membranes in vitro ]]> https://biorxiv.org/content/10.1101/278564v1?rss=1 Sundararajan, K. Vecchiarelli, A. G. Mizuuchi, K. Goley, E. 2018-03-08 doi:10.1101/278564 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Novel role of Lin28 signaling in regulation of mammalian PNS and CNS axon regeneration ]]> https://biorxiv.org/content/10.1101/281725v1?rss=1 Wang, X.-W. Liu, C.-M. Hall, P. A. Jiang, J.-J. Katchis, C. D. Kang, S. Dong, B. C. Li, S. Zhou, F.-Q. 2018-03-14 doi:10.1101/281725 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling ]]> https://biorxiv.org/content/10.1101/282103v1?rss=1 Hong, S.-R. Wang, C.-L. Huang, Y.-S. Chang, Y.-C. Chang, Y.-C. Pusapati, G. V. Lin, C.-Y. Hsu, N. Cheng, H.-C. Chiang, Y.-C. Huang, W.-E. Shaner, N. C. Rohatgi, R. Inoue, T. Lin, Y.-C. 2018-03-15 doi:10.1101/282103 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Calcium-activated chloride channels clamp odor-evoked spike activity in olfactory receptor neurons ]]> https://biorxiv.org/content/10.1101/282731v1?rss=1 Zak, J. D. Grimaud, J. Li, R.-c. Li, C.-c. Murthy, V. N. 2018-03-15 doi:10.1101/282731 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Targeting of NF-κB to Dendritic Spines is Required for Synaptic Signaling and Spine Development ]]> https://biorxiv.org/content/10.1101/283879v1?rss=1 Dresselhaus, E. C. Boersma, M. C. H. Meffert, M. K. 2018-03-17 doi:10.1101/283879 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Mathematical modelling of molecular heterogeneity identifies novel markers and subpopulations in complex tumors ]]> https://biorxiv.org/content/10.1101/283903v1?rss=1 Chen, L. Wang, N. Clarke, R. Zhang, Z. Wang, Y. 2018-03-17 doi:10.1101/283903 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Glutamatergic facilitation of neural responses in MT enhances motion perception in humans ]]> https://biorxiv.org/content/10.1101/283994v1?rss=1 Schallmo, M.-P. Millin, R. Kale, A. M. Kolodny, T. Edden, R. A. E. Bernier, R. A. Murray, S. O. 2018-03-17 doi:10.1101/283994 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Improved Analysis of Phage ImmunoPrecipitation Sequencing (PhIP-Seq) Data Using a Z-score Algorithm ]]> https://biorxiv.org/content/10.1101/285916v1?rss=1 Yuan, T. Mohan, D. Laserson, U. Ruczinski, I. Baer, A. Larman, H. B. 2018-04-26 doi:10.1101/285916 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Low frequency and rare coding variation contributes to multiple sclerosis risk ]]> https://biorxiv.org/content/10.1101/286617v1?rss=1 230 identified by genome-wide association studies (Patsopoulos et al., 2017). Multiple strands of evidence suggest that the majority of the remaining heritability is also due to the additive effects of individual variants, rather than epistatic interactions between these variants, or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that as much as 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common variant signals, which highlight a key role for regulatory T cell homeostasis and regulation, IFN{gamma} biology and NF{kappa}B signaling in MS pathogenesis. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS. ]]> International Multiple Sclerosis Genetics Consortium, Mitrovic, M. Patsopoulos, N. Beecham, A. Dankowski, T. Goris, A. Dubois, B. Dhooghe, M.-B. Lemmens, R. Van Damme, P. Fitzgerald, K. Bach Sondergaard, H. Sellebjerg, F. Sorensen, P. S. Ullum, H. Wegner Thoerner, L. Werge, T. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Gourraud, P.-A. Andlauer, T. Pongratz, V. Buck, D. Gasperi, C. Graetz, C. Bayas, A. Heesen, C. Kumpfel, T. Linker, R. Paul, F. Stangel, M. Tackenberg, B. Then Bergh, F. Warnke, C. Wiend 2018-03-23 doi:10.1101/286617 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription ]]> https://biorxiv.org/content/10.1101/290338v1?rss=1 Saberi, A. Zhu, R. Kwon, C. 2018-03-28 doi:10.1101/290338 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Propagation of information along the cortical hierarchy as a function of attention while reading and listening to stories ]]> https://biorxiv.org/content/10.1101/291526v1?rss=1 Regev, M. Simony, E. Lee, K. Tan, K. M. Chen, J. Hasson, U. 2018-04-08 doi:10.1101/291526 Cold Spring Harbor Laboratory Press 2018-04-08 <![CDATA[ Differential human mobility and local variation in human infection attack rate ]]> https://biorxiv.org/content/10.1101/291674v1?rss=1 Haw, D. J. Cummings, D. A. T. Lessler, J. Salje, H. Read, J. M. Riley, S. 2018-03-31 doi:10.1101/291674 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Movement imitation depends on an abstract trajectory representation in dorsal premotor cortex ]]> https://biorxiv.org/content/10.1101/294207v1?rss=1 Wong, A. L. Jax, S. A. Smith, L. A. Buxbaum, L. J. Krakauer, J. W. 2018-04-03 doi:10.1101/294207 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Effect Size and Power in fMRI Group Analysis ]]> https://biorxiv.org/content/10.1101/295048v1?rss=1 0.8), while sample sizes closer to 80 are required to reliably recover regions with medium effect sizes (0.5 < d < 0.8). We find little difference in results when using volumetric or surface based data with respect to standard mass-univariate group analysis. Finally, we conclude that special care is needed when estimating effect sizes, particularly for small sample sizes. ]]> Geuter, S. Qi, G. Welsh, R. C. Wager, T. D. Lindquist, M. A. 2018-04-06 doi:10.1101/295048 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ First in-human PET study of 3 novel tau radiopharmaceuticals: RO6958948 ]]> https://biorxiv.org/content/10.1101/296764v1?rss=1 HC (threshold of p<0.001, cluster size k>50).nnConclusions[18F]RO-948 demonstrates superior characteristics to [11C]RO-643 and [18F]RO-963 for characterization of tau pathology in AD. Regional binding data and kinetic properties of RO-948 compare favorably with existing other tau PET tracers. ]]> Wong, D. F. Comley, R. A. Kuwabara, H. Rosenberg, P. Resnick, S. M. Ostrowitzki, S. Vozzi, C. Boess, F. Oh, E. Lyketsos, C. G. Horner, M. Gobbi, L. Klein, G. George, N. Gapasin, L. Kitzmiller, K. Roberts, J. Sevigny, J. Nandi, A. Brasic, J. Mishra, C. Thambisetty, M. Mogekar, A. Mathur, A. Albert, M. Dannals, R. F. Borroni, E. 2018-04-11 doi:10.1101/296764 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Multiple brain networks mediating stimulus-pain relationships in humans ]]> https://biorxiv.org/content/10.1101/298927v1?rss=1 Geuter, S. Losin, E. A. R. Roy, M. Atlas, L. Y. Schmidt, L. Krishnan, A. Koban, L. Wager, T. D. Lindquist, M. A. 2018-04-11 doi:10.1101/298927 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ A planarian nidovirus expands the limits of RNA genome size ]]> https://biorxiv.org/content/10.1101/299776v1?rss=1 Saberi, A. Gulyaeva, A. A. Brubacher, J. Newmark, P. A. Gorbalenya, A. 2018-04-11 doi:10.1101/299776 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ SLC6A4 binding site and acute prosocial effects of (+/-)-3,4-methylendioxymethamphetamine (MDMA) are evolutionarily conserved in Octopus bimaculoides. ]]> https://biorxiv.org/content/10.1101/301192v1?rss=1 Dolen, G. Edsinger, E. 2018-04-15 doi:10.1101/301192 Cold Spring Harbor Laboratory Press 2018-04-15 <![CDATA[ Epigenetic changes induced by Bacteroides fragilis toxin ]]> https://biorxiv.org/content/10.1101/301374v1?rss=1 Allen, J. Hao, S. Sears, C. L. Timp, W. 2018-04-15 doi:10.1101/301374 Cold Spring Harbor Laboratory Press 2018-04-15 <![CDATA[ Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced de-novo mutation in survival outliers of glioblastoma ]]> https://biorxiv.org/content/10.1101/302042v1?rss=1 Hwang, T. Mathios, D. McDonald, K. L. Daris, I. Park, S.-H. Burger, P. C. Kim, S. Dho, Y.-S. Carolyn, H. Bettegowda, C. Shin, J. H. Lim, M. Park, C.-K. 2018-04-16 doi:10.1101/302042 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ CNV Neurons Are Rare in Aged Human Neocortex ]]> https://biorxiv.org/content/10.1101/303404v1?rss=1 Chronister, W. D. Wierman, M. B. Burbulis, I. E. Wolpert, M. J. Haakenson, M. F. Kleinman, J. E. Hyde, T. Weinberger, D. R. Bekiranov, S. McConnell, M. J. 2018-04-21 doi:10.1101/303404 Cold Spring Harbor Laboratory Press 2018-04-21 <![CDATA[ A member of the ferlin calcium sensor family is essential for Toxoplasma gondii rhoptry secretion ]]> https://biorxiv.org/content/10.1101/304048v1?rss=1 nView larger version (58K):norg.highwire.dtl.DTLVardef@505202org.highwire.dtl.DTLVardef@138400aorg.highwire.dtl.DTLVardef@1f468beorg.highwire.dtl.DTLVardef@1089d34_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Coleman, B. I. Saha, S. Sato, S. Engelberg, K. Ferguson, D. J. P. Coppens, I. Lodoen, M. B. Gubbels, M.-J. 2018-04-18 doi:10.1101/304048 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Sensorimotor cortical-subthalamic network dynamics during force generation ]]> https://biorxiv.org/content/10.1101/306332v1?rss=1 Alhourani, A. Korzeniewska, A. Wozny, T. Lipski, W. Kondylis, E. Ghuman, A. Crone, N. Crammond, D. Turner, R. Richardson, R. M. 2018-04-25 doi:10.1101/306332 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Transcranial photoacoustic imaging of NMDA-evoked focal circuit dynamics in rat forebrain ]]> https://biorxiv.org/content/10.1101/308585v1?rss=1 Kang, J. Kadam, S. D. Elmore, J. S. Sullivan, B. J. Valentine, H. Malla, A. P. Grace, A. A. Rahmim, A. Loew, L. M. Baumann, M. Gjedde, A. Boctor, E. M. Wong, D. F. 2018-04-26 doi:10.1101/308585 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing ]]> https://biorxiv.org/content/10.1101/310458v1?rss=1 Luo, R. Sedlazeck, F. J. Lam, T.-W. Schatz, M. 2018-04-28 doi:10.1101/310458 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Identification of small regulatory RNAs involved in persister formation ]]> https://biorxiv.org/content/10.1101/310631v1?rss=1 Zhang, S. Liu, S. Wu, N. Zhang, W. Zhang, Y. 2018-04-30 doi:10.1101/310631 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/310961v1?rss=1 Liu, S. Wu, N. Zhang, S. Zhang, Y. Zhang, W. Zhang, Y. 2018-04-30 doi:10.1101/310961 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Identification of Polynucleotide Phosphorylase (PNPase) in Escherichia coli Involved in Persister Formation ]]> https://biorxiv.org/content/10.1101/310987v1?rss=1 Wu, N. Zhang, Y. Zhang, S. Yuan, Y. Liu, S. Cui, P. Zhang, W. Zhang, Y. 2018-04-30 doi:10.1101/310987 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ FORGe: prioritizing variants for graph genomes ]]> https://biorxiv.org/content/10.1101/311720v1?rss=1 Pritt, J. Langmead, B. 2018-04-30 doi:10.1101/311720 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants ]]> https://biorxiv.org/content/10.1101/311985v1?rss=1 Luo, R. Lam, T.-W. Schatz, M. 2018-05-01 doi:10.1101/311985 Cold Spring Harbor Laboratory Press 2018-05-01 <![CDATA[ Enhanced context reveals the scope of somatic missense mutations driving human cancers ]]> https://biorxiv.org/content/10.1101/313296v1?rss=1 Tokheim, C. Karchin, R. 2018-05-02 doi:10.1101/313296 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification ]]> https://biorxiv.org/content/10.1101/313411v1?rss=1 Kalinin, A. A. Allyn-Feuer, A. Ade, A. Fon, G.-V. Meixner, W. Dilworth, D. de Wet, J. R. Higgins, G. A. Zheng, G. Creekmore, A. Wiley, J. W. Verdone, J. E. Veltri, R. W. Pienta, K. J. Coffey, D. S. Athey, B. D. Dinov, I. D. 2018-05-03 doi:10.1101/313411 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ SQuIRE: Software for Quantifying Interspersed Repeat Elements ]]> https://biorxiv.org/content/10.1101/313999v1?rss=1 Yang, W. R. Ardeljan, D. Pacyna, C. N. Payer, L. M. Burns, K. H. 2018-05-04 doi:10.1101/313999 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Systems Analysis of the 22q11.2 Microdeletion Syndrome Converges on a Mitochondrial Interactome Necessary for Synapse Function and Behavior ]]> https://biorxiv.org/content/10.1101/315143v1?rss=1 Gokhale, A. Freeman, A. A. Hartwig, C. Bassell, J. L. Zlatic, S. A. Sapp, C. Vadlamudi, T. Abudulai, F. Crocker, A. Werner, E. Wen, Z. Repetto, G. M. Gogos, J. A. Claypool, S. M. Forsyth, J. K. Bearden, C. Gausier, J. Lewis, D. A. Seyfried, N. T. Faundez, V. 2018-05-04 doi:10.1101/315143 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets ]]> https://biorxiv.org/content/10.1101/315598v1?rss=1 Huo, B.-X. Zeater, N. Lin, M. K. Takahashi, Y. S. Hanada, M. Nagashima, J. Lee, B. C. Grunert, U. Miller, M. I. Rosa, M. Okano, H. Martin, P. R. Mitra, P. P. 2018-05-07 doi:10.1101/315598 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset ]]> https://biorxiv.org/content/10.1101/315804v1?rss=1 Lin, M. K. Takahashi, Y. S. Huo, B.-X. Hanada, M. Nagashima, J. Hata, J. Tolpygo, A. S. Ram, K. Lee, B. C. Miller, M. I. Rosa, M. G. P. Sasaki, E. Iriki, A. Okano, H. Mitra, P. P. 2018-05-08 doi:10.1101/315804 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ TRAF6 directs Foxp3 localization and facilitates Treg function through K63-type ubiquitination ]]> https://biorxiv.org/content/10.1101/316000v1?rss=1 Lu, L. Ni, X. Tao, J. Gu, J. Park, B. V. Chen, Z. Newman, S. Shen, H. Wang, X. Li, B. Blazar, B. R. Barbi, J. Pan, F. 2018-05-07 doi:10.1101/316000 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Voltage-sensitive dye delivery through the blood brain barrier using adenosine receptor agonist Regadenoson ]]> https://biorxiv.org/content/10.1101/316505v1?rss=1 Pak, R. W. Kang, J. Valentine, H. Loew, L. M. Thorek, D. L. Boctor, E. M. Wong, D. F. Kang, J. U. 2018-05-07 doi:10.1101/316505 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Comprehensive Glycoproteomic Analysis of Chinese Hamster Ovary Cells ]]> https://biorxiv.org/content/10.1101/318865v1?rss=1 Yang, G. Hu, Y. Sun, S. Ouyang, C. Yang, W. Betenbaugh, M. Zhang, H. 2018-05-09 doi:10.1101/318865 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ AI-MHC: an allele-integrated deep learning framework for improving Class I & Class II HLA-binding predictions ]]> https://biorxiv.org/content/10.1101/318881v1?rss=1 Sidhom, J.-W. Pardoll, D. Baras, A. 2018-05-25 doi:10.1101/318881 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Recalibration of path integration in hippocampal place cells ]]> https://biorxiv.org/content/10.1101/319269v1?rss=1 Jayakumar, R. P. Madhav, M. S. Savelli, F. Blair, H. T. Cowan, N. J. Knierim, J. J. 2018-05-11 doi:10.1101/319269 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ A double dissociation in sensitivity to verb and noun semantics across cortical networks. ]]> https://biorxiv.org/content/10.1101/319640v1?rss=1 Elli, G. V. Lane, C. Bedny, M. 2018-05-10 doi:10.1101/319640 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Conformational heterogeneity allows access to DNA in longer Transcription Activator-Like Effector (TALE) arrays. ]]> https://biorxiv.org/content/10.1101/319749v1?rss=1 Geiger-Schuller, K. Mitra, J. Ha, T. Barrick, D. 2018-05-10 doi:10.1101/319749 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Deciphering the metabolic perturbation in hepatic alveolar echinococcosis: a 1H NMR-based metabolomics study ]]> https://biorxiv.org/content/10.1101/320333v1?rss=1 Lin, C. Zhang, L. Wei, Z. Cheng, K.-K. Shen, G. Dong, J. Chen, Z. Fan, H. 2018-05-14 doi:10.1101/320333 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in E. coli ]]> https://biorxiv.org/content/10.1101/320481v1?rss=1 Weng, X. Bohrer, C. H. Bettridge, K. Lagda, A. C. Cagliero, C. Jin, D. J. Xiao, J. 2018-05-11 doi:10.1101/320481 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ MS-PyCloud: An open-source, cloud computing-based pipeline for LC-MS/MS data analysis ]]> https://biorxiv.org/content/10.1101/320887v1?rss=1 Chen, L. Zhang, B. Schnaubelt, M. Shah, P. Aiyetan, P. Chan, D. Zhang, H. Zhang, Z. 2018-05-13 doi:10.1101/320887 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ Expression of novel fusion antiviral proteins Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) in Escherichia coli and their inhibition of protein synthesis and of hepatitis B virus in vitro ]]> https://biorxiv.org/content/10.1101/322040v1?rss=1 21818. The fusion protein was further optimized using in silico tools, produced in E. coli in vivo expression system, purified by three-step process from soluble lysate and protein synthesis inhibition activity assayed. Results showed that the optimized protein RTA mutant-Pokeweed antiviral protein isoform 1 from leaves (RTAM-PAP1) could be recovered and purified from soluble lysates with gain of function activity on protein synthesis inhibition with an IC50 of 0.03nM (1.82ng/ml). Collectively, our results demonstrate that RTA-PAPs are amenable to effective production and purification in native form, possess significant antiviral activity against HBV in vitro with a high therapeutic index and, thus, meriting further development as potential antiviral agents against chronic HBV infection. ]]> Hassan, Y. Ogg, S. Ge, H. 2018-05-15 doi:10.1101/322040 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Cryptsim: Modeling the evolutionary dynamics of the progression of Barrett’s esophagus to esophageal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/323485v1?rss=1 Mallo, D. Kostadinov, R. Cisneros, L. Kuhner, M. K. Maley, C. C. 2018-05-16 doi:10.1101/323485 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ T Cell Repertoire Evolution After Allogeneic Bone Marrow Transplantation: An Organizational Perspective ]]> https://biorxiv.org/content/10.1101/326744v1?rss=1 Meier, J. Fawaz, M. Abdeen, H. Reed, J. Kanakry, C. Luznik, L. Toor, A. 2018-05-21 doi:10.1101/326744 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Molecular phenotyping using networks, diffusion, and topology: soft tissue sarcoma ]]> https://biorxiv.org/content/10.1101/328054v1?rss=1 Mathews, J. Pouryahya, M. Moosmueller, C. Kevrekidis, I. Deasy, J. Tannenbaum, A. 2018-05-24 doi:10.1101/328054 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer with CancerInSilico ]]> https://biorxiv.org/content/10.1101/328807v1?rss=1 Sherman, T. D. Kagohara, L. T. Cao, R. Cheng, R. Satriano, M. Considine, M. Krigsfeld, G. Ranaweera, R. Tang, Y. Jablonski, S. Stein-O'Brien, G. Gaykalova, D. Weiner, L. M. Chung, C. Fertig, E. 2018-05-23 doi:10.1101/328807 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size ]]> https://biorxiv.org/content/10.1101/329672v1?rss=1 Rosenbloom, D. I. S. Bacchetti, P. Stone, M. Deng, X. Bosch, R. J. Richman, D. D. Siliciano, J. D. Mellors, J. W. Deeks, S. G. Ptak, R. G. Hoh, R. Keating, S. M. Dimapasoc, M. Massanella, M. Lai, J. Sobolewski, M. D. Kulpa, D. A. Busch, M. P. Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group, 2018-06-06 doi:10.1101/329672 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ REVA: a rank-based multi-dimensional measure of correlation ]]> https://biorxiv.org/content/10.1101/330498v1?rss=1 Afsari, B. Favorov, A. Fertig, E. J. Cope, L. 2018-05-25 doi:10.1101/330498 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise ]]> https://biorxiv.org/content/10.1101/332825v1?rss=1 Pertea, M. Shumate, A. Pertea, G. Varabyou, A. Chang, Y.-C. Madugundu, A. K. Pandey, A. Salzberg, S. 2018-05-28 doi:10.1101/332825 Cold Spring Harbor Laboratory Press 2018-05-28 <![CDATA[ Deconvoluting Virome-Wide Antiviral Antibody Profiling Data ]]> https://biorxiv.org/content/10.1101/333625v1?rss=1 Monaco, D. Kottapalli, S. Yuan, T. Breitwieser, F. Anderson, D. Wijaya, L. Tan, K. Chia, W. N. Kammers, K. Caturegli, M. Waugh, K. Rewers, M. Wang, L.-F. Larman, H. 2018-05-30 doi:10.1101/333625 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells ]]> https://biorxiv.org/content/10.1101/333658v1?rss=1 Rosenberg, A. Z. Wright, C. Fox-Talbot, K. Rajpurohit, A. Williams, C. Porter, C. Kovbasnjuk, O. McCall, M. N. Shin, J. H. Halushka, M. K. 2018-05-30 doi:10.1101/333658 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians ]]> https://biorxiv.org/content/10.1101/333690v1?rss=1 Esposito, U. Das, R. Pirooznia, M. Elhaik, E. 2018-05-30 doi:10.1101/333690 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Convolving Pre-Trained Convolutional Neural Networks at Various Magnifications to Extract Diagnostic Features for Digital Pathology ]]> https://biorxiv.org/content/10.1101/333773v1?rss=1 Sidhom, J.-W. Baras, A. 2018-05-30 doi:10.1101/333773 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Proteomics reveals ablation of placental growth factor inhibits the insulin resistance pathways in diabetic mouse retina ]]> https://biorxiv.org/content/10.1101/338368v1?rss=1 Lennikov, M. S. Lennikov, A. Tang, S. Huang, H. 2018-06-04 doi:10.1101/338368 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Long-range chromatin interactions on the inactive X and at Hox clusters are regulated by the non-canonical SMC protein Smchd1. ]]> https://biorxiv.org/content/10.1101/342212v1?rss=1 Jansz, N. Keniry, A. Trussart, M. Bildsoe, H. Beck, T. Tonks, I. D. Mould, A. W. Hickey, P. Breslin, K. Iminitoff, M. Ritchie, M. McGlinn, E. Kay, G. F. Murphy, J. M. Blewitt, M. 2018-06-08 doi:10.1101/342212 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants ]]> https://biorxiv.org/content/10.1101/342386v1?rss=1 Sedlazeck, F. J. Lemmon, Z. Soyk, S. Salerno, W. J. Lippman, Z. Schatz, M. C. 2018-06-08 doi:10.1101/342386 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries ]]> https://biorxiv.org/content/10.1101/343293v1?rss=1 Shrine, N. Guyatt, A. L. Erzurumluoglu, A. M. Jackson, V. E. Hobbs, B. D. Melbourne, C. Batini, C. Fawcett, K. A. Song, K. Sakornsakolpat, P. Li, X. Boxall, R. Reeve, N. F. Obeidat, M. Zhao, J. H. Wielscher, M. Understanding Society Scientific Group, Weiss, S. Kentistou, K. A. Cook, J. P. Sun, B. B. Zhou, J. Hui, J. Karrasch, S. Imboden, M. Harris, S. E. Marten, J. Enroth, S. Kerr, S. M. Surakka, I. Vitart, V. Lehtimäki, T. Allen, R. J. Bakke, P. S. Beaty, T. H. Bleecker, E. R. Bosse, Y. Brandsma, C.-A. Chen, Z. Crapo, J. D. Danesh, J. DeMeo, 2018-06-12 doi:10.1101/343293 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Improving Corticostriatal Parcellation Through Multilevel Bagging with PyBASC ]]> https://biorxiv.org/content/10.1101/343392v1?rss=1 Nikolaidis, A. Vogelstein, J. Bellec, P. Milham, M. 2018-06-11 doi:10.1101/343392 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ E-cadherin represses anoikis resistance in sarcomas through both signaling and mechanical mechanisms ]]> https://biorxiv.org/content/10.1101/347815v1?rss=1 Jolly, M. K. Ware, K. E. Xu, S. Gilja, S. Shetler, S. Yang, Y. Wang, X. Austin, G. Hish, A. J. Bartholf DeWitt, S. George, J. T. Kreulen, R. T. Boss, M.-K. Lazarides, A. L. Kerr, D. L. Gerber, D. G. Armstrong, A. J. Dewhirst, M. W. Eward, W. C. Levine, H. Somarelli, J. A. 2018-06-15 doi:10.1101/347815 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles ]]> https://biorxiv.org/content/10.1101/347955v1?rss=1 Kim, J. Han, K. Y. Khanna, N. Ha, T. Belmont, A. S. 2018-06-15 doi:10.1101/347955 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion ]]> https://biorxiv.org/content/10.1101/351387v1?rss=1 25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology. ]]> Gutierrez, J. M. Feizi, A. Li, S. Kallehauge, T. B. Hefzi, H. Grav, L. M. Ley, D. Hizal, D. B. Betenbaugh, M. J. Voldborg, B. Kildegaard, H. F. Lee, G. M. Palsson, B. O. Nielsen, J. Lewis, N. 2018-06-20 doi:10.1101/351387 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Electrocorticographic responses to time-compressed speech vary across the cortical auditory hierarchy ]]> https://biorxiv.org/content/10.1101/354464v1?rss=1 Davidesco, I. Thesen, T. Honey, C. J. Melloni, L. Doyle, W. Devinsky, O. Ghitza, O. Schroeder, C. Poeppel, D. Hasson, U. 2018-06-22 doi:10.1101/354464 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Expanded genetic landscape of chronic obstructive pulmonary disease reveals heterogeneous cell type and phenotype associations ]]> https://biorxiv.org/content/10.1101/355644v1?rss=1 Sakornsakolpat, P. Prokopenko, D. Lamontagne, M. Reeve, N. F. Guyatt, A. L. Jackson, V. E. Shrine, N. Qiao, D. Bartz, T. M. Kim, D. K. Lee, M. K. Latourelle, J. C. Li, X. Morrow, J. D. Obeidat, M. Wyss, A. B. Zhou, X. Bakke, P. Barr, R. G. Beaty, T. H. Belinsky, S. A. Brusselle, G. G. Crapo, J. D. Jong, K. d. DeMeo, D. L. Fingerlin, T. E. Gharib, S. A. Gulsvik, A. Hall, I. P. Hokanson, J. E. Kim, W. J. Lomas, D. A. London, S. J. Meyers, D. A. O'Connor, G. T. Rennard, S. I. Schwartz, D. A. Sliwinski, P. Sparrow, D. Strachan, D. P. Tal-Singer, R. Tesfaig 2018-06-26 doi:10.1101/355644 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ Canonical Wnt signaling regulates patterning, differentiation and nucleogenesis in mouse hypothalamus and prethalamus. ]]> https://biorxiv.org/content/10.1101/355750v1?rss=1 Newman, E. Wu, D. Taketo, M. M. Zhang, J. Blackshaw, S. 2018-06-26 doi:10.1101/355750 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ ATP synthase K+- and H+-flux drive ATP synthesis and enable mitochondrial K+-uniporter function ]]> https://biorxiv.org/content/10.1101/355776v1?rss=1 106-fold K+ excess vs H+) to drive ATP synthesis with the H+:K+ permeability of ~106:1. F1Fo can be upregulated by endogenous survival-related proteins (Bcl-xL, Mcl-1) and synthetic molecules (diazoxide, pinacidil) to increase its chemo-mechanical efficiency via IF1. Increasing K+- and H+-driven ATP synthesis enables F1Fo to operate as a primary mitochondrial K+-uniporter regulating energy supply-demand matching, and as the recruitable mitochondrial KATP-channel that can limit ischemia-reperfusion injury. Isolated mitochondria in the presence of K+ can sustain ~3.5-fold higher ATP-synthesis-flux (vs K+ absence) driven by a 2.7:1 K+:H+ stoichiometry with unaltered OxPhos coupling. Excellent agreement between F1Fo single-molecule and intact-mitochondria experiments is consistent with K+-transport through ATP synthase driving a major fraction of ATP synthesis. ]]> Juhaszova, M. Kobrinsky, E. Zorov, D. B. Nuss, B. Yaniv, Y. Fishbein, K. W. de Cabo, R. Montoliu, L. Gabelli, S. B. Aon, M. A. Cortassa, S. Sollott, S. J. 2018-06-26 doi:10.1101/355776 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ EnsembleCNV: An ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data ]]> https://biorxiv.org/content/10.1101/356667v1?rss=1 Zhang, Z. Cheng, H. Hong, X. Di Narzo, A. F. Franzen, O. Peng, S. Ruusalepp, A. Kovacic, J. C. Bjorkegren, J. L. Wang, X. Hao, K. 2018-06-27 doi:10.1101/356667 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ OTUB1 non-catalytically regulates the stability of the E2 ubiquitin conjugating enzyme UBE2E1 ]]> https://biorxiv.org/content/10.1101/359414v1?rss=1 Pasupala, N. Morrow, M. E. Que, L. T. Malynn, B. A. Ma, A. Wolberger, C. 2018-06-29 doi:10.1101/359414 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ TCR/ITK signaling via mTOR tunes CD8+ T cell homeostatic proliferation, metabolism, and anti-tumor effector function ]]> https://biorxiv.org/content/10.1101/359604v1?rss=1 Huang, W. Luo, J. August, A. 2018-06-29 doi:10.1101/359604 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Thyroid hormone signaling specifies cone subtypes in human retinal organoids ]]> https://biorxiv.org/content/10.1101/359950v1?rss=1 Eldred, K. C. Hadyniak, S. E. Hussey, K. A. Brennerman, B. Zhang, P. Chamling, X. Sluch, V. M. Welsbie, D. S. Hattar, S. Taylor, J. Wahlin, K. Zack, D. J. Johnston, R. J. 2018-06-30 doi:10.1101/359950 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ DNMT3A-NPM1 mutated acute myeloid leukaemia shows sensitivity to a PARP1 inhibitor combined with daunorubicin in an in vitro model ]]> https://biorxiv.org/content/10.1101/362103v1?rss=1 Gafencu, G. A. Pileczki, V. Jurj, A. Magdo, L. Selicean, C. Ola, R. Ghiaur, G. Berindan-Neagoe, I. Tomuleasa, C. 2018-07-05 doi:10.1101/362103 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ The immune cell landscape in kidneys of lupus nephritis patients ]]> https://biorxiv.org/content/10.1101/363051v1?rss=1 Arazi, A. Rao, D. A. Berthier, C. C. Davidson, A. Liu, Y. Hoover, P. J. Chicoine, A. Eisenhaure, T. M. Jonsson, A. H. Li, S. Lieb, D. J. Browne, E. P. Noma, A. Sutherby, D. Steelman, S. Smilek, D. E. Tosta, P. Apruzzese, W. Massarotti, E. Dall'Era, M. Park, M. Kamen, D. L. Furie, R. A. Payan-Schober, F. Buyon, J. P. Petri, M. A. Putterman, C. Kalunian, K. C. Woodle, E. S. Lederer, J. A. Hildeman, D. A. Nusbaum, C. Wofsy, D. Kretzler, M. Anolik, J. H. Brenner, M. B. The Accelerating Medicines Partnership in RA/SLE network, Hacohen, N. Diamond, B. 2018-07-07 doi:10.1101/363051 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Identification of substrates for the conserved prolyl hydroxylase Ofd1 using quantitative proteomics in fission yeast ]]> https://biorxiv.org/content/10.1101/363747v1?rss=1 Gu, H. Hughes, B. T. Espenshade, P. J. 2018-07-06 doi:10.1101/363747 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Parkinson-associated SNCA enhancer variants revealed by open chromatin in mouse dopamine neurons ]]> https://biorxiv.org/content/10.1101/364257v1?rss=1 2,300 putative enhancers assayed in mice reveals enrichment for MB cis-regulatory elements (CRE), data reinforced by transgenic analyses of six additional sequences in zebrafish and mice. One CRE, within intron 4 of the familial PD gene SNCA, directs reporter expression in catecholaminergic neurons of transgenic mice and zebrafish. Sequencing of this CRE in 986 PD patients and 992 controls reveals two common variants associated with elevated PD risk. To assess potential mechanisms of action, we screened >20,000 DNA interacting proteins and identify a subset whose binding is impacted by these enhancer variants. Additional genotyping across the SNCA locus identifies a single PD-associated haplotype, containing the minor alleles of both of the aforementioned PD-risk variants. Our work posits a model for how common variation at SNCA may modulate PD risk and highlights the value of cell context-dependent guided searches for functional non-coding variation. ]]> McClymont, S. A. Hook, P. W. Soto, A. I. Reed, X. Law, W. D. Kerans, S. J. Waite, E. L. Briceno, N. J. Thole, J. F. Heckman, M. G. Diehl, N. N. Wszolek, Z. K. Moore, C. D. Zhu, H. Akiyama, J. A. Dickel, D. E. Visel, A. Pennacchio, L. A. Ross, O. A. Beer, M. A. McCallion, A. S. 2018-07-08 doi:10.1101/364257 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut ]]> https://biorxiv.org/content/10.1101/364505v1?rss=1 Crook, N. Ferreiro, A. Gasparrini, A. Pesesky, M. Gibson, M. Wang, B. Sun, X. Condiotte, Z. Dobrowolski, S. Peterson, D. Dantas, G. 2018-07-08 doi:10.1101/364505 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ NHA2 promotes cyst development in an in vitro model of polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/364679v1?rss=1 Prasad, H. Dang, D. K. Kondapalli, K. C. Natarajan, N. Cebotaru, V. Rao, R. 2018-07-07 doi:10.1101/364679 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ BCG overexpressing an endogenous STING agonist provides enhanced protection against pulmonary tuberculosis ]]> https://biorxiv.org/content/10.1101/365411v1?rss=1 Bishai, W. R. Dey, R. J. Dey, B. Singh, A. K. Praharaj, M. 2018-07-09 doi:10.1101/365411 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Closed-Loop Control of Active Sensing Movements Regulates Sensory Slip. ]]> https://biorxiv.org/content/10.1101/366609v1?rss=1 Biswas, D. Arend, L. A. Stamper, S. A. Vagvölgyi, B. P. Fortune, E. S. Cowan, N. J. 2018-07-10 doi:10.1101/366609 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ The creation of sexual dimorphism in Drosophila gonad stem cell niches ]]> https://biorxiv.org/content/10.1101/367268v1?rss=1 Camara, N. Whitworth, C. Van Doren, M. 2018-07-11 doi:10.1101/367268 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Genetic data and cognitively-defined late-onset Alzheimer’s disease subgroups ]]> https://biorxiv.org/content/10.1101/367615v1?rss=1 1.30). There was substantial variation across studies in the proportions of people in each subgroup. In each study, higher proportions of people with isolated substantial relative memory impairment had [≥]1 APOE e4 allele than any other subgroup (overall p= 1.5 x 10-27). Across subgroups, there were 33 novel suggestive loci across the genome with p<10-5 and an extreme OR compared to controls, of which none had statistical evidence of heterogeneity and 30 had ORs in the same direction across all datasets. These data support the biological coherence of cognitively-defined subgroups and nominate novel genetic loci. ]]> Mukherjee, S. Mez, J. Trittschuh, E. Saykin, A. J. Gibbons, L. E. Fardo, D. W. Wessels, M. Bauman, J. Moore, M. Choi, S.-E. Gross, A. L. Rich, J. Louden, D. K. Sanders, R. E. Grabowski, T. J. Bird, T. D. McCurry, S. M. Snitz, B. E. Kamboh, M. I. Lopez, O. L. De Jager, P. L. Bennett, D. A. Keene, C. D. Larson, E. B. Crane, P. K. 2018-07-11 doi:10.1101/367615 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Mendelian Randomization Analysis Using Mixture Models (MRMix) for Genetic Effect-Size-Distribution Leads to Robust Estimation of Causal Effects ]]> https://biorxiv.org/content/10.1101/367821v1?rss=1 Qi, G. Chatterjee, N. 2018-07-13 doi:10.1101/367821 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO) ]]> https://biorxiv.org/content/10.1101/368282v1?rss=1 Yang, W. Ao, M. Hu, Y. Li, Q. Zhang, H. 2018-07-13 doi:10.1101/368282 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Short hairpin RNAs artifactually impair cell growth and suppress clustered microRNA expression. ]]> https://biorxiv.org/content/10.1101/372920v1?rss=1 Powers, J. da Rocha, E. Pearson, D. Missios, P. de Soysa, T. Y. Barragan, J. Cahan, P. Daley, G. 2018-07-20 doi:10.1101/372920 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection ]]> https://biorxiv.org/content/10.1101/374728v1?rss=1 Sluch, V. M. Chamling, X. Wenger, C. Duan, Y. Rice, D. S. Zack, D. J. 2018-07-23 doi:10.1101/374728 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing. ]]> https://biorxiv.org/content/10.1101/376301v1?rss=1 Martinez-Viaud, K. A. Lawley, C. T. Vergara, M. M. Ben-Zvi, G. Biniashvili, T. Baruch, K. St. Leger, J. Le, J. Natarjan, A. Rivera, M. Gillergan, N. Jaeger, E. Steffy, B. Zimin, A. 2018-07-24 doi:10.1101/376301 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Neural underpinnnings of auditory salience in natural soundscapes ]]> https://biorxiv.org/content/10.1101/376525v1?rss=1 Huang, N. Elhilali, M. 2018-08-07 doi:10.1101/376525 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Development and Application of a High-Content Virion Display Human GPCR Array ]]> https://biorxiv.org/content/10.1101/377754v1?rss=1 85% coverage) in the envelope of human herpes simplex virus-1 and immobilized on glass to form a high-content Virion Display (VirD) array. Using this array, we found that 50% of the tested commercial anti-GPCR antibodies (mAbs) is ultra-specific, and that the vast majority of those VirD-GPCRs, which failed to be recognized by the commercial mAbs, could bind to their canonical ligands, indicating that they were folded correctly. Next, we used the VirD-GPCR arrays to examine binding specificity of two known peptide ligands and recovered expected interactions, as well as new off-target interactions, three of which were confirmed with real-time kinetics measurements. Finally, we explored the possibility of discovering novel pathogen targets by probing VirD-GPCR arrays with live group B Streptococcus (GBS), a common Gram-positive bacterium causing neonatal meningitis. Using cell invasion assays and a mouse model of hematogenous meningitis, we showed that inhibition of one of the five newly identified GPCRs, CysLTR1, greatly reduced GBS penetration in brain-derived endothelial cells and in mouse brains. Therefore, our work demonstrated that the VirD-GPCR array holds great potential for high-throughput, unbiased screening for small molecule drugs, affinity reagents, and deorphanization. ]]> Syu, G.-D. Wang, S.-C. Ma, G. Liu, S. Pearce, D. Prakash, A. Henson, B. Weng, L.-C. Ghosh, D. Ramos, P. Eichinger, D. Pino, I. Dong, X. Xiao, J. Wang, S. Tao, N. Kim, K. S. Desai, P. J. Zhu, H. 2018-07-26 doi:10.1101/377754 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells. ]]> https://biorxiv.org/content/10.1101/378950v1?rss=1 Clark, B. Stein-O'Brien, G. Shiau, F. Cannon, G. Davis, E. Sherman, T. Rajaii, F. James-Esposito, R. Gronostajski, R. Fertig, E. Goff, L. Blackshaw, S. 2018-07-27 doi:10.1101/378950 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Dynamic recovery from depression enables rate encoding in inhibitory synapses ]]> https://biorxiv.org/content/10.1101/379081v1?rss=1 Huang, S. Bridi, M. Kirkwood, A. 2018-07-27 doi:10.1101/379081 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ A Moonlighting Role for SPCA2 in E-cadherin Biogenesis and Suppression of Epithelial-Mesenchymal Transition ]]> https://biorxiv.org/content/10.1101/379586v1?rss=1 nView larger version (28K):norg.highwire.dtl.DTLVardef@6b1e14org.highwire.dtl.DTLVardef@83edbborg.highwire.dtl.DTLVardef@16cbc5corg.highwire.dtl.DTLVardef@1c2752a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dang, D. K. Llongueras, J. P. Prasad, H. Ogunmola, I. Makena, M. R. Rao, R. 2018-07-28 doi:10.1101/379586 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ Activin signaling informs the graded pattern of terminal mitosis and hair cell differentiation in the mammalian cochlea ]]> https://biorxiv.org/content/10.1101/380055v1?rss=1 Prajapati-DiNubila, M. Benito-Gonzalez, A. Golden, E. J. Zhang, S. Doetzlhofer, A. 2018-07-30 doi:10.1101/380055 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Episodic Memory Can Replace Active Storage in Visual Working Memory ]]> https://biorxiv.org/content/10.1101/381848v1?rss=1 Schurgin, M. W. Cunningham, C. A. Egeth, H. E. Brady, T. F. 2018-08-01 doi:10.1101/381848 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Multilayer network analysis of miRNA and protein expression profiles in breast cancer patients ]]> https://biorxiv.org/content/10.1101/384768v1?rss=1 Zhang, Y. Chen, J. Wang, D. Cong, W. Lai, B. S. Yi, Z. 2018-08-03 doi:10.1101/384768 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Can patients with cerebellar disease switch learning mechanisms to reduce their adaptation deficits? ]]> https://biorxiv.org/content/10.1101/386466v1?rss=1 Wong, A. L. Marvel, C. L. Taylor, J. A. Krakauer, J. W. 2018-08-07 doi:10.1101/386466 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Motor Cortex Excitability Reflects the Subjective Value of Reward and Mediates its Effects on Incentive Motivated Performance ]]> https://biorxiv.org/content/10.1101/387332v1?rss=1 Galaro, J. K. Celnik, P. A. Chib, V. S. 2018-08-08 doi:10.1101/387332 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Persistent activity in primate auditory cortex evoked by sensory stimulation ]]> https://biorxiv.org/content/10.1101/387837v1?rss=1 Cooke, J. E. Lee, J. J. Bartlett, E. L. Wang, X. Bendor, D. 2018-08-09 doi:10.1101/387837 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer ]]> https://biorxiv.org/content/10.1101/388264v1?rss=1 Guo, C. C. Majewski, T. Zhang, L. Yao, H. Bodaruk, J. Wang, Y. Zhang, S. Wang, Z. Lee, J. G. Lee, S. Cogdell, D. Zhang, M. Wei, P. Grossman, H. B. Kamat, A. Duplisea, J. J. Ferguson, J. E. Huang, H. Dadhania, V. Dinney, C. Weinstein, J. Baggerly, K. McConkey, D. J. Czerniak, B. 2018-08-09 doi:10.1101/388264 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ tudor-domain containing protein 5-prime promotes male sexual identity in the Drosophila germline and is repressed in females by Sex lethal ]]> https://biorxiv.org/content/10.1101/388850v1?rss=1 Primus, S. Pozmanter, C. Baxter, K. Van Doren, M. 2018-08-09 doi:10.1101/388850 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Are these cardiomyocytes? Protocol development reveals impact of sample preparation on the accuracy of identifying cardiomyocytes by flow cytometry ]]> https://biorxiv.org/content/10.1101/388926v1?rss=1 Waas, M. Weerasekera, R. Kropp, E. M. Romero-Tejeda, M. Poon, E. Boheler, K. R. Burridge, P. W. Gundry, R. 2018-08-09 doi:10.1101/388926 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ IDH1R132H acts as a tumor suppressor in glioma via epigenetic upregulation of the DNA damage response ]]> https://biorxiv.org/content/10.1101/389817v1?rss=1 Nunez, F. J. Mendez, F. M. Kadilaya, P. Alghamri, M. S. Savelieff, M. Koschmann, C. Calinescu, A.-A. Kamran, N. Patel, R. Guo, M. Z. Carney, S. Garcia-Fabiani, M. B. Haase, S. Edwards, M. Ljungman, M. Qin, T. Sartor, M. Tagett, R. Venneti, S. Brosnan-Cashman, J. Meeker, A. Gorbunova, V. Zhao, L. Kramer, D. Zhang, L. Lyssiotis, C. A. Jones, L. Herting, C. Ross, J. Hambardzumyan, D. Hervey-Jumper, S. Figueroa, M. E. Lowenstein, P. R. Castro, M. G. 2018-08-10 doi:10.1101/389817 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Inactivation of medial frontal cortex changes risk preference ]]> https://biorxiv.org/content/10.1101/390021v1?rss=1 Stuphorn, V. Chen, X. 2018-08-10 doi:10.1101/390021 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ The capsule of Cryptococcus neoformans modulates phagosomal pH through its acid-base properties ]]> https://biorxiv.org/content/10.1101/390328v1?rss=1 DeLeon-Rodriguez, C. M. Fu, M. S. Corbali, M. O. Cordero, R. J. Casadevall, A. 2018-08-13 doi:10.1101/390328 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ \"Visual\" Cortices of Congenitally Blind Adults Respond to Executive Demands ]]> https://biorxiv.org/content/10.1101/390450v1?rss=1 Loiotile, R. E. Bedny, M. 2018-08-13 doi:10.1101/390450 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Quality of eyeglass prescriptions from a low-cost wavefront autorefractor evaluated in rural India: results of a 708-participant field study ]]> https://biorxiv.org/content/10.1101/390625v1?rss=1 Durr, N. J. Dave, S. R. Lim, D. Joseph, S. Ravilla, T. D. Lage, E. 2018-08-13 doi:10.1101/390625 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Pharmacokinetics, Side Effects, and Anti-Hyperalgesic Efficacy of The Mglu5 Antagonist Fenobam. ]]> https://biorxiv.org/content/10.1101/391383v1?rss=1 Cavallone, L. F. Montana, M. C. Frey, K. Kallogjeri, D. Wages, J. M. Rodebaugh, T. L. Doshi, T. Kharasch, E. D. Gereau, R. W. 2018-08-15 doi:10.1101/391383 Cold Spring Harbor Laboratory Press 2018-08-15 <![CDATA[ Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species. ]]> https://biorxiv.org/content/10.1101/395004v1?rss=1 nView larger version (81K):norg.highwire.dtl.DTLVardef@dd1c07org.highwire.dtl.DTLVardef@5b1109org.highwire.dtl.DTLVardef@bb6714org.highwire.dtl.DTLVardef@16c66f0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stein-O'Brien, G. L. Clark, B. S. Sherman, T. Zibetti, C. Hu, Q. Sealfon, R. Liu, S. Qian, J. Colantuoni, C. Blackshaw, S. Goff, L. A. Fertig, E. J. 2018-08-20 doi:10.1101/395004 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole genome sequencing studies ]]> https://biorxiv.org/content/10.1101/395046v1?rss=1 Chen, H. Huffman, J. E. Brody, J. A. Wang, C. Lee, S. Li, Z. Gogarten, S. M. Sofer, T. Bielak, L. F. Bis, J. C. Blangero, J. Bowler, R. P. Cade, B. E. Cho, M. H. Correa, A. Curran, J. E. de Vries, P. S. Glahn, D. C. Guo, X. Johnson, A. D. Kardia, S. Kooperberg, C. Lewis, J. P. Liu, X. Mathias, R. A. Mitchell, B. D. O'Connell, J. R. Peyser, P. A. Post, W. S. Reiner, A. P. Rich, S. S. Rotter, J. I. Silverman, E. K. Smith, J. A. Vasan, R. S. Wilson, J. G. Yanek, L. R. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Hematology and Hemos 2018-08-20 doi:10.1101/395046 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ High-dose rifamycins enable shorter oral treatment in a murine model of Mycobacterium ulcerans disease ]]> https://biorxiv.org/content/10.1101/395095v1?rss=1 Omansen, T. F. Almeida, D. Converse, P. J. Li, S.-Y. Lee, J. Stienstra, Y. van der Werf, T. S. Grosset, J. H. Nuermberger, E. 2018-08-19 doi:10.1101/395095 Cold Spring Harbor Laboratory Press 2018-08-19 <![CDATA[ On the Number of Driver Nodes for Controlling a Boolean Network to Attractors ]]> https://biorxiv.org/content/10.1101/395442v1?rss=1 Hou, W. Ruan, P. Ching, W.-K. Akutsu, T. 2018-08-20 doi:10.1101/395442 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ GBAT: a gene-based association method for robust trans-gene regulation detection ]]> https://biorxiv.org/content/10.1101/395970v1?rss=1 Liu, X. Mefford, J. A. Dahl, A. Subramaniam, M. Battle, A. Price, A. L. Zaitlen, N. 2018-08-20 doi:10.1101/395970 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ cAMP stimulates SLC26A3 activity in human colon by a CFTR-dependent mechanism that does not require CFTR activity ]]> https://biorxiv.org/content/10.1101/396408v1?rss=1 Tse, C.-M. Yin, J. Singh, V. Sarker, R. Lin, R. Verkman, A. S. Turner, J. R. Donowitz, M. 2018-08-20 doi:10.1101/396408 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics ]]> https://biorxiv.org/content/10.1101/397653v1?rss=1 Nune, M. Morgan, M. T. Connell, Z. McCullough, L. Jbara, M. Sun, H. Brik, A. Formosa, T. Wolberger, C. 2018-08-22 doi:10.1101/397653 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Life Inside A Dinosaur Bone: A Thriving Microbiome ]]> https://biorxiv.org/content/10.1101/400176v1?rss=1 Saitta, E. T. Liang, R. Lau, C. Y. Brown, C. M. Longrich, N. R. Kaye, T. G. Novak, B. J. Salzberg, S. Donohoe, P. Dickinson, M. Vinther, J. Bull, I. D. Brooker, R. A. Martin, P. Abbott, G. D. Knowles, T. D. Penkman, K. Onstott, T. C. 2018-09-07 doi:10.1101/400176 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Assessing 16S marker gene survey data analysis methods using mixtures of human stool sample DNA extracts. ]]> https://biorxiv.org/content/10.1101/400226v1?rss=1 Olson, N. D. Kumar, M. S. Li, S. Hao, S. Timp, W. Salit, M. L. Stine, O. C. Corrada Bravo, H. 2018-08-25 doi:10.1101/400226 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways ]]> https://biorxiv.org/content/10.1101/401729v1?rss=1 Ochsner, S. Abraham, D. Martin, K. Ding, W. McOwiti, A. Wang, Z. Andreano, K. Hamilton, R. Chen, Y. Hamilton, A. Gantner, M. Dehart, M. Qu, S. Hilsenbeck, S. Becnel, L. Bridges, D. Maayan, A. Huss, J. Stossi, F. Foulds, C. Kralli, A. McDonnell, D. McKenna, N. 2018-08-27 doi:10.1101/401729 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Optimizing non-invasive sampling of an infectious bat virus ]]> https://biorxiv.org/content/10.1101/401968v1?rss=1 Giles, J. R. Peel, A. J. Wells, K. Plowright, R. K. McCallum, H. Restif, O. 2018-08-28 doi:10.1101/401968 Cold Spring Harbor Laboratory Press 2018-08-28 <![CDATA[ Sensitive period for cognitive repurposing of human visual cortex ]]> https://biorxiv.org/content/10.1101/402321v1?rss=1 Kanjlia, S. Pant, R. Bedny, M. 2018-08-28 doi:10.1101/402321 Cold Spring Harbor Laboratory Press 2018-08-28 <![CDATA[ What can facial mechanoreceptors tell the mouse brain about whisking? ]]> https://biorxiv.org/content/10.1101/402883v1?rss=1 Severson, K. S. Xu, D. Yang, H. O'Connor, D. 2018-08-29 doi:10.1101/402883 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Overlapping but asymmetrical relationships between schizophrenia and autism revealed by brain connectivity ]]> https://biorxiv.org/content/10.1101/403212v1?rss=1 Yoshihara, Y. Lisi, G. Yahata, N. Fujino, J. Matsumoto, Y. Miyata, J. Sugihara, G. Urayama, S.-i. Kubota, M. Yamashita, M. Hashimoto, R. Ichikawa, N. Cahn, W. van Haren, N. E. M. Mori, S. Okamoto, Y. Kasai, K. Kato, N. Imamizu, H. Kahn, R. S. Sawa, A. Kawato, M. Murai, T. Morimoto, J. Takahashi, H. 2018-09-07 doi:10.1101/403212 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Fatigue induces long lasting detrimental changes in motor skill learning ]]> https://biorxiv.org/content/10.1101/406520v1?rss=1 Branscheidt, M. Kassavetis, P. Rogers, D. Lindquist, M. A. Celnik, P. 2018-09-03 doi:10.1101/406520 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Evidence for gene-environment correlation in child feeding: Links between common genetic variation for BMI in children and parental feeding practices ]]> https://biorxiv.org/content/10.1101/407221v1?rss=1 Selzam, S. McAdams, T. A. Coleman, J. R. I. Carnell, S. O'Reilly, P. F. Plomin, R. Llewellyn, C. H. 2018-09-04 doi:10.1101/407221 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Modular preprocessing pipelines can reintroduce artifacts into fMRI data ]]> https://biorxiv.org/content/10.1101/407676v1?rss=1 Lindquist, M. Geuter, S. Wager, T. Caffo, B. 2018-09-04 doi:10.1101/407676 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts ]]> https://biorxiv.org/content/10.1101/408492v1?rss=1 Fresard, L. Smail, C. Smith, K. S. Ferraro, N. M. Teran, N. A. Kernohan, K. D. Bonner, D. Li, X. Marwaha, S. Zappala, Z. Balliu, B. Davis, J. R. Liu, B. Prybol, C. J. Kholer, J. N. Zastrow, D. B. Fisk, D. G. Grove, M. E. Davidson, J. M. Hartley, T. Joshi, R. Strober, B. J. Utiramerur, S. Care4Rare Canada Consortium, Undiagnosed Diseases Network, Lind, L. Ingelsson, E. Battle, A. Bejerano, G. Bernstein, J. A. Ashley, E. A. Boycott, K. M. Merker, J. D. Wheeler, M. T. Montgomery, S. B. 2018-09-04 doi:10.1101/408492 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Flexible backbone assembly and refinement of symmetrical homomeric complexes ]]> https://biorxiv.org/content/10.1101/409730v1?rss=1 nView larger version (64K):norg.highwire.dtl.DTLVardef@1e4834borg.highwire.dtl.DTLVardef@167bd2eorg.highwire.dtl.DTLVardef@1b52510org.highwire.dtl.DTLVardef@1945a02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Roy Burman, S. S. Yovanno, R. A. Gray, J. J. 2018-09-06 doi:10.1101/409730 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Resting-state functional connectivity, cortical GABA and neuroactive steroids in peripartum and peripartum depressed women: a functional magnetic imaging and resonance study ]]> https://biorxiv.org/content/10.1101/411405v1?rss=1 Deligiannidis, K. M. Fales, C. L. Kroll-Desrosiers, A. R. Shaffer, S. A. Villamarin, V. Tan, Y. Hall, J. E. Frederick, B. B. Sikoglu, E. M. Edden, R. A. Rothschild, A. J. Moore, C. M. 2018-09-07 doi:10.1101/411405 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ No cell is an island: circulating T cell:monocyte complexes are markers of immune perturbations ]]> https://biorxiv.org/content/10.1101/411553v1?rss=1 Burel, J. G. Pomaznoy, M. Lindestam Arlehamn, C. S. Weiskopf, D. da Silva Antunes, R. Schulten, V. Babor, M. Seumois, G. Greenbaum, J. A. Premawansa, S. Premawansa, G. Wijewickrama, A. Tippalagama, R. deSilva, A. D. Gilman, R. H. Saito, M. Taplitz, R. Vijayanand, P. Sette, A. Peters, B. 2018-09-07 doi:10.1101/411553 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Optimal features for auditory categorization ]]> https://biorxiv.org/content/10.1101/411611v1?rss=1 95% accuracy could be accomplished using only 10 - 20 features per call type. Most importantly, predictions of the tuning properties of putative neurons selective for such features accurately matched some previously observed responses of superficial layer neurons in primary auditory cortex. Such a feature-based approach succeeded in categorizing calls of other species such as guinea pigs and macaque monkeys, and could also solve other complex classification tasks such as caller identification. Our results suggest that high-level neural representations of sounds are based on task-dependent features optimized for specific computational goals. ]]> Liu, S. T. Wang, X. Sadagopan, S. 2018-09-08 doi:10.1101/411611 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Agrobacterium tumefaciens divisome proteins regulate the transition from polar growth to cell division ]]> https://biorxiv.org/content/10.1101/412759v1?rss=1 Howell, M. L. Aliashkevich, A. Sundararajan, K. Daniel, J. J. Lariviere, P. J. Goley, E. Cava, F. Brown, P. J. 2018-09-10 doi:10.1101/412759 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ PISD is a mitochondrial disease gene causing skeletal dysplasia, cataracts and white matter changes ]]> https://biorxiv.org/content/10.1101/413070v1?rss=1 Shutt, T. E. Zhao, T. Goedhart, C. M. Sam, P. Lingrell, S. Cornish, A. Lamont, R. E. Bernier, F. P. Sinasac, D. Parboosingh, J. Vance, J. Claypool, S. M. Innes, M. 2018-09-12 doi:10.1101/413070 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ First Whole-Body Three-Dimensional Tomographic Imaging of Alpha Particle Emitting Radium-223 ]]> https://biorxiv.org/content/10.1101/414649v1?rss=1 Abou, D. S. Rittenbach, A. Tomlinson, R. E. Finley, P. A. Tsui, B. Simons, B. W. Ulmert, D. Riddle, R. C. Thorek, D. L. 2018-09-26 doi:10.1101/414649 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Stem cell mitotic drive ensures asymmetric epigenetic inheritance ]]> https://biorxiv.org/content/10.1101/416446v1?rss=1 Ranjan, R. Snedeker, J. Chen, X. 2018-09-13 doi:10.1101/416446 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform ]]> https://biorxiv.org/content/10.1101/417618v1?rss=1 Holm, J. B. Humphrys, M. Robinson, C. K. Settles, M. L. Ott, S. Fu, L. Yang, H. Gajer, P. He, X. McComb, E. J. Gravitt, P. Ghanem, K. G. Brotman, R. M. Ravel, J. 2018-09-14 doi:10.1101/417618 500 bp amplicon regions on the Illumina HiSeq 2500 platform]]> Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Progressive Mycobacterium abscessus lung infection in C3HeB/FeJ mice associated with corticosteroid administration ]]> https://biorxiv.org/content/10.1101/418491v1?rss=1 Maggioncalda, E. C. Story-Roller, E. Ammerman, N. C. Nuermberger, E. L. Lamichhane, G. 2018-09-14 doi:10.1101/418491 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Transformation of Speech Sequences in Human Sensorimotor Circuits ]]> https://biorxiv.org/content/10.1101/419358v1?rss=1 Müsch, K. Himberger, K. Tan, K. M. Valiante, T. A. Honey, C. J. 2018-09-16 doi:10.1101/419358 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy ]]> https://biorxiv.org/content/10.1101/420372v1?rss=1 Xi, W. Beer, M. A. 2018-09-27 doi:10.1101/420372 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay ]]> https://biorxiv.org/content/10.1101/424499v1?rss=1 Liang, X. Ho, M. C. W. Wu, M. N. Holy, T. E. Taghert, P. H. 2018-09-21 doi:10.1101/424499 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Covariate Assisted Principal Regression for Covariance Matrix Outcomes ]]> https://biorxiv.org/content/10.1101/425033v1?rss=1 Zhao, Y. Wang, B. Mostofsky, S. Caffo, B. Luo, X. 2018-09-23 doi:10.1101/425033 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Heritability enrichment in open chromatin reveals cortical layer contributions to schizophrenia ]]> https://biorxiv.org/content/10.1101/427484v1?rss=1 Hook, P. W. McCallion, A. S. 2018-09-26 doi:10.1101/427484 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Redefining Nephrotic Syndrome in Molecular Terms: Outcome-associated molecular clusters and patient stratification with noninvasive surrogate biomarkers ]]> https://biorxiv.org/content/10.1101/427880v1?rss=1 Mariani, L. H. Eddy, S. Martini, S. Eichinger, F. Godfrey, B. Nair, V. Adler, S. G. Appel, G. B. Athavale, A. Barisoni, L. Brown, E. Cattran, D. C. Dell, K. M. Derebail, V. Fervenza, F. C. Fornoni, A. Gadegbeku, C. A. Gibson, K. L. Gipson, D. Greenbaum, L. A. Hingorani, S. R. Hlandunewich, M. A. Hogan, J. Holzman, L. B. Jefferson, J. A. Kaskel, F. J. Kopp, J. B. Lafayette, R. A. Lemley, K. V. Lieske, J. C. Lin, J.-J. Myers, K. E. Nachman, P. H. Nast, C. C. Neu, A. M. Reich, H. N. Sambandam, K. Sedor, J. R. Sethna, C. B. Srivastava, T. Trachtman, H. Tran 2018-09-27 doi:10.1101/427880 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Autoamplification and competition drive symmetry breaking: Initiation of centriole duplication by the PLK4-STIL network ]]> https://biorxiv.org/content/10.1101/430264v1?rss=1 Leda, M. Holland, A. J. Goryachev, A. B. 2018-09-29 doi:10.1101/430264 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Computational modeling of the crosstalk between macrophage polarization and tumor cell plasticity in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/430520v1?rss=1 Li, X. Jolly, M. K. George, J. T. Pienta, K. J. Levine, H. 2018-10-13 doi:10.1101/430520 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Hexameric helicase G40P unwinds DNA in single base pair steps ]]> https://biorxiv.org/content/10.1101/431882v1?rss=1 Schlierf, M. Wang, G. Chen, X. S. Ha, T. 2018-10-01 doi:10.1101/431882 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Cell-type-specific methylome-wide association studies implicate neurodegenerative processes and neuroimmune communication in major depressive disorder ]]> https://biorxiv.org/content/10.1101/432088v1?rss=1 Chan, R. F. Turecki, G. Shabalin, A. A. Guintivano, J. Zhao, M. Xie, L. Y. van Grootheest, G. Kaminsky, Z. A. Dean, B. Penninx, B. W. J. H. Aberg, K. A. van den Oord, E. J. C. G. 2018-10-03 doi:10.1101/432088 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Genetic signatures of human cytomegalovirus variants acquired by seronegative glycoprotein B vaccinees ]]> https://biorxiv.org/content/10.1101/432922v1?rss=1 Nelson, C. S. Vera Cruz, D. Su, M. Xie, G. Vandergrift, N. Pass, R. Forman, M. Diener-West, M. Koelle, K. Arav-Boger, R. Permar, S. R. 2018-10-02 doi:10.1101/432922 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Epithelial WNT2B and Desert Hedgehog are necessary for human colonoid regeneration after bacterial cytotoxin injury ]]> https://biorxiv.org/content/10.1101/434639v1?rss=1 In, J. G. Yin, J. Doucet, M. Cole, R. N. DeVine, L. Donowitz, M. Zachos, N. C. Blutt, S. E. Estes, M. K. Kovbasnjuk, O. 2018-10-03 doi:10.1101/434639 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Leveraging evolutionary relationships to improve Anopheles genome assemblies ]]> https://biorxiv.org/content/10.1101/434670v1?rss=1 Waterhouse, R. M. Aganezov, S. Anselmetti, Y. Lee, J. Ruzzante, L. Reijnders, M. J. Berard, S. George, P. Hahn, M. W. Howell, P. I. Kamali, M. Koren, S. Lawson, D. Maslen, G. Peery, A. Phillippy, A. M. Sharakhova, M. V. Tannier, E. Unger, M. F. Zhang, S. V. Alekseyev, M. A. Besansky, N. J. Chauve, C. Emrich, S. J. Sharakhov, I. V. 2018-10-04 doi:10.1101/434670 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Unsupervised deconvolution of molecular heterogeneity uncovers novel signatures and glia-neuron ratio ]]> https://biorxiv.org/content/10.1101/435677v1?rss=1 Chen, L. Wang, N. Liu, C. Herrington, D. Clarke, R. Zhang, Z. Wang, Y. 2018-10-05 doi:10.1101/435677 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ TIN2 functions with TPP1/POT1 to stimulate telomerase processivity ]]> https://biorxiv.org/content/10.1101/435958v1?rss=1 Pike, A. M. Strong, M. A. Ouyang, J. P. T. Connelly, C. J. Greider, C. W. 2018-10-05 doi:10.1101/435958 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Reporter Ion Data Analysis Reduction (R.I.D.A.R) for isobaric proteomics quantification studies ]]> https://biorxiv.org/content/10.1101/437210v1?rss=1 nView larger version (14K):norg.highwire.dtl.DTLVardef@1bcf00eorg.highwire.dtl.DTLVardef@134510eorg.highwire.dtl.DTLVardef@1b594b4org.highwire.dtl.DTLVardef@35e268_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jenkins, C. Norris, A. O'Neill, M. Das, S. Andresson, T. Orsburn, B. 2018-10-07 doi:10.1101/437210 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Comparative validation of breast cancer risk prediction models and projections for future risk stratification ]]> https://biorxiv.org/content/10.1101/440347v1?rss=1 3% five-year risk). Additional information on MD and a PRS based on 172 variants is expected to increase this to ~3.6 million, and among them, ~155,000 invasive breast cancer cases are expected within five years.nnConclusionsiCARE models based on classical risk factors perform similarly or better than BCRAT or IBIS. Addition of MD and PRS can lead to substantial improvements in risk stratification. Independent prospective validation of integrated models is needed prior to clinical evaluation risk stratified breast cancer screening and prevention. ]]> Pal Choudhury, P. Wilcox, A. Brook, M. Zhang, Y. Ahearn, T. Orr, N. Coulson, P. Schoemaker, M. J. Jones, M. E. Gail, M. H. Swerdlow, A. J. Chatterjee, N. Garcia-Closas, M. 2018-10-19 doi:10.1101/440347 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Biofilm Structures of Borrelia burgdorferi Not Only Display More Tolerance to Lyme Antibiotics But Also Cause More Severe Pathology In a Mouse Arthritis Model: Implications for Understanding Persistence, PTLDS and Treatment ]]> https://biorxiv.org/content/10.1101/440461v1?rss=1 Feng, J. Li, T. Zhang, Y. 2018-10-11 doi:10.1101/440461 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ The Infectious Bronchitis Virus Coronavirus Envelope Protein Alters Golgi pH to Protect Spike Protein and Promote Release of Infectious Virus ]]> https://biorxiv.org/content/10.1101/440628v1?rss=1 Westerbeck, J. W. Machamer, C. E. 2018-10-11 doi:10.1101/440628 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Minimal phenotyping yields GWAS hits of low specificity for major depression ]]> https://biorxiv.org/content/10.1101/440735v1?rss=1 Cai, N. Kendler, K. Flint, J. 2018-10-11 doi:10.1101/440735 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Galectin-1 promotes the invasion of bladder cancer urothelia through their matrix milieu ]]> https://biorxiv.org/content/10.1101/441642v1?rss=1 Balakrishnan, A. Pally, D. Gondkar, K. Naito, S. Sidransky, D. Chatterjee, A. Kumar, P. Bhat, R. 2018-10-12 doi:10.1101/441642 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ Response of extremophile microbiome to a rare rainfall reveals a two-step adaptation mechanism ]]> https://biorxiv.org/content/10.1101/442525v1?rss=1 Uritskiy, G. Getsin, S. Munn, A. Gomez-Silva, B. Davila, A. Glass, B. Taylor, J. DiRuggiero, J. 2018-10-13 doi:10.1101/442525 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ On statistical tests of functional connectome fingerprinting ]]> https://biorxiv.org/content/10.1101/443556v1?rss=1 Wang, Z. Sair, H. Crainiceanu, C. Lindquist, M. Landman, B. A. Resnick, S. Vogelstein, J. T. Caffo, B. S. 2018-10-15 doi:10.1101/443556 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ TADs pair homologous chromosomes to promote interchromosomal gene regulation ]]> https://biorxiv.org/content/10.1101/445627v1?rss=1 Viets, K. Sauria, M. Chernoff, C. Anderson, C. Tran, S. Dove, A. Goyal, R. Voortman, L. Taylor, J. Johnston, R. J. 2018-10-16 doi:10.1101/445627 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ High residual prevalence of vaccine serotype Streptococcus pneumoniae carriage 4 to 6 years after introduction of 13-valent pneumococcal conjugate vaccine in Malawi: a prospective serial cross-sectional study ]]> https://biorxiv.org/content/10.1101/445999v1?rss=1 Swarthout, T. D. Fronterre, C. Lourenco, J. Obolski, U. Gori, A. Bar-Zeev, N. Everett, D. Kamngona, A. W. Mwalukomo, T. S. Mataya, A. A. Mwansambo, C. Banda, M. Gupta, S. Diggle, P. French, N. Heyderman, R. S. 2018-10-26 doi:10.1101/445999 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics ]]> https://biorxiv.org/content/10.1101/446039v1?rss=1 Zhang, H. Zhao, N. Ahearn, T. U. Wheeler, W. Garcia-Closas, M. Chatterjee, N. 2018-10-17 doi:10.1101/446039 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis ]]> https://biorxiv.org/content/10.1101/447367v1?rss=1 Vosa, U. Claringbould, A. Westra, H.-J. Bonder, M. J. Deelen, P. Zeng, B. Kirsten, H. Saha, A. Kreuzhuber, R. Kasela, S. Pervjakova, N. Alvaes, I. Fave, M.-J. Agbessi, M. Christiansen, M. Jansen, R. Seppälä, I. Tong, L. Teumer, A. Schramm, K. Hemani, G. Verlouw, J. Yaghootkar, H. Sönmez, R. Andrew, A. A. Kukushkina, V. Kalnapenkis, A. Rüeger, S. Porcu, E. Kronberg-Guzman, J. Kettunen, J. Powell, J. Lee, B. Zhang, F. Arindrarto, W. Beutner, F. BIOS Consortium, Brugge, H. i2QTL Consortium, Dmitrieva, J. Elansary, M. Fairfax, B. P. Georges, M. He 2018-10-19 doi:10.1101/447367 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Testing the Regulatory Consequences of 1,049 Schizophrenia Associated Variants With a Massively Parallel Reporter Assay ]]> https://biorxiv.org/content/10.1101/447557v1?rss=1 Myint, L. Wang, R. Boukas, L. Hansen, K. D. Goff, L. A. Avramopoulos, D. 2018-10-19 doi:10.1101/447557 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Evaluation of the causal effect of fibrinogen on incident coronary heart disease via Mendelian randomization ]]> https://biorxiv.org/content/10.1101/448381v1?rss=1 Ward-Caviness, C. K. de Vries, P. S. Wiggins, K. L. Huffman, J. E. Yanek, L. R. Bielak, L. F. Giulianini, F. Guo, X. Kleber, M. E. Kacprowski, T. Gross, S. Petersman, A. Davey Smith, G. Hartwig, F. P. Bowden, J. Hemani, G. Muller-Nuraysid, M. Strauch, K. Koenig, W. Waldenberger, M. Meitinger, T. Pankratz, N. Boerwinkle, E. Tang, W. Fu, Y.-P. Johnson, A. D. Song, C. de Maat, M. P. Uitterlinden, A. G. Franco, O. H. Brody, J. A. McKnight, B. Chen, Y.-D. I. Psaty, B. M. Mathias, R. A. Becker, D. M. Peyser, P. A. Smith, J. A. Bielinski, S. J. Ridker, P. M. Ta 2018-10-19 doi:10.1101/448381 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Genome-wide association and functional studies identify 46 novel loci for alcohol consumption and suggest common genetic mechanisms with neuropsychiatric disorders ]]> https://biorxiv.org/content/10.1101/453332v1?rss=1 Evangelou, E. Gao, H. Chu, C. Ntritsos, G. Blakeley, P. Butts, A. R. Pazoki, R. Suzuki, H. Koskeridis, F. Yiorkas, A. M. Karaman, I. Elliott, J. Aeschbacher, S. Bartz, T. M. Baumeister, S. E. Braund, P. S. Brown, M. R. Brody, J. A. Clarke, T.-K. Dimou, N. Faul, J. D. Homuth, G. Jackson, A. U. Kentistou, K. A. Joshi, P. K. Lemaitre, R. N. Lind, P. A. Lyytikainen, L.-P. Mangino, M. Milaneschi, Y. Nelson, C. P. Nolte, I. M. Perala, M.-M. Polasek, O. Porteous, D. Ratliff, S. M. Smith, J. A. Stancakova, A. Teumer, A. Tuominen, S. Theriault, S. Vangipurapu, J 2018-10-30 doi:10.1101/453332 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Activation of SEDS-PBP cell wall synthases by an essential regulator of bacterial division ]]> https://biorxiv.org/content/10.1101/453415v1?rss=1 Lariviere, P. J. Mahone, C. R. Santiago-Collazo, G. Howell, M. Daitch, A. K. Zeinert, R. Chien, P. Brown, P. J. Goley, E. D. 2018-10-25 doi:10.1101/453415 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Association between chronic hepatitis C virus infection and myocardial infarction in people living with HIV in the United States ]]> https://biorxiv.org/content/10.1101/453860v1?rss=1 Williams-Nguyen, J. Hawes, S. E. Nance, R. M. Lindström, S. Heckbert, S. R. Kim, H. N. Mathews, W. C. Cachay, E. R. Budoff, M. J. Hurt, C. B. Hunt, P. W. Geng, E. Moore, R. D. Mugavero, M. J. Peter, I. Kitahata, M. M. Saag, M. S. Crane, H. M. Delaney, J. A. A. 2018-10-26 doi:10.1101/453860 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ NanoMEA: a versatile platform for high-throughput analysis of structure-function relationships in human stem cell-derived excitable cells and tissues ]]> https://biorxiv.org/content/10.1101/453886v1?rss=1 Smith, A. S. T. Choi, E. Gray, K. Macadangdang, J. Ahn, E. H. Clark, E. C. Tyler, P. Laflamme, M. A. Tung, L. Wu, J. C. Murry, C. E. Kim, D.-H. 2018-10-26 doi:10.1101/453886 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Heritability and genetic variance of dementia with Lewy bodies ]]> https://biorxiv.org/content/10.1101/454249v1?rss=1 Guerreiro, R. Escott-Price, V. Hernandez, D. Kun-Rodrigues, C. Ross, O. Orme, T. Neto, J. L. Carmona, S. Dehghani, N. Eicher, J. D. Shepherd, C. Parkkinen, L. Darwent, L. Heckman, M. G. Scholz, S. Troncoso, J. Pletnikova, O. Dawson, T. Rosenthal, L. Ansorge, O. Clarimon, J. Lleo, A. Morenas-Rodriguez, E. Clark, L. Honig, L. Marder, K. Lemstra, A. Rogaeva, E. St. George-Hyslop, P. Londos, E. Zetterberg, H. Barber, I. Braae, A. Brown, K. Morgan, K. Troakes, C. Al-Sarraj, S. Lashley, T. Holton, J. Compta, Y. Van Deerlin, V. Serrano, G. Beach, T. Lesage, 2018-10-26 doi:10.1101/454249 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Validation of a low-cost, carbon dioxide-based cryoablation system for percutaneous tumor ablation ]]> https://biorxiv.org/content/10.1101/454413v1?rss=1 Surtees, B. Young, S. Hu, Y. Wang, G. McChesney, E. Kuroki, G. Acree, P. Thomas, S. Blair, T. Rastogi, S. Kraitchman, D. L. Weiss, C. Sukumar, S. Harvey, S. C. Durr, N. J. 2018-10-26 doi:10.1101/454413 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ fruitless functions downstream of doublesex to promote sexual dimorphism of the gonad stem cell niche ]]> https://biorxiv.org/content/10.1101/454546v1?rss=1 Zhou, H. Whitworth, C. Pozmanter, C. Van Doren, M. 2018-10-26 doi:10.1101/454546 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ JHU-2545 Selectively Shields Salivary Glands and Kidneys during PSMA-Targeted Radiotherapy ]]> https://biorxiv.org/content/10.1101/457085v1?rss=1 Nedelcovych, M. T. Dash, R. P. Wu, Y. Choi, E. Y. Lapidus, R. S. Majer, P. Abou, D. Penet, M.-F. Nikolopoulou, A. Amor-Coarasa, A. Babich, J. Thorek, D. L. Rais, R. Kratochwil, C. Slusher, B. S. 2018-10-30 doi:10.1101/457085 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ SNP2SIM: A modular workflow for standardizing molecular simulation and functional analysis of protein variants ]]> https://biorxiv.org/content/10.1101/457192v1?rss=1 McCoy, M. D. Shivakumar, V. Nimmagadda, S. Jafri, M. S. Madhavan, S. 2018-10-30 doi:10.1101/457192 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Mutations in Rv2983 as a novel determinant of resistance to nitroimidazole drugs in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/457754v1?rss=1 Rifat, D. Li, S.-Y. Ioerger, T. Lanoix, J.-P. Lee, J. Bashiri, G. Sacchettini, J. Nuermberger, E. 2018-10-31 doi:10.1101/457754 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Nanopore native RNA sequencing of a human poly(A) transcriptome ]]> https://biorxiv.org/content/10.1101/459529v1?rss=1 Workman, R. E. Tang, A. Tang, P. S. Jain, M. Tyson, J. R. Zuzarte, P. C. Gilpatrick, T. Razaghi, R. Quick, J. Sadowski, N. Holmes, N. Goes de Jesus, J. Jones, K. Snutch, T. P. Loman, N. J. Paten, B. Loose, M. W. Simpson, J. T. Olsen, H. E. Brooks, A. N. Akeson, M. Timp, W. 2018-11-09 doi:10.1101/459529 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data ]]> https://biorxiv.org/content/10.1101/459693v1?rss=1 Chaguza, C. HEINSBROEK, E. GLADSTONE, R. A. TAFATATHA, T. ALAERTS, M. PENO, C. CORNICK, J. E. MUSICHA, P. BAR-ZEEV, N. KAMNGONA, A. KADIOGLU, A. MCGEE, L. HANAGE, W. P. BREIMAN, R. F. HEYDERMAN, R. S. FRENCH, N. EVERETT, D. B. BENTLEY, S. D. 2018-11-01 doi:10.1101/459693 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ The human claustrum is functionally connected to cognitive networks and involved in cognitive control ]]> https://biorxiv.org/content/10.1101/461319v1?rss=1 Krimmel, S. R. White, M. G. Panicker, M. H. Barrett, F. S. Mathur, B. N. Seminowicz, D. A. 2018-11-03 doi:10.1101/461319 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ Modeling the relative role of human mobility, land-use and climate factors on dengue outbreak emergence in Sri Lanka ]]> https://biorxiv.org/content/10.1101/462150v1?rss=1 Zhang, Y. Riera, J. Ostrow, K. Siddiqui, S. de Silva, H. Sarkar, S. Fernando, L. Gardner, L. 2018-11-09 doi:10.1101/462150 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ DeepTCR: a deep learning framework for revealing structural concepts within TCR Repertoire ]]> https://biorxiv.org/content/10.1101/464107v1?rss=1 Sidhom, J.-W. Larman, H. B. Pardoll, D. M. Baras, A. S. 2018-11-07 doi:10.1101/464107 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Performance Limitations in Sensorimotor Control: Tradeoffs between Neural Computing and Accuracy in Tracking Fast Movements ]]> https://biorxiv.org/content/10.1101/464230v1?rss=1 Saxena, S. Sarma, S. V. Dahleh, M. 2018-11-07 doi:10.1101/464230 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Consensus sequence design as a general strategy to create hyperstable, biologically active proteins ]]> https://biorxiv.org/content/10.1101/466391v1?rss=1 Sternke, M. Tripp, K. W. Barrick, D. 2018-11-08 doi:10.1101/466391 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Tamoxifen improves glucose tolerance in a delivery, sex, and strain-dependent manner in mice ]]> https://biorxiv.org/content/10.1101/467266v1?rss=1 Ceasrine, A. M. Lin, E. E. Lumelsky, D. N. Ruiz-Otero, N. Boehm, E. D. Kuruvilla, R. 2018-11-09 doi:10.1101/467266 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements ]]> https://biorxiv.org/content/10.1101/468181v1?rss=1 Li, S. Cha, S. W. Heffner, K. Hizal, D. B. Bowen, M. Chaerkady, R. Cole, R. Tejwani, V. Kaushik, P. Henry, M. Meleady, P. Sharfstein, S. Betenbaugh, M. Bafna, V. Lewis, N. 2018-11-12 doi:10.1101/468181 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Ischemic Preconditioning and Left Ventricular Dysfunction: A Novel Mechanism & Model for Pulseless Electrical Activity ]]> https://biorxiv.org/content/10.1101/468710v1?rss=1 Patil, K. D. Tunin, R. S. Fink, S. J. Tao, S. Halperin, H. R. 2018-11-12 doi:10.1101/468710 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome ]]> https://biorxiv.org/content/10.1101/469312v1?rss=1 400-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity. ]]> Monachino, E. Jergic, S. Lewis, J. S. Xu, Z.-Q. Lo, A. T. Y. O Shea, V. L. Berger, J. M. Dixon, N. E. van Oijen, A. M. 2018-11-13 doi:10.1101/469312 Cold Spring Harbor Laboratory Press 2018-11-13 <![CDATA[ Chance is an important element in phagolysosomal acidification that favors the macrophage ]]> https://biorxiv.org/content/10.1101/470617v1?rss=1 Dragotakes, Q. Stouffer, K. Fu, M. S. Leon-Rodriguez, C. M. Freij, J. B. Bergman, A. Casadevall, A. 2018-11-15 doi:10.1101/470617 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits ]]> https://biorxiv.org/content/10.1101/471748v1?rss=1 Wheeler, H. E. Ploch, S. Barbeira, A. N. Bonazzola, R. Siahpirani, A. F. Saha, A. Battle, A. Roy, S. Im, H. K. 2018-11-19 doi:10.1101/471748 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Prefix-Free Parsing for Building Big BWTs ]]> https://biorxiv.org/content/10.1101/472399v1?rss=1 Boucher, C. Gagie, T. Kuhnle, A. Langmead, B. Manzini, G. Mun, T. 2018-11-19 doi:10.1101/472399 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]]> https://biorxiv.org/content/10.1101/472423v1?rss=1 Kuhnle, A. Mun, T. Boucher, C. Gagie, T. Langmead, B. Manzini, G. 2018-11-19 doi:10.1101/472423 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage ]]> https://biorxiv.org/content/10.1101/474049v1?rss=1 Venkei, Z. G. Choi, C. P. Feng, S. Jacobsen, S. E. Kim, J. K. Yamashita, Y. M. 2018-11-19 doi:10.1101/474049 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Infection with Persister Forms of Staphylococcus aureus Causes a Chronic Persistent Skin Infection with More Severe Lesion that Takes Longer to Heal and is not Eradicated by the Current Recommended Treatment in Mice ]]> https://biorxiv.org/content/10.1101/476465v1?rss=1 Yee, R. Yuan, Y. Brayton, C. Leal, A. T. Feng, J. Shi, W. Behrens, A. Zhang, Y. 2018-11-23 doi:10.1101/476465 Cold Spring Harbor Laboratory Press 2018-11-23 <![CDATA[ Accurate action potential inference from a calcium sensor protein through biophysical modeling ]]> https://biorxiv.org/content/10.1101/479055v1?rss=1 20 Hz, while requiring less training data. These results demonstrate the utility of quantitative, biophysically grounded models for complex biological data. ]]> Greenberg, D. S. Wallace, D. J. Voit, K.-M. Wuertenberger, S. Czubayko, U. Monsees, A. Handa, T. Vogelstein, J. T. Seifert, R. Groemping, Y. Kerr, J. N. 2018-11-29 doi:10.1101/479055 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains ]]> https://biorxiv.org/content/10.1101/481598v1?rss=1 Luperchio, T. R. Sauria, M. E. G. Hoskins, V. E. Xianrong, W. DeBoy, E. Gaillard, M.-C. Tsang, P. Pekrun, K. Ach, R. A. Yamada, A. Taylor, J. Reddy, K. L. 2018-11-29 doi:10.1101/481598 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Vitamin D status and risk of incident tuberculosis disease: a systematic review and individual participant data meta-analysis ]]> https://biorxiv.org/content/10.1101/481739v1?rss=1 75nmol/L. We estimated the association between vitamin D and incident TB using conditional logistic regression in the Peru cohort and generalized linear mixed models in the meta-analysis. FindingsIn Peru, baseline VDD was associated with a statistically insignificant increase in incident TB (aOR 1{middle dot}70, 95% CI 0{middle dot}84-3{middle dot}46; p=0{middle dot}14). We identified seven studies for the meta-analysis and analyzed 3544 participants. Individuals with VDD and very low vitamin D (<25nmol/L) had increased TB risk (aOR 1{middle dot}48, 95% CI 1{middle dot}04-210;p=0{middle dot} 03 and aOR 2 08, 95% CI 0{middle dot}88-4{middle dot}92; p trend=002 respectively). Among HIV-positive patients, VDD and very low vitamin D conferred a 2-fold (aOR 2.18, 95% CI 1{middle dot} 22-3{middle dot}90; p=0{middle dot} 01) and 4-fold (aOR 4{middle dot}28, 95% CI 0{middle dot}85-21{middle dot}44; p trend=0{middle dot}01) increased risk of TB respectively. InterpretationOur findings suggest vitamin D predicts TB risk in a dose-dependent manner and vitamin D supplementation may play a role in TB prevention. FundingNational Institute of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID), National Institute on Drug Abuse (NIDA), National Institute of Mental Health (NIMH), International Maternal Pediatric Adolescent AIDS Clinical Trials Group (IMPAACT), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Dental and Craniofacial Research (NIDCR), Boehringer-Ingelheim, Bristol-Myers Squibb, Gilead Sciences, GlaxoSmithKline, Foundation, Ujala Foundation, Wyncote Foundation, NIH - Fogarty International Center Program of International Training Grants in Epidemiology Related to AIDS, NIAID Byramjee Jeejeebhoy Medical College HIV Clinical Trials Unit, NIAIDs Baltimore-Washington-India Clinical Trials Unit, National Commission on Biotechnology, the Higher Education Commission, International Research Support Initiative Program of the Higher Education Commission Government of Pakistan, the Bill and Melinda Gates Foundation, and the NIH Fogarty International Center. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSNumerous studies have found lower serum vitamin D levels among patients with active TB disease compared to healthy controls. However, research has not clarified whether low vitamin D increases TB risk or whether TB disease leads to decreased vitamin D levels. We conducted PubMed and Medline searches for all studies available through December 31, 2017 on the association between vitamin D status and TB disease. We included the following keywords: "vitamin D," "vitamin D deficiency," "hypovitaminosis D," "25-hydroxyvitamin D," "1,25-dihydroxyvitamin D," "vitamin D2," "vitamin D3," "ergocalciferol," "cholecalciferol," and "tuberculosis." We found only seven studies had prospectively evaluated the impact of baseline vitamin D levels on risk of progression to TB disease. We report here the results of a case control study nested within a large prospective longitudinal cohort study of household contacts of TB cases and the results of an individual participant data (IPD) metaanalysis of available evidence on the association between vitamin D levels and incident TB disease. Added value of this studyWe demonstrated that low vitamin D levels predicts risk of future progression to TB disease in a dose-dependent manner. Implications of all the available evidenceThese findings suggest the possibility that vitamin D supplementation among individuals at high risk for developing TB disease might play a role in TB prevention efforts. ]]> Aibana, O. Huang, C.-C. Aboud, S. Arnedo-Pena, A. Becerra, M. C. Bellido-Blasco, J. B. Bhosale, R. Calderon, R. Chiang, S. Contreras, C. Fawzi, W. W. Molly, F. F. Galea, J. T. Garcia-Ferrer, D. Gil-Fortuno, M. Gomila-Sard, B. Gupta, A. Gupte, N. Hussain, R. Iborra-Millet, J. Iqbal, N. T. Juan-Cerdan, J. V. Kinikar, A. Lecca, L. Mave, V. Meseguer-Ferrer, N. Montepiedra, G. Mugusi, F. M. Owolabi, O. A. Parsonnet, J. Roach-Poblete, F. Romeu-Garcia, M. A. Spector, S. A. Sudfeld, C. R. Tenforde, M. W. Togun, T. O. Yataco, R. Zhang, Z. Murray, M. B. 2018-11-30 doi:10.1101/481739 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Early Visual Experience Shapes Binocularity in the Mouse Thalamocortical Pathway ]]> https://biorxiv.org/content/10.1101/484774v1?rss=1 Huh, C. Y. L. Abdelaal, K. Salinas, K. J. Gu, D. Zeitoun, J. Figueroa Velez, D. X. Peach, J. P. Fowlkes, C. C. Gandhi, S. P. 2018-12-02 doi:10.1101/484774 Cold Spring Harbor Laboratory Press 2018-12-02 <![CDATA[ C. elegans models of Marfan and Marfan-like Syndromes reveal trafficking defects of the type II TGFβ receptor as a potential novel disease mechanism ]]> https://biorxiv.org/content/10.1101/486381v1?rss=1 Lin, J. Vora, M. Kane, N. S. Gleason, R. J. Padgett, R. W. 2018-12-03 doi:10.1101/486381 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood ]]> https://biorxiv.org/content/10.1101/486498v1?rss=1 0.1, p < 0.01). These genes were significantly enriched for toxic substance response and xenobiotic metabolism functions, and gene sets involved in chromatin regulation and systemic lupus erythematosus were significantly upregulated (FDR q < 0.05). In contrast, 66 genes were differentially-expressed between Non-TD and TD cord blood, including only 8 genes that were also differentially-expressed in ASD.nnConclusionsThis is the first study to identify perinatal gene expression differences in umbilical cord blood specific to ASD. The results of this meta-analysis across two prospective ASD cohorts support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology. ]]> Mordaunt, C. E. Park, B. Y. Bakulski, K. M. Feinberg, J. I. Croen, L. A. Ladd-Acosta, C. Newschaffer, C. J. Volk, H. E. Ozonoff, S. Hertz-Picciotto, I. LaSalle, J. M. Schmidt, R. J. Fallin, D. D. 2018-12-04 doi:10.1101/486498 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Predicting complex genetic phenotypes using error propagation in weighted networks ]]> https://biorxiv.org/content/10.1101/487348v1?rss=1 El-Mhamdi, E.-M. Kucharavy, A. Guerraoui, R. Li, R. 2018-12-21 doi:10.1101/487348 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ The consensus molecular classification of muscle-invasive bladder cancer ]]> https://biorxiv.org/content/10.1101/488460v1?rss=1 Kamoun, A. de Reynies, A. Allory, Y. Sjodahl, G. Robertson, A. G. Seiler, R. Hoadley, K. Al-Ahmadie, H. Choi, W. Groeneveld, C. S. Castro, M. A. A. Fontugne, J. Eriksson, P. Mo, Q. Zlotta, A. Hartmann, A. Dinney, C. P. Bellmunt, J. Powles, T. Malats, N. Chan, K. S. Kim, W. Y. McConkey, D. J. Black, P. C. Dyrskjot, L. Hoglund, M. Lerner, S. P. Real, F. X. Radvanyi, F. The Bladder Cancer Molecular Taxonomy Group, 2018-12-07 doi:10.1101/488460 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud ]]> https://biorxiv.org/content/10.1101/488643v1?rss=1 Moreno, P. Pireddu, L. Roger, P. Goonasekera, N. Afgan, E. van den Beek, M. He, S. Larsson, A. Ruttkies, C. Schober, D. Johnson, D. Rocca-Serra, P. Weber, R. J. M. Gruening, B. Salek, R. Kale, N. Perez-Riverol, Y. Papatheodorou, I. Spjuth, O. Neumann, S. 2018-12-07 doi:10.1101/488643 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Dissociating task acquisition from expression during learning reveals latent knowledge ]]> https://biorxiv.org/content/10.1101/489450v1?rss=1 Kuchibhotla, K. V. Hindmarsh Sten, T. Papadoyannis, E. C. Elnozahy, S. Fogelson, K. Kumar, R. Boubenec, Y. Holland, P. C. Ostojic, S. Froemke, R. C. 2018-12-09 doi:10.1101/489450 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Petrosal morphology and cochlear function in Mesozoic stem therians ]]> https://biorxiv.org/content/10.1101/490367v1?rss=1 Harper, T. Rougier, G. 2018-12-07 doi:10.1101/490367 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ In vivo epigenetic editing of sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene ]]> https://biorxiv.org/content/10.1101/491779v1?rss=1 Peter, C. J. Saito, A. Hasegawa, Y. Tanaka, Y. Perez, G. Alway, E. Espesio-gil, S. Fayyad, T. Ratner, C. Dincer, A. Gupta, A. Devi, L. Pappas, J. G. Lalonde, F. M. Butman, J. A. Han, J. C. Akbarian, S. Kamiya, A. 2018-12-10 doi:10.1101/491779 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ A connectional hub in the rostral anterior cingulate cortex links areas of emotion and cognitive control ]]> https://biorxiv.org/content/10.1101/492157v1?rss=1 Tang, W. Jbabdi, S. Cottaar, M. Zhu, Z. Grisot, G. Yendiki, A. Haber, S. N. 2018-12-10 doi:10.1101/492157 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ The effect of tissue composition on gene co-expression ]]> https://biorxiv.org/content/10.1101/492223v1?rss=1 Zhang, Y. Cuerdo, J. Halushka, M. K. McCall, M. N. 2018-12-10 doi:10.1101/492223 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Diffeomorphic registration with intensity transformation and missing data: Application to 3D digital pathology of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/494005v1?rss=1 Tward, D. J. Brown, T. Kageyama, Y. Patel, J. Hou, Z. Mori, S. Albert, M. Troncoso, J. Miller, M. 2018-12-11 doi:10.1101/494005 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Ultra-Efficient Short Read Sequencing of Immune Receptor Repertoires ]]> https://biorxiv.org/content/10.1101/494062v1?rss=1 Montagne, J. Zheng, X. Pinal-Fernandez, I. Milisenda, J. Christopher-Stine, L. Lloyd, T. Mammen, A. Larman, H. B. 2018-12-13 doi:10.1101/494062 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Distinct ipRGC subpopulations mediate light’s acute and circadian effects on body temperature and sleep ]]> https://biorxiv.org/content/10.1101/496323v1?rss=1 Rupp, A. C. Ren, M. Altimus, C. Fernandez, D. Richardson, M. Turek, F. Hattar, S. Schmidt, T. M. 2018-12-13 doi:10.1101/496323 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ The cortico-striatal circuit regulates sensorimotor gating via Disc1/Huntingtin-mediated Bdnf transport ]]> https://biorxiv.org/content/10.1101/497446v1?rss=1 Jaaro-Peled, H. Kumar, S. Hughes, D. Kim, S.-H. Zoubovsky, S. Hirota-Tsuyada, Y. Zala, D. Sumitomo, A. Bruyere, J. Katz, B. M. Huang, B. Flores, R. Narayan, S. Hou, Z. Economides, A. N. Hikida, T. Wetsel, W. C. Deisseroth, K. Mori, S. Brandon, N. J. Tanaka, M. Ishizuka, K. Houslay, M. D. Saudou, F. Dzirasa, K. Sawa, A. Tomoda, T. 2018-12-14 doi:10.1101/497446 Cold Spring Harbor Laboratory Press 2018-12-14 <![CDATA[ In vitro activity of the new β-lactamase inhibitors relebactam and vaborbactam in combination with β-lactams against Mycobacterium abscessus complex clinical isolates ]]> https://biorxiv.org/content/10.1101/499830v1?rss=1 Kaushik, A. Ammerman, N. C. Lee, J. Martins, O. Kreiswirth, B. N. Lamichhane, G. Parrish, N. M. Nuermberger, E. 2018-12-19 doi:10.1101/499830 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Antibody-mediated immobilization of virions in mucus ]]> https://biorxiv.org/content/10.1101/500538v1?rss=1 Jensen, M. Wang, Y.-Y. Lai, S. Forest, M. G. McKinley, S. A. 2018-12-19 doi:10.1101/500538 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Proteomic Analyses of Morphological Variants of Borrelia burgdorferi Shed New Light on Persistence Mechanisms: Implications for Pathogenesis, Diagnosis and Treatment ]]> https://biorxiv.org/content/10.1101/501080v1?rss=1 Feng, J. Zhang, Y. 2018-12-19 doi:10.1101/501080 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ The mechanism of cross-talk between histone H2B ubiquitination and H3 methylation by Dot1L ]]> https://biorxiv.org/content/10.1101/501098v1?rss=1 Worden, E. J. Hoffmann, N. Hicks, C. Wolberger, C. 2018-12-19 doi:10.1101/501098 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Dashing: Fast and Accurate Genomic Distances with HyperLogLog ]]> https://biorxiv.org/content/10.1101/501726v1?rss=1 Baker, D. N. Langmead, B. 2018-12-20 doi:10.1101/501726 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ ASCOT identifies key regulators of neuronal subtype-specific splicing ]]> https://biorxiv.org/content/10.1101/501882v1?rss=1 Ling, J. P. Wilks, C. Charles, R. Ghosh, D. Jiang, L. Santiago, C. P. Pang, B. Venkataraman, A. Clark, B. S. Nellore, A. Langmead, B. Blackshaw, S. 2018-12-20 doi:10.1101/501882 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ The elasticity of individual protocadherin 15 molecules implicates cadherins as the gating springs for hearing ]]> https://biorxiv.org/content/10.1101/503029v1?rss=1 Bartsch, T. F. Hengel, F. E. Oswald, A. Dionne, G. Chipendo, I. V. Mangat, S. S. El Shatanofy, M. Shapiro, L. Mueller, U. Hudspeth, A. J. 2018-12-20 doi:10.1101/503029 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing ]]> https://biorxiv.org/content/10.1101/504993v1?rss=1 60Gb whole-genome nanopore sequencing data for each of four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231) including repetitive regions inaccessible by short read sequencing. Using the long reads, we find that we can observe phased methylation and chromatin accessibility, large scale pattern changes, and genetic changes such as structural variations from a single assay. ]]> Lee, I. Razaghi, R. Gilpatrick, T. Sadowski, N. Sedlazeck, F. Timp, W. 2018-12-22 doi:10.1101/504993 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API ]]> https://biorxiv.org/content/10.1101/505222v1?rss=1 Desvignes, T. Loher, P. Eilbeck, K. Ma, J. Urgese, G. Fromm, B. Sydes, J. Aparicio-Puerta, E. Barrera, V. Espin, R. Londin, E. Telonis, A. G. Ficarra, E. Friedlander, M. R. Postlethwait, J. H. Rigoutsos, I. Hackenberg, M. Vlachos, I. S. Halushka, M. K. Pantano, L. 2018-12-25 doi:10.1101/505222 Cold Spring Harbor Laboratory Press 2018-12-25 <![CDATA[ Introducing RpsA Point Mutation Δ438A or D123A into the Chromosome of M. tuberculosis Confirms its Role in Causing Resistance to Pyrazinamide ]]> https://biorxiv.org/content/10.1101/505297v1?rss=1 Shi, W. Cui, P. Niu, H. Zhang, S. Tonjum, T. Zhu, B. Zhang, Y. 2019-01-10 doi:10.1101/505297 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Activation of NIX-mediated mitophagy and replication by an interferon regulatory factor homologue of human herpesvirus ]]> https://biorxiv.org/content/10.1101/506113v1?rss=1 Vo, M. T. Smith, B. J. Nicholas, J. Choi, Y. B. 2018-12-25 doi:10.1101/506113 Cold Spring Harbor Laboratory Press 2018-12-25 <![CDATA[ Cloud Bursting Galaxy: Federated Identity and Access Management ]]> https://biorxiv.org/content/10.1101/506238v1?rss=1 Jalili, V. Afgan, E. Taylor, J. Goecks, J. 2018-12-26 doi:10.1101/506238 Cold Spring Harbor Laboratory Press 2018-12-26 <![CDATA[ A Regulatory Loop between the Retinoid-Related Orphan Nuclear Receptor NHR-23 and let-7 family microRNAs Modulates the C. elegans Molting Cycle ]]> https://biorxiv.org/content/10.1101/506261v1?rss=1 Patel, R. Frand, A. R. 2018-12-25 doi:10.1101/506261 Cold Spring Harbor Laboratory Press 2018-12-25 <![CDATA[ Functional dissection of Alzheimer’s disease brain gene expression signatures in humans and mouse models ]]> https://biorxiv.org/content/10.1101/506873v1?rss=1 Wan, Y.-W. Al-Ouran, R. Mangleburg, C. G. Lee, T. V. Allison, K. Neuner, S. Kaczorowski, C. Phillip, V. Howell, G. Martini-Stoica, H. Zheng, H. Kim, J. W. Dawson, V. Dawson, T. Pao, P.-C. Tsai, L.-H. Haure-Mirande, J.-V. Wang, M. Ehrlich, M. E. Mei, H. Zhong, X. Chakrabarty, P. Levites, Y. Golde, T. E. Levey, A. I. Accelerating Medicines Partnership-Alzheimer Disease Consortium, Logsdon, B. Mangravite, L. Liu, Z. Shulman, J. M. 2019-01-03 doi:10.1101/506873 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species ]]> https://biorxiv.org/content/10.1101/508085v1?rss=1 nView larger version (47K):norg.highwire.dtl.DTLVardef@1750006org.highwire.dtl.DTLVardef@548dbdorg.highwire.dtl.DTLVardef@1257cb1org.highwire.dtl.DTLVardef@1d8072_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tan, Y. Cahan, P. 2018-12-31 doi:10.1101/508085 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Identifying Changepoints in Biomarkers During the Preclinical Phase of AD ]]> https://biorxiv.org/content/10.1101/508820v1?rss=1 Younes, L. Albert, M. Moghekar, A. Soldan, A. Pettigrew, C. Miller, M. 2018-12-31 doi:10.1101/508820 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Recruitment and disruption of value encoding during alcohol seeking ]]> https://biorxiv.org/content/10.1101/513911v1?rss=1 Ottenheimer, D. Wang, K. Haimbaugh, A. Janak, P. H. Richard, J. M. 2019-01-07 doi:10.1101/513911 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Perceptions and Prospects in Life Sciences in a Heterogenous Latin American Population ]]> https://biorxiv.org/content/10.1101/514216v1?rss=1 Ferreira, L. M. R. Carosso, G. A. Lopez-Videla, B. Vaca Diez, G. Rivera-Betancourt, L. I. Rodriguez, Y. Ordonez, D. G. Montellano Duran, N. Alatriste-Gonzalez, D. K. Vacaflores, A. Bohorquez, S. Gonzalez Auza, L. Schuetz, C. Alexander-Savino, C. Gandarilla Cuellar, O. Mostajo Radji, M. A. 2019-01-07 doi:10.1101/514216 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Contribution of pretomanid to novel regimens containing bedaquiline with either linezolid or moxifloxacin and pyrazinamide in murine models of tuberculosis ]]> https://biorxiv.org/content/10.1101/514661v1?rss=1 Xu, J. Li, S.-Y. Almeida, D. Tasneen, R. Barnes-Boyle, K. Converse, P. J. M Upton, A. Mdluli, K. Fotouhi, N. Nuermberger, E. 2019-01-08 doi:10.1101/514661 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ Activity of a long-acting injectable bedaquiline formulation in a paucibacillary mouse model of latent tuberculosis infection ]]> https://biorxiv.org/content/10.1101/515692v1?rss=1 Kaushik, A. Ammerman, N. C. TYAGI, S. Saini, V. Vervoort, I. Lachau-Durand, S. Nuermberger, E. Andries, K. 2019-01-09 doi:10.1101/515692 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Highly-accurate long-read sequencing improves variant detection and assembly of a human genome ]]> https://biorxiv.org/content/10.1101/519025v1?rss=1 Wenger, A. M. Peluso, P. Rowell, W. J. Chang, P.-C. Hall, R. J. Concepcion, G. T. Ebler, J. Fungtammasan, A. Kolesnikov, A. Olson, N. D. Toepfer, A. Chin, C.-S. Alonge, M. Mahmoud, M. Qian, Y. Phillippy, A. M. Schatz, M. C. Myers, G. DePristo, M. A. Ruan, J. Marschall, T. Sedlazeck, F. J. Zook, J. M. Li, H. Koren, S. Carroll, A. Rank, D. R. Hunkapiller, M. W. 2019-01-13 doi:10.1101/519025 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery ]]> https://biorxiv.org/content/10.1101/519231v1?rss=1 Zhang, X. A. Yates, A. Vasilevsky, N. Gourdine, J. Carmody, L. C. Danis, D. Joachimiak, M. P. Ravanmehr, V. Pfaff, E. R. Champion, J. Robasky, K. Xu, H. Fecho, K. Walton, N. A. Zhu, R. Ramsdill, J. Mungall, C. Kohler, S. Haendel, M. A. McDonald, C. Vreeman, D. J. Peden, D. B. Chute, C. G. Robinson, P. N. 2019-01-13 doi:10.1101/519231 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Fast and accurate reference-guided scaffolding of draft genomes ]]> https://biorxiv.org/content/10.1101/519637v1?rss=1 Alonge, M. Soyk, S. Ramakrishnan, S. Wang, X. Goodwin, S. Sedlazeck, F. J. Lippman, Z. B. Schatz, M. C. 2019-01-13 doi:10.1101/519637 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Improved state change estimation in dynamic functionalconnectivity using hidden semi-Markov models ]]> https://biorxiv.org/content/10.1101/519868v1?rss=1 Shappell, H. M. Caffo, B. S. Pekar, J. J. Lindquist, M. 2019-01-14 doi:10.1101/519868 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways ]]> https://biorxiv.org/content/10.1101/519967v1?rss=1 Lam, M. Hill, W. D. Trampush, J. W. Yu, J. Knowles, E. Davies, G. Stahl, E. Huckins, L. Liewald, D. C. Djurovic, S. Melle, I. Sundet, K. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Hartmann, A. M. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Attix, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. Avramopoulos, D. Hatzimanolis, A. Arking, D. E. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, 2019-01-20 doi:10.1101/519967 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Select β-lactam combinations exhibit synergy against Mycobacterium abscessus in vitro ]]> https://biorxiv.org/content/10.1101/522649v1?rss=1 Story-Roller, E. Maggioncalda, E. Lamichhane, G. 2019-01-17 doi:10.1101/522649 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit ]]> https://biorxiv.org/content/10.1101/525360v1?rss=1 Razi, A. Davis, J. H. Hao, Y. Jahagirdar, D. Thurlow, B. Basu, K. Jain, N. Gomez-Blanco, J. Britton, R. A. Vargas, J. Guarne, A. Woodson, S. Williamson, J. Ortega, J. 2019-01-20 doi:10.1101/525360 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Platelet-neutrophil aggregates promote skin pathology in psoriasis ]]> https://biorxiv.org/content/10.1101/526236v1?rss=1 Herster, F. Bittner, Z. Codrea, M. C. Archer, N. Heister, M. Loeffler, M. W. Heumos, S. Wegner, J. Businger, R. Schindler, M. Stegner, D. Schaekel, K. Grabbe, S. Ghoreschi, K. Miller, L. Weber, A. N. R. 2019-01-22 doi:10.1101/526236 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ YAP/TAZ as a Novel Regulator of cell volume ]]> https://biorxiv.org/content/10.1101/528133v1?rss=1 Perez Gonzalez, N. A. Rochman, N. D. Yao, K. Tao, J. Tran Le, M.-T. Flanary, S. Sablich, L. Toler, B. Crentsil, E. Takaesu, F. Lambrus, B. Huang, J. Fu, V. Holland, A. An, S. Wirtz, D. Guan, K.-L. Sun, S. 2019-01-23 doi:10.1101/528133 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Tanycyte-independent control of hypothalamic leptin signaling ]]> https://biorxiv.org/content/10.1101/528794v1?rss=1 Yoo, S. Cha, D. Kim, D. W. Hoang, T. Blackshaw, S. 2019-01-23 doi:10.1101/528794 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ The impact of coregistration of gradient recalled echo images on quantitative susceptibility and R2* mapping at 7T ]]> https://biorxiv.org/content/10.1101/529891v1?rss=1 Choi, S. Li, X. Harrison, D. 2019-01-24 doi:10.1101/529891 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Commonly used insect repellents hide human odors from Anopheles mosquitoes ]]> https://biorxiv.org/content/10.1101/530964v1?rss=1 Afify, A. J. Betz, J. F. Riabinina, O. Potter, C. J. 2019-01-25 doi:10.1101/530964 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Cell Type Classification and Unsupervised MorphologicalPhenotype Identification from Low-Res Images with DeepLearning ]]> https://biorxiv.org/content/10.1101/533216v1?rss=1 Yao, K. Rochman, N. Sun, S. 2019-01-29 doi:10.1101/533216 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ The enigmatic role of fungal annexins: the case of Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/536193v1?rss=1 Maryam, M. Fu, M. S. Alanio, A. Camacho, E. Diego, G. Faneuff, E. E. Grossman, N. T. Casadevall, A. Coelho, C. 2019-01-31 doi:10.1101/536193 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Improving Proteinuria Screening with Mailed Smartphone Urinalysis Testing in Previously Unscreened Patients with Hypertension: a Randomized Controlled Trial ]]> https://biorxiv.org/content/10.1101/536995v1?rss=1 Leddy, J. Green, J. Yule, C. Molecavage, J. Coresh, J. Chang, A. R. 2019-02-08 doi:10.1101/536995 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Functional intra-operative guidance of the cavernous nerve network using near-infrared cyanine voltage-sensitive dye imaging: relevance for nerve-sparing radical prostatectomy ]]> https://biorxiv.org/content/10.1101/537274v1?rss=1 Kang, J. Le, H. N. D. Karakus, S. Malla, A. P. Harraz, M. M. Kang, J. U. Burnett, A. L. Boctor, E. M. 2019-02-01 doi:10.1101/537274 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Manganese-induced Parkinsonism in mice is reduced using a novel contaminated water sediment exposure model. ]]> https://biorxiv.org/content/10.1101/541664v1?rss=1 Freeman, D. M. O'Neal, R. Zhang, Q. Bouwer, E. J. Wang, Z. 2019-02-05 doi:10.1101/541664 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ A shared pathway of exosome biogenesis operates at plasma and endosome membranes ]]> https://biorxiv.org/content/10.1101/545228v1?rss=1 5-fold more efficiently than endosome-localized CD63. Furthermore, we show that redirecting CD63 from endosomes to the plasma membrane by mutating its endocytosis signal (CD63/Y235A) increased its exosomal secretion ~6-fold, whereas redirecting CD9 to endosomes by adding an endosome targeting signal (CD9/YEVM) reduced its exosomal secretion ~5-fold. These data demonstrate that the plasma membrane is a major site of exosome biogenesis, and more importantly, that cells possess a common pathway for exosome protein budding that operates at both plasma and endosome membranes. Using a combination of single-particle interferometry reflectance (SPIR) imaging and immunofluorescence (IF) microscopy, we also show that variations in exosome composition are controlled by differential intracellular protein trafficking rather than by separate mechanisms of exosome biogenesis. This new view of exosome biogenesis offers a simple explanation for the pronounced compositional heterogeneity of exosomes and a validated roadmap for exosome engineering. SummaryThis study of exosome cargo protein budding reveals that cells use a common pathway for budding exosomes from plasma and endosome membranes, providing a new mechanistic explanation for exosome heterogeneity and a rational roadmap for exosome engineering. ]]> Gould, S. Fordjour, F. K. Daaboul, G. 2019-02-11 doi:10.1101/545228 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ The Telomerase Reverse Transcriptase (TERT) and p53 Regulate Mammalian PNS and CNS Axon Regeneration downstream of c-Myc ]]> https://biorxiv.org/content/10.1101/547026v1?rss=1 Ma, J.-J. Xu, R.-J. Ju, X. Wang, W.-H. Luo, Z.-P. Liu, C.-M. Yang, L. Li, B. Chen, J.-Q. Meng, B. Yang, H.-L. Zhou, F.-Q. Saijilafu, 2019-02-13 doi:10.1101/547026 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ The Genetic Basis of Transcriptional and Spatial Heterogeneity of Squamous Features in Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/548354v1?rss=1 Hayashi, A. Fan, J. Chen, R. Makohon-Moore, A. P. Zhong, Y. Hong, J. Sakamoto, H. Attiyeh, M. A. Kohutek, Z. A. Zhang, L. Huang, J. Boumiza, A. Kappagantula, R. Baez, P. Wood, L. D. Hruban, R. H. Marta, L. Chadalavada, K. Nanjangud, G. J. Basturk, O. Klimstra, D. S. Overholtzer, M. Iacobuzio-Donahue, C. A. 2019-02-14 doi:10.1101/548354 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma. ]]> https://biorxiv.org/content/10.1101/548818v1?rss=1 Lee, B. Sahoo, A. Marchica, J. Sawada, J. Sahoo, S. Layng, F. I. A. L. Finlay, D. Mazar, J. Joshi, P. Komatsu, M. Vuori, K. Powis, G. de Jong, P. R. Ray, A. Perera, R. J. 2019-02-13 doi:10.1101/548818 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Preferential Binding of Anti-Neutrophil Cytoplasmic Antibodies to an Unexpected Epitope of a Chimeric Proteinase 3 Mutant ]]> https://biorxiv.org/content/10.1101/549063v1?rss=1 Casal Moura, M. Thompson, G. E. Nelson, D. A. Fussner, L. A. Hummel, A. M. Jenne, D. E. Emerling, D. Volkmuth, W. Fervenza, F. C. Kallenberg, C. G. M. Langford, C. A. McCune, J. W. Merkel, P. A. Monach, P. A. Seo, P. Spiera, R. F. St. Clair, E. W. Ytterberg, S. R. Stone, J. H. Robinson, W. H. Pang, Y.-P. Specks, U. 2019-02-14 doi:10.1101/549063 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene ]]> https://biorxiv.org/content/10.1101/549626v1?rss=1 Saferali, A. Yun, J. H. Parker, M. M. Sakornsakolpat, P. Chase, R. P. Lamb, A. Hobbs, B. D. Boezen, M. H. Dai, X. de Jong, K. Beaty, T. H. Wei, W. Zhou, X. Silverman, E. K. Cho, M. H. Castaldi, P. J. Hersh, C. P. COPDGene Investigators, and the International COPD Genetics Consortium Investigators, 2019-02-14 doi:10.1101/549626 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Endogenous and exogenous control of visuospatial selective attention in freely behaving mice ]]> https://biorxiv.org/content/10.1101/550822v1?rss=1 You, W.-K. Mysore, S. P. 2019-02-15 doi:10.1101/550822 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Autonomously replicating linear plasmids facilitate the analysis of replication origin function in Candida albicans ]]> https://biorxiv.org/content/10.1101/551127v1?rss=1 Bijlani, S. Thevandavakkam, M. A. Tsai, H.-J. Berman, J. 2019-02-15 doi:10.1101/551127 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Thermal sensors improve wrist-worn position tracking ]]> https://biorxiv.org/content/10.1101/552174v1?rss=1 Son, J. Clucas, J. White, C. Vogelstein, J. Milham, M. Klein, A. 2019-02-21 doi:10.1101/552174 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Delivering on the Vision of Bench to Bedside: A Rare Disease Funding Community Collaboration to Develop Effective Therapies for Neurofibromatosis Type 1 Tumors ]]> https://biorxiv.org/content/10.1101/552976v1?rss=1 La Rosa, S. Browder, V. Bakker, A. C. Blakeley, J. O. Verma, S. K. Wong, L. M. Morris, J. A. Bora, N. 2019-02-19 doi:10.1101/552976 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population. ]]> https://biorxiv.org/content/10.1101/553214v1?rss=1 Kessler, M. D. Loesch, D. P. Perry, J. A. Heard-Costa, N. L. Cade, B. E. Wang, H. Daya, M. Ziniti, J. Datta, S. Celedon, J. C. Soto-Quiros, M. E. Avila, L. Weiss, S. T. Barnes, K. Redline, S. S. Vasan, R. Johnson, A. D. Mathias, R. A. Hernandez, R. Wilson, J. G. Nickerson, D. A. Abecasis, G. Browning, S. R. Sebastian Zoellner, S. O'Connell, J. R. Mitchell, B. D. O'Connor, T. D. 2019-02-19 doi:10.1101/553214 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Cryptococcus neoformans secretes small molecules that inhibit IL-1β inflammasome-dependent secretion ]]> https://biorxiv.org/content/10.1101/554048v1?rss=1 Bürgel, P. H. Marina, C. L. Saavedra, P. H. V. Albuquerque, P. Holanda, P. H. Castro, R. d. A. Heyman, H. Coelho, C. Cordero, R. J. B. Casadevall, A. Nosanchuk, J. Nakayasu, E. May, R. C. Tavares, A. H. Bocca, A. 2019-02-19 doi:10.1101/554048 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Evaluating Invasive EEG Implantations in Medically Refractory Epilepsy with Functional Scalp EEG Recordings and Structural Imaging Data ]]> https://biorxiv.org/content/10.1101/554667v1?rss=1 Li, A. Palepu, A. Fitzgerald, Z. Hu, K. Costacurta, J. Bulacio, J. Martinez-Gonzalez, J. Sarma, S. 2019-02-19 doi:10.1101/554667 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Discovery of several thousand highly diverse circular DNA viruses ]]> https://biorxiv.org/content/10.1101/555375v1?rss=1 Tisza, M. J. Pastrana, D. V. Welch, N. L. Stewart, B. Peretti, A. Starrett, G. J. Pang, Y.-Y. S. Varsani, A. Krishnamurthy, S. R. Pesavento, P. A. McDermott, D. H. Murphy, P. M. Whited, J. L. Miller, B. Brenchley, J. M. Rosshart, S. P. Rehermann, B. Doorbar, J. Ta'ala, B. A. Pletnikova, O. Troncoso, J. Resnick, S. M. Segall, A. M. Buck, C. B. 2019-02-19 doi:10.1101/555375 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells ]]> https://biorxiv.org/content/10.1101/555540v1?rss=1 Joshi, P. Seki, T. Bergano, A. Marchica, J. Kitamura, S. Perera, R. J. 2019-02-20 doi:10.1101/555540 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Treatment-shortening effect of a novel regimen combining high-dose rifapentine and clofazimine in pathologically distinct mouse models of tuberculosis ]]> https://biorxiv.org/content/10.1101/556654v1?rss=1 Saini, V. Ammerman, N. C. Chang, Y. S. Tasneen, R. Chaisson, R. Jain, S. K. Nuermburger, E. Grosset, J. H. 2019-02-21 doi:10.1101/556654 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter ]]> https://biorxiv.org/content/10.1101/557637v1?rss=1 Woldemeskel, S. A. Alvarez, L. Daitch, A. K. Zeinert, R. Bhargava, A. Gonzalez, D. Collier, J. Chien, P. Cava, F. Goley, E. 2019-02-22 doi:10.1101/557637 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Multi-ancestry analysis of gene-sleep interactions in 126,926 individuals identifies multiple novel blood lipid loci that contribute to our understanding of sleep-associated adverse blood lipid profile ]]> https://biorxiv.org/content/10.1101/559393v1?rss=1 Noordam, R. Bos, M. M. Wang, H. Winkler, T. W. Bentley, A. R. Kilpeläinen, T. de Vries, P. S. Sung, Y. J. Schwander, K. Cabe, B. E. Manning, A. Aschard, H. Brown, M. R. Chen, H. Franceschini, N. Musani, S. K. Richard, M. Vojinovic, D. Aslibekyan, S. Bartz, T. M. de las Fuentes, L. Feitosa, M. Horimoto, A. R. Ilkov, M. Kho, M. Kraja, A. Li, C. Lim, E. Liu, Y. Mook-Kanamori, D. O. Rankinen, T. Tajuddin, S. M. van der Spek, A. Wang, Z. Marten, J. Laville, V. Alver, M. Evangelou, E. Graff, M. E. He, M. Kühnel, B. Lyytikäinen, L.