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