bioRxiv Channel: University of California, San Diego https://biorxiv.org This feed contains articles for bioRxiv Channel "University of California, San Diego" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Efficient synergistic single-cell genome assembly ]]> https://biorxiv.org/content/10.1101/002972v1?rss=1 Narjes S. Movahedi Zeinab Taghavi Mallory Embree Harish Nagarajan Karsten Zengler Hamidreza Chitsaz 2014-02-24 doi:10.1101/002972 Cold Spring Harbor Laboratory Press 2014-02-24 <![CDATA[ Inhibition of protein translation by the DISC1-Boymaw fusion gene from a Scottish family with major psychiatric disorders ]]> https://biorxiv.org/content/10.1101/005710v1?rss=1 Baohu Ji Kerin Higa Minjung Kim Lynn Zhou Jared Young Mark Geyer Xianjin Zhou 2014-05-31 doi:10.1101/005710 Cold Spring Harbor Laboratory Press 2014-05-31 <![CDATA[ Boymaw, Overexpressed in Brains with Major Psychiatric Disorders, May Encode a Small Protein to Inhibit Mitochondrial Function and Protein Translation ]]> https://biorxiv.org/content/10.1101/005728v1?rss=1 Baohu Ji Minjung Kim Kerin Higa Xianjin Zhou 2014-05-31 doi:10.1101/005728 Cold Spring Harbor Laboratory Press 2014-05-31 <![CDATA[ Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele ]]> https://biorxiv.org/content/10.1101/017871v1?rss=1 Roy Ronen Glenn Tesler Ali Akbari Shay Zakov Noah A Rosenberg Vineet Bafna 2015-04-10 doi:10.1101/017871 Cold Spring Harbor Laboratory Press 2015-04-10 <![CDATA[ Selection for Intermediate Genotypes Enables a Key Innovation in Phage Lambda ]]> https://biorxiv.org/content/10.1101/018606v1?rss=1 Alita Burmeister Richard Lenski Justin Meyer 2015-04-27 doi:10.1101/018606 Cold Spring Harbor Laboratory Press 2015-04-27 <![CDATA[ Evolution of organismal stoichiometry in a 50,000-generation experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/021360v1?rss=1 Caroline B. Turner Brian D. Wade Justin R. Meyer Richard E. Lenski 2015-06-29 doi:10.1101/021360 Cold Spring Harbor Laboratory Press 2015-06-29 <![CDATA[ SSCM: A method to analyze and predict the pathogenicity of sequence variants ]]> https://biorxiv.org/content/10.1101/021527v1?rss=1 Sharad Vikram Matthew D Rasmussen Eric A Evans Imran S Haque 2015-06-26 doi:10.1101/021527 Cold Spring Harbor Laboratory Press 2015-06-26 <![CDATA[ Remodeling of the interphase chromatin domain structures in embryonic stem cells by targeted placement of human-specific regulatory loci ]]> https://biorxiv.org/content/10.1101/022913v1?rss=1 Gennadi Glinsky 2015-07-21 doi:10.1101/022913 Cold Spring Harbor Laboratory Press 2015-07-21 <![CDATA[ Endogenous human stem cell-associated retroviruses ]]> https://biorxiv.org/content/10.1101/024273v1?rss=1 Gennadi Glinsky 2015-08-10 doi:10.1101/024273 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Effects of reference databases’ refinements on the validity of molecular definitions of 15,371 candidate human-specific regulatory sequences ]]> https://biorxiv.org/content/10.1101/026435v1?rss=1 Gennadi Glinsky 2015-09-09 doi:10.1101/026435 Cold Spring Harbor Laboratory Press 2015-09-09 <![CDATA[ Molecular stripping in the NFκB/IκB/DNA genetic regulatory network ]]> https://biorxiv.org/content/10.1101/027912v1?rss=1 Davit Potoyan Weihua Zheng Elizabeth Komives Peter Wolynes 2015-10-02 doi:10.1101/027912 Cold Spring Harbor Laboratory Press 2015-10-02 <![CDATA[ Conservation patterns’ analysis of 18,364 candidate human-specific regulatory sequences revealed two distinct pathways of the human regulatory DNA divergence ]]> https://biorxiv.org/content/10.1101/029975v1?rss=1 Gennadi Glinsky 2015-10-27 doi:10.1101/029975 Cold Spring Harbor Laboratory Press 2015-10-27 <![CDATA[ Frequency and complexity of de novo structural mutation in autism ]]> https://biorxiv.org/content/10.1101/030270v1?rss=1 William M Brandler Danny Antaki Madhusudan Gujral Amina Noor Gabriel Rosanio Timothy R Chapman Daniel J Barrera Guan Ning Lin Dheeraj Malhotra Amanda C Watts Lawrence C Wong Jasper A Estabillo Therese E Gadomski Oanh Hong Karin V Fuentes Fajardo Abhishek Bhandari Renius Owen Michael Baughn Jeffrey Yuan Terry Solomon Alexandra G Moyzis Stephan J Sanders Gail E Reiner Keith K Vaux Charles M Strom Kang Zhang Alysson R Muotri Natacha Akshoomoff Suzanne M Leal Karen Pierce Eric Courchesne Lilia M Iakoucheva Christina Corsello Jonathan Sebat 2015-10-30 doi:10.1101/030270 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Reconstitution of CO2 regulation of SLAC1 anion channel and function of CO2-permeable PIP2;1 aquaporin as carbonic anhydrase 4 interactor ]]> https://biorxiv.org/content/10.1101/030296v1?rss=1 Cun Wang Honghong Hu Xue Qin Brian Zeise Danyun Xu Wouter-Jan Rappel Walter F Boron Julian I Schroeder 2015-11-10 doi:10.1101/030296 Cold Spring Harbor Laboratory Press 2015-11-10 <![CDATA[ Analysis of protein-coding genetic variation in 60,706 humans ]]> https://biorxiv.org/content/10.1101/030338v1?rss=1 Exome Aggregation Consortium Monkol Lek Konrad Karczewski Eric Minikel Kaitlin Samocha Eric Banks Timothy Fennell Anne O'Donnell-Luria James Ware Andrew Hill Beryl Cummings Taru Tukiainen Daniel Birnbaum Jack Kosmicki Laramie Duncan Karol Estrada Fengmei Zhao James Zou Emma Pierce-Hoffman Joanne Berghout David Cooper Nicole Deflaux Mark DePristo Ron Do Jason Flannick Menachem Fromer Laura Gauthier Jackie Goldstein Namrata Gupta Daniel Howrigan Adam Kiezun Mitja Kurki Ami Levy Moonshine Pradeep Natarajan Lorena Orozco Gina Peloso Ryan Poplin Manuel Rivas Valentin Ruano-Rubio Samuel Rose Douglas 2015-10-30 doi:10.1101/030338 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Targeted mutations on 3D hub loci alter spatial interaction environment ]]> https://biorxiv.org/content/10.1101/030999v1?rss=1 Bo Ding Lina Zheng David Medovoy Wei Wang 2015-11-09 doi:10.1101/030999 Cold Spring Harbor Laboratory Press 2015-11-09 <![CDATA[ Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors ]]> https://biorxiv.org/content/10.1101/036665v1?rss=1 Yoshinao Katsu Satomi Kohno Kaori Oka Michael E Baker 2016-01-14 doi:10.1101/036665 Cold Spring Harbor Laboratory Press 2016-01-14 <![CDATA[ Best Practices in Docking and Activity Prediction ]]> https://biorxiv.org/content/10.1101/039446v1?rss=1 Manuel Rueda Ruben Abagyan 2016-02-12 doi:10.1101/039446 Cold Spring Harbor Laboratory Press 2016-02-12 <![CDATA[ Tunable bet hedging in yeast responses to osmotic stress ]]> https://biorxiv.org/content/10.1101/039982v1?rss=1 Yoshikazu Hirate Samuel Bottani Wyming Lee Pang Suzannah Rutherford 2016-02-18 doi:10.1101/039982 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Combating Chagas Disease Through Inhibition of Tiam1, a Rho GTPase Guanine Nucleotide Exchange Factor ]]> https://biorxiv.org/content/10.1101/040121v1?rss=1 Chirag Krishna Li Xie Philip Bourne Celine DerMarderossian 2016-02-18 doi:10.1101/040121 Cold Spring Harbor Laboratory Press 2016-02-18 <![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[ Microarray analysis identifies malignant field signatures in biopsy samples at diagnosis predicting the likelihood of lethal disease in patients with localized Gleason 6 and 7 prostate cancer. ]]> https://biorxiv.org/content/10.1101/040519v1?rss=1 Gennadi Glinsky 2016-02-21 doi:10.1101/040519 Cold Spring Harbor Laboratory Press 2016-02-21 <![CDATA[ Hierarchical cortical transcriptome disorganization in autism ]]> https://biorxiv.org/content/10.1101/042937v1?rss=1 Michael V Lombardo Eric Courchesne Nathan E Lewis Tiziano Pramparo 2016-03-10 doi:10.1101/042937 Cold Spring Harbor Laboratory Press 2016-03-10 <![CDATA[ A method for downstream analysis of gene set enrichment results facilitates the biological interpretation of vaccine efficacy studies ]]> https://biorxiv.org/content/10.1101/043158v1?rss=1 Yan Tan Jernej Godec Felix Wu Pablo Tamayo Jill P Mesirov W Nicholas Haining 2016-04-11 doi:10.1101/043158 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Finding De novo methylated DNA motifs ]]> https://biorxiv.org/content/10.1101/043810v1?rss=1 Vu Ngo Wei Wang 2016-03-15 doi:10.1101/043810 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Testing pseudo-linear models of responses to natural scenes in primate retina ]]> https://biorxiv.org/content/10.1101/045336v1?rss=1 Alexander Heitman Nora Brackbill Martin Greschner Alexander Sher Alan M. Litke E.J. Chichilnisky 2016-03-24 doi:10.1101/045336 Cold Spring Harbor Laboratory Press 2016-03-24 <![CDATA[ Zfp423 regulates Sonic hedgehog signaling via primary cilium function ]]> https://biorxiv.org/content/10.1101/046961v1?rss=1 CHEN-JEI HONG Bruce A. Hamilton 2016-04-05 doi:10.1101/046961 Cold Spring Harbor Laboratory Press 2016-04-05 <![CDATA[ Assembly of Long Error-Prone Reads Using de Bruijn Graphs ]]> https://biorxiv.org/content/10.1101/048413v1?rss=1 Yu Lin Jeffrey Yuan Mikhail Kolmogorov Max W. Shen Pavel A. Pevzner 2016-04-13 doi:10.1101/048413 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/048942v1?rss=1 Dmitry Antipov Nolan Hartwick Max Shen Mikhail Raiko Alla Lapidus Pavel Pevzner 2016-04-15 doi:10.1101/048942 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Omics Discovery Index - Discovering and Linking Public Omics Datasets ]]> https://biorxiv.org/content/10.1101/049205v1?rss=1 Yasset Perez-Riverol Mingze Bai Felipe Leprevost Silvano Squizzato Young Mi Park Ove Kenneth Haug Adam J. Carroll Dylan Spalding Justin Paschall Mingxun Wang Noemi del-Toro Tobias Ternent Peng Zhang Nicola Buso Nuno Bandeira Eric Deutsch David S. Campbell Ronald C. Beavis Reza Salek Alexey Nesvizhskii Susanna-Assunta Sansone Christoph Steinbeck Rodrigo Lopez Juan Antonio Vizcaino Peipei Ping Henning Hermjakob 2016-04-18 doi:10.1101/049205 Cold Spring Harbor Laboratory Press 2016-04-18 <![CDATA[ Nonsinusoidal oscillations underlie pathological phase-amplitude coupling in the motor cortex in Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/049304v1?rss=1 Scott R Cole Erik J Peterson Roemer van der Meij Coralie de Hemptinne Philip A Starr Bradley Voytek 2016-04-19 doi:10.1101/049304 Cold Spring Harbor Laboratory Press 2016-04-19 <![CDATA[ Membrane tension is a key determinant of bud morphology in clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/050484v1?rss=1 Julian E. Hassinger George Oster David G. Drubin Padmini Rangamani 2016-04-27 doi:10.1101/050484 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Subiculum neurons map the current axis of travel ]]> https://biorxiv.org/content/10.1101/050641v1?rss=1 Jacob M Olson Kanyanat Tongprasearth Douglas M Nitz 2016-04-27 doi:10.1101/050641 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Reduced spatial integration in the ventral visual cortex underlies face recognition deficits in developmental prosopagnosia ]]> https://biorxiv.org/content/10.1101/051102v1?rss=1 Nathaniel Witthoft Sonia Poltoratski Mai Nguyen Golijeh Golarai Alina Liberman Karen F LaRocque Mary E Smith Kalanit Grill-Spector 2016-04-29 doi:10.1101/051102 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Separating spandrels from phenotypic targets of selection in adaptive molecular evolution ]]> https://biorxiv.org/content/10.1101/051862v1?rss=1 Stevan A Springer Michael Manhart Alexandre V Morozov 2016-05-05 doi:10.1101/051862 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Corticosteroid and progesterone transactivation of mineralocorticoid receptors from Amur sturgeon and tropical gar ]]> https://biorxiv.org/content/10.1101/053199v1?rss=1 Akira Sugimoto Kaori Oka Rui Sato Shinji Adachi Michael E. Baker Yoshinao Katsu 2016-05-13 doi:10.1101/053199 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ Transformation of Independent Oscillatory Inputs into Temporally Precise Rate Codes ]]> https://biorxiv.org/content/10.1101/054163v1?rss=1 David Tingley Andrew Alexander Laleh Quinn Andrea Chiba Douglas Nitz 2016-05-18 doi:10.1101/054163 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Scanning the Horizon: challenges and solutions for neuroimaging research ]]> https://biorxiv.org/content/10.1101/059188v1?rss=1 Russell Poldrack Chris I Baker Joke Durnez Krzysztof Gorgolewski Paul M Matthews Marcus Munafo Thomas Nichols Jean-Baptiste Poline Edward Vul Tal Yarkoni 2016-06-16 doi:10.1101/059188 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution ]]> https://biorxiv.org/content/10.1101/060756v1?rss=1 74%) of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on our previous findings, we repeated our analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support our published inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis. ]]> Tomislav Domazet-Loso Anne-Ruxanda Carvunis M. Mar Alba Matin S Sestak Robert Bakaric Rafik Neme Diethard Tautz 2016-06-26 doi:10.1101/060756 Cold Spring Harbor Laboratory Press 2016-06-26 <![CDATA[ Evaluating the diagnostic utility of applying a machine learning algorithm to diffusion tensor MRI measures in individuals with major depressive disorder ]]> https://biorxiv.org/content/10.1101/061119v1?rss=1 David M Schnyer Peter G Clasen Christopher Gonzalez Christopher G Beevers 2016-06-29 doi:10.1101/061119 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Preparatory encoding of the fine scale of human spatial attention ]]> https://biorxiv.org/content/10.1101/061259v1?rss=1 Bradley Voytek Jason Samaha Camarin E Rolle Zachery Greenberg Navdeep Gill Shai Porat Tahim Kader Sabahat Rahman Rick Malzyner Adam Gazzaley 2016-06-29 doi:10.1101/061259 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Assessment of single cell RNA-seq normalization methods ]]> https://biorxiv.org/content/10.1101/064329v1?rss=1 Bo Ding Lina Zheng Wei Wang 2016-07-17 doi:10.1101/064329 Cold Spring Harbor Laboratory Press 2016-07-17 <![CDATA[ Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/064683v1?rss=1 Michael V Lombardo Hyang Mi Moon Jennifer Su Theo D Palmer Eric Courchesne Tiziano Pramparo 2016-07-19 doi:10.1101/064683 Cold Spring Harbor Laboratory Press 2016-07-19 <![CDATA[ Mutations in EBF3 disturb transcriptional profiles and underlie a novel syndrome of intellectual disability, ataxia and facial dysmorphism ]]> https://biorxiv.org/content/10.1101/067454v1?rss=1 Frederike Leonie Harms Katta Mohan Girisha Andrew Alexander Hardigan Fanny Kortum Anju Shukla Malik Alawi Ashwin Dalal Lauren Brady Mark Tarnopolsky Lynne M. Bird Sophia Ceulemans Martina Bebin Kevin M. Bowling Susan M. Hiatt Edward J. Lose Michelle Primiano Wendy K. Chung Jane Juusola Zeynep C. Akdemir Matthew Bainbridge Wu-Lin Charng Margaret Drummond-Borg Mohammad K. Eldomery Ayman W. El-Hattab Mohammed A.M. Saleh Stephane Bezieau Benjamin Cogne Bertrand Isidor Sebastien Kury James R. Lupski Richard M. Myers Gregory M. Cooper Kerstin Kutsche 2016-08-03 doi:10.1101/067454 Cold Spring Harbor Laboratory Press 2016-08-03 <![CDATA[ Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes ]]> https://biorxiv.org/content/10.1101/072470v1?rss=1 Morgan N Price Kelly M Wetmore Robert Jordan Waters Mark Callaghan Jayashree Ray Jennifer V Kuehl Ryan A Melnyk Jacob S Lamson Yumi Suh Zuelma Esquivel Harini Sadeeshkumar Romy Chakraborty Benjamin E Rubin James Bristow Matthew J Blow Adam P Arkin Adam M Deutschbauer 2016-08-31 doi:10.1101/072470 Cold Spring Harbor Laboratory Press 2016-08-31 <![CDATA[ A living vector field reveals constraints on galactose network induction in yeast ]]> https://biorxiv.org/content/10.1101/073817v1?rss=1 Sarah R. Stockwell Scott A. Rifkin 2016-09-06 doi:10.1101/073817 Cold Spring Harbor Laboratory Press 2016-09-06 <![CDATA[ Assessing data quality in citizen science - preprint ]]> https://biorxiv.org/content/10.1101/074104v1?rss=1 Margaret Kosmala Andrea Wiggins Alexandra Swanson Brooke Simmons 2016-09-08 doi:10.1101/074104 Cold Spring Harbor Laboratory Press 2016-09-08 <![CDATA[ MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQ ]]> https://biorxiv.org/content/10.1101/074294v1?rss=1 Rongxin Fang Miao Yu Guoqiang Li Sora Chee Tristin Liu Anthony Schmitt Bing Ren 2016-09-09 doi:10.1101/074294 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Predicting binding free energies: Frontiers and benchmarks ]]> https://biorxiv.org/content/10.1101/074625v1?rss=1 David L. Mobley Michael K. Gilson 2016-09-11 doi:10.1101/074625 Cold Spring Harbor Laboratory Press 2016-09-11 <![CDATA[ A large collection of novel nematode-infecting microsporidia and their diverse interactions with C. elegans and other related nematodes ]]> https://biorxiv.org/content/10.1101/074757v1?rss=1 Gaotian Zhang Martin Sachse Marie-Christine Prevost Robert J Luallen Emily Troemel Marie-Anne Felix 2016-09-12 doi:10.1101/074757 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ Personalized genetic assessment of age associated Alzheimers disease risk ]]> https://biorxiv.org/content/10.1101/074864v1?rss=1 Rahul S. Desikan Chun Chieh Fan Yunpeng Wang Andrew J. Schork Howard J. Cabral Adrienne Cupples Wesley K. Thompson Lilah Besser Walter A. Kukull Dominic Holland Chi-Hua Chen James B. Brewer David S. Karow Karolina Kauppi Aree Witoelar Celeste M. Karch Luke W. Bonham Jennifer S. Yokoyama Howard J. Rosen Bruce L. Miller William P. Dillon David M. Wilson Christopher P. Hess Margaret Pericak-Vance Jonathan L. Haines Lindsay A. Farrer Richard Mayeux John Hardy Alison M. Goate Bradley T. Hyman Gerard D. Schellenberg Linda K. McEvoy Ole A. Andreassen Anders N. Dale 2016-09-13 doi:10.1101/074864 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset ]]> https://biorxiv.org/content/10.1101/077248v1?rss=1 Michael R. Shirts Christoph Klein Jason M. Swails Jian Yin Michael K. Gilson David L. Mobley David A. Case Ellen D. Zhong 2016-09-25 doi:10.1101/077248 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ Genome-wide profiling of heritable and de novo STR variations ]]> https://biorxiv.org/content/10.1101/077727v1?rss=1 Thomas Willems Dina Zielinski Assaf Gordon Melissa Gymrek Yaniv Erlich 2016-09-27 doi:10.1101/077727 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria ]]> https://biorxiv.org/content/10.1101/079137v1?rss=1 Kevin S Bonham Benjamin E Wolfe Rachel J Dutton 2016-10-05 doi:10.1101/079137 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP ]]> https://biorxiv.org/content/10.1101/080929v1?rss=1 Kim, D. Seo, S. W. Nam, H. Guzman, G. I. Gao, Y. Palsson, B. O. 2016-10-16 doi:10.1101/080929 Cold Spring Harbor Laboratory Press 2016-10-16 <![CDATA[ Field Potential Reflects the Balance of Synaptic Excitation and Inhibition ]]> https://biorxiv.org/content/10.1101/081125v1?rss=1 Gao, R. D. Peterson, E. J. Voytek, B. 2016-10-14 doi:10.1101/081125 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ p53 dynamically directs TFIID assembly on target gene promoters ]]> https://biorxiv.org/content/10.1101/083014v1?rss=1 Coleman, R. A. Qiao, Z. Singh, S. K. Peng, C. S. Cianfrocco, M. Zhang, Z. Song, L. Piasecka, A. Aldeborgh, H. Basishvili, G. Rice, W. Liu, W.-L. 2016-10-24 doi:10.1101/083014 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ Spatial tuning shifts increase the discriminability and fidelity of population codes in visual cortex ]]> https://biorxiv.org/content/10.1101/086892v1?rss=1 Vo, V. A. Sprague, T. Serences, J. 2016-11-10 doi:10.1101/086892 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Modulation of Body Mass Composition using Vestibular Nerve Stimulation. ]]> https://biorxiv.org/content/10.1101/087692v1?rss=1 McGeoch, P. D. McKeown, J. Ramachandran, V. S. 2016-11-14 doi:10.1101/087692 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations ]]> https://biorxiv.org/content/10.1101/088815v1?rss=1 Duncan, L. Yilmaz, Z. Walters, R. Goldstein, J. Antilla, V. Bulik-Sullivan, B. Ripke, S. Adan, R. Alfredsson, L. Ando, T. Andreassen, O. Aschauer, H. Baker, J. Barrett, J. Bencko, V. Bergen, A. Berrettini, W. Birgegard, A. Boni, C. Boraska Perica, V. Brandt, H. Bughardt, R. Carlberg, L. Cassina, M. Cesta, C. Cichon, S. Clementi, M. Cohen-Woods, S. Coleman, J. Cone, R. Courtet, P. Crawford, S. Crow, S. Crowley, J. Danner, U. Davis, O. de Zaan, M. Dedoussis, G. Degortes, D. DeSocio, J. Dick, D. Dikeos, D. Dina, C. Ding, B. Dmitrzak-Weglarz, M. Docampo 2016-11-25 doi:10.1101/088815 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ A genetic risk score to guide age-specific, personalized prostate cancer screening ]]> https://biorxiv.org/content/10.1101/089383v1?rss=1 Seibert, T. M. Fan, C. C. Wang, Y. Zuber, V. Karunamuni, R. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Nielsen, S. F. Weischer, M. Bisbjerg, R. Roder, M. A. Iversen, P. Key, T. J. Travis, R. C. Neal, D. E. Donovan, J. L. Hamdy, F. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, L. Brenner, H. 2016-11-25 doi:10.1101/089383 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls ]]> https://biorxiv.org/content/10.1101/092163v1?rss=1 Buckley, A. R. Standish, K. A. Bhutani, K. Ideker, T. Harismendy, O. Carter, H. Schork, N. J. 2016-12-07 doi:10.1101/092163 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Incorporating the Rate of Transcriptional Change Improves Construction of Transcription Factor Regulatory Networks ]]> https://biorxiv.org/content/10.1101/093807v1?rss=1 Desai, J. Sartor, R. C. Lawas, L. M. Jagadish SV, K. Doherty, C. J. 2016-12-24 doi:10.1101/093807 Cold Spring Harbor Laboratory Press 2016-12-24 <![CDATA[ A Data Citation Roadmap for Scholarly Data Repositories ]]> https://biorxiv.org/content/10.1101/097196v1?rss=1 Fenner, M. Crosas, M. Grethe, J. Kennedy, D. Hermjakob, H. Rocca-Serra, P. Berjon, R. Karcher, S. Martone, M. Clark, T. 2016-12-28 doi:10.1101/097196 Cold Spring Harbor Laboratory Press 2016-12-28 <![CDATA[ Polymer dynamics of Alp7A reveals two ‘critical’ concentrations that govern dynamically unstable actin-like proteins ]]> https://biorxiv.org/content/10.1101/098954v1?rss=1 Petek, N. A. Derman, A. I. Royal, J. A. Pogliano, J. Mullins, D. 2017-01-10 doi:10.1101/098954 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ Comprehensive characterization of neutrophil genome topology ]]> https://biorxiv.org/content/10.1101/100198v1?rss=1 Zhu, Y. Gong, K. Denholtz, M. Chandra, V. Kamps, M. P. Alber, F. Murre, C. 2017-01-15 doi:10.1101/100198 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Uniform Resolution of Compact Identifiers for Biomedical Data ]]> https://biorxiv.org/content/10.1101/101279v1?rss=1 Wimalaratne, S. Juty, N. Kunze, J. Janee, G. McMurry, J. A. Beard, N. Jimenez, R. Grethe, J. Hermjakob, H. Clark, T. 2017-01-18 doi:10.1101/101279 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Paternally inherited noncoding structural variants contribute to autism ]]> https://biorxiv.org/content/10.1101/102327v1?rss=1 Brandler, W. M. Antaki, D. Gujral, M. Kleiber, M. L. Maile, M. S. Hong, O. Chapman, T. R. Tan, S. Tandon, P. Pang, T. Tang, S. C. Vaux, K. K. Yang, Y. Harrington, E. Juul, S. Turner, D. J. Kingsmore, S. F. Gleeson, J. G. Kakaradov, B. Telenti, A. Venter, J. C. Corominas, R. Cormand, B. Rueda, I. Messer, K. S. Nievergelt, C. M. Arranz, M. J. Courchesne, E. Pierce, K. Muotri, A. R. Iakoucheva, L. M. Hervas, A. Corsello, C. Sebat, J. 2017-03-29 doi:10.1101/102327 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ A toolkit for tissue-specific protein degradation in C. elegans ]]> https://biorxiv.org/content/10.1101/104398v1?rss=1 Wang, S. Tang, N. H. Lara-Gonzalez, P. Prevo, B. Cheerambathur, D. K. Chisholm, A. D. Desai, A. Oegema, K. 2017-01-30 doi:10.1101/104398 Cold Spring Harbor Laboratory Press 2017-01-30 <![CDATA[ Preprint: Environmentally-Friendly Workflow Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking For the Discovery of Potent Anti-Viral Leads From Plants ]]> https://biorxiv.org/content/10.1101/106153v1?rss=1 nView larger version (23K):norg.highwire.dtl.DTLVardef@191802aorg.highwire.dtl.DTLVardef@1755ab8org.highwire.dtl.DTLVardef@196edf5org.highwire.dtl.DTLVardef@1e0a1e0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nothias, L.-F. Boutet-Mercey, S. Cachet, X. De La Torre, E. Laboureur, L. Gallard, J.-F. Retailleau, P. Brunelle, A. Dorrestein, P. C. Costa, J. Bedoya, L. M. Roussi, F. Leyssen, P. Alcami, J. Paolini, J. Litaudon, M. Touboul, D. 2017-02-05 doi:10.1101/106153 Cold Spring Harbor Laboratory Press 2017-02-05 <![CDATA[ Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism ]]> https://biorxiv.org/content/10.1101/107425v1?rss=1 Du, B. Zielinski, D. C. Palsson, B. O. 2017-02-09 doi:10.1101/107425 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ Modeling prediction error improves power of transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/108316v1?rss=1 Bhutani, K. Sarkar, A. Park, Y. Kellis, M. Schork, N. J. 2017-02-14 doi:10.1101/108316 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ Significance estimation for large scale untargeted metabolomics annotations ]]> https://biorxiv.org/content/10.1101/109389v1?rss=1 Scheubert, K. Hufsky, F. Petras, D. Wang, M. Nothias, L.-F. Duehrkop, K. Bandeira, N. Dorrestein, P. Boecker, S. 2017-02-17 doi:10.1101/109389 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories ]]> https://biorxiv.org/content/10.1101/113050v1?rss=1 Giraldez, M. D. Spengler, R. M. Etheridge, A. Godoy, P. M. Barczak, A. J. Srinivasan, S. De Hoff, P. L. Tanriverdi, K. Courtright, A. Lu, S. Khoory, J. Rubio, R. Baxter, D. Driedonks, T. A. P. Buermans, H. P. J. Nolte-'t Hoen, E. N. M. Jiang, H. Wang, K. Ghiran, I. Wang, Y. Van Keuren-Jensen, K. Freedman, J. E. Woodruff, P. G. Laurent, L. C. Erle, D. J. Galas, D. J. Tewari, M. 2017-05-17 doi:10.1101/113050 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ A yield-cost tradeoff governs Escherichia coli's decision between fermentation and respiration in carbon-limited growth ]]> https://biorxiv.org/content/10.1101/113183v1?rss=1 Mori, M. Marinari, E. De Martino, A. 2017-03-02 doi:10.1101/113183 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Decoys reveal the genetic and biochemical roles of redundant plant E3 ubiquitin ligases ]]> https://biorxiv.org/content/10.1101/115071v1?rss=1 Lee, C.-M. Feke, A. Adamchek, C. Webb, K. Pruneda-Paz, J. Bennett, E. J. Kay, S. A. Gendron, J. M. 2017-03-11 doi:10.1101/115071 Cold Spring Harbor Laboratory Press 2017-03-11 <![CDATA[ Optimizing Pedigrees: Using a Biasing System to Determine Likely Inheritance Systems ]]> https://biorxiv.org/content/10.1101/116160v1?rss=1 Ang, J. Y. 2017-03-15 doi:10.1101/116160 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ Cysteine Proteases Of Hookworm Necator Americanus As Virulence Factors And Implications For Future Drug Design: A Bioinformatics-Based Study ]]> https://biorxiv.org/content/10.1101/116921v1?rss=1 Banerjee, A. 2017-03-17 doi:10.1101/116921 Cold Spring Harbor Laboratory Press 2017-03-17 <![CDATA[ Guiding the design of bacterial signaling interactions using a coevolutionary landscape ]]> https://biorxiv.org/content/10.1101/116947v1?rss=1 Cheng, R. R. Haglund, E. Tiee, N. Morcos, F. Levine, H. Adams, J. A. Jennings, P. A. Onuchic, J. N. 2017-03-16 doi:10.1101/116947 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Genetic Variation In Adaptability And Pleiotropy In Budding Yeast ]]> https://biorxiv.org/content/10.1101/121749v1?rss=1 Jerison, E. R. Kryazhimskiy, S. Mitchell, J. Bloom, J. S. Kruglyak, L. Desai, M. M. 2017-03-29 doi:10.1101/121749 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ The ubiquity of directional and reciprocating motion in enzymes out of equilibrium ]]> https://biorxiv.org/content/10.1101/121848v1?rss=1 Slochower, D. R. Gilson, M. K. 2017-04-19 doi:10.1101/121848 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures ]]> https://biorxiv.org/content/10.1101/122689v1?rss=1 Bradley, A. R. Rose, A. S. Pavelka, A. Valasatava, Y. Duarte, J. M. Prlic, A. Rose, P. W. 2017-04-05 doi:10.1101/122689 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Four-Sphere Head Model For EEG Signals Revisited ]]> https://biorxiv.org/content/10.1101/124875v1?rss=1 Naess, S. Chintaluri, C. Ness, T. B. Dale, A. M. Einevoll, G. T. Wojcik, D. K. 2017-04-06 doi:10.1101/124875 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ A Versatile Genetic Tool For Post-Translational Control Of Gene Expression With A Small Molecule In Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/130120v1?rss=1 Sethi, S. Wang, J. W. 2017-04-24 doi:10.1101/130120 Cold Spring Harbor Laboratory Press 2017-04-24 <![CDATA[ Evolutionarily Conserved Roles For Blood-Brain Barrier Xenobiotic Transporters In Endogenous Steroid Partitioning And Behavior ]]> https://biorxiv.org/content/10.1101/131698v1?rss=1 Hindle, S. Munji, R. Dolghih, E. Gaskins, G. Orng, S. Ishimoto, H. Soung, A. DeSalvo, M. Kitamoto, T. Keiser, M. Jacobson, M. Daneman, R. Bainton, R. 2017-04-29 doi:10.1101/131698 Cold Spring Harbor Laboratory Press 2017-04-29 <![CDATA[ Diagnostic, Infection Timing and Incidence Surveillance Applications of High Dynamic Range Chemiluminescent HIV Immuno-Assay Platforms ]]> https://biorxiv.org/content/10.1101/132332v1?rss=1 Grebe, E. Welte, A. Hall, J. Keating, S. M. Facente, S. N. Marson, K. Martin, J. N. Little, S. J. Price, M. A. Kallas, E. G. Busch, M. P. Pilcher, C. D. Murphy, G. CEPHIA, 2017-05-03 doi:10.1101/132332 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ FCS In Closed Systems And Application For Membrane Nanotubes ]]> https://biorxiv.org/content/10.1101/134742v1?rss=1 Jiang, Y. Melnykov, A. Elson, E. L. 2017-05-05 doi:10.1101/134742 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Convergence of Wnt, Growth Factor and Trimeric G protein signals on Daple ]]> https://biorxiv.org/content/10.1101/137125v1?rss=1 Aznar, N. Dunkel, Y. Sun, N. Satterfield, K. He, F. Lopez-Sanchez, I. Ghassemian, M. Sahoo, D. Kufareva, I. Ghosh, P. 2017-06-12 doi:10.1101/137125 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Mapping The Malaria Parasite Drug-Able Genome Using In Vitro Evolution And Chemogenomics ]]> https://biorxiv.org/content/10.1101/139386v1?rss=1 Cowell, A. N. Istvan, E. S. Lukens, A. K. Gomez-Lorenzo, M. G. Vanaerschot, M. Sakata-Kato, T. Flannery, E. L. Magistrado, P. Abraham, M. Lamonte, G. M. Williams, R. M. Franco, V. Arriago, I. Linares, M. Bopp, S. Corey, V. Gnadig, N. F. Coburn-Flynn, O. Reimer, C. Gupta, P. Murithi, J. M. Fuchs, O. Sasaki, E. Kim, S. W. Teng, C. Wang, L. T. Willis, P. Siegel, D. Tanaseichuk, O. Zhong, Y. Zhou, Y. Otillie, S. Gamo, F.-J. Lee, M. C. S. Goldberg, D. E. Fidock, D. A. Wirth, D. F. Winzeler, E. A. 2017-05-22 doi:10.1101/139386 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements ]]> https://biorxiv.org/content/10.1101/141028v1?rss=1 Zhou, H. Kolodner, R. Putnam, C. D. Liang, J. Li, B.-z. Tan, A. P. 2017-05-23 doi:10.1101/141028 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ Forces driving cell sorting in Hydra ]]> https://biorxiv.org/content/10.1101/142976v1?rss=1 Cochet-Escartin, O. Locke, T. T. Shi, W. H. Steele, R. E. Collins, E.-M. S. 2017-05-27 doi:10.1101/142976 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ An Intracellular Pathogen Response Pathway Promotes Proteostasis In C. elegans ]]> https://biorxiv.org/content/10.1101/145235v1?rss=1 Reddy, K. C. Dror, T. Sowa, J. N. Panek, J. Chen, K. Lim, E. S. Wang, D. Troemel, E. R. 2017-06-02 doi:10.1101/145235 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ LSD1/KDM1A Maintains Genome-wide Homeostasis of Transcriptional Enhancers ]]> https://biorxiv.org/content/10.1101/146357v1?rss=1 Agarwal, S. Garay, P. M. Porter, R. S. Brookes, E. Murata-Nakamura, Y. Macfarlan, T. S. Ren, B. Iwase, S. 2017-06-05 doi:10.1101/146357 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ Homology-based hydrogen bond information improves crystallographic structures in the PDB ]]> https://biorxiv.org/content/10.1101/147231v1?rss=1 van Beusekom, B. Touw, W. G. Tatineni, M. Somani, S. Rajagopal, G. Luo, J. Gilliland, G. L. Perrakis, A. Joosten, R. P. 2017-06-07 doi:10.1101/147231 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ PinAPL-Py: a web-service for the analysis of CRISPR-Cas9 Screens ]]> https://biorxiv.org/content/10.1101/147462v1?rss=1 Spahn, P. N. Bath, T. Weiss, R. J. Kim, J. Esko, J. D. Lewis, N. E. Harismendy, O. 2017-06-08 doi:10.1101/147462 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ Akt/PKB enhances non-canonical Wnt signals by compartmentalizing β-Catenin ]]> https://biorxiv.org/content/10.1101/149351v1?rss=1 Aznar, N. Sun, N. Dunkel, Y. Ear, J. Buschman, M. Ghosh, P. 2017-06-13 doi:10.1101/149351 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/150581v1?rss=1 Sarkar, P. Switzer, A. Peters, C. Pogliano, J. Wigneshweraraj, S. 2017-06-15 doi:10.1101/150581 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology ]]> https://biorxiv.org/content/10.1101/150623v1?rss=1 Savas, J. N. Wang, Y.-Z. DeNardo, L. A. Martinez-Bartolome, S. McClatchy, D. B. Hark, T. J. Shanks, N. F. Cozzolino, K. A. Lavallee-Adam, M. Smukowski, S. N. Park, S. K. Kelly, J. W. Koo, E. H. Nakagawa, T. Masliah, E. Ghosh, A. Yates, J. R. 2017-06-15 doi:10.1101/150623 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Enhanced cross-modal activation of sensory cortex in mouse models of autism ]]> https://biorxiv.org/content/10.1101/150839v1?rss=1 Hattori, R. Südhof, T. C. Yamakawa, K. Hensch, T. K. 2017-08-20 doi:10.1101/150839 Cold Spring Harbor Laboratory Press 2017-08-20 <![CDATA[ Evolution of steroid specificity in human, chicken, alligator, frog and zebrafish mineralocorticoid receptors: Allosteric interactions affect steroid specificity ]]> https://biorxiv.org/content/10.1101/151233v1?rss=1 Katsu, Y. Oka, K. Baker, M. E. 2017-06-16 doi:10.1101/151233 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Proximity labeling reveals an extensive steady-state stress granule interactome and insights to neurodegeneration ]]> https://biorxiv.org/content/10.1101/152520v1?rss=1 100 previously unknown SG proteins in human cells, about 10% of which localize to SGs in a cell type- or stress type-dependent manner. Supporting a link between SG proteins and neurodegeneration, we demonstrate aberrant SG composition and subcellular distribution in iPSC-derived motor neurons from ALS patients, and identify several known and previously unidentified SG proteins that modify toxicity of mutant FUS and TDP-43 overexpression in Drosophila. We show that even in an unstressed steady-state, SG proteins form a densely-connected protein interaction network (PIN) and propose a model in which existing RNPs coalesce rapidly into microscopically visible granules that can act as gateways to pathological protein aggregation.nnHighlights O_LIAPEX proximity labeling of dynamic RNP granules identifies over 100 novel SG proteinsnC_LIO_LISG proteins form a densely-connected protein interaction network in unstressed cellsnC_LIO_LISystematic immunofluorescence analysis reveals stress- and cell type-specific SG compositionnC_LIO_LIALS motor neurons contain SGs with distinct content and subcellular distributionnC_LI ]]> Markmiller, S. Soltanieh, S. Server, K. Mak, R. Jin, W. Luo, E. Krach, F. Kankel, M. W. Sen, A. Bennett, E. J. Lecuyer, E. Yeo, G. 2017-06-20 doi:10.1101/152520 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Lis1 has two opposing modes of regulating cytoplasmic dynein ]]> https://biorxiv.org/content/10.1101/152645v1?rss=1 DeSantis, M. E. Cianfrocco, M. A. Htet, Z. M. Tran, P. T. Reck-Peterson, S. L. Leschziner, A. E. 2017-06-20 doi:10.1101/152645 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Differential roles of sleep spindles and sleep slow oscillations in memory consolidation ]]> https://biorxiv.org/content/10.1101/153007v1?rss=1 Wei, Y. Krishnan, G. P. Komarov, M. Bazhenov, M. 2017-06-21 doi:10.1101/153007 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Predator-secreted sulfolipids induce fear-like defense responses in C. elegans ]]> https://biorxiv.org/content/10.1101/153056v1?rss=1 Liu, Z. Kariya, M. J. Chute, C. D. Pribadi, A. K. Leinwand, S. G. Tong, A. Curran, K. P. Bose, N. Schroeder, F. C. Srinivasan, J. Chalasani, S. 2017-06-21 doi:10.1101/153056 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Polygenic hazard scores in preclinical Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/156331v1?rss=1 Tan, C. H. Sugrue, L. P. Broce, I. J. Tong, E. Tan, J. Hess, C. P. Dillon, W. P. Bonham, L. W. Yokoyama, J. S. Rabinovici, G. D. Rosen, H. J. Miller, B. L. Hyman, B. T. Schellenberg, G. D. Besser, L. M. Kukull, W. A. Karch, C. M. Brewer, J. B. Kauppi, K. McEvoy, L. K. Andreassen, O. A. Dale, A. M. Fan, C. C. Desikan, R. S. 2017-06-27 doi:10.1101/156331 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Immune-related genetic enrichment in frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/157875v1?rss=1 Broce, I. J. Karch, C. M. Wen, N. Fan, C. C. Wang, Y. Hong Tan, C. Kouri, N. Ross, O. A. Höglinger, G. U. Muller, U. Hardy, J. - International FTD-Genomics Consortium (IFGC), Momeni, P. Hess, C. P. Dillon, W. P. Miller, Z. A. Bonham, L. W. Rabinovici, G. D. Rosen, H. J. Schellenberg, G. D. Franke, A. Karlsen, T. H. Veldink, J. H. Ferrari, R. Yokoyama, J. S. Miller, B. L. Andreassen, O. A. Dale, A. M. Desikan, R. S. Sugrue, L. P. 2017-06-30 doi:10.1101/157875 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Positive Feedback Between Contractile Ring Myosin and Ring-Directed Cortical Flow Drives Cytokinesis ]]> https://biorxiv.org/content/10.1101/161133v1?rss=1 Khaliullin, R. Green, R. Shi, L. Berns, M. Gomez-Cavazos, J. S. Desai, A. Oegema, K. 2017-07-08 doi:10.1101/161133 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics ]]> https://biorxiv.org/content/10.1101/164640v1?rss=1 Bose, A. Platt, D. E. Parida, L. Paschou, P. Drineas, P. 2017-07-17 doi:10.1101/164640 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Estimating inflation in GWAS summary statistics due to variance distortion from cryptic relatedness ]]> https://biorxiv.org/content/10.1101/164939v1?rss=1 Holland, D. Fan, C.-C. Frei, O. Shadrin, A. A. Smeland, O. B. Sundar, V. S. Andreassen, O. A. Dale, A. M. 2017-07-17 doi:10.1101/164939 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Polygenic hazard score: an enrichment marker for Alzheimer’s associated amyloid and tau deposition ]]> https://biorxiv.org/content/10.1101/165373v1?rss=1 Tan, C. H. Fan, C. C. Mormino, E. C. Sugrue, L. P. Broce, I. J. Hess, C. P. Dillion, W. P. Bonham, L. W. Yokoyama, J. S. Karch, C. M. Brewer, J. B. Rabinovici, G. D. Miller, B. L. Schellenberg, G. D. Kauppi, K. Feldman, H. A. Holland, D. McEvoy, L. K. Hyman, B. T. Andreassen, O. A. Dale, A. M. Desikan, R. S. 2017-07-18 doi:10.1101/165373 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ ssbio: A Python Framework for Structural Systems Biology ]]> https://biorxiv.org/content/10.1101/165506v1?rss=1 Mih, N. Brunk, E. Chen, K. Catoiu, E. Sastry, A. Kavvas, E. Monk, J. M. Zhang, Z. Palsson, B. O. 2017-07-18 doi:10.1101/165506 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Systematic mapping of chromatin state landscapes during mouse development ]]> https://biorxiv.org/content/10.1101/166652v1?rss=1 Gorkin, D. Barozzi, I. Zhang, Y. Lee, A. Y. Lee, B. Zhao, Y. Wildberg, A. Ding, B. Zhang, B. Wang, M. Strattan, J. S. Davidson, J. M. Qiu, Y. Afzal, V. Akiyama, J. A. Plajzer-Frick, I. Pickle, C. S. Kato, M. Garvin, T. H. Pham, Q. T. Harrington, A. N. Mannion, B. J. Lee, E. A. Fukuda-Yuzawa, Y. He, Y. Preissl, S. Chee, S. Williams, B. A. Trout, D. Amrhein, H. Yang, H. Cherry, J. M. Shen, Y. Ecker, J. R. Wang, W. Dickel, D. E. Visel, A. Pennacchio, L. A. Ren, B. 2017-07-21 doi:10.1101/166652 Cold Spring Harbor Laboratory Press 2017-07-21 <![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[ Category learning biases sensory representations in visual cortex. ]]> https://biorxiv.org/content/10.1101/170845v1?rss=1 Ester, E. F. Sprague, T. C. Serences, J. T. 2017-08-01 doi:10.1101/170845 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ Role of KCC2-Dependent Potassium Efflux in 4-Aminopyridine-Induced Epileptiform Synchronization ]]> https://biorxiv.org/content/10.1101/171488v1?rss=1 Gonzalez, O. C. Shiri, Z. Krishnan, G. P. Myers, T. L. Williams, S. Avoli, M. Bazhenov, M. 2017-08-03 doi:10.1101/171488 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Dissociable components of the reward circuit are involved in appraisal versus choice ]]> https://biorxiv.org/content/10.1101/172320v1?rss=1 Shenhav, A. Karmarkar, U. R. 2017-08-03 doi:10.1101/172320 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ The antibody repertoire of colorectal cancer ]]> https://biorxiv.org/content/10.1101/176768v1?rss=1 Cha, S. W. Bonissone, S. Na, S. Pevzner, P. A. Bafna, V. 2017-08-15 doi:10.1101/176768 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ When conflict cannot be avoided: executive control dominates early selective sensory modulations during cognitive conflict ]]> https://biorxiv.org/content/10.1101/177394v1?rss=1 Itthipuripat, S. Deering, S. Serences, J. 2017-08-17 doi:10.1101/177394 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Building a genome browser with GIVE ]]> https://biorxiv.org/content/10.1101/177832v1?rss=1 Cao, X. Zheng, A. Zhong, S. 2017-08-18 doi:10.1101/177832 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid ]]> https://biorxiv.org/content/10.1101/179127v1?rss=1 Ponce-de-Leon, M. Tamarit, D. Calle-Espinosa, J. Mori, M. Latorre, A. Montero, F. Pereto, J. 2017-08-21 doi:10.1101/179127 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ A neural algorithm for a fundamental computing problem ]]> https://biorxiv.org/content/10.1101/180471v1?rss=1 Dasgupta, S. Stevens, C. F. Navlakha, S. 2017-08-25 doi:10.1101/180471 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments ]]> https://biorxiv.org/content/10.1101/180646v1?rss=1 130 PTM sites in Escherichia coli to unravel how PTMs regulate cell metabolism and fitness in response to environmental changes, such as the glucose-acetate diauxie. Using a new metabolic modeling approach, we found a significant fraction of post-translationally modified enzymes are predicted to control shifts in pathway usage following evolutionarily-important environmental changes. Genetic screens using Multiplex Automated Genome Engineering confirmed that these PTMs impact cellular fitness, especially under dynamically changing environments. Finally, mechanisms of how individual PTMs impact protein function were detailed using molecular dynamics simulations and enzyme assays for enolase, transaldolase, and serine hydroxymethyltransferase. Thus, by integrating whole-cell data and pathway modeling with detailed biochemical analysis, we unraveled how individual PTMs regulate enzymes, pathways, and phenotypes to adapt to sudden environmental changes. ]]> Brunk, E. Chang, R. L. Xia, J. Hefzi, H. Yurkovich, J. T. Kim, D. Buckmiller, E. Wang, H. Yang, C. Palsson, B. O. Church, G. Lewis, N. E. 2017-08-25 doi:10.1101/180646 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ CXCR4 involvement in neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/181693v1?rss=1 Bonham, L Karch, C Fan, C Tan, C Geier, E Wang, Y Wen, N Broce, I Li, Y Barkovich, M Ferrari, R Hardy, J Momeni, P Höeglinger, G Müller, U Hess, C Sugrue, L Dillon, W Schellenberg, G Miller, B Andreassen, O Dale, A Barkovich, A Yokoyama, J Desikan, R 2017-08-29 doi:10.1101/181693 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Functional characterization of 3D-protein structures informed by human genetic diversity ]]> https://biorxiv.org/content/10.1101/182287v1?rss=1 Hicks, M. Bartha, I. di Iulio, J. Abagyan, R. Venter, J. C. Telenti, A. 2017-08-29 doi:10.1101/182287 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection ]]> https://biorxiv.org/content/10.1101/183764v1?rss=1 LaMonte, G. Orjuela-Sanchez, P. Wang, L. Li, S. Swann, J. Cowell, A. Zou, B. Y. Abdel- Haleem Mohamed, A. Villa-Galarce, Z. Moreno, M. Tong-Rios, C. Vinetz, J. Lewis, N. Winzeler, E. A. 2017-10-02 doi:10.1101/183764 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Reversal of molecular pathology by RNA-targeting Cas9 in a myotonic dystrophy mouse model ]]> https://biorxiv.org/content/10.1101/184408v1?rss=1 Batra, R. Nelles, D. A. Krach, F. Thomas, J. D. Snjader, L. Blue, S. M. Aigner, S. Swanson, M. S. Yeo, G. W. 2017-09-04 doi:10.1101/184408 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Alpha oscillations control cortical gain by modulating excitatory-inhibitory background activity. ]]> https://biorxiv.org/content/10.1101/185074v1?rss=1 Peterson, E. J. Voytek, B. 2017-09-07 doi:10.1101/185074 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Origin of Slow Spontaneous Resting-State Neuronal Fluctuations in Brain Networks ]]> https://biorxiv.org/content/10.1101/186098v1?rss=1 Krishnan, G. P. Gonzalez, O. C. Bazhenov, M. 2017-09-07 doi:10.1101/186098 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci ]]> https://biorxiv.org/content/10.1101/190892v1?rss=1 Thurner, M. van de Bunt, M. Gaulton, K. Barrett, A. Bennett, A. J. Torres, J. M. Nylander, V. Mahajan, A. Bell, C. G. Lowe, R. Beck, S. Rakyan, V. K. Gloyn, A. L. McCarthy, M. I. 2017-09-19 doi:10.1101/190892 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Multi-platform discovery of haplotype-resolved structural variation in human genomes ]]> https://biorxiv.org/content/10.1101/193144v1?rss=1 Chaisson, M. J. P. Sanders, A. D. Zhao, X. Malhotra, A. Porubsky, D. Rausch, T. Gardner, E. J. Rodriguez, O. Guo, L. Collins, R. L. Fan, X. Wen, J. Handsaker, R. E. Fairley, S. Kronenberg, Z. N. Kong, X. Hormozdiari, F. Lee, D. Wenger, A. M. Hastie, A. Antaki, D. Audano, P. Brand, H. Cantsilieris, S. Cao, H. Cerveira, E. Chen, C. Chen, X. Chin, C.-S. Chong, Z. Chuang, N. T. Church, D. M. Clarke, L. Farrell, A. Flores, J. Galeev, T. David, G. Gujral, M. Guryev, V. Haynes-Heaton, W. Korlach, J. Kumar, S. Kwon, J. Y. Lee, J. E. Lee, J. Lee, W.-P. Lee, 2017-09-23 doi:10.1101/193144 Cold Spring Harbor Laboratory Press 2017-09-23 <![CDATA[ CYK-4 functions independently of its centralspindlin partner ZEN-4 to cellularize oocytes in germline syncytia ]]> https://biorxiv.org/content/10.1101/196279v1?rss=1 Lee, K.-Y. Green, R. A. Gutierrez, E. Gomez-Cavazos, J. S. Kolotuev, I. Wang, S. Desai, A. Groisman, A. Oegema, K. 2017-09-29 doi:10.1101/196279 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Mapping Cortical Brain Asymmetry in 17,141 Healthy Individuals Worldwide via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/196634v1?rss=1 Kong, X.-Z. Mathias, S. Guadalupe, T. Abe, C. Agartz, I. Akudjedu, T. N. Aleman, A. Alhusaini, S. Allen, N. B. Ames, D. Andreassen, O. A. Armstrong, N. J. Bergo, F. Bastin, M. E. Batalla, A. Bauer, J. Baune, B. Baur, R. Biederman, J. Blaine, S. K. Boedhoe, P. Boen, E. Bose, A. Bralten, J. Brandeis, D. Brem, S. Brodaty, H. Bröhl, H. Buitelaar, J. Bürger, C. Bülow, R. Calhoun, V. Calvo, A. Canales-Rodriguez, E. J. Canive, J. M. Cannon, D. M. Caparelli, E. C. Castellanos, F. X. Cavalleri, G. L. Cendes, F. Chaim-Avancini, T. M. Chant 2017-10-01 doi:10.1101/196634 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Evolving building blocks of rhythm: How human cognition creates music via cultural transmission ]]> https://biorxiv.org/content/10.1101/198390v1?rss=1 Ravignani, A. Thompson, B. Grossi, T. Delgado, T. Kirby, S. 2017-10-04 doi:10.1101/198390 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Revisiting microbe-metabolite interactions: doing better than random ]]> https://biorxiv.org/content/10.1101/2019.12.10.871905v1?rss=1 Morton, J. McDonald, D. Aksenov, A. Nothias-Scaglia, L.-F. Foulds, J. Quinn, R. A. Badri, M. Swenson, T. Van Goethem, M. Northen, T. Vazquez-Baeza, Y. Wang, M. Bokulich, N. Watters, A. Song, S. J. Bonneau, R. Dorrestein, P. Knight, R. 2019-12-16 doi:10.1101/2019.12.10.871905 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants ]]> https://biorxiv.org/content/10.1101/2019.12.11.873398v1?rss=1 Luo, C. Liu, H. Xie, F. Armand, E. J. Siletti, K. Bakken, T. Fang, R. Doyle, W. I. Hodge, R. D. Hu, L. Wang, B.-A. Zhang, Z. Preissl, S. Lee, D.-S. Zhou, J. Niu, S.-Y. Castanon, R. Bartlett, A. Rivkin, A. Wang, X. Lucero, J. Nery, J. R. Davis, D. A. Mash, D. C. Dixon, J. R. Linnarsson, S. Lein, E. Behrens, M. M. Ren, B. Mukamel, E. A. Ecker, J. R. 2019-12-12 doi:10.1101/2019.12.11.873398 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ High-throughput screening of the ReFRAME library identifies potential drug repurposing candidates for Trypanosoma cruzi ]]> https://biorxiv.org/content/10.1101/2019.12.11.873711v1?rss=1 Bernatchez, J. A. Chen, E. Hull, M. V. McNamara, C. W. McKerrow, J. H. Siqueira-Neto, J. L. 2019-12-16 doi:10.1101/2019.12.11.873711 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Voluntary and involuntary orienting of attention elicit similar lateralized changes in alpha activity and slow potential shifts over visual cortex ]]> https://biorxiv.org/content/10.1101/2019.12.12.874818v1?rss=1 Keefe, J. M. Stoermer, V. S. 2019-12-13 doi:10.1101/2019.12.12.874818 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Polycomb-mediated repression compensates for loss of postnatal DNA methylation in excitatory neurons ]]> https://biorxiv.org/content/10.1101/2019.12.20.883694v1?rss=1 Li, J. Pinto-Duarte, A. Zander, M. Lai, C.-Y. Osteen, J. Fang, L. Luo, C. Lucero, J. D. Gomez-Castanon, R. Nery, J. R. Silva-Garcia, I. Pang, Y. Sejnowski, T. J. Powell, S. B. Ecker, J. R. Mukamel, E. A. Behrens, M. M. 2019-12-20 doi:10.1101/2019.12.20.883694 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ HIV Care Prioritization using Phylogenetic Branch Length ]]> https://biorxiv.org/content/10.1101/2019.12.20.885202v1?rss=1 Moshiri, N. Smith, D. M. Mirarab, S. 2019-12-23 doi:10.1101/2019.12.20.885202 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats ]]> https://biorxiv.org/content/10.1101/2019.12.23.887158v1?rss=1 Mikheenko, A. Bzikadze, A. V. Gurevich, A. Miga, K. H. Pevzner, P. A. 2019-12-23 doi:10.1101/2019.12.23.887158 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Reclassification of SLC22 Transporters: Analysis of OAT, OCT, OCTN, and other Family Members Reveals 8 Functional Subgroups ]]> https://biorxiv.org/content/10.1101/2019.12.23.887299v1?rss=1 Engelhart, D. C. Granados, J. Nigam, S. K. Shi, D. Saier, M. H. Baker, M. E. 2019-12-26 doi:10.1101/2019.12.23.887299 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Parkinson's Disease-linked LRRK2 structure and model for microtubule interaction ]]> https://biorxiv.org/content/10.1101/2020.01.06.895367v1?rss=1 Deniston, C. K. Salogiannis, J. Mathea, S. Snead, D. M. Lahiri, I. Donosa, O. Watanabe, R. Böhning, J. Shiau, A. K. Knapp, S. Villa, E. Reck-Peterson, S. L. Leschziner, A. E. 2020-01-06 doi:10.1101/2020.01.06.895367 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ The Latent Genetic Structure of Impulsivity and its Relation to Internalizing Psychopathology ]]> https://biorxiv.org/content/10.1101/2020.01.07.897231v1?rss=1 Gustavson, D. E. Friedman, N. P. Fontanillas, P. Elson, S. L. the 23andMe Research Team, Palmer, A. A. Sanchez-Roige, S. 2020-01-08 doi:10.1101/2020.01.07.897231 Cold Spring Harbor Laboratory Press 2020-01-08 <![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[ Electrophysiological Frequency Band Ratio Measures Conflate Periodic and Aperiodic Neural Activity ]]> https://biorxiv.org/content/10.1101/2020.01.11.900977v1?rss=1 Donoghue, T. Dominguez, J. Voytek, B. 2020-01-11 doi:10.1101/2020.01.11.900977 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS. ]]> https://biorxiv.org/content/10.1101/2020.01.13.905091v1?rss=1 Aksenov, A. Laponogov, I. Zhang, Z. Doran, S. Belluomo, I. Veselkov, D. Bittremieux, W. Nothias, L. F. Nothias-Esposito, M. Maloney, K. N. Misra, B. B. Melnik, A. V. Jones, K. L. Dorrestein, K. Panitchpakdi, M. Ernst, M. van der Hooft, J. J. J. Gonzalez, M. Carazzone, C. Amézquita, A. Callewaert, C. Morton, J. Quinn, R. A. Bouslimani, A. Albarracin Orio, A. Petras, D. Smania, A. M. Couvillion, S. P. Burnet, M. C. Nicora, C. D. Zink, E. Metz, T. O. Artaev, V. Humston-Fulmer, E. Gregor, R. Meijler, M. M. Mizrahi, I. Eyal, S. Anderson, B. Dutton, R. J. 2020-01-14 doi:10.1101/2020.01.13.905091 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus ]]> https://biorxiv.org/content/10.1101/2020.01.16.909333v1?rss=1 Ma, J. Do, M. Le Gros, M. A. Peskin, C. S. Larabell, C. A. Mori, Y. Isaacson, S. A. 2020-01-17 doi:10.1101/2020.01.16.909333 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Mechanical Instability of Adherens Junctions Overrides Intrinsic Quiescence of Hair Follicle Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.01.17.909937v1?rss=1 Biswas, R. Banerjee, A. Lembo, S. Zhao, Z. Lakshmanan, V. Nakasaki, M. Kutyavin, V. Wright, G. Palakodeti, D. Ross, R. Jamora, C. Vasioukhin, V. Yan, J. Raghavan, S. 2020-01-17 doi:10.1101/2020.01.17.909937 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Lipid Sponge Droplets as Programmable Synthetic Organelles ]]> https://biorxiv.org/content/10.1101/2020.01.20.913350v1?rss=1 Bhattacharya, A. Niederholtmeyer, H. Podolsky, K. A. Bhattacharya, R. Song, J.-J. Brea, R. J. Tsai, C.-H. Sinha, S. K. Devaraj, N. K. 2020-01-21 doi:10.1101/2020.01.20.913350 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ AmpliconReconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer ]]> https://biorxiv.org/content/10.1101/2020.01.22.916031v1?rss=1 150kb) with next-generation sequencing (NGS) to resolve fCNAs at single-nucleotide resolution. AR uses an NGS-derived breakpoint graph alongside OM scaffolds to produce high-fidelity reconstructions. After validating performance by extensive simulations, we used AR to reconstruct fCNAs in seven cancer cell lines to reveal the complex architecture of ecDNA, breakage-fusion-bridge cycles, and other complex rearrangements. By distinguishing between chromosomal and extrachromosomal origins, and by reconstructing the rearrangement signatures associated with a given fCNAs generative mechanism, AR enables a more thorough understanding of the origins of fCNAs, and their functional consequences. ]]> Luebeck, J. Coruh, C. Dehkordi, S. R. Lange, J. T. Turner, K. M. Deshpande, V. Pai, D. A. Zhang, C. Rajkumar, U. Law, J. A. Mischel, P. S. Bafna, V. 2020-01-23 doi:10.1101/2020.01.22.916031 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Systematically gap-filling the genome-scale model of CHO cells ]]> https://biorxiv.org/content/10.1101/2020.01.27.921296v1?rss=1 Fouladiha, H. Marashi, S.-A. Li, S. Vaziri, B. Lewis, N. E. 2020-01-27 doi:10.1101/2020.01.27.921296 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function ]]> https://biorxiv.org/content/10.1101/2020.01.30.925917v1?rss=1 Shen, Z. Hoeksema, M. Ouyang, Z. Benner, C. Glass, C. 2020-01-31 doi:10.1101/2020.01.30.925917 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A single-cell RNAseq atlas of the pathogenic stage of Schistosoma mansoni identifies a key regulator of blood feeding ]]> https://biorxiv.org/content/10.1101/2020.02.03.932004v1?rss=1 Wendt, G. Zhao, L. Chen, R. Lu, C. O'Donoghue, A. J. Caffrey, C. R. Collins, J. 2020-02-03 doi:10.1101/2020.02.03.932004 Cold Spring Harbor Laboratory Press 2020-02-03 <![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[ Structure-function analysis of the maize bulliform cell cuticle and its role in dehydration and leaf rolling ]]> https://biorxiv.org/content/10.1101/2020.02.06.937011v1?rss=1 Matschi, S. Vasquez, M. F. Bourgault, R. Steinbach, P. Chamness, J. Kaczmar, N. Gore, M. A. Molina, I. Smith, L. G. 2020-02-07 doi:10.1101/2020.02.06.937011 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator ]]> https://biorxiv.org/content/10.1101/2020.02.13.948422v1?rss=1 Bergstrom, E. N. Barnes, M. Martincorena, I. Alexandrov, L. B. 2020-02-14 doi:10.1101/2020.02.13.948422 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Fluid and crystallised intelligence are associated with distinct regionalisation patterns of cortical morphology ]]> https://biorxiv.org/content/10.1101/2020.02.13.948596v1?rss=1 Palmer, C. E. Zhao, W. Loughnan, R. J. Fan, C.-C. Thompson, W. K. Dale, A. M. Jernigan, T. L. 2020-02-14 doi:10.1101/2020.02.13.948596 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans. ]]> https://biorxiv.org/content/10.1101/2020.02.18.955245v1?rss=1 How, J. J. Navlakha, S. Chalasani, S. H. 2020-02-19 doi:10.1101/2020.02.18.955245 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Novelty-seeking impairment in addiction ]]> https://biorxiv.org/content/10.1101/2020.02.19.955989v1?rss=1 Cogliati Dezza, I. Noel, X. Cleeremans, A. Yu, A. 2020-02-21 doi:10.1101/2020.02.19.955989 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Slow Axonal Transport and Presynaptic Targeting of Clathrin Packets ]]> https://biorxiv.org/content/10.1101/2020.02.20.958140v1?rss=1 Ganguly, A. Wernert, F. Phan, S. BOASSA, D. Das, U. Sharma, R. Caillol, G. Han, X. Yates, J. R. Ellisman, M. Leterrier, C. Roy, S. 2020-02-20 doi:10.1101/2020.02.20.958140 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Systematic functional analysis of Rab GTPasesreveals limits of neuronal robustness in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.02.21.959452v1?rss=1 Kohrs, F. E. Daumann, I.-M. Pavlovic, B. Jin, E. J. Lin, S.-C. Port, F. Kiral, F. R. Wolfenberg, H. Mathejczyk, T. F. Chan, C.-C. Boutros, M. Hiesinger, P. R. 2020-02-22 doi:10.1101/2020.02.21.959452 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Improved reference genome of the arboviral vector Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2020.02.28.969527v1?rss=1 Palatini, U. Masri, R. Cosme, L. V. Koren, S. Thibaud-Nissen, F. Biedler, J. K. Krsticevic, F. Johnston, S. Halbach, R. Crawford, J. E. Antoshechkin, I. Failloux, A.-B. Pischedda, E. Marconcini, M. Ghurye, J. Rhie, A. Sharma, A. Karagodin, D. A. Jentette, J. Gamez, S. Miesen, P. Caccone, A. Sharakhova, M. V. Tu, Z. Papathanos, P. A. van Rij, R. P. Akbari, O. S. Powell, J. Phillippy, A. M. Bonizzoni, M. 2020-02-28 doi:10.1101/2020.02.28.969527 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Lipid availability influences the metabolic maturation of human pluripotent stem cell-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.03.14.991927v1?rss=1 Zhang, H. Badur, M. G. Spiering, S. Divakaruni, A. Meurs, N. E. Yu, M. S. Colas, A. R. Murphy, A. N. Mercola, M. Metallo, C. M. 2020-03-15 doi:10.1101/2020.03.14.991927 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Discovering biomarkers of chemotherapy resistance using in vitro evolution in haploid human cells ]]> https://biorxiv.org/content/10.1101/2020.03.17.982181v1?rss=1 Jado, J. C. Dow, M. Fonseca, G. Carolino, K. Ideker, T. Carter, H. Winzeler, E. 2020-03-18 doi:10.1101/2020.03.17.982181 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines ]]> https://biorxiv.org/content/10.1101/2020.03.17.995290v1?rss=1 Lin, D. Yalamanchili, H. Zhang, X. Lewis, N. E. Alves, C. L. Groot, J. Arnsdorf, J. Peterson Bjorn, S. Wulff, T. Rude Voldborg, B. G. Zhou, Y. Zhang, B. 2020-03-18 doi:10.1101/2020.03.17.995290 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Nitrogen starvation and stationary phase lipophagy have distinct molecular mechanisms ]]> https://biorxiv.org/content/10.1101/2020.03.17.996082v1?rss=1 Kumar, R. Rahman, M. A. Nazarko, T. Y. 2020-03-18 doi:10.1101/2020.03.17.996082 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses ]]> https://biorxiv.org/content/10.1101/2020.03.18.997296v1?rss=1 Poudel, S. Tsunemoto, H. Seif, Y. Sastry, A. V. Szubin, R. Xu, S. Machado, H. Olson, C. Anand, A. Pogliano, J. Nizet, V. Palsson, B. 2020-03-20 doi:10.1101/2020.03.18.997296 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Transcriptome-wide profiles of circular RNA and RNA binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression ]]> https://biorxiv.org/content/10.1101/2020.03.19.997478v1?rss=1 Okholm, T. L. H. Sathe, S. Park, S. S. Kamstrup, A. B. Rasmussen, A. M. Shankar, A. Fristrup, N. Nielsen, M. M. Vang, S. Dyrskjoet, L. Aigner, S. Damgaard, C. K. Yeo, G. Pedersen, J. S. 2020-03-20 doi:10.1101/2020.03.19.997478 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Multiplexed photo-activation of mRNA with single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.03.19.999631v1?rss=1 Zhang, D. Jin, S. Piao, X. Devaraj, N. K. 2020-03-20 doi:10.1101/2020.03.19.999631 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2020.03.21.001693v1?rss=1 Kubo, N. Ishii, H. Xiong, X. Bianco, S. Meitinger, F. Hu, R. Hocker, J. D. Conte, M. Gorkin, D. Yu, M. Li, B. Dixon, J. Hu, M. Nicodemi, M. Zhao, H. Ren, B. 2020-03-23 doi:10.1101/2020.03.21.001693 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Structural insights into assembly and function of the RSC chromatin remodeling complex ]]> https://biorxiv.org/content/10.1101/2020.03.24.006361v1?rss=1 Leschziner, A. E. Baker, R. W. Reimer, J. M. Dominguez, R. Carman, P. J. Arakawa, T. 2020-03-25 doi:10.1101/2020.03.24.006361 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ DDX5 targets tissue-specific RNAs to promote intestine tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.03.25.006668v1?rss=1 Abbasi, N. Long, T. Li, Y. Ma, E. Yee, B. A. Patel, P. R. Sayed, I. M. Varki, N. Das, S. Ghosh, P. Yeo, G. W. Huang, W. J. M. 2020-03-26 doi:10.1101/2020.03.25.006668 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Incorporation of a nucleoside analog maps genome repair sites in post-mitotic human neurons ]]> https://biorxiv.org/content/10.1101/2020.03.25.008490v1?rss=1 Reid, D. A. Reed, P. J. Schlachetzki, J. C. M. Chou, G. Chandran, S. Lu, A. T. McClain, C. A. Ooi, J. H. Jones, J. R. Linker, S. B. Tsui, E. C. Ricciardulli, A. S. Lau, S. Schafer, S. T. Horvath, S. Dixon, J. R. Hah, N. Glass, C. K. Gage, F. H. 2020-03-26 doi:10.1101/2020.03.25.008490 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Self-administration of heroin by vapor inhalation in female Wistar rats ]]> https://biorxiv.org/content/10.1101/2020.03.30.016725v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Taffe, M. A. 2020-03-31 doi:10.1101/2020.03.30.016725 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse ]]> https://biorxiv.org/content/10.1101/2020.03.31.016972v1?rss=1 Bakken, T. E. Jorstad, N. L. Hu, Q. Lake, B. B. Tian, W. Kalmbach, B. E. Crow, M. Hodge, R. D. Krienen, F. M. Sorensen, S. A. Eggermont, J. Yao, Z. Aevermann, B. D. Aldridge, A. I. Bartlett, A. Bertagnolli, D. Casper, T. Castanon, R. G. Crichton, K. Daigle, T. L. Dalley, R. Dee, N. Dembrow, N. Diep, D. Ding, S.-L. Dong, W. Fang, R. Fischer, S. Goldman, M. Goldy, J. Graybuck, L. T. Herb, B. R. Hou, X. Kancherla, J. Kroll, M. Lathia, K. Lew, B. v. Li, Y. E. Liu, C. S. Liu, H. Mahurkar, A. McMillen, D. Miller, J. A. Moussa, M. Nery, J. R. Orvis, J. Ow 2020-04-01 doi:10.1101/2020.03.31.016972 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Granadaene Photobleaching Reduces the Virulence and Increases Antimicrobial Susceptibility of Streptococcus agalactiae ]]> https://biorxiv.org/content/10.1101/2020.03.31.019372v1?rss=1 Jusuf, S. Dong, P.-T. Hui, J. Ulloa, E. R. Liu, G. Y. Cheng, J.-X. 2020-04-01 doi:10.1101/2020.03.31.019372 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain ]]> https://biorxiv.org/content/10.1101/2020.04.01.019612v1?rss=1 Zhang, Z. Zhou, J. Tan, P. Pang, Y. Rivkin, A. Kirchgessner, M. A. Williams, E. Lee, C.-T. Liu, H. Franklin, A. D. Miyazaki, P. A. Bartlett, A. Aldridge, A. Vu, M. Boggeman, L. Fitzpatrick, C. Nery, J. Castanon, R. G. Rashid, M. Jacobs, M. Ito, T. Dominguez, B. Niu, S.-Y. Smith, J. B. O'Connor, C. Lee, K.-F. Jin, X. Mukamel, E. A. Behrens, M. M. Ecker, J. R. Callaway, E. M. 2020-04-03 doi:10.1101/2020.04.01.019612 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.04.01.020792v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@c2c756org.highwire.dtl.DTLVardef@1ad1c03org.highwire.dtl.DTLVardef@a4136org.highwire.dtl.DTLVardef@13f403f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kellman, B. P. Baghdassarian, H. M. Pramparo, T. Shamie, I. Gazestani, V. H. Begzati, A. Li, S. Nalabolu, S. Murray, S. Lopez, L. Pierce, K. Courchesne, E. Lewis, N. E. 2020-04-03 doi:10.1101/2020.04.01.020792 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Rapid community-driven development of a SARS-CoV-2 tissue simulator ]]> https://biorxiv.org/content/10.1101/2020.04.02.019075v1?rss=1 Wang, Y. Heiland, R. Craig, M. Davis, C. L. Ford Versypt, A. N. Jenner, A. Ozik, J. Collier, N. Cockrell, C. Becker, A. An, G. Glazier, J. A. Narayanan, A. Smith, A. M. Macklin, P. 2020-04-05 doi:10.1101/2020.04.02.019075 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Mutational profiling of micro-dissected pre-malignant lesions from archived specimens ]]> https://biorxiv.org/content/10.1101/2020.04.05.026708v1?rss=1 Nachmanson, D. Steward, J. Yao, H. Jeong, E. O'Keefe, T. J. Hasteh, F. Jepsen, K. Hirst, G. L. Esserman, L. J. Borowsky, A. D. Harismendy, O. 2020-04-06 doi:10.1101/2020.04.05.026708 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ POMK Regulates Dystroglycan Function via LARGE-mediated Elongation of Matriglycan ]]> https://biorxiv.org/content/10.1101/2020.04.06.007948v1?rss=1 Walimbe, A. S. Yang, T. Yonekawa, T. Venzke, D. Anderson, M. E. Torelli, S. Manzur, A. Yu, L. Devereaux, M. Cuellar, M. Prouty, S. O'Campo Landa, S. Muntoni, F. Campbell, K. P. 2020-04-07 doi:10.1101/2020.04.06.007948 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Physical and mental health characteristics of adults with subjective cognitive decline: A study of 3,407 people aged 18-81 years from an MTurk-based U.S. national sample ]]> https://biorxiv.org/content/10.1101/2020.04.07.029553v1?rss=1 Van Patten, R. Nguyen, T. Mahmood, Z. Lee, E. Daly, R. Palmer, B. Wu, T.-C. Tu, X. Jeste, D. V. Twamley, E. 2020-04-07 doi:10.1101/2020.04.07.029553 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Visual function restoration in genetically blind mice via endogenous cellular reprogramming ]]> https://biorxiv.org/content/10.1101/2020.04.08.030981v1?rss=1 Fu, X. Zhu, J. Duan, Y. Li, G. Cai, H. Zheng, L. Zhang, C. Jin, Z. Fu, X.-D. Zhang, K. 2020-04-08 doi:10.1101/2020.04.08.030981 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia ]]> https://biorxiv.org/content/10.1101/2020.04.09.033555v1?rss=1 Bachireddy, P. Ennis, C. Nguyen, V. Clement, K. Gohil, S. H. Shukla, S. A. Forman, J. Barkas, N. Freeman, S. Bavli, N. Elagina, L. Leshchiner, I. Mohammad, A. W. Rassenti, L. Z. Kipps, T. J. Brown, J. R. Getz, G. A. Ho, V. T. Gnirke, A. Neuberg, D. Soiffer, R. J. Ritz, J. Alyea, E. P. Kharchenko, P. V. Wu, C. J. 2020-04-10 doi:10.1101/2020.04.09.033555 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ A New Form of Decellularized Extracellular Matrix Hydrogel for Treating Ischemic Tissue via Intravascular Infusion ]]> https://biorxiv.org/content/10.1101/2020.04.10.028076v1?rss=1 Spang, M. T. Lazerson, T. S. Bhatia, S. Corbitt, J. Sandoval, G. Luo, C. Osborn, K. G. Cabrales, P. Kwon, E. Contijoch, F. Reeves, R. R. DeMaria, A. N. Christman, K. L. 2020-04-12 doi:10.1101/2020.04.10.028076 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Sensitivity to Monoclonal Antibody 447-52D and an Open Env Trimer Conformation Correlate Poorly with Inhibition of HIV-1 Infectivity by SERINC5 ]]> https://biorxiv.org/content/10.1101/2020.04.10.036483v1?rss=1 Angerstein, A. O. Stoneham, C. A. Ramirez, P. W. Guatelli, J. C. Vollbrecht, T. 2020-04-12 doi:10.1101/2020.04.10.036483 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ An aptamer-based magnetic flow cytometer using matched filtering ]]> https://biorxiv.org/content/10.1101/2020.04.14.041210v1?rss=1 Huang, C.-C. Ray, P. Chan, M. Zhou, X. Hall, D. A. 2020-04-15 doi:10.1101/2020.04.14.041210 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ An Autophagy-Dependent Tubular Lysosomal Network Synchronizes Degradative Activity Required for Muscle Remodeling ]]> https://biorxiv.org/content/10.1101/2020.04.15.043075v1?rss=1 Murakawa, T. Kiger, A. A. Sakamaki, Y. Fukuda, M. Fujita, N. 2020-04-16 doi:10.1101/2020.04.15.043075 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Incremental language comprehension difficulty predicts activity in the language network but not the multiple demand network ]]> https://biorxiv.org/content/10.1101/2020.04.15.043844v1?rss=1 Wehbe, L. Blank, I. A. Shain, C. Futrell, R. Levy, R. von der Malsburg, T. Smith, N. Gibson, E. Fedorenko, E. 2020-04-17 doi:10.1101/2020.04.15.043844 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals ]]> https://biorxiv.org/content/10.1101/2020.04.16.044016v1?rss=1 10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment. ]]> Riva, L. Yuan, S. Yin, X. Martin-Sancho, L. Matsunaga, N. Burgstaller, S. Pache, L. De Jesus, P. Hull, M. V. Chang, M. Chan, J. F. W. Cao, J. Kwok-Man Poon, V. Herbert, K. Nguyen, T.-T. Pu, Y. Nguyen, C. Rubanov, A. Martinez-Sobrido, L. Lui, W.-C. Miorin, L. White, K. Johnson, J. R. Benner, C. Sun, R. Schultz, P. Su, A. I. Garcia-Sastre, A. Chatterjee, A. Yuen, K.-Y. Chanda, S. 2020-04-17 doi:10.1101/2020.04.16.044016 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes ]]> https://biorxiv.org/content/10.1101/2020.04.20.052068v1?rss=1 Moshiri, N. 2020-04-21 doi:10.1101/2020.04.20.052068 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Structural Basis of CD4 Downregulation by HIV-1 Nef ]]> https://biorxiv.org/content/10.1101/2020.04.21.054007v1?rss=1 Kwon, Y. Kaake, R. Echeverria, I. Suarez, M. Stoneham, C. Ramirez, P. W. Kress, J. Singh, R. Sali, A. Krogan, N. J. Guatelli, J. Jia, X. 2020-04-23 doi:10.1101/2020.04.21.054007 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development. ]]> https://biorxiv.org/content/10.1101/2020.04.24.060822v1?rss=1 Haist, J. Neumann, S. A. Al-Bassam, M. M. Lindenberg, S. Elliot, M. A. Tschowri, N. 2020-04-25 doi:10.1101/2020.04.24.060822 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. ]]> https://biorxiv.org/content/10.1101/2020.04.25.061598v1?rss=1 Ma, Q. Srivastav, S. P. Gamez, S. Feitosa-Suntheimer, F. Patterson, E. I. Johnson, R. Matson, E. Gold, A. Brackney, D. Connor, J. Colpitts, T. Hughes, G. Rasgon, J. Nolan, T. Akbari, O. S. Lau, N. 2020-04-27 doi:10.1101/2020.04.25.061598 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens ]]> https://biorxiv.org/content/10.1101/2020.04.25.061994v1?rss=1 Rajput, A. Seif, Y. Choudhary, K. S. Dalldorf, C. Poudel, S. Monk, J. Palsson, B. O. 2020-04-26 doi:10.1101/2020.04.25.061994 Cold Spring Harbor Laboratory Press 2020-04-26 <![CDATA[ What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data ]]> https://biorxiv.org/content/10.1101/2020.04.26.057943v1?rss=1 Richelle, A. Kellman, B. P. Wenzel, A. T. Chiang, A. W. T. Reagan, T. Gutierrez, J. M. Joshi, C. Li, S. Liu, J. K. Masson, H. Lee, J. Li, Z. Heirendt, L. Trefois, C. Juarez, E. F. Bath, T. Borland, D. Mesirov, J. P. Robasky, K. Lewis, N. E. 2020-04-28 doi:10.1101/2020.04.26.057943 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome ]]> https://biorxiv.org/content/10.1101/2020.04.26.062638v1?rss=1 Rychel, K. Sastry, A. V. Palsson, B. 2020-04-28 doi:10.1101/2020.04.26.062638 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures ]]> https://biorxiv.org/content/10.1101/2020.04.27.064584v1?rss=1 Ho, R. Workman, M. J. Mathkar, P. Wu, K. Kim, K. J. ORourke, J. G. Kellogg, M. Montel, V. Banuelos, M. G. Aladesuyi, O. Diaz-Garcia, S. Oheb, D. Huang, S. Khrebtukova, I. Watson, L. Ravits, J. Taylor, K. Baloh, R. H. Svendsen, C. N. 2020-04-28 doi:10.1101/2020.04.27.064584 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization ]]> https://biorxiv.org/content/10.1101/2020.04.27.065417v1?rss=1 Rodionova, I. A. Gao, Y. Sastry, A. V. Monk, J. wong, n. Szubin, R. Lim, H. Zhang, Z. Saier, M. H. Palsson, B. O. 2020-04-29 doi:10.1101/2020.04.27.065417 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ The TAT Protein Transduction Domain as an Intra-articular Drug-Delivery Technology ]]> https://biorxiv.org/content/10.1101/2020.04.28.066902v1?rss=1 Mailhiot, S. E. Thompson, M. A. Eguchi, A. Dinkel, S. Lotz, M. K. Dowdy, S. F. June, R. K. 2020-04-30 doi:10.1101/2020.04.28.066902 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Super-selective reconstruction of causal and direct connectivity with application to in-vitro iPSC neuronal networks ]]> https://biorxiv.org/content/10.1101/2020.04.28.067124v1?rss=1 Puppo, F. PrTh, D. Bang, A. Silva, G. A. 2020-04-30 doi:10.1101/2020.04.28.067124 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Determinants of Selective Fidelity in Diversity-Generating Retroelements ]]> https://biorxiv.org/content/10.1101/2020.04.29.068544v1?rss=1 Handa, S. Reyna, A. Wiryaman, T. Ghosh, P. 2020-04-30 doi:10.1101/2020.04.29.068544 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2020.04.30.069377v1?rss=1 Liu, H. Zhou, J. Tian, W. Luo, C. Bartlett, A. Aldridge, A. Lucero, J. Osteen, J. K. Nery, J. R. Chen, H. Rivkin, A. Castanon, R. G. Clock, B. Li, Y. E. Hou, X. Poirion, O. B. Preissl, S. O'Connor, C. Boggeman, L. Fitzpatrick, C. Nunn, M. Mukamel, E. A. Zhang, Z. Callaway, E. M. Ren, B. Dixon, J. R. Behrens, M. M. Ecker, J. R. 2020-04-30 doi:10.1101/2020.04.30.069377 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media ]]> https://biorxiv.org/content/10.1101/2020.04.30.070904v1?rss=1 Seif, Y. Poudel, S. Tsunemoto, H. Szubin, R. Meehan, M. J. Olson, C. Rajput, A. Alarcon, G. Lamsa, A. Dillon, N. Vrbanac, A. Sugie, J. Daesh, S. Monk, J. Dorrestein, P. Knight, R. Pogliano, J. Feist, A. Palsson, B. Nizet, V. 2020-05-01 doi:10.1101/2020.04.30.070904 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Sleep Deficits and Cannabis Use Behaviors: An Analysis of Shared Genetics Using Linkage Disequilibrium Score Regression and Polygenic Risk Prediction ]]> https://biorxiv.org/content/10.1101/2020.05.02.053983v1?rss=1 Winiger, E. A. Ellingson, J. M. Morrison, C. L. Corley, R. P. Pasman, J. A. Wall, T. L. Hopfer, C. J. Hewitt, J. K. 2020-05-03 doi:10.1101/2020.05.02.053983 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility ]]> https://biorxiv.org/content/10.1101/2020.05.04.077271v1?rss=1 Sastry, A. V. Dillon, N. Poudel, S. Hefner, Y. Xu, S. Szubin, R. Feist, A. Nizet, V. Palsson, B. 2020-05-04 doi:10.1101/2020.05.04.077271 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree ]]> https://biorxiv.org/content/10.1101/2020.05.04.077636v1?rss=1 Tripathi, A. Vazquez-Baeza, Y. Gauglitz, J. M. Wang, M. Duhrkop, K. Esposito-Nothias, M. Acharya, D. Ernst, M. van der Hooft, J. J. J. Zhu, Q. McDonald, D. Gonzalez, A. Handelsman, J. Fleischauer, M. Ludwig, M. Bocker, S. NOTHIAS, L. F. Knight, R. Dorrestein, P. C. 2020-05-05 doi:10.1101/2020.05.04.077636 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Vision does not impact walking performance in Argentine ants ]]> https://biorxiv.org/content/10.1101/2020.05.05.079582v1?rss=1 Clifton, G. Holway, D. Gravish, N. 2020-05-06 doi:10.1101/2020.05.05.079582 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media ]]> https://biorxiv.org/content/10.1101/2020.05.06.079640v1?rss=1 Rajput, A. Poudel, S. Tsunemoto, H. Meehan, M. Szubin, R. Olson, C. Seif, Y. Lamsa, A. Dillon, N. Vrbanac, A. Sugie, J. Dahesh, S. Monk, J. Dorrestein, P. Pogliano, J. Nizet, V. Feist, A. Palsson, B. O. 2020-05-07 doi:10.1101/2020.05.06.079640 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ In situ detection of protein interactions for recombinant therapeutic enzymes ]]> https://biorxiv.org/content/10.1101/2020.05.06.081885v1?rss=1 Samoudi, M. Kuo, C.-C. Robinson, C. M. Shams-Ud-Doha, K. Schinn, S.-M. Kol, S. Weiss, L. Petersen Bjorn, S. Voldborg, B. G. Rosa Campos, A. Lewis, N. E. 2020-05-07 doi:10.1101/2020.05.06.081885 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes ]]> https://biorxiv.org/content/10.1101/2020.05.07.081604v1?rss=1 Karottki, K. J. l. C. Hefzi, H. Li, S. Pedersen, L. E. Spahn, P. Ruckerbauer, D. Bort, J. H. Thomas, A. Lee, J. S. Borth, N. Lee, G. M. Kildegaard, H. F. Lewis, N. E. 2020-05-08 doi:10.1101/2020.05.07.081604 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Comment on 'Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism' ]]> https://biorxiv.org/content/10.1101/2020.05.08.084376v1?rss=1 Le Treut, G. Si, F. Li, D. Jun, S. 2020-05-10 doi:10.1101/2020.05.08.084376 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Computing temporal sequences associated with dynamic patterns on the C. elegans connectome ]]> https://biorxiv.org/content/10.1101/2020.05.08.085191v1?rss=1 George, V. K. Puppo, F. Silva, G. A. 2020-05-10 doi:10.1101/2020.05.08.085191 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Germline mutagenesis of Nasonia vitripennis through ovarian delivery of CRISPR-Cas9 ribonucleoprotein ]]> https://biorxiv.org/content/10.1101/2020.05.10.087494v1?rss=1 Chaverra-Rodriguez, D. Dalla Benetta, E. Heu, C. C. Rasgon, J. Ferree, P. M. Akbari, O. S. 2020-05-10 doi:10.1101/2020.05.10.087494 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum ]]> https://biorxiv.org/content/10.1101/2020.05.10.087585v1?rss=1 800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link a significant fraction of them to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of non-coding risk variants associated with various neurological disease and traits in humans. To facilitate the dissemination of information, we have set up a web portal (http://catlas.org/mousebrain). ]]> Li, Y. Preissl, S. Hou, X. Zhang, z. Zhang, K. Fang, R. Qiu, Y. Poirion, O. Li, B. Yan, Y. Liu, H. Wang, X. Han, J. Y. Lucero, J. Kuan, S. Gorkin, D. Nunn, M. Mukamel, E. A. Behrens, M. M. Ecker, J. R. Ren, B. 2020-05-11 doi:10.1101/2020.05.10.087585 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.05.12.090688v1?rss=1 Morshed, N. Ralvenius, W. T. Nott, A. Watson, L. A. Rodriguez, F. H. Akay, L. A. Joughin, B. A. Pao, P.-C. Penney, J. LaRocque, L. Mastroeni, D. Tsai, L.-H. White, F. M. 2020-05-14 doi:10.1101/2020.05.12.090688 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Catestatin (CST) is a key mediator of the immunoendocrine regulation of cardiovascular function ]]> https://biorxiv.org/content/10.1101/2020.05.12.092254v1?rss=1 Ying, W. Tang, K. Avolio, E. Schilling, J. M. Pasqua, T. Liu, M. A. Mahata, S. Bandyopadhyay, G. K. Das, S. Sahoo, D. Webster, N. J. Patel, H. H. Ghosh, P. Mahata, S. K. 2020-05-14 doi:10.1101/2020.05.12.092254 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Structural and Dynamic Basis of Molecular Recognition between Acyltransferase and Carrier Protein in E. coli Fatty Acid Synthesis ]]> https://biorxiv.org/content/10.1101/2020.05.15.098798v1?rss=1 Misson, L. E. Mindrebo, J. T. Davis, T. D. Patel, A. McCammon, J. A. Noel, J. P. Burkart, M. D. 2020-05-15 doi:10.1101/2020.05.15.098798 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein ]]> https://biorxiv.org/content/10.1101/2020.05.17.100685v1?rss=1 Ye, Q. West, A. M. V. Silletti, S. Corbett, K. D. 2020-05-17 doi:10.1101/2020.05.17.100685 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development ]]> https://biorxiv.org/content/10.1101/2020.05.18.101071v1?rss=1 Geusz, R. J. Wang, A. Chiou, J. Lancman, J. J. Wetton, N. Kefalopoulou, S. Wang, J. Qiu, Y. Yan, J. Aylward, A. Ren, B. Dong, P. D. S. Gaulton, K. J. Sander, M. 2020-05-19 doi:10.1101/2020.05.18.101071 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes ]]> https://biorxiv.org/content/10.1101/2020.05.19.104992v1?rss=1 Kavvas, E. Feist, A. Antoniewicz, M. R. Palsson, B. Monk, J. Ding, Y. Long, C. 2020-05-20 doi:10.1101/2020.05.19.104992 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Travelling spindles create necessary conditions for spike-timing-dependent plasticity in humans ]]> https://biorxiv.org/content/10.1101/2020.05.21.079152v1?rss=1 Dickey, C. W. Sargsyan, A. Madsen, J. R. Eskandar, E. N. Cash, S. S. Halgren, E. 2020-05-22 doi:10.1101/2020.05.21.079152 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Spatial Confidence Sets for Standardized Effect Size Images ]]> https://biorxiv.org/content/10.1101/2020.05.21.108761v1?rss=1 Bowring, A. Telschow, F. Schwartzman, A. Nichols, T. E. 2020-05-25 doi:10.1101/2020.05.21.108761 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.21.109694v1?rss=1 Gao, Y. Bang, I. Seif, Y. Nam, G. Sastry, A. V. Chen, K. Monk, J. Choudhary, K. S. Seo, S. W. Lee, E.-Y. Kim, D. Palsson, B. 2020-05-22 doi:10.1101/2020.05.21.109694 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Towards complete and error-free genome assemblies of all vertebrate species ]]> https://biorxiv.org/content/10.1101/2020.05.22.110833v1?rss=1 Rhie, A. McCarthy, S. A. Fedrigo, O. Damas, J. Formenti, G. Koren, S. Uliano-Silva, M. Chow, W. Fungtammasan, A. Gedman, G. L. Cantin, L. J. Thibaud-Nissen, F. Haggerty, L. Lee, C. Ko, B. J. Kim, J. Bista, I. Smith, M. Haase, B. Mountcastle, J. Winkler, S. Paez, S. Howard, J. Vernes, S. C. Lama, T. M. Grutzner, F. C. Warren, W. C. Balakrishnan, C. Burt, D. George, J. M. Biegler, M. Iorns, D. Digby, A. Eason, D. Edwards, T. Wilkinson, M. Turner, G. F. Meyer, A. Kautt, A. F. Franchini, P. Detrich, H. W. Svardal, H. Wagner, M. Naylor, G. J. P. Pippel, M 2020-05-23 doi:10.1101/2020.05.22.110833 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Explication of CB1 receptor contributions to the hypothermic effects of Δ9-tetrahydrocannabinol (THC) when delivered by vapor inhalation or parenteral injection in rats ]]> https://biorxiv.org/content/10.1101/2020.05.22.111468v1?rss=1 Nguyen, J. D. Creehan, K. M. Grant, Y. Vandewater, S. A. Kerr, T. M. Taffe, M. A. 2020-05-26 doi:10.1101/2020.05.22.111468 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Autism genetics perturb prenatal neurodevelopment through a hierarchy of broadly-expressed and brain-specific genes ]]> https://biorxiv.org/content/10.1101/2020.05.23.112623v1?rss=1 Gazestani, V. H. Chiang, A. W. Courchesne, E. Lewis, N. E. 2020-05-26 doi:10.1101/2020.05.23.112623 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Emergence and Propagation of Epistasis in Metabolic Networks ]]> https://biorxiv.org/content/10.1101/2020.05.24.113001v1?rss=1 Kryazhimskiy, S. 2020-05-26 doi:10.1101/2020.05.24.113001 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Variable Number Tandem Repeats mediate the expression of proximal genes ]]> https://biorxiv.org/content/10.1101/2020.05.25.114082v1?rss=1 Bakhtiari, M. Park, J. Ding, Y.-C. Shleizer-Burko, S. Neuhausen, S. L. Halldorsson, B. V. Stefansson, K. Gymrek, M. Bafna, V. 2020-05-25 doi:10.1101/2020.05.25.114082 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Neuronal timescales are functionally dynamic and shaped by cortical microarchitecture ]]> https://biorxiv.org/content/10.1101/2020.05.25.115378v1?rss=1 Gao, R. van den Brink, R. L. Pfeffer, T. Voytek, B. 2020-05-26 doi:10.1101/2020.05.25.115378 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.27.119784v1?rss=1 Flamholz, A. I. Dugan, E. Blikstad, C. Gleizer, S. Ben-Nissan, R. Amram, S. Antonovsky, N. Ravishankar, S. Noor, E. Bar-Even, A. Milo, R. Savage, D. 2020-05-27 doi:10.1101/2020.05.27.119784 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR) ]]> https://biorxiv.org/content/10.1101/2020.05.31.126623v1?rss=1 Kellman, B. P. Zhang, Y. Logomasini, E. Meinhardt, E. Chiang, A. W. T. Sorrentino, J. T. LIang, C. Bao, B. Zhou, Y. Akases, S. Sogabe, I. Kuoka, T. Wilson, I. B. H. Campbell, M. P. Neelamegham, S. Krambeck, F. J. Aoki-Kinoshita, K. F. Lewis, N. E. 2020-06-01 doi:10.1101/2020.05.31.126623 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Deep sncRNA-seq of the PPMI cohort to study Parkinson's disease progression ]]> https://biorxiv.org/content/10.1101/2020.06.01.127092v1?rss=1 Kern, F. Fehlmann, T. Violich, I. Alsop, E. Hutchins, E. Kahraman, M. Grammes, N. L. Guimaraes, P. Backes, C. Poston, K. Casey, B. Balling, R. Geffers, L. Krueger, R. Galasko, D. Mollenhauer, B. Meese, E. Wyss-Coray, T. Craig, D. W. Van Keuren-Jensen, K. Keller, A. 2020-06-01 doi:10.1101/2020.06.01.127092 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Evolutionarily related small viral fusogens hijack distinct but modular actin nucleation pathways to drive cell-cell fusion ]]> https://biorxiv.org/content/10.1101/2020.06.03.130740v1?rss=1 Chan, K. M. C. Arthur, A. L. Morstein, J. Jin, M. Bhat, A. Schlesinger, D. Son, S. Stevens, D. A. Drubin, D. G. Fletcher, D. A. 2020-06-04 doi:10.1101/2020.06.03.130740 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2020.06.07.138933v1?rss=1 Machado, H. Seif, Y. Sakoulas, G. Olson, C. A. Szubin, R. Palsson, B. Nizet, V. Feist, A. M. 2020-06-07 doi:10.1101/2020.06.07.138933 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution ]]> https://biorxiv.org/content/10.1101/2020.06.12.147033v1?rss=1 Lawson, C. L. Kryshtafovych, A. Adams, P. D. Afonine, P. Baker, M. L. Barad, B. A. Bond, P. Burnley, T. Cao, R. Cheng, J. Chojnowski, G. Cowtan, K. Dill, K. A. DiMaio, F. Farrell, D. Fraser, J. S. Herzik, M. A. Hoh, S. W. Hou, J. Hung, L.-W. Igaev, M. Joseph, A. P. Kihara, D. Kumar, D. Mittal, S. Monastyrskyy, B. Olek, M. Palmer, C. Patwardhan, A. Perez, A. Pfab, J. Pintilie, G. D. Richardson, J. S. Rosenthal, P. B. Sarkar, D. Schaefer, L. U. Schmid, M. F. Schroeder, G. F. Shekhar, M. Si, D. Singharoy, A. Terashi, G. Terwilliger, T. C. Vaiana, A. Wan 2020-06-15 doi:10.1101/2020.06.12.147033 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Adipose tissue macrophages orchestrate β cell adaptation in obesity through secreting miRNA-containing extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2020.06.12.148809v1?rss=1 Gao, H. Luo, Z. Jin, Z. Ji, Y. Ying, W. 2020-06-13 doi:10.1101/2020.06.12.148809 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Decoding of persistent multiscale structures in complex biological networks ]]> https://biorxiv.org/content/10.1101/2020.06.16.151555v1?rss=1 Zheng, F. Zhang, S. Churas, C. Pratt, D. Bahar, I. Ideker, T. 2020-06-17 doi:10.1101/2020.06.16.151555 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Machine Learning Models Identify Inhibitors of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.06.16.154765v1?rss=1 Gawriljuk, V. O. Kyaw Zin, P. P. Foil, D. H. Bernatchez, J. Beck, S. Beutler, N. Ricketts, J. Yang, L. Rogers, T. Puhl, A. C. Zorn, K. M. Lane, T. R. Godoy, A. S. Olivia, G. Siqueira-Neto, J. L. Madrid, P. Ekins, S. 2020-06-16 doi:10.1101/2020.06.16.154765 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Structural mimicry confers robustness in the cyanobacterial circadian clock ]]> https://biorxiv.org/content/10.1101/2020.06.17.158394v1?rss=1 Heisler, J. Swan, J. A. Palacios, J. G. Sancar, C. Ernst, D. C. Spangler, R. K. Bagshaw, C. R. Tripathi, S. Crosby, P. Golden, S. S. Partch, C. L. LiWang, A. 2020-06-19 doi:10.1101/2020.06.17.158394 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Reconstitution of an intact clock that generates circadian DNA binding in vitro ]]> https://biorxiv.org/content/10.1101/2020.06.18.158576v1?rss=1 Chavan, A. G. Ernst, D. C. Fang, M. Sancar, C. Partch, C. L. Golden, S. S. LiWang, A. 2020-06-19 doi:10.1101/2020.06.18.158576 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ An Analysis of SARS-CoV-2 Using ViReport ]]> https://biorxiv.org/content/10.1101/2020.06.20.163162v1?rss=1 Song, M. J. Moshiri, N. 2020-06-21 doi:10.1101/2020.06.20.163162 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Phosphoproteomics after nitrate treatments reveal an important role for PIN2 phosphorylation in control of root system architecture. ]]> https://biorxiv.org/content/10.1101/2020.06.22.164640v1?rss=1 Vega, A. Fredes, I. O'Brien, J. Shen, Z. Otvos, K. Benkova, E. Briggs, S. Gutierrez, R. A. 2020-06-23 doi:10.1101/2020.06.22.164640 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species ]]> https://biorxiv.org/content/10.1101/2020.06.23.162792v1?rss=1 Hanna, E. M. Zhang, X. Eide, M. Fallahi, S. Furmanek, T. Yadetie, F. Zielinski, D. C. Goksoyr, A. Jonassen, I. 2020-06-24 doi:10.1101/2020.06.23.162792 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Elucidation of regulatory modes for five two-component systems in Escherichia coli reveals novel relationships ]]> https://biorxiv.org/content/10.1101/2020.06.23.168344v1?rss=1 Choudhary, K. S. Kleinmanns, J. A. Decker, K. Sastry, A. V. Gao, Y. Szubin, R. Seif, Y. Palsson, B. O. 2020-06-24 doi:10.1101/2020.06.23.168344 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Systematic evaluation of parameterization for genome-scale metabolic models of cultured mammalian cells ]]> https://biorxiv.org/content/10.1101/2020.06.24.169938v1?rss=1 Schinn, S.-M. Morrison, C. Wei, W. Zhang, L. Lewis, N. E. 2020-06-26 doi:10.1101/2020.06.24.169938 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor ]]> https://biorxiv.org/content/10.1101/2020.06.25.172403v1?rss=1 Zhao, P. Praissman, J. L. Grant, O. C. Cai, Y. Xiao, T. Rosenbalm, K. E. Aoki, K. Kellman, B. P. Bridger, R. Barouch, D. H. Brindley, M. A. Lewis, N. E. Tiemeyer, M. Chen, B. Woods, R. J. Wells, L. 2020-06-26 doi:10.1101/2020.06.25.172403 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Tissue specific muscle extracellular matrix hydrogel improves skeletal muscle regeneration in vivo over non-matched tissue source ]]> https://biorxiv.org/content/10.1101/2020.06.30.181164v1?rss=1 Ungerleider, J. L. Dzieciatkowska, M. Hansen, K. C. Christman, K. L. 2020-07-01 doi:10.1101/2020.06.30.181164 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation ]]> https://biorxiv.org/content/10.1101/2020.07.02.183459v1?rss=1 Kim, M. Harmanci, A. O. Bossuat, J.-P. Carpov, S. Cheon, J. H. Chilotti, I. Cho, W. Froelicher, D. Gama, N. Georgieva, M. Hong, S. Hubaux, J.-P. Kim, D. Lauter, K. Ma, Y. Ohno-Machado, L. Sofia, H. J. Son, Y. Song, Y. Troncoso-Pastoriza, J. R. Jiang, X. 2020-07-04 doi:10.1101/2020.07.02.183459 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Alcohol Dependence Differentially Alters Orbitofrontal Cortex Representations of Inferred Decision-Making and Outcomes ]]> https://biorxiv.org/content/10.1101/2020.07.03.186148v1?rss=1 Cazares, C. Schreiner, D. C. Gremel, C. M. 2020-07-04 doi:10.1101/2020.07.03.186148 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[ Repurposed Drugs Block Toxin-Driven Platelet Clearance by the Hepatic Ashwell-Morell Receptor to Clear Staphylococcus aureus Bacteremia ]]> https://biorxiv.org/content/10.1101/2020.07.06.190322v1?rss=1 Sun, J. Uchiyama, S. Olson, J. Morodomi, Y. Cornax, I. Ando, N. Kohno, Y. Kyaw, M. M. T. Aguilar, B. Haste, N. M. Kanaji, S. Kanaji, T. Rose, W. E. Sakoulas, G. Marth, J. D. Nizet, V. 2020-07-07 doi:10.1101/2020.07.06.190322 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains ]]> https://biorxiv.org/content/10.1101/2020.07.07.192526v1?rss=1 Hui Huang Quan Zhu Adam Jussila Yuanyuan Han Bogdan Bintu Colin Kern Mattia Conte Yanxiao Zhang Simona Bianco Andrea Chiariello Miao Yu Rong Hu Ivan Juric Ming Hu Mario Nicodemi Xiaowei Zhuang Bing Ren 2020-07-08 doi:10.1101/2020.07.07.192526 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Reference data based insights expand understanding of human metabolomes ]]> https://biorxiv.org/content/10.1101/2020.07.08.194159v1?rss=1 Julia M Gauglitz Wout Bittremieux Candace L Williams Kelly C Weldon Morgan W Panitchpakdi Francesca Di Ottavio Christine M Aceves Elizabeth Brown Nicole C Sikora Alan K. Jarmusch Cameron Martino Anupriya Tripathi Erfan Sayyari Justin Shaffer Roxana Coras Fernando Vargas Lindsay DeRight Goldasich Tara Schwartz MacKenzie Bryant Gregory Humphrey Abigail J. Johnson Katharina Spengler Pedro Belda-Ferre Edgar Diaz Daniel McDonald Qiyun Zhu Dominic S. Nguyen Emmanuel O. Elijah Mingxun Wang Clarisse Marotz Kate E. Sprecher Daniela Vargas-Robles Dana Withrow Gail Ackerm 2020-07-11 doi:10.1101/2020.07.08.194159 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2 ]]> https://biorxiv.org/content/10.1101/2020.07.13.198069v1?rss=1 Schmidt, S. H. Weng, J.-H. Aoto, P. C. Boassa, D. Mathea, S. Silletti, S. Hu, J. Wallbott, M. Komives, E. A. Knapp, S. Herberg, F. W. Taylor, S. S. 2020-07-14 doi:10.1101/2020.07.13.198069 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 ]]> https://biorxiv.org/content/10.1101/2020.07.14.201616v1?rss=1 Clausen, T. M. Sandoval, D. R. Spliid, C. B. Pihl, J. Painter, C. D. Thacker, B. E. Glass, C. A. Narayanan, A. Majowicz, S. A. Zhang, Y. Torres, J. L. Golden, G. J. Porell, R. Garretson, A. F. Laubach, L. Feldman, J. Yin, X. Pu, Y. Hauser, B. Caradonna, T. M. Kellman, B. P. Martino, C. Gordts, P. L. S. M. Leibel, S. L. Chanda, S. K. Schmidt, A. G. Godula, K. Jose, J. Corbett, K. D. Ward, A. B. Carlin, A. F. Esko, J. D. 2020-07-14 doi:10.1101/2020.07.14.201616 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Nef enhances HIV-1 replication and infectivity independently of SERINC3 and SERINC5 in CEM T cells ]]> https://biorxiv.org/content/10.1101/2020.07.15.205757v1?rss=1 Ramirez, P. W. Angerstein, A. A. Suarez, M. Vollbrecht, T. Wallace, J. O'Connell, R. M. Guatelli, J. 2020-07-17 doi:10.1101/2020.07.15.205757 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity ]]> https://biorxiv.org/content/10.1101/2020.07.16.206680v1?rss=1 Oliveira, A. S. Ibarra, A. A. Bermudez, I. Casalino, L. Gaieb, Z. Shoemark, D. K. Gallagher, T. Sessions, R. B. Amaro, R. E. Mulholland, A. J. 2020-07-17 doi:10.1101/2020.07.16.206680 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ The Argo: A 65,536 channel recording system for high density neural recording in vivo ]]> https://biorxiv.org/content/10.1101/2020.07.17.209403v1?rss=1 Sahasrabuddhe, K. Khan, A. A. Singh, A. P. Stern, T. M. Ng, Y. Tadic, A. Orel, P. LaReau, C. Pouzzner, D. Nishimura, K. Boergens, K. M. Shivakumar, S. Hopper, M. S. Kerr, B. Hanna, M.-E. S. Edgington, R. J. McNamara, I. Fell, D. Gao, P. Babaie-Fishani, A. Veijalainen, S. Klekachev, A. V. Stuckey, A. M. Luyssaert, B. Kozai, T. D. Y. Xie, C. Gilja, V. Dierickx, B. Kong, Y. Straka, M. Sohal, H. S. Angle, M. R. 2020-07-17 doi:10.1101/2020.07.17.209403 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Biased orientation representations can be explained by experience with non-uniform training set statistics ]]> https://biorxiv.org/content/10.1101/2020.07.17.209536v1?rss=1 Henderson, M. M. Serences, J. 2020-07-18 doi:10.1101/2020.07.17.209536 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut. ]]> https://biorxiv.org/content/10.1101/2020.07.20.212498v1?rss=1 Zhi, H. Behnsen, J. Aron, A. Subramanian, V. Liu, J. Gerner, R. Petras, D. Green, K. Price, S. Camacho, J. Hillman, H. Tjokrosurjo, J. Montaldo, N. Hoover, E. Treacy-Abarca, S. Gilston, B. Skaar, E. Chazin, W. Garneau-Tsodikova, S. Lawrenz, M. Perry, R. Nuccio, S.-P. Dorrestein, P. Raffatellu, M. 2020-07-21 doi:10.1101/2020.07.20.212498 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner ]]> https://biorxiv.org/content/10.1101/2020.07.21.214932v1?rss=1 1/2 log10 increased infectivity in human cells expressing the human ACE2 protein as the viral receptor. The increased binding/fusion activity of the D614G Spike protein was corroborated in a cell fusion assay using Spike and ACE2 proteins expressed in different cells. These results are consistent with the possibility that the Spike D614G mutant increases the infectivity of SARS-CoV2. ]]> Ogawa, J. Zhu, W. Tonnu, N. Singer, O. Hunter, T. Ryan (Firth), A. L. Pao, G. M. 2020-07-22 doi:10.1101/2020.07.21.214932 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.23.217067v1?rss=1 Espin Palazon, R. Campbell, C. A. Fursova, O. Cheng, X. Snella, E. McCune, A. Li, L. Solchenberger, B. Schmid, B. Sahoo, D. Morton, M. Traver, D. 2020-07-23 doi:10.1101/2020.07.23.217067 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease ]]> https://biorxiv.org/content/10.1101/2020.07.23.218784v1?rss=1 Sztain, T. Amaro, R. E. McCammon, J. A. 2020-07-24 doi:10.1101/2020.07.23.218784 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Evolution of regulatory signatures in primate cortical neurons at cell type resolution ]]> https://biorxiv.org/content/10.1101/2020.07.24.219881v1?rss=1 Kozlenkov, A. Vermunt, M. W. Apontes, P. Li, J. Hao, K. Sherwood, C. C. Hof, P. R. Ely, J. J. Wegner, M. Mukamel, E. A. Creyghton, M. P. Koonin, E. V. Dracheva, S. 2020-07-27 doi:10.1101/2020.07.24.219881 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ E-cigarettes compromise the gut barrier and trigger gut inflammation ]]> https://biorxiv.org/content/10.1101/2020.07.29.227348v1?rss=1 90% of e-cigarette e-liquids as the source of harm. Given the ever-expanding importance of the integrity of the gut barrier for host fitness, and impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health. SIGNIFICANCEThe safety of electronic cigarettes has been questioned amidst emerging evidence that they may derail our immune system and increase our susceptibility to infections. Despite these insights, their impact on the most critical entity that separates trillions of microbes from the largest immune system in our body, i.e., the gut barrier, remains unexplored. Using a combination of mouse models, gut transcriptomics, and murine and human gut-derived organoids, here we show that chronic exposure to aerosols of electronic-cigarette disrupts the gut barrier, increases its susceptibility to bacterial infections and triggers inflammation. Given the importance of the gut barrier in the maintenance of immune homeostasis, these findings provide valuable insights into the potential long-term harmful effects of electronic cigarettes on health. ]]> Sharma, A. Lee, J. Fonseca, A. Moshensky, A. Kothari, T. Ibrahim, I. S. Ibeawuchi, S.-R. Pranadinata, R. Ear, J. Sahoo, D. Crotty-Alexander, L. Ghosh, P. Das, S. 2020-07-30 doi:10.1101/2020.07.29.227348 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein ]]> https://biorxiv.org/content/10.1101/2020.07.30.228023v1?rss=1 Lu, S. Ye, Q. Singh, D. Villa, E. Cleveland, D. W. Corbett, K. D. 2020-07-31 doi:10.1101/2020.07.30.228023 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ A genetic probe for visualizing glutamatergic synapses and vesicles by 3D electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.07.31.230995v1?rss=1 Steinkellner, T. Madany, M. Haberl, M. G. Zell, V. Li, C. Hu, J. Mackey, M. Ramachandra, R. Adams, S. Ellisman, M. H. Hnasko, T. BOASSA, D. 2020-08-03 doi:10.1101/2020.07.31.230995 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi ]]> https://biorxiv.org/content/10.1101/2020.08.02.233056v1?rss=1 Adolfi, A. Gantz, V. M. Jasinskiene, N. Lee, H.-F. Hwang, K. Bulger, E. A. Ramaiah, A. Bennett, J. B. Terradas, G. Emerson, J. J. Marshall, J. M. Bier, E. James, A. A. 2020-08-02 doi:10.1101/2020.08.02.233056 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment ]]> https://biorxiv.org/content/10.1101/2020.08.03.234146v1?rss=1 Marlow, J. Spietz, R. Kim, K.-Y. Ellisman, M. Girguis, P. Hatzenpichler, R. 2020-08-03 doi:10.1101/2020.08.03.234146 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Ventral Pallidum GABA Neurons Mediate Motivation Underlying Risky Choice ]]> https://biorxiv.org/content/10.1101/2020.08.04.221960v1?rss=1 Farrell, M. R. Esteban, J. Faget, L. Floresco, S. B. Hnasko, T. S. Mahler, S. V. 2020-08-04 doi:10.1101/2020.08.04.221960 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival ]]> https://biorxiv.org/content/10.1101/2020.08.05.238758v1?rss=1 Agelidis, A. Turturice, B. A. Suryawanshi, R. K. Yadavalli, T. Jaishankar, D. Ames, J. Hopkins, J. Koujah, L. Patil, C. D. Hadigal, S. R. Kyzar, E. J. Campeau, A. Wozniak, J. M. Gonzalez, D. J. Vlodavsky, I. Li, J.-p. Perkins, D. L. Finn, P. W. Shukla, D. 2020-08-06 doi:10.1101/2020.08.05.238758 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ White Matter Disruption in Pediatric Traumatic Brain Injury: Results from ENIGMA Pediatric msTBI ]]> https://biorxiv.org/content/10.1101/2020.08.06.237271v1?rss=1 Dennis, E. L. Caeyenberghs, K. Hoskinson, K. R. Merkley, T. L. Suskauer, S. J. Asarnow, R. F. Babikian, T. Bartnik-Olson, B. Bickart, K. Bigler, E. D. Ewing-Cobbs, L. Figaji, A. Giza, C. C. Hunsaker-Goodrich, N. J. Hodges, C. B. Hovenden, E. S. Irimia, A. Königs, M. Levin, H. S. Lindsey, H. M. Max, J. E. Newsome, M. R. Olsen, A. Ryan, N. P. Schmidt, A. T. Spruiell, M. S. Wade, B. S. Ware, A. L. Watson, C. G. Wheeler, A. L. Yeates, K. O. Zielinski, B. A. Kochunov, P. Jahanshad, N. Thompson, P. M. Tate, D. F. Wilde, E. A. 2020-08-07 doi:10.1101/2020.08.06.237271 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi ]]> https://biorxiv.org/content/10.1101/2020.08.09.229716v1?rss=1 Kalogriopoulos, N. Lopez-Sanchez, I. Lin, C. Ngo, T. Midde, K. Roy, S. Aznar, N. Murray, F. Garcia-Marcos, M. Kufareva, I. Ghassemian, M. Ghosh, P. 2020-08-10 doi:10.1101/2020.08.09.229716 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation ]]> https://biorxiv.org/content/10.1101/2020.08.10.243634v1?rss=1 Kuo, C.-C. Chiang, W.-T. Lewis, N. E. 2020-08-10 doi:10.1101/2020.08.10.243634 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato ]]> https://biorxiv.org/content/10.1101/2020.08.10.244665v1?rss=1 Nachappa, P. Challacombe, J. F. Margolies, D. C. Nechols, J. R. Whitfield, A. E. Rotenberg, D. 2020-08-11 doi:10.1101/2020.08.10.244665 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development ]]> https://biorxiv.org/content/10.1101/2020.08.10.244814v1?rss=1 Breuss, M. W. Yang, X. Antaki, D. Schlachetzki, J. C. M. Lana, A. A. Xu, X. Chai, G. Stanley, V. Song, Q. Fang Newmeyer, T. Nguyen, A. Cao, B. Nott, A. McEvoy-Venneri, J. Pasillas, M. P. Nahas, S. Van Der Kraan, L. Ding, Y. NIMH Brain Somatic Mosaicism Network, Glass, C. K. Gleeson, J. G. 2020-08-10 doi:10.1101/2020.08.10.244814 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Reelin deficiency contributes to long-term behavioral abnormalities induced by chronic adolescent exposure to Δ9-tetrahydrocannabinol in mice ]]> https://biorxiv.org/content/10.1101/2020.08.10.245449v1?rss=1 Iemolo, A. Nur, A. Montilla-Perez, P. Risbrough, V. B. Telese, F. 2020-08-13 doi:10.1101/2020.08.10.245449 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ A cohesin-independent mechanism modulates recombination activity along meiotic chromosomes ]]> https://biorxiv.org/content/10.1101/2020.08.11.247122v1?rss=1 Heldrich, J. Markowitz, T. E. Vale-Silva, L. A. Hochwagen, A. 2020-08-12 doi:10.1101/2020.08.11.247122 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning ]]> https://biorxiv.org/content/10.1101/2020.08.13.250159v1?rss=1 Rychel, K. Decker, K. Sastry, A. V. Phaneuf, P. V. Poudel, S. Palsson, B. O. 2020-08-14 doi:10.1101/2020.08.13.250159 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity ]]> https://biorxiv.org/content/10.1101/2020.08.17.238444v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@14ff1ecorg.highwire.dtl.DTLVardef@193d84corg.highwire.dtl.DTLVardef@15d6f9eorg.highwire.dtl.DTLVardef@14b16c6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. Diagram of hypothesis for bacterial mediation of SARS-CoV-2 infection through heparan sulfate (HS).It is well known that host microbes groom the mucosa where they reside. Recent investigations have shown that HS, a major component of mucosal layers, is necessary for SARS-CoV-2 infection. In this study we examine the impact of microbial modification of HS on viral attachment. C_FIG ]]> Martino, C. Kellman, B. P. Sandoval, D. R. Clausen, T. M. Marotz, C. A. Song, S. J. Wandro, S. Zaramela, L. S. Salido Benitez, R. A. Zhu, Q. Armingol, E. Vazquez-Baeza, Y. McDonald, D. Sorrentino, J. T. Taylor, B. Belda-Ferre, P. Liang, C. Zhang, Y. Schifanella, L. Klatt, N. R. Havulinna, A. S. Jousilahti, P. Huang, S. Haiminen, N. Parida, L. Kim, H.-C. Swafford, A. D. Zengler, K. Cheng, S. Inouye, M. Niiranen, T. Jain, M. Salomaa, V. Esko, J. D. Lewis, N. E. Knight, R. 2020-08-18 doi:10.1101/2020.08.17.238444 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome ]]> https://biorxiv.org/content/10.1101/2020.08.18.253443v1?rss=1 Lombardo, M. V. Eyler, L. Pramparo, T. Gazestani, V. H. Hagler, D. J. Chen, C.-H. Dale, A. M. Seidlitz, J. Bethlehem, R. A. I. Bertelsen, N. Carter Barnes, C. Lopez, L. Campbell, K. Lewis, N. E. Pierce, K. Courchesne, E. 2020-08-18 doi:10.1101/2020.08.18.253443 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Longitudinal changes in aperiodic and periodic activity in electrophysiological recordings in the first seven months of life ]]> https://biorxiv.org/content/10.1101/2020.08.18.256016v1?rss=1 Schaworonkow, N. Voytek, B. 2020-08-18 doi:10.1101/2020.08.18.256016 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Color compensation in anomalous trichromats assessed with fMRI ]]> https://biorxiv.org/content/10.1101/2020.08.18.256701v1?rss=1 Tregillus, K. E. Isherwood, Z. J. Vanston, J. E. Engel, S. A. MacLeod, D. I. A. Kuriki, I. Webster, M. A. 2020-08-19 doi:10.1101/2020.08.18.256701 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Long-range sequential dependencies precede complex syntactic production in language acquisition ]]> https://biorxiv.org/content/10.1101/2020.08.19.256792v1?rss=1 Sainburg, T. Mai, A. Gentner, T. Q. 2020-08-20 doi:10.1101/2020.08.19.256792 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ BDNF/TrkB signaling endosomes mediate long-distance dendritic growth by activating CREB/PI3K-mTOR-dependent translation in neuronal cell bodies. ]]> https://biorxiv.org/content/10.1101/2020.08.22.262923v1?rss=1 Bronfman, F. C. Moya-Alvarado, G. 2020-08-24 doi:10.1101/2020.08.22.262923 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a healthy human microbiome ]]> https://biorxiv.org/content/10.1101/2020.08.24.265504v1?rss=1 Han, Z. Thuy-Boun, P. S. Pfeiffer, W. Vartabedian, V. F. Torkamani, A. Teijaro, J. R. Wolan, D. W. 2020-08-24 doi:10.1101/2020.08.24.265504 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Heterologous expression of cryptomaldamide in a cyanobacterial host ]]> https://biorxiv.org/content/10.1101/2020.08.26.267179v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@660caforg.highwire.dtl.DTLVardef@1cab871org.highwire.dtl.DTLVardef@130de4org.highwire.dtl.DTLVardef@f50c64_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Taton, A. Ecker, A. Diaz, B. Moss, N. A. Anderson, B. Reher, R. Leao, T. F. Simkovsky, R. Dorrestein, P. C. Gerwick, L. Gerwick, W. H. Golden, J. W. 2020-08-26 doi:10.1101/2020.08.26.267179 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Regulation of Vacuole Morphology by PIEZO Channels in Spreading Earth Moss ]]> https://biorxiv.org/content/10.1101/2020.08.27.269282v1?rss=1 Radin, I. Richardson, R. A. Weiner, E. R. Bascom, C. S. Bezanilla, M. Haswell, E. 2020-08-27 doi:10.1101/2020.08.27.269282 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Hyperbolic geometry of gene expression ]]> https://biorxiv.org/content/10.1101/2020.08.27.270264v1?rss=1 Zhou, Y. Sharpee, T. 2020-08-28 doi:10.1101/2020.08.27.270264 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates ]]> https://biorxiv.org/content/10.1101/2020.08.28.263020v1?rss=1 Geusz, R. J. Wang, A. Lam, D. K. Vinckier, N. K. Alysandratos, K.-D. Roberts, D. A. Wang, J. Kefalopoulou, S. Qiu, Y. Chiou, J. Gaulton, K. J. Ren, B. Kotton, D. N. Sander, M. 2020-08-29 doi:10.1101/2020.08.28.263020 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin ]]> https://biorxiv.org/content/10.1101/2020.08.29.273516v1?rss=1 Swanson, L. A. B. Katkar, G. D. Tam, J. Pranadinata, R. Chareddy, Y. Coates, J. E. Amandachar, M. S. Castillo, V. Olson, J. Nizet, V. Kufareva, I. Das, S. Ghosh, P. 2020-08-30 doi:10.1101/2020.08.29.273516 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ A Genome-wide CRISPR-Cas9 Screen Identifies Host Factors Essential for Optimal Plasmodium Liver Stage Development. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275867v1?rss=1 Vijayan, K. Arang, N. Wei, L. Morrison, R. Geiger, R. Parks, R. K. Lewis, A. J. Mast, F. D. Douglass, A. N. Kain, H. S. Aitchison, J. D. Johnson, J. S. Aderem, A. Kaushansky, A. 2020-09-01 doi:10.1101/2020.08.31.275867 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Coupled Control of Distal Axon Integrity and Somal Responses to Axonal Damage by the Palmitoyl Acyltransferase ZDHHC17 ]]> https://biorxiv.org/content/10.1101/2020.09.01.276287v1?rss=1 Niu, J. Sanders, S. Jeong, H.-K. Holland, S. Sun, Y. Collura, K. Hernandez, L. Huang, H. Hayden, M. R. Smith, G. Hu, Y. Jin, Y. Thomas, G. 2020-09-01 doi:10.1101/2020.09.01.276287 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[ The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types ]]> https://biorxiv.org/content/10.1101/2020.09.01.278879v1?rss=1 Gillespie, T. H. Tripathy, S. Sy, M. F. Martone, M. E. Hill, S. L. 2020-09-02 doi:10.1101/2020.09.01.278879 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration ]]> https://biorxiv.org/content/10.1101/2020.09.02.278663v1?rss=1 95% of the HMO content in human milk. Through our models, we propose candidate genes for elongation, branching, fucosylation, and sialylation of HMOs. We further explored selected enzyme activities through kinetic assay and their co-regulation through transcription factor analysis. These results provide the molecular basis of HMO biosynthesis necessary to guide progress in HMO research and application with the ultimate goal of understanding and improving infant health and development. SO_SCPLOWIGNIFICANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWWith the HMO biosynthesis network resolved, we can begin to connect genotypes with milk types and thereby connect clinical infant, child and even adult outcomes to specific HMOs and HMO modifications. Knowledge of these pathways can simplify the work of synthetic reproduction of these HMOs providing a roadmap for improving infant, child, and overall human health with the specific application of a newly limitless source of nutraceuticals for infants and people of all ages. ]]> Kellman, B. P. Richelle, A. Yang, J.-Y. E. Chapla, D. G. Chiang, A. W.-T. Najera, J. Bao, B. Koga, N. Mohammad, M. A. Bruntse, A. B. Haymond, M. W. Bode, L. Lewis, N. E. 2020-09-03 doi:10.1101/2020.09.02.278663 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations ]]> https://biorxiv.org/content/10.1101/2020.09.02.279265v1?rss=1 Rees, E. Creeth, H. Hwu, H.-G. Chen, W. J. Tsuang, M. Glatt, S. Rey, R. Kirov, G. Walters, J. Holmans, P. Owen, M. O'Donovan, M. 2020-09-02 doi:10.1101/2020.09.02.279265 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ A genome-scale metabolic network model synergizes with statistical learning to predict amino acid concentrations in Chinese Hamster Ovary cell cultures ]]> https://biorxiv.org/content/10.1101/2020.09.02.279687v1?rss=1 Schinn, S.-M. Morrison, C. Wei, W. Zhang, L. Lewis, N. E. 2020-09-03 doi:10.1101/2020.09.02.279687 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ A balance between matrix deformation and the coordination of turning events governs directed neutrophil migration in 3-D matrices ]]> https://biorxiv.org/content/10.1101/2020.09.02.868505v1?rss=1 Francois, J. Kandasamy, A. Yeh, Y.-T. Ayala, C. Meili, R. Chien, S. Lasheras, J. C. del Alamo, J. C. 2020-09-02 doi:10.1101/2020.09.02.868505 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ A vapor inhalation method for delivering heroin alters nociception, body temperature and spontaneous activity in female and male rats ]]> https://biorxiv.org/content/10.1101/2020.09.03.281857v1?rss=1 Gutierrez, A. Creehan, K. M. Taffe, M. A. 2020-09-04 doi:10.1101/2020.09.03.281857 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ The structure, function, and evolution of a complete human chromosome 8 ]]> https://biorxiv.org/content/10.1101/2020.09.08.285395v1?rss=1 Logsdon, G. A. Vollger, M. R. Hsieh, P. Mao, Y. Liskovykh, M. A. Koren, S. Nurk, S. Mercuri, L. Dishuck, P. C. Rhie, A. de Lima, L. G. Porubsky, D. Bzikadze, A. V. Kremitzki, M. Graves-Lindsay, T. A. Jain, C. Hoekzema, K. Murali, S. C. Munson, K. M. Baker, C. Sorenson, M. Lewis, A. M. Surti, U. Gerton, J. L. Larionov, V. Ventura, M. Miga, K. H. Phillippy, A. M. Eichler, E. E. 2020-09-08 doi:10.1101/2020.09.08.285395 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Protecting synapses from amyloid β-associated degeneration by manipulations of Wnt/planar cell polarity signaling ]]> https://biorxiv.org/content/10.1101/2020.09.09.273011v1?rss=1 Feng, B. Freitas, A. Tian, R. Lee, Y. R. Grewal, A. Wang, J. Zou, Y. 2020-09-09 doi:10.1101/2020.09.09.273011 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association ]]> https://biorxiv.org/content/10.1101/2020.09.11.291724v1?rss=1 287,000 candidate cis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner. ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases. ]]> Hocker, J. D. Poirion, O. B. Zhu, F. Buchanan, J. Zhang, K. Chiou, J. Wang, T.-M. Hou, X. Li, Y. E. Zhang, Y. Farah, E. Wang, A. McCulloch, A. D. Gaulton, K. J. Ren, B. Chi, N. C. Preissl, S. 2020-09-12 doi:10.1101/2020.09.11.291724 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Real-time structural motif searching in proteins using an inverted index strategy ]]> https://biorxiv.org/content/10.1101/2020.09.11.293977v1?rss=1 160,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids. Author summaryThe Protein Data Bank (PDB) provides open access to more than 160,000 three-dimensional structures of proteins, nucleic acids, and biological complexes. Similarities between PDB structures give valuable functional and evolutionary insights but such resemblance may not be evident at sequence or global structure level. Throughout the database, there are recurring structural motifs - groups of modest numbers of residues in proximity that, for example, support catalytic activity. Identification of common structural motifs can unveil subtle similarities between proteins and serve as fingerprints for configurations such as the His-Asp-Ser catalytic triad found in serine proteases or the zinc coordination site found in Zinc Finger DNA-binding domains. We present a highly efficient yet flexible strategy that allows users for the first time to search for arbitrary structural motifs across the entire PDB archive in real-time. Our approach scales favorably with the increasing number and complexity of deposited structures, and, also, has the potential to be adapted for other applications in a macromolecular context. ]]> Bittrich, S. Burley, S. K. Rose, A. S. 2020-09-12 doi:10.1101/2020.09.11.293977 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Optimizing Mitochondrial Maintenance in Extended Neuronal Projections ]]> https://biorxiv.org/content/10.1101/2020.09.11.294207v1?rss=1 Agrawal, A. Koslover, E. F. 2020-09-12 doi:10.1101/2020.09.11.294207 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Context influences how individuals with misophonia respond to sounds ]]> https://biorxiv.org/content/10.1101/2020.09.12.292391v1?rss=1 Edelstein, M. Monk, B. Ramachandran, V. S. Rouw, R. 2020-09-15 doi:10.1101/2020.09.12.292391 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Deciphering the postsynaptic calcium-mediated energy homeostasis through mitochondria-endoplasmic reticulum contact sites using systems modeling ]]> https://biorxiv.org/content/10.1101/2020.09.12.294827v1?rss=1 Leung, A. K. Ohadi, D. Pekkurnaz, G. Rangamani, P. 2020-09-13 doi:10.1101/2020.09.12.294827 Cold Spring Harbor Laboratory Press 2020-09-13 <![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[ The flexibility of ACE2 in the context of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.09.16.300459v1?rss=1 Barros, E. P. Casalino, L. Gaieb, Z. Dommer, A. C. Wang, Y. Fallon, L. Raguette, L. Belfon, K. Simmerling, C. L. Amaro, R. E. 2020-09-16 doi:10.1101/2020.09.16.300459 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Scalable Models of Antibody Evolution and Benchmarking of Clonal Tree Reconstruction Methods ]]> https://biorxiv.org/content/10.1101/2020.09.17.302505v1?rss=1 Zhang, C. Bzikadze, A. V. Safonova, Y. Mirarab, S. 2020-09-20 doi:10.1101/2020.09.17.302505 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides ]]> https://biorxiv.org/content/10.1101/2020.09.19.304303v1?rss=1 Muntjewerff, E. M. Tang, K. Lutter, L. Christoffersson, G. Nicolasen, M. J. T. Gao, H. Katkar, G. D. Das, S. Beest, M. t. Ying, W. Ghosh, P. El Aidy, S. Oldenburg, B. van den Bogaart, G. Mahata, S. K. 2020-09-20 doi:10.1101/2020.09.19.304303 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ AI-guided discovery of the invariant host response to viral pandemics ]]> https://biorxiv.org/content/10.1101/2020.09.21.305698v1?rss=1 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them. Added value of this studyThis work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the cytokine storm mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs. Implications of all the available evidenceThe ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs. ]]> Sahoo, D. Katkar, G. D. Khandelwal, S. Behroozikhah, M. Claire, A. Castillo, V. Tindle, C. Fuller, M. Taheri, S. Rogers, T. F. Beutler, N. Ramirez, S. Rawlings, S. A. Pretorius, V. Smith, D. Burton, D. R. Alexander, L. C. Duran, J. M. Crotty, S. Dan, J. M. Das, S. Ghosh, P. 2020-09-22 doi:10.1101/2020.09.21.305698 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.21.307363v1?rss=1 Seirup, M. Sengupta, S. Swanson, S. McIntosh, B. E. Collins, M. Chu, L.-F. Cheng, Z. Gorkin, D. Duffin, B. Bolin, J. M. Argus, C. Stewart, R. Thomson, J. A. 2020-09-22 doi:10.1101/2020.09.21.307363 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Clinical interpretation of integrative molecular profiles to guide precision cancer medicine ]]> https://biorxiv.org/content/10.1101/2020.09.22.308833v1?rss=1 Reardon, B. Moore, N. D. Moore, N. Kofman, E. Aldubayan, S. Cheung, A. Conway, J. Elmarakeby, H. Imamovic, A. Kamran, S. C. Keenan, T. Keliher, D. Konieczkowski, D. J. Liu, D. Mouw, K. Park, J. Vokes, N. Dietlein, F. Van Allen, E. M. 2020-09-23 doi:10.1101/2020.09.22.308833 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection ]]> https://biorxiv.org/content/10.1101/2020.09.22.308965v1?rss=1 Song, G. He, W.-t. Callaghan, S. Anzanello, F. Huang, D. Ricketts, J. Torres, J. L. Beutler, N. Peng, L. Vargas, S. Cassell, J. Parren, M. Yang, L. Ignacio, C. Smith, D. M. Voss, J. E. Nemazee, D. Ward, A. B. Rogers, T. Burton, D. R. Andrabi, R. 2020-09-23 doi:10.1101/2020.09.22.308965 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Impacted Spike Frequency Adaptation Associated with Reduction of KCNQ2/3 Promotes Seizure Activity in Temporal Lobe Epilepsy ]]> https://biorxiv.org/content/10.1101/2020.09.25.313254v1?rss=1 Rong, L. R. Cheng, J. S. Shuo, T. Bei, L. Yang, L. Lei, J. Hong, N. Yi, W. Q. Di, Z. S. Jing, G. R. 2020-09-28 doi:10.1101/2020.09.25.313254 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Tissue topography steers migrating Drosophila border cells ]]> https://biorxiv.org/content/10.1101/2020.09.27.316117v1?rss=1 Dai, W. Guo, X. Cao, Y. S. Mondo, J. A. Campanale, J. P. Montell, B. J. Burrous, H. Streichan, S. Gov, N. Rappel, W.-J. Montell, D. 2020-09-28 doi:10.1101/2020.09.27.316117 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Evolution of Modularity, Interactome and Functions of GIV/Girdin (CCDC88A) from Invertebrates to Vertebrates ]]> https://biorxiv.org/content/10.1101/2020.09.28.317172v1?rss=1 Ear, J. Ali Abd El-Hafeez, A. Roy, S. Ngo, T. Rajapakse, N. Choi, J. Khandelwal, S. Ghassemian, M. McCaffrey, L. Kufareva, I. Sahoo, D. Ghosh, P. 2020-09-28 doi:10.1101/2020.09.28.317172 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Functional Landscape of SARS-CoV-2 Cellular Restriction ]]> https://biorxiv.org/content/10.1101/2020.09.29.319566v1?rss=1 Martin-Sancho, L. Lewinski, M. K. Pache, L. Stoneham, C. YIN, X. Pratt, D. Churas, C. Rosenthal, S. B. Liu, S. De Jesus, P. D. O'Neill, A. M. Gounder, A. P. Nguyen, C. Pu, Y. Oom, A. L. Miorin, L. Rodriguez-Frandsen, A. Urbanowski, M. Shaw, M. L. Chang, M. W. Benner, C. Frieman, M. Garcia-Sastre, A. Ideker, T. Hultquist, J. F. Guatelli, J. Chanda, S. 2020-09-30 doi:10.1101/2020.09.29.319566 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ History-driven modulations of population codes in early visual cortex during visual search ]]> https://biorxiv.org/content/10.1101/2020.09.30.321729v1?rss=1 Adam, K. C. S. Serences, J. T. 2020-10-02 doi:10.1101/2020.09.30.321729 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome ]]> https://biorxiv.org/content/10.1101/2020.10.01.322701v1?rss=1 Ho, B. Ryback, D. Benson, B. Torres, P. J. Quinn, R. A. Thackray, V. G. Kelley, S. T. 2020-10-01 doi:10.1101/2020.10.01.322701 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Cellular Anatomy of the Mouse Primary Motor Cortex ]]> https://biorxiv.org/content/10.1101/2020.10.02.323154v1?rss=1 Munoz-Castaneda, R. Zingg, B. Matho, K. S. Wang, Q. Chen, X. Foster, N. N. Narasimhan, A. Li, A. Hirokawa, K. E. Huo, B. Banerjee, S. Korobkova, L. Park, C. S. Park, Y.-G. Bienkowski, M. S. Chon, U. Wheeler, D. W. Li, X. Wang, Y. Kelly, K. An, X. Attili, S. M. Bowman, I. Bludova, A. Cetin, A. Ding, L. Drewes, R. D'Orazi, F. Elowsky, C. Fischer, S. Galbavy, W. Gao, L. Gillis, J. Groblewski, P. A. Gou, L. Hahn, J. D. Hatfield, J. T. Hintiryan, H. Huang, J. Kondo, H. Kuang, X. Lesnar, P. Li, X. Li, Y. Lin, M. Liu, L. Lo, D. Mizrachi, J. Mok, S. Nae 2020-10-02 doi:10.1101/2020.10.02.323154 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion ]]> https://biorxiv.org/content/10.1101/2020.10.02.323915v1?rss=1 Yu, A. Pak, A. J. He, P. Monje-Galvan, V. Casalino, L. Gaieb, Z. Dommer, A. C. Amaro, R. E. Voth, G. A. 2020-10-02 doi:10.1101/2020.10.02.323915 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Benchmarking ensemble docking methods as a scientific outreach project ]]> https://biorxiv.org/content/10.1101/2020.10.02.324343v1?rss=1 Gan, J. L. Kumar, D. Chen, C. Taylor, B. C. Jagger, B. R. Amaro, R. E. Lee, C. T. 2020-10-04 doi:10.1101/2020.10.02.324343 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Single-cell data and correlation analysis support the independent double adder model in both Escherichia coli and Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2020.10.06.315820v1?rss=1 Le Treut, G. Si, F. Li, D. Jun, S. 2020-10-08 doi:10.1101/2020.10.06.315820 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets ]]> https://biorxiv.org/content/10.1101/2020.10.06.327080v1?rss=1 Cantrell, K. Fedarko, M. W. Rahman, G. McDonald, D. Yang, Y. Zaw, T. Gonzalez, A. Janssen, S. Estaki, M. Haiminen, N. Beck, K. L. Zhu, Q. Sayyari, E. Morton, J. Tripathi, A. Gauglitz, J. M. Marotz, C. Matteson, N. L. martino, c. Sanders, J. G. Carrieri, A. P. Song, S. J. Swafford, A. D. Dorrestein, P. Andersen, K. G. PARIDA, L. Kim, H.-C. Vazquez-Baeza, Y. Knight, R. 2020-10-08 doi:10.1101/2020.10.06.327080 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome ]]> https://biorxiv.org/content/10.1101/2020.10.07.328740v1?rss=1 Ohta, M. Zhao, Z. Wu, D. Wang, S. Harrison, J. L. Gomez-Cavazos, J. S. Desai, A. Oegema, K. 2020-10-07 doi:10.1101/2020.10.07.328740 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen ]]> https://biorxiv.org/content/10.1101/2020.10.08.332510v1?rss=1 Van Nostrand, E. L. Barnhill, S. A. Shishkin, A. A. Nelles, D. A. Byeon, E. Nguyen, T. Wong, Y. C. E. Gianneschi, N. C. Yeo, G. W. 2020-10-09 doi:10.1101/2020.10.08.332510 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Activation of MAP3K DLK and LZK in Purkinje Cells Causes Rapid and Slow Degeneration Depending on Signaling Strength ]]> https://biorxiv.org/content/10.1101/2020.10.09.332940v1?rss=1 Jin, Y. Li, Y. Ritchie, E. M. Steinke, C. L. Qi, C. Chen, L. Zheng, B. 2020-10-09 doi:10.1101/2020.10.09.332940 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Fetal innate immunity contributes to the induction of atypical behaviors in a mouse model of maternal immune activation ]]> https://biorxiv.org/content/10.1101/2020.10.09.333815v1?rss=1 Nichols, E. K. Chuang, H.-C. Davis, M. T. Geiger, K. M. Li, R. Z. Arnold, M. L. Lin, P. M. Misra, R. Coscoy, L. Saijo, K. 2020-10-10 doi:10.1101/2020.10.09.333815 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells ]]> https://biorxiv.org/content/10.1101/2020.10.09.334045v1?rss=1 Shamie, I. S. Duttke, S. H. la Cour Karottki, K. J. Han, C. Z. Hansen, A. H. Hefzi, H. Xiong, K. Li, S. Roth, S. Tao, J. Lee, G. M. Glass, C. K. Kildegaard, H. F. Benner, C. Lewis, N. E. 2020-10-10 doi:10.1101/2020.10.09.334045 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Aberrant Epithelial Differentiation Contributes to Pathogenesis in a Murine Model of Congenital Tufting Enteropathy ]]> https://biorxiv.org/content/10.1101/2020.10.12.330522v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@6700d7org.highwire.dtl.DTLVardef@6855b9org.highwire.dtl.DTLVardef@1d41207org.highwire.dtl.DTLVardef@1eb9f05_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Das, B. Okamoto, K. Rabalais, J. Young, J. Barrett, K. E. Sivagnanam, M. 2020-10-12 doi:10.1101/2020.10.12.330522 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Cross-modal orienting of exogenous attention results in visual-cortical facilitation, not suppression ]]> https://biorxiv.org/content/10.1101/2020.10.13.338210v1?rss=1 Keefe, J. M. Pokta, E. Stoermer, V. S. 2020-10-14 doi:10.1101/2020.10.13.338210 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Targeted millisecond-scale activation of cells using non-invasive Sonogenetics ]]> https://biorxiv.org/content/10.1101/2020.10.14.338699v1?rss=1 Duque, M. Lee-Kubli, C. Tufail, Y. Magaram, U. Lopez, J. M. Edsinger, E. Vasan, A. Shiao, R. Weiss, C. Friend, J. Chalasani, S. H. 2020-10-15 doi:10.1101/2020.10.14.338699 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Temporal stability of human sperm mosaic mutations results in life-long threat of transmission to offspring ]]> https://biorxiv.org/content/10.1101/2020.10.14.339796v1?rss=1 Yang, X. Breuss, M. W. Xu, X. Antaki, D. James, K. N. Stanley, V. Ball, L. L. George, R. D. Wirth, S. A. Cao, B. Nguyen, A. McEvoy-Venneri, J. Chai, G. Nahas, S. Van Der Kraan, L. Ding, Y. Sebat, J. Gleeson, J. G. 2020-10-14 doi:10.1101/2020.10.14.339796 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Diverse viral proteases activate the NLRP1 inflammasome ]]> https://biorxiv.org/content/10.1101/2020.10.16.343426v1?rss=1 Tsu, B. V. Beierschmitt, C. Ryan, A. P. Agarwal, R. Mitchell, P. S. Daugherty, M. D. 2020-10-17 doi:10.1101/2020.10.16.343426 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules ]]> https://biorxiv.org/content/10.1101/2020.10.19.344077v1?rss=1 Shams, A. Higgins, S. A. Fellmann, C. Laughlin, T. J. Oakes, B. L. Lew, R. Lukarska, M. Arnold, M. Staahl, B. Doudna, J. A. Savage, D. 2020-10-19 doi:10.1101/2020.10.19.344077 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Markov State Models and NMR Uncover an Overlooked Allosteric Loop in p53 ]]> https://biorxiv.org/content/10.1101/2020.10.19.346023v1?rss=1 Barros, E. P. Demir, O. Soto, J. Cocco, M. J. Amaro, R. E. 2020-10-19 doi:10.1101/2020.10.19.346023 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Tracking changes in behavioural dynamics using prediction error ]]> https://biorxiv.org/content/10.1101/2020.10.19.346080v1?rss=1 Lorimer, T. Goodridge, R. Bock, A. K. Agarwal, V. Saberski, E. Sugihara, G. Rifkin, S. A. 2020-10-21 doi:10.1101/2020.10.19.346080 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Functional Connectome Fingerprinting Using Shallow Feedforward Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.10.19.346189v1?rss=1 Sarar, G. Rao, B. Liu, T. 2020-10-21 doi:10.1101/2020.10.19.346189 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Higher-order hub cells involved in feedforward motifs as critical factors in epileptic network instability ]]> https://biorxiv.org/content/10.1101/2020.10.20.340364v1?rss=1 Hadjiabadi, D. H. Lovett-Barron, M. Raikov, I. Sparks, F. Liao, Z. Baraban, S. C. Leskovec, J. Losonczy, A. Deisseroth, K. Soltesz, I. 2020-10-21 doi:10.1101/2020.10.20.340364 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity ]]> https://biorxiv.org/content/10.1101/2020.10.21.336578v1?rss=1 Stormo, A. E. D. FitzGibbon, M. Shavarebi, F. Earley, E. M. Lum, L. S. Verschueren, E. Swaney, D. L. Skibinski, G. Ravisankar, A. van Haren, J. Davis, E. J. Johnson, J. R. Von Dollen, J. Mirescu, C. Iaccarino, C. Dauer, W. T. Nichols, R. J. Wittmann, T. Cox, T. C. Finkbeiner, S. Krogan, N. J. Oakes, S. A. Hiniker, A. 2020-10-21 doi:10.1101/2020.10.21.336578 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells ]]> https://biorxiv.org/content/10.1101/2020.10.23.347534v1?rss=1 Mellott, D. Tseng, C.-T. Drelich, A. Fajtova, P. Chenna, B. C. Kostomiris, D. Hsu, J. C. Zhu, J. Taylor, Z. Tat, V. Katzfuss, A. Li, L. Giardini, M. A. Skinner, D. Hirata, K. Beck, S. Carlin, A. F. Clark, A. E. Berreta, L. Maneval, D. Frueh, F. Hurst, B. L. Wang, H. Kocurek, K. I. Raushel, F. M. O'Donoghue, A. Siqueira-Neto, J. L. Meek, T. D. McKerrow, J. H. 2020-10-24 doi:10.1101/2020.10.23.347534 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Sleep spindles coordinate corticostriatal reactivations during the emergence of automaticity ]]> https://biorxiv.org/content/10.1101/2020.10.25.354282v1?rss=1 Lemke, S. M. Ramanathan, D. S. Darevsky, D. Egert, D. G. Berke, J. Ganguly, K. 2020-10-25 doi:10.1101/2020.10.25.354282 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase ]]> https://biorxiv.org/content/10.1101/2020.10.27.356436v1?rss=1 Xia, Z. Tang, M. Zhang, H. Gimple, R. Prager, B. Tang, H. Sun, C. Liu, F. Lin, P. Mei, Y. Du, R. Rich, J. Xie, Q. 2020-10-27 doi:10.1101/2020.10.27.356436 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ BrainGENIE: The Brain Gene Expression and Network Imputation Engine ]]> https://biorxiv.org/content/10.1101/2020.10.27.356766v1?rss=1 Hess, J. L. Chen, S. Quinn, T. P. Neuropsychiatric Consortium for Analysis and Sharing of Transcriptomes, Kong, S. W. Cairns, M. Tsuang, M. Faraone, S. V. Glatt, S. J. 2020-10-27 doi:10.1101/2020.10.27.356766 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Towards Biophysically-Based Neuromorphic Computing at Scale: Markov Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission ]]> https://biorxiv.org/content/10.1101/2020.10.27.358390v1?rss=1 Wagner, M. S. Bartol, T. M. Sejnowski, T. J. Cauwenberghs, G. 2020-10-28 doi:10.1101/2020.10.27.358390 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Catestatin reduces hyperglycemia in insulin-resistant mice by redirecting glucose-6-phosphate from the gluconeogenic to the glycogenic pathway ]]> https://biorxiv.org/content/10.1101/2020.10.31.363481v1?rss=1 Bandyopadhyay, G. K. Tang, K. Webster, N. J. G. van den Bogaart, G. Mahata, S. K. 2020-11-01 doi:10.1101/2020.10.31.363481 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Associations between Early Midlife Lifestyle Behaviors, Young Adult Cognitive Reserve and Advanced Predicted Brain Age in Late Midlife ]]> https://biorxiv.org/content/10.1101/2020.11.02.362780v1?rss=1 Franz, C. E. Hatton, S. N. Elman, J. A. Warren, T. Gillespie, N. A. Whitsel, N. A. Puckett, O. K. Dale, A. M. Eyler, L. T. Fennema-Notestine, C. Hagler, D. J. Hauger, R. L. McKenzie, R. Neale, M. C. Panizzon, M. S. Pearce, R. C. Reynolds, C. R. Sanderson-Cimino, M. Toomey, R. Tu, X. Xian, H. Lyons, M. J. Kremen, W. 2020-11-03 doi:10.1101/2020.11.02.362780 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4 ]]> https://biorxiv.org/content/10.1101/2020.11.02.365742v1?rss=1 50 million SNPs and InDels provided by five inbred strains of mice on the responses of macrophages to interleukin 4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Remarkably, of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage determining and signal-dependent transcription factors driving late enhancer activation. These studies further revealed mechanisms by which non-coding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity. ]]> Hoeksema, M. A. Shen, Z. Holtman, I. R. Zheng, A. Spann, N. Cobo, I. Gymrek, M. Glass, C. K. 2020-11-03 doi:10.1101/2020.11.02.365742 Cold Spring Harbor Laboratory Press 2020-11-03 <![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[ Elemental Mapping of Labeled Biological Specimens at Intermediate Energy Loss in an Energy-Filtered TEM acquired using a Direct Detection Device ]]> https://biorxiv.org/content/10.1101/2020.11.02.365940v1?rss=1 Ramachandra, R. Mackey, M. R. Hu, J. Peltier, S. T. Nguyen-Huu, X. Ellisman, M. H. Adams, S. R. 2020-11-03 doi:10.1101/2020.11.02.365940 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Protein Structural Alignments From Sequence ]]> https://biorxiv.org/content/10.1101/2020.11.03.365932v1?rss=1 Morton, J. Strauss, C. Blackwell, R. Berenberg, D. Gligorijevic, V. Bonneau, R. 2020-11-04 doi:10.1101/2020.11.03.365932 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Genetically encoded ratiometric biosensor for probing lysosomal pH in mammalian cells and C. elegans ]]> https://biorxiv.org/content/10.1101/2020.11.04.368654v1?rss=1 Chin, M. Y. Patwardhan, A. R. Ang, K.-H. Wang, A. L. Alquezar, C. Welch, M. Grabe, M. Arkin, M. R. Kao, A. W. 2020-11-04 doi:10.1101/2020.11.04.368654 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/2020.11.06.371724v1?rss=1 Overbey, E. G. Saravia-Butler, A. M. Zhang, Z. Rathi, K. S. Fogle, H. da Silveira, W. A. Barker, R. J. Bass, J. J. Beheshti, A. Berrios, D. C. Blaber, E. A. Cekanaviciute, E. Costa, H. A. Davin, L. B. Fisch, K. M. Gebre, S. G. Geniza, M. Gilbert, R. Gilroy, S. Hardiman, G. Herranz, R. Kidane, Y. H. Kruse, C. P. S. Lee, M. D. Liefeld, T. Lewis, N. G. McDonald, J. T. Meller, R. Mishra, T. Perera, I. Ray, S. Reinsch, S. Rosenthal, S. B. Strong, M. Szewczyk, N. J. Tahimic, C. G. T. Taylor, D. M. Vandenbrink, J. P. Villacampa, A. Weging, S. Wolverton, C. Wya 2020-11-10 doi:10.1101/2020.11.06.371724 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ The unfolded protein response links tumor aneuploidy to local immune dysregulation ]]> https://biorxiv.org/content/10.1101/2020.11.10.377358v1?rss=1 Xian, S. Searles, S. T. Sahani, P. Weller, T. C. Jepsen, K. Carter, H. Zanetti, M. 2020-11-11 doi:10.1101/2020.11.10.377358 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ CoaTran: Coalescent tree simulation along a transmission network ]]> https://biorxiv.org/content/10.1101/2020.11.10.377499v1?rss=1 Moshiri, N. 2020-11-11 doi:10.1101/2020.11.10.377499 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ VGLUT modulates sex differences in dopamine neuron vulnerability to age-related neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.11.11.379008v1?rss=1 Buck, S. A. Steinkellner, T. Aslanoglou, D. Villeneuve, M. Bhatte, S. H. Childers, V. C. Rubin, S. A. De Miranda, B. R. O'Leary, E. I. Neureiter, E. G. Fogle, K. J. Palladino, M. J. Logan, R. W. Glausier, J. R. Fish, K. N. Lewis, D. A. Greenamyre, J. T. Bonci, A. McCabe, B. D. Cheetham, C. E. Hnasko, T. S. Freyberg, Z. 2020-11-12 doi:10.1101/2020.11.11.379008 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection ]]> https://biorxiv.org/content/10.1101/2020.11.12.380634v1?rss=1 Sundaramoorthy, E. Ryan, A. P. Fulzele, A. Leonard, M. Daugherty, M. D. Bennett, E. J. 2020-11-12 doi:10.1101/2020.11.12.380634 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Defining the ultrastructure of the hematopoietic stem cell niche by correlative light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.11.12.380790v1?rss=1 Agarwala, S. Kim, K.-Y. Phan, S. Ju, S. Kong, Y. E. Castillon, G. A. Bushong, E. A. Ellisman, M. H. Tamplin, O. J. 2020-11-13 doi:10.1101/2020.11.12.380790 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities ]]> https://biorxiv.org/content/10.1101/2020.11.13.370387v1?rss=1 Shaffer, J. P. Marotz, C. Belda-Ferre, P. Martino, C. Wandro, S. Estaki, M. Salido, R. A. Carpenter, C. S. Zaramela, L. S. Minich, J. J. Bryant, M. B. Sanders, K. Fraraccio, S. Ackermann, G. Humphrey, G. Swafford, A. D. Miller-Montgomery, S. Knight, R. 2020-11-14 doi:10.1101/2020.11.13.370387 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.11.14.382473v1?rss=1 Yang, X. Xu, X. Breuss, M. W. Antaki, D. Ball, L. L. Chung, C. Li, C. George, R. D. Wang, Y. Bae, T. Abyzov, A. Sebat, J. Gleeson, J. G. 2020-11-16 doi:10.1101/2020.11.14.382473 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Challenges in Benchmarking Metagenomic Profilers ]]> https://biorxiv.org/content/10.1101/2020.11.14.382994v1?rss=1 Sun, Z. Huang, S. Zhang, M. Zhu, Q. Haiminen, N. Carrieri, A.-P. Vazquez-Baeza, Y. Parida, L. Kim, H.-C. Knight, R. Liu, Y.-Y. 2020-11-16 doi:10.1101/2020.11.14.382994 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ osr1 couples intermediate mesoderm cell fate with temporal dynamics of vessel progenitor cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.11.14.383141v1?rss=1 Perens, E. Diaz, J. Quesnel, A. Askary, A. Crump, G. Yelon, D. 2020-11-15 doi:10.1101/2020.11.14.383141 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Immunological memory to SARS-CoV-2 assessed for greater than six months after infection ]]> https://biorxiv.org/content/10.1101/2020.11.15.383323v1?rss=1 Dan, J. M. Mateus, J. Kato, Y. Hastie, K. M. Faliti, C. Ramirez, S. I. Frazier, A. Yu, E. D. Grifoni, A. Rawlings, S. A. Peters, B. Krammer, F. Simon, V. Saphire, E. O. Smith, D. Weiskopf, D. Sette, A. Crotty, S. 2020-11-16 doi:10.1101/2020.11.15.383323 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning ]]> https://biorxiv.org/content/10.1101/2020.11.17.385757v1?rss=1 Jiang, Y. Rensi, S. wang, s. Altman, R. B. 2020-11-20 doi:10.1101/2020.11.17.385757 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Transient genomic instability drives tumorigenesis through accelerated clonal evolution ]]> https://biorxiv.org/content/10.1101/2020.11.17.387753v1?rss=1 Shoshani, O. Bakker, B. Wang, Y. Kim, D. H. Maldonado, M. Demarest, M. A. Artates, J. Zhengyu, O. Mark, A. Wardenaar, R. Sasik, R. Spierings, D. C. Vitre, B. Fisch, K. Foijer, F. Cleveland, D. W. 2020-11-17 doi:10.1101/2020.11.17.387753 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Aberrant gliogenesis and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids ]]> https://biorxiv.org/content/10.1101/2020.11.19.387639v1?rss=1 Trudler, D. Ghatak, S. Parker, J. Talantova, M. Grabauskas, T. Noveral, S. M. Teranaka, M. Luevanos, M. Dolatabadi, N. Bakker, C. Lopez, K. Sultan, A. Chan, A. Choi, Y. Kawaguchi, R. Schork, N. Stankiewicz, P. Garcia-Bassets, I. Kozbial, P. Rosenfeld, M. G. Nakanishi, N. Geschwind, D. Chan, S. F. Ambasudhan, R. Lipton, S. A. 2020-11-19 doi:10.1101/2020.11.19.387639 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.19.390187v1?rss=1 Casalino, L. Dommer, A. C. Gaieb, Z. Barros, E. P. Sztain, T. Ahn, S.-H. Trifan, A. Brace, A. Ma, H. Lee, H. Turilli, M. Bogetti, A. Khalid, S. Chong, L. Simmerling, C. Hardy, D. Maia, J. Phillips, J. Kurth, T. Stern, A. Huang, L. McCalpain, J. Tatineni, M. Gibbs, T. Stone, J. E. Jha, S. Ramanathan, A. Amaro, R. E. 2020-11-20 doi:10.1101/2020.11.19.390187 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ MetENP/MetENPWeb: An R package and web application for metabolomics enrichment and pathway analysis in Metabolomics Workbench ]]> https://biorxiv.org/content/10.1101/2020.11.20.391912v1?rss=1 Choudhary, K. S. Fahy, E. Coakley, K. Sud, M. Maurya, M. R. Subramaniam, S. 2020-11-21 doi:10.1101/2020.11.20.391912 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Caenorhabditis elegans junctophilin has tissue-specific functions and regulates neurotransmission with extended-synaptotagmin ]]> https://biorxiv.org/content/10.1101/2020.11.20.392142v1?rss=1 Piggott, C. A. Wu, Z. Nurrish, S. Xu, S. Kaplan, J. M. Chisholm, A. D. Jin, Y. 2020-11-21 doi:10.1101/2020.11.20.392142 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Inferring the spatial code of cell-cell interactions and communication across a whole animal body ]]> https://biorxiv.org/content/10.1101/2020.11.22.392217v1?rss=1 Armingol, E. Joshi, C. J. Baghdassarian, H. Shamie, I. Ghaddar, A. Chan, J. Her, H.-L. O'Rourke, E. J. Lewis, N. E. 2020-11-22 doi:10.1101/2020.11.22.392217 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ SEPIA: Simulation-based Evaluation of Prioritization Algorithms ]]> https://biorxiv.org/content/10.1101/2020.11.23.394890v1?rss=1 Almaraz, K. Jang, T. Lewis, M. Ngo, T. Song, M. Moshiri, N. 2020-11-24 doi:10.1101/2020.11.23.394890 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology ]]> https://biorxiv.org/content/10.1101/2020.11.24.396820v1?rss=1 Young, C. Meng, S. Moshiri, N. 2020-11-25 doi:10.1101/2020.11.24.396820 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Selective transport of fluorescent proteins into the phage nucleus ]]> https://biorxiv.org/content/10.1101/2020.11.25.398438v1?rss=1 Nguyen, K. T. Sugie, J. Khanna, K. MacKennon, E. E. Birkholz, E. A. Lee, J. Beierschmitt, C. Villa, E. Pogliano, J. 2020-11-25 doi:10.1101/2020.11.25.398438 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Recurrent dynamics of prefrontal cortex during context-dependent decision-making ]]> https://biorxiv.org/content/10.1101/2020.11.27.401539v1?rss=1 Cohen, Z. DePasquale, B. Aoi, M. C. Pillow, J. W. 2020-11-27 doi:10.1101/2020.11.27.401539 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Divergent pallidal pathways underlying distinct Parkinsonian behavioral deficits ]]> https://biorxiv.org/content/10.1101/2020.11.27.401554v1?rss=1 Lim, B. Lilascharoen, V. Wang, E. H.-J. Do, N. Pate, S. C. Tran, A. N. Wang, X.-Y. Park, Y.-G. Chung, K. 2020-11-27 doi:10.1101/2020.11.27.401554 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Multielectrode Cortical Stimulation Selectively Induces Unidirectional Wave Propagation in Biophysical/Neural Model ]]> https://biorxiv.org/content/10.1101/2020.11.28.402289v1?rss=1 Halgren, A. S. Siegel, Z. Golden, R. Bazhenov, M. 2020-11-29 doi:10.1101/2020.11.28.402289 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis ]]> https://biorxiv.org/content/10.1101/2020.11.29.400614v1?rss=1 Blair, A. Hu, R. K. Farah, E. N. Pollard, K. S. Przytycki, P. F. Kathiriya, I. S. Bruneau, B. G. 2020-11-30 doi:10.1101/2020.11.29.400614 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution ]]> https://biorxiv.org/content/10.1101/2020.11.30.405589v1?rss=1 Zhang, C. Zhao, Y. Braun, E. L. Mirarab, S. 2020-12-02 doi:10.1101/2020.11.30.405589 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Light-activated tetrazines enable live-cell spatiotemporal control of bioorthogonal reactions ]]> https://biorxiv.org/content/10.1101/2020.12.01.405423v1?rss=1 Liu, L. Zhang, D. Johnson, M. Devaraj, N. K. 2020-12-02 doi:10.1101/2020.12.01.405423 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveals a path to selective inhibitors ]]> https://biorxiv.org/content/10.1101/2020.12.01.406264v1?rss=1 Rathinaswamy, M. K. Gaieb, Z. Fleming, K. D. Borsari, C. Harris, N. J. Moeller, B. J. Wymann, M. P. Amaro, R. E. Burke, J. E. 2020-12-02 doi:10.1101/2020.12.01.406264 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq ]]> https://biorxiv.org/content/10.1101/2020.12.03.387894v1?rss=1 Benaglio, P. Newsome, J. Han, J. Y. Chiou, J. Aylward, A. Corban, S. Okino, M.-L. Kaur, J. Gorkin, D. Gaulton, K. J. 2020-12-03 doi:10.1101/2020.12.03.387894 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE2 ]]> https://biorxiv.org/content/10.1101/2020.12.04.409144v1?rss=1 Lei, Y. Zhang, J. Schiavon, C. R. He, M. Chen, L. Shen, H. Zhang, Y. Yin, Q. Cho, Y. Andrade, L. Shadel, G. S. Hepokoski, M. Lei, T. Wang, H. Zhang, J. Yuan, J. X.- J. Malhotra, A. Manor, U. Wang, S. Yuan, Z.-Y. Shyy, J. Y.-J. 2020-12-04 doi:10.1101/2020.12.04.409144 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Mechanism for differential recruitment of orbitostriatal transmission during outcomes and actions in alcohol dependence ]]> https://biorxiv.org/content/10.1101/2020.12.04.411819v1?rss=1 Gremel, C. M. Renteria, R. Cazares, C. Baltz, E. T. Schreiner, D. C. Yalcinbas, E. A. Steinkellner, T. Hnasko, T. S. 2020-12-04 doi:10.1101/2020.12.04.411819 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Cancer-specific overmethylation of histone H3 lysines is necessary for methionine addiction and malignancy ]]> https://biorxiv.org/content/10.1101/2020.12.04.412437v1?rss=1 Yamamoto, J. Inubushi, S. Han, Q. Tashiro, Y. Sun, Y. Sugisawa, N. Hamada, K. Nishino, H. Aoki, Y. Miyake, K. Matsuyama, R. Bouvet, M. Endo, I. Hoffman, R. M. 2020-12-06 doi:10.1101/2020.12.04.412437 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Hawkmoths use wingstroke-to-wingstroke frequency modulation for aerial recovery to vortex ring perturbations ]]> https://biorxiv.org/content/10.1101/2020.12.07.413781v1?rss=1 Gau, J. Gemilere, R. LDS-VIP FM subteam, Lynch, J. Gravish, N. Sponberg, S. 2020-12-08 doi:10.1101/2020.12.07.413781 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Quantifying liquid-liquid phase separation property of chromatin under physiological conditions using Hi-MS and Hi-C ]]> https://biorxiv.org/content/10.1101/2020.12.07.415489v1?rss=1 Shi, M. You, K. Hou, C. Chen, T. Liang, Z. Liu, M. Wang, J. Wei, T. Qin, J. Chen, Y. Li, T. Zhang, M. Q. 2020-12-08 doi:10.1101/2020.12.07.415489 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases ]]> https://biorxiv.org/content/10.1101/2020.12.08.416750v1?rss=1 Tarke, A. Sidney, J. Kidd, C. K. Dan, J. M. Ramirez, S. I. Yu, E. D. Mateus, J. da Silva Antunes, R. Moore, E. Rubiro, P. Methot, N. Phillips, E. J. Mallal, S. Frazier, A. Rawlings, S. Greenbaum, J. A. Peters, B. Smith, D. M. Crotty, S. Weiskopf, D. Grifoni, A. Sette, A. 2020-12-09 doi:10.1101/2020.12.08.416750 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Identification of a Novel Susceptibility Marker for SARS-CoV-2 Infection in Human Subjects and Risk Mitigation with a Clinically Approved JAK Inhibitor in Human/Mouse Cells ]]> https://biorxiv.org/content/10.1101/2020.12.09.416586v1?rss=1 Spalinger, M. R. Hai, R. Li, J. Santos, A. N. Nordgren, T. M. Tremblay, M. L. Eckmann, L. Hanson, E. Scharl, M. Wu, X. Boland, B. S. McCole, D. F. 2020-12-09 doi:10.1101/2020.12.09.416586 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Integrated scRNA-seq analysis identifies conserved transcriptomic features of mononuclear phagocytes in mouse and human atherosclerosis ]]> https://biorxiv.org/content/10.1101/2020.12.09.417535v1?rss=1 Zernecke, A. Erhard, F. Weinberger, T. Schulz, C. Ley, K. Saliba, A.-E. Cochain, C. 2020-12-10 doi:10.1101/2020.12.09.417535 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Effects of early life adversity on maternal effort and glucocorticoids in wild olive baboons ]]> https://biorxiv.org/content/10.1101/2020.12.11.418095v1?rss=1 Patterson, S. K. Hinde, K. Bond, A. B. Trumble, B. C. Strum, S. C. Silk, J. B. 2020-12-11 doi:10.1101/2020.12.11.418095 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ TCRMatch: Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors ]]> https://biorxiv.org/content/10.1101/2020.12.11.418426v1?rss=1 Chronister, W. D. Crinklaw, A. Mahajan, S. Vita, R. Kosaloglu-Yalcin, Z. Yan, Z. Greenbaum, J. A. Jessen, L. E. Nielsen, M. Christley, S. Cowell, L. G. Sette, A. Peters, B. 2020-12-11 doi:10.1101/2020.12.11.418426 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422541v1?rss=1 Ding, B. Liu, Y. Liu, Z. Zheng, L. Xu, P. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wei, W. Wang, W. 2020-12-14 doi:10.1101/2020.12.13.422541 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data ]]> https://biorxiv.org/content/10.1101/2020.12.13.422543v1?rss=1 Yu, M. Abnousi, A. Zhang, Y. Li, G. Lee, L. Chen, Z. Fang, R. Wen, J. Sun, Q. Li, Y. Ren, B. Hu, M. 2020-12-15 doi:10.1101/2020.12.13.422543 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Regulatory elements can be essential for maintaining broad chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422554v1?rss=1 Liu, Y. Ding, B. Zheng, L. Xu, P. Liu, Z. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wang, W. Wei, W. 2020-12-13 doi:10.1101/2020.12.13.422554 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Distinguishing the behavioral potencies of α-pyrrolidino-phenone cathinone stimulants ]]> https://biorxiv.org/content/10.1101/2020.12.14.422779v1?rss=1 Taffe, M. A. Nguyen, J. D. Vandewater, S. A. Grant, Y. Dickerson, T. J. 2020-12-15 doi:10.1101/2020.12.14.422779 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ FOXO1 mitigates the SMAD3/FOXL2C134W Transcriptomic Effect in a Model of Human Adult Granulosa Cell Tumor ]]> https://biorxiv.org/content/10.1101/2020.12.15.422901v1?rss=1 Secchi, C. Benaglio, P. Mulas, F. Belli, M. Stupack, D. Shimasaki, S. 2020-12-16 doi:10.1101/2020.12.15.422901 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ A Theory of Synaptic Transmission ]]> https://biorxiv.org/content/10.1101/2020.12.17.423159v1?rss=1 Wang, B. Dudko, O. 2020-12-19 doi:10.1101/2020.12.17.423159 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ Adaptive integration of self-motion and goals in posterior parietal cortex ]]> https://biorxiv.org/content/10.1101/2020.12.19.423589v1?rss=1 Alexander, A. S. Tung, J. C. Chapman, G. W. Shelley, L. E. Hasselmo, M. E. Nitz, D. A. 2020-12-20 doi:10.1101/2020.12.19.423589 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L ]]> https://biorxiv.org/content/10.1101/2020.12.23.424111v1?rss=1 Ashhurst, A. Tang, A. Fajtova, P. Yoon, M. Aggarwal, A. Stoye, A. Larance, M. Beretta, L. Drelich, A. Skinner, D. Li, L. Meek, T. McKerrow, J. Hook, V. Tseng, C.-T. Turville, S. G. Gerwick, W. O'Donoghue, A. Payne, R. J. 2020-12-25 doi:10.1101/2020.12.23.424111 Cold Spring Harbor Laboratory Press 2020-12-25 <![CDATA[ The N-terminal Tail of C. elegans CENP-A Interacts with KNL-2 and is Essential for Centromeric Chromatin Assembly ]]> https://biorxiv.org/content/10.1101/2020.12.28.424576v1?rss=1 de Groot, C. Houston, J. Davis, B. Gerson-Gurwitz, A. Monen, J. Oegema, K. Shiau, A. K. Desai, A. 2020-12-28 doi:10.1101/2020.12.28.424576 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Preventing post-surgical cardiac adhesions with a catechol-functionalized oxime hydrogel ]]> https://biorxiv.org/content/10.1101/2020.12.29.424755v1?rss=1 Fujita, M. Policastro, G. M. Burdick, A. Lam, H. T. Ungerleider, J. Braden, R. L. Huang, D. Osborn, K. Omens, J. H. Madani, M. Christman, K. 2020-12-30 doi:10.1101/2020.12.29.424755 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses ]]> https://biorxiv.org/content/10.1101/2020.12.30.424898v1?rss=1 2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants, and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance. ]]> Xie, Q. Yu, Q. Jobe, T. O. Pham, A. Ge, C. Guo, Q. Liu, J. Liu, H. Zhang, H. Zhao, Y. Xue, S. Hauser, F. Schroeder, J. I. 2021-01-02 doi:10.1101/2020.12.30.424898 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface ]]> https://biorxiv.org/content/10.1101/2020.12.31.424868v1?rss=1 Zost, S. J. Dong, J. Gilchuk, I. M. Gilchuk, P. Thornburg, N. J. Bangaru, S. Kose, N. Finn, J. A. Bombardi, R. Soto, C. Nargi, R. S. Irving, R. P. Suryadevara, N. Westover, J. B. Carnahan, R. H. Turner, H. L. Li, S. Ward, A. B. Crowe, J. E. 2021-01-03 doi:10.1101/2020.12.31.424868 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Comprehensive multi-omics study of the molecular perturbations induced by simulated diabetes on coronary artery endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.06.425584v1?rss=1 Moreno-Ulloa, A. Delgado De la Herran, H. C. Alvarez Delgado, C. Mendoza Porras, O. Carballo Castaneda, R. A. Villarreal, F. 2021-01-08 doi:10.1101/2021.01.06.425584 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Restoration of deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells ]]> https://biorxiv.org/content/10.1101/2021.01.07.425558v1?rss=1 Spahn, P. Zhang, X. Hu, Q. Hamaker, N. Hefzi, H. Li, S. Kuo, C.-C. Huang, Y. Lee, J. Ly, P. Lee, K. Lewis, N. E. 2021-01-07 doi:10.1101/2021.01.07.425558 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains ]]> https://biorxiv.org/content/10.1101/2021.01.08.426013v1?rss=1 Gao, Y. Poudel, S. Seif, Y. Shen, Z. Palsson, B. O. 2021-01-09 doi:10.1101/2021.01.08.426013 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Nucleus accumbens neurons encode initiation and vigor of reward approach behavior ]]> https://biorxiv.org/content/10.1101/2021.01.12.425739v1?rss=1 Levcik, D. Sugi, A. H. Pochapski, J. A. Baltazar, G. Pulido, L. N. Villas-Boas, C. Aguilar-Rivera, M. Fuentes-Flores, R. Nicola, S. M. Da Cunha, C. 2021-01-12 doi:10.1101/2021.01.12.425739 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ The SLIM1 transcription factor regulates arsenic sensitivity in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.01.12.426316v1?rss=1 Jobe, T. O. Yu, Q. Hauser, F. Xie, Q. Meng, Y. Maassen, T. Kopriva, S. Schroeder, J. 2021-01-13 doi:10.1101/2021.01.12.426316 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk ]]> https://biorxiv.org/content/10.1101/2021.01.13.426472v1?rss=1 Chiou, J. Geusz, R. Okino, M.-L. Han, J. Y. Miller, M. Benaglio, P. Huang, S. Korgaonkar, K. Heller, S. Kleger, A. Preissl, S. Gorkin, D. Sander, M. Gaulton, K. J. 2021-01-15 doi:10.1101/2021.01.13.426472 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent ]]> https://biorxiv.org/content/10.1101/2021.01.13.426522v1?rss=1 Waschke, L. Donoghue, T. Fiedler, L. Smith, S. Garrett, D. D. Voytek, B. Obleser, J. 2021-01-14 doi:10.1101/2021.01.13.426522 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ A triple-negative matrix-producing breast carcinoma is arrested by tumor-targeting Salmonella typhimurium A1-R in a PDOX model ]]> https://biorxiv.org/content/10.1101/2021.01.14.426747v1?rss=1 Hamada, K. Yamamoto, J. Hozumi, C. Zhao, M. Murata, T. Sugisawa, N. Sun, Y. Aoki, Y. Nishino, H. Bouvet, M. Tsunoda, T. Hoffman, R. M. 2021-01-16 doi:10.1101/2021.01.14.426747 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors ]]> https://biorxiv.org/content/10.1101/2021.01.18.427081v1?rss=1 Puppo, F. Sadegh, S. Trujillo, C. Thunemann, M. Campbell, E. Vandenberghe, M. Shan, X. Akkouh, I. A. Miller, E. W. Bloodgood, B. L. Silva, G. A. Dale, A. M. Einevoll, G. T. Djurovic, S. Andreassen, O. A. Muotri, A. R. Devor, A. 2021-01-19 doi:10.1101/2021.01.18.427081 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Alignment of biomedical data repositories with open, FAIR, citable and trustworthy principles ]]> https://biorxiv.org/content/10.1101/2021.01.19.427362v1?rss=1 Murphy, F. Bar-Sinai, M. Martone, M. E. 2021-01-20 doi:10.1101/2021.01.19.427362 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution ]]> https://biorxiv.org/content/10.1101/2021.01.27.428469v1?rss=1 1000s viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure, and enable the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit. ]]> Gallardo, C. M. Wang, S. Montiel-Garcia, D. J. Little, S. J. Smith, D. M. Routh, A. L. Torbett, B. E. 2021-01-28 doi:10.1101/2021.01.27.428469 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Phage Cocktails can Prevent the Evolution of Phage-Resistant Enterococcus ]]> https://biorxiv.org/content/10.1101/2021.01.27.428553v1?rss=1 Wandro, S. Ghatbale, P. Attai, H. Hendrickson, C. Samillano, C. Suh, J. Pride, D. T. Whiteson, K. 2021-01-28 doi:10.1101/2021.01.27.428553 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework ]]> https://biorxiv.org/content/10.1101/2021.01.28.428578v1?rss=1 Auddya, D. Zhang, X. Gulati, R. Vasan, R. Garikipati, K. Rangamani, P. Rudraraju, S. 2021-01-29 doi:10.1101/2021.01.28.428578 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.01.29.428890v1?rss=1 Berndt, A. J. Smalley, T. N. Ren, B. Badary, A. Sproles, A. Fields, F. Torres-Tiji, Y. Heredia, V. Mayfield, S. P. 2021-01-30 doi:10.1101/2021.01.29.428890 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Non cell-autonomous effect of astrocytes on cerebral cavernous malformations ]]> https://biorxiv.org/content/10.1101/2021.01.29.428891v1?rss=1 Lopez-Ramirez, M. A. A. Soliman, S. I. Hale, P. Lai, C. C. Pham, A. Estrada, E. J. McCurdy, S. Girard, R. Verma, R. Moore, T. Lightle, R. Hobson, N. Shenkar, R. Poulsen, O. Haddad, G. G. Daneman, R. Gongol, B. Sun, H. Lagarrigue, F. Awad, I. A. Ginsberg, M. 2021-02-01 doi:10.1101/2021.01.29.428891 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Complementary Maps for Location and Environmental Structure in CA1 and Subiculum ]]> https://biorxiv.org/content/10.1101/2021.02.01.428537v1?rss=1 Olson, J. M. Johnson, A. B. Chang, L. Tao, E. L. Wang, X. Nitz, D. A. 2021-02-02 doi:10.1101/2021.02.01.428537 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Potential global impact of the N501Y mutation on MHC-II presentation and immune escape ]]> https://biorxiv.org/content/10.1101/2021.02.02.429431v1?rss=1 Castro, A. Carter, H. Zanetti, M. 2021-02-03 doi:10.1101/2021.02.02.429431 Cold Spring Harbor Laboratory Press 2021-02-03 <![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[ The purine nucleoside phosphorylase pnp-1 regulates epithelial cell resistance to infection in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.02.03.429531v1?rss=1 Tecle, E. Chhan, C. B. Franklin, L. Underwood, R. S. Hanna-Rose, W. Troemel, E. R. 2021-02-03 doi:10.1101/2021.02.03.429531 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells ]]> https://biorxiv.org/content/10.1101/2021.02.04.429675v1?rss=1 Chen, P. Fiaux, P. Li, B. Zhang, K. Kubo, N. Jiang, S. Hu, R. Wu, S. Wang, M. Wang, W. McVicker, G. P. Mischel, P. Ren, B. 2021-02-05 doi:10.1101/2021.02.04.429675 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Derived loss of signal complexity and plasticity in a genus of weakly electric fish ]]> https://biorxiv.org/content/10.1101/2021.02.06.430027v1?rss=1 Saenz, D. E. Gu, T. Ban, Y. Winemiller, K. O. Markham, M. R. 2021-02-08 doi:10.1101/2021.02.06.430027 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data ]]> https://biorxiv.org/content/10.1101/2021.02.10.430563v1?rss=1 Bandrowski, A. Grethe, J. S. Pilko, A. Gillespie, T. H. Pine, G. Patel, B. Surles-Zeiglera, M. Martone, M. E. 2021-02-10 doi:10.1101/2021.02.10.430563 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates ]]> https://biorxiv.org/content/10.1101/2021.02.10.430696v1?rss=1 S Arunachalam, P. Walls, A. C. Golden, N. Atyeo, C. Fischinger, S. Li, C. Aye, P. Navarro, M. J. Lai, L. Edara, V. V. Roltgen, K. Rogers, K. Shirreff, L. Ferrell, D. E. Wrenn, S. Pettie, D. Kraft, J. C. Miranda, M. C. Kepl, E. Sydeman, C. Brunette, N. Murphy, M. Fiala, B. Carter, L. White, A. G. Trisal, M. Hsieh, C.-L. Russell-Lodrigue, K. Monjure, C. Dufour, J. Doyle-Meyer, L. Bohm, R. B. Maness, N. J. Roy, C. Plante, J. A. Plante, K. S. Zhu, A. Gorman, M. J. Shin, S. Shen, X. Fontenot, J. Gupta, S. O Hagan, D. T. Most, R. V. D. Rappuoli, R. Coffma 2021-02-11 doi:10.1101/2021.02.10.430696 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ What are housekeeping genes? ]]> https://biorxiv.org/content/10.1101/2021.02.14.431149v1?rss=1 Joshi, C. J. Ke, W. Drangowska-Way, A. O'Rourke, E. J. Lewis, N. E. 2021-02-16 doi:10.1101/2021.02.14.431149 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ APPLES-2: Faster and More Accurate Distance-based Phylogenetic Placement using Divide and Conquer ]]> https://biorxiv.org/content/10.1101/2021.02.14.431150v1?rss=1 Balaban, M. Roush, D. Zhu, Q. Mirarab, S. 2021-02-14 doi:10.1101/2021.02.14.431150 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ A glycan gate controls opening of the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.02.15.431212v1?rss=1 Sztain, T. E. Ahn, S.-H. Bogetti, A. T. Casalino, L. Goldsmith, J. A. McCool, R. S. Kearns, F. L. McCammon, J. A. McLellan, J. S. Chong, L. Amaro, R. E. 2021-02-16 doi:10.1101/2021.02.15.431212 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Plant trait heterosis is quantitatively associated with expression heterosis of plastid ribosomal proteins ]]> https://biorxiv.org/content/10.1101/2021.02.16.431485v1?rss=1 Birdseye, D. De Boer, L. Shen, Z. Bai, H. Zhou, P. Schmelz, E. A. Springer, N. M. Briggs, S. 2021-02-17 doi:10.1101/2021.02.16.431485 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Shared long-term and short-term memory representational formats in occipital and parietal cortex ]]> https://biorxiv.org/content/10.1101/2021.02.16.431528v1?rss=1 Vo, V. A. Sutterer, D. W. Foster, J. J. Sprague, T. C. Awh, E. Serences, J. T. 2021-02-16 doi:10.1101/2021.02.16.431528 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ A cell atlas of chromatin accessibility across 25 adult human tissues ]]> https://biorxiv.org/content/10.1101/2021.02.17.431699v1?rss=1 Zhang, K. Hocker, J. D. Miller, M. Hou, X. Chiou, J. Poirion, O. B. Qiu, Y. Li, Y. E. Gaulton, K. J. Wang, A. Preissl, S. Ren, B. 2021-02-17 doi:10.1101/2021.02.17.431699 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Pyrazinamide action is driven by the cell envelope stress response in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.02.17.431758v1?rss=1 Thiede, J. M. Dillon, N. Howe, M. D. Modlin, S. J. Aflakpui, R. Hoffner, S. Valafar, F. Minato, Y. Baughn, A. D. 2021-02-18 doi:10.1101/2021.02.17.431758 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Constructing An Adult Orofacial Premotor Atlas In Allen Mouse CCF ]]> https://biorxiv.org/content/10.1101/2021.02.18.431923v1?rss=1 Takatoh, J. Park, J. H. Lu, J. Li, S. Thompson, P. M. Han, B.-X. Zhao, S. Kleinfeld, D. Friedman, B. Wang, F. 2021-02-19 doi:10.1101/2021.02.18.431923 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Parallel Characterization of cis-Regulatory Elements for Multiple Genes UsingCRISPRpath ]]> https://biorxiv.org/content/10.1101/2021.02.19.431931v1?rss=1 Ren, X. Wang, M. Li, B. Jamieson, K. Zheng, L. Jones, I. R. Li, B. Takagi, M. A. Lee, J. Maliskova, L. Tam, T. W. Yu, M. Hu, R. Lee, L. Abnousi, A. Li, G. Li, Y. Hu, M. Ren, B. Wang, W. Shen, Y. 2021-02-19 doi:10.1101/2021.02.19.431931 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Precision Diffusion Imaging ]]> https://biorxiv.org/content/10.1101/2021.02.19.432023v1?rss=1 Seider, N. A. Adeyemo, B. Miller, R. Newbold, D. J. Hampton, J. M. Scheidter, K. M. Rutlin, J. Laumann, T. O. Roland, J. L. Montez, D. F. Van, A. N. Zheng, A. Marek, S. Kay, B. P. Bretthorst, G. L. Schlaggar, B. L. Greene, D. J. Wang, Y. Petersen, S. E. Gordon, E. M. Snyder, A. Z. Shimony, J. S. Dosenbach, N. U. 2021-02-20 doi:10.1101/2021.02.19.432023 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Bacterial Cytological Profiling Identifies Rhodanine-containing PAINS Analogs as Specific Inhibitors of E. coli Thymidylate Kinase in Vivo ]]> https://biorxiv.org/content/10.1101/2021.02.22.432404v1?rss=1 Montano, E. T. Nideffer, J. F. Sugie, J. Enustun, E. Shapiro, A. B. Tsunemoto, H. Derman, A. Pogliano, K. Pogliano, J. 2021-02-25 doi:10.1101/2021.02.22.432404 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Clinical Phage Microbiology:A suggested framework and recommendations for the in-vitro matching steps ‎of phage therapy ]]> https://biorxiv.org/content/10.1101/2021.02.23.432393v1?rss=1 Gelman, D. Yerushalmy, O. Ben-Porat, S. Rakov, C. Alkalay-Oren, S. Adler, K. Khalifa, L. Abdalrhman, M. Coppenhagen-Glazer, S. Aslam, S. Schooley, R. T. Nir-Paz, R. Hazan, R. 2021-02-23 doi:10.1101/2021.02.23.432393 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Widespread ripples synchronize human cortical activity ]]> https://biorxiv.org/content/10.1101/2021.02.23.432582v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Jiang, X. Rosen, B. Q. Kajfez, S. Stedelin, B. Shih, J. J. Ben-Haim, S. Raslan, A. M. Madsen, J. R. Eskandar, E. N. Gonzalez-Martinez, J. Cash, S. S. Halgren, E. 2021-02-24 doi:10.1101/2021.02.23.432582 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Csf1r-GCaMP5 Reporter Mice Reveal Immune Cell Communication in Vitro and in Vivo ]]> https://biorxiv.org/content/10.1101/2021.02.24.432710v1?rss=1 Taghdiri, N. Calcagno, D. M. Fu, Z. R. Huang, K. Kohler, R. H. Weissleder, R. Coleman, T. P. King, K. R. 2021-02-24 doi:10.1101/2021.02.24.432710 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq ]]> https://biorxiv.org/content/10.1101/2021.02.26.433126v1?rss=1 Massarat, A. R. Sen, A. Jaureguy, J. Tyndale, S. T. Fu, Y. Erikson, G. McVicker, G. 2021-02-27 doi:10.1101/2021.02.26.433126 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters ]]> https://biorxiv.org/content/10.1101/2021.02.26.433127v1?rss=1 Schaworonkow, N. Voytek, B. 2021-02-28 doi:10.1101/2021.02.26.433127 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Tetraspanin immunocapture phenotypes extracellular vesicles according to biofluid source but may limit identification of multiplexed cancer biomarkers ]]> https://biorxiv.org/content/10.1101/2021.03.02.433595v1?rss=1 Mizenko, R. R. Brostoff, T. Rojalin, T. Koster, H. J. Swindell, H. S. Leiserowitz, G. S. Wang, A. Carney, R. P. 2021-03-03 doi:10.1101/2021.03.02.433595 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Targeting Biofilm of MDR Providencia stuartii by Phages Using a Catheter Model ]]> https://biorxiv.org/content/10.1101/2021.03.02.433687v1?rss=1 Rakov, C. Ben-Porat, S. Alkalay-Oren, S. Yerushalmy, O. Abdalrhman, M. Gronovich, N. Huang, L. S. Pride, D. T. Coppenhagen-Glazer, S. Nir Paz, R. Hazan, R. 2021-03-03 doi:10.1101/2021.03.02.433687 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Predicting functional consequences of mutations using molecular interaction network features ]]> https://biorxiv.org/content/10.1101/2021.03.05.433991v1?rss=1 Ozturk, K. Carter, H. 2021-03-08 doi:10.1101/2021.03.05.433991 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius. ]]> https://biorxiv.org/content/10.1101/2021.03.08.432323v1?rss=1 O'Neill, A. M. Worthing, K. A. Kulkarni, N. Li, F. Nakatsuji, T. Mills, R. H. Cheng, J. Y. Gonzalez, D. J. Norris, J. M. Gallo, R. L. 2021-03-08 doi:10.1101/2021.03.08.432323 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1 ]]> https://biorxiv.org/content/10.1101/2021.03.08.434337v1?rss=1 Gandhi, S. Mitterhoff, R. Rapoport, R. Eden, S. Goren, A. Simon, I. 2021-03-08 doi:10.1101/2021.03.08.434337 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Effect of chronic JUUL aerosol inhalation on inflammatory states of the brain, lung, heart and colon in mice ]]> https://biorxiv.org/content/10.1101/2021.03.09.434442v1?rss=1 Moshensky, A. Brand, C. Alhaddad, H. Shin, J. Masso-Silva, J. A. Advani, I. Gunge, D. Sharma, A. Mehta, S. Jahan, A. Nilaad, S. Almarghalani, D. Pham, J. Perera, S. Park, K. Al-Kolla, R. Moon, H. Das, S. Byun, M. Shah, Z. Sari, Y. Heller Brown, J. Crotty Alexander, L. E. 2021-03-10 doi:10.1101/2021.03.09.434442 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Structural connectome quantifies tumor invasion and predicts survival in glioblastoma patients ]]> https://biorxiv.org/content/10.1101/2021.03.09.434656v1?rss=1 Wei, Y. Li, C. Cui, Z. Mayrand, R. C. Zou, J. Wong, A. L. K. C. Sinha, R. Matys, T. Schönlieb, C.-B. Price, S. J. 2021-03-10 doi:10.1101/2021.03.09.434656 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ The geometry of face memory ]]> https://biorxiv.org/content/10.1101/2021.03.12.435023v1?rss=1 She, L. Benna, M. K. Shi, Y. Fusi, S. Tsao, D. Y. 2021-03-12 doi:10.1101/2021.03.12.435023 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Structural Covariance Networks in Post-Traumatic Stress Disorder: A Multisite ENIGMA-PGC Study ]]> https://biorxiv.org/content/10.1101/2021.03.13.432212v1?rss=1 Rakesh, G. Sun, D. Logue, M. Clarke-Rubright, E. O Leary, B. M. Haswell, C. Xie, H. Thompson, P. Dennis, E. Jahanshad, N. Koch, S. Frijling, J. Nawijn, L. Olff, M. van Zuiden, M. Rashid, F. Zhu, X. De Bellis, M. Daniels, J. K. Sierk, A. Manthey, A. Stevens, J. S. Jovanovic, T. Stein, M. B. Shenton, M. van der Werff, S. J. A. van der Wee, N. J. A. Vermeiren, R. R. J. M. Schmahl, C. Herzog, J. Kaufman, M. L. O'Connor, L. Lebois, L. A. M. Baker, J. T. Gruber, S. A. Wolff, J. D. Wolf, E. J. Winternitz, S. Gonenc, A. Ressler, K. J. Hofmann, D. Bryant, R. A. 2021-03-16 doi:10.1101/2021.03.13.432212 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Using synthetic MR images for field map-less distortion correction ]]> https://biorxiv.org/content/10.1101/2021.03.13.435270v1?rss=1 Montez, D. F. Van, A. N. Miller, R. L. Seider, N. A. Marek, S. Zheng, A. Newbold, D. J. Scheidter, K. Feczko, E. Perrone, A. J. Miranda Dominguez, O. Earl, E. A. Kay, B. P. Jha, A. K. Sotiras, A. Laumann, T. O. Greene, D. J. Gordon, E. M. Tisdall, M. D. van der Kouwe, A. Fair, D. A. Dosenbach, N. U. F. 2021-03-15 doi:10.1101/2021.03.13.435270 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Open Data Commons for Preclinical Traumatic Brain Injury Research: Empowering Data Sharing and Big Data Analytics ]]> https://biorxiv.org/content/10.1101/2021.03.15.435178v1?rss=1 Chou, A. C. Torres-Espin, A. Huie, J. R. Krukowski, K. Lee, S. Nolan, A. Guglielmetti, C. Hawkins, B. E. Chaumeil, M. M. Manley, G. T. Beattie, M. S. Bresnahan, J. C. Martone, M. E. Grethe, J. S. Rosi, S. Ferguson, A. R. 2021-03-16 doi:10.1101/2021.03.15.435178 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Morphological principles of neuronal mitochondria ]]> https://biorxiv.org/content/10.1101/2021.03.15.435547v1?rss=1 Mendelsohn, R. Garcia, G. C. Bartol, T. M. Lee, C. T. Khandelwal, P. Liu, E. Spencer, D. J. Husar, A. Bushong, E. A. Phan, S. Perkins, G. Ellisman, M. H. Skupin, A. Sejnowski, T. J. Rangamani, P. 2021-03-16 doi:10.1101/2021.03.15.435547 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Meiotic Cas9 expression mediates genotype conversion in the male and female mouse germline ]]> https://biorxiv.org/content/10.1101/2021.03.16.435716v1?rss=1 Weitzel, A. J. Grunwald, H. A. Levina, R. Gantz, V. M. Hedrick, S. M. Bier, E. Cooper, K. L. 2021-03-17 doi:10.1101/2021.03.16.435716 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ iPSC-derived pancreatic progenitors are an optimal model system to study T2D regulatory variants active during fetal development of the pancreas ]]> https://biorxiv.org/content/10.1101/2021.03.17.435846v1?rss=1 D'Antonio-Chronowska, A. Donovan, M. K. R. Fujita, K. Salgado, B. M. Matsui, H. Arthur, T. D. Nguyen, J. P. D'Antonio, M. Frazer, K. A. 2021-03-17 doi:10.1101/2021.03.17.435846 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Proteomic Organellar Mapping Reveals Modulation of Peroxisomes by HIV-1 ]]> https://biorxiv.org/content/10.1101/2021.03.17.435902v1?rss=1 Oom, A. L. Stoneham, C. A. Lewinski, M. K. Richards, A. Wozniak, J. Gonzalez, D. Krogan, N. J. Guatelli, J. 2021-03-18 doi:10.1101/2021.03.17.435902 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ CONSULT: Accurate contamination removal using locality-sensitive hashing ]]> https://biorxiv.org/content/10.1101/2021.03.18.436035v1?rss=1 Rachtman, E. Bafna, V. Mirarab, S. 2021-03-19 doi:10.1101/2021.03.18.436035 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ EMBED: a low dimensional reconstruction of gut microbiome dynamics based on ecological normal modes ]]> https://biorxiv.org/content/10.1101/2021.03.18.436036v1?rss=1 Shahin, M. Ji, B. W. Dixit, P. D. 2021-03-19 doi:10.1101/2021.03.18.436036 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Closed-Loop Control between Two GTPase Switches makes the Secretory Functions of the Golgi Responsive to Growth Factors ]]> https://biorxiv.org/content/10.1101/2021.03.18.436048v1?rss=1 Qiao, L. Lo, I.-C. Midde, K. Aznar, N. Abd El-Hafeez, A. A. Lopez-Sanchez, I. Gupta, V. Farquhar, M. Rangamani, P. Ghosh, P. 2021-03-19 doi:10.1101/2021.03.18.436048 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ CCL28 modulates neutrophil responses and impacts the trajectory of mucosal infections ]]> https://biorxiv.org/content/10.1101/2021.03.19.436197v1?rss=1 Perez-Lopez, A. Silva, S. Dillon, N. Brandt, S. Gerner, R. Lee, M. Melchior, K. Torres-Ruiz, J. Sosa-Hernandez, V. Cervantes-Diaz, R. Perez-Fragoso, A. Romero-Ramirez, S. Gomez-Martin, D. Maravillas-Montero, J. Nuccio, S.-P. Nizet, V. Raffatellu, M. 2021-03-20 doi:10.1101/2021.03.19.436197 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Novelty-related engagement of VTA and anterior hippocampus propagate changes in cortical network plasticity at different scales ]]> https://biorxiv.org/content/10.1101/2021.03.22.436448v1?rss=1 Cowan, E. T. Fain, M. R. O'Shea, I. Ellman, L. M. Murty, V. P. 2021-03-22 doi:10.1101/2021.03.22.436448 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.03.22.436522v1?rss=1 Sandoval, D. R. Mandel Clausen, T. Nora, C. Magida, J. A. Cribbs, A. P. Denardo, A. Clark, A. E. Garretson, A. F. Coker, J. K. C. Narayanan, A. Majowicz, S. A. Philpott, M. Johansson, C. Dunford, J. E. Spliid, C. B. Golden, G. J. Payne, N. C. Tye, M. A. Nowell, C. J. Griffis, E. R. Piermatteo, A. Grunddal, K. V. Alle, T. Hauser, B. M. Feldman, J. Caradonna, T. M. Pu, Y. Yin, X. McVicar, R. N. Kwong, E. M. Tsimikas, S. Schmidt, A. G. Ballatore, C. Zengler, K. Chanda, S. K. Weiss, R. J. Downes, M. Evans, R. M. Croker, B. A. Leibel, S. L. Jose, J. Mazitsch 2021-03-23 doi:10.1101/2021.03.22.436522 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Parasitic nematode fatty acid- and retinol-binding proteins compromise host immunity by interfering with host lipid signaling pathways ]]> https://biorxiv.org/content/10.1101/2021.03.25.436866v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@48f582org.highwire.dtl.DTLVardef@1ee4292org.highwire.dtl.DTLVardef@1548248org.highwire.dtl.DTLVardef@13574d6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Parks, S. Nguyen, C. Nasrolahi, S. Juncaj, D. Lu, D. Ramaswamy, R. Dhillon, H. Buchman, A. Akbari, O. S. Yamanaka, N. Boulanger, M. J. Dillman, A. R. 2021-03-25 doi:10.1101/2021.03.25.436866 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ aPC/PAR1 confers endothelial anti-apoptotic activity via a discrete β-arrestin-2 mediated SphK1-S1PR1-Akt signaling axis ]]> https://biorxiv.org/content/10.1101/2021.03.27.437291v1?rss=1 Molinar-Inglis, O. Birch, C. A. Nicholas, D. Cisneros-Aguirre, M. Patwardhan, A. Chen, B. Grimsey, N. J. Gomez-Menzies, P. K. Lin, H. Coronel, L. J. Lawson, M. A. Patel, H. H. Trejo, J. 2021-03-27 doi:10.1101/2021.03.27.437291 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ A protective broadly cross-reactive human antibody defines a conserved site of vulnerability on beta-coronavirus spikes ]]> https://biorxiv.org/content/10.1101/2021.03.30.437769v1?rss=1 Zhou, P. Yuan, M. Song, G. Beutler, N. Shaabani, N. Huang, D. He, W.-t. Zhu, X. Callaghan, S. Yong, P. Anzanello, F. Peng, L. Ricketts, J. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Nemazee, D. Teijaro, J. R. Rogers, T. Wilson, I. A. Burton, D. R. Andrabi, R. 2021-03-31 doi:10.1101/2021.03.30.437769 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ An ammonium transporter is a non-canonical olfactory receptor for ammonia ]]> https://biorxiv.org/content/10.1101/2021.03.31.437861v1?rss=1 Vulpe, A. Kim, H. S. Ballou, S. Wu, S.-T. Grabe, V. Nava Gonzales, C. Sachse, S. Jeanne, J. M. Su, C.-Y. Menuz, K. 2021-03-31 doi:10.1101/2021.03.31.437861 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ The SPARC DRC: Building a resource for the autonomic nervous system community ]]> https://biorxiv.org/content/10.1101/2021.04.01.438136v1?rss=1 Osanlouy, M. Bandrowski, A. de Bono, B. Brooks, D. Cassara, A. M. Christie, R. Ebrahimi, N. Gillespie, T. Grethe, J. S. Guercio, L. A. Heal, M. Lin, M. Kuster, N. Martone, M. E. Neufeld, E. Nickerson, D. P. Soltani, E. G. Tappan, S. Wagenaar, J. B. Zhuang, K. Hunter, P. J. 2021-04-04 doi:10.1101/2021.04.01.438136 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN ]]> https://biorxiv.org/content/10.1101/2021.04.02.438274v1?rss=1 Moeller, N. H. Shi, K. Demir, O. Banerjee, S. Yin, L. Belica, C. Durfee, C. Amaro, R. E. Aihara, H. 2021-04-04 doi:10.1101/2021.04.02.438274 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures ]]> https://biorxiv.org/content/10.1101/2021.04.04.438427v1?rss=1 Zhu, Q. Huang, S. Gonzalez, A. McGrath, I. McDonald, D. Haiminen, N. Armstrong, G. Vazquez-Baeza, Y. Yu, J. Kuczynski, J. Sepich-Poore, G. D. Swafford, A. D. Das, P. Shaffer, J. P. Lejzerowicz, F. Belda-Ferre, P. Havulinna, A. S. Meric, G. Niiranen, T. Lahti, L. Salomaa, V. Kim, H.-C. Jain, M. Inouye, M. Gilbert, J. Knight, R. 2021-04-06 doi:10.1101/2021.04.04.438427 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser ]]> https://biorxiv.org/content/10.1101/2021.04.05.438475v1?rss=1 Petras, D. Phelan, V. V. Acharya, D. D. Allen, A. E. Aron, A. T. Bandeira, N. Belle-Oudry, D. Boecker, S. Bowen, B. P. Cummings, D. A. Deutsch, J. M. Fahy, E. Garg, N. Gregor, R. Handelsman, J. Navarro-Hoyos, M. Jarmusch, A. K. Jarmusch, S. A. Louie, K. B. Maloney, K. N. Marty, M. T. Meijler, M. M. Mizrahi, I. Molina-Santiago, C. Neve, R. L. Northen, T. R. Panitchpakdi, M. Pullman, B. Puri, A. W. Schmid, R. Subramaniam, S. Thukral, M. Vasquez-Castro, F. Dorrestein, P. C. Wang, M. 2021-04-06 doi:10.1101/2021.04.05.438475 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Sensory readout accounts for adaptation ]]> https://biorxiv.org/content/10.1101/2021.04.06.438664v1?rss=1 Sheehan, T. C. Serences, J. T. 2021-04-08 doi:10.1101/2021.04.06.438664 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Ubiquitin specific protease 1 expression and function in T cell immunity ]]> https://biorxiv.org/content/10.1101/2021.04.08.439046v1?rss=1 Omilusik, K. D. Nadjsombati, M. S. Yoshida, T. M. Shaw, L. A. Goulding, J. Goldrath, A. W. 2021-04-09 doi:10.1101/2021.04.08.439046 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ PRECISE 2.0: an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure ]]> https://biorxiv.org/content/10.1101/2021.04.08.439047v1?rss=1 Lamoureux, C. R. Decker, K. T. Sastry, A. V. McConn, J. L. Gao, Y. Palsson, B. O. 2021-04-11 doi:10.1101/2021.04.08.439047 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ NaCT (SLC13A5) facilitates citrate import and metabolism under nutrient-limited conditions ]]> https://biorxiv.org/content/10.1101/2021.04.08.439058v1?rss=1 Kumar, A. Cordes, T. Thalacker-Mercer, A. E. Pajor, A. M. Murphy, A. N. Metallo, C. M. 2021-04-10 doi:10.1101/2021.04.08.439058 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ State dependence of neural networks on past history and stimulus presentation in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.04.09.439242v1?rss=1 Cecere, Z. T. Yemini, E. Sharpee, T. O. Chalasani, S. H. 2021-04-11 doi:10.1101/2021.04.09.439242 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.12.439539v1?rss=1 Yoo, B. B. Griffiths, J. A. Thuy-Boun, P. Cantu, V. Weldon, K. Challis, C. Sweredoski, M. J. Chan, K. Y. Thron, T. M. Sharon, G. Moradian, A. Humphrey, G. Zhu, Q. Shaffer, J. Wolan, D. W. Dorrestein, P. Knight, R. Gradinaru, V. Mazmanian, S. 2021-04-13 doi:10.1101/2021.04.12.439539 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Adolescent Binge Drinking is Associated with Accelerated Decline of Gray Matter Volume ]]> https://biorxiv.org/content/10.1101/2021.04.13.439749v1?rss=1 Infante, M. A. Zhang, Y. Brumback, T. Brown, S. Colrain, I. Baker, F. Clark, D. Goldston, D. Nagel, B. Nooner, K. Zhao, Q. Pohl, K. Sullivan, E. Pfefferbaum, A. Tapert, S. Thompson, W. K. 2021-04-14 doi:10.1101/2021.04.13.439749 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Germline variants that influence the tumor immune microenvironment also drive response to immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.04.14.436660v1?rss=1 8000 tumors reveals novel cancer risk factors and targets for immunotherapy. ]]> Pagadala, M. Wu, V. H. Perez-Guijarro, E. Kim, H. Castro, A. Talwar, J. Gonzalez-Colin, C. Cao, S. Schmiedel, B. Salem, R. Morris, G. Harismendy, O. Patel, S. P. Mesirov, J. P. Zanetti, M. Day, C.-P. Fan, C. C. Thompson, W. K. Merlino, G. Gutkind, J. S. Vijayanand, P. Carter, H. 2021-04-15 doi:10.1101/2021.04.14.436660 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ A multiscale model predicts the sensitivity of Chlorella vulgaris to light and nitrogen levels in photobioreactors ]]> https://biorxiv.org/content/10.1101/2021.04.14.439858v1?rss=1 Tibocha-Bonilla, J. D. Zuniga, C. Broddrick, J. T. Zengler, K. Godoy-Silva, R. D. 2021-04-16 doi:10.1101/2021.04.14.439858 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Mindfulness Training Alters Resting-State EEG Dynamics in Novice Practitioners via Mindful Breathing and Body-scan ]]> https://biorxiv.org/content/10.1101/2021.04.16.439387v1?rss=1 Ng, H.-Y. H. Wu, C. W. Huang, F.-Y. Cheng, Y.-T. Guu, S.-F. Huang, C.-M. Hsu, C.-F. Chao, Y.-P. Jung, T.-P. Chuang, C.-H. 2021-04-16 doi:10.1101/2021.04.16.439387 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ System-level effects of CO2 and RuBisCO concentration on carbon isotope fractionation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440233v1?rss=1 Garcia, A. K. Kedzior, M. Taton, A. Li, M. Young, J. Kacar, B. 2021-04-20 doi:10.1101/2021.04.20.440233 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Chemoenzymatic Generation of Phospholipid Membranes Mediated by Type I Fatty Acid Synthase ]]> https://biorxiv.org/content/10.1101/2021.04.21.440816v1?rss=1 Devaraj, N. Burkart, M. Khanal, S. Brea Fernandez, R. J. 2021-04-22 doi:10.1101/2021.04.21.440816 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Expression of fatty acyl-CoA ligase drives one-pot de novo synthesis of membrane-bound vesicles in a cell free transcription-translation system ]]> https://biorxiv.org/content/10.1101/2021.04.22.440977v1?rss=1 Bhattacharya, A. Cho, C. J. Brea, R. J. Devaraj, N. K. 2021-04-22 doi:10.1101/2021.04.22.440977 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Rapid blood acid-base regulation by European sea bass (Dicentrarchus labrax) in response to sudden exposure to high environmental CO2 ]]> https://biorxiv.org/content/10.1101/2021.04.22.441026v1?rss=1 Montgomery, D. W. Kwan, G. T. Davison, W. G. Finlay, J. Berry, A. Simpson, S. Engelhard, G. H. Birchenough, S. N. Tresguerres, M. Wilson, R. W. 2021-04-23 doi:10.1101/2021.04.22.441026 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ RNA-CLAMP Enables Photo-activated Control of CRISPR-Cas9 Gene Editing by Site-specific Intramolecular Cross-linking of the sgRNA ]]> https://biorxiv.org/content/10.1101/2021.04.22.441030v1?rss=1 Devaraj, N. K. Zhang, D. Jin, S. Liu, L. Tota, E. Li, Z. Piao, X. 2021-04-23 doi:10.1101/2021.04.22.441030 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Generalization of Cortical Multivariate Genome-Wide Associations Within and Across Samples ]]> https://biorxiv.org/content/10.1101/2021.04.23.441215v1?rss=1 1,000 dimensionality for each). By deploying a replication method that aggregates discovered effects distributed across multiple phenotypes, termed PolyVertex Score (PVS), we demonstrate a higher replication yield and comparable replication rate of discovered loci for MOSTest (# replicated loci: 348-845, replication rate: 94-95%) in independent data when compared with the established min-P approach (# replicated loci: 31-68, replication rate: 65-80%). An out-of-sample replication of discovered loci was conducted with a sample of 8,336 individuals from the Adolescent Brain Cognitive Development(R) (ABCD) study, who are on average 50 years younger than UK Biobank individuals. We observe a higher replication yield and comparable replication rate of MOSTest compared to min-P. This finding underscores the importance of using well-powered multivariate techniques for both discovery and replication of high dimensional phenotypes in Genome-Wide Association studies. ]]> Loughnan, R. J. Shadrin, A. A. Frei, O. van der Meer, D. Zhao, W. Palmer, C. E. Thompson, W. E. Makowski, C. Jernigan, T. Andreassen, O. Fan, C. C. Dale, A. 2021-04-24 doi:10.1101/2021.04.23.441215 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ The nematode worm C. elegans chooses between bacterial foods exactly as if maximizing economic utility ]]> https://biorxiv.org/content/10.1101/2021.04.25.441352v1?rss=1 Katzen, A. Chung, H.-K. Harbaugh, W. Iacono, C. D. Jackson, N. Yu, S. Flavell, S. W. Glimcher, P. Lockery, S. 2021-04-26 doi:10.1101/2021.04.25.441352 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Subcellular Organization of Viral Particles During Maturation of Nucleus-Forming Jumbo Phage ]]> https://biorxiv.org/content/10.1101/2021.04.26.441357v1?rss=1 Chaikeeratisak, V. Khanna, K. Nguyen, K. T. Egan, M. E. Enustun, E. Armbruster, E. Pogliano, K. Villa, E. Pogliano, J. 2021-04-26 doi:10.1101/2021.04.26.441357 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Suboptimal proteome allocation during changing environments constrains bacterial response and growth recovery ]]> https://biorxiv.org/content/10.1101/2021.04.28.441780v1?rss=1 Balakrishnan, R. Hwa, T. Cremer, J. 2021-04-28 doi:10.1101/2021.04.28.441780 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Systematic morphological and morphometric analysis of identified olfactory receptor neurons in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.04.28.441861v1?rss=1 Nava Gonzales, C. McKaughan, Q. Bushong, E. A. Cauwenberghs, K. Ng, R. Madany, M. Ellisman, M. H. Su, C.-Y. 2021-04-29 doi:10.1101/2021.04.28.441861 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure ]]> https://biorxiv.org/content/10.1101/2021.04.29.441258v1?rss=1 Francis, J. M. Leistritz-Edwards, D. Dunn, A. Tarr, C. Lehman, J. Dempsey, C. Hamel, A. Rayon, V. Liu, G. Wang, Y. Wille, M. Durkin, M. Hadley, K. Sheen, A. Roscoe, B. Ng, M. Rockwell, G. Manto, M. Gienger, E. Nickerson, J. MGH COVID-19 Collection and Processing Team, Moarefi, A. Noble, M. Malia, T. Bardwell, P. D. Gordon, W. Swain, J. Skoberne, M. Sauer, K. Harris, T. Goldrath, A. W. Shalek, A. K. Coyle, A. J. Benoist, C. Pregibon, D. C. 2021-04-29 doi:10.1101/2021.04.29.441258 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ SmProt: a reliable repository with comprehensive annotation of small proteins identified from ribosome profiling ]]> https://biorxiv.org/content/10.1101/2021.04.29.441405v1?rss=1 Li, Y. Zhou, H. Chen, X. Zheng, Y. Kang, Q. Hao, D. Zhang, L. Song, T. Luo, H. Hao, Y. Chen, Y. Chen, R. Zhang, P. He, S. 2021-04-30 doi:10.1101/2021.04.29.441405 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Metabolic adaptation to progressive mitochondrial dysfunction in aging POLGD257A mice ]]> https://biorxiv.org/content/10.1101/2021.04.29.441996v1?rss=1 Lim, E. W. Handzlik, M. K. Trefts, E. Gengatharan, J. M. Shaw, R. J. Metallo, C. M. 2021-04-29 doi:10.1101/2021.04.29.441996 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ In heart failure reactivation of RNA-binding proteins drives the transcriptome into a fetal state ]]> https://biorxiv.org/content/10.1101/2021.04.30.442191v1?rss=1 D'Antonio, M. Nguyen, J. P. Arthur, T. D. Matsui, H. Donovan, M. K. R. DAntonio-Chronowska, A. Frazer, K. A. 2021-05-01 doi:10.1101/2021.04.30.442191 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Impaired T-cell and antibody immunity after COVID-19 infection in chronically immunosuppressed transplant recipients ]]> https://biorxiv.org/content/10.1101/2021.05.03.442371v1?rss=1 Ashokkumar, C. Rohan, V. Kroemer, A. H. Rao, S. Mazariegos, G. Higgs, B. W. Nadig, S. Almeda, J. Dhani, H. Khan, K. Yazigi, N. Ekong, U. Kaufman, S. Betancourt-Garcia, M. M. Mukund, K. Sethi, P. Mehrotra, S. Soltys, K. Singh, M. S. Bond, G. Khanna, A. Ningappa, M. Spishock, B. Sindhi, E. Atale, N. Saunders, M. Baliga, P. Fishbein, T. Subramaniam, S. Sindhi, R. 2021-05-04 doi:10.1101/2021.05.03.442371 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing ]]> https://biorxiv.org/content/10.1101/2021.05.04.442591v1?rss=1 Bickhart, D. M. Kolmogorov, M. Tseng, E. Portik, D. Korobeynikov, A. Tolstoganov, I. Uritskiy, G. Liachko, I. Sullivan, S. T. Shin, S. B. Zorea, A. Andreu, V. P. Panke-Buisse, K. Medema, M. H. Mizrahi, I. Pevzner, P. A. Smith, T. P. 2021-05-04 doi:10.1101/2021.05.04.442591 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Insights into the L3 to L4 developmental program through proteomics ]]> https://biorxiv.org/content/10.1101/2021.05.06.439182v1?rss=1 Bennuru, S. Meng, Z. McKerrow, J. H. Lustigman, S. Nutman, T. B. 2021-05-06 doi:10.1101/2021.05.06.439182 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Development of a Cell Surface Display System in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.05.06.442888v1?rss=1 Molino, J. V. D. Carpine, R. Gademann, K. Mayfield, S. Sieber, S. 2021-05-06 doi:10.1101/2021.05.06.442888 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells ]]> https://biorxiv.org/content/10.1101/2021.05.06.442935v1?rss=1 Mahoney, M. Damalanka, V. C. Tartell, M. Chung, D. H. Lourenco, A. L. Pwee, D. Mayer Bridwell, A. E. Hoffmann, M. Voss, J. Karmakar, P. Azouz, N. P. Klinger, A. M. Rothlauf, P. W. Thompson, C. E. Lee, M. Klampfer, L. Stallings, C. Rothenberg, M. E. Pöhlmann, S. Whelan, S. P. J. O'Donoghue, A. J. Craik, C. S. Janetka, J. W. 2021-05-06 doi:10.1101/2021.05.06.442935 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Discoidin Domain Receptor 2 regulates AT1 receptor expression in Angiotensin II-stimulated cardiac fibroblasts via fibronectin-dependent Integrin-β1 signalling ]]> https://biorxiv.org/content/10.1101/2021.05.06.442987v1?rss=1 Titus, A. S. V, H. Wang, M. Lakkatta, E. G. Kailasam, S. 2021-05-07 doi:10.1101/2021.05.06.442987 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Stochastic simulations reveal that dendritic spine morphology regulates synaptic plasticity in a deterministic manner ]]> https://biorxiv.org/content/10.1101/2021.05.06.442994v1?rss=1 Holst, M. V. Bell, M. K. Lee, C. T. Rangamani, P. 2021-05-06 doi:10.1101/2021.05.06.442994 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function ]]> https://biorxiv.org/content/10.1101/2021.05.06.443037v1?rss=1 Rajderkar, S. Barozzi, I. Zhu, Y. Hu, R. Zhang, Y. Li, B. Fukuda-Yuzawa, Y. Kelman, G. Akeza, A. Blow, M. J. Pham, Q. Harrington, A. N. Godoy, J. Meky, E. M. von Maydell, K. Novak, C. S. Plajzer-Frick, I. Afzal, V. Tran, S. Talkowski, M. E. Llyod, K. C. K. Ren, B. Dickel, D. E. Visel, A. Pennacchio, L. A. 2021-05-07 doi:10.1101/2021.05.06.443037 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Endoplasmic Reticulum morphological regulation by RTN4/NOGO modulates neuronal regeneration by slowing luminal transport ]]> https://biorxiv.org/content/10.1101/2021.05.10.441946v1?rss=1 Konno, T. Parutto, P. Bailey, D. M. D. Davi, V. Crapart, C. Awadelkareem, M. A. Hockings, C. Brown, A. Xiang, K. M. Agrawal, A. Chambers, J. E. Werp, M. V. Koning, K. Metzakopian, E. Westrate, L. Koslover, E. Avezov, E. 2021-05-10 doi:10.1101/2021.05.10.441946 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope ]]> https://biorxiv.org/content/10.1101/2021.05.10.443506v1?rss=1 Hetzer, M. W. tyagi, s. Chen, F. Huang, J. 2021-05-11 doi:10.1101/2021.05.10.443506 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Cortical ripples provide the conditions for consolidation during NREM sleep in humans ]]> https://biorxiv.org/content/10.1101/2021.05.11.443637v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Jiang, X. Rosen, B. Q. Kajfez, S. Eskandar, E. N. Gonzalez-Martinez, J. Cash, S. S. Halgren, E. 2021-05-13 doi:10.1101/2021.05.11.443637 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions ]]> https://biorxiv.org/content/10.1101/2021.05.12.443892v1?rss=1 Honda, T. Cremer, J. Mancini, L. Zhang, Z. Pilizota, T. Hwa, T. 2021-05-12 doi:10.1101/2021.05.12.443892 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach ]]> https://biorxiv.org/content/10.1101/2021.05.17.444458v1?rss=1 Sun, D. Adduru, V. R. Phillips, R. D. Bouchard, H. C. Sotiras, A. Michael, A. M. Baker, F. C. Tapert, S. F. Brown, S. A. Clark, D. B. Goldston, D. Nooner, K. B. Nagel, B. J. Thompson, W. K. De Bellis, M. Morey, R. A. 2021-05-17 doi:10.1101/2021.05.17.444458 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A systems-guided approach to discover the intracellular target of a novel evolution-drug lead ]]> https://biorxiv.org/content/10.1101/2021.05.17.444532v1?rss=1 Chowdhury, S. Zielinski, D. C. Dalldorf, C. Rodrigues, J. V. Palsson, B. Shakhnovich, E. 2021-05-18 doi:10.1101/2021.05.17.444532 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Effects of vapor exposure to Δ9-tetrahydrocannabinol (THC) in the Maine Lobster (Homarus americanus) ]]> https://biorxiv.org/content/10.1101/2021.05.24.445508v1?rss=1 Gutierrez, A. Creehan, K. M. Turner, M. Tran, R. N. Kerr, T. M. Nguyen, J. D. Taffe, M. A. 2021-05-25 doi:10.1101/2021.05.24.445508 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Optimal dimensionality selection for independent component analysis of transcriptomic data ]]> https://biorxiv.org/content/10.1101/2021.05.26.445885v1?rss=1 McConn, J. L. Lamoureux, C. R. Poudel, S. Palsson, B. O. Sastry, A. V. 2021-05-27 doi:10.1101/2021.05.26.445885 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA ]]> https://biorxiv.org/content/10.1101/2021.05.27.445689v1?rss=1 Bergstrom, E. N. Luebeck, J.-C. Petljak, M. Bafna, V. Mischel, P. S. Harris, R. Alexandrov, L. B. 2021-05-27 doi:10.1101/2021.05.27.445689 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium ]]> https://biorxiv.org/content/10.1101/2021.05.27.445969v1?rss=1 60 established anthropometric loci in Hispanic/Latino populations at genome-wide significance--representing up to 30% of previously-reported index SNP anthropometric associations. Trans-ethnic meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our novel findings demonstrate that future studies may also benefit from leveraging differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification. ]]> Fernandez-Rhodes, L. Graff, M. Buchanan, V. L. Justice, A. E. Highland, H. M. Guo, X. Young, K. L. Adhikari, K. Allred, N. P. Below, J. E. Bradfield, J. Pereira, A. C. Glover, L. Kim, D. Lilly, A. G. Shrestha, P. Thomas, A. G. Zhang, X. Chen, M. Chiang, C. Pulit, S. Horimoto, A. Krieger, J. E. Guindo-Martinez, M. Preuss, M. Schumann, C. Smit, R. A. J. Torres-Mejia, G. Acuna-Alonzo, V. Bedoya, G. Bortolini, M.-C. Canizales-Quinteros, S. Gallo, C. Gonzalez-Jose, R. Poletti, G. Rothhammer, F. Hakonarson, H. Adler, S. G. Igo, R. Iyengar, S. Nicholas, S. B. 2021-05-29 doi:10.1101/2021.05.27.445969 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Rapid evolution of bacterial AB5 toxin B subunits independent of A subunits: sialic acid binding preferences correlate with host range and toxicity ]]> https://biorxiv.org/content/10.1101/2021.05.28.446168v1?rss=1 Khan, N. Sasmal, A. Khedri, Z. Secrest, P. Verhagen, A. Srivastava, S. Varki, N. Chen, X. Yu, H. Beddoe, T. Paton, A. W. Paton, J. C. Varki, A. 2021-05-28 doi:10.1101/2021.05.28.446168 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Pro-regenerative Extracellular Matrix Hydrogel Prevents and Mitigates Pathological Alterations of Pelvic Muscles Following Birth Injury ]]> https://biorxiv.org/content/10.1101/2021.05.28.446170v1?rss=1 Duran, P. Sesillo, F. B. Burnett, L. Menefee, S. A. Cook, M. Zazueta-Damian, G. Dzieciatkowska, M. Do, E. French, S. Shah, M. M. Sanvictores, C. Hansen, K. Shtrahman, M. Christman, K. L. Alperin, M. 2021-05-28 doi:10.1101/2021.05.28.446170 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Sialoglycan microarray encoding reveals differential sialoglycan binding of phylogenetically-related bacterial AB5 toxin B subunits ]]> https://biorxiv.org/content/10.1101/2021.05.28.446191v1?rss=1 113,000 likely linear sialyltrisaccharides in nature. Notably a biantennary N-glycan with two terminal sialyltrisaccharides could thus have >1010 potential combinations and a triantennary N-glycan with three terminal sequences, >1015 potential combinations. While all possibilities likely do not exist in nature, sialoglycans encode enormous diversity. While glycomic approaches are used to probe such diverse sialomes, naturally-occurring bacterial AB5 toxin B subunits are simpler tools to track the dynamic sialome in biological systems. Sialoglycan microarray was utilized to compare sialoglycan-recognizing bacterial toxin B subunits. Unlike the poor correlation between B subunits and species phylogeny, there is stronger correlation with Sia-epitope preferences. Further supporting this pattern, we report a B subunit (YenB) from Yersinia enterocolitica (broad host range) recognizing almost all sialoglycans in the microarray, including 4-O-acetylated-Sias not recognized by a Y. pestis orthologue (YpeB). Differential Sia-binding patterns were also observed with phylogenetically-related B subunits from Escherichia coli (SubB), Salmonella Typhi (PltB), S. Typhimurium (ArtB), extra-intestinal E.coli (EcPltB), Vibrio cholera (CtxB), and cholera family homologue of E. coli (EcxB). ]]> Sasmal, A. Khan, N. Khedri, Z. Kellman, B. P. Srivastava, S. Verhagen, A. Yu, H. Bruntse, A. B. Diaz, S. Varki, N. Beddoe, T. Paton, A. W. Paton, J. C. Chen, X. Lewis, N. E. Varki, A. 2021-05-29 doi:10.1101/2021.05.28.446191 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Development and applications of sialoglycan-recognizing probes (SGRPs) with defined specificities: exploring the dynamic mammalian sialoglycome ]]> https://biorxiv.org/content/10.1101/2021.05.28.446202v1?rss=1 Srivastava, S. Verhagen, A. Sasmal, A. Wasik, B. R. Diaz, S. Yu, H. Bensing, B. A. Khan, N. Khedri, Z. Secrest, P. Sullam, P. Varki, N. Chen, X. Parrish, C. R. Varki, A. 2021-05-28 doi:10.1101/2021.05.28.446202 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Identification of Leucinostatins from Ophiocordyceps sp. as Antiparasitic Agents Against Trypanosoma cruzi ]]> https://biorxiv.org/content/10.1101/2021.05.30.446362v1?rss=1 Bernatchez, J. A. Kil, Y.-S. Barbosa da Silva, E. Thomas, D. McCall, L.-I. Wendt, K. L. Souza, J. M. Ackermann, J. McKerrow, J. H. Cichewicz, R. H. Siqueira-Neto, J. L. 2021-05-31 doi:10.1101/2021.05.30.446362 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Molecular foundations of Precambrian uniformitarianism ]]> https://biorxiv.org/content/10.1101/2021.05.31.446354v1?rss=1 Kedzior, M. Garcia, A. K. Li, M. Taton, A. Adam, Z. R. Young, J. N. Kacar, B. 2021-05-31 doi:10.1101/2021.05.31.446354 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.31.446440v1?rss=1 Borner, K. Teichmann, S. A. Quardokus, E. M. Gee, J. Browne, K. Osumi-Sutherland, D. Herr, B. W. Bueckle, A. Paul, H. Haniffa, M. A. Jardine, L. Bernard, A. Ding, S.-L. Miller, J. A. Lin, S. Halushka, M. Boppana, A. Longacre, T. A. Hickey, J. Lin, Y. Valerius, M. T. He, Y. Pryhuber, G. Sun, X. Jorgensen, M. Radtke, A. Wasserfall, C. Ginty, F. Ho, J. Sunshine, J. Beuschel, R. T. Brusko, M. Lee, S. Malhotra, R. Jain, S. Weber, G. 2021-06-01 doi:10.1101/2021.05.31.446440 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ CDK12 is Necessary to Promote Epidermal Differentiation through Transcription Elongation ]]> https://biorxiv.org/content/10.1101/2021.06.01.446524v1?rss=1 Sen, G. Li, J. Tiwari, M. Chen, Y. 2021-06-01 doi:10.1101/2021.06.01.446524 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies ]]> https://biorxiv.org/content/10.1101/2021.06.01.446591v1?rss=1 Ye, Q. Lu, S. Corbett, K. D. 2021-06-01 doi:10.1101/2021.06.01.446591 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Gene regulatory networks underlying human microglia maturation ]]> https://biorxiv.org/content/10.1101/2021.06.02.446636v1?rss=1 Coufal, N. G. Glass, C. Han, C. Li, R. Z. Hansen, E. Bennett, H. Poirion, O. Buchanan, J. Challacombe, J. Fixsen, B. Trescott, S. Schlachetzki, J. Preissl, S. Wang, A. O'Connor, C. Warden, A. S. Shriram, S. Kim, R. Nguyen, C. Schafer, D. Ramirez, G. Anavim, S. A. Johnson, A. Sajti, E. Gupta, M. Ben-Haim, S. Gonda, D. D. Levy, M. L. Laurent, L. 2021-06-02 doi:10.1101/2021.06.02.446636 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein aggregates within processing bodies ]]> https://biorxiv.org/content/10.1101/2021.06.02.446820v1?rss=1 Fenix, A. M. Miyaoka, Y. Bertero, A. Blue, S. Spindler, M. J. Tan, K. K. B. Perez-Bermejo, J. A. Chan, A. H. Mayer, S. J. Nguyen, T. Russell, C. R. Lizarraga, P. Truong, A. So, P.-L. Kulkarni, A. Chetal, K. Sathe, S. Sniadecki, N. J. Yeo, G. W. Murry, C. E. Salomonis, N. 2021-06-03 doi:10.1101/2021.06.02.446820 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Spatially heterogeneous microstructural development within subcortical regions from 9-13 years ]]> https://biorxiv.org/content/10.1101/2021.06.04.446984v1?rss=1 Palmer, C. E. Pecheva, D. Iversen, J. R. Hagler, D. J. Sugrue, L. Nedelec, P. Fan, C. Thompson, W. Jernigan, T. L. Dale, A. M. 2021-06-06 doi:10.1101/2021.06.04.446984 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Microstructural development across white matter from 9-13 years ]]> https://biorxiv.org/content/10.1101/2021.06.04.447102v1?rss=1 Palmer, C. E. Pecheva, D. Iversen, J. R. Hagler, D. J. Sugrue, L. Nedelec, P. Fan, C. Thompson, W. Jernigan, T. L. Dale, A. M. 2021-06-06 doi:10.1101/2021.06.04.447102 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Behavioral effects of ethanol in the Red Swamp Crayfish(Procambarus clarkii) ]]> https://biorxiv.org/content/10.1101/2021.06.05.447220v1?rss=1 Gutierrez, A. Creehan, K. M. de Guglielmo, G. Roberts, A. J. A. Taffe, M. A. 2021-06-07 doi:10.1101/2021.06.05.447220 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Estimating the absolute number of axons connecting different cortical areas in humans with diffusion MRI ]]> https://biorxiv.org/content/10.1101/2021.06.07.447453v1?rss=1 Rosen, B. Q. Halgren, E. 2021-06-08 doi:10.1101/2021.06.07.447453 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation ]]> https://biorxiv.org/content/10.1101/2021.06.08.447518v1?rss=1 Orth, M. F. Surdez, D. Marchetto, A. Grossetete, S. Gerke, J. S. Zaidi, S. Alonso, J. Sastre, A. Baulande, S. Sill, M. Cidre-Aranaz, F. Ohmura, S. Kirchner, T. Hauck, S. M. Reischl, E. Gymrek, M. Pfister, S. M. Strauch, K. Delattre, O. Grunewald, T. G. P. 2021-06-08 doi:10.1101/2021.06.08.447518 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo ]]> https://biorxiv.org/content/10.1101/2021.06.10.447994v1?rss=1 Gao, Y. Lim, H. G. Verkler, H. Szubin, R. Quach, D. Rodionova, I. Chen, K. Yurkovich, J. Cho, B.-K. Palsson, B. O. 2021-06-11 doi:10.1101/2021.06.10.447994 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers ]]> https://biorxiv.org/content/10.1101/2021.06.11.447968v1?rss=1 Lange, J. T. Chen, C. Y. Pichugin, Y. Xie, F. Tang, J. Hung, K. L. Yost, K. E. Shi, Q. Erb, M. L. Rajkumar, U. Wu, S. Swanton, C. Liu, Z. Huang, W. Chang, H. Y. Bafna, V. Henssen, A. G. Werner, B. Mischel, P. S. 2021-06-11 doi:10.1101/2021.06.11.447968 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Structural Basis for Cytoplasmic Dynein-1 Regulation by Lis1 ]]> https://biorxiv.org/content/10.1101/2021.06.11.448119v1?rss=1 Gillies, J. P. Reimer, J. M. Karasmanis, E. P. Lahiri, I. Htet, Z. M. Leschziner, A. E. Reck-Peterson, S. L. 2021-06-11 doi:10.1101/2021.06.11.448119 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion function for retrotranslocation of ER multi-spanning membrane substrates ]]> https://biorxiv.org/content/10.1101/2021.06.15.448428v1?rss=1 Nejatfard, A. Wauer, N. Bhaduri, S. Conn, A. Gourkanti, S. Singh, N. Kuo, T. Kandel, R. R. Amaro, R. E. Neal, S. E. 2021-06-15 doi:10.1101/2021.06.15.448428 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ The predicted bZIP transcription factor ZIP-1 promotes resistance to intracellular infection in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.06.17.448850v1?rss=1 Lazetic, V. Wu, F. Cohen, L. B. Reddy, K. C. Chang, Y.-T. Gang, S. S. Bhabha, G. Troemel, E. R. 2021-06-17 doi:10.1101/2021.06.17.448850 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Stem Cell Microarrays for Assessing Growth Factor Signaling in Engineered Glycan Microenvironments ]]> https://biorxiv.org/content/10.1101/2021.06.19.448747v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@42584forg.highwire.dtl.DTLVardef@1b3defcorg.highwire.dtl.DTLVardef@1f4796borg.highwire.dtl.DTLVardef@14f6e23_HPS_FORMAT_FIGEXP M_FIG C_FIG The present study describes the integration of glycosaminoglycan-protein conjugates into a hydrogel-supported stem cell microarray platform to analyze the activity of extracellular glycans in growth factor signaling. Such platforms can enable rapid development and optimization of functional glycomaterials for stem cell-based regenerative therapies. ]]> Michalak, A. L. Trieger, G. W. Trieger, K. A. Godula, K. 2021-06-20 doi:10.1101/2021.06.19.448747 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Disruption of VGLUT1 in cholinergic medial habenula projections increases nicotine self-administration ]]> https://biorxiv.org/content/10.1101/2021.06.19.449108v1?rss=1 Souter, E. A. Chen, Y.-C. Zell, V. Lallai, V. Steinkellner, T. Conrad, W. S. Wisden, W. Harris, K. D. Fowler, C. D. Hnasko, T. S. 2021-06-20 doi:10.1101/2021.06.19.449108 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Exploring cell surface-nanopillar interactions with 3D super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2021.06.21.449280v1?rss=1 Roy, A. R. Zhang, W. Jahed, Z. Tsai, C.-T. Cui, B. Moerner, W. E. 2021-06-22 doi:10.1101/2021.06.21.449280 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ The noncoding RNA PRANCR regulates splicing of Fibronectin-1 to control keratinocyte proliferation and migration ]]> https://biorxiv.org/content/10.1101/2021.06.22.449364v1?rss=1 Otten, A. B. Amarbayar, O. Cai, P. Cheng, B. Qu, K. Sun, B. 2021-06-22 doi:10.1101/2021.06.22.449364 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Leveraging Allele-Specific Expression for Therapeutic Response Gene Discovery in Glioblastoma. ]]> https://biorxiv.org/content/10.1101/2021.06.22.449493v1?rss=1 Sen, A. Prager, B. C. Park, D. Zhu, Z. Gimple, R. C. Bernatchez, J. A. Beck, S. Clark, A. E. Siqueira-Neto, J. L. Rich, J. N. McVicker, G. P. 2021-06-22 doi:10.1101/2021.06.22.449493 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Mice are not automatons; subjective experience in premotor circuits guides behavior ]]> https://biorxiv.org/content/10.1101/2021.06.23.449617v1?rss=1 Schreiner, D. C. Cazares, C. Renteria, R. Gremel, C. M. 2021-06-24 doi:10.1101/2021.06.23.449617 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Multivariate genome-wide association studies on the tissue compartments of human brain identify novel loci underpinning brain development and neuropsychiatric outcomes. ]]> https://biorxiv.org/content/10.1101/2021.06.24.449723v1?rss=1 Fan, C. C. Loughnan, R. Pechva, D. Chen, C.-H. Hagler, D. Thompson, W. K. van der Meer, D. Frei, O. Andreassen, O. Dale, A. M. 2021-06-24 doi:10.1101/2021.06.24.449723 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Protein Kinase C gamma Mutations Drive Spinocerebellar Ataxia Type 14 by Impairing Autoinhibition ]]> https://biorxiv.org/content/10.1101/2021.06.24.449810v1?rss=1 Pilo, C. A. Kornev, A. P. Baffi, T. R. Kunkel, M. T. Huang, L.-C. Longman, C. Kannan, N. A. Taylor, S. S. Gorrie, G. Newton, A. C. 2021-06-24 doi:10.1101/2021.06.24.449810 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Photoinactivation of Catalase Sensitizes Wide-Ranging Bacteria to ROS-Producing Agents and Immune Cells ]]> https://biorxiv.org/content/10.1101/2021.06.24.449847v1?rss=1 Dong, P.-T. Jusuf, S. Hui, J. Zhan, Y. Zhu, Y. Liu, G. Y. Cheng, J.-X. 2021-06-24 doi:10.1101/2021.06.24.449847 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.06.28.450262v1?rss=1 Serwas, D. Akamatsu, M. Moayed, A. Vegesna, K. Vasan, R. Hill, J. M. Schoeneberg, J. Davies, K. M. Rangamani, P. Drubin, D. G. 2021-06-29 doi:10.1101/2021.06.28.450262 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline ]]> https://biorxiv.org/content/10.1101/2021.06.30.450555v1?rss=1 Palmer, C. E. Sheth, C. Marshall, A. Adise, S. Baker, F. Chang, L. Clark, D. Dagher, R. Dowling, G. Gonzalez, M. Haist, F. Herting, M. Huber, R. Jernigan, T. LeBlanc, K. Lee, K. Lisdahl, K. Neigh, G. Patterson, M. Renshaw, P. Rhee, K. Tapert, S. Thompson, W. Uban, K. Sowell, E. Yurgelun-Todd, D. 2021-06-30 doi:10.1101/2021.06.30.450555 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Optimal balancing of clinical factors in large scale clinical RNA-Seq studies ]]> https://biorxiv.org/content/10.1101/2021.06.30.450639v1?rss=1 CHIANG, A. W. T. Gazestani, V. H. Altieri, M. G. Courchesne, E. Lewis, N. E. 2021-07-01 doi:10.1101/2021.06.30.450639 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection ]]> https://biorxiv.org/content/10.1101/2021.07.01.450045v1?rss=1 Yoo, R. Rychel, K. Poudel, S. Al-bulushi, T. Yuan, Y. Chauhan, S. Lamoureux, C. Palsson, B. Sastry, A. V. 2021-07-02 doi:10.1101/2021.07.01.450045 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ The Effect of a Fennel Extract on the STAT Signaling and Intestinal Barrier Function ]]> https://biorxiv.org/content/10.1101/2021.07.01.450766v1?rss=1 Rabalais, J. Kozan, P. Lu, T. Durali, N. Okamoto, K. Das, B. McGeough, M. D. Lee, J. B. Barrett, K. E. Marchelletta, R. Sivagnanam, M. 2021-07-02 doi:10.1101/2021.07.01.450766 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ A PKA Inhibitor Motif within Smoothened Controls Hedgehog Signal Transduction ]]> https://biorxiv.org/content/10.1101/2021.07.05.451193v1?rss=1 Happ, J. T. Arveseth, C. D. Bruystens, J. Bertinetti, D. Nelson, I. B. Olivieri, C. Hedeen, D. S. Zhu, J.