-P. Marques-Vidal, P. No 2019-02-25 doi:10.1101/559393 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Samovar: Single-sample mosaic SNV calling with linked reads ]]> https://biorxiv.org/content/10.1101/560532v1?rss=1 Darby, C. A. Fitch, J. R. Brennan, P. J. Kelly, B. J. Bir, N. Magrini, V. Leonard, J. Cottrell, C. E. Gastier-Foster, J. M. Wilson, R. K. Mardis, E. R. White, P. Langmead, B. Schatz, M. C. 2019-02-25 doi:10.1101/560532 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples ]]> https://biorxiv.org/content/10.1101/560839v1?rss=1 Aganezov, S. Raphael, B. J. 2019-02-25 doi:10.1101/560839 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Recollection and prior knowledge recruit the left angular gyrus during recognition ]]> https://biorxiv.org/content/10.1101/561910v1?rss=1 non-recollected or correctly rejected non-famous faces) and when prior knowledge was accessed in the absence of recollection (i.e., famous > non-famous correct rejections). This pattern was unique to the left AG, and was not present in any other regions of the lateral inferior parietal lobe. Furthermore, the response profile of the left AG was consistent with accounts of recollection strength. Recollection-related activity was greater for faces with longer exposures at encoding than those with shorter exposures and was greater for stimuli with prior knowledge than those without, despite prior knowledge being incidental to the recognition decision. Therefore, the left AG is recruited during the access of both task-specific recollection and general prior knowledge, with greater activity as the amount of retrieved information increases, irrespective of its episodic or semantic nature. Significance StatementThe human angular gyrus (AG) is often implicated in our ability to remember past events. A separate line of research examining our ability to represent general knowledge has also highlighted the AG as a core region of interest. To reconcile these separate views of AG function, we used fMRI to test whether the human left AG was sensitive to remembering details from a specific study episode (i.e., recollection) or more general prior knowledge, within the same participants. Overall, activity in the left AG was sensitive to both recollection and prior knowledge, suggesting any complete functional account of the left AG during retrieval must consider its sensitivity to both kinds of mnemonic representations. ]]> Bellana, B. Ladyka-Wojcik, N. Lahan, S. Moscovitch, M. Grady, C. 2019-02-26 doi:10.1101/561910 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Prototheca zopfii Genotype II induces mitochondrial apoptosis in models of bovine mastitis ]]> https://biorxiv.org/content/10.1101/562983v1?rss=1 Shahid, M. Cobo, E. R. Chen, L. Cavalcante, P. A. Barkema, H. W. Gao, J. Xu, S. Liu, Y. Knight, C. G. Kastelic, J. P. Han, B. 2019-02-27 doi:10.1101/562983 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program ]]> https://biorxiv.org/content/10.1101/563866v1?rss=1 400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency <1% and 46% are singletons. These rare variants provide insights into mutational processes and recent human evolutionary history. The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and extends the reach of nearly all genome-wide association studies to include variants down to ~0.01% in frequency. ]]> Taliun, D. Harris, D. N. Kessler, M. D. Carlson, J. Szpiech, Z. A. Torres, R. Gagliano Taliun, S. A. Corvelo, A. Gogarten, S. M. Min Kang, H. Pitsillides, A. N. LeFaive, J. Lee, S.-b. Tian, X. Browning, B. L. Das, S. Emde, A.-K. Clarke, W. E. Loesch, D. P. Shetty, A. C. Blackwell, T. W. Wong, Q. Aguet, F. Albert, C. Alonso, A. Ardlie, K. G. Aslibekyan, S. Auer, P. L. Barnard, J. Barr, R. G. Becker, L. C. Beer, R. L. Benjamin, E. J. Bielak, L. F. Blangero, J. Boehnke, M. Bowden, D. W. Brody, J. A. Burchard, E. G. Cade, B. E. Casella, J. F. Chalazan, B. L 2019-03-06 doi:10.1101/563866 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Epithelial retinoid acid receptor β regulates serum amyloid A expression and vitamin A-dependent intestinal immunity ]]> https://biorxiv.org/content/10.1101/563908v1?rss=1 Gattu, S. Bang, Y.-J. Pendse, M. Dende, C. Chara, A. L. Harris, T. A. Wang, Y. Ruhn, K. A. Kuang, Z. Sockanathan, S. Hooper, L. V. 2019-03-01 doi:10.1101/563908 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Dengue after Zika: characterizing impacts of Zika emergence on endemic dengue transmission ]]> https://biorxiv.org/content/10.1101/567537v1?rss=1 Borchering, R. K. Huang, A. Mier-y-Teran-Romero, L. Rojas, D. P. P. Rodriguez-Barraquer, I. Katzelnick, L. C. Martinez, S. D. King, G. D. Cinkovich, S. C. Lessler, J. Cummings, D. A. T. 2019-03-08 doi:10.1101/567537 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ GSTM1 copy number is not associated with risk of kidney failure in a large cohort ]]> https://biorxiv.org/content/10.1101/567651v1?rss=1 Zhang, Y. Zafar, W. Hartzel, D. N. Williams, M. S. Tin, A. Chang, A. R. Regeneron Genetics Center, Lee, M. T. M. 2019-03-06 doi:10.1101/567651 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation ]]> https://biorxiv.org/content/10.1101/568527v1?rss=1 Kalesh, K. Lukauskas, S. Borg, A. J. Snijders, A. P. Leung, A. K. L. Haskard, D. O. DiMaggio, P. A. 2019-03-05 doi:10.1101/568527 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Neural basis of approximate number system develops independent of visual experience ]]> https://biorxiv.org/content/10.1101/573436v1?rss=1 Kanjlia, S. Feigenson, L. Bedny, M. 2019-03-11 doi:10.1101/573436 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia ]]> https://biorxiv.org/content/10.1101/574509v1?rss=1 Tam, O. Rozhkov, N. V. Shaw, R. Kim, D. Hubbard, I. Fennessey, S. Propp, N. The NYGC ALS Consortium, Fagegaltier, D. Ostrow, L. W. Phatnani, H. Ravits, J. Dubnau, J. Gale Hammell, M. 2019-03-11 doi:10.1101/574509 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Feature Selection and Dimension Reduction for Single Cell RNA-Seq based on a Multinomial Model ]]> https://biorxiv.org/content/10.1101/574574v1?rss=1 Townes, F. W. Hicks, S. C. Aryee, M. J. Irizarry, R. A. 2019-03-11 doi:10.1101/574574 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Differential effects of two HDAC inhibitors with distinct concomitant DNA hypermethylation or hypomethylation in breast cancer cells ]]> https://biorxiv.org/content/10.1101/578062v1?rss=1 Kalle, A. M. Wang, Z. 2019-03-14 doi:10.1101/578062 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ An open resource of structural variation for medical and population genetics ]]> https://biorxiv.org/content/10.1101/578674v1?rss=1 Collins, R. L. Brand, H. Karczewski, K. J. Zhao, X. Alflödi, J. Khera, A. V. Francioli, L. C. Gauthier, L. D. Wang, H. Watts, N. A. Solomonson, M. O'Donnell-Luria, A. Baumann, A. Munshi, R. Lowther, C. Walker, M. Whelan, C. Huang, Y. Brookings, T. Sharpe, T. Stone, M. R. Valkanas, E. Fu, J. Tiao, G. Laricchia, K. M. Stevens, C. Gupta, N. Margolin, L. The Genome Aggregation Database (gnomAD) Productio, The gnomAD Consortium, Spertus, J. A. Taylor, K. D. Lin, H. J. Rich, S. S. Post, W. Chen, Y.-D. I. Rotter, J. I. Nusbaum, C. Philippakis, A. Lander, E 2019-03-14 doi:10.1101/578674 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ The speed of human social interaction perception ]]> https://biorxiv.org/content/10.1101/579375v1?rss=1 Isik, L. Mynick, A. Pantazis, D. Kanwisher, N. 2019-03-16 doi:10.1101/579375 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Neuronal histone methyltransferase EZH2 regulates neuronal morphogenesis, synaptic plasticity, and cognitive behavior of mice ]]> https://biorxiv.org/content/10.1101/582908v1?rss=1 Zhang, M. Zhang, Y. Xu, Q. Crawford, J. Qian, C. Wang, G.-H. Lewis, E. Hall, P. Dolen, G. Huganir, R. L. Qian, J. Dong, X. Pletnikov, M. V. Liu, C.-M. Zhou, F.-Q. 2019-03-20 doi:10.1101/582908 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Interleukin 17 and senescence regulate the foreign body response ]]> https://biorxiv.org/content/10.1101/583757v1?rss=1 Chung, L. Maestas, D. Lebid, A. Mageau, A. Rosson, G. D. Wu, X. Wolf, M. T. Tam, A. Wang, X. Vanderzee, I. Andorko, J. I. Narain, R. Sadlter, K. Fan, H. Cihakova, D. Jourdan Le Saux, C. Housseau, F. Pardoll, D. Elisseeff, J. 2019-03-20 doi:10.1101/583757 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ The mechanisms of dynamin-actin interaction ]]> https://biorxiv.org/content/10.1101/586461v1?rss=1 Zhang, R. Gerassimov, N. Lee, D. M. Jimah, J. R. Kim, S. Luvsanjav, D. Winkelman, J. Mettlen, M. Abrams, M. E. Kalia, R. Keene, P. Pandey, P. Ravaux, B. Kim, J. H. Ditlev, J. A. Zhang, G. Rosen, M. K. Frost, A. Alto, N. M. Gardel, M. Schmid, S. L. Hinshaw, J. E. Chen, E. H. 2019-03-25 doi:10.1101/586461 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Machine Learning-Assisted Digital PCR and Melt Enables Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test ]]> https://biorxiv.org/content/10.1101/587543v1?rss=1 nView larger version (35K):norg.highwire.dtl.DTLVardef@184e367org.highwire.dtl.DTLVardef@16db02forg.highwire.dtl.DTLVardef@49e48corg.highwire.dtl.DTLVardef@13bb1d6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Athamanolap, P. Hsieh, K. O'Keefe, C. M. Zhang, Y. Yang, S. Wang, J. 2019-03-24 doi:10.1101/587543 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Recovery of trait heritability from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/588020v1?rss=1 Wainschtein, P. Jain, D. P. Yengo, L. Zheng, Z. TOPMed Anthropometry Working Group, Trans-Omics for Precision Medicine Consortium, Cupples, L. A. Shadyab, A. H. McKnight, B. Shoemaker, B. M. Mitchell, B. D. Psaty, B. M. Kooperberg, C. Roden, D. Darbar, D. Arnett, D. K. Regan, E. A. Boerwinkle, E. Rotter, J. I. Allison, M. A. McDonald, M.-L. N. Chung, M. K. Smith, N. L. Ellinor, P. T. Vasan, R. S. Mathias, R. A. Rich, S. S. Heckbert, S. R. Redline, S. Guo, X. Chen, Y.-D. I. Liu, C.-T. Andrade, M. d. Yanek, L. R. Albert, C. M. Hernandez, R. D. McGarvey, S. 2019-03-25 doi:10.1101/588020 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ A sensitive period in the neural phenotype of language in blind individuals ]]> https://biorxiv.org/content/10.1101/592345v1?rss=1 Pant, R. Kanjlia, S. Bedny, M. 2019-03-29 doi:10.1101/592345 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ Emergence and molecular basis of azithromycin resistance in typhoidal Salmonella in Dhaka, Bangladesh ]]> https://biorxiv.org/content/10.1101/594531v1?rss=1 Hooda, Y. Saha, S. Sajib, M. S. I. Rahman, H. Luby, S. P. Bondy-Denomy, J. Santosham, M. Andrews, J. Saha, S. 2019-04-05 doi:10.1101/594531 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Differential expression of glutamate transporters and monoaminergic genes in major depression and suicide. ]]> https://biorxiv.org/content/10.1101/596403v1?rss=1 Powers, B. Kleinman, J. E. Hyde, T. M. Ajilore, O. Leow, A. Sodhi, M. 2019-04-03 doi:10.1101/596403 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Ancestry-specific polygenic scores and SNP heritability of 25(OH)D in African- and European-ancestry populations ]]> https://biorxiv.org/content/10.1101/596619v1?rss=1 Hatchell, K. E. Lu, Q. Hebbring, S. J. Michos, E. D. Wood, A. C. Engelman, C. D. 2019-04-04 doi:10.1101/596619 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ New β-Lactamase Inhibitors Nacubactam and Zidebactam Improve the In Vitro Activity of β-Lactam Antibiotics Against Mycobacterium abscessus Complex Clinical Isolates ]]> https://biorxiv.org/content/10.1101/597765v1?rss=1 Kaushik, A. Ammerman, N. Parrish, N. M. Nuermberger, E. 2019-04-04 doi:10.1101/597765 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Validation of new tools to identify expanded repeats: an intronic pentamer expansion in RFC1 causes CANVAS ]]> https://biorxiv.org/content/10.1101/597781v1?rss=1 Rafehi, H. Szmulewicz, D. Bennett, M. Sobreira, N. Pope, K. Smith, K. Gillies, G. Diakumis, P. Dolzhenko, E. Eberle, M. Barcina, M. G. Breen, D. Chancellor, A. Cremer, P. Delatycki, M. Fogel, B. Hackett, A. Halmagyi, G. M. Kapetanovic, S. Lang, A. Mossman, S. Mu, W. Patrikios, P. Perlman, S. Rosemargy, I. Storey, E. Watson, S. Wilson, M. Zee, D. Valle, D. Amor, D. Bahlo, M. Lockhart, P. J. 2019-04-04 doi:10.1101/597781 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Ensemble modeling of auditory streaming reveals potential sources of bistability across the perceptual hierarchy ]]> https://biorxiv.org/content/10.1101/598631v1?rss=1 Little, D. F. Snyder, J. S. Elhilali, M. F. 2019-04-05 doi:10.1101/598631 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ The full-length transcriptome of C. elegans using direct RNA sequencing ]]> https://biorxiv.org/content/10.1101/598763v1?rss=1 Roach, N. P. Sadowski, N. Alessi, A. F. Timp, W. Taylor, J. Kim, J. K. 2019-04-04 doi:10.1101/598763 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ On the prediction of protein abundance from RNA ]]> https://biorxiv.org/content/10.1101/599373v1?rss=1 Magnusson, R. Rundquist, O. Kim, M. J. Hellberg, S. Na, C. H. benson, m. Gomez-Cabrero, D. Kockum, I. S. Tegner, J. Piehl, F. Jagodic, M. Mellergard, J. Altafini, C. Ernerudh, J. Jenmalm, M. C. Nestor, C. E. Kim, M.-S. Gustafsson, M. 2019-04-04 doi:10.1101/599373 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery ]]> https://biorxiv.org/content/10.1101/599514v1?rss=1 Lee, B. Mahmud, I. Marchica, J. Derezinski, P. Qi, F. Wang, F. Joshi, P. Valerio, F. Rivera, I. Patel, V. Pavlovich, C. P. Garrett, T. Schroth, G. P. Sun, Y. Perera, R. J. 2019-04-04 doi:10.1101/599514 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Cholera in Internally Displaced Persons Camps in Borno State--Nigeria, 2017: A qualitative study of the multi-sectorial emergency response to stop the spread of the outbreak ]]> https://biorxiv.org/content/10.1101/599787v1?rss=1 5000 cases occurred in six local government areas. This qualitative study evaluated perspectives about the emergency response to this outbreak.nnMethods/FindingsWe conducted 39 key informant interviews and focused group discussions, and reviewed 21 documents with participants involved with surveillance, water-sanitation-hygiene, case management, oral cholera vaccine, communications, logistics, and coordination. Qualitative data analysis used thematic techniques comprising key-words-in-context, word-repetition, and key-sector-terms.nnAuthorities were alerted quickly, but outbreak declaration took 12 days due to a 10 day delay waiting for culture confirmation. Outbreak investigation revealed several potential transmission channels, but a leaking latrine around the index cases house was not repaired for >7 days.nnUse of chlorine disinfectant was initially not accepted by the community due to rumors that it would sterilize women. This could have been avoided with improved community consultation. Initially, key messages were communicated in Hausa, although Kanuri was the primary language; later this was corrected. Planning would have benefited using exercise drills to identify weaknesses, and inventory sharing to avoid stock outs.nnThe response by the Rural Water Supply and Sanitation Agency was perceived to be slow and an increased risk from Eid El Jabir festival with increased movement and food sharing was not recognized. Case management was provided at treatment centers, but some partners were concerned that their work was recognized asking, "who gets the glory and the data?"nnOCV was provided to nearly one million people and it distribution benefited from a robust polio vaccine structure; however, logistical problems related to payment of staff needed resolution.nnInitial coordination was thought to be slow, but improved by activating an Emergency Operations Centre. The Borno Ministry of Health used an Incident Management System to coordinate multi-sectoral response activities.nnThese were informed by daily reviews of epi curves and geo-coordinate maps. The synergy between partners and government improved when each recognized the governments leadership role.nnConclusions/SignificanceDespite a timely alert of the outbreak, the delayed declaration led to a slowed initial response, but this improved during the course of the outbreak. OCV distribution was efficient and benefited from the OPV infrastructure. Improvements in laboratory capacity are urgently needed.nnAuthor SummaryIn August 2017, a cholera outbreak started in the Muna Garage Internally Displaced Persons (IPDs) camp in Borno State, Nigeria. By October, it appeared in six local government areas with a total of 5,340 cases reported including 61 deaths. We evaluated the perspectives of the emergency response by the government of Nigeria and implementing partners to stop the outbreak. We conducted 39 interviews and group discussions and also studied 21 documents related to the outbreak response. We found that epidemiologic surveillance timely alerted the health authorities about the outbreak, but the outbreak was declared 12 days later, awaiting for culture confirmation. This led to delays in the initial response. We also observed that conditions in the IDPs camps like overflowing latrines, overcrowding, and open defecation were highly favorable to cholera transmission. Improved IDP camp conditions are needed to prevent cholera and other water born infections and strengthened laboratory capacity is needed to enable a more rapid response. ]]> Ngwa, M. C. Wondimagegnehu, A. Okudo, I. Owili, C. Ugochukwu, U. Peter, C. Devaux, I. Pezzoli, L. Ihekweazu, C. Sack, D. A. 2019-04-06 doi:10.1101/599787 Cold Spring Harbor Laboratory Press 2019-04-06 <![CDATA[ The Dialysis Procedure Triggers Autonomic Imbalance and Cardiac Arrhythmias: Insights from Continuous 14-day ECG Monitoring ]]> https://biorxiv.org/content/10.1101/601542v1?rss=1 Rogovoy, N. M. Howell, S. J. Lee, T. L. Hamilton, C. Perez-Alday, E. A. Kabir, M. M. Li-Pershing, Y. Zhang, Y. Kim, E. D. Fitzpatrick, J. Monroy-Trujillo, J. M. Estrella, M. M. Sozio, S. M. Jaar, B. G. Parekh, R. S. Tereshchenko, L. G. 2019-04-12 doi:10.1101/601542 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ YAP controls cell migration and invasion through a Rho-GTPase switch ]]> https://biorxiv.org/content/10.1101/602052v1?rss=1 Shah, S. R. Tippens, N. D. Park, J. Mohyeldin, A. Wang, S. Vela, G. Martinez-Gutierrez, J. C. Margolis, S. S. Schmidt, S. Xia, S. Levchenko, A. Quinones-Hinojosa, A. 2019-04-08 doi:10.1101/602052 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Basal Contamination of Bulk Sequencing: Lessons from the GTEx dataset ]]> https://biorxiv.org/content/10.1101/602367v1?rss=1 Nieuwenhuis, T. O. Yang, S. Pillalamarri, V. Arking, D. Rosenberg, A. Z. McCall, M. N. Halushka, M. K. 2019-04-08 doi:10.1101/602367 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Evolved resistance to GAPDH inhibition results in loss of the Warburg Effect but retains a different state of glycolysis ]]> https://biorxiv.org/content/10.1101/602557v1?rss=1 Liberti, M. V. Allen, A. E. Ramesh, V. Dai, Z. Singleton, K. R. Guo, Z. Liu, J. O. Wood, K. C. Locasale, J. W. 2019-04-09 doi:10.1101/602557 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations ]]> https://biorxiv.org/content/10.1101/604173v1?rss=1 10Gb+) to generate a median 165X coverage at 10 genomic loci with a median length of 18kb, representing a several hundred-fold improvement over the 2-3X coverage achieved without enrichment. We performed a pilot run on the smaller Flongle flow cell (Capacity ~1Gb), generating a median coverage of 30X at 11 genomic loci with a median length of 18kb. Using panels of guide RNAs, we show that the high coverage data from this method enables us to (1) profile DNA methylation patterns at cancer driver genes, (2) detect structural variations at known hot spots, and (3) survey for the presence of single nucleotide mutations. Together, this provides a low-cost method that can be applied even in low resource settings to directly examine cellular DNA. This technique has extensive clinical applications for assessing medically relevant genes and has the versatility to be a rapid and comprehensive diagnostic tool. We demonstrate applications of this technique by examining the well-characterized GM12878 cell line as well as three breast cell lines (MCF-10A, MCF-7, MDA-MB-231) with varying tumorigenic potential as a model for cancer.nnContributionsTG and WT constructed the study. TG performed the experiments. TG, IL, and FS analyzed the data. TG, JG, ER, RB and AH and developed the method. TG and WT wrote the paper ]]> Gilpatrick, T. Lee, I. Graham, J. E. Raimondeau, E. Bowen, R. Heron, A. Sedlazeck, F. Timp, W. 2019-04-11 doi:10.1101/604173 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ EM-LDDMM for 3D to 2D registration ]]> https://biorxiv.org/content/10.1101/604405v1?rss=1 Tward, D. Miller, M. 2019-04-10 doi:10.1101/604405 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Google searches accurately forecast RSV hospitalizations ]]> https://biorxiv.org/content/10.1101/607119v1?rss=1 0.95) and low phase differences were seen between counts of hospitalizations and search volume in WA, MD, FL, and CT. Searching for RSV began in FL and radiated outward and three distinct transmission clusters were identified: the south and northeast, the northwest and Appalachia, and the center of the country. Calculated initiation dates for prophylaxis closely followed those calculated using traditional data sources (correlation = 0.84).nnConclusionsThis work validates searches as a proxy for RSV hospitalizations. Search query surveillance of RSV is a rapid and no-cost addition to traditional RSV hospitalization surveillance and may be useful for medical and public health decision-making. ]]> Althouse, B. M. Weinberger, D. M. Scarpino, S. V. Pitzer, V. Ayers, J. W. Wenger, E. Fung, I. C.-H. Dredze, M. Hu, H. 2019-04-26 doi:10.1101/607119 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition ]]> https://biorxiv.org/content/10.1101/608380v1?rss=1 Kwon, P. S. Ren, S. Kwon, S.-J. Kizer, M. E. Kuo, L. Zhou, F. Zhang, F. Kim, D. Fraser, K. Kramer, L. D. Seeman, N. C. Dordick, J. S. Linhardt, R. J. Chao, J. Wang, X. 2019-04-13 doi:10.1101/608380 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ TAPAS: A Thresholding Approach for Probability Map Automatic Segmentation in Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/609156v1?rss=1 Valcarcel, A. Muschelli, J. Pham, D. Martin, M. L. Yushkevich, P. Calabresi, P. Bakshi, R. Shinohara, R. 2019-04-22 doi:10.1101/609156 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ Evaluation of mitochondrial DNA copy number estimation techniques ]]> https://biorxiv.org/content/10.1101/610238v1?rss=1 Longchamps, R. J. Castellani, C. A. Newcomb, C. E. Sumpter, J. A. Lane, J. Grove, M. L. Guallar, E. Pankratz, N. Taylor, K. D. Rotter, J. I. Boerwinkle, E. Arking, D. 2019-04-16 doi:10.1101/610238 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Connectal Coding: Discovering the Structures Linking Cognitive Phenotypes to Individual Histories ]]> https://biorxiv.org/content/10.1101/610501v1?rss=1 Vogelstein, J. T. Bridgeford, E. W. Pedigo, B. D. Chung, J. Levin, K. Mensh, B. Priebe, C. E. 2019-04-26 doi:10.1101/610501 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Role of human induced pluripotent stem cell-derived spinal cord astrocytes in the functional maturation of motor neurons in a multielectrode array system ]]> https://biorxiv.org/content/10.1101/614297v1?rss=1 Taga, A. Dastgheyb, R. Habela, C. Joseph, J. Richard, J.-P. Gross, S. K. Lauria, G. Lee, G. Haughey, N. Maragakis, N. J. 2019-04-19 doi:10.1101/614297 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Radiator: a cloud-based framework for deploying reusable bioinformatics tools ]]> https://biorxiv.org/content/10.1101/614594v1?rss=1 Lo, E. K. Schwab, R. M. Burke, Z. Cahan, P. 2019-04-20 doi:10.1101/614594 Cold Spring Harbor Laboratory Press 2019-04-20 <![CDATA[ Toward A Reproducible, Scalable Framework for Processing Large Neuroimaging Datasets ]]> https://biorxiv.org/content/10.1101/615161v1?rss=1 Johnson, E. C. Wilt, M. Rodriguez, L. M. Norman-Tenazas, R. Rivera, C. Drenkow, N. Kleissas, D. LaGrow, T. J. Cowley, H. P. Downs, J. Matelsky, J. Hughes, M. Reilly, E. Wester, B. Dyer, E. Kording, K. Gray-Roncal, W. 2019-04-22 doi:10.1101/615161 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ PanoView: An iterative clustering for single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/616862v1?rss=1 Hu, M.-W. Kim, D. W. Liu, S. Zack, D. Blackshaw, S. Qian, J. 2019-04-23 doi:10.1101/616862 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ De novo Classification of Mouse B Cell Types using Surfaceome Proteotype Maps ]]> https://biorxiv.org/content/10.1101/620344v1?rss=1 van Oostrum, M. Mueller, M. Klein, F. Bruderer, R. Zhang, H. Pedrioli, P. Reiter, L. Tsapogas, P. Rolink, A. Wollscheid, B. 2019-04-26 doi:10.1101/620344 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Genome Sequencing Unveils a New Regulatory Landscape of Platelet Reactivity ]]> https://biorxiv.org/content/10.1101/621565v1?rss=1 Keramati, A. R. Chen, M.-H. Rodriguez, B. A. T. Yanek, L. R. Gaynor, B. J. Ryan, K. Brody, J. NHLBI Trans-Omics for Precision Consortium, NHLBI TOPMed Hematology & Hemostasis Working Group, Kammers, K. Kanchan, K. Iyer, K. Kowalski, M. H. Pitsillides, A. N. Cupples, L. A. Shuldiner, A. R. O'Connell, J. R. Mitchell, B. D. Faraday, N. Taub, M. A. Becker, L. C. Lewis, J. P. Mathias, R. A. Johnson, A. D. 2019-05-16 doi:10.1101/621565 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ A new class of disordered elements controls DNA replication through initiator self-assembly ]]> https://biorxiv.org/content/10.1101/623058v1?rss=1 Parker, M. W. Bell, M. Mir, M. Kao, J. A. Darzacq, X. Botchan, M. R. Berger, J. M. M. 2019-04-29 doi:10.1101/623058 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ A methodology for morphological feature extraction and unsupervised cell classification ]]> https://biorxiv.org/content/10.1101/623793v1?rss=1 Bhaskar, D. Lee, D. Knutsdottir, H. Tan, C. Zhang, M. Dean, P. Roskelley, C. Edelstein-Keshet, L. 2019-04-30 doi:10.1101/623793 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Comparison of vibrotactile and joint-torque feedback in a myoelectric upper-limb prosthesis ]]> https://biorxiv.org/content/10.1101/623926v1?rss=1 Thomas, N. Ung, G. McGarvey, C. Brown, J. 2019-04-30 doi:10.1101/623926 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Deleting a UBE3A substrate rescues impaired hippocampal physiology and learning in Angelman syndrome mice ]]> https://biorxiv.org/content/10.1101/625418v1?rss=1 1-2% of patients with autism spectrum disorders - a further indication of the significant role it plays in brain development. Altered expression of UBE3A, an E3 ubiquitin ligase, is hypothesized to lead to impaired levels of its target proteins, but identifying the contribution of individual UBE3A targets to UBE3A-dependent deficits remains of critical importance. Ephexin5 is a putative UBE3A substrate that has restricted expression early in development, regulates synapse formation during hippocampal development, and is abnormally elevated in AS mice, modeled by maternally-derived Ube3a gene deletion. Here, we report that Ephexin5 is a direct substrate of UBE3A ubiquitin ligase activity. Furthermore, removing Ephexin5 from AS mice specifically rescued hippocampus-dependent behaviors, CA1 physiology, and deficits in dendritic spine number. Our findings identify Ephexin5 as a key driver of hippocampal dysfunction and related behavioral deficits in AS mouse models. These results demonstrate the exciting potential of targeting Ephexin5, and possibly other UBE3A substrates, to improve symptoms of AS and other UBE3A-related developmental disorders. ]]> Sell, G. Xin, W. Cook, E. Zbinden, M. Schaffer, T. OMeally, R. Cole, R. Bonci, A. Margolis, S. 2019-05-02 doi:10.1101/625418 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Knocking out non-muscle myosin II in retinal ganglion cells promotes long-distance optic nerve regeneration ]]> https://biorxiv.org/content/10.1101/625707v1?rss=1 Wang, X.-W. Yang, S.-G. Zhang, C. Ma, J.-J. Zhang, Y. Yang, B.-B. Weng, Y.-L. Ming, G.-L. Anish, K. R. XXX, S. Zhou, F.-Q. 2019-05-02 doi:10.1101/625707 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Screening human embryos for polygenic traits has limited utility ]]> https://biorxiv.org/content/10.1101/626846v1?rss=1 Karavani, E. Zuk, O. Zeevi, D. Atzmon, G. Barzilai, N. Stefanis, N. C. Hatzimanolis, A. Smyrnis, N. Avramopoulos, D. Kruglyak, L. Lam, M. Lencz, T. Carmi, S. 2019-05-05 doi:10.1101/626846 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Bile acid metabolism is altered in multiple sclerosis and supplementation ameliorates neuroinflammation ]]> https://biorxiv.org/content/10.1101/627356v1?rss=1 Bhargava, P. Mische, L. Smith, M. D. Harrington, E. Fitzgerald, K. C. Martin, K. Kim, S. Reyes, A. A. Gonzalez-Cardona, J. Volsko, C. Singh, S. Varanasi, K. Sotirchos, E. S. Nourbakhsh, B. Dutta, R. Mowry, E. M. Waubant, E. Calabresi, P. A. 2019-05-07 doi:10.1101/627356 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Targetable cellular signaling events drive arterial rupture in knock-in mouse models of vascular Ehlers-Danlos Syndrome ]]> https://biorxiv.org/content/10.1101/627653v1?rss=1 Bowen, C. J. Giadrosic, J. F. C. Rykiel, G. Burger, Z. Davis, E. C. Helmers, M. R. Gallo MacFarlane, E. Dietz, H. C. 2019-05-08 doi:10.1101/627653 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Alphavirus nsP3 ADP-ribosylhydrolase Activity Disrupts Stress Granule Formation ]]> https://biorxiv.org/content/10.1101/629881v1?rss=1 Jayabalan, A. K. Griffin, D. E. Leung, A. K. L. 2019-06-20 doi:10.1101/629881 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Protein structure prediction and design in a biologically-realistic implicit membrane ]]> https://biorxiv.org/content/10.1101/630715v1?rss=1 Alford, R. F. Fleming, P. J. Fleming, K. G. Gray, J. J. 2019-05-08 doi:10.1101/630715 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ The evolution of nitroimidazole antibiotic resistance in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/631127v1?rss=1 Lee, B. M. Almeida, D. V. Afriat-Jurnou, L. Aung, H. L. Forde, B. M. Hards, K. Pidot, S. J. Ahmed, F. H. Mohamed, A. E. Taylor, M. C. West, N. P. Stinear, T. P. Greening, C. Beatson, S. A. Cook, G. M. Nuermberger, E. L. Jackson, C. J. 2019-05-08 doi:10.1101/631127 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Determinants of FtsZ C-terminal linker-dependent regulation of cell wall metabolism in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/632075v1?rss=1 Sundararajan, K. Barrows, J. M. Goley, E. D. 2019-05-08 doi:10.1101/632075 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Paragraph: A graph-based structural variant genotyper for short-read sequence data ]]> https://biorxiv.org/content/10.1101/635011v1?rss=1 Chen, S. Krusche, P. Dolzhenko, E. Sherman, R. M. Petrovski, R. Schlesinger, F. Kirsche, M. Bentley, D. R. Schatz, M. S. Sedlazeck, F. J. Eberle, M. A. 2019-05-10 doi:10.1101/635011 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding ]]> https://biorxiv.org/content/10.1101/635045v1?rss=1 Roodgar, M. Babveyh, A. Huong, L. Zhou, W. Sinha, R. Lee, H. Hanks, J. B. Avula, M. Jiang, L. Lee, H. Song, G. Chaib, H. Weissman, I. Batzoglou, S. Holmes, S. Smith, D. G. Mankowski, J. L. Prost, S. Snyder, M. P. 2019-05-11 doi:10.1101/635045 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ Cross-species blastocyst chimerism between nonhuman primates using iPSCs ]]> https://biorxiv.org/content/10.1101/635250v1?rss=1 Roodgar, M. Suchy, F. P. Bajpai, V. K. Bhadury, J. Vilches-Moure, J. G. Oikonomopoulos, A. Wu, J. C. Mankowski, J. L. Loh, K. M. Nakauchi, H. VandeVoort, C. Snyder, M. P. 2019-05-11 doi:10.1101/635250 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ Rational design of a synthetic farnesyl-electrostatic switch based on the hypervariable region of K-Ras4b ]]> https://biorxiv.org/content/10.1101/635839v1?rss=1 Kim, A. K. Inoue, T. 2019-05-15 doi:10.1101/635839 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Reduced Cognitive Performance in Aged Rats Correlates with Increased Excitation/Inhibition Ratio in the Dentate Gyrus in Response to Lateral Entorhinal Input ]]> https://biorxiv.org/content/10.1101/637439v1?rss=1 Tran, T. Bridi, M. Gallagher, M. Kirkwood, A. 2019-05-14 doi:10.1101/637439 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ The Pontine Nuclei are an Integrative Cortico-Cerebellar Link Critical for Dexterity ]]> https://biorxiv.org/content/10.1101/637447v1?rss=1 Guo, J.-Z. Sauerbrei, B. Cohen, J. Mischiati, M. Graves, A. Pisanello, F. Branson, K. Hantman, A. 2019-05-14 doi:10.1101/637447 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Ablation of tanycytes of the arcuate nucleus and median eminence increases visceral adiposity and decreases insulin sensitivity in male mice. ]]> https://biorxiv.org/content/10.1101/637587v1?rss=1 Yoo, S. Cha, D. Kim, S. Jiang, L. Adebesin, M. Wolfe, A. Riddle, R. Aja, S. Blackshaw, S. 2019-05-16 doi:10.1101/637587 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Programmed Switch in The Mitochondrial Degradation Pathways During Human Retinal Ganglion Cell Differentiation from Stem Cells is Critical for RGC Survival ]]> https://biorxiv.org/content/10.1101/638585v1?rss=1 Das, A. Bell, C. M. Berlinicke, C. A. Marsh-Armstrong, N. Zack, D. J. 2019-05-15 doi:10.1101/638585 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia ]]> https://biorxiv.org/content/10.1101/638650v1?rss=1 Fuller, G. G. Han, T. Freeberg, M. A. Moresco, J. J. Yates, J. R. Kim, J. K. 2019-05-17 doi:10.1101/638650 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ An All-to-All Approach to the Identification of Sequence-Specific Readers for Epigenetic DNA Modifications on Cytosine ]]> https://biorxiv.org/content/10.1101/638700v1?rss=1 Song, G. Wang, G. Luo, X. Cheng, Y. Song, Q. Wan, J. Moore, C. Song, H. Jin, P. Qian, J. Zhu, H. 2019-05-16 doi:10.1101/638700 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Antibiotic treatment shapes antigen presentation during chronic TB infection, offering novel targets for therapeutic vaccination ]]> https://biorxiv.org/content/10.1101/638742v1?rss=1 Chuang, Y.-M. Dutta, N. K. Pinn, M. L. Hung, C.-F. Karakousis, P. C. 2019-05-15 doi:10.1101/638742 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ An optimized protocol for iDISCO+ rat brain clearing, imaging, and analysis ]]> https://biorxiv.org/content/10.1101/639674v1?rss=1 Branch, A. Tward, D. Vogelstein, J. T. Wu, Z. Gallagher, M. 2019-05-17 doi:10.1101/639674 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Leader cells in collective chemotaxis: optimality and tradeoffs ]]> https://biorxiv.org/content/10.1101/642157v1?rss=1 Hopkins, A. Camley, B. A. 2019-05-18 doi:10.1101/642157 Cold Spring Harbor Laboratory Press 2019-05-18 <![CDATA[ Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding ]]> https://biorxiv.org/content/10.1101/642223v1?rss=1 Okafor, I. Singh, D. Wang, Y. Jung, M. Wang, H. Mallon, J. Bailey, S. Lee, J. K. Ha, T. 2019-05-20 doi:10.1101/642223 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Single cell RNA-seq in regenerative and fibrotic biomaterial environments defines new macrophage subsets ]]> https://biorxiv.org/content/10.1101/642389v1?rss=1 Sommerfeld, S. D. Cherry, C. Schwab, R. M. Chung, L. Maestas, D. R. Laffont, P. Stein, J. E. Tam, A. Housseau, F. Taube, J. M. Pardoll, D. M. Cahan, P. Elisseeff, J. H. 2019-05-20 doi:10.1101/642389 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Impact of rare and common genetic variants on diabetes diagnosis by hemoglobin A1c in multi-ancestry cohorts: The Trans-Omics for Precision Medicine Program. ]]> https://biorxiv.org/content/10.1101/643932v1?rss=1 Sarnowski, C. Leong, A. Raffield, L. M. Wu, P. de Vries, P. S. DiCorpo, D. Guo, X. Xu, H. Liu, Y. Zheng, X. Hu, Y. Brody, J. A. Goodarzi, M. O. Hidalgo, B. A. Highland, H. M. Jain, D. Liu, C.-T. Naik, R. P. Perry, J. A. Porneala, B. C. Selvin, E. Wessel, J. Psaty, B. M. Curran, J. E. Peralta, J. M. Blangero, J. Kooperberg, C. Mathias, R. Johnson, A. D. Reiner, A. P. Mitchell, B. D. Cupples, L. A. Vasan, R. S. Correa, A. Morrison, A. C. Boerwinkle, E. Rotter, J. I. Rich, S. S. Manning, A. K. Dupuis, J. Meigs, J. B. the TOPMed Diabetes working group, t 2019-05-28 doi:10.1101/643932 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ The structural unit of melanin in the cell wall of the fungal pathogen Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/644484v1?rss=1 Camacho, E. Vij, R. Chrissian, C. Prados-Rosales, R. Gil, D. O'Meally, R. N. Cordero, R. J. Cole, R. N. McCaffery, J. M. Stark, R. E. Casadevall, A. 2019-05-21 doi:10.1101/644484 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Weaker neural suppression in autism ]]> https://biorxiv.org/content/10.1101/645846v1?rss=1 Schallmo, M.-P. Kolodny, T. Kale, A. M. Millin, R. Flevaris, A. V. Edden, R. A. E. Gerdts, J. Bernier, R. A. Murray, S. O. 2019-05-26 doi:10.1101/645846 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ Cancer/Testis Antigens Differentially Expressed In Indolent And Aggressive Prostate Cancer: Potential New Biomarkers And Targets For Immunotherapies ]]> https://biorxiv.org/content/10.1101/646869v1?rss=1 Kagohara, L. Carleton, N. M. Takahashi, S. Shiraishi, T. Mooney, S. M. Vessella, R. L. Getzenberg, R. H. Kulkarni, P. Veltri, R. W. 2019-05-23 doi:10.1101/646869 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ A role for Toxoplasma gondii chloroquine resistance transporter in bradyzoite viability and digestive vacuole maintenance ]]> https://biorxiv.org/content/10.1101/647669v1?rss=1 Kannan, G. Di Cristina, M. Schultz, A. J. Huynh, M.-H. Wang, F. Schultz, T. L. Lunghi, M. Coppens, I. Carruthers, V. B. 2019-05-24 doi:10.1101/647669 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Nanomechanics and co-transcriptional folding of Spinach and Mango ]]> https://biorxiv.org/content/10.1101/650119v1?rss=1 10 pN and refolding occurred at lower forces showing hysteresis. Binding of the cognate fluorogen, TO1, did not significantly alter the mechanical stability of Mangos. In addition to K+, which is needed to stabilize the GQ cores, Mg2+ was needed to obtain full mechanical stability of the aptamers. Co-transcriptional folding analysis using superhelicases showed that co-transcriptional folding reduces misfolding and allows a folding pathway different from refolding. As the fundamental cellular processes like replication, transcription etc. exert pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold. ]]> Mitra, J. Ha, T. 2019-05-24 doi:10.1101/650119 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Modeling binary and graded cone cell fate patterning in the mouse retina ]]> https://biorxiv.org/content/10.1101/650606v1?rss=1 Eldred, K. C. Avelis, C. M. Johnston, R. J. Roberts, E. 2019-05-26 doi:10.1101/650606 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ Castration-mediated IL-8 Promotes Myeloid Infiltration and Prostate Cancer Progression ]]> https://biorxiv.org/content/10.1101/651083v1?rss=1 Lopez-Bujanda, Z. A. Haffner, M. C. Chaimowitz, M. G. Chowdhury, N. Venturini, N. J. Obradovic, A. Hansen, C. S. Jackow, J. Sfanos, K. S. Bieberich, C. J. Hurley, P. J. Selby, M. J. Korman, A. J. Christiano, A. M. De Marzo, A. M. Drake, C. G. 2019-05-27 doi:10.1101/651083 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Streamlining effects of extra telomeric repeat on telomere folding revealed by fluorescence-force spectroscopy ]]> https://biorxiv.org/content/10.1101/651919v1?rss=1 Mitra, J. Ha, T. 2019-05-27 doi:10.1101/651919 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Evaluation of Natural and Botanical Medicines for Activity against Growing and Non-growing Forms of B. burgdorferi ]]> https://biorxiv.org/content/10.1101/652057v1?rss=1 Feng, J. Leone, J. Schweig, S. Zhang, Y. 2019-05-27 doi:10.1101/652057 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Origins, admixture dynamics and homogenization of the African gene pool in the Americas ]]> https://biorxiv.org/content/10.1101/652701v1?rss=1 Gouveia, M. H. Borda, V. Leal, T. P. Moreira, R. G. Bergen, A. W. Aquino, M. M. Araujo, G. S. Araujo, N. M. Kehdy, F. S. G. Liboredo, R. Machado, M. Magalhaes, W. C. S. Michelin, L. A. Rodrigues, M. R. Rodrigues-Soares, F. Sant Anna, H. P. Santolalla, M. L. Scliar, M. O. Soares-Souza, G. Zamudio, R. Zolini, C. Dean, M. Gilman, R. H. Guio, H. Rocha, J. Pereira, A. C. Barreto, M. L. Horta, B. L. Lima-Costa, M. F. Mbulaiteye, S. M. Chanock, S. J. Tishkoff, S. A. Yeager, M. Tarazona-Santos, E. 2019-05-28 doi:10.1101/652701 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Multi-ethnic genome-wide association study of decomposed cardioelectric phenotypes illustrates strategies to identify and characterize evidence of shared genetic effects for complex traits ]]> https://biorxiv.org/content/10.1101/654012v1?rss=1 Baldassari, A. R. Avery, C. L. Highland, H. M. Arking, D. R. Buyske, S. Darbar, D. Gondalia, R. Graff, M. R. Guo, X. R. Heckbert, S. R. Hindorff, L. A. Hodonsky, C. J. Ida Chen, Y.-D. Kaplan, R. C. Peters, U. Post, W. Reiner, A. P. Shohet, R. V. Sotoodehnia, N. Tao, R. Taylor, K. D. Yao, J. D. Kenny, E. D. Lin, H. J. Soliman, E. Z. Whitsel, E. A. North, K. E. Kooperberg, C. Rotters, j. Seyerle, A. A. 2019-05-31 doi:10.1101/654012 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Mitonuclear interactions influence Alzheimer’s disease risk ]]> https://biorxiv.org/content/10.1101/654400v1?rss=1 Andrews, S. J. Fulton-Howard, B. Patterson, C. McFall, G. P. Gross, A. Michaelis, E. K. Goate, A. M. J. Swerdlow, R. H. Pa, J. the Alzheimers Disease Neuroimaging Initiative, 2019-05-31 doi:10.1101/654400 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Brain-synthesized estrogens regulate cortical migration in a sexually divergent manner ]]> https://biorxiv.org/content/10.1101/654731v1?rss=1 Sellers, K. Denley, M. C. Saito, A. Kamiya, A. Srivastava, D. P. 2019-05-31 doi:10.1101/654731 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ IF3 licenses newly made 30S subunits for translation during stress ]]> https://biorxiv.org/content/10.1101/655696v1?rss=1 Sharma, I. M. Woodson, S. A. 2019-05-31 doi:10.1101/655696 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Let-7 miRNAs control auditory sensory progenitor behavior in the vertebrate inner ear ]]> https://biorxiv.org/content/10.1101/655993v1?rss=1 Evsen, L. Zhang, S. Doetzlhofer, A. 2019-05-31 doi:10.1101/655993 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ EpCAM Aptamer siRNA chimeras: Therapeutic efficacy in epithelial cancer cells. ]]> https://biorxiv.org/content/10.1101/656199v1?rss=1 nView larger version (48K):norg.highwire.dtl.DTLVardef@1ce89daorg.highwire.dtl.DTLVardef@bc5daeorg.highwire.dtl.DTLVardef@aa4ceforg.highwire.dtl.DTLVardef@a1159e_HPS_FORMAT_FIGEXP M_FIG C_FIG Illustration showing how EpCAM aptamer-mediated silencing of PLK1 could control the cell cycle progression at multiple number of check points and induce apoptosis involving hyper and hypophosphorylation of variety of signalling molecules ]]> Elchuri, S. V. Balasubramanyam, J. Badrinarayanan, L. Dhaka, B. Gowda, H. Pandey, A. Subramanian, K. Lakshmi, B. S. 2019-06-06 doi:10.1101/656199 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Targeting glutamine metabolism enhances tumor specific immunity by inhibiting the generation of MDSCs and reprogramming tumor associated macrophages ]]> https://biorxiv.org/content/10.1101/656553v1?rss=1 Oh, M.-H. Sun, I.-H. Zhao, L. Leone, R. Sun, I.-M. Xu, W. Collins, S. L. Tam, A. J. Blosser, R. L. Patel, C. H. Englert, J. Arwood, M. L. Wen, J. Chan-Li, Y. Majer, P. Rais, R. Slusher, B. S. Horton, M. R. Powell, J. D. 2019-06-03 doi:10.1101/656553 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Single cell RNA-Seq analysis identifies molecular mechanisms controlling hypothalamic patterning and differentiation. ]]> https://biorxiv.org/content/10.1101/657148v1?rss=1 Kim, D. W. Washington, P. W. Wang, Z. Q. Lin, S. Sun, C. Jiang, L. Blackshaw, S. 2019-06-05 doi:10.1101/657148 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Toward computational design of protein crystals with improved resolution ]]> https://biorxiv.org/content/10.1101/657262v1?rss=1 Jeliazkov, J. R. Robinson, A. C. Garcia-Moreno E., B. Berger, J. M. Gray, J. J. 2019-06-02 doi:10.1101/657262 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Recounting the FANTOM Cage Associated Transcriptome ]]> https://biorxiv.org/content/10.1101/659490v1?rss=1 Imada, E. L. Sanchez, D. F. Collado-Torres, L. Wilks, C. Matam, T. Dinalankara, W. Stupnikov, A. Lobo, F. P. Yip, C.-W. Yasuzawa, K. Kondo, N. Itoh, M. Suzuki, H. Kasukawa, T. Hon, C. C. de Hoon, M. Shin, J. W. Carninci, P. W. Jaffe, A. E. Leek, J. E. Favorov, A. V. Franco, G. R. Langmead, B. R. Marchionni, L. 2019-06-04 doi:10.1101/659490 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Assessing aneuploidy with repetitive element sequencing. ]]> https://biorxiv.org/content/10.1101/660258v1?rss=1 Douville, C. Cohen, J. D. Ptak, J. Popoli, M. Schaefer, J. Silliman, N. Dobbyn, L. Schoen, R. E. Tie, J. Gibbs, P. Goggins, M. Wolfgang, C. L. Wang, T.-L. Shih, I.-M. Karchin, R. Lennon, A. M. Hruban, R. H. Tomasetti, C. Bettegowda, C. Kinzler, K. W. Papadopoulos, N. Vogelstein, B. 2019-06-05 doi:10.1101/660258 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Targeting destabilized DNA G-quadruplexes and aberrant splicing in drug-resistant glioblastoma ]]> https://biorxiv.org/content/10.1101/661660v1?rss=1 Tiek, D. M. Razaghi, R. Jin, L. Sadowski, N. Alamillo-Ferrer, C. Hogg, J. R. Haddad, B. R. Drewry, D. H. Wells, C. I. Pickett, J. E. Zuercher, W. J. Timp, W. Riggins, R. B. 2019-06-05 doi:10.1101/661660 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ A Computational Model of the Underlying Mechanisms of Temporal Coding in the Auditory Cortex ]]> https://biorxiv.org/content/10.1101/661751v1?rss=1 Lee, J. H. Wang, X. Bendor, D. 2019-06-06 doi:10.1101/661751 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ A robust benchmark for germline structural variant detection ]]> https://biorxiv.org/content/10.1101/664623v1?rss=1 98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping. ]]> Zook, J. M. Hansen, N. F. Olson, N. D. Chapman, L. M. Mullikin, J. C. Xiao, C. Sherry, S. Koren, S. Phillippy, A. M. Boutros, P. C. Ebrahim, S. M. Huang, V. Rouette, A. Alexander, N. Mason, C. C. Hajirasouliha, I. C. Ricketts, C. C. Lee, J. Tearle, R. Fiddes, I. T. Barrio, A. M. Wala, J. Carroll, A. Ghaffari, N. C. Rodriguez, O. L. Bashir, A. Jackman, S. Farrell, J. J. Wenger, A. M. Alkan, C. Soylev, A. Schatz, M. C. Garg, S. Church, G. Marschall, T. Chen, K. Fan, X. English, A. C. Rosenfeld, J. D. Zhou, W. Mills, R. E. Sage, J. M. Davis, J. R. Kaiser 2019-06-09 doi:10.1101/664623 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ DNA shape complements sequence-based representations of transcription factor binding sites ]]> https://biorxiv.org/content/10.1101/666735v1?rss=1 DeFord, P. M. Taylor, J. 2019-06-17 doi:10.1101/666735 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ A theoretical model of neural maturation during the spinal cord neurogenesis ]]> https://biorxiv.org/content/10.1101/668640v1?rss=1 Joshi, P. Skromne, I. 2019-06-12 doi:10.1101/668640 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Neural correlates of perceptual switching while listening to bistable auditory streaming stimuli ]]> https://biorxiv.org/content/10.1101/669424v1?rss=1 Higgins, N. C. Little, D. F. Yerkes, B. D. Nave, K. M. Kuruvilla-Mathew, A. Elhilali, M. Snyder, J. S. 2019-06-13 doi:10.1101/669424 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ The Non-random Location of Autosomal Genes that Participate in X Inactivation ]]> https://biorxiv.org/content/10.1101/669929v1?rss=1 Migeon, B. R. 2019-06-14 doi:10.1101/669929 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs ]]> https://biorxiv.org/content/10.1101/669994v1?rss=1 Seifuddin, F. Singh, K. Suresh, A. Chen, Y.-C. Chaitankar, V. Tunc, I. Ruan, X. Li, P. Chen, Y. Cao, H. Lee, R. S. Goes, F. S. Zandi, P. P. Jafri, M. S. Pirooznia, M. 2019-06-13 doi:10.1101/669994 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. ]]> https://biorxiv.org/content/10.1101/671099v1?rss=1 DOrazio, K. N. Wu, C. C.-C. Sinha, N. Loll-Krippleber, R. Brown, G. W. Green, R. 2019-06-14 doi:10.1101/671099 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Functions of ventral visual cortex after bilateral hippocampal loss ]]> https://biorxiv.org/content/10.1101/673228v1?rss=1 Kim, J. G. Gregory, E. Landau, B. McCloskey, M. Turk-Browne, N. B. Kastner, S. 2019-06-18 doi:10.1101/673228 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Mitochondrial DNA Copy Number (mtDNA-CN) Can Influence Mortality and Cardiovascular Disease via Methylation of Nuclear DNA CpGs ]]> https://biorxiv.org/content/10.1101/673293v1?rss=1 Castellani, C. A. Longchamps, R. J. Sumpter, J. A. Newcomb, C. E. Lane, J. A. Grove, M. L. Bressler, J. Brody, J. A. Floyd, J. S. Bartz, T. M. Taylor, K. D. Wang, P. Tin, A. Coresh, J. Pankow, J. S. Fornage, M. Guallar, E. O'Rourke, B. Pankratz, N. Liu, C. Levy, D. Sotoodehnia, N. Boerwinkle, E. Arking, D. E. 2019-06-18 doi:10.1101/673293 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Class of antiretroviral drugs and anemia risk in the current treatment era ]]> https://biorxiv.org/content/10.1101/674549v1?rss=1 Harding, B. N. Whitney, B. M. Nance, R. M. Crane, H. M. Burkholder, G. Moore, R. D. Mathews, W. C. Eron, J. J. Hunt, P. W. Volberding, P. Rodriguez, B. Mayer, K. H. Saag, M. S. Kitahata, M. M. Heckbert, S. R. Delaney, J. A. C. 2019-06-21 doi:10.1101/674549 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Astrocyte subdomains respond independently in vivo ]]> https://biorxiv.org/content/10.1101/675769v1?rss=1 Lopez Hidalgo, M. Kellner, V. Schummers, J. 2019-06-20 doi:10.1101/675769 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Syngap Splice Variants Display Heterogeneous Spatio-Temporal Expression And Subcellular Distribution In The Developing Mammalian Brain ]]> https://biorxiv.org/content/10.1101/681148v1?rss=1 Gou, G. Roca-Fernandez, A. Kilinc, M. Serrano, E. Reig-Viader, R. Araki, Y. Huganir, R. L. de Quintana-Schmidt, C. Rumbaugh, G. Bayes, A. 2019-06-26 doi:10.1101/681148 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ No evidence for motor recovery-related cortical reorganization after stroke using resting-state fMRI ]]> https://biorxiv.org/content/10.1101/681320v1?rss=1 Branscheidt, M. Ejaz, N. Xu, J. Widmer, M. Harran, M. D. Cortes, J. C. Kitago, T. Celnik, P. Hernandez-Castillo, C. Diedrichsen, J. Luft, A. Krakauer, J. W. 2019-06-26 doi:10.1101/681320 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities ]]> https://biorxiv.org/content/10.1101/683367v1?rss=1 Armstrong, N. J. Mather, K. A. Sargurupremraj, M. Knol, M. J. Malik, R. Satizabal, C. L. Yanek, L. R. Wen, W. Gudnason, V. Dueker, N. D. Elliott, L. T. Hofer, E. Jahanshad, N. Li, S. Logue, M. A. Luciano, M. Scholz, M. Smith, A. V. Trompet, S. S. Vojinovic, D. Xia, R. Alfaro-Almagro, F. Ames, D. Amin, N. Amouyel, P. Beiser, A. S. Brodaty, H. Deary, I. J. Fennema-Notestine, C. Gampawar, P. G. Gottesman, R. F. Griffanti, L. Jack, C. R. Jenkinson, M. Jiang, J. Kral, B. G. Kwok, J. B. Lampe, L. Liewald, D. C. Maillard, P. Marchini, J. Bastin, M. E. Mazoyer 2019-06-27 doi:10.1101/683367 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Behavioral training of marmosets and electrophysiological recording from the cerebellum ]]> https://biorxiv.org/content/10.1101/683706v1?rss=1 Sedaghat-Nejad, E. Herzfeld, D. J. Hage, P. Karbasi, K. Palin, T. Wang, X. Shadmehr, R. 2019-06-27 doi:10.1101/683706 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Tel1 activation by the MRX complex is sufficient for telomere length regulation but not for the DNA damage response in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/684522v1?rss=1 Keener, R. Connelly, C. J. Greider, C. W. 2019-06-27 doi:10.1101/684522 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder ]]> https://biorxiv.org/content/10.1101/685586v1?rss=1 Alberry, B. L. Castellani, C. A. Singh, S. M. 2019-06-28 doi:10.1101/685586 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ A Drug Combination Approach Targeting Both Growing Bacteria and Dormant Persisters Eradicate Persistent Staphylococcus aureus Biofilm Infection ]]> https://biorxiv.org/content/10.1101/686097v1?rss=1 Yee, R. Yuan, Y. Tarff, A. Brayton, C. Gour, N. Feng, J. Shi, W. Zhang, Y. 2019-06-28 doi:10.1101/686097 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Ranking of Major Classes of Antibiotics for Activity against Stationary Phase Pseudomonas aeruginosa and Identification of Clinafloxacin + Cefuroxime + Gentamicin Drug Combination that Eradicates Persistent P. aeruginosa Infection in a Murine Cystic Fibrosis Model ]]> https://biorxiv.org/content/10.1101/686105v1?rss=1 Yuan, Y. Yee, R. Gour, N. Dong, X. Feng, J. Shi, W. Zhang, Y. 2019-06-30 doi:10.1101/686105 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ Inhibition of neutral sphingomyelinase-2 facilitates remyelination ]]> https://biorxiv.org/content/10.1101/686287v1?rss=1 Haughey, N. J. Agarwal, A. Smith, M. Khuder, S. Baxi, E. Thomas, A. Rojas, C. Moniruzzman, M. Slusher, B. S. Burgles, D. Calabresi, P. Yoo, S. W. 2019-06-28 doi:10.1101/686287 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Monocarboxylate transporter 1 in Schwann cells is critical for maintenance of sensory nerve myelination during aging ]]> https://biorxiv.org/content/10.1101/686832v1?rss=1 Jha, M. K. Lee, Y. Russell, K. Yang, F. Dastgheyb, R. Deme, P. Ament, X. H. Chen, W. Liu, Y. Guan, Y. Polydefkis, M. J. Hoke, A. Haughey, N. J. Rothstein, J. D. Morrison, B. M. 2019-06-28 doi:10.1101/686832 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Hepatitis E as a cause of adult hospitalization in Bangladesh: Results from an acute jaundice surveillance study in six tertiary hospitals, 2014-2017 ]]> https://biorxiv.org/content/10.1101/688721v1?rss=1 Paul, R. Nazneen, A. Banik, K. C. Sumon, S. A. Paul, K. K. Akram, A. Uzzaman, M. S. Iqbal, T. Tejada-Strop, A. Kamili, S. Luby, S. P. Gidding, H. F. Hayen, A. Gurley, E. S. 2019-07-02 doi:10.1101/688721 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Factors associated with unsuppressed viremia in women living with HIV on lifelong ART in a multi-country cohort study: US-PEPFAR PROMOTE study. ]]> https://biorxiv.org/content/10.1101/688945v1?rss=1 200 copies/ml) among African women on lifelong cART.nnMethodsThis analysis was based on baseline data of the PROMOTE longitudinal cohort study at 8 sites in Uganda, Malawi, Zimbabwe and South Africa. The study enrolled 1987 women living with HIV who initiated lifelong cART at least 1 year previously to assesses long-term safety and effectiveness of cART. Socio-demographic, clinical, and cART adherence data were collected. We used multivariable Poisson regression with robust variance to identify factors associated with unsuppressed viremia.nnResultsAt enrolment, 1947/1987 (98%) women reported taking cART. Of these, HIV-1 remained detectable in 293/1934 (15%), while 216/1934 (11.2%) were considered unsuppressed (>200 copies/ml). The following factors were associated with an increased risk of unsuppressed viremia: not having household electricity (adjusted prevalence rate ratio (aPRR) 1.74, 95% confidence interval (CI) 1.28-2.36, p<0.001); self-reported missed cART doses (aPRR 1.63, 95% CI 1.24-2.13, p<0.001); recent hospitalization (aPRR 2.48, 95% CI 1.28-4.80, p=0.007) and experiencing abnormal vaginal discharge in the last three months (aPRR 1.88; 95% CI 1.16-3.04, p=0.010). Longer time on cART (aPRR 0.75, 95% CI 0.64-0.88, p<0.001) and being older (aPRR 0.77, 95% CI 0.76-0.88, p<0.001) were associated with reduced risk of unsuppressed viremia.nnConclusionSocioeconomic barriers such as poverty, not being married, young age, and self-reported missed doses remain key predictors of unsuppressed viremia. Targeted interventions are needed to improve cART adherence among women living with HIV with this risk factor profile. ]]> Atuhaire, P. Hanley, S. Yende-Zuma, N. Aizire, J. Stranix-Chibanda, L. Makanani, B. Milala, B. Cassim, H. Taha, T. Fowler, M. G. 2019-07-01 doi:10.1101/688945 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Genetic contributions to variation in human stature in prehistoric Europe ]]> https://biorxiv.org/content/10.1101/690545v1?rss=1 Cox, S. L. Ruff, C. B. Maier, R. M. Mathieson, I. 2019-07-02 doi:10.1101/690545 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ A Systems Immunology Approach Identifies Cytokine-Induced STAT Signaling Pathways Critical to Rheumatoid Arthritis Disease Activity and Treatment Response ]]> https://biorxiv.org/content/10.1101/691865v1?rss=1 Bridges, S. L. Ptacek, J. Hawtin, R. E. Sun, D. Louie, B. Evensen, E. Mittleman, B. Cesano, A. Cavet, G. Bingham, C. O. Cofield, S. S. Curtis, J. R. Danila, M. I. Raman, C. Furie, R. Genovese, M. C. Robinson, W. H. Levesque, M. C. Moreland, L. W. Nigrovic, P. A. Shadick, N. A. O'Dell, J. R. Thiele, G. M. Clair, E. W. S. Striebich, C. C. Hale, M. B. Khalili, H. Batliwalla, F. Aranow, C. Mackay, M. Diamond, B. Nolan, G. P. Gregersen, P. K. 2019-07-08 doi:10.1101/691865 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Cross-species Functional Alignment Reveals Evolutionary Hierarchy Within the Connectome ]]> https://biorxiv.org/content/10.1101/692616v1?rss=1 Xu, T. Nenning, K.-H. Schwartz, E. Hong, S.-J. Vogelstein, J. T. Fair, D. A. Schroeder, C. E. Margulies, D. S. Smallwood, J. Milham, M. P. Langs, G. 2019-07-04 doi:10.1101/692616 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Transcriptome assembly from long-read RNA-seq alignments with StringTie2 ]]> https://biorxiv.org/content/10.1101/694554v1?rss=1 Kovaka, S. Zimin, A. V. Pertea, G. M. Razaghi, R. Salzberg, S. L. Pertea, M. 2019-07-08 doi:10.1101/694554 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures ]]> https://biorxiv.org/content/10.1101/699041v1?rss=1 Sherman, T. Gao, T. Fertig, E. 2019-07-11 doi:10.1101/699041 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Aging skeletal muscle proteomics finds changes in spliceosome, immune factors, proteostasis and mitochondria ]]> https://biorxiv.org/content/10.1101/700468v1?rss=1 Ubaida-Mohien, C. Lyashkov, A. Gonzalez-Freire, M. Tharakan, R. Shardell, M. Ruin Moaddel, R. Semba, R. D. Chia, C. W. Gorospe, M. Sen, R. Ferrucci, L. 2019-07-11 doi:10.1101/700468 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping ]]> https://biorxiv.org/content/10.1101/700864v1?rss=1 Ramilowski, J. A. Yip, C. W. Agrawal, S. Chang, J.-C. Ciani, Y. Kulakovskiy, I. V. Mendez, M. Ooi, J. L. C. Petri, A. Roos, L. Severin, J. Yasuzawa, K. Ouyang, J. F. Parkinson, N. Abugessaisa, I. Akalin, A. Antonov, I. Arner, E. Bonetti, A. Bono, H. Borsari, B. Brombacher, F. Cannistraci, C. Cardenas, R. Cardon, M. Chang, H. Dostie, J. Ducoli, L. Favorov, A. Fort, A. Garrido, D. Gil, N. Gimenez, J. Guler, R. Handoko, L. Harshbarger, J. Hasegawa, A. Hasegawa, Y. Hashimoto, K. Hayatsu, N. Heutink, P. Hirose, T. Imada, E. L. Itoh, M. Kaczkowski, B. Kan 2019-07-14 doi:10.1101/700864 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ BRCA1 Mediated Homologous Recombination and S Phase DNA Repair Pathways Restrict LINE-1 Retrotransposition in Human Cells ]]> https://biorxiv.org/content/10.1101/701458v1?rss=1 Sun, X. Mita, P. Kahler, D. J. Li, D. Wudzinska, A. Yun, C. Bader, J. S. Fenyo, D. Boeke, J. D. 2019-07-13 doi:10.1101/701458 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Node-Specific Heritability in the Mouse Connectome ]]> https://biorxiv.org/content/10.1101/701755v1?rss=1 Wang, N. Anderson, R. J. Ashbrook, D. G. Gopalakrishnan, V. Park, Y. Priebe, C. E. Qi, Y. Vogelstein, J. T. Williams, R. W. Johnson, G. A. 2019-07-16 doi:10.1101/701755 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ A Comprehensive Evaluation of Methods for Mendelian Randomization Using Realistic Simulations of Genome-wide Association Studies ]]> https://biorxiv.org/content/10.1101/702787v1?rss=1 Qi, G. Chatterjee, N. 2019-07-15 doi:10.1101/702787 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology ]]> https://biorxiv.org/content/10.1101/702845v1?rss=1 Fu, Y. Yogurtcu, O. N. Kothari, R. Thorkelsdottir, G. Sodt, A. J. Johnson, M. E. 2019-07-15 doi:10.1101/702845 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Identification of essential oils with strong activity against stationary phase uropathogenic Escherichia coli ]]> https://biorxiv.org/content/10.1101/702951v1?rss=1 Xiao, S. Cui, P. Shi, W. Zhang, Y. 2019-07-15 doi:10.1101/702951 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Identification of selection and inhibition components in a go/nogo task from EEG spectra using a machine learning model ]]> https://biorxiv.org/content/10.1101/705525v1?rss=1 DeLaRosa, B. Spence, J. Motes, M. To, W. T. Vanneste, S. Hart, J. Kraut, M. 2019-07-17 doi:10.1101/705525 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ P granules protect RNA interference genes from silencing by piRNAs ]]> https://biorxiv.org/content/10.1101/707562v1?rss=1 Ouyang, J. P. Folkmann, A. Bernard, L. Lee, C.-Y. Seroussi, U. Charlesworth, A. G. Claycomb, J. M. Seydoux, G. 2019-07-18 doi:10.1101/707562 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure. ]]> https://biorxiv.org/content/10.1101/708495v1?rss=1 Karakousis, P. C. Matern, W. M. Bader, J. Jenquin, R. L. 2019-07-19 doi:10.1101/708495 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Intranasal inoculation of Cryptococcus neoformans in mice produces nasal infection with rapid brain dissemination ]]> https://biorxiv.org/content/10.1101/709204v1?rss=1 Coelho, C. Camacho, E. Salas, A. Alanio, A. Casadevall, A. 2019-07-20 doi:10.1101/709204 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Rational Design of a Protein Kinase A Nuclear-cytosol Translocation Reporter ]]> https://biorxiv.org/content/10.1101/709766v1?rss=1 Kim, A. K. Inoue, T. 2019-07-20 doi:10.1101/709766 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Multi-ancestry GWAS of the electrocardiographic PR interval identifies 210 loci underlying cardiac conduction ]]> https://biorxiv.org/content/10.1101/712398v1?rss=1 Ntalla, I. Weng, L.-C. Cartwright, J. H. Hall, A. Sveinbjornsson, G. Tucker, N. R. Seung Young, C. Chaffin, M. D. Roselli, C. Barnes, M. R. Mifsud, B. Warren, H. R. Hayward, C. Marten, J. Cranley, J. J. Concas, M. P. Gasparini, P. Boutin, T. Kolcic, I. Polasek, O. Rudan, I. Araujo, N. M. Lima-Costa, M. F. Ribeiro, A. L. P. Souza, R. P. Tarazona-Santos, E. Giedraitis, V. Ingelsson, E. Mahajan, A. Morris, A. P. Del Greco M., F. Foco, L. Gogele, M. Hicks, A. A. Cook, J. P. Lind, L. Lindgren, C. M. Sundstrom, J. Nelson, C. P. Riaz, M. B. Samani, N. J. Sinag 2019-07-24 doi:10.1101/712398 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Temporal integration of narrative information in a hippocampal amnesic patient ]]> https://biorxiv.org/content/10.1101/713180v1?rss=1 Zuo, X. Honey, C. J. Barense, M. D. Crombie, D. Norman, K. A. Hasson, U. Chen, J. 2019-07-24 doi:10.1101/713180 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Shaky Scaffolding: Age Differences In Cerebellar Activation Revealed Through Activation Likelihood Estimation Meta-Analysis ]]> https://biorxiv.org/content/10.1101/716530v1?rss=1 Bernard, J. Nguyen, A. D. Hausman, H. K. Maldonado, T. Ballard, H. K. Eakin, S. M. Lokshina, Y. Goen, J. R. M. 2019-07-26 doi:10.1101/716530 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Quantitative intravital imaging of Plasmodium falciparum sporozoites: A novel platform to test malaria intervention strategies ]]> https://biorxiv.org/content/10.1101/716878v1?rss=1 Hopp, C. S. Kanatani, S. Archer, N. K. Miller, R. J. Liu, H. Chiou, K. Miller, L. S. Sinnis, P. 2019-07-30 doi:10.1101/716878 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia ]]> https://biorxiv.org/content/10.1101/717876v1?rss=1 Hoang, T. Wang, J. Boyd, P. Wang, F. Santiago, C. Jiang, L. Lahne, M. Todd, L. Saez, C. Yoo, S. Keuthan, C. Palazzo, I. Squires, N. Campbell, W. Jia, M. Rajaii, F. Parayil, T. Wang, G. Ash, J. Fischer, A. Hyde, D. Qian, J. Blackshaw, S. 2019-07-30 doi:10.1101/717876 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Perampanel rescues cortical gamma dysregulation associated with parvalbumin interneuron GluA2 upregulation in epileptic Syngap1+/- mice ]]> https://biorxiv.org/content/10.1101/718965v1?rss=1 Sullivan, B. J. Ammanuel, S. Kipnis, P. A. Araki, Y. Huganir, R. L. Kadam, S. D. 2019-07-30 doi:10.1101/718965 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Delineation of the First Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency ]]> https://biorxiv.org/content/10.1101/719047v1?rss=1 Beck, D. B. Petracovici, A. He, C. Moore, H. W. Louie, R. J. Ansar, M. Douzgou, S. Sithambaram, S. Cottrell, T. Santos-Cortez, R. L. P. Prijoles, E. J. Bend, R. Keren, B. Mignot, C. Nougues, M.-C. Ounap, K. Reimand, T. Pajusalu, S. Zahid, M. Saqib, M. A. N. Buratti, J. Seaby, E. G. McWalter, K. Telegrafi, A. Baldridge, D. Shinawi, M. Leal, S. M. Schaefer, G. B. Stevenson, R. E. Banka, S. Bonasio, R. Fahrner, J. A. 2019-07-31 doi:10.1101/719047 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Divergence: An R Package for Divergence Analysis of Omics Data ]]> https://biorxiv.org/content/10.1101/720391v1?rss=1 Dinalankara, W. Ke, Q. Geman, D. Marchionni, L. 2019-08-13 doi:10.1101/720391 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Organoid-derived Duodenum Intestine-Chip for preclinical drug assessment in a human relevant system ]]> https://biorxiv.org/content/10.1101/723015v1?rss=1 Kasendra, M. Luc, R. Yin, J. Manatakis, D. V. Apostolou, A. Sunuwar, L. Obrigewitch, J. Hamilton, G. A. Donowitz, M. Karalis, K. 2019-08-04 doi:10.1101/723015 Cold Spring Harbor Laboratory Press 2019-08-04 <![CDATA[ Single-cell RNA-seq highlights heterogeneity in human primary Wharton’s Jelly mesenchymal stem/stromal cells cultured in vitro ]]> https://biorxiv.org/content/10.1101/723130v1?rss=1 Sun, C. Wang, L. Wang, H. Huang, T. Zhang, X. 2019-08-02 doi:10.1101/723130 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers ]]> https://biorxiv.org/content/10.1101/723825v1?rss=1 Zhang, Y. Wilcox, A. N. Zhang, H. Choudhury, P. P. Easton, D. F. Milne, R. L. Simard, J. Hall, P. Michailidou, K. Dennis, J. Schmidt, M. K. Chang-Claude, J. Gharahkhani, P. Whiteman, D. Campbell, P. T. Hoffmeister, M. Jenkins, M. Peters, U. Hsu, L. Gruber, S. B. Casey, G. Schmit, S. L. O'Mara, T. A. Spurdle, A. B. Thompson, D. J. Tomlinson, I. Vivo, I. D. Landi, M. T. Law, M. H. Iles, M. M. Demenais, F. Kumar, R. MacGregor, S. Bishop, D. T. Ward, S. V. Bondy, M. L. Houlston, R. Wiencke, J. K. Melin, B. Barnholtz-Sloan, J. Kinnersley, B. Wrensch, M. R. 2019-08-09 doi:10.1101/723825 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ NF-κB signaling regulates the formation of proliferating Muller glia-derived progenitor cells in the avian retina. ]]> https://biorxiv.org/content/10.1101/724260v1?rss=1 Palazzo, I. Deistler, K. Hoang, T. V. Blackshaw, S. Fischer, A. J. 2019-08-02 doi:10.1101/724260 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ It takes two vanilloid ligand bindings per channel to transduce painful capsaicin stimuli ]]> https://biorxiv.org/content/10.1101/725598v1?rss=1 Liu, T.-Y. Chu, Y. Mei, H.-R. Chang, D. S. Chuang, H.-h. 2019-08-12 doi:10.1101/725598 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Cytochrome P450 26b1-mediated specification of vestibular striola and central zones is required for transient responses in linear acceleration ]]> https://biorxiv.org/content/10.1101/726232v1?rss=1 Ono, K. Keller, J. Ramirez, O. L. Garrido, A. G. Zobeiri, O. Chang, V. Vijayakumar, S. Ayiotis, A. Duester, G. Santina, C. C. D. Jones, S. M. Cullen, K. Eatock, R. A. Wu, D. K. 2019-08-06 doi:10.1101/726232 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering ]]> https://biorxiv.org/content/10.1101/726547v1?rss=1 Sharma, G. Colantuoni, C. Goff, L. A. Stein-O'Brien, G. L. Fertig, E. 2019-08-06 doi:10.1101/726547 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Trans-epithelial Fluid Pumping Performance of Renal Epithelial Cells and Mechanics of Cystic Expansion ]]> https://biorxiv.org/content/10.1101/727313v1?rss=1 Choudhury, M. I. Li, Y. Mistriotis, P. Dixon, E. E. Yang, J. Maity, D. Walker, R. Benson, M. Martin, L. Koroma, F. Qian, F. Konstantopoulos, K. Woodward, O. M. Sun, S. X. 2019-08-06 doi:10.1101/727313 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Identification of essential oils with activity against stationary phase Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/727883v1?rss=1 Xiao, S. Cui, P. Shi, W. Zhang, Y. 2019-08-07 doi:10.1101/727883 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Integrated single cell and bulk multi-omics reveals heterogeneity and early changes in pathways associated with cetuximab resistance in HNSCC sensitive cell lines ]]> https://biorxiv.org/content/10.1101/729384v1?rss=1 Kagohara, L. T. Zamuner, F. Considine, M. Allen, J. Yegnasubramanian, S. Gaykalova, D. A. Fertig, E. J. 2019-08-08 doi:10.1101/729384 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Post-EMT: Cadherin-11 mediates cancer hijacking fibroblasts ]]> https://biorxiv.org/content/10.1101/729491v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@11317f1org.highwire.dtl.DTLVardef@88fffaorg.highwire.dtl.DTLVardef@5da692org.highwire.dtl.DTLVardef@62f6ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kang, W. Fan, Y. Du, Y. Tonkova, E. A. Hsu, Y.-H. Tan, K. V. Alexander, S. Wong, B. S. Yang, H. Luo, J. Yao, K. Yang, J. Hu, X. Liu, T. Gan, Y. Zhang, J. Zhao, J. J. Konstantopoulos, K. Friedl, P. Khong, P. L. Lu, A. Hung, M.-C. Brenner, M. B. Segall, J. E. Gu, Z. 2019-08-09 doi:10.1101/729491 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ The gastrointestinal development ‘parts list’: transcript profiling of embryonic gut development in wildtype and Ret-deficient mice ]]> https://biorxiv.org/content/10.1101/730010v1?rss=1 Chatterjee, S. Nandakumar, P. Auer, D. Gabriel, S. B. Chakravarti, A. 2019-08-08 doi:10.1101/730010 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells ]]> https://biorxiv.org/content/10.1101/730358v1?rss=1 Hardison, R. C. Zhang, Y. Keller, C. A. Xiang, G. Heuston, E. An, L. C. Lichtenberg, J. Giardine, B. M. Bodine, D. Mahony, S. Li, Q. Yue, F. Weiss, M. J. Blobel, G. A. Taylor, J. Hughes, J. Higgs, D. R. Gottgens, B. 2019-08-26 doi:10.1101/730358 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ DNA methylation change in neurotrophic genes with aging and delirium evidenced from three independent cohorts ]]> https://biorxiv.org/content/10.1101/730382v1?rss=1 Saito, T. Braun, P. R. Daniel, S. Jellison, S. S. Hellman, M. Shinozaki, E. Lee, S. Cho, H. R. Yoshino, A. Toda, H. Shinozaki, G. 2019-08-08 doi:10.1101/730382 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify candidate risk genes and biological pathways ]]> https://biorxiv.org/content/10.1101/730952v1?rss=1 Fernandez, T. V. Williams, Z. P. Kline, T. Rajendran, S. Augustine, F. Wright, N. Sullivan, C. A. W. Olfson, E. Abdallah, S. B. Liu, W. Hoffman, E. J. Gupta, A. R. Singer, H. S. 2019-08-13 doi:10.1101/730952 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis ]]> https://biorxiv.org/content/10.1101/731729v1?rss=1 Xiang, G. Keller, C. A. Heuston, E. F. Giardine, B. M. An, L. Wixom, A. Q. Miller, A. Cockburn, A. Lichtenberg, J. Gottgens, B. Li, Q. Bodine, D. Mahony, S. Taylor, J. Blobel, G. A. Weiss, M. J. Cheng, Y. Yue, F. Hughes, J. Higgs, D. R. Zhang, Y. Hardison, R. C. 2019-08-10 doi:10.1101/731729 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Loss of tissue non-specific alkaline phosphatase (TNAP) enzyme activity in cerebral microvessels is coupled to persistent neuroinflammation and behavioral deficits in late sepsis ]]> https://biorxiv.org/content/10.1101/732008v1?rss=1 Nwafor, D. C. Chakraborty, S. Brichacek, A. L. Jun, S. Gambill, C. A. Wang, W. Engler-Chiurazzi, E. B. Dakhlallah, D. A. Benkovic, S. A. Brown, C. M. 2019-08-12 doi:10.1101/732008 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling ]]> https://biorxiv.org/content/10.1101/732024v1?rss=1 Lex, R. K. Ji, Z. Falkenstein, K. N. Zhou, W. Henry, J. L. Ji, H. Vokes, S. A. 2019-08-11 doi:10.1101/732024 Cold Spring Harbor Laboratory Press 2019-08-11 <![CDATA[ Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins ]]> https://biorxiv.org/content/10.1101/732057v1?rss=1 Lee, C.-Y. S. Putnam, A. Lu, T. He, S. Ouyang, J. P. T. Seydoux, G. 2019-08-11 doi:10.1101/732057 Cold Spring Harbor Laboratory Press 2019-08-11 <![CDATA[ Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality ]]> https://biorxiv.org/content/10.1101/732552v1?rss=1 Levitan, A. Gale, A. N. Dalton, E. K. Kozan, D. W. Cunningham, K. W. Sharan, R. Berman, J. 2019-08-12 doi:10.1101/732552 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ The Secretomes of Painful Versus Nonpainful Human Schwannomatosis Tumor Cells Differentially Influence Sensory Neuron Gene Expression and Sensitivity ]]> https://biorxiv.org/content/10.1101/734699v1?rss=1 Ostrow, K. L. Donaldson, K. J. Caterina, M. J. Belzberg, A. Hoke, A. 2019-08-15 doi:10.1101/734699 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Telomere-to-telomere assembly of a complete human X chromosome ]]> https://biorxiv.org/content/10.1101/735928v1?rss=1 Miga, K. H. Koren, S. Rhie, A. Vollger, M. R. Gershman, A. Bzikadze, A. Brooks, S. Howe, E. Porubsky, D. Logsdon, G. A. Schneider, V. A. Potapova, T. Wood, J. Chow, W. Armstrong, J. Fredrickson, J. Pak, E. Tigyi, K. Kremitzki, M. Markovic, C. Maduro, V. Dutra, A. Bouffard, G. G. Chang, A. M. Hansen, N. F. Thibaud-Nissen, F. Schmitt, A. D. Belton, J.-M. Selvaraj, S. Dennis, M. Y. Soto, D. C. Sahasrabudhe, R. Kaya, G. Quick, J. Loman, N. J. Holmes, N. Loose, M. Surti, U. Risques, R. a. Lindsay, T. A. G. Fulton, R. Hall, I. Paten, B. Howe, K. Timp, W. 2019-08-16 doi:10.1101/735928 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Catecholaminergic axons in the neocortex of adult mice regrow following brain injury ]]> https://biorxiv.org/content/10.1101/737072v1?rss=1 Dougherty, S. E. Kajstura, T. J. Jin, Y. Chan-Cortes, M. H. Kota, A. Linden, D. 2019-08-15 doi:10.1101/737072 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ The paltry power of priors versus populations ]]> https://biorxiv.org/content/10.1101/737676v1?rss=1 Zhan, J. Arking, D. Bader, J. S. 2019-08-16 doi:10.1101/737676 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Genetic modifiers of risk and age at onset in GBA associated Parkinson disease and Lewy body dementia ]]> https://biorxiv.org/content/10.1101/738351v1?rss=1 10-fold. An outstanding question in the field is what other genetic factors that influence GBA-associated risk for disease, and whether these overlap with known PD risk variants.nnUsing multiple, large case-control datasets, totalling 217,165 individuals (22,757 PD cases, 13,431 PD proxy cases, 622 LBD cases and 180,355 controls), we identified 1,772 PD cases, 711 proxy cases and 7,624 controls with a GBA variant (p.E326K, p.T369M or p.N370S). We performed a genome-wide association study and analysed the most recent PD-associated genetic risk score to detect genetic influences on GBA risk and age at onset. We attempted to replicate our findings in two independent datasets, including the personal genetics company 23andMe, Inc. and whole-genome sequencing data. Our analysis showed that the overall PD genetic risk score modifies risk for disease and decreases age at onset in carriers of GBA variants. Notably, this effect was consistent across all tested GBA risk variants. Dissecting this signal demonstrated that variants in close proximity to SNCA and CTSB (encoding cathepsin B) are the most significant contributors. Risk variants in the CTSB locus were identified to decrease mRNA expression of CTSB. Additional analyses suggest a possible genetic interaction between GBA and CTSB and GBA p.N370S neurons were shown to have decreased Cathepsin B expression compared to controls. These data provide a genetic basis for modification of GBA-associated PD risk and age at onset and demonstrate that variability at genes implicated in lysosomal function exerts the largest effect on GBA associated risk for disease. Further, these results have important implications for selection of GBA carriers for therapeutic interventions. ]]> Blauwendraat, C. Reed, X. Krohn, L. Heilbron, K. Bandres-Ciga, S. Tan, M. Gibbs, J. R. Hernandez, D. G. Kumaran, R. Langston, R. Bonet Ponce, L. Alcalay, R. Hassin-Baer, S. Greenbaum, L. Iwaki, H. Leonard, H. Grenn, F. P. Ruskey, J. A. Sabir, M. Ahmed, S. Makarious, M. B. Pihlstrom, L. Toft, M. van Hilten, J. J. Marinus, J. Schulte, C. Sharma, M. Brockmann, K. Siitonen, A. Majamaa, K. Eerola-Rautio, J. Tienari, P. The 23andMe Research Team, Pantelyat, A. Hillis-Trupe, A. Dawson, T. Rosenthal, L. Albert, M. Resnick, S. M. Ferrucci, L. Morris, C. M. Ple 2019-08-18 doi:10.1101/738351 Cold Spring Harbor Laboratory Press 2019-08-18 <![CDATA[ Prolonged tonic pain in healthy humans disrupts intrinsic brain networks implicated in pain modulation ]]> https://biorxiv.org/content/10.1101/740779v1?rss=1 Meeker, T. J. Schmid, A.-C. Keaser, M. L. Khan, S. Gullapalli, R. P. Dorsey, S. G. Greenspan, J. D. Seminowicz, D. 2019-08-21 doi:10.1101/740779 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Leveraging shared connectivity to aggregate heterogeneous datasets into a common response space ]]> https://biorxiv.org/content/10.1101/741975v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Norman, K. A. Hasson, U. 2019-08-21 doi:10.1101/741975 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21 ]]> https://biorxiv.org/content/10.1101/743526v1?rss=1 Mukhopadhyay, N. Bishop, M. Mortillo, M. Chopra, P. Ketmanski, J. B. Taub, M. A. Moreno, L. M. Valencia-Ramirez, L. C. Restrepo, C. Wehby, G. L. Hecht, J. T. Deleyiannis, F. Butali, A. Weinberg, S. M. Beaty, T. H. Murray, J. C. Leslie, E. J. Feingold, E. Marazita, M. L. 2019-08-22 doi:10.1101/743526 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ LINE-1 ORF2P EXPRESSION IS NEARLY IMPERCEPTIBLE IN HUMAN CANCERS ]]> https://biorxiv.org/content/10.1101/744425v1?rss=1 Ardeljan, D. Wang, X. Oghbaie, M. Taylor, M. S. Husband, D. Deshpande, V. Steranka, J. P. Gorbounov, M. Yang, W. R. Sie, B. Larman, H. B. Jiang, H. Molloy, K. R. Altukhov, I. Li, Z. McKerrow, W. Fenyo, D. Burns, K. H. LaCava, J. 2019-08-22 doi:10.1101/744425 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution ]]> https://biorxiv.org/content/10.1101/744540v1?rss=1 LU, L. Liu, X. Huang, W.-K. Giusti-Rodriguez, P. Cui, J. Zhang, S. Xu, W. Wen, Z. Ma, S. Rosen, J. D. Xu, Z. Bartels, C. Riki Kawaguchi, R. Hu, M. Scacheri, P. Rong, Z. Li, Y. Sullivan, P. F. Song, H. Ming, G.-l. Li, Y. Jin, F. 2019-08-22 doi:10.1101/744540 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Omic-Sig: Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions ]]> https://biorxiv.org/content/10.1101/746123v1?rss=1 Lih, T.-S. M. Clark, D. J. Zhang, H. 2019-09-05 doi:10.1101/746123 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Protein-surfactant-polysaccharide nanoparticles increase the catalytic activity of an engineered β-lactamase maltose-activated switch enzyme ]]> https://biorxiv.org/content/10.1101/746560v1?rss=1 Fuenzalida Werner, J. P. xiong, T. Moerschbacher, B. M. Ostermeier, M. Goycoolea, F. M. 2019-08-24 doi:10.1101/746560 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Spooky interaction at a distance in cave and surface dwelling electric fishes ]]> https://biorxiv.org/content/10.1101/747154v1?rss=1 Fortune, E. Andanar, N. Madhav, M. Jayakumar, R. Cowan, N. J. Bichuette, M. E. Soares, D. 2019-08-29 doi:10.1101/747154 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes ]]> https://biorxiv.org/content/10.1101/747568v1?rss=1 Ranallo-Benavidez, T. R. Jaron, K. S. Schatz, M. C. 2019-08-26 doi:10.1101/747568 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37-45 ]]> https://biorxiv.org/content/10.1101/749317v1?rss=1 Roy Burman, S. S. Nance, M. L. Jeliazkov, J. R. Labonte, J. W. Lubin, J. H. Biswas, N. Gray, J. J. 2019-08-30 doi:10.1101/749317 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ scHLAcount: Allele-specific HLA expression from single-cell gene expression data ]]> https://biorxiv.org/content/10.1101/750612v1?rss=1 Darby, C. A. Stubbington, M. J. T. Marks, P. J. Martinez Barrio, A. Fiddes, I. T. 2019-08-29 doi:10.1101/750612 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Expression of endoplasmic reticulum mannosyl-oligosaccharide α1, 2-mannosidase regulates tumorigenicity of prostate cancer cells ]]> https://biorxiv.org/content/10.1101/750984v1?rss=1 Toonstra, C. Wang, X. Höti, N. Pan, J. Zhang, h. 2019-09-11 doi:10.1101/750984 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Primary cilia deficiency in neural crest cells causes Anterior Segment Dysgenesis ]]> https://biorxiv.org/content/10.1101/752105v1?rss=1 Iomini, C. Portal, C. Lwigale, P. Rompolas, P. 2019-08-30 doi:10.1101/752105 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets ]]> https://biorxiv.org/content/10.1101/752469v1?rss=1 2 patients, with 61.7% of these derived from driver mutations. Our results provide a new method for neoantigen prediction with high performance characteristics and demonstrate its utility in large data sets across human cancers.nnSynopsisWe developed a new in silico predictor of Major Histocompatibility Complex (MHC) ligand binding and demonstrated its utility to assess potential neoantigens and immunogenic missense mutations (IMMs) in 6613 TCGA patients. ]]> Shao, X. M. Bhattacharya, R. Huang, J. Sivakumar, I. K. A. Tokheim, C. Zheng, L. Kaminow, B. Omdahl, A. Bonsack, M. Riemer, A. B. Velculescu, V. Anagnostou, V. Pagel, K. Karchin, R. 2019-08-31 doi:10.1101/752469 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Designing Peptides on a Quantum Computer ]]> https://biorxiv.org/content/10.1101/752485v1?rss=1 Mulligan, V. K. Melo, H. Merritt, H. I. Slocum, S. Weitzner, B. D. Watkins, A. M. Renfrew, P. D. Pelissier, C. Arora, P. S. Bonneau, R. 2019-09-02 doi:10.1101/752485 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts ]]> https://biorxiv.org/content/10.1101/755652v1?rss=1 Tesina, P. Lessen, L. N. Buschauer, R. Cheng, J. Wu, C. C.-C. Berninghausen, O. Buskirk, A. R. Becker, T. Beckmann, R. Green, R. 2019-09-04 doi:10.1101/755652 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ OmicsX: a web server for integrated OMICS analysis ]]> https://biorxiv.org/content/10.1101/755918v1?rss=1 Pan, J. Qian, J. Zhang, H. 2019-09-09 doi:10.1101/755918 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ OmicsOne: Associate Omics Data with Phenotypes in One-Click ]]> https://biorxiv.org/content/10.1101/756544v1?rss=1 Hu, Y. Ao, M. Zhang, H. 2019-09-05 doi:10.1101/756544 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Deep Learning-Based Analysis of Macaque Corneal Sub-Basal Nerve Fibers in Confocal Microscopy Images ]]> https://biorxiv.org/content/10.1101/758433v1?rss=1 Oakley, J. D. Russakoff, D. B. Weinberg, R. L. McCarron, M. E. Izzi, J. M. Mankowski, J. L. 2019-09-05 doi:10.1101/758433 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ B cell Compartmentalisation in Blood and Cerebrospinal Fluid of HIV- Infected Ugandans with Cryptococcal Meningitis ]]> https://biorxiv.org/content/10.1101/759092v1?rss=1 Okurut, S. Meya, D. B. Olobo, J. Bohjanen, P. R. Bwanga, F. Eller, M. A. Boulware, D. Huppler Hullsiek, K. Pratap, H. Manabe, Y. C. Palmer, B. Janoff, E. Jallow, F. 2019-09-06 doi:10.1101/759092 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities from Global Deserts ]]> https://biorxiv.org/content/10.1101/761262v1?rss=1 Qu, E. B. Omelon, C. Oren, A. Meslier, V. Cowan, D. A. Maggs-Koelling, G. L. DiRuggiero, J. 2019-09-08 doi:10.1101/761262 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Constructing and Forgetting Temporal Context in the Human Cerebral Cortex ]]> https://biorxiv.org/content/10.1101/761593v1?rss=1 Chien, H.-Y. S. Honey, C. J. 2019-09-08 doi:10.1101/761593 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Regulatory non-coding small RNAs are diverse and abundant in an extremophilic microbial community ]]> https://biorxiv.org/content/10.1101/761684v1?rss=1 Gelsinger, D. Uritskiy, G. V. Reddy, R. Munn, A. Farney, K. DiRuggiero, J. 2019-09-08 doi:10.1101/761684 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Improved metagenomic analysis with Kraken 2 ]]> https://biorxiv.org/content/10.1101/762302v1?rss=1 Wood, D. E. Lu, J. Langmead, B. 2019-09-07 doi:10.1101/762302 Cold Spring Harbor Laboratory Press 2019-09-07 <![CDATA[ Hippocampal place cells encode local surface texture boundaries ]]> https://biorxiv.org/content/10.1101/764282v1?rss=1 Wang, C.-H. Monaco, J. D. Knierim, J. J. 2019-09-10 doi:10.1101/764282 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Variability in locomotor dynamics reveals the critical role of feedback in task control ]]> https://biorxiv.org/content/10.1101/764621v1?rss=1 Uyanik, I. Sefati, S. Stamper, S. A. Cho, K.-A. Ankarali, M. M. Fortune, E. S. Cowan, N. 2019-09-10 doi:10.1101/764621 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ A Pairwise Distance Distribution Correction (DDC) algorithm for blinking-free super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/768051v1?rss=1 Bohrer, C. H. Yang, X. Weng, X. Tenner, B. Ross, B. Mcquillen, R. Zhang, J. Roberts, E. Xiao, J. 2019-09-12 doi:10.1101/768051 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Disulfide disruption reverses mucus dysfunction in allergic airway disease ]]> https://biorxiv.org/content/10.1101/768424v1?rss=1 Morgan, L. E. Shenoy, S. K. Raclawska, D. Emezienna, N. A. Richardson, V. L. Hara, N. Harder, A. Q. El-Batal, H. M. Magin, C. M. Villalon, D. E. G. Duncan, G. Hanes, J. S. Suk, J. S. Thornton, D. J. Holguin, F. Janssen, W. J. Thelin, W. R. Evans, C. M. 2019-09-14 doi:10.1101/768424 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ MetroNome - a visual data exploration platform for integrating human genotypic and phenotypic data across diseases ]]> https://biorxiv.org/content/10.1101/769646v1?rss=1 Stolte, C. Shi, K. Lapchyk, N. Novod, N. Abhyankar, A. Ostrow, L. W. Phatnani, H. Bloom, T. 2019-09-14 doi:10.1101/769646 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Mutations in the SPTLC1 gene are a cause of amyotrophic lateral sclerosis that may be amenable to serine supplementation ]]> https://biorxiv.org/content/10.1101/770339v1?rss=1 Johnson, J. O. Chia, R. Kumaran, R. Alahmady, N. Miller, D. E. Abramzon, Y. Faghri, F. Renton, A. E. Topp, S. D. Pliner, H. A. Gibbs, J. R. Ding, J. Smith, N. Landeck, N. Nalls, M. A. Cookson, M. R. Pletnikova, O. Troncoso, J. Scholz, S. W. Sabir, M. S. Ahmed, S. Dalgard, C. L. Troakes, C. Jones, A. R. Shatunov, A. Iacoangeli, A. Al Khleifat, A. Ticozzi, N. Silani, V. Gellera, C. Blair, I. P. Dobson-Stone, C. Kwok, J. B. England, B. K. Bonkowski, E. S. The International ALS Genomics Consortium, The ITALSGEN Consortium, The FALS Sequencing Consortium, 2019-09-19 doi:10.1101/770339 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Saccade vigor as an implicit measure of subjective economic value ]]> https://biorxiv.org/content/10.1101/770560v1?rss=1 Yoon, T. Jaleel, A. Ahmed, A. A. Shadmehr, R. 2019-09-16 doi:10.1101/770560 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Mechanical Stimuli Affect E. coli Heat Stable Enterotoxin-cyclic GMP Signaling in a Human Enteroid Intestine-Chip Diarrhea Model ]]> https://biorxiv.org/content/10.1101/772608v1?rss=1 sunuwar, l. Yin, J. Kasendra, m. karalis, k. Kaper, J. Fleckenstein, J. M. Donowitz, M. 2019-09-18 doi:10.1101/772608 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ The Hrq1 helicase stimulates Pso2 translesion nuclease activity to promote DNA inter-strand crosslink repair ]]> https://biorxiv.org/content/10.1101/773267v1?rss=1 Rogers, C. M. Lee, C.-Y. Parkins, S. Buehler, N. J. Wenzel, S. Martinez-Marquez, F. Takagi, Y. Myong, S. Bochman, M. L. 2019-09-18 doi:10.1101/773267 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ A Subcutaneous Implant of Tenofovir Alafenamide Fumarate Causes Local Inflammation and Tissue Necrosis in Rabbits and Macaques ]]> https://biorxiv.org/content/10.1101/775452v1?rss=1 Su, J. Simpson, S. M. Sung, S. Bryndza-Tfaily, E. Veazey, R. S. Marzinke, M. A. Qiu, J. Watrous, D. Widanapathirana, L. Pearson, E. Peet, M. M. Karunakaran, D. Grasperge, B. Dobek, G. Cain, C. M. Hope, T. J. Kiser, P. F. 2019-09-19 doi:10.1101/775452 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Reconstructing an epigenetic landscape using a genetic ‘pulling’ approach ]]> https://biorxiv.org/content/10.1101/777557v1?rss=1 Assaf, M. Be'er, S. Roberts, E. 2019-09-23 doi:10.1101/777557 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Δ9-Tetrahydrocannabinol (THC) impairs visual working memory performance ]]> https://biorxiv.org/content/10.1101/778068v1?rss=1 Adam, K. C. S. Doss, M. K. Pabon, E. Vogel, E. K. de Wit, H. 2019-09-23 doi:10.1101/778068 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development. ]]> https://biorxiv.org/content/10.1101/779694v1?rss=1 Lu, Y. Shiau, F. Yi, W. Lu, S. Wu, Q. Pearson, J. Kallman, A. Hoang, T. Zhong, S. Zuo, Z. Zhao, F. Zhang, M. Tsai, N. Zhou, Y. He, S. Zhang, J. Stein-O'Brien, G. Sherman, T. D. Duan, X. Fertig, E. J. Goff, L. Zack, D. Handa, J. T. Xu, T. Bremner, R. Blackshaw, S. Wang, X. Clark, B. S. 2019-10-02 doi:10.1101/779694 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Thalamocortical network connectivity controls spatiotemporal dynamics of cortical and thalamic traveling waves ]]> https://biorxiv.org/content/10.1101/780239v1?rss=1 Bhattacharya, S. Le Cauchois, M. B. Iglesias, P. A. Chen, Z. S. 2019-09-23 doi:10.1101/780239 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Signaling Diversity Enabled by Rap1-Regulated Plasma Membrane ERK with Distinct Temporal Dynamics ]]> https://biorxiv.org/content/10.1101/781716v1?rss=1 Keyes, J. Ganesan, A. Molinar-Inglis, O. Hamidzadeh, A. Ling, M. Trejo, J. Levchenko, A. Zhang, J. 2019-09-25 doi:10.1101/781716 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats ]]> https://biorxiv.org/content/10.1101/781823v1?rss=1 Krishnan, V. Xu, J. Mendoza, G. A. Koretsky, A. Anderson, S. Pelled, G. 2019-09-25 doi:10.1101/781823 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Persistent Cyfip1 expression is required to maintain the adult subventricular zone neurogenic niche ]]> https://biorxiv.org/content/10.1101/781856v1?rss=1 Habela, C. W. Yoon, K.-J. Kim, N. Taga, A. Bell, K. Bergles, D. Maragakis, N. J. Ming, G.-l. Song,, H. 2019-09-25 doi:10.1101/781856 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ A functional cortical network for sensorimotor sequence generation ]]> https://biorxiv.org/content/10.1101/783050v1?rss=1 Xu, D. Chen, Y. Delgado, A. M. Hughes, N. C. Zhang, L. Dong, M. O'Connor, D. H. 2019-09-27 doi:10.1101/783050 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ In silico analysis of long non-coding RNAs in medulloblastoma and its subgroups ]]> https://biorxiv.org/content/10.1101/783092v1?rss=1 Joshi, P. Perera, R. J. 2019-09-26 doi:10.1101/783092 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Human Rotavirus Diarrhea Is Associated with Altered Trafficking and Expression of Apical Membrane Transport Proteins ]]> https://biorxiv.org/content/10.1101/784264v1?rss=1 Zachos, N. C. Baetz, N. W. Gupta, A. Kapoor, A. Cole, R. N. Verkman, A. S. Turner, J. R. Estes, M. K. Donowitz, M. 2019-09-26 doi:10.1101/784264 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Harmonization of large multi-site imaging datasets: Application to 10,232 MRIs for the analysis of imaging patterns of structural brain change throughout the lifespan ]]> https://biorxiv.org/content/10.1101/784363v1?rss=1 Pomponio, R. Erus, G. Habes, M. Doshi, J. Srinivasan, D. Mamourian, E. Bashyam, V. Fan, Y. Launer, L. J. Masters, C. L. Maruff, P. Zhuo, C. Nasrallah, I. M. Völzke, H. Johnson, S. C. Fripp, J. Koutsouleris, N. Satterthwaite, T. D. Wolf, D. Gur, R. Gur, R. Morris, J. Albert, M. Grabe, H. J. Resnick, S. M. Bryan, R. N. Wolk, D. A. Shinohara, R. T. Shou, H. Davatzikos, C. 2019-09-26 doi:10.1101/784363 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs ]]> https://biorxiv.org/content/10.1101/785584v1?rss=1 He, Y. Chhetri, S. B. Arvanitis, M. Srinivasan, K. Aguet, F. Ardlie, K. G. Barbeira, A. N. Bonazzola, R. Im, H. K. GTEx Consortium, Brown, C. D. Battle, A. 2019-10-06 doi:10.1101/785584 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Reward timing and its expression by inhibitory interneurons in the mouse primary visual cortex ]]> https://biorxiv.org/content/10.1101/785824v1?rss=1 Monk, K. J. Allard, S. Hussain Shuler, M. G. 2019-09-30 doi:10.1101/785824 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Diverse transcriptomic signatures across human tissues identify functional rare genetic variation ]]> https://biorxiv.org/content/10.1101/786053v1?rss=1 Ferraro, N. M. Strober, B. J. Einson, J. Li, X. Aguet, F. Barbeira, A. N. Castel, S. E. Davis, J. R. Hilliard, A. T. Kotis, B. Park, Y. Scott, A. J. Smail, C. Tsang, E. K. Ardlie, K. G. Assimes, T. L. Hall, I. Im, H. K. GTEx Consortium, Lappalainen, T. Mohammadi, P. Montgomery, S. B. Battle, A. 2019-10-03 doi:10.1101/786053 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ C9orf72 arginine-rich dipeptide repeat proteins disrupt importin β-mediated nuclear import ]]> https://biorxiv.org/content/10.1101/787473v1?rss=1 Hayes, L. R. Duan, L. Bowen, K. Kalab, P. Rothstein, J. D. 2019-09-30 doi:10.1101/787473 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ The GTEx Consortium atlas of genetic regulatory effects across human tissues ]]> https://biorxiv.org/content/10.1101/787903v1?rss=1 Aguet, F. Barbeira, A. N. Bonazzola, R. Brown, A. Castel, S. E. Jo, B. Kasela, S. Kim-Hellmuth, S. Liang, Y. Oliva, M. Parsana, P. E. Flynn, E. Fresard, L. Gaamzon, E. R. Hamel, A. R. He, Y. Hormozdiari, F. Mohammadi, P. Munoz-Aguirre, M. Park, Y. Saha, A. Segrc, A. V. Strober, B. J. Wen, X. Wucher, V. Das, S. Garrido-Martin, D. Gay, N. R. Handsaker, R. E. Hoffman, P. J. Kashin, S. Kwong, A. Li, X. MacArthur, D. Rouhana, J. M. Stephens, M. Todres, E. Vinuela, A. Wang, G. Zou, Y. The GTEx Consortium, Brown, C. D. Cox, N. Dermitzakis, E. Engelhardt, 2019-10-03 doi:10.1101/787903 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data ]]> https://biorxiv.org/content/10.1101/791665v1?rss=1 200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics. ]]> Goubert, C. Thomas, J. Payer, L. M. Kidd, J. M. Feusier, J. Watkins, W. S. Burns, K. H. Jorde, L. B. Feschotte, C. 2019-10-03 doi:10.1101/791665 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Targeting the Pregnane X Receptor Using Microbial Metabolite Mimicry ]]> https://biorxiv.org/content/10.1101/792671v1?rss=1 Dvorak, Z. Felix Kopp, F. Costello, C. M. Kemp, J. S. Li, H. Vrzalova, A. Stepankova, M. Iveta Bartonkov, I. Poulikova, K. Vyhlidalova, B. Nordstroem, L. U. Karunaratne, C. Ranhotra, H. Mun, K. S. Naren, A. P. Murray, I. Perdew, G. H. Brtko, J. Toporova, L. Schon, A. Wallace, B. Walton, W. G. Redinbo, M. R. Sun, K. Beck, A. Kortagere, S. Neary, M. C. Chandran, A. Vishveshwara, S. Cavalluzzi, M. M. Lentini, G. Cui, J. Y. Gu, H. March, J. C. Chaterjee, S. Matson, A. Wright, D. Flannigan, K. L. Hirota, S. A. Mani, S. 2019-10-04 doi:10.1101/792671 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control ]]> https://biorxiv.org/content/10.1101/792994v1?rss=1 Hickey, K. L. Dickson, K. Cogan, J. Z. Replogle, J. M. Schoof, M. D'Orazio, K. N. Sinha, N. K. Frost, A. Green, R. Kostova, K. K. Weissman, J. S. 2019-10-03 doi:10.1101/792994 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes ]]> https://biorxiv.org/content/10.1101/793026v1?rss=1 Thomas, S. N. Friedrich, B. Schnaubelt, M. Chan, D. W. Zhang, H. Aebersold, R. 2019-10-03 doi:10.1101/793026 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Long non-coding RNA gene regulation and trait associations across human tissues ]]> https://biorxiv.org/content/10.1101/793091v1?rss=1 de Goede, O. M. Ferraro, N. M. Nachun, D. C. Rao, A. Aguet, F. Barbeira, A. N. Castel, S. E. Kim-Hellmuth, S. Park, Y. Scott, A. J. Strober, B. J. GTEx Consortium, Brown, C. D. Wen, X. Hall, I. M. Battle, A. Lappalainen, T. Im, H. K. Ardlie, K. G. Quertermous, T. Kirkegaard, K. Montgomery, S. B. 2019-10-04 doi:10.1101/793091 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Cerebral atherosclerosis contributes to Alzheimer’s dementia independently of its hallmark amyloid and tau pathologies ]]> https://biorxiv.org/content/10.1101/793349v1?rss=1 Wingo, A. Fan, W. Doung, D. M. Gerasimov, E. S. Dammer, E. B. White, B. Thambisetty, M. Troncoso, J. Schneider, J. A. Lah, J. J. Bennett, D. A. Seyfried, N. Levey, A. I. Wingo, T. S. 2019-10-13 doi:10.1101/793349 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation ]]> https://biorxiv.org/content/10.1101/794297v1?rss=1 Pagel, K. A. Kim, R. Moad, K. Busby, B. Zheng, L. Hynes-Grace, M. Tokheim, C. Ryan, M. Karchin, R. 2019-10-06 doi:10.1101/794297 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Measurement of organ-specific and acute-phase blood protein levels in early Lyme disease ]]> https://biorxiv.org/content/10.1101/795344v1?rss=1 Zhou, Y. Qin, S. Sun, M. Tang, L. Yan, X. Kim, T.-K. Caballero, J. Glusman, G. Brunkow, M. E. Soloski, M. J. Rebman, A. W. Scanvarda, C. Cooper, D. Omenn, G. S. Moritz, R. L. Wormser, G. P. Price, N. D. Aucoutt, J. N. Hood, L. 2019-10-08 doi:10.1101/795344 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Herpes Simplex Virus type 1 Inflammasome Activation in Human Macrophages is Dependent on NLRP3, ASC, and Caspase-1 ]]> https://biorxiv.org/content/10.1101/796235v1?rss=1 Karaba, A. H. Figueroa, A. Massaccesi, G. Botto, S. DeFilippis, V. R. Cox, A. 2019-10-07 doi:10.1101/796235 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Insights from a survey-based analysis of the academic job market ]]> https://biorxiv.org/content/10.1101/796466v1?rss=1 Fernandes, J. D. Sarabipour, S. Smith, C. T. Niemi, N. M. Jadavji, N. M. Kozik, A. J. Holehouse, A. S. Pejaver, V. Symmons, O. Bisson Filho, A. W. Haage, A. 2019-10-09 doi:10.1101/796466 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Astrocyte redox dysregulation causes prefrontal hypoactivity: sulforaphane treats non-ictal pathophysiology in ALDH7A1-mediated epilepsy ]]> https://biorxiv.org/content/10.1101/796474v1?rss=1 Faust, T. E. Xin, W. Lee, B. J. Agarwal, A. Saha, S. Palen, T. Cash-Padgett, T. Wood, D. Bonci, A. Fahey, J. W. Jaaro-Peled, H. Bergles, D. E. Sawa, A. 2019-10-07 doi:10.1101/796474 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Chemogenetic inhibition in the dorsal striatum reveals regional specificity of direct and indirect pathway control of action sequencing. ]]> https://biorxiv.org/content/10.1101/796698v1?rss=1 Garr, E. Delamater, A. R. 2019-10-07 doi:10.1101/796698 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Definition of naturally processed peptides reveals convergent presentation of autoantigenic topoisomerase-I epitopes in scleroderma ]]> https://biorxiv.org/content/10.1101/798249v1?rss=1 Tiniakou, E. Fava, A. McMahan, Z. Guhr, T. N. O'Meally, R. N. Shah, A. A. Wigley, F. M. Cole, R. N. Boin, F. Darrah, E. 2019-10-08 doi:10.1101/798249 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides ]]> https://biorxiv.org/content/10.1101/798579v1?rss=1 Wangen, J. R. Green, R. 2019-10-09 doi:10.1101/798579 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ The conserved DNMT1 dependent methylation regions in human cells are vulnerable to environmental rotenone. ]]> https://biorxiv.org/content/10.1101/798587v1?rss=1 Freeman, D. M. Lou, D. Li, Y. Martos, S. N. Wang, Z. 2019-10-09 doi:10.1101/798587 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Persons post-stroke restore step length symmetry by walking asymmetrically ]]> https://biorxiv.org/content/10.1101/799775v1?rss=1 Padmanabhan, P. Rao, K. S. Gulhar, S. Cherry-Allen, K. M. Leech, K. A. Roemmich, R. T. 2019-10-10 doi:10.1101/799775 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ A powerful subset-based gene-set analysis method identifies novel associations and improves interpretation in UK Biobank ]]> https://biorxiv.org/content/10.1101/799791v1?rss=1 Dutta, D. VandeHaar, P. Scott, L. Boehnke, M. Lee, S. 2019-10-10 doi:10.1101/799791 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Sequential and efficient neural-population coding of complex task information ]]> https://biorxiv.org/content/10.1101/801654v1?rss=1 Koay, S. A. Thiberge, S. Y. Brody, C. Tank, D. W. 2019-10-13 doi:10.1101/801654 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Optimal Experimental Design for Big Data: Applications in Brain Imaging ]]> https://biorxiv.org/content/10.1101/802629v1?rss=1 Bridgeford, E. W. Wang, S. Yang, Z. Wang, Z. Xu, T. Craddock, C. Kiar, G. Gray-Roncal, W. Priebe, C. E. Caffo, B. Milham, M. Zuo, X.-N. Consortium for Reliability and Reproducibility, Vogelstein, J. T. 2019-10-13 doi:10.1101/802629 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ A Consensus Proteomic Analysis of Alzheimer’s Disease Brain and Cerebrospinal Fluid Reveals Early Changes in Energy Metabolism Associated with Microglia and Astrocyte Activation ]]> https://biorxiv.org/content/10.1101/802959v1?rss=1 2000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brain that may serve as therapeutic targets and fluid biomarkers for the disease. ]]> Johnson, E. Dammer, E. B. Duong, D. M. Ping, L. Zhou, M. Yin, L. Higginbotham, L. A. Guajardo, A. White, B. Troncoso, J. C. Thambisetty, M. Montine, T. J. Lee, E. B. Trojanowski, J. Q. Beach, T. G. Reiman, E. M. Haroutunian, V. Wang, M. Schadt, E. Zhang, B. Dickson, D. W. Ertekin-Taner, N. Golde, T. E. Petyuk, V. A. De Jager, P. L. Bennett, D. A. Wingo, T. S. Rangaraju, S. Hajjar, I. Shulman, J. M. Lah, J. J. Levey, A. I. Seyfried, N. T. 2019-10-13 doi:10.1101/802959 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ A history-derived reward prediction error signal in ventral pallidum ]]> https://biorxiv.org/content/10.1101/807842v1?rss=1 Ottenheimer, D. J. Bari, B. A. Sutlief, E. Fraser, K. M. Kim, T. H. Richard, J. M. Cohen, J. Y. Janak, P. H. 2019-10-17 doi:10.1101/807842 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Mitochondrial Dysfunction Induces Epigenetic Dysregulation by H3K27 Hyperacetylation to Perturb Active Enhancers in Parkinson’s Disease Models ]]> https://biorxiv.org/content/10.1101/808246v1?rss=1 Huang, M. Lou, D. Charli, A. Kong, D. Jin, H. Anantharam, V. Kanthasamy, A. Wang, Z. Kanthasamy, A. 2019-10-17 doi:10.1101/808246 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Semiparametric Partial Common Principal Component Analysis for Covariance Matrices ]]> https://biorxiv.org/content/10.1101/808527v1?rss=1 Wang, B. Luo, X. Zhao, Y. Caffo, B. S. 2019-10-17 doi:10.1101/808527 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome ]]> https://biorxiv.org/content/10.1101/809798v1?rss=1 Marrano, A. Britton, M. Zaini, P. A. Zimin, A. Workman, R. Puiu, D. Bianco, L. Di Pierro, E. A. Allen, B. Chakraborty, S. Troggio, M. Leslie, C. Timp, W. Dendekar, A. Salzberg, S. Neale, D. B. 2019-10-17 doi:10.1101/809798 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Evolutionary Origins of Recurrent Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/811133v1?rss=1 Sakamoto, H. Attiyeh, M. Gerold, J. Makohon-Moore, A. P. Hayashi, A. Hong, J. Kappagantula, R. Zhang, L. Melchor, J. Reiter, J. Heyde, A. Bielski, C. Penson, A. Chakravarty, D. O'Reilly, E. Wood, L. Hruban, R. H. Nowak, M. A. Socci, N. Taylor, B. S. Iacobuzio-Donahue, C. A. 2019-10-31 doi:10.1101/811133 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ CTRL: a label-free method for dynamic measurement of single-cell volume ]]> https://biorxiv.org/content/10.1101/817189v1?rss=1 Yao, K. Rochman, N. Sun, S. 2019-10-24 doi:10.1101/817189 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Collateral fitness effects of mutations ]]> https://biorxiv.org/content/10.1101/820068v1?rss=1 Mehlhoff, J. D. Stearns, F. W. Rohm, D. Wang, B. Tsou, E.-Y. Dutta, N. Hsiao, M.-H. Gonzalez, C. E. Rubin, A. F. Ostermeier, M. 2019-10-29 doi:10.1101/820068 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Analysis of putative cis-regulatory elements regulating blood pressure variation ]]> https://biorxiv.org/content/10.1101/820522v1?rss=1 Nandakumar, P. Lee, D. Hoffmann, T. J. Ehret, G. Arking, D. Ranatunga, D. Li, M. Grove, M. L. Boerwinkle, E. Schaefer, C. Kwok, P.-Y. Iribarren, C. Risch, N. Chakravarti, A. 2019-10-27 doi:10.1101/820522 Cold Spring Harbor Laboratory Press 2019-10-27 <![CDATA[ Establishment of an eHAP1 Human Haploid Cell Line Hybrid Reference Genome Assembled from Short and Long Reads ]]> https://biorxiv.org/content/10.1101/822593v1?rss=1 90% complete BUSCO scores. We further assessed the eHAP1 long read data for structural variants using Sniffles and identify a variety of rearrangements, including a previously established Philadelphia translocation. Finally, we demonstrate how some of these variants overlap open chromatin regions, potentially impacting regulatory regions.nnConclusionsBy integrating both long and short reads, we generated a high-quality reference assembly for eHAP1 cells. We identify structural variants using long reads, including some that may impact putative regulatory elements. The union of long and short reads demonstrates the utility in combining sequencing platforms to generate a high-quality reference genome de novo solely from low coverage data. We expect the resulting eHAP1 genome assembly to provide a useful resource to enable novel experimental applications in this important model cell line. ]]> Law, W. D. Warren, R. L. McCallion, A. S. 2019-10-29 doi:10.1101/822593 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex ]]> https://biorxiv.org/content/10.1101/823781v1?rss=1 Perzel Mandell, K. A. Price, A. J. Wilton, R. Collado Torres, L. Tao, R. Eagles, N. J. Szalay, A. S. Hyde, T. M. Weinberger, D. Kleinman, J. E. Jaffe, A. E. 2019-10-30 doi:10.1101/823781 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Keratin 14-dependent disulfides regulate epidermal homeostasis and barrier function via 14-3-3sigma and YAP1 ]]> https://biorxiv.org/content/10.1101/824219v1?rss=1 Guo, Y. Leacock, K. A. Redmond, C. Jaskula-Ranga, V. Coulombe, P. A. 2019-10-30 doi:10.1101/824219 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection ]]> https://biorxiv.org/content/10.1101/825117v1?rss=1 Illingworth, C. Raghwani, J. Serwadda, D. Sewankambo, N. K. Robb, M. Eller, M. Redd, A. Quinn, T. Lythgoe, K. 2019-10-30 doi:10.1101/825117 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Collective MAPK Signaling Dynamics Coordinates Epithelial Homeostasis ]]> https://biorxiv.org/content/10.1101/826917v1?rss=1 Aikin, T. J. Peterson, A. F. Pokrass, M. J. Clark, H. R. Regot, S. 2019-10-31 doi:10.1101/826917 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Cerebellar patients have intact feedback control that can be leveraged to improve reaching ]]> https://biorxiv.org/content/10.1101/827113v1?rss=1 Zimmet, A. M. Bastian, A. J. Cowan, N. 2019-11-01 doi:10.1101/827113 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Mapping the micro-proteome of the nuclear lamina and lamin associated domains ]]> https://biorxiv.org/content/10.1101/828210v1?rss=1 Cutler, J. A. Wong, X. Hoskins, V. E. Gordon, M. Madugundu, A. K. Pandey, A. Reddy, K. L. 2019-11-02 doi:10.1101/828210 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Experimental Determination of the Force of Malaria Infection Reveals a Non-Linear Relationship to Mosquito Sporozoite Loads ]]> https://biorxiv.org/content/10.1101/830299v1?rss=1 Aleshnick, M. Ganusov, V. Nasir, G. Yenokyan, G. Sinnis, P. 2019-11-04 doi:10.1101/830299 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Recovering rearranged cancer chromosomes from karyotype graphs ]]> https://biorxiv.org/content/10.1101/831057v1?rss=1 Aganezov, S. Zban, I. Aksenov, V. Alexeev, N. Schatz, M. C. 2019-11-05 doi:10.1101/831057 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Metastatic function of METTL18 in breast cancer via actin methylation and Src ]]> https://biorxiv.org/content/10.1101/831701v1?rss=1 Kim, H. G. Kim, J. H. Yang, W. S. Park, J. G. Lee, Y. G. Kim, E. Hong, Y. H. Jo, M. Lee, C. Y. Kim, S. H. Sung, N. Y. Yi, Y.-S. Ratan, Z. A. Kim, S. Yoo, B. C. Kang, S.-U. Kim, Y. B. Kim, S. Paik, H.-J. Lee, J. E. Nam, S. J. Parameswaran, N. Han, J.-W. Cho, J. Y. 2019-11-05 doi:10.1101/831701 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/P38 signaling ]]> https://biorxiv.org/content/10.1101/833467v1?rss=1 Grit, J. L. Johnson, B. K. Essenburg, C. J. Dischinger, P. S. Campbell, S. Triche, T. J. Graveel, C. R. Steensma, M. R. 2019-12-02 doi:10.1101/833467 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Cell-type Specific Learning of Attentional Gating in Primate Striatum ]]> https://biorxiv.org/content/10.1101/837740v1?rss=1 Banaie Boroujeni, K. Hassani, S.-A. Oemisch, M. Womelsdorf, T. 2019-11-11 doi:10.1101/837740 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ EXoO-Tn: Tag-n-Map the Tn Antigen in the Human Proteome ]]> https://biorxiv.org/content/10.1101/840298v1?rss=1 Yang, W. Ao, M. Song, A. Xu, Y. Zhang, H. 2019-11-13 doi:10.1101/840298 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Affinity-engineered human antibodies detect celiac disease gluten pMHC complexes and inhibit T-cell activation ]]> https://biorxiv.org/content/10.1101/840561v1?rss=1 Frick, R. Hoydahl, L. S. Hodnebrug, I. Kumari, S. Berntsen, G. Jeliazkov, J. R. Gunnarsen, K. S. Frigstad, T. Vik, E. S. Lundin, K. E. A. Yaqub, S. Jahnsen, J. Gray, J. J. Sollid, L. M. Sandlie, I. Loset, G. A. 2019-11-15 doi:10.1101/840561 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome ]]> https://biorxiv.org/content/10.1101/841262v1?rss=1 Worden, E. J. Zhang, X. Wolberger, C. 2019-11-13 doi:10.1101/841262 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ The role of integrin αv and CD44 in GBM migration in human brain ]]> https://biorxiv.org/content/10.1101/841726v1?rss=1 Binder, Z. A. Kim, S. H. J. Wu, P.