-F. Capener, J. L. Bröckel, J. W. Vu, L. King, C. C. Ruiz-Perez, V. L. Veglia, G. Herberg, F. W. Taylor, S. S. Myers, B. R. 2021-07-06 doi:10.1101/2021.07.05.451193 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.07.05.451222v1?rss=1 He, W.-t. Yuan, M. Callaghan, S. Musharrafieh, R. Song, G. Silva, M. Beutler, N. Lee, W.-H. Yong, P. Torres, J. L. Melo, M. Zhou, P. Zhao, F. Zhu, X. Peng, L. Huang, D. Anzanello, F. Ricketts, J. Parren, M. Garcia, E. Ferguson, M. Rinaldi, W. Rawlings, S. A. Nemazee, D. Smith, D. M. Briney, B. Safonova, Y. Rogers, T. Crotty, S. Irvine, D. J. Ward, A. B. Wilson, I. A. Burton, D. R. Andrabi, R. 2021-07-06 doi:10.1101/2021.07.05.451222 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development ]]> https://biorxiv.org/content/10.1101/2021.07.06.449578v1?rss=1 Suban, S. Schwarz, R. Sendersky, E. Golden, S. S. 2021-07-06 doi:10.1101/2021.07.06.449578 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Ca2+-dependent liquid-liquid phase separation underlies intracellular Ca2+ stores. ]]> https://biorxiv.org/content/10.1101/2021.07.06.451223v1?rss=1 Mayfield, J. E. Pollak, A. J. Worby, C. A. Xu, J. C. Tandon, V. Newton, A. C. Dixon, J. E. 2021-07-06 doi:10.1101/2021.07.06.451223 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Early adaptation in a microbial community is dominated by mutualism-enhancing mutations ]]> https://biorxiv.org/content/10.1101/2021.07.07.451547v1?rss=1 Venkataram, S. Kuo, H.-Y. Hom, E. F. Y. Kryazhimskiy, S. 2021-07-09 doi:10.1101/2021.07.07.451547 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Microbiome divergence of marine gastropod species separated by the Isthmus of Panama ]]> https://biorxiv.org/content/10.1101/2021.07.08.451645v1?rss=1 Neu, A. T. Torchin, M. E. Allen, E. E. Roy, K. 2021-07-09 doi:10.1101/2021.07.08.451645 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Flexible utilization of spatial- and motor-based codes for the storage of visuo-spatial information ]]> https://biorxiv.org/content/10.1101/2021.07.08.451663v1?rss=1 Henderson, M. M. Rademaker, R. L. Serences, J. T. 2021-07-09 doi:10.1101/2021.07.08.451663 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Glycocalyx engineering with heparan sulfate mimetics attenuates Wnt activity during adipogenesis to promote glucose uptake and metabolism. ]]> https://biorxiv.org/content/10.1101/2021.07.08.451710v1?rss=1 Trieger, G. Pessentheiner, A. Purcell, S. Green, C. R. DeForest, N. Willert, K. Majithia, A. Metallo, C. Godula, K. Gordts, P. 2021-07-09 doi:10.1101/2021.07.08.451710 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2 ]]> https://biorxiv.org/content/10.1101/2021.07.11.451941v1?rss=1 Cheung, C. Y. Huang, T.-T. Chow, N. Zhang, S. Zhao, Y. Wong, C. C. Boassa, D. Phan, S. Ellisman, M. H. Yates, J. R. Xu, S. Yu, Z. Zhang, Y. Zhang, R. Ng, L. L. Ko, B. C. B. 2021-07-11 doi:10.1101/2021.07.11.451941 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ An intestinally secreted host factor limits bacterial colonization but promotes microsporidia invasion of C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.12.452088v1?rss=1 El Jarkass, H. T. Mok, C. Schertzberg, M. R. Fraser, A. G. Troemel, E. R. Reinke, A. W. 2021-07-12 doi:10.1101/2021.07.12.452088 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.07.14.452426v1?rss=1 270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n = 58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time the impact of age and antipsychotic treatment on chromatin organization. ]]> Zhu, B. Ainsworth, R. I. Wang, Z. Sierra, S. Deng, C. Callado, L. F. Meana, J. J. Wang, W. Lu, C. Gonzalez-Maeso, J. 2021-07-16 doi:10.1101/2021.07.14.452426 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Asymmetric Arp2/3-mediated actin assembly facilitates clathrin-mediated endocytosis at stalled sites in genome-edited human stem cells. ]]> https://biorxiv.org/content/10.1101/2021.07.16.452693v1?rss=1 Jin, M. Shirazinejad, C. Wang, B. Yan, A. Schöneberg, J. Upadhyayula, S. Xu, K. Drubin, D. G. 2021-07-16 doi:10.1101/2021.07.16.452693 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence ]]> https://biorxiv.org/content/10.1101/2021.07.16.452756v1?rss=1 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles. ]]> Salido, R. A. Cantu, V. J. Clark, A. E. Leibel, S. L. Foroughishafiei, A. Saha, A. Hakim, A. Nouri, A. Lastrella, A. L. Castro-Martinez, A. Plascencia, A. Kapadia, B. Xia, B. Ruiz, C. Marotz, C. Maunder, D. Lawrence, E. S. Smoot, E. W. Eisner, E. Crescini, E. S. Kohn, L. Franco Vargas, L. Chacon, M. Betty, M. Machnicki, M. Wu, M. Y. Baer, N. A. Belda-Ferre, P. DeHoff, P. Saever, P. Ostrander, R. T. Tsai, R. Sathe, S. Aigner, S. Morgan, S. C. Ngo, T. T. Barber, T. Cheung, W. Carlin, A. F. Yeo, G. W. Laurent, L. Fielding-Miller, R. Knight, R. 2021-07-20 doi:10.1101/2021.07.16.452756 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Artificial Intelligence-rationalized balanced PPARα/γ dual agonism resets the dysregulated macrophage processes in inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2021.07.18.452807v1?rss=1 Katkar, G. Sayed, I. M. Amandachar, M. Castillo, V. Vidales, E. Toobian, D. Usmani, F. F. Sawires, J. R. Leriche, G. Yang, J. Sandborn, W. J. Das, S. Sahoo, D. Ghosh, P. 2021-07-19 doi:10.1101/2021.07.18.452807 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data ]]> https://biorxiv.org/content/10.1101/2021.07.19.452699v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@8e1759org.highwire.dtl.DTLVardef@9ee7d5org.highwire.dtl.DTLVardef@866f04org.highwire.dtl.DTLVardef@1e27b29_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phaneuf, P. V. Zielinski, D. C. Yurkovich, J. T. Johnsen, J. Szubin, R. Yang, L. Kim, S. H. Schulz, S. Wu, M. Dalldorf, C. Ozdemir, E. Palsson, B. O. Feist, A. 2021-07-20 doi:10.1101/2021.07.19.452699 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ An Orally Available Cathepsin L Inhibitor Protects Lungs Against SARS-CoV-2-Induced Diffuse Alveolar Damage in African Green Monkeys ]]> https://biorxiv.org/content/10.1101/2021.07.20.453127v1?rss=1 Frueh, F. W. Maneval, D. C. Bohm, R. P. Dufour, J. P. Blair, R. V. Simpson, S. Powell, K. Aye, P. P. Golden, N. A. ROY, C. J. Spencer, S. Russell-Lodrigue, K. Plante, K. S. Plante, J. A. McKerrow, J. H. Rappaport, J. 2021-07-21 doi:10.1101/2021.07.20.453127 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ GIV/Girdin binds BRCA1 and links trimeric G-proteins to DNA damage response ]]> https://biorxiv.org/content/10.1101/2021.07.21.452842v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@3d5202org.highwire.dtl.DTLVardef@1d32d89org.highwire.dtl.DTLVardef@152a85dorg.highwire.dtl.DTLVardef@1ab9953_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINon-receptor G protein modulator, GIV/Girdin binds BRCA1 C_LIO_LIBinding occurs in both canonical and non-canonical modes C_LIO_LIGIV sequesters BRCA1 away from dsDNA breaks, suppresses HR C_LIO_LIActivation of Gi by GIV enhances Akt signals, favors NHEJ C_LI IN BRIEFIn this work, the authors show that heterotrimeric G protein signaling that is triggered by non-receptor GEF, GIV/Girdin, in response to double-stranded DNA breaks is critical for decisive signaling events which favor non-homologous end-joining (NHEJ) and inhibit homologous recombination (HR). ]]> Abd El-Hafeez, A. A. Sun, N. Chakraborty, A. Ear, J. Roy, S. Chamarthi, P. Rajapakse, N. Das, S. Luker, K. E. Hazra, T. K. Luker, G. D. Ghosh, P. 2021-07-22 doi:10.1101/2021.07.21.452842 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Characterization of cocaine addiction-like behavior in heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.22.453410v1?rss=1 500 outbred heterogeneous stock (HS) rats using an extended cocaine self-administration paradigm (6 h/daily). We analyzed individual differences in escalation of intake, progressive-ratio (PR) responding, continued use despite adverse consequences (contingent foot shocks), and irritability-like behavior during withdrawal. Principal component analysis showed that escalation of intake, progressive ratio responding, and continued use despite adverse consequences loaded onto a single factor that was distinct from irritability-like behaviors. Categorizing rats into resilient, mild, moderate, and severe addiction-like phenotypes showed that females exhibited higher addiction-like behaviors, with a lower proportion of resilient individuals compared to males. These findings suggest that, in genetically diverse rats with extended drug access, escalation of intake, continued use despite adverse consequences, and PR responding are highly correlated measures of a shared underlying construct. Furthermore, our results highlight sex differences in resilience to addiction-like behaviors. ]]> de Guglielmo, G. Carrette, L. Kallupi, M. Brennan, M. Boomhower, B. Maturin, L. Conlisk, D. Sedighim, S. Tieu, L. Pavlich, M. Martinez, A. Velarde, N. Kononoff, J. Kimbrough, A. Simpson, S. Smith, L. Shankar, K. Krook, C. Avelar, A. Schweitzer, P. Woods, L. S. Palmer, A. A. George, O. 2021-07-23 doi:10.1101/2021.07.22.453410 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Transcriptional regulatory features associated with Coccidioides immitis phase transition ]]> https://biorxiv.org/content/10.1101/2021.07.22.453417v1?rss=1 Duttke, S. H. Beyhan, S. Singh, R. Neal, S. E. Viriyakosol, S. Fierer, J. Kirkland, T. N. Stajich, J. E. Benner, C. Carlin, A. 2021-07-22 doi:10.1101/2021.07.22.453417 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Leptin protects against the development and expression of cocaine addiction-like behavior in heterogenous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.22.453426v1?rss=1 Carrette, L. L. G. Corral, C. Crook, C. Boomhower, B. Brennan, M. Ortez, C. Shankar, K. Simpson, S. Maturin, L. de Guglielmo, G. Solberg-Woods, L. Palmer, A. A. George, O. 2021-07-23 doi:10.1101/2021.07.22.453426 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Individual differences in members of Actinobacteria, Bacteroidetes, and Firmicutes is associated with resistance or vulnerability to addiction-like behaviors in heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.23.453592v1?rss=1 Simpson, S. de Guglielmo, G. Brennan, M. Maturin, L. Peters, G. Jia, H. Andrews, S. Solberg-Woods, L. Palmer, A. George, O. 2021-07-24 doi:10.1101/2021.07.23.453592 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent ]]> https://biorxiv.org/content/10.1101/2021.07.26.453919v1?rss=1 Luna, E. Parkar, S. G. Kirmiz, N. Hartel, S. Hearn, E. Hossine, M. Kurdian, A. Mendoza, C. Orr, K. Padilla, L. Ramirez, K. Salcedo, P. Serrano, E. Choudhury, B. Paulchakrabarti, M. Parker, C. T. Huynh, S. Cooper, K. Flores, G. E. 2021-07-28 doi:10.1101/2021.07.26.453919 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ An atlas of healthy and injured cell states and niches in the human kidney ]]> https://biorxiv.org/content/10.1101/2021.07.28.454201v1?rss=1 400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (n = 42) and disease (n = 42) kidneys. This has provided a high resolution cellular atlas of 100 cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations for major cell types spanning the entire kidney. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several segments. Molecular signatures of these states permitted their localization within injury neighborhoods using spatial transcriptomics, and large-scale 3D imaging analysis of [~]1.2 million neighborhoods provided linkages to active immune responses. These analyses further defined biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that were associated with a decline in kidney function during chronic kidney disease. This human kidney cell atlas, including injury cell states and neighborhoods, will be a valuable resource for future studies. ]]> Lake, B. B. Menon, R. Winfree, S. Hu, Q. Ferreira, R. M. Kalhor, K. Barwinska, D. Otto, E. A. Ferkowicz, M. Diep, D. Plongthongkum, N. Knoten, A. Urata, S. Naik, A. S. Eddy, S. Zhang, B. Wu, Y. Salamon, D. Williams, J. C. Wang, X. Balderrama, K. S. Hoover, P. Murray, E. Vijayan, A. Chen, F. Waikar, S. S. Rosas, S. Wilson, F. P. Palevsky, P. M. Kiryluk, K. Sedor, J. R. Toto, R. D. Parikh, C. Kim, E. H. Macosko, E. Z. Kharchenko, P. V. Gaut, J. P. Hodgin, J. B. Eadon, M. T. Dagher, P. C. El-Achkar, T. M. Zhang, K. Kretzler, M. Jain, S. KPMP Consortium, 2021-07-29 doi:10.1101/2021.07.28.454201 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators ]]> https://biorxiv.org/content/10.1101/2021.07.28.454220v1?rss=1 Rajput, A. Tsunemoto, H. Sastry, A. V. Szubin, R. Rychel, K. Sugie, J. Pogliano, J. Palsson, B. 2021-07-28 doi:10.1101/2021.07.28.454220 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ The timescale and magnitude of aperiodic activity decreases with cortical depth in humans, macaques and mice ]]> https://biorxiv.org/content/10.1101/2021.07.28.454235v1?rss=1 Halgren, M. Kang, R. Voytek, B. Ulbert, I. Fabo, D. Eross, L. G. Wittner, L. Madsen, J. Doyle, W. K. Devinsky, O. Halgren, E. Harnett, M. T. Cash, S. S. 2021-07-29 doi:10.1101/2021.07.28.454235 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius ]]> https://biorxiv.org/content/10.1101/2021.07.28.454237v1?rss=1 Chauhan, S. M. Poudel, S. Rychel, K. Lamoureux, C. Yoo, R. Al Bulushi, T. Yuan, Y. Palsson, B. Sastry, A. V. 2021-07-29 doi:10.1101/2021.07.28.454237 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML ]]> https://biorxiv.org/content/10.1101/2021.07.30.454489v1?rss=1 Krivdova, G. Voisin, V. Schoof, E. M. Marhon, S. A. Murison, A. J. McLeod, J. L. Gabra, M. Zeng, A. G. Van Nostrand, E. L. Aigner, S. J. Shishkin, A. A. Yee, B. A. Hermans, K. G. Trotman-Grant, A. G. Mbong, N. Kennedy, J. A. Gan, O. I. Wagenblast, E. De Carvalho, D. D. LAB, S. Minden, M. D. Bader, G. D. Yeo, G. W. Dick, J. E. Lechman, E. R. 2021-07-30 doi:10.1101/2021.07.30.454489 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ The role of muscle stem cells and fibro-adipogenic progenitors in female pelvic floor muscle regeneration following birth injury ]]> https://biorxiv.org/content/10.1101/2021.07.30.454534v1?rss=1 Boscolo Sesillo, F. Rajesh, V. Wong, M. Duran, P. Baynes, B. Laurent, L. C. Christman, K. Sacco, A. Alperin, M. 2021-07-31 doi:10.1101/2021.07.30.454534 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Mechanisms governing protective pregnancy-induced adaptions of the pelvic floor muscles in the rat pre-clinical model ]]> https://biorxiv.org/content/10.1101/2021.08.01.454675v1?rss=1 0.05). However, the myofibers remained significantly longer in load+/pregnancy hormones- compared to load- /pregnancy hormones- in coccygeus (13.33{+/-}0.94 vs 9.97{+/-}0.26 mm, P<0.0001) and pubocaudalis (21.20{+/-}0.52 vs 19.52{+/-}0.34 mm, P<0.04) and not different from load+/pregnancy hormones+ (12.82{+/-}0.30 and 22.53{+/-}0.32mm, respectively, P>0.1), indicating that sustained load induced sarcomerogenesis in these muscles. Intramuscular collagen content in load+/pregnancy hormones- group was significantly greater relative to controls in coccygeus (6.55{+/-}0.85 vs 3.11{+/-}0.47{micro}g/mg, P<0.001) and pubocaudalis (5.93{+/-}0.79 vs 3.46{+/-}0.52 {micro}g/mg, P<0.05) and not different from load+/pregnancy hormones+ (7.45{+/-}0.65 and 6.05{+/-}0.62 {micro}g/mg, respectively, P>0.5). Iliocaudalis required both mechanical and endocrine cues for sarcomerogenesis. Tibialis anterior was not affected by mechanical or endocrine alterations. Despite equivalent extent of adaptations, load-induced changes were only partially protective against sarcomere hyperelongation. ConclusionsLoad induces plasticity of the intrinsic pelvic floor muscle components that renders protection against mechanical birth injury. The protective effect, which varies between individual muscles and strain magnitudes, is further augmented by the presence of pregnancy hormones. Maximizing impact of mechanical load on pelvic floor muscles during pregnancy, such as with specialized pelvic floor muscle stretching regimens, is a potentially actionable target for augmenting pregnancy-induced adaptations to decrease birth injury in women who may otherwise have incomplete antepartum muscle adaptations. AJOG at a GlanceO_LIWhy was the study conducted? O_LITo determine the role of mechanical load, uncoupled from the hormonal milieu of pregnancy, in driving protective pregnancy-induced adaptations previously discovered in the rat pelvic floor muscles. C_LI C_LIO_LIWhat are the key findings? O_LIMechanical load, in the absence of pregnancy hormones, induces sarcomerogenesis and extracellular matrix remodeling in rat pelvic floor muscles. C_LIO_LILoad-induced adaptations are partially protective against mechanical pelvic floor muscle injury consequent to parturition-associated strains. C_LI C_LIO_LIWhat does this study add to what is already known? O_LIThe effect of sustained increased mechanical load, uncoupled from the hormonal milieu of pregnancy, on pelvic floor muscle plasticity has not been previously studied. C_LIO_LIModulating pelvic floor muscles stretch antepartum, such as with specialized pelvic floor physical therapy regimens, could be a promising approach for augmentation of protective muscle adaptations in women. C_LI C_LI ]]> Rieger, M. M. Wong, M. Burnett, L. A. Boscolo Sesillo, F. Baynes, B. Alperin, M. 2021-08-02 doi:10.1101/2021.08.01.454675 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ A vibrissa pathway that activates the limbic system ]]> https://biorxiv.org/content/10.1101/2021.08.02.454720v1?rss=1 Kleinfeld, D. Deschenes, M. Elbaz, M. Callado Perez, A. Foo, C. Zhao, S. Demers, M. 2021-08-04 doi:10.1101/2021.08.02.454720 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Near-Zero Phase-Lag Hyperscanning in a Novel Wireless EEG System ]]> https://biorxiv.org/content/10.1101/2021.08.04.454932v1?rss=1 Chuang, C.-H. Lu, S.-W. Chao, Y.-P. Peng, P.-H. Hsu, H.-C. Jung, T.-P. 2021-08-06 doi:10.1101/2021.08.04.454932 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ The genetic etiology of longitudinal measures of predicted brain ageing in a population-based sample of mid to late-age males ]]> https://biorxiv.org/content/10.1101/2021.08.04.455143v1?rss=1 Gillespie, N. A. Hatton, S. N. Hagler, D. H. Dale, A. M. Elman, J. A. McEvoy, L. K. Elyer, L. T. Fennema-Notestine, C. Logue, M. W. McKenzie, R. E. Puckett, O. K. Tu, X. M. Whitsel, N. Xian, H. Reynolds, C. A. Panizzon, M. S. Lyons, M. J. Neale, M. C. Kremen, W. S. Franz, C. 2021-08-06 doi:10.1101/2021.08.04.455143 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region ]]> https://biorxiv.org/content/10.1101/2021.08.04.455157v1?rss=1 Turakhia, Y. Thornlow, B. Hinrichs, A. S. Mcbroome, J. Ayala, N. Ye, C. De Maio, N. Haussler, D. Lanfear, R. Corbett-Detig, R. 2021-08-05 doi:10.1101/2021.08.04.455157 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Interleukin-33 coordinates a microglial phagocytic response and limits corticothalamic excitability and seizure susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.05.455250v1?rss=1 Han, R. T. Vainchtein, I. D. Schlachetzki, J. C. M. Cho, F. S. Dorman, L. C. Johung, T. Ahn, E. Barron, J. T. Inoue, H. N. Joshi, A. Molofsky, A. B. Glass, C. K. Paz, J. T. Molofsky, A. V. 2021-08-06 doi:10.1101/2021.08.05.455250 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Broad-spectrum in vitro antiviral activity of ODBG-P-RVn: an orally-available, lipid-modified monophosphate prodrug of remdesivir parent nucleoside (GS-441524) ]]> https://biorxiv.org/content/10.1101/2021.08.06.455494v1?rss=1 Lo, M. K. Shrivastava-Ranjan, P. Chatterjee, P. Flint, M. Beadle, J. R. Valiaeva, N. Schooley, R. Hostetler, K. Y. Montgomery, J. Spiropoulou, C. F. 2021-08-08 doi:10.1101/2021.08.06.455494 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Tankyrase interacts with the allosteric site of glucokinase and inhibits its glucose-sensing function in the beta cell ]]> https://biorxiv.org/content/10.1101/2021.08.08.454510v1?rss=1 Chi, N.-W. Eisemann, T. Yeh, T.-Y. J. Roy, S. Chi, T. J. Lu, S. H. Pascal, J. M. Osborn, O. 2021-08-08 doi:10.1101/2021.08.08.454510 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Safety and efficacy of a new vaginal gel, Feminilove, for the treatment of symptoms associated with vaginal dryness and vulvovaginal atrophy in women: an in vitro and in vivo study ]]> https://biorxiv.org/content/10.1101/2021.08.17.455703v1?rss=1 Gonzalez, A. Lee, R. Booshehri, L. Grady, D. Vaddi, V. Ip, C. Mitchell, C. Cheung, W. W. 2021-08-18 doi:10.1101/2021.08.17.455703 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Long-term p21 and p53 trends regulate the frequency of mitosis events and cell cycle arrest ]]> https://biorxiv.org/content/10.1101/2021.08.17.456721v1?rss=1 Tran, A. P. Tralie, C. J. Moosmüller, C. Belkhatir, Z. Reyes, J. Levine, A. J. Deasy, J. O. Tannenbaum, A. R. 2021-08-19 doi:10.1101/2021.08.17.456721 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway ]]> https://biorxiv.org/content/10.1101/2021.08.23.457403v1?rss=1 Farre, J.-C. Carolino, K. Devanneaux, L. Subramani, S. 2021-08-23 doi:10.1101/2021.08.23.457403 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.08.24.457187v1?rss=1 Lam, M. T. Y. Duttke, S. H. Odish, M. F. Le, H. D. Hansen, E. A. Nguyen, C. T. Trescott, S. Kim, R. Deota, S. Chang, M. W. Patel, A. Hepokoski, M. Alotaibi, M. Rolfsen, M. Perofsky, K. Warden, A. S. Foley, J. Ramirez, S. I. Dan, J. M. Abbott, R. Crotty, S. Crotty-Alexander, L. E. Malhotra, A. Panda, S. Benner, C. W. Coufal, N. G. 2021-08-24 doi:10.1101/2021.08.24.457187 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Amphetamine alters the Reward Positivity in humans and mice ]]> https://biorxiv.org/content/10.1101/2021.08.25.457689v1?rss=1 Cavanagh, J. F. Olguin, S. Talledo, J. Kotz, J. Roberts, B. Nungary, J. A. Sprock, J. Gregg, D. Bhakta, S. G. Light, G. A. Swerdlow, N. R. Young, J. W. Brigman, J. L. 2021-08-27 doi:10.1101/2021.08.25.457689 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Redesigning the Eterna100 for the Vienna 2 folding engine ]]> https://biorxiv.org/content/10.1101/2021.08.26.457839v1?rss=1 Koodli, R. V. Rudolfs, B. Wayment-Steele, H. K. Eterna Structure Designers, Das, R. 2021-08-28 doi:10.1101/2021.08.26.457839 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ The OPAQUE1/DISCORIDA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize ]]> https://biorxiv.org/content/10.1101/2021.08.29.458084v1?rss=1 Nan, Q. Liang, H. Mendoza, J. Liu, L. Fulzele, A. Wright, A. J. Bennett, E. J. Rasmussen, C. Facette, M. R. 2021-08-30 doi:10.1101/2021.08.29.458084 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ ZetaSuite, A Computational Method for Analyzing Multi-dimensional High-throughput Data, Reveals Genes with Opposite Roles in Cancer Dependency ]]> https://biorxiv.org/content/10.1101/2021.08.29.458095v1?rss=1 Hao, Y. Shao, C. Zhao, G. Fu, X.-D. 2021-08-30 doi:10.1101/2021.08.29.458095 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B ]]> https://biorxiv.org/content/10.1101/2021.08.30.458235v1?rss=1 McCann, J. Cristini, A. Law, E. LEE, S. Tellier, M. Carpenter, M. Beghe, C. Kim, J. Jarvis, M. C. Stefanovska, B. Temiz, N. A. Bergstrom, E. N. Salamango, D. Brown, M. Murphy, S. Alexandrov, L. Miller, K. Gromak, N. Harris, R. 2021-08-31 doi:10.1101/2021.08.30.458235 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease ]]> https://biorxiv.org/content/10.1101/2021.09.01.458619v1?rss=1 D'Antonio, M. Arthur, T. D. Nguyen, J. P. Matsui, H. D'Antonio-Chronowska, A. Frazer, K. A. 2021-09-02 doi:10.1101/2021.09.01.458619 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes ]]> https://biorxiv.org/content/10.1101/2021.09.02.458788v1?rss=1 Steinbrenner, A. D. Saldivar, E. Hodges, N. Chaparro, A. F. Schmelz, E. A. 2021-09-03 doi:10.1101/2021.09.02.458788 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Distinct stress-dependent signatures of cellular and extracellular tRNA-derived small RNAs (tDRs) ]]> https://biorxiv.org/content/10.1101/2021.09.03.458085v1?rss=1 Li, G. Manning, A. Bagi, A. Yang, X. Howard, J. Chan, P. P. Sweeney, T. Li, H. Laurent, B. D. Kontaridis, M. I. Laurent, L. C. Jensen, K. V. K. Aranki, S. F. Muehlschlegel, J. D. Kitchen, R. Lowe, T. M. Das, S. 2021-09-04 doi:10.1101/2021.09.03.458085 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population ]]> https://biorxiv.org/content/10.1101/2021.09.06.459155v1?rss=1 Parker, C. C. Philip, V. Gatti, D. M. Kasparek, S. Kreuzman, A. Kuffler, L. Mansky, B. Masneuf, S. Sharif, K. Sluys, E. Taterra, D. Taylor, W. M. Thomas, M. Polesskaya, O. Palmer, A. A. Holmes, A. Chesler, E. 2021-09-06 doi:10.1101/2021.09.06.459155 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes ]]> https://biorxiv.org/content/10.1101/2021.09.06.459165v1?rss=1 Mendes, M. Russell, A. B. 2021-09-06 doi:10.1101/2021.09.06.459165 Cold Spring Harbor Laboratory Press 2021-09-06 <![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[ Semisynthesis of functional transmembrane proteins in GUVs ]]> https://biorxiv.org/content/10.1101/2021.09.08.459519v1?rss=1 Podolsky, K. A. Masubuchi, T. Debelouchina, G. T. Hui, E. Devaraj, N. K. 2021-09-08 doi:10.1101/2021.09.08.459519 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Engineered bacteria detect tumor DNA in vivo ]]> https://biorxiv.org/content/10.1101/2021.09.10.459858v1?rss=1 Cooper, R. M. Wright, J. A. Ng, J. Q. Goyne, J. M. Suzuki, N. Lee, Y. K. Ichinose, M. Radford, G. Thomas, E. M. Vrbanac, L. Knight, R. Woods, S. L. Worthley, D. L. Hasty, J. 2021-09-11 doi:10.1101/2021.09.10.459858 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Ankfn1 vestibular defects in zebrafish require mutations in both ancestral and derived paralogs. ]]> https://biorxiv.org/content/10.1101/2021.09.11.459924v1?rss=1 Ross, K. D. Ren, J. Zhang, R. Chi, N. C. Hamilton, B. A. 2021-09-12 doi:10.1101/2021.09.11.459924 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation ]]> https://biorxiv.org/content/10.1101/2021.09.16.459846v1?rss=1 Yeh, Y.-T. Skinner, D. E. Criado-Hidalgo, E. Chen, N. S. Garcia-De Herreros, A. El-Sakary, N. Liu, L. Zhang, S. Chien, S. Lasheras, J. C. del Alamo, J. C. Caffrey, C. R. 2021-09-17 doi:10.1101/2021.09.16.459846 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ CRISPR-Cas Inhibits Natural Transformation through Altruistic Group Defense and Self-Sacrifice ]]> https://biorxiv.org/content/10.1101/2021.09.16.460680v1?rss=1 Cooper, R. M. Hasty, J. 2021-09-16 doi:10.1101/2021.09.16.460680 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ A BioID-derived proximity interactome for SARS-CoV-2 proteins ]]> https://biorxiv.org/content/10.1101/2021.09.17.460814v1?rss=1 May, D. G. Martin-Sancho, L. Anschau, V. Liu, S. Chrisopulos, R. J. Scott, K. L. Halfmann, C. T. Pena, R. D. Pratt, D. Campos, A. R. Roux, K. J. 2021-09-21 doi:10.1101/2021.09.17.460814 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Context-aware deconvolution of cell-cell communication with Tensor-cell2cell ]]> https://biorxiv.org/content/10.1101/2021.09.20.461129v1?rss=1 Armingol, E. Baghdassarian, H. Martino, C. Perez-Lopez, A. Knight, R. Lewis, N. E. 2021-09-23 doi:10.1101/2021.09.20.461129 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Origin of electroneutrality in living system ]]> https://biorxiv.org/content/10.1101/2021.09.21.461264v1?rss=1 Akbari, A. Palsson, B. O. 2021-09-24 doi:10.1101/2021.09.21.461264 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Extrasynaptic signaling enables an asymmetric juvenile motor circuit to produce a symmetric mature gait. ]]> https://biorxiv.org/content/10.1101/2021.09.21.461278v1?rss=1 Lu, Y. Ahamed, T. Mulcahy, B. Witvliet, D. Guan, S. A. Hung, W. Meng, J. Wen, Q. Samuel, A. Zhen, M. 2021-09-24 doi:10.1101/2021.09.21.461278 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ The connection between Rap1 and Talin1 in CD4+ T Lymphocytes ]]> https://biorxiv.org/content/10.1101/2021.09.22.461411v1?rss=1 Lagarrigue, F. Tan, B. Du, Q. Fan, Z. Lopez-Ramirez, M. A. Gingras, A. R. Qi, W. Sun, H. 2021-09-23 doi:10.1101/2021.09.22.461411 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Self-Administration of entactogen psychostimulants dysregulates GABA and Kappa Opioid Receptor signaling in the central nucleus of the amygdala of female Wistar rats ]]> https://biorxiv.org/content/10.1101/2021.09.24.461477v1?rss=1 Khom, S. Nguyen, J. D. Vandewater, S. A. Grant, Y. Roberto, M. Taffe, M. A. 2021-09-24 doi:10.1101/2021.09.24.461477 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Phostensin Enables Lymphocyte Integrin Activation and Population of Peripheral Lymphoid Organs ]]> https://biorxiv.org/content/10.1101/2021.09.24.461584v1?rss=1 Ginsberg, M. Sun, H. Gingras, A. Lee, H. Lagarrigue, F. Fox, J. W. Sherman, N. E. 2021-09-24 doi:10.1101/2021.09.24.461584 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Towards Understanding Comprehensive Morphometric Changes and Its Correlation with Cognition and Exposure to Fighting in Active Professional Boxers ]]> https://biorxiv.org/content/10.1101/2021.09.25.461817v1?rss=1 Mishra, V. R. Zhuang, X. Sreenivasan, K. R. Cordes, D. Ritter, A. Banks, S. Bernick, C. 2021-09-28 doi:10.1101/2021.09.25.461817 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Pre-mRNA Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the pre-mRNA Splice Site Signal ]]> https://biorxiv.org/content/10.1101/2021.09.27.462007v1?rss=1 Glasser, E. Maji, D. Biancon, G. Keedakkatt Puthenpeedikakkal, A. M. Cavender, C. Tebaldi, T. Pulvino, M. J. Jenkins, J. L. Mathews, D. H. Halene, S. Kielkopf, C. L. 2021-09-27 doi:10.1101/2021.09.27.462007 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Nanocrown electrodes for robust and scalable intracellular recordings of cardiomyocytes for cardiotoxicity screening ]]> https://biorxiv.org/content/10.1101/2021.09.28.462181v1?rss=1 99% success rates in obtaining intracellular access through electroporation, allowing reliable and simultaneous iAP recordings from up to 57 human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs). The accuracy of nanocrown electrode recordings is validated by simultaneous patch clamp recording from the same cell. Nanocrown electrodes enable prolonged iAP recording for continual monitoring of the same cells upon the sequential addition of four to five incremental drug doses. In this way, the dose-response data is self-referencing, which avoids the cell-to-cell variations inherent to hPSC-CMs. We are hopeful that this technology development is a step towards establishing an iAP screening assay for preclinical evaluation of drug-induced arrhythmogenicity. ]]> Jahed, Z. Yang, Y. Tsai, C.-T. Foster, E. P. McGuire, A. F. Yang, H. Liu, A. Forro, C. Yan, Z. Ke, X. J. Zhao, M.-T. Zheng, W. Li, X. Li, T. Pawlosky, A. Wu, J. C. Cui, B. 2021-09-30 doi:10.1101/2021.09.28.462181 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Integrated Regulation of PKA by Fast and Slow Neurotransmission in the Nucleus Accumbens Controls Plasticity and Stress Responses ]]> https://biorxiv.org/content/10.1101/2021.09.29.462408v1?rss=1 Thomas, R. Hernandez, A. Benavides, D. R. Li, W. Tan, C. Plattner, F. Chakraborti, A. Pozzo-Miller, L. Taylor, S. S. Bibb, J. A. 2021-10-01 doi:10.1101/2021.09.29.462408 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviours in the chick embryo ]]> https://biorxiv.org/content/10.1101/2021.10.03.462938v1?rss=1 Chuai, M. Serrano-Najere, G. Serra, M. Mahadavan, L. Weijer, C. J. 2021-10-03 doi:10.1101/2021.10.03.462938 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Novelty detection in early olfactory processing of the honey bee, Apis mellifera ]]> https://biorxiv.org/content/10.1101/2021.10.06.463371v1?rss=1 Lei, H. Haney, S. Jernigan, C. M. Cook, C. Guo, X. Smith, B. Bazhenov, M. 2021-10-08 doi:10.1101/2021.10.06.463371 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ The long-term effects of repeated heroin vapor inhalation during adolescence on measures of nociception and anxiety-like behavior in adult Wistar rats ]]> https://biorxiv.org/content/10.1101/2021.10.06.463404v1?rss=1 Gutierrez, A. Harvey, E. L. Creehan, K. M. Taffe, M. A. 2021-10-08 doi:10.1101/2021.10.06.463404 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Cytoplasmic dynein-1 cargo diversity is mediated by the combinatorial assembly of FTS-Hook-FHIP complexes ]]> https://biorxiv.org/content/10.1101/2021.10.07.463551v1?rss=1 Christensen, J. R. Kendrick, A. A. Troung, J. B. Aguilar-Maldonado, A. Adani, V. Dzieciatkowska, M. Reck-Peterson, S. L. 2021-10-08 doi:10.1101/2021.10.07.463551 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Disrupted intrinsic connectivity links to language and social deficits in toddlers with autism ]]> https://biorxiv.org/content/10.1101/2021.10.08.463640v1?rss=1 Xiao, Y. Wen, T. H. Kupis, L. Eyler, L. T. Goel, D. Lombardo, M. V. Pierce, K. Courchesne, E. 2021-10-09 doi:10.1101/2021.10.08.463640 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ HORmon: automated annotation of human centromeres ]]> https://biorxiv.org/content/10.1101/2021.10.12.464028v1?rss=1 Kunyavskaya, O. Dvorkina, T. Bzikadze, A. V. Alexandrov, I. Pevzner, P. A. 2021-10-12 doi:10.1101/2021.10.12.464028 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Multimodal tubulin binding by the yeast kinesin-8, Kip3, underlies its motility and depolymerization ]]> https://biorxiv.org/content/10.1101/2021.10.12.464151v1?rss=1 Arellano-Santoyo, H. Hernandez-Lopez, R. A. Stokasimov, E. Wang, R. Y. Pellman, D. Leschziner, A. E. 2021-10-13 doi:10.1101/2021.10.12.464151 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition ]]> https://biorxiv.org/content/10.1101/2021.10.14.464447v1?rss=1 Lu, S. Hu, J. Arogundade, O. A. Goginashvili, A. Vazquez-Sanchez, S. Diedrich, J. K. Gu, J. Blum, J. Oung, S. Yu, H. Ravits, J. Liu, C. Yates, J. R. Cleveland, D. W. 2021-10-15 doi:10.1101/2021.10.14.464447 Cold Spring Harbor Laboratory Press 2021-10-15 <![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[ Diverse chemical functionalization of nucleobases within long RNAs using sulfinate salts ]]> https://biorxiv.org/content/10.1101/2021.10.19.465008v1?rss=1 Hirlinger, A. Bassi, T. G. Grayson, L. Vantourout, J. C. Toor, N. 2021-10-19 doi:10.1101/2021.10.19.465008 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound ]]> https://biorxiv.org/content/10.1101/2021.10.19.465031v1?rss=1 Kunselman, E. Minich, J. J. Horwith, M. Gilbert, J. Allen, E. 2021-10-19 doi:10.1101/2021.10.19.465031 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults ]]> https://biorxiv.org/content/10.1101/2021.10.20.465206v1?rss=1 Nguyen, J. P. iPSCORE Consortium, D'Antonio-Chronowska, A. Fujita, K. Salgado, B. M. Matsui, H. Arthur, T. D. Donovan, M. K. D'Antonio, M. Frazer, K. A. 2021-10-21 doi:10.1101/2021.10.20.465206 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ A focal adhesion kinase-YAP signaling axis drives drug tolerant persister cells and residual disease in lung cancer ]]> https://biorxiv.org/content/10.1101/2021.10.23.465573v1?rss=1 Haderk, F. Fernandez-Mendez, C. Cech, L. Yu, J. Meraz, I. M. Olivas, V. Barbosa Rabago, D. Kerr, D. L. Gomez, C. Allegakoen, D. V. Guan, J. Shah, K. N. Herrington, K. A. Gbenedio, O. M. Nanjo, S. Majidi, M. Tamaki, W. Rotow, J. K. McCoach, C. E. Riess, J. W. Gutkind, J. S. Tang, T. T. Post, L. Huang, B. Santisteban, P. Goodarzi, H. Bandyopadhyay, S. Kuo, C. J. Roose, J. P. Wu, W. Blakely, C. M. Roth, J. A. Bivona, T. G. 2021-10-24 doi:10.1101/2021.10.23.465573 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ A Cytoskeletal Vortex Drives Phage Nucleus Rotation During Jumbo Phage Replication inE. coli ]]> https://biorxiv.org/content/10.1101/2021.10.25.465362v1?rss=1 Birkholz, E. A. Laughlin, T. G. Suslov, S. Armbruster, E. Lee, J. Wittmann, J. Corbett, K. D. Villa, E. Pogliano, J. 2021-10-26 doi:10.1101/2021.10.25.465362 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies ]]> https://biorxiv.org/content/10.1101/2021.10.25.465810v1?rss=1 Vezina, B. Judd, L. M. McDougall, F. K. Boardman, W. S. Power, M. L. Hawkey, J. Brisse, S. Monk, J. M. Holt, K. E. Wyres, K. L. 2021-10-26 doi:10.1101/2021.10.25.465810 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Conditional depletion reveals temporal requirements for the oscillating transcription factor NHR-23/NR1F1 in C. elegans larval progression ]]> https://biorxiv.org/content/10.1101/2021.10.27.465992v1?rss=1 Johnson, L. C. Aguilera, J. D. Levenson, M. T. Rechtsteiner, A. D. Vo, A. A. Ragle, J. M. Ward, J. D. 2021-10-27 doi:10.1101/2021.10.27.465992 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Sex differences in migraine: A twin study ]]> https://biorxiv.org/content/10.1101/2021.10.27.466155v1?rss=1 Fitzgerald, M. C. Saelzler, U. G. Panizzon, M. S. 2021-10-28 doi:10.1101/2021.10.27.466155 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ FEMA: Fast and efficient mixed-effects algorithm for population-scale whole brain imaging data ]]> https://biorxiv.org/content/10.1101/2021.10.27.466202v1?rss=1 Fan, C. C. Palmer, C. E. Iverson, J. Pecheva, D. Thompson, W. K. Hagler, D. Jernigan, T. L. Dale, A. M. 2021-10-28 doi:10.1101/2021.10.27.466202 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Two parallel pathways are required for ultrasound-evoked behavioral changes in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.10.29.466533v1?rss=1 Magaram, U. Weiss, C. Vasan, A. Reddy, K. C. Friend, J. Chalasani, S. H. 2021-11-02 doi:10.1101/2021.10.29.466533 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Mem3DG: Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry ]]> https://biorxiv.org/content/10.1101/2021.10.30.466618v1?rss=1 Zhu, C. Lee, C. T. Rangamani, P. 2021-10-31 doi:10.1101/2021.10.30.466618 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Behavioral context affects social signal representations within single primate prefrontal cortex neurons ]]> https://biorxiv.org/content/10.1101/2021.11.01.466818v1?rss=1 Jovanovic, V. Fishbein, A. R. de la Mothe, L. Lee, K.-F. Miller, C. T. 2021-11-03 doi:10.1101/2021.11.01.466818 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Discovery of a carbonic anhydrase-Rubisco supercomplex within the alpha-carboxysome ]]> https://biorxiv.org/content/10.1101/2021.11.05.467472v1?rss=1 Blikstad, C. Dugan, E. J. Laughlin, T. G. Liu, M. D. Shoemaker, S. R. Remis, J. P. Savage, D. F. 2021-11-05 doi:10.1101/2021.11.05.467472 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations ]]> https://biorxiv.org/content/10.1101/2021.11.10.468164v1?rss=1 Hattori, R. Komiyama, T. 2021-11-13 doi:10.1101/2021.11.10.468164 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes ]]> https://biorxiv.org/content/10.1101/2021.11.11.468006v1?rss=1 Russell, B. J. Brown, S. D. Saran, A. R. Mai, I. Lingaraju, A. Siguenza, N. Maissy, E. Dantas Machado, A. C. Pinto, A. F. M. Miyamoto, Y. Richter, R. A. Ho, S. B. Eckmann, L. Hasty, J. Saghatelian, A. Knight, R. Zarrinpar, A. 2021-11-12 doi:10.1101/2021.11.11.468006 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Synchrony and idiosyncrasy in the gut microbiome of wild primates ]]> https://biorxiv.org/content/10.1101/2021.11.24.469913v1?rss=1 Bjork, J. R. Dasari, M. R. Roche, K. Grieneisen, L. Gould, T. J. Grenier, J.-C. Yotova, V. Gottel, N. Jansen, D. Gesquiere, L. R. Gordon, J. B. Learn, N. H. Wango, T. L. Mututua, R. S. Warutere, J. K. Siodi, L. i. Mukherjee, S. Barreiro, L. B. Alberts, S. C. Gilbert, J. A. Tung, J. Blekhman, R. Archie, E. 2021-11-24 doi:10.1101/2021.11.24.469913 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Evolution of Human-specific Alleles Protecting Cognitive Function of Grandmothers ]]> https://biorxiv.org/content/10.1101/2021.11.26.470088v1?rss=1 Saha, S. Khan, N. Comi, T. Verhagen, A. Sasmal, A. Diaz, S. Yu, H. Chen, X. Akey, J. M. Frank, M. Gagneux, P. Varki, A. 2021-11-26 doi:10.1101/2021.11.26.470088 Cold Spring Harbor Laboratory Press 2021-11-26 <![CDATA[ Functionalizing lipid sponge droplets with DNA ]]> https://biorxiv.org/content/10.1101/2021.11.28.470255v1?rss=1 Cho, C. Niederholtmeyer, H. Seo, H. Bhattacharya, A. Devaraj, N. K. 2021-11-28 doi:10.1101/2021.11.28.470255 Cold Spring Harbor Laboratory Press 2021-11-28 <![CDATA[ COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2021.11.28.470269v1?rss=1 1000 human lung transcriptomic datasets associated with various lung conditions using two viral pandemic signatures (ViP and sViP) and one covid lung-derived signature. Upon identifying similarities between COVID-19 and idiopathic pulmonary fibrosis (IPF), we subsequently dissected the basis for such similarity from molecular, cytopathic, and immunologic perspectives using a panel of IPF-specific gene signatures, alongside signatures of alveolar type II (AT2) cytopathies and of prognostic monocyte-driven processes that are known drivers of IPF. Transcriptome-derived findings were used to construct protein-protein interaction (PPI) network to identify the major triggers of AT2 dysfunction. Key findings were validated in hamster and human adult lung organoid (ALO) pre-clinical models of COVID-19 using immunohistochemistry and qPCR. FindingsCOVID-19 resembles IPF at a fundamental level; it recapitulates the gene expression patterns (ViP and IPF signatures), cytokine storm (IL15-centric), and the AT2 cytopathic changes, e.g., injury, DNA damage, arrest in a transient, damage-induced progenitor state, and senescence-associated secretory phenotype (SASP). These immunocytopathic features were induced in pre-clinical COVID models (ALO and hamster) and reversed with effective anti-CoV-2 therapeutics in hamsters. PPI-network analyses pinpointed ER stress as one of the shared early triggers of both diseases, and IHC studies validated the same in the lungs of deceased subjects with COVID-19 and SARS-CoV-2-challenged hamster lungs. Lungs from tg-mice, in which ER stress is induced specifically in the AT2 cells, faithfully recapitulate the host immune response and alveolar cytopathic changes that are induced by SARS-CoV-2. InterpretationLike IPF, COVID-19 may be driven by injury-induced ER stress that culminates into progenitor state arrest and SASP in AT2 cells. The ViP signatures in monocytes may be key determinants of prognosis. The insights, signatures, disease models identified here are likely to spur the development of therapies for patients with IPF and other fibrotic interstitial lung diseases. FundingThis work was supported by the National Institutes for Health grants R01-GM138385 and AI155696 and funding from the Tobacco-Related disease Research Program (R01RG3780). One Sentence SummarySevere COVID-19 triggers cellular processes seen in fibrosing Interstitial Lung Disease RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSIn its aftermath, the COVID-19 pandemic has left many survivors, almost a third of those who recovered, with a mysterious long-haul form of the disease which culminates in a fibrotic form of interstitial lung disease (post-COVID-19 ILD). Post-COVID-19 ILD remains a largely unknown entity. Currently, we lack insights into the core cytopathic features that drive this condition. Added value of this studyUsing an AI-guided approach, which involves the use of sets of gene signatures, protein-protein network analysis, and a hamster model of COVID-19, we have revealed here that COVID-19 -lung fibrosis resembles IPF, the most common form of ILD, at a fundamental level--showing similar gene expression patterns in the lungs and blood, and dysfunctional AT2 processes (ER stress, telomere instability, progenitor cell arrest, and senescence). These findings are insightful because AT2 cells are known to contain an elegant quality control network to respond to intrinsic or extrinsic stress; a failure of such quality control results in diverse cellular phenotypes, of which ER stress appears to be a point of convergence, which appears to be sufficient to drive downstream fibrotic remodeling in the lung. Implications of all the available evidenceBecause unbiased computational methods identified the shared fundamental aspects of gene expression and cellular processes between COVID-19 and IPF, the impact of our findings is likely to go beyond COVID-19 or any viral pandemic. The insights, tools (disease models, gene signatures, and biomarkers), and mechanisms identified here are likely to spur the development of therapies for patients with IPF and, other fibrotic interstitial lung diseases, all of whom have limited or no treatment options. To dissect the validated prognostic biomarkers to assess and track the risk of pulmonary fibrosis and develop therapeutics to halt fibrogenic progression. ]]> Sinha, S. Castillo, V. Espinoza, C. R. Tindle, C. Fonseca, A. G. Dan, J. M. Katkar, G. D. Das, S. Sahoo, D. Ghosh, P. 2021-11-30 doi:10.1101/2021.11.28.470269 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ MuDCoD: Multi-Subject Community Detection in Personalized Dynamic Gene Networks from Single Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2021.11.30.470619v1?rss=1 Sapci, A. O. B. Lu, S. Tastan, O. Keles, S. 2021-12-01 doi:10.1101/2021.11.30.470619 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches ]]> https://biorxiv.org/content/10.1101/2021.12.02.471004v1?rss=1 Thornlow, B. Ye, C. De Maio, N. McBroome, J. Hinrichs, A. S. Lanfear, R. Turakhia, Y. Corbett-Detig, R. 2021-12-03 doi:10.1101/2021.12.02.471004 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Pandemic-scale phylogenetics ]]> https://biorxiv.org/content/10.1101/2021.12.03.470766v1?rss=1 Ye, C. Thornlow, B. Kramer, A. M. McBroome, J. Hinrichs, A. S. Corbett-Detig, R. Turakhia, Y. 2021-12-06 doi:10.1101/2021.12.03.470766 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ A remote lecture series roadmap to equity, diversity, and inclusion in STEM ]]> https://biorxiv.org/content/10.1101/2021.12.05.471284v1?rss=1 Boyle, E. A. Goldberg, G. Schmok, J. C. Burgado, J. Izidro Layng, F. Grunwald, H. A. Balotin, K. M. Cuoco, M. S. Chang, K.-C. Ecklu-Mensah, G. Arakaki, A. K. S. Ahmed, N. Garcia Arceo, X. Jagannatha, P. Pekar, J. Iyer, M. DASL Alliance, Yeo, G. W. 2021-12-07 doi:10.1101/2021.12.05.471284 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung ]]> https://biorxiv.org/content/10.1101/2021.12.05.471312v1?rss=1 Gaddis, N. Fortriede, J. Guo, M. Bardes, E. E. Kouril, M. Tabar, S. Burns, K. Ardini-Poleske, M. E. Loos, S. Schnell, D. Jin, K. Iyer, B. Du, Y. Korte, J. Munshi, R. Smith, V. Herbst, A. Kitzmiller, J. A. Clair, G. C. Carson, J. Adkins, J. Morrisey, E. E. Pryhuber, G. S. Misra, R. Whitsett, J. A. Sun, X. Heathorn, T. Paten, B. Prasath, V. B. S. Xu, Y. Tickle, T. Aronow, B. J. Salomonis, N. 2021-12-06 doi:10.1101/2021.12.05.471312 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Design of M protein immunogens to elicit broadly reactive antibodies against Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2021.12.07.471543v1?rss=1 220 M types, as defined by the M protein hypervariable region (HVR), has been considered to limit its utility as a vaccine immunogen due to type-specificity in the antibody response. Surprisingly, a multi-HVR immunogen in clinical vaccine trials elicited M type cross-reactivity. The basis for this cross-reactivity is unknown but may be due in part to antibody recognition of a three-dimensional (3D) pattern conserved in many M protein HVRs that confers binding to human C4b-binding protein (C4BP). To test this hypothesis, we asked whether a single M protein immunogen carrying the 3D pattern would elicit cross-reactivity against other M types carrying the 3D pattern. We found that a 34-amino acid sequence of M2 protein bearing the 3D pattern retained full C4BP-binding capacity when fused to a coiled coil-stabilizing sequence from GCN4. This immunogen, called M2G, elicited cross-reactive antibodies against a number of M types that carry the 3D pattern but not against those that lack the 3D pattern. The M2G antiserum recognized M proteins as displayed natively on the Strep A surface, and promoted the opsonophagocytic killing of Strep A strains expressing these M proteins. As C4BP-binding is a conserved virulence trait of Strep A, targeting the 3D pattern may prove advantageous in vaccine design. ]]> Wang, K.-C. Nizet, V. Ghosh, P. 2021-12-07 doi:10.1101/2021.12.07.471543 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Vascular proteome responses precede organ dysfunction in sepsis ]]> https://biorxiv.org/content/10.1101/2021.12.07.471579v1?rss=1 Sorrentino, J. T. Golden, G. J. Morris, C. Painter, C. Nizet, V. Campos, A. R. Smith, J. W. Karlsson, C. A. Q. Malmström, J. Lewis, N. E. Esko, J. D. Gomez Toledo, A. 2021-12-09 doi:10.1101/2021.12.07.471579 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Dopamine D2Rs Coordinate Cue-Evoked Changes in Striatal Acetylcholine Levels ]]> https://biorxiv.org/content/10.1101/2021.12.08.471871v1?rss=1 Kellendonk, C. Martyniuk, K. M. Torres-Herraez, A. Rubinstein, M. Labouesse, M. A. 2021-12-11 doi:10.1101/2021.12.08.471871 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling ]]> https://biorxiv.org/content/10.1101/2021.12.10.472112v1?rss=1 Biering, S. B. Tramontini Gomes de Sousa, F. Tjang, L. V. Pahmeier, F. Ruan, R. Blanc, S. F. Patel, T. S. Worthington, C. M. Glasner, D. R. Castillo-Rojas, B. Servellita, V. Lo, N. T. Wong, M. P. Warnes, C. M. Sandoval, D. R. Clausen, T. M. Santos, Y. A. Ortega, V. Aguilar-Carreno, H. Esko, J. D. Chiu, C. Y. Pak, J. E. Beatty, P. R. Harris, E. 2021-12-13 doi:10.1101/2021.12.10.472112 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy ]]> https://biorxiv.org/content/10.1101/2021.12.14.472731v1?rss=1 Liu, M. Hernandez-Morales, A. C. Clark, J. Le, T. T. Biswas, B. Bishop-Lilly, K. A. Henry, M. S. Quinones, J. Hamilton, T. Schooley, R. Salka, S. Young, R. F. Gill, J. J. 2021-12-16 doi:10.1101/2021.12.14.472731 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Distinguishing COVID-19 infection and vaccination history by T cell reactivity ]]> https://biorxiv.org/content/10.1101/2021.12.15.472874v1?rss=1 Yu, E. D. Wang, E. Garrigan, E. Goodwin, B. Sutherland, A. Chang, J. Galvez, R. I. Mateus, J. Rawlings, S. A. Smith, D. M. Frazier, A. Weiskopf, D. Dan, J. M. Crotty, S. Grifoni, A. Sette, A. da Silva Antunes, R. 2021-12-17 doi:10.1101/2021.12.15.472874 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Neural signature of everyday function in older adults at-risk of cognitive impairment ]]> https://biorxiv.org/content/10.1101/2021.12.16.472826v1?rss=1 De Sanctis, P. Wagner, J. Molholm, S. Foxe, J. J. Blumen, H. Horsthuis, D. 2021-12-17 doi:10.1101/2021.12.16.472826 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Transcriptomes and metabolism define mouse and human MAIT cell heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.12.20.473182v1?rss=1 Chandra, S. Ascui, G. Riffelmacher, T. Chawla, A. Ramirez-Suastegui, C. Castelan, V. C. Seumois, G. Simon, H. Murray, M. P. Seo, G.-Y. Premlal, A. L. R. Verstichel, G. Li, Y. Lin, C.-H. Greenbaum, J. Lamberti, J. Murthy, R. Nigro, J. Cheroutre, H. Ottensmeier, C. H. Hedrick, S. M. Lu, L.-F. Vijayanand, P. Kronenberg, M. 2021-12-21 doi:10.1101/2021.12.20.473182 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark ]]> https://biorxiv.org/content/10.1101/2021.12.20.473592v1?rss=1 Fang, X. Westh, H. Kemp, M. Ellermann-Eriksen, S. Palsson, B. O. Johansen, H. K. Monk, J. M. 2021-12-23 doi:10.1101/2021.12.20.473592 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A vascularized 3D model of the human pancreatic islet for ex vivo study of immune cell-islet interaction ]]> https://biorxiv.org/content/10.1101/2021.12.21.473744v1?rss=1 Bender, R. H. F. O'Donnell, B. T. Shergill, B. Pham, B. Q. Juat, D. J. Hatch, M. S. Shirure, V. S. Wortham, M. Nguyen-Ngoc, K.-V. Jun, Y. Gaetani, R. Christman, K. L. Teyton, L. George, S. C. Sander, M. Hughes, C. C. 2021-12-23 doi:10.1101/2021.12.21.473744 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Theta oscillations in the prefrontal-hippocampal circuit do not couple to respiration-related oscillations ]]> https://biorxiv.org/content/10.1101/2021.12.22.473834v1?rss=1 Srikanth, S. Le, D. Hu, Y. Leutgeb, J. K. Leutgeb, S. 2021-12-23 doi:10.1101/2021.12.22.473834 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.12.22.473864v1?rss=1 Rodionova, I. A. Gao, Y. Lim, H. G. Saier, M. H. Palsson, B. Monk, J. Rodionov, D. A. Szubin, R. 2021-12-23 doi:10.1101/2021.12.22.473864 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Mistimed feeding disrupts circadian rhythms of male mating behavior and female preovulatory LH surges in mice ]]> https://biorxiv.org/content/10.1101/2021.12.27.474267v1?rss=1 Kukino, A. Walbeek, T. J. Sun, L. J. Watt, A. T. Park, J. H. Kauffman, A. S. Butler, M. P. 2021-12-28 doi:10.1101/2021.12.27.474267 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Control of bacterial anti-phage signaling by a WYL domain transcription factor ]]> https://biorxiv.org/content/10.1101/2022.01.04.474952v1?rss=1 Blankenchip, C. L. Nguyen, J. V. Lau, R. K. Ye, Q. Gu, Y. Corbett, K. D. 2022-01-04 doi:10.1101/2022.01.04.474952 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.01.05.475095v1?rss=1 Santos, L. H. Kronenberger, T. Almeida, R. G. Barbosa da Silva, E. Rocha, R. E. O. Oliveira, J. C. Barreto, L. V. Skinner, D. Fajtova, P. Giardini, M. A. Woodworth, B. Bardine, C. Lourenco, A. L. Craik, C. S. Poso, A. Podust, L. M. McKerrow, J. H. Siqueira-Neto, J. L. O'Donoghue, A. J. da Silva Junior, E. N. Ferreira, R. 2022-01-05 doi:10.1101/2022.01.05.475095 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Quantifying biological carbon pump pathways with a data-constrained mechanistic model ensemble approach ]]> https://biorxiv.org/content/10.1101/2022.01.07.475464v1?rss=1 Stukel, M. R. Decima, M. Landry, M. R. 2022-01-10 doi:10.1101/2022.01.07.475464 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37 ]]> https://biorxiv.org/content/10.1101/2022.01.11.475926v1?rss=1 Kolesinski, P. Wang, K.-C. Hirose, Y. Nizet, V. Ghosh, P. 2022-01-11 doi:10.1101/2022.01.11.475926 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains ]]> https://biorxiv.org/content/10.1101/2022.01.11.475931v1?rss=1 Yuan, Y. Seif, Y. Rychel, K. Yoo, R. Chauhan, S. M. Poudel, S. Al-bulushi, T. Palsson, B. Sastry, A. V. 2022-01-11 doi:10.1101/2022.01.11.475931 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ GR-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction ]]> https://biorxiv.org/content/10.1101/2022.01.12.475507v1?rss=1 Duttke, S. Montilla-Perez, P. Chang, M. W. Li, H. Chen, H. Carrette, L. L. G. de Guglielmo, G. George, O. Palmer, A. A. Benner, C. Telese, F. 2022-01-12 doi:10.1101/2022.01.12.475507 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.01.12.475688v1?rss=1 Ye, C. Thornlow, B. Hinrichs, A. S. Torvi, D. Lanfear, R. Corbett-Detig, R. Turakhia, Y. 2022-01-13 doi:10.1101/2022.01.12.475688 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Endogenous 1-deoxysphingolipid synthesis compromises anchorage-independent growth and plasma membrane endocytosis in cancer cells ]]> https://biorxiv.org/content/10.1101/2022.01.19.476986v1?rss=1 Cordes, T. Kuna, R. S. McGregor, G. H. Khare, S. V. Gengatharan, J. Muthusamy, T. Metallo, C. M. 2022-01-22 doi:10.1101/2022.01.19.476986 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Wildlife and Marine Mammal Spatial Observatory: Observation and automated detection of Southern Right Whales in multispectral satellite imagery ]]> https://biorxiv.org/content/10.1101/2022.01.20.477141v1?rss=1 Houegnigan, L. Romero Merino, E. Vermeulen, E. Block, J. Safari, P. Moreno-Noguer, F. Nadeu, C. 2022-01-22 doi:10.1101/2022.01.20.477141 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Post-embryonic maturation of the C. elegans motor circuit ]]> https://biorxiv.org/content/10.1101/2022.01.24.477421v1?rss=1 Mulcahy, B. Witvliet, D. Mitchell, J. K. Schalek, R. Berger, D. Wu, Y. Holmyard, D. Lu, Y. Ahamed, T. Samuel, A. D. Chisholm, A. D. Lichtman, J. W. Zhen, M. 2022-01-25 doi:10.1101/2022.01.24.477421 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Mindin is essential for cutaneous fibrogenesis in a new mouse model of systemic sclerosis ]]> https://biorxiv.org/content/10.1101/2022.01.26.477822v1?rss=1 Rana, I. Kataria, S. Tan, T.-L. Hajam, E. Y. Kashyap, D. K. Saha, D. Ajnabi, J. Paul, S. Jayappa, S. Ananthan, A. S. Kumar, P. Zaarour, R. F. J, H. Samuel, R. George, R. Danda, D. Jacob, P. M. Dey, R. Perundurai, D. He, Y.-W. Varga, J. Varghese, S. Jamora, C. 2022-01-28 doi:10.1101/2022.01.26.477822 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 ]]> https://biorxiv.org/content/10.1101/2022.01.27.477154v1?rss=1 Simkovsky, R. Parnasa, R. Wang, J. Nagar, E. Zecharia, E. Suban, S. Yegorov, Y. Veltman, B. Sendersky, E. Schwarz, R. Golden, S. S. 2022-01-28 doi:10.1101/2022.01.27.477154 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Gnas ablation in CD11c+ cells prevents high-fat diet-induced obesity by elevating adipose tissue catecholamine levels and thermogenesis ]]> https://biorxiv.org/content/10.1101/2022.01.27.478070v1?rss=1 Zeng, L. Herdman, D. S. Lee, J. Tao, A. Das, M. Bertin, S. Eckmann, L. Mahata, S. K. Devulapalli, S. Patel, H. Molina, A. J. A. Osborn, O. Corr, M. Raz, E. Webster, N. J. G. 2022-01-28 doi:10.1101/2022.01.27.478070 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Interplay between rule learning and rule switching in a perceptual categorization task ]]> https://biorxiv.org/content/10.1101/2022.01.29.478330v1?rss=1 Bouchacourt, F. Tafazoli, S. Mattar, M. G. Buschman, T. J. Daw, N. D. 2022-01-30 doi:10.1101/2022.01.29.478330 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ AI-assisted Discovery of an Ethnicity-influenced Driver of Cell Transformation in Esophageal and Gastroesophageal Junction Adenocarcinomas ]]> https://biorxiv.org/content/10.1101/2022.01.30.478408v1?rss=1 Ghosh, P. Campos, V. J. Vo, D. T. Guccione, C. Goheen-Holland, V. Tindle, C. Mazzini, G. S. He, Y. Alexandrov, L. Lippman, S. M. Gurski, R. Das, S. Curtius, K. Yadlapati, R. Sahoo, D. 2022-02-01 doi:10.1101/2022.01.30.478408 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings ]]> https://biorxiv.org/content/10.1101/2022.02.01.478759v1?rss=1 Cantu, V. J. Sanders, K. Belda-Ferre, P. Salido, R. A. Tsai, R. Austin, B. Jordan, W. Asudani, M. Walster, A. Magallanes, C. G. Valentine, H. D. Majnoonian, A. Wijaya, C. Omaleki, V. Aigner, S. Baer, N. A. Betty, M. Castro-Martinez, A. Cheung, W. De Hoff, P. Eisner, E. Hakim, A. Lastrella, A. L. Lawrence, E. S. Ngo, T. T. Ostrander, R. T. Plascencia, A. Sathe, S. Smoot, E. W. Carlin, A. F. Yeo, G. W. Laurent, L. C. Manlutac, A. L. Fielding-Miller, R. Knight, R. 2022-02-03 doi:10.1101/2022.02.01.478759 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Epigenetic cell memory: The gene's inner chromatin modification circuit ]]> https://biorxiv.org/content/10.1101/2022.02.02.476953v1?rss=1 Bruno, S. Williams, R. J. Del Vecchio, D. 2022-02-03 doi:10.1101/2022.02.02.476953 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Nutrient gradients mediate creation of highly resistant layers in structured microbial populations during antibiotic exposures ]]> https://biorxiv.org/content/10.1101/2022.02.02.478895v1?rss=1 Stevanovic, M. Boukéké-Lesplulier, T. Hupe, L. Hasty, J. Bittihn, P. Schultz, D. 2022-02-03 doi:10.1101/2022.02.02.478895 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Exploring the frame effect ]]> https://biorxiv.org/content/10.1101/2022.02.10.479960v1?rss=1 Cavanagh, P. Anstis, S. Lisi, M. Wexler, M. Maechler, M. 't Hart, B. M. Shams-Ahmar, M. Saleki, S. 2022-02-10 doi:10.1101/2022.02.10.479960 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Examining clustered somatic mutations with SigProfilerClusters ]]> https://biorxiv.org/content/10.1101/2022.02.11.480117v1?rss=1 Bergstrom, E. N. Kundu, M. Tbeileh, N. Alexandrov, L. B. 2022-02-14 doi:10.1101/2022.02.11.480117 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission ]]> https://biorxiv.org/content/10.1101/2022.02.13.480251v1?rss=1 Aggarwal, A. Liu, R. Chen, Y. Ralowicz, A. J. Bergerson, S. J. Tomaska, F. Hanson, T. L. Hasseman, J. P. Reep, D. Tsegaye, G. Yao, P. Ji, X. Kloos, M. Walpita, D. Patel, R. Tilberg, P. W. Mohar, B. The GENIE Project Team, Looger, L. Marvin, J. Hoppa, M. Konnerth, A. Kleinfeld, D. Schreiter, E. R. Podgorski, K. 2022-02-15 doi:10.1101/2022.02.13.480251 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP ]]> https://biorxiv.org/content/10.1101/2022.02.13.480296v1?rss=1 Manakov, S. A. Shishkin, A. A. Yee, B. A. Shen, K. A. Cox, D. C. Park, S. S. Foster, H. M. Chapman, K. B. Yeo, G. W. Van Nostrand, E. L. 2022-02-14 doi:10.1101/2022.02.13.480296 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Nuclear Receptor 5A2 Regulation of Agrp underlies Olanzapine-induced Hyperphagia ]]> https://biorxiv.org/content/10.1101/2022.02.15.480590v1?rss=1 Zapata, R. C. Zhang, D. Libster, A. Porcu, A. Montilla-Perez, P. Zhang, Z. Correa, S. M. Telese, F. Osborn, O. 2022-02-18 doi:10.1101/2022.02.15.480590 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Substrate topology and cognate immunity modulate antibacterial toxicity of Tae cell wall hydrolases ]]> https://biorxiv.org/content/10.1101/2022.02.15.480620v1?rss=1 Radkov, A. Sapiro, A. Flores, S. Henderson, C. Saunders, H. Kim, R. Massa, S. Thompson, S. Mateusiak, C. Biboy, J. Zhao, Z. Starita, L. M. Hatleberg, W. Vollmer, W. Russell, A. B. Simorre, J.-P. Anthony-Cahill, S. Brzovic, P. Hayes, B. Chou, S. 2022-02-16 doi:10.1101/2022.02.15.480620 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ The Conserved CNOT1 Interaction Motif of Tristetraprolin Regulates ARE-mRNA Decay Independently of the p38 MAPK-MK2 Kinase Pathway ]]> https://biorxiv.org/content/10.1101/2022.02.15.480631v1?rss=1 Carreno, A. Lykke-Andersen, J. 2022-02-16 doi:10.1101/2022.02.15.480631 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Mitochondrial mRNA localization is governed by translation kinetics and spatial transport ]]> https://biorxiv.org/content/10.1101/2022.02.16.480701v1?rss=1 Arceo, X. G. Koslover, E. F. Zid, B. M. Brown, A. I. 2022-02-17 doi:10.1101/2022.02.16.480701 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Assessing base-resolution DNA mechanics on the genome scale ]]> https://biorxiv.org/content/10.1101/2022.02.16.480786v1?rss=1 Jiang, W.-j. Hu, C. Yi, X. Xu, Q. Lou, T. Wang, H. Zhou, J. Zhu, H. Li, Y. Wen, Y. Fan, R. Shen, J. Wong, C. C. Zheng, X. Wu, H.-J. 2022-02-19 doi:10.1101/2022.02.16.480786 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ An NKX-COUP-TFII genomic code for mucosal vascular addressins and organ morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.02.17.480956v1?rss=1 Dinh, t. t. Xiang, M. Rajaraman, A. Wang, Y. Salazar, N. Roper, W. Rhee, S. Brulois, K. O'Hara, E. Keifel, H. Dinh, T. Gonzalez, D. Bao, E. Red-Horse, K. Balogh, P. Gabris, F. Gaszner, B. Berta, G. Pan, J. Butcher, E. 2022-02-19 doi:10.1101/2022.02.17.480956 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using Mycobacterium tuberculosis Isolates ]]> https://biorxiv.org/content/10.1101/2022.02.18.481113v1?rss=1 Elghraoui, A. Mirarab, S. Swenson, K. M. Valafar, F. 2022-02-19 doi:10.1101/2022.02.18.481113 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees ]]> https://biorxiv.org/content/10.1101/2022.02.19.481132v1?rss=1 Zhang, C. Mirarab, S. 2022-02-20 doi:10.1101/2022.02.19.481132 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Quantitative sequence basis for the E. coli transcriptional regulatory network ]]> https://biorxiv.org/content/10.1101/2022.02.20.481200v1?rss=1 = 0.8) for 84% (57/68) of valid E. coli regulons identified from top-down analysis of RNA-seq data. We found that: 1) While regulatory motif strength is the most important sequence feature for determining regulon membership, additional features such as DNA shape substantially influence membership; 2) complex regulons involving multiple interacting regulators could be unraveled by machine learning; 3) investigating regulons where initial ML models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, while regulon structure can appear to be variable across estimation methods and strains, we found that strong regulatory sequence features underlie both the genes that appear most consistently in regulons across estimation methods as well as the core regulon genes in the Fur pan-regulon. This work develops a quantitative understanding of the sequence basis of the TRN and suggests a path towards computationally-guided control of transcriptional regulation for synthetic biology applications. ]]> Qiu, S. Lamoureux, C. Akbari, A. Palsson, B. O. Zielinski, D. C. 2022-02-20 doi:10.1101/2022.02.20.481200 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Long-term learning transforms prefrontal cortex selectivity during working memory ]]> https://biorxiv.org/content/10.1101/2022.02.22.481537v1?rss=1 Miller, J. Tambini, A. Kiyonaga, A. D'Esposito, M. 2022-02-23 doi:10.1101/2022.02.22.481537 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Novel and Reported Compensatory Mutations in rpoABC Associate Specifically with Predominant Mycobacterium tuberculosis Rifampicin Resistance Marker rpoB:S450L ]]> https://biorxiv.org/content/10.1101/2022.02.22.481565v1?rss=1 Conkle-Gutierrez, D. Ramirez-Busby, S. M. Gorman, B. M. Elghraoui, A. Hoffner, S. E. Elmaraachli, W. Valafar, F. 2022-02-24 doi:10.1101/2022.02.22.481565 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation ]]> https://biorxiv.org/content/10.1101/2022.02.24.481768v1?rss=1 Oliver, A. Cavalheri, H. B. Lima, T. G. Jones, N. T. Podell, S. Zarate, D. Allen, E. Burton, R. S. Shurin, J. B. 2022-02-24 doi:10.1101/2022.02.24.481768 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2022.02.25.481990v1?rss=1 314,000 single-cell RA synovial cell atlas with 77 cell states from T, B/plasma, natural killer, myeloid, stromal, and endothelial cells. We stratified tissue samples into six distinct cell type abundance phenotypes (CTAPs) individually enriched for specific cell states. These CTAPs demonstrate the striking diversity of RA synovial inflammation, ranging from marked enrichment of T and B cells (CTAP-TB) to a congregation of specific myeloid, fibroblast, and endothelial cells largely lacking lymphocytes (CTAP-EFM). Disease-relevant cytokines, histology, and serology metrics are associated with certain CTAPs. This comprehensive RA synovial atlas and molecular, tissue-based CTAP stratification reveal new insights into RA pathology and heterogeneity, which could lead to novel targeted-treatment approaches in RA. ]]> Zhang, F. Jonsson, A. H. Nathan, A. Wei, K. Millard, N. Xiao, Q. Gutierrez-Arcelus, M. Apruzzese, W. Watts, G. F. M. Weisenfeld, D. Kang, J. B. Rumker, L. Mears, J. Slowikowski, K. Weinand, K. Orange, D. E. Rangel-Moreno, J. Geraldino-Pardilla, L. Deane, K. D. Tabechian, D. Ceponis, A. Firestein, G. S. Maybury, M. Sahbudin, I. Ben-Artzi, A. Mandelin, A. M. Nerviani, A. Rivellese, F. Pitzalis, C. Hughes, L. B. Horowitz, D. DiCarlo, E. Gravallese, E. M. Boyce, B. F. Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus 2022-02-28 doi:10.1101/2022.02.25.481990 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Multi-omic analysis along the gut-brain axis points to a functional architecture of autism ]]> https://biorxiv.org/content/10.1101/2022.02.25.482050v1?rss=1 Morton, J. T. Jin, D.-m. Mills, R. Shao, Y. Rahman, G. Harold-Berding, K. Needham, B. D. Zurita, M. F. David, M. Averina, O. Kovtun, A. Noto, A. Mussap, M. Wang, M. Frank, D. Li, E. Zhou, W. Fanos, V. Danilenko, V. Wall, D. P. Cardenas, P. A. Baldeon, M. xavier, r. j. Mazmanian, S. Knight, R. Gilbert, J. Donovan, S. Lawley, T. Carpenter, B. Bonneau, R. Taroncher-Oldenburg, G. 2022-02-26 doi:10.1101/2022.02.25.482050 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ RNA fluorescence in situ hybridization (FISH) to visualize microbial colonization and infection in the Caenorhabditis elegans intestines ]]> https://biorxiv.org/content/10.1101/2022.02.26.482129v1?rss=1 Rivera, D. Lazetic, V. Troemel, E. R. Luallen, R. J. 2022-02-28 doi:10.1101/2022.02.26.482129 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy and improves prediction ]]> https://biorxiv.org/content/10.1101/2022.02.28.481967v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@1641108org.highwire.dtl.DTLVardef@9a24eeorg.highwire.dtl.DTLVardef@1eeae99org.highwire.dtl.DTLVardef@108db7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hindley, G. Shadrin, A. A. van der Meer, D. Parker, N. Cheng, W. O'Connell, K. S. Bahrami, S. Lin, A. Karadag, N. Holen, B. Bjella, T. Fan, C. C. Uelan, T. Djurovic, S. Smeland, O. B. Frei, O. Dale, A. Andreassen, O. 2022-03-02 doi:10.1101/2022.02.28.481967 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Temporal responses of bumblebee gustatory neurons encode sugar identity ]]> https://biorxiv.org/content/10.1101/2022.02.28.482341v1?rss=1 Parkinson, R. Kessler, S. Scott, J. Simpson, A. Bu, J. Pattrick, J. Mahdi, A. Miriyala, A. Wright, G. 2022-03-02 doi:10.1101/2022.02.28.482341 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Regulation associated modules reflect 3D genome modularity associated with chromatin activity ]]> https://biorxiv.org/content/10.1101/2022.03.02.482718v1?rss=1 Zheng, L. Wang, W. 2022-03-04 doi:10.1101/2022.03.02.482718 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[ A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities ]]> https://biorxiv.org/content/10.1101/2022.03.07.483343v1?rss=1 Shaffer, J. P. Carpenter, C. S. Martino, C. P. Salido, R. A. Bryant, M. Sanders, K. Schwartz, T. Humphrey, G. Swafford, A. D. Knight, R. 2022-03-08 doi:10.1101/2022.03.07.483343 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Comparative transcriptomics of the Drosophila olfactory subsystems identifies a support cell-expressed Osiris protein required for pheromone sensing ]]> https://biorxiv.org/content/10.1101/2022.03.09.483212v1?rss=1 Scalzotto, M. Ng, R. Cruchet, S. Saina, M. Armida, J. Su, C.-Y. Benton, R. 2022-03-12 doi:10.1101/2022.03.09.483212 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair ]]> https://biorxiv.org/content/10.1101/2022.03.10.483754v1?rss=1 Barr, J. Gentile, M. E. Lee, S. Kotas, M. Fernanda de Mello Costa, M. Holcomb, N. P. Jaquish, A. Palashikar, G. Matsumoto, I. Margolskee, R. Cohen, N. A. Sun, X. Vaughan, A. E. 2022-03-11 doi:10.1101/2022.03.10.483754 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ The KASH5 protein involved in meiotic chromosomal movements is a novel dynein activating adaptor ]]> https://biorxiv.org/content/10.1101/2022.03.11.483947v1?rss=1 Agrawal, R. Gillies, J. P. Zang, J. L. Zhang, J. Garrott, S. R. Shibuya, H. Nandakumar, J. DeSantis, M. E. 2022-03-12 doi:10.1101/2022.03.11.483947 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Opiate responses are controlled by interactions of Oprm1 and Fgf12 loci in the murine BXD family: Correspondence to human GWAS finding ]]> https://biorxiv.org/content/10.1101/2022.03.11.483993v1?rss=1 Lemen, P. M. Hatoum, A. S. Dickson, P. E. Mittleman, G. Agrawal, A. Reiner, B. C. Berrettini, W. Ashbrook, D. G. Gunturkun, H. Mulligan, M. K. Williams, R. W. Chen, H. 2022-03-12 doi:10.1101/2022.03.11.483993 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Mesoaccumbal glutamate neurons drive reward via glutamate release, but aversion via dopamine co-release ]]> https://biorxiv.org/content/10.1101/2022.03.17.484767v1?rss=1 Warlow, S. M. Zell, V. Hunker, A. C. Zweifel, L. Hnasko, T. S. 2022-03-18 doi:10.1101/2022.03.17.484767 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Cloning of Nine Glucocorticoid Receptor Isoforms from the Slender African lungfish (Protopterus dolloi) ]]> https://biorxiv.org/content/10.1101/2022.03.19.484994v1?rss=1 Katsu, Y. Oana, S. Lin, X. Hyodo, S. Bianchetti, L. Baker, M. E. 2022-03-20 doi:10.1101/2022.03.19.484994 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential ]]> https://biorxiv.org/content/10.1101/2022.03.25.485695v1?rss=1 Carlessi, R. Denisenko, E. Boslem, E. Koehn-Gaone, J. Main, N. Bakar, N. D. B. A. Shirolkar, G. D. Jones, M. Poppe, D. Dwyer, B. J. Jackaman, C. Tjiam, M. C. Lister, R. Karin, M. Fallowfield, J. A. Kendall, T. J. Forbes, S. J. Olynyk, J. K. Yeoh, G. Forrest, A. R. R. Ramm, G. A. Febbraio, M. A. Tirnitz-Parker, J. E. E. 2022-03-27 doi:10.1101/2022.03.25.485695 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sudden unexpected death in epilepsy is prevented by blocking postictal hypoxia ]]> https://biorxiv.org/content/10.1101/2022.03.25.485818v1?rss=1 George, A. Farrell, J. S. Colangeli, R. Wall, A. K. Gom, R. C. Kesler, M. T. de la Hoz, C. L. Perera, T. Rho, J. M. Kurrasch, D. Teskey, G. C. 2022-03-28 doi:10.1101/2022.03.25.485818 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ A spatial genome aligner for multiplexed DNA-FISH ]]> https://biorxiv.org/content/10.1101/2022.03.25.485845v1?rss=1 Jia, B. B. Jussila, A. P. Kern, J. C. Zhu, Q. Ren, B. 2022-03-27 doi:10.1101/2022.03.25.485845 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sperm mosaicism predicts transmission of de novo mutations to human blastocysts ]]> https://biorxiv.org/content/10.1101/2022.03.28.486034v1?rss=1 Yang, X. Stanley, V. McEvoy-Venneri, J. Xu, X. Morales, A. J. Gleeson, J. G. Breuss, M. W. 2022-03-28 doi:10.1101/2022.03.28.486034 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Characterization of a miniaturized ultrasound transducer customized for oral health applications ]]> https://biorxiv.org/content/10.1101/2022.03.31.486598v1?rss=1 Qi, B. Hariri, A. Khazaeinezhad, R. Fu, L. Jokerst, J. V. 2022-04-01 doi:10.1101/2022.03.31.486598 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ An untargeted metabolomics analysis of exogenous chemicals in human milk and transfer to the infant ]]> https://biorxiv.org/content/10.1101/2022.03.31.486633v1?rss=1 Thomas, S. P. Gauglitz, J. M. Tripathi, A. Vargas, F. Bertrand, K. Chambers, C. D. Kim, J. H. Dorrestein, P. C. Tsunoda, S. M. 2022-04-01 doi:10.1101/2022.03.31.486633 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity ]]> https://biorxiv.org/content/10.1101/2022.04.04.487013v1?rss=1 Anand, A. Patel, A. Chen, K. Olson, C. A. Phaneuf, P. V. Lamoureux, C. Hefner, Y. Szubin, R. Feist, A. Palsson, B. 2022-04-05 doi:10.1101/2022.04.04.487013 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.04.04.487056v1?rss=1 Catoiu, E. A. Phaneuf, P. V. Monk, J. Palsson, B. 2022-04-06 doi:10.1101/2022.04.04.487056 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2022.04.04.487074v1?rss=1 Rajput, A. Tsunemoto, H. Sastry, A. V. Szubin, R. Rychel, K. Chauhan, S. M. Pogliano, J. Palsson, B. 2022-04-06 doi:10.1101/2022.04.04.487074 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.04.05.487060v1?rss=1 Oh, C.-k. Nakamura, T. Beutler, N. Zhang, X. Pina-Crespo, J. Talantova, M. Ghatak, S. Trudler, D. Carnevale, L. N. McKercher, S. R. Bakowski, M. A. Diedrich, J. K. Roberts, A. J. Woods, A. K. Chi, V. Gupta, A. K. Rosenfeld, M. A. Kearns, F. L. Casalino, L. Shaabani, N. Liu, H. Wilson, I. A. Amaro, R. E. Burton, D. R. Yates, J. R. Becker, C. Rogers, T. F. Chatterjee, A. K. Lipton, S. A. 2022-04-05 doi:10.1101/2022.04.05.487060 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Comprehensive multiomic profiling of somatic mutations in malformations of cortical development ]]> https://biorxiv.org/content/10.1101/2022.04.07.487401v1?rss=1 Chung, C. Yang, X. Bae, T. Vong, K. I. Mittal, S. Donkels, C. Phillips, W. Marsh, A. P. L. Breuss, M. W. Ball, L. L. Garcia, C. A. B. George, R. D. Gu, J. Xu, M. Barrows, C. James, K. N. Stanley, V. Nidhiry, A. Khoury, S. Howe, G. Xu, X. Copeland, B. Antaki, D. Wang, Y. Kim, S. H. Kang, H.-C. Schulze-Bonhage, A. Haas, C. A. Urbach, H. Prinz, M. Sattar, S. Nespeca, M. Gonda, D. D. Imai, K. Takahashi, Y. Chen, R. Tsai, J.-W. Conti, V. Guerrini, R. Devinsky, O. Silva, W. A. Machado, H. R. Mathern, G. W. Abyzov, A. Baldassari, S. Boulac, S. Focal Corti 2022-04-08 doi:10.1101/2022.04.07.487401 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Reelin deficiency exacerbates cocaine-induced hyperlocomotion by enhancing neuronal activity in the dorsomedial striatum. ]]> https://biorxiv.org/content/10.1101/2022.04.12.488105v1?rss=1 de Guglielmo, G. Iemolo, A. Nur, A. Turner, A. Montilla-Perez, P. Telese, F. 2022-04-13 doi:10.1101/2022.04.12.488105 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins to promote corticospinal axon repair after injury ]]> https://biorxiv.org/content/10.1101/2022.04.14.488293v1?rss=1 Romaus-Sanjurjo, D. Saikia, J. M. Kim, H. J. Tsai, K. M. Le, G. Q. Zheng, B. 2022-04-14 doi:10.1101/2022.04.14.488293 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Molecular diversity and phenotypic pleiotropy of genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their impacts on pathophysiology of Modern Humans. ]]> https://biorxiv.org/content/10.1101/2022.04.19.488808v1?rss=1 Glinsky, G. 2022-04-19 doi:10.1101/2022.04.19.488808 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues ]]> https://biorxiv.org/content/10.1101/2022.04.25.489471v1?rss=1 Yu, M. Zemke, N. R. Chen, Z. Juric, I. Hu, R. Raviram, R. Abnousi, A. Fang, R. Zhang, Y. Gorkin, D. U. Li, Y. Zhao, Y. Lee, H. R. Schmitt, A. D. Qiu, Y. Dickel, D. E. Visel, A. Pennacchio, L. Hu, M. Ren, B. 2022-04-26 doi:10.1101/2022.04.25.489471 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Coupling of NOD2 to GIV is Required for Bacterial Sensing ]]> https://biorxiv.org/content/10.1101/2022.04.26.489574v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@139a1feorg.highwire.dtl.DTLVardef@ba5354org.highwire.dtl.DTLVardef@b4d933org.highwire.dtl.DTLVardef@11fe12e_HPS_FORMAT_FIGEXP M_FIG GRAPHIC ABSTRACT C_FIG HIGHLIGHTSO_LIGIV is a functional and direct interactor of the terminal LRR repeat of NOD2 C_LIO_LIMice lacking M[FE] GIV develop dysbiosis, protracted ileocolitis and sepsis C_LIO_LIMDP/NOD2-dependent protective host responses require GIV C_LIO_LICD-risk NOD2 1007fs variant lacking the terminal LRR#10 cannot bind GIV C_LI ]]> Katkar, G. D. Anandachar, M. S. Sinha, S. Ibeawuchi, S.-R. Espinoza, C. R. Coates, J. Malhotra, Y. S. Mullick, M. Castillo, V. Vo, D. T. Sahoo, D. Ghosh, P. 2022-04-27 doi:10.1101/2022.04.26.489574 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage ]]> https://biorxiv.org/content/10.1101/2022.04.27.489752v1?rss=1 Lau, R. K. Enustun, E. Gu, Y. Nguyen, J. V. Corbett, K. D. 2022-04-27 doi:10.1101/2022.04.27.489752 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ An auto-inhibited state of protein kinase G and implications for selective activation ]]> https://biorxiv.org/content/10.1101/2022.04.28.489861v1?rss=1 Sharma, R. Kim, J. J. Qin, L. Henning, P. Akimoto, M. VanSchouwen, B. Kaur, G. Sankaran, B. MacKenzie, K. R. Melacini, G. Casteel, D. E. Herberg, F. W. Kim, C. W. 2022-04-28 doi:10.1101/2022.04.28.489861 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Accelerated aging induced by stress in experimental murine ocular hypertension. ]]> https://biorxiv.org/content/10.1101/2022.05.01.490248v1?rss=1 Xu, Q. Rydz, C. Nguyen Huu, V. A. Rocha, L. Palomino La Torre, C. Lee, I. Cho, W. Jabari, M. Donello, J. Weinreb, R. N. Lyon, D. C. Ju, W.-K. Foik, A. Skowronska-Krawczyk, D. 2022-05-02 doi:10.1101/2022.05.01.490248 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Repeated birth injuries lead to pelvic floor muscle dysfunction and impairment in regeneration ]]> https://biorxiv.org/content/10.1101/2022.05.02.490259v1?rss=1 Duran, P. Zelus, E. French, S. Burnett, L. Christman, K. Alperin, M. 2022-05-02 doi:10.1101/2022.05.02.490259 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Neuroinflammation plays a critical role in cerebral cavernous malformation disease ]]> https://biorxiv.org/content/10.1101/2022.05.09.491214v1?rss=1 Lopez-Ramirez, M. A. Lai, C. C. Nelsen, B. Frias-Anaya, E. Gallego-Gutierrez, H. Orecchioni, M. Sun, H. Mesarwi, O. A. Ley, K. Gongol, B. 2022-05-10 doi:10.1101/2022.05.09.491214 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Liquid-like assembly of VASP drives actin polymerization and bundling ]]> https://biorxiv.org/content/10.1101/2022.05.09.491236v1?rss=1 Graham, K. D. Chandrasekaran, A. Wang, L. Ladak, A. Lafer, E. M. Rangamani, P. Stachowiak, J. C. 2022-05-10 doi:10.1101/2022.05.09.491236 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Voluntary and forced exposure to ethanol vapor produces similar escalation of alcohol drinking but differential recruitment of brain regions related to stress, habit, and reward in male rats. ]]> https://biorxiv.org/content/10.1101/2022.05.11.491572v1?rss=1 de Guglielmo, G. Simpson, S. Kimbrough, A. Conlisk, D. Baker, R. Cantor, M. Kallupi, M. George, O. 2022-05-12 doi:10.1101/2022.05.11.491572 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Genome-wide selection inference at short tandem repeats ]]> https://biorxiv.org/content/10.1101/2022.05.12.491726v1?rss=1 Huang, B. Durvasula, A. Mousavi, N. Ziaei-Jam, H. Maksimov, M. Lohmueller, K. E. Gymrek, M. 2022-05-13 doi:10.1101/2022.05.12.491726 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ CD133+ Intercellsome Mediates Direct Cell-Cell Communication to Offset Intracellular Signaling Deficit ]]> https://biorxiv.org/content/10.1101/2022.05.16.492226v1?rss=1 Kaneko, K. Liang, Y. Liu, Q. Chen, W. S. Feng, G.-S. 2022-05-17 doi:10.1101/2022.05.16.492226 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Guided construction of single cell reference for human and mouse lung ]]> https://biorxiv.org/content/10.1101/2022.05.18.491687v1?rss=1 Guo, M. Morley, M. P. Wu, Y. Du, Y. Zhao, S. Wagner, A. Kouril, M. Jin, K. Gaddis, N. Kitzmiller, J. A. Stewart, K. Basil, M. C. Lin, S. M. Ying, Y. Babu, A. Wikenheiser-Brokamp, K. A. Mun, K. S. Naren, A. P. Lin, S. Clair, G. Adkins, J. N. Pryhuber, G. S. Misra, R. S. Aronow, B. J. Tickle, T. L. Salomonis, N. Sun, X. Morrisey, E. E. Whitsett, J. A. Xu, Y. 2022-05-20 doi:10.1101/2022.05.18.491687 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ The regulatory landscapes of human ovarian ageing ]]> https://biorxiv.org/content/10.1101/2022.05.18.492547v1?rss=1 Suh, Y. Jin, C. Wang, X. Hudgins, A. Gamliel, A. Pei, M. Kim, S. Contreras, D. Hoeijmakers, J. Campisi, J. Lobo, R. Williams, Z. Rosenfeld, M. G. 2022-05-19 doi:10.1101/2022.05.18.492547 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons ]]> https://biorxiv.org/content/10.1101/2022.05.19.492359v1?rss=1 Mitchell, J. W. Midillioglu, I. Wang, B. Han, C. Wildonger, J. 2022-05-20 doi:10.1101/2022.05.19.492359 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Scalable power analysis and effect size exploration of microbiome community differences with Evident ]]> https://biorxiv.org/content/10.1101/2022.05.19.492684v1?rss=1 Rahman, G. McDonald, D. Gonzalez, A. Vazquez-Baeza, Y. Jiang, L. Casals-Pascual, C. Peddada, S. Hakim, D. Dilmore, A. H. Nowinski, B. Knight, R. 2022-05-20 doi:10.1101/2022.05.19.492684 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology ]]> https://biorxiv.org/content/10.1101/2022.05.19.492707v1?rss=1 Coker, J. Zhalnina, K. Marotz, C. Thiruppathy, D. Tjuanta, M. D'Elia, G. Hailu, R. Mahosky, T. Rowan, M. Northen, T. Zengler, K. 2022-05-19 doi:10.1101/2022.05.19.492707 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ A GATA factor radiation in Caenorhabditis rewired the endoderm specification network ]]> https://biorxiv.org/content/10.1101/2022.05.20.492851v1?rss=1 Darragh, A. C. Rifkin, S. A. 2022-05-21 doi:10.1101/2022.05.20.492851 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Radiation and diversification of GATA-domain-containing proteins in the genus Caenorhabditis ]]> https://biorxiv.org/content/10.1101/2022.05.20.492891v1?rss=1 Darragh, A. C. Rifkin, S. A. 2022-05-21 doi:10.1101/2022.05.20.492891 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Epitranscriptomic Modification of MicroRNA Increases Atherosclerosis Susceptibility ]]> https://biorxiv.org/content/10.1101/2022.05.21.492858v1?rss=1 He, M. Dong, J. Zhang, Y. Han, S. Y. Wang, C. Gongol, B. Kang, J. Huang, H.-Y. Shyy, J. Y.-J. 2022-05-21 doi:10.1101/2022.05.21.492858 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains ]]> https://biorxiv.org/content/10.1101/2022.05.25.493525v1?rss=1 Poudel, S. Hefner, Y. Szubin, R. Sastry, A. V. Gao, Y. Nizet, V. Palsson, B. O. 2022-05-26 doi:10.1101/2022.05.25.493525 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Adipocytes reprogram carbon and nitrogen metabolism to maintain lipogenic flux in the absence of Bckdha ]]> https://biorxiv.org/content/10.1101/2022.05.27.493780v1?rss=1 Green, C. R. Wessendorf-Rodriguez, K. A. Turner, R. Hover, J. D. Murphy, A. N. Wallace, M. Metallo, C. M. 2022-05-29 doi:10.1101/2022.05.27.493780 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Topography of mutational signatures in human cancer ]]> https://biorxiv.org/content/10.1101/2022.05.29.493921v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@abf065org.highwire.dtl.DTLVardef@33ad99org.highwire.dtl.DTLVardef@ca37b6org.highwire.dtl.DTLVardef@fa7c6_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIComprehensive topography analysis of mutational signatures encompassing 82,890,857 somatic mutations in 5,120 whole-genome sequenced tumours integrated with 516 tissue-matched topographical features from the ENCODE project. C_LIO_LIThe accumulation of somatic mutations from most mutational signatures is affected by nucleosome occupancy, histone modifications, CTCF binding sites, transcribed regions, or replication strand/timing. C_LIO_LIMutational signatures with related aetiologies are consistently characterized by similar genome topographies across tissue types. C_LIO_LITopography analysis allows both separating signatures from different aetiologies and understanding the genomic specificity of clustered somatic mutations. C_LIO_LIA comprehensive online resource, disseminate through the COSMIC signatures database, that allows researchers to explore the interactions between somatic mutational processes and genome architecture within and across cancer types. C_LI ]]> Otlu-Saritas, B. Diaz-Gay, M. Vermes, I. Bergstrom, E. N. Barnes, M. Alexandrov, L. B. 2022-05-29 doi:10.1101/2022.05.29.493921 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Preparing glycomics data for robust statistical analysis with GlyCompareCT ]]> https://biorxiv.org/content/10.1101/2022.05.31.494178v1?rss=1 Zhang, Y. Sridevi, K. Bao, B. Chiang, W.-T. Sorrentino, J. T. Schinn, S.-M. Kellman, B. P. Lewis, N. E. 2022-06-01 doi:10.1101/2022.05.31.494178 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ The conserved AAA-ATPase PCH-2 distributes its regulation of meiotic prophase events by remodeling multiple meiotic HORMADs in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.05.31.494220v1?rss=1 Russo, A. E. Giacopazzi, S. Deshong, A. Menon, M. Ortiz, V. A. Ego, K. M. Corbett, K. D. Bhalla, N. 2022-05-31 doi:10.1101/2022.05.31.494220 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Lis1 binding regulates force-induced detachment of cytoplasmic dynein from microtubules ]]> https://biorxiv.org/content/10.1101/2022.06.02.494578v1?rss=1 Kusakci, E. Htet, Z. M. Gillies, J. P. Reck-Peterson, S. L. Yildiz, A. 2022-06-03 doi:10.1101/2022.06.02.494578 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Relating neighborhood deprivation to childhood obesity in the ABCD Study(R): evidence for theories of neuroinflammation and neuronal stress ]]> https://biorxiv.org/content/10.1101/2022.06.04.494818v1?rss=1 Adise, S. Marshall, A. T. Kan, E. Gonzalez, M. Sowell, E. R. 2022-06-06 doi:10.1101/2022.06.04.494818 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Longitudinal assessment of brain structure and behavior in youth with rapid weight gain: Potential contributing causes and consequences ]]> https://biorxiv.org/content/10.1101/2022.06.04.494820v1?rss=1 38lbs); 63% of the WG group were healthy weight at 9-to-10-years-old. ResultsA five-fold cross-validated logistic elastic-net regression revealed that rapid weight gain was associated with structural variation amongst 39 brain features at 9-to-10-years-old in regions involved with executive functioning, appetitive control, and reward sensitivity. Two years later, WG youth showed differences in change over time in several of these regions and performed worse on measures of impulsivity. ConclusionsThese findings suggest that brain structure in pre-adolescence may predispose some to rapid weight gain and that weight gain itself may alter maturational brain change in regions important for food intake and impulsivity. Behavioral interventions that target inhibitory control may improve trajectories of brain maturation and facilitate healthier behaviors. ]]> Adise, S. Marshall, A. T. Hahn, S. Zhao, S. Kan, E. Rhee, K. Herting, M. M. Sowell, E. R. 2022-06-06 doi:10.1101/2022.06.04.494820 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ CryoEM Structures of the Nitrogenase Complex During Catalytic Turnover ]]> https://biorxiv.org/content/10.1101/2022.06.05.494884v1?rss=1 Rutledge, H. L. Cook, B. D. Nguyen, H. P. M. Herzik, M. A. Tezcan, F. A. 2022-06-05 doi:10.1101/2022.06.05.494884 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Modeling membrane curvature generation using mechanics and machine learning ]]> https://biorxiv.org/content/10.1101/2022.06.06.495017v1?rss=1 Malingen, S. A. Rangamani, P. 2022-06-06 doi:10.1101/2022.06.06.495017 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Distinct roles of dentate gyrus and medial entorhinal cortex inputs for phase precession and temporal correlations in hippocampal CA3 place cells ]]> https://biorxiv.org/content/10.1101/2022.06.07.491859v1?rss=1 Ahmadi, S. Sasaki, T. Sabariego, M. Leibold, C. Leutgeb, S. Leutgeb, J. K. 2022-06-09 doi:10.1101/2022.06.07.491859 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Strengthening of enterococcal biofilms by Esp ]]> https://biorxiv.org/content/10.1101/2022.06.09.495547v1?rss=1 Spiegelman, L. Bahn-Suh, A. Montano, E. Zhang, L. Hura, G. Patras, K. Kumar, A. Tezcan, A. Nizet, V. Tsutakawa, S. Ghosh, P. 2022-06-09 doi:10.1101/2022.06.09.495547 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Bento: A toolkit for subcellular analysis of spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2022.06.10.495510v1?rss=1 Mah, C. K. Ahmed, N. Lam, D. Monell, A. Kern, C. Han, Y. Cesnik, A. J. Lundberg, E. Zhu, Q. Carter, H. W. Yeo, G. W. 2022-06-13 doi:10.1101/2022.06.10.495510 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Design principles of dose-response alignment in coupled GTPase switches ]]> https://biorxiv.org/content/10.1101/2022.06.14.496184v1?rss=1 Qiao, L. Ghosh, P. Rangamani, P. 2022-06-15 doi:10.1101/2022.06.14.496184 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2022.06.15.496350v1?rss=1 Wan, Y. C. Troemel, E. R. Reinke, A. W. 2022-06-17 doi:10.1101/2022.06.15.496350 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ A Generalized Reinforcement Learning-Based Deep Neural Network (GRL-DNN) Agent Model for Diverse Cognitive Constructs ]]> https://biorxiv.org/content/10.1101/2022.06.17.496500v1?rss=1 Nair, S. S. Muddapu, V. R. C, V. Balasubramani, P. P. Mishra, J. Ramanathan, D. S. Chakravarthy, V. S. 2022-06-20 doi:10.1101/2022.06.17.496500 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ White matter and literacy: a dynamic system in flux ]]> https://biorxiv.org/content/10.1101/2022.06.21.497048v1?rss=1 Roy, E. Richie-Halford, A. Kruper, J. Narayan, M. Bloom, D. Brown, T. T. Jernigan, T. L. McCandliss, B. D. Rokem, A. Yeatman, J. D. 2022-06-25 doi:10.1101/2022.06.21.497048 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ VPS13A and VPS13C influence lipid droplet abundance ]]> https://biorxiv.org/content/10.1101/2022.06.21.497109v1?rss=1 Chen, S. Roberts, M. A. Chen, C.-Y. Markmiller, S. Wei, H.-G. Yeo, G. W. Granneman, J. G. Olzmann, J. A. Ferro-Novick, S. 2022-06-23 doi:10.1101/2022.06.21.497109 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Myeloid reprogramming by JAK inhibition enhances checkpoint blockade therapy ]]> https://biorxiv.org/content/10.1101/2022.06.24.497435v1?rss=1 Zak, J. Pratumchai, I. Marro, B. S. Marquardt, K. L. Beheshti Zavareh, R. Lairson, L. L. Oldstone, M. B. A. Varner, J. A. Bachanova, V. Teijaro, J. 2022-06-26 doi:10.1101/2022.06.24.497435 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Culture-Independent Detection and Identification of Leptospira Serovars ]]> https://biorxiv.org/content/10.1101/2022.06.24.497575v1?rss=1 200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches--such as multi-locus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test--are tedious and expensive, and require isolation of the organisms in culture media--a protracted and incredibly inefficient process-- precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay--targeting a Leptospira-unique gene encoding a putative polysaccharide flippase--that provides intra-species, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI ("rage one"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum and urine, with no detectable off-target amplification--even of the genetically related but low virulence group II pathogenic (formerly "intermediate") or non-pathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine-samples and environmental samples containing varied and complex microbial species-consortia. And holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies. ]]> Matthias, M. A. Lubar, A. Lanka Acharige, S. S. Chaiboonma, K. N. Pilau, N. N. Marroquin, A. S. Jayasundara, D. Agampodi, S. B. Vinetz, J. M. 2022-06-25 doi:10.1101/2022.06.24.497575 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice ]]> https://biorxiv.org/content/10.1101/2022.06.27.497828v1?rss=1 Abdel-Haq, R. Schlachetzki, J. C. M. Boktor, J. C. Cantu-Jungles, T. M. Thron, T. Zhang, M. Bostick, J. W. Khazaei, T. Chilakala, S. Morais, L. H. Humphrey, G. Keshavarzian, A. Katz, J. E. Thomson, M. Knight, R. Gradinaru, V. Hamaker, B. R. Glass, C. K. Mazmanian, S. K. 2022-06-30 doi:10.1101/2022.06.27.497828 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ A pals-25 gain-of-function allele triggers systemic resistance against natural pathogens of C. elegans ]]> https://biorxiv.org/content/10.1101/2022.06.28.497889v1?rss=1 Gang, S. S. Grover, M. Reddy, K. C. Raman, D. Chang, Y.-T. Ekiert, D. C. Barkoulas, M. Troemel, E. R. 2022-07-01 doi:10.1101/2022.06.28.497889 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades ]]> https://biorxiv.org/content/10.1101/2022.06.30.498375v1?rss=1 Kodera, S. M. Sharma, A. Martino, C. Dsouza, M. Grippo, M. Lutz, H. Knight, R. Gilbert, J. A. Negri, M. C. Allard, S. M. 2022-07-01 doi:10.1101/2022.06.30.498375 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Dendrite architecture determines mitochondrial distribution patterns in vivo ]]> https://biorxiv.org/content/10.1101/2022.07.01.497972v1?rss=1 Donovan, E. J. Agrawal, A. Liberman, N. Kalai, J. Chua, J. N. Koslover, E. F. Barnhart, E. L. 2022-07-03 doi:10.1101/2022.07.01.497972 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses ]]> https://biorxiv.org/content/10.1101/2022.07.05.498913v1?rss=1 Kumar, T. Bryant, M. Cantrell, K. Song, S. J. McDonald, D. Tubb, H. M. Farmer, S. Lukacz, E. S. Brubaker, L. Knight, R. 2022-07-06 doi:10.1101/2022.07.05.498913 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Co-opted Genes of Algal Origin Protect C. elegans against Cyanogenic Toxins ]]> https://biorxiv.org/content/10.1101/2022.07.06.498920v1?rss=1 Wang, B. Pandey, T. Long, Y. Delgado-Rodriguez, S. Daugherty, M. D. Ma, D. K. 2022-07-06 doi:10.1101/2022.07.06.498920 Cold Spring Harbor Laboratory Press 2022-07-06 <![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[ Chemokine CXCL4 interactions with extracellular matrix proteoglycans mediate wide-spread non-receptor mediated immune cell recruitment ]]> https://biorxiv.org/content/10.1101/2022.07.10.499282v1?rss=1 Gray, A. L. Karlsson, R. Roberts, A. R. Ridley, A. J. Pun, N. Hughes, C. Medina-Ruiz, L. Birchenough, H. Salanga, C. Yates, E. A. Turnbull, J. E. Handel, T. M. Graham, G. Jowitt, T. A. Schiessl, I. Richter, R. P. Miller, R. L. Dyer, D. P. 2022-07-10 doi:10.1101/2022.07.10.499282 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Antiviral function and viral antagonism of the rapidly evolving dynein activating adapter NINL ]]> https://biorxiv.org/content/10.1101/2022.07.11.499552v1?rss=1 Stevens, D. A. Beierschmitt, C. Mahesula, S. Corley, M. R. Salogiannis, J. Tsu, B. V. Cao, B. Ryan, A. P. Reck-Peterson, S. L. Daugherty, M. D. 2022-07-11 doi:10.1101/2022.07.11.499552 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein ]]> https://biorxiv.org/content/10.1101/2022.07.13.498973v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@7758f8org.highwire.dtl.DTLVardef@172396aorg.highwire.dtl.DTLVardef@176612org.highwire.dtl.DTLVardef@2e320c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Frenkel, A. Zecharia, E. Gomez-Perez, D. Yegorov, Y. Sendersky, E. Jacobs, A. Benichou, J. Stierhof, Y.-D. Parnasa, R. Golden, S. S. Kemen, E. Schwarz, R. 2022-07-13 doi:10.1101/2022.07.13.498973 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Decline of intrinsic cerebrospinal fluid outflow in healthy humans with age detected by non-contrast spin-labeling MRI ]]> https://biorxiv.org/content/10.1101/2022.07.14.500033v1?rss=1 Malis, V. Bae, W. C. Yamamoto, A. McEvoy, L. K. McDonald, M. A. Miyazaki, M. 2022-07-18 doi:10.1101/2022.07.14.500033 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Integrated multi-cohort analysis of the Parkinson's disease gut metagenome ]]> https://biorxiv.org/content/10.1101/2022.07.20.500694v1?rss=1 Boktor, J. C. Sharon, G. Verhagen Metman, L. A. Hall, D. A. Engen, P. A. Zreloff, Z. Hakim, D. J. Bostick, J. W. Ousey, J. Lange, D. Humphrey, G. Ackermann, G. Carlin, M. Knight, R. Keshavarzian, A. Mazmanian, S. K. 2022-07-21 doi:10.1101/2022.07.20.500694 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays). ]]> https://biorxiv.org/content/10.1101/2022.07.21.500061v1?rss=1 Murphy, K. M. Dowd, T. Khalil, A. Char, S. N. Yang, B. Endelman, B. J. Shih, P. M. Topp, C. N. Schmelz, E. A. Zerbe, P. 2022-07-22 doi:10.1101/2022.07.21.500061 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Identification of pre-existing microbiome and metabolic vulnerabilities to escalation of oxycodone self-administration and identification of a causal role of short-chain fatty acids in addiction-like behaviors. ]]> https://biorxiv.org/content/10.1101/2022.07.23.501268v1?rss=1 Simpson, S. Kimbrough, A. Peters, G. Wellmeyer, E. Mclellan, R. Walker, N. Jia, H. Hu, S. Iyer, M. Sathish, V. Sedighim, S. Kallupi, M. Brennan, M. Maturin, L. Hughes, T. Xie, T. Espinoza, V. Carrette, L. Smith, L. C. Seaman, J. Solberg-Woods, L. Palmer, A. de Guglielmo, G. George, O. 2022-07-23 doi:10.1101/2022.07.23.501268 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness ]]> https://biorxiv.org/content/10.1101/2022.07.25.501481v1?rss=1 Keller, L. J. Nguyen, T. H. Liu, L. Lakemeyer, M. Gelsinger, D. J. Chanin, R. Ngo, N. Lum, K. M. Faucher, F. Ipock, P. Niphakis, M. Bhatt, A. S. O'Donoghue, A. j. Huang, K. Bogyo, M. 2022-07-26 doi:10.1101/2022.07.25.501481 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Epigenome-wide meta-analysis of BMI in nine population-based cohorts: examining the utility of methylation as a biomarker of BMI ]]> https://biorxiv.org/content/10.1101/2022.07.26.498234v1?rss=1 Do, W. L. Sun, D. Meeks, K. A. Dugue, P.-A. Demerath, E. W. Guan, W. Li, S. Chen, W. Milne, R. L. Adeyemo, A. Agyemang, C. Nassir, R. Manson, J. E. Shadyab, A. H. Hou, L. Horvath, S. Assimes, T. L. Bhatti, P. Jordahl, K. M. Baccarelli, A. A. Smith, A. Staimez, L. R. Stein, A. D. Whitsel, E. A. Narayan, K. M. V. Conneely, K. N. 2022-07-27 doi:10.1101/2022.07.26.498234 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Radiogenomics of C9orf72 expansion carriers reveals global transposable element de-repression and enables prediction of thalamic atrophy and clinical impairment ]]> https://biorxiv.org/content/10.1101/2022.07.28.501897v1?rss=1 Bonham, L. W. Geier, E. G. Sirkis, D. W. Leong, J. K. Ramos, E. M. Wang, Q. Karydas, A. Lee, S. E. Sturm, V. E. Sawyer, R. P. Friedberg, A. Ichida, J. K. Gitler, A. D. Sugrue, L. Cordingley, M. Bee, W. Weber, E. Kramer, J. Rankin, K. P. Rosen, H. J. Boxer, A. L. Seeley, W. W. Ravits, J. Miller, B. L. Yokoyama, J. S. 2022-07-31 doi:10.1101/2022.07.28.501897 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Breathing and Tilting: Mesoscale simulations illuminate influenza glycoprotein vulnerabilities ]]> https://biorxiv.org/content/10.1101/2022.08.02.502576v1?rss=1 Casalino, L. Seitz, C. Lederhofer, J. Tsybovsky, Y. Wilson, I. A. Kanekiyo, M. Amaro, R. E. 2022-08-03 doi:10.1101/2022.08.02.502576 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ The hologenome of Osedax frankpressi reveals the genetic interplay for the symbiotic digestion of vertebrate bone ]]> https://biorxiv.org/content/10.1101/2022.08.04.502725v1?rss=1 Moggioli, G. Panossian, B. Sun, Y. Thiel, D. Martin-Zamora, F. M. Tran, M. Clifford, A. M. Goffredi, S. K. Rimskaya-Korsakova, N. Jekelly, G. Tresguerres, M. Qian, P.-Y. Qiu, J.-W. Rouse, G. W. Henry, L. M. Martin-Duran, J. M. 2022-08-05 doi:10.1101/2022.08.04.502725 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Predicting regional somatic mutation rates using DNA motifs ]]> https://biorxiv.org/content/10.1101/2022.08.04.502732v1?rss=1 Liu, c. Wang, Z. Wang, J. Liu, C. Wang, M. Ngo, V. Wang, W. 2022-08-05 doi:10.1101/2022.08.04.502732 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Detecting boolean asymmetric relationships with a loop counting technique and its implications for analyzing heterogeneity within gene expression datasets ]]> https://biorxiv.org/content/10.1101/2022.08.04.502792v1?rss=1 Zhou, H. Rangan, A. V. Lin, W. Labra, S. R. Lipton, S. A. Schork, N. J. 2022-08-05 doi:10.1101/2022.08.04.502792 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins ]]> https://biorxiv.org/content/10.1101/2022.08.04.502797v1?rss=1 Hirose, Y. Poudel, S. Sastry, A. V. Szubin, R. Zielinski, D. C. Lim, H. G. Menon, N. D. Bergsten, H. Uchiyama, S. Hanada, T. Kawabata, S. Palsson, B. O. Nizet, V. 2022-08-04 doi:10.1101/2022.08.04.502797 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Development of Highly Selective Epoxyketone-based Plasmodium Proteasome Inhibitors with Negligible Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2022.08.06.502205v1?rss=1 Almaliti, J. Fajtova, P. Calla, J. LaMonte, G. M. Feng, M. Rocamora, F. Ottilie, S. Glukhov, E. Boura, E. Suhandynata, R. T. Momper, J. D. Gilson, M. K. Winzeler, E. A. Gerwick, W. H. O'Donoghue, A. J. 2022-08-07 doi:10.1101/2022.08.06.502205 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ The Impact of Population Stratification on the Analysis of Multimodal Neuroimaging Derived Measures ]]> https://biorxiv.org/content/10.1101/2022.08.06.503037v1?rss=1 Huang, T.-H. Fan, C. C. Thompson, W. Loughnan, R. 2022-08-11 doi:10.1101/2022.08.06.503037 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Orbitofrontal cortex populations are differentially recruited to support actions ]]> https://biorxiv.org/content/10.1101/2022.08.08.503227v1?rss=1 Cazares, C. Schreiner, D. C. Valencia, M. L. Gremel, C. M. 2022-08-09 doi:10.1101/2022.08.08.503227 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ The genetic and environmental etiology of blood-based biomarkers related to the risks of Alzheimer's Disease in a population-based sample of early old age men ]]> https://biorxiv.org/content/10.1101/2022.08.09.503234v1?rss=1 Gillespie, N. A. Rissman, R. A. Elman, J. A. McKenzie, R. E. Tu, X. M. Reynolds, C. A. Lyons, M. J. Eglit, G. M. L. Neale, M. C. Franz, C. Kremen, W. S. 2022-08-11 doi:10.1101/2022.08.09.503234 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Fast, Efficient Multimodal Image Normalisation Tool (FEMINisT) for the Adolescent Brain and Cognitive Development study: the FEMINisT ABCD Atlas ]]> https://biorxiv.org/content/10.1101/2022.08.09.503395v1?rss=1 Pecheva, D. Iversen, J. R. Palmer, C. E. Watts, R. Jernigan, T. L. Hagler, D. J. Dale, A. M. 2022-08-11 doi:10.1101/2022.08.09.503395 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules ]]> https://biorxiv.org/content/10.1101/2022.08.10.503527v1?rss=1 Shaked, I. Foo, C. Liu, R. Cui, Y. Ji, X. Broggini, T. Mächler, P. Sundd, P. Devor, A. Friedman, B. Kleninfeld, D. 2022-08-13 doi:10.1101/2022.08.10.503527 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters ]]> https://biorxiv.org/content/10.1101/2022.08.10.503534v1?rss=1 Chaturvedi, S. Beutler, N. Pablo, M. Vasen, G. Chen, X. Calia, G. Buie, L. Rodick, R. Smith, D. Rogers, T. Weinberger, L. 2022-08-11 doi:10.1101/2022.08.10.503534 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ A thermodynamically-consistent model for ATP production in mitochondria ]]> https://biorxiv.org/content/10.1101/2022.08.16.500715v1?rss=1 Garcia, G. C. Bartol, T. M. Sejnowski, T. J. Rangamani, P. 2022-08-16 doi:10.1101/2022.08.16.500715 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling ]]> https://biorxiv.org/content/10.1101/2022.08.17.504291v1?rss=1 Leung, A. Rangamani, P. 2022-08-18 doi:10.1101/2022.08.17.504291 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression ]]> https://biorxiv.org/content/10.1101/2022.08.19.504467v1?rss=1 Liu, C. Wang, W. 2022-08-22 doi:10.1101/2022.08.19.504467 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Remarkable Sex-Specific Differences at Single-Cell Resolution in Neonatal Hyperoxic Lung Injury ]]> https://biorxiv.org/content/10.1101/2022.08.19.504541v1?rss=1 35000 cells isolated from the lungs of neonatal male and female C57BL/6 mice exposed to 95% FiO2 between PND1-5 (saccular stage of lung development) or normoxia and euthanized at PND7 (alveolar stage of lung development). ScRNAseq identified 22 cell clusters with distinct populations of endothelial, epithelial, mesenchymal, and immune cells. Our data identified that the distal lung vascular endothelium (composed of aerocytes and general capillary endothelial cells) is exquisitely sensitive to hyperoxia exposure with the emergence of an intermediate capillary endothelial population with both aCaP and gCaP markers. We also identified a myeloid derived suppressor cell population from the lung neutrophils. Sexual dimorphism was evident in all lung cell subpopulations but was striking among the lung immune cells. Finally, we identified that the specific intercellular communication networks and the ligand-receptor pairs that are impacted by neonatal hyperoxia exposure. ]]> Cantu Gutierrez, M. E. Cantu, A. Dong, X. Leek, C. Sajti, E. Lingappan, K. 2022-08-19 doi:10.1101/2022.08.19.504541 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.08.23.504974v1?rss=1 Kumpornsin, K. Kochakarn, T. Yeo, T. Luth, M. Pearson, R. D. Hoshizaki, J. Schindler, K. Mok, S. Park, H. Uhlemann, A.-C. Cubel, S. M. Franco, V. Gomez-Lorenzo, M. Gamo, F.-J. Winzeler, E. Fidock, D. A. Chookajorn, T. Lee, M. C. 2022-08-23 doi:10.1101/2022.08.23.504974 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ MicroRNA-218 instructs proper assembly of hippocampal networks ]]> https://biorxiv.org/content/10.1101/2022.08.24.505085v1?rss=1 Taylor, S. Kobayashi, M. Vilella, A. Tiwari, D. Zolboot, N. Hartzell, A. Girgiss, C. Abaci, Y. De Sanctis, C. Bellenchi, G. C. Darnell, R. B. Gross, C. Zoli, M. Berg, D. K. Lippi, G. 2022-08-25 doi:10.1101/2022.08.24.505085 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Interpretable Prediction of mRNA Abundance from Promoter Sequence using Contextual Regression Models ]]> https://biorxiv.org/content/10.1101/2022.08.27.505543v1?rss=1 Wang, S. Wang, W. 2022-08-29 doi:10.1101/2022.08.27.505543 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ A pharmacoproteomic landscape of organotypic intervention responses in gram-negative sepsis ]]> https://biorxiv.org/content/10.1101/2022.08.29.503941v1?rss=1 Mohanty, T. Karlsson, C. A. Q. Chao, Y. Malmstrom, E. Bratanis, E. Grentzmann, A. Morch, M. Nizet, V. Malmstrom, L. Linder, A. Shannon, O. Malmstrom, J. 2022-08-29 doi:10.1101/2022.08.29.503941 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Polycomb response elements reduce leaky expression of Cas9 under temperature-inducible Hsp70Bb promoter in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.08.29.505746v1?rss=1 Warsinger-Pepe, N. Chang, C. Desroberts, C. R. Akbari, O. S. 2022-08-29 doi:10.1101/2022.08.29.505746 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assemblyprior to nuclear dissolution ]]> https://biorxiv.org/content/10.1101/2022.09.01.505886v1?rss=1 Rocha, H. Simoes, P. A. Budrewicz, J. Lara-Gonzalez, P. Xavier de Carvalho, A. Dumont, J. Desai, A. Gassmann, R. 2022-09-02 doi:10.1101/2022.09.01.505886 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Effect of time spent on active learning on exam performance: A controlled case study on a course with different instructors but identical teaching materials ]]> https://biorxiv.org/content/10.1101/2022.09.01.506238v1?rss=1 Cen, X. Lee, R. J. Maloy, J. P. Owens, M. T. 2022-09-03 doi:10.1101/2022.09.01.506238 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Defining antigen targets to dissect vaccinia virus (VACV) and Monkeypox virus (MPXV)-specific T cell responses in humans ]]> https://biorxiv.org/content/10.1101/2022.09.06.506534v1?rss=1 Grifoni, A. Zhang, Y. Tarke, A. Sidney, J. Rubiro, P. Reina-Campos, M. Filaci, G. Dan, J. M. Scheuermann, R. H. Sette, A. 2022-09-07 doi:10.1101/2022.09.06.506534 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala ]]> https://biorxiv.org/content/10.1101/2022.09.08.506493v1?rss=1 Zhou, J. L. de Guglielmo, G. Ho, A. J. Kallupi, M. Li, H.-R. Chitre, A. S. Carrette, L. L. G. George, O. Palmer, A. A. McVicker, G. P. Telese, F. 2022-09-12 doi:10.1101/2022.09.08.506493 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ A small-molecule myosin inhibitor as a targeted multi-stage antimalarial ]]> https://biorxiv.org/content/10.1101/2022.09.09.507317v1?rss=1 50-fold selectivity against cardiac, skeletal, and smooth muscle myosins. KNX-115 inhibits the blood and liver stages of Plasmodium with an EC50 of about 100 nanomolar, with negligible liver cell toxicity. In addition, KNX-115 inhibits sporozoite cell traversal and blocks the gametocyte to oocyst conversion in the mosquito. KNX-115 displays a similar killing profile to pyrimethamine and parasites are totally killed after 96 hours of treatment. In line with its novel mechanism of action, KNX-115 is equally effective at inhibiting a panel of Plasmodium strains resistant to experimental and marketed antimalarials. In vitro evolution data likely suggests a refractory potential of KNX-115 in developing parasite resistance. ]]> Trivedi, D. V. Karabina, A. Bergnes, G. Racca, A. Wander, H. Jung, S. Mittal, N. Huijs, T. Ouchida, S. Ruijgrok, P. V. Song, D. Wittlin, S. Mukherjee, P. Chakraborty, A. Winzeler, E. A. Burrows, J. N. Laleu, B. Spudich, A. Ruppel, K. Dechering, K. Nag, S. Spudich, J. 2022-09-10 doi:10.1101/2022.09.09.507317 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Two Synaptic Convergence Motifs Define Functional Roles for Inputs to Cochlear Nucleus Bushy Cells ]]> https://biorxiv.org/content/10.1101/2022.09.10.507000v1?rss=1 Spirou, G. A. Kersting, M. Carr, S. Razzaq, B. Alves-Pinto, C. Y. Dawson, M. Ellisman, M. H. Manis, P. B. 2022-09-10 doi:10.1101/2022.09.10.507000 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Phosphorylation of Gαi shapes canonical Gα(i)βγ/GPCR signaling ]]> https://biorxiv.org/content/10.1101/2022.09.11.507491v1?rss=1 Roy, S. Silas, A. J. Ghassemian, M. Kufareva, I. Ghosh, P. 2022-09-12 doi:10.1101/2022.09.11.507491 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ TandemAligner: a new parameter-free framework for fast sequence alignment ]]> https://biorxiv.org/content/10.1101/2022.09.15.507041v1?rss=1 Bzikadze, A. V. Pevzner, P. A. 2022-09-17 doi:10.1101/2022.09.15.507041 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Cortico-cortical and hippocampo-cortical co-rippling are facilitated by thalamo-cortical spindles and upstates, but not by thalamic ripples ]]> https://biorxiv.org/content/10.1101/2022.09.15.507471v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Kajfez, S. Rosen, B. Q. Pati, S. Halgren, E. 2022-09-17 doi:10.1101/2022.09.15.507471 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Eliminating Genes for a Two Component System Increases PHB Productivity in Cupriavidus basilensis 4G11 Under PHB Suppressing, Non-Stress Conditions ]]> https://biorxiv.org/content/10.1101/2022.09.19.508597v1?rss=1 Sander, K. B. Abel, A. J. Friedline, S. Sharpless, W. Skerker, J. M. B. Deutschbauer, A. Clark, D. S. Arkin, A. P. 2022-09-20 doi:10.1101/2022.09.19.508597 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Host specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome ]]> https://biorxiv.org/content/10.1101/2022.09.21.508960v1?rss=1 Tsu, B. V. Agarwal, R. Gokhale, N. S. Kulsuptrakul, J. Ryan, A. P. Castro, L. K. Beierschmitt, C. M. Turcotte, E. A. Fay, E. J. Vance, R. E. Hyde, J. L. Savan, R. Mitchell, P. S. Daugherty, M. D. 2022-09-22 doi:10.1101/2022.09.21.508960 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[ Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms ]]> https://biorxiv.org/content/10.1101/2022.09.22.509046v1?rss=1 Bennett, H. Troutman, T. D. Zhou, E. Spann, N. J. Link, V. M. Seidman, J. S. Nickl, C. K. Abe, Y. Sakai, M. Pasillas, M. P. Marlman, J. M. Guzman, C. Hosseini, M. Schnabl, B. Glass, C. K. 2022-09-23 doi:10.1101/2022.09.22.509046 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Regulation of the Phage Lambda Viral Packaging Motor's Grip and DNA End-clamp Mechanism ]]> https://biorxiv.org/content/10.1101/2022.09.24.509349v1?rss=1 Rawson, B. Yang, Q. Catalano, C. E. Smith, D. E. 2022-09-25 doi:10.1101/2022.09.24.509349 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ RNA recoding in cephalopods tailors microtubule motor protein function ]]> https://biorxiv.org/content/10.1101/2022.09.25.509396v1?rss=1 Rangan, K. J. Reck-Peterson, S. L. 2022-09-25 doi:10.1101/2022.09.25.509396 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Ultrastructure of synaptic connectivity within sub-regions of the SCN revealed by genetically encoded EM tag and SBEM ]]> https://biorxiv.org/content/10.1101/2022.09.26.509467v1?rss=1 Calligaro, H. Shoghi, A. Chen, X. Kim, K.-Y. Liu, Y. H. Khov, B. Finander, B. Le, H. Ellisman, M. H. Panda, S. 2022-09-26 doi:10.1101/2022.09.26.509467 Cold Spring Harbor Laboratory Press 2022-09-26 <![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[ A di-arginine additive for dissociation of gold nanoparticle aggregates: A matrix-insensitive approach with applications in protease detection ]]> https://biorxiv.org/content/10.1101/2022.09.30.508454v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@13a6f3org.highwire.dtl.DTLVardef@35b42dorg.highwire.dtl.DTLVardef@1c8249forg.highwire.dtl.DTLVardef@dc8236_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Retout, M. Jin, Z. Mantri, Y. Borum, R. Creyer, M. Yim, W. He, T. Chang, Y.-C. Jokerst, J. 2022-10-03 doi:10.1101/2022.09.30.508454 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Optical Metabolic Imaging Uncovers Sex- and Diet-dependent Lipid Changes in Aging Drosophila Brain ]]> https://biorxiv.org/content/10.1101/2022.10.01.510416v1?rss=1 Li, Y. Chang, P. Sankaran, S. Jang, H. Nie, Y. Zeng, A. Hussain, S. Wu, J. Y. Chen, X. Shi, L. 2022-10-03 doi:10.1101/2022.10.01.510416 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Vascular tortuosity quantification as an outcome metric of the oxygen-induced retinopathy model of ischemic retinopathy ]]> https://biorxiv.org/content/10.1101/2022.10.02.510568v1?rss=1 Marra, K. V. Chen, J. S. Robles-Holmes, H. K. Miller, J. Wei, G. Ideguchi, Y. Ly, K. B. Prenner, S. Erdogmus, D. Ferrara, N. Campbell, J. P. Friedlander, M. Nudleman, E. 2022-10-04 doi:10.1101/2022.10.02.510568 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Artificial Intelligence Guided Discovery of Gastric Cancer Continuum ]]> https://biorxiv.org/content/10.1101/2022.10.05.510975v1?rss=1 Vo, D. T. Ghosh, P. Sahoo, D. 2022-10-07 doi:10.1101/2022.10.05.510975 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model ]]> https://biorxiv.org/content/10.1101/2022.10.06.511147v1?rss=1 Mai, U. Charvel, E. Mirarab, S. 2022-10-08 doi:10.1101/2022.10.06.511147 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ PLK-1 tethered on BUB-1 directs CDC-20 kinetochore recruitment to ensure timelyembryonic mitoses ]]> https://biorxiv.org/content/10.1101/2022.10.07.511323v1?rss=1 Houston, J. Ohta, M. Gomez-Cavazos, J. S. Deep, A. Corbett, K. D. Oegema, K. Lara-Gonzalez, P. Kim, T. Desai, A. 2022-10-07 doi:10.1101/2022.10.07.511323 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus ]]> https://biorxiv.org/content/10.1101/2022.10.07.511350v1?rss=1 Heffel, M. G. Zhou, J. Zhang, Y. Lee, D.-S. Hou, K. Pastor Alonso, O. Abuhanna, K. Schmitt, A. D. Li, T. Haeussler, M. Wick, B. Zhang, M. J. Xie, F. Ziffra, R. S. Mukamel, E. A. Eskin, E. Pasaniuc, B. Ecker, J. R. Dixon, J. Nowakowski, T. J. Paredes, M. F. Luo, C. 2022-10-08 doi:10.1101/2022.10.07.511350 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Structures of human cytoplasmic dynein in complex with the lissencephaly 1 protein, LIS1 ]]> https://biorxiv.org/content/10.1101/2022.10.08.511426v1?rss=1 Reimer, J. M. DeSantis, M. E. Reck-Peterson, S. L. Leschziner, A. E. 2022-10-08 doi:10.1101/2022.10.08.511426 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ TRB3 augments IL1β-TLR4 signaling by engaging Flightless-homolog 1. ]]> https://biorxiv.org/content/10.1101/2022.10.09.511391v1?rss=1 Gonuguntla, S. Humphrey, R. K. Gorantla, A. Hao, E. Jhala, U. S. 2022-10-10 doi:10.1101/2022.10.09.511391 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ MS2Prop: A machine learning model that directly predicts chemical properties from mass spectrometry data for novel compounds ]]> https://biorxiv.org/content/10.1101/2022.10.09.511482v1?rss=1 Voronov, G. Frandsen, A. Bargh, B. Healey, D. Lightheart, R. Kind, T. Dorrestein, P. C. Colluru, V. Butler, T. 2022-10-10 doi:10.1101/2022.10.09.511482 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Lis1 relieves cytoplasmic dynein-1 auto-inhibition by acting as a molecular wedge ]]> https://biorxiv.org/content/10.1101/2022.10.10.511666v1?rss=1 Karasmanis, E. P. Reimer, J. M. Kendrick, A. A. Rodriguez, J. A. Truong, J. B. Lahiri, I. Reck-Peterson, S. L. Leschziner, A. E. 2022-10-11 doi:10.1101/2022.10.10.511666 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters ]]> https://biorxiv.org/content/10.1101/2022.10.11.511793v1?rss=1 Diner, R. E. Zimmer-Faust, A. Cooksey, E. Allard, S. Kodera, S. M. Kunselman, E. Garodia, Y. Allen, A. E. Griffith, J. Gilbert, J. A. 2022-10-11 doi:10.1101/2022.10.11.511793 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Endosomal removal and disposal of dysfunctional, immunostimulatory mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2022.10.12.511955v1?rss=1 Newman, L. E. Tadepalle, N. Novak, S. W. Schiavon, C. R. Rojas, G. R. Chevez, J. A. Lemersal, I. Medina, M. Rocha, S. Towers, C. G. Grotjahn, D. A. Manor, U. Shadel, G. S. 2022-10-12 doi:10.1101/2022.10.12.511955 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Smaller total and subregional cerebellar volumes in posttraumatic stress disorder: a mega-analysis by the ENIGMA-PGC PTSD workgroup ]]> https://biorxiv.org/content/10.1101/2022.10.13.512111v1?rss=1 Huggins, A. A. Baird, C. L. Briggs, M. Laskowitz, S. Fouda, S. Haswell, C. C. Sun, D. Salminen, L. E. Jahanshad, N. Thomopoulos, S. I. Veltman, D. J. Frijling, J. L. Olff, M. van Zuiden, M. Koch, S. B. J. Nawijn, L. Wang, L. Zhu, Y. Li, G. Stein, D. J. Ipser, J. Seedat, S. du Plessis, S. van den Heuvel, L. L. Suarez-Jimenez, B. Zhu, X. Kim, Y. He, X. Zilcha-Mano, S. Lazarov, A. Neria, Y. Stevens, J. S. Ressler, K. J. Jovanovic, T. van Rooij, S. J. H. Fani, N. Hudson, A. R. Mueller, S. C. Sierk, A. Manthey, A. Walter, H. Daniels, J. K. Schmahl, C. Herz 2022-10-17 doi:10.1101/2022.10.13.512111 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Machine-guided cell-fate engineering ]]> https://biorxiv.org/content/10.1101/2022.10.14.512279v1?rss=1 Appleton, E. M. Tao, J. Fonseca, G. J. Liu, S. Glass, C. H. Church, G. M. 2022-10-14 doi:10.1101/2022.10.14.512279 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A fast-killing tyrosine amide ((S)-SW228703) with blood and liver-stage antimalarial activity associated with the Cyclic Amine Resistance Locus (PfCARL) ]]> https://biorxiv.org/content/10.1101/2022.10.16.512381v1?rss=1 Imlay, L. S. Lawong, A. K. Gahalawat, S. Kumar, A. Xing, C. Mittal, N. Wittlin, S. Churchyard, A. Niederstrasser, H. Crespo-Fernandez, B. Posner, B. Gamo, F.-J. S. Baum, J. Winzeler, E. Laleu, B. Ready, J. M. Phillips, M. A. 2022-10-17 doi:10.1101/2022.10.16.512381 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ A Computational Model for Storing Memories in the Synaptic Structures of the Brain ]]> https://biorxiv.org/content/10.1101/2022.10.21.513291v1?rss=1 George, V. K. Morar, V. N. Silva, G. A. 2022-10-22 doi:10.1101/2022.10.21.513291 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences ]]> https://biorxiv.org/content/10.1101/2022.10.21.513318v1?rss=1 Moshiri, N. 2022-10-24 doi:10.1101/2022.10.21.513318 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Localized APP pathology in the hippocampus is sufficient to result in progressive disorganization of the timing of neuronal firing patterns ]]> https://biorxiv.org/content/10.1101/2022.10.24.513188v1?rss=1 Viana da Silva, S. Haberl, M. G. Gaur, K. Patel, R. Narayan, G. Ledakis, M. Fu, M. L. Koo, E. H. Leutgeb, J. K. Leutgeb, S. 2022-10-25 doi:10.1101/2022.10.24.513188 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ The Molecular Signatures Database Revisited: Extending Support for Mouse Data ]]> https://biorxiv.org/content/10.1101/2022.10.24.513539v1?rss=1 Castanza, A. S. Recla, J. M. Eby, D. Thorvaldsdottir, H. Bult, C. J. Mesirov, J. P. 2022-10-25 doi:10.1101/2022.10.24.513539 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ EUGENe: A Python toolkit for predictive analyses of regulatory sequences ]]> https://biorxiv.org/content/10.1101/2022.10.24.513593v1?rss=1 Klie, A. Stites, H. Jores, T. Carter, H. 2022-10-26 doi:10.1101/2022.10.24.513593 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function ]]> https://biorxiv.org/content/10.1101/2022.10.24.513614v1?rss=1 Lewis, B. M. Cho, C. Y. Her, H.-L. Hunter, T. Yeo, G. W. 2022-10-26 doi:10.1101/2022.10.24.513614 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Capturing differences in the regulation of LRRK2 dynamics and conformational states by small molecule kinase inhibitors ]]> https://biorxiv.org/content/10.1101/2022.10.24.513618v1?rss=1 Weng, J.-H. Ma, W. Wu, J. Silletti, S. McCammon, J. A. Taylor, S. S. 2022-10-25 doi:10.1101/2022.10.24.513618 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response ]]> https://biorxiv.org/content/10.1101/2022.10.25.513771v1?rss=1 Chudnovskiy, A. Nakandakari-Higa, S. Castro, T. B. Cui, A. Lin, C.-H. Sade-Feldman, M. Phillips, B. K. Pae, J. Mesin, L. Bortolatto, J. Schweitzer, L. D. Pasqual, G. Lu, L.-F. Hacohen, N. Victora, G. D. 2022-10-25 doi:10.1101/2022.10.25.513771 Cold Spring Harbor Laboratory Press 2022-10-25 <![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[ Time of Sample Collection Critical for Microbiome Replicability ]]> https://biorxiv.org/content/10.1101/2022.10.26.513817v1?rss=1 Allaband, C. Lingaraju, A. Ramos, S. F. Kumar, T. Javaheri, H. Tiu, M. D. Machado, A. C. D. Richter, R. A. Elijah, E. Haddad, G. G. Leone, V. A. Dorrestein, P. C. Knight, R. Zarrinpar, A. 2022-10-28 doi:10.1101/2022.10.26.513817 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Low Temperature and High Hydrostatic Pressure Have Compounding Negative Effects on Marine Microbial Motility ]]> https://biorxiv.org/content/10.1101/2022.10.26.513967v1?rss=1 Mullane, K. K. Bartlett, D. H. Nishiyama, M. Kurihara, T. 2022-10-27 doi:10.1101/2022.10.26.513967 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Heritability estimation of cognitive phenotypes in the ABCD Study using mixed models ]]> https://biorxiv.org/content/10.1101/2022.10.28.512918v1?rss=1 Smith, D. M. Loughnan, R. J. Friedman, N. P. Parekh, P. Frei, O. Thompson, W. K. Andreassen, O. Neale, M. Jernigan, T. L. Dale, A. 2022-10-31 doi:10.1101/2022.10.28.512918 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Alveolar epithelial type 1 cells serve as a cell of origin for lung adenocarcinoma with distinct molecular and phenotypic presentation ]]> https://biorxiv.org/content/10.1101/2022.10.29.514334v1?rss=1 Yang, M. Shen, H. Flodby, P. Koss, M. Bassiouni, R. Liu, Y. Jashashvilli, T. Stueve, T. R. Mullen, D. J. Ryan, A. L. Carpten, J. Castaldi, A. Wallace, W. D. Zhou, B. Borok, MD, Z. Marconett, C. N. 2022-10-31 doi:10.1101/2022.10.29.514334 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Unraveling the coordinated dynamics of protein- and metabolite-mediated cell-cell communication ]]> https://biorxiv.org/content/10.1101/2022.11.02.514917v1?rss=1 Armingol, E. Larsen, R. O. Cequeira, M. Baghdassarian, H. Lewis, N. E. 2022-11-03 doi:10.1101/2022.11.02.514917 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Improving annotation propagation on molecular networks through random walks: Introducing ChemWalker ]]> https://biorxiv.org/content/10.1101/2022.11.04.514505v1?rss=1 Borelli, T. C. Arini, G. S. Feitosa, L. G. P. Dorrestein, P. C. Lopes, N. P. da Silva, R. R. 2022-11-05 doi:10.1101/2022.11.04.514505 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Methadone alters transcriptional programs associated with synapse formation in human cortical organoids ]]> https://biorxiv.org/content/10.1101/2022.11.04.515240v1?rss=1 Dwivedi, I. Zhou, D. Caldwell, A. B. Subramaniam, S. Haddad, G. G. 2022-11-05 doi:10.1101/2022.11.04.515240 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Whole-body gene expression atlas of an adult metazoan ]]> https://biorxiv.org/content/10.1101/2022.11.06.515345v1?rss=1 Ghaddar, A. Armingol, E. Huynh, C. Gevirtzman, L. Lewis, N. E. Waterston, R. O'Rourke, E. 2022-11-06 doi:10.1101/2022.11.06.515345 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Biophysical modeling of actin-mediated structural plasticity reveals mechanical adaptation in dendritic spines ]]> https://biorxiv.org/content/10.1101/2022.11.06.515372v1?rss=1 Bonilla-Quintana, M. Rangamani, P. 2022-11-06 doi:10.1101/2022.11.06.515372 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Rapid iPSC inclusionopathy models shed light on formation, consequence and molecular subtype of alpha-synuclein inclusions ]]> https://biorxiv.org/content/10.1101/2022.11.08.515615v1?rss=1 Lam, I. Ndayisaba, A. Lewis, A. J. Fu, Y. Sagredo, G. T. Zaccagnini, L. Sandoe, J. Sanz, R. L. Vahdatshoar, A. Martin, T. D. Morshed, N. Ichihashi, T. Tripathi, A. Ramalingam, N. Oettgen-Suazo, C. Bartels, T. Schabinger, M. Hallacli, E. Jiang, X. Verma, A. Tea, C. Wang, Z. Hakozaki, H. Yu, X. Hyles, K. Park, C. Theunissen, T. W. Wang, H. Jaenisch, R. Lindquist, S. Stevens, B. Stefanova, N. Wenning, G. Luk, K. C. Sanchez Pernaute, R. Gomez-Esteban, J. C. Felsky, D. Kiyota, Y. Sahni, N. Yi, S. S. Chung, C.-Y. Stahlberg, H. Ferrer, I. Schoneberg, J. Ell 2022-11-09 doi:10.1101/2022.11.08.515615 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2022.11.09.512793v1?rss=1 Kobayashi-Ishihara, M. Smutna, K. F. Alonso, F. E. Argilaguet, J. Esteve-Codina, A. Geiger, K. Genesca, M. Grau-Exposito, J. Duran-Castells, C. Rogenmoser, S. Böttcher, R. Jungfleisch, J. Oliva, B. Martinez, J. P. Li, M. David, M. Yamagishi, M. Ruiz-Riol, M. Brander, C. Tsunetsugu-Yokota, Y. Buzon, M. J. Diez, J. Meyerhans, A. 2022-11-09 doi:10.1101/2022.11.09.512793 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ A comparative atlas of single-cell chromatin accessibility in the human brain ]]> https://biorxiv.org/content/10.1101/2022.11.09.515833v1?rss=1 Li, Y. E. Preissl, S. Miller, M. Johnson, N. D. Wang, Z. Jiao, H. Zhu, C. Wang, Z. Xie, Y. Poirin, O. Kern, C. Pinto-Duarte, A. Tian, W. Siletti, K. Emerson, N. Osteen, J. Lucero, J. Lin, L. Yang, Q. Espinoza, S. Zhu, Q. Zemke, N. Yanny, A. M. Nyhus, J. Dee, N. Casper, T. Shapovalova, N. Hirschstein, D. Hodge, R. D. Linnarsson, S. Bakken, T. E. Levi, B. Keene, C. D. Shang, J. Lein, E. S. Wang, A. Behrens, M. M. Ecker, J. R. Ren, B. 2022-11-10 doi:10.1101/2022.11.09.515833 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations ]]> https://biorxiv.org/content/10.1101/2022.11.10.516058v1?rss=1 Ojha, A. A. Srivastava, A. Votapka, L. Amaro, R. E. 2022-11-12 doi:10.1101/2022.11.10.516058 Cold Spring Harbor Laboratory Press 2022-11-12 <![CDATA[ Inferring a cell's capabilities from omics data with ImmCellFie ]]> https://biorxiv.org/content/10.1101/2022.11.16.516672v1?rss=1 Masson, H. O. Borland, D. Reilly, J. Telleria, A. Shrivastava, S. Watson, M. Bustillo, L. Li, Z. Capps, L. Kellman, B. P. King, Z. A. Richelle, A. Lewis, N. E. Robasky, K. 2022-11-17 doi:10.1101/2022.11.16.516672 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cas9-mediated tagging of endogenous loci using HITAG ]]> https://biorxiv.org/content/10.1101/2022.11.16.516691v1?rss=1 Kim, J. Kratz, A. Sheng, J. Zhang, L. Singh, B. K. Chavez, A. 2022-11-17 doi:10.1101/2022.11.16.516691 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD ]]> https://biorxiv.org/content/10.1101/2022.11.17.516859v1?rss=1 Li, J. Jaiswal, M. K. Chien, J.-F. Kozlenkov, A. Zhou, P. Gardashli, M. Pregent, L. J. Engelberg-Cook, E. Dickson, D. W. Belzil, V. V. Mukamel, E. A. Dracheva, S. 2022-11-17 doi:10.1101/2022.11.17.516859 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Adult consequences of repeated nicotine vapor inhalation in adolescent rats ]]> https://biorxiv.org/content/10.1101/2022.11.17.516984v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Grant, Y. Taffe, M. A. 2022-11-18 doi:10.1101/2022.11.17.516984 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Plasmodium exoerythrocytic parasites redirect trafficking of human proteins to the parasitophorous vacuole ]]> https://biorxiv.org/content/10.1101/2022.11.22.517223v1?rss=1 Calla, J. Mittal, N. LaMonte, G. Liffner, B. Godinez-Macias, K. Carolino, K. Walker, G. T. Zou, B. Y. Paytas, E. Guerra, L. Tong-Rios, C. Campo, B. Vinetz, J. M. Gamboa, D. Raffatellu, M. Absalon, S. Winzeler, E. 2022-11-23 doi:10.1101/2022.11.22.517223 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Structure of LRRK1 and mechanisms of autoinhibition and activation ]]> https://biorxiv.org/content/10.1101/2022.11.22.517582v1?rss=1 Reimer, J. M. Dickey, A. M. Lin, Y. X. Abrisch, R. G. Mathea, S. Chatterjee, D. Fay, E. J. Daugherty, M. D. Reck-Peterson, S. L. Leschziner, A. E. 2022-11-23 doi:10.1101/2022.11.22.517582 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Cross-species analysis identifies conserved transcriptional mechanisms of neutrophil maturation ]]> https://biorxiv.org/content/10.1101/2022.11.28.518146v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@d46deaorg.highwire.dtl.DTLVardef@7c2647org.highwire.dtl.DTLVardef@b535eeorg.highwire.dtl.DTLVardef@e7dc38_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kirchberger, S. Shoeb, M. R. Lazic, D. Fischer, K. Shaw, L. E. Nogueira, F. Rifatbegovic, F. Bozsaky, E. Ladenstein, R. Bodenmiller, B. Lion, T. Traver, D. Farlik, M. Taschner-Mandl, S. Halbritter, F. Distel, M. 2022-11-28 doi:10.1101/2022.11.28.518146 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ A new theoretical framework jointly explains behavioral and neural variability across subjects performing flexible decision-making ]]> https://biorxiv.org/content/10.1101/2022.11.28.518207v1?rss=1 Pagan, M. Tang, V. D. Aoi, M. C. Pillow, J. W. Mante, V. Sussillo, D. Brody, C. D. 2022-11-28 doi:10.1101/2022.11.28.518207 Cold Spring Harbor Laboratory Press 2022-11-28 <![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[ Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding ]]> https://biorxiv.org/content/10.1101/2022.12.02.518910v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@167b370org.highwire.dtl.DTLVardef@135b62dorg.highwire.dtl.DTLVardef@14b5e9forg.highwire.dtl.DTLVardef@1311e84_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementA Golgi-localized molecular circuitry has been recently implicated in the orchestration of secrete-and-sense auto-/paracrine loops that impart self-sufficiency in growth signaling, a.k.a., growth signaling autonomy. Using a transdisciplinary approach, this work shows that growth signaling autonomy is uniquely induced in tumor cells that are in circulation. Circulating tumor cells (CTCs) represent a brutish and risky phase in the lifetime of tumor cells when they are exposed to the immune system and hemodynamic sheer forces, all in the setting of growth factor starvation. Cancer cells appear to rely on the autonomy circuit to survive and enhance their fitness to seed metastases. Autonomy generates the kind of eat-what-you-kill entrepreneurial spirit which minimizes the risk of CTCs dying on an otherwise risky journey. ]]> Sinha, S. Farfel, A. Luker, K. E. Sahoo, D. Parker, B. A. Yeung, K. Luker, G. D. Ghosh, P. 2022-12-05 doi:10.1101/2022.12.02.518910 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Nanoscaled discovery of a shunt rifamycin from Salinispora arenicola using a three-colour GFP-tagged Staphylococcus aureus macrophage infection assay. ]]> https://biorxiv.org/content/10.1101/2022.12.04.519019v1?rss=1 Pham, N. T. Alves, J. Sargison, F. A. Cullum, R. Wildenhain, J. Fenical, W. Butler, M. S. Mead, D. Duggan, B. M. Fitzgerald, J. R. La Clair, J. J. Auer, M. 2022-12-04 doi:10.1101/2022.12.04.519019 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Deciphering the determinants of recombinant protein yield across the human secretome ]]> https://biorxiv.org/content/10.1101/2022.12.12.520152v1?rss=1 Masson, H. O. Kuo, C.-C. Malm, M. Lundqvist, M. Sivertsson, A. Berling, A. Tegel, H. Hober, S. Uhlen, M. Grassi, L. Hatton, D. Rockberg, J. Lewis, N. E. 2022-12-14 doi:10.1101/2022.12.12.520152 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening ]]> https://biorxiv.org/content/10.1101/2022.12.13.520335v1?rss=1 Kim, S. H. Shin, S. Baek, M. Xiong, K. Karottki, K. J. l. C. Hefzi, H. Grav, L. M. Pedersen, L. E. Kildegaard, H. F. Lewis, N. E. Lee, J. S. Lee, G. M. 2022-12-14 doi:10.1101/2022.12.13.520335 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data ]]> https://biorxiv.org/content/10.1101/2022.12.16.520793v1?rss=1 Lee, L. Yu, H. Jia, B. B. Jussila, A. Zhu, C. Chen, J. Xie, L. Hafner, A. Strambio-De-Castillia, C. Boettiger, A. Ren, B. Li, Y. Hu, M. 2022-12-19 doi:10.1101/2022.12.16.520793 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ The ins and outs of membrane bending by intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2022.12.17.520884v1?rss=1 Yuan, F. Houser, J. Sangani, A. Wang, L. Lafer, E. Rangamani, P. Stachowiak, J. 2022-12-17 doi:10.1101/2022.12.17.520884 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.12.17.520895v1?rss=1 Wirthlin, M. E. Schmid, T. A. Elie, J. E. Zhang, X. Shvareva, V. A. Rakuljic, A. Ji, M. B. Bhat, N. S. Kaplow, I. M. Schäffer, D. E. Lawler, A. J. Annaldasula, S. Lim, B. Azim, E. Zoonomia Consortium, Meyer, W. K. Yartsev, M. M. Pfenning, A. R. 2022-12-18 doi:10.1101/2022.12.17.520895 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Greengenes2 enables a shared data universe for microbiome studies ]]> https://biorxiv.org/content/10.1101/2022.12.19.520774v1?rss=1 McDonald, D. Jiang, Y. Balaban, M. Cantrell, K. Zhu, Q. Gonzalez, A. Morton, J. T. Nicolaou, G. Parks, D. Karst, S. M. Albertsen, M. Hugenholtz, P. DeSantis, T. Mirarab, S. Knight, R. 2022-12-20 doi:10.1101/2022.12.19.520774 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study ]]> https://biorxiv.org/content/10.1101/2022.12.20.521181v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@1e7eadcorg.highwire.dtl.DTLVardef@ec127eorg.highwire.dtl.DTLVardef@b21f14org.highwire.dtl.DTLVardef@1690c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tissink, E. Shadrin, A. A. van der Meer, D. Parker, N. Hindley, G. Roelfs, D. Frei, O. Fan, C. C. Nagel, M. Naerland, T. Budisteanu, M. Djurovic, S. Westlye, L. T. van den Heuvel, M. Posthuma, D. Kaufmann, T. Dale, A. M. Andreassen, O. 2022-12-20 doi:10.1101/2022.12.20.521181 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance ]]> https://biorxiv.org/content/10.1101/2022.12.20.521246v1?rss=1 View larger version (83K): org.highwire.dtl.DTLVardef@187f455org.highwire.dtl.DTLVardef@ba0798org.highwire.dtl.DTLVardef@148b175org.highwire.dtl.DTLVardef@17a8f8c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rychel, K. Tan, J. Patel, A. Lamoureux, C. Hefner, Y. Szubin, R. Johnsen, J. Mohamed, E. T. T. Phaneuf, P. V. Anand, A. Olson, C. A. Park, J. H. Sastry, A. V. Yang, L. Feist, A. M. Palsson, B. O. 2022-12-23 doi:10.1101/2022.12.20.521246 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function ]]> https://biorxiv.org/content/10.1101/2022.12.22.521485v1?rss=1 Parra-Rivas, L. A. Madhivanan, K. Wang, L. Boyer, N. P. Prakashchand, D. D. Aulston, B. D. Pizzo, D. P. Branes-Guerrero, K. Tang, Y. Das, U. Scott, D. A. Rangamani, P. Roy, S. 2022-12-23 doi:10.1101/2022.12.22.521485 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ An Activity-Based Nanosensor for Minimally-Invasive Measurement of Protease Activity in Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2022.12.26.521967v1?rss=1 Kudryashev, J. A. Madias, M. I. Kandell, R. M. Lin, Q. X. Kwon, E. J. 2022-12-27 doi:10.1101/2022.12.26.521967 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Structural damping renders the insect exoskeleton mechanically insensitive to non-sinusoidal deformations ]]> https://biorxiv.org/content/10.1101/2022.12.27.522009v1?rss=1 Wold, E. Lynch, J. Gravish, N. Sponberg, S. 2022-12-27 doi:10.1101/2022.12.27.522009 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories ]]> https://biorxiv.org/content/10.1101/2022.12.27.522024v1?rss=1 Fang, J. Castillon, G. Phan, S. McArdle, S. Hariharan, C. Ellisman, M. H. Deniz, A. A. Saphire, E. O. 2022-12-27 doi:10.1101/2022.12.27.522024 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Predicting alcohol-related memory problems in older adults: A machine learning study with multi-domain features ]]> https://biorxiv.org/content/10.1101/2022.12.30.522330v1?rss=1 Kamarajan, C. Pandey, A. K. Chorlian, D. B. Meyers, J. L. Kinreich, S. Pandey, G. Subbie Saenz de Viteri, S. Zhang, J. Kuang, W. Barr, P. B. Aliev, F. Anokhin, A. P. Plawecki, M. H. Kuperman, S. Almasy, L. Merikangas, A. Brislin, S. J. Bauer, L. Hesselbrock, V. Chan, G. Kramer, J. Lai, D. Hartz, S. Bierut, L. J. McCutcheon, V. V. Bucholz, K. K. Dick, D. M. Schuckit, M. A. Edenberg, H. J. Porjesz, B. 2023-01-02 doi:10.1101/2022.12.30.522330 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Functional pathways for metabolic network-based data analysis: the MetPath algorithm ]]> https://biorxiv.org/content/10.1101/202226v1?rss=1 Mattei, G. Zielinski, D. C. Gan, Z. Ramazzotti, M. Palsson, B. O. 2017-10-12 doi:10.1101/202226 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data ]]> https://biorxiv.org/content/10.1101/2023.01.05.522928v1?rss=1 Moshiri, N. 2023-01-06 doi:10.1101/2023.01.05.522928 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Supramolecular fibrous hydrogel augmentation of uterosacral ligament suspension for treatment of pelvic organ prolapse ]]> https://biorxiv.org/content/10.1101/2023.01.08.522930v1?rss=1 Miller, B. Wolfe, W. Gentry, J. L. Grewal, M. G. Highley, C. B. De Vita, R. Vaughan, M. H. Caliari, S. R. 2023-01-09 doi:10.1101/2023.01.08.522930 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ High-dimensional phenotyping to define the genetic basis of cellular morphology ]]> https://biorxiv.org/content/10.1101/2023.01.09.522731v1?rss=1 Tegtmeyer, M. Arora, J. Asgari, S. Cimini, B. A. Peirent, E. Liyanage, D. Way, G. P. Weisbart, E. Nathan, A. Amariuta, T. Eggan, K. Haghighi, M. McCarroll, S. A. Carpenter, A. E. Singh, S. Nehme, R. Raychaudhuri, S. 2023-01-09 doi:10.1101/2023.01.09.522731 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Low Rate Hippocampal Delay Period Activity Encodes Behavioral Experience ]]> https://biorxiv.org/content/10.1101/2023.01.09.523199v1?rss=1 Athanasiadis, M. Masserini, S. Yuan, L. Fetterhoff, D. Leutgeb, J. K. Leutgeb, S. Leibold, C. 2023-01-09 doi:10.1101/2023.01.09.523199 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes ]]> https://biorxiv.org/content/10.1101/2023.01.09.523365v1?rss=1 Singh, H. W. Creamer, K. E. Chase, A. B. Klau, L. J. Podell, S. Jensen, P. R. 2023-01-10 doi:10.1101/2023.01.09.523365 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Distinguishing response from stimulus driven history biases ]]> https://biorxiv.org/content/10.1101/2023.01.11.523637v1?rss=1 Sheehan, T. C. Serences, J. T. 2023-01-13 doi:10.1101/2023.01.11.523637 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Automated quantitative trait locus analysis (AutoQTL) ]]> https://biorxiv.org/content/10.1101/2023.01.12.523835v1?rss=1 Freda, P. J. Ghosh, A. Zhang, E. Luo, T. Chitre, A. Polesskaya, O. St. Pierre, C. L. Gao, J. Martin, C. D. Chen, H. Garcia-Martinez, A. G. Wang, T. Han, W. Ishiwari, K. Meyer, P. Lamparelli, A. King, C. P. Palmer, A. A. Li, R. Moore, J. H. 2023-01-15 doi:10.1101/2023.01.12.523835 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ The mitochondrial multi-omic response to exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2023.01.13.523698v1?rss=1 Amar, D. Gay, N. R. Jimenez-Morales, D. Jean Beltran, P. M. Ramaker, M. E. Natarajan Raja, A. Zhao, B. Sun, Y. Marwaha, S. Gaul, D. Hershman, S. G. Xia, A. Lanza, I. Fernandez, F. M. Montgomery, S. B. Hevener, A. L. Ashley, E. Walsh, M. J. Sparks, L. M. Burant, C. F. Rector, R. S. Thyfault, J. Wheeler, M. T. Goodpaster, B. H. Coen, P. M. Schenk, S. Bodine, S. C. Lindholm, M. E. MoTrPAC Study Group, 2023-01-13 doi:10.1101/2023.01.13.523698 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.01.15.524171v1?rss=1 Lazetic, V. Blanchard, M. J. Bui, T. Troemel, E. R. 2023-01-18 doi:10.1101/2023.01.15.524171 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Bridging Big Data: Procedures for Combining Non-equivalent Cognitive Measures from the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/2023.01.16.524331v1?rss=1 Kennedy, E. Vadlamani, S. Lindsey, H. M. Lei, P.-W. Pugh, M. J. Adamson, M. Alda, M. Alonso-Lana, S. Ambrogi, S. Anderson, T. J. Arango, C. Asarnow, R. Avram, M. Ayesa-Arriola, R. Babikian, T. Banaj, N. Bird, L. J. Borgwardt, S. Brodtmann, A. Brosch, K. Caeyenberghs, K. Calhoun, V. D. Chiaravalloti, N. D. Cifu, D. X. Crespo-Facorro, B. Dalrymple-Alford, J. C. Dams-O'Connor, K. Dannlowski, U. Darby, D. Davenport, N. DeLuca, J. Diaz-Caneja, C. M. Disner, S. G. Dobryakova, E. Ehrlich, S. Esopenko, C. Ferrarelli, F. Frank, L. E. Franz, C. Fuentes-Claramonte, 2023-01-19 doi:10.1101/2023.01.16.524331 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Mixed Lineage Leukemia (Mll1) establishes global histone H3K4 trimethylation and stem like memory Cd8 T cell formation ]]> https://biorxiv.org/content/10.1101/2023.01.18.524461v1?rss=1 Getzler, A. J. Frederick, M. A. Diao, H. Milner, J. J. Belanger, S. Chen, R. Tsuda, S. M. Albao, D. Kim, J. Crotty, S. Goldrath, A. Pipkin, M. E. 2023-01-20 doi:10.1101/2023.01.18.524461 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures ]]> https://biorxiv.org/content/10.1101/2023.01.22.525049v1?rss=1 Kleven, H. Gillespie, T. H. Zehl, L. Dickscheid, T. Bjaalie, J. G. Martone, M. E. Leergaard, T. B. 2023-01-23 doi:10.1101/2023.01.22.525049 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Neurophysiological signatures of cortical micro-architecture ]]> https://biorxiv.org/content/10.1101/2023.01.23.525101v1?rss=1 Shafiei, G. Fulcher, B. D. Voytek, B. Satterthwaite, T. D. Baillet, S. Misic, B. 2023-01-23 doi:10.1101/2023.01.23.525101 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase ]]> https://biorxiv.org/content/10.1101/2023.01.23.525207v1?rss=1 Tota, E. M. Devaraj, N. K. 2023-01-23 doi:10.1101/2023.01.23.525207 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing ]]> https://biorxiv.org/content/10.1101/2023.01.24.525307v1?rss=1 Kleninfeld, D. Yao, P. Liu, R. Thunemann, M. Boggini, T. 2023-01-24 doi:10.1101/2023.01.24.525307 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways ]]> https://biorxiv.org/content/10.1101/2023.01.26.525555v1?rss=1 Monda, J. K. Ge, X. Hunkeler, M. Donovan, K. A. Ma, M. W. Jin, C. Y. Leonard, M. Fischer, E. S. Bennett, E. J. 2023-01-26 doi:10.1101/2023.01.26.525555 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Normative Modeling of Brain Morphometry Across the Lifespan using CentileBrain: Algorithm Benchmarking and Model Optimization ]]> https://biorxiv.org/content/10.1101/2023.01.30.523509v1?rss=1 Ge, R. Yu, Y. Qi, Y. X. Fan, Y. V. Chen, S. Gao, C. Haas, S. S. Modabbernia, A. New, F. Agartz, I. Asherson, P. Ayesa-Arriola, R. Banaj, N. Banaschewski, T. Baumeister, S. Bertolino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buckner, R. Buitelaar, J. K. Cannon, D. M. Caseras, X. Cervenka, S. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Haan, L. de Zubicaray, G. I. Di Giorgio, A. Erk, S. Fisher, S. E. Franke, B. Frodl, T. Glahn, D. C. Grotegerd, D. Gruber, O. Gruner, P. Gur, R. E. G 2023-01-31 doi:10.1101/2023.01.30.523509 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages ]]> https://biorxiv.org/content/10.1101/2023.01.30.526059v1?rss=1 Chen, H. I. Turakhia, Y. Bejerano, G. Kingsley, D. M. 2023-01-31 doi:10.1101/2023.01.30.526059 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations ]]> https://biorxiv.org/content/10.1101/2023.01.30.526328v1?rss=1 20-fold improvement in statistical power over existing methods. We then use BIRDMAn to identify antibiotic-mediated perturbations undetected by other DA methods due to subject-level heterogeneity. Finally, we demonstrate how BIRDMAn can construct state-of-the-art cancer-type classifiers using The Cancer Genome Atlas (TCGA) dataset, with substantial accuracy improvements over random forests and existing DA tools across multiple sequencing centers. Collectively, BIRDMAn extracts more informative biological signals while accounting for study-specific experimental conditions than existing approaches. ]]> Rahman, G. Morton, J. T. Martino, C. Sepich-Poore, G. D. Allaband, C. Guccione, C. Chen, Y. Hakim, D. Estaki, M. Knight, R. 2023-02-02 doi:10.1101/2023.01.30.526328 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ B3GALT6 Promotes Dormant Breast Cancer Cell Survival and Recurrence by Enabling Heparan Sulfate-Mediated FGF Signaling ]]> https://biorxiv.org/content/10.1101/2023.01.31.526529v1?rss=1 Sreekumar, A. Lu, M. Choudhury, B. Pan, T.-c. Pant, D. K. Sterner, C. J. Belka, G. K. Toriumi, T. Benz, B. Escobar-Aguirre, M. Marino, F. E. Esko, J. D. Chodosh, L. A. 2023-02-03 doi:10.1101/2023.01.31.526529 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE ]]> https://biorxiv.org/content/10.1101/2023.02.01.526488v1?rss=1 Chongsaritsinsuk, J. Steigmeyer, A. D. Mahoney, K. E. Rosenfeld, M. A. Lucas, T. M. Ince, D. Kearns, F. L. Battison, A. S. Hollenhorst, M. A. Shon, J. Tiemeyer, K. H. Attah, V. Kwon, C. Bertozzi, C. R. Ferracane, M. J. Amaro, R. E. Malaker, S. A. 2023-02-03 doi:10.1101/2023.02.01.526488 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Force transmission and SUN-KASH higher-order assembly in the LINC complex models ]]> https://biorxiv.org/content/10.1101/2023.02.02.526920v1?rss=1 Yerima, G. Domkam, N. Ornowski, J. Jahed, Z. Mofrad, M. R. K. 2023-02-03 doi:10.1101/2023.02.02.526920 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal ]]> https://biorxiv.org/content/10.1101/2023.02.03.526066v1?rss=1 Kudtarkar, P. Costanzo, M. Sun, Y. Jang, D. Koesterer, R. Mychaleckyj, J. C. Nayak, U. Onengut-Gumuscu, S. Rich, S. S. Flannick, J. A. Gaulton, K. J. Burtt, N. P. 2023-02-05 doi:10.1101/2023.02.03.526066 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ An integrated map of cell type-specific gene expression in pancreatic islets ]]> https://biorxiv.org/content/10.1101/2023.02.03.526994v1?rss=1 Elgamal, R. Kudtarkar, P. Melton, R. Mummey, H. Benaglio, P. Okino, M.-L. Gaulton, K. J. 2023-02-04 doi:10.1101/2023.02.03.526994 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue ]]> https://biorxiv.org/content/10.1101/2023.02.03.527012v1?rss=1 Many, G. M. Sanford, J. A. Sagendorf, T. J. Hou, Z. Nigro, P. Whytock, K. L. Amar, D. Caputo, T. Gay, N. R. Gaul, D. A. Hirshman, M. F. Jimenez-Morales, D. Lindholm, M. E. Muehlbauer, M. J. Vamvini, M. Bergman, B. C. Fernandez, F. M. Goodyear, L. J. Ortlund, E. A. Sparks, L. M. Xia, A. Adkins, J. N. Bodine, S. C. Newgard, C. B. Schenk, S. Study Group, T. M. 2023-02-04 doi:10.1101/2023.02.03.527012 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator ]]> https://biorxiv.org/content/10.1101/2023.02.03.527015v1?rss=1 Khandekar, A. Vangara, R. Barnes, M. Diaz-Gay, M. Abbasi, A. Bergstrom, E. N. Steele, C. D. Pillay, N. Alexandrov, L. B. 2023-02-04 doi:10.1101/2023.02.03.527015 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Curing GFP-itis in Bacteria with Base Editors: Development of a Genome Editing Science Program Implemented with High School Biology Students ]]> https://biorxiv.org/content/10.1101/2023.02.06.527367v1?rss=1 Vasquez, C. A. Evanoff, M. Ranzau, B. L. Gu, S. Deters, E. Komor, A. C. 2023-02-07 doi:10.1101/2023.02.06.527367 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Exploring the consequences of redirecting an exocytic Rab onto endocytic vesicles. ]]> https://biorxiv.org/content/10.1101/2023.02.09.527811v1?rss=1 Novick, P. J. Li, X. Liu, D. Griffis, E. 2023-02-10 doi:10.1101/2023.02.09.527811 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Generative Molecular Design and Experimental Validation of Selective Histamine H1 Inhibitors ]]> https://biorxiv.org/content/10.1101/2023.02.14.528391v1?rss=1 McLoughlin, K. S. Shi, D. Mast, J. E. Bucci, J. Williams, J. P. Jones, W. D. Miyao, D. Nam, L. Osswald, H. L. Zegelman, L. Allen, J. E. Bennion, B. J. Paulson, A. K. Abagyan, R. Head, M. S. Brase, J. M. 2023-02-16 doi:10.1101/2023.02.14.528391 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Selective loss of specific subsets of hair cell and spiral ganglion cell types in an outbred mouse model of age-related hearing loss ]]> https://biorxiv.org/content/10.1101/2023.02.15.528661v1?rss=1 Boussaty, E. C. Tedeschi, N. Novotny, M. Ninoyu, Y. Du, E. Draf, C. Zhang, Y. Scheuermann, R. H. Friedman, R. A. 2023-02-15 doi:10.1101/2023.02.15.528661 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2023.02.16.528701v1?rss=1 De Jesus, D. F. Zhang, Z. Brown, N. K. Li, X. Gaffrey, M. J. Kahraman, S. Wei, J. Hu, J. Basile, G. Xiao, L. Rana, T. M. Mathews, C. E. Powers, A. C. Atkinson, M. A. Eizirik, D. L. Dhe-Paganon, S. Parent, A. V. Qian, W.-J. He, C. Kulkarni, R. N. 2023-02-16 doi:10.1101/2023.02.16.528701 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Tracking and curating putative SARS-CoV-2 recombinants with RIVET ]]> https://biorxiv.org/content/10.1101/2023.02.17.529036v1?rss=1 Smith, K. Ye, C. Turakhia, Y. 2023-02-19 doi:10.1101/2023.02.17.529036 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Next-generation CRISPR gene-drive systems using Cas12a nuclease ]]> https://biorxiv.org/content/10.1101/2023.02.20.529271v1?rss=1 Sanz Juste, S. Okamoto, E. M. Feng, X. Del Amo, V. L. 2023-02-20 doi:10.1101/2023.02.20.529271 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Proteome allocation is linked to transcriptional regulation through a modularized transcriptome ]]> https://biorxiv.org/content/10.1101/2023.02.20.529291v1?rss=1 Patel, A. McGrosso, D. Hefner, Y. Campeau, A. Sastry, A. V. Maurya, S. Rychel, K. Gonzalez, D. J. Palsson, B. O. 2023-02-21 doi:10.1101/2023.02.20.529291 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Release of extracellular matrix components after human traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2023.02.23.529754v1?rss=1 Bambrick, M. Johnson, M. D. Esko, J. D. Choudhury, B. Gomez Toledo, A. Staley, K. J. Duhaime, A.-C. 2023-02-24 doi:10.1101/2023.02.23.529754 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Atypical Chemokine Receptor 3 'Senses' CXC Chemokine Receptor 4 Activation Through GPCR Kinase Phosphorylation ]]> https://biorxiv.org/content/10.1101/2023.02.25.530029v1?rss=1 Schafer, C. T. Chen, Q. Tesmer, J. J. G. Handel, T. M. 2023-02-26 doi:10.1101/2023.02.25.530029 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Small Molecule in situ Resin Capture - an Organism Independent Strategy for Natural Product Discovery. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530684v1?rss=1 Bogdanov, A. Salib, M. N. Chase, A. B. Hammerlindl, H. Muskat, M. N. Luedtke, S. O'Donoghue, A. J. Wu, L. F. Altschuler, S. J. Molinski, T. F. Jensen, P. R. 2023-03-03 doi:10.1101/2023.03.02.530684 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ CD4+ T cells display a spectrum of recall dynamics during re-infection with malaria parasites. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530907v1?rss=1 Lee, H. J. Moreira, M. d. L. Li, S. Williams, C. G. Skinner, O. P. Asad, S. Asatsuma, T. Bramhall, M. L. Jiang, Z. Engel, J. A. Soon, M. S. F. Straube, J. Barrera, I. Murray, E. Chen, F. Nideffer, J. F. Jagannathan, P. Haque, A. 2023-03-03 doi:10.1101/2023.03.02.530907 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Light-Guided Rabies Virus Tracing for Neural Circuit Analysis ]]> https://biorxiv.org/content/10.1101/2023.03.04.531104v1?rss=1 Zhang, S. Ma, Y. Ngamkanjanarat, W. Takahashi, S. Gibbs, D. Coleman, T. Doan, S. Kyriakakis, P. 2023-03-06 doi:10.1101/2023.03.04.531104 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Chromatin binding by HORMAD proteins regulates meiotic recombination initiation ]]> https://biorxiv.org/content/10.1101/2023.03.04.531117v1?rss=1 Milano, C. R. Ur, S. N. Gu, Y. Tromer, E. C. Zhang, J. Hochwagen, A. Corbett, K. D. 2023-03-05 doi:10.1101/2023.03.04.531117 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method ]]> https://biorxiv.org/content/10.1101/2023.03.05.531179v1?rss=1 Mikhaylov, V. Rzepka, M. Kawamura, T. Xia, Y. Chang, P. L. Zhou, S. Pham, L. Modi, N. Yao, L. Perez-Agustin, A. Pagans, S. Boles, T. C. Lei, M. Wang, Y. Garcia-Bassets, I. Chen, Z. 2023-03-06 doi:10.1101/2023.03.05.531179 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ FBP1 is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness ]]> https://biorxiv.org/content/10.1101/2023.03.05.531181v1?rss=1 Gu, L. Zhu, Y. Watari, K. Lee, M. Liu, J. Perez, S. Thai, M. Mayfield, J. Zhang, B. Rocha, K. C. e. Li, F. Kim, L. Jones, A. C. Wierzbicki, I. H. Liu, X. Newton, A. C. Kisseleva, T. Lee, J. H. Ying, W. Gonzalez, D. J. Saltiel, A. Simon, M. C. Karin, M. 2023-03-05 doi:10.1101/2023.03.05.531181 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors ]]> https://biorxiv.org/content/10.1101/2023.03.06.531398v1?rss=1 Lange, M. Granados, A. VijayKumar, S. Bragantini, J. Ancheta, S. Santhosh, S. Borja, M. Kobayashi, H. McGeever, E. Solak, A. C. Yang, B. Zhao, X. Liu, Y. Detweiler, A. Paul, S. Mekonen, H. Lao, T. Banks, R. Jacobo, A. Balla, K. Awayan, K. D'souza, S. Haase, R. Dizeux, A. Pourquie, O. Gomez-Sjoberg, R. Huber, G. Serra, M. Neff, N. Pisco, A. Royer, L. A. 2023-03-07 doi:10.1101/2023.03.06.531398 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks ]]> https://biorxiv.org/content/10.1101/2023.03.07.531453v1?rss=1 Li, H.-H. Su, M. P. Wu, S.-C. Tsou, H.-H. Chang, M.-C. Cheng, Y.-C. Tsai, K.-N. Wang, H.-W. Chen, G.-H. Tang, C.-K. Chung, P.-J. Tsai, W.-T. Huang, L.-R. Yueh, Y. A. Chen, H.-W. Pan, C.-Y. Akbari, O. Chang, H.-H. Yu, G.-Y. Marshall, J. M. CHEN, C.-H. 2023-03-07 doi:10.1101/2023.03.07.531453 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Synaptic changes in pallidostriatal circuits observed in parkinsonian model triggers abnormal beta synchrony with accurate spatio-temporal properties across the basal ganglia ]]> https://biorxiv.org/content/10.1101/2023.03.07.531640v1?rss=1 40Hz), whereas strong pallidostriatal loops drive low-{beta} (10-15Hz) oscillations. We show that pathophysiological strengthening of striatal and pallidal synapses following dopamine depletion leads to the emergence of synchronized oscillatory activity in the mid-{beta} range with spike-phase relationships between BG neuronal populations in-line with experiments. Furthermore, inhibition of GPe, contrary to STN, abolishes oscillations. Our modeling study uncovers the neural mechanisms underlying PD {beta} oscillations and may thereby guide the future development of therapeutic strategies. Significance statementIn Parkinsons disease, neural activity in subcortical nuclei called the basal ganglia displays abnormal oscillatory synchronization that constitutes an important biomarker for therapeutic effectiveness. The neural mechanisms for the generation of these oscillations remain unknown. Here, in a theoretical neuronal network model strongly constrained by anatomical and physiological data, we show that specific circuit modifications in basal ganglia connectivity during Parkinsons disease lead to the emergence of synchronized oscillatory activity in the network with properties that strongly agree with available experimental evidence. This and future theoretical investigations of the neural mechanisms underlying abnormal neuronal activity in Parkinsons disease are necessary to guide the future development of therapeutic strategies to ameliorate symptoms. ]]> Azizpour Lindi, S. Mallet, N. P. Leblois, A. 2023-03-10 doi:10.1101/2023.03.07.531640 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolopyrimidines as Potential Candidates to Treat Human African Trypanosomiasis ]]> https://biorxiv.org/content/10.1101/2023.03.11.532093v1?rss=1 Monti, L. Liu, L. J. Varricchio, C. Lucero, B. Alle, T. Yang, W. Bem-Shalom, I. Gilson, M. Brunden, K. R. Brancale, A. Caffrey, C. R. Ballatore, C. 2023-03-11 doi:10.1101/2023.03.11.532093 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics ]]> https://biorxiv.org/content/10.1101/2023.03.11.532245v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1edcea0org.highwire.dtl.DTLVardef@198a3c8org.highwire.dtl.DTLVardef@28d394org.highwire.dtl.DTLVardef@5a9dbb_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefThis work creates a prospectively biobanked phenotyped-genotyped Crohns disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTSO_LIProspectively biobanked CD-organoids recapitulate the disease epithelium in patients C_LIO_LIThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypes C_LIO_LIOne subtype shows impaired microbial clearance, another increased cellular senescence C_LIO_LIPhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics C_LI ]]> Tindle, C. Katkar, G. Fonseca, A. Taheri, S. Lee, J. Maity, P. Sayed, I. Ibeawuchi, S.-R. Vidales, E. Pranadinata, R. Fuller, M. Stec, D. Anandachar, M. S. Perry, K. Lee, H. Ear, J. Boland, B. Sandborn, W. Sahoo, D. Das, S. Ghosh, P. 2023-03-13 doi:10.1101/2023.03.11.532245 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ The landscape of cancer rewired GPCR signaling axes ]]> https://biorxiv.org/content/10.1101/2023.03.13.532291v1?rss=1 Raimondi, F. Arora, C. Matic, M. Rosa, N. D. O. Nemati, L. Clubb, L. Kargas, G. Vukotic, R. Licata, L. Wu, G. Gutkind, J. S. 2023-03-14 doi:10.1101/2023.03.13.532291 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome ]]> https://biorxiv.org/content/10.1101/2023.03.13.532310v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@196aefforg.highwire.dtl.DTLVardef@1bafcadorg.highwire.dtl.DTLVardef@122f502org.highwire.dtl.DTLVardef@35afd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Venkatraman, K. Lee, C. T. Garcia, G. C. Mahapatra, A. Perkins, G. Kim, K.-Y. Pasolli, H. A. Phan, S. Lippincott-Schwartz, J. Ellisman, M. Rangamani, P. Budin, I. 2023-03-15 doi:10.1101/2023.03.13.532310 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.03.16.532226v1?rss=1 Jones, A. C. Kornev, A. P. Weng, J.-H. Manning, G. C. Taylor, S. S. Newton, A. C. 2023-03-16 doi:10.1101/2023.03.16.532226 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Multiomic Analysis of Intercellular Communication through Tumor-Stroma Tunnels in Breast Cancers ]]> https://biorxiv.org/content/10.1101/2023.03.18.533175v1?rss=1 Sinha, S. Callow, B. Farfel, A. Roy, S. Chen, S. Rajendran, S. Buschhaus, J. Luker, K. E. Ghosh, P. Luker, G. D. 2023-03-21 doi:10.1101/2023.03.18.533175 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium ]]> https://biorxiv.org/content/10.1101/2023.03.18.533282v1?rss=1 Dunlap, G. S. Wagner, A. Meednu, N. Zhang, F. Jonsson, A. H. Wei, K. Sakaue, S. Nathan, A. Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (A, Bykerk, V. P. Donlin, L. T. Goodman, S. M. Firestein, G. S. Boyle, D. L. Holers, V. M. Moreland, L. W. Tabechian, D. Pitzalis, C. Filer, A. Raychaudhuri, S. Brenner, M. B. Rao, D. A. Anolik, J. 2023-03-21 doi:10.1101/2023.03.18.533282 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome Study ]]> https://biorxiv.org/content/10.1101/2023.03.21.533195v1?rss=1 Ecklu-Mensah, G. Choo-Kang, C. Maseng, M. G. Donato, S. Bovet, P. Bedu-Addo, K. Plange-Rhule, J. Forrester, T. E. Lambert, E. V. Rae, D. Luke, A. Layden, B. T. O'Keefe, S. Gilbert, J. A. Dugas, L. R. 2023-03-22 doi:10.1101/2023.03.21.533195 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition ]]> https://biorxiv.org/content/10.1101/2023.03.21.533564v1?rss=1 Lee, K. Cho, K. Morey, R. Cook-Andersen, H. 2023-03-23 doi:10.1101/2023.03.21.533564 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Unrecognized Potent Activities of Colistin Against Clinically Important mcr+ Enterobacteriaceae Revealed in Synergy with Host Immunity ]]> https://biorxiv.org/content/10.1101/2023.03.21.533661v1?rss=1 Kumaraswamy, M. Riestra, A. Flores, A. Uchiyama, S. Dahesh, S. Bondsater, G. Nilsson, V. Chang, M. Seo, H. Sakoulas, G. Nizet, V. 2023-03-21 doi:10.1101/2023.03.21.533661 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium ]]> https://biorxiv.org/content/10.1101/2023.03.21.533663v1?rss=1 Cordoza, J. L. Chen, P. Y.-T. Blaustein, L. R. Lima, S. T. Fiore, M. F. Chekan, J. R. Moore, B. S. McKinnie, S. M. K. 2023-03-21 doi:10.1101/2023.03.21.533663 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Flux exponent control predicts metabolic dynamics from network structure ]]> https://biorxiv.org/content/10.1101/2023.03.23.533708v1?rss=1 Xiao, F. Li, J. S. Doyle, J. C. 2023-03-25 doi:10.1101/2023.03.23.533708 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Kinetochore dynein is sufficient to biorient chromosomes and remodel the outer kinetochore ]]> https://biorxiv.org/content/10.1101/2023.03.23.534015v1?rss=1 Prevo, B. Cheerambathur, D. Earnshaw, W. C. Desai, A. 2023-03-24 doi:10.1101/2023.03.23.534015 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Pulmonary vein flow split effects in patient-specific simulations of left atrial flow ]]> https://biorxiv.org/content/10.1101/2023.03.24.534045v1?rss=1 Duran, E. Garcia-Villalba, M. Martinez-Legazpi, P. Gonzalo, A. McVeigh, E. Kahn, A. M. Bermejo, J. Flores, O. del Alamo, J. C. 2023-03-25 doi:10.1101/2023.03.24.534045 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network ]]> https://biorxiv.org/content/10.1101/2023.03.24.534160v1?rss=1 Karabay, E. T. Turnlund, A. Grear, J. Fraley, S. I. Katira, P. 2023-03-27 doi:10.1101/2023.03.24.534160 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Scaling deep phylogenetic embedding to ultra-large reference trees: a tree-aware ensemble approach ]]> https://biorxiv.org/content/10.1101/2023.03.27.534201v1?rss=1 Jiang, Y. McDonald, D. Knight, R. Mirarab, S. 2023-03-29 doi:10.1101/2023.03.27.534201 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Tools and methods for high-throughput single-cell imaging with the mother machine ]]> https://biorxiv.org/content/10.1101/2023.03.27.534286v1?rss=1 Thiermann, R. Sandler, M. Ahir, G. Sauls, J. T. Schroeder, J. W. Brown, S. D. Le Treut, G. Si, F. Li, D. Wang, J. Jun, S. 2023-03-29 doi:10.1101/2023.03.27.534286 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Hyperconnectivity of two separate long-range cholinergic systems contributes to the reorganization of the brain functional connectivity during nicotine withdrawal in male mice ]]> https://biorxiv.org/content/10.1101/2023.03.29.534836v1?rss=1 Carrette, L. L. G. Kimbrough, A. Davoudian, P. A. Kwan, A. C. Collazo, A. George, O. 2023-03-31 doi:10.1101/2023.03.29.534836 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Role of DNA-DNA sliding friction and non-equilibrium dynamics in viral genome ejection and packaging ]]> https://biorxiv.org/content/10.1101/2023.04.03.535472v1?rss=1 Fizari, M. Keller, N. Jardine, P. J. Smith, D. E. 2023-04-05 doi:10.1101/2023.04.03.535472 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis ]]> https://biorxiv.org/content/10.1101/2023.04.04.535621v1?rss=1 Reich, M. M. Tabor, T. Liefeld, T. joshi, j. Kim, F. Thorvaldsdottir, H. Blankenberg, D. Mesirov, J. P. 2023-04-06 doi:10.1101/2023.04.04.535621 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Development of subunit selective substrates for Trichomonas vaginalis proteasome ]]> https://biorxiv.org/content/10.1101/2023.04.05.535794v1?rss=1 Fajtova, P. Hurysz, B. Miyamoto, Y. Serafim, M. Jiang, Z. Trujillo, D. F. Liu, L. J. Somani, U. Almaliti, J. Myers, S. Caffrey, C. Gerwick, W. H. Kirk, C. J. Boura, E. Eckmann, L. O'Donoghue, A. J. 2023-04-06 doi:10.1101/2023.04.05.535794 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex ]]> https://biorxiv.org/content/10.1101/2023.04.08.536119v1?rss=1 Zemke, N. R. Armand, E. J. Wang, W. Lee, S. Zhou, J. Li, Y. E. Liu, H. Tian, W. Nery, J. R. Castanon, R. G. Bartlett, A. Osteen, J. K. Li, D. Zhuo, X. Xu, V. Miller, M. Krienen, F. M. Zhang, Q. Taskin, N. Ting, J. Feng, G. McCarroll, S. A. Callaway, E. M. Wang, T. Behrens, M. Lein, E. S. Ecker, J. R. Ren, B. 2023-04-08 doi:10.1101/2023.04.08.536119 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Do perineuronal nets stabilize the engram of a synaptic circuit? ]]> https://biorxiv.org/content/10.1101/2023.04.09.536164v1?rss=1 Lev-Ram, V. Palida, S. Deerinck, T. J. Bushong, E. A. Toyoma, B. H. Perez, A. McClatchy, D. B. Prichard, D. R. Savas, J. N. Ellisman, M. H. Yates, J. R. Tsien, R. Y. 2023-04-09 doi:10.1101/2023.04.09.536164 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Diverse Gut Pathogens Exploit the Host Engulfment Pathway via a Conserved Mechanism ]]> https://biorxiv.org/content/10.1101/2023.04.09.536168v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@21dbcorg.highwire.dtl.DTLVardef@ee27ccorg.highwire.dtl.DTLVardef@176f2c4org.highwire.dtl.DTLVardef@3c55e6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Anandachar, M. S. Agyekum, B. Sinha, S. Roy, S. Ibeawuchi, S.-R. Gementera, H. Amamoto, A. Katkar, G. D. Ghosh, P. 2023-04-09 doi:10.1101/2023.04.09.536168 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack ]]> https://biorxiv.org/content/10.1101/2023.04.10.536170v1?rss=1 Nobori, T. Monell, A. Lee, T. A. Zhou, J. Nery, J. R. Ecker, J. R. 2023-04-10 doi:10.1101/2023.04.10.536170 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Spatial proteomics of human diabetic kidney disease, from health to class III ]]> https://biorxiv.org/content/10.1101/2023.04.12.534028v1?rss=1 Kondo, A. McGrady, M. Nallapothula, D. Ali, H. Trevino, A. E. Lam, A. Preska, R. D'Angio, H. B. Wu, Z. Lopez, L. N. Badhesha, H. K. Vargas, C. R. Ramesh, A. Wiegley, N. Han, S. S. Dall'Era, M. Jen, K.-Y. Mayer, A. Afkarian, M. 2023-04-12 doi:10.1101/2023.04.12.534028 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Automatic Discovery of Cognitive Strategies with Tiny Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/2023.04.12.536629v1?rss=1 Ji-An, L. Benna, M. K. Mattar, M. G. 2023-04-13 doi:10.1101/2023.04.12.536629 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Building functional circuits in multispecies brains. ]]> https://biorxiv.org/content/10.1101/2023.04.13.536815v1?rss=1 Throesch, B. Imtiaz, M. K. Munoz-Castaneda, R. Sakurai, M. James, K. N. Rodriguez, A. Martin, G. S. Lippi, G. Kuprianov, S. Wu, Z. Osten, P. Belmonte, J. C. I. Wu, J. Baldwin, K. K. 2023-04-15 doi:10.1101/2023.04.13.536815 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae ]]> https://biorxiv.org/content/10.1101/2023.04.15.537036v1?rss=1 Morrill, S. R. Saha, S. Varki, A. P. Lewis, W. G. Ram, S. Lewis, A. L. 2023-04-15 doi:10.1101/2023.04.15.537036 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain ]]> https://biorxiv.org/content/10.1101/2023.04.16.536509v1?rss=1 Liu, H. Zeng, Q. Zhou, J. Bartlett, A. Wang, B.-A. Berube, P. Tian, W. Kenworthy, M. Altshul, J. Nery, J. R. Chen, H. Castanon, R. G. Zu, S. Li, Y. E. Lucero, J. Osteen, J. K. Pinto-Duarte, A. Lee, J. Rink, J. Cho, S. Emerson, N. Nunn, M. O'Connor, C. Yao, Z. Tasic, B. Smith, K. A. Zeng, H. Luo, C. Dixon, J. R. Ren, B. Behrens, M. M. Ecker, J. R. 2023-04-18 doi:10.1101/2023.04.16.536509 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Incongruence between transcriptional and vascular pathophysiological cell states ]]> https://biorxiv.org/content/10.1101/2023.04.16.537057v1?rss=1 Fernandez-Chacon, M. Muhleder, S. Regano, A. Garcia-Ortega, L. Torroja, C. Lytvyn, M. Sanchez-Munoz, M. S. Casquero-Garcia, V. Camafeita, E. Vazquez, J. Benguria, A. Dopazo, A. Sanchez-Cabo, F. Carter, H. Benedito, R. 2023-04-17 doi:10.1101/2023.04.16.537057 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Distinct blood CD3+ CD14+ T Cell-Monocyte complexes harbor HIV and are dynamic, glucose-dependent, and increased in individuals with glucose intolerance ]]> https://biorxiv.org/content/10.1101/2023.04.24.538020v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@fdc324org.highwire.dtl.DTLVardef@168fc4org.highwire.dtl.DTLVardef@138a9a0org.highwire.dtl.DTLVardef@1087108_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICirculating CD3+ CD14+ T cell-monocyte complexes are higher in individuals with diabetes. C_LIO_LICD3+ CD14+ T cell-monocytes complexes comprise a heterogenous group of functional and dynamic cell-cell interactions. C_LIO_LIThe proportion of CD3+ CD14+ T cell-monocyte complexes is positively associated with fasting blood glucose and negatively with plasma IL-10 levels and CD4+ T regulatory cells. C_LIO_LICD3+ CD14+ T cell-monocyte complexes are metabolically flexible and can utilize both glycolysis and oxidative phosphorylation for their energy requirements. C_LIO_LIIn persons with treated HIV, CD3+ CD14+ T cell-monocytes have more detectable HIV DNA than circulating CD4+ T cells alone. C_LI ]]> Wanjalla, C. N. Simmons, J. Oakes, J. Zhang, X. Nochowivz, C. Priest, S. Bailin, S. S. Watten, C. M. Mashayekhi, M. Beasley, H. K. Wang, J. Meenderink, L. M. Sheng, Q. Stolze, J. Gangula, R. Chopra, A. Gabriel, C. L. Temu, T. Pakala, S. Wilfong, E. M. Gianella, S. Phillips, E. J. Harrison, D. G. Hinton, A. Kalams, S. A. Mallal, S. A. Koethe, J. R. 2023-04-26 doi:10.1101/2023.04.24.538020 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution ]]> https://biorxiv.org/content/10.1101/2023.04.26.538152v1?rss=1 Epstein, H. E. Brown, T. Akinrinade, A. O. McMinds, R. Pollock, F. J. Sonett, D. Smith, S. Bourne, D. G. Carpenter, C. S. Knight, R. Willis, B. L. Medina, M. Lamb, J. B. Thurber, R. V. Zaneveld, J. R. 2023-04-26 doi:10.1101/2023.04.26.538152 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ TorsinA is essential for the timing and localization of neuronal nuclear pore complex biogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.26.538491v1?rss=1 Kim, S. Phan, S. Shaw, T. R. Ellisman, M. H. Veatch, S. L. Barmada, S. J. Pappas, S. S. Dauer, W. T. 2023-04-27 doi:10.1101/2023.04.26.538491 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols ]]> https://biorxiv.org/content/10.1101/2023.04.28.538741v1?rss=1 Forry, S. P. Servetas, S. L. Kralj, J. G. Soh, K. Hadjithomas, M. Carlin, M. de Amorim, M. G. Bartelli, T. F. Bustamante, J. P. Cassol, I. Chalita, M. Dias-Neto, E. Gohl, D. Kazantseva, J. Menzel, P. Moda, B. S. Neuberger-Castillo, L. Nunes, D. Peralta, R. D. Saliou, A. Schwarzer, R. Takenaka, I. K. T. M. Wang, J. Knight, R. Jackson, S. A. 2023-04-28 doi:10.1101/2023.04.28.538741 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by L. iners regardless of HPV status ]]> https://biorxiv.org/content/10.1101/2023.05.05.539619v1?rss=1 Vargas Robles, D. Romaguera, J. Alvarado-Velez, I. Tosado-Rodriguez, E. Dominicci-Maura, A. Sanchez, M. Wiggin, K. Martinez-Ferrer, M. Gilbert, J. A. Forney, L. J. Godoy-Vitorino, F. 2023-05-09 doi:10.1101/2023.05.05.539619 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Robust identification of perturbed cell types in single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.05.06.539326v1?rss=1 Nicol, P. B. Paulson, D. Qian, G. Liu, X. S. Irizarry, R. A. Sahu, A. D. 2023-05-08 doi:10.1101/2023.05.06.539326 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Optogenetic inhibition of Gα signalling alters and regulates circuit functionality and early circuit formation ]]> https://biorxiv.org/content/10.1101/2023.05.06.539674v1?rss=1 Lockyer, J. L. Reading, A. Vicenzi, S. Delandre, C. Marshall, O. J. Gasperini, R. Foa, L. Lin, J. Y.-l. 2023-05-08 doi:10.1101/2023.05.06.539674 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ The subiculum encodes environmental geometry ]]> https://biorxiv.org/content/10.1101/2023.05.07.539721v1?rss=1 Sun, Y. Nitz, D. A. Xu, X. Giocomo, L. M. 2023-05-07 doi:10.1101/2023.05.07.539721 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Molecular signatures associated with successful implantation of the human blastocyst ]]> https://biorxiv.org/content/10.1101/2023.05.09.539763v1?rss=1 Cook-Andersen, H. Chousal, J. N. Srinivasan, S. Lee, K. To, C. Cho, K. Zhang, W. Yeo, A. L. Garzo, V. G. Parast, M. M. Laurent, L. C. 2023-05-09 doi:10.1101/2023.05.09.539763 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection ]]> https://biorxiv.org/content/10.1101/2023.05.10.540184v1?rss=1 Bajpe, H. Rychel, K. Lamoureux, C. Sastry, A. V. Palsson, B. O. 2023-05-10 doi:10.1101/2023.05.10.540184 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Generalized fear following acute stress is caused by change in co-transmitter identity of serotonergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.10.540268v1?rss=1 Li, H.-q. L. Jiang, W. Ling, L. Gupta, V. Chen, C. Pratelli, M. Godavarthi, S. K. Spitzer, N. C. 2023-05-11 doi:10.1101/2023.05.10.540268 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.05.16.541025v1?rss=1 Rodionova, I. A. Lim, H. Rodionov, D. A. Hutchison, Y. Dalldorf, C. Gao, Y. Monk, J. Palsson, B. O. 2023-05-16 doi:10.1101/2023.05.16.541025 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family ]]> https://biorxiv.org/content/10.1101/2023.05.16.541042v1?rss=1 Rajput, A. Chauhan, S. M. Mohite, O. S. Hyun, J. C. Ardalani, O. Jahn, L. J. Sommer, M. O. Palsson, B. O. 2023-05-16 doi:10.1101/2023.05.16.541042 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Deep learning and host variable embedding augment microbiome-based simultaneous detection of multiple diseases ]]> https://biorxiv.org/content/10.1101/2023.05.16.541058v1?rss=1 Wu, S. Li, Z. Chen, Y. Zhang, M. Sun, Y. Xing, J. Zhao, F. Huang, S. Knight, R. Su, X. 2023-05-18 doi:10.1101/2023.05.16.541058 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Identification of the bacteriophage nucleus protein interaction network ]]> https://biorxiv.org/content/10.1101/2023.05.18.541317v1?rss=1 Enustun, E. Deep, A. Gu, Y. Nguyen, K. T. Chaikeeratisak, V. Armbruster, E. Ghassemian, M. Villa, E. Pogliano, J. Corbett, K. D. 2023-05-18 doi:10.1101/2023.05.18.541317 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Unsupervised Machine Learning Identifies Chromatin Accessibility Regulatory Networks that Define Cell State Transitions in Pluripotency ]]> https://biorxiv.org/content/10.1101/2023.05.20.541447v1?rss=1 Arthur, T. D. Nguyen, J. P. D'Antonio-Chronowska, A. Matsui, H. Silva, N. Joshua, I. N. iPSCORE Consortium, Young Greenwald, W. W. D'Antonio, M. Pera, M. F. Frazer, K. A. 2023-05-22 doi:10.1101/2023.05.20.541447 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Do cortical co-ripples bind lines, letters, words, meanings, strategy and action in reading? ]]> https://biorxiv.org/content/10.1101/2023.05.20.541597v1?rss=1 12cm), especially when many areas were co-rippling. General co-activation, indexed by non-oscillatory high gamma, was mainly confined to early latencies in fusiform and earlier visual areas, preceding co-ripples. These findings suggest that widespread synchronous co-ripples may assist the integration of multiple cortical areas for sustained periods during cognition. One Sentence SummaryWidespread visual, wordform, semantic, executive and response areas phase-lock at 90Hz during integrative semantic processing. ]]> Garrett, J. C. Verzhbinsky, I. A. Kaestner, E. Carlson, C. Doyle, W. K. Devinsky, O. Thesen, T. Halgren, E. 2023-05-22 doi:10.1101/2023.05.20.541597 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ A pancreatic cancer mouse model with human immunity ]]> https://biorxiv.org/content/10.1101/2023.05.24.542127v1?rss=1 Miyamura, N. Suzuki, K. Friedman, R. A. Floratos, A. Kunisada, Y. Masuda, K. Lowy, A. M. Tsuji, M. Sugahara, K. N. 2023-05-24 doi:10.1101/2023.05.24.542127 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Projectome-defined subtypes and modular intra-hypothalamic subnetworks of peptidergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.25.542241v1?rss=1 Jiao, Z. Gao, T. Wang, X. Zhang, W. Biglari, N. Boxer, E. E. Steuernagel, L. Ding, X. Yu, Z. Li, M. Hao, M. Zhou, H. Cao, X. Li, S. Jiang, T. Qi, J. Jia, X. Feng, Z. Ren, B. Chen, Y. Shi, X. Wang, D. Wang, X. Han, L. Liang, Y. Wang, C. Li, E. Hu, Y. Tao, Z. Li, H. Xiang, Y. Xu, M. Chang, H.-C. Zhang, Y. Xu, H.-t. Yan, J. Li, A. Luo, Q. Stoop, R. Sternson, S. Bruning, J. C. Poo, M.-m. Anderson, D. J. Gong, H. Sun, Y. Xu, X.-H. 2023-05-25 doi:10.1101/2023.05.25.542241 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Glaucoma-associated Optineurin mutations increase transmitophagy in a vertebrate optic nerve ]]> https://biorxiv.org/content/10.1101/2023.05.26.542507v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@c1d3d4org.highwire.dtl.DTLVardef@13a33e6org.highwire.dtl.DTLVardef@2544beorg.highwire.dtl.DTLVardef@c456a5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jeong, Y. Davis, c.-h. Muscarella, A. Deshpande, V. Kim, K.-Y. Ellisman, M. Marsh-Armstrong, N. 2023-05-30 doi:10.1101/2023.05.26.542507 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses ]]> https://biorxiv.org/content/10.1101/2023.05.26.542519v1?rss=1 Zhao, J. Chen, K. Palsson, B. O. Yang, L. 2023-05-26 doi:10.1101/2023.05.26.542519 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species ]]> https://biorxiv.org/content/10.1101/2023.05.26.542542v1?rss=1 Hyun, J. C. Monk, J. M. Szubin, R. Hefner, Y. Palsson, B. 2023-05-28 doi:10.1101/2023.05.26.542542 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Replication initiation in bacteria: precision control based on protein counting ]]> https://biorxiv.org/content/10.1101/2023.05.26.542547v1?rss=1 Fu, H. Xiao, F. Jun, S. 2023-05-27 doi:10.1101/2023.05.26.542547 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization ]]> https://biorxiv.org/content/10.1101/2023.05.28.542535v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@553e82org.highwire.dtl.DTLVardef@7add7dorg.highwire.dtl.DTLVardef@637549org.highwire.dtl.DTLVardef@1a9236a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phan, T. M. Kim, Y. C. Debelouchina, G. Mittal, J. 2023-05-30 doi:10.1101/2023.05.28.542535 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Emergence of Darwinian evolution in Bayesian collectives ]]> https://biorxiv.org/content/10.1101/2023.05.29.542733v1?rss=1 Csillag, M. Giaffar, H. Szathmary, E. Czegel, D. 2023-06-01 doi:10.1101/2023.05.29.542733 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Efficient multi-fidelity computation of blood coagulation under flow ]]> https://biorxiv.org/content/10.1101/2023.05.29.542763v1?rss=1 Guerrero-Hurtado, M. Garcia-Villalba, M. Gonzalo, A. Martinez-Legazpi, P. Kahn, A. M. McVeigh, E. Bermejo, J. del Alamo, J. C. Flores, O. 2023-06-01 doi:10.1101/2023.05.29.542763 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.05.30.542936v1?rss=1 Castillon, G. A. Phan, S. Hu, J. Boassa, D. Adams, S. R. Ellisman, M. H. 2023-05-31 doi:10.1101/2023.05.30.542936 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Cell motility modes are selected by the interplay of mechanosensitive adhesion and membrane tension ]]> https://biorxiv.org/content/10.1101/2023.05.31.543156v1?rss=1 Chen, Y. Saintillan, D. Rangamani, P. 2023-06-01 doi:10.1101/2023.05.31.543156 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ A novel method for tracking nitrogen kinetics in vivo and ex vivo using radioactive nitrogen-13 gas and Positron Emission Tomography ]]> https://biorxiv.org/content/10.1101/2023.06.01.543280v1?rss=1 Ashworth, E. Ogawa, R. Vera, D. R. Lindholm, P. 2023-06-05 doi:10.1101/2023.06.01.543280 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ A Boltzmann model predicts glycan structures from lectin binding ]]> https://biorxiv.org/content/10.1101/2023.06.03.543532v1?rss=1 Yom, A. CHIANG, W.-T. Lewis, N. 2023-06-06 doi:10.1101/2023.06.03.543532 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Activation of the TRIF pathway and downstream targets results in the development of precancerous lesions during infection with Helicobacter. ]]> https://biorxiv.org/content/10.1101/2023.06.04.543598v1?rss=1 Bali, P. Lozano-Pope, I. Hernandez, J. Estrada, M. V. Corr, M. Turner, M. A. Bouvet, M. Benner, C. Obonyo, M. 2023-06-06 doi:10.1101/2023.06.04.543598 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Engineering cell and nuclear morphology on nano topography by contact-free protein micropatterning ]]> https://biorxiv.org/content/10.1101/2023.06.05.543791v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1b3a13dorg.highwire.dtl.DTLVardef@1edbdaorg.highwire.dtl.DTLVardef@1f3e40corg.highwire.dtl.DTLVardef@100d6fc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sarikhani, E. Pushpa Meganathan, D. Rahmani, K. Tsai, C.-T. Marquez-Serrano, A. Li, X. Santoro, F. Cui, B. Hyldgaard Klausen, L. Jahed, Z. 2023-06-07 doi:10.1101/2023.06.05.543791 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle ]]> https://biorxiv.org/content/10.1101/2023.06.06.542650v1?rss=1 Birnbaum, S. K. Cohen, J. D. Belfi, A. Murray, J. I. Adams, J. R. G. Chisholm, A. D. Sundaram, M. V. 2023-06-07 doi:10.1101/2023.06.06.542650 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The chromatin landscape of healthy and injured cell types in the human kidney ]]> https://biorxiv.org/content/10.1101/2023.06.07.543965v1?rss=1 Gisch, D. L. Brennan, M. Lake, B. B. Basta, J. Keller, M. Melo Ferreira, R. Akilesh, S. Ghag, R. Lu, C. Cheng, Y.-H. Collins, K. S. Parikh, S. V. Rovin, B. H. Robbins, L. Conklin, K. Y. Diep, D. Zhang, B. Knoten, A. Barwinska, D. Asghari, M. Sabo, A. R. Ferkowicz, M. J. Sutton, T. A. Kelly, K. J. De Boer, I. H. Rosas, S. E. Kiryluk, K. Hodgin, J. B. Alakwaa, F. Jefferson, N. Gaut, J. P. Gehlenborg, N. Phillips, C. L. El-Achkar, T. M. Dagher, P. C. Hato, T. Zhang, K. Himmelfarb, J. Kretzler, M. Mollah, S. Kidney Precision Medicine Project, Jain, S. Ra 2023-06-10 doi:10.1101/2023.06.07.543965 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Large-scale map of RNA binding protein interactomes across the mRNA life-cycle ]]> https://biorxiv.org/content/10.1101/2023.06.08.544225v1?rss=1 Rothamel, K. Street, L. Brannan, K. Jin, W. Rhine, K. Al-Azzam, N. Wolin, E. Bokor, B. Abdou, A. Doron-Mandel, E. W. Kim, J. Ma, Y. Ahdout, J. Dong, K. Madrigel, A. Mujumba, M. Jovanovic, M. Yeo, G. W. 2023-06-08 doi:10.1101/2023.06.08.544225 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration. ]]> https://biorxiv.org/content/10.1101/2023.06.12.544338v1?rss=1 Correia, J. C. Jannig, P. R. Gosztyla, M. L. Cervenka, I. Ducommun, S. Praestholm, S. M. Dumont, K. D. Liu, Z. Liang, Q. Edsgard, D. Emanuelsson, O. Gregorevic, P. Westerblad, H. Venckunas, T. Brazaitis, M. Kamandulis, S. Lanner, J. T. Yeo, G. W. Ruas, J. L. 2023-06-13 doi:10.1101/2023.06.12.544338 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ High-Resolution Characterization of Human Brain Cortex with High-Fidelity Spatial Transcriptomic Slides (HiFi-Slides) ]]> https://biorxiv.org/content/10.1101/2023.06.12.544625v1?rss=1 Xu, T. Zhu, E. Zhang, C. Calandrelli, R. Lin, P. Zhong, S. 2023-06-13 doi:10.1101/2023.06.12.544625 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration ]]> https://biorxiv.org/content/10.1101/2023.06.16.545370v1?rss=1 Liefeld, T. Huang, E. Wenzel, A. T. Yoshimoto, K. Sharma, A. K. Sicklick, J. K. Mesirov, J. P. Reich, M. M. 2023-06-18 doi:10.1101/2023.06.16.545370 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Nyctinastic leaf folding mimic reduces herbivory by Chromacris trogon grasshoppers (Orthoptera:Romaleidae) ]]> https://biorxiv.org/content/10.1101/2023.06.16.545391v1?rss=1 Bell, A. B. 2023-06-18 doi:10.1101/2023.06.16.545391 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Spatiotemporal Control of Genomics and Epigenomics by Ultrasound ]]> https://biorxiv.org/content/10.1101/2023.06.21.544125v1?rss=1 Wu, Y. Huang, Z. Liu, Y. Yoon, C.-W. Sun, K. Situ, Y. Ho, P. Yuan, Z. Zhu, L. Eyquem, J. Zhao, Y. Liu, T. Kwong, G. A. Chien, S. Wang, Y. 2023-06-23 doi:10.1101/2023.06.21.544125 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Liquid-like condensates mediate competition between actin branching and bundling ]]> https://biorxiv.org/content/10.1101/2023.06.23.546267v1?rss=1 Graham, K. Chandrasekaran, A. Wang, L. Yang, N. Lafer, E. M. Rangamani, P. Stachowiak, J. C. 2023-06-26 doi:10.1101/2023.06.23.546267 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Luminal transport rates through intact endoplasmic reticulum limit the magnitude of localized Ca2+ signals ]]> https://biorxiv.org/content/10.1101/2023.06.23.546357v1?rss=1 Crapart, C. Scott, Z. C. Konno, T. Sharma, A. Bailey, D. M. Avezov, E. Koslover, E. F. 2023-06-26 doi:10.1101/2023.06.23.546357 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ CaBLAM! A high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase ]]> https://biorxiv.org/content/10.1101/2023.06.25.546478v1?rss=1 Lambert, G. G. Crespo, E. L. Murphy, J. Boassa, D. Luong, S. Hu, J. Sprecher, B. Tree, M. O. Orcutt, R. Heydari, D. Bell, A. B. Torreblanca Zanca, A. Hakimi, A. Lipscombe, D. Moore, C. I. Hochgeschwender, U. Shaner, N. C. 2023-06-26 doi:10.1101/2023.06.25.546478 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Cell Type- and Tissue-specific Enhancers in Craniofacial Development ]]> https://biorxiv.org/content/10.1101/2023.06.26.546603v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@7595a9org.highwire.dtl.DTLVardef@1b48b81org.highwire.dtl.DTLVardef@32fe86org.highwire.dtl.DTLVardef@1e41fed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rajderkar, S. S. Paraiso, K. Amaral, M. L. Kosicki, M. Cook, L. Darbellay, F. Spurrell, C. Osterwalder, M. Zhu, Y. Wu, H. Afzal, S. Y. Blow, M. Kelman, G. Barozzi, I. Fukuda-Yuzawa, Y. Akiyama, J. A. Afzal, V. Tran, S. Plajzer-Frick, I. Novak, C. S. Kato, M. Hunter, R. D. von Maydell, K. Wang, A. Lin, L. Preissl, S. Lisgo, S. Ren, B. Dickel, D. E. Pennacchio, L. A. Visel, A. 2023-06-26 doi:10.1101/2023.06.26.546603 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain ]]> https://biorxiv.org/content/10.1101/2023.06.28.546457v1?rss=1 Luo, Z. Wen, X. Zhao, W. Nguyen, T. Wan, X. Richard, J. L. C. Zhong, S. 2023-06-29 doi:10.1101/2023.06.28.546457 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2023.07.03.547507v1?rss=1 Inamo, J. Keegan, J. Griffith, A. Ghosh, T. Horisberger, A. Howard, K. Pulford, J. Murzin, E. Hancock, B. Jonsson, A. H. Seifert, J. Feser, M. L. Norris, J. M. Cao, Y. Apruzzese, W. Bridges, S. L. Bykerk, V. Goodman, S. Donlin, L. Firestein, G. S. Perlman, H. Bathon, J. M. Hughes, L. B. Tabechian, D. Filer, A. Pitzalis, C. H. Anolik, J. Moreland, L. Guthridge, J. M. James, J. A. Brenner, M. B. Raychaudhuri, S. Sparks, J. A. The Accelerating Medicines Partnership RA/SLE Network, Holers, V. M. Deane, K. D. Lederer, J. A. Rao, D. A. Zhang, F. 2023-07-04 doi:10.1101/2023.07.03.547507 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Covalent macrocyclic proteasome inhibitors mitigate resistance in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2023.07.03.547579v1?rss=1 Bennett, J. M. Ward, K. E. Muir, R. Kabeche, S. Yoo, E. Yeo, T. Lam, G. Berger, G. Faucher, F. F. Lin, G. Gerwick, W. H. Yeh, E. Fidock, D. A. Bogyo, M. 2023-07-03 doi:10.1101/2023.07.03.547579 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Exposure to constant artificial light alters honey bee sleep rhythms and disrupts sleep ]]> https://biorxiv.org/content/10.1101/2023.07.03.547605v1?rss=1 Kim, A. Y. Velazquez, A. Saavedra, B. Smarr, B. Nieh, J. C. 2023-07-04 doi:10.1101/2023.07.03.547605 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains ]]> https://biorxiv.org/content/10.1101/2023.07.04.547722v1?rss=1 Goudarzi, S. Pagadala, M. Klie, A. Talwar, J. Carter, H. 2023-07-07 doi:10.1101/2023.07.04.547722 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ A conserved antigen induces respiratory Th17-mediated serotype-independent protection against pneumococcal superinfection ]]> https://biorxiv.org/content/10.1101/2023.07.07.548156v1?rss=1 Liu, X. Van Maele, L. Matarazzo, L. Soulard, D. Alves Duarte da Silva, V. de Bakker, V. Denereaz, J. Bock, F. P. Taschner, M. Gruber, S. Nizet, V. Sirard, J.-C. Veening, J.-W. 2023-07-07 doi:10.1101/2023.07.07.548156 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment ]]> https://biorxiv.org/content/10.1101/2023.07.10.548264v1?rss=1 Diaz-Gay, M. Vangara, R. Barnes, M. Wang, X. Islam, S. M. A. Vermes, I. Narasimman, N. B. Yang, T. Jiang, Z. Moody, S. Senkin, S. Brennan, P. Stratton, M. Alexandrov, L. B. 2023-07-11 doi:10.1101/2023.07.10.548264 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.07.10.548468v1?rss=1 Kim, J. Y. Yang, J. E. Mitchell, J. W. English, L. A. Yang, S. Z. Tenpas, T. Dent, E. W. Wildonger, J. Wright, E. R. 2023-07-11 doi:10.1101/2023.07.10.548468 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Systems Age: A single blood methylation test to quantify aging heterogeneity across 11 physiological systems ]]> https://biorxiv.org/content/10.1101/2023.07.13.548904v1?rss=1 Sehgal, R. Meer, M. Shadyab, A. H. Casanova, R. Manson, J. E. Bhatti, P. Crimmins, E. M. Assimes, T. L. Whitsel, E. A. Higgins-Chen, A. T. Levine, M. 2023-07-17 doi:10.1101/2023.07.13.548904 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection ]]> https://biorxiv.org/content/10.1101/2023.07.14.548955v1?rss=1 Aiyer, S. Baldwin, P. R. Tan, S. M. Shan, Z. Oh, J. Mehrani, A. Bowman, M. E. Louie, G. Passos, D. O. Đorđevic-Marquardt, S. Mietzsch, M. Hull, J. A. Hoshika, S. Barad, B. A. Grotjahn, D. McKenna, R. Agbandje-Mckenna, M. Benner, S. A. Noel, J. P. Wang, D. Tan, Y. Z. Lyumkis, D. 2023-07-15 doi:10.1101/2023.07.14.548955 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Glycan-specific IgM is critical for human immunity to Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.07.14.548956v1?rss=1 Hendriks, A. M. Kerkman, P. F. Varkila, M. R. Haitsma-Mulier, J. L. Ali, S. ten Doesschate, T. van der Vaart, T. W. de Haas, C. J. C. Aerts, P. C. Cremer, O. L. Bonten, M. J. Nizet, V. Liu, G. Y. Codee, J. D. C. Rooijakkers, S. H. van Strijp, J. A. van Sorge, N. M. 2023-07-14 doi:10.1101/2023.07.14.548956 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ The MEK-ERK signaling pathway promotes maintenance of cardiac chamber identity ]]> https://biorxiv.org/content/10.1101/2023.07.17.549343v1?rss=1 Yao, Y. Yelon, D. 2023-07-19 doi:10.1101/2023.07.17.549343 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Contrasting roles of different mismatch repair proteins in basal-like breast cancer ]]> https://biorxiv.org/content/10.1101/2023.07.20.549745v1?rss=1 Mo, J. Borcherding, N. Jo, S. Tithi, T. I. Cho, E. Cash, C. E. Honda, M. Ahmed, K. K. kolb, R. Weigel, R. Spies, M. Zhang, W. 2023-07-22 doi:10.1101/2023.07.20.549745 Cold Spring Harbor Laboratory Press 2023-07-22 <![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[ Altered Fhod3 Expression Involved in Progressive High-Frequency Hearing Loss via Dysregulation of Actin Polymerization Stoichiometry in The Cuticular Plate ]]> https://biorxiv.org/content/10.1101/2023.07.20.549974v1?rss=1 Boussaty, E. C. Ninoyu, Y. Andrade, L. Li, Q. Ohyama, T. Wahlin, K. J. Manor, U. Friedman, R. A. 2023-07-25 doi:10.1101/2023.07.20.549974 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia ]]> https://biorxiv.org/content/10.1101/2023.07.21.549930v1?rss=1 Haney, M. Palovics, R. Munson, C. Long, C. Johansson, P. Yip, O. Dong, W. Rawat, E. West, E. Schlachetzki, J. Tsai, A. P.-Y. Guldner, I. Lamichhane, B. Smith, A. Schaum, N. Calcuttawala, K. Shin, A. Wang, Y.-H. Wang, C. Koutsodendris, N. Serrano, G. E. Beach, T. Reiman, E. M. Glass, C. Abu-Remaileh, M. M. Enejder, A. Huang, Y. Wyss-Coray, T. 2023-07-25 doi:10.1101/2023.07.21.549930 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction ]]> https://biorxiv.org/content/10.1101/2023.07.26.550757v1?rss=1 Poudel, S. Hyun, J. C. Hefner, Y. Monk, J. Nizet, V. Palsson, B. O. 2023-07-29 doi:10.1101/2023.07.26.550757 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework ]]> https://biorxiv.org/content/10.1101/2023.07.26.550768v1?rss=1 Liang, C. Murray, S. Li, Y. Lee, R. Low, A. Sasaki, S. Chiang, W.-T. Lin, W.-J. Mathews, J. Barnes, W. Lewis, N. E. 2023-07-28 doi:10.1101/2023.07.26.550768 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus ]]> https://biorxiv.org/content/10.1101/2023.07.27.550855v1?rss=1 Liang, Z. Gilbreath, C. Liu, W. Wang, Y. Zhang, M. Q. Zhang, D.-E. Wu, S. Fu, X.-D. 2023-07-27 doi:10.1101/2023.07.27.550855 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Sex, gender diversity, and brain structure in children ages 9 to 11 years old ]]> https://biorxiv.org/content/10.1101/2023.07.28.551036v1?rss=1 Torgerson, C. Ahmadi, H. Choupan, J. Fan, C. C. Blosnich, J. R. Herting, M. 2023-07-29 doi:10.1101/2023.07.28.551036 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Transformation of value signaling in a striatopallidal circuit ]]> https://biorxiv.org/content/10.1101/2023.08.01.551547v1?rss=1 Lee, D. Liu, L. Root, C. M. 2023-08-03 doi:10.1101/2023.08.01.551547 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ An AI-assisted Investigation of Tumor-Associated Macrophages and their Polarization in Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2023.08.01.551559v1?rss=1 Dadlani, E. Dash, T. Sahoo, D. 2023-08-03 doi:10.1101/2023.08.01.551559 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ scMD: cell type deconvolution using single-cell DNA methylation references ]]> https://biorxiv.org/content/10.1101/2023.08.03.551733v1?rss=1 Cai, M. Zhou, J. McKennan, C. Wang, J. 2023-08-06 doi:10.1101/2023.08.03.551733 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.04.551992v1?rss=1 Quiroz, E. J. Kim, S. Gautam, L. K. Borok, Z. Kintner, C. Ryan, A. L. 2023-08-04 doi:10.1101/2023.08.04.551992 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes ]]> https://biorxiv.org/content/10.1101/2023.08.04.552006v1?rss=1 Goodheart, J. A. Rio, R. A. Taraporevala, N. F. Fiorenza, R. A. Barnes, S. R. Morrill, K. Jacob, M. A. C. Whitesel, C. Masterson, P. Batzel, G. O. Johnston, H. T. Ramirez, M. D. Katz, P. S. Lyons, D. 2023-08-06 doi:10.1101/2023.08.04.552006 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Analysis of 8839 pan-primate retroviral LTR elements with regulatory functions during human embryogenesis reveals their global impacts on evolution of Modern Humans. ]]> https://biorxiv.org/content/10.1101/2023.08.06.552206v1?rss=1 Glinsky, G. 2023-08-07 doi:10.1101/2023.08.06.552206 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Rats Chasing the Dragon: A new heroin inhalation method ]]> https://biorxiv.org/content/10.1101/2023.08.09.552712v1?rss=1 Gutierrez, A. Taffe, M. A. 2023-08-14 doi:10.1101/2023.08.09.552712 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains ]]> https://biorxiv.org/content/10.1101/2023.08.10.552793v1?rss=1 Gu, Y. Li, H. Deep, A. Enustun, E. Zhang, D. Corbett, K. D. 2023-08-10 doi:10.1101/2023.08.10.552793 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ A fluorescent sex-sorting technique for insects with the demonstration in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.08.11.553026v1?rss=1 Liu, J. Rayes, D. Akbari, O. 2023-08-14 doi:10.1101/2023.08.11.553026 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Estimating the Total Variance Explained by Whole-Brain Imaging for Zero-inflated Outcomes ]]> https://biorxiv.org/content/10.1101/2023.08.14.553270v1?rss=1 Ren, J. Loughnan, R. J. Xu, B. Thompson, W. K. Fan, C. C. 2023-08-16 doi:10.1101/2023.08.14.553270 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Co-Occurrence Network Analysis Reveals The Alterations Of The Skin Microbiome And Metabolome In Atopic Dermatitis Patients ]]> https://biorxiv.org/content/10.1101/2023.08.17.553735v1?rss=1 Portal Gomes, P. W. Mannochio-Russo, H. Mao, J. Zhao, H. N. Tipton, C. D. Ancira, J. Dorrestein, P. C. Li, M. 2023-08-18 doi:10.1101/2023.08.17.553735 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Identification of human skin microbiome odorants that manipulate mosquito landing behavior - towards engineering a repellent skin flora ]]> https://biorxiv.org/content/10.1101/2023.08.19.553996v1?rss=1 Coutinho-Abreu, I. V. Jamshidi, O. Raban, R. Atabakhsh, K. Merriman, J. A. Fischbach, M. A. Akbari, O. S. 2023-08-21 doi:10.1101/2023.08.19.553996 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Acquired stress resilience through bacteria-to-nematode horizontal gene transfer ]]> https://biorxiv.org/content/10.1101/2023.08.20.554039v1?rss=1 Pandey, T. Kalluraya, C. Wang, B. Xu, T. Huang, X. Guang, S. Daugherty, M. D. Ma, D. K. 2023-08-21 doi:10.1101/2023.08.20.554039 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Correlating stress reduction and eye movement patterns in a world famous Kyoto Japanese garden ]]> https://biorxiv.org/content/10.1101/2023.08.21.554170v1?rss=1 Goto, S. Takase, H. Yamaguchi, K. Tamoki, K. Sun, M. Koga, A. Tiankai, L. Poy, I. Herrup, K. 2023-08-23 doi:10.1101/2023.08.21.554170 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ ]]> https://biorxiv.org/content/10.1101/2023.08.21.554211v1?rss=1 Tao, A. J. Jiang, J. Gadbois, G. E. Goyal, P. Boyle, B. T. Mumby, E. J. Myers, S. A. English, J. G. Ferguson, F. M. 2023-08-25 doi:10.1101/2023.08.21.554211 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ A data-driven approach for timescale decomposition of biochemical reaction networks ]]> https://biorxiv.org/content/10.1101/2023.08.21.554230v1?rss=1 Akbari, A. Haiman, Z. B. Palsson, B. O. 2023-08-25 doi:10.1101/2023.08.21.554230 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Impairment of the SKN-1A/NRF1 proteasome surveillance pathway triggers tissue-specific protective immune responses against distinct natural pathogens in C. elegans. ]]> https://biorxiv.org/content/10.1101/2023.08.22.554255v1?rss=1 Grover, M. Gang, S. S. Troemel, E. Barkoulas, M. 2023-08-23 doi:10.1101/2023.08.22.554255 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ A simple solid media assay for detection of synergy between bacteriophages and antibiotics ]]> https://biorxiv.org/content/10.1101/2023.08.23.554535v1?rss=1 Khong, E. Oh, J. Jiminez, J. M. Liu, R. Dunham, S. J. B. Monsibais, A. Rhoads, A. Ghatbale, P. Garcia, A. Cobian-Güemes, A. G. Blanc, A. Chiu, M. Kuo, P. Proost, M. Kline, A. Aslam, S. Schooley, R. Whiteson, K. Fraley, S. Pride, D. T. 2023-08-25 doi:10.1101/2023.08.23.554535 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ S-Nitrosylation of CRTC1 in Alzheimer's disease impairs CREB-dependent gene expression induced by neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.08.25.554320v1?rss=1 Zhang, X. Vlkolinsky, R. Wu, C. Dolatabadi, N. Scott, H. Prikhodko, O. Blanco, M. Lang, N. Pina-Crespo, J. Nakamura, T. Roberto, M. Lipton, S. A. 2023-08-27 doi:10.1101/2023.08.25.554320 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Fe-TAMLs as a new class of small molecule peroxidase probes for correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.08.25.554352v1?rss=1 Adams, S. R. Mackey, M. R. Ramachandra, R. Deerinck, T. J. Castillon, G. A. Phan, S. Hu, J. Boassa, D. Ngo, J. T. Ellisman, M. H. 2023-08-26 doi:10.1101/2023.08.25.554352 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris ]]> https://biorxiv.org/content/10.1101/2023.08.27.555018v1?rss=1 Leavitt, W. D. Waldbauer, J. Venceslau, S. S. Sim, M. S. Zhang, L. Boidi, F. J. Plummer, S. Diaz, J. M. Pereira, I. A. C. Bradley, A. S. 2023-08-27 doi:10.1101/2023.08.27.555018 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene GUT fecal stabilization ]]> https://biorxiv.org/content/10.1101/2023.08.29.555241v1?rss=1 Isokaanta, H. Pinto da Silva, L. Karu, N. Kallonen, T. Aatsinki, A. K. Hankemeier, T. Schimmel, L. Diaz, E. Hyotylainen, T. Dorrestein, P. C. Knight, R. Oresic, M. Daouk, R. K. Dickens, A. M. Lamichhane, S. 2023-08-29 doi:10.1101/2023.08.29.555241 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2023.08.30.555359v1?rss=1 Yang, X. Jones, I. R. Chen, P. B. Yang, H. Ren, X. Zheng, L. Li, B. Li, Y. E. Sun, Q. Wen, J. Beaman, C. Cui, X. Li, Y. Wang, W. Hu, M. Ren, B. Shen, Y. 2023-08-30 doi:10.1101/2023.08.30.555359 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Network effects of traumatic brain injury: from infra slow to high frequency oscillations ]]> https://biorxiv.org/content/10.1101/2023.08.31.555809v1?rss=1 Marsh, B. Huang, M. Bazhenov, M. 2023-09-03 doi:10.1101/2023.08.31.555809 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Protein Kinase Structure and Dynamics: Role of the αC-β4 Loop ]]> https://biorxiv.org/content/10.1101/2023.08.31.555822v1?rss=1 Wu, J. Jonniya, N. A. Hirakis, S. P. Olivieri, C. Veglia, G. Kornev, A. P. Taylor, S. S. 2023-09-01 doi:10.1101/2023.08.31.555822 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Inhibition of Parkinsons Disease-related LRRK2 by type-I and type-II kinase inhibitors: activity and structures ]]> https://biorxiv.org/content/10.1101/2023.09.07.556689v1?rss=1 Leschziner, A. E. Sanz Murillo, M. Suarez, A. V. Dederer, V. Chatterjee, D. Louro, J. A. Knapp, S. Mathea, S. 2023-09-09 doi:10.1101/2023.09.07.556689 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Elf1 promotes Rad26 interaction with lesion-arrested Pol II for transcription-coupled repair ]]> https://biorxiv.org/content/10.1101/2023.09.08.556893v1?rss=1 Sarsam, R. Xu, J. Lahiri, I. Gong, W. Oh, J. Zhou, Z. Chong, J. Hao, N. Li, S. Wang, D. Leschziner, A. E. 2023-09-10 doi:10.1101/2023.09.08.556893 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure ]]> https://biorxiv.org/content/10.1101/2023.09.08.556894v1?rss=1 Yoon, J. Zhang, Y. M. Her, C. Grant, R. A. Ponomarenko, A. M. Ackermann, B. E. Debelouchina, G. Shoulders, M. D. 2023-09-12 doi:10.1101/2023.09.08.556894 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Adult consequences of repeated nicotine and Δ9-tetrahydrocannabinol (THC) vapor inhalation in adolescent rats ]]> https://biorxiv.org/content/10.1101/2023.09.08.556932v1?rss=1 Gutierrez, A. Creehan, K. M. Grant, Y. Taffe, M. A. 2023-09-14 doi:10.1101/2023.09.08.556932 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Distinct 3D contacts and phenotypic consequences of adjacent non-coding loci in the epigenetically quiescent regions ]]> https://biorxiv.org/content/10.1101/2023.09.11.557110v1?rss=1 Wu, P. Wang, W. 2023-09-13 doi:10.1101/2023.09.11.557110 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis ]]> https://biorxiv.org/content/10.1101/2023.09.11.557221v1?rss=1 Ren, B. Zhang, K. Zemke, N. Armand, E. 2023-09-15 doi:10.1101/2023.09.11.557221 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Categorization dynamically alters representations in human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.11.557257v1?rss=1 Henderson, M. M. Serences, J. T. Rungratsameetaweemana, N. 2023-09-13 doi:10.1101/2023.09.11.557257 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks ]]> https://biorxiv.org/content/10.1101/2023.09.13.557626v1?rss=1 Gopalakrishnan, S. Johnson, W. Gomez, M. A. V. Icten, E. Tat, J. Lay, F. Diep, J. Gomez, N. Stevens, J. Schlegel, F. Rolandi, P. Kontoravdi, C. Lewis, N. E. 2023-09-17 doi:10.1101/2023.09.13.557626 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Reinstatement of CDX2 as a differentiation therapy for colorectal cancers ]]> https://biorxiv.org/content/10.1101/2023.09.13.557628v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@16eeb1eorg.highwire.dtl.DTLVardef@10e308borg.highwire.dtl.DTLVardef@9512f0org.highwire.dtl.DTLVardef@10e74eb_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIn this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk. HighlightsO_LIAn ML framework (CANDiT) identifies target for differentiation therapy for CRCs C_LIO_LITherapy induces crypt differentiation and CSC-specific cytotoxicity C_LIO_LICDX2-low state predicts therapeutic response; restoration improves prognosis C_LIO_LITherapy dismantles stemness via reactivation of stress polarity signaling C_LI ]]> Sinha, S. Alcantara, J. Perry, K. Castillo, V. Espinoza, C. R. Taheri, S. Vidales, E. Tindle, C. Adel, A. Amirfakhri, S. Sawires, J. R. Yang, J. Bouvet, M. Sahoo, D. Ghosh, P. 2023-09-17 doi:10.1101/2023.09.13.557628 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2023.09.13.557637v1?rss=1 Crits-Christoph, A. Levy, J. I. Pekar, J. Goldstein, S. A. Singh, R. Hensel, Z. Gangavarapu, K. Rogers, M. B. Moshiri, N. Garry, R. f. Holmes, E. C. Koopmans, M. P. G. Lemey, P. Popescu, S. Rambaut, A. Robertson, D. L. Suchard, M. A. Wertheim, J. Rasmussen, A. L. Andersen, K. G. Worobey, M. Debarre, F. 2023-09-14 doi:10.1101/2023.09.13.557637 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling ]]> https://biorxiv.org/content/10.1101/2023.09.13.557646v1?rss=1 Gopalakrishnan, S. Johnson, W. Valderrama-Gomez, M. A. Icten, E. Tat, J. Ingram, M. Shek, C. F. Chan, P. K. Schlegel, F. Rolandi, P. Kontoravdi, C. Lewis, N. E. 2023-09-17 doi:10.1101/2023.09.13.557646 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Machine assisted annotation in neuroanatomy ]]> https://biorxiv.org/content/10.1101/2023.09.13.557658v1?rss=1 Qian, K. Kleinfeld, D. Friedman, B. Freund, Y. 2023-09-14 doi:10.1101/2023.09.13.557658 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA ]]> https://biorxiv.org/content/10.1101/2023.09.14.557527v1?rss=1 Okholm, T. L. H. Kamstrup, A. B. Nielsen, M. M. Hollensen, A. K. Graversgaard, M. L. Kristensen, L. S. Vang, S. Park, S. S. Yeo, G. W. Dyrskjot, L. Kjems, J. Pedersen, J. S. Damgaard, C. K. 2023-09-14 doi:10.1101/2023.09.14.557527 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Cold Storage and Cryopreservation Methods for Spermatozoa of the Sea Urchin, Lytechinus pictus . ]]> https://biorxiv.org/content/10.1101/2023.09.14.557644v1?rss=1 90% development and producing larvae that successfully undergo metamorphosis to juvenile sea urchins. Sperm of these two species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis. Main PointsO_LISperm can maintain fertilizing capacity ex vivo for 5-10 weeks when stored at 0{degrees}C. C_LIO_LIWhen freezing in liquid nitrogen no stepwise addition of cryoprotectant, or stepwise drop in temperature are required. C_LIO_LIA standard fertilization assay is presented to score cleavage stage sea urchin embryos produced by cryopreserved sperm. C_LIO_LISperm frozen and thawed more than once can produce larvae. C_LI ]]> Vacquier, V. Hamdoun, A. 2023-09-15 doi:10.1101/2023.09.14.557644 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Generating Novel Leads for Drug Discovery using LLMs with Logical Feedback ]]> https://biorxiv.org/content/10.1101/2023.09.14.557698v1?rss=1 Brahmavar, S. B. Srinivasan, A. Dash, T. Krishnan, S. R. Vig, L. Roy, A. Aduri, R. 2023-09-17 doi:10.1101/2023.09.14.557698 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Structural and dynamic changes in P-Rex1 upon activation by PIP3 and inhibition by IP4 ]]> https://biorxiv.org/content/10.1101/2023.09.15.557836v1?rss=1 Ravala, S. K. Adame-Garcia, S. R. Li, S. Chen, C.-L. Cianfrocco, M. A. Gutkind, J. S. Cash, J. N. Tesmer, J. J. G. 2023-09-16 doi:10.1101/2023.09.15.557836 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Variability in the phytoplankton response to upwelling across an iron limitation mosaic within the California Current System ]]> https://biorxiv.org/content/10.1101/2023.09.22.558967v1?rss=1 Lin, Y. Torano, O. Whitehouse, L. Pierce, E. Till, C. P. Hurst, M. Freiberger, R. Mellett, T. Maldonado, M. T. Guo, J. Sutton, M. Zeitz, D. Marchetti, A. 2023-09-23 doi:10.1101/2023.09.22.558967 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A phage nucleus-associated RNA-binding protein is required for jumbo phage infection ]]> https://biorxiv.org/content/10.1101/2023.09.22.559000v1?rss=1 Enustun, E. Armbruster, E. G. Lee, J. Zhang, S. Yee, B. A. Gu, Y. Deep, A. Naritomi, J. T. Liang, Q. Aigner, S. Adler, B. A. Cress, B. F. Doudna, J. A. Chaikeeratisak, V. Cleveland, D. W. Ghassemian, M. Yeo, G. W. Pogliano, J. Corbett, K. D. 2023-09-22 doi:10.1101/2023.09.22.559000 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Next-generation genetic sexing strain establishment in the agricultural pest Ceratitis capitata ]]> https://biorxiv.org/content/10.1101/2023.09.29.560088v1?rss=1 Davydova, S. Liu, J. Kandul, N. P. Braswell, W. E. Akbari, O. S. Meccariello, A. 2023-10-01 doi:10.1101/2023.09.29.560088 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Light-induced trapping of endogenous proteins reveals spatiotemporal roles of microtubule and kinesin-1 in dendrite patterning of Drosophila sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.09.30.560303v1?rss=1 Xu, Y. Wang, B. Bush, I. Saunders, H. A. Wildonger, J. Han, C. 2023-10-02 doi:10.1101/2023.09.30.560303 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ A mobile intron facilitates interference competition between co-infecting viruses ]]> https://biorxiv.org/content/10.1101/2023.09.30.560319v1?rss=1 Birkholz, E. A. Morgan, C. J. Laughlin, T. G. Lau, R. K. Prichard, A. Rangarajan, S. Meza, G. N. Lee, J. Armbruster, E. G. Suslov, S. Pogliano, K. Meyer, J. R. Villa, E. Corbett, K. D. Pogliano, J. 2023-09-30 doi:10.1101/2023.09.30.560319 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.10.02.560584v1?rss=1 Buck, S. A. Rubin, S. A. Kunkhyen, T. Treiber, C. D. Xue, X. Fenno, L. E. Mabry, S. J. Sundar, V. R. Yang, Z. Shah, D. Ketchesin, K. D. Becker-Krail, D. D. Vasylieva, I. Smith, M. C. Weisel, F. J. Wang, W. Erickson-Oberg, M. Q. O'Leary, E. I. Aravind, E. Ramakrishnan, C. Kim, Y. S. Wu, Y. Quick, M. Coleman, J. A. MacDonald, W. A. Elbakri, R. De Miranda, B. R. Palladino, M. J. McCabe, B. D. Fish, K. N. Seney, M. L. Rayport, S. Mingote, S. Deisseroth, K. Hnasko, T. S. Awatramani, R. Watson, A. M. Waddell, S. Cheetham, C. E. Logan, R. W. Freyberg, Z. 2023-10-03 doi:10.1101/2023.10.02.560584 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ CASTER: Direct species tree inference from whole-genome alignments ]]> https://biorxiv.org/content/10.1101/2023.10.04.560884v1?rss=1 Zhang, C. Nielsen, R. Mirarab, S. 2023-10-06 doi:10.1101/2023.10.04.560884 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Structure-Function Coupling in Highly Sampled Individual Brains ]]> https://biorxiv.org/content/10.1101/2023.10.04.560909v1?rss=1 Rajesh, A. Seider, N. A. Newbold, D. J. Adeyemo, B. Marek, S. Greene, D. J. Snyder, A. Z. Shimony, J. S. Laumann, T. O. Dosenbach, N. U. F. Gordon, E. M. 2023-10-05 doi:10.1101/2023.10.04.560909 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model ]]> https://biorxiv.org/content/10.1101/2023.10.06.560776v1?rss=1 Bottom-Tanzer, S. Corella, S. Meyer, J. Sommer, M. Bolanos, L. Murphy, T. Quinones, S. Heiney, S. Shtrahman, M. Whalen, M. Oren, R. Higley, M. J. Cardin, J. A. Noubary, F. Armbruster, M. Dulla, C. 2023-10-06 doi:10.1101/2023.10.06.560776 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Encoding extracellular modification of artificial cell membranes using engineered self-translocating proteins ]]> https://biorxiv.org/content/10.1101/2023.10.06.561148v1?rss=1 Harjung, A. Fracassi, A. Devaraj, N. 2023-10-06 doi:10.1101/2023.10.06.561148 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Changes in electrophysiological aperiodic activity during cognitive control in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2023.10.09.561166v1?rss=1 Monchy, N. Modolo, J. Houvenaghel, J.-F. Voytek, B. Duprez, J. 2023-10-10 doi:10.1101/2023.10.09.561166 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Inputs to the locus coeruleus from the periaqueductal gray and rostroventral medulla shape opioid-mediated descending pain modulation ]]> https://biorxiv.org/content/10.1101/2023.10.10.561768v1?rss=1 Lubejko, S. T. Livrizzi, G. Patel, J. Yung, J. Yaksh, T. L. Banghart, M. R. 2023-10-10 doi:10.1101/2023.10.10.561768 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Environment-driven trends in fish larval abundance predict fishery recruitment in two temperature reef congeners: mechanisms and implications for management ]]> https://biorxiv.org/content/10.1101/2023.10.11.561723v1?rss=1 Mason, E. T. J. Thompson, A. R. Semmens, B. X. 2023-10-16 doi:10.1101/2023.10.11.561723 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Hidden evolutionary constraints dictate the retention of coronavirus accessory genes ]]> https://biorxiv.org/content/10.1101/2023.10.12.561935v1?rss=1 Goldstein, S. A. Feeley, T. M. Babler, K. M. Hilbert, Z. A. Downhour, D. M. Moshiri, N. Elde, N. C. 2023-10-14 doi:10.1101/2023.10.12.561935 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Metabolic bypass rescues aberrant S-nitrosylation-induced TCA cycle inhibition and synapse loss in Alzheimer's disease human neurons ]]> https://biorxiv.org/content/10.1101/2023.10.12.562118v1?rss=1 Andreyev, A. Y. Yang, H. Doulias, P.-T. Dolatabadi, N. Zhang, X. Luevanos, M. Blanco, M. Baal, C. Putra, I. Nakamura, T. Ischiropoulos, H. Tannenbaum, S. R. Lipton, S. A. 2023-10-17 doi:10.1101/2023.10.12.562118 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Long chain monomethyl branched-chain fatty acid levels in human milk vary with gestational weight gain ]]> https://biorxiv.org/content/10.1101/2023.10.13.561203v1?rss=1 O'Sullivan, A. Brady, E. Lafferty, L. O'Shea, F. O'Regan, Z. Meurs, N. Baldini, M. Gengatharan, J. Metallo, C. M. Wallace, M. 2023-10-17 doi:10.1101/2023.10.13.561203 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Resting-state is not enough: alpha and mu rhythms change shape across development, but lack diagnostic sensitivity ]]> https://biorxiv.org/content/10.1101/2023.10.13.562301v1?rss=1 Bender, A. Voytek, B. Schaworonkow, N. 2023-10-17 doi:10.1101/2023.10.13.562301 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Emergent effects of synaptic connectivity on cortical sleep slow wave amplitude, density and propagation in a large-scale thalamocortical network model of the human brain ]]> https://biorxiv.org/content/10.1101/2023.10.15.562408v1?rss=1 Marsh, B. Zuloaga, M. G. N. Rosen, B. Q. Sokolov, Y. Delanois, J. E. Gonzalez, O. C. Krishnan, G. P. Halgren, E. Bazhenov, M. 2023-10-17 doi:10.1101/2023.10.15.562408 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ GRAMD2+ alveolar type I cell plasticity facilitates cell state transitions in organoid culture ]]> https://biorxiv.org/content/10.1101/2023.10.17.560801v1?rss=1 Shen, H. Chen, W. Liu, Y. Castaldi, A. Castillo, J. Horie, M. Flodby, P. Sundar, S. Li, C. Ji, Y. Minoo, P. Marconett, C. N. Zhou, B. Borok, Z. 2023-10-18 doi:10.1101/2023.10.17.560801 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia ]]> https://biorxiv.org/content/10.1101/2023.10.17.562767v1?rss=1 Fricker, A. D. Padilla, L. Luna, E. Choudhury, B. Hughes, E. R. Panzetta, M. E. Valdivia, R. Flores, G. E. 2023-10-17 doi:10.1101/2023.10.17.562767 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Eukaryotic chemotaxis under periodic stimulation shows temporal gradient dependence ]]> https://biorxiv.org/content/10.1101/2023.10.17.562804v1?rss=1 Karmakar, R. Karanam, A. R. Tang, M.-H. Rappel, W.-J. 2023-10-19 doi:10.1101/2023.10.17.562804 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement ]]> https://biorxiv.org/content/10.1101/2023.10.23.563531v1?rss=1 Handa, S. Biswas, T. Chakraborty, J. Paul, B. G. Ghosh, P. 2023-10-23 doi:10.1101/2023.10.23.563531 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain ]]> https://biorxiv.org/content/10.1101/2023.10.24.563814v1?rss=1 Chung, C. Yang, X. Hevner, R. Kennedy, K. Vong, K. L. Liu, Y. Patel, A. Nedunuri, R. Barton, S. T. Barrows, C. Stanley, V. Mittal, S. Breuss, M. W. Schlachetzki, J. C. M. Gleeson, J. G. 2023-10-25 doi:10.1101/2023.10.24.563814 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens ]]> https://biorxiv.org/content/10.1101/2023.10.24.563841v1?rss=1 Nuqui, X. Casalino, L. Zhou, L. Shehata, M. Wang, A. Tse, A. L. Ojha, A. Kearns, F. L. Rosenfeld, M. A. Miller, E. H. Acreman, C. M. Ahn, S.-H. Chandran, K. McLellan, J. S. Amaro, R. E. 2023-10-25 doi:10.1101/2023.10.24.563841 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Oxycodone Self-Administration in Female Rats is Enhanced by Δ9-tetrahydrocannabinol, but not by Cannabidiol, in a Progressive Ratio Procedure ]]> https://biorxiv.org/content/10.1101/2023.10.26.564282v1?rss=1 Nguyen, J. D. Grant, Y. Yang, C. Gutierrez, A. Taffe, M. A. 2023-10-31 doi:10.1101/2023.10.26.564282 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Benchmarking of small and large variants across tandem repeats ]]> https://biorxiv.org/content/10.1101/2023.10.29.564632v1?rss=1 English, A. Dolzhenko, E. Ziaei-Jam, H. Olson, N. D. Mckenzie, S. De Coster, W. Park, J. Gu, B. Wagner, J. Eberle, M. Gymrek, M. Chaisson, M. Zook, J. M. Sedlazeck, F. J. 2023-11-01 doi:10.1101/2023.10.29.564632 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Brain Injury Knowledge Ontology (BIKO) for traumatic brain injury: Formalizing concepts and methods used in translational traumatic brain injury research. ]]> https://biorxiv.org/content/10.1101/2023.10.29.564650v1?rss=1 Surles-Zeigler, M. Sincomb, T. Dixon, C. E. Imam, F. Gillespie, T. H. Grethe, J. S. Ferguson, A. R. Martone, M. E. 2023-11-01 doi:10.1101/2023.10.29.564650 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ The Generation and Propagation of the Human Alpha Rhythm ]]> https://biorxiv.org/content/10.1101/202564v1?rss=1 Halgren, M. Devinsky, O. Doyle, W. K. Bastuji, H. Rey, M. Mak-McCully, R. Chauvel, P. Ulbert, I. Fabo, D. Wittner, L. Heit, G. Eskandar, E. Mandell, A. Cash, S. S. 2017-11-18 doi:10.1101/202564 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Simulating human sleep spindle MEG and EEG from ion channel and circuit level dynamics ]]> https://biorxiv.org/content/10.1101/202606v1?rss=1 Rosen, B. Q. Krishnan, G. Sanda, P. Komarov, M. Sejnowski, T. Rulkov, N. Bazhenov, M. Halgren, E. 2017-10-13 doi:10.1101/202606 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Alpha-band oscillations track the retrieval of precise spatial representations from long-term memory ]]> https://biorxiv.org/content/10.1101/207860v1?rss=1 Sutterer, D. W. Foster, J. J. Serences, J. T. Vogel, E. K. Awh, E. 2018-02-18 doi:10.1101/207860 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Quantification of autism recurrence risk by direct assessment of paternal sperm mosaicism ]]> https://biorxiv.org/content/10.1101/208165v1?rss=1 90x) whole genome sequencing of four paternal sperm samples, which detected 12/355 transmitted de novo single nucleotide variants that were mosaic above 2% AF, and more than two dozen additional, non-transmitted mosaic variants in paternal sperm. Our results demonstrate that germline mosaicism is an underestimated phenomenon, which has important implications for clinical practice and in understanding the basis of human disease. Genetic analysis of sperm can assess individualized recurrence risk following the birth of a child with a de novo disease, as well as the risk in any male planning to have children. ]]> Breuss, M. Kleiber, M. George, R. D. Antaki, D. James, K. N. Ball, L. L. Hong, O. Garcia, C. A. B. Musaev, D. Nguyen, A. McEvoy-Venneri, J. Knox, R. Sticca, E. Devinsky, O. Gymrek, M. Sebat, J. Gleeson, J. G. 2017-10-24 doi:10.1101/208165 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Id proteins suppress E2A-driven innate-like T cell development prior to TCR selection ]]> https://biorxiv.org/content/10.1101/208728v1?rss=1 Roy, S. Moore, A. J. Love, C. Reddy, A. Rajagopalan, D. Dave, S. S. Li, L. Murre, C. Zhuang, Y. 2017-10-25 doi:10.1101/208728 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Sequence Transfer Learning for Neural Decoding ]]> https://biorxiv.org/content/10.1101/210732v1?rss=1 Elango, V. Patel, A. N. Miller, K. J. Gilja, V. 2017-10-29 doi:10.1101/210732 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data ]]> https://biorxiv.org/content/10.1101/210997v1?rss=1 Liu, C. Wang, W. 2017-10-29 doi:10.1101/210997 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Quantitative proteomic analysis of auxin signaling during seedling development ]]> https://biorxiv.org/content/10.1101/211532v1?rss=1 Kelley, D. Shen, Z. Walley, J. W. Chapman, E. J. Briggs, S. P. Estelle, M. 2017-10-30 doi:10.1101/211532 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Processive movement of actin by biased polymerization: a new paradigm of axonal transport ]]> https://biorxiv.org/content/10.1101/212449v1?rss=1 Chakrabarty, N. Dubey, P. Tang, Y. Ganguly, A. Ladt, K. Leterrier, C. Jung, P. Roy, S. 2017-11-01 doi:10.1101/212449 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction ]]> https://biorxiv.org/content/10.1101/212639v1?rss=1 1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. ]]> Herbert, Z. T. Kershner, J. P. Butty, V. L. Thimmapuram, J. Choudhari, S. Alekseyev, Y. O. Fan, J. Podnar, J. W. Wilcox, E. Gipson, J. Gillaspy, A. Jepsen, K. BonDurant, S. S. Morris, K. Berkeley, M. LeClerc, A. Simpson, S. D. Sommerville, G. Grimmett, L. Adams, M. Levine, S. S. 2017-11-01 doi:10.1101/212639 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Selective Recruitment of Cortical Neurons by Electrical Stimulation ]]> https://biorxiv.org/content/10.1101/213017v1?rss=1 Komarov, M. Malerba, P. Nunez, P. Halgren, E. Bazhenov, M. 2017-11-02 doi:10.1101/213017 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ A linear-time algorithm to sample the dual-birth model ]]> https://biorxiv.org/content/10.1101/226423v1?rss=1 Moshiri, N. 2017-11-28 doi:10.1101/226423 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ Catalytic potential and disturbance rejection of glycolytic kinases in the human red blood cell ]]> https://biorxiv.org/content/10.1101/227058v1?rss=1 Yurkovich, J. T. Alcantar, M. A. Haiman, Z. B. Palsson, B. O. 2017-11-30 doi:10.1101/227058 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ RIFRAF: a frame-resolving consensus algorithm ]]> https://biorxiv.org/content/10.1101/227520v1?rss=1 Eren, K. Murrell, B. 2017-12-03 doi:10.1101/227520 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Multi-scale model of the proteomic and metabolic consequences of reactive oxygen species ]]> https://biorxiv.org/content/10.1101/227892v1?rss=1 Yang, L. Mih, N. Yurkovich, J. T. Park, J. H. Seo, S. Kim, D. Monk, J. M. Lloyd, C. J. Tan, J. Gao, Y. Broddrick, J. T. Chen, K. Heckmann, D. Feist, A. M. Palsson, B. O. 2017-12-02 doi:10.1101/227892 Cold Spring Harbor Laboratory Press 2017-12-02 <![CDATA[ Assembly-free and alignment-free sample identification using genome skims ]]> https://biorxiv.org/content/10.1101/230409v1?rss=1 Sarmashghi, S. Bohmann, K. Gilbert, M. T. P. Bafna, V. Mirarab, S. 2017-12-08 doi:10.1101/230409 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons ]]> https://biorxiv.org/content/10.1101/230474v1?rss=1 Eren, K. Weaver, S. Ketteringham, R. Valentyn, M. Laird Smith, M. Kumar, V. Mohan, S. Kosakovsky Pond, S. L. Murrell, B. 2017-12-07 doi:10.1101/230474 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ Integrated analysis of anatomical and electrophysiological human intracranial data ]]> https://biorxiv.org/content/10.1101/230912v1?rss=1 Stolk, A. Griffin, S. van der Meij, R. Dewar, C. Saez, I. Lin, J. J. Piantoni, G. Schoffelen, J.-M. Knight, R. T. Oostenveld, R. 2017-12-08 doi:10.1101/230912 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Genome wide association study of behavioral, physiological and gene expression traits in a multigenerational mouse intercross ]]> https://biorxiv.org/content/10.1101/230920v1?rss=1 Gonzales, N. M. Seo, J. Hernandez-Cordero, A. I. St. Pierre, C. L. Gregory, J. S. Distler, M. G. Abney, M. Canzar, S. Lionikas, A. Palmer, A. A. 2017-12-08 doi:10.1101/230920 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Study of the mitotic chromatin shows involvement of histone modifications in bookmarking and reveals nucleosome deposition patterns ]]> https://biorxiv.org/content/10.1101/233056v1?rss=1 Javasky, E. Shamir, I. Gandhi, S. Egri, S. Sandler, O. Kaplan, N. Jaffe, J. D. Goren, A. Simon, I. 2017-12-12 doi:10.1101/233056 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ The Anorexia Nervosa Genetics Initiative: Overview and Methods ]]> https://biorxiv.org/content/10.1101/234013v1?rss=1 Thornton, L. M. Munn-Chernoff, M. A. Baker, J. H. Jureus, A. Parker, R. Henders, A. K. Larsen, J. T. Petersen, L. Watson, H. J. Yilmaz, Z. Kirk, K. M. Gordon, S. Leppa, V. M. Martin, F. C. Whiteman, D. C. Olsen, C. M. Werge, T. Pedersen, N. L. Kaye, W. Bergen, A. W. Halmi, K. A. Strober, M. Kaplan, A. S. Woodside, D. B. Mitchell, J. Johnson, C. L. Brandt, H. Crawford, S. Horwood, L. J. Boden, J. M. Pearson, J. F. Duncan, L. E. Grove, J. Mattheisen, M. Jordan, J. Kennedy, M. A. Birgegard, A. Lichtenstein, P. Norring, C. Wade, T. D. Montgomery, G. Martin, 2017-12-15 doi:10.1101/234013 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Bivariate Gaussian Mixture Model of GWAS (BGMG)quantifies polygenic overlap between complex traitsbeyond genetic correlation ]]> https://biorxiv.org/content/10.1101/240275v1?rss=1 Frei, O. Holland, D. Smeland, O. B. Shadrin, A. A. Fan, C. C. Witoelar, A. Wang, Y. Djurovic, S. Thompson, W. Andreassen, O. A. Dale, A. M. 2017-12-27 doi:10.1101/240275 Cold Spring Harbor Laboratory Press 2017-12-27 <![CDATA[ IMPROVEMENTS TO BAYESIAN GENE ACTIVITY STATE ESTIMATION FROM GENOME-WIDE TRANSCRIPTOMICS DATA ]]> https://biorxiv.org/content/10.1101/241000v1?rss=1 Disselkoen, C. Hekman, N. Gilbert, B. Benson, S. Anderson, M. DeJongh, M. Best, A. Tintle, N. 2017-12-29 doi:10.1101/241000 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ Viral gain-of-function experiments uncover residues under diversifying selection in nature ]]> https://biorxiv.org/content/10.1101/242495v1?rss=1 Maddamsetti, R. Johnson, D. T. Spielman, S. J. Petrie, K. L. Marks, D. S. Meyer, J. R. 2018-01-03 doi:10.1101/242495 Cold Spring Harbor Laboratory Press 2018-01-03 <![CDATA[ Assembly of Long Error-Prone Reads Using Repeat Graphs ]]> https://biorxiv.org/content/10.1101/247148v1?rss=1 Kolmogorov, M. Yuan, J. Lin, Y. Pevzner, P. 2018-01-12 doi:10.1101/247148 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Characterizing concentration-dependent neural dynamics of 4-aminopyridine-induced epileptiform activity ]]> https://biorxiv.org/content/10.1101/252726v1?rss=1 Myers, T. L. Gonzalez, O. C. Stein, J. B. Bazhenov, M. 2018-01-24 doi:10.1101/252726 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Beyond synthetic lethality: multiple gene interaction types play a key functional role in cancer ]]> https://biorxiv.org/content/10.1101/253120v1?rss=1 Magen, A. Das, A. Sang Lee, J. Sharmin, M. Lugo, A. Gutkind, S. Ruppin, E. Hannenhalli, S. 2018-01-24 doi:10.1101/253120 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Sex-specific impact of prenatal androgens on intrinsic functional connectivity between social brain default mode subsystems ]]> https://biorxiv.org/content/10.1101/253310v1?rss=1 Lombardo, M. V. Auyeung, B. Pramparo, T. Quartier, A. Courraud, J. Holt, R. J. Waldman, J. Ruigrok, A. Mooney, N. Lai, M.-C. Kundu, P. Bullmore, E. T. Mandel, J.-L. Piton, A. Baron-Cohen, S. 2018-01-25 doi:10.1101/253310 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish ]]> https://biorxiv.org/content/10.1101/254854v1?rss=1 Brennan, R. S. Healy, T. M. Bryant, H. J. La, M. V. Schulte, P. M. Whitehead, A. 2018-01-27 doi:10.1101/254854 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ Social behavior and anxiety contribute to nicotine self-administration in adolescent outbred rats ]]> https://biorxiv.org/content/10.1101/257097v1?rss=1 Wang, T. Han, W. Chitre, A. Polesskaya, O. Solberg Woods, L. C. Palmer, A. A. Chen, H. 2018-01-30 doi:10.1101/257097 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Trans-ancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/257311v1?rss=1 Walters, R. K. Adams, M. J. Adkins, A. E. Aliev, F. Bacanu, S.-A. Batzler, A. Bertelsen, S. Biernacka, J. Bigdeli, T. B. Chen, L.-S. Clarke, T.-K. Chou, Y.-L. Degenhardt, F. Docherty, A. R. Fontanillas, P. Foo, J. Fox, L. Frank, J. Giegling, I. Gordon, S. Hack, L. -, Hartz, S. M. Heilmann-Heimbach, S. Herms, S. Hodgkinson, C. Hoffmann, P. Hottenga, J.-J. Kennedy, M. A. Alanne-Kinnunen, M. Konte, B. Lahti, J. Lahti-Pulkkinen, M. Ligthart, L. Loukola, A.-M. Maher, B. S. Mbarek, H. McIntosh, A. M. McQueen, M. B. Milaneschi, Y. Palviainen, T. Pearson, J. 2018-03-10 doi:10.1101/257311 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation ]]> https://biorxiv.org/content/10.1101/258194v1?rss=1 Arora, K. Corbett, K. D. 2018-02-01 doi:10.1101/258194 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Local Cortical Activity Of Distant Brain Areas Can Time-Lock To The Respiratory Rhythm In The Freely Behaving Rat ]]> https://biorxiv.org/content/10.1101/259457v1?rss=1 Rojas-Libano, D. Wimmer del Solar, J. Aguilar, M. Montefusco-Siegmund, R. Maldonado, P. E. 2018-02-04 doi:10.1101/259457 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ Theta bursts precede, and spindles follow, cortical and thalamic downstates in human NREM sleep ]]> https://biorxiv.org/content/10.1101/260786v1?rss=1 Gonzalez, C. E. Mak-McCully, R. Cash, S. Chauvel, P. Bastuji, H. Rey, M. Halgren, E. 2018-02-06 doi:10.1101/260786 Cold Spring Harbor Laboratory Press 2018-02-06 <![CDATA[ ClusterPicker-II: Massively scalable transmission clustering using phylogenetic trees ]]> https://biorxiv.org/content/10.1101/261354v1?rss=1 Moshiri, A. N. 2018-02-07 doi:10.1101/261354 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues ]]> https://biorxiv.org/content/10.1101/261594v1?rss=1 Tsang, T. K. Bushong, E. A. Boassa, D. Hu, J. Romoli, B. Phan, S. Dulcis, D. Su, C.-Y. Ellisman, M. H. 2018-02-07 doi:10.1101/261594 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP pathways in macrophages ]]> https://biorxiv.org/content/10.1101/263434v1?rss=1 Muse, E. D. Yu, S. Edillor, C. R. Tao, J. Spann, N. J. Troutman, T. D. Seidman, J. S. Henke, A. Roland, J. T. Ozeki, K. A. McDonald, J. G. Bahadorani, J. Tsimikas, S. Grossman, T. R. Tremblay, M. S. Glass, C. K. 2018-02-11 doi:10.1101/263434 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ Transcriptional Activation of a Cartilaginous Fish (Elephant Shark, Callorhinchus milii) Mineralocorticoid Receptor by Corticosteroids, Progestins and Spironolactone ]]> https://biorxiv.org/content/10.1101/265348v1?rss=1 Katsu, Y. Kohno, S. Oka, K. Lin, X. Otake, S. Pillai, N. E. Takagi, W. Hyodo, S. Venkatesh, B. Baker, M. E. 2018-02-13 doi:10.1101/265348 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ MARGE: Mutation Analysis for Regulatory Genomic Elements ]]> https://biorxiv.org/content/10.1101/268839v1?rss=1 Link, V. M. Romanoski, C. E. Metzler, D. Glass, C. K. 2018-02-21 doi:10.1101/268839 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing ]]> https://biorxiv.org/content/10.1101/273433v1?rss=1 Ganem, N. S. Ben-Asher, N. Manning, A. C. Deffit, S. N. Washburn, M. C. Wheeler, E. C. Yeo, G. W. Ben-Naim Zgayer, O. Mantsur, E. Hundley, H. A. Lamm, A. T. 2018-02-28 doi:10.1101/273433 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Strong Episodic Selection for Natural Competence for Transformation Due to Host-Pathogen Dynamics ]]> https://biorxiv.org/content/10.1101/275651v1?rss=1 Palmer, N. D. Cartwright, R. A. 2018-03-03 doi:10.1101/275651 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures ]]> https://biorxiv.org/content/10.1101/277277v1?rss=1 Choudhary, K. S. Mih, N. Monk, J. Kavvas, E. Yurkovich, J. T. Sakoulas, G. Palsson, B. O. 2018-03-06 doi:10.1101/277277 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA ]]> https://biorxiv.org/content/10.1101/283812v1?rss=1 Welkie, D. G. Rubin, B. E. Chang, Y.-G. Diamond, S. Rifkin, S. A. LiWang, A. Golden, S. S. 2018-03-17 doi:10.1101/283812 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Nuisance Effects and the Limitations of Nuisance Regression in Dynamic Functional Connectivity fMRI ]]> https://biorxiv.org/content/10.1101/285239v1?rss=1 Nalci, A. Rao, B. D. Liu, T. T. 2018-03-21 doi:10.1101/285239 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Changes in the genetic requirements for microbial interactions with increasing community complexity ]]> https://biorxiv.org/content/10.1101/290353v1?rss=1 Morin, M. Pierce, E. C. Dutton, R. J. 2018-03-28 doi:10.1101/290353 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Development of a joint evolutionary model for the genome and the epigenome ]]> https://biorxiv.org/content/10.1101/293076v1?rss=1 Lu, J. Cao, X. Zhong, S. 2018-04-02 doi:10.1101/293076 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ An inter-chromosomal transcription hub activates the unfolded protein response in plasma cells ]]> https://biorxiv.org/content/10.1101/295915v1?rss=1 Bortnick, A. He, Z. Aubrey, M. Chandra, V. Denholtz, M. Chen, K. Lin, Y. C. Murre, C. 2018-04-06 doi:10.1101/295915 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences ]]> https://biorxiv.org/content/10.1101/297267v1?rss=1 Moshiri, N. Ragonnet-Cronin, M. Wertheim, J. O. Mirarab, S. 2018-04-07 doi:10.1101/297267 Cold Spring Harbor Laboratory Press 2018-04-07 <![CDATA[ Parameterizing neural power spectra ]]> https://biorxiv.org/content/10.1101/299859v1?rss=1 Haller, M. Donoghue, T. Peterson, E. Varma, P. Sebastian, P. Gao, R. Noto, T. Knight, R. T. Shestyuk, A. Voytek, B. 2018-04-11 doi:10.1101/299859 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome ]]> https://biorxiv.org/content/10.1101/300483v1?rss=1 Chen, W. Yan, Z. Li, S. Huang, N. Huang, X. Zhang, J. Zhong, S. 2018-04-12 doi:10.1101/300483 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Assessing key decisions for transcriptomic data integration in biochemical networks ]]> https://biorxiv.org/content/10.1101/301945v1?rss=1 Richelle, A. Joshi, C. Lewis, N. E. 2018-04-16 doi:10.1101/301945 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Cycle-by-cycle analysis of neural oscillations ]]> https://biorxiv.org/content/10.1101/302000v1?rss=1 Cole, S. R. Voytek, B. 2018-04-16 doi:10.1101/302000 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Development and validation of a phenotypic high-content imaging assay for assessing the antiviral activity of small-molecule inhibitors targeting the Zika virus ]]> https://biorxiv.org/content/10.1101/302927v1?rss=1 Bernatchez, J. A. Yang, Z. Coste, M. Li, J. Beck, S. Liu, Y. Clark, A. E. Zhu, Z. Luna, L. A. Sohl, C. Purse, B. W. Li, R. Siqueira-Neto, J. L. 2018-04-17 doi:10.1101/302927 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ A novel sialylation site on Neisseria gonorrhoeae lipooligosaccharide links heptose II lactose expression with pathogenicity ]]> https://biorxiv.org/content/10.1101/302968v1?rss=1 Ram, S. Gulati, S. Lewis, L. A. Chakraborti, S. Zheng, B. DeOliveira, R. B. Reed, G. W. Cox, A. D. Li, J. St. Michael, F. Stupak, J. Su, X.-H. Saha, S. Landig, C. S. Varki, A. RICE, P. A. 2018-04-17 doi:10.1101/302968 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Movement-related activity dominates cortex during sensory-guided decision making ]]> https://biorxiv.org/content/10.1101/308288v1?rss=1 Musall, S. Kaufman, M. T. Gluf, S. Churchland, A. 2018-04-25 doi:10.1101/308288 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Enzyme promiscuity shapes evolutionary innovation and optimization ]]> https://biorxiv.org/content/10.1101/310946v1?rss=1 Guzman, G. I. Sandberg, T. E. LaCroix, R. A. Nyerges, A. Papp, H. de Raad, M. King, Z. A. Northen, T. R. Notebaart, R. A. Pal, C. Palsson, B. O. Papp, B. Feist, A. M. 2018-05-03 doi:10.1101/310946 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Mechanistic Origins of Dynamic Instability in Filaments from the Phage Tubulin, PhuZ ]]> https://biorxiv.org/content/10.1101/311498v1?rss=1 Zehr, E. A. Rohu, A. Liu, Y. Verba, K. A. Pogliano, J. Grigorieff, N. Agard, D. A. 2018-04-30 doi:10.1101/311498 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Two Isoforms of the Guanine Nucleotide Exchange Factor, Daple/CCDC88C Cooperate as Tumor Suppressors ]]> https://biorxiv.org/content/10.1101/312934v1?rss=1 Dunkel, Y. Ear, J. Mittal, Y. Lim, B. Liu, L. Holda, M. Nitsche, U. Barbazan, J. Goel, A. Janssen, K.-P. Aznar, N. Ghosh, P. 2018-05-02 doi:10.1101/312934 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria ]]> https://biorxiv.org/content/10.1101/315499v1?rss=1 Peters, J. M. Koo, B.-M. Patino, R. Heussler, G. E. Hearne, C. C. Inclan, Y. Hawkins, J. S. Lu, C. H. S. Harden, M. M. Osadnik, H. Peters, J. E. Engel, J. N. Dutton, R. J. Grossman, A. D. Gross, C. A. Rosenberg, O. S. 2018-05-05 doi:10.1101/315499 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Spatial gene-by-environment mapping for schizophrenia reveals locale of upbringing effects beyond urban-rural differences ]]> https://biorxiv.org/content/10.1101/315820v1?rss=1 Fan, C. C. McGrath, J. J. Appadurai, V. Buil, A. Gandal, M. J. Schork, A. J. Mortensen, P. B. Agerbo, E. Geschwind, S. A. Geschwind, D. Werge, T. Thompson, W. K. Pedersen, C. B. 2018-05-11 doi:10.1101/315820 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics ]]> https://biorxiv.org/content/10.1101/318972v1?rss=1 Heckmann, D. Zielinski, D. C. Palsson, B. O. 2018-05-10 doi:10.1101/318972 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Links between environment, diet, and the hunter-gatherer microbiome ]]> https://biorxiv.org/content/10.1101/319673v1?rss=1 Fragiadakis, G. K. Smits, S. A. Sonnenburg, E. D. Van Treuren, W. Reid, G. Knight, R. Manjurano, A. Changalucha, J. Dominguez-Bello, M. G. Leach, J. Sonnenburg, J. L. 2018-05-15 doi:10.1101/319673 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution ]]> https://biorxiv.org/content/10.1101/320747v1?rss=1 Phaneuf, P. V. Gosting, D. Palsson, B. Feist, A. 2018-05-15 doi:10.1101/320747 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ The Repertoire of Mutational Signatures in Human Cancer ]]> https://biorxiv.org/content/10.1101/322859v1?rss=1 Alexandrov, L. Kim, J. Haradhvala, N. J. Huang, M. N. Ng, A. W. T. Boot, A. Covington, K. R. Gordenin, D. A. Bergstrom, E. Lopez-Bigas, N. Klimczak, L. J. McPherson, J. R. Morganella, S. Sabarinathan, R. Wheeler, D. A. Mustonen, V. Getz, G. Rozen, S. G. Stratton, M. R. PCAWG Mutational Signatures Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net, 2018-05-15 doi:10.1101/322859 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ TreeSwift: a massively scalable Python package for trees ]]> https://biorxiv.org/content/10.1101/325522v1?rss=1 Moshiri, N. 2018-05-18 doi:10.1101/325522 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Hyperactive Rac1 drives MAPK-independent proliferation in melanoma by assembly of a mechanosensitive dendritic actin network ]]> https://biorxiv.org/content/10.1101/326710v1?rss=1 Mohan, A. S. Dean, K. M. Kasitinon, S. Y. Isogai, T. Siruvallur Murali, V. Han, S. J. Roudot, P. Groisman, A. Welf, E. Danuser, G. 2018-05-22 doi:10.1101/326710 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Relevance of coral geometry in the outcomes of the coral-algal benthic war ]]> https://biorxiv.org/content/10.1101/327031v1?rss=1 George, E. E. Mullinix, J. Meng, F. Bailey, B. Edwards, C. Felts, B. Haas, A. Hartmann, A. C. Mueller, B. Nulton, J. Roach, T. N. F. Salamon, P. Silveira, C. B. Vermeij, M. J. A. Rohwer, F. L. Luque, A. 2018-05-24 doi:10.1101/327031 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Impact of MMP-2 and MMP-9 activation on wound healing, tumor growth and RACPP cleavage ]]> https://biorxiv.org/content/10.1101/327791v1?rss=1 Ellies, L. G. Hingorani, D. V. Lippert, C. N. Crisp, J. L. Savariar, E. N. Hasselmann, J. P. C. Kuo, C. P. C. Nguyen, Q. T. Tsien, R. Y. Whitney, M. A. 2018-05-21 doi:10.1101/327791 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Using global t-SNE to preserve inter-cluster data structure ]]> https://biorxiv.org/content/10.1101/331611v1?rss=1 Zhou, Y. Sharpee, T. 2018-05-25 doi:10.1101/331611 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Using deep whole genome sequence, transcriptome and epigenome data to characterize the mutational burden of induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/334870v1?rss=1 D'Antonio, M. Benaglio, P. Jakubosky, D. A. Greenwald, W. W. Matsui, H. Donovan, M. K. R. Li, H. Smith, E. N. D'Antonio-Chronowska, A. Frazer, K. A. 2018-05-30 doi:10.1101/334870 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ PI(4,5)P2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding ]]> https://biorxiv.org/content/10.1101/341248v1?rss=1 Johnson, K. A. Budicini, M. R. Urata, S. Bhattarai, N. Gerstman, B. S. Chapagain, P. P. Li, S. Stahelin, R. V. 2018-06-07 doi:10.1101/341248 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 ]]> https://biorxiv.org/content/10.1101/343913v1?rss=1 Gao, Y. Yurkovich, J. T. Seo, S. W. Kabimoldayev, I. Drager, A. Chen, K. Sastry, A. V. Fang, X. Mih, N. Yang, L. Eichner, J. Cho, B.-K. Kim, D. Palsson, B. O. 2018-06-11 doi:10.1101/343913 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ The Evolution of White Matter Microstructural Changes After Mild Traumatic Brain Injury: A Longitudinal DTI and NODDI Study ]]> https://biorxiv.org/content/10.1101/345629v1?rss=1 Palacios, E. Owen, J. P. Yuh, E. L. Wang, M. B. Vassar, M. J. Ferguson, A. R. Diaz-Arrastia, R. Giacino, J. T. Okonkwo, D. O. Robertson, C. S. Stein, M. B. Temkin, N. Jain, S. McCrea, M. Mac Donald, C. L. Manley, G. T. Mukherjee, P. TRACK-TBI Investigators, 2018-06-14 doi:10.1101/345629 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Prognostic Relevance of CCDC88C (Daple) Transcripts in the Peripheral Blood of Patients with Malignant Melanoma ]]> https://biorxiv.org/content/10.1101/346551v1?rss=1 Dunkel, Y. Reid, A. Ear, J. Aznar, N. Millward, M. Gray, E. Pearce, R. Ziman, M. Ghosh, P. 2018-06-13 doi:10.1101/346551 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages ]]> https://biorxiv.org/content/10.1101/347716v1?rss=1 Gauglitz, J. M. Aceves, C. M. Aksenov, A. A. Aleti, G. Almaliti, J. Bouslimani, A. Brown, E. A. Campeau, A. Caraballo-Rodriguez, A. M. Chaar, R. da Silva, R. R. Demko, A. M. Di Ottavio, F. Elijah, E. Ernst, M. Ferguson, L. P. Holmes, X. van der Hooft, J. J. J. Jarmusch, A. K. Jiang, L. Kang, K. B. Koester, I. Kwan, B. Ni, B. Li, J. Li, Y. Melnik, A. V. Molina-Santiago, C. Oom, A. L. Panitchpakdi, M. W. Petras, D. Quinn, R. Sikora, N. C. Spengler, K. Teke, B. Tripathi, A. Ul-Hasan, S. Vargas, F. Vrbanac, A. Vu, A. Q. Wang, S. C. Weldon, K. Wilson, K. W 2018-06-15 doi:10.1101/347716 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite ]]> https://biorxiv.org/content/10.1101/350991v1?rss=1 Lieven, C. Beber, M. E. Olivier, B. G. Bergmann, F. T. Babaei, P. Bartell, J. A. Blank, L. M. Chauhan, S. Correia, K. Diener, C. Dräger, A. Ebert, B. E. Edirisinghe, J. N. Fleming, R. M. T. Garcia-Jimenez, B. van Helvoirt, W. Henry, C. Hermjakob, H. Herrgard, M. J. Kim, H. U. King, Z. Koehorst, J. J. Klamt, S. Klipp, E. Lakshmanan, M. Le Novere, N. Lee, D.-Y. Lee, S. Y. Lee, S. Lewis, N. E. Ma, H. Machado, D. Mahadevan, R. Maia, P. Mardinoglu, A. Medlock, G. L. Monk, J. Nielsen, J. Nielsen, L. K. Nogales, J. Nookaew, I. Resendis, O. Palsson, B. 2018-06-21 doi:10.1101/350991 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry ]]> https://biorxiv.org/content/10.1101/351130v1?rss=1 Zhang, F. Wei, K. Slowikowski, K. Fonseka, C. Y. Rao, D. A. Kelly, S. Goodman, S. M. Tabechian, D. Hughes, L. B. Salomon-Escoto, K. Watts, G. F. M. Apruzzese, W. Lieb, D. J. Boyle, D. L. Mandelin, A. M. Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Boyce, B. F. DiCarlo, E. Gravallese, E. M. Gregersen, P. K. Moreland, L. Firestein, G. S. Hacohen, N. Nusbaum, C. Lederer, J. A. Perlman, H. Pitzalis, C. Filer, A. Holers, V. M. Bykerk, V. P. Donlin, L. T. Anolik, J. H. Brenner, M. B. Raychaudhuri, S. 2018-06-20 doi:10.1101/351130 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion ]]> https://biorxiv.org/content/10.1101/351387v1?rss=1 25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology. ]]> Gutierrez, J. M. Feizi, A. Li, S. Kallehauge, T. B. Hefzi, H. Grav, L. M. Ley, D. Hizal, D. B. Betenbaugh, M. J. Voldborg, B. Kildegaard, H. F. Lee, G. M. Palsson, B. O. Nielsen, J. Lewis, N. 2018-06-20 doi:10.1101/351387 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Allele-specific NKX2-5 binding underlies multiple genetic associations with human EKG traits ]]> https://biorxiv.org/content/10.1101/351411v1?rss=1 Benaglio, P. D'Antonio-Chronowska, A. Greenwald, W. W. DeBoever, C. Li, H. Drees, F. Singhal, S. Matsui, H. D'Antonio, M. Smith, E. N. Frazer, K. A. 2018-06-20 doi:10.1101/351411 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Communication and quorum sensing in non-living mimics of eukaryotic cells ]]> https://biorxiv.org/content/10.1101/352666v1?rss=1 Niederholtmeyer, H. Chaggan, C. Devaraj, N. K. 2018-06-20 doi:10.1101/352666 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION ]]> https://biorxiv.org/content/10.1101/352674v1?rss=1 Justice, A. E. Karaderi, T. Highland, H. M. Young, K. L. Graff, M. Lu, Y. Turcot, V. Auer, P. L. Fine, R. S. Guo, X. Schurmann, C. Lempradl, A. Marouli, E. Mahajan, A. Winkler, T. W. Locke, A. E. Medina-Gomez, C. Esko, T. Vedantam, S. Giri, A. Lo, K. S. Alfred, T. Mudgal, P. Ng, M. C. Heard-Costa, N. C. Feitosa, M. F. Manning, A. K. Willems, S. M. Sivapalaratnam, S. Abecasis, G. Alam, D. S. Allison, M. Amouyel, P. Arzumanyan, Z. Balkau, B. Bastarache, L. Bergmann, S. Bielak, L. F. Blüher, M. Boehnke, M. Boeing, H. Boerwinkle, E. Böger, 2018-06-30 doi:10.1101/352674 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ CDeep3M - Plug-and-Play cloud based deep learning for image segmentation of light, electron and X-ray microscopy ]]> https://biorxiv.org/content/10.1101/353425v1?rss=1 Haberl, M. Churas, C. Tindall, L. Boassa, D. Phan, S. Bushong, E. A. Madany, M. Akay, R. Deerinck, T. J. Peltier, S. T. Ellisman, M. H. 2018-06-21 doi:10.1101/353425 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ TP53 mutations promote immunogenic activity in breast cancer ]]> https://biorxiv.org/content/10.1101/354779v1?rss=1 Liu, Z. Jiang, Z. Gao, Y. Wang, L. Chen, C. Wang, X. 2018-06-24 doi:10.1101/354779 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ Evidence that recurrent Group A streptococcus tonsillitis is animmunosusceptibility disease involving antibody deficiency and aberrant Tfh cells ]]> https://biorxiv.org/content/10.1101/356741v1?rss=1 Dan, J. M. Havenar-Daughton, C. Kendric, K. Kaushik, K. Rosales, S. Anderson, E. LaRock, C. Vijayanand, P. Seumois, G. Layfield, D. Cutress, R. Ottensmeier, C. Lindestam Arlehamn, C. Sette, A. Nizet, V. Bothwell, M. Brigger, M. Crotty, S. 2018-06-27 doi:10.1101/356741 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans ]]> https://biorxiv.org/content/10.1101/357756v1?rss=1 Reddy, K. C. Dror, T. Underwood, R. S. Osman, G. A. Desjardins, C. A. Cuomo, C. A. Barkoulas, M. Troemel, E. R. 2018-06-28 doi:10.1101/357756 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Peak p-values and false discovery rate inference in neuroimaging ]]> https://biorxiv.org/content/10.1101/358051v1?rss=1 Schwartzman, A. Telschow, F. 2018-06-28 doi:10.1101/358051 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Breakdown of spatial coding and neural synchronization in epilepsy ]]> https://biorxiv.org/content/10.1101/358580v1?rss=1 Shuman, T. Aharoni, D. Cai, D. J. Lee, C. R. Chavlis, S. Taxidis, J. Flores, S. E. Cheng, K. Javaherian, M. Kaba, C. C. Shtrahman, M. Kakhurin, K. I. Masmanidis, S. Khakh, B. S. Poirazi, P. Silva, A. J. Golshani, P. 2018-06-29 doi:10.1101/358580 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ VPAC1 couples with TRPV4 channel to promote calcium-dependent gastric cancer progression ]]> https://biorxiv.org/content/10.1101/360404v1?rss=1 Tang, B. Wu, J. Zhu, M. X. Sun, X. Liu, J. Xie, R. Dong, T. X. Xiao, Y. Carethers, J. M. Yang, S.-M. Dong, H. 2018-07-02 doi:10.1101/360404 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ Beauty-in-averageness and its contextual modulations: A Bayesian statistical account ]]> https://biorxiv.org/content/10.1101/360651v1?rss=1 Ryali, C. Yu, A. J. 2018-07-04 doi:10.1101/360651 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Computational modeling of social face perception in humans: Leveraging the active appearance model ]]> https://biorxiv.org/content/10.1101/360776v1?rss=1 Guan, J. Ryali, C. Yu, A. J. 2018-07-03 doi:10.1101/360776 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Ad-Seq, a genome-wide DNA-adduct profiling assay ]]> https://biorxiv.org/content/10.1101/364794v1?rss=1 Harismendy, O. Howell, S. 2018-07-08 doi:10.1101/364794 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria ]]> https://biorxiv.org/content/10.1101/367797v1?rss=1 Ortega, F. E. Koslover, E. F. Theriot, J. A. 2018-07-12 doi:10.1101/367797 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Dorsal Premotor Contributions to Auditory Rhythm Perception: Causal Transcranial Magnetic Stimulation Studies of Interval, Tempo, and Phase ]]> https://biorxiv.org/content/10.1101/368597v1?rss=1 Ross, J. M. Iversen, J. R. Balasubramaniam, R. R. 2018-07-13 doi:10.1101/368597 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Overview of the SAMPL6 host-guest binding affinity prediction challenge ]]> https://biorxiv.org/content/10.1101/371724v1?rss=1 Rizzi, A. Murkli, S. McNeill, J. N. Yao, W. Sullivan, M. Gilson, M. K. Chiu, M. W. Isaacs, L. Gibb, B. C. Mobley, D. L. Chodera, J. D. 2018-07-19 doi:10.1101/371724 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Spatial Control of Neuronal Metabolism Through Glucose-Mediated Mitochondrial Transport Regulation ]]> https://biorxiv.org/content/10.1101/372284v1?rss=1 Agrawal, A. Pekkurnaz, G. Koslover, E. F. 2018-07-18 doi:10.1101/372284 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Co-occurring genetic alterations in the RAS pathway promote resistance to MET inhibitor treatment in non-small cell lung cancer with a MET exon 14 skipping mutation ]]> https://biorxiv.org/content/10.1101/374181v1?rss=1 Rotow, J. K. Gui, P. Wu, W. Raymond, V. M. Lanman, R. B. Kaye, F. J. Peled, N. Fece de la Cruz, F. Nadres, B. Corcoran, R. B. Yeh, I. Bastian, B. C. Starostik, P. Newsom, K. Olivas, V. R. Wolff, A. M. Fraser, J. S. Collisson, E. A. McCoach, C. E. Blakely, C. M. Bivona, T. G. 2018-07-22 doi:10.1101/374181 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ A conserved mechanism for meiotic chromosome organization through self-assembly of a filamentous chromosome axis core ]]> https://biorxiv.org/content/10.1101/375220v1?rss=1 West, A. M. V. Rosenberg, S. C. Ur, S. N. Lehmer, M. K. Ye, Q. Hagemann, G. Caballero, I. Uson, I. Herzog, F. Corbett, K. D. 2018-07-24 doi:10.1101/375220 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ A nonlinear simulation framework supports adjusting for age when analyzing BrainAGE. ]]> https://biorxiv.org/content/10.1101/377648v1?rss=1 Le, T. T. Kuplicki, R. McKinney, B. A. Yeh, H.-w. Thompson, W. K. Tulsa 1000 Investigators, Paulus, M. P. 2018-07-26 doi:10.1101/377648 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Episodic Memory Can Replace Active Storage in Visual Working Memory ]]> https://biorxiv.org/content/10.1101/381848v1?rss=1 Schurgin, M. W. Cunningham, C. A. Egeth, H. E. Brady, T. F. 2018-08-01 doi:10.1101/381848 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ TreeN93: a non-parametric distance-based method for inferring viral transmission clusters ]]> https://biorxiv.org/content/10.1101/383190v1?rss=1 Moshiri, N. 2018-08-02 doi:10.1101/383190 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Long-read amplicon denoising ]]> https://biorxiv.org/content/10.1101/383794v1?rss=1 Kumar, V. Vollbrecht, T. Chernyshev, M. Mohan, S. Hanst, B. Bavafa, N. Lorenzo, A. Ketteringham, R. Eren, K. Golden, M. Oliveira, M. F. Murrell, B. 2018-08-03 doi:10.1101/383794 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions ]]> https://biorxiv.org/content/10.1101/384099v1?rss=1 Richelle, A. Chiang, A. W. T. Kuo, C.-C. Lewis, N. E. 2018-08-03 doi:10.1101/384099 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive ]]> https://biorxiv.org/content/10.1101/386441v1?rss=1 1000 TB data worth of raw sequence data) into a single unified dataset of allelic read counts for nearly 300,000 variants of biomedical relevance curated by NCBI dbSNP, where germline variants were detected in a median of 912 sequencing runs, and somatic variants were detected in a median of 4,876 sequencing runs, suggesting that this dataset facilitates identification of sequencing runs that harbor variants of interest. Allelic read counts obtained using a targeted alignment were very similar to read counts obtained from whole genome alignment. Analyzing allelic read count data for matched DNA and RNA samples from tumors, we find that RNA-seq can also recover variants identified by WXS, suggesting that reprocessed allelic read counts can support variant detection across different library strategies in SRA. This study provides a rich database of known human variants across SRA samples that can support future meta-analyses of human sequence variation. ]]> Tsui, B. Y. Dow, M. Skola, D. Carter, H. 2018-08-07 doi:10.1101/386441 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Human pluripotent stem cell-derived brain pericyte-like cells induce blood-brain barrier properties ]]> https://biorxiv.org/content/10.1101/387100v1?rss=1 Stebbins, M. J. Gastfriend, B. D. Canfield, S. G. Lee, M.-S. Richards, D. Faubion, M. G. Li, W.-J. Daneman, R. Palecek, S. P. Shusta, E. V. 2018-08-07 doi:10.1101/387100 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Human frontoparietal cortex represents behaviorally-relevant target status during invariant object recognition ]]> https://biorxiv.org/content/10.1101/387498v1?rss=1 Henderson, M. M. Serences, J. 2018-08-09 doi:10.1101/387498 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Reconciling fMRI and EEG indices of attentional modulations in human visual cortex ]]> https://biorxiv.org/content/10.1101/391193v1?rss=1 Itthipuripat, S. Sprague, T. Serences, J. 2018-08-13 doi:10.1101/391193 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA ]]> https://biorxiv.org/content/10.1101/396275v1?rss=1 Yang, E.-W. Bahn, J. H. Hsiao, E. Y.-H. Tan, B. X. Sun, Y. Fu, T. Zhou, B. Van Nostrand, E. L. Pratt, G. A. Freese, P. Wei, X. Quinones-Valdez, G. Urban, A. E. Graveley, B. R. Burge, C. B. Yeo, G. W. Xiao, X. 2018-08-20 doi:10.1101/396275 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ The genetic architecture of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/399402v1?rss=1 Grasby, K. L. Jahanshad, N. Painter, J. N. Colodro-Conde, L. Bralten, J. Hibar, D. P. Lind, P. A. Pizzagalli, F. Ching, C. R. McMahon, M. A. Shatokhina, N. Zsembik, L. C. P. Agartz, I. Alhusaini, S. Almeida, M. A. Alnaes, D. Amlien, I. K. Andersson, M. Ard, T. Armstrong, N. J. Ashley-Koch, A. Bernard, M. Brouwer, R. M. Buimer, E. E. Bülow, R. Bürger, C. Cannon, D. M. Chakravarty, M. Chen, Q. Cheung, J. W. Couvy-Duchesne, B. Dale, A. M. Dalvie, S. de Araujo, T. K. de Zubicaray, G. I. de Zwarte, S. M. den Braber, A. Doan, N. T. Dohm, K. Ehrlich, S. Engel 2018-09-03 doi:10.1101/399402 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Planar cell polarity pathway and development of the human visual cortex ]]> https://biorxiv.org/content/10.1101/404558v1?rss=1 Shin, J. Ma, S. Hofer, E. Patel, Y. Roshchupkin, G. Sousa, A. M. Jian, X. Gottesmann, R. Mosley, T. H. Fornage, M. Saba, Y. Pirpamer, L. Schmidt, R. Schmidt, H. Mazoyer, B. Carrion-Castillo, A. Bis, J. Li, S. Yang, Q. Luciano, M. Karama, S. Lewis, L. Bastin, M. Harris, M. A. Deary, I. Wardlaw, J. M. Scholz, M. Loeffler, M. Witte, V. Beyer, F. Villringer, A. Adams, H. H. Ikrum, M. A. Kremen, W. S. Gillespie, N. A. Sestan, N. Pausova, Z. Seshadri, S. Paus, T. 2018-08-31 doi:10.1101/404558 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Social integration predicts mitochondrial DNA copy number in rhesus macaques ]]> https://biorxiv.org/content/10.1101/408849v1?rss=1 Debray, R. Snyder-Mackler, N. Kohn, J. Wilson, M. Barreiro, L. Tung, J. 2018-09-06 doi:10.1101/408849 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Genetic Determinants of Cortical Structure (Thickness, Surface Area and Volumes) among Disease Free Adults in the CHARGE Consortium ]]> https://biorxiv.org/content/10.1101/409649v1?rss=1 Hofer, E. Roshchupkin, G. V. Adams, H. Knol, M. Lin, H. Li, S. Zare, H. Ahmad, S. Armstrong, N. Satizabal, C. Bernard, M. Bis, J. Gillespie, N. Luciano, M. Mishra, A. Scholz, M. Teumer, A. Xia, R. Jian, X. Mosley, T. Saba, Y. Pirpamer, L. Seiler, S. Becker, J. Carmichael, O. Rotter, J. Psaty, B. Lopez, O. Amin, N. Lee, S. Yang, Q. Himali, J. Maillard, P. Beiser, A. DeCarli, C. Karama, S. Lewis, L. Bastin, M. Harris, M. Deary, I. Witte, V. Beyer, F. Loeffler, M. Mather, K. Schofield, P. Thalamuthu, A. Kwok, J. Wright, M. Ames, D. Trollor, J. Jia 2018-09-09 doi:10.1101/409649 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments ]]> https://biorxiv.org/content/10.1101/411835v1?rss=1 Juric, I. Yu, M. Abnousi, A. Raviram, R. Fang, R. Zhao, Y. Zhang, Y. Yang, Y. Li, Y. Ren, B. Hu, M. 2018-09-08 doi:10.1101/411835 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism ]]> https://biorxiv.org/content/10.1101/414912v1?rss=1 Cheng, C. O'brien, E. J. McCloskey, D. Utrilla, J. Olson, C. LaCroix, R. A. Sandberg, T. E. Feist, A. M. Palsson, B. O. King, Z. A. 2018-09-12 doi:10.1101/414912 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Active protein neddylation or ubiquitylation is dispensable for stress granule dynamics ]]> https://biorxiv.org/content/10.1101/418848v1?rss=1 Markmiller, S. Fulzele, A. Higgins, R. Yeo, G. Bennett, E. J. 2018-09-15 doi:10.1101/418848 Cold Spring Harbor Laboratory Press 2018-09-15 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Split-miniSOG for detecting and localizing intracellular protein-protein interactions: application to correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/423566v1?rss=1 BOASSA, D. Lemieux, S. P. Lev-Ram, V. Hu, J. Xiong, Q. Phan, S. Mackey, M. Ramachandra, R. Adams, S. R. Tsien, R. Y. Ellisman, M. H. Ngo, J. T. 2018-09-21 doi:10.1101/423566 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity ]]> https://biorxiv.org/content/10.1101/423590v1?rss=1 Chiang, A. W. T. Li, S. Kellman, B. P. Chattopadhyay, G. Zhang, Y. Kuo, C.-C. Gutierrez, J. M. Ghazi, F. Schmeisser, H. Menard, P. Petersen Bjorn, S. Voldborg, B. G. Rosenberg, A. S. Puig, M. Lewis, N. E. 2018-09-21 doi:10.1101/423590 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ A Cortico- Basal Ganglia Model for choosing an optimal rehabilitation strategy in Hemiparetic Stroke ]]> https://biorxiv.org/content/10.1101/423863v1?rss=1 Chakravarthy, S. Muralidharan, V. Narayanamurthy, R. Jayakumar, S. Elango, S. 2018-09-21 doi:10.1101/423863 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ A Sparse Unreliable Distributed Code Underlies the Limits of Behavioral Discrimination ]]> https://biorxiv.org/content/10.1101/424713v1?rss=1 Sriram, B. Cruz-Martin, A. Li, L. Reinagel, P. Ghosh, A. 2018-09-23 doi:10.1101/424713 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Repeated Δ9-tetrahydrocannabinol (THC) vapor inhalation during adolescence: Sex differences inacute thermoregulatory tolerance and in feeding during adulthood ]]> https://biorxiv.org/content/10.1101/426064v1?rss=1 Nguyen, J. D. Creehan, K. M. Kerr, T. M. Taffe, M. A. 2018-09-25 doi:10.1101/426064 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Visualizing metabolic network dynamics through time-series metabolomics data ]]> https://biorxiv.org/content/10.1101/426106v1?rss=1 Buchweitz, L. F. Yurkovich, J. T. Blessing, C. Kohler, V. Schwarzkopf, F. King, Z. A. Yang, L. Johannsson, F. Sigurjonsson, O. Rolfsson, O. Heinrich, J. Draeger, A. 2018-09-26 doi:10.1101/426106 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Asymmetric ephaptic inhibition between compartmentalized olfactory receptor neurons ]]> https://biorxiv.org/content/10.1101/427252v1?rss=1 Zhang, Y. Tsang, T. K. Bushong, E. A. Chu, L.-A. Chiang, A.-S. Ellisman, M. H. Reingruber, J. Su, C.-Y. 2018-09-25 doi:10.1101/427252 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Extracellular matrix components are required to protect Bacillus subtilis colonies from T6SS-dependent Pseudomonas invasion and modulate co-colonization of plant ]]> https://biorxiv.org/content/10.1101/429001v1?rss=1 Molina-Santiago, C. Pearson, J. R. Navarro, Y. Berlanga-Clavero, M. V. Caraballo-Rodriguez, A. M. Petras, D. Cazorla, F. M. de Vicente, A. Dorrestein, P. C. Romero, D. 2018-10-05 doi:10.1101/429001 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance ]]> https://biorxiv.org/content/10.1101/432666v1?rss=1 Cirelli, K. M. Carnathan, D. G. Nogal, B. Rodriguez, O. L. Martin, J. T. Upadhyay, A. A. Enemuo, C. A. Gebru, E. H. Choe, Y. Viviano, F. Nakao, C. Pauthner, M. Reiss, S. Cottrell, C. A. Bastidas, R. Gibson, W. Wolabaugh, A. N. Melo, M. B. Cosette, B. Kuman, V. Patel, N. Tokatlian, T. Menis, S. Kulp, D. W. Burton, D. R. Murrell, B. Bosinger, S. E. Schief, W. R. Ward, A. B. Watson, C. T. Silvestri, G. Irvine, D. J. Crotty, S. 2018-10-01 doi:10.1101/432666 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores ]]> https://biorxiv.org/content/10.1101/432906v1?rss=1 Rabiee, M. Mirarab, S. 2018-10-02 doi:10.1101/432906 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ TCR-pMHC bond length controls TCR ligand discrimination ]]> https://biorxiv.org/content/10.1101/433938v1?rss=1 Sasmal, D. K. Feng, W. Roy, S. Leung, P. He, Y. Cai, C. Cao, G. Lian, H. Qin, J. Hui, E. Schreiber, H. Adams, E. Huang, J. 2018-10-03 doi:10.1101/433938 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Multi-allele species reconstruction using ASTRAL ]]> https://biorxiv.org/content/10.1101/439489v1?rss=1 Rabiee, M. Sayyari, E. Mirarab, S. 2018-10-11 doi:10.1101/439489 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Measuring the average power of neural oscillations ]]> https://biorxiv.org/content/10.1101/441626v1?rss=1 40 hours of human M/EEG and ECoG, we show that in all cases it is not.nC_LIO_LIThis effect is demonstrated in simple simulation of an event-related task.nC_LIO_LIOverinflated power estimates are reduced via log-transformation or median power.nC_LI ]]> Izhikevich, L. Gao, R. Peterson, E. Voytek, B. 2018-10-13 doi:10.1101/441626 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Cell Mechanics at the Rear Act To Steer the Direction of Cell Migration ]]> https://biorxiv.org/content/10.1101/443408v1?rss=1 Allen, G. M. Lee, K. C. Barnhart, E. L. Tsuchida, M. A. Wilson, C. A. Gutierrez, E. Groisman, A. Mogilner, A. Theriot, J. A. 2018-10-15 doi:10.1101/443408 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Comparative genetic architectures of schizophrenia in East Asian and European populations ]]> https://biorxiv.org/content/10.1101/445874v1?rss=1 Lam, M. Chen, C.-Y. Li, Z. Martin, A. Bryois, J. Ma, X. Gaspar, H. Ikeda, M. Benyamin, B. Brown, B. Liu, R. Zhou, W. Huan, L. Kamatani, Y. Kim, S.-W. Kubo, M. Kusumawardhani, A. Liu, C.-M. Ma, H. Periyasamy, S. Takahashi, A. Wang, Q. Xu, Z. Yu, H. Zhu, F. Psychiatric Genomics Consortium - Schizophrenia Working Group, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and Netherland (GREAT-CN), Chen, W. Faraone, S. Glatt, S. He, L. Hyman, S. Hwu, H.-G. Li, T. McCarroll, S. Neale, B. Sklar, P. Wildenauer, D. Yu, X. Zh 2018-10-17 doi:10.1101/445874 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ The RNA-binding protein AATF coordinates rRNA maturation ]]> https://biorxiv.org/content/10.1101/446260v1?rss=1 Kaiser, R. Ignarski, M. Van Nostrand, E. L. Frese, C. Jain, M. Cukoski, S. Heinen, H. Schaechter, M. Bunte, K. Frommolt, P. Keller, P. Helm, M. Bohl, K. Höhne, M. Schermer, B. Benzing, T. Höpker, K. Dieterich, C. Yeo, G. W. Mueller, R.-U. Fabretti, F. 2018-10-17 doi:10.1101/446260 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network ]]> https://biorxiv.org/content/10.1101/446666v1?rss=1 Hu, J. Li, Y. Hao, Y. Zheng, T. Parada, G. Wu, H. Lin, S. Wang, S. Zhao, X. Goldman, R. Cai, S. Guo, M. 2018-10-17 doi:10.1101/446666 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Homogenization of capillary flow and oxygenation in deeper cortical layers correlates with increased oxygen extraction ]]> https://biorxiv.org/content/10.1101/450932v1?rss=1 Li, B. Esipova, T. V. Sencan, I. Kılıc, K. Fu, B. Desjardins, M. Moeini, M. Kura, S. Yaseen, M. A. Lesage, F. Ostergaard, L. Devor, A. Boas, D. A. Vinogradov, S. A. Sakadzic, S. 2018-10-23 doi:10.1101/450932 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic β-cell function ]]> https://biorxiv.org/content/10.1101/451542v1?rss=1 Wortham, M. Benthuysen, J. R. Wallace, M. Savas, J. N. Mulas, F. Divakaruni, A. S. Liu, F. Albert, V. Taylor, B. L. Sui, Y. Saez, E. Murphy, A. N. Yates, J. R. Metallo, C. M. Sander, M. 2018-10-24 doi:10.1101/451542 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Hippocampal theta bursting and waveform shape reflect CA1 spiking patterns ]]> https://biorxiv.org/content/10.1101/452987v1?rss=1 Cole, S. R. Voytek, B. 2018-10-25 doi:10.1101/452987 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Heritability and genetic variance of dementia with Lewy bodies ]]> https://biorxiv.org/content/10.1101/454249v1?rss=1 Guerreiro, R. Escott-Price, V. Hernandez, D. Kun-Rodrigues, C. Ross, O. Orme, T. Neto, J. L. Carmona, S. Dehghani, N. Eicher, J. D. Shepherd, C. Parkkinen, L. Darwent, L. Heckman, M. G. Scholz, S. Troncoso, J. Pletnikova, O. Dawson, T. Rosenthal, L. Ansorge, O. Clarimon, J. Lleo, A. Morenas-Rodriguez, E. Clark, L. Honig, L. Marder, K. Lemstra, A. Rogaeva, E. St. George-Hyslop, P. Londos, E. Zetterberg, H. Barber, I. Braae, A. Brown, K. Morgan, K. Troakes, C. Al-Sarraj, S. Lashley, T. Holton, J. Compta, Y. Van Deerlin, V. Serrano, G. Beach, T. Lesage, 2018-10-26 doi:10.1101/454249 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells ]]> https://biorxiv.org/content/10.1101/456491v1?rss=1 HIGASHIJIMA, Y. MATSUI, Y. SHIMAMURA, T. TSUTSUMI, S. NAKAKI, R. ABE, Y. LINK, V. M. OSAKA, M. YOSHIDA, M. WATANABE, R. TANAKA, T. TAGUCHI, A. MIURA, M. INOUE, T. NANGAKU, M. KIMURA, H. FURUKAWA, T. ABURATANI, H. WADA, Y. GLASS, C. K. KANKI, Y. 2018-11-11 doi:10.1101/456491 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ The Molecular Basis of Monopolin Recruitment to the Kinetochore ]]> https://biorxiv.org/content/10.1101/456798v1?rss=1 Plowman, R. Singh, N. Duro, E. Payan, A. Corbett, K. D. Marston, A. L. 2018-10-30 doi:10.1101/456798 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Image processing and analysis methods for the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/457739v1?rss=1 Hagler, D. J. Hatton, S. N. Makowski, C. Cornejo, M. D. Fair, D. A. Dick, A. S. Sutherland, M. T. Casey, B. J. Barch, D. M. Harms, M. P. Watts, R. Bjork, J. M. Garavan, H. P. Hilmer, L. Pung, C. J. Sicat, C. S. Kuperman, J. Bartsch, H. Xue, F. Heitzeg, M. M. Laird, A. R. Trinh, T. T. Gonzalez, R. Tapert, S. F. Riedel, M. C. Squeglia, L. M. Hyde, L. W. Rosenberg, M. D. Earl, E. A. Howlett, K. D. Baker, F. C. Soules, M. Diaz, J. Ruiz de Leon, O. Thompson, W. K. Neale, M. C. Herting, M. Sowell, E. R. Alvarez, R. P. Hawes, S. W. Sanchez, M. Bodurka, J. Bre 2018-11-04 doi:10.1101/457739 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Intermittent abstinence potentiates oxycodone self-administration under extended access conditions and alters brain reward sensitivity ]]> https://biorxiv.org/content/10.1101/460048v1?rss=1 Nguyen, J. Grant, Y. Taffe, M. 2018-11-02 doi:10.1101/460048 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae ]]> https://biorxiv.org/content/10.1101/463620v1?rss=1 Kang, K. B. Ernst, M. van der Hooft, J. J. J. da Silva, R. R. Park, J. Medema, M. H. Sung, S. H. Dorrestein, P. C. 2018-11-07 doi:10.1101/463620 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements ]]> https://biorxiv.org/content/10.1101/468181v1?rss=1 Li, S. Cha, S. W. Heffner, K. Hizal, D. B. Bowen, M. Chaerkady, R. Cole, R. Tejwani, V. Kaushik, P. Henry, M. Meleady, P. Sharfstein, S. Betenbaugh, M. Bafna, V. Lewis, N. 2018-11-12 doi:10.1101/468181 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model ]]> https://biorxiv.org/content/10.1101/472688v1?rss=1 Torres, P. Ho, B. Arroyo, P. Sau, L. Chen, A. Kelley, S. Thackray, V. 2018-11-19 doi:10.1101/472688 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Modulation of RNA-dependent interactions in stress granules prevents persistent TDP-43 accumulation in ALS/FTD ]]> https://biorxiv.org/content/10.1101/474577v1?rss=1 Fang, M. Y. Markmiller, S. Dowdle, W. E. Vu, A. Q. Bushway, P. J. Ding, S. Mercola, M. M. Lewcock, J. W. Yeo, G. 2018-11-20 doi:10.1101/474577 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Reconstitution of eukaryotic chromosomes and manipulation of DNA N6-methyladenine alters chromatin and gene expression ]]> https://biorxiv.org/content/10.1101/475384v1?rss=1 Beh, L. Y. Debelouchina, G. T. Clay, D. M. Thompson, R. E. Lindblad, K. A. Hutton, E. R. Bracht, J. R. Sebra, R. P. Muir, T. W. Landweber, L. F. 2018-11-20 doi:10.1101/475384 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state ]]> https://biorxiv.org/content/10.1101/481283v1?rss=1 Stamenova, E. K. Durand, N. Dudchenko, O. Shamim, M. S. Huang, S.-C. Jiang, Y. Bochkov, I. D. Rao, S. S. P. Lander, E. S. Gnirke, A. Aiden, E. L. 2018-11-29 doi:10.1101/481283 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Mechanism of action of methotrexate against Zika virus ]]> https://biorxiv.org/content/10.1101/481440v1?rss=1 Beck, S. Bernatchez, J. A. Zhu, Z. Oliveira, M. F. Smith, D. M. Siqueira-Neto, J. L. 2018-11-29 doi:10.1101/481440 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Mutations In PIK3C2A Cause Syndromic Short Stature, Skeletal Abnormalities, and Cataracts Associated With Ciliary Dysfunction ]]> https://biorxiv.org/content/10.1101/488411v1?rss=1 Tiosano, D. Baris Feldman, H. Chen, A. Hitzert, M. M. Schueler, M. Gulluni, F. Wiesener, A. Bergua, A. Mory, A. Copeland, B. Gleeson, J. G. Rump, P. van Meer, H. Sival, D. A. Haucke, V. Kriwinsky, J. Knaup, K. X. Reis, A. Hauer, N. N. Hirsch, E. Roepman, R. Pfundt, R. Thiel, C. T. Wiesener, M. S. Aslanyan, M. G. Buchner, D. A. 2018-12-07 doi:10.1101/488411 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Rapid screening of engineered microbial therapies in a 3-D multicellular model ]]> https://biorxiv.org/content/10.1101/491159v1?rss=1 Harimoto, T. Singer, Z. Velazquez, O. Zhang, J. Castro, S. Hinchliffe, T. Mather, W. Danino, T. 2018-12-10 doi:10.1101/491159 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers ]]> https://biorxiv.org/content/10.1101/491845v1?rss=1 Fan, S. Tang, J. Li, N. Zhao, Y. Ai, R. Zhang, K. Wang, M. Du, W. Wang, W. 2018-12-18 doi:10.1101/491845 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Schizophrenia risk conferred by protein-coding de novo mutations ]]> https://biorxiv.org/content/10.1101/495036v1?rss=1 Howrigan, D. Rose, S. A. Samocha, K. E. Fromer, M. Cerrato, F. Chen, W. J. Churchhouse, C. Chambert, K. Chandler, S. D. Daly, M. J. Dumont, A. Genovese, G. Hwu, H.-G. Laird, N. Kosmicki, J. A. Moran, J. Roe, C. Singh, T. Wang, S.-H. Faraone, S. Glatt, S. McCarroll, S. Tsuang, M. Neale, B. 2018-12-13 doi:10.1101/495036 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ The molecular architecture of engulfment during Bacillus subtilis sporulation ]]> https://biorxiv.org/content/10.1101/498220v1?rss=1 Khanna, K. Lopez-Garrido, J. Zhao, Z. Watanabe, R. Yuan, Y. Pogliano, K. Villa, E. 2018-12-16 doi:10.1101/498220 Cold Spring Harbor Laboratory Press 2018-12-16 <![CDATA[ Beyond SNP Heritability: Polygenicity and Discoverability of Phenotypes Estimated with a Univariate Gaussian Mixture Model ]]> https://biorxiv.org/content/10.1101/498550v1?rss=1 1%. We apply the model to diverse phenotypes and validate the implementation with simulations. We find model polygenicities ranging from [~=] 2 x 10-5 to [~=] 4 x 10-3, with discoverabilities similarly ranging over two orders of magnitude. A power analysis allows us to estimate the proportions of phenotypic variance explained additively by causal SNPs at current sample sizes, and map out sample sizes required to explain larger portions of additive SNP heritability. The model also allows for estimating residual inflation. ]]> Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Sundar, V. S. Thompson, P. Andreassen, O. A. Dale, A. M. 2018-12-17 doi:10.1101/498550 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Structures of the PKA RIα holoenzyme with the FLHCC driver J-PKAcα or wild type PKAcα ]]> https://biorxiv.org/content/10.1101/505347v1?rss=1 Cao, B. Lu, T.-W. Martinez Fiesco, J. Tomasini, M. Fan, L. Simon, S. Taylor, S. Zhang, P. 2018-12-22 doi:10.1101/505347 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ Cryo-EM Structure of OSCA1.2 from Oryza sativa: Mechanical basis of hyperosmolality-gating in Plants ]]> https://biorxiv.org/content/10.1101/505453v1?rss=1 Maity, K. Heumann, J. McGrath, A. P. Kopcho, N. J. Hsu, P.-K. Lee, C.-W. Mapes, J. H. Garza, D. Krishnan, S. Morgan, G. P. Medrano-Soto, A. Hendargo, K. J. Klose, T. Rees, S. D. Saier, M. H. Pineros, M. Komives, E. A. Schroeder, J. I. Chang, G. Stowell, M. H. B. 2018-12-30 doi:10.1101/505453 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Partitioning the genetic architecture of amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/505693v1?rss=1 3 million people. We found strong genetic enrichment between ALS and a number of disparate traits including frontotemporal dementia, coronary artery disease, C-reactive protein, celiac disease and memory function. Beyond C9ORF72, we detected novel genetic signal within numerous loci including GIPC1, ELMO1 and COL16A and confirmed previously reported variants, such as ATXN2, KIF5A, UNC13A and MOBP. We found that ALS variants form a small-world co-expression network characterized by highly inter-connected hub genes. This network clustered into smaller sub-networks, each associated with a unique function. Altered gene expression of several sub-networks and hubs was over-represented in neuropathological samples from ALS patients and SOD1 G93A mice. Our collective findings indicate that the genetic architecture of ALS can be partitioned into distinct components where some genes are highly important for developing disease. These findings have implications for stratification and enrichment strategies for ALS clinical trials. ]]> Broce, I. J. Fan, C. C. Olney, N. T. Lomen-Hoerth, C. Finkbeiner, S. Atassi, N. Cudkowicz, M. E. Yokoyama, J. S. Kao, A. Dillon, W. P. Glastonbury, C. M. Hess, C. P. van Rheenen, W. Veldink, J. H. Al-Chalabi, A. Andreassen, O. A. Dale, A. M. Seeley, W. W. Sugrue, L. P. Karch, C. M. Miller, B. L. Desikan, R. S. 2018-12-23 doi:10.1101/505693 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ Cooperation of dominant oncogenes with regulatory germline variants shapes clinical outcomes in childhood cancer ]]> https://biorxiv.org/content/10.1101/506659v1?rss=1 Musa, J. Cidre-Aranaz, F. Aynaud, M.-M. Orth, M. F. Mirabeau, O. Varon, M. Grossetete, S. Surdez, D. Ohmura, S. Gerke, J. S. Marchetto, A. Dallmayer, M. Baldauf, M. C. Gartlgruber, M. Westermann, F. Stein, S. Hoelting, T. L. B. Knott, M. Sannino, G. Li, J. Romero-Perez, L. Hartmann, W. Dirksen, U. Gymrek, M. Anderson, N. D. Shlien, A. Rotblat, B. Kirchner, T. Delattre, O. Grunewald, T. G. P. 2018-12-27 doi:10.1101/506659 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Evolutionary loss of foot muscle during development with characteristics of atrophy and no evidence of cell death ]]> https://biorxiv.org/content/10.1101/512590v1?rss=1 Tran, M. P. Tsutsumi, R. Erberich, J. M. Chen, K. D. Flores, M. D. Cooper, K. L. 2019-01-06 doi:10.1101/512590 Cold Spring Harbor Laboratory Press 2019-01-06 <![CDATA[ Visual-olfactory integration in the human disease vector mosquito, Aedes aegypti ]]> https://biorxiv.org/content/10.1101/512996v1?rss=1 Vinauger, C. Van Breugel, F. Locke, L. Tobin, K. Dickinson, M. Fairhall, A. Akbari, O. Riffell, J. 2019-01-07 doi:10.1101/512996 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B ]]> https://biorxiv.org/content/10.1101/513366v1?rss=1 Shi, K. Demir, O. Carpenter, M. A. Banerjee, S. Harki, D. A. Amaro, R. E. Harris, R. S. Aihara, H. 2019-01-07 doi:10.1101/513366 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Geometric control of frequency modulation of cAMP oscillations due to Ca2+-bursts in dendritic spines ]]> https://biorxiv.org/content/10.1101/520643v1?rss=1 Ohadi, D. Rangamani, P. 2019-01-15 doi:10.1101/520643 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines ]]> https://biorxiv.org/content/10.1101/521740v1?rss=1 Ohadi, D. Schmitt, D. L. Calabrese, B. Halpain, S. Zhang, J. Rangamani, P. 2019-01-16 doi:10.1101/521740 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Global phylogeography and ancient evolution of the widespread human gut virus crAssphage ]]> https://biorxiv.org/content/10.1101/527796v1?rss=1 Edwards, R. Vega, A. Norman, H. Ohaeri, M. C. Levi, K. Dinsdale, E. Cinek, O. Aziz, R. McNair, K. Barr, J. Bibby, K. Brouns, S. Cazares, A. de Jonge, P. A. Desnues, C. Diaz-Munoz, S. Fineran, P. Kurilshikov, A. Lavigne, R. Mazankova, K. McCarthy, D. Nobrega, F. Reyes, A. Tapia, G. Trefault, N. Tyakht, A. Vinuesa, P. Wagemans, J. Zhernakova, A. Aarestrup, F. Ahmadov, G. Alassaf, A. Anton, J. Asangba, A. Billings, E. Cantu, A. Carlton, J. Cazares Lopez, D. Cho, G.-S. Condeff, T. Cortes, P. Cranfield, M. Cuevas, D. De la Iglesia, R. Decewicz, P. Doane, 2019-01-26 doi:10.1101/527796 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Planning Face, Hand, and Leg Movements: Anatomical Constraints on Preparatory Inhibition. ]]> https://biorxiv.org/content/10.1101/529107v1?rss=1 Labruna, L. Tischler, C. Cazares, C. Greenhouse, I. Duque, J. Lebon, F. Ivry, R. B. 2019-01-26 doi:10.1101/529107 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage ]]> https://biorxiv.org/content/10.1101/530204v1?rss=1 Li, Z.-R. Li, J. Cai, W. Lai, J. McKinnie, S. Zhang, W.-P. Moore, B. Zhang, W. Qian, P.-Y. 2019-01-24 doi:10.1101/530204 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Activity of Selected Nucleoside Analogue ProTides against Zika Virus in Human Neural Stem Cells ]]> https://biorxiv.org/content/10.1101/533497v1?rss=1 Bernatchez, J. A. Coste, M. Beck, S. Wells, G. A. Luna, L. A. Clark, A. E. Zhu, Z. Sohl, C. D. Purse, B. W. Siqueira-Neto, J. L. 2019-01-29 doi:10.1101/533497 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Characteristics of Beta Waveform Shape in Parkinson's Disease Detected with Scalp Electroencephalography ]]> https://biorxiv.org/content/10.1101/534396v1?rss=1 Jackson, N. Cole, S. C. Voytek, B. Swann, N. C. 2019-01-29 doi:10.1101/534396 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs ]]> https://biorxiv.org/content/10.1101/534479v1?rss=1 Lee, C. T. Laughlin, J. G. Angliviel de La Beaumelle, N. Amaro, R. McCammon, J. A. Ramamoorthi, R. Holst, M. J. Rangamani, P. 2019-01-29 doi:10.1101/534479 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Occupation and Parkinson disease in Women's Health Initiative Observational Study ]]> https://biorxiv.org/content/10.1101/535732v1?rss=1 Burstyn, I. LaCroix, A. Z. Litvan, I. Wallace, R. B. Checkoway, H. 2019-02-01 doi:10.1101/535732 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids ]]> https://biorxiv.org/content/10.1101/538421v1?rss=1 Huang, Q. Chan, K. Y. Tobey, I. G. Chan, Y. A. Poterba, T. Boutros, C. L. Balazs, A. B. Daneman, R. Bloom, J. M. Seed, C. Deverman, B. E. 2019-02-01 doi:10.1101/538421 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ DLITE: Dynamic Local Intercellular Tension Estimation ]]> https://biorxiv.org/content/10.1101/541144v1?rss=1 Vasan, R. Maleckar, M. M. Williams, C. D. Rangamani, P. 2019-02-05 doi:10.1101/541144 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Age and sex-dependent patterns of gut microbial diversity in human adults ]]> https://biorxiv.org/content/10.1101/544270v1?rss=1 de la Cuesta-Zuluaga, J. Kelley, S. T. Chen, Y. Esobar, J. S. Mueller, N. T. Ley, R. E. McDonald, D. Huang, S. Swafford, A. D. Knight, R. Thackray, V. 2019-02-08 doi:10.1101/544270 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Implementations of the chemical structural and compositional similarity metric in R and Python ]]> https://biorxiv.org/content/10.1101/546150v1?rss=1 Brejnrod, A. D. Ernst, M. Dworzynski, P. Rasmussen, L. B. Dorrestein, P. van der Hooft, J. Arumugam, M. 2019-02-11 doi:10.1101/546150 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes ]]> https://biorxiv.org/content/10.1101/549816v1?rss=1 Thompson, L. R. Haroon, M. F. Shibl, A. A. Cahill, M. J. Ngugi, D. K. Williams, G. J. Morton, J. Knight, R. Goodwin, K. D. Stingl, U. 2019-02-14 doi:10.1101/549816 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Flower-like patterns in multi-species biofilms ]]> https://biorxiv.org/content/10.1101/550996v1?rss=1 Xiong, L. Cao, Y. Cooper, R. Rappel, W.-J. Hasty, J. Tsimring, L. 2019-02-15 doi:10.1101/550996 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ EpiAlignment: alignment with both DNA sequence and epigenomic data ]]> https://biorxiv.org/content/10.1101/562199v1?rss=1 Lu, J. Cao, X. Zhong, S. 2019-02-27 doi:10.1101/562199 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ The laminar profile of sleep spindles in humans ]]> https://biorxiv.org/content/10.1101/563221v1?rss=1 Ujma, P. P. Hajnal, B. Bodizs, R. Gombos, F. Eross, L. Wittner, L. Halgren, E. Cash, S. Ulbert, I. Fabo, D. 2019-02-28 doi:10.1101/563221 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease ]]> https://biorxiv.org/content/10.1101/564161v1?rss=1 D'Antonio, M. Reyna, J. D'Antonio-Chronowska, A. Bonder, M.-J. Jakubosky, D. Matsui, H. Smith, E. N. Stegle, O. Nariai, N. Frazer, K. A. 2019-02-28 doi:10.1101/564161 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing ]]> https://biorxiv.org/content/10.1101/564443v1?rss=1 Edge, P. Bansal, V. 2019-03-01 doi:10.1101/564443 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Heterozygous variants in KMT2E cause a spectrum of neurodevelopmental disorders and epilepsy ]]> https://biorxiv.org/content/10.1101/566091v1?rss=1 O'Donnell-Luria, A. H. Pais, L. S. Faundes, V. Wood, J. C. Sveden, A. Luria, V. Abou Jamra, R. Accogli, A. Amburgey, K. Anderlid, B.-M. Azzarello-Burri, S. Basinger, A. A. Bianchini, C. Bird, L. M. Buchert, R. Carre, W. Ceulemans, S. Charles, P. Cox, H. Culliton, L. Curro, A. Deciphering Developmental Disorders (DDD) Study, Demurger, F. Dowling, J. J. Duban-Bedu, B. Dubourg, C. Escobar, L. F. Ferrarini, A. Haack, T. B. Hashim, M. Heide, S. Helbig, K. L. Helbig, I. Heredia, R. Heron, D. Isidor, B. Jonasson, A. R. Joset, P. Keren, B. Kok, F. Kroes, H. Y 2019-03-05 doi:10.1101/566091 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ The Tangent copy-number inference pipeline for cancer genome analyses ]]> https://biorxiv.org/content/10.1101/566505v1?rss=1 Tabak, B. Saksena, G. Oh, C. Gao, G. F. Hill Meyers, B. Reich, M. Schumacher, S. E. Westlake, L. C. Berger, A. C. Carter, S. L. Cherniack, A. D. Meyerson, M. Beroukhim, R. Getz, G. 2019-03-05 doi:10.1101/566505 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Interaction of Hippocampal Ripples and Cortical Slow Waves Leads to Coordinated Large-Scale Sleep Rhythm ]]> https://biorxiv.org/content/10.1101/568881v1?rss=1 Sanda, P. Malerba, P. Jiang, X. Krishnan, G. Cash, S. Halgren, E. Bazhenov, M. 2019-03-05 doi:10.1101/568881 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Can sleep protect memories from catastrophic forgetting? ]]> https://biorxiv.org/content/10.1101/569038v1?rss=1 Gonzalez, O. C. Sokolov, Y. Krishnan, G. Bazhenov, M. 2019-03-07 doi:10.1101/569038 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Identification of DNA motifs that regulate DNA methylation ]]> https://biorxiv.org/content/10.1101/573352v1?rss=1 Wang, M. Zhang, K. Ngo, V. Liu, C. Fan, S. Whitaker, J. W. Chen, Y. Ai, R. Chen, Z. Wang, J. Zheng, L. Wang, W. 2019-03-11 doi:10.1101/573352 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia ]]> https://biorxiv.org/content/10.1101/574509v1?rss=1 Tam, O. Rozhkov, N. V. Shaw, R. Kim, D. Hubbard, I. Fennessey, S. Propp, N. The NYGC ALS Consortium, Fagegaltier, D. Ostrow, L. W. Phatnani, H. Ravits, J. Dubnau, J. Gale Hammell, M. 2019-03-11 doi:10.1101/574509 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Quantifying and understanding well-to-well contamination in microbiome research ]]> https://biorxiv.org/content/10.1101/577718v1?rss=1 Minich, J. J. Sanders, J. Amir, A. Humphrey, G. Gilbert, J. A. Knight, R. 2019-03-14 doi:10.1101/577718 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Multiple memory tests in midlife improve prediction of mild cognitive impairment ]]> https://biorxiv.org/content/10.1101/584193v1?rss=1 Gustavson, D. E. Sanderson-Cimino, M. Elman, J. A. Franz, C. E. Panizzon, M. S. Jak, A. J. Reynolds, C. A. Lyons, M. J. Kremen, W. S. 2019-03-21 doi:10.1101/584193 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ A newly defined cullin-RING ubiquitin ligase promotes thermotolerance as part of the Intracellular Pathogen Response in C. elegans ]]> https://biorxiv.org/content/10.1101/586834v1?rss=1 Panek, J. Reddy, K. C. Luallen, R. J. Fulzele, A. Bennett, E. J. Troemel, E. R. 2019-03-23 doi:10.1101/586834 Cold Spring Harbor Laboratory Press 2019-03-23 <![CDATA[ Progressive recruitment of distal MEC-4 channels determines touch response strength in C. elegans ]]> https://biorxiv.org/content/10.1101/587014v1?rss=1 Katta, S. Sanzeni, A. Vergassola, M. Goodman, M. B. 2019-03-24 doi:10.1101/587014 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Recovery of trait heritability from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/588020v1?rss=1 Wainschtein, P. Jain, D. P. Yengo, L. Zheng, Z. TOPMed Anthropometry Working Group, Trans-Omics for Precision Medicine Consortium, Cupples, L. A. Shadyab, A. H. McKnight, B. Shoemaker, B. M. Mitchell, B. D. Psaty, B. M. Kooperberg, C. Roden, D. Darbar, D. Arnett, D. K. Regan, E. A. Boerwinkle, E. Rotter, J. I. Allison, M. A. McDonald, M.-L. N. Chung, M. K. Smith, N. L. Ellinor, P. T. Vasan, R. S. Mathias, R. A. Rich, S. S. Heckbert, S. R. Redline, S. Guo, X. Chen, Y.-D. I. Liu, C.-T. Andrade, M. d. Yanek, L. R. Albert, C. M. Hernandez, R. D. McGarvey, S. 2019-03-25 doi:10.1101/588020 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Predicting primary production in the southern California Current Ecosystem from chlorophyll, nutrient concentrations, and irradiance ]]> https://biorxiv.org/content/10.1101/590240v1?rss=1 Stukel, M. Goericke, R. Landry, M. R. 2019-03-28 doi:10.1101/590240 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ A conserved acidic cluster motif in SERINC5 confers resistance to antagonism by HIV-1 Nef ]]> https://biorxiv.org/content/10.1101/590646v1?rss=1 Stoneham, C. Ramirez, P. W. Singh, R. Suarez, M. Debray, A. Lim, C. Jia, X. Xiong, Y. Guatelli, J. 2019-03-27 doi:10.1101/590646 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Resting networks and personality predict attack speed in social spiders ]]> https://biorxiv.org/content/10.1101/591453v1?rss=1 Hunt, E. R. Mi, B. Geremew, R. Fernandez, C. Wong, B. M. Pruitt, J. N. Pinter-Wollman, N. 2019-03-28 doi:10.1101/591453 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Common DNA sequence variation influences 3-dimensional conformation of the human genome ]]> https://biorxiv.org/content/10.1101/592741v1?rss=1 Gorkin, D. Qiu, Y. Hu, M. Fletez-Brant, K. Liu, T. Schmitt, A. Noor, A. Chiou, J. Gaulton, K. Sebat, J. Li, Y. Hansen, K. Ren, B. 2019-03-30 doi:10.1101/592741 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome ]]> https://biorxiv.org/content/10.1101/594010v1?rss=1 Claesen, J. Spagnolo, J. B. Flores Ramos, S. Kurita, K. L. Byrd, A. L. Aksenov, A. A. Melnik, A. V. Wong, W. R. Wang, S. Hernandez, R. D. Donia, M. S. Dorrestein, P. C. Kong, H. H. Segre, J. A. Linington, R. G. Fischbach, M. A. Lemon, K. P. 2019-03-30 doi:10.1101/594010 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ StanDep: capturing transcriptomic variability improves context-specific metabolic models ]]> https://biorxiv.org/content/10.1101/594861v1?rss=1 Joshi, C. J. Schinn, S.-M. Richelle, A. Shamie, I. O'Rourke, E. J. Lewis, N. 2019-04-01 doi:10.1101/594861 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ Nuisance effects in inter-scan functional connectivity estimates before and after nuisance regression ]]> https://biorxiv.org/content/10.1101/603183v1?rss=1 Nalci, A. Luo, W. Liu, T. T. 2019-04-09 doi:10.1101/603183 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects ]]> https://biorxiv.org/content/10.1101/604371v1?rss=1 Young Greenwald, W. W. D'Antonio-Chronowska, A. Benaglio, P. Matsui, H. Smith, E. N. D'Antonio, M. Frazer, K. A. 2019-04-09 doi:10.1101/604371 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations ]]> https://biorxiv.org/content/10.1101/607267v1?rss=1 Sanchez C., H. M. Bennett, J. B. Wu, S. L. Rasic, G. Akbari, O. S. Marshall, J. M. 2019-04-12 doi:10.1101/607267 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Motto: Representing motifs in consensus sequences with minimum information loss ]]> https://biorxiv.org/content/10.1101/607408v1?rss=1 Wang, M. Wang, D. Zhang, K. Ngo, V. Fan, S. Wang, W. 2019-04-13 doi:10.1101/607408 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Methods for the generation of heritable germline mutations in the disease vector Culex quinquefasciatus using CRISPR/Cas9. ]]> https://biorxiv.org/content/10.1101/609206v1?rss=1 Li, M. Li, T. Liu, N. Raban, R. Wang, X. Akbari, O. 2019-04-16 doi:10.1101/609206 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Activation of a Protein Kinase Via Asymmetric Allosteric Coupling of Structurally Conserved Signaling Modules ]]> https://biorxiv.org/content/10.1101/611772v1?rss=1 Hao, Y. England, J. P. Belluci, L. Paci, E. Hodges, H. C. Taylor, S. S. Maillard, R. A. 2019-04-18 doi:10.1101/611772 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Sex-dependent polygenic effects on the clinical progressions of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/613893v1?rss=1 Fan, C. C. Banks, S. J. Thompson, W. K. Chen, C.-H. McEvoy, L. K. Tan, C. H. Kukull, W. Bennett, D. A. Farrer, L. A. Mayeux, R. Schellenberg, G. D. Andreassen, O. A. Desikan, R. Dale, A. M. 2019-04-18 doi:10.1101/613893 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Fast and Accurate Clustering of Single Cell Epigenomes Reveals Cis-Regulatory Elements in Rare Cell Types ]]> https://biorxiv.org/content/10.1101/615179v1?rss=1 Fang, R. Preissl, S. Hou, X. Lucero, J. Wang, X. Motamedi, A. Shiau, A. K. Mukamel, E. A. Zhang, Y. Behrens, M. M. Ecker, J. Ren, B. 2019-04-22 doi:10.1101/615179 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ Homeostatic mechanisms may shape the type and duration of oscillatory modulation. ]]> https://biorxiv.org/content/10.1101/615450v1?rss=1 Peterson, E. J. Voytek, B. 2019-04-22 doi:10.1101/615450 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ Catestatin improves insulin sensitivity in diet-induced obese mice: in vivo and in silico validation ]]> https://biorxiv.org/content/10.1101/615997v1?rss=1 Mahata, S. K. Dasgupta, A. Bandyopadhyay, K. Ray, I. Bandyopadhyay, G. K. Chowdhury, N. De, R. K. 2019-04-22 doi:10.1101/615997 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells ]]> https://biorxiv.org/content/10.1101/618330v1?rss=1 Jin, W. Mulas, F. Gaertner, B. Sui, Y. Wang, J. Zeng, C. Vinckier, N. Wang, A. Nguyen-Ngoc, K.-V. Chiou, J. Kaestner, K. H. Frazer, K. Carrano, A. C. Shih, H.-P. Sander, M. 2019-04-25 doi:10.1101/618330 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ A genetic hazard score to personalize prostate cancer screening, applied to population data ]]> https://biorxiv.org/content/10.1101/619718v1?rss=1 Huynh-Le, M.-P. Fan, C. C. Karunamuni, R. Walsh, E. I. Turner, E. L. Lane, J. A. Martin, R. M. Neal, D. E. Donovan, J. L. Hamdy, F. C. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Key, T. J. Travis, R. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Thibodeau, S. N. McDonnell, S. K. Schaid, D. J. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, 2019-04-26 doi:10.1101/619718 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ The Escherichia coli Transcriptome Consists of Independently Regulated Modules ]]> https://biorxiv.org/content/10.1101/620799v1?rss=1 Sastry, A. V. Gao, Y. Szubin, R. Hefner, Y. Xu, S. Kim, D. Choudhary, K. S. Yang, L. King, Z. A. Palsson, B. O. 2019-04-29 doi:10.1101/620799 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences ]]> https://biorxiv.org/content/10.1101/621532v1?rss=1 Vakirlis, N. Acar, O. Hsu, B. Castilho Coelho, N. Van Oss, S. B. Wacholder, A. Medetgul-Ernar, K. Ianotta, J. McLysaght, A. Camacho, C. J. O'Donnell, A. F. Ideker, T. Carvunis, A.-R. 2019-04-29 doi:10.1101/621532 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Pupillary dilation responses as a midlife indicator of risk for Alzheimer’s Disease: Association with Alzheimer’s disease polygenic risk ]]> https://biorxiv.org/content/10.1101/624767v1?rss=1 Kremen, W. Panizzon, M. Elman, J. A. Granholm, E. Andreassen, O. A. Dale, A. Gillespie, N. Gustavson, D. E. Logue, M. Lyons, M. Neale, M. Reynolds, C. Whitsel, N. Franz, C. 2019-05-02 doi:10.1101/624767 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Single-cell chromatin accessibility analysis of mammary gland development reveals cell state transcriptional regulators and cellular lineage relationships ]]> https://biorxiv.org/content/10.1101/624957v1?rss=1 Chung, C.-Y. Ma, Z. Dravis, C. Preissl, S. Poirion, O. Luna, G. Hou, X. Giraddi, R. R. Ren, B. Wahl, G. M. 2019-05-02 doi:10.1101/624957 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Mammalian gene expression variability is explained by underlying cell state ]]> https://biorxiv.org/content/10.1101/626424v1?rss=1 Foreman, R. Wollman, R. 2019-05-03 doi:10.1101/626424 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Spatial Confidence Sets for Raw Effect Size Images ]]> https://biorxiv.org/content/10.1101/631473v1?rss=1 Bowring, A. Telschow, F. Schwartzman, A. Nichols, T. 2019-05-08 doi:10.1101/631473 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Polygenic Score of Intelligence is More Predictive of Crystallized than Fluid Performance Among Children ]]> https://biorxiv.org/content/10.1101/637512v1?rss=1 Loughnan, R. Palmer, C. E. Thompson, W. K. Dale, A. M. Jernigan, T. L. Fan, C. C. 2019-05-15 doi:10.1101/637512 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ metaFlye: scalable long-read metagenome assembly using repeat graphs ]]> https://biorxiv.org/content/10.1101/637637v1?rss=1 Kolmogorov, M. Rayko, M. Yuan, J. Polevikov, E. Pevzner, P. 2019-05-15 doi:10.1101/637637 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier ]]> https://biorxiv.org/content/10.1101/641506v1?rss=1 Chen, Z. Gabizon, R. Bustamante, C. Yao, T. Lee, A. Diaz-Celis, C. Koslover, E. F. Brown, A. I. Song, A. 2019-05-17 doi:10.1101/641506 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Inverted encoding models estimate sensible channel responses for sensible models ]]> https://biorxiv.org/content/10.1101/642710v1?rss=1 Sprague, T. C. Boynton, G. M. Serences, J. 2019-05-21 doi:10.1101/642710 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ The olfactory basis of orchid pollination by mosquitoes ]]> https://biorxiv.org/content/10.1101/643510v1?rss=1 Lahondere, C. Vinauger, C. Okubo, R. Wolff, G. Akbari, O. Riffell, J. 2019-05-27 doi:10.1101/643510 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Mitochondrial morphology provides a mechanism for energy buffering at synapses ]]> https://biorxiv.org/content/10.1101/643551v1?rss=1 Garcia, G. C. Bartol, T. M. Phan, S. Bushong, E. A. Perkins, G. Sejnowski, T. J. Ellisman, M. H. Skupin, A. 2019-05-20 doi:10.1101/643551 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Human iPSC gene signatures and X chromosome dosage impact response to WNT inhibition and cardiac differentiation fate ]]> https://biorxiv.org/content/10.1101/644633v1?rss=1 D'Antonio-Chronowska, A. Donovan, M. K. R. Benaglio, P. Young Greenwald, W. W. W. Ward, M. C. Matsui, H. Fujita, K. Hashem, S. Soncin, F. Parast, M. Adler, E. Smith, E. N. D'Antonio, M. Frazer, K. A. 2019-05-24 doi:10.1101/644633 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Plasticity of cell migration resulting from mechanochemical coupling ]]> https://biorxiv.org/content/10.1101/644880v1?rss=1 Cao, Y. Ghabache, E. Rappel, W.-J. 2019-05-21 doi:10.1101/644880 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences ]]> https://biorxiv.org/content/10.1101/645762v1?rss=1 Godoy, P. M. Barczak, A. J. DeHoff, P. Srinivasan, S. Das, S. Erle, D. J. Laurent, L. C. 2019-05-24 doi:10.1101/645762 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ PHLPP1 Counter-regulates STAT1-mediated Inflammatory Signaling ]]> https://biorxiv.org/content/10.1101/647883v1?rss=1 Cohen Katsenelson, K. Stender, J. D. Kawashima, A. T. Lorden, G. Uchiyama, S. Nizet, V. Glass, C. K. Newton, A. C. 2019-05-24 doi:10.1101/647883 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Age dependence of modern clinical risk groups for localized prostate cancer -- a population-based study ]]> https://biorxiv.org/content/10.1101/648519v1?rss=1 Huynh-Le, M.-P. Myklebust, T. A. Feng, C. Karunamuni, R. Johannesen, T. B. Dale, A. M. Andreassen, O. A. Seibert, T. M. 2019-05-24 doi:10.1101/648519 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ On the impact of biomass composition in constraint-based flux analysis ]]> https://biorxiv.org/content/10.1101/652040v1?rss=1 Lakshmanan, M. Long, S. Ang, K. S. Lewis, N. E. Lee, D.-Y. 2019-05-28 doi:10.1101/652040 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Tyr1 phosphorylation promotes the phosphorylation of Ser2 on the C-terminal domain of RNA polymerase II by P-TEFb ]]> https://biorxiv.org/content/10.1101/652214v1?rss=1 Zhang, Y. Mayfield, J. E. Irani, S. Escobar, E. E. Zhang, Z. Burkholder, N. T. Robinson, M. R. Mehaffey, M. R. Sipe, S. N. Yang, W. Prescott, N. A. Kathuria, K. Liu, Z. Brodbelt, J. 2019-05-28 doi:10.1101/652214 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events ]]> https://biorxiv.org/content/10.1101/653097v1?rss=1 Bergstrom, E. N. Huang, M. N. Mahto, U. Barnes, M. Stratton, M. R. Rozen, S. G. Alexandrov, L. B. 2019-05-29 doi:10.1101/653097 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Ventral Pallidum is Essential for Cocaine Reinstatement After Voluntary Abstinence ]]> https://biorxiv.org/content/10.1101/653741v1?rss=1 Farrell, M. R. Ruiz, C. M. Castillo, E. Faget, L. Khanbijian, C. Liu, S. Schoch, H. Rojas, G. Hnasko, T. S. Mahler, S. V. 2019-05-30 doi:10.1101/653741 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in IGH-CRLF2 patients ]]> https://biorxiv.org/content/10.1101/654418v1?rss=1 Badri, S. Carella, B. Lhoumaud, P. Castro, D. M. Raviram, R. Watters, A. Bonneau, R. M. Skok, J. A. 2019-05-31 doi:10.1101/654418 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids ]]> https://biorxiv.org/content/10.1101/654756v1?rss=1 Quinn, R. A. Vrbanac, A. Melnik, A. V. Patras, K. A. Christy, M. Nelson, A. T. Aksenov, A. A. Tripathi, A. Humphrey, G. da Silva, R. Bussell, R. Thron, T. Wang, M. Vargas, F. Gauglitz, J. Meehan, M. J. Poulsen, O. Boland, B. S. Chang, J. T. Sandborn, W. J. Lim, M. Garg, N. Lumeng, J. Kazmierczak, B. I. Jain, R. Egan, M. Rhee, K. E. Haddad, G. G. Siegel, D. Mazmanian, S. Nizet, V. Knight, R. Dorrestein, P. C. 2019-06-03 doi:10.1101/654756 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ The cohesin loader NIPBL interacts with pre-ribosomal RNA and treacle to regulate ribosomal RNA synthesis ]]> https://biorxiv.org/content/10.1101/658492v1?rss=1 Kong, X. Chen, Y.-Y. Lin, J. Flowers, E. Van Nostrand, E. Blue, S. Chau, J. Ma, C. I.-H. Mohr, I. Thai, R. Yao, C. Ball, A. Chien, R. Kawauchi, S. Santos, R. Calof, A. Lander, A. Shi, Y. Okuwaki, M. Yeo, G. W. Yokomori, K. 2019-06-03 doi:10.1101/658492 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Vapor inhalation of cannabidiol (CBD) in rats ]]> https://biorxiv.org/content/10.1101/659250v1?rss=1 Javadi-Paydar, M. Creehan, K. M. Kerr, T. M. Taffe, M. A. 2019-06-04 doi:10.1101/659250 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Behavioral and neural signatures of working memory in childhood ]]> https://biorxiv.org/content/10.1101/659409v1?rss=1 Rosenberg, M. D. Martinez, S. A. Rapuano, K. M. Conley, M. I. Cohen, A. O. Cornejo, M. D. Hagler, D. J. Anderson, K. M. Wager, T. D. Feczko, E. Earl, E. Fair, D. A. Barch, D. M. Watts, R. Casey, B. 2019-06-06 doi:10.1101/659409 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Semantic Fluency Predicts Six-Year Progression to Mild Cognitive Impairment in Middle-Aged Men ]]> https://biorxiv.org/content/10.1101/659417v1?rss=1 Gustavson, D. E. Elman, J. A. Panizzon, M. S. Franz, C. E. Zuber, J. Sanderson-Cimino, M. Reynolds, C. A. Jacobson, K. C. Xian, H. Jak, A. J. Toomey, R. Lyons, M. J. Kremen, W. A. 2019-06-04 doi:10.1101/659417 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Small-molecule control of super-Mendelian inheritance in gene drives ]]> https://biorxiv.org/content/10.1101/665620v1?rss=1 nView larger version (15K):norg.highwire.dtl.DTLVardef@1aa8522org.highwire.dtl.DTLVardef@a99c8org.highwire.dtl.DTLVardef@1f63636org.highwire.dtl.DTLVardef@1613408_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Lopez Del Amo, V. Leger, B. S. Cox, K. J. Gill, S. Bishop, A. L. Scanlon, G. D. Walker, J. A. Gantz, V. M. Choudhary, A. 2019-06-14 doi:10.1101/665620 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Stimulation augments spike sequence replay and memory consolidation during slow-wave sleep ]]> https://biorxiv.org/content/10.1101/670091v1?rss=1 Wei, Y. Krishnan, G. Marshall, L. Martinetz, T. BAZHENOV, M. 2019-06-13 doi:10.1101/670091 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction ]]> https://biorxiv.org/content/10.1101/672485v1?rss=1 Vasan, R. Rudraraju, S. Akamatsu, M. Garikipati, K. Rangamani, P. 2019-06-15 doi:10.1101/672485 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ Higher fitness yeast genotypes are less robust to deleterious mutations ]]> https://biorxiv.org/content/10.1101/675314v1?rss=1 Johnson, M. S. Martsul, A. Kryazhimskiy, S. Desai, M. M. 2019-06-20 doi:10.1101/675314 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ The Molecular and Microbial Microenvironments in Chronically Diseased Lungs ]]> https://biorxiv.org/content/10.1101/676148v1?rss=1 Garg, N. Melnik, A. V. Vasquez-Baeza, Y. Aksenov, A. Hyde, E. R. McAvoy, A. C. Wang, M. da Silva, R. Protsyuk, I. Wu, J. V. Bouslimani, A. Lim, Y. W. Luzzatto-Knaan, T. Comstock, W. Quinn, R. A. Wong, R. Humphrey, G. Ackermann, G. Spivey, T. Brouha, S. S. Bandeira, N. Lin, G. Y. Rohwer, F. Conrad, D. Alexandrov, T. Dorrestein, P. C. Knight, R. 2019-06-19 doi:10.1101/676148 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Altered White Matter Microstructural Organization in Post-Traumatic Stress Disorder across 3,049 Adults: Results from the PGC-ENIGMA PTSD Consortium ]]> https://biorxiv.org/content/10.1101/677153v1?rss=1 Dennis, E. Disner, S. E. Fani, N. Salminen, L. E. Logue, M. Clarke-Rubright, E. K. Haswell, C. C. Averill, C. Baugh, L. A. Bomyea, J. Bruce, S. E. Cha, J. Choi, K. Davenport, N. D. Densmore, M. du Plessis, S. Forster, G. L. Frijling, J. L. Gonenc, A. Gruber, S. Grupe, D. W. Guenette, J. P. Hayes, J. Hofmann, D. Ipser, J. Jovanovic, T. Kelly, S. Kennis, M. Kinzel, P. Koch, S. B. Koerte, I. Koopowitz, S. Korgaonkar, M. Krystal, J. Lebois, L. A. Li, G. Magnotta, V. A. Manthey, A. May, G. J. Menefee, D. S. Nawijn, L. Nelson, S. M. Neufeld, R. W. Nitschke, 2019-06-20 doi:10.1101/677153 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Aequorea victoria’s secrets ]]> https://biorxiv.org/content/10.1101/677344v1?rss=1 Lambert, G. G. Depernet, H. Gotthard, G. Schultz, D. T. Navizet, l. Lambert, T. Bindels, D. S. Levesque, V. Nero Moffatt, J. N. Salih, A. Royant, A. Shaner, N. C. 2019-06-19 doi:10.1101/677344 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/678797v1?rss=1 Akamatsu, M. Vasan, R. Serwas, D. Ferrin, M. Rangamani, P. Drubin, D. G. 2019-06-21 doi:10.1101/678797 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ A receptor for herbivore-associated molecular patterns mediates plant immunity ]]> https://biorxiv.org/content/10.1101/679803v1?rss=1 Steinbrenner, A. D. Munoz-Amatriain, M. Venegas, J. M. A. Lo, S. Shi, D. Holton, N. Zipfel, C. Abagyan, R. Huffaker, A. Close, T. J. Schmelz, E. A. 2019-06-22 doi:10.1101/679803 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Impact of insertion sequences on convergent evolution of Shigella species ]]> https://biorxiv.org/content/10.1101/680777v1?rss=1 Hawkey, J. Monk, J. M. Billman-Jacobe, H. Palsson, B. Holt, K. E. 2019-06-24 doi:10.1101/680777 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities ]]> https://biorxiv.org/content/10.1101/683367v1?rss=1 Armstrong, N. J. Mather, K. A. Sargurupremraj, M. Knol, M. J. Malik, R. Satizabal, C. L. Yanek, L. R. Wen, W. Gudnason, V. Dueker, N. D. Elliott, L. T. Hofer, E. Jahanshad, N. Li, S. Logue, M. A. Luciano, M. Scholz, M. Smith, A. V. Trompet, S. S. Vojinovic, D. Xia, R. Alfaro-Almagro, F. Ames, D. Amin, N. Amouyel, P. Beiser, A. S. Brodaty, H. Deary, I. J. Fennema-Notestine, C. Gampawar, P. G. Gottesman, R. F. Griffanti, L. Jack, C. R. Jenkinson, M. Jiang, J. Kral, B. G. Kwok, J. B. Lampe, L. Liewald, D. C. Maillard, P. Marchini, J. Bastin, M. E. Mazoyer 2019-06-27 doi:10.1101/683367 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses ]]> https://biorxiv.org/content/10.1101/685008v1?rss=1 Lee, J. Zhang, J. Chung, Y.-J. Kim, J. H. Kook, C. M. Gonzalez-Navajas, J. M. Herdman, D. S. Nürnberg, B. Insel, P. Corr, M. Tao, A. Yasuda, K. Rifkin, I. R. Broide, D. H. Sciammas, R. Webster, N. J. G. Raz, E. 2019-06-28 doi:10.1101/685008 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Convergent metatarsal fusion in jerboas and chickens is mediated by similarities and differences in the patterns of osteoblast and osteoclast activities ]]> https://biorxiv.org/content/10.1101/688036v1?rss=1 Gutierrez, H. L. Tsutsumi, R. Moore, T. Y. Cooper, K. L. 2019-07-01 doi:10.1101/688036 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Isolation of muscle stem cells from rat skeletal muscles ]]> https://biorxiv.org/content/10.1101/690776v1?rss=1 Boscolo Sesillo, F. Wong, M. Cortez, A. Alperin, M. 2019-07-03 doi:10.1101/690776 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Correcting for sparsity and non-independence in glycomic data through a system biology framework ]]> https://biorxiv.org/content/10.1101/693507v1?rss=1 Bao, B. Kellman, B. P. Chiang, A. W. T. York, A. K. Mohammad, M. A. Haymond, M. W. Bode, L. Lewis, N. E. 2019-07-05 doi:10.1101/693507 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ HORMA domain proteins and a Pch2-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity ]]> https://biorxiv.org/content/10.1101/694695v1?rss=1 Ye, Q. Lau, R. K. Mathews, I. T. Watrous, J. D. Azimi, C. S. Jain, M. Corbett, K. D. 2019-07-06 doi:10.1101/694695 Cold Spring Harbor Laboratory Press 2019-07-06 <![CDATA[ Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity ]]> https://biorxiv.org/content/10.1101/694703v1?rss=1 Lau, R. K. Ye, Q. Patel, L. Berg, K. R. Mathews, I. T. Watrous, J. D. Whiteley, A. T. Lowey, B. Mekalanos, J. J. Kranzusch, P. J. Jain, M. Corbett, K. 2019-07-07 doi:10.1101/694703 Cold Spring Harbor Laboratory Press 2019-07-07 <![CDATA[ Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders - findings from a Danish population-based study ]]> https://biorxiv.org/content/10.1101/699462v1?rss=1 Liu, X. Nudel, R. Thompson, W. K. Appadurai, V. Schork, A. J. Buil, A. Rasmussen, S. Allesoee, R. L. Werge, T. Mors, O. Boerglum, A. D. Hougaard, D. M. Mortensen, P. B. Nordentoft, M. Benros, M. E. 2019-07-11 doi:10.1101/699462 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex ]]> https://biorxiv.org/content/10.1101/701532v1?rss=1 Partlow, E. A. Baker, R. W. Beacham, G. M. Chappie, J. S. Leschziner, A. E. Hollopeter, G. 2019-07-13 doi:10.1101/701532 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Improved identification and differentiation from epileptiform activity of human hippocampal sharpwave-ripples during NREM sleep ]]> https://biorxiv.org/content/10.1101/702894v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Cash, S. S. S. Chauvel, P. Gale, J. Halgren, E. 2019-07-15 doi:10.1101/702894 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Coordination of human hippocampal sharpwave-ripples during NREM sleep with cortical theta bursts, spindles, downstates and upstates ]]> https://biorxiv.org/content/10.1101/702928v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Halgren, E. 2019-07-15 doi:10.1101/702928 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Posterior hippocampal spindle-ripples co-occur with neocortical theta-bursts and down-upstates, and phase-lock with parietal spindles during NREM sleep in humans ]]> https://biorxiv.org/content/10.1101/702936v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Halgren, E. 2019-07-15 doi:10.1101/702936 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ The potential for gas-free measurements of absolute oxygen metabolism during both baseline and activation states in the human brain ]]> https://biorxiv.org/content/10.1101/705186v1?rss=1 Liu, E. Y. Guo, J. Simon, A. B. Haist, F. Dubowitz, D. J. Buxton, R. B. 2019-07-16 doi:10.1101/705186 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes: Evidence of Natural Selection from GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/705285v1?rss=1 Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Andreassen, O. A. Dale, A. 2019-07-16 doi:10.1101/705285 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ The C. elegans RIG-I homolog drh-1 mediates the Intracellular Pathogen Response upon viral infection ]]> https://biorxiv.org/content/10.1101/707141v1?rss=1 Sowa, J. N. Jiang, H. Somasundaram, L. Xu, G. Wang, D. Troemel, E. 2019-07-18 doi:10.1101/707141 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks ]]> https://biorxiv.org/content/10.1101/709683v1?rss=1 Zhang, H. B. Kim, M. Chuang, J. H. Ruan, Y. 2019-07-20 doi:10.1101/709683 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ TMEM16F phospholipid scramblase mediates trophoblast fusion and placental development ]]> https://biorxiv.org/content/10.1101/711473v1?rss=1 Yang, H. Zhang, Y. Le, T. Grabau, R. Mohseni, Z. Kim, H. Natale, D. R. Feng, L. Pan, H. 2019-07-24 doi:10.1101/711473 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats using Deep Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/713198v1?rss=1 Jakubosky, D. Smith, E. N. D'Antonio, M. Bonder, M. J. Young Greenwald, W. W. Matsui, H. D'Antonio-Chronowska, A. i2QTL Consortium, HipSci Consortium, Stegle, O. Montgomery, S. B. DeBoever, C. Frazer, K. A. 2019-07-24 doi:10.1101/713198 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ ALS Motor Neurons Exhibit Hallmark Metabolic Defects That Are Rescued by Nicotinamide and SIRT3 Activation ]]> https://biorxiv.org/content/10.1101/713651v1?rss=1 Hor, J.-H. Mohamad Santosa, M. Lim, V. J. W. Ho, B. X. Taylor, A. Khong, Z. J. Ravits, J. Fan, Y. Liou, Y.-C. Soh, B.-S. Ng, S.-Y. 2019-08-02 doi:10.1101/713651 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Structural variant classes and short tandem repeats differentially impact gene expression and complex traits ]]> https://biorxiv.org/content/10.1101/714477v1?rss=1 Jakubosky, D. D'Antonio, M. Bonder, M. J. Smail, C. Donovan, M. K. R. Young Greenwald, W. W. D'Antonio-Chronowska, A. Matsui, H. i2QTL Consortium, Stegle, O. Smith, E. N. Montgomery, S. B. DeBoever, C. Frazer, K. A. 2019-07-25 doi:10.1101/714477 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signalling. ]]> https://biorxiv.org/content/10.1101/716647v1?rss=1 Vinckier, N. K. Patel, N. A. Wang, A. Wang, J. Shih, H.-P. Wang, J. Jhala, U. S. Rosenfeld, M. G. Benner, C. Sander, M. 2019-08-01 doi:10.1101/716647 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Skeletal Muscle mTORC1 Activation Increases Energy Expenditure and Reduces Longevity in Mice ]]> https://biorxiv.org/content/10.1101/720540v1?rss=1 Stephenson, E. J. Redd, J. R. Snyder, D. Tran, Q. T. Lu, B. Peloquin, M. J. Mulcahy, M. C. Harvey, I. Fisher, K. Han, J. C. Qi, N. Saltiel, A. R. Bridges, D. 2019-07-31 doi:10.1101/720540 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Predictive coding account of action perception: Evidence from effective connectivity in the Action Observation Network ]]> https://biorxiv.org/content/10.1101/722298v1?rss=1 Urgen, B. A. Saygin, A. P. 2019-08-01 doi:10.1101/722298 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ In vivo lineage conversion of vertebrate muscle into early endoderm-like cells ]]> https://biorxiv.org/content/10.1101/722967v1?rss=1 Campbell, C. Lancman, J. J. Espin-Palazon, R. Matalonga, J. He, J. Graves, A. Zeng, X.-X. I. Huisken, J. Traver, D. Dong, P. D. S. 2019-08-09 doi:10.1101/722967 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Relating visual production and recognition of objects in human visual cortex ]]> https://biorxiv.org/content/10.1101/724294v1?rss=1 Fan, J. Wammes, J. Gunn, J. Yamins, D. Norman, K. Turk-Browne, N. 2019-08-03 doi:10.1101/724294 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast ]]> https://biorxiv.org/content/10.1101/724617v1?rss=1 Jerison, E. R. Nguyen Ba, A. N. Desai, M. M. Kryazhimskiy, S. 2019-08-03 doi:10.1101/724617 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Laccase-mediated catalyzed fluorescent reporter deposition for live cell imaging ]]> https://biorxiv.org/content/10.1101/731539v1?rss=1 Cisneros, B. T. Devaraj, N. K. 2019-08-10 doi:10.1101/731539 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Variations in Brain Morphometry Among Healthy Preschoolers Born Very Preterm ]]> https://biorxiv.org/content/10.1101/734277v1?rss=1 Hasler, H. M. Brown, T. T. Akshoomoff, N. 2019-08-13 doi:10.1101/734277 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Movement abilities and brain development in preschoolers born very preterm ]]> https://biorxiv.org/content/10.1101/734319v1?rss=1 Hasler, H. M. Fuller, M. G. Vaucher, Y. E. Brown, T. T. Stiles, J. Dale, A. M. Jernigan, T. L. Akshoomoff, N. 2019-08-13 doi:10.1101/734319 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Formation of talin-vinculin pre-complexes dictates maturation of nascent adhesions by accelerated force transmission and vinculin recruitment ]]> https://biorxiv.org/content/10.1101/735183v1?rss=1 Han, S. J. Dean, K. Whitewood, A. J. Bachir, A. Guttierrez, E. Groisman, A. Horwitz, A. R. Goult, B. T. Danuser, G. 2019-08-14 doi:10.1101/735183 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway ]]> https://biorxiv.org/content/10.1101/735894v1?rss=1 LaMonte, G. M. Marapana, D. S. Gnadig, N. Ottilie, S. Luth, M. R. Worgall, T. S. Rocamora, F. Goldgof, G. M. Mohunlal, R. Kumar, T. R. S. Thompson, J. K. Vigil, E. Yang, J. Hutson, D. Johnson, T. Huang, J. Williams, R. M. Zou, B. Y. Cheung, A. L. Kumar, P. Egan, T. J. Lee, M. C. S. Siegel, D. Cowman, A. F. Fidock, D. A. Winzeler, E. A. 2019-08-15 doi:10.1101/735894 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Telomere-to-telomere assembly of a complete human X chromosome ]]> https://biorxiv.org/content/10.1101/735928v1?rss=1 Miga, K. H. Koren, S. Rhie, A. Vollger, M. R. Gershman, A. Bzikadze, A. Brooks, S. Howe, E. Porubsky, D. Logsdon, G. A. Schneider, V. A. Potapova, T. Wood, J. Chow, W. Armstrong, J. Fredrickson, J. Pak, E. Tigyi, K. Kremitzki, M. Markovic, C. Maduro, V. Dutra, A. Bouffard, G. G. Chang, A. M. Hansen, N. F. Thibaud-Nissen, F. Schmitt, A. D. Belton, J.-M. Selvaraj, S. Dennis, M. Y. Soto, D. C. Sahasrabudhe, R. Kaya, G. Quick, J. Loman, N. J. Holmes, N. Loose, M. Surti, U. Risques, R. a. Lindsay, T. A. G. Fulton, R. Hall, I. Paten, B. Howe, K. Timp, W. 2019-08-16 doi:10.1101/735928 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Dynamic regulation of immunity through post-translational control of defense transcript splicing ]]> https://biorxiv.org/content/10.1101/736249v1?rss=1 Dressano, K. Weckwerth, P. Poretsky, E. Takahashi, Y. Villarreal, C. Shen, Z. Schroeder, J. Briggs, S. Huffaker, A. 2019-08-15 doi:10.1101/736249 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Hippocampal subfield volumes are uniquely affected in PTSD and depression: International analysis of 31 cohorts from the PGC-ENIGMA PTSD Working Group ]]> https://biorxiv.org/content/10.1101/739094v1?rss=1 Salminen, L. E. Sämann, P. G. Zheng, Y. Dennis, E. L. Clarke, E. K. Jahanshad, N. Iglesias, J. E. Whelan, C. D. Bruce, S. E. Hayes, J. P. Seedat, S. Averill, C. L. Baugh, L. A. Bomyea, J. Bright, J. Buckle, C. J. Choi, K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. du Plessis, S. Elman, J. A. Fani, N. Forster, G. L. Franz, C. E. Frijling, J. L. Gonenc, A. Gruber, S. A. Grupe, D. W. Guenette, J. P. Haswell, C. C. Hofmann, D. Hollifield, M. Hosseini, B. Hudson, A. R. Ipser, J. Jovanovic, T. Kennedy-Krage, A. Kennis, M. King, A. Kinzel, P. 2019-08-21 doi:10.1101/739094 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems ]]> https://biorxiv.org/content/10.1101/740530v1?rss=1 Lim, B. J. Ackermann, B. E. Debelouchina, G. T. 2019-08-27 doi:10.1101/740530 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Trading Genome Vulnerability for Stable Genetic Inheritance: Active Retrotransposons Help Maintain Pericentromeric Heterochromatin Required for Faithful Cell Division ]]> https://biorxiv.org/content/10.1101/740753v1?rss=1 Hao, Y. Wang, D. Wu, S. Li, X. Shao, C. Zhang, P. Chen, J.-Y. Lim, D.-H. Fu, X.-D. He, S. Chen, R. 2019-08-20 doi:10.1101/740753 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Nutrient regulation of the islet epigenome controls adaptive insulin secretion ]]> https://biorxiv.org/content/10.1101/742403v1?rss=1 Wortham, M. Liu, F. Fleischman, J. Y. Wallace, M. Mulas, F. Vinckier, N. K. Harrington, A. R. Cross, B. R. Chiou, J. Patel, N. A. Sui, Y. Jhala, U. S. Shirihai, O. S. Huising, M. O. Gaulton, K. J. Metallo, C. M. Sander, M. 2019-08-21 doi:10.1101/742403 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Pharmacological inhibition of the heart of glass (HEG1)-Krev interaction trapped protein 1 (KRIT1) protein complex increases Kruppel-like Factors 4 and 2 (KLF4/2) expression in endothelial cells ]]> https://biorxiv.org/content/10.1101/744821v1?rss=1 Lopez-Ramirez, M. A. Haynes, M. K. Hale, P. Oukoloff, K. Bautista, M. Gongol, B. Shyy, J. Y. Ballatore, C. Sklar, L. A. Gingras, A. R. 2019-08-23 doi:10.1101/744821 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Evolution of resistance in vitro reveals a novel mechanism of artemisinin activity in Toxoplasma gondii. ]]> https://biorxiv.org/content/10.1101/746065v1?rss=1 Rozenberg, A. Luth, M. R. Behnke, M. Winzeler, E. Sibley, L. D. 2019-08-24 doi:10.1101/746065 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Enzyme-free synthesis of natural phospholipids in water ]]> https://biorxiv.org/content/10.1101/746156v1?rss=1 Liu, L. Zou, Y. Bhattacharya, A. Zhang, D. Lang, S. Q. Houk, K. N. Devaraj, N. K. 2019-08-24 doi:10.1101/746156 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Polygenic Prediction of Substance Use Disorders in Clinical and Population Samples ]]> https://biorxiv.org/content/10.1101/748038v1?rss=1 Barr, P. B. Ksinan, A. Su, J. Johnson, E. C. Meyers, J. L. Wetherill, L. Latvala, A. Aleive, F. Chan, G. Kuperman, S. Nurnberger, J. Kamarajan, C. Anokhin, A. Agrawal, A. Rose, R. J. Edenberg, H. J. Schuckit, M. Kaprio, J. Dick, D. M. 2019-08-30 doi:10.1101/748038 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance ]]> https://biorxiv.org/content/10.1101/749887v1?rss=1 Tan, J. Olson, C. A. Park, J. H. Sastry, A. V. Phaneuf, P. Yang, L. Szubin, R. Hefner, Y. Feist, A. M. Palsson, B. O. 2019-08-29 doi:10.1101/749887 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data ]]> https://biorxiv.org/content/10.1101/750471v1?rss=1 Jarmusch, A. K. Wang, M. Aceves, C. M. Advani, R. S. Aguire, S. Aksenov, A. A. Aleti, G. Aron, A. T. Bauermeister, A. Bolleddu, S. Bouslimani, A. Caraballo-Rodriguez, A. M. Chaar, R. Coras, R. Elijah, E. O. Ernst, M. Gauglitz, J. M. Gentry, E. C. Husband, M. Jarmusch, S. A. Jones, K. L. Kamenik, Z. Le Gouellec, A. Lu, A. McCall, L.-I. McPhail, K. L. Meehan, M. J. Melnik, A. V. Menezes, R. C. Montoya-Giraldo, Y. A. Nguyen, N. H. Nothias, L. F. Nothias-Esposito, M. Panitchpakdi, M. Petras, D. Quinn, R. Sikora, N. van der Hooft, J. J. J. Vargas, F. Vrbanac, 2019-08-29 doi:10.1101/750471 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production ]]> https://biorxiv.org/content/10.1101/751347v1?rss=1 Fouladiha, H. Marashi, S.-A. Torkashvand, F. Mahboudi, F. Lewis, N. Vaziri, B. 2019-09-01 doi:10.1101/751347 Cold Spring Harbor Laboratory Press 2019-09-01 <![CDATA[ Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion ]]> https://biorxiv.org/content/10.1101/754002v1?rss=1 Saxena, A. Sharma, V. Tran, M. P. Gutierrez, H. L. Erberich, J. M. Birmingham, A. Hiller, M. Cooper, K. L. 2019-08-31 doi:10.1101/754002 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Factors that influence the thymic selection of CD8αα intraepithelial lymphocytes ]]> https://biorxiv.org/content/10.1101/761601v1?rss=1 Kurd, N. S. Hoover, A. Yoon, J. Weist, B. M. Robey, E. A. 2019-09-12 doi:10.1101/761601 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Cross-Sectional and Longitudinal Validation of Serum Neurofilament Light Chain (NfL) as a Biomarker of Parkinson’s Disease Progression ]]> https://biorxiv.org/content/10.1101/762237v1?rss=1 Mollenhauer, B. Dakna, D. Liu, T.-Y. Galasko, D. Foroud, T. Zetterberg, H. Schade, S. Gera, R. Wang, W. Gao, F. Kruse, N. Frasier, M. Chahine, L. Coffey, C. S. Singleton, A. B. Simuni, T. Weintraub, D. Seibyl, J. Toga, A. W. Tanner, C. M. Kieburtz, K. Marek, K. Siderowf, A. Cedarbaum, J. M. Hutten, S. J. Trenkwalder, C. Graham, D. 2019-09-11 doi:10.1101/762237 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Network-based clustering for drug sensitivity prediction in cancer cell lines ]]> https://biorxiv.org/content/10.1101/764043v1?rss=1 Pouryahya, M. Oh, J. H. Mathews, J. C. Belkhatir, Z. Moosmuller, C. Deasy, J. O. Tannenbaum, A. R. 2019-09-18 doi:10.1101/764043 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Interferon stimulated genes mark pathogenic cells of the emergency myelopoietic response to sterile tissue injury in mice and humans ]]> https://biorxiv.org/content/10.1101/765404v1?rss=1 Ng, R. Calcagno, D. M. Toomu, A. Huang, K. Aguirre, A. Daniels, L. Fu, Z. King, K. 2019-09-11 doi:10.1101/765404 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries ]]> https://biorxiv.org/content/10.1101/765453v1?rss=1 Lee, C. T. Laughlin, J. G. Moody, J. B. Amaro, R. E. McCammon, J. A. Holst, M. J. Rangamani, P. 2019-09-11 doi:10.1101/765453 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Beyond the ecology of fear: non-lethal effects of predators are strong whereas those of parasites are diverse ]]> https://biorxiv.org/content/10.1101/766477v1?rss=1 Daversa, D. R. Hechinger, R. F. Madin, E. Fenton, A. 2019-09-18 doi:10.1101/766477 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Understanding the role of urban design in disease spreading ]]> https://biorxiv.org/content/10.1101/766667v1?rss=1 Brizuela, N. G. Garcia-Chan, N. Gutierrez Pulido, H. Chowell, G. 2019-09-12 doi:10.1101/766667 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Making the MOSTest of imaging genetics ]]> https://biorxiv.org/content/10.1101/767905v1?rss=1 van der Meer, D. Frei, O. Kaufmann, T. Shadrin, A. A. Devor, A. Smeland, O. B. Thompson, W. Fan, C. C. Holland, D. Westlye, L. T. Andreassen, O. A. Dale, A. 2019-09-14 doi:10.1101/767905 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ A Pairwise Distance Distribution Correction (DDC) algorithm for blinking-free super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/768051v1?rss=1 Bohrer, C. H. Yang, X. Weng, X. Tenner, B. Ross, B. Mcquillen, R. Zhang, J. Roberts, E. Xiao, J. 2019-09-12 doi:10.1101/768051 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Reliability of Mismatch Negativity Event-Related Potentials in a Multisite, Traveling Subjects Study ]]> https://biorxiv.org/content/10.1101/768408v1?rss=1 0.5). Reliability of MMN amplitude was greater than latency, and reliability with mastoid referencing significantly outperformed nose-referencing.nnConclusionsEEG preprocessing methods have a significant impact on the reliability of MMN amplitude. Within site MMN reliability can be excellent, consistent with prior single site studies.nnSignificanceWith standardized data collection and ERP processing, MMN can be reliably obtained in multisite studies, providing larger samples sizes within rare patient groups. ]]> Roach, B. Carrion, R. E. Hamilton, H. K. Bachman, P. Belger, A. Duncan, E. Johannesen, J. Light, G. A. Niznikiewicz, M. Addington, J. Bearden, C. E. Cadenhead, K. S. Cannon, T. D. Cornblatt, B. A. McGlashan, T. H. Perkins, D. O. Seidman, L. J. Tsuang, M. Walker, E. F. Woods, S. W. Mathalon, D. H. 2019-09-18 doi:10.1101/768408 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ centroFlye: Assembling Centromeres with Long Error-Prone Reads ]]> https://biorxiv.org/content/10.1101/772103v1?rss=1 Bzikadze, A. V. Pevzner, P. A. 2019-09-16 doi:10.1101/772103 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Annotation-Informed Causal Mixture Modeling (AI-MiXeR) reveals phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories ]]> https://biorxiv.org/content/10.1101/772202v1?rss=1 Shadrin, A. A. Frei, O. Smeland, O. B. Bettella, F. O`Connell, K. S. Gani, O. Bahrami, S. Uggen, T. K. E. Djurovic, S. Holland, D. Andreassen, O. A. Dale, A. M. 2019-09-16 doi:10.1101/772202 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Secondary Motor Cortex Transforms Spatial Information into Planned Action During Navigation ]]> https://biorxiv.org/content/10.1101/776765v1?rss=1 Olson, J. M. Li, J. Montgomery, S. E. Nitz, D. A. 2019-09-20 doi:10.1101/776765 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk association ]]> https://biorxiv.org/content/10.1101/778183v1?rss=1 Nott, A. Holtman, I. R. Coufal, N. G. Schlachetzki, J. C. M. Yu, M. Hu, R. Han, C. Z. Pena, M. Xiao, J. Wu, Y. Keuelen, Z. Pasillas, M. P. O'Connor, C. Schafer, S. T. Shen, Z. Rissman, R. A. Brewer, J. B. Gosselin, D. Gonda, D. D. Levy, M. L. Rosenfeld, M. G. McVicker, G. P. Gage, F. H. Ren, B. Glass, C. K. 2019-09-22 doi:10.1101/778183 Cold Spring Harbor Laboratory Press 2019-09-22 <![CDATA[ Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses ]]> https://biorxiv.org/content/10.1101/778605v1?rss=1 Zhang, H. Ahearn, T. Lecarpentier, J. Barnes, D. Beesley, J. Qi, G. Jiang, X. O'Mara, T. A. Zhao, N. Bolla, M. K. Dunning, A. M. Dennis, J. Wang, Q. Abu Ful, Z. Aittomaki, K. Andrulis, I. L. Anton-Culver, H. Arndt, V. Aronson, K. J. Arun, B. K. Auer, P. L. Azzollini, J. Barrowdale, D. Becher, H. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Bogdanova, N. V. Bojesen, S. E. Bonanni, B. Bondavalli, D. Borg, A. Brauch, H. Brenner, H. Briceno, I. Broeks, A. Brucker, S. Y. Bruning, T. Burwinkel, B. Buys, S. 2019-09-24 doi:10.1101/778605 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets ]]> https://biorxiv.org/content/10.1101/781328v1?rss=1 Mohite, O. S. Lloyd, C. J. Monk, J. M. Weber, T. Palsson, B. O. 2019-09-25 doi:10.1101/781328 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Systematic assessment of regulatory effects of human disease variants in pluripotent cells ]]> https://biorxiv.org/content/10.1101/784967v1?rss=1 Bonder, M. J. Smail, C. Gloudemans, M. J. Fresard, L. Jakubosky, D. D'Antonio, M. Li, X. Ferraro, N. M. Carcamo-Orive, I. Mirauta, B. Seaton, D. D. Cai, N. Horta, D. HipSci Consortium, iPSCORE Consortium, GENESiPS Consortium, PhLiPS Consortium, Smith, E. N. Frazer, K. A. Montgomery, S. B. Stegle, O. 2019-09-28 doi:10.1101/784967 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract ]]> https://biorxiv.org/content/10.1101/787358v1?rss=1 Sidhwani, P. Boezio, G. L. M. Yang, H. Chi, N. C. Roman, B. L. Stainier, D. Y. R. Yelon, D. 2019-09-30 doi:10.1101/787358 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ c-di-AMP hydrolysis by a novel type of phosphodiesterase promotes differentiation of multicellular bacteria ]]> https://biorxiv.org/content/10.1101/789354v1?rss=1 Latoscha, A. Drexler, D. J. Al-Bassam, M. M. Kaever, V. Findlay, K. C. Witte, G. Tschowri, N. 2019-10-01 doi:10.1101/789354 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs ]]> https://biorxiv.org/content/10.1101/790063v1?rss=1 Gauglitz, J. M. Morton, J. T. Tripathi, A. Hansen, S. Gaffney, M. Carpenter, C. Weldon, K. C. Shah, R. Parampil, A. Fidgett, A. Swafford, A. D. Knight, R. Dorrestein, P. C. 2019-10-02 doi:10.1101/790063 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Regional dynamics of fractal dimension of the LV endocardium from cine CT images ]]> https://biorxiv.org/content/10.1101/791731v1?rss=1 Manohar, A. Rossini, L. Colvert, G. Vigneault, D. M. Contijoch, F. Chen, M. Y. del Alamo, J. C. McVeigh, E. R. 2019-10-03 doi:10.1101/791731 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations ]]> https://biorxiv.org/content/10.1101/795005v1?rss=1 Rizzi, A. Jensen, T. Slochower, D. R. Aldeghi, M. Gapsys, V. Ntekoumes, D. Bosisio, S. Papadourakis, M. Henriksen, N. M. de Groot, B. L. Cournia, Z. Dickson, A. Michel, J. Gilson, M. K. Shirts, M. R. Mobley, D. L. Chodera, J. D. 2019-10-07 doi:10.1101/795005 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Vaping nicotine-containing electronic cigarettes produces addiction-like behaviors and cardiopulmonary abnormalities in rats ]]> https://biorxiv.org/content/10.1101/797084v1?rss=1 Smith, L. C. Kallupi, M. Tieu, L. Jaquish, A. Barr, J. Su, Y. Velarde, N. Sedighim, S. Klodnicki, M. Carrette, L. L. G. Sun, X. de Guglielmo, G. George, O. 2019-10-08 doi:10.1101/797084 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ The maize heterotrimeric G-protein β subunit controls shoot meristem development and immune responses. ]]> https://biorxiv.org/content/10.1101/797985v1?rss=1 Wu, Q. Xu, F. Liu, L. Char, S. N. Ding, Y. Schmelz, E. A. Yang, B. Jackson, D. 2019-10-08 doi:10.1101/797985 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ The effects of modified sialic acids on mucus and erythrocytes on influenza A virus HA and NA functions ]]> https://biorxiv.org/content/10.1101/800300v1?rss=1 Barnard, K. N. Alford-Lawrence, B. K. Buchholz, D. W. Wasik, B. R. LaClair, J. R. Yu, H. Honce, R. Ruhl, S. Pajic, P. Daugherity, E. K. Chen, X. Schultz-Cherry, S. Aguilar, H. C. Varki, A. Parrish, C. R. 2019-10-10 doi:10.1101/800300 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure ]]> https://biorxiv.org/content/10.1101/804401v1?rss=1 Vargas, F. Weldon, K. C. Sikora, N. Wang, M. Zhang, Z. Gentry, E. C. Panitchpakdi, M. W. Caraballo, M. Dorrestein, P. C. Jarmusch, A. K. 2019-10-15 doi:10.1101/804401 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ A simple mass-action model predicts protein timecourses from mRNA trajectories during a dynamic response in two strains of S. cerevisiae ]]> https://biorxiv.org/content/10.1101/805846v1?rss=1 Kuo, S. Egertson, J. Merrihew, G. MacCoss, M. J. Pollard, D. Rifkin, S. A. 2019-10-16 doi:10.1101/805846 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. ]]> https://biorxiv.org/content/10.1101/807008v1?rss=1 Van Nostrand, E. L. Pratt, G. A. Yee, B. A. Wheeler, E. C. Blue, S. M. Mueller, J. Park, S. S. Garcia, K. E. Gelboin-Burkhart, C. Nguyen, T. B. Rabano, I. Stanton, R. Sundararaman, B. Wang, R. Fu, X.-D. Graveley, B. R. Yeo, G. W. 2019-10-16 doi:10.1101/807008 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program ]]> https://biorxiv.org/content/10.1101/808568v1?rss=1 Denholtz, M. Zhu, Y. Doehrmann, S. He, Z. Lu, H. Isoda, T. Nizet, V. Murre, C. 2019-10-17 doi:10.1101/808568 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Structural Brain Imaging Studies Offer Clues about the Effects of the Shared Genetic Etiology among Neuropsychiatric Disorders ]]> https://biorxiv.org/content/10.1101/809582v1?rss=1 Radonjic, N. V. Hess, J. L. Rovira, P. Andreassen, O. Buitelaar, J. K. Ching, C. R. K. Franke, B. Hoogman, M. Jahanshad, N. McDonald, C. Schmaal, L. Sisodiya, S. M. Stein, D. J. van den Heuvel, O. A. van Erp, T. G. M. van Rooij, D. Veltman, D. J. Thompson, P. Faraone, S. V. 2019-10-17 doi:10.1101/809582 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ The γH2AX Peak in the S Phase After UV Irradiation Corresponds to the sites of DNA Replication and not DNA Damage ]]> https://biorxiv.org/content/10.1101/810689v1?rss=1 Dhuppar, S. Roy, S. Mazumder, A. 2019-10-21 doi:10.1101/810689 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ The polyvertex score (PVS): a whole-brain phenotypic prediction framework for neuroimaging studies ]]> https://biorxiv.org/content/10.1101/813915v1?rss=1 Zhao, W. Palmer, C. E. Thompson, W. K. Jernigan, T. L. Dale, A. M. Fan, C. C. 2019-10-22 doi:10.1101/813915 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Genetic and clinical analyses of psychosis spectrum symptoms in a large multi-ethnic youth cohort reveal significant link with ADHD. ]]> https://biorxiv.org/content/10.1101/814087v1?rss=1 Olde Loohuis, L. M. Mennigen, E. Ori, A. P. S. Perkins, D. Robinson, E. Addington, J. Cadenhead, K. S. Cornblatt, B. A. Mathalon, D. H. McGlashan, T. H. Seidman, L. J. Keshavan, M. Stone, W. Tsuang, M. T. Walker, E. F. Woods, S. W. Cannon, T. D. Gur, R. C. Gur, R. E. Bearden, C. E. Ophoff, R. A. 2019-10-22 doi:10.1101/814087 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Determining the association between cortical morphology and cognition in 10,145 children from the Adolescent Brain and Cognitive Development (ABCD) study using the MOSTest ]]> https://biorxiv.org/content/10.1101/816025v1?rss=1 Palmer, C. E. Zhao, W. E. Loughnan, R. J. Fan, C. C. Thompson, W. K. Jernigan, T. L. Dale, A. M. 2019-10-23 doi:10.1101/816025 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ The circadian clock and darkness control natural competence in cyanobacteria ]]> https://biorxiv.org/content/10.1101/822627v1?rss=1 Taton, A. Erikson, C. Yang, Y. Rubin, B. E. Rifkin, S. A. Golden, J. W. Golden, S. S. 2019-10-30 doi:10.1101/822627 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ N-terminal domain Increases Activation of Elephant Shark Glucocorticoid and Mineralocorticoid Receptors ]]> https://biorxiv.org/content/10.1101/822718v1?rss=1 Katsu, Y. Shariful, I. M. Lin, X. Takagi, W. Urushitani, H. Kohno, S. Hyodo, S. Baker, M. E. 2019-10-29 doi:10.1101/822718 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation ]]> https://biorxiv.org/content/10.1101/823096v1?rss=1 Hahn, W. C. Kim, J. W. Berrios, C. Kim, M. Schade, A. E. Adelmant, G. Yeerna, H. Damato, E. Iniguez, A. B. Swanson, S. K. Florens, L. Washburn, M. P. Stegmaier, K. Gray, N. S. Tamayo, P. Gjoerup, O. Marto, J. A. DeCaprio, J. 2019-10-29 doi:10.1101/823096 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds ]]> https://biorxiv.org/content/10.1101/824888v1?rss=1 Aron, A. T. Petras, D. Schmid, R. Gauglitz, J. M. Buttel, I. Antelo, L. Zhi, H. Saak, C. C. Malarney, K. P. Thines, E. Dutton, R. J. Raffatellu, M. Dorrestein, P. C. 2019-10-30 doi:10.1101/824888 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters ]]> https://biorxiv.org/content/10.1101/831941v1?rss=1 Rachtman, E. Balaban, M. Bafna, V. Mirarab, S. 2019-11-05 doi:10.1101/831941 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Resolving intrinsic ambiguities of the fMRI signal in the human brain ]]> https://biorxiv.org/content/10.1101/833681v1?rss=1 Liu, E. Y. Haist, F. Shin, D. D. Buxton, R. B. 2019-11-07 doi:10.1101/833681 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression and drug response ]]> https://biorxiv.org/content/10.1101/835918v1?rss=1 Zhang, P. Kitchen-Smith, I. Xiong, L. Stracquadanio, G. Brown, K. Richter, P. Wallace, M. Bond, E. Sahgal, N. Moore, S. Nornes, S. De Val, S. Surakhy, M. Sims, D. Wang, X. Bell, D. A. Zeron-Medina, J. Jiang, Y. Ryan, A. Selfe, J. Shipley, J. Kar, S. Pharoah, P. Loveday, C. Jansen, R. Grochola, L. F. Palles, C. Protheroe, A. Millar, V. Ebner, D. Pagadala, M. Blagden, S. P. Maughan, T. Domingo, E. Tomlinson, I. Turnbull, C. Carter, H. Bond, G. 2019-11-09 doi:10.1101/835918 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Co-Increasing Neuronal Noise and Beta Power in the Developing Brain ]]> https://biorxiv.org/content/10.1101/839258v1?rss=1 He, W. Donoghue, T. Sowman, P. F. Seymour, R. A. Brock, J. Crain, S. Voytek, B. Hillebrand, A. 2019-11-12 doi:10.1101/839258 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy ]]> https://biorxiv.org/content/10.1101/840520v1?rss=1 Oliver, A. LaMere, B. Weihe, C. Wandro, S. Lindsay, K. Wadhwa, P. Mills, D. Pride, D. T. Fiehn, O. Northen, T. de Raad, M. Li, H. Martiny, J. B. H. Lynch, S. Whiteson, K. 2019-11-13 doi:10.1101/840520 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Anthropomorphic left ventricular mesh phantom: a framework to investigate the accuracy of SQUEEZ using Coherent Point Drift for the detection of regional wall motion abnormalities ]]> https://biorxiv.org/content/10.1101/840595v1?rss=1 Manohar, A. Colvert, G. M. Schluchter, A. Contijoch, F. J. McVeigh, E. R. 2019-11-13 doi:10.1101/840595 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Predictive Coding Models for Pain Perception ]]> https://biorxiv.org/content/10.1101/843284v1?rss=1 Song, Y. Yao, M. Kemprecos, H. byrne, a. Xiao, Z. Zhang, Q. Singh, A. Wang, J. Chen, Z. S. 2019-11-18 doi:10.1101/843284 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Fluorescence correlation spectroscopy and photon count histograms in small domains. Part I: General theory ]]> https://biorxiv.org/content/10.1101/847129v1?rss=1 Elson, E. L. Jiang, Y. Xu, B. Melnykov, A. Genin, G. M. 2019-11-20 doi:10.1101/847129 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Antagonistic odor interactions in olfactory sensory neurons are widespread in freely breathing mice ]]> https://biorxiv.org/content/10.1101/847525v1?rss=1 Zak, J. D. Reddy, G. Vergassola, M. Murthy, V. N. 2019-11-20 doi:10.1101/847525 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Human-specific regulatory features of brain development manifest staggering breadth of associations with physiological processes and pathological conditions of H. sapiens ]]> https://biorxiv.org/content/10.1101/848762v1?rss=1 Glinsky, G. 2019-11-20 doi:10.1101/848762 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Economic, social, and physiological resilience predict brain structure and cognitive performance in 9 - 10-year-old children ]]> https://biorxiv.org/content/10.1101/852988v1?rss=1 Gonzalez, M. R. Palmer, C. E. Uban, K. A. Jernigan, T. L. Thompson, W. K. Sowell, E. R. 2019-11-25 doi:10.1101/852988 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Sub-2 A Resolution Structure Determination Using Single-Particle Cryo-EM at 200 keV ]]> https://biorxiv.org/content/10.1101/855643v1?rss=1 Wu, M. Lander, G. C. Herzik, M. A. 2019-11-26 doi:10.1101/855643 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Systematic analyses of factors required for adhesion of Salmonella enterica serovar Typhimurium to corn salad (Valerianella locusta) ]]> https://biorxiv.org/content/10.1101/855726v1?rss=1 Hensel, M. Elpers, L. Kretzschmar, J. Nuccio, S.-P. Bäumler, A. J. 2019-11-27 doi:10.1101/855726 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Identifying Brain Network Topology Changes in Task Processes and Psychiatric Disorders ]]> https://biorxiv.org/content/10.1101/866855v1?rss=1 Rezaeinia, P. Fairley, K. Pal, P. Meyer, F. Carter, R. M. 2019-12-06 doi:10.1101/866855 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Quantifying the polygenic architecture of the human cerebral cortex: Extensive genetic overlap between cortical thickness and surface area ]]> https://biorxiv.org/content/10.1101/868307v1?rss=1 van der Meer, D. Frei, O. Kaufmann, T. Chen, C.-H. Thompson, W. K. O'Connell, K. S. Monereo Sanchez, J. Linden, D. E. Westlye, L. T. Dale, A. M. Andreassen, O. A. 2019-12-06 doi:10.1101/868307 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Cognitive Functions Mediate the Effect of Preterm Birth on Mathematics Skills in Young Children ]]> https://biorxiv.org/content/10.1101/868547v1?rss=1 Adrian, J. A. Bakeman, R. Akshoomoff, N. Haist, F. 2019-12-08 doi:10.1101/868547 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ SODA: Multi-locus species delimitation using quartet frequencies ]]> https://biorxiv.org/content/10.1101/869396v1?rss=1 Rabiee, M. Mirarab, S. 2019-12-09 doi:10.1101/869396 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ GIV/Girdin and Exo70 Constitute the Core of the Mammalian Polarized Exocytic Machinery ]]> https://biorxiv.org/content/10.1101/870071v1?rss=1 Rohena, C. Rajapakse, N. Lo, I.-C. Novick, P. Sahoo, D. Ghosh, P. 2019-12-09 doi:10.1101/870071 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ GIV-Kindlin interaction is required for Kindlin-Mediated Integrin Recognition and Activation ]]> https://biorxiv.org/content/10.1101/870113v1?rss=1 Rohena, C. Kalogriopoulos, N. Rajapakse, N. Roy, S. Lopez-Sanchez, I. Ablack, J. Sahoo, D. Ghosh, P. 2019-12-10 doi:10.1101/870113 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Latent space visualization, characterization, and generation of diverse vocal communication signals ]]> https://biorxiv.org/content/10.1101/870311v1?rss=1 Sainburg, T. Thielk, M. Gentner, T. Q. 2019-12-11 doi:10.1101/870311 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites ]]> https://biorxiv.org/content/10.1101/870949v1?rss=1 Xu, F. Jimenez-Gonzalez, A. Einarsson, E. Astvaldsson, A. Peirasmaki, D. Eckmann, L. Andersson, J. O. Svärd, S. G. Jerlström-Hultqvist, J. 2019-12-10 doi:10.1101/870949 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Inference of Gorilla demographic and selective history from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/009191v1?rss=1 Kimberly F. McManus Joanna L. Kelley Shiya Song Krishna Veeramah August E. Woerner Laurie S. Stevison Oliver A. Ryder Great Ape Genome Project Jeffrey M. Kidd Jeffrey D. Wall Carlos D. Bustamante Michael F. Hammer 2014-09-17 doi:10.1101/009191 Cold Spring Harbor Laboratory Press 2014-09-17 <![CDATA[ Abnormal X Chromosome Inactivation in Females with Major Psychiatric Disorders ]]> https://biorxiv.org/content/10.1101/009555v1?rss=1 Baohu Ji Kerin K Higa John Kelsoe Xianjin Zhou 2014-09-23 doi:10.1101/009555 Cold Spring Harbor Laboratory Press 2014-09-23 <![CDATA[ On the scope and limitations of baker’s yeast as a model organism for studying human tissue-specific pathways ]]> https://biorxiv.org/content/10.1101/011858v1?rss=1 Shahin Mohammadi Baharak Saberidokht Shankar Subramaniam Ananth Grama 2014-11-26 doi:10.1101/011858 Cold Spring Harbor Laboratory Press 2014-11-26 <![CDATA[ Identification of an Arabidopsis Aminotransferase that Facilitates Tryptophan and Auxin Homeostasis ]]> https://biorxiv.org/content/10.1101/013821v1?rss=1 Michael Pieck Youxi Yuan Jason Godfrey Christopher Fisher Sanda Zolj Nicholas Thomas Connie Wu Julian Ramos Norman Lee Jennifer Normanly John Celenza 2015-01-16 doi:10.1101/013821 Cold Spring Harbor Laboratory Press 2015-01-16 <![CDATA[ Restoration of Sp4 in forebrain GABAergic neurons rescues hypersensitivity to ketamine in Sp4 hypomorphic mice ]]> https://biorxiv.org/content/10.1101/015677v1?rss=1 Kerin K Higa Baohu Ji Mahalah R Buell Risbrough B Victoria Susan B Powell Jared W Young Mark A Geyer Xianjin Zhou 2015-02-26 doi:10.1101/015677 Cold Spring Harbor Laboratory Press 2015-02-26 <![CDATA[ The C. elegans ephrin EFN-4 functions non-cell autonomously with heparan sulfate proteoglycans to promote axon outgrowth and branching ]]> https://biorxiv.org/content/10.1101/022756v1?rss=1 Alicia A Schwieterman Alyse N Steves Vivian Yee Cory J Donelson Aaron Pital Taylor Voyles Austin M Howard Danielle E Ereddia Kelsie S Effrein Jonathan L McMurry Brian D Ackley Andrew D Chisholm Martin L Hudson 2015-07-17 doi:10.1101/022756 Cold Spring Harbor Laboratory Press 2015-07-17 <![CDATA[ Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis ]]> https://biorxiv.org/content/10.1101/026948v1?rss=1 Jean Fan Neeraj Salathia Rui Liu Gwen Kaeser Yun Yung Joseph L Herman Fiona Kaper Jian-Bing Fan Kun Zhang Jerold Chun Peter Kharchenko 2015-09-16 doi:10.1101/026948 Cold Spring Harbor Laboratory Press 2015-09-16 <![CDATA[ Balanced Oscillatory Coupling Improves Information Flow ]]> https://biorxiv.org/content/10.1101/030304v1?rss=1 Erik J Peterson Bradley Voytek 2015-10-30 doi:10.1101/030304 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Resources for the comprehensive discovery of functional RNA elements ]]> https://biorxiv.org/content/10.1101/030486v1?rss=1 Balaji Sundararaman Lijun Zhan Steven Blue Rebecca Stanton Keri Elkins Sara Olson Xintao Wei Eric L Van Nostrand Stephanie C Huelga Brendan M Smalec Xiaofeng Wang Eurie L Hong Jean M Davidson Eric Lecuyer Brenton R Graveley Gene W Yeo 2015-11-03 doi:10.1101/030486 Cold Spring Harbor Laboratory Press 2015-11-03 <![CDATA[ Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/032474v1?rss=1 Dominic Holland Yunpeng Wang Wesley K Thompson Andrew Schork Chi-Hua Chen Min-Tzu Lo Aree Witoelar Thomas Werge Michael O'Donovan Ole A Andreassen Anders Dale 2015-11-21 doi:10.1101/032474 Cold Spring Harbor Laboratory Press 2015-11-21 <![CDATA[ Peroxisomes move by hitchhiking on early endosomes using the novel linker protein PxdA ]]> https://biorxiv.org/content/10.1101/034231v1?rss=1 John Salogiannis Martin J. Egan Samara L. Reck-Peterson 2015-12-11 doi:10.1101/034231 Cold Spring Harbor Laboratory Press 2015-12-11 <![CDATA[ The Arabidopsis Auxin F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram ]]> https://biorxiv.org/content/10.1101/034652v1?rss=1 Michael J Prigge Kathleen Greenham Yi Zhang Aaron Santner Cristina Castillejo Ronan C O'Malley Joseph R Ecker Mark Estelle 2015-12-17 doi:10.1101/034652 Cold Spring Harbor Laboratory Press 2015-12-17 <![CDATA[ Systematic identification of cooperation between DNA binding proteins in 3D space ]]> https://biorxiv.org/content/10.1101/036145v1?rss=1 Kai Zhang Nan Li Wei Wang 2016-01-07 doi:10.1101/036145 Cold Spring Harbor Laboratory Press 2016-01-07 <![CDATA[ Gene Expression Signatures of Sporadic ALS Motor Neuron Populations ]]> https://biorxiv.org/content/10.1101/038448v1?rss=1 Ranjan Batra Kasey Hutt Anthony Vu Stuart J Rabin Michael W Baughn Ryan T Libby Shawn Hoon John Ravits Gene W Yeo 2016-02-01 doi:10.1101/038448 Cold Spring Harbor Laboratory Press 2016-02-01 <![CDATA[ Rigidity of silicone substrates controls cell spreading and stem cell differentiation ]]> https://biorxiv.org/content/10.1101/040048v1?rss=1 25 kPa, have been classified as soft (adipogenic) [2,3], medium rigidity (myogenic)1, and hard (osteogenic) [1], respectively. In most studies, the soft substrates are hydrogels, and variations in their elastic moduli are usually accompanied by variations in the dry mass and porosity. The paradigm of the effect of substrate rigidity on the cellular functions has been challenged by Trappmann et al. [4], who claimed that cell spreading and differentiation on hydrogel substrates depend not on the elastic moduli of the substrates, but rather on their porosity, which affects the density of adhesion points between the substrate surface and the extracellular matrix (ECM) coating on it. This claim has been rebutted by Wen at al. [3], who have used hydrogel substrates with different porosities but identical elastic moduli to show that it is the elastic modulus rather than the porosity that is key to the effect of the substrate on cell spreading and differentiation. Both publications agree, however, that there is no appreciable effect of the substrate rigidity on either cell spreading or differentiation, if the substrate is made of a silicone gel rather than a hydrogel. This conclusion appears to contradict the findings of several other groups, who reported that when cells are plated on an array of flexible silicone microposts, their spreading and differentiation depend on the rigidity of the substrate [5], and that when cell are plated on silicone gels, their differentiation depends on the gel rigidity [6]. To resolve this contradiction, we used soft, medium, and hard silicone gel substrates with elastic moduli of 0.5, 16, and 64 kPa, respectively, (Fig.1) to perform experiments similar to those reported in Refs.4 and 3, testing the dependence of differentiation and spreading of MSCs and of spreading of fibroblasts and keratinocytes on the substrate rigidity. ]]> Grigory Vertelov Edgar Gutierrez Sin-Ae Lee Edward Ronan Alex Groisman Eugene Tkachenko 2016-02-19 doi:10.1101/040048 Cold Spring Harbor Laboratory Press 2016-02-19 <![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[ Control of Transposon-mediated Activation of the glpFK Operon of Escherichia coli by two DNA binding Proteins ]]> https://biorxiv.org/content/10.1101/046649v1?rss=1 Zhongge Zhang Milton H. Saier 2016-03-31 doi:10.1101/046649 Cold Spring Harbor Laboratory Press 2016-03-31 <![CDATA[ Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/047720v1?rss=1 Robert J Luallen Aaron W Reinke Linda Tong Michael R Botts Marie-Anne Felix Emily R Troemel 2016-04-08 doi:10.1101/047720 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Immune DNA signature of T-cell infiltration in breast tumor exomes ]]> https://biorxiv.org/content/10.1101/047753v1?rss=1 Eric Levy Rachel Marty Valentina Garate-Calderon Brian Woo Michelle Dow Ricardo Armisen Hannah Carter Olivier Harismendy 2016-04-08 doi:10.1101/047753 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Rapid hyperosmotic-induced Ca2+ responses in Arabidopsis thaliana exhibit sensory potentiation and establish involvement of plastidial KEA transporters ]]> https://biorxiv.org/content/10.1101/048330v1?rss=1 Aaron Benjamin Stephan Eric Yang Hans-Henning Kunz Julian I. Schroeder 2016-04-13 doi:10.1101/048330 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Paradoxical signaling regulates structural plasticity in dendritic spines ]]> https://biorxiv.org/content/10.1101/050492v1?rss=1 Padmini Rangamani Michael G. Levy Shahid M. Khan George Oster 2016-04-27 doi:10.1101/050492 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Shear-induced nitric oxide production by endothelial cells ]]> https://biorxiv.org/content/10.1101/051946v1?rss=1 Krishna Sriram Justin G. Laughlin Padmini Rangamani Daniel M. Tartakovsky 2016-05-05 doi:10.1101/051946 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Detection of human adaptation during the past 2,000 years ]]> https://biorxiv.org/content/10.1101/052084v1?rss=1 Yair Field Evan A Boyle Natalie Telis Ziyue Gao Kyle J Gaulton David Golan Loic Yengo Ghislain Rocheleau Philippe Froguel Mark I McCarthy Jonathan K Pritchard 2016-05-07 doi:10.1101/052084 Cold Spring Harbor Laboratory Press 2016-05-07 <![CDATA[ Cell-to-cell spread of microsporidia causes C. elegans organs to form syncytia ]]> https://biorxiv.org/content/10.1101/053181v1?rss=1 Keir M Balla Robert J Luallen Malina A Bakowski Emily R Troemel 2016-05-13 doi:10.1101/053181 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ Harnessing Molecular Motors for Nanoscale Pulldown in Live Cells ]]> https://biorxiv.org/content/10.1101/053744v1?rss=1 Jonathan E Bird Melanie Barzik Meghan Drummond Daniel C Sutton Spencer M Goodman Eva L Morozko Stacey M Cole Jennifer Skidmore Diana Syam Elizabeth A Wilson Tracy Fitzgerald Atteeq U Rehman Donna M Martin Erich T Boger Inna A Belyantseva Thomas B Friedman 2016-06-07 doi:10.1101/053744 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ Rapidly evolving homing CRISPR barcodes ]]> https://biorxiv.org/content/10.1101/055863v1?rss=1 Reza Kalhor Prashant Mali George M Church 2016-05-27 doi:10.1101/055863 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling ]]> https://biorxiv.org/content/10.1101/057174v1?rss=1 Justin W Walley Zhouxin Shen Maxwell R McReynolds Steven P Briggs 2016-06-05 doi:10.1101/057174 Cold Spring Harbor Laboratory Press 2016-06-05 <![CDATA[ Distinct Cellular States Determine Calcium Signaling Response ]]> https://biorxiv.org/content/10.1101/059287v1?rss=1 Jason Yao Roy Wollman 2016-06-16 doi:10.1101/059287 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ Williams Syndrome-Specific Neuroarchitectural Profile and Its Associations with Cognitive Features ]]> https://biorxiv.org/content/10.1101/060764v1?rss=1 Chun Chieh Fan Timothy T. Brown Hauke Bartsch Joshua M. Kuperman Donald J. Hagler Andrew Schork Eric Halgren Anders Dale 2016-06-26 doi:10.1101/060764 Cold Spring Harbor Laboratory Press 2016-06-26 <![CDATA[ Metabolic complementation in bacterial communities: necessary conditions and optimality ]]> https://biorxiv.org/content/10.1101/064121v1?rss=1 Matteo Mori Miguel Ponce-de-Leon Juli Pereto Francisco Montero Montero 2016-07-15 doi:10.1101/064121 Cold Spring Harbor Laboratory Press 2016-07-15 <![CDATA[ An introduction to linear stability analysis for deciphering spatial patterns in signaling networks ]]> https://biorxiv.org/content/10.1101/065474v1?rss=1 Jasmine Nirody Padmini Rangamani 2016-07-23 doi:10.1101/065474 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Chaotic propagation of spatial cytoskeletal instability modulates integrity of podocyte foot processes ]]> https://biorxiv.org/content/10.1101/065839v1?rss=1 Cibele V Falkenberg Evren U Azeloglu Mark Stothers Thomas J Deerinck Yibang Chen John C He Mark H. Ellisman James C. Hone Ravi Iyengar Leslie M. Loew 2016-07-26 doi:10.1101/065839 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion ]]> https://biorxiv.org/content/10.1101/066944v1?rss=1 Zachary Andrew King Edward J O'Brien Adam M Feist Bernhard O Palsson 2016-08-01 doi:10.1101/066944 Cold Spring Harbor Laboratory Press 2016-08-01 <![CDATA[ ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions ]]> https://biorxiv.org/content/10.1101/069021v1?rss=1 Haythem Latif Stephen Federowicz Ali Ebrahim Janna Tarasova Richard Szubin Jose Utrilla Karsten Zengler Bernhard Palsson 2016-08-11 doi:10.1101/069021 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Pulsatile lipid vesicles under osmotic stress ]]> https://biorxiv.org/content/10.1101/070342v1?rss=1 Morgan Chabanon James C.S. Ho Bo Liedberg Atul N. Parikh Padmini Rangamani 2016-08-18 doi:10.1101/070342 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ A new foreperiod effect on single-trial phase coherence.\\ Part I: existence and relevance ]]> https://biorxiv.org/content/10.1101/072371v1?rss=1 Joaquin Rapela Marissa Westerfield Jeanne Townsend Scott Makeig 2016-08-30 doi:10.1101/072371 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Hand2 Inhibits Kidney Specification While Promoting Vein Formation Within the Posterior Mesoderm ]]> https://biorxiv.org/content/10.1101/075036v1?rss=1 Elliot A. Perens Zayra V. Garavito-Aguilar Gina P. Guio-Vega Karen T. Pena Yocheved L. Schindler Deborah Yelon 2016-09-13 doi:10.1101/075036 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ PDGF signaling directs cardiomyocyte movement toward the midline during heart tube assembly ]]> https://biorxiv.org/content/10.1101/076703v1?rss=1 Joshua Bloomekatz Reena Singh Owen W.J. Prall Ariel C. Dunn Megan Vaughan Chin-San Loo Richard P. Harvey Deborah Yelon 2016-09-21 doi:10.1101/076703 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Change-point detection without needing to detect change-points? ]]> https://biorxiv.org/content/10.1101/077719v1?rss=1 Chaitanya K Ryali Angela J Yu 2016-09-27 doi:10.1101/077719 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ CLEAR: Composition of Likelihoods for Evolve And Resequence Experiments ]]> https://biorxiv.org/content/10.1101/080085v1?rss=1 Arya Iranmehr Ali Akbari Christian Schlötterer Vineet Bafna 2016-10-10 doi:10.1101/080085 Cold Spring Harbor Laboratory Press 2016-10-10 <![CDATA[ Complete coverage of space favors modularity of the grid system in the brain ]]> https://biorxiv.org/content/10.1101/081356v1?rss=1 Sanzeni, A. Balasubramanian, V. Tiana, G. Vergassola, M. 2016-10-16 doi:10.1101/081356 Cold Spring Harbor Laboratory Press 2016-10-16 <![CDATA[ Deconstructing cell size control into physiological modules in Escherichia coli ]]> https://biorxiv.org/content/10.1101/081422v1?rss=1 Si, F. Li, D. Cox, S. E. Sauls, J. T. Azizi, O. Schwartz, A. B. Erickstad, M. J. Jun, Y. Li, X. Jun, S. 2016-10-17 doi:10.1101/081422 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ The human functional genome defined by genetic diversity ]]> https://biorxiv.org/content/10.1101/082362v1?rss=1 di Iulio, J. Bartha, I. Wong, E. Yu, H.-C. Hicks, M. Shah, N. Lavrenko, V. Kirkness, E. Fabani, M. Yang, D. Jung, I. Biggs, W. Ren, B. Venter, J. C. Telenti, A. 2016-10-21 doi:10.1101/082362 Cold Spring Harbor Laboratory Press 2016-10-21 <![CDATA[ Single cell analysis of lincRNA expression during human blastocyst differentiation identifies TERT (+) multi-lineage precursor cells ]]> https://biorxiv.org/content/10.1101/084087v1?rss=1 Durruthy-Durruthy, J. Wossidlo, M. Sebastiano, V. Glinsky, G. 2016-10-28 doi:10.1101/084087 Cold Spring Harbor Laboratory Press 2016-10-28 <![CDATA[ Feature-coding transitions to conjunction-coding with progression through human visual cortex ]]> https://biorxiv.org/content/10.1101/085381v1?rss=1 Cowell, R. A. Serences, J. T. 2016-11-03 doi:10.1101/085381 Cold Spring Harbor Laboratory Press 2016-11-03 <![CDATA[ Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals ]]> https://biorxiv.org/content/10.1101/086504v1?rss=1 Boehme, U. Otto, T. D. Cotton, J. Steinbiss, S. Sanders, M. Oyola, S. O. Nicot, A. Gandon, S. Patra, K. P. Herd, C. Bushell, E. Modrzynska, K. K. Billker, O. Vinetz, J. M. Rivero, A. Newbold, C. I. Berriman, M. 2016-11-08 doi:10.1101/086504 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ T cell co-stimulatory receptor CD28 is a primary target for PD-1-mediated inhibition ]]> https://biorxiv.org/content/10.1101/086652v1?rss=1 Hui, E. Cheung, J. Zhu, J. Su, X. Taylor, M. J. Wallweber, H. A. Sasmal, D. K. Huang, J. Kim, J. M. Mellman, I. Vale, R. D. 2016-11-09 doi:10.1101/086652 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Natural Genetic Variation Modifies Gene Expression Dynamics at the Protein Level During Pheromone Response in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/090480v1?rss=1 Pollard, D. A. Asamoto, C. K. Rahnamoun, H. Abendroth, A. S. Lee, S. R. Rifkin, S. A. 2016-11-29 doi:10.1101/090480 Cold Spring Harbor Laboratory Press 2016-11-29 <![CDATA[ Non-linear tradeoffs allow cooperation to evolve from Prisoner’s Dilemma to Snow Drift ]]> https://biorxiv.org/content/10.1101/091041v1?rss=1 Chao, L. Elena, S. 2016-12-06 doi:10.1101/091041 Cold Spring Harbor Laboratory Press 2016-12-06 <![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[ A framework to interpret short tandem repeat variation in humans ]]> https://biorxiv.org/content/10.1101/092734v1?rss=1 Gymrek, M. Willems, T. Erlich, Y. Reich, D. E. 2016-12-09 doi:10.1101/092734 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ DataMed: Finding useful data across multiple biomedical data repositories ]]> https://biorxiv.org/content/10.1101/094888v1?rss=1 Ohno-Machado, L. Sansone, S.-A. Alter, G. Fore, I. Grethe, J. Xu, H. Gonzalez-Beltran, A. Rocca-Serra, P. Soysal, E. Zong, N. Kim, H.-e. bioCADDIE Consortium, 2016-12-17 doi:10.1101/094888 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Blood flow directs arterial-venous remodeling through Notch activation and endothelial cell migration ]]> https://biorxiv.org/content/10.1101/095307v1?rss=1 Weijts, B. Gutierrez, E. Saikin, S. K. Ablooglu, A. J. Traver, D. Groisman, A. Tkachenko, E. 2016-12-19 doi:10.1101/095307 Cold Spring Harbor Laboratory Press 2016-12-19 <![CDATA[ In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase ]]> https://biorxiv.org/content/10.1101/097600v1?rss=1 Carbone, C. B. Kern, N. Fernandes, R. A. Hui, E. Su, X. Garcia, K. C. Vale, R. 2016-12-31 doi:10.1101/097600 Cold Spring Harbor Laboratory Press 2016-12-31 <![CDATA[ Evolution of the Mineralocorticoid Receptor: Sequence, Structure and Function ]]> https://biorxiv.org/content/10.1101/098921v1?rss=1 Baker, M. E. Katsu, Y. 2017-01-06 doi:10.1101/098921 Cold Spring Harbor Laboratory Press 2017-01-06 <![CDATA[ A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information ]]> https://biorxiv.org/content/10.1101/100305v1?rss=1 Luo, Y. Zhao, X. Zhou, J. Yang, J. Zhang, Y. Kuang, W. Peng, J. Chen, L. Zeng, J. 2017-01-13 doi:10.1101/100305 Cold Spring Harbor Laboratory Press 2017-01-13 <![CDATA[ Spatially periodic activation patterns of retrosplenial cortex encode route sub-spaces and distance travelled ]]> https://biorxiv.org/content/10.1101/100537v1?rss=1 Alexander, A. S. Nitz, D. A. 2017-01-15 doi:10.1101/100537 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Multi-generational silencing dynamics control cell aging ]]> https://biorxiv.org/content/10.1101/102210v1?rss=1 Li, Y. Jin, M. O'Laughlin, R. Tsimring, L. S. Pillus, L. Hasty, J. Hao, N. 2017-01-22 doi:10.1101/102210 Cold Spring Harbor Laboratory Press 2017-01-22 <![CDATA[ COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression ]]> https://biorxiv.org/content/10.1101/106559v1?rss=1 Lloyd, C. J. Ebrahim, A. Yang, L. King, Z. A. Catoiu, E. O'Brien, E. J. Liu, J. K. Palsson, B. O. 2017-02-07 doi:10.1101/106559 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Multi-tissue polygenic models for transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/107623v1?rss=1 Park, Y. Sarkar, A. K. Bhutani, K. Kellis, M. 2017-02-10 doi:10.1101/107623 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers ]]> https://biorxiv.org/content/10.1101/110239v1?rss=1 Yan, J. Chen, S.-A. A. Local, A. Liu, T. Qiu, Y. Lee, A.-Y. Jung, I. Preissl, S. Rivera, C. M. Wang, C. Ishii, H. Fang, R. Ye, Z. Ge, K. Hu, M. Ren, B. 2017-02-21 doi:10.1101/110239 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ SV2: Accurate Structural Variation Genotyping and De Novo Mutation Detection ]]> https://biorxiv.org/content/10.1101/113498v1?rss=1 Antaki, D. Brandler, W. M. Sebat, J. 2017-03-03 doi:10.1101/113498 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data ]]> https://biorxiv.org/content/10.1101/117812v1?rss=1 McMurry, J. Juty, N. Blomberg, N. Burdett, A. Conlin, T. Conte, N. Courtot, M. Deck, J. Dumontier, M. Fellows, D. Gonzalez-Beltran, A. Gormanns, P. Grethe, J. Hastings, J. Hermjakob, H. Heriche, J.-K. Ison, J. Jimenez, R. Jupp, S. Kunze, J. Laibe, C. Le Novere, N. Malone, J. R. Martin, M.-J. McEntyre, J. Morris, C. Muilu, J. Mueller, W. Rocca-Serra, P. Sansone, S.-A. Sariyar, M. Snoep, J. Stanford, N. J. Soiland-Reyes, S. Swainston, N. Washington, N. Williams, A. Wimalaratne, S. Winfree, L. Wolstencroft, K. Goble, C. Mungall, C. Haendel, M. Parkinson, 2017-03-20 doi:10.1101/117812 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/118737v1?rss=1 Kubo, N. Ishii, H. Gorkin, D. Meitinger, F. Xiong, X. Fang, R. Liu, T. Ye, Z. Li, B. Dixon, J. Desai, A. Zhao, H. Ren, B. 2017-03-20 doi:10.1101/118737 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields ]]> https://biorxiv.org/content/10.1101/125229v1?rss=1 Shao, M. Ma, J. Wang, S. 2017-04-07 doi:10.1101/125229 Cold Spring Harbor Laboratory Press 2017-04-07 <![CDATA[ Predicting Protein Binding Affinity With Word EmbeddingsAnd Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/128223v1?rss=1 Mazzaferro, C. 2017-04-18 doi:10.1101/128223 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Integrative Single-Cell Analysis By Transcriptional And Epigenetic States In Human Adult Brain ]]> https://biorxiv.org/content/10.1101/128520v1?rss=1 Lake, B. Cheng, S. Sos, B. Fan, J. Yung, Y. Kaeser, G. Duong, T. Gao, D. Chun, J. Kharchenko, P. Zhang, K. 2017-04-19 doi:10.1101/128520 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ Estimating Degree Of Polygenicity, Causal Effect Size Variance, And Confounding Bias In GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/133132v1?rss=1 Holland, D. Fan, C.-C. Frei, O. Shadrin, A. A. Smeland, O. B. Sundar, V. S. ENIGMA, Andreassen, O. A. Dale, A. M. 2017-05-24 doi:10.1101/133132 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ BugBase Predicts Organism Level Microbiome Phenotypes ]]> https://biorxiv.org/content/10.1101/133462v1?rss=1 Ward, T. Larson, J. Meulemans, J. Hillmann, B. Lynch, J. Sidiropoulos, D. Spear, J. Caporaso, G. Blekhman, R. Knight, R. Fink, R. Knights, D. 2017-05-02 doi:10.1101/133462 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Precision Medicine Screening Using Whole Genome Sequencing And Advanced Imaging To Identify Disease Risk In Adults ]]> https://biorxiv.org/content/10.1101/133538v1?rss=1 Perkins, B. A. Caskey, C. T. Brar, P. Dec, E. Karow, D. Kahn, A. Hou, C. Shah, N. Boeldt, D. Coughlin, E. Hands, G. Lavrenko, V. Yu, J. Procko, A. Appis, J. Dale, A. M. Guo, L. Jonsson, T. J. Wittmann, B. M. Bartha, I. Ramakrishnan, S. Bernal, A. Brewer, J. Brewerton, S. Biggs, W. H. Turpaz, Y. Telenti, A. Venter, J. C. 2017-05-03 doi:10.1101/133538 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ MutPred2: inferring the molecular and phenotypic impact of amino acid variants ]]> https://biorxiv.org/content/10.1101/134981v1?rss=1 Pejaver, V. Urresti, J. Lugo-Martinez, J. Pagel, K. A. Lin, G. N. Nam, H.-J. Mort, M. Cooper, D. N. Sebat, J. Iakoucheva, L. M. Mooney, S. D. Radivojac, P. 2017-05-09 doi:10.1101/134981 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells ]]> https://biorxiv.org/content/10.1101/135384v1?rss=1 Chu, W. K. Edge, P. Lee, H. S. Bansal, V. Bafna, V. Huang, X. Zhang, K. 2017-05-08 doi:10.1101/135384 Cold Spring Harbor Laboratory Press 2017-05-08 <![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[ Gaussian Curvature Directs The Distribution Of Spontaneous Curvature On Bilayer Membrane Necks ]]> https://biorxiv.org/content/10.1101/137091v1?rss=1 Chabanon, M. Rangamani, P. 2017-05-12 doi:10.1101/137091 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness ]]> https://biorxiv.org/content/10.1101/139121v1?rss=1 Nogales, J. Gudmundsson, S. Duque, E. Ramos, J. L. Palsson, B. O. 2017-05-19 doi:10.1101/139121 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ The Human Cytoplasmic Dynein Interactome Reveals Novel Activators Of Motility ]]> https://biorxiv.org/content/10.1101/143743v1?rss=1 Redwine, W. B. DeSantis, M. E. Hollyer, I. Htet, Z. M. Tran, P. T. Swanson, S. K. Florens, L. Washburn, M. P. Reck-Peterson, S. L. 2017-05-30 doi:10.1101/143743 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Genetics of the Research Domain Criteria (RDoC): genome-wide association study of delay discounting ]]> https://biorxiv.org/content/10.1101/146936v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - The 23andMe Research Team, Pandit, A. Schmidt, E. Forster, J. Abecasis, G. R. Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-07 doi:10.1101/146936 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Genome-wide association study of Alcohol Use Disorder Identification Test (AUDIT) scores in 20,328 research participants of European ancestry ]]> https://biorxiv.org/content/10.1101/147397v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - the 23andMe Research Team, Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-15 doi:10.1101/147397 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals ]]> https://biorxiv.org/content/10.1101/149781v1?rss=1 Getz, M. Swanson, L. Sahoo, D. Ghosh, P. Rangamani, P. 2017-06-13 doi:10.1101/149781 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ The role of traction in membrane curvature generation ]]> https://biorxiv.org/content/10.1101/157313v1?rss=1 Alimohamadi, H. Vasan, R. Hassinger, J. E. Stachowiak, J. Rangamani, P. 2017-06-29 doi:10.1101/157313 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ Single nucleus analysis of the chromatin landscape in mouse forebrain development ]]> https://biorxiv.org/content/10.1101/159137v1?rss=1 Preissl, S. Fang, R. Zhao, Y. Raviram, R. Zhang, Y. Sos, B. C. Huang, H. Gorkin, D. U. Afzal, V. Dickel, D. E. Kuan, S. Visel, A. Pennacchio, L. A. Zhang, K. Ren, B. 2017-07-04 doi:10.1101/159137 Cold Spring Harbor Laboratory Press 2017-07-04 <![CDATA[ Common Piezo1 allele in African populations causes xerocytosis and attenuates Plasmodium infection ]]> https://biorxiv.org/content/10.1101/159830v1?rss=1 Ma, S. Cahalan, S. Lohia, R. LaMonte, G. Zeng, W. Murthy, S. Paytas, E. Grubaugh, N. D. Gamini, R. Berry, L. Lukacs, V. Whitwam, T. Loud, M. Su, A. I. Andersen, K. G. Winzeler, E. A. Honore, E. Wengelnik, K. Patapoutian, A. 2017-07-06 doi:10.1101/159830 Cold Spring Harbor Laboratory Press 2017-07-06 <![CDATA[ Rapid and scalable preparation of bacterial lysates for cell-free gene expression ]]> https://biorxiv.org/content/10.1101/162768v1?rss=1 Didovyk, A. Tonooka, T. Tsimring, L. Hasty, J. 2017-07-12 doi:10.1101/162768 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Defining the synaptic mechanisms that tune CA3-CA1 reactivation during sharp-wave ripples. ]]> https://biorxiv.org/content/10.1101/164699v1?rss=1 Malerba, P. Jones, M. W. Bazhenov, M. 2017-07-18 doi:10.1101/164699 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus ]]> https://biorxiv.org/content/10.1101/166744v1?rss=1 He, Y. Hariharan, M. Gorkin, D. U. Dickel, D. E. Luo, C. Castanon, R. G. Nery, J. R. Lee, A. Y. Williams, B. A. Trout, D. Amrhein, H. Fang, R. Chen, H. Li, B. Visel, A. Pennacchio, L. Ren, B. Ecker, J. 2017-07-21 doi:10.1101/166744 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Systems-level identification of transcription factors critical for mouse embryonic development ]]> https://biorxiv.org/content/10.1101/167197v1?rss=1 Zhang, K. Wang, M. Zhao, Y. Wang, W. 2017-07-21 doi:10.1101/167197 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Genomewide association study identifies 30 loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/173062v1?rss=1 Stahl, E. Forstner, A. McQuillin, A. Ripke, S. Ophoff, R. Scott, L. Cichon, S. Andreassen, O. A. Sklar, P. Kelsoe, J. Breen, G. 2017-08-07 doi:10.1101/173062 Cold Spring Harbor Laboratory Press 2017-08-07 <![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[ Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms ]]> https://biorxiv.org/content/10.1101/176024v1?rss=1 Rastogi, A. Maheswari, U. Dorrell, R. G. Maumus, F. Rocha Jimenez Vieira, F. Kustka, A. McCarthy, J. Allen, A. E. Kersey, P. Bowler, C. Tirichine, L. 2017-08-14 doi:10.1101/176024 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Ligand-regulated entry into the HRD ERAD pathway: The dark side of allostery ]]> https://biorxiv.org/content/10.1101/177311v1?rss=1 Wangeline, M. A. Hampton, R. Y. 2017-08-18 doi:10.1101/177311 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A Large-Scale Binding and Functional Map of Human RNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/179648v1?rss=1 Van Nostrand, E. L. Freese, P. Pratt, G. A. Wang, X. Wei, X. Blue, S. M. Dominguez, D. Cody, N. A. L. Olson, S. Sundararaman, B. Xiao, R. Zhan, L. Bazile, C. Benoit Bouvrette, L. P. Chen, J. Duff, M. O. Garcia, K. Gelboin-Burkhart, C. Hochman, A. Lambert, N. J. Li, H. Nguyen, T. B. Palden, T. Rabano, I. Sathe, S. Stanton, R. Louie, A. L. Aigner, S. Bergalet, J. Zhou, B. Su, A. Wang, R. Yee, B. A. Fu, X.-D. Lecuyer, E. Burge, C. B. Graveley, B. Yeo, G. W. 2017-08-23 doi:10.1101/179648 Cold Spring Harbor Laboratory Press 2017-08-23 <![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[ Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor ]]> https://biorxiv.org/content/10.1101/182964v1?rss=1 Doshi, R. McGrath, A. P. Pineros, M. A. Szewczyk, P. Garza, D. M. Kochian, L. V. Chang, G. 2017-08-31 doi:10.1101/182964 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ A neural decoder for learned vocal behavior ]]> https://biorxiv.org/content/10.1101/193987v1?rss=1 Arneodo, E. Chen, S. Gilja, V. Gentner, T. Q. 2017-09-26 doi:10.1101/193987 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ A distributed algorithm to maintain and repair the trail networks of arboreal ants ]]> https://biorxiv.org/content/10.1101/194480v1?rss=1 Chandrasekhar, A. Gordon, D. M. Navlakha, S. 2017-09-27 doi:10.1101/194480 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Thalamocortical and Intracortical Laminar Connectivity Determines Sleep Spindle Properties ]]> https://biorxiv.org/content/10.1101/195552v1?rss=1 Krishnan, G. P. Rosen, B. Q. Chen, J.-Y. Muller, L. Sejnowski, T. J. Cash, S. S. Halgren, E. Bazhenov, M. 2017-09-28 doi:10.1101/195552 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Coupling of autonomic and central events during sleep boosts declarative memory consolidation ]]> https://biorxiv.org/content/10.1101/195586v1?rss=1 Naji, M. Krishnan, G. McDevitt, E. A. Bazhenov, M. Mednick, S. C. 2017-09-28 doi:10.1101/195586 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Dissociable signatures of visual salience and behavioral relevance across attentional priority maps in human cortex ]]> https://biorxiv.org/content/10.1101/196642v1?rss=1 Sprague, T. Itthipuripat, S. Vo, V. Serences, J. T. 2017-10-02 doi:10.1101/196642 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Cell surface vimentin is involved in matrix stiffness-dependent infection of endothelial cells by Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/198739v1?rss=1 Bastounis, E. E. Yeh, Y.-T. Theriot, J. A. 2017-10-05 doi:10.1101/198739 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Computational model of brainstem circuit for state dependent control of hypoglossal motoneurons ]]> https://biorxiv.org/content/10.1101/199117v1?rss=1 Naji, M. Komarov, M. Krishnan, G. Malhotra, A. Powell, F. Rukhadze, I. Fenik, V. Bazhenov, M. 2017-10-05 doi:10.1101/199117 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Is N-Hacking Ever OK? A Simulation-based study ]]> https://biorxiv.org/content/10.1101/2019.12.12.868489v1?rss=1 Reinagel, P. 2019-12-16 doi:10.1101/2019.12.12.868489 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ ASTRAL-Pro: quartet-based species tree inference despite paralogy ]]> https://biorxiv.org/content/10.1101/2019.12.12.874727v1?rss=1 Zhang, C. Scornavacca, C. Molloy, E. Mirarab, S. 2019-12-13 doi:10.1101/2019.12.12.874727 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis ]]> https://biorxiv.org/content/10.1101/2019.12.14.850305v1?rss=1 Han, W. Ma, X. Balibar, C. J. Baxter Rath, C. M. Benton, B. Bermingham, A. Casey, F. Chi-Leon, B. Cho, M.-K. Frank, A. O. Frommlet, A. Ho, C.-M. Lee, P. S. Li, M. Lingel, A. Ma, S. Merritt, H. Ornelas, E. de Pascale, G. Prathapam, R. Prosen, K. R. Rasper, D. Ruzin, A. Sawyer, W. Shaul, J. Shen, X. Shia, S. Steffek, M. Subramanian, S. Vo, J. Wang, F. Wartchow, C. Uehara, T. 2019-12-15 doi:10.1101/2019.12.14.850305 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Visualizing 'omic feature rankings and log-ratios using Qurro ]]> https://biorxiv.org/content/10.1101/2019.12.17.880047v1?rss=1 Fedarko, M. W. Martino, C. Morton, J. T. Gonzalez, A. Rahman, G. Marotz, C. A. Minich, J. J. Allen, E. E. Knight, R. 2019-12-18 doi:10.1101/2019.12.17.880047 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Implications of TP53 Allelic State for Genome Stability, Clinical Presentation and Outcomes in Myelodysplastic Syndromes ]]> https://biorxiv.org/content/10.1101/2019.12.19.868844v1?rss=1 Bernard, E. Nannya, Y. Hasserjian, R. P. Devlin, S. M. Tuechler, H. Medina-Martinez, J. S. Yoshizato, T. Shiozawa, Y. Saiki, R. Malcovati, L. Levine, M. F. Arango, J. E. Zhou, Y. Sole, F. Cargo, C. A. Haase, D. Creignou, M. Germing, U. Zhang, Y. Gundem, G. Sarian, A. van de Loosdrecht, A. A. Jadersten, M. Tobiasson, M. Kosmider, O. Follo, M. Y. Thol, F. Pinheiro, R. F. Santini, V. Kotsianidis, I. Boultwood, J. Santos, F. P. S. Schanz, J. Kasahara, S. Ishikawa, T. Tsurumi, H. Takaori-Kondo, A. Kiguchi, T. Polprasert, C. Bennett, J. M. Klimek, V. M. Savon 2019-12-19 doi:10.1101/2019.12.19.868844 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling ]]> https://biorxiv.org/content/10.1101/2019.12.19.882985v1?rss=1 DelGiorno, K. E. Chung, C.-Y. Maurer, H. C. Weiser Novak, S. Giraddi, R. R. Wang, D. Naeem, R. F. Fang, L. Andrade, L. R. Lytle, N. K. Ali, W. H. Tsui, C. Gubbala, V. B. Ridinger-Saison, M. Ohmoto, M. O'Connor, C. Erikson, G. Shokhirev, M. N. Urade, Y. Matsumoto, I. Vavinskaya, V. Singh, P. K. Manor, U. Olive, K. P. Wahl, G. 2019-12-20 doi:10.1101/2019.12.19.882985 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA Epilepsy study ]]> https://biorxiv.org/content/10.1101/2019.12.19.883405v1?rss=1 Hatton, S. N. Huynh, K. H. Bonilha, L. Abela, E. Alhusaini, S. Altmann, A. N. Alvim, M. K. Balachandra, A. R. Bargallo, N. Bartolini, E. Bender, B. Bernasconi, A. Bernasconi, N. Bernhardt, B. Caldairou, B. Caligiuri, M. E. Carr, S. J. Cavalleri, G. L. Cendes, F. Concha, L. Davoodi-Bojd, E. Desmond, P. M. Devinsky, O. Doherty, C. P. Domin, M. Duncan, J. S. Niels, N. K. Foley, S. F. Gambardella, A. Gleichgerrcht, E. Hamandi, K. Ishikawa, A. Keller, S. S. Kochunov, P. V. Kotikalapudi, R. Kreilkamp, B. A. Kwan, P. Labate, A. Langner, S. Lenge, M. Liu, M. Lu 2019-12-20 doi:10.1101/2019.12.19.883405 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Empirical dynamic modeling reveals ecological drivers of dengue dynamics ]]> https://biorxiv.org/content/10.1101/2019.12.20.883363v1?rss=1 Nova, N. Deyle, E. R. Shocket, M. MacDonald, A. J. Childs, M. Rypdal, M. Sugihara, G. Mordecai, E. A. 2019-12-20 doi:10.1101/2019.12.20.883363 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Log Transformation Improves Dating of Phylogenies ]]> https://biorxiv.org/content/10.1101/2019.12.20.885582v1?rss=1 Mai, U. Mirarab, S. 2019-12-21 doi:10.1101/2019.12.20.885582 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Sequestration of Methane by Symbiotic Deep-Sea Annelids: Ancient and Future Implications of Redefining the Seep Influence ]]> https://biorxiv.org/content/10.1101/2019.12.23.887653v1?rss=1 Goffredi, S. K. Tilic, E. Mullin, S. W. Dawson, K. S. Keller, A. Lee, R. Wu, F. Levin, L. A. Rouse, G. W. Cordes, E. Orphan, V. J. 2019-12-27 doi:10.1101/2019.12.23.887653 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ A Novel Chloroplast Super-Complex Consisting of the ATP Synthase and Photosystem I Reaction Center ]]> https://biorxiv.org/content/10.1101/2019.12.25.888495v1?rss=1 Bhaduri, S. Singh, S. K. Cohn, W. Hasan, S. S. Whitelegge, J. P. Cramer, W. A. 2019-12-27 doi:10.1101/2019.12.25.888495 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ The String Decomposition Problem and its Applications to Centromere Assembly ]]> https://biorxiv.org/content/10.1101/2019.12.26.888685v1?rss=1 Dvorkina, T. Bzikadze, A. V. Pevzner, P. A. 2019-12-26 doi:10.1101/2019.12.26.888685 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ A Molecular Pathway for Arterial-Specific Association of Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2019.12.27.889782v1?rss=1 Stratman, A. N. Burns, M. C. Farrelly, O. M. Davis, A. E. Li, W. Pham, V. N. Castranova, D. Yano, J. J. Goddard, L. M. Nguyen, O. Venero Galanternik, M. Bolan, T. J. Kahn, M. L. Mukouyama, Y. Weinstein, B. M. 2019-12-28 doi:10.1101/2019.12.27.889782 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Dual role of auxin in regulating plant defense and bacterial virulence gene expression during Pseudomonas syringae PtoDC3000 pathogenesis. ]]> https://biorxiv.org/content/10.1101/2019.12.29.881581v1?rss=1 Djami-Tchatchou, A. T. Harrison, G. A. Harper, C. P. Wang, R. Prigge, M. J. Estelle, M. Kunkel, B. N. 2019-12-30 doi:10.1101/2019.12.29.881581 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Sequence, Structure and Context Preferences of Human RNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/201996v1?rss=1 Dominguez, D. Freese, P. Alexis, M. S. Su, A. Hochman, M. Palden, T. Bazile, C. Lambert, N. J. Van Nostrand, E. L. Pratt, G. A. Yeo, G. W. Graveley, B. Burge, C. B. 2017-10-12 doi:10.1101/201996 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ DNA damage induced during mitosis undergoes DNA repair synthesis ]]> https://biorxiv.org/content/10.1101/2020.01.03.893784v1?rss=1 Gomez Godinez, V. Kabbara, S. Cohen, S. Sherman, A. Wu, T. Kong, X. Maravillas-Montero, J. L. Shi, Z. Preece, D. Yokomori, K. Berns, M. 2020-01-03 doi:10.1101/2020.01.03.893784 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ A qualitative difference in decision-making of rats vs. humans explained by quantitative differences in behavioral variability ]]> https://biorxiv.org/content/10.1101/2020.01.05.895268v1?rss=1 Nguyen, Q. N. Reinagel, P. 2020-01-06 doi:10.1101/2020.01.05.895268 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Lipid-specific labeling of enveloped viruses with quantum dots for single-virus tracking ]]> https://biorxiv.org/content/10.1101/2020.01.06.895805v1?rss=1 Zhang, L.-J. Wang, S. Xia, L. Lv, C. Tang, H.-W. Xiao, G. Pang, D.-W. 2020-01-06 doi:10.1101/2020.01.06.895805 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance ]]> https://biorxiv.org/content/10.1101/2020.01.06.896316v1?rss=1 Gaidarenko, O. Mills, D. W. Vernet, M. Hildebrand, M. 2020-01-07 doi:10.1101/2020.01.06.896316 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling ]]> https://biorxiv.org/content/10.1101/2020.01.06.896365v1?rss=1 Johnson, J. R. Crosby, D. C. Hultquist, J. F. Li, D. Marlett, J. Swann, J. Hüttenhain, R. Verschueren, E. Johnson, T. L. Newton, B. W. Shales, M. Beltrao, P. Frankel, A. D. Marson, A. Fregoso, O. I. Young, J. A. Krogan, N. J. 2020-01-07 doi:10.1101/2020.01.06.896365 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Regulation of HDAC2-PDX1 by RNF125 defines pancreatic cancer development ]]> https://biorxiv.org/content/10.1101/2020.01.06.896555v1?rss=1 Hasnis, E. Kim, H. Verma, S. Feng, Y. Almog, R. Matsliah, S. Vavinskaya, V. Alelbaum, R. Ben-Ishay, O. Tuveson, D. Sears, R. Ronai, Z. A. 2020-01-07 doi:10.1101/2020.01.06.896555 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Long-term warming weakens stabilizing effects of biodiversity in aquatic ecosystems ]]> https://biorxiv.org/content/10.1101/2020.01.06.896746v1?rss=1 Chang, C.-W. Ye, H. Miki, T. Deyle, E. R. Souissi, S. Anneville, O. Adrian, R. Chiang, Y.-R. Ichise, S. Kumagai, M. Matsuzaki, S.-i. S. Shiah, F.-K. Wu, J.-T. Hsieh, C.-h. Sugihara, G. 2020-01-07 doi:10.1101/2020.01.06.896746 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication ]]> https://biorxiv.org/content/10.1101/2020.01.07.897082v1?rss=1 Badouin, H. Velt, A. Gindraud, F. Flutre, T. Dumas, V. Vautrin, S. Marande, W. Corbi, J. Sallet, E. Ganofsky, J. Santoni, S. Guyot, D. Ricciardelli, E. Jepsen, K. Kafer, J. Berges, H. Duchene, E. Picard, F. Hugueney, P. Tavares, R. Bacilieri, R. Rustenholz, C. Marais, G. A. 2020-01-08 doi:10.1101/2020.01.07.897082 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Enhanced triacylglycerol (TAG) and protein accumulation in transgenic diatom Thalassiosira pseudonana with altered photosynthetic pigmentation ]]> https://biorxiv.org/content/10.1101/2020.01.07.897850v1?rss=1 Gaidarenko, O. Yee, D. P. Hildebrand, M. 2020-01-08 doi:10.1101/2020.01.07.897850 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ UDP-glucose dehydrogenase Ugd in E. coli is activated by Gmd and RffD, is inhibited by CheY, and regulates swarming ]]> https://biorxiv.org/content/10.1101/2020.01.08.899336v1?rss=1 Rodionova, I. A. Zhang, Z. Aboulwafa, M. Saier, M. H. 2020-01-09 doi:10.1101/2020.01.08.899336 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity ]]> https://biorxiv.org/content/10.1101/2020.01.10.900951v1?rss=1 Ngo, T. Stephens, B. S. Gustavsson, M. Holden, L. G. Abagyan, R. Handel, T. M. Kufareva, I. 2020-01-11 doi:10.1101/2020.01.10.900951 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Transport Phenomena in Fluid Films with Curvature Elasticity ]]> https://biorxiv.org/content/10.1101/2020.01.14.906917v1?rss=1 Mahapatra, A. Saintillan, D. Rangamani, P. 2020-01-15 doi:10.1101/2020.01.14.906917 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods. ]]> https://biorxiv.org/content/10.1101/2020.01.15.908111v1?rss=1 Menke, J. Roelandse, M. Ozyurt, B. I. Martone, M. E. Bandrowski, A. E. 2020-01-18 doi:10.1101/2020.01.15.908111 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ mosaicFlye: Resolving long mosaic repeats using long error-prone reads ]]> https://biorxiv.org/content/10.1101/2020.01.15.908285v1?rss=1 Bankevich, A. Pevzner, P. 2020-01-16 doi:10.1101/2020.01.15.908285 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning ]]> https://biorxiv.org/content/10.1101/2020.01.16.909861v1?rss=1 Gao, C. Welch, J. D. 2020-01-17 doi:10.1101/2020.01.16.909861 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ AAV Ablates Neurogenesis in the Adult Murine Hippocampus ]]> https://biorxiv.org/content/10.1101/2020.01.18.911362v1?rss=1 Johnston, S. T. Parylak, S. L. Kim, S. Mac, N. Lim, C. Gallina, I. Bloyd, C. Newberry, A. Saavedra, C. Novák, O. Goncalves, J. T. Gage, F. H. Shtrahman, M. 2020-01-19 doi:10.1101/2020.01.18.911362 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ The effect of statistical normalisation on network propagation scores ]]> https://biorxiv.org/content/10.1101/2020.01.20.911842v1?rss=1 Picart-Armada, S. Thompson, W. K. Buil, A. Perera-Lluna, A. 2020-01-20 doi:10.1101/2020.01.20.911842 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Functional anatomy of the full length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis ]]> https://biorxiv.org/content/10.1101/2020.01.21.913772v1?rss=1 Stephens, B. S. Ngo, T. Kufareva, I. Handel, T. M. 2020-01-21 doi:10.1101/2020.01.21.913772 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Wnt signaling determines body axis polarity in regenerating Hydra tissue ]]> https://biorxiv.org/content/10.1101/2020.01.22.915702v1?rss=1 Wang, R. Steele, R. Collins, E.-M. 2020-01-23 doi:10.1101/2020.01.22.915702 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Giant magnetoresistive biosensors for real-time quantitative detection of protease activity ]]> https://biorxiv.org/content/10.1101/2020.01.26.917476v1?rss=1 Adem, S. Jain, S. Sveiven, M. Zhou, X. O'Donoghue, A. J. Hall, D. A. 2020-01-27 doi:10.1101/2020.01.26.917476 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Transcriptomic Organization of Human Posttraumatic Stress Disorder ]]> https://biorxiv.org/content/10.1101/2020.01.27.921403v1?rss=1 Girgenti, M. J. Wang, J. Ji, D. Cruz, D. Traumatic Stress Brain Research Study Group, The Million Veteran Program, Stein, M. B. Gelernter, J. Young, K. A. Huber, B. R. Williamson, D. E. Friedman, M. J. Krystal, J. H. Zhao, H.-y. Duman, R. S. 2020-01-28 doi:10.1101/2020.01.27.921403 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway ]]> https://biorxiv.org/content/10.1101/2020.01.28.924217v1?rss=1 Allemann, M. N. Allen, E. E. 2020-01-29 doi:10.1101/2020.01.28.924217 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Early detection of biomarkers for circulating tumor cells in Bone marrow and Peripheral blood in a fast-progressing gastric cancer model. ]]> https://biorxiv.org/content/10.1101/2020.01.29.925727v1?rss=1 Bali, P. Lozano-Pope, I. Pachow, C. Obonyo, M. 2020-01-30 doi:10.1101/2020.01.29.925727 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2020.01.31.929117v1?rss=1 Bamberger, T. C. Pankow, S. Martinez-Bartolome, S. Ma, M. Diedrich, J. K. Rissman, R. A. Yates, J. R. 2020-02-02 doi:10.1101/2020.01.31.929117 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Fast transport of RNA granules by direct interactions with KIF5A/KLC1 motors prevents axon degeneration ]]> https://biorxiv.org/content/10.1101/2020.02.02.931204v1?rss=1 Segal, R. A. Seo, H.-S. Adelmant, G. Walensky, L. Marto, J. A. Dhe-Paganon, S. Fukuda, Y. Pazyra-Murphy, M. F. Tasdemir-Yilmaz, O. E. Li, Y. Rose, L. Yeoh, Z. C. Vangos, N. E. Geffken, E. A. Bird, G. H. 2020-02-03 doi:10.1101/2020.02.02.931204 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Zebrafish Kit ligands cooperate with erythropoietin to promote erythroid cell expansion ]]> https://biorxiv.org/content/10.1101/2020.02.03.931634v1?rss=1 Oltova, J. Svoboda, O. Svatonova, P. Kolar, M. Bartunek, P. 2020-02-03 doi:10.1101/2020.02.03.931634 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Regulation of peroxisome and lipid droplet hitchhiking by PxdA and the DipA phosphatase ]]> https://biorxiv.org/content/10.1101/2020.02.03.932616v1?rss=1 Salogiannis, J. Christensen, J. R. Aguilar-Maldonado, A. Shukla, N. Reck-Peterson, S. L. 2020-02-04 doi:10.1101/2020.02.03.932616 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Twist, Snail, and Sox9 form an allosterically regulated complex, the EMTosome, on a bipartite E-box site. ]]> https://biorxiv.org/content/10.1101/2020.02.03.932962v1?rss=1 McCracken, D. Peng, H. P. Ayyanathan, K. Jiang, Y. L. Welsh, S. Yang, J. Kennedy, E. Rauscher, F. J. Gardini, A. Rauscher, F. J. 2020-02-05 doi:10.1101/2020.02.03.932962 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Microstructural meal pattern analysis reveals that nicotine is a potent anti-anorectic drug despite producing long-term anorexigenic effects ]]> https://biorxiv.org/content/10.1101/2020.02.04.934414v1?rss=1 Shankar, K. Ambroggi, F. George, O. 2020-02-05 doi:10.1101/2020.02.04.934414 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Telomere length heterogeneity in ALT cells is maintained by PML-dependent localization of the BTR complex to telomeres ]]> https://biorxiv.org/content/10.1101/2020.02.07.938753v1?rss=1 Loe, T. K. Li, J. Zhang, Y. Azeroglu, B. Boddy, M. N. Lazzerini Denchi, E. 2020-02-07 doi:10.1101/2020.02.07.938753 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance ]]> https://biorxiv.org/content/10.1101/2020.02.07.938894v1?rss=1 Rapaport, F. Boisson, B. Gregor, A. Beziat, V. Boisson-Dupuis, S. Bustamante, J. Jouanguy, E. Puel, A. Rosain, J. Zhang, Q. Zhang, S.-Y. Gleeson, J. Quintana-Murci, L. Casanova, J.-L. Abel, L. Patin, E. 2020-02-08 doi:10.1101/2020.02.07.938894 Cold Spring Harbor Laboratory Press 2020-02-08 <![CDATA[ Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling ]]> https://biorxiv.org/content/10.1101/2020.02.07.939256v1?rss=1 Amar, M. Pramod, A. B. Herrera, V. M. Yu, N.-K. Qiu, L. R. Zhang, P. Moran-Losada, P. Trujillo, C. A. Ellegood, J. Urresti, J. Chau, K. Diedrich, J. Chen, J. Gutierrez, J. Sebat, J. Ramanathan, D. Lerch, J. P. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-02-12 doi:10.1101/2020.02.07.939256 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Strong inhibitory signaling underlies stable temporal dynamics and working memory in spiking neural networks ]]> https://biorxiv.org/content/10.1101/2020.02.11.944751v1?rss=1 Kim, R. Sejnowski, T. J. 2020-02-12 doi:10.1101/2020.02.11.944751 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Antagonistic roles of NOT1 paralogues in the timing of gene expression in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2020.02.12.945477v1?rss=1 Liu, Y. Rai, R. Lei, Z. Zhang, C. Rocamora, F. Featherstone, M. Bozdech, Z. 2020-02-12 doi:10.1101/2020.02.12.945477 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome ]]> https://biorxiv.org/content/10.1101/2020.02.16.951699v1?rss=1 Lee, J. S. Nair, N. U. Chapman, L. M. Sinha, S. Wang, K. Cha, H. Rubin, E. Berger, R. Lazar, V. Kurzrock, R. Gilbert, M. R. Hannenhalli, S. S. Lee, S.-H. Aldape, K. Ruppin, E. 2020-02-17 doi:10.1101/2020.02.16.951699 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ IRE1? regulates macrophage polarization, PD-L1 expression and tumor survival ]]> https://biorxiv.org/content/10.1101/2020.02.17.952457v1?rss=1 Zanetti, M. Batista, A. T. Rodvold, J. Xian, S. Searles, S. T. Lew, A. Iwawaki, T. Almanza, G. Weller, T. C. Lin, J. Jepsen, K. Carter, H. 2020-02-17 doi:10.1101/2020.02.17.952457 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Acoustogenetic Control of CAR T Cells via Focused Ultrasound ]]> https://biorxiv.org/content/10.1101/2020.02.18.955005v1?rss=1 WU, Y. Liu, Y. Huang, Z. Wang, X. Jin, Z. Li, J. Limsakul, P. Zhu, L. Allen, M. Pan, Y. Bussell, R. Jacobson, A. Liu, T. Chien, S. Wang, Y. 2020-02-19 doi:10.1101/2020.02.18.955005 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Commensal oral Rothia mucilaginosa produces enterobactin - a metal chelating siderophore ]]> https://biorxiv.org/content/10.1101/2020.02.20.956391v1?rss=1 Uranga, C. Arroyo, P. Duggan, B. M. Gerwick, W. H. Edlund, A. 2020-02-20 doi:10.1101/2020.02.20.956391 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ B cells expressing authentic naive human VRC01-class BCRs can be primed and recruited to germinal centers in multiple independent mouse models ]]> https://biorxiv.org/content/10.1101/2020.02.24.963629v1?rss=1 Huang, D. Abbott, R. K. Havenar-Daughton, C. Skog, P. Al-Kolla, R. Groschel, B. Blane, T. Menis, S. Tran, J. T. Thinnes, T. C. Volpi, S. A. Pintea, M. Voss, J. E. Phelps, N. Tingle, R. Rodriguez, A. R. Martin, G. S. Kupryianov, S. Schief, W. R. Nemazee, D. Crotty, S. 2020-02-26 doi:10.1101/2020.02.24.963629 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Deep neural networks identify context-specific determinants of transcription factor binding affinity ]]> https://biorxiv.org/content/10.1101/2020.02.26.965343v1?rss=1 Zheng, A. Lamkin, M. Wu, C. Su, H. Gymrek, M. 2020-02-27 doi:10.1101/2020.02.26.965343 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans ]]> https://biorxiv.org/content/10.1101/2020.02.26.966747v1?rss=1 Wilmanski, T. Diener, C. Rappaport, N. Patwardhan, S. Wiedrick, J. Lapidus, J. Earls, J. C. Zimmer, A. Glusman, G. Robinson, M. Yurkovich, J. T. Kado, D. M. Cauley, J. A. Zmuda, J. Lane, N. E. Magis, A. T. Lovejoy, J. C. Gibbons, S. M. Hood, L. Orwoll, E. S. Price, N. D. 2020-02-28 doi:10.1101/2020.02.26.966747 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ TP53 abnormalities correlate with immune infiltration and are associated with response to flotetuzumab, an investigational immunotherapy, in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2020.02.28.961391v1?rss=1 Lai, C. Vadakekolathu, J. Reeder, S. Church, S. E. Hood, T. Aldoss, I. Godwin, J. Wieduwilt, M. J. Arellano, M. Muth, J. Ravandi, F. Sweet, K. Altmann, H. Foulds, G. A. Stolzel, F. Middeke, J. M. Ciciarello, M. Curti, A. Valk, P. J. M. Lowenberg, B. Bornhauser, M. DiPersio, J. F. Davidson-Moncada, J. K. Rutella, S. 2020-02-28 doi:10.1101/2020.02.28.961391 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation ]]> https://biorxiv.org/content/10.1101/2020.03.01.955443v1?rss=1 Arneson, A. Felsheim, B. Chien, J. Ernst, J. 2020-03-02 doi:10.1101/2020.03.01.955443 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Molecular determinants and heterogeneity of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.03.02.973578v1?rss=1 Kurd, N. He, Z. Milner, J. Omilusik, K. Louis, T. Tsai, M. Widjaja, C. Kanbar, J. Olvera, J. Tysl, T. Quezada, L. Boland, B. Huang, W. Murre, C. Goldrath, A. Yeo, G. Chang, J. 2020-03-04 doi:10.1101/2020.03.02.973578 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition ]]> https://biorxiv.org/content/10.1101/2020.03.03.968750v1?rss=1 Stopfer, L. E. Mesfin, J. M. Joughin, B. A. Lauffenburger, D. A. White, F. 2020-03-04 doi:10.1101/2020.03.03.968750 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ The contribution of de novo tandem repeat mutations to autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/2020.03.04.974170v1?rss=1 Mitra, I. Mousavi, N. Ma, N. Lamkin, M. Yanicky, R. Shleizer-Burko, S. Gymrek, M. 2020-03-05 doi:10.1101/2020.03.04.974170 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Genetic elucidation of complex biochemical traits mediating maize innate immunity ]]> https://biorxiv.org/content/10.1101/2020.03.04.977355v1?rss=1 Ding, Y. Weckwerth, P. R. Poretsky, E. Murphy, K. M. Sims, J. Saldivar, E. Christensen, S. A. Char, S. N. Yang, B. Tong, A.-d. Shen, Z. Kremling, K. Buckler, E. S. Kono, T. J. Y. Nelson, D. R. Bohlmann, J. Bakker, M. G. Vaughan, M. M. Khalil, A. S. Betsiashvili, M. Briggs, S. Zerbe, P. Schmelz, E. A. Huffaker, A. 2020-03-05 doi:10.1101/2020.03.04.977355 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Functional delineation of tissue-resident CD8 T cell heterogeneity during infection and cancer ]]> https://biorxiv.org/content/10.1101/2020.03.05.979146v1?rss=1 Milner, J. J. Toma, C. He, Z. Kurd, N. S. Nguyen, Q. P. McDonald, B. Quezada, L. Widjaja, C. E. Witherden, D. A. Crowl, J. T. Yeo, G. W. Chang, J. T. Omilusik, K. D. Goldrath, A. W. 2020-03-06 doi:10.1101/2020.03.05.979146 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ One-Day Construction Of Multiplex Arrays to Harness Natural CRISPR Systems ]]> https://biorxiv.org/content/10.1101/2020.03.06.981316v1?rss=1 Cooper, R. M. Hasty, J. 2020-03-08 doi:10.1101/2020.03.06.981316 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Evidence for a biological source of widespread, reproducible nighttime oxygen spikes in tropical reef ecosystems has implications for coral health ]]> https://biorxiv.org/content/10.1101/2020.03.08.982645v1?rss=1 Calhoun, S. K. Haas, A. F. Takeshita, Y. Johnson, M. D. Fox, M. D. Kelly, E. L. A. Mueller, B. Vermeij, M. J. A. Kelly, L. W. Nelson, C. E. Price, N. N. Roach, T. N. F. Rohwer, F. Smith, J. E. 2020-03-09 doi:10.1101/2020.03.08.982645 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Combined membrane potential imaging and connectome of behavioral circuits in an annelid worm ]]> https://biorxiv.org/content/10.1101/2020.03.09.984013v1?rss=1 Ashaber, M. Tomina, Y. Kassraian-Fard, P. Bushong, E. A. Kristan, W. B. Ellisman, M. H. Wagenaar, D. A. 2020-03-10 doi:10.1101/2020.03.09.984013 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ ZNF423 orthologs are highly constrained in vertebrates but show domain-level plasticity across invertebrate lineages ]]> https://biorxiv.org/content/10.1101/2020.03.09.984518v1?rss=1 Hamilton, B. A. 2020-03-11 doi:10.1101/2020.03.09.984518 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Gamma activity accelerates during prefrontal development ]]> https://biorxiv.org/content/10.1101/2020.03.10.986281v1?rss=1 Bitzenhofer, S. H. Poepplau, J. A. Hanganu-Opatz, I. L. 2020-03-11 doi:10.1101/2020.03.10.986281 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research ]]> https://biorxiv.org/content/10.1101/2020.03.12.989400v1?rss=1 Sigmon, J. S. Blanchard, M. Baric, R. S. Bell, T. A. Brennan, J. Brockmann, G. A. Burks, A. W. Calabrese, M. Caron, K. M. Cheney, R. E. Ciavatta, D. Conlon, F. Darr, D. B. Faber, J. Franklin, C. Gershon, T. R. Gralinski, L. E. Gu, B. Gaines, C. H. Hagan, R. S. Heimsath, E. G. Heise, M. T. Hock, P. Ideraabdullah, F. Jennette, J. C. Kafri, T. Kashfeen, A. Kelada, S. N. P. Kulis, M. Kumar, V. Linnertz, C. L. Livraghi-Butrico, A. Lloyd, K. Loeser, R. Lutz, C. M. Lynch, R. M. Magnuson, T. Matsushima, G. K. McMullan, R. Miller, D. Mohlke, K. L. Moy, S. S. Mu 2020-03-14 doi:10.1101/2020.03.12.989400 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Maturational trajectories of white matter microstructure underlying the right presupplementary motor area reflect individual improvements in motor response cancellation in children and adolescents ]]> https://biorxiv.org/content/10.1101/2020.03.13.990507v1?rss=1 Madsen, K. S. Johansen, L. B. Thompson, W. K. Siebner, H. R. Jernigan, T. L. Baare, W. F. 2020-03-15 doi:10.1101/2020.03.13.990507 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Distinctive Gene and Protein Characteristics of Extremely Piezophilic Colwellia ]]> https://biorxiv.org/content/10.1101/2020.03.15.992594v1?rss=1 Peoples, L. M. Kyaw, T. S. Ugalde, J. U. Mullane, K. K. Chastain, R. A. Yayanos, A. A. Kusube, M. Methe, B. A. Bartlett, D. H. 2020-03-15 doi:10.1101/2020.03.15.992594 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Importance of polymorphic SNPs, short tandem repeats and structural variants for differential gene expression among inbred C57BL/6 and C57BL/10 substrains ]]> https://biorxiv.org/content/10.1101/2020.03.16.993683v1?rss=1 Mortazavi, M. Ren, Y. Saini, S. Antaki, D. Pierre, C. S. Williams, A. Sebat, J. Gymrek, M. Palmer, A. A. 2020-03-18 doi:10.1101/2020.03.16.993683 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ TRTools: a toolkit for genome-wide analysis of tandem repeats ]]> https://biorxiv.org/content/10.1101/2020.03.17.996033v1?rss=1 Mousavi, N. Margoliash, J. Pusarla, N. Saini, S. Yanicky, R. Gymrek, M. 2020-03-18 doi:10.1101/2020.03.17.996033 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners ]]> https://biorxiv.org/content/10.1101/2020.03.19.999193v1?rss=1 Pierce, E. C. Morin, M. Little, J. C. Liu, R. B. Tannous, J. Keller, N. P. Wolfe, B. E. Sanchez, L. M. Dutton, R. J. 2020-03-20 doi:10.1101/2020.03.19.999193 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth ]]> https://biorxiv.org/content/10.1101/2020.03.23.003236v1?rss=1 Lloyd, C. J. Monk, J. Ebrahim, A. Yang, L. Palsson, B. 2020-03-23 doi:10.1101/2020.03.23.003236 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning ]]> https://biorxiv.org/content/10.1101/2020.03.25.008664v1?rss=1 Gur, D. Bain, E. J. Johnson, K. Aman, A. J. Pasoili, A. Flynn, J. D. Allen, M. C. Deheyn, D. D. Lee, J. C. Lippincott-Schwartz, J. Parichy, D. M. 2020-03-25 doi:10.1101/2020.03.25.008664 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli ]]> https://biorxiv.org/content/10.1101/2020.03.28.985986v1?rss=1 Yu, H. Lu, S. Gasior, K. Singh, D. Tapia, O. Vazquez-Sanchez, S. Toprani, D. Beccari, M. Yates, J. R. Da Cruz, S. Newby, J. Larfaga, M. Gladfelter, A. Villa, E. Cleveland, D. W. 2020-03-29 doi:10.1101/2020.03.28.985986 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into an N-prenyltransferase ]]> https://biorxiv.org/content/10.1101/2020.03.31.014811v1?rss=1 Chekan, J. R. McKinnie, S. M. K. Noel, J. P. Moore, B. S. 2020-04-01 doi:10.1101/2020.03.31.014811 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ A common analgesic enhances the anti-tumour activity of 5-aza-2'-deoxycytidine through induction of oxidative stress ]]> https://biorxiv.org/content/10.1101/2020.03.31.017947v1?rss=1 Gleneadie, H. J. Baker, A. H. Batis, N. Bryant, J. Jiang, Y. Clokie, S. J. Mehanna, H. Garcia, P. Gendoo, D. M. Roberts, S. Molinolo, A. Gutkind, S. Scheven, B. A. Cooper, P. R. Khanim, F. Wiench, M. 2020-04-01 doi:10.1101/2020.03.31.017947 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Bedscales: A non-contact adherence-independent multi-person sensor for longitudinal physiologic monitoring in the home bed ]]> https://biorxiv.org/content/10.1101/2020.03.31.018523v1?rss=1 Harrington, N. Wei, Z. Hernandez-Pacheco, B. Biu, Q. DeYoung, P. N. Duwaik, B. Desai, A. S. Bhatt, D. L. Owens, R. L. Coleman, T. P. King, K. R. 2020-04-01 doi:10.1101/2020.03.31.018523 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated ]]> https://biorxiv.org/content/10.1101/2020.04.02.021535v1?rss=1 30-bp decrease using CRISPR/Cas9 mutagenesis. These findings provide implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation. ]]> Shen, Z. Tao, J. Fonseca, G. J. Glass, C. K. 2020-04-03 doi:10.1101/2020.04.02.021535 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ ZNF423 patient variants, truncations, and in-frame deletions in mice define an allele-dependent range of midline brain abnormalities ]]> https://biorxiv.org/content/10.1101/2020.04.04.024562v1?rss=1 Deshpande, O. Lara, R. Z. Zhang, O. R. Concepcion, D. Hamilton, B. A. 2020-04-05 doi:10.1101/2020.04.04.024562 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Therapeutic Reversal of Chemically Induced Parkinson Disease by Converting Astrocytes into Nigral Neurons ]]> https://biorxiv.org/content/10.1101/2020.04.06.028084v1?rss=1 Fu, X.-D. 2020-04-07 doi:10.1101/2020.04.06.028084 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila ]]> https://biorxiv.org/content/10.1101/2020.04.08.032177v1?rss=1 Hinzke, T. Kleiner, M. Meister, M. Schlueter, R. Hentschker, C. Pane-Farre, J. Hildebrandt, P. Felbeck, H. Sievert, S. M. Bonn, F. Voelker, U. Becher, D. Schweder, T. Markert, S. 2020-04-09 doi:10.1101/2020.04.08.032177 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2020.04.12.037580v1?rss=1 Wang, A. Chiou, J. A. Poirion, O. B. Buchanan, J. Valdez, M. J. Verheyden, J. M. Hou, X. Guo, M. Newsome, J. M. Kudtarkar, P. Faddah, D. A. Zhang, K. Young, R. E. Barr, J. Misra, R. Huyck, H. Rogers, L. Poole, C. Whitsett, J. A. Pryhuber, G. Xu, Y. Gaulton, K. J. Preissl, S. Sun, X. NHLBI LungMap Consortium, 2020-04-14 doi:10.1101/2020.04.12.037580 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ ISG15 drives immune pathology and respiratory failure during viral infection ]]> https://biorxiv.org/content/10.1101/2020.04.13.039321v1?rss=1 Shaabani, N. Zak, J. Johnson, J. L. Huang, Z. Nguyen, N. Lazar, D. C. Vartabedian, V. F. Honke, N. Prinz, M. Knobeloch, K.-P. Arimoto, K.-i. Zhang, D.-E. Catz, S. D. Teijaro, J. R. 2020-04-14 doi:10.1101/2020.04.13.039321 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry ]]> https://biorxiv.org/content/10.1101/2020.04.14.041459v1?rss=1 Kim, S. Y. Jin, W. Sood, A. Montgomery, D. W. Grant, O. C. Fuster, M. M. Fu, L. Dordick, J. S. Woods, R. J. Zhang, F. Linhardt, R. J. 2020-04-15 doi:10.1101/2020.04.14.041459 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Automated docking refinement and virtual compound screening with absolute binding free energy calculations ]]> https://biorxiv.org/content/10.1101/2020.04.15.043240v1?rss=1 Heinzelmann, G. Gilson, M. K. 2020-04-16 doi:10.1101/2020.04.15.043240 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization ]]> https://biorxiv.org/content/10.1101/2020.04.16.044255v1?rss=1 Mortensen, M. S. Rasmussen, M. A. Stokholm, J. Brejnrod, A. D. Balle, C. Thorsen, J. Krogfelt, K. A. Bisgaard, H. Sorensen, S. J. 2020-04-17 doi:10.1101/2020.04.16.044255 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Weight Sensitivity of Temporal SNR Metrics in multi-echo fMRI ]]> https://biorxiv.org/content/10.1101/2020.04.20.049460v1?rss=1 Liu, T. Li, B. Chen, C. Fernandez, B. Yang, B. Banerjee, S. 2020-04-23 doi:10.1101/2020.04.20.049460 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Determining the Depth Limit of Bioluminescent Sources in Scattering Media ]]> https://biorxiv.org/content/10.1101/2020.04.21.044982v1?rss=1 Raghuram, A. Ye, F. Adams, J. K. Shaner, N. Robinson, J. Veeraraghavan, A. 2020-04-23 doi:10.1101/2020.04.21.044982 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ G protein-regulated endocytic trafficking of adenylyl cyclase type 9 ]]> https://biorxiv.org/content/10.1101/2020.04.23.057026v1?rss=1 Lazar, A. M. Irannejad, R. Baldwin, T. A. Sundaram, A. B. Gutkind, J. S. Inoue, A. Dessauer, C. W. Von Zastrow, M. 2020-04-25 doi:10.1101/2020.04.23.057026 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Dynamics of Brain Structure and its Genetic Architecture over the Lifespan ]]> https://biorxiv.org/content/10.1101/2020.04.24.031138v1?rss=1 Brouwer, R. M. Klein, M. Grasby, K. L. Schnack, H. G. Jahanshad, N. Teeuw, J. Thomopoulos, S. I. Sprooten, E. Franz, C. E. Gogtay, N. Kremen, W. Panizzon, M. S. Olde Loohuis, L. M. Whelan, C. D. Aghajani, M. Alloza, C. Alnaes, D. Artiges, E. Ayesa-Arriola, R. Barker, G. J. Blok, E. Boen, E. Breukelaar, I. A. Bright, J. K. Buimer, E. E. Bülow, R. Cannon, D. M. Ciufolini, S. Crossley, N. A. Damatac, C. G. Dazzan, P. de Mol, C. L. de Zwarte, S. M. Desrivieres, S. Diaz-Caneja, C. M. Doan, N. T. Dohm, K. Fröhner, J. H. Goltermann, J. Grigis, A. Grotegerd, D 2020-04-27 doi:10.1101/2020.04.24.031138 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Regulatory interactions between Vax1, Pax6, and miR-7 regionalize the lateral Ventricular-Subventricular Zone during post-natal Olfactory Bulb neurogenesis in mice ]]> https://biorxiv.org/content/10.1101/2020.04.24.059428v1?rss=1 Core, N. Erni, A. Mellon, P. L. Hoffmann, H. M. Beclin, C. Cremer, H. 2020-04-25 doi:10.1101/2020.04.24.059428 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ A transcriptional regulatory atlas of coronavirus infection of human cells ]]> https://biorxiv.org/content/10.1101/2020.04.24.059527v1?rss=1 Ochsner, S. A. McKenna, N. 2020-04-25 doi:10.1101/2020.04.24.059527 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Matrix factorization recovers consistent regulatory signals from disparate datasets ]]> https://biorxiv.org/content/10.1101/2020.04.26.061978v1?rss=1 Sastry, A. V. Hu, A. Heckmann, D. Poudel, S. Kavvas, E. Palsson, B. O. 2020-04-27 doi:10.1101/2020.04.26.061978 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Inhibition of the NLRP3 inflammasome prevents ovarian aging ]]> https://biorxiv.org/content/10.1101/2020.04.26.062646v1?rss=1 Navarro-Pando, J. M. Alcocer-Gomez, E. Castejon-Vega, B. Muntane, J. Wang, C. Hoffman, H. M. Sanz, A. Mbalaviele, G. Ryffel, B. Cordero, M. D. 2020-04-28 doi:10.1101/2020.04.26.062646 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Expanding magnetic organelle biogenesis in the domain Bacteria ]]> https://biorxiv.org/content/10.1101/2020.04.27.061960v1?rss=1 Lin, W. Zhang, W. Paterson, G. A. Zhu, Q. Zhao, X. Knight, R. Bazylinski, D. A. Roberts, A. P. Pan, Y. 2020-04-28 doi:10.1101/2020.04.27.061960 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells ]]> https://biorxiv.org/content/10.1101/2020.04.27.065227v1?rss=1 Panwar, B. Schmiedel, B. J. Liang, S. White, B. Rodriquez, E. Kalunian, K. McKnight, A. J. Soloff, R. Seumois, G. Vijayanand, P. Ay, F. 2020-04-29 doi:10.1101/2020.04.27.065227 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.04.28.062679v1?rss=1 View larger version (96K): org.highwire.dtl.DTLVardef@10715caorg.highwire.dtl.DTLVardef@27af76org.highwire.dtl.DTLVardef@17083a6org.highwire.dtl.DTLVardef@1d31f9f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIExtensive lncRNA translation and microprotein production during human pancreas development C_LIO_LIA small-scale loss-of-function screen shows most translated lncRNAs are dispensable C_LIO_LILINC00261 is highly translated and regulates endocrine cell differentiation C_LIO_LIDeleting LINC00261s evolutionary young microproteins reveals no essential roles C_LI ]]> Gaertner, B. van Heesch, S. Schneider-Lunitz, V. Schulz, J. F. Witte, F. Blachut, S. Nguyen, S. Wong, R. Matta, I. Hubner, N. Sander, M. 2020-04-29 doi:10.1101/2020.04.28.062679 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Representative diatom and coccolithophore species exhibit divergent responses throughout simulated upwelling cycles ]]> https://biorxiv.org/content/10.1101/2020.04.30.071480v1?rss=1 Lampe, R. H. Hernandez, G. Lin, Y. Y. Marchetti, A. 2020-05-01 doi:10.1101/2020.04.30.071480 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate ]]> https://biorxiv.org/content/10.1101/2020.05.01.072231v1?rss=1 Ruess, H. Lee, J. Guzman, C. Malladi, V. D'Orso, I. 2020-05-02 doi:10.1101/2020.05.01.072231 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake. ]]> https://biorxiv.org/content/10.1101/2020.05.03.074617v1?rss=1 Rodionova, I. A. Rodionov, D. A. Gao, Y. Yoo, R. Sastry, A. Saier, M. Palsson, B. O. 2020-05-03 doi:10.1101/2020.05.03.074617 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) ]]> https://biorxiv.org/content/10.1101/2020.05.03.075499v1?rss=1 Robinson, J. T. Thorvaldsdottir, H. Turner, D. Mesirov, J. P. 2020-05-05 doi:10.1101/2020.05.03.075499 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability ]]> https://biorxiv.org/content/10.1101/2020.05.04.074443v1?rss=1 Parisian, A. D. Koga, T. Miki, S. Johann, P. D. Kool, M. Crawford, J. R. Furnari, F. 2020-05-05 doi:10.1101/2020.05.04.074443 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Interhemispheric callosal projections enforce response fidelity and frequency tuning in auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.05.05.079012v1?rss=1 Slater, B. J. Isaacson, J. S. 2020-05-06 doi:10.1101/2020.05.05.079012 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Nucleoid openness profiling links bacterial genome structure to phenotype ]]> https://biorxiv.org/content/10.1101/2020.05.07.082990v1?rss=1 Al-Bassam, M. M. Moyne, O. Chapin, N. Zengler, K. 2020-05-07 doi:10.1101/2020.05.07.082990 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Interactive MS/MS Visualization with the Metabolomics Spectrum Resolver Web Service ]]> https://biorxiv.org/content/10.1101/2020.05.09.086066v1?rss=1 Wang, M. Rogers, S. Bittremieux, W. Chen, C. Dorrestein, P. C. Schymanski, E. L. Schulze, T. Neumann, S. Meier, R. 2020-05-10 doi:10.1101/2020.05.09.086066 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Ion Identity Molecular Networking in the GNPS Environment ]]> https://biorxiv.org/content/10.1101/2020.05.11.088948v1?rss=1 Schmid, R. Petras, D. Nothias, L.-F. Wang, M. Aron, A. T. Jagels, A. Tsugawa, H. Rainer, J. Garcia-Aloy, M. Duehrkop, K. Korf, A. Pluskal, T. Kamenik, Z. Jarmusch, A. K. Caraballo-Rodriguez, A. M. Weldon, K. Nothias-Esposito, M. Aksenov, A. A. Bauermeister, A. Albarracin-Orio, A. Grundmann, C. O. Vargas, F. Koester, I. Gauglitz, J. M. Gentry, E. C. Hoevelmann, Y. Kalinina, S. A. Pendergraft, M. A. Panitchpakdi, M. W. Tehan, R. Le Gouellec, A. Aleti, G. Mannochio Russo, H. Arndt, B. Huebner, F. Hayen, H. Zhi, H. Raffatellu, M. Prather, K. A. Aluwihare, L. 2020-05-13 doi:10.1101/2020.05.11.088948 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Strain-dependent modifier genes determine survival in Zfp423 mice ]]> https://biorxiv.org/content/10.1101/2020.05.12.091629v1?rss=1 Alcaraz, W. A. Liu, Z. Valdes, P. Chen, E. Valdovino Gonzalez, A. G. Wade, S. Wong, C. Kim, E. Chen, H.