-H. Giri, A. Gallia, G. L. Pardo, C. A. Wirtz, D. 2019-11-16 doi:10.1101/841726 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Type II Alexander disease caused by splicing errors and aberrant overexpression of an uncharacterized GFAP isoform. ]]> https://biorxiv.org/content/10.1101/842229v1?rss=1 A;p.(Arg430His) while in Family 3 we identified a synonymous variant in the adjacent nucleotide, NM 001363846.1:c.1290C>A;p.(Arg430Arg). Using RNA and protein analysis of brain autopsy samples, and a mini-gene splicing reporter assay, we demonstrate both variants result in upregulation of the lambda isoform. We assessed other GFAP variants in the ClinVar database for predicted aberrant splicing and using the same assay demonstrated significant changes to splicing for two selected variants. Our approach demonstrates the importance of characterizing the effect of GFAP variants on mRNA splicing in order to inform future pathophysiologic and therapeutic study for Alexander disease. ]]> Helman, G. Takanohashi, A. Hagemann, T. L. Perng, M. D. Walkiewicz, M. Woidill, S. Sase, S. Cross, Z. Du, Y. Zhao, L. Waldman, A. Haake, B. C. Fatemi, A. Brenner, M. Sherbini, O. Messing, A. Vanderver, A. Simons, C. 2019-11-21 doi:10.1101/842229 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Tet2 negatively regulates memory fidelity ]]> https://biorxiv.org/content/10.1101/843581v1?rss=1 Zengeler, K. E. Gettens, C. P. Smith, H. C. Caron, M. M. Zhang, X. Howard, A. H. Boitnott, A. R. Gogliettino, A. R. Reda, A. Malachowsky, B. G. Zhong, C. Song, H. Kaas, G. A. Kennedy, A. J. 2019-11-25 doi:10.1101/843581 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Nuclear GAPDH signaling mediates pathological cardiac hypertrophy ]]> https://biorxiv.org/content/10.1101/844902v1?rss=1 Zhang, M. Kariya, T. Numata, G. Ramos, A. Sasaki, H. Iwakiri, M. Sasaki, M. Koitabashi, N. Zhu, G. Tsujimura, T. Lee, D.-i. Tristan, C. Shahani, N. Tsuchiya, Y. Jaaro-Peled, H. Slusher, B. S. Kass, D. Taguchi, K. Horiguchi, Y. Saitoh, T. Ishizuka, K. Sawa, A. Takimoto, E. 2019-11-16 doi:10.1101/844902 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Standardizing Human Brain Parcellations ]]> https://biorxiv.org/content/10.1101/845065v1?rss=1 Myers, P. E. Arvapalli, G. C. Ramachandran, S. C. Pisner, D. A. Frank, P. F. Lemmer, A. D. Bridgeford, E. W. Nikolaidis, A. Vogelstein, J. T. 2019-11-25 doi:10.1101/845065 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Integration of Odor-Induced Activity of Kenyon Cells in an Electrotonically Compact Drosophila Mushroom Body Output Neuron (MBON) ]]> https://biorxiv.org/content/10.1101/847244v1?rss=1 Hafez, O. Escribano, B. Pielage, J. Niebur, E. 2019-11-20 doi:10.1101/847244 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Characterization of OTUB1 activation and inhibition by different E2 enzymes ]]> https://biorxiv.org/content/10.1101/847806v1?rss=1 Que, L. T. Morrow, M. E. Wolberger, C. 2019-11-20 doi:10.1101/847806 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing ]]> https://biorxiv.org/content/10.1101/847855v1?rss=1 Aganezov, S. Goodwin, S. Sherman, R. Sedlazeck, F. J. Arun, G. Bhatia, S. Lee, I. Kirsche, M. Wappel, R. Kramer, M. Kostroff, K. Spector, D. L. Timp, W. McCombie, W. R. Schatz, M. C. 2019-11-19 doi:10.1101/847855 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ Mitochondrial DNA Copy Number and Incident Atrial Fibrillation ]]> https://biorxiv.org/content/10.1101/848085v1?rss=1 Zhao, D. Bartz, T. Sotoodehnia, N. Post, W. Heckbert, S. Alonso, A. Longchamps, R. J. Castellani, C. A. Hong, Y. S. Rotter, J. I. Lin, H. O'Rourke, B. Pankratz, N. Lane, J. Yang, S. Guallar, E. Arking, D. 2019-11-20 doi:10.1101/848085 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ FtsW exhibits distinct processive movements driven by either septal cell wall synthesis or FtsZ treadmilling in E. coli ]]> https://biorxiv.org/content/10.1101/850073v1?rss=1 Yang, X. McQuillen, R. Lyv, Z. Phillips-Mason, P. De La Cruz, A. McCausland, J. W. Liang, H. DeMeester, K. E. Grimes, C. L. de Boer, P. Xiao, J. 2019-11-21 doi:10.1101/850073 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes ]]> https://biorxiv.org/content/10.1101/850529v1?rss=1 Mordaunt, C. E. Jianu, J. M. Laufer, B. Zhu, Y. Dunaway, K. W. Bakulski, K. M. Feinberg, J. I. Volk, H. E. Lyall, K. Croen, L. A. Newschaffer, C. J. Ozonoff, S. Hertz-Picciotto, I. Fallin, M. D. Schmidt, R. J. LaSalle, J. M. 2019-11-21 doi:10.1101/850529 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Neurocognitive mechanisms of social inferences in typical and autistic adolescents ]]> https://biorxiv.org/content/10.1101/850552v1?rss=1 Rosenblau, G. Korn, C. W. Dutton, A. Lee, D. Pelphrey, K. 2019-11-21 doi:10.1101/850552 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Purinergic signaling in cochlear supporting cells reduces hair cell excitability by increasing the extracellular space ]]> https://biorxiv.org/content/10.1101/852756v1?rss=1 Babola, T. A. Kersbergen, C. J. Wang, H. C. Bergles, D. E. 2019-12-03 doi:10.1101/852756 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale ]]> https://biorxiv.org/content/10.1101/853614v1?rss=1 Varga, M. J. Loggia, S. Fu, Y. Yogurtcu, O. N. Johnson, M. E. 2019-11-24 doi:10.1101/853614 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism ]]> https://biorxiv.org/content/10.1101/857813v1?rss=1 McCausland, J. W. Yang, X. Lyu, Z. Söderström, B. W. Xiao, J. Liu, J. 2019-11-28 doi:10.1101/857813 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus ]]> https://biorxiv.org/content/10.1101/859025v1?rss=1 Graziano, V. Walker, F. C. Kennedy, E. A. Wei, J. Ettayebi, K. Simoes, M. Filler, R. Hassan, E. Hsieh, L. L. Kolawole, A. O. Wobus, C. Lindesmith, L. C. Baric, R. S. Estes, M. Orchard, R. C. Baldridge, M. T. Wilen, C. 2019-11-28 doi:10.1101/859025 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ A Novel LysR-Type Global Regulator RpvA Controls Persister Formation and Virulence in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/861500v1?rss=1 Han, J. Liu, Z. Xu, T. Shi, W. Xu, X. Wang, S. Ji, L. Xu, Y. Peng, Q. Li, W. Zhang, Y. 2019-12-02 doi:10.1101/861500 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Fibroblast Protection of Borrelia burgdorferi from Doxycycline, Cefuroxime and Daptomycin Combination is Eliminated by Oregano or Carvacrol Essential Oil ]]> https://biorxiv.org/content/10.1101/861575v1?rss=1 Bai, C. Yang, H. Cui, P. Quan, R. Zhang, Y. 2019-12-02 doi:10.1101/861575 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ A non-mosaic humanized mouse model of Down syndrome, trisomy of the long arm of human chromosome 21 in mouse chromosome background ]]> https://biorxiv.org/content/10.1101/862433v1?rss=1 Reeves, R. H. Kazuki, Y. Gao, F. Li, Y. Moyer, A. Devenney, B. Hiramatsu, K. Miyagawa-Tomita, S. Abe, S. Kazuki, K. Kajitani, N. Uno, N. Takehara, S. Takiguchi, M. Yamakawa, M. Hasegawa, A. Shimizu, R. Matsukura, S. Noda, N. Ogonuki, N. Inoue, K. Matoba, S. Ogura, A. Florea, L. D. Savonenko, A. Xiao, M. Wu, D. Batista, D. Yang, J. Qiu, Z. Singh, N. Richstemeier, J. Takeuchi, T. Oshimura, M. 2019-12-02 doi:10.1101/862433 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Nodal Fragility of Intracranial EEG Networks: Towards an EEG Fingerprint for the Epileptogenic Zone ]]> https://biorxiv.org/content/10.1101/862797v1?rss=1 Li, A. Fitzgerald, Z. Cajigas, I. Brusko, D. Claudio, A. Jagid, J. Kanner, A. Hopp, J. Chen, S. Haagensen, J. Johnson, E. Crone, N. Anderson, W. Inati, S. Zaghloul, K. Bulacio, J. Martinez, J. Sarma, S. 2019-12-03 doi:10.1101/862797 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ An updated antennal lobe atlas for the yellow fever mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.1101/865675v1?rss=1 Shankar, S. McMeniman, C. J. 2019-12-05 doi:10.1101/865675 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Interdependent regulation of stereotyped and stochastic photoreceptor fates in the fly eye ]]> https://biorxiv.org/content/10.1101/865717v1?rss=1 Miller, A. C. Urban, E. Lyons, E. L. Herman, T. G. Johnston, R. J. 2019-12-05 doi:10.1101/865717 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome ]]> https://biorxiv.org/content/10.1101/866558v1?rss=1 Cho, M. H. Wrabl, J. O. Taylor, J. Hilser, V. J. 2019-12-05 doi:10.1101/866558 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order ]]> https://biorxiv.org/content/10.1101/867069v1?rss=1 Gemmell, N. Rutherford, K. Prost, S. Tollis, M. Winter, D. J. Macey, J. R. Adelson, D. L. Suh, A. Bertozzi, T. Grau, J. Organ, C. Gardner, P. Muffato, M. Patricio, M. Billis, K. Martin, F. J. Flicek, P. Petersen, B. Kang, L. Michalak, P. Buckley, T. Wilson, M. A. Cheng, Y. Miller, H. Schott, R. K. Jordan, M. Newcomb, R. Arroyo, J. I. Valenzuela, N. Hore, T. A. Renart, J. Peona, V. Peart, C. Warmuth, V. ZENG, L. Kortschak, D. Raison, J. M. Zapata, V. V. Wu, Z. Santesmasses, D. Mariotti, M. Guigo, R. Rupp, S. Twort, V. Dussex, N. Taylor, H. R. Abe, H 2019-12-08 doi:10.1101/867069 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild ]]> https://biorxiv.org/content/10.1101/867341v1?rss=1 Humble, E. Dobrynin, P. Senn, H. Chuven, J. Scott, A. F. Mohr, D. W. Dudchenko, O. Omer, A. D. Colaric, Z. Lieberman Aiden, E. Wildt, D. Oliagi, S. Tamazian, G. Pukazhenthi, B. Ogden, R. Koepfli, K.-P. 2019-12-08 doi:10.1101/867341 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Asymptotic limits of sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/868406v1?rss=1 Albert, S. T. Jang, J. Sheahan, H. R. Teunissen, L. Vandevoorde, K. Shadmehr, R. 2019-12-08 doi:10.1101/868406 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Neural Correlates of Working Memory Training: Evidence for Plasticity in Older Adults ]]> https://biorxiv.org/content/10.1101/869164v1?rss=1 Iordan, A. D. Cooke, K. A. Moored, K. D. Katz, B. Buschkuehl, M. Jaeggi, S. M. Polk, T. A. Peltier, S. J. Jonides, J. Reuter-Lorenz, P. A. 2019-12-10 doi:10.1101/869164 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ TBK1 regulates autophagic clearance of soluble mutant huntingtin and inhibits aggregation/toxicity in different models of Huntington's disease ]]> https://biorxiv.org/content/10.1101/869586v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1368abeorg.highwire.dtl.DTLVardef@1cecff4org.highwire.dtl.DTLVardef@b6b7c5org.highwire.dtl.DTLVardef@1daf53d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG ]]> Hegde, R. N. Chiki, A. Petricca, L. Martufi, P. Arbez, N. Mouchiroud, L. Auwerx, J. Landles, C. Bates, G. P. Singh-Bains, M. K. Curtis, M. A. Faull, R. L. M. Ross, C. A. Caricasole, A. Lashuel, H. A. 2019-12-10 doi:10.1101/869586 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Regulation of heterotopic ossification through local inflammatory monocytes in a mouse model of aberrant wound healing ]]> https://biorxiv.org/content/10.1101/871574v1?rss=1 Huber, A. K. Sorkin, M. Hwang, C. Carson, W. F. Menon, R. Li, J. Vasquez, K. Pagani, C. Patel, N. Li, S. Visser, N. Niknafs, Y. Loder, S. Scola, M. Nycz, D. Gallagher, K. McCauley, L. Xu, J. James, A. Agarwal, S. Kunkel, S. Mishina, Y. Levi, B. 2019-12-11 doi:10.1101/871574 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Exploring Cryptococcus neoformans capsule structure and assembly with a hydroxylamine-armed fluorescent probe ]]> https://biorxiv.org/content/10.1101/871665v1?rss=1 Crawford, C. Cordero, R. J. B. Guazzelli, L. Wear, M. P. Oscarson, S. Casadevall, A. 2019-12-11 doi:10.1101/871665 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ IVT-seq reveals extreme bias in RNA-sequencing ]]> https://biorxiv.org/content/10.1101/005371v1?rss=1 1000 in vitro transcribed (IVT) RNAs from a full-length human cDNA library and sequenced them with poly-A and total RNA-seq, the most common protocols. Because each cDNA is full length and we show IVT is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find [~]50% of transcripts have > 2-fold and [~]10% have > 10-fold differences in within-transcript sequence coverage. Strikingly, we also find > 6% of transcripts have regions of high, unpredictable sequencing coverage, where the same transcript varies dramatically in coverage between samples, confounding accurate determination of their expression. To get at causal factors, we used a combination of experimental and computational approaches to show that rRNA depletion is responsible for the most significant variability in coverage and that several sequence determinants also strongly influence representation.nnConclusionsIn sum, these results show the utility of IVT-seq in promoting better understanding of bias introduced by RNA-seq and suggest caution in its interpretation. Furthermore, we find that rRNA-depletion is responsible for substantial, unappreciated biases in coverage. Perhaps most importantly, these coverage biases introduced during library preparation suggest exon level expression analysis may be inadvisable. ]]> Nicholas F Lahens Ibrahim Halil Kavakli Ray Zhang Katharina Hayer Michael B Black Hannah Dueck Angel Pizarro Junhyong Kim Rafael A Irizarry Russell S Thomas Gregory R Grant John B Hogenesch 2014-05-21 doi:10.1101/005371 Cold Spring Harbor Laboratory Press 2014-05-21 <![CDATA[ Avoiding test set bias with rank-based prediction ]]> https://biorxiv.org/content/10.1101/005983v1?rss=1 Prasad Patil Peirre-Olivier Bachant-Winner Benjamin Haibe-Kains Jeffrey T Leek 2014-06-06 doi:10.1101/005983 Cold Spring Harbor Laboratory Press 2014-06-06 <![CDATA[ Correspondence between resting state activity and brain gene expression ]]> https://biorxiv.org/content/10.1101/021071v1?rss=1 Guang-Zhong Wang T. Grant Belgard Deng Mao Leslie Chen Stefano Berto Todd Preuss Hanzhang Lu Daniel Geschwind Genevieve Konopka 2015-06-16 doi:10.1101/021071 Cold Spring Harbor Laboratory Press 2015-06-16 <![CDATA[ Impact of the X chromosome and sex on regulatory variation ]]> https://biorxiv.org/content/10.1101/024117v1?rss=1 Kimberly R Kukurba Princy Parsana Kevin S Smith Zachary Zappala David A Knowles Marie-Julie Favé Xin Li Xiaowei Zhu James B Potash Myrna M Weissman Jianxin Shi Anshul Kundaje Douglas F Levinson Philip Awadalla Sara Mostafavi Alexis Battle Stephen B Montgomery 2015-08-07 doi:10.1101/024117 Cold Spring Harbor Laboratory Press 2015-08-07 <![CDATA[ Predicting intensities of Zika infection and microcephaly using transmission intensities of other arboviruses ]]> https://biorxiv.org/content/10.1101/041095v1?rss=1 Isabel Rodriguez-Barraquer Henrik Salje Justin Lessler Derek AT Cummings 2016-02-24 doi:10.1101/041095 Cold Spring Harbor Laboratory Press 2016-02-24 <![CDATA[ Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9 ]]> https://biorxiv.org/content/10.1101/048371v1?rss=1 2 s-1 upon introduction of mismatches proximal to the protospacer adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 12 base pairs in length, which prevent DNA cleavage, still allow the formation of a stable complex (off-rate < 0.006 s-1), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome editing thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading. ]]> Digvijay Singh Samuel H. Sternberg Jingyi Fei Taekjip Ha Jennifer A. Doudna 2016-04-13 doi:10.1101/048371 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications ]]> https://biorxiv.org/content/10.1101/049452v1?rss=1 Elisabeth M Bik Arturo Casadevall Ferric C Fang 2016-04-20 doi:10.1101/049452 Cold Spring Harbor Laboratory Press 2016-04-20 <![CDATA[ α4-containing GABAA receptors on dopamine D2 receptor-expressing neurons mediate instrumental responding for conditioned reinforcers, and its potentiation by cocaine ]]> https://biorxiv.org/content/10.1101/055822v1?rss=1 Tom Macpherson Claire I Dixon Patricia H Janak Delia Belelli Jeremy J Lambert David N Stephens Sarah King 2016-05-27 doi:10.1101/055822 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ Population and individual effects of non-coding variants inform genetic risk factors ]]> https://biorxiv.org/content/10.1101/065144v1?rss=1 Mauro Pala Zachary Zappala Mara Marongiu Xin Li Joe R Davis Roberto Cusano Francesca Crobu Kimberly R Kukurba Frederic Reiner Riccardo Berutti Maria G Piras Antonella Mulas Magdalena Zoledziewska Michele Marongiu Fabio Busonero Andrea Maschio Maristella Steri Carlo Sidore Serena Sanna Edoardo Fiorillo Alexis Battle John Novembre Chris Jones Andrea Angius Goncalo R Abecasis David Schlessinger Francesco Cucca Stephen B Montgomery 2016-07-21 doi:10.1101/065144 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ AN INTERNATIONAL INTER-LABORATORY DIGITAL PCR STUDY DEMONSTRATES HIGH REPRODUCIBILITY FOR THE MEASUREMENT OF A RARE SEQUENCE VARIANT ]]> https://biorxiv.org/content/10.1101/077917v1?rss=1 Alexandra S Whale Alison S Devonshire George Karlin-Neumann Jack Regan Leanne Javier Simon Cowen Ana Fernandez-Gonzalez Gerwyn M Jones Nicholas Redshaw Julia Beck Andreas W Berger Valerie Combaret Nina Dahl Kjersgaard Lisa Davis Frederic Fina Tim Forshew Rikke Fredslund Andersen Silvia Galbiati Alvaro Gonzalez Hernandez Charles Haynes Filip Janku Roger Lacave Justin Lee Vilas Mistry Alexandra Pender Anne Pradines Charlotte Proudhon Lao Saal Elliot Stieglitz Bryan Ulrich Carole A Foy Helen Parkes Svilen Tzonev Jim Huggett 2016-09-28 doi:10.1101/077917 Cold Spring Harbor Laboratory Press 2016-09-28 <![CDATA[ Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/128124v1?rss=1 Phan, B. N. Page, S. C. Campbell, M. N. Bohlen, J. F. Thaxton, C. L. Simon, J. M. Burke, E. E. Shin, J. H. Kennedy, A. J. Sweatt, J. D. Philpot, B. D. Jaffe, A. E. Maher, B. J. 2017-04-18 doi:10.1101/128124 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ A Neuropeptide Signaling System That Rapidly Enforces Paternity In The Aedes aegypti Mosquito ]]> https://biorxiv.org/content/10.1101/136150v1?rss=1 500 eggs she will produce during her [~]4-6 week lifespan in the laboratory (2). Successful mating is capable of inducing lifetime refractoriness to subsequent insemination by other males, enforcing the paternity of the first male (3-5). In other species, males use diverse strategies to assure the paternity of their offspring, for instance physical barriers such as mating plugs found in mice (6) and Anopheline mosquitoes (7), and anti-aphrodisiac pheromones used by Drosophila melanogaster males to tag female flies as non-virgin (8). Another widely used strategy in insects is the transfer of biologically active male seminal proteins, produced by the male accessory gland and secreted into the ejaculatory duct along with sperm during insemination, to affect the sexual receptivity of the female (3, 9-13). Perhaps the best-characterized male seminal fluid protein in insects is the Drosophila fly sex peptide (11), which acts on the sex peptide receptor in the female to suppress receptivity and trigger egg production (12). Drosophila sex peptide receptor mutant females will readily remate with multiple males, and wild-type females that mate with sex peptide mutant males remain sexually receptive. ]]> Duvall, L. B. Basrur, N. S. Molina, H. McMeniman, C. J. Vosshall, L. B. 2017-05-09 doi:10.1101/136150 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Genome-Wide Association Study Reveals Genetic Link Between Diarrhea-Associated Entamoeba histolytica Infection And Inflammatory Bowel Disease ]]> https://biorxiv.org/content/10.1101/137448v1?rss=1 Wojcik, G. L. Marie, C. Abhyankar, M. M. Yoshida, N. Watanabe, K. Mychaleckyj, J. Kirkpatrick, B. D. Rich, S. S. Concannon, P. Haque, R. Tsokos, G. C. Petri, W. A. Duggal, P. 2017-05-12 doi:10.1101/137448 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Refining The Accuracy Of Validated Target Identification Through Coding Variant Fine-Mapping In Type 2 Diabetes ]]> https://biorxiv.org/content/10.1101/144410v1?rss=1 1.36. Second, we used GWAS data from 50,160 T2D cases and 465,272 controls to fine-map associated coding variants in their regional context, with and without additional weighting, to account for the global enrichment of complex trait association signals in coding exons. We demonstrate convincing support (posterior probability >80% under the "annotation-weighted" model) that coding variants are causal for the association at 16 of the 40 signals (including novel signals involving POC5 p.His36Arg, ANKH p.Arg187Gln, WSCD2 p.Thr113Ile, PLCB3 p.Ser778Leu, and PNPLA3 p.Ile148Met). However, one third of coding variant association signals represent "false leads" at which naive analysis would have led to an erroneous inference regarding the effector transcript mediating the signal. Accurate identification of validated targets is dependent on correct specification of the contribution of coding and non-coding mediated mechanisms at associated loci. ]]> Mahajan, A. Morris, A. P. Rotter, J. I. McCarthy, M. I. 2017-05-31 doi:10.1101/144410 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Quantifying the Risk and Cost of Active Monitoring for Infectious Diseases ]]> https://biorxiv.org/content/10.1101/156497v1?rss=1 Reich, N. G. Lessler, J. Varma, J. K. Vora, N. M. 2017-06-28 doi:10.1101/156497 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Patterns of sedentary and active time accumulation are associated with mortality in US adults: The NHANES study ]]> https://biorxiv.org/content/10.1101/182337v1?rss=1 Di, J. Leroux, A. Urbanek, J. Varadhan, R. Spira, A. Schrack, J. Zipunnikov, V. 2017-08-31 doi:10.1101/182337 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Timescales of influenza A/H3N2 antibody dynamics ]]> https://biorxiv.org/content/10.1101/183111v1?rss=1 Kucharski, A. Cummings, D. Riley, S. 2017-08-31 doi:10.1101/183111 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Identification of environmental and genetic factors important for Cryptococcus neoformans titan cell formation using new in vitro inducing conditions ]]> https://biorxiv.org/content/10.1101/191668v1?rss=1 10 {micro}m and up to 100 {micro}m). We found and optimized in vitro conditions that produce titan cells in order to identify the ancestry of titan cells, the environmental determinants, and the key gene regulators of titan cell formation. Titan cells generated in vitro harbor the main characteristics of titan cells produced in vivo including their large cell size (>10 {micro}m), polyploidy with a single nucleus, large vacuole, dense capsule, and thick cell wall. Here we show titan cells derived from the enlargement of progenitor cells in the population independent of yeast growth rate. Change in the incubation medium, hypoxia, nutrient starvation and low pH were the main factors that trigger titan cell formation, while quorum sensing factors like the initial inoculum concentration, pantothenic acid, and the quorum sensing peptide Qsp1p also impacted titan cell formation. Inhibition of ergosterol, protein and nucleic acid biosynthesis altered titan cell formation, as did serum, phospholipids and anti-capsular antibodies in our settings. We explored genetic factors important for titan cell formation using three approaches. Using H99-derivative strains with natural genetic differences, we showed that titan cell formation was dependent on LMP1 and SGF29 genes. By screening a gene deletion collection, we also confirmed that GPR4/5-RIM101, and CAC1 genes were required to generate titan cells and that the PKR1, TSP2, USV101 genes negatively regulated titan cell formation. Furthermore, analysis of spontaneous Pkr1 loss-of-function clinical isolates confirmed the important role of the Pkr1 protein as a negative regulator of titan cell formation. Through development of a standardized and robust in vitro assay, our results provide new insights into titan cell biogenesis with the identification of multiple important factors/pathways.nnAuthor SummaryCryptococcus neoformans is a yeast that is capable of morphological change upon interaction with the host. Particularly, in the lungs of infected mice, a subpopulation of yeast enlarges, producing cells up to 100 {micro}m in cell body diameter - referred to as titan cells. Along with their large size, the titan cells have other unique characteristics such as thickened cell wall, dense capsule, polyploidization, large vacuole with peripheral nucleus and cellular organelles. The generation of a large number of such cells outside the lungs of mice has been described but was not reproducible nor standardized. Here we report standardized, reproducible, robust conditions for generation of titan cells and explored the environmental and genetic factors underlying the genesis of these cells. We showed that titan cells were generated upon stresses such as change in the incubation medium, nutrient deprivation, hypoxia and low pH. Using collections of well characterized reference strains and clinical isolates, we validated with our model that the cAMP/PKA/Rim101 pathway is a major genetic determinant of titan cell formation. This study opens the way for a more comprehensive picture of the ontology of morphological changes in Cryptococcus neoformans and its impact on pathobiology of this deadly pathogen. ]]> Hommel, B. Mukaremera, L. Cordero, R. J. B. Desjardins, C. A. Sturny-Leclere, A. Perfect, J. Fraser, J. A. Casadevall, A. Cuomo, C. A. Dromer, F. Nielsen, K. Alanio, A. 2017-09-20 doi:10.1101/191668 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Hierarchical brain network for face and voice integration of emotion expression ]]> https://biorxiv.org/content/10.1101/197426v1?rss=1 Jodie Davies-Thompson Giulia V Elli Mohamed Rezk Stefania Benetti Markus Johannes Van Ackeren Olivier Collignon Suvranu De Xavier Intes 2017-10-02 doi:10.1101/197426 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ MRI tracking reveals selective accumulation of stem cell-derived magneto-extracellular vesicles in sites of injury ]]> https://biorxiv.org/content/10.1101/2019.12.22.885764v1?rss=1 Han, Z. Liu, S. Pei, Y. Ding, Z. Li, Y. Weiss, R. G. van Zijl, P. C. Bulte, J. W. M. Cheng, L. Liu, G. 2019-12-23 doi:10.1101/2019.12.22.885764 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ A Length Penalized Probabilistic Principal Curve Algorithm With Applications To Handwritten Digits And Pharmacologic Colon Imaging ]]> https://biorxiv.org/content/10.1101/2020.01.04.894964v1?rss=1 Chen, H. Weld, E. Hendrix, C. Caffo, B. 2020-01-06 doi:10.1101/2020.01.04.894964 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ T cell responses induced by attenuated flavivirus vaccination are specific and show limited cross-reactivity with other flavivirus species. ]]> https://biorxiv.org/content/10.1101/2020.01.17.911099v1?rss=1 Grifoni, A. Voic, H. Dhanda, S. K. Kidd, C. K. Brien, J. D. Buus, S. Stryhn, A. Durbin, A. P. Whitehead, S. Diehl, S. A. de Silva, A. D. Balmaseda, A. Harris, E. Weiskopf, D. Sette, A. 2020-01-20 doi:10.1101/2020.01.17.911099 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods ]]> https://biorxiv.org/content/10.1101/2020.01.29.925974v1?rss=1 Hou, W. Ji, Z. Ji, H. Hicks, S. C. 2020-01-30 doi:10.1101/2020.01.29.925974 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Gold-standard diagnostics are tarnished by lytic bacteriophage ]]> https://biorxiv.org/content/10.1101/2020.01.30.926832v1?rss=1 Nelson, E. J. Grembi, J. A. Chao, D. L. Andrews, J. R. Alexandrova, L. Rodriguez, P. H. Ramachandran, V. V. Sayeed, M. A. Wamala, J. Debes, A. K. Sack, D. A. Hryckowian, A. J. Haque, F. Khatun, S. Rahman, M. M. Chien, A. Spormann, A. M. Schoolnik, G. K. 2020-01-31 doi:10.1101/2020.01.30.926832 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by E. coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex ]]> https://biorxiv.org/content/10.1101/2020.02.04.932780v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1068460org.highwire.dtl.DTLVardef@dcd6d9org.highwire.dtl.DTLVardef@9d4727org.highwire.dtl.DTLVardef@1aa8e47_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sreenivasan, R. Shkel, I. A. Chhabra, M. Drennan, A. Heitkamp, S. Wang, H.-C. Sridevi, M. A. Plaskon, D. McNerney, C. Callies, K. Cimperman, C. K. Record, M. T. 2020-02-04 doi:10.1101/2020.02.04.932780 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Hippocampal and cortical mechanisms at retrieval explain variability in episodic remembering in older adults ]]> https://biorxiv.org/content/10.1101/2020.02.11.940668v1?rss=1 Trelle, A. N. Carr, V. A. Guerin, S. A. Thieu, M. K. Jayakumar, M. Guo, W. Nadiadwala, A. Corso, N. K. Hunt, M. P. Litovsky, C. P. Tanner, N. J. Deutsch, G. K. Bernstein, J. D. Harrison, M. B. Khazenzon, A. M. Jiang, J. Sha, S. J. Fredericks, C. A. Rutt, B. K. Mormino, E. C. Kerchner, G. A. Wagner, A. D. 2020-02-12 doi:10.1101/2020.02.11.940668 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2020.02.11.941351v1?rss=1 Lopez de Maturana, E. Rodriguez, J. Alonso, L. Lao, O. Molina-Montes, E. Martin-Antoniano, I. Gomez-Rubio, P. Lawlor, R. Carrato, A. Hidalgo, M. Iglesias, M. Molero, X. Lohr, M. Michalski, C. Perea, J. O'Rorke, M. Barbera, V. Tardon, A. Farre, A. Munoz-Bellvis, L. Crnogorac-Jurcevic, T. Dominguez-Munoz, E. Gress, T. Greenhaf, W. Sharp, L. Arnes, L. Cecchini, L. Balsells, J. Costello, E. Ilzarbe, L. Kleeff, J. Kong, B. Marquez, M. Mora, J. O'Driscoll, D. Scarpa, A. Ye, W. Yu, J. Investigators, P. Garcia-Closas, M. Kogevinas, M. Rothman, N. Silverman, D. 2020-02-12 doi:10.1101/2020.02.11.941351 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.02.28.969931v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@fcf6borg.highwire.dtl.DTLVardef@1fab44dorg.highwire.dtl.DTLVardef@53629dorg.highwire.dtl.DTLVardef@6f3de5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Maynard, K. E. Collado-Torres, L. Weber, L. M. Uytingco, C. Barry, B. K. Williams, S. R. Catallini, J. L. Tran, M. N. Besich, Z. Tippani, M. Chew, J. Yin, Y. Kleinman, J. E. Hyde, T. M. Rao, N. Hicks, S. C. Martinowich, K. Jaffe, A. E. 2020-02-28 doi:10.1101/2020.02.28.969931 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Creation of an Open Science Dataset from PREVENT-AD, a Longitudinal Cohort Study of Pre-symptomatic Alzheimer's Disease. ]]> https://biorxiv.org/content/10.1101/2020.03.04.976670v1?rss=1 Tremblay-Mercier, J. Madjar, C. Das, S. Dyke, S. O. M. Etienne, P. Lafaille-Magnan, M.-E. Bellec, P. Collins, D. L. Rajah, M. N. Bohbot, V. D. Leoutsakos, J.-M. Iturria-Medina, Y. Kat, J. Hoge, R. D. Gauthier, S. Chakravarty, M. M. Poline, J.-B. Rosa-Neto, P. Villeneuve, S. Evans, A. C. Poirier, J. Breitner, J. C. S. the PREVENT-AD Research Group, 2020-03-05 doi:10.1101/2020.03.04.976670 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Injectable Nanoelectrodes Enable Wireless Deep Brain Stimulation of Native Tissue in Freely Moving Mice ]]> https://biorxiv.org/content/10.1101/2020.03.14.978676v1?rss=1 Kozielski, K. L. Jahanshahi, A. Gilbert, H. B. Yu, Y. Erin, O. Francisco, D. Alosaimi, F. Temel, Y. Sitti, M. 2020-03-15 doi:10.1101/2020.03.14.978676 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Learning to Control the Brain through Adaptive Closed-Loop Patterned Stimulation ]]> https://biorxiv.org/content/10.1101/2020.03.14.992198v1?rss=1 Tafazoli, S. MacDowell, C. J. Che, Z. Letai, K. C. Steinhardt, C. Buschman, T. J. 2020-03-16 doi:10.1101/2020.03.14.992198 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Single-shot Mesoporous Silica Rods Scaffold for Induction of Humoral Responses Against Small Antigens ]]> https://biorxiv.org/content/10.1101/2020.03.17.993808v1?rss=1 Dellacherie, M. O. Li, A. Lu, B. Y. Verbeke, C. S. Gu, L. Stafford, A. Doherty, E. J. Mooney, D. J. 2020-03-18 doi:10.1101/2020.03.17.993808 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Evaluating features of scientific conferences: A call for improvements ]]> https://biorxiv.org/content/10.1101/2020.04.02.022079v1?rss=1 Sarabipour, S. Schwessinger, B. Mumoki, F. N. Mwakilili, A. D. Khan, A. Debat, H. J. Saez, P. Seah, S. Mestrovic, T. 2020-04-03 doi:10.1101/2020.04.02.022079 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Genetic diversity of Anopheles coustani in high malaria transmission foci in southern and central Africa ]]> https://biorxiv.org/content/10.1101/2020.04.04.020537v1?rss=1 Ciubotariu, I. I. Jones, C. M. Kobayashi, T. Bobanga, T. Muleba, M. Pringle, J. C. Stevenson, J. C. Carpi, G. Norris, D. E. 2020-04-05 doi:10.1101/2020.04.04.020537 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Subpopulations of stressed Y. pseudotuberculosis preferentially survive doxycycline treatment within host tissues ]]> https://biorxiv.org/content/10.1101/2020.04.13.039222v1?rss=1 Raneses, J. R. Ellison, A. L. Liu, B. Davis, K. M. 2020-04-13 doi:10.1101/2020.04.13.039222 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Identifying Neural Signatures Mediating Behavioral Symptoms and Psychosis Onset: High-Dimensional Whole Brain Functional Mediation Analysis ]]> https://biorxiv.org/content/10.1101/2020.04.15.043034v1?rss=1 Chén, O. Y. Cao, H. Phan, H. Nagels, G. Reinen, J. M. Gou, J. Qian, T. Di, J. Prince, J. Cannon, T. D. de Vos, M. 2020-04-16 doi:10.1101/2020.04.15.043034 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ A Solanum lycopersicoides reference genome facilitates biological discovery in tomato ]]> https://biorxiv.org/content/10.1101/2020.04.16.039636v1?rss=1 Powell, A. F. Courtney, L. E. Schmidt, M. H.- W. Feder, A. Vogel, A. Xu, Y. Lyon, D. A. Dumschott, K. E. McHale, M. Suplice, R. Bao, K. Duhan, A. Hallab, A. Denton, A. K. Mueller, L. A. Alseekh, S. Lie, J. Martin, C. Fernie, A. R. Hind, S. R. Martin, G. B. Fei, Z. Giovannoni, J. J. Strickler, S. R. Usadel, B. 2020-04-18 doi:10.1101/2020.04.16.039636 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Tension causes structural unfolding of intracellular intermediate filaments ]]> https://biorxiv.org/content/10.1101/2020.04.22.054379v1?rss=1 Fleissner, F. Kumar, S. Klein, N. Wirth, D. Dhiman, R. Schneider, D. Bonn, M. Parekh, S. H. 2020-04-24 doi:10.1101/2020.04.22.054379 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Toxoplasma ferlin1 is a versatile and dynamic mediator of microneme trafficking and secretion ]]> https://biorxiv.org/content/10.1101/2020.04.27.063628v1?rss=1 Tagoe, D. N. Drozda, A. A. Coppens, I. Coleman, B. I. Gubbels, M.-J. 2020-04-28 doi:10.1101/2020.04.27.063628 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Topologically correct synthetic reconstruction of pathogen social behavior found in deep tissue sites ]]> https://biorxiv.org/content/10.1101/2020.04.27.065144v1?rss=1 Clark, S. A. Thibault, D. Shull, L. M. Davis, K. M. Aunins, E. van Opijnen, T. Isberg, R. R. 2020-04-29 doi:10.1101/2020.04.27.065144 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Toxoplasma TgATG9 is critical for autophagy and long-term persistence in tissue cysts ]]> https://biorxiv.org/content/10.1101/2020.05.13.093401v1?rss=1 Smith, D. Kannan, G. Coppens, I. Wang, F. Nugyen, H. M. Cerutti, A. Schultz, T. L. B. Rimple, P. Di Cristina, M. Besteiro, S. Carruthers, V. B. 2020-05-15 doi:10.1101/2020.05.13.093401 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression ]]> https://biorxiv.org/content/10.1101/2020.05.21.102756v1?rss=1 Workman, R. E. Pammi, T. Nguyen, B. T. K. Graeff, L. W. Smith, E. Sebald, S. M. Stoltzfus, M. J. Modell, J. W. 2020-05-21 doi:10.1101/2020.05.21.102756 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ A novel mechanism of natural killer cell response to anti-CTLA-4 therapy identified by integrative analysis of mouse and human tumors ]]> https://biorxiv.org/content/10.1101/2020.05.31.125625v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1ca0c13org.highwire.dtl.DTLVardef@1dedc51org.highwire.dtl.DTLVardef@5277eforg.highwire.dtl.DTLVardef@4007c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Davis-Marcisak, E. F. Fitzgerald, A. A. Kessler, M. D. Danilova, L. Jaffee, E. M. Zaidi, N. Weiner, L. M. Fertig, E. J. 2020-05-31 doi:10.1101/2020.05.31.125625 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Ribosome rescue inhibitors clear Neisseria gonorrhoeae in vivo using a new mechanism ]]> https://biorxiv.org/content/10.1101/2020.06.04.132530v1?rss=1 Aron, Z. D. Mehrani, A. Hoffer, E. D. Connolly, K. L. Torhan, M. C. Alumasa, J. N. Srinivas, P. Cabrera, M. Hosangadi, D. Barbor, J. S. Cardinale, S. C. Kwasny, S. M. Morin, L. R. Butler, M. M. Opperman, T. J. Bowlin, T. L. Jerse, A. E. Stagg, S. M. Dunham, C. M. Keiler, K. C. 2020-06-05 doi:10.1101/2020.06.04.132530 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Cocaine-induced neuron subtype mitochondrial dynamics through Egr3 transcriptional regulation ]]> https://biorxiv.org/content/10.1101/2020.06.27.175349v1?rss=1 Cole, S. Chandra, R. Harris, M. Patel, I. Wang, T. Kim, H. Jensen, L. Russo, S. Turecki, G. Gancarz-Kausch, A. Dietz, D. Lobo, M. K. 2020-06-29 doi:10.1101/2020.06.27.175349 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Antifungal activity of 2,3-diphenyl-2,3-dihydro-1,3-thiaza-4-ones against two human pathogenic fungi ]]> https://biorxiv.org/content/10.1101/2020.06.27.175711v1?rss=1 Liporagi Lopes, L. C. Sobhi, H. F. Silverberg, L. J. Cordero, R. J. Casadevall, A. 2020-06-27 doi:10.1101/2020.06.27.175711 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum ]]> https://biorxiv.org/content/10.1101/2020.07.18.210385v1?rss=1 Pholcharee, T. Oyen, D. Flores-Garcia, Y. Gonzalez-Paez, G. Han, Z. Williams, K. L. Volkmuth, W. Emerling, D. Locke, E. King, C. R. Zavala, F. Wilson, I. A. 2020-07-18 doi:10.1101/2020.07.18.210385 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Paracoccidioides HSP90 can be found in the cell surface and is a target for antibodies with therapeutic potential ]]> https://biorxiv.org/content/10.1101/2020.07.29.198804v1?rss=1 Moura, A. N. D. Oliveira, D. S. L. d. Paredes, V. Rocha, L. B. Casadevall, A. Albuquerque, P. Felipe, M. S. S. Piazza, R. M. F. Nicola, A. M. 2020-07-29 doi:10.1101/2020.07.29.198804 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Faster Cryptococcus melanization increases virulence in experimental and human cryptococcosis ]]> https://biorxiv.org/content/10.1101/2020.07.29.222794v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@41c48borg.highwire.dtl.DTLVardef@1ce8e1eorg.highwire.dtl.DTLVardef@1d4568corg.highwire.dtl.DTLVardef@17e2003_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sousa, H. R. d. Oliveira, G. P. d. Frazao, S. d. O. Gorgonha, K. C. d. M. Rosa, C. P. Garcez, E. M. Lucas, J. Correia, A. F. Freitas, W. F. d. Paes, H. C. Trilles, L. Lazera, M. d. S. Pinto, V. L. Felipe, M. S. S. Casadevall, A. Silva-Pereira, I. Albuquerque, P. Nicola, A. M. 2020-07-29 doi:10.1101/2020.07.29.222794 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. ]]> https://biorxiv.org/content/10.1101/2020.08.06.240358v1?rss=1 Chou, H.-C. Bhalla, K. Demerdesh, O. E. Klingbeil, O. Hanington, K. Aganezov, S. Andrews, P. Alsudani, H. Chang, K. Vakoc, C. R. Schatz, M. C. McCombie, W. R. Stillman, B. 2020-08-06 doi:10.1101/2020.08.06.240358 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ An Epitope-based Malaria Vaccine Targeting the Junctional Domain of Circumsporozoite Protein ]]> https://biorxiv.org/content/10.1101/2020.08.07.241802v1?rss=1 Jelinkova, L. Jhun, H. Eaton, A. Petrovsky, N. Zavala, F. Chackerian, B. 2020-08-07 doi:10.1101/2020.08.07.241802 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Evaluation of pneumococcal serotyping in nasopharyngeal carriage isolates by latex agglutination, whole genome sequencing (PneumoCaT) and DNA microarray in a high pneumococcal carriage prevalence population in Malawi ]]> https://biorxiv.org/content/10.1101/2020.08.17.255224v1?rss=1 Swarthout, T. D. Gori, A. Bar-Zeev, N. Kamng'ona, A. W. Mwalukomo, T. S. Bonomali, F. Nyirenda, R. Brown, C. Msefula, J. Everett, D. Mwansambo, C. Gould, K. Hinds, J. Heyderman, R. French, N. 2020-08-18 doi:10.1101/2020.08.17.255224 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ BDNF/TrkB signaling endosomes mediate long-distance dendritic growth by activating CREB/PI3K-mTOR-dependent translation in neuronal cell bodies. ]]> https://biorxiv.org/content/10.1101/2020.08.22.262923v1?rss=1 Bronfman, F. C. Moya-Alvarado, G. 2020-08-24 doi:10.1101/2020.08.22.262923 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ PieParty: Visualizing cells from scRNA-seq data as pie charts ]]> https://biorxiv.org/content/10.1101/2020.08.25.267021v1?rss=1 Kurtenbach, S. Dollar, J. J. Durante, M. A. Harbour, J. W. 2020-08-26 doi:10.1101/2020.08.25.267021 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Temporal uncertainty affects the visual processing of predicted stimulus properties ]]> https://biorxiv.org/content/10.1101/2020.08.26.265884v1?rss=1 Nara, S. Lizarazu, M. Richter, C. G. Dima, D. C. Bourguignon, M. Molinaro, N. 2020-08-27 doi:10.1101/2020.08.26.265884 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Creating Clear and Informative Image-based Figures for Scientific Publications ]]> https://biorxiv.org/content/10.1101/2020.10.08.327718v1?rss=1 Jambor, H. Antonietti, A. Alicea, B. J. Audisio, T. L. Auer, S. Bhardwaj, V. Burgess, S. J. Ferling, I. Gazda, M. A. Hoeppner, L. H. Ilangovan, V. Lo, H. Olson, M. Mohamed, S. Y. Sarabipour, S. Varma, A. Walavalkar, K. Wissink, E. Weissgerber, T. L. 2020-10-08 doi:10.1101/2020.10.08.327718 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entireSARS-CoV-2 proteome and show kinetics of early differentiation ]]> https://biorxiv.org/content/10.1101/2020.10.08.330688v1?rss=1 Kared, H. Redd, A. D. Bloch, E. M. Bonny, T. S. Sumatoh, H. Kairi, F. Carbajo, D. Abel, B. Newell, E. W. Bettinotti, M. P. Benner, S. E. Patel, E. U. Littlefield, K. Laeyendecker, O. Shoham, S. Sullivan, D. Casadevall, A. Pekosz, A. Nardin, A. Fehlings, M. Tobian, A. A. Quinn, T. C. 2020-10-08 doi:10.1101/2020.10.08.330688 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Constitutive deletion of translin (Tsn) enhances locomotor response to amphetamine: role of developmental effects ]]> https://biorxiv.org/content/10.1101/2020.10.08.331447v1?rss=1 Fu, X. Shah, A. P. Keighron, J. Mou, T.-C. M. Ladenheim, B. Alt, J. Fukudome, D. Niwa, M. Sawa, A. Cadet, J.-L. Rais, R. Tanda, G. Baraban, J. M. 2020-10-09 doi:10.1101/2020.10.08.331447 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Ontology-Aware Deep Learning Enables Ultrafast, Accurate and Interpretable Source Tracking among Sub-Million Microbial Community Samples from Hundreds of Niches ]]> https://biorxiv.org/content/10.1101/2020.11.01.364208v1?rss=1 Ning, K. Zha, Y. Chong, H. Qiu, H. Kang, K. Dun, Y. Chen, Z. Cui, X. 2020-11-02 doi:10.1101/2020.11.01.364208 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design ]]> https://biorxiv.org/content/10.1101/2020.11.06.371963v1?rss=1 Weber, L. M. Hippen, A. A. Hickey, P. F. Berrett, K. C. Gertz, J. Doherty, J. A. Greene, C. S. Hicks, S. C. 2020-11-07 doi:10.1101/2020.11.06.371963 Cold Spring Harbor Laboratory Press 2020-11-07 <![CDATA[ Epigenome-wide study of brain DNA methylation among opioid users and controls ]]> https://biorxiv.org/content/10.1101/2020.11.10.377069v1?rss=1 Shu, C. Sosnowski, D. W. Tao, R. Deep-Soboslay, A. Kleinman, J. E. Hyde, T. M. Jaffe, A. E. Sabunciyan, S. Maher, B. S. 2020-11-11 doi:10.1101/2020.11.10.377069 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Whole Genome Sequence Analysis of Shigella from Malawi Identifies Fluoroquinolone Resistance ]]> https://biorxiv.org/content/10.1101/2020.11.20.391235v1?rss=1 Stenhouse, G. E. Jere, K. C. Peno, C. Bengtsson, R. J. Chinyama, E. Mandolo, J. Cain, A. K. Iturriza_Gomara, M. Bar-Zeev, N. Cunliffe, N. A. Cornick, J. Baker, K. S. 2020-11-20 doi:10.1101/2020.11.20.391235 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ distinct: a novel approach to differential distribution analyses ]]> https://biorxiv.org/content/10.1101/2020.11.24.394213v1?rss=1 Tiberi, S. Crowell, H. L. Weber, L. M. Samartsidis, P. Robinson, M. D. 2020-11-25 doi:10.1101/2020.11.24.394213 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Immunofocusing humoral immunity potentiates the functional efficacy of the AnAPN1 malaria transmission-blocking vaccine antigen ]]> https://biorxiv.org/content/10.1101/2020.11.29.402669v1?rss=1 Bender, N. G. Khare, P. Martinez, J. Tweedell, R. E. Nyasembe, V. O. Lopez-Gutierrez, B. Tripathi, A. Miller, D. Hamerly, T. Vela, E. M. Howard, R. F. Nsango, S. Cobb, R. R. Harbers, M. Dinglasan, R. R. 2020-11-29 doi:10.1101/2020.11.29.402669 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ An Optimized CRISPR/Cas9 Approach for Precise Genome Editing in Neurons ]]> https://biorxiv.org/content/10.1101/2020.11.30.402883v1?rss=1 FANG, H. L. Bygrave, A. M. Roth, R. H. Johnson, R. C. Huganir, R. L. 2020-11-30 doi:10.1101/2020.11.30.402883 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ The ecology of Nipah virus in Bangladesh: a nexus of land use change and opportunistic feeding behavior in bats ]]> https://biorxiv.org/content/10.1101/2020.11.30.404582v1?rss=1 McKee, C. D. Islam, A. Luby, S. P. Salje, H. Hudson, P. J. Plowright, R. K. Gurley, E. S. 2020-12-01 doi:10.1101/2020.11.30.404582 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ The genomic epidemiology of multi-drug resistant nontyphoidal Salmonella causing invasive disease in sub-Saharan Africa ]]> https://biorxiv.org/content/10.1101/2020.12.11.422246v1?rss=1 Park, S. E. Pham, D. T. Pak, G. D. Panzner, U. Espinoza, L. M. C. von Kalckreuth, V. Im, J. Mogeni, O. D. Schutt-Gerowitt, H. Crump, J. A. BREIMAN, R. F. Abu-Sarkodie, Y. Owusu-Dabo, E. Rakotozandrindrainy, R. Soura, A. B. Aseffa, A. Gasmelseed, N. Sooka, A. Keddy, K. H. May, J. Aaby, P. Biggs, H. M. Hertz, J. T. Montgomery, J. M. Cosmas, L. Olack, B. Fields, B. Sarpong, N. Razafindrabe, T. J. L. Raminosoa, T. M. Kabore, L. P. Sampo, E. Teferi, M. Yeshitela, B. Tayeb, M. A. E. Krumkamp, R. Dekker, D. M. Jaeger, A. Tall, A. Niang, A. Bjerregaard-Andersen, 2020-12-12 doi:10.1101/2020.12.11.422246 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Differential Expression of NPAS4 in the Dorsolateral Prefrontal Cortex Following Acute Opioid Intoxication ]]> https://biorxiv.org/content/10.1101/2020.12.23.424239v1?rss=1 Sosnowski, D. W. Jaffe, A. E. Tao, R. Deep-Soboslay, A. Kleinman, J. E. Hyde, T. M. Shu, C. Sabunciyan, S. Maher, B. S. 2020-12-23 doi:10.1101/2020.12.23.424239 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Intricate regulation of ribosome biogenesis genes in response to mTORC1 signaling ]]> https://biorxiv.org/content/10.1101/2021.01.04.425249v1?rss=1 Kumar, S. Mashkoor, M. Balamurugan, P. Grove, A. 2021-01-04 doi:10.1101/2021.01.04.425249 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver ]]> https://biorxiv.org/content/10.1101/2021.01.11.426100v1?rss=1 Hildebrandt, F. F. A. Andersson, A. Saarenpaa, S. Larsson, L. Van Hul, N. Kanatani, S. Masek, J. Ellis, E. Barragan, A. Mollbrink, A. Andersson, E. R. Lundeberg, J. Ankarklev, J. 2021-01-12 doi:10.1101/2021.01.11.426100 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Loss of C3aR induces immune infiltration and inflammatory microbiota in a novel spontaneous model of colon cancer ]]> https://biorxiv.org/content/10.1101/2021.01.18.426963v1?rss=1 Krieg, C. Carloni, S. Weber, L. M. Fosso, B. Hardiman, G. Mileti, E. El Aidy, S. Marzano, M. Pesole, G. Asnicar, F. Segata, N. Robinson, M. D. Guglietta, S. 2021-01-19 doi:10.1101/2021.01.18.426963 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Hinge Influences in Murine IgG Binding to Cryptococcus neoformans Capsule ]]> https://biorxiv.org/content/10.1101/2021.01.18.427174v1?rss=1 Oliveira, D. S. L. d. Paredes, V. Caixeta, A. V. Henriques, N. M. Wear, M. P. Albuquerque, P. Felipe, M. S. S. Casadevall, A. Nicola, A. M. 2021-01-19 doi:10.1101/2021.01.18.427174 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ High-order areas and auditory cortex both represent the high-level event structure of music ]]> https://biorxiv.org/content/10.1101/2021.01.26.428291v1?rss=1 Williams, J. A. Margulis, E. H. Nastase, S. A. Chen, J. Hasson, U. Norman, K. A. Baldassano, C. A. 2021-01-26 doi:10.1101/2021.01.26.428291 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor ]]> https://biorxiv.org/content/10.1101/2021.01.27.428431v1?rss=1 Righelli, D. Weber, L. M. Crowell, H. L. Pardo, B. Collado-Torres, L. Ghazanfar, S. Lun, A. T. Hicks, S. C. Risso, D. 2021-01-27 doi:10.1101/2021.01.27.428431 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Differential susceptibility of neuronal neurotransmitter phenotypes to HHV6 infection ]]> https://biorxiv.org/content/10.1101/2021.01.28.428686v1?rss=1 Bahramian, E. Furr, M. Wu, J. T. Ceballos, R. M. 2021-01-28 doi:10.1101/2021.01.28.428686 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Nitroxoline as a promising alternative drug for the treatment of Lyme disease based on an in-vitro study ]]> https://biorxiv.org/content/10.1101/2021.02.04.429852v1?rss=1 Alvarez-Manzo, H. S. Zhang, Y. Shi, W. Zhang, Y. 2021-02-05 doi:10.1101/2021.02.04.429852 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Placenta DNA methylation at ZNF300 is associated with fetal sex and placental morphology ]]> https://biorxiv.org/content/10.1101/2021.03.05.433992v1?rss=1 Ladd-Acosta, C. Andrews, S. V. Bakulski, K. M. Feinberg, J. I. Tryggvadottir, R. Yao, R. Croen, L. A. Hertz-Picciotto, I. Newschaffer, C. J. Salafia, C. M. Feinberg, A. P. Hansen, K. D. Fallin, M. D. 2021-03-07 doi:10.1101/2021.03.05.433992 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya ]]> https://biorxiv.org/content/10.1101/2021.03.10.434750v1?rss=1 Kariuki, S. Dyson, Z. A. Mbae, C. Ngetich, R. Kavai, S. Wairimu, C. Anyona, S. Gitau, N. Onsare, R. S. Ongandi, B. Duchene, S. Ali, M. Clemens, J. D. Holt, K. E. Dougan, G. 2021-03-10 doi:10.1101/2021.03.10.434750 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Differential expression of single-cell RNA-seq data using Tweedie models ]]> https://biorxiv.org/content/10.1101/2021.03.28.437378v1?rss=1 Mallick, H. Chatterjee, S. Chowdhury, S. Chatterjee, S. Rahnavard, A. Hicks, S. C. 2021-03-29 doi:10.1101/2021.03.28.437378 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ State dependence of neural networks on past history and stimulus presentation in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.04.09.439242v1?rss=1 Cecere, Z. T. Yemini, E. Sharpee, T. O. Chalasani, S. H. 2021-04-11 doi:10.1101/2021.04.09.439242 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Spatial genomics maps the structure, character and evolution of cancer clones ]]> https://biorxiv.org/content/10.1101/2021.04.16.439912v1?rss=1 Lomakin, A. Svedlund, J. Strell, C. Gataric, M. Shmatko, A. Park, J. S. Ju, Y. S. Dentro, S. Kleshchevnikov, V. Vaskivskyi, V. Li, T. Bayraktar, O. A. Moore, L. Pinder, S. Richardson, A. L. Campbell, P. J. Gerstung, M. Nilsson, M. Yates, L. R. 2021-04-16 doi:10.1101/2021.04.16.439912 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Redefining replication in multi-ancestry genome-wide association studies ]]> https://biorxiv.org/content/10.1101/2021.04.20.440612v1?rss=1 Smith, S. P. Shahamatdar, S. Cheng, W. Zhang, S. Paik, J. Graff, M. Haiman, C. A. Matise, T. C. North, K. E. Peters, U. Kenny, E. Gignoux, C. R. Wojcik, G. L. Crawford, L. Ramachandran, S. 2021-04-20 doi:10.1101/2021.04.20.440612 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data ]]> https://biorxiv.org/content/10.1101/2021.04.29.440149v1?rss=1 Pardo, B. Spangler, A. Weber, L. M. Hicks, S. C. Jaffe, A. E. Martinowich, K. Maynard, K. R. Collado-Torres, L. 2021-04-30 doi:10.1101/2021.04.29.440149 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Volumetric alteration of olfactory bulb and immune-related molecular changes in olfactory epithelium in first episode psychosis patients ]]> https://biorxiv.org/content/10.1101/2021.05.03.442464v1?rss=1 Yang, K. Hua, J. Etyemez, S. Paez, A. Prasad, N. Ishizuka, K. Sawa, A. Kamath, V. 2021-05-05 doi:10.1101/2021.05.03.442464 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Diversity and selection of SARS-CoV-2 minority variants in the early New York City outbreak ]]> https://biorxiv.org/content/10.1101/2021.05.05.442873v1?rss=1 Roder, A. Khalfan, M. Johnson, K. E. Ruchnewitz, D. Knoll, M. Banakis, S. Wang, W. Samanovic, M. I. Mulligan, M. J. Gresham, D. Laessig, M. Luksza, M. Ghedin, E. 2021-05-06 doi:10.1101/2021.05.05.442873 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Rapid Estimation of SNP Heritability using Predictive Process approximation in Large scale Cohort Studies ]]> https://biorxiv.org/content/10.1101/2021.05.12.443931v1?rss=1 Seal, S. Datta, A. Basu, S. 2021-05-14 doi:10.1101/2021.05.12.443931 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ A dentate gyrus-CA3 inhibitory circuit promotes evolution of hippocampal-cortical ensembles during memory consolidation ]]> https://biorxiv.org/content/10.1101/2021.05.21.445117v1?rss=1 Twarkowski, H. Steininger, V. Kim, M. J. Sahay, A. 2021-05-21 doi:10.1101/2021.05.21.445117 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ A homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium ]]> https://biorxiv.org/content/10.1101/2021.06.02.446828v1?rss=1 Van Winkle, J. A. Peterson, S. T. Kennedy, E. A. Wheadon, M. J. Ingle, H. Desai, C. Constant, D. A. Wright, A. P. Li, L. Artyomov, M. Lee, S. Baldridge, M. T. Nice, T. J. 2021-06-02 doi:10.1101/2021.06.02.446828 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Fungal extracellular vesicles are involved in intraspecies intracellular communication ]]> https://biorxiv.org/content/10.1101/2021.06.03.447024v1?rss=1 Bittencourt, T. A. Hatanaka, O. Pessoni, A. M. Freitas, M. S. Trentin, G. Santos, P. Rossi, A. Martinez-Rossi, N. M. Alves, L. R. Casadevall, A. Rodrigues, M. Almeida, F. 2021-06-05 doi:10.1101/2021.06.03.447024 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters ]]> https://biorxiv.org/content/10.1101/2021.06.16.448525v1?rss=1 Wuertz, K. M. Barkei, E. Chen, W.-h. Martinez, E. J. Naouar, I. E. Jagodzinski, L. Paquin-Proulx, D. Gromowski, G. D. Swafford, I. Ganesh, A. Dong, M. Zeng, X. Thomas, P. V. Sankhala, R. S. Hajduczki, A. Peterson, C. E. Kuklis, C. H. Soman, S. Wieczorek, L. Zemil, M. Anderson, A. Darden, J. Hernandez, H. Grove, H. Dussupt, V. Hack, H. de la Barrera, R. A. Zarling, S. N. Wood, J. F. Froude, J. W. Gagne, M. J. Henry, A. R. Mokhtari, E. B. Mudvari, P. Krebs, S. J. Pekosz, A. S. Currier, J. R. Kar, S. Porto, M. Winn, A. Radzyminski, K. Lewis, M. G. Vasan, 2021-06-16 doi:10.1101/2021.06.16.448525 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ GLI transcriptional repression is inert prior to Hedgehog pathway activation ]]> https://biorxiv.org/content/10.1101/2021.06.29.450392v1?rss=1 Lex, R. K. Zhou, W. Ji, Z. Falkenstein, K. N. Schuler, K. E. Windsor, K. E. Kim, J. D. Ji, H. Vokes, S. A. 2021-06-29 doi:10.1101/2021.06.29.450392 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples ]]> https://biorxiv.org/content/10.1101/2021.07.10.451910v1?rss=1 Hou, W. Ji, Z. Chen, Z. Wherry, E. J. Hicks, S. C. Ji, H. 2021-07-12 doi:10.1101/2021.07.10.451910 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Critical Assessment of Metagenome Interpretation - the second round of challenges ]]> https://biorxiv.org/content/10.1101/2021.07.12.451567v1?rss=1 Meyer, F. Fritz, A. Deng, Z.-L. Koslicki, D. Gurevich, A. Robertson, G. Zhu, J. Jia, H. Kola, A. Limasset, A. Kolmogorov, M. Egan, R. Rosen, G. L. Cristian, A. Zhao, Z. Gray, M. A. Nissen, J. Zeller, G. Paoli, L. Ruscheweyh, H.-J. Milanese, A. Sunagawa, S. Alser, M. Shi, L. Chen, B. Wang, Z. Wang, Z. Huang, P. You, R. Sun, F. Zhu, S. Bertrand, D. Tong, C. Li, C. Nagarajan, N. Renard, B. Malcher-Miranda, F. Piro, V. C. Chikhi, R. Vicedomini, R. Wang, Z. Thomas, A. Tremblay, J. Dabrowski, P. W. Nurk, S. Jorgensen, T. S. Willassen, N. P. Klemetsen, T 2021-07-12 doi:10.1101/2021.07.12.451567 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ NO-stressed Y. pseudotuberculosis have decreased cell division rates in the mouse spleen ]]> https://biorxiv.org/content/10.1101/2021.08.04.455180v1?rss=1 Liu, B. Davidson, R. K. Davis, K. M. 2021-08-05 doi:10.1101/2021.08.04.455180 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Nuclear SUN1 stabilizes endothelial cell junctions to regulate blood vessel formation ]]> https://biorxiv.org/content/10.1101/2021.08.11.455980v1?rss=1 Buglak, D. B. Gold, A. L. Marvin, A. P. Ricketts, S. N. Oatley, M. Tanke, N. T. Johnson, B. N. Bautch, V. L. 2021-08-11 doi:10.1101/2021.08.11.455980 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Protection against SARS-CoV-2 Beta Variant in mRNA-1273 Boosted Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2021.08.11.456015v1?rss=1 Corbett, K. S. Gagne, M. Wagner, D. O'Connell, S. Narpala, S. R. Flebbe, D. R. Andrew, S. F. Davis, R. L. Flynn, B. Johnston, T. S. Stringham, C. Lai, L. Valentin, D. Van Ry, A. Flinchbaugh, Z. Werner, A. P. Moliva, J. I. Sriparna, M. O'Dell, S. Schmidt, S. D. Tucker, C. Choi, A. Koch, M. Bock, K. W. Minai, M. Nagata, B. M. Alvarado, G. S. Henry, A. R. Laboune, F. Schramm, C. A. Zhang, Y. Wang, L. Choe, M. Boyoglu-Barnum, S. Shi, W. Lamb, E. Nurmukhambetova, S. T. Provost, S. J. Donaldson, M. M. Marquez, J. Todd, J.-P. M. Cook, A. Dodson, A. Pekosz, A 2021-08-12 doi:10.1101/2021.08.11.456015 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ The Rules of Pulsatile Neurostimulation ]]> https://biorxiv.org/content/10.1101/2021.08.18.456731v1?rss=1 Steinhardt, C. R. Mitchell, D. E. Cullen, K. E. Fridman, G. Y. 2021-08-19 doi:10.1101/2021.08.18.456731 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Critical Role for Isoprenoids in Apicoplast Biogenesis by Malaria Parasites ]]> https://biorxiv.org/content/10.1101/2021.08.19.456988v1?rss=1 Okada, M. Rajaram, K. Swift, R. P. Mixon, A. Maschek, J. A. Prigge, S. T. Sigala, P. A. 2021-08-19 doi:10.1101/2021.08.19.456988 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Characterization of USH1C/harmonin in the human retina provides insights into pathophysiology and therapy options for Usher syndrome ]]> https://biorxiv.org/content/10.1101/2021.08.27.457962v1?rss=1 Nagel-Wolfrum, K. Fadl, B. R. Becker, M. M. Wunderlich, K. A. Schaefer, J. Sturm, D. Guer, B. Kaplan, L. Goldmann, T. Brooks, M. Starostik, M. R. Apel, M. Fath, K. R. Stingl, K. Kohl, S. Andrade, M. Vetter, J. M. Pfeiffer, N. Grosche, A. A. Swaroop, A. Wolfrum, U. 2021-08-27 doi:10.1101/2021.08.27.457962 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Targeting metabolic adaptations in the breast cancer liver metastatic niche using dietary approaches to improve endocrine therapy efficacy ]]> https://biorxiv.org/content/10.1101/2021.09.07.458711v1?rss=1 Zuo, Q. Mogol, A. N. Liu, Y.-J. Casiano, A. S. Chien, C. Drnevich, J. Imir, O. B. Kulkoyluoglu-Cotul, E. Park, N. H. Shapiro, D. J. Park, B. H. Ziegler, Y. Katzenellenbogen, B. S. Aranda, E. O'Neill, J. D. Raghavendra, A. S. Tripathy, D. Madak-Erdogan, Z. 2021-09-07 doi:10.1101/2021.09.07.458711 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Variant surface glycoprotein expression in human African trypanosomiasis patients ]]> https://biorxiv.org/content/10.1101/2021.09.09.459620v1?rss=1 So, J. Sudlow, S. Sayeed, A. Grudda, T. Deborggraeve, S. Ngoyi, D. M. Desamber, D. K. Wickstead, B. Lejon, V. Mugnier, M. R. 2021-09-09 doi:10.1101/2021.09.09.459620 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Batch effects removal for microbiome data via conditional quantile regression (ConQuR) ]]> https://biorxiv.org/content/10.1101/2021.09.23.461592v1?rss=1 Ling, W. Zhao, N. Lulla, A. Plantinga, A. M. Fu, W. Zhang, A. Liu, H. Li, Z. Chen, J. Randolph, T. Koay, W. L. A. White, J. R. Launer, L. J. Fodor, A. A. Meyer, K. A. Wu, M. C. 2021-09-24 doi:10.1101/2021.09.23.461592 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Molecular assembly of measles and Nipah virus: specific lipid binding drives conformational change and matrix polymerization ]]> https://biorxiv.org/content/10.1101/2021.10.11.463969v1?rss=1 Norris, M. J. Husby, M. L. Kiosses, W. B. Yin, J. Rennick, L. J. Heiner, A. Harkins, S. S. Pokhrel, R. Schendel, S. L. Hastie, K. M. Landeras-Bueno, S. Li Salie, Z. Lee, B. Chapagain, P. P. Maisner, A. Duprex, W. P. Stahelin, R. V. Ollmann Saphire, E. 2021-10-11 doi:10.1101/2021.10.11.463969 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ New from old: discovery of the novel antibiotic actinomycin L in Streptomyces sp. MBT27 ]]> https://biorxiv.org/content/10.1101/2021.10.12.464064v1?rss=1 Machushynets, N. Elsayed, S. S. Du, C. Siegler, M. A. de la Cruz, M. Genilloud, O. Hankemeier, T. van Wezel, G. P. 2021-10-12 doi:10.1101/2021.10.12.464064 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ The Formation of a Stable Sliding Clamp Discriminates MSH2-MSH3 and MSH2-MSH6 Mismatch Interaction ]]> https://biorxiv.org/content/10.1101/2021.10.21.465318v1?rss=1 Britton, B. M. London, J. A. Martin-Lopez, J. Jones, N. D. Liu, J. Lee, J.-B. Fishel, R. 2021-10-21 doi:10.1101/2021.10.21.465318 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Tree-based Correlation Screen and Visualization for Exploring Phenotype-Cell Type Association in Multiple Sample Single-Cell RNA-Sequencing Experiments ]]> https://biorxiv.org/content/10.1101/2021.10.27.466024v1?rss=1 Zhang, B. Ji, Z. Ji, H. 2021-10-29 doi:10.1101/2021.10.27.466024 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function ]]> https://biorxiv.org/content/10.1101/2021.11.01.466782v1?rss=1 Bygrave, A. M. Sengupta, A. Jackert, E. P. Ahmed, M. Adenuga, B. Nelson, E. Goldschmidt, H. L. Johnson, R. C. Zhong, H. Yeh, F. L. Sheng, M. Huganir, R. L. 2021-11-02 doi:10.1101/2021.11.01.466782 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications ]]> https://biorxiv.org/content/10.1101/2021.11.01.466809v1?rss=1 Alvarez-Manzo, H. S. Davidson, R. K. Van Cauwelaert de Wyels, J. Cotten, K. L. Nguyen, B. Zhu, Z. Anthony, J. van Opijnen, T. Davis, K. M. 2021-11-01 doi:10.1101/2021.11.01.466809 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ A vaccine targeting the L9 epitope of the malaria circumsporozoite protein confers protection from blood-stage infection in a mouse challenge model ]]> https://biorxiv.org/content/10.1101/2021.11.10.465032v1?rss=1 Jelinkova, L. Flores-Garcia, Y. Shapiro, S. Roberts, B. T. Petrovsky, N. Zavala, F. Chackerian, B. 2021-11-11 doi:10.1101/2021.11.10.465032 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ The mouse mammary tumor virus intasome exhibits distinct dynamics on target DNA ]]> https://biorxiv.org/content/10.1101/2021.11.17.468995v1?rss=1 Baltierra-Jasso, L. E. Jones, N. D. Ballandras-Collas, A. Engelman, A. Fishel, R. Yoder, K. E. 2021-11-17 doi:10.1101/2021.11.17.468995 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Bet-hedging antimicrobial strategies in macrophage phagosome acidification drive the dynamics of Cryptococcus neoformans intracellular escape mechanisms ]]> https://biorxiv.org/content/10.1101/2021.11.29.470444v1?rss=1 Dragotakes, Q. Jacobs, E. Ramirez, L. S. Yoon, O. I. Perez-Stable, C. Eden, H. Pagnotta, J. Vij, R. Bergman, A. D'Alessio, F. Casadevall, A. 2021-11-29 doi:10.1101/2021.11.29.470444 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals ]]> https://biorxiv.org/content/10.1101/2021.12.06.471446v1?rss=1 Redd, A. Nardin, A. Kared, H. Bloch, E. M. Abel, B. Pekosz, A. Laeyendecker, O. Fehlings, M. Quinn, T. Tobian, A. A. 2021-12-09 doi:10.1101/2021.12.06.471446 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Pre-determined diversity in resistant fates emerges from homogenous cells after anti-cancer drug treatment ]]> https://biorxiv.org/content/10.1101/2021.12.08.471833v1?rss=1 Goyal, Y. Dardani, I. P. Busch, G. T. Emert, B. Fingerman, D. Kaur, A. Jain, N. Mellis, I. A. Li, J. Kiani, K. Fane, M. E. Weeraratna, A. T. Herlyn, M. Raj, A. 2021-12-09 doi:10.1101/2021.12.08.471833 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Brain regulatory program predates central nervous system evolution ]]> https://biorxiv.org/content/10.1101/2021.12.10.472178v1?rss=1 Faltine-Gonzalez, D. Z. Havrilak, J. A. Layden, M. J. 2021-12-13 doi:10.1101/2021.12.10.472178 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Non-toxigenic Vibrio cholerae challenge strains for evaluating vaccine efficacy and inferring mechanisms of protection ]]> https://biorxiv.org/content/10.1101/2021.12.17.473008v1?rss=1 Fakoya, B. Hullahalli, K. Rubin, D. H. F. Leitner, D. R. Chilengi, R. Sack, D. Waldor, M. K. 2021-12-18 doi:10.1101/2021.12.17.473008 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Nipah virus detection at bat roosts following spillover events in Bangladesh, 2012-2019 ]]> https://biorxiv.org/content/10.1101/2021.12.29.474445v1?rss=1 McKee, C. D. Islam, A. Rahman, M. Z. Khan, S. U. Rahman, M. Satter, S. M. Islam, A. Yinda, C. K. Epstein, J. H. Daszak, P. Munster, V. J. Hudson, P. J. Plowright, R. K. Luby, S. P. Gurley, E. S. 2021-12-30 doi:10.1101/2021.12.29.474445 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Modulation of sleep by trafficking of lipids through the Drosophila blood brain barrier ]]> https://biorxiv.org/content/10.1101/2022.02.17.480875v1?rss=1 Artiushin, G. Li, F. Sehgal, A. 2022-02-19 doi:10.1101/2022.02.17.480875 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Ethanol exposure alters Alzheimer's-related pathology, behavior, and metabolism ]]> https://biorxiv.org/content/10.1101/2022.02.18.481066v1?rss=1 Gironda, S. C. Day, S. M. Clarke, C. W. Snipes, J. A. Nicol, N. I. Kamran, H. Vaughan, W. Macauley, S. L. Weiner, J. L. 2022-02-20 doi:10.1101/2022.02.18.481066 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Kir6.2-containing KATP channels are necessary for glucose dependent increases in amyloid-beta and Alzheimer's-related pathology ]]> https://biorxiv.org/content/10.1101/2022.02.20.481215v1?rss=1 Grizzanti, J. Moritz, W. R. Pait, M. C. Stanley, M. Kaye, S. D. Carroll, C. M. Constantino, N. J. Deitelzweig, L. T. Nicol, N. I. Snipes, J. A. Kellar, D. Caesar, E. E. Dhillon, J. Remedi, M. S. Karch, C. Nichols, C. G. Holtzman, D. M. Macauley, S. L. 2022-02-20 doi:10.1101/2022.02.20.481215 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease ]]> https://biorxiv.org/content/10.1101/2022.03.02.480688v1?rss=1 Frazier, M. N. Wilson, I. M. Krahn, J. M. Butay, K. J. Dillard, L. B. Borgnia, M. J. N. Stanley, R. E. 2022-03-02 doi:10.1101/2022.03.02.480688 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Palo: Spatially-aware color palette optimization for single-cell and spatial data ]]> https://biorxiv.org/content/10.1101/2022.03.13.484080v1?rss=1 Hou, W. Ji, Z. 2022-03-14 doi:10.1101/2022.03.13.484080 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Melanization is an important antifungal defense mechanism in Galleria mellonella hosts ]]> https://biorxiv.org/content/10.1101/2022.04.02.486843v1?rss=1 Smith, D. F. Q. Dragotakes, Q. Kulkarni, M. Hardwick, J. M. Casadevall, A. 2022-04-03 doi:10.1101/2022.04.02.486843 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Identification of Antimalarial Compounds that Inhibit Apicomplexan AP2 Proteins ]]> https://biorxiv.org/content/10.1101/2022.04.05.487101v1?rss=1 2 for 50% (46/93) of AP2-EXP target genes. Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that are targeted against the ApiAP2 family of proteins. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics. Author SummaryPlasmodium parasites are the causative agent of malaria, which resulted in over 600,000 deaths in 2021. Due to resistance arising for every antimalarial therapeutic deployed to date, new drug targets and druggable pathways must be explored. To address this concern, we used a molecular docking screen to predict competitors of DNA binding by the parasite specific family of Apicomplexan AP2 (ApiAP2) transcription factor proteins for testing in vitro and in vivo. We find that ApiAP2 competing compounds have antimalarial activity consistent with the disruption of gene regulation. This work will further our understanding of both the biological role and targetability of parasite transcriptional regulation. ]]> Russell, T. J. De Silva, E. K. Crowley, V. Shaw-Saliba, K. Dube, N. Josling, G. Pasaje, C. F. A. Kouskoumvekaki, I. Panagiotou, G. Niles, J. C. JACOBS-LORENA, M. Okafor, C. D. Gamo, F.-J. Llinas, M. 2022-04-06 doi:10.1101/2022.04.05.487101 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Propofol disrupts alpha dynamics in distinct thalamocortical networks underlying sensory and cognitive function during loss of consciousness ]]> https://biorxiv.org/content/10.1101/2022.04.05.487190v1?rss=1 Weiner, V. S. Zhou, D. W. Kahali, P. Stephen, E. P. Peterfreund, R. A. Aglio, L. S. Szabo, M. D. Eskandar, E. N. Salazar-Gomez, A. F. Sampson, A. L. Cash, S. S. Brown, E. N. Purdon, P. L. 2022-04-08 doi:10.1101/2022.04.05.487190 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Unexpected proteinopathies in hippocampal PDE11A4 promote age-related cognitive decline of social associative memories ]]> https://biorxiv.org/content/10.1101/2022.04.08.487696v1?rss=1 Pilarzyk, K. ( Porcher, L. Capell, W. R. Burbano, S. D. Davis, J. Fisher, J. Gorny, N. Petrolle, S. Kelly, M. P. 2022-04-10 doi:10.1101/2022.04.08.487696 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Characterization of enterovirus D68 infection in four nonhuman primate species ]]> https://biorxiv.org/content/10.1101/2022.04.16.487524v1?rss=1 Dearing, J. Conte, A. Brooks, C. Zimina, A. Birch, S. M. Adney, D. R. Li, M. Rascon, A. Belov, G. A. Pekosz, A. Vermillion, M. S. 2022-04-17 doi:10.1101/2022.04.16.487524 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data ]]> https://biorxiv.org/content/10.1101/2022.04.20.488947v1?rss=1 Eagles, N. J. Wilton, R. Jaffe, A. E. Torres, L. C. 2022-04-21 doi:10.1101/2022.04.20.488947 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Identification of Transient Intermediates During Spliceosome Activation by Single Molecule Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/2022.04.23.488636v1?rss=1 Fu, X. Kaur, H. Rodgers, M. L. Montemayor, E. BUTCHER, S. E. Hoskins, A. 2022-04-23 doi:10.1101/2022.04.23.488636 Cold Spring Harbor Laboratory Press 2022-04-23 <![CDATA[ Data-driven Identification of Total RNA Expression Genes (TREGs) for Estimation of RNA Abundance in Heterogeneous Cell Types ]]> https://biorxiv.org/content/10.1101/2022.04.28.489923v1?rss=1 Huuki-Myers, L. A. Montgomery, K. D. Kwon, S. H. Page, S. C. Hicks, S. C. Maynard, K. R. Collado-Torres, L. 2022-04-29 doi:10.1101/2022.04.28.489923 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Fc-engineered antibodies leverage neutrophils to drive control of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.05.01.490220v1?rss=1 Irvine, E. B. Peters, J. M. Lu, R. Grace, P. S. Sixsmith, J. Wallace, A. Schneider, M. Shin, S. Karpinski, W. Hsiao, J. C. van Woudenbergh, E. Casadevall, A. Bryson, B. D. Cavacini, L. Alter, G. Fortune, S. M. 2022-05-01 doi:10.1101/2022.05.01.490220 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Non-Covalently Associated Streptavidin Multi-Arm Nanohubs Exhibit Mechanical and Thermal Stability in Protein-Network Materials ]]> https://biorxiv.org/content/10.1101/2022.05.09.491252v1?rss=1 Knoff, D. S. Kim, S. Y. Fajardo Cortes, K. A. Rivera, J. Altamirano, D. Kim, M. 2022-05-10 doi:10.1101/2022.05.09.491252 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ NMR as a readout to monitor and restore the integrity of complex chemoenzymatic reactions ]]> https://biorxiv.org/content/10.1101/2022.05.14.491371v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@11bc2e6org.highwire.dtl.DTLVardef@198ab6forg.highwire.dtl.DTLVardef@1f0747org.highwire.dtl.DTLVardef@116fcbf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Marincin, K. A. Hwang, Y. Kengmana, E. S. Meyers, D. J. Frueh, D. P. 2022-05-14 doi:10.1101/2022.05.14.491371 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ nnSVG: scalable identification of spatially variable genes using nearest-neighbor Gaussian processes ]]> https://biorxiv.org/content/10.1101/2022.05.16.492124v1?rss=1 Weber, L. M. Saha, A. Datta, A. Hansen, K. D. Hicks, S. C. 2022-05-16 doi:10.1101/2022.05.16.492124 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ A computational proposal for tracking multiple molecules in a multi-focus confocal setup ]]> https://biorxiv.org/content/10.1101/2022.05.17.492362v1?rss=1 Jazani, S. Xu, L. Sgouralis, I. Shepherd, D. P. Presse, S. 2022-05-19 doi:10.1101/2022.05.17.492362 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Inhibition of Tgfβ signaling enables durable ventricular pacing by TBX18 gene transfer ]]> https://biorxiv.org/content/10.1101/2022.06.02.493572v1?rss=1 Fan, J. Kim, N. K. Fernandez, N. Kim, T. Y. Li, J. Wolfson, D. Cho, H. C. 2022-06-03 doi:10.1101/2022.06.02.493572 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Disrupting cellular memory to overcome drug resistance ]]> https://biorxiv.org/content/10.1101/2022.06.16.496161v1?rss=1 Harmange, G. Reyes Hueros, R. A. Schaff, D. L. Emert, B. L. Saint-Antoine, M. M. Nellore, S. Fane, M. E. Alicea, G. M. Weeraratna, A. T. Singh, A. Shaffer, S. M. 2022-06-17 doi:10.1101/2022.06.16.496161 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ NRX-101, A RAPID-ACTING ANTI-DEPRESSANT, DOES NOT CAUSE NEUROTOXICITY FOLLOWING KETAMINE ADMINISTRATION IN PRECLINICAL MODELS ]]> https://biorxiv.org/content/10.1101/2022.06.18.496662v1?rss=1 Jordan, W. Siegel, R. Kumar, R. Javitt, J. C. 2022-06-20 doi:10.1101/2022.06.18.496662 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ RetroFun-RVS: a retrospective family-based framework for rare-variant analysis incorporating functional annotations ]]> https://biorxiv.org/content/10.1101/2022.06.21.497085v1?rss=1 Mangnier, L. Bureau, A. 2022-06-26 doi:10.1101/2022.06.21.497085 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Extravascular spaces are reservoirs of antigenic diversity in Trypanosoma brucei infection ]]> https://biorxiv.org/content/10.1101/2022.06.27.497797v1?rss=1 Beaver, A. Crilly, N. P. Hakim, J. Zhang, B. Bobb, B. Rijo-Ferreira, F. Figueiredo, L. M. Mugnier, M. R. 2022-06-27 doi:10.1101/2022.06.27.497797 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals ]]> https://biorxiv.org/content/10.1101/2022.07.11.499652v1?rss=1 Sohail, M. Chong, A. Y. Quinto-Cortes, C. D. Palma-Martinez, M. J. Ragsdale, A. Medina-Munoz, S. G. Barberena-Jonas, C. Delgado-Sanchez, G. Cruz-Hervert, L. P. Ferreyra-Reyes, L. Ferreira-Guerrero, E. Mongua-Rodriguez, N. Jimenez-Kaufmann, A. Moreno-Macias, H. Aguilar-Salinas, C. A. Auckland, K. Cortes, A. Acuna-Alonzo, V. Ioannidis, A. G. Gignoux, C. R. Wojcik, G. L. Fernandez-Valverde, S. L. Hill, A. V. S. Tusie-Luna, M. T. Mentzer, A. J. Novembre, J. Garcia-Garcia, L. Moreno-Estrada, A. 2022-07-13 doi:10.1101/2022.07.11.499652 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Structural and functional landscape of α-synuclein fibril conformations amplified from cerebrospinal fluid ]]> https://biorxiv.org/content/10.1101/2022.07.13.499896v1?rss=1 Sokratian, A. Zhou, Y. Xu, E. Viverette, E. Dillard, L. Yuan, Y. Li, J. Matarangas, A. Bouvette, J. Borgnia, M. J. Bartesaghi, A. West, A. 2022-07-13 doi:10.1101/2022.07.13.499896 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference ]]> https://biorxiv.org/content/10.1101/2022.07.20.500802v1?rss=1 Meng, X. Navoly, G. Giannakopoulou, O. DL, D. Koller, D. Pathak, G. Koen, N. Lin, K. Renteria, M. Feng, Y. Gaziano, J. M. Stein, D. Zar, H. Campbell, M. van Heel, D. Trivedi, B. Finer, S. McQuillin, A. Bass, N. Chundru, V. K. Martin, H. Huang, Q. Q. Valkovskaya, M. Kuo, P.-H. Chen, H.-C. Tsai, S.-J. Liu, Y.-L. Kendler, K. Peterson, R. Cai, N. Fang, Y. Sen, S. Scott, L. Burmeister, M. Loos, R. Preuss, M. Actkins, K. Davis, L. Uddin, M. Wani, A. Wildman, D. Ursano, R. Kessler, R. Kanai, M. Okada, Y. Sakaue, S. Rabinowitz, J. Maher, B. Uhl, G. Eato 2022-07-21 doi:10.1101/2022.07.20.500802 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ D-cycloserine, a mixed NMDAR agonist/antagonist is Not Susceptible to Self-administration, unlike S-ketamine Using an Intravenous Self-administration Model in Naive and Ketamine-habituated Sprague-Dawley Rats ]]> https://biorxiv.org/content/10.1101/2022.08.12.503713v1?rss=1 Javitt, D. C. Javitt, J. C. 2022-08-15 doi:10.1101/2022.08.12.503713 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ 3D RNA-scaffolded wireframe origami ]]> https://biorxiv.org/content/10.1101/2022.08.15.504019v1?rss=1 Parsons, M. F. Allan, M. F. Li, S. Shepherd, T. R. Ratanalert, S. Zhang, K. Pullen, K. M. Chiu, W. Rouskin, S. Bathe, M. 2022-08-16 doi:10.1101/2022.08.15.504019 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ The efficiency of Grignard Pure™ to inactivate airborne SARS-CoV-2 surrogate ]]> https://biorxiv.org/content/10.1101/2022.08.19.504307v1?rss=1 Desai, G. Ramachandran, G. Goldman, E. Galione, A. Lal, A. Choueiri, T. K. Fay, A. Jordan, W. Schaffner, D. W. Caravanos, J. Grignard, E. Mainelis, G. 2022-08-23 doi:10.1101/2022.08.19.504307 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ CRISPR Mediated Transactivation in the Human Disease Vector Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2022.08.31.505972v1?rss=1 Bui, M. Benetta, E. D. Dong, Y. Zhao, Y. Yang, T. Li, M. Antoshechkin, I. A. Buchman, A. Bottino-Rojas, V. James, A. A. Perry, M. W. Dimopoulos, G. Akbari, O. 2022-09-02 doi:10.1101/2022.08.31.505972 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ A neuroepithelial wave of BMP signalling drives anteroposterior specification of the tuberal hypothalamus ]]> https://biorxiv.org/content/10.1101/2022.08.31.506043v1?rss=1 Placzek, M. Chinnaiya, K. Burbridge, S. Jones, A. Kim, D. W. Place, E. Manning, E. Groves, I. Sun, C. Towers, M. Blackshaw, S. 2022-09-02 doi:10.1101/2022.08.31.506043 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Understanding changes in genetic literacy over time and in genetic research participants ]]> https://biorxiv.org/content/10.1101/2022.09.12.507568v1?rss=1 Little, I. D. Koehly, L. M. Gunter, C. 2022-09-14 doi:10.1101/2022.09.12.507568 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Affinity-matured homotypic interactions induce spectrum of PfCSP-antibody structures that influence protection from malaria infection ]]> https://biorxiv.org/content/10.1101/2022.09.20.508747v1?rss=1 Martin, G. Torres, J. L. Pholcharee, T. Oyen, D. Flores-Garcia, Y. Gibson, G. Moskovitz, R. Beutler, N. Jung, D. D. Copps, J. Lee, W.-H. Gonzalez-Paez, G. Emerling, D. MacGill, R. S. Locke, E. King, C. R. Zavala, F. Wilson, I. A. Ward, A. 2022-09-21 doi:10.1101/2022.09.20.508747 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Machine Learning Optimization of Candidate Antibodies Yields Highly Diverse Sub-nanomolar Affinity Antibody Libraries ]]> https://biorxiv.org/content/10.1101/2022.10.07.502662v1?rss=1 Li, L. Gupta, E. Spaeth, J. Shing, L. Jaimes, R. Caceres, R. S. Bepler, T. Walsh, M. E. 2022-10-07 doi:10.1101/2022.10.07.502662 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ The START domain potentiates HD-ZIPIII transcriptional activity ]]> https://biorxiv.org/content/10.1101/2022.10.08.511209v1?rss=1 Husbands, A. Y. Feller, A. Aggarwal, V. Dresden, C. E. Holub, A. S. Ha, T. Timmermans, M. C. P. 2022-10-08 doi:10.1101/2022.10.08.511209 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ A TMT-based quantitative proteomics approach toward α-syn PFF associated Lewy Body Dementia (LBD) using α-syn PFF-injected mouse brain tissues ]]> https://biorxiv.org/content/10.1101/2022.10.10.511662v1?rss=1 Akkentli, F. Jang, I. k. Choi, Y. Yoo, D. Oh, E. J.-H. Na, C. H. Ha, S. Kang, S.-U. 2022-10-11 doi:10.1101/2022.10.10.511662 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Deciphering the non-coding code of pathogenicity and sexual differentiation in the human malaria parasite. ]]> https://biorxiv.org/content/10.1101/2022.10.12.511630v1?rss=1 Batugedara, G. Lu, X. M. Abel, S. Chahine, Z. Hristov, B. Williams, D. Hollin, T. Wang, T. Cort, A. Lenz, T. Thompson, T. Prudhomme, J. Tripathi, A. K. Xu, G. Cudini, J. Dogga, S. Lawniczak, M. Stafford Noble, W. Sinnis, P. Le Roch, K. G. 2022-10-14 doi:10.1101/2022.10.12.511630 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ YAP condensates are highly organized hubs for YAP/TEAD transcription ]]> https://biorxiv.org/content/10.1101/2022.10.24.513621v1?rss=1 Hao, S. Fuehrer, H. Flores, E. Demmerle, J. Lippincott-Schwartz, J. Liu, Z. Sukenik, S. Cai, D. 2022-10-26 doi:10.1101/2022.10.24.513621 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Daily Artificial Gravity is Associated with Greater Neural Efficiency during Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2022.10.27.514043v1?rss=1 Tays, G. Hupfeld, K. McGregor, H. Beltran, N. Kofman, I. DeDios, Y. Mulder, E. Bloomberg, J. Mulavara, A. Wood, S. Seidler, R. 2022-10-28 doi:10.1101/2022.10.27.514043 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Equalizing epigenetically imprinted centromeres in early mammalian embryos ]]> https://biorxiv.org/content/10.1101/2022.10.27.514094v1?rss=1 Manske, G. Jorgensen, K. Ma, B. Aboelenain, M. Tower, C. Chakraborty, S. Ranjan, R. Das, A. Lampson, M. A. Black, B. E. Schindler, K. Chen, X. Hammoud, S. S. 2022-10-28 doi:10.1101/2022.10.27.514094 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.10.28.514241v1?rss=1 Weber, L. M. Divecha, H. R. Tran, M. N. Kwon, S. H. Spangler, A. Montgomery, K. D. Tippani, M. Bharadwaj, R. Kleinman, J. E. Page, S. C. Hyde, T. M. Collado-Torres, L. Maynard, K. R. Martinowich, K. Hicks, S. C. 2022-10-28 doi:10.1101/2022.10.28.514241 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Quorum sensing peptidic inhibitor rescue host immune system eradication: a novel QS infectivity mechanism ]]> https://biorxiv.org/content/10.1101/2022.10.28.514287v1?rss=1 Yehuda, A. Malach, E. Slamti, L. Shuan Kuo, S. Z. Lau, J. Whan Oh, M. Adeoye, J. Shlezinger, N. Lau, G. Lereclus, D. Hayouka, Z. 2022-10-30 doi:10.1101/2022.10.28.514287 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Bursting Translation on Single mRNAs in Live Cells ]]> https://biorxiv.org/content/10.1101/2022.11.07.515520v1?rss=1 Livingston, N. M. Kwon, J. Valera, O. Saba, J. A. Sinha, N. K. Reddy, P. Nelson, B. Wolfe, C. Ha, T. Green, R. Liu, J. Wu, B. 2022-11-08 doi:10.1101/2022.11.07.515520 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Voltage-gated sodium channel activity mediates sea urchin larval skeletal patterning through spatial regulation of Wnt5 expression ]]> https://biorxiv.org/content/10.1101/2022.11.18.517086v1?rss=1 Thomas, C. F. Hawkins, D. Y. Skidanova, V. Marrujo, S. R. Gibson, J. Ye, Z. Bradham, C. A. 2022-11-18 doi:10.1101/2022.11.18.517086 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Activity-regulated gene expression across cell types of the mouse hippocampus ]]> https://biorxiv.org/content/10.1101/2022.11.23.517593v1?rss=1 Nelson, E. D. Maynard, K. R. Nicholas, K. R. Tran, M. N. Divecha, H. R. Collado-Torres, L. Hicks, S. C. Martinowich, K. 2022-11-24 doi:10.1101/2022.11.23.517593 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Plasma after both SARS-CoV-2 boosted vaccination and COVID-19 potently neutralizes BQ1.1 and XBB. ]]> https://biorxiv.org/content/10.1101/2022.11.25.517977v1?rss=1 Sullivan, D. J. Franchini, M. Senefeld, J. Joyner, M. Casadevall, A. Focosi, D. 2022-11-28 doi:10.1101/2022.11.25.517977 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Cell dichotomous role of STING in pulmonary hypertension ]]> https://biorxiv.org/content/10.1101/2022.11.29.518422v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@7f5b50org.highwire.dtl.DTLVardef@143e485org.highwire.dtl.DTLVardef@4fe1a4org.highwire.dtl.DTLVardef@66fe26_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pham, A. T. Oliveira, A. C. Fu, C. Alves, M. D. Dupee, Z. Mukhsinova, L. Ebrahimi, E. Patel, H. Patel, R. Nguyen, A. jin, l. Bryant, A. J. 2022-11-29 doi:10.1101/2022.11.29.518422 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors ]]> https://biorxiv.org/content/10.1101/2022.12.04.519045v1?rss=1 Hippen, A. A. Omran, D. K. Weber, L. M. Jung, E. Drapkin, R. Doherty, J. A. Hicks, S. C. Greene, C. S. 2022-12-05 doi:10.1101/2022.12.04.519045 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves. ]]> https://biorxiv.org/content/10.1101/2022.12.05.518843v1?rss=1 Focosi, D. Quiroga, R. McConnell, S. Johnson, M. C. Casadevall, A. 2022-12-05 doi:10.1101/2022.12.05.518843 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ RNAP promoter search and transcription kinetics in live E. coli cells ]]> https://biorxiv.org/content/10.1101/2022.12.31.522404v1?rss=1 Bettridge, K. E. Harris, F. Yeyha, N. Xiao, J. 2023-01-03 doi:10.1101/2022.12.31.522404 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Ethyl Maltol Disrupts Iron Homeostasis in SH-SY5Y Neuroblastoma Cell Line ]]> https://biorxiv.org/content/10.1101/2023.01.02.522514v1?rss=1 Sun, Y. Bressler, J. P. 2023-01-03 doi:10.1101/2023.01.02.522514 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes ]]> https://biorxiv.org/content/10.1101/2023.01.09.523313v1?rss=1 De Luca, C. Gupta, A. Bortvin, A. 2023-01-10 doi:10.1101/2023.01.09.523313 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand cleavage in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.01.19.524782v1?rss=1 Kotagama, K. Grimme, A. L. Yang, B. Sakhawala, R. Yu, G. McJunkin, K. 2023-01-20 doi:10.1101/2023.01.19.524782 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments ]]> https://biorxiv.org/content/10.1101/2023.01.28.525943v1?rss=1 Sriworarat, C. Nguyen, A. B. Eagles, N. J. Collado-Torres, L. Martinowich, K. Maynard, K. R. Hicks, S. C. 2023-01-29 doi:10.1101/2023.01.28.525943 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Neurexin 3 is required for the specific S-cone to S-cone bipolar cell synapse in the mammalian retina ]]> https://biorxiv.org/content/10.1101/2023.02.13.527055v1?rss=1 Kunze, V. P. Angueyra, J. Ball, J. M. Thomsen, M. B. Li, X. Sabnis, A. Nadal-Nicolas, F. M. Li, W. 2023-02-14 doi:10.1101/2023.02.13.527055 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.02.15.528722v1?rss=1 Huuki-Myers, L. A. Spangler, A. Eagles, N. J. Montgomery, K. D. Kwon, S. H. Guo, B. Grant-Peters, M. Divecha, H. R. Tippani, M. Sriworarat, C. Nguyen, A. B. Ravichandran, P. Tran, M. N. Seyedian, A. PsychENCODE Consortium, Hyde, T. M. Kleinman, J. E. Battle, A. Page, S. C. Ryten, M. Hicks, S. C. Martinowich, K. Collado-Torres, L. Maynard, K. R. 2023-02-15 doi:10.1101/2023.02.15.528722 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Instructive and reorganizing effects of experience on development of human visual cortices ]]> https://biorxiv.org/content/10.1101/2023.02.21.528939v1?rss=1 Tian, M. Xiao, X. Hu, H. Cusack, R. Bedny, M. 2023-02-21 doi:10.1101/2023.02.21.528939 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ 2019-20 H1N1 clade A5a.1 viruses have better in vitro replication compared with the co-circulating A5a.2 clade ]]> https://biorxiv.org/content/10.1101/2023.02.26.530085v1?rss=1 Swanson, N. J. Marinho, P. Dziedzic, A. Jedlicka, A. Liu, H. Fenstermacher, K. Rothman, R. E. Pekosz, A. 2023-02-26 doi:10.1101/2023.02.26.530085 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Rapid molecular phenotypic antimicrobial susceptibility test for Neisseria gonorrhoeae based on propidium monoazide viability PCR ]]> https://biorxiv.org/content/10.1101/2023.03.01.530513v1?rss=1 Tjandra, K. C. Ram-Mohan, N. Abe, R. Wang, J. Yang, S. 2023-03-01 doi:10.1101/2023.03.01.530513 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Early transcriptional responses of human nasal epithelial cells to infection with Influenza A and SARS-CoV-2 virus differ and are influenced by physiological temperature ]]> https://biorxiv.org/content/10.1101/2023.03.07.531609v1?rss=1 Resnick, J. D. Beer, M. A. Pekosz, A. 2023-03-09 doi:10.1101/2023.03.07.531609 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ An Ensemble Penalized Regression Method for Multi-ancestry Polygenic Risk Prediction ]]> https://biorxiv.org/content/10.1101/2023.03.15.532652v1?rss=1 Zhang, J. Zhan, J. Jin, J. Ma, C. Zhao, R. Connell, J. O. Jiang, Y. 23andMe Research Team, Koelsch, B. L. Zhang, H. Chatterjee, N. 2023-03-16 doi:10.1101/2023.03.15.532652 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ escheR: Unified multi-dimensional visualizations with Gestalt principles ]]> https://biorxiv.org/content/10.1101/2023.03.18.533302v1?rss=1 Guo, B. Hicks, S. C. 2023-03-23 doi:10.1101/2023.03.18.533302 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Integrated Drivers of Basal and Acute Immunity in Diverse Human Populations ]]> https://biorxiv.org/content/10.1101/2023.03.25.534227v1?rss=1 Souquette, A. Allen, E. K. Oshansky, C. M. Tang, L. Wong, S.-s. Jeevan, T. Shi, L. Pounds, S. Elias, G. Kuan, G. Balmaseda, A. Zapata, R. Shaw-Saliba, K. Van Damme, P. Van Tendeloo, V. Dib, J. C. Ogunjimi, B. Webby, R. Schultz-Cherry, S. Pekosz, A. Rothman, R. Gordon, A. Thomas, P. G. 2023-03-25 doi:10.1101/2023.03.25.534227 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Control of working memory maintenance by theta-gamma phase amplitude coupling of human hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2023.04.05.535772v1?rss=1 Daume, J. Kaminski, J. Schjetan, A. G. P. Salimpour, Y. Khan, U. Reed, C. Andersen, W. Valiante, T. A. Mamelak, A. N. Rutishauser, U. 2023-04-06 doi:10.1101/2023.04.05.535772 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics ]]> https://biorxiv.org/content/10.1101/2023.04.10.536252v1?rss=1 Chan, T. F. Rui, X. Conti, D. V. Fornage, M. Graff, M. Haessler, J. Haiman, C. Highland, H. M. Jung, S. Y. Kenny, E. Kooperberg, C. Le Marchland, L. North, K. E. Tao, R. Wojcik, G. Gignoux, C. R. PAGE Consortium, Chiang, C. W. Mancuso, N. 2023-04-10 doi:10.1101/2023.04.10.536252 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Enhancer evolution as a driving force for lineage-specific paralog usage in the central nervous system. ]]> https://biorxiv.org/content/10.1101/2023.04.20.537653v1?rss=1 Fujimori, C. Sugimoto, K. Ishida, M. Yang, C. Kayo, D. Tomihara, S. Sano, K. Akazome, Y. Oka, Y. Kanda, S. 2023-04-21 doi:10.1101/2023.04.20.537653 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ BuGZ exhibits guanine nucleotide exchange factor toward tubulin ]]> https://biorxiv.org/content/10.1101/2023.05.09.539990v1?rss=1 Yon, W. J. Tran, J. R. Ha, T. Zheng, Y. Pedersen, R. T. 2023-05-09 doi:10.1101/2023.05.09.539990 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Anopheles salivary apyrase regulates blood meal hemostasis and drives malaria parasite transmission ]]> https://biorxiv.org/content/10.1101/2023.05.22.541827v1?rss=1 Pala, Z. R. Alves e Silva, T. L. Minai, M. Crews, B. Patino-Martinez, E. Carmona-Rivera, C. Valenzuela-Leon, P. C. Martin-Martin, I. Flores-Garcia, Y. Cachau, R. E. Srivastava, N. Moore, I. N. Alves, D. A. Kaplan, M. J. Fischer, E. Calvo, E. Vega-Rodriguez, J. 2023-05-22 doi:10.1101/2023.05.22.541827 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ ABI1 regulates transcriptional activity of Androgen Receptor by novel DNA and AR binding mechanism ]]> https://biorxiv.org/content/10.1101/2023.05.26.542350v1?rss=1 Porter, B. A. Li, X. Arya, N. Zhang, F. Kung, S. H. Y. Fazli, L. Zarni Oo, H. Li, Y. Marincin, K. Kukkonen, K. Urhonen, H. Ortiz, M. A. Kemraj, A. P. Corey, E. Dong, X. Kuznetsov, V. A. Nykter, M. Gleave, M. E. Bratslavsky, G. Urbanucci, A. Frueh, D. Bah, A. Kotula, L. 2023-05-26 doi:10.1101/2023.05.26.542350 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Essential role of the Conserved Oligomeric Golgi complex in Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/2023.05.30.542952v1?rss=1 Marsilia, C. Batra, M. Pokrovskaya, I. D. Wang, C. Chaput, D. Naumova, D. A. Lupashin, V. V. Suvorova, E. S. 2023-05-31 doi:10.1101/2023.05.30.542952 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness ]]> https://biorxiv.org/content/10.1101/2023.06.02.543338v1?rss=1 Mok, S. Yeo, T. Hong, D. Shears, M. J. Ross, L. S. Ward, K. E. Dhingra, S. K. Kanai, M. Bridgford, J. L. Tripathi, A. K. Mlambo, G. Burkhard, A. Y. Fairhurst, K. J. Gil-Iturbe, E. Park, H. Rozenberg, F. D. Kim, J. Mancia, F. Quick, M. Uhlemann, A.-C. Sinnis, P. Fidock, D. A. 2023-06-03 doi:10.1101/2023.06.02.543338 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ The Size of Fields in Biomedical Sciences ]]> https://biorxiv.org/content/10.1101/2023.06.13.544650v1?rss=1 Dragotakes, Q. Casadevall, A. 2023-06-14 doi:10.1101/2023.06.13.544650 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes ]]> https://biorxiv.org/content/10.1101/2023.06.14.544991v1?rss=1 Hippen, A. A. Davidson, N. R. Barnard, M. E. Weber, L. M. Gertz, J. Doherty, J. A. Hicks, S. C. Greene, C. S. 2023-06-15 doi:10.1101/2023.06.14.544991 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Degradation of amyloid beta species by multi-copper oxidases ]]> https://biorxiv.org/content/10.1101/2023.07.02.547398v1?rss=1 Yang, J. Ran, K. Ma, W. Chen, L. Chen, C. Zhang, C. M. Ye, H. Lu, Y. M. Ran, C. 2023-07-03 doi:10.1101/2023.07.02.547398 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Naturally segregating genetic variants contribute to thermal tolerance in a D. melanogaster model system. ]]> https://biorxiv.org/content/10.1101/2023.07.06.547110v1?rss=1 Williams-Simon, P. A. Oster, C. Moaton, J. A. Ghidey, R. Ngoma, E. Middleton, K. M. King, E. G. 2023-07-07 doi:10.1101/2023.07.06.547110 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ A transmission bottleneck for malaria? Quantification of sporozoite expelling from laboratory and natural P. falciparum infections ]]> https://biorxiv.org/content/10.1101/2023.08.03.551751v1?rss=1 Andolina, C. Graumans, W. Guelbeogo, M. Gemert, G.-J. v. Ramjith, J. Harouna, S. Soumanaba, Z. Stoter, R. van de Vegte-Bolmer, M. Pangos, M. Sinnis, P. Collins, K. Staedke, S. Tiono, A. Drakeley, C. Lanke, K. Bousema, T. 2023-08-06 doi:10.1101/2023.08.03.551751 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ The Influenza B Virus Victoria and Yamagata Lineages Display Distinct Cell Tropism and Infection Induced Host Gene Expression in Human Nasal Epithelial Cell Cultures ]]> https://biorxiv.org/content/10.1101/2023.08.04.551980v1?rss=1 Wilson, J. L. Akin, E. Zhou, R. Jedlicka, A. Dziedzic, A. Liu, H. Fenstermacher, K. K. Rothman, R. E. Pekosz, A. 2023-08-04 doi:10.1101/2023.08.04.551980 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Single-Molecule Reaction-Diffusion ]]> https://biorxiv.org/content/10.1101/2023.09.05.556378v1?rss=1 Xu, W. Jazani, S. Kilic, Z. Presse, S. 2023-09-06 doi:10.1101/2023.09.05.556378 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ The structure of a C. neoformans polysaccharide motif recognized by protective antibodies: a combined NMR and MD study ]]> https://biorxiv.org/content/10.1101/2023.09.06.556507v1?rss=1 Hargett, A. A. Azurmendi, H. F. Crawford, C. J. Wear, M. P. Oscarson, S. Casadevall, A. A. Freedberg, D. I. 2023-09-06 doi:10.1101/2023.09.06.556507 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ The tidyomics ecosystem: Enhancing omic data analyses ]]> https://biorxiv.org/content/10.1101/2023.09.10.557072v1?rss=1 Hutchison, W. J. Keyes, T. J. Crowell, H. L. Soneson, C. Mu, W. Park, J.-E. Davis, E. S. Nahid, A. A. Tang, M. Yuan, V. Axisa, P.-P. Kitt, J. W. Poon, C.-L. Sato, N. Gottardo, R. Morgan, M. Lee, S. Lawrence, M. Hicks, S. C. Nolan, G. P. Davis, K. L. Papenfuss, A. T. Love, M. I. Mangiola, S. 2023-09-13 doi:10.1101/2023.09.10.557072 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Suppression of progesterone by influenza A virus causes adverse maternal and fetal outcomes in mice ]]> https://biorxiv.org/content/10.1101/2023.09.11.557146v1?rss=1 Creisher, P. S. Parish, M. A. Lei, J. Liu, J. Perry, J. L. Campbell, A. D. Sherer, M. L. Burd, I. Klein, S. L. L. 2023-09-11 doi:10.1101/2023.09.11.557146 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2023.09.13.557637v1?rss=1 Crits-Christoph, A. Levy, J. I. Pekar, J. Goldstein, S. A. Singh, R. Hensel, Z. Gangavarapu, K. Rogers, M. B. Moshiri, N. Garry, R. f. Holmes, E. C. Koopmans, M. P. G. Lemey, P. Popescu, S. Rambaut, A. Robertson, D. L. Suchard, M. A. Wertheim, J. Rasmussen, A. L. Andersen, K. G. Worobey, M. Debarre, F. 2023-09-14 doi:10.1101/2023.09.13.557637 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Neutron Scattering Analysis of the Cryptococcus neoformans Polysaccharide Reveals Solution Rigidity and Repeating Fractal-like Structural Patterns ]]> https://biorxiv.org/content/10.1101/2023.09.22.559017v1?rss=1 Wang, Z. Teixeira, S. C. M. Strother, C. Bowen, A. Casadevall, A. Cordero, R. J. 2023-09-23 doi:10.1101/2023.09.22.559017 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ MultipleXed Population Selection and Enrichment single nucleus RNA sequencing (XPoSE-seq) enables sample identity retention during transcriptional profiling of rare populations ]]> https://biorxiv.org/content/10.1101/2023.09.27.559834v1?rss=1 Savell, K. E. Madangopal, R. Saravanan, P. Palaganas, R. G. Woods, K. D. Thompson, D. J. Drake, O. R. Brenner, M. B. Weber, S. J. Van Leer, E. Choi, J. H. Martin, T. L. Martin, J. C. Steinberg, M. K. Austin, J. W. Charendoff, C. I. Hope, B. T. 2023-09-29 doi:10.1101/2023.09.27.559834 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates -- MosAIC (Mosquito-Associated Isolate Collection) ]]> https://biorxiv.org/content/10.1101/2023.10.04.560816v1?rss=1 Foo, A. Brettell, L. E. Nichols, H. L. 2022 UW-Madison Capstone in Microbiology Students, Medina Munoz, M. Lysne, J. Dhokiya, V. Hoque, A. F. Brackney, D. E. Caragata, E. P. Hutchinson, M. Jacobs-Lorena, M. Lampe, D. J. Martin, E. Valiente Moro, C. Povelones, M. Short, S. M. Steven, B. Xu, J. Paustian, T. D. Rondon, M. R. Hughes, G. L. Coon, K. L. Heinz, E. 2023-10-04 doi:10.1101/2023.10.04.560816 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Spatially specific, closed-loop infrared thalamocortical deep brain stimulation ]]> https://biorxiv.org/content/10.1101/2023.10.04.560859v1?rss=1 Coventry, B. S. Lawlor, G. L. Bagnati, C. B. Krogmeier, C. Bartlett, E. L. 2023-10-06 doi:10.1101/2023.10.04.560859 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense ]]> https://biorxiv.org/content/10.1101/2023.10.22.562561v1?rss=1 Workman, R. E. Stoltzfus, M. J. Keith, N. C. Euler, C. W. Bondy-Denomy, J. Modell, J. W. 2023-10-22 doi:10.1101/2023.10.22.562561 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ New tools reveal PCP-dependent polarized mechanics in the cortex and cytoplasm of single cells during convergent extension ]]> https://biorxiv.org/content/10.1101/2023.11.07.566066v1?rss=1 Weng, S. Devitt, C. C. Nyaoga, B. M. Havnen, A. E. Alvarado, J. Wallingford, J. B. 2023-11-08 doi:10.1101/2023.11.07.566066 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Thermal and pigment characterization of environmental fungi in the urban heat island of Baltimore City ]]> https://biorxiv.org/content/10.1101/2023.11.10.566554v1?rss=1 Smith, D. F. Q. Faiez, T. S. Bencomo, A. Casadevall, A. 2023-11-10 doi:10.1101/2023.11.10.566554 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Axonal PLC-γ activity is required for BDNF long-distance signaling. ]]> https://biorxiv.org/content/10.1101/2023.11.10.566602v1?rss=1 Moya-Alvarado, G. Valero-Pena, X. Aguirre-Soto, A. Bronfman, F. C. 2023-11-12 doi:10.1101/2023.11.10.566602 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Spatially-resolved transcriptomics of human dentate gyrus across postnatal lifespan reveals heterogeneity in markers for proliferation, extracellular matrix, and neuroinflammation ]]> https://biorxiv.org/content/10.1101/2023.11.20.567883v1?rss=1 Ramnauth, A. D. Tippani, M. Divecha, H. R. Papariello, A. R. Miller, R. A. Pattie, E. A. Kleinman, J. E. Maynard, K. R. Collado-Torres, L. Hyde, T. M. Martinowich, K. Hicks, S. C. Page, S. C. 2023-11-21 doi:10.1101/2023.11.20.567883 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Estradiol Mediates Greater Germinal Center Responses to Influenza Vaccination in Female than Male Mice ]]> https://biorxiv.org/content/10.1101/2023.11.27.568847v1?rss=1 Dhakal, S. Park, H.-S. Seddu, K. Lee, J. Creisher, P. S. Davis, K. M. Hernandez, I. R. Maul, R. W. Klein, S. L. 2023-11-27 doi:10.1101/2023.11.27.568847 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ MetaVision3D: Automated framework for the Generation of Spatial Metabolome Atlas in 3D ]]> https://biorxiv.org/content/10.1101/2023.11.27.568931v1?rss=1 Ma, X. Shedlock, C. J. Medina, T. Ribas, R. Clarke, H. Hawkinson, T. Dande, P. Wu, L. Burke, S. N. Merritt, M. Vander Kooi, C. Gentry, M. Yadav, N. Chen, L. Sun, R. C. 2023-11-28 doi:10.1101/2023.11.27.568931 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex ]]> https://biorxiv.org/content/10.1101/2023.11.28.569011v1?rss=1 Ford, K. Zuin, E. Righelli, D. Medina, E. Schoch, H. Singletary, K. Muheim, C. Frank, M. G. Hicks, S. Risso, D. Peixoto, L. 2023-11-28 doi:10.1101/2023.11.28.569011 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Antibiotic skeletal diversification via differential enoylreductase recruitment and module iteration in trans-acyltransferase polyketide synthases ]]> https://biorxiv.org/content/10.1101/2023.11.30.569433v1?rss=1 Jian, X. Pang, F. Hobson, C. Jenner, M. Alkhalaf, L. M. Challis, G. L. 2023-11-30 doi:10.1101/2023.11.30.569433 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch ]]> https://biorxiv.org/content/10.1101/2023.12.05.570056v1?rss=1 Hertz, L. M. White, E. N. Kuznedelov, K. Cheng, L. Yu, A. M. Kakkaramadam, R. Severinov, K. Chen, A. Lucks, J. B. 2023-12-05 doi:10.1101/2023.12.05.570056 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Electrostatic encoding of genome organization principles within single native nucleosomes ]]> https://biorxiv.org/content/10.1101/2023.12.08.570828v1?rss=1 Park, S. Athreya, A. Carrizo, G. Benning, N. Mitchener, M. Bhanu, N. Garcia, B. Zhang, B. Muir, T. W. Pearce, E. Ha, T. 2023-12-09 doi:10.1101/2023.12.08.570828 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors ]]> https://biorxiv.org/content/10.1101/2023.12.13.571595v1?rss=1 Johnston, A. C. Alicea, G. M. Lee, C. C. Patel, P. V. Hanna, E. A. Vaz, E. Forjaz, A. Wan, Z. Nair, P. R. Lim, Y. Chen, T. Du, W. Kim, D. Nichakawade, T. D. Rebecca, V. W. Bonifant, C. L. Fan, R. Kiemen, A. L. Wu, P.-H. Wirtz, D. 2023-12-14 doi:10.1101/2023.12.13.571595 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Deep super-resolution imaging of thick tissue using structured illumination with adaptive optics ]]> https://biorxiv.org/content/10.1101/2023.12.21.572818v1?rss=1 Wang, J. Stoychev, D. Phillips, M. Pinto, D. M. S. Parton, R. M. Hall, N. Titlow, J. Faria, A. R. Wincott, M. Gala, D. Gerondopoulos, A. Irani, N. Dobbie, I. Schermelleh, L. Booth, M. Davis, I. 2023-12-22 doi:10.1101/2023.12.21.572818 Cold Spring Harbor Laboratory Press 2023-12-22 <![CDATA[ NRX-101 (D-Cycloserine + Lurasidone) , a Qualified Infectious Disease Product, is Active Against Drug-Resistant Urinary Pathogens In Vitro ]]> https://biorxiv.org/content/10.1101/2024.01.14.575572v1?rss=1 Sapko, M. T. Manyak, M. Panicucci, R. Javitt, J. C. 2024-01-14 doi:10.1101/2024.01.14.575572 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Integrating Safety, Security, Sustainability and Social Responsibility Principles into the U.S Bioeconomy ]]> https://biorxiv.org/content/10.1101/2024.02.05.578954v1?rss=1 Gronvall, G. K. Attal-Juncqua, A. Getz, J. Morhard, R. 2024-02-08 doi:10.1101/2024.02.05.578954 Cold Spring Harbor Laboratory Press 2024-02-08 <![CDATA[ Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2024.02.09.579665v1?rss=1 Huuki-Myers, L. A. Montgomery, K. D. Kwon, S. H. Cinquemani, S. Maden, S. K. Eagles, N. J. Kleinman, J. E. Hyde, T. M. Hicks, S. C. Maynard, K. R. Collado-Torres, L. 2024-02-12 doi:10.1101/2024.02.09.579665 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Glutathione metabolism impacts fungal virulence by modulating the redox environment ]]> https://biorxiv.org/content/10.1101/2024.02.19.581054v1?rss=1 Black, B. Roque da Silva, L. B. Hu, G. Qu, X. Smith, D. F. Magana, A. A. Horianopoulos, L. C. Caza, M. Attarian, R. Foster, L. J. Casadevall, A. Kronstad, J. W. 2024-02-19 doi:10.1101/2024.02.19.581054 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Transcriptomic analysis of the human habenula in schizophrenia ]]> https://biorxiv.org/content/10.1101/2024.02.26.582081v1?rss=1 Yalcinbas, E. A. Ajanaku, B. Nelson, E. D. Garcia-Flores, R. Montgomery, K. D. Stolz, J. M. Wu, J. Divecha, H. R. Chandra, A. Bharadwaj, R. A. Bach, S. Rajpurohit, A. Tao, R. Shin, J.-H. Kleinman, J. E. Hyde, T. M. Weinberger, D. R. Huuki-Myers, L. A. Collado-Torres, L. Maynard, K. R. 2024-02-27 doi:10.1101/2024.02.26.582081 Cold Spring Harbor Laboratory Press 2024-02-27 <![CDATA[ A Drosophila model to screen Alport syndrome COL4A5 variants for their functional pathogenicity ]]> https://biorxiv.org/content/10.1101/2024.03.06.583697v1?rss=1 Duan, J. Wen, P. Zhao, Y. van de Leemput, J. Lai, J. Fermin, D. Warady, B. A. Furth, S. L. Ng, D. K. Sampson, M. Han, Z. 2024-03-11 doi:10.1101/2024.03.06.583697 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584120v1?rss=1 Kubinski, H. C. Despres, H. W. Johnson, B. A. Schmidt, M. M. Jaffrani, S. A. Mills, M. G. Lokugamage, K. Dumas, C. M. Shirley, D. J. Estes, L. K. Pekosz, A. Crothers, J. W. Roychoudhury, P. Greninger, A. L. Jerome, K. R. Martorelli Di Genova, B. Walker, D. H. Ballif, B. A. Ladinsky, M. S. Bjorkman, P. J. Menachery, V. D. Bruce, E. A. 2024-03-11 doi:10.1101/2024.03.08.584120 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ UDP-6-glucose dehydrogenase in hormonally responsive breast cancers ]]> https://biorxiv.org/content/10.1101/2024.03.20.585919v1?rss=1 Price, M. J. Nguyen, A. D. Haines, C. Baeta, C. D. Byemerwa, J. Mukherjee, D. Artham, S. Kumar, V. Lavau, C. Wardell, S. Varghese, S. Goodwin, C. R. 2024-03-21 doi:10.1101/2024.03.20.585919 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ DNA damage drives antigen diversification through mosaic VSG formation in Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2024.03.22.582209v1?rss=1 Smith, J. E. Wang, K. J. Hakim, J. M. Beaver, A. K. Magesh, A. Gilligan-Steinberg, S. D. Zheng, J. So, J. Kennedy, E. M. Zhang, B. Akin, E. H. Mwakibete, L. Mugnier, M. R. 2024-03-22 doi:10.1101/2024.03.22.582209 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Theta-Gamma Phase-Amplitude Coupling Supports Working Memory Performance in the Human Hippocampus ]]> https://biorxiv.org/content/10.1101/2024.03.24.586454v1?rss=1 Salimpour, Y. Anderson, W. 2024-03-27 doi:10.1101/2024.03.24.586454 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ ZFAND6 is a subunit of a TRAF2-cIAP E3 ubiquitin ligase complex essential for mitophagy ]]> https://biorxiv.org/content/10.1101/2024.03.27.586763v1?rss=1 Shaikh, K. Bowman, M. McCormick, S. M. Gao, L. Zhang, J. Tawil, J. Kapoor, A. Arav-Boger, R. Choi, Y. B. Pekosz, A. Klein, S. L. Lanza, M. Fanburg-Smith, J. C. Garcia-Sastre, A. Norbury, C. C. Chroneos, Z. Harhaj, E. W. 2024-03-29 doi:10.1101/2024.03.27.586763 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons ]]> https://biorxiv.org/content/10.1101/2024.03.27.587011v1?rss=1 Sinha, I. R. Sandal, P. S. Burns, G. D. Mallika, A. P. Irwin, K. E. Cruz, A. L. F. Wang, V. Rodriguez, J. L. Wong, P. C. Ling, J. P. 2024-03-30 doi:10.1101/2024.03.27.587011 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression ]]> https://biorxiv.org/content/10.1101/2024.04.04.588105v1?rss=1 Maden, S. K. Huuki-Myers, L. A. Kwon, S. H. Collado-Torres, L. Maynard, K. R. Hicks, S. C. 2024-04-06 doi:10.1101/2024.04.04.588105 Cold Spring Harbor Laboratory Press 2024-04-06 <![CDATA[ Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species ]]> https://biorxiv.org/content/10.1101/2024.04.22.590602v1?rss=1 Phillips, R. A. Oh, S. Bach, S. V. Du, Y. Miller, R. A. Kleinman, J. E. Hyde, T. M. Hicks, S. C. Page, S. C. Martinowich, K. 2024-04-26 doi:10.1101/2024.04.22.590602 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Missing cell types in single-cell references impact deconvolution of bulk data but are detectable ]]> https://biorxiv.org/content/10.1101/2024.04.25.590992v1?rss=1 Ivich, A. Davidson, N. R. Grieshober, L. Li, W. Hicks, S. C. Doherty, J. A. Greene, C. S. 2024-04-28 doi:10.1101/2024.04.25.590992 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Mathematical model of intestinal lipolysis of a long-chain triglyceride ]]> https://biorxiv.org/content/10.1101/2024.05.01.592066v1?rss=1 Rezhdo, O. West, R. Kim, M. Ng, B. Saphier, S. Carrier, R. L. 2024-05-04 doi:10.1101/2024.05.01.592066 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Functional role of myosin-binding protein H in thick filaments of developing vertebrate fast-twitch skeletal muscle ]]> https://biorxiv.org/content/10.1101/2024.05.10.593199v1?rss=1 Mead, A. F. Wood, N. B. Nelson, S. R. Palmer, B. M. Yang, L. Previs, S. B. Ploysangngam, A. Kennedy, G. G. McAdow, J. F. Tremble, S. M. Cipolla, M. J. Ebert, A. M. Johnson, A. N. Gurnett, C. A. Previs, M. J. Warshaw, D. M. 2024-05-13 doi:10.1101/2024.05.10.593199 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ The Hippo-YAP/TAZ-TEAD axis promotes multipotency in bone marrow stromal cells ]]> https://biorxiv.org/content/10.1101/2024.05.14.594149v1?rss=1 Cheng, Y.