-H. M. Concepcion, D. Hamilton, B. A. 2020-05-13 doi:10.1101/2020.05.12.091629 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Sensitivity to food and cocaine cues are independent traits in a large sample of heterogeneous stock rats. ]]> https://biorxiv.org/content/10.1101/2020.05.13.066944v1?rss=1 King, C. P. Tripi, J. A. Hughson, A. R. Hovarth, A. P. Lamparelii, A. C. Holl, K. L. Chitre, A. S. Polesskaya, O. Richards, J. B. Solberg-Woods, L. C. Palmer, A. A. Robinson, T. E. Flagel, S. B. Meyer, P. J. 2020-05-14 doi:10.1101/2020.05.13.066944 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ I ncreased accuracy of signaling by hyperbolic odorant mixtures in a beneficial insect-plant relationship ]]> https://biorxiv.org/content/10.1101/2020.05.13.093864v1?rss=1 Ghaninia, M. Knauer, A. C. Schiestl, F. Sharpee, T. O. Smith, B. H. 2020-05-14 doi:10.1101/2020.05.13.093864 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Metabolite profiling of experimental cutaneous leishmaniasis lesions demonstrates significant perturbations in tissue phospholipids ]]> https://biorxiv.org/content/10.1101/2020.05.13.094649v1?rss=1 McCall, L.-I. Parab, A. McKerrow, J. Dorrestein, P. C. Thomas, D. Lostracco-Johnson, S. de Siquiera-Neto, J. L. 2020-05-15 doi:10.1101/2020.05.13.094649 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence ]]> https://biorxiv.org/content/10.1101/2020.05.14.096305v1?rss=1 Traver, D. Sahai, P. Pouget, C. Svoboda, O. 2020-05-15 doi:10.1101/2020.05.14.096305 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Mapping Cognitive Brain Functions at Scale ]]> https://biorxiv.org/content/10.1101/2020.05.14.097014v1?rss=1 Balasubramani, P. P. Ojeda, A. Maric, V. Le, H. Grennan, G. Alim, F. Zafar-Khan, M. Diaz-Delgado, J. Silveira, S. Ramanathan, D. Mishra, J. 2020-05-16 doi:10.1101/2020.05.14.097014 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ PI3Kγ inhibition suppresses microglia/TAM accumulation in glioblastoma microenvironment to promote exceptional temozolomide response ]]> https://biorxiv.org/content/10.1101/2020.05.14.097121v1?rss=1 Li, J. Kaneda, M. M. Ma, J. Li, M. Patel, K. Koga, T. Sarver, A. L. Furnari, F. Xu, B. Dhawan, S. Ning, J. Zhu, H. Wu, A. You, G. Jiang, T. Venteichera, A. S. Rich, J. N. Glass, C. K. Varner, J. A. Chen, C. C. 2020-05-16 doi:10.1101/2020.05.14.097121 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2020.05.15.038679v1?rss=1 Aylward, A. Okino, M.-L. Benaglio, P. Chiou, J. Beebe, E. Padilla, J. A. Diep, S. Gaulton, K. J. 2020-05-16 doi:10.1101/2020.05.15.038679 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ A characterization of the electrophysiological, morphological and input domains of vasoactive intestinal peptide (VIP) interneurons in the medial entorhinal cortex (MEC) ]]> https://biorxiv.org/content/10.1101/2020.05.15.097972v1?rss=1 Badrinarayanan, S. Manseau, F. Lim, B. K. Williams, S. Brandon, M. P. 2020-05-16 doi:10.1101/2020.05.15.097972 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2020.05.17.095000v1?rss=1 Brouwer, S. Barnett, T. C. Ly, D. Kasper, K. J. De Oliveira, D. M. Rivera-Hernandez, T. Cork, A. J. McIntyre, L. Jespersen, M. G. Richter, J. Schulz, B. L. Dougan, G. Nizet, V. Yuen, K.-Y. You, Y. McCormick, J. K. Sanderson-Smith, M. L. Davies, M. R. Walker, M. J. 2020-05-17 doi:10.1101/2020.05.17.095000 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Role of Inflammasome-independent Activation of IL-1β by the Pseudomonas aeruginosa Protease LasB ]]> https://biorxiv.org/content/10.1101/2020.05.18.101303v1?rss=1 Sun, J. LaRock, D. Skowronski, E. Kimmey, J. M. Olson, J. Jiang, Z. O'Donoghue, A. Nizet, V. LaRock, C. 2020-05-19 doi:10.1101/2020.05.18.101303 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Human Hair Graying is Naturally Reversible and Linked to Stress ]]> https://biorxiv.org/content/10.1101/2020.05.18.101964v1?rss=1 Rosenberg, A. Rausser, S. Ren, J. Mosharov, E. Sturm, G. M. Ogden, R. T. Patel, P. Soni, R. K. Lacefield, C. Paus, R. Picard, M. 2020-05-19 doi:10.1101/2020.05.18.101964 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Cell cycle-gated feedback control mediates desensitization to interferon stimulation ]]> https://biorxiv.org/content/10.1101/2020.05.18.103101v1?rss=1 Mudla, A. Jiang, Y. Arimoto, K.-i. Xu, B. Rajesh, A. Ryan, A. P. Wang, W. Daugherty, M. D. Zhang, D.-E. Hao, N. 2020-05-20 doi:10.1101/2020.05.18.103101 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions ]]> https://biorxiv.org/content/10.1101/2020.05.19.079962v1?rss=1 Dillon, N. A. Seif, Y. Tsunemoto, H. Poudel, S. Meehan, M. Szubin, R. Olson, C. Rajput, A. Alarcon, G. Lamsa, A. Vrbanac, A. Sugie, J. Dahesh, S. Monk, J. Dorrestein, P. Knight, R. Feist, A. Pogliano, J. Palsson, B. Nizet, V. 2020-05-20 doi:10.1101/2020.05.19.079962 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment ]]> https://biorxiv.org/content/10.1101/2020.05.19.105270v1?rss=1 Minich, J. J. Power, C. Melanson, M. Knight, R. Webber, C. Rough, K. Bott, N. J. Nowak, B. Allen, E. 2020-05-20 doi:10.1101/2020.05.19.105270 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Development of follicular dendritic cells in lymph nodes depends on retinoic acid mediated signaling ]]> https://biorxiv.org/content/10.1101/2020.05.20.106385v1?rss=1 Koning, J. J. Rajaraman, A. Reijmers, R. M. Konijn, T. Pan, J. Ware, C. F. Butcher, E. C. Mebius, R. E. 2020-05-21 doi:10.1101/2020.05.20.106385 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ On the effectiveness of small, discriminatively pre-trained language representation models for biomedical text mining ]]> https://biorxiv.org/content/10.1101/2020.05.20.107003v1?rss=1 Ozyurt, I. B. 2020-05-23 doi:10.1101/2020.05.20.107003 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ The emergence of SARS-CoV-2 in Europe and the US ]]> https://biorxiv.org/content/10.1101/2020.05.21.109322v1?rss=1 Worobey, M. Pekar, J. Larsen, B. B. Nelson, M. I. Hill, V. Joy, J. B. Rambaut, A. Suchard, M. A. Wertheim, J. O. Lemey, P. 2020-05-23 doi:10.1101/2020.05.21.109322 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Membrane bending by protein phase separation ]]> https://biorxiv.org/content/10.1101/2020.05.21.109751v1?rss=1 Yuan, F. Alimohamadi, H. Bakka, B. Trementozzi, A. N. Fawzi, N. L. Rangamani, P. Stachowiak, J. C. 2020-05-22 doi:10.1101/2020.05.21.109751 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Identification and physiological significance of temporal NFκB signaling codewords deployed by macrophages to classify immune threats ]]> https://biorxiv.org/content/10.1101/2020.05.23.112862v1?rss=1 Taylor, B. Adelaja, A. Liu, Y. Luecke, S. Hoffmann, A. 2020-05-26 doi:10.1101/2020.05.23.112862 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Hidden features of the malaria vectormosquito, Anopheles stephensi ,revealed by a high-quality referencegenome ]]> https://biorxiv.org/content/10.1101/2020.05.24.113019v1?rss=1 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively through male development and adulthood, suggesting an important role throughout male development. ConclusionCollectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate development of genetic control strategies of malaria transmission. ]]> Chakraborty, M. Ramaiah, A. Adolfi, A. Halas, P. Kaduskar, B. Ngo, L. T. Jayaprasad, S. Paul, K. Whadgar, S. Srinivasan, S. Subramani, S. Bier, E. James, A. Emerson, J. J. 2020-05-24 doi:10.1101/2020.05.24.113019 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ The gene cortex controls scale colour identity in Heliconius ]]> https://biorxiv.org/content/10.1101/2020.05.26.116533v1?rss=1 Livraghi, L. Hanly, J. J. Loh, L. S. Ren, A. Warren, I. A. Concha, C. Wright, C. Walker, J. M. Foley, J. Arenas-Castro, H. Brenes, L. R. Martin, A. McMillan, W. O. Jiggins, C. D. 2020-05-29 doi:10.1101/2020.05.26.116533 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ An improved CRISPR/dCas9 interference tool for neuronal gene suppression ]]> https://biorxiv.org/content/10.1101/2020.05.26.116822v1?rss=1 Duke, C. G. Bach, S. V. Revanna, J. S. Sultan, F. A. Southern, N. T. Davis, M. N. Gallus, N. V. N. Bauman, A. J. Phillips, R. A. Day, J. J. 2020-05-27 doi:10.1101/2020.05.26.116822 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Local sensitivity analysis of the 'Membrane shape equation'derived from the Helfrich energy ]]> https://biorxiv.org/content/10.1101/2020.05.26.117275v1?rss=1 Rangamani, P. Behzadan, A. Holst, M. 2020-05-28 doi:10.1101/2020.05.26.117275 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Plasmin cascade mediates thrombolytic events in SARS-CoV-2 infection via complement and platelet-activating systems ]]> https://biorxiv.org/content/10.1101/2020.05.28.120162v1?rss=1 Mukund, K. Mathee, K. Subramaniam, S. 2020-05-29 doi:10.1101/2020.05.28.120162 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Antineoplastic kinase inhibitors: a new class of potent anti-amoebic compounds ]]> https://biorxiv.org/content/10.1101/2020.05.28.120923v1?rss=1 Sauvey, C. Ehrenkaufer, G. Shi, D. Debnath, A. Abagyan, R. 2020-05-28 doi:10.1101/2020.05.28.120923 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Sofosbuvir protects human brain organoids against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.05.30.125856v1?rss=1 Mesci, P. Macia, A. Saleh, A. Martin-Sancho, L. YIN, X. Snethlage, C. Avansini, S. Chanda, S. Muotri, A. 2020-05-31 doi:10.1101/2020.05.30.125856 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.05.31.122085v1?rss=1 Busby, K. N. Fulzele, A. Zhang, D. Bennett, E. J. Devaraj, N. K. 2020-05-31 doi:10.1101/2020.05.31.122085 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Leveraging non-structural data to predict structures of protein-ligand complexes ]]> https://biorxiv.org/content/10.1101/2020.06.01.128181v1?rss=1 Paggi, J. M. Belk, J. A. Hollingsworth, S. A. Villanueva, N. Powers, A. S. Clark, M. J. Chemparathy, A. G. Tynan, J. E. Lau, T. K. Sunahara, R. K. Dror, R. O. 2020-06-02 doi:10.1101/2020.06.01.128181 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Sustained attention and vigilance deficits associated with HIV and a history of methamphetamine dependence ]]> https://biorxiv.org/content/10.1101/2020.06.03.132522v1?rss=1 Pocuca, N. Young, J. W. MacQueen, D. A. Letendre, S. Heaton, R. K. Geyer, M. A. Perry, W. Grant, I. Minassian, A. Translational Methamphetamine AIDS Research Center (TMARC), 2020-06-04 doi:10.1101/2020.06.03.132522 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Neural divergence and convergence for interoceptive and somatosensory attention and detection ]]> https://biorxiv.org/content/10.1101/2020.06.04.134288v1?rss=1 Herman, A. M. Palmer, C. E. Azevedo, R. Tsakiris, M. 2020-06-05 doi:10.1101/2020.06.04.134288 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Multivariate analysis reveals a generalizable human electrophysiological signature of working memory load ]]> https://biorxiv.org/content/10.1101/2020.06.04.135053v1?rss=1 250,000 trials), we demonstrate that multivariate analysis of EEG voltage topography provides a sensitive index of the number of items stored in WM that generalizes to novel human observers. Moreover, multivariate load detection ("mvLoad") can provide robust information at the single-trial level, exceeding the sensitivity of extant univariate approaches. We show that this method tracks WM load in a manner that is (1) independent of the spatial position of the memoranda, (2) precise enough to differentiate item-by-item increments in the number of stored items, (3) generalizable across distinct tasks and stimulus displays and (4) correlated with individual differences in WM behavior. Thus, this approach provides a powerful complement to univariate analytic approaches, enabling temporally-resolved tracking of online memory storage in humans. ]]> Adam, K. C. S. Vogel, E. K. Awh, E. 2020-06-05 doi:10.1101/2020.06.04.135053 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box ]]> https://biorxiv.org/content/10.1101/2020.06.05.133405v1?rss=1 Reader, J. van der Watt, M. E. Taylor, D. Le Manach, C. Mittal, N. Ottilie, S. Theron, A. Moyo, P. Erlank, E. Nardini, L. Venter, N. Lauterbach, S. Bezuidenhout, B. Horatscheck, A. van Heerden, A. Boyle, G. A. Calvo, D. Mancama, D. Coetzer, T. L. Winzeler, E. A. Duffy, J. Koekemoer, L. L. Basarab, G. Chibale, K. Birkholtz, L.-M. 2020-06-05 doi:10.1101/2020.06.05.133405 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways ]]> https://biorxiv.org/content/10.1101/2020.06.08.140079v1?rss=1 Serbyn, N. Bagdiul, I. Michel, A. H. Suhandynata, R. T. Zhou, H. Kornmann, B. Stutz, F. 2020-06-09 doi:10.1101/2020.06.08.140079 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ DYNC1LI2 regulates localization of the chaperone-mediated autophagy-receptor LAMP2A and improves cellular homeostasis in cystinosis ]]> https://biorxiv.org/content/10.1101/2020.06.09.142349v1?rss=1 Rahman, F. Johnson, J. L. Zhang, J. He, J. Cherqui, S. Catz, S. D. 2020-06-10 doi:10.1101/2020.06.09.142349 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Both HIV Infection and Conditional Tat Expression Decrease Prepulse Inhibition with Further Impairment by Methamphetamine History in Humans ]]> https://biorxiv.org/content/10.1101/2020.06.11.130666v1?rss=1 Walter, T. Young, J. Milienne-Petiot, M. Deben, D. S. Heaton, R. Letendre, S. Grelotti, D. Perry, W. Grant, I. Minassian, A. 2020-06-12 doi:10.1101/2020.06.11.130666 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein ]]> https://biorxiv.org/content/10.1101/2020.06.11.146522v1?rss=1 Casalino, L. Gaieb, Z. Dommer, A. C. Harbison, A. M. Fogarty, C. A. Barros, E. P. Taylor, B. C. Fadda, E. Amaro, R. E. 2020-06-11 doi:10.1101/2020.06.11.146522 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Hybrid analysis reveals how DNA sequence governs genomic location and DNA contacts of bacterial chromatin H-NS filaments ]]> https://biorxiv.org/content/10.1101/2020.06.11.146589v1?rss=1 Shen, B. A. Hustmyer, C. M. Roston, D. Wolfe, M. B. Jessen, E. D. Landick, R. 2020-06-12 doi:10.1101/2020.06.11.146589 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Co-Occurrence of Enzyme Domains Guides the Discovery of an Oxazolone Synthetase ]]> https://biorxiv.org/content/10.1101/2020.06.11.147165v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@20cb16org.highwire.dtl.DTLVardef@f54df0org.highwire.dtl.DTLVardef@cffa51org.highwire.dtl.DTLVardef@3b085d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> de Rond, T. Asay, J. E. Moore, B. S. 2020-06-12 doi:10.1101/2020.06.11.147165 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Learning the synaptic and intrinsic membrane dynamics underlying working memory in spiking neural network models ]]> https://biorxiv.org/content/10.1101/2020.06.11.147405v1?rss=1 Li, Y. Kim, R. Sejnowski, T. J. 2020-06-12 doi:10.1101/2020.06.11.147405 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ DNA glycosylase NEIL2 prevents Fusobacterium-mediated inflammation and DNA damage in colonic epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.06.11.147454v1?rss=1 Sayed, I. Chakraborty, A. Ali, A. Sharma, A. Sahan, A. Sahoo, D. Ghosh, P. Hazra, T. Das, S. 2020-06-12 doi:10.1101/2020.06.11.147454 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ The genetic organization of subcortical volumetric change is stable throughout the lifespan ]]> https://biorxiv.org/content/10.1101/2020.06.12.143834v1?rss=1 Fjell, A. Grydeland, H. Wang, Y. Amlien, I. K. Bartres-Faz, D. Brandmaier, A. Duzel, S. Elman, J. Franz, C. Haberg, A. Kietzmann, T. C. Kievit, R. A. Kremen, W. Krogsrud, S. K. Kuhn, S. A. Lindenberger, U. Macia, D. Mowinckel, A. M. Nyberg, L. Panizzon, M. Sole-Padulles, C. Sorensen, O. Westerhausen, R. Walhovd, K. B. 2020-06-12 doi:10.1101/2020.06.12.143834 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ PP2A:B56 Regulates Meiotic Chromosome Segregation in C. elegans Oocytes ]]> https://biorxiv.org/content/10.1101/2020.06.12.148254v1?rss=1 Bel Borja, L. Soubigou, F. Taylor, S. J. P. Fraguas Bringas, C. Budrewicz, J. Lara-Gonzalez, P. Sorensen-Turpin, C. G. Bembenek, J. N. Cheerambathur, D. K. Pelisch, F. 2020-06-13 doi:10.1101/2020.06.12.148254 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE ]]> https://biorxiv.org/content/10.1101/2020.06.15.134403v1?rss=1 Bickler, S. W. Cauvi, D. M. Fisch, K. M. Prieto, J. M. Gaidry, A. D. Thangarajah, H. Lazar, D. Ignacio, R. Gerstmann, D. R. Ryan, A. F. Bickler, P. E. De Maio, A. 2020-06-16 doi:10.1101/2020.06.15.134403 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Resident macrophages establish and control lipid stores via PDGFcc production ]]> https://biorxiv.org/content/10.1101/2020.06.15.152397v1?rss=1 Cox, N. Crozet, L. Holtman, I. R. Loyher, P.-L. Lazarov, T. Mass, E. Stanley, R. Glass, C. K. Geissmann, F. 2020-06-15 doi:10.1101/2020.06.15.152397 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals ]]> https://biorxiv.org/content/10.1101/2020.06.15.152546v1?rss=1 Celinskis, D. Friedman, N. Koksharov, M. Murphy, J. Gomez-Ramirez, M. Borton, D. Shaner, N. Hochgeschwender, U. Lipscombe, D. Moore, C. 2020-06-16 doi:10.1101/2020.06.15.152546 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Photoperiod-Induced Neurotransmitter Switching in the Circadian Pacemaker Regulates Hypothalamic Dopamine Expression ]]> https://biorxiv.org/content/10.1101/2020.06.16.155440v1?rss=1 Porcu, A. Booreddy, S. Welsh, D. K. Dulcis, D. 2020-06-17 doi:10.1101/2020.06.16.155440 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Differential covariance: A new method to estimate functional connectivity in fMRI ]]> https://biorxiv.org/content/10.1101/2020.06.16.155630v1?rss=1 lin, w. Chen, Y. Bukhari, Q. Krishnan, G. Bazhenov, M. Sejnowski, T. J. 2020-06-17 doi:10.1101/2020.06.16.155630 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Molecular mode of action of an Acyl Protein thioesterase ]]> https://biorxiv.org/content/10.1101/2020.06.18.157545v1?rss=1 Abrami, L. Audagnotto, M. Ho, S. Marcaida, M. J. Mesquita, F. Anward, M. Sandoz, P. A. Fonti, G. Pojer, F. Dal Peraro, M. van der Goot, F. G. 2020-06-19 doi:10.1101/2020.06.18.157545 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Mapping cell structure across scales by fusing protein images and interactions ]]> https://biorxiv.org/content/10.1101/2020.06.21.163709v1?rss=1 Qin, Y. Winsnes, C. F. Huttlin, E. L. Zheng, F. Ouyang, W. Park, J. Pitea, A. Kreisberg, J. F. Gygi, S. P. Harper, J. W. Ma, J. Lundberg, E. Ideker, T. 2020-06-22 doi:10.1101/2020.06.21.163709 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals ]]> https://biorxiv.org/content/10.1101/2020.06.22.164533v1?rss=1 Montano, E. T. Nideffer, J. F. Brumage, L. Erb, M. Derman, A. I. Davis, J. P. Estrada, E. Fu, S. Le, D. Vuppala, A. Tran, C. Luterstein, E. Lakkaraju, S. Panchagnula, S. Ren, C. Doan, J. Tran, S. Soriano, J. Fujita, Y. Gutala, P. Fujii, Q. Lee, M. Bui, A. Villarreal, C. Shing, S. R. Kim, S. Freeman, D. Racha, V. Ho, A. Kumar, P. Falah, K. Dawson, T. Enustun, E. Prichard, A. Gomez, A. Khanna, K. Trigg, S. Pogliano, K. Pogliano, J. 2020-06-22 doi:10.1101/2020.06.22.164533 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ A whole-cortex probabilistic diffusion tractography connectome ]]> https://biorxiv.org/content/10.1101/2020.06.22.166041v1?rss=1 Rosen, B. Q. Halgren, E. 2020-06-23 doi:10.1101/2020.06.22.166041 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ A Live-Cell Assay for the Detection of pre-microRNA-Protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.06.23.167734v1?rss=1 Rosenblum, S. L. Lorenz, D. A. Garner, A. L. 2020-06-24 doi:10.1101/2020.06.23.167734 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2. ]]> https://biorxiv.org/content/10.1101/2020.06.23.167791v1?rss=1 Krishnan, S. Krishnan, G. P. 2020-06-24 doi:10.1101/2020.06.23.167791 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ A Simple Procedure for Bacterial Expression and Purification of the Fragile X Protein Family ]]> https://biorxiv.org/content/10.1101/2020.06.24.169243v1?rss=1 Edwards, M. M. Xu, M. Joseph, S. 2020-06-26 doi:10.1101/2020.06.24.169243 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ The Human Fragile X Mental Retardation Protein Inhibits the Elongation Step of Translation through its RGG and C-terminal domains ]]> https://biorxiv.org/content/10.1101/2020.06.25.171967v1?rss=1 Athar, Y. M. Joseph, S. 2020-06-27 doi:10.1101/2020.06.25.171967 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism ]]> https://biorxiv.org/content/10.1101/2020.06.25.172262v1?rss=1 Urresti, J. Zhang, P. Moran-Losada, P. Yu, N.-K. Negraes, P. D. Trujillo, C. A. Antaki, D. Amar, M. Chau, K. Pramod, A. B. Diedrich, J. Tejwani, L. Romero, S. Sebat, J. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.25.172262 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Genetics of human gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2020.06.26.173724v1?rss=1 Kurilshikov, A. Medina-Gomez, C. Bacigalupe, R. Radjabzadeh, D. Wang, J. Demirkan, A. Le Roy, C. I. Raygoza Garay, J. A. Finnicum, C. Liu, X. Zhernakova, D. Bonder, M. J. Hansen, T. H. Frost, F. Ruhlemann, M. C. Turpin, W. Moon, J.-Y. Kim, H.-N. Lull, K. Barkan, E. Shah, S. A. Fornage, M. Szopinska-Tokov, J. Wallen, Z. Borisevich, D. Agreus, L. Andreasson, A. Bang, C. Bedrani, L. Bell, J. T. Bisgaard, H. Boehnke, M. Boomsma, D. I. Burk, R. D. Claringbould, A. Croitoru, K. Davies, G. Van Duijn, C. Duijts, L. Falony, G. Fu, J. van der Graaf, A. Hansen, T 2020-06-28 doi:10.1101/2020.06.26.173724 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ The N-terminus of GPR37L1 is proteolytically processed by matrix metalloproteases ]]> https://biorxiv.org/content/10.1101/2020.06.27.174847v1?rss=1 Coleman, J. L. J. Ngo, T. Smythe, R. E. Cleave, A. J. Jones, N. M. Graham, R. M. Smith, N. J. 2020-06-28 doi:10.1101/2020.06.27.174847 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Isoform transcriptome of developing human brain provides new insights into autism risk variants ]]> https://biorxiv.org/content/10.1101/2020.06.27.175489v1?rss=1 Chau, K. Zhang, P. Urresti, J. Amar, M. Pramod, A. B. Thomas, A. Corominas, R. Lin, G. N. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.27.175489 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ A Small Molecule Fluorogenic Probe for the Detection of Sphingosine in Living Cells ]]> https://biorxiv.org/content/10.1101/2020.06.27.175661v1?rss=1 Rudd, A. K. Mittal, N. Lim, E. W. Metallo, C. M. Devaraj, N. K. 2020-06-29 doi:10.1101/2020.06.27.175661 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Spatial metabolomics identifies localized chemical changes in heart tissue during chronic cardiac Chagas disease ]]> https://biorxiv.org/content/10.1101/2020.06.29.178038v1?rss=1 Dean, D. A. Gautham, Siqueira-Neto, J. L. McKerrow, J. H. Dorrestein, P. C. McCall, L.-I. 2020-06-29 doi:10.1101/2020.06.29.178038 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Local Field Potentials in a Pre-motor Region Predict Learned Vocal Sequences ]]> https://biorxiv.org/content/10.1101/2020.06.30.179861v1?rss=1 Brown, D. E. Chavez, J. I. Nguyen, D. H. Kadwory, A. Voytek, B. Arneodo, E. Gentner, T. Q. Gilja, V. 2020-06-30 doi:10.1101/2020.06.30.179861 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Biophysical modeling of the neural origin of EEG and MEG signals ]]> https://biorxiv.org/content/10.1101/2020.07.01.181875v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@47f029org.highwire.dtl.DTLVardef@e8244dorg.highwire.dtl.DTLVardef@a765c1org.highwire.dtl.DTLVardef@96550_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICurrent dipoles are computed from biophysically detailed simulated neuron and network activity C_LIO_LIExtracted current dipoles allow for accurate computation of EEG and MEG signals in simplified and detailed head models C_LIO_LICurrent-diplole approximation generally not suitable for accurate calculations of ECoG signals C_LIO_LIMethod provides biophysics-based link between detailed neural activity and systems-level signals C_LI ]]> Naess, S. Halnes, G. Hagen, E. Hagler, D. J. Dale, A. Einevoll, G. T. Ness, T. V. 2020-07-04 doi:10.1101/2020.07.01.181875 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Phosphoregulation of HORMA domain protein HIM-3 promotes asymmetric synaptonemal complex disassembly in meiotic prophase in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.07.01.182063v1?rss=1 Sato-Carlton, A. Nakamura-Tabuchi, C. Li, X. Boog, H. Lehmer, M. K. Rosenberg, S. C. Barroso, C. Martinez-Perez, E. Corbett, K. D. Carlton, P. M. 2020-07-01 doi:10.1101/2020.07.01.182063 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Development of a Synthetic Poxvirus-Based SARS-CoV-2 Vaccine ]]> https://biorxiv.org/content/10.1101/2020.07.01.183236v1?rss=1 Chiuppesi, F. Werner, M. S. Contreras, H. Nguyen, H. V. Martinez, J. Park, S. Nguyen, J. Kha, M. Iniguez, A. Zhou, Q. Kaltcheva, T. Levytskyy, R. Ebelt, N. D. Kang, T. H. Wu, X. Rogers, T. Manuel, E. R. Shostak, Y. Diamond, D. J. Wussow, F. 2020-07-02 doi:10.1101/2020.07.01.183236 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Title: Acetylcholine regulates pulmonary inflammation and facilitates the transition from active immunity to tissue repair during respiratory viral infection ]]> https://biorxiv.org/content/10.1101/2020.07.02.184226v1?rss=1 Horkowitz, A. P. Schwartz, A. V. Alvarez, C. A. Herrera, E. B. Thoman, M. L. Chatfield, D. A. Osborn, K. G. Feuer, R. George, U. Z. Phillips, J. A. 2020-07-02 doi:10.1101/2020.07.02.184226 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Heart Snapshot: a broadly validated smartphone measure of VO2max for collection of real world data ]]> https://biorxiv.org/content/10.1101/2020.07.02.185314v1?rss=1 Webster, D. E. Tummalacherla, M. Higgins, M. Wing, D. Ashley, E. Kelly, V. E. McConnell, M. V. Muse, E. D. Olgin, J. Mangravite, L. Godino, J. Kellen, M. Omberg, L. 2020-07-04 doi:10.1101/2020.07.02.185314 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota ]]> https://biorxiv.org/content/10.1101/2020.07.06.190181v1?rss=1 Aranda-Diaz, A. Ng, K. Thomsen, T. Real-Ramirez, I. Dahan, D. Dittmar, S. Gutierrez Gonzalez, C. Chavez, T. Vasquez, K. S. Nguyen, T. H. Yu, F. B. Higginbottom, S. K. Neff, N. Elias, J. E. Sonnenburg, J. L. Huang, K. C. 2020-07-06 doi:10.1101/2020.07.06.190181 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Activity Mapping the Acyl Carrier Protein - Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis ]]> https://biorxiv.org/content/10.1101/2020.07.09.196451v1?rss=1 Jeffrey T Mindrebo Laetitia Estelle Misson Mindrebo Caitlin Johnson Joseph P. Noel Michael Burkart 2020-07-10 doi:10.1101/2020.07.09.196451 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Temperature triggers provide quantitative predictions of multi-species fish spawning peaks ]]> https://biorxiv.org/content/10.1101/2020.07.10.196923v1?rss=1 0.97) between a single event in daily sea surface temperatures each spring, and peak fish egg abundance measurements the following summer, in 7 years of approximately weekly fish egg abundance data collected at Scripps Pier in La Jolla California. Even more surprising is that this event-based result persists despite the large and variable number of fish species involved (up to 46), and the large and variable time interval between trigger and response (up to ~3 months). To mitigate against potential over-fitting, we make a true out-of-sample prediction for the peak summer egg abundance that will be observed at Scripps Pier this year. ]]> Emma S. Choi Erik Saberski Tom Lorimer Cameron Smith Unduwap Kandage-don Ronald S. Burton George Sugihara 2020-07-10 doi:10.1101/2020.07.10.196923 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Wide phenotypic spectrum of human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations ]]> https://biorxiv.org/content/10.1101/2020.07.12.189621v1?rss=1 Rebecca SF Mok Wen-Bo Zhang Taimoor I Sheikh Isabella R Fernandes Leah C DeJong Matthew R Hildebrandt Marat Mufteev Deivid C Rodrigues Wei Wei Alina Piekna Jiajie Liu Alysson R Muotri John B Vincent Michael W Salter James Ellis 2020-07-12 doi:10.1101/2020.07.12.189621 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Tobacco, but not nicotine and flavor-less electronic cigarettes, induces ACE2 and immune dysregulation ]]> https://biorxiv.org/content/10.1101/2020.07.13.198630v1?rss=1 Lee, A. C. Chakladar, J. Li, W. T. Chen, C. Chang, E. Y. Wang-Rodriguez, J. Ongkeko, W. M. 2020-07-13 doi:10.1101/2020.07.13.198630 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Cigarette Smoke and Nicotine-Containing E-cigarette Vapor Downregulate Lung WWOX Expression Which is Associated with Increased Severity of Murine ARDS ]]> https://biorxiv.org/content/10.1101/2020.07.13.200832v1?rss=1 Zeng, Z. Chen, W. Moshensky, A. Khan, R. Alexander, L. C. Ware, L. B. Aldaz, C. M. Jacobson, J. R. Dudek, S. M. Natarajan, V. Machado, R. F. Singla, S. 2020-07-13 doi:10.1101/2020.07.13.200832 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Acidosis, Zinc and HMGB1 in Sepsis: A Common Connection Involving Sialoglycan Recognition ]]> https://biorxiv.org/content/10.1101/2020.07.15.198010v1?rss=1 Siddiqui, S. S. Dhar, C. Sundaramurthy, V. Sasmal, A. Yu, H. Bandala-Sanchez, E. Li, M. Zhang, X. Chen, X. Harrison, L. C. Xu, D. Varki, A. 2020-07-15 doi:10.1101/2020.07.15.198010 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications ]]> https://biorxiv.org/content/10.1101/2020.07.15.202929v1?rss=1 Prodanov, T. Bansal, V. 2020-07-16 doi:10.1101/2020.07.15.202929 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population ]]> https://biorxiv.org/content/10.1101/2020.07.17.207266v1?rss=1 Milner, J. Nguyen, H. Omilusik, K. Reina-Campos, M. Tsai, M. Toma, C. Delpoux, A. D. Boland, B. Hedrick, S. M. Chang, J. T. Goldrath, A. W. 2020-07-17 doi:10.1101/2020.07.17.207266 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Aβ-induced synaptic injury is mediated by presynaptic expression of amyloid precursor protein (APP) in hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2020.07.18.210344v1?rss=1 Vicario-Orri, E. Kasuga, K. Tyan, S.-H. Chiang, K. Viana da Silva, S. Bushong, E. A. DeLoach, K. Ling, I.-F. Luo, L. Ellisman, M. H. Leutgeb, S. Koo, E. H. 2020-07-20 doi:10.1101/2020.07.18.210344 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ Unique contributions of sensory discrimination and gamma synchronization deficits to cognitive, clinical, and psychosocial functional impairments in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.07.19.211193v1?rss=1 Koshiyama, D. Miyakoshi, M. Thomas, M. L. Joshi, Y. B. Molina, J. L. Tanaka-Koshiyama, K. Sprock, J. Braff, D. L. Swerdlow, N. R. Light, G. A. 2020-07-21 doi:10.1101/2020.07.19.211193 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Tractography-Pathology Correlations in Traumatic Brain Injury: A TRACK-TBI Study ]]> https://biorxiv.org/content/10.1101/2020.07.20.209668v1?rss=1 Nolan, A. L. Petersen, C. Iacono, D. Mac Donald, C. L. Mukherjee, P. van der Kouwe, A. Jain, S. Stevens, A. Diamond, B. R. Wang, R. Markowitz, A. J. Fischl, B. Perl, D. P. Manley, G. T. Keene, C. D. Diaz-Arrastia, R. Edlow, B. L. the TRACK-TBI Investigators, 2020-07-22 doi:10.1101/2020.07.20.209668 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Unique genomic features of crAss-like phages, the dominant component of the human gut virome ]]> https://biorxiv.org/content/10.1101/2020.07.20.212944v1?rss=1 Yutin, N. Benler, S. Shmakov, S. A. Wolf, Y. I. Tolstoy, I. Rayko, M. Antipov, D. Pevzner, P. A. Koonin, E. V. 2020-07-20 doi:10.1101/2020.07.20.212944 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease ]]> https://biorxiv.org/content/10.1101/2020.07.21.214874v1?rss=1 Alexanian, M. Przytycki, P. F. Micheletti, R. Padmanabhan, A. Ye, L. Travers, J. G. Gonzalez Teran, B. Duan, Q. Ranade, S. S. Felix, F. Linares-Saldana, R. Huang, Y. Andreoletti, G. Yang, J. Ivey, K. N. Jain, R. McKinsey, T. A. Rosenfeld, M. G. Gifford, C. Pollard, K. S. Haldar, S. M. Srivastava, D. 2020-07-22 doi:10.1101/2020.07.21.214874 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ ABCB-mediated auxin transport in outer root tissues regulates lateral root spacing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.07.22.206300v1?rss=1 CHEN, J. Hu, Y. Hao, P. Zhang, Y. Roth, O. Njo, M. Sterck, L. Hu, Y. Zhao, Y. Geisler, M. Shani, E. Beeckman, T. Vanneste, S. 2020-07-22 doi:10.1101/2020.07.22.206300 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Asymmetric localization of the cell division machinery during Bacillus subtilis sporulation ]]> https://biorxiv.org/content/10.1101/2020.07.22.216184v1?rss=1 Khanna, K. Lopez-Garrido, J. Sugie, J. Pogliano, K. Villa, E. 2020-07-22 doi:10.1101/2020.07.22.216184 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project ]]> https://biorxiv.org/content/10.1101/2020.07.23.216507v1?rss=1 Hansen, J. Sealfon, R. Menon, R. Eadon, M. T. Lake, B. B. Steck, B. Dobi, D. Parikh, S. Sidgel, T. K. Alexandrov, T. Schroeder, A. Otto, E. A. Anderton, C. R. Barwinska, D. Zheng, G. Rose, M. P. Shapiro, J. P. Velickovic, D. Pamreddy, A. Winfree, S. He, Y. de Boer, I. H. Hodgin, J. B. Nair, A. Sharma, K. Sarwal, M. Zhang, K. Himmelfarb, J. Laszik, Z. Rovin, B. Dagher, P. C. He, J. C. El-Achkar, T. M. Jain, S. Troyanskaya, O. G. Kretzler, M. Iyengar, R. Azeloglu, E. U. 2020-07-24 doi:10.1101/2020.07.23.216507 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[ Synapsin-caveolin-1 mitigates cognitive deficits and neurodegeneration in Alzheimer's disease mice ]]> https://biorxiv.org/content/10.1101/2020.07.24.220129v1?rss=1 Wang, S. Leem, J. Podvin, S. Hook, V. Kleschevnikov, N. Savchenko, P. Dhanani, M. Zhou, K. Kelly, I. Zhang, T. Miyanohara, A. Kleschevnikov, A. Wagner, S. Trojanowski, J. Roth, D. Patel, H. Patel, P. Head, B. P. 2020-07-25 doi:10.1101/2020.07.24.220129 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ A Novel CD206 Targeting Peptide Inhibits Bleomycin Induced Pulmonary Fibrosis in Mice ]]> https://biorxiv.org/content/10.1101/2020.07.27.218115v1?rss=1 Gheberemedhin, A. Salam, A. B. Adu-Addai, B. Noonan, S. Stratton, R. Ahmed, M. S. U. khantwal, C. Martin, G. Huixian, L. Andrews, C. Balasubramanyam, K. Udo, R. Henry, L. Jaynes, J. Yates, C. 2020-07-29 doi:10.1101/2020.07.27.218115 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ The ABCD Stop Signal Data: Response to Bissett et al. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223057v1?rss=1 Garavan, H. Hahn, S. Chaarani, B. Juliano, A. Allgaier, N. Yuan, D. K. Weigard, A. Orr, C. Watts, R. Wager, T. Ruiz de Leon, O. Hagler, D. Potter, A. 2020-07-28 doi:10.1101/2020.07.27.223057 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ ABO genetic variation in Neanderthals and Denisovans ]]> https://biorxiv.org/content/10.1101/2020.07.27.223628v1?rss=1 Fox, K. Huerta-Sanchez, E. Villanea, F. A. 2020-07-27 doi:10.1101/2020.07.27.223628 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ RNA-binding protein RBM3 negatively regulates innate lymphoid cells (ILCs) and lung inflammation ]]> https://biorxiv.org/content/10.1101/2020.07.27.223958v1?rss=1 Doherty, T. 2020-07-28 doi:10.1101/2020.07.27.223958 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Insights into the catalytic properties of the mitochondrial rhomboid protease PARL ]]> https://biorxiv.org/content/10.1101/2020.07.27.224220v1?rss=1 Lysyk, L. Brassard, R. Arutyunova, E. Siebert, V. Jiang, Z. Takyi, E. Morrison, M. Young, H. S. Lemberg, M. K. O'Donoghue, A. J. Lemieux, M. J. 2020-07-29 doi:10.1101/2020.07.27.224220 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Understanding the Human Brain using Brain Organoids and a Structure-Function Theory ]]> https://biorxiv.org/content/10.1101/2020.07.28.225631v1?rss=1 Silva, G. A. Muotri, A. R. White, C. 2020-07-28 doi:10.1101/2020.07.28.225631 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Plankton food webs of the Gulf of Mexico spawning grounds of Atlantic Bluefin tuna ]]> https://biorxiv.org/content/10.1101/2020.07.29.227116v1?rss=1 80% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). In contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <4% of net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on calanoid copepods and other suspension-feeding zooplankton that in turn derive much of their nutrition from diatoms and mixotrophic flagellates. This allows ABT larvae to maintain a comparatively low trophic level ([~]4.0 for pre-flexion larvae; [~]4.2 for post-flexion larvae) that increases trophic transfer from phytoplankton to larval fish. ]]> Stukel, M. R. Gerard, T. Kelly, T. B. Knapp, A. N. Laiz-Carrion, R. Lamkin, J. Landry, M. R. Malca, E. Selph, K. E. Shiroza, A. Shropshire, T. A. Swalethorp, R. R. 2020-07-30 doi:10.1101/2020.07.29.227116 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Spatial attention enhances the spatial selectivity of population codes during the first wave of visual processing ]]> https://biorxiv.org/content/10.1101/2020.07.30.228981v1?rss=1 Foster, J. J. Thyer, W. Wennberg, J. W. Awh, E. 2020-07-31 doi:10.1101/2020.07.30.228981 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ MOLECULAR DETERMINANTS OF THE ENDOCYTIC PROTEIN EPSIN CONTROLLING ITS LOCALIZATION AND FUNCTION IN CANCER CELL MIGRATION AND INVASION ]]> https://biorxiv.org/content/10.1101/2020.07.30.229195v1?rss=1 Madhivanan, K. Cao, L. Staiger, C. J. Aguilar, R. C. 2020-07-30 doi:10.1101/2020.07.30.229195 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics ]]> https://biorxiv.org/content/10.1101/2020.07.31.230334v1?rss=1 Haiman, Z. B. Zielinski, D. C. Koike, Y. Yurkovich, J. T. Palsson, B. O. 2020-07-31 doi:10.1101/2020.07.31.230334 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Injectable Myocardial Matrix Hydrogel Mitigates Negative Left Ventricular Remodeling in a Chronic Myocardial Infarction Model ]]> https://biorxiv.org/content/10.1101/2020.07.31.231449v1?rss=1 Diaz, M. D. Tran, E. Wassenaar, J. Spang, M. Gaetani, R. Luo, C. Braden, R. Hill, R. C. Hansen, K. C. DeMaria, A. N. Christman, K. 2020-08-02 doi:10.1101/2020.07.31.231449 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Myocardial matrix material supports a proliferative microenvironment for cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.07.31.231845v1?rss=1 Wang, R. M. Cattaneo, P. Luo, C. Camboa, N. Braden, R. Christman, K. Evans, S. 2020-08-02 doi:10.1101/2020.07.31.231845 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Mast Cells Contribute to the Immunomodulatory Effect of the Biomaterial Microenvironment in a Gender Specific Manner ]]> https://biorxiv.org/content/10.1101/2020.07.31.231852v1?rss=1 Wang, R. M. Ungerleider, J. Kawakami, Y. Kawakami, Y. Kawakami, T. Christman, K. 2020-08-02 doi:10.1101/2020.07.31.231852 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ NPC1-mTORC1 signaling Couples Cholesterol Sensing to Organelle Homeostasis and is a Targetable Pathway in Niemann-Pick type C ]]> https://biorxiv.org/content/10.1101/2020.08.02.233254v1?rss=1 Davis, O. B. Shin, H. R. Lim, C.-Y. Wu, E. Y. Kukurugya, M. Maher, C. F. Perera, R. M. Ordonez, P. Zoncu, R. 2020-08-02 doi:10.1101/2020.08.02.233254 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Specific OCRL1 patient mutations differentially impact Lowe Syndrome cellular phenotypes ]]> https://biorxiv.org/content/10.1101/2020.08.04.236612v1?rss=1 Ramadesikan, S. Skiba, L. Lee, J. Madhivanan, K. Sarkar, D. De La Fuente, A. Hanna, C. B. Hazbun, T. Kihara, D. Aguilar, R. C. 2020-08-05 doi:10.1101/2020.08.04.236612 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Paranode stability requires UNC5B expression by oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2020.08.06.234906v1?rss=1 de Faria, O. Nakamura, D. S. Clemot, S. Kim, D. Mocanu, M. V. Pilgram, R. Bin, J. M. Wong, E. W. Shmuel, A. Sadikot, A. Ackerman, S. L. Kennedy, T. E. 2020-08-07 doi:10.1101/2020.08.06.234906 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Identification of the keystone species in non-alcoholic fatty liver disease by causal inference and dynamic intervention modeling ]]> https://biorxiv.org/content/10.1101/2020.08.06.240655v1?rss=1 Wu, D. Jiao, N. Zhu, R. Zhang, Y. Gao, W. Fang, S. Li, Y. Cheng, S. Tian, C. Lan, P. Loomba, R. Zhu, L. 2020-08-07 doi:10.1101/2020.08.06.240655 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Influenza A virus NS1 protein binds as a dimer to the RNA-free PABP1 but not to the PABP1-Poly(A) RNA Complex ]]> https://biorxiv.org/content/10.1101/2020.08.10.245225v1?rss=1 de Rozieres, C. M. Joseph, S. 2020-08-10 doi:10.1101/2020.08.10.245225 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase ]]> https://biorxiv.org/content/10.1101/2020.08.12.248690v1?rss=1 Seitz, C. Casalino, L. Konecny, R. Huber, G. Amaro, R. E. McCammon, J. A. 2020-08-12 doi:10.1101/2020.08.12.248690 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Learned adaptive multiphoton illumination microscopy ]]> https://biorxiv.org/content/10.1101/2020.08.14.251314v1?rss=1 Pinkard, H. Baghdassarian, H. Mujal, A. Roberts, E. Hu, K. H. Friedman, D. H. Malenica, I. Shagam, T. Fries, A. Corbin, K. Krummel, M. F. Waller, L. 2020-08-15 doi:10.1101/2020.08.14.251314 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Abortive Intussusceptive Angiogenesis Causes Multi-Cavernous Vascular Malformations ]]> https://biorxiv.org/content/10.1101/2020.08.14.251744v1?rss=1 Li, W. Tran, V. Shaked, I. Xue, B. Moore, T. Lightle, R. Kleinfeld, D. Awad, I. A. Ginsberg, M. 2020-08-14 doi:10.1101/2020.08.14.251744 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD ]]> https://biorxiv.org/content/10.1101/2020.08.14.251876v1?rss=1 Jiao, N. Loomba, R. Yang, Z.-H. Wu, D. Fang, S. Bettencourt, R. Lan, P. Zhu, R. Zhu, L. 2020-08-14 doi:10.1101/2020.08.14.251876 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.17.253955v1?rss=1 Kim, H. Ding, Y.-H. Lu, S. Zuo, M.-Q. Conte, D. Dong, M.-Q. Mello, C. 2020-08-17 doi:10.1101/2020.08.17.253955 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Extracellular matrix and cyclic stretch alter fetal cardiomyocyte proliferation and maturation in a rodent model of heart hypoplasia ]]> https://biorxiv.org/content/10.1101/2020.08.17.254334v1?rss=1 Watson, M. C. Williams, C. Wang, R. M. Perreault, L. R. Sullivan, K. E. Stoppel, W. L. Black, L. D. 2020-08-18 doi:10.1101/2020.08.17.254334 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors ]]> https://biorxiv.org/content/10.1101/2020.08.19.257352v1?rss=1 Hunkeler, M. Jin, C. Y. Ma, M. W. Overwijn, D. Monda, J. K. Bennett, E. J. Fischer, E. S. 2020-08-19 doi:10.1101/2020.08.19.257352 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ An autonomous, but INSIG-modulated, role for the Sterol Sensing Domain in mallostery-regulated ERAD of yeast HMG-CoA reductase ]]> https://biorxiv.org/content/10.1101/2020.08.20.260133v1?rss=1 Wangeline, M. A. Hampton, R. Y. 2020-08-21 doi:10.1101/2020.08.20.260133 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ A home and rescue gene drive forces its inheritance stably persisting in populations ]]> https://biorxiv.org/content/10.1101/2020.08.21.261610v1?rss=1 Kandul, N. P. Liu, J. Bennett, J. B. Marshall, J. M. Akbari, O. 2020-08-23 doi:10.1101/2020.08.21.261610 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Functional validation of a finding from a mouse genome-wide association study demonstrates that a mutant allele of Azi2 alters sensitivity to methamphetamine ]]> https://biorxiv.org/content/10.1101/2020.08.22.262709v1?rss=1 Zhou, X. Barkley-Levenson, A. Montilla-Perez, P. Telese, F. Palmer, A. A. 2020-08-22 doi:10.1101/2020.08.22.262709 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Developmental stage-specific changes in protein synthesis differentially sensitize hematopoietic stem cells and erythroid progenitors to impaired ribosome biogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.22.262816v1?rss=1 Magee, J. A. Signer, R. A. J. 2020-08-23 doi:10.1101/2020.08.22.262816 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Assessment of research ethics education offerings of pharmacy master programs: a qualitative content analysis ]]> https://biorxiv.org/content/10.1101/2020.08.25.266023v1?rss=1 Ahmed, W. S. Nebeker, C. 2020-08-25 doi:10.1101/2020.08.25.266023 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ The population genetics of pleiotropy, and the evolution of collateral resistance and sensitivity in bacteria ]]> https://biorxiv.org/content/10.1101/2020.08.25.267484v1?rss=1 Ardell, S. M. Kryazhimskiy, S. 2020-08-25 doi:10.1101/2020.08.25.267484 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Rethinking Remdesivir: Synthesis of Lipid Prodrugs that Substantially Enhance Anti-Coronavirus Activity ]]> https://biorxiv.org/content/10.1101/2020.08.26.269159v1?rss=1 Schooley, R. T. Carlin, A. F. Beadle, J. R. Valiaeva, N. Zhang, X.-Q. Garretson, A. F. Smith, V. I. Murphy, J. A. Hostetler, K. Y. 2020-08-27 doi:10.1101/2020.08.26.269159 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ PIEZO ion channel is required for root mechanotransduction in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2020.08.27.270355v1?rss=1 Patapoutian, A. Mousavi, S. A. R. Dubin, A. E. Zeng, W.-Z. Coombs, A. M. Do, K. Ghadiri, D. A. Zhao, Y. Ge, C. 2020-08-28 doi:10.1101/2020.08.27.270355 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Neural vulnerability and hurricane-related media predict posttraumatic stress in youth ]]> https://biorxiv.org/content/10.1101/2020.08.27.271056v1?rss=1 Dick, A. S. Silva, K. Gonzalez, R. Sutherland, M. T. Laird, A. R. Thompson, W. K. Tapert, S. F. Squeglia, L. M. Gray, K. M. Nixon, S. J. Cottler, L. B. La Greca, A. M. Gurwitch, R. H. Comer, J. S. 2020-08-29 doi:10.1101/2020.08.27.271056 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors ]]> https://biorxiv.org/content/10.1101/2020.08.28.270454v1?rss=1 Hong, L. Ko, C. S. Kang, S. E. Pruneda-Paz, J. L. Roeder, A. H. K. 2020-08-30 doi:10.1101/2020.08.28.270454 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ De Novo Mutation in an Enhancer of EBF3 in simplex autism ]]> https://biorxiv.org/content/10.1101/2020.08.28.270751v1?rss=1 Padhi, E. M. Hayeck, T. J. Mannion, B. Chatterjee, S. Byrska-Bishop, M. Musunuri, R. Narzisi, G. Abhyankar, A. Cheng, Z. Hunter, R. D. Akiyama, J. Fries, L. E. Ng, J. Stong, N. Allen, A. S. Dickel, D. E. Bernier, R. A. Gorkin, D. U. Pennacchio, L. A. Zody, M. C. Turner, T. N. 2020-08-28 doi:10.1101/2020.08.28.270751 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing ]]> https://biorxiv.org/content/10.1101/2020.08.29.273565v1?rss=1 Martinez, N. M. Gilbert, W. V. Yeo, G. W. Su, A. Schaening, C. Burns, M. C. Nussbacher, J. K. Sathe, S. 2020-08-31 doi:10.1101/2020.08.29.273565 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275602v1?rss=1 Adam, K. Chang, L. Rangan, N. Serences, J. 2020-09-01 doi:10.1101/2020.08.31.275602 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Stability analysis of a signaling circuit with dual species of GTPase switches ]]> https://biorxiv.org/content/10.1101/2020.08.31.276311v1?rss=1 Stolerman, L. M. Ghosh, P. Rangamani, P. 2020-08-31 doi:10.1101/2020.08.31.276311 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Single-vessel cerebral blood flow fMRI to map blood velocity by phase-contrast imaging ]]> https://biorxiv.org/content/10.1101/2020.09.03.280636v1?rss=1 Chen, X. Jiang, Y. Choi, S. Pohmann, R. Scheffler, K. Kleninfeld, D. Yu, X. 2020-09-03 doi:10.1101/2020.09.03.280636 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis ]]> https://biorxiv.org/content/10.1101/2020.09.03.281675v1?rss=1 Terrey, M. Adamson, S. I. Gibson, A. L. Deng, T. Ishimura, R. Chuang, J. H. Ackerman, S. L. 2020-09-04 doi:10.1101/2020.09.03.281675 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Inherently confinable split-drive systems in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.09.03.282079v1?rss=1 Terradas, G. Buchman, A. B. Bennett, J. B. Shriner, I. Marshall, J. M. Akbari, O. S. Bier, E. 2020-09-03 doi:10.1101/2020.09.03.282079 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Differential gene expression reflects larval development and survival of monarch butterflies on different milkweed hosts ]]> https://biorxiv.org/content/10.1101/2020.09.05.284489v1?rss=1 Gonzalez-De-la-Rosa, P. M. Ramirez Loustalot-Laclette, M. Abreu-Goodger, C. Markow, T. A. 2020-09-06 doi:10.1101/2020.09.05.284489 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects ]]> https://biorxiv.org/content/10.1101/2020.09.06.285056v1?rss=1 Larkin, A. A. Garcia, C. A. Brock, M. L. Lee, J. A. Garcia, N. Ustick, L. J. Barbero, L. Carter, B. R. Sonnerup, R. E. Talley, L. Tarran, G. A. Volkov, D. L. Martiny, A. C. 2020-09-08 doi:10.1101/2020.09.06.285056 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.09.06.285387v1?rss=1 Fan, X. Masamsetti, V. P. Sun, J. Q. J. Engholm-Keller, K. Osteil, P. Studdert, J. Graham, M. E. Fossat, N. Tam, P. P. L. 2020-09-07 doi:10.1101/2020.09.06.285387 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Direct observation of RAG recombinase recruitment to chromatin and the IgH locus in live pro-B cells ]]> https://biorxiv.org/content/10.1101/2020.09.07.286484v1?rss=1 Lovely, G. A. Braikia, F.-Z. Singh, A. K. Schatz, D. Murre, C. Liu, Z. Sen, R. 2020-09-07 doi:10.1101/2020.09.07.286484 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity ]]> https://biorxiv.org/content/10.1101/2020.09.08.288233v1?rss=1 1000 fold more specific RNA editing. Taken together, we anticipate this comprehensive deaminase engineering will enable broader utility of the ADAR toolset for RNA biotechnology and therapeutic applications. ]]> Katrekar, D. Palmer, N. Xiang, Y. Saha, A. Meluzzi, D. Mali, P. 2020-09-09 doi:10.1101/2020.09.08.288233 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Mechanical principles governing the shapes of dendritic spines ]]> https://biorxiv.org/content/10.1101/2020.09.09.290650v1?rss=1 Alimohamadi, H. Bell, M. Halpain, S. Rangamani, P. 2020-09-10 doi:10.1101/2020.09.09.290650 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement ]]> https://biorxiv.org/content/10.1101/2020.09.09.290668v1?rss=1 Boyle, E. A. Becker, W. R. Bai, H. B. Chen, J. S. Doudna, J. A. Greenleaf, W. J. 2020-09-10 doi:10.1101/2020.09.09.290668 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Gene exchange networks define species-like units in marine prokaryotes ]]> https://biorxiv.org/content/10.1101/2020.09.10.291518v1?rss=1 12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes. ]]> Stepanauskas, R. Brown, J. M. Mai, U. Bezuidt, O. Pachiadaki, M. Brown, J. Biller, S. Berube, P. M. Record, N. R. Mirarab, S. 2020-09-10 doi:10.1101/2020.09.10.291518 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Orphan G protein-coupled receptor, GPR37L1: pharmacological toolbox empty once again ]]> https://biorxiv.org/content/10.1101/2020.09.11.290486v1?rss=1 Ngo, T. Wilkins, B. P. So, S. S. Keov, P. Chahal, K. K. Finch, A. M. Coleman, J. L. J. Kufareva, I. Smith, N. J. 2020-09-11 doi:10.1101/2020.09.11.290486 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Selective activation of FZD7 promotes mesendodermal differentiation of human pluripotent stem cells. ]]> https://biorxiv.org/content/10.1101/2020.09.14.297028v1?rss=1 Gumber, D. Do, M. Suresh Kumar, N. Wu, C. C. N. Carson, D. Gaasterland, T. Willert, K. 2020-09-14 doi:10.1101/2020.09.14.297028 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Optimal transcriptional regulation of cellular responses to sudden environmental shifts ]]> https://biorxiv.org/content/10.1101/2020.09.14.297317v1?rss=1 Schultz, D. Tsimring, L. S. 2020-09-15 doi:10.1101/2020.09.14.297317 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits ]]> https://biorxiv.org/content/10.1101/2020.09.16.300152v1?rss=1 Ward, S. Riley, C. Carey, E. M. Nguyen, J. Esener, S. Nimmerjahn, A. Sirbuly, D. J. 2020-09-17 doi:10.1101/2020.09.16.300152 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ The organization and developmental establishment ofcortical interneuron presynaptic circuits ]]> https://biorxiv.org/content/10.1101/2020.09.17.302117v1?rss=1 Pouchelon, G. Bollmann, Y. Fisher, E. Agba, C. K. Xu, Q. Ritola, K. D. Mirow, A. M. Kim, S. Cossart, R. Fishell, G. 2020-09-17 doi:10.1101/2020.09.17.302117 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ A De Novo Genome Assembly, Gene Annotation, And Expression Atlas For The Monarch Butterfly Danaus plexippus ]]> https://biorxiv.org/content/10.1101/2020.09.19.304162v1?rss=1 Ranz, J. M. Gonzalez, P. Clifton, B. Nazario, N. Hernandez-Cervantes, P. Palma-Martinez, M. Valdivia, D. Jimenez-Kaufman, A. Lu, M. Markow, T. A. Abreu-Goodger, C. 2020-09-20 doi:10.1101/2020.09.19.304162 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Altered lipid metabolism marks glioblastoma stem and non-stem cells in separate tumor niches ]]> https://biorxiv.org/content/10.1101/2020.09.20.304964v1?rss=1 Shakya, S. Gromovsky, A. Hale, J. Knudsen, A. Prager, B. Wallace, L. Penalva, L. O. Ivanova, P. Brown, H. A. Kristensen, B. Rich, J. Lathia, J. Brown, J. M. Hubert, C. G. 2020-09-20 doi:10.1101/2020.09.20.304964 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Multivariate GWAS elucidates the genetic architecture of alcohol consumption and misuse, corrects biases, and reveals novel associations with disease ]]> https://biorxiv.org/content/10.1101/2020.09.21.304196v1?rss=1 Mallard, T. T. Savage, J. E. Johnson, E. C. Huang, Y. Edwards, A. C. Hottenga, J. J. Grotzinger, A. D. Gustavson, D. E. Jennings, M. V. Anokhin, A. Dick, D. M. Edenberg, H. J. Kramer, J. R. Lai, D. Meyers, J. L. Pandey, A. K. Harden, K. P. Nivard, M. G. de Geus, E. J. Boomsma, D. I. Agrawal, A. Davis, L. K. Clarke, T.-K. Palmer, A. A. Sanchez-Roige, S. 2020-09-22 doi:10.1101/2020.09.21.304196 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna ]]> https://biorxiv.org/content/10.1101/2020.09.21.307181v1?rss=1 Ho, E. K. H. Bellis, E. S. Calkins, J. Adrion, J. R. Latta, L. C. Schaack, S. 2020-09-21 doi:10.1101/2020.09.21.307181 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia ]]> https://biorxiv.org/content/10.1101/2020.09.22.307728v1?rss=1 Karmeinski, D. Meusemann, K. Goodheart, J. A. Schroedl, M. Martynov, A. Korshunova, T. Wägele, H. Donath, A. 2020-09-23 doi:10.1101/2020.09.22.307728 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ RNA adenosine deaminase ADAR2 modulates T helper 17 cell effector function ]]> https://biorxiv.org/content/10.1101/2020.09.22.308221v1?rss=1 Ma, S. Cho, B. S. Li, Y. Abbasi, N. Yee, B. A. Sun, G. Luo, C. Chang, J. T. Zhou, B. Fu, X.-d. Yeo, G. W. Huang, W. J. M. 2020-09-22 doi:10.1101/2020.09.22.308221 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Functional Organization for Color Appearance Mechanisms in Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2020.09.22.309054v1?rss=1 Li, P. Garg, A. K. Zhang, L. A. Rashid, M. S. Callaway, E. M. 2020-09-23 doi:10.1101/2020.09.22.309054 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Resolving atomic site interactions of the Y. pestis outer membrane protein Ail with human serum in the bacterial cell envelope ]]> https://biorxiv.org/content/10.1101/2020.09.23.310672v1?rss=1 Kent, J. E. Fujimoto, L. M. Shn, K. Singh, C. Yao, Y. Park, S. Opella, S. J. Plano, G. V. Marassi, F. M. 2020-09-23 doi:10.1101/2020.09.23.310672 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ The quantitative metabolome is shaped by abiotic constraints ]]> https://biorxiv.org/content/10.1101/2020.09.26.315135v1?rss=1 Akbari, A. Yurkovich, J. T. Zielinski, D. C. Palsson, B. O. 2020-09-27 doi:10.1101/2020.09.26.315135 Cold Spring Harbor Laboratory Press 2020-09-27 <![CDATA[ THAP1 Modulates Oligodendrocyte Maturationby Regulating ECM Degradation in Lysosomes ]]> https://biorxiv.org/content/10.1101/2020.09.27.316133v1?rss=1 Yellajoshyula, D. Pappas, S. S. Rogers, A. Choudhury, B. Cookson, M. Reed, X. Shakkottai, V. Giger, R. Dauer, W. T. 2020-09-28 doi:10.1101/2020.09.27.316133 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Boolean Implication Analysis Improves Prediction Accuracy of In Silico Gene Reporting of Retinal Cell Types ]]> https://biorxiv.org/content/10.1101/2020.09.28.317313v1?rss=1 Subramanian, R. Sahoo, D. 2020-10-01 doi:10.1101/2020.09.28.317313 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities ]]> https://biorxiv.org/content/10.1101/2020.09.28.317438v1?rss=1 Pena Montenegro, T. D. Kleindienst, S. Allen, A. E. Eren, A. M. McCrow, J. Sanchez Calderon, J. D. Arnold, J. Joye, S. B. 2020-09-28 doi:10.1101/2020.09.28.317438 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate Promiscuity ]]> https://biorxiv.org/content/10.1101/2020.10.01.322594v1?rss=1 Bielinski, V. A. Brunson, J. K. Ghosh, A. Moosburner, M. A. Garza, E. A. Fussy, Z. Bai, J. McKinnie, S. M. K. Moore, B. Allen, A. E. Almo, S. C. Dupont, C. L. 2020-10-02 doi:10.1101/2020.10.01.322594 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Modulating the Blood-Brain Barrier by Light Stimulation of Molecular-Targeted Nanoparticles ]]> https://biorxiv.org/content/10.1101/2020.10.05.326843v1?rss=1 Li, X. Vemireddy, V. Cai, Q. Xiong, H. Kang, P. Li, X. Giannotta, M. Hayenga, H. Pan, E. Sirsi, S. Mateo, C. Kleinfeld, D. Greene, C. Campbell, M. Dejana, E. Bachoo, R. Qin, Z. 2020-10-07 doi:10.1101/2020.10.05.326843 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors ]]> https://biorxiv.org/content/10.1101/2020.10.06.323634v1?rss=1 Mor, M. Werbner, M. Alter, J. Safra, M. Chomsky, E. Hada-Neeman, S. Polonsky, K. Nowell, C. Clark, A. Roitburd-Berman, A. Ben-Shalom, N. Navon, M. Rafael, D. Sharim, H. Kiner, E. Griffis, E. Gershoni, J. M. Kobiler, O. Leibel, S. L. Zimhony, O. Carlin, A. F. Yaari, G. Dassau, M. Gal-Tanamy, M. Hagin, D. Croker, B. A. Freund, N. 2020-10-06 doi:10.1101/2020.10.06.323634 Cold Spring Harbor Laboratory Press 2020-10-06 <![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[ FARCI: Fast and Robust Connectome Inference ]]> https://biorxiv.org/content/10.1101/2020.10.07.330175v1?rss=1 Meamardoost, S. Bhattacharya, M. Hwang, E. Komiyama, T. Mewes, C. K. Wang, L. Zhang, Y. Gunawan, R. 2020-10-08 doi:10.1101/2020.10.07.330175 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Thousands of previously unknown phages discovered in whole-community human gut metagenomes ]]> https://biorxiv.org/content/10.1101/2020.10.07.330464v1?rss=1 Benler, S. Yutin, N. Antipov, D. Raykov, M. Shmakov, S. A. Gussow, A. B. Pevzner, P. A. Koonin, E. V. 2020-10-07 doi:10.1101/2020.10.07.330464 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Neural network dynamics underlying gamma synchronization deficits in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.10.07.330498v1?rss=1 Koshiyama, D. Miyakoshi, M. Joshi, Y. Molina, J. Tanaka-Koshiyama, K. Sprock, J. Braff, D. Swerdlow, N. Light, G. 2020-10-09 doi:10.1101/2020.10.07.330498 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Intercellular telomere transfer extends T cell lifespan ]]> https://biorxiv.org/content/10.1101/2020.10.09.331918v1?rss=1 Vaz, B. Vuotto, C. Valvo, S. D'Ambra, C. Esposito, F. M. Chiurchiu, V. Devine, O. Sanchez, M. Borsellino, G. Gilroy, D. Akbar, A. Dustin, M. Karin, M. Lanna, A. 2020-10-09 doi:10.1101/2020.10.09.331918 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP ]]> https://biorxiv.org/content/10.1101/2020.10.11.335273v1?rss=1 Sahin, M. Wong, W. Zhan, Y. Van Deynze, K. Koche, R. Leslie, C. S. 2020-10-11 doi:10.1101/2020.10.11.335273 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ Expansion of gamma-butyrolactone signaling molecule biosynthesis to phosphotriester natural products ]]> https://biorxiv.org/content/10.1101/2020.10.11.335315v1?rss=1 Kudo, Y. Awakawa, T. Du, Y.-L. Jordan, P. A. Creamer, K. E. Jensen, P. R. Linington, R. G. Ryan, K. S. Moore, B. S. 2020-10-11 doi:10.1101/2020.10.11.335315 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ ELOVL2 is required for robust visual function in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.10.13.336974v1?rss=1 Dasyani, M. Gao, F. Xu, Q. Van Fossan, D. Zhang, E. Pinto, A. F. M. Saghatelian, A. Skowronska-Krawczyk, D. Chao, D. L. 2020-10-13 doi:10.1101/2020.10.13.336974 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling ]]> https://biorxiv.org/content/10.1101/2020.10.14.340349v1?rss=1 Scott, K. Fraley, S. Rangamani, P. 2020-10-15 doi:10.1101/2020.10.14.340349 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Microbiome signatures in a fast and slow progressing gastric cancer murine model and their contribution to gastric carcinogenesis ]]> https://biorxiv.org/content/10.1101/2020.10.15.341701v1?rss=1 Bali, P. Coker, J. Pope, I. L. Zengler, K. Obonyo, M. 2020-10-15 doi:10.1101/2020.10.15.341701 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signaling-molecule diversity ]]> https://biorxiv.org/content/10.1101/2020.10.16.342204v1?rss=1 Creamer, K. E. Kudo, Y. Moore, B. S. Jensen, P. R. 2020-10-16 doi:10.1101/2020.10.16.342204 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Multivariate genomic analysis of 1.5 million people identifies genes related to addiction, antisocial behavior, and health ]]> https://biorxiv.org/content/10.1101/2020.10.16.342501v1?rss=1 Karlsson Linner, R. Mallard, T. T. Barr, P. B. Sanchez-Roige, S. Madole, J. W. Driver, M. N. Poore, H. E. Grotzinger, A. D. Tielbeek, J. J. Johnson, E. C. Liu, M. Zhou, H. Kember, R. Pasman, J. A. Verweij, K. J. H. Liu, D. Vrieze, S. Kranzler, H. Gelernter, J. Mullan Harris, K. Tucker-Drob, E. M. Waldman, I. D. Palmer, A. A. Harden, K. P. Koellinger, P. D. Dick, D. M. 2020-10-16 doi:10.1101/2020.10.16.342501 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.10.17.344002v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@1d1507aorg.highwire.dtl.DTLVardef@faa17forg.highwire.dtl.DTLVardef@80ceb1org.highwire.dtl.DTLVardef@81d61c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHuman lung organoids with mixed proximodistal epithelia are created C_LIO_LIProximal airway cells are critical for viral infectivity C_LIO_LIDistal alveolar cells are important for emulating host response C_LIO_LIBoth are required for the overzealous response in severe COVID-19 C_LI IN BRIEFAn integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19. ]]> Tindle, C. Fuller, M. Fonseca, A. Taheri, S. Ibeawuchi, S.-R. Beutler, N. Claire, A. Castillo, V. Hernandez, M. Russo, H. Duran, J. Crotty Alexander, L. E. Tipps, A. Lin, G. Thistlethwaite, P. A. Chattopadhyay, R. Rogers, T. F. Sahoo, D. Ghosh, P. Das, S. 2020-10-18 doi:10.1101/2020.10.17.344002 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Real-Time Observation of Structure and Dynamics during the Liquid-to-Solid Transition of FUS LC ]]> https://biorxiv.org/content/10.1101/2020.10.19.345710v1?rss=1 Berkeley, R. F. Kashefi, M. Debelouchina, G. T. 2020-10-19 doi:10.1101/2020.10.19.345710 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Cyclic-di-GMP induces STING-dependent ILC2 to ILC1 shift during innate type 2 lung inflammation ]]> https://biorxiv.org/content/10.1101/2020.10.19.345850v1?rss=1 Cavagnero, K. J. Doherty, T. A. Badrani, J. H. Naji, L. H. Lacasa, L. D. Strohm, A. N. Amadeo, M. B. Leng, A. S. 2020-10-19 doi:10.1101/2020.10.19.345850 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Circadian benefits of exercise training reflect metabolic and structural flexibility ]]> https://biorxiv.org/content/10.1101/2020.10.19.346015v1?rss=1 Duglan, D. Casanova Vallve, N. Vaughan, M. E. Handzlik, M. K. Fan, W. Yu, R. Liddle, C. Downes, M. Chan, A. B. Pariollaud, M. Afetian, M. E. Metallo, C. Evans, R. Lamia, K. A. 2020-10-21 doi:10.1101/2020.10.19.346015 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis ]]> https://biorxiv.org/content/10.1101/2020.10.20.347138v1?rss=1 Gong, S. Kirmizialtin, S. Chang, A. Mayfield, J. E. Zhang, Y. Johnson, K. A. 2020-10-20 doi:10.1101/2020.10.20.347138 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Evaluation of pigmentation gene knock-outs by CRISPR as potential targets for the genetic engineering of Culex quinquefasciatus ]]> https://biorxiv.org/content/10.1101/2020.10.21.349704v1?rss=1 Feng, X. Kambic, L. Nishimoto, J. H. Reed, F. A. Denton, J. A. Sutton, J. T. Gantz, V. M. 2020-10-22 doi:10.1101/2020.10.21.349704 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Multivariate genome-wide association study identifies 1735 unique genetic loci associated with cortical morphology. ]]> https://biorxiv.org/content/10.1101/2020.10.22.350298v1?rss=1 Shadrin, A. A. Kaufmann, T. van der Meer, D. Palmer, C. E. Makowski, C. Loughnan, R. J. Jernigan, T. L. Seibert, T. M. Hagler, D. J. Smeland, O. B. Chu, Y. Lin, A. Cheng, W. Hindley, G. Thompson, W. K. Fan, C. C. Holland, D. Westlye, L. T. Frei, O. Andreassen, O. A. Dale, A. M. 2020-10-23 doi:10.1101/2020.10.22.350298 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Distributed Phase Oscillatory Excitation Efficiently Produces Attractors Using Spike Timing Dependent Plasticity ]]> https://biorxiv.org/content/10.1101/2020.10.22.351379v1?rss=1 Wong, E. C. 2020-10-23 doi:10.1101/2020.10.22.351379 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA targets sites promotes commitment of mammalian nephron progenitor cells ]]> https://biorxiv.org/content/10.1101/2020.10.26.356410v1?rss=1 Guo, Q. Kim, A. D. Li, B. Ransick, A. Bugacov, H. Chen, X. Lindstrom, N. O. Brown, A. Oxburgh, L. Ren, B. McMahon, A. P. 2020-10-27 doi:10.1101/2020.10.26.356410 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Using a betting game to reveal the rich nature of visual working memories ]]> https://biorxiv.org/content/10.1101/2020.10.28.357442v1?rss=1 Jabar, S. B. Sreenivasan, K. K. Lentzou, S. Kanabar, A. Brady, T. F. Fougnie, D. 2020-10-30 doi:10.1101/2020.10.28.357442 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Neural basis of opioid-induced respiratory depression and its rescue ]]> https://biorxiv.org/content/10.1101/2020.10.28.359893v1?rss=1 Liu, S. Kim, D.-I. Oh, T. G. Pao, G. M. Kim, J. H. Palmiter, R. D. Banghart, M. M. Lee, K.-F. Evans, R. M. Han, S. 2020-10-29 doi:10.1101/2020.10.28.359893 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Optogenetic interrogation of the role of striatal patches in habit formation and inhibition of striatal dopamine ]]> https://biorxiv.org/content/10.1101/2020.10.29.359265v1?rss=1 Nadel, J. A. Pawelko, S. S. Scott, J. R. McLaughlin, R. Fox, M. Hollon, N. G. Howard, C. D. 2020-10-29 doi:10.1101/2020.10.29.359265 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Infant functional connectivity fingerprints predict long-term language and pre-literacy outcomes ]]> https://biorxiv.org/content/10.1101/2020.10.29.360081v1?rss=1 Yu, X. Ferradal, S. Sliva, D. D. Dunstan, J. Carruthers, C. Sanfilippo, J. Zuk, J. Zollei, L. Boyd, E. Gagoski, B. Grant, E. P. Gaab, N. 2020-10-29 doi:10.1101/2020.10.29.360081 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Unsupervised Learning of Brain State Dynamics during Emotion Imagery using High-Density EEG ]]> https://biorxiv.org/content/10.1101/2020.10.29.361394v1?rss=1 Hsu, S.-H. Lin, Y. Onton, J. Jung, T.-P. Makeig, S. 2020-10-30 doi:10.1101/2020.10.29.361394 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing ]]> https://biorxiv.org/content/10.1101/2020.10.31.337758v1?rss=1 Gupta, A. Peng, S. Leung, C. Y. Borin, J. M. Weitz, J. Meyer, J. R. 2020-11-01 doi:10.1101/2020.10.31.337758 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance ]]> https://biorxiv.org/content/10.1101/2020.11.02.365361v1?rss=1 Borin, J. M. Avrani, S. Barrick, J. E. Petrie, K. L. Meyer, J. R. 2020-11-02 doi:10.1101/2020.11.02.365361 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ With Childhood Hemispherectomy, One Hemisphere Can Support--But is Suboptimal for--Word and Face Recognition ]]> https://biorxiv.org/content/10.1101/2020.11.06.371823v1?rss=1 Granovetter, M. C. Ettensohn, L. Behrmann, M. 2020-11-08 doi:10.1101/2020.11.06.371823 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ A plant lipocalin is required for retinal-mediated de novo root organogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.09.375444v1?rss=1 Dickinson, A. J. Zhang, J. Luciano, M. Schnermann, M. Dinneny, J. R. Benfey, P. N. 2020-11-10 doi:10.1101/2020.11.09.375444 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ A scale-free, fully connected global transition network underlies known microbiome diversity ]]> https://biorxiv.org/content/10.1101/2020.11.11.376103v1?rss=1 Jing, G. Zhang, Y. Liu, L. Wang, Z. Sun, Z. Knight, R. Su, X. Xu, J. 2020-11-11 doi:10.1101/2020.11.11.376103 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Polygenic transcriptome risk scores improve portability of polygenic risk scores across ancestries ]]> https://biorxiv.org/content/10.1101/2020.11.12.373647v1?rss=1 Liang, Y. Pividori, M. Manichaikul, A. Palmer, A. A. Cox, N. J. Wheeler, H. E. Im, H. K. 2020-11-13 doi:10.1101/2020.11.12.373647 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ MUNIn (Multiple cell-type UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple cell types ]]> https://biorxiv.org/content/10.1101/2020.11.12.380782v1?rss=1 Liu, W. Abnousi, A. Zhang, Q. Li, Y. Hu, M. Yang, Y. 2020-11-13 doi:10.1101/2020.11.12.380782 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Lipid-specific protein oligomerization is regulated by two interfaces in Marburg virus matrix protein VP40 ]]> https://biorxiv.org/content/10.1101/2020.11.13.381350v1?rss=1 Amiar, S. Husby, M. L. Wijesinghe, K. J. Angel, S. Bhattarai, N. Gerstman, B. S. Chapagain, P. P. Li, S. Stahelin, R. V. 2020-11-14 doi:10.1101/2020.11.13.381350 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ The ant fungus garden acts as an external digestive system ]]> https://biorxiv.org/content/10.1101/2020.11.18.389361v1?rss=1 Caraballo-Rodriguez, A. M. Pucket, S. P. Kyle, K. E. Petras, D. da Silva, R. R. Nothias, L.-F. Ernst, M. van der Hooft, J. J. J. Tripathi, A. Wang, M. Balunas, M. J. Klassen, J. L. Dorrestein, P. C. 2020-11-20 doi:10.1101/2020.11.18.389361 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Genetic and pharmacological manipulations of glyoxalase 1 mediate ethanol withdrawal seizure susceptibility in mice ]]> https://biorxiv.org/content/10.1101/2020.11.19.389452v1?rss=1 Barkley-Levenson, A. M. Lee, A. Palmer, A. A. 2020-11-19 doi:10.1101/2020.11.19.389452 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ EcDNA hubs drive cooperative intermolecular oncogene expression ]]> https://biorxiv.org/content/10.1101/2020.11.19.390278v1?rss=1 Hung, K. L. Yost, K. E. Xie, L. Wu, S. Lange, J. T. Duffy, C. V. Kraft, K. Tang, J. Shi, Q. Rose, J. C. Corces, M. R. Granja, J. M. Li, R. Rajkumar, U. Tjian, R. Bafna, V. Mischel, P. S. Liu, Z. Chang, H. Y. 2020-11-20 doi:10.1101/2020.11.19.390278 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A Cre-dependent CRISPR/dCas9 activation system for gene expression regulation in neurons ]]> https://biorxiv.org/content/10.1101/2020.11.20.391987v1?rss=1 Carullo, N. V. N. Revanna, J. S. Tuscher, J. J. Bauman, A. J. Day, J. J. 2020-11-20 doi:10.1101/2020.11.20.391987 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Timing the SARS-CoV-2 Index Case in Hubei Province ]]> https://biorxiv.org/content/10.1101/2020.11.20.392126v1?rss=1 Pekar, J. Worobey, M. Moshiri, N. Scheffler, K. Wertheim, J. O. 2020-11-24 doi:10.1101/2020.11.20.392126 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Inhibition of Biofilm Formation by Modified Oxylipins from the Shipworm Symbiont Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2020.11.22.393314v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@145f68org.highwire.dtl.DTLVardef@183df5borg.highwire.dtl.DTLVardef@bcdb6corg.highwire.dtl.DTLVardef@e9b9e3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lacerna, N. M. Ramones, C. M. V. Robes, J. M. D. Picart, M. R. D. Tun, J. O. Miller, B. W. Haygood, M. G. Schmidt, E. W. Salvador-Reyes, L. Concepcion, G. P. 2020-11-22 doi:10.1101/2020.11.22.393314 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome ]]> https://biorxiv.org/content/10.1101/2020.11.22.393546v1?rss=1 Markaki, Y. Chong, J. G. Luong, C. Tan, S. Y. X. Wang, Y. Jacobson, E. C. Maestrini, D. Dror, I. Mistry, B. A. Schoeneberg, J. Banerjee, A. Guttman, M. Chou, T. Plath, K. 2020-11-23 doi:10.1101/2020.11.22.393546 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ The anti-inflammatory peptide Catestatin blocks chemotaxis ]]> https://biorxiv.org/content/10.1101/2020.11.23.393934v1?rss=1 Muntjewerff, E. M. Parv, K. Mahata, S. K. Phillipson, M. Christoffersson, G. van den Bogaart, G. 2020-11-24 doi:10.1101/2020.11.23.393934 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ The Drosophila Baramicin polypeptide gene protects against fungal infection ]]> https://biorxiv.org/content/10.1101/2020.11.23.394148v1?rss=1 Hanson, M. A. Cohen, L. B. Marra, A. Iatsenko, I. Wasserman, S. A. Lemaitre, B. 2020-11-23 doi:10.1101/2020.11.23.394148 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Competition-based screening secures the evolutionary stability of a defensive microbiome ]]> https://biorxiv.org/content/10.1101/2020.11.24.395384v1?rss=1 Worsley, S. F. Innocent, T. M. Holmes, N. A. Al-Bassam, M. M. Wilkinson, B. Murrell, J. C. Boomsma, J. J. Yu, D. W. Hutchings, M. I. 2020-11-24 doi:10.1101/2020.11.24.395384 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Non-linear manifold learning in fMRI uncovers a low-dimensional space of brain dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.25.398693v1?rss=1 Gao, S. Mishne, G. Scheinost, D. 2020-11-27 doi:10.1101/2020.11.25.398693 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Augmenter of Liver Regeneration Regulates Cellular Iron by Modulating Mitochondrial Transport of ATP-Binding Cassette B8 ]]> https://biorxiv.org/content/10.1101/2020.11.30.403295v1?rss=1 Ardehali, H. Chang, H.-C. Shapiro, J. S. Jiang, X. Senyei, G. Sato, T. Sawicki, K. 2020-11-30 doi:10.1101/2020.11.30.403295 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ 3D Genome Contributes to Protein-Protein Interactome ]]> https://biorxiv.org/content/10.1101/2020.11.30.404517v1?rss=1 Shi, Y. Cao, S. Zhang, M. Su, X. Guo, Z. Wang, J. Liu, T. Shi, H. He, G. 2020-12-01 doi:10.1101/2020.11.30.404517 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. ]]> https://biorxiv.org/content/10.1101/2020.12.01.404483v1?rss=1 Ho, J. S. Y. Mok, B. W.-Y. Campisi, L. Jordan, T. Yildiz, S. Parameswaran, S. Wayman, J. A. Gaudreault, N. N. Meekins, D. A. Indran, S. V. Morozov, I. Trujillo, J. D. Fstkchyan, Y. S. Rathnasinghe, R. Zhu, Z. Zheng, S. Zhao, N. White, K. Ray-Jones, H. Malysheva, V. Thiecke, M. J. Lau, S.-Y. Liu, H. Zhang, A. J. Lee, A. C.-Y. Liu, W.-C. Aydillo, T. Melo, B. S. Guccione, E. Sebra, R. Shum, E. Bakker, J. Kaufman, D. A. Moreira, A. Carossino, M. Balasuriya, U. B. R. Byun, M. Miraldi, E. R. Albrecht, R. A. Schotsaert, M. Garcia-Sastre, A. Chanda, S. K. Jeya 2020-12-01 doi:10.1101/2020.12.01.404483 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ AlphaTracker: A Multi-Animal Tracking and Behavioral Analysis Tool ]]> https://biorxiv.org/content/10.1101/2020.12.04.405159v1?rss=1 Chen, Z. Zhang, R. Zhang, Y. E. Fang, H.-S. Zhou, H. Rock, R. R. Bal, A. Padilla-Coreano, N. Keyes, L. Tye, K. M. Lu, C. 2020-12-06 doi:10.1101/2020.12.04.405159 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae ]]> https://biorxiv.org/content/10.1101/2020.12.04.411496v1?rss=1 Kramer, N. Tamir, R. Ben-Zvi, O. Jacques, S. L. Loya, Y. Wangpraseurt, D. 2020-12-06 doi:10.1101/2020.12.04.411496 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Is it all in our head? When subjective beliefs about receiving an intervention are better predictors of experimental results than the intervention itself ]]> https://biorxiv.org/content/10.1101/2020.12.06.411850v1?rss=1 Fassi, L. Cohen Kadosh, R. 2020-12-07 doi:10.1101/2020.12.06.411850 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Universal Spectrum Identifier for mass spectra ]]> https://biorxiv.org/content/10.1101/2020.12.07.415539v1?rss=1 Deutsch, E. W. Perez-Riverol, Y. Carver, J. Kawano, S. Mendoza, L. Van Den Bossche, T. Gabriels, R. Binz, P.-A. Pullman, B. Sun, Z. Shofstahl, J. Bittremieux, W. Mak, T. Klein, J. Zhu, Y. Lam, H. Vizcaino, J. A. Bandeira, N. 2020-12-09 doi:10.1101/2020.12.07.415539 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Mechanisms for Communicating in a Marmoset "Cocktail Party" ]]> https://biorxiv.org/content/10.1101/2020.12.08.416693v1?rss=1 Jovanovic, V. Miller, C. T. 2020-12-09 doi:10.1101/2020.12.08.416693 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[ Assembling Long Accurate Reads Using de Bruijn Graphs ]]> https://biorxiv.org/content/10.1101/2020.12.10.420448v1?rss=1 Bankevich, A. Bzikadze, A. V. Kolmogorov, M. Pevzner, P. 2020-12-11 doi:10.1101/2020.12.10.420448 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor ]]> https://biorxiv.org/content/10.1101/2020.12.13.422570v1?rss=1 Islam, S. M. A. Wu, Y. Diaz-Gay, M. Bergstrom, E. N. He, Y. Barnes, M. Vella, M. Wang, J. Teague, J. W. Clapham, P. Moody, S. Senkin, S. Li, Y. R. Riva, L. Zhang, T. Gruber, A. J. Vangara, R. Steele, C. D. Otlu, B. Khandekar, A. Abbasi, A. Humphreys, L. Syulyukina, N. Brady, S. W. Alexandrov, B. S. Pillay, N. Zhang, J. Adams, D. J. Marticorena, I. Wedge, D. C. Landi, M. T. Brennan, P. Stratton, M. R. Rozen, S. G. Alexandrov, L. B. 2020-12-13 doi:10.1101/2020.12.13.422570 Cold Spring Harbor Laboratory Press 2020-12-13 <![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 CRISPR endonuclease gene drive reveals two distinct mechanisms of inheritance bias ]]> https://biorxiv.org/content/10.1101/2020.12.15.421271v1?rss=1 Verkuijl, S. A. N. Gonzalez, E. Ang, J. X. D. Li, M. Kandul, N. P. Anderson, M. Akbari, O. S. Bonsall, M. Alphey, L. 2020-12-15 doi:10.1101/2020.12.15.421271 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Wild-type FUS corrects ALS-like disease induced by cytoplasmic mutant FUS through autoregulation. ]]> https://biorxiv.org/content/10.1101/2020.12.16.423060v1?rss=1 Sanjuan-Ruiz, I. Govea-Perez, N. McAlonis-Downes, M. Dieterle, S. Megat, S. Dirrig-Grosch, S. Picchiarelli, G. Piol, D. Zhu, Q. Myers, B. D. Lee, C.-Z. Cleveland, D. W. Lagier-Tourenne, C. Da Cruz, S. Dupuis, L. 2020-12-16 doi:10.1101/2020.12.16.423060 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Alternative splicing of GluN1 gates glycine-primed internalization of NMDA receptors ]]> https://biorxiv.org/content/10.1101/2020.12.18.423454v1?rss=1 Li, H. Rajani, V. Han, L. Chung, D. Cooke, J. Sengar, A. Salter, M. 2020-12-20 doi:10.1101/2020.12.18.423454 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Complex evolutionary dynamics govern the diversity and distribution of biosynthetic gene clusters and their encoded specialized metabolites ]]> https://biorxiv.org/content/10.1101/2020.12.19.423547v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@aef190org.highwire.dtl.DTLVardef@17536baorg.highwire.dtl.DTLVardef@5bf336org.highwire.dtl.DTLVardef@bc7d2f_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TEXTBOXSIGNIFICANCENatural products are traditionally exploited for their pharmaceutical potential; yet what is often overlooked is that the evolution of the biosynthetic gene clusters (BGCs) encoding these small molecules likely affects the diversification of the produced compounds and implicitly has an impact on the compounds activities and ecological functions. And while the prevailing dogma in natural product research attributes frequent and widespread horizontal gene transfer (HGT) as an integral driver of BGC evolution, we find that the majority of BGC diversity derives from processes of vertical descent, with HGT events being rare. This understanding can facilitate informed biosynthetic predictions to identify novel natural products, in addition to uncovering how these specialized metabolites contribute to the environmental distribution of microbes. C_TEXTBOX ]]> Chase, A. B. Sweeney, D. Muskat, M. N. Guillen-Matus, D. Jensen, P. R. 2020-12-20 doi:10.1101/2020.12.19.423547 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ The ENIGMA Toolbox: Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets ]]> https://biorxiv.org/content/10.1101/2020.12.21.423838v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@183a3f3org.highwire.dtl.DTLVardef@180d368org.highwire.dtl.DTLVardef@b752a3org.highwire.dtl.DTLVardef@1928c53_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lariviere, S. Paquola, C. Park, B.-y. Royer, J. Wang, Y. Benkarim, O. Vos de Wael, R. Valk, S. L. Thomopoulos, S. I. Kirschner, M. ENIGMA Consortium, Sisodiya, S. McDonald, C. Thompson, P. M. Bernhardt, B. 2020-12-22 doi:10.1101/2020.12.21.423838 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Selective Targeting of Ras Mutant Cancers via a New Small Molecule ]]> https://biorxiv.org/content/10.1101/2020.12.23.423300v1?rss=1 Tolani, B. Celli, A. Yao, Y. Tan, Y. Z. Fetter, R. Liem, C. R. de Smith, A. J. Vasanthakumar, T. Bisignano, P. Seiple, I. B. Rubinstein, J. L. Jost, M. Weissman, J. S. 2020-12-23 doi:10.1101/2020.12.23.423300 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Retracing the Evolutionary Trajectory of Adenine Base Editors Using Theoretical Approaches ]]> https://biorxiv.org/content/10.1101/2020.12.24.424366v1?rss=1 Rallapalli, K. L. Ranzau, B. L. Ganapathy, K. R. Komor, A. C. Lab, P. 2020-12-24 doi:10.1101/2020.12.24.424366 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ MHC-II constrains the natural neutralizing antibody response to the SARS-CoV-2 spike RBM in humans ]]> https://biorxiv.org/content/10.1101/2020.12.26.424449v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@d332ccorg.highwire.dtl.DTLVardef@1ac1a95org.highwire.dtl.DTLVardef@5688dorg.highwire.dtl.DTLVardef@1133d83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Castro, A. Ozturk, K. Zanetti, M. Carter, H. 2020-12-28 doi:10.1101/2020.12.26.424449 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma ]]> https://biorxiv.org/content/10.1101/2020.12.28.424451v1?rss=1 Andreano, E. Piccini, G. Licastro, D. Casalino, L. Johnson, N. V. Paciello, I. Dal Monego, S. Pantano, E. Manganaro, N. Manenti, A. Manna, R. Casa, E. Hyseni, I. Benincasa, L. Montomoli, E. Amaro, R. E. McLellan, J. S. Rappuoli, R. 2020-12-28 doi:10.1101/2020.12.28.424451 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Heterologous expression of methylxanthine synthesis enzymes in mammalian cells and their use as reporter proteins ]]> https://biorxiv.org/content/10.1101/2020.12.29.424659v1?rss=1 Cisneros, B. Devaraj, N. 2020-12-29 doi:10.1101/2020.12.29.424659 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ The structural basis for Ulp2 recruitment to the kinetochore ]]> https://biorxiv.org/content/10.1101/2020.12.30.424835v1?rss=1 Quan, Y. Hinshaw, S. M. Wang, P.-C. Harrison, S. C. Zhou, H. 2021-01-01 doi:10.1101/2020.12.30.424835 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing ]]> https://biorxiv.org/content/10.1101/2020.12.31.425022v1?rss=1 Rustici, G. Williams, E. Barzine, M. Brazma, A. Bumgarner, R. Chierici, M. Furlanello, C. Greger, L. Jurman, G. Miller, M. Ouellette, B. F. F. Quackenbush, J. Reich, M. Stoeckert, C. J. Taylor, R. C. Trutane, S. C. Weller, J. Wilhelm, B. Winegarden, N. 2021-01-03 doi:10.1101/2020.12.31.425022 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Histone H3K4me3 and H3K9me3 are super over-methylated in soft tissue sarcoma compared to normal muscle in patient-derived xenograft (PDX) mouse models: an indicator of cancer methionine addiction ]]> https://biorxiv.org/content/10.1101/2021.01.01.425040v1?rss=1 Aoki, Y. Hoffman, R. M. Nishida, K. Endo, I. Bouvet, M. Tashiro, Y. Inubushi, S. Hamada, K. Tome, Y. Yamamoto, J. 2021-01-05 doi:10.1101/2021.01.01.425040 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Comberons from single cell transcriptomics in endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.04.425317v1?rss=1 Domanskyi, S. Hakansson, A. Meng, M. Graff Zivin, J. S. Piermarocchi, C. Paternostro, G. Ferrara, N. 2021-01-05 doi:10.1101/2021.01.04.425317 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Simultaneous readout of multiple FRET pairs using photochromism ]]> https://biorxiv.org/content/10.1101/2021.01.06.425528v1?rss=1 Roebroek, T. Vandenberg, W. Sipieter, F. Hugelier, S. Stove, C. Zhang, J. Dedecker, P. 2021-01-06 doi:10.1101/2021.01.06.425528 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Microglial Neuropilin-1 trans-regulates oligodendrocyte expansion during development and remyelination ]]> https://biorxiv.org/content/10.1101/2021.01.07.425796v1?rss=1 Sherafat, A. Pfeiffer, F. Reiss, A. Wood, W. M. Nishiyama, A. 2021-01-07 doi:10.1101/2021.01.07.425796 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Unveiling unexpected complexity and multipotentiality of early heart fields ]]> https://biorxiv.org/content/10.1101/2021.01.08.425950v1?rss=1 Zhang, Q. Carlin, D. Zhu, F. Cattaneo, P. Ideker, T. Evans, S. Bloomekatz, J. Chi, N. C. 2021-01-09 doi:10.1101/2021.01.08.425950 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Interhemispheric connectivity endures across species: An allometric expose on the corpuscallosum ]]> https://biorxiv.org/content/10.1101/2021.01.10.426155v1?rss=1 Cipollini, B. Cottrell, G. W. 2021-01-11 doi:10.1101/2021.01.10.426155 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence ]]> https://biorxiv.org/content/10.1101/2021.01.11.426172v1?rss=1 Molina-Santiago, C. Vela-Corcia, D. Petras, D. Diaz-Martinez, L. Perez-Lorente, A. Sopena-Torres, S. Pearson, J. R. Caraballo-Rodriguez, A. M. Dorrestein, P. de Vicente, A. romero, d. 2021-01-11 doi:10.1101/2021.01.11.426172 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs ]]> https://biorxiv.org/content/10.1101/2021.01.12.426286v1?rss=1 Katrekar, D. Yen, J. Xiang, Y. Saha, A. Meluzzi, D. Savva, Y. Mali, P. 2021-01-13 doi:10.1101/2021.01.12.426286 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution ]]> https://biorxiv.org/content/10.1101/2021.01.12.426373v1?rss=1 Vrancken, B. Dellicour, S. Smith, D. M. Chaillon, A. 2021-01-13 doi:10.1101/2021.01.12.426373 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision ]]> https://biorxiv.org/content/10.1101/2021.01.13.426552v1?rss=1 Yu, L. Myers, G. Ku, C.-J. Schneider, E. Wang, Y. Singh, S. Jearawiriyapaisarn, N. White, A. Moriguchi, T. Khoriaty, R. Yamamoto, M. Rosenfeld, M. G. Pedron, J. Bushweller, J. H. Lim, K.-C. Engel, J. D. 2021-01-14 doi:10.1101/2021.01.13.426552 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ The genetic architecture of human cortical folding ]]> https://biorxiv.org/content/10.1101/2021.01.13.426555v1?rss=1 van der Meer, D. Kaufmann, T. Shadrin, A. A. Makowski, C. Frei, O. Roelfs, D. Monereo Sanchez, J. Linden, D. E. Rokicki, J. de Leeuw, C. Thompson, W. K. Loughnan, R. J. Fan, C. C. Thompson, P. M. Westlye, L. T. Andreassen, O. A. Dale, A. M. 2021-01-13 doi:10.1101/2021.01.13.426555 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion ]]> https://biorxiv.org/content/10.1101/2021.01.13.426627v1?rss=1 Schalk, F. Gostincar, C. Kreuzenbeck, N. B. Schantz-Conlon, B. Sommerwerk, E. Rabe, P. Burkhardt, I. Krüger, T. Kniemeyer, O. Brakhage, A. A. Gunde-Cimerman, N. De Beer, W. Z. Dickschat, J. S. Poulsen, M. Beemelmanns, C. 2021-01-15 doi:10.1101/2021.01.13.426627 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Dynamic molecular epidemiology reveals lineage-associated single-nucleotide variants that alter RNA structure in Chikungunya virus ]]> https://biorxiv.org/content/10.1101/2021.01.17.427002v1?rss=1 Spicher, T. Delitz, M. de Bernardi Schneider, A. Wolfinger, M. T. 2021-01-17 doi:10.1101/2021.01.17.427002 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Histone Deacetylase 2 (HDAC2) influences maturation and mitochondrial dynamics in human induced pluripotent stem cell derived neurons. ]]> https://biorxiv.org/content/10.1101/2021.01.18.427156v1?rss=1 Frankowski, H. Yeboah, F. Berry, B. Kinoshita, C. Lee, M. Evitts, K. Davis, J. Kinoshita, Y. Morrison, R. S. Young, J. E. 2021-01-18 doi:10.1101/2021.01.18.427156 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Generation and characterization of a laforin nanobody inhibitor ]]> https://biorxiv.org/content/10.1101/2021.01.20.426524v1?rss=1 Simmons, Z. R. Sharma, S. Wayne, J. Li, S. Vander Kooi, C. W. Gentry, M. S. 2021-01-20 doi:10.1101/2021.01.20.426524 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Regulation by Progestins, Corticosteroids and RU486 of Activation of Elephant Shark and Human Progesterone Receptors: An Evolutionary Perspective ]]> https://biorxiv.org/content/10.1101/2021.01.20.427507v1?rss=1 Lin, X. Takagi, W. T. Hyodo, S. Ijiri, S. Katsu, Y. K. Baker, M. E. 2021-01-21 doi:10.1101/2021.01.20.427507 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ DEPP: Deep Learning Enables Extending Species Trees using Single Genes ]]> https://biorxiv.org/content/10.1101/2021.01.22.427808v1?rss=1 Jiang, Y. Balaban, M. Zhu, Q. Mirarab, S. 2021-01-24 doi:10.1101/2021.01.22.427808 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology ]]> https://biorxiv.org/content/10.1101/2021.01.25.428167v1?rss=1 Terrey, M. Adamson, S. I. Chuang, J. H. Ackerman, S. L. 2021-01-25 doi:10.1101/2021.01.25.428167 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Discovery of an IKK2 Site that Allosterically Controls Its Activation ]]> https://biorxiv.org/content/10.1101/2021.01.27.428502v1?rss=1 Hotchkiss, S. J. Mulero, M. C. Chan, G. J. Biswas, T. Polley, S. Ohn, C. Konduri, S. Demir, O. Amaro, R. E. Ghosh, G. 2021-01-27 doi:10.1101/2021.01.27.428502 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT ]]> https://biorxiv.org/content/10.1101/2021.01.28.428636v1?rss=1 Sarmashghi, S. Balaban, M. Rachtman, E. Touri, B. Mirarab, S. Bafna, V. 2021-01-29 doi:10.1101/2021.01.28.428636 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Somatic mutational profiles and germline polygenic risk scores in human cancer ]]> https://biorxiv.org/content/10.1101/2021.01.28.428663v1?rss=1 Liu, Y. Gusev, A. Heng, Y. J. Alexandrov, L. B. Kraft, P. 2021-01-30 doi:10.1101/2021.01.28.428663 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Non-Canonical Projections from Ventral CA1 and Subicular Complex to CA3 Augments the Feedforward Hippocampal Trisynaptic Pathway ]]> https://biorxiv.org/content/10.1101/2021.02.01.429124v1?rss=1 Lin, X. Amarlraj, M. Blanton, C. Avila, B. Todd, H. Nitz, D. Xu, X. 2021-02-01 doi:10.1101/2021.02.01.429124 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ A modular platform for engineering function ofnatural and synthetic biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2021.02.03.429226v1?rss=1 Lasker, K. Boeynaems, S. Lam, V. Stainton, E. Jacquemyn, M. Daelemans, D. Villa, E. Holehouse, A. S. Gitler, A. Shapiro, L. 2021-02-03 doi:10.1101/2021.02.03.429226 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Pre-mutagenic and mutagenic changes imprinted on the genomes of mammalian cells after irradiation with a nail polish dryer ]]> https://biorxiv.org/content/10.1101/2021.02.03.429605v1?rss=1 A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of mammalian cells. These results have far-reaching implications in regard to public health and to preventing skin cancer due to consumer-based exposure to ultraviolet light from artificial sources. ]]> Zhivagui, M. Valenzuela, N. Yeh, Y.-Y. Dai, J. He, Y. Alexandrov, L. B. 2021-02-03 doi:10.1101/2021.02.03.429605 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ High fiber, whole foods dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids ]]> https://biorxiv.org/content/10.1101/2021.02.04.429869v1?rss=1 Oliver, A. Chase, A. B. Weihe, C. Orchanian, S. B. Riedel, S. F. Hendrickson, C. Lay, M. Massimelli Sewall, J. Martiny, J. B. Whiteson, K. 2021-02-05 doi:10.1101/2021.02.04.429869 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Large-scale tandem mass spectrum clustering using fast nearest neighbor searching ]]> https://biorxiv.org/content/10.1101/2021.02.05.429957v1?rss=1 Bittremieux, W. Laukens, K. Noble, W. S. Dorrestein, P. C. 2021-02-08 doi:10.1101/2021.02.05.429957 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ The role of IL-1 in adipose browning and muscle wasting in CKD-associated cachexia ]]> https://biorxiv.org/content/10.1101/2021.02.05.429984v1?rss=1 Cheung, W. W. Zheng, R. Hao, S. Wang, Z. Gonzalez, A. Zhou, P. Hoffman, H. M. Mak, R. H. 2021-02-07 doi:10.1101/2021.02.05.429984 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Targeting interleukin-1 for reversing fat browning and muscle wasting in infantile nephropathic cystinosis ]]> https://biorxiv.org/content/10.1101/2021.02.05.429989v1?rss=1 Cheung, W. W. Hao, S. Zheng, R. Wang, Z. Gonzalez, A. Zhou, P. Hoffman, H. M. Mak, R. H. 2021-02-07 doi:10.1101/2021.02.05.429989 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility ]]> https://biorxiv.org/content/10.1101/2021.02.05.429998v1?rss=1 Zou, J. Gopalakrishnan, S. Parker, C. C. Nicod, J. Mott, R. Cai, N. Lionikas, A. Davies, R. W. Palmer, A. A. Flint, J. 2021-02-07 doi:10.1101/2021.02.05.429998 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Methylomic alteration in peripheral blood lymphocytes of prodromal stage and first-episode Chinese Han schizophrenia patients ]]> https://biorxiv.org/content/10.1101/2021.02.07.430160v1?rss=1 Liu, Y. Lang, B. Smith, R. C. Wang, G. Wang, J. Liu, Y. Jin, H. Lyu, H. Davis, J. M. Guidotti, A. R. Zhao, J. Wu, R. 2021-02-09 doi:10.1101/2021.02.07.430160 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ A Human 3D neural assembloid model for SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.02.09.430349v1?rss=1 Gleeson, J. G. Wang, L. Sievert, D. Clark, A. E. Federman, H. Gastfriend, B. D. Shusta, E. Palecek, S. Carlin, A. Clark, A. E. 2021-02-09 doi:10.1101/2021.02.09.430349 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Catestatin regulates the colonic mucus layer in inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2021.02.09.430377v1?rss=1 Muntjewerff, E. Lutter, L. Tang, K. Kea-te Lindert, M. Fransen, J. Oldenburg, B. Mahata, S. K. van den Bogaart, G. 2021-02-10 doi:10.1101/2021.02.09.430377 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Customized de novo mutation detection for any variant calling pipeline: SynthDNM ]]> https://biorxiv.org/content/10.1101/2021.02.10.427198v1?rss=1 Lian, A. Guevara, J. Xia, K. Sebat, J. 2021-02-10 doi:10.1101/2021.02.10.427198 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Optimized CRISPR tools and site-directed transgenesis in Culex quinquefasciatus mosquitoes for gene drive development. ]]> https://biorxiv.org/content/10.1101/2021.02.10.430702v1?rss=1 Feng, X. Lopez Del Amo, V. Mameli, E. Lee, M. Bishop, A. L. Perrimon, N. Gantz, V. M. 2021-02-11 doi:10.1101/2021.02.10.430702 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Structure and mechanistic analyses of the gating mechanism of elongating ketosynthases ]]> https://biorxiv.org/content/10.1101/2021.02.13.431092v1?rss=1 Mindrebo, J. T. Chen, A. Kim, W. E. Re, R. N. Davis, T. D. Noel, J. P. Burkart, M. D. 2021-02-14 doi:10.1101/2021.02.13.431092 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape ]]> https://biorxiv.org/content/10.1101/2021.02.14.431043v1?rss=1 West, A. P. Barnes, C. O. Yang, Z. Bjorkman, P. J. 2021-02-15 doi:10.1101/2021.02.14.431043 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ The APOBEC3A deaminase drives episodic mutagenesis in cancer cells ]]> https://biorxiv.org/content/10.1101/2021.02.14.431145v1?rss=1 Petljak, M. Chu, K. Dananberg, A. Bergstrom, E. N. von Morgen, P. Alexandrov, L. Stratton, M. R. Maciejowski, J. 2021-02-14 doi:10.1101/2021.02.14.431145 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Dynamic association of IκBα to chromatin is regulated by acetylation and cleavage of histone H4 ]]> https://biorxiv.org/content/10.1101/2021.02.15.431217v1?rss=1 Espinosa, L. Bertran, J. Alvarez-Villanueva, D. Floor, M. Mulero, M. C. Vert, A. Guillen, Y. Arce, S. Batlle-Morera, L. Villa-Freixa, J. Ghosh, G. Bigas, A. Marruecos, L. 2021-02-16 doi:10.1101/2021.02.15.431217 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Nicotine-mediated recruitment of GABAergic neurons to a dopaminergic phenotype attenuates motor deficits in alpha-synuclein Parkinson's model. ]]> https://biorxiv.org/content/10.1101/2021.02.15.431290v1?rss=1 Lai, I.-C. Romoli, B. Keisler, M. Manfredsson, F. Powell, S. B. Dulcis, D. 2021-02-16 doi:10.1101/2021.02.15.431290 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing ]]> https://biorxiv.org/content/10.1101/2021.02.17.430112v1?rss=1 Ottilie, S. Luth, M. R. Hellemann, E. Goldgof, G. M. Vigil, E. Kumar, P. Cheung, A. L. Song, M. Godinez-Macias, K. P. Carolino, K. Yang, J. Lopez, G. Abraham, M. Tarsio, M. LeBlanc, E. Whitesell, L. Schenken, J. Gunawan, F. Patel, R. Smith, J. Love, M. S. Williams, R. M. McNamara, C. W. Gerwick, W. H. Ideker, T. Suzuki, Y. Wirth, D. F. Lukens, A. K. Kane, P. M. Cowen, L. E. Durrant, J. D. Winzeler, E. A. 2021-02-17 doi:10.1101/2021.02.17.430112 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Invariant Differential Expression Analysis Reveals Mechanism of Cancer Resistance to Cell Cycle Inhibitors ]]> https://biorxiv.org/content/10.1101/2021.02.17.431607v1?rss=1 Chatterjee, A. Pandey, S. Danda, R. Kumar R, R. S, M. Khetan, V. Rishi, P. S, R. Elchuri, S. V. Sahoo, D. 2021-02-17 doi:10.1101/2021.02.17.431607 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ A photoswitchable GPCR-based opsin for presynaptic silencing ]]> https://biorxiv.org/content/10.1101/2021.02.19.432008v1?rss=1 Copits, B. A. O'Neill, P. R. Gowrishankar, R. Yoo, J. J. Meshik, X. Parker, K. E. Spangler, S. M. Vasquez, A. M. Elerding, A. J. Stander, M. C. Kalyanaraman, V. Vogt, S. K. Samineni, V. K. Gautam, N. Sunahara, R. K. Gereau, R. W. Bruchas, M. R. 2021-02-20 doi:10.1101/2021.02.19.432008 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor ]]> https://biorxiv.org/content/10.1101/2021.02.22.432252v1?rss=1 Stoneham, C. A. Langer, S. De Jesus, P. Wozniak, J. Lapek, J. Deerinck, T. Thor, A. Pache, L. Chanda, S. Gonzalez, D. Ellisman, M. Guatelli, J. 2021-02-22 doi:10.1101/2021.02.22.432252 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees. ]]> https://biorxiv.org/content/10.1101/2021.02.27.433180v1?rss=1 Tarke, A. Sidney, J. Methot, N. Zhang, Y. Dan, J. M. Goodwin, B. Rubiro, P. Sutherland, A. da Silva Antunes, R. Fraizer, A. Rawlings, S. A. Smith, D. M. Peters, B. Scheuermann, R. H. Weiskopf, D. Crotty, S. Grifoni, A. Sette, A. 2021-03-01 doi:10.1101/2021.02.27.433180 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques ]]> https://biorxiv.org/content/10.1101/2021.02.27.433211v1?rss=1 800 genera detected across the five sites. Additionally, 39 genera were only detected using CD approaches revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in the delineation of sediment communities. This study provides important baseline data describing shallow water sediment microbial communities and evidence that standard cultivation techniques may be more effective than previously recognized. Originality-Significance StatementMarine sediments host some of the most diverse microbial communities on the planet. While these communities are critical for global nutrient cycling, the oceanic food web, and the maintenance of ecosystem dynamics, they remain poorly studied. Studies that have assessed sediment communities typically use culture-independent approaches, which have known biases and can miss ecologically important taxa. Here we describe microbial diversity in marine sediments using both culture-dependent and culture-independent approaches. Our culturing approach, sequencing communities as opposed to individual colonies, revealed an additional 39 genera that were not detected with culture-independent methods. Additionally, we cultured numerous, as-yet undescribed species, suggesting that traditional culturing practices can be more efficient than commonly thought. Moreover, our results indicate rare taxa play an important role in distinguishing microbial communities at different sites, thus highlighting the importance of deep sequencing and incorporating culture-dependent approaches for diversity assessments. ]]> Demko, A. M. Patin, N. V. Jensen, P. R. 2021-02-28 doi:10.1101/2021.02.27.433211 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning ]]> https://biorxiv.org/content/10.1101/2021.03.01.431313v1?rss=1 1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource. ]]> Greenwald, N. F. Miller, G. Moen, E. Kong, A. Kagel, A. Fullaway, C. C. McIntosh, B. J. Leow, K. Schwartz, M. S. Dougherty, T. Pavelchek, C. Cui, S. Camplisson, I. Bar-Tal, O. Singh, J. Fong, M. Chaudhry, G. Abraham, Z. Moseley, J. Warshawsky, S. Soon, E. Greenbaum, S. Risom, T. Hollmann, T. Keren, L. Graf, W. Angelo, M. Van Valen, D. 2021-03-02 doi:10.1101/2021.03.01.431313 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Taxon-specific phytoplankton growth, nutrient utilization, and light limitation in the oligotrophic Gulf of Mexico ]]> https://biorxiv.org/content/10.1101/2021.03.01.433426v1?rss=1 Yingling, N. Kelly, T. B. Shropshire, T. A. Landry, M. R. Selph, K. E. Knapp, A. N. Kranz, S. A. Stukel, M. R. 2021-03-02 doi:10.1101/2021.03.01.433426 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ When is it Worth Working for Water? A Utility Maximization Theory ]]> https://biorxiv.org/content/10.1101/2021.03.01.433467v1?rss=1 Reinagel, P. 2021-03-02 doi:10.1101/2021.03.01.433467 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naive human B cells ]]> https://biorxiv.org/content/10.1101/2021.03.01.433480v1?rss=1 Lee, J. H. Toy, L. Kos, J. T. Safonova, Y. Schief, W. R. Watson, C. T. Havenar-Daughton, C. Crotty, S. 2021-03-02 doi:10.1101/2021.03.01.433480 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Synthetic algal-bacteria consortia for space-efficient microalgal growth in a simple hydrogel system ]]> https://biorxiv.org/content/10.1101/2021.03.01.433490v1?rss=1 Martin, N. Bernat, T. Dinasquet, J. Stofko, A. Damon, A. Deheyn, D. Azam, F. Smith, J. Davey, M. P. Smith, A. G. Vignolini, S. Wangpraseurt, D. 2021-03-02 doi:10.1101/2021.03.01.433490 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Blockade of SARS-CoV-2 infection in-vitro by highly potent PI3K-α/mTOR/BRD4 inhibitor ]]> https://biorxiv.org/content/10.1101/2021.03.02.433604v1?rss=1 Acharya, A. Pandey, K. Thurman, M. Challagundla, K. B. Vann, K. R. Kutateladze, T. G. Morales, G. A. Durden, D. L. Byrareddy, S. N. 2021-03-03 doi:10.1101/2021.03.02.433604 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Slow, heterogeneous NFκB single molecule conformational dynamics and implications for function ]]> https://biorxiv.org/content/10.1101/2021.03.02.433616v1?rss=1 Chen, W. Liu, W. Wolynes, P. G. Komives, E. A. 2021-03-02 doi:10.1101/2021.03.02.433616 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Probiotic bacteria and bile acid profile are modulated by prebiotic diet and associate with facilitated diurnal clock/sleep realignment after chronic disruption of rhythms ]]> https://biorxiv.org/content/10.1101/2021.03.03.433775v1?rss=1 Thompson, R. S. Gaffney, M. K. Hopkins, S. Kelley, T. Gonzalez, A. Bowers, S. J. Vitaterna, M. H. Turek, F. W. Foxx, C. L. Lowry, C. A. Vargas, F. Dorrestein, P. C. Wright, K. P. Knight, R. Fleshner, M. 2021-03-04 doi:10.1101/2021.03.03.433775 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ BoolSim, a Graphical Interface for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling ]]> https://biorxiv.org/content/10.1101/2021.03.05.434139v1?rss=1 Karanam, A. R. He, D. Hsu, P.-K. Schulze, S. Dubeaux, G. Karmakar, R. Schroeder, J. Rappel, W.-J. 2021-03-07 doi:10.1101/2021.03.05.434139 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Nanoscale organization of Actin Filaments in the Red Blood Cell Membrane Skeleton ]]> https://biorxiv.org/content/10.1101/2021.03.07.434292v1?rss=1 Nowak, R. B. Alimohamadi, H. Pestonjamasp, K. Rangamani, P. Fowler, V. M. 2021-03-08 doi:10.1101/2021.03.07.434292 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ A novel nitrogen concentrating mechanism in the coral-algae symbiosome ]]> https://biorxiv.org/content/10.1101/2021.03.08.434475v1?rss=1 Thies, A. Quijada-Rodriguez, A. R. Zhouyao, H. Weihrauch, D. Tresguerres, M. 2021-03-09 doi:10.1101/2021.03.08.434475 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas ]]> https://biorxiv.org/content/10.1101/2021.03.09.434648v1?rss=1 Parekh, U. McDonald, D. Dailamy, A. Wu, Y. Cordes, T. Zhang, K. Tipps, A. Metallo, C. Mali, P. 2021-03-09 doi:10.1101/2021.03.09.434648 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Bayesian Multivariate Growth Mixture Modeling of Longitudinal Data: An Application to Alzheimer's Disease Study ]]> https://biorxiv.org/content/10.1101/2021.03.10.434854v1?rss=1 Lin, W. Donohue, M. C. Insel, P. Schwartzman, A. Thompson, W. K. 2021-03-12 doi:10.1101/2021.03.10.434854 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ A wild-derived antimutator drives germline mutation spectrum differences in a genetically diverse murine family ]]> https://biorxiv.org/content/10.1101/2021.03.12.435196v1?rss=1 A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily due to the activity of a C>A-dominated mutational signature known as SBS18. The B and D QTL haplotypes encode different alleles of the DNA repair gene Mutyh, which underlies the heritable colorectal cancer syndrome in which SBS18 was first identified. The B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species. ]]> Sasani, T. A. Ashbrook, D. G. Lu, L. Palmer, A. A. Williams, R. W. Pritchard, J. K. Harris, K. 2021-03-13 doi:10.1101/2021.03.12.435196 Cold Spring Harbor Laboratory Press 2021-03-13 <![CDATA[ Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. ]]> https://biorxiv.org/content/10.1101/2021.03.15.435499v1?rss=1 Blazie, S. M. Takayanagi-Kiya, S. McCulloch, K. M. Jin, Y. 2021-03-16 doi:10.1101/2021.03.15.435499 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Targeting Glioblastoma Signaling and Metabolism with A Re-Purposed Brain-Penetrant Drug ]]> https://biorxiv.org/content/10.1101/2021.03.16.435487v1?rss=1 Bi, J. Khan, A. Tang, J. Wu, S. Zhang, W. Gimple, R. C. Koga, T. Armando, A. M. Miki, S. Yang, H. Prager, B. Curtis, E. J. Wainwright, D. A. Furnari, F. B. Rich, J. N. Cloughesy, T. F. Quehenberger, O. Kornblum, H. I. Rzhetsky, A. Cravatt, B. F. Mischel, P. S. 2021-03-17 doi:10.1101/2021.03.16.435487 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ MLL3/MLL4 Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.17.435905v1?rss=1 Kubo, N. Hu, R. Ye, Z. Ren, B. 2021-03-18 doi:10.1101/2021.03.17.435905 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Assigning confidence to structural annotations from mass spectra with COSMIC ]]> https://biorxiv.org/content/10.1101/2021.03.18.435634v1?rss=1 Hoffmann, M. A. Nothias, L.-F. Ludwig, M. Fleischauer, M. Gentry, E. C. Witting, M. Dorrestein, P. C. Dührkop, K. Böcker, S. 2021-03-19 doi:10.1101/2021.03.18.435634 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Kawasaki Disease patient stratification and pathway analysis based on host transcriptomic and proteomic profiles ]]> https://biorxiv.org/content/10.1101/2021.03.18.435948v1?rss=1 Jackson, H. Menikou, S. Hamilton, S. McArdle, A. Shimizu, C. Galassini, R. Huang, H. Kim, J. Tremoulet, A. de Jonge, M. Kuijpers, T. W. Wright, V. Burns, J. Casals-Pascual, C. Herberg, J. Levin, M. Kaforou, M. The PERFORM Consortium, 2021-03-19 doi:10.1101/2021.03.18.435948 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Transcription Factor NF-κB Unravels Nucleosomes ]]> https://biorxiv.org/content/10.1101/2021.03.18.436050v1?rss=1 Stormberg, T. Filliaux, S. Baughman, H. Komives, E. Lyubchenko, Y. L. 2021-03-18 doi:10.1101/2021.03.18.436050 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ The Human Milk Oligosaccharide 3-Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice. ]]> https://biorxiv.org/content/10.1101/2021.03.19.433472v1?rss=1 Pessentheiner, A. R. Spann, N. J. Autran, C. A. Ramms, B. Chiang, A. W. T. Grunddal, K. V. Wang, Y. Quach, A. Booshehri, L. M. Hammond, A. Tognaccini, C. Latasiewicz, J. Witztum, j. L. Hoffman, H. M. Lewis, N. E. Glass, C. K. Bode, L. Gordts, P. L. S. M. 2021-03-20 doi:10.1101/2021.03.19.433472 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics ]]> https://biorxiv.org/content/10.1101/2021.03.19.436193v1?rss=1 Wu, Y. Lake, B. Sos, B. Chen, S. Duong, T. E. Yun, Y. C. Dong, W. Limaye, S. Chun, J. Zhang, K. 2021-03-19 doi:10.1101/2021.03.19.436193 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Proteome plasticity in response to persistent environmental change ]]> https://biorxiv.org/content/10.1101/2021.03.22.436511v1?rss=1 Domnauer, M. Zheng, F. Li, L. Zhang, Y. Chang, C. E. Unruh, J. Conkright-Fincham, J. McCroskey, S. Florens, L. Zhang, Y. Seidel, C. Fong, B. Schilling, B. Sharma, R. Ramanathan, A. Si, K. Zhou, C. 2021-03-22 doi:10.1101/2021.03.22.436511 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Genes identified in rodent studies of alcohol intake are enriched for heritability of human substance use ]]> https://biorxiv.org/content/10.1101/2021.03.22.436527v1?rss=1 Huggett, S. B. Johnson, E. C. Hatoum, A. S. Lai, D. Bubier, J. A. Chesler, E. C. Agrawal, A. A. Palmer, A. Edenberg, H. J. Palmer, R. H. C. 2021-03-23 doi:10.1101/2021.03.22.436527 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes ]]> https://biorxiv.org/content/10.1101/2021.03.24.436806v1?rss=1 Hempel, T. del Razo, M. J. Lee, C. T. Taylor, B. C. Amaro, R. E. Noe, F. 2021-03-25 doi:10.1101/2021.03.24.436806 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ An empirical pipeline for personalized diagnosis of Lafora disease mutations ]]> https://biorxiv.org/content/10.1101/2021.03.26.437206v1?rss=1 Brewer, M. K. Machio-Castello, M. Viana, R. Wayne, J. L. Kuchtova, A. Simmons, Z. R. Sternbach, S. Li, S. Garcia-Gimeno, M. A. Serratosa, J. Sanz, P. Vander Kooi, C. W. Gentry, M. S. 2021-03-26 doi:10.1101/2021.03.26.437206 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Single-Cell Transcriptomic Analysis of Livers During NLRP3 Inflammasome Activation Reveals a Novel Immune Niche ]]> https://biorxiv.org/content/10.1101/2021.03.31.437725v1?rss=1 Calcagno, D. M. Chu, A. Gaul, S. Taghdiri, N. Toomu, A. Leszczynska, A. Kaufmann, B. Wree, A. Geisler, L. Hoffman, H. M. Feldstein, A. E. King, K. R. 2021-03-31 doi:10.1101/2021.03.31.437725 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Acetylated α-tubulin residue K394 regulates microtubule stability to shape the growth of axon terminals ]]> https://biorxiv.org/content/10.1101/2021.04.01.438108v1?rss=1 Saunders, H. A. J. Johnson-Schlitz, D. M. Jenkins, B. V. Volkert, P. J. Yang, S. Z. Wildonger, J. 2021-04-02 doi:10.1101/2021.04.01.438108 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Anatomy and Development of the Pectoral Fin Vascular Network in the Zebrafish ]]> https://biorxiv.org/content/10.1101/2021.04.02.437283v1?rss=1 Paulissen, S. Castranova, D. M. Krispin, S. Burns, M. C. Weinstein, B. M. 2021-04-02 doi:10.1101/2021.04.02.437283 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers ]]> https://biorxiv.org/content/10.1101/2021.04.02.438263v1?rss=1 Mahapatra, A. Saintillan, D. Rangamani, P. 2021-04-04 doi:10.1101/2021.04.02.438263 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ THEM6-mediated lipid remodelling sustains stress resistance in cancer ]]> https://biorxiv.org/content/10.1101/2021.04.04.438378v1?rss=1 Blomme, A. Peter, C. Mui, E. Rodriguez Blanco, G. Mason, L. M. Jamieson, L. E. McGregor, G. H. Lilla, S. Ntala, C. Patel, R. Thiry, M. Kung, S. H. Ford, C. A. Rushworth, L. K. McGarry, D. J. Mason, S. Repiscak, P. Nixon, C. Salji, M. J. Markert, E. MacKay, G. M. Kamphorst, J. J. Graham, D. Faulds, K. Fazli, L. Gleave, M. E. Avezov, E. Edwards, J. Yin, H. Sumpton, D. Blyth, K. Close, P. Murphy, D. J. Zanivan, S. R. Leung, H. Y. 2021-04-04 doi:10.1101/2021.04.04.438378 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Cell-type specific circadian bioluminescence rhythms recorded from Dbp reporter mice reveal circadian oscillator misalignment ]]> https://biorxiv.org/content/10.1101/2021.04.04.438413v1?rss=1 Smith, C. B. van der Vinne, V. McCartney, E. Stowie, A. C. Leise, T. L. Martin-Burgos, B. Molyneux, P. C. Garbutt, L. A. Brodsky, M. H. Davidson, A. J. Harrington, M. E. Dallmann, R. Weaver, D. R. 2021-04-05 doi:10.1101/2021.04.04.438413 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity ]]> https://biorxiv.org/content/10.1101/2021.04.06.438579v1?rss=1 DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5 position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. Author SummaryThe novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein. ]]> Park, S. H. Siddiqi, H. Castro, D. De Angelis, A. Oom, A. L. Stoneham, C. Lewinski, M. Clark, A. Croker, B. Carlin, A. Guatelli, J. Opella, S. J. 2021-04-06 doi:10.1101/2021.04.06.438579 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ An AI-guided invariant signature places MIS-C with Kawasaki disease in a continuum of host immune responses ]]> https://biorxiv.org/content/10.1101/2021.04.11.439347v1?rss=1 Sahoo, D. Dattatray, G. Shimizu, C. Kim, J. Khandelwal, S. Tremoulet, A. H. Kanegaye, J. Bocchini, J. Das, S. Burns, J. C. Ghosh, P. Pediatric Emergency Medicine Kawasaki Disease Research Group, 2021-04-12 doi:10.1101/2021.04.11.439347 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Vacuole phase-partitioning boosts mitochondria activity and cell lifespan through an inter-organelle lipid pipeline ]]> https://biorxiv.org/content/10.1101/2021.04.11.439383v1?rss=1 Seo, A. Y. Sarkleti, F. Budin, I. Chang, C.-L. King, C. R. Kohlwein, S.-D. Sengupta, P. Lippincott-Schwartz, J. 2021-04-12 doi:10.1101/2021.04.11.439383 Cold Spring Harbor Laboratory Press 2021-04-12 <![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[ Underwater dual-magnification imaging for automated lake plankton monitoring ]]> https://biorxiv.org/content/10.1101/2021.04.14.439767v1?rss=1 Merz, E. Kozakiewicz, T. Reyes, M. Ebi, C. Isles, P. Baity Jesi, M. Roberts, P. L. D. Jaffe, J. S. Dennis, S. Hardeman, R. Stevens, N. Lorimer, T. Pomati, F. 2021-04-14 doi:10.1101/2021.04.14.439767 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity ]]> https://biorxiv.org/content/10.1101/2021.04.14.439786v1?rss=1 Zhou, B. Stueve, T. R. Mihalakakos, E. Miao, L. Mullen, D. J. Wang, Y. Liu, Y. Luo, J. Tran, E. Siegmund, K. D. Lynch, S. K. Ryan, A. L. Offringa, I. A. Borok, Z. Marconett, C. N. 2021-04-15 doi:10.1101/2021.04.14.439786 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Monosodium Urate Crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response ]]> https://biorxiv.org/content/10.1101/2021.04.14.439881v1?rss=1 Cobo, I. Cheng, A. Saich, J. Coras, R. Torres, A. Lana, A. J. Schlachetzki, J. Bryan, R. Terkeltaub, R. Lopez, E. Glass, C. K. Guma, M. 2021-04-14 doi:10.1101/2021.04.14.439881 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome ]]> https://biorxiv.org/content/10.1101/2021.04.16.440249v1?rss=1 Flores Ramos, S. Brugger, S. D. Fernandez Escapa, I. Skeete, C. A. Cotton, S. L. Eslami, S. M. Gao, W. Bomar, L. Tran, T. H. Jones, D. S. Minot, S. Roberts, R. J. Johnston, C. D. Lemon, K. P. 2021-04-18 doi:10.1101/2021.04.16.440249 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses ]]> https://biorxiv.org/content/10.1101/2021.04.17.440161v1?rss=1 Lucas, T. M. Gupta, C. Altman, M. O. Sanchez, E. Naticchia, M. R. Gagneux, P. Singharoy, A. Godula, K. 2021-04-17 doi:10.1101/2021.04.17.440161 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440649v1?rss=1 Garshott, D. M. An, H. Sundaramoorthy, E. Leonard, M. Vicary, A. Harper, J. W. Bennett, E. J. 2021-04-21 doi:10.1101/2021.04.20.440649 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.04.20.440657v1?rss=1 Tewari, A. K. Cheung, A. T. M. Crowdis, J. Conway, J. R. Camp, S. Y. Wankowicz, S. A. Livitz, D. G. Park, J. Lis, R. T. Boosma-Moody, A. He, M. X. AlDubayan, S. H. Zhang, Z. McKay, R. R. Leshchiner, I. Brown, M. Balk, S. Getz, G. Taplin, M.-E. Van Allen, E. 2021-04-21 doi:10.1101/2021.04.20.440657 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Chronic Presence of Blood Circulating Anti-NMDAR1 Autoantibodies Impairs Cognitive Function in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.22.440976v1?rss=1 Zhou, X. Yue, W. Caldwell, S. Risbrough, V. Powell, S. 2021-04-22 doi:10.1101/2021.04.22.440976 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Convergent, functionally independent signaling by mu and delta opioid receptors in hippocampal parvalbumin interneurons ]]> https://biorxiv.org/content/10.1101/2021.04.23.441199v1?rss=1 He, X. J. Patel, J. Weiss, C. E. Ma, X. Bloodgood, B. L. Banghart, M. R. 2021-04-24 doi:10.1101/2021.04.23.441199 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants ]]> https://biorxiv.org/content/10.1101/2021.04.24.438478v1?rss=1 Yan, C. Nayar, N. Zhao, H. Rhee, K. Lumeng, J. 2021-04-24 doi:10.1101/2021.04.24.438478 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2021.04.26.441469v1?rss=1 Croxford, M. Elbaum, M. Arigovindan, M. Kam, Z. Agard, D. A. Villa, E. Sedat, J. 2021-04-26 doi:10.1101/2021.04.26.441469 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Understanding double descent through the lens of principal component regression ]]> https://biorxiv.org/content/10.1101/2021.04.26.441538v1?rss=1 Lind, C. H. Yu, A. J. 2021-04-27 doi:10.1101/2021.04.26.441538 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ THC modifies the impact of heroin delivered by vapor inhalation in rats ]]> https://biorxiv.org/content/10.1101/2021.04.26.441541v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Javadi-Paydar, M. Grant, Y. Taffe, M. A. 2021-04-27 doi:10.1101/2021.04.26.441541 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Red blood cells protect oxygen transport with adrenergic sodium-proton exchangers in hypoxic and hypercapnic white seabass ]]> https://biorxiv.org/content/10.1101/2021.04.28.441819v1?rss=1 Harter, T. S. Clifford, A. M. Tresguerres, M. 2021-04-28 doi:10.1101/2021.04.28.441819 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Signatures of copy number alterations in human cancer ]]> https://biorxiv.org/content/10.1101/2021.04.30.441940v1?rss=1 Steele, C. D. Abbasi, A. Islam, A. S. M. Khandekar, A. Haase, K. Hames, S. Tarabichi, M. Lesluyes, T. Flanagan, A. M. Mertens, F. Van Loo, P. Alexandrov, L. B. Pillay, N. 2021-04-30 doi:10.1101/2021.04.30.441940 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression ]]> https://biorxiv.org/content/10.1101/2021.04.30.442101v1?rss=1 Rissman, R. A. Grundman, J. Spencer, B. Sarsoza, F. 2021-04-30 doi:10.1101/2021.04.30.442101 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Repeated administration of 2-hydroxypropyl-β-cyclodextrin (HPβCD) attenuates the chronic inflammatory response to experimental stroke ]]> https://biorxiv.org/content/10.1101/2021.05.03.442388v1?rss=1 Becktel, D. A. Zbesko, J. C. Frye, J. B. Chung, A. G. Hayes, M. Calderon, K. Grover, J. W. Li, A. Garcia, F. G. Tavera-Garcia, M. A. Schnellmann, R. G. Wu, H.-J. J. Nguyen, T.-V. V. Doyle, K. P. 2021-05-03 doi:10.1101/2021.05.03.442388 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Mapping the Central and Peripheral Projections of Lung Innervating Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2021.05.05.442702v1?rss=1 Su, Y. Barr, J. Jaquish, A. Xu, J. Verheyden, J. M. Sun, X. 2021-05-05 doi:10.1101/2021.05.05.442702 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Cecropins contribute to Drosophila host defense against fungal and Gram-negative bacterial infection ]]> https://biorxiv.org/content/10.1101/2021.05.06.442783v1?rss=1 Carboni, A. Hanson, M. A. Lindsay, S. A. Wasserman, S. A. Lemaitre, B. 2021-05-06 doi:10.1101/2021.05.06.442783 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Capturing the nature of events and event context using Hierarchical Event Descriptors (HED) ]]> https://biorxiv.org/content/10.1101/2021.05.06.442841v1?rss=1 Robbins, K. A. Truong, D. Appelhoff, S. Delorme, A. Makeig, S. 2021-05-07 doi:10.1101/2021.05.06.442841 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ GIV/Girdin, a Non-receptor Modulator for Gαi/s, Regulates Spatiotemporal Signaling during Sperm Capacitation and is Required for Male Fertility ]]> https://biorxiv.org/content/10.1101/2021.05.06.442927v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@f4901forg.highwire.dtl.DTLVardef@2211dforg.highwire.dtl.DTLVardef@c37ff5org.highwire.dtl.DTLVardef@105eed7_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGIV is highly expressed in spermatozoa, and is required for male fertility C_LIO_LIGIV is rapidly phosphoregulated during sperm capacitation C_LIO_LIIt enhances tyrosine-based signals in sperm tail, enhances motility C_LIO_LIIt suppresses cAMP in the sperm head, inhibits premature acrosome exocytosis C_LI ]]> Reynoso, S. Castillo, V. Katkar, G. D. Lopez-Sanchez, I. Taheri, S. Espinoza, C. R. Rohena, C. Sahoo, D. Gagneux, P. Ghosh, P. 2021-05-06 doi:10.1101/2021.05.06.442927 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ SPT6 loss Permits the Transdifferentiation of Keratinocytes into anIntestinal Fate that Recapitulates Barretts Metaplasia ]]> https://biorxiv.org/content/10.1101/2021.05.06.442930v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@8ce08aorg.highwire.dtl.DTLVardef@e98c83org.highwire.dtl.DTLVardef@107f521org.highwire.dtl.DTLVardef@16e7523_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIKeratinocytes transdifferentiate into the gut lineage upon depletion of SPT6 C_LIO_LISuch transdifferentiation recapitulates Barretts metaplasia, not the healthy gut C_LIO_LIAcid downregulates SPT6, which derails the expression and functions of TP63 C_LIO_LISuch downregulation precedes the metaplasia-dysplasia-neoplasia cascade C_LI ]]> Vo, D. Fuller, M. R. Tindle, C. Anandachar, M. Das, S. Sahoo, D. Ghosh, P. 2021-05-06 doi:10.1101/2021.05.06.442930 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Accuracy in near-perfect virus phylogenies ]]> https://biorxiv.org/content/10.1101/2021.05.06.442951v1?rss=1 Wertheim, J. O. Steel, M. Sanderson, M. J. 2021-05-06 doi:10.1101/2021.05.06.442951 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Endothelial Unc5B controls blood-brain barrier integrity ]]> https://biorxiv.org/content/10.1101/2021.05.06.442974v1?rss=1 Boye, K. Geraldo, L. H. M. furtado, J. Pibouin-fragner, L. Poulet, M. Kim, D. Nelson, B. Xu, Y. Jacob, L. Maissa, N. Tavitian, B. Agalliu, D. Claesson-Welsh, L. Ackerman, S. Eichmann, A. 2021-05-06 doi:10.1101/2021.05.06.442974 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Glycocalyx crowding with synthetic mucin mimetics strengthens interactions between soluble and virus-associated lectins and cell surface glycan receptors ]]> https://biorxiv.org/content/10.1101/2021.05.07.443169v1?rss=1 Honigfort, D. J. Altman, M. O. Gagneux, P. Godula, K. 2021-05-07 doi:10.1101/2021.05.07.443169 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ ]]> https://biorxiv.org/content/10.1101/2021.05.11.443641v1?rss=1 Nachmanson, D. Officer, A. Mori, H. Gordon, J. Evans, M. F. Steward, J. Yao, H. O'Keefe, T. Hasteh, F. Stein, G. S. Jepsen, K. Weaver, D. L. Hirst, G. Sprague, B. L. Esserman, L. J. Borowsky, A. D. Stein, J. L. Harismendy, O. 2021-05-12 doi:10.1101/2021.05.11.443641 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Serine 182 on RORγt regulates T helper 17 and regulatory T cell functions to resolve inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.14.444071v1?rss=1 Ma, S. Patel, S. Chen, N. Patel, P. R. Cho, B. S. Chang, J. T. Huang, W. J. M. 2021-05-16 doi:10.1101/2021.05.14.444071 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Distinct features of brain perivascular fibroblasts and mural cells revealed by in vivo two-photon imaging ]]> https://biorxiv.org/content/10.1101/2021.05.14.444194v1?rss=1 Bonney, S. K. Sullivan, L. T. Cherry, T. J. Daneman, R. Shih, A. Y. 2021-05-17 doi:10.1101/2021.05.14.444194 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Pan-ErbB inhibition protects from SARS-CoV-2 replication, inflammation, and injury ]]> https://biorxiv.org/content/10.1101/2021.05.15.444128v1?rss=1 Saul, S. Karim, M. Huang, P. T. Ghita, L. Chiu, W. Kumar, S. Bhalla, N. Leyssen, P. Cohen, C. A. Huie, K. E. Tindle, C. Sahoo, M. K. Sibai, M. Pinsky, B. A. Das, S. Ghosh, P. Dye, J. Solow-Cordero, D. E. Jin, J. Jochmans, D. Neyts, J. Narayanan, A. De Jonghe, S. Einav, S. 2021-05-16 doi:10.1101/2021.05.15.444128 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ The autophagy initiating kinase ULK1 is required for pancreatic cancer cell growth and survival ]]> https://biorxiv.org/content/10.1101/2021.05.15.444304v1?rss=1 Shaw, R. J. Brun, S. N. Lumibao, J. Limpert, A. Ren, H. Ianniciello, A. Cosford, N. Tiriac, H. Downes, M. Evans, R. Engle, D. D. 2021-05-17 doi:10.1101/2021.05.15.444304 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Feral and managed honey bees, Apis mellifera (Hymenoptera: Apidae), in southern California have similar levels of viral pathogens ]]> https://biorxiv.org/content/10.1101/2021.05.17.444546v1?rss=1 Geffre, A. C. Travis, D. Kohn, J. Nieh, J. 2021-05-18 doi:10.1101/2021.05.17.444546 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Subcellular localization of PKA catalytic subunits provides a basis for their distinct functions in the retina ]]> https://biorxiv.org/content/10.1101/2021.05.17.444584v1?rss=1 Roa, J. N. Ma, Y. Mikulski, Z. Xu, Q. Ilouz, R. Taylor, S. S. Skowronska-Krawczyk, D. 2021-05-18 doi:10.1101/2021.05.17.444584 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Detection of Small Fiber Neuronal Activity with Optically Pumped Magnetometers ]]> https://biorxiv.org/content/10.1101/2021.05.18.444539v1?rss=1 Bu, Y. Borna, A. Schwindt, P. Zeng, X. Huang, M. Baum, E. Rao, R. Kimball, D. Shah, V. Lerman, I. 2021-05-20 doi:10.1101/2021.05.18.444539 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ In-phase and in-antiphase connectivity in EEG ]]> https://biorxiv.org/content/10.1101/2021.05.19.444800v1?rss=1 O'Reilly, C. Lewis, J. D. Theilmann, R. J. Elsabbagh, M. Townsend, J. 2021-06-02 doi:10.1101/2021.05.19.444800 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Transient nuclear deformation primes epigenetic state and promotes cell reprogramming ]]> https://biorxiv.org/content/10.1101/2021.05.19.444886v1?rss=1 Song, Y. Soto, J. Chen, B. Zhao, W. Hoffman, T. Zhu, N. Peng, Q. Ly, C. Wong, P. K. Wang, Y. Rowat, A. C. Kurdistani, S. K. Li, S. 2021-05-21 doi:10.1101/2021.05.19.444886 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ A proteomics sample metadata representation for multiomics integration, and big data analysis. ]]> https://biorxiv.org/content/10.1101/2021.05.21.445143v1?rss=1 Dai, C. Fullgrabe, A. Pfeuffer, J. Solovyeva, E. Deng, J. Moreno, P. Kamatchinathan, S. Jaiswal Kundu, D. George, N. Fexova, S. Gruning, B. Foll, M. C. Griss, J. Vaudel, M. Audain, E. Locard-Paulet, M. Turewicz, M. Eisenacher, M. Uszkoreit, J. Van Den Bossche, T. Schwammle, V. Webel, H. Schulze, S. Bouyssie, D. Jayaram, S. Kumar Duggineni, V. Samaras, P. Wilhelm, M. Choi, M. Wang, M. Kohlbacher, O. Brazma, A. Papatheodorou, I. Bandeira, N. W. Deutsch, E. Vizcaino, J. A. Bai, M. Levitsky, L. Sachsenberg, T. Perez-Riverol, Y. 2021-05-23 doi:10.1101/2021.05.21.445143 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Transcriptional and Functional Activity of Canine Hemangiosarcoma to Support Hematopoiesis Demonstrate Bone Marrow Nurse Cell Ontogeny ]]> https://biorxiv.org/content/10.1101/2021.05.21.445198v1?rss=1 Kim, J. H. Schulte, A. J. Sarver, A. L. Angelos, M. G. Frantz, A. M. Foster, C. L. O'Brien, T. D. Cornax, I. O'Sullivan, M. G. Cheng, N. Lewellen, M. Oseth, L. Kumar, S. Bullman, S. Pedamallu, C. S. Goyal, S. M. Meyerson, M. Lund, T. C. Alfoldi, J. Lindblad-Toh, K. Breen, M. Dickerson, E. B. Kaufman, D. S. Modiano, J. F. 2021-05-23 doi:10.1101/2021.05.21.445198 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria ]]> https://biorxiv.org/content/10.1101/2021.05.24.445329v1?rss=1 Balakrishnan, R. Mori, M. Segota, I. Zhang, Z. Aebersold, R. Ludwig, C. Hwa, T. 2021-05-24 doi:10.1101/2021.05.24.445329 Cold Spring Harbor Laboratory Press 2021-05-24 <![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[ In vivo selection of nanobodies to target the tumor immune microenvironment for immunotherapy development ]]> https://biorxiv.org/content/10.1101/2021.05.26.445719v1?rss=1 Sekar, T. V. Elghonaimy, E. Swancutt, K. L. Whitney, M. Aguilera, T. A. 2021-05-29 doi:10.1101/2021.05.26.445719 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures ]]> https://biorxiv.org/content/10.1101/2021.05.28.446215v1?rss=1 Dhanwani, R. Rodrigues Lima-Junior, J. Sethi, A. Pham, J. Williams, G. Frazier, A. Xu, Y. Amara, A. W. Standaert, D. G. Goldman, J. G. Litvan, I. Alcalay, R. N. Peters, B. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2021-05-29 doi:10.1101/2021.05.28.446215 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Aldosterone, Dexamethasone and Triamcinolone Activate African Lungfish Mineralocorticoid Receptor: Increased Activation After Removal of the Amino-Terminal Domain ]]> https://biorxiv.org/content/10.1101/2021.05.28.446239v1?rss=1 Katsu, Y. Oana, S. Lin, X. Hyodo, S. Baker, M. E. 2021-05-30 doi:10.1101/2021.05.28.446239 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ ppx: Programmatic access to proteomics data repositories ]]> https://biorxiv.org/content/10.1101/2021.05.29.446304v1?rss=1 Fondrie, W. E. Bittremieux, W. Noble, W. S. 2021-05-30 doi:10.1101/2021.05.29.446304 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution ]]> https://biorxiv.org/content/10.1101/2021.05.30.446342v1?rss=1 Subramanian, A. Vernon, K. Zhou, Y. Marshall, J. Alimova, M. Zhang, F. Slyper, M. Waldman, J. Montesinos, M. Dionne, D. Nguyen, L. Cuoco, M. S. Dubinsky, D. Purnell, J. Keller, K. Turner, S. H. Grinkevich, E. Ghoshal, A. Weins, A. Villani, A.-C. Chang, S. Rosenblatt-Rosen, O. Shaw, J. L. Regev, A. Greka, A. 2021-05-30 doi:10.1101/2021.05.30.446342 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Gonadal sex patterns p21-induced cellular senescence in mouse and human glioblastoma ]]> https://biorxiv.org/content/10.1101/2021.06.02.446756v1?rss=1 Broestl, L. Grandison, L. Shenoy, S. Tallman, M. M. Rhee, G. Yang, W. Sponagel, J. Kfoury-Beaumont, N. Hill, C. M. Mao, D. D. Kim, A. H. Stewart, S. A. Venere, M. Luo, J. Rubin, J. B. 2021-06-02 doi:10.1101/2021.06.02.446756 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Optimizing microtubule arrangements for rapid cargo capture ]]> https://biorxiv.org/content/10.1101/2021.06.02.446824v1?rss=1 Mogre, S. S. Christensen, J. R. Reck-Peterson, S. L. Koslover, E. 2021-06-02 doi:10.1101/2021.06.02.446824 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Anal skin-like epithelium mediates colonic wound healing ]]> https://biorxiv.org/content/10.1101/2021.06.02.446836v1?rss=1 Liu, C. Y. Girish, N. Gomez, M. L. Dube, P. E. Washington, M. K. Simons, B. D. Polk, D. B. 2021-06-03 doi:10.1101/2021.06.02.446836 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Nuclear depletion of RNA binding protein ELAVL3 (HuC) in sporadic and familial amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2021.06.03.446017v1?rss=1 Diaz-Garcia, S. Ko, V. I. Vazquez-Sanchez, S. Chia, R. Arogundade, O. A. Rodriguez, M. J. Cleveland, D. W. Traynor, B. Ravits, J. 2021-06-03 doi:10.1101/2021.06.03.446017 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment ]]> https://biorxiv.org/content/10.1101/2021.06.04.446988v1?rss=1 Shaffer, J. P. Nothias, L.-F. Thompson, L. R. Jon, S. G. Salido, R. A. Couvillion, S. P. Brejnrod, A. D. Huang, S. Lejzerowicz, F. Lutz, H. L. Zhu, Q. Martino, C. Morton, J. T. Karthikeyan, S. Nothias-Esposito, M. Dührkop, K. Böcker, S. Kim, H. Aksenov, A. A. Bittremieux, W. Minich, J. J. Marotz, C. Bryant, M. M. Sanders, K. Schwartz, T. Humphrey, G. Vasquez-Baeza, Y. Tripathi, A. Parida, L. Carrieri, A. P. Haiminen, N. Beck, K. L. Das, P. Gonzalez, A. McDonald, D. Karst, S. M. Albertsen, M. Ackermann, G. DeReus, J. Thomas, T. Petras, D. Shade, A. St 2021-06-06 doi:10.1101/2021.06.04.446988 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Mutualistic interactions between B. subtilis and seeds dictate plant development ]]> https://biorxiv.org/content/10.1101/2021.06.07.447311v1?rss=1 Berlanga-Clavero, M. V. Molina-Santiago, C. Caraballo-Rodriguez, A. M. Petras, D. Diaz-Martinez, L. Perez-Garcia, A. de Vicente, A. Dorrestein, P. Romero, D. 2021-06-07 doi:10.1101/2021.06.07.447311 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ The interaction of enteric bacterial effectors with the host engulfment pathway control innate immune responses ]]> https://biorxiv.org/content/10.1101/2021.06.07.447447v1?rss=1 Sayed, I. M. Ibeawuchi, S.-R. Lie, D. Anandachar, M. S. Pranadinata, R. Raffatellu, M. Das, S. 2021-06-07 doi:10.1101/2021.06.07.447447 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Habitat Protection Indexes - new monitoring measures for the conservation of coastal and marine habitats ]]> https://biorxiv.org/content/10.1101/2021.06.09.447318v1?rss=1 Kumagai, J. A. Favoretto, F. Pruckner, S. Rogers, A. D. Weatherdon, L. V. Aburto-Oropeza, O. Niamir, A. 2021-06-10 doi:10.1101/2021.06.09.447318 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells ]]> https://biorxiv.org/content/10.1101/2021.06.10.447969v1?rss=1 Calandrelli, R. Wen, X. Nguyen, T. C. Chen, C.-J. Qi, Z. Chen, W. Yan, Z. Wu, W. Zaleta-Rivera, K. Hu, R. Yu, M. Wang, Y. Ma, J. Ren, B. Zhong, S. 2021-06-11 doi:10.1101/2021.06.10.447969 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ High-level language brain regions are sensitive to sub-lexical regularities ]]> https://biorxiv.org/content/10.1101/2021.06.11.447786v1?rss=1 Regev, T. I. Affourtit, J. Chen, X. Schipper, A. E. Bergen, L. Mahowald, K. Fedorenko, E. 2021-06-11 doi:10.1101/2021.06.11.447786 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Disentangling reward processes underlying payoff maximization from individual differences in gain frequency bias and reinforcement learning ]]> https://biorxiv.org/content/10.1101/2021.06.11.447974v1?rss=1 Balasubramani, P. P. Diaz-Delgado, J. Grennan, G. Zafar-Khan, M. Alim, F. Ramanathan, D. Mishra, J. 2021-06-13 doi:10.1101/2021.06.11.447974 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ Ultrasound mediated cellular deflection results in cellular depolarization ]]> https://biorxiv.org/content/10.1101/2021.06.11.447976v1?rss=1 Vasan, A. Orosco, J. Magaram, U. Weiss, C. Duque, M. Tufail, Y. Chalasani, S. H. Friend, J. 2021-06-13 doi:10.1101/2021.06.11.447976 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ Temperature-Inducible Precision Guided Sterile Insect Technique ]]> https://biorxiv.org/content/10.1101/2021.06.14.448312v1?rss=1 Kandul, N. P. Liu, J. Akbari, O. 2021-06-14 doi:10.1101/2021.06.14.448312 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ DOPAL initiates αSynuclein-mediated impaired proteostasis in neuronal projections leading to enhanced vulnerability in Parkinson's disease. ]]> https://biorxiv.org/content/10.1101/2021.06.15.448476v1?rss=1 Masato, A. Plotegher, N. Thor, A. Adams, S. Sandre, M. Cogo, S. De Lazzari, F. Fontana, C. M. Martinez, P. A. Strong, R. Bellucci, A. Bisaglia, M. Greggio, E. Dalla Valle, L. Boassa, D. Bubacco, L. 2021-06-16 doi:10.1101/2021.06.15.448476 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ EPAC1 Inhibition Protects the Heart from Doxorubicin-Induced Toxicity ]]> https://biorxiv.org/content/10.1101/2021.06.16.448655v1?rss=1 Mazevet, M. Ribeiro, M. Belhadef, A. Dayde, D. Llach, A. Laudette, M. Belleville, T. Mateo, P. Gressette, M. Lefebvre, F. Chen, J. Bachelot-Loza, C. Rucker-Martin, C. Lezoualch, F. Crozatier, B. Benitah, J.-P. Vozenin, M.-C. Fischmeister, R. Gomez, A.-M. Lemaire, C. Morel, E. 2021-06-17 doi:10.1101/2021.06.16.448655 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Bioluminescent Genetically Encoded Glutamate Indicator for Molecular Imaging of Neuronal Activity ]]> https://biorxiv.org/content/10.1101/2021.06.16.448690v1?rss=1 Petersen, E. D. Crespo, E. C. Lambert, G. G. Zanca, A. T. Orcutt, R. Hochgeschwender, U. Nathan, S. C. Gilad, A. 2021-06-17 doi:10.1101/2021.06.16.448690 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Parallel shifts of visual sensitivity and body colouration in replicate populations of extremophile fish. ]]> https://biorxiv.org/content/10.1101/2021.06.16.448734v1?rss=1 Owens, G. L. Veen, T. Moxley, D. R. Arias-Rodriguez, L. Tobler, M. L. Rennison, D. J. 2021-06-17 doi:10.1101/2021.06.16.448734 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Tau interactome mapping reveals dynamic processes in synapses and mitochondria associated with neurodegenerative disease ]]> https://biorxiv.org/content/10.1101/2021.06.17.448349v1?rss=1 Tracy, T. E. Madero-Perez, J. Swaney, D. Chang, T. S. Moritz, M. Konrad, C. Ward, M. E. Stevenson, E. Huttenhain, R. Kauwe, G. Mercedes, M. Sweetland-Martin, L. Chen, X. Mok, S.-A. Telpoukhovskaia, M. Min, S.-W. Wang, C. Dongmin Sohn, P. Martin, J. Zhou, Y. Manfredi, G. Coppola, G. Krogan, N. J. Geschwind, D. Gan, L. 2021-06-17 doi:10.1101/2021.06.17.448349 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Dynamical differential covariance recovers directional network structure in multiscale neural systems ]]> https://biorxiv.org/content/10.1101/2021.06.18.448901v1?rss=1 Chen, Y. Rosen, B. Q. Sejnowski, T. J. 2021-06-20 doi:10.1101/2021.06.18.448901 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Nanoscale surface topography reduces focal adhesions and cell stiffness by enhancing integrin endocytosis ]]> https://biorxiv.org/content/10.1101/2021.06.18.448920v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1599ab1org.highwire.dtl.DTLVardef@1bade3corg.highwire.dtl.DTLVardef@1543b28org.highwire.dtl.DTLVardef@f7cc15_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, X. Klausen, L. H. Zhang, W. Jahed, Z. Tsai, C.-T. Li, T. L. Cui, B. 2021-06-18 doi:10.1101/2021.06.18.448920 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Multiplexed Screening of Population-level Synthetic Gene Oscillator Libraries ]]> https://biorxiv.org/content/10.1101/2021.06.22.449269v1?rss=1 Lezia, A. Csicsery, N. Hasty, J. 2021-06-22 doi:10.1101/2021.06.22.449269 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Witnessing the Structural Evolution of an RNA Enzyme ]]> https://biorxiv.org/content/10.1101/2021.06.22.449496v1?rss=1 Portillo, X. Huang, Y.-T. Breaker, R. R. Horning, D. P. Joyce, G. F. 2021-06-22 doi:10.1101/2021.06.22.449496 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Molecular Features Underlying Shp1/Shp2 Discrimination by Immune Checkpoint Receptors ]]> https://biorxiv.org/content/10.1101/2021.06.23.449580v1?rss=1 Hui, E. Xu, X. Masubuchi, T. Zhao, Y. 2021-06-23 doi:10.1101/2021.06.23.449580 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Non-Newtonian Patient-specific Simulations of Left Atrial Hemodynamics ]]> https://biorxiv.org/content/10.1101/2021.06.24.449801v1?rss=1 Gonzalo, A. Garcia-Villalba, M. Rossini, L. Duran, E. Vigneault, D. Martinez-Legazpi, P. Flores, O. Bermejo, J. McVeigh, E. Kahn, A. del Alamo, J. C. 2021-06-25 doi:10.1101/2021.06.24.449801 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Stress-induced cross-feeding of internal metabolites provides a dynamic mechanism of microbial cooperation ]]> https://biorxiv.org/content/10.1101/2021.06.24.449802v1?rss=1 Amarnath, K. Narla, A. Pontrelli, S. Dong, J. Caglar, T. Taylor, B. R. Schwartzman, J. A. Sauer, U. Cordero, O. X. Hwa, T. 2021-06-24 doi:10.1101/2021.06.24.449802 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Host-parasite coevolution promotes innovation through deformations in fitness landscapes ]]> https://biorxiv.org/content/10.1101/2021.06.25.449783v1?rss=1 Gupta, A. Zaman, L. Strobel, H. M. Gallie, J. Burmeister, A. R. Kerr, B. Tamar, E. S. Kishony, R. Meyer, J. R. 2021-06-27 doi:10.1101/2021.06.25.449783 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ Transfer learning improves outcome predictions for ASD from gene expression in blood ]]> https://biorxiv.org/content/10.1101/2021.06.26.449864v1?rss=1 Robasky, K. Kim, R. Yi, H. Xu, H. Bao, B. Chang, A. W. T. Courchesne, E. Lewis, N. E. 2021-06-29 doi:10.1101/2021.06.26.449864 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Robust integration of single-cell cytometry datasets ]]> https://biorxiv.org/content/10.1101/2021.06.28.450128v1?rss=1 Pedersen, C. B. Dam, S. H. Barnkob, M. B. Leipold, M. D. Purroy, N. Rassenti, L. Z. Kipps, T. J. Nguyen, J. Lederer, J. A. Gohil, S. H. Wu, C. J. Olsen, L. R. 2021-06-28 doi:10.1101/2021.06.28.450128 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks ]]> https://biorxiv.org/content/10.1101/2021.07.01.450581v1?rss=1 Sastry, A. V. Poudel, S. Rychel, K. Yoo, R. Lamoureux, C. R. Chauhan, S. Haiman, Z. B. Al Bulushi, T. Seif, Y. Palsson, B. O. 2021-07-02 doi:10.1101/2021.07.01.450581 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Inducible Yeast Two-Hybrid with Quantitative Measures ]]> https://biorxiv.org/content/10.1101/2021.07.01.450807v1?rss=1 Hernandez, J. Ross, K. D. Hamilton, B. A. 2021-07-02 doi:10.1101/2021.07.01.450807 Cold Spring Harbor Laboratory Press 2021-07-02 <![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[ A Population-level Strain Genotyping Method to Study Pathogen Strain Dynamics in Human Infections ]]> https://biorxiv.org/content/10.1101/2021.07.02.450905v1?rss=1 Morgan, S. J. Durfey, S. L. Ravishankar, S. Jorth, P. Ni, W. Skerrett, D. Aitken, M. L. Mckone, E. F. Salipante, S. Radey, M. Singh, P. K. 2021-07-03 doi:10.1101/2021.07.02.450905 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Kinetic Properties of Microbial Exoenzymes Vary with Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile ]]> https://biorxiv.org/content/10.1101/2021.07.02.450965v1?rss=1 Alves, R. J. E. Callejas, I. A. Marschmann, G. L. Mooshammer, M. Singh, H. W. Whitney, B. Torn, M. S. Brodie, E. L. 2021-07-03 doi:10.1101/2021.07.02.450965 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Implicitly Learned Higher Order Associations Differentiates Recent and Remote Retrieval of Temporal Order Memory ]]> https://biorxiv.org/content/10.1101/2021.07.03.451031v1?rss=1 30 mins) are chosen deliberately to minimise the working memory contributions. We develop this paradigm initially using 4 order place associates and later extend it to 5 paired associates. Our results show that animals not only acquire these explicit (entry order to place) associations but also higher order associations that can only be inferred implicitly from the temporal order of these events. As an indicator of such higher order learning during the probe trail the mice exhibit predominantly prospective errors that declines proportionally with temporal distance. On the other hand, prior to acquiring the sequence the retrospective errors are dominant. Additionally, we also tested the nature of such acquisitions when temporal order CS is presented along with flavour as a compound stimulus comprising of order and flavour both simultaneously being paired with location. Results from these experiments indicate that the animal learns both order-place and flavour-place associations. Comparing with pure order place training, we find that the additional flavour in compound training did not interfere with the ability of the animals to acquire the order place associations. When tested remotely, pure order place associations could be retrieved only after a reminder training. Further higher order associations representing the temporal relationship between the events is markedly absent in the remote time. ]]> Shridhar, S. Singh, V. Bhatt, R. Kundu, S. Jayaprakash, B. 2021-07-04 doi:10.1101/2021.07.03.451031 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Transient beta modulates decision thresholds during human action-stopping ]]> https://biorxiv.org/content/10.1101/2021.07.05.447605v1?rss=1 Muralidharan, V. Aron, A. R. Schmidt, R. 2021-07-05 doi:10.1101/2021.07.05.447605 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth ]]> https://biorxiv.org/content/10.1101/2021.07.08.451571v1?rss=1 Tang, R. Shuldiner, E. G. Kelly, M. Murray, C. W. Hebert, J. D. Andrejka, L. Tsai, M. K. Cai, H. Li, Y.-C. Wahl, G. Jackson, P. K. Petrov, D. Winslow, M. M. 2021-07-09 doi:10.1101/2021.07.08.451571 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Allele-specific expression links diverse cis-regulatory mutations to recurrent gene dysregulation in high-risk neuroblastoma ]]> https://biorxiv.org/content/10.1101/2021.07.08.451695v1?rss=1 Sen, A. Huo, Y. Elster, J. Zage, P. E. McVicker, G. P. 2021-07-08 doi:10.1101/2021.07.08.451695 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Splicing Factor SRSF1 Deficiency in the Liver Triggers NASH-like Pathology via R-Loop Induced DNA Damage and Cell Death ]]> https://biorxiv.org/content/10.1101/2021.07.10.451875v1?rss=1 Arif, W. Mathur, B. Saikali, M. F. Chembazhi, U. V. Blue, S. M. Yee, B. A. Van Nostrand, E. L. Bangru, S. Hao, Q. Yeo, G. W. Prasanth, K. V. Anakk, S. Cummins, C. L. Kalsotra, A. 2021-07-11 doi:10.1101/2021.07.10.451875 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Altered costimulatory signals and hypoxia support chromatin landscapes limiting the functional potential of exhausted T cells in cancer ]]> https://biorxiv.org/content/10.1101/2021.07.11.451947v1?rss=1 Ford, B. R. Rittenhouse, N. L. Scharping, N. E. Vignali, P. D. A. Frisch, A. T. Peralta, R. Delgoffe, G. M. Poholek, A. C. 2021-07-12 doi:10.1101/2021.07.11.451947 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Critical Assessment of Metagenome Interpretation - the second round of challenges ]]> https://biorxiv.org/content/10.1101/2021.07.12.451567v1?rss=1 Meyer, F. Fritz, A. Deng, Z.-L. Koslicki, D. Gurevich, A. Robertson, G. Zhu, J. Jia, H. Kola, A. Limasset, A. Kolmogorov, M. Egan, R. Rosen, G. L. Cristian, A. Zhao, Z. Gray, M. A. Nissen, J. Zeller, G. Paoli, L. Ruscheweyh, H.-J. Milanese, A. Sunagawa, S. Alser, M. Shi, L. Chen, B. Wang, Z. Wang, Z. Huang, P. You, R. Sun, F. Zhu, S. Bertrand, D. Tong, C. Li, C. Nagarajan, N. Renard, B. Malcher-Miranda, F. Piro, V. C. Chikhi, R. Vicedomini, R. Wang, Z. Thomas, A. Tremblay, J. Dabrowski, P. W. Nurk, S. Jorgensen, T. S. Willassen, N. P. Klemetsen, T 2021-07-12 doi:10.1101/2021.07.12.451567 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ 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[ Effects of sub-threshold transcutaneous auricular vagus nerve stimulation on cerebral blood flow ]]> https://biorxiv.org/content/10.1101/2021.07.13.451709v1?rss=1 Chen, C. Mao, Y. Falahpour, M. MacNiven, K. H. Heit, G. Sharma, V. Alataris, K. Liu, T. T. 2021-07-14 doi:10.1101/2021.07.13.451709 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Temporal Analyses of Postnatal Liver Development and Maturation by Single Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.07.14.451852v1?rss=1 Liang, Y. Kaneko, K. Xin, B. Lee, J. Sun, X. Zhang, K. Feng, G.-S. 2021-07-14 doi:10.1101/2021.07.14.451852 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Over-Representation of Potential SP4 Target Genes within Schizophrenia-Risk Genes ]]> https://biorxiv.org/content/10.1101/2021.07.14.452377v1?rss=1 Zhou, X. 2021-07-15 doi:10.1101/2021.07.14.452377 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Single-nucleus cross-tissue molecular reference maps to decipher disease gene function ]]> https://biorxiv.org/content/10.1101/2021.07.19.452954v1?rss=1 Eraslan, G. Drokhlyansky, E. Anand, S. Subramanian, A. Fiskin, E. Slyper, M. Wang, J. Van Wittenberghe, N. Rouhana, J. M. Waldman, J. Ashenberg, O. Dionne, D. Win, T. S. Cuoco, M. S. Kuksenko, O. Branton, P. A. Marshall, J. L. Greka, A. Getz, G. Segre, A. V. Aguet, F. Rozenblatt-Rosen, O. Ardlie, K. G. Regev, A. 2021-07-19 doi:10.1101/2021.07.19.452954 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record ]]> https://biorxiv.org/content/10.1101/2021.07.19.453013v1?rss=1 Mongiardino Koch, N. Thompson, J. R. Hatch, A. S. McCowin, M. F. Armstrong, F. Coppard, S. E. Aguilera, F. Bronstein, O. Kroh, A. Mooi, R. Rouse, G. 2021-07-20 doi:10.1101/2021.07.19.453013 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Spatial and Temporal Organization of Composite Receptive Fields in the Songbird Auditory Forebrain ]]> https://biorxiv.org/content/10.1101/2021.07.21.453115v1?rss=1 Vahidi, N. W. 2021-07-22 doi:10.1101/2021.07.21.453115 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Individual difference in addiction-like behaviors and choice between cocaine versus food in Heterogeneous Stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.21.453270v1?rss=1 Sedighim, S. Carrette, L. L. Venniro, M. Shaham, Y. de Guglielmo, G. George, O. 2021-07-23 doi:10.1101/2021.07.21.453270 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ EXPRESSION OF A SECRETABLE, CELL-PENETRATING CDKL5 PROTEIN ENHANCES THE EFFICACY OF AAV VECTOR-MEDIATED GENE THERAPY FOR CDKL5 DEFICIENCY DISORDER. ]]> https://biorxiv.org/content/10.1101/2021.07.26.453746v1?rss=1 Medici, G. Tassinari, M. Galvani, G. Bastianini, S. Gennaccaro, L. Loi, M. Fuchs, C. Mottolese, N. Alvente, S. Berteotti, C. Bagget, H. R. Zoccoli, G. Giustetto, M. Muotri, A. R. Nakai, H. Trazzi, S. Ciani, E. 2021-07-26 doi:10.1101/2021.07.26.453746 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Mitochondria dysfunction in Charcot Marie Tooth 2B Peripheral Sensory Neuropathy ]]> https://biorxiv.org/content/10.1101/2021.07.28.454213v1?rss=1 Gu, Y. Guerra, F. Hu, M. Pope, A. Sung, K. Yang, W. Jetha, S. Shoff, T. A. Gunatilake, T. Dahlkamp, O. Shi, L. Z. Manganelli, F. Nolano, M. Zhou, Y. Ding, J. Bucci, C. Wu, C. 2021-07-28 doi:10.1101/2021.07.28.454213 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ The sensory code within sense of time ]]> https://biorxiv.org/content/10.1101/2021.07.29.454157v1?rss=1 Reinartz, S. Fassihi, A. Paz, L. Pulecchi, F. Gigante, M. Diamond, M. E. 2021-07-30 doi:10.1101/2021.07.29.454157 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Regulatory perturbations of ribosome allocation results in a trade-off between fast growth and adaptation capacity ]]> https://biorxiv.org/content/10.1101/2021.08.01.454633v1?rss=1 Hidalgo, D. Martinez-Ortiz, C. A. Palsson, B. Jimenez, J. I. Utrilla, J. 2021-08-02 doi:10.1101/2021.08.01.454633 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector ]]> https://biorxiv.org/content/10.1101/2021.08.02.454639v1?rss=1 Haas, B. Dobin, A. Ghandi, M. Van Arsdale, A. Tickle, T. L. Robinson, J. T. Gilliani, R. Kasif, S. Regev, A. 2021-08-04 doi:10.1101/2021.08.02.454639 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Helical Ordering of Envelope Associated Proteins and Glycoproteins in Respiratory Syncytial Virus Filamentous Virions ]]> https://biorxiv.org/content/10.1101/2021.08.04.455049v1?rss=1 Conley, M. J. Short, J. M. Hutchings, J. Burns, A. M. Streetley, J. Bakker, S. E. Jaffery, H. Stewart, M. Power, B. J. Zanetti, G. Fearns, R. Vijayakrishnan, S. Bhella, D. 2021-08-04 doi:10.1101/2021.08.04.455049 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Revealing how variations in antibody repertoires correlate with vaccine responses ]]> https://biorxiv.org/content/10.1101/2021.08.06.454618v1?rss=1 Safonova, Y. Shin, S. B. Kramer, L. Reecy, J. Watson, C. T. Smith, T. P. L. Pevzner, P. A. 2021-08-09 doi:10.1101/2021.08.06.454618 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ NFIC regulates ribosomal biology and ER stress in pancreatic acinar cells and suppresses PDAC initiation ]]> https://biorxiv.org/content/10.1101/2021.08.09.455477v1?rss=1 Cobo, i. Paliwal, S. Melia-Aloma, J. Torres, A. Martinez-Villarreal, J. Garcia, F. Millan, I. del Pozo, N. Park, J.-C. MacDonald, R. J. Munoz, J. Real, F. X. 2021-08-09 doi:10.1101/2021.08.09.455477 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ The Mismatch Between Neuroscience Graduate Training and Professional Skill Sets ]]> https://biorxiv.org/content/10.1101/2021.08.09.455678v1?rss=1 Shah, S. Juavinett, A. L. 2021-08-10 doi:10.1101/2021.08.09.455678 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny ]]> https://biorxiv.org/content/10.1101/2021.08.11.456014v1?rss=1 Diao, H. Chen, R. Tsuda, S. M. Wang, D. Frederick, M. A. Kim, J. Karunadharma, P. Martinez, G. Getzler, A. J. Toma, C. Milner, J. Venables, T. C. Martin, D. M. Goldrath, A. W. Crotty, S. Pipkin, M. E. 2021-08-11 doi:10.1101/2021.08.11.456014 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Proteomic analysis reveals different sets of proteins expressed during high temperature stress in two thermotolerant isolates of Trichoderma ]]> https://biorxiv.org/content/10.1101/2021.08.12.456037v1?rss=1 Poosapati, S. Viswanathaswamy, D. K. Ravulapalli, D. P. Kannan, M. 2021-08-12 doi:10.1101/2021.08.12.456037 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Autoimmune Alleles at the Major Histocompatibility Locus Modify Melanoma Susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.12.456166v1?rss=1 1%). However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte conserved antigens suggesting a potential relationship between antigen processing, binding, and cell-surface presentation. Overall, this study presents evidence that MHC-I autoimmune risk alleles modulate melanoma risk unaccounted for by current PRS. ]]> Talwar, J. Laub, D. Pagadala, M. Castro, A. Lewis, M. Luebeck, G. E. Morris, G. P. Salem, R. M. Thompson, W. K. Curtius, K. Zanetti, M. Carter, H. 2021-08-13 doi:10.1101/2021.08.12.456166 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Quaternary structure independent folding of voltage-gated ion channel pore domain subunits ]]> https://biorxiv.org/content/10.1101/2021.08.15.456357v1?rss=1 Arrigoni, C. Lolicato, M. Shaya, D. Rohaim, A. Findeisen, F. Colleran, C. M. Dominik, P. Kim, S. S. Schuermann, J. Kossiakoff, A. A. Minor, D. L. 2021-08-15 doi:10.1101/2021.08.15.456357 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Rapid fluctuations in functional connectivity of cortical networks encode spontaneous behavior ]]> https://biorxiv.org/content/10.1101/2021.08.15.456390v1?rss=1 Benisty, H. Moberly, A. H. Lohani, S. Barson, D. Coifman, R. R. Mishne, G. Cardin, J. A. Higley, M. J. 2021-08-15 doi:10.1101/2021.08.15.456390 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins ]]> https://biorxiv.org/content/10.1101/2021.08.16.455786v1?rss=1 Malm, M. Kuo, C.-C. Moradi Barzadd, M. Mebrahtu, A. Wistabacka, N. Razavi, R. Volk, A.-L. Lunqvist, M. Kotol, D. Edfors, F. Graslund, T. Chotteau, V. Field, R. Varley, P. G. Roth, R. G. Lewis, N. Hatton, D. Rockberg, J. 2021-08-17 doi:10.1101/2021.08.16.455786 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Physicochemical and Pharmacokinetic Properties Determining Drug Detection in Skin ]]> https://biorxiv.org/content/10.1101/2021.08.17.456720v1?rss=1 Bittremieux, W. Advani, R. Jarmusch, A. K. Aguirre, S. Lu, A. Dorrestein, P. C. Tsunoda, S. M. 2021-08-18 doi:10.1101/2021.08.17.456720 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Parallel pathways for rapid odor processing in lateral entorhinal cortex: Rate and temporal coding by layer 2 subcircuits ]]> https://biorxiv.org/content/10.1101/2021.08.19.456942v1?rss=1 Bitzenhofer, S. H. Westeinde, E. A. Zhang, H.-X. B. Isaacson, J. S. 2021-08-19 doi:10.1101/2021.08.19.456942 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Microscale concert hall acoustics to produce uniform ultrasound stimulation for targeted sonogenetics in hsTRPA1-transfected cells ]]> https://biorxiv.org/content/10.1101/2021.08.21.457135v1?rss=1 Vasan, A. Allein, F. Duque, M. Magaram, U. Boechler, N. Chalasani, S. H. Friend, J. 2021-08-22 doi:10.1101/2021.08.21.457135 Cold Spring Harbor Laboratory Press 2021-08-22 <![CDATA[ LRRK2 causes centrosomal deficits via phosphorylated Rab10 and RILPL1 at centriolar subdistal appendages ]]> https://biorxiv.org/content/10.1101/2021.08.23.457380v1?rss=1 Ordonez, A. J. L. Fernandez, B. Fasiczka, R. Naaldijk, Y. Fdez, E. Blanca Ramirez, M. Phan, S. Boassa, D. Hilfiker, S. 2021-08-24 doi:10.1101/2021.08.23.457380 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ A missense KCNQ1 Mutation Impairs Insulin Secretion in Neonatal Diabetes ]]> https://biorxiv.org/content/10.1101/2021.08.24.457485v1?rss=1 Zhou, Z. Gong, M. Pande, A. Lisewski, U. Röpke, T. Purfürst, B. Liang, L. Jia, S. Frühler, S. Margineanu, A. Zeng, C. Zhu, H. Kühnen, P. Khodaverdi, S. Krill, W. Chen, W. Sander, M. Raile, K. Izsvak, Z. 2021-08-26 doi:10.1101/2021.08.24.457485 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.08.25.457468v1?rss=1 Thakare, A. Ghosh, C. Alalamath, T. Kumar, N. Narang, H. Whadgar, S. Paul, K. Shrotri, S. Kumar, S. M, S. Rao, R. Chakraborty, M. Choudhary, B. Ghosh, S. K. Subramani, S. K. Swain, S. Srinivasan, S. 2021-08-27 doi:10.1101/2021.08.25.457468 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Systems analysis of the familial cardiomyopathy signaling network ]]> https://biorxiv.org/content/10.1101/2021.08.28.458032v1?rss=1 Khalilimeybodi, A. McCulloch, A. Omens, J. Saucerman, J. J. 2021-08-28 doi:10.1101/2021.08.28.458032 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Only females show a stable association between neuroticism and microstructural asymmetry of the cingulum across childhood and adolescence: A longitudinal DTI study ]]> https://biorxiv.org/content/10.1101/2021.08.31.458188v1?rss=1 Plachti, A. Baare, W. F. Johansen, L. B. Thompson, W. K. Siebner, H. R. Madsen, K. S. 2021-09-01 doi:10.1101/2021.08.31.458188 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Establishment of reference standards for multifaceted mosaic variant analysis ]]> https://biorxiv.org/content/10.1101/2021.08.31.458343v1?rss=1 Ha, Y.-J. Oh, M. J. Kim, J. Kim, J. Kang, S. Kim, H. S. Kim, S. 2021-08-31 doi:10.1101/2021.08.31.458343 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Functional connectivity of fMRI using differential covariance predicts structural connectivity and behavioral reaction times ]]> https://biorxiv.org/content/10.1101/2021.09.01.458609v1?rss=1 Chen, Y. Bukhari, Q. Lin, T. W. Sejnowski, T. J. 2021-09-03 doi:10.1101/2021.09.01.458609 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Ether Lipid Biosynthesis Promotes Lifespan Extension and Enables Diverse Prolongevity Paradigms ]]> https://biorxiv.org/content/10.1101/2021.09.02.457410v1?rss=1 Cedillo, L. Li, S. Ahsan, F. Emans, S. Adedoja, A. Dao, K. Li, Z. Peterson, N. Watrous, J. Jain, M. Das, S. Pukkila-Worley, R. Soukas, A. A. 2021-09-03 doi:10.1101/2021.09.02.457410 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Human spindle variability ]]> https://biorxiv.org/content/10.1101/2021.09.02.458632v1?rss=1 Gonzalez, C. E. Jiang, X. Gonzalez-Martinez, J. Halgren, E. 2021-09-03 doi:10.1101/2021.09.02.458632 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors ]]> https://biorxiv.org/content/10.1101/2021.09.03.458897v1?rss=1 Reher, R. Aron, A. T. Fajtova, P. Liu, C. Ben Shalom, I. Y. Bittremieux, W. Wang, M. Matos-Hernandez, M. L. Alexander, K. L. Caro-Diaz, E. J. Naman, C. B. Dorrestein, P. C. O'Donoghue, A. J. Gerwick, W. H. Petras, D. 2021-09-04 doi:10.1101/2021.09.03.458897 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Transcriptome phylogenies support ancient evolutionary transitions in bioluminescence traits of cypridinid ostracods ]]> https://biorxiv.org/content/10.1101/2021.09.03.458903v1?rss=1 Ellis, E. A. Goodheart, J. A. Hensley, N. M. Gonzalez, V. L. Reda, N. J. Rivers, T. J. Morin, J. G. Torres, E. Gerrish, G. A. Oakley, T. H. 2021-09-05 doi:10.1101/2021.09.03.458903 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Network Modeling Predicts Personalized Gene Expression and Drug Responses in Valve Myofibroblasts Cultured with Patient Sera ]]> https://biorxiv.org/content/10.1101/2021.09.04.458984v1?rss=1 Rogers, J. D. Aguado, B. A. Watts, K. Anseth, K. S. Richardson, W. J. 2021-09-06 doi:10.1101/2021.09.04.458984 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Cyclic mechanical stresses alter erythrocyte membrane composition and microstructure and trigger macrophage phagocytosis ]]> https://biorxiv.org/content/10.1101/2021.09.10.459518v1?rss=1 Garcia-Herreros, A. Yeh, Y.-T. Peng, Z. del Alamo, J. C. 2021-09-11 doi:10.1101/2021.09.10.459518 Cold Spring Harbor Laboratory Press 2021-09-11 <![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[ Probing neuropeptide volume transmission in vivo by a novel all-optical approach ]]> https://biorxiv.org/content/10.1101/2021.09.10.459853v1?rss=1 Xiong, H. Lacin, E. Ouyang, H. Naik, A. Xu, X. Xie, C. Youn, J. Kumar, K. Kern, T. Aisenberg, E. Kircher, D. Li, X. Zasadzinski, J. A. Mateo, C. Kleinfeld, D. Hrabetova, S. Slesinger, P. Qin, Z. 2021-09-11 doi:10.1101/2021.09.10.459853 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ A caged DAMGO for selective photoactivation of endogenous mu opioid receptors ]]> https://biorxiv.org/content/10.1101/2021.09.13.460181v1?rss=1 Ma, X. He, X. J. Banghart, M. R. 2021-09-14 doi:10.1101/2021.09.13.460181 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania ]]> https://biorxiv.org/content/10.1101/2021.09.14.460245v1?rss=1 Cuypers, B. Meysman, P. Erb, I. Bittremieux, W. Valkenborg, D. Baggerman, G. Mertens, I. Sundar, S. Khanal, B. Notredame, C. Dujardin, J.-C. Domagalska, M. A. Laukens, K. 2021-09-15 doi:10.1101/2021.09.14.460245 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Hidden conformations differentiate day and night in a circadian pacemaker ]]> https://biorxiv.org/content/10.1101/2021.09.14.460370v1?rss=1 Swan, J. Sandate, C. Chavan, A. Freeberg, A. Etwaru, D. Ernst, D. Palacios, J. Golden, S. LiWang, A. Lander, G. C. Partch, C. 2021-09-15 doi:10.1101/2021.09.14.460370 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ A Comparison of Methods to Harmonize Cortical Thickness Measurements Across Scanners and Sites ]]> https://biorxiv.org/content/10.1101/2021.09.22.461242v1?rss=1 Sun, D. Rakesh, G. Clarke-Rubright, E. K. Haswell, C. C. Logue, M. O'Leary, B. M. Cotton, A. S. Xie, H. Dennis, E. L. Jahanshad, N. Salminen, L. E. Thomopolous, S. I. Rashid, F. Ching, C. R. K. Koch, S. B. J. Frijling, J. L. Nawijn, L. van Zuiden, M. Zhu, X. Suarez-Jimenez, B. Sierk, A. Walter, H. Manthey, A. Stevens, J. S. Fani, N. van Rooij, S. J. H. Stein, M. Bomyea, J. Koerte, I. K. Choi, K. van der Werff, S. J. A. Vermeiren, R. R. J. M. Herzog, J. Lebois, L. A. M. Baker, J. T. Ressler, K. J. Olson, E. A. Straube, T. Korgaonkar, M. S. Andrew, E. Zhu, 2021-09-24 doi:10.1101/2021.09.22.461242 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ LXR agonist Prevents Peripheral Neuropathy and modifies PNS immune cells in Aged Mice ]]> https://biorxiv.org/content/10.1101/2021.09.22.461263v1?rss=1 Gavini, C. Elshareif, N. Germanwala, A. Aubert, G. Calcutt, N. Aubert, V. 2021-09-24 doi:10.1101/2021.09.22.461263 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ The impact of phosphorylated Pten at threonine 366 on cortical connectivity and behaviour ]]> https://biorxiv.org/content/10.1101/2021.09.22.461341v1?rss=1 Ledderose, J. Benitez, J. A. Roberts, A. J. Reed, R. Bintig, W. Sachdev, R. Furnari, F. Eickholt, B. 2021-09-24 doi:10.1101/2021.09.22.461341 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Salt leverages polyethylene terephthalate hydrolase (PETase) enzymatic activity via the predicted conformational switch ]]> https://biorxiv.org/content/10.1101/2021.09.23.461413v1?rss=1 Shiryaev, S. A. Cieplak, P. Chernov, A. V. 2021-09-23 doi:10.1101/2021.09.23.461413 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Disentangling heterogeneity of Malignant Pleural Mesothelioma through deep integrative omics analyses ]]> https://biorxiv.org/content/10.1101/2021.09.27.461908v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@b6c43corg.highwire.dtl.DTLVardef@10d45a9org.highwire.dtl.DTLVardef@58746eorg.highwire.dtl.DTLVardef@143f880_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mangiante, L. Alcala, N. Di Genova, A. Sexton-Oates, A. Gonzalez-Perez, A. Khandekar, A. Bergstrom, E. Kim, J. Giacobi, C. Le-Stang, N. Boyault, S. Cuenin, C. Tabone-Eglinger, S. Damiola, F. Voegele, C. Ardin, M. Michallet, M.-C. Soudade, L. Delhomme, T. Poret, A. Brevet, M. Copin, M.-C. Giusiano-Courcambeck, S. Damotte, D. Girard, C. Hofman, V. Hofman, P. Mouroux, J. Lacomme, S. Mazieres, J. Thomas de Montpreville, V. Perrin, C. Planchard, G. Rouquette, I. Sagan, C. Scherpereel, A. Thivolet, F. Vignaud, J.-M. Jean, D. Gilg Soit Ilg, A. Olaso, R. Meyer, 2021-09-29 doi:10.1101/2021.09.27.461908 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ GABAB receptor/HCN channel complexes in VTA dopamine neurons limit synaptic inhibition and prevent anxiety-like behavior ]]> https://biorxiv.org/content/10.1101/2021.09.27.461912v1?rss=1 Bettler, B. Rizzi, G. Fritzius, T. Perez-Garci, E. Porcu, A. Besseyrias, V. Gassmann, M. Tan, K. R. 2021-09-27 doi:10.1101/2021.09.27.461912 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Two helices control the dynamic crosstalk between the catalytic domains of LRRK2 ]]> https://biorxiv.org/content/10.1101/2021.09.29.462278v1?rss=1 Weng, J.-H. Aoto, P. C. Lorenz, R. Wu, J. Schmidt, S. H. Manschwetus, J. T. Kaila-Sharma, P. Mathea, S. Knapp, S. Herberg, F. W. Taylor, S. S. 2021-09-29 doi:10.1101/2021.09.29.462278 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Repurposing CAR targets in solid tumors via a pan-cancer single-cell transcriptome analysis ]]> https://biorxiv.org/content/10.1101/2021.09.29.462485v1?rss=1 Madan, S. Schaffer, A. A. Ruppin, E. 2021-10-01 doi:10.1101/2021.09.29.462485 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ INF2-mediated actin filament reorganization confers intrinsic resilience to neuronal ischemic injury ]]> https://biorxiv.org/content/10.1101/2021.10.01.462790v1?rss=1 Calabrese, B. Jones, S. Yamaguchi-Shiraishi, Y. Lingelbach, M. J. Manor, U. Svitkina, T. M. Higgs, H. N. Shih, A. Y. Halpain, S. 2021-10-01 doi:10.1101/2021.10.01.462790 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Structure selected RBM immunogens prime polyclonal memory responses that neutralize SARS-CoV-2 variants of concern ]]> https://biorxiv.org/content/10.1101/2021.10.01.462840v1?rss=1 Almanza, G. Kouznetsova, V. Clark, A. E. Olmedillas, E. Castro, A. Tsigelny, I. F. Wu, Y. Gao, G. F. Ollmann Saphire, E. Carlin, A. F. Zanetti, M. 2021-10-04 doi:10.1101/2021.10.01.462840 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ A mechanochemical model recapitulates distinct vertebrate gastrulation modes ]]> https://biorxiv.org/content/10.1101/2021.10.03.462928v1?rss=1 Serra, M. Najera, G. S. Chuai, M. Spandan, V. Weijer, C. J. Mahadevan, L. 2021-10-03 doi:10.1101/2021.10.03.462928 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Local conjugation of auxin by the GH3 amido synthetases is required for normaldevelopment of roots and flowers in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2021.10.04.463114v1?rss=1 Guo, R. Hu, Y. Aoi, Y. Hira, H. Ge, C. Dai, X. Kasahara, H. Zhao, Y. 2021-10-05 doi:10.1101/2021.10.04.463114 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2021.10.04.463121v1?rss=1 LaSalle, T. J. Gonye, A. L. K. Freeman, S. S. Kaplonek, P. Gushterova, I. Kays, K. R. Manakongtreecheep, K. Tantivit, J. Rojas-Lopez, M. Russo, B. C. Sharma, N. Thomas, M. F. Lavin-Parsons, K. M. Lilly, B. M. Mckaig, B. N. Charland, N. C. Khanna, H. K. Lodenstein, C. L. Margolin, J. D. Blaum, E. M. Lirofonis, P. B. Sonny, A. Bhattacharyya, R. P. Parry, B. A. Goldberg, M. B. Alter, G. Filbin, M. R. Villani, A. C. Hacohen, N. Sade-Feldman, M. 2021-10-05 doi:10.1101/2021.10.04.463121 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals ]]> https://biorxiv.org/content/10.1101/2021.10.05.463211v1?rss=1 50% of orange-red light available to the photosynthetic symbionts at mesophotic depths. We further show that upregulation of pink CPs in shallow-water corals during bleaching leads to a reduction of orange light by 10-20% compared to low-CP tissue. Thus, screening by CPs has an important role in mitigating the light-enhancing effect of coral tissue scattering during bleaching. Our results provide the first experimental quantification of the importance of GFP-like proteins in fine-tuning the light microclimate of corals during photoacclimation. ]]> Bollati, E. Lyndby, N. H. D'Angelo, C. Kühl, M. Wiedenmann, J. Wangpraseurt, D. 2021-10-07 doi:10.1101/2021.10.05.463211 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ A supervised fingerprint-based strategy to connect natural product mass spectrometry fragmentation data to their biosynthetic gene clusters ]]> https://biorxiv.org/content/10.1101/2021.10.05.463235v1?rss=1 Leao, T. F. Wang, M. da Silva, R. van der Hooft, J. J. J. Bauermeister, A. Brejnrod, A. D. Glukhov, E. Gerwick, L. Gerwick, W. H. Bandeira, N. Dorrestein, P. C. 2021-10-06 doi:10.1101/2021.10.05.463235 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds ]]> https://biorxiv.org/content/10.1101/2021.10.06.463301v1?rss=1 Sauvey, C. Ehrenkaufer, G. Blevitt, J. Jackson, P. Abagyan, R. 2021-10-07 doi:10.1101/2021.10.06.463301 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ A sensitive and specific genetically encodable biosensor for potassium ions ]]> https://biorxiv.org/content/10.1101/2021.10.07.463410v1?rss=1 Wu, S.-Y. Wen, Y. Serre, N. B. C. Laursen, C. C. H. Dietz, A. G. Taylor, B. R. Aggarwal, A. Rancic, V. Becker, M. Ballanyi, K. Podgorski, K. Hirase, H. Nedergaard, M. Fendrych, M. Lemieux, M. J. Eberl, D. F. Kay, A. R. Campbell, R. E. Shen, Y. 2021-10-09 doi:10.1101/2021.10.07.463410 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ A Proposed Unified Interphase Nucleus Chromosome Structure: Preliminary Preponderance of Evidence ]]> https://biorxiv.org/content/10.1101/2021.10.08.463051v1?rss=1 Sedat, J. McDonald, A. Cang, H. Lucas, J. S. Arigovindan, M. Kam, Z. Murre, C. Elbaum, M. 2021-10-09 doi:10.1101/2021.10.08.463051 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality ]]> https://biorxiv.org/content/10.1101/2021.10.10.463858v1?rss=1 Hawkey, J. Vezina, B. Monk, J. Judd, L. M. Harshegyi, T. Lopez-Fernandez, S. Rodrigues, C. Brisse, S. Holt, K. E. Wyres, K. L. 2021-10-11 doi:10.1101/2021.10.10.463858 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Catestatin selects for the colonization of antimicrobial-resistant gut bacterial communities ]]> https://biorxiv.org/content/10.1101/2021.10.11.463921v1?rss=1 Gonzalez-Davila, P. Schwalbe, M. Danewalia, A. Dalile, B. Verbeke, K. Mahata, S. K. El Aidy, S. 2021-10-11 doi:10.1101/2021.10.11.463921 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Spatial regulation of AMPK signaling revealed by a sensitive kinase activity reporter ]]> https://biorxiv.org/content/10.1101/2021.10.11.463987v1?rss=1 Schmitt, D. L. Curtis, S. D. Leung, A. Zhang, J.-f. Chen, M. He, C. Y. Mehta, S. Rangamani, P. Shaw, R. J. Zhang, J. 2021-10-11 doi:10.1101/2021.10.11.463987 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ MicroPET evidence for a hypersensitive neuroinflammatory profile of gp120 mouse model of HIV ]]> https://biorxiv.org/content/10.1101/2021.10.11.463989v1?rss=1 Young, J. W. Barback, C. V. Stolz, L. A. Groman, S. M. Vera, D. R. Hoh, C. Kotta, K. K. Minassian, A. Powell, S. B. Brody, A. L. 2021-10-12 doi:10.1101/2021.10.11.463989 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Chemical inhibition of auxin inactivation pathway uncovers the metabolic turnover of auxin homeostasis ]]> https://biorxiv.org/content/10.1101/2021.10.12.464031v1?rss=1 Fukui, K. Arai, K. Tanaka, Y. Aoi, Y. Kukshal, V. Jez, J. M. Kubes, M. F. Napier, R. Zhao, Y. Kasahara, H. Hayashi, K.-i. 2021-10-13 doi:10.1101/2021.10.12.464031 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.10.12.464152v1?rss=1 Ryu, J. K. Sozmen, E. G. Dixit, K. Montano, M. Matsui, Y. Liu, Y. Helmy, E. Deerinck, T. J. Yan, Z. Schuck, R. Acevedo, R. M. Spencer, C. M. Thomas, R. Pico, A. R. Zamvil, S. S. Lynch, K. L. Ellisman, M. H. Greene, W. C. Akassoglou, K. 2021-10-13 doi:10.1101/2021.10.12.464152 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Modular, robust and extendible multicellular circuit design in yeast ]]> https://biorxiv.org/content/10.1101/2021.10.13.464175v1?rss=1 Carignano, A. Chen, D. H. Mallory, C. Wright, C. Seelig, G. Klavins, E. 2021-10-14 doi:10.1101/2021.10.13.464175 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Microscopic Quantification of Oxygen Consumption across Cortical Layers ]]> https://biorxiv.org/content/10.1101/2021.10.13.464176v1?rss=1 Mächler, P. Fomin-Thunemann, N. Thunemann, M. Saetra, M. J. Desjardins, M. Kılıc, K. Sencan, I. Li, B. Saisan, P. Cheng, Q. Weldy, K. L. Boas, D. A. Buxton, R. B. Einevoll, G. T. Dale, A. M. Sakadzic, S. Devor, A. 2021-10-14 doi:10.1101/2021.10.13.464176 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ A Proposed Unified Mitotic Chromosome Architecture ]]> https://biorxiv.org/content/10.1101/2021.10.14.464227v1?rss=1 Sedat, J. McDonald, A. Kasler, H. G. Verdin, E. Cang, H. Murre, C. Elbaum, M. 2021-10-14 doi:10.1101/2021.10.14.464227 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Decoding of cortex-wide brain activity from local recordings of neural potentials ]]> https://biorxiv.org/content/10.1101/2021.10.14.464468v1?rss=1 Liu, X. Ren, C. Huang, Z. Wilson, M. Kim, J.-H. Lu, Y. Ramezani, M. Komiyama, T. Kuzum, D. 2021-10-16 doi:10.1101/2021.10.14.464468 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Immunogenic potential of neopeptides depends on parent protein subcellular location ]]> https://biorxiv.org/content/10.1101/2021.10.16.464599v1?rss=1 Castro, A. Kaabinejadian, S. Hildebrand, W. Zanetti, M. Carter, H. 2021-10-16 doi:10.1101/2021.10.16.464599 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Cellular perception of growth rate and the mechanistic origin of bacterial growth laws ]]> https://biorxiv.org/content/10.1101/2021.10.16.464649v1?rss=1 Wu, C. Balakrishnan, R. Mori, M. Manzanarez, G. Zhang, Z. Hwa, T. 2021-10-16 doi:10.1101/2021.10.16.464649 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation ]]> https://biorxiv.org/content/10.1101/2021.10.17.464753v1?rss=1 Chen, Y. S. Tracy, S. Harjono, V. Xu, F. Moresco, J. J. Yates, J. R. Zid, B. M. 2021-10-18 doi:10.1101/2021.10.17.464753 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Structural network alterations in focal and generalized epilepsy follow axes of epilepsy risk gene expression: An ENIGMA study ]]> https://biorxiv.org/content/10.1101/2021.10.18.464713v1?rss=1 Lariviere, S. Royer, J. Rodriguez-Cruces, R. Caligiuri, M. E. Gambardella, A. Concha, L. Keller, S. S. Cendes, F. Yasuda, C. L. Bonilha, L. Gleichgerrcht, E. Focke, N. K. Domin, M. von Podewills, F. Langner, S. Rummel, C. Wiest, R. Martin, P. Kotikalapudi, R. OBrien, T. J. Sinclair, B. Vivash, L. Desmond, P. M. Lui, E. Vaudano, A. E. Meletti, S. Tondelli, M. Alhusaini, S. Doherty, C. P. Cavalleri, G. L. Delanty, N. Kalviainen, R. Jackson, G. D. Kowalczyk, M. Mascalchi, M. Semmelroch, M. Thomas, R. H. Soltanian-Zadeh, H. Davoodi-Bojd, E. Zhang, J. Kreilka 2021-10-19 doi:10.1101/2021.10.18.464713 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Genome-wide association study of open fieldbehavior in outbred heterogeneous stock ratsidentifies multiple loci implicated inpsychiatric disorders ]]> https://biorxiv.org/content/10.1101/2021.10.18.464872v1?rss=1 Gunturkun, M. H. Wang, T. Chitre, A. S. Martinez, A. G. Holl, K. St. Pierre, C. Bimschleger, H. Gao, J. Cheng, R. Polesskaya, O. Solberg-Woods, L. C. Palmer, A. A. Chen, H. 2021-10-19 doi:10.1101/2021.10.18.464872 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ The landscape of extrachromosomal circular DNA in medulloblastoma ]]> https://biorxiv.org/content/10.1101/2021.10.18.464907v1?rss=1 Chapman, O. S. Luebeck, J. Wani, S. Tiwari, A. Pagadala, M. Wang, S. Larson, J. D. Lange, J. T. Wong, I. T.-L. Dehkordi, S. R. Chandran, S. Adam, M. Lin, Y. Juarez, E. Robinson, J. T. Sridhar, S. Malicki, D. M. Coufal, N. Levy, M. Crawford, J. R. Pomeroy, S. L. Rich, J. Scheuermann, R. Carter, H. Dixon, J. Mischel, P. S. Fraenkel, E. Wechsler-Reya, R. J. Bafna, V. Mesirov, J. P. Chavez, L. 2021-10-19 doi:10.1101/2021.10.18.464907 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks ]]> https://biorxiv.org/content/10.1101/2021.10.19.465028v1?rss=1 Hernandez Mesa, M. van der Brink, J. Louch, W. E. McCabe, K. Rangamani, P. 2021-10-19 doi:10.1101/2021.10.19.465028 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Discovery of Potent Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L ]]> https://biorxiv.org/content/10.1101/2021.10.19.465036v1?rss=1 Meewan, I. Kattoula, J. Kattoula, J. Skinner, D. Fajtov, P. Giardini, M. Woodworth, B. McKerrow, J. Siqueira-Neto, J. O'Donoghue, A. J. Abagyan, R. 2021-10-20 doi:10.1101/2021.10.19.465036 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Human milk oligosaccharides reduce murine group B Streptococcus vaginal colonization with minimal impact on the vaginal microbiota ]]> https://biorxiv.org/content/10.1101/2021.10.20.465155v1?rss=1 Mejia, M. E. Ottinger, S. Vrbanac, A. Babu, P. Zulk, J. Moorshead, D. Bode, L. Nizet, V. Patras, K. 2021-10-20 doi:10.1101/2021.10.20.465155 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Commensal bacteria promote type I interferon signaling to maintain immune tolerance ]]> https://biorxiv.org/content/10.1101/2021.10.21.464743v1?rss=1 Vasquez Ayala, A. Matsuo, K. Hsu, C.-Y. Carrillo Terrazas, M. Chu, H. 2021-10-21 doi:10.1101/2021.10.21.464743 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ E-Cannula reveals anatomical diversity in sharp-wave ripples as a driver for the recruitment of distinct hippocampal assemblies ]]> https://biorxiv.org/content/10.1101/2021.10.22.465514v1?rss=1 Liu, X. Terada, S. Kim, J. Lu, Y. Ramezani, M. Grosmark, A. D. Losonczy, A. Kuzum, D. 2021-10-24 doi:10.1101/2021.10.22.465514 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha ]]> https://biorxiv.org/content/10.1101/2021.10.25.465724v1?rss=1 Sahu, A. Wang, X. Munson, P. Klomp, J. Wang, X. Gu, S. Qian, G. Nicol, P. Zeng, Z. Wang, C. Tokheim, C. Zhang, W. Fu, J. Wang, J. Nair, N. Rens, J. Bourajjaj, M. Jansen, B. Leenders, I. Lemmers, J. Musters, M. Zanten, S. Zelst, L. Worthington, J. Brown, M. Liu, J. Juric, D. Meyer, C. Oubrie, A. Liu, X. S. Fisher, D. Flaherty, K. 2021-10-26 doi:10.1101/2021.10.25.465724 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes ]]> https://biorxiv.org/content/10.1101/2021.10.25.465795v1?rss=1 10,000 gene-CRE pairs that contribute to gene expression programs in different cell types in the mouse brain. ]]> Xie, F. Armand, E. J. Yao, Z. Liu, H. Bartlett, A. Behrens, M. M. Li, Y. E. Lucero, J. D. Luo, C. Nery, J. R. Pinto-Duarte, A. Poirion, O. Preissl, S. Rivkin, A. C. Tasic, B. Zeng, H. Ren, B. Ecker, J. R. Mukamel, E. A. 2021-10-28 doi:10.1101/2021.10.25.465795 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Some rats take more time to make easier perceptual decisions ]]> https://biorxiv.org/content/10.1101/2021.10.26.465587v1?rss=1 Reinagel, P. 2021-10-28 doi:10.1101/2021.10.26.465587 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Integration of GWAS and TWAS to elucidate the genetic architecture of natural variation for leaf cuticular conductance in maize ]]> https://biorxiv.org/content/10.1101/2021.10.26.465975v1?rss=1 Lin, M. Qiao, P. Matschi, S. Vasquez, M. Ramstein, G. P. Bourgault, R. Mohammadi, M. Scanlon, M. J. Molina, I. Smith, L. G. Gore, M. A. 2021-10-28 doi:10.1101/2021.10.26.465975 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Syrbactin-class dual constitutive- and immuno-proteasome inhibitor TIR-199 impedes myeloma-mediated bone degeneration in vivo. ]]> https://biorxiv.org/content/10.1101/2021.10.27.466109v1?rss=1 Tandon, V. Vala, R. M. Chen, A. Sah, R. Patel, H. M. Pirrung, M. C. Banerjee, S. 2021-10-27 doi:10.1101/2021.10.27.466109 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Cephalopod Retinal Development Shows Vertebrate-like Mechanisms of Neurogenesis ]]> https://biorxiv.org/content/10.1101/2021.10.28.466353v1?rss=1 Napoli, F. Daly, C. M. Neal, S. McCulloch, K. J. Zaloga, A. Liu, A. Koenig, K. M. 2021-10-28 doi:10.1101/2021.10.28.466353 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines ]]> https://biorxiv.org/content/10.1101/2021.10.29.466025v1?rss=1 Benaglio, P. Zhu, H. Okino, M.-L. Yan, J. Elgamal, R. Nariai, N. Beebe, E. Korgaonkar, K. Qiu, Y. Donovan, M. Chiou, J. Newsome, J. Kaur, J. Corban, S. Aylward, A. Taipale, J. Ren, B. Frazer, K. A. Sander, M. Gaulton, K. J. 2021-10-31 doi:10.1101/2021.10.29.466025 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1 Akey, C. Singh, D. Ouch, C. Echeverria, I. Nudelman, I. Varberg, J. M. Yu, Z. Fang, F. Shi, Y. Wang, J. Saltzberg, D. Song, K. Xu, C. Gumbart, J. Suslov, S. Unruh, J. Jaspersen, S. L. Chait, B. Sali, A. Menendez-Martinez, J. Ludke, S. J. Villa, E. Rout, M. 2021-10-29 doi:10.1101/2021.10.29.466335 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Selective Control of Synaptically-Connected Circuit Elements by All-Optical Synapses ]]> https://biorxiv.org/content/10.1101/2021.10.29.466531v1?rss=1 Prakash, M. Murphy, J. St Laurent, R. Friedman, N. Crespo, E. Bjorefeldt, A. Pal, A. Bhagat, Y. Kauer, J. A. Shaner, N. Lipscombe, D. Moore, C. Hochgeschwender, U. 2021-11-01 doi:10.1101/2021.10.29.466531 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Chronic Cochlear Implantation with and without Electric Stimulation in a Mouse Model Induces Robust Cochlear Influx of CX3CR1+/GFP Macrophages. ]]> https://biorxiv.org/content/10.1101/2021.10.31.466540v1?rss=1 Claussen, A. D. Vielman Quevedo, R. Higgins, T. Mostaert, B. Taifur Rahman, M. Kirk, J. R. Hirose, K. Hansen, M. R. 2021-11-03 doi:10.1101/2021.10.31.466540 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in PSC. ]]> https://biorxiv.org/content/10.1101/2021.10.31.466701v1?rss=1 Awoniyi, M. Wang, J. Ngo, B. Meadows, V. Tam, J. Viswanathan, A. Lai, Y. Montgomery, S. Farmer, M. Kummen, M. Thingholm, L. B. Schramm, C. Bang, C. Franke, A. Schnabl, B. Lu, K. Ting, J. P. Popov, Y. V. Hov, J. R. Francis, H. Sartor, R. B. 2021-11-01 doi:10.1101/2021.10.31.466701 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Initial efficacy determination and resistance profile of anti-Acinetobacter antibiotics, turnercyclamycins ]]> https://biorxiv.org/content/10.1101/2021.11.01.466777v1?rss=1 99% and >98% reduction in bacterial load compared to vehicle control in a thigh infection model at 25 and 12.5 mg/kg, respectively. This result closely reflected the anticipated effectiveness based upon in vitro activity and was similar to the colistin control. Acinetobacter strains resistant to colistin often harbor the mcr-1 resistance gene. Here, we show that the effectiveness of turnercyclamycins against Escherichia coli is not greatly altered by mcr-1 (0- to 2-fold) whereas there is a 16-fold increase in the colistin minimal inhibitory concentration when mcr-1 is present. These data suggest that turnercyclamycins are suitable for further investigation and optimization as anti-Acinetobacter lead compounds. ]]> Miller, B. W. Lim, A. L. Haygood, M. G. Schmidt, E. 2021-11-03 doi:10.1101/2021.11.01.466777 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism ]]> https://biorxiv.org/content/10.1101/2021.11.04.467239v1?rss=1 Broddrick, J. T. Ware, M. A. Jallet, D. Palsson, B. O. Peers, G. 2021-11-04 doi:10.1101/2021.11.04.467239 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ A Simple Method to Dual Site-Specifically Label a Protein Using Tryptophan Auxotrophic Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.11.04.467337v1?rss=1 Wu, T. Joseph, S. 2021-11-04 doi:10.1101/2021.11.04.467337 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Multi-site phosphorylation of yeast Mif2/CENP-C promotes inner kinetochore assembly ]]> https://biorxiv.org/content/10.1101/2021.11.04.467375v1?rss=1 Hinshaw, S. M. Quan, Y. Cai, J. Zhou, A. Zhou, H. 2021-11-05 doi:10.1101/2021.11.04.467375 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Age-induced P-bodies become detrimental and shorten the lifespan of yeast ]]> https://biorxiv.org/content/10.1101/2021.11.05.467477v1?rss=1 Choi, J. Wang, S. Li, Y. Hao, N. Zid, B. M. 2021-11-05 doi:10.1101/2021.11.05.467477 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Association of cochlear outer hair cell - type II spiral ganglion afferents with protection from noise-induced hearing loss ]]> https://biorxiv.org/content/10.1101/2021.11.06.467554v1?rss=1 Cederholm, J. M. E. Parley, K. E. Perera, C. J. Jonquieres, G. v. Pinyon, J. L. Julien, J.-P. Ryugo, D. K. Ryan, A. F. Housley, G. D. 2021-11-06 doi:10.1101/2021.11.06.467554 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Chromogranin A plays a crucial role in the age-related development of insulin resistance and hypertension ]]> https://biorxiv.org/content/10.1101/2021.11.08.467835v1?rss=1 Liu, M. A. Jati, S. Tang, K. van den Bogaart, G. Ghosh, G. Mahata, S. K. 2021-11-10 doi:10.1101/2021.11.08.467835 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2021.11.10.467836v1?rss=1 Papadas, A. Deb, G. Officer, A. Cicala, A. Hope, C. Emmerich, P. Wiesner, J. Pagenkopf, A. Matkowskyj, K. Deming, D. A. Politi, K. Abrams, S. Harismendy, O. Asimakopoulos, F. 2021-11-13 doi:10.1101/2021.11.10.467836 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Real-time motion monitoring improves functional MRI data quality in infants ]]> https://biorxiv.org/content/10.1101/2021.11.10.468084v1?rss=1 D'Andrea, C. B. Kenley, J. K. Montez, D. F. Mirro, A. E. Miller, R. L. Earl, E. A. Koller, J. M. Sung, S. Yacoub, E. Elison, J. T. Fair, D. Dosenbach, N. U. F. Rogers, C. Smyser, C. D. Greene, D. J. 2021-11-11 doi:10.1101/2021.11.10.468084 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Wnt5A Signaling Blocks Progression of Experimental Visceral Leishmaniasis ]]> https://biorxiv.org/content/10.1101/2021.11.12.468361v1?rss=1 Maity, S. Chakraborty, A. Mahata, S. K. Roy, S. Das, A. K. Sen, M. 2021-11-13 doi:10.1101/2021.11.12.468361 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol ]]> https://biorxiv.org/content/10.1101/2021.11.12.468428v1?rss=1 Dommer, A. Casalino, L. Kearns, F. Rosenfeld, M. Wauer, N. Ahn, S.-H. Russo, J. Oliveira, S. Morris, C. Bogetti, A. Trifan, A. Brace, A. Sztain, T. Clyde, A. Ma, H. Chennubhotla, C. Lee, H. Turilli, M. Khalid, S. Tamayo-Mendoza, T. Welborn, M. Christiansen, A. Smith, D. G. A. Qiao, Z. Sirumalla, S. K. O'Connor, M. Manby, F. Anandkumar, A. Hardy, D. Phillips, J. Stern, A. Romero, J. Clark, D. Dorrell, M. Maiden, T. Huang, L. McCalpin, J. Woods, C. Gray, A. Williams, M. Barker, B. Rajapaksha, H. Pitts, R. Gibbs, T. Stone, J. Zuckerman, D. Muholland, 2021-11-15 doi:10.1101/2021.11.12.468428 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Cortex-independent open-loop control of a voluntary orofacial motor action ]]> https://biorxiv.org/content/10.1101/2021.11.15.465585v1?rss=1 Elbaz, M. Demers, M. Kleinfeld, D. Ethier, C. Deschenes, M. 2021-11-16 doi:10.1101/2021.11.15.465585 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Extending and using anatomical vocabularies in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) project ]]> https://biorxiv.org/content/10.1101/2021.11.15.467961v1?rss=1 300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data. ]]> Surles-Zeigler, M. C. Sincomb, T. Gillespie, T. H. de Bono, B. Bresnahan, J. Mawe, G. M. Grethe, J. S. Tappan, S. Heal, M. Martone, M. E. 2021-11-19 doi:10.1101/2021.11.15.467961 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Upregulation of CREB1 and FOXO1 transcription factor pathways in Neuregulin-1 mediated neuroprotection following ischemic stroke ]]> https://biorxiv.org/content/10.1101/2021.11.17.468955v1?rss=1 Bennett, K. R. Surles-Zeigler, M. C. Augello, C. J. Ako, E. Rodgers, V. G. J. Ford, B. D. 2021-11-17 doi:10.1101/2021.11.17.468955 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and non-ischemic human hearts ]]> https://biorxiv.org/content/10.1101/2021.11.21.469462v1?rss=1 Parvatiyar, M. S. Landim-Vieira, M. Childers, M. C. Wacker, A. L. Garcia, M. R. He, H. Singh, R. Brundage, E. A. Johnston, J. R. Whitson, B. A. Chase, P. B. Janssen, P. M. Regnier, M. Biesiadecki, B. J. Pinto, J. R. 2021-11-22 doi:10.1101/2021.11.21.469462 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Non-Invasive Skin Sampling Detects Systemically Administered Drugs in Humans ]]> https://biorxiv.org/content/10.1101/2021.11.22.469638v1?rss=1 Panitchpakdi, M. Weldon, K. C. Jarmusch, A. K. Gentry, E. C. Choi, A. Sepulveda, Y. Aguirre, S. Sun, K. Momper, J. D. Dorrestein, P. C. Tsunoda, S. M. 2021-11-25 doi:10.1101/2021.11.22.469638 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Milk Exosomes Cross the Blood-Brain Barrier in Murine Cerebral Cortex Endothelial Cells and Promote Dendritic Complexity in the Hippocampus and Brain Function in C57BL/6J Mice ]]> https://biorxiv.org/content/10.1101/2021.11.24.469889v1?rss=1 Zhou, F. Ebea, P. Mutai, E. Sukreet, S. Navazesh, S. Dogan, H. Li, W. CUI, J. Ji, P. Ramirez, D. M. ZEMPLENI, J. 2021-11-25 doi:10.1101/2021.11.24.469889 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Transcriptional profiles of a foliar fungal endophyte (Pestalotiopsis, Ascomycota) and its endohyphal bacterium (Luteibacter, Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation ]]> https://biorxiv.org/content/10.1101/2021.11.24.469969v1?rss=1 Shaffer, J. P. Carter, M. E. Spraker, J. E. Clark, M. Smith, B. Hockett, K. L. Baltrus, D. A. Arnold, E. 2021-11-25 doi:10.1101/2021.11.24.469969 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Systemic LSD1 inhibition prevents aberrant remodeling of metabolism in obesity ]]> https://biorxiv.org/content/10.1101/2021.11.25.469928v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@17232dcorg.highwire.dtl.DTLVardef@6940a0org.highwire.dtl.DTLVardef@11d3deorg.highwire.dtl.DTLVardef@6cc0fd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ramms, B. Pollow, D. P. Zhu, H. Nora, C. Harrington, A. R. Omar, I. Gordts, P. Wortham, M. Sander, M. 2021-11-25 doi:10.1101/2021.11.25.469928 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH ]]> https://biorxiv.org/content/10.1101/2021.11.28.470285v1?rss=1 Hung, K. L. Luebeck, J. Dehkordi, S. R. Coruh, C. Law, J. A. Greenleaf, W. J. Mischel, P. S. Bafna, V. Chang, H. Y. 2021-11-29 doi:10.1101/2021.11.28.470285 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Chronic adolescent exposure to cannabis in mice leads to long-term sex-biased changes in gene expression networks across brain regions ]]> https://biorxiv.org/content/10.1101/2021.11.30.470393v1?rss=1 Telese, F. Zuo, Y. Iemolo, A. Montilla-Perez, P. Li, H.-R. Yang, X. 2021-12-01 doi:10.1101/2021.11.30.470393 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Elucidating the acid-base mechanisms underlying otolith overgrowth in fish exposed to ocean acidification ]]> https://biorxiv.org/content/10.1101/2021.11.30.470671v1?rss=1 Kwan, G. T. Tresguerres, M. 2021-12-01 doi:10.1101/2021.11.30.470671 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ CRISPR gene-drive systems based on Cas9 nickases promote super-Mendelian inheritance in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.12.01.470847v1?rss=1 50%). Current technologies employ a Cas9 that introduces DNA double-strand breaks into the opposing wildtype allele to replace it with a copy of the gene drive allele via DNA homology-directed repair. Yet, the use of different Cas9s versions is unexplored, and alternative approaches could increase the available toolkit for gene-drive designs. Here, we report a novel gene-drive approach that relies on Cas9 nickases that generate staggered paired nicks in DNA to propagate the engineered gene-drive cassette. We show that generating 5 overhangs in the system yields efficient allelic conversion. The nickase gene-drive arrangement produces large, stereotyped deletions that are advantageous for targeting essential genes. Indeed, our nickase approach should expand the repertoire for gene-drive designs aimed at applications in mosquitoes and beyond. ]]> Lopez del Amo, V. Sanz Juste, S. Gantz, V. M. 2021-12-02 doi:10.1101/2021.12.01.470847 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Mechanisms of modulation of pre-mRNA 3D structural scaffolds for splicing substrate definition ]]> https://biorxiv.org/content/10.1101/2021.12.01.470860v1?rss=1 Saha, K. Ghosh, G. 2021-12-01 doi:10.1101/2021.12.01.470860 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Secreted ORF8 is a pathogenic cause of severe Covid-19 and potentially targetable with select NLRP3 inhibitors ]]> https://biorxiv.org/content/10.1101/2021.12.02.470978v1?rss=1 Wu, X. Manske, M. K. Ruan, G. Nowakowski, K. E. Abeykoon, J. P. Tang, X. Yu, Y. Witter, T. L. Taupin, V. Paludo, J. Ansell, S. M. Badley, A. D. Schellenberg, M. Witzig, T. E. 2021-12-03 doi:10.1101/2021.12.02.470978 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Reduced Dimension, Biophysical Neuron Models Constructed From Observed Data ]]> https://biorxiv.org/content/10.1101/2021.12.03.471194v1?rss=1 Clark, R. E. Fuller, L. Platt, J. Abarbanel, H. 2021-12-05 doi:10.1101/2021.12.03.471194 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ A new substrate triggers susceptibility by uncoupling a bacterial multidrug resistance efflux pump ]]> https://biorxiv.org/content/10.1101/2021.12.04.471113v1?rss=1 Spreacker, P. J. Thomas, N. E. Beeninga, W. F. Brousseau, M. Hibbs, K. M. Henzler-Wildman, K. A. 2021-12-05 doi:10.1101/2021.12.04.471113 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ Genetic conversion of a split-drive into a full-drive element ]]> https://biorxiv.org/content/10.1101/2021.12.05.471291v1?rss=1 Terradas, G. Bennett, J. B. Li, Z. Marshall, J. M. Bier, E. 2021-12-06 doi:10.1101/2021.12.05.471291 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Tailer: A Pipeline for Sequencing-Based Analysis of Non-Polyadenylated RNA 3' End Processing ]]> https://biorxiv.org/content/10.1101/2021.12.06.471174v1?rss=1 Nicholson-Shaw, T. Lykke-Andersen, J. 2021-12-06 doi:10.1101/2021.12.06.471174 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with loss of proteostasis ]]> https://biorxiv.org/content/10.1101/2021.12.06.471495v1?rss=1 Paxman, J. Zhou, Z. O'Laughlin, R. Li, Y. Tian, W. Su, H. Jiang, Y. Holness, S. E. Stasiowski, E. Tsimring, L. Pillus, L. Hasty, J. Hao, N. 2021-12-07 doi:10.1101/2021.12.06.471495 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Microneedle-mediated intratumoral delivery of anti-CTLA-4 promotes cDC1-dependent eradication of oral squamous cell carcinoma with limited irAEs ]]> https://biorxiv.org/content/10.1101/2021.12.07.471658v1?rss=1 90% tumor response, which is dependent on CD8 T cells and conventional dendritic cell type 1 (cDC1). However, local-MN delivery limited the distribution of anti-CTLA-4 antibody from areas distal to draining lymphatic basins. Employing Foxp3-GFPDTR transgenic mice to interrogate irAEs in vivo, we found that local-MN delivery of anti-CTLA-4 protects animals from irAEs observed with systemic therapy. Taken together, our findings support the exploration of MN-intratumoral ICI delivery as a viable strategy for HNSCC treatment with reduced irAEs, and the opportunity to target cDC1s as part of multimodal treatment options to boost ICI therapy. ]]> Gilardi, M. Saddawi-Konefka, R. Wu, V. H. Lopez-Ramirez, M. A. Wang, Z. Soto, F. Steffen, D. J. Proietto, M. Mikulski, Z. Miki, H. Sharabi, A. Kupor, D. Rueda, R. Hollern, D. P. Wang, J. Gutkind, J. S. 2021-12-07 doi:10.1101/2021.12.07.471658 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Directional Tuning of Phase Precession Properties in the Hippocampus ]]> https://biorxiv.org/content/10.1101/2021.12.08.471702v1?rss=1 Yiu, Y.-H. Leutgeb, J. K. Leibold, C. 2021-12-09 doi:10.1101/2021.12.08.471702 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats ]]> https://biorxiv.org/content/10.1101/2021.12.09.472024v1?rss=1 Luu, G. T. Lizama-Chamu, I. McCaughey, C. S. Sanchez, L. M. Wang, M. 2021-12-13 doi:10.1101/2021.12.09.472024 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Discovery and synthesis of hydroxy-L-proline based blockers of the neutral amino acid transporters SLC1A4 (ASCT1) and SLC1A5 (ASCT2). ]]> https://biorxiv.org/content/10.1101/2021.12.14.470456v1?rss=1 Kavanaugh, M. P. Lyda, B. R. Leary, G. P. Silvius, D. Natale, N. R. Esslinger, C. S. Seaver, B. Farnsworth, J. 2021-12-16 doi:10.1101/2021.12.14.470456 Cold Spring Harbor Laboratory Press 2021-12-16 <![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[ A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations ]]> https://biorxiv.org/content/10.1101/2021.12.16.472881v1?rss=1 Thomas, M. Jensen, F. Averly, B. Demartsev, V. Manser, M. B. Sainburg, T. Roch, M. Strandburg-Peshkin, A. 2021-12-17 doi:10.1101/2021.12.16.472881 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Electrical activity between skin cells regulates melanoma initiation ]]> https://biorxiv.org/content/10.1101/2021.12.19.473393v1?rss=1 Tagore, M. Hergenreder, E. Suresh, S. Baron, M. Perlee, S. Melendez, S. Hollmann, T. J. Ideker, T. Studer, L. White, R. 2021-12-21 doi:10.1101/2021.12.19.473393 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ ORA47 is a transcriptional regulator of a general stress response hub ]]> https://biorxiv.org/content/10.1101/2021.12.20.473540v1?rss=1 Zeng, L. Chen, H. Wang, Y. Hicks, D. Ke, H. Pruneda-Paz, J. Dehesh, K. 2021-12-21 doi:10.1101/2021.12.20.473540 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Intramolecular interactions enhance the potency of gallinamide A analogs against Trypanosoma cruzi ]]> https://biorxiv.org/content/10.1101/2021.12.22.473926v1?rss=1 Da Silva, E. B. Sharma, V. Hernandez-Alvarez, L. Tang, A. H. Stoye, A. O'Donoghue, A. J. Gerwick, W. H. Payne, R. J. McKerrow, J. H. Podust, L. M. 2021-12-23 doi:10.1101/2021.12.22.473926 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Single cell RNA-seq identifies developing corneal cell fates in the human cornea organoid ]]> https://biorxiv.org/content/10.1101/2021.12.23.471999v1?rss=1 Maiti, G. Rocha Monteiro de Barros, M. Hu, N. Roshan, M. Wahlin, K. J. Chakravarti, S. 2021-12-24 doi:10.1101/2021.12.23.471999 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Crosstalk between biochemical signaling and trafficking determines AMPAR dynamics in synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2021.12.23.473965v1?rss=1 Bell, M. Rangamani, P. 2021-12-23 doi:10.1101/2021.12.23.473965 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Systemic influences of mammary cancer on monocytes in mice ]]> https://biorxiv.org/content/10.1101/2021.12.24.474104v1?rss=1 Robinson, A. Burgess, M. Webb, S. Louwe, P. Ouyang, Z. Skola, D. Han, C. Z. Batada, N. N. Gonzalez, V. Cassetta, L. Glass, C. K. Jenkins, S. J. Pollard, J. W. 2021-12-24 doi:10.1101/2021.12.24.474104 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Phylogeographic analysis reveals an ancient East African origin of the human herpes simplexvirus 2 dispersal out-of-Africa. ]]> https://biorxiv.org/content/10.1101/2022.01.03.474822v1?rss=1 Havens, J. L. Calvignac-Spencer, S. Merkel, K. Burrel, S. Boutolleau, D. Wertheim, J. O. 2022-01-04 doi:10.1101/2022.01.03.474822 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Calculation of centralities in protein kinase A ]]> https://biorxiv.org/content/10.1101/2022.01.03.474877v1?rss=1 Kornev, A. P. Aoto, P. Taylor, S. 2022-01-04 doi:10.1101/2022.01.03.474877 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Evaluating Human Mutation Databases for 'Treatability' Using Personalized Antisense Oligonucleotides ]]> https://biorxiv.org/content/10.1101/2022.01.04.474998v1?rss=1 Gleeson, J. G. Tang, I. Mittal, S. 2022-01-06 doi:10.1101/2022.01.04.474998 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Towards transboundary networks of climate-smart marine reserves in the Southern California Bight ]]> https://biorxiv.org/content/10.1101/2022.01.04.475006v1?rss=1 Arafeh-Dalmau, N. Munguia-Vega, A. Micheli, F. Vilalta-Navas, A. Villasenor-Derbez, J. C. Precoma-de la Mora, M. Schoeman, D. S. Medellin-Ortiz, A. Cavanaugh, K. C. Sosa-Nishizaki, O. Burnham, T. L. U. Knight, C. J. Woodson, C. B. Abas, M. Abadia-Cardoso, A. Aburto-Oropeza, O. Esgro, M. W. Espinosa-Andrade, N. Beas-Luna, R. Cardenas, N. Carr, M. H. Dale, K. E. Cisneros-Soberanis, F. Flores-Morales, A. L. Fulton, S. Garcia-Rodriguez, E. Giron-Nava, A. Gleason, M. G. Green, A. L. Hernandez-Velasco, A. Ibarra-Macias, B. Johnson, A. F. Lorda, J. Malpica-Cruz, L. M 2022-01-05 doi:10.1101/2022.01.04.475006 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release ]]> https://biorxiv.org/content/10.1101/2022.01.06.475261v1?rss=1 Bibel, B. Elkayam, E. Silletti, S. Komives, E. A. Joshua-Tor, L. 2022-01-06 doi:10.1101/2022.01.06.475261 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Functional oscillation of a multienzyme glucosome assembly during cell cycle progression ]]> https://biorxiv.org/content/10.1101/2022.01.06.475270v1?rss=1 Jeon, M. Schmitt, D. L. Kyoung, M. An, S. 2022-01-07 doi:10.1101/2022.01.06.475270 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ Localized Synaptic Potentiation is Necessary and Sufficient for Context Fear Memory ]]> https://biorxiv.org/content/10.1101/2022.01.09.475530v1?rss=1 Cardozo, L. M. Dillingham, B. C. Sousa, A. F. Dang, W. Job, N. Yoo, E. J. Ranamukhaarachchi, S. K. Yuan, Q. Mayford, M. 2022-01-11 doi:10.1101/2022.01.09.475530 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas ]]> https://biorxiv.org/content/10.1101/2022.01.10.475285v1?rss=1 Stopfer, L. E. Rettko, N. Leddy, O. Mesfin, J. M. Brown, E. Winski, S. Bryson, B. D. Wells, J. A. White, F. 2022-01-12 doi:10.1101/2022.01.10.475285 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Type I IFN promotes pathogenic inflammatory monocyte maturation during H5N1 infection ]]> https://biorxiv.org/content/10.1101/2022.01.10.475751v1?rss=1 Fourati, S. Jimenez-Morales, D. Hultquist, J. F. Chang, M. W. Benner, C. Krogan, N. J. Pache, L. Chanda, S. Sekaly, R.-P. Garcia-Sastre, A. Uccellini, M. B. 2022-01-11 doi:10.1101/2022.01.10.475751 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Machine-learning from Pseudomonas putida transcriptomes reveals its transcriptional regulatory network ]]> https://biorxiv.org/content/10.1101/2022.01.11.475908v1?rss=1 Lim, H. G. Rychel, K. Sastry, A. V. Mueller, J. Niu, W. Feist, A. M. Palsson, B. O. 2022-01-12 doi:10.1101/2022.01.11.475908 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Epigenetic dysregulation from chromosomal transit in micronuclei ]]> https://biorxiv.org/content/10.1101/2022.01.12.475944v1?rss=1 Agustinus, A. Raviram, R. Dameracharla, B. Luebeck, J. Stransky, S. Scipioni, L. Myers, R. DiBona, M. Duran, M. Weigelt, B. Yomtoubian, S. Toufektchan, E. Mischel, P. Mittal, V. Shah, S. Maciejowski, J. Gratton, E. Ly, P. Bakhoum, M. Landau, D. Bafna, V. Sidoli, S. David, Y. Bakhoum, S. F. 2022-01-12 doi:10.1101/2022.01.12.475944 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Epac1 regulates cellular SUMOylation by promoting the formation of SUMO-activating nuclear condensates ]]> https://biorxiv.org/content/10.1101/2022.01.12.476066v1?rss=1 Yang, W. Robichaux, W. G. Mei, F. C. Lin, W. Li, L. Pan, S. White, M. A. Chen, Y. Cheng, X. 2022-01-12 doi:10.1101/2022.01.12.476066 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease ]]> https://biorxiv.org/content/10.1101/2022.01.13.475329v1?rss=1 Jambeau, M. Meyer, K. D. Hruska-Plochan, M. Tabet, R. Lee, C.-Z. Ray-Soni, A. Aguilar, C. Savage, K. Mishra, N. Cavegn, N. Borter, P. Lin, C.-C. Jansen-West, K. Jiang, J. Freyermuth, F. Li, N. De Rossi, P. Perez-Berlanga, M. Jiang, X. Daughrity, L. M. Pereira, J. Narayanan, S. Gu, Y. Dhokai, S. Dalkilic-Liddle, I. Maniecka, Z. Weber, J. Workman, M. McAlonis-Downes, M. Berezovski, E. Zhang, Y.-J. Berry, J. Wainger, B. J. Kankel, M. W. Rushe, M. Hock, C. Nitsch, R. M. Cleveland, D. W. Petrucelli, L. Gendron, T. Montrasio, F. Grimm, J. Polymenidou, M. La 2022-01-15 doi:10.1101/2022.01.13.475329 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats ]]> https://biorxiv.org/content/10.1101/2022.01.15.476391v1?rss=1 Blanton, J. M. Peoples, L. M. Gerringer, M. E. Iacuniello, C. M. Gallo, N. D. Linley, T. D. Jamieson, A. J. Drazen, J. C. Bartlett, D. H. Allen, E. E. 2022-01-16 doi:10.1101/2022.01.15.476391 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Phenotypic dissection of epithelial lineages and therapeutic manipulation of differentiation programs in human Adenoid Cystic Carcinomas ]]> https://biorxiv.org/content/10.1101/2022.01.19.476843v1?rss=1 Viragova, S. Aparicio, L. Zhao, J. Valencia Salazar, L. E. Schurer, A. Dhuri, A. Sahoo, D. Moskaluk, C. A. Rabadan, R. Dalerba, P. 2022-01-21 doi:10.1101/2022.01.19.476843 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Molecular and connectomic vulnerability shape cross-disorder cortical abnormalities ]]> https://biorxiv.org/content/10.1101/2022.01.21.476409v1?rss=1 Hansen, J. Y. Shafiei, G. Y. Vogel, J. W. Smart, K. Bearden, C. E. Hoogman, M. Franke, B. van Rooij, D. Buitelaar, J. McDonald, C. R. Sisodiya, S. Schmaal, L. Veltman, D. J. van den Heuvel, O. A. Stein, D. J. van Erp, T. G. Ching, C. Andreassen, O. A. Hajek, T. Opel, N. Modinos, G. Aleman, A. van der Werf, Y. Jahanshad, N. Thomopoulos, S. I. Thompson, P. M. Carson, R. E. Dagher, A. Misic, B. 2022-01-21 doi:10.1101/2022.01.21.476409 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Immune-responsive biodegradable scaffolds for enhancing neutrophil regeneration ]]> https://biorxiv.org/content/10.1101/2022.01.21.477275v1?rss=1 Kerr, M. McBride, D. Johnson, W. Chumber, A. Najibi, A. Seo, B. R. Stafford, A. Scadden, D. Mooney, D. Shah, N. 2022-01-23 doi:10.1101/2022.01.21.477275 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Structural basis for Parkinson's Disease-linked LRRK2's binding to microtubules ]]> https://biorxiv.org/content/10.1101/2022.01.21.477284v1?rss=1 Snead, D. M. Matyszewski, M. Dickey, A. M. Lin, Y. X. Leschziner, A. E. Reck-Peterson, S. L. 2022-01-22 doi:10.1101/2022.01.21.477284 Cold Spring Harbor Laboratory Press 2022-01-22 <![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[ Chondroitin sulfates enhances the barrier function of basement membrane assembled by heparan sulfates ]]> https://biorxiv.org/content/10.1101/2022.01.23.477428v1?rss=1 Tao, C. Makrides, N. Wu, Y. Brooks, S. E. Esko, J. D. Zhang, X. 2022-01-24 doi:10.1101/2022.01.23.477428 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Decoding the IGF1 Signaling Gene Regulatory Network Behind Alveologenesis from A Mouse Model of Bronchopulmonary Dysplasia ]]> https://biorxiv.org/content/10.1101/2022.01.24.477613v1?rss=1 Gao, F. Li, C. Smith, S. Peinado, N. Kohbodi, G. Tran, E. Loh, E. Li, W. Borok, Z. Minoo, P. 2022-01-25 doi:10.1101/2022.01.24.477613 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Derlin Dfm1 Employs a Chaperone Function to Resolve Misfolded Membrane Protein Stress ]]> https://biorxiv.org/content/10.1101/2022.01.25.477788v1?rss=1 Kandel, R. R. Jung, J. Dysau, D. Kuo, T. Songster, L. Aguayo, A. Duttke, S. Benner, C. Neal, S. E. 2022-01-26 doi:10.1101/2022.01.25.477788 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Staphylococcus aureus prophages are gatekeepers of exogenous lipid utilization to control membrane flexibility and bacterial fitness ]]> https://biorxiv.org/content/10.1101/2022.01.27.478126v1?rss=1 Gloux, K. Zhou, B. Pathania, A. Pant, D. Gaudu, P. Trieu-Cuot, P. Gruss, A. 2022-01-31 doi:10.1101/2022.01.27.478126 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Single-cell Transcriptome and Accessible Chromatin Dynamics During Endocrine Pancreas Development ]]> https://biorxiv.org/content/10.1101/2022.01.28.478217v1?rss=1 Duvall, E. Benitez, C. M. Tellez, K. Enge, M. Pauerstein, P. T. Li, L. Baek, S. Quake, S. R. Smith, J. P. Sheffield, N. C. Kim, S. K. Arda, H. E. 2022-01-28 doi:10.1101/2022.01.28.478217 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathology ]]> https://biorxiv.org/content/10.1101/2022.01.31.478476v1?rss=1 Shen, W.-B. Logue, J. Yang, P. Baracco, L. Elahi, M. Reece, E. A. Wang, B. Li, L. Blanchard, T. Han, Z. Frieman, M. Rissman, R. A. Yang, P. 2022-02-01 doi:10.1101/2022.01.31.478476 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Growth cone macropinocytosis of neurotrophin receptor and neuritogenesis are regulated by Neuron Navigator 1 ]]> https://biorxiv.org/content/10.1101/2022.01.31.478516v1?rss=1 Powers, R. Daza, R. Koehler, A. E. Courchet, J. Calabrese, B. Hevner, R. Halpain, S. 2022-02-01 doi:10.1101/2022.01.31.478516 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Plankton energy flows using a global size-structured and trait-based model ]]> https://biorxiv.org/content/10.1101/2022.02.01.478546v1?rss=1 Negrete-Garcia, G. Luo, J. Y. Long, M. C. Lindsay, K. Levy, M. Barton, A. D. 2022-02-01 doi:10.1101/2022.02.01.478546 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Lymphatic-Preserving Treatment Sequencing with Immune Checkpoint Inhibition Unleashes cDC1-Dependent Antitumor Immunity in HNSCC ]]> https://biorxiv.org/content/10.1101/2022.02.01.478744v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@542d71org.highwire.dtl.DTLVardef@737ad0org.highwire.dtl.DTLVardef@183f519org.highwire.dtl.DTLVardef@505ce2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Saddawi-Konefka, R. O'Farrell, A. Faraji, F. Clubb, L. Allevato, M. M. Anang, N.-A. A. S. Jensen, S. M. Wang, Z. Wu, V. H. Yung, B. S. Al Msari, R. Franiak Pietryga, I. Molinolo, A. A. Mesirov, J. P. Simon, A. B. Fox, B. A. Bui, J. D. Sharabi, A. Cohen, E. E. W. Califano, J. A. Gutkind, J. S. 2022-02-03 doi:10.1101/2022.02.01.478744 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Control of Craniofacial Development by the Collagen Receptor, Discoidin Domain Receptor 2 ]]> https://biorxiv.org/content/10.1101/2022.02.03.479017v1?rss=1 Mohamed, F. F. Ge, C. Cowling, R. T. Ono, N. Binrayes, A.-A. Greenberg, B. Kaartinen, V. M. Franceschi, R. T. 2022-02-03 doi:10.1101/2022.02.03.479017 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Salp blooms increase carbon export 5-fold in the Southern Ocean ]]> https://biorxiv.org/content/10.1101/2022.02.07.479467v1?rss=1 Decima, M. Stukel, M. R. Nodder, S. Gutierrez, A. Selph, K. Lopes dos Santos, A. Safi, K. Kelly, T. Deans, F. Morales, S. E. Baltar, F. Latasa, M. Maxim, G. Pinkerton, M. 2022-02-08 doi:10.1101/2022.02.07.479467 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ De novo mass spectrometry peptide sequencing with a transformer model ]]> https://biorxiv.org/content/10.1101/2022.02.07.479481v1?rss=1 Yilmaz, M. Fondrie, W. E. Bittremieux, W. Oh, S. Noble, W. S. 2022-02-09 doi:10.1101/2022.02.07.479481 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Engineering Defensin α-helix to produce high-affinity SARS-CoV-2 Spike protein binding ligands. ]]> https://biorxiv.org/content/10.1101/2022.02.09.479781v1?rss=1 Fernandes, L. A. Gomes, A. A. Magalhaes, M. d. L. B. Ray, P. da Silva, G. F. 2022-02-10 doi:10.1101/2022.02.09.479781 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ A conserved biosynthetic gene cluster is regulated by quorum sensing in a shipworm symbiont ]]> https://biorxiv.org/content/10.1101/2022.02.10.479910v1?rss=1 Robes, J. M. D. Altamia, M. A. Murdock, E. G. Concepcion, G. P. Haygood, M. G. Puri, A. W. 2022-02-10 doi:10.1101/2022.02.10.479910 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Extensive in vitro and in vivo protein translation via in situ circularized RNAs ]]> https://biorxiv.org/content/10.1101/2022.02.11.480072v1?rss=1 Kumar, A. Palmer, N. Miyasaki, K. Finburgh, E. Xiang, Y. Portell, A. Dailamy, A. Suhardjo, A. Chew, W. L. Kwon, E. J. Mali, P. 2022-02-11 doi:10.1101/2022.02.11.480072 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Architecture and self-assembly of the jumbo bacteriophage nuclear shell ]]> https://biorxiv.org/content/10.1101/2022.02.14.480162v1?rss=1 Laughlin, T. G. Deep, A. Prichard, A. M. Seitz, C. Gu, Y. Enustun, E. Suslov, S. Khanna, K. Birkholz, E. A. Armbruster, E. McCammon, J. A. Amaro, R. E. Pogliano, J. Corbett, K. D. Villa, E. 2022-02-14 doi:10.1101/2022.02.14.480162 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Sequential increase of PHGDH expression with Alzheimer's pathology and symptoms ]]> https://biorxiv.org/content/10.1101/2022.02.15.480384v1?rss=1 Chen, X. Calandrelli, R. Girardini, J. Yan, Z. Tan, Z. Xu, X. Hiniker, A. Zhong, S. 2022-02-17 doi:10.1101/2022.02.15.480384 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages ]]> https://biorxiv.org/content/10.1101/2022.02.15.480533v1?rss=1 2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology. ]]> Neri, U. Wolf, Y. I. Roux, S. Camargo, A. P. Lee, B. D. Kazlauskas, D. Chen, I. M. Ivanova, N. Allen, L. Z. Paez-Espino, D. Bryant, D. A. Bhaya, D. Krupovic, M. RNA Virus Discovery Consortium, Dolja, V. V. Kyrpides, N. C. Koonin, E. V. Gophna, U. 2022-02-17 doi:10.1101/2022.02.15.480533 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Identification of a small molecule, Mebendazole, as a novel ethylene signaling activator reveals a role of ethylene signaling on the regulation of lateral root angles ]]> https://biorxiv.org/content/10.1101/2022.02.16.480742v1?rss=1 He, W. Zhang, L. Cao, M. Arakawa, N. Xiao, Y. Hou, Y. Busch, W. 2022-02-19 doi:10.1101/2022.02.16.480742 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Prey Size Spectra and Predator:Prey ratios of 7 Species of New Zealand Salps ]]> https://biorxiv.org/content/10.1101/2022.02.16.480784v1?rss=1 Fender, C. K. Decima, M. Gutierrez-Rodriguez, A. Selph, K. E. Yingling, N. Stukel, M. R. 2022-02-19 doi:10.1101/2022.02.16.480784 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Spatiotemporal analysis of axonal autophagosome-lysosome dynamics reveals limited fusion events trigger two-step maturation ]]> https://biorxiv.org/content/10.1101/2022.02.17.480915v1?rss=1 Cason, S. E. Mogre, S. S. Holzbaur, E. L. F. Koslover, E. F. 2022-02-18 doi:10.1101/2022.02.17.480915 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Systematic Evaluation of Different R-loop Mapping Methods: Achieving Consensus, Resolving Discrepancies and Uncovering Distinct Types of RNA:DNA Hybrids ]]> https://biorxiv.org/content/10.1101/2022.02.18.480986v1?rss=1 Chen, J.-Y. Lim, D.-H. Chen, L. Zhou, Y. Zhang, F. Shao, C. Zhang, X. Li, H. Wang, D. Zhang, D.-E. Fu, X.-D. 2022-02-19 doi:10.1101/2022.02.18.480986 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions ]]> https://biorxiv.org/content/10.1101/2022.02.21.481223v1?rss=1 Xiang, J. S. Mueller, J. R. Luo, E.-C. Yee, B. A. Schafer, D. Schmok, J. C. Tan, F. E. Rothamel, K. McVicar, R. N. Kwong, E. M. Jones, K. L. Her, H.-L. Chen, C.-Y. Vu, A. Q. Jin, W. Park, S. S. Le, P. Brannan, K. W. Kofman, E. R. Li, Y. Tankka, A. T. Dong, K. D. Song, Y. Carlin, A. F. Van Nostrand, E. L. Leibel, S. L. Yeo, G. W. 2022-02-24 doi:10.1101/2022.02.21.481223 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus ]]> https://biorxiv.org/content/10.1101/2022.02.22.481494v1?rss=1 Mahajan, A. Yan, W. Zidovska, A. Saintillan, D. Shelley, M. J. 2022-02-22 doi:10.1101/2022.02.22.481494 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations ]]> https://biorxiv.org/content/10.1101/2022.02.23.481658v1?rss=1 Salido, R. A. Martino, C. Karthikeyan, S. Huang, S. Rahman, G. Gonzalez, A. Zaramela, L. S. Beck, K. L. Bhute, S. Cantrell, K. Carrieri, A. P. Farmer, S. Haiminen, N. Humphrey, G. Kim, H.-C. Parida, L. Richter, R. A. Vazquez-Baeza, Y. Zengler, K. Swafford, A. Bartko, A. Knight, R. 2022-02-24 doi:10.1101/2022.02.23.481658 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ A Geometric View of Signal Sensitivity Metrics in multi-echo fMRI ]]> https://biorxiv.org/content/10.1101/2022.02.23.481688v1?rss=1 Liu, T. Li, B. Fernandez, B. Banerjee, S. 2022-02-25 doi:10.1101/2022.02.23.481688 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Gut microbiota transplantation drives the adoptive transfer of colonic genotype-phenotype characteristics between mice lacking catestatin and their wild type counterparts ]]> https://biorxiv.org/content/10.1101/2022.02.24.481402v1?rss=1 Gonzalez-Davila, P. Schwalbe, M. Danewalia, A. Wardenaar, R. Dalile, B. Verbeke, K. Mahata, S. K. El Aidy, S. 2022-02-24 doi:10.1101/2022.02.24.481402 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Conserved neuropeptidergic regulation of intestinal integrity in invertebrate models of aging ]]> https://biorxiv.org/content/10.1101/2022.02.24.481867v1?rss=1 Singh, A. Kaduskar, B. Reddy, K. C. Kumsta, C. Bier, E. Hansen, M. Chalasani, S. H. 2022-02-28 doi:10.1101/2022.02.24.481867 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ A loss-of-function cysteine mutant in fibulin-3 (EFEMP1) forms aberrant extracellular disulfide-linked homodimers and alters extracellular matrix composition ]]> https://biorxiv.org/content/10.1101/2022.02.25.481983v1?rss=1 C; p.Cys55Arg (C55R), disrupts F3 secretion, quaternary structure, and function by forming unique extracellular disulfide-linked homodimers. Dual cysteine mutants suggest that the C55R-induced disulfide species forms because of new availability of Cys70 on adjacent F3 monomers. Surprisingly, mutation of single cysteines located near C55 (i.e., C29, C42, C48, C61, C70, C159, and C171) also produced similar extracellular disulfide-linked dimers, suggesting that this is not a phenomenon isolated to the C55R mutant. To assess C55R functionality, F3 knockout (KO) retinal pigmented epithelial (RPE) were generated, followed by reintroduction of wild-type (WT) or C55R F3. F3 KO cells produced lower levels of the ECM remodeling enzyme, matrix metalloproteinase 2 and reduced formation of collagen VI ECM filaments, both of which were partially rescued by WT F3 overexpression. However, C55R F3 was unable to compensate for these same ECM-related defects. Our results highlight the unique behavior of particular cysteine mutations in F3 and uncover potential routes to restore C55R F3 loss-of-function. ]]> Woodard, D. R. Daniel, S. Nakahara, E. Abbas, A. DiCesare, S. M. Hulleman, J. D. 2022-02-27 doi:10.1101/2022.02.25.481983 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers ]]> https://biorxiv.org/content/10.1101/2022.02.28.482315v1?rss=1 Li, B.-Z. Kolodner, R. D. Putnam, C. D. 2022-03-01 doi:10.1101/2022.02.28.482315 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Balancing activation and costimulation of CAR tunes signaling dynamics and enhances therapeutic potency ]]> https://biorxiv.org/content/10.1101/2022.03.01.482445v1?rss=1 Sun, J. Duan, Y. Chen, J. Meng, X. Liu, L. Shang, K. Wu, X. Wang, Y. Huang, Z. Liu, H. Huang, Y. Zhou, C. Gao, X. Wang, Y. Sadelain, M. 2022-03-01 doi:10.1101/2022.03.01.482445 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice ]]> https://biorxiv.org/content/10.1101/2022.03.02.482700v1?rss=1 Maksimov, M. Ashbrook, D. G. BXD Sequencing Consortium, Villani, F. Colonna, V. Mousavi, N. Ma, N. Palmer, A. A. Gymrek, M. 2022-03-02 doi:10.1101/2022.03.02.482700 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Precocious sperm exchange in the simultaneously hermaphroditic nudibranch, Berghia stephanieae ]]> https://biorxiv.org/content/10.1101/2022.03.02.482740v1?rss=1 Taraporevala, N. F. Lesoway, M. P. Goodheart, J. A. Lyons, D. C. 2022-03-04 doi:10.1101/2022.03.02.482740 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Biologically-derived neoproteoglycans for profiling protein-glycosaminoglycan interactions ]]> https://biorxiv.org/content/10.1101/2022.03.04.482917v1?rss=1 500 binding proteins, making them prominent relays for sensing external stimuli and transducing cellular responses. However, their unique substructural protein-recognition domains that confer their binding specificity remain elusive. While the emergence of glycan arrays has rapidly enabled the profiling of ligand specificities of a range of glycan-binding proteins, their adaptation for the analysis of GAG-binding proteins has been considerably more challenging. Current GAG-microarrays primarily employ synthetically defined oligosaccharides, which capture only a fraction of the structural diversity of native GAG polysaccharides. Augmenting existing array platforms to include GAG structures purified from tissues or produced in cells with engineered glycan biosynthetic pathways may significantly advance the understanding of structure-activity relationships in GAG-protein interactions. Here, we demonstrate an efficient and tunable strategy to mimic cellular proteoglycan architectures by conjugating biologically-derived GAG chains to a protein scaffold, defined as neoproteoglycans (neoPGs). The use of a reactive fluorogenic linker enabled real-time monitoring of the conjugation reaction efficiency and tuning of the neoPG valency. Immobilization of the reagents on a 96-well array platform allowed for efficient probing of ligand binding and enzyme substrate specificity, including growth factors and the human sulfatase 1. The neoPGs can also be used directly as soluble probes to evaluate GAG-dependent growth factor signaling in cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/482917v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1a51f0org.highwire.dtl.DTLVardef@1f99e16org.highwire.dtl.DTLVardef@f9c5b9org.highwire.dtl.DTLVardef@242d9a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Porell, R. N. Follmar, J. L. Purcell, S. C. Timm, B. Laubach, L. K. Kozirovskiy, D. Thacker, B. E. Glass, C. A. Gordts, P. L. S. M. Godula, K. 2022-03-04 doi:10.1101/2022.03.04.482917 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Cell size asymmetries in the sea star embryo ]]> https://biorxiv.org/content/10.1101/2022.03.05.483134v1?rss=1 Barone, V. Byrne, M. Lyons, D. 2022-03-06 doi:10.1101/2022.03.05.483134 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Fish microbiomes 101: disentangling the rules governing marine fish mucosal microbiomes across 101 species ]]> https://biorxiv.org/content/10.1101/2022.03.07.483203v1?rss=1 Minich, J. J. Harer, A. Vechinski, J. Frable, B. W. Skelton, Z. Kunselman, E. Shane, M. Perry, D. Gonzalez, A. McDonald, D. Knight, R. Michael, T. P. Allen, E. E. 2022-03-08 doi:10.1101/2022.03.07.483203 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Candidates for Drug Repurposing to Address the Cognitive Symptoms in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2022.03.07.483231v1?rss=1 Koch, E. Kauppi, K. Chen, C.-H. 2022-03-07 doi:10.1101/2022.03.07.483231 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Enzyme-Responsive Nanoparticles for the Targeted Delivery of an MMP Inhibitor to the Heart post Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2022.03.07.483374v1?rss=1 Sullivan, H. Liang, Y. Worthington, K. Luo, C. Gianneschi, N. C. Christman, K. 2022-03-08 doi:10.1101/2022.03.07.483374 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Allosteric inhibitors of Zika virus NS2B-NS3 protease targeting protease in super-open conformation ]]> https://biorxiv.org/content/10.1101/2022.03.09.483711v1?rss=1 Meewan, I. Shiryaev, S. Huang, C.-T. Lin, Y.-W. Chuang, C.-H. Terskikh, A. Abagyan, R. 2022-03-11 doi:10.1101/2022.03.09.483711 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites ]]> https://biorxiv.org/content/10.1101/2022.03.10.483652v1?rss=1 Adams, C. Boonen, K. Laukens, K. Bittremieux, W. 2022-03-10 doi:10.1101/2022.03.10.483652 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ An integrated cell atlas of the human lung in health and disease ]]> https://biorxiv.org/content/10.1101/2022.03.10.483747v1?rss=1 Sikkema, L. Strobl, D. C. Zappia, L. Madissoon, E. Markov, N. S. Zaragosi, L.-E. Ansari, M. Arguel, M.-J. Apperloo, L. Becavin, C. Berg, M. Chichelnitskiy, E. Chung, M.-i. Collin, A. Gay, A. C. Hooshiar Kashani, B. Jain, M. Kapellos, T. Kole, T. M. Mayr, C. H. Papen, von, M. Peter, L. Ramirez-Suastegui, C. Schniering, J. Taylor, C. J. Walzthoeni, T. Xu, C. Bui, L. T. Donno, de, C. Dony, L. Guo, M. Gutierrez, A. J. Heumos, L. Huang, N. Ibarra, I. L. Jackson, N. D. Kadur Lakshminarasimha Murthy, P. Lotfollahi, M. Tabib, T. Talavera-Lopez, C. Travaglini, K. 2022-03-11 doi:10.1101/2022.03.10.483747 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ A distinct subset of oligodendrocyte lineage cells interact with the developing dorsal root entry during its genesis ]]> https://biorxiv.org/content/10.1101/2022.03.10.483786v1?rss=1 Green, L. Gallant, R. Brandt, J. Nichols, E. Smith, C. 2022-03-13 doi:10.1101/2022.03.10.483786 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Double NPY motifs at the N-terminus of Sso2 synergistically bind Sec3 to promote membrane fusion ]]> https://biorxiv.org/content/10.1101/2022.03.11.483902v1?rss=1 Peer, M. Yuan, H. Zhang, Y. Korbula, K. Novick, P. J. Dong, G. 2022-03-12 doi:10.1101/2022.03.11.483902 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Combining two Genetic Sexing Strains allows sorting of non-transgenic males for Aedes genetic control ]]> https://biorxiv.org/content/10.1101/2022.03.11.483912v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@761545org.highwire.dtl.DTLVardef@6e80f2org.highwire.dtl.DTLVardef@d3911dorg.highwire.dtl.DTLVardef@1dc19ce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lutrat, C. Burckbuchler, M. Olmo, R. P. Beugnon, R. Fontaine, A. Baldet, T. Bouyer, J. Marois, E. 2022-03-12 doi:10.1101/2022.03.11.483912 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Mutational footprint of platinum chemotherapy in a secondary thyroid cancer ]]> https://biorxiv.org/content/10.1101/2022.03.14.484002v1?rss=1 Schiantarelli, J. Pappa, T. Conway, J. Crowdis, J. Reardon, B. Dietlein, F. Huang, J. Stanizzi, D. Carey, E. Bosma-Moody, A. Imamovic, A. Han, S. Camp, S. Kofman, E. Shannon, E. Barletta, J. He, M. X. Liu, D. Park, J. Lorch, J. Van Allen, E. 2022-03-15 doi:10.1101/2022.03.14.484002 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ Heterogeneous multimeric metabolite ion species observed in LC-MS based metabolomics data sets ]]> https://biorxiv.org/content/10.1101/2022.03.15.484295v1?rss=1 El Abiead, Y. Bueschl, C. Panzenboeck, L. Wang, M. Doppler, M. Seidl, B. Zanghellini, J. Dorrestein, P. C. Koellensperger, G. 2022-03-17 doi:10.1101/2022.03.15.484295 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Cavitation Induced Fracture of Intact Brain Tissue ]]> https://biorxiv.org/content/10.1101/2022.03.15.484522v1?rss=1 Dougan, C. Song, Z. Fu, H. Crosby, A. J. Cai, S. Peyton, S. 2022-03-18 doi:10.1101/2022.03.15.484522 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Immune and Clotting Dysfunction Detected in Saliva and Blood Plasma after COVID-19. ]]> https://biorxiv.org/content/10.1101/2022.03.18.484814v1?rss=1 Jang, H. Choudhury, S. Yu, Y. Sievers, B. L. Gelbart, T. Singh, H. Rawlings, S. A. Tan, G. S. Smith, D. Freire, M. 2022-03-21 doi:10.1101/2022.03.18.484814 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples ]]> https://biorxiv.org/content/10.1101/2022.03.18.484889v1?rss=1 Lu, B. Curtius, K. Graham, T. A. Yang, Z. Barnes, C. P. 2022-03-20 doi:10.1101/2022.03.18.484889 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Dissociable Cellular and Genetic Mechanisms of Cortical Thinning at Different Life Stages ]]> https://biorxiv.org/content/10.1101/2022.03.21.484899v1?rss=1 60 years) in the patterns of association between inter-regional profiles of cortical thickness and expression profiles of marker genes for CA1 and S1 pyramidal cells, astrocytes, and microglia. Gene ontology and enrichment analyses indicated that each of the three life-stages was associated with different biological processes and cellular components: synaptic modeling in early life, neurotransmission in mid-life, and neurodegeneration in late-life. These findings provide mechanistic insights into age-related cortical thinning during typical development and aging. ]]> Modabbernia, A. Vidal-Pineiro, D. Agartz, I. Andreassen, O. A. Ayesa-Arriola, R. Bertolino, A. Boomsma, D. I. Bourque, J. Breier, A. Brouwer, R. M. Buitelaar, J. K. Canales-Rodriguez, E. J. Caseras, X. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Zubicaray, G. I. Dickie, E. W. Dima, D. Frenzel, S. Fisher, S. E. Franke, B. Glahn, D. C. Grabe, H.-J. Grotegerd, D. Gruber, O. Guerrero-Pedraza, A. Gur, R. E. Gur, R. C. Hartman, C. A. Hoekstra, P. J. Hulshoff Pol, H. E. Jahanshad, N. Jernigan, T. L. Jiang, J. Kalnin, A. J. Kochan, N. A. Mazoyer, 2022-03-22 doi:10.1101/2022.03.21.484899 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Chromatin-associated lncRNA Malat1 regulates Th17 effector program and promotes intestinal inflammation ]]> https://biorxiv.org/content/10.1101/2022.03.21.485192v1?rss=1 Ma, S. Zhou, B. Chen, N. Luo, C. Li, Y. Patel, P. R. Zheng, A. Patel, S. A. Hao, Y. Chang, J. T. Fu, X. Huang, W. J. M. 2022-03-23 doi:10.1101/2022.03.21.485192 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ SPACA6 structure reveals a conserved superfamily of gamete fusion-associated proteins ]]> https://biorxiv.org/content/10.1101/2022.03.23.484325v1?rss=1 Vance, T. D. R. Yip, P. Jimenez, E. Li, S. Gawol, D. Byrnes, J. Uson, I. Ziyyat, A. Lee, J. E. 2022-03-23 doi:10.1101/2022.03.23.484325 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq ]]> https://biorxiv.org/content/10.1101/2022.03.23.485509v1?rss=1 Vazquez, S. E. Mann, S. A. Bodansky, A. Kung, A. F. Quandt, Z. Ferre, E. M. N. Landegren, N. Eriksson, D. Bastard, P. Zhang, S.-Y. Liu, J. Mitchell, A. Mandel-Brehm, C. Miao, B. Sowa, G. Zorn, K. Chan, A. Y. Shimizu, C. Tremoulet, A. Lynch, K. Wilson, M. R. Kämpe, O. Dobbs, K. Delmonte, O. M. Notarangelo, L. D. Burns, J. C. Casanova, J.-L. Lionakis, M. S. Torgerson, T. R. Anderson, M. S. DeRisi, J. L. 2022-03-25 doi:10.1101/2022.03.23.485509 Cold Spring Harbor Laboratory Press 2022-03-25 <![CDATA[ Distinct bile salt hydrolase substrate preferences dictate C. difficile pathogenesis ]]> https://biorxiv.org/content/10.1101/2022.03.24.485529v1?rss=1 Foley, M. H. Walker, M. E. Stewart, A. K. O'Flaherty, S. Gentry, E. C. Allen, G. Patel, S. Pan, M. Beaty, V. V. Vanhoy, M. E. Dougherty, M. K. McGill, S. K. Gulati, A. Dorrestein, P. Baker, E. S. Redinbo, M. R. Barrangou, R. Theriot, C. M. 2022-03-24 doi:10.1101/2022.03.24.485529 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Two modes of mid-frontal theta suggest a role in conflict and error processing ]]> https://biorxiv.org/content/10.1101/2022.03.25.485421v1?rss=1 Muralidharan, V. Aron, A. R. Cohen, M. X. Schmidt, R. 2022-03-27 doi:10.1101/2022.03.25.485421 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ The general anesthetic isoflurane inhibits calcium activity in cerebrovascular endothelial cells and disrupts vascular tone ]]> https://biorxiv.org/content/10.1101/2022.03.25.485881v1?rss=1 Shi, L. Rodriguez-Contreras, A. 2022-03-27 doi:10.1101/2022.03.25.485881 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ CryoET Reveals Organelle Phenotypes in Huntington Disease Patient iPSC-Derived and Mouse Primary Neurons ]]> https://biorxiv.org/content/10.1101/2022.03.26.485912v1?rss=1 Wu, G.-H. Smith-Geater, C. Galaz-Montoya, J. G. Gu, Y. Gupte, S. R. Aviner, R. Mitchell, P. G. Hsu, J. Miramontes, R. Wang, K. Q. Geller, N. Danita, C. Joubert, L.-M. Schmid, M. F. Yeung, S. Frydman, J. Mobley, W. Wu, C. Thompson, L. M. Chiu, W. 2022-03-27 doi:10.1101/2022.03.26.485912 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces ]]> https://biorxiv.org/content/10.1101/2022.03.30.486421v1?rss=1 Peris, D. Ubbelohde, E. J. Kuang, M. C. Kominek, J. Langdon, Q. K. Adams, M. Koshalek, J. A. Hulfachor, A. B. Opulente, D. A. Hall, D. J. Hyma, K. Fay, J. C. Leducq, J.-B. Charron, G. Landry, C. R. Libkind, D. Goncalves, C. Goncalves, P. Sampaio, J. P. Wang, Q.-M. Bai, F.-Y. Wrobel, R. L. Hittinger, C. T. 2022-04-01 doi:10.1101/2022.03.30.486421 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ The molecular organization of flat and curved caveolae indicates bendable structural units at the plasma membrane. ]]> https://biorxiv.org/content/10.1101/2022.03.31.486578v1?rss=1 Matthaeus, C. Sochacki, K. Dickey, A. Puchkov, D. Haucke, V. Lehmann, M. Taraska, J. W. 2022-03-31 doi:10.1101/2022.03.31.486578 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Full-mouth photoacoustic/ultrasound imaging of the periodontal pocket with a compact intraoral transducer ]]> https://biorxiv.org/content/10.1101/2022.03.31.486608v1?rss=1 Fu, L. Khazaeinezhad, R. Hariri, A. Qi, B. Chen, C. Jokerst, J. V. 2022-04-01 doi:10.1101/2022.03.31.486608 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ cGASylation by a bacterial E1-E2 fusion protein primes antiviral immune signaling ]]> https://biorxiv.org/content/10.1101/2022.03.31.486616v1?rss=1 Ledvina, H. E. Ye, Q. Gu, Y. Quan, Y. Lau, R. K. Zhou, H. Corbett, K. D. Whiteley, A. T. 2022-03-31 doi:10.1101/2022.03.31.486616 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Active vision during prey-capture in wild marmoset monkeys ]]> https://biorxiv.org/content/10.1101/2022.04.01.486794v1?rss=1 Ngo, V. Miller, C. Gorman, J. De La Fuente, M. F. Souto, A. Schiel, N. 2022-04-05 doi:10.1101/2022.04.01.486794 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Collagen remodeling dictates pancreatic cancer bioenergetics and outcome through DDR1 activation or degradation ]]> https://biorxiv.org/content/10.1101/2022.04.02.486837v1?rss=1 Su, H. Yang, F. Fu, R. Trinh, B. Sun, N. Liu, J. Kumar, A. Baglieri, J. Siruno, J. Dozier, S. Nair, A. Filliol, A. Rosenthal, S. B. Santini, J. Metallo, C. M. Molina, A. Schwabe, R. F. Lowy, A. M. Brenner, D. Sun, B. Karin, M. 2022-04-04 doi:10.1101/2022.04.02.486837 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies ]]> https://biorxiv.org/content/10.1101/2022.04.03.486854v1?rss=1 Li, R. Mor, M. Ma, B. Clark, A. E. Alter, J. Werbner, M. Lee, J. Leibel, S. L. Carlin, A. F. Dassau, M. Gal-Tanamy, M. Croker, B. A. Xiang, Y. Freund, N. T. 2022-04-03 doi:10.1101/2022.04.03.486854 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Molecular-Dynamics Simulation Methods for Macromolecular Crystallography ]]> https://biorxiv.org/content/10.1101/2022.04.04.486986v1?rss=1 Wych, D. C. Aoto, P. C. Vu, L. Wolff, A. M. Mobley, D. L. Fraser, J. S. Taylor, S. S. Wall, M. E. 2022-04-05 doi:10.1101/2022.04.04.486986 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Mechanism-based crosslinking probes capture E. coli ketosynthase FabB in conformationally-distinct catalytic states. ]]> https://biorxiv.org/content/10.1101/2022.04.04.486996v1?rss=1 Chen, A. Mindrebo, J. T. Davis, T. D. Kim, W. E. Katsuyama, Y. Jiang, Z. Ohnishi, Y. Noel, J. P. Burkart, M. D. 2022-04-04 doi:10.1101/2022.04.04.486996 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Unaltered T cell responses to common antigens in individuals with Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2022.04.05.487195v1?rss=1 Williams, G. P. Muskat, K. Frazier, A. Xu, Y. Mateus, J. Grifoni, A. Antunes, R. d. S. Weiskopf, D. Amara, A. W. Standaert, D. G. Goldman, J. G. Litvan, I. Alcalay, R. N. Sulzer, D. Arlehamn, C. S. L. Sette, A. 2022-04-08 doi:10.1101/2022.04.05.487195 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Collateral sensitivity as a strategy to suppress resistance emergence: the challenge of diverse evolutionary pathways ]]> https://biorxiv.org/content/10.1101/2022.04.07.486819v1?rss=1 Mandt, R. E. K. Luth, M. R. Tye, M. A. Mazitschek, R. Ottilie, S. Winzeler, E. A. Lafuente-Monasterio, M. J. Gamo, F. J. Wirth, D. F. Lukens, A. K. 2022-04-07 doi:10.1101/2022.04.07.486819 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2022.04.07.487560v1?rss=1 Munro, D. Wang, T. Chitre, A. S. Polesskaya, O. Ehsan, N. Gao, J. Chen, H. Gusev, A. Solberg Woods, L. C. Saba, L. M. Palmer, A. A. Mohammadi, P. 2022-04-09 doi:10.1101/2022.04.07.487560 Cold Spring Harbor Laboratory Press 2022-04-09 <![CDATA[ Targeting N-Myc in Neuroblastoma with Selective Aurora Kinase A Degraders ]]> https://biorxiv.org/content/10.1101/2022.04.09.487756v1?rss=1 Tang, J. Moorthy, R. Demir, O. Baker, Z. D. Naumann, J. A. Jones, K. F. M. Grillo, M. J. Haefner, E. S. Shi, K. Levy, M. J. Aihara, H. Harris, R. S. Amaro, R. E. Levinson, N. M. Harki, D. A. 2022-04-10 doi:10.1101/2022.04.09.487756 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ A chemomechanical model of sperm locomotion reveals two modes of swimming ]]> https://biorxiv.org/content/10.1101/2022.04.10.487801v1?rss=1 Li, C. Chakrabarti, B. Castilla, P. Mahajan, A. Saintillan, D. 2022-04-10 doi:10.1101/2022.04.10.487801 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Olfactory receptor neurons generate multiple response motifs, increasing coding space dimensionality ]]> https://biorxiv.org/content/10.1101/2022.04.11.487908v1?rss=1 Kim, B. Haney, S. Milan, A. P. Joshi, S. Aldworth, Z. Kim, A. T. Rulkov, N. Bazhenov, M. Stopfer, M. A. 2022-04-12 doi:10.1101/2022.04.11.487908 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ An intrinsically disordered transcription activation domain alters the DNA binding affinity and specificity of NFκB p50/RelA ]]> https://biorxiv.org/content/10.1101/2022.04.11.487922v1?rss=1 Baughman, H. E. R. Narang, D. Chen, W. Suarez, A. C. V. Lee, J. Bachochin, M. J. Gunther, T. R. Wolynes, P. G. Komives, E. A. 2022-04-11 doi:10.1101/2022.04.11.487922 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Estimation of Left Ventricular Mechanical Activation Times from Motion-Corrected Cardiac 4DCT Images ]]> https://biorxiv.org/content/10.1101/2022.04.12.488106v1?rss=1 |35| ms has a significant effect on reclassifying patients based on their probabilities of responding to CRT; we investigated the effect of ResyncCT on the measured values of TOS over the LV. ResultsResyncCT had a pronounced effect on the TOS estimates; ResyncCT could potentially reclassify 23/24 (96%) subjects as either responders or non-responders to CRT. In 16/24 (67%) subjects, the differences in TOS that were sufficient to bring about a reclassification of CRT response were at least as large in surface area of the LV as one entire American Heart Association segment. ConclusionsWe demonstrated the clinical utility of ResyncCT in estimating LV mechanical activation times as times to onset of shortening in 24 human subjects. ResyncCT has a pronounced effect on the estimation of LV mechanical activation times; the differences in activation times between the ResyncCT and uncorrected images are heterogenous and subject specific. The effect of ResyncCT could potentially reclassify 96% of the subjects used in this study based on their probabilities of responding to CRT. The results reported in this study highlight the potential utility of ResyncCT in estimating timing of mechanical events of interest of the LV for CRT planning. ]]> Manohar, A. Yang, J. Pack, J. D. McVeigh, E. R. 2022-04-13 doi:10.1101/2022.04.12.488106 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Single acoustic closed loop stimulation in mice to modulate hippocampo-thalamo-cortical activity and performance ]]> https://biorxiv.org/content/10.1101/2022.04.16.488547v1?rss=1 Aksamaz, S. Moelle, M. Olubukola, A. E. Bazhenov, M. Marshall, L. 2022-04-16 doi:10.1101/2022.04.16.488547 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Persistent post-COVID-19 smell loss is associated with inflammatory infiltration and altered olfactory epithelial gene expression ]]> https://biorxiv.org/content/10.1101/2022.04.17.488474v1?rss=1 Finlay, J. B. Brann, D. H. Hachem, R. A. Jang, D. W. Oliva, A. D. Ko, T. Gupta, R. Wellford, S. A. Moseman, E. A. Jang, S. S. Yan, C. H. Matsunami, H. Tsukahara, T. Datta, S. R. Goldstein, B. J. 2022-04-18 doi:10.1101/2022.04.17.488474 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Systems-level identification of key transcription factors in immune cell specification ]]> https://biorxiv.org/content/10.1101/2022.04.21.489000v1?rss=1 Liu, c. Omilusik, K. Toma, C. Kurd, N. S. Chang, J. T. Goldrath, A. W. Wang, W. 2022-04-22 doi:10.1101/2022.04.21.489000 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Private and sub-family specific mutations of founder haplotypes in the BXD family reveal phenotypic consequences relevant to health and disease ]]> https://biorxiv.org/content/10.1101/2022.04.21.489063v1?rss=1 Ashbrook, D. G. Sasani, T. A. Maksimov, M. Gunturkun, M. H. Ma, N. Villani, F. Ren, Y.-y. Rothschild, D. Chen, H. Lu, L. Colonna, V. Dumont, B. L. Harris, K. Gymrek, M. Pritchard, J. K. Palmer, A. A. Williams, R. W. 2022-04-21 doi:10.1101/2022.04.21.489063 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ The kinase activity of the cancer stem cell marker DCLK1 drives gastric cancer progression by reprogramming the stromal tumor landscape ]]> https://biorxiv.org/content/10.1101/2022.04.21.489109v1?rss=1 Afshar-Sterle, S. Carli, A. L. E. O'Keefe, R. Tse, J. Fischer, S. Azimpour, A. I. Baloyan, D. Elias, L. Thilakasiri, P. Patel, O. Ferguson, F. M. Eissmann, M. F. Chand, A. L. Gray, N. S. Busuttil, R. Boussioutas, A. Lucet, I. Ernst, M. Buchert, M. 2022-04-21 doi:10.1101/2022.04.21.489109 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells ]]> https://biorxiv.org/content/10.1101/2022.04.22.489166v1?rss=1 Jaber-Hijazi, F. Swaminathan, K. Gilroy, K. Wenzel, A. T. Lagnado, A. Kirschner, K. Robertson, N. A. Reid, C. Fullarton, N. Pawlikowski, J. Blyth, K. Mesirov, J. P. Rai, T. S. Passos, J. F. Machesky, L. M. Adams, P. D. 2022-04-22 doi:10.1101/2022.04.22.489166 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development ]]> https://biorxiv.org/content/10.1101/2022.04.22.489215v1?rss=1 Nan, Q. Char, S. N. Yang, B. Facette, M. R. 2022-04-22 doi:10.1101/2022.04.22.489215 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ High precision magnetoencephalography reveals increased right-inferior frontal gyrus beta power during response conflict ]]> https://biorxiv.org/content/10.1101/2022.04.25.489434v1?rss=1 10,000) from 8 subjects during different levels of response conflict. We hypothesized that a R-IFG-triggered network for response inhibition is domain general and also involved in mediating response conflict. We therefore tested whether R-IFG showed increased beta power dependent on the level of response conflict. We also hypothesized that pre-SMA is an important node in response conflict processing, and tested whether pre-SMA theta power increased for response conflict trials. Using event-related spectral perturbations and linear mixed modeling, we found that both R-IFG beta and pre-SMA theta increased for response conflict trials, with the R-IFG beta increase specific to trials with strong response conflict. This result supports a more generalized role for R-IFG beta in response inhibition, beyond simple stopping behavior towards response switching. Significance StatementResponse inhibition is a core component of cognitive control. Neural mechanisms of response inhibition are typically studied using stopping paradigms. However, there is an unresolved debate regarding whether the response inhibition network is specific to stopping or generalizes to switching between tasks and overcoming conflict between competing response tendencies. Increased beta (12-30 Hz) in R-IFG has historically been interpreted as a marker of successful response inhibition in the stop-signal task. Here, we investigated the presence of this electrophysiological marker of response inhibition specifically during response conflict (switching). We found R-IFG beta power increased for trials with strong response conflict, and not for weak or no response conflict, thereby supporting a generalized role for R-IFG beta in response inhibition and switching. ]]> Daniel, P. L. Bonaiuto, J. J. Bestmann, S. Aron, A. R. Little, S. 2022-04-26 doi:10.1101/2022.04.25.489434 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ The 2',3' cyclic phosphatase Angel1 facilitates mRNA degradation during human ribosome-associated quality control ]]> https://biorxiv.org/content/10.1101/2022.04.28.489582v1?rss=1 Nicholson-Shaw, T. Ajaj, Y. Perelis, M. Fulzele, A. Yeo, G. W. Bennett, E. J. Lykke-Anderson, J. 2022-04-28 doi:10.1101/2022.04.28.489582 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Induction of neutralizing antibodies against SARS-CoV-2 variants by a multivalent mRNA-lipid nanoparticle vaccine encoding SARS-CoV-2/SARS-CoV Spike protein receptor-binding domains ]]> https://biorxiv.org/content/10.1101/2022.04.28.489834v1?rss=1 Zhang, Q. Tiwari, S. K. Wang, S. Wang, L. Li, W. Zhang, L. Rawlings, S. A. Cheng, Y. Jokerst, J. V. Rana, T. M. 2022-04-28 doi:10.1101/2022.04.28.489834 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ High resolution quantitative and functional MRI indicate lower myelination of thin and thick stripes in human secondary visual cortex ]]> https://biorxiv.org/content/10.1101/2022.04.28.489865v1?rss=1 Haenelt, D. Trampel, R. Nasr, S. Polimeni, J. Tootell, R. B. Sereno, M. I. Pine, K. Edwards, L. J. Helbling, S. Weiskopf, N. 2022-04-29 doi:10.1101/2022.04.28.489865 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Ablation of palladin in adult heart causes dilated cardiomyopathy associated with intercalated disc abnormalities ]]> https://biorxiv.org/content/10.1101/2022.04.29.489866v1?rss=1 Mastrototaro, G. Carullo, P. Zhang, J. Scellini, B. Piroddi, N. Nemska, S. Filomena, M. C. Serio, S. Otey, C. A. Tesi, C. Emrich, F. Linke, W. A. Poggesi, C. Boncompagni, S. Bang, M.-L. 2022-04-30 doi:10.1101/2022.04.29.489866 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ A resource for generating and manipulating human microglial states in vitro ]]> https://biorxiv.org/content/10.1101/2022.05.02.490100v1?rss=1 Dolan, M.-J. Therrien, M. Jereb, S. Kamath, T. Atkeson, T. Marsh, S. Goeva, A. Lojek, N. Murphy, S. White, C. Joung, J. Liu, B. Limone, F. Eggan, K. Hacohen, N. Bernstein, B. Glass, C. Leinonen, V. Blurton-Jones, M. Zhang, F. Epstein, C. B. Macosko, E. Stevens, B. 2022-05-02 doi:10.1101/2022.05.02.490100 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Interpretable deep learning to uncover the molecular binding patterns determining TCR-epitope interactions ]]> https://biorxiv.org/content/10.1101/2022.05.02.490264v1?rss=1 Dens, C. Bittremieux, W. Affaticati, F. Laukens, K. Meysman, P. 2022-05-02 doi:10.1101/2022.05.02.490264 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation ]]> https://biorxiv.org/content/10.1101/2022.05.03.490500v1?rss=1 Meshcheryakov, V. A. Pan, W. Li, T. Wang, Y. Ghosh, G. Wang, V. Y.-F. 2022-05-03 doi:10.1101/2022.05.03.490500 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Single cell transcriptomic profiling of tauopathy in a novel 3D neuron-astrocyte coculture model ]]> https://biorxiv.org/content/10.1101/2022.05.03.490513v1?rss=1 Rickner, H. D. Jiang, L. Hong, R. O'Neill, N. K. Medalla, M. Zhang, L. Shaw, D. Wolozin, B. Cheng, C. S. 2022-05-04 doi:10.1101/2022.05.03.490513 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Hemodynamic stress activates inflammatory responses and cell death through spectrin-dependent modulation of Store Operated Calcium Entry ]]> https://biorxiv.org/content/10.1101/2022.05.04.490549v1?rss=1 Hsieh, L. Tu, L. N. Smith, J. R. Ghassemian, M. Timms, A. Savan, R. Nigam, V. 2022-05-05 doi:10.1101/2022.05.04.490549 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Heterologous expression of a lycophyte protein enhances angiosperm seedling vigor ]]> https://biorxiv.org/content/10.1101/2022.05.06.490942v1?rss=1 Koh, S. W. H. Bascom, C. Berenguer, E. Ingram, G. Estelle, M. Hardtke, C. 2022-05-06 doi:10.1101/2022.05.06.490942 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Deep Reinforcement Learning for Optimal Experimental Design in Biology ]]> https://biorxiv.org/content/10.1101/2022.05.09.491138v1?rss=1 Treloar, N. J. Braniff, N. Ingalls, B. Barnes, C. P. 2022-05-10 doi:10.1101/2022.05.09.491138 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Hypoxic memory of tumor intrinsic type I interferon suppression promotes breast cancer metastasis ]]> https://biorxiv.org/content/10.1101/2022.05.12.491632v1?rss=1 Iriondo, O. Mecenas, D. Li, Y. Chin, C. R. Thomas, A. Amzaleg, Y. Ortiz, V. MacKay, M. Dickerson, A. Lee, G. Harotoonian, S. Benayoun, B. A. Smith, A. D. Mason, C. Yu, M. 2022-05-13 doi:10.1101/2022.05.12.491632 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission ]]> https://biorxiv.org/content/10.1101/2022.05.13.491776v1?rss=1 Stern, S. Zhang, L. Wang, M. Wright, R. Cordeiro, D. Peles, D. Hang, Y. Mendes, A. P. Baul, T. Roth, J. Coorapati, S. Boks, M. Pol, H. H. Brennand, K. J. Rethelyi, J. M. Kahn, R. S. Marchetto, M. C. Gage, F. H. 2022-05-13 doi:10.1101/2022.05.13.491776 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Mouse primary T cell phosphotyrosine proteomics enabled by BOOST ]]> https://biorxiv.org/content/10.1101/2022.05.13.491817v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@4a2742org.highwire.dtl.DTLVardef@57645borg.highwire.dtl.DTLVardef@17dbfacorg.highwire.dtl.DTLVardef@b2df00_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chua, X. Y. Callahan, K. P. Griffith, A. A. Hildebrandt, T. Fu, G. Hu, M. Wen, R. Salomon, A. 2022-05-13 doi:10.1101/2022.05.13.491817 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics ]]> https://biorxiv.org/content/10.1101/2022.05.15.490691v1?rss=1 Bittremieux, W. Avalon, N. E. Thomas, S. P. Kakhkhorov, S. A. Aksenov, A. A. Portal Gomes, P. W. Aceves, C. M. Caraballo Rodriguez, A. M. Gauglitz, J. M. Gerwick, W. H. Jarmusch, A. K. Kaddurah-Daouk, R. F. Kang, K. B. Kim, H. W. Kondic, T. Mannochio-Russo, H. Meehan, M. J. Melnik, A. Nothias, L.-F. O'Donovan, C. Panitchpakdi, M. Petras, D. Schmid, R. Schymanski, E. L. van der Hooft, J. J. J. Weldon, K. C. Yang, H. Zemlin, J. Wang, M. Dorrestein, P. C. 2022-05-15 doi:10.1101/2022.05.15.490691 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Interactive Neurorobotics: Behavioral and Neural Dynamics of Agent Interactions ]]> https://biorxiv.org/content/10.1101/2022.05.17.492233v1?rss=1 Leonardis, E. J. Breston, L. Lucero-Moore, R. Sena, L. Kohli, R. Schuster, L. Barton-Gluzman, L. Quinn, L. K. Wiles, J. Chiba, A. 2022-05-18 doi:10.1101/2022.05.17.492233 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Immunomodulatory Extracellular Matrix Hydrogel Mitigates Scar Formation in a Model of Tongue Fibrosis. ]]> https://biorxiv.org/content/10.1101/2022.05.17.492250v1?rss=1 Zelus, E. I. Panduro, A. Alperin, M. Vahabzadeh-Hagh, A. M. Christman, K. L. 2022-05-18 doi:10.1101/2022.05.17.492250 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ A neural theory for counting memories ]]> https://biorxiv.org/content/10.1101/2022.05.18.492502v1?rss=1 Dasgupta, S. Hattori, D. Navlakha, S. 2022-05-18 doi:10.1101/2022.05.18.492502 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness ]]> https://biorxiv.org/content/10.1101/2022.05.19.492686v1?rss=1 Makowski, C. Wang, H. Srinivasan, A. Qi, A. Qiu, Y. van der Meer, D. Frei, O. Zou, J. Visscher, P. M. Yang, J. Chen, C.-H. 2022-05-19 doi:10.1101/2022.05.19.492686 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Higher-order interactions shape microbial interactions as microbial community complexity increases ]]> https://biorxiv.org/content/10.1101/2022.05.19.492721v1?rss=1 Morin, M. A. Morrison, A. J. Harms, M. J. Dutton, R. J. 2022-05-20 doi:10.1101/2022.05.19.492721 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Mechanosensor Piezo1 Mediates Bimodal Patterns of Intracellular Signaling ]]> https://biorxiv.org/content/10.1101/2022.05.19.492730v1?rss=1 Pan, Y. Shi, L. Z. Preece, D. Gomez-Godinez, V. Yoon, C. W. Lu, S. Carmona, C. Woo, S.-H. Chien, S. W. Berns, M. Liu, L. Wang, Y. 2022-05-20 doi:10.1101/2022.05.19.492730 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Hippocampus as a generative circuit for predictive coding of future sequences ]]> https://biorxiv.org/content/10.1101/2022.05.19.492731v1?rss=1 Chen, Y. Zhang, H. Sejnowski, T. J. 2022-05-20 doi:10.1101/2022.05.19.492731 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Mechanoreceptor signal convergence and transformation in the dorsal horn flexibly shape a diversity of outputs to the brain ]]> https://biorxiv.org/content/10.1101/2022.05.20.492853v1?rss=1 Chirila, A. M. Rankin, G. Tseng, S.-Y. Emanuel, A. Chavez-Martinez, C. L. Zhang, D. Harvey, C. D. Ginty, D. D. 2022-05-20 doi:10.1101/2022.05.20.492853 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Lactational delivery of Triclosan promotes non-alcoholic fatty liver disease in newborn mice ]]> https://biorxiv.org/content/10.1101/2022.05.20.492880v1?rss=1 Weber, A. Yang, X. Mennillo, E. Ding, J. Watrous, J. Jain, M. Chen, S.-J. Karin, M. Tukey, R. 2022-05-21 doi:10.1101/2022.05.20.492880 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer involved in allergic diseases ]]> https://biorxiv.org/content/10.1101/2022.05.24.493112v1?rss=1 Chen, H. V. Fiaux, P. C. Sen, A. Luthra, I. Ho, A. J. Chen, A. R. Guruvayurappan, K. Lorenzini, M. H. O'Connor, C. McVicker, G. 2022-05-25 doi:10.1101/2022.05.24.493112 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Bridging between mouse and human enhancer-promoter long-range interactions in neural stem cells, to understand enhancer function in neurodevelopmental disease ]]> https://biorxiv.org/content/10.1101/2022.05.26.493430v1?rss=1 D'Aurizio, R. Catona, O. Pitasi, M. Li, Y. E. Ren, B. Nicolis, S. K. 2022-05-26 doi:10.1101/2022.05.26.493430 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ A proton pump enhancing photosynthesis links phagocytosis to marine phytoplankton symbiogenesis ]]> https://biorxiv.org/content/10.1101/2022.05.26.493626v1?rss=1 Yee, D. P. Samo, T. J. Abbriano, R. M. Shimasaki, B. Vernet, M. Mayali, X. Weber, P. K. Mitchell, B. G. Hildebrand, M. Tresguerres, M. 2022-05-28 doi:10.1101/2022.05.26.493626 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ A Role for Nup153 in Nuclear Assembly Reveals Differential Requirements for Targeting of Nuclear Envelope Constituents ]]> https://biorxiv.org/content/10.1101/2022.05.27.493435v1?rss=1 LaJoie, D. Turkmen, A. M. Mackay, D. R. Jensen, C. C. Aksenova, V. Niwa, M. Dasso, M. Ullman, K. S. 2022-05-28 doi:10.1101/2022.05.27.493435 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Affinity-optimizing variants within cardiac enhancers disrupt heart development and contribute to cardiac traits ]]> https://biorxiv.org/content/10.1101/2022.05.27.493636v1?rss=1 Jindal, G. A. Bantle, A. T. Solvason, J. J. Grudzien, J. L. D'Antonio-Chronowska, A. Lim, F. Le, S. H. Larsen, R. O. Klie, A. Frazer, K. A. Farley, E. K. 2022-05-29 doi:10.1101/2022.05.27.493636 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Affinity-optimizing variants within the ZRS enhancer disrupt limb development ]]> https://biorxiv.org/content/10.1101/2022.05.27.493789v1?rss=1 Lim, F. Ryan, G. E. Le, S. H. Solvason, J. J. Steffen, P. Farley, E. K. 2022-05-28 doi:10.1101/2022.05.27.493789 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation ]]> https://biorxiv.org/content/10.1101/2022.05.29.493926v1?rss=1 Jiang, K. Xie, Y. Zhu, Y. Wang, N. Luo, M. Oda, T. Guo, R. Yu, Z. Aizezi, Y. Zhang, L. Yan, Y. Zhang, Y. Bao, H. Wang, Y. Zhu, Z. Huang, A. Zhao, Y. Asami, T. Huang, H. Guo, H. 2022-05-30 doi:10.1101/2022.05.29.493926 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology ]]> https://biorxiv.org/content/10.1101/2022.05.31.494202v1?rss=1 Bell, M. Lee, C. T. Rangamani, P. 2022-06-01 doi:10.1101/2022.05.31.494202 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Retractions and rewards in science: An open question for reviewers and funders ]]> https://biorxiv.org/content/10.1101/2022.05.31.494225v1?rss=1 Ribeiro, M. D. Kalichman, M. Vasconcelos, S. M. 2022-06-01 doi:10.1101/2022.05.31.494225 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectral Alignment For Discovery of Structurally Related Molecules ]]> https://biorxiv.org/content/10.1101/2022.06.01.494370v1?rss=1 Bittremieux, W. Schmid, R. Huber, F. van der Hooft, J. J. J. Wang, M. Dorrestein, P. C. 2022-06-02 doi:10.1101/2022.06.01.494370 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Variable Number Tandem Repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG ]]> https://biorxiv.org/content/10.1101/2022.06.01.494371v1?rss=1 Ding, Y. C. Adamson, A. W. Bakhtiari, M. Patrick, C. Park, J. Laitman, Y. Weitzel, J. N. Bafna, V. Friedman, E. Neuhausen, S. L. 2022-06-02 doi:10.1101/2022.06.01.494371 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Enabled primarily controls filopodial morphology, not actin organization, in the TSM1 growth cone in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.06.01.494414v1?rss=1 Fang, H. Y. Forghani, R. Clarke, A. McQueen, P. G. Chandrasekaran, A. O'Neill, K. M. Losert, W. Papoian, G. A. Giniger, E. 2022-06-03 doi:10.1101/2022.06.01.494414 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Evaluation of Blood-Based Exosomes as Biomarkers for Aging-Related TDP-43 pathology ]]> https://biorxiv.org/content/10.1101/2022.06.03.487443v1?rss=1 Winston, C. N. Sukreet, S. Lynch, H. Lee, V. M. Y. Wilcock, D. M. Nelson, P. T. Rissman, R. A. 2022-06-06 doi:10.1101/2022.06.03.487443 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Polygenic Transcriptome Risk Scores Can Translate Genetic Results Between Species ]]> https://biorxiv.org/content/10.1101/2022.06.03.494719v1?rss=1 Santhanam, N. Sanchez-Roige, S. Liang, Y. Chitre, A. Munro, D. Chen, D. Cheng, R. Gao, J. George, A. M. Gileta, A. Holl, K. Hughson, A. King, C. P. Lamparelli, A. C. Martin, C. D. Martinez, A. G. Mi, S. St. Pierre, C. L. Tripi, J. Wang, T. Chen, H. Flagel, S. Ishiwari, K. Meyer, P. Saba, L. Woods, L. S. Polesskaya, O. Palmer, A. A. Im, H. K. 2022-06-05 doi:10.1101/2022.06.03.494719 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Super-resolution stimulated Raman Scattering microscopy with A-PoD ]]> https://biorxiv.org/content/10.1101/2022.06.04.494813v1?rss=1 Jang, H. Li, Y. Fung, A. Bagheri, P. Hoang, K. Skowronska-Krawczyk, D. Chen, X. Wu, J. Y. Bintu, B. Shi, L. 2022-06-05 doi:10.1101/2022.06.04.494813 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Formation of protein-mediated tubes is governed by a snapthrough transition ]]> https://biorxiv.org/content/10.1101/2022.06.07.494774v1?rss=1 Mahapatra, A. Rangamani, P. 2022-06-08 doi:10.1101/2022.06.07.494774 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ Site-specific C-terminal fluorescent labeling of Tau protein ]]> https://biorxiv.org/content/10.1101/2022.06.07.495075v1?rss=1 Bryan, L. Awasthi, S. Li, Y. Nirmalraj, P. N. Balog, S. Yang, J. Mayer, M. 2022-06-09 doi:10.1101/2022.06.07.495075 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP ]]> https://biorxiv.org/content/10.1101/2022.06.08.495357v1?rss=1 Lorenz, D. A. Shen, K. A. Her, H.-L. Rothamel, K. Hutt, K. R. Nojadera, A. C. Bruns, S. C. Manakov, S. A. Chapman, K. B. Yeo, G. W. 2022-06-09 doi:10.1101/2022.06.08.495357 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Genetic exchange in Leishmania is facilitated by IgM natural antibodies ]]> https://biorxiv.org/content/10.1101/2022.06.09.495557v1?rss=1 Serafim, T. D. Iniguez, E. F. Barletta, A. B. Doehl, J. S. P. Short, M. Lack, J. Cecilio, P. Nair, V. Disotuar, M. Wilson, T. Coutinho-Abreu, I. V. Oliveira, F. Meneses, C. Barillas-Mury, C. Andersen, J. Ribeiro, J. M. C. Beverley, S. M. Kamhawi, S. Valenzuela, J. G. 2022-06-10 doi:10.1101/2022.06.09.495557 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Multimodal monitoring of human cortical organoids implanted in mice using transparent graphene microelectrodes reveal functional connection between organoid and mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2022.06.16.496469v1?rss=1 Wilson, M. Thunemann, M. Liu, X. Lu, Y. Puppo, F. Adams, J. Kim, J.-H. Pizzo, D. Djurovic, S. Andreassen, O. Mansour, A. Gage, F. H. Muotri, A. R. Devor, A. Kuzum, D. 2022-06-17 doi:10.1101/2022.06.16.496469 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Phencyclidine and methamphetamine cause cognitive deficits by changing pyramidal neuron transmitter identity in the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2022.06.16.496480v1?rss=1 Pratelli, M. Thaker, A. Li, H. Godavarthi, S. Spitzer, N. C. 2022-06-17 doi:10.1101/2022.06.16.496480 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Endogenous Rab38 regulates LRRK2's membrane recruitment and substrate Rab phosphorylation in melanocytes ]]> https://biorxiv.org/content/10.1101/2022.06.20.496629v1?rss=1 Unapanta, A. Shavarebi, F. Porath, J. Balen, C. Nguyen, A. Tseng, J. Shen, Y. Liu, M. Lis, P. Di Pietro, S. Hiniker, A. 2022-06-20 doi:10.1101/2022.06.20.496629 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Molecular interactions underlying the phase separation of HP1: Role of phosphorylation, ligand and nucleic acid binding ]]> https://biorxiv.org/content/10.1101/2022.06.20.496886v1?rss=1 Her, C. Phan, T. M. Jovic, N. Kapoor, U. Ackermann, B. E. Rizuan, A. Kim, Y. Mittal, J. Debelouchina, G. T. 2022-06-20 doi:10.1101/2022.06.20.496886 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury and matrix remodeling in patients with stone disease ]]> https://biorxiv.org/content/10.1101/2022.06.22.497218v1?rss=1 Canela, V. H. Bowen, W. S. Ferreira, R. M. Lingeman, J. E. Sabo, A. R. Barwinska, D. Winfree, S. Lake, B. Cheng, Y.-H. LaFavers, K. Zhang, K. Coe, F. L. Worcester, E. Jain, S. Eadon, M. T. Williams, J. C. El-Achkar, T. M. Kidney Precision Medicine Project, 2022-06-26 doi:10.1101/2022.06.22.497218 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period ]]> https://biorxiv.org/content/10.1101/2022.06.24.497549v1?rss=1 Philpott, J. M. Freeberg, A. M. Park, J. Lee, K. Ricci, C. G. Hunt, S. R. Narasimamurthy, R. Segal, D. H. Robles, R. Cao, Y. D. Tripathi, S. McCammon, J. A. Virshup, D. M. Chiu, J. C. Lee, C. Partch, C. L. 2022-06-26 doi:10.1101/2022.06.24.497549 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Machine Learning Identifies Signatures of Macrophage Reactivity and Tolerance that Predict Disease Outcomes ]]> https://biorxiv.org/content/10.1101/2022.06.27.497783v1?rss=1 12,500 diverse datasets). This 338-gene signature identified macrophage polarization states at single-cell resolution, in physiology and across diverse human diseases, and in murine pre-clinical disease models. The signature consistently outperformed conventional signatures in the degree of transcriptome-proteome overlap, and in detecting disease states; it also prognosticated outcomes across diverse acute and chronic diseases, e.g., sepsis, liver fibrosis, aging and cancers. Crowd-sourced genetic and pharmacologic studies confirmed that model-rationalized interventions trigger predictable macrophage fates. These findings provide a formal and universally relevant definition of macrophage states and a predictive framework (http://hegemon.ucsd.edu/SMaRT) for the scientific community to develop macrophage-targeted precision diagnostics and therapeutics. One Sentence SummarySignatures of macrophage reactivity and tolerance (SMaRT) predict disease outcomes ]]> Ghosh, P. Sinha, S. Katkar, G. D. Vo, D. T. Taheri, S. Dang, D. Das, S. Sahoo, D. 2022-06-30 doi:10.1101/2022.06.27.497783 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Activity-driven extracellular volume expansion drives vertebrate axis elongation ]]> https://biorxiv.org/content/10.1101/2022.06.27.497799v1?rss=1 Michaut, A. Mongera, A. Gupta, A. Serra, M. Rigoni, P. Lee, J. G. Hall, A. R. Duarte, F. Mahadevan, L. Guevorkian, K. Pourquie, O. 2022-06-28 doi:10.1101/2022.06.27.497799 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Increasing Muscle Hypertrophy with a Natural Product Designed to Inhibit SIRT1 ]]> https://biorxiv.org/content/10.1101/2022.06.27.497838v1?rss=1 Pathak, S. Wallace, M. Athalye, S. Schenk, S. Langer, H. T. Baar, K. 2022-06-29 doi:10.1101/2022.06.27.497838 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Function and phylogeny support the independent evolution of acid-sensing ion channels in the Placozoa ]]> https://biorxiv.org/content/10.1101/2022.06.28.497943v1?rss=1 Elkhatib, W. Yanez-Guerra, L. A. Mayorova, T. D. Currie, M. A. Perera, M. Singh, A. Gauberg, J. Senatore, A. 2022-06-30 doi:10.1101/2022.06.28.497943 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ GLT8D1 mutations cause amyotrophic lateral sclerosis via disruption of neurotrophin signalling within membrane lipid rafts ]]> https://biorxiv.org/content/10.1101/2022.06.28.497990v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@1992dc4org.highwire.dtl.DTLVardef@18be04eorg.highwire.dtl.DTLVardef@333216org.highwire.dtl.DTLVardef@11d76c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Moll, T. Graves, E. Urbanek, A. Soni, N. Ranganathan, R. Higginbottom, A. Wang, S. Head, B. Cooper-Knock, J. Shaw, P. J. 2022-07-01 doi:10.1101/2022.06.28.497990 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Avian and Human Influenza Viruses Exhibit Distinct Glycoconjugate Receptor Specificities in Human Lung Cells ]]> https://biorxiv.org/content/10.1101/2022.06.29.498208v1?rss=1 Liang, C.-Y. Huang, I. Han, J. Manivasagam, S. Plung, J. Sturtz, M. Yu, Y. Kandasamy, M. Gourronc, F. A. Klingelhutz, A. J. Choudhury, B. Rong, L. Perez, J. T. Neelamegham, S. Manicassamy, B. 2022-06-30 doi:10.1101/2022.06.29.498208 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Longitudinal, Multi-platform Metagenomics Yields a High-quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities ]]> https://biorxiv.org/content/10.1101/2022.07.01.497845v1?rss=1 Saak, C. C. Pierce, E. C. Dinh, C. B. Portik, D. Hall, R. Ashby, M. Dutton, R. J. 2022-07-02 doi:10.1101/2022.07.01.497845 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors ]]> https://biorxiv.org/content/10.1101/2022.07.05.498881v1?rss=1 Fink, E. A. Bardine, C. Gahbauer, S. Singh, I. White, K. Gu, S. Wan, X. Ary, B. Glenn, I. O'Connell, J. O'Donnell, H. Fajtova, P. Lyu, J. Vigneron, S. Young, N. J. Kondratov, I. S. O'Donoghue, A. J. Moroz, Y. Taunton, J. Renslo, A. R. Irwin, J. J. Garcia-Sastre, A. Shoichet, B. K. Craik, C. S. 2022-07-06 doi:10.1101/2022.07.05.498881 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Large-scale capture of hidden fluorescent labels for training generalizable markerless motion capture models ]]> https://biorxiv.org/content/10.1101/2022.07.07.499213v1?rss=1 Butler, D. J. Keim, A. P. Ray, S. Azim, E. 2022-07-10 doi:10.1101/2022.07.07.499213 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ The crosstalk between microbial sensors ELMO1 and NOD2 shape intestinal immune responses ]]> https://biorxiv.org/content/10.1101/2022.07.09.499433v1?rss=1 Sharma, A. Achi, S. Ibeawuchi, S. R. Anandachar, M. S. Gementera, H. Chaudhury, U. Usmani, F. Vega, K. Sayed, I. Das, S. 2022-07-10 doi:10.1101/2022.07.09.499433 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Measurement of Cervical Neuronal Activity during Stress Challenge Using Novel Flexible Adhesive Surface Electrodes ]]> https://biorxiv.org/content/10.1101/2022.07.10.499484v1?rss=1 Bu, Y. Kurniawa, J. F. Prince, J. Nguyen, A. K. L. Ho, B. Sit, N. L. J. Pham, T. Wu, V. M. Tjhia, B. Shin, A. J. Wu, T.-c. Tu, X. Rao, R. Coleman, T. P. Lerman, I. 2022-07-11 doi:10.1101/2022.07.10.499484 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits ]]> https://biorxiv.org/content/10.1101/2022.07.12.499605v1?rss=1 Chitre, A. S. Hebda-Bauer, E. K. Blandino, P. Bimschleger, H. Nguyen, K.-M. Maras, P. Li, F. Ozel, A. B. Polesskaya, O. Cheng, R. Flagel, S. B. Watson, S. J. Li, J. Akil, H. Palmer, A. A. 2022-07-13 doi:10.1101/2022.07.12.499605 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning ]]> https://biorxiv.org/content/10.1101/2022.07.12.499746v1?rss=1 Meamardoost, S. Hwang, E. Bhattacharya, M. Ren, C. Wang, L. Mewes, C. Zhang, Y. Komiyama, T. Gunawan, R. 2022-07-14 doi:10.1101/2022.07.12.499746 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors ]]> https://biorxiv.org/content/10.1101/2022.07.13.499814v1?rss=1 Replogle, J. M. Bonnar, J. L. Pogson, A. N. Liem, C. R. Maier, N. K. Ding, Y. Russell, B. J. Wang, X. Leng, K. Guna, A. Norman, T. M. Pak, R. A. Ramos, D. M. Ward, M. E. Gilbert, L. A. Kampmann, M. Weissman, J. S. Jost, M. 2022-07-13 doi:10.1101/2022.07.13.499814 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Comparison of bacterial suppression by phage cocktails, dual-receptor generalists, and coevolutionarily trained phages ]]> https://biorxiv.org/content/10.1101/2022.07.14.500114v1?rss=1 Borin, J. M. Lee, J. J. Gerbino, K. R. Meyer, J. R. 2022-07-14 doi:10.1101/2022.07.14.500114 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Transcriptional Profiling of the Hippocampus in an F2 Cross of a Genetic Rat Model of Internalizing vs. Externalizing Behavior and Addiction Liability ]]> https://biorxiv.org/content/10.1101/2022.07.14.500129v1?rss=1 Hebda-Bauer, E. K. Hagenauer, M. H. Blandino, P. Meng, F. Chitre, A. S. Ozel, A. B. Arakawa, K. Flagel, S. B. Watson, S. J. Palmer, A. A. Li, J. Akil, H. 2022-07-15 doi:10.1101/2022.07.14.500129 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ The Type 9 Secretion System enables sharing of fungal mannan by human gut Bacteroides ]]> https://biorxiv.org/content/10.1101/2022.07.15.500217v1?rss=1 Buzun, E. Heunis, T. Cottam, C. Trost, M. Lowe, E. C. 2022-07-15 doi:10.1101/2022.07.15.500217 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Cortical polarity ensures its own asymmetric inheritance in the stomatal lineage to pattern the leaf surface ]]> https://biorxiv.org/content/10.1101/2022.07.15.500234v1?rss=1 Muroyama, A. Gong, Y. Hartman, K. S. Bergmann, D. C. 2022-07-16 doi:10.1101/2022.07.15.500234 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Identification of a Papain-Like Protease Inhibitor with Potential for Repurposing in Combination with an Mpro Protease Inhibitor for Treatment of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.07.18.500363v1?rss=1 Campagna, J. Jagodzinska, B. Alvarez, P. Yeun, C. Spilman, P. Enquist, K. M. Cohn, W. Fajtov, P. O'Donoghue, A. J. Arumugaswami, V. Li, M. M. H. Damoiseaux, R. John, V. 2022-07-18 doi:10.1101/2022.07.18.500363 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Metabolic network models of Gardnerella pangenome identify interactions in the vaginal environment ]]> https://biorxiv.org/content/10.1101/2022.07.18.500544v1?rss=1 Dillard, L. R. Glass, E. M. Lewis, A. L. Thomas-White, K. Papin, J. A. 2022-07-20 doi:10.1101/2022.07.18.500544 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Deep generative modeling and clustering of single cell Hi-C data ]]> https://biorxiv.org/content/10.1101/2022.07.19.500573v1?rss=1 Liu, Q. Zeng, W. Zhang, W. Wang, S. Chen, H. Jiang, R. Zhou, M. Zhang, S. 2022-07-20 doi:10.1101/2022.07.19.500573 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Adipocyte-secreted IL-6 sensitizes macrophages to IL-4 signaling ]]> https://biorxiv.org/content/10.1101/2022.07.19.500620v1?rss=1 Luan, D. A. Dadpey, B. Zaid, J. De Luca, J. H. Xia, W. Castle, J. Reilly, S. M. 2022-07-20 doi:10.1101/2022.07.19.500620 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference ]]> https://biorxiv.org/content/10.1101/2022.07.20.500802v1?rss=1 Meng, X. Navoly, G. Giannakopoulou, O. DL, D. Koller, D. Pathak, G. Koen, N. Lin, K. Renteria, M. Feng, Y. Gaziano, J. M. Stein, D. Zar, H. Campbell, M. van Heel, D. Trivedi, B. Finer, S. McQuillin, A. Bass, N. Chundru, V. K. Martin, H. Huang, Q. Q. Valkovskaya, M. Kuo, P.-H. Chen, H.-C. Tsai, S.-J. Liu, Y.-L. Kendler, K. Peterson, R. Cai, N. Fang, Y. Sen, S. Scott, L. Burmeister, M. Loos, R. Preuss, M. Actkins, K. Davis, L. Uddin, M. Wani, A. Wildman, D. Ursano, R. Kessler, R. Kanai, M. Okada, Y. Sakaue, S. Rabinowitz, J. Maher, B. Uhl, G. Eato 2022-07-21 doi:10.1101/2022.07.20.500802 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Optimizing immunostaining of archival fish samples to enhance museum collection potential ]]> https://biorxiv.org/content/10.1101/2022.07.21.501016v1?rss=1 Kwan, G. T. Frable, B. W. Thompson, A. R. Tresguerres, M. 2022-07-22 doi:10.1101/2022.07.21.501016 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Efficient in vivo neuronal genome editing in the mouse brain using nanocapsules containing CRISPR-Cas9 ribonucleoproteins ]]> https://biorxiv.org/content/10.1101/2022.07.24.501299v1?rss=1 80%), with occasional editing in cholinergic, calretinin, and parvalbumin interneurons. Glial activation was minimal and was localized along the needle tract. Our results demonstrate that the RNP NCs are capable of safe and efficient neuronal genome editing in vivo. SIGNIFICANCE STATEMENTModifying the DNA of cells in the brain could present opportunities for new treatments of neurological diseases. In this report, we describe a nanocapsule system designed to deliver the elements needed to modify the DNA of brain cells, also known as genome editing. These nanocapsules are created by chemically encapsulating the genome editing components, such that the nanocapsules are stable when prepared and biodegradable to release their payload upon entering cells. When injected into the mouse brain, our research shows that the nanocapsules lead to safe and efficient editing of DNA in neurons. ]]> Metzger, J. M. Wang, Y. Neuman, S. S. Snow, K. J. Murray, S. A. Lutz, C. M. Bondarenko, V. Felton, J. A. Gimse, K. Xie, R. Zhao, Y. Flowers, M. T. Simmons, H. A. Roy, S. Saha, K. Levine, J. Emborg, M. E. Gong, S. 2022-07-24 doi:10.1101/2022.07.24.501299 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Microcephaly-associated WDR62 mutations hamper Golgi apparatus-to-spindle pole shuttling in human neural progenitors ]]> https://biorxiv.org/content/10.1101/2022.07.24.501306v1?rss=1 dell'Amico, C. Angulo Salavarria, M. M. Takeo, Y. Saotome, I. Dell'Anno, M. T. Galimberti, M. Pellegrino, E. Cattaneo, E. Louvi, A. Onorati, M. 2022-07-26 doi:10.1101/2022.07.24.501306 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Extrachromosomal DNA in the cancerous transformation of Barrett's esophagus ]]> https://biorxiv.org/content/10.1101/2022.07.25.501144v1?rss=1 Luebeck, J. Ng, A. W. T. Galipeau, P. C. Li, X. Sanchez, C. A. Katz-Summercorn, A. Kim, H. Jammula, S. He, Y. Lippman, S. M. Verhaak, R. G. W. Maley, C. C. Alexandrov, L. B. Reid, B. J. Fitzgerald, R. C. Paulson, T. G. Chang, H. Y. Wu, S. Bafna, V. Mischel, P. S. 2022-07-25 doi:10.1101/2022.07.25.501144 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Diverse logics and grammar encode notochord enhancers ]]> https://biorxiv.org/content/10.1101/2022.07.25.501440v1?rss=1 Song, B. P. Ragsac, M. F. Tellez, K. Jindal, G. A. Grudzien, J. L. Le, S. H. Farley, E. K. 2022-07-27 doi:10.1101/2022.07.25.501440 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Multi-Molecular Hyperspectral PRM-SRS Imaging ]]> https://biorxiv.org/content/10.1101/2022.07.25.501472v1?rss=1 Shi, L. Zhang, W. Li, Y. Fung, A. A. Li, Z. Jang, H. Zha, H. Chen, X. Gao, F. Wu, J. Y. Sheng, H. Yao, J. Skowronska-Krawczyk, D. Jain, S. 2022-07-25 doi:10.1101/2022.07.25.501472 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Differential Analysis of Stromal-Epithelial Interactions between In Situ and Invasive Breast Cancer using Gene Expression Profiling ]]> https://biorxiv.org/content/10.1101/2022.07.30.502150v1?rss=1 Officer, A. Dempsey, A. M. Murrow, L. M. Gartner, Z. Tamayo, P. Yau, C. Harismendy, O. 2022-08-02 doi:10.1101/2022.07.30.502150 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis ]]> https://biorxiv.org/content/10.1101/2022.07.30.502165v1?rss=1 Bhaduri, S. Aguayo, A. Ohno, Y. Proietto, M. Jung, J. Wang, I. Kandel, R. Singh, N. Ibrahim, I. Fulzele, A. Bennett, E. J. Kihara, A. Neal, S. E. 2022-07-31 doi:10.1101/2022.07.30.502165 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Polymorphic short tandem repeats make widespread contributions to blood and serum traits ]]> https://biorxiv.org/content/10.1101/2022.08.01.502370v1?rss=1 Margoliash, J. Fuchs, S. Li, Y. Massarat, A. Goren, A. Gymrek, M. 2022-08-03 doi:10.1101/2022.08.01.502370 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Molecular formula discovery via bottom-up MS/MS interrogation ]]> https://biorxiv.org/content/10.1101/2022.08.03.502704v1?rss=1 5,000 novel molecular formulae unarchived in chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global peak annotation. This approach reveals peak interrelationships, allowing the systematic annotation of 37 fatty acid amide molecules in human fecal data, among other applications. All bioinformatics pipelines are available in a standalone software, BUDDY (https://github.com/HuanLab/BUDDY/). ]]> Xing, S. Shen, S. Xu, B. Huan, T. 2022-08-05 doi:10.1101/2022.08.03.502704 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Yeast and Mammalian Epsins Use Different Determinants for Localization and Function: Role of Clathrin/AP2/Ubiquitin Binding Motifs and Poly-Glutamine Stretches ]]> https://biorxiv.org/content/10.1101/2022.08.04.502746v1?rss=1 Madhivanan, K. Subramanian, S. Cao, L. Mukherjee, D. Sen, A. Hsieh, W.-C. Hanna, C. B. Wang, B. Chen, H. Staiger, C. J. Aguilar, R. C. 2022-08-05 doi:10.1101/2022.08.04.502746 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ The Nested Hierarchy of Overt, Mouthed, and Imagined Speech Activity Evident in Intracranial Recordings ]]> https://biorxiv.org/content/10.1101/2022.08.04.502829v1?rss=1 Soroush, P. Z. Herff, C. Ries, S. K. Shih, J. J. Schultz, T. Krusienski, D. J. 2022-08-06 doi:10.1101/2022.08.04.502829 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Depletion of Plasma Membrane PI4P by ORP5 Requires Hydrolysis by SAC1 in Acceptor Membranes ]]> https://biorxiv.org/content/10.1101/2022.08.04.502856v1?rss=1 Doyle, C. P. Timple, L. Hammond, G. R. 2022-08-05 doi:10.1101/2022.08.04.502856 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data ]]> https://biorxiv.org/content/10.1101/2022.08.05.502991v1?rss=1 Lee, L. Yu, M. Li, X. Zhu, C. Zhang, Y. Yu, H. Ren, B. Li, Y. Hu, M. 2022-08-06 doi:10.1101/2022.08.05.502991 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Live imaging of echinoderm embryos to illuminate evo-devo ]]> https://biorxiv.org/content/10.1101/2022.08.05.503002v1?rss=1 Barone, V. Lyons, D. C. 2022-08-06 doi:10.1101/2022.08.05.503002 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A Universal Language for Finding Mass Spectrometry Data Patterns ]]> https://biorxiv.org/content/10.1101/2022.08.06.503000v1?rss=1 Jarmusch, A. K. Aron, A. T. Petras, D. Phelan, V. V. Bittremieux, W. Acharya, D. D. Ahmed, M. M. A. Bauermeister, A. Bertin, M. J. Boudreau, P. D. Borges, R. M. Bowen, B. P. Brown, C. J. Chagas, F. O. Clevenger, K. D. Correia, M. S. P. Crandall, W. J. Crusemann, M. Damiani, T. Fiehn, O. Garg, N. Gerwick, W. H. Gilbert, J. R. Globisch, D. Gomes, P. W. P. Heuckeroth, S. James, C. A. Jarmusch, S. A. Kakhkhorov, S. A. Kang, K. B. Kersten, R. D. Kim, H. Kirk, R. D. Kohlbacher, O. Kontou, E. E. Liu, K. Lizama-Chamu, I. Luu, G. T. Luzzatto Knaan, T. Marty, M. T. 2022-08-07 doi:10.1101/2022.08.06.503000 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors ]]> https://biorxiv.org/content/10.1101/2022.08.07.503099v1?rss=1 Moghadasi, S. A. Heilmann, E. Moraes, S. N. Kearns, F. L. von Laer, D. Amaro, R. E. Harris, R. 2022-08-08 doi:10.1101/2022.08.07.503099 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Genome-Wide Association Study Finds Multiple Loci Associated with Intraocular Pressure in HS Rats ]]> https://biorxiv.org/content/10.1101/2022.08.16.503865v1?rss=1 Fowler, S. Wang, T. Munro, D. Kumar, A. Chitre, A. S. Hollingsworth, T. Martinez, A. G. St.Pierre, C. L. Bimschleger, H. Gao, J. Cheng, R. Mohammadi, P. Chen, H. Palmer, A. A. Polesskaya, O. Jablonski, M. M. 2022-08-17 doi:10.1101/2022.08.16.503865 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data ]]> https://biorxiv.org/content/10.1101/2022.08.16.504049v1?rss=1 90% accurate in dynamic spatial mitochondria simulations and are in agreement with published motility results in vitro. Using MitoTNT, we reveal correlated mitochondrial movement patterns, local fission and fusion fingerprints, asymmetric fission and fusion dynamics, cross-network transport patterns, and network-level responses to pharmacological manipulations. MitoTNT is implemented in python with a JupyterLab interface. The extendable and user-friendly design aims at making temporal network tracking accessible to the wider mitochondria community. ]]> Wang, Z. Natekar, P. Tea, C. Tamir, S. Hakozaki, H. Schoeneberg, J. 2022-08-17 doi:10.1101/2022.08.16.504049 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Cell-associated Transcriptional Alterations in the Retinal of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.08.18.502974v1?rss=1 Ngolab, J. Mark, A. Buchanan, J. Korouri, S. Preissl, S. Rosenthal, S. B. Wang, A. Fisch, K. M. Rissman, R. A. 2022-08-19 doi:10.1101/2022.08.18.502974 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Efficient meta-analysis of multivariate genome-wide association studies with Meta-MOSTest ]]> https://biorxiv.org/content/10.1101/2022.08.18.504383v1?rss=1 Lin, A. shadrin, a. van der Meer, D. Hindley, G. Cheng, W. Sonderby, I. E. Bahrami, S. S OConnell, K. Rahman, Z. Parker, N. B Smeland, O. Fan, C. Holland, D. Dale, A. Andreassen, O. Frei, O. 2022-08-18 doi:10.1101/2022.08.18.504383 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ The CD103-XCR1 axis mediates the recruitment of immunoregulatory dendritic cells after traumatic injury ]]> https://biorxiv.org/content/10.1101/2022.08.19.504399v1?rss=1 Lokwani, R. Ngo, T. B. DeStefano, S. Adusei, K. M. Bhuiyan, M. Josyula, A. Faust, M. Lin, A. Karkanitsa, M. Fathi, P. Sadtler, K. 2022-08-19 doi:10.1101/2022.08.19.504399 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Genomic and transcriptional profiling stratifies VQ myeloma lines into two clusters with distinct risk signatures and drug responses ]]> https://biorxiv.org/content/10.1101/2022.08.21.504657v1?rss=1 Flietner, E. Yu, M. Rajagopalan, A. Zhou, Y. Feng, Y. Veltri, A. Lasho, T. Wen, Z. Sun, Y. Patnaik, M. M. Callander, N. S. Asimakopoulos, F. Wang, D. Zhang, J. 2022-08-22 doi:10.1101/2022.08.21.504657 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Effective Matrix Designs for COVID-19 Group Testing ]]> https://biorxiv.org/content/10.1101/2022.08.22.504823v1?rss=1 Brust, D. Brust, J. J. 2022-08-23 doi:10.1101/2022.08.22.504823 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Combined loss of obscurin and obscurin-like 1 in murine hearts results in impaired diastolic dysfunction, altered metabolism and deregulated mitophagy. ]]> https://biorxiv.org/content/10.1101/2022.08.24.505098v1?rss=1 Fujita, K. Desmond, P. Blondelle, J. Sotak, M. Rajan, M. R. Clark, M. Esteve, E. Chan, Y. Gu, Y. Marrocco, V. Dalton, N. D. Ghassemian, M. Do, A. Klos, M. Peterson, K. L. Sheikh, F. Cho, Y. Borgeson, E. Lange, S. 2022-08-24 doi:10.1101/2022.08.24.505098 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Inaccurate fossil placement does not compromise tip-dated divergence times ]]> https://biorxiv.org/content/10.1101/2022.08.25.505200v1?rss=1 Koch, N. M. Garwood, R. J. Parry, L. A. 2022-08-26 doi:10.1101/2022.08.25.505200 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Regional and LTP-Dependent Variation of Synaptic Information Storage Capacity in Rat Hippocampus ]]> https://biorxiv.org/content/10.1101/2022.08.29.505464v1?rss=1 Samavat, M. Bartol, T. M. Bromer, C. Bowden, J. B. Hubbard, D. D. Hanka, D. C. Kuwajima, M. Mendenhall, J. M. Parker, P. H. Abraham, W. C. Harris, K. M. Sejnowski, T. J. 2022-08-31 doi:10.1101/2022.08.29.505464 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ A confinable female-lethal population suppression system in the malaria vector, Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/2022.08.30.505861v1?rss=1 Smidler, A. L. Pai, J. J. Apte, R. A. Sanchez C., H. M. Corder, R. M. Gutierrez, E. J. Thakre, N. Antoshechkin, I. Marshall, J. M. Akbari, O. 2022-08-30 doi:10.1101/2022.08.30.505861 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ CRISPR Mediated Transactivation in the Human Disease Vector Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2022.08.31.505972v1?rss=1 Bui, M. Benetta, E. D. Dong, Y. Zhao, Y. Yang, T. Li, M. Antoshechkin, I. A. Buchman, A. Bottino-Rojas, V. James, A. A. Perry, M. W. Dimopoulos, G. Akbari, O. 2022-09-02 doi:10.1101/2022.08.31.505972 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ A Metabolic Sum Rule Dictates Bacterial Response to Short-Chain Fatty Acid Stress ]]> https://biorxiv.org/content/10.1101/2022.08.31.506075v1?rss=1 Taylor, B. R. Patsalo, V. Okano, H. Shen, Y. Zhange, Z. Williamson, J. R. Rabinowitz, J. D. Hwa, T. 2022-08-31 doi:10.1101/2022.08.31.506075 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[ Imaging through Windansee electrode arrays reveals a small fraction of local neurons following surface MUA ]]> https://biorxiv.org/content/10.1101/2022.09.01.506113v1?rss=1 Thunemann, M. Hossain, L. Ness, T. V. Rogers, N. Lee, K. Lee, S.-H. Kılıc, K. Oh, H. Economo, M. N. Gilja, V. Einevoll, G. Dayeh, S. Devor, A. 2022-09-03 doi:10.1101/2022.09.01.506113 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Distinguishing Signal from Noise: Understanding Patterns of Non-Detections to Inform Accurate Quantitative Metabarcoding ]]> https://biorxiv.org/content/10.1101/2022.09.02.506420v1?rss=1 Gold, Z. Shelton, A. O. Casendino, H. R. Duprey, J. Gallego, R. Van Cise, A. Fisher, M. Jensen, A. J. D'Agnese, E. Andruszkiewicz Allan, E. Ramon-Laca, A. Garber-Yonts, M. Labare, M. Parsons, K. M. Kelly, R. P. 2022-09-02 doi:10.1101/2022.09.02.506420 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Mitotic tethering enables en masse inheritance of a shattered micronuclear chromosome ]]> https://biorxiv.org/content/10.1101/2022.09.08.507171v1?rss=1 Cleveland, D. W. Trivedi, P. Steele, C. D. Alexandrov, L. B. 2022-09-09 doi:10.1101/2022.09.08.507171 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Robust control of replication initiation in the absence of DnaA-ATP {leftrightharpoons} DnaA-ADP regulatory elements in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.09.08.507175v1?rss=1 Boesen, T. Charbon, G. Fu, H. Jensen, C. Li, D. Jun, S. Lobner-Olesen, A. 2022-09-08 doi:10.1101/2022.09.08.507175 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids ]]> https://biorxiv.org/content/10.1101/2022.09.09.507197v1?rss=1 Healy, T. M. Burton, R. S. 2022-09-13 doi:10.1101/2022.09.09.507197 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in nuclear condensates in plants ]]> https://biorxiv.org/content/10.1101/2022.09.09.507346v1?rss=1 Sun, T. Zeng, S. Wang, X. Owens, L. Fei, Z. Zhao, Y. Mazourek, M. Giovannoni, J. J. Li, L. 2022-09-11 doi:10.1101/2022.09.09.507346 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Postsynaptic receptors regulate presynaptic neurotransmitter stability ]]> https://biorxiv.org/content/10.1101/2022.09.10.507343v1?rss=1 Godavarthi, S. K. Hiramoto, M. Ignatyev, Y. Levin, J. B. Li, H. Pratelli, M. Borchardt, J. Czajkowski, C. M. Borodinsky, L. N. Sweeney, L. Cline, H. T. Spitzer, N. C. 2022-09-10 doi:10.1101/2022.09.10.507343 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options ]]> https://biorxiv.org/content/10.1101/2022.09.11.507475v1?rss=1 Kang, J. Y. Mishanina, T. V. Bao, Y. Chen, J. Llewellyn, E. Liu, J. Darst, S. A. Landick, R. 2022-09-11 doi:10.1101/2022.09.11.507475 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Cross-Modal Representation of Identity in Primate Hippocampus ]]> https://biorxiv.org/content/10.1101/2022.09.12.507611v1?rss=1 Tyree, T. Metke, M. Miller, C. 2022-09-13 doi:10.1101/2022.09.12.507611 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Developmental rate displays effects of inheritance but not of sex in inter-population hybrids of Tigriopus californicus ]]> https://biorxiv.org/content/10.1101/2022.09.13.507602v1?rss=1 Healy, T. M. Hargadon, A. C. Burton, R. S. 2022-09-15 doi:10.1101/2022.09.13.507602 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ APP family member dimeric complexes are formed predominantly in synaptic compartments ]]> https://biorxiv.org/content/10.1101/2022.09.13.507759v1?rss=1 Schilling, S. August, A. Meleux, M. Conradt, C. Tremmel, L. Teigler, S. Koo, E. H. Kins, S. Eggert, S. 2022-09-16 doi:10.1101/2022.09.13.507759 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.09.19.508543v1?rss=1 Grooms, N. W. F. W. F. Fitzgerald, M. Q. Schulting, L. G. Urena, S. E. Chung, S. H. 2022-09-19 doi:10.1101/2022.09.19.508543 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ DNA processing by the Kaposi's sarcoma-associated herpesvirus alkaline exonuclease SOX contributes to viral gene expression and infectious virion production ]]> https://biorxiv.org/content/10.1101/2022.09.19.508573v1?rss=1 Hartenian, E. Mendez, A. Didychuk, A. Khosla, S. Glaunsinger, B. A. 2022-09-19 doi:10.1101/2022.09.19.508573 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence ]]> https://biorxiv.org/content/10.1101/2022.09.19.508600v1?rss=1 Healy, T. M. Burton, R. S. 2022-09-19 doi:10.1101/2022.09.19.508600 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ FGF21 protects against hepatic lipotoxicity and macrophage activation to attenuate fibrogenesis in nonalcoholic steatohepatitis ]]> https://biorxiv.org/content/10.1101/2022.09.20.508654v1?rss=1 Liu, C. Schönke, M. Spoorenberg, B. Lambooij, J. van der Zande, H. Zhou, E. Tushuizen, M. E. Andreasson, A.-C. Park, A. Oldham, S. Uhrbom, M. Ahlstedt, I. Ikeda, Y. Wallenius, K. Peng, X.-R. Guigas, B. Boon, M. R. Wang, Y. Rensen, P. C. 2022-09-22 doi:10.1101/2022.09.20.508654 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Affinity-matured homotypic interactions induce spectrum of PfCSP-antibody structures that influence protection from malaria infection ]]> https://biorxiv.org/content/10.1101/2022.09.20.508747v1?rss=1 Martin, G. Torres, J. L. Pholcharee, T. Oyen, D. Flores-Garcia, Y. Gibson, G. Moskovitz, R. Beutler, N. Jung, D. D. Copps, J. Lee, W.-H. Gonzalez-Paez, G. Emerling, D. MacGill, R. S. Locke, E. King, C. R. Zavala, F. Wilson, I. A. Ward, A. 2022-09-21 doi:10.1101/2022.09.20.508747 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ A genetically encoded tool to increase cellular NADH/NAD+ ratio in living cells ]]> https://biorxiv.org/content/10.1101/2022.09.20.508785v1?rss=1 Heacock, M. L. Abdulaziz, E. N. Pan, X. Zuckerman, A. L. Violante, S. Yao, C. Cross, J. R. Cracan, V. 2022-09-20 doi:10.1101/2022.09.20.508785 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Temporal dynamics of the multi-omic response to endurance exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2022.09.21.508770v1?rss=1 MoTrPAC Study Group, Amar, D. Gay, N. R. Jean Beltran, P. M. Adkins, J. N. Almagro Armenteros, J. J. Ashley, E. Avila-Pacheco, J. Bae, D. Bararpour, N. Burant, C. Clish, C. Cutter, G. Dasari, S. Dennis, C. Evans, C. R. Fernandez, F. M. Gaul, D. Ge, Y. Gerszten, R. Goodyear, L. J. Hou, Z. Ilkayeva, O. Ivanova, A. A. Jimenez-Morales, D. Kachman, M. T. Keshishian, H. Kraus, W. E. Lanza, I. R. Li, J. Lindholm, M. E. Lira, A. C. Many, G. M. Marwaha, S. Miller, M. E. Muehlbauer, M. J. Nair, K. S. Nair, V. D. Natarajan Raja, A. Newgard, C. Ortlund, E. A. Pie 2022-09-23 doi:10.1101/2022.09.21.508770 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Validity of fecal sampling for characterizing temporal variation in threespine stickleback's gut microbiota ]]> https://biorxiv.org/content/10.1101/2022.09.22.509070v1?rss=1 Härer, A. Rennison, D. J. 2022-09-23 doi:10.1101/2022.09.22.509070 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis ]]> https://biorxiv.org/content/10.1101/2022.09.23.509066v1?rss=1 Härer, A. Rennison, D. J. 2022-09-23 doi:10.1101/2022.09.23.509066 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes ]]> https://biorxiv.org/content/10.1101/2022.09.25.509355v1?rss=1 Zhu, H. Wang, G. Nguyen-Ngoc, K.-V. Kim, D. Miller, M. Goss, G. Kovsky, J. Harrington, A. R. Saunders, D. Melton, R. Powers, A. C. Preissl, S. Spagnoli, F. M. Gaulton, K. J. Sander, M. 2022-09-26 doi:10.1101/2022.09.25.509355 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Reprogramming Adeno-Associated Virus Tropism Via Displayed Peptides Tiling Receptor-Ligands ]]> https://biorxiv.org/content/10.1101/2022.09.26.509383v1?rss=1 1 million AAV variants, were screened across 9 tissues in C57BL/6 mice. Tracking variant abundance, we identified >250,000 variants which packaged into capsids, and >15,000 variants which efficiently transduced at least one mouse organ. We individually validated 21 AAV variants with 74.3% of the organ tropism predictions accurately reproducing, confirming overall screen efficacy. Systematic ligand tiling enabled prediction of putative AAV-receptor interactions, which we successfully validated by targeted genetic perturbations. Comprehensive peptide tiling also enabled examination of homologous peptide activity. Interestingly, we observed functional peptides tended to be derived from specific domains on ligands. Notably, certain peptides also displayed consistent activity across mice strains, capsid insertion contexts, and capsid serotypes, including novel immune orthogonal serotypes. Further analyses of displayed peptides revealed that biophysical attributes were highly predictive of AAV variant packaging, and there was a machine learnable relationship between peptide sequence and tissue tropism. We anticipate this comprehensive ligand peptide tiling and display approach will enable engineering of tropism across diverse viral, viral-like, and non-viral delivery platforms, and shed light into basic receptor-ligand biology. ]]> Portell, A. Ford, K. M. Suhardjo, A. Rainaldi, J. Bublik, M. N. Sanghvi, M. Kumar, A. Wing, M. K. Palmer, N. D. Le, D. A. Kalahasti, N. Dailamy, A. Mali, P. 2022-09-26 doi:10.1101/2022.09.26.509383 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Mutational spectra distinguish SARS-CoV-2 replication niches ]]> https://biorxiv.org/content/10.1101/2022.09.27.509649v1?rss=1 T mutations in Omicron, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both upper and lower respiratory tracts (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalisable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while the mutational burden in Alpha varied consistent with changes in transmission source as social restrictions were lifted. This supports the use of mutational spectra to infer niches of established and emergent pathogens. ]]> Ruis, C. Peacock, T. P. Polo, L. M. Masone, D. Soledad Alvarez, M. Hinrichs, A. S. Turakhia, Y. Ye, C. McBroome, J. Corbett-Detig, R. Parkhill, J. Floto, R. A. 2022-09-28 doi:10.1101/2022.09.27.509649 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Simulated green turtle grazing reduces seagrass productivity and alters benthic community structure while triggering further disturbance by feeding stingrays ]]> https://biorxiv.org/content/10.1101/2022.09.27.509764v1?rss=1 Cannon, A. Hynes, M. G. Brandt, M. Wold, C. O'Dea, A. Altieri, A. Smith, J. E. 2022-09-28 doi:10.1101/2022.09.27.509764 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A Multivariate Approach to Understanding the Genetic Overlap between Externalizing Phenotypes and Substance Use Disorders ]]> https://biorxiv.org/content/10.1101/2022.09.27.509777v1?rss=1 .87) and similarly genetically correlated with external criteria, suggesting they did not represent meaningfully distinct dimensions. Results from this study can be used to inform future efforts to characterize genetic liability for broad externalizing as well as specific externalizing phenotypes. ]]> Poore, H. E. Hatoum, A. Mallard, T. T. Sanchez-Roige, S. Waldman, I. D. Palmer, A. A. Harden, K. P. Barr, P. B. Dick, D. M. 2022-09-28 doi:10.1101/2022.09.27.509777 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ kcna1a mutant zebrafish as a model of episodic ataxia type 1 and epilepsy ]]> https://biorxiv.org/content/10.1101/2022.09.28.509973v1?rss=1 Dogra, D. Meza-Santoscoy, P. L. Rehak, R. de la Hoz, C. L. R. Gavrilovici, C. Ibhazehiebo, K. Rho, J. M. Kurrasch, D. M. 2022-09-30 doi:10.1101/2022.09.28.509973 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Semi-supervised machine learning for sensitive open modification spectral library searching ]]> https://biorxiv.org/content/10.1101/2022.09.30.510366v1?rss=1 Arab, I. Fondrie, W. E. Laukens, K. Bittremieux, W. 2022-10-03 doi:10.1101/2022.09.30.510366 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ DELE1 oligomerization promotes integrated stress response activation ]]> https://biorxiv.org/content/10.1101/2022.10.01.510468v1?rss=1 Yang, J. Baron, K. R. Pride, D. E. Schneemann, A. Guo, X. Chen, W. Song, A. S. Aviles, G. Kampmann, M. Wiseman, R. L. Lander, G. C. 2022-10-02 doi:10.1101/2022.10.01.510468 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ The Ketogenic Diet Metabolite β-Hydroxybutyrate Promotes Mitochondrial Elongation via Deacetylation and Improves Autism-like Behavior in Zebrafish ]]> https://biorxiv.org/content/10.1101/2022.10.03.510695v1?rss=1 SHUTT, T. Uddin, G. M. Zaman, M. Kurrasch, D. Rho, J. Lacroix, R. Al Khatib, I. 2022-10-03 doi:10.1101/2022.10.03.510695 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Oscillations and aperiodic activity: Evidence for dynamic changes in both during memory encoding ]]> https://biorxiv.org/content/10.1101/2022.10.04.509632v1?rss=1 Preston, M. Schaworonkow, N. Voytek, B. 2022-10-07 doi:10.1101/2022.10.04.509632 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Chemical Imaging Reveals Diverse Functions of Tricarboxylic Acid Metabolites in Root Growth and Development ]]> https://biorxiv.org/content/10.1101/2022.10.04.510836v1?rss=1 Zhang, T. Noll, S. E. Peng, J. T. Klair, A. Tripka, A. Stutzman, N. Cheng, C. Zare, R. N. Dickinson, A. J. 2022-10-05 doi:10.1101/2022.10.04.510836 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Treatment of pancreatic cancer with irreversible electroporation and intratumoral CD40 antibody stimulates systemic immune responses that inhibit liver metastasis in an orthotopic model. ]]> https://biorxiv.org/content/10.1101/2022.10.04.510847v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1a42713org.highwire.dtl.DTLVardef@16be8org.highwire.dtl.DTLVardef@15362eaorg.highwire.dtl.DTLVardef@182f988_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Narayanan, J. S. S. Hayashi, T. Erdem, S. McArdle, S. Tiriac, H. Ray, P. Pu, M. Mikulski, Z. Miller, A. Messer, K. Carson, D. Schoenberger, S. P. White, R. R. 2022-10-06 doi:10.1101/2022.10.04.510847 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Unified and standardized mass spectrometry data processing in Python using spectrum_utils ]]> https://biorxiv.org/content/10.1101/2022.10.04.510894v1?rss=1 Bittremieux, W. Levitsky, L. I. Pilz, M. Sachsenberg, T. Wang, M. Dorrestein, P. C. 2022-10-07 doi:10.1101/2022.10.04.510894 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Identifying best practices for detecting inter-regional functional connectivity from EEG ]]> https://biorxiv.org/content/10.1101/2022.10.05.510753v1?rss=1 Pellegrini, F. Delorme, A. Nikulin, V. Haufe, S. 2022-10-07 doi:10.1101/2022.10.05.510753 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Genomic Analysis of Two Phlebotomine Sand Fly Vectors of Leishmania from the New and Old World ]]> https://biorxiv.org/content/10.1101/2022.10.05.510924v1?rss=1 McDowell, M. A. Labbe, F. Abdeladhim, M. Abrudan, J. Araki, A. S. Araujo, R. N. Arensburger, P. Beniot, J. B. Brazil, R. P. Bruno, R. V. Bueno da Silva Rivas, G. Carvalho de Abreu, V. Charamis, J. Coutinho-Abreu, I. da Costa-Latge, S. G. Darby, A. Dillon, V. Emrich, S. J. Fernandez-Medina, D. Figueiredo Gontijo, N. Flannley, C. M. Gatherer, D. Genta, F. A. Gesing, S. Giraldo-Calderon, G. I. Gomes, B. Aguiar, E. R. G. R. Hamarsheh, O. Hawksworth, M. Hendershot, J. M. Hickner, P. V. Imler, J.-L. Ioannidis, P. Jennings, E. C. Kamhawi, S. Karageorgiou, C. Kenned 2022-10-05 doi:10.1101/2022.10.05.510924 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Revealing Pentose Catabolism in Pseudomonas putida ]]> https://biorxiv.org/content/10.1101/2022.10.05.510959v1?rss=1 Park, M.-R. Gauttam, R. Fong, B. Chen, Y. Lim, H. G. Feist, A. Mukhopadhyay, A. Petzold, C. J. Simmons, B. A. Singer, S. W. 2022-10-05 doi:10.1101/2022.10.05.510959 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling ]]> https://biorxiv.org/content/10.1101/2022.10.06.511161v1?rss=1 Khalilimeybodi, A. Fraley, S. I. Rangamani, P. 2022-10-07 doi:10.1101/2022.10.06.511161 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ BUB-1 and CENP-C Recruit PLK-1 to Control Chromosome Alignment and Segregation During Meiosis I in C. elegans Oocytes ]]> https://biorxiv.org/content/10.1101/2022.10.07.511262v1?rss=1 Taylor, S. J. P. Bel Borja, L. Soubigou, F. Cheerambathur, D. K. Pelisch, F. 2022-10-07 doi:10.1101/2022.10.07.511262 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Circadian modulation by time-restricted feeding restores brain transcription and slows amyloid deposition in a mouse model of Alzheimer's disease. ]]> https://biorxiv.org/content/10.1101/2022.10.07.511346v1?rss=1 Whittaker, D. S. Akhmetova, L. Romero, H. Welsh, D. K. Colwell, C. S. Desplats, P. 2022-10-07 doi:10.1101/2022.10.07.511346 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Corticosteroid Activation of Atlantic Sea Lamprey Corticoid Receptor: Allosteric Regulation by the N-terminal Domain ]]> https://biorxiv.org/content/10.1101/2022.10.08.511437v1?rss=1 Katsu, Y. Lin, X. Ji, R. Chen, Z. Kamisaka, Y. Bamba, K. Baker, M. E. 2022-10-08 doi:10.1101/2022.10.08.511437 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites ]]> https://biorxiv.org/content/10.1101/2022.10.08.511447v1?rss=1 10 times more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable analysis of CLIP-seq data. ]]> Boyle, E. A. Her, H.-L. Mueller, J. R. Nguyen, G. G. Yeo, G. W. 2022-10-08 doi:10.1101/2022.10.08.511447 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Multiple-trait subsampling for optimized ancestral trait reconstruction ]]> https://biorxiv.org/content/10.1101/2022.10.11.511762v1?rss=1 Li, X. Trovao, N. S. Wertheim, J. O. Baele, G. de Bernardi Schneider, A. 2022-10-14 doi:10.1101/2022.10.11.511762 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A Bayesian Approach to Hyperbolic Multi-Dimensional Scaling ]]> https://biorxiv.org/content/10.1101/2022.10.12.511940v1?rss=1 Praturu, A. Sharpee, T. O. 2022-10-16 doi:10.1101/2022.10.12.511940 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Integrated Molecular Characterization of Intraductal Papillary Mucinous Neoplasms: An NCI Cancer Moonshot Precancer Atlas Pilot Project ]]> https://biorxiv.org/content/10.1101/2022.10.14.512148v1?rss=1 Semaan, A. Bernard, V. Wong, J. Makino, Y. Swartzlander, D. Rajapakshe, K. I. Lee, J. Officer, A. Schmidt, C. M. Wu, H. H. Scaife, C. L. Affolter, K. E. Nachmanson, D. Firpo, M. A. Yip-Schneider, M. Lowy, A. M. Harismendy, O. Sen, S. Maitra, A. A. Jakubek, Y. A. Guerrero, P. A. 2022-10-18 doi:10.1101/2022.10.14.512148 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Microscopic Imaging of Epigenetic Age ]]> https://biorxiv.org/content/10.1101/2022.10.16.512441v1?rss=1 Rodriguez, D. Fiengo, L. Alvarez-Kuglen, M. Qin, H. Farhy, C. Havas, A. Anderson, R. M. Adams, P. D. Sharpee, T. O. Terskikh, A. 2022-10-20 doi:10.1101/2022.10.16.512441 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ Metabolic homeostasis and growth in abiotic cells ]]> https://biorxiv.org/content/10.1101/2022.10.16.512448v1?rss=1 Akbari, A. Palsson, B. 2022-10-19 doi:10.1101/2022.10.16.512448 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ A tissue injury repair pathway distinct but parallel to host pathogen defense ]]> https://biorxiv.org/content/10.1101/2022.10.18.509515v1?rss=1 Liu, S. Hur, Y. H. Cai, X. Cong, Q. Yang, Y. Xu, C. Bilate, A. M. Gonzales, K. A. U. Cowley, C. J. Hurwitz, B. Luo, J.-D. Tseng, T. Gur-Cohen, S. Sribour, M. Omelchenko, T. Levorse, J. Pasolli, H. A. Thompson, C. B. Mucida, D. Fuchs, E. 2022-10-19 doi:10.1101/2022.10.18.509515 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ The epigenetic modifier DOT1L regulates gene regulatory networks necessary for cardiac patterning and cardiomyocyte cell cycle withdrawal ]]> https://biorxiv.org/content/10.1101/2022.10.18.512679v1?rss=1 Cattaneo, P. Hayes, M. G. Baumgarten, N. Hecker, D. Peruzzo, S. Kunderfranco, P. Larcher, V. Zhang, L. Contu, R. Fonseca, G. Spinozzi, S. Chen, J. Condorelli, G. Schulz, M. H. Guimaraes-Camboa, N. Evans, S. M. 2022-10-19 doi:10.1101/2022.10.18.512679 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Multimodal mapping of cell types and projections in the central nucleus of the amygdala ]]> https://biorxiv.org/content/10.1101/2022.10.19.512845v1?rss=1 Wang, Y. Krabbe, S. Eddison, M. Henry, F. Fleishman, G. Lemire, A. L. Wang, L. Korff, W. Tillberg, P. Lüthi, A. Sternson, S. 2022-10-22 doi:10.1101/2022.10.19.512845 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions ]]> https://biorxiv.org/content/10.1101/2022.10.22.513080v1?rss=1 Mori, M. Cheng, C. Taylor, B. R. Okano, H. Hwa, T. 2022-10-24 doi:10.1101/2022.10.22.513080 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Systematic loss of function screens identify pathway specific functional circular RNAs ]]> https://biorxiv.org/content/10.1101/2022.10.22.513321v1?rss=1 Liu, L. Neve, M. Perlaza-Jimenez, L. Hawdon, A. Conn, S. Zenker, J. Tamayo, P. Goodall, G. Rosenbluh, J. 2022-10-22 doi:10.1101/2022.10.22.513321 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Cortico-Striatal Beta-Oscillations as a Marker of Learned Reward Value ]]> https://biorxiv.org/content/10.1101/2022.10.24.513264v1?rss=1 Koloski, M. F. Hulyalkar, S. Tang, T. Wu, X. Fakhraei, L. Mishra, J. Ramanathan, D. S. 2022-10-25 doi:10.1101/2022.10.24.513264 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Maximal interferon induction by influenza lacking NS1 is infrequent owing to requirements for replication and export ]]> https://biorxiv.org/content/10.1101/2022.10.24.513459v1?rss=1 99% of cells in tissue-culture models of infection. Notably, the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1. What explains the observed rarity of interferon production in spite of the frequent loss of this, critical, antagonist? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral life cycle to prevent the triggering of an innate immune response. In doing so, we find that NS1 prevents the detection of de novo innate immune ligands, defective viral genomes, and viral export from the nucleus, although only generation of de novo ligands appears absolutely required for enhanced detection of virus in the absence of NS1. Due to this, the highest frequency of interferon production we observe (97% of infected cells) requires a high level of replication in the presence of defective viral genomes with NS1 bearing an inactivating mutation that does not impact its partner encoded on the same segment, NEP. This is incredibly unlikely to occur given the standard variation found within a viral population, and would generally require direct, artificial, intervention to achieve at an appreciable rate. Thus from our study, we procure at least a partial explanation for the seeming contradiction between high rates of replicative failure and the rarity of the interferon response to influenza infection. Author summaryThe production of interferons in response to viral threat is a potent barrier to successful infection. Viruses like influenza A virus encode potent interferon antagonists, suppressing detection of viral replication such that only an incredibly small number of cells successfully produce interferons. Strikingly, even in the absence of its major interferon antagonist, NS1, influenza still only induces an interferon response in a minority of infected cells. Using a combination of single-cell RNAseq, flow cytometry, and classical bulk methods, we explored how heterogeneity, both genetic and phenotypic, in a virus lacking NS1, explains the observed rarity of the interferon response. In doing so, we find that, in the absence of NS1, viral replication is absolutely required to induce an interferon response, and that both active export and the presence of defective viral genomes can greatly enhance, but are not strictly required, for the detection of this virus. The confluence of events which we find maximizes the host response is incredibly unlikely to occur alongside the absence of the NS1 protein via the most common forms of genetic variation in the viral population, perhaps explaining, in part, how a virus with such a high error rate nevertheless has such a high rate of success at evading cell intrinsic innate immunity. ]]> Vicary, A. C. Lekbua, A. Reddan, J. Rodriguez, Z. K. Mendes, M. Russell, A. B. 2022-10-24 doi:10.1101/2022.10.24.513459 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange ]]> https://biorxiv.org/content/10.1101/2022.10.24.513552v1?rss=1 Pillich, R. T. Chen, J. Churas, C. Fong, D. Gyori, B. M. Ideker, T. Karis, K. Liu, S. N. Ono, K. Pico, A. Pratt, D. 2022-10-25 doi:10.1101/2022.10.24.513552 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Extreme genome diversity and cryptic speciation in a harmful algal bloom forming eukaryote ]]> https://biorxiv.org/content/10.1101/2022.10.25.513657v1?rss=1 Wisecaver, J. H. Auber, R. P. Pendleton, A. L. Watervoort, N. F. Fallon, T. R. Riedling, O. L. Moore, B. S. Driscoll, W. W. 2022-10-26 doi:10.1101/2022.10.25.513657 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ A Clade-D Auxin Response Factor is a Major Regulator of Auxin Signaling in Physcomitrium patens. ]]> https://biorxiv.org/content/10.1101/2022.10.25.513742v1?rss=1 Bascom, C. S. Prigge, M. J. Szutu, W. Bantle, A. Irmak, S. Tu, D. Estelle, M. 2022-10-27 doi:10.1101/2022.10.25.513742 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A mind-body interface alternates with effector-specific regions in motor cortex ]]> https://biorxiv.org/content/10.1101/2022.10.26.513940v1?rss=1 Gordon, E. M. Chauvin, R. J. Van, A. N. Rajesh, A. Nielsen, A. Newbold, D. J. Lynch, C. J. Seider, N. A. Krimmel, S. R. Scheidter, K. M. Monk, J. Miller, R. L. Metoki, A. Montez, D. F. Zheng, A. Elbau, I. Madison, T. Nishino, T. Myers, M. J. Kaplan, S. D'Andrea, C. B. Demeter, D. V. Feigelis, M. Barch, D. M. Smyser, C. D. Rogers, C. E. Zimmerman, J. Botteron, K. N. Pruett, J. R. Willie, J. T. Brunner, P. Shimony, J. S. Kay, B. P. Marek, S. Norris, S. A. Gratton, C. Sylvester, C. M. Power, J. D. Liston, C. Greene, D. J. Roland, J. L. Petersen, S. E. Rai 2022-10-28 doi:10.1101/2022.10.26.513940 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Engineered vasculature induces functional maturation of pluripotent stem cell-derived islet organoids ]]> https://biorxiv.org/content/10.1101/2022.10.28.513298v1?rss=1 Nguyen Ngoc, K. V. Sai, S. Jun, Y. Bender, R. H. F. Kravets, V. Zhu, H. Hatch, C. J. Schlichting, M. Gaetani, R. Mallick, M. Hachey, S. J. Christman, K. George, S. C. Hughes, C. C. Sander, M. 2022-10-30 doi:10.1101/2022.10.28.513298 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Mice lacking Ptprd exhibit deficits in goal-directed behavior and female-specific impairments in sensorimotor gating ]]> https://biorxiv.org/content/10.1101/2022.10.28.514214v1?rss=1 Ho, E. Welch, A. Knowles, J. Dulawa, S. C. 2022-10-28 doi:10.1101/2022.10.28.514214 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors ]]> https://biorxiv.org/content/10.1101/2022.10.28.514263v1?rss=1 Mills, F. Lee, C. R. Howe, J. R. Li, H. Shao, S. Keisler, M. N. Lemieux, M. E. Taschbach, F. H. Keyes, L. R. Borio, M. R. Chen, H. S. Patel, R. R. Gross, A. L. Delahanty, J. Cazares, C. Maree, L. Wichmann, R. Pereira, T. D. Benna, M. K. Root, C. M. Tye, K. M. 2022-10-29 doi:10.1101/2022.10.28.514263 Cold Spring Harbor Laboratory Press 2022-10-29 <![CDATA[ Glutamine mimicry suppresses tumor progression through asparagine metabolism in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.10.31.514261v1?rss=1 Recouvreux, M. V. Galapate, C. M. Grenier, S. Esparza, E. Zhang, Y. Maganti, S. Naeem, R. Scott, D. A. Lowy, A. M. Tiriac, H. Commisso, C. 2022-11-01 doi:10.1101/2022.10.31.514261 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Cholinergic modulation supports DMN suppression during resting state ]]> https://biorxiv.org/content/10.1101/2022.11.01.514686v1?rss=1 Sanda, P. Hlinka, J. van den Berg, M. Bazhenov, M. Keliris, G. A. Krishnan, G. 2022-11-01 doi:10.1101/2022.11.01.514686 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Fine-scale variability in coral bleaching and mortality during a marine heatwave ]]> https://biorxiv.org/content/10.1101/2022.11.01.514760v1?rss=1 Yadav, S. Roach, T. McWilliam, M. J. Caruso, C. Rocha de Souza, M. Foley, C. Allen, C. Dilworth, J. Huckeba, J. Santoro, E. P. Wold, R. Simpson, J. Miller, S. Hancock, J. R. Drury, C. Madin, J. S. 2022-11-04 doi:10.1101/2022.11.01.514760 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck. ]]> https://biorxiv.org/content/10.1101/2022.11.04.515098v1?rss=1 Nigam, N. Bernard, B. Kim, S. Burkitt, K. Tsai, D. Robbins, Y. Sievers, C. Allen, C. T. Bennett, R. L. Tettey, T. T. Carter, B. Bao, R. Rinaldi, L. Lingen, M. W. Sater, H. Edmondson, E. F. Cheng, H. Luo, X. Brennan, K. Chen, C. Sevilla, S. Murali, M. Sakata, S. Takeuchi, K. Nakamura, Y. Uppaluri, R. Sunwoo, J. B. Van Waes, C. Licht, J. D. Hager, G. L. Saloura, V. 2022-11-04 doi:10.1101/2022.11.04.515098 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Flexible, Scalable, High Channel Count Stereo-Electrode for Recording in the Human Brain ]]> https://biorxiv.org/content/10.1101/2022.11.08.515705v1?rss=1 Lee, K. Paulk, A. C. Ro, Y. G. Cleary, D. R. Tonsfeldt, K. J. Kfir, Y. Pezaris, J. Tchoe, Y. Lee, J. Bourhis, A. M. Vatsyayan, R. Russman, S. M. Yang, J. C. Baohan, A. Richardson, M. Williams, Z. M. Fried, S. Raslan, A. Halgren, E. Cash, S. S. Dayeh, S. A. 2022-11-09 doi:10.1101/2022.11.08.515705 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Environmental luminance impairs socio-sexual recognition memory through a succinct retina to supraoptic nucleus circuit ]]> https://biorxiv.org/content/10.1101/2022.11.08.515735v1?rss=1 Huang, Y.-F. Liao, P.-Y. Yu, J.-H. Chen, S.-K. 2022-11-09 doi:10.1101/2022.11.08.515735 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Inflammation-Responsive Micellar Nanoparticles from Degradable Polyphosphoramidates for Targeted Delivery to Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2022.11.11.516224v1?rss=1 84%). Efficient MePTDO copolymerizations with norbornene-based monomers are demonstrated, including a norbornenyl monomer functionalized with a peptide substrate for inflammation-associated matrix metalloproteinases (MMPs). The resulting amphiphilic peptide brush copolymers self-assembled in aqueous solution to generate micellar nanoparticles (30 nm in diameter) which exhibit excellent cyto- and hemocompatibility and undergo MMP-induced assembly into micron scale aggregates. As MMPs are upregulated in the heart post-myocardial infarction (MI), the MMP-responsive micelles were applied to target and accumulate in the infarcted heart following intravenous administration in a rat model of MI. These particles displayed a distinct biodistribution and clearance pattern in comparison to non-degradable analogues. Specifically, accumulation at the site of MI, competed with elimination predominantly through the kidney rather than the liver. Together, these results suggest this as a promising new biodegradable platform for inflammation targeted delivery. ]]> Liang, Y. Sullivan, H. Carrow, K. Korpanty, J. Worthington, K. Luo, C. Christman, K. L. Gianneschi, N. C. 2022-11-11 doi:10.1101/2022.11.11.516224 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma-derived metabolite cues ]]> https://biorxiv.org/content/10.1101/2022.11.12.516288v1?rss=1 Kyle, K. E. Puckett, S. P. Caraballo Rodriguez, A. M. Rivera Chavez, J. Samples, R. M. Earp, C. E. Raja, H. A. Pearce, C. J. Ernst, M. van der Hooft, J. J. J. Adams, M. E. Oberlies, N. H. Dorrestein, P. C. Klassen, J. L. Balunas, M. J. 2022-11-13 doi:10.1101/2022.11.12.516288 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ The Src and Abl family kinases activate the Spleen Tyrosine Kinase to maximize phagocytosis and Leishmania infection ]]> https://biorxiv.org/content/10.1101/2022.11.14.513575v1?rss=1 Ullah, I. Barrie, U. Kernen, R. M. Mamula, E. T. Datta, A. Booshehri, L. M. Rhodes, E. L. Bradford, J. M. Wetzel, D. M. 2022-11-16 doi:10.1101/2022.11.14.513575 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Control of cell proliferation by memories of mitosis ]]> https://biorxiv.org/content/10.1101/2022.11.14.515741v1?rss=1 Meitinger, F. Davis, R. L. Martinez, M. B. Shiau, A. K. Oegema, K. Desai, A. 2022-11-16 doi:10.1101/2022.11.14.515741 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Diversified repertoire of phage defenses in Klebsiella pneumoniae: Bi-directional steering effects impacting antibiotic susceptibility ]]> https://biorxiv.org/content/10.1101/2022.11.14.516531v1?rss=1 Nang, S. C. Lu, J. Yu, H. Wickremasinghe, H. Azad, M. A. K. Han, M. Zhao, J. Rao, G. Bergen, P. J. Velkov, T. Sherry, N. McCarthy, D. T. Aslam, S. Schooley, R. T. Howden, B. P. Barr, J. J. Zhu, Y. Li, J. 2022-11-15 doi:10.1101/2022.11.14.516531 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ A dynamic epibiont community associated with the bone eating worm Osedax ]]> https://biorxiv.org/content/10.1101/2022.11.14.516544v1?rss=1 140 months) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests a transition from heterotrophy to autotrophy along the successional gradient, and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free living relatives, the Osedax epibionts were highly enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms ]]> Goffredi, S. Panossian, B. Brzechffa, C. Field, N. King, C. Moggioli, G. Rouse, G. W. Martin-Duran, J. M. Henry, L. 2022-11-16 doi:10.1101/2022.11.14.516544 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions ]]> https://biorxiv.org/content/10.1101/2022.11.16.515599v1?rss=1 Cornish, A. Gruber, A. Kinnersley, B. Chubb, D. Frangou, A. Caravagna, G. Noyvert, B. Lakatos, E. Wood, H. Arnedo-Pac, C. Culliford, R. Househam, J. Cross, W. Sud, A. Law, P. Ni Leathlobhair, M. Hawari, A. Thorn, S. Sherwood, K. Gul, G. Fernandez-Tajes, J. Zapata, L. Alexandrov, L. Murugaesu, N. Sosinsky, A. Mitchell, J. Lopez-Bigas, N. Quirke, P. Church, D. Tomlinson, I. Sottoriva, A. Graham, T. Wedge, D. Houlston, R. 2022-11-16 doi:10.1101/2022.11.16.515599 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ BDNF and TRiC-inspired Reagents Rescue Cortical Synaptic Deficits in a Mouse Model of Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2022.11.25.517123v1?rss=1 Gu, Y. Pope, A. Smith-Geater, C. Carmona, C. Johnstone, A. Shi, L. Chen, X. Santos, S. Bacon-Brenes, C. C. Shoff, T. Kleczko, K. M. Frydman, J. Thompson, L. M. Mobley, W. C. Wu, C. 2022-11-25 doi:10.1101/2022.11.25.517123 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Tissue- and sex-specific DNA damage tracks aging in rodents and humans ]]> https://biorxiv.org/content/10.1101/2022.11.28.518087v1?rss=1 Guilbaud, A. Ghanegolmohammadi, F. Wang, Y. Leng, J. Kreymerman, A. Gamboa Varela, J. Garbern, J. Elwell, H. Cao, F. Ricci-Blair, E. M. Liang, C. Balamkundu, S. Vidoudez, C. DeMott, M. S. Bedi, K. Margulies, K. B. Bennett, D. A. Palmer, A. A. Barkley-Levenson, A. Lee, R. T. Dedon, P. C. 2022-11-29 doi:10.1101/2022.11.28.518087 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ A general method for the development of multicolor biosensors with large dynamic ranges ]]> https://biorxiv.org/content/10.1101/2022.11.29.518186v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@9ae8b9org.highwire.dtl.DTLVardef@250477org.highwire.dtl.DTLVardef@482d03org.highwire.dtl.DTLVardef@833397_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hellweg, L. Edenhofer, A. Barck, L. Huppertz, M.-C. Frei, M. S. Tarnawski, M. Bergner, A. Koch, B. Johnsson, K. Hiblot, J. 2022-11-29 doi:10.1101/2022.11.29.518186 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures ]]> https://biorxiv.org/content/10.1101/2022.11.30.518285v1?rss=1 Tian, W. Zhou, J. Bartlett, A. Zeng, Q. Liu, H. Castanon, R. G. Kenworthy, M. Altshul, J. Valadon, C. Aldridge, A. Nery, J. R. Chen, H. Xu, J. Johnson, N. D. Lucero, J. Osteen, J. K. Emerson, N. Rink, J. Lee, J. Li, Y. Siletti, K. Liem, M. Claffey, N. OConnor, C. Yanny, A. M. Nyhus, J. Dee, N. Casper, T. Shapovalova, N. Hirschstein, D. Hodge, R. Levi, B. P. Keene, C. D. Linnarsson, S. Lein, E. Ren, B. Behrens, M. M. Ecker, J. R. 2022-12-01 doi:10.1101/2022.11.30.518285 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Hexokinase 2 localizes to the nucleus in response to glucose limitation but does not regulate gene expression ]]> https://biorxiv.org/content/10.1101/2022.11.30.518474v1?rss=1 Lesko, M. A. Chandrashekarappa, D. G. Jordahl, E. M. Oppenheimer, K. G. Bowman, R. W. Shang, C. Durrant, J. Schmidt, M. C. O'Donnell, A. F. 2022-12-05 doi:10.1101/2022.11.30.518474 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data ]]> https://biorxiv.org/content/10.1101/2022.12.04.519052v1?rss=1 Gopalakrishnan, S. Joshi, C. J. Valderrama Gomez, M. Icten, E. Rolandi, P. Johnson, W. Kontoravdi, C. Lewis, N. E. 2022-12-07 doi:10.1101/2022.12.04.519052 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Aβ-CT affective touch: Touch pleasantness ratings for gentle stroking and deep pressure exhibit dependence on A-fibers ]]> https://biorxiv.org/content/10.1101/2022.12.06.518627v1?rss=1 Case, L. Madian, N. McCall, M. Bradson, M. Liljencrantz, J. Goldstein, B. Alasha, V. Zimmerman, M. 2022-12-06 doi:10.1101/2022.12.06.518627 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ SpLitteR: Diploid genome assembly using linked TELL-Seq reads and assembly graphs ]]> https://biorxiv.org/content/10.1101/2022.12.08.519233v1?rss=1 Tolstoganov, I. Pevzner, P. A. Korobeynikov, A. 2022-12-12 doi:10.1101/2022.12.08.519233 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Context-dependent functions of mitochondria protein quality control in lung ]]> https://biorxiv.org/content/10.1101/2022.12.08.519642v1?rss=1 Xu, L. Tan, C. Barr, J. Talaba, N. McCulley, D. Shen, Y. Chung, W. K. Sun, X. 2022-12-10 doi:10.1101/2022.12.08.519642 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Regulation of Nuclear Transcription by Mitochondrial RNA ]]> https://biorxiv.org/content/10.1101/2022.12.10.519922v1?rss=1 Sriram, K. Qi, Z. Yuan, D. Malhi, N. K. Liu, X. Calandrelli, R. Luo, Y. Jin, S. Shi, J. Salas, M. Dang, R. Armstrong, B. Priceman, S. J. Wang, P. Liao, J. Natarajan, R. Zhong, S. Chen, Z. B. 2022-12-11 doi:10.1101/2022.12.10.519922 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Focused ultrasound-mediated brain genome editing ]]> https://biorxiv.org/content/10.1101/2022.12.10.519924v1?rss=1 Lao, Y.-H. Ji, R. Zhou, J. K. Snow, K. J. Kwon, N. Saville, E. He, S. Chauhan, S. Chi, C.-W. Datta, M. S. Zhang, H. Quek, C. H. Cai, S. Li, M. Gaitan, Y. Bechtel, L. Wu, S.-Y. Lutz, C. M. Tomer, R. Murray, S. A. Chavez, A. Konofagou, E. E. Leong, K. W. 2022-12-11 doi:10.1101/2022.12.10.519924 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Bulk and Mosaic Deletions of Egfr Reveal Regionally Defined Gliogenesis in the Developing Mouse Forebrain ]]> https://biorxiv.org/content/10.1101/2022.12.10.519926v1?rss=1 Zhang, X. Xiao, G. Johnson, C. A. Cai, Y. Horowitz, Z. Mennicke, C. Coffey, R. Haider, M. Threadgill, D. W. Eliscu, R. Oldham, M. C. Greenbaum, A. C. Ghashghaei, H. T. 2022-12-11 doi:10.1101/2022.12.10.519926 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Stathmin-2 loss leads to neurofilament-dependent axonal collapse driving motor and sensory denervation ]]> https://biorxiv.org/content/10.1101/2022.12.11.519794v1?rss=1 Lopez-Erauskin, J. Bravo-Hernandez, M. Presa, M. Baughn, M. W. Melamed, Z. Beccari, M. S. Agra de Almeida Quadros, A. R. Zuberi, A. Ling, K. Platoshyn, O. Nino-Jara, E. Ndayambaje, I. S. Arnold-Garcia, O. McAlonis-Downes, M. Cabrera, L. Artates, J. W. Ryan, J. Bennett, F. Jafar-nejad, P. Rigo, F. Marsala, M. Lutz, C. M. Cleveland, D. W. Lagier-Tourenne, C. 2022-12-12 doi:10.1101/2022.12.11.519794 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea ]]> https://biorxiv.org/content/10.1101/2022.12.11.519962v1?rss=1 Mongiardino Koch, N. Tilic, E. Miller, A. K. Stiller, J. Rouse, G. W. 2022-12-13 doi:10.1101/2022.12.11.519962 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ High Density Domain-Focused CRISPR Screens Reveal Epigenetic Regulators of HOX/MEIS Gene Expression in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2022.12.12.519332v1?rss=1 Barbosa, K. Deshpande, A. Perales, M. E. Xiang, P. Murad, R. Minkina, A. Robertson, N. A. Schischlik, F. Lei, X. Sun, Y. Brown, A. Doench, J. G. Humphries, K. Ruppin, E. Shendure, J. Mali, P. Adams, P. D. Deshpande, A. J. 2022-12-13 doi:10.1101/2022.12.12.519332 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. C 2022-12-13 doi:10.1101/2022.12.12.519838 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Proteomic discovery of chemical probes that perturb protein complexes in human cells ]]> https://biorxiv.org/content/10.1101/2022.12.12.520090v1?rss=1 Lazear, M. Remsberg, J. Jaeger, M. Rothamel, K. Her, H.-l. DeMeester, K. Njomen, E. Hogg, S. Rahman, J. Whitby, L. Won, S. J. Schafroth, M. Ogasawara, D. Yokoyama, M. Lindsey, G. Li, H. Germain, J. Barbas, S. Vaughan, J. Hanigan, T. Vartabedian, V. Reinhardt, C. Dix, M. Koo, S. J. Heo, I. Teijaro, J. Simon, G. Ghosh, B. Abdel-Wahab, O. Ahn, K. Saghatelian, A. Melillo, B. Schreiber, S. Yeo, G. Cravatt, B. 2022-12-13 doi:10.1101/2022.12.12.520090 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Neurodegeneration Risk Factor, EIF2AK3 (PERK), Influences Tau Protein Aggregation ]]> https://biorxiv.org/content/10.1101/2022.12.14.520487v1?rss=1 Park, G. Xu, K. Chea, L. Kim, K. Safarta, L. Song, K.-H. Wu, J. Park, S. Min, H. Hiramatsu, N. Han, J. Lin, J. H. 2022-12-15 doi:10.1101/2022.12.14.520487 Cold Spring Harbor Laboratory Press 2022-12-15 <![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[ Longitudinal development of category representations in ventral temporal cortex predicts word and face recognition ]]> https://biorxiv.org/content/10.1101/2022.12.23.521732v1?rss=1 Nordt, M. Gomez, J. Natu, V. S. Rezai, A. A. Finzi, D. Kular, H. Grill-Spector, K. 2022-12-23 doi:10.1101/2022.12.23.521732 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence ]]> https://biorxiv.org/content/10.1101/2022.12.23.521837v1?rss=1 Jin, W. Brannan, K. W. Kapeli, K. Park, S. S. Tan, H. Q. Gosztyla, M. L. Mujumdar, M. Ahdout, J. Henroid, B. Rothamel, K. Xiang, J. S. Wong, L. Yeo, G. W. 2022-12-23 doi:10.1101/2022.12.23.521837 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ A change in behavioral state switches the pattern of motor output that underlies rhythmic head and orofacial movements ]]> https://biorxiv.org/content/10.1101/2022.12.29.522264v1?rss=1 Kleinfeld, D. Liao, S.-M. 2022-12-30 doi:10.1101/2022.12.29.522264 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Integration of single-cell multiomic measurements across disease states with genetics identifies mechanisms of beta cell dysfunction in type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2022.12.31.522386v1?rss=1 Wang, G. Chiou, J. Zeng, C. Miller, M. Matta, I. Han, J. Y. Kadakia, N. Okino, M.-L. Beebe, E. Mallick, M. Camunas-Soler, J. dos Santos, T. Dai, X.-Q. Ellis, C. Hang, Y. Kim, S. K. Macdonald, P. E. Kandeel, F. R. Preiss, S. Gaulton, K. Sander, M. 2023-01-02 doi:10.1101/2022.12.31.522386 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cortex ]]> https://biorxiv.org/content/10.1101/2023.01.02.522381v1?rss=1 Ghisleni, A. Bonilla-Quintana, M. Crestani, M. Fukuzawa, A. Rangamani, P. Gauthier, N. 2023-01-02 doi:10.1101/2023.01.02.522381 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Multiomics atlas-assisted discovery of transcription factors enables specific cell state programming. ]]> https://biorxiv.org/content/10.1101/2023.01.03.522354v1?rss=1 Chung, H. K. Liu, C. Casillas, E. Mcdonald, B. Wang, J. Sun, M. Ma, S. Chen, D. Chick, B. Yang, Q. Hoffmann, F. Varanasi, S. K. Tripple, V. Cho, U. H. Ho, J. Hang, Y. Williams, A. Hargreaves, D. Kaech, S. M. Wang, W. 2023-01-03 doi:10.1101/2023.01.03.522354 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Sequence-to-sequence translation from mass spectra to peptides with a transformer model ]]> https://biorxiv.org/content/10.1101/2023.01.03.522621v1?rss=1 Fondrie, W. E. Yilmaz, M. Bittremieux, W. Nelson, R. Ananth, V. Oh, S. Noble, W. S. 2023-01-03 doi:10.1101/2023.01.03.522621 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2023.01.04.522696v1?rss=1 Dubey, S. M. Han, S. Stutzman, N. Prigge, M. J. Medvecka, E. Platre, M. P. Busch, W. Fendrych, M. Estelle, M. 2023-01-04 doi:10.1101/2023.01.04.522696 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ UFMTrack: Under-Flow Migration Tracker enabling analysis of the entire multi-step immune cell extravasation cascade across the blood-brain barrier in microfluidic devices ]]> https://biorxiv.org/content/10.1101/2023.01.04.522827v1?rss=1 Vladymyrov, M. Marchetti, L. Aydin, S. Soldati, S. G. N. Mossu, A. Pal, A. Gueissaz, L. Ariga, A. Engelhardt, B. 2023-01-06 doi:10.1101/2023.01.04.522827 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Thermodynamic limitations on brain oxygen metabolism: physiological implications ]]> https://biorxiv.org/content/10.1101/2023.01.06.522942v1?rss=1 Buxton, R. B. 2023-01-06 doi:10.1101/2023.01.06.522942 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Chemical inhibition of bromodomain proteins in insect stage African trypanosomes perturbs silencing of the Variant Surface Glycoprotein repertoire and results in widespread changes in the transcriptome ]]> https://biorxiv.org/content/10.1101/2023.01.09.523188v1?rss=1 Ashby, E. C. Havens, J. L. Hardin, J. Schulz, D. 2023-01-09 doi:10.1101/2023.01.09.523188 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity ]]> https://biorxiv.org/content/10.1101/2023.01.11.523512v1?rss=1 Yu, S. B. Sanchez, R. G. Papich, Z. D. Whisenant, T. C. Ghassemian, M. Koberstein, J. N. Stewart, M. L. Pekkurnaz, G. 2023-01-11 doi:10.1101/2023.01.11.523512 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates ]]> https://biorxiv.org/content/10.1101/2023.01.12.523844v1?rss=1 Chen, X. Wolfe, D. A. Sivadasan Bindu, D. Zhang, M. Taskin, N. Goertsen, D. Shay, T. F. Sullivan, E. Ravindra Kumar, S. Huang, S.-F. Arokiaraj, C. M. Plattner, V. Campos, L. J. Mich, J. K. Monet, D. Ngo, V. Ding, X. Omstead, V. Weed, N. Bishaw, Y. Gore, B. B. Lein, E. S. Akrami, A. Miller, C. Levi, B. P. Keller, A. Ting, J. T. Fox, A. S. Eroglu, C. Gradinaru, V. 2023-01-13 doi:10.1101/2023.01.12.523844 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ White matter network organization predicts memory decline after epilepsy surgery ]]> https://biorxiv.org/content/10.1101/2023.01.14.524071v1?rss=1 Stasenko, A. Kaestner, E. Arienzo, D. Schadler, A. Helm, J. L. Shih, J. Ben-Haim, S. McDonald, C. R. 2023-01-17 doi:10.1101/2023.01.14.524071 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Tipifarnib potentiates the antitumor effects of PI3Kα inhibition in PIK3CA- and HRAS-dysregulated HNSCC via convergent inhibition of mTOR activity ]]> https://biorxiv.org/content/10.1101/2023.01.17.523964v1?rss=1 45% of R/M HNSCC patients. By blocking feedback reactivation of mTORC1, tipifarnib may prevent adaptive resistance to additional targeted therapies, thereby enhancing their clinical utility. ]]> Smith, A. E. Chan, S. Wang, Z. McCloskey, A. Reilly, Q. Wang, J. Z. Patel, H. V. Koshizuka, K. Soifer, H. S. Kessler, L. Dayoub, A. Villaflor, V. Adkins, D. Bruce, J. Y. Ho, A. Perez, C. A. Hanna, G. J. Gasco Hernandez, A. Saunders, A. Dale, S. Gutkind, J. S. Burrows, F. Malik, S. 2023-01-20 doi:10.1101/2023.01.17.523964 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Increased TCR signaling in regulatory T cells is disengaged from TCR affinity ]]> https://biorxiv.org/content/10.1101/2023.01.17.523999v1?rss=1 Jing, Y. Kong, Y. Allard, D. Liu, B. Kolawole, E. Sprouse, M. Evavold, B. Bettini, M. Bettini, M. 2023-01-21 doi:10.1101/2023.01.17.523999 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Tiered Sympathetic Control of Cardiac Function Revealed by Viral Tracing and Single Cell Transcriptome Profiling ]]> https://biorxiv.org/content/10.1101/2023.01.18.524575v1?rss=1 Sharma, S. Littman, R. Tompkins, J. Arneson, D. Contreras, J. Dajani, A.-H. Ang, K. Tsanhani, A. Sun, X. Jay, P. Y. Herzog, H. Yang, X. Ajijola, O. A. 2023-01-19 doi:10.1101/2023.01.18.524575 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Acoustically Targeted Noninvasive Gene Therapy in Large Brain Regions ]]> https://biorxiv.org/content/10.1101/2023.01.19.524626v1?rss=1 Nouraein, S. Saenz, V. A. Del Mundo, H. C. Yiu, J. Szablowski, J. O. 2023-01-20 doi:10.1101/2023.01.19.524626 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Woronin bodies move dynamically and bidirectionally by hitchhiking on early endosomes in Aspergillus nidulans ]]> https://biorxiv.org/content/10.1101/2023.01.20.524968v1?rss=1 Songster, L. D. Bhuyan, D. Christensen, J. R. Reck-Peterson, S. L. 2023-01-21 doi:10.1101/2023.01.20.524968 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Sex, but not early life stress, effects on two-bottle choice alcohol drinking behaviors in mice ]]> https://biorxiv.org/content/10.1101/2023.01.21.524642v1?rss=1 Perry, T. W. Sneddon, E. A. Reichert, A. N. Schuh, K. M. Shand, N. A. Quinn, J. J. Radke, A. K. 2023-01-22 doi:10.1101/2023.01.21.524642 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome ]]> https://biorxiv.org/content/10.1101/2023.01.24.525211v1?rss=1 Johnson, K. E. Heisel, T. Allert, M. Furst, A. Yerabandi, N. Knights, D. Jacobs, K. M. Lock, E. F. Bode, L. Fields, D. A. Rudolph, M. C. Gale, C. A. Albert, F. W. Demerath, E. W. Blekhman, R. 2023-01-25 doi:10.1101/2023.01.24.525211 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ IRF1 regulates self-renewal and stress-responsiveness to support hematopoietic stem cell maintenance ]]> https://biorxiv.org/content/10.1101/2023.01.24.525321v1?rss=1 Rundberg Nilsson, A. J. Xian, H. Shalapour, S. Cammenga, J. Karin, M. 2023-01-24 doi:10.1101/2023.01.24.525321 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense ]]> https://biorxiv.org/content/10.1101/2023.01.26.525578v1?rss=1 Leibel, S. L. McVicar, R. N. Murad, R. Kwong, E. M. Clark, A. E. Alvarado, A. Grimmig, B. A. Nuryyev, R. Young, R. E. Lee, J. C. Peng, W. Zhu, Y. P. Griffis, E. Nowell, C. J. James, B. Alarcon, S. Malhotra, A. Gearing, L. J. Hertzog, P. J. Galapate, C. M. Galenkamp, K. M. O. Commisso, C. Smith, D. M. Sun, X. Carlin, A. F. Croker, B. A. Snyder, E. Y. 2023-01-27 doi:10.1101/2023.01.26.525578 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ How PTEN mutations degrade function at the membrane and life expectancy of carriers of mutations in the human brain ]]> https://biorxiv.org/content/10.1101/2023.01.26.525746v1?rss=1 JANG, H. Chen, J. Iakoucheva, L. M. Nussinov, R. 2023-01-27 doi:10.1101/2023.01.26.525746 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ The impact of extracellular matrix on the precision medicine utility of pancreatic cancer patient-derived organoids ]]> https://biorxiv.org/content/10.1101/2023.01.26.525757v1?rss=1 Lumibao, J. C. Okhovat, S. R. Peck, K. Lande, K. Zou, J. Engle, D. D. 2023-01-27 doi:10.1101/2023.01.26.525757 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Phenotypically Complex Living Materials Containing Engineered Cyanobacteria ]]> https://biorxiv.org/content/10.1101/2023.01.26.525792v1?rss=1 Datta, D. Weiss, E. L. Wangpraseurt, D. Hild, E. Chen, S. Golden, J. W. Golden, S. S. Pokorski, J. K. 2023-01-27 doi:10.1101/2023.01.26.525792 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Engineered Antiviral Sensor Targets Infected Mosquitoes ]]> https://biorxiv.org/content/10.1101/2023.01.27.525922v1?rss=1 Dalla Benetta, E. Lopez-Denman, A. J. Li, H.-H. Masri, R. A. Brogan, D. J. Bui, M. Yang, T. Li, M. Dunn, M. Klein, M. J. Jackson, S. Catalan, K. Blasdell, K. R. Tng, P. Antoshechkin, I. Alphey, L. S. Paradkar, P. N. Akbari, O. 2023-01-27 doi:10.1101/2023.01.27.525922 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Exponential increase in QTL detection with increased sample size. ]]> https://biorxiv.org/content/10.1101/2023.01.27.525982v1?rss=1 Chitre, A. S. Polesskaya, O. Munro, D. Cheng, R. Mohammadi, P. Holl, K. Gao, J. Bimschleger, H. V. Garcia Martinez, A. George, A. Gileta, A. F. Han, W. Horvath, A. Hughson, A. Ishiwari, K. King, C. P. Lamparelli, A. Versaggi, C. L. Martin, C. St. Pierre, C. L. Tripi, J. A. Richards, J. B. Wang, T. Chen, H. Flagel, S. B. Meyer, P. Robinson, T. E. Solberg Woods, L. C. Palmer, A. A. 2023-01-29 doi:10.1101/2023.01.27.525982 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Bacterial vaginosis is associated with increased amylolytic activity ]]> https://biorxiv.org/content/10.1101/2023.01.28.526025v1?rss=1 Hertzberger, R. Himschoot, L. Bruisten, S. Steenbergen, L. Lewis, W. Cools, P. Kort, R. 2023-01-29 doi:10.1101/2023.01.28.526025 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor ]]> https://biorxiv.org/content/10.1101/2023.01.31.526348v1?rss=1 Herrera, L. McGlynn, K. Gibbs, Z. Davis, A. J. Whitehurst, A. 2023-02-03 doi:10.1101/2023.01.31.526348 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis ]]> https://biorxiv.org/content/10.1101/2023.01.31.526474v1?rss=1 Alker, A. T. Aspiras, A. E. Dunbar, T. L. Farrell, M. V. Fedoriouk, A. Jones, J. E. Mikhail, S. R. Salcedo, G. Y. Moore, B. S. Shikuma, N. J. 2023-01-31 doi:10.1101/2023.01.31.526474 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ In vivo photopharmacology with light-activated opioid drugs ]]> https://biorxiv.org/content/10.1101/2023.02.02.526901v1?rss=1 McClain, S. P. Ma, X. Johnson, D. A. Johnson, C. A. Layden, A. E. Yung, J. C. Lubejko, S. T. Livrizzi, G. He, X. J. Zhou, J. Ventriglia, E. Rizzo, A. Levinstein, M. Gomez, J. L. Bonaventura, J. Michaelides, M. Banghart, M. R. 2023-02-04 doi:10.1101/2023.02.02.526901 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Automated Agnostic Designation of Pathogen Lineages ]]> https://biorxiv.org/content/10.1101/2023.02.03.527052v1?rss=1 McBroome, J. de Bernardi Schneider, A. Roemer, C. Wolfinger, M. T. Hinrichs, A. S. O'Toole, A. N. Ruis, C. Turakhia, Y. Rambaut, A. Corbett-Detig, R. 2023-02-05 doi:10.1101/2023.02.03.527052 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Gene panel selection for targeted spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.02.03.527053v1?rss=1 Zhang, Y. Petukhov, V. Biederstedt, E. Kharchenko, P. V. 2023-02-04 doi:10.1101/2023.02.03.527053 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice ]]> https://biorxiv.org/content/10.1101/2023.02.03.527064v1?rss=1 Borin, J. M. Liu, R. Wang, Y. Wu, T.-C. Chopyk, J. Huang, L. Kuo, P. Ghose, C. Meyer, J. R. Tu, X. M. Schnabl, B. Pride, D. T. 2023-02-04 doi:10.1101/2023.02.03.527064 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Brainstem Dbh+ Neurons Control Chronic Allergen-Induced Airway Hyperreactivity ]]> https://biorxiv.org/content/10.1101/2023.02.04.527145v1?rss=1 Su, Y. Xu, J. Zhu, Z. Yu, H. Nudell, V. S. Dash, B. Moya, E. Ye, L. Nimmerjahn, A. Sun, X. 2023-02-05 doi:10.1101/2023.02.04.527145 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth ]]> https://biorxiv.org/content/10.1101/2023.02.06.527228v1?rss=1 Neher, W. Rasmussen, C. G. Braybrook, S. A. Lazetic, V. Stowers, C. E. Mooney, P. T. Sylvester, A. W. Springer, P. S. 2023-02-06 doi:10.1101/2023.02.06.527228 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Mitochondrial metabolism in primary and metastatic human kidney cancers ]]> https://biorxiv.org/content/10.1101/2023.02.06.527285v1?rss=1 Bezwada, D. DeBerardinis, R. J. Lesner, N. P. Brooks, B. Vu, H. S. Wu, Z. Cai, L. Kasitinon, S. Kelekar, S. Cai, F. Aurora, A. B. Patrick, M. Leach, A. Ghandour, R. Zhang, Y. Do, D. Sudderth, J. Dumesnil, D. House, S. Rosales, T. Poole, A. M. Lotan, Y. Woldu, S. Bagrodia, A. Meng, X. Cadeddu, J. A. Mishra, P. Pedrosa, I. Kapur, P. Courtney, K. D. Malloy, C. R. Margulis, V. 2023-02-07 doi:10.1101/2023.02.06.527285 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Reply to: Caution Regarding the Specificities of Pan-Cancer Microbial Structure ]]> https://biorxiv.org/content/10.1101/2023.02.10.528049v1?rss=1 Sepich-Poore, G. D. Kopylova, E. Zhu, Q. Carpenter, C. Fraraccio, S. Wandro, S. Kosciolek, T. Janssen, S. Metcalf, J. Song, S. J. Kanbar, J. Miller-Montgomery, S. Heaton, R. Mckay, R. Patel, S. P. Swafford, A. D. Knight, R. 2023-02-13 doi:10.1101/2023.02.10.528049 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ The Small GTPase Rab7 Regulates Release of Mitochondria in Extracellular Vesicles in Response to Lysosomal Dysfunction ]]> https://biorxiv.org/content/10.1101/2023.02.11.528148v1?rss=1 Liang, W. Diao, R. Quiles, J. Najor, R. Chi, L. Woodall, B. Leon, L. Duran, J. Cauvi, D. De Maio, A. Adler, E. Gustafsson, A. B. 2023-02-13 doi:10.1101/2023.02.11.528148 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Flow augmentation from off-channel storage improves salmonid habitat and survival ]]> https://biorxiv.org/content/10.1101/2023.02.15.528508v1?rss=1 1.5 km downstream from the point of augmentation and had a marginal warming effect on stream temperature. During the wet year, both dissolved oxygen and water temperature effects were negligible. In both years, augmentation had a small but positive effect on invertebrate drift. Inter-pool movement of juvenile steelhead (Oncorhynchus mykiss) and stocked Coho Salmon (O. kisutch) increased due to augmentation during the dry summer. Flow augmentation also increased the survival probability for salmonids, with a larger effect during the dry summer (24% higher survival for Coho and 20% higher for steelhead), than during the wet summer (when no effect was observed for steelhead survival and Coho Salmon survival increased by 11%). This study indicates that appropriately designed and timed flow augmentations can improve conditions for rearing salmonids in small streams, particularly during dry years. More broadly it provides empirical evidence that efforts to restore summer streamflow in small, salmon-bearing streams can yield significant ecological benefits. ]]> Rossi, G. Obedzinski, M. Pneh, S. Pierce, S. N. Boucher, W. Flynn, K. Slaughter, W. Grantham, T. 2023-02-15 doi:10.1101/2023.02.15.528508 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Restructuring of olfactory representations in the fly brain around odor relationships in natural sources ]]> https://biorxiv.org/content/10.1101/2023.02.15.528627v1?rss=1 Yang, J.-Y. O'Connell, T. F. Hsu, W.-M. M. Bauer, M. S. Dylla, K. V. Sharpee, T. O. Hong, E. J. 2023-02-15 doi:10.1101/2023.02.15.528627 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ The mitochondrial regulation of smooth muscle cell proliferation in type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2023.02.15.528765v1?rss=1 Grumbach, I. M. Koval, O. M. Nguyen, E. Mittauer, D. J. Ait-Aissa, K. Chinchankar, W. Qian, L. Madesh, M. Dai, D.-F. 2023-02-16 doi:10.1101/2023.02.15.528765 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Exploiting heterogeneity in coupled, two plasmid systems for dynamic population adaptation ]]> https://biorxiv.org/content/10.1101/2023.02.19.529072v1?rss=1 Kumar, S. Lezia, A. Hasty, J. 2023-02-19 doi:10.1101/2023.02.19.529072 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Sex differences in patch-leaving foraging decisions in rats ]]> https://biorxiv.org/content/10.1101/2023.02.19.529135v1?rss=1 Garcia, M. Gupta, S. Wikenheiser, A. M. 2023-02-19 doi:10.1101/2023.02.19.529135 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Selective IL-27 production by intestinal regulatory T cells permits gut-specific regulation of Th17 immunity ]]> https://biorxiv.org/content/10.1101/2023.02.20.529261v1?rss=1 Lin, C.-H. Wu, C.-J. Cho, S. Patkar, R. Lin, L.-L. Chen, M.-C. Israelsson, E. Betts, J. Niedzielska, M. Patel, S. A. Duong, H. G. Gerner, R. R. Hsu, C.-Y. Catley, M. Maciewicz, R. A. Chu, H. Raffatellu, M. Chang, J. T. Lu, L.-F. 2023-02-21 doi:10.1101/2023.02.20.529261 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Arsenic is a potent co-mutagen of ultraviolet light ]]> https://biorxiv.org/content/10.1101/2023.02.22.529578v1?rss=1 Speer, R. M. Nandi, S. P. Cooper, K. L. Zhou, X. Yu, H. Guo, Y. Hudson, L. G. Alexandrov, L. B. Liu, K. J. 2023-02-23 doi:10.1101/2023.02.22.529578 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2023.02.23.529781v1?rss=1 Naka, H. Haygood, M. G. 2023-02-24 doi:10.1101/2023.02.23.529781 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Striatal enkephalin supports maintenance of conditioned cocaine reward during extinction ]]> https://biorxiv.org/content/10.1101/2023.02.23.529807v1?rss=1 Matsumura, K. Choi, I. B. Asokan, M. Le, N. N. Natividad, L. Dobbs, L. K. 2023-02-24 doi:10.1101/2023.02.23.529807 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Cooperativity between H3.3K27M and PDGFRA poses multiple therapeutic vulnerabilities in human iPSC-derived diffuse midline glioma avatars ]]> https://biorxiv.org/content/10.1101/2023.02.24.528982v1?rss=1 Skinner, K. R. Koga, T. Miki, S. Gruener, R. F. Grigore, F.-N. Torii, E. H. Seelig, D. M. Suzuki, Y. Kawauchi, D. Lin, B. Malicki, D. M. Chen, C. C. Benveniste, E. N. Patel, R. P. McFarland, B. C. Huang, R. S. Jones, C. Mackay, A. Miller, C. R. Furnari, F. B. 2023-02-24 doi:10.1101/2023.02.24.528982 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Estimating single cell clonal dynamics in human blood using coalescent theory ]]> https://biorxiv.org/content/10.1101/2023.02.24.529817v1?rss=1 Johnson, B. Shuai, Y. Schweinsberg, J. Curtius, K. 2023-02-27 doi:10.1101/2023.02.24.529817 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY ]]> https://biorxiv.org/content/10.1101/2023.02.24.529968v1?rss=1 Prichard, A. Lee, J. Laughlin, T. G. Lee, A. Thomas, K. P. Sy, A. Spencer, T. Asavavimol, A. Cafferata, A. Cameron, M. Chiu, N. Davydov, D. Desai, I. Diaz, G. Guereca, M. Hearst, K. Huang, L. Jacobs, E. Johnson, A. Kahn, S. Koch, R. Martinez, A. Norquist, M. Pau, T. Prasad, G. Saam, K. Sandhu, M. Sarabia, A. J. Schumaker, S. Sonin, A. Uyeno, A. Zhao, A. Corbett, K. Pogliano, K. Meyer, J. Grose, J. H. Villa, E. Dutton, R. Pogliano, J. 2023-02-25 doi:10.1101/2023.02.24.529968 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ Reduced steroid activation of elephant shark GR and MR after inserting four amino acids from the DBD of lamprey corticoid receptor-1 ]]> https://biorxiv.org/content/10.1101/2023.02.24.529974v1?rss=1 Katsu, Y. Zhang, J. Baker, M. E. 2023-02-25 doi:10.1101/2023.02.24.529974 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models ]]> https://biorxiv.org/content/10.1101/2023.02.26.530115v1?rss=1 Vezina, B. Watts, S. C. Hawkey, J. Cooper, H. B. Judd, L. M. Jenney, A. Monk, J. M. Holt, K. E. Wyres, K. L. 2023-02-27 doi:10.1101/2023.02.26.530115 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Active maintenance of CD8+ T cell naivety through regulation of global genome architecture ]]> https://biorxiv.org/content/10.1101/2023.02.26.530139v1?rss=1 Russ, B. E. Tsyganov, K. Quon, S. Yu, B. Li, J. Lee, J. K. Olshansky, M. He, Z. Harrison, P. F. Barugahare, A. See, M. Nuessing, S. Morey, A. E. Udupa, V. A. Bennett, T. J. Kallies, A. Murre, C. Collas, P. Powell, D. Goldrath, A. W. Turner, S. J. 2023-02-27 doi:10.1101/2023.02.26.530139 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Angiotensin II receptor inhibition ameliorates liver fibrosis and enhances hepatocellular carcinoma infiltration by effector T cells ]]> https://biorxiv.org/content/10.1101/2023.03.05.531188v1?rss=1 Gu, L. Zhu, Y. Lee, M. Nguyen, A. Ryujin, N. T. Huang, J. Chamseddine, S. Xiao, L. Mohamed, Y. I. Kaseb, A. O. Karin, M. Shalapour, S. 2023-03-06 doi:10.1101/2023.03.05.531188 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Inferring functional organization of posterior parietal cortex circuitry based on information flow ]]> https://biorxiv.org/content/10.1101/2023.03.08.531516v1?rss=1 Kang, J. U. Mooshagian, E. Snyder, L. H. 2023-03-09 doi:10.1101/2023.03.08.531516 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ A deep population reference panel of tandem repeat variation ]]> https://biorxiv.org/content/10.1101/2023.03.09.531600v1?rss=1 Ziaei Jam, H. Li, Y. DeVito, R. Mousavi, N. Ma, N. Lujumba, I. Adam, Y. Maksimov, M. Huang, B. Dolzhenko, E. Qiu, Y. Kakembo, F. E. Joseph, H. Onyido, B. Adeyemi, J. Bakhtiari, M. Park, J. Javadzadeh, S. Jjingo, D. Adebiyi, E. Bafna, V. Gymrek, M. 2023-03-12 doi:10.1101/2023.03.09.531600 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Optical coherence tomography of human fetal membrane sub-layers during dynamic loading ]]> https://biorxiv.org/content/10.1101/2023.03.09.531932v1?rss=1 0.8). Intact amniochorion bilayer and separated amnion and chorion were individually loaded, and the amnion layer was identified as the load-bearing layer within intact fetal membranes for both labored and C-section samples, consistent with prior work. Additionally, the rupture pressure and thickness of the amniochorion bilayer from the near-placental region were greater than those of the near-cervical region for labored samples. This location-dependent change in fetal membrane thickness was not attributable to the load-bearing amnion layer. Finally, the initial phase of the loading curve indicates that amniochorion bilayer from the near-cervical region is strain-hardened compared to the near-placental region in labored samples. Overall, these studies fill a gap in our understanding of the structural and mechanical properties of human fetal membranes at high resolution under dynamic loading events. ]]> Samimi, K. Contreras Guzman, E. Wu, M. Carlson, L. Feltovich, H. Hall, T. J. Myers, K. M. Oyen, M. L. Skala, M. C. 2023-03-12 doi:10.1101/2023.03.09.531932 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Generating high quality reference genomes from field collected specimens by optimizing preservation ]]> https://biorxiv.org/content/10.1101/2023.03.10.532097v1?rss=1 Minich, J. J. Moore, M. L. Allsing, N. A. Murray, E. R. Tran, L. Michael, T. P. 2023-03-12 doi:10.1101/2023.03.10.532097 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Metabolic energetics underlying attractors in neural models ]]> https://biorxiv.org/content/10.1101/2023.03.11.532220v1?rss=1 Buxton, R. B. Wong, E. C. 2023-03-13 doi:10.1101/2023.03.11.532220 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms ]]> https://biorxiv.org/content/10.1101/2023.03.13.532449v1?rss=1 Luu, G. T. Little, J. C. Pierce, E. C. Morin, M. Ertekin, C. A. Wolfe, B. E. Baars, O. Dutton, R. J. Sanchez, L. M. 2023-03-13 doi:10.1101/2023.03.13.532449 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ A mathematical model of the disruption of glucose homeostasis in cancer patients ]]> https://biorxiv.org/content/10.1101/2023.03.15.532725v1?rss=1 Salentine, N. Doria, J. Nguyen, C. Pinter, G. A. Wang, S. E. Hinow, P. 2023-03-15 doi:10.1101/2023.03.15.532725 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods ]]> https://biorxiv.org/content/10.1101/2023.03.15.532862v1?rss=1 Oslandsbotn, A. Forsch, N. Cloninger, A. 2023-03-16 doi:10.1101/2023.03.15.532862 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases ]]> https://biorxiv.org/content/10.1101/2023.03.17.533036v1?rss=1 Lampe, G. D. King, R. T. Halpin-Healy, T. S. Klompe, S. E. Hogan, M. I. Vo, P. L. H. Tang, S. Chavez, A. Sternberg, S. H. 2023-03-18 doi:10.1101/2023.03.17.533036 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Leptomeningeal anti-tumor immunity follows unique signaling principles ]]> https://biorxiv.org/content/10.1101/2023.03.17.533041v1?rss=1 Remsik, J. Tong, X. Kunes, R. Z. Li, M. J. Osman, A. Chabot, K. Sener, U. Wilcox, J. A. Isakov, D. Snyder, J. Bale, T. Chaligne, R. Pe'er, D. D. Boire, A. 2023-03-20 doi:10.1101/2023.03.17.533041 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Spatial-temporal expression analysis of lineage-restricted shell matrix proteins reveals shell field regionalization and distinct cell populations in the slipper snail Crepidula atrasolea ]]> https://biorxiv.org/content/10.1101/2023.03.18.532128v1?rss=1 Lopez-Anido, R. Batzel, G. O. Ramirez, G. Goodheart, J. A. Wang, Y. Neal, S. Lyons, D. C. 2023-03-21 doi:10.1101/2023.03.18.532128 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Quantification of elongation stalls and impact on gene expression in yeast ]]> https://biorxiv.org/content/10.1101/2023.03.19.533377v1?rss=1 Hou, W. Harjono, V. Harvey, A. T. Subramaniam, A. R. Zid, B. M. 2023-03-20 doi:10.1101/2023.03.19.533377 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Mutant Prion Protein Endoggresomes are Hubs for Local Axonal Organelle-Cytoskeletal Remodeling ]]> https://biorxiv.org/content/10.1101/2023.03.19.533383v1?rss=1 Chaiamarit, T. Verhelle, A. Chassefeyre, R. Shukla, N. Weiser Novak, S. Andrade, L. R. Manor, U. Encalada, S. E. 2023-03-21 doi:10.1101/2023.03.19.533383 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development ]]> https://biorxiv.org/content/10.1101/2023.03.20.533545v1?rss=1 Sur, A. Wang, Y. Capar, P. Margolin, G. Farrell, J. A. 2023-03-21 doi:10.1101/2023.03.20.533545 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Guidelines for Evaluating the Comparability of Down-Sampled GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/2023.03.21.533641v1?rss=1 Williams, C. M. Poore, H. Tanksley, P. T. Kweon, H. Courchesne-Krak, N. S. Londono-Correa, D. Mallard, T. T. Barr, P. Koellinger, P. D. Waldman, I. Sanchez-Roige, S. Harden, K. P. Palmer, A. A. Dick, D. D. Linner, R. K. 2023-03-24 doi:10.1101/2023.03.21.533641 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach ]]> https://biorxiv.org/content/10.1101/2023.03.21.533676v1?rss=1 Raja, R. Khanum, S. Aboulmouna, L. Maurya, M. R. Gupta, S. Subramaniam, S. Ramkrishna, D. 2023-03-23 doi:10.1101/2023.03.21.533676 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Microbial short-chain fatty acids regulate drug seeking and transcriptional control in a model of cocaine seeking ]]> https://biorxiv.org/content/10.1101/2023.03.22.533834v1?rss=1 Meckel, K. R. Simpson, S. Godino, A. Peck, E. G. George, O. Calipari, E. S. Hofford, R. S. Kiraly, D. 2023-03-24 doi:10.1101/2023.03.22.533834 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ A multi-omics strategy for the study of microbial metabolism: application to the human skin's microbiome ]]> https://biorxiv.org/content/10.1101/2023.03.26.532286v1?rss=1 120, n = 41) were analyzed by LC-MS/MS, yielding four metabolomics datasets for RP18 or HILIC separation in ESI+ or ESI- ionization mode. Following our data analysis strategy, we were able to obtain increasingly comprehensive structural and functional annotations, by applying the GNPS (Wang et al., Nat. Biotechnol. 2016), SIRIUS (Duhrkop et al. Nat. Methods 2019), and MicrobeMASST (Zuffa et al., bioRxiv 2023) tools. We finally combined the metabolomics data with a corresponding metagenomic sequencing dataset using MMvec (Morton et al., Nat. Methods 2019), gaining insights into the metabolic niche of one of the most prominent microbes on the human skin, Staphylococcus epidermidis. IMPORTANCESystems biology research on host-associated microbiota focuses on two fundamental questions: Which microbes are present and how do they interact with each other, their host, and the broader host environment? Metagenomics provides us with a direct answer to the first part of the question: it unveils the microbial inhabitants, e.g., on our skin, and can provide insight into their functional potential. Yet, it falls short in revealing their active role. Metabolomics shows us the chemical composition of the environment in which microbes thrive and the transformation products they produce. In particular, untargeted metabolomics has the potential to observe a diverse set of metabolites and is thus an ideal complement to metagenomics. However, this potential often remains underexplored due to the low annotation rates in MS-based metabolomics and the necessity for multiple experimental chromatographic and mass spectrometric conditions. Beyond detection, prospecting metabolites functional role in the host/microbiome metabolome requires identifying the biological processes and entities involved in their production and biotransformations. In the present study of the human scalp, we developed a strategy to achieve comprehensive structural and functional annotation of the metabolites in the human scalp environment, thus diving one step deeper into the interpretation of omics data. Leveraging a collection of openly accessible software tools and integrating microbiome data as a source of functional metabolite annotations, we finally identified the specific metabolic niche of Staphylococcus epidermidis, one of the key players of the human skin microbiome. ]]> Nothias, L.-F. Schmid, R. Garlet, A. Cameron, H. Leoty-Okombi, S. Andre-Frei, V. Fuchs, R. Dorrestein, P. Ternes, P. 2023-03-26 doi:10.1101/2023.03.26.532286 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ A network of CD163+ macrophages monitors enhanced permeability at the blood-dorsal root ganglion barrier ]]> https://biorxiv.org/content/10.1101/2023.03.27.534318v1?rss=1 Lund, H. Hunt, M. Kurtovic, Z. Sandor, K. Fereydouni, N. Julien, A. Goeritz, C. Han, J. Zhu, K. Harris, R. A. Lampa, J. Haglund, L. Yaksh, T. L. Svensson, C. I. 2023-03-27 doi:10.1101/2023.03.27.534318 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates ]]> https://biorxiv.org/content/10.1101/2023.03.27.534408v1?rss=1 Barghouth, P. G. Melemenidis, S. Montay-Gruel, P. Ollivier, J. Viswanathan, V. Jorge, P. G. Soto, L. Lau, B. C. Sadeghi, C. Edlabadkar, A. Manjappa, R. Wang, J. Le Bouteiller, M. Surucu, M. Yu, A. Bush, K. Skinner, L. Maxim, P. G. Loo, B. W. Limoli, C. L. Vozenin, M.-C. Frock, R. L. 2023-03-27 doi:10.1101/2023.03.27.534408 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Natural constraints explain working memory capacity limitations in sensory-cognitive models ]]> https://biorxiv.org/content/10.1101/2023.03.30.534982v1?rss=1 Xie, Y. Duan, Y. Cheng, A. Jiang, P. Cueva, C. J. Yang, G. R. 2023-03-30 doi:10.1101/2023.03.30.534982 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms ]]> https://biorxiv.org/content/10.1101/2023.04.03.535074v1?rss=1 Gruen, C. Yang, H. H. Sassano, A. Wu, E. Gopalan, V. Marie, K. L. Castro, A. Mehrabadi, F. R. Wu, C. H. Church, I. Needle, G. A. Smith, C. Chin, S. Ebersole, J. Marcelus, C. Fon, A. Liu, H. Malikic, S. Sahinalp, C. Carter, H. Hannenhalli, S. Day, C.-P. Lee, M. P. Merlino, G. Perez-Guijarro, E. 2023-04-05 doi:10.1101/2023.04.03.535074 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system ]]> https://biorxiv.org/content/10.1101/2023.04.04.535519v1?rss=1 Royseth, V. Hurysz, B. M. Kaczorowska, A. Dorawa, S. Fedoy, A.-E. Arsin, H. Serafim, M. Werbowy, O. Kaczorowski, T. Stokke, R. O'Donoghue, A. J. Steen, I. H. 2023-04-04 doi:10.1101/2023.04.04.535519 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Photoreceptor disc incisures form as an adaptive mechanism ensuring the completion of disc enclosure ]]> https://biorxiv.org/content/10.1101/2023.04.06.535932v1?rss=1 Lewis, T. R. Phan, S. Castillo, C. M. Kim, K.-Y. Coppenrath, K. Thomas, W. Hao, Y. Skiba, N. P. Horb, M. E. Ellisman, M. H. Arshavsky, V. Y. 2023-04-07 doi:10.1101/2023.04.06.535932 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Structured memory representations develop at multiple time scales in hippocampal-cortical networks ]]> https://biorxiv.org/content/10.1101/2023.04.06.535935v1?rss=1 Tambini, A. Miller, J. Ehlert, L. Kiyonaga, A. D'Esposito, M. 2023-04-07 doi:10.1101/2023.04.06.535935 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Frizzled2 receives the WntA morphogen during butterfly wing pattern formation ]]> https://biorxiv.org/content/10.1101/2023.04.11.536469v1?rss=1 Hanly, J. J. Loh, L. S. Mazo-Vargas, A. Rivera-Miranda, T. S. Livraghi, L. Tendolkar, A. Day, C. R. Liutikaite, N. Earls, E. A. Corning, O. B. D'Souza, N. Hermina-Perez, J. J. Mehta, C. Ainsworth, J. A. Rossi, M. McMillan, W. O. Perry, M. W. Martin, A. 2023-04-12 doi:10.1101/2023.04.11.536469 Cold Spring Harbor Laboratory Press 2023-04-12 <![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[ Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor ]]> https://biorxiv.org/content/10.1101/2023.04.13.536636v1?rss=1 Pang, Y. Huang, M. Fan, Y. Yeh, H.-W. Xiong, Y. Ng, H. L. Ai, H. 2023-04-14 doi:10.1101/2023.04.13.536636 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats ]]> https://biorxiv.org/content/10.1101/2023.04.13.536694v1?rss=1 de Jong, T. V. Pan, Y. Rastas, P. Munro, D. Tutaj, M. Akil, H. Benner, C. Chitre, A. S. Chow, W. Colonna, V. Dalgard, C. L. Demos, W. M. Doris, P. A. Garrison, E. Geurts, A. Gunturkun, H. M. Guryev, V. Hourlier, T. Howe, K. Huang, J. Kalbfleisch, T. Kim, P. Li, L. Mahaffey, S. Martin, F. J. Mohammadi, P. Ozel, A. B. Polesskaya, O. Pravenec, M. Prins, P. Sebat, J. Smith, J. R. Solberg Woods, L. C. Tabakoff, B. Tracey, A. Uliano-Silva, M. Villani, F. Wang, H. Sharp, B. M. Telese, F. Jiang, Z. Saba, L. Wang, X. Murphy, T. D. Palmer, A. A. Kwitek, A. E. 2023-04-14 doi:10.1101/2023.04.13.536694 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Rapid bacteria-phage coevolution drives the emergence of multi-scale networks ]]> https://biorxiv.org/content/10.1101/2023.04.13.536812v1?rss=1 Borin, J. M. Lee, J. J. Lucia-Sanz, A. Gerbino, K. R. Weitz, J. M. Meyer, J. R. 2023-04-14 doi:10.1101/2023.04.13.536812 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ EGFR+ lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth ]]> https://biorxiv.org/content/10.1101/2023.04.15.536974v1?rss=1 Kuhlmann-Hogan, A. Cordes, T. Xu, Z. Traina, K. Robles-Oteiza, C. Ayeni, D. Kwong, E. M. Levy, S. Nobari, M. Cheng, G. Z. Shaw, R. J. Leibel, S. L. Metallo, C. Politi, K. Kaech, S. M. 2023-04-17 doi:10.1101/2023.04.15.536974 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Sperm Whales Demographics in the Gulf of Alaska and Bering Sea/Aleutian Islands: An Overlooked Female Habitat ]]> https://biorxiv.org/content/10.1101/2023.04.16.537097v1?rss=1 Posdaljian, N. Solsona-Berga, A. Hildebrand, J. A. Soderstjerna, C. Wiggins, S. M. Lenssen, K. Baumann-Pickering, S. 2023-04-18 doi:10.1101/2023.04.16.537097 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Colocalization of Protein and microRNA Markers Reveals Unique Extracellular Vesicle Sub-Populations for Early Cancer Detection ]]> https://biorxiv.org/content/10.1101/2023.04.17.536958v1?rss=1 Li, Z. Guo, K. Gao, Z. Chen, J. Ye, Z. Wang, S. E. Yin, Y. Zhong, W. 2023-04-18 doi:10.1101/2023.04.17.536958 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ How can graph theory inform the dual-stream model of speech processing? a resting-state fMRI study of post-stroke aphasia ]]> https://biorxiv.org/content/10.1101/2023.04.17.537216v1?rss=1 Zhu, H. Fitzhugh, M. C. Keator, L. M. Johnson, L. Rorden, C. Bonilha, L. Fridriksson, J. Rogalsky, C. 2023-04-19 doi:10.1101/2023.04.17.537216 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ Targeting Sex Determination to Suppress Mosquito Populations ]]> https://biorxiv.org/content/10.1101/2023.04.18.537404v1?rss=1 Li, M. Kandul, N. P. Sun, R. Yang, T. Benetta, E. D. Brogan, D. J. Antoshechkin, I. Sanchez C., H. M. Zhan, Y. DeBeaubien, N. A. Loh, Y. M. Su, M. P. Montell, C. Marshall, J. M. Akbari, O. S. 2023-04-20 doi:10.1101/2023.04.18.537404 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Conserved enhancer logic controls the notochord expression of vertebrate Brachyury ]]> https://biorxiv.org/content/10.1101/2023.04.20.536761v1?rss=1 Kemmler, C. L. Smolikova, J. Moran, H. R. Mannion, B. J. Knapp, D. Lim, F. Czarkwiani, A. Hermosilla Aguayo, V. Rapp, V. Fitch, O. E. Boetschi, S. Selleri, L. Farley, E. Braasch, I. Yun, M. Visel, A. Osterwalder, M. Mosimann, C. Kozmik, Z. Burger, A. 2023-04-20 doi:10.1101/2023.04.20.536761 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors ]]> https://biorxiv.org/content/10.1101/2023.04.24.537925v1?rss=1 Lin, M. S. Jo, S.-Y. Luebeck, J. Chang, H. Y. Wu, S. Mischel, P. S. Bafna, V. 2023-04-24 doi:10.1101/2023.04.24.537925 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Shortwave infrared (SWIR) fluorescence imaging of peripheral organs in awake and freely moving mice ]]> https://biorxiv.org/content/10.1101/2023.04.26.538387v1?rss=1 Arus, B. A. Cosco, E. D. Yiu, J. Balba, I. Bischof, T. S. Sletten, E. M. Bruns, O. T. 2023-04-26 doi:10.1101/2023.04.26.538387 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Rit2 loss in dopaminergic neurons drives a progressive Parkinsonian phenotype ]]> https://biorxiv.org/content/10.1101/2023.04.26.538430v1?rss=1 Kearney, P. J. Zhang, Y. Tan, Y. Kahuno, E. Conklin, T. Fagan, R. R. Yue, Z. Melikian, H. E. Shaffer, S. A. Pavchinskiy, R. G. 2023-04-28 doi:10.1101/2023.04.26.538430 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Marine bacterial enrichment in the sea surface microlayer, and surface taxa aerosolization potential in the Western Mediterranean Sea ]]> https://biorxiv.org/content/10.1101/2023.04.26.538450v1?rss=1 Dinasquet, J. Zancker, B. Nicosia, A. Bigeard, E. Baudoux, A.-C. Engel, A. Guieu, C. Sellegri, K. 2023-04-26 doi:10.1101/2023.04.26.538450 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and without epistatic-like interactions ]]> https://biorxiv.org/content/10.1101/2023.04.26.538501v1?rss=1 Zhou, J. L. Guruvayurappan, K. Chen, H. V. Chen, A. R. McVicker, G. P. 2023-04-27 doi:10.1101/2023.04.26.538501 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Inferring secretory and metabolic pathway activity from omic data with secCellFie ]]> https://biorxiv.org/content/10.1101/2023.05.04.539316v1?rss=1 Masson, H. O. Samoudi, M. Robinson, C. M. Kuo, C.-C. Weiss, L. Shams Ud Doha, K. Campos, A. Tejwani, V. Dahodwala, H. Menard, P. Voldborg, B. G. Sharfstein, S. Lewis, N. 2023-05-07 doi:10.1101/2023.05.04.539316 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Chaotic neural dynamics facilitate probabilistic computations through sampling ]]> https://biorxiv.org/content/10.1101/2023.05.04.539470v1?rss=1 Terada, Y. Toyoizumi, T. 2023-05-05 doi:10.1101/2023.05.04.539470 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ CRISPR/Cas9-mediated mutagenesis of the Asian Citrus Psyllid, Diaphorina citri ]]> https://biorxiv.org/content/10.1101/2023.05.05.539615v1?rss=1 Chaverra-Rodriguez, D. Bui, M. Gilleland, C. L. Rasgon, J. L. Akbari, O. 2023-05-06 doi:10.1101/2023.05.05.539615 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ A riboswitch-controlled manganese exporter (Alx) tunes intracellular Mn2+ concentration in E. coli at alkaline pH ]]> https://biorxiv.org/content/10.1101/2023.05.07.539761v1?rss=1 Sharma, R. Mishanina, T. V. 2023-05-08 doi:10.1101/2023.05.07.539761 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Jumbo phages are active against extensively-drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. ]]> https://biorxiv.org/content/10.1101/2023.05.08.539869v1?rss=1 200kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the 3 separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment. ]]> Cobian-Guemes, A. G. Ghatbale, P. Blanc, A. N. Morgan, C. J. Garcia, A. Leonard, J. Huang, L. Kovalick, G. Proost, M. Chiu, M. Kuo, P. Oh, J. Karthikeyan, S. Knight, R. Pogliano, J. Schooley, R. Pride, D. 2023-05-08 doi:10.1101/2023.05.08.539869 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Evolving spike-protein N-glycosylation in SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2023.05.08.539897v1?rss=1 3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function. ]]> Baboo, S. Diedrich, J. K. Torres, J. L. Copps, J. Singh, B. Garrett, P. T. Ward, A. B. Paulson, J. C. Yates, J. R. 2023-05-09 doi:10.1101/2023.05.08.539897 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Linking bacterial tetrabromopyrrole biosynthesis to coral metamorphosis ]]> https://biorxiv.org/content/10.1101/2023.05.08.539906v1?rss=1 Alker, A. Farrell, M. Demko, A. Purdy, T. Adak, S. Moore, B. Sneed, J. Paul, V. Shikuma, N. J. 2023-05-09 doi:10.1101/2023.05.08.539906 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Computational Framework for Statistical Epistasis Supports XOR Penetrance Function in a Living System ]]> https://biorxiv.org/content/10.1101/2023.05.09.539940v1?rss=1 Batista, S. Madar, V. Freda, P. J. Bhandary, P. Ghosh, A. Chitre, A. S. Palmer, A. A. Moore, J. H. 2023-05-09 doi:10.1101/2023.05.09.539940 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Guard cell epigenomics reveals distinct abscisic acid and CO2 triggered chromatin remodeling during stomatal movements ]]> https://biorxiv.org/content/10.1101/2023.05.11.540345v1?rss=1 Seller, C. A. Schroeder, J. I. 2023-05-11 doi:10.1101/2023.05.11.540345 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Guild and Niche Determination Enable Targeted Alteration of the Microbiome ]]> https://biorxiv.org/content/10.1101/2023.05.11.540389v1?rss=1 Moyne, O. Al-Bassam, M. M. Lieng, C. Thiruppathy, D. Norton, G. J. Kumar, M. Haddad, E. Zaramela, L. S. Zengler, K. 2023-05-11 doi:10.1101/2023.05.11.540389 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Divergent host innate immune response to the smooth-to-rough M. abscessus adaptation to chronic infection ]]> https://biorxiv.org/content/10.1101/2023.05.15.540822v1?rss=1 Malcolm, K. C. Wheeler, E. A. Lenhart-Pendergrass, P. M. Rrysavy, N. M. Poch, K. R. Caceres, S. M. Calhoun, K. M. Serban, K. A. Nick, J. A. 2023-05-18 doi:10.1101/2023.05.15.540822 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Dynamic nuclear polarization illuminates key protein-lipid interactions in the native bacterial cell envelope ]]> https://biorxiv.org/content/10.1101/2023.05.18.541325v1?rss=1 Kent, J. E. Ackerman, B. E. Debelouchina, G. T. Marassi, F. M. 2023-05-18 doi:10.1101/2023.05.18.541325 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a ]]> https://biorxiv.org/content/10.1101/2023.05.18.541339v1?rss=1 Zhu, Y. Tazearslan, C. Rosenfeld, M. G. Fiser, A. Suh, Y. 2023-05-22 doi:10.1101/2023.05.18.541339 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.05.18.541360v1?rss=1 Chipman, L. B. Luc, S. Nicastro, I. A. Hulahan, J. J. Dann, D. C. Bodas, D. M. Pasquinelli, A. E. 2023-05-22 doi:10.1101/2023.05.18.541360 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells ]]> https://biorxiv.org/content/10.1101/2023.05.19.541501v1?rss=1 Naigles, B. Narla, A. Soroczynski, J. Tsimring, L. Hao, N. 2023-05-22 doi:10.1101/2023.05.19.541501 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Human co-ripples facilitate neuronal interactions between cortical locations. ]]> https://biorxiv.org/content/10.1101/2023.05.20.541588v1?rss=1 Verzhbinsky, I. A. Rubin, D. B. Kajfez, S. Bu, Y. Hochberg, L. R. Cash, S. S. Halgren, E. 2023-05-22 doi:10.1101/2023.05.20.541588 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters ]]> https://biorxiv.org/content/10.1101/2023.05.22.541294v1?rss=1 Garcia-Bernalt Diego, J. Singh, G. Jangra, S. Handrejk, K. Laporte, M. Chang, L. A. El Zahed, S. S. Pache, L. Chang, M. W. Warang, P. Aslam, S. Mena, I. Webb, B. T. Benner, C. Garcia-Sastre, A. Schotsaert, M. 2023-05-22 doi:10.1101/2023.05.22.541294 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Genetics of skeletal proportions in two different populations ]]> https://biorxiv.org/content/10.1101/2023.05.22.541772v1?rss=1 Bartell, E. Lin, K. Tsuo, K. Gan, W. Vedantam, S. Cole, J. B. Baronas, J. M. Yengo, L. Marouli, E. Amariuta, T. GIANT Consortium, Renthal, N. E. Jacobsen, C. M. Salem, R. Walters, R. G. Hirschhorn, J. N. 2023-05-23 doi:10.1101/2023.05.22.541772 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Tumor-resident regulatory T cells in pancreatic cancer express the αvβ5 integrin as a targetable activation marker ]]> https://biorxiv.org/content/10.1101/2023.05.24.542137v1?rss=1 Suzuki, K. Kunisada, Y. Miyamura, N. Eikawa, S. Hurtado de Mendoza, T. Mose, E. S. Lu, C. Kuroda, Y. Ruoslahti, E. Lowy, A. M. Sugahara, K. N. 2023-05-24 doi:10.1101/2023.05.24.542137 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method ]]> https://biorxiv.org/content/10.1101/2023.05.26.542489v1?rss=1 de Bernardi Schneider, A. Su, M. Hinrichs, A. S. Wang, J. Amin, H. Bell, J. Wadford, D. A. O'Toole, A. Scher, E. Perry, M. D. Turakhia, Y. De Maio, N. Hughes, S. Corbett-Detig, R. 2023-05-27 doi:10.1101/2023.05.26.542489 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Kinetic trapping organizes actin filaments within liquid-like protein droplets ]]> https://biorxiv.org/content/10.1101/2023.05.26.542517v1?rss=1 Chandrasekaran, A. Graham, K. Stachowiak, J. Rangamani, P. 2023-05-28 doi:10.1101/2023.05.26.542517 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Super-resolution imaging of neuronal structure with structured illumination microscopy ]]> https://biorxiv.org/content/10.1101/2023.05.26.542523v1?rss=1 Paul, T. C. Johnson, K. A. Hagen, G. M. 2023-05-26 doi:10.1101/2023.05.26.542523 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Phase-encoded fMRI tracks down brainstorms of natural language processing with sub-second precision ]]> https://biorxiv.org/content/10.1101/2023.05.29.542546v1?rss=1 Lei, V. L. C. Leong, T. I. Leong, C. T. Liu, L. Choi, C. U. Sereno, M. I. Li, D. Huang, R.-S. 2023-05-29 doi:10.1101/2023.05.29.542546 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Effective cell membrane tension protects red blood cells against malaria invasion ]]> https://biorxiv.org/content/10.1101/2023.05.30.542792v1?rss=1 Alimohamadi, H. Rangamani, P. 2023-05-31 doi:10.1101/2023.05.30.542792 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Efficient Analysis of Proteome-wide FPOP Data by FragPipe ]]> https://biorxiv.org/content/10.1101/2023.06.01.543263v1?rss=1 Ramirez, C. R. Espino, J. A. Jones, L. M. Polasky, D. A. Nesvizhskii, A. I. 2023-06-05 doi:10.1101/2023.06.01.543263 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model ]]> https://biorxiv.org/content/10.1101/2023.06.01.543315v1?rss=1 Phan, T. V. Mattingly, H. H. Vo, L. Marvin, J. S. Looger, L. L. Emonet, T. 2023-06-05 doi:10.1101/2023.06.01.543315 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Aeroplane wing, a new recessive autosomal phenotypic marker in malaria vector, Anopheles stephensi Liston ]]> https://biorxiv.org/content/10.1101/2023.06.05.543679v1?rss=1 Ghosh, C. M, S. Kumar, N. Ramanjini, C. K. Joshi, S. G. S, S. K. Subramani, S. Swain, S. 2023-06-07 doi:10.1101/2023.06.05.543679 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex ]]> https://biorxiv.org/content/10.1101/2023.06.06.543957v1?rss=1 Deng, S. Cai, J. Harrison, S. Zhou, H. Hinshaw, S. M. 2023-06-07 doi:10.1101/2023.06.06.543957 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Sustained growth and rapid dispersal of chitin-associated marine bacteria ]]> https://biorxiv.org/content/10.1101/2023.06.12.544524v1?rss=1 Guessous, G. Patsalo, V. Balakrishnan, R. Caglar, T. Williamson, J. Hwa, T. 2023-06-12 doi:10.1101/2023.06.12.544524 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ CRISPR-based gene drives generate super-Mendelian inheritance in the disease vector Culex quinquefasciatus. ]]> https://biorxiv.org/content/10.1101/2023.06.12.544656v1?rss=1 Harvey-Samuel, T. Feng, X. Okamoto, E. M. Purusothaman, D.-K. Leftwich, P. T. Alphey, L. Gantz, V. M. 2023-06-15 doi:10.1101/2023.06.12.544656 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Decoding Root Biogeography: Building Reduced Complexity Functional Rhizosphere Microbial Consortia ]]> https://biorxiv.org/content/10.1101/2023.06.12.544662v1?rss=1 Chen, M. Acharya, S. Yee, M. O. Kabugao, K. G. Chakraborty, R. 2023-06-12 doi:10.1101/2023.06.12.544662 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Mitochondria- and ER-associated actin are required for mitochondrial fusion ]]> https://biorxiv.org/content/10.1101/2023.06.13.544768v1?rss=1 Gatti, P. Schiavon, C. R. Manor, U. Germain, M. 2023-06-13 doi:10.1101/2023.06.13.544768 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets ]]> https://biorxiv.org/content/10.1101/2023.06.14.545018v1?rss=1 Nuhamunada, M. Mohite, O. S. Phaneuf, P. V. Palsson, B. Weber, T. 2023-06-15 doi:10.1101/2023.06.14.545018 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Reports of the death of brain-behavior associations have been greatly exaggerated ]]> https://biorxiv.org/content/10.1101/2023.06.16.545340v1?rss=1 Makowski, C. Brown, T. T. Zhao, W. Hagler, D. J. Parekh, P. Garavan, H. Nichols, T. E. Jernigan, T. L. Dale, A. M. 2023-06-16 doi:10.1101/2023.06.16.545340 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Efficient Sex Separation by Exploiting Differential Alternative Splicing of a Dominant Marker in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2023.06.16.545348v1?rss=1 Weng, S.-C. Antoshechkin, I. Marois, E. Akbari, O. S. 2023-06-16 doi:10.1101/2023.06.16.545348 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Neuronal Ndst1 depletion accelerates prion protein clearance and slows neurodegeneration in prion infection ]]> https://biorxiv.org/content/10.1101/2023.06.19.545528v1?rss=1 Aguilar Calvo, P. Malik, A. Sandoval, D. Barback, C. Orru, C. Standke, H. Thomas, O. Dwyer, C. Pizzo, D. Bapat, J. Soldau, K. Ogawa, R. Riley, M. Nilsson, P. kraus, a. caughey, b. Iliff, J. Esko, J. Vera, D. Sigurdson, C. J. 2023-06-20 doi:10.1101/2023.06.19.545528 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/2023.06.20.545666v1?rss=1 Dayton, H. Kiss, J. Wei, M. Chauhan, S. LaMarre, E. Cornell, W. C. Janakiraman, A. Min, W. Tomer, R. Price-Whelan, A. Nirody, J. A. Dietrich, L. E. 2023-06-20 doi:10.1101/2023.06.20.545666 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ GRAS1 non-coding RNA protects against DNA damage and cell death by binding NKAP ]]> https://biorxiv.org/content/10.1101/2023.06.20.545783v1?rss=1 Su, T. Kong, L. Cheung, D. Zhu, J. Chou, V. W.-H. Camden, N. Huang, C. McHugh, C. A. 2023-06-20 doi:10.1101/2023.06.20.545783 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Hypogonadal (Gnrh1hpg) mice reveal niche-specific influence of reproductive axis and sex on intestinal microbial communities ]]> https://biorxiv.org/content/10.1101/2023.06.20.545808v1?rss=1 Sisk-Hackworth, L. Brown, J. Sau, L. Levine, A. A. Tam, L. Y. I. Ramesh, A. Shah, R. S. Kelley-Thackray, E. T. Wang, S. Nguyen, A. Kelley, S. T. Thackray, V. G. 2023-06-20 doi:10.1101/2023.06.20.545808 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Multimodule imaging of the hierarchical equine hoof wall porosity and structure ]]> https://biorxiv.org/content/10.1101/2023.06.21.545722v1?rss=1 Jasiuk, I. Mahrous, M. A. Chadha, C. Robins, P. L. Bonney, C. Boateng, K. A. Meyers, M. 2023-06-23 doi:10.1101/2023.06.21.545722 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Probing the dissociation pathway of a kinetically labile transthyretin mutant ]]> https://biorxiv.org/content/10.1101/2023.06.21.545798v1?rss=1 Sun, X. Ferguson, J. A. Leach, B. I. Stanfield, R. L. Dyson, H. J. Wright, P. E. 2023-06-22 doi:10.1101/2023.06.21.545798 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Spatial and temporal distribution of ribosomes in single cells reveals aging differences between old and new daughters of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.06.21.545935v1?rss=1 Chao, L. Chen, C. K. Shi, C. Rang, C. U. 2023-06-23 doi:10.1101/2023.06.21.545935 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness ]]> https://biorxiv.org/content/10.1101/2023.06.23.546216v1?rss=1 Leineweber, W. Khalilimeybodi, A. Rangamani, P. Fraley, S. I. 2023-06-26 doi:10.1101/2023.06.23.546216 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Synapsin E-domain is essential for α-synuclein function ]]> https://biorxiv.org/content/10.1101/2023.06.24.546170v1?rss=1 Stavsky, A. Parra-Rivas, L. A. Tal, S. Madhivanan, K. Roy, S. Gitler, D. 2023-06-26 doi:10.1101/2023.06.24.546170 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Immortalization and transformation of primary cells mediated by engineered ecDNAs ]]> https://biorxiv.org/content/10.1101/2023.06.25.546239v1?rss=1 1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs, also known as "double minutes") in a spatiotemporally controlled manner in cancer cell lines and in primary cells derived from genetically engineered mice. With this strategy, ecDNA formation can be coupled with expression of fluorescent reporters or other selectable markers to enable the identification and tracking of ecDNA-containing cells. We demonstrate the feasibility of this approach by engineering MDM2-containing ecDNAs in near-diploid human cells, showing that GFP expression can be used to track ecDNA dynamics under physiological conditions or in the presence of specific selective pressures. We also apply this approach to generate mice harboring inducible Myc- and Mdm2-containing ecDNAs analogous to those spontaneously occurring in human cancers. We show that the engineered ecDNAs rapidly accumulate in primary cells derived from these animals, promoting proliferation, immortalization, and transformation. ]]> Pradella, D. Zhang, M. Gao, R. Melissa, Y. A. Gluchowska, K. M. Cendon Florez, Y. Mishra, T. La Rocca, G. Weigl, M. Jiao, Z. Nguyen, H. H. M. Grimm, F. Lisi, M. Mastroleo, C. Chen, K. Luebeck, J. Bafna, V. Antonescu, C. R. Ventura, A. 2023-06-26 doi:10.1101/2023.06.25.546239 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ A FRET-based excitatory luminopsin with improved efficacy of bioluminescence-driven activation ]]> https://biorxiv.org/content/10.1101/2023.06.26.545546v1?rss=1 Bjorefeldt, A. Murphy, J. Crespo, E. L. Prakash, M. Friedman, N. Brown, T. M. Lipscombe, D. Moore, C. I. Hochgeschwender, U. Shaner, N. C. 2023-06-26 doi:10.1101/2023.06.26.545546 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IkappaBalpha without requiring ATP ]]> https://biorxiv.org/content/10.1101/2023.06.27.546692v1?rss=1 Polley, S. Borar, P. Biswas, T. Huxford, T. Ghosh, G. 2023-06-27 doi:10.1101/2023.06.27.546692 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ RNF185 control of COL3A1 expression limits prostate cancer migration and metastatic potential. ]]> https://biorxiv.org/content/10.1101/2023.06.29.547118v1?rss=1 Van Espen, B. Oo, H. Z. Collins, C. Fazil, L. Molinolo, A. Murad, R. Gleave, M. Ronai, Z. A. 2023-07-01 doi:10.1101/2023.06.29.547118 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2023.06.30.547228v1?rss=1 Ishiwari, K. King, C. P. Martin, C. D. Tripi, J. A. George, A. M. Lamparelli, A. C. Chitre, A. Polesskaya, O. Richards, J. B. Solberg Woods, L. C. Gancarz, A. Palmer, A. A. Dietz, D. M. Mitchell, S. H. Meyer, P. J. 2023-07-03 doi:10.1101/2023.06.30.547228 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Immune-Epithelial Dynamics and Tissue Remodeling in Chronically Inflamed Nasal Epithelium via Multi-scaled Transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.07.01.547352v1?rss=1 Liao, G. Nakayama, T. Lee, I. T. Zhu, B. Overdevest, J. B. Yan, C. H. Zarabanda, D. Gall, P. A. Dholakia, S. S. Borchard, N. A. Yang, A. Kim, D. Bravo, D. T. Patel, Z. M. Hwang, P. H. Wagh, D. Coller, J. Philips, K. Chang, M. T. Lechner, M. Ma, Q. Li, Z. Nolan, G. Barouch, D. Nayak, J. V. Jiang, S. 2023-07-05 doi:10.1101/2023.07.01.547352 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Cognitive rehabilitation can improve brain injury-induced deficits in behavioral flexibility and impulsivity linked to impaired reward-feedback activity. ]]> https://biorxiv.org/content/10.1101/2023.07.02.547397v1?rss=1 Koloski, M. F. O'Hearn, C. M. Frankot, M. Giesler, L. P. Ramanathan, D. S. Vonder Haar, C. 2023-07-02 doi:10.1101/2023.07.02.547397 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Glioblastoma Mesenchymal Transition and Invasion are Dependent on a NF-κB/BRD2 Chromatin Complex ]]> https://biorxiv.org/content/10.1101/2023.07.03.546613v1?rss=1 vadla, r. Miki, S. Taylor, B. Kawauchi, D. Jones, B. M. Nathwani, N. Pham, P. Tsang, J. Nathanson, D. A. Furnari, F. B. 2023-07-03 doi:10.1101/2023.07.03.546613 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Reconstructing the Transcriptional Regulatory Network of Probiotic L. reuteri is Enabled by Transcriptomics and Machine Learning ]]> https://biorxiv.org/content/10.1101/2023.07.03.547516v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@118ec4corg.highwire.dtl.DTLVardef@141b0b7org.highwire.dtl.DTLVardef@1b8cf6forg.highwire.dtl.DTLVardef@3ab181_HPS_FORMAT_FIGEXP M_FIG C_FIG Comprehensive iModulon Workflow Overview. Our innovative workflow is grounded in the analysis of the LactoPRECISE compendium, a curated dataset containing 117 internally sequenced RNA-seq samples derived from a diversity of 50 unique conditions, encompassing an extensive range of 13 distinct condition types. We employ the power of Independent Component Analysis (ICA), a cutting-edge machine learning algorithm, to discern the underlying structure of iModulons within this wealth of data. In the subsequent stage of our workflow, the discovered iModulons undergo detailed scrutiny to uncover media-specific regulatory mechanisms governing metabolism, illuminate the context-dependent intricacies of gene expression, and predict pathways leading to the biosynthesis of probiotic secondary metabolites. Our workflow offers an invaluable and innovative lens through which to view probiotic strain design while simultaneously highlighting transformative approaches to data analytics in the field. ]]> Josephs-Spaulding, J. Rajput, A. Hefner, Y. Szubin, R. Balasubramanian, A. Li, G. Zielinski, D. C. Jahn, L. Sommer, M. Phaneuf, P. Palsson, B. O. 2023-07-03 doi:10.1101/2023.07.03.547516 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Cholinergic stimulation increases cortical spine formation via local inhibitory circuit ]]> https://biorxiv.org/content/10.1101/2023.07.05.547662v1?rss=1 Zhao, X. Zhang, Y. E. Yang, L. Yang, Y. 2023-07-06 doi:10.1101/2023.07.05.547662 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Enhanced cellular longevity arising from environmental fluctuations ]]> https://biorxiv.org/content/10.1101/2023.07.05.547867v1?rss=1 Liu, Y. Zhou, Z. Wu, S. Ni, G. Zhang, A. Tsimring, L. S. Hasty, J. Hao, N. 2023-07-07 doi:10.1101/2023.07.05.547867 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Dimensional and Categorical Solutions to Parsing Depression Heterogeneity in a Large Single-Site Sample ]]> https://biorxiv.org/content/10.1101/2023.07.05.547873v1?rss=1 Dunlop, K. Grosenick, L. Downar, J. Vila-Rodriguez, F. Gunning, F. M. Daskalakis, Z. Blumberger, D. M. Liston, C. 2023-07-07 doi:10.1101/2023.07.05.547873 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from the Marine Cyanobacterium Moorena producens JHB Discovered via Co-culture with Candida albicans ]]> https://biorxiv.org/content/10.1101/2023.07.06.547815v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@1b507d4org.highwire.dtl.DTLVardef@152376org.highwire.dtl.DTLVardef@1cb410dorg.highwire.dtl.DTLVardef@11bcabc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ngo, T.-E. Ecker, A. K. Guild, A. Remmel, A. Boudreau, P. B. Alexander, K. L. Naman, C. B. Glukhov, E. Avalon, N. E. Shende, V. V. Gerwick, L. Gerwick, W. H. 2023-07-06 doi:10.1101/2023.07.06.547815 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Impact of environmental factors on calling behavior in midshipman fish across ocean basins ]]> https://biorxiv.org/content/10.1101/2023.07.11.547287v1?rss=1 Kok, A. Kim, E. B. Rowell, T. J. Margolina, T. Joseph, J. E. Peavey Reeves, L. E. Hatch, L. T. Baumann-Pickering, S. 2023-07-11 doi:10.1101/2023.07.11.547287 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.07.12.548617v1?rss=1 Pekar, J. E. Lytras, S. Ghafari, M. Magee, A. F. Parker, E. Havens, J. L. Katzourakis, A. Vasylyeva, T. I. Suchard, M. A. Hughes, A. C. Hughes, J. Robertson, D. L. Dellicour, S. Worobey, M. Wertheim, J. O. Lemey, P. 2023-07-12 doi:10.1101/2023.07.12.548617 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Ventral pallidum GABA and glutamate neurons drive approach and avoidance through distinct modulation of VTA cell types ]]> https://biorxiv.org/content/10.1101/2023.07.12.548750v1?rss=1 Faget, L. Oriol, L. Lee, W.-C. Sargent, C. Ramanathan, D. Hnasko, T. S. 2023-07-12 doi:10.1101/2023.07.12.548750 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole ]]> https://biorxiv.org/content/10.1101/2023.07.13.548923v1?rss=1 Kim, H. Budin, I. 2023-07-13 doi:10.1101/2023.07.13.548923 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Linear modeling of brain activity during selectiveattention to continuous speech: the critical role of the N1 effect in event-related potentials to acoustic edges ]]> https://biorxiv.org/content/10.1101/2023.07.14.548994v1?rss=1 Mai, A. Hillyard, S. A. Strauss, D. J. 2023-07-16 doi:10.1101/2023.07.14.548994 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ C9orf72 gene networks in the human brain correlate with cortical thickness in C9-FTD and implicate vulnerable cell types ]]> https://biorxiv.org/content/10.1101/2023.07.17.549377v1?rss=1 Broce, I. Sirkis, D. Nillo, R. M. Bonham, L. W. Lee, S. E. Miller, B. L. Sturm, V. Sugrue, L. S. Desikan, R. Yokoyama, J. S. 2023-07-19 doi:10.1101/2023.07.17.549377 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Partitioning variance in cortical morphometry into genetic, environmental, and subject-specific components using a large adolescent sample ]]> https://biorxiv.org/content/10.1101/2023.07.17.549390v1?rss=1 Smith, D. M. Parekh, P. Kennedy, J. Loughnan, R. J. Frei, O. Nichols, T. E. Andreassen, O. A. Jernigan, T. L. Dale, A. M. 2023-07-19 doi:10.1101/2023.07.17.549390 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding ]]> https://biorxiv.org/content/10.1101/2023.07.18.549504v1?rss=1 Chen, Q. Schafer, C. T. Mukherjee, S. Gustavsson, M. Agrawal, P. Yao, X.-Q. Kossiakoff, A. A. Handel, T. Tesmer, J. J. G. 2023-07-19 doi:10.1101/2023.07.18.549504 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ The Brain Electroencephalogram Microdisplay for Precision Neurosurgery ]]> https://biorxiv.org/content/10.1101/2023.07.19.549735v1?rss=1 Tchoe, Y. Wu, T. U, H. S. Roth, D. M. Kim, D. Lee, J. Cleary, D. R. Pizarro, P. Tonsfeldt, K. J. Lee, K. Chen, P. C. Bourhis, A. M. Galton, I. Coughlin, B. Yang, J. C. Paulk, A. C. Halgren, E. Cash, S. S. Dayeh, S. A. 2023-07-21 doi:10.1101/2023.07.19.549735 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data ]]> https://biorxiv.org/content/10.1101/2023.07.20.549584v1?rss=1 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health. ]]> Zuffa, S. Schmid, R. Bauermeister, A. P. Gomes, P. W. Caraballo-Rodriguez, A. M. El Abiead, Y. Aron, A. T. Gentry, E. C. Zemlin, J. Meehan, M. J. Avalon, N. E. Cichewicz, R. H. Buzun, E. Carrillo Terrazas, M. Hsu, C.-Y. Oles, R. Vasquez Ayala, A. Zhao, J. Chu, H. Kuijpers, M. C. M. Jackrel, S. L. Tugizimana, F. Nephali, L. P. Dubery, I. A. Madala, N. E. Moreira, E. A. Costa-Lotufo, L. V. Lopes, N. P. Rezende-Teixeira, P. Jimenez, P. C. Rimal, B. Patterson, A. D. Traxler, M. F. Pessotti, R. d. C. Alvarado-Villalobos, D. Tamayo-Castillo, G. Chaverri, P. Escud 2023-07-20 doi:10.1101/2023.07.20.549584 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Cost-effectiveness of Precision Guided SIT for Control of Anopheles gambiae in the Upper River Region, The Gambia. ]]> https://biorxiv.org/content/10.1101/2023.07.20.549762v1?rss=1 Grendron, W. Raban, R. Mondal, A. Sanchez C., H. M. Smidler, A. Zilberman, D. Ilboudo, P. G. D'Alessandro, U. Marshall, J. M. Akbari, O. 2023-07-22 doi:10.1101/2023.07.20.549762 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ A positive association between gut microbiota diversity and vertebrate host performance in a field experiment ]]> https://biorxiv.org/content/10.1101/2023.07.20.549938v1?rss=1 Härer, A. Thompson, K. A. Schluter, D. Rennison, D. J. 2023-07-20 doi:10.1101/2023.07.20.549938 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Eliminating Malaria Vectors with Precision Guided Sterile Males ]]> https://biorxiv.org/content/10.1101/2023.07.20.549947v1?rss=1 99.5% male-sterility and >99.9% female-lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce population suppression in cage trials, and are predicted to eliminate wild A. gambiae populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, for the first time enabling scalable SIT-like confinable suppression in the species. ]]> Smidler, A. L. Apte, R. A. Pai, J. J. Chow, M. L. Chen, S. Mondal, A. Sanchez C., H. M. Antoshechkin, I. Marshall, J. M. Akbari, O. S. 2023-07-21 doi:10.1101/2023.07.20.549947 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Macrophage Xanthine Oxidoreductase Links LPS Induced Lung Inflammatory Injury to NLRP3 Inflammasome Expression and Mitochondrial Respiration ]]> https://biorxiv.org/content/10.1101/2023.07.21.550055v1?rss=1 Fini, M. A. Monks, J. A. Li, M. Gerasimovskaya, E. Paucek, P. Wang, K. Frid, M. G. Pugliese, S. C. Bratton, D. Yu, Y.-R. Irwin, D. Karin, M. Wright, R. M. Stenmark, K. R. 2023-07-21 doi:10.1101/2023.07.21.550055 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Metabolomic rearrangement controls the intrinsic microbial response to temperature changes ]]> https://biorxiv.org/content/10.1101/2023.07.22.550177v1?rss=1 Knapp, B. Willis, L. Gonzalez, C. Vashistha, H. Touma, J. J. Tikhonov, M. Ram, J. Salman, H. Elias, J. E. Huang, K. C. 2023-07-24 doi:10.1101/2023.07.22.550177 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Shallow networks run deep: Peripheral preprocessing facilitates odor classification ]]> https://biorxiv.org/content/10.1101/2023.07.23.550211v1?rss=1 Puri, P. Wu, S.-T. Su, C.-Y. Aljadeff, J. 2023-07-25 doi:10.1101/2023.07.23.550211 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ A Bayesian Regularized and Anotation-Informed Integrative Analysis of Cognition (BRAINIAC) ]]> https://biorxiv.org/content/10.1101/2023.07.24.550424v1?rss=1 Zablocki, R. Xu, B. Fan, C. Thompson, W. K. 2023-07-26 doi:10.1101/2023.07.24.550424 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Direct reprogramming of oral epithelial progenitor cells to cancer stem cells at single cell resolution in vivo ]]> https://biorxiv.org/content/10.1101/2023.07.24.550427v1?rss=1 Faraji, F. Ramirez, S. I. Clubb, L. Sato, K. Anguiano Quiroz, P. Y. Galloway, W. M. Mikulski, Z. Hoang, T. S. Medetgul-Ernar, K. Marangoni, P. Jones, K. B. Officer, A. Molinolo, A. A. Kim, K. Sakaguchi, K. Califano, J. A. Smith, Q. Klein, O. D. Tamayo, P. Gutkind, J. S. 2023-07-26 doi:10.1101/2023.07.24.550427 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies ]]> https://biorxiv.org/content/10.1101/2023.07.26.550749v1?rss=1 Shi, P. Martino, C. Han, R. Janssen, S. Buck, G. Serrano, M. Owzar, K. Knight, R. Shenhav, L. Zhang, A. R. 2023-07-29 doi:10.1101/2023.07.26.550749 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ The effective number of shared dimensions: A simple method for revealing shared structure between datasets ]]> https://biorxiv.org/content/10.1101/2023.07.27.550815v1?rss=1 Giaffar, H. Rullan Buxo, C. E. Aoi, M. 2023-07-28 doi:10.1101/2023.07.27.550815 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Antagonism of kappa opioid receptors worsens the development of L-DOPA-induced dyskinesia in a preclinical model of moderate dopamine depletion ]]> https://biorxiv.org/content/10.1101/2023.07.31.551112v1?rss=1 Flores, A. J. Bartlett, M. J. Seaton, B. T. Samtani, G. Sexauer, M. R. Weintraub, N. C. Siegenthaler, J. R. Lu, D. Heien, M. L. Porreca, F. Sherman, S. J. Falk, T. 2023-08-01 doi:10.1101/2023.07.31.551112 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ The evolution of borneol repellency in culicine mosquitoes ]]> https://biorxiv.org/content/10.1101/2023.08.01.548337v1?rss=1 Vainer, Y. Wang, Y. Huff, R. M. Ghaninia, M. Coutinho-Abreu, I. Sar-Shalom, E. Perets, D. Yakir, E. Rajamanickam, D. Warburg, A. Papathanos, P. A. Ignell, R. Riffell, J. A. Pitts, J. Bohbot, J. D. 2023-08-03 doi:10.1101/2023.08.01.548337 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Alzheimer's disease linked Aβ42 exerts product feedback inhibition on γsecretase impairing downstream cell signaling ]]> https://biorxiv.org/content/10.1101/2023.08.02.551596v1?rss=1 Zoltowska, K. M. Utpal, D. Lismont, S. Enzlein, T. Maesako, M. Houser, M. C. Gomes Moreira, D. Franco, M. L. Karachentsev, D. Becker, A. Hopf, C. Vilar, M. Berezovska, O. Mobley, W. Chavez-Gutierrez, L. 2023-08-02 doi:10.1101/2023.08.02.551596 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Single-linkage molecular clustering of viral pathogens ]]> https://biorxiv.org/content/10.1101/2023.08.03.551813v1?rss=1 Soto Miranda, M. Narvaez Romo, R. Moshiri, N. 2023-08-04 doi:10.1101/2023.08.03.551813 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme ]]> https://biorxiv.org/content/10.1101/2023.08.03.551874v1?rss=1 Adak, S. Ye, N. Calderone, L. A. Schafer, R. J. B. Lukowski, A. L. Pandelia, M.-E. Drennan, C. L. Moore, B. S. 2023-08-03 doi:10.1101/2023.08.03.551874 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS ]]> https://biorxiv.org/content/10.1101/2023.08.03.551876v1?rss=1 Ozturk, K. Panwala, R. Sheen, J. Ford, K. Payne, N. Zhang, D.-E. Hutter, S. Haferlach, T. Ideker, T. Mali, P. Carter, H. 2023-08-04 doi:10.1101/2023.08.03.551876 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A kinome-wide synthetic lethal CRISPR/Cas9 screen reveals that mTOR inhibition prevents adaptive resistance to CDK4/CDK6 blockade in HNSCC ]]> https://biorxiv.org/content/10.1101/2023.08.07.552216v1?rss=1 Goto, Y. Koshizuka, K. Ando, T. Izumi, H. Wu, X. Ford, K. Feng, X. Wang, Z. Arang, N. Allevato, M. M. Kishore, A. Mali, P. Gutkind, J. S. 2023-08-07 doi:10.1101/2023.08.07.552216 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ A bacterial sialidase mediates early life colonization by a pioneering gut commensal ]]> https://biorxiv.org/content/10.1101/2023.08.08.552477v1?rss=1 Buzun, E. Hsu, C.-Y. Sejane, K. Oles, R. E. Ayala, A. V. Loomis, L. R. Zhao, J. Rossitto, L.-A. McGrosso, D. Gonzalez, D. J. Bode, L. Chu, H. 2023-08-09 doi:10.1101/2023.08.08.552477 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Expansion of a frontostriatal salience network in individuals with depression ]]> https://biorxiv.org/content/10.1101/2023.08.09.551651v1?rss=1 21,000 minutes of fMRI data, we show that the frontostriatal salience network is expanded two-fold in most individuals with depression. This effect was replicable in multiple samples, including large-scale, group-average data (N=1,231 subjects), and caused primarily by network border shifts affecting specific functional systems, with three distinct modes of encroachment occurring in different individuals. Salience network expansion was unexpectedly stable over time, unaffected by changes in mood state, and detectable in children before the subsequent onset of depressive symptoms in adolescence. Longitudinal analyses of individuals scanned up to 62 times over 1.5 years identified connectivity changes in specific frontostriatal circuits that tracked fluctuations in specific symptom domains and predicted future anhedonia symptoms before they emerged. Together, these findings identify a stable trait-like brain network topology that may confer risk for depression and mood-state dependent connectivity changes in frontostriatal circuits that predict the emergence and remission of depressive symptoms over time. ]]> Lynch, C. J. Elbau, I. Ng, T. Ayaz, A. Zhu, S. Manfredi, N. Johnson, M. Wolk, D. Power, J. D. Gordon, E. M. Kay, K. Aloysi, A. Moia, S. Gaudes, C. C. Victoria, L. W. Solomonov, N. Goldwaser, E. Zebley, B. Grosenick, L. Downar, J. Vila-Rodriguez, F. Daskalakis, Z. J. Blumberger, D. M. Williams, N. Gunning, F. Liston, C. 2023-08-14 doi:10.1101/2023.08.09.551651 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Long-Term Exposure of Cells to Cdk4 Inhibitor Palbociclib Leads to Chromosomal Aberrations ]]> https://biorxiv.org/content/10.1101/2023.08.10.552830v1?rss=1 Kaulich, M. F. Dowdy, S. F. 2023-08-11 doi:10.1101/2023.08.10.552830 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ I feel your pain: Higher empathy is associated with higher posterior default mode network activity ]]> https://biorxiv.org/content/10.1101/2023.08.11.553004v1?rss=1 Oliva, V. Riegner, G. Dean, J. Khatib, L. Barrows, D. Chen, C. Mosbey, D. Lopez, C. Uvarova, A. Allen, A. Reyes, M. Fuentes, R. Jacobson, A. Liu, T. Zeidan, F. 2023-08-15 doi:10.1101/2023.08.11.553004 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses ]]> https://biorxiv.org/content/10.1101/2023.08.11.553011v1?rss=1 Lara-Gonzalez, P. Variyar, S. Budrewicz, J. Schlientz, A. Varshney, N. Bellaart, A. Moghareh, S. Nguyen, A. C. N. Oegema, K. Desai, A. 2023-08-12 doi:10.1101/2023.08.11.553011 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation ]]> https://biorxiv.org/content/10.1101/2023.08.11.553017v1?rss=1 Doud, M. B. Gupta, A. Li, V. Medina, S. J. De La Fuente, C. A. Meyer, J. R. 2023-08-14 doi:10.1101/2023.08.11.553017 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Gene editing in the Chagas disease vector Rhodnius prolixus by Cas9-mediated ReMOT Control ]]> https://biorxiv.org/content/10.1101/2023.08.14.553172v1?rss=1 Lima, L. Berni, M. Mota, J. Bressan, D. Julio, A. Cavalcante, R. Macias, V. Li, Z. Rasgon, J. L. Bier, E. Araujo, H. M. 2023-08-15 doi:10.1101/2023.08.14.553172 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5' cap trimethylation ]]> https://biorxiv.org/content/10.1101/2023.08.15.553431v1?rss=1 Ma, T. Xiong, E. S. Lardelli, R. M. Lykke-Anderson, J. 2023-08-17 doi:10.1101/2023.08.15.553431 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Robust and resource-optimal dynamic pattern formation of Min proteins in vivo ]]> https://biorxiv.org/content/10.1101/2023.08.15.553443v1?rss=1 ren, z. Weyer, H. Wurthner, L. Li, D. Sou, C. Villarreal, D. Frey, E. Jun, S. 2023-08-16 doi:10.1101/2023.08.15.553443 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization ]]> https://biorxiv.org/content/10.1101/2023.08.16.553610v1?rss=1 20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts. ]]> Kalhor, K. Chen, C.-j. Lee, H. S. Cai, M. Nafisi, M. Que, R. Yuan, Y. Song, J. Lake, B. Zhang, K. Kharchenko, P. Zhang, Y. Palmer, C. Chun, J. Jain, S. Knoten, A. Gaut, J. Keene, D. Lein, E. Fan, J.-B. 2023-08-18 doi:10.1101/2023.08.16.553610 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Differences in Oligomerization of the SARS-CoV-2 Envelope Protein, Poliovirus VP4, and HIV Vpu ]]> https://biorxiv.org/content/10.1101/2023.08.18.553902v1?rss=1 Townsend, J. A. Fapohunda, O. Wang, Z. Pham, H. Taylor, M. T. Kloss, B. Park, S. H. Opella, S. J. Aspinwall, C. A. Marty, M. T. 2023-08-20 doi:10.1101/2023.08.18.553902 Cold Spring Harbor Laboratory Press 2023-08-20 <![CDATA[ Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms. ]]> https://biorxiv.org/content/10.1101/2023.08.23.554369v1?rss=1 Santos, C. d. Shrestha, S. Cottam, M. A. Perkins, G. Lev-Ram, V. Roy, B. Acree, C. Kim, K.-Y. Deerinck, T. Cutler, M. Dean, D. Cartailler, J. P. MacDonald, P. E. Hetzer, M. W. Ellisman, M. H. Arrojo e Drigo, R. 2023-08-24 doi:10.1101/2023.08.23.554369 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Nitric Oxide modulates spontaneous Ca2+ release and ventricular arrhythmias during β adrenergic signalling through S-nitrosylation of Calcium/Calmodulin dependent kinase II ]]> https://biorxiv.org/content/10.1101/2023.08.23.554546v1?rss=1 Power, A. S. Asamudo, E. Worthington, L. P. Alim, C. C. Parackal, R. Wallace, R. S. Ebenebe, O. V. Heller Brown, J. Kohr, M. J. Bers, D. M. Erickson, J. 2023-08-25 doi:10.1101/2023.08.23.554546 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Where's Whaledo: A software toolkit for array localization of animal vocalizations. ]]> https://biorxiv.org/content/10.1101/2023.08.24.554565v1?rss=1 Snyder, E. R. Solsona-Berga, A. Baumann-Pickering, S. Frasier, K. E. Wiggins, S. M. Hildebrand, J. A. 2023-08-26 doi:10.1101/2023.08.24.554565 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Stratification of enterochromaffin cells by single-cell expression analysis ]]> https://biorxiv.org/content/10.1101/2023.08.24.554649v1?rss=1 Song, Y. Fothergill, L. J. Lee, K. S. Liu, B. Y. Koo, A. Perelis, M. Diwakarla, S. Callaghan, B. Huang, J. Wykosky, J. Furness, J. B. Yeo, G. W. 2023-08-25 doi:10.1101/2023.08.24.554649 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Glycolytic Metabolon Assembly on Mitochondria via Hexokinase O-GlcNAcylation Promotes Metabolic Efficiency ]]> https://biorxiv.org/content/10.1101/2023.08.26.554955v1?rss=1 Wang, H. Vant, J. Wu, Y. Sanchez, R. Micou, M. L. Zhang, A. Luczak, V. Yu, S. B. Jabbo, M. Yoon, S. Abushawish, A. A. Ghassemian, M. Griffis, E. Hammarlund, M. Singharoy, A. Pekkurnaz, G. 2023-08-27 doi:10.1101/2023.08.26.554955 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Spatiotemporal development of growth and death zones in expanding bacterial colonies driven by emergent nutrient dynamics ]]> https://biorxiv.org/content/10.1101/2023.08.27.554977v1?rss=1 Kannan, H. Sun, P. Caglar, T. Yao, P. Taylor, B. R. Sahu, K. Ge, D. Mori, M. Warren, M. Kleinfeld, D. Dong, J. Li, B. Hwa, T. 2023-08-27 doi:10.1101/2023.08.27.554977 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Orthogonal targeting of SAC1 to mitochondria implicates ORP2 as a major player in PM PI4P turnover ]]> https://biorxiv.org/content/10.1101/2023.08.28.555163v1?rss=1 Doyle, C. P. Rectenwald, A. Timple, L. Hammond, G. R. 2023-08-28 doi:10.1101/2023.08.28.555163 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ A systems vaccinology resource to develop and test computational models of immunity ]]> https://biorxiv.org/content/10.1101/2023.08.28.555193v1?rss=1 Shinde, P. Soldevila, F. Reyna, J. Aoki, M. Rasmussen, M. Willemsen, L. Kojima, M. Ha, B. Greenbaum, J. A. Overton, J. A. Guzman-Orozco, H. Nili, S. Orfield, S. Gygi, J. P. Antunes, R. d. S. Sette, A. Grant, B. J. Olsen, L. R. Konstorum, A. Guan, L. Ay, F. Kleinstein, S. H. Peters, B. 2023-08-29 doi:10.1101/2023.08.28.555193 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ A mathematical model for velocity-selective arterial spin labeling ]]> https://biorxiv.org/content/10.1101/2023.08.28.555232v1?rss=1 Liu, T. Wong, E. C. Bolar, D. Chen, C. Barnes, R. 2023-08-31 doi:10.1101/2023.08.28.555232 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Large-scale annotated dataset for cochlear hair cell detection and classification ]]> https://biorxiv.org/content/10.1101/2023.08.30.553559v1?rss=1 Buswinka, C. J. Rosenberg, D. B. Simikyan, R. G. Osgood, R. T. Fernandez, K. Nitta, H. Hayashi, Y. Liberman, L. W. Nguyen, E. Yildiz, E. Kim, J. Jarysta, A. Renauld, J. Wesson, E. Thapa, P. Bordiga, P. McMurtry, N. Llamas, J. Kitcher, S. R. Lopez-Porras, A. I. Cui, R. Behnammanesh, G. Bird, J. E. Ballesteros, A. Velez-Ortega, A. C. Edge, A. S. Deans, M. Gnedeva, K. Shrestha, B. R. Manor, U. Zhao, B. Ricci, A. J. Tarchini, B. Basch, M. Stepanyan, R. S. Landegger, L. D. Rutherford, M. Liberman, M. C. Walters, B. J. Kros, C. Richardson, G. P. Cunningham, L 2023-09-01 doi:10.1101/2023.08.30.553559 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ The CNS Microenvironment Promotes Leukemia Cell Survival by Disrupting Tumor Suppression and Cell Cycle Regulation in Pediatric T-cell Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2023.09.01.555887v1?rss=1 Enlund, S. Sinha, I. Neofytou, C. Ramilo Amor, A. Papadakis, K. Nilsson, A. Jiang, Q. Hermanson, O. Holm, F. 2023-09-05 doi:10.1101/2023.09.01.555887 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Bone Morphogenetic Protein (BMP) signaling upregulates expression of the E protein repressors, ID1 and ID3, in pancreatitis and pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.09.01.555987v1?rss=1 Raghunathan, M. K. Scully, K. M. Wehrmaker, A. Lowy, A. M. DelGiorno, K. E. Itkin-Ansari, P. 2023-09-05 doi:10.1101/2023.09.01.555987 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes ]]> https://biorxiv.org/content/10.1101/2023.09.06.556529v1?rss=1 Xu, J. Casanave, R. Chitre, A. S. Wang, Q. Nguyen, K.-M. Blake, C. Wagle, M. Cheng, R. Polesskaya, O. Palmer, A. A. Guo, S. 2023-09-06 doi:10.1101/2023.09.06.556529 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Converging Topographic Axes of Connectivity and Genetic Architectures Scaffold Cortical Patterning ]]> https://biorxiv.org/content/10.1101/2023.09.06.556618v1?rss=1 Li, D. Ma, L. Wang, Y. Lu, Y. Wang, H. Wang, Y. Gao, C. Cheng, L. Zhang, Y. Yang, Z. Eickhoff, S. Chen, C.-h. Chu, C. Fan, L. 2023-09-09 doi:10.1101/2023.09.06.556618 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Proteome partitioning constraints on long-term laboratory evolution ]]> https://biorxiv.org/content/10.1101/2023.09.08.556843v1?rss=1 Mori, M. Patsalo, V. Williamson, J. R. Scott, M. 2023-09-08 doi:10.1101/2023.09.08.556843 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics ]]> https://biorxiv.org/content/10.1101/2023.09.10.556910v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@ec7a9org.highwire.dtl.DTLVardef@563495org.highwire.dtl.DTLVardef@1965cd7org.highwire.dtl.DTLVardef@a9659d_HPS_FORMAT_FIGEXP M_FIG TOC. Schematic of the three systems used here. (A) 2009-H1N1-ungly is the unglycosylated, single protein NA system. (B) 2009-H1N1-gly is the glycosylated, single protein NA system. (C) 2009-H1N1-vir is the NA in the virion context. C_FIG ]]> Seitz, C. Deveci, I. McCammon, J. A. 2023-09-16 doi:10.1101/2023.09.10.556910 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Improving the discovery of rare variants associated with alcohol problems by leveraging machine learning phenotype prediction and functional information. ]]> https://biorxiv.org/content/10.1101/2023.09.11.557163v1?rss=1 Ahangari, M. Gentry, A. E. Hassan, M. Nguyen, T. H. Kendler, K. S. Bacanu, S.-A. Peterson, R. E. Riley, B. P. Webb, B. T. 2023-09-15 doi:10.1101/2023.09.11.557163 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Inhibiting Stromal Class I HDACs Curbs Pancreatic Cancer Progression ]]> https://biorxiv.org/content/10.1101/2023.09.12.557260v1?rss=1 Liang, G. Oh, T. G. Hah, N. Tiriac, H. Shi, Y. Truitt, M. L. Antal, C. E. Atkins, A. R. Li, Y. Fraser, C. Ng, S. Pinto, A. F. Nelson, D. C. Bashi, S. Banayo, E. Estepa, G. Dai, Y. Liddle, C. Yu, R. T. Hunter, T. Engle, D. Han, H. Von Hoff, D. D. Downes, M. Evans, R. M. 2023-09-14 doi:10.1101/2023.09.12.557260 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A ]]> https://biorxiv.org/content/10.1101/2023.09.12.557419v1?rss=1 Olivieri, C. Wang, Y. Walker, C. Subrahmanian, M. V. Ha, K. N. Bernlohr, D. A. Gao, J. Camilloni, C. Vendruscolo, M. Taylor, S. S. Veglia, G. 2023-09-15 doi:10.1101/2023.09.12.557419 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Self-supervised deep learning uncovers the semantic landscape of drug-induced latent mitochondrial phenotypes ]]> https://biorxiv.org/content/10.1101/2023.09.13.557636v1?rss=1 Natekar, P. Wang, Z. Arora, M. Hakozaki, H. Schoeneberg, J. 2023-09-14 doi:10.1101/2023.09.13.557636 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody ]]> https://biorxiv.org/content/10.1101/2023.09.14.557679v1?rss=1 Phan, T. Zitzmann, C. Chew, K. W. Smith, D. M. Daar, E. S. Wohl, D. A. Eron, J. J. Currier, J. S. Hughes, M. D. Choudhary, M. C. Deo, R. Li, J. Z. Ribeiro, R. M. Ke, R. Perelson, A. S. 2023-09-17 doi:10.1101/2023.09.14.557679 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Using the E. coli Alleleome in Strain Design ]]> https://biorxiv.org/content/10.1101/2023.09.17.558058v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1a8e843org.highwire.dtl.DTLVardef@28a134org.highwire.dtl.DTLVardef@16f6849org.highwire.dtl.DTLVardef@127b43c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phaneuf, P. V. Jarczynska, Z. D. Kandasamy, V. Chauhan, S. M. Feist, A. M. Palsson, B. O. 2023-09-17 doi:10.1101/2023.09.17.558058 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Data-Driven Strain Design Towards Mitigating Biomanufacturing Stresses ]]> https://biorxiv.org/content/10.1101/2023.09.17.558093v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1c8b4f6org.highwire.dtl.DTLVardef@1e08eacorg.highwire.dtl.DTLVardef@1b6fcb7org.highwire.dtl.DTLVardef@89554f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phaneuf, P. V. Kim, S. H. Rychel, K. Rode, C. Beulig, F. Palsson, B. O. Yang, L. 2023-09-18 doi:10.1101/2023.09.17.558093 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi ]]> https://biorxiv.org/content/10.1101/2023.09.18.558157v1?rss=1 Adler, B. A. Al-Shimary, M. J. Patel, J. R. Ambruster, E. Colognori, D. Charles, E. J. Miller, K. V. Lahiri, A. Trinidad, M. Boger, R. Nomburg, J. Beurnier, S. Cui, M. L. Barrangou, R. Mutalik, V. K. Schoeniger, J. S. Pogliano, J. A. Savage, D. F. Doudna, J. A. Cress, B. F. 2023-09-18 doi:10.1101/2023.09.18.558157 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits ]]> https://biorxiv.org/content/10.1101/2023.09.18.558222v1?rss=1 Ardalani, O. Phaneuf, P. V. Mohie, O. S. Nielsen, L. K. Palsson, B. 2023-09-20 doi:10.1101/2023.09.18.558222 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ RATTACA: Genetic predictions in Heterogeneous Stock rats offer a new tool for genetic correlation and experimental design ]]> https://biorxiv.org/content/10.1101/2023.09.18.558279v1?rss=1 Johnson, B. B. Sanches, T. M. Okamoto, M. H. Nguyen, K.-M. Ortez, C. A. Polesskaya, O. Palmer, A. A. 2023-09-19 doi:10.1101/2023.09.18.558279 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Parallel pathways carrying direction and orientation selective retinal signals to layer 4 of mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.18.558281v1?rss=1 Wang, H. Dey, O. Lagos, W. N. Behnam, N. Callaway, E. Stafford, B. 2023-09-18 doi:10.1101/2023.09.18.558281 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Intronic miR342 is a master regulator of cellular glycolysis in Foxp3+ regulatory CD4 T cells ]]> https://biorxiv.org/content/10.1101/2023.09.18.558294v1?rss=1 Yu, R. Li, S. Kim, S. Kim, G. Lu, L.