-H. Chan, C. H. R. Bian, Q. Merling, R. K. Kuznetsov, S. A. Robey, P. G. Cahan, P. 2024-05-17 doi:10.1101/2024.05.14.594149 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Clade-defining mutations in human H1N1 hemagglutinin protein from 2021-2023 have opposing effects on in vitro fitness and antigenic drift ]]> https://biorxiv.org/content/10.1101/2024.05.18.594815v1?rss=1 Swanson, N. J. Girish, J. Yunker, M. Liu, H. Norton, J. Han, C. Mostafa, H. Fenstermacher, K. Rothman, R. E. Pekosz, A. 2024-05-19 doi:10.1101/2024.05.18.594815 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ The major surface protein of malaria sporozoites is GPI-anchored to the plasma membrane ]]> https://biorxiv.org/content/10.1101/2024.05.21.595204v1?rss=1 Nagar, R. Castillo, S. S. G. Pinzon-Ortiz, M. Patray, S. Coppi, A. Kanatani, S. Moritz, R. L. Swearingen, K. E. Ferguson, M. A. J. Sinnis, P. 2024-05-21 doi:10.1101/2024.05.21.595204 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Urban wastewater contains a functional human antibody repertoire of mucosal origin ]]> https://biorxiv.org/content/10.1101/2024.06.02.597066v1?rss=1 Stephenson, S. Eid, W. Wong, C. H. Mercier, E. D'Aoust, P. M. Kabir, M. P. Baral, S. Gilbride, K. A. Oswald, C. Straus, S. E. Mackenzie, A. Delatolla, R. Graber, T. E. 2024-06-03 doi:10.1101/2024.06.02.597066 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Application of machine learning in a rodent malaria model for rapid, accurate, and consistent parasite counts ]]> https://biorxiv.org/content/10.1101/2024.06.05.597554v1?rss=1 Yanik, S. Yu, H. Chaiyawong, N. Adewale-Fasoro, O. Ribeiro Dinis, L. Narayanasamy, R. K. Lee, E. C. Lubonja, A. Li, B. Jaeger, S. SRINIVASAN, P. 2024-06-05 doi:10.1101/2024.06.05.597554 Cold Spring Harbor Laboratory Press 2024-06-05 <![CDATA[ SpotSweeper: spatially-aware quality control for spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.06.06.597765v1?rss=1 Totty, M. S. Hicks, S. C. Guo, B. 2024-06-09 doi:10.1101/2024.06.06.597765 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Weighted variance component test for the integrative multi-omics analysis of microbiome data ]]> https://biorxiv.org/content/10.1101/2024.06.14.599073v1?rss=1 Zhang, A. Ling, W. Little, A. Williams-Nguyen, J. S. Moon, J.-Y. Burk, R. D. Knight, R. Wang, D. D. Qi, Q. Kaplan, R. Zhao, N. Wu, M. 2024-06-17 doi:10.1101/2024.06.14.599073 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ A higher order PUF complex is central to regulation of C. elegans germline stem cells ]]> https://biorxiv.org/content/10.1101/2024.06.14.599074v1?rss=1 Qiu, C. Crittenden, S. L. Carrick, B. Dillard, L. Costa dos Santos, S. Dandey, V. Dutcher, R. Viverette, E. Wine, R. Woodworth, J. Campbell, Z. Wickens, M. Borgnia, M. J. Kimble, J. Hall, T. 2024-06-14 doi:10.1101/2024.06.14.599074 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ The Proton Resonance Enhancement for CEST imaging and Shift Exchange (PRECISE) family of RF pulse shapes for Chemical Exchange Saturation Transfer MRI ]]> https://biorxiv.org/content/10.1101/2024.06.19.599565v1?rss=1 Mohanta, Z. Stabinska, J. Barker, P. B. Gilad, A. McMahon, M. T. 2024-06-22 doi:10.1101/2024.06.19.599565 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Medial prefrontal cortex and nucleus reuniens are critical for working memory in an operant delayed nonmatch task ]]> https://biorxiv.org/content/10.1101/2024.07.03.601891v1?rss=1 Ciacciarelli, E. J. Dunn, S. D. Gohar, T. Sloand, T. J. Niedringhaus, M. West, E. A. 2024-07-03 doi:10.1101/2024.07.03.601891 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Spatial Transcriptomics and Single-Nucleus Multi-omics Analysis Revealing the Impact of High Maternal Folic Acid Supplementation on Offspring Brain Development ]]> https://biorxiv.org/content/10.1101/2024.07.12.603269v1?rss=1 Xie, H. Xu, X. Lin, Y. Yin, L. Serpa, P. d. S. Conacher, B. Pacholac, C. Carvallo, F. Hrubec, T. Farris, S. Zimmerman, K. Wang, X. 2024-07-16 doi:10.1101/2024.07.12.603269 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Persistent activity during working memory maintenance predicts long-term memory formation in the human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.07.15.603630v1?rss=1 Daume, J. Kaminski, J. Salimpour, Y. Anderson, W. S. Valiante, T. A. Mamelak, A. N. Rutishauser, U. 2024-07-16 doi:10.1101/2024.07.15.603630 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Somatic hypermutation-mediated paratope flexibility improves the cross-reactivity of human malaria antibodies ]]> https://biorxiv.org/content/10.1101/2024.07.24.604858v1?rss=1 Murugan, R. Hanke, A. Oludada, O. E. Costa, G. Flores-Garcia, Y. Mustafa, G. Li, K. Huntwork, R. H. C. Horn, G. Sekaran, M. Tomaras, G. Zavala, F. Levashina, E. A. Ketchem, R. R. Wade, R. C. Wardemann, H. 2024-07-24 doi:10.1101/2024.07.24.604858 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Cholecystokinin modulates age-dependent Thalamocortical Neuroplasticity ]]> https://biorxiv.org/content/10.1101/2024.07.31.605964v1?rss=1 Li, X. Feng, J. Hu, X. Zhou, P. Chen, T. Zheng, X. Jendrichovsky, P. Wang, X. Chen, M. Li, H. Chen, X. Zeng, D. Zhang, M. Xiao, Z. He, L. Bello, S. T. He, J. 2024-07-31 doi:10.1101/2024.07.31.605964 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum ]]> https://biorxiv.org/content/10.1101/204503v1?rss=1 Pattabiraman, C. Dias, M. Siddappa, S. Gowda, M. Shet, A. Smith, D. Muehlemann, B. Tamma, K. Solomon, T. Jones, T. Krishna, S. 2017-10-19 doi:10.1101/204503 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Integrin alpha 4/beta 1 (CD49d/CD29) is a component of the murine IgG3 receptor ]]> https://biorxiv.org/content/10.1101/207274v1?rss=1 Hawk, C. S. Coelho, C. de Oliveira, D. S. L. Paredes, V. Albuquerque, P. Bocca, A. L. dos Santos, A. C. Rusakova, V. Holemon, H. Felipe, M. S. S. Yagita, H. Nicola, A. M. Casadevall, A. 2017-10-21 doi:10.1101/207274 Cold Spring Harbor Laboratory Press 2017-10-21 <![CDATA[ Bayesian estimation of MSM population size in Côte d’Ivoire ]]> https://biorxiv.org/content/10.1101/213926v1?rss=1 Datta, A. Lin, W. Rao, A. Diouf, D. Kouame, A. Edwards, J. K. Bao, L. Louis, T. A. Baral, S. 2017-11-10 doi:10.1101/213926 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ Divalent metal cations potentiate the predatory capacity of amoeba for Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/214460v1?rss=1 Fu, M. S. Casadevall, A. 2017-11-05 doi:10.1101/214460 Cold Spring Harbor Laboratory Press 2017-11-05 <![CDATA[ Explanation implies causation? ]]> https://biorxiv.org/content/10.1101/218784v1?rss=1 Myint, L. Leek, J. T. Jager, L. R. 2017-11-13 doi:10.1101/218784 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ mRNA structure determines specificity of a polyQ-driven phase separation ]]> https://biorxiv.org/content/10.1101/233817v1?rss=1 Langdon, E. M. Billingsly, P. Ghanbari Niaki, A. McLaughlin, G. Weidmann, C. Gerbich, T. Termini, C. M. Weeks, K. M. Myong, S. Gladfelter, A. 2017-12-13 doi:10.1101/233817 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Disequilibrium in Gender Ratios among Authors who Contributed Equally ]]> https://biorxiv.org/content/10.1101/241554v1?rss=1 mixed gender > female-female. For mixed gender pairs males were more often at the first position although the disparity has lessened in the past decade. Among author associations claiming equal contribution and containing three or more individuals, males predominated in both the first position and number of gender exclusive groupings. Our results show a disequilibrium in gender ratios among authors who contributed equally from expected ratios had the ordering been done randomly or alphabetical. Given the importance of the first author position in assigning credit for a publication, the finding of fewer than expected females in associations involving shared contributions raises concerns about women not receiving their fair share of expected credit. The results suggest a need for journals to request clarity on the method used to decide author order among individuals claiming to have made equal contributions to a scientific publication. ]]> Broderick, N. A. Casadevall, A. 2017-12-31 doi:10.1101/241554 Cold Spring Harbor Laboratory Press 2017-12-31 <![CDATA[ Micro-hotspots of Risk in Urban Cholera Epidemics ]]> https://biorxiv.org/content/10.1101/248476v1?rss=1 Azman, A. Luquero Alcalde, F. J. Salje, H. Naibei, N. Adalbert, N. Ali, M. Bertuzzo, E. Finger, F. Toure, B. Massing, L. A. Ramazani, R. Cardon, A. Saga, B. Allan, M. Olson, D. Leglise, J. Porten, K. Lessler, J. 2018-01-18 doi:10.1101/248476 Cold Spring Harbor Laboratory Press 2018-01-18 <![CDATA[ Additional Essential Oils with High Activity against Stationary Phase Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/260091v1?rss=1 Feng, J. Shi, W. Miklossy, J. Zhang, Y. 2018-02-06 doi:10.1101/260091 Cold Spring Harbor Laboratory Press 2018-02-06 <![CDATA[ Serum-mediated cleavage of Bacillus anthracis Protective Antigen is a two-step process that involves a serum carboxypeptidase ]]> https://biorxiv.org/content/10.1101/267369v1?rss=1 Goldman, D. L. Nieves, E. Nakouzi, A. Rivera, J. Phyu, E. E. Win, T. H. Achkar, J. Casadevall, A. 2018-02-18 doi:10.1101/267369 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis ]]> https://biorxiv.org/content/10.1101/277442v1?rss=1 Uritskiy, G. V. DiRuggiero, J. Taylor, J. 2018-03-06 doi:10.1101/277442 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Mapping malaria by combining parasite genomic and epidemiologic data ]]> https://biorxiv.org/content/10.1101/288506v1?rss=1 Wesolowski, A. Taylor, A. Chang, H.-H. Verity, R. Tessema, S. Bailey, J. Perkins, T. A. Neafsey, D. Greenhouse, B. Buckee, C. O. 2018-03-26 doi:10.1101/288506 Cold Spring Harbor Laboratory Press 2018-03-26 <![CDATA[ Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDB ]]> https://biorxiv.org/content/10.1101/292904v1?rss=1 Rajapakse, V. N. Luna, A. Yamade, M. Loman, L. Varma, S. Sunshine, M. Iorio, F. Sousa, F. G. Elloumi, F. Aladjem, M. I. Thomas, A. Sander, C. Kohn, K. Benes, C. H. Garnett, M. Reinhold, W. C. Pommier, Y. 2018-04-02 doi:10.1101/292904 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Population dynamics of Escherichia coli in the gastrointestinal tracts of Tanzanian children ]]> https://biorxiv.org/content/10.1101/294934v1?rss=1 Richter, T. K. S. Hazen, T. H. Lam, D. Coles, C. L. Seidman, J. C. You, Y. Silbergeld, E. K. Fraser, C. M. Rasko, D. A. 2018-04-05 doi:10.1101/294934 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Improved single-molecule localization precision in astigmatism-based 3D superresolution imaging using weighted likelihood estimation ]]> https://biorxiv.org/content/10.1101/304816v1?rss=1 Bohrer, C. H. Yang, X. Lyu, Z. Wang, S.-C. Xiao, J. 2018-04-19 doi:10.1101/304816 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Opsonin-free, real-time imaging of Cryptococcus neoformans capsule during budding ]]> https://biorxiv.org/content/10.1101/313429v1?rss=1 Paes, H. C. Frazao, S. O. Rosa, C. P. Albuquerque, P. Casadevall, A. Felipe, M. S. Nicola, A. M. 2018-05-03 doi:10.1101/313429 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci ]]> https://biorxiv.org/content/10.1101/314880v1?rss=1 Azarian, T. Mitchell, P. Georgieva, M. Thompson, C. M. Ghoulia, A. Pollard, A. J. von Gottberg, A. du Plessis, M. Antonio, M. Kwambana-Adams, B. A. Clarke, S. C. Everett, D. Cornick, J. Sadowy, E. Hryniewicz, W. Skoczynska, A. Moisi, J. McGee, L. Beall, B. Metcalf, B. J. Breiman, R. F. Ho, P. Reid, R. O'Brien, K. L. Gladstone, R. Bentley, S. D. Hanage, W. P. 2018-05-04 doi:10.1101/314880 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Intersection of phosphate transport, oxidative stress and TOR signalling in Candida albicans virulence ]]> https://biorxiv.org/content/10.1101/317933v1?rss=1 Liu, N.-N. Uppuluri, P. Broggi, A. Besold, A. Ryman, K. Kambara, H. Solis, N. Lorenz, V. Qi, W. Acosta Zaldivar, M. Emami, S. N. Bao, B. An, D. Bonilla, F. Sola-Visner, M. Filler, S. Luo, H. R. Engstrom, Y. Ljungdahl, P. O. Culotta, V. C. Zanoni, I. Lopez-Ribot, J. L. Koehler, J. R. 2018-05-11 doi:10.1101/317933 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Peripheral blood DNA methylation and autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/320622v1?rss=1 Andrews, S. V. Sheppard, B. Windham, G. C. Schieve, L. A. Schendel, D. E. Croen, L. A. Chopra, P. Alisch, R. S. Newschaffer, C. J. Warren, S. T. Feinberg, A. P. Fallin, M. D. Ladd-Acosta, C. 2018-05-11 doi:10.1101/320622 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience ]]> https://biorxiv.org/content/10.1101/354621v1?rss=1 Casadevall, A. Bik, E. M. Fang, F. C. Kullas, A. Davis, R. J. 2018-06-24 doi:10.1101/354621 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ Impact of 10-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya ]]> https://biorxiv.org/content/10.1101/369876v1?rss=1 Hammitt, L. Etyang, A. O. Morpeth, S. C. Ojal, J. Mutuku, A. Mturi, N. Moisi, J. Adetifa, I. Karani, A. Akech, D. Otiende, M. Bwanaali, T. Wafula, J. Mataza, C. Mumbo, E. Tabu, C. Deloria Knoll, M. Bauni, E. Marsh, K. Williams, T. Kamau, T. Sharif, S. Levine, O. Scott, J. A. G. 2018-07-18 doi:10.1101/369876 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Deciphering the roles of N-glycans on collagen-platelet interactions ]]> https://biorxiv.org/content/10.1101/385179v1?rss=1 Toonstra, C. hu, Y. Zhang, H. 2018-08-05 doi:10.1101/385179 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Broad spectrum capture of clinical pathogens using engineered Fc-Mannose-Binding Lectin (FcMBL) enhanced by antibiotic treatment ]]> https://biorxiv.org/content/10.1101/387589v1?rss=1 Seiler, B. T. Cartwright, M. Dinis, A. L. M. Duffy, S. Lombardo, P. Cartwright, D. Super, E. H. Lanzaro, J. Dugas, K. Super, M. Ingber, D. E. 2018-08-08 doi:10.1101/387589 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Dragotcytosis: Elucidation of the Mechanism for Cryptococcus neoformans Macrophage-to-Macrophage Transfer ]]> https://biorxiv.org/content/10.1101/387688v1?rss=1 Dragotakes, Q. Fu, M. S. Casadevall, A. 2018-08-09 doi:10.1101/387688 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies ]]> https://biorxiv.org/content/10.1101/420315v1?rss=1 Azarian, T. Martinez, P. P. P. Arnold, B. J. Grant, L. R. Corander, J. Fraser, C. Croucher, N. Hammitt, L. Reed, R. Santosham, M. Weatherholtz, R. R. Bentley, S. D. O'Brien, K. L. Lipsitch, M. Hanage, W. P. 2018-09-18 doi:10.1101/420315 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia ]]> https://biorxiv.org/content/10.1101/426213v1?rss=1 Collado-Torres, L. Burke, E. E. Peterson, A. Shin, J. H. Straub, R. E. Rajpurohi, A. Semick, S. A. Ulrich, W. S. BrainSeq Consortium, Valencia, C. Tao, R. Deep-Soboslay, A. Hyde, T. M. Kleinman, J. E. Weinberger, D. R. Jaffe, A. E. 2018-09-26 doi:10.1101/426213 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Coverage and timeliness of vaccination and the validity of routine estimates: Insights from a Vaccine Registry in Kenya ]]> https://biorxiv.org/content/10.1101/427773v1?rss=1 Adetifa, I. M. O. Karia, B. Mutuku, A. Bwanaali, T. Makumi, A. Wafula, J. Chome, M. Mwatsuma, P. Bauni, E. Hammitt, L. Mataza, C. Tabu, C. Kamau, T. N. Williams, T. Scott, J. A. 2018-10-02 doi:10.1101/427773 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Setting the occasion for incentive motivation: implications for addiction ]]> https://biorxiv.org/content/10.1101/428409v1?rss=1 Fraser, K. M. Janak, P. H. 2018-09-26 doi:10.1101/428409 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ The buoyant cell density of Cryptococcus neoformans is affected by capsule size ]]> https://biorxiv.org/content/10.1101/429936v1?rss=1 Vij, R. Cordero, R. J. Casadevall, A. 2018-09-28 doi:10.1101/429936 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ Perfect Counterfactuals for Epidemic Simulations ]]> https://biorxiv.org/content/10.1101/451153v1?rss=1 Kaminsky, J. Keegan, L. T. Metcalf, C. J. E. Lessler, J. 2018-10-26 doi:10.1101/451153 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ A practical guide to methods controlling false discoveries in computational biology ]]> https://biorxiv.org/content/10.1101/458786v1?rss=1 Korthauer, K. Kimes, P. K. Duvallet, C. Reyes, A. Subramanian, A. Teng, M. Shukla, C. Alm, E. J. Hicks, S. C. 2018-10-31 doi:10.1101/458786 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Oligodendrocyte Precursor Cells Are Co-Opted by the Immune System to Cross-Present Antigen and Mediate Cytotoxicity ]]> https://biorxiv.org/content/10.1101/461434v1?rss=1 Kirby, L. Jin, J. Gonzalez-Cardona, J. Smith, M. Martin, K. Wang, J. Strasburger, H. Herbst, L. Alexis, M. Karnell, J. Davidson, T. Dutta, R. Goverman, J. Bergles, D. E. Calabresi, P. A. 2018-11-04 doi:10.1101/461434 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Expression variation analysis for tumor heterogeneity in single-cell RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/479287v1?rss=1 Davis-Marcisak, E. F. Orugunta, P. Stein-O'Brien, G. Puram, S. V. Roussos Torres, E. Hopkins, A. Jaffee, E. M. Favorov, A. V. Afsari, B. Goff, L. A. Fertig, E. J. 2018-11-27 doi:10.1101/479287 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Symmetric Intralimb Transfer of Skilled Isometric Force Production ]]> https://biorxiv.org/content/10.1101/491415v1?rss=1 Rajan, V. A. Hardwick, R. M. Celnik, P. A. 2018-12-09 doi:10.1101/491415 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Generation of Transgenic Human Malaria Parasites With Strong Fluorescence in the Transmission Stages ]]> https://biorxiv.org/content/10.1101/500793v1?rss=1 McLean, K. J. Straimer, J. Hopp, C. S. Vega-Rodriguez, J. Tripathi, A. Mlambo, G. Doumolin, P. C. Harris, C. T. Tong, X. Shears, M. J. Ankarklev, J. Kafsack, B. Fidock, D. A. Sinnis, P. 2018-12-18 doi:10.1101/500793 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Tumor mutational landscape is a record of the pre-malignant state ]]> https://biorxiv.org/content/10.1101/517565v1?rss=1 Kübler, K. Karlic, R. Haradhvala, N. J. Ha, K. Kim, J. Kuzman, M. Jiao, W. Gakkhar, S. Mouw, K. W. Braunstein, L. Z. Elemento, O. Biankin, A. V. Rooman, I. Miller, M. Karthaus, W. R. Nogiec, C. D. Juvenson, E. Curry, E. Mino-Kenudson, M. Ellisen, L. W. Brown, R. Gusev, A. Tomasetti, C. Lolkema, M. P. Steeghs, N. van Herpen, C. Kim, H.-G. Lee, H. Vlahovicek, K. Bernstein, B. E. Sawyers, C. L. Hoadley, K. A. Cuppen, E. Koren, A. Arndt, P. F. Louis, D. N. Stein, L. D. Foulkes, W. D. Polak, P. Getz, G. 2019-01-11 doi:10.1101/517565 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ A Vaccine Composed of Antigen Fused to a Ligand for a Receptor on Immature Dendritic Cells Elicits Protective Antibody Responses to Malaria Sporozoites in Infant Macaques ]]> https://biorxiv.org/content/10.1101/530840v1?rss=1 Markham, R. B. Luo, K. Gordy, J. Zavala, F. 2019-01-26 doi:10.1101/530840 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ IFN-alpha and 5-Aza-2-deoxycytidine enhance the anti-tumor efficacy of a dendritic-cell targeting MIP3alpha-Gp100-Trp2 DNA vaccine by affecting T-cell recruitment and tumor microenvironment gene expression ]]> https://biorxiv.org/content/10.1101/531616v1?rss=1 Gordy, J. Luo, K. Markham, R. 2019-01-26 doi:10.1101/531616 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Age and sex-dependent patterns of gut microbial diversity in human adults ]]> https://biorxiv.org/content/10.1101/544270v1?rss=1 de la Cuesta-Zuluaga, J. Kelley, S. T. Chen, Y. Esobar, J. S. Mueller, N. T. Ley, R. E. McDonald, D. Huang, S. Swafford, A. D. Knight, R. Thackray, V. 2019-02-08 doi:10.1101/544270 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Case-only analysis of gene-environment interactions using polygenic risk scores ]]> https://biorxiv.org/content/10.1101/555300v1?rss=1 Meisner, A. Kundu, P. Chatterjee, N. 2019-02-19 doi:10.1101/555300 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Reward prediction error modulates saccade vigor ]]> https://biorxiv.org/content/10.1101/555573v1?rss=1 Sedaghat-Nejad, E. Herzfeld, D. J. Shadmehr, R. 2019-02-20 doi:10.1101/555573 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Holding the arm still through subcortical mathematical integration of cortical commands ]]> https://biorxiv.org/content/10.1101/556282v1?rss=1 Albert, S. T. Hadjiosif, A. Jang, J. Krakauer, J. W. Shadmehr, R. 2019-02-24 doi:10.1101/556282 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Galectin-3 inhibits Paracoccidioides brasiliensis growth and impacts paracoccidioidomycosis through multiple mechanisms ]]> https://biorxiv.org/content/10.1101/557918v1?rss=1 Hatanaka, O. Rezende, C. P. Moreno, P. Fernandes, F. F. Oliveira-Brito, P. K. M. Martinez, R. Coelho, C. Roque-Barreira, M. C. Casadevall, A. Almeida, F. 2019-02-23 doi:10.1101/557918 Cold Spring Harbor Laboratory Press 2019-02-23 <![CDATA[ Identification of Genes Regulating Cell Death in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/569053v1?rss=1 Yee, R. Feng, J. Wang, J. Chen, J. ZHANG, Y. 2019-03-06 doi:10.1101/569053 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Iron-sulfur cluster repair contributes to Y. pseudotuberculosis survival within deep tissues ]]> https://biorxiv.org/content/10.1101/576454v1?rss=1 Davis, K. M. Krupp, J. Clark, S. Isberg, R. R. 2019-03-14 doi:10.1101/576454 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ A Methylation Density Binary Classifier for Predicting and Optimizing the Performance of Methylation Biomarkers in Clinical Samples ]]> https://biorxiv.org/content/10.1101/579839v1?rss=1 Miller, B. F. Pisanic, T. R. Margolin, G. Petrykowska, H. M. Athamanolap, P. Osei-Tutu, A. Annunziata, C. M. Wang, T.-H. Elnitski, L. 2019-03-18 doi:10.1101/579839 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Proteomic Analysis of Plasmodium Merosomes: The Link Between Liver and Blood Stages in Malaria ]]> https://biorxiv.org/content/10.1101/580266v1?rss=1 nView larger version (11K):norg.highwire.dtl.DTLVardef@5bd8b1org.highwire.dtl.DTLVardef@1ef4fb9org.highwire.dtl.DTLVardef@5b3833org.highwire.dtl.DTLVardef@c69c73_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shears, M. J. Sekhar Nirujogi, R. Swearingen, K. E. Renuse, S. Mishra, S. Jaipal Reddy, P. Moritz, R. L. Pandey, A. Sinnis, P. 2019-03-16 doi:10.1101/580266 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Orchestrating Single-Cell Analysis with Bioconductor ]]> https://biorxiv.org/content/10.1101/590562v1?rss=1 Amezquita, R. A. Carey, V. J. Carpp, L. N. Geistlinger, L. Lun, A. T. Marini, F. Rue-Albrecht, K. Risso, D. Soneson, C. Waldron, L. Pages, H. Smith, M. Huber, W. Morgan, M. Gottardo, R. Hicks, S. C. 2019-03-27 doi:10.1101/590562 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ The origins of anterograde interference in visuomotor adaptation ]]> https://biorxiv.org/content/10.1101/593996v1?rss=1 Lerner, G. Albert, S. Caffaro, P. A. Villalta, J. I. Jacobacci, F. Shadmehr, R. Della-Maggiore, V. 2019-03-31 doi:10.1101/593996 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Tau pathology in cognitively normal older adults: Associations with brain atrophy and cognitive decline ]]> https://biorxiv.org/content/10.1101/611186v1?rss=1 Ziontz, J. Bilgel, M. Shafer, A. Moghekar, A. Elkins, W. Helphrey, J. Gomez, G. June, D. McDonald, M. A. Dannals, R. F. Azad, B. B. Ferrucci, L. Wong, D. F. Resnick, S. M. 2019-04-26 doi:10.1101/611186 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ The impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa: a modeling study ]]> https://biorxiv.org/content/10.1101/617076v1?rss=1 Lee, E. C. Azman, A. S. Kaminsky, J. Moore, S. M. McKay, H. Lessler, J. 2019-04-26 doi:10.1101/617076 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites ]]> https://biorxiv.org/content/10.1101/642298v1?rss=1 Lindner, S. E. Swearingen, K. E. Shears, M. J. Walker, M. P. Vrana, E. N. Hart, K. J. Minns, A. M. Sinnis, P. Moritz, R. L. Kappe, S. H. 2019-05-20 doi:10.1101/642298 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Microbial Food Safety in the Maryland Direct-to-Consumer Poultry Supply Chain ]]> https://biorxiv.org/content/10.1101/643106v1?rss=1 Baron, P. Love, D. Ludwig, S. Dalton, K. Larsen, J. Innes, G. Davis, M. Heaney, C. 2019-05-20 doi:10.1101/643106 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Circulating electrolytes and the prevalence of atrial fibrillation and supraventricular ectopy: the Atherosclerosis Risk in Communities (ARIC) Study ]]> https://biorxiv.org/content/10.1101/645176v1?rss=1 Alonso, A. Rooney, M. Chen, L. Y. Norby, F. Saenger, A. Soliman, E. O'Neal, W. Hootman, K. Selvin, E. Lutsey, P. 2019-05-24 doi:10.1101/645176 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Design principles of ROS dynamic networks relevant to precision therapies for age-related diseases ]]> https://biorxiv.org/content/10.1101/647776v1?rss=1 Kolodkin, A. Prasad Sharma, R. Colangelo, A. M. Ignatenko, A. Martorana, F. Jennen, D. Briede, J. J. Brady, N. Barberis, M. Mondeel, T. D. G. A. Papa, M. Kumar, V. Peters, B. Skupin, A. Alberghina, L. Balling, R. Westerhoff, H. V. 2019-05-24 doi:10.1101/647776 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Large particle fluorescence-activated cell sorting enables high quality single cell RNA-sequencing and functional analysis of adult cardiomyocytes ]]> https://biorxiv.org/content/10.1101/654954v1?rss=1 Kannan, S. Miyamoto, M. Lin, B. Zhu, R. Murphy, S. Kass, D. Andersen, P. Kwon, C. 2019-05-30 doi:10.1101/654954 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ A many-to-one sensory circuit encodes oxygen levels and drives respiratory behaviour in Danio rerio ]]> https://biorxiv.org/content/10.1101/655084v1?rss=1 Yeh, C. M. Pao, G. M. Villa-Real, R. Rosales, K. DePasquale, E. Groisman, A. Chalasani, S. H. 2019-05-31 doi:10.1101/655084 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ The Impact of Antimalarial Resistance on the Genetic Structure of Plasmodium falciparum in the DRC ]]> https://biorxiv.org/content/10.1101/656561v1?rss=1 Verity, R. J. Aydemir, O. Brazeau, N. F. Watson, O. J. Hathaway, N. J. Mwandagalirwa, M. K. Marsh, P. W. Thwai, K. Fulton, T. Denton, M. Morgan, A. P. Parr, J. B. Tumwebaze, P. K. Conrad, M. Rosenthal, P. J. Ishengoma, D. S. Ngondi, J. Gutman, J. Mulenga, M. Norris, D. E. Moss, W. J. Mensah, B. A. Myers-Hansen, J. L. Ghansah, A. Tshefu, A. K. Ghani, A. C. Meshnick, S. R. Bailey, J. A. Juliano, J. J. 2019-05-31 doi:10.1101/656561 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Evading non-essential fetal oocyte attrition maximizes the ovarian reserve ]]> https://biorxiv.org/content/10.1101/656645v1?rss=1 Tharp, M. E. Malki, S. Bortvin, A. 2019-06-03 doi:10.1101/656645 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ On the emergence of Candida auris: climate change, azoles, swamps and birds ]]> https://biorxiv.org/content/10.1101/657635v1?rss=1 Casadevall, A. Kontoyiannis, D. P. Robert, V. 2019-06-03 doi:10.1101/657635 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ PIWI proteins as prognostic markers in cancer: a systematic review and meta-analysis ]]> https://biorxiv.org/content/10.1101/663468v1?rss=1 Mentis, A.-F. Dardiotis, E. Papavassiliou, A. G. 2019-06-14 doi:10.1101/663468 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ RanGTP induces an effector gradient of XCTK2 and importin α/β for spindle microtubule cross-linking ]]> https://biorxiv.org/content/10.1101/664821v1?rss=1 Ems-McClung, S. E. Emch, M. Zhang, S. Mahnoor, S. Weaver, L. N. Walczak, C. E. 2019-06-08 doi:10.1101/664821 Cold Spring Harbor Laboratory Press 2019-06-08 <![CDATA[ Vascular Progenitors Generated from Tankyrase Inhibitor-Regulated Diabetic Induced Pluripotent Stem Cells Potentiate Efficient Revascularization of Ischemic Retina ]]> https://biorxiv.org/content/10.1101/678599v1?rss=1 Park, T. S. Zimmerlin, L. Evans-Moses, R. Thomas, J. Huo, J. S. Kanherkar, R. He, A. Ruzgar, N. Metzger, S. Grebe, R. Bhutto, I. Lutty, G. Zambidis, E. T. 2019-06-25 doi:10.1101/678599 Cold Spring Harbor Laboratory Press 2019-06-25 <![CDATA[ Serosolver: an open source tool to infer epidemiological and immunological dynamics from serological data ]]> https://biorxiv.org/content/10.1101/730069v1?rss=1 Hay, J. A. Minter, A. Ainslie, K. Lessler, J. Kucharski, A. J. Riley, S. 2019-08-08 doi:10.1101/730069 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Deep learning for brains?: Different linear and nonlinear scaling in UK Biobank brain images vs. machine-learning datasets ]]> https://biorxiv.org/content/10.1101/757054v1?rss=1 Schulz, M.-A. Yeo, T. Vogelstein, J. Mourao-Miranada, J. Kather, J. Kording, K. Richards, B. A. Bzdok, D. 2019-09-06 doi:10.1101/757054 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ A finite vocabulary of antibody-antigen interaction enables predictability of paratope-epitope binding ]]> https://biorxiv.org/content/10.1101/759498v1?rss=1 Akbar, R. Jeliazkov, J. R. Robert, P. A. Snapkov, I. Pavlovic, M. Slabodkin, A. Weber, C. R. Safanova, Y. Sandve, G. K. Greiff, V. 2019-09-09 doi:10.1101/759498 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ CaMKII oxidation is a performance/disease trade-off in vertebrate evolution ]]> https://biorxiv.org/content/10.1101/767525v1?rss=1 Wang, Q. Hernandez-Ochoa, E. O. Viswanathan, M. C. Blum, I. D. Granger, J. M. Murphy, K. R. Wei, A.-C. Aja, S. Liu, N. Antonescu, C. M. Florea, L. D. Talbot, C. C. Mohr, D. Wagner, K. R. Regot, S. Lovering, R. M. Wu, M. N. Cammarato, A. Schneider, M. F. Bever, G. S. Anderson, M. E. 2019-09-12 doi:10.1101/767525 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses ]]> https://biorxiv.org/content/10.1101/778605v1?rss=1 Zhang, H. Ahearn, T. Lecarpentier, J. Barnes, D. Beesley, J. Qi, G. Jiang, X. O'Mara, T. A. Zhao, N. Bolla, M. K. Dunning, A. M. Dennis, J. Wang, Q. Abu Ful, Z. Aittomaki, K. Andrulis, I. L. Anton-Culver, H. Arndt, V. Aronson, K. J. Arun, B. K. Auer, P. L. Azzollini, J. Barrowdale, D. Becher, H. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Bogdanova, N. V. Bojesen, S. E. Bonanni, B. Bondavalli, D. Borg, A. Brauch, H. Brenner, H. Briceno, I. Broeks, A. Brucker, S. Y. Bruning, T. Burwinkel, B. Buys, S. 2019-09-24 doi:10.1101/778605 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE ]]> https://biorxiv.org/content/10.1101/795609v1?rss=1 Ji, Z. Zhou, W. Ji, H. 2019-10-07 doi:10.1101/795609 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Malaria parasite immune evasion and adaptation to its mosquito host is influenced by the acquisition of multiple blood meals ]]> https://biorxiv.org/content/10.1101/801480v1?rss=1 Kwon, H. Reynolds, R. A. Simoes, M. L. Dimopoulos, G. Smith, R. C. 2019-10-15 doi:10.1101/801480 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Genome-wide association study of cryptosporidiosis in infants implicates PRKCA ]]> https://biorxiv.org/content/10.1101/819052v1?rss=1 Wojcik, G. L. Korpe, P. S. Marie, C. Mychaleckyj, J. Kirkpatrick, B. D. Rich, S. S. Concannon, P. Faruque, A. S. G. Haque, R. Petri, W. Duggal, P. 2019-10-25 doi:10.1101/819052 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ A screening platform based on epitope editing for drug discovery ]]> https://biorxiv.org/content/10.1101/838896v1?rss=1 Zhu, B. Yang, J. Van, R. Ran, K. Yin, K. Liang, Y. Shen, N. Yin, W. Choi, S. H. Lu, Y. Wang, C. Shao, Y. Tanzi, R. E. Zhang, C. Cheng, Y. Zhang, Z. Ran, C. 2019-11-24 doi:10.1101/838896 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community ]]> https://biorxiv.org/content/10.1101/839134v1?rss=1 Uritskiy, G. Tisza, M. J. Gelsinger, D. Munn, A. Taylor, J. DiRuggiero, J. 2019-11-12 doi:10.1101/839134 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Oncologic Therapy Shapes the Fitness Landscape of ClonalHematopoiesis ]]> https://biorxiv.org/content/10.1101/848739v1?rss=1 Bolton, K. L. Ptashkin, R. N. Gao, T. Braunstein, L. Devlin, S. M. Kelly, D. Patel, M. Berthon, A. Syed, A. Yabe, M. Coombs, C. Caltabellotta, N. M. Walsh, M. Offit, K. Stadler, Z. Mandelker, D. Schulman, J. W. Patel, A. Philip, J. Bernard, E. Gundem, G. Arango, J. E. Levine, M. Medina, J. S. Farnhoud, N. Glodzik, D. Li, S. Robson, M. E. Lee, C. Pharoah, P. Stopsack, K. Spitzer, B. Mantha, S. Fagin, J. Boucai, L. Gibson, C. J. Ebert, B. L. Young, A. L. Druley, T. Takahashi, K. Gillis, N. Ball, M. Padron, E. Hyman, D. M. Baselga, J. Norton, L. Gardo 2019-11-20 doi:10.1101/848739 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Kidney Function and Blood Pressure: A Bi-directional Mendelian Randomisation Study ]]> https://biorxiv.org/content/10.1101/856674v1?rss=1 Yu, Z. Coresh, J. Qi, G. Grams, M. Boerwinkle, E. Snieder, H. Teumer, A. Pattaro, C. Kottgen, A. Chatterjee, N. Tin, A. 2019-11-29 doi:10.1101/856674 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ An optimized acetylcholine sensor for monitoring in vivo cholinergic activity ]]> https://biorxiv.org/content/10.1101/861690v1?rss=1 jing, m. Li, Y. Zeng, J. Huang, P. Skirzewski, M. Peng, W. Qian, T. Tan, K. Wu, R. Zhang, S. Pan, S. Xu, M. Li, H. Saksida, L. M. Prado, V. F. Bussey, T. Prado, M. A. M. Chen, L. Cheng, H. Li, Y. 2019-12-02 doi:10.1101/861690 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Confluence of timing and reward biases in perceptual decision-making dynamics ]]> https://biorxiv.org/content/10.1101/865501v1?rss=1 Shinn, M. Ehrlich, D. Lee, D. Murray, J. D. Seo, H. 2019-12-05 doi:10.1101/865501 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Variation in cell surface hydrophobicity among Cryptococcus neoformans strains influences interactions with amoeba ]]> https://biorxiv.org/content/10.1101/867598v1?rss=1 Vij, R. Crawford, C. Casadevall, A. 2019-12-06 doi:10.1101/867598 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Aurora B and C kinases regulate prophase exit and chromosome segregation during spermatogenesis ]]> https://biorxiv.org/content/10.1101/868836v1?rss=1 Wellard, S. R. Schindler, K. Jordan, P. 2019-12-11 doi:10.1101/868836 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Evaluation of p53 Immunohistochemical Expression Using Open-Source Software for Digital Image Analysis: A Tissue Microarray Study of Penile Squamous Cell Carcinomas ]]> https://biorxiv.org/content/10.1101/029850v1?rss=1 Alcides Chaux George J Netto Authur L Burnett 2015-10-26 doi:10.1101/029850 Cold Spring Harbor Laboratory Press 2015-10-26 <![CDATA[ RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing (RASL-seq) experiments ]]> https://biorxiv.org/content/10.1101/036061v1?rss=1 Erick R. Scott H. Benjamin Larman Ali Torkamani Nicholas J. Schork Nathan Wineinger Max Nanis Ryan C. Thompson Reza B. Beheshti Zavareh Luke L. Lairson Peter G. Schultz Andrew I. Su 2016-01-07 doi:10.1101/036061 Cold Spring Harbor Laboratory Press 2016-01-07 <![CDATA[ Molecular mechanisms of substrate-controlled ring dynamics and sub-stepping in a nucleic-acid dependent hexameric motor ]]> https://biorxiv.org/content/10.1101/069559v1?rss=1 Nathan D. Thomsen Michael R. Lawson Lea B. Witkowsky Song Qu James M. Berger 2016-08-16 doi:10.1101/069559 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Ligand-induced and small molecule control of substrate loading in a hexameric helicase ]]> https://biorxiv.org/content/10.1101/069773v1?rss=1 Michael R. Lawson Kevin Dyer James M. Berger 2016-08-16 doi:10.1101/069773 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3 ]]> https://biorxiv.org/content/10.1101/073908v1?rss=1 Jarrett Smith Deepika Calidas Helen Schmidt Tu Lu Dominique Rasoloson Geraldine Seydoux 2016-09-07 doi:10.1101/073908 Cold Spring Harbor Laboratory Press 2016-09-07 <![CDATA[ COPI Mediates Recycling Of An Exocytic SNARE From Endosomes By Recognition Of A Ubiquitin Sorting Signal ]]> https://biorxiv.org/content/10.1101/133546v1?rss=1 Xu, P. Hankins, H. Macdonald, C. Erlinger, S. J. Frazier, M. Diab, N. S. Piper, R. C. Jackson, L. P. MacGurn, J. A. Graham, T. R. 2017-05-03 doi:10.1101/133546 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces potentially functional transcripts ]]> https://biorxiv.org/content/10.1101/154856v1?rss=1 Anderson, J. L. Mulligan, T. S. Shen, M.-C. Wang, H. Scahill, C. M. Du, S. J. Busch-Nentwich, E. M. Farber, S. A. 2017-06-23 doi:10.1101/154856 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Large-Scale cognitive GWAS Meta-analysis Reveals Tissue-Specific Neural Expression and Potential Nootopic Drug Targets ]]> https://biorxiv.org/content/10.1101/176842v1?rss=1 Lam, M. Trampush, J. W. Yu, J. Knowles, E. Davies, G. Liewald, D. C. Starr, J. M. Djurovic, S. Melle, I. Sundet, K. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. J. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Attix, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. C. Avramopoulos, D. Hatzimanolis, A. Arking, D. E. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, T. D. London, E. Poldrack, R. A. 2017-08-16 doi:10.1101/176842 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ Sparse interaction between oligodendrocyte precursor cells (NG2+ cells) and nodes of Ranvier in the central nervous system ]]> https://biorxiv.org/content/10.1101/185801v1?rss=1 De Biase, L. M. Pucak, M. L. Kang, S. H. Rodriguez, S. N. Bergles, D. E. 2017-09-07 doi:10.1101/185801 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Islet architecture controls synchronous β cell response to glucose in the intact mouse pancreas in vivo ]]> https://biorxiv.org/content/10.1101/2019.12.11.873471v1?rss=1 Adams, M. T. Reissaus, C. A. Szulczewski, J. M. Dwulet, J. M. Lyman, M. R. Sdao, S. M. Nimkulrat, S. D. Ponik, S. M. Merrins, M. J. Benninger, R. K. P. Mirmira, R. G. Linnemann, A. K. Blum, B. 2019-12-12 doi:10.1101/2019.12.11.873471 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ A single cell transcriptional atlas of early synovial joint development ]]> https://biorxiv.org/content/10.1101/2019.12.23.887208v1?rss=1 Bian, Q. Cheng, Y.-H. Wilson, J. P. Kim, D. W. Wang, H. Blackshaw, S. Cahan, P. 2019-12-23 doi:10.1101/2019.12.23.887208 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Failure to maternally reprogram histone methylation causes developmental delay due to germline transcription in somatic tissues ]]> https://biorxiv.org/content/10.1101/2020.01.22.914580v1?rss=1 Carpenter, B. S. Lee, T. W. Plott, C. F. Brockett, J. S. Katz, D. 2020-01-23 doi:10.1101/2020.01.22.914580 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Regulation of human development by ubiquitin chain editing of chromatin remodelers ]]> https://biorxiv.org/content/10.1101/2020.01.23.917450v1?rss=1 Beck, D. Basar, M. A. Asmar, A. J. Thompson, J. Oda, H. Uehara, D. T. Saida, K. Bodurtha, J. d Souza, P. Mu, W. Baranano, K. W. Miyake, N. Wang, R. Kempers, M. Nishimura, Y. Okada, S. Kosho, T. Dale, R. Mitra, A. Macnamara, E. Undiagnosed Diseases Network, Matsumoto, N. Inazawa, J. Walkiewicz, M. Tifft, C. J. Aksentijevich, I. Kastner, D. L. Rocha, P. P. Werner, A. 2020-01-24 doi:10.1101/2020.01.23.917450 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets ]]> https://biorxiv.org/content/10.1101/2020.01.30.927129v1?rss=1 Erbe, R. Kess;ler, M. D. Favorov, A. V. Easwaran, H. Gaykalova, D. A. Fertig, E. J. 2020-01-31 doi:10.1101/2020.01.30.927129 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Spatiotemporal Dynamics of Orthographic and Lexical Processing in the Ventral Visual Pathway ]]> https://biorxiv.org/content/10.1101/2020.02.18.955039v1?rss=1 Woolnough, O. Donos, C. Rollo, P. S. Forseth, K. J. Lakretz, Y. Crone, N. E. Fischer-Baum, S. Dehaene, S. Tandon, N. 2020-02-19 doi:10.1101/2020.02.18.955039 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ A virion-based assay for glycoprotein thermostability reveals key determinants of filovirus entry and its inhibition ]]> https://biorxiv.org/content/10.1101/2020.02.25.965772v1?rss=1 Bortz, R. H. Wong, A. C. Grodus, M. G. Recht, H. Pulanco, M. C. Lasso, G. Anthony, S. J. Mittler, E. Jangra, R. K. Chandran, K. 2020-02-26 doi:10.1101/2020.02.25.965772 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating ]]> https://biorxiv.org/content/10.1101/2020.02.26.966754v1?rss=1 Drew, K. Lee, C. Cox, R. M. Dang, V. Devitt, C. C. Papoulas, O. Huizar, R. L. Marcotte, E. M. Wallingford, J. B. 2020-02-27 doi:10.1101/2020.02.26.966754 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Establishing Preclinical Withdrawal Syndrome Symptomatology Following Heroin Self-Administration in Male and Female Rats ]]> https://biorxiv.org/content/10.1101/2020.03.02.974006v1?rss=1 Gipson, C. D. Dunn, K. E. Bull, A. H. Ulangkaya, H. Hossain, A. 2020-03-04 doi:10.1101/2020.03.02.974006 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Evidence for oligodendrocyte progenitor cell heterogeneity in the adult mouse brain. ]]> https://biorxiv.org/content/10.1101/2020.03.06.981373v1?rss=1 Beiter, R. M. Fernandez-Castaneda, A. Rivet-Noor, C. Merchak, A. Bai, R. Slogar, E. Seki, S. M. Rosen, D. A. overall, c. c. Gaultier, A. 2020-03-08 doi:10.1101/2020.03.06.981373 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Structural and developmental principles of neuropil assembly in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.03.15.992222v1?rss=1 Moyle, M. W. Barnes, K. M. Kuchroo, M. Gonopolskiy, A. Duncan, L. H. Sengupta, T. Shao, L. Guo, M. Santella, A. Christensen, R. Kumar, A. Wu, Y. Moon, K. R. Wolf, G. Krishnaswamy, S. Bao, Z. Shroff, H. Mohler, W. Colon-Ramos, D. A. 2020-03-15 doi:10.1101/2020.03.15.992222 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Start codon disruption with CRISPR/Cas9 prevents murine Fuchs' endothelial corneal dystrophy ]]> https://biorxiv.org/content/10.1101/2020.03.18.996728v1?rss=1 Uehara, H. Zhang, X. Pereira, F. Narendran, S. Choi, S. Bhuvanagiri, S. Liu, J. Ravi Kumar, S. Bohner, A. Carroll, L. Archer, B. Zhang, Y. Liu, W. Gao, G. Ambati, J. Jun, A. S. Ambati, B. K. 2020-03-20 doi:10.1101/2020.03.18.996728 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Characterization of essential eggshell proteins from Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2020.04.06.027706v1?rss=1 Simington, C. J. Oscherwitz, M. E. Peterson, A. J. Rascon, A. A. Massani, B. B. Miesfeld, R. ISOE, J. 2020-04-07 doi:10.1101/2020.04.06.027706 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Astrocyte- and neuron-derived extracellular vesicles from Alzheimer's disease patients effect complement-mediated neurotoxicity ]]> https://biorxiv.org/content/10.1101/2020.04.14.041863v1?rss=1 Nogueras-Ortiz, C. J. Mahairaki, V. Delgado-Peraza, F. M. Das, D. Avgerinos, K. Hentschel, M. Goetzl, E. J. Mattson, M. P. Kapogiannis, D. 2020-04-16 doi:10.1101/2020.04.14.041863 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Development of mPing-based Activation Tags for Crop Insertional Mutagenesis ]]> https://biorxiv.org/content/10.1101/2020.04.22.055970v1?rss=1 Johnson, A. Mcassey, E. Diaz, S. Reagin, J. Parrilla, D. R. Nguyen, H. Stec, A. McDaniel, L. A. L. Clemente, T. E. Stupar, R. M. Parrott, W. A. Hancock, C. N. 2020-04-24 doi:10.1101/2020.04.22.055970 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Genetic inactivation of the translin/trax microRNA-degrading enzyme phenocopies the robust adiposity induced by Translin (Tsn) deletion ]]> https://biorxiv.org/content/10.1101/2020.04.25.060665v1?rss=1 Fu, X. Shah, A. P. Li, Z. Li, M. Tamashiro, K. L. Baraban, J. M. 2020-04-25 doi:10.1101/2020.04.25.060665 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Nature and effective range of non-cell autonomous activator and inhibitor peptides specifying plant stomatal patterning ]]> https://biorxiv.org/content/10.1101/2020.04.29.069211v1?rss=1 Zeng, S. Lo, E. K. W. Hazelton, B. J. Morales, M. F. Torii, K. 2020-05-01 doi:10.1101/2020.04.29.069211 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Experimental Stroke Induces Chronic Gut Dysbiosis and Neuroinflammation in Male Mice ]]> https://biorxiv.org/content/10.1101/2020.04.29.069575v1?rss=1 Brichacek, A. L. Nwafor, D. C. Benkovic, S. A. Chakraborty, S. Kenney, S. M. Mace, M. Jun, S. Gambill, C. A. Wang, W. Hu, H. Ren, X. Povroznik, J. M. Engler-Chiurazzi, E. B. Primerano, D. Denvir, J. Percifield, R. Infante, A. Franko, J. Schafer, R. Gemoets, D. E. Brown, C. M. 2020-05-01 doi:10.1101/2020.04.29.069575 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ A small molecule that binds an RNA repeat expansion stimulates its decay via the exosome complex ]]> https://biorxiv.org/content/10.1101/2020.05.11.088427v1?rss=1 100-fold specificity vs. many other RNAs and DNA. Interestingly, the compounds downstream effects are different in the two diseases, owing to the location of the repeat expansion. In DM1, r(CUG)exp is harbored in the 3 untranslated region (UTR) of and mRNA, and the compound has no effect on the RNAs abundance. In FECD, however, r(CUG)exp is located in an intron, and the small molecule, by binding the repeat expansion, facilitates excision of the intron, which is then degraded by the exosome complex exonuclease, hRRP6. Thus, structure-specific, RNA-targeting small molecules can act disease-specifically to affect biology, either by disabling its gain-of-function mechanism (DM1) or by stimulating quality control pathways to rid a disease-affected cell of a toxic RNA (FECD). Significance statementMany different diseases are caused by toxic structured RNAs. Herein, we designed a lead small molecule that binds a toxic structure and rescues disease biology. We show that a structure-specific small molecule can improve disease-associated defects in two diseases that share the common toxic RNA structure. In one disease, the toxic structure is harbored in an intron and causes its retention. The compound facilitates processing of a retained intron, enabling the disease-affected cell to remove the toxic RNA. ]]> Angelbello, A. J. Benhamou, R. I. Rzuczek, S. G. Choudhary, S. Tang, Z. Chen, J. L. Roy, M. Wang, K. W. Yildirim, I. Jun, A. S. Thornton, C. A. Disney, M. D. 2020-05-12 doi:10.1101/2020.05.11.088427 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ CREBBP and STAT6 co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma ]]> https://biorxiv.org/content/10.1101/2020.05.28.120212v1?rss=1 Xian, R. R. Xie, Y. Haley, L. M. Yonescu, R. Pallavajjala, A. Pittaluga, S. Jaffe, E. S. Duffield, A. S. McCall, C. M. Gheith, S. M. F. Gocke, C. D. 2020-05-31 doi:10.1101/2020.05.28.120212 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Functional melanoma cell heterogeneity is regulated by MITF-dependent cell-matrix interactions ]]> https://biorxiv.org/content/10.1101/2020.06.09.141747v1?rss=1 Spoerri, L. Tonnessen-Murray, C. A. Gunasingh, G. Hill, D. S. Beaumont, K. A. Jurek, R. J. Vanwalleghem, G. C. Fane, M. E. Daignault, S. M. Matigian, N. Scott, E. K. Smith, A. G. Stehbens, S. J. Schaider, H. Weninger, W. Gabrielli, B. Haass, N. K. 2020-06-11 doi:10.1101/2020.06.09.141747 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Immunoresolvents Support Skeletal Myofiber Regeneration via Actions on Myeloid and Muscle Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.06.12.148320v1?rss=1 Markworth, J. F. Brown, L. A. Lim, E. Floyd, C. Larouche, J. Castor-Macias, J. A. Sugg, K. B. Sarver, D. C. Macpherson, P. C. F. Davis, C. Aguilar, C. A. Maddipati, K. R. Brooks, S. V. 2020-06-13 doi:10.1101/2020.06.12.148320 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Clinical characteristics and primary management of patients diagnosed with prostate cancer between 2015 and 2019 at the Uganda Cancer Institute ]]> https://biorxiv.org/content/10.1101/2020.07.09.194936v1?rss=1 Paul Katongole Obondo J. Sande Mulumba Yusuf Moses Joloba Steven J Reynolds Nixon Niyonzima 2020-07-09 doi:10.1101/2020.07.09.194936 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ An orthogonal differentiation platform for genomically programming stem cells, organoids, and bioprinted tissues ]]> https://biorxiv.org/content/10.1101/2020.07.11.198671v1?rss=1 Mark Skylar-Scott Jeremy Huang Aric Lu Alex Ng Tomoya Duenki Lucy Nam Sarita Damaraju George Church Jennifer A. Lewis 2020-07-12 doi:10.1101/2020.07.11.198671 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Lamin C regulates genome organization after mitosis ]]> https://biorxiv.org/content/10.1101/2020.07.28.213884v1?rss=1 Wong, X. Hoskins, V. E. Harr, J. C. Gordon, M. Reddy, K. 2020-07-28 doi:10.1101/2020.07.28.213884 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Drug Screening with Zebrafish Visual Behavior Identifies Carvedilol as a Potential Treatment for Retinitis Pigmentosa ]]> https://biorxiv.org/content/10.1101/2020.07.28.225789v1?rss=1 Ganzen, L. Ko, M. J. Zhang, M. Xie, R. Chen, Y. Zhang, L. James, R. Mumm, J. van Rijn, R. Zhong, W. Pang, C. P. Zhang, M. Tsujikawa, M. Leung, Y. F. 2020-07-29 doi:10.1101/2020.07.28.225789 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Aggregation Tool for Genomic Concepts (ATGC): A deep learning framework for sparse genomic measures and its application to tumor mutational burden ]]> https://biorxiv.org/content/10.1101/2020.08.05.237206v1?rss=1 Anaya, J. Sidhom, J.-W. Cummings, C. A. Baras, A. S. The AACR Project GENIE Consortium, 2020-08-07 doi:10.1101/2020.08.05.237206 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Purinergic signaling controls spontaneous activityin the auditory system throughout early development ]]> https://biorxiv.org/content/10.1101/2020.08.11.246306v1?rss=1 Babola, T. A. Li, S. Wang, Z. Kersbergen, C. J. Elgoyhen, A. B. Coate, T. M. Bergles, D. E. 2020-08-12 doi:10.1101/2020.08.11.246306 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ A neurite-zippering mechanism, mediated by layer-specific expression of IgCAMs, regulates synaptic laminar specificity in the C. elegans nerve ring neuropil ]]> https://biorxiv.org/content/10.1101/2020.08.28.271437v1?rss=1 Sengupta, T. Koonce, N. L. Moyle, M. W. Duncan, L. H. Vazquez-Martinez, N. Han, X. Shao, L. Wu, Y. Santella, A. Fan, L. Bao, Z. Mohler, W. A. Shroff, H. Colon-Ramos, D. 2020-08-29 doi:10.1101/2020.08.28.271437 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ The Arf-GEF Steppke promotes F-actin accumulation, cell protrusions and tissue sealingduring Drosophila dorsal closure ]]> https://biorxiv.org/content/10.1101/2020.09.08.287102v1?rss=1 West, J. J. Harris, T. J. C. 2020-09-08 doi:10.1101/2020.09.08.287102 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Establishment of multiple novel patient-derived models of desmoplastic small round cell tumor enabling functional characterization of ERBB pathway signaling and pre-clinical evaluation of a novel targeted therapy approach ]]> https://biorxiv.org/content/10.1101/2020.09.22.308940v1?rss=1 Smith, R. S. Odintsov, I. Liu, Z. Hayashi, T. Lui, A. J. W. Vojnic, M. Suehara, Y. Mattar, M. S. Hmeljak, J. Ramirez, H. A. Shaw, M. Bui, G. Hartono, A. B. Gladstone, E. Magnan, H. Khodos, I. de Stanchina, E. La Quaglia, M. P. Yao, J. Lae, M. Lee, S. B. Spraggon, L. Pratilas, C. A. Ladanyi, M. Somwar, R. 2020-09-23 doi:10.1101/2020.09.22.308940 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Perilipin2 down-regulation in beta cells impairs insulin secretion under nutritional stress and damages mitochondria ]]> https://biorxiv.org/content/10.1101/2020.10.01.322974v1?rss=1 Mishra, A. Liu, S. Promes, J. Harata, M. Sivitz, W. Fink, B. Bhardwaj, G. O'Neill, B. Kang, C. Sah, R. Strack, S. Stephens, S. King, T. Jackson, L. Greenberg, A. Anokye-Danso, F. Ahima, R. Ankrum, J. A. Imai, Y. 2020-10-01 doi:10.1101/2020.10.01.322974 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Comprehensive identification of somatic nucleotide variants in human brain tissue ]]> https://biorxiv.org/content/10.1101/2020.10.10.332213v1?rss=1 Wang, Y. Bae, T. Thorpe, J. Sherman, M. A. Jones, A. G. Cho, S. Daily, K. Dou, Y. Ganz, J. Galor, A. Lobon, I. Pattni, R. Rosenbluh, C. Tomasi, S. Tomasini, L. Yang, X. Zhou, B. Akbarian, S. Ball, L. L. Bizzotto, S. Emery, S. B. Doan, R. Fasching, L. Jang, Y. Juan, D. Lizano, E. Moldovan, J. B. Narurkar, R. Oetjens, M. T. Sekar, S. Shin, J. H. Soriano, E. Straub, R. E. Zhou, W. Chess, A. Gleeson, J. G. Marques-Bonet, T. Park, P. J. Peters, M. A. Pevsner, J. Walsh, C. A. Weinberger, D. R. Brain Somatic Mosaicism Network, Vaccarino, F. M. Moran, J. V 2020-10-10 doi:10.1101/2020.10.10.332213 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader ]]> https://biorxiv.org/content/10.1101/2020.10.21.345918v1?rss=1 Puri, N. Fernandez, A. J. O'Shea Murray, V. L. McMillan, S. Keck, J. L. Berger, J. M. 2020-10-21 doi:10.1101/2020.10.21.345918 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu ]]> https://biorxiv.org/content/10.1101/2020.11.10.375675v1?rss=1 Goods, B. A. Askenase, M. H. Markarian, E. Beatty, H. E. Drake, R. Fleming, I. DeLong, J. H. Philip, N. H. Matouk, C. C. Awad, I. A. Zuccarello, M. Hanley, D. F. Love, J. C. Shalek, A. K. Sansing, L. H. 2020-11-12 doi:10.1101/2020.11.10.375675 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Biomarkers of lesion severity in a rodent model of nonarteritic anterior ischemic optic neuropathy (rNAION) ]]> https://biorxiv.org/content/10.1101/2020.11.18.388132v1?rss=1 Guo, Y. Mehabian, Z. Johnson, M. A. Miller, N. R. Henderson, A. Hamlyn, J. Bernstein, S. L. 2020-11-18 doi:10.1101/2020.11.18.388132 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ The Role of Aquaporin-4 in Optic Nerve Head Astrocytes in Experimental Glaucoma ]]> https://biorxiv.org/content/10.1101/2020.12.04.411322v1?rss=1 Kimball, E. Schaub, J. Quillen, S. Keuthan, C. Pease, M. E. Korneva, A. Quigley, H. 2020-12-04 doi:10.1101/2020.12.04.411322 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Total recall: episodic memory retrieval,choice, and memory confidence in the rat ]]> https://biorxiv.org/content/10.1101/2020.12.14.420174v1?rss=1 Joo, H. R. Liang, H. Chung, J. E. Geaghan-Breiner, C. Fan, J. L. Nachman, B. Kepecs, A. Frank, L. M. 2020-12-15 doi:10.1101/2020.12.14.420174 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Maladaptive oxidative stress cascade drives type I interferon hyperactivity in TNF activated macrophages promoting necrosis in murine tuberculosis granulomas ]]> https://biorxiv.org/content/10.1101/2020.12.14.422743v1?rss=1 Brownhill, E. Yabaji, S. M. Zhernovkov, V. Rukhlenko, O. S. Seidel, K. Bhattacharya, B. Chatterjee, S. Chen, H. A. Crossland, N. Bishai, W. Kholodenko, B. N. Gimelbrant, A. Kobzik, L. Kramnik, I. 2020-12-14 doi:10.1101/2020.12.14.422743 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Hypoxia Regulation of ndrgs ]]> https://biorxiv.org/content/10.1101/2020.12.16.422782v1?rss=1 Le, N. Hufford, T. M. Brewster, R. 2020-12-18 doi:10.1101/2020.12.16.422782 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Extensive High-Order Complexes within SARS-CoV-2 Proteome Revealed by Compartmentalization-Aided Interaction Screening ]]> https://biorxiv.org/content/10.1101/2020.12.26.424422v1?rss=1 Xu, W. Pei, G. Liu, H. Wang, J. Li, P. 2020-12-26 doi:10.1101/2020.12.26.424422 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ Adipocyte-specific deletion of the oxygen-sensor PHD2 sustains elevated energy expenditure at thermoneutrality ]]> https://biorxiv.org/content/10.1101/2021.01.05.425401v1?rss=1 GOMEZ SALAZAR, M. PRUNONOSA CERVERA, I. WANG, R. FRENCH, K. GARCIA-MARTIN, R. BLÜHER, M. SCHOFIELD, C. J. STIMSON, R. H. CHAVAKIS, T. GUDMUNDSSON, E. F. JENNINGS, L. L. GUDNASON, V. G. MORTON, N. M. EMILSSON, V. MICHAILIDOU, Z. 2021-01-06 doi:10.1101/2021.01.05.425401 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Phosphorylation of the selective autophagy receptor TAX1BP1 by canonical and noncanonical IκB kinases promotes its lysosomal localization and clearance of MAVS aggregates ]]> https://biorxiv.org/content/10.1101/2021.01.07.425702v1?rss=1 Choi, Y. B. Zhang, J. Vo, M. T. White, J. He, C. Harhaj, E. W. 2021-01-07 doi:10.1101/2021.01.07.425702 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Local Shifts in Inflammatory and Resolving Lipid Mediators in Response to Tendon Overuse ]]> https://biorxiv.org/content/10.1101/2021.01.08.425901v1?rss=1 Markworth, J. F. Sugg, K. B. Sarver, D. C. Maddipati, K. R. Brooks, S. V. 2021-01-09 doi:10.1101/2021.01.08.425901 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Human colorectal pre-cancer atlas identifies distinct molecular programs underlying two major subclasses of pre-malignant tumors ]]> https://biorxiv.org/content/10.1101/2021.01.11.426044v1?rss=1 Chen, B. McKinley, E. T. Simmons, A. J. Ramirez, M. A. Zhu, X. Southard-Smith, A. N. Markham, N. O. Sheng, Q. Drewes, J. Xu, Y. Heiser, C. N. Zhou, Y. Revetta, F. Berry, L. D. Zheng, W. Washington, M. K. Cai, Q. Sears, C. L. Goldenring, J. R. Franklin, J. L. Vandekar, S. Roland, J. T. Su, T. Huh, W. J. Liu, Q. Coffey, R. J. Shrubsole, M. J. Lau, K. 2021-01-13 doi:10.1101/2021.01.11.426044 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Decoding shared versus divergent transcriptomic signatures across cortico-amygdala circuitry in PTSD and depressive disorders ]]> https://biorxiv.org/content/10.1101/2021.01.12.426438v1?rss=1 Jaffe, A. E. Barry, B. K. Tao, R. Tran, M. N. Page, S. C. Maynard, K. R. Pattie, E. A. Nguyen, C. V. Deep-Soboslay, A. Bharadwaj, R. Young, K. A. Friedman, M. J. Williamson, D. E. Traumatic Stress Brain Research Group, Shin, J. H. Hyde, T. M. Martinowich, K. Kleinman, J. E. 2021-01-13 doi:10.1101/2021.01.12.426438 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites ]]> https://biorxiv.org/content/10.1101/2021.01.22.427624v1?rss=1 Lee, J. H. Mosher, E. P. Lee, Y.-S. Bumpus, N. N. Berger, J. M. 2021-01-23 doi:10.1101/2021.01.22.427624 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ Nuclear cholesterol is required for transcriptional repression by BASP1 ]]> https://biorxiv.org/content/10.1101/2021.01.24.427800v1?rss=1 Loats, A. E. Carrera, S. Fleming, A. F. Roberts, A. R. E. Sherrard, A. Toska, E. Medler, K. F. Roberts, S. G. E. 2021-01-26 doi:10.1101/2021.01.24.427800 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.01.28.428598v1?rss=1 Fasolino, M. Schwartz, G. W. Golson, M. Wang, Y. J. Morgan, A. Liu, C. Schug, J. Liu, J. Wu, M. Traum, D. Kondo, A. May, C. Goldman, N. Wang, W. HPAP Consortium, Feldman, M. Moore, J. Japp, A. Betts, M. Faryabi, R. B. Kaestner, K. Naji, A. Vahedi, G. 2021-01-29 doi:10.1101/2021.01.28.428598 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ A conversion from slow to fast memory in response to passive motion ]]> https://biorxiv.org/content/10.1101/2021.03.09.434594v1?rss=1 Javidialsaadi, M. Albert, S. T. Wang, J. 2021-03-10 doi:10.1101/2021.03.09.434594 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Direct Extraction of Signal and Noise Correlations from Two-Photon Calcium Imaging of Ensemble Neuronal Activity ]]> https://biorxiv.org/content/10.1101/2021.03.11.434932v1?rss=1 Rupasinghe, A. Francis, N. Liu, J. Bowen, Z. O. Kanold, P. Babadi, B. 2021-03-12 doi:10.1101/2021.03.11.434932 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Mapping origins of variation in neural trajectories of human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.03.17.435870v1?rss=1 Kim, S. K. Seo, S. Stein-O'Brien, G. Jaishankar, A. Ogawa, K. Micali, N. Wang, Y. Hyde, T. Kleinman, J. Voss, T. Fertig, E. Shin, J. H. Burli, R. Cross, A. J. Brandon, N. J. Weinberger, D. R. Chenoweth, J. G. Hoeppner, D. J. Sestan, N. Colantuoni, C. McKay, R. D. 2021-03-17 doi:10.1101/2021.03.17.435870 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Activity of Plasmodium vivax promoter elements in Plasmodium knowlesi, and a centromere-containing plasmid that expresses NanoLuc throughout the parasite life cycle ]]> https://biorxiv.org/content/10.1101/2021.03.30.437722v1?rss=1 Moraes Barros, R. R. Thawnashom, K. Gibson, T. J. Armistead, J. S. Caleon, R. L. Kaneko, M. Kite, W. A. Mershon, J. P. Brockhurst, J. K. Engels, T. Lambert, L. Orr-Gonzalez, S. Adams, J. H. Sa, J. M. Kaneko, O. Wellems, T. 2021-03-30 doi:10.1101/2021.03.30.437722 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ ALT Neuroblastoma Chemoresistance due to ATM Activation by Telomere Dysfunction is Reversible with the ATM Inhibitor AZD0156 ]]> https://biorxiv.org/content/10.1101/2021.04.06.438692v1?rss=1 Koneru, B. Farooqi, A. Nguyen, T. H. Chen, W. H. Hindle, A. Eslinger, C. Makena, M. R. Burrow, T. A. Wilson, J. Smith, A. Reddy, V. P. Cadogan, E. Durant, S. T. Reynolds, C. P. 2021-04-07 doi:10.1101/2021.04.06.438692 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ Electrophysiological measures from human iPSC-derived neurons are associated with schizophrenia clinical status and predict individual cognitive performance ]]> https://biorxiv.org/content/10.1101/2021.04.08.437289v1?rss=1 Page, S. C. Sripathy, S. R. Farinelli, F. Ye, Z. Wang, Y. Hiler, D. J. Pattie, E. A. Nguyen, C. V. Tippani, M. Moses, R. L. Chen, H.-Y. Tran, M. N. Eagles, N. J. Stolz, J. M. Catallini, J. L. Soudry, O. R. Dickinson, D. Berman, K. F. Apud, J. A. Weinberger, D. R. Martinowich, K. Jaffe, A. E. Straub, R. E. Maher, B. J. 2021-04-10 doi:10.1101/2021.04.08.437289 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Targeting cancer glycosylation repolarizes tumor-associated macrophages allowing effective immune checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2021.04.11.439323v1?rss=1 Stanczak, M. A. Mantuano, N. R. Kirchhammer, N. Sanin, D. E. Wang, J. Trefny, M. P. Monaco, G. Gray, M. A. Petrone, A. Kashyap, A. S. Glatz, K. Kasenda, B. Normington, K. Broderick, J. Peng, L. Pearce, O. M. Pearce, E. L. Bertozzi, C. R. Zippelius, A. Laeubli, H. 2021-04-11 doi:10.1101/2021.04.11.439323 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Molecular determinants of phase separation for Drosophila DNA replication licensing factors ]]> https://biorxiv.org/content/10.1101/2021.04.12.439485v1?rss=1 Parker, M. W. Kao, J. A. Huang, A. T. Berger, J. M. Botchan, M. R. 2021-04-12 doi:10.1101/2021.04.12.439485 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Protective efficacy of an orf virus-vector encoding the hemmagglutinin and the nucleoprotein of influenza A virus in swine ]]> https://biorxiv.org/content/10.1101/2021.04.19.440556v1?rss=1 Joshi, L. R. Knudsen, D. Pineyro, P. Dhakal, S. Renukaradhya, G. J. Diel, D. G. 2021-04-21 doi:10.1101/2021.04.19.440556 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification ]]> https://biorxiv.org/content/10.1101/2021.05.06.443021v1?rss=1 Su, E. Y. Spangler, A. Bian, Q. Kasamoto, J. Y. Cahan, P. 2021-05-07 doi:10.1101/2021.05.06.443021 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution ]]> https://biorxiv.org/content/10.1101/2021.05.07.443179v1?rss=1 Tan, Y. Spangler, A. Farid, M. Peng, D. Cahan, P. 2021-05-08 doi:10.1101/2021.05.07.443179 Cold Spring Harbor Laboratory Press 2021-05-08 <![CDATA[ Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole cell mechanics ]]> https://biorxiv.org/content/10.1101/2021.05.12.443683v1?rss=1 Vahabikashi, A. Sivagurunathan, S. Nicdao, F. A. S. Han, Y. L. Park, C. Y. Tran, J. R. Gundersen, G. G. Reddy, K. Luxton, G. G. Guo, M. Fredberg, J. J. Zheng, Y. Adam, S. A. Goldman, R. D. 2021-05-13 doi:10.1101/2021.05.12.443683 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Generation of potent cellular and humoral immunity against SARS-CoV-2 antigens via conjugation to a polymeric glyco-adjuvant ]]> https://biorxiv.org/content/10.1101/2021.05.20.445060v1?rss=1 Gray, L. T. Raczy, M. M. Briquez, P. S. Marchell, T. M. Alpar, A. T. Wallace, R. P. Volpatti, L. R. Sasso, M. S. Cao, S. Nguyen, M. Mansurov, A. Budina, E. Watkins, E. A. Solanki, A. Mitrousis, N. Reda, J. W. Yu, S. S. Tremain, A. C. Wang, R. Nicolaescu, V. Furlong, K. Dvorkin, S. Manicassamy, B. Randall, G. Wilson, D. S. Kwissa, M. Swartz, M. A. Hubbell, J. A. 2021-05-21 doi:10.1101/2021.05.20.445060 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Effects of vapor exposure to Δ9-tetrahydrocannabinol (THC) in the Maine Lobster (Homarus americanus) ]]> https://biorxiv.org/content/10.1101/2021.05.24.445508v1?rss=1 Gutierrez, A. Creehan, K. M. Turner, M. Tran, R. N. Kerr, T. M. Nguyen, J. D. Taffe, M. A. 2021-05-25 doi:10.1101/2021.05.24.445508 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.31.446440v1?rss=1 Borner, K. Teichmann, S. A. Quardokus, E. M. Gee, J. Browne, K. Osumi-Sutherland, D. Herr, B. W. Bueckle, A. Paul, H. Haniffa, M. A. Jardine, L. Bernard, A. Ding, S.-L. Miller, J. A. Lin, S. Halushka, M. Boppana, A. Longacre, T. A. Hickey, J. Lin, Y. Valerius, M. T. He, Y. Pryhuber, G. Sun, X. Jorgensen, M. Radtke, A. Wasserfall, C. Ginty, F. Ho, J. Sunshine, J. Beuschel, R. T. Brusko, M. Lee, S. Malhotra, R. Jain, S. Weber, G. 2021-06-01 doi:10.1101/2021.05.31.446440 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Retinoic acid exerts sexually dimorphic effects over muscle energy metabolism and function ]]> https://biorxiv.org/content/10.1101/2021.06.04.447134v1?rss=1 30%. Rdh10+/- male GM had impaired electron transport chain activity, and a 60% reduction in fasting ATP. The share of oxidative fibers increased, as did expression of the myogenic transcription factors Myog and Myf5. Centralized nuclei increased 5-fold in fibers--indicating muscle malady or repair. In Rdh10+/- female GM, RA decreased only 17%, due to a 1.8-fold increase in the estrogen-induced retinol dehydrogenase, Dhrs9. Rdh10+/- female GM did not amass TAG, increase oxidative fibers, decrease Glut1 mRNA or glucose, nor increase centralized nuclei. Expression of Myog and Myf5 decreased. Electron transport chain activity increased, elevating fasting ATP >3-fold. Thus, small decreases in skeletal muscle RA affect whole body energy use, insulin resistance and adiposity, in part through estrogen-related sexual dimorphic effects on mitochondria function. ]]> Zhao, Y. Vuckovic, M. Yoo, H. S. Fox, N. Rodriguez, A. McKessy, K. Napoli, J. L. 2021-06-04 doi:10.1101/2021.06.04.447134 Cold Spring Harbor Laboratory Press 2021-06-04 <![CDATA[ A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets ]]> https://biorxiv.org/content/10.1101/2021.06.07.447460v1?rss=1 Babin, B. M. Keller, L. J. Pinto, Y. Li, V. L. Eneim, A. Vance, S. E. Terrell, S. M. Bhatt, A. S. Long, J. Z. Bogyo, M. 2021-06-08 doi:10.1101/2021.06.07.447460 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ miR-544-3p mediates arthritis pain through regulation of FcγRI ]]> https://biorxiv.org/content/10.1101/2021.06.13.448256v1?rss=1 Liu, Y. Jeon, S.-M. Caterina, M. Qu, L. 2021-06-14 doi:10.1101/2021.06.13.448256 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Structural analysis of the C. elegans dauer larval anterior sensilla by Focused Ion Beam-Scanning Electron Microscopy ]]> https://biorxiv.org/content/10.1101/2021.06.29.449894v1?rss=1 Britz, S. Markert, S. M. Witvliet, D. Steyer, A. M. Troeger, S. Mulcahy, B. Kollmannsberger, P. Schwab, Y. Zhen, M. Stigloher, C. 2021-06-30 doi:10.1101/2021.06.29.449894 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays ]]> https://biorxiv.org/content/10.1101/2021.06.29.450369v1?rss=1 Stopsack, K. H. Tyekucheva, S. Wang, M. Gerke, T. A. Vaselkiv, J. B. Penney, K. L. Kantoff, P. W. Finn, S. P. Fiorentino, M. Loda, M. Lotan, T. L. Parmigiani, G. Mucci, L. A. 2021-06-30 doi:10.1101/2021.06.29.450369 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma ]]> https://biorxiv.org/content/10.1101/2021.07.03.450733v1?rss=1 Freeman, S. S. Sade-Feldman, M. Kim, J. Stewart, C. Gonye, A. L. K. Ravi, A. Arniella, M. B. Gushterova, I. LaSalle, T. J. Blaum, E. M. Yizhak, K. Frederick, D. T. Sharova, T. Leshchiner, I. Elagina, L. Spiro, O. G. Livitz, D. Rosebrock, D. Aguet, F. Carrot-Zhang, J. Ha, G. Lin, Z. Chen, J. H. Barzily-Rokni, M. Hammond, M. R. Vitzthum von Eckstaedt, H. C. Blackmon, S. M. Jiao, Y. J. Gabriel, S. Lawrence, D. P. Duncan, L. M. Stemmer-Rachamimov, A. O. Wargo, J. A. Flaherty, K. T. Sullivan, R. J. Boland, G. M. Meyerson, M. Getz, G. Hacohen, N. 2021-07-04 doi:10.1101/2021.07.03.450733 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Myosin-driven Nucleation of Actin Filaments Drives Stereocilia Development Critical for Hearing ]]> https://biorxiv.org/content/10.1101/2021.07.09.451618v1?rss=1 Moreland, Z. G. Jiang, F. Aguilar, C. Barzik, M. Gong, R. Shams, A. Faaborg-Andersen, C. Werth, J. C. Harley, R. Sutton, D. C. Cole, S. M. Parker, A. Morse, S. Wilson, E. Takagi, Y. Sellers, J. R. Brown, S. D. Friedman, T. B. Alushin, G. M. Bowl, M. R. Bird, J. E. 2021-07-10 doi:10.1101/2021.07.09.451618 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Nuclear hormone receptors promote gut and glia detoxifying enzyme induction and protect C. elegans from the mold P. brevicompactum ]]> https://biorxiv.org/content/10.1101/2021.07.15.452486v1?rss=1 Wallace, S. W. Lizzappi, M. C. Hur, H. Liang, Y. Shaham, S. 2021-07-15 doi:10.1101/2021.07.15.452486 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ An atlas of healthy and injured cell states and niches in the human kidney ]]> https://biorxiv.org/content/10.1101/2021.07.28.454201v1?rss=1 400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (n = 42) and disease (n = 42) kidneys. This has provided a high resolution cellular atlas of 100 cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations for major cell types spanning the entire kidney. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several segments. Molecular signatures of these states permitted their localization within injury neighborhoods using spatial transcriptomics, and large-scale 3D imaging analysis of [~]1.2 million neighborhoods provided linkages to active immune responses. These analyses further defined biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that were associated with a decline in kidney function during chronic kidney disease. This human kidney cell atlas, including injury cell states and neighborhoods, will be a valuable resource for future studies. ]]> Lake, B. B. Menon, R. Winfree, S. Hu, Q. Ferreira, R. M. Kalhor, K. Barwinska, D. Otto, E. A. Ferkowicz, M. Diep, D. Plongthongkum, N. Knoten, A. Urata, S. Naik, A. S. Eddy, S. Zhang, B. Wu, Y. Salamon, D. Williams, J. C. Wang, X. Balderrama, K. S. Hoover, P. Murray, E. Vijayan, A. Chen, F. Waikar, S. S. Rosas, S. Wilson, F. P. Palevsky, P. M. Kiryluk, K. Sedor, J. R. Toto, R. D. Parikh, C. Kim, E. H. Macosko, E. Z. Kharchenko, P. V. Gaut, J. P. Hodgin, J. B. Eadon, M. T. Dagher, P. C. El-Achkar, T. M. Zhang, K. Kretzler, M. Jain, S. KPMP Consortium, 2021-07-29 doi:10.1101/2021.07.28.454201 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Predictive framework of macrophage activation ]]> https://biorxiv.org/content/10.1101/2021.08.02.454825v1?rss=1 Sanin, D. E. Ge, Y. Marinkovic, E. Kabat, A. M. Castoldi, A. Caputa, G. Grzes, K. M. Curtis, J. D. Willenborg, S. Dichtl, S. Reinhardt, S. Dahl, A. Pearce, E. L. Eming, S. A. Gerbaulet, A. Roers, A. Murray, P. J. Pearce, E. J. 2021-08-04 doi:10.1101/2021.08.02.454825 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Overexpression of the SETD2 WW domain inhibits the phosphor-IWS1/SETD2 interaction and the oncogenic AKT/IWS1 RNA splicing program. ]]> https://biorxiv.org/content/10.1101/2021.08.12.454141v1?rss=1 Laliotis, G. I. Chavdoula, E. Anastas, V. Singh, S. Kenney, A. I. Achaya, S. Yount, J. S. Sehgal, L. Tsichlis, P. N. 2021-08-12 doi:10.1101/2021.08.12.454141 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas ]]> https://biorxiv.org/content/10.1101/2021.08.14.456365v1?rss=1 Webster, A. L. H. Sanders, M. A. Patel, K. Dietrich, R. Noonan, R. J. Lach, F. P. White, R. R. Goldfarb, A. Hadi, K. Edwards, M. M. Donovan, F. X. Jung, M. Sridhar, S. Fedrigo, O. Tian, H. Rosiene, J. Heineman, T. Kennedy, J. A. Bean, L. Rosti, O. Tryon, R. Gonzalez, A.-M. Rosenberg, A. Luo, J.-D. Carrol, T. Velleuer, E. Rastatter, J. C. Wells, S. I. Surralles, J. Bagby, G. MacMillan, M. L. Wagner, J. E. Cancio, M. Boulad, F. Scognamiglio, T. Vaughan, R. Koren, A. Imielinski, M. Chandrasekharappa, S. Auerbach, A. D. Singh, B. Kutler, D. I. Campbell, P. 2021-08-16 doi:10.1101/2021.08.14.456365 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar ]]> https://biorxiv.org/content/10.1101/2021.08.17.456619v1?rss=1 Lieberman, N. A. Lin, M. J. Xie, H. Shretha, L. Nguyen, T. Huang, M.-L. Haynes, A. M. Romeis, E. Wang, Q.-Q. Zhang, R.-L. Kou, C.-X. Ciccarese, G. Dal Conte, I. Cusini, M. Drago, F. Nakayama, S.-i. Lee, K. Ohnishi, M. Konda, K. A. Vargas, S. K. Eguiluz, M. Caceres, C. Klausner, J. D. Mitja, O. Rompalo, A. Mulcahy, F. Hook, E. W. Lukehart, S. Casto, A. M. Roychoudhury, P. DiMaio, F. Giacani, L. Greninger, A. L. 2021-08-17 doi:10.1101/2021.08.17.456619 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ PRMT5 promotes symmetric dimethylation of RNA processing proteins and modulates activated T cell alternative splicing and Ca2+/NFAT signaling ]]> https://biorxiv.org/content/10.1101/2021.08.24.457384v1?rss=1 Sengupta, S. West, K. O. Sanghvi, S. Laliotis, G. Agosto, L. M. Lynch, K. W. Tsichlis, P. Singh, H. Patrick, K. L. Guerau-de-Arellano, M. 2021-08-26 doi:10.1101/2021.08.24.457384 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Signaling and transcriptional networks governing late synovial joint development ]]> https://biorxiv.org/content/10.1101/2021.08.25.457383v1?rss=1 Bian, Q. Cheng, Y.-H. Su, E. Y. Tan, Y. Kim, D. W. Wang, H. Yoo, S. Blackshaw, S. Cahan, P. 2021-08-27 doi:10.1101/2021.08.25.457383 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ The pigtail macaque (Macaca nemestrina) model of COVID-19 reproduces diverse clinical outcomes and reveals new and complex signatures of disease ]]> https://biorxiv.org/content/10.1101/2021.08.28.458047v1?rss=1 Melton, A. Doyle-Meyers, L. A. Blair, R. V. Midkiff, C. Melton, H. J. Russell-Lodrigue, K. Aye, P. P. Schiro, F. Fahlberg, M. Szeltner, D. Spencer, S. Beddingfield, B. J. Goff, K. Golden, N. Penney, T. Picou, B. Hensley, K. Chandler, K. E. Plante, J. A. Plante, K. S. Weaver, S. C. Roy, C. J. Hoxie, J. A. Gao, H. Montefiori, D. C. Mankowski, J. L. Bohm, R. P. Rappaport, J. Maness, N. J. 2021-08-30 doi:10.1101/2021.08.28.458047 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ Pathogenic, but not non-pathogenic, Rickettsia manipulate inflammasome-dependent IL-1 responses to facilitate their replication and host dissemination. ]]> https://biorxiv.org/content/10.1101/2021.09.08.459437v1?rss=1 Voss, O. H. Cobb, J. Rivera Diaz, N. Sanchez, R. DeTolla, L. Rahman, M. S. Azad, A. F. 2021-09-08 doi:10.1101/2021.09.08.459437 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Active growth signalling promotes cancer cell sensitivity to the CDK7 inhibitor ICEC0942 ]]> https://biorxiv.org/content/10.1101/2021.09.10.459733v1?rss=1 Wilson, G. Sava, G. Vuina, K. Huard, C. Meneguello, L. Coulombe-Huntington, J. Bertomeu, T. Maizels, R. Lauring, J. Tyers, M. Ali, S. Bertoli, C. de Bruin, R. A. M. 2021-09-10 doi:10.1101/2021.09.10.459733 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ "Understanding Cortical Arousals during Sleep from Leg Movements: A Pilot Study." ]]> https://biorxiv.org/content/10.1101/2021.09.14.460395v1?rss=1 Bansal, K. Garcia, J. Feltch, C. Earley, C. Robucci, R. Banerjee, N. Brooks, J. 2021-09-14 doi:10.1101/2021.09.14.460395 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Amyloid β oligomer selective antibodies for Alzheimers therapeutics and diagnostics ]]> https://biorxiv.org/content/10.1101/2021.09.20.460817v1?rss=1 Viola, K. L. Bicca, M. A. Bebenek, A. M. Kranz, D. L. Nandwana, V. Waters, E. A. Haney, C. R. Lee, M. Gupta, A. Brahmbhatt, Z. Huang, W. Chang, T.-T. Peck, A. Valdez, C. Dravid, V. P. Klein, W. L. 2021-09-21 doi:10.1101/2021.09.20.460817 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of juvenile myogenic progenitors ]]> https://biorxiv.org/content/10.1101/2021.09.28.462168v1?rss=1 Wei, X. Lienhard, M. Murgai, A. Franke, J. Poehle-Kronawitter, S. Kotsaris, G. Wu, H. Boerno, S. Timmermann, B. Glauben, R. Stricker, S. 2021-09-30 doi:10.1101/2021.09.28.462168 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ The proposed promiscuity value of an HLA can vary significantly depending on the source data used ]]> https://biorxiv.org/content/10.1101/2021.10.01.462828v1?rss=1 Anaya, J. Baras, A. S. 2021-10-06 doi:10.1101/2021.10.01.462828 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2021.10.04.463121v1?rss=1 LaSalle, T. J. Gonye, A. L. K. Freeman, S. S. Kaplonek, P. Gushterova, I. Kays, K. R. Manakongtreecheep, K. Tantivit, J. Rojas-Lopez, M. Russo, B. C. Sharma, N. Thomas, M. F. Lavin-Parsons, K. M. Lilly, B. M. Mckaig, B. N. Charland, N. C. Khanna, H. K. Lodenstein, C. L. Margolin, J. D. Blaum, E. M. Lirofonis, P. B. Sonny, A. Bhattacharyya, R. P. Parry, B. A. Goldberg, M. B. Alter, G. Filbin, M. R. Villani, A. C. Hacohen, N. Sade-Feldman, M. 2021-10-05 doi:10.1101/2021.10.04.463121 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Defunctionalizing Intracellular Organelles with Genetically-Encoded Molecular Tools Based on Engineered Phospholipase A/Acyltransferases (PLAATs) ]]> https://biorxiv.org/content/10.1101/2021.10.10.463806v1?rss=1 Watanabe, S. Nihongaki, Y. Itoh, K. Watanabe, S. Inoue, T. 2021-10-10 doi:10.1101/2021.10.10.463806 Cold Spring Harbor Laboratory Press 2021-10-10 <![CDATA[ Endothelial Cell-Specific Molecule-1 Inhibits Albuminuria in Diabetic Mice ]]> https://biorxiv.org/content/10.1101/2021.10.14.464296v1?rss=1 Zheng, X. Higdon, L. Gaudet, A. Shah, M. Balistieri, A. Li, C. Nadai, P. Palaniappan, L. Yang, X. Santo, B. Ginley, B. Wang, X. Myakala, K. Nallagatla, P. Levi, M. Sarder, P. Rosenberg, A. Maltzman, J. Caires, N. Bhalla, V. 2021-10-15 doi:10.1101/2021.10.14.464296 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Bilaterally Reduced Rolandic Beta Band Activity in Minor Stroke Patients ]]> https://biorxiv.org/content/10.1101/2021.10.15.464457v1?rss=1 Kulasingham, J. P. Brodbeck, C. Khan, S. Marsh, E. B. Simon, J. Z. 2021-10-16 doi:10.1101/2021.10.15.464457 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Behavioral phenotyping of Zip8 393T-KI mice for in vivo study of schizophrenia pathogenesis ]]> https://biorxiv.org/content/10.1101/2021.10.18.464839v1?rss=1 Terrillion, C. E. Kang, B.-h. Melia, J. M. 2021-10-18 doi:10.1101/2021.10.18.464839 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ The anterior insular cortex associates temporally discontiguous stimuli during threat learning ]]> https://biorxiv.org/content/10.1101/2021.10.19.465048v1?rss=1 Namkung, H. Lockhart, S. de Chabot, J. Guttman, L. Isehak, I. Kwon, H.-B. Sawa, A. 2021-10-20 doi:10.1101/2021.10.19.465048 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ KIBRA-PKCγ signaling pathway modulates memory performance in mice and humans ]]> https://biorxiv.org/content/10.1101/2021.10.26.465926v1?rss=1 Tian, M. Chen, Q. Graves, A. R. Goldschmidt, H. L. Johnson, R. C. Weinberger, D. R. Huganir, R. L. 2021-10-28 doi:10.1101/2021.10.26.465926 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Circadian regulation of lung repair and regeneration ]]> https://biorxiv.org/content/10.1101/2021.11.20.469376v1?rss=1 Naik, A. Forrest, K. Issah, Y. Valekunja, U. Reddy, A. B. Hennessy, E. Brooks, T. Babu, A. Morley, M. Grant, G. R. FitzGerald, G. A. Sehgal, A. Worthen, G. S. Frank, D. B. Morrisey, E. E. Sengupta, S. 2021-11-20 doi:10.1101/2021.11.20.469376 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Endogenous Syngap1 Alpha Splice Forms Promote Cognitive Function and Seizure Protection ]]> https://biorxiv.org/content/10.1101/2021.12.05.471306v1?rss=1 Kilinc, M. Rumbaugh, G. Miller, C. A. Lynch, G. Coba, M. Bayes, A. Araki, Y. Gou, G. Reich, A. Graham, N. Hartel, N. Wilkinson, B. Lauterborn, J. Le, A. Rojas, C. Creson, T. K. Arora, V. 2021-12-09 doi:10.1101/2021.12.05.471306 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Ca2+ Mediates HIF-dependent Upregulation of Aquaporin 1 in Pulmonary Arterial Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2021.12.06.471473v1?rss=1 Yun, X. JIang, H. Semenza, G. Shimoda, L. 2021-12-06 doi:10.1101/2021.12.06.471473 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children ]]> https://biorxiv.org/content/10.1101/2021.12.18.473308v1?rss=1 Boribong, B. P. LaSalle, T. J. Bartsch, Y. C. Ellett, F. Loiselle, M. E. Davis, J. P. Gonye, A. L. K. Hajizadeh, S. Kreuzer, J. Pillai, S. Haas, W. Edlow, A. G. Fasano, A. Alter, G. Irimia, D. Sade-Feldman, M. Yonker, L. M. 2021-12-20 doi:10.1101/2021.12.18.473308 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Nucleoplasmic Lamin C Rapidly Accumulates at Sites of Nuclear Envelope Rupture with BAF and cGAS ]]> https://biorxiv.org/content/10.1101/2022.01.05.475028v1?rss=1 Kono, Y. Adam, S. A. Reddy, K. Zheng, Y. Medalia, O. Goldman, R. D. Kimura, H. Shimi, T. 2022-01-05 doi:10.1101/2022.01.05.475028 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Accounting for motion in fMRI: What part of the spectrum are we characterizing in autism spectrum disorder? ]]> https://biorxiv.org/content/10.1101/2022.01.12.476077v1?rss=1 Nebel, M. B. Lidstone, D. Wang, L. Benkeser, D. Mostofsky, S. H. Risk, B. B. 2022-01-13 doi:10.1101/2022.01.12.476077 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Task-specific neural processes underlying conflict resolution during cognitive control ]]> https://biorxiv.org/content/10.1101/2022.01.16.476535v1?rss=1 Xiao, Y. Chou, C.-C. Cosgrove, G. R. Crone, N. E. Stone, S. Madsen, J. R. Reucroft, I. Weisholtz, D. Shih, Y.-C. Yu, H.-Y. Anderson, W. S. Kreiman, G. 2022-01-18 doi:10.1101/2022.01.16.476535 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade ]]> https://biorxiv.org/content/10.1101/2022.02.02.478819v1?rss=1 700 proteins) at three timepoints on 174 metastatic melanoma patients treated with ICB. We leverage independent training and testing cohorts to build a predictor of immunotherapy response that outperforms several tissue-based approaches. We found 217 differentially expressed proteins between ICB responders (R) and non-responders (NR), including a co-regulated module of proteins enriched in certain NR patients. By analyzing single-cell RNA-sequencing data of tumor biopsies from 32 patients, we dissected the relative contribution of cells in the tumor to proteins in circulation. The majority of proteins in the co-regulated NR module derived from tumor and myeloid cells. Amongst myeloid cells, we identified a subset of tumor-associated macrophages (TAMs) with a suppressive phenotype that expressed high levels of the co-regulated NR module, thus suggesting they are key drivers of non-response signatures. Together, our data demonstrates the utility of plasma proteomics in biomarker discovery and in understanding the biology of host response to tumors. ]]> Mehta, A. Rucevic, M. Sprecher, E. Parikh, M. Chem, J. Frederick, D. T. Woods, E. Bi, L. Lieb, D. Hultin-Rosenberg, L. Guess, J. Park, R. J. Schneider, A. Michaud, W. Miao, B. Kasumova, G. Kim, M. S. Bai, X. Jenkins, R. W. Klempner, S. J. Gonye, A. L. Yizhak, K. Sade-Feldman, M. Liu, D. Sullivan, R. J. Flaherty, K. T. Hacohen, N. Boland, G. M. 2022-02-05 doi:10.1101/2022.02.02.478819 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ STAT3 gain-of-function mutations connect leukemia with autoimmune disease by pathological dysregulation of NKG2Dhi CD8 killer T cells ]]> https://biorxiv.org/content/10.1101/2022.02.11.480027v1?rss=1 Masle-Farquhar, E. Jackson, K. J. L. Peters, T. J. Al-Eryani, G. Singh, M. Payne, K. J. Rao, G. Apps, G. Kingham, J. Jara, C. J. Skvortsova, K. Swarbrick, A. Ma, C. Suan, D. Uzel, G. Chua, I. Leiding, J. W. Heiskanen, K. Preece, K. Kainulainen, L. O'Sullivan, M. Cooper, M. A. Seppänen, M. R. J. Mustjoki, S. Brothers, S. Vogel, T. P. Brink, R. Tangye, S. G. Reed, J. H. Goodnow, C. C. 2022-02-11 doi:10.1101/2022.02.11.480027 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ A single 2'-O-methylation of ribosomal RNA gates assembly of a functionalribosome ]]> https://biorxiv.org/content/10.1101/2022.02.16.480697v1?rss=1 Yelland, J. N. Bravo, J. P. K. Black, J. J. Taylor, D. W. Johnson, A. 2022-02-16 doi:10.1101/2022.02.16.480697 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Read depth correction for somatic mutations ]]> https://biorxiv.org/content/10.1101/2022.02.16.480761v1?rss=1 Anaya, J. Baras, A. S. 2022-02-19 doi:10.1101/2022.02.16.480761 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Cohesin is required for meiotic spindle assembly independent of its role in cohesion in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.03.10.483728v1?rss=1 McNally, K. P. Danlasky, B. M. Barroso, C. Gong, T. Li, W. Martinez-Perez, E. McNally, F. J. 2022-03-10 doi:10.1101/2022.03.10.483728 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ A cancer stem cell population underlies a multi-lineage phenotype and drug resistance in prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.03.24.484651v1?rss=1 Beshiri, M. L. Capaldo, B. J. Lake, R. Ku, A. T. Burner, D. Tice, C. M. Tran, C. Kostas, J. Alilin, A. N. Yin, J. Agarwal, S. Morris, S. A. Karzai, F. H. Lotan, T. L. Dahut, W. L. Sowalsky, A. G. Kelly, K. 2022-03-27 doi:10.1101/2022.03.24.484651 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism ]]> https://biorxiv.org/content/10.1101/2022.03.26.485862v1?rss=1 D'Ignazio, L. Jacomini, R. S. Qamar, B. Benjamin, K. J. M. Arora, R. Sawada, T. Evans, T. A. Diffenerfer, K. E. Pankonin, A. R. Hendriks, W. T. Hyde, T. M. Kleinman, J. E. Weinberger, D. Bragg, D. C. Paquola, A. C. Erwin, J. A. 2022-03-27 doi:10.1101/2022.03.26.485862 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Helical remodeling augments 5-lipoxygenase activity ]]> https://biorxiv.org/content/10.1101/2022.03.31.486615v1?rss=1 Gallegos, E. M. Reed, T. D. Mathes, F. A. Guevara, N. Neau, D. Huang, W. Newcomer, M. E. Gilbert, N. C. 2022-03-31 doi:10.1101/2022.03.31.486615 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ The effect of sleep continuity disruption on multimodal emotion processing and regulation: a laboratory-based, randomized, controlled experiment in good sleepers ]]> https://biorxiv.org/content/10.1101/2022.04.22.489209v1?rss=1 Reid, M. Omlin, X. Espie, C. Sharman, R. Tamm, S. Kyle, S. 2022-04-22 doi:10.1101/2022.04.22.489209 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ DeepTMB: An uncertainty-aware deep calibration of tumor mutational burden with a synthetic tumor-only dataset ]]> https://biorxiv.org/content/10.1101/2022.04.22.489230v1?rss=1 Anaya, J. Baras, A. S. 2022-04-25 doi:10.1101/2022.04.22.489230 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Replication-competent HIV-1 in human alveolar macrophages and monocytes despite nucleotide pools with elevated dUTP ]]> https://biorxiv.org/content/10.1101/2022.05.03.490432v1?rss=1 Cui, J. Meshesha, M. Churgulia, N. Merlo, C. Fuchs, E. Breakey, J. Stivers, J. T. 2022-05-04 doi:10.1101/2022.05.03.490432 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ MPZ-T124M mouse model replicates human axonopathy and suggest alteration in axo-glia communication ]]> https://biorxiv.org/content/10.1101/2022.05.09.491190v1?rss=1 Shackleford, G. Marziali, L. N. Sasaki, Y. Weinstock, N. I. Rossor, A. M. Silvestri, N. Wilson, E. R. Hurley, E. Kidd, G. J. Manohar, S. M. Ding, D. Salvi, R. J. Feltri, M. L. D'Antonio, M. Wrabetz, L. 2022-05-10 doi:10.1101/2022.05.09.491190 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Glia-mediated cerebellar pain modulation ]]> https://biorxiv.org/content/10.1101/2022.05.18.489807v1?rss=1 Kim, S. H. Lee, J. Roh, S.-E. Jang, M. Kim, S. Lee, J. H. Seo, J. Hwang, J. Y. Lee, Y.-S. Shigetomi, E. Lee, C. J. J. Koizumi, S. KIM, S. K. Kim, S. J. 2022-05-19 doi:10.1101/2022.05.18.489807 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Loss-of-function mutation in human Oxidation Resistance gene 1 disrupts the spatial-temporal regulation of histone arginine methylation in early brain development ]]> https://biorxiv.org/content/10.1101/2022.05.24.493324v1?rss=1 Lin, X. Wang, W. Yang, M. Damseh, N. Sousa, M. M. L. d. Jacob, F. Lang, A. Kristiansen, E. Pannone, M. Kissova, M. Almaas, R. Kusnierczyk, A. Siller, R. Shahrour, M. Al-Ashhab, M. Abu-Libdeh, B. Tang, W. Slupphaug, G. Elpeleg, O. Boe, S. O. Eide, L. Sullivan, G. J. Rinholm, J. E. Song, H. Ming, G.-L. Van Loon, B. Edvardson, S. Ye, J. Bjoras, M. 2022-05-24 doi:10.1101/2022.05.24.493324 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities ]]> https://biorxiv.org/content/10.1101/2022.05.30.493851v1?rss=1 Zhang, Y. Remillard, D. Onubogu, U. Karakyriakou, B. Asiaban, J. N. Ramos, A. R. Bowland, K. Bishop, T. R. Ott, C. J. Janiszewska, M. Cravatt, B. F. Erb, M. A. 2022-05-30 doi:10.1101/2022.05.30.493851 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Circulating plasma IL-13 and periostin are dysregulated type 2 inflammatory biomarkers in prurigo nodularis: a cluster analysis ]]> https://biorxiv.org/content/10.1101/2022.06.07.495051v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@101432dorg.highwire.dtl.DTLVardef@1e16d01org.highwire.dtl.DTLVardef@bb8edborg.highwire.dtl.DTLVardef@19fd785_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Single-plex plasma immunoassays of prurigo nodularis vs. controls (a) Plasma single-plex immunoassays (b) Heatmap of Z-scored biomarker levels for each patient, delineated by cluster. PN, prurigo nodularis; HC, healthy control C_FIG ConclusionsThis study demonstrates elevation of IL-13 and periostin in PN patients with distinct clusters with varying degrees of type 2 inflammation. Given this heterogeneity, further biomarker studies with single-cell resolution will provide better guidance towards future precision medicine approaches in the treatment of PN. ]]> Parthasarathy, V. Cravero, K. Deng, J. Sun, Z. Engle, S. Auxier, A. Hahn, N. Sims, J. T. Okragly, A. Alphonse, M. P. Kwatra, S. G. 2022-06-09 doi:10.1101/2022.06.07.495051 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles ]]> https://biorxiv.org/content/10.1101/2022.06.13.495966v1?rss=1 Vettkoetter, D. Schneider, M. Liewald, J. Zeiler, S. Guldan, J. Watanabe, S. Gottschalk, A. 2022-06-14 doi:10.1101/2022.06.13.495966 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress ]]> https://biorxiv.org/content/10.1101/2022.06.21.497008v1?rss=1 Saab, J. J. A. Dzierozynski, L. N. Jonker, P. B. Zhu, Z. Chen, R. N. Oh, M. Sheehan, C. Macleod, K. F. Weber, C. R. Muir, A. 2022-06-25 doi:10.1101/2022.06.21.497008 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ The nuclear GAPDH-HMGB cascade in cortical microglia regulates cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2022.06.21.497065v1?rss=1 Ramos, A. Ishizuka, K. Namkung, H. Hayes, L. N. Saito, A. Sengupta, A. Srivastava, R. Calva, C. Hayashida, A. Elkins, N. Palen, T. Carloni, E. Tsujimura, T. Gallego, J. A. Robinson, D. G. Malhotra, A. K. Ikemoto, S. Rais, R. Slusher, B. S. Niwa, M. Saitoh, T. Takimoto, E. Sawa, A. 2022-06-21 doi:10.1101/2022.06.21.497065 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ The discovery of genome-wide mutational dependence in naturally evolving populations ]]> https://biorxiv.org/content/10.1101/2022.06.24.497504v1?rss=1 Green, A. G. Vargas, R. Marin, M. G. Freschi, L. Xie, J. Farhat, M. R. 2022-06-28 doi:10.1101/2022.06.24.497504 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ TCF4 trinucleotide repeat expansions and UV irradiation are associated with ferroptosis susceptibility in Fuchs endothelial corneal dystrophy ]]> https://biorxiv.org/content/10.1101/2022.06.27.497862v1?rss=1 Saha, S. Skeie, J. M. Schmidt, G. A. Eggleston, T. Shevalye, H. Sales, C. S. Phruttiwanichakun, P. Field, M. Rinkoski, T. A. Fautsch, M. P. Baratz, K. H. Roy, M. Jun, A. S. Salem, A. K. Greiner, M. A. 2022-06-28 doi:10.1101/2022.06.27.497862 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes ]]> https://biorxiv.org/content/10.1101/2022.07.06.498900v1?rss=1 Hildebrandt, R. P. Moss, K. R. Janusz-Kaminska, A. Knudson, L. A. Denes, L. T. Saxena, T. Boggupalli, D. Li, Z. Lin, K. Bassell, G. J. Wang, E. T. 2022-07-06 doi:10.1101/2022.07.06.498900 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast ]]> https://biorxiv.org/content/10.1101/2022.07.10.499442v1?rss=1 Brielle, E. S. Fleisher, J. Wynne-Jones, S. Broomandskhoshbacht, N. Callan, K. Curtis, E. Iliev, L. Lawson, A. M. Oppenheimer, J. Qiu, L. Stewardson, K. Workman, N. Zalzala, F. Ayodo, G. Gidna, A. Kabiru, A. Kwekason, A. Mabulla, A. Manthi, F. K. Ndiema, E. Ogola, C. Sawchuk, E. Al-Gazali, L. Ali, B. R. Ben-Salem, S. Letellier, T. Pierron, D. Radimilahy, C. Rakotoarisoa, J.-A. Culleton, B. Mallick, S. Rohland, N. Patterson, N. Mwenje, M. A. Ahmed, K. B. Mohamed, M. M. Williams, S. Monge, J. Kusimba, S. Prendergast, M. Reich, D. Kusimba, C. 2022-07-11 doi:10.1101/2022.07.10.499442 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Engineered Adhesion Molecules Drive Synapse Organization ]]> https://biorxiv.org/content/10.1101/2022.07.18.500465v1?rss=1 Hale, W. D. Sudhof, T. C. Huganir, R. L. 2022-07-18 doi:10.1101/2022.07.18.500465 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny ]]> https://biorxiv.org/content/10.1101/2022.08.02.502389v1?rss=1 Lieberman, N. A. P. Armstrong, T. D. Chung, B. Pfalmer, D. Hennelly, C. M. Haynes, A. Romeis, E. Wang, Q.-Q. Zhang, R.-L. Kou, C.-X. Ciccarese, G. Dal Conte, I. Cusini, M. Drago, F. Nakayama, S.-i. Lee, K. Ohnishi, M. Konda, K. A. Vargas, S. K. Eguiluz, M. Caceres, C. F. Klausner, J. D. Mitja, O. Rompalo, A. Mulcahy, F. Hook, E. W. Hoffman, I. F. Matoga, M. M. Zheng, H. Yang, B. Lopez-Medina, E. Ramirez, L. G. Radolf, J. D. Hawley, K. L. Salazar, J. C. Lukehart, S. A. Sena, A. C. Parr, J. B. Giacani, L. Greninger, A. L. 2022-08-02 doi:10.1101/2022.08.02.502389 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Loss of retinogeniculate synaptic function in the DBA/2J mouse model of glaucoma. ]]> https://biorxiv.org/content/10.1101/2022.08.15.503974v1?rss=1 Smith, J. C. Zhang, K. Y. Sladek, A. Thompson, J. Bierlein, E. R. Bhandari, A. Van Hook, M. J. 2022-08-15 doi:10.1101/2022.08.15.503974 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Specialized germline P-bodies are required to specify germ cell fate in C. elegans embryos ]]> https://biorxiv.org/content/10.1101/2022.08.15.504042v1?rss=1 Cassani, M. Seydoux, G. 2022-08-15 doi:10.1101/2022.08.15.504042 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Perturbations of the T-cell immune repertoire in kidney transplant rejection ]]> https://biorxiv.org/content/10.1101/2022.08.24.505187v1?rss=1 Sigdel, T. Fields, P. A. Liberto, J. Damm, I. Kerwin, M. Hood, J. Towfighi, P. Sirota, M. Robins, H. Sarwal, M. M. 2022-08-26 doi:10.1101/2022.08.24.505187 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Disassembly of embryonic keratin filaments promotes pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2022.08.27.504988v1?rss=1 Kawalerski, R. R. Torrente Goncalves, M. Pan, C.-H. Tseng, R. Roa-Pena, L. Leiton, C. V. Torre-Healy, L. A. Boyle, T. Chowdhury, S. Snider, N. T. Shroyer, K. R. Escobar-Hoyos, L. F. 2022-08-28 doi:10.1101/2022.08.27.504988 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Mesenchymal stem cell culture within perfusion bioreactors incorporating 3D-printed scaffolds enables improved extracellular vesicle yield with preserved bioactivity ]]> https://biorxiv.org/content/10.1101/2022.08.30.505860v1?rss=1 Kronstadt, S. M. Patel, D. B. Born, L. J. Levy, D. Lerman, M. J. Mahadik, B. McLoughlin, S. T. Fasuyi, A. Fowlkes, L. Hoorens van Heyningen, L. Aranda, A. Abadchi, S. N. Chang, K.-H. Hsu, A. T. W. Bengali, S. Harmon, J. W. Fisher, J. P. Jay, S. M. 2022-09-01 doi:10.1101/2022.08.30.505860 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Reorganizing Niche Architecture Still Preserves Organ Function in the Hair Follicle ]]> https://biorxiv.org/content/10.1101/2022.09.06.506764v1?rss=1 Wei, H. Du, S. Parksong, J. Pasolli, H. A. Regot, S. Gonzalez, L. E. Xin, T. Greco, V. 2022-09-08 doi:10.1101/2022.09.06.506764 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ PI 4-kinases promote cell surface expansion and facilitate tissue morphogenesis during Drosophila cellularization and gastrulation ]]> https://biorxiv.org/content/10.1101/2022.09.09.507384v1?rss=1 Chen, W. Bergstein, V. He, B. 2022-09-10 doi:10.1101/2022.09.09.507384 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Two Synaptic Convergence Motifs Define Functional Roles for Inputs to Cochlear Nucleus Bushy Cells ]]> https://biorxiv.org/content/10.1101/2022.09.10.507000v1?rss=1 Spirou, G. A. Kersting, M. Carr, S. Razzaq, B. Alves-Pinto, C. Y. Dawson, M. Ellisman, M. H. Manis, P. B. 2022-09-10 doi:10.1101/2022.09.10.507000 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation ]]> https://biorxiv.org/content/10.1101/2022.09.14.507992v1?rss=1 Xin, T. Gallini, S. Gonzalez, D. Gonzalez, L. E. Regot, S. Greco, V. 2022-09-17 doi:10.1101/2022.09.14.507992 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Immune-related molecular changes in the olfactory epithelium, structural alteration in the olfactory bulb, and psychosis ]]> https://biorxiv.org/content/10.1101/2022.09.23.509224v1?rss=1 Yang, K. Hasegawa, Y. Hua, J. Dower, M. Etyemez, S. Prasad, N. Duvall, L. G. Paez, A. K. Smith, A. Lane, A. P. Ishizuka, K. Kamath, V. Kamiya, A. Sawa, A. 2022-09-26 doi:10.1101/2022.09.23.509224 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ The promiscuous development of an unconventional Qa1b-restricted T cell population ]]> https://biorxiv.org/content/10.1101/2022.09.26.509583v1?rss=1 Manoharan Valerio, M. A. Arana, K. Guan, J. Wei Chan, S. Kurd, N. S. Lee, A. Shastri, N. Robey, E. 2022-09-27 doi:10.1101/2022.09.26.509583 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ KapBeta2 is a modifier of the C9orf72-linked glycine-arginine dipeptide neurotoxicity ]]> https://biorxiv.org/content/10.1101/2022.09.30.510384v1?rss=1 cicardi, M. e. Kankate, V. Sriramoji, S. Krishnamurthy, K. ShamamandriMarkandaiah, S. Verdone-Morris, B. Girdhar, A. Nelson, A. T. Rivas, L. B. Boehringer, A. Haeusler, A. Pasinelli, P. Guo, L. Trotti, D. 2022-10-03 doi:10.1101/2022.09.30.510384 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy ]]> https://biorxiv.org/content/10.1101/2022.10.03.510678v1?rss=1 Yoshida, T. Latt, K. Z. Rosenberg, A. Z. Santo, B. A. Myakala, K. Ishimoto, Y. Zhao, Y. Shrivastav, S. Jones, B. A. Yang, X. Wang, X. Tutino, V. M. Sarder, P. Levi, M. Okamoto, K. Winkler, C. A. Kopp, J. B. 2022-10-07 doi:10.1101/2022.10.03.510678 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Human sialidase activity is vital for dengue virus serotype 2 infection ]]> https://biorxiv.org/content/10.1101/2022.10.05.511017v1?rss=1 St Clair, L. A. Pujari, P. G. Perera, R. 2022-10-05 doi:10.1101/2022.10.05.511017 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A human DCC variant causing mirror movement disorder reveals an essential role for the Wave regulatory complex in Netrin/DCC signaling ]]> https://biorxiv.org/content/10.1101/2022.10.13.511954v1?rss=1 Chaudhari, K. Zhang, K. Yam, P. T. Zang, Y. Kramer, D. A. Schlienger, S. Calabretta, S. Collins, M. Srour, M. Chen, B. Charron, F. Bashaw, G. J. 2022-10-17 doi:10.1101/2022.10.13.511954 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ NIS metastable intermediates provide insights into conformational transition between principal thermodynamic states ]]> https://biorxiv.org/content/10.1101/2022.10.13.512170v1?rss=1 View larger version (80K): org.highwire.dtl.DTLVardef@e826e0org.highwire.dtl.DTLVardef@1504d00org.highwire.dtl.DTLVardef@ef7104org.highwire.dtl.DTLVardef@1e4c95f_HPS_FORMAT_FIGEXP M_FIG For Table of Contents Only C_FIG ]]> Chakrabarti, M. Amzel, L. M. Lau, A. Y. 2022-10-17 doi:10.1101/2022.10.13.512170 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ CRISPR correction of GBA mutation in hiPSCs restores normal function to Gaucher macrophages and increases their susceptibility to Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.11.26.517656v1?rss=1 Ramalingam, S. Kumar, A. Krug, S. Mohan, H. Rao, D. N. Bishai, W. R. Chandrasegaran, S. 2022-11-26 doi:10.1101/2022.11.26.517656 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ The Epithelial Na+ Channel UNC-8 promotes an endocytic mechanism that recycles presynaptic components from old to new boutons in remodeling neurons ]]> https://biorxiv.org/content/10.1101/2022.11.29.518248v1?rss=1 Cuentas-Condori, A. Chen, S. Krout, M. Gallick, K. Tipps, J. Flautt, L. Richmond, J. E. E. Miller, D. M. 2022-12-01 doi:10.1101/2022.11.29.518248 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Pre-epidemic evolution of the USA300 clade and a molecular key for classification ]]> https://biorxiv.org/content/10.1101/2022.12.05.519169v1?rss=1 Bianco, C. Moustafa, A. OBrien, K. Martin, M. Read, T. Kreiswirth, B. N. Planet, P. 2022-12-05 doi:10.1101/2022.12.05.519169 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Senescent Schwann cells induced by aging and chronic denervation impair axonal regeneration after peripheral nerve injury ]]> https://biorxiv.org/content/10.1101/2022.12.07.519441v1?rss=1 Fuentes-Flores, A. Geronimo-Olvera, C. Necunir-Ibarra, D. S. Patel, S. K. Bons, J. Wright, M. C. Geschwind, D. Höke, A. Gomez-Sanchez, J. A. Schilling, B. Campisi, J. Court, F. A. 2022-12-08 doi:10.1101/2022.12.07.519441 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Focal adhesion assembly requires phosphorylation signaling ]]> https://biorxiv.org/content/10.1101/2022.12.19.521109v1?rss=1 Kumar, S. Stainer, A. Dubrulle, J. Simpkins, C. Cooper, J. 2022-12-19 doi:10.1101/2022.12.19.521109 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Progressive spreading of DNA methylation in the GSTP1 promoter CpG island across transitions from precursors to invasive prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.12.21.521517v1?rss=1 Gupta, H. Inoue, H. Nakai, Y. Nakayama, M. Jones, T. Hicks, J. Kumar, B. Gurel, M. Nelson, W. G. De Marzo, A. M. Yegnasubramanian, S. 2022-12-22 doi:10.1101/2022.12.21.521517 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ SUMOylation of the Cardiac Sodium Channel NaV1.5 Modifies Inward Current and Cardiac Excitability ]]> https://biorxiv.org/content/10.1101/2022.12.26.521675v1?rss=1 Yoon, J.-Y. Greiner, A. Jacobs, J. S. Kim, Y.-R. Rasmussen, T. P. Kutschke, W. Matasic, D. S. Vikram, A. Gaddam, R. R. Mehdi, H. Irani, K. London, B. 2022-12-26 doi:10.1101/2022.12.26.521675 Cold Spring Harbor Laboratory Press 2022-12-26 <![CDATA[ Oncogene-like addiction to aneuploidy in human cancers ]]> https://biorxiv.org/content/10.1101/2023.01.09.523344v1?rss=1 Girish, V. Lakhani, A. A. Scaduto, C. M. Thompson, S. L. Brown, L. M. Hagenson, R. A. Sausville, E. L. Mendelson, B. E. Lukow, D. A. Yuan, M. L. Kandikuppa, P. K. Stevens, E. C. Lee, S. N. Salovska, B. Li, W. Smith, J. C. Taylor, A. M. Martienssen, R. A. Liu, Y. Sun, R. Sheltzer, J. M. 2023-01-10 doi:10.1101/2023.01.09.523344 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs ]]> https://biorxiv.org/content/10.1101/2023.01.18.523629v1?rss=1 Grit, J. L. McGee, L. E. Tovar, E. A. Essenburg, C. J. Wolfrum, E. Beddows, I. Williams, K. Sheridan, R. Schipper, J. Adams, M. Arumugam, M. Vander Woude, T. Gurunathan, S. Field, J. M. Wulfkuhle, J. Petricoin, E. F. Graveel, C. R. Steensma, M. 2023-01-19 doi:10.1101/2023.01.18.523629 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Super-enhancer driven expression of BAHCC1 promotes melanomacell proliferation and genome stability ]]> https://biorxiv.org/content/10.1101/2023.01.18.524519v1?rss=1 Berico, P. Nogaret, M. Gambi, G. Davidson, G. Cigrang, M. Vokshi, B. Le Gras, S. Mengus, G. Ye, T. Dalmasso, M. Compe, E. Bertolotto, C. Davidson, I. Coin, F. 2023-01-20 doi:10.1101/2023.01.18.524519 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Reprogramming Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti-PD1 Therapy ]]> https://biorxiv.org/content/10.1101/2023.01.26.525680v1?rss=1 Chen, J. Amoozgar, Z. LIU, X. Aoki, S. Liu, Z. Shin, S. Matsui, A. Pu, Z. Lei, P.-J. Datta, M. Zhu, L. Ruan, Z. Shi, L. Staiculescu, D. Inoue, K. Munn, L. L. Fukumura, D. Huang, P. Bardeesy, N. Ho, W. J. Jain, R. Duda, D. G. 2023-01-27 doi:10.1101/2023.01.26.525680 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ HIV viral protein R induces loss of DCT1-type renal tubules ]]> https://biorxiv.org/content/10.1101/2023.02.02.526686v1?rss=1 Latt, K. Z. Yoshida, T. Shrivastav, S. Abedini, A. Reece, J. M. Lee, H. Okamoto, K. Heymann, J. Zhao, Y. Chung, J.-Y. Hewitt, S. Jose, P. A. Winkler, C. A. Knepper, M. A. Kino, T. Rosenberg, A. Z. Susztak, K. Kopp, J. B. 2023-02-03 doi:10.1101/2023.02.02.526686 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Reinforcement-Based Processes Actively Regulate MotorExploration Along Redundant Solution Manifolds ]]> https://biorxiv.org/content/10.1101/2023.02.08.527668v1?rss=1 Roth, A. M. Calalo, J. A. Lokesh, R. Sullivan, S. R. Grill, S. Jeka, J. J. van der Kooij, K. Carter, M. J. Cashaback, J. G. A. 2023-02-09 doi:10.1101/2023.02.08.527668 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Perinuclear damage from nuclear envelope deterioration elicits stress responses that contribute to LMNA cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.02.14.528563v1?rss=1 Sikder, K. Phillips, E. Zhong, Z. Wang, N. Saunders, J. Mothy, D. Kossenkov, A. Schneider, T. Nichtova, Z. Csordas, G. Margulies, K. B. Choi, J. C. 2023-02-14 doi:10.1101/2023.02.14.528563 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity ]]> https://biorxiv.org/content/10.1101/2023.02.23.529804v1?rss=1 Zheng, R. Dunlap, M. Lyu, J. Gonzalez-Figueroa, C. Bobkov, G. Harvey, S. E. Chan, T. W. Quinones-Valdez, G. Choudhury, M. Vuong, A. Flynn, R. A. Chang, H. Y. Xiao, X. Cheng, C. 2023-02-24 doi:10.1101/2023.02.23.529804 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Cutaneous jet-injection of naked mRNA vaccine induces robust immune responses without systemic vaccine spillage ]]> https://biorxiv.org/content/10.1101/2023.02.27.530188v1?rss=1 Abbasi, S. Matsui-Masai, M. Hayashi, A. Tockary, T. Akinaga, S. Kataoka, K. Uchida, S. 2023-02-27 doi:10.1101/2023.02.27.530188 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling ]]> https://biorxiv.org/content/10.1101/2023.02.28.530493v1?rss=1 Khatib, T. O. Amanso, A. M. Pedro, B. Knippler, C. M. Summerbell, E. R. Zohbi, N. M. Konen, J. M. Mouw, J. K. Marcus, A. I. 2023-03-01 doi:10.1101/2023.02.28.530493 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Extracellular vesicle-localized miR-203 mediates neural crest-placode communication required for trigeminal ganglia formation ]]> https://biorxiv.org/content/10.1101/2023.03.14.532527v1?rss=1 Bernardi, Y. E. Sanchez-Vasquez, E. Piacentino, M. L. Urrutia, H. Rossi, I. Alcantara Saraiva, K. L. Pereira-Neves, A. Ramirez, M. I. Bronner, M. E. de Miguel, N. Strobl-Mazzulla, P. H. 2023-03-15 doi:10.1101/2023.03.14.532527 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Structural insights into TRPV4-Rho GTPase signaling complex function and disease ]]> https://biorxiv.org/content/10.1101/2023.03.15.532784v1?rss=1 Lee, S.-Y. Kwon, D. H. Zhang, F. Sumner, C. McCray, B. A. Sullivan, J. Kumar, M. 2023-03-15 doi:10.1101/2023.03.15.532784 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Reduction of Spermine Synthase Suppresses Tau Accumulation Through Autophagy Modulation in Tauopathy ]]> https://biorxiv.org/content/10.1101/2023.03.17.533015v1?rss=1 Tao, X. Liu, J. Diaz-Perez, Z. Foley, J. R. Stewart, T. M. Casero, R. A. Zhai, G. 2023-03-19 doi:10.1101/2023.03.17.533015 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Induced pluripotent stem cell-derived extracellular vesicles promote wound repair in a diabetic mouse model via an anti-inflammatory immunomodulatory mechanism ]]> https://biorxiv.org/content/10.1101/2023.03.19.533334v1?rss=1 Levy, D. Abadchi, S. N. Shababi, N. Ravari, M. R. Pirolli, N. H. Bergeron, C. Obiorah, A. Mokhtari-Esbuie, F. Gheshlaghi, S. Abraham, J. M. Smith, I. M. Powsner, E. Solomon, T. Harmon, J. W. Jay, S. M. 2023-03-23 doi:10.1101/2023.03.19.533334 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ APOL1 kidney risk variants in glomerular diseases modeled in transgenic mice ]]> https://biorxiv.org/content/10.1101/2023.03.27.534273v1?rss=1 Yoshida, T. Latt, K. Z. Santo, B. A. Shrivastav, S. Zhao, Y. Fenaroli, P. Chung, J.-Y. Hewitt, S. M. Tutino, V. M. Sarder, P. Rosenberg, A. Z. Winkler, C. A. Kopp, J. B. 2023-03-27 doi:10.1101/2023.03.27.534273 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Synthetically mannosylated antigens induce antigen-specific humoral tolerance and reduce anti-drug antibody responses to immunogenic biologics ]]> https://biorxiv.org/content/10.1101/2023.04.07.534593v1?rss=1 Wallace, R. P. Refvik, K. C. Antane, J. T. Brünggel, K. Tremain, A. C. Raczy, M. R. Alpar, A. T. Nguyen, M. Solanki, A. Slezak, A. J. Watkins, E. A. Lauterbach, A. L. Wilson, D. S. Hubbell, J. A. 2023-04-07 doi:10.1101/2023.04.07.534593 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Regression models for partially localized fMRI connectivity analyses ]]> https://biorxiv.org/content/10.1101/2023.04.20.537694v1?rss=1 Smith, B. B. Zhao, Y. Lindquist, M. A. Caffo, B. 2023-04-20 doi:10.1101/2023.04.20.537694 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Genetic basis of aposematic coloration in a mimetic radiation of poison frogs ]]> https://biorxiv.org/content/10.1101/2023.04.20.537757v1?rss=1 Linderoth, T. Aguilar-Gomez, D. White, E. Twomey, E. Stuckert, A. Bi, K. Ko, A. Graham, N. Rocha, J. L. Chang, J. MacManes, M. D. Summers, K. Nielsen, R. 2023-04-21 doi:10.1101/2023.04.20.537757 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.08.539795v1?rss=1 Cronin, S. J. F. Yu, W. Hale, A. Crabtree, M. Korecka, J. Sealey, M. Licht-Mayer, S. Turnes, B. da Luz Scheffer, D. Somlyay, M. Cikes, D. Nagy, V. Wolf, A. Reither, H. Weidinger, A. Chabloz, A. Kavirayani, A. Rao, S. Andrews, N. Latremoliere, A. Costigan, M. Kozlov, A. Douglas, G. Freitas, F. C. Pifl, C. Konrat, R. Mahad, D. J. Bagby, S. Isacson, O. Walz, R. Hallett, P. Latini, A. Woolf, C. J. Je, S. Channon, K. Penninger, J. Tretiakov, E. Onji, M. An, M. Fox, J. Gomez-Diaz, C. Harkany, T. 2023-05-09 doi:10.1101/2023.05.08.539795 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.05.18.541360v1?rss=1 Chipman, L. B. Luc, S. Nicastro, I. A. Hulahan, J. J. Dann, D. C. Bodas, D. M. Pasquinelli, A. E. 2023-05-22 doi:10.1101/2023.05.18.541360 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ The structure of NAD+ consuming protein Acinetobacter baumannii TIR domain shows unique kinetics and conformations. ]]> https://biorxiv.org/content/10.1101/2023.05.19.541320v1?rss=1 Klontz, E. Obi, J. O. Wang, Y. Glendening, G. Carr, J. Tsibouris, C. Buddula, S. Nallar, S. Soares, A. Beckett, D. Redzic, J. S. Eisenmesser, E. Palm, C. Schmidt, K. Scudder, A. Obiorah, T. Essuman, K. Milbrandt, J. Diantonio, A. Ray, K. Snyder, M. L. Deredge, D. Snyder, G. A. 2023-05-20 doi:10.1101/2023.05.19.541320 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Suppression of tumor cell lactate-generating signaling pathways eradicates murine PTEN/p53-deficient aggressive-variant prostate cancer via macrophage phagocytosis ]]> https://biorxiv.org/content/10.1101/2023.05.23.540590v1?rss=1 Chaudagar, K. K. Hieromnimon, H. Kelley, A. Labadie, B. Shafran, J. Rameshbabu, S. Drovetsky, C. Bynoe, K. Solanki, A. Markiewicz, E. Fan, X. Loda, M. Patnaik, A. 2023-05-23 doi:10.1101/2023.05.23.540590 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Pharmaceutical agent cetylpyridinium chloride inhibits immune mast cell function by interfering with calcium mobilization ]]> https://biorxiv.org/content/10.1101/2023.05.23.541979v1?rss=1 Obeng, B. Potts, C. M. West, B. E. Burnell, J. E. Fleming, P. J. Shim, J. K. Kinney, M. S. Ledue, E. L. Sangroula, S. Vazquez, A. Y. B. Gosse, J. A. 2023-05-24 doi:10.1101/2023.05.23.541979 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ A phosphorylation-deficient ribosomal protein eS6 is largely functional in Arabidopsis thaliana, rescuing mutant defects from global translation and gene expression to photosynthesis and growth ]]> https://biorxiv.org/content/10.1101/2023.05.30.542942v1?rss=1 Dasgupta, A. Camacho, R. A. U. Enganti, R. Cho, S. K. Tucker, L. L. Torreverde, J. S. Abraham, P. E. von Arnim, A. G. 2023-05-31 doi:10.1101/2023.05.30.542942 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Type 4 pili mediated natural competence in Fusobacterium nucleatum ]]> https://biorxiv.org/content/10.1101/2023.06.09.544391v1?rss=1 Sanders, B. E. Umana, A. Nguyen, T. T. D. Williams, K. J. Yoo, C. C. Casasanta, M. A. Wozniak, B. Slade, D. J. 2023-06-09 doi:10.1101/2023.06.09.544391 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ A Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) Binary Classification Platform for Tabular Data ]]> https://biorxiv.org/content/10.1101/2023.06.20.545752v1?rss=1 Nasimian, A. Younus, S. Hammarlund, E. U. Pienta, K. J. Rönnstrand, L. Kazi, J. U. 2023-06-24 doi:10.1101/2023.06.20.545752 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Brooklyn plots to identify co-expression dysregulation in single cell sequencing ]]> https://biorxiv.org/content/10.1101/2023.06.21.545951v1?rss=1 Patil, A. H. Halushka, M. K. 2023-06-24 doi:10.1101/2023.06.21.545951 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Using energy to go downhill - a genoprotective role for ATPase activity in DNA topoisomerase II ]]> https://biorxiv.org/content/10.1101/2023.06.27.546777v1?rss=1 Bandak, A. F. Blower, T. R. Nitiss, K. c. Shah, V. Nitiss, J. L. Berger, J. M. 2023-06-27 doi:10.1101/2023.06.27.546777 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Social and genetic diversity in first farmers of central Europe ]]> https://biorxiv.org/content/10.1101/2023.07.07.548126v1?rss=1 Gelabert, P. Bickle, P. Hofmann, D. Teschler-Nicola, M. Anders, A. Huang, X. Olalde, I. Fournier, R. Ringbauer, H. Akbari, A. Cheronet, O. Lazaridis, I. Broomandkhoshbacht, N. Fernandes, D. M. Buttinger, K. Callan, K. Candilio, F. Bravo, G. Curtis, E. Ferry, M. Keating, D. Freilich, S. Kearns, A. Harney, E. Lawson, A. M. Mandl, K. Michel, M. Oberreiter, V. Oppenheimer, J. Sawyer, S. Schattke, C. Ozdogan, K. T. T. Qiu, L. Workman, N. Zalzala, F. Mallick, S. Mah, M. Micco, A. Pieler, F. Pavuk, J. Lazar, C. Skrivanko, M. K. Slaus, M. Bedic, Z. Novotny, 2023-07-09 doi:10.1101/2023.07.07.548126 Cold Spring Harbor Laboratory Press 2023-07-09 <![CDATA[ Bacterial sepsis triggers stronger transcriptomic responses in larger primates ]]> https://biorxiv.org/content/10.1101/2023.07.11.548565v1?rss=1 McMinds, R. Jiang, R. H. Adapa, S. R. Cornelius Ruhs, E. Munds, R. A. Leiding, J. W. Downs, C. Martin, L. B. 2023-07-11 doi:10.1101/2023.07.11.548565 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Cardiomyocyte-specific adenylyl cyclase type-8 overexpression induces cell-autonomous activation of RelA and non-cell-autonomous myocardial and systemic inflammation ]]> https://biorxiv.org/content/10.1101/2023.07.15.549173v1?rss=1 Kumar, V. Bermea, K. C. Kumar, D. Singh, A. Verma, A. Kaileh, M. Sen, R. Lakatta, E. G. Adamo, L. 2023-07-16 doi:10.1101/2023.07.15.549173 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Loss of REP1 impacts choroidal melanogenesis in choroideremia ]]> https://biorxiv.org/content/10.1101/2023.07.20.549875v1?rss=1 Sarkar, H. Tracey-White, D. Hagag, A. M. Burgoyne, T. Jensen, L. D. Edwards, M. Moosajee, M. 2023-07-20 doi:10.1101/2023.07.20.549875 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ FLN-2 functions in parallel to LINC complexes and Cdc42/actin pathways during P-cell nuclear migration through constricted spaces in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.08.04.552041v1?rss=1 Ma, L. Kuhn, J. Chang, Y.-T. Elnatan, D. Luxton, G. G. Starr, D. A. 2023-08-06 doi:10.1101/2023.08.04.552041 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Long-term combination therapy with Metformin and Oxymetholone in a Fanconi Anemia mouse model ]]> https://biorxiv.org/content/10.1101/2023.08.16.553572v1?rss=1 Grompe, M. Dorrell, C. S. Peters, A. M. Zhang, Q. Balaji, N. Mochizuki-Kashio, M. Major, A. Finegold, M. J. Liu, C. Lu, K. 2023-08-16 doi:10.1101/2023.08.16.553572 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Combined Mek inhibition and Pparg activation Eradicates Muscle Invasive Bladder cancer in a Mouse Model of BBN-induced Carcinogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.19.553961v1?rss=1 Tate, T. Plumber, S. A. Al-Ahmadie, H. Chen, X. Choi, W. Lu, C. Viny, A. D. Batourina, E. Gretarsson, K. Alija, B. Molotkov, A. Wiessner, G. Mckiernan, J. M. McConkey, D. J. Dinney, C. Czerniak, B. Mendelsohn, C. L. 2023-08-21 doi:10.1101/2023.08.19.553961 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Spatial and temporal control of lysis by the lambda holin ]]> https://biorxiv.org/content/10.1101/2023.09.08.556860v1?rss=1 Cahill, J. Holt, A. Theodore, M. Moreland, R. O Leary, C. Martin, C. Bettridge, K. Xiao, J. Young, R. 2023-09-11 doi:10.1101/2023.09.08.556860 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species ]]> https://biorxiv.org/content/10.1101/2023.09.20.558718v1?rss=1 95% cell type specificity) with variable expression levels, and the astrocyte enhancer-AAVs show multiple distinct expression patterns reflecting the spatial distribution of astrocyte cell types. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity across transgenes and in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs. ]]> Mich, J. K. Sunil, S. Johansen, N. Martinez, R. A. Leytze, M. Gore, B. B. Mahoney, J. T. Ben-Simon, Y. Bishaw, Y. Brouner, K. Campos, J. Canfield, R. Casper, T. Dee, N. Egdorf, T. Gary, A. Gibson, S. Goldy, J. Groce, E. L. Hirschstein, D. Loftus, L. Lusk, N. Malone, J. Martin, N. X. Monet, D. Omstead, V. Opitz-Araya, X. Oster, A. Alice Pom, C. Potekhina, L. Reding, M. Rimorin, C. Ruiz, A. Sedeno-Cortes, A. E. Shapovalova, N. V. Taormina, M. Taskin, N. Tieu, M. Valera Cuevas, N. J. Weed, N. Way, S. W. Yao, Z. McMillen, D. A. Kunst, M. McGraw, M. Thya 2023-09-21 doi:10.1101/2023.09.20.558718 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Improvisation and Live Accompaniment Increase Motor Response and Reward During a Music Playing Task ]]> https://biorxiv.org/content/10.1101/2023.09.28.559982v1?rss=1 Palumbo, A. Groves, K. Vidal, E. L. M. Turry, A. Raghavan, P. Schambra, H. Voelbel, G. Ripolles, P. 2023-09-29 doi:10.1101/2023.09.28.559982 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ MAP1B Regulates Cortical Neuron Interstitial Axon Branching Through the Tubulin Tyrosination Cycle ]]> https://biorxiv.org/content/10.1101/2023.10.02.560024v1?rss=1 Ziak, J. Dorskind, J. Trigg, B. Sudarsanam, S. Hand, R. Kolodkin, A. L. 2023-10-02 doi:10.1101/2023.10.02.560024 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Aquaporin 1 confers apoptosis resistance in pulmonary arterial smooth muscle cells from the SU5416 hypoxia rat model ]]> https://biorxiv.org/content/10.1101/2023.10.05.561143v1?rss=1 Yun, X. Niedermeyer, S. Andrade, M. Jiang, H. Suresh, K. Kolb, T. Damarla, M. Shimoda, L. 2023-10-06 doi:10.1101/2023.10.05.561143 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ A Novel Interaction Between Aquaporin 1 and Caspase-3 in Pulmonary Arterial Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2023.10.05.561144v1?rss=1 Niedermeyer, S. Yun, X. Trujillo, M. Andrade, M. Kolb, T. Suresh, K. Damarla, M. Shimoda, L. 2023-10-06 doi:10.1101/2023.10.05.561144 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Serum-deprivation response of ARPE-19 cells; expression patterns relevant to age-related macular degeneration. ]]> https://biorxiv.org/content/10.1101/2023.10.12.562023v1?rss=1 Peterson, K. M. Mishra, S. Asaki, E. Powell, J. I. He, Y. Berger, A. Rajapakse, D. Wistow, G. 2023-10-12 doi:10.1101/2023.10.12.562023 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Aberrant macrophage activation and failed regeneration of pulmonary epithelium promote tuberculosis progression uniquely in lung tissue ]]> https://biorxiv.org/content/10.1101/2023.10.17.562695v1?rss=1 Yabaji, S. M. Lo, M. Lata, S. Gavrish, I. Tseng, A. E. O'Connel, A. K. Gertje, H. P. Mazzilli, S. Tan, S. Thurman, C. E. Bishai, W. R. Crossland, N. Kobzik, L. Kramnik, I. 2023-10-20 doi:10.1101/2023.10.17.562695 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types ]]> https://biorxiv.org/content/10.1101/2023.11.06.565867v1?rss=1 Mandlbauer, A. Sun, Q. Popitsch, N. Schwickert, T. Spanova, M. Wang, J. Ameres, S. L. Busslinger, M. Cochella, L. 2023-11-06 doi:10.1101/2023.11.06.565867 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ A small-molecule TrkB ligand improves dendritic spine phenotypes and atypical behaviors in female Rett syndrome mice ]]> https://biorxiv.org/content/10.1101/2023.11.09.566435v1?rss=1 Medeiros, D. Ayala-Baylon, K. Egido-Betancourt, H. Miller, E. Chapleau, C. A. Robinson, H. A. Phillips, M. L. Yang, T. Longo, F. Li, W. Pozzo-Miller, L. 2023-11-12 doi:10.1101/2023.11.09.566435 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Transcriptional profile of the rat cardiovascular system at single cell resolution ]]> https://biorxiv.org/content/10.1101/2023.11.14.567085v1?rss=1 Arduini, A. Fleming, S. J. Xiao, L. Hall, A. W. Akkad, A.-D. Chaffin, M. D. Bendinelli, K. J. Tucker, N. R. Papangeli, I. Mantineo, H. Babadi, M. Stegmann, C. M. Garcia-Cardena, G. Lindsay, M. E. Klattenhoff, C. Ellinor, P. T. 2023-11-16 doi:10.1101/2023.11.14.567085 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Allosteric Competition and Inhibition in AMPA Receptors ]]> https://biorxiv.org/content/10.1101/2023.11.28.569057v1?rss=1 Hale, W. D. Romero, A. M. Gonzalez, C. U. Jayaraman, V. Lau, A. Y. Huganir, R. L. Twomey, E. C. 2023-11-28 doi:10.1101/2023.11.28.569057 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit γ2 ]]> https://biorxiv.org/content/10.1101/2023.11.28.569079v1?rss=1 Hale, W. D. Romero, A. M. Huganir, R. L. Twomey, E. C. 2023-11-28 doi:10.1101/2023.11.28.569079 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Transcriptional correlates of cocaine-associated learning in striatal ARC ensembles. ]]> https://biorxiv.org/content/10.1101/2023.12.13.571585v1?rss=1 Salery, M. Godino, A. Xu, Y. Q. Fullard, J. F. Durand-de Cuttoli, R. LaBanca, A. R. Holt, L. M. Russo, S. J. Roussos, P. Nestler, E. J. 2023-12-14 doi:10.1101/2023.12.13.571585 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Spatial analysis of NOS2 and COX2 interaction with T-effector cells reveals immunosuppressive landscapes associated with poor outcome in ER- breast cancer patients ]]> https://biorxiv.org/content/10.1101/2023.12.21.572867v1?rss=1 Ridnourl, L. A. Cheng, R. Y. Heinz, W. F. Pore, M. Gonzalez, A. L. Femino, E. L. Moffat, R. Wink, A. L. Imtiaz, F. Coutinho, L. Butcher, D. Edmondson, E. F. Rangel, C. Wong, S. T. Lipkowitz, S. Glynn, S. McVicar, D. W. Vitek, M. P. Li, X. Anderson, S. K. Paolocci, N. Hewitt, S. M. Ambs, S. Billiar, T. R. Chang, J. C. Lockett, S. J. Wink, D. A. 2023-12-23 doi:10.1101/2023.12.21.572867 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Beyond benchmarking: towards predictive models of dataset-specific single-cell RNA-seq pipeline performance ]]> https://biorxiv.org/content/10.1101/2024.01.02.572650v1?rss=1 Fang, C. Selega, A. Campbell, K. R. 2024-01-02 doi:10.1101/2024.01.02.572650 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ Single dopaminergic neuron DAN-c1 in Drosophila larval brain mediates aversive olfactory learning through D2-like receptors ]]> https://biorxiv.org/content/10.1101/2024.01.15.575767v1?rss=1 Qi, C. Qian, C. Steijvers, E. Colvin, R. A. Lee, D. 2024-01-16 doi:10.1101/2024.01.15.575767 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Characterization of non-monotonic relationships between tumor mutational burden and clinical outcomes ]]> https://biorxiv.org/content/10.1101/2024.01.16.575937v1?rss=1 Anaya, J. Kung, J. Baras, A. S. 2024-01-20 doi:10.1101/2024.01.16.575937 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Single-nucleus RNA sequencing reveals cellular and molecular dynamics of white and brown adipose tissue in a mouse model of type-2 diabetes ]]> https://biorxiv.org/content/10.1101/2024.02.06.578860v1?rss=1 Gaynor, T. L. Hsu, I. Krstevski, C. Farrugia, G. E. Dona, M. S. Cohen, C. D. Drew, B. G. Pinto, A. R. 2024-02-07 doi:10.1101/2024.02.06.578860 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Complex carbohydrate utilization by gut bacteria modulates host food preference ]]> https://biorxiv.org/content/10.1101/2024.02.13.580152v1?rss=1 Yu, K. B. Son, C. Chandra, A. Paramo, J. Novoselov, A. Ozcan, E. Kazmi, S. Lum, G. Lopez-Romero, A. Lynch, J. Hsiao, E. Y. 2024-02-14 doi:10.1101/2024.02.13.580152 Cold Spring Harbor Laboratory Press 2024-02-14 <![CDATA[ AI-driven Classification of Cancer-Associated Fibroblasts Using Morphodynamic and Motile Features ]]> https://biorxiv.org/content/10.1101/2024.02.22.581611v1?rss=1 Kang, M. Min, C. Devarasou, S. Shin, J. H. 2024-02-25 doi:10.1101/2024.02.22.581611 Cold Spring Harbor Laboratory Press 2024-02-25 <![CDATA[ Transcriptomic signature and pro-osteoclastic secreted factors of abnormal bone marrow stromal cells in fibrous dysplasia ]]> https://biorxiv.org/content/10.1101/2024.02.23.581225v1?rss=1 Michel, Z. Raborn, L. N. Spencer, T. Pan, K. S. Martin, D. Roszko, K. L. Wang, Y. Robey, P. Boyce, A. Collins, M. T. de Castro, L. F. 2024-02-28 doi:10.1101/2024.02.23.581225 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ Gluk4-containing kainate receptors regulate synaptic communication in the motor cortex and reduce axon degeneration in adult mice ]]> https://biorxiv.org/content/10.1101/2024.02.29.582867v1?rss=1 Ricci, R. Fletcher, J. L. Makowiecki, K. Pepper, R. Fortune, A. Cullen, C. L. Connelly, W. M. Charlesworth, J. Blackburn, N. B. Pitman, K. A. Young, K. 2024-03-02 doi:10.1101/2024.02.29.582867 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ TREM1 disrupts myeloid bioenergetics and cognitive function in aging and Alzheimer disease models ]]> https://biorxiv.org/content/10.1101/2024.03.05.583562v1?rss=1 Andreasson, K. I. Wilson, E. N. Wang, C. Xin, M. Panchal, M. Rabinowitz, J. D. Minhas, P. S. Swarovski, M. S. Benitez, J. A. R. Durairaj, A. S. Chaney, A. Iweka, C. A. Buckwalter, M. S. Ennerfelt, H. E. Umans, J. Huang, J. Zera, K. A. McReynolds, M. R. Greicius, M. D. James, M. L. Mehta, S. S. Le Guen, Y. Tan, Y. J. Zuckerman, A. J. Blacher, E. Gauba, E. Serrano, G. E. Cropper, H. Jain, P. Liu, Q. 2024-03-11 doi:10.1101/2024.03.05.583562 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance ]]> https://biorxiv.org/content/10.1101/2024.03.05.583602v1?rss=1 Yabaji, S. M. Zhernovkov, V. Araveti, P. B. Lata, S. Rukhlenko, O. S. Abdullatif, S. A. Alekseev, Y. Ma, Q. Dayama, G. Lau, N. C. Bishai, W. R. Crossland, N. A. Campbell, J. D. Kholodenko, B. N. Gimelbrant, A. A. Kobzik, L. Kramnik, I. 2024-03-10 doi:10.1101/2024.03.05.583602 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Human mobility and malaria risk in peri-urban and rural communities in the Peruvian Amazon ]]> https://biorxiv.org/content/10.1101/2024.03.11.584373v1?rss=1 Gomez, J. Grosso, A. Guzman-Guzman, M. Garcia Castillo, S. Castro, M. C. Torres, K. Vinetz, J. M. Gamboa, D. 2024-03-11 doi:10.1101/2024.03.11.584373 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation ]]> https://biorxiv.org/content/10.1101/2024.03.12.584710v1?rss=1 Crain, A. T. Butler, M. B. Hill, C. A. Huynh, M. McGinty, R. K. Duronio, R. J. 2024-03-18 doi:10.1101/2024.03.12.584710 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ High-fidelity enhanced AsCas12a knock-in mice for efficient multiplexed gene editing, disease modeling and orthogonal immunogenetics ]]> https://biorxiv.org/content/10.1101/2024.03.14.585126v1?rss=1 Tang, K. Zhou, X. Fang, S.-Y. Vandenbulcke, E. Du, A. Shen, J. Cao, H. Zhou, J. Chen, K. Xin, S. Zhou, L. Lin, S. H. Majety, M. Ling, X. Lam, S. Z. Chow, R. Bai, S. Nottoli, T. Booth, C. Liu, C. Dong, M. B. Chen, S. 2024-03-16 doi:10.1101/2024.03.14.585126 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Preeclamptic phenotype in transgenic mice with fetuses carrying APOL1 risk variants ]]> https://biorxiv.org/content/10.1101/2024.03.20.586039v1?rss=1 Yoshida, T. Latt, K. Z. Shrivastav, S. Lu, H. Reidy, K. J. Charlton, J. R. Zhao, Y. Winkler, C. A. Reznik, S. E. Rosenberg, A. Z. Kopp, J. B. 2024-03-21 doi:10.1101/2024.03.20.586039 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ Tissue-Specific Dynamics of TCF4 Triplet Repeat Instability Revealed by Optical Genome Mapping ]]> https://biorxiv.org/content/10.1101/2024.03.27.587034v1?rss=1 Zarouchlioti, C. Efthymiou, S. Fracchini, S. Dominik, N. Bhattacharyya, N. Liu, S. Abreu Costa, M. Szabo, A. Sadan, A. N. Jun, A. Bugiardini, E. Houlden, H. Cortese, A. Skalicka, P. Dudakova, L. Muthusamy, K. Cheetham, M. E. Hardcastle, A. J. Liskova, P. Tuft, S. J. Davidson, A. 2024-03-30 doi:10.1101/2024.03.27.587034 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Conditioned medium from painful schwannomatosis tumors increases pain behaviors in mice. ]]> https://biorxiv.org/content/10.1101/2024.04.06.588413v1?rss=1 Rubright, R. Caterina, M. Belzberg, A. Ostrow, K. L. 2024-04-10 doi:10.1101/2024.04.06.588413 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Transiently Worse Postural Effects After Vestibulo-ocular Reflex Gain-Down Adaptation in Healthy Adults ]]> https://biorxiv.org/content/10.1101/2024.04.09.588711v1?rss=1 Arduino, C. Schubert, M. C. Anson, E. R. 2024-04-13 doi:10.1101/2024.04.09.588711 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ The Genetic Origin of the Indo-Europeans ]]> https://biorxiv.org/content/10.1101/2024.04.17.589597v1?rss=1 View larger version (91K): org.highwire.dtl.DTLVardef@127de98org.highwire.dtl.DTLVardef@87010aorg.highwire.dtl.DTLVardef@1554627org.highwire.dtl.DTLVardef@170dd63_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure:C_FLOATNO The origin of Indo-Anatolian and Indo-European languages. Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green). C_FIG ]]> Lazaridis, I. Patterson, N. Anthony, D. Vyazov, L. Fournier, R. Ringbauer, H. Olalde, I. Khokhlov, A. A. Kitov, E. P. Shishlina, N. I. Ailincai, S. C. Agapov, D. S. Agapov, S. A. Batieva, E. Bauyrzhan, B. Bereczki, Z. Buzhilova, A. Changmai, P. Chizhevsky, A. A. Ciobanu, I. Constantinescu, M. Csanyi, M. Dani, J. Dashkovskiy, P. K. Evinger, S. Faifert, A. Flegontov, P. N. Frinculeasa, A. Frinculeasa, M. N. Hajdu, T. Higham, T. Jarosz, P. Jelinek, P. Khartanovich, V. I. Kirginekov, E. N. Kiss, V. Kitova, A. Kiyashko, A. V. Koledin, J. Korolev, A. Kosintsev 2024-04-18 doi:10.1101/2024.04.17.589597 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ A genomic history of the North Pontic Region from the Neolithic to the Bronze Age ]]> https://biorxiv.org/content/10.1101/2024.04.17.589600v1?rss=1 Nikitin, A. G. Lazaridis, I. Patterson, N. Ivanova, S. Videiko, M. Dergachev, V. Kotova, N. Lillie, M. Potekhina, I. Krenz-Niedbała, M. Łukasik, S. Makhortykh, S. Renson, V. Shephard, H. Sirbu, G. Svyryd, S. Tkachuk, T. Włodarczak, P. Callan, K. Curtis, E. Harney, E. Iliev, L. Kearns, A. Lawson, A. M. Michel, M. Mah, M. Micco, A. Oppenheimer, J. Qiu, L. Workman, J. N. Zalzala, F. Mallick, S. Rohland, N. Reich, D. 2024-04-18 doi:10.1101/2024.04.17.589600 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Single-cell transcriptional and epigenetic mapping reveals cellular and molecular mechanisms driving non-ischemic cardiac fibrosis ]]> https://biorxiv.org/content/10.1101/2024.05.09.593315v1?rss=1 Krstevski, C. Farrugia, G. E. Hsu, i. Dona, M. S. I. Gaynor, T. L. Cohen, C. D. Harper, R. L. Harrison, T. I. Claridge, B. Drack, A. Lelliott, P. Kiriazis, H. Brown, A. McMullen, J. R. Donner, D. G. Lal, S. Greening, D. W. Pinto, A. R. 2024-05-13 doi:10.1101/2024.05.09.593315 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex. ]]> https://biorxiv.org/content/10.1101/2024.05.09.593355v1?rss=1 Ge, T. Brickner, D. G. Zehr, K. VanBelzen, J. Zhang, W. Caffalette, C. Ungerleider, S. Marcou, N. Chait, B. Rout, M. Brickner, J. 2024-05-13 doi:10.1101/2024.05.09.593355 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Striatal output regulates the postnatal maturation of cortical circuits ]]> https://biorxiv.org/content/10.1101/2024.05.10.593512v1?rss=1 Deemyad, T. Janecek, M. Shih, Y.-C. Valle, V. D'Agostino, A. Perez, M. Ketchesin, K. Silva, S. Peixoto, R. 2024-05-11 doi:10.1101/2024.05.10.593512 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Spatial Profiling of Metals through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging ]]> https://biorxiv.org/content/10.1101/2024.05.22.594980v1?rss=1 Stopka, S. Bodineau, C. Baquer, G. Lin, J.-R. Hossain, M. A. Regan, M. S. Ruiz, D. F. Fletcher, S.-M. Pourquie, O. Lutsenko, S. Payne, C. Agar, J. N. Mazitschek, R. McDannold, N. Sorger, P. K. Santagata, S. Agar, N. 2024-05-23 doi:10.1101/2024.05.22.594980 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ A novel variant in ADPRS disrupts ARH3 stability and subcellular localization in childrenwith neurodegeneration and respiratory failure ]]> https://biorxiv.org/content/10.1101/2024.06.14.597428v1?rss=1 G, p.His182Arg) encoding the mono(ADP-ribosyl) hydrolase ARH3 found in 2 patients with childhood-onset neurodegeneration with stress-induced ataxia and seizures (CONDSIAS). MethodsGenetic testing via exome sequencing was used to identify the underlying disease cause in two siblings with developmental delay, seizures, progressive muscle weakness, and respiratory failure following an episodic course. Studies in a cell culture model uncover biochemical and cellular consequences of the identified genetic change. ResultsThe ARH3H182R variant affects a highly conserved residue in the active site of ARH3, leading to protein instability, degradation, and reduced expression. ARH3H182R additionally fails to localize to the nucleus. The combination of reduced expression and mislocalization of ARH3H182R resulted in accumulation of mono-ADP ribosylated species in cells. ConclusionsThe childrens clinical course combined with the biochemical characterization of their genetic variant develops our understanding of the pathogenic mechanisms driving CONDSIAS and highlights a critical role for ARH3-regulated ADP ribosylation in nervous system integrity. ]]> Bannister, M. Bray, S. Aggarwal, A. Billington, C. Nguyen, H. D. 2024-06-14 doi:10.1101/2024.06.14.597428 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.06.14.598925v1?rss=1 Mato-Blanco, X. Kim, S.-K. Jourdon, A. Ma, S. Tebbenkamp, A. T. N. Liu, F. Duque, A. Vaccarino, F. M. Sestan, N. Colantuoni, C. Rakic, P. Santpere, G. Micali, N. 2024-06-14 doi:10.1101/2024.06.14.598925 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study ]]> https://biorxiv.org/content/10.1101/2024.06.18.599628v1?rss=1 Rua, A. J. Mitchell, W. Claypool, S. M. Alder, N. N. Alexandrescu, A. T. 2024-06-22 doi:10.1101/2024.06.18.599628 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Comprehensive assessment of recessive, pathogenic AARS1 alleles in a humanized yeast model reveals loss-of-function and dominant-negative effects ]]> https://biorxiv.org/content/10.1101/2024.06.20.599900v1?rss=1 Kuo, M. E. Parish, M. Jonatzke, K. E. Antonellis, A. 2024-06-24 doi:10.1101/2024.06.20.599900 Cold Spring Harbor Laboratory Press 2024-06-24 <![CDATA[ Post-transcriptional regulation by the CCR4-NOT deadenylase complex maintains redox homeostasis in insulin biosynthesis in mouse pancreatic β cells ]]> https://biorxiv.org/content/10.1101/2024.06.26.599433v1?rss=1 Yanagiya, A. Stoney, P. N. Tara, Y. Takaoka, S. Vares, G. Higa, R. Friedman, N. R. Villar-Briones, A. Yamamoto, T. 2024-06-29 doi:10.1101/2024.06.26.599433 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Uridine Phosphorylase-1 supports metastasis of mammary cancer by altering immune and extracellular matrix landscapes of the lung ]]> https://biorxiv.org/content/10.1101/2024.07.02.601676v1?rss=1 Whyte, D. Vande Voorde, J. Sumpton, D. Dhayade, S. Dornier, E. Moore, M. Novo, D. Peters, J. Wiesheu, R. Mackey, J. B. McFarlane, A. J. Fercoq, F. Fisher, S. Dehesa Caballero, C. Gilroy, K. Redmond, K. L. Mitchell, L. E. Anderson, E. Thomson, G. Dzierozynski, L. N. Apiz Saab, J. J. Lewis, C. A. Muir, A. Halbrook, C. J. Strathdee, D. Jackstadt, R. Nixon, C. Dunne, P. Steele, C. W. Carlin, L. M. Macpherson, I. R. Roberts, E. W. Coffelt, S. B. Blyth, K. Sansom, O. J. Norman, J. C. Clarke, C. J. 2024-07-04 doi:10.1101/2024.07.02.601676 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Antimicrobial cetylpyridinium chloride suppresses mast cell function by targeting tyrosine phosphorylation of Syk kinase ]]> https://biorxiv.org/content/10.1101/2024.07.04.602096v1?rss=1 Obeng, B. Bennett, L. J. West, B. E. Wagner, D. J. Fleming, P. J. Tasker, M. N. Lorenger, M. K. Smith, D. R. Systuk, T. Plummer, S. M. Eom, J. Paine, M. D. Frangos, C. T. Wilczek, M. P. Shim, J. K. Maginnis, M. S. Gosse, J. A. 2024-07-08 doi:10.1101/2024.07.04.602096 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Chromatin endogenous cleavage provides a global view of RNA polymerase II transcription kinetics ]]> https://biorxiv.org/content/10.1101/2024.07.08.602535v1?rss=1 VanBelzen, J. Sakelaris, B. Brickner, D. G. Marcou, N. Riecke, H. Mangan, N. Brickner, J. H. 2024-07-08 doi:10.1101/2024.07.08.602535 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ A common pathway controls cell size in the sepal and leaf epidermis leading to a non-random pattern of giant cells ]]> https://biorxiv.org/content/10.1101/2024.07.26.605215v1?rss=1 Clark, F. K. Weissbart, G. Wang, X. Harline, K. Li, C.-B. Formosa-Jordan, P. Roeder, A. H. K. 2024-07-29 doi:10.1101/2024.07.26.605215 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ TRPV5, TRPV6, TRPM6, and TRPM7 do not contribute to hair-cell mechanotransduction ]]> https://biorxiv.org/content/10.1101/204172v1?rss=1 Morgan, C. P. Zhao, H. LeMasurier, M. Xiong, W. Pan, B. Avenarius, M. R. Bateschell, M. Larisch, R. Ricci, A. J. Mueller, U. Barr-Gillespie, P. G. 2017-10-16 doi:10.1101/204172 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ Postnatal Tendon Growth and Remodeling Requires Platelet-Derived Growth Factor Receptor Signaling ]]> https://biorxiv.org/content/10.1101/208991v1?rss=1 Sugg, K. B. Markworth, J. F. Disser, N. P. Rizzi, A. M. Talarek, J. R. Sarver, D. C. Brooks, S. V. Mendias, C. L. 2017-10-25 doi:10.1101/208991 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ New Cell Fate Potentials and Switching Kinetics Uncovered in a Classic Bistable Genetic Switch ]]> https://biorxiv.org/content/10.1101/215061v1?rss=1 Fang, X. Liu, Q. Bohrer, C. Hensel, Z. Han, W. Wang, J. Xiao, J. 2017-11-07 doi:10.1101/215061 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Comparing neurotransmitter metabolism in the brain of patients with symptomatic and aysmptomatic Alzheimer’s disease and healthy individuals ]]> https://biorxiv.org/content/10.1101/220699v1?rss=1 Snowden, S. G. Ebshiana, A. Hye, A. Yang, A. Olga, P. Richard, O. John, T. Cristina, L.-Q. Madhav, T. 2017-11-17 doi:10.1101/220699 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Spatial organization of single mRNPs at different stages of the gene expression pathway ]]> https://biorxiv.org/content/10.1101/237008v1?rss=1 Adivarahan, S. Rahman, S. Zenklusen, D. 2017-12-19 doi:10.1101/237008 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Liquid-like P granules require ATP hydrolysis to avoid solidification ]]> https://biorxiv.org/content/10.1101/245878v1?rss=1 Smith, J. Seydoux, G. 2018-01-10 doi:10.1101/245878 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ ATP-dependent force generation and membrane scission by ESCRT-III and Vps4 ]]> https://biorxiv.org/content/10.1101/262170v1?rss=1 Schoeneberg, J. Yan, S. Righini, M. Remec Pavlin, M. Lee, I.-H. Carlson, L.-A. Bahrami, A. H. Goldman, D. H. Ren, X. Hummer, G. Bustamante, C. Hurley, J. 2018-02-07 doi:10.1101/262170 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Diverse progenitor cells preserve salivary gland ductal architecture after radiation induced damage ]]> https://biorxiv.org/content/10.1101/295501v1?rss=1 May, A. Cruz Pacheco, N. Emmerson, E. Siedel, K. Nathan, S. Muench, M. O. Klein, O. D. Knox, S. M. 2018-04-05 doi:10.1101/295501 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Structure of the Human Volume Regulated Anion Channel ]]> https://biorxiv.org/content/10.1101/323584v1?rss=1 Kefauver, J. M. Saotome, K. Dubin, A. E. Pallesen, J. Cottrell, C. A. Hong, G. Cahalan, S. M. Qiu, Z. Crowley, C. S. Whitwam, T. Lee, W.-H. Ward, A. B. Patapoutian, A. 2018-05-16 doi:10.1101/323584 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Glutathione shapes glutamatergic transmission ]]> https://biorxiv.org/content/10.1101/325530v1?rss=1 Koga, M. Parker, G. M. Hester, L. D. Y, T. Kamiya, A. Snyder, S. H. Sawa, A. Sedlak, T. W. 2018-05-18 doi:10.1101/325530 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution ]]> https://biorxiv.org/content/10.1101/374140v1?rss=1 Gao, R. Asano, S. M. Upadhyayula, S. Pisarev, I. Milkie, D. E. Liu, T.-L. Singh, V. Graves, A. Huynh, G. H. Zhao, Y. Bogovic, J. Colonell, J. Ott, C. M. Zugates, C. Tappan, S. Rodriguez, A. Mosaliganti, K. R. Megason, S. G. Lippincott-Schwartz, J. Hantman, A. Rubin, G. M. Kirchhausen, T. Saalfeld, S. Aso, Y. Boyden, E. S. Betzig, E. 2018-07-23 doi:10.1101/374140 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Planar cell polarity pathway and development of the human visual cortex ]]> https://biorxiv.org/content/10.1101/404558v1?rss=1 Shin, J. Ma, S. Hofer, E. Patel, Y. Roshchupkin, G. Sousa, A. M. Jian, X. Gottesmann, R. Mosley, T. H. Fornage, M. Saba, Y. Pirpamer, L. Schmidt, R. Schmidt, H. Mazoyer, B. Carrion-Castillo, A. Bis, J. Li, S. Yang, Q. Luciano, M. Karama, S. Lewis, L. Bastin, M. Harris, M. A. Deary, I. Wardlaw, J. M. Scholz, M. Loeffler, M. Witte, V. Beyer, F. Villringer, A. Adams, H. H. Ikrum, M. A. Kremen, W. S. Gillespie, N. A. Sestan, N. Pausova, Z. Seshadri, S. Paus, T. 2018-08-31 doi:10.1101/404558 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ A High Avidity Biosensor Reveals PI(3,4)P2 is Predominantly a Class I PI3K Signaling Product ]]> https://biorxiv.org/content/10.1101/410811v1?rss=1 Goulden, B. Pacheco, J. Dull, A. Zewe, J. Deiters, A. Hammond, G. R. 2018-09-06 doi:10.1101/410811 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ A second generation IL-2 receptor-targeted diphtheria fusion toxin exhibits anti-tumor activity and synergy with anti-PD-1 in melanoma ]]> https://biorxiv.org/content/10.1101/420158v1?rss=1 Cheung, L. S. Fu, J. Kumar, P. Kumar, A. Urbanowski, M. E. Ihms, E. A. Parveen, S. Bullen, C. K. Patrick, G. Harrison, R. Murphy, J. R. Pardoll, D. M. Bishai, W. 2018-09-17 doi:10.1101/420158 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ GWAS-driven Pathway Analyses and Functional Validation Suggest GLIS1 as a Susceptibility Gene for Mitral Valve Prolapse ]]> https://biorxiv.org/content/10.1101/433268v1?rss=1 Yu, M. Georges, A. Tucker, N. R. Kyryachenko, S. Toomer, K. Schott, J.-J. Delling, F. N. Ellinor, P. T. Levine, R. A. Slaugenhaupt, S. A. Hagege, A. A. Dina, C. Jeunemaitre, X. Milan, D. J. Norris, R. A. Bouatia-Naji, N. 2018-10-02 doi:10.1101/433268 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Factors Affecting Electroconvulsive Therapy Ictal Outcomes: Duration and Postictal Suppression ]]> https://biorxiv.org/content/10.1101/433789v1?rss=1 Ingram, W. M. Weston, C. Lu, W. D. Hodge, C. B. Poler, S. M. Nahi, F. T. Larson, S. 2018-10-02 doi:10.1101/433789 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Integrating brain methylome with GWAS for psychiatric risk gene discovery ]]> https://biorxiv.org/content/10.1101/440206v1?rss=1 Han, S. Lin, Y. Wang, M. Goes, F. S. Tan, K. Zandi, P. Hyde, T. Weinberger, D. R. Potash, J. B. Kleinman, J. E. Jaffe, A. E. 2018-10-11 doi:10.1101/440206 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ A machine learning approach to predicting autism risk genes: Validation of known genes and discovery of new candidates ]]> https://biorxiv.org/content/10.1101/463547v1?rss=1 Lin, Y. Rajadhyaksha, A. Potash, J. Han, S. 2018-11-07 doi:10.1101/463547 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Transcriptional suppression from KMT2D loss disrupts cell cycle and hypoxic responses in neurodevelopmental models of Kabuki syndrome ]]> https://biorxiv.org/content/10.1101/484410v1?rss=1 70%) of patients diagnosed with the congenital, multisystem intellectual disability (ID) disorder Kabuki syndrome 1 (KS1). Critical roles for KMT2D are established in various non-neural tissues, but the effects of KMT2D loss in brain cell development have not been described. We conducted parallel studies of proliferation, differentiation, transcription, and chromatin profiling in KMT2D-deficient human and mouse models to define KMT2D-regulated functions in neurodevelopmental contexts, including adult-born hippocampal NSPCs in vivo and in vitro. We report cell-autonomous defects in proliferation, cell cycle, and survival, accompanied by early NSPC maturation in several KMT2D-deficient model systems. Transcriptional suppression in KMT2D-deficient cells indicated strong perturbation of hypoxia-responsive metabolism pathways. Functional experiments confirmed abnormalities of cellular hypoxia responses in KMT2D-deficient neural cells, and accelerated NSPC maturation in vivo. Together, our findings support a model in which loss of KMT2D function suppresses expression of oxygen-responsive gene programs important to neural progenitor maintenance, resulting in precocious neuronal differentiation in a mouse model of KS1.nnGraphical AbstractnnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/484410v3_ufig1.gif" ALT="Figure 1">nView larger version (22K):norg.highwire.dtl.DTLVardef@55dd1aorg.highwire.dtl.DTLVardef@1270c80org.highwire.dtl.DTLVardef@a5bda2org.highwire.dtl.DTLVardef@144df37_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carosso, G. A. Boukas, L. Augustin, J. J. Nguyen, H. N. Winer, B. L. Cannon, G. H. Robertson, J. D. Zhang, L. Hansen, K. D. Goff, L. A. Bjornsson, H. T. 2018-12-02 doi:10.1101/484410 Cold Spring Harbor Laboratory Press 2018-12-02 <![CDATA[ The integrated stress response mediates type I interferon driven necrosis in Mycobacterium tuberculosis granulomas ]]> https://biorxiv.org/content/10.1101/499467v1?rss=1 Bhattacharya, B. Xiao, S. Chatterjee, S. Urbanowski, M. Ordonez, A. Ihms, E. A. Agrahari, G. Lun, S. Berland, R. Pichugin, A. Gao, Y. Connor, J. Ivanov, A. Yan, B.-S. Kobzik, L. Jain, S. Bishai, W. Kramnik, I. 2018-12-19 doi:10.1101/499467 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma ]]> https://biorxiv.org/content/10.1101/508549v1?rss=1 Huang, H. H.-L. Ferguson, I. D. Thornton, A. M. Lam, C. Y. T. Lin, Y.-H. T. Bastola, P. Mariano, M. C. Marcoulis, M. D. Malato, J. Phojanakong, P. Hann, B. C. Brooks, A. N. Wiita, A. P. 2018-12-30 doi:10.1101/508549 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Identifying small proteins by ribosome profiling with stalled initiation complexes ]]> https://biorxiv.org/content/10.1101/511675v1?rss=1 Weaver, J. S. Mohammad, F. Buskirk, A. Storz, G. 2019-01-04 doi:10.1101/511675 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ The Toxoplasma Vacuolar H+-ATPase regulates intracellular pH, and impacts the maturation of essential secretory proteins ]]> https://biorxiv.org/content/10.1101/515296v1?rss=1 Stasic, A. J. Chasen, N. M. Dykes, E. J. Vella, S. A. Asady, B. Starai, V. J. Moreno, S. 2019-01-09 doi:10.1101/515296 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ The role of SLC7A5 (LAT1) in endocrine therapy resistant breast cancer ]]> https://biorxiv.org/content/10.1101/555342v1?rss=1 Sevigny, C. M. Sengupta, S. Luo, Z. Liu, X. Hu, R. Zhang, Z. Jin, L. Pearce, D. A. Demas, D. Shajahan-Haq, A. N. Clarke, R. 2019-02-21 doi:10.1101/555342 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Human cortical neural stem cells generate regional organizer states in vitro before committing to excitatory neuronal fates ]]> https://biorxiv.org/content/10.1101/577544v1?rss=1 Micali, N. Kim, S.-K. Diaz-Bustamante, M. Stein-O'Brien, G. Seo, S. Shin, J.-H. Rash, B. G. Ma, S. Olivares, N. A. Arellano, J. Maynard, K. R. Fertig, E. J. Cross, A. J. Burli, R. Brandon, N. J. Weinberger, D. R. Chenoweth, J. G. Hoeppner, D. J. Sestan, N. Rakic, P. Colantuoni, C. McKay, R. D. 2019-03-15 doi:10.1101/577544 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Serum Flt3 ligand is a biomarker of progenitor cell mass and prognosis in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/588319v1?rss=1 1185pg/ml was associated with higher overall survival (p = 0.0119). Serial measurement of Flt3L in patients who had received a hematopoietic stem cell transplant for AML further illustrated the potential value of declining Flt3L to identify relapse. Together these observations suggest that measurement of Flt3L provides a non-invasive estimate of progenitor cell mass in most patients with AML, with the potential to inform clinical decisions.nnGraphical abstractnnO_FIG O_LINKSMALLFIG WIDTH=151 HEIGHT=200 SRC="FIGDIR/small/588319_ufig1.gif" ALT="Figure 1">nView larger version (21K):norg.highwire.dtl.DTLVardef@132f3f3org.highwire.dtl.DTLVardef@2e033eorg.highwire.dtl.DTLVardef@d70598org.highwire.dtl.DTLVardef@b0648a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Milne, P. Wilhelm-Benartzi, C. Grunwald, M. R. Bigley, V. Publicover, A. Pagan, S. Marr, H. Jones, G. Dickinson, A. Grech, A. Burnett, A. Russell, N. Levis, M. Knapper, S. Collin, M. 2019-03-25 doi:10.1101/588319 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Precocious Chondrocyte Differentiation Disrupts Skeletal Growth in Kabuki Syndrome Mice ]]> https://biorxiv.org/content/10.1101/599878v1?rss=1 Fahrner, J. A. Lin, W.-Y. Riddle, R. C. Boukas, L. DeLeon, V. B. Chopra, S. Lad, S. E. Luperchio, T. R. Hansen, K. D. Bjornsson, H. T. 2019-04-05 doi:10.1101/599878 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Complete blood count with differential: An effective diagnostic for IBS subtype in the context of BMI? ]]> https://biorxiv.org/content/10.1101/608208v1?rss=1 Robinson, J. Boulineaux, C. Butler, K. Joseph, P. Murray, M. Pocock, S. Sherwin, L. Turkington, S. Weaver, K. Henderson, W. 2019-04-18 doi:10.1101/608208 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/645929v1?rss=1 Roberts Buceta, P. M. Romanelli-Cedrez, L. Babcock, S. J. Xun, H. VonPaige, M. L. Higley, T. W. Schlatter, T. D. Davis, D. C. Drexelius, J. A. Culver, J. C. Carrera, I. Shepherd, J. N. Salinas, G. 2019-05-22 doi:10.1101/645929 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ Multi-ethnic analysis shows genetic risk and environmental predictors interact to influence 25(OH)D concentration and optimal vitamin D intake ]]> https://biorxiv.org/content/10.1101/652941v1?rss=1 20ng/ml) increased as genetic risk decreased (72% vs 89% in the highest vs lowest risk categories; p=0.018).nnConclusionsAvailable UV radiation and vitamin D intake interact with genetics to influence 25(OH)D. Individuals with higher genetic risk of deficiency may require more vitamin D exposure to maintain optimal 25(OH)D concentrations. Overall, the results showcase the importance of incorporating both environmental and genetic factors into analyses, as well as the potential for gene-environment interactions to inform personalized dosing of vitamin D.nnSources of SupportO_ST_ABSARICC_ST_ABSThe Atherosclerosis Risk in Communities Study is carried out as a collaborative study supported by National Heart, Lung, and Blood Institute contracts (HHSN268201100005C, HHSN268201100006C, HHSN268201100007C, HHSN268201100008C, HHSN268201100009C, HHSN268201100010C, HHSN268201100011C, and HHSN268201100012C). The authors thank the staff and participants of the ARIC study for their important contributions.nnFunding for GENEVA was provided by National Human Genome Research Institute grant U01HG004402 (E. Boerwinkle).nnMESAMESA and the MESA SHARe project are conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with MESA investigators. Support for MESA is provided by contracts HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1-TR-001881, and DK063491.nnThe MESA CARe data used for the analyses described in this manuscript were obtained through Genetics (accession numbers). Funding for CARe genotyping was provided by NHLBI Contract N01-HC-65226.nnFunding support for the Vitamin D dataset was provided by grant HL096875nnWHIThe WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through contracts HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C. This manuscript was not prepared in collaboration with investigators of the WHI, has not been reviewed and/or approved by the Womens Health Initiative (WHI), and does not necessarily reflect the opinions of the WHI investigators or the NHLBI.nnWHI PAGE is funded through the NHGRI Population Architecture Using Genomics and Epidemiology (PAGE) network (Grant Number U01 HG004790). Assistance with phenotype harmonization, SNP selection, data cleaning, meta-analyses, data management and dissemination, and general study coordination, was provided by the PAGE Coordinating Center (U01HG004801-01).nnFunding support for WHI GARNET was provided through the NHGRI Genomics and Randomized Trials Network (GARNET) (Grant Number U01 HG005152). Assistance with phenotype harmonization and genotype cleaning, as well as with general study coordination, was provided by the GARNET Coordinating Center (U01 HG005157). Assistance with data cleaning was provided by the National Center for Biotechnology Information. Funding support for genotyping, which was performed at the Broad Institute of MIT and Harvard, was provided by the NIH Genes, Environment and Health Initiative [GEI] (U01 HG004424). The datasets used for the analyses described in this manuscript were obtained from dbGaP at http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap through dbGa Paccession phs000200.v11.p3.nnFunding for WHI SHARe genotyping was provided by NHLBI Contract N02-HL-64278.nnOtherKEH was supported by an NLM training grant to the Computation and Informatics in Biology and Medicine Training Program (NLM 5T15LM007359). Computational resources were supported by a core grant to the Center for Demography and Ecology at the University of Wisconsin-Madison (P2C HD047873).nnJM was supported by the Department of Ophthalmology and Visual Sciences, and by an unrestricted grant to the Department of Ophthalmology and Visual Sciences from the Research to Prevent Blindness, and by National Institutes of Health, National Eye Institute grants R01 EY016686, R01 EY025292. ]]> Hatchell, K. E. Lu, Q. Mares, J. A. Michos, E. D. Wood, A. C. Engelman, C. D. 2019-05-28 doi:10.1101/652941 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ The effect of sex and underlying disease on the genetic association of QT interval and sudden cardiac death ]]> https://biorxiv.org/content/10.1101/664300v1?rss=1 Mitchell, R. N. Ashar, F. N. Jarvelin, M.-R. Froguel, P. Sotoodehnia, N. Brody, J. A. Sebert, S. Huikuri, H. Rioux, J. Goyette, P. Newcomb, C. E. Junttila, M. J. Arking, D. E. 2019-06-09 doi:10.1101/664300 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ Insulin-like growth factor 1 receptor signaling in tenocytes is required for adult tendon growth ]]> https://biorxiv.org/content/10.1101/670026v1?rss=1 Disser, N. P. Sugg, K. B. Talarek, J. R. Sarver, D. C. Rourke, B. J. Mendias, C. L. 2019-06-13 doi:10.1101/670026 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Probing the Subcellular Distribution of Phosphatidylinositol Reveals a Surprising Lack at the Plasma Membrane ]]> https://biorxiv.org/content/10.1101/677039v1?rss=1 Zewe, J. Miller, A. Sangappa, S. Wills, R. Goulden, B. Hammond, G. R. 2019-06-19 doi:10.1101/677039 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ A new data-driven cell population discovery and annotation method for single-cell data, FAUST, reveals correlates of clinical response to cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/702118v1?rss=1 Greene, E. Finak, G. D'Amico, L. A. Bhardwaj, N. Church, C. D. Morishima, C. Ramchurren, N. Taube, J. M. Nghiem, P. T. Cheever, M. A. Fling, S. P. Gottardo, R. 2019-07-13 doi:10.1101/702118 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework ]]> https://biorxiv.org/content/10.1101/709428v1?rss=1 Brnich, S. E. Abou Tayoun, A. N. Couch, F. J. Cutting, G. Greenblatt, M. S. Heinen, C. D. Kanavy, D. M. Luo, X. McNulty, S. M. Starita, L. M. Tavtigian, S. V. Wright, M. W. Harrison, S. M. Biesecker, L. G. Berg, J. S. 2019-07-25 doi:10.1101/709428 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Cryptococcus neoformans evades pulmonary immunity by modulating xylose transport ]]> https://biorxiv.org/content/10.1101/741017v1?rss=1 Li, L. X. Hole, C. R. Rangel-Moreno, J. Khader, S. A. Doering, T. L. 2019-08-20 doi:10.1101/741017 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Novel genetic determinants of telomere length from a multi-ethnic analysis of 75,000 whole genome sequences in TOPMed ]]> https://biorxiv.org/content/10.1101/749010v1?rss=1 1 independent signal. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). We further identified two novel genes, DCLRE1B (SNM1B) and PARN, using a multi-variant gene-based approach. ]]> Taub, M. A. Weinstock, J. S. Iyer, K. R. Yanek, L. R. Conomos, M. P. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Reiner, A. P. Mathias, R. A. 2019-09-04 doi:10.1101/749010 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ ERR agonism reverses mitochondrial dysfunction and inflammation in aging ]]> https://biorxiv.org/content/10.1101/755801v1?rss=1 Wang, X. X. Takahashi, S. Libby, A. E. Myakala, K. Jones, B. A. Bhasin, K. Qi, Y. Krausz, K. Zerfas, P. Panov, J. velenosi, t. J. patel, d. P. Daneshpajouhnejad, P. Ginley, B. Sarder, P. Titievsky, A. Sharov, V. Ostretsov, B. Kopp, J. B. Rosenberg, A. Z. Gonzalez, F. J. Guha, U. Brodsky, L. Burris, T. Levi, M. 2019-09-05 doi:10.1101/755801 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ IL-10 Promotes Endothelial Progenitor Cell Driven Wound Neovascularization and Enhances Healing via STAT3. ]]> https://biorxiv.org/content/10.1101/760165v1?rss=1 Balaji, S. steen, e. wang, x. Vangapandu, H. V. Templeman, N. Blum, A. J. Moles, C. M. Li, H. narmoneva, d. a. Crombleholme, T. m. butte, m. j. bollyky, p. l. keswani, s. g. 2019-09-08 doi:10.1101/760165 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Prostaglandin D2 Signaling is Not Involved in Rat Hindlimb Tendon Healing ]]> https://biorxiv.org/content/10.1101/778126v1?rss=1 Sarver, D. C. Sugg, K. B. Talarek, J. R. Swanson, J. B. Oliver, D. J. Hinken, A. C. Kramer, H. F. Mendias, C. L. 2019-09-23 doi:10.1101/778126 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ EAGLE: an algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interaction ]]> https://biorxiv.org/content/10.1101/781427v1?rss=1 Gao, T. Qian, J. 2019-09-25 doi:10.1101/781427 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Counteracting resistance to targeted therapy in melanoma by inhibiting discoidin domain receptors ]]> https://biorxiv.org/content/10.1101/857904v1?rss=1 Sala, M. Allain, N. Henriet, E. Uguen, A. Di-Tommaso, S. Dupuy, J.-W. Gerard, E. Dugot-Senant, N. Rousseau, B. Merlio, J.-P. Pham-Ledart, A. Vergier, B. Moreau, V. Saltel, F. Raymond, A.-A. 2019-12-03 doi:10.1101/857904 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Genome-wide Association Study of Pediatric Obsessive-Compulsive Traits: Shared Genetic Risk between Traits and Disorder ]]> https://biorxiv.org/content/10.1101/858241v1?rss=1 Burton, C. L. Lemire, M. Xiao, B. Corfield, E. C. Erdman, L. Bralten, J. Poelmans, G. Yu, D. Shaheen, S.-M. Goodale, T. OCD Working Group of the Psychiatric Genomics Consortium, Soreni, N. Hanna, G. L. Fitzgerald, K. D. Rosenberg, D. Nestadt, G. Paterson, A. D. Strug, L. Schachar, R. J. Crosbie, J. Arnold, P. D. 2019-11-29 doi:10.1101/858241 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2024.08.12.607630v1?rss=1 Sotomayor, B. Donahue, T. C. Mahajan, S. P. Taw, M. N. Hulbert, S. W. Bidstrup, E. J. Owitipana, D. N. Pang, A. Yang, X. Ghosal, S. Alabi, C. A. Azadi, P. Gray, J. J. Jewett, M. C. Wang, L.-X. DeLisa, M. P. 2024-08-12 doi:10.1101/2024.08.12.607630 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Spontaneous calcium transients in hair cell stereocilia ]]> https://biorxiv.org/content/10.1101/2024.08.12.607658v1?rss=1 Hussain, S. Sedlacek, M. Cui, R. Zhang-Hooks, W. Bergles, D. E. Shin, J.-B. Kindt, K. Kachar, B. 2024-08-13 doi:10.1101/2024.08.12.607658 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ The role of mitochondrial complex I in the proinflammatory response to polylactide implants ]]> https://biorxiv.org/content/10.1101/2024.08.12.607680v1?rss=1 Maduka, C. V. Makela, A. V. Tundo, A. Ural, E. Stivers, K. B. Alhaj, M. Narayan, R. Goodman, S. B. Ashammakhi, N. Elisseeff, J. H. Hankenson, K. D. Contag, C. H. 2024-08-15 doi:10.1101/2024.08.12.607680 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Circulating extracellular microRNAs in the blood promote sociability in mice ]]> https://biorxiv.org/content/10.1101/2024.08.12.605506v1?rss=1 Dohi, E. Matoba, K. Garcia, P. A. Francis-Oliveira, J. Anguiano, F. Kochi, T. Badrani, J. H. See, J. Ito, N. Mitani, R. Rose, I. V. Choi, E. Y. Imai, T. Crossman, D. K. Pletnikov, M. V. Witwer, K. W. Niwa, M. Kano, S. 2024-08-16 doi:10.1101/2024.08.12.605506 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Complete genome sequences of two new strains of the shipworm endosymbiont, Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2024.08.13.607755v1?rss=1 Gasser, M. T. Flatau, R. Altamia, M. A. Filone, C. M. Distel, D. L. 2024-08-16 doi:10.1101/2024.08.13.607755 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Improving the accuracy of cerebral blood flow measurement by phase contrast MRI ]]> https://biorxiv.org/content/10.1101/2024.08.13.607816v1?rss=1 yang, x. 2024-08-16 doi:10.1101/2024.08.13.607816 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ scatterbar: an R package for visualizing proportional data across spatially resolved coordinates ]]> https://biorxiv.org/content/10.1101/2024.08.14.606810v1?rss=1 Velazquez, D. Fan, J. 2024-08-16 doi:10.1101/2024.08.14.606810 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Calcium tunneling through the entoplasmic reticulum and transfer to other organelles for optimal signaling in Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/2024.08.15.608087v1?rss=1 Li, Z.-H. Asady, B. Chang, L. Hortua Triana, M. A. Li, C. Coppens, I. Moreno, S. N. 2024-08-16 doi:10.1101/2024.08.15.608087 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Serum Amyloid P Secreted by Bone Marrow Adipocytes Drives Skeletal Amyloidosis ]]> https://biorxiv.org/content/10.1101/2024.08.15.608092v1?rss=1 Kumar, S. Song, K. Wang, J. Baghel, M. S. Wong, P. Cao, X. Wan, M. 2024-08-16 doi:10.1101/2024.08.15.608092 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ WheresWalker: a pipeline for rapid mutation mapping using whole genome sequencing ]]> https://biorxiv.org/content/10.1101/2024.08.14.607950v1?rss=1 Feltes, M. Zimin, A. V. Angel, S. Pansari, N. Hensley, M. R. Anderson, J. L. Shen, M.-C. Klemek, M. Shen, Y. Ginde, V. S. Truong, V. P. Kozan, H. Le, N. V. Wilson, M. H. Salzberg, S. L. Farber, S. A. 2024-08-17 doi:10.1101/2024.08.14.607950 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Comparison of test-retest reproducibility of DESPOT and 3D-QALAS for water T1 and T2 mapping ]]> https://biorxiv.org/content/10.1101/2024.08.15.608081v1?rss=1 Simegn, G. L. Gagoski, B. Song, Y. Dean, D. C. Hupfelda, K. E. Murali-Manohara, S. Davies-Jenkinsa, C. W. Simicic, D. Wisnowskij, J. Yedavallia, V. Gudmundson, A. T. Zollner, H. J. Oeltzschner, G. Edden, R. A. E. 2024-08-19 doi:10.1101/2024.08.15.608081 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT) ]]> https://biorxiv.org/content/10.1101/2024.08.16.608281v1?rss=1 Lu, J. Satten, G. A. Meyer, K. A. Launer, L. J. Ling, W. Zhao, N. 2024-08-19 doi:10.1101/2024.08.16.608281 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Uncovering Astrocyte Morphological Dynamics Using Optical Diffraction Tomography and Shape-based Trajectory Inference ]]> https://biorxiv.org/content/10.1101/2024.08.16.608356v1?rss=1 Anantha, P. Raj, P. Saracino, E. Kim, J. H. Kim, J. H. Convertino, A. Gu, L. Barman, I. 2024-08-19 doi:10.1101/2024.08.16.608356 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Functional Regrowth of Norepinephrine Axons in the Adult Mouse Brain Following Injury ]]> https://biorxiv.org/content/10.1101/2024.08.19.608684v1?rss=1 Cooke, P. R. Linden, D. J. 2024-08-20 doi:10.1101/2024.08.19.608684 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Transcriptional Dynamics of Sleep Deprivation and Subsequent Recovery Sleep in the Male Mouse Cortex ]]> https://biorxiv.org/content/10.1101/2024.08.20.607983v1?rss=1 Popescu, A. Ottaway, C. Ford, K. Patterson, T. W. Ingiosi, A. M. Medina, E. Hicks, S. C. Singletary, K. Peixoto, L. 2024-08-21 doi:10.1101/2024.08.20.607983 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ ActSort: An active-learning accelerated cell sorting algorithm for large-scale calcium imaging datasets ]]> https://biorxiv.org/content/10.1101/2024.08.21.609011v1?rss=1 Jiang, Y. Akengin, H. O. Zhou, J. Aslihak, M. A. Li, Y. Hernandez, O. Ebrahimi, S. Zhang, Y. Inan, H. Jaidar, O. Miranda, C. Dinc, F. Blanco-Pozo, M. Schnitzer, M. J. 2024-08-22 doi:10.1101/2024.08.21.609011 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration ]]> https://biorxiv.org/content/10.1101/2024.08.21.609017v1?rss=1 Playter, C. Golloshi, R. Garretson, J. H. Gonzalez, A. R. Olajide, T. H. Saad, A. Benson, S. J. McCord, R. P. 2024-08-22 doi:10.1101/2024.08.21.609017 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ On the relationship between serotype, chemotype and genotype for Cryptococcus spp. including a method for including polysaccharide structure in strain characterization ]]> https://biorxiv.org/content/10.1101/2024.08.22.609096v1?rss=1 Wear, M. P. Greengo, S. McConnell, S. Xu, A. Lopes, L. L. Majumdar, A. Casadevall, A. 2024-08-22 doi:10.1101/2024.08.22.609096 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Polyploid cancer cells reveal signatures of chemotherapy resistance ]]> https://biorxiv.org/content/10.1101/2024.08.19.608632v1?rss=1 Schmidt, M. J. Naghdloo, A. Prabakar, R. K. Kamal, M. Cadaneanu, R. Garraway, I. P. Lewis, M. Aparicio, A. Kuhn, P. Pienta, K. J. Amend, S. R. Hicks, J. 2024-08-23 doi:10.1101/2024.08.19.608632 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Solving the "Blind men and the elephant problem": Additive deep learning of complex high dimensional models from partial faceted datasets ]]> https://biorxiv.org/content/10.1101/2024.08.22.609223v1?rss=1 Wu, Y. Wu, P.-H. Chambliss, A. Wirtz, D. Sun, S. 2024-08-23 doi:10.1101/2024.08.22.609223 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Tactile Mechanisms and Afferents Underlying the Rat Pup Transport Response ]]> https://biorxiv.org/content/10.1101/2024.08.23.609194v1?rss=1 Ni, Z. Neifert, C. Rosete, A. Albeely, A. M. Yang, Y. Pratelli, M. Brecht, M. Clemens, A. M. 2024-08-23 doi:10.1101/2024.08.23.609194 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing ]]> https://biorxiv.org/content/10.1101/2024.08.25.608519v1?rss=1 Zhao, R. Lu, J. Zhou, W. Zhao, N. Ji, H. 2024-08-26 doi:10.1101/2024.08.25.608519 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Effects of connectivity hyperalignment (CHA) on estimated brain network properties: from coarse-scale to fine-scale ]]> https://biorxiv.org/content/10.1101/2024.08.27.609817v1?rss=1 Farahani, F. V. Nebel, M. B. Wager, T. Lindquist, M. A. 2024-08-28 doi:10.1101/2024.08.27.609817 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Auditory feedback effect of self-pacing treadmill walking in comparison to overground walking ]]> https://biorxiv.org/content/10.1101/2024.08.28.610096v1?rss=1 Evans, T. Reissman, M. E. Reissman, T. Shelhamer, M. Chaudhari, A. M. W. 2024-08-29 doi:10.1101/2024.08.28.610096 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Integer topological defects provide a new way to quantify and classify cell sheets ]]> https://biorxiv.org/content/10.1101/2024.08.28.610106v1?rss=1 Zhao, Z. Li, H. Yao, Y. Zhao, Y. Serra, F. Kawaguchi, K. Zhang, H. Chate, H. Sano, M. 2024-08-30 doi:10.1101/2024.08.28.610106 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Single-Molecule Studies of Cognate and Near-Cognate Elongation in an in vitro Eukaryotic Translation System ]]> https://biorxiv.org/content/10.1101/2024.08.29.609187v1?rss=1 Fritsch, C. Bhattacharya, A. Ng, M. Y. Li, H. Nelson, P. C. Cooperman, B. S. Goldman, Y. E. 2024-08-30 doi:10.1101/2024.08.29.609187 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Stable White Matter Structure in the First Three Years after Psychosis Onset ]]> https://biorxiv.org/content/10.1101/2024.08.29.610312v1?rss=1 Van Dyken, P. C. Yang, K. Faria, A. V. Sawa, A. MacKinley, M. Khan, A. R. Palaniyappan, L. 2024-08-30 doi:10.1101/2024.08.29.610312 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Decreasing ZAP Poly(ADP-ribose) Binding Enhances Antiviral Activity Against Alphaviruses ]]> https://biorxiv.org/content/10.1101/2024.08.30.610567v1?rss=1 Cheng, S.-J. Griffin, D. E. Abraham, R. Leung, A. K. L. 2024-08-31 doi:10.1101/2024.08.30.610567 Cold Spring Harbor Laboratory Press 2024-08-31 <![CDATA[ Yersinia pseudotuberculosis growth arrest during type-III secretion system expression is associated with altered ribosomal protein expression and decreased gentamicin susceptibility ]]> https://biorxiv.org/content/10.1101/2024.09.02.610769v1?rss=1 Greene, J. Snyder, R. A. Cotten, K. L. Huiszoon, R. Chu, S. Braza, R. E. D. Chapin, A. A. Stine, J. M. Bentley, W. E. Ghodssi, R. Davis, K. M. 2024-09-02 doi:10.1101/2024.09.02.610769 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ A FUCCI sensor reveals complex cell cycle organization of Toxoplasma endodyogeny ]]> https://biorxiv.org/content/10.1101/2024.09.02.610821v1?rss=1 Batra, M. Marsilia, C. Awshah, D. Hawkins, L. M. Wang, C. Chaput, D. Naumova, D. A. Suvorova, E. S. 2024-09-03 doi:10.1101/2024.09.02.610821 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Disrupted Post-Transcriptional Regulation of Gene Expression as A Hallmark of Fatty Liver Progression ]]> https://biorxiv.org/content/10.1101/2024.09.02.610906v1?rss=1 Takaoka, S. Jaso-Vera, M. E. Ruan, X. 2024-09-03 doi:10.1101/2024.09.02.610906 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Sweet science: Exploring the impact of fructose and glucose on brown adipocyte differentiation using optical diffraction tomography ]]> https://biorxiv.org/content/10.1101/2024.09.04.611269v1?rss=1 Anantha, P. Wu, X. Elsaid, S. Raj, P. Barman, I. Tee, S. S. 2024-09-04 doi:10.1101/2024.09.04.611269 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms ]]> https://biorxiv.org/content/10.1101/2024.09.04.610850v1?rss=1 Wenz, B. M. He, Y. Chen, N.-C. Pickrell, J. K. Li, J. H. Dudek, M. F. Li, T. Keener, R. Voight, B. F. Brown, C. D. Battle, A. 2024-09-05 doi:10.1101/2024.09.04.610850 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Mechanosensing by Piezo1 regulates osteoclast differentiation via PP2A-Akt axis in periodontitis ]]> https://biorxiv.org/content/10.1101/2024.09.04.611049v1?rss=1 Shindo, S. Nakamura, S. Hawthorne, A. Heidari, A. Pastore, M. R. Okamoto, M. Suzuki, M. Salinas, M. Minond, D. Bontempo, A. Cayabyab, M. Yang, Y. Crane, J. L. Hernandez, M. Vardar, S. Hardigan, P. Han, X. Kaltman, S. Kawai, T. 2024-09-05 doi:10.1101/2024.09.04.611049 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ The small MAF transcription factor MAFG co-opts MITF to promote melanoma progression ]]> https://biorxiv.org/content/10.1101/2024.09.03.611024v1?rss=1 Vera, O. Martinez, M. Soto-Vargas, Z. Wang, K. Xu, X. Ruiz-Buceta, S. Mecozzi, N. Chadourne, M. Posorske, B. Angarita, A. Bok, I. Liu, Q. Murikipudi, H. Kim, Y. Messina, J. L. Tsai, K. Y. Major, M. Lau, E. K. Yu, X. Ibanez-de-Caceres, I. Karreth, F. A. 2024-09-06 doi:10.1101/2024.09.03.611024 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Mitochondrial morphodynamics are modulated by physiological range of temperature and influence host cell outcomes during influenza infection ]]> https://biorxiv.org/content/10.1101/2024.09.06.611682v1?rss=1 Pekosz, A. McLoughlin, G. J. 2024-09-06 doi:10.1101/2024.09.06.611682 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Computational Study of the Excitation of Human Induced Pluripotent Stem-Cell Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2024.09.03.611054v1?rss=1 Shetty, R. Samurkashian, R. Tung, L. 2024-09-07 doi:10.1101/2024.09.03.611054 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Temperature Sensitive Glutamate Gating of AMPA-subtype iGluRs ]]> https://biorxiv.org/content/10.1101/2024.09.05.611422v1?rss=1 Kumar Mondal, A. Carrillo, E. Jayaraman, V. Twomey, E. C. 2024-09-07 doi:10.1101/2024.09.05.611422 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ MYC plus class IIa HDAC inhibition potentiates mitochondrial dysfunction in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2024.09.04.610116v1?rss=1 Park, J. Chen, Y.-Y. Cao, J. J. An, J. Yen, R.-W. C. Outen, J. D. Baylin, S. B. Topper, M. J. 2024-09-08 doi:10.1101/2024.09.04.610116 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Calibration of FRET-based biosensors using multiplexed biosensor barcoding ]]> https://biorxiv.org/content/10.1101/2024.09.04.610346v1?rss=1 Wu, J.-W. Yang, J.-M. Chen, C.-C. Au, G. Wang, S. Chern, G.-W. Huang, C.-H. 2024-09-08 doi:10.1101/2024.09.04.610346 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Limited O-specific polysaccharide (OSP)-specific functional antibody responses in young children with Shigella infection in Bangladesh ]]> https://biorxiv.org/content/10.1101/2024.09.04.611236v1?rss=1 Bernshtein, B. Zhiteneva, J. A. Janardhanan, J. Wagh, C. Kelly, M. Verma, S. Jung, W. Basher, S. R. Amin, M. A. Mahamud, S. Rajib, N. H. Chowdhury, F. Khan, A. I. Charles, R. C. Xu, P. Kovac, P. Chakraborty, S. Kaminski, R. W. Alter, G. Bhuiyan, T. R. Qadri, F. Ryan, E. T. 2024-09-08 doi:10.1101/2024.09.04.611236 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan ]]> https://biorxiv.org/content/10.1101/2024.09.06.611254v1?rss=1 Xu, Y. K. T. Bush, A. Musheyev, E. Kim, A. A. Zhang, S. Eugenin von Bernhardi, J. Sulam, J. Bergles, D. E. 2024-09-08 doi:10.1101/2024.09.06.611254 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Dimerization-dependent gel-like condensation with dsDNA underpins the activation of human cGAS ]]> https://biorxiv.org/content/10.1101/2024.09.08.611895v1?rss=1 Sohn, J. Lueck, J. Strom, A. Wu, S. Wendorff, H. 2024-09-08 doi:10.1101/2024.09.08.611895 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ A fluid droplet harvests the force generated by shrinking microtubules in living cells ]]> https://biorxiv.org/content/10.1101/2024.09.09.612121v1?rss=1 Morelli, K. Meier, S. M. Zhao, A. Choudhury, M. Willis, M. Barral, Y. Vogel, J. 2024-09-10 doi:10.1101/2024.09.09.612121 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Desmoplakin mutations in cardiac fibroblasts cause TGF?1-mediated pathological fibrogenesis in desmoplakin cardiomyopathy via beclin-1 regulation ]]> https://biorxiv.org/content/10.1101/2024.09.09.612149v1?rss=1 Chen, H. V. Wei, C. Chan, S. F. Saguner, A. M. Brunckhorst, C. B. Duru, F. Marine, J. E. James, C. A. Calkins, H. Judge, D. Shou, W. 2024-09-11 doi:10.1101/2024.09.09.612149 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Differential Immunoregulation by Human Surfactant Protein A Variants Determines Severity of SARS-CoV-2-induced Lung Disease ]]> https://biorxiv.org/content/10.1101/2024.09.11.612497v1?rss=1 Jacob, I. B. Lawal, A. O. Mahmoud, S. S. Kopsack, E. M. Reynolds, E. S. Meng, Q. Fan, H. Massa, P. T. Thangamani, S. Jia, H. Wang, G. 2024-09-13 doi:10.1101/2024.09.11.612497 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering ]]> https://biorxiv.org/content/10.1101/2024.09.10.612244v1?rss=1 Benoit, M. Jenike, K. M. Satterlee, J. W. Ramakrishnan, S. Gentile, I. Hendelman, A. Passalacqua, M. J. Suresh, H. Shohat, H. Robitaille, G. M. Fitzgerald, B. Alonge, M. M. Wang, X. Santos, R. He, J. Ou, S. Golan, H. Green, Y. Swartwood, K. Sierra, G. P. Orejuela, A. Fornaguera, F. Goodwin, S. McCombie, W. R. Kizito, E. B. Gagnon, E. Knapp, S. Sarkinen, T. Frary, A. Gillis, J. Van Eck, J. Schatz, M. C. Lippman, Z. B. 2024-09-14 doi:10.1101/2024.09.10.612244 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Data-driven determination of 1H-MRS basis set composition ]]> https://biorxiv.org/content/10.1101/2024.09.11.612503v1?rss=1 Davies-Jenkins, C. W. Zollner, H. J. Simicic, D. Alcicek, S. Edden, R. A. E. Oeltzschner, G. 2024-09-15 doi:10.1101/2024.09.11.612503 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Virally-Mediated Enhancement of Efferent Inhibition Reduces Acoustic Trauma in Wild Type Murine Cochleas. ]]> https://biorxiv.org/content/10.1101/2024.09.12.612688v1?rss=1 Slika, E. Fuchs, P. A. Beers Wood, M. 2024-09-15 doi:10.1101/2024.09.12.612688 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Muscle spindles provide flexible sensory feedback for movement sequences ]]> https://biorxiv.org/content/10.1101/2024.09.13.612899v1?rss=1 Olson, W. P. Chokshi, V. B. Kim, J. J. Cowan, N. O'Connor, D. H. 2024-09-15 doi:10.1101/2024.09.13.612899 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Phase-Dependent Stimulation of the Hippocampus: A Computational Modeling Approach ]]> https://biorxiv.org/content/10.1101/2024.09.14.613022v1?rss=1 Lee, H.-P. Arginteanu, T. Kudela, P. Anderson, W. salimpour, y. 2024-09-15 doi:10.1101/2024.09.14.613022 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ PIP5K-Ras bistability initiates plasma membrane symmetry breaking to regulate cell polarity and migration ]]> https://biorxiv.org/content/10.1101/2024.09.15.613115v1?rss=1 Deng, Y. Banerjee, T. Pal, D. S. Banerjee, P. Zhan, H. D. Borleis, J. Iglesias, P. A. Devreotes, P. 2024-09-15 doi:10.1101/2024.09.15.613115 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ The Pattern and Staging of Brain Atrophy in Spinocerebellar Ataxia Type 2 (SCA2): MRI Volumetrics from ENIGMA-Ataxia ]]> https://biorxiv.org/content/10.1101/2024.09.16.613281v1?rss=1 2.5) in the cerebellar white matter (WM), middle cerebellar peduncle, pons, and corticospinal tract. Very large effects (d>1.5) were also evident in the superior cerebellar, inferior cerebellar, and cerebral peduncles. In cerebellar grey matter (GM), large effects (d>0.8) mapped to areas related to both motor coordination and cognitive tasks. Strong correlations (|r|>0.4) between volume and disease severity largely mirrored these groupwise outcomes. Stratification by disease severity showed a degeneration pattern beginning in cerebellar and pontine WM in pre-clinical subjects; spreading to the cerebellar GM and cerebro-cerebellar/corticospinal WM tracts; then finally involving the thalamus, striatum, and cortex in severe stages. InterpretationThe magnitude and pattern of brain atrophy evolves over the course of SCA2, with widespread, non-uniform involvement across the brainstem, cerebellar tracts, and cerebellar cortex; and late involvement of the cerebral cortex and striatum. ]]> Robertson, J. W. Adanyeguh, I. M. Bender, B. Boesch, S. Brunetti, A. Cocozza, S. Coutinho, L. Deistung, A. Diciotti, S. Dogan, I. Durr, A. Fernandez-Ruiz, J. Göricke, S. L. Grisoli, M. Han, S. Mariotti, C. Marzi, C. Mascalchi, M. Mochel, F. Nachbauer, W. Nanetti, L. Nigri, A. Ono, S. E. Onyike, C. U. Prince, J. L. Reetz, K. Romanzetti, S. Sacca, F. Synofzik, M. Teive, H. A. G. Thomopoulos, S. I. Thompson, P. M. Timmann, D. Ying, S. H. Harding, I. H. Hernandez-Castillo, C. R. 2024-09-17 doi:10.1101/2024.09.16.613281 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Optimized CRISPR inhibition and activation opens key avenues for systematic biological exploration in zebrafish. ]]> https://biorxiv.org/content/10.1101/2024.09.16.613289v1?rss=1 Barrientos, N. B. Shoppell, E. A. Boyd, R. J. Culotta, V. C. McCallion, A. S. 2024-09-19 doi:10.1101/2024.09.16.613289 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory ]]> https://biorxiv.org/content/10.1101/2024.09.17.613333v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@50a256org.highwire.dtl.DTLVardef@1d1f8c9org.highwire.dtl.DTLVardef@24688borg.highwire.dtl.DTLVardef@4ba3b4_HPS_FORMAT_FIGEXP M_FIG C_FIG Overview of the main components of the experiments conducted. Figure created using BioRender.com. ]]> Alam El Din, D.-M. Moenkemoeller, L. Loeffler, A. Habibollahi, F. Schenkman, J. Mitra, A. van der Molen, T. Ding, L. Laird, J. Schenke, M. Johnson, E. Kagan, B. Hartung, T. Smirnova, L. 2024-09-19 doi:10.1101/2024.09.17.613333 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ RIPK1 is essential for Herpes Simplex Virus-triggered ZBP1-dependent necroptosis in human cells ]]> https://biorxiv.org/content/10.1101/2024.09.17.613393v1?rss=1 Amusan, O. T. Wang, S. Yin, C. Koehler, H. S. Li, Y. Tenev, T. Wilson, R. Bellenie, B. Zhang, T. Wang, J. liu, c. seong, k. Poorbaghi, S. L. Yates, J. Shen, Y. Upton, J. W. Meier, P. Balachandra, S. Guo, H. 2024-09-19 doi:10.1101/2024.09.17.613393 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Contrasting Cognitive, Behavioral, and Physiological Responses to Breathwork vs. Naturalistic Stimuli in Reflective Chamber and VR Headset Environments ]]> https://biorxiv.org/content/10.1101/2024.09.17.613581v1?rss=1 Simonian, N. Johnson, M. A. Lynch, C. Wang, G. Kumaravel, V. Kuhn, T. Schoeller, F. Reggente, N. 2024-09-19 doi:10.1101/2024.09.17.613581 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Viral-mediated Oct4 overexpression and inhibition of Notch signaling synergistically induce neurogenic competence in mammalian Muller glia. ]]> https://biorxiv.org/content/10.1101/2024.09.18.613666v1?rss=1 Le, N. Awad, S. Palazzo, I. Hoang, T. Blackshaw, S. 2024-09-19 doi:10.1101/2024.09.18.613666 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Global remodeling of ADP-ribosylation by PARP1 suppresses influenza A virus infection ]]> https://biorxiv.org/content/10.1101/2024.09.19.613696v1?rss=1 Zhang, Z. Uribe, I. Davis, K. A. McPherson, R. L. Larson, G. P. Badiee, M. Tran, V. Ledwith, M. P. Feltman, E. Yu, S. Cai, Y. Chang, C.-Y. Yang, X. Ma, Z. Chang, P. Kuhn, J. H. Leung, A. K. L. Mehle, A. 2024-09-19 doi:10.1101/2024.09.19.613696 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Visualizing nuclear pore complex plasticity with Pan-Expansion Microscopy ]]> https://biorxiv.org/content/10.1101/2024.09.18.613744v1?rss=1 Morgan, K. J. Carley, E. Coyne, A. N. Rothstein, J. D. Lusk, C. P. King, M. C. 2024-09-20 doi:10.1101/2024.09.18.613744 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Altered development and network connectivity in a human neuronal model of 15q11.2 deletion-related neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2024.09.19.613912v1?rss=1 Habela, C. W. Liu, S. Taga, A. Dastgheyb, R. Haughey, N. Bergles, D. E. Song, H. Ming, G.-L. Maragakis, N. J. 2024-09-20 doi:10.1101/2024.09.19.613912 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Modulating DNA Polα Enhances Cell Reprogramming Across Species ]]> https://biorxiv.org/content/10.1101/2024.09.19.613993v1?rss=1 Ranjan, R. Ma, B. Gleason, R. J. Liao, Y. Bi, Y. Davis, B. E. M. Yang, G. Clark, M. Mahajan, V. Condon, M. Broderick, N. A. Chen, X. 2024-09-20 doi:10.1101/2024.09.19.613993 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks ]]> https://biorxiv.org/content/10.1101/2024.09.18.613544v1?rss=1 McDaniel, J. H. Patel, V. Olson, N. D. He, H.-J. He, Z. Schmitt, A. Sikkink, K. Sedlazeck, F. Doddapaneni, H. Jhangiani, S. N. Muzny, D. M. Gingras, M.-C. Mehta, H. Paulin, L. F. Hastie, A. R. Yu, H.-C. Weigman, V. Rojas, A. Kennedy, K. Remington, J. Gonzalez, I. Sudkamp, M. Wiseman, K. Lajoie, B. Levy, S. Jain, M. Akeson, S. Narzisi, G. Steinsnyder, Z. Reeves, C. Shelton, J. Kingan, S. B. Lambert, C. Bayabyan, P. Wenger, A. M. McLaughlin, I. J. Adamson, A. Kingsley, C. Wescott, M. Kim, Y. Paten, B. Park, J. Violich, I. Miga, K. H. Gardner, J. McNul 2024-09-22 doi:10.1101/2024.09.18.613544 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ SMoRe GloS: An efficient and flexible framework for inferring global sensitivity of agent-based model parameters ]]> https://biorxiv.org/content/10.1101/2024.09.18.613723v1?rss=1 Bergman, D. R. Jackson, T. L. Jain, H. V. Norton, K.-A. 2024-09-22 doi:10.1101/2024.09.18.613723 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Tau P301S Transgenic Mice Develop Gait and Eye Movement Impairments That Mimic Progressive Supranuclear Palsy ]]> https://biorxiv.org/content/10.1101/2024.09.20.614197v1?rss=1 Creed, R. B. Harris, S. C. Sridhar, S. du Lac, S. Zee, D. S. Dunn, F. A. Bouvier, G. Nelson, A. B. 2024-09-23 doi:10.1101/2024.09.20.614197 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Widespread brain activity increases in frontal lobe seizures with impaired consciousness ]]> https://biorxiv.org/content/10.1101/2024.09.20.614207v1?rss=1 Salardini, E. Vaddiparti, A. Kumar, A. Martin, R. A. Gebere, R. Z. Arencibia, C. A. Dhakar, M. B. Grover, E. H. Quraishi, I. H. Sternberg, E. J. George, I. C. Sivaraju, A. Bonito, J. Zaveri, H. P. Gober, L. M. Ahmed, S. Ghoshal, S. Wu, K. Farooque, P. Hirsch, L. J. Damisah, E. Gerrard, J. L. Spencer, D. D. Yoo, J. Y. Young, J. J. Friedman, D. Shum, J. Blumenfeld, H. 2024-09-23 doi:10.1101/2024.09.20.614207 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in pancreatic cancer immunotherapy pathologic responders ]]> https://biorxiv.org/content/10.1101/2024.09.22.613714v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@d5e1a5org.highwire.dtl.DTLVardef@1d14012org.highwire.dtl.DTLVardef@c57c6corg.highwire.dtl.DTLVardef@16baa56_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIIntegrated multi-modal spatial profiling of human PDAC tumors from neoadjuvant immunotherapy clinical trials reveal diverse spatial niches enriched in TLS. C_LIO_LITLS maturity is influenced by tumor location and the cellular neighborhoods in which TLS immune cells are recruited. C_LIO_LIUnsupervised machine learning of genome-wide signatures on spatial transcriptomics data characterizes the TLS-enriched TME and associates TLS transcriptomes with survival outcomes in PDAC. C_LIO_LIInteractions of spatially variable gene expression patterns showed TLS maturation is coupled with immunoglobulin distribution and ECM remodeling in pathologic responders. C_LIO_LIIntratumoral plasma cell and immunoglobin gene expression spatial dynamics demonstrate trafficking of TLS-driven humoral immunity in the PDAC TME. C_LI SignificanceWe report a spatial multi-omics atlas of PDAC tumors from a series of immunotherapy neoadjuvant clinical trials. Intratumorally, pathologic responders exhibit mature TLS that propagate plasma cells into malignant niches. Our findings offer insights on the role of TLS-associated humoral immunity and stromal remodeling during immunotherapy treatment. ]]> Sidiropoulos, D. N. Shin, S. M. Wetzel, M. Girgis, A. A. Bergman, D. Danilova, L. Perikala, S. Shu, D. H. Montagne, J. M. Deshpande, A. Leatherman, J. Dequiedt, L. Jacobs, V. Ogurtsova, A. Mo, G. Yuan, X. Lvovs, D. Stein-O'Brien, G. Yarchoan, M. Zhu, Q. Harper, E. I. Weeraratna, A. T. Kiemen, A. L. Jaffee, E. M. Zheng, L. Ho, W. J. Anders, R. A. Fertig, E. J. Kagohara, L. T. 2024-09-23 doi:10.1101/2024.09.22.613714 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ SGLT2 inhibitors protect against diabetic cardiomyopathy and atrial fibrillation through a CaMKII independent mechanism ]]> https://biorxiv.org/content/10.1101/2024.09.23.614368v1?rss=1 Severino, A. Reyes-Gaido, O. E. Nguyen, P. Elkarim, A. Luczak, E. D. Mesubi, O. O. 2024-09-23 doi:10.1101/2024.09.23.614368 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Vascular responses of hypercapnia challenge in mice ]]> https://biorxiv.org/content/10.1101/2024.09.20.614141v1?rss=1 Yang, X. Li, Y. Wei, Z. 2024-09-24 doi:10.1101/2024.09.20.614141 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity ]]> https://biorxiv.org/content/10.1101/2024.09.20.614172v1?rss=1 Tarbox, H. E. Branch, A. Fried, S. D. 2024-09-24 doi:10.1101/2024.09.20.614172 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ What has AlphaFold3 learned about antibody and nanobody docking, and what remains unsolved? ]]> https://biorxiv.org/content/10.1101/2024.09.21.614257v1?rss=1 Hitawala, F. N. Gray, J. J. 2024-09-24 doi:10.1101/2024.09.21.614257 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Naturally occurring variation in a cytochrome P450 modifies thiabendazole responses independent of beta-tubulin ]]> https://biorxiv.org/content/10.1101/2024.09.23.614411v1?rss=1 Collins, J. Dilks, C. M. Hahnel, S. R. Rodriguez, B. Fox, B. W. Redman, E. Yu, J. Cooke, B. Sihuta, K. Zamanian, M. Roy, P. J. Schroeder, F. C. Gilleard, J. S. Andersen, E. C. 2024-09-24 doi:10.1101/2024.09.23.614411 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets ]]> https://biorxiv.org/content/10.1101/2024.09.23.614419v1?rss=1 Papaiakovou, M. Waeschenbach, A. Ajibola, O. Ajjampur, S. S. Anderson, R. M. Bailey, R. Benjamin Chung, J. Cambra Pelleja, M. Caro, N. R. Chaima, D. Cimino, R. O. Cools, P. Cossa, A. Dunn, J. Galagan, S. Gandasegui, J. Grau Pujol, B. Houlder, E. Ibikounle, M. Jenkins, T. P. Kalua, K. Kjetland, E. F. Krolewiecki, A. J. Levecke, B. Luty, A. J. MacDonald, A. Mandomando, I. Manuel, M. Martinez Valladares, M. Mejia, R. Mekonnen, Z. Messa, A. Mpairwe, H. Muchisse, O. Munoz, J. Mwinzi, P. Novela, V. Odiere, M. R. Sacoor, C. Walson, J. L. Williams, S. A. Witek 2024-09-24 doi:10.1101/2024.09.23.614419 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues ]]> https://biorxiv.org/content/10.1101/2024.09.24.614640v1?rss=1 Asami, S. Yin, C. Garza, L. A. Kalhor, R. 2024-09-24 doi:10.1101/2024.09.24.614640 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Why do we have so many excitatory neurons? ]]> https://biorxiv.org/content/10.1101/2024.09.24.614724v1?rss=1 Wang, Q. Cardona, A. Zlatic, M. Vogelstein, J. Priebe, C. 2024-09-24 doi:10.1101/2024.09.24.614724 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Targeting CCRL2 enhances therapeutic outcomes in a tuberculosis mouse model ]]> https://biorxiv.org/content/10.1101/2024.09.23.614576v1?rss=1 Wang, T. Quijada, D. Ahmenda, T. Castillo, J. R. Naji, N. S. Peske, J. D. Karakousis, P. C. Paul, S. Karantanos, T. Karanika, S. 2024-09-25 doi:10.1101/2024.09.23.614576 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ A genetically encoded fluorescent sensor enables sensitive and specific detection of IDH mutant associated oncometabolite D-2-hydroxyglutarate ]]> https://biorxiv.org/content/10.1101/2024.09.25.615072v1?rss=1 Choate, K. A. Konickson, W. W. L. Jennings, M. J. Mann, P. B. Winn, R. J. Kamson, D. O. Pratt, E. P. S. 2024-09-27 doi:10.1101/2024.09.25.615072 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Gestational arsenite exposure alters maternal postpartum heart size and induces Ca2+ handling dysregulation in cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2024.09.25.615085v1?rss=1 Taube, N. Steiner, M. Ebenebe-Kasonde, O. V. Kabir, R. Garbus-Grant, H. Alam El Din, S.-M. Illingworth, E. Wang, N. Lin, B. L. Kohr, M. J. 2024-09-27 doi:10.1101/2024.09.25.615085 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Intranasal therapies for neonatal hypoxic-ischemic encephalopathy: Systematic review, synthesis, and implications for global accessibility to care ]]> https://biorxiv.org/content/10.1101/2024.09.26.615156v1?rss=1 Cavanagh, A. S. Kuter, N. Sollinger, B. I. Aziz, K. Turnbill, V. Martin, L. J. Northington, F. J. 2024-09-27 doi:10.1101/2024.09.26.615156 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ HuBMAPR: an R Client for the HuBMAP Data Portal ]]> https://biorxiv.org/content/10.1101/2024.09.26.615227v1?rss=1 Hou, C. Ghazanfar, S. Marini, F. Morgan, M. Hicks, S. C. 2024-09-27 doi:10.1101/2024.09.26.615227 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Unified Sampling and Ranking for Protein Docking with DFMDock ]]> https://biorxiv.org/content/10.1101/2024.09.27.615401v1?rss=1 Chu, L.-S. Sarma, S. Gray, J. J. 2024-09-28 doi:10.1101/2024.09.27.615401 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ A Water Relaxation Atlas for Age and Region specific Metabolite Concentration Correction ]]> https://biorxiv.org/content/10.1101/2024.09.27.615424v1?rss=1 Simegn, G. L. Song, y. Murali-Manohar, S. Zollner, H. J. Davies-Jenkins, C. W. Simicic, D. Hupfeld, K. E. Gudmundson, A. T. Musaka, E. Carter, E. Hui, S. C. N. Yedavalli, V. Oeltzschner, G. C. N. Dean, D. C. Ceritoglu, C. Ratnanather, T. Porges, E. Edden, R. 2024-09-30 doi:10.1101/2024.09.27.615424 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Endosomal hyper-acidification via proton-activated chloride channel deletion in neurons impairs AMPA receptor endocytosis and LTD ]]> https://biorxiv.org/content/10.1101/2024.09.27.615471v1?rss=1 Chen, K. Yang, J. Liu, B. Jiang, C. Koylass, N. Zhang, Z. Sun, S. Huganir, R. L. Qiu, Z. 2024-09-30 doi:10.1101/2024.09.27.615471 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors ]]> https://biorxiv.org/content/10.1101/2024.09.28.615606v1?rss=1 Singh, U. S. Harbach, R. E. Hii, J. Chang, M. S. Somboon, P. Prakash, A. Sarma, D. Broomfield, B. Morgan, K. Albert, S. Das, A. Linton, Y.-M. Carlton, J. M. Walton, C. 2024-09-30 doi:10.1101/2024.09.28.615606 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden ]]> https://biorxiv.org/content/10.1101/2024.09.30.615839v1?rss=1 Camacho, E. Dong, Y. Chrissian, C. Cordero, R. J. Saraiva, R. G. Anglero-Rodriguez, Y. Smith, D. F. Q. Jacobs, E. Hartshorn, I. Patino-Medina, J. A. DePasquale, M. Dziedzic, A. Jedlicka, A. Smith, B. Mlambo, G. Tripathi, A. Broderick, N. A. Stark, R. E. Dimopoulos, G. Casadevall, A. 2024-09-30 doi:10.1101/2024.09.30.615839 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Iterative sacrificial 3D printing and polymer casting to create complex vascular grafts and multi-compartment bioartificial organs ]]> https://biorxiv.org/content/10.1101/2024.09.29.615298v1?rss=1 Brassard, J. A. Sidharthan, S. D. Orimi, H. E. Vdovenko, D. Rioux, Y. Wang, H. Champion, K. Lemaire, F. Moeun, B. N. Zhao, J. Liang, S. Kieffer, T. J. Tchervenkov, J. I. Soulez, G. Begin-Drolet, A. Ruel, J. Leask, R. L. Paraskevas, S. Hoesli, C. A. 2024-10-01 doi:10.1101/2024.09.29.615298 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells ]]> https://biorxiv.org/content/10.1101/2024.09.29.615728v1?rss=1 Sarabipour, S. Kinghorn, K. Quigley, K. M. Kovacs-Kasa, A. Annex, B. H. Bautch, V. L. Mac Gabhann, F. 2024-10-01 doi:10.1101/2024.09.29.615728 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Branched actin polymerization drives invasive protrusion formation to promote myoblast fusion during skeletal muscle regeneration ]]> https://biorxiv.org/content/10.1101/2024.09.30.615960v1?rss=1 Lu, Y. Walji, T. Pandey, P. Zhou, C. Habela, C. W. Snapper, S. Li, R. Chen, E. 2024-10-01 doi:10.1101/2024.09.30.615960 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and Ca2+ ]]> https://biorxiv.org/content/10.1101/2024.09.30.615856v1?rss=1 Tsai, S.-J. Gong, Y. Dabbs, A. Zahra, F. Xu, J. Geske, A. Caterina, M. J. Gould, S. J. 2024-10-02 doi:10.1101/2024.09.30.615856 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Age dependency of neurometabolite T1 relaxation times ]]> https://biorxiv.org/content/10.1101/2024.09.30.615917v1?rss=1 Murali-Manohar, S. Zoellner, H. J. Hupfeld, K. E. Song, Y. Carter, E. E. Yedavalli, V. Hui, S. C. N. Simicic, D. Gudmundson, A. T. Simegn, G. L. Davies-Jenkins, C. W. Oeltzschner, G. Porges, E. C. Edden, R. A. E. 2024-10-02 doi:10.1101/2024.09.30.615917 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ MORC-1 is a key component of the C. elegans CSR-1 germline gene licensing mechanism ]]> https://biorxiv.org/content/10.1101/2024.10.02.616347v1?rss=1 Kirshner, J. A. Picard, C. L. Weiser, N. E. Mehta, N. Feng, S. Murphy, V. N. Vakhnovetsky, A. Alessi, A. F. Xiao, C. Inoki, K. El Mouridi, S. Frokjaer-Jensen, C. Jacobsen, S. E. Kim, J. K. 2024-10-02 doi:10.1101/2024.10.02.616347 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain ]]> https://biorxiv.org/content/10.1101/2024.10.01.616090v1?rss=1 Khatib, L. Song, S. J. Dilmore, A. H. Sanders, J. G. Brennan, C. Hernandez, A. R. Myers, T. Oles, R. Farmer, S. Cowart, C. Birmingham, A. Diaz, E. A. Nizet, O. Gilbert, K. Litwin, N. Das, P. Nowinski, B. Bryant, M. Tribelhorn, C. Sanders-Bodai, K. Chaumont, S. Knol, J. Roeselers, G. Laiola, M. Shetty, S. A. Veiga, P. Tap, J. Derrien, M. Koutnikova, H. Cotillard, A. Lay, C. Tovar, A. R. Torres, N. Arteaga, L. Gonzalez, A. McDonald, D. Bartko, A. Knight, R. 2024-10-03 doi:10.1101/2024.10.01.616090 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Reconstructing the deep phylogeny of the MAPK signaling network: functional specialization via multi-tier coevolutionary expansion ]]> https://biorxiv.org/content/10.1101/2024.10.01.616093v1?rss=1 Huang, E. Parksong, J. Peterson, A. F. Torres, F. Regot, S. Bever, G. S. 2024-10-03 doi:10.1101/2024.10.01.616093 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ An inducible and reversible system to regulate unsaturated fatty acid biosynthesis in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.10.01.616130v1?rss=1 Battista, B. Hernandez-Cravero, B. Colaiacovo, M. P. Cochella, L. Binolfi, A. de Mendoza, D. 2024-10-03 doi:10.1101/2024.10.01.616130 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Fully Hyperbolic Neural Networks: A Novel Approach to Studying Aging Trajectories ]]> https://biorxiv.org/content/10.1101/2024.10.01.616153v1?rss=1 Ramirez, H. Tabarelli, D. Brancaccio, A. Belardinelli, P. Marsh, E. B. Funke, M. Mosher, J. Maestu, F. Xu, M. Pantazis, D. 2024-10-03 doi:10.1101/2024.10.01.616153 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Machine learning sparse reaction-diffusion models from stochastic dynamics and spatiotemporal patterns ]]> https://biorxiv.org/content/10.1101/2024.10.02.616367v1?rss=1 Abubaker-Sharif, B. Devreotes, P. N. Iglesias, P. A. 2024-10-03 doi:10.1101/2024.10.02.616367 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Female-germline specific protein Sakura interacts with Otu and is crucial for germline stem cell renewal and differentiation and oogenesis ]]> https://biorxiv.org/content/10.1101/2024.10.04.616675v1?rss=1 Azlan, A. Zhu, L. Fukunaga, R. 2024-10-04 doi:10.1101/2024.10.04.616675 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Separate timescales for spatial and anatomical information processing during action observation ]]> https://biorxiv.org/content/10.1101/2024.10.07.616993v1?rss=1 Baptiste, W. M. McAteer, S. Moreno-Verdu, M. Van Caenegem, E. E. Du, Y. Hardwick, R. M. 2024-10-07 doi:10.1101/2024.10.07.616993 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Geometry-induced competitive release in a meta-population model of range expansions in disordered environments ]]> https://biorxiv.org/content/10.1101/2024.10.07.614155v1?rss=1 Nunez, J. G. Beller, D. A. 2024-10-08 doi:10.1101/2024.10.07.614155 Cold Spring Harbor Laboratory Press 2024-10-08 <![CDATA[ Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restriction. ]]> https://biorxiv.org/content/10.1101/2024.10.07.617070v1?rss=1 Grace, P. S. Peters, J. M. Sixsmith, J. Lu, R. Fenderson, B. A. Vickers, A. Slein, M. D. Irvine, E. B. McKitrick, T. Wei, M.-H. Cummings, R. D. Wallace, A. Cavacini, L. Choudhary, A. K. Proulx, M. K. Sundling, C. Källenius, G. Reljic, R. Ernst, J. D. Casadevall, A. Locht, C. Pinter, A. Sassetti, C. M. Bryson, B. D. Fortune, S. M. Alter, G. 2024-10-11 doi:10.1101/2024.10.07.617070 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Odorant receptors tuned to isothiocyanates in Drosophila melanogaster and their evolutionary expansion in herbivorous relatives ]]> https://biorxiv.org/content/10.1101/2024.10.08.617316v1?rss=1 Matsunaga, T. Reisenman, C. E. Goldman-Huertas, B. M. Rajshekar, S. Suzuki, H. C. Tadres, D. Wong, J. Louis, M. Ramirez, S. R. Whiteman, N. K. 2024-10-11 doi:10.1101/2024.10.08.617316 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ CREB3 gain of function variants protect against ALS ]]> https://biorxiv.org/content/10.1101/2024.10.10.617542v1?rss=1 Megat, S. Marques, C. Hernan Godoy, M. Sellier, C. Stuart-Lopez, G. Dirrig-Grosch, S. Gorin, C. Brunet, A. Fischer, M. Keime, C. Kessler, P. Mendoza-Parra, M. A. Scholz, S. W. Ferrucci, L. Ludolph, A. Traynor, B. Chio, A. Dupuis, L. Rouaux, C. 2024-10-11 doi:10.1101/2024.10.10.617542 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization ]]> https://biorxiv.org/content/10.1101/2024.10.08.617296v1?rss=1 Vinayak, V. Basir, R. Golloshi, R. Toth, J. M. Sant'Anna, L. Lakadamyali, M. McCord, R. P. Shenoy, V. 2024-10-12 doi:10.1101/2024.10.08.617296 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Expectation generation and its effect on subsequent pain and visual perception ]]> https://biorxiv.org/content/10.1101/2024.10.10.617570v1?rss=1 Botvinik-Nezer, R. Geuter, S. Lindquist, M. A. Wager, T. D. 2024-10-12 doi:10.1101/2024.10.10.617570 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Sex-specific effects of intensity and dose of physical activity on BOLD-fMRI cerebrovascular reactivity and cerebral pulsatility ]]> https://biorxiv.org/content/10.1101/2024.10.10.617666v1?rss=1 Potvin-Jutras, Z. Intzandt, B. Mohammadi, H. Liu, P. Chen, J. J. Gauthier, C. J. 2024-10-12 doi:10.1101/2024.10.10.617666 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Light modulates glucose and lipid homeostasis via the sympathetic nervous system ]]> https://biorxiv.org/content/10.1101/2024.10.11.617839v1?rss=1 Chen, X. Lin, E. Haghighatian, M. Shepard, L. W. Hattar, S. Kuruvilla, R. Zhao, H. 2024-10-12 doi:10.1101/2024.10.11.617839 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Bond-centric modular design of protein assemblies ]]> https://biorxiv.org/content/10.1101/2024.10.11.617872v1?rss=1 Wang, S. Favor, A. Kibler, R. D. Lubner, J. M. Borst, A. J. Coudray, N. Redler, R. Chiang, H. T. Sheffler, W. Hsia, Y. Li, Z. Ekiert, D. C. Bhabha, G. Pozzo, L. D. Baker, D. 2024-10-12 doi:10.1101/2024.10.11.617872 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ DeepPaint: A deep-learning package for Cell Painting Image Classification ]]> https://biorxiv.org/content/10.1101/2024.10.08.617198v1?rss=1 Luna, D. Johnson, E. Dunphy, L. McQuillen, R. J. 2024-10-13 doi:10.1101/2024.10.08.617198 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Fentanyl reinforcement history has sex-specific effects on multi-step decision-making ]]> https://biorxiv.org/content/10.1101/2024.10.10.617707v1?rss=1 Garr, E. Cheng, Y. Castell, L. Dong, A. Shuai, C. Wang, Y. Min, J. Camhi, Z. Nay, A. Malloy, N. Janak, P. H. 2024-10-14 doi:10.1101/2024.10.10.617707 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Light-guided actin polymerization drives directed motility in protocells ]]> https://biorxiv.org/content/10.1101/2024.10.14.617543v1?rss=1 Matsubayashi, H. T. Razavi, S. Rock, T. W. Nakajima, D. Nakamura, H. Kramer, D. A. Matsuura, T. Chen, B. Murata, S. Nomura, S.-i. M. Inoue, T. 2024-10-15 doi:10.1101/2024.10.14.617543 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ A human high-fidelity DNA polymerase holoenzyme has a wide range of lesion bypass activities ]]> https://biorxiv.org/content/10.1101/2024.10.14.618244v1?rss=1 Dannenberg, R. L. Cardina, J. A. Washington, H. Gao, S. Greenberg, M. M. Hedglin, M. 2024-10-17 doi:10.1101/2024.10.14.618244 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Illumination mediates a switch in both active sensing and control in weakly electric fish ]]> https://biorxiv.org/content/10.1101/2024.10.15.618597v1?rss=1 Yeh, H. Yang, Y. Biswas, D. Cowan, N. J. 2024-10-17 doi:10.1101/2024.10.15.618597 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Role of dopamine in reward expectation and predictability during execution of action sequences ]]> https://biorxiv.org/content/10.1101/2024.10.16.618735v1?rss=1 Magnard, R. Cheng, Y. Zhou, J. Province, H. Thiriet, N. Janak, P. H. Vandaele, Y. 2024-10-17 doi:10.1101/2024.10.16.618735 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Uncovering locomotor learning dynamics in people with Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2024.10.17.618863v1?rss=1 Kim, A. Schweighofer, N. Petzinger, G. M. Finley, J. M. 2024-10-17 doi:10.1101/2024.10.17.618863 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Chromatin Buffers Torsional Stress During Transcription ]]> https://biorxiv.org/content/10.1101/2024.10.15.618270v1?rss=1 Qian, J. Lubkowska, L. Zhang, S. Tan, C. Hong, Y. Fulbright, R. M. Inman, J. T. Kay, T. M. Jeong, J. Gotte, D. Berger, J. M. Kashlev, M. Wang, M. D. 2024-10-18 doi:10.1101/2024.10.15.618270 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Human Topoisomerase IIα Promotes Chromatin Condensation Via a Phase Transition ]]> https://biorxiv.org/content/10.1101/2024.10.15.618281v1?rss=1 Wu, M. Beck, C. Lee, J. H. Fulbright, R. M. Jeong, J. Inman, J. T. Woodhouse, M. V. Berger, J. M. Wang, M. D. 2024-10-18 doi:10.1101/2024.10.15.618281 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Why do bats fly into cave doors? Inattentional blindness in echolocating animals ]]> https://biorxiv.org/content/10.1101/2024.10.16.618711v1?rss=1 Finger, N. M. Eveland, K. E. Yin, X. Moss, C. F. 2024-10-18 doi:10.1101/2024.10.16.618711 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Divergent and Convergent TMEM106B Pathology in Murine Models of Neurodegeneration and Human Disease ]]> https://biorxiv.org/content/10.1101/2024.10.16.618765v1?rss=1 Du, M. Akerman, S. C. Fare, C. Ruan, L. Vidensky, S. Mamedova, L. Lee, J. Rothstein, J. D. D. 2024-10-18 doi:10.1101/2024.10.16.618765 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Glioblastoma Treatment by Systemic Actinium-225 alpha-particle Dendrimer-radioconjugates is Improved by Chemotherapy ]]> https://biorxiv.org/content/10.1101/2024.10.17.618960v1?rss=1 Nair, R. R. Sarkar, A. Hariharan, P. Gabrielson, K. L. Wu, T. Liu, C. Sharma, A. Liyanage, W. Bhujwalla, Z. M. Vidaver, M.-F. P. Kannan, R. M. Sofou, S. 2024-10-19 doi:10.1101/2024.10.17.618960 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ TRIM24 directs replicative stress responses to maintain ALT telomeres via chromatin signaling ]]> https://biorxiv.org/content/10.1101/2024.10.18.618947v1?rss=1 Kim, D. Bhargava, R. Wang, S.-C. Lee, D. Patel, R. Oh, S. Bowman, R. W. Na, C. H. O'Sullivan, R. J. Miller, K. M. 2024-10-19 doi:10.1101/2024.10.18.618947 Cold Spring Harbor Laboratory Press 2024-10-19 <![CDATA[ Cannabidiol (CBD) potentiates physiological and behavioral markers of hypothalamic-pituitary-adrenal (HPA) axis responsivity in female and male mice ]]> https://biorxiv.org/content/10.1101/2024.10.17.618869v1?rss=1 Jenkins, B. W. Spina, H. A. Nicholson, K. Newman, A. E. M. Khokhar, J. Y. 2024-10-21 doi:10.1101/2024.10.17.618869 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ ZNFX1 is a Novel Master Regulator in Epigenetically-induced Pathogen Mimicry and Inflammasome Signaling in Cancer ]]> https://biorxiv.org/content/10.1101/2024.10.18.618659v1?rss=1 Stojanovic, L. Abbotts, R. Tripathi, K. Coon, C. M. Rajendran, S. Abbasi Farid, E. Hostetter, G. Guarnieri, J. W. Wallace, D. C. Liu, S. Wan, J. Calendo, G. Marker, R. Gohari, Z. Inayatullah, M. M. A. Tiwari, V. K. Kader, T. Santagata, S. Drapkin, R. Kommoss, S. Pfisterer, J. Konecny, G. E. Coopergard, R. Issa, J.-P. Winterhoff, B. J. N. Topper, M. J. Sandusky, G. E. Miller, K. D. Baylin, S. B. Nephew, K. P. Rassool, F. V. 2024-10-21 doi:10.1101/2024.10.18.618659 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Neural and behavioral reinstatement jointly reflect retrieval of narrative events ]]> https://biorxiv.org/content/10.1101/2024.10.19.619187v1?rss=1 Nau, M. Greene, A. Tarder-Stoll, H. Lossio-Ventura, J. A. Pereira, F. Chen, J. Baldassano, C. Baker, C. 2024-10-21 doi:10.1101/2024.10.19.619187 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Inter-laboratory harmonization of microsphere immunoassays for SARS-CoV-2 antibody detection in dried blood spots and oral fluids ]]> https://biorxiv.org/content/10.1101/2024.10.19.619238v1?rss=1 DeRosa, K. L. Pisanic, N. Kruczynski, K. Heaney, C. D. Styer, L. M. MANTIS, N. J. 2024-10-22 doi:10.1101/2024.10.19.619238 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Mitochondrial fission controls astrocyte morphogenesis and organization in the cortex ]]> https://biorxiv.org/content/10.1101/2024.10.22.619706v1?rss=1 Salazar, M. P. R. Kolanukuduru, S. Ramirez, V. Lyu, B. Sejourne, G. Sesaki, H. Yu, G. Eroglu, C. 2024-10-23 doi:10.1101/2024.10.22.619706 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Sex-biased effect of sodium leak channel NALCN deletion in striatal Drd2 spiny projection neurons ]]> https://biorxiv.org/content/10.1101/2024.10.23.619832v1?rss=1 Castell, L. Naon, C. Rogliardo, A. Makrini, L. Avrillon, M. Mignon, A. Bernat, C. Lory, P. Bertaso, F. Monteil, A. Bosch-Bouju, C. Valjent, E. 2024-10-23 doi:10.1101/2024.10.23.619832 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ α-Synuclein Strain Dynamics Correlate with Cognitive Shifts in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.10.22.619694v1?rss=1 Gadhave, K. Xu, E. Wang, N. Zhang, X. Deyell, J. Yang, J. Wang, A. Cha, Y. Kumbhar, R. Liu, H. Niu, L. Chen, R. Zhang, S. Bakker, C. Jin, L. Liang, Y. Ying, M. Dawson, V. L. Dawson, T. M. Rosenthal, L. S. Mao, X. 2024-10-24 doi:10.1101/2024.10.22.619694 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Epigenetic control of Topoisomerase 1 activity presents a cancer vulnerability ]]> https://biorxiv.org/content/10.1101/2024.10.22.619113v1?rss=1 Lee, T. Qiao, C. X. Kuzin, V. Shi, Y. Ramanaranayan, V. Wu, T. Zhou, X. Corujo, D. Buschbeck, M. Baranello, L. Oberdoerffer, P. 2024-10-25 doi:10.1101/2024.10.22.619113 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ CRB2 Depletion Induces YAP Signaling and Disrupts Mechanosensing in Podocytes ]]> https://biorxiv.org/content/10.1101/2024.10.22.619513v1?rss=1 Sun, Y. Kronenberg, N. M. Sethi, S. K. Dash, S. N. Kovalik, M. E. Sempowski, B. Strickland, S. Raina, R. Sperati, C. J. Tian, X. Ishibe, S. Hall, G. Gather, M. C. 2024-10-25 doi:10.1101/2024.10.22.619513 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Automated segmentation of synchrotron-scanned fossils ]]> https://biorxiv.org/content/10.1101/2024.10.23.619778v1?rss=1 During, M. A. D. Matelsky, J. K. Gustafsson, F. K. Voeten, D. F. A. E. Chen, D. Wester, B. A. Kording, K. P. Ahlberg, P. E. Schön, T. B. 2024-10-25 doi:10.1101/2024.10.23.619778 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ A high throughput single molecule platform to study DNA supercoiling effect on protein-DNA interactions ]]> https://biorxiv.org/content/10.1101/2024.10.24.620099v1?rss=1 Lee, H. Hwang, J. Rashid, F. London, J. A. Fishel, R. Berger, J. M. Myong, S. Ha, T. 2024-10-25 doi:10.1101/2024.10.24.620099 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Single-Cell Proteomic and Transcriptomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes ]]> https://biorxiv.org/content/10.1101/2024.10.23.619905v1?rss=1 Woo, J. Loycano, M. Amanullah, M. Qian, J. Amend, S. Pienta, K. Zhang, h. 2024-10-28 doi:10.1101/2024.10.23.619905 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.10.27.620437v1?rss=1 Jank, L. Singh, S. S. Lee, J. Dhukhwa, A. Siavoshi, F. Joshi, D. Minney, V. Gupta, K. Ghimire, S. Deme, P. Schoeps, V. A. Soman, K. Ladakis, D. Smith, M. Borkowski, K. Newman, J. Baranzini, S. E. Waubant, E. L. Fitzgerald, K. C. Mangalam, A. K. Haughey, N. Kornberg, M. D. Chamling, X. Calabresi, P. A. Bhargava, P. 2024-10-28 doi:10.1101/2024.10.27.620437 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Transcriptional profiles of murine oligodendrocyte precursor cells across the lifespan ]]> https://biorxiv.org/content/10.1101/2024.10.27.620502v1?rss=1 Heo, D. Kim, A. A. Neumann, B. Doze, V. N. Xu, Y. K. T. Mironova, Y. A. Slosberg, J. Goff, L. A. Franklin, R. J. M. Bergles, D. E. 2024-10-28 doi:10.1101/2024.10.27.620502 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency ]]> https://biorxiv.org/content/10.1101/2024.10.26.620318v1?rss=1 Koehnke, T. Karigane, D. Hilgart, E. Fan, A. C. Kayamori, K. Miyauchi, M. Collins, C. T. Suchy, F. P. Rangavajhula, A. Feng, Y. Nakauchi, Y. Martinez-Montes, E. Fowler, J. Loh, K. M. Nakauchi, H. Koldobskiy, M. A. Feinberg, A. P. Majeti, R. 2024-10-29 doi:10.1101/2024.10.26.620318 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation ]]> https://biorxiv.org/content/10.1101/2024.10.26.620414v1?rss=1 Feinberg, A. P. Lo, E. K. Idrizi, A. Tryggvadottir, R. Zhou, W. Hou, W. Ji, H. Cahan, P. 2024-10-29 doi:10.1101/2024.10.26.620414 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML ]]> https://biorxiv.org/content/10.1101/2024.10.26.620422v1?rss=1 Hilgart, E. Zhou, W. Martinez-Montes, E. Idrizi, A. Tryggvadottir, R. Gondek, L. P. Majeti, R. Ji, H. Koldobskiy, M. Feinberg, A. P. 2024-10-29 doi:10.1101/2024.10.26.620422 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Exploring the adhesion properties of extracellular vesicles for functional assays ]]> https://biorxiv.org/content/10.1101/2024.10.28.620659v1?rss=1 Pachane, B. C. Carlson, B. Queen, S. Selistre-de-Araujo, H. S. Witwer, K. W. 2024-10-30 doi:10.1101/2024.10.28.620659 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Sensitivity of Cerebellar Reaching Ataxia to Kinematic and Dynamic Demands ]]> https://biorxiv.org/content/10.1101/2024.10.28.620711v1?rss=1 Oh, K. Cao, D. Cowan, N. Bastian, A. J. 2024-10-30 doi:10.1101/2024.10.28.620711 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment ]]> https://biorxiv.org/content/10.1101/2024.11.01.621152v1?rss=1 Tolman, N. Li, T. Balasubramanian, R. Li, G. Bupp-Chickering, V. Kelly, R. A. Simon, M. Peregrin, J. Montgomery, C. Stamer, W. D. Qian, J. John, S. W. M. 2024-11-01 doi:10.1101/2024.11.01.621152 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ New Insights Into The Melanin Structure Of Lomentospora prolificans ]]> https://biorxiv.org/content/10.1101/2024.11.01.621558v1?rss=1 Liporagi Lopes, L. Chrissian, C. Kacirani, A. Camacho, E. Stark, R. E. Casadevall, A. 2024-11-01 doi:10.1101/2024.11.01.621558 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Improved pangenomic classification accuracy with chain statistics ]]> https://biorxiv.org/content/10.1101/2024.10.29.620953v1?rss=1 Brown, N. K. Shivakumar, V. S. Langmead, B. 2024-11-02 doi:10.1101/2024.10.29.620953 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ GeneCover: A Combinatorial Approach for Label-free Marker Gene Selection ]]> https://biorxiv.org/content/10.1101/2024.10.30.621151v1?rss=1 Wang, A. Hicks, S. C. Geman, D. Younes, L. 2024-11-03 doi:10.1101/2024.10.30.621151 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Inhibition of Yes-Associated Protein (YAP) with Verteporfin Enhances Radiosensitivity in Chordoma by Inducing G2M Arrest and Inhibiting the DNA Damage Response ]]> https://biorxiv.org/content/10.1101/2024.11.03.621728v1?rss=1 Akinduro, O. O. Meade, P. S. Schiapparelli, P. Whitehead, R. Tzeng, S. Y. Rosenfeld, S. S. Kim, S. Palena, C. Gokaslan, Z. L. Green, J. J. Hinojosa, A. Q. 2024-11-04 doi:10.1101/2024.11.03.621728 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ A consensus definition for deep layer 6 excitatory neurons in mouse neocortex ]]> https://biorxiv.org/content/10.1101/2024.11.04.621933v1?rss=1 Kim, S.-J. Babola, T. A. Lee, K. Matney, C. J. Spiegel, A. C. Liew, M. H. Schulteis, E. M. Coye, A. E. Proskurin, M. Kang, H. Kim, J. A. Chevee, M. Lee, K. Kanold, P. O. Goff, L. A. Kim, J. Brown, S. P. 2024-11-05 doi:10.1101/2024.11.04.621933 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ xIV-LDDMM Toolkit: A Suite of Image-Varifold Based Technologies for Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales ]]> https://biorxiv.org/content/10.1101/2024.11.04.621983v1?rss=1 Stouffer, K. Chen, X. Zeng, H. Charlier, B. Younes, L. Trouve, A. Miller, M. I. 2024-11-05 doi:10.1101/2024.11.04.621983 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Electrical Coordinated Reset Stimulation Induces Network Desynchronization in an in Vivo Model of Status Epilepticus ]]> https://biorxiv.org/content/10.1101/2024.11.06.621943v1?rss=1 Ehrens, D. Aeed, F. Otor, Y. Charu, V. Razavi, B. Sarma, S. V. Schiller, Y. Tass, P. A. 2024-11-07 doi:10.1101/2024.11.06.621943 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ TIA1 Mediates Divergent Inflammatory Responses to Tauopathy in Microglia and Macrophages ]]> https://biorxiv.org/content/10.1101/2024.11.06.622325v1?rss=1 Webber, C. J. Van Der Spek, S. Cruz, A. L. F. Puri, S. Zhang, C. Aw, J. T. M. Papadimitriou, G.