-F. Kim, D. Min, B. 2023-09-22 doi:10.1101/2023.09.18.558294 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Selective capture of circulating metastatic cancer cell clusters from lung cancer patients reveals a unique genomic profile that identifies anti-metastatic molecular therapeutic targets. ]]> https://biorxiv.org/content/10.1101/2023.09.19.558270v1?rss=1 Kouhmareh, K. Martin, E. Finlay, D. Bhadada, A. Hernandez-Vargas, H. Downey, F. Allen, J. K. Teriete, P. 2023-09-22 doi:10.1101/2023.09.19.558270 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation ]]> https://biorxiv.org/content/10.1101/2023.09.19.558457v1?rss=1 70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation. ]]> Baron, M. Tagore, M. Wall, P. Zheng, F. Barkley, D. Yanai, I. Yang, J. Kiuru, M. White, R. Ideker, T. 2023-09-22 doi:10.1101/2023.09.19.558457 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR, ATF3, GATA3, HNF1B, POU2F2, and TFCP2 transcription factors as potential candidates to explain incomplete penetrance ]]> https://biorxiv.org/content/10.1101/2023.09.19.558496v1?rss=1 Leal-Gutierrez, J. D. Munro, D. Chen, D. Cheng, R. Wang, T. Chen, H. Meyer, P. Ishiwari, K. Robinson, T. Rau, C. Garrett, M. 2023-09-19 doi:10.1101/2023.09.19.558496 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection ]]> https://biorxiv.org/content/10.1101/2023.09.20.558163v1?rss=1 Armbruster, E. Lee, J. Hutchings, J. VanderWal, A. Enustun, E. Adler, B. Aindow, A. Deep, A. Rodriguez, Z. Morgan, C. Ghassemian, M. Charles, E. Cress, B. Savage, D. Doudna, J. Pogliano, K. Corbett, K. Villa, E. Pogliano, J. 2023-09-21 doi:10.1101/2023.09.20.558163 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Immunohistochemical and ultrastructural characterization of the inner ear epithelial cells of splitnose rockfish (Sebastes diploproa) ]]> https://biorxiv.org/content/10.1101/2023.09.22.558895v1?rss=1 Kwan, G. T. Prime, K. J. Andrade, L. R. Tresguerres, M. 2023-09-23 doi:10.1101/2023.09.22.558895 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Spine apparatus modulates Ca2+ in spines through spatial localization of sources and sinks ]]> https://biorxiv.org/content/10.1101/2023.09.22.558941v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1a2aa64org.highwire.dtl.DTLVardef@60a7c5org.highwire.dtl.DTLVardef@1a68303org.highwire.dtl.DTLVardef@e3743f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract. Factors governing the dynamics of Ca2+ in dendritic spines include plasma membrane geometry, RyR distribution and ER laminarity. C_FIG ]]> Hernandez Mesa, M. Garcia, G. C. Hoerndli, F. McCabe, K. J. Rangamani, P. 2023-09-22 doi:10.1101/2023.09.22.558941 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Genomic insights into Lactobacillaceae: Analyzing the Alleleome of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants ]]> https://biorxiv.org/content/10.1101/2023.09.22.558971v1?rss=1 Harke, A. S. Josephs-Spaulding, J. Mohite, O. S. Chauhan, S. M. Ardalani, O. Palsson, B. Phaneuf, P. V. 2023-09-22 doi:10.1101/2023.09.22.558971 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ A 3D Printed Ventilated Perfused Lung Model Platform to Dissect the Lung's Response to Viral Infection in the Presence of Respiration ]]> https://biorxiv.org/content/10.1101/2023.09.24.559194v1?rss=1 Derman, I. D. Alioglu, M. A. Banerjee, D. Holton, S. E. Klunk, D. N. Nagamine, M. Rizvi, S. H. A. Mikacenic, C. Celik, N. Castaneda, D. C. Prajakta, W. Chen, P. Schotsaert, M. Peeples, M. E. Palucka, K. Koff, J. Ozbolat, I. T. 2023-09-24 doi:10.1101/2023.09.24.559194 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies ]]> https://biorxiv.org/content/10.1101/2023.09.25.558915v1?rss=1 Medina-Munoz, H. C. Kofman, E. Jagannatha, P. Boyle, E. A. Yu, T. Jones, K. L. Mueller, J. R. Lykins, G. D. Doudna, A. T. Park, S. S. Blue, S. M. Ranzau, B. L. Kohli, R. M. Komor, A. C. Yeo, G. W. 2023-09-25 doi:10.1101/2023.09.25.558915 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Modeling Cardiomyocyte Signaling and Metabolism Predicts Genotype to Phenotype Mechanisms in Hypertrophic Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2023.09.25.559356v1?rss=1 Khalilimeybodi, A. Rangamani, P. 2023-09-26 doi:10.1101/2023.09.25.559356 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Bacterial antiviral defense pathways encode eukaryotic-like ubiquitination systems ]]> https://biorxiv.org/content/10.1101/2023.09.26.559546v1?rss=1 Chambers, L. R. Ye, Q. Cai, J. Gong, M. Ledvina, H. E. Zhou, H. Whiteley, A. T. Suhandynata, R. T. Corbett, K. D. 2023-09-26 doi:10.1101/2023.09.26.559546 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice ]]> https://biorxiv.org/content/10.1101/2023.09.28.558803v1?rss=1 Lee, J. Wellenstein, K. Rahnavard, A. Nelson, A. T. Holter, M. Cummings, B. P. Yeliseyev, V. Castoldi, A. Clish, C. B. Bry, L. Siegel, D. Kahn, B. B. 2023-09-29 doi:10.1101/2023.09.28.558803 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Light management by algal aggregates in living photosynthetic hydrogels. ]]> https://biorxiv.org/content/10.1101/2023.09.28.559714v1?rss=1 Chua, S. T. Smith, A. Murthy, S. Murace, M. Yang, H. Kuhl, M. Cicuta, P. Smith, A. G. Wangpraseurt, D. Vignolini, S. 2023-09-28 doi:10.1101/2023.09.28.559714 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Forward Genetic Stomatal CO2 Response Screen in Grass Brachypodium distachyon Reveals Central Function of a MAP Kinase in Early Stomatal CO2 Signal Transduction ]]> https://biorxiv.org/content/10.1101/2023.09.28.559842v1?rss=1 Lopez, B. N. K. Ceciliato, P. H. O. Rangel, F. Salem, E. Kernig, K. Takahashi, Y. Chow, K. Zhang, L. Sidhom, M. Seitz, C. Sibout, R. Laudencia, D. Woods, D. P. McCammon, J. A. Vogel, J. Schroeder, J. I. 2023-09-29 doi:10.1101/2023.09.28.559842 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ IL-1B-mediated inflammatory signaling drives ineffective erythropoiesis in early-stage myelodysplastic syndromes ]]> https://biorxiv.org/content/10.1101/2023.09.28.560018v1?rss=1 Adema, V. Ganan-Gomez, I. Ma, F. Rodriguez-Sevilla, J. J. Chien, K. Yang, H. Thongon, N. Kanagal-Shamanna, R. Loghavi, S. Montalban-Bravo, G. Hammond, D. Gu, Y. Tan, R. Tan, L. Lorenzi, P. Al-Atrash, G. Clise-Dwyer, K. Bejar, R. Pellegrini, M. Garcia-Manero, G. Colla, S. 2023-09-30 doi:10.1101/2023.09.28.560018 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Antagonists of the stress and opioid systems restore the functional connectivity of the prefrontal cortex during alcohol withdrawal through divergent mechanisms. ]]> https://biorxiv.org/content/10.1101/2023.09.30.560339v1?rss=1 Carrette, L. L. G. Santos, A. Brennan, M. Othman, D. Collazo, A. George, O. 2023-10-02 doi:10.1101/2023.09.30.560339 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria ]]> https://biorxiv.org/content/10.1101/2023.10.01.559299v1?rss=1 Martiniano, R. Haber, M. Almarri, M. A. Mattiangeli, V. Kuijpers, M. C. M. Chamel, B. Breslin, E. M. Littleton, J. Almahari, S. Aloraifi, F. Bradley, D. G. Lombard, P. Durbin, R. 2023-10-01 doi:10.1101/2023.10.01.559299 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Modeling stereospecific drug interactions with beta-adrenergic receptors ]]> https://biorxiv.org/content/10.1101/2023.10.01.560334v1?rss=1 View larger version (82K): org.highwire.dtl.DTLVardef@e8a838org.highwire.dtl.DTLVardef@7c2743org.highwire.dtl.DTLVardef@f5ac43org.highwire.dtl.DTLVardef@100a3d3_HPS_FORMAT_FIGEXP M_FIG Norepinephrine (NE) bound active-state beta-1 adrenergic receptor (1AR) in complex with the stimulatory G protein (Gs) heterotrimer embedded in a lipid bilayer. When expressed at the plasma membrane, the 1AR is oriented such that the ligand binding pocket (*) is accessible to ligands from the extracellular side (Ex.) of the membrane. The Gs (red), G (blue), and G{gamma} (yellow) subunits comprise the Gs heterotrimer. Nucleotides GDP or GTP bind G at the P-loop (**). Inset: Representative image of NE bound within the orthosteric ligand binding pocket. C_FIG ]]> Dawson, J. R. D. DeMarco, K. R. Han, Y. Bekker, S. Clancy, C. E. Yarov-Yarovoy, V. Vorobyov, I. 2023-10-01 doi:10.1101/2023.10.01.560334 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ NanoNERF: A nanoscale NERF blaster replica made of DNA ]]> https://biorxiv.org/content/10.1101/2023.10.02.560388v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1d7619forg.highwire.dtl.DTLVardef@14a16dforg.highwire.dtl.DTLVardef@123b531org.highwire.dtl.DTLVardef@14cb703_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO A nanoscale replica of the NERF Maverick Rev-6 a) Original NERF Maverick Rev-6 toy, b) rendering of the NanoNERF structure in oxView. Gray lines represent individual DNA strands. NanoNERF length: 100 nm; width of barrel: 35 nm; thickness: 2 nm; c) Scan of a NanoNERF blaster acquired in an Atomic Force Microscope. C_FIG ]]> Takiguchi, L. P. Rober, M. B. Olvera, J. G. Shipley, W. Wacker, A. L. Fantasia, R. J. Liu, B. Kosuri, P. 2023-10-03 doi:10.1101/2023.10.02.560388 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Alterations in DNA 5-hydroxymethylation Patterns in the Hippocampus of an Experimental Model of Refractory Epilepsy ]]> https://biorxiv.org/content/10.1101/2023.10.03.560698v1?rss=1 Bahabry, R. Hauser, R. M. Sanchez, R. Sint Jago, S. Ianov, L. Stuckey, R. Parrish, R. Ver Hoef, L. Lubin, F. 2023-10-05 doi:10.1101/2023.10.03.560698 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ A dual-pathway architecture enables chronic stress to promote habit formation ]]> https://biorxiv.org/content/10.1101/2023.10.03.560731v1?rss=1 Giovanniello, J. R. Paredes, N. Wiener, A. Ramirez-Armenta, K. Oragwam, C. Uwadia, H. O. Lim, K. Nnamdi, G. Wang, A. Sehgal, M. Reis, F. M. Sias, A. C. Silva, A. J. Adhikari, A. Malvaez, M. Wassum, K. M. 2023-10-03 doi:10.1101/2023.10.03.560731 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Localized synthesis of molecular chaperones sustains neuronal proteostasis ]]> https://biorxiv.org/content/10.1101/2023.10.03.560761v1?rss=1 Alecki, C. Rizwan, J. Le, P. Jacob-Tomas, S. Xu, J. S. M. Minotti, S. Wu, T. Durham, H. Yeo, G. W. Vera, M. 2023-10-03 doi:10.1101/2023.10.03.560761 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Analysis of the Diverse Antigenic Landscape of the Malaria Invasion Protein RH5 Identifies a Potent Vaccine-Induced Human Public Antibody Clonotype ]]> https://biorxiv.org/content/10.1101/2023.10.04.560576v1?rss=1 Barrett, J. R. Pipini, D. Wright, N. D. Cooper, A. J. R. Gorini, G. Quinkert, D. Lias, A. M. Davies, H. Rigby, C. Aleshnick, M. Williams, B. G. Bradshaw, W. J. Paterson, N. G. Martinson, T. Kirtley, P. Picard, L. Wiggins, C. D. Donnellan, F. R. King, L. D. W. Wang, L. T. Popplewell, J. F. Silk, S. E. Swain, J. d. R. Skinner, K. Kotraiah, V. Noe, A. R. MacGill, R. S. King, C. R. Birkett, A. J. Soisson, L. A. Minassian, A. M. Lauffenburger, D. A. Miura, K. Long, C. A. Wilder, B. K. Koekemoer, L. Tan, J. Nielsen, C. M. McHugh, K. Draper, S. J. 2023-10-04 doi:10.1101/2023.10.04.560576 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5 ]]> https://biorxiv.org/content/10.1101/2023.10.04.560669v1?rss=1 Wang, L. T. Cooper, A. J. R. Farrell, B. Miura, K. Diouf, A. Muller-Sienerth, N. Crosnier, C. Purser, L. Maciuszek, M. Barrett, J. R. McHugh, K. Tucker, C. Li, S. Doumbo, S. Doumtabe, D. Pyo, C.-W. Nielsen, C. M. Silk, S. E. Kayentao, K. Ongoiba, A. Zhao, M. Nguyen, D. C. Lee, F. E.-H. Minassian, A. M. Geraghty, D. E. Traore, B. Seder, R. A. Crompton, P. D. Wright, G. J. Long, C. A. Draper, S. J. Higgins, M. K. Tan, J. 2023-10-06 doi:10.1101/2023.10.04.560669 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Chimpanzees and bonobos reinstate an interrupted triadic game ]]> https://biorxiv.org/content/10.1101/2023.10.05.560857v1?rss=1 60% of subjects on first trial), with no group differences in the way of reengagement. Infant bonobos rarely reengaged and never did so on their first trial. Importantly, when infants reengaged passive partners, they mostly deployed (tactile) signals, yet rarely game-related behaviours (GRBs) as commonly observed in adults. These findings might explain negative results of earlier research. Bonobos and chimpanzees may thus have motivational foundations for joint commitment, although this capacity might develop over lifetime. We discuss this finding in relation to evolutionary and developmental theories on joint commitment. ]]> Heesen, R. Bangerter, A. Zuberbuhler, K. Iglesias, K. Rossano, F. Guery, J.-P. Genty, E. 2023-10-06 doi:10.1101/2023.10.05.560857 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Improving vocal communication with a ketogenic diet in a mouse model of autism ]]> https://biorxiv.org/content/10.1101/2023.10.05.561083v1?rss=1 Möhrle, D. Murari, K. Rho, J. M. Cheng, N. 2023-10-05 doi:10.1101/2023.10.05.561083 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Cellular Calcium Activity at Depth Predicted from Surface Potential Recordings using Ultra-high Density Transparent Graphene Arrays ]]> https://biorxiv.org/content/10.1101/2023.10.05.561133v1?rss=1 Ramezani, M. Kim, J.-H. Liu, X. Ren, C. Alothman, A. De- Eknamkul, C. Wilson, M. Cubukcu, E. Gilja, V. Komiyama, T. Kuzum, D. 2023-10-08 doi:10.1101/2023.10.05.561133 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ LRP1 and p75 Neurotrophin Receptor Collaborate to Trigger Pro-inflammatory Cell-signaling in Response to Extracellular Tau ]]> https://biorxiv.org/content/10.1101/2023.10.06.561299v1?rss=1 Mantuano, E. Azmoon, P. Poudel, B. Zampieri, C. Gonias, S. L. 2023-10-07 doi:10.1101/2023.10.06.561299 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ A model of marmoset monkey vocal turn-taking ]]> https://biorxiv.org/content/10.1101/2023.10.07.561358v1?rss=1 Grijseels, D. Fairbank, D. Miller, C. 2023-10-07 doi:10.1101/2023.10.07.561358 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Computational modeling establishes mechanotransduction as a potent entrainment cue for the mammalian circadian clock ]]> https://biorxiv.org/content/10.1101/2023.10.09.561563v1?rss=1 Francis, E. A. Rangamani, P. 2023-10-10 doi:10.1101/2023.10.09.561563 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Biocomposite Thermoplastic Polyurethanes Containing Evolved Bacterial Spores as Living Fillers to Facilitate Polymer Disintegration ]]> https://biorxiv.org/content/10.1101/2023.10.10.561602v1?rss=1 Kim, H. S. Noh, M. H. White, E. M. Kandefer, M. V. Wright, A. F. Datta, D. Lim, H. G. Smiggs, E. Locklin, J. J. Rahman, M. A. Feist, A. M. Pokorski, J. K. 2023-10-12 doi:10.1101/2023.10.10.561602 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Substructure of the brain's Cingulo-Opercular network ]]> https://biorxiv.org/content/10.1101/2023.10.10.561772v1?rss=1 5 hours of resting state functional connectivity (RSFC) and task data, we identified three anatomically and functionally distinct CON subnetworks within each individual. These three distinct subnetworks were linked to Decisions, Actions, and Feedback (including pain processing), respectively, in convergence with a meta-analytic task database. These Decision, Action and Feedback subnetworks represent pathways by which the brain establishes top-down goals, transforms those goals into actions, implemented as movements, and processes critical action feedback such as pain. ]]> D'Andrea, C. B. Laumann, T. O. Newbold, D. J. Nelson, S. M. Nielsen, A. N. Chauvin, R. Marek, S. Greene, D. J. Dosenbach, N. U. F. Gordon, E. M. 2023-10-10 doi:10.1101/2023.10.10.561772 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ FluxNorm: Toolbox for metabolic flux assay normalization by in situ cell counting ]]> https://biorxiv.org/content/10.1101/2023.10.13.562314v1?rss=1 Djaja, N. A. Bracha, T. Yu, S. B. Wang, H. Carlson, N. M. Pekkurnaz, G. 2023-10-14 doi:10.1101/2023.10.13.562314 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Epigenome erosion in Alzheimer's disease brain cells and induced neurons ]]> https://biorxiv.org/content/10.1101/2023.10.15.562394v1?rss=1 Ecker, J. R. Gage, F. H. Wang, B. Jones, J. Zhou, J. Tian, W. Wu, Y. Wang, W. Berube, P. Bartlett, A. Castanon, R. G. Nery, J. R. Chen, H. Kenworthy, M. Altshul, J. Valadon, C. Wang, Y. Kang, A. Goodman, R. Liem, M. Claffey, N. O'Connor, C. Metcalf, J. Luo, C. 2023-10-18 doi:10.1101/2023.10.15.562394 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Recruitment limitation increases susceptibility to fishing-induced collapse in a spawning aggregation fishery ]]> https://biorxiv.org/content/10.1101/2023.10.16.562228v1?rss=1 Mason, E. T. J. Riecke, T. V. Bellquist, L. F. Pondella, D. J. Semmens, B. X. 2023-10-19 doi:10.1101/2023.10.16.562228 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Restoring AIBP deficiency in the retina provides neuroprotection in glaucoma ]]> https://biorxiv.org/content/10.1101/2023.10.16.562633v1?rss=1 Ju, W.-K. Ha, Y. Choi, S. Kim, K.-Y. Bastola, T. Kim, J. Weinreb, R. N. Zhang, W. Miller, Y. I. Choi, S.-H. 2023-10-17 doi:10.1101/2023.10.16.562633 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Trophic Efficiency Facilitates Larval Shortbelly Rockfish (Sebastes jordani) Development ]]> https://biorxiv.org/content/10.1101/2023.10.18.562988v1?rss=1 Kwan, G. T. Walsh, K. A. Thompson, A. R. Ben-Aderet, N. J. Fennie, H. W. Semmens, B. X. Swalethorp, R. 2023-10-21 doi:10.1101/2023.10.18.562988 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones ]]> https://biorxiv.org/content/10.1101/2023.10.19.562961v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1c1f554org.highwire.dtl.DTLVardef@d16b02org.highwire.dtl.DTLVardef@c856e1org.highwire.dtl.DTLVardef@bfd248_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Thukral, M. Aron, A. T. Rabines, A. J. Petras, D. Preston, C. M. Zheng, H. Fussy, Z. James, C. Ussler, W. Lucas, A. J. Anderson, C. R. Scholin, C. A. Dorrestein, P. C. Ryan, J. P. Allen, A. E. 2023-10-20 doi:10.1101/2023.10.19.562961 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study ]]> https://biorxiv.org/content/10.1101/2023.10.21.562994v1?rss=1 Kerestes, R. Perry, A. Vivash, L. O'Brien, T. Alvim, M. K. M. Arienzo, D. Aventurato, I. K. Ballerini, A. Baltazar, G. F. Bargallo, N. Bender, B. Brioschi, R. Bürkle, E. Caligiuri, M. E. Cendes, F. de Tisi, J. Duncan, J. S. Engel, J. P. Foley, S. Fortunato, F. Gambardella, A. Giacomini, T. Guerrini, R. Hall, G. Hamandi, K. Ives-Deliperi, V. Joao, R. B. Keller, S. S. Kleiser, B. Labate, A. Lenge, M. Marotta, C. Martin, P. Mascalchi, M. Meletti, S. Owens-Walton, C. Parodi, C. b. Pascual-Diaz, S. Powell, D. Rao, J. Rebsamen, M. Reiter, J. Riva, A. Rüeb 2023-10-23 doi:10.1101/2023.10.21.562994 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Effect of Human Infant Gut Microbiota on Mouse Behavior, Dendritic Complexity, and Myelination ]]> https://biorxiv.org/content/10.1101/2023.10.24.563309v1?rss=1 DUBEY, H. Roychoudhury, R. Alex, A. Best, C. Liu, S. White, A. Carlson, A. Azcarate-Peril, M. A. Mansfield, L. Knickmeyer, R. C. 2023-10-27 doi:10.1101/2023.10.24.563309 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers ]]> https://biorxiv.org/content/10.1101/2023.10.24.563645v1?rss=1 Mu, P. Xu, Y. Wang, Z. Sjostrom, M. Deng, S. Wang, C. Jonhson, N. Gonzalez, J. Li, X. Metang, L. Rodriguez, C. Mukherji, A. Wainwright, G. Yu, X. Yang, Y. Barnes, S. Hofstad, M. Zhu, H. Hanker, A. He, H. Chen, Y. Wang, Z. Raj, G. Arteaga, C. Feng, F. Wang, Y. Wang, T. 2023-10-27 doi:10.1101/2023.10.24.563645 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Development of neural circuits for social motion perception in schooling fish ]]> https://biorxiv.org/content/10.1101/2023.10.25.563839v1?rss=1 Zada, D. Schulze, L. Yu, J.-H. Tarabishi, P. Napoli, J. L. Lovett-Barron, M. 2023-10-27 doi:10.1101/2023.10.25.563839 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Nuclear Pyruvate Dehydrogenase Complex Regulates Histone Acetylation and Transcriptional Regulation in the Ethylene Response ]]> https://biorxiv.org/content/10.1101/2023.10.25.564010v1?rss=1 Shao, Z. Bian, L. Ahmadi, S. K. Daniel, T. J. Belmonte, M. A. Burns, J. G. Kotla, P. Bi, Y. Shen, Z. Xu, S.-L. Wang, Z.-Y. Briggs, S. P. Qiao, H. 2023-10-27 doi:10.1101/2023.10.25.564010 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.10.25.564014v1?rss=1 Ramirez, S. I. Lopez, P. G. Faraji, F. Parikh, U. M. Heaps, A. Ritz, J. Moser, C. Eron, J. J. Wohl, D. A. Currier, J. S. Daar, E. S. Greninger, A. L. Klekotka, P. Grifoni, A. Weiskopf, D. Sette, A. Peters, B. Hughes, M. D. Chew, K. W. Smith, D. M. Crotty, S. ACTIV-2/A5401 Study Team, 2023-10-26 doi:10.1101/2023.10.25.564014 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ A glycolytic metabolite restores DNA repair activity of polynucleotide kinase 3-phosphatase in polyglutamine (PolyQ) diseases ]]> https://biorxiv.org/content/10.1101/2023.10.26.564220v1?rss=1 CHAKRABORTY, A. Miller, W. Huai, W. Biswas, T. Mandal, S. M. Bosca, L. Ghosh, G. Hazra, T. 2023-10-26 doi:10.1101/2023.10.26.564220 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes ]]> https://biorxiv.org/content/10.1101/2023.10.26.564281v1?rss=1 Miller, E. C. Faucher, R. Hart, P. B. Rincon-Sandoval, M. Santaquiteria, A. White, W. T. Baldwin, C. C. Miya, M. Betancur-R, R. Tornabene, L. Evans, K. Arcila, D. 2023-10-30 doi:10.1101/2023.10.26.564281 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Medial temporal lobe functional network architecture supports sleep-related emotional memory processing in older adults ]]> https://biorxiv.org/content/10.1101/2023.10.27.564260v1?rss=1 Chappel-Farley, M. G. Adams, J. N. Betzel, R. N. Janecek, J. C. Sattari, N. S. Berisha, D. E. Meza, N. J. Niknazar, H. Kim, S. Dave, A. Chen, I. Y. Lui, K. K. Neikrug, A. B. Benca, R. M. Yassa, M. A. Mander, B. A. 2023-11-01 doi:10.1101/2023.10.27.564260 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Reliability of high-quantity human brain organoids for modeling microcephaly, glioma invasion, and drug screening ]]> https://biorxiv.org/content/10.1101/2023.10.29.564523v1?rss=1 Ramani, A. Pasquini, G. Gerkau, N. Vinchure, O. S. Gabriel, E. Rothenaigner, I. Lin, S. Altinisk, N. Rathinam, D. Mirsaidi, A. Goureau, O. Ricci-Vitiani, L. Q. d'alessandris, G. Pallini, R. Wollnik, B. Muotri, A. Jurisch-Yaksi, N. Rose, C. R. Busskamp, V. Hadian, K. Gopalakrishnan, J. 2023-10-30 doi:10.1101/2023.10.29.564523 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ A Neanderthal Origin of Genetic Variants Associated with Asthma ]]> https://biorxiv.org/content/10.1101/2023.10.30.564624v1?rss=1 Day, A. S. H. Gaulton, K. J. 2023-11-02 doi:10.1101/2023.10.30.564624 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Deep Phenotyping of Sleep in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.10.30.564733v1?rss=1 Keles, M. F. Sapcı, A. O. B. Brody, C. Palmer, I. Le, C. Tastan, O. Keles, S. Wu, M. 2023-11-02 doi:10.1101/2023.10.30.564733 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models ]]> https://biorxiv.org/content/10.1101/2023.10.31.564882v1?rss=1 Shao, Y. Magee, A. F. Vasylyeva, T. I. Suchard, M. A. 2023-11-02 doi:10.1101/2023.10.31.564882 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Distinct Activation Mechanisms of CXCR4 and ACKR3 Revealed by Single-Molecule Analysis of their Conformational Landscapes ]]> https://biorxiv.org/content/10.1101/2023.10.31.564925v1?rss=1 Schafer, C. T. Pauszek, R. F. Gustavsson, M. Handel, T. M. Millar, D. P. 2023-11-02 doi:10.1101/2023.10.31.564925 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome. ]]> https://biorxiv.org/content/10.1101/2023.10.31.564956v1?rss=1 Tsukuda, S. Harris, J. Magri, A. Balfe, P. Wing, P. A. Siddiqui, A. McKeating, J. 2023-11-01 doi:10.1101/2023.10.31.564956 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. ]]> https://biorxiv.org/content/10.1101/2023.10.31.565004v1?rss=1 Nguyen, T. B. Miramontes, R. Chillon-Marinas, C. Maimon, R. Vazquez-Sanchez, S. Lau, A. L. McClure, N. R. England, W. E. Singha, M. Stocksdale, J. T. Jang, K.-H. Jung, S. McKnight, J. I. Ho, L. N. Faull, R. L. M. Steffan, J. S. Reidling, J. C. Jang, C. Lee, G. Cleveland, D. W. Lagier-Tourenne, C. Spitale, R. C. Thompson, L. M. 2023-11-02 doi:10.1101/2023.10.31.565004 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Resting state global brain activity induces bias in fMRI motion estimates ]]> https://biorxiv.org/content/10.1101/2023.10.31.565023v1?rss=1 Mao, Y. Chen, C. Nguyen, T. Liu, T. 2023-11-02 doi:10.1101/2023.10.31.565023 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ TPXL-1 Activates Aurora A to Clear Contractile Ring Components from the Polar Cortex During Cytokinesis ]]> https://biorxiv.org/content/10.1101/202895v1?rss=1 Mangal, S. Sacher, J. Kim, T. Osorio, D. S. Motegi, F. Carvalho, A. X. Oegema, K. Zanin, E. 2017-10-13 doi:10.1101/202895 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Antagonism in olfactory receptor neurons and its implications for the perception of odor mixtures ]]> https://biorxiv.org/content/10.1101/204354v1?rss=1 Reddy, G. Zak, J. Vergassola, M. Murthy, V. N. 2017-10-16 doi:10.1101/204354 Cold Spring Harbor Laboratory Press 2017-10-16 <![CDATA[ A simple, consistent estimator of heritability for genome-wide association studies ]]> https://biorxiv.org/content/10.1101/204446v1?rss=1 Schwartzman, A. Schork, A. J. Zablocki, R. Thompson, W. K. 2017-10-17 doi:10.1101/204446 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Juicebox.js provides a cloud-based visualization system for Hi-C data ]]> https://biorxiv.org/content/10.1101/205740v1?rss=1 Robinson, J. Turner, D. Durand, N. C. Thorvaldsdottir, H. Mesirov, J. P. Aiden, E. L. 2017-10-19 doi:10.1101/205740 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Normative Brain Size Variation and the Remodeling of Brain Shape in Humans ]]> https://biorxiv.org/content/10.1101/205930v1?rss=1 Reardon, P. K. Vandekar, S. N. Liu, S. Patel, R. Park, M. T. M. Alexander-Bloch, A. Seidlitz, J. Clasen, L. S. Blumenthal, J. D. Giedd, J. N. Gur, R. C. Gur, R. E. Lerch, J. P. Chakravarty, M. M. Satterthwaite, T. D. Shinohara, R. T. Raznahan, A. 2017-10-19 doi:10.1101/205930 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Learning-induced sequence reactivation during sharp-wave ripples: a computational study ]]> https://biorxiv.org/content/10.1101/207894v1?rss=1 Malerba, P. Tsimring, K. Bazhenov, M. 2017-10-23 doi:10.1101/207894 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Germline determinants of the somatic mutation landscape in 2,642 cancer genomes ]]> https://biorxiv.org/content/10.1101/208330v1?rss=1 T mutagenesis at CpG dinucleotides, a ubiquitous mutational process acting across tissues. Analysis of somatic structural variation exposed complex rearrangement patterns, involving cycles of templated insertions and tandem duplications, in BRCA1-deficient tumours. Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer types. We further inferred over a hundred polymorphic L1/LINE elements with somatic retrotransposition activity in cancer. Our study highlights the major impact of rare and common germline variants on mutational landscapes in cancer. ]]> Waszak, S. M. Tiao, G. Zhu, B. Rausch, T. Muyas, F. Rodriguez-Martin, B. Rabionet, R. Yakneen, S. Escaramis, G. Li, Y. Saini, N. Roberts, S. A. Demidov, G. M. Pitkanen, E. Delaneau, O. Heredia-Genestar, J. M. Weischenfeldt, J. Shringarpure, S. S. Chen, J. Nakagawa, H. Alexandrov, L. B. Drechsel, O. Dursi, L. J. Segre, A. V. Garrison, E. Erkek, S. Habermann, N. Urban, L. Khurana, E. Cafferkey, A. Hayashi, S. Imoto, S. Aaltonen, L. A. Alvarez, E. G. Baez-Ortega, A. Bailey, M. Bosio, M. Bruzos, A. L. Buchhalter, I. Bustamante, C. D. Calabrese, C. DiBiase, 2017-11-01 doi:10.1101/208330 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ N-acetyl-2-aminofluorene (AAF) processing in adult rat hepatocytes in primary culture occurs by high-affinity low-velocity and low-affinity high-velocity AAF metabolite-forming systems ]]> https://biorxiv.org/content/10.1101/209072v1?rss=1 7-OH-AAF > 3-OH-AAF > N-OH-AAF > aminofluorene (AF) > 1-OH-AAF. Lineweaver-Burk analyses revealed two principal classes of metabolism: System I (high-affinity and low-velocity), Km[APPARENT] = 1.64 x 10-7 M and VMAX[APPARENT] = 0.1 nmols/106 cells/day; and, System II (low-affinity and high-velocity), Km[APPARENT] = 3.25 x 10-5 M and VMAX[APPARENT] = 1000 nmols/106 cells/day. A third system of metabolism of AAF to AF, with Km[APPARENT] and VMAX[APPARENT] constants of 9.6 x 10-5 M and 4.7 nmols/106 cells/day, was also observed. Evidence provided in this report and its companion paper suggests selective roles and intracellular locations for System I- and System II-mediated AAF metabolite formation during hepatocarcinogenesis, although some of the molecules and mechanisms responsible for multi-system processing remain to be fully defined. ]]> Koch, K. S. Moran, T. Shier, W. T. Leffert, H. L. 2017-10-26 doi:10.1101/209072 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ High-affinity low-capacity and low-affinity high-capacity N-acetyl-2-aminofluorene (AAF) macromolecular binding sites are revealed during the growth cycle of adult rat hepatocytes in primary culture ]]> https://biorxiv.org/content/10.1101/209130v1?rss=1 Koch, K. S. Moran, T. Shier, W. T. T. Leffert, H. L. 2017-10-26 doi:10.1101/209130 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Nuclear Abl Drives Extracellular-Vesicle Transfer of miR-34c to Induce Bystander Effects of Radiation ]]> https://biorxiv.org/content/10.1101/209767v1?rss=1 Rastogi, S. Hwang, A. Chan, J. Wang, J. Y. 2017-10-26 doi:10.1101/209767 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ In vivo RNA targeting of point mutations via suppressor tRNAs and adenosine deaminases ]]> https://biorxiv.org/content/10.1101/210278v1?rss=1 Katrekar, D. Mali, P. 2017-10-27 doi:10.1101/210278 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Accounting for Apparent Deviations between Calorimetric and van’t Hoff Enthalpies ]]> https://biorxiv.org/content/10.1101/210351v1?rss=1 Kantonen, S. A. Henriksen, N. M. Gilson, M. K. 2017-10-27 doi:10.1101/210351 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Sharing genetic admixture and diversity of public biomedical datasets ]]> https://biorxiv.org/content/10.1101/210716v1?rss=1 Harismendy, O. Kim, J. Xu, X. Ohno-Machado, L. 2017-10-28 doi:10.1101/210716 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Bayesian estimation of MSM population size in Côte d’Ivoire ]]> https://biorxiv.org/content/10.1101/213926v1?rss=1 Datta, A. Lin, W. Rao, A. Diouf, D. Kouame, A. Edwards, J. K. Bao, L. Louis, T. A. Baral, S. 2017-11-10 doi:10.1101/213926 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB. ]]> https://biorxiv.org/content/10.1101/219006v1?rss=1 Santos-Zavaleta, A. Sanchez-Perez, M. Salgado, H. Velazquez-Ramirez, D. A. Gama-Castro, S. Tierrafria, V. H. Busby, S. Fang, X. Palsson, B. Galagan, J. Collado-Vides, J. 2017-11-13 doi:10.1101/219006 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Heterogeneous origins of human sleep spindles in different cortical layers ]]> https://biorxiv.org/content/10.1101/221234v1?rss=1 Donald J Hagler Istvan Ulbert Lucia Wittner Lorand Eross Joseph R Madsen Orrin Devinsky Werner Doyle Daniel Fabo Sydney S Cash Eric Halgren 2017-11-17 doi:10.1101/221234 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Replay of large-scale spatio-temporal patterns from waking during subsequent slow-wave sleep in human cortex ]]> https://biorxiv.org/content/10.1101/221275v1?rss=1 Jiang, X. Shamie, I. Doyle, W. Friedman, D. Dugan, P. Devinsky, O. Eskandar, E. Cash, S. S. Thesen, T. Halgren, E. 2017-11-17 doi:10.1101/221275 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Targeted Genotyping of Variable Number Tandem Repeats with adVNTR ]]> https://biorxiv.org/content/10.1101/221754v1?rss=1 Bakhtiari, M. Shleizer-Burko, S. Gymrek, M. Bansal, V. Bafna, V. 2017-11-18 doi:10.1101/221754 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ DDX3 is exploited by Arenaviruses to suppress type I interferons and favor their replication ]]> https://biorxiv.org/content/10.1101/224725v1?rss=1 Loureiro, M. E. Zorzetto-Fernandes, A. L. Radoshitzky, S. Chi, X. Dallari, S. Marooki, N. Leger, P. Foscaldi, S. Sharma, S. Lopez, N. de la Torre, J. C. Bavari, S. Zuniga, E. 2017-11-25 doi:10.1101/224725 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ Solubilization kinetics determines the pulsatory dynamics of lipid vesicles exposed to surfactant ]]> https://biorxiv.org/content/10.1101/225946v1?rss=1 Chabanon, M. Rangamani, P. 2018-02-01 doi:10.1101/225946 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ The promiscuous estrogen receptor: evolution of physiological estrogens and response to phytochemicals and endocrine disruptors ]]> https://biorxiv.org/content/10.1101/228064v1?rss=1 Baker, M. E. Lathe, R. 2017-12-04 doi:10.1101/228064 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Inhibition of Glyoxalase 1 reduces alcohol self-administration in dependent and nondependent rats ]]> https://biorxiv.org/content/10.1101/230995v1?rss=1 de Guglielmo, G. Conlisk, D. Barkley-Levenson, A. Palmer, A. George, O. 2017-12-08 doi:10.1101/230995 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Predictions of Protein-Protein Interactions in Schistosoma Mansoni ]]> https://biorxiv.org/content/10.1101/233072v1?rss=1 White Bear, J. Barkan, D. T. Davis, F. P. Sali, A. 2017-12-12 doi:10.1101/233072 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ Template-based prediction of vigilance fluctuations in resting-state fMRI ]]> https://biorxiv.org/content/10.1101/234179v1?rss=1 Falahpour, M. Chang, C. Wong, C. W. Liu, T. 2017-12-14 doi:10.1101/234179 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Genome-wide association analysis of lifetime cannabis use (N=184,765) identifies new risk loci, genetic overlap with mental health, and a causal influence of schizophrenia on cannabis use ]]> https://biorxiv.org/content/10.1101/234294v1?rss=1 Pasman, J. A. Verweij, K. J. H. Gerring, Z. Stringer, S. Sanchez-Roige, S. Treur, J. L. Abdellaoui, A. Nivard, M. G. Baselmans, B. M. L. Ong, J.-S. Ip, H. F. van der Zee, M. D. Bartels, M. Day, F. R. Fontanillas, P. Elson, S. L. the 23andMe Research Team, de Wit, H. Davis, L. K. MacKillop, J. International Cannabis Consortium, Derringer, J. L. Branje, S. J. T. Hartman, C. A. Heath, A. C. van Lier, P. A. C. Madden, P. A. F. Magi, R. Meeus, W. Montgomery, G. W. Oldehinkel, A. J. Pausova, Z. Ramos-Quiroga, J. A. Paus, T. Ribases, M. Kaprio, J. Boks, M. P. M 2018-01-08 doi:10.1101/234294 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Glyoxalase (GLO1) inhibition or genetic overexpression does not alter ethanol locomotor effects: implications for GLO1 as a therapeutic target in alcohol use disorders ]]> https://biorxiv.org/content/10.1101/239624v1?rss=1 Barkley-Levenson, A. M. Lagarda, F. A. Palmer, A. A. 2017-12-25 doi:10.1101/239624 Cold Spring Harbor Laboratory Press 2017-12-25 <![CDATA[ An ordered pattern of Ana2 phosphorylation by Plk4 is required for centriole assembly ]]> https://biorxiv.org/content/10.1101/240374v1?rss=1 McLamarrah, T. A. Buster, D. W. Galletta, B. J. Boese, C. J. Ryniawec, J. M. Hollingsworth, N. A. Byrnes, A. E. Brownlee, C. W. Slep, K. C. Rusan, N. M. Rogers, G. C. 2017-12-28 doi:10.1101/240374 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control ]]> https://biorxiv.org/content/10.1101/240747v1?rss=1 Matthews, B. J. Dudchenko, O. Kingan, S. Koren, S. Antoshechkin, I. Crawford, J. E. Glassford, W. J. Herre, M. Redmond, S. N. Rose, N. H. Weedall, G. D. Wu, Y. Batra, S. S. Brito-Sierra, C. A. Buckingham, S. D. Campbell, C. L. Chan, S. Cox, E. Evans, B. R. Fansiri, T. Filipovic, I. Fontaine, A. Gloria-Soria, A. Hall, R. Joardar, V. S. Jones, A. K. Kay, R. G. G. Kodali, V. Lee, J. Lycett, G. J. Mitchell, S. N. Muehling, J. Murphy, M. R. Omer, A. Partridge, F. A. Peluso, P. Aiden, A. P. Ramasamy, V. Rasic, G. Roy, S. Saavedra-Rodriguez, K. Sharan, S. Sha 2017-12-29 doi:10.1101/240747 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ Generalizing Genetic Risk Scores from Europeans to Hispanics/Latinos ]]> https://biorxiv.org/content/10.1101/242404v1?rss=1 Grinde, K. E. Qi, Q. Thornton, T. A. Liu, S. Shadyab, A. H. Chan, K. H. K. Reiner, A. P. Sofer, T. 2018-01-04 doi:10.1101/242404 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ BOFdat: generating biomass objective function stoichiometric coefficients from experimental data ]]> https://biorxiv.org/content/10.1101/243881v1?rss=1 Lachance, J.-C. Monk, J. M. Lloyd, C. J. Seif, Y. Palsson, B. O. Rodrigue, S. Feist, A. M. King, Z. A. Jacques, P.-E. 2018-01-05 doi:10.1101/243881 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Exploring protein orthogonality in immune space: a case study with AAV and Cas9 orthologs ]]> https://biorxiv.org/content/10.1101/245985v1?rss=1 Moreno, A. M. Palmer, N. Aleman, F. Chen, G. Pla, A. Chew, W. L. Law, M. Mali, P. 2018-01-10 doi:10.1101/245985 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Chemogenetic Manipulations of Ventral Tegmental Area Dopamine Neurons Reveal Multifaceted Roles in Cocaine Abuse ]]> https://biorxiv.org/content/10.1101/246595v1?rss=1 Mahler, S. V. Brodnik, Z. D. Cox, B. M. Buchta, W. C. Bentzley, B. S. Cope, Z. A. Lin, E. C. Riedy, M. D. Scofield, M. D. Messinger, J. Riegel, A. C. Espana, R. A. Aston-Jones, G. 2018-02-26 doi:10.1101/246595 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package ]]> https://biorxiv.org/content/10.1101/247692v1?rss=1 140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. ]]> Mermelstein, D. J. Lin, C. Nelson, G. Kretsch, R. McCammon, J. A. Walker, R. C. 2018-01-15 doi:10.1101/247692 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants ]]> https://biorxiv.org/content/10.1101/253534v1?rss=1 Farnaes, L. Hildreth, A. Sweeney, N. Clark, M. Chowdhury, S. Nahas, S. Cakici, J. Benson, W. Kaplan, R. Kronick, R. Bainbridge, M. Friedman, J. Gold, J. Ding, Y. Veeraraghavan, N. Dimmock, D. kingsmore, S. RCIGM Investigators, 2018-01-26 doi:10.1101/253534 Cold Spring Harbor Laboratory Press 2018-01-26 <![CDATA[ Ferroptosis-like signaling facilitates a potent innate defense against Plasmodium infection ]]> https://biorxiv.org/content/10.1101/257287v1?rss=1 Kain, H. S. Arang, N. Glennon, E. Douglass, A. N. Dudgeon, D. R. Johnson, J. S. Aderem, A. Kaushansky, A. 2018-01-31 doi:10.1101/257287 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ GITAR: An open source tool for analysis and visualization of Hi-C data ]]> https://biorxiv.org/content/10.1101/259515v1?rss=1 Calandrelli, R. Wu, Q. Guan, J. Zhong, S. 2018-02-04 doi:10.1101/259515 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ Crystallizing the Parkinson’s Disease Protein LRRK2 Under Microgravity Conditions ]]> https://biorxiv.org/content/10.1101/259655v1?rss=1 Mattea, S. Baptista, M. Reichert, P. Spinale, A. Wu, J. Allaire, M. Fiske, B. Knapp, S. 2018-02-04 doi:10.1101/259655 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ Swedish Nerve Growth Factor Mutation (NGFR100W) Defines a Role for TrkA and p75NTR in Nociception ]]> https://biorxiv.org/content/10.1101/266643v1?rss=1 Sung, K. Ferrari, L. F. Yang, W. Chung, C. Zhao, X. Gu, Y. Lin, S. Zhang, K. Cui, B. Pearn, M. L. P. L. Maloney, M. T. Mobley, W. C. Levine, J. D. Wu, C. 2018-02-16 doi:10.1101/266643 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ Streptococcal Lancefield polysaccharides are critical cell wall determinants for human group IIA secreted phospholipase A2 to exert its bactericidal effects ]]> https://biorxiv.org/content/10.1101/269779v1?rss=1 van Hensbergen, V. P. Movert, E. de Maat, V. Le Breton, Y. Lambeau, G. Payre, C. Kahn, F. Henningham, A. Nizet, V. Van Strijp, J. A. G. Carlsson, F. McIver, K. S. van Sorge, N. M. 2018-02-22 doi:10.1101/269779 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ Hedgehog signaling controls progenitor differentiation timing during heart development ]]> https://biorxiv.org/content/10.1101/270751v1?rss=1 Rowton, M. Hoffmann, A. D. Steimle, J. D. Yang, X. H. Guzzetta, A. Lazarevic, S. Kim, C. Deng, N. Lu, E. Jacobs-Li, J. Yu, S. Hanson, E. Perez-Cervantes, C. Chan, S. S.-K. Ikegami, K. Garry, D. J. Kyba, M. Moskowitz, I. P. 2018-02-23 doi:10.1101/270751 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Brainstem control of urethral sphincter relaxation and scent marking behavior ]]> https://biorxiv.org/content/10.1101/270801v1?rss=1 Keller, J. A. Chen, J. Simpson, S. Wang, E. H.-J. Lilascharoen, V. George, O. Lim, B. K. Stowers, L. 2018-02-23 doi:10.1101/270801 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom ]]> https://biorxiv.org/content/10.1101/271635v1?rss=1 swalethorp, R. Dinasquet, J. Logares, R. Bertilsson, S. Kjellerup, S. Krabberod, A. Moksnes, P.-O. Nielsen, T. Riemann, L. 2018-02-26 doi:10.1101/271635 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Repeat-specific functions for the C-terminal domain of RNA polymerase II in budding yeast ]]> https://biorxiv.org/content/10.1101/274274v1?rss=1 Babokhov, M. Mosaheb, M. M. Baker, R. W. Fuchs, S. M. 2018-03-01 doi:10.1101/274274 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Crowding tunes 3D collagen fibrils and reveals matrix regulation of cancer cell morphogenesis ]]> https://biorxiv.org/content/10.1101/274696v1?rss=1 Han, A. Ranamukhaarachchi, S. Velez, D. O. Kumar, A. Engler, A. J. Fraley, S. I. 2018-03-02 doi:10.1101/274696 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ Genome-wide association study meta-analysis of the Alcohol Use Disorder Identification Test (AUDIT) in two population-based cohorts (N=141,958) ]]> https://biorxiv.org/content/10.1101/275917v1?rss=1 Sanchez-Roige, S. Palmer, A. A. Fontanillas, P. Elson, S. 23andMe Research Team, Substance Use Disorder Working Group of the Psychiatric Genomics Consortium, Adams, M. J. Howard, D. M. Edenberg, H. J. Davies, G. Crist, R. C. Deary, I. McIntosh, A. M. Clarke, T. K. 2018-03-06 doi:10.1101/275917 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Visualizing single-cell RNA-seq datasets with Similarity Weighted Nonnegative Embedding (SWNE) ]]> https://biorxiv.org/content/10.1101/276261v1?rss=1 Wu, Y. Tamayo, P. Zhang, K. 2018-03-05 doi:10.1101/276261 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ A reference haplotype panel for genome-wide imputation of short tandem repeats ]]> https://biorxiv.org/content/10.1101/277673v1?rss=1 Saini, S. Mitra, I. Gymrek, M. 2018-03-06 doi:10.1101/277673 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ American Gut: an Open Platform for Citizen-Science Microbiome Research ]]> https://biorxiv.org/content/10.1101/277970v1?rss=1 McDonald, D. Hyde, E. R. Debelius, J. W. Morton, J. T. Gonzalez, A. Ackermann, G. Aksenov, A. A. Behsaz, B. Brennan, C. Chen, Y. DeRight Goldasicha, L. Dorrestein, P. C. Dunn, R. R. Fahimipourg, A. K. Gaffney, J. Gilbert, J. A. Gogul, G. Green, J. L. Hugenholtz, P. Humphrey, G. Huttenhower, C. Jackson, M. A. Janssen, S. Jeste, D. V. Jiang, L. Kelley, S. T. Knights, D. Kosciolek, T. Ladau, J. Leach, J. Marotz, C. Meleshko, D. Melnik, A. V. Metcalf, J. L. Mohimani, H. Montassier, E. Navas-Molina, J. Nguyen, T. T. Peddada, S. Pevzner, P. Pollard, K. S. Rah 2018-03-07 doi:10.1101/277970 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Dysregulation of the engulfment pathway in the gut fuels Inflammatory Bowel Disease ]]> https://biorxiv.org/content/10.1101/280172v1?rss=1 Suarez, K. Lim, E. Singh, S. Pereira, M. Joosen, L. P. Ibeawuchi, S.-R. Dunkel, Y. Mittal, Y. Ho, S. B. Chattopadhyay, R. Guma, M. Boland, B. S. Dulai, P. S. Sandborn, W. J. Ghosh, P. Das, S. 2018-03-12 doi:10.1101/280172 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ A homing CRISPR mouse resource for barcoding and lineage tracing ]]> https://biorxiv.org/content/10.1101/280289v1?rss=1 Kalhor, R. Kalhor, K. Leeper, K. Graveline, A. Mali, P. Church, G. M. 2018-03-12 doi:10.1101/280289 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Escher-FBA: A web application for interactive flux balance analysis ]]> https://biorxiv.org/content/10.1101/281600v1?rss=1 Rowe, E. G. Palsson, B. O. King, Z. A. 2018-03-13 doi:10.1101/281600 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Human Puf-A, a Novel Component of 90S Pre-ribosome, Links Ribosome Biogenesis to Cancer Progression ]]> https://biorxiv.org/content/10.1101/281857v1?rss=1 Yu, J. Cho, H.-C. Huang, Y. Hung, J.-T. Lai, L.-C. Wang, S.-H. Liu, Y.-H. Cho, I.-M. Kuo, M.-W. Cheng, P.-Y. Ho, M.-Y. Lin, R.-J. Yu, A. L. 2018-03-13 doi:10.1101/281857 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Insulin Signaling-independent Activation of DAF-16 Shapes the Transcriptome during Normal Aging ]]> https://biorxiv.org/content/10.1101/284083v1?rss=1 Li, S.-T. Zhao, H.-Q. Zhang, P. Liang, C.-Y. Zhang, Y.-P. Hsu, A.-L. Dong, M.-Q. 2018-03-22 doi:10.1101/284083 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ High dimensional analyses of cells dissociated from cryopreserved synovial tissue ]]> https://biorxiv.org/content/10.1101/284844v1?rss=1 Donlin, L. T. Rao, D. A. Wei, K. Slowikowski, K. McGeachy, M. J. Turner, J. D. Meednu, N. Mizoguchi, F. Gutierrez-Arcelus, M. Lieb, D. J. Keegan, J. Muskat, K. Hillman, J. Rozo, C. Ricker, E. Eisenhaure, T. M. Li, S. Browne, E. P. Chicoine, A. Sutherby, D. Noma, A. Nusbaum, C. Kelly, S. Pernis, A. B. Ivashkiv, L. B. Goodman, S. M. Robinson, W. H. Utz, P. J. Lederer, J. A. Gravallese, E. M. Boyce, B. F. Hacohen, N. Pitzalis, C. Gregersen, P. K. Firestein, G. S. Raychaudhuri, S. Moreland, L. W. Holers, M. Bykerk, V. P. Filer, A. Boyle, D. L. Brenner, M. B 2018-03-19 doi:10.1101/284844 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Shared genetic contribution to type 1 and type 2 diabetes risk ]]> https://biorxiv.org/content/10.1101/285304v1?rss=1 Aylward, A. J. Chiou, J. Okino, M.-L. Kadakia, N. Gaulton, K. J. 2018-05-07 doi:10.1101/285304 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Phosphoserine acidic cluster motifs in the cytoplasmic domains of transmembrane proteins bind distinct basic regions on the μ subunits of clathrin adaptor protein complexes ]]> https://biorxiv.org/content/10.1101/286633v1?rss=1 Singh, R. Stoneham, C. Lim, C. jia, X. Guenaga, J. Wyatt, R. Wertheim, J. o. Xiong, Y. Guatelli, J. 2018-03-21 doi:10.1101/286633 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Perturbed functional networks in Alzheimers Disease reveal opposing roles for TGIF and EGR3 ]]> https://biorxiv.org/content/10.1101/286674v1?rss=1 Canchi, S. Raao, B. Masliah, D. Rosenthal, S. B. Sasik, R. Fisch, K. M. Jager, P. D. Bennett, D. A. Rissman, R. A. 2018-03-22 doi:10.1101/286674 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Cystinosin regulates kidney inflammation through its interaction with galectin-3 ]]> https://biorxiv.org/content/10.1101/289702v1?rss=1 Lobry, T. Miller, R. Nevo, N. Rocca, C. J. Zhang, J. Catz, S. D. Moore, F. Bailleux, A. Guerrera, I. C. Gubler, M.-C. Cheung, W. W. Mak, R. Montier, T. Antignac, C. Cherqui, S. 2018-03-27 doi:10.1101/289702 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Temperature-dependent estimation of Gibbs energies using an updated group contribution method ]]> https://biorxiv.org/content/10.1101/289918v1?rss=1 Du, B. Zhang, Z. Gruber, S. Yurkovich, J. Palsson, B. Zielinski, D. 2018-03-27 doi:10.1101/289918 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos ]]> https://biorxiv.org/content/10.1101/293134v1?rss=1 Biase, F. Wu, Q. Calandrelli, R. Rivas-Astroza, M. Zhou, S. Zhong, S. 2018-04-02 doi:10.1101/293134 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Pancreatic islet chromatin accessibility and conformation defines distal enhancer networks of type 2 diabetes risk ]]> https://biorxiv.org/content/10.1101/299388v1?rss=1 Greenwald, W. W. Chiou, J. Yan, J. Qiu, Y. Dai, N. Wang, A. Nariai, N. Aylward, A. Han, J. Y. Kadakia, N. Barrufet, L. Okino, M.-L. Drees, F. Vinckier, N. Minichiello, L. Gorkin, D. Avruch, J. Frazer, K. Sander, M. Ren, B. Gaulton, K. 2018-04-20 doi:10.1101/299388 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Large time step discrete-time modeling of sharp wave activity in hippocampal area CA3. ]]> https://biorxiv.org/content/10.1101/303917v1?rss=1 Malerba, P. Rulkov, N. F. Bazhenov, M. 2018-04-18 doi:10.1101/303917 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Sub-2 A Ewald Curvature Corrected Single-Particle Cryo-EM ]]> https://biorxiv.org/content/10.1101/305599v1?rss=1 Tan, Y. Z. Aiyer, S. Mietzsch, M. Hull, J. A. McKenna, R. Grieger, J. Samulski, R. J. Baker, T. S. Agbandje-McKenna, M. Lyumkis, D. 2018-04-21 doi:10.1101/305599 Cold Spring Harbor Laboratory Press 2018-04-21 <![CDATA[ Genome Wide Association Scan identifies new variants associated with a cognitive predictor of dyslexia. ]]> https://biorxiv.org/content/10.1101/309336v1?rss=1 Gialluisi, A. Andlauer, T. F. Mirza-Schreiber, N. Moll, K. Hoffmann, P. Ludwig, K. U. Czamara, D. Francks, C. St Pourcain, B. Brandler, W. Honbolygo, F. Toth, D. Csepe, V. Huguet, G. Morris, A. P. Hulslander, J. Willcutt, E. G. DeFries, J. C. Olson, R. K. Smith, S. D. Pennington, B. F. Vaessen, A. Maurer, U. Lyytinen, H. Peyrard-Janvid, M. Leppanen, P. H. Brandeis, D. Bonte, M. Stein, J. F. Talcott, J. Fauchereau, F. Bourgeron, T. Monaco, A. P. Ramus, F. Landerl, K. Kere, J. Scerri, T. S. Paracchini, S. Fisher, S. E. Schumacher, J. Nothen, M. M. Muller- 2018-05-02 doi:10.1101/309336 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Site-specific transgenesis of the D. melanogaster Y-chromosome using CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/310318v1?rss=1 Buchman, A. Akbari, O. 2018-04-27 doi:10.1101/310318 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ Genome-wide Association Study for Noise-induced Cochlear Synaptopathy. ]]> https://biorxiv.org/content/10.1101/311407v1?rss=1 Lavinsky, J. Dermanaki, P. S. Wang, J. Friedman, R. A. 2018-04-30 doi:10.1101/311407 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ N-linked glycosylation of the antagonist Short gastrulation increases the functional complexity of BMP signals ]]> https://biorxiv.org/content/10.1101/316448v1?rss=1 Negreiros, E. Herszterg, S. Kang, K.-H. Camara, A. Dias, W. Carneiro, K. Bier, E. Todeschini, A. Araujo, H. 2018-05-07 doi:10.1101/316448 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ On the Development of Sesamoid Bones ]]> https://biorxiv.org/content/10.1101/316901v1?rss=1 Eyal, S. Rubin, S. Krief, S. Levin, L. Zelzer, E. 2018-05-08 doi:10.1101/316901 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Can the presence of neural probes be neglected in computational modeling of extracellular potentials? ]]> https://biorxiv.org/content/10.1101/318741v1?rss=1 Buccino, A. Kuchta, M. Jaeger, K. Ness, T. Mardal, K.-A. Cauwenberghs, G. Tveito, A. 2018-05-10 doi:10.1101/318741 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Extensile motor activity drives coherent motions in a model of interphase chromatin ]]> https://biorxiv.org/content/10.1101/319756v1?rss=1 Saintillan, D. Shelley, M. J. Zidovska, A. 2018-05-10 doi:10.1101/319756 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression ]]> https://biorxiv.org/content/10.1101/319962v1?rss=1 Yang, L. Ebrahim, A. Lloyd, C. J. Saunders, M. A. Palsson, B. O. 2018-05-15 doi:10.1101/319962 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Evaluating the information content of shallow shotgun metagenomics ]]> https://biorxiv.org/content/10.1101/320986v1?rss=1 Hillmann, B. Al-Ghalith, G. A. Shields-Cutler, R. Zhu, Q. Gohl, D. Beckman, K. B. Knight, R. Knights, D. 2018-05-12 doi:10.1101/320986 Cold Spring Harbor Laboratory Press 2018-05-12 <![CDATA[ Did a plant-herbivore arms race drive chemical diversity in Euphorbia? ]]> https://biorxiv.org/content/10.1101/323014v1?rss=1 Ernst, M. Nothias-Scaglia, L.-F. van der Hooft, J. Silva, R. R. Saslis-Lagoudakis, C. H. Grace, O. M. Martinez-Swatson, K. Hassemer, G. Funez, L. T. Simonsen, H. Medema, M. H. Staerk, D. Nilsson, N. Lovato, P. Dorrestein, P. Ronsted, N. 2018-05-15 doi:10.1101/323014 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Organized spatial patterns of activated β2 integrins in arresting neutrophils ]]> https://biorxiv.org/content/10.1101/323279v1?rss=1 Fan, Z. Kiosses, W. B. Zajonc, D. M. Arnaout, M. A. Gutierrez, E. Groisman, A. Ley, K. 2018-05-16 doi:10.1101/323279 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Bone Morphology is Regulated Modularly by Global and Regional Genetic Programs ]]> https://biorxiv.org/content/10.1101/324293v1?rss=1 Eyal, S. Kult, S. Rubin, S. Krief, S. Pineault, K. M. Wellik, D. Zelzer, E. 2018-05-16 doi:10.1101/324293 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Model-driven design and evolution of non-trivial synthetic syntrophic pairs ]]> https://biorxiv.org/content/10.1101/327270v1?rss=1 Lloyd, C. J. King, Z. Sandberg, T. Hefner, Y. Olson, C. Phaneuf, P. O'Brien, E. Feist, A. 2018-05-21 doi:10.1101/327270 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ The Y-ome defines the thirty-four percent of Escherichia coli genes that lack experimental evidence of function ]]> https://biorxiv.org/content/10.1101/328591v1?rss=1 Ghatak, S. King, Z. A. Sastry, A. Palsson, B. O. 2018-05-23 doi:10.1101/328591 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size ]]> https://biorxiv.org/content/10.1101/329672v1?rss=1 Rosenbloom, D. I. S. Bacchetti, P. Stone, M. Deng, X. Bosch, R. J. Richman, D. D. Siliciano, J. D. Mellors, J. W. Deeks, S. G. Ptak, R. G. Hoh, R. Keating, S. M. Dimapasoc, M. Massanella, M. Lai, J. Sobolewski, M. D. Kulpa, D. A. Busch, M. P. Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group, 2018-06-06 doi:10.1101/329672 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ IL-11 is a therapeutic target in idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/336537v1?rss=1 Cook, S. Ng, B. Dong, J. Viswanathan, S. DAgostino, G. Widjaja, A. Lim, W.-W. Ko, N. Tan, J. Chothani, S. Huang, B. Xie, C. Chacko, A.-M. Guimaraes-Camboa, N. Evans, S. Byrne, A. Maher, T. Liang, J. Noble, P. Schafer, S. 2018-06-02 doi:10.1101/336537 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ Correction of respiratory artifacts in MRI head motion estimates ]]> https://biorxiv.org/content/10.1101/337360v1?rss=1 Fair, D. A. Miranda-Dominguez, O. Snyder, A. Z. Perrone, A. A. Earl, E. A. Van, A. N. Koller, J. M. Feczko, E. Klein, R. L. Mirro, A. E. Hampton, J. M. Adeyemo, B. Laumann, T. O. Gratton, C. Greene, D. J. Schlaggar, B. Hagler, D. Watts, R. Garavan, H. Barch, D. M. Nigg, J. T. Petersen, S. E. Dale, A. Feldstein-Ewing, S. W. Nagel, B. J. Dosenbach, N. U. F. 2018-06-07 doi:10.1101/337360 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Simultaneous representation of sensory and mnemonic information in human visual cortex ]]> https://biorxiv.org/content/10.1101/339200v1?rss=1 Rademaker, R. L. Chunharas, C. Serences, J. T. 2018-06-05 doi:10.1101/339200 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Cryptic Dispersal Networks Connect Habitat Patches in ways not Captured by Distance ]]> https://biorxiv.org/content/10.1101/341123v1?rss=1 Germain, R. M. Jones, N. T. Grainger, T. N. 2018-06-08 doi:10.1101/341123 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Growth adaptation of gnd and sdhCB Escherichia coli deletion strains diverges from a similar initial perturbation of the transcriptome ]]> https://biorxiv.org/content/10.1101/342683v1?rss=1 McCloskey, D. Xu, S. Sandberg, T. E. Brunk, E. Hefner, Y. Szubin, R. Feist, A. M. Palsson, B. O. 2018-06-20 doi:10.1101/342683 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions ]]> https://biorxiv.org/content/10.1101/342709v1?rss=1 McCloskey, D. Xu, S. Sandberg, T. E. Brunk, E. Hefner, Y. Szubin, R. Feist, A. M. Palsson, B. O. 2018-06-20 doi:10.1101/342709 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria ]]> https://biorxiv.org/content/10.1101/343558v1?rss=1 Cekanaviciute, E. Probstel, A.-K. Thomann, A. Runia, T. Casaccia, P. Katz Sand, I. Crabtree, E. Singh, S. Morrissey, J. Barba, P. Gomez, R. Knight, R. Mazmanian, S. Graves, J. Cree, B. C. A. Zamvil, S. S. Baranzini, S. 2018-06-11 doi:10.1101/343558 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex ]]> https://biorxiv.org/content/10.1101/344556v1?rss=1 Handa, S. Jiang, Y. Tao, S. Foreman, R. Schinazi, R. Miller, J. F. Ghosh, P. 2018-06-12 doi:10.1101/344556 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Engineered resistance to Zika virus in transgenic Ae. aegypti expressing a polycistronic cluster of synthetic miRNAs ]]> https://biorxiv.org/content/10.1101/344697v1?rss=1 Buchman, A. Gamez, S. Li, M. Antoshechkin, I. Lee, h.-H. Wang, S.-W. Chen, C.-H. Klein, M. J. Duchmemin, J.-B. Paradkar, P. N. Akbari, O. S. 2018-06-12 doi:10.1101/344697 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages ]]> https://biorxiv.org/content/10.1101/345835v1?rss=1 Fonseca, G. J. Tao, J. Westin, E. M. Duttke, S. H. Spann, N. J. Strid, T. Shen, Z. Stender, J. D. Link, V. M. Benner, C. Glass, C. K. 2018-06-13 doi:10.1101/345835 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data ]]> https://biorxiv.org/content/10.1101/350181v1?rss=1 Fernandez-Tajes, J. Gaulton, K. J. van de Bunt, M. Torres, J. Mahajan, A. Mahajan, A. Gloyn, A. L. Lage, K. McCarthy, M. I. 2018-06-20 doi:10.1101/350181 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Integration of phased Hi-C and molecular phenotype data to study genetic and epigenetic effects on chromatin looping ]]> https://biorxiv.org/content/10.1101/352682v1?rss=1 Greenwald, W. W. Li, H. Benaglio, P. Jakubosky, D. Matsui, H. Schmitt, A. Selvaraj, S. D'Antonio, M. D'Antonio-Chrownowska, A. Smith, E. N. Frazer, K. A. 2018-06-20 doi:10.1101/352682 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ MODE for detecting and estimating genetic causal variants ]]> https://biorxiv.org/content/10.1101/357228v1?rss=1 Sundar, V. Fan, C.-C. Holland, D. Dale, A. 2018-06-27 doi:10.1101/357228 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ SCuPhr: A Probabilistic Framework for Cell Lineage Tree Reconstruction ]]> https://biorxiv.org/content/10.1101/357442v1?rss=1 Koptagel, H. Jun, S.-H. Lagergren, J. 2018-06-29 doi:10.1101/357442 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Imputation of Behavioral Candidate Gene Repeat Polymorphisms in 486,551 Publicly-Available UK Biobank Individuals. ]]> https://biorxiv.org/content/10.1101/358267v1?rss=1 0.96 for all four VNTR polymorphisms and one modifying SNP, depending on the reference and target dataset. We describe the imputation procedures of these candidate polymorphisms in 486,551 UK Biobank individuals, and have made the imputed polymorphism data available to UK Biobank researchers. This resource, provided to the community, will allow the most rigorous tests to-date of the roles of these polymorphisms in behavioral and psychiatric phenotypes. ]]> Border, R. Smolen, A. Corley, R. Stallings, M. Brown, S. Conger, R. Derringer, J. Donnellan, M. B. Haberstick, B. C. Hewitt, J. Hopfer, C. Krauter, K. McQueen, M. B. Wall, T. L. Keller, M. C. Evans, L. 2018-06-29 doi:10.1101/358267 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Genetic heterogeneity in Anopheles darlingi related to biting behavior in western Amazon ]]> https://biorxiv.org/content/10.1101/358556v1?rss=1 Campos, M. Alonso, D. P. Conn, J. E. Vinetz, J. Emerson, K. J. Ribolla, P. E. M. 2018-06-28 doi:10.1101/358556 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Nested oscillatory dynamics in cortical organoids model early human brain network development ]]> https://biorxiv.org/content/10.1101/358622v1?rss=1 Trujillo, C. A. Gao, R. Negraes, P. D. Chaim, I. A. Domissy, A. Vandenberghe, M. Devor, A. Yeo, G. W. Voytek, B. Muotri, A. R. 2018-06-29 doi:10.1101/358622 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Thyroid hormone signaling specifies cone subtypes in human retinal organoids ]]> https://biorxiv.org/content/10.1101/359950v1?rss=1 Eldred, K. C. Hadyniak, S. E. Hussey, K. A. Brennerman, B. Zhang, P. Chamling, X. Sluch, V. M. Welsbie, D. S. Hattar, S. Taylor, J. Wahlin, K. Zack, D. J. Johnston, R. J. 2018-06-30 doi:10.1101/359950 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ Timing between cortical slow oscillations and heart rate bursts during sleep predicts perceptual speed, but not offline consolidation ]]> https://biorxiv.org/content/10.1101/360867v1?rss=1 Naji, M. Krishnan, G. P. McDevitt, E. A. Bazhenov, M. Mednick, S. C. 2018-07-03 doi:10.1101/360867 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Profiling the genome-wide landscape of tandem repeat expansions ]]> https://biorxiv.org/content/10.1101/361162v1?rss=1 Mousavi, N. Shleizer-Burko, S. Gymrek, M. 2018-07-03 doi:10.1101/361162 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Prospective Study of Polygenic Risk, Protective Factors, and Incident Depression Following Combat Deployment in US Army Soldiers ]]> https://biorxiv.org/content/10.1101/361725v1?rss=1 Choi, K. Chen, C.-Y. Ursano, R. Sun, X. Jain, S. Kessler, R. Koenen, K. Wang, M.-J. Wynn, G. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Campbell-Sills, L. Stein, M. Smoller, J. 2018-07-06 doi:10.1101/361725 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline ]]> https://biorxiv.org/content/10.1101/362558v1?rss=1 Grunwald, H. A. Gantz, V. M. Poplawski, G. Xu, X.-r. S. Bier, E. Cooper, K. L. 2018-07-04 doi:10.1101/362558 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ The immune cell landscape in kidneys of lupus nephritis patients ]]> https://biorxiv.org/content/10.1101/363051v1?rss=1 Arazi, A. Rao, D. A. Berthier, C. C. Davidson, A. Liu, Y. Hoover, P. J. Chicoine, A. Eisenhaure, T. M. Jonsson, A. H. Li, S. Lieb, D. J. Browne, E. P. Noma, A. Sutherby, D. Steelman, S. Smilek, D. E. Tosta, P. Apruzzese, W. Massarotti, E. Dall'Era, M. Park, M. Kamen, D. L. Furie, R. A. Payan-Schober, F. Buyon, J. P. Petri, M. A. Putterman, C. Kalunian, K. C. Woodle, E. S. Lederer, J. A. Hildeman, D. A. Nusbaum, C. Wofsy, D. Kretzler, M. Anolik, J. H. Brenner, M. B. The Accelerating Medicines Partnership in RA/SLE network, Hacohen, N. Diamond, B. 2018-07-07 doi:10.1101/363051 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Ancestral Roles of the Fam20C Family of Secreted Protein Kinases Revealed by Functional Analysis in C. elegans ]]> https://biorxiv.org/content/10.1101/363440v1?rss=1 Gerson-Gurwitz, A. Worby, C. A. Lee, K.-Y. Khaliullin, R. Bouffard, J. Cheerambathur, D. Cram, E. J. Oegema, K. Dixon, J. E. Desai, A. 2018-07-06 doi:10.1101/363440 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Disparate expression specificities coded by a shared Hox-C enhancer ]]> https://biorxiv.org/content/10.1101/364216v1?rss=1 Miller, S. W. Posakony, J. W. 2018-07-07 doi:10.1101/364216 Cold Spring Harbor Laboratory Press 2018-07-07 <![CDATA[ Testing Causal Bidirectional Influences between Physical Activity and Depression using Mendelian Randomization ]]> https://biorxiv.org/content/10.1101/364232v1?rss=1 Choi, K. Chen, C.-Y. Stein, M. Klimentidis, Y. Wang, M.-J. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Koenen, K. Smoller, J. 2018-07-08 doi:10.1101/364232 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ The role of meaning in visual memory: Face-selective brain activity predicts memory for ambiguous face stimuli ]]> https://biorxiv.org/content/10.1101/366641v1?rss=1 Brady, T. F. Alvarez, G. A. Stoermer, V. 2018-07-10 doi:10.1101/366641 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ Noninvasive Vagus Nerve Stimulation Alters Neural Response and Physiological Autonomic Tone to Noxious Thermal Challenge ]]> https://biorxiv.org/content/10.1101/367979v1?rss=1 Lerman, I. Davis, B. Huang, M. Huang, C. Sorkin, L. Proudfoot, J. Zhong, E. Kimball, D. Rao, R. Simon, B. Spadoni, A. Strigo, I. Baker, D. Simmons, A. 2018-07-12 doi:10.1101/367979 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Engrafted parenchymal brain macrophages differ from host microglia in transcriptome, epigenome and responsiveness to challenge ]]> https://biorxiv.org/content/10.1101/369942v1?rss=1 Shemer, A. Grozovski, J. Leng Tay, T. Tao, J. Volaski, A. Suess, P. Ardura-Fabregat, A. Gross, M. Kim, J.-S. David, E. Chappell-Maor, L. Thielecke, L. Glass, C. K. Cornils, K. Prinz, M. Jung, S. 2018-07-16 doi:10.1101/369942 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Comparative structural dynamic analysis of GTPases ]]> https://biorxiv.org/content/10.1101/370197v1?rss=1 Li, H. Yao, X.-Q. Grant, B. J. 2018-07-16 doi:10.1101/370197 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Genome-wide analysis in UK Biobank identifies over 100 QTLs associated with muscle mass variability in middle age individuals ]]> https://biorxiv.org/content/10.1101/370312v1?rss=1 Hernandez Cordero, A. I. Gregory, J. S. Douglas, A. Lionikas, A. 2018-07-16 doi:10.1101/370312 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Plasmodium falciparum Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis ]]> https://biorxiv.org/content/10.1101/371484v1?rss=1 Istvan, E. S. Das, S. Bhatnagar, S. Beck, J. R. Owen, E. LLinas, M. Ganesan, S. M. Niles, J. C. Winzeler, E. A. Vaidya, A. B. Goldberg, D. E. 2018-07-18 doi:10.1101/371484 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Protein aggregation and membrane bending govern nanotube morphology. ]]> https://biorxiv.org/content/10.1101/373811v1?rss=1 Alimohamadi, H. Ovryn, B. Rangamani, P. 2018-07-20 doi:10.1101/373811 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Two central pattern generators from the crab, Cancer borealis, respond robustly and differentially to extreme extracellular pH ]]> https://biorxiv.org/content/10.1101/374405v1?rss=1 Haley, J. A. Hampton, D. Marder, E. 2018-07-22 doi:10.1101/374405 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome ]]> https://biorxiv.org/content/10.1101/375634v1?rss=1 Innocent, T. Holmes, N. Al Bassam, M. Schiott, M. Scheuring, I. Wilkinson, B. Hutchings, M. I. Boomsma, J. J. Yu, D. 2018-07-24 doi:10.1101/375634 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Adaptation of Bacillus subtilis upon interaction with Setophoma terrestris results in loss of surfactin and plipastatin production ]]> https://biorxiv.org/content/10.1101/376590v1?rss=1 Albarracin Orio, A. G. Tobares, R. A. Petras, D. Sayago, P. Juncosa, F. Dorrestein, P. Smania, A. M. Ducasse, D. 2018-07-25 doi:10.1101/376590 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Modelling bistable tumour population dynamics to design effective treatment strategies ]]> https://biorxiv.org/content/10.1101/381418v1?rss=1 Akhmetzhanov, A. R. Kim, J. W. Sullivan, R. Beckman, R. A. Tamayo, P. Yeang, C.-H. 2018-07-31 doi:10.1101/381418 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development ]]> https://biorxiv.org/content/10.1101/381608v1?rss=1 Vain, T. Raggi, S. Ferro, N. Barange, D. K. Kieffer, M. Ma, Q. Doyle, S. M. Thelander, M. Parizkova, B. Novak, O. Ismail, A. Enquist, P. A. Rigal, A. Łangowska, M. Harborough, S. R. Zhang, Y. Ljung, K. Callis, J. Almqvist, F. Kepinski, S. Estelle, M. Pauwels, L. Robert, S. 2018-07-31 doi:10.1101/381608 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium ]]> https://biorxiv.org/content/10.1101/386367v1?rss=1 Bell, M. Bartol, T. Sejnowski, T. Rangamani, P. 2018-08-07 doi:10.1101/386367 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ EGFR confers exquisite specificity of Wnt9a-Fzd9b signaling in hematopoietic stem cell development ]]> https://biorxiv.org/content/10.1101/387043v1?rss=1 Grainger, S. Nguyen, N. Richter, J. Setayesh, J. Lonquich, B. Oon, C. H. Wozniak, J. M. Barahona, R. Kamei, C. N. Houston, J. Carrillo-Terrazas, M. Drummon, I. A. Gonzalez, D. Willert, K. Traver, D. 2018-08-07 doi:10.1101/387043 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Genome-wide association study, replication, and mega-analysis using a dense marker panel in a multi-generational mouse advanced intercross line ]]> https://biorxiv.org/content/10.1101/387613v1?rss=1 Zhou, X. St. Pierre, C. L. Gonzales, N. M. Cheng, R. Chitre, A. S. Sokoloff, G. Palmer, A. A. 2018-08-08 doi:10.1101/387613 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ Mathematical modelling reveals how MeCP2 restrains transcriptional elongation in human neurons ]]> https://biorxiv.org/content/10.1101/391904v1?rss=1 Cholewa-Waclaw, J. Shah, R. Webb, S. Chhatbar, K. Ramsahoye, B. Pusch, O. Yu, M. Greulich, P. Waclaw, B. Bird, A. 2018-08-14 doi:10.1101/391904 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Structural basis for ligand modulation of the CCR2 conformational landscape ]]> https://biorxiv.org/content/10.1101/392068v1?rss=1 Taylor, B. C. Lee, C. T. Amaro, R. E. 2018-08-14 doi:10.1101/392068 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ A human cell model of cardiac pathophysiological valvulogenesis ]]> https://biorxiv.org/content/10.1101/397422v1?rss=1 Neri, T. Hiriart, E. Van Vliet, P. Faure, E. Norris, R. Farhat, B. Lefrancois, J. Moore-Morris, T. Zaffran, S. Faustino, R. Zambon, A. Devisgnes, J.-P. Salgado, D. Sugi, Y. Levine, R. de la Pompa, J. L. Terzic, A. Evans, S. Markwald, R. Puceat, m. 2018-08-22 doi:10.1101/397422 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Validation of the protein kinase PfCLK3 as a multi-stage cross species malarial drug target ]]> https://biorxiv.org/content/10.1101/404459v1?rss=1 400 genes essential for parasite survival. Through this mechanism, blocking PfCLK3 activity not only results in rapid killing of asexual blood stage parasites but is also effective on sporozoites and gametocytes as well as showing parasiticidal activity in all Plasmodium species tested. Hence, our data establishes PfCLK3 as a target with the potential to deliver both symptomatic treatment and transmission blocking in malaria. ]]> Alam, M. Sanchez-Azqueta, A. Janha, O. Flannery, E. Mahindra, A. Mapesa, K. Brancucci, N. Antonova-Koch, Y. Crouch, K. Simwela, N. V. Akinwale, J. Mitcheson, D. Solyakov, L. Dudek, K. Jones, C. Zapatero, C. Doerig, C. Nwakanma, D. C. Vazquez, M.-J. Colmenarejo, G. Lafuente, M.-J. Leon, M. L. Waters, A. P. Jamieson, A. G. Alvaro, L. E. Marti, M. Winzeler, E. A. Gamo, F. J. Tobin, A. 2018-08-31 doi:10.1101/404459 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ USP21 and OTUD3 Antagonize Regulatory Ribosomal Ubiquitylation and Ribosome-Associated Quality Control ]]> https://biorxiv.org/content/10.1101/407726v1?rss=1 Garshott, D. M. Sundaramoorthy, E. Leonard, M. Bennett, E. J. 2018-09-04 doi:10.1101/407726 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Maternal Circulating MicroRNAs Control the Placental Response to Alcohol ]]> https://biorxiv.org/content/10.1101/409854v1?rss=1 Tseng, A. M. Mahnke, A. H. Wells, A. B. Salem, N. A. Allan, A. M. Roberts, V. H. J. Newman, N. Walter, N. A. R. Kroenke, C. D. Grant, K. A. Akison, L. K. Moritz, K. M. Chambers, C. D. Miranda, R. C. 2018-09-06 doi:10.1101/409854 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ No cell is an island: circulating T cell:monocyte complexes are markers of immune perturbations ]]> https://biorxiv.org/content/10.1101/411553v1?rss=1 Burel, J. G. Pomaznoy, M. Lindestam Arlehamn, C. S. Weiskopf, D. da Silva Antunes, R. Schulten, V. Babor, M. Seumois, G. Greenbaum, J. A. Premawansa, S. Premawansa, G. Wijewickrama, A. Tippalagama, R. deSilva, A. D. Gilman, R. H. Saito, M. Taplitz, R. Vijayanand, P. Sette, A. Peters, B. 2018-09-07 doi:10.1101/411553 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Reduced Medial Frontal Positivity During the Stimulus-Response Interval Precedes Action Errors and Explains Task Deficits in Attention-Deficit Hyperactivity Disorder ]]> https://biorxiv.org/content/10.1101/412494v1?rss=1 Burwell, S. J. Makeig, S. Iacono, W. G. Malone, S. M. 2018-09-09 doi:10.1101/412494 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Genome-wide association studies of impulsive personality traits (BIS-11 and UPPSP) and drug experimentation in up to 22,861 adult research participants ]]> https://biorxiv.org/content/10.1101/414854v1?rss=1 0.5) with drug experimentation and other substance use traits measured in independent cohorts, including smoking initiation, and lifetime cannabis use. Several UPPSP and BIS subscales were genetically correlated with attention-deficit/hyperactivity disorder (rg = 0.30-0.51, p < 8.69 x 10-3), supporting their validity as endophenotypes.nnConclusionsOur findings demonstrate a role for common genetic contributions to individual differences in impulsivity. Furthermore, our study is the first to provide a genetic dissection of the relationship between different types of impulsive personality traits and various psychiatric disorders. ]]> Sanchez-Roige, S. Fontanillas, P. Elson, S. L. the 23andMe Research Team, Gray, J. C. de Wit, H. MacKillop, J. Palmer, A. A. 2018-09-13 doi:10.1101/414854 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses ]]> https://biorxiv.org/content/10.1101/415976v1?rss=1 Hauser, F. Ceciliato, P. H. d. O. Lin, Y.-C. Guo, D. Gregerson, J. Abbasi, N. Youhanna, D. Park, J. Dubeaux, G. Shani, E. Poomchongkho, N. Schroeder, J. 2018-09-16 doi:10.1101/415976 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ Natural variation in the C. elegans autophagy response and clearance of intracellular microsporidia ]]> https://biorxiv.org/content/10.1101/418749v1?rss=1 Balla, K. Lazetic, V. Troemel, E. 2018-09-16 doi:10.1101/418749 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ The speed-accuracy tradeoff reveals flexible access to accumulating sensory evidence during human decision making ]]> https://biorxiv.org/content/10.1101/420430v1?rss=1 Nelli, S. Itthipuripat, S. Rungratsameetaweemana, N. Serences, J. 2018-09-17 doi:10.1101/420430 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets ]]> https://biorxiv.org/content/10.1101/420521v1?rss=1 Sedova, M. Iyer, M. Li, Z. Jaroszewski, L. Post, K. W. Hrabe, T. Porta-Pardo, E. Godzik, A. 2018-09-18 doi:10.1101/420521 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ The spatial chronnectome reveals a dynamic interplay between functional segregation and integration ]]> https://biorxiv.org/content/10.1101/427450v1?rss=1 Iraji, A. DeRamus, T. Lewis, N. Yaesoubi, M. Stephen, J. M. Erhardt, E. Belger, A. Ford, J. McEwen, S. Mathalon, D. Mueller, B. Pearlson, G. Potkin, S. Preda, A. Turner, J. Vaidya, J. van Erp, T. Calhoun, V. 2018-09-25 doi:10.1101/427450 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity ]]> https://biorxiv.org/content/10.1101/428557v1?rss=1 Nechemia-Arbely, Y. H. Miga, K. Shoshani, O. Aslanian, A. A. McMahon, M. Lee, A. Y. Fachinetti, D. R. Yates, J. Ren, B. Cleveland, D. 2018-09-27 doi:10.1101/428557 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ A phylogenomic resolution of the sea urchin tree of life ]]> https://biorxiv.org/content/10.1101/430595v1?rss=1 Mongiardino Koch, N. Coppard, S. E. Lessios, H. A. Briggs, D. E. Mooi, R. Rouse, G. W. 2018-09-29 doi:10.1101/430595 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease ]]> https://biorxiv.org/content/10.1101/431510v1?rss=1 Aleti, G. Baker, J. L. Tang, X. Alvarez, R. Boltelho, M. Tran, N. C. Melnik, A. V. Zhong, C. Ernst, M. Dorrestein, P. C. Edlund, A. 2018-10-02 doi:10.1101/431510 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein ]]> https://biorxiv.org/content/10.1101/432187v1?rss=1 Handa, S. Shaw, K. L. Ghosh, P. 2018-10-01 doi:10.1101/432187 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Genetic risk for coronary heart disease alters the influence of Alzheimer’s genetic risk on mild cognitive impairment ]]> https://biorxiv.org/content/10.1101/432443v1?rss=1 Elman, J. A. Panizzon, M. S. Logue, M. W. Gillespie, N. A. Neale, M. C. Reynolds, C. A. Gustavson, D. E. Andreassen, O. A. Dale, A. M. Franz, C. E. Lyons, M. J. Kremen, W. S. 2018-10-03 doi:10.1101/432443 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Multi-species mosaicism of evolutionary origins of genomic loci harboring 59,732 human-specific regulatory sequences reflects a complex continuous speciation process of the human lineage ]]> https://biorxiv.org/content/10.1101/432625v1?rss=1 Glinsky, G. 2018-10-03 doi:10.1101/432625 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Expression of a recombinant high affinity IgG Fc receptor by engineered NK cells as a docking platform for therapeutic mAbs to target cancer cells ]]> https://biorxiv.org/content/10.1101/432849v1?rss=1 Snyder, K. Hullsiek, R. Mishra, H. Mendez, D. Li, Y. Rogich, A. Kaufman, D. Wu, J. Walcheck, B. 2018-10-02 doi:10.1101/432849 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ The Effects of Global Signal Regression on Estimates of Resting-state BOLD fMRI and EEG Vigilance Correlations ]]> https://biorxiv.org/content/10.1101/433912v1?rss=1 Falahpour, M. Nalci, A. Liu, T. 2018-10-03 doi:10.1101/433912 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Time calibrated morpho-molecular classification of Nassellaria (Radiolaria) ]]> https://biorxiv.org/content/10.1101/435123v1?rss=1 Mendez Sandin, M. Pillet, L. Biard, T. Poirier, C. Bigeard, E. Romac, S. Suzuki, N. Not, F. 2018-10-04 doi:10.1101/435123 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Transcriptional organization of autism spectrum disorder and its connection to ASD risk genes and phenotypic variation ]]> https://biorxiv.org/content/10.1101/435917v1?rss=1 Gazestani, V. H. Pramparo, T. Nalabolu, S. Kellman, B. P. Murry, S. Lopez, L. Pierce, K. Courchesne, E. Lewis, N. E. 2018-10-05 doi:10.1101/435917 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci ]]> https://biorxiv.org/content/10.1101/440230v1?rss=1 Smith, E. N. D'Antonio-Chronowska, A. Greenwald, W. W. Borja, V. Aguiar, L. R. Pogue, R. Matsui, H. Borooah, S. D'Antonio, M. Ayyagari, R. Frazer, K. A. 2018-10-11 doi:10.1101/440230 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers ]]> https://biorxiv.org/content/10.1101/441295v1?rss=1 Chatterjee, N. Pazarentzos, E. Hrustanovic, G. Lin, L. Verschueren, E. Johnson, J. R. Hofree, M. Yan, J. J. Olivas, V. Newton, B. W. Dollen, J. V. Earnshaw, C. H. Flanagan, J. Chan, E. Asthana, S. Ideker, T. Wu, W. Mayekar, M. K. Suzuki, J. Barad, B. Kirichok, Y. Fraser, J. Weiss, W. A. Krogan, N. J. Tulpule, A. Sabnis, A. J. Bivona, T. G. 2018-10-11 doi:10.1101/441295 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Antigen receptor locus dynamics is orchestrated near the sol-gel phase transition to enforce stepwise VDJ gene rearrangement ]]> https://biorxiv.org/content/10.1101/441444v1?rss=1 Khanna, N. Zhang, J. Dudko, O. Murre, C. 2018-10-12 doi:10.1101/441444 Cold Spring Harbor Laboratory Press 2018-10-12 <![CDATA[ Geometric principles of second messenger dynamics in dendritic spines. ]]> https://biorxiv.org/content/10.1101/444489v1?rss=1 Cugno, A. Bartol, T. M. Sejnowski, T. J. Iyengar, R. Rangamani, P. 2018-10-16 doi:10.1101/444489 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Identification of essential regulatory elements in the human genome ]]> https://biorxiv.org/content/10.1101/444562v1?rss=1 telenti, a. Wells, A. C. Heckerman, D. Torkamani, A. Ren, B. di Iulio, J. 2018-10-16 doi:10.1101/444562 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Lipid unsaturation properties govern the sensitivity of membranes to photo-induced oxidative stress ]]> https://biorxiv.org/content/10.1101/451591v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@c17ecdorg.highwire.dtl.DTLVardef@16bc938org.highwire.dtl.DTLVardef@167a85eorg.highwire.dtl.DTLVardef@5ee754_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bour, A. Kruglik, S. G. Chabanon, M. Rangamani, P. Puff, N. Bonneau, S. 2018-10-24 doi:10.1101/451591 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Kinematic and Thermodynamic Limits on the Enhanced Diffusion of Enzymes ]]> https://biorxiv.org/content/10.1101/451682v1?rss=1 Feng, M. Gilson, M. K. 2018-10-24 doi:10.1101/451682 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Directed evolution of split APEX peroxidase ]]> https://biorxiv.org/content/10.1101/452888v1?rss=1 Han, Y. Martell, J. Branon, T. Boassa, D. Shechner, D. Ellisman, M. Ting, A. 2018-10-25 doi:10.1101/452888 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Orbitofrontal neuron ensembles contribute to inhibitory control ]]> https://biorxiv.org/content/10.1101/452938v1?rss=1 Balasubramani, P. P. Hayden, B. 2018-10-25 doi:10.1101/452938 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior ]]> https://biorxiv.org/content/10.1101/453746v1?rss=1 Rouse, A. G. 2018-10-25 doi:10.1101/453746 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Association between chronic hepatitis C virus infection and myocardial infarction in people living with HIV in the United States ]]> https://biorxiv.org/content/10.1101/453860v1?rss=1 Williams-Nguyen, J. Hawes, S. E. Nance, R. M. Lindström, S. Heckbert, S. R. Kim, H. N. Mathews, W. C. Cachay, E. R. Budoff, M. J. Hurt, C. B. Hunt, P. W. Geng, E. Moore, R. D. Mugavero, M. J. Peter, I. Kitahata, M. M. Saag, M. S. Crane, H. M. Delaney, J. A. A. 2018-10-26 doi:10.1101/453860 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect ]]> https://biorxiv.org/content/10.1101/457333v1?rss=1 Deshpande, V. Luebeck, J. Bakhtiari, M. Nguyen, N.-P. D. Turner, K. M. Schwab, R. Carter, H. Mischel, P. S. Bafna, V. 2018-10-30 doi:10.1101/457333 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways ]]> https://biorxiv.org/content/10.1101/458562v1?rss=1 Nievergelt, C. M. Maihofer, A. X. Klengel, T. Atkinson, E. G. Chen, C.-Y. Choi, K. W. Coleman, J. R. I. Dalvie, S. Duncan, L. E. Logue, M. W. Provost, A. Ratanatharathorn, A. Stein, M. B. Torres, K. Aiello, A. E. Almli, L. M. Amstadter, A. B. Andersen, S. B. Andreassen, O. A. Arbisi, P. A. Ashley-Koch, A. E. Austin, S. B. Avdibegovic, E. Babic, D. Baekvad-Hansen, M. Baker, D. G. Beckham, J. C. Bierut, L. J. Bisson, J. I. Boks, M. P. Bolger, E. A. Borglum, A. D. Bradley, B. Brashear, M. Breen, G. Bryant, R. A. Bustamante, A. C. Bybjerg-Grauholm, J. Calabres 2018-11-01 doi:10.1101/458562 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking ]]> https://biorxiv.org/content/10.1101/469940v1?rss=1 Wagner, J. Churas, C. Liu, S. Swift, R. Chiu, M. Shao, C. Feher, V. Burley, S. Gilson, M. Amaro, R. 2018-11-18 doi:10.1101/469940 Cold Spring Harbor Laboratory Press 2018-11-18 <![CDATA[ Excitability changes in the motor cortex in preparation for self-paced and cue-guided movements: a transcranial magnetic stimulation study ]]> https://biorxiv.org/content/10.1101/470153v1?rss=1 Ibanez, J. Hannah, R. Rocchi, L. Rothwell, J. C. 2018-11-14 doi:10.1101/470153 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells ]]> https://biorxiv.org/content/10.1101/470963v1?rss=1 Ren, B. Li, G. Liu, Y. Fang, R. Kellis, M. Zhang, Y. 2018-11-14 doi:10.1101/470963 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Tissue mechanics and somatosensory neural responses govern touch sensation in C. elegans ]]> https://biorxiv.org/content/10.1101/471904v1?rss=1 Sanzeni, A. Katta, S. Petzold, B. Pruitt, B. L. Goodman, M. B. Vergassola, M. 2018-11-16 doi:10.1101/471904 Cold Spring Harbor Laboratory Press 2018-11-16 <![CDATA[ Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs ]]> https://biorxiv.org/content/10.1101/472019v1?rss=1 Yan, Z. Huang, N. Wu, W. Chen, W. Jiang, Y. Chen, J. Huang, X. Wen, X. Xu, J. Jin, Q. Zhang, K. Chen, Z. Chien, S. Zhong, S. 2018-11-19 doi:10.1101/472019 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ SYNPLA: A synapse-specific method for identifying learning-induced synaptic plasticity loci ]]> https://biorxiv.org/content/10.1101/473314v1?rss=1 Dore, K. Pao, Y. Soria Lopez, J. Aronson, S. Zhan, H. Ghosh, S. Merrill, S. Zador, A. M. Malinow, R. Kebschull, J. M. 2018-11-19 doi:10.1101/473314 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ APPLES: Fast Distance-based Phylogenetic Placement ]]> https://biorxiv.org/content/10.1101/475566v1?rss=1 Balaban, M. Sarmashghi, S. Mirarab, S. 2018-11-23 doi:10.1101/475566 Cold Spring Harbor Laboratory Press 2018-11-23 <![CDATA[ A learned embedding for efficient joint analysis of millions of mass spectra ]]> https://biorxiv.org/content/10.1101/483263v1?rss=1 May, D. H. Bilmes, J. Noble, W. S. 2018-11-29 doi:10.1101/483263 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ 3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains ]]> https://biorxiv.org/content/10.1101/485961v1?rss=1 Zhang, Y. Li, T. Preissl, S. Grinstein, J. Farah, E. Destici, E. Lee, A. Y. Chee, S. Qiu, Y. Ma, K. Ye, Z. Zhu, Q. Huang, H. Hu, R. Fang, R. Evans, S. Chi, N. Ren, B. 2018-12-04 doi:10.1101/485961 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ The Ca2+ sensor protein CMI1 fine tunes root development, auxin distribution and responses ]]> https://biorxiv.org/content/10.1101/488536v1?rss=1 Hazak, O. Mamon, E. Lavy, M. Sternberg, H. Behera, S. Schmitz-Thom, I. Bloch, D. Dementiev, O. Gutman, I. Danziger, T. Schwarz, N. Abuzeineh, A. Mockaitis, K. Estelle, M. Hirsch, J. Kudla, J. Yalovsky, S. 2018-12-05 doi:10.1101/488536 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra ]]> https://biorxiv.org/content/10.1101/491506v1?rss=1 nView larger version (19K):norg.highwire.dtl.DTLVardef@1382d8borg.highwire.dtl.DTLVardef@13636a4org.highwire.dtl.DTLVardef@3d7decorg.highwire.dtl.DTLVardef@1161d62_HPS_FORMAT_FIGEXP M_FIG Integration of MS2LDA substructure discovery with MAGMa spectral annotations and ClassyFire term predictions complemented with MotifDB significantly advance metabolite annotation.nnC_FIG Complex metabolite mixtures are challenging to unravel. Mass spectrometry (MS) is a widely used and sensitive technique to obtain structural information on complex mixtures. However, just knowing the molecular masses of the mixtures constituents is almost always insufficient for confident assignment of the associated chemical structures. Structural information can be augmented through MS fragmentation experiments whereby detected metabolites are fragmented giving rise to MS/MS spectra. However, how can we maximize the structural information we gain from fragmentation spectra?nnWe recently proposed a substructure-based strategy to enhance metabolite annotation for complex mixtures by considering metabolites as the sum of (bio)chemically relevant moieties that we can detect through mass spectrometry fragmentation approaches. Our MS2LDA tool allows us to discover - unsupervised - groups of mass fragments and/or neutral losses termed Mass2Motifs that often correspond to substructures. After manual annotation, these Mass2Motifs can be used in subsequent MS2LDA analyses of new datasets, thereby providing structural annotations for many molecules that are not present in spectral databases.nnHere, we describe how additional strategies, taking advantage of i) combinatorial in-silico matching of experimental mass features to substructures of candidate molecules, and ii) automated machine learning classification of molecules, can facilitate semi-automated annotation of substructures. We show how our approach accelerates the Mass2Motif annotation process and therefore broadens the chemical space spanned by characterized motifs. Our machine learning model used to classify fragmentation spectra learns the relationships between fragment spectra and chemical features. Classification prediction on these features can be aggregated for all molecules that contribute to a particular Mass2Motif and guide Mass2Motif annotations.nnTo make annotated Mass2Motifs available to the community, we also present motifDB: an open database of Mass2Motifs that can be browsed and accessed programmatically through an API. MotifDB is integrated within ms2lda.org, allowing users to efficiently search for characterized motifs in their own experiments. We expect that with an increasing number of Mass2Motif annotations available through a growing database we can more quickly gain insight in the constituents of complex mixtures. That will allow prioritization towards novel or unexpected chemistries and faster recognition of known biochemical building blocks. ]]> Rogers, S. Wei Ong, C. Wandy, J. Ernst, M. Ridder, L. van der Hooft, J. J. J. 2018-12-09 doi:10.1101/491506 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits ]]> https://biorxiv.org/content/10.1101/495226v1?rss=1 Feupe Fotsing, S. Wang, C. Saini, S. Shleizer-Burko, S. Goren, A. Gymrek, M. 2018-12-13 doi:10.1101/495226 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ LIN-15B promotes enrichment of H3K9me2 on the promoters of a subset of germline genes that are repressed in somatic cells in C. elegans ]]> https://biorxiv.org/content/10.1101/497438v1?rss=1 Rechtsteiner, A. Costello, M. E. Egelhofer, T. A. Garrigues, J. M. Strome, S. Petrella, L. 2018-12-17 doi:10.1101/497438 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Precision Medicine Advancements Using Whole Genome Sequencing, Noninvasive Whole Body Imaging, and Functional Diagnostics ]]> https://biorxiv.org/content/10.1101/497560v1?rss=1 400, Relative Risk of 7.2), 8.0% had arrhythmia found on continuous rhythm monitoring, 6.5% had cardiac conduction disorders found on EKG, 2% had previously undetected tumors detected by WB MRI, and 2.5% had previously undetected aneurysms detected by non-contrast MRI/MRA. Using family histories, personal histories, and test results, clinical and phenotypic findings were correlated with genomic findings in 130 study participants (63.1%) with high to moderate penetrance variants, suggesting the precision health platform improves the diagnostic process in asymptomatic individuals who were at risk. Cardiovascular and endocrine diseases achieved considerable clinical associations between MSFs and clinical phenotypes (89% and 72%, respectively). These findings demonstrate the value of integrating WGS and noninvasive clinical assessments for a rapid and integrated point-of-care clinical diagnosis of age-related diseases that contribute to premature mortality. ]]> Hou, Y.-C. C. Yu, H.-C. Martin, R. Schenker-Ahmed, N. M. Hicks, M. Cirulli, E. T. Cohen, I. V. Jonsson, T. J. Heister, R. Napier, L. Leon Swisher, C. Dominguez, S. Tang, H. Li, W. Barea, J. Rybak, C. Smith, E. Duchicela, K. Doney, M. Brar, P. Hernandez, N. Kirkness, E. F. Kahn, A. M. Venter, J. C. Karow, D. S. Caskey, C. T. 2018-12-17 doi:10.1101/497560 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Genome-wide association study of diabetic kidney disease highlights biology involved in renal basement membrane collagen ]]> https://biorxiv.org/content/10.1101/499616v1?rss=1 Salem, R. Todd, J. N. Sandholm, N. Cole, J. B. Chen, W.-M. Andrews, D. Pezzolesi, M. G. MCKEIGUE, P. M. Hiraki, L. T. Qiu, C. Nair, V. Liao, C. D. Cao, J. J. Valo, E. Onengut-Gumuscu, S. Smiles, A. M. MCGURNAGHAN, S. Haukka, J. K. Harjutsalo, V. Brennan, E. P. van Zuydam, N. Ahlqvist, E. Doyle, R. Ahluwalia, T. S. Lajer, M. Hughes, M. F. Park, J. Skupien, J. Spiliopoulou, A. Liu, A. Menon, R. Boustany-Kari, C. M. Kang, H. M. Nelson, R. G. Klein, R. Klein, B. E. Lee, K. E. Gao, X. Mauer, M. Maeastroni, S. Caramori, M. L. de Boer, I. H. Miller, R. G. Gu 2018-12-19 doi:10.1101/499616 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Fibroblast growth factor receptors function redundantly during zebrafish embryonic development ]]> https://biorxiv.org/content/10.1101/501023v1?rss=1 Leerberg, D. M. Hopton, R. E. Draper, B. W. 2018-12-20 doi:10.1101/501023 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Antimalarial drug mefloquine kills both trophozoite and cyst stages of Entamoeba ]]> https://biorxiv.org/content/10.1101/501999v1?rss=1 Sauvey, C. Ehrenkaufer, G. Debnath, A. Abagyan, R. 2018-12-20 doi:10.1101/501999 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Community venomics reveals intra-species variations in venom composition of a local population of Vipera kaznakovi in Northeastern Turkey ]]> https://biorxiv.org/content/10.1101/503276v1?rss=1 Petras, D. Hempel, B.-F. Gocmen, B. Karis, M. Whiteley, G. Wagstaff, S. C. Heiss, P. Casewell, N. R. Nalbantsoy, A. Suessmuth, R. D. 2018-12-20 doi:10.1101/503276 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ A biophysical computational model for memory trace transfer from hippocampus to neocortex ]]> https://biorxiv.org/content/10.1101/503524v1?rss=1 Liu, X. Kuzum, D. 2018-12-21 doi:10.1101/503524 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ A Rap1 binding site and lipid-dependent helix in talin F1 domain cooperate in integrin activation ]]> https://biorxiv.org/content/10.1101/504894v1?rss=1 Gingras, A. Lagarrigue, F. Cuevas, M. Zorovich, M. Valadez, A. Lopez-Ramirez, M. A. Seban, N. McLaughlin, W. Ginsberg, M. 2018-12-21 doi:10.1101/504894 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Genomic perspectives on adaptation and conservation in the endangered long-tailed goral (Naemorhedus caudatus). ]]> https://biorxiv.org/content/10.1101/505156v1?rss=1 Weber, J. A. Chung, O. Kim, J. Jun, J. Lee, H. Jho, S. Cho, Y. S. Kim, D.-S. Paek, W. k. Kim, S. Lee, H. Lee, S. Edwards, J. S. Cook, J. A. An, J. Bhak, J. 2018-12-23 doi:10.1101/505156 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ Full Atomistic Model Of Prion Structure And Conversion ]]> https://biorxiv.org/content/10.1101/505271v1?rss=1 Spagnolli, G. Rigoli, M. Orioli, S. Sevillano, A. M. Faccioli, P. Wille, H. Biasini, E. Requena, J. R. 2018-12-22 doi:10.1101/505271 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ HiCluster: A Robust Single-Cell Hi-C Clustering Method Based on Convolution and Random Walk ]]> https://biorxiv.org/content/10.1101/506717v1?rss=1 Zhou, J. Ma, J. Chen, Y. Cheng, C. Bao, B. Peng, J. Sejnowski, T. Dixon, J. Ecker, J. 2018-12-27 doi:10.1101/506717 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ HOOK3 is a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein and KIF1C ]]> https://biorxiv.org/content/10.1101/508887v1?rss=1 Kendrick, A. A. Redwine, W. B. Tran, P. T. Pontano Vaites, L. Dzieciatkowska, M. Harper, J. W. Reck-Peterson, S. L. 2018-12-31 doi:10.1101/508887 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Perceptions and Prospects in Life Sciences in a Heterogenous Latin American Population ]]> https://biorxiv.org/content/10.1101/514216v1?rss=1 Ferreira, L. M. R. Carosso, G. A. Lopez-Videla, B. Vaca Diez, G. Rivera-Betancourt, L. I. Rodriguez, Y. Ordonez, D. G. Montellano Duran, N. Alatriste-Gonzalez, D. K. Vacaflores, A. Bohorquez, S. Gonzalez Auza, L. Schuetz, C. Alexander-Savino, C. Gandarilla Cuellar, O. Mostajo Radji, M. A. 2019-01-07 doi:10.1101/514216 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Genomewide Analyses of Psychological Resilience in US Army Soldiers ]]> https://biorxiv.org/content/10.1101/516716v1?rss=1 Stein, M. Choi, K. W. Jain, S. Campbell-Sills, L. Chen, C.-Y. Gelernter, J. He, F. Heeringa, S. G. Maihofer, A. X. Nievergelt, C. M. Nock, M. K. Ripke, S. Sun, X. Kessler, R. C. Smoller, J. W. Ursano, R. J. 2019-01-20 doi:10.1101/516716 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ A Note on Computing Interval Overlap Statistics ]]> https://biorxiv.org/content/10.1101/517987v1?rss=1 Sarmashghi, S. Bafna, V. 2019-01-11 doi:10.1101/517987 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Cell Fate Determining Molecular Switches and Signaling Pathway in Pax7-expressing Somitic Mesoderm ]]> https://biorxiv.org/content/10.1101/518084v1?rss=1 Fung, C. W. Han, Z. Zhou, S. Wu, Z. Wu, A. R. 2019-01-11 doi:10.1101/518084 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments ]]> https://biorxiv.org/content/10.1101/521872v1?rss=1 Behsaz, B. Mohimani, H. Gurevich, A. Prjibelski, A. Fisher, M. F. Smarr, L. Dorrestein, P. C. Mylne, J. S. Pevzner, P. A. 2019-01-16 doi:10.1101/521872 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/523043v1?rss=1 Gao, J. Gileta, A. F. Bimschleger, H. V. St. Pierre, C. L. Gopalakrishnan, S. Palmer, A. A. 2019-01-23 doi:10.1101/523043 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Aβ-Positivity Predicts Cognitive Decline but Cognition Also Predicts Progression to Aβ-Positivity ]]> https://biorxiv.org/content/10.1101/523787v1?rss=1 Elman, J. A. Panizzon, M. S. Franz, C. E. Gustavson, D. E. Sanderson, M. E. Lyons, M. J. Kremen, W. S. 2019-01-17 doi:10.1101/523787 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores ]]> https://biorxiv.org/content/10.1101/526475v1?rss=1 Lewis, V. Saunders, L. Larson, T. A. Bain, E. Sturiale, S. Gur, D. Chowdhury, S. Flynn, J. Allen, M. Deheyn, D. Lee, J. Simon, J. Lippincott-Schwartz, J. Raible, D. Parichy, D. 2019-01-22 doi:10.1101/526475 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Optimal sparse olfactory representations persist in a plastic network ]]> https://biorxiv.org/content/10.1101/528125v1?rss=1 Assisi, C. Stopfer, M. Bazhenov, M. 2019-01-23 doi:10.1101/528125 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ YAP/TAZ as a Novel Regulator of cell volume ]]> https://biorxiv.org/content/10.1101/528133v1?rss=1 Perez Gonzalez, N. A. Rochman, N. D. Yao, K. Tao, J. Tran Le, M.-T. Flanary, S. Sablich, L. Toler, B. Crentsil, E. Takaesu, F. Lambrus, B. Huang, J. Fu, V. Holland, A. An, S. Wirtz, D. Guan, K.-L. Sun, S. 2019-01-23 doi:10.1101/528133 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Members of the Arabidopsis auxin receptor gene family are essential early in embryogenesis and have broadly overlapping functions ]]> https://biorxiv.org/content/10.1101/529248v1?rss=1 Prigge, M. J. Kadakia, N. Greenham, K. Estelle, M. 2019-01-23 doi:10.1101/529248 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins ]]> https://biorxiv.org/content/10.1101/529289v1?rss=1 Tsuboi, T. Viana, M. P. Xu, F. Yu, J. Chanchani, R. Arceo, X. G. Tutucci, E. Choi, J. Chen, Y. S. Singer, R. H. Rafelski, S. M. Zid, B. M. 2019-01-25 doi:10.1101/529289 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Dedifferentiation orchestrated through remodeling of the chromatin landscape defines PSEN1 mutation-induced Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/531202v1?rss=1 Caldwell, A. B. Liu, Q. Schroth, G. P. Tanzi, R. E. Galasko, D. R. Yuan, S. H. Wagner, S. L. Subramaniam, S. 2019-01-29 doi:10.1101/531202 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/539379v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@12ba2f9org.highwire.dtl.DTLVardef@1d88c15org.highwire.dtl.DTLVardef@1d4f21eorg.highwire.dtl.DTLVardef@16396aa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4:C_FLOATNO (A-D) Coverage tracks of the PSBS genomic regions from five low NPQ (A and B) and five high NPQ (C and D) Arabidopsis accessions aligned with the TAIR 10 Col-0 reference genome (low NPQ accession; A and C) and KBS-Mac-74 genome (high NPQ accession; B and D). Values along x-axes indicate the base pair distance relative to the PSBS transcription start site. Genes along the track are coloured green and the intergenic region is coloured pink. (E) Graphical view of the alignment of the TAIR 10 Col-0 and the KBS-Mac-74 PSBS genomic regions. Axis values refer to base pair positions within the respective tracks. (F) Comparison of the average relative PsbS protein abundance between low and high NPQ accessions. Error bars represent standard deviations. N=30; *** P < 0.001 with paired Students T test. C_FIG ]]> Rungrat, T. Almonte, A. A. Cheng, R. Gollan, P. J. Stuart, T. Aro, E.-M. Borevitz, J. O. Pogson, B. Wilson, P. B. 2019-02-03 doi:10.1101/539379 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation: Mapping the Neoantigen to 3D Genome ]]> https://biorxiv.org/content/10.1101/539387v1?rss=1 Shang, X. Zhang, M. Meng, L. Su, X. Li, Q. Lin, M. Zou, X. Luo, Q. Zhai, Y. He, K. Wang, L. Da, L. Cai, W. T. Han, Z.-g. Shi, Y. 2019-02-03 doi:10.1101/539387 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Reproducible Risk Loci and Psychiatric Comorbidities in Anxiety: Results from ~200,000 Million Veteran Program Participants ]]> https://biorxiv.org/content/10.1101/540245v1?rss=1 Levey, D. F. Gelernter, J. Polimanti, R. Zhou, H. Cheng, Z. Aslan, M. Quaden, R. Concato, J. Radhakrishnan, K. Bryois, J. Sullivan, P. F. the Million Veteran Program, Stein, M. 2019-02-05 doi:10.1101/540245 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Oligogenic effects of 16p11.2 copy number variation on craniofacial development ]]> https://biorxiv.org/content/10.1101/540732v1?rss=1 Qiu, Y. Arbogast, T. Martin Lorenzo, S. Li, H. Shih, T. Ellen, R. Hong, O. Cho, S. Shanta, O. Timothy, P. Corsello, C. Deutsch, C. K. Chevalier, C. Davis, E. E. Iakoucheva, L. M. Herault, Y. Katasanis, N. Messer, K. Sebat, J. 2019-02-05 doi:10.1101/540732 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Ligand dependent gene regulation by transient ER clustered enhancers ]]> https://biorxiv.org/content/10.1101/541540v1?rss=1 Saravanan, B. Soota, D. Islam, Z. Jayani, R. S. Mann, R. Farooq, U. Meel, S. Walavalkar, K. Gayen, S. Singh, A. K. Hannenhalli, S. Notani, D. 2019-02-05 doi:10.1101/541540 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors ]]> https://biorxiv.org/content/10.1101/546481v1?rss=1 50 GPCRs, including many targets for approved drugs, hitherto largely unrecognized as targets of interest in cancer. GPCR mRNA signatures characterize specific tumor types, indicate survival and correlate with expression of cancer-related pathways. Tumor GPCR mRNA signatures have prognostic relevance for survival and correlate with expression of numerous cancer-related genes and pathways. GPCR expression in tumors is largely independent of staging/grading/metastasis/driver mutations and GPCRs expressed in cancer cell lines parallels that measured in tumors. Certain GPCRs are frequently mutated and appear to be hotspots, serving as bellwethers of accumulated genomic damage. CNV of GPCRs while common, does not generally correlate with mRNA expression. We suggest a previously under-appreciated role for GPCRs in cancer, perhaps as functional oncogenes, biomarkers, surface antigens and pharmacological targets. ]]> Sriram, K. Moyung, K. Corriden, R. Carter, H. Insel, P. A. 2019-02-11 doi:10.1101/546481 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Direct Visualization of Live Zebrafish Glycan via Single-step Metabolic Labeling with Fluorophore-tagged Nucleotide Sugars ]]> https://biorxiv.org/content/10.1101/548016v1?rss=1 Hong, S. Sahai-Hernandez, P. Traver, D. Wu, P. 2019-02-12 doi:10.1101/548016 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards ]]> https://biorxiv.org/content/10.1101/551978v1?rss=1 Lind, A. Lai, Y. Y. Y. Mostovoy, Y. Holloway, A. K. Iannucci, A. Mak, A. C. Fondi, M. Orlandini, V. Eckalbar, W. L. Milan, M. Rovatsos, M. Kichigin, I. G. Makunin, A. I. Trifonov, V. Schijlen, E. Kratochvil, L. Fani, R. Jessop, T. S. Patarnello, T. Hicks, J. W. Ryder, O. A. Mendelson, J. R. Ciofi, C. Kwok, P.-Y. A. Pollard, K. S. Bruneau, B. 2019-02-15 doi:10.1101/551978 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ rSeqTU -- a machine-learning based R package for prediction of bacterial transcription units ]]> https://biorxiv.org/content/10.1101/553057v1?rss=1 Niu, S.-Y. Liu, B. Ma, Q. Chou, W.-C. 2019-02-18 doi:10.1101/553057 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Metabolic basis of brain-like electrical signalling in bacterial communities ]]> https://biorxiv.org/content/10.1101/553305v1?rss=1 Martinez-Corral, R. Liu, J. Prindle, A. Suel, G. M. Garcia-Ojalvo, J. 2019-02-18 doi:10.1101/553305 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Future sea-level rise drives rocky intertidal habitat loss and benthic community change ]]> https://biorxiv.org/content/10.1101/553933v1?rss=1 Kaplanis, N. Edwards, C. B. Eynaud, Y. Smith, J. E. 2019-02-18 doi:10.1101/553933 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Activity-dependent maturation of prefrontal gamma oscillations sculpts cognitive performance ]]> https://biorxiv.org/content/10.1101/558957v1?rss=1 Bitzenhofer, S. H. Poepplau, J. A. Chini, M. Marquardt, A. Hanganu-Opatz, I. 2019-02-22 doi:10.1101/558957 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Avant-garde assembly-line biosynthesis expands diversity of cyclic lipodepsipeptide products ]]> https://biorxiv.org/content/10.1101/560987v1?rss=1 Zhang, J. J. Tang, X. Huan, T. Ross, A. C. Moore, B. S. 2019-02-25 doi:10.1101/560987 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Photoperiod-induced neurotransmitter plasticity declines with aging: an epigenetic regulation? ]]> https://biorxiv.org/content/10.1101/563213v1?rss=1 Pritchard, R. Chen, H. Romoli, B. Spitzer, N. C. Dulcis, D. 2019-02-27 doi:10.1101/563213 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Mouth Function Determines The Shape Oscillation Pattern In Regenerating Hydra Tissue Spheres ]]> https://biorxiv.org/content/10.1101/565465v1?rss=1 Wang, R. Goel, T. Khazoyan, K. Sabry, Z. Quan, H. J. Diamond, P. H. Collins, E.-M. S. 2019-03-04 doi:10.1101/565465 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Genomic decoding of neuronal depolarization by stimulus-specific NPAS4 heterodimers ]]> https://biorxiv.org/content/10.1101/565721v1?rss=1 Brigidi, G. S. Hayes, M. G. B. Hartzell, A. L. Texari, L. Lin, P.-A. Bartlett, A. Ecker, J. R. Benner, C. Heinz, S. Bloodgood, B. L. 2019-03-03 doi:10.1101/565721 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ Value-driven attentional capture enhances distractor representations in early visual cortex ]]> https://biorxiv.org/content/10.1101/567354v1?rss=1 Itthipuripat, S. Vo, V. A. Sprague, T. C. Serences, J. 2019-03-04 doi:10.1101/567354 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Bone marrow transplantation rescues monocyte recruitment defect and improves cystic fibrosis in mice ]]> https://biorxiv.org/content/10.1101/570135v1?rss=1 Fan, Z. Miller, J. Herro, R. Ehinger, E. Conrad, D. J. Mikulski, Z. Zhu, Y. P. Marcovecchio, P. M. Hedrick, C. C. Ley, K. 2019-03-06 doi:10.1101/570135 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Fear Learning Induces Long-Lasting Changes in Gene Expression and Pathway Specific Presynaptic Growth ]]> https://biorxiv.org/content/10.1101/571331v1?rss=1 Dillingham, B. C. Cameron, P. Pieraut, S. Cardozo, L. M. Yoo, E. J. Maximov, A. Stowers, L. Mayford, M. 2019-03-09 doi:10.1101/571331 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels ]]> https://biorxiv.org/content/10.1101/572305v1?rss=1 Estelle, M. Salehin, M. Li, B. Tang, M. Katz, E. Song, L. Ecker, J. Kliebenstein, D. 2019-03-10 doi:10.1101/572305 Cold Spring Harbor Laboratory Press 2019-03-10 <![CDATA[ Engineered phenotype patterns in microbial populations ]]> https://biorxiv.org/content/10.1101/575068v1?rss=1 Bittihn, P. Didovyk, A. Tsimring, L. S. Hasty, J. 2019-03-13 doi:10.1101/575068 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Glioblastomas derived from genetically modified pluripotent stem cells recapitulate pathobiology ]]> https://biorxiv.org/content/10.1101/576009v1?rss=1 Koga, T. Benitez, J. A. Chaim, I. A. Markmiller, S. Parisian, A. D. Turner, K. M. Hessenauer, F. M. D'Antonio, M. Nguyen, N.-p. D. Saberi, S. Ma, J. Miki, S. Boyer, A. D. Ravits, J. Frazer, K. A. Bafna, V. Chen, C. C. Mischel, P. S. Yeo, G. W. Furnari, F. B. 2019-03-13 doi:10.1101/576009 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Coordinated development of the mouse extrahepatic bile duct: implications for neonatal susceptibility to biliary injury ]]> https://biorxiv.org/content/10.1101/576256v1?rss=1 nView larger version (27K):norg.highwire.dtl.DTLVardef@1685e52org.highwire.dtl.DTLVardef@1086478org.highwire.dtl.DTLVardef@1fc3f55org.highwire.dtl.DTLVardef@1a20a5f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khandekar, G. Llewellyn, J. Kriegermeier, A. Waisbourd-Zinman, O. Johnson, N. Du, Y. Giwa, R. Liu, X. Kisseleva, T. Russo, P. A. Theise, N. D. Wells, R. G. 2019-03-13 doi:10.1101/576256 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Simple Framework for Constructing Functional Spiking Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/579706v1?rss=1 Kim, R. Li, Y. Sejnowski, T. J. 2019-03-15 doi:10.1101/579706 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Analysis of Genetically Regulated Gene Expression identifies a trauma type specific PTSD gene, SNRNP35 ]]> https://biorxiv.org/content/10.1101/581124v1?rss=1 Huckins, L. M. Breen, M. S. Chatzinakos, C. Hartmann, J. Klengel, T. da Silva Almeida, A. C. Dobbyn, A. Girdhar, K. Hoffman, G. E. Klengel, C. Logue, M. Lori, A. Morrison, F. G. Nguyen, H. T. Park, Y. Ruderfer, D. Sloofman, L. van Rooij, S. J. PTSD Working Group of the Psychiatric Genomics Con, Baker, D. Chen, C.-Y. Cox, N. Duncan, L. Geyer, M. A. Glatt, S. Im, H. K. Maihofer, A. Risbrough, V. B. Smoller, J. W. Stein, D. J. Yehuda, R. Liberzon, I. Koenen, K. C. Jovanovic, T. Kellis, M. Miller, M. W. Bacanu, S.-A. Nievergelt, C. Buxbaum, J. D. Sklar, P. 2019-03-19 doi:10.1101/581124 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Identification of histological features to predict MUC2 expression in colon cancer tissues ]]> https://biorxiv.org/content/10.1101/584292v1?rss=1 Periyakoil, P. K. Clarke, M. Sahoo, D. 2019-03-21 doi:10.1101/584292 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Linalool acts as a fast and reversible anesthetic in Hydra ]]> https://biorxiv.org/content/10.1101/584946v1?rss=1 Goel, T. Wang, R. Martin, S. Lanphear, E. Collins, E.-M. S. 2019-03-24 doi:10.1101/584946 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ 3.1A structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids ]]> https://biorxiv.org/content/10.1101/585547v1?rss=1 Lahiri, I. Xu, J. Han, B. G. Oh, J. Wang, D. DiMaio, F. Leschziner, A. E. 2019-03-22 doi:10.1101/585547 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Tamoxifen Suppresses Pancreatic β-Cell Proliferation in Mice ]]> https://biorxiv.org/content/10.1101/586602v1?rss=1 Ahn, S.-H. Granger, A. Rankin, M. M. Lam, C. J. Cox, A. R. Kushner, J. A. 2019-03-22 doi:10.1101/586602 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ NOD1 mediates non-canonical inflammasome processing of interleukin-18 in epithelial cells to Helicobacter pylori infection. ]]> https://biorxiv.org/content/10.1101/587212v1?rss=1 Tran, L. S. Ying, L. D'Costa, K. Wray-McCann, G. Kerr, G. Le, L. Allison, C. C. Ferrand, J. Chaudhry, H. Emery, J. De Paoli, A. Creed, S. Kaparakis-Liaskos, M. Como, J. Dowling, J. Johanesen, P. A. Kufer, T. A. Pedersen, J. S. Mansell, A. Philpott, D. J. Elgass, K. Abud, H. E. Nachbur, U. Croker, B. A. Masters, S. L. Ferrero, R. L. 2019-03-24 doi:10.1101/587212 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Nilotinib, an approved leukemia drug, inhibits Smoothened signaling in Hedgehog-dependent medulloblastoma ]]> https://biorxiv.org/content/10.1101/588897v1?rss=1 Chahal, K. K. Li, J. Kufareva, I. Parle, M. Durden, D. D. Wechsler-Reya, R. Chen, C. C. Abagyan, R. 2019-03-25 doi:10.1101/588897 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data. ]]> https://biorxiv.org/content/10.1101/591016v1?rss=1 Wang, M. Jarmusch, A. K. Vargas, F. Aksenov, A. A. Gauglitz, J. Weldon, K. Petras, D. da Silva, R. Quinn, R. Melnik, A. van der Hooft, J. J. J. Rodriguez, A. M. C. Nothias, L. F. Aceves, C. M. Panitchpakdi, M. Brown, E. Di Ottavio, F. Sikora, N. Elijah, E. O. Labarta-Bajo, L. Gentry, E. G. Shalapour, S. Kyle, K. E. Puckett, S. P. Watrous, J. D. Carpenter, C. S. Bouslimani, A. Ernst, M. Swafford, A. D. Zuniga, E. I. Balunas, M. J. Klassen, J. L. Loomba, R. Knight, R. Bandeira, N. Dorrestein, P. C. 2019-03-28 doi:10.1101/591016 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ TreeCluster: clustering biological sequences using phylogenetic trees ]]> https://biorxiv.org/content/10.1101/591388v1?rss=1 Balaban, M. Moshiri, N. Mai, U. Mirarab, S. 2019-03-28 doi:10.1101/591388 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Mitochondria supply ATP to the ER through a mechanism antagonized by cytosolic Ca2+ ]]> https://biorxiv.org/content/10.1101/591685v1?rss=1 Yong, J. Bischof, H. Siirin, M. Murphy, A. N. Malli, R. Kaufman, R. J. 2019-03-27 doi:10.1101/591685 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy ]]> https://biorxiv.org/content/10.1101/594184v1?rss=1 nView larger version (52K):norg.highwire.dtl.DTLVardef@20c737org.highwire.dtl.DTLVardef@1f714faorg.highwire.dtl.DTLVardef@823560org.highwire.dtl.DTLVardef@7e6219_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIHigh grade serous ovarian carcinoma tumors contain PTK2 (FAK) 8q24.3 gains associated with prognostic differences.nC_LIO_LIKMF, a new murine ovarian cancer model with K-Ras, Myc, and FAK gene gains and intrinsic platinum resistance.nC_LIO_LIFAK activation in tumors surviving platinum chemotherapy promotes cancer stem cell survival.nC_LIO_LIFAK facilitates a {beta}-catenin-Myc signaling axis controlling gene expression supporting platinum resistance.nC_LIO_LIFAK activity is essential for KMF tumor growth and is a targetable cellular adaptation of platinum resistance.nC_LI ]]> Diaz Osterman, C. J. Ozmadenci, D. Kleinschmidt, E. G. Taylor, K. N. Barrie, A. M. Jiang, S. Bean, L. M. Sulzmaier, F. J. Jean, C. Tancioni, I. Anderson, K. Uryu, S. Cordasco, E. A. Li, J. Chen, X. L. Fu, G. Ojalill, M. Rappu, P. Heino, J. Mark, A. M. Xu, G. Fisch, K. M. Kolev, V. N. Weaver, D. T. Pachter, J. A. Gyorffy, B. McHale, M. T. Connolly, D. C. Molinolo, A. Stupack, D. G. Schlaepfer, D. D. 2019-03-30 doi:10.1101/594184 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Biomolecular Contrast Agents for Optical Coherence Tomography ]]> https://biorxiv.org/content/10.1101/595157v1?rss=1 Lu, G. J. Chou, L.-d. Malounda, D. Patel, A. K. Welsbie, D. S. Chao, D. L. Ramalingam, T. Shapiro, M. G. 2019-03-31 doi:10.1101/595157 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Generation of Temperature Sensitive Mutations with Error-Prone PCR in a Gene Encoding a Component of the Spindle Pole Body in Fission Yeast ]]> https://biorxiv.org/content/10.1101/595447v1?rss=1 Tang, N. H. Fong, C. S. Masuda, H. Jourdain, I. Yukawa, M. Toda, T. 2019-04-01 doi:10.1101/595447 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ Quantifying the mechanics of locomotion of the schistosome pathogen with respect to changes in its physical environment ]]> https://biorxiv.org/content/10.1101/599993v1?rss=1 Zhang, S. Skinner, D. Joshi, P. Criado-Hidalgo, E. Yeh, Y.-T. Lasheras, J. C. Caffrey, C. R. del Alamo, J. C. 2019-04-05 doi:10.1101/599993 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ A Theoretical Model of Telomere Length Regulation ]]> https://biorxiv.org/content/10.1101/602037v1?rss=1 Ishii, H. 2019-04-08 doi:10.1101/602037 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Not just one p: Multivariate GWAS of psychiatric disorders and their cardinal symptoms reveal two dimensions of cross-cutting genetic liabilities ]]> https://biorxiv.org/content/10.1101/603134v1?rss=1 Mallard, T. T. Karlsson Linner, R. Okbay, A. Grotzinger, A. D. de Vlaming, R. Meddens, S. F. W. Tucker-Drob, E. M. Kendler, K. Keller, M. C. Koellinger, P. D. Harden, K. P. 2019-04-09 doi:10.1101/603134 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes ]]> https://biorxiv.org/content/10.1101/605642v1?rss=1 Sen, A. Tyndale, S. T. Fu, Y. Erikson, G. McVicker, G. 2019-04-11 doi:10.1101/605642 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data ]]> https://biorxiv.org/content/10.1101/612994v1?rss=1 Gopalakrishnan, S. Dash, S. Maranas, C. 2019-04-18 doi:10.1101/612994 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Exercise enhances motor skill learning by neurotransmitter switching in the adult midbrain ]]> https://biorxiv.org/content/10.1101/613539v1?rss=1 Li, H.-q. Spitzer, N. C. 2019-04-18 doi:10.1101/613539 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ An improved method to produce clinical scale natural killer cells from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/614792v1?rss=1 Zhu, H. Kaufman, D. S. 2019-04-21 doi:10.1101/614792 Cold Spring Harbor Laboratory Press 2019-04-21 <![CDATA[ PD-L1:CD80 Heterodimer Triggers CD28 While Repressing Both PD-1 and CTLA4 Pathways ]]> https://biorxiv.org/content/10.1101/615138v1?rss=1 Zhao, Y. Lin, C.-H. Lee, C. Xu, X. Huang, Z. Xiao, C. Bui, J. Lu, L.-F. Hui, E. 2019-04-21 doi:10.1101/615138 Cold Spring Harbor Laboratory Press 2019-04-21 <![CDATA[ Three-dimensional Monolayer Stress Microscopy ]]> https://biorxiv.org/content/10.1101/616987v1?rss=1 Serrano, R. Aung, A. Yeh, Y.-T. Varghese, S. Lasheras, J. C. del Alamo, J. C. 2019-04-23 doi:10.1101/616987 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ FIREcaller: an R package for detecting frequently interacting regions from Hi-C data ]]> https://biorxiv.org/content/10.1101/619288v1?rss=1 Crowley, C. Yang, Y. Qiu, Y. Hu, B. Won, H. Ren, B. Hu, M. Li, Y. 2019-04-29 doi:10.1101/619288 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ A new method for inferring timetrees from temporally sampled molecular sequences ]]> https://biorxiv.org/content/10.1101/620187v1?rss=1 Miura, S. Tamura, K. Kosakovsky Pond, S. L. Huuki, L. A. Priest, J. Deng, J. Kumar, S. 2019-04-26 doi:10.1101/620187 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Hairless as a novel component of the Notch signaling pathway ]]> https://biorxiv.org/content/10.1101/621367v1?rss=1 Miller, S. W. Movsesyan, A. Zhang, S. Fernandez, R. Posakony, J. W. 2019-04-29 doi:10.1101/621367 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Formation of multinucleated variant endothelial cells with altered mitochondrial function in cultured coronary endothelium under simulated diabetes ]]> https://biorxiv.org/content/10.1101/622407v1?rss=1 Delgado De la Herran, H. C. Donis Maturano, L. Alvarez Delgado, C. Villarreal, F. Moreno Ulloa, A. 2019-04-29 doi:10.1101/622407 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments ]]> https://biorxiv.org/content/10.1101/624486v1?rss=1 Zheng, A. Lamkin, M. Qiu, Y. Ren, K. Goren, A. Gymrek, M. 2019-05-01 doi:10.1101/624486 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Red blood cell-derived extracellular vesicles mediate intercellular communication in ischemic heart failure ]]> https://biorxiv.org/content/10.1101/624841v1?rss=1 Das, A. Valkov, N. Salvador, A. M. Kur, I. Ziegler, O. Yeri, A. Garcia, F. C. Lu, S. Khamesra, A. Xiao, C. Rodosthenous, R. Li, G. Srinivasan, S. Toxavidis, V. Tigges, J. Laurent, L. C. Momma, S. Ghiran, I. Das, S. 2019-05-02 doi:10.1101/624841 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Changes in lipid composition and ultrastructure associated with functional maturation of the cuticle during adult maize leaf development ]]> https://biorxiv.org/content/10.1101/625343v1?rss=1 Bourgault, R. Matschi, S. Vasquez, M. Qiao, P. Sonntag, A. Charlebois, C. Mohammadi, M. Scanlon, M. J. Smith, L. G. Molina, I. 2019-05-02 doi:10.1101/625343 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Differential local stability governs the metamorphic fold-switch of bacterial virulence factor RfaH ]]> https://biorxiv.org/content/10.1101/629477v1?rss=1 40% deuteron incorporation) and its flexibility only decreases in the {beta}-folded state. Computationally-predicted {Delta}Gs agree with these results by displaying similar anisotropic stability within the tip of the -hairpin and on neighboring N-terminal domain residues. Remarkably, the {beta}-folded state shows comparable stability to non-metamorphic homologs. Our findings provide information critical for understanding the metamorphic behavior of RfaH and other chameleon proteins, and for devising targeted strategies to combat bacterial diseases.nnSignificanceInfections caused by Gram-negative bacteria are a worldwide health threat due to rapid acquisition of antibiotic resistance. RfaH, a protein essential for virulence in several Gram-negative pathogens, undergoes a large-scale structural rearrangement in which one RfaH domain completely refolds. Refolding transforms RfaH from an inactive state that restricts RfaH recruitment to a few target genes into an active state that binds to, and couples, transcription and translation machineries to elicit dramatic activation of gene expression. However, the molecular basis of this unique conformational change is poorly understood. Here, we combine molecular dynamics and structural biology to unveil the hotspots that differentially stabilize both states of RfaH. Our findings provide novel insights that will guide design of inhibitors blocking RfaH action. ]]> Galaz-Davison, P. Molina, J. A. Silletti, S. Komives, E. A. Knauer, S. H. Artsimovitch, I. Ramirez-Sarmiento, C. A. 2019-05-08 doi:10.1101/629477 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ An epigenetic landscape governs early fate decision in cellular aging ]]> https://biorxiv.org/content/10.1101/630921v1?rss=1 Li, Y. Jiang, Y. Paxman, J. O'Laughlin, R. Pillus, L. Tsimring, L. S. Hasty, J. Hao, N. 2019-05-07 doi:10.1101/630921 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ DYRK2 activates heat shock factor 1 promoting resistance to proteotoxic stress and tumour growth in triple-negative breast cancer ]]> https://biorxiv.org/content/10.1101/633560v1?rss=1 Moreno, R. Banerjee, S. Jackson, A. W. Quinn, J. Baillie, G. Dixon, J. E. Dinkova-Kostova, A. T. Edwards, J. de la Vega, L. 2019-05-09 doi:10.1101/633560 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Geometric state-space of protein-induced spontaneous curvature on helicoidal ramps in organelle membranes ]]> https://biorxiv.org/content/10.1101/635466v1?rss=1 Chabanon, M. Rangamani, P. 2019-05-11 doi:10.1101/635466 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ Dissociation of disease phenotype and allele silencing in hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/642421v1?rss=1 Dainis, A. Zaleta-Rivera, K. Ribeiro, A. Chang, A. C. H. Shang, C. Lan, F. Burridge, P. W. Wu, J. C. Chang, A. C. Y. Pruitt, B. L. Wheeler, M. Ashley, E. 2019-06-12 doi:10.1101/642421 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Gating Mechanism of β-Ketoacyl-ACP Synthases ]]> https://biorxiv.org/content/10.1101/644518v1?rss=1 Mindrebo, J. Patel, A. Kim, W. Davis, T. Chen, A. Bartholow, T. La Clair, J. McCammon, J. A. Noel, J. Burkart, M. 2019-05-21 doi:10.1101/644518 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers and Nanopore sequencing ]]> https://biorxiv.org/content/10.1101/645903v1?rss=1 10,000 bp in length with a mean error-rate of 0.0049-0.0006% and chimera rate <0.022%. ]]> Karst, S. M. Ziels, R. Kirkegaard, R. H. Albertsen, M. 2019-05-24 doi:10.1101/645903 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Novel Small Molecules Targeting the Intrinsically Disordered Structural Ensemble of α-Synuclein Protect Against Diverse α-Synuclein Mediated Dysfunctions ]]> https://biorxiv.org/content/10.1101/646505v1?rss=1 Toth, G. Neumann, T. Berthet, A. Masliah, E. Spencer, B. Tao, J. Jobling, M. Gardai, S. Bertoncini, C. Cremades, N. Bova, M. Ballaron, S. Chen, X.-H. Mao, W. Nguyen, P. Tabios, M. Tambe, M. Rochet, J.-C. Junker, H.-D. Schwizer, D. Sekul, R. Ott, I. Anderson, J. Szoke, B. Hoffman, W. Christodoulou, J. Yednock, T. Agard, D. Schenk, D. McConlogue, L. 2019-05-24 doi:10.1101/646505 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Nod-like receptors are critical for gut-brain axis signaling ]]> https://biorxiv.org/content/10.1101/647032v1?rss=1 Pusceddu, M. Barboza, M. Schneider, M. Stokes, P. Sladek, J. Torres Fuentes, C. Goldfild, L. Gillis, S. Brust-Mascher, I. Rabasa, G. Wong, K. Lebrilla, C. Byndloss, M. Maisonneuve, C. Baumler, A. J. Philpott, D. J. Ferrero, R. Barrett, K. E. Reardon, C. Gareau, M. 2019-05-24 doi:10.1101/647032 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Multiplex secretome engineering enhances recombinant protein production and purity ]]> https://biorxiv.org/content/10.1101/647214v1?rss=1 Kol, S. Ley, D. Wulff, T. Decker, M. Arnsdorf, J. Gutierrez, J. M. Chiang, A. W. Pedersen, L. E. Kildegaard, H. F. Lee, G. M. Lewis, N. 2019-05-24 doi:10.1101/647214 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ StrainHub: A phylogenetic tool to construct pathogen transmission networks ]]> https://biorxiv.org/content/10.1101/650283v1?rss=1 de Bernardi Schneider, A. Ford, C. T. Hostager, R. Williams, J. Cioce, M. Catalyürek, U. V. Wertheim, J. O. Janies, D. 2019-05-31 doi:10.1101/650283 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Host-microbe interactions in the chemosynthetic Riftia pachyptila symbiosis ]]> https://biorxiv.org/content/10.1101/651323v1?rss=1 Hinzke, T. Kleiner, M. Breusing, C. Felbeck, H. Haesler, R. Sievert, S. M. Schlueter, R. Rosenstiel, P. Reusch, T. B. H. Schweder, T. Markert, S. 2019-05-27 doi:10.1101/651323 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models ]]> https://biorxiv.org/content/10.1101/652537v1?rss=1 Facompre, N. D. Rajagopalan, P. Sahu, V. Pearson, A. T. Montone, K. T. James, C. D. Gleber-Netto, F. O. Weinstein, G. S. Jalaly, J. Lin, A. Rustgi, A. K. Nakagawa, H. Califano, J. A. Pickering, C. R. White, E. A. Windle, B. A. Morgan, I. M. Cohen, R. B. Gimotty, P. A. Basu, D. 2019-05-30 doi:10.1101/652537 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools ]]> https://biorxiv.org/content/10.1101/654459v1?rss=1 Ernst, M. Kang, K. B. Caraballo-Rodriguez, A. M. Nothias, L.-F. Wandy, J. Wang, M. Rogers, S. Medema, M. H. Dorrestein, P. C. van der Hooft, J. J. J. 2019-05-31 doi:10.1101/654459 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ A many-to-one sensory circuit encodes oxygen levels and drives respiratory behaviour in Danio rerio ]]> https://biorxiv.org/content/10.1101/655084v1?rss=1 Yeh, C. M. Pao, G. M. Villa-Real, R. Rosales, K. DePasquale, E. Groisman, A. Chalasani, S. H. 2019-05-31 doi:10.1101/655084 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ A Protein Kinase A-Regulated Network Encodes Short- and Long-Lived Cellular Memory ]]> https://biorxiv.org/content/10.1101/656009v1?rss=1 Jiang, Y. AkhavanAghdam, Z. Li, Y. Zid, B. M. Hao, N. 2019-05-31 doi:10.1101/656009 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Adaptive laboratory evolution of Escherichia coli under acid stress ]]> https://biorxiv.org/content/10.1101/659706v1?rss=1 Du, B. Olson, C. A. Sastry, A. V. Fang, X. Phaneuf, P. V. Chen, K. Wu, M. Szubin, R. Xu, S. Gao, Y. Hefner, Y. Feist, A. M. Palsson, B. O. 2019-06-04 doi:10.1101/659706 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ DECODING THE MECHANOCHEMISTRY OF NEURITE PLASTICITY ]]> https://biorxiv.org/content/10.1101/661975v1?rss=1 Pearce, K. Bell, M. Linthicum, W. Wen, Q. Srinivasan, J. Rangamani, P. Scarlata, S. 2019-06-06 doi:10.1101/661975 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Laboratory evolution of Escherichia coli enables life based on fluorinated amino acids ]]> https://biorxiv.org/content/10.1101/665950v1?rss=1 Agostini, F. Sinn, L. Petras, D. Schipp, C. J. Kubyshkin, V. Berger, A. A. Rappsilber, J. Dorrestein, P. C. Budisa, N. Koksch, B. 2019-06-10 doi:10.1101/665950 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Non-uniform distribution of myosin-mediated forces governs red blood cell curvature through tension modulation ]]> https://biorxiv.org/content/10.1101/668582v1?rss=1 Alimohamadi, H. S. Smith, A. M. Fowler, V. Rangamani, P. 2019-06-12 doi:10.1101/668582 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ BTLA and PD-1 employ distinct phosphatases to differentially repress T cell signaling ]]> https://biorxiv.org/content/10.1101/669812v1?rss=1 Xu, X. Fulzele, A. Zhao, Y. Wu, Z. Hu, Y. Jiang, Y. Ma, Y. Wang, H. Fu, G. Bennett, E. HUI, E. 2019-06-14 doi:10.1101/669812 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Cellular deconvolution of GTEx tissues powers eQTL studies to discover thousands of novel disease and cell-type associated regulatory variants ]]> https://biorxiv.org/content/10.1101/671040v1?rss=1 Donovan, M. K. R. D'Antonio-Chronowska, A. D'Antonio, M. Frazer, K. A. 2019-06-13 doi:10.1101/671040 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Novel syngeneic animal model of tobacco-associated oral cancer reveals the activity of in situ anti-CTLA-4 ]]> https://biorxiv.org/content/10.1101/672527v1?rss=1 70% of HNSCC lesions respond to intratumoral anti-CTLA-4. This syngeneic HNSCC mouse model provides a platform for the development of novel immunotherapeutic options for HNSCC. ]]> Wang, Z. Wu, V. H. Allevato, M. M. Gilardi, M. He, Y. Callejas-Valera, J. L. Vitale-Cross, L. Martin, D. Amornphimoltham, P. Mcdermott, J. Goto, Y. Molinolo, A. A. Sharabi, A. B. Cohen, E. E. W. Chen, Q. Lyons, G. Alexandrov, L. B. Gutkind, J. S. 2019-06-15 doi:10.1101/672527 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ TWIST1 homo- and heterodimers orchestrate specificity control in embryonic stem cell lineage differentiation and craniofacial development ]]> https://biorxiv.org/content/10.1101/672824v1?rss=1 Fan, X. Waardenberg, A. J. Demuth, M. Osteil, P. Sun, J. Loebel, D. A. F. Graham, M. Tam, P. P. L. Fossat, N. 2019-06-16 doi:10.1101/672824 Cold Spring Harbor Laboratory Press 2019-06-16 <![CDATA[ Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae ]]> https://biorxiv.org/content/10.1101/674333v1?rss=1 de Bernardi Schneider, A. Jacob Machado, D. Janies, D. A. 2019-06-18 doi:10.1101/674333 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Class of antiretroviral drugs and anemia risk in the current treatment era ]]> https://biorxiv.org/content/10.1101/674549v1?rss=1 Harding, B. N. Whitney, B. M. Nance, R. M. Crane, H. M. Burkholder, G. Moore, R. D. Mathews, W. C. Eron, J. J. Hunt, P. W. Volberding, P. Rodriguez, B. Mayer, K. H. Saag, M. S. Kitahata, M. M. Heckbert, S. R. Delaney, J. A. C. 2019-06-21 doi:10.1101/674549 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Symmetry breaking transition towards directional locomotion in Physarum microplasmodia ]]> https://biorxiv.org/content/10.1101/675942v1?rss=1 Zhang, S. Lasheras, J. C. del Alamo, J. C. 2019-06-19 doi:10.1101/675942 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ hunchback promoters can readout morphogenetic positional information in less than a minute ]]> https://biorxiv.org/content/10.1101/676684v1?rss=1 Desponds, J. Vergassola, M. Walczak, A. M. 2019-06-19 doi:10.1101/676684 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/678763v1?rss=1 nView larger version (22K):norg.highwire.dtl.DTLVardef@d6291borg.highwire.dtl.DTLVardef@24db3aorg.highwire.dtl.DTLVardef@1b4f65borg.highwire.dtl.DTLVardef@199d243_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, S. Zhang, Q. Hui, H. Agrawal, K. Karris, M. A. Y. Rana, T. 2019-06-21 doi:10.1101/678763 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ The effect of sample size on polygenic hazard models for prostate cancer ]]> https://biorxiv.org/content/10.1101/679092v1?rss=1 Karunamuni, R. Huynh-Le, M.-P. Fan, C. Eeles, R. Easton, D. Kote-Jarai, Z. Al Olama, A. A. Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. Nordestgaard, B. Key, T. Travis, R. Neal, D. Donovan, J. Hamdy, F. Pharoah, P. Pashayan, N. Khaw, K.-T. Thibodeau, S. McDonnell, S. Schaid, D. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, L. Brenner, H. Schöttker, B. Holleczek, B. Park, J. Sellers, T. Lin, H.-Y. Slavov, C. Kaneva, R. Mitev, V. Batra, 2019-06-21 doi:10.1101/679092 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Reconstructing neural representations of tactile space ]]> https://biorxiv.org/content/10.1101/679241v1?rss=1 Tame, L. Tucciarelli, R. Sadibolova, R. Sereno, M. I. Longo, M. 2019-06-21 doi:10.1101/679241 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Protein:Protein Interactions in the Cytoplasmic Membrane Influencing Sugar Transport and Phosphorylation Activities of the E. coli Phosphotransferase System. ]]> https://biorxiv.org/content/10.1101/681411v1?rss=1 Saier, M. H. Aboulwafa, M. Zhang, Z. 2019-06-26 doi:10.1101/681411 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Lis1 promotes the formation of maximally activated cytoplasmic dynein-1 complexes ]]> https://biorxiv.org/content/10.1101/683052v1?rss=1 nView larger version (37K):norg.highwire.dtl.DTLVardef@1acc26corg.highwire.dtl.DTLVardef@1107393org.highwire.dtl.DTLVardef@113eab4org.highwire.dtl.DTLVardef@95f6f4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Lis1 increases microtubule binding and the velocity of activated dynein complexes. a. Schematic of the current model for dynein activation. Dynein is autoinihibited in the Phi conformation, opens and then adopts a parallel conformation that is seen in the activated dynein complex, which includes dynactin and an activating adaptor. Maximally activated dynein contains two dynein dimers (dynein A and B, far right) b. Schematic of the dynein motor domain with AAA+ ATPase domains colored in rainbow, highlighting the two Lis1 binding sites in yeast dynein, "sitering" at AAA3/4 and "sitestalk" on dyneins stalk, which leads to dyneins microtubule binding domain (MTBD). Lis1 is shown in orange to the right c. Schematic of the activating adaptor constructs used in this study. d. Binding density (mean {+/-} s.e.m. dynein) of dynein alone on microtubules in the absence (white circles) or presence (black circles) of 300 nM Lis1. Data was normalized to a density of 1.0 in the absence of Lis1. Statistical analysis was performed using a two-tailed unpaired t test; ****, p<0.0001; n = 12 replicates for each condition. e. Binding density (mean {+/-} s.e.m) of dynein/ dynactin/ activating adaptor complexes on microtubules in the absence (white circles) or presence (black circles) of 300 nM Lis1. The activating adaptors used are indicated. Data was normalized to a density of 1.0 in the absence of Lis1. Statistical analysis was performed using a two-tailed unpaired t test; ****, p<0.0001; n = 12 replicates for each condition. f. Velocity of dynein/ dynactin/ activating adaptor complexes in the absence (white circles) or presence (black circles) of 300 nM Lis1. The median and interquartile range are shown and the activating adaptors used are indicated. Statistical analysis was performed using a two-tailed Mann-Whitney test; ****, p<0.0001; ns, p=0.3498; n (individual single molecule events) = 506 (BicD2-S no Lis1), 569 (BicD2-S with Lis1), 496 (BicD2-L no Lis1), 505 (BicD2-L with Lis1), 454 (Hook3 no Lis1), 471 (Hook3 with Lis1), 490 (Ninl no Lis1), 582 (Ninl with Lis1). g. Percent processive runs (mean {+/-} s.e.m.) of dynein/ dynactin/ Hook3 complexes in a higher salt buffer (60 mM KOAc versus 30 mM KOAc in our standard motility buffer) in the absence (white circles) or presence (black circles) of 300 nM Lis1. Statistical analysis was performed using a one-way ANOVA and Tukeys multiple comparisons test; ****, p<0.0001; n = 3 replicates per condition. h. Schematic of the peroxisome relocation assay. i. Peroxisome velocity in human U2OS cells with scrambled or Lis1 siRNA knockdown. The median and interquartile range are shown. Statistical analysis was performed using a two-tailed unpaired t test; ***, p=0.0002; n (average peroxisome velocity per cell) = 30 per condition. More than 7 events were measured per cell.nnC_FIG ]]> Htet, Z. M. Gillies, J. P. Baker, R. W. Leschziner, A. E. DeSantis, M. E. Reck-Peterson, S. L. 2019-06-27 doi:10.1101/683052 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Computational analysis of transcriptome signature repurposes low dose trifluoperazine for the treatment of fragile X syndrome in mouse model ]]> https://biorxiv.org/content/10.1101/683169v1?rss=1 Ding, Q. Sethna, F. Wu, X.-T. Miao, Z. Chen, P. Zhang, Y. Xiao, H. Feng, W. Feng, Y. Li, X. Wang, H. 2019-06-27 doi:10.1101/683169 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Split-gene drive system provides flexible application for safe laboratory investigation and potential field deployment ]]> https://biorxiv.org/content/10.1101/684597v1?rss=1 Lopez del Amo, V. Bishop, A. L. Sanchez C., H. M. Bennett, J. B. Feng, X. Marshall, J. M. Bier, E. Gantz, V. M. 2019-06-27 doi:10.1101/684597 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Removal of early senescent cells protects retinal ganglion cells loss in experimental ocular hypertension. ]]> https://biorxiv.org/content/10.1101/684811v1?rss=1 Rocha, L. R. Nguyen Huu, V. A. Palomino La torre, C. Xu, Q. Jabari, M. Krawczyk, M. Weinreb, R. N. Skowronska-Krawczyk, D. 2019-06-27 doi:10.1101/684811 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Discovering functional sequences with RELICS, an analysis method for CRISPR regulatory screens ]]> https://biorxiv.org/content/10.1101/687293v1?rss=1 Fiaux, P. C. Chen, H. McVicker, G. 2019-06-30 doi:10.1101/687293 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ NEIL2 plays a critical role in limiting inflammation and preserving genomic integrity in H. pylori-infected gastric epithelial cells ]]> https://biorxiv.org/content/10.1101/687962v1?rss=1 Sahan, A. Z. Venkova, T. Sayed, I. M. Beswick, E. Reyes, V. Pinchuk, I. Sahoo, D. Ghosh, P. Hazra, T. K. Das, S. 2019-07-02 doi:10.1101/687962 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Natural selection shapes codon usage in the human genome ]]> https://biorxiv.org/content/10.1101/688051v1?rss=1 Dhindsa, R. S. Copeland, B. R. Mustoe, A. M. Goldstein, D. B. 2019-07-01 doi:10.1101/688051 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Interleaved training prevents catastrophic forgetting in spiking neural networks ]]> https://biorxiv.org/content/10.1101/688622v1?rss=1 Bazhenov, M. Golden, R. Delanois, J. E. 2019-07-01 doi:10.1101/688622 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ A non-acidic method using hydroxyapatite and phosphohistidine monoclonal antibodies allows enrichment of phosphopeptides containing non-conventional phosphorylations for mass spectrometry analysis. ]]> https://biorxiv.org/content/10.1101/691352v1?rss=1 Adam, K. Fuhs, S. Meisenhelder, J. Aslanian, A. Diedrich, J. K. Moresco, J. J. La Clair, J. Yates, J. R. Hunter, T. 2019-07-03 doi:10.1101/691352 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing ]]> https://biorxiv.org/content/10.1101/692608v1?rss=1 Chen, S. Lake, B. Zhang, K. 2019-07-04 doi:10.1101/692608 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Single cell chromatin accessibility reveals pancreatic islet cell type- and state-specific regulatory programs of diabetes risk ]]> https://biorxiv.org/content/10.1101/693671v1?rss=1 Chiou, J. Zeng, C. Cheng, Z. Han, J. Y. Schlichting, M. Huang, S. Wang, J. Sui, Y. Deogaygay, A. Okino, M.-L. Qiu, Y. Sun, Y. Kudtarkar, P. Fang, R. Preissl, S. Sander, M. Gorkin, D. Gaulton, K. 2019-07-09 doi:10.1101/693671 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Decoding WW Domain Tandem-mediated Target Recognitions in Tissue Growth and Cell Polarity ]]> https://biorxiv.org/content/10.1101/694976v1?rss=1 Zhang, M. Lin, Z. Yang, Z. Xie, R. Ji, Z. Guan, K.-L. 2019-07-07 doi:10.1101/694976 Cold Spring Harbor Laboratory Press 2019-07-07 <![CDATA[ Mapping Vector Field of Single Cells ]]> https://biorxiv.org/content/10.1101/696724v1?rss=1 Qiu, X. Zhang, Y. Yang, D. Hosseinzadeh, S. Wang, L. Yuan, R. Xu, S. Ma, Y. Replogle, J. Darmanis, S. Xing, J. Weissman, J. 2019-07-09 doi:10.1101/696724 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Updated phylogeny of Chikungunya virus reveals lineage-specific RNA architecture ]]> https://biorxiv.org/content/10.1101/698522v1?rss=1 de Bernardi Schneider, A. Ochsenreiter, R. Hostager, R. Hofacker, I. L. Janies, D. Wolfinger, M. T. 2019-07-11 doi:10.1101/698522 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Transfer of Septin Rings to Cytokinetic Remnants Directs Age-Sensitive ER stress Surveillance Cell Cycle Re-entry ]]> https://biorxiv.org/content/10.1101/698829v1?rss=1 Chao, J. T. Pina, F. Onishi, M. Cohen, Y. Schuldiner, M. Niwa, M. 2019-07-13 doi:10.1101/698829 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Temporal cascade of frontal, motor and muscle processes underlying human action-stopping ]]> https://biorxiv.org/content/10.1101/700088v1?rss=1 Jana, S. Hannah, R. Muralidharan, V. Aron, A. R. 2019-07-14 doi:10.1101/700088 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping ]]> https://biorxiv.org/content/10.1101/700864v1?rss=1 Ramilowski, J. A. Yip, C. W. Agrawal, S. Chang, J.-C. Ciani, Y. Kulakovskiy, I. V. Mendez, M. Ooi, J. L. C. Petri, A. Roos, L. Severin, J. Yasuzawa, K. Ouyang, J. F. Parkinson, N. Abugessaisa, I. Akalin, A. Antonov, I. Arner, E. Bonetti, A. Bono, H. Borsari, B. Brombacher, F. Cannistraci, C. Cardenas, R. Cardon, M. Chang, H. Dostie, J. Ducoli, L. Favorov, A. Fort, A. Garrido, D. Gil, N. Gimenez, J. Guler, R. Handoko, L. Harshbarger, J. Hasegawa, A. Hasegawa, Y. Hashimoto, K. Hayatsu, N. Heutink, P. Hirose, T. Imada, E. L. Itoh, M. Kaczkowski, B. Kan 2019-07-14 doi:10.1101/700864 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Remodeling of the C. elegans Non-coding RNA Transcriptome by Heat Shock ]]> https://biorxiv.org/content/10.1101/706820v1?rss=1 Schreiner, W. P. Pagliuso, D. C. Garrigues, J. M. Chen, J. S. Aalto, A. P. Pasquinelli, A. E. 2019-07-18 doi:10.1101/706820 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Long-lasting Analgesia via Targeted in vivo Epigenetic Repression of Nav1.7 ]]> https://biorxiv.org/content/10.1101/711812v1?rss=1 Moreno, A. M. Catroli, G. F. Aleman, F. Pla, A. Woller, S. A. Hu, M. Yaksh, T. Mali, P. 2019-07-24 doi:10.1101/711812 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Seagrass mediates microalgal community structure at a distance ]]> https://biorxiv.org/content/10.1101/712612v1?rss=1 Jacobs-Palmer, E. Gallego, R. Ramon-Laca, A. Kunselman, E. Cribari, K. Horwith, M. Kelly, R. P. 2019-07-24 doi:10.1101/712612 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction ]]> https://biorxiv.org/content/10.1101/712950v1?rss=1 Calandrelli, R. Xu, L. Luo, Y. Wu, W. Fan, X. Nguyen, T. Chen, C. Sriram, K. Natarajan, R. Chen, Z. Zhong, S. 2019-07-24 doi:10.1101/712950 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Pyruvate Kinase M Links Glucose Availability to Protein Synthesis ]]> https://biorxiv.org/content/10.1101/715086v1?rss=1 Kejiou, N. S. Ilan, L. Aigner, S. Luo, E. Rabano, I. Rajakulendran, N. Najafabadi, H. S. Angers, S. Yeo, G. W. Palazzo, A. F. 2019-07-25 doi:10.1101/715086 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Meta-analysis of longitudinal epigenome-wide association studies of military cohorts reveals multiple CpG sites associated with post-traumatic stress disorder ]]> https://biorxiv.org/content/10.1101/716068v1?rss=1 Snijders, C. Maihofer, A. X. Ratanatharathorn, A. Baker, D. G. Boks, M. P. Geuze, E. Jain, S. Kessler, R. C. Pishva, E. Risbrough, V. B. Stein, M. B. Ursano, R. J. Vermetten, E. Vinkers, C. PGC PTSD EWAS Consortium, Smith, A. K. Uddin, M. Rutten, B. P. F. Nievergelt, C. M. 2019-07-26 doi:10.1101/716068 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Tyrosine-based Signals Converge on Daple*PARD3 Complex to Fine-tune Polarized Planar Cell Migration ]]> https://biorxiv.org/content/10.1101/717041v1?rss=1 Ear, J. Saklecha, A. Ghassemian, M. Kufareva, I. Ghosh, P. 2019-07-27 doi:10.1101/717041 Cold Spring Harbor Laboratory Press 2019-07-27 <![CDATA[ Altered phosphorylation of the proteasome subunit Rpt6 has minimal impact on synaptic plasticity and learning ]]> https://biorxiv.org/content/10.1101/719195v1?rss=1 Scudder, S. L. Gonzales, F. R. Howell, K. K. Stein, I. S. Dozier, L. E. Anagnostaras, S. G. Zito, K. Patrick, G. N. 2019-07-30 doi:10.1101/719195 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Serotonergic plasticity in the dorsal raphe nucleus characterizes susceptibility and resilience to anhedonia ]]> https://biorxiv.org/content/10.1101/719286v1?rss=1 Prakash, N. Stark, C. J. Keisler, M. N. Luo, L. Der-Avakian, A. Dulcis, D. 2019-07-30 doi:10.1101/719286 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus ]]> https://biorxiv.org/content/10.1101/721555v1?rss=1 Minich, J. Petrus, S. Michael, J. D. Michael, T. P. Knight, R. Allen, E. 2019-08-01 doi:10.1101/721555 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ IgEvolution: clonal analysis of antibody repertoires ]]> https://biorxiv.org/content/10.1101/725424v1?rss=1 Safonova, Y. Pevzner, P. A. 2019-08-13 doi:10.1101/725424 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Gram-positive and Gram-negative Bacteria Share Common Principles to Coordinate Growth and the Cell Cycle at the Single-cell Level ]]> https://biorxiv.org/content/10.1101/726596v1?rss=1 Sauls, J. T. Cox, S. E. Doh, Q. Castillo, V. Ghulam-Jelani, Z. Jun, S. 2019-08-06 doi:10.1101/726596 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ The interaction between elapsed time and decision accuracy differs between humans and rats performing the same visual motion discrimination task ]]> https://biorxiv.org/content/10.1101/726703v1?rss=1 Shevinsky, C. A. Reinagel, P. 2019-08-07 doi:10.1101/726703 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Indirect actuation reduces flight power requirements in Manduca sexta via elastic energy exchange ]]> https://biorxiv.org/content/10.1101/727743v1?rss=1 Gau, J. Gravish, N. Sponberg, S. 2019-08-07 doi:10.1101/727743 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Comparing the microbial communities of natural and supplemental nests of an endangered ecosystem engineer ]]> https://biorxiv.org/content/10.1101/727966v1?rss=1 Thoemmes, M. S. Cove, M. V. 2019-08-07 doi:10.1101/727966 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Rough substrates constrain walking speed in ants through modulation of stride frequency and not stride length ]]> https://biorxiv.org/content/10.1101/731380v1?rss=1 Clifton, G. Holway, D. Gravish, N. 2019-08-13 doi:10.1101/731380 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Assessing the motivational effects of ethanol in mice using a discrete-trial current-intensity intracranial self-stimulation procedure ]]> https://biorxiv.org/content/10.1101/731612v1?rss=1 Barkley-Levenson, A. M. Der-Avakian, A. Palmer, A. A. 2019-08-10 doi:10.1101/731612 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Addition of Genetics to Quantitative MRI Facilitates Earlier Prediction of Dementia: A Non-invasive Alternative to Amyloid Measures ]]> https://biorxiv.org/content/10.1101/731661v1?rss=1 Schenker-Ahmed, N. M. Bulsara, N. Yang, L. Huang, L. Iranmehr, A. Wu, J. Graff, A. M. Dadakova, T. Chung, H.-K. Tkach, D. Shomorony, I. Shah, N. Garst, P. Heister, R. Bureeva, S. Delport, W. Karow, D. S. Brewer, J. B. Swisher, C. L. 2019-08-11 doi:10.1101/731661 Cold Spring Harbor Laboratory Press 2019-08-11 <![CDATA[ Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 ]]> https://biorxiv.org/content/10.1101/733576v1?rss=1 nView larger version (18K):norg.highwire.dtl.DTLVardef@8765f2org.highwire.dtl.DTLVardef@136235aorg.highwire.dtl.DTLVardef@14aef76org.highwire.dtl.DTLVardef@af33d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Deutsch, E. W. Lane, L. Overall, C. M. Bandeira, N. Baker, M. S. Pineau, C. Moritz, R. L. Corrales, F. Orchard, S. Van Eyk, J. E. Paik, Y.-K. Weintraub, S. T. Vandenbrouck, Y. Omenn, G. S. 2019-08-13 doi:10.1101/733576 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Detection and quantification of GPCR mRNA: An assessment and implications of data from high-content methods ]]> https://biorxiv.org/content/10.1101/734863v1?rss=1 nView larger version (21K):norg.highwire.dtl.DTLVardef@1a47e41org.highwire.dtl.DTLVardef@5ce56corg.highwire.dtl.DTLVardef@da5330org.highwire.dtl.DTLVardef@18b8215_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sriram, K. Wiley, S. Z. Moyung, K. Gorr, M. W. Salmeron, C. Marucut, J. French, R. P. Lowy, A. M. Insel, P. A. 2019-08-15 doi:10.1101/734863 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ STABILITY ANALYSIS OF A BULK-SURFACE REACTION MODEL FOR MEMBRANE-PROTEIN CLUSTERING ]]> https://biorxiv.org/content/10.1101/736165v1?rss=1 Stolerman, L. M. Getz, M. Llewellyn Smith, S. G. Holst, M. Rangamani, P. 2019-08-15 doi:10.1101/736165 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Deep Learning-Based Point-Scanning Super-Resolution Imaging ]]> https://biorxiv.org/content/10.1101/740548v1?rss=1 nView larger version (90K):norg.highwire.dtl.DTLVardef@fbf19aorg.highwire.dtl.DTLVardef@b2cc88org.highwire.dtl.DTLVardef@921e1corg.highwire.dtl.DTLVardef@f6c5af_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fang, L. Monroe, F. Novak, S. W. Kirk, L. Schiavon, C. R. Yu, S. B. Zhang, T. Wu, M. Kastner, K. Kubota, Y. Zhang, Z. Pekkurnaz, G. Mendenhall, J. Harris, K. Howard, J. Manor, U. 2019-08-21 doi:10.1101/740548 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Characterization of the brain functional architecture of psychostimulant withdrawal using single-cell whole brain imaging ]]> https://biorxiv.org/content/10.1101/743799v1?rss=1 Kimbrough, A. Smith, L. C. Kallupi, M. Simpson, S. Collazo, A. George, O. 2019-08-22 doi:10.1101/743799 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Environmental sensing in dynamic quorum responses ]]> https://biorxiv.org/content/10.1101/745091v1?rss=1 Chu, E. K. Groisman, A. Levchenko, A. 2019-09-05 doi:10.1101/745091 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Nanoluciferase-based Method for Detecting Gene Expression in C. elegans ]]> https://biorxiv.org/content/10.1101/745927v1?rss=1 Sfarcic, I. Bui, T. Daniels, E. C. Troemel, E. R. 2019-08-24 doi:10.1101/745927 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Photo-Disassembly of Membrane Microdomains Revives Conventional Antibiotics against MRSA ]]> https://biorxiv.org/content/10.1101/747626v1?rss=1 Hui, J. Dong, P.-T. Liang, L. Mandal, T. Li, J. Ulloa, E. R. Zhan, Y. Jusuf, S. Zong, C. Seleem, M. N. Liu, G. Y. Cui, Q. Cheng, J.-X. 2019-09-26 doi:10.1101/747626 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Interactions across life stages and thermal tolerance plasticity in Tigriopus californicus ]]> https://biorxiv.org/content/10.1101/751040v1?rss=1 Healy, T. M. Bock, A. K. Burton, R. S. 2019-08-30 doi:10.1101/751040 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization ]]> https://biorxiv.org/content/10.1101/755025v1?rss=1 Tang, X. Kudo, Y. Baker, J. LaBonte, S. Jordan, P. McKinnie, S. Guo, J. Huan, T. Moore, B. Edlund, A. 2019-09-04 doi:10.1101/755025 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Normal human lymph node T follicular helper cells and germinal center B cells accessed via fine needle aspirations ]]> https://biorxiv.org/content/10.1101/757534v1?rss=1 Havenar-Daughton, C. Newton, I. Zare, S. Reiss, S. Suh, M. J. Hasteh, F. Crotty, S. 2019-09-05 doi:10.1101/757534 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Example Based Hebbian Learning may be sufficient to support Human Intelligence ]]> https://biorxiv.org/content/10.1101/758375v1?rss=1 Wong, E. C. 2019-09-05 doi:10.1101/758375 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ A two-stage approach to identifying and validating modifiable factors for the prevention of depression ]]> https://biorxiv.org/content/10.1101/759753v1?rss=1 90th percentile) for clinically significant depression at follow-up based on their (i) polygenic risk, or (ii) reported traumatic life events. Using a factors-wide design corrected for multiple testing and adjusted for potential confounders, we identified modifiable factors associated with follow-up depression in the full sample and among at-risk individuals. Using a two-sample Mendelian randomization (MR) design, we then examined which significant factors showed potential causal influences on depression risk, or vice versa.nnResultsA range of baseline modifiable factors were prospectively associated with follow-up depression, including factors related to social engagement, physical activity, media use, and diet. MR follow-up analyses provided further support for the effects of social support-seeking, TV use, and other factors on depression risk.nnConclusionAs the field increasingly quantifies the role of genetic factors in complex conditions such as depression, knowledge of modifiable factors that could offset ones genetic risk has become highly relevant. Here, we present an approach to screening for potentially modifiable factors that may offset the risk of depression in general and among at-risk individuals. In light of the burden of disease associated with depression and the urgent need for actionable preventive strategies, this approach could help prioritize candidates for follow-up studies including clinical trials for depression prevention. ]]> Choi, K. W. Stein, M. B. Nishimi, K. Ge, T. Coleman, J. R. Chen, C.-Y. Ratanatharathorn, A. Zheutlin, A. B. Dunn, E. C. 23andMe Research Team, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Breen, G. Koenen, K. C. Smoller, J. W. 2019-09-08 doi:10.1101/759753 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ ODORANT RECEPTOR INHIBITION IS FUNDAMENTAL TO ODOR ENCODING ]]> https://biorxiv.org/content/10.1101/760033v1?rss=1 Pfister, P. Smith, B. C. Evans, B. J. Brann, J. H. Trimmer, C. Sheik, M. Arroyave, R. Reddy, G. Jeong, H.-Y. Raps, D. A. Peterlin, Z. Vergassola, M. Rogers, M. E. 2019-09-05 doi:10.1101/760033 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ The PAR2 signal peptide prevents premature receptor cleavage and activation ]]> https://biorxiv.org/content/10.1101/760769v1?rss=1 Liu, B. Lee, G. Wu, J. Deming, J. Kuei, C. Harrington, A. Wang, L. Towne, J. Lovenberg, T. Liu, C. Sun, S. 2019-09-06 doi:10.1101/760769 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Interplay between persistent activity and activity-silent dynamics in prefrontal cortex during working memory ]]> https://biorxiv.org/content/10.1101/763938v1?rss=1 Barbosa, J. Stein, H. Martinez, R. Galan, A. Adam, K. Li, S. Valls-Sole, J. Constantinidis, C. Compte, A. 2019-09-12 doi:10.1101/763938 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Genomic Characterization of Posttraumatic Stress Disorder in a Large US Military Veteran Sample ]]> https://biorxiv.org/content/10.1101/764001v1?rss=1 Stein, M. B. Levey, D. F. Cheng, Z. Wendt, F. R. Harrington, K. Cho, K. Quaden, R. Radhakrishnan, K. Girgenti, M. J. Ho, Y.-L. A. Posner, D. PTSD Working Group of the Psychiatric Genomics Consortium, Traumatic Stress Brain Research Study Group, VA Million Veteran Program, VA Cooperative Studies Program, Aslan, M. Duman, R. S. Zhao, H. Polimanti, R. Concato, J. Gelernter, J. 2019-09-10 doi:10.1101/764001 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction ]]> https://biorxiv.org/content/10.1101/765396v1?rss=1 Johnson, K. Hagen, G. M. 2019-09-11 doi:10.1101/765396 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Physiology-forward identification of bile acid sensitive vomeronasal receptors ]]> https://biorxiv.org/content/10.1101/766592v1?rss=1 Wong, W. M. Cao, J. Zhang, X. Doyle, W. I. Leon Mercado, L. Gautron, L. Meeks, J. P. 2019-09-12 doi:10.1101/766592 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Coordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance ]]> https://biorxiv.org/content/10.1101/767871v1?rss=1 Bi, M. Zhang, Z. Wang, H. Xue, P. Hernandez, K. Fu, X. De angelis, C. Gao, Z. Ruan, J. Jin, V. Wang, Q. Marangoni, E. Huang, T. H.-M. Chen, L. Glass, C. K. Li, W. Schiff, R. Liu, Z. 2019-09-16 doi:10.1101/767871 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers ]]> https://biorxiv.org/content/10.1101/767996v1?rss=1 Heckmann, D. Campeau, A. Lloyd, C. J. Phaneuf, P. Hefner, Y. Carrillo-Terrazas, M. Feist, A. M. Gonzalez, D. J. Palsson, B. O. 2019-09-12 doi:10.1101/767996 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Viral host-range evolvability changes in response to fluctuating selection ]]> https://biorxiv.org/content/10.1101/771998v1?rss=1 Mouchka, M. E. Dorsey, D. M. Malcangio, G. L. Medina, S. J. Stuart, E. C. Meyer, J. R. 2019-09-18 doi:10.1101/771998 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Δ9-Tetrahydrocannabinol (THC) impairs visual working memory performance ]]> https://biorxiv.org/content/10.1101/778068v1?rss=1 Adam, K. C. S. Doss, M. K. Pabon, E. Vogel, E. K. de Wit, H. 2019-09-23 doi:10.1101/778068 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Signaling Diversity Enabled by Rap1-Regulated Plasma Membrane ERK with Distinct Temporal Dynamics ]]> https://biorxiv.org/content/10.1101/781716v1?rss=1 Keyes, J. Ganesan, A. Molinar-Inglis, O. Hamidzadeh, A. Ling, M. Trejo, J. Levchenko, A. Zhang, J. 2019-09-25 doi:10.1101/781716 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ A Missense Point Mutation in Nerve Growth Factor (NGFR100W) Results in Selective Peripheral Sensory Neuropathy ]]> https://biorxiv.org/content/10.1101/784660v1?rss=1 Yang, W. Sung, K. Xu, W. Rodriguez, M. J. Wu, A. Santos, S. A. Fang, S. Uber, R. K. Dong, S. X. Guillory, B. C. Orain, X. Raus, J. Jolivalt, C. Calcutt, N. Ding, J. Rissman, R. A. Wu, C. 2019-09-27 doi:10.1101/784660 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Prefrontal high-gamma in ECoG tags periodicity of musical rhythms in perception and imagination ]]> https://biorxiv.org/content/10.1101/784991v1?rss=1 Herff, S. A. Herff, C. Milne, A. J. Johnson, G. Krusienski, D. J. 2019-09-30 doi:10.1101/784991 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Structure-Based Function Prediction using Graph Convolutional Networks ]]> https://biorxiv.org/content/10.1101/786236v1?rss=1 200,000 protein structures, including many homology-predicted structures, greatly expanding the reach and applications of the method. Our model learns general structure-function relationships by robustly predicting functions of proteins with [≤] 40% sequence identity to the training set. We show that our GCN architecture predicts functions more accurately than Convolutional Neural Networks trained on sequence data alone and previous competing methods. Using class activation mapping, we automatically identify structural regions at the residue-level that lead to each function prediction for every confidently predicted protein, advancing site-specific function prediction. We use our method to annotate PDB and SWISS-MODEL proteins, making several new confident function predictions spanning both fold and function classifications. ]]> Gligorijevic, V. Renfrew, P. D. Kosciolek, T. Leman, J. K. Cho, K. Vatanen, T. Berenberg, D. Taylor, B. C. Fisk, I. M. Xavier, R. J. Knight, R. Bonneau, R. A. 2019-10-04 doi:10.1101/786236 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Metabolic dysregulation of the lysophospholipid/autotaxin axis in the chromosome 9p21 gene SNP rs10757274 ]]> https://biorxiv.org/content/10.1101/789768v1?rss=1 Meckelmann, S. Hawksworth, J. White, D. Andrews, R. Rodrigues, P. O'Connor, A. Alvarez Jarreta, J. Tyrrell, V. Hinz, C. Zhou, Y. Williams, J. Aldrovandi, M. Watkins, W. J. Engler, A. Slatter, D. Allen, S. Acharya, J. Mitchell, J. Cooper, J. Aoki, J. Kano, K. Humphries, S. O'Donnell, V. B. 2019-10-02 doi:10.1101/789768 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Loss of AKAP1 triggers Drp1 dephosphorylation-mediated mitochondrial fragmentation and loss in retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/790139v1?rss=1 Edwards, G. Perkins, G. A. Kim, K.-Y. Kong, Y. Lee, Y. Choi, S.-H. Skowronska-Krawczyk, D. Weinreb, R. N. Zangwill, L. Strack, S. Ju, W.-K. 2019-10-02 doi:10.1101/790139 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ The Lipid Elongation Enzyme ELOVL2 is a molecular regulator of aging in the retina ]]> https://biorxiv.org/content/10.1101/795559v1?rss=1 Skowronska-Krawczyk, D. Chen, D. Chao, D. L. Rocha, L. Kolar, M. Nguyen Huu, V. A. Krawczyk, M. Dasyani, M. Wang, T. Jabari, M. Jafari, M. Ross, K. D. Saghatelian, A. Hamilton, B. A. Zhang, K. 2019-10-07 doi:10.1101/795559 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Calcium Imaging Reveals Host-Graft Synaptic Network Formation in Spinal Cord Injury ]]> https://biorxiv.org/content/10.1101/795583v1?rss=1 Ceto, S. Sekiguchi, K. J. Takashima, Y. Nimmerjahn, A. Tuszynski, M. H. 2019-10-07 doi:10.1101/795583 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Systems-level physiology of the human red blood cell is computed from metabolic and macromolecular mechanisms ]]> https://biorxiv.org/content/10.1101/797258v1?rss=1 95% of proteome mass fraction), and several macromolecular mechanisms. Proteomics data are used to place quantitative constraints on individual protein complexes that catalyze metabolic reactions, as well as a total proteome capacity constraint. We explicitly describe molecular mechanisms--such as hemoglobin binding and the formation and detoxification of reactive oxygen species--and takes standard hematological variables (e.g., hematocrit, hemoglobin concentration) as input, allowing for personalized physiological predictions. This model is built from first principles and allows for direct computation of physiologically meaningful quantities such as the oxygen dissociation curve and an accurate computation of the flux state of the metabolic network. More broadly, this work represents an important step toward including the proteome and its function in whole-cell models of human cells. ]]> Yurkovich, J. T. Yang, L. Palsson, B. O. 2019-10-08 doi:10.1101/797258 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas ]]> https://biorxiv.org/content/10.1101/805010v1?rss=1 Siegle, J. H. Jia, X. Durand, S. Gale, S. Bennett, C. Graddis, N. Heller, G. Ramirez, T. K. Choi, H. Luviano, J. A. Groblewski, P. A. Arkhipov, A. Bernard, A. Billeh, Y. N. Brown, D. Buice, M. A. Cain, N. Caldejon, S. Casal, L. Cho, A. Chvilicek, M. Cox, T. Dai, K. Denman, D. J. de Vries, S. E. J. Esposito, L. Farrell, C. Feng, D. Galbraith, J. Garrett, M. Gelfand, E. C. Hancock, N. Harris, J. A. Howard, R. Hu, B. Hytnen, R. Iyer, R. Jessett, E. Kato, I. Kiggens, J. Lecoq, J. Ledochowitsch, P. Lee, J. H. Leon, A. Li, Y. Liang, E. Long, F. Mace, K. 2019-10-16 doi:10.1101/805010 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Phytotransferrin endocytosis mediates a direct cell surface-to-chloroplast iron trafficking axis in marine diatoms ]]> https://biorxiv.org/content/10.1101/806539v1?rss=1 Turnsek, J. Brunson, J. K. Deerinck, T. J. Obornik, M. Horak, A. Bielinski, V. A. Allen, A. E. 2019-10-16 doi:10.1101/806539 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Computational approach to identifying universal macrophage biomarker ]]> https://biorxiv.org/content/10.1101/807347v1?rss=1 Dang, D. Taheri, S. Das, S. Prince, L. A. Ghosh, P. Sahoo, D. 2019-10-17 doi:10.1101/807347 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator ]]> https://biorxiv.org/content/10.1101/809905v1?rss=1 Ordyan, M. Bartol, T. M. Kennedy, M. B. Rangamani, P. Sejnowski, T. J. 2019-10-18 doi:10.1101/809905 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Mother machine image analysis with MM3 ]]> https://biorxiv.org/content/10.1101/810036v1?rss=1 Sauls, J. T. Schroeder, J. W. Brown, S. D. Le Treut, G. Si, F. Li, D. Wang, J. D. Jun, S. 2019-10-18 doi:10.1101/810036 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Hitching a Ride: Mechanics of Organelle Transport Through Linker-Mediated Hitchhiking ]]> https://biorxiv.org/content/10.1101/811372v1?rss=1 Mogre, S. S. Christensen, J. R. Reck-Peterson, S. L. Koslover, E. F. 2019-10-20 doi:10.1101/811372 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Errors associated with compound specific δ15N analysis of amino acids in preserved fish samples purified by high pressure liquid chromatography ]]> https://biorxiv.org/content/10.1101/812065v1?rss=1 Swalethorp, R. Aluwihare, L. Thompson, A. R. Ohman, M. D. Landry, M. R. 2019-10-21 doi:10.1101/812065 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Network analyses implicate a role for PHYTOCHROME-mediated light signaling in the regulation of cuticle development in plant leaves ]]> https://biorxiv.org/content/10.1101/812107v1?rss=1 Qiao, P. Bourgault, R. Mohammadi, M. Smith, L. G. Gore, M. A. Molina, I. Scanlon, M. J. 2019-10-21 doi:10.1101/812107 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Feature-based Molecular Networking in the GNPS Analysis Environment ]]> https://biorxiv.org/content/10.1101/812404v1?rss=1 Nothias, L. F. Petras, D. Schmid, R. Duehrkop, K. Rainer, J. Sarvepalli, A. Protsyuk, I. Ernst, M. Tsugawa, H. Fleischauer, M. Aicheler, F. Aksenov, A. Alka, O. Allard, P.-M. Barsch, A. Cachet, X. Caraballo, M. Da Silva, R. Dang, T. Garg, N. Gauglitz, J. M. Gurevich, A. Isaac, G. Jarmusch, A. K. Kamenik, Z. Kang, K. B. Kessler, N. Koester, I. Korf, A. Le Gouellec, A. Ludwig, M. Martin H., C. McCall, L.-I. McSayles, J. Meyer, S. Mohimani, H. Morsy, M. Moyne, O. Neumann, S. Neuweger, H. Nguyen, N. H. Esposito-Nothias, M. Paolini, J. Phelan, V. Pluskal, 2019-10-20 doi:10.1101/812404 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Canonical host-pathogen tradeoffs subverted by mutations with dual benefits ]]> https://biorxiv.org/content/10.1101/818492v1?rss=1 Beardmore, R. E. Gudelj, I. Meyer, J. R. Hewlett, M. Pena-Miller, R. 2019-10-24 doi:10.1101/818492 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Neuronal transcriptome analyses reveal novel neuropeptide modulators of excitation and inhibition imbalance in C. elegans ]]> https://biorxiv.org/content/10.1101/821769v1?rss=1 McCulloch, K. Zhou, K. Jin, Y. 2019-10-28 doi:10.1101/821769 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Deep functional synthesis: a machine learning approach to gene functional enrichment ]]> https://biorxiv.org/content/10.1101/824086v1?rss=1 Wang, S. Ma, J. Fong, S. Rensi, S. Han, J. Peng, J. Pratt, D. Altman, R. Ideker, T. 2019-11-13 doi:10.1101/824086 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Secondary metabolic symbiosis in shipworms (Teredinidae) ]]> https://biorxiv.org/content/10.1101/826933v1?rss=1 Altamia, M. A. Lin, Z. Trindade-Silva, A. E. Uy, I. D. Shipway, J. R. Veras Wilke, D. Concepcion, G. P. Distel, D. L. Schmidt, E. W. Haygood, M. G. 2019-10-31 doi:10.1101/826933 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project ]]> https://biorxiv.org/content/10.1101/828665v1?rss=1 El-Achkar, T. M. Eadon, M. T. Menon, R. Lake, B. B. Sigdel, T. K. Alexandrov, T. Parikh, S. Zhang, G. Dobi, D. Dunn, K. W. Otto, E. A. Anderton, C. R. Carson, J. M. Luo, J. Park, C. Hamidi, H. Zhou, J. Hoover, P. Schroeder, A. Joanes, M. Azeloglu, E. Sealfon, R. Winfree, S. Steck, B. He, Y. D'Agati, V. D. Iyengar, R. Troyanskaya, O. G. Barisoni, L. Gaut, J. Zhang, K. Laszik, Z. Rovin, B. Dagher, P. C. Sharma, K. Sarwal, M. Hodgin, J. B. Alpers, C. E. Kretzler, M. Jain, S. For the Kidney Precision Medicine Project, 2019-11-06 doi:10.1101/828665 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota ]]> https://biorxiv.org/content/10.1101/828749v1?rss=1 Minich, J. J. Jantawongsri, K. Johnston, C. Bowie, K. Bowman, J. P. Knight, R. Nowak, B. Allen, E. E. 2019-11-02 doi:10.1101/828749 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks ]]> https://biorxiv.org/content/10.1101/829192v1?rss=1 150X coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship which translates dog to human years, aligns the timing of major physiological milestones between the two species, and extends to mice. Conserved changes center on specific developmental gene networks which are sufficient to capture the effects of anti-aging interventions in multiple mammals. These results establish methylation not only as a diagnostic age readout but as a cross-species translator of physiological aging milestones. ]]> Wang, T. Ma, J. Hogan, A. N. Fong, S. Licon, K. Tsui, B. Kreisberg, J. F. Adams, P. D. Carvunis, A.-R. Bannasch, D. Ostrander, E. A. Ideker, T. 2019-11-04 doi:10.1101/829192 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Brainstem organoids from human pluripotent stem cells contain neural crest population ]]> https://biorxiv.org/content/10.1101/829275v1?rss=1 Eura, N. Matsui, T. K. Luginbuhl, J. Matsubayashi, M. Nanaura, H. Shiota, T. Kinugawa, K. Iguchi, N. Kiriyama, T. Zheng, C. Kouno, T. Lan, Y. J. Kongpracha, P. Wiriyasermkul, P. Sakaguchi, Y. M. Nagata, R. Komeda, T. Morikawa, N. Kitayoshi, F. Jong, M. Kobashigawa, S. Nakanishi, M. Hasegawa, M. Saito, Y. Shiromizu, T. Nishimura, Y. Kasai, T. Takeda, M. Kobayashi, H. Inagaki, Y. Tanaka, Y. Makinodan, M. Kishimoto, T. Kuniyasu, H. Nagamori, S. Muotri, A. R. Shin, J. W. Sugie, K. Mori, E. 2019-11-04 doi:10.1101/829275 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Serine and glycine are essential for human muscle progenitor cell population expansion ]]> https://biorxiv.org/content/10.1101/833798v1?rss=1 nView larger version (32K):norg.highwire.dtl.DTLVardef@438298org.highwire.dtl.DTLVardef@32f66dorg.highwire.dtl.DTLVardef@1d08aeeorg.highwire.dtl.DTLVardef@511c7f_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Gheller, B. J. Blum, J. E. Bender, E. L. Gheller, M. E. Lim, E. W. Handzlik, M. K. Stover, P. J. Field, M. S. Cosgrove, B. D. Metallo, C. M. Thalacker-Mercer, A. E. 2019-11-07 doi:10.1101/833798 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ The thermodynamics of thinking: connections between neural activity, energy metabolism and blood flow ]]> https://biorxiv.org/content/10.1101/833855v1?rss=1 Buxton, R. B. 2019-11-07 doi:10.1101/833855 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Bionic 3D printed corals ]]> https://biorxiv.org/content/10.1101/834051v1?rss=1 Wangpraseurt, D. You, S. Azam, F. Jacucci, G. Gaidarenko, O. Hildebrand, M. Kuhl, M. Smith, A. G. Davey, M. P. Smith, A. Deheyn, D. D. Chen, S. Vignolini, S. 2019-11-08 doi:10.1101/834051 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Genome-wide association study for maize leaf cuticular conductance identifies candidate genes involved in the regulation of cuticle development ]]> https://biorxiv.org/content/10.1101/835892v1?rss=1 Gore, M. A. Smith, L. G. Lin, M. Matschi, S. Vasquez, M. Chamness, J. Kaczmar, N. Baseggio, M. Miller, M. Stewart, E. Qiao, P. Scanlon, M. J. Molina, I. 2019-11-09 doi:10.1101/835892 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ The in situ structure of Parkinson’s disease-linked LRRK2 ]]> https://biorxiv.org/content/10.1101/837203v1?rss=1 Watanabe, R. Buschauer, R. Boehning, J. Audagnotto, M. Lasker, K. Lu, T. W. Boassa, D. Taylor, S. Villa, E. 2019-11-10 doi:10.1101/837203 Cold Spring Harbor Laboratory Press 2019-11-10 <![CDATA[ The urinary tract microbiome in older women exhibits host genetics and environmental influences ]]> https://biorxiv.org/content/10.1101/838367v1?rss=1 0.15)). Age, menopausal status, prior UTI and host genetics were top among factors defining the urobiome. Increased composition was associated with older age, contrary to previous findings. ]]> Adebayo, A. S. Ackermann, G. Bowyer, R. C. E. Wells, P. M. Humphrey, G. Knight, R. Spector, T. D. Steves, C. J. 2019-11-12 doi:10.1101/838367 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Spiking Recurrent Networks as a Model to Probe Neuronal Timescales Specific to Working Memory ]]> https://biorxiv.org/content/10.1101/842302v1?rss=1 Kim, R. Sejnowski, T. J. 2019-11-15 doi:10.1101/842302 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules ]]> https://biorxiv.org/content/10.1101/842740v1?rss=1 Ludwig, M. Nothias, L.-F. Dührkop, K. Koester, I. Fleischauer, M. Hoffmann, M. A. Petras, D. Vargas, F. Morsy, M. Aluwihare, L. Dorrestein, P. Böcker, S. 2019-11-16 doi:10.1101/842740 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Tfam knockdown results in reduction of mtDNA copy number, OXPHOS deficiency and abnormalities in zebrafish embryos ]]> https://biorxiv.org/content/10.1101/843318v1?rss=1 Otten, A. Kamps, R. Lindsey, P. Gerards, M. Pendeville Samain, H. Muller, M. van Tienen, F. Smeets, B. 2019-11-14 doi:10.1101/843318 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids ]]> https://biorxiv.org/content/10.1101/843474v1?rss=1 Di, L. Fu, Y. Sun, Y. Li, J. Liu, L. Yao, J. Wang, G. Wu, Y. Lao, K. Lee, R. W. Zheng, G. Xu, J. Oh, J. Wang, D. Xie, X. S. Huang, Y. Wang, J. 2019-11-15 doi:10.1101/843474 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Temporally-precise disruption of prefrontal cortex informed by the timing of beta bursts impairs human action-stopping ]]> https://biorxiv.org/content/10.1101/843557v1?rss=1 Hannah, R. Muralidharan, V. Sundby, K. K. Aron, A. R. 2019-11-18 doi:10.1101/843557 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis ]]> https://biorxiv.org/content/10.1101/850305v1?rss=1 Han, W. Ma, X. Balibar, C. J. Baxter Rath, C. M. Benton, B. Bermingham, A. Casey, F. Chie-Leon, B. Cho, M.-K. Frank, A. O. Frommlet, A. Ho, C.-M. Lee, P. S. Li, M. Lingel, A. Ma, S. Merritt, H. Ornelas, E. de Pascale, G. Prathapam, R. Prosen, K. R. Rasper, D. Ruzin, A. Sawyer, W. Shaul, J. Shen, X. Shia, S. Steffek, M. Subramanian, S. Vo, J. Wang, F. Wartchow, C. Uehara, T. 2019-12-17 doi:10.1101/850305 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Evolutionary Stalling in the Optimization of the Translation Machinery ]]> https://biorxiv.org/content/10.1101/850644v1?rss=1 Venkataram, S. Monasky, R. Sikaroodi, S. H. Kryazhimskiy, S. Kacar, B. 2019-11-24 doi:10.1101/850644 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing ]]> https://biorxiv.org/content/10.1101/852947v1?rss=1 Chen, Z. Pham, L. Wu, T.-C. Mo, G. Xia, Y. Chang, P. Porter, D. Phan, T. Che, H. Tran, H. Bansal, V. Shaffer, J. Belda-Ferre, P. Humphrey, G. Knight, R. Pevzner, P. Pham, S. Wang, Y. Lei, M. 2019-11-29 doi:10.1101/852947 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Face familiarity detection with complex synapses ]]> https://biorxiv.org/content/10.1101/854059v1?rss=1 Ji-An, L. Stefanini, F. Benna, M. K. Fusi, S. 2019-11-25 doi:10.1101/854059 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Genetic Association Study of Childhood Aggression across raters, instruments and age ]]> https://biorxiv.org/content/10.1101/854927v1?rss=1 Ip, H. F. van der Laan, C. M. Brikell, I. Sanchez-Mora, C. Nolte, I. M. St Pourcain, B. Bolhuis, K. Palviainen, T. Zafarmand, H. Colodro-Conde, L. Gordon, S. Zayats, T. Aliev, F. Jiang, C. Wang, C. A. Saunders, G. Karhunen, V. Hammerschlag, A. R. Adkins, D. E. Border, R. Peterson, R. E. Prinz, J. A. Thiering, E. Seppälä, I. Vilor-Tejedor, N. Ahluwalia, T. S. Day, F. R. Hottenga, J.-J. Allegrini, A. G. Krapohl, E. M. L. Rimfeld, K. Chen, Q. Lu, Y. Martin, J. Soler Artigas, M. Rovira, P. Bosch, R. Espanol, G. Ramos Quiroga, J. A. Neumann, A. Ensink, J. 2019-11-29 doi:10.1101/854927 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Frequent extrachromosomal oncogene amplification drives aggressive tumors ]]> https://biorxiv.org/content/10.1101/859306v1?rss=1 Kim, H. Nguyen, N. Turner, K. Wu, S. Liu, J. Deshpande, V. Namburi, S. Chang, H. Y. Beck, C. Mischel, P. S. Bafna, V. Verhaak, R. G. W. 2019-11-28 doi:10.1101/859306 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ Maternal Obesity and Western-style Diet Impair Fetal and Juvenile Offspring Skeletal Muscle Insulin-Stimulated Glucose Transport in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/864082v1?rss=1 Campodonico-Burnett, W. Hetrick, B. Wesolowski, S. R. Schenk, S. Takahashi, D. L. Dean, T. A. Sullivan, E. L. Kievit, P. Gannon, M. Aagaard-Tillery, K. Friedman, J. E. McCurdy, C. E. 2019-12-03 doi:10.1101/864082 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Functional connectivity differences in early infancy precede autism symptoms: a multivariate pattern analysis ]]> https://biorxiv.org/content/10.1101/866939v1?rss=1 Dickinson, A. Daniel, M. Marin, A. Goanker, B. Dapretto, M. McDonald, N. M. Jeste, S. 2019-12-06 doi:10.1101/866939 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order ]]> https://biorxiv.org/content/10.1101/867069v1?rss=1 Gemmell, N. Rutherford, K. Prost, S. Tollis, M. Winter, D. J. Macey, J. R. Adelson, D. L. Suh, A. Bertozzi, T. Grau, J. Organ, C. Gardner, P. Muffato, M. Patricio, M. Billis, K. Martin, F. J. Flicek, P. Petersen, B. Kang, L. Michalak, P. Buckley, T. Wilson, M. A. Cheng, Y. Miller, H. Schott, R. K. Jordan, M. Newcomb, R. Arroyo, J. I. Valenzuela, N. Hore, T. A. Renart, J. Peona, V. Peart, C. Warmuth, V. ZENG, L. Kortschak, D. Raison, J. M. Zapata, V. V. Wu, Z. Santesmasses, D. Mariotti, M. Guigo, R. Rupp, S. Twort, V. Dussex, N. Taylor, H. R. Abe, H 2019-12-08 doi:10.1101/867069 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Thousands of missing variants in the UK BioBankare recoverable by genome realignment ]]> https://biorxiv.org/content/10.1101/868570v1?rss=1 Jia, T. Munson, B. Lango Allen, H. Ideker, T. Majithia, A. R. 2019-12-10 doi:10.1101/868570 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Adverse caregiving in infancy blunts neural processing of the mother: Translating across species ]]> https://biorxiv.org/content/10.1101/870261v1?rss=1 Opendak, M. M. Theisen, E. Blomkvist, A. Hollis, K. Lind, T. Sarro, E. Lundstrom, J. N. Tottenham, N. Dozier, M. Wilson, D. Sullivan, R. 2019-12-10 doi:10.1101/870261 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ A multi-dimensional, time-lapse, high content screening platform for the flatworm pathogen causing schistosomiasis ]]> https://biorxiv.org/content/10.1101/872069v1?rss=1 Chen, S. Suzuki, B. M. Dohrmann, J. Singh, R. Arkin, M. R. Caffrey, C. R. 2019-12-11 doi:10.1101/872069 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Ligand-Dependent Mechanisms of C-C Chemokine Receptor 5 (CCR5) Trafficking Revealed by APEX2 Proximity Labeling Proteomics ]]> https://biorxiv.org/content/10.1101/2023.11.01.565224v1?rss=1 Gu, S. Maurya, S. Lona, A. Borrega-Roman, L. Salanga, C. Gonzalez, D. J. Kufareva, I. Handel, T. 2023-11-03 doi:10.1101/2023.11.01.565224 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom ]]> https://biorxiv.org/content/10.1101/2023.11.02.565333v1?rss=1 Brunson, J. K. Thukral, M. Ryan, J. P. Anderson, C. R. Kolody, B. C. James, C. C. Chavez, F. P. Leaw, C. P. Rabines, A. J. Venepally, P. Zheng, H. Kudela, R. M. Smith, G. J. Moore, B. S. Allen, A. E. 2023-11-05 doi:10.1101/2023.11.02.565333 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Zinc stimulation of coastal productivity in low carbon dioxide environments ]]> https://biorxiv.org/content/10.1101/2023.11.05.565706v1?rss=1 Kell, R. M. Subhas, A. V. Schanke, N. L. Lees, L. E. Chmiel, R. J. Rao, D. Brisbin, M. M. M. Moran, D. M. McIlvin, M. R. Bolinesi, F. Mangoni, O. Casotti, R. Balestra, C. Horner, T. Dunbar, R. B. Allen, A. E. DiTullio, G. R. Saito, M. A. 2023-11-05 doi:10.1101/2023.11.05.565706 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2023.11.06.565757v1?rss=1 Oliveira, A. S. F. Kearns, F. L. Rosenfeld, M. A. Casalino, L. F. Berger, I. Schaffitzel, C. Davidson, A. D. Amaro, R. E. Mulholland, A. J. 2023-11-08 doi:10.1101/2023.11.06.565757 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Arousal as a universal embedding for spatiotemporal brain dynamics ]]> https://biorxiv.org/content/10.1101/2023.11.06.565918v1?rss=1 Raut, R. V. Rosenthal, Z. P. Wang, X. Miao, H. Zhang, Z. Lee, J.-M. Raichle, M. E. Bauer, A. Q. Brunton, S. L. Brunton, B. W. Kutz, J. N. 2023-11-08 doi:10.1101/2023.11.06.565918 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Bacterial Diversity and Chemical Ecology of Natural Product-Producing Bacteria from Great Salt Lake Sediment ]]> https://biorxiv.org/content/10.1101/2023.11.07.565188v1?rss=1 Bring Horvath, E. R. Brazelton, W. J. Kim, M. C. Cullum, R. Mulvey, M. A. Fenical, W. Winter, J. M. 2023-11-08 doi:10.1101/2023.11.07.565188 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Both mOTS-words and pOTS-words prefer emoji stimuli over text stimuli during a reading task ]]> https://biorxiv.org/content/10.1101/2023.11.07.565794v1?rss=1 Dalski, A. Kular, H. Jorgensen, J. G. Grill-Spector, K. Grotheer, M. 2023-11-09 doi:10.1101/2023.11.07.565794 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow ]]> https://biorxiv.org/content/10.1101/2023.11.07.565977v1?rss=1 Malmstrom, J. Chowdhury, S. Gomez Toledo, A. Hjortswang, E. Sorrentino, J. T. Lewis, N. E. Blackberg, A. Ekstrom, S. Izadi, A. Nordenfelt, P. Malmstrom, L. Rasmussen, M. 2023-11-09 doi:10.1101/2023.11.07.565977 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Universal Digital High Resolution Melt for the detection of pulmonary mold infections ]]> https://biorxiv.org/content/10.1101/2023.11.09.566457v1?rss=1 Goshia, T. Aralar, A. Wiederhold, N. P. Jenks, J. D. Mehta, S. R. Sinha, M. Karmakar, A. Sharma, A. Shrivastava, R. Sun, H. White, P. L. Hoenigl, M. Fraley, S. I. 2023-11-09 doi:10.1101/2023.11.09.566457 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ CONSULT-II: Accurate taxonomic identification and profiling using locality-sensitive hashing ]]> https://biorxiv.org/content/10.1101/2023.11.07.566115v1?rss=1 Sapci, A. O. B. Rachtman, E. Mirarab, S. 2023-11-10 doi:10.1101/2023.11.07.566115 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Social isolation recruits amygdala-cortical circuitry to escalate alcohol drinking ]]> https://biorxiv.org/content/10.1101/2023.11.09.566421v1?rss=1 Patel, R. Patarino, M. Kim, K. Pamintuan, R. Taschbach, F. Li, H. Lee, C. van Hoek, A. Castro, R. Cazares, C. Miranda, R. Jia, C. Delahanty, J. Batra, K. Keyes, L. Libster, A. Wichmann, R. W. Pereira, T. Benna, M. Tye, K. M. 2023-11-10 doi:10.1101/2023.11.09.566421 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Dissecting Multiparametric Cerebral Hemodynamics using Integrated Ultrafast Ultrasound and Multispectral Photoacoustic Imaging ]]> https://biorxiv.org/content/10.1101/2023.11.07.566048v1?rss=1 Chen, H. Mirg, S. Gaddale, P. Agrawal, S. Li, M. Nguyen, V. Xu, T. Li, Q. Liu, J. Tu, W. Liu, X. Drew, P. J. Zhang, N. Gluckman, B. J. Kothpalli, S.-R. 2023-11-11 doi:10.1101/2023.11.07.566048 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants ]]> https://biorxiv.org/content/10.1101/2023.11.09.566459v1?rss=1 Prigge, M. J. Morffy, N. De Neve, A. Szutu, W. Juarez, M. J. A. Johnson, K. Do, N. Lavy, M. Hake, S. Strader, L. Estelle, M. Richardson, A. E. 2023-11-13 doi:10.1101/2023.11.09.566459 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Dilated cardiomyopathy mutation in beta-cardiac myosin enhances actin activation of the power stroke and phosphate release ]]> https://biorxiv.org/content/10.1101/2023.11.10.566646v1?rss=1 Bodt, S. M. Ge, J. Ma, W. Rasicci, D. V. Desetty, R. McCammon, J. A. Yengo, C. M. 2023-11-13 doi:10.1101/2023.11.10.566646 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput ]]> https://biorxiv.org/content/10.1101/2023.11.11.566649v1?rss=1 Kennedy, P. H. Deh Sheikh, A. A. Balakar, M. Jones, A. C. Olive, M. E. Hedge, M. Matias, M. I. Pirete, N. Burt, R. Levy, J. Little, T. Hogan, P. G. Liu, D. R. Doench, J. G. Newton, A. C. Gottschalk, R. A. de Boer, C. Alarcon, S. Newby, G. Myers, S. A. 2023-11-14 doi:10.1101/2023.11.11.566649 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Cell type-specific effects of age and sex on human cortical neurons ]]> https://biorxiv.org/content/10.1101/2023.11.11.566717v1?rss=1 Chien, J.-F. Liu, H. Wang, B.-A. Luo, C. Bartlett, A. Castanon, R. Johnson, N. D. Nery, J. R. Osteen, J. Li, J. Altshul, J. Kenworthy, M. Valadon, C. Liem, M. Claffey, N. O'Connor, C. Seeker, L. A. Ecker, J. R. Behrens, M. M. Mukamel, E. A. 2023-11-15 doi:10.1101/2023.11.11.566717 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Development of LRRK2 designed ankyrin-repeat proteins ]]> https://biorxiv.org/content/10.1101/2023.11.14.567123v1?rss=1 Dederer, V. Sanz Murillo, M. Karasmanis, E. P. Hatch, K. S. Chatterjee, D. Preuss, F. Abdul Azeez, K. R. Nguyen, L. V. Galicia, C. Dreier, B. Pluckthun, A. Versees, W. Mathea, S. Leschziner, A. E. Reck-Peterson, S. L. Knapp, S. 2023-11-15 doi:10.1101/2023.11.14.567123 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ O-antigen biosynthesis mediates evolutionary trade-offs within a simple community ]]> https://biorxiv.org/content/10.1101/2023.11.15.566321v1?rss=1 Spencer-Drakes, T. C. J. Sarabia, A. Heussler, G. Pierce, E. C. Morin, M. Dutton, R. J. Villareal, S. 2023-11-15 doi:10.1101/2023.11.15.566321 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ High quality, high throughput, and low-cost simultaneous video recording of 60 animals in operant chambers using PiRATeMC ]]> https://biorxiv.org/content/10.1101/2023.11.13.566747v1?rss=1 Ramborger, J. Kalra, S. Smith, A. C. George, O. 2023-11-16 doi:10.1101/2023.11.13.566747 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Optimal Tree Metric Matching Enables Phylogenomic Branch Length Reconciliation ]]> https://biorxiv.org/content/10.1101/2023.11.13.566962v1?rss=1 Arasti, S. Tabaghi, P. Tabatabaee, Y. Mirarab, S. 2023-11-16 doi:10.1101/2023.11.13.566962 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies ]]> https://biorxiv.org/content/10.1101/2023.11.14.567106v1?rss=1 Ma, J. Ting, S. Tam, B. Pham, T. Reich, M. M. Mesirov, J. Tamayo, P. Kim, W. 2023-11-16 doi:10.1101/2023.11.14.567106 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5 ]]> https://biorxiv.org/content/10.1101/2023.11.15.567150v1?rss=1 Dawson, J. R. D. Wadman, G. M. Zhang, P. Gu, S. Shroka, T. Borrega-Roman, L. Salanga, C. Handel, T. M. Kufareva, I. 2023-11-17 doi:10.1101/2023.11.15.567150 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Use of dye sensitizers for increased photoacoustic mechanosensation ]]> https://biorxiv.org/content/10.1101/2023.11.15.567262v1?rss=1 Rafeedi, T. Becerra, L. L. Root, N. Qi, B. Fu, L. Esparza, G. Qie, Y. Sasi, L. Rouw, R. Jokerst, J. Lipomi, D. J. 2023-11-17 doi:10.1101/2023.11.15.567262 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Environment-independent distribution of mutational effects emerges from microscopic epistasis ]]> https://biorxiv.org/content/10.1101/2023.11.18.567655v1?rss=1 Ardell, S. Martsul, A. Johnson, M. S. Kryazhimskiy, S. 2023-11-18 doi:10.1101/2023.11.18.567655 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback ]]> https://biorxiv.org/content/10.1101/2023.11.21.567575v1?rss=1 Coelho, C. H. Bloom, N. Ramirez, S. I. Parikh, U. M. Heaps, A. Sieg, S. F. Greninger, A. Ritz, J. Moser, C. Eron, J. J. Currier, J. S. Klekotka, P. Wohl, D. A. Daar, E. S. Li, J. Hughes, M. D. Chew, K. W. Smith, D. M. Crotty, S. Accelerating COVID-19 Therapeutic Interventions and Vaccines: 2/A5401 (ACTIV-2/A5401) Study Team, 2023-11-22 doi:10.1101/2023.11.21.567575 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2023.11.21.568070v1?rss=1 Crawford, J. E. Beebe, N. Bonizzoni, M. Caputo, B. Carter, B. H. Chen, C.-H. Cosme, L. De Marco, C. M. della Torre, A. Estallo, E. L. Guo, X. Liu, W.-L. Maringer, K. Mains, J. Maynard, A. Mogi, M. Livdahl, T. Rose, N. H. Scarafia, P. Y. Severson, D. Stein, M. Surendran, S. N. Tuno, N. Wahid, I. Wang, X. Xu, J. Yan, G. Yee, D. Armbruster, P. A. Caccone, A. White, B. 2023-11-22 doi:10.1101/2023.11.21.568070 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Polyglucosan body density in the aged mouse hippocampus is controlled by a novel modifier locus on chromosome 1 ]]> https://biorxiv.org/content/10.1101/2023.11.22.567373v1?rss=1 Gomez-Pascual, A. Glikman, D. M. Ng, H. X. Tomkins, J. E. Lu, L. Xu, Y. Ashbrook, D. G. Kaczorowski, C. Kempermann, G. Killmar, J. Mozhui, K. Aebersold, R. Williams, E. G. Williams, R. W. Overall, R. W. Jucker, M. de Bakker, D. E. M. 2023-11-22 doi:10.1101/2023.11.22.567373 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Engineering luminopsins with improved coupling efficiencies ]]> https://biorxiv.org/content/10.1101/2023.11.22.568342v1?rss=1 Slaviero, A. Gorantla, N. Simkins, J. W. Crespo, E. L. Ikefuama, E. C. Tree, M. O. Prakash, M. Bjorefeldt, A. Barnett, L. M. Lambert, G. G. Lipscombe, D. Moore, C. I. Shaner, N. C. Hochgeschwender, U. 2023-11-22 doi:10.1101/2023.11.22.568342 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Human extracellular sulfatases use a dual mechanism for regulation of growth factor interactions with heparan sulfate proteoglycans ]]> https://biorxiv.org/content/10.1101/2023.11.22.568358v1?rss=1 Timm, B. M. Follmar, J. L. Porell, R. N. Glass, K. Thacker, B. E. Glass, C. A. Godula, K. 2023-11-22 doi:10.1101/2023.11.22.568358 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Genome wide detection of somatic mosaicism at short tandem repeats ]]> https://biorxiv.org/content/10.1101/2023.11.22.568371v1?rss=1 Sehgal, A. Ziaei Jam, H. Shen, A. Gymrek, M. 2023-11-23 doi:10.1101/2023.11.22.568371 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Activatable prodrug for controlled release of an antimicrobial peptide via the proteases overexpressed in Candida albicans and Porphyromonas gingivalis ]]> https://biorxiv.org/content/10.1101/2023.11.27.568833v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1e9cf5corg.highwire.dtl.DTLVardef@12cb36forg.highwire.dtl.DTLVardef@1b862f7org.highwire.dtl.DTLVardef@697946_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Amer, L. Retout, M. Jokerst, J. V. 2023-11-27 doi:10.1101/2023.11.27.568833 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer ]]> https://biorxiv.org/content/10.1101/2023.11.28.569082v1?rss=1 Schmidt, T. T. Tyer, C. Rughani, P. Haggblom, C. Jones, J. R. Dai, X. Frazer, K. A. Gage, F. H. Juul, S. Hickey, S. Karlseder, J. 2023-11-29 doi:10.1101/2023.11.28.569082 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Upper bound on the mutational burden imposed by a CRISPR-Cas9 gene-drive element ]]> https://biorxiv.org/content/10.1101/2023.11.28.569142v1?rss=1 Overton, M. S. Guy, S. E. Chen, X. Martsul, A. Carolino, K. Akbari, O. Meyer, J. R. Kryazhimskiy, S. 2023-11-29 doi:10.1101/2023.11.28.569142 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population ]]> https://biorxiv.org/content/10.1101/2023.11.29.566473v1?rss=1 Okamoto, F. Chitre, A. S. Sanches, T. M. Chen, D. Munro, D. NIDA Center for GWAS in Outbred Rats, Polesskaya, O. Palmer, A. A. 2023-11-29 doi:10.1101/2023.11.29.566473 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Investigation of astrocytes' morphological changes in response to laser-induced shockwave ]]> https://biorxiv.org/content/10.1101/2023.11.29.569124v1?rss=1 Pouladian, P. Ho, J. Perez, N. Wakida, N. M. Gomez Godinez, V. Preece, D. 2023-11-30 doi:10.1101/2023.11.29.569124 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Perineuronal nets and the neuronal extracellular matrix can be imaged by genetically encoded labeling of HAPLN1 in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2023.11.29.569151v1?rss=1 Lemieux, S. P. Lev-Ram, V. Tsien, R. Y. Ellisman, M. H. 2023-11-30 doi:10.1101/2023.11.29.569151 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Understanding and exploitation of host stress responses to protein production using novel transcriptomic analytics ]]> https://biorxiv.org/content/10.1101/2023.11.30.569415v1?rss=1 Rode, C. Beulig, F. Jonsson, M. Jahn, L. Noerholm, M. H. H. Palsson, B. O. Ozdemir, E. Yang, L. 2023-12-01 doi:10.1101/2023.11.30.569415 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations ]]> https://biorxiv.org/content/10.1101/2023.11.30.569436v1?rss=1 Zhou, Z. Kim, J. Huang, A. Y. Nolan, M. Park, J. Doan, R. Shin, T. Miller, M. B. Chhouk, B. Morillo, K. Yeh, R. C. Kenny, C. Neil, J. E. Lee, C.-Z. Ohkubo, T. Ravits, J. Ansorge, O. Ostrow, L. W. Lagier-Tourenne, C. Lee, E. A. Walsh, C. A. 2023-12-01 doi:10.1101/2023.11.30.569436 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Intracellular Ebola Virus nucleocapsid assembly revealed by in situ cryo-electron tomography. ]]> https://biorxiv.org/content/10.1101/2023.12.01.569666v1?rss=1 Watanabe, R. Zyla, D. Parekh, D. Hong, C. Jones, Y. Schendel, S. L. Wan, W. Castillon, G. Saphire, E. O. 2023-12-02 doi:10.1101/2023.12.01.569666 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence ]]> https://biorxiv.org/content/10.1101/2023.12.03.569753v1?rss=1 Khan, A. H. Patel, R. J. Viana, M. P. Rafelski, S. M. Brown, A. I. Zid, B. M. Tsuboi, T. 2023-12-03 doi:10.1101/2023.12.03.569753 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ A foundational atlas of autism protein interactions reveals molecular convergence ]]> https://biorxiv.org/content/10.1101/2023.12.03.569805v1?rss=1 Wang, B. Vartak, R. Zaltsman, Y. Naing, Z. Z. C. Hennick, K. M. Polacco, B. J. Bashir, A. Eckhardt, M. Bouhaddou, M. Xu, J. Sun, N. Lasser, M. Zhou, Y. Guiley, K. Z. Chan, U. Kaye, J. A. Khare, P. Drake, S. Drury, V. Burke, D. F. Gonzalez, S. Alkhairy, S. Morris, M. Baum, T. Krasnoff, R. Wang, S. Pham, P. Arbalaez, J. Pratt, D. Chag, S. Rolland, T. Bourgeron, T. Finkbeiner, S. Bandyopadhay, S. Ideker, T. Beltrao, P. Willsey, H. R. Obernier, K. Nowakowski, T. J. Huttenhain, R. State, M. W. Willsey, A. J. Krogan, N. J. 2023-12-03 doi:10.1101/2023.12.03.569805 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Innate extracellular Hsp70 inflammatory properties are mediated by the interaction of Siglec-E and LOX-1 receptors ]]> https://biorxiv.org/content/10.1101/2023.12.01.569623v1?rss=1 Borges, T. J. Lima, K. Murshid, A. Lape, I. T. Zhao, Y. Rigo, M. M. Lang, B. J. Siddiqui, S. S. Hui, E. Riella, L. V. Bonorino, C. Calderwood, S. K. 2023-12-04 doi:10.1101/2023.12.01.569623 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Tumor microenvironmental determinants of high-risk DCIS progression ]]> https://biorxiv.org/content/10.1101/2023.12.01.569676v1?rss=1 5cm in size with at least one additional high-risk feature: young age (<45 years), high nuclear grade, hormone receptor negativity, HER2 positivity, the presence of comedonecrosis, or a palpable mass. The tumor immune microenvironment was characterized using multiplex immunofluorescence to identify immune cells and their spatial relationships within the ducts and stroma. Gene copy number analysis and whole exome DNA sequencing identified the mutational burden and driver mutations, and quantitative whole-transcriptome/gene expression analyses were performed. There was no association between the percent of the DCIS genome characterized by copy number variants (CNAs) and recurrence events (DCIS or invasive). Mutations, especially missense mutations, in the breast cancer driver genes PIK3CA and TP53 were common in this high-risk DCIS cohort (47% of evaluated lesions). Tumor infiltrating lymphocyte (TIL) density was higher in DCIS lesions with TP53 mutations (p=0.0079) compared to wildtype lesions, but not in lesions with PIK3CA mutations (p=0.44). Immune infiltrates were negatively associated with hormone receptor status and positively associated with HER2 expression. High levels of CD3+CD8-T cells were associated with good outcomes with respect to any subsequent recurrence (DCIS or invasive cancer), whereas high levels of CD3+Foxp3+ Treg cells were associated with poor outcomes. Spatial proximity analyses of immune cells and tumor cells demonstrated that close proximity of T cells with tumor cells was associated with good outcomes with respect to any recurrence as well as invasive recurrences. Interestingly, we found that myoepithelial continuity (distance between myoepithelial cells surrounding the involved ducts) was significantly lower in DCIS lesions compared to normal tissue (p=0.0002) or to atypical ductal hyperplasia (p=0.011). Gene set enrichment analysis identified several immune pathways associated with low myoepithelial continuity and a low myoepithelial continuity score was associated with better outcomes, suggesting that gaps in the myoepithelial layer may allow access/interactions between immune infiltrates and tumor cells. Our study demonstrates the immune microenvironment of DCIS, in particular the spatial proximity of tumor cells and T cells, and myoepithelial continuity are important determinants for progression of disease. ]]> Glencer, A. Ramalingam, K. Schindler, N. Mori, H. Ghule, P. Lee, K. C. Nachmanson, D. Officer, A. Harismendy, O. Stein, J. L. Stein, G. Weaver, D. Yau, C. Hirst, G. L. Campbell, M. J. Esserman, L. J. Borowsky, A. D. 2023-12-04 doi:10.1101/2023.12.01.569676 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Cell-type-specific 3D-genome organization and transcription regulation in the brain ]]> https://biorxiv.org/content/10.1101/2023.12.04.570024v1?rss=1 Liu, S. Zheng, P. Wang, C. Y. Jia, B. B. Zemke, N. R. Ren, B. Zhuang, X. 2023-12-05 doi:10.1101/2023.12.04.570024 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Discovery of anthelmintic small molecules in the Medicines for Malaria Ventures COVID and Global Health Priority Boxes using an infrared-based assay for Caenorhabditis elegans motility ]]> https://biorxiv.org/content/10.1101/2023.12.09.570935v1?rss=1 100 {micro}M. ConclusionsA C. elegans motility assay was optimized and used to screen two recently-released, small molecule libraries. One or more of these three novel active compounds might serve as starting points for the development of new anthelmintics. ]]> Caffrey, C. Liu, L. Sun, Y. U. 2023-12-10 doi:10.1101/2023.12.09.570935 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ A Bayesian Approach to Non-Metric Hyperbolic Multi-Dimensional Scaling ]]> https://biorxiv.org/content/10.1101/2023.12.08.570871v1?rss=1 Jolis, M. Praturu, A. Sharpee, T. O. 2023-12-11 doi:10.1101/2023.12.08.570871 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Molecular Determinants and Signaling Effects of PKA RIα Phase Separation ]]> https://biorxiv.org/content/10.1101/2023.12.10.570836v1?rss=1 Hardy, J. C. Pool, E. H. Bruystens, J. G. H. Zhou, X. Li, Q. Zhou, D. R. Palay, M. Tan, G. Chen, L. Choi, J. L. C. Lee, H. N. Strack, S. Wang, D. Taylor, S. S. Mehta, S. Zhang, J. 2023-12-11 doi:10.1101/2023.12.10.570836 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Towards a Brighter Constellation: Multi-Organ Neuroimaging of Neural and Vascular Dynamics in the Spinal Cord and Brain ]]> https://biorxiv.org/content/10.1101/2023.12.25.573323v1?rss=1 Celinskis, D. Black, C. J. Murphy, J. Barrios-Anderson, A. Friedman, N. Shaner, N. C. Saab, C. Gomez-Ramirez, M. Lipscombe, D. Borton, D. A. Moore, C. I. 2023-12-27 doi:10.1101/2023.12.25.573323 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Phago-mixotrophy of small eukaryotic phytoplankton might alleviate iron limitation in HNLC Southern Ocean ]]> https://biorxiv.org/content/10.1101/2024.01.08.574519v1?rss=1 Ong, D. R. Y. Gutierrez-Rodriguez, A. Safi, K. A. Marie, D. Selph, K. E. Stukel, M. R. Decima, M. Lopes dos Santos, A. 2024-01-08 doi:10.1101/2024.01.08.574519 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus ]]> https://biorxiv.org/content/10.1101/2024.01.12.574766v1?rss=1 Samavat, M. Bartol, T. M. Bromer, C. Hubbard, D. D. Hanka, D. C. Kuwajima, M. Mendenhall, J. M. Parker, P. H. Bowden, J. B. Abraham, W. Sejnowski, T. J. Harris, K. M. 2024-01-14 doi:10.1101/2024.01.12.574766 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Methyl substituted β-lactam framework based antibiotics and β-lactamase inhibitors: Proof of concept by computations ]]> https://biorxiv.org/content/10.1101/2024.01.14.575563v1?rss=1 Thakkur, V. Das, C. K. Verma, S. Saha, S. Nair, N. N. 2024-01-14 doi:10.1101/2024.01.14.575563 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ The Interaction of NF-κB Transcription Factor with Centromeric Chromatin ]]> https://biorxiv.org/content/10.1101/2024.02.13.580208v1?rss=1 Filliaux, S. B. Bertelsen, C. Baughman, H. E. R. Komives, E. A. A. Lyubchenko, Y. L. 2024-02-16 doi:10.1101/2024.02.13.580208 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing ]]> https://biorxiv.org/content/10.1101/2024.02.15.580594v1?rss=1 Zhu, K. Jones, M. G. Luebeck, J. Bu, X. Yi, H. Hung, K. L. Wong, I. T.-L. Zhang, S. Mischel, P. S. Chang, H. Y. Bafna, V. 2024-02-16 doi:10.1101/2024.02.15.580594 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex ]]> https://biorxiv.org/content/10.1101/2024.02.17.580791v1?rss=1 Pradhan, B. Deep, A. Koenig, J. Baaske, M. Corbett, K. Kim, E. 2024-02-17 doi:10.1101/2024.02.17.580791 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ MU-BRAIN: MUltiethnic Brain Rna-seq for Alzheimer INitiative ]]> https://biorxiv.org/content/10.1101/2024.02.20.581250v1?rss=1 Yang, Z. Cieza, B. Reyes-Dumeyer, D. Lee, A. Ma, Y. Yilmaz, E. Lantigua, R. Miller, G. Brown, L. Honig, L. Ciener, B. Leskinin, S. Sivakumar, S. Vardarajan, B. Dugger, B. Jin, L.-W. Murray, M. Dickson, D. Rissman, R. Hiniker, A. Pericak-Vance, M. Vance, J. Foroud, T. Kizil, C. Teich, A. Mayeux, R. Tosto, G. 2024-02-23 doi:10.1101/2024.02.20.581250 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ A multi-symptomatic model of heroin use disorder in rats reveals distinct behavioral profiles and neuronal correlates of heroin vulnerability versus resiliency ]]> https://biorxiv.org/content/10.1101/2024.02.22.581440v1?rss=1 Kuhn, B. N. Cannella, N. Crow, A. Lunerti, V. Gupta, A. Walterhouse, S. Allen, C. Chalhoub, R. Dereschewitz, E. Roberts, A. Cockerham, M. Beeson, A. Nall, R. Palmer, A. A. Hardiman, G. Solberg-Woods, L. Chung, D. Ciccocioppo, R. Kalivas, P. 2024-02-23 doi:10.1101/2024.02.22.581440 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2024.02.22.581624v1?rss=1 Rychel, K. Chen, K. Catoiu, E. A. Olson, C. A. Sandberg, T. E. Gao, Y. Xu, S. Hefner, Y. Szubin, R. Patel, A. Feist, A. M. Palsson, B. 2024-02-23 doi:10.1101/2024.02.22.581624 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Activity-dependent regulation of vascular cholesterol metabolism acts as a negative feedback mechanism for neurovascular coupling ]]> https://biorxiv.org/content/10.1101/2024.02.23.581685v1?rss=1 Profaci, C. P. Foreman, K. L. Spieth, L. Coelho-Santos, V. Berghoff, S. A. Fontaine, J. T. Jeffrey, D. A. Palecek, S. P. Shusta, E. V. Saher, G. Shih, A. Y. Dabertrand, F. Daneman, R. 2024-02-23 doi:10.1101/2024.02.23.581685 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Design, optimization, and inference of multiphasic decay of infectious virus particles ]]> https://biorxiv.org/content/10.1101/2024.02.23.581735v1?rss=1 Seurat, J. Gerbino, K. Meyer, J. R. Borin, J. Weitz, J. 2024-02-23 doi:10.1101/2024.02.23.581735 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ A worldwide ENIGMA study on epilepsy-related gray and white matter compromise across the adult lifespan ]]> https://biorxiv.org/content/10.1101/2024.03.02.583073v1?rss=1 Chen, J. Ngo, A. Rodriguez-Cruces, R. Royer, J. Caligiuri, M. E. Gambardella, A. Concha, L. Keller, S. S. Cendes, F. Yasuda, C. L. Alvim, M. K. M. Bonilha, L. Gleichgerrcht, E. Focke, N. K. Kreilkamp, B. Domin, M. von Podewils, F. Langner, S. Rummel, C. Wiest, R. Martin, P. Kotikalapudi, R. Bender, B. O'Brien, T. J. Sinclair, B. Vivash, L. Kwan, P. Desmond, P. M. Lui, E. Duma, G. M. Bonanni, P. Ballerini, A. Vaudano, A. E. Meletti, S. Tondelli, M. Alhusaini, S. Doherty, C. P. Cavalleri, G. L. Delanty, N. Kälviäinen, R. Jackson, G. Kowalczyk, M. Masca 2024-03-06 doi:10.1101/2024.03.02.583073 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Effects of access condition on substance use disorder-like phenotypes in male and female rats self-administering MDPV or cocaine ]]> https://biorxiv.org/content/10.1101/2024.03.04.583431v1?rss=1 Doyle, M. R. Beltran, N. M. Bushnell, M. S. Syed, M. Acosta, V. Desai, M. Rice, K. C. Serafine, K. M. Gould, G. G. Daws, L. C. Collins, G. T. 2024-03-08 doi:10.1101/2024.03.04.583431 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Understanding flux switching in metabolic networks through an analysis of synthetic lethals ]]> https://biorxiv.org/content/10.1101/2024.03.05.583461v1?rss=1 Manojna, S. Malpani, T. Mohite, O. S. Nath, S. Raman, K. 2024-03-09 doi:10.1101/2024.03.05.583461 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors ]]> https://biorxiv.org/content/10.1101/2024.03.05.583605v1?rss=1 Xu, W. Hsu, P.-K. Moshiri, N. Yu, S. Rosing, T. 2024-03-08 doi:10.1101/2024.03.05.583605 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads ]]> https://biorxiv.org/content/10.1101/2024.03.08.584032v1?rss=1 Eidi, M. Abdolalizadeh, S. Nasirpour, M. H. Zahiri, J. Garshasbi, M. 2024-03-10 doi:10.1101/2024.03.08.584032 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Cytokine and Chemokine Receptor Profiles in Adipose Tissue Vasculature Unravel Endothelial Cell Responses in HIV ]]> https://biorxiv.org/content/10.1101/2024.03.10.584280v1?rss=1 Obare, L. M. Priest, S. Ismael, A. Mashayekhi, M. Zhang, X. Stolze, L. Sheng, Q. Vue, Z. Neikirk, K. Beasley, H. Gabriel, C. Temu, T. Gianella, S. Mallal, S. Koethe, J. Hinton, A. Bailin, S. Wanjalla, C. N. 2024-03-12 doi:10.1101/2024.03.10.584280 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS ]]> https://biorxiv.org/content/10.1101/2024.03.11.584522v1?rss=1 Weaver, S. Davila-Conn, V. M. Ji, D. Avila-Rios, S. Leigh Brown, A. Wertheim, J. Kosakovsky Pond, S. L. 2024-03-14 doi:10.1101/2024.03.11.584522 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Host evolution improves genetic circuit function in complex growth environments ]]> https://biorxiv.org/content/10.1101/2024.03.13.583595v1?rss=1 Zhang, J. T. Lezia, A. Emmanuele, P. Wu, M. Olson, C. A. Feist, A. T. Hasty, J. 2024-03-13 doi:10.1101/2024.03.13.583595 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Genome-Wide Association Study in Outbred Heterogeneous Stock Rats Identifies Multiple Loci for the Incentive Salience of Reward Cues. ]]> https://biorxiv.org/content/10.1101/2024.03.13.584852v1?rss=1 King, C. P. Chitre, A. S. Leal-Gutierrez, J. D. Tripi, J. A. Hughson, A. Horvath, A. Lamparelli, A. C. George, A. Martin, C. St. Pierre, C. L. Bimschleger, H. V. Gao, J. Cheng, R. Nguyen, K.-M. Holl, K. L. Polesskaya, O. Ishiwari, K. Chen, H. Solberg-Woods, L. C. Palmer, A. A. Robinson, T. E. Flagel, S. B. Meyer, P. J. 2024-03-18 doi:10.1101/2024.03.13.584852 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ Lysine-Cysteine-Serine-Tryptophan Inserted into the DNA-Binding Domain of Human Mineralocorticoid Receptor Increases Transcriptional Activation by Aldosterone ]]> https://biorxiv.org/content/10.1101/2024.03.14.585051v1?rss=1 Katsu, Y. Zhang, J. Baker, M. E. 2024-03-15 doi:10.1101/2024.03.14.585051 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Astrocyte CCN1 stabilizes neural circuits in the adult brain ]]> https://biorxiv.org/content/10.1101/2024.03.14.585077v1?rss=1 Sancho, L. Boisvert, M. M. Dawoodtabar, T. Burgado, J. Wang, E. Allen, N. J. 2024-03-14 doi:10.1101/2024.03.14.585077 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Transposable element methylation state predicts age and disease ]]> https://biorxiv.org/content/10.1101/2024.03.15.585206v1?rss=1 Morandini, F. Lu, J. Y. Rechsteiner, C. Shadyab, A. H. Casanova, R. Snively, B. Seluanov, A. Gorbunova, V. 2024-03-16 doi:10.1101/2024.03.15.585206 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Intra-species quantification reveals differences in activity and sleep levels in the yellow fever mosquito, Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2024.03.16.585223v1?rss=1 Ajayi, O. Susanto, E. E. Wang, L. Kennedy, J. Ledezma, A. Harris, A. Smith, E. S. Chakraborty, S. Wynne, N. E. Sylla, M. Akorli, J. Otoo, S. Rose, N. H. Vinauger, C. Benoit, J. B. 2024-03-19 doi:10.1101/2024.03.16.585223 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.03.17.585262v1?rss=1 Leventhal, M. J. Zanella, C. A. Kang, B. Peng, J. Gritsch, D. Liao, Z. Bukhari, H. Wang, T. Pao, P.-C. Danquah, S. Benetatos, J. Nehme, R. Farhi, S. Tsai, L.-H. Dong, X. Scherzer, C. Feany, M. B. Fraenkel, E. 2024-03-17 doi:10.1101/2024.03.17.585262 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Representing the dynamics of natural marmoset vocal behaviors in frontal cortex ]]> https://biorxiv.org/content/10.1101/2024.03.17.585423v1?rss=1 Li, J. Aoi, M. C. Miller, C. 2024-03-17 doi:10.1101/2024.03.17.585423 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ mLiftOver: Harmonizing Data Across Infinium DNA Methylation Platforms ]]> https://biorxiv.org/content/10.1101/2024.03.18.585415v1?rss=1 Chen, B. H. Zhou, W. 2024-03-19 doi:10.1101/2024.03.18.585415 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Light-gated Integrator for Highlighting Kinase Activity in Living Cells ]]> https://biorxiv.org/content/10.1101/2024.03.18.585554v1?rss=1 Lin, W. Phatarphekar, A. Zhong, Y. Liu, L. Kwon, H.-B. Gerwick, W. H. Wang, Y. Mehta, S. Zhang, J. 2024-03-20 doi:10.1101/2024.03.18.585554 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression ]]> https://biorxiv.org/content/10.1101/2024.03.19.585820v1?rss=1 Dilmore, A. H. Kuplicki, R. McDonald, D. Kumar, M. Estaki, M. Youngblut, N. D. Tyakht, A. Ackermann, G. Blach, C. MahmoudianDehkordi, S. Dunlop, B. Bhattacharyya, S. Guinjoan, S. Mandaviya, P. Ley, R. Kaddurah-Daouk, R. Paulus, M. P. Knight, R. Alzheimer Gut Microbiome Project Consortium, 2024-03-19 doi:10.1101/2024.03.19.585820 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted ]]> https://biorxiv.org/content/10.1101/2024.03.20.585130v1?rss=1 Reina-Campos, M. Monell, A. Ferry, A. Luna, V. Cheung, K. Galletti, G. Scharping, N. E. Takehara, K. Quon, S. Boland, B. Lin, Y. H. Wong, W. H. Indralingam, C. S. Yeo, G. W. Chang, J. T. Heeg, M. Goldrath, A. W. 2024-03-25 doi:10.1101/2024.03.20.585130 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Bioinformatic prediction and high throughput in vivo screening to identify cis-regulatory elements for the development of algal synthetic promoters ]]> https://biorxiv.org/content/10.1101/2024.03.20.585996v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@1869cd4org.highwire.dtl.DTLVardef@a25d8dorg.highwire.dtl.DTLVardef@1abd96forg.highwire.dtl.DTLVardef@1501bc8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Torres-Tiji, Y. Sethuram, H. Gupta, A. McCauley, J. Dutra-Molino, J.