-Z. Roberts, R. Jiang, K. Tran, T. N. Zhang, L. Taylor, A. K. Wang, Z. Porter, J. Sotiropoulos, I. Emili, A. Silva, J. M. Li, H. Wolozin, B. 2024-11-07 doi:10.1101/2024.11.06.622325 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination ]]> https://biorxiv.org/content/10.1101/2024.11.07.622519v1?rss=1 Deveryshetty, J. Mistry, A. Pangeni, S. Ghoneim, M. Tokmina, M. Kaushik, V. Taddei, A. Ha, T. Bothner, B. Antony, E. 2024-11-07 doi:10.1101/2024.11.07.622519 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Sticky enzymes: increased metabolic efficiency via substrate-dependent enzyme clustering ]]> https://biorxiv.org/content/10.1101/2024.11.05.622105v1?rss=1 Martinez-Calvo, A. Zhou, J. Zhang, Y. Wingreen, N. S. 2024-11-08 doi:10.1101/2024.11.05.622105 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ A consensus variant-to-function score to functionally prioritize variants for disease ]]> https://biorxiv.org/content/10.1101/2024.11.07.622307v1?rss=1 0.95) variants than non-functionally informed fine-mapping. We further constructed tissue/cell line-specific cV2F scores that prioritize variants based on regulatory potential in specific tissues/cell lines, attaining high heritability enrichment for tissue-related diseases/traits (15.6x, s.e. 2.3) while providing independent information (average correlation of 0.27 with the primary cV2F score). We highlight examples of GWAS loci for which cV2F pinpoints causal variants with high confidence and elucidates their functional role. ]]> Fabiha, T. Raine, I. Kundu, S. Pampari, A. Abramov, S. Boytsov, A. Strouse, K. Dura, K. Fang, W. Kerner, G. Butts, J. Ali, T. Gschwind, A. Mualim, K. S. Moore, J. E. Weng, Z. Ulirsch, J. Ji, H. E. Vierstra, J. Reddy, T. E. Montgomery, S. B. Engreitz, J. Kundaje, A. Tewhey, R. Price, A. Dey, K. 2024-11-09 doi:10.1101/2024.11.07.622307 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Commonalities and differences in the Cryptococcus neoformans response to ingestion by protozoal and mammalian phagocytic cells suggests host cell metabolism as a target for intracellular survival ]]> https://biorxiv.org/content/10.1101/2024.11.08.622732v1?rss=1 Dragotakes, Q. Jacobs, E. Gerbig, G. Greengo, S. Jedlicka, A. Dziedzic, A. Casadevall, A. 2024-11-09 doi:10.1101/2024.11.08.622732 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ MOSAIC: A Pipeline for MicrobiOme Studies Analytical Integration and Correction ]]> https://biorxiv.org/content/10.1101/2024.11.07.622561v1?rss=1 Fu, C. Lu, J. Zhao, N. Ling, W. 2024-11-11 doi:10.1101/2024.11.07.622561 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS ]]> https://biorxiv.org/content/10.1101/2024.11.08.622670v1?rss=1 15 months) survival at single-cell resolution. Long-term survivors showed a significant reduction of immunosuppressive monocytes, and an expansion of effector lymphocytes after combination therapy. Further immune profiling suggests that gamma delta T cell activation through primed dendritic cells was associated with global interferon activation in the bone marrow microenvironment of long-term survivors. Short-term survivors exhibited elevated inflammation and senescence-like gene signatures that were not resolved by combination therapy. We propose that distinct bone marrow microenvironment features, such as senescence-associated inflammation or immunosuppressive monocyte presence, could improve patient stratification for HMA and immunotherapy combinations in HMA-R/R MDS patients. ]]> Jang, H. J. Urrutia, G. Orskov, A. D. Kim, H. J. Nelson, S. A. Nguyen, A. V. Lee, H. Burgos, R. S. Johnson, B. K. Wegener, M. Becker, K. Adams, M. Sheridan, R. Ramjan, Z. H. Givan, S. A. Zebley, C. C. Youngblood, B. Issa, J.-P. Topper, M. J. Baer, M. R. Baylin, S. B. Triche, T. J. O'Connell, C. L. Gronbaek, K. Jones, P. A. 2024-11-11 doi:10.1101/2024.11.08.622670 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Thermodynamics of Bivalent Heterotrimer Association in the Notch Signaling Pathway ]]> https://biorxiv.org/content/10.1101/2024.11.09.622674v1?rss=1 Cook, C. Ramsey, K. M. Barrick, D. 2024-11-11 doi:10.1101/2024.11.09.622674 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Heterogeneous Effects of Src Inhibition on Determinants of Metastasis in Preclinical Models of Human Bladder Cancer ]]> https://biorxiv.org/content/10.1101/2024.11.09.622804v1?rss=1 Aragaki, K. Wehrenberg, B. Hayashi, Y. McConkey, D. 2024-11-11 doi:10.1101/2024.11.09.622804 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Prenatal Arsenic Exposure and Gene Expression in Fetal Liver, Heart, Lung, and Placenta ]]> https://biorxiv.org/content/10.1101/2024.11.10.622821v1?rss=1 Rychlik, K. A. Kashiwagi, C. M. Liao, J.-S. Mathur, A. Illingworth, E. J. Sanchez, S. S. Kleensang, A. Maertens, A. Sille, F. C. M. 2024-11-11 doi:10.1101/2024.11.10.622821 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures ]]> https://biorxiv.org/content/10.1101/2024.11.11.622992v1?rss=1 Manshour, N. Ren, J. Esmaili, F. Bergstrom, E. Xu, D. 2024-11-11 doi:10.1101/2024.11.11.622992 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation ]]> https://biorxiv.org/content/10.1101/2024.11.12.623260v1?rss=1 Devlin, K. L. Leach, D. T. Stratton, K. G. Lamichhane, G. Lin, V. Beatty, K. E. 2024-11-12 doi:10.1101/2024.11.12.623260 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Sparse matrix factorization of GWAS summary statistics robust to sample sharing improves detection and interpretation of factors with diverse genetic architectures ]]> https://biorxiv.org/content/10.1101/2024.11.12.623313v1?rss=1 Omdahl, A. R. Weinstock, J. S. Keener, R. Chhetri, S. B. Arvanitis, M. Battle, A. 2024-11-14 doi:10.1101/2024.11.12.623313 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ International multi-cohort analysis identifies novel framework for quantifying immune dysregulation in critical illness: results of the SUBSPACE consortium ]]> https://biorxiv.org/content/10.1101/2024.11.12.623298v1?rss=1 Moore, A. R. Zheng, H. Ganesan, A. Hasin-Brumshtein, Y. Maddali, M. V. Levitt, J. E. van der Poll, T. Scicluna, B. Giamarellos-Bourboulis, E. J. Kotsaki, A. Martin-Loeches, I. Garduno, A. Rothman, R. E. Sevransky, J. Wright, D. W. Atreya, M. R. Moldawer, L. L. Efron, P. A. Marcela, K. Karvunidis, T. Giannini, H. M. Meyer, N. J. Sweeney, T. E. Rogers, A. J. Khatri, P. 2024-11-15 doi:10.1101/2024.11.12.623298 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Redefining the spliceosomal introns of the sexually transmitted parasite Trichomonas vaginalis and its close relatives in columbid birds ]]> https://biorxiv.org/content/10.1101/2024.11.13.623467v1?rss=1 Callejas-Hernandez, F. Shiratori, M. Sullivan, S. A. Blow, F. Carlton, J. M. 2024-11-15 doi:10.1101/2024.11.13.623467 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins. ]]> https://biorxiv.org/content/10.1101/2024.11.14.623618v1?rss=1 Kelpsch, D. J. Zhang, L. Thierer, J. H. Koren, K. Kumar, U. Lin, Y. Hensley, M. R. Sohn, M. Liu, J. O. Lectka, T. Mumm, J. S. Farber, S. A. 2024-11-15 doi:10.1101/2024.11.14.623618 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Chromosomal Instability in Human Trophoblast Stem Cells and Placentas ]]> https://biorxiv.org/content/10.1101/2024.11.15.623799v1?rss=1 Wang, D. Cearlock, A. Lane, K. Jan, I. McCoy, R. Yang, M. 2024-11-17 doi:10.1101/2024.11.15.623799 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Quiescent Infections of Elephant Endotheliotropic Herpesviruses and Elephant Gammaherpesviruses in African Elephants in Botswana, Gabon, Kenya, South Africa and USA ]]> https://biorxiv.org/content/10.1101/2024.11.17.624021v1?rss=1 Pearson, V. R. Hayward, G. S. 2024-11-17 doi:10.1101/2024.11.17.624021 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ A proposed framework for evaluating meat alternatives ]]> https://biorxiv.org/content/10.1101/2024.11.18.624184v1?rss=1 Semper, C. Kolta, C. Kinney, M. Giali, J. Rogers, M. Blaustein-Rejto, D. Rowat, A. C. Ogilvie, O. J. Hutmacher, R. Wee, J. Emery, I. Domigan, L. J. Shelke, K. 2024-11-20 doi:10.1101/2024.11.18.624184 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Inhibition of Cardiac p38 Highlights the Role of the Phosphoproteome in Heart Failure Progression ]]> https://biorxiv.org/content/10.1101/2024.11.20.624554v1?rss=1 Sedighi, S. Liu, T. OMeally, R. Cole, R. N. O'Rourke, B. Foster, D. B. 2024-11-20 doi:10.1101/2024.11.20.624554 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Defining the parameters for sorting of different RNA cargo into Extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2024.11.20.624351v1?rss=1 Batish, M. Abdelgawad, A. Huang, Y. Gololobova, O. Yu, Y. Parashar, V. Witwer, K. W. 2024-11-21 doi:10.1101/2024.11.20.624351 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ A deep neural network to de-noise single-cell RNAsequencing data ]]> https://biorxiv.org/content/10.1101/2024.11.20.624552v1?rss=1 Sharifitabar, M. Kazempour, S. Razavian, J. Sajedi, S. Solhjoo, S. Zare, H. 2024-11-21 doi:10.1101/2024.11.20.624552 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ SFPQ-TFE3 gene fusion reciprocally regulates mTORC1 activity and induces lineage plasticity in a novel mouse model of renal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2024.11.21.624702v1?rss=1 Asrani, K. Amaral, A. Woo, J. Abadchi, S. N. Vidotto, T. Feng, K. Liu, H. B. Kasbe, M. Baba, M. Oike, Y. Outeda, P. Watnick, T. Rosenberg, A. Z. Schmidt, L. S. Linehan, M. Argani, P. Lotan, T. L. 2024-11-22 doi:10.1101/2024.11.21.624702 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Cryo-EM Structure of AAA + ATPase Thorase Reveals Novel Helical Filament Formation ]]> https://biorxiv.org/content/10.1101/2024.11.22.624887v1?rss=1 Dar, M. A. Louder, R. Cortes, M. Chen, R. Ma, Q. Chakrabarti, M. Umanah, G. K. Dawson, T. M. Dawson, V. L. 2024-11-22 doi:10.1101/2024.11.22.624887 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Dysregulated airway epithelial antiviral immunity in Down Syndrome impairs type III IFN response and amplifies airway inflammation during RSV infection. ]]> https://biorxiv.org/content/10.1101/2024.11.22.624921v1?rss=1 Chorvinsky, E. Bhattacharya, S. Bera, B. S. Welham, A. L. Hussain Ismat, K. Lawlor, C. M. Preciado, D. Gomez Villalobos, J. Morizono, H. Pillai, D. Gutierrez, M. J. Jaiswal, J. Nino, G. 2024-11-25 doi:10.1101/2024.11.22.624921 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Inflammation in Areas of Fibrosis Precedes Loss of Kidney Function in Lupus Nephritis ]]> https://biorxiv.org/content/10.1101/2024.11.25.625225v1?rss=1 15 ml/min at 3 years from biopsy. Immune cell phenotype was defined by serial immunohistochemistry (13-plex). ResultsIFTA was observed in 88/124 (71%) biopsies, and i-IFTA was identified in 76/88 (86%) cases. The distribution of i-IFTA grades was heterogenous across all IFTA grades. In patients with moderate-to-severe IFTA (>25%), the degree of i-IFTA was associated with a higher risk of significant GFR loss: 0/2 (0%), 1/3 (33%), 3/4 (75%), and 7/9 (78%) for i-IFTA grades 0, 1, 2, and 3, respectively (p = 0.028). Multiplexed histology revealed that i-IFTA was mostly composed of CD163+ macrophages and CD4 T cells, followed by CD8 T cells and granulocytes. ConclusionI-IFTA is frequently observed in LN and is dominated by macrophages and T cells. For patients with baseline IFTA >25%, the degree of i-IFTA emerged as a predictor of GFR loss. These data support the routine scoring of i-IFTA in LN due to its prognostic implications and nominate i-IFTA as a potential therapeutic target. LAY SUMMARYScar tissue often contains immune cells, but we still do not fully understand their role. In lupus nephritis (LN), this is typically dismissed as "nonspecific inflammation". However, our study analyzed kidney biopsies from 124 people with LN and found that inflammation in scarred areas may predict future kidney function loss. Specifically, we identified a type of immune cell, CD163+ macrophages, that may contribute to scarring and kidney damage. Our findings suggest that routinely assessing inflammation in scarred areas could help predict kidney health in LN patients and highlight a possible new target for therapies to prevent kidney damage. ]]> Malvica, S. Fenaroli, P. Lee, C.-Y. Louis, S. Celia, A. I. Bagnasco, S. Yang, X. Hodgin, J. B. Buyon, J. Magder, L. Petri, M. Accelerating Medicines Partnership: RA/SLE Network, Rosenberg, A. Fava, A. 2024-11-26 doi:10.1101/2024.11.25.625225 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ MULTIPLE, REDUNDANT CARBOXYLIC ACID TRANSPORTERS SUPPORT MITOCHONDRIAL METABOLISM IN PLASMODIUM FALCIPARUM ]]> https://biorxiv.org/content/10.1101/2024.11.26.624872v1?rss=1 Prigge, S. T. Llinas, M. Rajaram, K. Nair, S. C. Rangel, G. W. Munro, J. T. 2024-11-26 doi:10.1101/2024.11.26.624872 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Quantifying information stored in synaptic connections rather than in firing patterns of neural networks ]]> https://biorxiv.org/content/10.1101/2024.11.26.625447v1?rss=1 Fan, X. Mysore, S. P. 2024-11-26 doi:10.1101/2024.11.26.625447 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ How sturdy is your memory palace? Reliable room representations predict subsequent reinstatement of placed objects ]]> https://biorxiv.org/content/10.1101/2024.11.26.625465v1?rss=1 Masis-Obando, R. Norman, K. A. Baldassano, C. 2024-11-26 doi:10.1101/2024.11.26.625465 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Changes in interlimb coordination induced by within-stride changes in treadmill speed ]]> https://biorxiv.org/content/10.1101/2024.11.27.625740v1?rss=1 Hall, B. L. Roemmich, R. T. Banks, C. L. 2024-11-27 doi:10.1101/2024.11.27.625740 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification ]]> https://biorxiv.org/content/10.1101/2024.11.27.625726v1?rss=1 Kang, J. Rashid, F. Murray, P. J. Merino-Urteaga, R. Gavrilov, M. Shang, T. Jo, W. Ahmed, A. Aksel, T. Barrick, D. Berger, J. M. Ha, T. 2024-11-29 doi:10.1101/2024.11.27.625726 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Robust characterization of selectivity of individual neurons to distinct task-relevant behavioral states using calcium imaging ]]> https://biorxiv.org/content/10.1101/2024.11.30.626195v1?rss=1 Huang, H. Shah, G. Adwanikar, H. Mysore, S. 2024-12-01 doi:10.1101/2024.11.30.626195 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Identification of a Highly Functional Effector CD8+ T Cell Program After Transplantation in Mice and Humans ]]> https://biorxiv.org/content/10.1101/2024.11.26.625263v1?rss=1 Cohen, G. S. Freibaum, J. S. Leathem, R. P. Hatano, R. Morimoto, C. Krummey, S. M. 2024-12-02 doi:10.1101/2024.11.26.625263 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Approximate Bayesian computation supports a high incidence of chromosomal mosaicism in blastocyst-stage human embryos ]]> https://biorxiv.org/content/10.1101/2024.11.26.625484v1?rss=1 Yang, Q. Carioscia, S. A. Isada, M. McCoy, R. C. 2024-12-02 doi:10.1101/2024.11.26.625484 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Integration of spatial multiplexed protein imaging and transcriptomics in the human kidney tracks the regenerative potential timeline of proximal tubules ]]> https://biorxiv.org/content/10.1101/2024.11.26.625544v1?rss=1 Asghari, M. Sabo, A. R. Barwinska, D. Melo Ferreira, R. Ferkowicz, M. Bowen, W. Cheng, Y. Gisch, D. Gulbronson, C. Phillips, C. L. Kelly, K. J. Sutton, T. A. Williams, J. Vazquez, M. O'Toole, J. Palevsky, P. Rosas, S. Waikar, S. S. Kiryluk, K. Parikh, C. Hodgins, J. Sarder, P. De Boer, I. Himmelfarb, J. Kretzler, M. Kidney Precision Medicine Project, Jain, S. Eadon, M. Winfree, S. El-Achkar, T. M. Dagher, P. C. 2024-12-02 doi:10.1101/2024.11.26.625544 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Study design and the sampling of deleterious rare variants in biobank-scale datasets ]]> https://biorxiv.org/content/10.1101/2024.12.02.626424v1?rss=1 Steiner, M. C. Rice, D. P. Biddanda, A. Ianni-Ravn, M. K. Porras, C. Novembre, J. 2024-12-02 doi:10.1101/2024.12.02.626424 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ A method for authenticating the fidelity of Cryptococcus neoformans knockout collections ]]> https://biorxiv.org/content/10.1101/2024.12.03.626716v1?rss=1 Jacobs, E. Dragotakes, Q. Kulkarni, M. Dziedzic, A. Jedlicka, A. Hardwick, J. M. Casadevall, A. 2024-12-04 doi:10.1101/2024.12.03.626716 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Dynamic modulation of IRE1α-XBP1 signaling by adenovirus ]]> https://biorxiv.org/content/10.1101/2024.11.30.626188v1?rss=1 Jang, Y. Bunz, F. 2024-12-05 doi:10.1101/2024.11.30.626188 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Ubiquitin Ligase ITCH Regulates Life Cycle of SARS-CoV-2 Virus ]]> https://biorxiv.org/content/10.1101/2024.12.04.624804v1?rss=1 Xiang, Q. Wouters, C. Chang, P. Lu, Y.-N. Liu, M. Wang, H. Yang, J. Pekosz, A. Zhang, Y. Wang, J. 2024-12-05 doi:10.1101/2024.12.04.624804 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Structural Dynamics of the Dengue Virus Non-structural 5 (NS5) Interactions with Promoter Stem Loop A (SLA) ]]> https://biorxiv.org/content/10.1101/2024.12.03.626708v1?rss=1 Obi, J. O. Kihn, K. C. McQueen, L. Fields, J. K. Snyder, G. A. Deredge, D. J. 2024-12-06 doi:10.1101/2024.12.03.626708 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ In vivo detection of HIV-1 antisense transcripts in untreated and ART-treated individuals ]]> https://biorxiv.org/content/10.1101/2024.12.06.627170v1?rss=1 Capoferri, A. A. Sklutuis, R. Famuyiwa, T. O. Pathak, S. Li, R. Rausch, J. W. Luke, B. T. Hoh, R. Deeks, S. G. Mellors, J. W. Coffin, J. M. Groebner, J. L. Romerio, F. Kearney, M. F. 2024-12-06 doi:10.1101/2024.12.06.627170 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Dysregulation of cellular iron predisposes chemotherapy resistant cancer cells to ferroptosis ]]> https://biorxiv.org/content/10.1101/2024.12.05.626685v1?rss=1 Loftus, L. Rolle, L. T. A. Cherry, C. Patatanian, M. Orzolek, L. Wang, B. Pienta, K. Amend, S. R. 2024-12-10 doi:10.1101/2024.12.05.626685 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Investing in Open Science: Key Considerations for Funders ]]> https://biorxiv.org/content/10.1101/2024.12.09.627554v1?rss=1 Cobb-Lewis, D. E. Snyder, D. Dumanis, S. Thibault, R. Marebwa, B. Clark, E. St.Clair, L. Kirsch, L. Durborow, M. Riley, E. A. U. 2024-12-10 doi:10.1101/2024.12.09.627554 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Neural mechanisms underlying the effects of cognitive fatigue on physical effort-based decision-making ]]> https://biorxiv.org/content/10.1101/2024.12.06.627274v1?rss=1 Dryzer, M. Chib, V. S. 2024-12-11 doi:10.1101/2024.12.06.627274 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Inhibition of DKK-1 by WAY262611 Inhibits Osteosarcoma Metastasis ]]> https://biorxiv.org/content/10.1101/2024.12.10.627181v1?rss=1 Tal, A. Gunawardana-Zeigler, S. Peng, D. Tan, Y. Perez, N. M. Offenbacher, R. Kastner, L. Ciero, P. Randolph, M. E. Gong, Y. Deng, H.-W. Cahan, P. Loeb, D. M. 2024-12-11 doi:10.1101/2024.12.10.627181 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Regimen comprising clarithromycin, clofazimine and bedaquiline is more efficacious than monotherapy in a mouse model of chronic Mycobacterium avium lung infection ]]> https://biorxiv.org/content/10.1101/2024.12.11.627976v1?rss=1 Rimal, B. Howe, R. A. Panthi, C. M. Lamichhane, G. 2024-12-11 doi:10.1101/2024.12.11.627976 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Perceptual choice and motor signals in mouse somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2024.12.06.627272v1?rss=1 Minamisawa, G. Dong, M. O'Connor, D. H. 2024-12-12 doi:10.1101/2024.12.06.627272 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Cells Prioritize the Regulation of Cell Mass Density ]]> https://biorxiv.org/content/10.1101/2024.12.10.627803v1?rss=1 Fu, J. Ni, Q. Wu, Y. Gupta, A. Ge, Z. Yang, H. Afrida, Y. Barman, I. Sun, S. 2024-12-12 doi:10.1101/2024.12.10.627803 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity ]]> https://biorxiv.org/content/10.1101/2024.12.12.627852v1?rss=1 Fisher, R. J. Park, K. Lee, K. Pinjusic, K. Vanasse, A. Ennis, C. S. Ficcaro, S. Marto, J. Stransky, S. Duke-Cohan, J. Geethadevi, A. Raabe, E. H. Sidoli, S. Hicks, C. W. Keskin, D. Wu, C. J. Cole, P. A. Alani, R. M. 2024-12-12 doi:10.1101/2024.12.12.627852 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ A core set of neural states underlying memory reactivation of naturalistic events in the posterior medial cortex ]]> https://biorxiv.org/content/10.1101/2024.12.11.627957v1?rss=1 Lee, Y. Lee, H. Chen, J. 2024-12-16 doi:10.1101/2024.12.11.627957 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation ]]> https://biorxiv.org/content/10.1101/2024.12.16.628723v1?rss=1 Billingsley, K. J. Meredith, M. Daida, K. Alvarez Jerez, P. Negi, S. Malik, L. Genner, R. M. Moller, A. Zheng, X. Gibson, S. B. Mastoras, M. Baker, B. Kouam, C. Paquette, K. Jarreau, P. Makarious, M. B. Moore, A. Hong, S. Vitale, D. Shah, S. Monlong, J. Pantazis, C. B. Asri, M. Shafin, K. Carnevali, P. Marenco, S. Auluck, P. Mandal, A. Miga, K. H. Rhie, A. Reed, X. Ding, J. Cookson, M. R. Nalls, M. Singleton, A. Miller, D. E. Chaisson, M. Timp, W. Gibbs, J. R. Phillippy, A. M. Kolmogorov, M. Jain, M. Sedlazeck, F. J. Paten, B. Blauwendraat, C. 2024-12-18 doi:10.1101/2024.12.16.628723 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Linkage-based ortholog refinement in bacterial pangenomes with CLARC ]]> https://biorxiv.org/content/10.1101/2024.12.18.629228v1?rss=1 Ojeda, I. G. Palace, S. G. Martinez, P. P. Azarian, T. Grant, L. R. Hammitt, L. Hanage, B. Lipsitch, M. 2024-12-20 doi:10.1101/2024.12.18.629228 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Syngap1 and the development of murine neocortical progenitor cells ]]> https://biorxiv.org/content/10.1101/2024.12.18.629233v1?rss=1 Barao, S. Hong, I. Mueller, U. Huganir, R. L. 2024-12-20 doi:10.1101/2024.12.18.629233 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Image Processing in the Acute to Chronic Pain Signatures (A2CPS) Project ]]> https://biorxiv.org/content/10.1101/2024.12.19.627509v1?rss=1 Sadil, P. Arfanakis, K. Bhuiyan, E. H. Caffo, B. Calhoun, V. D. Clauw, D. J. DeLano, M. C. Ford, J. C. Gattu, R. Guo, X. Harris, R. E. Ichesco, E. Johnson, M. A. Jung, H. Kahn, A. B. Kaplan, C. M. Leloudas, N. Lindquist, M. A. Luo, Q. Mulderink, T. A. Peltier, S. J. Prasad, P. V. Sica, C. Urrutia, J. Vance, C. G. Wager, T. D. Xuan, Y. Zhou, X. J. Zhou, Y. Shu, D. C. The Acute to Chronic Pain Signatures Consortium, 2024-12-20 doi:10.1101/2024.12.19.627509 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Common and distinct neural correlates of social interaction perception and theory of mind ]]> https://biorxiv.org/content/10.1101/2024.12.19.628993v1?rss=1 Miao, Z. Jung, H. Kragel, P. A. Sadil, P. Lindquist, M. A. Wager, T. D. 2024-12-20 doi:10.1101/2024.12.19.628993 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Ongoing loss of viable neurons for weeks after mild perinatal hypoxia-ischemia ]]> https://biorxiv.org/content/10.1101/2024.12.19.629457v1?rss=1 McNally, M. Lau, L. A. Granak, S. Hike, D. Liu, X. Yu, X. Donahue, R. Chibnik, L. Ortiz, J. Che, A. Northington, F. Staley, K. J. 2024-12-20 doi:10.1101/2024.12.19.629457 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Test-retest reliability of TMS-evoked potentials over fMRI-based definitions of non-motor cortical targets ]]> https://biorxiv.org/content/10.1101/2024.12.20.629675v1?rss=1 Sayali, C. Gogulski, J. Grano, I. Lioumis, P. Barrett, F. S. 2024-12-20 doi:10.1101/2024.12.20.629675 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Detecting Clinically Relevant Topological Structures in Multiplexed Spatial Proteomics Imaging Using TopKAT ]]> https://biorxiv.org/content/10.1101/2024.12.18.628976v1?rss=1 Samorodnitsky, S. Campbell, K. M. Little, A. Ling, W. Zhao, N. Chen, Y.-C. Wu, M. 2024-12-21 doi:10.1101/2024.12.18.628976 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data ]]> https://biorxiv.org/content/10.1101/2024.12.20.629764v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@11a452forg.highwire.dtl.DTLVardef@1b44cb9org.highwire.dtl.DTLVardef@190dbdorg.highwire.dtl.DTLVardef@d4f66b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Badia-i-Mompel, P. Casals-Franch, R. Wessels, L. Müller-Dott, S. Trimbour, R. Yang, Y. Ramirez Flores, R. O. Saez-Rodriguez, J. 2024-12-21 doi:10.1101/2024.12.20.629764 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ MRS-Sim: Open-Source Framework for Simulating Realistic In Vivo-like MR Spectroscopy Data ]]> https://biorxiv.org/content/10.1101/2024.12.20.629645v1?rss=1 LaMaster, J. T. Oeltzschner, G. Li, Y. 2024-12-22 doi:10.1101/2024.12.20.629645 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Combined inhibition of SHP2 overcomes adaptive resistance to type 1 BRAF inhibitors in BRAF V600E-driven high-grade glioma ]]> https://biorxiv.org/content/10.1101/2024.12.21.629454v1?rss=1 Ayanlaja, A. A. Chang, M. Lalwani, K. Ioannou, M. Wang, J. Jagtap, S. Yang, Y. Gartrell, R. D. Pratilas, C. A. Schreck, K. C. 2024-12-22 doi:10.1101/2024.12.21.629454 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Histone H4 limits transcription of the histone locus in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.12.23.630206v1?rss=1 Ahmad, K. Wooten, M. Takushi, B. N. Vidaurre, V. Chen, X. Henikoff, S. 2024-12-24 doi:10.1101/2024.12.23.630206 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans ]]> https://biorxiv.org/content/10.1101/2024.12.22.629724v1?rss=1 Sullivan, S. A. Orosco, J. C. Callejas-Hernandez, F. Blow, F. Lee, H. Ranallo-Benavidez, T. Peters, A. Raidal, S. Girard, Y. A. Johnson, C. K. Rogers, K. Gerhold, R. Mangelson, H. Liachko, I. Srivastava, H. Chandler, C. Berenberg, D. Bonneau, R. Huang, P.-J. Yeh, Y.-M. Lee, C.-C. Liu, H. Tang, P. Chen, T.-W. Schatz, M. Carlton, J. M. 2024-12-25 doi:10.1101/2024.12.22.629724 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Overexpression of Xanthophyll Cycle Genes Leads to Faster NPQ Acclimation in the C4 Monocot Setaria viridis ]]> https://biorxiv.org/content/10.1101/2024.12.23.630197v1?rss=1 Stone, W. D. Acosta-Gamboa, L. Kang, X. zhang, f. Owens, L. Li, L. Thielen, P. M. Jander, G. Gore, M. A. Lawton, T. J. 2024-12-25 doi:10.1101/2024.12.23.630197 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Nectin-4 PET For Optimizing Enfortumab Vedotin Dose-Response In Urothelial Carcinoma ]]> https://biorxiv.org/content/10.1101/2024.12.25.630315v1?rss=1 Mishra, A. Sharma, A. K. Gupta, K. Banka, D. Johnson, B. A. Hoffman-Censits, J. Huang, P. McConkey, D. J. Nimmagadda, S. 2024-12-25 doi:10.1101/2024.12.25.630315 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation ]]> https://biorxiv.org/content/10.1101/2024.12.26.629296v1?rss=1 Moore, J. E. Pratt, H. E. Fan, K. Phalke, N. Fisher, J. Elhajjajy, S. I. Andrews, G. Gao, M. Shedd, N. Fu, Y. Lacadie, M. C. Meza, J. Ganna, M. Choudhury, E. Swofford, R. Farrell, N. P. Pampari, A. Ramalingam, V. Reese, F. Borsari, B. Yu, X. Wattenberg, E. S. Ruiz-Romero, M. Razavi-Mohseni, M. Xu, J. Galeev, T. Beer, M. A. Guigo, R. Gerstein, M. Engreitz, J. M. Ljungman, M. Reddy, T. E. Snyder, M. Epstein, C. B. Gaskell, E. Bernstein, B. E. Dickel, D. E. Visel, A. Pennacchio, L. A. Mortazavi, A. Kundaje, A. Weng, Z. 2024-12-26 doi:10.1101/2024.12.26.629296 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ Pro-cognitive reshaping of neuronal dynamics by a human CSF-based factor ]]> https://biorxiv.org/content/10.1101/2024.12.26.629959v1?rss=1 Dos Santos, M. Forrest, M. P. Bomba-Warczak, E. K. Parnell, E. Edassery, S. L. Yang, K. Hayes, L. N. Coughlin, J. M. Eckman, B. L. Lammert, C. Martin-de-Saavedra, M. D. Barbolina, M. Sawa, A. Savas, J. Penzes, P. 2024-12-26 doi:10.1101/2024.12.26.629959 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ Ultrastructural membrane dynamics of mouse and human cortical synapses ]]> https://biorxiv.org/content/10.1101/2024.12.26.630393v1?rss=1 Eddings, C. R. Fan, M. Imoto, Y. Itoh, K. McDonald, X. Eilers, J. Anderson, W. S. Worley, P. F. Lippmann, K. Nauen, D. W. Watanabe, S. 2024-12-26 doi:10.1101/2024.12.26.630393 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data ]]> https://biorxiv.org/content/10.1101/2024.12.23.629682v1?rss=1 Nasr, E. Amato, P. Bhardwaj, A. Blankenberg, D. Brites, D. Cumbo, F. Do, K. Ferrari, E. Griffin, T. J. Gruening, B. Hiltemann, S. Jagtap, P. Mehta, S. Metris, K. L. Momin, S. Oba, A. Pavloudi, C. Pechlivanis, N. Peguilhan, R. Psomopoulos, F. Rosic, N. Schatz, M. C. Schiml, V. C. Siguret, C. Soranzo, N. Stubbs, A. Van Heusden, P. Vohra, M. microGalaxy Community, Zierep, P. Batut, B. 2024-12-27 doi:10.1101/2024.12.23.629682 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Huntingtin interactome reveals huntingtin role in regulation of double strand break DNA damage response (DSB/DDR), chromatin remodeling and RNA processing pathways ]]> https://biorxiv.org/content/10.1101/2024.12.27.630542v1?rss=1 Ratovitski, T. Holland, C. D. O'Meally, R. N. Shevelkin, A. V. Shi, T. Cole, R. N. Jiang, M. Ross, C. A. 2024-12-28 doi:10.1101/2024.12.27.630542 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Evidence for distinct networks underlying symptom clusters of posttraumatic stress disorder ]]> https://biorxiv.org/content/10.1101/2024.12.31.630851v1?rss=1 Hauner, K. K. Chau, A. Krueger, F. Gordon, B. Grafman, J. 2024-12-31 doi:10.1101/2024.12.31.630851 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2024.12.30.630810v1?rss=1 Queen, J. Cing, Z. Minsky, H. Nandi, A. Southward, T. Ferri, J. McMann, M. Iyadorai, T. Vadivelu, J. Roslani, A. Loke, M. F. Wanyiri, J. White, J. R. Drewes, J. L. Sears, C. L. 2025-01-01 doi:10.1101/2024.12.30.630810 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Visual experience contributes to separation of face and language responses in the ventral stream ]]> https://biorxiv.org/content/10.1101/2024.12.18.629198v1?rss=1 Saccone, E. J. LNU, A. Murty, N. A. R. Kim, J. S. Tian, M. KANWISHER, N. G. Bedny, M. 2025-01-02 doi:10.1101/2024.12.18.629198 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Differential effect of supercoiling on bacterial transcription in topological domains ]]> https://biorxiv.org/content/10.1101/2025.01.02.631060v1?rss=1 Goldberg, B. I. Yehya, N. Xiao, J. Meyer, S. 2025-01-02 doi:10.1101/2025.01.02.631060 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Searching for Sequence Features that Control DNA Cyclizability ]]> https://biorxiv.org/content/10.1101/2025.01.02.631081v1?rss=1 Gordiychuk, M. Park, J. Basu, A. Ha, T. Bialek, W. Zhang, Y. 2025-01-02 doi:10.1101/2025.01.02.631081 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ The atypical filament assembly underpins the inflammasome-independent functions of IFI16. ]]> https://biorxiv.org/content/10.1101/2025.01.02.631089v1?rss=1 Garg, A. Niedzialkowska, E. Zhou, J. Moh, J. Egelman, E. Sohn, J. 2025-01-02 doi:10.1101/2025.01.02.631089 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Neuronal LAG3 facilitates pathogenic α-synuclein neuron-to-neuron propagation ]]> https://biorxiv.org/content/10.1101/2025.01.03.631221v1?rss=1 Yang, X. Jeong, D. Madeo, G. Kumbhar, R. Wang, N. Niu, L. Hu, J. Li, S. Gadhave, K. Chen, R. Akkentli, F. Workman, C. J. Vignali, D. A. A. Ying, M. Bonci, A. Dawson, V. L. Dawson, T. Mao, X. 2025-01-04 doi:10.1101/2025.01.03.631221 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Early Noise Exposure and Changes in Medial Olivocochlear Strength Alters Auditory Pathway Development ]]> https://biorxiv.org/content/10.1101/2025.01.03.631257v1?rss=1 Castagna, V. C. Boero, L. E. Di Guilmi, M. N. Fuchs, P. A. Lauer, A. M. Elgoyhen, A. B. Gomez-Casati, M. E. 2025-01-04 doi:10.1101/2025.01.03.631257 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Mumemto: efficient maximal matching across pangenomes ]]> https://biorxiv.org/content/10.1101/2025.01.05.631388v1?rss=1 Shivakumar, V. S. Langmead, B. 2025-01-05 doi:10.1101/2025.01.05.631388 Cold Spring Harbor Laboratory Press 2025-01-05 <![CDATA[ Toward a privacy-preserving predictive foundation model of single-cell transcriptomics with federated learning and tabular modeling ]]> https://biorxiv.org/content/10.1101/2025.01.06.631427v1?rss=1 Ding, J. Lin, J. Jiang, S. Wang, Y. Mao, Z. Fang, Z. Tang, J. Li, M. Qiu, X. 2025-01-06 doi:10.1101/2025.01.06.631427 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Fast and flexible minimizer digestion with digest ]]> https://biorxiv.org/content/10.1101/2025.01.02.631161v1?rss=1 Zheng, A. Lee, I. Shivakumar, V. S. Ahmed, O. S. Langmead, B. 2025-01-08 doi:10.1101/2025.01.02.631161 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Behavioral and neural sound classification: Insights from natural and synthetic sounds ]]> https://biorxiv.org/content/10.1101/2025.01.06.631484v1?rss=1 Ogg, M. 2025-01-08 doi:10.1101/2025.01.06.631484 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ TGFBR2-High mesenchymal glioma stem cells phenocopy regulatory T cells to suppress CD4+ and CD8+ T cell function ]]> https://biorxiv.org/content/10.1101/2025.01.07.631757v1?rss=1 Johnson, A. L. Khela, H. S. Korleski, J. Sall, S. Li, Y. Zhou, W. Smith-Connor, K. Lopez-Bertoni, H. Laterra, J. 2025-01-08 doi:10.1101/2025.01.07.631757 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression ]]> https://biorxiv.org/content/10.1101/2025.01.07.631784v1?rss=1 Guinn, S. Perez, B. Tandurella, J. A. Ramani, M. Lee, J. W. Zabransky, D. J. Kartalia, E. Patel, J. Zlomke, H. Nicolson, N. Shin, S. Barrett, B. Sun, N. Hernandez, A. Coyne, E. Cannon, C. Gross, N. E. Charmsaz, S. Cho, Y. Leatherman, J. Lyman, M. Mitchell, J. T. Kagohara, L. T. Goggins, M. G. Lafaro, K. J. He, J. Shubert, C. Burns, W. Zheng, L. Fertig, E. J. Jaffee, E. M. Burkhart, R. A. Ho, W. J. Zimmerman, J. W. 2025-01-08 doi:10.1101/2025.01.07.631784 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Revealing hidden knowledge in amnestic mice ]]> https://biorxiv.org/content/10.1101/2025.01.09.632026v1?rss=1 Santi, A. Moore, S. Fogelson, K. A. Wang, A. Lawlor, J. Amato, J. Burke, K. Lauer, A. M. Kuchibhotla, K. V. 2025-01-09 doi:10.1101/2025.01.09.632026 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Rapid "recycling" of logical algorithm representations in fronto-parietal reasoning systems following computer programming instructions ]]> https://biorxiv.org/content/10.1101/2025.01.08.631982v1?rss=1 Liu, Y.-F. Bedny, M. 2025-01-10 doi:10.1101/2025.01.08.631982 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Decoding Gene Networks Controlling Hypothalamic and Prethalamic Neuron Development. ]]> https://biorxiv.org/content/10.1101/2025.01.10.632449v1?rss=1 Kim, D. W. Duncan, L. Xu, J. Chang, M. Sorensen, S. S. Terrillin, C. Kanold, P. Place, E. S. Blackshaw, S. 2025-01-11 doi:10.1101/2025.01.10.632449 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ AUTO-SP: automated sample preparation for analyzing proteins and protein modifications ]]> https://biorxiv.org/content/10.1101/2025.01.08.631960v1?rss=1 0.98). Additionally, >14,000 ubiquitinated peptides were identified in the PDX samples when using AUTO-SP for ubiquitin enrichment, while unique pathways were enriched from the basal-like and luminal subtypes. AUTO-SP demonstrated its efficacy to provide reliable and reproducible sample preparation procedure for MS-based proteomic and PTM analyses. ]]> Lih, T. M. Jiao, L. Chen, L. Woo, J. Wang, Y. Zhang, H. 2025-01-13 doi:10.1101/2025.01.08.631960 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ OcuPair, a novel photo-crosslinkable dendrimer-hyaluronic acid hydrogel bandage/bioadhesive for corneal injuries and temporary corneal repair ]]> https://biorxiv.org/content/10.1101/2025.01.08.632042v1?rss=1 Kambhampati, S. P. Sharma, R. Lin, H. Appiani, S. Cleland, J. L. Yiu, S. C. Rangaramanujam, K. 2025-01-13 doi:10.1101/2025.01.08.632042 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Microscopic Control of Cortical Flows in Polarized C. elegans Zygotes ]]> https://biorxiv.org/content/10.1101/2025.01.12.632635v1?rss=1 White, E. Li, Y. Kadzik, R. Qiu, Y. Dinner, A. Munro, E. 2025-01-13 doi:10.1101/2025.01.12.632635 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Prolyl isomerase FKBP12 reduces axon growth and negatively regulates microtubule polymerization by inhibiting CRMP2A ]]> https://biorxiv.org/content/10.1101/2025.01.13.632804v1?rss=1 Weissova, R. Sabo, J. Chafai, D. E. Ziak, J. Buran, P. Bodakuntla, S. Janke, C. Lansky, Z. Balastik, M. 2025-01-13 doi:10.1101/2025.01.13.632804 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants ]]> https://biorxiv.org/content/10.1101/2025.01.12.632622v1?rss=1 Milburn, G. Morris, C. M. Kosola, E. Patel-Tupper, D. Liu, J. Pham, D. H. Acosta-Gamboa, L. Stone, W. D. Pardi, S. Hillman, K. McHargue, W. E. Becker, E. Kang, X. Sumner, J. Bailey, C. Thielen, P. M. Jander, G. Kane, C. N. McAdam, S. A. M. Lawton, T. J. Nusinow, D. A. Zhang, F. Gore, M. A. Cheng, J. Niyogi, K. K. Zhang, R. 2025-01-15 doi:10.1101/2025.01.12.632622 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Longitudinal T cell repertoire analysis reveals dynamic clonal T cell populations in Ulcerative Colitis ]]> https://biorxiv.org/content/10.1101/2025.01.13.632427v1?rss=1 Briggs, K. C. Lin, J. S. Chaaban, L. Parian, A. Lazarev, M. Selaru, F. M. Housseau, F. Smith, K. N. Melia, J. M. 2025-01-17 doi:10.1101/2025.01.13.632427 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant ]]> https://biorxiv.org/content/10.1101/2025.01.13.632473v1?rss=1 Yang, B. Rutkowski, N. Ruta, A. Gray-Gaillard, E. Maestas, D. R. Kelly, S. H. Krishnan, K. Wu, X. Wu, S. Chen, A. M. Amelung, C. D. Mejias, J. C. Hooks, J. S. T. Vanderzee, I. Mensah, P. Celik, N. Eric, M. Abraham, P. Tam, A. Gerecht, S. Housseau, F. Pardoll, D. M. Sears, C. Elisseeff, J. 2025-01-17 doi:10.1101/2025.01.13.632473 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ Native nucleosome-positioning elements for the investigation of nucleosome repositioning ]]> https://biorxiv.org/content/10.1101/2025.01.17.633597v1?rss=1 Chen, R.-W. Stoeber, S. D. Nodelman, I. M. Chen, H. Yang, L. Bowman, G. Bai, L. Poirier, M. G. 2025-01-19 doi:10.1101/2025.01.17.633597 Cold Spring Harbor Laboratory Press 2025-01-19 <![CDATA[ Telomeric SUMO level influences the choices of APB formation pathways and ALT efficiency ]]> https://biorxiv.org/content/10.1101/2025.01.16.633463v1?rss=1 Zhao, R. Wivagg, A. Lackner, R. M. Salsman, J. Dellaire, G. Matunis, M. J. Chenoweth, D. M. Zhao, X. Zhang, H. 2025-01-20 doi:10.1101/2025.01.16.633463 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Autoantibody hotspots reveal origin and impact of immunogenic XIST ribonucleoprotein complex ]]> https://biorxiv.org/content/10.1101/2025.01.16.633465v1?rss=1 Yan, B. Lee, J. Srinivasan, S. Shi, Q. Dou, D. R. Davuluri, S. Nandyala, S. Woods, A. Leatherman, G. Zhao, Y. Reggiardo, R. E. Sawant, M. Thiam, H. R. Shah, A. A. Fiorentino, D. F. Chung, L. S. Chang, H. Y. 2025-01-20 doi:10.1101/2025.01.16.633465 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Glycan-reactive antibodies isolated from human HIV-1 vaccine trial participants show broad pathogen cross-reactivity ]]> https://biorxiv.org/content/10.1101/2025.01.17.633475v1?rss=1 Jamieson, P. J. Shen, X. Abu-Shmais, A. A. Wasdin, P. T. Janowska, K. Edwards, R. J. Scapellato, G. Richardson, S. I. Manamela, N. P. Liu, S. Barr, M. Gillespie, R. A. Mimms, J. Suryadevara, N. Sornberger, T. A. Zost, S. Parks, R. Flaherty, S. Janke, A. K. Howard, B. N. Suresh, Y. P. Ruprecht, R. M. Crowe, J. E. Carnahan, R. H. Bailey, J. R. Masaru, K. Haynes, B. F. Moore, P. L. Acharya, P. Montefiori, D. C. Kalams, S. A. Lu, S. Georgiev, I. S. 2025-01-20 doi:10.1101/2025.01.17.633475 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ Binding affinities for 2D protein dimerization benefit from enthalpic stabilization ]]> https://biorxiv.org/content/10.1101/2025.01.16.633485v1?rss=1 Jhaveri, A. Chhibber, S. Kulkarni, N. Johnson, M. E. 2025-01-21 doi:10.1101/2025.01.16.633485 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Multi-Region Brain Organoid: Fusion Organoid with Cerebral, Endothelial and Mid-Hindbrain Components ]]> https://biorxiv.org/content/10.1101/2025.01.20.633788v1?rss=1 Kshirsagar, A. Mnatsakanyan, H. Kulkarni, S. Guo, J. Cheng, K. Bohra, O. Badr, C. E. Kathuria, A. 2025-01-21 doi:10.1101/2025.01.20.633788 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Combinations comprising dual β-lactams and a β-lactamase inhibitor achieve optimal synergistic inhibition of Mycobacterium abscessus growth ]]> https://biorxiv.org/content/10.1101/2025.01.20.633926v1?rss=1 Rimal, B. Xie, Y. Panthi, C. M. Devlin, K. L. Beatty, K. E. Lamichhane, G. 2025-01-21 doi:10.1101/2025.01.20.633926 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Multifunctional bending magnet beamline with a capillary optic for X-ray fluorescence studies of metals in tissue sections ]]> https://biorxiv.org/content/10.1101/2025.01.18.633695v1?rss=1 Roter, B. Crawford, A. M. Jin, Q. Glowacki, A. T. Lai, B. Marin, F. S. Maxey, E. R. Shi, X. Culotta, V. C. Wildeman, A. S. Patel, N. K. O'Halloran, T. V. Jacobsen, C. 2025-01-22 doi:10.1101/2025.01.18.633695 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Mapping brain function underlying naturalistic motor observation and imitation using high-density diffuse optical tomography ]]> https://biorxiv.org/content/10.1101/2025.01.21.634109v1?rss=1 Yang, D. George, T. Sobolewski, C. McMorrow, S. Pacheco, C. King, K. Rochowiak, R. Daniels-Day, E. Park, S. Speh, E. Lidstone, D. Santra, R. Crocetti, D. Nebel, M. B. Tuncgenc, B. Vidal, R. Marrus, N. M. Mostofsky, S. H. Eggebrecht, A. T. 2025-01-22 doi:10.1101/2025.01.21.634109 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Three annotated chromosome-level de novo genome assemblies of Lomentospora prolificans provide evidence for a chromosomal translocation event ]]> https://biorxiv.org/content/10.1101/2025.01.21.634120v1?rss=1 Grossman, N. T. Fan, Y. Zimin, A. V. Wear, M. P. Jedlicka, A. Dziedzic, A. Liporagi-Lopes, L. Timp, W. Casadevall, A. 2025-01-22 doi:10.1101/2025.01.21.634120 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Automatic detection of fluorescently labeled synapses in volumetric in vivo imaging data ]]> https://biorxiv.org/content/10.1101/2025.01.22.634278v1?rss=1 Chen, Z. Coste, G. I. Li, E. Huganir, R. L. Charles, A. Graves, A. R. 2025-01-22 doi:10.1101/2025.01.22.634278 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Mef2c Controls Postnatal Callosal Axon Targeting by Regulating Sensitivity to Ephrin Repulsion ]]> https://biorxiv.org/content/10.1101/2025.01.22.634300v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@108c788org.highwire.dtl.DTLVardef@163c6c3org.highwire.dtl.DTLVardef@18e6d8borg.highwire.dtl.DTLVardef@1b9f9e4_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIMef2c is required for the development of L4 and L5 neurons in the embryonic neocortex C_LIO_LIPostnatally, Mef2c is enriched in L2/3 neurons and is required for axon targeting C_LIO_LIL2/3-specific Mef2c deletion leads to EphA6 upregulation C_LIO_LIMef2c deletion in L2/3 neurons sensitizes them to EfnA5 repulsion in the contralateral cortex C_LI ]]> Sudarsanam, S. Guzman-Clavel, L. Dar, N. Ziak, J. Shahid, N. Jin, X. O. Kolodkin, A. L. 2025-01-22 doi:10.1101/2025.01.22.634300 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ The microbiome of the human facial skin is unique compared to that of other hominids ]]> https://biorxiv.org/content/10.1101/2025.01.22.634396v1?rss=1 Degregori, S. Manus, M. Qu, E. Mendall, C. Baker, J. Hopper, L. Amato, K. R. Lieberman, T. 2025-01-24 doi:10.1101/2025.01.22.634396 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Dual Probe Ligation In Situ Hybridization with Rolling-Circle Amplification for High-Plex Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.01.22.634417v1?rss=1 Maguire, S. Credle, J. Bertelson, E. Lee, S. Cha, B. Xie, D. Kirk, G. Ray, D. George, L. Suru, A. Maalouf, A. Ikenaga, C. Lloyd, T. Llosa, N. Larman, H. B. 2025-01-24 doi:10.1101/2025.01.22.634417 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Spontaneous spatial sorting by cell shape in growing colonies of rod-like bacteria ]]> https://biorxiv.org/content/10.1101/2025.01.22.634274v1?rss=1 Ratman, M. Gonzalez Nunez, J. Beller, D. A. 2025-01-25 doi:10.1101/2025.01.22.634274 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Attenuated adenosine mediated immune-dampening increases natural killer cell activity in early age-related macular degeneration ]]> https://biorxiv.org/content/10.1101/2025.01.22.634301v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1516bfaorg.highwire.dtl.DTLVardef@87f505org.highwire.dtl.DTLVardef@1e725caorg.highwire.dtl.DTLVardef@622717_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Illustra tion of pro posed mechanism underlying NK cell-RPE interaction in early AMD pathogenesis. Dysregulated NK cell communicate s with stressed RPE in early AMD immunopathology. Aberrant AMD aqueous humor and retina shows increased NK cells and NK effector molecules like IFN{gamma} with reduced MDSC and adenosine in human subjects, don or eye and animal model. Activated NK cells interaction with RPE causes dysfunction and pyroptotic cell death via Gasdermin-E pathway in AMD.. Created with BioRender.com C_FIG ]]> Nair, A. P. Ghosh, S. Babu, V. S. Praveen, M. Xin, Y. Sahu, G. R. Vaidya, T. A. Debnath, J. Raja, K. Gadde, S. G. K. MB, T. Shetty, N. Saxena, A. Shetty, R. Hose, S. Deshpande, V. Chakrabarthy, K. Handa, J. T. Qian, J. Sethu, S. Sinha, D. Ghosh, A. 2025-01-25 doi:10.1101/2025.01.22.634301 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ An anti-amyloidogenic approach to specifically block memory consolidation in mice for therapeutic intervention ]]> https://biorxiv.org/content/10.1101/2025.01.27.635080v1?rss=1 Lopez-Garcia, P. McGreevy, K. R. Vaquero, M. E. Ramirez de Mingo, D. Palle, A. Popiel, H. A. Santi, A. Nagai, Y. Trejo, J. L. Carrion-Vazquez, M. 2025-01-28 doi:10.1101/2025.01.27.635080 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Cigarette smoke and biological age induce degenerative heterogeneity in retinalpigment epithelium ]]> https://biorxiv.org/content/10.1101/2025.01.27.635096v1?rss=1 Singh, K. jin, y. Hu, M. Pallazo, I. Cano,, M. Hoang, T. Bhutto, I. Wang, S. Sinha, D. Blackshaw, S. Qian, J. Handa, J. T. 2025-01-28 doi:10.1101/2025.01.27.635096 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ mRNA lipid nanoparticle-incorporated nanofiber-hydrogel composite generates a local immunostimulatory niche for cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.01.27.633179v1?rss=1 Zhu, Y. Yao, Z.-C. Li, S. Ma, J. Wei, C. Yu, D. Stelzel, J. L. Ni, B. Y. X. Miao, Y. Van Batavia, K. Lu, X. Lin, J. Dai, Y. Kong, J. Shen, R. Goodier, K. D. Liu, X. Cheng, L. Vuong, I. Howard, G. P. Livingston, N. K. Choy, J. Schneck, J. P. Doloff, J. C. Reddy, S. K. Hickey, J. W. Mao, H.-Q. 2025-01-29 doi:10.1101/2025.01.27.633179 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Deep Learning-Powered Colloidal Digital SERS for Precise Monitoring of Cell Culture Media ]]> https://biorxiv.org/content/10.1101/2025.02.03.636280v1?rss=1 Zheng, P. Wu, L. Lee, M. K. H. Nelson, A. Betenbaugh, M. Barman, I. 2025-02-04 doi:10.1101/2025.02.03.636280 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ A CD25-CCR7 complex initiates non-canonical IL-2 signaling ]]> https://biorxiv.org/content/10.1101/2025.02.03.636356v1?rss=1 Kim, S. H. J. Lee, H. Gingras, A. Ley, K. Spangler, J. B. Ginsberg, M. H. 2025-02-04 doi:10.1101/2025.02.03.636356 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Hypoxia-induced histone methylation and NF-κB activation in pancreas cancer fibroblasts promote EMT-supportive growth factor secretion ]]> https://biorxiv.org/content/10.1101/2025.01.30.635486v1?rss=1 Kowalewski, K. M. Adair, S. J. Talkington, A. Wieder, J. Pitarresi, J. R. Perez-Vale, K. Chu, B. Dolatshahi, S. Sears, R. Stanger, B. Z. Bauer, T. W. Lazzara, M. J. 2025-02-05 doi:10.1101/2025.01.30.635486 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Partially differentiated enterocytes in ileal and distal-colonic human F508del-CF-enteroids 1 secrete fluid in response to forskolin and linaclotide. ]]> https://biorxiv.org/content/10.1101/2025.02.03.636268v1?rss=1 Rong, Y. Zhang, Z. de Jonge, H. Lin, R.-X. Yu, H. Sarker, R. Boffelli, D. Zwick, R. K. Klein, O. Tse, M. Donowitz, M. K. Singh, V. 2025-02-08 doi:10.1101/2025.02.03.636268 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Feedback and feedforward control are differentially delayed in cerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2025.02.09.637327v1?rss=1 Cao, D. Wilkinson, M. G. T. Bastian, A. J. Cowan, N. J. 2025-02-10 doi:10.1101/2025.02.09.637327 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Cethromycin Pharmacokinetics and Pharmacodynamics for Single Dose Cure of Plasmodium berghei Liver Stages ]]> https://biorxiv.org/content/10.1101/2025.02.10.637401v1?rss=1 Kennedy, G. J. West, R. M. Poti, K. Bobb, B. Ippolito, M. M. Marzinke, M. A. Kaludov, N. Sullivan, D. J. 2025-02-11 doi:10.1101/2025.02.10.637401 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ High density probes reveal medullary seizure and rapid medullary shutdown in a model of fatal apnea in seizure ]]> https://biorxiv.org/content/10.1101/2025.02.10.637524v1?rss=1 Budde, R. B. Irazoqui, P. P. RoaFiore, L. A. 2025-02-12 doi:10.1101/2025.02.10.637524 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.02.11.637688v1?rss=1 Ma, X. Wei, X. Niu, m. Zhang, C. Peng, Z. Liu, W. Yan, J. Su, X. Lu, S. Cui, W. Sesaki, H. Zong, W.-X. Ni, H.-M. Ding, W.-X. 2025-02-12 doi:10.1101/2025.02.11.637688 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ An ex vivo and in vitro investigation of extracellular vesicle interactions with B cells of Macaca nemestrina and humans ]]> https://biorxiv.org/content/10.1101/2025.02.12.637883v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@bd28e3org.highwire.dtl.DTLVardef@c76b28org.highwire.dtl.DTLVardef@4c2e44org.highwire.dtl.DTLVardef@1719771_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pachane, B. C. Rodriguez, B. V. Shirk, E. N. Gololobova, O. Carlson, B. Queen, S. E. Erickson, L. D. Selistre-de-Araujo, H. S. Witwer, K. W. 2025-02-16 doi:10.1101/2025.02.12.637883 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Dynamic and Biphasic Regulation of Cell Migration by Ras ]]> https://biorxiv.org/content/10.1101/2025.02.13.638204v1?rss=1 Lin, Y. Parajon, E. Yuan, Q. Ye, S. Qin, G. Deng, Y. Borleis, J. Koyfman, A. Iglesias, P. A. Konstantopoulos, K. Robinson, D. N. Devreotes, P. N. 2025-02-16 doi:10.1101/2025.02.13.638204 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Mechanistic computational modeling of sFLT1 secretion dynamics ]]> https://biorxiv.org/content/10.1101/2025.02.12.637983v1?rss=1 Gill, A. Kinghorn, K. Bautch, V. L. Mac Gabhann, F. 2025-02-17 doi:10.1101/2025.02.12.637983 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Hip stabilization in an australopithecine-like hip: the influence of shape on muscle activation ]]> https://biorxiv.org/content/10.1101/2025.02.13.637980v1?rss=1 Kramer, P. A. Sylvester, A. D. 2025-02-17 doi:10.1101/2025.02.13.637980 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data ]]> https://biorxiv.org/content/10.1101/2025.02.17.638651v1?rss=1 Liu, H. Ma, Z. Lih, T. M. Chen, L. Hu, Y. Wang, Y. Sun, Z. Huang, Y. Xu, Y. Zhang, H. 2025-02-17 doi:10.1101/2025.02.17.638651 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ SUMO2 Promotes Histone Pre-mRNA Processing by Stabilizing Histone Locus Body Interactions and Facilitating U7 snRNP Assembly ]]> https://biorxiv.org/content/10.1101/2025.02.15.638447v1?rss=1 He, S. Lyu, P. Skinner, M. W. Desotell, A. Foley, B. McCaig, C. M. Wang, W. Qian, J. Tong, L. Marzluff, W. F. Matunis, M. J. 2025-02-18 doi:10.1101/2025.02.15.638447 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ Neuromodulation in neural organoids with shell MEAs ]]> https://biorxiv.org/content/10.1101/2025.02.18.637712v1?rss=1 Acha, C. George, D. Diaz, L. C. Ouyang, Z. Alam El Din, D.-M. M. Surlekar, H. Moghadas, B. Rayasam, P. S. R. Lai, Y.-C. Smirnova, L. Caffo, B. S. Johnson, E. C. Gracias, D. H. 2025-02-19 doi:10.1101/2025.02.18.637712 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ A novel peptidoglycan deacetylase modulates daughter cell separation in E. coli ]]> https://biorxiv.org/content/10.1101/2025.02.18.638797v1?rss=1 Hernandez-Rocamora, V. Martorana, A. Belloso, A. Ballesteros, D. Zaccaria, M. Perez, A. Iorga, B. Abia, D. Gray, J. Breukink, E. Xiao, J. Pazos, M. Polissi, A. Vollmer, W. 2025-02-19 doi:10.1101/2025.02.18.638797 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization ]]> https://biorxiv.org/content/10.1101/2025.02.18.638941v1?rss=1 Sang, M. Johnson, M. E. 2025-02-23 doi:10.1101/2025.02.18.638941 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Inhibition of methylthioadenosine phosphorylase provides protection from experimental acute kidney injury ]]> https://biorxiv.org/content/10.1101/2025.02.19.639065v1?rss=1 Saliba, A. Chen, Y. Nelson, J. W. Vetcha, A. Wang, W. W. Kang, L. Ragi, N. Maity, S. Rabb, H. Reeves, W. B. Sharma, K. 2025-02-23 doi:10.1101/2025.02.19.639065 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ S. pombe telomerase RNA: secondary structure and flexible-scaffold function ]]> https://biorxiv.org/content/10.1101/2025.02.22.638514v1?rss=1 McMurdie, K. Peeney, A. N. Mefford, M. A. Baumann, P. Zappulla, D. C. 2025-02-23 doi:10.1101/2025.02.22.638514 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ EvANI benchmarking workflow for evolutionary distance estimation ]]> https://biorxiv.org/content/10.1101/2025.02.23.639716v1?rss=1 Majidian, S. Hwang, S. Zakeri, M. Langmead, B. 2025-02-23 doi:10.1101/2025.02.23.639716 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ A Metabolite-Based Resistance Mechanism Against Malaria ]]> https://biorxiv.org/content/10.1101/2025.02.20.639306v1?rss=1 10-fold higher ratio of unconjugated bilirubin over parasite burden, compared to symptomatic malaria. Genetic suppression of bilirubin synthesis by biliverdin reductase A (BVRA) (4) increased parasite virulence and malaria mortality in mice. Accumulation of unconjugated bilirubin in plasma, via genetic inhibition of hepatic conjugation by UDP glucuronosyltransferase family 1 member A1 (UGT1A1) (5), was protective against malaria in mice. Unconjugated bilirubin inhibited P. falciparum proliferation in red blood cells (RBC) via a mechanism that suppressed mitochondrial pyrimidine synthesis. Moreover, unconjugated bilirubin inhibited hemozoin (Hz) crystallization and compromised the parasites food vacuole. In conclusion, jaundice represents a metabolic response to Plasmodium spp. infection that limits malaria severity. ]]> Figueiredo, A. Trikha Rastogi, S. Ramos, S. Nogueira, F. De Villiers, K. Goncalves de Sousa, A. G. Votborg-Novel, L. von Wedel, C. Tober-Lau, P. Jentho, E. Pagnotta, S. Mesquita, M. Cardoso, S. Bortolussi, G. Muro, A. F. Tranfield, E. M. Thibaud, J. Duarte, D. Sousa, A. L. Pinto, S. N. Kitoko, J. Mombo-Ngoma, G. Mischlinger, J. Junttila, S. Alenquer, M. Amorim, M. J. Vasavda, C. Bosma, P. J. Violante, S. Drotleff, B. Paixao, T. Portugal, S. Kurth, F. Elo, L. L. Paul, B. D. Martins, R. Soares, M. P. 2025-02-26 doi:10.1101/2025.02.20.639306 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation ]]> https://biorxiv.org/content/10.1101/2025.02.24.639687v1?rss=1 Lalli, J. L. Bortvin, A. N. McCoy, R. C. Werling, D. M. 2025-02-28 doi:10.1101/2025.02.24.639687 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Comprehensive identification of β-lactam antibiotic polypharmacology in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.02.25.640225v1?rss=1 Devlin, K. L. Hutchinson, E. Dearing, H. N. Levine, S. R. Reid, D. J. Leach, D. T. Griggs, L. H. Lomas, G. X. Gorham, L. J. Wright, A. T. Lamichhane, G. Lin, V. Beatty, K. E. 2025-02-28 doi:10.1101/2025.02.25.640225 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition ]]> https://biorxiv.org/content/10.1101/2025.02.28.640732v1?rss=1 0.05. At {beta} diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100{beta} (p=0.002) and {beta}-Amyloid 1-42 fragment ({beta}A-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower {beta}A-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, {beta}A-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (modelsp<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV. Author SummaryHIV can affect brain health and mental well-being, even in people on successful antiretroviral therapy. The reasons behind this are still unclear. HIV also influences the communities of microbes and viruses living in the human body, and recent research suggests that the human virome, the collection of all viruses within the body, may play a role in cognitive functions, mood, and brain health. For a long time, scientists believed that the cerebrospinal fluid (CSF), which surrounds the brain, was sterile, while robust evidence has shown that the CSF hosts its own unique virome. Via advanced genetic sequencing (shotgun metagenomics), we analyzed the CSF virome in people with and without HIV looking for possible links to neuroinflammation, cognitive performance, and depression. We found that while HIV infection does affect the composition of CSF viral communities, there were no remarkable differences in the CSF virome of individuals with and without HIV. Most viral sequences appeared to come outside the brain. A higher abundance of non-human viral sequences, such as viruses of bacteria, plants, fungi, and animals, was associated with neuroinflammation and poorer cognitive performance. On the other hand, a higher abundance of human viruses correlated with better cognitive function and healthier signature of neuromarkers. These findings provide new insights into the presence and characteristics of the human CSF virome and how it might influence brain health. They also suggest new potential mechanisms of HIV-associated neuropathology. ]]> Trunfio, M. Scutari, R. Fox, V. Vuaran, E. Dastgheyb, R. M. Fini, V. Granaglia, A. Balbo, F. Tortarolo, D. Bonora, S. Perno, C. F. Di Perri, G. Alteri, C. Calcagno, A. 2025-02-28 doi:10.1101/2025.02.28.640732 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Development of an image-guided non-vitrectomy subretinal access approach for trans-scleral cell and gene therapy delivery ]]> https://biorxiv.org/content/10.1101/2025.02.25.640217v1?rss=1 Singh, M. S. Guo, S. Toomey, C. B. McNally, M. M. Harris-Bookman, S. Li, K. V. Agakishiev, D. Wei, S. Lee, S. Perrino, K. Wolfe, K. C. Kang, J. 2025-03-01 doi:10.1101/2025.02.25.640217 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Phagosome-mediated anti-bacterial immunity is governed by the proton-activated chloride channel in peritoneal macrophages ]]> https://biorxiv.org/content/10.1101/2025.02.27.640612v1?rss=1 Cheng, H. Y. Chu, J. Limjunyawong, N. Chen, J. Ye, Y. Chen, K. H. Koylass, N. Sun, S. Dong, X. Qiu, Z. 2025-03-02 doi:10.1101/2025.02.27.640612 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Atypical functional connectome in congenitally blind humans ]]> https://biorxiv.org/content/10.1101/2025.02.28.640746v1?rss=1 Koba, C. Falco-Roget, J. Collignon, O. Raczy, K. Bedny, M. Tian, M. Szwed, M. Stroh, A.-L. 2025-03-02 doi:10.1101/2025.02.28.640746 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Minimum biomechanical energy expenditure predicts upper-limb motor strategies in individuals with limb loss ]]> https://biorxiv.org/content/10.1101/2025.02.27.640462v1?rss=1 Hunt, C. L. Greene, R. J. Lee, I. Kaliki, R. R. Thakor, N. V. 2025-03-04 doi:10.1101/2025.02.27.640462 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Effectiveness of Digital Dispersion Compensation in OCT ]]> https://biorxiv.org/content/10.1101/2025.02.27.640677v1?rss=1 Liu, F. Li, X. 2025-03-04 doi:10.1101/2025.02.27.640677 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Effective Multiple Scattering Correction for Accurate Quantitative OCT ]]> https://biorxiv.org/content/10.1101/2025.02.28.640668v1?rss=1 Lee, C.-Y. Li, X. 2025-03-06 doi:10.1101/2025.02.28.640668 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Magnetically Labeled iPSC-Derived Extracellular Vesicles Enable MRI/MPI-Guided Regenerative Therapy for Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2025.03.02.641040v1?rss=1 Wang, W. Han, Z. Aafreen, S. Zivko, C. Gololobova, O. Wei, Z. Cotin, G. Felder-Flesch, D. Mahairaki, V. Witwer, K. W. Bulte, J. W. M. Weiss, R. G. Liu, G. 2025-03-10 doi:10.1101/2025.03.02.641040 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Artery-on-chip demonstrates smooth muscle function comparable to both healthy and diseased living tissues ]]> https://biorxiv.org/content/10.1101/2025.03.06.641764v1?rss=1 Yarbrough, D. Chen, R. Shoemaker, J. Yu, E. Ataam, J. A. Amelung, C. Karakikes, I. Gerecht, S. 2025-03-11 doi:10.1101/2025.03.06.641764 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Endothelial-pericyte interactions regulate angiogenesis via VEGFR2 signaling during retinal development and disease ]]> https://biorxiv.org/content/10.1101/2025.03.08.642174v1?rss=1 Lin, Y. Warren, E. Macklin, B. Ramirez, L. Gerecht, S. 2025-03-11 doi:10.1101/2025.03.08.642174 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Psychedelics Align Brain Activity with Context ]]> https://biorxiv.org/content/10.1101/2025.03.09.642197v1?rss=1 Stoliker, D. Novelli, L. Khajehnejad, M. Biabani, M. Barta, T. Greaves, M. D. Williams, M. Chopra, S. Bazin, O. Simonsson, O. Chambers, R. Barrett, F. Deco, G. Seth, A. Preller, K. H. Carhart-Harris, R. Sundram, S. Egan, G. F. Razi, A. 2025-03-11 doi:10.1101/2025.03.09.642197 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Monkey See, Model Knew: Large Language Models Accurately Predict Visual Brain Responses in Humans and Non-Human Primates ]]> https://biorxiv.org/content/10.1101/2025.03.05.641284v1?rss=1 Conwell, C. MacMahon, E. Jagadeesh, A. Vinken, K. Sharma, S. Prince, J. S. Alvarez, G. A. Konkle, T. Livingstone, M. Isik, L. 2025-03-12 doi:10.1101/2025.03.05.641284 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Single cell transcriptomic analyses of human heart failure with preserved ejection fraction ]]> https://biorxiv.org/content/10.1101/2025.03.06.641949v1?rss=1 75% of droplets to individual patients. From eight pooled samples (19 HFpEF, 24 controls), we recovered 48,886 nuclei and identified 14 cell types. Cardiomyocytes (5159 differentially expressed [DE] genes, 36%) and fibroblasts (5905 DE genes, 49%) showed the most DE genes, while endothelial cells (2143), pericytes (1812), and macrophages (1405) had fewer. Enriched pathways common to multiple cell types included transcription/translation, immune activation, metabolism, and protein quality control. Of 7848 DE genes identified via pseudo-bulk snRNA-seq, 51% were DE in fibroblasts and 47% in cardiomyocytes, compared to <20% in other cell types. Unlike dilated cardiomyopathy (DCM), sub-clustering fibroblasts did not reveal an activated fibroblast population in HFpEF. Comparative analysis between HFpEF and DCM identified transcriptional differences primarily in cardiomyocytes. ConclusionsThis study demonstrates the power of genotype-based demultiplexing for single-cell transcriptomic analyses of small endomyocardial biopsies and identifies cardiomyocytes as the principal cell type with distinct transcriptional changes in HFpEF versus DCM. These findings, coupled with differential gene expression and functional pathway analyses, illuminate HFpEF pathways and may nominate compelling targets for future mechanistic studies and therapeutic efforts for HFpEF. Clinical PerspectiveWhat is new? We successfully used genotype-based demultiplexing to perform single nucleus RNA-seq from myocardial biopsies. The snRNA-seq analysis revealed distinct enrichment of pathways related to transcription/translation, immune activation, metabolism, and protein quality control across multiple cell types in HFpEF. In contrast to DCM, HFpEF is distinguished by the absence of an activated fibroblast population and a predominance of transcriptional differences within cardiomyocytes, highlighting a distinct disease mechanism. What are the clinical implications? The cell-selective HFpEF myocardial transcriptional landscape highlights altered metabolism, protein translation and quality control, immune activation and growth/matrix organization. These pathways provide compelling new targets for developing effective treatments. ]]> Hahn, V. S. Chaffin, M. Simonson, B. Jenkin, S. Mulligan, A. S. Bedi, K. Margulies, K. B. Klattenhoff, C. Sharma, K. Kass, D. A. Ellinor, P. T. 2025-03-12 doi:10.1101/2025.03.06.641949 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Gold Nanocages with a Long SPR Peak Wavelength as Contrast Agents for Optical Coherence Tomography Imaging at 1060 nm ]]> https://biorxiv.org/content/10.1101/2025.03.09.642209v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@179a727org.highwire.dtl.DTLVardef@1cd1e4eorg.highwire.dtl.DTLVardef@180ce47org.highwire.dtl.DTLVardef@166a779_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, Y. Xi, J. Lee, D. Ramella-Roman, J. Li, X. 2025-03-13 doi:10.1101/2025.03.09.642209 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Comparison of oviposition and adult trapping to monitor wMel introgression for Wolbachia-based vector control ]]> https://biorxiv.org/content/10.1101/2025.03.10.642347v1?rss=1 Nelson, E. Pereira, T. N. Ribeiro, E. M. d. C. Mafra e Silva, B. D. Camillo, C. Rodrigues da Costa, T. Teixeira, M. M. Ko, A. I. Cummings, D. A. Moreira, L. A. 2025-03-13 doi:10.1101/2025.03.10.642347 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Longitudinal changes in functional connectivity networks in the first year following stroke ]]> https://biorxiv.org/content/10.1101/2025.03.10.642404v1?rss=1 Tao, Y. Schnur, T. T. Ding, J. Martin, R. Rapp, B. 2025-03-13 doi:10.1101/2025.03.10.642404 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Sub-second Fluctuation between Top-Down and Bottom-Up Modes Distinguishes Diverse Human Brain States ]]> https://biorxiv.org/content/10.1101/2025.03.12.642768v1?rss=1 Park, Y. Cha, Y. Kim, H. Kim, Y. Woo, J. H. Cho, H. Mashour, G. A. Xu, T. Lee, U. Hong, S.-J. Honey, C. Moon, J.-Y. 2025-03-13 doi:10.1101/2025.03.12.642768 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Single-Cell Analysis Reveals Tissue-Specific T Cell Adaptation and Clonal Distribution Across the Human Gut-Liver-Blood Axis ]]> https://biorxiv.org/content/10.1101/2025.03.11.642626v1?rss=1 Ran, R. Uslu, M. Siddiqui, M. F. Brubaker, D. Trapecar, M. 2025-03-14 doi:10.1101/2025.03.11.642626 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.03.12.642800v1?rss=1 Young, J. Cho, N. W. Lucas, C.-H. G. Najem, H. Mirchia, K. Chen, W. C. Seo, K. Zakimi, N. Daggubati, V. Casey-Clyde, T. Nguyen, M. P. Chen, A. Phillips, J. J. Ozawa, T. Aghi, M. Taylor, J. DeRisi, J. L. Bhaduri, A. Berger, M. S. Heimberger, A. B. Butowski, N. Spitzer, M. H. Raleigh, D. R. 2025-03-14 doi:10.1101/2025.03.12.642800 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Independent mechanisms of benzimidazole resistance across Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2025.03.13.643047v1?rss=1 Shaver, A. O. McKeown, R. Reyes Otero, J. M. Andersen, E. C. 2025-03-15 doi:10.1101/2025.03.13.643047 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition ]]> https://biorxiv.org/content/10.1101/2025.03.13.643053v1?rss=1 Wang, Q. Kong, X. Song, H. Wang, L. Li, L. Hou, X. Renuse, S. Cheng, R. Khan, M. K. H. Fang, L. Lotan, T. L. Park, B. H. Weroha, S. J. Zhou, H. Pandey, A. Wu, X. 2025-03-15 doi:10.1101/2025.03.13.643053 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Tetraspanin positivity as a function of extracellular vesicle size measured by a modified immuno-TEM protocol ]]> https://biorxiv.org/content/10.1101/2025.03.13.643132v1?rss=1 Fagundez, P. Olivera, A. Gololobova, O. O. Li Calzi, M. Cayota, A. Witwer, K. Mendez, E. Tosar, J. P. 2025-03-15 doi:10.1101/2025.03.13.643132 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Progressively reduced cerebral oxygen metabolism and elevated plasma NfL levels in the zQ175DN mouse model of Huntington disease ]]> https://biorxiv.org/content/10.1101/2025.03.16.643551v1?rss=1 Wu, Q. Yao, M. Liu, H. Kakazu, A. Ouyang, Y. Liu, C. Li, R. Yang, F. Wang, A. Surasinghe, S. Gerochi, D. Baldo, B. Jahn, S. Tang, H. Lu, H. Wei, Z. Duan, W. 2025-03-16 doi:10.1101/2025.03.16.643551 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ Gold Nanocages as Scattering Contrast Agents for Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/2025.03.14.643380v1?rss=1 Chen, Y. Xi, J. Lee, D. Ramella-Roman, J. Li, X. 2025-03-17 doi:10.1101/2025.03.14.643380 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Setdb2 Regulates Inflammatory Trigger-Induced Trained Immunity of Macrophages Through Two Different Epigenetic Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.03.18.644013v1?rss=1 Jaiswal, A. Halasz, L. Williams, D. L. Osborne, T. 2025-03-19 doi:10.1101/2025.03.18.644013 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Immortalization and Characterization of Schwann Cell Lines Derived from NF1 Associated Cutaneous Neurofibromas ]]> https://biorxiv.org/content/10.1101/2025.03.19.643702v1?rss=1 Li, H. Pemov, A. Allaway, R. J. Muir, D. F. Chang, L.-J. Banerjee, J. Scott, A. J. Nagy, J. M. Liu, J. Carrio, M. Mazuelas, H. Yachnis, A. Lee, S. Y. Zhang, X. Lyu, Y. Stewart, D. R. Hirbe, A. Blakeley, J. O. Serra, E. Wallis, D. Wallace, M. R. 2025-03-20 doi:10.1101/2025.03.19.643702 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ A novel enterococcus phage endolysin Lys22 with a wide host range against mixed biofilm of Enterococcus faecalis, Staphylococcus aureus and Acinetobacter baumannii ]]> https://biorxiv.org/content/10.1101/2025.03.11.642608v1?rss=1 Yang, Z. Du, X. Hu, N. Feng, M.-a. Xu, J. Jiang, H. Zhang, N. Huang, H. Li, J. Shi, H. 2025-03-21 doi:10.1101/2025.03.11.642608 Cold Spring Harbor Laboratory Press 2025-03-21 <![CDATA[ Biochemical analysis of human eIF4E-DCP2 interaction: Implications for the relationship between translation initiation and decapping ]]> https://biorxiv.org/content/10.1101/2025.03.21.644491v1?rss=1 Coller, J. Mandell, Z. 2025-03-22 doi:10.1101/2025.03.21.644491 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species ]]> https://biorxiv.org/content/10.1101/2025.03.20.644351v1?rss=1 Chao, K.-H. Mao, A. Liu, A. Salzberg, S. L. Pertea, M. 2025-03-23 doi:10.1101/2025.03.20.644351 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors ]]> https://biorxiv.org/content/10.1101/2025.03.23.644666v1?rss=1 Muratspahic, E. Feldman, D. Kim, D. E. Qu, X. Bratovianu, A.-M. Rivera-Sanchez, P. Dimitri, F. Cao, J. Cary, B. P. Belousoff, M. J. Keov, P. Chen, Q. Ren, Y. Fine, J. Sappington, I. Schlichthaerle, T. Zhang, J. Z. Pillai, A. Mihaljevic, L. Bauer, M. Torres, S. V. Motmaen, A. Lee, G. R. Tran, L. Wang, X. Goreshnik, I. Vafeados, D. K. Svendsen, J. E. Hosseinzadeh, P. Lindegaard, N. Brandt, M. Waltenspühl, Y. Deibler, K. Oostdyk, L. Cao, W. Anantharaman, L. Stewart, L. Halloran, L. Spangler, J. B. Sexton, P. M. Roth, B. L. Krumm, B. E. Wootten, D. Tate, 2025-03-23 doi:10.1101/2025.03.23.644666 Cold Spring Harbor Laboratory Press 2025-03-23 <![CDATA[ Glutamate indicators with increased sensitivity and tailored deactivation rates ]]> https://biorxiv.org/content/10.1101/2025.03.20.643984v1?rss=1 Aggarwal, A. Negrean, A. Chen, Y. Iyer, R. Reep, D. Liu, A. Palutla, A. Xie, M. E. MacLennan, B. Hagihara, K. M. Kinsey, L. W. Sun, J. L. Yao, P. Zheng, J. Tsang, A. Tsegaye, G. Zhang, Y. Patel, R. H. Arthur, B. J. Hiblot, J. Leippe, P. Tarnawski, M. Marvin, J. S. Vevea, J. D. Turaga, S. C. Tebo, A. G. Carandini, M. Rossi, L. F. Kleinfeld, D. Konnerth, A. Svoboda, K. Turner, G. C. Hasseman, J. Podgorski, K. 2025-03-24 doi:10.1101/2025.03.20.643984 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Translating the Post-Mortem Brain Multi-Omics Molecular Taxonomy of Alzheimer's Dementia to Living Humans ]]> https://biorxiv.org/content/10.1101/2025.03.20.644323v1?rss=1 Iturria-Medina, Y. Poole, V. N. Zammit, A. R. de Paiva Lopes, K. Vialle, R. A. Yu, L. Tasaki, S. Batalha, C. Hong, J. H. Sanchez-Rodriguez, L. Geddes, M. R. Abadir, P. Ortlund, E. A. De Jager, P. Menon, V. Schnaider Beeri, M. Buchman, A. S. Levin, Y. Morgenstern, D. Schneider, J. A. Kaddurah-Daouk, R. Wyss-Coray, T. Seyfried, N. Poulakis, K. Rosa-Neto, P. Wang, Y. Bennett, D. A. 2025-03-24 doi:10.1101/2025.03.20.644323 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids ]]> https://biorxiv.org/content/10.1101/2025.03.20.644422v1?rss=1 McNerney, C. Santiago, C. Eldred, K. C. Glass, I. Reh, T. A. Hernandez, A. Blackshaw, S. Lord, N. Johnston, R. J. 2025-03-24 doi:10.1101/2025.03.20.644422 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Anti-citrullinated protein antibodies arise during affinity maturation of germline antibodies to carbamylated proteins in rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2025.03.22.644346v1?rss=1 Escarra-Senmarti, M. Chungyoun, M. Ferris, D. Gray, J. J. Andrade, F. 2025-03-25 doi:10.1101/2025.03.22.644346 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Lignature: A Comprehensive Database of Ligand Signatures to Predict Cell-Cell Communication ]]> https://biorxiv.org/content/10.1101/2025.03.22.644770v1?rss=1 Xin, Y. Amanullah, M. Qian, C. Zhou, C. Qian, J. 2025-03-25 doi:10.1101/2025.03.22.644770 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Using Random Forests to Infer Nonlinear Step Selection Effects ]]> https://biorxiv.org/content/10.1101/2025.03.27.644749v1?rss=1 Koshute, P. Robinette, M. Fagan, W. F. 2025-03-28 doi:10.1101/2025.03.27.644749 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Elimination of senescent cells with senolytic host-directed therapy reduces tuberculosis progression in mice ]]> https://biorxiv.org/content/10.1101/2025.03.28.645957v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@1ce7eeeorg.highwire.dtl.DTLVardef@1ef55d4org.highwire.dtl.DTLVardef@1ebef03org.highwire.dtl.DTLVardef@98b61f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMtb lung infection results in recruitment of both restrictive and permissive myeloid cells to the nascent granuloma. C_LIO_LIMtb infection induces certain permissive myeloid cells to enter a senescent state, characterized by cell cycle arrest and they promote local immunosuppression. C_LIO_LITreatment with a Senolytic drug cocktail, which kills senescent cells, augments host resistance against Mtb proliferation, lethality and immunopathology. C_LI ]]> Bishai, W. Shee, S. Martinez-Martinez, Y. B. Koleske, B. Yabaji, S. M. Kobzik, L. Kramnik, I. 2025-03-28 doi:10.1101/2025.03.28.645957 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Multiple Wnt signaling pathways direct epithelial tubule interconnection in the regenerating zebrafish kidney ]]> https://biorxiv.org/content/10.1101/2025.03.26.645545v1?rss=1 Kamei, C. N. Sampson, W. G. B. Albertz, C. Aries, O. Wolf, A. Upadhyay, R. Hughes, S. Schenk, H. Bonnet, F. Draper, B. B. W. McCracken, K. Marciano, D. Oxburgh, L. Drummond, I. A. 2025-03-29 doi:10.1101/2025.03.26.645545 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Use of Droplet Digital PCR for Consistent Detection of TMPRSS2:ERG Gene Fusion Transcripts Initiated In Vitro ]]> https://biorxiv.org/content/10.1101/2025.03.26.645503v1?rss=1 Check, M. H. Ernst, S. E. Sfanos, K. S. 2025-03-30 doi:10.1101/2025.03.26.645503 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Temporal and Spatial Scales of Resting-state Human Cortical Activity Throughout Lifespan ]]> https://biorxiv.org/content/10.1101/2025.03.28.645952v1?rss=1 Bero, J. Humphries, C. Li, Y. Kumar, A. Lee, H. Shinn, M. Murray, J. D. Vickery, T. Lee, D. 2025-03-30 doi:10.1101/2025.03.28.645952 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Antigen-presenting cancer-associated fibroblasts in murine pancreatic tumors differentially control regulatory T cell phenotype and function via CXCL9 and CCL22 ]]> https://biorxiv.org/content/10.1101/2025.03.27.645833v1?rss=1 Maru, S. Y. Wetzel, M. Mitchell, J. T. Gross, N. E. Andaloori, L. Howe, K. Kartalia, E. Mo, G. Leatherman, J. Ho, W. J. Fertig, E. J. Kagohara, L. T. Pearce, E. J. Jaffee, E. M. 2025-04-01 doi:10.1101/2025.03.27.645833 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA ]]> https://biorxiv.org/content/10.1101/2025.04.01.643995v1?rss=1 Paul, T. Lee, I.-R. Pangeni, S. Rashid, F. Yang, O. Antony, E. Berger, J. M. Myong, S. Ha, T. 2025-04-01 doi:10.1101/2025.04.01.643995 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Compact lens-based dual-channel adaptive optics scanning laser ophthalmoscopy for in-vivo three-dimensional retinal imaging in mice ]]> https://biorxiv.org/content/10.1101/2025.03.31.645335v1?rss=1 Li, Z. Mary, S. Johnson, T. V. Yi, J. 2025-04-02 doi:10.1101/2025.03.31.645335 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Optimizing Artificial Neural Network Models to Predict Brain-Age from Functional MRI ]]> https://biorxiv.org/content/10.1101/2025.03.28.645964v1?rss=1 Ogg, M. Kitchell, L. 2025-04-03 doi:10.1101/2025.03.28.645964 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Identifying potential biomarkers of response to CCR5Δ32 HSCT in HIV infection ]]> https://biorxiv.org/content/10.1101/2025.03.30.646188v1?rss=1 Chang, J. Gabhann, F. M. 2025-04-03 doi:10.1101/2025.03.30.646188 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Developing a zebrafish xenograft model of diffuse midline glioma ]]> https://biorxiv.org/content/10.1101/2025.03.31.646163v1?rss=1 Wang, K. Graziano, G. Ceisel, A. Xiao, H. Banerjee, S. Yu, Y. Galanternik, M. V. Weinstein, B. M. Eberhart, C. G. Mumm, J. S. Raabe, E. H. 2025-04-03 doi:10.1101/2025.03.31.646163 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling ]]> https://biorxiv.org/content/10.1101/2025.03.31.646342v1?rss=1 Hallinan, C. Ji, H. J. Salzberg, S. L. Fan, J. 2025-04-03 doi:10.1101/2025.03.31.646342 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Discovery and therapeutic exploitation of Master Regulatory miRNAs in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.04.01.646663v1?rss=1 Abounader, R. Saha, S. Zhang, Y. Gibert, M. K. Dube, C. Hanif, F. Mulcahy, E. Bednarek, S. Marcinkiewicz, P. Wang, X. Kwak, G. Hudson, K. Sun, Y. Dinda, M. Saha, T. Guessous, F. Cruickshanks, N. Colon, R. R. Dell'Olio, L. G. Anbu, R. Kefas, B. Kumar, P. Klibanov, A. L. Schiff, D. Suk, J. S. Hanes, J. Mata, J. Hafner, M. 2025-04-03 doi:10.1101/2025.04.01.646663 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Accelerated Discovery of Cell Migration Regulators Using Label-Free Deep Learning-Based Automated Tracking ]]> https://biorxiv.org/content/10.1101/2025.04.01.646705v1?rss=1 wu, p.-h. Wirtz, D. Chu, T. lim, y. Sun, Y. 2025-04-03 doi:10.1101/2025.04.01.646705 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Aging reduces excitatory bandwidth, alters spectral tuning curve diversity, and reduces sideband inhibition in L2/3 of primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2025.04.02.646797v1?rss=1 Maximov, K. O. Kanold, P. 2025-04-03 doi:10.1101/2025.04.02.646797 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ 5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins ]]> https://biorxiv.org/content/10.1101/2025.04.02.646885v1?rss=1 Hayes, L. R. Zaepfel, B. Duan, L. Starner, A. C. Bartels, M. D. Rothacher, R. L. Martin, S. French, R. Zhang, Z. Sinha, I. R. Ling, J. P. Sun, S. Ayala, Y. M. Coller, J. Van Nostrand, E. L. Florea, L. Kalab, P. 2025-04-03 doi:10.1101/2025.04.02.646885 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Glycolysis-enhancing alpha 1-adrenergic antagonists are neuroprotective in Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2025.04.03.647018v1?rss=1 Zhang, Q. Schultz, J. Simmering, J. Kirkpatrick, B. Q. Weber, M. A. Skuodas, S. Hicks, T. Pierce, G. Laughlin, M. Bertolli, A. X. Larson, T. Thangavel, R. Oya, M. Meyerholz, D. Aldridge, G. Fassler, J. Narayanan, N. S. 2025-04-03 doi:10.1101/2025.04.03.647018 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods ]]> https://biorxiv.org/content/10.1101/2025.03.31.646356v1?rss=1 Forjaz, A. Kramer, D. Shen, Y. Bea, H. Tsapatsis, M. Ping, J. Queiroga, V. Han, K. S. Joshi, S. Grubel, C. Beery, M. L. Kusmartseva, I. Atkinson, M. A. Kiemen, A. L. Wirtz, D. 2025-04-04 doi:10.1101/2025.03.31.646356 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ JACUZI-SD: An automated, high-throughput, minimally stressful approach to sleep depriving larval zebrafish. ]]> https://biorxiv.org/content/10.1101/2025.04.03.647099v1?rss=1 Elias, L. J. Khoo, H. Kroll, F. Zhang, C. Hur, S. C. Rihel, J. Blackshaw, S. 2025-04-04 doi:10.1101/2025.04.03.647099 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1 ]]> https://biorxiv.org/content/10.1101/2025.04.04.647291v1?rss=1 1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs. ]]> Hariharan, V. White, J. A. Dragoni, F. Fray, E. J. Pathoulas, N. Moskovljevic, M. Zhang, H. Singhal, A. Lai, J. Beg, S. A. Scully, E. P. Gilliams, E. A. Block, D. S. Keruly, J. Moore, R. D. Siliciano, J. D. Simonetti, F. R. Siliciano, R. F. 2025-04-04 doi:10.1101/2025.04.04.647291 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ Nonlinear integration of sensory and motor inputs by a single neuron in C. elegans. ]]> https://biorxiv.org/content/10.1101/2025.04.05.647390v1?rss=1 Ray, A. Gordus, A. G. 2025-04-06 doi:10.1101/2025.04.05.647390 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Chemical Compensation to Mechanical Loss in CellMechanosensation ]]> https://biorxiv.org/content/10.1101/2025.04.02.646640v1?rss=1 Ni, Q. Ge, Z. Sen, A. Wu, Y. Fu, J. Amitrano, A. Srivastava, N. Konstantopoulos, K. Sun, S. 2025-04-07 doi:10.1101/2025.04.02.646640 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Protein diffusion controls how single cells respond to electric fields ]]> https://biorxiv.org/content/10.1101/2025.04.09.647627v1?rss=1 Nwogbaga, I. Belliveau, N. M. Singh, A. R. Sun, D. Mulenga, N. Theriot, J. A. Camley, B. A. 2025-04-10 doi:10.1101/2025.04.09.647627 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Loss of the ESX-5 secretion locus in Mycobacterium tuberculosis reshapes the mycomembrane and enhances ESX-1 substrate secretion ]]> https://biorxiv.org/content/10.1101/2025.04.11.648440v1?rss=1 550 g/mol) antimicrobial compounds, suggesting that an intact ESX-5 system is required for M.tb to exclude such molecules. Our findings suggest that removing the ESX-5 system from M.tb fundamentally alters the properties of the mycobacterial OMM and impacts the expression and secretion activity of other ESX systems. Significance StatementMycobacterium tuberculosis (M.tb) uses the ESX-5 secretion system to export numerous proteins that shape host-pathogen interactions. Here, we found that deleting ESX-5 from M.tb not only prevented the secretion of many ESX-5 substrates but also impacted other ESX systems. The M.tb {Delta}esx5 mutant had increased ESX-1 substrate secretion but reduced ESX-3 expression. In addition, the M.tb {Delta}esx5 mutant displayed altered cell surface morphology and increased vulnerability to large antibiotic drugs, suggesting a critical role for ESX-5 for maintaining outer membrane integrity. These findings highlight ESX-5 as a central modulator of secretion and cell envelope composition with implications for drug targeting and vaccine development. ]]> Koleske, B. Rajagopalan, S. Schill, C. Lun, S. Vilcheze, C. Das, L. Gupta, M. Martinez-Martinez, Y. B. Jacobs, W. R. Bishai, W. R. 2025-04-11 doi:10.1101/2025.04.11.648440 Cold Spring Harbor Laboratory Press 2025-04-11 <![CDATA[ Microbes regulate glomerular filtration rate in health and chronic kidney disease in mice ]]> https://biorxiv.org/content/10.1101/2025.04.08.647647v1?rss=1 Xu, J. Verma, E. Sanchez, J. Gharaie, S. Jeong, S. Gooya, M. Gupta, K. Rabb, H. Pluznick, J. L. 2025-04-14 doi:10.1101/2025.04.08.647647 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images ]]> https://biorxiv.org/content/10.1101/2025.04.11.648464v1?rss=1 Matos-Romero, V. Gomez-Becerril, J. Forjaz, A. Dequiedt, L. Newton, T. Joshi, S. Shen, Y. Hanna, E. Nair, P. R. Sivasubramanian, A. Wang, J. Lasse-Opsahl, E. L. Bell, A. T. F. Czum, J. Steenbergen, C. Dai, D.-F. Wood, L. D. Kagohara, L. T. Fertig, E. J. Pasca di Magliano, M. Shatzel, J. McCarty, O. J. Lo, J. O. Rosenberg, A. Hruban, R. H. Munoz-Barrutia, A. Wirtz, D. Kiemen, A. L. 2025-04-14 doi:10.1101/2025.04.11.648464 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Spatial distribution of cytoskeleton-mediated feedback controls cell polarization: a computational study ]]> https://biorxiv.org/content/10.1101/2025.04.12.648264v1?rss=1 Banerjee, P. Kuhn, J. Pal, D. S. Deng, Y. Banerjee, T. Devreotes, P. N. Iglesias, P. A. 2025-04-14 doi:10.1101/2025.04.12.648264 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ An Essential Adaptor for Apicoplast Fission and Inheritance in Malaria Parasites ]]> https://biorxiv.org/content/10.1101/2025.04.12.648511v1?rss=1 Blauwkamp, J. A. Rajaram, K. Staggers, S. R. Harrigan, O. Doud, E. H. Prigge, S. T. Sun, S. Y. Absalon, S. 2025-04-14 doi:10.1101/2025.04.12.648511 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Unpacking similarity effects in visual memory search: categorical, semantic, and visual contributions ]]> https://biorxiv.org/content/10.1101/2025.04.09.647918v1?rss=1 Shang, L. Yeh, L.-C. Zhao, Y. Peelen, M. V. 2025-04-15 doi:10.1101/2025.04.09.647918 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Neuronal titration of Snca via enhancer disruption mitigates disease onset in a Parkinson's disease mouse model ]]> https://biorxiv.org/content/10.1101/2025.04.09.648026v1?rss=1 Boyd, R. J. Kho, A. R. McClymont, S. Loftus, S. K. Ko, H. McCallion, A. S. 2025-04-15 doi:10.1101/2025.04.09.648026 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ The Maternal Effect of SKN-1B and DAF-7 on Intergenerational Pathogen Avoidance Learning in C. elegans. ]]> https://biorxiv.org/content/10.1101/2025.04.14.648668v1?rss=1 Paisner, R. Bekele, M. Onyia, E. Gordus, A. G. 2025-04-15 doi:10.1101/2025.04.14.648668 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Autophagy-Dependent Regulation of YAP1 by STK38 Governs Recruitment of Differentiated Cells as Progenitor Cells During Regeneration ]]> https://biorxiv.org/content/10.1101/2025.04.14.648819v1?rss=1 Zeng, Y. Huang, Y.-Z. Li, Q. K. Ho, R. Bark, S. J. Willet, S. G. Mills, J. C. 2025-04-16 doi:10.1101/2025.04.14.648819 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ A community-consensus reconstruction of Chinese Hamster metabolism enables structural systems biology analyses to decipher metabolic rewiring in lactate-free CHO cells ]]> https://biorxiv.org/content/10.1101/2025.04.10.647063v1?rss=1 70% of its 7377 metabolites, enabling deeper exploration of the link between molecular structure and cellular metabolism. We used iCHO3K to contextualize transcriptomics and metabolomics data from a CHO cell line in which lactate secretion is abolished. We found the reduced glycolytic flux and enhanced TCA cycle flux were accompanied by an elevated NADH and PEP levels in these cells, consistent with experimental measurements. Leveraging iCHO3Ks structural annotations, we identified candidate binding interactions of NADH and PEP with glycolytic enzymes showing model-predicted differential flux, suggesting novel allosteric regulation associated with the observed decrease in glucose uptake and glycolysis. Overall, iCHO3K offers a valuable framework for systematic integration of omics data, improved flux predictions, and structure-guided insights, thus advancing CHO cell engineering and enhancing biomanufacturing efficiency. ]]> Di Giusto, P. Choi, D.-H. Antonakoudis, A. Duraikannan, V. G. Craveur, P. Cowie, N. L. Ganapathy, T. Ramesh, K. Benavidez-Lopez, S. Orellana, C. A. Jimenez, N. E. Dworkin, L. A. Morrissey, J. Marin de Mas, I. Strain, B. Valdez-Cruz, N. A. Trujillo-Roldan, M. A. Marzluf, J. Martinez, V. S. Zehetner, L. Altamirano, C. Vega-Letter, A. M. Priem, B. Cao, H. C. Hold, M. Ma, J. Hong, Y. Gopalakrishnan, S. Enuh, B. M. Tarzi, C. Pang, K. T. Angione, C. Zanghellini, J. Kontoravdi, C. Hefzi, H. Betenbaugh, M. J. Nielsen, L. K. Lakshmanan, M. Lee, D.-Y. Richelle, A. 2025-04-17 doi:10.1101/2025.04.10.647063 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Gliomas organize as liquid crystals: three-dimensional nematic order, disclinations and quasi-long-range order ]]> https://biorxiv.org/content/10.1101/2025.04.14.648711v1?rss=1 Argento, A. E. Varela, M. L. Singh, G. Visnuk, D. P. Jacobovitz, B. Rutherford, M. E. Edwards, M. B. Chaboche, Q. Orringer, D. A. Heth, J. A. Castro, M. G. Beller, D. A. Blanch-Mercader, C. Lowenstein, P. 2025-04-17 doi:10.1101/2025.04.14.648711 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Detection of Aggressive Mesenchymal Glioblastoma by Mannose-Weighted CEST MRI ]]> https://biorxiv.org/content/10.1101/2025.04.15.648948v1?rss=1 Ghaemi, B. Lopez-Bertoni, H. Kuddannaya, S. Sall, S. Laterra, J. Liu, G. Bulte, J. 2025-04-17 doi:10.1101/2025.04.15.648948 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Uncovering Shared and Tissue-Specific Molecular Adaptations to Intermittent Fasting in Liver, Brain, and Muscle ]]> https://biorxiv.org/content/10.1101/2025.04.13.648650v1?rss=1 Fan, Y. De Silva, S. Tabassum, N. I. Peng, X. Lim, V. Cheng, X. Datta, K. K. Lowe, R. Johns, T. G. Mattson, M. P. Mathivanan, S. Sobey, C. G. Okun, E. Liu, Y. U. Chen, G. Lai, M. K. P. Jo, D.-G. Gunaratne, J. Arumugam, T. V. 2025-04-18 doi:10.1101/2025.04.13.648650 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Photodisruption of the inner limiting membrane promotes retinal engraftment of stem-cell derived retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/2025.04.14.648093v1?rss=1 De Coster, E. De Clerck, K. De Clercq, C. Li, W. Punj, D. Vanmeerhaeghe, B. De Smedt, S. Braeckmans, K. Hadady, H. Remaut, K. Johnson, T. V. Peynshaert, K. 2025-04-19 doi:10.1101/2025.04.14.648093 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Write and read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing. ]]> https://biorxiv.org/content/10.1101/2025.04.14.648727v1?rss=1 Bertocchi, U. Grunwald, A. Goldner, G. Eitan, E. Avraham, S. Deek, J. Michaeli, Y. Yao, B. Listgarten, J. Simpson, J. T. Timp, W. Ebenstein, Y. 2025-04-19 doi:10.1101/2025.04.14.648727 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ From Decay to Rhythm: Sustained Biological Oscillators Require More Than Chemistry Alone ]]> https://biorxiv.org/content/10.1101/2025.04.15.648857v1?rss=1 Wu, Y. Sun, S. 2025-04-19 doi:10.1101/2025.04.15.648857 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Fast and accessible morphology-free functional fluorescence imaging analysis ]]> https://biorxiv.org/content/10.1101/2025.04.15.648462v1?rss=1 Estrada Berlanga, A. A. Kang, G. Kwok, A. Broggini, T. Lawlor, J. Kuchibhotla, K. Kleninfeld, D. Mishne, G. Charles, A. 2025-04-20 doi:10.1101/2025.04.15.648462 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Improved Injury Detection Through Harmonizing Multi-Site Neuroimaging Data after Experimental TBI: A Translational Outcomes Project in NeuroTrauma (TOP-NT) Consortium Study ]]> https://biorxiv.org/content/10.1101/2025.04.15.649026v1?rss=1 5%) and skewness, which introduced significant variation in non-outlier sites. After removal of one outlier site and harmonization using a global sham population, harmonization displayed an increase in effect size in data that displayed group level effects (p<0.01) in both univariate and voxel-level volumes of pathology. This was characterized by movement toward similar distributions in voxel measurements (Kolmogorov-Smirnov p<<0.001 to >0.01) and statistical power increases within the ipsilateral cortex. Harmonization improved statistical power and frequency of significant differences in areas with existing group differences, thus improving the ability to detect regions affected by injury rather than by other confounds. These findings indicate the utility of NeuroCombat in reproducible data collection, where biological differences can be accurately revealed to allow for greater reliability in multi-site neuroimaging studies. Significance StatementThis project demonstrates the utility of NeuroCombat in reducing site effects in multi-site rodent imaging. We also demonstrate that harmonization improves the ability to distinguish between sham and injured rats at the voxel level and increase statistical power and effect size in areas of injury. Multi-center studies are becoming more common to allow for increased efficiency in data collection, and with conservative approaches and analysis into the datasets, NeuroCombat can be utilized to improve study reliability and reproducibility. ]]> Kislik, G. Fox, R. Korotcov, A. V. Zhou, J. Febo, M. Moghadas, B. Bibic, A. Zou, Y. Wan, J. Koehler, R. C. Adebayo, T. Burns, M. P. McCabe, J. T. Wang, K. K. Huie, J. R. Ferguson, A. R. Harris, N. G. The TOP-NT Investigators, 2025-04-20 doi:10.1101/2025.04.15.649026 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Cold Quad-Modal Nanocomplex for Precise and Quantitative in Vivo Stem Cell Tracking ]]> https://biorxiv.org/content/10.1101/2025.04.16.649154v1?rss=1 Shakeri-Zadeh, A. Wang, C. Kuddannaya, S. Yousf, S. Bulte, J. 2025-04-20 doi:10.1101/2025.04.16.649154 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Mechanism of USP21 autoinhibition and histone H2AK119 deubiquitination ]]> https://biorxiv.org/content/10.1101/2025.04.17.649347v1?rss=1 Rahman, S. Morgan, M. T. Hicks, C. W. Gwizdala, A. Wolberger, C. 2025-04-21 doi:10.1101/2025.04.17.649347 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ HIV IMPAIRS AND EXPLOITS PULMONARY TH17 AND TH22 CELL-MEDIATED IMMUNE RESPONSES TO MYCOBACTERIUM TUBERCULOSIS ]]> https://biorxiv.org/content/10.1101/2025.04.16.649152v1?rss=1 Martinez-Martinez, Y. B. Huante, M. B. Naqvi, K. F. Shah, M. N. Lisinicchia, J. G. Files, M. A. Perez, J. Gelman, B. B. Endsley, M. A. Endsley, J. J. 2025-04-22 doi:10.1101/2025.04.16.649152 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Privacy-Preserving Generative AI Framework for Synthetic Multimodal Eye Movement Data ]]> https://biorxiv.org/content/10.1101/2025.04.21.649786v1?rss=1 Rahman, A. Bachina, P. Patel, V. Green, K. E. 2025-04-22 doi:10.1101/2025.04.21.649786 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories ]]> https://biorxiv.org/content/10.1101/2025.04.21.649824v1?rss=1 Grimm, S. L. Jangid, R. Bartolomei, M. S. Dolinoy, D. C. Aylor, D. L. Mutlu, G. M. Biswal, S. Zhang, B. Wang, T. TaRGET II Consortium, Coarfa, C. Walker, C. L. 2025-04-22 doi:10.1101/2025.04.21.649824 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Proviruses in CD4+ T cells reactive to autologous antigens contribute to nonsuppressible HIV-1 viremia ]]> https://biorxiv.org/content/10.1101/2025.04.19.649587v1?rss=1 Wu, F. Moskovjlevic, M. Dragoni, F. Jayaraman, S. Board, N. L. Camilo-Contreras, A. Bernal, S. Hariharan, V. Zhang, H. Lai, J. Singhal, A. Poulin, S. Chano, F. Chamberland, A. Tremblay, C. Zoltik, M. Hoffmann, C. J. Jones, J. L. Larman, H. B. Montaner, L. J. Siliciano, J. D. Siliciano, R. F. Simonetti, F. R. 2025-04-23 doi:10.1101/2025.04.19.649587 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Short Report: A Meta-Analysis of the Effects of Sleep Deprivation on the Cortical Transcriptome in Animal Models ]]> https://biorxiv.org/content/10.1101/2025.04.21.648791v1?rss=1 19,000 re-analyzed microarray and RNA-Seq datasets. Eight studies met our systematic inclusion/exclusion criteria. These studies characterized the effect of 18 SD interventions on gene expression in the mouse cerebral cortex (collective n=293). For each gene with sufficient data (n=16,290), we fit a random effects meta-analysis model to the SD effect sizes (log(2) fold changes). Our meta-analysis revealed 182 differentially expressed genes in response to SD (false discovery rate: FDR<0.05), most of which (115/182) showed similar effects (FDR<0.05) in an independent large dataset (GSE114845: n=86 RNA-Seq samples from n=222 mice). Gene-set enrichment analysis revealed down-regulation in pathways related to stress response (e.g., glucocorticoid receptor Nr3c1), vasculature, growth and development, and upregulation related to stress, inflammation, and neuropeptide signalling. Exploratory analyses suggested that recovery sleep (included in six contrasts: range: 1-18 hrs), could reverse the impact of SD on gene expression. Our meta-analysis provides a useful reference database illustrating the diverse molecular impact of SD on the rodent cerebral cortex. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/648791v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@52984dorg.highwire.dtl.DTLVardef@8d1174org.highwire.dtl.DTLVardef@174ed85org.highwire.dtl.DTLVardef@195e8bf_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Rhoads, C. A. Hagenauer, M. H. Xiong, J. Hernandez, E. Nguyen, D. M. Saffron, A. Flandreau, E. I. Watson, S. Akil, H. 2025-04-23 doi:10.1101/2025.04.21.648791 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.04.21.649828v1?rss=1 Zhang, R. Qi, J. McKasson, M. Choi, J. Gutierrez, V. Brennan, C. Hong, S. Chour, W. Ng, R. H. Xie, J. Yuan, D. Webster, A. Sidhu, S. K. Anderson, A. Chen, D. Edmark, R. Murray, K. M. Li, S. McDonald, C. Rowen, L. Wang, S. Rasheed, Y. Su, Y. Wagner, J. R. Chen, J. Narwaly, K. Fu, J. Duven, A. Forman, S. J. Song, M. Priceman, S. Brown, C. E. Ribas, A. Wong, D. Paulson, K. G. Drescher, C. W. Puig-Saus, C. Goldman, J. D. Trimble, C. L. Heath, J. R. 2025-04-23 doi:10.1101/2025.04.21.649828 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testicular stem cells ]]> https://biorxiv.org/content/10.1101/2025.04.19.649648v1?rss=1 Urban, J. Ringwalt, D. Urban, J. Xue, W. Gleason, R. Zhao, K. Chen, X. 2025-04-24 doi:10.1101/2025.04.19.649648 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Systemic trafficking of mRNA lipid nanoparticle vaccine following intramuscular injection generates potent tissue-specific T cell response ]]> https://biorxiv.org/content/10.1101/2025.04.21.649878v1?rss=1 Wei, C. Zhu, Y. Lu, X. Goodier, K. D. Yu, D. Liu, X. Choy, J. Tellez Calderon, A. Ma, J. Su, Y. Lin, J. Li, S. Schneck, J. P. Murphy, S. C. Mao, H.-Q. 2025-04-24 doi:10.1101/2025.04.21.649878 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ The representation of mood in primate anterior insular cortex ]]> https://biorxiv.org/content/10.1101/2025.04.22.650010v1?rss=1 Rust, N. C. Yang, Y.-P. C. Hacker, C. M. Stuphorn, V. 2025-04-25 doi:10.1101/2025.04.22.650010 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice ]]> https://biorxiv.org/content/10.1101/2025.04.23.650260v1?rss=1 Yao, M. Sun, N. Linville, R. Wei, Z. Kakazu, A. Ouyang, Y. Li, R. Du, L. Wang, H. Zhou, Y. Jiang, Y. Zhang, Z. Li, A. Lu, H. Xu, J. Kellis, M. Heiman, M. Duan, W. 2025-04-29 doi:10.1101/2025.04.23.650260 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Complex cooperativity in DNA origami revealed via design dependent defectivity ]]> https://biorxiv.org/content/10.1101/2025.04.23.650292v1?rss=1 Majikes, J. Hasni, A. Haridas, S. Robertson, J. Pintar, A. Zwolak, M. Liddle, J. A. 2025-04-29 doi:10.1101/2025.04.23.650292 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. ]]> https://biorxiv.org/content/10.1101/2025.04.25.650540v1?rss=1 Weir, K. Lyu, P. Kandoi, S. An, R. Pannullo, N. Palaxxo, I. Tangeman, J. Shi, J. DeVries, S. Merriman, D. Qian, J. Blackshaw, S. 2025-04-29 doi:10.1101/2025.04.25.650540 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Backpropagation through time training of an unrolled Hodgkin Huxley model for automatic conductance estimation ]]> https://biorxiv.org/content/10.1101/2025.04.27.650871v1?rss=1 Li, Y. 2025-04-29 doi:10.1101/2025.04.27.650871 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ MPI-Guided Photothermal Therapy of Prostate Cancer using Stem Cell Delivery of Magnetotheranostic Nanoflowers ]]> https://biorxiv.org/content/10.1101/2025.04.27.650870v1?rss=1 Ghamei, B. Rosu, A. Kuddannaya, S. Laurent, G. Bazzi, R. Roux, S. Sakeri-Zadeh, A. Bulte, J. 2025-04-30 doi:10.1101/2025.04.27.650870 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Chromatix: a differentiable, GPU-accelerated wave-optics library ]]> https://biorxiv.org/content/10.1101/2025.04.29.651152v1?rss=1 Deb, D. Both, G.-J. Bezzam, E. Kohli, A. Yang, S. Chaware, A. Allier, C. Cai, C. Anderberg, G. Eybposh, M. H. Schneider, M. C. Heintzmann, R. Rivera-Sanchez, F. A. Simmerer, C. Meng, G. Tormes-Vaquerano, J. Han, S. Shanmugavel, S. C. Maruvada, T. Yang, X. Kim, Y. Diederich, B. Joo, C. Waller, L. Durr, N. J. Pegard, N. C. La Riviere, P. J. Horstmeyer, R. Chowdhury, S. Turaga, S. C. 2025-05-02 doi:10.1101/2025.04.29.651152 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis. ]]> https://biorxiv.org/content/10.1101/2025.05.01.651492v1?rss=1 Leavey, P. Jiang, L. Pannullo, N. Santiago, C. Blackshaw, S. 2025-05-02 doi:10.1101/2025.05.01.651492 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Mesenchymal WNT2B is Required for the Development and Function of the Human Intestine ]]> https://biorxiv.org/content/10.1101/2025.05.01.651727v1?rss=1 Singh, A. Poling, H. M. Foulke-Abel, J. Sundaram, N. Al Reza, A. Joseph, S. Elseht, A. Srivasta, K. Krutko, M. Mayhew, C. N. Breault, D. Wells, J. M. Thiagarajah, J. R. O'Connell, A. E. Kovbasnjuk, O. Helmrath, M. A. 2025-05-02 doi:10.1101/2025.05.01.651727 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal ]]> https://biorxiv.org/content/10.1101/2025.05.02.651747v1?rss=1 Mitchell, J. T. Stapleton, O. Krishnan, K. Nagaraj, S. Lvovs, D. Cherry, C. Poissonnier, A. Horton, W. Adey, A. Rao, V. Huff, A. Zimmerman, J. W. Kagohara, L. T. Zaidi, N. Coussens, L. M. Jaffee, E. M. Elisseeff, J. H. Fertig, E. J. 2025-05-03 doi:10.1101/2025.05.02.651747 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin ]]> https://biorxiv.org/content/10.1101/2025.05.02.651992v1?rss=1 Liang, J. Wang, Y. Demmerle, J. He, B. J. Ricketts, C. J. Linehan, W. M. Zang, C. Cai, D. 2025-05-03 doi:10.1101/2025.05.02.651992 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ Harmonized Protocol for Subfield Segmentation in the Hippocampal Body on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.04.29.651039v1?rss=1 Daugherty, A. M. Carr, V. Canada, K. Radman, G. Brown, T. Augustinack, J. Amunts, K. Bakker, A. Berron, D. Burggren, A. Chetelat, G. de Flores, R. Ding, S.-L. Huang, Y. Insausti, R. Johnson, E. Kanel, P. Keresztes, A. Kedo, O. Kennedy, K. M. Lee, J. Malykhin, N. Martinez, A. Mueller, S. Mulligan, E. Ofen, N. Palombo, D. Pasquini, L. Pluta, J. Raz, N. Riggins, T. Rodrigue, K. M. Saifullah, S. Schlichting, M. L. Stark, C. Wang, L. Yushkevich, P. La Joie, R. Wisse, L. Olsen, R. the Alzheimers Disease Neuroimaging Initiative, the Hippocampal Subfields Gro 2025-05-04 doi:10.1101/2025.04.29.651039 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Disease-associated loci share properties with response eQTLs under common environmental exposures ]]> https://biorxiv.org/content/10.1101/2025.04.30.651602v1?rss=1 Lin, W. Li, M. Allen, O. Burnett, J. Popp, J. M. Stephens, M. Battle, A. Gilad, Y. 2025-05-04 doi:10.1101/2025.04.30.651602 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Data-driven feedback augments ultrasound nanotheranostics in brain tumors ]]> https://biorxiv.org/content/10.1101/2025.05.01.651328v1?rss=1 Lee, H. Menezes, V. Zeng, S. Kim, C. Baseman, C. M. Kim, J. H. Padmanabhan, S. Premdas, P. Djeddar, N. Bryksin, A. V. Pandey, N. Anastasiadis, P. Kim, A. J. MacDonald, T. J. Bettegowda, C. Woodworth, G. F. Hermann, F. J. Arvanitis, C. 2025-05-07 doi:10.1101/2025.05.01.651328 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Adaptive learning of a naturalistic bimanual task in virtual reality ]]> https://biorxiv.org/content/10.1101/2025.05.01.651653v1?rss=1 Varghese, R. Rossi, C. Malone, L. A. Bastian, A. J. 2025-05-07 doi:10.1101/2025.05.01.651653 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes ]]> https://biorxiv.org/content/10.1101/2025.05.01.651657v1?rss=1 Sadri, G. Nadakal, S. T. Lauer, W. A. Kos, J. Singh, P. Elliott, E. M. Kaiser, C. Ford, E. E. Richardson, N. Hudson, E. Linden, N. Danesh, A. Powell, J. Warburton, P. Soto, J. Emery, M. Deikus, G. Lee, G. Q. Lamers, S. Reynolds, S. J. Galiwango, R. M. Prodger, J. L. Tomusange, S. Kityamuweesi, T. Han, T. Jones, R. B. Tobian, A. A. R. Engelman, A. N. Sebra, R. Morgello, S. Redd, A. D. Sachs, D. Rouchka, E. Smith, M. L. 2025-05-07 doi:10.1101/2025.05.01.651657 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Detecting neuroplastic effects induced by ketamine in healthy human subjects: a multimodal approach ]]> https://biorxiv.org/content/10.1101/2025.05.01.651686v1?rss=1 Agnorelli, C. Peill, J. Sawicka, G. Kurtin, D. L. Shatalina, E. Ahmad, K. Wall, M. B. Rua, C. Godfrey, K. Ertl, N. Searle, G. Zhou, K. Weiss, B. Fagiolini, A. Carhart-Harris, R. Matthews, P. M. Rabiner, E. Nutt, D. Erritzoe, D. 2025-05-07 doi:10.1101/2025.05.01.651686 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Conserved and lineage-restricted gene regulatory programs modulate developmental cnidocyte specification in Nematostella vectensis. ]]> https://biorxiv.org/content/10.1101/2025.05.08.652877v1?rss=1 Danladi, B. Al-Shaer, L. Havrilak, J. A. Faltine-Gonzalez, D. Z. Jia, K. Forwood, W. Dubuc, T. Musser, J. Layden, M. J. 2025-05-09 doi:10.1101/2025.05.08.652877 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Personalized Gut-Liver Microphysiological System Maps Donor-Specific Tissue Resident Immunity and Reveals a Conserved Metabolic Crosstalk ]]> https://biorxiv.org/content/10.1101/2025.05.05.652244v1?rss=1 Uslu, M. Ran, R. Siddiqui, M. F. Liang, J. Raechal, L. Dogsa, M. Perrot, C. Lieberman, L. A. Brubaker, D. K. Trapecar, M. 2025-05-10 doi:10.1101/2025.05.05.652244 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ APOE genotype confers context dependent neurovascular vulnerability in immune-vascularized human forebrain organoids ]]> https://biorxiv.org/content/10.1101/2025.05.08.652864v1?rss=1 Fang, H. Liao, X. Bullen, C. K. Pu, R. Wang, H. Condoleo, J. Cheat, S. Chen, X. Zhang, Y. Zhang, S. Huo, D. Lissit, K. Yang, A. Jarvis, K. Neifert, S. Huang, Y. Bishai, W. Jain, S. K. Dawson, T. Dawson, V. L. Xu, J. 2025-05-10 doi:10.1101/2025.05.08.652864 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Spatially Organized IGF1 mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs ]]> https://biorxiv.org/content/10.1101/2025.05.08.652851v1?rss=1 Xu, J. Lissit, K. Huo, D. Eacker, S. M. Zhang, S. Yang, A. Huang, Y. Dawson, T. Dawson, V. L. 2025-05-12 doi:10.1101/2025.05.08.652851 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ A key role for Canoes intrinsically disordered region in linking cell junctions to the cytoskeleton ]]> https://biorxiv.org/content/10.1101/2025.05.10.653259v1?rss=1 Jensen, C. Gurley, N. Mathias, A. Wolfsbrrg, L. Xiao, Y. Zhou, Z. Slep, K. C. Peifer, M. 2025-05-13 doi:10.1101/2025.05.10.653259 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Serine auxotrophy is a targetable vulnerability driven by PSAT1 suppression in AML ]]> https://biorxiv.org/content/10.1101/2025.05.13.651470v1?rss=1 Sinanidis, I. Tsakiroglou, P. Dubner, B. Foertsch, R. Gondek, J. Choi, I. Paun, B. Zhao, L. Ghiaur, G. Dalton, W. B. 2025-05-14 doi:10.1101/2025.05.13.651470 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Peroxisomes regulate virulence and cell density sensing in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/2025.05.14.654083v1?rss=1 Jacobs, E. Dragotakes, Q. dos Santos, S. R. Smith, D. F. Smith, B. Wolf, J. M. Coelho, C. Casadevall, A. 2025-05-14 doi:10.1101/2025.05.14.654083 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ A Transcriptomic Atlas of Healthy Human Skin Links Regional Identity to Inflammatory Disease. ]]> https://biorxiv.org/content/10.1101/2025.05.10.653184v1?rss=1 Marella, S. Bogle, R. Fox, J. Tsoi, L. C. Xing, X. Gu, Y. Kirma, J. Sarkar, M. K. van Drongelen, V. Klein, B. Kozlow, J. H. Harms, P. Gallagher, K. Naik, S. Rebecca, V. W. Andersen, B. Nakamura, M. Kahlenberg, J. M. Modlin, R. L. Billi, A. C. Gudjonsson, J. E. 2025-05-15 doi:10.1101/2025.05.10.653184 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Automated high-throughput patch clamp electrophysiology of hiPSC-derived neuronal models ]]> https://biorxiv.org/content/10.1101/2025.05.12.653142v1?rss=1 Farinelli, F. Ostlund, I. Sripathy, S. R. Das, D. Shim, G. Myung, S. Straub, R. E. Maher, B. J. 2025-05-15 doi:10.1101/2025.05.12.653142 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ NvashA function reveals temporal differences in neural subtype generation in cnidarians ]]> https://biorxiv.org/content/10.1101/2025.05.12.653478v1?rss=1 Havrilak, J. A. Cheng, M. Al-Shaer, L. Leach, W. B. Yagodich, M. Faltine-Gonzalez, D. Z. Layden, M. J. 2025-05-15 doi:10.1101/2025.05.12.653478 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Rainbow Nucleus Charts Dynamic Interactome of Membrane-less Organelles ]]> https://biorxiv.org/content/10.1101/2025.05.14.654140v1?rss=1 Ye, S. Benhamou Goldfajn, N. So, C. L. Inoue, T. Cai, D. 2025-05-15 doi:10.1101/2025.05.14.654140 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Early development of direction selectivity in higher visual cortex ]]> https://biorxiv.org/content/10.1101/2025.05.15.654265v1?rss=1 Khamiss, D. C. Lempel, A. A. Nanfito, B. R. Nielsen, K. J. 2025-05-17 doi:10.1101/2025.05.15.654265 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Deep Blood Proteomics Identifies over 12,000 Proteins Providing Valuable Information about the State of the Human Body ]]> https://biorxiv.org/content/10.1101/2025.05.15.654311v1?rss=1 Sun, Z. Lih, T. M. Hoang, T. Chen, S.