-V. Pathania, R. Saxton, L. Kang, K. Hillson, N. J. Mayfield, S. P. 2024-03-21 doi:10.1101/2024.03.20.585996 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ An essential and highly selective protein import pathway encoded by nucleus-forming phage ]]> https://biorxiv.org/content/10.1101/2024.03.21.585822v1?rss=1 Morgan, C. J. Enustun, E. Armbruster, E. G. Birkholz, E. A. Prichard, A. Forman, T. Aindow, A. Wannasrichan, W. Peters, S. Inlow, K. Shepherd, I. L. Razavilar, A. Chaikeeratisak, V. Adler, B. A. Cress, B. F. Doudna, J. A. Pogliano, K. Villa, E. Corbett, K. D. Pogliano, J. 2024-03-21 doi:10.1101/2024.03.21.585822 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ ChemPrint: An AI-Driven Framework for Enhanced Drug Discovery ]]> https://biorxiv.org/content/10.1101/2024.03.22.586314v1?rss=1 Umansky, T. Ramesh, N. Woods, V. Russell, S. M. Smith, D. M. Haders, D. 2024-03-27 doi:10.1101/2024.03.22.586314 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Thermal tolerance of mosquito eggs is associated with urban adaptation and human interactions ]]> https://biorxiv.org/content/10.1101/2024.03.22.586322v1?rss=1 Chakraborty, S. Zigmond, E. Shah, S. Sylla, M. Akorli, J. Otoo, S. Rose, N. H. McBride, C. S. Armbruster, P. A. Benoit, J. B. 2024-03-27 doi:10.1101/2024.03.22.586322 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer ]]> https://biorxiv.org/content/10.1101/2024.03.22.586352v1?rss=1 Allemann, M. N. Kato, R. Alexander, W. G. Giannone, R. J. Kamimura, N. Masai, E. Michener, J. K. 2024-03-23 doi:10.1101/2024.03.22.586352 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay ]]> https://biorxiv.org/content/10.1101/2024.03.24.586510v1?rss=1 Sun, B. Ding, T. Zhou, W. Porter, T. S. Lew, M. D. 2024-03-27 doi:10.1101/2024.03.24.586510 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin, Lytechinus pictus. ]]> https://biorxiv.org/content/10.1101/2024.03.26.586777v1?rss=1 Jackson, E. W. Romero, E. Lee, Y. Kling, S. Tjeerdema, E. Hamdoun, A. 2024-03-29 doi:10.1101/2024.03.26.586777 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ A Hollow TFG Condensate Spatially Compartmentalizes the Early Secretory Pathway ]]> https://biorxiv.org/content/10.1101/2024.03.26.586876v1?rss=1 Wegeng, W. R. Bogus, S. M. Ruiz, M. Chavez, S. R. Noori, K. S. M. Niesman, I. R. Ernst, A. M. 2024-03-27 doi:10.1101/2024.03.26.586876 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Multiple and subject-specific roles of uncertainty in reward-guided decision-making ]]> https://biorxiv.org/content/10.1101/2024.03.27.587016v1?rss=1 Paunov, A. L'Hotellier, M. He, Z. Guo, D. Yu, A. Meyniel, F. 2024-03-30 doi:10.1101/2024.03.27.587016 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling ]]> https://biorxiv.org/content/10.1101/2024.03.27.587044v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@11687e4org.highwire.dtl.DTLVardef@33b146org.highwire.dtl.DTLVardef@1bb6bcborg.highwire.dtl.DTLVardef@1a1e47e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, H. Peralta, A. G. Schoffelen, S. Hansen, A. H. Arnsdorf, J. Schinn, S.-M. Skidmore, J. Choudhury, B. Paulchakrabarti, M. Voldborg, B. G. Chiang, A. W. T. Lewis, N. E. 2024-03-30 doi:10.1101/2024.03.27.587044 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes ]]> https://biorxiv.org/content/10.1101/2024.03.27.587047v1?rss=1 Franco-Enzastiga, U. Inturi, N. N. Natarajan, K. Mwirigi, J. M. Mazhar, K. Schlachetzki, J. C. Schumacher, M. Price, T. J. 2024-03-30 doi:10.1101/2024.03.27.587047 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ The Molecular Architecture of the Nuclear Basket ]]> https://biorxiv.org/content/10.1101/2024.03.27.587068v1?rss=1 Singh, D. Soni, N. Hutchings, J. Echeverria, I. Shaikh, F. Duquette, M. Suslov, S. Li, Z. van Eeuwen, T. Molloy, K. Shi, Y. Wang, J. Guo, Q. Chait, B. T. Fernandez-Martinez, J. Rout, M. P. Sali, A. Villa, E. 2024-03-28 doi:10.1101/2024.03.27.587068 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Glycoengineered recombinant alpha1-antitrypsin results in comparable in vitro and in vivo activities to human plasma-derived protein ]]> https://biorxiv.org/content/10.1101/2024.03.27.587088v1?rss=1 Rocamora, F. Schoffelen, S. Arnsdorf, J. Toth, E. A. Abdul, Y. Cleveland, T. E. Bjorn, S. P. Wu, M. Y. M. McElvaney, N. G. Voldborg, B. G. R. Fuerst, T. R. Lewis, N. E. 2024-03-30 doi:10.1101/2024.03.27.587088 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Learning from Machine Learning: advancing from static to dynamic facial function quantification ]]> https://biorxiv.org/content/10.1101/2024.03.28.584911v1?rss=1 Kalavacherla, S. Mills, M. D. Greene, J. 2024-04-01 doi:10.1101/2024.03.28.584911 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Open-source, high performance miniature multiphoton microscopy systems for freely behaving animals ]]> https://biorxiv.org/content/10.1101/2024.03.29.586663v1?rss=1 Madruga, B. A. Dorian, C. C. Sehgal, M. Silva, A. J. Shtrahman, M. Aharoni, D. Golshani, P. 2024-03-31 doi:10.1101/2024.03.29.586663 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers ]]> https://biorxiv.org/content/10.1101/2024.03.29.586681v1?rss=1 Tang, J. Weiser, N. E. Wang, G. Chowdhry, S. Curtis, E. J. Zhao, Y. Wong, I. T.-L. Marinov, G. K. Li, R. Hanoian, P. Tse, E. Hansen, R. Plum, J. Steffy, A. Milutinovic, S. Meyer, S. T. Altemose, N. Curtis, C. Greenleaf, W. J. Bafna, V. Benkovic, S. J. Pinkerton, A. B. Kasibhatla, S. Hassig, C. A. Mischel, P. S. Chang, H. Y. 2024-03-29 doi:10.1101/2024.03.29.586681 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Sensitive Fluorescent Biosensor Reveals Differential Subcellular Regulation of PKC ]]> https://biorxiv.org/content/10.1101/2024.03.29.587373v1?rss=1 Su, Q. Zhang, J. Lin, W. Zhang, J.-f. Newton, A. C. Mehta, S. Yang, J. Zhang, J. 2024-03-30 doi:10.1101/2024.03.29.587373 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Discovery of RdRp Thumb-1 as a novel broad-spectrum antiviral family of targets and MDL-001 as a potent broad-spectrum inhibitor thereof - Part I: A Bioinformatics and Deep Learning Approach ]]> https://biorxiv.org/content/10.1101/2024.03.29.587401v1?rss=1 Woods, V. Umansky, T. Ramesh, N. Russell, S. M. Garvey, D. Smith, D. M. Haders, D. 2024-04-03 doi:10.1101/2024.03.29.587401 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Extracellular vesicles-based point-of-care testing for the diagnosis and monitoring of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.03.31.587511v1?rss=1 Li, X. Chen, J. yang, y. Cai, H. Ao, Z. Xing, Y. Li, k. Yang, K. Wallace, A. Friend, J. Lee, L. P. Wang, N. Guo, F. 2024-04-02 doi:10.1101/2024.03.31.587511 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Empowering STEM Students: A University-wide Mentorship Program Fostering Retention and Belonging ]]> https://biorxiv.org/content/10.1101/2024.04.02.587784v1?rss=1 Ravishankar, S. Spencer-Drakes, T. C. J. Fernandes, I. H. Hayes, M. I. Coopwood, S. Spencers, I. Neal, S. E. 2024-04-02 doi:10.1101/2024.04.02.587784 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ APOBEC shapes tumor evolution and age at onset of lung cancer in smokers ]]> https://biorxiv.org/content/10.1101/2024.04.02.587805v1?rss=1 Zhang, T. Sang, J. Hoang, P. Zhao, W. Rosenbaum, J. Johnson, K. Klimczak, L. McElderry, J. Klein, A. Wirth, C. Bergstrom, E. Diaz Gay, M. Vangara, R. Colon-Matos, F. Hutchinson, A. Lawrence, S. Cole, N. Zhu, B. Przytycka, T. Shi, J. Caporaso, N. Homer, R. Pesatori, A. Consonni, D. Imielin _ski, M. Chanock, S. Wedge, D. Gordenin, D. Alexandrov, L. Harris, R. Landi, M. 2024-04-03 doi:10.1101/2024.04.02.587805 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration ]]> https://biorxiv.org/content/10.1101/2024.04.02.587832v1?rss=1 Liu, D. Webber, H. C. Bian, F. Xu, Y. Prakash, M. Feng, X. Yang, M. Yang, H. You, I.-J. Li, L. Liu, L. Liu, P. Huang, H. Chang, C.-Y. Liu, L. Shah, S. H. La Torre, A. Welsbie, D. S. Sun, Y. Duan, X. Goldberg, J. L. Braun, M. Lansky, Z. Hu, Y. 2024-04-03 doi:10.1101/2024.04.02.587832 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Onco-Circuit Addiction and Onco-Nutrient mTORC1 Signaling Vulnerability in a Model of Aggressive T Cell Malignancy ]]> https://biorxiv.org/content/10.1101/2024.04.03.587917v1?rss=1 Wang, X. Cornish, A. E. Do, M. H. Brunner, J. S. Hsu, T.-W. Xu, Z. Malik, I. Edwards, C. Capistrano, K. J. Zhang, X. Ginsberg, M. H. Finley, L. W. S. Lim, M. S. Horwitz, S. M. Li, M. O. 2024-04-04 doi:10.1101/2024.04.03.587917 Cold Spring Harbor Laboratory Press 2024-04-04 <![CDATA[ Unique functional neuroimaging signatures of genetic versus clinical high risk for psychosis ]]> https://biorxiv.org/content/10.1101/2024.04.03.587988v1?rss=1 Schleifer, C. H. Chang, S. E. Amir, C. M. O'Hora, K. P. Fung, H. Kang, J. W. D. Kushan-Wells, L. Daly, E. Di Fabio, F. Frascarelli, M. Gudbrandsen, M. Kates, W. R. Murphy, D. Addington, J. Anticevic, A. Cadenhead, K. S. Cannon, T. D. Cornblatt, B. A. Keshavan, M. Mathalon, D. H. Perkins, D. O. Stone, W. Walker, E. Woods, S. W. Uddin, L. Q. Kumar, K. Hoftman, G. D. Bearden, C. E. 2024-04-05 doi:10.1101/2024.04.03.587988 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ 12/15-Lipoxygenases mediate neuropathic-like pain hypersensitivity in female mice ]]> https://biorxiv.org/content/10.1101/2024.04.04.588153v1?rss=1 Brown, B. Chen, I. Miliano, C. Murdaugh, L. B. Dong, Y. Eddinger, K. A. Yaksh, T. L. Burton, M. D. Buczynski, M. Gregus, A. M. 2024-04-08 doi:10.1101/2024.04.04.588153 Cold Spring Harbor Laboratory Press 2024-04-08 <![CDATA[ Integrated multiomic analysis identifies TRIP13 as a mediator of alveolar epithelial type II cell dysfunction in idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2024.04.05.588292v1?rss=1 St. Pierre, L. Berhan, A. Sung, E. K. Alvarez, J. R. Wang, H. Ji, Y. Liu, Y. Yu, H. V. Meier, A. Afshar, K. Golts, E. Lin, G. Y. Castaldi, A. Calvert, B. Ryan, A. Zhou, B. Offringa, I. Marconett, C. N. Borok, Z. 2024-04-12 doi:10.1101/2024.04.05.588292 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Elasmobranchs Exhibit Species-Specific Epidermal Microbiomes Guided by Denticle Topography ]]> https://biorxiv.org/content/10.1101/2024.04.05.588334v1?rss=1 Goodman, A. Z. Papudeshi, B. Mora, M. F. Kerr, E. N. Torres, M. Nero Moffatt, J. Lima, L. F. Niesman, I. Moreno, I. Y. Doane, M. Dinsdale, E. A. 2024-04-06 doi:10.1101/2024.04.05.588334 Cold Spring Harbor Laboratory Press 2024-04-06 <![CDATA[ Genome-wide profiling of the hierarchical control of autophagy dynamics using deep learning ]]> https://biorxiv.org/content/10.1101/2024.04.06.588104v1?rss=1 Chica, N. Andersen, A. N. Orellana-Munoz, S. Garcia, I. Nguea P, A. Ayuda-Duran, P. Hakensbakken, L. Rodningen, E. Putnam, C. D. Zucknick, M. Rusten, T. E. Enserink, J. M. 2024-04-06 doi:10.1101/2024.04.06.588104 Cold Spring Harbor Laboratory Press 2024-04-06 <![CDATA[ Diet and Size-at-Birth Affect Larval Rockfish Condition and Survival ]]> https://biorxiv.org/content/10.1101/2024.04.07.588270v1?rss=1 Walsh, K. A. Thompson, A. R. Kwan, G. T. Semmens, B. X. Fennie, H. W. Swalethorp, R. 2024-04-10 doi:10.1101/2024.04.07.588270 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Chemical tools to define and manipulate interferon-inducible Ubl protease USP18 ]]> https://biorxiv.org/content/10.1101/2024.04.08.588544v1?rss=1 Davis, G. J. Omole, A. O. Jung, Y. Rut, W. Holewinski, R. Suazo, K. F. Kim, H.-R. Yang, M. Andresson, T. Drag, M. Yoo, E. 2024-04-08 doi:10.1101/2024.04.08.588544 Cold Spring Harbor Laboratory Press 2024-04-08 <![CDATA[ Automated, image-based quantification of peroxisome characteristics with perox-per-cell ]]> https://biorxiv.org/content/10.1101/2024.04.08.588597v1?rss=1 Neal, M. L. Shukla, N. Mast, F. D. Farre, J.-C. Pacio, T. M. Raney-Plourde, K. E. Prasad, S. Subramani, S. Aitchison, J. D. 2024-04-12 doi:10.1101/2024.04.08.588597 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Terrestrial 3D Laser Scanning for Ecosystem and Fire Effects Monitoring ]]> https://biorxiv.org/content/10.1101/2024.04.09.587551v1?rss=1 Murphy, M. C. Loudermilk, E. L. L. Pokswinski, S. Williams, B. Link, E. Lienesch, L. Douglas, L. Skowronski, N. S. Gallagher, M. R. Maxwell, A. Snitker, G. Hawley, C. M. Wallace, D. Payne, I. Yurkiewicz, T. Sanchez Meador, A. Anderson, C. Jackson, M. Parsons, R. Floca, M. Nealey, I. Altintas, I. Hiers, J. K. Wallace, J. 2024-04-09 doi:10.1101/2024.04.09.587551 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves ]]> https://biorxiv.org/content/10.1101/2024.04.09.588685v1?rss=1 Lin, M. Bacher, H. Bourgault, R. Qiao, P. Matschi, S. Vasquez, M. F. Mohammadi, M. van Boerdonk, S. Scanlon, M. J. Smith, L. G. Molina, I. Gore, M. A. 2024-04-12 doi:10.1101/2024.04.09.588685 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Breaking Down the Bottlebrush: Atomically-Detailed Structural Dynamics of Mucins ]]> https://biorxiv.org/content/10.1101/2024.04.09.588790v1?rss=1 Kearns, F. Rosenfeld, M. Amaro, R. E. 2024-04-13 doi:10.1101/2024.04.09.588790 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci ]]> https://biorxiv.org/content/10.1101/2024.04.10.588874v1?rss=1 Arthur, T. D. Nguyen, J. P. D'Antonio-Chronowska, A. Jaureguy, J. Silva, N. Henson, B. iPSCORE Consortium, Panopoulos, A. D. Belmonte, J. C. I. D'Antonio, M. McVicker, G. Frazer, K. A. 2024-04-11 doi:10.1101/2024.04.10.588874 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Microglia drive diurnal variation in susceptibility to inflammatory blood-brain barrier breakdown ]]> https://biorxiv.org/content/10.1101/2024.04.10.588924v1?rss=1 Lawrence, J. H. Patel, A. King, M. W. Nadarajah, C. J. Daneman, R. Musiek, E. S. 2024-04-14 doi:10.1101/2024.04.10.588924 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Regulation of lung cancer initiation and progression by the stem cell determinant Musashi ]]> https://biorxiv.org/content/10.1101/2024.04.11.589053v1?rss=1 Barber, A. G. Quintero, C. M. Hamilton, M. Rajbhandari, N. Sasik, R. Zhang, Y. Kim, C. Husain, H. Sun, X. Reya, T. 2024-04-15 doi:10.1101/2024.04.11.589053 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ A Novel Simple ImmunoAssay for Quantification of Blood Anti-NMDAR1 Autoantibodies ]]> https://biorxiv.org/content/10.1101/2024.04.11.589086v1?rss=1 Vaughn, M. N. Powell, S. Risbrough, V. Zhou, X. 2024-04-15 doi:10.1101/2024.04.11.589086 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. ]]> https://biorxiv.org/content/10.1101/2024.04.11.589096v1?rss=1 Qadir, M. M. F. Elgamal, R. M. Song, K. Kudtarkar, P. Sakamuri, S. S. V. P. Katakam, P. V. El-Dahr, S. Kolls, J. K. Gaulton, K. J. Mauvais-Jarvis, F. 2024-04-14 doi:10.1101/2024.04.11.589096 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus ]]> https://biorxiv.org/content/10.1101/2024.04.12.589303v1?rss=1 Aksenov, A. A. Blacutt, A. Ginnan, N. Rolshausen, P. Melnik, A. V. Lotfi, A. Gentry, E. C. Ramasamy, M. Zuniga, C. Zengler, K. Mandadi, K. Dorrestein, P. C. Roper, C. 2024-04-15 doi:10.1101/2024.04.12.589303 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Super-resolution Left Ventricular Flow and Pressure Mapping by Navier-Stokes-Informed Neural Networks ]]> https://biorxiv.org/content/10.1101/2024.04.12.589319v1?rss=1 Maidu, B. Martinez-Legazpi, P. Guerrero-Hurtado, M. Nguyen, C. M. Gonzalo, A. Kahn, A. M. Bermejo, J. Flores, O. del Alamo, J. C. 2024-04-15 doi:10.1101/2024.04.12.589319 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ The microtubule regulator EFA-6 forms spatially restricted cortical foci dependent on its intrinsically disordered region and interactions with tubulins ]]> https://biorxiv.org/content/10.1101/2024.04.14.588158v1?rss=1 Sandhu, A. Lyu, X. Wan, X. Meng, X. Tang, N. H. Gonzalez, G. Syed, I. N. Chen, L. Jin, Y. Chisholm, A. D. 2024-04-14 doi:10.1101/2024.04.14.588158 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Bacteriophage {Phi}21s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity ]]> https://biorxiv.org/content/10.1101/2024.04.15.589635v1?rss=1 Gerbino, K. R. Borin, J. M. Ardell, S. M. Lee, J. J. Corbett, K. D. Meyer, J. R. 2024-04-15 doi:10.1101/2024.04.15.589635 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ The Sodium/Glucose Cotransporter 2 Inhibitor Empagliflozin Inhibits Long QT 3 Late Sodium Currents in a Mutation Specific Manner ]]> https://biorxiv.org/content/10.1101/2024.04.15.589662v1?rss=1 Lunsonga, L. Fatehi, M. Long, W. Barr, A. Gruber, B. E. Chattopadhyay, A. Barakat, K. Edwards, A. G. Light, P. E. 2024-04-22 doi:10.1101/2024.04.15.589662 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes ]]> https://biorxiv.org/content/10.1101/2024.04.16.589618v1?rss=1 50 kilobases in 258k individuals from 6 general population cohorts with assessments of general cognitive abilities. We performed a CNV-GWAS and functional burden analyses, which tested 6502 gene-sets defined by tissue and cell-type transcriptomics as well as gene ontology disrupted by all rare coding CNVs. CNV-GWAS identified a novel duplication at 2q12.3 associated with higher performance in cognitive ability. Among the 864 gene-sets associated with cognitive ability, only 11% showed significant effects for both deletions and duplication. Accordingly, we systematically observed negative correlations between deletion and duplication effect sizes across all levels of biological observations. We quantified the preferential effects of deletions versus duplication using tagDS, a new normalized metric. Cognitive ability was preferentially affected by cortical, presynaptic, and negative-regulation gene-sets when duplicated. In contrast, preferential effects of deletions were observed for subcortical, post-synaptic, and positive-regulation gene-sets. A large proportion of gene-sets assigned to non-brain organs were associated with cognitive ability due to low tissue specificity genes, which were associated with higher sensitive to haploinsufficiency. Overall, most biological functions associated with cognitive ability are divided into those sensitive to either deletion or duplications. ]]> Huguet, G. Renne, T. Poulain, C. Dubuc, A. Kumar, K. Kazem, S. Engchuan, W. B. Shanta, O. Douard, E. Proulx, C. Jean-Louis, M. Saci, Z. Mollon, J. Schultz, L. M. Knowles, E. E. Cox, S. R. Porteous, D. Davies, G. Redmond, P. Harris, S. E. Schumann, G. Dumas, G. Labbe, A. Pausova, Z. Paus, T. Scherer, S. W. Sebat, J. Almasy, L. Glahn, D. C. Jacquemont, S. 2024-04-17 doi:10.1101/2024.04.16.589618 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors ]]> https://biorxiv.org/content/10.1101/2024.04.16.589761v1?rss=1 Usyk, M. Hayes, R. B. Knight, R. Gonzalez, A. Li, H. Osman, I. Weber, J. S. Ahn, J. 2024-04-20 doi:10.1101/2024.04.16.589761 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Organelle-targeted Laurdans measure heterogeneity in subcellular membranes and their responses to saturated lipid stress ]]> https://biorxiv.org/content/10.1101/2024.04.16.589828v1?rss=1 Wong, A. M. Budin, I. 2024-04-20 doi:10.1101/2024.04.16.589828 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1 ]]> https://biorxiv.org/content/10.1101/2024.04.18.590103v1?rss=1 Dion, W. Tao, Y. Chambers, M. Zhao, S. Arbuckle, R. K. Sun, M. Kubra, S. Nie, Y. Ye, M. Larsen, M. B. Camarco, D. Ickes, E. DuPont, C. Wang, H. Wang, B. Liu, S. Pi, S. Chen, B. B. Chen, Y. Chen, X. Zhu, B. 2024-04-21 doi:10.1101/2024.04.18.590103 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells ]]> https://biorxiv.org/content/10.1101/2024.04.18.590148v1?rss=1 Chang, L. Xie, Y. Taylor, B. Wang, Z. Sun, J. Tan, T. R. Bejar, R. Chen, C. C. Furnari, F. B. Hu, M. Ren, B. 2024-04-22 doi:10.1101/2024.04.18.590148 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Conservation of C4BP-binding Sequence Patterns in Streptococcus pyogenes M and Enn Proteins ]]> https://biorxiv.org/content/10.1101/2024.04.22.590534v1?rss=1 Kolesinski, P. McGowan, M. Botteaux, A. Smeesters, P. R. Ghosh, P. 2024-04-22 doi:10.1101/2024.04.22.590534 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ PACS-1 variant protein is aberrantly localized in C. elegans model of PACS1/PACS2 syndromes ]]> https://biorxiv.org/content/10.1101/2024.04.22.590644v1?rss=1 Byrd, D. T. Han, Z. C. Piggott, C. A. Jin, Y. 2024-04-26 doi:10.1101/2024.04.22.590644 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Two modes in the velocity statistics in cautious walks of laboratory rodents ]]> https://biorxiv.org/content/10.1101/2024.04.23.590757v1?rss=1 Midzyanovskaya, I. Rebik, A. Idzhilova, O. Strelkov, V. Komarova, N. Chichigina, O. 2024-04-28 doi:10.1101/2024.04.23.590757 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Synaptic architecture of a memory engram in the mouse hippocampus ]]> https://biorxiv.org/content/10.1101/2024.04.23.590812v1?rss=1 Uytiepo, M. Ellisman, M. Maximov, A. 2024-04-25 doi:10.1101/2024.04.23.590812 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ The attenuation of activity-based anorexia by obese adipose tissue transplant is AgRP neuron-dependent. ]]> https://biorxiv.org/content/10.1101/2024.04.23.590824v1?rss=1 Yoon, D. J. Zhang, J. Zapata, R. Ulivieri, M. Libster, A. M. McMurray, M. S. Osborn, O. Dulawa, S. C. 2024-04-26 doi:10.1101/2024.04.23.590824 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Establishing comprehensive quaternary structural proteomes from genome sequence ]]> https://biorxiv.org/content/10.1101/2024.04.24.590993v1?rss=1 Catoiu, E. A. Mih, N. Lu, M. Palsson, B. O. 2024-04-28 doi:10.1101/2024.04.24.590993 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Membrane curvature catalyzes actin nucleation through nano-scale condensation of N-WASP-FBP17 ]]> https://biorxiv.org/content/10.1101/2024.04.25.591054v1?rss=1 ZHU, K. Guo, X. Chandrasekaran, A. Miao, X. RANGAMANI, P. ZHAO, W. MIAO, Y. 2024-04-25 doi:10.1101/2024.04.25.591054 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening ]]> https://biorxiv.org/content/10.1101/2024.04.25.591187v1?rss=1 Jones, K. F. Demir, O. Wyllie, M. K. Grillo, M. J. Morris, C. Hirakis, S. P. Kardile, R. D. Walters, M. A. Harris, R. S. Amaro, R. E. Harki, D. A. 2024-04-25 doi:10.1101/2024.04.25.591187 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ State of the Interactomes: an evaluation of molecular networks for generating biological insights ]]> https://biorxiv.org/content/10.1101/2024.04.26.587073v1?rss=1 Wright, S. N. Colton, S. Schaffer, L. V. Pillich, R. T. Churas, C. Pratt, D. Ideker, T. 2024-04-29 doi:10.1101/2024.04.26.587073 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Mimicking opioid analgesia in cortical pain circuits ]]> https://biorxiv.org/content/10.1101/2024.04.26.591113v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@d294c0org.highwire.dtl.DTLVardef@123d4f4org.highwire.dtl.DTLVardef@1720deborg.highwire.dtl.DTLVardef@efc632_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> James, J. G. McCall, N. M. Hsu, A. I. Oswell, C. S. Salimando, G. J. Mahmood, M. Wooldridge, L. M. Wachira, M. Jo, A. Sandoval Ortega, R. A. Wojick, J. A. Beattie, K. Farinas, S. A. Chehimi, S. N. Rodrigues, A. Ejoh, L. L. Kimmey, B. A. Lo, E. Azouz, G. Vasquez, J. J. Banghart, M. R. Creasy, K. T. Beier, K. T. Ramakrishnan, C. Crist, R. C. Reiner, B. C. Deisseroth, K. Yttri, E. A. Corder, G. 2024-04-29 doi:10.1101/2024.04.26.591113 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ RBC-GEM: a Knowledge Base for Systems Biology of Human Red Blood Cell Metabolism ]]> https://biorxiv.org/content/10.1101/2024.04.26.591249v1?rss=1 Haiman, Z. B. Palsson, B. D'Alessandro, A. 2024-04-28 doi:10.1101/2024.04.26.591249 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Loop Catalog: a comprehensive HiChIP database of human and mouse samples ]]> https://biorxiv.org/content/10.1101/2024.04.26.591349v1?rss=1 Reyna, J. Fetter, K. Ignacio, R. Ali Marandi, C. C. Rao, N. Jiang, Z. Figueroa, D. S. Bhattacharyya, S. Ay, F. 2024-04-29 doi:10.1101/2024.04.26.591349 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Direct and indirect regulation of β- glucocerebrosidase by the transcription factors USF2 and ONECUT2 ]]> https://biorxiv.org/content/10.1101/2024.04.28.591482v1?rss=1 Aguzzi, A. Yin, J.-A. Vocadlo, D. J. Ging, K. Lukas, F. Zhu, Y. Schlachetzki, J. Gilormini, P.-A. Chen, X. Boeck, D. Serdiuk, T. Marques, A. Pisano, C. Trevisan, C. Sellitto, S. Deen, M. Armani, A. Dhingra, A. Glass, C. Heutink, P. 2024-04-28 doi:10.1101/2024.04.28.591482 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Modulation of calcium signaling on demand to decipher the molecular mechanisms of primary aldosteronism ]]> https://biorxiv.org/content/10.1101/2024.04.29.591306v1?rss=1 Fedlaoui, B. Cosentino, T. Al Sayed, Z. R. Giscos-Douriez, I. Faedda, N. Fayad, M. Hulot, J.-S. Magnus, C. Sternson, S. M. Travers-Allard, S. Baron, S. Fernandes-Rosa, F. L. Zennaro, M.-C. Boulkroun, S. 2024-05-02 doi:10.1101/2024.04.29.591306 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Dynamic mechanisms for membrane skeleton transitions ]]> https://biorxiv.org/content/10.1101/2024.04.29.591779v1?rss=1 Bonilla-Quintana, M. Ghisleni, A. Gauthier, N. C. Rangamani, P. 2024-05-02 doi:10.1101/2024.04.29.591779 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Feeling Senseless Sensations: A Crossmodal study of mismatching tactile and virtual visual experience ]]> https://biorxiv.org/content/10.1101/2024.04.30.591838v1?rss=1 Lehser, C. Hillyard, S. A. Strauss, D. J. 2024-05-01 doi:10.1101/2024.04.30.591838 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation ]]> https://biorxiv.org/content/10.1101/2024.05.01.591800v1?rss=1 Wang, S. Li, W. Wang, L. Tiwari, S. K. Bray, W. Wu, L. Li, N. Hui, H. Clark, A. Zhang, Q. Zhang, L. Carlin, A. Rana, T. M. 2024-05-03 doi:10.1101/2024.05.01.591800 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Uterus and cervix anatomical changes and cervix stiffness evolution throughout pregnancy ]]> https://biorxiv.org/content/10.1101/2024.05.01.592023v1?rss=1 Louwagie, E. M. Russell, S. R. Hairston, J. C. Nottman, C. Nhan-Chang, C.-L. Fuchs, K. Gyamfi-Bannerman, C. Booker, W. Andrikopoulou, M. Friedman, A. Zork, N. Wapner, R. Vink, J. Mourad, M. Feltovich, H. House, M. Myers, K. 2024-05-03 doi:10.1101/2024.05.01.592023 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Tuning ice thickness using the chameleon for high-quality cryoEM data collection ]]> https://biorxiv.org/content/10.1101/2024.05.01.592094v1?rss=1 McGuire, K. L. Cook, B. D. Narehood, S. M. Herzik, M. A. 2024-05-04 doi:10.1101/2024.05.01.592094 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Human striatal progenitor cells that contain inducible safeguards and overexpress BDNF rescue Huntington's disease phenotypes in R6/2 mice ]]> https://biorxiv.org/content/10.1101/2024.05.01.592095v1?rss=1 Simmons, D. A. Selvaraj, S. Chen, T. Cao, G. Sauto Camelo, T. McHugh, T. L. M. Gonzalez, S. Martin, R. Simanauskaite, J. Uchida, N. Porteus, M. Longo, F. M. 2024-05-01 doi:10.1101/2024.05.01.592095 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Subcellular imaging of lipids and sugars using genetically encoded proximity sensors ]]> https://biorxiv.org/content/10.1101/2024.05.01.592120v1?rss=1 Moore, W. M. Brea, R. J. Knittel, C. Wrightsman, E. Hui, B. Loui, J. Ancajas, C. F. Best, M. D. Devaraj, N. K. Budin, I. 2024-05-03 doi:10.1101/2024.05.01.592120 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ The global fish and invertebrate abundance value of mangroves ]]> https://biorxiv.org/content/10.1101/2024.05.02.591889v1?rss=1 zu Ermgassen, P. Worthington, T. A. Gair, J. R. Garnett, E. E. Mukherjee, N. Longley-Wood, K. Nagelkerken, I. Abrantes, K. Aburto-Oropeza, O. Acosta, A. Araujo, A. R. d. R. Baker, R. Barnett, A. Beitl, C. M. Benzeev, R. Brookes, J. Castellanos-Galindo, G. A. Ching Chong, V. Connolly, R. M. Cunha-Lignon, M. Dahdouh-Guebas, F. Diele, K. Dwyer, P. G. Friess, D. A. Grove, T. Hoq, M. E. Huijbers, C. Hutchinson, N. Johnson, A. F. Johnson, R. Knight, J. Krumme, U. Kuguru, B. Lee, S. Y. Lobo, A. S. Lugendo, B. R. Meynecke, J.-O. Nzaka Munga, C. Olds, A. D. Parret 2024-05-05 doi:10.1101/2024.05.02.591889 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Viral overexpression of human alpha-synuclein in mouse substantia nigra dopamine neurons results in hyperdopaminergia but no neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.05.03.592188v1?rss=1 Moreno, S. Limani, F. Ludwig, I. Gilbert, C. Pifl, C. Hnasko, T. S. Steinkellner, T. 2024-05-05 doi:10.1101/2024.05.03.592188 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ IFN-γ activates an immune-like regulatory network in the cardiac vascular endothelium ]]> https://biorxiv.org/content/10.1101/2024.05.03.592380v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@e66966org.highwire.dtl.DTLVardef@111da44org.highwire.dtl.DTLVardef@110a8f5org.highwire.dtl.DTLVardef@c4997b_HPS_FORMAT_FIGEXP M_FIG C_FIG Paired RNA-seq and ATAC-seq was generated for induced pluripotent stem cell derived cardiovascular progenitor cells (CVPCs) treated with interferon-gamma (IFN{gamma}) and matched controls to model the effect of the pro-inflammatory cytokine on human cardiac tissue. Using the RNA-seq, transcriptomic changes were characterized by performing differential gene expression analysis, integrating gene expression data from hundreds of samples of adult cardiac tissues, and using single cell RNA-seq to evaluate cell type-specificity. Using the ATAC-seq, epigenomic changes were characterized by performing differential chromatin accessibility and transcription factor binding analyses, and annotating ATAC-seq peaks with chromatin states from over 800 tissues. Genetic variants in risk loci associated with cardiac diseases were intersected with ATAC-seq peaks to evaluate whether they were in chromatin that is only accessible after IFN{gamma} treatment. The findings demonstrate the utility of using CVPCs to model the effects of cytokines on cardiac tissues and provide the framework for conducting large scale studies to further evaluate GWAS loci that are explained by context-specific regulatory variation. ]]> Arthur, T. D. Joshua, I. N. Nguyen, J. P. D'Antonio-Chronowska, A. iPSCORE Consortium, Frazer, K. A. D'Antonio, M. 2024-05-05 doi:10.1101/2024.05.03.592380 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Proteome profiling identifies a link between the mitochondrial pathways and host-microbial sensor ELMO1 following Salmonella infection. ]]> https://biorxiv.org/content/10.1101/2024.05.03.592405v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@72862org.highwire.dtl.DTLVardef@1ec4a5borg.highwire.dtl.DTLVardef@5b805org.highwire.dtl.DTLVardef@17466d7_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementHost microbial sensing is critical in infection and inflammation. Among these sensors, ELMO1 has emerged as a key regulator, finely tuning innate immune signaling and discriminating between pathogenic and non-pathogenic bacteria through interactions with microbial effectors like SifA of Salmonella. In this study, we employed Multinotch MS3-Tandem Mass Tag (TMT) multiplexed proteomics to determine the proteome alterations mediated by ELMO1 in macrophages following WT and SifA mutant Salmonella infection. Our findings highlight a substantial enrichment of host proteins associated with metabolic pathways and mitochondrial functions. Notably, we validated the mitochondrial fission protein DRP1 that is upregulated in ELMO1-depleted macrophages and in ELMO1 knockout mice intestine after infection. Furthermore, we demonstrated that Salmonella-induced changes in cellular energetics are influenced by the presence of ELMO1. This work shed light on a possible novel link between mitochondrial dynamics and microbial sensing in modulating immune responses. ]]> Achi, S. McGrosso, D. Tocci, S. Ibeawuchi, S.-R. Sayed, I. M. Gonzalez, D. J. Das, S. 2024-05-03 doi:10.1101/2024.05.03.592405 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Liquid-like condensates that bind actin can polymerize and bundle actin filaments ]]> https://biorxiv.org/content/10.1101/2024.05.04.592527v1?rss=1 Walker, C. Graham, K. Torres, A. Wang, L. Lafer, E. M. Rangamani, P. Stachowiak, J. 2024-05-04 doi:10.1101/2024.05.04.592527 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Genetic Inactivation of the beta1 adrenergic receptor prevents Cerebral Cavernous Malformations in zebrafish ]]> https://biorxiv.org/content/10.1101/2024.05.05.592554v1?rss=1 Li, W. McCurdy, S. Lopez-Ramirez, M. A. Lee, H.-S. 2024-05-05 doi:10.1101/2024.05.05.592554 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Persistent effects of repeated adolescent and adult heroin vapor inhalation in female Wistar rats ]]> https://biorxiv.org/content/10.1101/2024.05.06.592492v1?rss=1 Gutierrez, A. Taffe, M. A. 2024-05-10 doi:10.1101/2024.05.06.592492 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes ]]> https://biorxiv.org/content/10.1101/2024.05.06.592768v1?rss=1 Luebeck, J. Huang, E. Kim, F. Liefeld, T. Dameracharla, B. Ahuja, R. Schreyer, D. Prasad, G. Adamaszek, M. Kenkre, R. Agashe, T. Torvi, D. Tabor, T. Giurgiu, M. Kim, S. Kim, H. Bailey, P. Verhaak, R. G. W. Deshpande, V. B. Reich, M. M. Mischel, P. S. Mesirov, J. Bafna, V. 2024-05-10 doi:10.1101/2024.05.06.592768 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Network approach reveals preferential T-cell and macrophage association with α-linked β-cells in early stage of insulitis in NOD mice. ]]> https://biorxiv.org/content/10.1101/2024.05.06.592831v1?rss=1 Balasenthilkumaran, N. V. . Whitesell, J. C. Pyle, L. Friedman, R. Kravets, V. 2024-05-10 doi:10.1101/2024.05.06.592831 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Dopey-dependent regulation of extracellular vesicles maintains neuronal morphology ]]> https://biorxiv.org/content/10.1101/2024.05.07.591898v1?rss=1 Park, S. Noblett, N. Pitts, L. Colavita, A. Wehman, A. M. Jin, Y. Chisholm, A. D. 2024-05-08 doi:10.1101/2024.05.07.591898 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Extensive folding variability between homologous chromosomes in mammalian cells ]]> https://biorxiv.org/content/10.1101/2024.05.08.591087v1?rss=1 Irastorza-Azcarate, I. Kukalev, A. Kempfer, R. Thieme, C. J. Mastrobuoni, G. Markowski, J. Loof, G. Sparks, T. M. Brookes, E. Natarajan, K. N. Sauer, S. Fisher, A. G. Nicodemi, M. Ren, B. Schwarz, R. F. Kempa, S. Pombo, A. 2024-05-10 doi:10.1101/2024.05.08.591087 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Evolutionary and functional analyses reveal conserved and non-conserved functions of vertebrate RIP kinases ]]> https://biorxiv.org/content/10.1101/2024.05.09.593370v1?rss=1 Fay, E. J. Isterabadi, K. Rezanka, C. M. Le, J. Daugherty, M. D. 2024-05-13 doi:10.1101/2024.05.09.593370 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Asesino: a nucleus-forming phage that lacks PhuZ ]]> https://biorxiv.org/content/10.1101/2024.05.10.593592v1?rss=1 Prichard, A. Sy, A. Meyer, J. R. Villa, E. Pogliano, J. 2024-05-11 doi:10.1101/2024.05.10.593592 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70 ]]> https://biorxiv.org/content/10.1101/2024.05.10.593630v1?rss=1 Morizono, M. A. McGuire, K. L. Birouty, N. I. Herzik, M. A. 2024-05-13 doi:10.1101/2024.05.10.593630 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Active vision in freely moving marmosets using head-mounted eye tracking ]]> https://biorxiv.org/content/10.1101/2024.05.11.593707v1?rss=1 Singh, V. P. Li, J. Mitchell, J. Miller, C. 2024-05-12 doi:10.1101/2024.05.11.593707 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Y chromosome linked UTY modulates sex differences in valvular fibroblast methylation in response to nanoscale extracellular matrix cues ]]> https://biorxiv.org/content/10.1101/2024.05.13.593760v1?rss=1 Gorashi, R. M. Baddour, T. Chittle, S. J. Velez, N. E. F. Wenning, M. A. Anseth, K. S. Mestroni, L. Pena, B. Guo, P. Aguado, B. A. 2024-05-14 doi:10.1101/2024.05.13.593760 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Successful Cardiac Resynchronization Therapy Reduces Negative Septal Work in Patient-Specific Models of Dyssynchronous Heart Failure ]]> https://biorxiv.org/content/10.1101/2024.05.13.593804v1?rss=1 Craine, A. Krishnamurthy, A. Villongco, C. T. Vincent, K. Krummen, D. E. Narayan, S. M. Kerckhoffs, R. C. P. Omens, J. H. Contijoch, F. McCulloch, A. D. 2024-05-14 doi:10.1101/2024.05.13.593804 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Genetic and environmental contributions to eigengene expression ]]> https://biorxiv.org/content/10.1101/2024.05.13.593914v1?rss=1 Gillespie, N. A. Bell, T. R. Hearn, G. C. Hess, J. L. Tsuang, M. T. Lyons, M. J. Franz, C. E. Kremen, W. S. Glatt, S. J. 2024-05-15 doi:10.1101/2024.05.13.593914 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Gill ionocyte remodeling mediates blood pH regulation in rockfish (Sebastes diploproa) exposed to environmentally relevant hypercapnia ]]> https://biorxiv.org/content/10.1101/2024.05.13.593928v1?rss=1 Kwan, G. T. Clifford, A. M. Prime, K. J. Harter, T. S. Tresguerres, M. 2024-05-15 doi:10.1101/2024.05.13.593928 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Plastic microfibers found in high numbers around Kantamanto, the world's largest secondhand textile market in Accra, Ghana ]]> https://biorxiv.org/content/10.1101/2024.05.13.593950v1?rss=1 20x to >100x greater, respectively, than those reported from other metropolises around the world. A comparison of concentrations from water in the adjacent Korle Lagoon was similarly striking, with up to 45x more microfibers, and up to 200x more microplastics than what has previously been reported for lagoon waters worldwide. Beyond the microscale, the issue of whole garments as waste was also demonstrated, with a strong similarity found between the global brand garment tags from fashion items discarded in the market and those that were washed up on nearby beaches, highlighting the need for more holistic regulatory frameworks to address textile waste. ]]> Deheyn, D. D. Ayesu, J. The Or Foundation, Skinner, B. 2024-05-15 doi:10.1101/2024.05.13.593950 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ plantMASST - Community-driven chemotaxonomic digitization of plants ]]> https://biorxiv.org/content/10.1101/2024.05.13.593988v1?rss=1 Gomes, P. W. P. Mannochio-Russo, H. Schmid, R. Zuffa, S. Damiani, T. Quiros-Guerrero, L.-M. Caraballo-Rodriguez, A. M. Zhao, H. N. Yang, H. Xing, S. Charron-Lamoureux, V. Chigumba, D. N. Sedio, B. E. Myers, J. A. Allard, P.-M. Harwood, T. V. Tamayo-Castillo, G. Kang, K. B. Defossez, E. Koolen, H. H. F. da Silva, M. N. e Silva, C. Y. Y. Rasmann, S. Walker, T. W. N. Glauser, G. Chaves-Fallas, J. M. David, B. Kim, H. Lee, K. H. Kim, M. J. Choi, W. J. Keum, Y.-S. de Lima, E. J. S. P. de Medeiros, L. S. Bataglion, G. A. Costa, E. V. da Silva, F. M. A. Carvalho, 2024-05-15 doi:10.1101/2024.05.13.593988 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Mitochondrial dysfunction heightens the integrated stress response to drive ALS pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.05.13.594000v1?rss=1 Landry, C. A. Costanzo, J. Neto, M. M. Zatz, M. Schaffer, A. E. Hatzoglou, M. Muotri, A. R. Miranda, H. C. 2024-05-14 doi:10.1101/2024.05.13.594000 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics ]]> https://biorxiv.org/content/10.1101/2024.05.14.594051v1?rss=1 Munro, D. Ehsan, N. Esmaeili-Fard, S. M. Gusev, A. Palmer, A. A. Mohammadi, P. 2024-05-15 doi:10.1101/2024.05.14.594051 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Protein structure, a genetic encoding for glycosylation ]]> https://biorxiv.org/content/10.1101/2024.05.15.594261v1?rss=1 Kellman, B. Sandoval, D. Zaytseva, O. Brock, K. Baboo, S. Nachmanson, D. Irvine, E. Armingol, E. Mih, N. Zhang, Y. Jeffris, M. Bartels, P. Nguyen, T. Tam, A. Gasman, S. Ilan, S. Shamie, I. Diedrich, J. Wang, X. van Woudenbergh, E. Altman, M. Aylward, A. Bao, B. Castro, A. Sorrentino, J. Chiang, A. Campbell, M. Bartsch, Y. Aguilar-Calvo, P. Sigurdson, C. Alter, G. Lauc, G. Yates, Y. Marks, D. Lisacek, F. Lewis, N. 2024-05-15 doi:10.1101/2024.05.15.594261 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Cathepsin X is a conserved cell death protein involved in algal response to environmental stress ]]> https://biorxiv.org/content/10.1101/2024.05.15.594278v1?rss=1 Mizrachi, A. Sadeh, M. Ben-Dor, S. Dym, O. Ku, C. Feldmesser, E. Zarfin, A. Brunson, J. K. Allen, A. E. Jinkerson, R. E. Schatz, D. Vardi, A. 2024-05-15 doi:10.1101/2024.05.15.594278 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Intrinsic skeletal muscle function and contraction-stimulated glucose uptake do not vary by time-of-day in mice ]]> https://biorxiv.org/content/10.1101/2024.05.15.594323v1?rss=1 Fitzgerald, L. S. Bremner, S. N. Ward, S. R. Cho, Y. Schenk, S. 2024-05-18 doi:10.1101/2024.05.15.594323 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network ]]> https://biorxiv.org/content/10.1101/2024.05.15.594334v1?rss=1 Kellman, B. Mariethoz, J. Zhang, Y. Shaul, S. Jeffris, M. Sandoval, D. Jeffris, M. Armingol, E. Bao, B. Lisacek, F. Bojar, D. Lewis, N. 2024-05-15 doi:10.1101/2024.05.15.594334 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations ]]> https://biorxiv.org/content/10.1101/2024.05.15.594372v1?rss=1 Ghandian, S. Albarghouthi, L. Nava, K. Sharma, S. R. R. Minaud, L. Beckett, L. Saito, N. DeCarli, C. Rissman, R. A. Teich, A. F. Jin, L.-W. Dugger, B. N. Keiser, M. J. 2024-05-17 doi:10.1101/2024.05.15.594372 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ The Endoplasmic Reticulum as an Active Liquid Network ]]> https://biorxiv.org/content/10.1101/2024.05.15.594381v1?rss=1 Scott, Z. C. Steen, S. B. Huber, G. Westrate, L. M. Koslover, E. F. 2024-05-16 doi:10.1101/2024.05.15.594381 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ The dithiocarbamate pesticides maneb and mancozeb disturb the metabolism of lipids and xenobiotics in an in vitro model of metabolic dysfunction-associated steatotic liver disease ]]> https://biorxiv.org/content/10.1101/2024.05.16.594496v1?rss=1 Petitjean, K. Dicara, G. Bristeau, S. Coppens-Exandier, H. Amalric, L. Baran, N. Savary, C. C. Corlu, A. Loyer, P. Fromenty, B. 2024-05-18 doi:10.1101/2024.05.16.594496 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A ]]> https://biorxiv.org/content/10.1101/2024.05.16.594558v1?rss=1 Jain, S. Trinidad, M. Nguyen, T. B. Jones, K. Diaz Neto, S. Ge, F. Glagovsky, A. Jones, C. Moran, G. Wang, B. Rahimi, K. Zeynep Calici, S. Cedillo, L. R. Berardelli, S. Ozden, B. Chen, K. Katsonis, P. Williams, A. Lichtarge, O. Rana, S. Pradhan, S. Srinivasan, R. Sajeed, R. Joshi, D. Faraggi, E. Jernigan, R. Kloczkowski, A. Xu, J. Song, Z. Ozkan, S. Padilla, N. de la Cruz, X. Acuna-Hidalgo, R. Grafmuller, A. Jimenez Barron, L. T. Manfredi, M. Savojardo, C. Babbi, G. Martelli, P. L. Casadio, R. Sun, Y. Zhu, S. Shen, Y. Pucci, F. Rooman, M. Cia, G. R 2024-05-19 doi:10.1101/2024.05.16.594558 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ iLipidome: enhancing statistical power and interpretability using hidden biosynthetic interdependencies in the lipidome ]]> https://biorxiv.org/content/10.1101/2024.05.16.594607v1?rss=1 Lin, W.-J. CHIANG, A. W. T. Zhou, E. H. Liang, C. Liu, C.-H. Ma, W.-L. Cheng, W.-C. Lewis, N. E. 2024-05-21 doi:10.1101/2024.05.16.594607 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription ]]> https://biorxiv.org/content/10.1101/2024.05.17.594600v1?rss=1 Wagner, T. Priyanka, P. Micheletti, R. Friedman, M. J. Nair, S. J. Gamliel, A. Taylor, H. Song, X. Cho, M. Oh, S. Li, W. Han, J. Ohgi, K. A. Abrass, M. D'Antonio-Chronowska, A. D'Antonio, M. Hazuda, H. Duggirala, R. Blangero, J. Ding, S. Guzmann, C. Frazer, K. Aggarwal, A. K. Zemljic-Harpf, A. E. Rosenfeld, M. G. Suh, Y. 2024-05-19 doi:10.1101/2024.05.17.594600 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ Disruptors of sestrin-MAPK interactions rejuvenate T cells and expand TCR specificity ]]> https://biorxiv.org/content/10.1101/2024.05.17.594698v1?rss=1 Lanna, A. D'Ambra, C. Rinaldi, F. Chocarro De Erauso, L. Delpero, M. Capitani, M. Karin, M. 2024-05-21 doi:10.1101/2024.05.17.594698 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC ]]> https://biorxiv.org/content/10.1101/2024.05.19.594824v1?rss=1 Tran, N. L. Jiang, J. Ma, M. Gadbois, G. E. Gulay, K. C. M. Verano, A. Zhou, H. Huang, C.-T. Scott, D. A. Bang, A. G. Tiriac, H. Lowy, A. M. Wang, E. S. Ferguson, F. M. 2024-05-21 doi:10.1101/2024.05.19.594824 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Freeform robotic optical coherence tomography beyond the optical field-of-view limit ]]> https://biorxiv.org/content/10.1101/2024.05.21.595073v1?rss=1 Fang, R. Zhang, P. Zhang, T. Kim, D. Sun, E. Kuranov, R. Kweon, J. Huang, A. Zhang, H. F. 2024-05-23 doi:10.1101/2024.05.21.595073 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis ]]> https://biorxiv.org/content/10.1101/2024.05.21.595139v1?rss=1 Lieu, D. J. Crowder, M. K. Kryza, J. R. Tamilselvam, B. Kaminski, P. J. Kim, I.-J. Li, Y. Jeong, E. Enkhbaatar, M. Chen, H. Son, S. B. Mok, H. Bradley, K. A. Phillips, H. Blanke, S. R. 2024-05-23 doi:10.1101/2024.05.21.595139 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Antibodies targeting Crimean-Congo hemorrhagic fever virus GP38 limit vascular leak and viral spread ]]> https://biorxiv.org/content/10.1101/2024.05.23.595578v1?rss=1 Pahmeier, F. Monticelli, S. R. Feng, X. Hjorth, C. K. Wang, A. Kuehne, A. I. Bakken, R. R. Batchelor, T. G. Lee, S. E. Middlecamp, M. Stuart, L. Abelson, D. M. McLellan, J. S. Biering, S. B. Herbert, A. S. Chandran, K. Harris, E. 2024-05-23 doi:10.1101/2024.05.23.595578 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Spatial Modeling Algorithms for Reactions and Transport (SMART) in Biological Cells ]]> https://biorxiv.org/content/10.1101/2024.05.23.595604v1?rss=1 Francis, E. A. Laughlin, J. G. Dokken, J. S. Finsberg, H. N. T. Lee, C. T. Rognes, M. E. Rangamani, P. 2024-05-25 doi:10.1101/2024.05.23.595604 Cold Spring Harbor Laboratory Press 2024-05-25 <![CDATA[ Quantifying acyl-chain diversity in isobaric compound lipids containing monomethyl branched-chain fatty acids ]]> https://biorxiv.org/content/10.1101/2024.05.28.596332v1?rss=1 Green, C. R. Kolar, M. J. McGregor, G. H. Nelson, A. T. Wallace, M. Metallo, C. 2024-05-29 doi:10.1101/2024.05.28.596332 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Predicting Primary Graft Dysfunction in Lung Transplantation: Machine Learning-Guided Biomarker Discovery ]]> https://biorxiv.org/content/10.1101/2024.05.24.595368v1?rss=1 Nord, D. Brunson, J. C. Langerude, L. Moussa, H. Gill, B. Machuca, T. Rackauskas, M. Sharma, A. K. Lin, C. Emtiazjoo, A. Atkinson, C. 2024-05-30 doi:10.1101/2024.05.24.595368 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ LiveLattice: Real-time visualization of tilted light-sheet microscopy data using a memory-efficient transformation algorithm ]]> https://biorxiv.org/content/10.1101/2024.05.28.596280v1?rss=1 Wang, Z. Hakozaki, H. McMahon, G. Medina-Carbonero, M. Schoeneberg, J. 2024-05-30 doi:10.1101/2024.05.28.596280 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Cardiolipin remodeling maintains the inner mitochondrial membrane in cells with saturated lipidomes ]]> https://biorxiv.org/content/10.1101/2024.05.29.596368v1?rss=1 Venkatraman, K. Budin, I. 2024-05-30 doi:10.1101/2024.05.29.596368 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES ]]> https://biorxiv.org/content/10.1101/2024.05.27.596098v1?rss=1 Gupta, A. Mirarab, S. Turakhia, Y. 2024-06-01 doi:10.1101/2024.05.27.596098 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ D-Serine inhibits non-ionotropic NMDA receptor signaling ]]> https://biorxiv.org/content/10.1101/2024.05.29.596266v1?rss=1 Barragan, E. V. Anisimova, M. Vijayakumar, V. Coblentz, A. C. Park, D. K. Salaka, R. J. Nisan, A. F. K. Petshow, S. Dore, K. Zito, K. Gray, J. A. 2024-06-01 doi:10.1101/2024.05.29.596266 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ The use of vocal coordination in male African elephant group departures: evidence of active leadership and consensus ]]> https://biorxiv.org/content/10.1101/2024.05.31.596833v1?rss=1 O'Connell-Rodwell, C. E. Berezin, J. L. Pignatelli, A. Rodwell, T. C. 2024-06-01 doi:10.1101/2024.05.31.596833 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Transportome remodeling of a symbiotic microalga inside a planktonic host ]]> https://biorxiv.org/content/10.1101/2024.06.01.596945v1?rss=1 Juery, C. Auladell, A. Fussy, Z. Chevalier, F. Yee, D. Pelletier, E. Corre, E. Allen, A. E. Richter, D. Decelle, J. 2024-06-01 doi:10.1101/2024.06.01.596945 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ A synthetic skin microbial community (SkinCom) enables reproducible investigations of the human skin microbiome ]]> https://biorxiv.org/content/10.1101/2024.06.01.596969v1?rss=1 Lekbua, A. Thiruppathy, D. Coker, J. Weng, Y. Askarian, F. Kousha, A. Marotz, C. Hauw, A. Nizet, V. Zengler, K. 2024-06-01 doi:10.1101/2024.06.01.596969 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Data-driven modeling of E. coli transcriptional regulation ]]> https://biorxiv.org/content/10.1101/2024.05.30.596718v1?rss=1 Dalldorf, C. Hughes, G. Li, G. Palsson, B. Zielinski, D. C. 2024-06-03 doi:10.1101/2024.05.30.596718 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Extracellular Respiration is a Latent Energy Metabolism in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2024.05.30.596743v1?rss=1 Kundu, B. B. Krishnan, J. Szubin, R. Patel, A. Palsson, B. O. Zielinski, D. C. Ajo-Franklin, C. M. 2024-06-03 doi:10.1101/2024.05.30.596743 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions ]]> https://biorxiv.org/content/10.1101/2024.06.01.596973v1?rss=1 Volz, S. Malone, J. R. Guseman, A. J. Gronenborn, A. M. Marqusee, S. 2024-06-03 doi:10.1101/2024.06.01.596973 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Frontotemporal dementia-like disease progression elicited by seeded aggregation and spread of FUS ]]> https://biorxiv.org/content/10.1101/2024.06.03.593639v1?rss=1 Vazquez-Sanchez, S. Tilkin, B. Gasset-Rosa, F. Zhang, S. Piol, D. McAlonis-Downes, M. Artates, J. Govea-Perez, N. Verresen, Y. Guo, L. Cleveland, D. W. Shorter, J. Da Cruz, S. 2024-06-03 doi:10.1101/2024.06.03.593639 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Profiling ranked list enrichment scoring in sparse data elucidates algorithmic tradeoffs ]]> https://biorxiv.org/content/10.1101/2024.06.03.597180v1?rss=1 Wenzel, A. T. Jun, J. Tamayo, P. Mesirov, J. P. 2024-06-04 doi:10.1101/2024.06.03.597180 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ An Infusible Extracellular Matrix Biomaterial Improves Survival in a Model of Severe Systemic Inflammation ]]> https://biorxiv.org/content/10.1101/2024.06.05.597616v1?rss=1 Karkanitsa, M. L. Wang, R. Lyons, A. C. Mesfin, J. M. Chen, A. Spang, M. T. Quintero, F. Sadtler, K. Christman, K. L. 2024-06-06 doi:10.1101/2024.06.05.597616 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Spectrin condensates provide a nidus for assembling the periodic axonal structure ]]> https://biorxiv.org/content/10.1101/2024.06.05.597638v1?rss=1 Boyer, N. P. Sharma, R. Wiesner, T. Delamare, A. Pelletier, F. Leterrier, C. Roy, S. 2024-06-06 doi:10.1101/2024.06.05.597638 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors ]]> https://biorxiv.org/content/10.1101/2024.06.06.597667v1?rss=1 Wu, P. Liu, Z. Zheng, L. Zhou, Z. Wang, W. Lu, C. 2024-06-08 doi:10.1101/2024.06.06.597667 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Disruption of Core Stress Granule Protein Aggregates Promotes CNS Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2024.06.07.597743v1?rss=1 Sahoo, P. K. Hanovice, N. Ward, P. Agrawal, M. A. Smith, T. P. SiMa, H. Dulin, J. N. Vaughn, L. S. Tuszynski, M. Welshhans, K. Benowitz, L. English, A. Houle, J. D. Twiss, J. L. 2024-06-08 doi:10.1101/2024.06.07.597743 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Optimization of systemic AAV9 gene therapy in Niemann-Pick disease type C1 mice ]]> https://biorxiv.org/content/10.1101/2024.06.07.597901v1?rss=1 Mylvara, A. V. Gibson, A. L. Gu, T. Davidson, C. D. Incao, A. A. Melnyk, K. Pierre-Jacques, D. Cologna, S. M. Venditti, C. P. Porter, F. Pavan, W. J. 2024-06-08 doi:10.1101/2024.06.07.597901 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Ventral tegmental area interneurons revisited: GABA and glutamate projection neurons make local synapses ]]> https://biorxiv.org/content/10.1101/2024.06.07.597996v1?rss=1 Oriol, L. Chao, M. Kollman, G. J. Dowlat, D. S. Singhal, S. M. Steinkellner, T. Hnasko, T. S. 2024-06-08 doi:10.1101/2024.06.07.597996 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ The Pangenome of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2024.06.07.598014v1?rss=1 Chauhan, S. M. Ardalani, O. Hyun, J. C. Phaneuf, P. V. Monk, J. M. Palsson, B. O. 2024-06-08 doi:10.1101/2024.06.07.598014 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Long term rescue of Alzheimer deficits in vivo by one-time gene-editing of App C-terminus. ]]> https://biorxiv.org/content/10.1101/2024.06.08.598099v1?rss=1 Aulston, B. Gimse, K. Bazick, H. O. Kramar, E. A. Pizzo, D. P. Parra-Rivas, L. A. Sun, J. Branes-Guerrero, K. Cheka, N. Bagheri, N. Satyadev, N. Carlson-Stevermer, J. Saito, T. Saido, T. C. Audhya, A. Wood, M. A. Zylka, M. J. Saha, K. Roy, S. 2024-06-09 doi:10.1101/2024.06.08.598099 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares ]]> https://biorxiv.org/content/10.1101/2024.06.07.597819v1?rss=1 Mattessich, M. Reyna, J. Aron, E. Ay, F. Kilmer, M. Kleinstein, S. H. Konstorum, A. 2024-06-10 doi:10.1101/2024.06.07.597819 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Dopamine-driven Increase in IL-1β in Myeloid Cells is Mediated by Differential Dopamine Receptor Expression and Exacerbated by HIV ]]> https://biorxiv.org/content/10.1101/2024.06.09.598137v1?rss=1 Matt, S. Nolan, R. Manikandan, S. Agarwal, Y. Channer, B. Oteju, O. Daniali, M. Canagarajah, J. A. LuPone, T. Mompho, K. Runner, K. Nickoloff-Bybel, E. Li, B. Niu, M. Schlachetzki, J. Fox, H. Gaskill, P. J. 2024-06-10 doi:10.1101/2024.06.09.598137 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Chromogranin A Deficiency Attenuates Tauopathy by Altering Epinephrine Alpha-Adrenergic Receptor Signaling ]]> https://biorxiv.org/content/10.1101/2024.06.11.598548v1?rss=1 Jati, S. Munoz-Mayorga, D. Shahabi, S. Tang, K. Tao, Y. Dickson, D. W. Litvan, I. Ghosh, G. W. Mahata, S. K. Chen, X. 2024-06-12 doi:10.1101/2024.06.11.598548 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Missing data approaches for longitudinal neuroimaging research: Examples from the Adolescent Brain and Cognitive Development (ABCD) Study ]]> https://biorxiv.org/content/10.1101/2024.06.12.598732v1?rss=1 Li, L. Bayat, M. Hayes, T. Thompson, W. K. Gard, A. M. S. Dick, A. S. 2024-06-13 doi:10.1101/2024.06.12.598732 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts ]]> https://biorxiv.org/content/10.1101/2024.06.12.598766v1?rss=1 I snRNAs consistently increase adenosine-to-inosine editing efficiency for genes with higher exon counts, perturb substantially fewer genes in the transcriptome, and localize more persistently to the nucleus where ADAR is expressed. A>I snRNAs can also edit pre-mRNA 3' splice sites to promote splicing changes. Finally, snRNA fusions to H/ACA box snoRNAs (U>{Psi} snRNAs) increase targeted RNA pseudouridylation efficiency. Altogether, our results advance the protein-free RNA base conversion toolbox and enhance minimally invasive RNA targeting technologies to treat genetic diseases. ]]> Smargon, A. A. Pant, D. Glynne, S. Gomberg, T. A. Yeo, E. W. 2024-06-13 doi:10.1101/2024.06.12.598766 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes ]]> https://biorxiv.org/content/10.1101/2024.06.13.597128v1?rss=1 Moakley, D. F. Campbell, M. Anglada-Girotto, M. Feng, H. Califano, A. Au, E. Zhang, C. 2024-06-16 doi:10.1101/2024.06.13.597128 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ PSSR2: a user-friendly Python package for democratizing deep learning-based point-scanning super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2024.06.16.599221v1?rss=1 Stites, H. C. Manor, U. 2024-06-16 doi:10.1101/2024.06.16.599221 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Weighted variance component test for the integrative multi-omics analysis of microbiome data ]]> https://biorxiv.org/content/10.1101/2024.06.14.599073v1?rss=1 Zhang, A. Ling, W. Little, A. Williams-Nguyen, J. S. Moon, J.-Y. Burk, R. D. Knight, R. Wang, D. D. Qi, Q. Kaplan, R. Zhao, N. Wu, M. 2024-06-17 doi:10.1101/2024.06.14.599073 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Increasing certainty in systems biology models using Bayesian multimodel inference ]]> https://biorxiv.org/content/10.1101/2024.06.16.599231v1?rss=1 Linden-Santangeli, N. Zhang, J. Kramer, B. Rangamani, P. 2024-06-17 doi:10.1101/2024.06.16.599231 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures ]]> https://biorxiv.org/content/10.1101/2024.06.16.599236v1?rss=1 Sun, Y. Lucas, M. V. Cline, C. C. Menezes, M. C. Kim, S. Badami, F. S. Narayan, M. Wu, W. Daskalakis, Z. J. Etkin, A. Saggar, M. 2024-06-17 doi:10.1101/2024.06.16.599236 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Posterior parietal cortex maps progress along routes sharing the same meta-structure ]]> https://biorxiv.org/content/10.1101/2024.06.17.599318v1?rss=1 Johnson, A. B. Nitz, D. A. 2024-06-17 doi:10.1101/2024.06.17.599318 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles ]]> https://biorxiv.org/content/10.1101/2024.06.17.599381v1?rss=1 Kassim, Y. M. Rosenberg, D. B. Renero, A. Das, S. Rahman, S. Al Shammaa, I. Salim, S. Huang, Z. Huang, K. Ninoyu, Y. Friedman, R. A. Indzhykulian, A. A. Manor, U. 2024-06-17 doi:10.1101/2024.06.17.599381 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals ]]> https://biorxiv.org/content/10.1101/2024.06.19.599758v1?rss=1 Oles, R. E. Terrazas, M. C. Loomis, L. R. Neal, M. J. Paulchakrabarti, M. Zuffa, S. Hsu, C.-Y. Vasquez Ayala, A. Lee, M. H. Tribelhorn, C. Belda-Ferre, P. Bryant, M. Zemlin, J. Young, J. Dulai, P. Sandborn, W. J. Sivagnanam, M. Raffatellu, M. Pride, D. Dorrestein, P. C. Zengler, K. Choudhury, B. Knight, R. Chu, H. 2024-06-19 doi:10.1101/2024.06.19.599758 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Cell of origin alters myeloid-mediated immunosuppression in lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.06.19.599651v1?rss=1 Yang, M. Shulkin, N. Gonzalez, E. Castillo, J. Yan, C. Zhang, K. Arvanitis, L. Borok, Z. Wallace, W. D. Raz, D. Torres, E. T. R. Marconett, C. N. 2024-06-23 doi:10.1101/2024.06.19.599651 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike ]]> https://biorxiv.org/content/10.1101/2024.06.24.600393v1?rss=1 Tse, A. L. Acreman, C. M. Ricardo-Lax, I. Berrigan, J. Lasso, G. Balogun, T. Kearns, F. L. Casalino, L. McClain, G. L. Chandran, A. M. Lemeunier, C. Amaro, R. E. Rice, C. M. Jangra, R. K. McLellan, J. S. Chandran, K. Miller, E. H. 2024-06-27 doi:10.1101/2024.06.24.600393 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Advancing coral micropropagation for coral restoration and reef engineering ]]> https://biorxiv.org/content/10.1101/2024.06.25.600690v1?rss=1 Walton, E. Badder, L. Galindo-Martinez, C. Berry, D. Tresguerres, M. Wangpraseurt, D. 2024-06-29 doi:10.1101/2024.06.25.600690 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ A large-scale optogenetic neurophysiology platform for improving accessibility in NHP behavioral experiments ]]> https://biorxiv.org/content/10.1101/2024.06.25.600719v1?rss=1 View larger version (67K): org.highwire.dtl.DTLVardef@179542eorg.highwire.dtl.DTLVardef@85ab3aorg.highwire.dtl.DTLVardef@1ac8deeorg.highwire.dtl.DTLVardef@19a0831_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Griggs, D. J. Bloch, J. Stanis, N. Zhou, J. Fisher, S. Jahanian, H. Yazdan-Shahmorad, A. 2024-06-29 doi:10.1101/2024.06.25.600719 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis ]]> https://biorxiv.org/content/10.1101/2024.06.26.600548v1?rss=1 Garg, B. Khan, S. Sheikh Babu, D. Mose, E. Gulay, K. Sharma, S. Sood, D. Wenzel, A. T. Martsinkovskiy, A. Patel, J. Jaquish, D. Lambies, G. D Ippolito, A. Austgen, K. Johnston, B. Orlando, D. Jang, G. H. Gallinger, S. Goodfellow, E. Brodt, P. Commisso, C. Tamayo, P. Mesirov, J. P. Tiriac, H. Lowy, A. M. 2024-06-30 doi:10.1101/2024.06.26.600548 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Endosomal actin branching, fission and receptor recycling require FCHSD2 recruitment by MICAL-L1 ]]> https://biorxiv.org/content/10.1101/2024.06.27.601011v1?rss=1 Frisby, D. Murakonda, A. B. Ashraf, B. Dhawan, K. Almeida-Souza, L. Naslavsky, N. Caplan, S. 2024-06-30 doi:10.1101/2024.06.27.601011 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Break-induced replication is activated to repair R-loop-associated double-strand breaks in SETX-deficient cells ]]> https://biorxiv.org/content/10.1101/2024.06.29.601361v1?rss=1 Wu, T. Li, Y. Shi, L. Z. Wu, X. 2024-06-30 doi:10.1101/2024.06.29.601361 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Aspartic proteases are abundant and active in acidified wound fluid ]]> https://biorxiv.org/content/10.1101/2024.06.30.601389v1?rss=1 Barbosa da Silva, E. Crane, M. Liu, L. Gelsinger, D. J. Jordon, A. McKinney, R. L. Eberson, C. P. Jamieson, A. O'Donoghue, A. J. 2024-06-30 doi:10.1101/2024.06.30.601389 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Phosphorylation-induced flexibility of proto-oncogenic Bcl3 regulates transcriptional activation by NF-κB p52 homodimer ]]> https://biorxiv.org/content/10.1101/2024.06.30.601400v1?rss=1 Pan, W. Biswas, T. Shahabi, S. Suryajaya, W. Vasquez, A. Du, Q. Ghosh, G. Wang, V. Y.-F. 2024-06-30 doi:10.1101/2024.06.30.601400 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Membrane Curvature Promotes ER-PM Contact Formation via Junctophilin-EHD Interactions ]]> https://biorxiv.org/content/10.1101/2024.06.29.601287v1?rss=1 Yang, Y. Valencia, L. A. Lu, C.-H. Nakamoto, M. L. Tsai, C.-T. Liu, C. Yang, H. Zhang, W. Jahed, Z. Lee, W.-R. Santoro, F. Liou, J. Wu, J. C. Cui, B. 2024-07-01 doi:10.1101/2024.06.29.601287 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ Density-dependent network structuring within and across wild animal systems ]]> https://biorxiv.org/content/10.1101/2024.06.28.601262v1?rss=1 58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals, and insects. 80% of systems exhibited strong positive relationships between local density and network centrality. However, >80% of relationships were nonlinear and 75% became shallower at higher values, signifying that demographic and behavioural processes counteract densitys effects, thereby producing saturating trends [11-15]. Densitys effect was much stronger and less saturating for spatial than social networks, such that individuals become disproportionately spatially connected rather than socially at higher densities. Consequently, ecological processes that depend on spatial connections (e.g. indirect pathogen transmission, resource competition, and territory formation) are likely more density-dependent than those involving social interactions (e.g. direct pathogen transmission, aggression, and social learning). These findings reveal fundamental ecological rules governing societal structuring, with widespread implications. Identifying scaling rules based on processes that generalise across systems, such as these patterns of density dependence, might provide the ability to predict network structures in novel systems. ]]> Albery, G. F. Becker, D. J. Firth, J. A. Silk, M. Sweeny, A. R. Wal, E. V. Webber, Q. Allen, B. Babayan, S. A. Barve, S. Begon, M. Birtles, R. J. Block, T. A. Block, B. A. Bradley, J. E. Budischak, S. Buesching, C. Burthe, S. J. Carlisle, A. B. Caselle, J. E. Cattuto, C. Chaine, A. S. Chapple, T. Cheney, B. J. Clutton-Brock, T. Collier, M. Curnick, D. J. Delahay, R. J. Farine, D. R. Fenton, A. Ferretti, F. Fielding, H. Foroughirad, V. Frere, C. Gardner, M. G. Geffen, E. Godfrey, S. S. Graham, A. L. Hammond, P. S. Henrich, M. Heurich, M. Hopwood, P. Ila 2024-07-02 doi:10.1101/2024.06.28.601262 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ The oncofetal protein IMP1 regulates the transcriptomic landscape to drive early events in pancreatic cancer progression and growth ]]> https://biorxiv.org/content/10.1101/2024.06.28.601273v1?rss=1 Hacariz, O. Messina-Pacheco, J. Goodfellow, E. Leibovitch, M. Lowy, A. Perrino, S. Jean-Claude, B. Gao, Z.-H. Gregorieff, A. Brodt, P. 2024-07-02 doi:10.1101/2024.06.28.601273 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Cooperativity among clustered κB sites within promoters and enhancers dictates transcriptional specificity of NF-κB RelA along with specific cofactors ]]> https://biorxiv.org/content/10.1101/2024.07.03.601930v1?rss=1 Shahabi, S. Biswas, T. Shen, Y. Zou, Y. Sanahmadi, R. Ghosh, G. 2024-07-03 doi:10.1101/2024.07.03.601930 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Parallel Synapses with Transmission Nonlinearities Enhance Neuronal Classification Capacity ]]> https://biorxiv.org/content/10.1101/2024.07.01.601490v1?rss=1 Song, Y. Benna, M. K. 2024-07-04 doi:10.1101/2024.07.01.601490 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Compressive Pangenomics Using Mutation-Annotated Networks ]]> https://biorxiv.org/content/10.1101/2024.07.02.601807v1?rss=1 Walia, S. Motwani, H. Smith, K. Corbett-Detig, R. Turakhia, Y. 2024-07-04 doi:10.1101/2024.07.02.601807 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Control of Modular Tissue Flows Shaping the Embryo in Avian Gastrulation ]]> https://biorxiv.org/content/10.1101/2024.07.04.601785v1?rss=1 Serrano Najera, G. Plum, A. M. Steventon, B. Weijer, C. J. Serra, M. 2024-07-08 doi:10.1101/2024.07.04.601785 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Evidence for low affinity of GABA at the vesicular monoamine transporter VMAT2. Implications for transmitter co-release from dopamine neurons ]]> https://biorxiv.org/content/10.1101/2024.07.04.602053v1?rss=1 Limani, F. Srinivasan, S. Hanzlova, M. La Batide-Alanore, S. Klotz, S. Hnasko, T. S. Steinkellner, T. 2024-07-08 doi:10.1101/2024.07.04.602053 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication ]]> https://biorxiv.org/content/10.1101/2024.07.10.602835v1?rss=1 Yin, X. Pu, Y. Yuan, S. Pache, L. Churas, C. Weston, S. Riva, L. Simons, L. M. Cisneros, W. Clausen, T. de Jesus, P. Kim, H. N. Fuentes, D. Whitelock, J. Esko, J. Lord, M. Mena, I. Garcia-Sastre, A. Hultquist, J. Frieman, M. Ideker, T. Pratt, D. Martin-Sancho, L. Chanda, S. 2024-07-10 doi:10.1101/2024.07.10.602835 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Single-cell transcriptomics reveal differences between chorionic and basal plate cytotrophoblasts and trophoblast stem cells ]]> https://biorxiv.org/content/10.1101/2024.07.12.603155v1?rss=1 Morey, R. E. Soncin, F. Kallol, S. Sah, N. Manalo, Z. Bui, T. Slamecka, J. Cheung, V. C. Pizzo, D. Requena, D. F. Chang, C.-W. Farah, O. Kittle, R. Meads, M. Horii, M. Fisch, K. Parast, M. M. 2024-07-16 doi:10.1101/2024.07.12.603155 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Insights into the role of root exudates in bacteriophage infection dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.15.603626v1?rss=1 Novak, V. van Winden, M. C. M. Harwood, T. V. Neurath, R. Kosina, S. M. Louie, K. B. Sullivan, M. B. Roux, S. Zengler, K. Mutalik, V. K. Northen, T. R. 2024-07-18 doi:10.1101/2024.07.15.603626 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Logical Network Perturbations Guide Precise Target Prioritization for Drug Development ]]> https://biorxiv.org/content/10.1101/2024.07.16.602603v1?rss=1 Sinha, S. McLaren, E. G. Mullick, M. Singh, S. Boland, B. S. Ghosh, P. 2024-07-19 doi:10.1101/2024.07.16.602603 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import ]]> https://biorxiv.org/content/10.1101/2024.07.17.604013v1?rss=1 Chang, Y.-T. Barad, B. A. Rahmani, H. Zid, B. M. Grotjahn, D. A. 2024-07-19 doi:10.1101/2024.07.17.604013 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Engineering the novel extremophile alga Chlamydomonas pacifica for high lipid and high starch production as a path to developing commercially relevant strains ]]> https://biorxiv.org/content/10.1101/2024.07.18.604193v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@84948eorg.highwire.dtl.DTLVardef@352616org.highwire.dtl.DTLVardef@1577082org.highwire.dtl.DTLVardef@19b8644_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gupta, A. Dutra Molino, J. V. Wnuk-Fink, K. M. Bruckbauer, A. Tessman, M. Kang, K. Diaz, C. J. Saucedo, B. Malik, A. Mayfield, S. P. 2024-07-19 doi:10.1101/2024.07.18.604193 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification ]]> https://biorxiv.org/content/10.1101/2024.07.19.604374v1?rss=1 Cook, B. D. Narehood, S. M. McGuire, K. L. Li, Y. Tezcan, A. F. Herzik, M. A. 2024-07-22 doi:10.1101/2024.07.19.604374 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ An arylsulphonamide that targets cell wall biosynthesis in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.07.22.604653v1?rss=1 Allen, R. Ames, L. Baldin, V. P. Butts, A. Henry, K. J. Quach, D. Sugie, J. Pogliano, J. Parish, T. 2024-07-23 doi:10.1101/2024.07.22.604653 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Gene expression changes in long-term memory unlikely to replicate in the long term ]]> https://biorxiv.org/content/10.1101/2024.07.22.604349v1?rss=1 Mukamel, E. A. Yu, Z. 2024-07-24 doi:10.1101/2024.07.22.604349 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Sequencing 1206 genomes reveals origin and movement of Aedes aegypti driving increased dengue risk ]]> https://biorxiv.org/content/10.1101/2024.07.23.604830v1?rss=1 Crawford, J. E. Balcazar, D. Redmond, S. Rose, N. H. Youd, H. A. Lucas, E. R. Sudirman Made Ali, R. Al-Nazawi, A. M. Badolo, A. CHEN, C.-H. Cosme, L. V. Henke, J. A. Hung, K. Y. Kluh, S. Liu, W. -L. Maringer, K. Micieli, M. V. Pless, E. Sombie, A. R. Surendran, S. N. Wahid, I. Armbruster, P. A. Weetman, D. McBride, C. S. Gloria-Soria, A. Powell, J. R. White, B. J. 2024-07-24 doi:10.1101/2024.07.23.604830 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ All atom molecular dynamics simulations enable ensemble refinement of flexible and mismodelled cryo-EM derived RNA structures ]]> https://biorxiv.org/content/10.1101/2024.07.24.604258v1?rss=1 Posani, E. Janos, P. Haack, D. Toor, N. Bonomi, M. Magistrato, A. Bussi, G. 2024-07-24 doi:10.1101/2024.07.24.604258 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports persistent co-existence of diverse lineages ]]> https://biorxiv.org/content/10.1101/2024.07.24.605038v1?rss=1 Vezina, B. Cooper, H. B. Rethoret-Pasty, M. Brisse, S. Monk, J. M. Holt, K. E. Wyres, K. L. 2024-07-25 doi:10.1101/2024.07.24.605038 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Modulation of Neuronal Excitability and Plasticity by BHLHE41 Conveys Lithium Non-Responsiveness ]]> https://biorxiv.org/content/10.1101/2024.07.25.605130v1?rss=1 Rossner, M. J. Stephan, M. Papiol, S. Zhang, M. Song, J. Frommeyer, S. M. Haupt, H. Jensen, N. Kannaiyan, N. Gupta, R. Schuler, P. Pickelmann, P. McCarthy, M. J. Schulte, E. Lande, M. Falkai, P. Scheuss, V. Schulze, T. G. Zhang, W. 2024-07-25 doi:10.1101/2024.07.25.605130 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Cell surface ribonucleoproteins cluster with heparan sulfate to regulate growth factor signaling ]]> https://biorxiv.org/content/10.1101/2024.07.25.605163v1?rss=1 Flynn, R. A. Chair, P. Perr, J. Kageler, L. Lebedenko, C. G. Dias, J. M. L. Yankova, E. Esko, J. D. Tzelepis, K. 2024-07-25 doi:10.1101/2024.07.25.605163 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Testing the causal impact of amyloidosis on total Tau using a genetically informative sample of adult male twins. ]]> https://biorxiv.org/content/10.1101/2024.07.23.602498v1?rss=1 Gillespie, N. Neale, M. C. Panizzon, M. S. McKenzie, R. E. Tu, X. M. Reynolds, C. M. Lyons, M. J. Rissman, R. A. Elman, J. A. Franz, C. E. Kremen, W. S. 2024-07-26 doi:10.1101/2024.07.23.602498 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Genomic Epidemiology of Monkeypox Virus During the 2022 Outbreak in New York City ]]> https://biorxiv.org/content/10.1101/2024.07.23.604793v1?rss=1 Akther, S. Su, M. Wang, J. C. Amin, H. Taki, F. De La Cruz, N. Chowdhury, M. Clabby, T. Kopping, E. Ruiz, V. E. Leelawong, M. Latash, J. Johnson, K. Baumgartner, J. Wong, M. Olsen, A. Fowler, R. C. Pekar, J. C. Havens, J. L. Vasylyeva, T. I. Wertheim, J. O. Hughes, S. Omoregie, E. 2024-07-26 doi:10.1101/2024.07.23.604793 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Degradability tunes ECM stress relaxation and cellular mechanics ]]> https://biorxiv.org/content/10.1101/2024.07.28.605514v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@13a701dorg.highwire.dtl.DTLVardef@196bb05org.highwire.dtl.DTLVardef@d04613org.highwire.dtl.DTLVardef@1a8b1d1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Narasimhan, B. N. Fraley, S. I. 2024-07-29 doi:10.1101/2024.07.28.605514 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Deciphering the transcriptional regulatory network of Yarrowia lipolytica using machine learning ]]> https://biorxiv.org/content/10.1101/2024.07.29.605545v1?rss=1 Kerssemakers, A. A. J. Krishnan, J. Rychel, K. Zielinski, D. C. Palsson, B. Sudarsan, S. 2024-07-30 doi:10.1101/2024.07.29.605545 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Anisotropic Articular Cartilage Biofabrication based on Decellularized Extracellular Matrix ]]> https://biorxiv.org/content/10.1101/2024.07.30.605411v1?rss=1 Puiggali-Jou, A. Hui, I. Baldi, L. Frischknecht, R. Asadikorayem, M. Janiak, J. Chansoria, P. McCabe, M. C. Stoddart, M. J. Hansen, K. Christman, K. L. Zenobi, M. 2024-07-30 doi:10.1101/2024.07.30.605411 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ RESP2: An uncertainty aware multi-target multi-property optimization AI pipeline for antibody discovery ]]> https://biorxiv.org/content/10.1101/2024.07.30.605700v1?rss=1 = 85%. Popular generative AI techniques evaluated on the same datasets achieve success rates of 1.5% or less by comparison. Next we use the receptor binding domain (RBD) of the COVID-19 spike protein as a case study, and discover a highly human antibody with broad (mid to high-affinity) binding to at least 8 different variants of the RBD. These results illustrate the advantages of this pipeline for antibody discovery against a challenging target. A Python package that enables users to utilize the RESP pipeline on their own targets is available at https://github.com/Wang-lab-UCSD/RESP2, together with code needed to reproduce the experiments in this paper. ]]> Parkinson, J. Hard, R. Ko, Y. S. Wang, W. 2024-07-31 doi:10.1101/2024.07.30.605700 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Prediction of Threonine-Tyrosine Kinase Receptor-LigandUnbinding Kinetics with Multiscale Milestoning andMetadynamics ]]> https://biorxiv.org/content/10.1101/2024.08.01.606239v1?rss=1 View larger version (99K): org.highwire.dtl.DTLVardef@59d2dborg.highwire.dtl.DTLVardef@12244c4org.highwire.dtl.DTLVardef@d0a8a5org.highwire.dtl.DTLVardef@f01a4b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Votapka, L. W. Ojha, A. A. Asada, N. Amaro, R. E. 2024-08-02 doi:10.1101/2024.08.01.606239 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ CRISPR-RNA binding drives structural ordering that primes Cas7-11 for target cleavage ]]> https://biorxiv.org/content/10.1101/2024.08.01.606276v1?rss=1 Lin, C. P. Li, H. Brogan, D. J. Wang, T. Akbari, O. S. Komives, E. A. 2024-08-02 doi:10.1101/2024.08.01.606276 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Ordering molecular diversity in untargeted metabolomics via molecular community networking ]]> https://biorxiv.org/content/10.1101/2024.08.02.606356v1?rss=1 Coler, E. A. Melnik, A. Lotfi, A. Moradi, D. Ahiadu, B. Portal Gomes, P. W. Patan, A. Dorrestein, P. C. Barnes, S. Boginski, V. Semenov, A. Aksenov, A. A. 2024-08-02 doi:10.1101/2024.08.02.606356 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer ]]> https://biorxiv.org/content/10.1101/2024.07.31.606057v1?rss=1 Havas, A. Lande, K. Rajesh, A. Evensen, K. G. Varanasi, S. K. Shang, L. Schmidt, E. Lee, J. Kim, K. Teneche, M. G. Hoffmann, F. LaPorte, M. Davis, A. Grier, A. Reisz, J. A. Tharp, K. Gandhi, A. Lei, X. Proulx, J. Miller, K. N. Sacco, A. Shadel, G. S. Niedernhofer, L. Feng, G.-S. D'Alesssandro, A. Kaech, S. Williams, A. Adams, P. D. 2024-08-03 doi:10.1101/2024.07.31.606057 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Modeling collagen fibril degradation as a function of matrix microarchitecture ]]> https://biorxiv.org/content/10.1101/2024.08.10.607470v1?rss=1 Debnath, B. Narasimhan, B. N. Fraley, S. I. Rangamani, P. 2024-08-12 doi:10.1101/2024.08.10.607470 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Engineered Nanotopographies Induce Transient Openings in the Nuclear Membrane ]]> https://biorxiv.org/content/10.1101/2024.08.13.605467v1?rss=1 Sarikhani, E. Patel, V. Li, Z. Meganathan, D. P. Rahmani, K. Sadr, L. Hosseini, R. Visda, D. Shukla, S. Naghsh-Nilchi, H. Balaji, A. McMahon, G. Chen, S. Schoneberg, J. McHugh, C. A. Shi, L. Jahed, Z. 2024-08-16 doi:10.1101/2024.08.13.605467 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling ]]> https://biorxiv.org/content/10.1101/2024.08.14.607921v1?rss=1 50% of tested strains. The multi-phage cocktail maintains bacterial growth suppression and prevents the emergence of phage-resistant strains throughout our 40-hour assay. These findings suggest specialized phage cocktails may be an effective avenue of treatment for recalcitrant STM infections resistant to current antibiotics. IMPORTANCEPhage therapy could provide a vital strategy in the fight against antimicrobial resistance (AMR) bacterial infections; however, significant knowledge gaps remain. This study investigates phage cocktail development for the opportunistic pathogen Stenotrophomonas maltophilia (STM). Our findings contribute novel phages, their lytic characteristics, and limitations when exposed to an array of clinically relevant STM strains. Eighteen bacteriophages were isolated from wastewater influent from Escondido, California, and subjected to genomic analysis. We investigated genetically distinct phages to establish their infection kinetics and developed them into a phage cocktail. Our findings suggest that a genetically distinct STM phage cocktail provides an effective strategy for bacterial suppression of host strain B28B and five other clinically relevant STM strains. Phage therapy against STM remains poorly understood, as only 39 phages have been previously isolated. Future research into the underlying mechanism of how phage cocktails overwhelm the host bacteria will provide essential information that could aid in optimizing phage applications and impact alternative treatment options. ]]> Monsibais, A. N. Tea, O. Ghatbale, P. Phan, J. Lam, K. Paulson, M. Tran, N. Suder, D. S. Blanc, A. Samillano, C. Suh, J. Dunham, S. J. B. Gonen, S. Pride, D. T. Whiteson, K. 2024-08-16 doi:10.1101/2024.08.14.607921 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Formation of giant ER sheets by pentadecanoic acid causes lipotoxicity in fission yeast ]]> https://biorxiv.org/content/10.1101/2024.08.15.608187v1?rss=1 Hoshikawa, Y. Shirota, N. Tsugawa, H. Kimura, S. Matsuyama, A. Yashiroda, Y. Kakeya, H. Arita, M. Iizumi, R. Yoshida, M. Nishimura, S. 2024-08-17 doi:10.1101/2024.08.15.608187 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining ]]> https://biorxiv.org/content/10.1101/2024.08.16.608241v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@4d3daaorg.highwire.dtl.DTLVardef@10b6d49org.highwire.dtl.DTLVardef@133da4forg.highwire.dtl.DTLVardef@141ae7e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, B. Pashkova, L. Pieters, P. A. Harke, A. S. Palsson, B. O. Phaneuf, P. V. 2024-08-19 doi:10.1101/2024.08.16.608241 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Engagement in moderate-intensity physical activity supports overnight emotional memory retention in older adults ]]> https://biorxiv.org/content/10.1101/2024.08.16.608272v1?rss=1 Chappel-Farley, M. G. Berisha, D. E. Dave, A. Sanders, R. M. Kline, C. E. Janecek, J. C. Sattari, N. Lui, K. K. Chen, I. Y. Neikrug, A. B. Benca, R. M. Yassa, M. A. Mander, B. A. 2024-08-19 doi:10.1101/2024.08.16.608272 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor ]]> https://biorxiv.org/content/10.1101/2024.08.17.608367v1?rss=1 Takagi, H. Ito, S. Shim, J. S. Kubota, A. Hempton, A. K. Lee, N. Suzuki, T. Yang, C. Nolan, C. T. Bubb, K. L. Alexandre, C. M. Kurihara, D. Sato, Y. Tada, Y. Kiba, T. Pruneda-Paz, J. L. Queitsch, C. Cuperus, J. T. Imaizumi, T. 2024-08-19 doi:10.1101/2024.08.17.608367 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes ]]> https://biorxiv.org/content/10.1101/2024.08.19.607671v1?rss=1 Tang, Y. J. Xu, H. Hughes, N. W. Kim, S. H. Ruiz, P. Shuldiner, E. G. Lopez, S. S. Hebert, J. D. Karmakar, S. Andrejka, L. Dolcen, N. Boross, G. Chu, P. Detrick, C. Pierce, S. E. Ashkin, E. L. Greenleaf, W. Voss, A. K. Thomas, T. van de Rijn, M. Petrov, D. Winslow, M. M. 2024-08-20 doi:10.1101/2024.08.19.607671 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Intermittent Theta Burst Stimulation Drives Bi-Directional Changes in Excitability in Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/2024.08.19.608693v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@113f13dorg.highwire.dtl.DTLVardef@4317d7org.highwire.dtl.DTLVardef@d25dd5org.highwire.dtl.DTLVardef@10e6e3f_HPS_FORMAT_FIGEXP M_FIG C_FIG SummaryElectrical theta burst stimulation (TBS) with different inter-train intervals (ITIs) was first used to characterize bidirectional synaptic plasticity in brain slices. Despite a lack of understanding of mechanism, TBS has been adopted by rTMS research and clinical protocols to drive plasticity in the human brain, with variable results. To uncover how TBS modulates excitability in vivo, we systematically screen the impact of electrical TBS with different ITIs on rodent cortical neurons. Short inter-train intervals (4-10s) increased calcium activity in both glutamatergic and GABAergic neurons during stimulation, whereas extended ITIs (20s) yielded modest but significant activation of glutamatergic cells and minimal activation of GABAergic cells. TBS with an ITI of 20s emerged as a plasticity "sweet spot" that maximized long-term activation of glutamatergic neurons, potentially through suppression of GABAergic neurons(1-3). Translating our novel iTBS electrical stimulation protocol to rTMS interventions has the potential to deliver heightened plasticity and improved therapeutic outcomes. HighlightsSystematic manipulation of inter-train intervals (ITIs) reveals an optimal 20s ITI for TBS-induced plasticity. Extended ITIs enhance excitability in glutamatergic neurons while suppressing GABAergic activity. PV interneurons are preferentially recruited during short-interval TBS, limiting sustained plasticity. ]]> Salimi, M. Nazari, M. Mishler, J. Mishra, J. Ramanathan, D. 2024-08-20 doi:10.1101/2024.08.19.608693 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Multi-Modal Large Language Model Enables Protein Function Prediction ]]> https://biorxiv.org/content/10.1101/2024.08.19.608729v1?rss=1 Huo, M. Guo, H. Cheng, X. Singh, D. Rahmani, H. Li, S. Gerlof, P. Ideker, T. Grotjahn, D. A. Villa, E. Song, L. Xie, P. 2024-08-20 doi:10.1101/2024.08.19.608729 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Development of the Follow-Up Discourse Observation Protocol (FUDOP) for characterizing instructor active-learning follow-up behaviors ]]> https://biorxiv.org/content/10.1101/2024.08.20.608824v1?rss=1 Cen, X. Kight, M. Lee, R. Kranzfelder, P. Lo, S. M. Maloy, J. Owens, M. T. 2024-08-22 doi:10.1101/2024.08.20.608824 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Olfactory receptor coexpression and co-option in the dengue mosquito ]]> https://biorxiv.org/content/10.1101/2024.08.21.608847v1?rss=1 Adavi, E. D. dos Anjos, V. L. Kotb, S. Metz, H. C. Tian, D. Zhao, Z. Zung, J. L. Rose, N. H. McBride, C. S. 2024-08-22 doi:10.1101/2024.08.21.608847 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Genetically encoded fluorescent sensors for visualizing polyamine levels, uptake, and distribution ]]> https://biorxiv.org/content/10.1101/2024.08.21.609037v1?rss=1 Tamura, R. Chen, J. De Jaeger, M. Morris, J. F. Scott, D. A. Vangheluwe, P. Looger, L. L. 2024-08-22 doi:10.1101/2024.08.21.609037 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Tactile Mechanisms and Afferents Underlying the Rat Pup Transport Response ]]> https://biorxiv.org/content/10.1101/2024.08.23.609194v1?rss=1 Ni, Z. Neifert, C. Rosete, A. Albeely, A. M. Yang, Y. Pratelli, M. Brecht, M. Clemens, A. M. 2024-08-23 doi:10.1101/2024.08.23.609194 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Enrichment analysis for spatial and single-cell metabolomics accounting for molecular ambiguity ]]> https://biorxiv.org/content/10.1101/2024.08.23.609355v1?rss=1 Wadie, B. Molenaar, M. R. Vieira, L. M. Alexandrov, T. 2024-08-23 doi:10.1101/2024.08.23.609355 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ E-cigarettes increase the risk of adenoma formation in murine colorectal cancer model. ]]> https://biorxiv.org/content/10.1101/2024.08.23.609469v1?rss=1 Sayed, I. M. Chakraborty, A. Inouye, K. Dugan, L. Tocci, S. Advani, I. Park, K. Hazra, T. K. Das, S. Crotty Alexander, L. E. 2024-08-26 doi:10.1101/2024.08.23.609469 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ A link between aging and persistence ]]> https://biorxiv.org/content/10.1101/2024.08.24.609520v1?rss=1 Proenca, A. M. Rang, C. U. Chao, L. 2024-08-26 doi:10.1101/2024.08.24.609520 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks ]]> https://biorxiv.org/content/10.1101/2024.08.24.609531v1?rss=1 Ko, Y. S. Parkinson, J. Wang, W. 2024-08-26 doi:10.1101/2024.08.24.609531 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Multi-scale reactor designs extend the physical limits of CO2 fixation ]]> https://biorxiv.org/content/10.1101/2024.08.28.610213v1?rss=1 Akbari, A. Palsson, B. O. 2024-08-30 doi:10.1101/2024.08.28.610213 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Integrated Dual-Channel Retrograde Signaling Directs Stress Responses by Degrading the HAT1/TPL/IMPalpha-9 Suppressor Complex and Activating CAMTA3 ]]> https://biorxiv.org/content/10.1101/2024.08.29.610327v1?rss=1 Zeng, L. Guo, J. Palayam, M. Rodriguez, C. Gomez Mendez, M. F. Wang, Y. Ven, W. v. d. Pruneda-Paz, J. Shabek, N. Dehesh, K. 2024-08-30 doi:10.1101/2024.08.29.610327 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Metacognition in Putative Magno- and Parvocellular Vision ]]> https://biorxiv.org/content/10.1101/2024.08.31.610587v1?rss=1 Pilipenko, A. Samaha, J. Nukala, V. De La Torre, J. 2024-09-02 doi:10.1101/2024.08.31.610587 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Methods for high throughput discovery of fluoroprobes that recognize tau fibril polymorphs ]]> https://biorxiv.org/content/10.1101/2024.09.02.610853v1?rss=1 Carroll, E. C. Yang, H. E. Jones, J. G. Oehler, A. Charvat, A. F. Montgomery, K. M. Yung, A. Millbern, Z. Vinueza, N. R. Degrado, W. F. Mordes, D. A. Condello, C. Gestwicki, J. E. 2024-09-02 doi:10.1101/2024.09.02.610853 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Genome-Wide Mapping of RNA-Protein Associations via Sequencing ]]> https://biorxiv.org/content/10.1101/2024.09.04.611288v1?rss=1 Qi, Z. Xue, S. Chen, J. Zhao, W. Johnson, K. Wen, X. Richard, J. L. C. Zhong, S. 2024-09-04 doi:10.1101/2024.09.04.611288 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Decoupling Coldness and Softness in Tactile Wetness Perception Using Tunable Hydrogels ]]> https://biorxiv.org/content/10.1101/2024.09.03.611060v1?rss=1 Becerra, L. L. Root, N. Clark, A. Rafeedi, T. Brown, W. Chen, A. X. Qie, Y. Blau, R. Miller, J. Kapadia, K. Ng, T. N. Rouw, R. Lipomi, D. J. 2024-09-05 doi:10.1101/2024.09.03.611060 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ A Distinct Alternative mRNA Splicing Profile Identifies the Oncogenic CD44 Transcript Variant 3 in KMT2A-Rearranged Pediatric T-cell Acute Lymphoblastic Leukemia Cells ]]> https://biorxiv.org/content/10.1101/2024.09.05.611385v1?rss=1 Ramilo Amor, A. Enlund, S. Sinha, I. Jiang, Q. Hermanson, O. Nilsson, A. Shirazi Fard, S. Holm, F. 2024-09-06 doi:10.1101/2024.09.05.611385 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Acetylation of lysine 82 initiates TDP-43 nuclear loss of function by disrupting its nuclear import ]]> https://biorxiv.org/content/10.1101/2024.09.04.611121v1?rss=1 Zhang, S. Vazquez-Sanchez, S. Lu, S. Baughn, M. W. Lim, J. Oung, S. Gao, L. Diedrich, J. K. Yates, J. R. Yu, H. Ravits, J. Cleveland, D. W. 2024-09-07 doi:10.1101/2024.09.04.611121 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Planar cell polarity coordination in a cnidarian embryo provides clues to animal body axis evolution ]]> https://biorxiv.org/content/10.1101/2024.09.05.609312v1?rss=1 Uveira, J. Donati, A. Leria, M. Lechable, M. Lahaye, F. Vesque, C. Houliston, E. Momose, T. 2024-09-07 doi:10.1101/2024.09.05.609312 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Enhancer activation from transposable elements in extrachromosomal DNA ]]> https://biorxiv.org/content/10.1101/2024.09.04.611262v1?rss=1 Kraft, K. Murphy, S. E. Jones, M. G. Shi, Q. Bhargava-Shah, A. Luong, C. Hung, K. L. He, B. J. Li, R. Park, S. K. Weiser, N. E. Luebeck, J. Bafna, V. Boeke, J. D. Mischel, P. S. Boettiger, A. N. Chang, H. Y. 2024-09-08 doi:10.1101/2024.09.04.611262 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes ]]> https://biorxiv.org/content/10.1101/2024.09.04.611290v1?rss=1 Shinde, P. Willemsen, L. Anderson, M. Aoki, M. Basu, S. Burel, J. G. Cheng, P. Dastidar, S. G. Dunleavy, A. Einav, T. Forschmiedt, J. Fourati, S. Garcia, J. Gibson, W. Greenbaum, J. A. Guan, L. Guan, W. Gygi, J. P. Ha, B. Hou, J. Hsiao, J. Huang, Y. Jansen, R. Kakoty, B. Kang, Z. Kobie, J. J. Kojima, M. Konstorum, A. Lee, J. Lewis, S. A. Li, A. Lock, E. F. Mahita, J. Mendes, M. Meng, H. Neher, A. Nili, S. Orfield, S. Overton, J. Pai, N. Parker, C. Qian, B. Rasmussen, M. Reyna, J. Richardson, E. Safo, S. Sorenson, J. Srinivasan, A. Thrupp, N. Tip 2024-09-08 doi:10.1101/2024.09.04.611290 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx ]]> https://biorxiv.org/content/10.1101/2024.09.07.611813v1?rss=1 Xiao, K. Park, S. Stachowiak, J. Rangamani, P. 2024-09-08 doi:10.1101/2024.09.07.611813 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Behavioral state and stimulus strength regulate the role of somatostatin interneurons in stabilizing network activity ]]> https://biorxiv.org/content/10.1101/2024.09.09.612138v1?rss=1 Cammarata, C. M. Pei, Y. Shields, B. C. Lim, S. S. X. Hawley, T. Li, J. Y. St. Amand, D. Brunel, N. Tadross, M. R. Glickfeld, L. L. 2024-09-10 doi:10.1101/2024.09.09.612138 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Efficient genome replication in influenza A virus requires NS2 and sequence beyond the canonical promoter ]]> https://biorxiv.org/content/10.1101/2024.09.10.612348v1?rss=1 Swaminath, S. Mendes, M. Zhang, Y. Remick, K. A. Mejia, I. Guereca, M. te Velthuis, A. J. W. Russell, A. B. 2024-09-10 doi:10.1101/2024.09.10.612348 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing ]]> https://biorxiv.org/content/10.1101/2024.09.11.612086v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@12609e5org.highwire.dtl.DTLVardef@53a128org.highwire.dtl.DTLVardef@794e63org.highwire.dtl.DTLVardef@9835f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Song, L. Alker, A. T. P. Oromi-Bosch, A. Swartz, S. E. Martinson, J. N. V. Arora, J. Wang, A. M. Rovinsky, R. Smith, S. J. Pierce, E. C. Deutschbauer, A. M. Doudna, J. A. Cress, B. F. Rubin, B. E. 2024-09-11 doi:10.1101/2024.09.11.612086 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Targeting the Schwann Cell EP2/cAMP Nanodomain to Block Pain but not Inflammation ]]> https://biorxiv.org/content/10.1101/2024.09.10.612200v1?rss=1 Nassini, R. Landini, L. Marini, M. Chieca, M. Souza Monteiro de Araujo, D. Montini, M. Pensieri, P. Abruzzese, V. D. De Siena, G. Zhang, J. De Giorgi, V. Romitelli, A. Brancolini, G. Tonello, R. Peach, C. J. Mastricci, A. Scuffi, I. Tesi, M. Jensen, D. D. Schmidt, B. L. Bunnett, N. W. De Logu, F. Geppetti, P. 2024-09-14 doi:10.1101/2024.09.10.612200 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Cholinergic feedback for context-specific modulation of sensory representations ]]> https://biorxiv.org/content/10.1101/2024.09.10.612274v1?rss=1 Yu, B. Yue, Y. Ren, C. Yun, R. Lim, B. Komiyama, T. 2024-09-14 doi:10.1101/2024.09.10.612274 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Decoding Specificity of Cyanobacterial MysDs in Mycosporine-Like Amino Acid Biosynthesis through Heterologous Expression in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.09.14.613006v1?rss=1 Zheng, X. Xie, P. Cai, A. C. Jiang, Y. Huang, S. Ma, X. Su, H. Wang, B. 2024-09-15 doi:10.1101/2024.09.14.613006 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Combined transcriptomic, connectivity, and activity profiling of the medial amygdala using highly amplified multiplexed in situ hybridization (hamFISH) ]]> https://biorxiv.org/content/10.1101/2024.09.14.613026v1?rss=1 Edwards, M. D. Yin, Z. Sueda, R. Gubanova, A. Xu, C. S. Lakner, V. Murchie, M. Lee, C.-Y. Ng, K. Farrell, K. Faraway, R. Ganguly, S. Jacobs, E. Bintu, B. Isogai, Y. 2024-09-15 doi:10.1101/2024.09.14.613026 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Evaluating and Comparing Measures of Aperiodic Neural Activity ]]> https://biorxiv.org/content/10.1101/2024.09.15.613114v1?rss=1 Donoghue, T. Hammonds, R. Lybrand, E. Waschke, L. Gao, R. Voytek, B. 2024-09-15 doi:10.1101/2024.09.15.613114 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Manipulating attentional priority creates a trade-off between memory and sensory representations in human visual cortex ]]> https://biorxiv.org/content/10.1101/2024.09.16.613302v1?rss=1 Rademaker, R. L. Serences, J. 2024-09-16 doi:10.1101/2024.09.16.613302 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2 ]]> https://biorxiv.org/content/10.1101/2024.09.17.613365v1?rss=1 Raig, N. D. Surridge, K. J. Sanz-Murillo, M. Dederer, V. Kramer, A. Schwalm, M. P. Elson, L. Chatterjee, D. Mathea, S. Hanke, T. Leschziner, A. E. Reck-Peterson, S. L. Knapp, S. 2024-09-18 doi:10.1101/2024.09.17.613365 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Lateral prefrontal cortex controls interplay between working memory and actions ]]> https://biorxiv.org/content/10.1101/2024.09.17.613601v1?rss=1 Kiyonaga, A. Miller, J. D'Esposito, M. 2024-09-18 doi:10.1101/2024.09.17.613601 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygen-inducedlung injury ]]> https://biorxiv.org/content/10.1101/2024.09.13.612775v1?rss=1 Abe, Y. Spann, N. J. Tang, W. Zeng, F. Richard, J. L. C. Seymour, C. Jansky, S. Mooney, M. Huff, R. Chanthavixay, K. Dhar, D. Ganguly, S. Guo, J. L. Lopez, D. M. Longaker, M. T. Benner, C. Glass, C. Sajti, E. 2024-09-19 doi:10.1101/2024.09.13.612775 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Untargeted and Semi-Targeted Metabolomics Approach for Profiling Small Intestinal and Fecal Metabolome Using High-Resolution Mass Spectrometry ]]> https://biorxiv.org/content/10.1101/2024.09.16.613180v1?rss=1 TRONEL, a. Roger-Margueritat, m. Plazy, C. Cunin, v. Mohanty, I. Dorrestein, P. C. Soranzo, T. LE GOUELLEC, a. 2024-09-19 doi:10.1101/2024.09.16.613180 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Metabolic growth coupling strategies for in vivo enzyme selection systems ]]> https://biorxiv.org/content/10.1101/2024.09.16.613188v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@15d5a10org.highwire.dtl.DTLVardef@1c4067aorg.highwire.dtl.DTLVardef@856ce9org.highwire.dtl.DTLVardef@1b14cdb_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG HighlightsO_LIEnzyme selection system designs link enzyme activities to global metabolic processes. C_LIO_LIEnzymes can be categorized based on growth-couplable reaction stoichiometries. C_LIO_LIA database of strain designs for building enzyme selection systems was created. C_LIO_LIEnzyme selection systems enable optimization of a range product synthesis pathways. C_LIO_LIApplication recommendations: weakly coupled enzyme activities can have practical advantages. C_LI ]]> Alter, T. B. Pieters, P. A. Lloyd, C. J. Feist, A. M. Ozdemir, E. Palsson, B. O. Zielinski, D. C. 2024-09-19 doi:10.1101/2024.09.16.613188 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?rss=1 The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Accept-reject decision-making revealed via a quantitative and ethological study of C. elegans foraging ]]> https://biorxiv.org/content/10.1101/2024.09.18.613674v1?rss=1 Haley, J. A. Chen, T. Aoi, M. Chalasani, S. H. 2024-09-19 doi:10.1101/2024.09.18.613674 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Glycosite Mapping and in situ Mass Spectrometry Imaging of MUC2 Glycopeptides via On-slide Digestion with Mucinase StcE ]]> https://biorxiv.org/content/10.1101/2024.09.16.613285v1?rss=1 Lowery, S. C. Tran, I. P. Grimsley, G. Stubler, R. Mahoney, K. E. Lucas, T. M. Charkoftaki, G. Santos-Neto, A. Varki, N. Vasiliou, V. Drake, R. R. Malaker, S. A. 2024-09-20 doi:10.1101/2024.09.16.613285 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Functional connectivity is dominated by aperiodic, rather than oscillatory, coupling ]]> https://biorxiv.org/content/10.1101/2024.09.18.613682v1?rss=1 Monchy, N. Duprez, J. Houvenaghel, J.-F. Legros, A. Voytek, B. Modolo, J. 2024-09-20 doi:10.1101/2024.09.18.613682 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Antipsychotic-like effects of the selective Rho-kinase 2 inhibitor KD025 in genetic and pharmacological mouse models of schizophrenia ]]> https://biorxiv.org/content/10.1101/2024.09.16.613372v1?rss=1 Tanaka, R. Liao, J. Liu, Y. Zhu, W. Fukuzawa, K. Kondo, M. Sawahata, M. Mori, D. Mouri, A. Kubota, H. Tachibana, D. Kobayashi, Y. Matsuzaki, T. Nagai, T. Nabeshima, T. Kaibuchi, K. Ozaki, N. Mizoguchi, H. Yamada, K. 2024-09-21 doi:10.1101/2024.09.16.613372 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development ]]> https://biorxiv.org/content/10.1101/2024.09.17.612508v1?rss=1 Fan, A. T. Gadbois, G. E. Huang, H.-T. Jiang, J. Sigua, L. H. Smith, E. R. Wu, S. Dunne-Dombrink, K. Goyal, P. Tao, A. J. Sellers, W. B. Fischer, E. S. Donovan, K. A. Ferguson, F. 2024-09-21 doi:10.1101/2024.09.17.612508 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Sex-specific effects of early life unpredictability on hippocampal and amygdala responses to novelty in adolescents ]]> https://biorxiv.org/content/10.1101/2024.09.20.614130v1?rss=1 Davis, E. P. Leonard, B. Jirsaraie, R. Keator, D. Small, S. Sandman, C. A. Risbrough, V. Stern, H. S. Glynn, L. Yassa, M. A. Baram, T. Z. Rasmussen, J. 2024-09-23 doi:10.1101/2024.09.20.614130 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Human untargeted metabolomics in the gut microbiome era: ethanol vs methanol ]]> https://biorxiv.org/content/10.1101/2024.09.23.614605v1?rss=1 Zuffa, S. Charron-Lamoureux, V. Brennan, C. Ambre, A. Knight, R. Dorrestein, P. C. 2024-09-23 doi:10.1101/2024.09.23.614605 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS ]]> https://biorxiv.org/content/10.1101/2024.09.19.613975v1?rss=1 Xu, J. Zhu, K. Cai, J. Kockan, C. Dokmai, N. Cho, H. Woodruff, D. Sahinalp, C. 2024-09-24 doi:10.1101/2024.09.19.613975 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Small mammals and their burrows shape the distribution of Coccidioides in soils: a long-term ecological experiment ]]> https://biorxiv.org/content/10.1101/2024.09.21.613892v1?rss=1 Head, J. R. Camponuri, S. K. Weaver, A. K. Montoya, L. Lee, E. Radosevich, M. T. Jones, I. Wagner, R. Bhattachan, A. Campbell, G. Keeney, N. Collender, P. A. Heaney, A. K. Couper, L. Colvin, K. A. Larios, L. Bean, W. T. Taylor, J. Remais, J. V. 2024-09-24 doi:10.1101/2024.09.21.613892 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Evolutionary fingerprint in rodent PD1 confers weakened activity and enhanced tumor immunity compared to human PD1 ]]> https://biorxiv.org/content/10.1101/2024.09.21.614250v1?rss=1 Masubuchi, T. Chen, L. Marcel, N. Wen, G. A. Caron, C. Zhang, J. Zhao, Y. Morris, G. P. Chen, X. Hedrick, S. M. Lu, L.-F. Wu, C. Zou, Z. Bui, J. D. Hui, E. 2024-09-24 doi:10.1101/2024.09.21.614250 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Tumor-induced endothelial RhoA activation mediates tumor cell transendothelial migration and metastasis ]]> https://biorxiv.org/content/10.1101/2024.09.22.614304v1?rss=1 Sajib, M. S. Zahra, F. T. Lamprou, M. Akwii, R. G. Park, J. H. Osorio, M. Tullar, P. Doci, C. L. Zhang, C. Huveneers, S. van Buul, J. D. Wang, M.-H. Markiewski, M. M. Srivastava, S. K. Zheng, Y. Gutkind, J. S. Hu, J. Bickel, U. Maeda, D. Y. Zebala, J. A. Lionakis, M. S. Trasti, S. Mikelis, C. M. 2024-09-24 doi:10.1101/2024.09.22.614304 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Comprehensive proteolytic profiling of Aedes aegypti mosquito midgut extracts: Unraveling the blood meal protein digestion system ]]> https://biorxiv.org/content/10.1101/2024.09.23.614410v1?rss=1 O'Donoghue, A. J. Lui, C. Simington, C. J. Montermoso, S. Moreno-Galvez, E. Serafim, M. S. M. Burata, O. E. Lucero, R. M. Nguyen, J. T. Fong, D. Tran, K. Millan, N. Gallimore, J. M. Parungao, K. A. Fong, J. Suzuki, B. M. Jiang, Z. Isoe, J. Rascon, A. A. 2024-09-24 doi:10.1101/2024.09.23.614410 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Robotic Visible-Light Optical Coherence Tomography Visualizes Segmental Schlemms Canal Anatomy and Segmental Pilocarpine Response ]]> https://biorxiv.org/content/10.1101/2024.09.23.614542v1?rss=1 Fang, R. Zhang, P. Kim, D. Kweon, J. Sun, C. Huang, A. Zhang, H. F. 2024-09-25 doi:10.1101/2024.09.23.614542 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Genomic signatures of coral adaptation and recovery following a mass mortality event ]]> https://biorxiv.org/content/10.1101/2024.09.23.614560v1?rss=1 Fifer, J. E. Speare, K. Leinbach, S. Hendricks, S. Davies, S. W. Rose, N. Burkepile, D. Adam, T. Hofmann, G. Strader, M. 2024-09-25 doi:10.1101/2024.09.23.614560 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Adaptation to high pressure; insights from the genome of an evolved Escherichia coli strain with increased piezotolerance ]]> https://biorxiv.org/content/10.1101/2024.09.24.613341v1?rss=1 Allemann, M. N. Ma, S. Sztain, T. Bartholow, T. G. G. Marshall, I. P. G. McCammon, A. Burkart, M. Allen, E. E. Bartlett, D. H. Marietou, A. 2024-09-25 doi:10.1101/2024.09.24.613341 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ The Proteostasis Network is a Therapeutic Target in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2024.09.24.614781v1?rss=1 Lam, K. Kim, Y. J. Ong, C. M. Liu, A. Z. Zhou, F. J. Sunshine, M. J. Chua, B. A. Vicenzi, S. Ford, P. Zhou, J.-H. Hong, Y. Bennett, E. J. Crews, L. A. Ball, E. D. Signer, R. A. J. 2024-09-26 doi:10.1101/2024.09.24.614781 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models ]]> https://biorxiv.org/content/10.1101/2024.09.24.614797v1?rss=1 Raman, K. Kratochvil, M. Olivier, B. G. Konig, M. Sengupta, P. Baskaran, D. K. K. Nguyen, T. V. N. Lobo, D. Wilken, S. E. Tiwari, K. K. Raghu, A. K. Palanikumar, I. Raajaraam, L. Ibrahim, M. Balakrishnan, S. Umale, S. Bergmann, F. Malpani, T. Satagopam, V. P. Schneider, R. Beber, M. E. Keating, S. Anton, M. Renz, A. Lakshmanan, M. Lee, D.-Y. Koduru, L. Mostolizadeh, R. Dias, O. Cunha, E. Oliveira, A. Lee, Y. Q. Zengler, K. Santibanez-Palominos, R. Kumar, M. Barberis, M. Puniya, B. L. Helikar, T. Dinh, H. V. Suthers, P. F. Maranas, C. D. Casini, I. Logh 2024-09-26 doi:10.1101/2024.09.24.614797 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Bulk and selective autophagy cooperate to remodel a fungal proteome in response to changing nutrient availability ]]> https://biorxiv.org/content/10.1101/2024.09.24.614842v1?rss=1 Telusma, B. Farre, J.-C. Cui, D. S. Subramani, S. Davis, J. H. 2024-09-26 doi:10.1101/2024.09.24.614842 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Intestinal Epithelial PTPN2 Limits Pathobiont Colonization by Immune-Directed Antimicrobial Responses ]]> https://biorxiv.org/content/10.1101/2024.09.24.614848v1?rss=1 Chatterjee, P. Spalinger, M. R. Acevedo, C. Gries, C. M. Manz, S. Canale, V. Santos, A. N. Shawki, A. Sayoc-Becerra, A. Lei, H. Crawford, M. S. Eckmann, L. Borneman, J. McCole, D. 2024-09-26 doi:10.1101/2024.09.24.614848 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Concurrent single-pulse (sp) TMS/fMRI to reveal the causal connectome in healthy and patient populations ]]> https://biorxiv.org/content/10.1101/2024.09.25.614833v1?rss=1 Glick, C. C. Gajawelli, N. Sun, Y. Badami, F. Saggar, M. Etkin, A. 2024-09-26 doi:10.1101/2024.09.25.614833 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia ]]> https://biorxiv.org/content/10.1101/2024.09.25.615004v1?rss=1 Vong, K. I. Alvarez, Y. D. Noel, G. Barton, S. T. Chung, C. Howarth, R. Meave, N. Zhang, Q. Jiwani, F. Barrows, C. Patel, A. Kingsmore, S. F. White, M. D. Yang, X. Gleeson, J. G. 2024-09-26 doi:10.1101/2024.09.25.615004 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Different signaling interpretations by PKC eta and theta control T cell function and exhaustion ]]> https://biorxiv.org/content/10.1101/2024.09.26.615103v1?rss=1 Mann, T. H. Knox, H. M. Ma, S. Furgiuele, J. Globig, A.-M. LaPorta, M. Chung, H. K. McDonald, B. Ghassemian, M. Zhao, S. Tseng, H. Farsakoglu, Y. Tripple, V. Koo, J. Newton, A. C. Kaech, S. M. 2024-09-27 doi:10.1101/2024.09.26.615103 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Radical Protein Footprinting in Mammalian Whole Blood ]]> https://biorxiv.org/content/10.1101/2024.09.29.615683v1?rss=1 Tobin, L. Misra, S. K. Liu, H. Jones, L. M. Sharp, J. S. 2024-09-29 doi:10.1101/2024.09.29.615683 Cold Spring Harbor Laboratory Press 2024-09-29 <![CDATA[ Temporal Dynamics of Nucleus Accumbens Neurons in Male Mice During Reward Seeking ]]> https://biorxiv.org/content/10.1101/2024.09.27.615291v1?rss=1 Schall, T. A. Li, K.-l. Qi, X. Lee, B. T. Wright, W. J. Alpaugh, E. E. Zhao, R. J. Liu, J. Li, Q. Zeng, B. Wang, L. Huang, Y. H. Schlueter, O. Nestler, E. J. Nieh, E. H. Dong, Y. 2024-09-30 doi:10.1101/2024.09.27.615291 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation ]]> https://biorxiv.org/content/10.1101/2024.09.28.614012v1?rss=1 Brewer, J. J. Inlow, K. Mooney, R. A. Bosch, B. Olinares, P. D. B. Marcelino, L. P. Chait, B. T. Landick, R. Gelles, J. Campbell, E. A. Darst, S. A. 2024-09-30 doi:10.1101/2024.09.28.614012 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Cryo-EM visualizes multiple steps of dynein activation pathway ]]> https://biorxiv.org/content/10.1101/2024.09.28.615567v1?rss=1 Kendrick, A. Nguyen, K. MA, W. Karasmanis, E. Amaro, R. E. Reck-Peterson, S. Leschziner, A. 2024-09-30 doi:10.1101/2024.09.28.615567 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Multi-Modal Large Language Model Enables All-Purpose Prediction of Drug Mechanisms and Properties ]]> https://biorxiv.org/content/10.1101/2024.09.29.615524v1?rss=1 Liang, Y. Zhang, R. Li, Y. Huo, M. Ma, Z. Singh, D. Gao, C. Rahmani, H. Bandi, S. Zhang, L. Weinreb, R. Malhotra, A. Grotjahn, D. A. Awdishu, L. Ideker, T. Gilson, M. Xie, P. 2024-10-01 doi:10.1101/2024.09.29.615524 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ A Novel Engineered U7 Small Nuclear RNA Scaffold Greatly Increases in vitro and in vivo ADAR-Mediated Programmable RNA Base Editing ]]> https://biorxiv.org/content/10.1101/2024.09.29.615721v1?rss=1 Byrne, S. M. Burleigh, S. M. Fragoza, R. Jiang, Y. Saava, Y. Pabon, R. Rainaldi, J. Portell, A. Mali, P. Briggs, A. W. 2024-10-01 doi:10.1101/2024.09.29.615721 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ The Deubiquitinating Enzyme Otub2 Modulates Pancreatic Beta-Cells Function and Survival ]]> https://biorxiv.org/content/10.1101/2024.09.30.615641v1?rss=1 Oshry, M. Isaac, R. Boura-Halfon, S. Sampson, S. Lev, S. Zick, Y. Vinik, Y. 2024-10-01 doi:10.1101/2024.09.30.615641 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Group B streptococci lyse endothelial cells to infect the brain in a zebrafish meningitis model ]]> https://biorxiv.org/content/10.1101/2024.10.01.616123v1?rss=1 Ravishankar, S. Tuohey, S. M. Ramos, N. O. Uchiyama, S. Hayes, M. I. Nizet, V. Madigan, C. A. 2024-10-01 doi:10.1101/2024.10.01.616123 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ N-Acetyl-2-Aminofluorene (AAF): In vivo temporal expression patterns of growth cycle-dependent macromolecular binding constants KD are revealed by primary cultures of premalignant hepatocytes derived from a multi-cyclic hepatocarcinogenic feeding regimen ]]> https://biorxiv.org/content/10.1101/2024.09.30.615953v1?rss=1 Koch, K. S. Moran, T. Sell, S. Leffert, H. L. 2024-10-02 doi:10.1101/2024.09.30.615953 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ An engineered chromatin protein with enhanced preferential binding of H3K27me3 over H3K9me3 ]]> https://biorxiv.org/content/10.1101/2024.10.02.616304v1?rss=1 Franklin, K. A. Priode, J. H. Steppe, P. Haynes, K. A. 2024-10-02 doi:10.1101/2024.10.02.616304 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Soil depth determines the microbial communities in Sorghum bicolor fields ]]> https://biorxiv.org/content/10.1101/2024.10.02.616346v1?rss=1 Murray, E. R. Minich, J. J. Saxton, J. de Gracia, M. Eck, N. Allsing, N. Kitony, J. Patel-Jhawar, K. Allen, E. E. Michael, T. P. Shakoor, N. 2024-10-02 doi:10.1101/2024.10.02.616346 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain ]]> https://biorxiv.org/content/10.1101/2024.10.01.616090v1?rss=1 Khatib, L. Song, S. J. Dilmore, A. H. Sanders, J. G. Brennan, C. Hernandez, A. R. Myers, T. Oles, R. Farmer, S. Cowart, C. Birmingham, A. Diaz, E. A. Nizet, O. Gilbert, K. Litwin, N. Das, P. Nowinski, B. Bryant, M. Tribelhorn, C. Sanders-Bodai, K. Chaumont, S. Knol, J. Roeselers, G. Laiola, M. Shetty, S. A. Veiga, P. Tap, J. Derrien, M. Koutnikova, H. Cotillard, A. Lay, C. Tovar, A. R. Torres, N. Arteaga, L. Gonzalez, A. McDonald, D. Bartko, A. Knight, R. 2024-10-03 doi:10.1101/2024.10.01.616090 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Determining sex differences in drug combinations targeting aortic valve myofibroblast activation using an artificial intelligence derived platform ]]> https://biorxiv.org/content/10.1101/2024.10.02.615251v1?rss=1 Vogt, B. J. Wang, P. Chavez, M. Guo, P. Chow, E. K.-H. Ho, D. Aguado, B. A. 2024-10-03 doi:10.1101/2024.10.02.615251 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems ]]> https://biorxiv.org/content/10.1101/2024.10.02.615924v1?rss=1 Novak, V. Andeer, P. F. King, E. Calabria, J. Fitzpatrick, C. Kelm, J. M. Wippel, K. Kosina, S. M. Daum, C. Zane, M. Yadav, A. Chen, M. Russ, D. Adams, C. A. Owens, T. K. Lee, B. Ding, Y. Sordo, Z. Chakraborty, R. Roux, S. Deutschbauer, A. M. Ushizima, D. Zengler, K. Arsova, B. Dangl, J. Schulze-Lefert, P. Watt, M. Vogel, J. Northen, T. R. 2024-10-03 doi:10.1101/2024.10.02.615924 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Conserved chromatin regulators control the transcriptional immune response to intracellular pathogens in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.10.03.616425v1?rss=1 Tecle, E. Li, S. Blanchard, M. J. Bui, T. Chhan, C. B. Underwood, R. S. Bakowski, M. A. Troemel, E. R. Lazetic, V. 2024-10-04 doi:10.1101/2024.10.03.616425 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases ]]> https://biorxiv.org/content/10.1101/2024.10.04.615514v1?rss=1 Weisburd, B. Dolzhenko, E. Bennett, M. F. Danzi, M. C. English, A. Hiatt, L. Tanudisastro, H. Kurtas, N. E. Jam, H. Z. Brand, H. Sedlazeck, F. J. Gymrek, M. Dashnow, H. Eberle, M. A. Rehm, H. L. 2024-10-05 doi:10.1101/2024.10.04.615514 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2024.10.04.616668v1?rss=1 Sen, A. Xu, Z. Tyndale, S. Yasis, J. Cho, C. Y. Bump, R. Chandran, S. Luo, L. Fu, Y. Petersen, L. K. Shokhirev, M. Kuo, D. J. McVicker, G. P. Dixon, J. R. 2024-10-05 doi:10.1101/2024.10.04.616668 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Comprehensive sequencing of the lung neuroimmune landscape in response to asthmatic induction ]]> https://biorxiv.org/content/10.1101/2024.10.04.616730v1?rss=1 McSwiggin, H. Wang, R. Magalhaes, R. D. M. Zhu, F. Doherty, T. A. Yan, W. Jendzjowsky, N. 2024-10-05 doi:10.1101/2024.10.04.616730 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding ]]> https://biorxiv.org/content/10.1101/2024.10.05.616664v1?rss=1 Zhang, Y. Liu, Y. Ma, Z. Li, M. Xu, C. Gong, H. 2024-10-05 doi:10.1101/2024.10.05.616664 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Growth-coupled microbial biosynthesis of the animal pigment xanthommatin ]]> https://biorxiv.org/content/10.1101/2024.10.04.616593v1?rss=1 Bushin, L. B. Alter, T. B. Alvan-Vargas, M. V. G. Dürr, L. Olson, E. C. Avila, M. J. Puiggene, O. Kim, T. Deravi, L. F. Feist, A. M. Nikel, P. I. Moore, B. S. 2024-10-06 doi:10.1101/2024.10.04.616593 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models ]]> https://biorxiv.org/content/10.1101/2024.10.06.616870v1?rss=1 Zhang, L. Guo, H. Schaffer, L. V. Ko, Y. S. Singh, D. Rahmani, H. Grotjahn, D. Villa, E. Gilson, M. Wang, W. Ideker, T. Xing, E. Xie, P. 2024-10-06 doi:10.1101/2024.10.06.616870 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Alzheimer's disease-associated genotypes differentially influence chronic evoked seizure outcomes and antiseizure medicine activity in aged mice ]]> https://biorxiv.org/content/10.1101/2024.10.06.616921v1?rss=1 Knox, K. Davidson, S. Lehmann, L. Skinner, E. Lo, A. Jayadev, S. Barker-Haliski, M. 2024-10-07 doi:10.1101/2024.10.06.616921 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Empirically establishing drug exposure records directly from untargeted metabolomics data ]]> https://biorxiv.org/content/10.1101/2024.10.07.617109v1?rss=1 Zhao, H. N. Kvitne, K. E. Brungs, C. Mohan, S. Charron-Lamoureux, V. Bittremieux, W. Tang, R. Schmid, R. Lamichhane, S. El Abiead, Y. Andalibi, M. S. Mannochio-Russo, H. Ambre, M. Avalon, N. E. Bryant, M. Caraballo-Rodriguez, A. M. Maya, M. C. Chin, L. Ellis, R. J. Franklin, D. Girod, S. Gomes, P. W. P. Hansen, L. Heaton, R. Iudicello, J. E. Jarmusch, A. K. Khatib, L. Letendre, S. Magyari, S. McDonald, D. Mohanty, I. Cumsille, A. Moore, D. J. Rajkumar, P. Ross, D. H. Sapre, H. Shahneh, M. R. Z. Thomas, S. P. Tribelhorn, C. Tubb, H. M. Walker, C. Wang, C 2024-10-10 doi:10.1101/2024.10.07.617109 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription ]]> https://biorxiv.org/content/10.1101/2024.10.08.616922v1?rss=1 Ren, X. Zheng, L. Maliskova, L. Tam, T. W. Sun, Y. Liu, H. Lee, J. Takagi, M. A. Li, B. Ren, B. Wang, W. Shen, Y. 2024-10-10 doi:10.1101/2024.10.08.616922 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ TRIM37 employs peptide motif recognition and substrate-dependent oligomerization to prevent ectopic spindle pole assembly ]]> https://biorxiv.org/content/10.1101/2024.10.09.617493v1?rss=1 Bellaart, A. Brambila, A. Xu, J. Diaz, F. M. Deep, A. Anzola, J. Meitinger, F. Ohta, M. Corbett, K. D. Desai, A. Oegema, K. 2024-10-10 doi:10.1101/2024.10.09.617493 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Metabolomic Profiling Reveals Potential of Fatty Acids as Regulators of Stem-like Exhausted CD8 T Cells During Chronic Viral Infection ]]> https://biorxiv.org/content/10.1101/2024.10.07.617124v1?rss=1 Kazane, K. R. Labarta-Bajo, L. Zangwill, D. R. Liimatta, K. Vargas, F. Weldon, K. C. Dorrestein, P. C. Zuniga, E. I. 2024-10-11 doi:10.1101/2024.10.07.617124 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Biodiversity forecasting in natural plankton communities reveals temperature and biotic interactions as key predictors ]]> https://biorxiv.org/content/10.1101/2024.10.10.617676v1?rss=1 Merz, E. pomati, f. Saavedra, S. Gilarranz, L. 2024-10-13 doi:10.1101/2024.10.10.617676 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork ]]> https://biorxiv.org/content/10.1101/2024.10.11.617674v1?rss=1 Kay, T. M. Inman, J. T. Lubkowska, L. Le, T. T. Qian, J. Hall, P. M. Wang, D. Kashlev, M. Wang, M. D. 2024-10-13 doi:10.1101/2024.10.11.617674 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ ExoSloNano: Multi-Modal Nanogold Tags for identi-fication of Macromolecules in Live Cells & Cryo-Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2024.10.12.617288v1?rss=1 Young, L. N. Sherrard, A. Zhou, H. Shaikh, F. Hutchings, J. Riggi, M. Rosen, M. K. Giraldez, A. Villa, E. 2024-10-13 doi:10.1101/2024.10.12.617288 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4 ]]> https://biorxiv.org/content/10.1101/2024.10.13.618094v1?rss=1 Bhaduri, S. E. Braza, M. K. E. Stanchev, S. Bach, K. Tauber, M. Al-Bawab, R. Liu, L. J. Trujillo, D. F. Solorio-Kirpichyan, K. Srivastava, A. Sanlley-Hernandez, J. O'Donoghue, A. J. Lemberg, M. K. Amaro, R. E. Strisovsky, K. Neal, S. E. 2024-10-13 doi:10.1101/2024.10.13.618094 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Retinoid X Receptor Signaling Mediates Cancer Cell Lipid Metabolism in the Leptomeninges ]]> https://biorxiv.org/content/10.1101/2024.10.13.618083v1?rss=1 Tong, X. Remsik, J. Brook, J. Pentrova, B. Li, M. J. Snyder, J. Sidharta, M. Chabot, K. Estrera, R. Osei-Guyening, I. Nobre, A. R. L. C. Wang, H. Osman, A. Piedrafita-Ortiz, S. Wong, A. Manoranjan, B. Zhou, T. Murali, R. Xu, L. Koche, R. He, Y. Kanarek, N. Boire, A. 2024-10-15 doi:10.1101/2024.10.13.618083 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Epigenetic trajectory predicts development of clinical rheumatoid arthritis in ACPA+ individuals: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA) ]]> https://biorxiv.org/content/10.1101/2024.10.15.618490v1?rss=1 Prideaux, E. B. Boyle, D. L. Choi, E. Buckner, J. H. Robinson, W. H. Holers, V. M. Deane, K. D. Firestein, G. S. Wang, W. 2024-10-16 doi:10.1101/2024.10.15.618490 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Annotating full-scan MS data using tandem MS libraries ]]> https://biorxiv.org/content/10.1101/2024.10.14.618269v1?rss=1 Xing, S. Charron-Lamoureux, V. El Abiead, Y. Dorrestein, P. C. 2024-10-17 doi:10.1101/2024.10.14.618269 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Epigenetic and 3D genome reprogramming during the aging of human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.14.618338v1?rss=1 Zemke, N. Lee, S. Mamde, S. Yang, B. Berchtold, N. Garduno, M. Indralingam, H. Bartosik, W. Lau, P. Dong, K. Yang, A. Tani, Y. Chen, C. Zeng, Q. Ajith, V. Tong, L. Seng, C. Li, D. Wang, T. Xu, X. Ren, B. 2024-10-17 doi:10.1101/2024.10.14.618338 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Automatic Detection and Extraction of Key Resources from Tables in Biomedical Papers ]]> https://biorxiv.org/content/10.1101/2024.10.15.618379v1?rss=1 Ozyurt, I. B. Bandrowski, A. 2024-10-17 doi:10.1101/2024.10.15.618379 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ The role of auxin-mediated gene activation in the bryophyte, Physcomitrium patens ]]> https://biorxiv.org/content/10.1101/2024.10.15.618431v1?rss=1 Bascom, C. S. Tu, D. Estelle, M. 2024-10-17 doi:10.1101/2024.10.15.618431 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Dark Microglia Are Abundant in Normal Postnatal Development, where they Remodel Synapses via Phagocytosis and Trogocytosis, and Are Dependent on TREM2 ]]> https://biorxiv.org/content/10.1101/2024.10.15.618087v1?rss=1 Vecchiarelli, H. A. Bisht, K. Sharma, K. P. Weiser Novak, S. Traetta, M. E. Garcia-Segura, M. E. St-Pierre, M.-K. Savage, J. C. Willis, C. Picard, K. Bordeleau, M. Vernoux, N. Khakpour, M. Garg, R. Loewen, S. M. Murray, C. J. Grinberg, Y. Y. Faustino, J. Halvorson, T. Lau, V. Pluchino, S. Vexler, Z. S. Carson, M. J. Manor, U. Peruzzotti-Jametti, L. Tremblay, M.-E. 2024-10-18 doi:10.1101/2024.10.15.618087 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Discovery and Biosynthesis of Sulfenicin and Its New-to-Nature Acylsulfenic Acid Functional Group ]]> https://biorxiv.org/content/10.1101/2024.10.16.618611v1?rss=1 Xue, D. Zou, H. Lv, W. Madden, M. D. Lian, X. Xu, M. Pulliam, C. Older, E. A. Hou, L. Campbell, A. de Rond, T. Awakawa, T. Yuan, C. Moore, B. S. Li, J. 2024-10-18 doi:10.1101/2024.10.16.618611 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injury ]]> https://biorxiv.org/content/10.1101/2024.10.16.618727v1?rss=1 Shen, Z. Feng, B. Lim, W. Woo, T. Liu, Y. Vicenzi, S. Wang, J. Kwon, B. K. Zou, Y. 2024-10-18 doi:10.1101/2024.10.16.618727 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Hybrid incompatibility emerges at the one-cell stage in interspecies Caenorhabditis embryos ]]> https://biorxiv.org/content/10.1101/2024.10.19.619171v1?rss=1 Bloom, J. Green, R. A. Desai, A. Oegema, K. Rifkin, S. A. 2024-10-21 doi:10.1101/2024.10.19.619171 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Nanoscale curvature of the plasma membrane regulates mechanoadaptation through nuclear deformation and rupture ]]> https://biorxiv.org/content/10.1101/2024.10.18.619165v1?rss=1 View larger version (84K): org.highwire.dtl.DTLVardef@ec6d5aorg.highwire.dtl.DTLVardef@1ff6ec2org.highwire.dtl.DTLVardef@c09f46org.highwire.dtl.DTLVardef@18df50_HPS_FORMAT_FIGEXP M_FIG C_FIG This study uses experiments and biophysical modeling to examine the response and adaptation of cells to nanoscale topography of surfaces. It is shown that cytoskeletal assembly and nuclear localization of transcription regulatory factors such as YAP/TAZ can be tuned by nanoscale membrane curvature and nuclear deformation and rupture due to substrate nanotopography. ]]> Francis, E. A. Sarikhani, E. Patel, V. Meganathan, D. P. Jahed, Z. Rangamani, P. 2024-10-22 doi:10.1101/2024.10.18.619165 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ The YTHDF Proteins Shape the Brain Gene Signatures of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.10.23.619425v1?rss=1 Tasaki, S. Avey, D. R. Kearns, N. A. Iatrou, A. Yu, C. De Tissera, S. Vyas, H. Xu, J. Flood, D. J. Rothamel, K. Wingo, A. P. Wingo, T. S. Seyfried, N. T. De Jager, P. L. Yeo, G. Gaiteri, C. Bennett, D. A. Wang, Y. 2024-10-23 doi:10.1101/2024.10.23.619425 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Inhibition of PIM kinase in tumor associated macrophages suppresses inflammasome 1 activation and sensitizes prostate cancer to immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.10.21.618756v1?rss=1 Clements, A. N. Casillas, A. L. Flores, C. E. Liou, H. Toth, R. K. Chauhan, S. S. Sutterby, K. Deshmukh, S. K. Wu, S. Xiu, J. Farrell, A. Radovich, M. Nabhan, C. Heath, E. I. McKay, R. R. Subah, N. Centuori, S. Wheeler, T. J. Cress, A. E. Rogers, G. C. Wilson, J. E. Recio-Boiles, A. Warfel, N. A. 2024-10-24 doi:10.1101/2024.10.21.618756 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Efficient secretion of a plastic degrading enzyme from the green algae Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2024.10.23.619606v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@108e29dorg.highwire.dtl.DTLVardef@55ceaborg.highwire.dtl.DTLVardef@173793eorg.highwire.dtl.DTLVardef@1d14c3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Molino, J. V. D. Saucedo, B. Kang, K. Walsh, C. Diaz, C. J. Tessman, M. Mayfield, S. P. 2024-10-24 doi:10.1101/2024.10.23.619606 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Simulated larvae dispersion of the invasive sun-coral (Tubastrea spp.) along Rio de Janeiro's coast: the role of submesoscale filaments on offshore transport and connectivity ]]> https://biorxiv.org/content/10.1101/2024.10.23.619824v1?rss=1 Calado, L. Cosensa, B. Moraes, F. L. P. d. Dias Luko, C. Mizrahi, D. Xavier, F. C. Batista, D. Domingos, R. Calazans, S. Araujo, F. Coutinho, R. 2024-10-24 doi:10.1101/2024.10.23.619824 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Mechanistic genotype-phenotype translation using hierarchical transformers ]]> https://biorxiv.org/content/10.1101/2024.10.23.619940v1?rss=1 1,395 variants within 20 systems and include epistatic interactions among variants, e.g. between APOA4 and CETP in phospholipid transfer. This work positions hierarchical graph transformers as a next-generation approach to polygenic risk. ]]> Lee, I. Wallace, Z. Park, S. Nam, H. Majithia, A. Ideker, T. 2024-10-24 doi:10.1101/2024.10.23.619940 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.10.22.619657v1?rss=1 2) and do not co-amplify other oncogenes on the same ecDNA particles. In contrast, PDGFRA ecDNAs have lower mean copy number (mean of 15 copies per cell), are under weaker positive selection and frequently co-amplify other oncogenes on the same ecDNA. Evolutionary modeling suggests that EGFR ecDNAs often accumulate prior to clonal expansion. EGFR structural variants, including vIII and c-terminal deletions are under strong positive selection, are found exclusively on ecDNA, and are intermixed with wild-type EGFR ecDNAs. Simulations show EGFRvIII ecDNA likely arises after ecDNA formation in a cell with high wild-type EGFR copy number (> 10) before the onset of the most recent clonal expansion. This remains true even in cases of co-selection and co-amplification of multiple oncogenic ecDNA species in a subset of patients. Overall, our results suggest a potential time window in which early ecDNA detection may provide an opportunity for more effective intervention. HighlightsO_LIecDNA is the most common mechanism of focal oncogene amplification in IDHwt glioblastoma. C_LIO_LIEGFR and its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis. C_LIO_LIWild-type and variant EGFR ecDNA heteroplasmy (co-occurrence) is common with EGFRvIII or c-terminal deletions being derived from EGFR wild-type ecDNA prior to the most recent clonal expansion. C_LIO_LITumors with ecDNA amplified EGFR versus PDGFRA exhibit different evolutionary trajectories. C_LIO_LISPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer. C_LIO_LIA delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention. C_LI ]]> Noorani, I. Haughey, M. Luebeck, J. Rowan, A. Grönroos, E. Terenzi, F. Wong, I. T.-L. Kittel, J. Bailey, C. Weeden, C. Bell, D. Joo, E. Barbe, V. Jones, M. G. Nye, E. Green, M. Meader, L. Norton, E. J. Fabian, M. Kanu, N. Jamal-Hanjani, M. Santarius, T. Nicoll, J. Boche, D. Chang, H. Y. Bafna, V. Huang, W. Mischel, P. S. Swanton, C. Werner, B. 2024-10-25 doi:10.1101/2024.10.22.619657 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ AI-readiness for Biomedical Data: Bridge2AI Recommendations ]]> https://biorxiv.org/content/10.1101/2024.10.23.619844v1?rss=1 Clark, T. Caufield, H. Mohan, J. A. Al Manir, S. Amorim, E. Eddy, J. Gim, N. Gow, B. Goar, W. Haendel, M. Hansen, J. N. Harris, N. Hermjakob, H. McWeeney, S. K. Nebeker, C. Nikolov, M. Shaffer, J. Sheffield, N. Sheynkman, G. Stevenson, J. Mungall, C. Chen, J. Y. Wagner, A. Kong, S. W. Ghosh, S. S. Patel, B. Williams, A. Munoz-Torres, M. C. 2024-10-25 doi:10.1101/2024.10.23.619844 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Oncogenic Alterations, Race, and Survival in US Veterans with Metastatic Prostate Cancer Undergoing Somatic Tumor Next Generation Sequencing ]]> https://biorxiv.org/content/10.1101/2024.10.24.620071v1?rss=1 Valle, L. F. Li, J. Desai, H. Hausler, R. Haroldsen, C. Chatwal, M. S. Ojo, M. Kelley, M. J. Rebbeck, T. Rose, B. S. Rettig, M. B. Nickols, N. G. Garraway, I. P. Yamoah, K. Maxwell, K. N. 2024-10-25 doi:10.1101/2024.10.24.620071 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ HT SpaceM: A High-Throughput and Reproducible Method for Small-Molecule Single-Cell Metabolomics ]]> https://biorxiv.org/content/10.1101/2024.10.24.620114v1?rss=1 Delafiori, J. Shahraz, M. Eisenbarth, A. Hilsenstein, V. Drotleff, B. Bailoni, A. Wadie, B. Ekelöf, M. Mattausch, A. Alexandrov, T. 2024-10-25 doi:10.1101/2024.10.24.620114 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Explicitly Acquired Interrelations Among Mental Schema Reduces Cognitive Load and Facilitates Emergence of Novel Responses in Mice and Artificial Neural Networks. ]]> https://biorxiv.org/content/10.1101/2024.10.23.619968v1?rss=1 Singh, V. P. Shridhar, S. Kundu, S. Bhatt, R. Jayaprakash, B. 2024-10-26 doi:10.1101/2024.10.23.619968 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ EEG-VLM Toolbox: Extending voxel-based lesion mapping to multi-dimensional EEG data ]]> https://biorxiv.org/content/10.1101/2024.10.25.620269v1?rss=1 Hardstone, R. Ostrowski, L. Dusang, A. N. Lopez-Larraz, E. Jesser, J. Cash, S. S. Cramer, S. C. Hochberg, L. R. Ramos-Murguialday, A. Lin, D. J. 2024-10-26 doi:10.1101/2024.10.25.620269 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas ]]> https://biorxiv.org/content/10.1101/2024.10.25.620311v1?rss=1 Weber, C. J. Weitzel, A. J. Liu, A. Y. Gacasan, E. G. Sah, R. L. Cooper, K. L. 2024-10-26 doi:10.1101/2024.10.25.620311 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Developing a Multiscale Neural Connectivity Knowledgebase of the Autonomic Nervous System ]]> https://biorxiv.org/content/10.1101/2024.10.25.620360v1?rss=1 Imam, F. T. Gillespie, T. H. Ziogas, I. Surles-Zeigler, M. C. Tappan, S. Ozyurt, B. Boline, J. de Bono, B. Grethe, J. S. Martone, M. E. 2024-10-28 doi:10.1101/2024.10.25.620360 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria ]]> https://biorxiv.org/content/10.1101/2024.10.28.620613v1?rss=1 Mukherjee, S. D. Batagello, C. Adler, A. Agudelo, J. Zampini, A. Suryavanshi, M. Nguyen, A. Orr, T. Dearing, D. Monga, M. Miller, A. W. 2024-10-28 doi:10.1101/2024.10.28.620613 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Structure of a Putative Terminal Amidation Domain in Natural Product Biosynthesis ]]> https://biorxiv.org/content/10.1101/2024.10.28.620694v1?rss=1 Rankin, M. R. Khare, D. Gerwick, L. Sherman, D. H. Gerwick, W. H. Smith, J. L. 2024-10-28 doi:10.1101/2024.10.28.620694 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Scalable Fabrication of a Tough and Recyclable Spore-Bearing Biocomposite Thermoplastic Polyurethane ]]> https://biorxiv.org/content/10.1101/2024.10.25.620092v1?rss=1 Kim, H. S. White, E. Crane, G. Patel, K. Noh, M. H. Rahman, M. A. Feist, A. Locklin, J. Pokorski, J. 2024-10-29 doi:10.1101/2024.10.25.620092 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2024.10.27.620507v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@116edb1org.highwire.dtl.DTLVardef@4f010corg.highwire.dtl.DTLVardef@cde718org.highwire.dtl.DTLVardef@1ff0841_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Label-free indicators of diabetic nephropathies. C_FIG ]]> Fung, A. A. Li, Z. Boote, C. Markov, P. P. Jain, S. A. Shi, L. 2024-10-29 doi:10.1101/2024.10.27.620507 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy ]]> https://biorxiv.org/content/10.1101/2024.10.29.620861v1?rss=1 Lee, S.-Y. Roh, H. Gonzalez-Perez, D. Mackey, M. R. Kim, K.-Y. Hoces, D. McLaughlin, C. Adams, S. R. Nguyen, K. Luginbuhl, D. J. Luo, L. Udeshi, N. Carr, S. A. Hernandez-Lopez, R. A. Ellisman, M. Alcalde, M. Ting, A. Y. 2024-10-29 doi:10.1101/2024.10.29.620861 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Pattern-based genome mining guides discovery of the antibiotic indanopyrrole A from a marine streptomycete. ]]> https://biorxiv.org/content/10.1101/2024.10.29.620887v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@14d6080org.highwire.dtl.DTLVardef@fa89b5org.highwire.dtl.DTLVardef@66fdddorg.highwire.dtl.DTLVardef@1a4f7f9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sweeney, D. Bogdanov, A. Chase, A. B. Castro-Falcon, G. Trinidad-Javier, A. Dahesh, S. Nizet, V. Jensen, P. R. 2024-10-29 doi:10.1101/2024.10.29.620887 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Identification of a large cohort of Enterobacter jumbo phages with broad host ranges across pathogenic Gammaproteobacteria ]]> https://biorxiv.org/content/10.1101/2024.10.29.620934v1?rss=1 Kanhirun, N. Blanc, A. Aindow, A. You, M. Antani, J. D. Ghatbale, P. Leonard, J. Garcia, A. G. Nghiem, K. Whiteson, K. Schooley, R. Turner, P. Pogliano, J. Guemes, A. G. C. Pride, D. T. 2024-10-29 doi:10.1101/2024.10.29.620934 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation ]]> https://biorxiv.org/content/10.1101/2024.10.25.620329v1?rss=1 Mawass, W. Matheson, J. Hernandez, U. Berg, J. J. Masel, J. 2024-10-30 doi:10.1101/2024.10.25.620329 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Systemic inflammation and lymphocyte activation precede rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2024.10.25.620344v1?rss=1 He, Z. Glass, M. C. Venkatesan, P. Feser, M. L. Lazaro, L. Okada, L. Y. Tran, N. T. T. He, Y. D. Rachid Zaim, S. Bennett, C. E. Ravisankar, P. Dornisch, E. M. Arishi, N. A. Asamoah, A. G. Barzideh, S. Becker, L. A. Bemis, E. A. Buckner, J. H. Collora, C. E. Criley, M. A. L. Demoruelle, M. K. Fleischer, C. L. Garber, J. Genge, P. C. Gong, Q. Graybuck, L. T. Gustafson, C. E. Hattel, B. C. Hernandez, V. Heubeck, A. T. Kawelo, E. K. Krishnan, U. Kuan, E. L. Kuhn, K. A. LaFrance, C. M. Lee, K. J. Li, R. Lord, C. Mettey, R. R. Moss, L. Musgrove, B. Nguyen, K. 2024-10-30 doi:10.1101/2024.10.25.620344 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Genomic Analysis of Progenitors in Viral Infection Implicates Glucocorticoids as Suppressors of Plasmacytoid Dendritic Cell Generation ]]> https://biorxiv.org/content/10.1101/2024.10.28.620771v1?rss=1 Jo, Y. Greene, T. T. Zhang, K. Chiale, C. Fang, Z. Dallari, S. Marooki, N. Wang, W. Zuniga, E. I. 2024-10-30 doi:10.1101/2024.10.28.620771 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ The CYK-4 GAP domain regulates cortical targeting of centralspindlin to promote contractile ring assembly and facilitate ring dissolution ]]> https://biorxiv.org/content/10.1101/2024.10.29.620943v1?rss=1 Schlientz, A. J. Lee, K.-Y. Gomez-Cavazos, J. S. Lara-Gonzalez, P. Desai, A. Oegema, K. 2024-10-30 doi:10.1101/2024.10.29.620943 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ RATS: Unsupervised manifold learning using low-distortion alignment of tangent spaces ]]> https://biorxiv.org/content/10.1101/2024.10.31.621292v1?rss=1 Kohli, D. Nieuwenhuis, J. S. Cloninger, A. Mishne, G. Narain, D. 2024-10-31 doi:10.1101/2024.10.31.621292 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Tenascin-C from the tissue microenvironment promotes muscle stem cell self-renewal through Annexin A2 ]]> https://biorxiv.org/content/10.1101/2024.10.29.620732v1?rss=1 Loreti, M. Cecchini, A. Kaufman, C. D. Stamenkovic, C. Renero, A. Nicoletti, C. Kervadec-Badillo, A. Guarnaccia, G. Mayer, D. K. COLAS, A. Puri, P. L. Sacco, A. 2024-11-01 doi:10.1101/2024.10.29.620732 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ A Structural Mechanism for Noncanonical GPCRSignal Transduction in the Hedgehog Pathway ]]> https://biorxiv.org/content/10.1101/2024.10.31.621410v1?rss=1 Steiner, W. P. Iverson, N. Venkatakrishnan, V. Wu, J. Stepniewski, T. M. Michaelson, Z. Broeckel, J. Zhu, J.-F. Bruystens, J. Lee, A. Nelson, I. Bertinetti, D. Arveseth, C. D. Tan, G. Spaltenstein, P. Xu, J. Huttenhain, R. Kay, M. Herberg, F. W. Selent, J. Anand, G. S. Dunbrack, R. L. Taylor, S. S. Myers, B. R. 2024-11-01 doi:10.1101/2024.10.31.621410 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ To impute or not to impute in untargeted metabolomics - that is the compositional question ]]> https://biorxiv.org/content/10.1101/2024.10.28.620738v1?rss=1 Krutkin, D. D. Thomas, S. Zuffa, S. Rajkumar, P. Knight, R. Dorrestein, P. C. Kelley, S. T. 2024-11-02 doi:10.1101/2024.10.28.620738 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time ]]> https://biorxiv.org/content/10.1101/2024.10.30.621190v1?rss=1 Hernandez Mesa, M. McCabe, K. Rangamani, P. 2024-11-03 doi:10.1101/2024.10.30.621190 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds ]]> https://biorxiv.org/content/10.1101/2024.10.31.621412v1?rss=1 Mannochio-Russo, H. Charron-Lamoureux, V. van Faassen, M. Lamichhane, S. Goncalves Nunes, W. D. Deleray, V. Patan, A. Vittali, K. Rajkumar, P. El Abiead, Y. Zhao, H. N. Portal Gomes, P. W. Mohanty, I. Lee, C. Sund, A. Sharma, M. Liu, Y. Pattynama, D. Walker, G. T. Norton, G. J. Khatib, L. Andalibi, M. S. Wang, C. X. Ellis, R. J. Moore, D. J. Iudicello, J. E. Franklin, D. Letendre, S. Chin, L. Walker, C. Renwick, S. Zemlin, J. Meehan, M. J. Song, X. Kasper, D. Burcham, Z. Kim, J. J. Kadakia, S. Raffatellu, M. Bode, L. Zengler, K. Wang, M. Siegel, D. Kn 2024-11-03 doi:10.1101/2024.10.31.621412 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Association of oropharyngeal cancer recurrence with tumor-intrinsic and immune-mediated sequelae of reduced genomic instability ]]> https://biorxiv.org/content/10.1101/2024.10.31.621311v1?rss=1 Sannigrahi, M. K. Raghav, L. Rich, D. J. Schrank, T. P. Califano, J. A. Lukens, J. N. Sun, L. Morgan, I. M. Cohen, R. B. Lin, A. Liu, X. Brown, E. J. You, J. Mirabello, L. Mishra, S. K. Shimunov, D. Brody, R. M. Pearson, A. T. Gimotty, P. A. Diab, A. Jalaly, J. B. Basu, D. 2024-11-04 doi:10.1101/2024.10.31.621311 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Polymorphic tandem repeats shape single-cell gene expression across the immune landscape ]]> https://biorxiv.org/content/10.1101/2024.11.02.621562v1?rss=1 5.4 million blood-derived cells across 1,925 individuals in two cohorts [Cuomo et al., accompanying manuscript], and perform meta-analysis to characterize the impact of variation in >1.7 million TR loci on immune cell type-specific gene expression. We identify >69,000 single-cell expression TR loci (sc-eTRs), 30.7% of which are specific to one of 28 immune cell types, and reveal dynamic regulatory effects using cell-state inference. Matched single-cell ATAC sequencing profiles from >3.4 million nuclei in 922 individuals [Xue et al., accompanying manuscript]. uncover chromatin accessibility QTLs for nearly one-third of expression-associated TRs, supporting coordinated effects on cis-regulatory architecture. Fine-mapping implicates 1,490 TRs as candidate causal drivers of gene expression in 6.1% of tested genes, and colocalization analyses highlight >200 genes in which TRs likely mediate genetic associations with immune and hematological traits. Together, these results provide a genome-wide, multiomic view of TR-mediated regulation in the human immune system, establishing TRs as key contributors to cell type-specific regulatory variation and complex trait architecture. ]]> Tanudisastro, H. A. Cuomo, A. S. E. Weisburd, B. Welland, M. Spenceley, E. Franklin, M. Xue, A. Bowen, B. Wing, K. Tang, O. Gray, M. Reis, A. L. M. Margoliash, J. Kurtas, E. N. Pullin, J. Lee, A. S. Brand, H. Harper, M. Bobowik, K. Silk, M. Marshall, J. Bakiris, V. Swapna Madala, B. Uren, C. Bartie, C. Senabouth, A. Dashnow, H. Fearnley, L. Dolzhenko, E. Qiao, Z. Grieve, S. Nguyen, T. Talkowski, M. Alexander, S. I. Siggs, O. M. Gruenschloss, L. Nicholas, H. R. Piscionere, J. Simons, C. Wallace, C. Gymrek, M. Deveson, I. W. Hewitt, A. W. Figtree, G. A. 2024-11-04 doi:10.1101/2024.11.02.621562 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS ]]> https://biorxiv.org/content/10.1101/2024.11.03.621734v1?rss=1 Nourreddine, S. Doctor, Y. Dailamy, A. Forget, A. Lee, Y.-H. Chinn, B. Khaliq, H. Polacco, B. Muralidharan, M. Pan, E. Zhang, Y. Sigaeva, A. Hansen, J. N. Gao, J. Parker, J. A. Obernier, K. Clark, T. Chen, J. Y. Metallo, C. Lundberg, E. Ideker, T. Krogan, N. Mali, P. 2024-11-04 doi:10.1101/2024.11.03.621734 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ F2,6BP restores mitochondrial genome integrity in Huntingtons Disease ]]> https://biorxiv.org/content/10.1101/2024.11.04.621834v1?rss=1 Chakraborty, A. Mandal, S. M. Mankevich, M. Sreenivasmurthy, S. G. Hegde, M. Ghosh, G. Hazra, T. 2024-11-04 doi:10.1101/2024.11.04.621834 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ PgtE protease enables virulent Salmonella to evade C3-mediated serum and neutrophil killing ]]> https://biorxiv.org/content/10.1101/2024.11.05.622138v1?rss=1 Lee, M. H. Perez-Lopez, A. Knodler, L. Nguyen, G. Walker, G. T. Behnsen, J. Silva, S. Celli, J. Tamin, M. A. Liang, M. H. Melchior, K. Argueta, F. A. Nuccio, S.-P. Raffatellu, M. 2024-11-05 doi:10.1101/2024.11.05.622138 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Ultrastructural correlates of circadian structural plasticity ]]> https://biorxiv.org/content/10.1101/2024.11.06.622332v1?rss=1 Ispizua, J. I. Rodriguez-Caron, M. Tassara, F. J. Keun-young, K. Perkins, C. I. Barzi, M. Carpio-Romero, C. Hansen, C. N. Gargiulo, J. Rosato, E. de la iglesia, H. Ellisman, M. Ceriani, M. F. 2024-11-07 doi:10.1101/2024.11.06.622332 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Competition strategies driving resource partitioning in chitin degrading communities ]]> https://biorxiv.org/content/10.1101/2024.11.07.622309v1?rss=1 Pontrelli, S. Guessous, G. Trouillon, J. Krishna, A. Hwa, T. Sauer, U. 2024-11-07 doi:10.1101/2024.11.07.622309 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Tardigrade Dsup: Interactions with DNA and protection of cells from oxidative stress ]]> https://biorxiv.org/content/10.1101/2024.11.06.622393v1?rss=1 Ni, G. S. Su, H. Zhu, Y. Dhiman, A. Zhou, H.-X. Lin, W. Hao, N. 2024-11-08 doi:10.1101/2024.11.06.622393 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ RBPMS and RBPMS2 Cooperate to Safeguard Cardiac Splicing ]]> https://biorxiv.org/content/10.1101/2024.11.07.622565v1?rss=1 Wu, T. Chen, Z. Zhang, Z. Zhou, X. Gu, Y. Dinenno, F. A. Chen, J. 2024-11-08 doi:10.1101/2024.11.07.622565 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ The development of aperiodic neural activity in the human brain ]]> https://biorxiv.org/content/10.1101/2024.11.08.622714v1?rss=1 Cross, Z. R. Gray, S. M. Dede, A. J. O. Rivera, Y. M. Yin, Q. Vahidi, P. Rau, E. M. B. Cyr, C. Holubecki, A. M. Asano, E. Lin, J. J. McManus, O. K. Sattar, S. Saez, I. Girgis, F. King-Stephens, D. Weber, P. B. Laxer, K. D. Schuele, S. U. Rosenow, J. M. Wu, J. Y. Kam, S. K. Raskin, J. S. Chang, E. F. Shaikhouni, A. Brunner, P. Roland, J. L. Braga, R. M. Knight, R. T. Ofen, N. Johnson, E. L. 2024-11-09 doi:10.1101/2024.11.08.622714 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.11.09.622759v1?rss=1 Bai, D. Mo, S. Zhang, R. Luo, Y. Gao, J. Yang, J. P. Wu, Q. Singh, D. Rahmani, H. Amariuta, T. Grotjahn, D. Zhong, S. Lewis, N. Wang, W. Ideker, T. Xing, E. Xie, P. 2024-11-11 doi:10.1101/2024.11.09.622759 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Surface remodeling and inversion of cell-matrix interactions underlies community recognition and dispersal in Vibrio cholerae biofilms ]]> https://biorxiv.org/content/10.1101/2024.11.11.623042v1?rss=1 Moreau, A. P. Nguyen, D. T. Hinbest, A. Zamora, A. Weerasekera, R. Matej, K. Zhou, X. Sanchez, S. Rodriguez-Brenes, I. A. Tai, J.-S. B. Nadell, C. D. Ng, W.-L. Gordon, V. D. Komarova, N. L. Olson, R. Li, Y. Yan, J. 2024-11-12 doi:10.1101/2024.11.11.623042 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Influenza A virus transcription generates capped cRNAs that activate RIG-I ]]> https://biorxiv.org/content/10.1101/2024.11.12.623191v1?rss=1 Elshina, E. Pitre, E. Mendes, M. Schweibenz, B. French, H. Park, J. W. Wang, W. Marcotrigiano, J. Russell, A. B. te Velthuis, A. J. W. 2024-11-12 doi:10.1101/2024.11.12.623191 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Lysosomes cell autonomously regulate myeloid cell states and immune responses ]]> https://biorxiv.org/content/10.1101/2024.11.11.623074v1?rss=1 Tejwani, L. Balak, C. Skuja, L. L. Tatarakis, D. Rana, A. Fitzgerald, G. A. Ha, C. de Melo, G. L. Sun, E. W. Heffner, C. M. Simon, M. J. Dugas, J. C. Sarrafha, L. Liang, E. Sandmann, T. Glass, C. K. Di Paolo, G. 2024-11-13 doi:10.1101/2024.11.11.623074 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Sequence specificity of an essential nuclear localization sequence in Mcm3 ]]> https://biorxiv.org/content/10.1101/2024.11.14.623588v1?rss=1 Wang, Z. Zhang, Y. J. Zhang, Q.-y. Bilsborrow, K. Leslie, M. Suhandynata, R. T. Zhou, H. 2024-11-14 doi:10.1101/2024.11.14.623588 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ ecPath detects ecDNA in tumors from histopathology images ]]> https://biorxiv.org/content/10.1101/2024.11.13.623494v1?rss=1 Choudhury, M. Liu, L. Yadav, A. Chapman, O. S. Ahmadi, Z. Younis, R. Sharma, C. Goel, N. Sridhar, S. Kenkre, R. Dutta, A. Wang, S. Shulman, E. Dhruba, S. R. Tai, H. D. Tharp, K. Paul, M. Malicki, D. Yip, K. Ruppin, E. Chavez, L. Sinha, S. 2024-11-15 doi:10.1101/2024.11.13.623494 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ A reconstruction of the mammalian secretory pathway identifies mechanisms regulating antibody production ]]> https://biorxiv.org/content/10.1101/2024.11.14.623668v1?rss=1 30% of mammalian proteins, orchestrating their synthesis, modification, trafficking, and quality control. However, its complexity-- spanning multiple organelles and dependent on coordinated protein interactions--limits our ability to decipher how protein secretion is controlled in biomedical and biotechnological applications. To advance such research, we present secRecon--a comprehensive reconstruction of the mammalian secretory pathway, comprising 1,127 manually curated genes organized within an ontology of 77 secretory process terms, annotated with functional roles, subcellular localization, protein interactions, and complex composition. Using secRecon to integrate multi-omics data, we identified distinct secretory topologies in antibody-producing plasma cells compared to CHO cells. Genes within proteostasis, translocation, and N-glycosylation are deficient in CHO cells, highlighting them as potential engineering targets to boost secretion capacity. Applying secRecon to single-cell transcriptomics and SEC-seq data, we uncovered secretory pathway signatures underlying secretion diversity among IgG-secreting plasma cells. Different transcriptomic clusters had unique secretory phenotypes characterized by variations in the unfolded protein response (UPR), endoplasmic reticulum-associated degradation (ERAD), and vesicle trafficking pathways. Additionally, we discovered specific secretory machinery genes as new markers for plasma cell differentiation. These findings demonstrate secRecon can identify mechanisms regulating protein secretion and guide diverse studies in biomedical research and biotechnology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/623668v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@f9f865org.highwire.dtl.DTLVardef@122db7forg.highwire.dtl.DTLVardef@1788a1aorg.highwire.dtl.DTLVardef@b2b2bd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Masson, H. Tat, J. Di Giusto, P. Antonakoudis, A. Shamie, I. Baghdassarian, H. Samoudi, M. Robinson, C. M. Kuo, C.-C. Koga, N. Singh, S. Gezalyan, A. Li, Z. Movsessian, A. Richelle, A. Lewis, N. E. 2024-11-15 doi:10.1101/2024.11.14.623668 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Novel CRITR-seq approach reveals influenza transcription is modulated by NELF and is a key event precipitating an interferon response ]]> https://biorxiv.org/content/10.1101/2024.11.14.623683v1?rss=1 Vicary, A. C. Jordan, S. N. Z. Mendes, M. Swaminath, S. Castro, L. K. Porter, J. S. Russell, A. B. 2024-11-15 doi:10.1101/2024.11.14.623683 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Secreted cytokines from inflammatory macrophages modulate sex differences in valvular interstitial cells on hydrogel biomaterials ]]> https://biorxiv.org/content/10.1101/2024.11.15.623805v1?rss=1 Felix Velez, N. E. Tu, K. Guo, P. Reeves, R. R. Aguado, B. A. 2024-11-15 doi:10.1101/2024.11.15.623805 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Detecting interspecific positive selection using convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2024.11.18.624117v1?rss=1 West, C. Walker, C. R. Arasti, S. Vasilev, V. Xu, X. De Maio, N. Goldman, N. 2024-11-19 doi:10.1101/2024.11.18.624117 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2024.11.18.624205v1?rss=1 Xue, J. Allaband, C. Zuffa, S. Poulsen, O. Meadows, J. Zhou, D. Dorrestein, P. C. Knight, R. Haddad, G. G. 2024-11-19 doi:10.1101/2024.11.18.624205 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation ]]> https://biorxiv.org/content/10.1101/2024.11.18.624210v1?rss=1 Wang, Y. Zhang, Y. Leung, V. Heydari-Seradj, S. Sonmez, U. Servin-Vences, R. Lipomi, D. J. Ye, L. Patapoutian, A. 2024-11-19 doi:10.1101/2024.11.18.624210 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Comparative single-cell lineage bias in human and murine hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2024.11.19.624262v1?rss=1 Shamie, I. Bliss-Moreau, M. Lee, J. C. Mathieu, R. Hoffman, H. M. Geng, B. Lewis, N. E. Zhu, Y. P. Croker, B. A. 2024-11-19 doi:10.1101/2024.11.19.624262 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Context-dependent effects of ivermectin residues on dung insects: Interactions with environmental stressors, size, and sex in a sepsid fly (Sepsis neocynipsea) ]]> https://biorxiv.org/content/10.1101/2024.11.18.623968v1?rss=1 Walker, J. Mathews, B. J. Rohner, P. T. 2024-11-20 doi:10.1101/2024.11.18.623968 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ The Protein Language Visualizer: Sequence Similarity Networks for the Era of Language Models ]]> https://biorxiv.org/content/10.1101/2024.11.19.624229v1?rss=1 Herrera, J. E. Garcia, M. F. M. Bermejo, S. M. Jasso, A. L. Shi, K. Mead, D. Veskimägi, S. M. O'Connor, M. Siordia, A. Roethler, N. Jinich, A. 2024-11-21 doi:10.1101/2024.11.19.624229 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback ]]> https://biorxiv.org/content/10.1101/2024.11.19.624388v1?rss=1 Härer, A. Kurstjens, E. Rennison, D. J. 2024-11-21 doi:10.1101/2024.11.19.624388 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Ancient climate changes and relaxed selection shape cave colonisation in North American cavefishes ]]> https://biorxiv.org/content/10.1101/2024.11.20.624529v1?rss=1 Hart, P. Rincon-Sandoval, M. Melendez-Vazquez, F. Armbruster, J. Troyer, E. Bierstein, O. Gough, B. Betancur-R, R. Niemiller, M. Arcila, D. 2024-11-21 doi:10.1101/2024.11.20.624529 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Age-associated modulation of TREM1/2- expressing macrophages promotes melanoma progression and metastasis ]]> https://biorxiv.org/content/10.1101/2024.11.20.624563v1?rss=1 Scotegagna, M. Murad, R. Bina, P. Feng, Y. Porritt, R. Terskikh, A. Tian, X. Adams, P. D. Vuori, K. Ronai, Z. A. 2024-11-21 doi:10.1101/2024.11.20.624563 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Targeting eIF4G1-dependent translation in melanoma ]]> https://biorxiv.org/content/10.1101/2024.11.20.624566v1?rss=1 Feng, Y. Radaeva, M. Amiri, M. Deshpande, A. Olson, S. Jovanovic, P. Amiri, M. Pass, I. Deng, Q. Lazar, I. Murad, R. Molinolo, A. Kim, H. Sergienko, E. Villaneuva, J. Topisirovic, I. Jackson, M. Sonenberg, N. Cherkasov, A. Ronai, Z. A. 2024-11-21 doi:10.1101/2024.11.20.624566 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway ]]> https://biorxiv.org/content/10.1101/2024.11.21.623953v1?rss=1 Ye, Q. Gong, M. Chambers, L. R. Corbett, K. D. 2024-11-21 doi:10.1101/2024.11.21.623953 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Structural diversity and oligomerization of bacterial ubiquitin-like proteins ]]> https://biorxiv.org/content/10.1101/2024.11.21.623966v1?rss=1 Gong, M. Ye, Q. Gu, Y. Chambers, L. R. Bobkov, A. A. Arakawa, N. K. Matyszewski, M. Corbett, K. D. 2024-11-21 doi:10.1101/2024.11.21.623966 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Diminished gap junction coupling under diabetogenic conditions does not drive loss of functional β-cell sub-populations ]]> https://biorxiv.org/content/10.1101/2024.11.20.624571v1?rss=1 Levitt, C. H. Isaacs, D. Hansen, M. S. Kravets, V. Briggs, J. K. Benninger, R. K. 2024-11-22 doi:10.1101/2024.11.20.624571 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease ]]> https://biorxiv.org/content/10.1101/2024.11.21.624724v1?rss=1 Tibocha-Bonilla, J. D. Santibanez-Palominos, R. Weng, Y. Kumar, M. Zengler, K. 2024-11-22 doi:10.1101/2024.11.21.624724 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Developmentally-regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation ]]> https://biorxiv.org/content/10.1101/2024.11.26.625531v1?rss=1 Riley, E. P. Lyda, J. A. Reyes-Matte, O. Sugie, J. Kasu, I. R. Enustun, E. Armbruster, E. Ravishankar, S. Isaacson, R. L. Camp, A. H. Garrido, J. L. Pogliano, K. 2024-11-26 doi:10.1101/2024.11.26.625531 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Sensory Entrained TMS (seTMS) enhances motor cortex excitability ]]> https://biorxiv.org/content/10.1101/2024.11.26.625537v1?rss=1 Ross, J. M. Forman, L. Gogulski, J. D. Hassan, U. Cline, C. C. Parmigiani, S. Truong, J. Hartford, J. W. Chen, N.-F. Fujioka, T. Makeig, S. Pascual-Leone, A. Keller, C. 2024-11-27 doi:10.1101/2024.11.26.625537 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Stage-specific CAR-mediated signaling generates naive-like, TCR-null CAR T cells from induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2024.11.25.624041v1?rss=1 Yoo, S. P. Yuan, X. Engstrom, C. Chang, P. C. Li, S. Lathrop, L. E. Lagosh, J. A. Seet, C. S. Kohn, D. B. Crooks, G. M. 2024-11-28 doi:10.1101/2024.11.25.624041 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ BPMs regulate Arabidopsis seedling development by promoting auxin-independent degradation of the Aux/IAA protein IAA10 ]]> https://biorxiv.org/content/10.1101/2024.11.26.625463v1?rss=1 Ban, Z. Hou, Y.-J. Ku, E. Zhu, Y. Hu, Y. Karadanaian, N. Zhao, Y. Estelle, M. 2024-11-28 doi:10.1101/2024.11.26.625463 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Glycocalyx-induced formation of membrane tubes ]]> https://biorxiv.org/content/10.1101/2024.11.27.625577v1?rss=1 Xiao, K. Rangamani, P. 2024-11-28 doi:10.1101/2024.11.27.625577 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography ]]> https://biorxiv.org/content/10.1101/2024.12.01.626131v1?rss=1 Zhou, H. Hutchings, J. Shiozaki, M. Zhao, X. Doolittle, L. K. Yang, S. Yan, R. Jean, N. Riggi, M. Yu, Z. Villa, E. Rosen, M. K. 2024-12-02 doi:10.1101/2024.12.01.626131 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ How much is 'enough'? Considerations for functional connectivity reliability in pediatric naturalistic fMRI ]]> https://biorxiv.org/content/10.1101/2024.12.02.626468v1?rss=1 Rai, S. S. Godfrey, K. J. Graff, K. Tansey, R. Merrikh, D. Yin, S. Feigelis, M. Demeter, D. V. Vanderwal, T. Greene, D. J. Bray, S. L. 2024-12-02 doi:10.1101/2024.12.02.626468 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Loss of chromogranin A and catestatin affect pancreatic islet homeostasis, endocrine function, and neurotransmitters ]]> https://biorxiv.org/content/10.1101/2024.11.29.626063v1?rss=1 Muntjewerff, E. M. Epremidze, D. Nezhyva, M. Bootsma, M. Mannaa, A. Ikebuchi, H. Nilsson, A. M. Andren, P. Jansson, E. Mahata, S. K. Christoffersson, G. 2024-12-03 doi:10.1101/2024.11.29.626063 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Macropinocytosis controls metabolic stress-driven CAF subtype identity in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2024.11.29.625709v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@40b38eorg.highwire.dtl.DTLVardef@1cc6a3borg.highwire.dtl.DTLVardef@15283e8org.highwire.dtl.DTLVardef@5214d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhang, Y. Ling, L. Maganti, S. Hope, J. L. Galapate, C. M. Carrette, F. Duong-Polk, K. Bagchi, A. Scott, D. A. Lowy, A. M. Bradley, L. M. Commisso, C. 2024-12-05 doi:10.1101/2024.11.29.625709 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Dynamic Control of Argonautes by a Rapidly Evolving Immunological Switch ]]> https://biorxiv.org/content/10.1101/2024.11.30.626165v1?rss=1 Ewe, C. K. Teichman, G. Knott, M. M. Anava, S. Gingold, H. Bardan Sarmiento, M. Troemel, E. Rechavi, O. 2024-12-05 doi:10.1101/2024.11.30.626165 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Inhibition of RhoA-mediated secretory autophagy in megakaryocytes mitigates myelofibrosis in mice ]]> https://biorxiv.org/content/10.1101/2024.12.04.626665v1?rss=1 Becker, I. C. Barrachina, M. N. Lykins, J. Camacho, V. Stone, A. P. Chua, B. A. Signer, R. A. Machlus, K. R. Whiteheart, S. W. Roweth, H. G. Italiano, J. E. 2024-12-05 doi:10.1101/2024.12.04.626665 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Experimental Phage Evolution Results in Expanded Host Ranges Against MDR and XDR Klebsiella pneumoniae Isolates ]]> https://biorxiv.org/content/10.1101/2024.12.05.627030v1?rss=1 Ghatbale, P. Blanc, A. Leonard, J. Bates, M. Garcia, A. Nunes, D. D. G. Hitchcock, N. Shiach, J. Bardaro, R. Sah, G. P. Ghose, C. Whiteson, K. Schooley, R. White, R. A. Cobian-Guemes, A. G. Meyer, J. R. Pride, D. T. 2024-12-05 doi:10.1101/2024.12.05.627030 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ SUMO Inhibition Plus CD40 Agonism Increases Anti-Tumor Immunogenicity Through Interferon Mediated Macrophage Activation ]]> https://biorxiv.org/content/10.1101/2024.12.03.626688v1?rss=1 Li, K. Y. Courelli, A. Lee, H. J. De Mendoza, T. H. Martsinkovskiy, A. Mose, E. Patel, J. Ng, I. Sun, S. Tharuka, M. D. N. Tiriac, H. Chen, Y. Lowy, A. M. 2024-12-07 doi:10.1101/2024.12.03.626688 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Disruption of basal CXCR4 oligomers impairs oncogenic properties in lymphoid neoplasms ]]> https://biorxiv.org/content/10.1101/2024.12.06.627249v1?rss=1 Mobach, S. Bergkamp, N. D. Ma, Z. Haselager, M. V. Anbuhl, S. M. Jurriens, D. van den Bor, J. Wang, Z. Crudden, C. J. Roos, J. L. Perez Almeria, C. V. Boergonje, R. Lohse, M. J. Bosma, R. Eldering, E. Siderius, M. Wu, W. Spaargaren, M. Tonino, S. H. Kater, A. P. Smit, M. J. Heukers, R. 2024-12-07 doi:10.1101/2024.12.06.627249 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Orchestration of SARS-CoV-2 Nsp4 and host-cell ESCRT proteins induces morphological changes of the endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/2024.12.08.627411v1?rss=1 Kifer, A. Pina, F. Codallos, N. Hermann, A. Ziegler, L. Niwa, M. 2024-12-10 doi:10.1101/2024.12.08.627411 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Comparison of Transcriptional Activation by Corticosteroids of Human MR (Ile-180) and Human MR Haplotype (Ile180Val) ]]> https://biorxiv.org/content/10.1101/2024.12.08.627066v1?rss=1 Katsu, Y. Zhang, J. Ao, Y. Baker, M. E. 2024-12-11 doi:10.1101/2024.12.08.627066 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Histone H3 tail modifications required for meiosis in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.12.09.627563v1?rss=1 Prichard, A. Johansson, M. Kirkpatrick, D. T. Clarke, D. 2024-12-11 doi:10.1101/2024.12.09.627563 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Regulatory interactions between APOBEC3B N- and C-terminal domains ]]> https://biorxiv.org/content/10.1101/2024.12.11.628032v1?rss=1 Braza, K. Demir, O. Ahn, S.-H. Morris, C. Calvo-Tusell, C. McGuire, K. Carpenter, M. Chen, Y. de la Pena Avalos, B. Casalino, L. Aihara, H. Harris, R. S. Amaro, R. E. 2024-12-12 doi:10.1101/2024.12.11.628032 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Mu-opioid receptor activation potentiates excitatory transmission at the habenulo-peduncular synapse ]]> https://biorxiv.org/content/10.1101/2024.12.10.627842v1?rss=1 Singhal, S. M. Szlaga, A. Chen, Y.-C. Conrad, W. S. Hnasko, T. S. 2024-12-16 doi:10.1101/2024.12.10.627842 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Highly recurrent multi-nucleotide mutations in SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2024.12.14.628346v1?rss=1 De Maio, N. Smith, K. Turakhia, Y. Goldman, N. 2024-12-16 doi:10.1101/2024.12.14.628346 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Exploring Bioelectricity with Ace2N-mNeon during Zebrafish Embryogenesis ]]> https://biorxiv.org/content/10.1101/2024.12.12.628143v1?rss=1 Wu, Z. Oliveira Silva, R. Hoessein, R. Marques Trujillo, F. Gotti, J. Ganapathy, S. Gao, Z. Brinks, D. 2024-12-17 doi:10.1101/2024.12.12.628143 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Synergistic Neural Circuits for Novelty and Goal-Directed Behavior ]]> https://biorxiv.org/content/10.1101/2024.12.16.628816v1?rss=1 Elliott, B. L. O'Brien, K. Fain, M. Ellman, L. M. Murty, V. P. 2024-12-17 doi:10.1101/2024.12.16.628816 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Capturing the Conformational Heterogeneity of HSPB1 Chaperone Oligomers at Atomic Resolution ]]> https://biorxiv.org/content/10.1101/2024.12.16.628790v1?rss=1 Berkeley, R. F. Plonski, A. P. Phan, T. Grohe, K. Becker, L. Wegner, S. Herzik, M. A. Mittal, J. Debelouchina, G. T. 2024-12-20 doi:10.1101/2024.12.16.628790 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Predicting Future Development of Stress-Induced Anhedonia From Cortical Dynamics and Facial Expression ]]> https://biorxiv.org/content/10.1101/2024.12.18.629202v1?rss=1 Coley, A. Batra, K. Delahanty, J. Keyes, L. Pamintuan, R. Ramot, A. Hagemann, J. Lee, C. Liu, V. Adivikolanu, H. Cressy, J. Jia, C. Massa, F. LeDuke, D. Gabir, M. Durubeh, B. linderhof, L. Patel, R. Wichmann, R. Li, H. Fischer, K. Pereira, T. Tye, K. 2024-12-20 doi:10.1101/2024.12.18.629202 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures ]]> https://biorxiv.org/content/10.1101/2024.12.18.629229v1?rss=1 Li, H. Pham, M. C. Teng, J. O'Connor, K. C. Noviello, C. M. Hibbs, R. E. 2024-12-20 doi:10.1101/2024.12.18.629229 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Bacteria-powered living materials enable coral larval settlement ]]> https://biorxiv.org/content/10.1101/2024.12.18.629188v1?rss=1 5-fold compared to uncoated control substrates. Brink can be applied as a coating or 3D bioprinted, leading to various potential applications for integration with reef engineering. Our approach underscores the potential of using functional living materials for augmented ecosystem engineering and reef rehabilitation. SynopsisThis study introduces a functional and sustainable bacteria-powered living material that enhances coral settlement, promoting coral reef rehabilitation and ecosystem resilience. ]]> Levy, N. Kundu, S. Freckelton, M. L. Dinasquet, J. Flores, I. Galindo-Martinez, C. T. Tresguerres, M. De La Garza, V. Sun, Y. Karimi, Z. Drury, C. Jury, C. P. Hancock, J. Chen, S. Hadfield, M. G. R3D Consortium, Wangpraseurt, D. 2024-12-21 doi:10.1101/2024.12.18.629188 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ MrHAMER2: high-accuracy long-read RNA sequencing to decode isoform-specific variation in viral transcripts during latency ]]> https://biorxiv.org/content/10.1101/2024.12.19.629526v1?rss=1 Gallardo, C. M. Albert, J. L. Qazi, A. A. Ventura, R. L. Deshmukh, S. Beliakova-Bethell, N. Torbett, B. E. 2024-12-22 doi:10.1101/2024.12.19.629526 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Pearling Drives Mitochondrial DNA Nucleoid Distribution ]]> https://biorxiv.org/content/10.1101/2024.12.21.629917v1?rss=1 Landoni, J. C. Lycas, M. D. Macuada, J. Jaccard, R. Obara, C. J. Moore, A. S. Ben Nejma, S. Hoffman, D. Lippincott-Schwartz, J. Marshall, W. Sturm, G. Manley, S. 2024-12-22 doi:10.1101/2024.12.21.629917 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ A self-limiting Sterile Insect Technique alternative for Ceratitis capitata ]]> https://biorxiv.org/content/10.1101/2024.12.23.629662v1?rss=1 Davydova, S. Liu, J. Liu, Y. Prince, K. Mann, J. Kandul, N. P. Braswell, W. E. Champer, J. Akbari, O. S. Meccariello, A. 2024-12-23 doi:10.1101/2024.12.23.629662 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ FAIRSCAPE: An Evolving AI-readiness Framework for Biomedical Research ]]> https://biorxiv.org/content/10.1101/2024.12.23.629818v1?rss=1 Al Manir, S. Levinson, M. A. Niestroy, J. Churas, C. Parker, J. A. Clark, T. 2024-12-23 doi:10.1101/2024.12.23.629818 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Investigating the Role of Glyoxalase 1 as a Therapeutic Target for Cocaine and Oxycodone Use Disorder ]]> https://biorxiv.org/content/10.1101/2024.12.23.630123v1?rss=1 Alcantara, E. Doyle, M. R. Ortez, C. A. Ilustrisimo, A. Stromberg, B. Barkley-Levenson, A. M. Palmer, A. A. 2024-12-23 doi:10.1101/2024.12.23.630123 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Afadin Sorts Different Retinal Neuron Types into Accurate Cellular Layers ]]> https://biorxiv.org/content/10.1101/2024.12.24.630272v1?rss=1 Lum, M. R. Patel, S. Graham, H. K. Zhao, M. Yi, Y. Li, L. Yao, M. La Torre, A. Della Santina, L. Han, Y. Hu, Y. Welsbie, D. S. Duan, X. 2024-12-25 doi:10.1101/2024.12.24.630272 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Long-Term Reactivation of Multiple Sub-Assemblies in the Hippocampus and Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/2024.12.25.630328v1?rss=1 Tatsuno, M. Fellous, J.-M. 2024-12-25 doi:10.1101/2024.12.25.630328 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina ]]> https://biorxiv.org/content/10.1101/2024.12.28.630634v1?rss=1 Yuan, Y. Biswas, P. Zemke, N. Dang, K. Wu, Y. D Antonio, M. Xie, Y. Yang, Q. Dong, K. Lau, P. K. Li, D. Seng, C. Bartosik, W. Buchanan, J. Lin, L. Lancione, R. Wang, K. Lee, S. Gibbs, Z. Ecker, J. Frazer, K. Wang, T. Preissl, S. Wang, A. Ayyagari, R. Ren, B. 2024-12-29 doi:10.1101/2024.12.28.630634 Cold Spring Harbor Laboratory Press 2024-12-29 <![CDATA[ Catestatin improves heart metabolic flexibility by promoting mitochondrial structure and function ]]> https://biorxiv.org/content/10.1101/2024.12.29.630689v1?rss=1 Chirasani, V. R. Kal, S. Biswas, N. Mahata, S. Tang, K. Pasqua, T. Avolio, E. Jati, S. Bandyopadhyay, G. Head, B. P. Patel, H. H. van den Bogaart, G. Sahoo, D. Senapati, S. Mahata, S. K. 2024-12-30 doi:10.1101/2024.12.29.630689 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Circuit dynamics of approach-avoidance conflict in humans ]]> https://biorxiv.org/content/10.1101/2024.12.31.630927v1?rss=1 Staveland, B. R. Oberschulte, J. Kim-McManus, O. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. J. Hsu, M. Knight, R. T. 2025-01-01 doi:10.1101/2024.12.31.630927 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress ]]> https://biorxiv.org/content/10.1101/2024.12.31.630809v1?rss=1 Shukla, N. Neal, M. Farre, J.-C. Mast, F. D. Truong, L. Simon, T. Miller, L. Aitchison, J. Subramani, S. 2025-01-02 doi:10.1101/2024.12.31.630809 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ A fetal oncogene NUAK2 is an emerging therapeutic target in glioblastoma. ]]> https://biorxiv.org/content/10.1101/2024.12.31.630965v1?rss=1 Jo, H. Dalvi, A. Yang, W. Morozova, E. Munoz, S. Glasgow, S. M. 2025-01-02 doi:10.1101/2024.12.31.630965 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ In vivo itaconate tracing reveals degradation pathway and turnover kinetics ]]> https://biorxiv.org/content/10.1101/2025.01.02.629617v1?rss=1 Cordes, T. F. Willenbockel, H. F. Williams, A. T. Lucas, A. Dowerg, B. Cabrales, P. Metallo, C. M. 2025-01-02 doi:10.1101/2025.01.02.629617 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Dissection of ergosterol metabolism reveals a pathway optimized for membrane phase separation ]]> https://biorxiv.org/content/10.1101/2025.01.05.631358v1?rss=1 Juarez-Contreras, I. Lopes, L. J. S. Holt, J. Yu-Liao, L. O'Shea, K. Ruiz-Ruiz, J. Sodt, A. Budin, I. 2025-01-05 doi:10.1101/2025.01.05.631358 Cold Spring Harbor Laboratory Press 2025-01-05 <![CDATA[ Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.01.06.631511v1?rss=1 Yadav, S. Pan, X. Li, S. Martin, P. L. Hoang, N. Chen, K. Karhadkar, A. Malhotra, J. Zuckerman, A. L. Munan, S. Klose, M. K. Wang, L. Cracan, V. Parkhitko, A. 2025-01-06 doi:10.1101/2025.01.06.631511 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Mirror effect of genomic deletions and duplications on cognitive ability across the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2025.01.06.631492v1?rss=1 Kumar, K. Kazem, S. Huguet, G. Renne, T. Engchuan, W. Jean-Louis, M. Kopal, J. Saci, Z. Thiruvahindrapuram, B. MacDonald, J. R. Mollon, J. Schultz, L. M. Knowles, E. E. M. Porteous, D. Davies, G. Redmond, P. Harris, S. E. Cox, S. R. Schumann, G. Pausova, Z. Greenwood, C. M. T. Paus, T. Scherer, S. W. Almasy, L. Sebat, J. Glahn, D. Dumas, G. Jacquemont, S. 2025-01-07 doi:10.1101/2025.01.06.631492 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif ]]> https://biorxiv.org/content/10.1101/2025.01.06.631586v1?rss=1 Alegrio-Louro, J. Cruz-Becerra, G. Kadonaga, J. T. Leschziner, A. E. 2025-01-08 doi:10.1101/2025.01.06.631586 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation ]]> https://biorxiv.org/content/10.1101/2025.01.07.631779v1?rss=1 Leerberg, D. M. Avillion, G. Priya, R. Stainier, D. Y. R. Yelon, D. 2025-01-08 doi:10.1101/2025.01.07.631779 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ The spinal premotor network driving scratching flexor and extensor alternation ]]> https://biorxiv.org/content/10.1101/2025.01.08.631866v1?rss=1 Yao, M. Nagamori, A. Azim, E. Sharpee, T. Goulding, M. Golomb, D. Gatto, G. 2025-01-08 doi:10.1101/2025.01.08.631866 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Revealing hidden knowledge in amnestic mice ]]> https://biorxiv.org/content/10.1101/2025.01.09.632026v1?rss=1 Santi, A. Moore, S. Fogelson, K. A. Wang, A. Lawlor, J. Amato, J. Burke, K. Lauer, A. M. Kuchibhotla, K. V. 2025-01-09 doi:10.1101/2025.01.09.632026 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Molecular and structural basis of a subfamily of PrfH rescuing both the damaged and intact ribosomes stalled in translation ]]> https://biorxiv.org/content/10.1101/2025.01.09.632186v1?rss=1 Tian, Y. Li, Q. Fatma, S. Jiang, J. Jin, H. Zeng, F. Huang, R. H. 2025-01-10 doi:10.1101/2025.01.09.632186 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor ]]> https://biorxiv.org/content/10.1101/2025.01.09.632202v1?rss=1 Grant, Z. L. Kuang, S. Zhang, S. Horrillo, A. J. Rao, K. S. Kameswaran, V. Joubran, C. Lau, P. K. Dong, K. Yang, B. Bartosik, W. M. Zemke, N. R. Ren, B. Kathiriya, I. S. Pollard, K. S. Bruneau, B. G. 2025-01-12 doi:10.1101/2025.01.09.632202 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Markers of mitochondrial function and oxidative metabolism in female skeletal muscle do not display intrinsic circadian regulation ]]> https://biorxiv.org/content/10.1101/2025.01.08.631231v1?rss=1 Fitzgerald, L. S. Spurrier, C. S. R. Lau, N. Melamed, M. Burnett, L. A. Meyer, G. A. Gui, C. Hevener, A. L. Sanford, J. A. Schenk, S. 2025-01-13 doi:10.1101/2025.01.08.631231 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ T cells are necessary for development of PCOS reproductive symptoms in a letrozole-induced mouse model of PCOS ]]> https://biorxiv.org/content/10.1101/2025.01.08.631835v1?rss=1 Ujagar, N. Velez, L. De Robles, G. Nguyen, C. Wiggins, K. Kim, J. Naidu, N. Angulo, J. A. Kaufmann, A. S. Thackray, V. G. Banaszewska, B. Wysocka, E. Duleba, A. Seldin, M. M. Nicholas, D. A. 2025-01-13 doi:10.1101/2025.01.08.631835 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Extending empirical dynamic modeling to cross-sectional data beyond traditional time series. ]]> https://biorxiv.org/content/10.1101/2025.01.10.628762v1?rss=1 Deyle, E. R. Pao, G. Sugihara, G. 2025-01-15 doi:10.1101/2025.01.10.628762 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Effects of increasing hydrostatic pressures on marine microbial enzymatic activities ]]> https://biorxiv.org/content/10.1101/2025.01.12.632627v1?rss=1 Balmonte, J. P. Arnosti, C. Bartlett, D. H. Caddell, S. Glud, R. N. 2025-01-15 doi:10.1101/2025.01.12.632627 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Unintended bias in the pursuit of collinearity solutions in fMRI analysis ]]> https://biorxiv.org/content/10.1101/2025.01.14.633053v1?rss=1 Mumford, J. A. Demidenko, M. I. Bjork, J. M. Garavan, H. P. Hagler, D. J. Nelson, S. M. Wager, T. D. Poldrack, R. A. 2025-01-15 doi:10.1101/2025.01.14.633053 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Stress Granules Underlie Acute Myeloid Leukemia Stem Cell Survival and Stress Adaptation ]]> https://biorxiv.org/content/10.1101/2025.01.14.632811v1?rss=1 Tajik, A. Tsao, E. Jahangiri, S. Seale, B. Yee, B. A. Naritomi, J. T. Balde, Z. Cathelin, S. Chahi, A. K. Li, L. Chen, H. T. Wong, N. Liu, L. Joshi, P. Moreira, S. McCloskey, C. W. Khan, S. Rothamel, K. L. Boutzen, H. Bansal, S. Zeng, A. G. X. Aigner, S. Lu, Y. Dick, J. E. Kislinger, T. Khokha, R. Minden, M. D. Gingras, A.-C. Yeo, G. W. Hope, K. J. 2025-01-17 doi:10.1101/2025.01.14.632811 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics ]]> https://biorxiv.org/content/10.1101/2025.01.15.633240v1?rss=1 Laub, D. Ho, A. Jaureguy, J. Klie, A. Salem, R. M. McVicker, G. Carter, H. 2025-01-17 doi:10.1101/2025.01.15.633240 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis ]]> https://biorxiv.org/content/10.1101/2025.01.16.633226v1?rss=1 Kim, H. Y. Mizrahi, O. Lee, W. Rosenthal, S. B. Han, C. Yee, B. A. Blue, S. M. Diaz, J. Jonnalagadda, J. Hokutan, K. Jang, H. Ma, C.-T. Bobkov, A. Sergienko, E. Jackson, M. R. Stefanovic, B. Kisseleva, T. Yeo, G. W. Brenner, D. A. 2025-01-18 doi:10.1101/2025.01.16.633226 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ Periodic Obstacles Regulate Membrane Tension Propagation to Enable Localized Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.01.14.632796v1?rss=1 Catala, F. Bonilla-Quintana, M. Sanfeliu-Cerdan, N. Rangamani, P. Krieg, M. 2025-01-19 doi:10.1101/2025.01.14.632796 Cold Spring Harbor Laboratory Press 2025-01-19 <![CDATA[ A Single-Cell Atlas of the Upper Respiratory Epithelium Reveals Heterogeneity in Cell Types and Patterning Strategies ]]> https://biorxiv.org/content/10.1101/2025.01.16.633456v1?rss=1 Sun, X. Foote, A. 2025-01-21 doi:10.1101/2025.01.16.633456 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period ]]> https://biorxiv.org/content/10.1101/2025.01.17.633651v1?rss=1 Gravina Ricci, C. Philpott, J. M. Torgrimson, M. R. Freeberg, A. M. Narasimamurthy,, R. Pecora de Barros, E. Amaro, R. E. Virshup, D. M. McCammon, J. A. Partch, C. L. 2025-01-22 doi:10.1101/2025.01.17.633651 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Regionally specific resting-state beta neural power predicts brain injury and symptom recovery in adolescents with concussion: a longitudinal study ]]> https://biorxiv.org/content/10.1101/2025.01.22.633765v1?rss=1 Edgar, J. C. Blaskey, L. Chen, Y. Podolak, O. E. Murray, D. L. McNamee, M. Konka, K. Berman, J. I. Roberts, T. P. L. Huang, M. Arbogast, K. B. Master, C. L. 2025-01-23 doi:10.1101/2025.01.22.633765 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Dynamic activity of Erg promotes aging of the hematopoietic system ]]> https://biorxiv.org/content/10.1101/2025.01.23.634563v1?rss=1 Yano, M. Sugden, W. Wang, D. Badalamenti, B. Cote, P. Chin, D. Goldstein, J. George, S. Rodrigues-Luiz, G. F. da Rocha, E. L. Li, H. North, T. Gryder, B. Rowe, G. 2025-01-23 doi:10.1101/2025.01.23.634563 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement. ]]> https://biorxiv.org/content/10.1101/2025.01.20.633730v1?rss=1 Sapci, A. O. B. Mirarab, S. 2025-01-24 doi:10.1101/2025.01.20.633730 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Lipid Nanoparticles for the Delivery of CRISPR/Cas9 Machinery to Enable Site-Specific Integration of CFTR and Mutation-Agnostic Disease Rescue ]]> https://biorxiv.org/content/10.1101/2025.01.22.633938v1?rss=1 Foley, R. A. Ayoub, P. G. Sinha, V. Juett, C. Sanoyca, A. Duggan, E. C. Lathrop, L. E. Bhatt, P. Coote, K. Illek, B. Gomperts, B. N. Kohn, D. B. Jonas, S. J. 2025-01-24 doi:10.1101/2025.01.22.633938 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Path of differentiation defines human macrophage identity ]]> https://biorxiv.org/content/10.1101/2025.01.24.634694v1?rss=1 Frenis, K. Badalamenti, B. Mamigonian, O. Weng, C. Wang, D. Fierstein, S. Cote, P. Khong, H. Li, H. Lummertz da Rocha, E. Sankaran, V. Rowe, R. G. 2025-01-24 doi:10.1101/2025.01.24.634694 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis ]]> https://biorxiv.org/content/10.1101/2025.01.23.634541v1?rss=1 11,000 rare genes in 2,377 strains); and 5) The aromatic amino acids and branched chain amino acids pathways are enriched with rare genes, with Acetolactate synthase having 29 distinct genes. Thus, analysis of GPRs across the pangenome reveals a complex dynamic evolutionary history of metabolism, revealing the role of conserved, fragmented, and horizontally transferred metabolic genes. ]]> Ardalani, O. Phaneuf, P. V. Krishnan, J. Li, G. Burrows, J. Nielsen, L. K. Palsson, B. O. 2025-01-25 doi:10.1101/2025.01.23.634541 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ A brainstem map of orofacial rhythms ]]> https://biorxiv.org/content/10.1101/2025.01.27.635041v1?rss=1 Kaku, H. Liu, L. D. Gao, R. West, S. Liao, S.-M. Finkelstein, A. Kleinfeld, D. Thomas, A. Tipparaju, S. L. Svoboda, K. Li, N. 2025-01-27 doi:10.1101/2025.01.27.635041 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Mental exploration of future choices during immobility theta oscillations ]]> https://biorxiv.org/content/10.1101/2025.02.03.636313v1?rss=1 Wang, M. Yuan, L. Leutgeb, S. Leutgeb, J. K. 2025-02-03 doi:10.1101/2025.02.03.636313 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ A CD25-CCR7 complex initiates non-canonical IL-2 signaling ]]> https://biorxiv.org/content/10.1101/2025.02.03.636356v1?rss=1 Kim, S. H. J. Lee, H. Gingras, A. Ley, K. Spangler, J. B. Ginsberg, M. H. 2025-02-04 doi:10.1101/2025.02.03.636356 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D ]]> https://biorxiv.org/content/10.1101/2025.02.01.636064v1?rss=1 Chowdhury, B. Zhu, K. Li, C. Luebeck, J. Chapman, O. S. Kraft, K. Zhang, S. Chavez, L. Henssen, A. G. Mischel, P. S. Chang, H. Bafna, V. 2025-02-06 doi:10.1101/2025.02.01.636064 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Drosophila embryo cellularization is modulated by the viscoelastic dynamics of cortical-membrane interactions ]]> https://biorxiv.org/content/10.1101/2025.02.07.637185v1?rss=1 Stark, K. Bonilla-Quintana, M. Sokac, A. M. Rangamani, P. 2025-02-08 doi:10.1101/2025.02.07.637185 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Cystinosin is involved in Na+/H+ Exchanger 3 trafficking in the proximal tubular cells: new insights in the renal Fanconi syndrome in cystinosis ]]> https://biorxiv.org/content/10.1101/2025.02.12.637793v1?rss=1 Khare, V. Farre, J. C. Rocca, C. Kbaich, M. A. Tang, C. Ma, X. Biederman, K. Mathur, I. Grau, R. A. B.- Sivakumar, A. Chen, R. Catz, S. D. Cherqui, S. 2025-02-12 doi:10.1101/2025.02.12.637793 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods ]]> https://biorxiv.org/content/10.1101/2025.02.13.637864v1?rss=1 Goodheart, J. A. Fiorenza, R. Rio, R. Lopez-Anido, R. N. Martin, N. J. Herrlinger, T. J. Tarvin, R. D. Lyons, D. C. 2025-02-17 doi:10.1101/2025.02.13.637864 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Joint linear modeling of transcriptomics and proteomics is predictive of cancer metastasis ]]> https://biorxiv.org/content/10.1101/2025.02.15.638428v1?rss=1 Sharma, R. Meimetis, N. Begzati, A. Nagar, S. D. Kellman, B. Baghdassarian, H. M. 2025-02-20 doi:10.1101/2025.02.15.638428 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss ]]> https://biorxiv.org/content/10.1101/2025.02.20.639320v1?rss=1 Tabatabaee, Y. Zhang, C. Arasti, S. Mirarab, S. 2025-02-21 doi:10.1101/2025.02.20.639320 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements ]]> https://biorxiv.org/content/10.1101/2025.02.17.638454v1?rss=1 Tiwari, A. Paithane, U. Friedlein, J. Tashiro, K. Saulnier, O. Barbosa, K. O. Trinh, Q. Hall, B. Saha, S. Soni, A. Nakashima, T. Bobkov, A. A. Fujimoto, L. M. Murad, R. Maurya, S. Saraswat, M. Sarmashghi, S. Lange, J. T. Wu, S. Masihi, M. B. Ghosh, S. Hemmati, G. Chapman, O. S. Hendrikse, L. D. James, B. Luebeck, J.-C. Eisemann, T. Tzaridis, T. Rohila, D. Leary, R. Varshney, J. Konety, B. Dehm, S. M. Kawakami, Y. Beroukhim, R. Largaespada, D. Stein, L. D. Chavez, L. Suzuki, H. Weiss, W. A. Zhao, J. Deshpande, A. Wechsler-Reya, R. J. Taylor, M. D. Bag 2025-02-22 doi:10.1101/2025.02.17.638454 Cold Spring Harbor Laboratory Press 2025-02-22 <![CDATA[ D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes ]]> https://biorxiv.org/content/10.1101/2025.03.07.642081v1?rss=1 Kearns, F. Bogetti, A. Calvo-Tussell, C. Braza, M. K. Casalino, L. Gramm, A. J. Braet, S. M. Rosenfeld, M. Rajapaksha, H. Barker, B. Anand, G. S. Chong, L. Ahn, S.-H. Amaro, R. E. 2025-03-11 doi:10.1101/2025.03.07.642081 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Neural Mechanisms Linking Global Maps to First-Person Perspectives ]]> https://biorxiv.org/content/10.1101/2025.03.03.641106v1?rss=1 Lui, H. W. Chrastil, E. R. Nitz, D. A. Krichmar, J. L. 2025-03-12 doi:10.1101/2025.03.03.641106 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Obesity Increases Atherosclerosis Susceptibility via Inter-tissue miR-30e-SLC7A11 Axis ]]> https://biorxiv.org/content/10.1101/2025.03.06.641950v1?rss=1 Wang, C. She, J. Qian, X. Wu, H. Hao, W. Liang, X. Guo, N. Dai, X. He, F. He, S. Zhang, J. Lei, Y. Zhuo, X. Li, H. Luo, Y. Deng, K. Liu, Y. Gao, S. Yuan, X. Liu, H. Bai, T. Xiong, Y. Shyy, J. Y.-J. Yuan, Z.-Y. 2025-03-12 doi:10.1101/2025.03.06.641950 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Glassy Adhesion Dynamics Govern Transitions Between Sub-Diffusive and Super-Diffusive Cell Migration on Viscoelastic Substrates ]]> https://biorxiv.org/content/10.1101/2025.03.11.642113v1?rss=1 Sharma, V. Adebowale, O. Gong, Z. Chaudhuri, O. Shenoy, V. 2025-03-14 doi:10.1101/2025.03.11.642113 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Silencing KRIT1 Partially Reverses the Effects of Disturbed Flow onThe Endothelial Cell Transcriptome ]]> https://biorxiv.org/content/10.1101/2025.03.12.642862v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@a20119org.highwire.dtl.DTLVardef@1f62f68org.highwire.dtl.DTLVardef@1a26d71org.highwire.dtl.DTLVardef@bf3c82_HPS_FORMAT_FIGEXP M_FIG C_FIG Endothelial cells respond to blood flow by expressing transcription factors such as Kruppel-Like Factors 2 and 4 (KLF2 and KLF4). Under oscillatory shear stress (OS) conditions, characterized by disturbed flow, KLF2 and KLF4 are suppressed in endothelial cells, which is linked to an atheroprone gene program that includes increased inflammation and risk of atherosclerosis (unhealthy endothelium). Our work shows that silencing of endothelial KRIT1 under OS increases expression of KLF2 and KLF4 mRNA levels as well as the expression of a protective gene program associated with resilience to inflammation, hypoxia, and angiogenesis, similar to those observed under pulsatile shear stress conditions (healthy endothelium). ]]> Meecham, A. McCurdy, S. Frias-Anaya, E. Li, W. Gallego-Gutierrez, H. Ngyuen, P. Yi-Shuan Li, J. Chien, S. Shyy, J. Y.-J. Ginsberg, M. Lopez-Ramirez, M. A. 2025-03-14 doi:10.1101/2025.03.12.642862 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants ]]> https://biorxiv.org/content/10.1101/2025.03.13.642450v1?rss=1 Patel, A. Banwani, N. Mink, R. Prabhakaran, D. M. Khairnar, S. V. Feist, A. M. Palsson, B. O. Anand, A. 2025-03-15 doi:10.1101/2025.03.13.642450 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Bifunctional Phagocytic Synapse Enhancers for Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.03.13.642658v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@1673fd4org.highwire.dtl.DTLVardef@18fa319org.highwire.dtl.DTLVardef@11cf680org.highwire.dtl.DTLVardef@7b8784_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sabatino, V. Fleisch, S. Tang, C. Muller, F. M. Labao-Almeida, C. Khaw, W. T. Hogan, S. Hicks, D. R. Fontes, M. Coelho, A. R. Yang, W. Sarkar, I. Shome, D. Vidal, A. V. Cabeza-Cabrerizo, M. Rohm, T. Reijmers, R. M. Kaymak, D. Gerster, F. Baker, D. Fior, R. Hutter, G. Bernardes, G. J. L. 2025-03-15 doi:10.1101/2025.03.13.642658 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Genetic risk in endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.03.16.643481v1?rss=1 Mamde, S. Rose, S. Prater, K. E. Cochoit, A. Smith, I. Johnson, C. S. C. Strohbehn, S. Rolf, B. Lin, K. Garden, G. Blue, E. Young, J. E. Jayadev, S. 2025-03-17 doi:10.1101/2025.03.16.643481 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Computational Analysis of Threonine Ladders on Distinct Beta-Solenoid Scaffolds, with Implications for the Design of Novel Antifreeze Proteins ]]> https://biorxiv.org/content/10.1101/2025.03.18.644030v1?rss=1 Calia, C. N. Paesani, F. 2025-03-19 doi:10.1101/2025.03.18.644030 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Uncoupling overeating and fat storage by modulation of different serotonergic receptors ]]> https://biorxiv.org/content/10.1101/2025.03.18.644037v1?rss=1 Clark, C. Zapata, R. C. Newman, I. R. Osborn, O. Petrascheck, M. 2025-03-19 doi:10.1101/2025.03.18.644037 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Pcdh20 is a POU2F3 target gene required for proper tuft cell microvillus formation ]]> https://biorxiv.org/content/10.1101/2025.03.18.644042v1?rss=1 Ankenbauer, K. E. Yang, Y. Chung, C.-Y. Andrade, L. R. Weiser Novak, S. Jarvis, B. Ali Hanel, W. H. Liu, J. Sarkisian, V. Dani, N. Krystofiak, E. Hu, G. Ebrahim, S. Kachar, B. Gong, Q. Wahl, G. Manor, U. Lau, K. DelGiorno, K. E. 2025-03-20 doi:10.1101/2025.03.18.644042 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Differential representations of spatial location by aperiodic and alpha oscillatory activity in working memory ]]> https://biorxiv.org/content/10.1101/2025.03.21.644412v1?rss=1 Bender, A. Zhao, C. Vogel, E. K. Awh, E. Voytek, B. 2025-03-22 doi:10.1101/2025.03.21.644412 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ Glutamate indicators with increased sensitivity and tailored deactivation rates ]]> https://biorxiv.org/content/10.1101/2025.03.20.643984v1?rss=1 Aggarwal, A. Negrean, A. Chen, Y. Iyer, R. Reep, D. Liu, A. Palutla, A. Xie, M. E. MacLennan, B. Hagihara, K. M. Kinsey, L. W. Sun, J. L. Yao, P. Zheng, J. Tsang, A. Tsegaye, G. Zhang, Y. Patel, R. H. Arthur, B. J. Hiblot, J. Leippe, P. Tarnawski, M. Marvin, J. S. Vevea, J. D. Turaga, S. C. Tebo, A. G. Carandini, M. Rossi, L. F. Kleinfeld, D. Konnerth, A. Svoboda, K. Turner, G. C. Hasseman, J. Podgorski, K. 2025-03-24 doi:10.1101/2025.03.20.643984 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ The external rumen of dung beetles: Complex interactions between larvae and their ontogenetic environments shape growth and life history ]]> https://biorxiv.org/content/10.1101/2025.03.21.644625v1?rss=1 McConnell, N. J. Rohner, P. T. 2025-03-24 doi:10.1101/2025.03.21.644625 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Evolved microbial diversity enables combinatoric biosensing in complex environments ]]> https://biorxiv.org/content/10.1101/2025.03.24.645055v1?rss=1 Hasty, J. Chiang, A. J. Csicsery, N. O'Laughlin, R. Baumgart, L. Stasiowski, E. Nguyen, P. Doughty, A. Ashraf, M. Mink, R. Olson, E. C. Ferry, M. Feist, A. M. Hao, N. Zengler, K. 2025-03-24 doi:10.1101/2025.03.24.645055 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Conformational dynamics and activation of membrane-associated human Group IVA cytosolic phospholipase A2 (cPLA2) ]]> https://biorxiv.org/content/10.1101/2025.03.22.644760v1?rss=1 Braza, M. K. E. Dennis, E. A. Amaro, R. E. 2025-03-25 doi:10.1101/2025.03.22.644760 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway ]]> https://biorxiv.org/content/10.1101/2025.03.28.646030v1?rss=1 Doherty, E. E. Adler, B. A. Yoon, P. H. Hsieh, K. Loi, K. Armbuster, E. G. Lahiri, A. Bolling, C. S. Wilcox, X. E. Akkati, A. Iavarone, A. T. Pogliano, J. Doudna, J. A. 2025-03-30 doi:10.1101/2025.03.28.646030 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations ]]> https://biorxiv.org/content/10.1101/2025.03.29.646120v1?rss=1 Kuo, H.-Y. Kryazhimskiy, S. 2025-04-03 doi:10.1101/2025.03.29.646120 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ PEAS: Detection of Clustered Differences in Genomic Data ]]> https://biorxiv.org/content/10.1101/2025.03.31.646436v1?rss=1 Skola, D. D. Glass, C. 2025-04-05 doi:10.1101/2025.03.31.646436 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Glycoengineering of the hepatitis C virus E2 glycoprotein leads to improved biochemical properties and enhanced immunogenicity ]]> https://biorxiv.org/content/10.1101/2025.04.02.646860v1?rss=1 Kulakova, L. Li, K. H. Chiang, A. W. T. Schwoerer, M. P. Schoffelen, S. Elkholy, K. Chao, K. L. Shahid, S. Kumar, B. Murray, N. B. Archer-Hartmann, S. Azadi, P. Voldborg, B. G. Marin, A. Mariuzza, R. A. Andrianov, A. K. Ploss, A. Lewis, N. E. Toth, E. A. Fuerst, T. R. 2025-04-07 doi:10.1101/2025.04.02.646860 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Minimal Correlation but Complementary Diagnostic Utility for Plasma Cell-free RNA and Proteins ]]> https://biorxiv.org/content/10.1101/2025.04.09.647972v1?rss=1 0.93). Analysis of KD subtypes revealed distinct cfRNA and protein signatures, with one group showing molecular similarity to MIS-C. These findings underscore the complementary nature of cfRNA and protein profiling and highlight the utility of integrating multiple blood analytes to improve disease classification and deepen our understanding of complex inflammatory conditions. ]]> Bliss, A. Loy, C. J. Kim, J. Shimizu, C. Lenz, J. S. Belcher, E. Tremoulet, A. H. Burns, J. C. De Vlaminck, I. 2025-04-10 doi:10.1101/2025.04.09.647972 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Selectivity profiles and substrate recognition of Rab phosphorylating kinases ]]> https://biorxiv.org/content/10.1101/2025.04.09.647999v1?rss=1 Chatterjee, D. Dederer, V. Nguyen, L. V. Wendel, M. Abdul Azeez, K. R. Mahesula, S. Stengel, F. Reck-Peterson, S. Mathea, S. 2025-04-10 doi:10.1101/2025.04.09.647999 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ 4D mitochondrial network assumes distinct and predictive phenotypes through human lung and intestinal epithelial development ]]> https://biorxiv.org/content/10.1101/2025.04.09.648043v1?rss=1 McMahon, G. Agarwal, D. Arora, M. Wang, Z. Hakozaki, H. Schöneberg, J. 2025-04-10 doi:10.1101/2025.04.09.648043 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Sexually distinct multi omic responses to progressive endurance exercise training in the rat lung. Findings from MoTrPAC ]]> https://biorxiv.org/content/10.1101/2025.04.10.647997v1?rss=1 Many, G. Sagendorf, T. J. Mitchell, H. D. Sanford, J. A. Cohen, S. Misra, R. Estevao, I. L. Diaz Ludovico, I. Gaul, D. A. Lindholm, M. E. Ushakumary, M. G. Pino, J. Musi, N. Nie, J. Fernandez, F. Ortlund, E. A. Esser, K. A. Bodine, S. C. Schenk, S. Clair, G. C. Adkins, J. N. 2025-04-16 doi:10.1101/2025.04.10.647997 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Benchmarking single cell transcriptome matching methods for incremental growth of reference atlases ]]> https://biorxiv.org/content/10.1101/2025.04.10.648034v1?rss=1 Hu, J. Peng, B. Pankajam, A. V. Xu, B. Deshpande, V. A. Bueckle, A. D. Herr, B. W. Borner, K. Dupont, C. L. Scheuermann, R. H. Zhang, Y. 2025-04-16 doi:10.1101/2025.04.10.648034 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ mspms: A Comprehensive R Package and Graphic Interface for Multiplex Substrate Profiling by Mass Spectrometry Analysis ]]> https://biorxiv.org/content/10.1101/2025.04.14.648679v1?rss=1 Bayne, C. Hurysz, B. Gonzalez, D. J. O'Donoghue, A. 2025-04-19 doi:10.1101/2025.04.14.648679 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Real-world objects scaffold visual working memory for features: Increased neural delay activity when colors are remembered as part of meaningful objects ]]> https://biorxiv.org/content/10.1101/2025.04.15.645785v1?rss=1 Chung, Y. H. Brady, T. F. Stoermer, V. S. 2025-04-20 doi:10.1101/2025.04.15.645785 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Fast and accessible morphology-free functional fluorescence imaging analysis ]]> https://biorxiv.org/content/10.1101/2025.04.15.648462v1?rss=1 Estrada Berlanga, A. A. Kang, G. Kwok, A. Broggini, T. Lawlor, J. Kuchibhotla, K. Kleninfeld, D. Mishne, G. Charles, A. 2025-04-20 doi:10.1101/2025.04.15.648462 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ The 4th GPCR Dock: assessment of blind predictions for GPCR-ligand complexes in the era of AlphaFold ]]> https://biorxiv.org/content/10.1101/2025.04.18.647407v1?rss=1 Chitsazi, R. Wu, Y. GPCR Dock 2021 participants, Stevens, R. C. Zhao, S. Kufareva, I. 2025-04-20 doi:10.1101/2025.04.18.647407 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Synaptic Spine Head Morphodynamics from Graph Grammar Rules for Actin Dynamics ]]> https://biorxiv.org/content/10.1101/2025.04.18.649558v1?rss=1 Hur, M. Bartol, T. Rangamani, P. Sejnowski, T. Mjolsness, E. 2025-04-21 doi:10.1101/2025.04.18.649558 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain ]]> https://biorxiv.org/content/10.1101/2025.04.21.648266v1?rss=1 Zeng, Q. Tian, W. Klein, A. Bartlett, A. Liu, H. Nery, J. R. Castanon, R. G. Osteen, J. Johnson, N. Wang, W. Ding, W. Chen, H. Altshul, J. Kenworthy, M. Valadon, C. Owens, W. Wu, Z. Amaral, M. L. Song, Y. Baez-Becerra, C. T. Cho, S. Chen, C. Willier, J. Cao, S. Rink, J. Lee, J. Barcoma, A. Arzavala, J. Emerson, N. Lu, Y. R. Ren, B. Behrens, M. M. Ecker, J. R. 2025-04-21 doi:10.1101/2025.04.21.648266 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging ]]> https://biorxiv.org/content/10.1101/2025.04.21.649585v1?rss=1 Amaral, M. L. Mamde, S. Miller, M. Hou, X. Arzavala, J. Osteen, J. Walker Smoot, E. Yang, Q. Eisner, E. Zeng, Q. Baez-Becerra, C. T. Olness, J. Kern, J. C. Rink, J. Johnson, N. Barcoma, A. Cho, S. Cao, S. Emerson, N. Lee, J. Willier, J. Loe, T. Jiao, H. Zu, S. Zhu, Q. Preissl, S. Wang, A. Ecker, J. Behrens, M. M. Ren, B. 2025-04-23 doi:10.1101/2025.04.21.649585 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ A Lipid Prodrug Strategy Enhances Targeted Protein Degrader CNS Pharmacokinetics ]]> https://biorxiv.org/content/10.1101/2025.04.18.649560v1?rss=1 Leconte, G. Gadbois, G. E. Sepulveda, Y. Schwarz, A. Chang, E. Suhandynata, R. T. Momper, J. D. Ferguson, F. 2025-04-24 doi:10.1101/2025.04.18.649560 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Domoic acid biosynthesis and genome expansion in Nitzschia navis-varingica ]]> https://biorxiv.org/content/10.1101/2025.04.19.649686v1?rss=1 Wood-Rocca, S. M. Allsing, N. Ashida, Y. Mochizuki, M. Moore, M. L. Füssy, Z. Kotaki, Y. Puilingi, C. Maeno, Y. Beattie, A. W. Allen, A. E. Yotsu-Yamashita, M. Michael, T. P. Moore, B. S. 2025-04-24 doi:10.1101/2025.04.19.649686 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Dynamic Contrastive Learning with Pretrained Deep Language Model Enhances Metagenome Binning for Contigs ]]> https://biorxiv.org/content/10.1101/2025.04.20.649691v1?rss=1 Zou, B. Zhang, Z. Tao, R. Gu, N. Zhang, L. 2025-04-24 doi:10.1101/2025.04.20.649691 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to α-synuclein ]]> https://biorxiv.org/content/10.1101/2025.04.21.649867v1?rss=1 Freuchet, A. Johansson, E. Frazier, A. Litvan, I. Goldman, J. G. Alcalay, R. N. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2025-04-24 doi:10.1101/2025.04.21.649867 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ T cell responses towards PINK1 and α-synuclein are elevated in prodromal Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.04.21.649871v1?rss=1 Johansson, E. Freuchet, A. Williams, G. P. Michealis, T. Frazier, A. Litvan, I. Goldman, J. G. Alcalay, R. N. Standaert, D. G. Amara, A. W. Stover, N. Fon, E. A. Postuma, R. B. Sidney, J. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2025-04-24 doi:10.1101/2025.04.21.649871 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Aperiodic neural timescales in prefrontal cortex dilate with increased task abstraction ]]> https://biorxiv.org/content/10.1101/2025.04.21.649913v1?rss=1 Cellier, D. Riddle, J. Hammonds, R. Frohlich, F. Voytek, B. 2025-04-24 doi:10.1101/2025.04.21.649913 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ DNA Methylation Dynamics of Dose-dependent Acute Exercise, Training Adaptation, and Detraining ]]> https://biorxiv.org/content/10.1101/2025.04.22.650067v1?rss=1 Hariharan, M. Patel, S. Song, H. Rehman, A. Barragan, C. Bartlett, A. Castanon, R. Nery, J. Rothenberg, V. Chen, H. Tian, W. Ding, W. Wang, W. McAdam, J. Graham, Z. Lavin, K. Bamman, M. Broderick, T. Ecker, J. 2025-04-25 doi:10.1101/2025.04.22.650067 Cold Spring Harbor Laboratory Press 2025-04-25 <![CDATA[ Excitation-Inhibition Balance and Fronto-Limbic Connectivity Drive TMS Treatment Outcomes in Refractory Depression ]]> https://biorxiv.org/content/10.1101/2025.04.23.648963v1?rss=1 Momi, D. Wang, Z. Oveisi, M. P. Kadak, K. Bastiaens, S. P. Lissemore, J. I. Noda, Y. Downar, J. Vila Rodriguez, F. Strafella, R. Daskalakis, Z. J. Zrenner, C. Zomorrodi, R. Rolle, C. E. Saggar, M. Williams, N. Keller, C. J. Blumberger, D. M. Voineskos, D. Griffiths, J. D. 2025-04-29 doi:10.1101/2025.04.23.648963 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Estimating fMRI Timescale Maps ]]> https://biorxiv.org/content/10.1101/2025.04.23.650300v1?rss=1 Riegner, G. Davenport, S. Voytek, B. Schwartzman, A. 2025-04-29 doi:10.1101/2025.04.23.650300 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Gut bacteria degrade purines via the 2,8-dioxopurine pathway ]]> https://biorxiv.org/content/10.1101/2025.04.24.650524v1?rss=1 Liu, Y. Zhou, Z. Bryce Jarman, J. Chen, H. Miranda-Velez, M. Terkeltaub, R. Dodd, D. 2025-04-29 doi:10.1101/2025.04.24.650524 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment ]]> https://biorxiv.org/content/10.1101/2025.04.25.650693v1?rss=1 Calderon, R. I. Sah, N. Huang, M. Kittle, R. H. Shaik, W. Chousal, J. N. Kallol, S. Bui, T. Morey, R. Mitre, A. Fogarty, N. M. E. Gerri, C. Zheng, C. DeHoff, P. M. Home, P. Niakan, K. Cook-Andersen, H. Fisch, K. M. Paul, S. Soncin, F. 2025-04-29 doi:10.1101/2025.04.25.650693 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Tulp3 quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress Zfp423 mutations in mice. ]]> https://biorxiv.org/content/10.1101/2025.04.25.650726v1?rss=1 McCoy, C. A. Concepcion, D. Mezody, M. G. Lara, R. Z. Deshpande, O. Liang, C. Long, R. Hamilton, B. A. 2025-04-29 doi:10.1101/2025.04.25.650726 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Maternal Immune Activation Disrupts Epigenomic and Functional Maturation of Cortical Excitatory Neurons ]]> https://biorxiv.org/content/10.1101/2025.04.28.651094v1?rss=1 Lai, C.-Y. Arzavala, J. Duarte, A. P. Wang, S. Li, J. Liu, H. Osteen, J. Castanon, R. G. Nery, J. R. Powell, S. B. Ecker, J. R. Mukamel, E. A. Behrens, M. M. 2025-04-29 doi:10.1101/2025.04.28.651094 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants ]]> https://biorxiv.org/content/10.1101/2025.04.30.651506v1?rss=1 LaMere, S. Xiong, H. Wang, W. LaMere, B. Moshiri, N. 2025-04-30 doi:10.1101/2025.04.30.651506 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Molecular and Spatial Organization of the Primary Olfactory System and its Responses to Social Odors ]]> https://biorxiv.org/content/10.1101/2025.05.02.651832v1?rss=1 Bintu, B. Isogai, Y. Zhuang, X. Dulac, C. 2025-05-02 doi:10.1101/2025.05.02.651832 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Sex-specific transcriptional signatures of oxycodone persist during withdrawal and abstinence in the suprachiasmatic nucleus of heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2025.04.29.651331v1?rss=1 Delorme, T. C. Sambare, S. Williams, B. R. Gamble, M. C. Solberg-Woods, L. Maturin, L. Palmer, A. A. George, O. Logan, R. 2025-05-04 doi:10.1101/2025.04.29.651331 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ CircRNA hypomethylation in the human amygdala implicates FKBP5 in alcohol use disorder ]]> https://biorxiv.org/content/10.1101/2025.05.04.652083v1?rss=1 Ghandour, T. Glausier, J. R. Asok, A. Doyle, M. R. Campo, P. Colnaghi, L. Lewis, D. A. Kandel, D. B. Kandel, E. R. de Guglielmo, G. Huang, S.-s. C. Melas, P. A. 2025-05-04 doi:10.1101/2025.05.04.652083 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ The LOTUS domain of Oskar promotes localisation of both protein and mRNA components of Drosophila germ plasm ]]> https://biorxiv.org/content/10.1101/2025.05.02.651258v1?rss=1 Repouliou, A. Srouji, J. R. Rivard, E. L. Leschziner, A. Extavour, C. G. 2025-05-06 doi:10.1101/2025.05.02.651258 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Mechanisms and Plasticity in Leaves and Leaflets in a Creeping Legume, Mimosa pudica ]]> https://biorxiv.org/content/10.1101/2025.05.03.652067v1?rss=1 Kellogg, M. T. 2025-05-06 doi:10.1101/2025.05.03.652067 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ A Cluster of Acidic Residues in the Cytoplasmic Domain of SARS-CoV-2 Spike is Required for Virion-Incorporation and Infectivity ]]> https://biorxiv.org/content/10.1101/2025.05.04.652125v1?rss=1 Stoneham, C. A. Singh, R. De Leon, A. Tafelmeyer, P. Acosta, F. Fuori, A. Anderson, M. Ramirez, P. W. Schwartzer-Sperber, H. S. Pillai, S. K. Lewinski, M. K. Guatelli, J. 2025-05-06 doi:10.1101/2025.05.04.652125 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Integrative Single-Cell Analysis of Autism Spectrum Disorder Animal Models Reveal Convergent Transcriptomic Dysregulation Involved in Excitatory-Inhibitory Imbalance and Glial Disfunction ]]> https://biorxiv.org/content/10.1101/2025.05.05.651905v1?rss=1 Nani, J. V. Duque, V. J. Muotri, A. R. Mecawi, A. d. S. 2025-05-06 doi:10.1101/2025.05.05.651905 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ A Preclinical Alcohol BioBank: Samples from Behaviorally Characterized HS Rats for AUD Research ]]> https://biorxiv.org/content/10.1101/2025.04.30.651600v1?rss=1 Doyle, M. R. Campo, P. Dirik, S. Balaguer, M. Martinez, A. R. Kallupi, M. de Guglielmo, G. 2025-05-07 doi:10.1101/2025.04.30.651600 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ 3D Printed Nerve Guidance Conduit for Biologics-Free Nerve Regeneration and Vascular Integration ]]> https://biorxiv.org/content/10.1101/2025.04.30.651603v1?rss=1 Schimelman, J. Berry, D. B. Johnson, S. Shi, R. Brown, S. Nguyen, Q. T. Chen, S. 2025-05-07 doi:10.1101/2025.04.30.651603 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression ]]> https://biorxiv.org/content/10.1101/2025.05.01.651692v1?rss=1 Tankka, A. Einstein, J. M. Zhou, C. J. Pham, V. N. Zhang, Y. Naritomi, J. T. Nguyen, G. G. Mizrahi, O. Perelis, M. Sarsam, J. Tan, F. E. Kaufman, D. S. Antal, C. E. Yeo, G. W. 2025-05-07 doi:10.1101/2025.05.01.651692 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Identification and Overexpression of Endogenous Transcription Factors to Enhance Lipid Accumulation in the Commercially Relevant Species Chlamydomonas pacifica ]]> https://biorxiv.org/content/10.1101/2025.05.01.651737v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@8ab995org.highwire.dtl.DTLVardef@19dff1forg.highwire.dtl.DTLVardef@1d865aborg.highwire.dtl.DTLVardef@1fafd12_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com. ]]> Gupta, A. Oliver, A. Molino, J. V. D. Wnuk-Fink, K. M. Tessman, M. Kang, K. Santo, E. d. E. Torres-Tiji, Y. Burkart, M. Mayfield, S. 2025-05-07 doi:10.1101/2025.05.01.651737 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Chronic nicotine treatment enhanced cognition and reduced neuroinflammation in the gp120 transgenic mouse model of neuroHIV ]]> https://biorxiv.org/content/10.1101/2025.05.03.651604v1?rss=1 Ayoub, S. M. Dexter, T. Noback, M. Flesher, M. M. Achim, C. Fields, J. A. Minassian, A. Brody, A. Young, J. W. 2025-05-07 doi:10.1101/2025.05.03.651604 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain ]]> https://biorxiv.org/content/10.1101/2025.05.02.651738v1?rss=1 Brann, D. H. Tsukahara, T. Tau, C. Kalloor, D. Lubash, R. Thamarai Kannan, L. Klimpert, N. Kollo, M. Escamilla-Del-Arenal, M. Bintu, B. Bozza, T. Datta, S. R. 2025-05-08 doi:10.1101/2025.05.02.651738 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Regulation of the branched-chain amino acid pathway and its crosstalk to carbon metabolism in yeast ]]> https://biorxiv.org/content/10.1101/2025.05.05.652184v1?rss=1 Escalera-Fanjul, X. Bolaji, O. Drotleff, B. DeLuna, A. Alexandrov, T. Klipp, E. 2025-05-09 doi:10.1101/2025.05.05.652184 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Competition, Mutualism, and Host Immune Control in a Cancer Microbiome ]]> https://biorxiv.org/content/10.1101/2025.05.06.652496v1?rss=1 Abbasi, E. Abbasi, A. Akcay, E. 2025-05-11 doi:10.1101/2025.05.06.652496 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Structural Covariance Network Properties Predictive of Early Adolescent Alcohol Initiation ]]> https://biorxiv.org/content/10.1101/2025.05.08.652983v1?rss=1 Byrne, H. Visontay, R. Devine, E. K. Wade, N. E. Jacobus, J. Squeglia, L. M. Mewton, L. 2025-05-11 doi:10.1101/2025.05.08.652983 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Synaptic dynamics govern spatial integration in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2025.05.11.653343v1?rss=1 Li, J. Y. Cammarata, C. M. Glickfeld, L. L. 2025-05-12 doi:10.1101/2025.05.11.653343 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Social Exclusion Amplifies Behavioral Responses to Physical Pain via Insular Neuromodulation ]]> https://biorxiv.org/content/10.1101/2025.05.09.653162v1?rss=1 Jia, C. Tran, A. Aloboudi, F. Say, E. Thao, N. Lee, C. R. Batra, K. Nguyen, A. Bal, A. Nono, N. N. Delahanty, J. Chan, M. G. Keyes, L. R. Patel, R. R. Wichmann, R. Taschbach, F. Li, Y. Benna, M. K. Pereira, T. D. Li, H. Tye, K. M. 2025-05-13 doi:10.1101/2025.05.09.653162 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ 1-Deoxysphingolipids dysregulate membrane properties and cargo trafficking in the early secretory pathway ]]> https://biorxiv.org/content/10.1101/2025.05.13.652513v1?rss=1 Tsai, Y.-T. Frederic-Lipp, N. Varma, R. Seidel, O. Laguerre, A. Solorio-Kirpichyan, K. Wong, A. Brea, R. J. McGregor, G. H. Cordes, T. Devaraj, N. K. Kuerschner, L. Neal, S. E. Metallo, C. Budin, I. 2025-05-13 doi:10.1101/2025.05.13.652513 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ FEMA-Long: Modeling unstructured covariances for discovery of time-dependent effects in large-scale longitudinal datasets ]]> https://biorxiv.org/content/10.1101/2025.05.09.653146v1?rss=1 Parekh, P. Parker, N. Pecheva, D. Frei, E. Vaudel, M. Smith, D. M. Rigby, A. Jahołkowski, P. Sonderby, I. E. Birkenaes, V. Bakken, N. R. Fan, C. C. Makowski, C. Kopal, J. Loughnan, R. J. Hagler, D. J. van der Meer, D. Johansson, S. Njolstad, P. R. Jernigan, T. L. Thompson, W. K. Frei, O. Shadrin, A. A. Nichols, T. E. Andreassen, O. A. Dale, A. M. 2025-05-15 doi:10.1101/2025.05.09.653146 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Two-Dimensional Nonlinear Structured Illumination Microscopy with rsEGFP2 ]]> https://biorxiv.org/content/10.1101/2025.05.11.653285v1?rss=1 Li, S. Tamura, R. Banzai, K. Kamiyama, D. Kner, P. 2025-05-15 doi:10.1101/2025.05.11.653285 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Skeletonization of neuronal processes using Discrete Morse techniques from computational topology ]]> https://biorxiv.org/content/10.1101/2025.05.12.653477v1?rss=1 Banerjee, S. Stam, C. Tward, D. J. Savoia, S. Wang, Y. Mitra, P. P. 2025-05-15 doi:10.1101/2025.05.12.653477 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Cellular metabolic state controls mitochondrial RNA kinetics ]]> https://biorxiv.org/content/10.1101/2025.05.13.653903v1?rss=1 Reardon, S. D. Bautista, C. Cole, S. C. Cicero, J. Mishanina, T. V. 2025-05-15 doi:10.1101/2025.05.13.653903 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Sustainable production of plastic-degrading enzymes in Chlamydomonas pacifica ]]> https://biorxiv.org/content/10.1101/2025.05.14.654053v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@10065a3org.highwire.dtl.DTLVardef@110c456org.highwire.dtl.DTLVardef@1c9efc6org.highwire.dtl.DTLVardef@9ceea1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Diaz, C. J. Dutra Molino, J. V. Saucedo, B. Kang, K. do Espirito Santo, E. Tessman, M. Gupta, A. Burkart, M. D. Simkovsky, R. Mayfield, S. 2025-05-15 doi:10.1101/2025.05.14.654053 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Smed-pou4-2 regulates mechanosensory neuron regeneration and function in planarians ]]> https://biorxiv.org/content/10.1101/2025.05.15.654132v1?rss=1 McCubbin, R. A. Auwal, M. A. Wang, S. Zepeda, S. A. Sasik, R. Zeller, R. W. Ross, K. G. Zayas, R. M. 2025-05-16 doi:10.1101/2025.05.15.654132 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Inhibition of phosphodiesterase 4B as a novel therapeutic strategy for the treatment of refractory epilepsy ]]> https://biorxiv.org/content/10.1101/2025.05.13.653835v1?rss=1 Kinch, C. D. Kesler, M. Dogra, D. D. Morin, K. Ibhazehiebo, K. Noschang, C. G. Rho, J. M. Kurrasch, D. 2025-05-17 doi:10.1101/2025.05.13.653835 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ sKL/mKL Transcript Ratio and Protein Localization Define a Species- and Region-Specific Klotho Signature in the CNS and AD Progression ]]> https://biorxiv.org/content/10.1101/2025.05.13.653838v1?rss=1 Blanch, R. Esandi, J. Guerrero-Yagüe, R. Del Rey, J. Roig-Soriano, J. Lleo, A. Carro, E. Mestre-Frances, N. Devau, G. Ferrer, I. Meseguer, A. Lanciego, J. L. Almolda, B. Bosch, A. Chillon, M. 2025-05-17 doi:10.1101/2025.05.13.653838 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ A cold-inducible phospholipid--protein interaction in brown fat mitochondria optimizes thermogenic capacity ]]> https://biorxiv.org/content/10.1101/2025.05.15.654206v1?rss=1 Shimanaka, Y. Tol, M. J. Rocha-Roa, C. Jellinek, M. J. Cui, L. Bender, A. Bedard, A. H. Milner, M. G. Melillo, B. Shoucri, B. M. Wong, A. Williams, K. J. Stiles, L. Shum, M. Weston, T. A. Cohn, W. Whitelegge, J. P. Budin, I. Bertholet, A. M. Cravatt, B. F. Young, S. G. Houten, S. M. Argmann, C. Ford, D. A. Liesa, M. Shirihai, O. S. Vanni, S. Tontonoz, P. 2025-05-18 doi:10.1101/2025.05.15.654206 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Redirecting cytomegalovirus immunity against pancreas cancer for immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.05.15.654308v1?rss=1 Marrocco, R. Patel, J. Medari, R. Salu, P. Lucero-Meza, E. Brunel, S. Martsinkovskiy, A. Sun, S. Gulay, K. Jaljuli, M. Mose, E. Lowy, A. Benedict, C. A. Hurtado de Mendoza, T. 2025-05-19 doi:10.1101/2025.05.15.654308 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ An origin for a eukaryotic lipid transfer protein fold in Asgard archaea ]]> https://biorxiv.org/content/10.1101/2025.05.16.653879v1?rss=1 Lipp, N.