-Y. Xu, J. Lin, D. C. Wang, Y. Woo, J. Huang, Y. Chen, L. Liu, H. Alpern, M. Milosevic, J. He, H.-Z. Chaerkady, R. Wang, Q. Zhang, H. 2025-05-20 doi:10.1101/2025.05.15.654311 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Flexible sensitivity to inputs during skilled tongue movements ]]> https://biorxiv.org/content/10.1101/2025.05.18.654702v1?rss=1 Dasgupta, R. Dong, M. O'Connor, D. H. 2025-05-21 doi:10.1101/2025.05.18.654702 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Increased vulnerability to noise exposure of low spontaneous rate type 1C spiral ganglion neuron synapses with inner hair cells (Pre-Print) ]]> https://biorxiv.org/content/10.1101/2025.05.19.654865v1?rss=1 Reijntjes, D. O. J. Burke, K. Paul, S. Mueller, U. Glowatzki, E. Lauer, A. M. 2025-05-21 doi:10.1101/2025.05.19.654865 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ 3D organoids containing endothelial and neural cells generation by serial inductions of differentiation on human iPSC-derived embryoid bodies ]]> https://biorxiv.org/content/10.1101/2025.05.20.653559v1?rss=1 Wang, T. Bagnell, A. McDonald, V. Gastfriend, B. D. Steiner, J. P. Elkahloun, A. G. Johnson, K. Langston, R. G. Cookson, M. R. Nath, A. 2025-05-21 doi:10.1101/2025.05.20.653559 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Characterising the association between posterior parietal metabolite levels and cortical macrostructure in a cohort spanning childhood to adulthood. ]]> https://biorxiv.org/content/10.1101/2025.05.20.655054v1?rss=1 Thomson, A. R. pasanta, d. Edden, R. A. E. Arichi, T. Chai, X. J. Puts, N. 2025-05-21 doi:10.1101/2025.05.20.655054 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Intercellular communication in the brain via dendritic nanotubular network ]]> https://biorxiv.org/content/10.1101/2025.05.20.655147v1?rss=1 Chang, M. Kruessel, S. Parajuli, L. K. Kim, J. Lee, D. Merodio, A. Kwon, J. Okabe, S. Kwon, H. 2025-05-21 doi:10.1101/2025.05.20.655147 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Shared and distinct cortical mechanisms for working memory and decision-making. ]]> https://biorxiv.org/content/10.1101/2025.05.21.655340v1?rss=1 Seo, H. Lee, D. Murray, S. K. 2025-05-21 doi:10.1101/2025.05.21.655340 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Dissecting Rate-Limiting Processes in Biomolecular Condensate Exchange Dynamics ]]> https://biorxiv.org/content/10.1101/2025.05.16.654578v1?rss=1 Kliegman, R. Kengmana, E. Schulman, R. Zhang, Y. 2025-05-22 doi:10.1101/2025.05.16.654578 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Tuning the interaction of a ParA-type ATPase with its partner separates bacterial organelle positioning from partitioning ]]> https://biorxiv.org/content/10.1101/2025.05.22.655647v1?rss=1 Byrne, J. A. Swasthi, H. M. Hu, L. Azaldegui, C. A. Liu, J. Vecchiarelli, A. G. 2025-05-22 doi:10.1101/2025.05.22.655647 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ In vivo CRISPR screening identifies NF1/RASA1/TP53 co-mutations and downstream MEK signaling as a common key mechanism of sinonasal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.05.19.654661v1?rss=1 Vu, K. P. Gunti, S. Viswanathan, R. Nandal, A. Larkin, R. Cho, S. Zou, J. Ramolia, S. Hoke, A. T. K. Barbosa, S. M. Gallia, G. L. Rooper, L. M. Floudas, C. S. Cheng, H. Miller, C. N. Guest, M. R. Notaro, M. Raziuddin, A. Sun, Z. Wu, X. Faraji, F. Lechner, M. Comoglio, F. Edmondson, E. F. Chari, R. London, N. R. 2025-05-23 doi:10.1101/2025.05.19.654661 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ The shape of attention: How cognitive goals sculpt cortical representation of speech. ]]> https://biorxiv.org/content/10.1101/2025.05.22.655464v1?rss=1 Huet, M.-P. Elhilali, M. 2025-05-23 doi:10.1101/2025.05.22.655464 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Aeromonas: Genomic Insights into an Environmental Pathogen and Reservoir of Antimicrobial Resistance ]]> https://biorxiv.org/content/10.1101/2025.05.22.655522v1?rss=1 Singh, N. Golicha, R. O. Thakur, C. Beale, M. A. Dorman, M. J. Cazares, A. Taylor-Brown, A. Johura, F.-T. Rashid, M. u. Monira, S. Zohura, F. Parveen, T. Bhuiyan, S. I. Sultana, M. Mohan, B. Domman, D. George, C. M. Kariuki, S. Alam, M. Taneja, N. Thomson, N. R. 2025-05-23 doi:10.1101/2025.05.22.655522 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Human-Specific Suppression of Hepatic Fatty Acid Catabolism by RNA-Binding Protein HuR ]]> https://biorxiv.org/content/10.1101/2025.05.22.655551v1?rss=1 Takaoka, S. Jaso-Vera, M. E. Ruan, X. 2025-05-23 doi:10.1101/2025.05.22.655551 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Partitioned Multi-MUM finding for scalable pangenomics ]]> https://biorxiv.org/content/10.1101/2025.05.20.654611v1?rss=1 Shivakumar, V. S. Langmead, B. 2025-05-25 doi:10.1101/2025.05.20.654611 Cold Spring Harbor Laboratory Press 2025-05-25 <![CDATA[ StringTie3 Improves Total RNA-seq Assembly by Resolving Nascent and Mature Transcripts ]]> https://biorxiv.org/content/10.1101/2025.05.21.655404v1?rss=1 Shinder, I. Pertea, G. Hu, R. Rudnick, Z. Pertea, M. 2025-05-26 doi:10.1101/2025.05.21.655404 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress ]]> https://biorxiv.org/content/10.1101/2025.05.21.655305v1?rss=1 Liao, J. N. Betances, I. Tian, S. Shen, E. Ye, Z. Basu, A. Trcek, T. 2025-05-27 doi:10.1101/2025.05.21.655305 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Movi Color: fast and accurate long-read classification with the move structure ]]> https://biorxiv.org/content/10.1101/2025.05.22.655637v1?rss=1 Tan, S. Majidian, S. Langmead, B. Zakeri, M. 2025-05-27 doi:10.1101/2025.05.22.655637 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ End Processing in NHEJ by Polymerase {lambda} and PNKP is coordinated during short-range synapsis ]]> https://biorxiv.org/content/10.1101/2025.05.25.656038v1?rss=1 Vogt, A. Kaminski, A. M. Pedersen, L. C. Naila, T. Tomkinson, A. E. Lees-Miller, S. P. Kunkel, T. A. He, Y. 2025-05-27 doi:10.1101/2025.05.25.656038 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes ]]> https://biorxiv.org/content/10.1101/2025.05.25.654911v1?rss=1 Singh, S. Patel, S. K. Matsuura, R. Velazquez, D. Sun, Z. Noel, S. Rabb, H. Fan, J. 2025-05-28 doi:10.1101/2025.05.25.654911 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Marker genes for predicting cytokine release syndrome in vitro before CAR T cell infusion ]]> https://biorxiv.org/content/10.1101/2025.05.26.655341v1?rss=1 Chen, M. Wu, T. Hu, Y. Liu, Q. Chen, M. Zhang, J. Du, Y. Ouyang, F. Huang, Y. 2025-05-29 doi:10.1101/2025.05.26.655341 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ mt.surv: Multi-Threshold Survival Analysis for Associating Continuous Predictor Variables with Time-to-Event Outcomes ]]> https://biorxiv.org/content/10.1101/2025.05.29.656703v1?rss=1 Loncar, A. J. Hoyd, R. Liu, Y. Dravillas, C. Dhrubo, D. Spakowicz, D. J. 2025-05-29 doi:10.1101/2025.05.29.656703 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Recovery of retinal terminal fields after traumatic brain injury: evidence of collateral sprouting and sexual dimorphism ]]> https://biorxiv.org/content/10.1101/2025.05.28.656451v1?rss=1 Alexandris, A. S. Yi, J. Liu, C. Belamarich, J. Alam, Z. Vats, A. Peng, A. Welsbie, D. S. Zack, D. J. Koliatsos, V. E. 2025-06-01 doi:10.1101/2025.05.28.656451 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.05.28.656689v1?rss=1 Grimont, A. Falvo, D. J. Sisso, W. J. Zumbo, P. Chan, C. W. Santos, F. Pan, G. Cleveland, M. Yaron, T. Osterhoudt, A. S. Meng, Y. Zafra, M. P. Fall, W. B. Rendeiro, A. F. Hissong, E. Yantiss, R. K. Betel, D. Magnuson, M. A. Leach, S. D. Rustgi, A. K. Dow, L. E. Chandwani, R. 2025-06-01 doi:10.1101/2025.05.28.656689 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Multimodal retinal imaging by visible light optical coherence tomography and phosphorescence lifetime ophthalmoscopy in the mouse eye ]]> https://biorxiv.org/content/10.1101/2025.05.29.656845v1?rss=1 Nolen, S. L. Li, Z. Wang, J. El Khatib, M. Vinogradov, S. A. Yi, J. 2025-06-01 doi:10.1101/2025.05.29.656845 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Macrophages Lacking TSC2 have mTORC1-dependent GPNMB Augmentation Ameliorating Cardiac Ischemia-Reperfusion Injury ]]> https://biorxiv.org/content/10.1101/2025.05.29.656917v1?rss=1 Keykhaei, M. Koleini, N. Meddeb, M. Tajdini, M. Rezaee, M. Huang, Q. Panesar, T. Adamo, L. Ranek, M. Kass, D. A. 2025-06-01 doi:10.1101/2025.05.29.656917 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Targeting Neutrophil Extracellular Traps to inhibit Colon Cancer Tumor Necrosis and Metastasis ]]> https://biorxiv.org/content/10.1101/2025.05.30.657122v1?rss=1 Gazzara, E. Adrover, J. M. Lui, A. Han, S. Aminzada, Z. Bhandari, N. Sivetz, N. Shirue, V. S. Shergill, B. S. Curtis, M. B. George, S. C. Cicala, A. Rishi, A. Chung, C. Devoe, C. Huang, H. Weiss, M. Lou, E. Tuveson, D. A. Beyaz, S. Westcott, P. M. K. Egeblad, M. Gholami, S. 2025-06-03 doi:10.1101/2025.05.30.657122 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Adhesive implant interfaces prevent fibrosis by disrupting mechanobiological feedback ]]> https://biorxiv.org/content/10.1101/2025.06.01.657311v1?rss=1 Jafari, M. Aymon, B. Hong, Y. Shakiba, D. Genin, G. M. Zhao, X. Alisafaei, F. 2025-06-03 doi:10.1101/2025.06.01.657311 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Clinical Trypanosoma cruzi isolates share a common antigen repertoire that is absent from culture adapted strains ]]> https://biorxiv.org/content/10.1101/2025.06.04.657671v1?rss=1 Hakim, J. M. C. Gutierrez Guarnizo, S. A. Duran, A. Malaga-Machacha, E. Duque, C. Singer, L. Colanzi, R. Sherbuk, J. E. Gilman, R. Bern, C. Messenger, L. A. Mugnier, M. R. Working Group on Chagas Disease in Bolivia and Peru, 2025-06-04 doi:10.1101/2025.06.04.657671 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ ezscore-f: A Set of Freely Available, Validated Sleep Stage Classifiers for Forehead EEG ]]> https://biorxiv.org/content/10.1101/2025.06.02.657451v1?rss=1 Coon, W. G. Zerr, P. Milsap, G. Sikder, N. Smith, M. Dresler, M. Reid, M. 2025-06-06 doi:10.1101/2025.06.02.657451 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Extracellular Vesicles from Multiple Sclerosis White Matter Exhibit Synaptic, Mitochondrial, Complement, and Aging-related Pathway Dysregulation ]]> https://biorxiv.org/content/10.1101/2025.06.02.657509v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@1f88da5org.highwire.dtl.DTLVardef@11b7ee9org.highwire.dtl.DTLVardef@291d9forg.highwire.dtl.DTLVardef@157cb73_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jank, L. Satheesh Kumar, M. K. Ryu, T. Thapa, R. Gololobova, O. Niepokny, T. Calabresi, P. A. Witwer, K. W. Dutta, R. Na, C. H. Bhargava, P. 2025-06-06 doi:10.1101/2025.06.02.657509 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Temporally-segregated dual functions for Gfi1 in the development of retinal direction-selectivity ]]> https://biorxiv.org/content/10.1101/2025.06.03.657700v1?rss=1 Chaudhari, K. Guzman-Clavel, L. E. Kolodkin, A. L. 2025-06-06 doi:10.1101/2025.06.03.657700 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Cardiac fibroblasts counterbalance cardiomyocytes in LMNA cardiomyopathy pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.05.657412v1?rss=1 Sikder, K. Phillips, E. Bouhrira, N. Mothy, D. Wang, N. Bonne, G. Margulies, K. B. Choi, J. C. 2025-06-06 doi:10.1101/2025.06.05.657412 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Lack of mRNA Methylation in Schwann Cells Results in Demyelination and Regenerative Failure ]]> https://biorxiv.org/content/10.1101/2025.06.03.657089v1?rss=1 Sari, M. C. Johnson, A. Yu, A. T. Mi, R. Chen, W. Hu, X. Harris, T. G. Tuffaha, S. Swarup, V. Kawaguchi, R. Ming, G.-L. Hoke, A. 2025-06-07 doi:10.1101/2025.06.03.657089 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Preliminary insights into salivary proteomic versus targeted biomarker profiles associated with acute physical fatigue ]]> https://biorxiv.org/content/10.1101/2025.06.04.657971v1?rss=1 Lindsey, B. Bowden, K. Shaul, Y. Petricoin, E. Caswell, S. V. Alhammad, R. Elayadi, A. N. Martin, J. 2025-06-08 doi:10.1101/2025.06.04.657971 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ Affordable plasmonic biosensing: democratizing SERS with scalable, field-compatible substrate fabrication ]]> https://biorxiv.org/content/10.1101/2025.06.05.658202v1?rss=1 Arora, S. Ginde, V. Tanwar, S. Chazli, M. E. Bhatt, R. Edelman, E. Paria, D. Barman, I. 2025-06-09 doi:10.1101/2025.06.05.658202 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Ultrafast endocytosis in mouse cortical inhibitory synapses ]]> https://biorxiv.org/content/10.1101/2025.06.06.658279v1?rss=1 Eddings, C. R. Watanabe, S. 2025-06-09 doi:10.1101/2025.06.06.658279 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Development of a Novel Benzodiazepine to Delineate Peripheral GABA-A Signaling Mechanisms in Visceral Pain Syndromes ]]> https://biorxiv.org/content/10.1101/2025.06.08.658501v1?rss=1 Poslusney, M. S. Li, Q. Buchler, I. P. Huang, Y. Liu, L. Zhu, Y. Kulkarni, S. Carr, G. DeBrosse, A. White, N. Peters, D. Barrow, J. C. Pasricha, P. J. 2025-06-09 doi:10.1101/2025.06.08.658501 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ PIVOT: an open-source tool for multi-omic spatial data registration ]]> https://biorxiv.org/content/10.1101/2025.06.08.658506v1?rss=1 Forjaz, A. Romero, V. M. Reucroft, I. Eminizer, M. Kramer, D. Higuera, D. Mojdeganlou, H. Guerrero, P. A. Min, J. Wetzel, M. Lvovs, D. Valentin, A. Shin, S. M. Xuan, Y. Sears, R. C. Chin, K. Maitra, A. Fertig, E. J. Ho, W. J. Kagohara, L. T. Wood, L. D. Wirtz, D. Sidiropoulos, D. N. Kiemen, A. L. 2025-06-09 doi:10.1101/2025.06.08.658506 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Acute induction of IFNα is responsible for the attenuation of the live measles vaccine ]]> https://biorxiv.org/content/10.1101/2025.06.09.658652v1?rss=1 Edwards, J. Yoon, S. Brockhurst, J. K. Rennick, L. J. Duprex, W. P. Coppens, I. Pekosz, A. Griffin, D. E. 2025-06-09 doi:10.1101/2025.06.09.658652 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Neural and behavioral consequences of bilateral maps in primary somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2025.06.10.658919v1?rss=1 Chokshi, V. B. Chang, Y.-T. Ra, D. M. Erzurumlu, R. S. O'Connor, D. H. 2025-06-11 doi:10.1101/2025.06.10.658919 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Application and Characterization of the Multiple Instance Learning Framework in Flow Cytometry ]]> https://biorxiv.org/content/10.1101/2025.06.10.658646v1?rss=1 Ding, Z. Baras, A. 2025-06-12 doi:10.1101/2025.06.10.658646 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Cancer systems immunology reveals myeloid - T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer ]]> https://biorxiv.org/content/10.1101/2025.06.09.658361v1?rss=1 Gonzalez, E. Kreger, J. Liu, Y. Wu, X. Barbetta, A. Baugh, A. Al-Zubeidy, B. Jang, J. Shin, S. M. Jacobo, M. Stearns, V. Connolly, R. M. Ho, W. Emamaullee, J. MacLean, A. L. Roussos Torres, E. T. 2025-06-13 doi:10.1101/2025.06.09.658361 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Applying Self-Supervised Tissue Patch Encoders to Enable Cellular Graph Encoding ]]> https://biorxiv.org/content/10.1101/2025.06.10.658651v1?rss=1 Ding, Z. Baras, A. 2025-06-15 doi:10.1101/2025.06.10.658651 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Effects of Ambient Temperature During Pregnancy on Newborn Birthweight ]]> https://biorxiv.org/content/10.1101/2025.06.10.658978v1?rss=1 Nargund, R. Marchesoni, J. Bareja, A. W. Sosnowski, D. Peng, G. Hoyo, C. Pan, W. K. Murphy, S. 2025-06-15 doi:10.1101/2025.06.10.658978 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain ]]> https://biorxiv.org/content/10.1101/2025.06.10.658982v1?rss=1 180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. ]]> Petkova, M. D. Januszewski, M. Blakely, T. Herrera, K. J. Schuhknecht, G. F. P. Tiller, R. Choi, J. Schalek, R. L. Boulanger-Weil, J. Peleg, A. Wu, Y. Wang, S. Troidl, J. Kumar Vohra, S. Wei, D. Lin, Z. Bahl, A. Tapia, J. C. Iyer, N. Miller, Z. T. Hebert, K. B. Pavarino, E. C. Taylor, M. Deng, Z. Stingl, M. Hockling, D. Hebling, A. Wang, R. C. Zhang, L. L. Dvorak, S. Faik, Z. King, K. I. Goel, P. Wagner-Carena, J. Aley, D. Chalyshkan, S. Contreas, D. Li, X. Muthukumar, A. V. Vernaglia, M. S. Tapia Carrasco, T. Melnychuck, S. Yan, T. Dalal, A. DiMarti 2025-06-15 doi:10.1101/2025.06.10.658982 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Cell type specific CaMKII activation patterns revealed by CaMKAR, a bioactivity reporter deployable in living cells ]]> https://biorxiv.org/content/10.1101/2025.06.11.658946v1?rss=1 Severino, A. Reyes Gaido, O. E. Liu, B. Lopez-Cecetaite, G. A. Wei, A.-C. Rosales-Soto, G. Hernandez-Ochoa, E. O. Luczak, E. D. 2025-06-15 doi:10.1101/2025.06.11.658946 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ DCPS modulates TDP-43 mediated neurodegeneration through P-body regulation ]]> https://biorxiv.org/content/10.1101/2025.06.13.659508v1?rss=1 Ye, Y. Zhang, Z. Yu, X. Zhu, C. Wright, N. Asbury, J. Huang, Y. Wang, W. Gomez-Isaza, L. Troncoso, J. He, C. Sun, S. 2025-06-15 doi:10.1101/2025.06.13.659508 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms ]]> https://biorxiv.org/content/10.1101/2025.06.02.657494v1?rss=1 Fu, T.-M. Liu, G. Milkie, D. E. Ruan, X. Gorlitz, F. Shi, Y. Ferro, V. Divekar, N. S. Wang, W. York, H. M. Kilic, V. Mueller, M. Liang, Y. Daugird, T. A. Gacha-Garay, M. J. Larkin, K. A. Adikes, R. C. Harrison, N. Shirazinejad, C. Williams, S. Nourse, J. L. Sheu, S.-H. Gao, L. Li, T. Mondal, C. Achour, K. Hercule, W. Stabley, D. Emmerich, K. Dong, P. Drubin, D. Liu, Z. J. Clapham, D. Mumm, J. S. Koyama, M. Killilea, A. Bravo-Cordero, J. J. Keene, C. D. Luo, L. Kirchhausen, T. Pathak, M. M. Arumugam, S. Nunez, J. K. Gao, R. G. Matus, D. Q. Martin, B. 2025-06-16 doi:10.1101/2025.06.02.657494 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Architecture, Activation, and Conformational Plasticity in the GluA4 AMPA Receptor ]]> https://biorxiv.org/content/10.1101/2025.06.12.659357v1?rss=1 Hale, W. D. Huganir, R. L. Twomey, E. C. 2025-06-16 doi:10.1101/2025.06.12.659357 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Modeling cellular influence delineates functionally relevant cellular neighborhoods in primary and metastatic pancreatic ductal adenocarcinoma. ]]> https://biorxiv.org/content/10.1101/2025.06.12.659314v1?rss=1 Cho, Y. Lee, J. W. Shin, S. M. Hernandez, A. G. Yuan, X. Schneider, J. Hooper, J. E. Wood, L. D. Jaffee, E. M. Deshpande, A. Ho, W. J. 2025-06-17 doi:10.1101/2025.06.12.659314 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ CrebA regulation of secretory capacity: Genome-wide transcription profiling coupled with in vivo DNA binding studies ]]> https://biorxiv.org/content/10.1101/2025.06.12.659381v1?rss=1 Andrew, D. J. Jackson, D. M. Peng, D. Shinde, S. Holenarasipura, A. Cahan, P. 2025-06-17 doi:10.1101/2025.06.12.659381 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Cell barcoding with tandem fluorescent proteins enables high-throughput signaling dynamics analysis ]]> https://biorxiv.org/content/10.1101/2025.06.17.660155v1?rss=1 Wu, J.-W. Yang, J.-M. Wang, S. Chen, Y. Huang, C.-H. 2025-06-20 doi:10.1101/2025.06.17.660155 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Tau-seed interactome analysis reveals distinct functional signatures in Alzheimer's disease across model systems. ]]> https://biorxiv.org/content/10.1101/2025.06.17.660179v1?rss=1 Martinez, P. Patel, H. You, Y. Lopes, D. Amaro, A. Jury-Garfe, N. Min, Y. Redding-Ochoa, J. Dutta, S. Rochet, C. Ertekin-Taner, N. Troncoso, J. Lasagna-Reeves, C. A. 2025-06-20 doi:10.1101/2025.06.17.660179 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Volume Control for a Cortical Network ]]> https://biorxiv.org/content/10.1101/2025.06.19.660597v1?rss=1 Wang, R. Fridman, G. Y. 2025-06-21 doi:10.1101/2025.06.19.660597 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ A Multi-State Structural Genomics Approach Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases ]]> https://biorxiv.org/content/10.1101/2025.06.17.660194v1?rss=1 Wagenknecht, J. B. Haque, N. Jorge, S. D. Ratnasinghe, B. D. Urrutia, R. A. Gahl, W. A. Ziegler, S. G. Zimmermann, M. T. 2025-06-23 doi:10.1101/2025.06.17.660194 Cold Spring Harbor Laboratory Press 2025-06-23 <![CDATA[ daf-16/FOXO promotes the activity of ligand-bound DAF-12/NHR to coordinate dauer recovery and post-dauer seam cell fate ]]> https://biorxiv.org/content/10.1101/2025.06.18.660181v1?rss=1 Wirick, M. J. Smith, I. T. Olson, B. S. Alessi, A. F. Galagali, H. Lalk, K. Schmidt, M. N. Ranke, K. J. Kim, J. K. Karp, X. 2025-06-24 doi:10.1101/2025.06.18.660181 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Multisensory integration for active mechanosensation in Drosophila flight ]]> https://biorxiv.org/content/10.1101/2025.06.20.660728v1?rss=1 Mills, K. M. Cowan, N. J. Suver, M. P. 2025-06-24 doi:10.1101/2025.06.20.660728 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Phase separation of PGL-3 driven by structured domains that oligomerize and interact with terminal RGG motifs. ]]> https://biorxiv.org/content/10.1101/2025.06.23.660947v1?rss=1 Kuroiwa, R. Sharma, P. Putnam, A. Fried, S. D. Seydoux, G. 2025-06-24 doi:10.1101/2025.06.23.660947 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ MAPseq2: a sensitive and cost-effective barcoded connectomics method ]]> https://biorxiv.org/content/10.1101/2025.06.23.661165v1?rss=1 Kim, H. Qi, H. Washington, C. Liang, X. Kebschull, J. M. 2025-06-24 doi:10.1101/2025.06.23.661165 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ SLAy-ing oversplitting errors in high-density electrophysiology spike sorting ]]> https://biorxiv.org/content/10.1101/2025.06.20.660590v1?rss=1 Koukuntla, S. DeWeese, T. Cheng, A. Mildren, R. Lawrence, A. Graves, A. R. Colonell, J. Harris, T. D. Charles, A. S. 2025-06-25 doi:10.1101/2025.06.20.660590 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Biocatalytic Construction of a CEST MRI Nucleoside Probe: Synthesis and Evaluation of 5-Methyl-5,6-dihydrothymidine ]]> https://biorxiv.org/content/10.1101/2025.06.25.661137v1?rss=1 Al-Hilfi, A. Franco, E. A. C. Grady, C. J. Mohanta, Z. McMahon, M. T. Bazayeva, M. Li, Z. Merz, K. M. Gilad, A. A. 2025-06-25 doi:10.1101/2025.06.25.661137 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Testing Sensorimotor Timing in a Living Laboratory: Behavioral Signatures of a Neural Oscillator ]]> https://biorxiv.org/content/10.1101/2025.06.25.661347v1?rss=1 Serre, H. Harrigian, K. Park, S.-W. Sternad, D. 2025-06-25 doi:10.1101/2025.06.25.661347 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Mapping the projectional architecture of the mouse midbrain dopaminergic system using cell type-specific barcoding ]]> https://biorxiv.org/content/10.1101/2025.06.25.661405v1?rss=1 Kim, H. Xu, C. Washington, C. Lowmann, M. Kebschull, J. M. 2025-06-26 doi:10.1101/2025.06.25.661405 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Sensitizing Immune-Refractory Ovarian Tumors via p53 Mutation-Tailored Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.06.23.661120v1?rss=1 Chatterjee, R. Simoni-Nieves, A. Truong, A. Lindzen, M. Ozmen, F. Cherry, C. Zwicky, P. Mukherjee, S. Selvadurai, B.-R. Salame, T. M. Gupta, N. Giri, S. Kramarski, L. Avraham, Y. Weizman, E. Ozmen, T. Noronha, A. Chakrabarti, P. Ramesh-Kumar, D. Downward, J. Dahan, R. Amit, I. Velculescu, V. Brenton, J. Mills, G. Oren, M. Yarden, Y. 2025-06-27 doi:10.1101/2025.06.23.661120 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Antibiotic-induced microbiota depletion impairs the pro-regenerative response to a biological scaffold in mice ]]> https://biorxiv.org/content/10.1101/2025.06.23.661121v1?rss=1 Rutkowski, N. N. Yang, B. Gray-Gaillard, E. Ruta, A. Mejias, J. C. Patatanian, M. Cherry, C. Stivers, K. B. Ramanujam, S. Price, N. L. Housseau, F. Pardoll, D. M. Sears, C. L. Elisseeff, J. 2025-06-27 doi:10.1101/2025.06.23.661121 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Cross-species proteomics quantification pipeline distinguishes donor versus host extracellular matrix in explanted biomaterials ]]> https://biorxiv.org/content/10.1101/2025.06.24.661315v1?rss=1 Cahalane, R. M. Meuris, B. Matamalas, J. T. Blaser, M. C. Billaud, M. Kasai, T. Hendrickx, A. Goeminne, L. J. Muehlschlegel, J. Rega, F. Aikawa, M. McNamara, L. Singh, S. A. Clift, C. L. Aikawa, E. 2025-06-27 doi:10.1101/2025.06.24.661315 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Integrated Spatial Analysis of Ovarian Precancerous Lesions ]]> https://biorxiv.org/content/10.1101/2025.06.24.661327v1?rss=1 Chang, T.-Y. Chien, Y.-W. Chen, S.-H. Sokolow, A. Wang, Y. Wang, B. G. Numan, T. Chui, M. H. Stone, R. Pisanic, T. Papadopoulos, N. Wang, T.-L. Douville, C. Cope, L. Shih, I.-M. 2025-06-27 doi:10.1101/2025.06.24.661327 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Phosphoglycerate Kinase Can Adopt a Topologically Misfolded Form that is More Stable than its Native State ]]> https://biorxiv.org/content/10.1101/2025.06.24.661412v1?rss=1 Xia, Y. Amann, B. Gillilan, R. E. Sharma, P. Sen, S. Fleming, K. G. Fried, S. D. 2025-06-27 doi:10.1101/2025.06.24.661412 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Core microRNAs regulate neural crest delamination and condensation in the developing trigeminal ganglion ]]> https://biorxiv.org/content/10.1101/2025.06.27.661967v1?rss=1 Marquez, R. B. Sanchez Vazquez, E. Alonso, A. M. Bernardi, Y. E. Santillan, E. M. Lwigale, P. Cochella, L. Bronner, M. Strobl-Mazzulla, P. H. 2025-06-28 doi:10.1101/2025.06.27.661967 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Why Meaning Survives Noise: The Spatiotemporal Abstraction Theory ]]> https://biorxiv.org/content/10.1101/2025.06.28.662092v1?rss=1 Fridman, G. Y. 2025-06-28 doi:10.1101/2025.06.28.662092 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Identifying out-of-voxel echoes in edited MRS with phase cycle inversion ]]> https://biorxiv.org/content/10.1101/2025.06.26.661810v1?rss=1 Shams, Z. Gad, A. Gudmundson, A. T. Murali-Manohar, S. Davies-Jenkins, C. W. Simegn, G. L. Simicic, D. Song, Y. Yedavalli, V. Zöllner, H. J. Oeltzschner, G. Edden, R. A. E. 2025-06-29 doi:10.1101/2025.06.26.661810 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons ]]> https://biorxiv.org/content/10.1101/2025.06.28.661837v1?rss=1 Sinha, I. S. Ye, Y. Li, Y. Sandal, P. S. Wong, P. C. Sun, S. Ling, J. P. 2025-06-29 doi:10.1101/2025.06.28.661837 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Mechanisms of Ion Permeation in the AMPA Receptor Ion Channel ]]> https://biorxiv.org/content/10.1101/2025.06.27.662003v1?rss=1 Montano Romero, A. Yovanno, R. A. Lau, A. Y. Twomey, E. C. 2025-06-30 doi:10.1101/2025.06.27.662003 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ MYCBP interacts with Sakura and Otu and is essential for germline stem cell renewal and differentiation and oogenesis ]]> https://biorxiv.org/content/10.1101/2025.07.01.662550v1?rss=1 Azlan, A. Fukunaga, R. 2025-07-02 doi:10.1101/2025.07.01.662550 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Tonotopically distinct OFF responses arise in the mouse auditory midbrain following sideband suppression ]]> https://biorxiv.org/content/10.1101/2025.07.02.662630v1?rss=1 Parker, P. D. Lauer, A. M. Bergles, D. E. 2025-07-03 doi:10.1101/2025.07.02.662630 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Ptbp1 is not required for retinal neurogenesis and cell fate specification. ]]> https://biorxiv.org/content/10.1101/2025.07.02.662808v1?rss=1 Appel, H. Carmen-Orozco, R. Santiago, C. Hoang, T. Blackshaw, S. 2025-07-03 doi:10.1101/2025.07.02.662808 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Genetics of growth rate in induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.07.02.662844v1?rss=1 Lee, B. N. Taylor, H. J. Cipriani, F. Narisu, N. Robertson, C. C. Swift, A. J. Sinha, N. Yan, T. Bonnycastle, L. L. Dale, N. Butt, A. Parsaud, H. Semrau, S. NYSCF Global Stem Cell Array Team, GENESiPS Consortium, iPSCORE Consortium, Knowles, J. W. Carcamo-Orive, I. D'Antonio-Chronowska, A. Frazer, K. A. Biesecker, L. G. Noggle, S. Erdos, M. R. Paull, D. Collins, F. S. Taylor, D. L. 2025-07-03 doi:10.1101/2025.07.02.662844 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ DTH: A nonparametric test for homogeneity of multivariate dispersions ]]> https://biorxiv.org/content/10.1101/2025.06.29.662200v1?rss=1 Roy, A. Satten, G. Zhao, N. 2025-07-04 doi:10.1101/2025.06.29.662200 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Targeted ablation and regeneration of enteric nervous system neurons in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.07.01.660701v1?rss=1 Shah, M. A. Moran, K. K. Rueckert, H. Sharrock, A. V. Ackerley, D. F. Mumm, J. S. Ganz, J. 2025-07-04 doi:10.1101/2025.07.01.660701 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Comparative genomics and phylogenomics of the Mustelinae lineage (Mustelidae, Carnivora) ]]> https://biorxiv.org/content/10.1101/2025.07.01.662473v1?rss=1 Totikov, A. A. Tomarovsky, A. A. Perelman, P. L. Bulyonkova, T. M. Serdyukova, N. A. Yakupova, A. R. Mohr, D. Foerster, D. W. Grau Jipoulou, J. H. Beklemisheva, V. R. Sidorov, M. Miranda, I. Farelo, L. Abramov, A. V. Krasheninnikova, K. Mukhacheva, A. S. Panov, V. V. Balanovska, E. Cherkasov, N. Zub, K. Scott, A. F. Melo-Ferreira, J. Okhlopkov, I. M. Zhuk, A. Koepfli, K.-P. Kliver, S. 2025-07-04 doi:10.1101/2025.07.01.662473 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Low and high frequency signatures of impaired consciousness in temporal lobe seizures ]]> https://biorxiv.org/content/10.1101/2025.07.01.662627v1?rss=1 Yadav, T. Litvinov, B. P. Culler, G. W. Kumar, A. Khalaf, A. Song, Y. Brinkmann, B. H. Joseph, B. Ahmad, Z. Gunawardane, N. Ramirez, V. C. Quraishi, I. H. START Clinical Trial Research Consortium, Jobst, B. C. Worrell, G. Blumenfeld, H. 2025-07-04 doi:10.1101/2025.07.01.662627 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Subtype-Specific Roles of Nigrostriatal Dopaminergic Neurons in Motor and Associative Learning ]]> https://biorxiv.org/content/10.1101/2025.07.03.663035v1?rss=1 Habib, A. Riccobono, G. T. Tian, L. Basu, D. Sun, L. Chang, L. Martinez-Smith, V. Wang, L. Le, W. Cai, H. 2025-07-04 doi:10.1101/2025.07.03.663035 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ CaMKII monomers are sufficient for GluN2B binding, co-condensation, and synaptic potentiation ]]> https://biorxiv.org/content/10.1101/2025.07.04.663188v1?rss=1 Brown, C. N. Barker, C. M. Miller, C. N. Aoto, J. Coultrap, S. J. Bayer, K. U. 2025-07-04 doi:10.1101/2025.07.04.663188 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Copper-Containing ROS-Scavenging Nanozyme Paradoxically Drives Alpha-Synucleinopathy by Amplifying Nitrosative Stress ]]> https://biorxiv.org/content/10.1101/2025.07.01.661317v1?rss=1 Li, S. Mao, Y. Wang, N. Zhang, J. Zhi, X. Chen, Y. Si, J. Yang, Q. Kumbhar, R. Joeng, D. Song, J.-Y. Yang, X. Kang, B. G. Khandekar, A. Park, J. Gao, Y. Yu, S. Chen, R. Zhang, S. Han, J. Dawson, V. L. Liu, P. Han, S. Dawson, T. He, W. Mao, X. 2025-07-05 doi:10.1101/2025.07.01.661317 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production ]]> https://biorxiv.org/content/10.1101/2025.07.02.662322v1?rss=1 Lin, J. Hu, Y. Pial, T. H. Goodier, K. D. Yu, D. Guise, M. Brailsford, P. Choi-Ali, M. Li, S. Zhu, Y. Ma, J. Cheng, L. Lu, X. Korinetz, N. Wang, J. Curk, T. Mao, H.-Q. 2025-07-05 doi:10.1101/2025.07.02.662322 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Screening of a pooled library of chimeric antigen receptor T cells based on secretory function ]]> https://biorxiv.org/content/10.1101/2025.07.02.662376v1?rss=1 2 million cells screened), compatibility with downstream sequencing, and tunable antigen presentation make it ideal for identifying CAR constructs associated with various time-dependent secretion phenotypes. ]]> Soemardy, C. Mei, A. Castellanos-Rueda, R. Espinoza, N. G. Kizerwetter, M. Spangler, J. B. Reddy, S. T. Di Carlo, D. 2025-07-05 doi:10.1101/2025.07.02.662376 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ CASZ1 regulates the rate at which outer hair cells mature and is required for hearing ]]> https://biorxiv.org/content/10.1101/2025.07.04.663233v1?rss=1 Nakano, Y. Driver, E. C. Wiechert, S. C. Peguero, B. Boger, E. T. Allamargot, C. Hipp, R. Doetzlhofer, A. Morell, R. J. Kelley, M. W. Banfi, B. 2025-07-05 doi:10.1101/2025.07.04.663233 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Music-evoked reactivation during continuous perception is associated with enhanced subsequent recall of naturalistic events ]]> https://biorxiv.org/content/10.1101/2025.07.05.663273v1?rss=1 Williams, J. A. Margulis, E. H. Baldassano, C. Hasson, U. Chen, J. Norman, K. A. 2025-07-06 doi:10.1101/2025.07.05.663273 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Intravital Multimodal Imaging of Human Cortical Organoids for Chronic Stroke Treatment in Mice ]]> https://biorxiv.org/content/10.1101/2025.07.05.663297v1?rss=1 Wang, J. Qiao, G. Tan, H. Li, M. Wang, K. Xu, J. Janowski, M. Fu, T.-M. Walczak, P. Liang, Y. 2025-07-06 doi:10.1101/2025.07.05.663297 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Staphylococcus aureus exhibits spatiotemporal heterogeneity in Sae activity during kidney abscess development ]]> https://biorxiv.org/content/10.1101/2025.07.08.663646v1?rss=1 Anil, A. Braza, R. E. Liu, B. Altouma, V. Adedeji, C. Welling, A. Ellison, A. L. Check, M. H. Irnov, I. Prescott, R. Torres, V. J. Davis, K. M. 2025-07-08 doi:10.1101/2025.07.08.663646 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Rapid Prototyping of Microfluidic Devices with Stereolithographic 3D Printing ]]> https://biorxiv.org/content/10.1101/2025.07.10.662041v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@126ff02org.highwire.dtl.DTLVardef@1301c7forg.highwire.dtl.DTLVardef@19edb96org.highwire.dtl.DTLVardef@6256b5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mason, H. G. Hu, C.-H. Cordova, L. S. Hakami, R. M. Veneziano, R. 2025-07-11 doi:10.1101/2025.07.10.662041 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Characterization of astrocyte density in the Pitt-Hopkins Syndrome mouse model of ASD ]]> https://biorxiv.org/content/10.1101/2025.07.10.664109v1?rss=1 Stump, S. M. Bohlen, J. F. Phan, B. Maher, B. 2025-07-12 doi:10.1101/2025.07.10.664109 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Spatiotemporal Abstraction Theory: Re-Interpretation of Localized Cortical Networks ]]> https://biorxiv.org/content/10.1101/2025.07.07.663596v1?rss=1 Fridman, G. Y. 2025-07-14 doi:10.1101/2025.07.07.663596 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ IL-33 promotes transcriptional and metabolic adaptations of tissue-resident Th2 cells ]]> https://biorxiv.org/content/10.1101/2025.07.09.663905v1?rss=1 Kania, A. K. Sanin, D. E. Gu, X. Kokosinski, E. Smith, A. Pearce, E. L. Pearce, E. J. 2025-07-14 doi:10.1101/2025.07.09.663905 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Dynamic extracellular interactions with AMPA receptors ]]> https://biorxiv.org/content/10.1101/2025.07.11.664166v1?rss=1 Merrion, H. G. Barber, C. N. Renuse, S. S. Cutler, J. Kreimer, S. Bygrave, A. M. Meyers, D. J. Hale, W. D. Pandey, A. Huganir, R. L. 2025-07-14 doi:10.1101/2025.07.11.664166 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ The DNA damage response pathway is required for multiciliated cell differentiation ]]> https://biorxiv.org/content/10.1101/2025.07.13.664567v1?rss=1 Jewett, C. E. Holland, A. J. Pearson, C. G. 2025-07-14 doi:10.1101/2025.07.13.664567 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Statistically valid explainable black-box machine learning: applications in sex classification across species using brain imaging ]]> https://biorxiv.org/content/10.1101/2025.07.09.664026v1?rss=1 0.80 on human data, and > 0.70 on macaque data, while NEOFIT identifies statistically significant features aligned with sex-dimorphic neuroanatomy. Our results demonstrate that the proposed framework not only enhances classification performance but also provides clear, interpretable insights into the neuroanatomical features that distinguish sexes. These methodological advancements pave the way for improved diagnostic tools and contribute to a deeper understanding of the evolutionary basis of sex differences in brain structure. ]]> Liu, T. Dey, J. Xu, B. Alldritt, S. S. Nenning, K.-H. Byeon, K. Xu, T. Vogelstein, J. 2025-07-15 doi:10.1101/2025.07.09.664026 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Pde10a gates light responses in the SCN to regulate circadian photoentrainment ]]> https://biorxiv.org/content/10.1101/2025.07.14.664763v1?rss=1 Komal, R. Thomsen, M. Wang, H. Yang, S. Tang, Q. Zhao, H. Hattar, S. 2025-07-15 doi:10.1101/2025.07.14.664763 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Given the birds, where is the flock? Visual estimation of the location of collections of points ]]> https://biorxiv.org/content/10.1101/2025.07.10.664170v1?rss=1 Ota, K. Wu, Q. Mamassian, P. Maloney, L. 2025-07-16 doi:10.1101/2025.07.10.664170 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Low levels of H5N1 HA and NA antibodies in the human population are boosted by seasonal A/H1N1 infection but not by A/H3N2 infection or influenza vaccination ]]> https://biorxiv.org/content/10.1101/2025.07.13.664638v1?rss=1 Werner, A. P. Schneider, C. G. Akin, E. Hayes, J. Fenstermacher, K. Rothman, R. E. Coughlan, L. Pekosz, A. 2025-07-16 doi:10.1101/2025.07.13.664638 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis ]]> https://biorxiv.org/content/10.1101/2025.07.11.664335v1?rss=1 Cohen, C. D. He, J. H. Bermea, K. C. Rousseau, S. T. Luo, A. Ebenebe, O. V. D. Casella, K. Palescandolo, E. Lavine, K. J. Shenderov, E. Halushka, M. Adamo, L. 2025-07-17 doi:10.1101/2025.07.11.664335 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes ]]> https://biorxiv.org/content/10.1101/2025.07.17.663733v1?rss=1 Dang, H. Edwards, C. E. Kato, T. Reidel, B. Meganck, R. M. Esther, C. R. Ehre, C. Fulcher, M. L. Bailey, A. B. Cooley, M. R. Mikami, Y. Asakura, T. Hawkins, P. E. Saito, M. Meyers, J. L. Konopka, K. Gerayeli, F. V. Park, H. Y. Sin, D. D. Livraghi-Butrico, A. Okuda, K. Pickles, R. J. Klein, S. L. Randell, S. H. O'Neal, W. K. Baric, R. S. Boucher, R. C. 2025-07-17 doi:10.1101/2025.07.17.663733 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Increased vaccine efficacy against tuberculosis with a recombinant BCG overexpressing the STING agonist cyclic di AMP ]]> https://biorxiv.org/content/10.1101/2025.07.17.665241v1?rss=1 Singh, D. Um, P. Arora, G. Alvarez, X. Dick, E. Shivanna, V. Mehra, S. Bishai, W. R. 2025-07-17 doi:10.1101/2025.07.17.665241 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Developmental Immunotoxicity of Low-dose Inorganic Arsenic Reprograms Macrophages Inducing Tumor-promoting Phenotypes ]]> https://biorxiv.org/content/10.1101/2025.07.14.663593v1?rss=1 Illingworth, E. J. Sanchez, S. S. Rychlik, K. A. Kleensang, A. Lopez-Cecetaite, G. A. Rodriguez Steube, M. C. Mathur, A. Sadhukhan, P. Medina-Cleghorn, D. A. Nomura, D. Smith, M. T. Hoque, M. O. Sille, F. C. M. 2025-07-18 doi:10.1101/2025.07.14.663593 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Gradient scheme optimization for PRESS-localized edited MRS using weighted pathway suppression ]]> https://biorxiv.org/content/10.1101/2025.07.14.664705v1?rss=1 Simegn, G. L. Shams, Z. Murali Manohar, S. V. Simicic, D. Gad, A. Song, Y. Yedavalli, V. Davies-Jenkins, C. Gudmundson, A. T. Zollner, H. J. Oeltzschner, G. Edden, R. 2025-07-18 doi:10.1101/2025.07.14.664705 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ TabSyM: A Generative Pipeline for Small Multi-Cohort Omics Tabular Data ]]> https://biorxiv.org/content/10.1101/2025.07.14.664738v1?rss=1 Yu, N. Wang, Y. Olsen, L. K. Zhang, B. Zhang, h. Liu, Z. 2025-07-18 doi:10.1101/2025.07.14.664738 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Myc and Kras cooperate in adult acinar cells to drive phenotypic heterogeneity, metastasis, and therapeutic resistance in a novel pancreatic cancer mouse model ]]> https://biorxiv.org/content/10.1101/2025.07.14.664767v1?rss=1 English, I. A. Worth, P. J. MacPherson-Hawthorne, K. A. Vergara, M. Pelz, K. Kiemen, A. L. Shah, V. M. Blise, K. E. Pelz, C. Tsuda, M. Heskett, M. B. Farrell, A. S. Allen-Petersen, B. L. Jimenez, P. Joly, M. M. Thoma, M. C. Eng, J. R. Daniel, C. J. Wang, X. Cunningham, M. Salgado-Garza, G. Phipps, J. L. Betts, C. Sivagnanam, S. Morgan, T. K. Wood, L. D. Coussens, L. M. Brody, J. R. Langer, E. M. Sears, R. C. 2025-07-18 doi:10.1101/2025.07.14.664767 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Benchmarking the Impact of Anatomical Segmentation on In Vivo Magnetic Resonance Spectroscopy ]]> https://biorxiv.org/content/10.1101/2025.07.15.664931v1?rss=1 Archibald, J. Igwe, K. C. Kaiser, A. Landheer, K. Lee, J. Kramer, J. L. K. Zolch, N. Gudmundson, A. Zollner, H. J. Fleischer, C. C. Oeltzschner, G. Near, J. Mikkelsen, M. 2025-07-18 doi:10.1101/2025.07.15.664931 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Quality control of single-cell ATAC-seq data without peak calling using Chromap ]]> https://biorxiv.org/content/10.1101/2025.07.15.664951v1?rss=1 Ahmed, O. Zhang, H. Langmead, B. Song, L. 2025-07-18 doi:10.1101/2025.07.15.664951 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Whole blood transcriptional signatures of age and survival identified in Long Life Family and Integrative Longevity Omics Studies ]]> https://biorxiv.org/content/10.1101/2025.07.15.664976v1?rss=1 Li, M. Song, Z. Reed, E. Karagiannis, T. T. Andersen, S. Brent, M. Mateusiak, C. Acharya, S. Jung, W. S. Liao, S. Wojczynski, M. K. Feitosa, M. F. O'Connell, J. R. Montasser, M. E. Thorpe, R. J. Arbeev, K. Milman, S. Tai, A. Perls, T. T. Sebastiani, P. Monti, S. 2025-07-18 doi:10.1101/2025.07.15.664976 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Genetically encoded assembly recorder temporally resolves cellular histories in cellulo and in vivo ]]> https://biorxiv.org/content/10.1101/2025.07.16.664392v1?rss=1 Yan, Y. Lu, J. Li, Z. Zhao, Z.-H. Shay, T. F. Wang, S. Lei, Y. Wang, Y. Chen, W. Parker, P. Yang, H. Qi, A. Sun, Y. Bergles, D. Baker, D. Lin, D. 2025-07-18 doi:10.1101/2025.07.16.664392 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection ]]> https://biorxiv.org/content/10.1101/2025.07.16.664785v1?rss=1 Merritt, B. Ratcliff, J. Ta, S. Osis, G. Mauldin, M. Thielen, P. M. 2025-07-18 doi:10.1101/2025.07.16.664785 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A live tumor fragment platform to assess immunotherapy response in core needle biopsies while addressing challenges of tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.07.18.663728v1?rss=1 Ramasubramanian, T. S. Adstamongkonkul, P. Scribano, C. Johnson, C. Caenepeel, S. Hrycyniak, L. Vedder, L. C. Dana, N. Baltes, C. Browning, T. Chen, Y.-I. Dietz, T. Flietner, E. Kaplewski, N. Kellner, A. Korrer, M. Liu, C. Marhefke, N. McDonnell, P. Nasreen, A. Pope, V. Prasad, A. Richardson, J. Schneider, S. Schultz, M. Sood, C. Sunil, A. von Euw, E. Wait, E. Wargowski, E. Advani, P. Broome, B. Bruckbauer, A. Godwin, A. Kokabi, N. Martin, R. Robaina, M. Toia, G. Routh, J. Friedl, A. Eliceiri, K. Szulczewski, M. Johnson, S. Oliner, J. Galon, J. Capi 2025-07-18 doi:10.1101/2025.07.18.663728 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Increased Exertion Variability is Linked to Disruptions in Effort Assessment in Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2025.07.16.665234v1?rss=1 Dryzer, M. H. Nourbakhsh, B. Keller, J. Chib, V. S. 2025-07-21 doi:10.1101/2025.07.16.665234 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Goal Uncertainty Attenuates Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.07.18.665537v1?rss=1 Padmanabhan, S. Shadmehr, R. S. Klatzky, R. Tsay, J. S. 2025-07-23 doi:10.1101/2025.07.18.665537 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Prematurity Reprograms Cerebellar Development and Long-Term Behavior ]]> https://biorxiv.org/content/10.1101/2025.07.22.664624v1?rss=1 Sanidas, G. Simonti, G. Ghaemmaghami, J. Woyshner, K. Wolff, N. Byrd, C. Triantafyllou, M. Lowe, C. Salisbury, H. Goldstein, E. Sathyanesan, A. Vidva, R. Koutroulis, I. O Brien, G. Sidiropoulos, D. Gallo, V. Kratimenos, P. 2025-07-24 doi:10.1101/2025.07.22.664624 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ CRABS-ROC, A Respirometry Protocol For Overcoming Substrate Limitations, Reveals Excess Brain Mitochondrial Complex I Capacity ]]> https://biorxiv.org/content/10.1101/2025.07.23.666392v1?rss=1 2-fold excess Complex I capacity beyond the uncoupled OCR of cells metabolizing glucose and pyruvate. Furthermore, we demonstrate that CRABS-ROC can expose a Complex I deficit in isolated harlequin mutant brain mitochondria that display wild-type levels of Complex I-substrate-linked respiration despite having about half the normal level of Complex I. Thus, CRABS-ROC should be broadly useful for studies on mitochondrial function because it can both reveal excess ETC capacity and unmask ETC alterations that may be missed by the most widely used methods. ]]> Zhang, N. Roelofs, B. A. Bordt, E. A. Piskoun, B. Robertson, C. L. Polster, B. M. 2025-07-24 doi:10.1101/2025.07.23.666392 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Continuous partitioning of neuronal variability ]]> https://biorxiv.org/content/10.1101/2025.07.23.666404v1?rss=1 Rupasinghe, A. Charles, A. S. Pillow, J. W. 2025-07-27 doi:10.1101/2025.07.23.666404 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Oscillatory signal decoding within the ERK cascade ]]> https://biorxiv.org/content/10.1101/2025.07.24.666680v1?rss=1 Ganesan, A. Lee, H. N. Tenner, B. Mehta, S. Levchenko, A. Zhang, J. 2025-07-28 doi:10.1101/2025.07.24.666680 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Origin and novel transport pathways of bacterial hopanoids ]]> https://biorxiv.org/content/10.1101/2025.07.29.667474v1?rss=1 Lawrence, E. C. Pan, H. Ollikainen, N. Belin, B. J. 2025-07-29 doi:10.1101/2025.07.29.667474 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Precision fMRI reveals densely interdigitated network patches with conserved motifs in the lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2025.07.24.666468v1?rss=1 Ladwig, Z. Kermani, K. Z. Dworetsky, A. Labora, N. Hernandez, J. J. Dorn, M. Smith, D. M. Nee, D. E. Braga, R. M. Petersen, S. E. Gratton, C. 2025-07-30 doi:10.1101/2025.07.24.666468 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ A spinal origin for the obligate flexor synergy in the non-human primate: Implications for control of reaching ]]> https://biorxiv.org/content/10.1101/2025.07.28.666086v1?rss=1 Glover, I. S. Baker, A. M. Krakauer, J. W. Baker, S. N. 2025-07-30 doi:10.1101/2025.07.28.666086 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ A lncRNA drives developmentally-timed decay of all members of an essential microRNA family ]]> https://biorxiv.org/content/10.1101/2025.07.30.667716v1?rss=1 Grimme, A. L. Li, L. Scholl, A. Donnelly, B. F. Channamraju, N. Vieux, K.-F. Zhou, L. Seydoux, G. Xie, M. McJunkin, K. 2025-07-31 doi:10.1101/2025.07.30.667716 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Formate reduces ischemic injury in female hearts lacking alcohol dehydrogenase 5 ]]> https://biorxiv.org/content/10.1101/2025.07.29.667470v1?rss=1 Garbus-Grant, H. Ebenebe-Kasonde, O. V. Kabir, R. Kohr, M. J. 2025-08-01 doi:10.1101/2025.07.29.667470 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Sleep pressure is differentially regulated by molecularly distinct subtypes of Lhx6-positive and Lhx6-negative neurons of the zona incerta. ]]> https://biorxiv.org/content/10.1101/2025.07.30.667705v1?rss=1 Chandler, P. W. Lee, S. S. Duncan, L. Kim, D. W. T. Wu, M. Blackshaw, S. 2025-08-01 doi:10.1101/2025.07.30.667705 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Longitudinal TCR repertoires in ulcerative colitis patients show features distinguishing disease states ]]> https://biorxiv.org/content/10.1101/2025.07.31.667918v1?rss=1 Rahman, S. Farah, M. Kwok, A. Varghese, J. Xu, B. Daraie, A. Greenstein, J. Taylor, C. Soley, N. Yan, A. Vatsaraj, I. Harris, C. Melia, J. Briggs, K. 2025-08-01 doi:10.1101/2025.07.31.667918 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Effects of sex and pre-exposure on Δ9-tetrahydrocannabinol (THC) vapor self-administration in rats ]]> https://biorxiv.org/content/10.1101/2025.08.01.668172v1?rss=1 Moore, C. F. Weerts, E. M. 2025-08-01 doi:10.1101/2025.08.01.668172 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource ]]> https://biorxiv.org/content/10.1101/2025.07.28.667191v1?rss=1 Zhang, B. A. Miao, B. Fu, S. Coarfa, C. Kumar, R. Kuntala, P. K. Park, B. Colacino, J. A. Svobada, L. K. Shao, W. Xing, X. Li, D. Liu, S. Hamanaka, R. B. Lalancette, C. Sartor, M. A. Krapp, C. Crawford, G. E. Patisaul, H. B. Wiltshire, T. Aylor, D. L. Biswal, S. Mutlu, G. M. Rajagopalan, S. Tang, W.-Y. Dolinoy, D. C. Wang, T. Bartolomei, M. S. Walker, C. L. Grimm, S. L. Ruiz-Echartea, E. Katz, T. Jangid, R. 2025-08-02 doi:10.1101/2025.07.28.667191 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Chronic activation of a key exercise signal transducer, CaMKII, drives skeletal muscle aging and sarcopenia ]]> https://biorxiv.org/content/10.1101/2025.07.30.667744v1?rss=1 Bene, M. R. Chung, T. Fountain, W. A. Rosales-Soto, G. Hernandez-Ochoa, E. Antonescu, C. Florea, L. Jeong, S. J. Le, A. Xue, Q.-L. Hoke, A. Abadir, P. Wang, Q. 2025-08-02 doi:10.1101/2025.07.30.667744 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Early-life Exposure to Arsenic Primes the Offspring to Increased Asthma Risk: Transcriptome and Epigenome Analysis ]]> https://biorxiv.org/content/10.1101/2025.08.01.668223v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1f5394eorg.highwire.dtl.DTLVardef@855bf8org.highwire.dtl.DTLVardef@1592328org.highwire.dtl.DTLVardef@1133ec4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Maternal iAs exposure and study design to assess offspring asthma risk. A) Schematic shows the exposure window in which F0 dams received iAs in drinking water from preconception through lactation, followed by collection of F1 progeny for transcriptomic and methylomic analysis. A subset of 5-month-old F1 progenies were assessed for the HDM allergen-induced airway reactivity and airway inflammation. B) Lung resistance was assessed following methacholine (30mg/mL) challenge. C) BAL cells were stained with Diff-Quick, and eosinophil counts are shown. Each datapoint represents a pup from an individual dam; error bars indicate SEM. Five to six dams were used. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/668223v1_fig2.gif" ALT="Figure 2"> View larger version (23K): org.highwire.dtl.DTLVardef@7dc1b1org.highwire.dtl.DTLVardef@378529org.highwire.dtl.DTLVardef@1076fe3org.highwire.dtl.DTLVardef@142d801_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Blood transcriptome profiles and predicted canonical pathways and regulatory networks. A) Numbers of differentially expressed genes (DEGs) identified in male and female progeny are illustrated with a Venn diagram. Enriched canonical pathways ranked by the p value are shown. B) Using the set of DEGs common in both sexes, Ingenuity Pathway Analysis (IPA) highlights TGF as a central upstream regulator linking overlapping DEGs related to extracellular matrix signaling (orange), inflammation (yellow), and embryonic development/cell metabolism (blue). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/668223v1_fig3.gif" ALT="Figure 3"> View larger version (23K): org.highwire.dtl.DTLVardef@1732b53org.highwire.dtl.DTLVardef@216332org.highwire.dtl.DTLVardef@1f794d1org.highwire.dtl.DTLVardef@14b62df_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Blood methylome analysis and associations between miR-101c and TGF-related differentially expressed genes. A) Number of differentially methylated CpGs (DMCs) identified in male and female progeny are illustrated with a Venn diagram. There are four DMCs overlapping DMCs annotated to miR-101c. B) Expression levels of miR-101c are shown. C) IPA-derived network linking this miRNA to TGF-related DEGs. Each datapoint represents a pup from an individual dam; error bars indicate SEM. Four to five dams were used. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/668223v1_fig4.gif" ALT="Figure 4"> View larger version (38K): org.highwire.dtl.DTLVardef@482e86org.highwire.dtl.DTLVardef@e666bdorg.highwire.dtl.DTLVardef@631538org.highwire.dtl.DTLVardef@10618f6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Relationship between iAs-induced blood transcriptional changes and allergen-induced AHR. This figure presents correlation patterns between baseline blood DEGs expression changes prior to HDM challenge and subsequent changes in AHR. Pearson correlation coefficients are depicted using a color gradient to distinguish positive (blue) and negative (peach) associations. * Positive correlation: r>0.8, p<0.05; ^ negative correlation: r<-0.8, p<0.05 C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/668223v1_fig5.gif" ALT="Figure 5"> View larger version (20K): org.highwire.dtl.DTLVardef@150d27eorg.highwire.dtl.DTLVardef@12b4edeorg.highwire.dtl.DTLVardef@4702a8org.highwire.dtl.DTLVardef@1ff9600_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5.C_FLOATNO Circulating miR-101c levels in progeny exposed to maternal iAs. Plasma levels of miR-101c and COL3A1 protein are shown at different developmental stages. A) Relative expression of miR-101c across F1 progeny at juvenile (3 weeks of age) and adult (5 months of age) prenatally exposed to iAs. B) Levels of COL3A1 protein are shown at juvenile and adult F1 progeny. Each datapoint represents a pup from an individual dam, error bars indicate SEM. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/668223v1_fig6.gif" ALT="Figure 6"> View larger version (46K): org.highwire.dtl.DTLVardef@d0ec76org.highwire.dtl.DTLVardef@5468a2org.highwire.dtl.DTLVardef@1a17e85org.highwire.dtl.DTLVardef@17956ce_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 6.C_FLOATNO Comparison of transcriptional patterns across tissues and developmental stages. Expression changes (FC: fold changes vs. unexposed) of DEGs and miR-101c are compared between blood and lung tissues in both A) juvenile (3 weeks of age) and B) adult (5 months of age) progeny. Blue and orange bars represent FC in blood from male and female progeny, respectively. Black bars represent FC in lung tissues. Solid bars indicate statistically significant changes. C_FIG O_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/668223v1_fig7.gif" ALT="Figure 7"> View larger version (22K): org.highwire.dtl.DTLVardef@131ef23org.highwire.dtl.DTLVardef@14b0652org.highwire.dtl.DTLVardef@8c1b30org.highwire.dtl.DTLVardef@4cf6d9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 7.C_FLOATNO Fetal lung and amniotic fluid levels of miR-101c. Relative levels of miR-101c are shown in fetal lung tissues and matched amniotic fluid at embryonic day 16. Data illustrate expression patterns in the context of maternal iAs exposure. Each datapoint represents a pup from an individual dam, error bars indicate SEM. C_FIG GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/668223v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e25f49org.highwire.dtl.DTLVardef@1dddc22org.highwire.dtl.DTLVardef@9f4244org.highwire.dtl.DTLVardef@1b787e9_HPS_FORMAT_FIGEXP M_FIG C_FIG Description: F1 progeny prenatally exposed to iAs were assessed for blood transcriptomic and DNA methylome analysis at 5 months of age. Correlation analysis between transcriptional changes and allergen-induced airway hyperresponsiveness (AHR) was conducted to examine the epigenetic impact of maternal iAs exposure on offspring asthma risk. ]]> Sun, Y. Watfa, M. Sun, Q. Rajasundaram, D. Schlegel, B. Yeung-Luk, B. Pulczinski, J. Park, B. Barchowsky, A. Mitzner, W. Biswal, S. Tang, W. Y. 2025-08-03 doi:10.1101/2025.08.01.668223 Cold Spring Harbor Laboratory Press 2025-08-03 <![CDATA[ Structural and functional characterisation of a reconstructed ancestral strigolactone receptor ]]> https://biorxiv.org/content/10.1101/2025.08.03.668049v1?rss=1 Tuckey, A. J. Marshall, A. C. Rothzerg, E. Bennett, T. Bond, C. S. Waters, M. T. 2025-08-04 doi:10.1101/2025.08.03.668049 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Modeling hidden cognitive states reveals acute and chronic effects of fentanyl on decision-making ]]> https://biorxiv.org/content/10.1101/2025.08.04.668448v1?rss=1 Zhang, Z. Janak, P. H. Garr, E. 2025-08-05 doi:10.1101/2025.08.04.668448 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Structural Repertoire of HCV Broadly Neutralizing Antibodies Targeting the E2 Front Layer Supersite ]]> https://biorxiv.org/content/10.1101/2025.08.04.668577v1?rss=1 Wilcox, X. E. Punia, R. Mimms, J. Frumento, N. Bailey, J. R. Flyak, A. I. 2025-08-06 doi:10.1101/2025.08.04.668577 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Data-driven simulations elucidate how lymphocyte motility behaviors drive cell-cell interactions within germinal centers ]]> https://biorxiv.org/content/10.1101/2025.08.05.668700v1?rss=1 Sivakumar, N. Min, C. Choe, K. Beguelin, W. Phillip, J. M. Mac Gabhann, F. 2025-08-07 doi:10.1101/2025.08.05.668700 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ A colorimetric method for detecting virulent bacteriophage to Vibrio cholerae in fecal and environmental samples ]]> https://biorxiv.org/content/10.1101/2025.08.07.669158v1?rss=1 Luo, W. Dinowitz, D. Camilli, A. Andrews, J. R. da Silva, K. E. Debes, A. K. Sayeed, M. A. Nelson, E. J. Sack, D. A. 2025-08-07 doi:10.1101/2025.08.07.669158 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Kinematic Dissection of Arm Paresis after Focal New M1, Old M1 and Red Nucleus Lesions in Non-Human Primates ]]> https://biorxiv.org/content/10.1101/2025.08.06.668715v1?rss=1 Baines, A. Poll, A. Baker, A. M. Krakauer, J. W. Baker, S. N. 2025-08-08 doi:10.1101/2025.08.06.668715 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation ]]> https://biorxiv.org/content/10.1101/2025.08.07.669196v1?rss=1 Yan, J. Cho, H. S. Luo, R. Beer, M. A. Li, W. Huangfu, D. 2025-08-08 doi:10.1101/2025.08.07.669196 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Loss of DAXX induces alternative lengthening of telomeres (ALT)-associated hallmarks in prostate cancer cells in a context-specific manner ]]> https://biorxiv.org/content/10.1101/2025.08.06.668744v1?rss=1 Mori, J. O. Da, J. Kim, J. Rizzo, A. Davis, C. Lanza, C. Brosnan-Cashman, J. A. Meeker, A. K. Heaphy, C. M. Graham, M. K. 2025-08-09 doi:10.1101/2025.08.06.668744 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Cell-type-selective synaptogenesis during the development of excitatory connectivity in the mammalian neocortex ]]> https://biorxiv.org/content/10.1101/2025.08.08.669371v1?rss=1 Gutman-Wei, A. Y. Sudarsanam, S. Cabalinan, A. G. Shahid, N. Shi, A. Guzman Clavel, L. E. Spindler-Krage, S. M. Agarwal, A. Kolodkin, A. L. Brown, S. P. 2025-08-09 doi:10.1101/2025.08.08.669371 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Attenuated CaV1.2-BK channel protein interaction in bipolar disorder ]]> https://biorxiv.org/content/10.1101/2025.08.08.669447v1?rss=1 Srivastava, R. Genduso, N. Ishizuka, K. Sawa, A. 2025-08-10 doi:10.1101/2025.08.08.669447 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease ]]> https://biorxiv.org/content/10.1101/2025.08.07.669006v1?rss=1 Markov, N. S. Esposito, A. J. Senkow, K. J. Schleck, M. J. Cusick, L. Yu, Z. Sokolenko, Y. V. Diaz, E. Jonasson, E. Swaminathan, S. Lu, Z. Nafikova, R. A. Fenske, S. Bunyan, E. G. Perez-Leonor, X. G. Abdala-Valencia, H. Flozak, A. S. Joshi, N. Argento, C. A. Malsin, E. S. Reyfman, P. A. Puchalski, J. T. Gulati, M. Carns, M. Aren, K. Cooper, P. R. Field, N. S. Mohsin, S. Shawabkeh, M. Soriano, A. Gundersheimer, A. N. Goldberg, I. A. Damore, B. Peltekian, A. K. Agrawal, A. Cheung, C. Perez, S. Teaw, S. Williams, A. Page, N. Kujawski, S. E. Odell, W. Gune 2025-08-11 doi:10.1101/2025.08.07.669006 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Survey of benzimidazole resistance in ascarid parasites of poultry ]]> https://biorxiv.org/content/10.1101/2025.08.12.669876v1?rss=1 Collins, J. Choo, R. Shaver, A. O. Schaye, E. S. Volpe, T. Nunn, L. Lightly, M. E. Niel, K. R. Frye, E. M. Zamanian, M. Andersen, E. C. 2025-08-12 doi:10.1101/2025.08.12.669876 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Paracrine Bone-Derived Senescent Secretome Induces Spatially Patterned ECM and Biomechanical Vulnerability in Human Brain Organoids ]]> https://biorxiv.org/content/10.1101/2025.08.11.669674v1?rss=1 Kim, C. Ofria, L. D. Kshirsagar, A. Gomez Flores, E. Kulkarni, S. Liu, A. Y. Kirkland, J. L. Kathuria, A. Tilton, M. 2025-08-13 doi:10.1101/2025.08.11.669674 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ ClpA- and ClpAP-Catalyzed Unfolding and Translocation are Differentially Coupled to ATP Binding ]]> https://biorxiv.org/content/10.1101/2025.08.12.669770v1?rss=1 Islam, L. Banwait, J. K. Lucius, A. L. 2025-08-13 doi:10.1101/2025.08.12.669770 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ A population-scale atlas of blood and tissue in lupus nephritis ]]> https://biorxiv.org/content/10.1101/2025.08.11.669754v1?rss=1 Gurajala, S. Sugiarto, N. W. Curtis, M. Eisenhaure, T. M. Arazi, A. Fava, A. Xiao, Q. Mears, J. Rovin, B. Berthier, C. C. Izmirly, P. M. Barnas, J. L. Hoover, P. J. Peters, M. Raychowdhury, R. Horisberger, A. Sakaue, S. Zhao, Y. Furie, R. A. Belmont, H. M. Hildeman, D. A. Woodle, E. S. Dall'Era, M. Putterman, C. Kamen, D. L. McMahon, M. A. Grossman, J. Kalunian, K. C. Hodgin, J. B. Payan-Schober, F. Apruzzese, W. Perlman, H. Cuda, C. M. Wofsy, D. Guthridge, J. M. Anolik, J. H. James, J. A. Accelerating Medicines Partnerships Rheumatoid Arthritis/Systemic Lu 2025-08-14 doi:10.1101/2025.08.11.669754 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ In vivo bioreactor matures iPSC-CMs for MLP disease modeling ]]> https://biorxiv.org/content/10.1101/2025.08.11.669708v1?rss=1 Murphy, S. Cho, G. Limphong, P. Lee, D. Kwon, C. 2025-08-15 doi:10.1101/2025.08.11.669708 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS) ]]> https://biorxiv.org/content/10.1101/2025.08.13.665980v1?rss=1 Cottrell, T. R. Roskes, J. S. Fotheringham, M. Cohen, E. Zhang, B. Engle, L. L. Wang, D. Will, E. Sunshine, J. C. Jimenez-Sanchez, D. Zheng, Z. Caushi, J. X. Zhang, J. D'Amiano, N. Stein-Deutsch, J. Uttam, S. Pirie, K. Vlaminck, D. Mataj, M. Fiorante, A. Espinosa, N. Popa, T. Ogurtsova, A. Soto-Diaz, S. Eminizer, M. Tabrisky, S. Jorquera, A. Skidmore, J. Medvedev, D. Chaft, J. E. Brahmer, J. R. Conroy, M. Reuss, J. E. Danilova, L. Ji, H. Forde, P. M. Pardoll, D. M. Smith, K. N. Green, B. F. Szalay, A. S. Taube, J. M. 2025-08-15 doi:10.1101/2025.08.13.665980 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Characterizing Post-Mortem Brain Molecular Taxonomy of Cognitive Resilience and Translating it to Living Humans ]]> https://biorxiv.org/content/10.1101/2025.08.13.670106v1?rss=1 Batalha, C. M. P. F. Yu, L. Zammit, A. R. Poole, V. N. Buchman, A. S. Lopes, K. d. P. Vialle, R. Abadir, P. Nidadavolu, L. Wyss-Coray, T. Seyfried, N. T. Wang, Y. Tasaki, S. De Jager, P. L. Iturria-Medina, Y. Bennett, D. A. 2025-08-18 doi:10.1101/2025.08.13.670106 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Uncertainty and reward histories have distinct effects on decisions after wins and losses ]]> https://biorxiv.org/content/10.1101/2025.08.14.670176v1?rss=1 Kalhan, S. Magnard, R. Cheng, Y. Janak, P. H. 2025-08-19 doi:10.1101/2025.08.14.670176 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Characterizing the Ion-Conductive State of the α7-Nicotinic Acetylcholine Receptor via Single-Channel Measurements and Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/2025.08.15.670429v1?rss=1 Sultan, N. Cymes, G. Chen, A. Brooks, B. Grosman, C. Damjanovic, A. 2025-08-19 doi:10.1101/2025.08.15.670429 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Symptomatic treatment by a BBB-permeable AAV engineered to restore TDP-43 function slows motor neuron disease and prevents paralysis ]]> https://biorxiv.org/content/10.1101/2025.08.14.670400v1?rss=1 20 months, grip strength and body weight remained normal, and no histopathological abnormalities were observed, underscoring a favorable safety profile for this gene therapy. These results provide preclinical proof-of-concept that BBB-crossing AAV delivery of CTR can rescue motor neuron disease through the restoration of TDP-43 function, offering a promising mechanism-based therapeutic strategy for ALS. ]]> Peethambaran Mallika, A. Yu, J. Sitzman, O. Baghel, M. S. Renganathan, S. Sinha, I. R. Melnikova, T. Ling, J. P. Wong, P. C. 2025-08-20 doi:10.1101/2025.08.14.670400 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ The Cancer/Testis Antigen FATE1 Antagonizes Fission and Preserves Mitochondrial Network Integrity under Cytotoxic Stress ]]> https://biorxiv.org/content/10.1101/2025.08.18.670752v1?rss=1 Lang, V. Zahn, J. T. Tonse, D. P. Brady, N. R. Hamacher-Brady, A. 2025-08-20 doi:10.1101/2025.08.18.670752 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Missing data in single-cell transcriptomes reveals transcriptional shifts ]]> https://biorxiv.org/content/10.1101/2025.08.15.669765v1?rss=1 Chen, R. Chung, Y.-C. Kelly, B. Moore, H. Lvovs, D. Basu, S. Gueguen, P. M. Sanin, D. E. 2025-08-21 doi:10.1101/2025.08.15.669765 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal ]]> https://biorxiv.org/content/10.1101/2025.08.15.670438v1?rss=1 Balasubramanian, R. Tolman, N. Li, T. Hannan, A. Bupp-Chickering, V. Polanco, K. Bhandari, A. Zhou, S. Simon, M. Peregrin, J. Montgomery, C. Kizhatil, K. Qian, J. John, S. 2025-08-21 doi:10.1101/2025.08.15.670438 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML ]]> https://biorxiv.org/content/10.1101/2025.08.17.670714v1?rss=1 Naji, N. S. Ahmedna, T. Peske, J. D. Zeng, X. Perkins, B. Thompson, Z. Nichakawade, T. D. Lee, B. S. Watson, E. Chatzilygeroudi, T. Luo, L. Paun, B. Klausner, M. An, Y. Supeanu, T. Gojo, I. Ghiaur, G. DeZern, A. E. Levis, M. J. Resar, L. Jones, R. J. Karanika, S. Paul, S. Karantanos, T. 2025-08-21 doi:10.1101/2025.08.17.670714 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Oncolytic peptide NF27 effectively inhibits tumor growth and eradicates tumors in multiple cancer types ]]> https://biorxiv.org/content/10.1101/2025.08.17.668569v1?rss=1 Furukawa, N. Chao, A. R. Yang, W. Patil, A. Christenson, E. S. Mirando, A. C. Pandey, N. B. Popel, A. S. 2025-08-22 doi:10.1101/2025.08.17.668569 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ 3D map-guided modeling of functional endometrial tissue using multi-compartment assembloids ]]> https://biorxiv.org/content/10.1101/2025.08.22.671545v1?rss=1 REN, K. DUARTE, V. ZHOU, X. D. HO, B. FORJAZ, A. CRAWFORD, A. ALICEA-REBECCA, G. M. JOSHI, S. NAIR, P. R. HANNA, E. A. WIRTZ, D. 2025-08-23 doi:10.1101/2025.08.22.671545 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Evaluating the Effectiveness of Parameter-Efficient Fine-Tuning in Genomic Classification Tasks ]]> https://biorxiv.org/content/10.1101/2025.08.21.671544v1?rss=1 Berman, D. Jimenez, D. Ta, S. Merritt, B. Narayan, V. Ratcliff, J. 2025-08-26 doi:10.1101/2025.08.21.671544 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Puromycin-sensitive aminopeptidase acts as an inhibitory auxiliary subunit of volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2025.08.24.671966v1?rss=1 Zheng, W. Hagino, T. Wang, H. Cheng, H. Y. Koylass, N. Chen, K. H. Wang, H. Mani, S. Mondal, A. K. Twomey, E. C. Qiu, Z. 2025-08-27 doi:10.1101/2025.08.24.671966 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Actinium-225 dendrimer-radioconjugates combined with low-dose standard-of-care chemotherapy: site-independent treatment of triple negative breast cancer metastases ]]> https://biorxiv.org/content/10.1101/2025.08.25.670941v1?rss=1 Hariharan, P. Nair, R. Sarkar, A. Gabrielson, K. L. Wu, T. Liu, C. Liyanage, W. Kannan, R. M. Sofou, S. 2025-08-27 doi:10.1101/2025.08.25.670941 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ UNC-45A Drives ATP-Independent Microtubule Destabilization via Defect Recognition and Repair Inhibition Contributing to Neurite Dystrophy ]]> https://biorxiv.org/content/10.1101/2025.08.26.671351v1?rss=1 Hoshino, A. Castle, B. T. Shetty, M. Khan, H. Meints, J. Pletnikova, O. Lee, M. K. Troncoso, J. Odde, D. J. Bazzaro, M. 2025-08-27 doi:10.1101/2025.08.26.671351 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Robust representation and non-linear spectral integration of simple and complex harmonic sounds in layers 4 and 2/3 of primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2025.08.26.672221v1?rss=1 Chen, Y. Chen, C.-T. Gui, Y. Kanold, P. O. 2025-08-27 doi:10.1101/2025.08.26.672221 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Self-Assembling Synthetic Peptides Remodel Mitochondrial Properties via Nanopore Formation ]]> https://biorxiv.org/content/10.1101/2025.08.26.672490v1?rss=1 Nguyen, N. T. H. Fujita, S. Takeuchi, N. Kawano, R. Inoue, T. 2025-08-27 doi:10.1101/2025.08.26.672490 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Decitabine reverses innate immune gene suppression in rare melanomas ]]> https://biorxiv.org/content/10.1101/2025.08.24.671992v1?rss=1 MacBeth, M. L. Bagby, S. M. Borgers, J. S. W. Turner, J. A. Anderson, K. C. Whitty, P. A. Hartman, S. Yacob, B. Rebecca, V. W. Davila, E. Pitts, T. M. Medina, T. M. Patel, S. P. McCarter, M. D. Robinson, W. A. Tobin, R. P. Couts, K. L. 2025-08-28 doi:10.1101/2025.08.24.671992 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Tafazzin-Mediated Cardiolipin Remodeling Controls Metabolic Stress Response and Effector Function of Inflammatory T Cells ]]> https://biorxiv.org/content/10.1101/2025.08.25.672061v1?rss=1 Zhao, X. Hochrein, S. M. Eckstein, M. Wu, H. Sinning, K. Ermer, K. J. Puhl, S.-L. Eilers, M. Schmitz, W. Stigloher, C. Claypool, S. M. Maack, C. Dudek, J. Vaeth, M. 2025-08-28 doi:10.1101/2025.08.25.672061 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Intrinsic Gestational Timing Governs Human Cerebellar Development After Preterm Birth ]]> https://biorxiv.org/content/10.1101/2025.09.01.673244v1?rss=1 Sanidas, G. Simonti, G. Ghaemmaghami, J. Woyshner, K. Vidva, R. Wolff, N. Triantafyllou, M. Lowe, C. Vij, A. Pettersen, H. P. S. Chandereng, T. Koutroulis, I. O'Brein, G. Sidiropoulos, D. N. Gallo, V. Kratimenos, P. 2025-09-02 doi:10.1101/2025.09.01.673244 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Biological landscape of acute illness in children in sub-Saharan Africa and South Asia ]]> https://biorxiv.org/content/10.1101/2025.09.01.672585v1?rss=1 Mudibo, E. O. Sande, C. Ngari, M. M. Jenkins, B. Singa, B. O. Lancioni, C. L. Diallo, A. H. Mbale, E. Mupere, E. John, M. Bamouni, R. M. Prendergast, A. J. McGrath, C. J. Koulman, A. Bandsma, R. H. J. Tickell, K. D. Walson, J. L. Berkley, J. A. Gonzales, G. B. Njunge, J. M. 2025-09-03 doi:10.1101/2025.09.01.672585 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling ]]> https://biorxiv.org/content/10.1101/2025.09.01.673503v1?rss=1 Fu, Y. Mathew, D. Wang, M. Chen, X. E. Lin, K. Schaff, D. L. Shaffer, S. M. Pardoll, D. Jackson, C. Zhang, N. 2025-09-04 doi:10.1101/2025.09.01.673503 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ A neural network with episodic memory learns causal relationships between narrative events ]]> https://biorxiv.org/content/10.1101/2025.09.01.673596v1?rss=1 Song, H. Lu, Q. Nguyen, T. T. Chen, J. Leong, Y. C. Rosenberg, M. D. Ching, S. Zacks, J. M. 2025-09-05 doi:10.1101/2025.09.01.673596 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ HIF-1α and RhoA Drive Enhanced Motility and Aerotaxis of Polyaneuploid Prostate Cancer Cells in Hypoxia ]]> https://biorxiv.org/content/10.1101/2025.09.03.673887v1?rss=1 Hosny, N. Li, S. Amend, S. R. Gatenby, R. Pienta, K. Brown, J. Qu, J. Austin, R. H. 2025-09-05 doi:10.1101/2025.09.03.673887 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome ]]> https://biorxiv.org/content/10.1101/2025.09.02.673778v1?rss=1 Canner, S. W. Lu, L. Takeshita, S. S. Gray, J. J. 2025-09-06 doi:10.1101/2025.09.02.673778 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Clinical and molecular features of primary gliosarcoma with digital spatial whole-transcriptome analysis of glial and mesenchymal components ]]> https://biorxiv.org/content/10.1101/2025.09.02.673845v1?rss=1 Wood, M. D. Zangirolani, G. Lee, J. Neff, T. Zhang, K. Corless, C. L. 2025-09-07 doi:10.1101/2025.09.02.673845 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Poly(ADP-ribose) Polymerase 1 Deficiency Attenuates Amyloid Pathology, Neurodegeneration, and Cognitive Decline in a Familial Alzheimer Disease Model ]]> https://biorxiv.org/content/10.1101/2025.09.06.674313v1?rss=1 Jhaldiyal, A. Kumari, M. Tripathi, T. Khan, R. Wang, J. Guttman, L. Biswas, D. Pasupuleti, A. Aggarwal, A. Pandya, S. Chou, S.-C. Panicker, N. Monghekar, A. Albert, M. Bekris, L. Leverenz, J. Kam, T.-I. Dawson, T. Dawson, V. L. 2025-09-07 doi:10.1101/2025.09.06.674313 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection ]]> https://biorxiv.org/content/10.1101/2025.09.03.673836v1?rss=1 Koneru, R. Anant, M. M.-G. Kim, H. Cheron, J. Kebschull, J. M. 2025-09-08 doi:10.1101/2025.09.03.673836 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ TDP-43 loss of function drives aberrant splicing in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.09.04.673943v1?rss=1 500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD. ]]> Brenton, J. W. Follett, J. Nirujogi, R. Toomey, C. E. Lopez-Garcia, P. Evans, J. R. Lee, Y. J. Syed, K. M. Rocamora Perez, G. Fairbrother-Browne, A. D'Sa, K. Grant-Peters, M. Lachica, J. Hicks, A. R. Wagen, A. Z. O'Callaghan, B. Macpherson, H. Montgomery, K.-a. Busquets, O. Reynolds, R. H. Garcia Ruiz, S. Cao, T. Chen, Z. Plun-Favreau, H. Wong, P. C. Farrer, M. Lashley, T. Soldner, F. Hockemeyer, D. Alessi, D. Wood, N. W. Hardy, J. Rio, D. C. Jaunmuktane, Z. Gustavsson, E. K. Gandhi, S. Ryten, M. 2025-09-09 doi:10.1101/2025.09.04.673943 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology Images ]]> https://biorxiv.org/content/10.1101/2025.09.04.674228v1?rss=1 Hallinan, C. Lucas, C.-H. G. Fan, J. 2025-09-09 doi:10.1101/2025.09.04.674228 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Perinatal Exposure to Metal Mixtures Disrupts Neuronal Function and Behavior ]]> https://biorxiv.org/content/10.1101/2025.09.05.673216v1?rss=1 Pandey, N. C. Karimi, B. Bhobe, A. Pagadala, S. Pandey, S. Sanchez, S. S. Yeung-Luk, B. Rivera, E. Kohr, M. J. Riess, B. Nachman, K. E. Biswal, S. Sille, F. C. M. Graves, A. R. 2025-09-11 doi:10.1101/2025.09.05.673216 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Dual checkpoint blockade of glioblastoma with Anti-PD-1 and Anti-LAG-3 promotes expansion of tumor-reactive T cell clones along a unique pathway of differentiation ]]> https://biorxiv.org/content/10.1101/2025.09.06.674490v1?rss=1 Wang, M. Fu, Y. Bom, S. Ning, Y. Matthews, D. Zhang, M. Lucas, C.-H. Choi, J. Zeng, Z. Zhang, T. Ji, H. Yegnasubramanian, V. Weingart, J. Bettegowda, C. Smith, K. N. Lim, M. Pardoll, D. Zhang, N. R. Jackson, C. 2025-09-11 doi:10.1101/2025.09.06.674490 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging. ]]> https://biorxiv.org/content/10.1101/2025.09.09.673285v1?rss=1 Lyu, P. Palazzo, I. jin, y. Campbell, L. Santiago, C. Carmen-Orzoco, R. Hoang, T. Tangeman, J. Park, A. Yang, S. Shao, J. Chen, R. Hyde, D. Qian, J. Blackshaw, S. 2025-09-11 doi:10.1101/2025.09.09.673285 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens ]]> https://biorxiv.org/content/10.1101/2025.09.10.675374v1?rss=1 Ravichandran, P. Bach, S. V. Phillips, R. A. Valentine, M. R. Eagles, N. J. Du, Y. Rosario, I. D. Miller, R. A. Divecha, H. R. Tippani, M. Montgomery, K. D. Kleinman, J. E. Han, S. Page, S. C. Hyde, T. M. Torres, L. C. Battle, A. Martinowich, K. Hicks, S. C. Maynard, K. 2025-09-11 doi:10.1101/2025.09.10.675374 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Characterizing intra- and inter-tumor heterogeneity in ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.15.676244v1?rss=1 Li, W. Grieshober, L. Gertz, J. Ivich, A. Doherty, J. A. Greene, C. S. Hicks, S. C. 2025-09-15 doi:10.1101/2025.09.15.676244 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Differential Regulation of NHE3 Expression in Type 1 and Type 2 Diabetic Intestine: Impaired Endosomal Regulation of NHE3 Expression in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2025.09.10.675364v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@eabf0aorg.highwire.dtl.DTLVardef@1a46891org.highwire.dtl.DTLVardef@cd2d5corg.highwire.dtl.DTLVardef@5d185b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Singh, V. Lin, R.-X. Sunuwar, L. Yang, J. Donowitz, M. Sarker, R. 2025-09-16 doi:10.1101/2025.09.10.675364 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Fast Dynamic Whole-Body In Vivo Cytometry Using Magnetic Particle Imaging ]]> https://biorxiv.org/content/10.1101/2025.09.11.675624v1?rss=1 Shakeri-Zadeh, A. Kuddannaya, S. Chu, C. Sood, K. Itoo, A. Zivko, C. MACHAIRAKI, V. Walczak, P. Bulte, J. 2025-09-16 doi:10.1101/2025.09.11.675624 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Impact of > 24 h sustained wakefulness and subsequent recovery sleep on time-dependent changes in microRNA factors of individuals with post-acute phase mild traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2025.09.11.675463v1?rss=1 Brager, A. J. Edwards, K. Pattinson, C. Peyer, J. Gill, J. 2025-09-17 doi:10.1101/2025.09.11.675463 24 h sustained wakefulness and subsequent recovery sleep on time-dependent changes in microRNA factors of individuals with post-acute phase mild traumatic brain injury]]> Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ vsgseq2: an updated pipeline for analysis of the diversity and abundance of population-wide Trypanosoma brucei VSG expression ]]> https://biorxiv.org/content/10.1101/2025.09.12.675796v1?rss=1 Oldrieve, G. R. Larcombe, S. Krasilnikova, M. Mugnier, M. R. Matthews, K. R. 2025-09-17 doi:10.1101/2025.09.12.675796 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus ]]> https://biorxiv.org/content/10.1101/2025.09.12.675843v1?rss=1 Srivastava, H. R. Berenberg, D. Qassab, O. Wang, Z. Bonneau, R. Carlton, J. M. 2025-09-17 doi:10.1101/2025.09.12.675843 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Altered NPTX2 dynamics associated with impaired cognitive aging ]]> https://biorxiv.org/content/10.1101/2025.09.15.676156v1?rss=1 Haberman, R. P. Delgado, A. Xiao, M. Koh, M. T. Becker, A. A. Ji, S. Worley, P. F. Gallagher, M. Branch, A. E. 2025-09-17 doi:10.1101/2025.09.15.676156 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Prelamin A Does Not Promote Atherosclerosis or Vascular Smooth Muscle Loss ]]> https://biorxiv.org/content/10.1101/2025.09.15.676432v1?rss=1 Wang, Y. Joseph, L. C. Östlund, C. Kuriakose, G. Hsu, W. Michaelis, S. Worman, H. 2025-09-18 doi:10.1101/2025.09.15.676432 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Library Size in Spatial ATAC-seq: Technical Confounder or Biology? ]]> https://biorxiv.org/content/10.1101/2025.09.15.676443v1?rss=1 Ji, K. X. Ji, H. 2025-09-18 doi:10.1101/2025.09.15.676443 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Modulating Glutamine Metabolism Reprograms Pro-Inflammatory Differentiation in Macrophages ]]> https://biorxiv.org/content/10.1101/2025.09.16.675216v1?rss=1 Qi, S. Fan, J. Wu, D.-S. Ganguly, S. Shih, I.-M. Wang, T.-L. 2025-09-18 doi:10.1101/2025.09.16.675216 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ TDP-43 pathology triggers SRRM4-dependent cryptic splicing of G3BP1 in ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.09.17.676845v1?rss=1 Fakim, H. Ghosh, A. Amzallag, E. Danino, Y. M. Triassi, V. Brown, A.-L. Pal, N. Deshaies, J.-E. Dubinski, A. Lacombe, A. Fauchon, C. Esfahani, A. M. Ling, K. Rigo, F. Jafar-nejad, P. NYGC ALS Consortium, Francis, N. J. Trempe, J.-F. Fratta, P. Coyne, A. N. Hornstein, E. Velde, C. V. 2025-09-18 doi:10.1101/2025.09.17.676845 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ KM-GPT: An Automated Pipeline for Reconstructing Individual Patient Data from Kaplan-Meier Plots ]]> https://biorxiv.org/content/10.1101/2025.09.15.676421v1?rss=1 Zhao, Y. Sun, H. Ding, Y. Xu, Y. 2025-09-19 doi:10.1101/2025.09.15.676421 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Screening of a kinase library in human Huntington disease iPSC derived striatal precursor neurons reveals a neuroprotective effect of PKC alpha and PKC beta1 inhibition ]]> https://biorxiv.org/content/10.1101/2025.09.18.677178v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@256d6org.highwire.dtl.DTLVardef@1931e7borg.highwire.dtl.DTLVardef@1b6598borg.highwire.dtl.DTLVardef@b0bbb5_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHD patient-derived iPSC-based striatal precursor neurons (ISPNs) were used to screen and identify neuroprotective compounds. C_LIO_LIThe PKC-/{beta}1 inhibitor GO6976 rescues HD ISPNs from mutant huntingtin (HTT)-induced toxicity. C_LIO_LIThe phosphorylation of PKC-/{beta}1 is elevated in HD cell and tissues, and PKC-/{beta}1 interact with both wild-type and mutant huntingtin. C_LIO_LIOverexpression of PKC-/{beta}1 is toxic to HD ISPNs, while its knockdown protects the neurons. C_LI ]]> Jiang, M. Shi, T. Miryala, R. Rodriguez, M. Wang, R. Sultania, R. Guttman, L. Johnston, J. Li, Y. Cui, A. Belkas, K. Xue, Y. Um, Y. Yuan, A. Holland, C. Troncoso, J. C. Duan, W. Ratovitski, T. Smith, W. Ross, C. A. 2025-09-19 doi:10.1101/2025.09.18.677178 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Transcytosis-mediated anterograde transport of TrkA receptors controls formation of presynaptic sites in sympathetic neurons ]]> https://biorxiv.org/content/10.1101/2025.09.18.677078v1?rss=1 Moya-Alvarado, G. Markert, S. Raychaudhuri, S. Tachoute, M. Watanabe, S. Kuruvilla, R. 2025-09-21 doi:10.1101/2025.09.18.677078 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Kidney kallikrein-1 contributes to cleavage of gamma-ENaC in vivo ]]> https://biorxiv.org/content/10.1101/2025.09.19.677394v1?rss=1 Curry, J. N. Su, X.-T. Wu, Q. Maeoka, Y. Yang, C.-L. Delpire, E. Fenton, R. F. Welling, P. A. Ellison, D. H. 2025-09-21 doi:10.1101/2025.09.19.677394 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Predicting dynamic expression patterns in budding yeast with a fungal DNA language model ]]> https://biorxiv.org/content/10.1101/2025.09.19.677475v1?rss=1 Chao, K.-H. Magzoub, M. M. Stoops, E. Hackett, S. R. Linder, J. Kelley, D. R. 2025-09-21 doi:10.1101/2025.09.19.677475 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ A complete diploid human genome benchmark for personalized genomics ]]> https://biorxiv.org/content/10.1101/2025.09.21.677443v1?rss=1 Hansen, N. F. Dwarshuis, N. Ji, H. J. Rhie, A. Loucks, H. Logsdon, G. A. Vollger, M. R. Storer, J. M. Kim, J. Adam, E. Altemose, N. Antipov, D. Asri, M. Barreira, S. Bohaczuk, S. C. Bzikadze, A. V. Carioscia, S. A. Carroll, A. Chao, K.-H. Chu, Y. Das, A. Ebert, P. English, A. Fleharty, M. Fleming, L. E. Formenti, G. Guarracino, A. Hartley, G. A. Jenike, K. Kalleberg, J. Kang, Y. King, R. Lipovac, J. Mastoras, M. Mitchell, M. W. Negi, S. Olson, N. D. Oshima, K. K. Paulin, L. F. Pickett, B. D. Porubsky, D. Ranchalis, J. Ranjan, D. Rautiainen, M. Riethm 2025-09-21 doi:10.1101/2025.09.21.677443 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ 3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors ]]> https://biorxiv.org/content/10.1101/2025.09.21.677628v1?rss=1 Forjaz, A. Queiroga, V. Li, Y. Hernandez, A. Crawford, A. Qin, X. Zhong, M. Tsapatsis, M. Joshi, S. Kramer, D. Nizet, O. Bea, H. Li, Y. Qin, S. O Flynn, R. Yang, M. Pratt, B. Wu, F. Gensbigler, P. Blecher, M. Wu, P.-H. Kagohara, L. T. Shih, I. M. Zwicker, D. Atkinson, M. A. Shi, L. Fan, R. Kiemen, A. L. Wirtz, D. 2025-09-21 doi:10.1101/2025.09.21.677628 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Comparative Connectomics Highlights Conserved Architectural Synaptic Motifs in the Drosophila Mushroom Body ]]> https://biorxiv.org/content/10.1101/2025.09.22.677863v1?rss=1 Rivlin, P. K. Robinette, M. Matelsky, J. K. Wester, B. 2025-09-22 doi:10.1101/2025.09.22.677863 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ In Vitro Evidence to Support Amphotericin B and Flucytosine Combination Therapy for Talaromycosis ]]> https://biorxiv.org/content/10.1101/2025.09.23.677804v1?rss=1 Natesan Sambath, H. Vitsupakorn, S. Sreerama Reddy, K. Brown, L. Nguyen Thi Mai, T. Burke, M. Liu, J. Evans, E. Giamberardino, C. Perfect, J. Ngo Thi, H. Le, T. 2025-09-25 doi:10.1101/2025.09.23.677804 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Inferring the Metabolic Objectives of Mammalian Cells via Inverse Modeling of Fluxomics and Metabolomics ]]> https://biorxiv.org/content/10.1101/2025.09.23.677837v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@5c507aorg.highwire.dtl.DTLVardef@a7b544org.highwire.dtl.DTLVardef@6db0d4org.highwire.dtl.DTLVardef@17464e2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIObjFind-M, an inverse FBA framework, infers reaction-level metabolic objectives from fluxomic and metabolomic data. C_LIO_LIATP synthase (Complex V) emerges as the top reaction, supported by NADH-generating TCA reactions such as the -ketoglutarate dehydrogenase complex. C_LIO_LICHO cells suppress formation of toxic or wasteful byproducts while emphasizing energy-efficient flux routing. C_LIO_LIGrowth vs. non-growth phases reveal shifts between biosynthesis and oxidative phosphorylation. C_LIO_LIHigh recombinant protein producers emphasize citrate shuttling and beta-oxidation, linking energy with secretory capacity. C_LIO_LIATP demand maximization provides the most accurate generalizable FBA objective C_LI ]]> Morrissey, J. Monteiro, M. Betenbaugh, M. Kontoravdi, C. 2025-09-25 doi:10.1101/2025.09.23.677837 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Exploring endothelial cell environments across organs in spatially resolved omics data ]]> https://biorxiv.org/content/10.1101/2025.09.23.678129v1?rss=1 Jain, Y. Jepson, J. Chen, R. Maier, E. Herr, B. W. Puig-Barbe, A. Quardokus, E. M. Qaurooni, D. Yapp, C. Ewing, S. L. Enninful, A. Farzad, N. Bueckle, A. Easter, Q. T. Matuck, B. Zhu, C. Monte, E. M. Purkerson, J. M. Jehrio, M. Misra, R. S. Fan, R. Ginty, F. Karunamurthy, A. Fan, J. Campbell-Thompson, M. Pryhuber, G. S. Byrd, K. M. Hickey, J. W. Börner, K. 2025-09-25 doi:10.1101/2025.09.23.678129 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Development of a Human iPSC-Derived "Corticospinal Tract-on-a-Chip" for Neurodegenerative Disease Research ]]> https://biorxiv.org/content/10.1101/2025.09.24.678092v1?rss=1 CHARALAMPOPOULOU, A. Taga, A. RUST, K. LUCIANI, E. MARSHALL, K. MONTGOMERY, E. MANSINGHKA, A. SINGH, R. ZHAO, Y. O'KEEFE, C. Wang, J. VENKATESAN, A. Habela, C. W. Maragakis, N. J. 2025-09-25 doi:10.1101/2025.09.24.678092 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Regulation of Glypican 6-mediated Wnt activation maintains TDP-43 nuclear localization in neurons ]]> https://biorxiv.org/content/10.1101/2025.09.24.678385v1?rss=1 Zhang, N. Sockanathan, S. 2025-09-25 doi:10.1101/2025.09.24.678385 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes ]]> https://biorxiv.org/content/10.1101/2025.09.24.675449v1?rss=1 Varabyou, A. Artamonov, M. Cheng, S. Bolton, D. L. Salzberg, S. L. Pertea, M. 2025-09-26 doi:10.1101/2025.09.24.675449 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Evolution of the rate, spectrum, and fitness effects of mutation under minimal selection in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.09.24.678306v1?rss=1 Saber, S. Rifat, M. M. I. Rahimi, F. Snyder, M. Singh, A. Eickwort, B. Newhall, Y. Rajaei, M. Saxena, A. S. Tanny, R. Katju, V. Andersen, E. C. Zhou, J. Baer, C. F. 2025-09-26 doi:10.1101/2025.09.24.678306 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Fine-tuning sequence to function deep learning models on large-scale proteomic data improves the accuracy of variant effect prediction ]]> https://biorxiv.org/content/10.1101/2025.09.26.678908v1?rss=1 0.05) that are enriched for regulatory regions. We evaluated the generalizability of our model on a fine-tuned Borzoi model trained jointly on varying numbers of genes and observed that these models consistently outperform the pre-trained Borzoi model, the single-gene models yield more accurate results. Together this work demonstrates the importance of including larger sample sizes and rare variants in sequence to function models for variant effect prediction and demonstrates feasibility that these models are capable of highly accurate variant effect prediction. ]]> Vaz, E. Wang, L. Galvin, J. Keener, R. Battle, A. 2025-09-27 doi:10.1101/2025.09.26.678908 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Blocking apoptosis promotes survival and alters developmental dynamics of human retinal ganglion cells in retinal organoids ]]> https://biorxiv.org/content/10.1101/2025.09.27.678991v1?rss=1 Zhang, J. S. Guy, B. Santiago, C. P. Tiozzo, C. Sreenath, M. Chen, Y.-W. Blackshaw, S. Johnston, R. J. 2025-09-28 doi:10.1101/2025.09.27.678991 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Low Dose GLP-1 Therapy Attenuates Pathological Cardiac and Hepatic Remodelling in HFpEF Independent of Weight Loss ]]> https://biorxiv.org/content/10.1101/2025.09.26.678829v1?rss=1 Elbatreek, M. Li, Z. Yu, X. Gehred, N. D. Gromova, T. Chen, J. Muraoka, N. Jensen, M. Kartha, V. Carrico, C. Allerton, T. D. Bowdish, M. E. Chikwe, J. Shah, S. Woulfe, K. C. McKinsey, T. A. Yoo, E. Polhemus, D. J. Vondriska, T. M. Goodchild, T. T. Lefer, D. J. 2025-09-29 doi:10.1101/2025.09.26.678829 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Hyper-migratory CAR T cells alleviate ovarian cancer metastatic burden and improve prognosis ]]> https://biorxiv.org/content/10.1101/2025.09.28.679084v1?rss=1 Nair, P. R. Hanna, E. Joshi, S. Duarte Alvarado, V. Bonifant, C. Wirtz, D. 2025-09-30 doi:10.1101/2025.09.28.679084 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Overcoming rapaprotin resistance through inhibition of P-glycoprotein ]]> https://biorxiv.org/content/10.1101/2025.09.28.679086v1?rss=1 Liu, J. O. Zhang, Q. Asbell, T. Rao, A. V. S. Pasunooti, K. Zhang, J. Rees, M. G. Roth, J. A. 2025-09-30 doi:10.1101/2025.09.28.679086 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Characterization of the cardiac proteome of wild-type transthyretin amyloidosis cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2025.09.29.679210v1?rss=1 Rhodehamel, M. Jani, V. Gross, R. Dewan, K. Mulay, A. Koleini, N. Foster, M. Sharma, K. Aslam, M. I. Vaishnav, J. Bowles, D. E. Kass, D. A. Ranek, M. J. 2025-09-30 doi:10.1101/2025.09.29.679210 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ A multi-muscular, redundant strategy for free-flight roll stability ]]> https://biorxiv.org/content/10.1101/2025.09.29.679272v1?rss=1 Ludlow, B. K. Dhawan, S. Whitehead, S. C. Teoh, H. K. Ehrhardt, E. Cowan, N. Dickerson, B. H. Cohen, I. 2025-10-01 doi:10.1101/2025.09.29.679272 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Reward-reset interval timing drives patch foraging decisions through neural state transitions in dorsomedial striatum ]]> https://biorxiv.org/content/10.1101/2025.09.29.679309v1?rss=1 Sutlief, E. Zhang, S. Forsberg, K. Kaneko, R. Shuler, M. G. H. 2025-10-01 doi:10.1101/2025.09.29.679309 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Cancer cells surviving cisplatin chemotherapy increase stress-induced OMA1 activity and mitochondrial fragmentation ]]> https://biorxiv.org/content/10.1101/2025.09.29.679325v1?rss=1 Li, M. McCullum, C. A. Rolle, L. T. Ni, Q. Ge, Z. Sun, S. Pienta, K. J. Amend, S. R. 2025-10-01 doi:10.1101/2025.09.29.679325 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.09.30.679260v1?rss=1 Li, Y. Dou, X. Xiao, Y. Zhang, Z. Ye, Y. Wright, N. Chang, K. Liu, C. Troncoso, J. C. He, C. Sun, S. 2025-10-02 doi:10.1101/2025.09.30.679260 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Machine-Learning-Guided Video Analysis Identifies Sound-Evoked Pain Behaviors from Facial Grimace and Body Cues in Mice ]]> https://biorxiv.org/content/10.1101/2025.09.30.679579v1?rss=1 Seicol, B. J. Valles, A. Kohler, A. Glowatzki, E. Wood, M. B. 2025-10-02 doi:10.1101/2025.09.30.679579 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response ]]> https://biorxiv.org/content/10.1101/2025.09.30.679608v1?rss=1 Ruta, A. Krishnan, K. Woo, J. Mejias, J. C. Gray-Gaillard, E. F. Maestas, D. R. Nguyen, H. H. Rindone, A. N. Cherry, C. Patatanian, M. Yu, F. H. Yang, B. Amelung, C. King, C. D. Schilling, B. Gerecht, S. Fertig, E. J. Huyer, L. D. Pardoll, D. M. Elisseeff, J. H. 2025-10-02 doi:10.1101/2025.09.30.679608 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet ]]> https://biorxiv.org/content/10.1101/2025.10.01.679366v1?rss=1 Kim, J. Rosen, B. D. Fumagalli, S. E. Kuhn, K. L. Long, A. Schoenebeck, J. J. Wu-Cavener, L. Zimin, A. V. Cavener, D. Smith, T. P. L. Phillippy, A. M. Koren, S. Rhie, A. 2025-10-02 doi:10.1101/2025.10.01.679366 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow ]]> https://biorxiv.org/content/10.1101/2025.10.02.679940v1?rss=1 Yang, Y. Fan, Y. Jain, S. Ding, Z. Liu, H. Horenberg, A. Sun, H. Killer, M. S. Chandra, A. Chandran, M. Yap, L. Dalan, R. Chen, J. Verma, N. K. Cheung, C. Risbud, M. Bozec, A. Ramadan, K. Cohen-Solal, M. Grayson, W. Ramasamy, S. K. Kusumbe, A. P. 2025-10-03 doi:10.1101/2025.10.02.679940 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Circulating Lipids are Associated with PTSD Severity and Predict Symptomatic PTSD in a Cohort of Veterans and Service Members ]]> https://biorxiv.org/content/10.1101/2025.10.02.680007v1?rss=1 Silvey, S. Cowart, L. A. Liu, J. Yue, Y. Allegood, J. Gill, J. Devoto, C. Horvath, P. Valadka, A. 2025-10-03 doi:10.1101/2025.10.02.680007 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Brain Iron as a Surrogate Biomarker of Pathological TDP-43 Identifies Brain Region-Specific Signatures in Ageing, Alzheimer's Disease and Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/2025.10.02.680028v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@9c54b3org.highwire.dtl.DTLVardef@17cb415org.highwire.dtl.DTLVardef@12dabeorg.highwire.dtl.DTLVardef@1d72f95_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITDP-43 brain pathology occurs in normal ageing from early in the fourth decade, characterised by a 4.5-fold increase in hippocampus pathology from the sixth decade. C_LIO_LITDP-43 brain pathology is detectable in 90% of AD cases, with a disease-signature of increased amygdala pathology relative to age-matched controls. C_LIO_LIIn ALS, TDP-43 is nearly ubiquitous in amygdala, hippocampus and frontal cortex. C_LIO_LIHippocampus high brain ferritin distinguishes AD from and age-matched controls C_LIO_LIBrain ferritin is a brain region-specific marker of TDP-43 pathology in ageing and disease, with amygdala ferritin explaining 87% of the variance in amygdala TDP-43 pathology in ALS, and 66% of amygdala TDP-43 pathology in AD C_LIO_LIIn AD, ferritin levels for all three brain regions explain between 43-81% of variance in their TDP-43 pathology levels C_LI ]]> Waldron, F. M. Spence, H. Taso, O. S. Read, F. L. Sinha, I. R. Irwin, K. E. Wong, P. C. Ling, J. P. Gregory, J. M. 2025-10-03 doi:10.1101/2025.10.02.680028 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Desmoglein-2 deficiency results in cardiac dysfunction by compromising both Z-disc- and intercalated disc-mediated mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.10.03.680335v1?rss=1 Landim-Vieira, M. Jani, V. P. Shiel, E. Rastegarpouyani, H. Engel, M. Paradine, F. Chastain, R. Farra, W. Ma, W. Toepfer, C. Chase, P. B. Kass, D. A. Pinto, J. R. Chelko, S. P. 2025-10-04 doi:10.1101/2025.10.03.680335 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Matrix stiffness induces endothelial network senescence ]]> https://biorxiv.org/content/10.1101/2025.10.05.680536v1?rss=1 Song, J. Rindone, A. N. Guan, Y. Daswani, P. S. Elisseeff, J. Gerecht, S. 2025-10-06 doi:10.1101/2025.10.05.680536 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Optimization of velocity receptor transduction in CAR T cells ]]> https://biorxiv.org/content/10.1101/2025.10.05.680548v1?rss=1 Jiang, X. Queiroga, V. Hanna, E. A. Wirtz, D. 2025-10-06 doi:10.1101/2025.10.05.680548 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Clonal dynamics of monozygotic twinning in early human embryogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.05.680569v1?rss=1 Yoon, C. J. Nam, C. H. N. Lee, S. M. Choi, E. S. Bae, J. H. Kim, H. Lim, J. Kim, R. Derom, C. Meireson, E. Weyers, S. Park, J. W. Lee, J. Sung, J. Griffith, O. L. Griffith, M. Jun, J. K. Ju, Y. S. 2025-10-06 doi:10.1101/2025.10.05.680569 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ A TCR-mimic bispecific antibody reduces HIV-1 provirus and delays viral rebound in HLA-matched humanized mice ]]> https://biorxiv.org/content/10.1101/2025.10.06.680344v1?rss=1 Yuan, Z. Board, N. L. Zhao, M. Zu, G. Sengupta, S. Li, Q. Siliciano, J. D. Siliciano, R. F. Montaner, L. J. 2025-10-06 doi:10.1101/2025.10.06.680344 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Design and Synthesis of Peptide-Polyester Conjugates for Cell-Mediated Scaffold Degradation ]]> https://biorxiv.org/content/10.1101/2025.10.06.680674v1?rss=1 Sinad, K. V. G. Hunt, N. K. Singh, S. Seims, K. B. Wu, Y. Pashuck, E. T. Grayson, W. L. Chow, L. W. 2025-10-06 doi:10.1101/2025.10.06.680674 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag ]]> https://biorxiv.org/content/10.1101/2025.10.06.680180v1?rss=1 Liao, Y. Zhou, W. Jiang, M.-Z. Yu, K. Wang, Z. J. Drummond, T. Ding, M. Zhao, Y. Pino, I. Taverna, S. D. Ji, H. Zhu, H. 2025-10-07 doi:10.1101/2025.10.06.680180 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Engineering substrate selectivity in the human sodium/iodide symporter (NIS) ]]> https://biorxiv.org/content/10.1101/2025.10.07.681042v1?rss=1 Llorente-Esteban, A. Sabbineni, H. Hoffsmith, K. Manville, R. W. Lopez-Gonzalez, D. Reyna-Neyra, A. Leyva, A. Abbott, G. W. Bianchet, M. A. Carrasco, N. 2025-10-08 doi:10.1101/2025.10.07.681042 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Effects of oral cannabidiol (CBD) on spontaneous opioid withdrawal in male and female rats ]]> https://biorxiv.org/content/10.1101/2025.10.08.680984v1?rss=1 Jenkins, B. W. Pang, C. Kuang, R. Y. Weerts, E. M. Moore, C. F. 2025-10-09 doi:10.1101/2025.10.08.680984 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Arm dominance emerges through asymmetric practice of complex trajectory shapes inherent to tool-use ]]> https://biorxiv.org/content/10.1101/2025.10.08.680998v1?rss=1 Arac, A. Jeong Lee, N. Y. Krakauer, J. W. 2025-10-09 doi:10.1101/2025.10.08.680998 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Synchronized path-integration recalibration but distinct landmark-control dynamics in head direction and CA1 place cells ]]> https://biorxiv.org/content/10.1101/2025.10.08.681135v1?rss=1 Jayakumar, R. P. Sueoka, Y. Ferreyros, M. K. Li, B. Y. Madhav, M. S. Chen, X. Knierim, J. J. Cowan, N. J. 2025-10-10 doi:10.1101/2025.10.08.681135 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Complement Factor H and its C. elegans homolog regulate IFT52/OSM-6 and CNG channel localization in sensory neurons ]]> https://biorxiv.org/content/10.1101/2025.10.10.681644v1?rss=1 Oshima, Y. Hussey, K. Hagen, J. Smit-McBride, Z. Moorthy, M. Matsubara, J. A. Flajnik, M. Johnston, R. J. Vogel, B. E. 2025-10-13 doi:10.1101/2025.10.10.681644 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Uncertainty-Gated Min-Cost Flows for In Vivo NanoScale Synaptic Plasticity Tracking ]]> https://biorxiv.org/content/10.1101/2025.10.10.681691v1?rss=1 100,000 dynamic, submicrometer particles is difficult even for state-of-the-art algorithms. Moreover, most algorithms rely on an isotropic uncertainty ball, assigning equal weight to the lateral plane (XY) and to the noisier axial dimension (Z), leading to poorer performance. To address these challenges and accurately track synapses in vivo, we developed SynTrack. We formulated SynTrack as a Maximum A Posteriori estimation problem under the anisotropic uncertainty ball, along with a fully temporally connected spatio-temporal graph to overcome long-term occlusions. SynTrack achieves a mean track length of 0.51 {micro}m with a Multiple Object Tracking Accuracy (MOTA) score of 88.8%, on par with MOTA scores of expert annotators but with massively increased speed and scalability. Over two weeks, we successfully track 65,000 synapses in 5.6 out of 8 imaging sessions on average, with 20,000 synapses being tracked in at least seven sessions. We present SynTrack as a state-of-the-art algorithm capable of high-resolution and fidelity tracking of synapse dynamics in behaving mice with unprecedented detail. ]]> Kumar, S. Coste, G. I. Premathilaka, D. Huganir, R. L. Graves, A. R. Charles, A. S. Miller, M. I. 2025-10-13 doi:10.1101/2025.10.10.681691 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/2025.10.11.681280v1?rss=1 Huang, K.-T. Yang, Y.-H. Lin, M.-J. Lai, S.-K. Chou, T.-H. Lee, C.-Y. Hung, T.-K. Hsu, C.-L. Yang, Y.-C. Chen, C.-Y. Chen, P.-L. Hsu, J. S. 2025-10-13 doi:10.1101/2025.10.11.681280 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Direct cell reprogramming by a designed agonist inducing HER2-FGFR proximity ]]> https://biorxiv.org/content/10.1101/2025.10.12.681903v1?rss=1 Keshri, R. Exposit, M. Abedi, M. R Hicks, D. Foreman, Z. Phal, A. Lim, Y. C. Barrett, P. Sniezek, C. Lin, J. Schlichthaerle, T. J Robinson, A. Detraux, D. Ching, T. C. Wu, K. Coventry, B. Chang, L. S.T. Smith, A. L Mack, D. K Schweppe, D. Martin, B. E. Hristova, K. Mathieu, J. Baker, D. Ruohola-Baker, H. 2025-10-13 doi:10.1101/2025.10.12.681903 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus ]]> https://biorxiv.org/content/10.1101/2025.10.13.682095v1?rss=1 Nekrutenko, A. Callan, D. Van Den Beek, M. Baker, D. Rogers, D. Maier, W. Guerler, A. Clawson, H. Cain, S. Beavers, K. Haeussler, M. Gruning, B. Kosakowsky Pond, S. 2025-10-14 doi:10.1101/2025.10.13.682095 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Mechanisms of sex differences in acute and long COVID sequelae in mice ]]> https://biorxiv.org/content/10.1101/2025.10.13.682101v1?rss=1 Liu, J. A. Chaulagain, S. Creisher, P. S. Zhong, W. Zhang, T. Taddese, M. Shi, K. Park, H.-S. Hcnir, H. Arnold, A. P. Baric, R. S. Barahona, N. B. Engler-Chiurazzi, E. B. Zwezdaryk, K. J. Thio, C. L. Balagopal, A. Harkema, J. R. Thompson, E. A. Pekosz, A. Cox, A. L. Klein, S. L. 2025-10-14 doi:10.1101/2025.10.13.682101 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Characterization of chemotaxis in soybean symbiont Bradyrhizobium diazoefficiens ]]> https://biorxiv.org/content/10.1101/2025.10.14.682368v1?rss=1 Lubin, M. Teixeira, D. Belin, B. J. 2025-10-14 doi:10.1101/2025.10.14.682368 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Repeat associated non-AUG translation as a common mechanism for the polyGln ataxias ]]> https://biorxiv.org/content/10.1101/2025.10.14.682372v1?rss=1 Banez-Coronel, M. Zu, T. Aldridge, M. Guo, S. Ajredini, R. Morrison, D. Tays, A. B. Pletnikova, O. Yachnis, A. T. Troncoso, J. Paulson, H. L. McLoughlin, H. S. Ashizawa, T. Subramony, S. H. Ranum, L. 2025-10-15 doi:10.1101/2025.10.14.682372 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Parallel circadian-like oscillations in LTP and excitation inhibition balance in mouse CA1 reverse direction after puberty ]]> https://biorxiv.org/content/10.1101/2025.10.15.682451v1?rss=1 valdivia, g. moreno, c. He, K. contreras, d. tran, T. Ramnaugh, A. D. Xu, W. Contreras, A. Fernandez, D. C. Severin, D. Hattar, S. Gallagher, M. kirkwood, a. 2025-10-15 doi:10.1101/2025.10.15.682451 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Movi 2: Fast and Space-Efficient Queries on Pangenomes ]]> https://biorxiv.org/content/10.1101/2025.10.16.682873v1?rss=1 Zakeri, M. Brown, N. K. Gagie, T. Langmead, B. 2025-10-17 doi:10.1101/2025.10.16.682873 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Improved inference of latent neural states from calcium imaging data ]]> https://biorxiv.org/content/10.1101/2025.10.17.682993v1?rss=1 Keeley, S. Zoltowski, D. M. Charles, A. Pillow, J. W. 2025-10-17 doi:10.1101/2025.10.17.682993 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Noncanonical amino acid incorporation enables minimally disruptive labeling of stress granule and TDP-43 proteinopathy ]]> https://biorxiv.org/content/10.1101/2025.10.17.683020v1?rss=1 Chen, H. Wang, H. Lu, Y.-N. Chen, P. Zheng, Z. Zhang, T. Wang, J. 2025-10-17 doi:10.1101/2025.10.17.683020 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Cognitive Resilience in Aging Degus is Linked to CA3 Hippocampal GABAergic Integrity ]]> https://biorxiv.org/content/10.1101/2025.10.18.682786v1?rss=1 Ibaceta-Gonzalez, C. Neira, D. Ardiles, N. M. Baeza-Araya, N. kirkwood, a. Moya, P. Palacios, A. G. 2025-10-19 doi:10.1101/2025.10.18.682786 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells ]]> https://biorxiv.org/content/10.1101/2025.10.19.682634v1?rss=1 Liu, J. Xia, Y. Mog, B. Gliech, C. Shaw, E. Ferris, D. Moritz, B. Awosika, T. DiNapoli, S. Glavaris, S. Kaeo, K. J. Li, Y. Marcou, N. Pearlman, A. H. Ahmedna, T. Bugrovsky, R. Sanz, I. Bettegowda, C. Paul, S. Duarte-Alvarado, V. Wirtz, D. Goldman, D. W. Petri, M. A. Kinzler, K. W. Zhou, S. Andrade, F. Vogelstein, B. Konig, M. F. 2025-10-19 doi:10.1101/2025.10.19.682634 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Transcriptomic and protein analysis of human cortex reveals genes and pathways linked to NPTX2 disruption in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.10.17.683150v1?rss=1 Lao, Y. Xiao, M.-F. Ji, S. Piras, I. S. Bonfitto, A. Song, S. Aldabergenova, A. Na, C.-H. Sloan, J. Trejo, A. Geula, C. Rogalski, E. J. Kawas, C. H. Corrada, M. M. Serrano, G. E. Beach, T. G. Troncoso, J. C. Huentelman, M. J. Barnes, C. A. Worley, P. F. Colantuoni, C. 2025-10-20 doi:10.1101/2025.10.17.683150 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Computational modeling of hormone- and cytokine-dependent proliferation of endometrial cells in 3D co-culture ]]> https://biorxiv.org/content/10.1101/2025.10.18.682837v1?rss=1 Mbuguiro, W. Holt, S. E. Griffith, L. G. Gnecco, J. S. Mac Gabhann, F. 2025-10-20 doi:10.1101/2025.10.18.682837 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Transcriptomic profiling of the middle temporal gyrus reveals differential glial/neuronal dysregulation across Alzheimer disease and aging. ]]> https://biorxiv.org/content/10.1101/2025.10.19.683343v1?rss=1 Piras, I. S. Bonfitto, A. Song, S. Aldabergenova, A. Sloan, J. Trejo, A. Troncoso, J. Geula, C. Rogalski, E. J. Kawas, C. H. Corrada, M. Beach, T. G. Serrano, G. E. Worley, P. F. Barnes, C. A. Huentelman, M. J. 2025-10-20 doi:10.1101/2025.10.19.683343 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Exploring Size Exclusion Chromatography Columns 20 and 35 nm Pore Size Effect for Isolation of Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2025.10.20.682612v1?rss=1 Kaszala, B. Scarsella, V. Bomb, K. Fay, J. Smith, B. Gokulnath, P. Desai, R. Kulkarni, R. N. Das, S. Garcia-Contreras, M. 2025-10-20 doi:10.1101/2025.10.20.682612 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Ventral striatal astrocytes contribute to reinforcement learning ]]> https://biorxiv.org/content/10.1101/2025.10.20.683205v1?rss=1 Pai, J. Sogukpinar, F. Ogasawara, K. Smith, G. J. Fiocchi, F. R. Dai, Y. Wu, Y. Frank, M. J. Ching, S. Lucantonio, F. Papouin, T. Pignatelli, M. Hiratani, N. Monosov, I. E. 2025-10-20 doi:10.1101/2025.10.20.683205 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Tumor-associated macrophages protect glioblastoma cells from ferroptosis by inducing the release of ferritin-bound iron via exosomes. ]]> https://biorxiv.org/content/10.1101/2025.10.21.683804v1?rss=1 Sahu, A. P. Palsa, K. Shenoy, G. Slagle-Webb, B. Connor, J. R. 2025-10-22 doi:10.1101/2025.10.21.683804 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Efficacies of sequenced monotherapies of Mycobacterium avium lung infection in mouse ]]> https://biorxiv.org/content/10.1101/2025.10.22.684001v1?rss=1 Howe, R. A. Rimal, B. Khandelwal, J. Panthi, C. M. Lamichhane, G. 2025-10-22 doi:10.1101/2025.10.22.684001 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ FOXI3 Promotes Migration and Proliferation in Prostate Cancer Bone Metastases, Modulated by FGF8. ]]> https://biorxiv.org/content/10.1101/2025.10.22.683826v1?rss=1 Mukherjee, A. Jones, J. Hollern, D. p. Byrd, W. A. Rayburn, T. S. Williams, O. G. Knight, C. S. Yates, C. C. 2025-10-23 doi:10.1101/2025.10.22.683826 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence with Existing Human Data ]]> https://biorxiv.org/content/10.1101/2025.10.23.683091v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1062c5eorg.highwire.dtl.DTLVardef@4ae148org.highwire.dtl.DTLVardef@c747corg.highwire.dtl.DTLVardef@1b3a713_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIChronic stress is linked to many human psychiatric disorders involving the prefrontal cortex (PFC). C_LIO_LIMeta-analysis showed that stressed mice had less gene expression for glia and neural activity in the PFC. C_LIO_LIPFC gene expression in chronically stressed mice mirrors patterns seen in psychiatric patients. C_LI Plain Language SummaryChronic stress has been shown to have lasting effects on the brain, contributing to cognitive impairments and the risk of psychiatric disorders such as anxiety, depression, and post-traumatic stress disorder. The prefrontal cortex, a brain region that is important for behavioral and attentional control, is sensitive to chronic stress. We combined information from six public mouse datasets to identify consistent effects of chronic stress on gene expression (mRNA) in the prefrontal cortex. In these studies, mice that had experienced chronic stress showed a decreased amount of mRNA related to a variety of non-neuronal support cells (glia) and blood vessels, and general neural activity. The mouse chronic stress signature overlapped with gene-activity patterns reported in human psychiatric conditions, suggesting a biological bridge between chronic stress and the onset of psychopathology. ]]> Xiong, J. Hagenauer, M. H. Rhoads, C. A. Flandreau, E. I. Rempel-Clower, N. L. Hernandez, E. Nguyen, D. M. Saffron, A. Duan, T. Q. Watson, S. Akil, H. 2025-10-24 doi:10.1101/2025.10.23.683091 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Aromatic residues in mobile regions distal to the active site support the closed conformation of E. coli DXPS ]]> https://biorxiv.org/content/10.1101/2025.10.24.684457v1?rss=1 Kramer, L. J. Austin, S. L. Majumdar, A. Smith, N. D. Woodcock, H. L. Freel Meyers, C. L. 2025-10-25 doi:10.1101/2025.10.24.684457 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Stress drives the hippocampus to prioritize statistical prediction over episodic encoding ]]> https://biorxiv.org/content/10.1101/2025.10.25.683838v1?rss=1 Zhou, I. Bai, Z. Huang, Y. Wijaya, E. G. Sherman, B. E. Turk-Browne, N. B. Goldfarb, E. V. 2025-10-26 doi:10.1101/2025.10.25.683838 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Machine Vision Enabled Lateral Flow Immunoassay Using Functionalized Gold Nanoparticles for Point-of-Care Cardiac Biomarker Detection ]]> https://biorxiv.org/content/10.1101/2025.10.22.683875v1?rss=1 0.99). Overall, these results demonstrate that machine vision-enhanced AuNPs-LFIA offers an efficient, sensitive and reliable strategy for point-of- care testing (POCT) in cardiovascular diagnostics, particularly in resource-limited settings. ]]> Lu, Y. Peng, X. Yin, Z. Fan, X. Fan, J. Mi, Y. Li, G. 2025-10-27 doi:10.1101/2025.10.22.683875 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Enhancing enzymatic bioconjugation efficiency via installation of a substrate recruitment domain ]]> https://biorxiv.org/content/10.1101/2025.10.27.684804v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1a3b274org.highwire.dtl.DTLVardef@18eeedorg.highwire.dtl.DTLVardef@ee0aaeorg.highwire.dtl.DTLVardef@1ff3fa1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shelby, C. Kuzelka, K. P. Ellis, J. M. Yao, Z. McCue, A. C. Park, R. Nair, S. K. Bowers, A. Kuhlman, B. 2025-10-27 doi:10.1101/2025.10.27.684804 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Identification and functional characterization of an AMD associated c-ABL binding SNP streak within the ARMS2 gene promoter region ]]> https://biorxiv.org/content/10.1101/2025.10.27.684937v1?rss=1 Zhang, P.-W. Liu, S. Li, W. Fan, L. Li, S. Wan, Z.-H. Berlinicke, C. A. Merbs, S. L. Zack, D. J. 2025-10-27 doi:10.1101/2025.10.27.684937 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ VIDEO - Visual Integration of Drosophila Enhancer Organization: A tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes ]]> https://biorxiv.org/content/10.1101/2025.10.27.684897v1?rss=1 Andrew, D. J. Ajay, V. Laughner, N. Cahan, P. 2025-10-28 doi:10.1101/2025.10.27.684897 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Ventral tegmental area dopamine controls timing variability ]]> https://biorxiv.org/content/10.1101/2025.10.27.684913v1?rss=1 Weber, M. A. Sivakumar, K. Bova, A. Tabakovic, E. Conlon, M. Oya, M. Singh, A. Cole, R. Espinoza, A. Kim, Y. Narayanan, N. 2025-10-28 doi:10.1101/2025.10.27.684913 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Tracking Sleep-Linked Brain Fluid Dynamics Using Modified fNIRS: A Novel Noninvasive Window into Glymphatic Function ]]> https://biorxiv.org/content/10.1101/2025.10.27.684357v1?rss=1 Gupta, S. Amyot, F. Coon, W. G. Pollatou, A. Skeiky, L. Seenivasan, S. Kenny, K. Lee, A. Lettieri, M. Penafiel, A. Yalewayker, S. Cheraghpour, E. Sheth, P. Metzger, E. Scholl, C. Werner, J. K. 2025-10-29 doi:10.1101/2025.10.27.684357 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ CRISPR-mediated transcriptional activation as a mutation-independent therapeutic strategy for SYNGAP1-related intellectual disability ]]> https://biorxiv.org/content/10.1101/2025.10.28.685100v1?rss=1 Sichlinger, L. Reilly, M. Arora, S. Zhang, S. Marotta, N. Rodriguez-Acevedo, K. L. Hooks, M. Czarnecki, K. S. Winter, J. J. Waxman, E. A. Dungan, L. V. Hong, I. Araki, Y. Johnson, R. Huganir, R. L. Pavani, G. French, D. L. Davidson, B. L. Prosser, B. L. Heller, E. A. 2025-10-29 doi:10.1101/2025.10.28.685100 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Using endocytosis to switch between chemoattraction and chemorepulsion ]]> https://biorxiv.org/content/10.1101/2025.10.28.685129v1?rss=1 Luettgen, G. K. Camley, B. A. 2025-10-30 doi:10.1101/2025.10.28.685129 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Comparing Kinetic versus Stoichiometric Priorities in Hybrid Models of CHO Metabolism ]]> https://biorxiv.org/content/10.1101/2025.10.28.685134v1?rss=1 Khare, P. A. Ndahiro, N. Klaubert, S. Ma, E. Bertalan, T. Kevrekidis, Y. Harcum, S. W. Betenbaugh, M. 2025-10-30 doi:10.1101/2025.10.28.685134 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Spatial analysis reveals the cellular microenvironments and mechanisms of inflammation and kidney injury in acute interstitial nephritis ]]> https://biorxiv.org/content/10.1101/2025.10.29.684811v1?rss=1 Baker, M. L. Kakade, V. R. Budiman, T. Weiss, M. Cunningham, J. M. Sadarangani, S. Lerner, G. Moeckel, G. Rosenberg, A. Z. Parikh, C. R. Kluger, Y. Moledina, D. G. Cantley, L. G. 2025-10-30 doi:10.1101/2025.10.29.684811 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Structure-based Predictions of Conformational B Cell Epitopes by Protein Language Model and Deep Learning ]]> https://biorxiv.org/content/10.1101/2025.10.29.685313v1?rss=1 Zhang, Y. Vilicich, F. Kuang, X. Liu, Y. Zhang, G. Su, Z. Wu, Y. 2025-10-30 doi:10.1101/2025.10.29.685313 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus ]]> https://biorxiv.org/content/10.1101/2025.10.29.685354v1?rss=1 Mulvey, B. Divecha, H. R. Tippani, M. Bach, S. V. Bharadwaj, R. Del Rosario, I. Maguire, S. E. Miller, R. A. Salisbury, A. J. Chandra, A. Oster, B. A. Montgomery, K. D. Kwon, S. H. Algrain, H. A. Papariello, A. R. Huuki-Myers, L. A. Kleinman, J. E. Collado-Torres, L. Hyde, T. M. Han, S. Hicks, S. C. Weinberger, D. R. Page, S. C. Maynard, K. R. Martinowich, K. 2025-10-31 doi:10.1101/2025.10.29.685354 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ State-dependent release of extracellular particles with distinct α2,6-sialylation patterns and small RNA cargo related to neuroinflammation ]]> https://biorxiv.org/content/10.1101/2025.10.30.684535v1?rss=1 Garcia-Contreras, M. Lima, C. Alsop, E. Kaszala, B. Meechoovet, B. Purnell, B. Jiang, N. Saftics, A. Tang, C. Walsh, O. D. Holland, S. Fay, J. Smith, B. Sigdel, K. P. Van Keuren-Jensen, K. Jovanovic-Talisman, T. Das, S. 2025-10-31 doi:10.1101/2025.10.30.684535 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ RNA G-Quadruplexes Function as a Tunable Switch of FUS Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.10.31.685846v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1db3ea8org.highwire.dtl.DTLVardef@eec825org.highwire.dtl.DTLVardef@96187eorg.highwire.dtl.DTLVardef@2204ce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carey, J. L. Hayashi, M. Welebob, E. Ganser, L. R. Wang, H. Buckhaults, K. DePierro, J. A. Shi, Z. Shorter, J. Myong, S. Haeusler, A. Guo, L. 2025-11-01 doi:10.1101/2025.10.31.685846 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Quantitative Calibration of a Spatial QSP Model Identifies Fibroblast Impact on HCC Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.10.31.685939v1?rss=1 Zhang, S. Wang, H. Cho, Y. Wong, W. Yarchoan, M. Jaffee, E. M. Ho, W. J. Kagohara, L. T. Fertig, E. J. Popel, A. S. Deshpande, A. 2025-11-04 doi:10.1101/2025.10.31.685939 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight ]]> https://biorxiv.org/content/10.1101/2025.11.02.686144v1?rss=1 Teoh, H. K. Biswas, D. Leung, A. Ludlow, B. K. Whitehead, S. C. Ehrhard, E. Dickinson, M. H. Beatus, T. Cowan, N. Cohen, I. 2025-11-04 doi:10.1101/2025.11.02.686144 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas ]]> https://biorxiv.org/content/10.1101/2025.11.03.686234v1?rss=1 Noller, K. Lai, J. Lesperance, D. Adkins, R. S. Elhossiny, A. Guerrero, P. A. Rajapakshe, K. I. Maitra, A. Giglio, M. Mahurkar, A. White, O. Pasca di Magliano, M. Ochs, M. F. Kagohara, L. T. Wood, L. D. Karchin, R. Fertig, E. J. 2025-11-04 doi:10.1101/2025.11.03.686234 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Mitotic bypass and endocycling promote cancer cell survival after genotoxic chemotherapy ]]> https://biorxiv.org/content/10.1101/2025.11.03.686258v1?rss=1 Truskowski, K. Rolle, L. Butler, G. Yang, M. E. Pienta, K. J. Amend, S. R. 2025-11-04 doi:10.1101/2025.11.03.686258 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology ]]> https://biorxiv.org/content/10.1101/2025.11.04.686570v1?rss=1 Zhan, L. Yu, D. Ivankovic, F. Niarchou, M. Domenech-Salgado, L. Barr, C. L. Benarroch, F. Budman, C. L. Cath, D. C. Freimer, N. B. Garrido, H. Grados, M. A. Gross-Tsur, V. Herrera-Amighetti, L. King, R. A. Kurlan, R. Leckman, J. F. Lyon, G. J. McMahon, W. M. Pauls, D. L. Pollak, Y. Robertson, M. M. Romero, R. Rouleau, G. A. Sandor, P. Singer, H. S. Giusti-Rodriguez, P. Davis, L. K. Mathews, C. A. Scharf, J. M. Ophoff, R. A. 2025-11-05 doi:10.1101/2025.11.04.686570 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Staying in the loop to make ends meet: roles and regulation of GlmR in Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2025.11.05.686802v1?rss=1 Suits, L. Khan, S. Bhattacharya, D. Dimitrova, S. Eswara, P. J. 2025-11-05 doi:10.1101/2025.11.05.686802 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ The scaffold protein PRR14L links the PP2A-TACC3 axis to mitotic fidelity and sensitivity to MPS1 inhibition ]]> https://biorxiv.org/content/10.1101/2025.11.04.686150v1?rss=1 Liu, A. Z. Narkar, A. Li, K. Bertomeu, T. Johnson, B. A. Coulombe-Huntington, J. Dong, Y. Zhu, J. Tyers, M. Li, R. 2025-11-06 doi:10.1101/2025.11.04.686150 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Base editing and nanoparticle transfection of airway cell types essential for treatment of cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2025.11.06.687048v1?rss=1 Kavanagh, E. W. Joynt, A. T. Pion, A. R. Eastman, A. C. Parr, A. I. Starego, K. L. Jain, M. Shannon, S. R. Yoo, E. Newby, G. A. Tzeng, S. Y. Sharma, N. Green, J. J. Cutting, G. R. 2025-11-06 doi:10.1101/2025.11.06.687048 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Extra-ciliary role for polycystins in regulation of Ezrin and renal tubular morphology ]]> https://biorxiv.org/content/10.1101/2025.11.05.684799v1?rss=1 Dixon, E. E. Zapf, A. M. Halperin Kuhns, V. L. Basquin, D. Park, R. M. Coleman, R. Franklin, L. Lane-Harris, A. C. Hofherr, A. Kottgen, M. Qian, F. Welling, P. A. Watnick, T. J. Woodward, O. M. 2025-11-07 doi:10.1101/2025.11.05.684799 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework ]]> https://biorxiv.org/content/10.1101/2025.11.06.686996v1?rss=1 Damjanovic, A. Carnevale, V. Hater, T. Sultan, N. Rossetti, G. Diaz, S. Carloni, P. 2025-11-07 doi:10.1101/2025.11.06.686996 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Na+/H+ Exchanger Isoform 1 Regulates Apoptosis Susceptibility in Pulmonary Arterial Smooth Muscle from the Sugen/Hypoxia model of Pulmonary Hypertension ]]> https://biorxiv.org/content/10.1101/2025.11.06.687041v1?rss=1 Andrade, M. R. Yun, X. Croglio, M. Niedermeyer, S. Jiang, H. Philip, N. Murray, S. Munson, M. Suresh, K. Damarla, M. Huetsch, J. Shimoda, L. 2025-11-08 doi:10.1101/2025.11.06.687041 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Functional Effects of CD33 SNP rs12459419 on Microglial Gene Regulation and Alzheimer's Disease Risk ]]> https://biorxiv.org/content/10.1101/2025.11.07.684725v1?rss=1 Lu, Y. 2025-11-08 doi:10.1101/2025.11.07.684725 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Region-specific proteomic analysis of aging rhesus macaques following chronic glutamate-carboxypeptidase-II (GCPII) inhibition elucidates potential treatment strategies for sporadic Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.11.07.687004v1?rss=1 2,400 proteins across experimental conditions, and label-free quantification revealed region-specific differential expression patterns paralleling known vulnerability gradients in sAD. Gene ontology enrichment of vulnerable regions implicated pathways governing protein deneddylation, amyloid and tau-associated processes, synaptic plasticity, mitochondrial homeostasis, and oxidative stress, revealing putative targets for therapeutic intervention in sAD. These findings demonstrate that GCPII inhibition engages distinct, region-selective molecular programs in the aging primate cortex, consistent with the protection of circuits most vulnerable to sAD. By mapping the proteomic shifts that occur with treatment, we reveal molecular signatures that not only serve as candidate biomarkers but also highlight novel mechanistic pathways contributing to calcium-driven degeneration in sAD. As such, more focused investigations into these pathways of therapeutic interest are warranted, in addition to the analysis of key post-translational modifications and their potential roles in sAD. ]]> Steigmeyer, A. D. Battison, A. S. Liebman, I. R. van Dyck, C. H. Slusher, B. S. Arnsten, A. F. Malaker, S. A. Datta, D. 2025-11-10 doi:10.1101/2025.11.07.687004 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures ]]> https://biorxiv.org/content/10.1101/2025.11.09.687475v1?rss=1 Makarov, M. Krystufek, R. Fricek, M. Manriquez-Sandoval, E. Dutta, S. Kormanik, J. M. Kalvoda, T. Verner, V. Bednarova, L. Charnavets, T. Lebl, M. Brown, S. M. Hadravova, R. Konvalinka, J. Singharoy, A. Fried, S. D. Hlouchova, K. 2025-11-10 doi:10.1101/2025.11.09.687475 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics ]]> https://biorxiv.org/content/10.1101/2025.11.10.687605v1?rss=1 Xie, J. Win, P. W. Newcomb, C. E. Zeng, S. Castellani, C. A. Arking, D. 2025-11-11 doi:10.1101/2025.11.10.687605 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications ]]> https://biorxiv.org/content/10.1101/2025.11.10.687672v1?rss=1 Cieslak, M. Irfanoglu, M. O. Meisler, S. L. Salo, T. Raikes, A. C. Cook, P. A. Chung, A. W. Lee, E. G. Li, R. Li, X. Pecheva, D. Fair, D. A. Smyser, C. D. Harms, M. P. Landman, B. A. Wisnowski, J. L. Huang, H. Alexander, A. L. Satterthwaite, T. D. 2025-11-11 doi:10.1101/2025.11.10.687672 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ The Drosophila ovary produces three follicle waves similar to those in mice ]]> https://biorxiv.org/content/10.1101/2025.11.11.687893v1?rss=1 Fu, W. Y. Spradling, A. C. 2025-11-12 doi:10.1101/2025.11.11.687893 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Visual landmark coding and dynamic coupling with path integration circuits in area 29e of the rodent parahippocampal cortex ]]> https://biorxiv.org/content/10.1101/2025.11.11.687899v1?rss=1 Secer, G. Krishnan, B. Cowan, N. Knierim, J. J. 2025-11-12 doi:10.1101/2025.11.11.687899 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Wasserstein Critics Outperform Discriminatorsin Adversarial Deconfounding of Gene Expression Data ]]> https://biorxiv.org/content/10.1101/2025.11.12.688061v1?rss=1 Reid, K. Guven, E. 2025-11-13 doi:10.1101/2025.11.12.688061 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2025.11.12.688126v1?rss=1 Zhao, W. Fertig, E. J. Stein-O'Brien, G. L. 2025-11-13 doi:10.1101/2025.11.12.688126 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ A tale of two distinct actin networks underlies the entire life cycle of focal adhesion ]]> https://biorxiv.org/content/10.1101/2025.11.12.688129v1?rss=1 Dong, R. ishii, K. Plotnikov, S. V. Liu, J. 2025-11-13 doi:10.1101/2025.11.12.688129 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ A patient derived missense mouse model of Kabuki syndrome 1 ]]> https://biorxiv.org/content/10.1101/2025.11.13.688040v1?rss=1 Halldorsdottir, S. T. Vinod, M. Gunnlaugsson, H. O. Bjornsdottir, E. D. Luperchio, T. Fahrner, J. A. Ulfig, A. Bjornsson, H. T. 2025-11-14 doi:10.1101/2025.11.13.688040 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Human resistin is critical to activation of the NLRP3 inflammasome in macrophages ]]> https://biorxiv.org/content/10.1101/2025.11.13.688330v1?rss=1 Kariyawasam, U. Skinner, J. Lam, W. Chakrabarti, R. Cox, A. Hassoun, P. M. Lin, Q. Johns, R. 2025-11-14 doi:10.1101/2025.11.13.688330 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases ]]> https://biorxiv.org/content/10.1101/2025.11.14.688538v1?rss=1 Sathe, A. Zhang, M. Bai, X. Kang, J. I. Meka, R. Sun, H. Grimes, S. M. Khan, A. Liu, M. Luksik, A. S. Lim, M. Petrisch, C. K. Jackson, C. M. Vogel, H. Shen, J. Gephart, M. Han, S. Ji, H. 2025-11-16 doi:10.1101/2025.11.14.688538 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ A membrane-driven biochemical oscillator tunable by the volume to surface area ratio ]]> https://biorxiv.org/content/10.1101/2025.11.14.688573v1?rss=1 Fischer, J. Greenberg, E. Ying, Y. M. Takeshita, S. S. Foley, S. L. Johnson, M. E. 2025-11-16 doi:10.1101/2025.11.14.688573 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024 ]]> https://biorxiv.org/content/10.1101/2025.11.14.688517v1?rss=1 Isaac, K. J. Cox, K. E. L. Ho, K. Y. Humphries, E. M. Kucher, N. Leek, J. T. Mosher, S. Schatz, M. C. Tan, F. J. Hoffman, A. M. 2025-11-17 doi:10.1101/2025.11.14.688517 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Comparative Molecular Docking and Toxicity Profiling of Buspirone and Tandospirone Targeting the HTR1A Receptor ]]> https://biorxiv.org/content/10.1101/2025.11.17.688977v1?rss=1 Lu, Y. 2025-11-18 doi:10.1101/2025.11.17.688977 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ CANVAS causing AAGGG repeat expansions cause tissue-specific reduction in RFC1 expression and increase sensitivity to DNA damage ]]> https://biorxiv.org/content/10.1101/2025.11.18.688292v1?rss=1 Curro, R. Dominik, N. Facchini, S. Schnekenberg, R. P. Perini, C. Ronco, R. Rugginini, B. Ghia, A. Bione, S. Tagliaferri, N. Grupelli, G. P. Lowe, S. A. Hicks, A. R. Vegezzi, E. Simone, R. Bertini, A. Abati, E. Velasco, R. Sereno, M. Gutierrez-Gutierrez, G. Thomas, S. Alberti, P. Khurana, V. Attems, J. Troakes, C. Gustavsson, E. K. Lignani, G. Qiu, Y. Sleigh, J. N. Tucci, A. Fratta, P. Isaacs, A. Lim, Y. M. Jaunmuktane, Z. Brandner, S. Bennett, D. L. Przedborski, S. Opal, P. Hoke, A. Kuo, S.-H. Reilly, M. M. Houlden, H. Ryten, M. Cavaletti, G. Argyri 2025-11-18 doi:10.1101/2025.11.18.688292 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ CUSP: Complex Spike Sorting from Multi-electrode Array Recordings with U-net Sequence-to-Sequence Prediction ]]> https://biorxiv.org/content/10.1101/2025.11.18.689109v1?rss=1 Bao, C. Mildren, R. Charles, A. Cullen, K. E. 2025-11-18 doi:10.1101/2025.11.18.689109 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Mutational divergence in local populations of the selfing nematode Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.11.19.689209v1?rss=1 Felix, M.-A. Wei, X. Richaud, A. Tanny, R. E. Andersen, E. C. 2025-11-19 doi:10.1101/2025.11.19.689209 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Harmonized Protocol for Segmentation of the Hippocampal Tail on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG) ]]> https://biorxiv.org/content/10.1101/2025.11.20.689476v1?rss=1 0.98; Averaged Dice Similarity Coefficient = 0.92) and inter-rater reliability (Averaged ICC(2,k) > 0.98; Averaged Dice Similarity Coefficient = 0.86) and offers a practical framework for replicable segmentation. By establishing standardized guidelines, this protocol enhances comparability of findings across developmental, aging, and clinical research and is compatible with ongoing technological advances. ]]> de Flores, R. Canada, K. L. Brown, T. Gervais, N. J. Maass, A. Radman, G. Shine, J. Tucker, H. L. Molloy, E. N. Adams, J. N. Reinke, M. B. Bakker, A. Berron, D. Dalton, M. A. Kennedy, K. M. La Joie, R. Mueller, S. G. Ofen, N. Olsen, R. K. Raz, N. Riggins, T. Rodrigue, K. M. Stark, C. Wang, L. Wisse, L. E. Yushkevich, P. A. Carr, V. A. Daugherty, A. M. Alzheimer's Disease Neuroimaging Initiative, Hippocampal Subfields Group, 2025-11-20 doi:10.1101/2025.11.20.689476 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Orchestrating Spatial Transcriptomics Analysis with Bioconductor ]]> https://biorxiv.org/content/10.1101/2025.11.20.688607v1?rss=1 Crowell, H. L. Dong, Y. Billato, I. Cai, P. Emons, M. Gunz, S. Guo, B. Li, M. Mahmoud, A. Manukyan, A. Pages, H. Panwar, P. Rao, S. Sargeant, C. J. Shepherd Kern, L. Ramos, M. Sun, J. Totty, M. Carey, V. J. Chen, Y. Collado-Torres, L. Ghazanfar, S. Hansen, K. D. Martinowich, K. Maynard, K. R. Patrick, E. Righelli, D. Risso, D. Tiberi, S. Waldron, L. Gottardo, R. Robinson, M. D. Hicks, S. C. Weber, L. M. 2025-11-21 doi:10.1101/2025.11.20.688607 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ cpiVAE: Robust and Interpretable Cross-Platform Proteomics Imputation ]]> https://biorxiv.org/content/10.1101/2025.11.20.689433v1?rss=1 Li, Y. Duong, T. Rooney, M. R. Ballantyne, C. M. Coresh, J. Brody, J. A. Sotoodehnia, N. Arking, D. E. Bader, J. S. 2025-11-21 doi:10.1101/2025.11.20.689433 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL ]]> https://biorxiv.org/content/10.1101/2025.11.20.689441v1?rss=1 95% of the adult population with diverse outcomes ranging from benign latency to cancers and autoimmune diseases. Immunological control of EBV infection is known to be an important determinant of EBV infection outcomes. However, species-specific viral tropism and limited infection models have impeded mechanistic insights into early host-immune control of EBV infection. Here, we use ex vivo infection of peripheral blood mononuclear cells (PBMCs), rather than routinely used B cell enriched culture systems, to study immune and viral dynamics during primary EBV infection. We combined bulk RNA sequencing, EBV transcript enrichment, and flow cytometry to characterize cellular responses across Days 1, 7-8, and 14 post-infection. Early infection triggered a monocyte-specific antiviral response marked by changes in the expression of genes associated with lipid metabolism (LIPA, lysosomal acid lipase) and chemotaxis (CCR1 and CCR2). Inhibitors of LIPA increased EBV titers during primary infection, indicating that LIPA is part of an early monocyte-driven antiviral response. At later timepoints post-infection, donor-dependent variability in lymphoblastoid cell line (LCL) outgrowth was associated with divergent immune states. Donors that failed to generate LCLs demonstrated increased frequencies of CD8+ T cells and reduced numbers of regulatory T cells (CD4CD25FOXP3). EBV transcriptomics revealed that LCL-failed donors exhibited elevated early lytic gene expression but did not establish a type III latency program. Our findings suggest that individual variations in immune cell composition and gene expression may account for differences in the immune response to EBV. These findings define temporal immune and viral signatures that predict transformation outcome and highlight intact PBMCs as a tractable model to study EBV pathogenesis in a genetically diverse, human-specific context. AUTHOR SUMMARYIndividual variation in response to Epstein-Barr virus (EBV) infection can lead to diverse pathogenic outcomes, ranging from cancers to autoimmune disease. To study this variation, we analyzed immune cell response and viral dynamics during the ex vivo primary EBV infection of peripheral blood mononuclear cells (PBMCs) from donors that either fail or succeed to generate lymphoblastoid cell lines (LCLs). Flow cytometry and RNA-seq revealed a rapid monocyte-specific antiviral response among all donors marked by genes associated with lipid metabolism (LIPA) and chemotaxis (CCR1 and CCR2). LIPA inhibition increased EBV titers during primary infection, demonstrating a functional antiviral role. At later timepoints, donor-specific differences in CD8+ T cells and Treg subsets, along with EBV gene expression, were correlated with successful LCL outgrowth. Treatment with the Treg-depleting antibody RG6292 suppressed viral transformation in donors that otherwise supported LCL outgrowth, confirming a functional role for Tregs in shaping early EBV infection outcomes. Viral transcript enrichment-seq revealed an upregulation of early lytic and failure to sustain latent gene expression correlating with failure to generate LCL. These findings highlight intact PBMCs as a tractable model to study EBV viral-host interaction in a genetically diverse, human-specific context, and that Tregs play a key determining role in viral transformation. ]]> Yoon, L. MacMullen, L. N. Castro Munoz, L. J. Gu, A. Bregman, J. Campion, M. S. Srivastava, A. Xian, R. R. Ambinder, R. F. Kossenkov, A. Soldan, S. S. Lieberman, P. M. 2025-11-21 doi:10.1101/2025.11.20.689441 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.11.20.689569v1?rss=1 Zhou, H. Chen, H. Rudnick, Z. Baalbaki, S. I. Lee, Y. J. Lugo-Martinez, J. 2025-11-21 doi:10.1101/2025.11.20.689569 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Myeloid cell recruitment propels right ventricular dysfunction in HFpEF via sterile inflammation. ]]> https://biorxiv.org/content/10.1101/2025.11.21.689863v1?rss=1 Jaeschke, L. Kocana, C. Chitroceanu, A. M. Winkler, A. Kleitke, H. Fahjen, P. Faidel, D. Asmus, E. Meiser, M. Stamatiades, E. G. Hublitz, K. W. Zach, V. Kretzler, L. Zurkan, D. Perret, P.-L. von der Ohe, L. A. Simmons, S. Gillan, J. L. Franz, K. Alasfar, L. Hahn, V. S. Sharma, K. Reynolds, E. Schiattarella, G. G. Van Linthout, S. Pieske, B. Hegemann, N. Mertins, P. Edelmann, F. Kuebler, W. M. Grune, J. 2025-11-23 doi:10.1101/2025.11.21.689863 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2025.11.23.690031v1?rss=1 Yehya, N. Bohrer, C. H. Yu, Q. Hathcock, D. Goldberg, B. I. Leng, S. Harris, F. E. Hendrix, H. White, M. Leng, F. Meyer, S. Tu, Y. Xiao, J. 2025-11-23 doi:10.1101/2025.11.23.690031 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Sphingosine-1-phosphate receptor modulators resensitize FLT3-ITD acute myeloid leukemia cells with NRAS mutations to FLT3 inhibitors ]]> https://biorxiv.org/content/10.1101/2025.11.21.689510v1?rss=1 Baer, M. R. Chatterjee, A. Ali, M. K. M. Bailey, C. M. Liu, Y. Small, D. Smith, C. C. Traer, E. C. Wang, Y. Silvestri, G. 2025-11-24 doi:10.1101/2025.11.21.689510 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Determining gene specificity from multivariate single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2025.11.21.689845v1?rss=1 Swarna, N. P. Booeshaghi, A. S. Rebboah, E. Gordon, M. G. Kathail, P. Li, T. Alvarez, M. Ye, C. J. Wold, B. J. Mortazavi, A. Pachter, L. 2025-11-24 doi:10.1101/2025.11.21.689845 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes ]]> https://biorxiv.org/content/10.1101/2025.11.21.689847v1?rss=1 Clifton, K. Jiang, V. Peixoto, R. d. S. Singh, S. Matsuura, R. Rabb, H. Fan, J. 2025-11-25 doi:10.1101/2025.11.21.689847 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Sex and experience dependent regulation of synaptic protein turnover ]]> https://biorxiv.org/content/10.1101/2025.11.24.690161v1?rss=1 Heo, S. Zhang, S. Mun, D.-G. Pandey, A. Bygrave, A. M. Huganir, R. L. 2025-11-25 doi:10.1101/2025.11.24.690161 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Integrative multi-omic analysis identifies key transcription factors and target proteins in renal cell carcinoma and its subtypes ]]> https://biorxiv.org/content/10.1101/2025.11.23.690024v1?rss=1 Chhetri, S. B. Winter, T. D. Machiela, M. J. Brown, K. Battle, A. Purdue, M. P. Chanock, S. J. Dutta, D. 2025-11-26 doi:10.1101/2025.11.23.690024 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ A mouse model of classical trigeminal neuralgia via intradural compression of the trigeminal nerve ]]> https://biorxiv.org/content/10.1101/2025.11.24.690061v1?rss=1 Abdulrahim, M. Xu, R. Chen, Y. Nair, S. Xu, Q. Zhang, Y. Das, O. Gensler, R. Feghali, J. Ahmad, A. K. Jackson, C. Huang, J. Comair, Y. Bettegowda, C. Dong, X. 2025-11-26 doi:10.1101/2025.11.24.690061 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy ]]> https://biorxiv.org/content/10.1101/2025.11.24.690135v1?rss=1 Babu, V. S. Ghosh, S. Bammidi, S. Jiwon, R. Sharma, R. Meyer, D. Hose, S. Pattabiraman, P. P. Sahel, J.-A. Kidley, N. J. Braz, N. F. Slater, M. J. Lang, S. Ghosh, A. Yi, J. Sripathi, S. Rangaramanujam, K. Bharti, K. Sinha, D. 2025-11-26 doi:10.1101/2025.11.24.690135 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Dynamic changes in mRNA isoform usage during human retinal development ]]> https://biorxiv.org/content/10.1101/2025.11.26.689062v1?rss=1 Keuthan, C. J. Parthiban, S. Chang, Y.-Y. Shan, X. Chang, X. Yan, E. Cavalier, S. Timp, W. Hicks, S. C. Zack, D. J. 2025-11-26 doi:10.1101/2025.11.26.689062 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Mapping spatial gradients in spatial transcriptomics data with score matching ]]> https://biorxiv.org/content/10.1101/2025.11.24.690257v1?rss=1 Wang, A. Geman, D. Chitra, U. Younes, L. 2025-11-27 doi:10.1101/2025.11.24.690257 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Sensorineural regulation of skull healing implicates FGF1 signaling in non-healing bone ]]> https://biorxiv.org/content/10.1101/2025.11.24.690319v1?rss=1 Horenberg, A. L. Villapudua-Gastelum, C. Xu, M. Zeng, E. Dias, S. Sinha, T. Archer, M. Scheller, E. L. Pathak, A. James, A. Grayson, W. 2025-11-28 doi:10.1101/2025.11.24.690319 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala ]]> https://biorxiv.org/content/10.1101/2025.11.25.690517v1?rss=1 Magnard, R. Gonzalez-Padilla, D. Yalcinbas, E. A. Chaloux-Pinette, E. Eagles, N. J. Totty, M. S. Janak, P. H. Collado-Torres, L. Maynard, K. R. 2025-11-28 doi:10.1101/2025.11.25.690517 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Anionic Lipid Trafficking and Cell Mechanics RegulateMembrane Electrical Potential in Non-Excitable Tissue Cells ]]> https://biorxiv.org/content/10.1101/2025.11.25.690536v1?rss=1 Ge, Z. Ni, Q. Yan, Y. Wu, Y. Si, B. R. Fu, J. LIN, D. Konstantopoulos, K. Li, Y. Sun, S. 2025-11-28 doi:10.1101/2025.11.25.690536 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and intra-tumoral mucosal associated invariant T (MAIT) cell activation ]]> https://biorxiv.org/content/10.1101/2025.11.25.690539v1?rss=1 Birla, P. Yang, L. Shan, W. Minamisawa, S. Dhaygude, O. Manoj, H. Zheng, Y. Fan, H. Beauregard, H. Smith, K. N. Shaikh, F. Y. Sears, C. L. Pardoll, D. M. Housseau, F. 2025-11-29 doi:10.1101/2025.11.25.690539 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Ultrafast CTCF dynamics control cohesin barrier function ]]> https://biorxiv.org/content/10.1101/2025.11.25.690553v1?rss=1 Rudnizky, S. Murray, P. J. Sorensen, E. W. Koenig, T. J. R. Pangeni, S. Merino-Urteaga, R. Chhabra, H. Caccianini, L. Davidson, I. F. Osorio-Valeriano, M. Hook, P. W. Meneses, P. Hao, J. Zarb, J. S. Hatzakis, N. S. Timp, W. Farnung, L. Vos, S. M. Peters, J.-M. Aksimentiev, A. Ha, T. 2025-11-29 doi:10.1101/2025.11.25.690553 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Can We Extract Physics-like Energies from Generative Protein Diffusion Models? ]]> https://biorxiv.org/content/10.1101/2025.11.28.690021v1?rss=1 Sarma, S. S. Truscott, H. H. Xu, D. Reid, K. Chu, L.-S. Chen, J. Gray, J. J. 2025-11-29 doi:10.1101/2025.11.28.690021 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Aridity drives global convergence of desert microbiomes and biogeochemical activities ]]> https://biorxiv.org/content/10.1101/2025.11.29.691269v1?rss=1 Leung, P. M. Bay, S. K. Wong, W. W. Jirapanjawat, T. Archer, S. D. Beaman, J. Cherif, A. Chown, S. L. Cowan, D. A. Demergasso, C. de los Rios, A. DiRuggiero, J. Elberling, B. Frey, B. Gillor, O. Graham, D. W. Gupta, P. Hogg, I. D. Juottonen, H. Kytöviita, M.-M. Makhalanyane, T. Meredith, L. K. Nguyen-Dinh, T. Prieme, A. Ramond, J.-B. Siciliano, S. D. Tan, G. Y. A. Warren-Rhodes, K. A. Wieler, N. Cook, P. L. M. Delgado-Baquerizo, M. Greening, C. 2025-11-29 doi:10.1101/2025.11.29.691269 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Domain-specific decoupling of co-chaperone and ligase functions in STUB1 underlies biochemical and clinical heterogeneity in SCA48 ]]> https://biorxiv.org/content/10.1101/2025.11.26.690709v1?rss=1 Altinok, S. Paulakonis, E. Almeida, M. F. Hwang, I. Sanchez-Hodge, R. DOvidio, C. Roper, G. Irons, G. Vargas, E. Peng, I. Saeed, M. Pathan, A. Ronnebaum, S. M. Shi, C.-h. Ranek, M. J. Scaglione, K. M. Page, R. C. Brown, N. G. Schisler, J. C. 2025-11-30 doi:10.1101/2025.11.26.690709 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ CAFT: A Compositional Log-Linear Model for Microbiome Data with Zero Cells ]]> https://biorxiv.org/content/10.1101/2025.11.26.690468v1?rss=1 Satten, G. A. Li, M. Zhao, N. 2025-12-01 doi:10.1101/2025.11.26.690468 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Metabolic and Redox Pathway Dysregulation in HIV-Associated Coronary Endothelial Dysfunction ]]> https://biorxiv.org/content/10.1101/2025.11.26.690743v1?rss=1 Keole, K. S. Bukhari, S. Minhas, A. Cohen, C. D. Wallace, A. Piggott, D. Leucker, T. M. Sun, K. Adamo, L. Hays, A. 2025-12-01 doi:10.1101/2025.11.26.690743 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Local B cell maturation and mast cell regulation of choroid plexus function in early life. ]]> https://biorxiv.org/content/10.1101/2025.11.27.690721v1?rss=1 Ali-Moussa, S. Blas-Medina, A. Josephides, J. Mirabeau, O. Bouteau, I. Matijevic, T. Kovacs, M. Pakulska, V. Pangan, A. R. Thomas, C. Hasselblatt, M. Dong, X. Matondo, M. Gaudenzio, N. Jonsson, F. Travier, L. Deczkowska, A. 2025-12-01 doi:10.1101/2025.11.27.690721 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Image-based Morphological Profiling Reveals Signatures of Radiation Exposure ]]> https://biorxiv.org/content/10.1101/2025.11.27.691043v1?rss=1 Tiburzi, O. Dunphy, L. Ton, S. McQuillen, R. Hunt, A. 2025-12-01 doi:10.1101/2025.11.27.691043 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching ]]> https://biorxiv.org/content/10.1101/2025.11.28.691195v1?rss=1 Xu, D. Chu, L.-S. Gray, J. J. 2025-12-01 doi:10.1101/2025.11.28.691195 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Genetic analysis of pyrimidine biosynthetic enzymes in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2025.11.30.691290v1?rss=1 Rajaram, K. Sievert, M. L. Elahi, R. Dillard, L. B. Blauwkamp, J. Absalon, S. Prigge, S. T. 2025-12-01 doi:10.1101/2025.11.30.691290 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ The pKa values of buried ionizable amino acids can be determined by the thermodynamic stability of the protein ]]> https://biorxiv.org/content/10.64898/2025.11.30.690581v1?rss=1 Hurst, M. Kougentakis, C. Robinson, A. Garcia-Moreno, B. 2025-12-02 doi:10.64898/2025.11.30.690581 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ ClustSIGNAL identifies cell types and subtypes using an adaptive smoothing approach for scalable spatial clustering ]]> https://biorxiv.org/content/10.64898/2025.11.30.691081v1?rss=1 Panwar, P. Guo, B. Zhou, H. Hicks, S. C. Ghazanfar, S. 2025-12-02 doi:10.64898/2025.11.30.691081 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Electrodiffusion active pump model with asymmetric immersed chemical potentials ]]> https://biorxiv.org/content/10.64898/2025.11.30.691367v1?rss=1 Lee, P. Sun, S. 2025-12-02 doi:10.64898/2025.11.30.691367 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Vascular smooth muscle cell loss, but not neuroinflammation, drives cerebrovascular reactivity impairment in Alzheimer disease ]]> https://biorxiv.org/content/10.64898/2025.12.01.691642v1?rss=1 yang, x. Li, Y. Yao, M. Bibic, A. Duan, W. Lu, H. Wei, Z. 2025-12-03 doi:10.64898/2025.12.01.691642 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A developmentally regulated long-range enhancer-promoter contact mediates human neural development ]]> https://biorxiv.org/content/10.64898/2025.12.01.691702v1?rss=1 Bready, D. Wang, S. Ravn-Boess, N. Frenster, J. Sabio, J. Kushmakov, R. Clark, F. Guerrero, A. Lapierre, C. Galbraith, K. Do, C. Lhoumaud, P. Prado, J. Jiang, A. Haddock, S. Kim, C. D. Snuderl, M. Lionnet, T. Tsirigos, A. Skok, J. Placantonakis, D. G. 2025-12-03 doi:10.64898/2025.12.01.691702 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ The long noncoding RNA Peanut (Gm11454) promotes neurogenesis and rod photoreceptor differentiation during postnatal retinal development. ]]> https://biorxiv.org/content/10.64898/2025.12.02.691925v1?rss=1 Hostetler, J. E. Shiau, F. Zhang, X. Chen, S. Ruzycki, P. A. Blackshaw, S. Clark, B. 2025-12-03 doi:10.64898/2025.12.02.691925 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Myelin density dictates region-specific vulnerability of oligodendrocyte lineage cells during aging ]]> https://biorxiv.org/content/10.64898/2025.12.02.691836v1?rss=1 Skaf, A. Eugenin von Bernhardi, J. Dimou, L. 2025-12-05 doi:10.64898/2025.12.02.691836 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Hyperintense signals in cerebral blood flow maps acquired with pseudo-continuous arterial spin labeling MRI in mice ]]> https://biorxiv.org/content/10.64898/2025.12.02.691929v1?rss=1 Yang, X. Li, Y. Bibic, A. Wei, Z. 2025-12-05 doi:10.64898/2025.12.02.691929 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Coordination of spike timing among the neurons of the cerebellum ]]> https://biorxiv.org/content/10.64898/2025.12.03.692114v1?rss=1 Fakharian, M. A. Taeckens, E. A. Vasserman, A. N. Shoup, A. Shadmehr, R. 2025-12-08 doi:10.64898/2025.12.03.692114 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Genetic Background and Sex Modulate Androgen Responses in Human Brain Microphysiological System ]]> https://biorxiv.org/content/10.64898/2025.12.03.692130v1?rss=1 Schenke, M. Laird, J. Rittenhouse, A. Kucheryavenko, V. Neuhaus, W. Chen, O. Sabunciyan, S. Maertens, A. Smirnova, L. 2025-12-08 doi:10.64898/2025.12.03.692130 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.03.692228v1?rss=1 Watson, M. A. Devrukhkar, P. R. Murad, N. F. Wu, F. Kim, M. J. Anvari, H. Tran, U. Martin, N. Tran, T. Zaza, G. Schneider, K. Soygur, B. Shanes, E. D. Wirtz, D. Pavone, M. G. Melov, S. Wu, P.-H. Furman, D. Duncan, F. E. Schilling, B. 2025-12-08 doi:10.64898/2025.12.03.692228 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Tuberculous meningitis alters the proteomic landscape of brain-derived extracellular vesicles ]]> https://biorxiv.org/content/10.64898/2025.12.08.692466v1?rss=1 Rodriguez, B. V. Damiba, N. N. L. Beaubien, N. Puca, D. Foster, D. B. Das, S. Tucker, E. 2025-12-08 doi:10.64898/2025.12.08.692466 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Scalable and Adaptive Spatiotemporal Modeling for Task-Based fMRI Analysis ]]> https://biorxiv.org/content/10.64898/2025.12.04.692389v1?rss=1 Choi, J. Datta, A. Lindquist, M. 2025-12-09 doi:10.64898/2025.12.04.692389 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Enhanced ex vivo 3D whole-brain mapping and automated analysis of Parkinson's disease pathologies in mice ]]> https://biorxiv.org/content/10.64898/2025.12.05.692595v1?rss=1 Combes, B. F. Henrich, M. T. Karatsoli, M. Kollmorgen, S. Rosenau, A. K. Nilsson, P. R. Chen, R. Dawson, V. L. Dawson, T. M. Oertel, W. H. Razansky, D. Karayannis, T. Rominger, A. Hock, C. Nitsch, R. M. Geibl, F. F. Ni, R. 2025-12-09 doi:10.64898/2025.12.05.692595 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir ]]> https://biorxiv.org/content/10.64898/2025.12.07.692769v1?rss=1 Garcia, M. A. Farrell-Sherman, A. Zhuo, J. Fray, E. J. Zinsser, A. M. Aydin, B. Sowers, K. Li, H. Lopez, B. M. Abeyta-Lopez, A. Chu, T. Lubbeck, D. Chae, M. Varriale, J. Westfall, D. H. Lai, J. Hoh, R. Dalhuisen, T. Simonetti, F. R. Peluso, M. J. Deeks, S. G. Siliciano, R. F. Cohn, L. B. Siliciano, J. D. 2025-12-09 doi:10.64898/2025.12.07.692769 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Neuronal PARIS-STAT3 axis drives tau pathology and glial activation in Alzheimers disease ]]> https://biorxiv.org/content/10.64898/2025.12.06.692741v1?rss=1 Song, J.-Y. Akkentili, F. Jo, H. Park, J. Ha, S. Redding_Ochoa, J. Troncoso, J. Kang, S.-U. Dawson, V. L. Dawson, T. 2025-12-10 doi:10.64898/2025.12.06.692741 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Neuromuscular Signals Shape Fatigue and Effort-Based Decision-Making in Humans ]]> https://biorxiv.org/content/10.64898/2025.12.06.692763v1?rss=1 Casamento-Moran, A. Kim, A. Lee, J. L. Chib, V. S. 2025-12-10 doi:10.64898/2025.12.06.692763 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ An integrated workflow for structural virology with a 100 keV electron microscope ]]> https://biorxiv.org/content/10.64898/2025.12.08.693081v1?rss=1 Pathirage, R. Dutta, M. Parsons, R. J. Lella, M. Atwood, E. Zhang, Q. E. May, A. Johnson, A. Huang, X. Flemming, J. Kumar, U. Marayati, B. F. Spurrier, M. A. Liu, C. Zhuo, J. Song, K. Devkota Adhikari, R. Sammour, S. Ilevbare, V. Abram, C. Diaz, M. Guzman, A. Rai, J. Skelly, A. N. Hogarty, M. P. Anasti, K. Purro, M. Lindsay, M. Alam, S. M. Weissman, D. Herschhorn, A. Hahn, B. H. Shaw, G. M. Sharma, A. Heaton, N. S. Edwards, R. J. Henderson, R. Denny, T. Saunders, K. O. Siliciano, J. D. Siliciano, R. F. Haynes, B. F. Janowska, K. Acharya, P. 2025-12-10 doi:10.64898/2025.12.08.693081 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Vascular Microbleeds Without Brain Atrophy: A Microvascular Signature of Mid-Stage 5xFAD Pathology ]]> https://biorxiv.org/content/10.64898/2025.12.08.692809v1?rss=1 yang, x. Li, Y. Bibic, A. Wang, J. Wan, M. Duan, W. Lu, H. Wei, Z. 2025-12-11 doi:10.64898/2025.12.08.692809 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ A transition zone enriched WIF1⁺ basal cell subtype is associated with benign prostatic hyperplasia ]]> https://biorxiv.org/content/10.64898/2025.12.08.692826v1?rss=1 Wang, R. Zheng, Q. Graham, M. K. Vaghasia, A. Liu, J. Gregg, J. Jones, T. Gupta, A. Castagna, N. Zhang, Y. Schuebel, K. Meyers, J. Skaist, A. Hoyle, D. Yang, Y. Nelson, W. G. De Marzo, A. M. Yegnasubramanian, S. 2025-12-11 doi:10.64898/2025.12.08.692826 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes ]]> https://biorxiv.org/content/10.64898/2025.12.08.693002v1?rss=1 Moya, N. D. Wang, B. Tanny, R. E. Sauria, M. E. G. O'Connor, L. M. Khorshidian, A. McKeown, R. Gosse, C. Dilks, C. M. Crombie, T. A. Zhang, G. Rais, E. Frezal, L. Dang, V. D. Haryoso, E. Devi, M. P. Gimond, C. Cook, D. E. Hsu, J.-C. Shaver, A. O. Zdraljevic, S. Richaud, A. Wen, T. Mehraj, A. H, S. Arulprakasam, K. R. Koury, E. J. Roberto, N. M. Schaye, E. S. Singh, V. Tarno, H. Ailion, M. Paaby, A. B. Zhao, Z. Cutter, A. D. Wang, J. Rockman, M. V. Braendle, C. Andersen, E. C. 2025-12-11 doi:10.64898/2025.12.08.693002 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Engineering immunotoxin-equipped effector cells and evaluation in primary human immune cells ]]> https://biorxiv.org/content/10.64898/2025.12.09.691975v1?rss=1 Pearlman, A. H. Mog, B. J. Hwang, M. S. Rincon-Torroella, J. DiNapoli, S. R. Paul, S. Douglass, J. Hsiue, E. H.-C. Glavaris, S. A. Pardoll, D. M. Papadopoulos, N. Kinzler, K. W. Bettegowda, C. Zhou, S. Vogelstein, B. Konig, M. F. 2025-12-11 doi:10.64898/2025.12.09.691975 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Esc1-mediated anchoring regulates telomere clustering in response to metabolic changes. ]]> https://biorxiv.org/content/10.64898/2025.12.09.692953v1?rss=1 Ruault, M. Loiodice, i. Keister, B. D. Even, A. Garnier, M. Perez, M. B. Waterman, D. P. Haber, J. E. Blagoev, K. B. Scolari, V. Taddei, A. 2025-12-11 doi:10.64898/2025.12.09.692953 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Do Pseudosequences Matter in Neoantigen Prediction? ]]> https://biorxiv.org/content/10.64898/2025.12.09.693250v1?rss=1 Valeria, A. Karchin, R. 2025-12-12 doi:10.64898/2025.12.09.693250 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology ]]> https://biorxiv.org/content/10.64898/2025.12.09.693329v1?rss=1 Finney, C. A. An, L. Winchester, L. M. Vogel, J. Wilkins, H. M. Burns, J. M. Swerdlow, R. H. Slawson, C. Rothstein, J. D. Global Neurodegeneration Proteomics Consortium, Lutz, M. W. Saloner, R. Shvetcov, A. 2025-12-12 doi:10.64898/2025.12.09.693329 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.64898/2025.12.15.694292v1?rss=1 Devlin, K. L. Hutchinson, E. Leach, D. T. Nelson, W. C. Gorham, L. J. Lamichhane, G. Lin, V. S. Beatty, K. E. 2025-12-15 doi:10.64898/2025.12.15.694292 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ spaTransfer: transfer learning for single-cell and spatialtranscriptomics data using non-negative matrix factorization ]]> https://biorxiv.org/content/10.64898/2025.12.12.694021v1?rss=1 Fang, C. Montgomery, K. D. Maguire, S. E. Ramnauth, A. D. Guo, B. Miller, R. Kleinmann, J. E. Hyde, T. M. Martinowich, K. Maynard, K. R. Page, S. C. Hicks, S. C. 2025-12-16 doi:10.64898/2025.12.12.694021 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Versatile high-speed volumetric imaging from microscopic to macroscopic scale by self-adaptive oblique plane microscopy ]]> https://biorxiv.org/content/10.64898/2025.12.16.694458v1?rss=1 3x3 mm2 FOV) with a sweeping 0.32 mm wide volume section at 100 Hz. In optically cleared mouse brain, the flexibility allows a screen-and-zoom capability by sequentially imaging the whole brain at low-and-high magnifications to locate and resolve subcellular structures such as dendritic tress and spines. By offering a switchable imaging resolution, volume, and speed, the self-adaptive OPM achieves a versatile platform for studying a wide range of multi-cellular model system, whether in vivo or fixed and optically cleared. ]]> Meyer, D. Kroeschell, G. Lu, X. Hoang, L. Wang, H. Li, S. Xu, Y. K. T. Tan, L. Mumm, J. S. Bergles, D. E. Yi, J. 2025-12-18 doi:10.64898/2025.12.16.694458 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ p53 preserves genome stability in dividing cells under hypo-osmotic stress ]]> https://biorxiv.org/content/10.64898/2025.12.17.694541v1?rss=1 Wong, B. S. Ghosh, A. K. Cui, H. Li, K. Johnson, B. A. Sethi, K. Lee, Y. Zhu, J. Sun, S. X. Li, R. 2025-12-18 doi:10.64898/2025.12.17.694541 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Ectopic engraftment of nociceptive neurons derived from hPSCs for pain relief and joint homeostasis ]]> https://biorxiv.org/content/10.64898/2025.12.16.694733v1?rss=1 View larger version (70K): org.highwire.dtl.DTLVardef@15f0948org.highwire.dtl.DTLVardef@5a59bforg.highwire.dtl.DTLVardef@1ba4439org.highwire.dtl.DTLVardef@1d518d1_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIhPSC-derived nociceptors (hPSC-NNs) as Decoy Engraftment for Cellular Interception and Repair (DECIR) when transplanted into the knee joint, extending beyond conventional regenerative strategies C_LIO_LICD200 serves as a clinically actionable surface marker for the purification of hPSC-NNs C_LIO_LIEctopic grafting of CD200high hPSC-NNs delivers dual benefits, alleviating pain and modulating the neuro-immune environment within joint tissues C_LIO_LIProteomic analyses reveal that CD200highhPSC-NNs sequester inflammatory mediators and secrete reparative factors to support joint homeostasis C_LI ]]> Dong, X. Lee, G. Wang, Z. P. Zhang, W. Cao, X. Peng, J. Wang, J. Wu, Z. 2025-12-19 doi:10.64898/2025.12.16.694733 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Wnt-presenting materials sustain H3K14-acetylation in human skeletal stem cells for tissue engineering and bone repair ]]> https://biorxiv.org/content/10.64898/2025.12.18.694408v1?rss=1 Becquart, P. Tournier, P. Junyent, S. Ma, B. Liu, Y. Tang, Y. Chen, X. Fang, D. Kusumbe, A. Habib, S. J. 2025-12-19 doi:10.64898/2025.12.18.694408 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Phenotypes and Cellular Mechanics of Primary Human Aorta- and Pluripotent Stem Cell-derived Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.64898/2025.12.18.694995v1?rss=1 Huang, C.-Y. Wu, S. C. M. Kissling, M. Arking, A. Chen, Y.-W. Hall, F. D. Sivarajan, S. Yezzi, H. Reich, D. H. Boheler, K. R. 2025-12-22 doi:10.64898/2025.12.18.694995 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity ]]> https://biorxiv.org/content/10.64898/2025.12.18.695193v1?rss=1 Velazquez, D. Hallinan, C. An, R. Clifton, K. Fan, J. 2025-12-22 doi:10.64898/2025.12.18.695193 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data ]]> https://biorxiv.org/content/10.64898/2025.12.18.695273v1?rss=1 Anyaso-Samuel, S. C. Li, S. Herrera-Ossa, G. Vogtmann, E. Wang, X. Hua, X. Qin, F. Zhao, W. Rahman, M. Yang, X. Brown, K. Zhu, B. Moore, S. Abnet, C. Zhang, T. Landi, M. T. Yu, K. Albert, P. Shi, J. 2025-12-22 doi:10.64898/2025.12.18.695273 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Biliverdin Reductase Catalytic Activity Is Essential for Malaria Resistance ]]> https://biorxiv.org/content/10.64898/2025.12.19.694840v1?rss=1 Mesquita, M. Figueiredo, A. Rastogi, S. T. Ramos, S. Pagnotta, S. Carlos, A. R. Cardoso, S. Novoa, A. Mallo, M. Paul, B. Jentho, E. Soares, M. 2025-12-22 doi:10.64898/2025.12.19.694840 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping ]]> https://biorxiv.org/content/10.64898/2025.12.19.695003v1?rss=1 Flores, J. P. Perreault, A. Drum, Z. A. Xu, C. Cruz Alonso, D. Petros, G. Wu, Y. Kim, H. Quiroga-Barber, I. Y. Sahasrabudhe, I. Demmerle, J. Wang, G. G. Cai, D. Phanstiel, D. H. 2025-12-22 doi:10.64898/2025.12.19.695003 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ A Digital Twin to Optimize Treatment Efficacy of Targeted Alpha-particle Therapies by Antibody-Radioconjugate Cocktails Against Solid Tumors ]]> https://biorxiv.org/content/10.64898/2025.12.19.695379v1?rss=1 Kavousanakis, M. Macher, R. Kevrekidis, Y. Sofou, S. 2025-12-22 doi:10.64898/2025.12.19.695379 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology ]]> https://biorxiv.org/content/10.64898/2025.12.19.695392v1?rss=1 Santos, A. R. d. Bonifaz, A. Bombassaro, A. Machado, A. C. d. S. Rodrigues, A. M. Borman, A. M. Chakrabarti, A. Chowdhary, A. Rediguieri, B. Johnson, E. M. Hagen, F. Queiroz-Telles Filho, F. Gonzalez, G. M. Garcia-Effron, G. Dib Ferreira Gremiao, I. Meis, J. F. Takahashi, J. P. F. Borba-Santos, L. P. MSC, M. Cappellan, P. Samia Nogueira Brilhante, R. Pereira, S. A. Goncalvez, S. S. Kidd, S. E. Zhang, S. X. Rudramurthy, S. M. Rozental, S. Cordoba, S. B. De Groot, T. Liu, W. Wiederhold, N. P. Meijer, E. F. J. Lockhart, S. R. Dufresne, P. 2025-12-23 doi:10.64898/2025.12.19.695392 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Guiding treatment response by spatiotemporal control of α-particle deposition in solid tumors: the case for 'affinity cocktails' of antibody-radioconjugates ]]> https://biorxiv.org/content/10.64898/2025.12.22.696075v1?rss=1 Nair, R. Sarkar, A. Hariharan, P. Kavousanakis, M. E. Chaudhari, R. Bastiaannet, R. Gabrielson, K. L. Sofou, S. 2025-12-25 doi:10.64898/2025.12.22.696075 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells ]]> https://biorxiv.org/content/10.64898/2025.12.25.696246v1?rss=1 Yuda, R. A. A. Bea, H. Kellett, V. Kim, J. Yang, F. Choijilsuren, H. B. Park, Y. Fu, Y. Ha, Z. Choi, J. Luo, L. Z. Sun, Z. Gao, B. Jeong, S. Resar, L. M. S. Jung, M. 2025-12-26 doi:10.64898/2025.12.25.696246 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Profiling miRNAs involved in Human Oligodendrocyte Precursor Cell Differentiation and Maturation ]]> https://biorxiv.org/content/10.64898/2025.12.25.696416v1?rss=1 Barzegar, M. Dhukhwa, A. Patel, V. N. Velasquez, F. C. Das, S. Patil, A. H. Halushka, M. K. Zack, D. Chamling, X. 2025-12-26 doi:10.64898/2025.12.25.696416 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Identification of molecular and clinical ALS subgroups based on TDP-43 loss of function molecular markers from population-based patient-derived iPS motor neurons ]]> https://biorxiv.org/content/10.64898/2025.12.28.696512v1?rss=1 Cheng, T. tripathi, s. Guo, Y. vedula, P. Li, R. Potanin, M. Soley, N. Yan, A. Y. Vatsaraj, I. Harris, C. Greenstein, J. Taylor, C. O. Coyne, A. Rothstein, J. D. 2025-12-29 doi:10.64898/2025.12.28.696512 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study ]]> https://biorxiv.org/content/10.64898/2025.12.30.697050v1?rss=1 Nekrutenko, A. Callan, D. Van Den Beek, M. Baker, D. Rogers, D. Guerler, A. Chilton, J. Clawson, H. Cain, S. O'Meara, T. Beavers, K. Schatz, M. Haeussler, M. Gruning, B. Goecks, J. Pond, S. K. 2025-12-31 doi:10.64898/2025.12.30.697050 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Ultrastructural changes at auditory nerve synapses following moderate noise exposure ]]> https://biorxiv.org/content/10.64898/2025.12.30.697061v1?rss=1 Gorman, D. Wong, N. F. Schupbach, C. W. DiCenso, S. L. Xu-Friedman, S. C. Boergens, K. M. Lauer, A. M. Salles, A. Xu-Friedman, M. A. 2025-12-31 doi:10.64898/2025.12.30.697061 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Rescuing Neurodevelopmental Deficits in AMPA Receptor Gain-of-Function Mutant ]]> https://biorxiv.org/content/10.64898/2025.12.30.697121v1?rss=1 Chen, C.-M. Huang, Y.-M. Chung, C.-C. Johnson, R. C. Tsai, C.-Y. Chen, Y.-H. Tan, H. L. Hsiao, F.-Y. Huganir, R. L. Chiu, S.-L. 2025-12-31 doi:10.64898/2025.12.30.697121 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Endothelial TLR4 signaling drives tissue inflammation, Claudin-5 internalization, and vascular barrier breakdown in a mouse model of neonatal meningitis ]]> https://biorxiv.org/content/10.64898/2025.12.31.697193v1?rss=1 Seegren, P. V. Rattner, A. Smallwood, P. M. Nathans, J. 2026-01-02 doi:10.64898/2025.12.31.697193 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology ]]> https://biorxiv.org/content/10.64898/2026.01.05.697007v1?rss=1 Robasky, K. Morrissey, J. Riedl, M. Dräger, A. Borth, N. Betenbaugh, M. J. Lewis, N. E. 2026-01-05 doi:10.64898/2026.01.05.697007 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Determination of diagnostic cycle threshold (Ct) cut-offs for qPCR-based prevalence surveys of soil-transmitted helminth infections ]]> https://biorxiv.org/content/10.64898/2026.01.05.697616v1?rss=1 Manuel, M. Pilotte, N. Timothy, J. W. S. Galagan, S. R. Israel, G. J. Connors, C. T. Omballa, V. Voss, M. Dadwal, U. Gonzalez, A. Ahlonsou, J. Chaima, D. Zondervenni Manoharan, Z. Rains, D. Asbjornsdottir, K. H. Williams, S. Luty, A. J. Ibikounle, M. Kalua, K. Bailey, R. L. Pullan, R. L. Walson, J. L. Ajjampur, S. S. R. 2026-01-05 doi:10.64898/2026.01.05.697616 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Regulatory T cells clonally expand and contribute to stromal cell function in fibrotic response to synthetic implants ]]> https://biorxiv.org/content/10.64898/2026.01.05.697727v1?rss=1 Mejias, J. C. Krishnan, K. Ruta, A. Ramanujam, A. S. Gray-Gaillard, E. F. Huyer, L. D. Maestas, D. R. Nagaraj, S. Yu, F. H. Rindone, A. N. Abraham, P. Browne, M. Fertig, E. J. Pardoll, D. M. Elisseeff, J. H. 2026-01-06 doi:10.64898/2026.01.05.697727 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Drug-tolerant persister cells reallocate carbon sources to fuel antioxidant metabolism for survival ]]> https://biorxiv.org/content/10.64898/2026.01.05.697775v1?rss=1 Li, M. Priem, B. Loftus, L. V. Betenbaugh, M. J. Pienta, K. J. Amend, S. R. 2026-01-06 doi:10.64898/2026.01.05.697775 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ SCREWx: A Screwless, Chronic, Recoverable, and Lightweight Neuropixels fixture for freely-moving rodents ]]> https://biorxiv.org/content/10.64898/2026.01.06.697790v1?rss=1 Cheng, A. DeWeese, T. Zhou, Y. Sueoka, Y. Koukuntla, S. Green, M. Cullen, K. Knierim, J. Graves, A. Harris, T. 2026-01-06 doi:10.64898/2026.01.06.697790 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Importins recognize the winged-helix fold of ETS transcription factors to mediate nuclear import ]]> https://biorxiv.org/content/10.64898/2026.01.06.697953v1?rss=1 McConville, M. Lankford, K. Bernardes, N. E. Walterscheid, A. Valadez, C. Brower, A. Chook, Y. M. Liszczak, G. 2026-01-06 doi:10.64898/2026.01.06.697953 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration ]]> https://biorxiv.org/content/10.64898/2026.01.06.697893v1?rss=1 Song, J.-J. Park, H. Choi, Y. Ryu, T. Shin, J. Kim, S.-H. Park, A. Wang, J. Biswas, D. Chou, S.-C. Ha, S. Jang, Y. Shin, Y. Chen, G. Hong, I. Wemmie, J. Svenningsson, P. Troncoso, J. Xu, J. Na, C. H. Dawson, V. L. Dawson, T. Kam, T.-I. 2026-01-07 doi:10.64898/2026.01.06.697893 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1 ]]> https://biorxiv.org/content/10.64898/2026.01.06.697917v1?rss=1 Shen, K. Su, R. Ji, Y. Zhang, W. Liu, X. Chai, X. Wang, J. Liu, B. Li, A. Wu, H. Wang, T. Zhou, X. Jiang, Z. Zhu, H. H. Dong, L. Zhu, Y. Dong, B. Pan, J. Wang, Q. Xue, W. 2026-01-07 doi:10.64898/2026.01.06.697917 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ High performance sorting of motor unit action potentials with EMUsort ]]> https://biorxiv.org/content/10.64898/2026.01.06.697952v1?rss=1 O'Connell, S. Michaels, J. A. Wang, R. Mamidipaka, S. Venkatesh, M. Aresh, N. Pachitariu, M. Pruszynski, J. A. Sober, S. J. Pandarinath, C. 2026-01-07 doi:10.64898/2026.01.06.697952 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Lipid-mediated reinforcement of FGF/MAPK signaling enables robust otic placode specification ]]> https://biorxiv.org/content/10.64898/2026.01.06.698011v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@12001ceorg.highwire.dtl.DTLVardef@56b35aorg.highwire.dtl.DTLVardef@1902eaorg.highwire.dtl.DTLVardef@e8817_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Peralta, S. R. Maiorana, N. Piacentino, M. L. 2026-01-07 doi:10.64898/2026.01.06.698011 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ mAbClust with AlphaFold 3 avoids hallucinations to define a quaternary broadly neutralizing HCV epitope ]]> https://biorxiv.org/content/10.64898/2026.01.06.698032v1?rss=1 Paul, H. T. Mimms, J. L. Aboueid, H. Sanchez Buitrago, L. Kulakova, L. Wilcox, X. Kuhn, K. Zhang, H. Toth, E. A. Skinner, N. Flyak, A. I. Ofek, G. Larman, H. B. Fuerst, T. R. Ray, S. C. Cox, A. L. Bailey, J. R. 2026-01-07 doi:10.64898/2026.01.06.698032 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Substrate stiffness and cellular microenvironment regulate cell and junction mechanics in iPSC-derived brain microvascular endothelial cells ]]> https://biorxiv.org/content/10.64898/2026.01.06.698052v1?rss=1 Yan, L. Gupta, U. Wang, H. Schrump, D. S. Stroka, K. M. 2026-01-07 doi:10.64898/2026.01.06.698052 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Protein tyrosine phosphatase receptor type kappa (PTPRκ) regulates Superior ON-Direction Selective Ganglion Cell development, facilitating image stabilization ]]> https://biorxiv.org/content/10.64898/2026.01.07.698158v1?rss=1 Lin, T.-H. Balraj, A. Al-Khindi, T. Kiraly, J. K. Dunn, F. A. Kolodkin, A. L. 2026-01-07 doi:10.64898/2026.01.07.698158 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Targeting EZH2 Oncogenic Splicing: Decoding the Regulatory Network and Antisense Correction ]]> https://biorxiv.org/content/10.64898/2026.01.07.697981v1?rss=1 Islam, M. R. Nagar, P. McNaughton, N. Heeamoni, S. A. Hasan, M. M. Kandel, S. Tsakiroglou, P. Dalton, W. B. Abdel-Wahab, O. Krainer, A. R. Rahman, M. A. 2026-01-08 doi:10.64898/2026.01.07.697981 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ A continuous viral vaccine biomanufacturing platform utilizing multiple bioreactor configurations ]]> https://biorxiv.org/content/10.64898/2026.01.09.698222v1?rss=1 90% viability. Peclet number-fit tracer studies confirmed near-ideal plug flow in the PFR, yielding a 10 h residence time and progressive infection as measured by gp64 signaling. Finally, a pCSTR with a residence time of 48 h exhibited sustained recombinant protein production. An integrated pilot cascade incorporating all reactors ran continuously for 5 days, maintaining stable CSTR cell densities and a measurable increase in infected cell diameter from 14.5 m to 16.1 m. Western blotting and EM of [~]100 nm VLPs in pCSTR effluent demonstrated platform success. Digital twin mechanistic models across four distinct stages of bioreactor operation and Hill-type relationships for rBV infection kinetics predicted cell growth and death for a 7-day run, demonstrating promise for designing continuous systems in silico and building a quantitative framework for scale-up and optimization. Our multi-stage reactor configuration represents a cell host- and product-agnostic production scheme, particularly for processes prone to product heterogeneity, and paves the way towards a true end-to-end continuous platform for myriad modalities in the future. ]]> Sargunas, J. Preim, B. Carman, D. Sarvari, T. Nold, N. M. Sharma, V. Pekosz, A. Heldt, C. L. Betenbaugh, M. 2026-01-11 doi:10.64898/2026.01.09.698222 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Dissociation of Diffusion and Perfusion Responses After Intracerebral Hemorrhage ]]> https://biorxiv.org/content/10.64898/2026.01.09.698716v1?rss=1 yang, x. Li, Y. Bibic, A. Wei, Z. 2026-01-12 doi:10.64898/2026.01.09.698716 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Threshold-Free Neural Network Models for Swim Bout Detection of Larval Zebrafish ]]> https://biorxiv.org/content/10.64898/2026.01.11.698899v1?rss=1 Wang, H. Kroeschell, G. Zhu, Y. Mumm, J. S. Yi, J. 2026-01-12 doi:10.64898/2026.01.11.698899 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Sox8 and Sox9 regulate differentiation and nuclear positioning of retinal Muller glia. ]]> https://biorxiv.org/content/10.64898/2026.01.12.698638v1?rss=1 Pannullo, N. Datta, D. Santiago, C. Tangeman, J. Jiang, L. Duncan, L. Blackshaw, S. 2026-01-13 doi:10.64898/2026.01.12.698638 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Gene dosage imbalance disrupts systemic metabolism in the Dp16 Down syndrome mouse model ]]> https://biorxiv.org/content/10.64898/2026.01.13.699318v1?rss=1 Chen, F. Saqib, M. Nguyen, C. M. Sarver, D. C. Yu, Y. E. Aja, S. Seldin, M. M. Wong, G. W. 2026-01-14 doi:10.64898/2026.01.13.699318 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Acute priming using elevated fluid viscosity recovers young-like single-cellsurveillance behaviors in aged human T cells ]]> https://biorxiv.org/content/10.64898/2026.01.13.699374v1?rss=1 Dance, Y. Amitrano, A. Saffron, A. Min, C. Thompson, L. Ge, Z. Smith, I. Macaluso, N. Ezenwanne, C. Milcik, N. Fennell, A. Pyndell, K. Stroka, K. Walston, J. Sun, S. Konstantopoulos, K. Phillip, J. M. 2026-01-14 doi:10.64898/2026.01.13.699374 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ An ancestral haplotype of P2RX5 yields a B-cell surface marker and a promising multi-lineage immunotherapy target ]]> https://biorxiv.org/content/10.64898/2026.01.14.698748v1?rss=1 Ang, Z. Castro, A. Paruzzo, L. Schimdt, C. Hasanali, Z. S. Hayer, K. E. Stella, F. Soldan, S. S. Diz, M. T. Kwok, C. Sainos, P. K. Ji, K. Krohl, P. J. Fine, J. Sehgal, P. Martinez, D. Spangler, J. B. Riley, J. L. Vogl, D. T. Porazzi, P. Pillai, V. Lieberman, P. M. Allman, D. Ruella, M. Thomas-Tikhonenko, A. 2026-01-14 doi:10.64898/2026.01.14.698748 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ The origin and evolution of amphibious hearing in pinnipeds ]]> https://biorxiv.org/content/10.64898/2026.01.14.699601v1?rss=1 Rule, J. P. Park, T. Kattan, M. Grohe, C. Taszus, R. Palmer, S. M. Hocking, D. P. Adams, J. W. Evans, A. R. Brennan, I. G. Pollock, T. I. Sanfelice, D. Marx, F. G. Kohno, N. Sabol, M. Stoessel, A. Flynn, J. J. Cooper, N. 2026-01-15 doi:10.64898/2026.01.14.699601 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Guessing reveals internal models of perceptual precision ]]> https://biorxiv.org/content/10.64898/2026.01.15.699528v1?rss=1 Myers, C. F. Firestone, C. Halberda, J. P. 2026-01-16 doi:10.64898/2026.01.15.699528 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ B7-H3-targeted natural killer cells effectively kill atypical teratoid / rhabdoid tumors and extend survival in orthotopic xenografts ]]> https://biorxiv.org/content/10.64898/2026.01.15.699746v1?rss=1 Choe, T. Chakravarti, S. Holl, N. J. Zinsky, M. T. Jones, D. G. Guchhait, S. Rahnama, R. Vorri, S. C. Amaral, A. Lucas, C.-H. G. Raabe, E. H. Bonifant, C. 2026-01-16 doi:10.64898/2026.01.15.699746 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Genetic architecture of miRNA expression in human brain and its contribution to brain disorders ]]> https://biorxiv.org/content/10.64898/2026.01.15.699788v1?rss=1 Patil, A. H. Rajpurohit, A. Lee, Y. K. Montoya, C. Wright, C. Pertia, G. Hyde, T. M. Kleinman, J. E. Shin, J. H. Weinberger, D. R. Hwang, T. 2026-01-16 doi:10.64898/2026.01.15.699788 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ NON-REDUNDANT ROLES OF COPPER TRANSPORTERS ATP7A AND ATP7B IN NORADRENERGIC SIGNALING ]]> https://biorxiv.org/content/10.64898/2026.01.15.699802v1?rss=1 ROY, S. Wang, Y. Aja, S. Sinha, N. Crawford, A. MacRenaris, K. Wade, A. Kim, K. Muchenditsi, A. Torres-Hernandez, L. Na, C.-H. Kralli, A. Petris, M. Taylor, A. O'Halloran, T. Tressler, C. Glunde, K. lutsenko, S. 2026-01-16 doi:10.64898/2026.01.15.699802 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing ]]> https://biorxiv.org/content/10.64898/2026.01.16.699998v1?rss=1 Hartweger, H. Ruprecht, C. Yao, K.-H. Laffont, P. Lima dos Reis, G. Zhou, P. Hägglöf, T. Binet, L. Loewe, M. Hong, J. P. Xiao, T. Sefik, E. Hernandez, B. Gazumyan, A. Jankovic, M. Seaman, M. S. Costa, G. Nelson, S. A. Clark, J. Kanatani, S. Wilson, P. C. Krammer, F. Levashina, E. A. Julien, J.-P. Wardemann, H. Sinnis, P. Stamatatos, L. Flavell, R. A. Nussenzweig, M. C. 2026-01-18 doi:10.64898/2026.01.16.699998 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Deconvolved tumor adipocyte proportions and high grade serous ovarian carcinoma survival ]]> https://biorxiv.org/content/10.64898/2026.01.14.699527v1?rss=1 Ivich, A. Grieshober, L. Davidson, N. R. Akatsu, G. Y. Peres, L. C. Hicks, S. C. Marks, J. R. Schildkraut, J. M. Doherty, J. A. Greene, C. S. 2026-01-19 doi:10.64898/2026.01.14.699527 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ The heat-ramp method to study regulated cell death in a pathogenic yeastCryptococcus neoformans ]]> https://biorxiv.org/content/10.64898/2026.01.19.700367v1?rss=1 Kulkarni, M. Liu, Y. Cheng, Q. Zhu, C. Kuhn, K. Shen, A. Jin, B. Casadevall, A. Lamb, H. M. Stolp, Z. D. Hardwick, J. M. 2026-01-19 doi:10.64898/2026.01.19.700367 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Fibrin barriers limit vancomycin penetration into staphylococcal abscess communities and maintain S. aureus in an unstressed, transcriptionally-responsive state ]]> https://biorxiv.org/content/10.64898/2026.01.20.700504v1?rss=1 Farhang, P. A. Huang, T. Braza, R. E. D. Anil, A. Davis, K. M. 2026-01-20 doi:10.64898/2026.01.20.700504 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Memory erasure by dopamine-gated retrospective learning ]]> https://biorxiv.org/content/10.64898/2026.01.17.700100v1?rss=1 Jeong, H. Zsembik, L. Farouq, F. Chakraborty, R. Belur, N. Zhou, M. Sanders, A. D. Wang, S. X. Srinivasan, A. Cox, S. M. L. Garr, E. Brooke, S. Janak, P. H. Leyton, M. Chen, R. Namboodiri, V. M. K. 2026-01-21 doi:10.64898/2026.01.17.700100 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ PFKFB2 Gates a Relationship Between Cardiac Glycolytic Regulation and Electrophysiological Function ]]> https://biorxiv.org/content/10.64898/2026.01.19.699308v1?rss=1 Harold, K. M. Blankenship, H. E. Minor, K. E. Mulligan, A. S. Loveland, B. L. Lee, C. F. Kinter, M. Kass, D. A. Stavrakis, S. Beckstead, M. J. Humphries, K. M. 2026-01-22 doi:10.64898/2026.01.19.699308 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Soft tissue morphology of the vomeronasal organ in Lontra canadensis and its osteological correlate: Implications for the evolution of the caniform accessory olfactory system ]]> https://biorxiv.org/content/10.64898/2026.01.19.700381v1?rss=1 Palmer, S. M. Foster, W. Capshaw, G. Michaud, M. Cooke, S. B. 2026-01-22 doi:10.64898/2026.01.19.700381 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Tailored Cell Cycle Modulation Enhances AAV Manufacturing: Balancing Arrest with Adaptive Stress Responses ]]> https://biorxiv.org/content/10.64898/2026.01.19.700387v1?rss=1 Wen, J. Sargunas, J. Carman, D. Greenshtein, N. Betenbaugh, M. 2026-01-22 doi:10.64898/2026.01.19.700387 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Neuronal microscale biophysical instability mediates macroscale network dynamics shaping pathological manifestations ]]> https://biorxiv.org/content/10.64898/2026.01.20.697254v1?rss=1 Kumar, V. Sanchez Franco, V. M. Ferry, F. S. Xie, Y. Hutson, A. N. Zhang, Y. J. Daniels, S. D. Nguyen, D. L. Spera, L. K. Snyder, E. M. Knauss, A. Sudhakar, S. L. Duan, G. Y. Paul, E. M. Tabuchi, M. 2026-01-22 doi:10.64898/2026.01.20.697254 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ FAK Inhibition Remodels the Metastatic ECM and Restores CD8+ T Cell Trafficking and Immunosurveillance ]]> https://biorxiv.org/content/10.64898/2026.01.21.700837v1?rss=1 Barth, N. D. Peng, B. Papanicolaou, M. Moughari, F. A. Duran, C. L. McGinnis, C. S. Dawson, J. C. Webb, E. R. Muir, M. Laing, F. Jung, Y. He, X.-Y. Satpathy, A. Egeblad, M. Haider, S. Natrajan, R. Oktay, M. H. Entenberg, D. Brunton, V. G. 2026-01-23 doi:10.64898/2026.01.21.700837 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Environmental and mutational modulation of collateral fitness effects informs their mechanisms ]]> https://biorxiv.org/content/10.64898/2026.01.22.699087v1?rss=1 Goff, C. Tsou, E.-Y. Mehlhoff, J. D. Ostermeier, M. 2026-01-23 doi:10.64898/2026.01.22.699087 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A genetically encoded microtubule bundler for causal dissection of microtubule bundling in cells ]]> https://biorxiv.org/content/10.64898/2026.01.22.700042v1?rss=1 Watari, S. Chinen, T. Kunitatsu, Y. Saitou, T. Takahashi, Y. Matsuura, K. Inoue, T. Inaba, H. 2026-01-23 doi:10.64898/2026.01.22.700042 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Encephalitic Alphavirus Infection Induces PARP-1 Hyperactivation Mediated Energy Collapse in Motor Neurons ]]> https://biorxiv.org/content/10.64898/2026.01.23.701280v1?rss=1 Williams, R. E. Pieterse, L. Patel, S. S. McLaren, M. W. Elrick, M. Griffin, D. E. 2026-01-23 doi:10.64898/2026.01.23.701280 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis ]]> https://biorxiv.org/content/10.64898/2026.01.23.701410v1?rss=1 Sanaullah, A. Brown, N. K. Shakya, P. Deegutla, A. Naseri, A. Langmead, B. Zhi, D. Zhang, S. 2026-01-25 doi:10.64898/2026.01.23.701410 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Fetal Thymic Expression Defines the Immunogenicity of Tumor Associated Antigens ]]> https://biorxiv.org/content/10.64898/2026.01.25.701584v1?rss=1 Long, A. H. Tooker, K. R. Pathoulas, N. M. Beppler, C. Bilich, T. Shankar, V. Bracey, N. A. Davis, M. M. 2026-01-27 doi:10.64898/2026.01.25.701584 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Multi-omics integration of malignant peripheral nerve sheath tumors identifies potential targets based on chromosome 8q status ]]> https://biorxiv.org/content/10.64898/2026.01.26.701599v1?rss=1 Garana, B. Wang, J. J. Acar, S. Oztosun, G. Makri, S. C. Borcherding, D. C. Zou, Y. Hutchinson-Bunch, C. Gritsenko, M. A. Piehowski, P. Pratilas, C. A. Hirbe, A. Gosline, S. J. 2026-01-27 doi:10.64898/2026.01.26.701599 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates ]]> https://biorxiv.org/content/10.64898/2026.01.27.702063v1?rss=1 Sweeten, A. P. Schatz, M. Phillippy, A. M. 2026-01-28 doi:10.64898/2026.01.27.702063 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Transforming macromolecular structures into simulations of self-assembly ]]> https://biorxiv.org/content/10.64898/2026.01.27.702082v1?rss=1 Ying, Y. M. Sang, M. Au, G. Chhibber, S. Du, Y. Fischer, J. A. Foley, S. L. Guo, S. Herzog-Pohl, I. Liu, Z. Roscom, H. Sohail, H. Takeshita, S. S. Johnson, M. E. 2026-01-28 doi:10.64898/2026.01.27.702082 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice ]]> https://biorxiv.org/content/10.64898/2026.01.22.701181v1?rss=1 Casaletto, J. A. Scott, R. T. Rathod, A. Jain, A. Chandar, A. Adapala, A. Prajapati, A. Nautiyal, A. Jayaraman, A. Boddu, A. Kelam, A. Jain, A. Pham, B. Shastry, D. Narayanan, D. Kosaraju, E. Paley, E. Uribe, F. P. Shahid, I. Ye, I. Wu, J. Lin, J. Srinivas, K. Della Monica, M. P. Hitt, M. Lin, M. Volkan, M. Kharya, M. Kaul, M. Jaffer, M. A. Ali, M. Chang, N. Z. Ashri, N. Couderc, N. B. Paladugu, P. Hiremath, R. Pathak, R. Dogra, S. Srinivas, S. Samaddar, S. Gopinath, S. Sawant, S. Cai, S. Pala, V. Nair, V. Shi, Z. Narayanan, S. Mundackal Thomas, D 2026-01-29 doi:10.64898/2026.01.22.701181 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Distinct control of T cell proliferation and effector function by partitioning of intracellular sulfur from cysteine ]]> https://biorxiv.org/content/10.64898/2026.01.27.702014v1?rss=1 Kelly, B. Cha, M. Gremelspacher, T. Martin, J. L. Andreis, M. Carrizo, G. E. Gidley, M. Stanczak, M. A. Apostolova, P. Sanin, D. E. Majumdar, A. Pearce, E. L. 2026-01-29 doi:10.64898/2026.01.27.702014 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A role for aquaporin (Aqp1) in the control of Cryptococcus neoformans cell morphology ]]> https://biorxiv.org/content/10.64898/2026.01.29.702379v1?rss=1 Stempinski, P. R. Patino-Medina, J. A. Hernandez, F. G. Jimenez, I. A. Rodrigues dos Santos Junior, S. Agre, P. Casadevall, A. 2026-01-29 doi:10.64898/2026.01.29.702379 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ BlueNuclei: automated identification and classification of live and dead transfected neurons using interpretable features ]]> https://biorxiv.org/content/10.64898/2026.01.29.702657v1?rss=1 Zha, Z. Jin, J. Margolis, R. L. Taliun, D. 2026-02-02 doi:10.64898/2026.01.29.702657 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Predicting early bactericidal activity of tuberculosis drug combinations using a translational pharmacokinetic-pharmacodynamic modeling approach ]]> https://biorxiv.org/content/10.64898/2026.01.29.702705v1?rss=1 de Castro Suarez, N. Nuermberger, E. L. Ernest, J. Savic, R. M. 2026-02-02 doi:10.64898/2026.01.29.702705 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Reinnervation of Muscle Targets Enhances the Separability of Motor Unit Signals Following Peripheral Nerve Transfers ]]> https://biorxiv.org/content/10.64898/2026.01.30.700058v1?rss=1 Quinn, K. N. Wang, S. Qin, L. Orsini, A. A. Griffith, K. Suresh, R. Kang, F. Perkins, P. L. Joshi, N. Lowe, A. L. Tuffaha, S. Thakor, N. V. 2026-02-02 doi:10.64898/2026.01.30.700058 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds ]]> https://biorxiv.org/content/10.64898/2026.01.31.703034v1?rss=1 Garcia, J. Ruta, A. Yu, F. Mejias, J. Pena, A. Rutkowski, N. Gray-Gaillard, E. Dubois, C. Cherry, C. Browne, M. Stivers, K. Maestas, D. Krishnan, K. Bell, A. Fertig, E. J. Cooney, C. Cooney, D. Byrne, P. Hillel, A. Smith, K. Ji, H. Anders, r. Pardoll, D. Ellisseeff, J. 2026-02-03 doi:10.64898/2026.01.31.703034 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Tissue Injury and Biomaterial Treatment Modulate Tumor Growth and Response to Immunotherapy ]]> https://biorxiv.org/content/10.64898/2026.02.02.703323v1?rss=1 Ruta, A. Gray-Gaillard, E. F. Garcia, J. A. Davenport Huyer, L. Mathkour, Y. Cherry, C. Patatanian, M. Mejias, J. C. Maestas, D. R. Krishnan, K. Abraham, P. Wolf, M. T. Smith, K. N. Pardoll, D. M. Elisseeff, J. H. 2026-02-04 doi:10.64898/2026.02.02.703323 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Multi-Objective Bayesian Optimization for Data-Efficient Bioprocess Development ]]> https://biorxiv.org/content/10.64898/2026.02.02.703372v1?rss=1 Ma, E. Morrissey, J. Duan, S. Lu, Z. Ranpura, S. Arora, S. Dabek, A. Liu, C. Gheorghe, A.-G. Fong, L. K. W. Sani, M. Vrljicak, P. Demirhan, D. Betenbaugh, M. 2026-02-04 doi:10.64898/2026.02.02.703372 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ APOE ε4 defines a systemic immune endophenotype independent of clinical trajectory in amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.64898/2026.02.02.703399v1?rss=1 Shvetcov, A. Thomson, S. Kwan, S. Thompson, T. G. Rothstein, J. D. Finney, C. A. 2026-02-04 doi:10.64898/2026.02.02.703399 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Film Recall Reveals Intact Event Memory but Impaired Sequence Memory in Temporal Lobe Epilepsy Patients ]]> https://biorxiv.org/content/10.64898/2026.02.03.702007v1?rss=1 Zhang, H. Farahani, F. Tefera, E. Botnick, B. Thapaliya, B. Lee, H. Borges, H. Zhang, W. Barr, W. Henin, S. Shi, Y. Chen, J. Liu, A. 2026-02-05 doi:10.64898/2026.02.03.702007 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Defining and rescuing pathomechanisms of myotubularin and autophagy disruption in a novel human cell model of Charcot-Marie-Tooth Type 4B3 ]]> https://biorxiv.org/content/10.64898/2026.02.03.703518v1?rss=1 Sharma, M. Mao, X. S. Stumpf, S. C. Wang, L. Chua, J. 2026-02-05 doi:10.64898/2026.02.03.703518 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ The changing contributions of weakness and the flexor synergy to post-stroke arm function over time: A kinematic re-examination of Twitchell ]]> https://biorxiv.org/content/10.64898/2026.02.03.703629v1?rss=1 Avni, I. Arac, A. Goldhamer, N. Binyamin-Netser, R. Kramer, S. Bar-Haim, S. Krakauer, J. W. Shmuelof, L. 2026-02-06 doi:10.64898/2026.02.03.703629 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ MV-ComBat and MV-CovBat: Multivariate Frameworks for Joint Harmonization of Multi-Metric Neuroimaging Data ]]> https://biorxiv.org/content/10.64898/2026.02.05.704069v1?rss=1 Ren, Z. Sadil, P. Lindquist, M. 2026-02-09 doi:10.64898/2026.02.05.704069 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Metabolic plasticity and virulence of Cryptococcus neoformans are regulated by mitochondrial homeostasis ]]> https://biorxiv.org/content/10.64898/2026.02.06.704083v1?rss=1 Patino-Medina, J. A. Camacho, E. Casadevall, A. 2026-02-10 doi:10.64898/2026.02.06.704083 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Cajal-Retzius fate specification is disrupted by constitutive activation of β-Catenin in hem progenitors ]]> https://biorxiv.org/content/10.64898/2026.02.09.704731v1?rss=1 Singh, A. Parichha, A. Datta, D. Chatterjee, M. Tole, S. 2026-02-10 doi:10.64898/2026.02.09.704731 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Intrathecal (G4C2)149 delivery in C9orf72-deficient mice yields mild motor dysfunction and ALS/FTD pathological hallmarks ]]> https://biorxiv.org/content/10.64898/2026.02.09.704060v1?rss=1 Russell, K. A. Shahrabi, A. A. Akerman, S. C. Byrne, M. D. Rothstein, J. D. Trotti, D. Jensen, B. K. Haeusler, A. R. 2026-02-11 doi:10.64898/2026.02.09.704060 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS ]]> https://biorxiv.org/content/10.64898/2026.02.09.704902v1?rss=1 Avila, T. U. Wang, J. Adams, L. Hu, E. Beltran, A. A. Kozlenkov, A. Urhekar, S. Gonzalez, A. B. M. Lee, H.-G. Calabrese, J. M. Dracheva, S. Beltran, A. S. Mah, W. Won, H. 2026-02-11 doi:10.64898/2026.02.09.704902 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Distinct spatial and non-spatial response properties of excitatory narrow-spike and burst-firing neurons in the marmoset auditory cortex ]]> https://biorxiv.org/content/10.64898/2026.02.10.705046v1?rss=1 Chen, C. Remington, E. D. Wang, X. 2026-02-11 doi:10.64898/2026.02.10.705046 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ TRIM32-UBQLN2-p62 axis promotes TDP-43 inclusion formation and amyloid aggregation through shuttle condensates ]]> https://biorxiv.org/content/10.64898/2026.02.11.705390v1?rss=1 He, Z. Zhou, J. Zhang, R. Meng, F. Nauen, D. W. Troncoso, J. C. Worley, P. F. Zhang, W. 2026-02-14 doi:10.64898/2026.02.11.705390 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Cortical maps diverge, representations converge along cortical hierarchy ]]> https://biorxiv.org/content/10.64898/2026.02.12.702420v1?rss=1 Petre, B. Lindquist, M. A. Wager, T. 2026-02-14 doi:10.64898/2026.02.12.702420 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Substrate binding and activation mechanism of the essential bacterial septal cell wall synthase FtsW ]]> https://biorxiv.org/content/10.64898/2026.02.13.705525v1?rss=1 Yepes, M. Yehya, N. N. Perez, A. Xiong, R. Britton, B. Lau, A. Y. Xiao, J. 2026-02-14 doi:10.64898/2026.02.13.705525 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Cell Ploidy Modulates Nucleolar Size via Dosage of Nucleolar Organizing Regions ]]> https://biorxiv.org/content/10.64898/2026.02.13.705825v1?rss=1 Bi, T. Rastogi, V. Zeineldin, M. Johnson, B. A. Dong, Y. Li, M. Larman, T. C. 2026-02-16 doi:10.64898/2026.02.13.705825 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex ]]> https://biorxiv.org/content/10.64898/2026.02.16.706214v1?rss=1 Kwon, S. H. Guo, B. Fang, C. Tippani, M. Bach, S. V. Miller, R. A. Maguire, S. E. Iatrou, A. Pertea, G. Eagles, N. J. Valentine, M. R. Oh, S. Jajoo, A. Balakundi, V. Du, Y. Nguyen, A. B. Zhang, R. Kaipa, U. M. Divecha, H. R. Lobana, J. S. Kleinman, J. E. Han, S. Daskalakis, N. P. Hyde, T. M. Collado-Torres, L. Page, S. C. Maynard, K. R. Hicks, S. C. Martinowich, K. 2026-02-17 doi:10.64898/2026.02.16.706214 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Brain morphological pattern is associated with the presence, severity, and transition of transdiagnostic psychiatric disorders in preadolescents ]]> https://biorxiv.org/content/10.64898/2026.02.17.706371v1?rss=1 kuang, n. Hammond, C. J. Salmeron, B. J. Xiao, X. Wang, D. Murray, L. Gu, H. Zhai, T. Zheng, H. Hill, J. Scavinicky, M. Lu, H. Janes, A. Ross, T. J. Yang, Y. 2026-02-18 doi:10.64898/2026.02.17.706371 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Insulin resistance modifies longitudinal multi-omics responses to habitual diet ]]> https://biorxiv.org/content/10.64898/2026.02.17.706440v1?rss=1 Park, H. Shen, X. Perelma, D. Berry, P. Lu, Y. Battersby, R. Miryam Schussler Fiorenza, S. Celli, A. Bejikian, C. Snyder, M. 2026-02-18 doi:10.64898/2026.02.17.706440 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ 3D, multi-omic imaging reveals molecular biomarkers of the pre-metastatic niche in lung cancer ]]> https://biorxiv.org/content/10.64898/2026.02.18.706515v1?rss=1 Michel, J. Forjaz, A. Queiroga, V. Casella, K. Stivers, K. Nguyen, H. Browne, M. Chen, F. Tam, A. Dhaygude, O. Fan, H. Maehira, H. Lin, C. T. Gray-Gaillard, E. Benducci, T. Yamauchi, S. Shoyombo, I. Xu, Z. Shenderov, E. Huang, P. Wirtz, D. Elisseeff, J. Chen, Y. Brock, M. V. Kiemen, A. L. Housseau, F. 2026-02-18 doi:10.64898/2026.02.18.706515 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study ]]> https://biorxiv.org/content/10.64898/2026.02.19.706769v1?rss=1 Wirbel, J. Saber, W. Martens, M. J. Peled, J. U. Andermann, T. M. Fei, T. Brooks, E. F. Doyle, B. Pincus, N. B. Jenq, R. R. Bar, M. Bolanos-Meade, J. Bratrude, B. Chhabra, S. Choi, S. W. Clark, W. Das, S. Elmariah, H. Gooptu, M. Holtan, S. G. Jones, R. J. Levine, J. E. Logan, B. R. Al Malki, M. M. Murthy, H. S. Rashidi, A. Rezvani, A. R. Riches, M. L. Runaas, L. Sandhu, K. Spahn, A. Sung, A. D. van den Brink, M. R. M. Horowitz, M. M. Hamadani, M. Kean, L. S. Perales, M.-A. Bhatt, A. S. 2026-02-20 doi:10.64898/2026.02.19.706769 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Epigenetic control of microglial mitochondrial immunity by KAT7 drives Alzheimer's disease pathogenesis ]]> https://biorxiv.org/content/10.64898/2026.02.19.706884v1?rss=1 Liu, Y. Fan, M. Ye, Y. Cheng, H. Y. Sun, S. Qiu, Z. 2026-02-20 doi:10.64898/2026.02.19.706884 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Discovery and dynamic pharmacology of μ-opioid receptor positive allosteric modulators ]]> https://biorxiv.org/content/10.64898/2026.02.20.707058v1?rss=1 O'Brien, E. S. Wang, J. Tanguturi, P. Li, M. White, E. Shiimura, Y. Paul, B. Appourchaux, K. Krishna Kumar, K. Huang, W. Majumdar, S. Traynor, J. R. Streicher, J. M. Chen, C. Kobilka, B. 2026-02-21 doi:10.64898/2026.02.20.707058 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation ]]> https://biorxiv.org/content/10.64898/2026.02.20.707063v1?rss=1 Shohat, H. Ciren, D. Arrones, A. Gentile, I. Ramakrishnan, S. Hendelman, A. Jenike, K. M. Brown, N. L. Luna-Ramos, J. Passalacqua, M. J. Satterlee, J. W. Fitzgerald, B. Baraja-Fonseca, V. Robitaille, G. M. Seman, B. M. Gillis, J. Van Eck, J. Prohens, J. Schatz, M. C. Lippman, Z. B. 2026-02-21 doi:10.64898/2026.02.20.707063 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Bottom-up and generative computations both uniquely explain social brain responses ]]> https://biorxiv.org/content/10.64898/2026.02.20.707082v1?rss=1 Malik, M. Kim, M. Shu, T. Liu, S. Isik, L. 2026-02-21 doi:10.64898/2026.02.20.707082 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Benchmarking foundation models for splice site and exon annotation ]]> https://biorxiv.org/content/10.64898/2026.02.22.707219v1?rss=1 He, Z. Florea, L. 2026-02-23 doi:10.64898/2026.02.22.707219 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity ]]> https://biorxiv.org/content/10.64898/2026.02.23.707200v1?rss=1 Russ, D. Saha, C. Paul, K. Zheng, Z. Law, T. F. Anguita-Maeso, M. Lundberg, D. S. Fitzpatrick, C. R. Dangl, J. L. 2026-02-24 doi:10.64898/2026.02.23.707200 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Formate reduces ischemic injury in the male heart by increasing protein S-nitrosation ]]> https://biorxiv.org/content/10.64898/2026.02.24.707768v1?rss=1 Garbus-Grant, H. Kabir, R. Ebenebe, O. V. Patel, P. Ashok, D. Quiroga, D. Das, S. O'Rourke, B. Crabtree, M. Kohr, M. J. 2026-02-26 doi:10.64898/2026.02.24.707768 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ The zinc metalloprotease ZMPSTE24 binds a distinct topological isoform of the tail-anchored protein IFITM3 ]]> https://biorxiv.org/content/10.64898/2026.02.27.708584v1?rss=1 Spear, E. D. Shilagardi, K. Sarju, S. Michaelis, S. 2026-03-02 doi:10.64898/2026.02.27.708584 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ An Inositol Receptor Orchestrates Carbon Utilization and Fungal Virulence ]]> https://biorxiv.org/content/10.64898/2026.03.02.708983v1?rss=1 Wang, Y. Tancer, R. Wear, M. Jackson, K. M. Zhang, Y. Gao, Y.-G. Nielsen, k. Casadevall, A. Xue, C. 2026-03-02 doi:10.64898/2026.03.02.708983 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Modulation of exploration-avoidance behaviors by vmPFC-projecting BLA neurons ]]> https://biorxiv.org/content/10.64898/2026.03.01.708792v1?rss=1 Huang, H. Mysore, S. Adwanikar, H. 2026-03-03 doi:10.64898/2026.03.01.708792 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Perceiving latent dynamics: Innate and coachable visual estimation of limb damping ]]> https://biorxiv.org/content/10.64898/2026.03.02.708982v1?rss=1 Huang, T. Huber, M. E. Brown, J. D. West, A. M. 2026-03-04 doi:10.64898/2026.03.02.708982 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Cryo-EM reveals a right-handed double-helix dimer architecture of PCDH15 critical for mechanotransduction ]]> https://biorxiv.org/content/10.64898/2026.03.02.709101v1?rss=1 Liang, X. Pathak, R. Qiu, X. Dillard, L. Twomey, E. C. Mueller, U. 2026-03-04 doi:10.64898/2026.03.02.709101 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Recovering signatures of archaic introgression using ancestral recombination graphs ]]> https://biorxiv.org/content/10.64898/2026.03.03.709416v1?rss=1 Zhang, Y. Biddanda, A. Johnson, S. A. O'Dushlaine, C. Moorjani, P. 2026-03-04 doi:10.64898/2026.03.03.709416 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Deep Learning Enabled 3D Multi-Omic Analysis Reveals Molecular Signatures of Heterogeneous Response to Chemotherapy in Pancreatic Cancer ]]> https://biorxiv.org/content/10.64898/2026.03.03.709150v1?rss=1 Forjaz, A. Mojdeganlou, H. Valentin, A. Wetzel, M. Lvovs, D. Deshpande, A. Shin, S. M. Piya, S. Rajapakshe, K. I. Guerrero, P. A. Pedro, B. A. Sidiropoulos, D. N. Wu, P.-H. Bernard Pagan, V. Demystifying Pancreatic Cancer Therapies TeamLab, Wirtz, D. Fertig, E. J. Kagohara, L. T. Ho, W. J. Kiemen, A. L. Wood, L. D. 2026-03-05 doi:10.64898/2026.03.03.709150 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Subclonal Complete Loss of CDKN1B as a Common Genomic Alteration in Prostate Cancer: Associations with Race and Prostate Cancer Outcomes ]]> https://biorxiv.org/content/10.64898/2026.03.03.709424v1?rss=1 Sfanos, K. Morton, R. Flores, J. Sosa, R. Ernst, S. Mummert, L. Hicks, J. Lotan, T. L. Lu, J. Jing, Y. Joshu, C. De Marzo, A. M. 2026-03-05 doi:10.64898/2026.03.03.709424 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Extent of damage to descending output from cortex rather than to specific cortical regions drives the emergence of flexor synergy in non-human primates ]]> https://biorxiv.org/content/10.64898/2026.03.04.709517v1?rss=1 Baines, A. Glover, I. S. Baker, A. M. Krakauer, J. W. Baker, S. N. 2026-03-06 doi:10.64898/2026.03.04.709517 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Clathrin is an Intrinsic Driver of Membrane Fission ]]> https://biorxiv.org/content/10.64898/2026.03.05.709932v1?rss=1 Bouzos, N. Foley, S. L. Potamianos, A. Jacobs, C. O. Johnson, M. E. Zeno, W. F. 2026-03-06 doi:10.64898/2026.03.05.709932 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ The Kinetic Intron Hypothesis ]]> https://biorxiv.org/content/10.64898/2026.03.04.709683v1?rss=1 Tisdale, G. 2026-03-07 doi:10.64898/2026.03.04.709683 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Epigenetic Silencing of Carotid Body TRPM7 Attenuates Hypertension in Obese Mice ]]> https://biorxiv.org/content/10.64898/2026.03.05.709322v1?rss=1 Shin, M. K. Roy, A. Paudel, O. Gudapati, S. Sham, J. Tang, W.-Y. Polotsky, V. 2026-03-07 doi:10.64898/2026.03.05.709322 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Positive Affect Modulates Early Valuation and Conflict Processing in Social Decision-Making ]]> https://biorxiv.org/content/10.64898/2026.03.05.709732v1?rss=1 Liu, Z. Liu, Y. Li, W. Cui, R. Liu, X. 2026-03-07 doi:10.64898/2026.03.05.709732 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ A Modular Framework for Automated Segmentation and Analysis of AFM Imaging of Chromatin Organization ]]> https://biorxiv.org/content/10.64898/2026.03.06.708946v1?rss=1 Sorensen, E. W. Pangeni, S. Merino-Urteaga, R. Murray, P. J. Rudnizky, S. Liao, T.-W. Rashid, F. Hwang, J. Yamadi, M. Feng, X. A. Zähringer, J. Gu, S. Davidson, I. F. Caccianini, L. Osorio-Valeriano, M. Farnung, L. Vos, S. Peters, J.-M. Berger, J. M. Wu, C. Hatzakis, N. S. Kirkegaard, J. B. Ha, T. 2026-03-07 doi:10.64898/2026.03.06.708946 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Reprogramming of neuronal genome function and phenotype by astrocytes ]]> https://biorxiv.org/content/10.64898/2026.03.07.710282v1?rss=1 200 astrocyte-responsive TF genes uncovered discrete functional clusters that promote neuronal maturity or stemness C_LIO_LIAstrocyte-responsive TF genes reprogram neuronal electrophysiology and neurite morphology C_LI ]]> Li, B. Hagy, K. Safi, A. Beer, M. A. Barrera, A. Geraghty, S. Rai, R. Pederson, A. N. Reisman, S. J. Love, M. I. Sullivan, P. F. Eroglu, C. Crawford, G. E. Gersbach, C. A. 2026-03-07 doi:10.64898/2026.03.07.710282 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ MS-BCR-DB: an integrated BCR repertoire database to mine humoral multiple sclerosis signatures ]]> https://biorxiv.org/content/10.64898/2026.03.05.709606v1?rss=1 Ballerini, C. Cardente, N. Abbate, M. F. Le Quy, K. Rincon, N. Wolfram, L. Lossius, A. Portaccio, E. Amato, M. P. Ballerini, C. Greiff, V. 2026-03-08 doi:10.64898/2026.03.05.709606 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes ]]> https://biorxiv.org/content/10.64898/2026.03.06.710148v1?rss=1 Nguyen, M. Schatz, M. 2026-03-08 doi:10.64898/2026.03.06.710148 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ Structured Schemas for LLM-Modeler Collaboration in Quantitative Systems Pharmacology Model Calibration ]]> https://biorxiv.org/content/10.64898/2026.03.05.709623v1?rss=1 Eliason, J. Popel, A. S. 2026-03-09 doi:10.64898/2026.03.05.709623 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ The extreme diversity of retinal amacrine cells has deep evolutionary roots ]]> https://biorxiv.org/content/10.64898/2026.03.07.710289v1?rss=1 Tommasini, D. Monavarfeshani, A. Dinesh, V. Hahn, J. Tangeman, J. Marre, O. Blackshaw, S. Puthussery, T. Sanes, J. Shekhar, K. 2026-03-09 doi:10.64898/2026.03.07.710289 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Monitoring Autonomic Tone During Spinal Cord Neuromodulation Using Wearble AURIS Sensor ]]> https://biorxiv.org/content/10.64898/2026.03.07.709943v1?rss=1 0.46). While time-domain shifts trended toward significance, complexity metrics showed robust sequential responses with large effect sizes, including the SD1/SD2 ratio (d = 1.474) and the DFA ratio (d = 1.091). These findings validate a sensor architecture that is durable, accessible, and provides the necessary technical foundation for closed-loop feedback and non-invasive clinical trials. ]]> Bohluli, R. S. Lopez, A. F. Perkins, P. L. Griffith, K. M. Babu, A. Cho, S.-M. Thakor, N. V. 2026-03-10 doi:10.64898/2026.03.07.709943 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Multivalent weak contacts shape chaperone-nascent protein interactions ]]> https://biorxiv.org/content/10.64898/2026.03.09.709851v1?rss=1 Rajasekaran, N. Toptygin, D. Liao, T.-W. Hilser, V. J. Ha, T. Kaiser, C. M. 2026-03-10 doi:10.64898/2026.03.09.709851 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery ]]> https://biorxiv.org/content/10.64898/2026.03.09.710548v1?rss=1 704.2 {micro}g/mL) indicating that they may be useful as scaffolds for future optimization for therapeutic applications. None of our peptides were found to considerably inhibit the emerging pathogen C. auris, suggesting the need for pathogen-specific down-selection of candidate peptides. Overall, we present a proof-of-principle, generative-AI-based approach for the rapid design of de novo antifungal peptides. ]]> Berman, D. S. Lewis, L. M. Curtis, T. D. Tiburzi, O. N. Smith, D. F. Casadevall, A. Dunphy, L. 2026-03-10 doi:10.64898/2026.03.09.710548 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Identification of compounds that repress DUX4 expression in facioscapulohumeral muscular dystrophy ]]> https://biorxiv.org/content/10.64898/2026.03.09.710626v1?rss=1 Chang, N. Moore, H. P. Himeda, C. L. O'Brien, T. E. Thomas, W. Jones, T. I. Jones, P. L. 2026-03-11 doi:10.64898/2026.03.09.710626 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders ]]> https://biorxiv.org/content/10.64898/2026.03.09.710649v1?rss=1 Zhou, J. Liu, C. Liu, X. Zhang, Y. Wei, Y. Shin, J. H. Maher, B. LIU, C. Luo, C. Wang, K. Weinberger, D. Han, S. 2026-03-11 doi:10.64898/2026.03.09.710649 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Exploring Links between Brain Image-Derived Phenotypes and Accelerometer-Measured Physical Activity in the UK Biobank ]]> https://biorxiv.org/content/10.64898/2026.03.10.710798v1?rss=1 Zhang, D. Leroux, A. Crainiceanu, C. M. Lindquist, M. A. 2026-03-11 doi:10.64898/2026.03.10.710798 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Cell-type-specific sustained value representations in the claustrum ]]> https://biorxiv.org/content/10.64898/2026.03.10.710905v1?rss=1 Taha, A. B. An, S. Y. Kim, S.-J. Daly, R. Cohen, J. Y. Brown, S. P. 2026-03-11 doi:10.64898/2026.03.10.710905 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Monocytes are biological sensors of aging and frailty in humans ]]> https://biorxiv.org/content/10.64898/2026.03.10.710601v1?rss=1 Min, C. Ezenwanne, C. Dance, Y. Macaluso, N. Thompson, L. Nidadavolu, L. Katuri, A. Szczesny, C. Langdon, J. Pearce, E. Abadir, P. Walston, J. Phillip, J. M. 2026-03-12 doi:10.64898/2026.03.10.710601 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Bat eye movements resolve a long-standing question in gaze control ]]> https://biorxiv.org/content/10.64898/2026.03.10.710949v1?rss=1 Chang, H. H. V. Capshaw, G. Skandalis, D. Moss, C. F. Cullen, K. E. 2026-03-12 doi:10.64898/2026.03.10.710949 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ SpotGraphs: Graph-based analysis of spatially resolved transcriptional data in R ]]> https://biorxiv.org/content/10.64898/2026.03.12.711347v1?rss=1 Lee, A. J. Sanin, D. E. 2026-03-16 doi:10.64898/2026.03.12.711347 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ A Deep Quantitative Proteome Turnover Platform for Human iPSC-derived Neurons ]]> https://biorxiv.org/content/10.64898/2026.03.14.711828v1?rss=1 Hao, L. Frankenfield, A. M. Shih, J. Zhang, T. Ni, J. Mazli, W. N. A. b. Lo, E. Liu, Y. Wang, J. 2026-03-16 doi:10.64898/2026.03.14.711828 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ A microfluidic platform for multi-marker profiling of extracellular vesicles from single-cell-derived clones ]]> https://biorxiv.org/content/10.64898/2026.03.13.711619v1?rss=1 Kim, J. Petrisor, D. Stoianovici, D. Amend, S. Pienta, K. Kim, C.-J. 2026-03-17 doi:10.64898/2026.03.13.711619 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Evidence that the protein phosphatase activity of PTEN contributes to embryonic development and tumour suppression in mice ]]> https://biorxiv.org/content/10.64898/2026.03.14.711778v1?rss=1 Tibarewal, P. Spinelli, L. Kriplani, N. Wise, H. Poncet, N. Marzano, G. Anderson, K. E. Grzes, K. M. Varyova, Z. Adil, M. Downes, C. P. Hawkins, P. T. Stephens, L. R. Storey, K. G. Cantrell, D. A. Vanhaesebroeck, B. Leslie, N. R. 2026-03-17 doi:10.64898/2026.03.14.711778 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer ]]> https://biorxiv.org/content/10.64898/2026.03.15.711961v1?rss=1 Park, W. Umeda, S. Hilmi, M. O'Connor, C. A. Sharma, R. Tezcan, N. Zhang, H. Zhu, Y. Schwartz, C. Yaqubie, A. Varghese, A. M. Soares, K. Florou, V. Kim, D. Maron, S. Argiles, G. Balogun, F. McIntyre, C. Kim, D. Yu, K. H. Chou, J. F. Hayashi, A. Keane, F. Khalil, D. N. Chatila, W. K. Capanu, M. Chaligne, R. Pishvaian, M. J. Bandlamudi, C. Lecomte, N. Berger, M. Basturk, O. Balachandran, V. Pe'er, D. Rousseau, B. Greenbaum, B. Sfeir, A. Iacobuzio-Donahue, C. A. Riaz, N. O'Reilly, E. M. 2026-03-17 doi:10.64898/2026.03.15.711961 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Convergent cortical temporal axis: common cortical oscillatory modes ]]> https://biorxiv.org/content/10.64898/2026.03.16.711992v1?rss=1 Liu, X. Wang, S. Wu, X. Long, S. He, L. Liu, L. Cui, R. Yang, G. 2026-03-17 doi:10.64898/2026.03.16.711992 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Loss of KMT2D accelerates hypertrophic chondrocyte differentiation and senescence by increasing mitochondrial ROS production ]]> https://biorxiv.org/content/10.64898/2026.03.18.712470v1?rss=1 Halldorsdottir, S. T. Ulfig, A. Petursson, S. Bjornsson, H. T. 2026-03-19 doi:10.64898/2026.03.18.712470 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ A bifunctional H/ACA snoRNP mediates both pseudouridylation and rRNA scaffolding during ribosome assembly ]]> https://biorxiv.org/content/10.64898/2026.03.20.713187v1?rss=1 Hafner, J. Thoms, M. Hamze, H. Forstner, A. Alidou-D'Anjou, I. Hebbachi, H. Kalinina, M. Hausharter, A. Favre, S. Lebaron, S. Ismail, S. Denk, T. Schlick, K. Fröhlich, T. Bhutada, P. Farquar, E. Schindlmaier, K. Sormaz, S. Hurt, E. Kressler, D. Henry, Y. Woodson, S. Dragon, F. Beckmann, R. Henras, A. K. Pertschy, B. 2026-03-21 doi:10.64898/2026.03.20.713187 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Acceleration and Velocity Dissociate Temporal Phases of Postural Control in Rhesus Macaques ]]> https://biorxiv.org/content/10.64898/2026.03.20.713289v1?rss=1 Leavitt Brown, O. M. E. Ramadan, B. A. Cullen, K. E. 2026-03-21 doi:10.64898/2026.03.20.713289 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Modes of programmed macrophage cell death govern outcome of cutaneous wound healing ]]> https://biorxiv.org/content/10.64898/2026.03.19.712831v1?rss=1 Injarabian, L. Reiche, N. Willenborg, S. Welcker, D. Bai, Y. Schoenenberg, E. Sanin, D. E. Tanevski, J. Pasparakis, M. Kashkar, H. Eming, S. A. 2026-03-22 doi:10.64898/2026.03.19.712831 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Computational aberration-corrected volumetric imaging of single retinal cells in the living eye ]]> https://biorxiv.org/content/10.64898/2026.03.21.712744v1?rss=1 20{o} FOV with >23 Hz volume rate. We leverage this structural and functional imaging modality to investigate three key aspects of CNS physiology through the living mouse retina, including: microglial process dynamics, vascular perfusion, and light evoked calcium fluxes in inner retinal neurons. PI-SLO is a versatile non-invasive platform for in vivo investigation of retinal and CNS physiology at the cellular level. ]]> Feng, G. Godinez, D. R. Li, Z. Nolen, S. Cho, H. Kimball, E. Duh, E. J. Johnson, T. V. Yi, J. 2026-03-24 doi:10.64898/2026.03.21.712744 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ ExposoGraph: An Interactive Platform for Carcinogen Bioactivation and Detoxification Pathway Visualization ]]> https://biorxiv.org/content/10.64898/2026.03.22.713456v1?rss=1 Pienta, K. Kazi, J. U. 2026-03-24 doi:10.64898/2026.03.22.713456 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ HIV-1 infection does not confer intrinsic resistance to cell death induced by cytotoxic T lymphocytes ]]> https://biorxiv.org/content/10.64898/2026.03.23.713717v1?rss=1 Bachmann, N. Kim, B. Simonetti, F. R. Kovacs, C. M. Hoh, R. Deeks, S. G. Siliciano, J. D. Siliciano, R. F. 2026-03-25 doi:10.64898/2026.03.23.713717 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Highly Stable Mn(V)-Nitrido and Nitrogen-Atom Transfer Reactivity within a De Novo Protein ]]> https://biorxiv.org/content/10.64898/2026.03.23.713767v1?rss=1 Thomas, J. Yadav, S. Oyala, P. H. Carta, V. Goldberg, D. P. Mann, S. I. 2026-03-25 doi:10.64898/2026.03.23.713767 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Repetitive extragenic palindrome (REP) elements are local, context-dependent, dual 3'UTR regulators in Escherichia coli ]]> https://biorxiv.org/content/10.64898/2026.03.23.713779v1?rss=1 Harris, F. E. Hu, Y. Verma, S. Adhya, S. Zhou, W. Xiao, J. 2026-03-25 doi:10.64898/2026.03.23.713779 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Deep-learning-enabled morphodynamic analysis of drug responses in a biomimetic fibrin-based 3D glioblastoma invasion model ]]> https://biorxiv.org/content/10.64898/2026.03.24.713307v1?rss=1 Dong, Z. Kethireddy, S. Kim, D. Ting, P. Lal, B. Lee, K. Kim, D.-H. Ahn, E. H. 2026-03-26 doi:10.64898/2026.03.24.713307 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ Mirdametinib and abemaciclib cooperate in atypical teratoid rhabdoid tumor to decrease proliferation and suppress tumor growth ]]> https://biorxiv.org/content/10.64898/2026.03.24.714018v1?rss=1 Liang, J. Deng, Y. Geethadevi, A. Malebranche, K. Findlay, T. R. Eberhart, C. G. Rubens, J. Raabe, E. H. 2026-03-27 doi:10.64898/2026.03.24.714018 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ FATE (Fish Aquarium with a Turbulent Environment): a turbulence-control facility for quantifying fish-flow interactions and collective behavior ]]> https://biorxiv.org/content/10.64898/2026.03.25.714166v1?rss=1 Calicchia, M. A. Ni, R. 2026-03-27 doi:10.64898/2026.03.25.714166 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Strategic template filtering accelerates fragment-based peptide docking ]]> https://biorxiv.org/content/10.64898/2026.03.26.714397v1?rss=1 Trabelsi, N. Varga, J. K. Khramushin, A. Lyskov, S. Schueler-Furman, O. 2026-03-30 doi:10.64898/2026.03.26.714397 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ A Reproducible Dual-Model Constraint-Based Framework for Exploring Hepatic Energy Metabolism Under Stachys affinis-Derived Short-Chain Fatty Acid Scenarios ]]> https://biorxiv.org/content/10.64898/2026.03.26.714589v1?rss=1 Nguyen, A. T. Nguyen, B. A. 2026-03-30 doi:10.64898/2026.03.26.714589 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ ATF4 Coordinates Transcriptomic and Structural Adaptations in Aging Muscle ]]> https://biorxiv.org/content/10.64898/2026.03.27.711928v1?rss=1 Crabtree, A. Khan, M. M. Scudese, E. Hernandez Perez, C. P. Venkhatesh, P. Marshall, A. G. Rodriguez, B. Garza Lopez, E. Ochayi, O. M. Dantas, E. H. M. Martin, P. Baffi, M. Scartoni, F. Mungai, M. Neikirk, K. Streeter, J. Pereira, R. O. Dai, D. F. Le, H. Mobley, H. Afolabi, J. Mobley, B. C. Wanjalla, C. N. Hall, D. Berry, J. Kovtun, O. Schafer, J. C. Schaffer, S. Katti, P. Evans, C. Kinder, A. George, J. G. McReynolds, M. Kirabo, A. Masenga, S. K. Hinton, A. 2026-03-30 doi:10.64898/2026.03.27.711928 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Haplotype-resolved centromeric chromatin organization from a complete diploid human genome ]]> https://biorxiv.org/content/10.64898/2026.03.27.714900v1?rss=1 Xu, Y. Loucks, H. Menendez, J. Ryabov, F. Lucas, J. K. Cechova, M. Morina, L. Xu, E. Dubocanin, D. Chittenden, C. Asri, M. Violich, I. Ortiz, C. Gardner, J. M. V. Hillaker, T. O'Rourke, S. McNulty, B. Potapova, T. A. Mitchell, M. W. Schwartz, J. P. Straight, A. F. Gerton, J. L. Timp, W. Alexandrov, I. A. Altemose, N. Miga, K. H. 2026-03-31 doi:10.64898/2026.03.27.714900 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Acyl Carrier Protein is Essential for Apicoplast Biogenesis in Malaria Parasites Independent of Fatty Acid Synthesis ]]> https://biorxiv.org/content/10.64898/2026.03.29.713301v1?rss=1 Geher, S. W. R. Falekun, S. Pita-Aquino, J. N. Swift, R. P. Okada, M. Jami-Alahmadi, Y. Wohlschlegel, J. A. Prigge, S. T. Sigala, P. A. 2026-03-31 doi:10.64898/2026.03.29.713301 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Signal, noise, and bias in phylogenetic inference:potential and limits to the resolution of phylogenetic trees in the phylogenomic era ]]> https://biorxiv.org/content/10.64898/2026.03.30.714540v1?rss=1 Dornburg, A. Su, Z. T. Jin, Y. Fisk, N. Townsend, J. P. 2026-04-01 doi:10.64898/2026.03.30.714540 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ STAPLE: automating spatial transcriptomics analysis and AI interpretation ]]> https://biorxiv.org/content/10.64898/2026.03.30.715127v1?rss=1 Lvovs, D. Quinn, J. Forjaz, A. Santana-Cruz, I. Stapleton, O. Vavikolanu, K. Wetzel, M. Data Science Hub TeamLab, Demystifying Pancreatic Cancer Therapies TeamLab, Pagan, V. B. Herb, B. R. Favorov, A. Kagohara, L. T. Kiemen, A. L. Maitra, A. Sidiropoulos, D. N. Tansey, W. Wood, L. Deshpande, A. Noble, M. Fertig, E. J. 2026-04-01 doi:10.64898/2026.03.30.715127 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Eye-head coordination during goal-directed orienting in mice ]]> https://biorxiv.org/content/10.64898/2026.03.30.715285v1?rss=1 Verdone, B. M. Chang, H. H. V. Roberts, D. C. Cullen, K. E. 2026-04-01 doi:10.64898/2026.03.30.715285 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Comparative transcriptomic analysis reveals signatures of selection for orb-weaving behavior in spiders ]]> https://biorxiv.org/content/10.64898/2026.03.30.715290v1?rss=1 Runnels, C. Miller, J. Gordus, A. G. 2026-04-01 doi:10.64898/2026.03.30.715290 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ The association of extracellular vesicle (EV)-cargo miR-330-3p with postoperative delirium and a potential mechanism of tau phosphorylation and neuron toxicity ]]> https://biorxiv.org/content/10.64898/2026.03.30.715460v1?rss=1 Fujimori, T. Chakraborty, S. Miyagawa, A. Tak, H. Yamaguchi, A. Hogue, C. W. Brown, C. H. Das, S. 2026-04-01 doi:10.64898/2026.03.30.715460 Cold Spring Harbor Laboratory Press 2026-04-01