-F. Budin, I. 2025-05-20 doi:10.1101/2025.05.16.653879 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Electrical Stimulation Rejuvenates Tunicates: Altered Stem Cell and Immune Activity ]]> https://biorxiv.org/content/10.1101/2025.05.17.654683v1?rss=1 Domen, J. Voskoboynik, Y. Levy, T. Domen, E. M. Ishizuka, K. j. Palmeri, K. j. Anselmi, C. Rolander, T. Neff, N. F. Detweiler, A. M. Weissman, I. L. Gandy, K. L. Sahoo, D. Voskoboynik, A. 2025-05-21 doi:10.1101/2025.05.17.654683 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Analgesic actions of Intrathecal NaV 1.7 antisense in rats: loss of antagonist channel binding, message depletion, and neuraxial distribution of oligonucleotide ]]> https://biorxiv.org/content/10.1101/2025.05.19.654680v1?rss=1 Malange, K. Lemes, J. B. P. Noble, B. Anchondo, Y. Urbina, C. M. Jadhav, S. Dochnal, S. A. Kambalimath, C. Alvarez, P. Fitzsimmons, B. Mazur, C. Kordasiewicz, H. Dore, K. Zhao, H. Yaksh, T. L. 2025-05-21 doi:10.1101/2025.05.19.654680 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ The anterior olfactory nucleus mediates curious exploration evoked by novel odors ]]> https://biorxiv.org/content/10.1101/2025.05.19.654779v1?rss=1 De Plus, R. Martijn, B. Giaffar, H. Eleonore, S. Kondrakiewicz, K. Aydin, C. Haesler, S. 2025-05-21 doi:10.1101/2025.05.19.654779 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Perivascular space mediated the interaction between sleep, and brain functional connectivity in the healthy aging population ]]> https://biorxiv.org/content/10.1101/2025.05.19.654921v1?rss=1 Shih, N.-C. Contreras, J. Mack, W. J. Choupan, J. 2025-05-21 doi:10.1101/2025.05.19.654921 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ 3D organoids containing endothelial and neural cells generation by serial inductions of differentiation on human iPSC-derived embryoid bodies ]]> https://biorxiv.org/content/10.1101/2025.05.20.653559v1?rss=1 Wang, T. Bagnell, A. McDonald, V. Gastfriend, B. D. Steiner, J. P. Elkahloun, A. G. Johnson, K. Langston, R. G. Cookson, M. R. Nath, A. 2025-05-21 doi:10.1101/2025.05.20.653559 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Perinatal Fentanyl Exposure Drives Enduring Addiction Risk and Central Amygdala Gene Dysregulation ]]> https://biorxiv.org/content/10.1101/2025.05.20.655167v1?rss=1 Wood, C. P. Shin, Y. Balaguer, M. G. Campo, P. Dirik, S. Montoya, B. A. Cook, G. M. R. Palermo, G. M. Naghshineh, P. K. Morgan, A. Rahman, S. R. M. U. Palmer, A. A. Telese, F. de Guglielmo, G. 2025-05-21 doi:10.1101/2025.05.20.655167 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Enhanced Production of HCV E1E2 Subunit Vaccine Candidates via Protein-Protein Interaction Identification in Glycoengineered CHO cells ]]> https://biorxiv.org/content/10.1101/2025.05.20.655202v1?rss=1 Wu, M. Y. M. Rocamora, F. Robinson, C. Shin, S. Toth, E. A. Fuerst, T. Maurya, S. Lewis, N. E. 2025-05-23 doi:10.1101/2025.05.20.655202 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus ]]> https://biorxiv.org/content/10.1101/2025.05.22.655576v1?rss=1 Qiao, L. Alfonzo-Mendez, M. Taraska, J. W. Rangamani, P. 2025-05-23 doi:10.1101/2025.05.22.655576 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Association of RhoGEF Ect2 with Desmoplakin Supports RhoA Activity at Intercellular Junctions: Implications for Carvajal Disease ]]> https://biorxiv.org/content/10.1101/2025.05.21.655405v1?rss=1 Zarkoob, H. Kam, C. Koetsier, J. Jaiganesh, A. McCarthy, E. Kelsell, D. Sheikh, F. Godsel, L. M. Green, K. J. 2025-05-24 doi:10.1101/2025.05.21.655405 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography ]]> https://biorxiv.org/content/10.1101/2025.05.23.655666v1?rss=1 Duong, T. E. Diep, D. Conklin, K. Y. Bui, I. Purkerson, J. M. Boone, E. Olness, J. Patel, S. Peng, B. Kern, J. C. Zhao, Z. Misra, R. S. Huyck, H. L. Verheyden, J. M. Borok, Z. Zhang, Y. Scheuermann, R. H. Zhu, Q. Deutsch, G. Hagood, J. S. Sun, X. Zhang, K. Pryhuber, G. 2025-05-24 doi:10.1101/2025.05.23.655666 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ The Mechanism of Histone Ubiquitylation by the ASB9-CUL5 Ubiquitin Ligase ]]> https://biorxiv.org/content/10.1101/2025.05.21.655409v1?rss=1 Komives, E. A. Lee, N. H. Alipranti, F. X. Li, H. Lin, C. P. 2025-05-26 doi:10.1101/2025.05.21.655409 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Systems modeling reveals that store-operated calcium entry modulates force and fatigue during exercise ]]> https://biorxiv.org/content/10.1101/2025.05.22.655415v1?rss=1 Francis, E. A. Hamid, J. Kumar, A. Rangamani, P. 2025-05-27 doi:10.1101/2025.05.22.655415 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Coherent Structures in Active Flows on Dynamic Surfaces ]]> https://biorxiv.org/content/10.1101/2025.05.23.655805v1?rss=1 Santhosh, S. Zhu, C. Fencil, B. Serra, M. 2025-05-27 doi:10.1101/2025.05.23.655805 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites ]]> https://biorxiv.org/content/10.1101/2025.05.26.656146v1?rss=1 Xiang, J. S. Zhao, K. X. Tadri, L. Tamaru, K. Yee, B. A. Rothamel, K. Schmok, J. C. Mueller, J. R. Park, S. S. Madrigal, A. A. McVicar, R. N. Kwong, E. M. Croker, B. A. Clark, A. E. Carlin, A. F. Acevedo, C. McCole, D. F. O'Leary, S. E. Hai, R. Leibel, S. L. Yeo, G. W. 2025-05-28 doi:10.1101/2025.05.26.656146 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Genetic Mapping in Diversity Outbred Mice Identifies Novel Loci and Candidate Genes for Anxiety-Like Behavior and Genetic Subgroups Predictive of Ethanol Consumption ]]> https://biorxiv.org/content/10.1101/2025.05.27.656445v1?rss=1 Tatom, Z. Mignogna, K. M. Macleod, L. Sergi, Z. Miles, M. F. 2025-05-28 doi:10.1101/2025.05.27.656445 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Evaluating the pathogenicity, stability, and stereochemical effects of variants of unknown significance in TREM2 using orthogonal structural analyses ]]> https://biorxiv.org/content/10.1101/2025.05.25.656054v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@c426b1org.highwire.dtl.DTLVardef@1c859f1org.highwire.dtl.DTLVardef@88ea70org.highwire.dtl.DTLVardef@d777f4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pillai, J. Sung, K. Shi, L. Wu, C. 2025-05-29 doi:10.1101/2025.05.25.656054 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Development of a Charge-Resistant Embedding Media for High-Performance Serial Block Face Imaging of Cells and Tissues ]]> https://biorxiv.org/content/10.1101/2025.05.28.656661v1?rss=1 Deerinck, T. Peltier, S. Ellisman, M. 2025-05-29 doi:10.1101/2025.05.28.656661 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Rules of engagement: determinants of chemokine receptor activation and selectivity by CCL27 and CCL28 ]]> https://biorxiv.org/content/10.1101/2025.05.27.656466v1?rss=1 Huang, M. Celniker, A. F. Chitsazi, R. Dyer, D. P. Jansma, A. L. Kufareva, I. Salanga, C. L. Handel, T. 2025-06-01 doi:10.1101/2025.05.27.656466 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Nonequivalence of Zfp423 premature termination codons in mice. ]]> https://biorxiv.org/content/10.1101/2025.05.30.656936v1?rss=1 Concepcion, D. Liang, C. Kim, D. Hamilton, B. A. 2025-06-02 doi:10.1101/2025.05.30.656936 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ The interferon response signature links to increased expression of transposable elements in neutrophils of systemic lupus erythematosus patients ]]> https://biorxiv.org/content/10.1101/2025.05.30.657099v1?rss=1 Arteaga-Vazquez, L. J. Sepulveda, H. Villalobos, B. Suzuki, K. Kalunian, K. Ay, F. Boothby, M. R. Rao, A. 2025-06-03 doi:10.1101/2025.05.30.657099 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ A genetically encoded bifunctional enzyme mitigates redox imbalance and lipotoxicity via engineered Gro3P-Glycerol shunt ]]> https://biorxiv.org/content/10.1101/2025.06.02.657195v1?rss=1 Pan, X. Munan, S. Zuckerman, A. L. Pon, A. Violante, S. Cross, J. R. Shah, H. Cracan, V. 2025-06-05 doi:10.1101/2025.06.02.657195 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Systems modeling and uncertainty quantification of AMP-activated protein kinase signaling ]]> https://biorxiv.org/content/10.1101/2025.06.02.657503v1?rss=1 Linden-Santangeli, N. Zhang, J. Kramer, B. Rangamani, P. 2025-06-05 doi:10.1101/2025.06.02.657503 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ GeneChat: A Multi-Modal Large Language Model for Gene Function Prediction ]]> https://biorxiv.org/content/10.1101/2025.06.05.658031v1?rss=1 Dhanasekar, S. Saranathan, A. Xie, P. 2025-06-06 doi:10.1101/2025.06.05.658031 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Comprehensive molecular impact mapping of common and rare variants at GWAS loci ]]> https://biorxiv.org/content/10.1101/2025.06.05.658079v1?rss=1 7 times as many contexts as Enformer, which allows for better detection of variant effects at expression quantitative trait loci (eQTLs). We also introduce DNACipher Deep Variant Impact Mapping (DVIM), a method to identify variants with molecular effects at genome-wide association study (GWAS) loci. Application of DVIM to type 1 diabetes (T1D) reduced the mean fine-mapping credible set size from 24 to 1.4 variants per signal. DVIM variants had significantly higher fine-mapping posterior probabilities, and their predicted effects were supported by single-nucleus ATAC-seq and luciferase assays. DVIM also detected 6547 rare variants with molecular effects at 96% of GWAS T1D loci, and these were enriched for associations with immune traits. In summary, DNACipher DVIM prioritises common and rare variants at GWAS loci by predicting molecular effects across a broad range of contexts. ]]> Balderson, B. Tule, S. Okino, M.-L. Rieger, W. J. Corban, S. Jaureguy, J. Palpant, N. Gaulton, K. J. Boden, M. McVicker, G. 2025-06-06 doi:10.1101/2025.06.05.658079 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Examining the Role of Extrachromosomal DNA in 1,216 Lung Cancers ]]> https://biorxiv.org/content/10.1101/2025.06.03.657117v1?rss=1 Khandekar, A. Hoang, P. H. Luebeck, J. Diaz-Gay, M. Zhao, W. McElderry, J. P. Hartman, C. Miraftab, M. Lee, O. W. Barnao, K. M. Bergstrom, E. N. Yang, Y. Nowak, M. A. Rothman, N. Homer, R. Yang, S.-R. Lan, Q. Wedge, D. C. Yang, L. Chanock, S. J. Zhang, T. Alexandrov, L. B. Landi, M. T. 2025-06-07 doi:10.1101/2025.06.03.657117 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Parkinson's disease-vulnerable and -resilient dopamine neurons display opposite responses to excitatory input ]]> https://biorxiv.org/content/10.1101/2025.06.03.657460v1?rss=1 Hadjas, L. C. Kollman, G. J. Linderhof, L. Xia, M. Mansur, S. Saint-Pierre, M. Lim, B. Lee, E. B. Cicchetti, F. Awatramani, R. Hollon, N. G. Hnasko, T. S. 2025-06-07 doi:10.1101/2025.06.03.657460 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ TH5487 specifically targets NLRP3 in FCAS patients resistant to MCC950 ]]> https://biorxiv.org/content/10.1101/2025.06.05.658156v1?rss=1 Lackner, A. Leonidas, L. Macapagal, A. Lee, H. Xu, H. Qiu, Y. Campos, M. Cabral, J. E. Onyuru, J. Kulkarni, S. Albrecht, L. Hoffman, H. M. McNulty, R. 2025-06-09 doi:10.1101/2025.06.05.658156 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2025.06.06.658321v1?rss=1 Kazachkova, M. Otlu-Saritas, B. Diaz-Gay, M. Abbasi, A. Moody, S. Perdomo, S. Wedge, D. C. Brennan, P. Stratton, M. Alexandrov, L. B. 2025-06-09 doi:10.1101/2025.06.06.658321 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Interlinked roles for HEB and Id3 in fetal gamma-delta T cell commitment and functional programming ]]> https://biorxiv.org/content/10.1101/2025.06.08.658490v1?rss=1 Selvaratnam, J. S. Barbosa da Rocha, J. D. Rajan, V. Wang, H. Reddy, E. C. Gams, M. S. Murre, C. Guidos, C. J. Zuniga-Pflucker, J. C. Anderson, M. K. 2025-06-09 doi:10.1101/2025.06.08.658490 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Constitutive activation and allosteric mechanisms underlying Gi/Gq signaling bias in SUCNR1 revealed by AlphaFold-based modeling and enhanced sampling simulations ]]> https://biorxiv.org/content/10.1101/2025.06.08.658530v1?rss=1 Shenol, A. Petersen, J. E. Lückmann, M. Frimurer, T. McCammon, J. A. Schwartz, T. W. Ma, W. 2025-06-10 doi:10.1101/2025.06.08.658530 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ A single-cell fixed RNA profiling of liver fibrosis progression and regression reveals SEMA4D and LMCD1 as key mediators of fibrogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.12.657772v1?rss=1 Pham, D. M. Thuy, L. T. T. Hoang, H. Nguyen, H. T. Pham, A. T. Ikenaga, H. Fuji, H. Yuasa, H. Matsubara, T. Vu, H. T. Yi, C. Yamagishi, R. Ohtani, N. Oikawa, D. Tokunaga, F. Kisseleva, T. Brenner, D. Iwakiri, Y. Sancho, J. G. Kawada, N. 2025-06-12 doi:10.1101/2025.06.12.657772 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Boolean Network Modeling Identifies Cognitive Resilience in the First Murine Model of Asymptomatic Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2025.06.11.659207v1?rss=1 Jati, S. Taheri, S. Kal, S. Sinha, S. Head, B. P. Mahata, S. K. Sahoo, D. 2025-06-13 doi:10.1101/2025.06.11.659207 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Conditions enabling the persistence of cooperating ribozymes without cellular encapsulation ]]> https://biorxiv.org/content/10.1101/2025.06.10.658808v1?rss=1 Peng, Z. Plum, A. M. Kartha, R. Jacobson, E. M. Baum, D. A. 2025-06-14 doi:10.1101/2025.06.10.658808 Cold Spring Harbor Laboratory Press 2025-06-14 <![CDATA[ Enhanced Sampling on Domain/Motif Level with Kinetic Accelerated Molecular Dynamics ]]> https://biorxiv.org/content/10.1101/2025.06.14.659665v1?rss=1 Wei, H. 2025-06-14 doi:10.1101/2025.06.14.659665 Cold Spring Harbor Laboratory Press 2025-06-14 <![CDATA[ Environmental modifications of dung beetle larvae shape their growth and life history. ]]> https://biorxiv.org/content/10.1101/2025.06.10.658956v1?rss=1 McConnell, N. J. Rohner, P. T. 2025-06-15 doi:10.1101/2025.06.10.658956 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Condensate-driven chromatin organization via elastocapillary interactions ]]> https://biorxiv.org/content/10.1101/2025.06.12.659369v1?rss=1 Zhao, H. Strom, A. R. Eeftens, J. M. Haataja, M. Kosmrlj, A. Brangwynne, C. P. 2025-06-15 doi:10.1101/2025.06.12.659369 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Mechanochemical feedback between confinement and actin crosslinking drives the shape dynamics of liquid-like droplets ]]> https://biorxiv.org/content/10.1101/2025.06.13.659650v1?rss=1 Mansour, D. Jordan, D. Walker, C. Chandrasekaran, A. Lee, C. T. Graham, K. Stachowiak, J. Rangamani, P. 2025-06-15 doi:10.1101/2025.06.13.659650 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Bipartite chromatin recognition by Hop1 from two diverged holozoa ]]> https://biorxiv.org/content/10.1101/2025.06.14.659699v1?rss=1 Rodriguez, A. A. Cirulli, A. E. Chau, K. Nguyen, J. Ye, Q. Corbett, K. D. 2025-06-15 doi:10.1101/2025.06.14.659699 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Formation of extracellular vesicles depends on mechanical feedback of the cortex and the glycocalyx ]]> https://biorxiv.org/content/10.1101/2025.06.14.659723v1?rss=1 Xiao, K. Rangamani, P. 2025-06-15 doi:10.1101/2025.06.14.659723 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Terrigenous inputs link nutrient dynamics to microbial communities in a tropical lagoon ]]> https://biorxiv.org/content/10.1101/2025.06.11.659169v1?rss=1 John, C. Silbiger, N. J. Adam, T. C. Barnas, D. M. Bistolas, K. S. Carpenter, R. C. Castaneda, N. Donahue, M. J. Donovan, M. K. Enright, L. N. Epstein, H. E. Gallagher, J. P. Jorissen, H. Kerlin, J. R. Leidholt, S. L. McLachlan, R. H. Molina, N. Mullenmeister, C. A. Neumann, K. Renzi, J. J. Silva, D. P. Speare, K. E. Swift, S. Vompe, A. D. Kelly, L. W. Zeff, M. Nelson, C. E. Thurber, R. V. Burkepile, D. E. 2025-06-17 doi:10.1101/2025.06.11.659169 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Improving Recombinant Antibody Production Using FcBAR: An In Situ Approach to Detect and Amplify Protein-Protein Interactions ]]> https://biorxiv.org/content/10.1101/2025.06.12.659199v1?rss=1 Wu, M. Y. M. Rocamora, F. Samoudi, M. Robinson, C. Kuo, C.-C. Pristovsek, N. Grav, L. M. Kildegaard, H. F. Lee, G. M. Campos, A. R. Lewis, N. E. 2025-06-17 doi:10.1101/2025.06.12.659199 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Spectral disruption of inter-hemispheric resting-state BOLD coherence at vasomotor frequency (~0.1 Hz) links vascular dysfunction to functional connectivity loss in carotid artery stenosis ]]> https://biorxiv.org/content/10.1101/2025.06.12.659378v1?rss=1 Choi, S. Hoffmann, G. Schneider, S. Kaczmarz, S. Kleinfeld, D. Yu, X. Sorg, C. Preibisch, C. 2025-06-17 doi:10.1101/2025.06.12.659378 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Thymic DC2 are heterogenous and include a novel population of transitional dendritic cells ]]> https://biorxiv.org/content/10.1101/2025.06.13.659520v1?rss=1 Hogquist, K. A. Voboril, M. Sulczewski, F. B. Martinez, R. J. Ashby, K. M. Valerio, M. M. Idoyaga, J. 2025-06-18 doi:10.1101/2025.06.13.659520 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Gastric cancer treatment target identified from an accelerated Helicobacter-induced gastric cancer mouse model ]]> https://biorxiv.org/content/10.1101/2025.06.14.659641v1?rss=1 Kurstjens, E. M. Cox, K. Bali, P. Amirfakhri, S. Hernandez, J. Lozano-Pope, I. Benner, C. Bouvet, M. Obonyo, M. 2025-06-20 doi:10.1101/2025.06.14.659641 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Single cell transcriptomics in a treatment-segregated cohort exposes a STAT3-regulated therapeutic gap in idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.06.16.659944v1?rss=1 McKenna, N. Ochsner, S. A. Cohen, A. W. Cala-Garcia, J. Echartea, M. E. Grimm, S. L. Poli, F. Castillo, R. C. Zuluaga, J. D. Poli, S. Adams, T. S. Pineda, R. Moss, B. Ryter, S. Pillich, R. T. Villalba, J. Kato, K. Hecker, L. Celada, L. J. Sauler, M. Koenigshoff, M. Kaminski, N. Raby, B. Agarwal, S. K. Tsoyi, K. Coarfa, C. Rosas, I. 2025-06-21 doi:10.1101/2025.06.16.659944 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ A balance between nucleating and elongating actin filaments controls deformation of protein condensates ]]> https://biorxiv.org/content/10.1101/2025.06.18.660423v1?rss=1 Walker, C. Mansour, D. Effiong, U. Jordan, D. Wang, L. Lafer, E. M. Alvarado, J. Belardi, B. Rangamani, P. Stachowiak, J. C. Rangamani, P. 2025-06-21 doi:10.1101/2025.06.18.660423 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ The chromatin remodeler LET-418/Mi-2 regulates the intracellular pathogen response in the C. elegans intestine ]]> https://biorxiv.org/content/10.1101/2025.06.17.659900v1?rss=1 Rajopadhye, S. A. Lazetic, V. Rodriguez Crespo, D. Troemel, E. Meister, P. Wicky, C. 2025-06-22 doi:10.1101/2025.06.17.659900 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Development of PROTACs for targeted degradation of oncogenic TRK fusions ]]> https://biorxiv.org/content/10.1101/2025.06.18.660465v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@6c78f7org.highwire.dtl.DTLVardef@179dcdeorg.highwire.dtl.DTLVardef@1939988org.highwire.dtl.DTLVardef@144c718_HPS_FORMAT_FIGEXP M_FIG C_FIG JWJ-01-378 recruits cereblon (CRBN) to induce potent and selective degradation of oncogenic TRK fusions, leading to a collapse in downstream signaling and loss of cancer cell viability. Graphical abstract was created using Biorender.com. ]]> Kumar, S. Jiang, J. Donald-Paladino, M. S. Chen, J. Gutierrez, A. Federation, A. J. Szulzewsky, F. Holland, E. C. Ferguson, F. M. Nabet, B. 2025-06-24 doi:10.1101/2025.06.18.660465 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Ultra-fast and Efficient Network Embedding for Gigascale Biological Datasets ]]> https://biorxiv.org/content/10.1101/2025.06.18.660497v1?rss=1 Knight, R. Zhao, J. Pierre Both, J. 2025-06-24 doi:10.1101/2025.06.18.660497 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ The titin N2A-MARP signalosome constrains muscle longitudinal hypertrophy in response to stretch ]]> https://biorxiv.org/content/10.1101/2025.06.19.660595v1?rss=1 Van der Pijl, R. Gohlke, J. Strom, J. Peters, E. Shen, S. Conijn, S. Hourani, Z. Lange, S. Chen, J. Langlais, P. Labeit, S. Granzier, H. L. Ottenheijm, C. 2025-06-25 doi:10.1101/2025.06.19.660595 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Simulating Scalp EEG from Ultrahigh-Density ECoG Data Illustrates Cortex to Scalp Projection Patterns ]]> https://biorxiv.org/content/10.1101/2025.06.24.660870v1?rss=1 Shirazi, S. Y. Onton, J. Makeig, S. 2025-06-25 doi:10.1101/2025.06.24.660870 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Microbiome variations in osteoarthritis reflect aging and metabolic factors, not the disease ]]> https://biorxiv.org/content/10.1101/2025.06.24.661261v1?rss=1 Bevc, K. Malfertheiner, L. Neuenschwander, S. Tran, V. D. T. Pagni, M. Pantiukh, K. Jagura, M. Niiranen, T. Knight, R. T. Salomaa, V. Havulinna, A. S. Org, E. Eklund, K. K. Barreto, G. Zenobi, M. von Mering, C. 2025-06-25 doi:10.1101/2025.06.24.661261 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation ]]> https://biorxiv.org/content/10.1101/2025.06.25.661606v1?rss=1 Cheng, C. Bennett, B. D. Savalia, P. Asrari, H. Biel, C. Evans, K. A. Tang, R. Thrash, C. 2025-06-25 doi:10.1101/2025.06.25.661606 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ The microbial fingerprint: fine-scale environmental, genetic, and temporal factors drive the reef metagenome during coral spawning ]]> https://biorxiv.org/content/10.1101/2025.06.23.661127v1?rss=1 Scott, C. B. Nixon, E. N. Huzar, A. K. Matz, M. V. 2025-06-27 doi:10.1101/2025.06.23.661127 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Accurate Prediction of ecDNA in Interphase Cancer Cells using Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/2025.06.23.661188v1?rss=1 Rajkumar, U. Prasad, G. Curtis, E. J. Wong, I. T.-L. Yan, X. Zhang, S. Brückner, L. Turner, K. Wiese, J. Wahl, J. Wu, S. Theissen, J. Fischer, M. Chang, H. Y. Henssen, A. G. Mischel, P. S. Bafna, V. 2025-06-27 doi:10.1101/2025.06.23.661188 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Interleaved Replay of Novel and Familiar Memory Traces During Slow-Wave Sleep Prevents Catastrophic Forgetting ]]> https://biorxiv.org/content/10.1101/2025.06.25.661579v1?rss=1 Golden, R. Saxena, R. Gonzalez, O. C. Delanois, J. E. Kilianski, S. McNaughton, B. L. Bazhenov, M. 2025-06-29 doi:10.1101/2025.06.25.661579 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain ]]> https://biorxiv.org/content/10.1101/2025.06.25.661599v1?rss=1 Huang, H. Shi, C. H. Yang, W. Crespo, J. P. Bhatnagar, J. Curatolo, J. Murad, R. Shah, P. Campos, A. Houser, A. Porritt, R. A. Zhang, T. Xiao, Q. Feng, S. Yip, K. Y. Huang, T. Y. 2025-06-29 doi:10.1101/2025.06.25.661599 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Long-Term Effects of Adolescent 5F-MDMB-PICA Intravenous self-administration: Neurobehavioral Consequences and medial Prefrontal Cortex Dysfunction in Adult Mice ]]> https://biorxiv.org/content/10.1101/2025.06.26.661592v1?rss=1 Caria, F. Libster, A. Desfor, S. Telese, F. Di Chiara, G. De Luca, M. A. 2025-06-29 doi:10.1101/2025.06.26.661592 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Simultaneous recording of spikes and calcium signals in odor-evoked responses of Drosophila antennal neurons ]]> https://biorxiv.org/content/10.1101/2025.06.27.662059v1?rss=1 Xiao, Y. Wu, S.-T. Xuan, Y. Rifkin, S. Su, C.-Y. 2025-06-29 doi:10.1101/2025.06.27.662059 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Improved Genotype Inference Reveals Cis- and Trans-Driven Variation in the Loss-of-Heterozygosity Rates in Yeast ]]> https://biorxiv.org/content/10.1101/2025.06.26.661874v1?rss=1 Overton, M. S. Kryazhimskiy, S. 2025-06-30 doi:10.1101/2025.06.26.661874 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ CD47 blockade enhances immunoradiotherapy response in head and neck squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.06.29.662015v1?rss=1 Monther, A. Al-Msari, R. Saddawi-Konefka, R. Fassardi, S. Tang, C. Philips, C. Sen, P. Mohammadzadeh, P. Decker, K. Miyauchi, S. Roy, S. Jones, R. Gutkind, S. Sharabi, A. Califano, J. 2025-06-30 doi:10.1101/2025.06.29.662015 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles ]]> https://biorxiv.org/content/10.1101/2025.06.30.662372v1?rss=1 Zuffa, S. Thomas, S. Mohanty, I. El Abiead, Y. Deleray, V. Kvitne, K. E. Kousha, A. Suzuki, E. Tsai, C.-M. Nguyen, G. Ho, B. Liu, G. Y. Nizet, V. Dorrestein, P. C. Askarian, F. Tsunoda, S. M. 2025-06-30 doi:10.1101/2025.06.30.662372 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Persistent Activation of Endothelial Cells is Linked to Thrombosis and Inflammation in Cerebral Cavernous Malformation Disease ]]> https://biorxiv.org/content/10.1101/2025.06.29.662238v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1297edforg.highwire.dtl.DTLVardef@1488e27org.highwire.dtl.DTLVardef@6cae62org.highwire.dtl.DTLVardef@12cb282_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gallego-Gutierrez, H. Frias-Anaya, E. Bui, C. Zhao, L. Hsu, E. Indralingam, H. S. Korbelin, J. Trejo, J. Steinberg, J. Zemke, N. R. Lopez-Ramirez, M. A. 2025-07-02 doi:10.1101/2025.06.29.662238 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Genetics of growth rate in induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.07.02.662844v1?rss=1 Lee, B. N. Taylor, H. J. Cipriani, F. Narisu, N. Robertson, C. C. Swift, A. J. Sinha, N. Yan, T. Bonnycastle, L. L. Dale, N. Butt, A. Parsaud, H. Semrau, S. NYSCF Global Stem Cell Array Team, GENESiPS Consortium, iPSCORE Consortium, Knowles, J. W. Carcamo-Orive, I. D'Antonio-Chronowska, A. Frazer, K. A. Biesecker, L. G. Noggle, S. Erdos, M. R. Paull, D. Collins, F. S. Taylor, D. L. 2025-07-03 doi:10.1101/2025.07.02.662844 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ A novel subtyping method for TNBC with implications for prognosis and therapy ]]> https://biorxiv.org/content/10.1101/2025.07.04.663242v1?rss=1 Mesrizadeh, Z. Mukund, K. Zabaleta, J. Valle, L. D. Tomsic, J. Neuhausen, S. L. Ding, Y. C. Seewaldt, V. Ochoa, A. Miele, L. Subramaniam, S. 2025-07-08 doi:10.1101/2025.07.04.663242 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Targeting Aurora kinases as essential cell cycle regulators to deliver multi-stage antimalarials against Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2025.07.10.663886v1?rss=1 1000x selectivity towards the parasite without concerns about mammalian cell toxicity. Importantly, we identified PfArk1 as the principal vulnerable Ark family member, with specific inhibition of PfArk1 as the primary target for hesperadin and the human anaplastic lymphoma kinase (ALK) inhibitor TAE684. Hesperadins whole-cell and protein activity validates it as a unique PfArk1 tool compound. Inhibition of PfArk1 results in the parasites inability to complete mitotic processes, presenting with unsegregated, multi-lobed nuclei caused by aberrant microtubule organization. This suggests that PfArk1 is the main Aur mitotic kinase in proliferative stages of Plasmodium, characterized by bifunctional AurA and B activity. This paves the way for drug discovery campaigns based on hesperadin targeting PfArk1. ]]> Langeveld, H. Maepa, K. Maree, M. Thibaud, J. L. Salomane, N. Bridgwater, R. Famodimu, M. T. Godoy, L. C. Pasaje, C. F. A. Boonyalai, N. de Souza, M. L. Fong, J. Rabie, T. Theart, R. P. Ghidelli-Disse, S. Niles, J. C. Lee, M. C. S. Winzeler, E. A. Delves, M. J. Chibale, K. Wicht, K. J. Coulson, L. B. Birkholtz, L.-M. 2025-07-10 doi:10.1101/2025.07.10.663886 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS ]]> https://biorxiv.org/content/10.1101/2025.07.08.663251v1?rss=1 Sang, X. Jiao, H. Meng, Q. Fang, X. Sundaram, K. S. Zhou, J. Xu, Y. Alvarado, A. I. W. Nuryyev, R. L. Ourenik, J. Ourednik, V. Huang, I. S. Liu, X. Mei, Y. Qian, T. Ciechanover, A. Pizzo, D. P. Lane, M. A. Zholudeva, L. V. An, J. Snyder, E. Y. Hu, H. Huang, Z. 2025-07-11 doi:10.1101/2025.07.08.663251 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ The mevalonate pathway of isoprenoid biosynthesis supports metabolic flexibility in Mycobacterium marinum ]]> https://biorxiv.org/content/10.1101/2025.07.11.664281v1?rss=1 Qabar, C. Baidoo, E. E. Akyuz Turumtay, E. Qayum, T. Keasling, J. D. Madigan, C. Portnoy, D. A. Cox, J. S. 2025-07-14 doi:10.1101/2025.07.11.664281 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ An increase of NPY1 expression leads to inhibitory phosphorylation of PIN-FORMED (PIN) proteins and suppression of pinoid (pid) null mutants ]]> https://biorxiv.org/content/10.1101/2025.07.14.664678v1?rss=1 Mudgett, M. Shen, Z. Kang, R. Dai, X. Briggs, S. P. Zhao, Y. 2025-07-14 doi:10.1101/2025.07.14.664678 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Complementary cortical and thalamic contributions to cell-type-specific striatal activity dynamics during movement ]]> https://biorxiv.org/content/10.1101/2025.07.11.664473v1?rss=1 Gjoni, E. Sristi, R. D. Liu, H. Dror, S. Lin, X. O'Neil, K. Arroyo, O. M. Hong, S. W. Kim, H. Liu, J. Blumenstock, S. Lim, B. Mishne, G. Komiyama, T. 2025-07-17 doi:10.1101/2025.07.11.664473 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Improved Mutation Detection in Duplex Sequencing Data with Sample-Specific Error Profiles ]]> https://biorxiv.org/content/10.1101/2025.07.13.664565v1?rss=1 Cheng, Y. Nandi, S. Culibrk, L. Kristin, A. Stuewe, I. Al-Azzam, S. Petljak, M. Alexandrov, L. B. 2025-07-18 doi:10.1101/2025.07.13.664565 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Genome-wide association study of cocaine self-administration behavior in Heterogeneous Stock rats ]]> https://biorxiv.org/content/10.1101/2025.07.17.660811v1?rss=1 Lara, M. K. Carrette, L. L. G. Sanches, T. M. Polesskaya, O. Avelar, A. Beeson, A. Beldjoud, H. Boomhower, B. Brennan, M. Chen, D. China, L. Chitre, A. S. Conlisk, D. E. Fannon, M. Johnson, B. B. Keung, E. Kimbrough, A. Kononoff, J. Martinez, A. R. Maturin, L. Nguyen, K.-M. Morgan, A. Mosquera, J. Othman, D. Plasil, S. L. Ramborger, J. Schweitzer, P. Sedighim, S. Seshie, O. Shankar, K. Sichel, B. Simpson, S. Smith, L. C. Sneddon, E. A. Tieu, L. Velarde, N. Zahedi, S. Solberg Woods, L. C. Kallupi, M. de Guglielmo, G. Palmer, A. George, O. 2025-07-18 doi:10.1101/2025.07.17.660811 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Ras-Responsive Element Binding Protein 1 regulates survival of Group 3 medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.07.16.665230v1?rss=1 Beigi Masihi, M. Chambers, K. Friedman, R. Pampou, S. Gudenas, B. L. Torrejon, J. Lee, C. Furnari, G. Chau, L. Q. GC, S. Lin, Y. Chapman, O. S. Skowron, P. Garzia, L. Taylor, M. D. Chavez, L. Ayrault, O. Northcott, P. A. Karan, C. Wechsler-Reya, R. J. 2025-07-21 doi:10.1101/2025.07.16.665230 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape ]]> https://biorxiv.org/content/10.1101/2025.07.17.664328v1?rss=1 James, F. Churas, C. Pratt, D. Luna, A. 2025-07-21 doi:10.1101/2025.07.17.664328 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Activation of IL-17+ ILC subsets in IL-18R-deficient mice during fungal allergen exposure ]]> https://biorxiv.org/content/10.1101/2025.07.17.665289v1?rss=1 Strohm, A. Civello, B. Badrani, J. Lacasa, L. Cavagnero, K. Portillo, A. Amadeo, M. Naji, L. Leng, A. Baum, R. Wang, X. McGee, H. Huang, Y.-A. Doherty, T. 2025-07-21 doi:10.1101/2025.07.17.665289 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Hedgehog and Bmp signaling pathways play opposing roles during establishment of the cardiac inflow tract in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.07.19.665705v1?rss=1 Robertson, R.-C. A. Knight, H. G. Lipovsky, C. Ren, J. Chi, N. C. Yelon, D. 2025-07-22 doi:10.1101/2025.07.19.665705 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ The genome of the early diverged amphioxus, Asymmetron lucayanum, illuminates the evolution of genome architecture and gene repertoires in cephalochordates ]]> https://biorxiv.org/content/10.1101/2025.07.21.665930v1?rss=1 Ren, Y. Miao, Z. Lin, C.-Y. Yang, L. Li, H. Holland, L. Z. Cho, S.-J. Yu, J.-K. Yue, J.-X. 2025-07-22 doi:10.1101/2025.07.21.665930 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Zebrafish larval GPR132b differentially influences wound repair and infection control ]]> https://biorxiv.org/content/10.1101/2025.07.21.666068v1?rss=1 Mercado Soto, N. Schoen, T. Stuntebeck, J. Garcia, N. M. Halley, M. Keller, N. P. Huttenlocher, A. 2025-07-22 doi:10.1101/2025.07.21.666068 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ An allosteric network governs Tom70 conformational dynamics to coordinate mitochondrial import ]]> https://biorxiv.org/content/10.1101/2025.07.19.665690v1?rss=1 Bachochin, M. J. Mcguire, K. L. Cook, B. D. Ye, Q. Silletti, S. Corbett, K. D. Komives, E. A. Herzik, M. A. 2025-07-23 doi:10.1101/2025.07.19.665690 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Looks can be deceiving: discordances in phylogeny and morphology within loricate choanoflagellates ]]> https://biorxiv.org/content/10.1101/2025.07.22.666139v1?rss=1 Galvez-Morante, A. Rutaganira, F. U. Palenik, B. Richter, D. J. 2025-07-23 doi:10.1101/2025.07.22.666139 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Fluorescence recovery after photobleaching reveals different 1 behaviour2 of tropomyosin isoforms Tpm3.1 and Tpm4.2 in dendritic spines ]]> https://biorxiv.org/content/10.1101/2025.07.22.666217v1?rss=1 Tomanic, T. Stefen, H. Paric, E. Chien, A. Fath, T. 2025-07-23 doi:10.1101/2025.07.22.666217 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Integrated single-nuclei and spatial transcriptomic profiling of human sacrococcygeal teratomas reveals heterogeneity in cellular composition and X-chromosome inactivation ]]> https://biorxiv.org/content/10.1101/2025.07.21.665156v1?rss=1 Rojas, E. J. Giannikou, K. Huang, B. J. Cho, S.-J. Cordero, M. Pena, D. Vu, L. Bagrodia, A. Derderian, S. C. MacKenzie, T. C. Laird, D. J. 2025-07-24 doi:10.1101/2025.07.21.665156 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Precision functional mapping reveals less inter-individual variability in the child vs. adult human brain ]]> https://biorxiv.org/content/10.1101/2025.07.21.665760v1?rss=1 Demeter, D. V. Feigelis, M. DAndrea, C. B. Ali, S. A. Baim, A. R. Koithan, E. Stearns, J. Zreik, S. Ahern, J. Park, S. Chang, S. E. Miller, R. L. Hampton, J. M. Schlaggar, B. L. Marek, S. Gordon, E. M. Dosenbach, N. U. Gratton, C. Greene, D. J. 2025-07-24 doi:10.1101/2025.07.21.665760 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.07.25.666579v1?rss=1 Faizi, K. Mehta, P. Maida, A. Humphreys, T. Berrigan, E. McKee-Reid, L. McCorkell, R. Tagade, A. Rumbelow, J. Showalter, J. Brent, L. Coroenne, C. Rigaud, A. Chandrasekhar, A. Navlakha, S. Martin, A. Pradal, C. Lee, S. Busch, W. Platre, M. P. 2025-07-26 doi:10.1101/2025.07.25.666579 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Intrinsic noise reveals the stability of a neuronal network ]]> https://biorxiv.org/content/10.1101/2025.07.23.666219v1?rss=1 Reyes, M. B. Huerta, R. Carelli, P. V. Pinto, R. D. Rabinovich, M. I. Selverston, A. I. 2025-07-27 doi:10.1101/2025.07.23.666219 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ NeoPrecis: Enhancing Immunotherapy Response Prediction through Integration of Qualified Immunogenicity and Clonality-Aware Neoantigen Landscapes ]]> https://biorxiv.org/content/10.1101/2025.07.23.666355v1?rss=1 Lee, K.-H. Sears, T. J. Zanetti, M. Carter, H. 2025-07-27 doi:10.1101/2025.07.23.666355 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Sensory Entrained TMS (seTMS) enhances motor cortex plasticity ]]> https://biorxiv.org/content/10.1101/2025.07.23.666433v1?rss=1 Ross, J. M. Forman, L. Hassan, U. Gogulski, J. Truong, J. Cline, C. C. Parmigiani, S. Chen, N.-F. Hartford, J. W. Fujioka, T. Makeig, S. Pascual-Leone, A. Keller, C. J. 2025-07-27 doi:10.1101/2025.07.23.666433 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Cryopreservation of Sea Urchin (Lytechinus pictus) Embryos and Development Through Metamorphosis ]]> https://biorxiv.org/content/10.1101/2025.07.23.666466v1?rss=1 Vacquier, V. Hamdoun, A. 2025-07-27 doi:10.1101/2025.07.23.666466 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Oscillatory signal decoding within the ERK cascade ]]> https://biorxiv.org/content/10.1101/2025.07.24.666680v1?rss=1 Ganesan, A. Lee, H. N. Tenner, B. Mehta, S. Levchenko, A. Zhang, J. 2025-07-28 doi:10.1101/2025.07.24.666680 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Slow wave stimulation using a smartwatch improves sleep quality ]]> https://biorxiv.org/content/10.1101/2025.07.28.666762v1?rss=1 Whitmore, N. W. Chan, S. W. Dulski, A. Podrug, A. Hidalgo, N. Obi, N. Viswanath, V. K. Freedman, M. S. Nathan, V. Maes, P. 2025-07-29 doi:10.1101/2025.07.28.666762 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Human Strategy Adaptation in Reinforcement Learning Resembles Policy Gradient Ascent ]]> https://biorxiv.org/content/10.1101/2025.07.28.667308v1?rss=1 Xiong, H.-D. Ji-An, L. Wilson, R. C. Mattar, M. G. 2025-07-31 doi:10.1101/2025.07.28.667308 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Spatial specificity of the functional gradient echo and spin echo BOLD signal across cortical depth at 7 T ]]> https://biorxiv.org/content/10.1101/2025.07.28.667324v1?rss=1 Haenelt, D. Trampel, R. Chaimow, D. Shmuel, A. Sereno, M. I. Weiskopf, N. 2025-07-31 doi:10.1101/2025.07.28.667324 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Phasor diagrams clock oscillatory hemodynamic switching between overt speech production and micro resting states ]]> https://biorxiv.org/content/10.1101/2025.07.29.667380v1?rss=1 Huang, R.-S. Wang, M. Leong, T. I. Lei, U. M. Sereno, M. I. Li, D. Lei, V. L. C. 2025-08-01 doi:10.1101/2025.07.29.667380 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Effects of wasting disease on sea star populations in southern California: Variations over a 40-year period ]]> https://biorxiv.org/content/10.1101/2025.07.30.667779v1?rss=1 Schroeter, S. Dixon, J. Dayton, P. Smith, R. Parnell, P. E. 2025-08-02 doi:10.1101/2025.07.30.667779 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ CD133+ Vesicles Mediate Resistance to RAS-ERK Inhibition Regulated by YAP Activation in Liver Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.07.31.667712v1?rss=1 Zhang, S. Feng, X. Quan, E. Kaneko, K. Feng, G.-s. 2025-08-02 doi:10.1101/2025.07.31.667712 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ RNA triggers chronic stress during neuronal aging ]]> https://biorxiv.org/content/10.1101/2025.08.04.668575v1?rss=1 Rhine, K. Epstein, E. Carlson, N. M. Ge, X. Mizrahi, O. Kamat, A. Hermann, A. Brothers, W. R. Ravits, J. Bennett, E. J. Pekkurnaz, G. Yeo, G. W. 2025-08-05 doi:10.1101/2025.08.04.668575 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Structural mechanisms for the recruitment of factor H by Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2025.08.05.668778v1?rss=1 Kumar, A. Wang, K.-C. Ghosh, P. 2025-08-05 doi:10.1101/2025.08.05.668778 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Comparative analysis of plasma and bone marrow nutrient levels in pediatric B-ALL patients ]]> https://biorxiv.org/content/10.1101/2025.08.05.668707v1?rss=1 Abbott, K. L. Ali, A. Munim, M. B. Bagchi, D. P. Kunchok, T. Waite, M. Wiggers, C. R. M. Dimitrov, B. Harris, M. H. Knoechel, B. Silverman, L. B. Vander Heiden, M. G. Pikman, Y. 2025-08-07 doi:10.1101/2025.08.05.668707 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality ]]> https://biorxiv.org/content/10.1101/2025.08.07.667992v1?rss=1 Palmer, C. R. Song, J. Yang, B. Chen, C.-J. Diep, D. Conklin, K. Plongthongkum, N. Indralingam, H. S. Liu, C. S. Kurtz, J. Hu, Q. Ransom, L. Shahnaee, A. Hiniker, A. Hodge, R. D. Keene, C. D. Lein, E. Kharchenko, P. Zemke, N. Chun, J. Ren, B. Zhang, K. 2025-08-07 doi:10.1101/2025.08.07.667992 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ A Scalable Toolkit for Modeling 3D Surface-based Brain Geometry ]]> https://biorxiv.org/content/10.1101/2025.08.06.668521v1?rss=1 Im, Y. Nabulsi, L. Kang, M. J. Y. Thomopoulos, S. I. Zuluaga, A. M. D. Dale, A. M. Karuk, A. Giorgio, A. D. Mwangi, B. Gutman, B. Overs, B. Jaramillo, C. L. McDonald, C. Stein, D. Cannon, D. M. Glahn, D. Hidalgo-Mazzei, D. Pecheva, D. Grotegerd, D. Pomarol-Clotet, E. Vieta, E. Olie, E. Cherto, E. V. Sambataro, F. Howells, F. Scheffler, F. Busatto, G. Anmella, G. Zunta-Soares, G. B. Roberts, G. Temmingh, H. Gotlib, I. Agartz, I. Soares, J. C. Karantonis, J. A. Prisciandaro, J. Fullerton, J. M. Radua, J. Savitz, J. Houenou, J. Sim, K. Harada, K. Berger, 2025-08-09 doi:10.1101/2025.08.06.668521 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Targeting FSP1 triggers ferroptosis in lung cancer ]]> https://biorxiv.org/content/10.1101/2025.08.07.668766v1?rss=1 Wu, K. Vaughan, A. J. Bossowski, J. P. Hao, Y. Ziogou, A. Kim, S. M. Kim, T. H. Nakamura, M. N. Pillai, R. Mancini, M. Rajalingam, S. Han, M. Nakamura, T. Wang, L. Chung, S. Simeone, D. Shackelford, D. Kang, Y. P. Conrad, M. Papagiannakopoulos, T. 2025-08-11 doi:10.1101/2025.08.07.668766 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Ultrafast and Ultralarge Distance-Based Phylogenetics Using DIPPER ]]> https://biorxiv.org/content/10.1101/2025.08.12.669583v1?rss=1 Walia, S. Chen, Z. Tseng, Y.-H. Turakhia, Y. 2025-08-12 doi:10.1101/2025.08.12.669583 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions ]]> https://biorxiv.org/content/10.1101/2025.08.11.669795v1?rss=1 Richter, S. M. Brook, N. Guseman, A. 2025-08-13 doi:10.1101/2025.08.11.669795 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ CT-induced disease generates epithelial cell-derived L-lactate that promotes Vibrio cholerae growth in the small intestine ]]> https://biorxiv.org/content/10.1101/2025.08.12.669941v1?rss=1 Gutierrez, M. d. l. P. Hall, J. L. Winter, S. E. Rivera-Chavez, F. 2025-08-13 doi:10.1101/2025.08.12.669941 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo ]]> https://biorxiv.org/content/10.1101/2025.08.12.669999v1?rss=1 Brandenburg, J. M. Trinks, A. Vojtasova, D. Monaco, A. A. Arsie, R. Hu, M. Hamdoun, A. Jenniches, C. Landthaler, M. Bluthgen, N. Garfield, D. 2025-08-13 doi:10.1101/2025.08.12.669999 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use ]]> https://biorxiv.org/content/10.1101/2025.08.13.670183v1?rss=1 Cyphert, E. L. Liu, C. Chu, V. T. Dubey, A. Liu, M. Zhong, Z. Cockey, J. R. Diaz, E. C. G. Morales, A. L. Nixon, J. C. Garcia, M. Zeng, S. Rohatgi, S. Wong, J. Arjyal, R. Mekonen, H. Neff, N. Lee, J. Shea, M. K. Fu, X. Booth, S. L. Leifer, C. A. Singh, A. Langelier, C. R. Hernandez, C. J. 2025-08-13 doi:10.1101/2025.08.13.670183 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ A population-scale atlas of blood and tissue in lupus nephritis ]]> https://biorxiv.org/content/10.1101/2025.08.11.669754v1?rss=1 Gurajala, S. Sugiarto, N. W. Curtis, M. Eisenhaure, T. M. Arazi, A. Fava, A. Xiao, Q. Mears, J. Rovin, B. Berthier, C. C. Izmirly, P. M. Barnas, J. L. Hoover, P. J. Peters, M. Raychowdhury, R. Horisberger, A. Sakaue, S. Zhao, Y. Furie, R. A. Belmont, H. M. Hildeman, D. A. Woodle, E. S. Dall'Era, M. Putterman, C. Kamen, D. L. McMahon, M. A. Grossman, J. Kalunian, K. C. Hodgin, J. B. Payan-Schober, F. Apruzzese, W. Perlman, H. Cuda, C. M. Wofsy, D. Guthridge, J. M. Anolik, J. H. James, J. A. Accelerating Medicines Partnerships Rheumatoid Arthritis/Systemic Lu 2025-08-14 doi:10.1101/2025.08.11.669754 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Recombinant proteasome provides new avenues for anti-malarial drug development. ]]> https://biorxiv.org/content/10.1101/2025.08.13.670186v1?rss=1 Fajtova, P. Zhang, H. Urich, L. da Silva, E. B. da Silva, C. H. Almaliti, J. Al-Hindy, M. Boura, E. Fidock, D. A. Kirkman, L. Lin, G. Bogyo, M. Gerwick, W. H. Zhao, J. O'Donoghue, A. J. 2025-08-14 doi:10.1101/2025.08.13.670186 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Reduced efficacy of an anti-toxin vaccine from senescence-driven attenuation of toxin virulence ]]> https://biorxiv.org/content/10.1101/2025.08.14.670416v1?rss=1 Du, X. Tseng, C.-W. Bjanes, E. Gage, H. Swan, J. Tsai, C. M. Hajam, I. Gonzalez, C. Lin, B. Nizet, V. Liu, G. Y. 2025-08-14 doi:10.1101/2025.08.14.670416 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data ]]> https://biorxiv.org/content/10.1101/2025.08.11.666099v1?rss=1 Mohseni Ahooyi, T. Stear, B. Simmons, J. A. Metzger, V. T. Kumar, P. Evangelista, J. E. Clarke, D. J. B. Xie, Z. Kim, H. Jenkins, S. L. Maurya, M. R. Ramachandran, S. Fahy, E. Imam, F. T. Kokash, N. Roth, M. E. Fullem, R. Jevtic, D. Mihajlovic, A. Tiemeyer, M. Gillespie, T. H. Bakker, C. Schroeder, A. J. Markowski, J. Nedzel, J. Hill, D. D. Terry, J. Nemarich, C. Park, P. Ardlie, K. G. Vora, J. Mazumder, R. Ranzinger, R. de Bono, B. Subramaniam, S. Grethe, J. S. Yang, J. J. Lambert, C. G. Resnick, A. Milosavljevic, A. Ma'ayan, A. Silverstein, J. C. Tay 2025-08-15 doi:10.1101/2025.08.11.666099 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Increased atherosclerosis and expression of inflammarafts in macrophage foam cells in AIBP-deficient mice ]]> https://biorxiv.org/content/10.1101/2025.08.12.669996v1?rss=1 Miller, Y. I. Li, S. Nazarenkov, N. Alekseeva, E. Navia-Pelaez, J. M. Secrest, P. Gordts, P. L. Heinz, S. 2025-08-15 doi:10.1101/2025.08.12.669996 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Aberrant recursive splicing in a human disease locus ]]> https://biorxiv.org/content/10.1101/2025.08.14.666599v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@171156borg.highwire.dtl.DTLVardef@13553baorg.highwire.dtl.DTLVardef@bee7forg.highwire.dtl.DTLVardef@156f19e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Boone, P. M. Harripaul, R. Yadav, R. Grzybowski, M. Hanafy, M. K. Lee, A. C. Choi, E. Y. Collins, R. L. Polesskaya, O. Makhortova, N. Larson, M. O. Kayir, H. Wang, Y. Avila, R. A. Frie, J. A. Eed, A. Albeely, A. M. Venmuri, S. Ayoub, S. M. Lemanski, J. M. Ben-Isvy, D. Zhao, X. Sanchis-Juan, A. Handley, M. Erdin, S. de Esch, C. Mohajeri, K. Chen, C. Tovar, P. G. Salani, M. Oliveira, M. M. Tai, D. J. C. Currall, B. McGraw, C. Slaughenhaupt, S. Doan, R. Gao, D. Gusella, J. F. Sanchez-Roige, S. Young, J. Khokar, J. Geurts, A. M. Palmer, A. A. Talkowski, M 2025-08-15 doi:10.1101/2025.08.14.666599 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Distributed theta networks support the control of working memory: Evidence from scalp and intracranial EEG ]]> https://biorxiv.org/content/10.1101/2025.08.14.670214v1?rss=1 Shi, L. Chattopadhyay, K. Gray, S. M. Yarbrough, J. B. King-Stephens, D. Saez, I. Girgis, F. Shaikhouni, A. Schuele, S. U. Rosenow, J. M. Asano, E. Kim-McManus, O. Sattar, S. Knight, R. T. Johnson, E. L. 2025-08-15 doi:10.1101/2025.08.14.670214 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Acidic vacuole-containing organisms are a majority of the eukaryotic microbial community in oligotrophic Argo Basin waters (eastern Indian Ocean) ]]> https://biorxiv.org/content/10.1101/2025.08.14.670408v1?rss=1 Selph, K. E. Yingling, N. Traboni, C. Landry, M. R. 2025-08-15 doi:10.1101/2025.08.14.670408 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Measuring Joint Pain Through Tibio-Femoral Flexion: technique validation and assessment of behavior in response to different analgesics in rats ]]> https://biorxiv.org/content/10.1101/2025.08.13.669963v1?rss=1 Malange, K. F. Menezes de Souza, D. Lemes, J. B. P. Portugal, L. C. Parada, C. A. 2025-08-18 doi:10.1101/2025.08.13.669963 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Sinking particle export within and beneath the euphotic zone in the eastern Indian Ocean ]]> https://biorxiv.org/content/10.1101/2025.08.14.670365v1?rss=1 Stukel, M. R. Biard, T. Decima, M. Fender, C. K. Kehinde, O. Kelly, T. B. Kranz, S. A. Landry, M. R. Yingling, N. 2025-08-19 doi:10.1101/2025.08.14.670365 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Interpretable EEG Biomarkers for Neurological Disease Models in Mice Using Bag-of-Waves Classifiers ]]> https://biorxiv.org/content/10.1101/2025.08.14.670397v1?rss=1 Achuri, M. I. C. Lara, M. K. Rabbo, K. A. Wilson, B. T. Meek, A. Mahoney, J. M. Hernan, A. E. Brockmeier, A. J. 2025-08-20 doi:10.1101/2025.08.14.670397 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility ]]> https://biorxiv.org/content/10.1101/2025.08.14.670424v1?rss=1 Yao, M. Libster, A. M. Desfor, S. Malhotra, F. Castorena, N. Montilla-Perez, P. Telese, F. 2025-08-20 doi:10.1101/2025.08.14.670424 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Subcellular assessment of algal carbon storage and chloroplasts across the microenvironmental landscape of a photosymbiotic coral ]]> https://biorxiv.org/content/10.1101/2025.08.19.671130v1?rss=1 Grundy, A. Kramer, N. Jakobsen, S. Kuhl, M. Decelle, J. Wangpraseurt, D. 2025-08-20 doi:10.1101/2025.08.19.671130 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ DFFB suppresses interferon to enable cancer persister cell regrowth ]]> https://biorxiv.org/content/10.1101/2025.08.15.670603v1?rss=1 Williams, A. F. Gervasio, D. A. G. Turkal, C. E. Stuhlfire, A. E. Wang, M. X. Mauch, B. E. Plawat, R. Nguyen, A. H. Paw, M. H. Hairani, M. Lathrop, C. P. Harris, S. H. Page, J. L. Hangauer, M. J. 2025-08-21 doi:10.1101/2025.08.15.670603 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Toggling of NKG2A expression drives functional specialization of iPSC-derived CAR NK cells ]]> https://biorxiv.org/content/10.1101/2025.08.20.671199v1?rss=1 Kanaya, M. Philippon, C. Netskar, H. Saetersmoen, M. L. Cieslar-Pobuda, A. Torralba-Raga, L. Casoni, G. P. Hammer, Q. Vincenti, M. Wiiger, M. T. Krokeide, S. Hoel, H. J. Ask, E. H. Kosugi-Kanaya, M. Kveberg, L. Chu, H.-y. Groff, B. Miller, J. S. Lee, T. Kaufman, D. S. Goodridge, j. P. Valameher, B. Pfefferle, A. Malmberg, K.-J. 2025-08-23 doi:10.1101/2025.08.20.671199 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ CCL26 and CXCL12 Promote Release of Insulin-Sensitizing Adipose Tissue Macrophage sEVs from Subcutaneous Adipose Tissue in Obesity ]]> https://biorxiv.org/content/10.1101/2025.08.20.670151v1?rss=1 Lee, Y. S. 2025-08-24 doi:10.1101/2025.08.20.670151 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Spatial transcriptomic profiling of the human aortic valve reveals cellular sex differences near sites of calcification ]]> https://biorxiv.org/content/10.1101/2025.08.20.671175v1?rss=1 Baddour, T. Ninh, V. K. Gorashi, R. M. Pena, R. King, K. R. Aguado, B. A. 2025-08-24 doi:10.1101/2025.08.20.671175 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ The Darwin-Godel Drug Discovery Machine (DGDM): A Self-Improving AI Framework ]]> https://biorxiv.org/content/10.1101/2025.08.21.671415v1?rss=1 Wu, X. Zhang, X. Kang, Y. Xu, Q. Wang, H. Chen, Z. 2025-08-25 doi:10.1101/2025.08.21.671415 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9 ]]> https://biorxiv.org/content/10.1101/2025.08.25.672025v1?rss=1 Ahsan, M. Saha, A. Ramos, D. Strohkendl, I. Skeens, E. Lisi, G. P. Taylor, D. W. Palermo, G. 2025-08-26 doi:10.1101/2025.08.25.672025 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Transcriptional Readthrough at Atf4 Locus Suppresses Rps19bp1 and Impairs Heart Development ]]> https://biorxiv.org/content/10.1101/2025.08.26.672495v1?rss=1 Zhang, Z. Wu, T. Chen, Z. Chen, D. liang, Z. Adams, C. M. Gu, Y. Ye, M. Barroga, F. Evans, S. M. Zhou, X. Chen, J. 2025-08-29 doi:10.1101/2025.08.26.672495 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Molecular Architecture and Function Mechanism of Tri-heteromeric GluN1-N2-N3A NMDA Receptors ]]> https://biorxiv.org/content/10.1101/2025.08.25.672209v1?rss=1 Kou, Z. Yao, F. Zhang, T. Nan, S. Xie, C. Wang, B. Sun, Y. 2025-08-30 doi:10.1101/2025.08.25.672209 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ METTL13 Promotes Pre-Leukemic Transformation and the Development of Pediatric Leukemia ]]> https://biorxiv.org/content/10.1101/2025.08.29.673071v1?rss=1 Enlund, S. Lim, C.-E. Hoang, I. Joshi, S. Ramilo Amor, A. Thomsson, C. Sinha, I. Shirazi Fard, S. Nilsson, A. Hermanson, O. Jiang, Q. Holm, F. 2025-08-30 doi:10.1101/2025.08.29.673071 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ The dietary emulsifier polysorbate-80 induces lipid accumulation and cell death in intestinal epithelial cells via ferroptosis ]]> https://biorxiv.org/content/10.1101/2025.08.29.673091v1?rss=1 Saiz-Gonzalo, G. Singh, R. Hanrahan, N. Cluzel, G. Manning, C. Quilter, K. Crowley, T. Srutkova, D. Hudcovic, T. Schwarzer, M. Marcone, S. O Sullivan, J. Joyce, S. A. Melgar, S. 2025-08-31 doi:10.1101/2025.08.29.673091 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Aberrant Hippo-YAP/TEAD signaling drives malignant transcriptional reprogramming in external auditory canal squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.08.27.672711v1?rss=1 Sato, K. Komune, N. Ono, M. Hongo, T. Nakano, T. Koike, K. Itoyama, S. Taguchi, K. Mimori, K. Gutkind, J. S. Masuda, M. Nakagawa, T. 2025-09-01 doi:10.1101/2025.08.27.672711 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Trophic specialization enhances growth performance in larvae of southern bluefin, albacore, and skipjack tunas from the eastern Indian Ocean ]]> https://biorxiv.org/content/10.1101/2025.08.28.672816v1?rss=1 LAIZ-CARRION, R. BORREGO-SANTOS, R. QUINTANILLA, J. M. QUEZADA-ROMEGIALLI, C. MALCA, E. SWALETHORP, R. ABASCAL, F. PENNINO, M. G. VARGAS, M. GODOY-BERMUDEZ, M. A. DIE, D. LANDRY, M. R. 2025-09-02 doi:10.1101/2025.08.28.672816 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Germline stem cell isolation, lineage tracing, and aging in a protochordate ]]> https://biorxiv.org/content/10.1101/2025.08.31.673173v1?rss=1 Levy, T. Anselmi, C. Ishizuka, K. J. Gordon, T. Voskoboynik, Y. McGeever, E. Detweiler, A. M. Levin, L. Palmeri, K. J. Liu, D. D. Sinha, R. Ohene-Gambill, B. F. Raveh, T. Morri, M. Vanni, V. Manni, L. Sahoo, D. Neff, N. F. Rosental, B. Weissman, I. L. Voskoboynik, A. 2025-09-02 doi:10.1101/2025.08.31.673173 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Platelet factor 4 modulates endothelial cell antimicrobial activity to enhance bacterial clearance and improve sepsis outcomes ]]> https://biorxiv.org/content/10.1101/2025.09.02.673783v1?rss=1 Ngo, A. T. P. Ortmann, W. Skidmore, A. Kim, H. Oberg, J. Sarkar, A. Bochenek, V. Levine, N. Rauova, L. Chernysh, I. Martinez, Z. Diorio, C. Goulian, M. Nizet, V. Poncz, M. Gollomp, K. L. 2025-09-03 doi:10.1101/2025.09.02.673783 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Calorie Restriction modulates beta cell IP3R activity to regulate Ca2+ homeostasis and cell network connectivity ]]> https://biorxiv.org/content/10.1101/2025.09.01.673520v1?rss=1 Pfabe, J. dos Santos, C. Cutler, M. Acree, C. Habashy, A. Cambraia, A. Perkins, G. Ellisman, M. Slak Rupnik, M. Arrojo e Drigo, R. 2025-09-04 doi:10.1101/2025.09.01.673520 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Tissue geometry and mechanochemical feedback initiate rotational migration in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.09.03.674060v1?rss=1 Schwabach, S. Santhosh, S. Williams, A. M. Cetera, M. Serra, M. Horne-Badovinac, S. 2025-09-04 doi:10.1101/2025.09.03.674060 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Cellular mechanism linking endoplasmic reticulum inheritance and cell cycle regulation of the nuclear genome ]]> https://biorxiv.org/content/10.1101/2025.09.04.674221v1?rss=1 Lai, Y.-S. Chao, J. Niwa, M. 2025-09-04 doi:10.1101/2025.09.04.674221 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Exploring the roles of trophic mode and microbial prey size in grazing pathways of tropical oligotrophic waters of the eastern Indian Ocean ]]> https://biorxiv.org/content/10.1101/2025.09.02.673656v1?rss=1 Traboni, C. Cawley, G. F. Selph, K. E. Landry, M. R. Decima, M. 2025-09-05 doi:10.1101/2025.09.02.673656 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Sensory Compression as a Unifying Principle for Action Chunking and Time Coding in the Brain ]]> https://biorxiv.org/content/10.1101/2025.09.05.674585v1?rss=1 Kumar, S. Le Cauchois, M. B. Mathis, A. Duncker, L. Howlett, J. R. Mattar, M. G. 2025-09-06 doi:10.1101/2025.09.05.674585 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Erucamide regulates retinal neurovascular crosstalk ]]> https://biorxiv.org/content/10.1101/2025.09.02.673793v1?rss=1 Wei, G. Chatterjee, S. Yang, Q. Vijayakumar, S. Ogasawara, D. Giles, S. Westenskow, P. Wang, J. Fan, R. Pham, H. Aguilar, E. Robinson, J. Usui-Ouchi, A. Bonelli, R. Eade, K. Siuzdak, G. Cravatt, B. Sailor, M. J. Boger, D. Friedlander, M. 2025-09-07 doi:10.1101/2025.09.02.673793 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Proteome-wide impact of LRRK1 and 2 inhibitors on protein interactions and phosphorylation ]]> https://biorxiv.org/content/10.1101/2025.09.03.674114v1?rss=1 Jansen, J. Wendel, M. Raig, N. D. Kraus, T. V. Surridge, K. J. Mahesula, S. Richter-Muller, N. Mathea, S. Reck-Peterson, S. L. Knapp, S. Stengel, F. 2025-09-07 doi:10.1101/2025.09.03.674114 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Evidence for hierarchical representations of written and spoken words from an open-science human neuroimaging dataset ]]> https://biorxiv.org/content/10.1101/2025.09.07.674741v1?rss=1 Banerjee, S. Jin, K. Nikolov, P. Cho, P. Pendri, V. R. Chang, L. Damera, S. R. Riesenhuber, M. 2025-09-08 doi:10.1101/2025.09.07.674741 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Translating clinical gene sequencing into a foundational representation of tumor subtype ]]> https://biorxiv.org/content/10.1101/2025.09.08.674723v1?rss=1 30,000 tumors with extensive molecular knowledge, yielding a model that accurately reconstructs held-out genetic profiles (demonstrating strong generalization) and determines subtype representations from altered molecular pathways (enabling model interpretability). We evaluate MutationProjector in independent tasks related to prediction of immunotherapy response, prediction of chemotherapy response, and classification of metastasis, recording leading performance in all areas. Each task identifies key biomarkers of interest, including KMT2A and KRAS-STK11 alterations which govern immunotherapy response. ]]> Kong, J. Lee, I. Boecher, D. Singhal, A. Kelly, M. Moon, J. Ahn, C. H. Ock, C.-Y. Kumar, T. Sears, T. J. Laub, D. Wright, S. Wall, P. Carter, H. Wang, Z. Ideker, T. 2025-09-09 doi:10.1101/2025.09.08.674723 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ TNF signaling drives expansion of Reg4+ epithelial cells in colitis. ]]> https://biorxiv.org/content/10.1101/2025.09.08.674949v1?rss=1 Gadeock, S. Girish, N. Liu, C. Y. Huang, Y. Grikscheit, T. C. Polk, D. B. 2025-09-09 doi:10.1101/2025.09.08.674949 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ TNF Receptor 1 regulates colonic mesenchymal cell diversity and the epithelial stem cell niche. ]]> https://biorxiv.org/content/10.1101/2025.09.08.674957v1?rss=1 Gadeock, S. Girish, N. Liu, C. Y. Huang, Y. Grikscheit, T. C. Polk, D. B. 2025-09-09 doi:10.1101/2025.09.08.674957 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Redox regulation of neuroinflammatory pathways contributes to damage in Alzheimers disease brain ]]> https://biorxiv.org/content/10.1101/2025.09.08.674963v1?rss=1 Carnevale, L. N. Banerjee, P. Zhang, X. Navarro, J. Raspur, C. K. Nakamura, T. Schahrer, E. Scott, H. Lang, N. Diedrich, J. K. Yates, J. R. Lipton, S. A. 2025-09-09 doi:10.1101/2025.09.08.674963 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Redefining Parkinson's Disease by Dysregulated Genetic Networks in Distinct Cell Types ]]> https://biorxiv.org/content/10.1101/2025.09.09.674964v1?rss=1 Yang, J. Baldeschi, A. C. Kong, J. Mattson, N. Schiksnis, E. Wright, S. N. Park, S. Lee, I. roybon, l. Ideker, T. 2025-09-13 doi:10.1101/2025.09.09.674964 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ A phenotypic brain organoid atlas for neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2025.09.12.675864v1?rss=1 Wang, L. Nakamura, Y. Li, J. Sievert, D. Liu, Y. Nguyen, T. Jetti, P. S. Thai, E. Zhou, R. Y. Weng, J. Meave, N. Yadavilli, M. Howarth, R. Camey, K. Banka, N. Owusu-Hammond, C. Barrows, C. Kingsmore, S. F. Zaki, M. S. Mukamel, E. A. Gleeson, J. G. 2025-09-13 doi:10.1101/2025.09.12.675864 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Time-Restricted Feeding Attenuates Kidney Damage and Preserves Renal Function in Mouse Model of Chronic Kidney Disease ]]> https://biorxiv.org/content/10.1101/2025.09.08.674986v1?rss=1 Lin, T. Rey-Serra, C. Tituana, J. Cannata, P. Le, H. Glina, A. Sahoo, D. Lamas, S. Chaix, A. Panda, S. 2025-09-14 doi:10.1101/2025.09.08.674986 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response ]]> https://biorxiv.org/content/10.1101/2025.09.13.676059v1?rss=1 Fang, J. Lam, D. C. Mah, C. Tanner, H. M. Comi, T. Cai, Y. Chen, C. te Velthuis, A. J. W. Brangwynne, C. P. Yeo, G. W. Saphire, E. O. 2025-09-14 doi:10.1101/2025.09.13.676059 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Systematic Mapping of Protein Interactions Underlying IL-2 Secretion in Human T Cells ]]> https://biorxiv.org/content/10.1101/2025.09.09.675165v1?rss=1 Shin, S. Rocamora, F. Lewis, N. E. 2025-09-15 doi:10.1101/2025.09.09.675165 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Evaluating the Contribution of Genome 3D Folding to Variation in Human Height Using Machine Learning ]]> https://biorxiv.org/content/10.1101/2025.09.09.675195v1?rss=1 Gu, W. Gilbertson, E. Baranzini, S. E. Salem, R. Capra, J. A. 2025-09-15 doi:10.1101/2025.09.09.675195 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Revisiting daily growth and survival insights of Southern bluefin tuna (Thunnus maccoyii) larvae in the eastern Indian Ocean ]]> https://biorxiv.org/content/10.1101/2025.09.10.675289v1?rss=1 Borrego-Santos, R. Quintanilla, J. M. Laiz-Carrion, R. Garcia, A. Malca, E. Abascal, F. Die, D. J. Riveiro, I. Swalethorp, R. Landry, M. R. 2025-09-16 doi:10.1101/2025.09.10.675289 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ QSProteome: A Community-Driven Interactive Platform for Large-Scale Exploration and Evaluation of Predicted Protein Complex Structures. ]]> https://biorxiv.org/content/10.1101/2025.09.10.675416v1?rss=1 54,000 models within 14 weeks. To promote iterative refinement, QSProteome includes a gamified re-curation workflow that transitions users from training modules into live curation, enabling the community-led assessment of 1,547 ABC transporter complexes. Together, these components form a dynamic, scalable infrastructure for proteome-scale structural biology. By unifying modeling, validation, and annotation in a reusable, searchable, and community-extensible framework, QSProteome enables proteome-scale structure accessibility and reuse--powering discovery, annotation, and collaborative refinement across the structural biology community. ]]> Catoiu, E. A. Kambo, D. Rodriguez, B. Vear, K. Wang, Z. Akpata, J. Shah, J. Ayoub, R. Hofmann, M. Ananda, K. Tantry, A. Gupta, I. Anwyl, R. Faucher, C. Nichols, J. Ton, B. Marchal, L. O. Palsson, B. O. 2025-09-16 doi:10.1101/2025.09.10.675416 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Distributed and drifting signals for working memory load in human cortex ]]> https://biorxiv.org/content/10.1101/2025.09.15.676305v1?rss=1 Adam, K. C. S. Awh, E. Serences, J. T. 2025-09-16 doi:10.1101/2025.09.15.676305 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Methamphetamine and α-pyrrolidinopentiophenone (α-PVP) Intravenous Self-Administration in Female and Male Rats ]]> https://biorxiv.org/content/10.1101/2025.09.12.675933v1?rss=1 Gutierrez, A. Grant, Y. Vandewater, S. A. Taffe, M. A. 2025-09-17 doi:10.1101/2025.09.12.675933 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Ovarian Tumor FAK Inhibition Releases Omega-3 Fatty Acids Stimulating GATA6 Peritoneal Macrophage CXCL13 Production Enhancing Immunotherapy ]]> https://biorxiv.org/content/10.1101/2025.09.12.675975v1?rss=1 Chen, X. L. Tharp, K. M. Ojalill, M. Ozmadenci, D. Boyer, A. Hannen, T. J. Lawson, C. Lee, H. J. Xia, M. Tahon, E. Zhang, Y. Minor, C. Khan, S. U. Anderson, C. C. Nemkov, T. Rose, M. Estrada, M. V. Molinolo, A. A. Warren, E. Penalosa, P. Eskander, R. K. McHale, M. T. Wang, S. E. Connolly, D. C. Fisch, K. M. Stupack, D. G. Schlaepfer, D. D. 2025-09-17 doi:10.1101/2025.09.12.675975 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Systematic evaluation of the impact of promoter proximal short tandem repeats on expression ]]> https://biorxiv.org/content/10.1101/2025.09.14.676153v1?rss=1 Zhang, X. Lingzhi, Z. Wang, E. Benton, S. Modolo, E. Maksimov, M. Shleizer-Burko, S. Gong, Q. Wang, C. Lamkin, M. Mendenhall, E. Gymrek, M. Goren, A. 2025-09-17 doi:10.1101/2025.09.14.676153 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Transport of sphingolipids by yeast Npc2 supports phase separation of the vacuole membrane ]]> https://biorxiv.org/content/10.1101/2025.09.14.676161v1?rss=1 Kim, H. Lipp, N.-F. Juarez-Contreras, I. Wong, A. M. Budin, I. 2025-09-17 doi:10.1101/2025.09.14.676161 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ The DREAM complex links somatic mutation, lifespan, and disease ]]> https://biorxiv.org/content/10.1101/2025.09.15.676396v1?rss=1 Koch, Z. Nandi, S. P. Licon, K. Bujarrabal-Dueso, A. Meyer, D. H. Saeed, S. Perampalam, P. Dick, F. A. Schumacher, B. Alexandrov, L. B. Ideker, T. 2025-09-18 doi:10.1101/2025.09.15.676396 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Exploiting TGF-β-mediated Stromal Programming in Homologous Recombination-Deficient Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.16.676458v1?rss=1 Roger, E. Mummey, H. M. Zimmer, E. Srinivasan, D. Härle, A. Moubri, L. Beutel, A. K. Singh, R. Ekizce, M. Melzer, M. K. Lee, Y. Silva, A. Härle, L. Engleitner, T. Arnold, F. Morawe, M. Naggay, B. Schneider, J. Gilberg, L. Mosler, J. P. Ludwig, C. Meng, C. Hirschenberger, M. Hunszinger, V. Kluck, K. Kirchner, M. Volckmar, A.-L. Wirth, M. Alhamdani, M. S. S. Hoheisel, J. D. Löhr, J.- M. Seufferlein, T. Abaei, A. Kemkemer, R. Rad, R. Budczies, J. Mulaw, M. Hermann, P. C. Hänle, M. Sparrer, K. M. Halbrook, C. J. Gaulton, K. J. Steinestel, K. Stenzinge 2025-09-18 doi:10.1101/2025.09.16.676458 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Resting-State fMRI and the Risk of Overinterpretation: Noise, Mechanisms, and a Missing Rosetta Stone ]]> https://biorxiv.org/content/10.1101/2025.09.16.676611v1?rss=1 Chen, G. Cai, Z. Kording, K. P. Liu, T. Faskowitz, J. Bandettini, P. A. Biswal, B. Taylor, P. A. 2025-09-19 doi:10.1101/2025.09.16.676611 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ RobPicker: A Meta Learning Framework for Robust Identification of Macromolecules in Cryo-Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2025.09.16.676650v1?rss=1 Hosseini, R. Liang, Y. Singh, D. Rahmani, H. Choe, S. Lee, J. Xu, M. Segal, E. Zou, J. Williamson, J. Grotjahn, D. A. Villa, E. Xie, P. 2025-09-19 doi:10.1101/2025.09.16.676650 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Age associations with cortical and subcortical brain structure in adolescents age 9-17 ]]> https://biorxiv.org/content/10.1101/2025.09.18.677236v1?rss=1 Smith, D. M. Rigby, A. Pecheva, D. M. Parekh, P. Becker, A. Loughnan, R. J. Nichols, T. Jernigan, T. Dale, A. 2025-09-19 doi:10.1101/2025.09.18.677236 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure ]]> https://biorxiv.org/content/10.1101/2025.09.17.676618v1?rss=1 Yuan, Y. Hefner, Y. Szubin, R. Sung, J. Palsson, B. 2025-09-20 doi:10.1101/2025.09.17.676618 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Detection of multiple per- and polyfluoroalkyl substances (PFAS) using a biological brain-based gas sensor ]]> https://biorxiv.org/content/10.1101/2025.09.17.676814v1?rss=1 McLane-Svoboda, S. B. Joshi, S. McLane-Svoboda, A. K. Stout, C. Bazhenov, M. Saha, D. 2025-09-20 doi:10.1101/2025.09.17.676814 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Effects of 6-methyl nicotine in middle aged female rats with a history of nicotine vapor self-administration ]]> https://biorxiv.org/content/10.1101/2025.09.15.676338v1?rss=1 Taffe, M. A. Coons, T. R. Doran, T. A. Grant, Y. Vandewater, S. A. 2025-09-21 doi:10.1101/2025.09.15.676338 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Phytoplankton community structure and photophysiological strategies in the oligotrophic Indian Ocean spawning ground of Southern Bluefin Tuna ]]> https://biorxiv.org/content/10.1101/2025.09.18.677227v1?rss=1 Goes, J. Gomes, H. Wu, X. Kranz, S. Swalethorp, R. Wu, J. Tirkey, A. Landry, M. 2025-09-21 doi:10.1101/2025.09.18.677227 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Human milk components interact with infant genomics to modulate gut microbiota, childhood asthma and atopy ]]> https://biorxiv.org/content/10.1101/2025.09.19.676891v1?rss=1 Stickley, S. A. Fang, Z. Y. Ambalavanan, A. George, E. Petersen, C. Dai, D. L. Y. Moossavi, S. Miliku, K. Bode, L. Field, C. J. Mandhane, P. J. Simons, E. Moraes, T. J. Surette, M. G. Azad, M. B. Turvey, S. E. Subbarao, P. Duan, Q. 2025-09-21 doi:10.1101/2025.09.19.676891 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ A complete diploid human genome benchmark for personalized genomics ]]> https://biorxiv.org/content/10.1101/2025.09.21.677443v1?rss=1 Hansen, N. F. Dwarshuis, N. Ji, H. J. Rhie, A. Loucks, H. Logsdon, G. A. Vollger, M. R. Storer, J. M. Kim, J. Adam, E. Altemose, N. Antipov, D. Asri, M. Barreira, S. Bohaczuk, S. C. Bzikadze, A. V. Carioscia, S. A. Carroll, A. Chao, K.-H. Chu, Y. Das, A. Ebert, P. English, A. Fleharty, M. Fleming, L. E. Formenti, G. Guarracino, A. Hartley, G. A. Jenike, K. Kalleberg, J. Kang, Y. King, R. Lipovac, J. Mastoras, M. Mitchell, M. W. Negi, S. Olson, N. D. Oshima, K. K. Paulin, L. F. Pickett, B. D. Porubsky, D. Ranchalis, J. Ranjan, D. Rautiainen, M. Riethm 2025-09-21 doi:10.1101/2025.09.21.677443 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Investigation of Double-Stranded DNA Donors and CRISPR-Cas9 RNP for Universal Correction of Mutations Causing Cystic Fibrosis in Human Airway Cells ]]> https://biorxiv.org/content/10.1101/2025.09.21.677613v1?rss=1 Sinha, V. Ayoub, P. G. Juett, C. J. Lathrop, L. E. Foley, R. A. Sims, R. A. Long, J. D. Duggan, E. C. Fernandes, N. Illek, B. Gomperts, B. N. Jonas, S. J. Kohn, D. B. 2025-09-21 doi:10.1101/2025.09.21.677613 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ 3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors ]]> https://biorxiv.org/content/10.1101/2025.09.21.677628v1?rss=1 Forjaz, A. Queiroga, V. Li, Y. Hernandez, A. Crawford, A. Qin, X. Zhong, M. Tsapatsis, M. Joshi, S. Kramer, D. Nizet, O. Bea, H. Li, Y. Qin, S. O Flynn, R. Yang, M. Pratt, B. Wu, F. Gensbigler, P. Blecher, M. Wu, P.-H. Kagohara, L. T. Shih, I. M. Zwicker, D. Atkinson, M. A. Shi, L. Fan, R. Kiemen, A. L. Wirtz, D. 2025-09-21 doi:10.1101/2025.09.21.677628 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Computational method for mapping mass signatures along developmental gradients reveals a novel role for a monosaccharide tetrose in maize salt-stress response. ]]> https://biorxiv.org/content/10.1101/2025.09.22.677919v1?rss=1 Sama, A. M. Cahill, S. B. Luo, S. Tripka, A. L. Meng, Y. Noll, S. E. Zare, R. N. Shah, P. Dickinson, A. J. 2025-09-24 doi:10.1101/2025.09.22.677919 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Neuronal detection of social actions directs collective escape behavior ]]> https://biorxiv.org/content/10.1101/2025.09.24.678087v1?rss=1 Yu, J.-H. Milan, J. Meyerhof, G. T. Napoli, J. L. Lovett-Barron, M. 2025-09-24 doi:10.1101/2025.09.24.678087 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Chronic stress facilitates behavioral engagement and alters lateral habenula activity during flexible decision making in a sex-dependent manner ]]> https://biorxiv.org/content/10.1101/2025.09.24.678366v1?rss=1 Wright, H. R. Fisher, Z. D. G. Schmid, R. M. Westbrook, S. R. Abeshima, R. A. Giannotti, G. McLaughlin, R. J. 2025-09-25 doi:10.1101/2025.09.24.678366 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Central carbon metabolism switching in lytic versus temperate coral reef viral communities ]]> https://biorxiv.org/content/10.1101/2025.09.25.676695v1?rss=1 Kelman, J. Khan, M. Umunna, C. Brainard, R. Donohue, G. Edwards, R. A. Falta, N. A. George, E. E. Gorham, E. Grasis, J. Green, K. Haas, A. F. Halsey, K. Hester, E. Jacob, S. Karatas, A. L. Lim, Y. W. Little, M. Sandin, S. Segnitz, J. Serota, M. Shahwan, N. Simmons, G. Smith, J. E. Tripathi, I. Wegley Kelly, L. Woodward, L. Yang, N. Young, C. Zgliczynski, B. Rohwer, F. Knowles, B. 2025-09-28 doi:10.1101/2025.09.25.676695 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Flexible Working Memory in the Peripheral Nervous System ]]> https://biorxiv.org/content/10.1101/2025.09.26.678884v1?rss=1 Yang, S. Dong, Y. Kiyonaga, A. 2025-09-28 doi:10.1101/2025.09.26.678884 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Human dorsal root ganglia neuronal cell line to study nociceptive signaling: a new pipeline for pain therapy. ]]> https://biorxiv.org/content/10.1101/2025.09.27.674468v1?rss=1 Dochnal, S. A. Du, Y. Malange, K. F. Bryant, J. Bandari, D. Borges Paes Lemes, J. Whitford, A. L. Cliffe, A. R. Mali, P. Dore, K. Miller, Y. I. Yaksh, T. L. 2025-09-28 doi:10.1101/2025.09.27.674468 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression ]]> https://biorxiv.org/content/10.1101/2025.09.24.678347v1?rss=1 Al-Azzam, S. Stuewe, I. Sharma, S. Yamada-Hara, M. Tanaka, A. Stringer, K. Behnam, M. Al-Azzam, N. Nandi, S. Zhivagui, M. Duong, J. Yang, T. Herdman, S. Corr, M. Webster, N. J. G. Raz, E. Alexandrov, L. B. Bertin, S. 2025-09-29 doi:10.1101/2025.09.24.678347 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ ONC206 demonstrates potent anti-tumorigenic activity and is a potential novel therapeutic strategy for high-risk medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.09.25.678693v1?rss=1 Tzaridis, T. D. Liu, J. Chien, F. L. Malhotra, A. Zhu, D. Gershon, I. Zhang, H. Velazquez Vega, J. E. Schniederjan, M. Sposito, T. Adams, P. D. Allen, J. E. Prabhu, V. V. Wechsler-Reya, R. MacDonald, T. J. 2025-09-29 doi:10.1101/2025.09.25.678693 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.09.29.678849v1?rss=1 Wang, W. Berube, P. Yang, B. Castanon, R. Bartlett, A. Komandur, K. Nery, J. R. Barragan, C. Kenworthy, M. Valadon, C. Altshul, J. Petrella, A. Chan, D. Chen, C. Acerbo, A. S. Luo, J. Jain, M. Soma, E. Chen, H. Liem, M. Marrin, M. O'Connor, C. Zemke, N. Oakley, D. H. Ren, B. Hyman, B. T. Ecker, J. R. 2025-09-30 doi:10.1101/2025.09.29.678849 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Flexible gaze reinstatement during working memory for natural scenes ]]> https://biorxiv.org/content/10.1101/2025.09.29.678115v1?rss=1 Dong, Y. Hung, Y. Gaspariani, L. Kiyonaga, A. 2025-10-01 doi:10.1101/2025.09.29.678115 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing ]]> https://biorxiv.org/content/10.1101/2025.09.30.679624v1?rss=1 Eisemann, T. Masihi, M. B. Tzaridis, T. Pister, V. Youm, I. Chambers, K. R. Dutta, A. Wenzel, A. T. Chin, K. Pomeroy, S. L. Mesirov, J. P. Fraenkel, E. Bagchi, A. Chavez, L. Wechsler-Reya, R. J. 2025-10-02 doi:10.1101/2025.09.30.679624 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Qimai: a multi-agent framework for zero-shot DNA-protein interaction prediction ]]> https://biorxiv.org/content/10.1101/2025.09.30.679628v1?rss=1 Wang, W. Liu, c. Yao, M. 2025-10-02 doi:10.1101/2025.09.30.679628 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing ]]> https://biorxiv.org/content/10.1101/2025.10.01.679626v1?rss=1 Fan, W. Xu, F. Kuranov, R. Zambrano, R. Chen, J. Wu, J. Lee, S. H. Trang, K. Q. Mirza, R. Simon, S. Lavinsky, F. Liu, X. Goldberg, J. L. Huang, A. S. Schuman, J. S. Zhang, H. F. 2025-10-03 doi:10.1101/2025.10.01.679626 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors ]]> https://biorxiv.org/content/10.1101/2025.10.01.679859v1?rss=1 Castaldi, A. Chin, J. S. Ma, B. Chang, M. W. Samimi, K. Allen, A. Pinon-Rose, W. Castillo, J. Zamani, P. Xie, M. Arias, N. Solaimanpour, K. Liu, Y. Shen, H. Scott, B. T. Horie, M. Flodby, P. Kasirer-Friede, A. Dang, K. Buchanan, J. Lancione, R. Miller, M. Yang, Q. Benner, C. Marconett, C. Wang, A. Zhou, B. Sun, X. Borok, Z. 2025-10-03 doi:10.1101/2025.10.01.679859 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Progressive Loss of Astrocytic AIBP Expression during Alzheimer's Disease Pathology ]]> https://biorxiv.org/content/10.1101/2025.10.03.680289v1?rss=1 Ding, S. Choi, S.-H. Kim, Y. S. Nazarenkov, N. Miller, Y. I. 2025-10-03 doi:10.1101/2025.10.03.680289 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Tertiary lymphoid structures support the development of allergen-specific progenitor CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2025.10.03.680350v1?rss=1 Bangs, D. J. Hondowicz, B. Abadie, K. Savard, R. Weiss, M. Karakousi, T. Skene, P. J. ImmGenT, Lund, A. W. Goldrath, A. W. Heeg, M. Pepper, M. 2025-10-05 doi:10.1101/2025.10.03.680350 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Incentive Salience, not Psychomotor Sensitization or Tolerance, Drives Escalation of Cocaine Self-Administration in Heterogeneous Stock Rats ]]> https://biorxiv.org/content/10.1101/2025.10.04.680105v1?rss=1 Ramborger, J. Mosquera, J. Brennan, M. Sichel, B. Othman, D. Plasil, S. Sneddon, E. A. Bonnet Zahedi, S. Morgan, A. Chonwattanagul, S. Bai, K. China, L. La, T. Maturin, L. Carrette, L. L. G. George, O. 2025-10-06 doi:10.1101/2025.10.04.680105 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Photoaffinity labeling of protein targets in a complex metazoan: proof-of-concept using a probe for Schistosoma mansoni tubulin ]]> https://biorxiv.org/content/10.1101/2025.10.04.680471v1?rss=1 Lucero, B. Alle, T. Bufano, M. Yao, Y. Brunden, K. R. Brancale, A. Ballatore, C. Francisco, K. R. Caffrey, C. R. 2025-10-06 doi:10.1101/2025.10.04.680471 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting ]]> https://biorxiv.org/content/10.1101/2025.10.06.680814v1?rss=1 Berkeley, R. F. Cook, B. D. Ji, D. Foroughi, A. He, Y. Bachochin, M. J. Herzik, M. A. 2025-10-06 doi:10.1101/2025.10.06.680814 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Commensal Escherichia coli colonization triggers Peyer's patch development ]]> https://biorxiv.org/content/10.1101/2025.10.06.680803v1?rss=1 Gerner, R. R. Walker, G. T. Klaus, S. M. Melchior, K. Hossain, S. Siada, K. Hsu, C.-Y. Albicoro, F. J. Santus, W. Patkar, R. Carrillo-Terrazas, M. Norton, G. J. Thelen, F. Perez-Lopez, A. Sharma, P. Wong, M. P. Lei, V. Ransohoff, R. M. Lo, D. D. Lane, T. E. Reboldi, A. Nuccio, S.-P. Behnsen, J. Zuniga, E. I. Lu, L.-F. Tukel, C. Chu, H. Raffatellu, M. 2025-10-07 doi:10.1101/2025.10.06.680803 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Cerebral cortical structures linked to intelligence ]]> https://biorxiv.org/content/10.1101/2025.10.06.680808v1?rss=1 Chou, C.-J. Fiecas, M. del Re, E. C. Vuoksimaa, E. Chen, C.-H. 2025-10-07 doi:10.1101/2025.10.06.680808 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Structural and biochemical basis for cannabinoid cyclase activity in marine bacterial flavoenzymes ]]> https://biorxiv.org/content/10.1101/2025.10.07.680811v1?rss=1 Love, A. C. Sirohi, H. Hubert, F. M. Kao, Y.-C. Quinnell, D. E. Gappy, R. Sheehy, M. Hsu, J. Lee, A. Zangwill, L. Palfey, B. A. Chang, G. Moore, B. S. 2025-10-07 doi:10.1101/2025.10.07.680811 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ PTH-Induced Behavioral and Metabolic Alterations in Mouse Models of Hyperparathyroidism ]]> https://biorxiv.org/content/10.1101/2025.10.07.681037v1?rss=1 Zhang, L. Chen, Y. Liu, Y. Liu, N. Wu, Y. Du, Z. Li, B. Sun, W. Yang, F. 2025-10-08 doi:10.1101/2025.10.07.681037 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Prenatal Acetaminophen Exposure Does Not Disrupt Human Fetal Brain Development in Cortical Organoid Models ]]> https://biorxiv.org/content/10.1101/2025.10.07.681041v1?rss=1 Trovo, L. Kucera, G. Gomez, G. de Souza, J. S. Muotri, A. R. Iakoucheva, L. M. 2025-10-08 doi:10.1101/2025.10.07.681041 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding. ]]> https://biorxiv.org/content/10.1101/2025.10.07.681056v1?rss=1 Saia-Cereda, V. M. Sharma, A. Flanagan, K. Elmsaouri, S. Steiner, S. Benassi, S. Reis-de-Oliveira, G. Whiteley, J. T. Chandrabhatta, A. Mendes, A. P. Randolph-Moore, L. Xenitopoulos, D. Jetzer, M. Oefner, R. Benner, C. Santos, R. Yeo, G. W. Marchetto, M. C. 2025-10-08 doi:10.1101/2025.10.07.681056 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Structure-Activity Relationship and Target Investigation of Thiophen-2-yl-Pyrimidines against Schistosoma species ]]> https://biorxiv.org/content/10.1101/2025.10.07.681061v1?rss=1 20 {micro}M against three mammalian cell lines. Further, paralytic potency, as measured by the EC50 value for adult S. mansoni motility, was increased 14.5-fold (538 vs. 37 nM), and plasma half-life (t1/2) was improved 3-fold, from 0.48 to 1.51 h for a 40% loss in maximum plasma concentration (Cmax). In washout experiments, 38 produced a sustained paralysis of both juvenile and adult S. mansoni, possibly suggesting a broader in vitro efficacy spectrum compared to PZQ, which is inactive against the juvenile parasite. Also, the two other medically important species, Schistosoma haematobium and Schistosoma japonicum, were susceptible to 38. Finally, to identify potential protein targets, we synthesized a TPP photoaffinity labeling (PAL) probe that labeled several S. mansoni proteins by SDS-PAGE fluorescence analysis, although, notably, not tubulin, suggesting that the antischistosomal activity of 38 is a function of engaging other targets. Future work with the TPP series will aim to decrease toxicity further while improving PK properties to better support in vivo efficacy testing. ]]> Francisco, K. R. Lucero, B. Yohannan, D. Varricchio, C. Lam, A. Sebastiani, J. Liu, L. J. Sun, Y. U. Jacinto, J. Renzulli, M. Monti, L. Brancale, A. Ballatore, C. Alle, T. Caffrey, C. R. 2025-10-08 doi:10.1101/2025.10.07.681061 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Chronic kidney disease exacerbates hyperlipidemia and atherosclerosis via miR-148a-3p targeting SIK1/AMPKα1 in liver ]]> https://biorxiv.org/content/10.1101/2025.10.08.681287v1?rss=1 Huang, Y. Li, T. Hu, E. Zhang, P. Feng, X. Fan, H. Wang, Z. Lei, Y. Wang, C. Yang, W. Wang, L. Liu, P. Du, B. Wu, Y. Li, W. Feng, J. Bai, X. Wu, H. Li, J. Shyy, J. Y.-J. Yuan, Z.-Y. Zhou, J. 2025-10-10 doi:10.1101/2025.10.08.681287 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Astrocyte SEMA3C reduction improves Rett Syndrome phenotypes ]]> https://biorxiv.org/content/10.1101/2025.10.10.681027v1?rss=1 Lyon, K. A. Paumier, A. Kandikonda, A. Melendez, A. Allen, N. J. 2025-10-12 doi:10.1101/2025.10.10.681027 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ An extremophilic Nocardiopsis strain from Great Salt Lake expands the taxonomic range of mycolic acid biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.10.11.681818v1?rss=1 Scott, A. F. Jin, T. Bring Horvath, E. R. Krull, N. K. Iizumi, R. Bender, A. Murphy, B. T. Fenical, W. Winter, J. 2025-10-12 doi:10.1101/2025.10.11.681818 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ Imaging Cellular Metabolic Rewiring with SuMMIT-SRS ]]> https://biorxiv.org/content/10.1101/2025.10.10.681769v1?rss=1 Li, Y. Li, Z. Li, Y. Rhine, K. Ranamukhaarachchi, S. Qin, S. Jang, H. Villazon, J. Bai, Z. Fraley, S. I. Yeo, G. W. Fan, R. Shi, L. 2025-10-13 doi:10.1101/2025.10.10.681769 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Targeted Intestinal Cooling Offers Superior Brain Protection in the Mouse Stroke Model ]]> https://biorxiv.org/content/10.1101/2025.10.10.681764v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1aa07cdorg.highwire.dtl.DTLVardef@1e64569org.highwire.dtl.DTLVardef@d6f178org.highwire.dtl.DTLVardef@1871862_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPost-stroke body surface cooling-induced hypothermia demonstrated marginally neuroprotective effects compared to normothermic conditions in the mouse model. C_LIO_LITargeted deep cooling of the intestine after a stroke resulted in a significantly greater reduction in stroke injury areas and volume, as well as lower mortality rates and fewer functional deficits, compared to body surface cooling-induced hypothermia and normothermic conditions. C_LI ]]> Liu, C. Park, Y. Hu, K. Olivasa, Y. Hu, B. 2025-10-14 doi:10.1101/2025.10.10.681764 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney ]]> https://biorxiv.org/content/10.1101/2025.10.12.681746v1?rss=1 Trim, W. V. Oh, S. Diakova, M. Petrova, K. Ichimura, T. Takakura, A. Karmakar, R. Norrelykke, S. F. F. Peshkin, L. Bonventre, J. V. Kirschner, M. W. 2025-10-14 doi:10.1101/2025.10.12.681746 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ New Quantitative Cost-Impact Effectiveness Indexes to Assist in Publication Decisions by Researchers in the Open Access Era ]]> https://biorxiv.org/content/10.1101/2025.10.10.681750v1?rss=1 Hardy, J. C. Vu, C. K. Wang, D. 2025-10-15 doi:10.1101/2025.10.10.681750 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ The C. elegans immune switch proteins PALS-25 and PALS-22 localizeto mitochondria and regulate fragmentation ]]> https://biorxiv.org/content/10.1101/2025.10.13.682198v1?rss=1 Gang, S. S. Strul, M. W. Troemel, E. 2025-10-15 doi:10.1101/2025.10.13.682198 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ The impact of microplastic contamination in cow manure on reproductive behavior and larval survival in the dung beetle Onthophagus taurus ]]> https://biorxiv.org/content/10.1101/2025.10.14.682200v1?rss=1 McConnell, N. Galindo Lovell, J. Walker, J. Mathews, B. J. Morton, S. G. Shurin, J. B. Rohner, P. T. 2025-10-15 doi:10.1101/2025.10.14.682200 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ ULK1/2 Inhibitors that Degrade ATG13 Effectively Target KRAS-Mutant Cancers ]]> https://biorxiv.org/content/10.1101/2025.10.14.682402v1?rss=1 Hagan, P. M. Ren, H. Brun, S. N. Layng, F. I. A. L. Panickar, D. R. Lambert, L. J. Celeridad, M. Das, R. Ling, L. Zhang, Y. Limpert, A. S. Sheffler, D. J. Commisso, C. Shaw, R. J. Cosford, N. D. P. 2025-10-15 doi:10.1101/2025.10.14.682402 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Senescent Activated Naive B Cells Promote Anti-Citrullinated Antigen T Cell Responses and the Transition to Clinical Rheumatoid Arthritis ]]> https://biorxiv.org/content/10.1101/2025.10.14.682430v1?rss=1 View larger version (85K): org.highwire.dtl.DTLVardef@153b185org.highwire.dtl.DTLVardef@1aba6eeorg.highwire.dtl.DTLVardef@5c886eorg.highwire.dtl.DTLVardef@10109a3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wu, X. Zhang, M. Moon, J.-S. Song, E. K. Abrams, J. C. van Dam, L. S. Sharpe, O. Feser, M. Moss, L. Ho, P. P. Smith, M. H. Donlin, L. H. Buckner, J. H. James, E. A. Firestein, G. S. Okamoto, Y. Lanz, T. V. Meffre, E. Holers, V. M. Deane, K. D. Robinson, W. H. 2025-10-15 doi:10.1101/2025.10.14.682430 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Ivermectin Reduces Withdrawal-Induced Alcohol Intake via CeA GABAergic Enhancement ]]> https://biorxiv.org/content/10.1101/2025.10.14.682432v1?rss=1 Campo, P. Qiao, R. Doyle, M. R. Munro, D. Johnson, B. J. Palmer, A. A. Kallupi, M. de Guglielmo, G. 2025-10-15 doi:10.1101/2025.10.14.682432 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Towards In Situ Dynamics of DNA-bound Full-Length p53 Tetramer ]]> https://biorxiv.org/content/10.1101/2025.10.14.682466v1?rss=1 Demir, O. Barros, E. P. Amaro, R. E. 2025-10-15 doi:10.1101/2025.10.14.682466 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ AAV Kills Dividing Cells by Depleting PARP1 and Other DNA Damage Response Proteins ]]> https://biorxiv.org/content/10.1101/2025.10.14.682484v1?rss=1 Friese, S. Zai, J. Luzbetak, G. Khanna, N. Gesperger, J. Liu, C.-H. Roos, W. Al-Rahahleh, R. Willardson, M. Yang, F. Fu, D. Han, Y. Lintag, N. Saykham, J. Le, J. Al-Delaimy, E. Soutipan, N. Duong, E. Rich, J. Marchetto, M. C. Rosenfeld, M. Sobol, R. W. Shtrahman, M. 2025-10-15 doi:10.1101/2025.10.14.682484 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry. ]]> https://biorxiv.org/content/10.1101/2025.10.15.682631v1?rss=1 1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented. ]]> Krull, N. K. Strobel, M. Saulog, J. Zaroubi, L. Paulo, B. S. Timba, M. Braun, D. R. Mingolelli, G. Raherisoanjato, J. Shepherd, R. A. Scott, A. F. De Silva, C. Fergusson, C. Daniel, Z. Pokharel, S. K. Romanowski, S. Hernandez, A. Monge-Loria, M. Dylla, C. E. Natu, M. M. Petukhova, V. Z. Garg, N. Jensen, P. R. Blachowicz, A. Cassilly, C. D. Guan, L. Stevens, C. D. Winter, J. M. McKinnie, S. M. K. Adaikpoh, B. I. Carlson, S. McCauley, E. P. Metcalf, W. W. Bugni, T. S. Mullowney, M. W. Pamer, E. G. Henke, M. T. Barton, H. Carter, D. O. Eustaquio, A. S. Lini 2025-10-15 doi:10.1101/2025.10.15.682631 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Adventitial leptin receptor-expressing fibroblasts are preferential contributors to fibrotic remodeling of the heart post infarction ]]> https://biorxiv.org/content/10.1101/2025.10.14.682477v1?rss=1 Larcher, V. Fischer, A. Zhang, L. Almolla, O. Chiesa, M. Andriani, F. Wernet, C. Serio, S. Tombor, L. S. Peruzzo, S. Mukherjee, D. Bussani, R. Zacchigna, S. Adams, R. H. Dimmeler, S. Evans, S. M. Cattaneo, P. Guimaraes-Camboa, N. 2025-10-16 doi:10.1101/2025.10.14.682477 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ PHOX2B polyalanine repeat mutation has a profound impact on the transcriptome of neuronal progenitor cells in Haddad syndrome ]]> https://biorxiv.org/content/10.1101/2025.10.15.682708v1?rss=1 10 fold differentially expressed genes. In the patient cells there was a significant enrichment of genes related to neuronal development and synapse organization mainly driven by L1CAM interactions and synaptogenesis signaling pathway. Our result not only highlight the use of a suitable model of HS but also provide a clear path for future experimental validation and downstream targets with potential therapeutic values. ]]> Stobdan, T. Ventrapragada, V. Yao, H. Zhou, D. Dwivedi, I. Lesser, D. Haddad, G. G. 2025-10-16 doi:10.1101/2025.10.15.682708 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ An unconventional HxD motif orchestrates coatomer-dependent coronavirus morphogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.16.682669v1?rss=1 Mohona, S. Shakya, A. K. Singh, S. Kearns, F. L. Jemison, K. Erramilli, S. K. Dey, D. Qing, E. Jennings, B. C. Doray, B. Kossiakoff, A. A. Amaro, R. E. Klose, T. Gallagher, T. Hasan, S. S. 2025-10-17 doi:10.1101/2025.10.16.682669 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Toll-like Receptor 4 Contributes to PCOS-like Metabolic and Reproductive Pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.10.16.682907v1?rss=1 Wiggins, K. Del Mundo, Z. Ayala, J. Naidu, N. Saba, A. Garcia, C. Nguyen, C. Ujagar, N. De La Torre, J.-J. De Robles, G. Rivera, A. Trinh, D. Tinoco, R. Kauffman, A. S. Thackray, V. G. Agrawal, A. Seldin, M. M. Sanchez, G. P. Nicholas, D. 2025-10-17 doi:10.1101/2025.10.16.682907 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Primate ACC encodes natural vocal interactions in a cocktail party ]]> https://biorxiv.org/content/10.1101/2025.10.17.683014v1?rss=1 Lefevre, A. Pal Singh, V. Tyree, T. Li, J. Duhamel, J.-R. Miller, C. 2025-10-17 doi:10.1101/2025.10.17.683014 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Intersection of transient cell states with stable cell types in hippocampus ]]> https://biorxiv.org/content/10.1101/2025.10.17.683151v1?rss=1 Olmstead, J. A. King, L. E. Bloodgood, B. L. 2025-10-19 doi:10.1101/2025.10.17.683151 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ ACE2 Phosphorylation Modulates Angiogenesis via the Activator Protein-1 ]]> https://biorxiv.org/content/10.1101/2025.10.17.683185v1?rss=1 Shyy, J. Y.-J. Lei, Y. Xing, Y. Lei, Y. Liu, Q. Wei, T.-Y. W. Li, B. He, F. Wu, Z. Wang, L. Wang, C. Hao, W. Zhang, J. Xiong, Y. Zhou, J. Wang, X. Yuan, Z.-Y. 2025-10-19 doi:10.1101/2025.10.17.683185 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Mathematical Modeling of Bone Remodeling after Surgical Menopause ]]> https://biorxiv.org/content/10.1101/2025.10.19.683313v1?rss=1 Nelson, A. C. Yeo, E. F. Zhang, Y. Cook, C. V. Fischer-Holzhausen, S. Keeler Bruce, L. Dutta, P. Gholami, S. Smith, B. J. Ford Versypt, A. N. 2025-10-20 doi:10.1101/2025.10.19.683313 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex ]]> https://biorxiv.org/content/10.1101/2025.10.20.683548v1?rss=1 Hayward, R. E. Berkeley, R. F. Gao, Z. Garhammer, M. Morizono, M. A. Njomen, E. Li, H. DeMeester, K. E. Cociorva, V. Herzik, M. A. Hartl, F.-U. Melillo, B. Cravatt, B. F. 2025-10-20 doi:10.1101/2025.10.20.683548 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Brain Dynamics of Mental Manipulation ]]> https://biorxiv.org/content/10.1101/2025.10.20.683458v1?rss=1 30 Hz) and slower (< 30 Hz) dynamics in primary and secondary auditory areas, suggesting a decrease in local excitability. Second, there is a distributed increase in oscillatory synchrony (6-10 Hz), which predicts imagery vividness and task performance. This evidence points to a key role of local excitability and inter-areal synchrony in the manipulation of thought. ]]> Quiroga-Martinez, D. R. He, T. Fernandez-Rubio, G. Bonetti, L. Blenkmann, A. O. Endestad, T. Solbakk, A.-K. Meling, T. R. Fabricius, M. E. McManus, O. K. Willie, J. T. Brunner, P. Dastjerdi, M. Lin, J. Knight, R. 2025-10-21 doi:10.1101/2025.10.20.683458 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Integrated multiomics reveals inflammation-driven excessive erythrocytosis in subjects with Monge's disease ]]> https://biorxiv.org/content/10.1101/2025.10.20.683487v1?rss=1 Azad, P. Caldwell, A. Villafuerte, F. C. Banihani, S. Zhou, D. Subramaniam, S. Haddad, G. G. 2025-10-21 doi:10.1101/2025.10.20.683487 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Disruption of Marrow Microenvironments in Chronic Lymphocytic Leukemia by High-Resolution Synchrotron Micro-Computed Tomography ]]> https://biorxiv.org/content/10.1101/2025.10.20.683519v1?rss=1 Lee, I. K. Obata, Y. Pomicter, A. D. Williams, J. A. Kikani, B. Jensen, C. E. Sborov, D. W. Stephens, D. M. Acevedo, C. 2025-10-21 doi:10.1101/2025.10.20.683519 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Memory recall errors reflect interacting sensory and mnemonic representations ]]> https://biorxiv.org/content/10.1101/2025.10.20.683560v1?rss=1 Kular, H. Serences, J. 2025-10-21 doi:10.1101/2025.10.20.683560 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Maternal transmission of a plastid structure enhances offspring fitness ]]> https://biorxiv.org/content/10.1101/2025.10.21.683706v1?rss=1 Carrier, T. J. Rufino-Navarro, A. Knoop, T. Repnik, U. Caraballo-Rodriguez, A. M. Needham, D. M. Bang, C. Franzenburg, S. Bramkamp, M. Rath, W. Biastoch, A. Hernandez, J. C. Hentschel, U. 2025-10-22 doi:10.1101/2025.10.21.683706 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies ]]> https://biorxiv.org/content/10.1101/2025.10.22.683934v1?rss=1 Dame, H. B. Kopalle, H. Minana, B. Klaft, Z. Fahey, J. McWatters, D. Rao, V. Suresh, R. Aigner, S. Hammer, M. F. Yuskaitis, C. J. Wong, M. Teaney, N. Zhang, C. Thompson, M. Lehner, B. Bennett, C. F. Valcarcel, J. Yeo, E. Burge, C. Dulla, C. Oudin, M. J. 2025-10-22 doi:10.1101/2025.10.22.683934 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Catestatin suppresses melanoma progression and drug resistance through multitargeted modulation of signaling pathways ]]> https://biorxiv.org/content/10.1101/2025.10.22.684062v1?rss=1 Kal, S. Jati, S. Tang, K. Webster, N. J. Corti, A. Mahata, S. K. 2025-10-24 doi:10.1101/2025.10.22.684062 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Analysis of environmental data during a lagrangian experiment: The influence of vertical movements. ]]> https://biorxiv.org/content/10.1101/2025.10.23.680922v1?rss=1 Romero-Fernandez, P. Vargas-Garcia, E. Borrego-Santos, R. Laiz-Carrion, R. L. QUINTANILLA, J. M. Landry, M. R. Kranz, S. A. Stukel, M. R. Kelly, T. B. Vargas-Yanez, M. 2025-10-24 doi:10.1101/2025.10.23.680922 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Targeting serine dehydratase supports amino acid homeostasis and skin repair ]]> https://biorxiv.org/content/10.1101/2025.10.23.683531v1?rss=1 Joulia, E. Ashley, E. L. Tseng, P. Arechiga, C. Liang, Y. Laguerre, A. Ruchhoeft, M. L. Rainaldi, J. Handzlik, M. K. Fallon, R. J. Kim, H. Y. Mali, P. Brenner, D. A. Kisseleva, T. Zheng, Y. Gantner, M. L. Metallo, C. M. 2025-10-24 doi:10.1101/2025.10.23.683531 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease ]]> https://biorxiv.org/content/10.1101/2025.10.24.684434v1?rss=1 View larger version (11K): org.highwire.dtl.DTLVardef@159d7bcorg.highwire.dtl.DTLVardef@16289c5org.highwire.dtl.DTLVardef@43156forg.highwire.dtl.DTLVardef@344a58_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yao, C. Y. Joseph, S. 2025-10-24 doi:10.1101/2025.10.24.684434 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Interregional human assembloids recapitulate fetal brain morphologies and enhance neuronal complexity ]]> https://biorxiv.org/content/10.1101/2025.10.24.684445v1?rss=1 Antunes, A. S. L. M. Athie, M. C. P. Silveira, A. C. C. Renner, J. Dias, E. V. Santos, J. V. R. d. Hrvoj-Mihic, B. Canateli, C. Meidanis, J. Muotri, A. R. Rasia-Filho, A. A. Avansini, S. H. 2025-10-25 doi:10.1101/2025.10.24.684445 Cold Spring Harbor Laboratory Press 2025-10-25 <![CDATA[ Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm ]]> https://biorxiv.org/content/10.1101/2025.10.25.684559v1?rss=1 Li, S. Aston, K. Gleeson, J. G. Quinlan, A. Yang, X. Sudmant, P. H. 2025-10-26 doi:10.1101/2025.10.25.684559 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Exploring the intrinsic and extrinsic determinants of heterogeneity in a β-cell network ]]> https://biorxiv.org/content/10.1101/2025.10.26.684303v1?rss=1 Khaddaj, A. Browne, S. Choi, W. Kravets, V. Edwards, A. G. 2025-10-26 doi:10.1101/2025.10.26.684303 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Long-term prevention of aneuploidy in human pluripotent stem cells by fine-tuning GSK3 activity ]]> https://biorxiv.org/content/10.1101/2025.10.27.684724v1?rss=1 De Jaime-Soguero, A. Romitti, M. Costagliola, S. Jauch, A. Willert, K. Foijer, F. Perez Acebron, S. 2025-10-27 doi:10.1101/2025.10.27.684724 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Mutating different α-tubulin acetylation sites has distinct effects on axon terminal morphogenesis in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2025.10.27.684845v1?rss=1 Than, H. Welch, C. J. Schauer, E. Trujillo, S. P. Wildonger, J. 2025-10-27 doi:10.1101/2025.10.27.684845 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Systems modeling of mitochondrial dynamics in different exercise regimes ]]> https://biorxiv.org/content/10.1101/2025.10.27.684912v1?rss=1 Khalilimeybodi, A. Qiao, L. Leung, A. McCulloch, A. D. Schenk, S. Rangamani, P. 2025-10-28 doi:10.1101/2025.10.27.684912 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Differentiating the Roles of Metabolic Similarity and Ionic Coupling in Determining the Beta Hub Cell Phenotype ]]> https://biorxiv.org/content/10.1101/2025.10.27.684924v1?rss=1 Devold, I. S. Rokstad, H. Velazquez, J. Browne, S. Edwards, A. G. Kravets, V. 2025-10-28 doi:10.1101/2025.10.27.684924 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ A FINITE ELEMENT FRAMEWORK FOR BULK-SURFACE COUPLED PDES TO SOLVE MOVING BOUNDARY PROBLEMS IN BIOPHYSICS ]]> https://biorxiv.org/content/10.1101/2025.10.27.684936v1?rss=1 Contri, A. Massing, A. Rangamani, P. 2025-10-28 doi:10.1101/2025.10.27.684936 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Control of Synaptic Communication through Molecularly Engineered Bioluminescence Light Emission and Sensing ]]> https://biorxiv.org/content/10.1101/2025.10.27.684942v1?rss=1 Slaviero, A. N. Prakash, M. Bell, E. Schumaker, R. Crespo, E. L. Tree, M. O. Lambert, G. G. Moore, C. I. Shaner, N. C. Lipscombe, D. Hochgeschwender, U. 2025-10-28 doi:10.1101/2025.10.27.684942 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.10.28.685084v1?rss=1 Hensen, T. Khatib, L. Patel, L. McDonald, D. Gonzalez, A. Mahmoudiandehkordi, S. Blach, C. Alzheimer Gut Microbiome Project Consortium, Knight, R. Kaddurah-Daouk, R. Thiele, I. 2025-10-29 doi:10.1101/2025.10.28.685084 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Spatiotemporal Microbial Ecoevolutionary Dynamics on the International Space Station ]]> https://biorxiv.org/content/10.1101/2025.10.28.685245v1?rss=1 Hill, M. S. Simpson, A. C. Minnis, V. Salas Garcia, M. C. Mahnert, A. Lax, S. Rushton, E. Chung, R. Bone, D. Parker, C. W. Allard, S. M. Matty, M. Venkateswaran, K. Gilbert, J. A. 2025-10-29 doi:10.1101/2025.10.28.685245 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Coupling Step-Wise Motility and Traction Force Patterns in chemotaxing cells ]]> https://biorxiv.org/content/10.1101/2025.10.28.685178v1?rss=1 Rappel, W.-J. Echeverria-Alar, S. 2025-10-30 doi:10.1101/2025.10.28.685178 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Stimulation with ECoG electrodes modulates cortical activity and sensory processing in the awake mouse brain ]]> https://biorxiv.org/content/10.1101/2025.10.28.685211v1?rss=1 Ji, N. Fan, J. L. Lee, K. Tchoe, Y. Ganji, M. Vatsyayan, R. Yoon, H. Y. Garrett, J. Dayeh, S. A. Halgren, E. 2025-10-30 doi:10.1101/2025.10.28.685211 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Disruption of the Lacunar Canalicular Network in Type 2 Diabetes: Impaired Osteocyte Connectivity in Zucker Diabetic Rats ]]> https://biorxiv.org/content/10.1101/2025.10.29.683583v1?rss=1 Sieverts, M. Gyulassy, A. Juluru, I. Pascucci, V. Acevedo, C. 2025-10-30 doi:10.1101/2025.10.29.683583 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ A more comprehensive and reliable analysis of individual differences with generalized random forest for high-dimensional data: validation and guidelines ]]> https://biorxiv.org/content/10.1101/2025.10.28.685232v1?rss=1 Lee, J. Park, J. J. Pak, M. Choi, S. Y. Cha, J. 2025-10-31 doi:10.1101/2025.10.28.685232 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review ]]> https://biorxiv.org/content/10.1101/2025.10.29.685397v1?rss=1 Robinson, J. T. Thorvaldsdottir, H. Mesirov, J. P. 2025-10-31 doi:10.1101/2025.10.29.685397 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Extracellular matrix rigidity controls breast cancer metastasis via TYK2-mediated mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.10.30.681251v1?rss=1 Hu, Z. Majeski, H. E. Mestre-Farrera, A. Cai, S. Lalezarzadeh, A. Zhang, Y. Arimoto, K.-I. Zhang, D.-E. Piwnica-Worms, H. Fattet, L. Yang, J. 2025-10-31 doi:10.1101/2025.10.30.681251 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Integrated metabolomic and genomic insights into amino acid incorporation within the hybrid polyketide-alkaloid antibiotic TLN-05220 ]]> https://biorxiv.org/content/10.1101/2025.10.30.685158v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@4402e8org.highwire.dtl.DTLVardef@11af789org.highwire.dtl.DTLVardef@1717c5borg.highwire.dtl.DTLVardef@19b6529_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cordoza, J. L. Johnson, R. A. Whiteley, A. E. Horta, C. A. Nicholas, J. C. Owen, D. M. Rodriguez-Velandia, L. Luu, G. R. Petukhova, V. Z. Calhoun, J. T. Sanchez, L. M. McKinnie, S. M. K. Watts, K. R. 2025-10-31 doi:10.1101/2025.10.30.685158 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires ]]> https://biorxiv.org/content/10.1101/2025.10.30.685465v1?rss=1 Paco, K. Mendivil, M. P. Zhang, Z. Zebardast, S. Davila, C. Mooney, R. M. Olatoyinbo, P. Yang, T. Bassi, S. Gonzales, V. Chen, E. Ashraf, F. B. Roman, I. C. Felix, J. R. Alam, R. M. Lay, J. A. Johal, M. S. Le Roch, K. G. Tolstorukov, I. Hernandez, J. B. da Silva, F. L. B. Lonardi, S. Sazinsky, M. H. Ray, A. 2025-10-31 doi:10.1101/2025.10.30.685465 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Integrative Multi-Omics Identifies CDK1 as a Key Signaling Regulator of CD4+ T Cell Effector Function ]]> https://biorxiv.org/content/10.1101/2025.10.30.685551v1?rss=1 Servaas, N. H. Bauersachs, H. G. Abreu, L. Claringbould, A. Berest, I. Schwarz, J. J. Stein, F. Faelth-Savitski, M. Eismann, L. Reddington, J. P. Zaugg, J. B. 2025-10-31 doi:10.1101/2025.10.30.685551 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ From microbial diversity to function; evaluating dimensionality reduction methods ]]> https://biorxiv.org/content/10.1101/2025.10.30.685628v1?rss=1 Chamberlain, E. J. Boulton, W. Connors, E. Calianos, T. Bowman, J. Creamean, J. Mock, T. Kim, H. H. 2025-10-31 doi:10.1101/2025.10.30.685628 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Sensory receptor expansion and neural accommodation in butterfly color vision ]]> https://biorxiv.org/content/10.1101/2025.10.30.685642v1?rss=1 Gao, K. Ainsworth, J. Donati, A. Zhao, Y. Ragsac, M. F. Genduso, C. Andre, Z. Tomlinson, A. Perry, M. W. 2025-10-31 doi:10.1101/2025.10.30.685642 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Shared Binding Site but Divergent Resistance Profiles Uncover Novel Resistance Mechanisms in Plasmodium HSP90 Inhibitors ]]> https://biorxiv.org/content/10.1101/2025.10.30.684657v1?rss=1 Ko, F.-H. Lukens, A. de Souza, M. L. Foy, A. Hsiao, J. Ndiaye, T. Okombo, J. Yeo, T. Park, H. Uhlemann, A.-C. Boonyalai, N. Kumpornsin, K. Girling, G. Pasaje, C. Godoy, L. Ottilie, S. Durst, G. L. Chatterjee, A. Niles, J. Lee, M. Fidock, D. A. Wirth, D. F. Winzeler, E. 2025-11-01 doi:10.1101/2025.10.30.684657 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ A chromatin-associated pool of Aurora A controls kinetochore-microtubule attachments to ensure chromosome biorientation ]]> https://biorxiv.org/content/10.1101/2025.10.31.685952v1?rss=1 Meaders, J. L. Rodriguez, A. A. Variyar, S. Park, S. Cirulli, A. E. Oegema, K. Corbett, K. D. Desai, A. 2025-11-01 doi:10.1101/2025.10.31.685952 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS ]]> https://biorxiv.org/content/10.1101/2025.10.31.685813v1?rss=1 Le, P. Lal, N. Xu, S. Mumford, S. Huang, M. Yang, D. Mizrahi, O. Hoover, B. Mei, Y. Rothamel, K. Her, H.-L. Blue, S. Shneider, N. Yeo, G. W. 2025-11-02 doi:10.1101/2025.10.31.685813 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Rapid-Response, High-Gain Inkjet-Printed Organic Electrochemical Transistors with Geometry-Optimized Design for Neural Recording and Biosensing ]]> https://biorxiv.org/content/10.1101/2025.11.01.686019v1?rss=1 Khoury, F. Habli, Z. Daorah, J. Xu, Y. Obeid, M. Cauwenberghs, G. Khraiche, M. 2025-11-03 doi:10.1101/2025.11.01.686019 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Activated protein C promotes beta-arrestin-2- and c-Src-dependent caveolin-1 (Cav1) phosphorylation and alters Cav1 association with PAR1 and GRK5 ]]> https://biorxiv.org/content/10.1101/2025.11.02.686166v1?rss=1 Qin, H. Orduna-Castillo, L. Molinar-Inglis, O. Gonzalez Ramirez, M. Lopez-Ramirez, M. A. Bardeleben, C. Trejo, J. 2025-11-03 doi:10.1101/2025.11.02.686166 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants ]]> https://biorxiv.org/content/10.1101/2025.11.02.686167v1?rss=1 Gonzalez Ramirez, M. L. Orduna-Castillo, L. B. Bardeleben, C. Qin, H. Lin, Y. Birch, C. A. Kufareva, I. Trejo, J. 2025-11-03 doi:10.1101/2025.11.02.686167 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Dormant viral pathways underlie space-induced neural senescence: a neuroprotective strategy for spaceflight and neurological diseases ]]> https://biorxiv.org/content/10.1101/2025.11.02.686043v1?rss=1 Martins, A. M. Nakashima, H. Macia, A. Umeyama, T. Miyashita, S. Nascimento, L. L. Coelho, L. B. Mesci, P. Viirre, E. Suarez, N. Saleh, A. Savchenko, A. Freitas, B. Leite, A. L. Assis, D. M. Ishizu, M. Owa, T. Hoshino, M. Yates, J. R. Nakashiima, K. Muotri, A. R. 2025-11-04 doi:10.1101/2025.11.02.686043 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart ]]> https://biorxiv.org/content/10.1101/2025.11.02.686137v1?rss=1 1,800 genes and at whole-organ 3D imaging scale C_LIO_LICombines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics C_LIO_LIGenerates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution C_LIO_LIIntroduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets C_LI ]]> Kern, C. Zhang, Q. Lu, Y. Eschbach, J. Zeng, Z. Farah, E. N. Tai, C.-Y. Yang, K. Jenie, I. Yao, F. Zhao, Z. Ma, Q. Padilla, C. G. Monell, A. Moghadami, S. Zhu, F. Li, B. Hou, A. Tucker, G. Ellison, D. Chi, N. C. Qiu, X. Zhu, Q. Bintu, B. 2025-11-04 doi:10.1101/2025.11.02.686137 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Derivation of functional early gestation decidual natural killer cell subtypes from induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2025.11.03.685424v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@9b182dorg.highwire.dtl.DTLVardef@507037org.highwire.dtl.DTLVardef@f73238org.highwire.dtl.DTLVardef@1021ce0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cheung, V. C. DaCosta, C. Jaimez, J. Arora, H. Caron, C. Slamecka, J. Fierro, M. Meads, M. Fisch, K. Morey, R. E. Pant, D. Kaufman, D. S. Horii, M. Bui, J. D. Parast, M. M. 2025-11-05 doi:10.1101/2025.11.03.685424 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Labile iron overload reprograms microglia and neurons for lipid droplet synthesis in the aging brain ]]> https://biorxiv.org/content/10.1101/2025.11.03.686315v1?rss=1 Cunha e Rocha, K. Xiang, Q. Qian, C. Wang, L. Yuan, W. Beldona, V. Duan, Y. Veras, L. Abolmaali, D. An, G. Park, J. Lim, W. Chen, X. Ying, W. 2025-11-05 doi:10.1101/2025.11.03.686315 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ BudFinder: A Masked Auto-Encoder Vision Transformer Framework for Yeast Budding Detection ]]> https://biorxiv.org/content/10.1101/2025.11.04.686463v1?rss=1 5-fold reduction compared to prior methods while maintaining comparable accuracy. Author SummaryOur work addresses a longstanding challenge in in live-cell time-lapse microscopy analysis, namely, automating cellular division tracking while minimizing the amount of training data required. Traditionally, scientists identify each division event by manually inspecting thousands of time-lapse images, a process that is both tedious and prone to bias. While automated tools exist, they often require large amounts of annotated data to work effectively, limiting their use across different experimental setups. To overcome these barriers, we developed BudFinder, which can recognize and track cell divisions with far less training data. Using yeast replicative aging data as an example, we first trained a model to understand what a yeast cell "looks like", using tens of thousands of segmented yeast cell images entrapped in our custom-built microfluidic device. Then, we taught it to detect budding events directly from time-lapse movies. This approach reduces the need for manual labeling by more than five-fold compared to previous structures in place, while maintaining accuracy comparable to existing methods. By making high-throughput analysis of cellular division more accessible, our work paves the way for faster and more scalable quantification of cellular dynamics. ]]> Nguyen, P. Mousavi Karimi, Z. Layer, A. Wan, M. Su, H. Hasty, J. Hao, N. 2025-11-05 doi:10.1101/2025.11.04.686463 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Large-scale discovery of neural enhancers for cis-regulation therapies ]]> https://biorxiv.org/content/10.1101/2025.11.04.686611v1?rss=1 McDiarmid, T. A. Page, N. F. Chardon, F. M. Daza, R. M. Chen, G. T. Kosicki, M. James, L. M. Nourie, H. C. Laboy-Cintron, D. Lee, A. S. Vij, P. Calderon, D. Lalanne, J.-B. Martin, B. K. Fink, K. Talkowski, M. E. Muotri, A. R. Philpot, B. D. Pennacchio, L. A. Geschwind, D. H. Sanders, S. J. Ahituv, N. Shendure, J. 2025-11-05 doi:10.1101/2025.11.04.686611 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish ]]> https://biorxiv.org/content/10.1101/2025.11.04.686673v1?rss=1 Plominsky, A. M. Allen, E. E. Sims, N. A. Minich, J. J. Podell, S. Oliver, A. Henriquez-Castillo, C. Augyte, S. Lowell-Hawkins, J. 2025-11-05 doi:10.1101/2025.11.04.686673 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686660v1?rss=1 Perets, E. A. Spies, J. A. Cheong, J. H. Shi, L. Asamoto, D. K. Holehouse, A. S. Kim, J. E. Min, W. Neu, J. Yan, E. C. Y. 2025-11-06 doi:10.1101/2025.11.04.686660 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Identification of Protein Cargo in Extracellular Vesicles from Macrophages in Progressing and Regressing Tumors ]]> https://biorxiv.org/content/10.1101/2025.11.05.685429v1?rss=1 Zhu, Y. Cai, J. Suhandynata, R. T. Bui, J. D. 2025-11-06 doi:10.1101/2025.11.05.685429 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Exploring the neuroimmune cellular landscape in the skin of subjects with fibromyalgia. ]]> https://biorxiv.org/content/10.1101/2025.11.05.686713v1?rss=1 Morado-Urbina, C. Agashkov, K. Hunt, M. Tejos-Bravo, M. af Ekenstam, K. Fanton, S. Venckute-Larsson, S. Sandor, K. Linderoth, E. Kuliszkiewicz, A. Arlestig, T. Lofgren, M. Kosek, E. Svensson, C. 2025-11-06 doi:10.1101/2025.11.05.686713 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Omnidirectional 3D Printing of Anisotropic Nanofibrous Peptide Hydrogels ]]> https://biorxiv.org/content/10.1101/2025.11.06.687046v1?rss=1 Farsheed, A. C. Makhoul, J. T. Chew-Martinez, D. Maldonado, E. Liu, J. Yu, L. T. Gorostieta-Salas, E. Jones, J. R. Gage, F. H. Hartgerink, J. D. 2025-11-08 doi:10.1101/2025.11.06.687046 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Modeling Phage Therapy ]]> https://biorxiv.org/content/10.1101/2025.11.08.687339v1?rss=1 De Boer, R. j. Schooley, R. Perelson, A. S. 2025-11-08 doi:10.1101/2025.11.08.687339 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Intrinsic ion dynamics underlies the temporal nature of resting-state functional connectivity ]]> https://biorxiv.org/content/10.1101/2025.11.08.687387v1?rss=1 Gonzalez, O. C. Sanda, P. Hlinka, J. Bazhenov, M. Krishnan, G. 2025-11-09 doi:10.1101/2025.11.08.687387 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ MetaboliteChat: A Unified Multimodal Large Language Model for Interactive Metabolite Analysis and Functional Insights ]]> https://biorxiv.org/content/10.1101/2025.11.07.687008v1?rss=1 Guo, Z. Duan, D. Liang, Y. Patil, A. Xie, P. 2025-11-10 doi:10.1101/2025.11.07.687008 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Structured Neural Variability from Repeated Naturalistic Video Watching Experiences ]]> https://biorxiv.org/content/10.1101/2025.11.07.687258v1?rss=1 Yang, M. Chen, P.-h. A. Brandt, A. M. Sadhukha, S. Farrens, M. Jolly, E. Chang, L. J. 2025-11-10 doi:10.1101/2025.11.07.687258 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Spatial transcriptomics reveals distinct inflammatory and adaptive immune properties of rheumatoid arthritis synovial fibroblasts ]]> https://biorxiv.org/content/10.1101/2025.11.08.687060v1?rss=1 0.5) and Reactome pathway (FDR<0.02) analysis. ResultsDEG analysis of RA compared to OA revealed distinct gene signatures across regions and cell types. RA lining fibroblasts exhibited a strong pro-inflammatory and matrix-destructive signature, while RA sublining fibroblasts showed an unexpected role in antigen presentation and adaptive immunity. RA lining macrophages exhibited enrichment for interleukin signaling, extracellular matrix organization, and translation-related pathways. In contrast, sublining macrophages showed minimal transcriptional differences between RA and OA, suggesting limited pathogenic involvement. Comparison between lining and sublining within RA showed that lining fibroblasts display a higher activated phenotype than sublining cells. ConclusionSpatial transcriptomic analysis uncovers distinct region- and cell-type-specific transcriptional profiles in RA synovium. Lining fibroblasts are highly activated and destructive, and sublining fibroblasts contribute surprisingly to adaptive immunity. This data provides clues to region-cell-type-specific functions that could be exploited to identify novel therapeutic targets. ]]> Machado, C. R. L. Yao, M. Boyle, D. L. Benschop, R. J. Parker, J. T. Wang, W. Firestein, G. S. 2025-11-10 doi:10.1101/2025.11.08.687060 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2025.11.08.687255v1?rss=1 Mesfin, J. M. Chen, A. Lyons, Q. P. Nguyen, M. B. Karkanitsa, M. L. Yu, J. Ninh, V. K. Gardner, E. Wong, E. G. Paleti, S. N. Cheng, J. Bridgelal, B. D. Reimold, K. E. Cao, S. Uhre, C. Luo, C. G. Fu, Z. King, K. R. Christman, K. L. 2025-11-10 doi:10.1101/2025.11.08.687255 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ The blood proteome predicts the impact of circulating factors on age-related mitochondrial health ]]> https://biorxiv.org/content/10.1101/2025.11.09.687483v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@905c12org.highwire.dtl.DTLVardef@18ca82forg.highwire.dtl.DTLVardef@175d397org.highwire.dtl.DTLVardef@966faa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Heimler, S. R. Bergstrom, J. Sun, N. S. Tanaka, T. Moore, A. Z. Candia, J. Chen, B. H. Tian, Q. Bektas, A. Fantoni, G. Dunn, C. Kaileh, M. Sen, R. Ferrucci, L. Molina, A. J. A. 2025-11-11 doi:10.1101/2025.11.09.687483 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Hippocampal indexing alters the stability landscape of synaptic weight space allowing life-long learning ]]> https://biorxiv.org/content/10.1101/2025.11.10.687549v1?rss=1 Gonzalez, O. C. Golden, R. Delanois, J. E. McNaughton, B. L. Bazhenov, M. 2025-11-11 doi:10.1101/2025.11.10.687549 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ An infusible decellularized extracellular matrix material binds to vasculature in infarcted myocardium and induces pro-reparative gene expression following acute myocardial infarction through inherent avidity and bioactive signaling ]]> https://biorxiv.org/content/10.1101/2025.11.12.687915v1?rss=1 Nguyen, M. B. Chen, A. Ninh, V. K. McCabe, M. C. Lyons, Q. P. Luo, C. Bridgelal, B. D. Uhre, C. Reimold, K. E. Cao, S. Hansen, K. C. King, K. R. Christman, K. L. 2025-11-13 doi:10.1101/2025.11.12.687915 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Scalable prediction of symmetric protein complex structures ]]> https://biorxiv.org/content/10.1101/2025.11.14.688531v1?rss=1 8 times the limit of existing machine learning methods. The results demonstrate that protein complexes can be modeled at significantly improved speeds and scales, making Plica-1 a promising tool for protein engineering and drug development. ]]> Yu, V. S. Demsko, P. Castells-Graells, R. Parker, H. Huang, A. Chen, C. Huang, M. Srinivasan, V. Ajjarapu, K. Tofighbakhsh, N. Yu, R. Lake, M. Glanzman, D. Warren, S. Alzagatiti, J. 2025-11-15 doi:10.1101/2025.11.14.688531 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation ]]> https://biorxiv.org/content/10.1101/2025.11.14.688492v1?rss=1 Melendez, D. Sapci, A. O. B. Bafna, V. Mirarab, S. 2025-11-16 doi:10.1101/2025.11.14.688492 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Minute-scale single-cell transcriptomics enables dynamic modeling of cellular behavior ]]> https://biorxiv.org/content/10.1101/2025.11.15.688181v1?rss=1 Asthana, K. Jambor, A. N. Wang, W. 2025-11-17 doi:10.1101/2025.11.15.688181 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Neural ensembles for music production recruit more language instruments as rhythmic complexity increases ]]> https://biorxiv.org/content/10.1101/2025.11.16.688175v1?rss=1 Lei, U. M. Tian, Y. Wang, M. Mu, Y. Choi, C. U. Ho Weatherly, K. I. C. Sereno, M. I. Li, D. Lei, V. L. C. Huang, R.-S. 2025-11-17 doi:10.1101/2025.11.16.688175 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ pH-induced structural changes in SARS-CoV-2 spike variants ]]> https://biorxiv.org/content/10.1101/2025.11.17.688702v1?rss=1 Oliveira, A. S. F. Tulli, L. Kearns, K. L. Casalino, L. Rosenfeld, M. A. Berger, I. Schaffitzel, C. Davidson, A. D. Haddrell, A. E. Reid, J. P. Amaro, R. E. Mulholland, A. J. 2025-11-17 doi:10.1101/2025.11.17.688702 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Aging alters tumor cell - T cell crosstalk to promote breast cancer progression ]]> https://biorxiv.org/content/10.1101/2025.11.17.688754v1?rss=1 Yin, S. Yeung, K. T. Mamde, S. Lin, K. Gandhi, A. Lei, X. Davis, A. Arnold, R. Yang, J. Adams, P. D. 2025-11-17 doi:10.1101/2025.11.17.688754 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Insular error network enables self-correcting intracranial brain-computer interface ]]> https://biorxiv.org/content/10.1101/2025.11.17.688824v1?rss=1 Weger, P. Ottenhoff, M. C. Verwoert, M. Gimple, S. V. Ostrowski, L. Colon, A. Wagner, L. van Dijk, J. P. Temel, Y. Kubben, P. Herff, C. 2025-11-17 doi:10.1101/2025.11.17.688824 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Inhibiting Glycan Degradation Prevents HIV-Induced Inflammaging and Cognitive Impairment ]]> https://biorxiv.org/content/10.1101/2025.11.17.688839v1?rss=1 Giron, L. B. Borjabad, A. Hadas, E. Granche, J. de Menezes, E. G. M. Premeaux, T. A. He, H. Yeung, S. T. T. Singh, S. Friday, C. Glover, J. Balboa, E. Dopkin, D. Burrows, M. Secreto, A. Skuli, N. Tateno, H. Denton, P. W. Palella, F. Corley, M. J. J. Ndhlovu, L. Norris, P. J. Tassiopoulos, K. Volsky, D. J. Abdel-Mohsen, M. 2025-11-17 doi:10.1101/2025.11.17.688839 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Capturing Translation in Action with Protein Synthesis Profiling ]]> https://biorxiv.org/content/10.1101/2025.11.17.688896v1?rss=1 Matta, C. A. Ten, Z. Q. Joseph, S. 2025-11-17 doi:10.1101/2025.11.17.688896 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Structure and mechanism of microtubule stabilization and motor regulation by MAP9 ]]> https://biorxiv.org/content/10.1101/2025.11.17.688911v1?rss=1 Cetin, B. Taheri, A. Golcuk, M. Monroy, B. Y. Fernandes, J. Ori-McKenney, K. M. Gur, M. Nogales, E. Yildiz, A. 2025-11-17 doi:10.1101/2025.11.17.688911 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Deoxyguanosine Kinase Deficiency Couples Purine Metabolism to Innate Immune Activation and Lipid Accumulation in Hepatocytes ]]> https://biorxiv.org/content/10.1101/2025.11.18.688341v1?rss=1 Corey, M. Rayadurgam, M. Jung, J. Gibbons, A. Reddy, N. Vatanmakanian, M. Kakugawa, K. Saminathan, P. Sharma, S. Y. 2025-11-18 doi:10.1101/2025.11.18.688341 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Astrocytic RNA degradation suppresses calcium signaling to support synapse function and restrain anxiety ]]> https://biorxiv.org/content/10.1101/2025.11.18.689044v1?rss=1 Lituma, P. J. Deveci, A. Barrio-Alonso, E. Tan, K. Wilkinson, M. F. Castillo, P. E. Colak, D. 2025-11-18 doi:10.1101/2025.11.18.689044 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Maternal glucocorticoids and behavior shape offspring developmental trade-offs in wild baboons ]]> https://biorxiv.org/content/10.1101/2025.11.18.689046v1?rss=1 Patterson, S. K. Hinde, K. Bowen Bond, A. Trumble, B. C. Lu, A. Strum, S. C. Silk, J. B. 2025-11-18 doi:10.1101/2025.11.18.689046 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Dataset Documentation for Responsible AI: Analysis of Suitability and Usage for Health Datasets ]]> https://biorxiv.org/content/10.1101/2025.11.18.689064v1?rss=1 Heinke, A. Huang, L. Simpkins, K. U. Kalaw, F. G. P. Karsolia, A. Singh, K. Soundarajan, S. Nebeker, C. Baxter, S. L. Lee, C. S. Lee, A. Y. Patel, B. 2025-11-19 doi:10.1101/2025.11.18.689064 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Charting the Undiscovered Metabolome with Synthetic Multiplexing ]]> https://biorxiv.org/content/10.1101/2025.11.18.689170v1?rss=1 Patan, A. Xing, S. Charron-Lamoureux, V. Hu, Z. Deleray, V. Agongo, J. El Abiead, Y. Mannochio-Russo, H. Mohanty, I. Gouda, H. Zemlin, J. Rajkumar, P. Lee, C. Leanos, D. Weimann, N. Tsuda, W. Giddings, S. Bui, T. Kvitne, K. E. Zhao, H. N. Zuffa, S. Nguyen, V. Andrade, A. Goncalves Nunes, W. D. Caraballo-Rodriguez, A. M. Caetano David, L. Carver, J. Bandeira, N. Wang, M. Burnett, L. Siegel, D. Dorrestein, P. C. 2025-11-19 doi:10.1101/2025.11.18.689170 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Dengue Virus NS1 Binds Ephrin B1 to Trigger Endothelial Dysfunction ]]> https://biorxiv.org/content/10.1101/2025.11.19.689067v1?rss=1 Pahmeier, F. Hammond, S. R. Flory, C. Feng, X. Lee, S. E. Jimenez-Posada, E. V. Duarte, E. M. Cardona-Ospina, J. A. Ball, A. H. Lee, N. E. Leung, K. Tjang, L. V. Beatty, P. R. Biering, S. B. Scaturro, P. Harris, E. 2025-11-19 doi:10.1101/2025.11.19.689067 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ GABA-glutamate corelease is a mechanism for state-dependent neurotransmission ]]> https://biorxiv.org/content/10.1101/2025.11.19.689286v1?rss=1 Warlow, S. M. Dowlat, D. S. Hollon, N. G. Faget, L. Oriol, L. Zell, V. Zweifel, L. Hnasko, T. S. 2025-11-19 doi:10.1101/2025.11.19.689286 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Targeting peptide-MHC complexes with designed T cell receptors and antibodies ]]> https://biorxiv.org/content/10.1101/2025.11.19.689381v1?rss=1 Motmaen, A. Jude, K. M. Wang, N. Minervina, A. Feldman, D. Lichtenstein, M. A. Ebenezer, A. Correnti, C. Thomas, P. G. Garcia, K. C. Baker, D. Bradley, P. 2025-11-20 doi:10.1101/2025.11.19.689381 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Force-responsive symmetric cell divisions orient stomata along global tissue axes ]]> https://biorxiv.org/content/10.1101/2025.11.19.689402v1?rss=1 Hartman, K. S. Lopez, B. Y. Gonzalez, J. H. Goetz, M. E. Cleveland, A. Muroyama, A. 2025-11-20 doi:10.1101/2025.11.19.689402 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Cognitive Performance and Brain-Predicted Age Difference in Bipolar Disorder ]]> https://biorxiv.org/content/10.1101/2025.11.20.681142v1?rss=1 Ng, H. X. Sutherland, A. Eyler, L. 2025-11-21 doi:10.1101/2025.11.20.681142 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis ]]> https://biorxiv.org/content/10.1101/2025.11.20.689413v1?rss=1 Ori, D. Okude, H. Konishi, R. Murase, M. Hiroki, S. Takahara, S. Tanaka, T. Toyodome, R. Kano, N. Kawasaki, T. Ishii, K. Kobiyama, K. Nakashima, H. Nakashima, K. Sasai, M. Yamamoto, M. Kumagai, Y. Tsuru, A. Kohno, K. Kawai, T. 2025-11-21 doi:10.1101/2025.11.20.689413 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ YOLito: A generalizable model for automated mosquito detection ]]> https://biorxiv.org/content/10.1101/2025.11.20.689454v1?rss=1 Sar-Shalom, E. Kassner, Z. Sarig, A. Vinauger, C. Coutinho-Abreu, I. Triana, M. F. Bouzada, L. I. Pitts, J. Stensmyr, M. C. Akbari, O. Papathanos, P. A. Bohbot, J. D. 2025-11-21 doi:10.1101/2025.11.20.689454 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Phosphorylation remodels the mitotic centrosome matrix to generate bipartite gamma-tubulin complex docking sites ]]> https://biorxiv.org/content/10.1101/2025.11.20.689565v1?rss=1 Ohta, M. Arakawa, O. Gu, Y. Tian, W. Corbett, K. D. Desai, A. Oegema, K. 2025-11-21 doi:10.1101/2025.11.20.689565 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ A user-friendly machine-learning program to quantify stomatal features from fluorescence images ]]> https://biorxiv.org/content/10.1101/2025.11.20.689597v1?rss=1 Angres, G. J. Gillert, A. Muroyama, A. 2025-11-21 doi:10.1101/2025.11.20.689597 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Comparison of Brain Age Algorithms in Bipolar Disorder ]]> https://biorxiv.org/content/10.1101/2025.11.20.689600v1?rss=1 Ng, H. X. Eyler, L. 2025-11-21 doi:10.1101/2025.11.20.689600 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery. ]]> https://biorxiv.org/content/10.1101/2025.11.21.689547v1?rss=1 Street, L. A. Majumdar, M. Rothamel, K. L. Gogus, E. Brar, G. A. Yeo, G. W. Rube, T. Jovanovic, M. 2025-11-21 doi:10.1101/2025.11.21.689547 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Cannabis-enriched oral Actinomyces induces anxiety-like behavior via impairing mitochondria and GABA signaling ]]> https://biorxiv.org/content/10.1101/2025.11.21.689724v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@120b0b1org.highwire.dtl.DTLVardef@1304782org.highwire.dtl.DTLVardef@a6aa77org.highwire.dtl.DTLVardef@17d6d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Salman, T. Luo, Z. Johnson, D. Noorani, A. A. Wan, Z. Bordieanu, B. Ye, Z.-w. Penrod-Martin, R. Xian, H. Fitting, S. Kalivas, P. Jiang, W. 2025-11-22 doi:10.1101/2025.11.21.689724 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy ]]> https://biorxiv.org/content/10.1101/2025.11.21.689741v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@1897489org.highwire.dtl.DTLVardef@1420587org.highwire.dtl.DTLVardef@178e8ddorg.highwire.dtl.DTLVardef@1003b44_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Karafin, M. S. Issaian, A. V. Bevers, S. Reisz, J. A. Hay, A. Keele, G. R. Dzieciatkowska, M. Cendali, F. I. Haiman, Z. B. Key, A. M. Nemkov, T. Stephenson, D. Marsh, E. Moore, A. Palha, M. S. Legenzov, E. A. Lamb, D. R. Deng, X. Stone, M. Hansen, K. Kleinman, S. Norris, P. J. Busch, M. P. Vallese, F. Palsson, B. O. Spitalnik, S. Kao, J. P. Roubinian, N. H. Janetzko, J. Page, G. P. Eisenmesser, E. Z. Zimring, J. C. Buehler, P. W. D'Alessandro, A. 2025-11-22 doi:10.1101/2025.11.21.689741 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Multiple Quality Control Checkpoints Safeguard Small Nuclear RNA Biogenesis and Prevent Assembly of Aberrant Spliceosomes ]]> https://biorxiv.org/content/10.1101/2025.11.21.689835v1?rss=1 Ma, T. Huntington, C. Song, Z. Lardelli, R. M. Van Nostrand, E. L. Lykke-Anderson, J. 2025-11-23 doi:10.1101/2025.11.21.689835 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Histone H2A Ubiquitination Mediates the Establishment of Reactivation-Competent HSV-1 Latent Infection ]]> https://biorxiv.org/content/10.1101/2025.11.23.690028v1?rss=1 Boehlke, J. M. Dochnal, S. A. Misra, C. S. Cliffe, A. R. Boutell, C. Francois, A. 2025-11-23 doi:10.1101/2025.11.23.690028 Cold Spring Harbor Laboratory Press 2025-11-23 <![CDATA[ Cytokine and Immunoglobulin Dynamics in Phage Therapy: Insights from Clinical Cases ]]> https://biorxiv.org/content/10.1101/2025.11.21.689765v1?rss=1 Ritter, S. R. Clark, J. R. Salazar, K. C. Aslam, S. Maresso, A. W. 2025-11-24 doi:10.1101/2025.11.21.689765 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Machine Learning Analysis of the Human Initiator Reveals New Insights into the Interrelationships between the TATA box, Initiator, and DPR ]]> https://biorxiv.org/content/10.1101/2025.11.21.689830v1?rss=1 Rhyne-Carrigg, T. E. Vo ngoc, L. Medrano, C. Gillespie, K. E. Kadonaga, J. T. 2025-11-24 doi:10.1101/2025.11.21.689830 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Glycerol suppresses lactose-dependent growth of Streptococcus pyogenes through a transcription-independent mechanism ]]> https://biorxiv.org/content/10.1101/2025.11.24.690200v1?rss=1 Bando, A. Hirose, Y. Bertolla, O. M. Takemoto, N. Brouwer, S. O'Donohue, J. Ono, M. Ikeda, E. Nizet, V. Walker, M. J. Kawabata, S. 2025-11-24 doi:10.1101/2025.11.24.690200 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Improved spike-in normalization clarifies the relationship between active histone modifications and transcription ]]> https://biorxiv.org/content/10.1101/2025.11.25.690627v1?rss=1 Patel, L. Cao, Y. Xu, T. Xu, T. Dishon, T. Zhang, L. Mendenhall, E. Heinz, S. Simon, I. Benner, C. Goren, A. 2025-11-26 doi:10.1101/2025.11.25.690627 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ AKAP1 regulates mitochondrial and synaptic homeostasis to enable neuroprotection and repair in retinal ganglion cell degeneration ]]> https://biorxiv.org/content/10.1101/2025.11.24.689866v1?rss=1 Bastola, T. Kim, K.-Y. Shen, Z. Perkins, G. A. Poudel, M. Gomez, V. Lim, Y. Choi, H. Won, J. Y. Choi, S.-H. Ellisman, M. H. Weinreb, R. N. Ju, W.-K. 2025-11-27 doi:10.1101/2025.11.24.689866 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Inferring Local Protein Structural Similarity from Sequence Alone ]]> https://biorxiv.org/content/10.1101/2025.11.24.690129v1?rss=1 Ma, Z. Herrera, J. E. Bethel, N. P. Jinich, A. 2025-11-27 doi:10.1101/2025.11.24.690129 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ The HMGN Proteins Are Transcriptional Regulatory Factors in Humans ]]> https://biorxiv.org/content/10.1101/2025.11.27.690916v1?rss=1 Cruz-Becerra, G. Zau, J. Purow-Ruderman, R. Dao, A. Delatte, B. Chapin, N. Kassavetis, G. A. Kadonaga, J. T. 2025-11-28 doi:10.1101/2025.11.27.690916 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Systemic immune dysregulation in hypertensive disorders of pregnancy persists years after delivery ]]> https://biorxiv.org/content/10.1101/2025.11.25.690209v1?rss=1 Sabayev, M. Ganio, E. A. Stelzer, I. A. Sato, M. Cambriel, A. Bonham, T. A. Juvan, Z. N. Diop, M. Iyer, P. Sedan, O. Aghaeepour, N. Angst, M. S. Shaw, G. M. Stevenson, D. K. Stefanick, M. L. Boyd, H. A. Melbye, M. Hlatky, M. A. Winn, V. D. Gaudilliere, B. Feyaerts, D. 2025-11-29 doi:10.1101/2025.11.25.690209 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Deep Red Blood Cell Proteome Defines the Band 3 N-Terminus Interactome as a Regulator of Hypoxic Adaptation via BLVRB-Dependent S-Nitroso Transfer ]]> https://biorxiv.org/content/10.1101/2025.11.29.691178v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@122468org.highwire.dtl.DTLVardef@114428dorg.highwire.dtl.DTLVardef@11d40c4org.highwire.dtl.DTLVardef@1870fb7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDeep proteomics defines a complete, contamination-free RBC proteome (3,775 proteins) C_LIO_LICross-linking proteomics maps an oxygen-sensitive Band 3-centered interactome C_LIO_LIO2-dependent BLVRB-Band 3 binding regulates metabolism via S-nitrosation of GAPDH C_LIO_LIBand 3 N-terminus is required for hypoxic remodeling and exercise tolerance in vivo C_LI ]]> Issaian, A. V. Dzieciatkowska, M. Bevers, S. Zohreh, S. Hay, A. Saviola, A. Redzic, J. S. Reisz, J. A. Keele, G. R. Cendali, F. I. Haiman, Z. B. Nemkov, T. Stephenson, D. Lisk, C. Vallese, F. Palsson, B. O. King, S. B. Page, G. P. Doctor, A. Hudson, K. E. Hansen, K. C. Irwin, D. C. Mohandas, N. Zimring, J. C. Eisenmesser, E. Z. D'Alessandro, A. 2025-11-30 doi:10.1101/2025.11.29.691178 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Rethinking Alzheimers: Novel miRNAs Illuminate a Disease Beyond the Brain ]]> https://biorxiv.org/content/10.1101/2025.11.27.690929v1?rss=1 Novotny, J. S. Carna, M. Dammer, E. B. Mao, Z. Stokin, G. B. 2025-12-01 doi:10.1101/2025.11.27.690929 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Proteostasis Stress Drives Stem Cell Aging, Clonal Hematopoiesis and Leukemia ]]> https://biorxiv.org/content/10.1101/2025.11.27.690982v1?rss=1 Zhou, F. J. Le, M. Wang, H. C. Yang, W. Wang, H.-Y. Tiwari, A. Cen, X. Sunshine, M. J. Magee, J. A. Signer, R. A. 2025-12-01 doi:10.1101/2025.11.27.690982 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ ClustSIGNAL identifies cell types and subtypes using an adaptive smoothing approach for scalable spatial clustering ]]> https://biorxiv.org/content/10.64898/2025.11.30.691081v1?rss=1 Panwar, P. Guo, B. Zhou, H. Hicks, S. C. Ghazanfar, S. 2025-12-02 doi:10.64898/2025.11.30.691081 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Dual-targeting snRNA gene therapy rescues STMN2 and UNC13A splicing in TDP-43 proteinopathies ]]> https://biorxiv.org/content/10.64898/2025.12.01.691001v1?rss=1 Gomberg, T. Elmsaouri, S. Kopalle, H. M. Baughn, M. W. Beccari, M. S. McAlonis-Downes, M. Artates, J. W. Pant, D. Mak, H. Smargon, A. A. Sander, T. C. Garcia, E. Lee, D. P. Cleveland, D. W. Yeo, G. W. 2025-12-03 doi:10.64898/2025.12.01.691001 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Elucidating an anterior cingulate circuit for self-initiated actions and rescue of Parkinsonian akinesia ]]> https://biorxiv.org/content/10.64898/2025.12.01.691607v1?rss=1 Ulloa Severino, F. Lu, B. Kim, J. Friedman, A. Roshchina, M. Johnson, S. Bakhurin, K. Eroglu, C. Yin, H. 2025-12-03 doi:10.64898/2025.12.01.691607 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ The mitotic stopwatch synergizes with mild p53 activation to halt cell proliferation ]]> https://biorxiv.org/content/10.64898/2025.12.02.691971v1?rss=1 Mierzwa, B. E. Meitinger, F. Desai, A. Oegema, K. 2025-12-03 doi:10.64898/2025.12.02.691971 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization ]]> https://biorxiv.org/content/10.64898/2025.12.02.691876v1?rss=1 Berackey, B. T. Tan, Z. Wu, G. Das, S. C. Li, R. Esser, B. Ye, Q. Nafisi, M. Park, S. S. Sequeira Mendieta, P. A. Berry, J. Mamdani, F. Zhu, Q. Holmes, T. C. Li, D. Wang, T. Behrens, M. M. Ren, B. Ecker, J. R. Bintu, B. Xu, X. 2025-12-05 doi:10.64898/2025.12.02.691876 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Widespread remodeling of the RNA editome underlies transcriptional and clinical heterogeneity in pediatric acute lymphoblastic leukemia ]]> https://biorxiv.org/content/10.64898/2025.12.03.692208v1?rss=1 Jiang, Q. 2025-12-06 doi:10.64898/2025.12.03.692208 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Asymmetric mitochondrial trafficking maintains network morphology by balancing perinuclear biogenesis ]]> https://biorxiv.org/content/10.64898/2025.12.08.692722v1?rss=1 Winter, J. Landoni, J. C. Holt, K. Ben Nejma, S. Durmus, E. B. Kleele, T. Koslover, E. F. Manley, S. 2025-12-08 doi:10.64898/2025.12.08.692722 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine ]]> https://biorxiv.org/content/10.64898/2025.12.08.692990v1?rss=1 Suzuki, E. Deleray, V. Zemlin, J. Kousha, A. Nonoguchi, H. Sun, D. Tsai, C.-M. Zuffa, S. Kvitne, K. E. Dorrestein, P. C. Tsunoda, S. M. Nizet, V. Liu, G. Y. Askarian, F. 2025-12-08 doi:10.64898/2025.12.08.692990 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Investigation of CNS damage following HIV infection and methamphetamine exposure using human iPSC-derived microglia and 3D cerebral assembloid models ]]> https://biorxiv.org/content/10.64898/2025.12.06.692767v1?rss=1 Tiwari, S. K. Baidwan, G. Trescott, S. Jakhmola, S. Coufal, N. G. Rana, T. M. 2025-12-10 doi:10.64898/2025.12.06.692767 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Windows to the goal: Pupillary working memory signatures prospectively adapt to task demands ]]> https://biorxiv.org/content/10.64898/2025.12.06.692784v1?rss=1 Dong, Y. Hung, Y.-c. Xie, C. Kiyonaga, A. 2025-12-10 doi:10.64898/2025.12.06.692784 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Domestic goats can follow the direction of human voices to solve a hidden-object task ]]> https://biorxiv.org/content/10.64898/2025.12.08.692563v1?rss=1 Watson, S. K. Nawroth, C. McElligott, A. G. Rossano, F. Townsend, S. W. 2025-12-10 doi:10.64898/2025.12.08.692563 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Integration of artificial intelligence and high-content screening enabled identification of drugs for long-term treatment of cerebral cavernous malformation disease ]]> https://biorxiv.org/content/10.64898/2025.12.08.693036v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@17bfadforg.highwire.dtl.DTLVardef@936708org.highwire.dtl.DTLVardef@15171ceorg.highwire.dtl.DTLVardef@69029_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Frias-Anaya, E. Gallego-Gutierrez, H. Bui, C. Birrueta, J. O. Steinberg, J. Niesman, I. Gongol, B. Nguyen, B. Sawhney, A. Mizushima, Z. Kilpatrick, B. Awad, I. A. Patel, H. H. Trejo, J. Momper, J. D. Taddei, A. Lopez-Ramirez, M. A. 2025-12-11 doi:10.64898/2025.12.08.693036 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Y-linked editors for invasive rodent control ]]> https://biorxiv.org/content/10.64898/2025.12.08.693037v1?rss=1 Verma, P. Akbari, O. S. Marshall, J. M. 2025-12-11 doi:10.64898/2025.12.08.693037 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Sparse, random sampling is sufficient for central tolerance ]]> https://biorxiv.org/content/10.64898/2025.12.09.693230v1?rss=1 Meyer, H. V. Dasgupta, S. Banerjee, A. Lin, Y. Prabakar, R. K. Chapin, S. R. Kiingsford, C. Navlakha, S. 2025-12-12 doi:10.64898/2025.12.09.693230 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ The Impact of Variant Calling on Substitution Mutational Signature Inference ]]> https://biorxiv.org/content/10.64898/2025.12.09.693327v1?rss=1 Jiang, Z. Au, J. Kazachkova, M. Diaz-Gay, M. Vangara, R. Alexandrov, L. B. 2025-12-12 doi:10.64898/2025.12.09.693327 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations ]]> https://biorxiv.org/content/10.64898/2025.12.11.693698v1?rss=1 Merzliakov, S. Dong, G. Castro, A. Bihie, M. Nichols-Evans, Y. Carter, H. Huang, K.-l. 2025-12-14 doi:10.64898/2025.12.11.693698 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Transcriptional Activation of Estrogen Receptor-alpha and Estrogen Receptor-beta from Elephant Shark (Callorhynchus milii) ]]> https://biorxiv.org/content/10.64898/2025.12.11.693795v1?rss=1 Ao, Y. Narita, H. Takagi, W. Hyodo, S. Baker, M. E. Katsu, Y. 2025-12-14 doi:10.64898/2025.12.11.693795 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Mammalian Cells Integrate Endoplasmic Reticulum and Nuclear Envelope signals to time mitotic entry ]]> https://biorxiv.org/content/10.64898/2025.12.12.693814v1?rss=1 Shiozaki, Y. Codallos, N. Saik, N. Jenkins, D. Lara-Gonzalez, P. Shiau, A. Ullman, K. Niwa, M. 2025-12-15 doi:10.64898/2025.12.12.693814 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Structural Dynamics and Allosteric Communication of a SARS-Like Bat Coronavirus Spike Glycoprotein ]]> https://biorxiv.org/content/10.64898/2025.12.12.693972v1?rss=1 Balogun, T. Kearns, F. Calvo-Tusell, C. Tse, A. L. Acreman, C. M. Casalino, L. Lasso, G. Miller, E. H. Chandran, K. McLellan, J. S. Amaro, R. E. 2025-12-15 doi:10.64898/2025.12.12.693972 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Proteostasis Remodeling Across Development Defines Fetal, Neonatal, and Adult Hematopoietic Stem Cell States ]]> https://biorxiv.org/content/10.64898/2025.12.12.694052v1?rss=1 Yu, H. Kim, Y. J. Chen, K. Liu, A. Z. Sunshine, M. J. Signer, R. A. 2025-12-15 doi:10.64898/2025.12.12.694052 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Enterocloster citroniae and related gut microbiome species modulate Vibrio cholerae biofilm formation through the production of bioactive small molecules ]]> https://biorxiv.org/content/10.64898/2025.12.15.694346v1?rss=1 Pauer, H. Nasiri, S. Magalhaes, N. Nguyen, V. Ferreira, N. Ferreira, L. Bradshaw, A. Kirby, K. Sabapathy, T. Udensi, C. G. Feofanova, V. Moreira, D. Parente, T. Wilde, J. Pride, D. T. Allen-Vercoe, E. Antunes, C. 2025-12-16 doi:10.64898/2025.12.15.694346 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ RPE pseudopods maintain photoreceptor outer segment renewal despite subretinal space expansion in Adam9 knockout mice ]]> https://biorxiv.org/content/10.64898/2025.12.16.694731v1?rss=1 Lewis, T. R. Castillo, C. M. Phan, S. Shores, C. Hayase, K. K. Kim, K.-Y. Ellisman, M. Alekseev, O. Burns, M. E. Arshavsky, V. Y. 2025-12-19 doi:10.64898/2025.12.16.694731 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Tunable multivalent Fe(II)-based glycoassemblies as mimetics for native high-mannose glycans. ]]> https://biorxiv.org/content/10.64898/2025.12.17.694979v1?rss=1 1000-fold range in KD for Fe(II) iminopyridine complexes that can be tuned by factors such as saccharide tether length and number of sugars displayed. Through leveraging systematic molecular-level modifications, we demonstrate that tunable Fe(II) glycan assemblies can be used both as mimetics for high mannose glycans as well as competitive inhibitors for native glycan binding. ]]> Hall, E. Sung, Y.-S. Priest, C. W. Stauber, J. M. Guseman, A. J. 2025-12-19 doi:10.64898/2025.12.17.694979 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ In-cell cryo-electron tomography reveals differential effects of type I and type II kinase inhibitors on LRRK2 filament formation and microtubule association ]]> https://biorxiv.org/content/10.64898/2025.12.18.694444v1?rss=1 Basiashvili, T. Hutchings, J. Chen, S. Karasmanis, E. P. Flaherty, W. A. Leschziner, A. E. Villa, E. 2025-12-19 doi:10.64898/2025.12.18.694444 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Collagen remodeling promotes a GPCR-mediated mechanosensory immune checkpoint in ADGRG1+ CD8+ T cells and serves as a spatial biomarker of response to immunotherapy ]]> https://biorxiv.org/content/10.64898/2025.12.19.695209v1?rss=1 Srivastava, S. Powers, J. J. Mehta, J. H. Marzban, S. Nozaki, R. Karanam, L. S. Torrez, J. Bharambe, H. S. Faraji, F. Chaudhary, R. Bordignon, P. Giliberti, J. Slebos, R. J. C. Johnson, J. O. Gantenbee, C. Song, X. Cassano, M. Guevara-Patino, J. A. Nguyen, D. T. Anderson, A. R. A. Yamauchi, M. West, J. Gutkind, J. S. Chung, C. H. Amelio, A. L. 2025-12-22 doi:10.64898/2025.12.19.695209 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Aging-induced hepatocyte CD44 drives IL6/STAT3 signaling and associates with impaired neighboring T cell function. ]]> https://biorxiv.org/content/10.64898/2025.12.20.695732v1?rss=1 Gandhi, A. Lande, K. Li, Y. Hoffman, F. A. LaPorte, M. Tan, S. Evensen, G. Portillo, B. Teneche, M. G. Arnold, R. Rajesh, A. Proulx, J. Yin, S. Havas, A. P. Miciano, C. Yang, Q. Smoot, E. Mamde, S. Davis, A. Yip, K. Wang, A. Ren, B. Williams, A. Kaech, S. Adams, P. D. 2025-12-22 doi:10.64898/2025.12.20.695732 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Regulatable In Vivo Gene Expression via Adaptamers ]]> https://biorxiv.org/content/10.64898/2025.12.21.695777v1?rss=1 Bryant, J. Herron, L. Doctor, Y. McRae, F. Wang, J. Hirsch, T. Portell, A. Kumar, S. Mali, P. 2025-12-22 doi:10.64898/2025.12.21.695777 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.64898/2025.12.19.695410v1?rss=1 Wirth, C. Zhang, T. Diaz-Gay, M. Steele, C. D. Hoang, P. H. Yang, Y. Khandekar, A. Zhao, W. Sang, J. Leduc, C. Baine, M. K. Travis, W. D. Sholl, L. M. Joubert, P. Homer, R. Yang, S.-R. Tran, T.-V.-T. McElderry, J. P. Hartman, C. Miraftab, M. Lee, O. W. Jones, K. M. Zhu, B. Santamaria, J. M. Schabath, M. B. Yendamuri, S. S. Manczuk, M. Lissowska, J. Swiatkowska, B. Mukeria, A. Shangina, O. Zaridze, D. Holcatova, I. Janout, V. Mates, D. Ognjanovic, S. Savic, M. Kontic, M. Bosse, Y. Rothberg, B. E. G. Christiani, D. C. Gaborieau, V. Brennan, P. Liu, G. 2025-12-23 doi:10.64898/2025.12.19.695410 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Closed-loop acoustic stimulation modified by cathodal tDCS is beneficial for retention ]]> https://biorxiv.org/content/10.64898/2025.12.19.695567v1?rss=1 Hoefer, T. Hoesel, T. Hansen, K. Moelle, M. Peifer, C. Bazhenov, M. Marshall, L. 2025-12-23 doi:10.64898/2025.12.19.695567 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Resolution of collided ribosomes by ZNF598 is required for adipocyte energy dissipation ]]> https://biorxiv.org/content/10.64898/2025.12.19.695646v1?rss=1 KASSOUF, T. Ryder, L. El Ghoz, K. Kucharski, B. A. Dollet, L. Dziaczkowski, F. Snieckute, G. Chen, S. Martinez, J. F. Malinska, D. Loza-Valdes, A. Sliwinska, M. A. Bennett, E. Gerhart-Hines, Z. Bekker-Jensen, S. Sumara, G. 2025-12-23 doi:10.64898/2025.12.19.695646 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A neurorecording toolkit for longitudinal assessments of transplanted human cortical organoids in vivo ]]> https://biorxiv.org/content/10.64898/2025.12.20.695690v1?rss=1 Herrema, K. E. Kharitonova, E. K. Bogatova, D. Wilson, M. Martin, E. A. Chung, C. Puppo, F. Klorfeld-Auslender, S. Boucher, P. Tsai, L.-H. Muotri, A. R. Kuzum, D. Devor, A. O'Shea, T. M. Zeldich, E. Thunemann, M. 2025-12-23 doi:10.64898/2025.12.20.695690 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Longitudinal Neurocognitive Trajectories in a Large Cohort of Youth Who Use Cannabis: Combining Self-Report and Toxicology ]]> https://biorxiv.org/content/10.64898/2025.12.20.695698v1?rss=1 Wade, N. E. Sullivan, R. M. Wallace, A. L. Visontay, R. Szpak, V. Lisdahl, K. M. Huestis, M. A. Goncalves, P. D. Byrne, H. Mewton, L. Jacobus, J. Tapert, S. F. 2025-12-23 doi:10.64898/2025.12.20.695698 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Multiplexed Pan Soluble Ligandome Assaying via OASIS ]]> https://biorxiv.org/content/10.64898/2025.12.21.695830v1?rss=1 Lee, Y.-H. Doctor, Y. Zhang, Y. Kumar, S. Rainaldi, J. Pan, E. Mali, P. 2025-12-23 doi:10.64898/2025.12.21.695830 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado ]]> https://biorxiv.org/content/10.64898/2025.12.22.695989v1?rss=1 Groh, J. S. dos Santos, M. F. S. de Dios, E. A. Ackerman, G. Solares, E. Focht, E. Seymour, D. Gaut, B. S. Arpaia, M. L. Coop, G. 2025-12-24 doi:10.64898/2025.12.22.695989 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Oncogene c-Myc Regulates Upper Respiratory Epithelial Repair for Host Immunity During Acute Influenza Infection ]]> https://biorxiv.org/content/10.64898/2025.12.22.696065v1?rss=1 Foote, A. G. Sun, X. 2025-12-24 doi:10.64898/2025.12.22.696065 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Single-cell chiral symmetry breaking under confinement ]]> https://biorxiv.org/content/10.64898/2025.12.23.696323v1?rss=1 Echeverria-Alar, S. Narasimhan, B. N. Fraley, S. I. Rappel, W.-J. 2025-12-25 doi:10.64898/2025.12.23.696323 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Temporal Multi-Omic Analysis Uncovers Sex-Biased Molecular Programs Underlying Skeletal Muscle Adaptation to Endurance Training ]]> https://biorxiv.org/content/10.64898/2025.12.26.696612v1?rss=1 Many, G. Jin, C. Day, N. Smith, G. R. Iyer, G. Sanford, J. A. Bareja, A. Jimenez-Morales, D. Voos, K. Leach, D. T. A. Goodyear, L. Goodpaster, B. Ortlund, E. A. Burant, C. F. Gaul, D. Viggars, M. R. Kohrt, W. Snyder, M. Fernandez, F. Esser, K. A. Bodine, S. Huffman, K. Kraus, W. Newgard, C. Hevener, A. L. Qian, W.-J. Schenk, S. Adkins, J. N. Lindholm, M. E. 2025-12-27 doi:10.64898/2025.12.26.696612 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Multimodal spatial transcriptomics determines repeat expansion, huntingtin aggregation, and selective cortical neuron loss in Huntington Disease ]]> https://biorxiv.org/content/10.64898/2025.12.26.696622v1?rss=1 50% loss, closely linked to very large (>380{+/-}55) somatic expansions. Intranuclear aggregation was most prevalent at intermediate somatic repeat expansion (220-300 CAGs) and was accompanied by broader transcriptional changes. In contrast, chandelier and somatostatin+ inhibitory interneurons are lost despite only modest repeat expansion or aggregation. These data provide a comprehensive resource and establish a broadly applicable framework for connecting repeat expansion and protein pathology across diverse cell types. Short Bullet pointsO_LIDevelopment of a novel, multimodal spatial transcriptomics platform enables definition of RNA transcriptomes with subcellular resolution, somatic repeat expansions, and protein accumulation in cells within tissue sections C_LIO_LIGeneration of two complementary datasets for HD and control cortex: 428,173 cells to quantify comprehensively cell-type vulnerability, and a deeper multimodal dataset in which CAG repeat expansion, huntingtin aggregation, six additional pathological readouts, and expression of 1,128 genes were measured in 185,721 cells, providing a comprehensive resource for the neurodegeneration community. C_LIO_LIDeep layer excitatory neuron loss (L5-6 NP and L6b) was associated with very large somatic CAG expansions (>380{+/-}55), while selective inhibitory neuron loss (chandelier and somatostatin interneurons) occurred with modest CAG repeat expansion or huntingtin intranuclear aggregation C_LIO_LIIntranuclear aggregation, not somatic repeat expansion, was more predictive of transcriptional changes, including chromatin remodeling and RNA export factors C_LI ]]> Vazquez-Sanchez, S. Arnold-Garcia, O. Chillon-Marinas, C. Maimon, R. McNair, K. Dai, Y. Jimenez-Villegas, N. Cui, J. Thompson, L. M. Lopez-Erauskin, J. Bintu, B. Cleveland, D. W. 2025-12-27 doi:10.64898/2025.12.26.696622 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Neutrophil-neuronal crosstalk drives arthritis-induced pain ]]> https://biorxiv.org/content/10.64898/2025.12.27.696652v1?rss=1 Kurtovic, Z. Vazquez Mora, J. A. Ye, S. Dochnal, S. Sandor, K. Ur Rasheed, M. S. Arvidsson, S. D. Bersellini Farinotti, A. Agalave, N. Wangberg, G. Hunt, M. A. Simon, N. Doring, J. D. M. Kuliszkiewicz, A. Ponce Gomez, L. Lopez Delgado, G. E. Martinez Martinez, A. Mendoza Sanchez, E. Makhmudova, K. Munoz Islas, E. Bollmann, M. Svensson, M. Krock, E. Haglund, L. Jimenez Andrade, J. M. Yaksh, T. L. Lund, H. Svensson, C. I. 2025-12-27 doi:10.64898/2025.12.27.696652 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ The ecology of carbon sequestration in coastal upwelling ecosystems ]]> https://biorxiv.org/content/10.64898/2025.12.29.696936v1?rss=1 half of the BCP in EBUSs), as well as subduction of organic matter and vertically migrating zooplankton and fish. We suggest that a plug-flow-reactor conceptual model can be used to link BCP results with physical circulation changes within EBUSs to predict whether climate change will lead to increased or decreased biologically mediated CO2 uptake. ]]> Stukel, M. R. Aluwihare, L. I. Bianchi, D. Forrer, H. J. Messie, M. 2025-12-30 doi:10.64898/2025.12.29.696936 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Template-based RNA structure prediction advanced through a blind code competition ]]> https://biorxiv.org/content/10.64898/2025.12.30.696949v1?rss=1 Lee, Y. He, S. Oda, T. Rao, G. J. Kim, Y. Kim, R. Kim, H. Heng, C. K. Kowerko, D. Li, H. Nguyen, H. Sampathkumar, A. Enrique Gomez, R. Chen, M. Yoshizawa, A. Kuraishi, S. Ogawa, K. Zou, S. Paullier, A. Zhao, B. Chen, H.-L. Hsu, T.-A. Hirano, T. Gezelle, J. G. Haack, D. Hong, Y. Jadhav, S. Koirala, D. Kretsch, R. C. Lewicka, A. Li, S. Marcia, M. Piccirilli, J. Rudolfs, B. Srivastava, Y. Steckelberg, A.-L. Su, Z. Toor, N. Wang, L. Yang, Z. Zhang, K. Zou, J. Baker, D. Chen, S.-J. Chiu, W. Demkin, M. Favor, A. Hummer, A. M. Joshi, C. K. Kryshtafovyc 2025-12-30 doi:10.64898/2025.12.30.696949 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Glycomimetic Lysosome-targeting Chimeras (GLYTACs) for Degradation of Growth Factors and Growth Factor Receptors in Cancer Cells. ]]> https://biorxiv.org/content/10.64898/2025.12.30.696977v1?rss=1 Follmar, J. L. Tabuchi, T. Godula, K. 2025-12-30 doi:10.64898/2025.12.30.696977 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq ]]> https://biorxiv.org/content/10.64898/2026.01.01.697286v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@1ed0805org.highwire.dtl.DTLVardef@a9c0d9org.highwire.dtl.DTLVardef@b411fborg.highwire.dtl.DTLVardef@8a12e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xu, T. Wang, J. Shin, Y. Cao, Y. Zhang, L. Modolo, E. Dishon, T. Fisher, J. Norton, M. Fry, C. Farjoun, Y. Mendenhall, E. Heinz, S. Benner, C. Goren, A. 2026-01-02 doi:10.64898/2026.01.01.697286 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Targeted 3'-end RNA sequencing uncovers cryptic polyadenylation in Huntington's disease linked to somatic instability and CAG repeat purity ]]> https://biorxiv.org/content/10.64898/2026.01.03.697463v1?rss=1 Velasco-Bilbao, A. Manterola, M. Herrero-Reiriz, A. Carazo-Hidalgo, M. Misiukiewicz, A. Arnold-Garcia, O. Perez-Navarro, E. Hallegger, M. Ule, J. Rabano, A. Lopez de Munain, A. Olejniczak, M. Brito, V. Blazquez, L. 2026-01-03 doi:10.64898/2026.01.03.697463 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ Catestatin ameliorates tauopathy and amyloidogenesis via adrenergic inhibition ]]> https://biorxiv.org/content/10.64898/2026.01.04.697519v1?rss=1 Jati, S. Kal, S. Munoz-Mayorga, D. Tang, K. Sahoo, D. Chen, X. Mahata, S. K. 2026-01-04 doi:10.64898/2026.01.04.697519 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ TubercuProbe: A Cross-Attention Graph-Sequence Model for Cross-Species Chemoproteomic Discovery in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.64898/2026.01.04.697588v1?rss=1 2M ChEMBL compound-protein pairs (predominantly human targets), TubercuProbe achieves R2=0.77 (MSE=0.45) for continuous affinity prediction and transfers effectively to binary cysteine reactivity prediction (CysDB AUPRC=0.63). Ablation studies reveal that pretrained features are highly transferable across freezing strategies ({Delta}AUPRC<0.03), suggesting the model captures fundamental protein-molecule interaction patterns. As a case study, we prioritize cysteine-reactive electrophiles and molecular glues for three Mtb virulence proteins (PtpB, SapM, Rv3671c), providing candidate probes for prospective ABPP validation. Orthogonal comparison with Boltz-2 structure predictions shows moderate correlation (Pearson r{approx}0.69). TubercuProbe provides a lightweight, sequence-driven first-pass ranker that enables pre-experimental prioritization--reducing the time, cost, and experimental burden of chemoproteomic discovery in biosafety-restricted systems. We discuss extensions toward multitask learning that jointly predicts non-covalent binding and covalent reactivity, recognizing that effective covalent probes must both reach their target and react once there. ]]> Chalamalasetty, A. Mishra, A. R. Ferguson, F. Sanchez-Lengeling, B. Barraza-Chavez, J. M. Jinich, A. 2026-01-05 doi:10.64898/2026.01.04.697588 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ P-Rex2 exhibits unique structural features and regulatory mechanisms distinct from the closely related RhoGEF P-Rex1 ]]> https://biorxiv.org/content/10.64898/2026.01.05.697791v1?rss=1 Anderson, L. K. Marde, R. Muma, G. Nayak, V. Phan, C. Li, S. Cash, J. 2026-01-05 doi:10.64898/2026.01.05.697791 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Neurobiological Signatures of Endometriosis: Characterizing Pain, Cognition, and Brain Morphology ]]> https://biorxiv.org/content/10.64898/2026.01.05.696004v1?rss=1 Murata, E. M. Natividad, G. Gabay, A. Grotzinger, H. Santander, T. Giudicessi, A. Fitzgerald, M. Iadipaolo, A. Agarwal, S. K. Panizzon, M. S. Jacobs, E. G. 2026-01-06 doi:10.64898/2026.01.05.696004 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Chromosome axis protein SYCP2 recruits HORMAD2 to enable meiotic synapsis quality control in mice ]]> https://biorxiv.org/content/10.64898/2026.01.06.697704v1?rss=1 Raveendran, K. Valerio-Cabrera, S. Gope, A. Telychko, V. George, G. Richter, C. Scholte, T. Weigel, M. M. Bondarieva, A. Petzold, A. Dahl, A. Corbett, K. D. Toth, A. 2026-01-06 doi:10.64898/2026.01.06.697704 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Partitioning Fraction of Variance Explained into Strong Localized Effects and Weak Diffuse Effects ]]> https://biorxiv.org/content/10.64898/2026.01.06.697735v1?rss=1 Nan, F. Azriel, D. Schwartzman, A. 2026-01-07 doi:10.64898/2026.01.06.697735 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Evolution at experimental epidemic fronts speeds up parasite spread ]]> https://biorxiv.org/content/10.64898/2026.01.06.697932v1?rss=1 Raina, M. Allotta, M. Lombard, J. Deshpande, J. N. Sanchez, C. Gougat-Barbera, C. Gammuto, L. Petroni, G. Kaltz, O. Zilio, G. 2026-01-07 doi:10.64898/2026.01.06.697932 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Ecological Interactions Drive Metabolomic Diversification in Amazonian Pseudonocardia Symbionts ]]> https://biorxiv.org/content/10.64898/2026.01.05.697768v1?rss=1 Grundmann, C. O. Melo, W. G. P. Caraballo Rodriguez, A. M. Guardia, N. U. A. Migliorini, I. L. da Silva, R. R. Dorrestein, P. C. Lopes, N. P. Currie, C. R. Clardy, J. Pupo, M. T. 2026-01-08 doi:10.64898/2026.01.05.697768 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Latent Regulatory Programs Generate Synthetic T Cell States with Enhanced Therapeutic Potential ]]> https://biorxiv.org/content/10.64898/2026.01.07.698190v1?rss=1 5,000-fold antigen-dependent expansion and antitumor activity, contrasting sharply with its native function in driving terminal differentiation. scGOF-seq further identified TF modules that cooperate with cMyc GOF to promote robust CD8 T cell responses in solid tumors. Together, these findings establish GOF perturbation as a powerful strategy for revealing latent immune regulatory programs and engineering synthetic immune states with therapeutic potential. One-Sentence SummaryIn vivo single-cell gain-of-function screening reveals latent transcriptional programs that can reprogram T cells into highly functional synthetic states. ]]> Pratt, B. M. Mullins, G. N. Brown, N. Green, W. D. Modliszewski, J. Xie, F. van Rooyen, L. Zhabotynsky, V. Jambor, A. N. Cannon, G. Green, J. M. Kennedy, A. Alicea Paunto, C. d. M. Shi, H. Merritt, E. Egawa, T. Somasundaram, A. Wang, W. Thaxton, J. E. Dotti, G. Chung, H. K. Milner, J. J. 2026-01-08 doi:10.64898/2026.01.07.698190 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules ]]> https://biorxiv.org/content/10.64898/2026.01.07.698252v1?rss=1 Deleray, V. Charron-Lamoureux, V. Vittali, K. Mannochio-Russo, H. Wang, C. X. Walker, C. Zengler, K. Siegel, D. Dorrestein, P. C. 2026-01-08 doi:10.64898/2026.01.07.698252 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Statistical Atlas-Based Surrogate Model of Biventricular Wall Mechanics ]]> https://biorxiv.org/content/10.64898/2026.01.07.697811v1?rss=1 97%, demonstrating good fidelity to the simulated ground truth. This approach may enable accurate prediction of ventricular wall mechanics without computationally expensive finite element analysis, offering a more feasible method for rapid, subject-specific cardiac modeling. ]]> Robles, A. Konanur, R. Qi, A. Finsberg, H. Sundnes, J. McCulloch, A. D. 2026-01-09 doi:10.64898/2026.01.07.697811 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Benchmarking Peptide Spectral Library Search ]]> https://biorxiv.org/content/10.64898/2026.01.08.698418v1?rss=1 Xu, H. Bandeira, N. 2026-01-09 doi:10.64898/2026.01.08.698418 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity ]]> https://biorxiv.org/content/10.64898/2026.01.08.698420v1?rss=1 Montgomery, T. L. Nelson, E. A. Downs, L. A. Heney, E. R. Lee, M. F. J. Martino, C. McDonald, D. Rahman, G. Knight, R. Krementsov, D. N. 2026-01-09 doi:10.64898/2026.01.08.698420 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Orthogonally targeted tumor radiosensitization using cell penetrating peptide-ATM inhibitor conjugates to stimulate anti-tumor immune responses ]]> https://biorxiv.org/content/10.64898/2026.01.09.698736v1?rss=1 Dhawan, K. Allevato, M. M. Lesperance, J. Camargo, M. F. Cheng, M. M. Mortaja, M. Zareh, B. Hingorani, D. Adams, S. R. Gutkind, J. S. Advani, S. J. 2026-01-12 doi:10.64898/2026.01.09.698736 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Self-Organized Pattern Formation of a Common Tropical Alga ]]> https://biorxiv.org/content/10.64898/2026.01.13.699319v1?rss=1 McNamara, D. E. Lester, C. Edwards, C. B. Smith, J. E. Sandin, S. 2026-01-14 doi:10.64898/2026.01.13.699319 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Templating and confining calcium phosphate mineralization within designed protein assemblies ]]> https://biorxiv.org/content/10.64898/2026.01.14.699524v1?rss=1 Yu, L. T. Pyles, H. Li, X. Borst, A. J. Bethel, N. P. Kwon, P. S. Weidle, C. Kibler, R. D. Carr, K. D. Liu, Y. Moroz, S. Zhang, S. DeYoreo, J. J. Baker, D. 2026-01-14 doi:10.64898/2026.01.14.699524 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Drought tolerance of Aedes aegypti mosquito eggs is influenced by adaptation to local climate conditions and associations with humans ]]> https://biorxiv.org/content/10.64898/2026.01.15.699549v1?rss=1 Chakraborty, S. Zigmond, E. Levan, K. Kennedy, J. Vaka, A. Arya, T. Shah, S. Uhran, M. Harris, A. Sylla, M. Akorli, J. Otoo, S. Rose, N. Holmes, C. Xiao, Y. Benoit, J. B. 2026-01-15 doi:10.64898/2026.01.15.699549 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance ]]> https://biorxiv.org/content/10.64898/2026.01.14.699484v1?rss=1 Baker, J. L. Tang, J. Guo, M. Farias-da-Silva, F. F. Barbisan, M. Burnside, M. Crofton, K. Williams, S. Rao, S. Lee, M. Drucker, S. G. Higashi, D. L. Merrit, J. Hirose, Y. Jan-Willem, V. Nizet, V. 2026-01-16 doi:10.64898/2026.01.14.699484 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Illuminating spatial dynamics of glutamine metabolism with a sensitive genetically encoded biosensor ]]> https://biorxiv.org/content/10.64898/2026.01.15.699810v1?rss=1 Scully, J. M. Sun, M. J. Das, S. Arias, N. J. Kapelczak, E. D. Robinson, T. D. Vineall, K. G. Dean, T. S. TeSlaa, T. Divakaruni, A. S. Schmitt, D. L. 2026-01-16 doi:10.64898/2026.01.15.699810 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Rigor and Transparency in two neurotrauma-publishing journals: editorial policies improve transparent reporting. ]]> https://biorxiv.org/content/10.64898/2026.01.16.699952v1?rss=1 Bandrowski, A. E. Namburi, A. Ferguson, A. R. Floyd, C. L. Martone, M. E. PRECISE-TBI Authors, T. 2026-01-19 doi:10.64898/2026.01.16.699952 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Transforming Growth Factor β1 Modulates Sex Differences in Cardiac Myofibroblast Activation on Hydrogel Biomaterials ]]> https://biorxiv.org/content/10.64898/2026.01.16.699818v1?rss=1 Faust, M. N. Nguyen, A. K. Gorashi, R. M. Felix Velez, N. E. Loud, M. C. Aguado, B. A. 2026-01-20 doi:10.64898/2026.01.16.699818 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Circulating biomarkers in serum from aortic valve stenosis patients predict sex-specific drug responses in valve myofibroblasts ]]> https://biorxiv.org/content/10.64898/2026.01.16.700010v1?rss=1 Vogt, B. J. Chavez, M. Felix Velez, N. E. Gorashi, R. M. Reeves, R. R. Aguado, B. A. 2026-01-20 doi:10.64898/2026.01.16.700010 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Curcumin Alleviates Systemic Inflammation and Gut Dysbiosis Induced by Circadian Rhythm Disruption in a Rodent Model of Jet Lag ]]> https://biorxiv.org/content/10.64898/2026.01.18.698756v1?rss=1 Mandyam, T. Licamele, M. Besmer, M. Peters, G. Simpson, S. 2026-01-20 doi:10.64898/2026.01.18.698756 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Co-option of Lysosomal Machinery for Biomineralization ]]> https://biorxiv.org/content/10.64898/2026.01.19.700231v1?rss=1 Rangarajan-Paul, M. Nichols, S. A. Tresguerres, M. 2026-01-20 doi:10.64898/2026.01.19.700231 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Direct binding of chromosome axis and cohesin complexes underlies meiotic chromosome architecture in fungi and plants ]]> https://biorxiv.org/content/10.64898/2026.01.19.700424v1?rss=1 Mendez Diaz, F. Huo, J. Corbett, K. D. 2026-01-20 doi:10.64898/2026.01.19.700424 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Deconvolving Phylogenetic Distance Mixtures ]]> https://biorxiv.org/content/10.64898/2026.01.18.700179v1?rss=1 Arasti, S. Sapci, A. O. B. Rachtman, E. El-Kebir, M. Mirarab, S. 2026-01-21 doi:10.64898/2026.01.18.700179 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ A Clinically Silent Resistance Phenotype That Promotes Acinetobacter baumannii Survival During Colistin Therapy ]]> https://biorxiv.org/content/10.64898/2026.01.20.700680v1?rss=1 Yaqub, M. Bonde, N. Maity, T. Arugonda, R. Du, Z. Rudra, C. Tiwari, S. Olea-Ozuna, R. J. Nandy, S. Boll, J. Monk, J. Dillon, N. 2026-01-21 doi:10.64898/2026.01.20.700680 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Computational pipeline reveals nature's untapped reservoir of halogenating enzymes ]]> https://biorxiv.org/content/10.64898/2026.01.20.700248v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@ebae51org.highwire.dtl.DTLVardef@10188f0org.highwire.dtl.DTLVardef@1c55684org.highwire.dtl.DTLVardef@b311bd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Szenei, J. Burke, A. Liong, A. Korenskaia, A. Lukowski, A. L. Ziemert, N. Nikel, P. I. Leao, P. N. Moore, B. S. Weber, T. Blin, K. 2026-01-22 doi:10.64898/2026.01.20.700248 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution ]]> https://biorxiv.org/content/10.64898/2026.01.21.700733v1?rss=1 Wacker, A. Fantasia, R. J. Tenner, B. J. Wu, J. Monell, N. A. Kosuri, P. 2026-01-22 doi:10.64898/2026.01.21.700733 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Environmental Fungi Modulate the Vaginal Mycobiome and Cervical Disease Progression in Hispanic Women ]]> https://biorxiv.org/content/10.64898/2026.01.21.700834v1?rss=1 Godoy-Vitorino, F. Vargas Robles, D. Bolanos-Rosero, B. Pagan-Zayas, N. Cortes-Nazario, A. Wiggin, K. Allard, S. Romaguera, J. Gilbert, J. A. 2026-01-22 doi:10.64898/2026.01.21.700834 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Heterologous betacoronavirus spike immunization in nonhuman primates elicits cross-reactive antibodies that neutralize both sarbeco- and merbecoviruses ]]> https://biorxiv.org/content/10.64898/2026.01.22.700386v1?rss=1 Dueker, K. Capozzola, T. Feng, Z. Lin, R. N. Hurtado, J. Bangaru, S. Yuan, M. Beutler, N. Garcia, E. He, W.-t. Callaghan, S. Avillion, G. Vo, L. Li, X. Torres, J. L. Musharrafieh, R. Song, G. Mishra, N. Sharma, P. Yong, P. Anzanello, F. Kaczmarek-Michaels, K. Ben-Akiva, E. Silva, M. Melo, M. Makhdoomi, M. Westfall-Gomez, E. Rinaldi, W. Ferguson, M. Safonova, Y. Crotty, S. Irvine, D. J. Rogers, T. Ward, A. B. Briney, B. Wilson, I. A. Burton, D. R. andrabi, R. 2026-01-23 doi:10.64898/2026.01.22.700386 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ CRISPR-mediated conditional mutagenesis of Smad1/5/8 reveals BMP/GDF signaling restricts postnatal bone overgrowth ]]> https://biorxiv.org/content/10.64898/2026.01.22.701170v1?rss=1 Levina, R. Weitzel, A. J. Liu, A. Y. Low, B. E. Ford, P. W. Halaby, H. Grunwald, H. A. Gacasan, E. G. Moharrer, Y. Sah, R. L. Bennett, E. J. Boerckel, J. D. Wiles, M. V. Cooper, K. L. 2026-01-23 doi:10.64898/2026.01.22.701170 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A Manifold-Based Measure of Transcriptional Entropy for Quantifying Aging in Single Cells ]]> https://biorxiv.org/content/10.64898/2026.01.24.701460v1?rss=1 Yang, Y. Hess, P. R. Huang, S. Teneche, M. G. Wang, H. Miller, K. N. Davis, A. E. Miciano, C. Li, K. Y. Mamde, S. Yip, K. Ren, B. Yang, Q. Smoot, E. Wang, A. Johnson, B. Wilson, P. Adams, P. D. Zhang, N. R. 2026-01-24 doi:10.64898/2026.01.24.701460 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ Csf1r-mediated depletion of midbrain microglia prevents dopaminergic neuron loss during chronic colitis ]]> https://biorxiv.org/content/10.64898/2026.01.23.700559v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1bf7217org.highwire.dtl.DTLVardef@1db66c0org.highwire.dtl.DTLVardef@136ef2eorg.highwire.dtl.DTLVardef@190f641_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. C_FIG ]]> Kutscherauer, R. K. Stolzer, I. Neumaier, E. E. Dedden, M. Kielkowski, P. Xiang, W. Grotemeyer, A. Prinz, M. Masuda, T. Knobeloch, K.-P. Rothhammer, V. Zundler, S. Schlachetzki, J. C. Winkler, J. Guenther, C. Suess, P. 2026-01-26 doi:10.64898/2026.01.23.700559 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Sonogenetic control of cardiomyocytes and cardiac pacing using exogenous Transient Receptor Potential A1 channels ]]> https://biorxiv.org/content/10.64898/2026.01.24.701376v1?rss=1 Zhang, L. Zhang, J. Wang, T.-M. Walsh, C. Sheikh, F. Chalasani, S. H. Friend, J. 2026-01-26 doi:10.64898/2026.01.24.701376 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ BiomarkerKB: FAIR and Integrated Biomarker Knowledge Connecting Biomolecular and Clinical Data Types ]]> https://biorxiv.org/content/10.64898/2026.01.26.701395v1?rss=1 Masood, D. Kim, M. Vora, J. Kahsay, R. McNeeley, P. Kim, S. Kulkarni, S. V. Natale, D. A. Maurya, M. Ramachandran, S. Gupta, S. Bologa, C. G. DeNapoli, T. S. Metzger, V. T. Kumar, P. Ahmed, N. Evangelista, J. E. Kelly, S. C. Sepulveda, J. Ma'ayan, A. Silverstein, J. Taylor, D. M. Crichton, D. J. Mahabal, A. Yang, J. J. Lambert, C. G. Subramaniam, S. Tiemeyer, M. Ranzinger, R. Mazumder, R. 2026-01-27 doi:10.64898/2026.01.26.701395 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Efficient and scalable Python implementation of ANCOM-BC for omics differential abundance testing ]]> https://biorxiv.org/content/10.64898/2026.01.26.701398v1?rss=1 Wu, Z. Lin, H. Morton, J. Zhu, Q. 2026-01-28 doi:10.64898/2026.01.26.701398 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Spatial transcriptomics reveals brain-wide circadian disruption in an Alzheimer's disease model ]]> https://biorxiv.org/content/10.64898/2026.01.26.701799v1?rss=1 Gelber, A. Romero, H. Burrows, D. Whittaker, D. S. Carlin, D. Mukamel, E. A. Desplats, P. 2026-01-28 doi:10.64898/2026.01.26.701799 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data ]]> https://biorxiv.org/content/10.64898/2026.01.24.701521v1?rss=1 Mannochio-Russo, H. Goncalves Nunes, W. D. Xing, S. de Oliveira, F. Caraballo-Rodriguez, A. M. Portal Gomes, P. W. Charron-Lamoureux, V. Agongo, J. Avalon, N. E. Bui, T. Cancelada, L. Chevrette, M. G. Cumsille, A. de Araujo, M. B. De Graeve, M. Deleray, V. Donia, M. S. Dzveta, M. B. El Abiead, Y. Ellis, R. J. Franklin, D. Garg, N. Gouda, H. Hamany Djande, C. Y. Hiskia, A. Ho, B. N. Hughes, C. C. Hwang, S. Iliakopoulou, S. Iudicello, J. E. Jarmusch, A. K. Kaloudis, T. Koester, I. Konkel, R. Koolen, H. H. F. Kvitne, K. E. La Rosa, S. L. Lam, A. Lamichhane, S 2026-01-29 doi:10.64898/2026.01.24.701521 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ SUMO2 Deletion Changes Chromatin Accessibility and Enhances Cytotoxic T Cell Activation and Tumor Infiltration ]]> https://biorxiv.org/content/10.64898/2026.01.27.700738v1?rss=1 Don, N. T. M. Chen, D.-H. Amaral, M. L. J. Ren, T. Kuang, Y. Huang, S.-T. Chilakapati, N. Ren, B. Schoenberger, S. P. Zheng, Y. Chen, Y. 2026-01-29 doi:10.64898/2026.01.27.700738 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons ]]> https://biorxiv.org/content/10.64898/2026.01.28.702385v1?rss=1 Heffel, M. G. Xu, H. Pastor-Alonso, O. Li, X. Baig, M. S. Irfan Ghoor, R. Li, R. Kern, C. Kum, J. Zhang, Y. Paino, J. Tsai, M. J. Tai, C.-Y. Tucker, G. Zhao, Z. Hou, A. von Behren, Z. Bhade, M. Li, S. Sandoval, K. Scholes, J. Codrea, F. Calimlim, J. Liao, E. K. Leung, G. Kim, J. Eskin, E. Flint, J. Cotter, J. A. Pasaniuc, B. Bintu, B. Zhu, Q. Mukamel, E. A. Ernst, J. Paredes, M. F. Luo, C. 2026-01-29 doi:10.64898/2026.01.28.702385 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A high fermentable fiber Western diet reduces indole levels ]]> https://biorxiv.org/content/10.64898/2026.01.27.702025v1?rss=1 Priyadarshini, M. Jorgensen, J. Stauffer, S. R. C. Issa, L. Pandya, N. Nnyamah, C. Xu, K. Boyett, J. E. Kular, P. Mhatre, A. Brahambhatt, V. H. Gilbert, J. A. Khan, M. W. Wicksteed, B. Dai, Y. Layden, B. T. 2026-01-30 doi:10.64898/2026.01.27.702025 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Endothelial MRG15 Is a Mechanosensitive Suppressor of Atherosclerosis ]]> https://biorxiv.org/content/10.64898/2026.01.28.702256v1?rss=1 Li, Y. Lin, X. Ma, J. Jiang, Q. Lin, J. Qu, L. Ding, Q. Wei, X. Zhi, X. Zhang, P. Shyy, J. Y.- J. Osto, E. Dai, Y. Guo, J. Meng, D. 2026-01-30 doi:10.64898/2026.01.28.702256 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Flexibility of cell fates and functions across sex determination systems revealed by comparative single-cell analyses ]]> https://biorxiv.org/content/10.64898/2026.01.29.701242v1?rss=1 Acemel, R. D. Tezak, B. M. Chung, V. W. Y. Hurtado, A. Albertson, S. Weber, C. J. Capel, B. Lupianez, D. G. 2026-01-30 doi:10.64898/2026.01.29.701242 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.01.29.702575v1?rss=1 Zhang, W. Ding, W. Li, K. Chang, L. Klein, A. Baez-Becerra, C. T. Rink, J. A. Bartlett, A. Chen, H. Schenker, N. Johansen, N. Mollenkopf, T. Fu, Y. Yang, X. Liu, S. Seng, C. Miao, B. Liu, T. Zhu, Q. Hodge, R. D. Bakken, T. E. Lein, E. S. Hawrylycz, M. Xu, X. Behrens, M. M. Ren, B. Ecker, J. R. Wang, T. Li, D. 2026-01-30 doi:10.64898/2026.01.29.702575 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Neural representations of dynamic social interactions ]]> https://biorxiv.org/content/10.64898/2026.02.01.703160v1?rss=1 Kwon, D. Jolly, E. Chang, L. Shim, W. M. 2026-02-02 doi:10.64898/2026.02.01.703160 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Forward Programming Identifies Inducers of Blood-Brain Barrier Properties in Human Pluripotent Stem Cell-Derived Endothelial Cells ]]> https://biorxiv.org/content/10.64898/2026.02.02.699492v1?rss=1 Tamhankar, S. Ding, Y. Yaghoobi Hashjin, F. Boutom, S. M. Daneman, R. Palecek, S. P. Shusta, E. V. 2026-02-03 doi:10.64898/2026.02.02.699492 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain ]]> https://biorxiv.org/content/10.64898/2026.02.02.703166v1?rss=1 750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. C_LI ]]> Xie, Y. Chang, L. Zhong, G. Rink, J. A. Baez-Becerra, T. Armand, E. Ding, W. Li, K. Boone, E. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Huang, B. Wang, Z. Barcoma, A. S. Willier, J. K. Knutson, K. W. Liu, J. Cho, S. Cao, S. Russo, K. G. Young, C. K. Arzavala, J. Sanchez, Y. Bikkina, A. Schenker-Ahmed, N. Kern, C. Zhao, Z. Klein, A. Flores, J. Tai, C.-Y. Olness, J. Monell, A. Moghadami, S. Barragan, C. Chen, C. Owens, W. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Emerson, N. Osteen, J. Lucero, J. Li, D. Hodge, R. D. Wang, T. Keene, 2026-02-03 doi:10.64898/2026.02.02.703166 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Simultaneous optimization of lignocellulosic sugar catabolism via systematic laboratory evolution in dynamic conditions ]]> https://biorxiv.org/content/10.64898/2026.02.02.702459v1?rss=1 Feist, A. M. Woo, S. Lim, H. G. Norton-Baker, B. Lind, T. M. Gladden, N. E. Chen, Y. Eng, T. Johnson, C. W. Mukhopadhyay, A. Petzold, C. J. Guss, A. M. Beckham, G. T. 2026-02-04 doi:10.64898/2026.02.02.702459 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ The CD8 immgenT framework as a universal reference of mouse CD8 Tαβ cell differentiation states ]]> https://biorxiv.org/content/10.64898/2026.02.02.703365v1?rss=1 200,000 single-cell transcriptomes and 128-plex surface proteomes from 734 samples spanning multiple perturbations, tissues, and timepoints. Unbiased analysis identifies 21 states encompassing naive, effector, circulating memory, tissue-resident memory, progenitor-exhausted, and terminally-exhausted compartments, among others. These states re-emerge with striking molecular convergence across acute/chronic infections, cancer, autoimmunity, aging, and homeostasis, showing that near-identical transcriptional programs support protective or dysfunctional outcomes depending on developmental history and microenvironment. Classic archetypes map to discrete clusters but exhibit unappreciated heterogeneity and overlap, cautioning against rigid nomenclature. We provide validated combinatorial markers, flow cytometry gating strategies, and immgenT reference-based integration for reproducible annotation of new datasets. This universal coordinate system harmonizes fragmented CD8 T cell literature and clarifies relationships across diverse immune challenges. ]]> Galletti, G. Globig, A.-M. Barreiro, O. Heim, T. A. Liu, S. Borys, S. M. Casey, O. Monell, A. T. Patravali, D. Scharping, N. E. Quon, S. Takehara, K. K. Ferry, A. Cheung, K. P. Duong, E. Shinkawa, T. Spranger, S. Behar, S. M. Kaech, S. M. Goldrath, A. W. Zemmour, D. ImmgenT Project, 2026-02-04 doi:10.64898/2026.02.02.703365 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Rapid optogenetic manipulation of autophagy reveals that the nuclear pore complex is a robust autophagy substrate ]]> https://biorxiv.org/content/10.64898/2026.02.03.703609v1?rss=1 Mondal, P. Cyril, A. Mamriev, D. Parham, L. Wierzbicki, I. Shen, C. Gonzalez, D. J. DAngelo, M. A. Towers, C. G. 2026-02-04 doi:10.64898/2026.02.03.703609 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.02.03.703645v1?rss=1 Chang, L. Li, K. Xie, Y. Zhong, G. Rink, J. A. Baez-Becerra, C. T. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Wang, Z. Zu, S. Kern, J. C. Zhao, Z. Boone, E. Flores, J. Monell, A. Olness, J. Barragan, C. Osgood, E. Owens, W. Schenker-Ahmed, N. Zhang, W. Liu, D. Barcoma, A. S. Willier, J. K. Knutson, K. W. Russo, K. G. Liu, J. Cho, S. Arzavala, J. Young, C. K. Sundaram, G. V. Manning, A. C. Sanchez, Y. Bikkina, A. Berry, J. Gao, X. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Zhu, C. Zemke, N. R. Ding, W. Klein, A. Fu, Y. Johansen, N. B 2026-02-04 doi:10.64898/2026.02.03.703645 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Active gaze behavior organizes V1 activity in freely-moving marmosets ]]> https://biorxiv.org/content/10.64898/2026.02.05.704079v1?rss=1 Li, J. Singh, V. P. Mitchell, J. F. Huk, A. C. Miller, C. T. 2026-02-07 doi:10.64898/2026.02.05.704079 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Structural basis of caveolin-driven membrane bending ]]> https://biorxiv.org/content/10.64898/2026.02.05.703862v1?rss=1 Connelly, S. M. Bergner, L. Tiwari, A. Brant, T. S. Medford, S. Ramesh, S. Tidwell, E. D. Yoo, Y. Xiao, K. Gentry, J. Chang, L. Han, B. Rangamani, P. Doktorova, M. Kenworthy, A. K. Mosalaganti, S. Ohi, M. D. 2026-02-08 doi:10.64898/2026.02.05.703862 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ Highly Sensitive Chemigenetic FRET-Based Kinase Biosensors ]]> https://biorxiv.org/content/10.64898/2026.02.06.702961v1?rss=1 He, X. Zhou, D. R. Huan, Y. Berriman-Rozen, Z. Mehta, S. Chen, Y. Frei, M. S. Zhang, J. 2026-02-09 doi:10.64898/2026.02.06.702961 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ A time-calibrated phylogeny of hummingbirds supports stepwise diversification in the Andes ]]> https://biorxiv.org/content/10.64898/2026.02.06.704360v1?rss=1 da Fonseca, R. R. Graves, G. R. R. Mirarab, S. Winkelmann, I. E. Claramunt, S. Fonseca, M. M. Samaniego Castruita, J. A. Penaloza, F. Li, C. Rocha, S. Escalona, M. Sanz Moreta, L. Albrechtsen, A. Warnow, T. Fjeldsa, J. Gilbert, M. T. P. Rahbek, C. 2026-02-09 doi:10.64898/2026.02.06.704360 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin ]]> https://biorxiv.org/content/10.64898/2026.02.09.704686v1?rss=1 Adepoju, L. A. McKaig, J. M. Salcedo, R. S. R. Martinez, A. Buessecker, S. Skoog, E. J. Elbon, C. E. Paris, E. R. Desmarais, M. Sephus, C. D. Pozarycki, C. Hegelein, V. Quartini, E. S. Schartup, A. T. Doran, P. T. Carr, C. E. Ingall, E. D. Bartlett, D. H. Murali, R. Raven, M. R. Dekas, A. E. Bowman, J. S. Schmidt, B. E. Glass, J. B. 2026-02-09 doi:10.64898/2026.02.09.704686 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Metabolic Perturbation Exacerbates Sinoatrial Node Dysfunction in Heart Failure ]]> https://biorxiv.org/content/10.64898/2026.02.06.704519v1?rss=1 Ren, L. Liu, Y. Zhang, H. Diloretto, D. A. Zheng, Y. Caudal, A. Xie, M. Zeng, W. Woltz, R. L. Shin, H. S. Ngo, R. Q. Perkins, G. A. Grigorean, G. Yamoah, E. N. Wu, J. C. Chiamvimonvat, N. Thai, P. N. 2026-02-10 doi:10.64898/2026.02.06.704519 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Whole-Brain Co-Mapping of Gene Expression and NeuronalActivity at Cellular Resolution in Behaving Zebrafish ]]> https://biorxiv.org/content/10.64898/2026.02.07.704095v1?rss=1 Marquez Legorreta, E. Fleishman, G. M. Hesselink, L. W. Eddison, M. Smeets, K. Stringer, C. Keller, P. J. Narayan, S. Chen, A. B. Mensh, B. D. Sternson, S. M. Englitz, B. Tillberg, P. W. Ahrens, M. B. 2026-02-10 doi:10.64898/2026.02.07.704095 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Proteostasis sustains T cell differentiation potential and tumor-infiltrating lymphocyte function ]]> https://biorxiv.org/content/10.64898/2026.02.08.704716v1?rss=1 Scharping, N. Ge, X. Matias, M. Jiang, F. Cafferata, A. Heeg, M. Monell, A. T. Galletti, G. Cheung, K. Rock, A. Thao, N. Shuttleworth, S. Bauer, M. Takehara, K. Ferry, A. Quon, S. Koss, B. Myers, S. Bennett, E. J. Goldrath, A. W. 2026-02-10 doi:10.64898/2026.02.08.704716 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Existence of Causation without Correlation in Transcriptional Networks ]]> https://biorxiv.org/content/10.64898/2026.02.09.704821v1?rss=1 Pao, G. M. Deyle, E. R. Ye, H. Ogawa, J. Guaderrma, M. Ku, M. Lorimer, T. M. Tonnu, N. U. Saberski, E. Park, J. Ke, E. Wittenberg, C. Verma, I. M. Sugihara, G. 2026-02-10 doi:10.64898/2026.02.09.704821 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Rp-vasa: a bona fide Primordial Germ Cell marker that drives embryonic expression in the Chagas disease vector Rhodnius prolixus ]]> https://biorxiv.org/content/10.64898/2026.02.09.704890v1?rss=1 Martins, G. Berni, M. Guedes-Silva, T. Vieira, J. Cardoso, M. Pane, A. Gantz, V. M. Bier, E. Araujo, H. M. 2026-02-11 doi:10.64898/2026.02.09.704890 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Compositional decoding of neural activity enhances generalization in handwriting BCIs ]]> https://biorxiv.org/content/10.64898/2026.02.09.704932v1?rss=1 Narasimha, S. M. Huang, J. Sristi, R. D. Gilja, V. Mishne, G. 2026-02-11 doi:10.64898/2026.02.09.704932 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia ]]> https://biorxiv.org/content/10.64898/2026.02.10.704353v1?rss=1 Rossi, F. Sportelli, L. Kikidis, G. C. Grassi, G. Di Camillo, F. Bertolino, A. Blasi, G. Borcuk, C. Fusco, D. Hyde, T. M. Kleinman, J. E. Marnetto, D. Pellegrini, S. Rampino, A. Vitiello, B. ripke, s. Braun, A. Kraft, J. Belangero, S. I. Menezes, P. R. Arango, C. Walters, J. O'Donovan, M. C. Owen, M. J. Braff, D. Corvin, A. Morris, D. W. Domenici, E. van Os, J. Atbasoglu, E. Saka, M. C. Di Forti, M. baune, B. T. Pato, C. N. McQuillin, A. Golimbet, V. Kondratyev, N. Escott-Price, V. Gareeva, A. Khusnutdinova, E. Cervilla, J. A. Rivera, M. Laurent-Levins 2026-02-11 doi:10.64898/2026.02.10.704353 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ PRECISE TBI Model Catalog: Increasing Accessibility and Reproducibility in TBI research ]]> https://biorxiv.org/content/10.64898/2026.02.10.704562v1?rss=1 Surles-Zeigler, M. C. Holmes, L. Sincomb, T. Martone, M. E. Grethe, J. Ferguson, A. R. Dixon, C. E. 2026-02-12 doi:10.64898/2026.02.10.704562 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.02.12.705594v1?rss=1 Ding, W. Klein, A. Baez-Becerra, C. T. Rink, J. A. Bartlett, A. Zeng, Q. Wang, R. Castanon, R. G. Nery, J. R. Osgood, E. Owens, W. Petrella, A. Chen, C. Acerbo, A. S. Barcoma, A. S. Liu, J. Russo, K. G. Knutson, K. W. Young, C. K. Willier, J. K. Barragan, C. Arzavala, J. Cho, S. Altshul, J. Chan, D. Soma, E. Luo, J. Jain, M. Velazquez, S. Schenker-Ahmed, N. Sundaram, G. V. Manning, A. C. Sanchez, Y. Bikkina, A. Fu, S. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Berry, J. Kern, C. Boone, E. Tian, W. Wu, Y. Hariharan, M. Fu, Y. Xie, Y. L 2026-02-14 doi:10.64898/2026.02.12.705594 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Rhomboid protease Rhbdl2 regulates macrophage recruitment and wound regeneration in zebrafish ]]> https://biorxiv.org/content/10.64898/2026.02.13.705804v1?rss=1 Gourkanti, S. Ramakrishnan, G. Munoz, Y. Chavez, R. M. Cheung, J. Dohnalek, J. Schoen, T. J. Martin, K. Lovett-Barron, M. E. Whisenant, T. Strisovsky, K. Neal, S. E. 2026-02-15 doi:10.64898/2026.02.13.705804 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ A scalable approach to resolving variants of uncertain significance ]]> https://biorxiv.org/content/10.64898/2026.02.14.705848v1?rss=1 90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine. ]]> Tejura, M. Chen, Y. McEwen, A. E. Stewart, R. Sverchkov, Y. Laval, F. Woo, I. Zeiberg, D. Shen, R. Fayer, S. Stone, J. Smith, N. Casadei, S. Wang, Z. R. Snyder, M. Capodanno, B. J. Gupta, P. Benazouz, M. Jain, S. Heidl, S. Muffley, L. Dong, S. Lin, K. Hitz, B. C. Gabdank, I. Da, E. Y. Best, S. Grindstaff, S. Reinhart, D. Rodriguez-Salas, L. Seid, O. Vandi, A. J. Wenman, C. Wheelock, M. K. Pendyala, S. Holmes, D. Xu, A. Hosokai, A. Tixhon, M. Reno, C. Ewald, J. D. Spirohn-Fitzgerald, K. Teelucksingh, T. Hao, T. Chen, Z. S. Haghighi, M. Hamid, A. K. 2026-02-15 doi:10.64898/2026.02.14.705848 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ scAmp analyzes focal gene amplifications at single-cell resolution ]]> https://biorxiv.org/content/10.64898/2026.02.14.705928v1?rss=1 Jones, M. G. Weiser, N. E. Hung, K. L. Yan, X. Agarwal, S. Luebeck, J. Gnanasekar, A. Howitt, B. E. Curtis, E. J. Yu, K. Rose, J. C. Kraft, K. Amiri, V. V. P. Satpathy, L. Bafna, V. Mischel, P. S. Chang, H. Y. 2026-02-15 doi:10.64898/2026.02.14.705928 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.64898/2026.02.13.705822v1?rss=1 Yang, C.-J. Yeh, Y.-C. Hsiao, C. Liu, Y.-H. Lu, M. R. Liu, Y.-C. Liti, G. Tsai, I. J. Ke, H.-M. 2026-02-16 doi:10.64898/2026.02.13.705822 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ A Druggable G Protein Checkpoint in Cholesterol Efflux ]]> https://biorxiv.org/content/10.64898/2026.02.15.705962v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@1b1c85org.highwire.dtl.DTLVardef@1ed9f6aorg.highwire.dtl.DTLVardef@17d153forg.highwire.dtl.DTLVardef@fdf47b_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC blurbLipid-associated macrophages drive immunometabolic disease. Katkar et al. show that disabling a GIV-dependent G-protein brake restores cholesterol efflux, reverses plaque lipid accumulation, and establishes reverse cholesterol transport as a druggable therapeutic axis. HighlightsO_LIStatins slow but rarely reverse plaque burden, leaving residual risk driven by LAM dysfunction C_LIO_LIGIV (CCDC88A) non-canonically modulates Gi to suppress macrophage cholesterol efflux C_LIO_LIGIV loss or inhibition restores ABCA1 activity via transcriptional and post-translational control C_LIO_LIBlocking the GIV[bullet]Gi checkpoint defats LAMs, regresses plaques, and relieves systemic lipid overload C_LIO_LIIdentifies a druggable node that redefines RCT restoration as a therapeutic paradigm in immunometabolic disease C_LI ]]> Katkar, G. Anandachar, M. S. Espinoza, C. Estanol, M. Biggs, C. Nacayama, M. Hsu, S.-T. Tam, E. Mukharjee, R. McLaren, E. Aviles, S. Castillo, V. Mullick, M. Yang, J. Kaufmann, B. Sinha, S. Ghosh, P. 2026-02-17 doi:10.64898/2026.02.15.705962 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Histone variant H2A.Z mutant suppresses the senescence-associated secretory phenotype ]]> https://biorxiv.org/content/10.64898/2026.02.16.706244v1?rss=1 Chua, Z. M. Tanaka, H. Abele, A. Rajesh, A. Marcos, T. G. Lei, X. Miller, K. Davis, A. Cano Macip, C. Haddadin, L. Dasgupta, N. Adams, P. D. 2026-02-17 doi:10.64898/2026.02.16.706244 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Regulation of the Balance between Concentric and Eccentric Cardiac Hypertrophy by a CDC14A-KMT5A Signaling Pathway ]]> https://biorxiv.org/content/10.64898/2026.02.16.706249v1?rss=1 Li, X. Li, J. Tan, Y. Samuelsson, A.-M. Nguyen, V. B. Nair, R. V. Colombe, A.-S. Grimm, D. Rosenfeld, M. G. Kapiloff, M. S. 2026-02-17 doi:10.64898/2026.02.16.706249 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Potassium-Selective Nanoelectrode Arrays for Single-Cell Profiling of human iPSC-Derived Cardiomyocytes ]]> https://biorxiv.org/content/10.64898/2026.02.13.705576v1?rss=1 Meganathan, D. P. Banzon, R. Casanova, A. Sarikhani, E. Mahato, K. Vu, H. Reade, S. Ambika Devarajan, I. Tahir, A. Sasi, L. Spain, L. Wang, J. Jahed, Z. 2026-02-18 doi:10.64898/2026.02.13.705576 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ The Role of Glycan Structures in Modulating GM-CSF Bioactivity: Insights from Glycoengineering ]]> https://biorxiv.org/content/10.64898/2026.02.17.706267v1?rss=1 Cagdas, E. Skovbakke, S. L. Agullet, J. P. Dworkin, L. A. Scapin, G. Hefzi, H. Fremming, K. S. Schoffhelen, S. Putkaradze, N. Voldborg, B. Grav, L. M. Nielsen, L. K. Goletz, S. G. Lewis, N. E. 2026-02-18 doi:10.64898/2026.02.17.706267 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Genetic Architecture of Addiction-Relevant Behaviors in Outbred Sprague-Dawley Rats Reveals Loci for Anxiety-Like and Nociceptive Traits ]]> https://biorxiv.org/content/10.64898/2026.02.18.706481v1?rss=1 Chitre, A. S. Hebda-Bauer, E. K. Emery, M. A. Li, F. Nguyen, K.-M. Wang, Y. Cheng, R. Polesskaya, O. Watson, S. J. Li, J. Akil, H. Palmer, A. A. 2026-02-19 doi:10.64898/2026.02.18.706481 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing ]]> https://biorxiv.org/content/10.64898/2026.02.18.706685v1?rss=1 Palmer, D. Chauvier, A. Silva, T. F. D. Ontiveros, A. Bussi, G. Walter, N. G. Mishanina, T. V. 2026-02-19 doi:10.64898/2026.02.18.706685 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Unlocking the Bile Acid Universe: Advanced Workflows and a Multidimensional Library of 280 Unique Species ]]> https://biorxiv.org/content/10.64898/2026.02.18.706700v1?rss=1 Zhang, G. Vincent, E. C. Disselkoen, S. M. Dodds, J. N. DuVal-Smith, Q. Patan, A. Mohanty, I. Deleray, V. Zhang, J. Thiessen, P. A. Bolton, E. E. Schymanski, E. L. Dorrestein, P. C. Theriot, C. M. Baker, E. S. 2026-02-19 doi:10.64898/2026.02.18.706700 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ A predictive mechanochemical modeling framework for the deformation and remodeling of the nuclear lamina ]]> https://biorxiv.org/content/10.64898/2026.02.19.706840v1?rss=1 Francis, E. A. Sarikhani, E. Naghsh-Nilchi, H. Jahed, Z. Rangamani, P. 2026-02-20 doi:10.64898/2026.02.19.706840 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Neural circuits regulating social dominance implement a strategy predicted by evolutionary game theory ]]> https://biorxiv.org/content/10.64898/2026.02.20.706896v1?rss=1 Ventimiglia, D. Chamiec-Case, E. Lee, C. S. Ruff, B. Asahina, K. 2026-02-21 doi:10.64898/2026.02.20.706896 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Data-driven RNA phenotyping captures genetically regulated dimensions of the transcriptome ]]> https://biorxiv.org/content/10.64898/2026.02.20.707100v1?rss=1 Munro, D. Gusev, A. Palmer, A. A. Mohammadi, P. 2026-02-21 doi:10.64898/2026.02.20.707100 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ Cortical oscillations reflect opponent ensemble dynamics through coordinated multifrequency activity ]]> https://biorxiv.org/content/10.64898/2026.02.20.707132v1?rss=1 Mishler, J. H. Salimi, M. Koloski, M. F. Rembado, I. Shilyansky, C. Mishra, J. Ramanathan, D. 2026-02-23 doi:10.64898/2026.02.20.707132 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Reln haploinsufficiency alters fentanyl-induced striatal activity and adaptive responding without affecting opioid reinforcement ]]> https://biorxiv.org/content/10.64898/2026.02.21.707172v1?rss=1 Telese, F. Litif, C. Libster, A. M. Desfor, S. Huang, T. Liaw, L. Cheng, A. 2026-02-23 doi:10.64898/2026.02.21.707172 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Statins and genetic inhibition of the mevalonate pathway activate an ATF3-STMN2 regenerative program ]]> https://biorxiv.org/content/10.64898/2026.02.23.707492v1?rss=1 Nolan, M. Aryal, S. Ndayambaje, I. S. Cao, M. Lee, P. Hovde, M. Yun, S. Wlaschin, J. Held, A. Beaussant, H. Wymann, B. Lee, C.-Z. Lim, S. M. Jiang, X. Ramesh, N. Agra Almeida Quadros, A. R. Boulos, A. Zinter, N. Salem, S. El-Tayar, L. Beccari, M. Presa, M. Jourdan Ferraras Reyes, C. Ruan, Y. Y. Griesman, G. Aguilar, C. Hawrot, J. Wheeler, H. Melamed, Z. P. Kleinstiver, B. Albers, M. W. Cleveland, D. E. Tanzi, R. M. Lutz, C. D. Hubbard, R. Kobayashi, D. Ward, M. R.R. Alves, C. Wainger, B. Le Pichon, C. Lagier-Tourenne, C. 2026-02-24 doi:10.64898/2026.02.23.707492 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ A generalized synthetic control algorithm for sparse functional data ]]> https://biorxiv.org/content/10.64898/2026.02.23.707582v1?rss=1 Shao, L. Pohl, K. M. Thompson, W. K. 2026-02-25 doi:10.64898/2026.02.23.707582 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Geomorphic evolution of a Caribbean biological hotspot ]]> https://biorxiv.org/content/10.64898/2026.02.24.707483v1?rss=1 O'Dea, A. Titcomb, M. Anderson, L. H. de Gracia, B. Flantua, S. Hynes, M. G. Parsons, T. Schloeder, C. Braun, M. J. 2026-02-25 doi:10.64898/2026.02.24.707483 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Spore-Based Biocomposite Thermoplastic Polyesters with Enhanced Toughness and Programmable Disintegration ]]> https://biorxiv.org/content/10.64898/2026.02.24.707801v1?rss=1 90%) after extrusion and exhibited improved mechanical performance (up to 41% toughness improvement compared to neat polymers). End-of-life behavior was evaluated in a microbially-limited composting environment, where spore-containing PCL exhibited nearly complete disintegration within five months, corresponding to a [~]7-fold increase in degradation kinetics relative to neat PCL. Finally, 3D printing of biocomposite PCL was demonstrated through fused deposition modeling and direct ink writing methodologies. Together, this work demonstrated the successful extension of spore-based engineered living materials from thermoplastic polyurethane to multiple thermoplastic polyesters. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/707801v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4eaafaorg.highwire.dtl.DTLVardef@bb17c2org.highwire.dtl.DTLVardef@114e4ceorg.highwire.dtl.DTLVardef@b9bd0c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kim, H. S. Fan, E. Chandra, A. Meyer, E. Tang, J. Noh, M. H. Feist, A. M. Pokorski, J. K. 2026-02-26 doi:10.64898/2026.02.24.707801 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Mitotic bookmarking by Prox1 preserves mammalian neuronal lineage identity memory via promoting timely H3K27me3 restoration ]]> https://biorxiv.org/content/10.64898/2026.02.25.707603v1?rss=1 Wong, C. Liu, J. Yang, H. Li, H. Luo, X. Li, T. Chen, Z. Chu, J. Shen, Y. Long, S. Zhang, Y. Song, Y. 2026-02-26 doi:10.64898/2026.02.25.707603 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Identifying Robust Subclonal Structures through Tumor Progression Tree Alignment ]]> https://biorxiv.org/content/10.64898/2026.02.25.708046v1?rss=1 Gilbert, J. Wu, C. H. Knittel, H. Schäffer, A. A. Malikic, S. Sahinalp, C. 2026-02-27 doi:10.64898/2026.02.25.708046 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ A Translational Model of MASLD-Associated HFpEF Defines Mitochondrial Dysfunction and Cardiac Plasticity During Disease Progression and Regression ]]> https://biorxiv.org/content/10.64898/2026.02.26.708088v1?rss=1 50. Liver fibrosis emerged as a strong predictor of cardiac dysfunction. Remarkably, dietary reversal restored hepatic architecture, normalized cardiac function, and improved survival, revealing marked plasticity of the liver-heart axis. Mechanistic analyses revealed coordinated mitochondrial dysfunction, altered substrate utilization, and extracellular matrix remodeling in the left ventricle, with strong concordance to human HFpEF transcriptomic signatures. Ultrastructural studies confirmed mitochondrial injury and sarcomeric disorganization, linking metabolic failure to impaired cardiomyocyte performance. Together, these findings identify mitochondrial dysfunction as a central mediator of MASLD-associated HFpEF and establish the Foz/Foz model as a powerful platform for dissecting liver-to-heart signaling pathways and testing mechanism-based therapeutic strategies. STRUCTURED ABSTRACTO_ST_ABSBackgroundC_ST_ABSMetabolic dysfunction associated steatotic liver disease (MASLD) and its advanced form, MASH, are closely linked to heart failure with preserved ejection fraction (HFpEF). However, the mechanisms driving MASLD-associated HFpEF and its reversibility remain poorly understood, largely due to the lack of robust preclinical models. Here, we established a translational model of MASLD-associated HFpEF and applied functional and transcriptomic analyses of the left ventricle (LV) to define the mechanisms underlying cardiac dysfunction and its reversibility. MethodsAlms1-/- (Foz/Foz) mice and wild-type littermates were fed normal chow (NC) or Western diet (WD) for up to 34w. Reversibility was modeled by switching WD-fed Foz/Foz mice at 12w back to NC for 12w. Cardiac assessment included echocardiography, invasive hemodynamics with dobutamine stimulation, histopathology, electron microscopy and isolated cardiomyocyte contractility. LV transcriptomes were profiled by bulk RNA sequencing and analyzed by differential expression and pathway enrichment. ResultFoz/Foz mice on WD for 24w developed metabolic syndrome and MASH with advanced liver fibrosis. Cardiac phenotyping showed LV hypertrophy, impaired cardiomyocyte contractility, reduced {beta}-adrenergic reserve, elevated plasma BNP, and increased mortality while the ejection fraction was preserved (>50%), consistent with HFpEF. Liver fibrosis was a strong predictor of HFpEF. Switching WD-fed Foz/Foz mice at 12w to normal chow diet reversed hepatic fibrosis, restored LV function, and reduced mortality, demonstrating plasticity of the liver-heart axis. LV transcriptome during disease progression and regression revealed mitochondrial dysfunction, altered substrate utilization, extracellular matrix remodeling, and metabolic stress as central drivers of HFpEF, with strong overlap to human HFpEF signatures. Cardiac electron microscopy revealed swollen mitochondria with disrupted cristae, which normalized following dietary intervention. ConclusionsMitochondrial dysfunction and fibroinflammatory remodeling are central mediators of MASLD-associated HFpEF. Reversal of hepatic and cardiac phenotypes with dietary intervention, together with elucidation of underlying pathways, establish the Foz/Foz model as a robust translational platform for mechanistic and therapeutic discovery targeting the liver-heart axis. ]]> Ganguly, S. Gunes, B. Gu, Y. Suarez, J. Gupta, G. Ishizuka, K. Murad, R. Kisseleva, T. Dillmann, W. Peterson, K. Adler, E. Brenner, D. Dhar, D. 2026-02-28 doi:10.64898/2026.02.26.708088 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ A Hidden Binding Pocket in the β- ketoacyl-ACP Synthase FabB ]]> https://biorxiv.org/content/10.64898/2026.02.26.708327v1?rss=1 Jiang, Z. Friedman, A. J. Thompson, A. Andrzejewski, S. J. Mains, K. Sankaran, B. Burkart, M. J. Shirts, M. R. Fox, J. M. 2026-02-28 doi:10.64898/2026.02.26.708327 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Refinement of Nucleus Accumbens Neuronal Dynamics During Cocaine Self-Administration Training ]]> https://biorxiv.org/content/10.64898/2026.02.26.708295v1?rss=1 Jin, L. Qi, X. Liu, J. Wright, W. J. Schall, T. A. Li, K.-L. Zeng, B. Wang, C. Wang, L. Dong, Y. 2026-03-02 doi:10.64898/2026.02.26.708295 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Computational modelling of natural cell-to-cell heterogeneity reveals key parameters that control the diversity of human pancreatic islet β-cell excitability in response to glucose ]]> https://biorxiv.org/content/10.64898/2026.02.27.708039v1?rss=1 Goswami, I. Koepke, J. Baghelani, M. Macdonald, P. E. Kravets, V. Light, P. E. Edwards, A. G. 2026-03-02 doi:10.64898/2026.02.27.708039 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Derlin-mediated ERAD of lipid regulator ORMDL3 safeguards mitochondrial function ]]> https://biorxiv.org/content/10.64898/2026.02.27.708653v1?rss=1 Scott, N. A. Afolabi, J. Marshall, A. G. Schafer, J. C. Baskerville, V. R. Prasad, P. Kadam, A. A. Som de Cerff, C. Whisenant, T. Phillips, M. A. Tomar, D. McReynolds, M. Hinton, A. Neal, S. E. 2026-03-03 doi:10.64898/2026.02.27.708653 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Transcriptomic profiling of mouse mammary tumors enables prognostic and predictive biomarker discovery for human breast cancers ]]> https://biorxiv.org/content/10.64898/2026.02.28.707759v1?rss=1 Sutcliffe, M. D. Mott, K. R. Yilmaz-Swenson, T. Felsheim, B. M. Lobanov, A. V. Michmerhuizen, A. R. Raedler, P. D. Okumu, D. O. He, X. Pfefferle, A. D. Dance-Barnes, S. East, M. P. Hollern, D. P. Elston, T. C. Johnson, G. L. Perou, C. M. 2026-03-03 doi:10.64898/2026.02.28.707759 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum ]]> https://biorxiv.org/content/10.64898/2026.03.01.708876v1?rss=1 Green, A. A. Vashist, T. D. Jakhmola, S. Chen, X. Baidwan, G. Buchanan, J. Tiwari, S. K. Griffin, E. Howell, A. Lee, Y. Moore, D. J. Gianella, S. Smith, D. M. Zhu, Q. Walss-Bass, C. Wang, A. Mukamel, E. A. Gaulton, K. J. Rana, T. M. 2026-03-03 doi:10.64898/2026.03.01.708876 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Enabling Megascale Microbiome Analysis with DartUniFrac ]]> https://biorxiv.org/content/10.64898/2026.03.01.708916v1?rss=1 Zhao, J. McDonald, D. Sfiligoi, I. Lladser, M. E. Patel, L. Weng, Y. Khatib, L. Degregori, S. Gonzalez, A. Lozupone, C. Knight, R. 2026-03-03 doi:10.64898/2026.03.01.708916 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ A new mRNA antigen vaccine induces potent B and T cell responses and in vivo protection against SARS-CoV-2 ]]> https://biorxiv.org/content/10.64898/2026.03.02.709177v1?rss=1 Wen, J. Moon, J. Tucciarone, L. Bu, T.-H. Sun, A. Y. Miller, R. Timis, J. Wu, L. Smith, D. M. Shresta, S. Gaulton, K. J. Rana, T. M. 2026-03-03 doi:10.64898/2026.03.02.709177 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation ]]> https://biorxiv.org/content/10.64898/2026.03.03.709330v1?rss=1 75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-{gamma} in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4 T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance. ]]> Charron-Lamoureux, V. Kelly, P. Zuffa, S. Patan, A. Sala-Climent, M. Walker, C. Zhao, H. N. Xing, S. Gouda, H. Agongo, J. Reilly, E. R. Sallam, L. Shore, S. F. H. Ghoshal, S. Harpavat, A. K. Murugesan, M. P. Yadav, S. Versalovic, J. Orlovsky, V. El Abiead, Y. Kvitne, K. E. Markle, J. G. Norton, G. J. Walker, G. T. Lee, M. H. Hu, Z. Carrillo Terrazas, M. Zong, D. M. Zarrinpar, A. Raffatellu, M. Martin, A. Chin, L. Devkota, S. Gonzalez, A. Ackermann, G. Patel, L. Weng, Y. Knight, R. Russell, R. K. Hansen, R. Svolos, V. Gkikas, K. Rattray, N. J. Siegel, 2026-03-04 doi:10.64898/2026.03.03.709330 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Cannabis Use by People with HIV is Associated with an Anti-Inflammatory Immunometabolic Phenotype in Monocyte-Derived Macrophages ]]> https://biorxiv.org/content/10.64898/2026.03.04.709579v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@15fb1adorg.highwire.dtl.DTLVardef@189d79corg.highwire.dtl.DTLVardef@aa6a89org.highwire.dtl.DTLVardef@3852f8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ford, M. Halcrow, P. W. Laird, A. Leyva, B. Boustani, A. Spencer, M. Melcher, J. Walter, K. Hong, D. Funk, G. Searson, E. Le, A. A. Ellis, R. J. Letendre, S. Marcondes, M. C. G. Schlachetzki, J. Iudicello, J. Fields, J. A. 2026-03-06 doi:10.64898/2026.03.04.709579 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Engineered OAA lectins as selective and sensitive high mannose glycan targeting tools ]]> https://biorxiv.org/content/10.64898/2026.03.04.709641v1?rss=1 Ackermann, B. E. Hall, E. Mariscal, V. T. Clark, A. Corbett, K. D. Carlin, A. Guseman, A. 2026-03-06 doi:10.64898/2026.03.04.709641 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma ]]> https://biorxiv.org/content/10.64898/2026.03.05.709911v1?rss=1 Taylor, B. Dong, W. Keal, T. Wang, Z. Saravanan, B. Gibbs, Z. A. Miyake, Y. Kawauchi, D. Vadla, R. Banerjee, A. Elkassih, O. Kashyap, S. Jones, B. M. Malukhina, K. Nafisi, M. Loe, T. H. Bendik, J. McAllister, T. Xie, Y. Chang, L. Chen, C. Ren, B. Furnari, F. Bintu, B. 2026-03-07 doi:10.64898/2026.03.05.709911 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Computed atlas of the human GPCR-G protein signaling complexes ]]> https://biorxiv.org/content/10.64898/2026.03.07.710286v1?rss=1 Miglionico, P. Matic, M. Franchini, L. Arai, H. Nemati Fard, L. A. Arora, C. Gherghinescu, M. DeOliveira Rosa, N. Ryoji, K. Gutkind, J. S. Orlandi, C. Inoue, A. Raimondi, F. 2026-03-10 doi:10.64898/2026.03.07.710286 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Lipoxins Regulate Intercalated Disk-Associated Signaling and Immune Remodeling in Dilated Cardiomyopathy ]]> https://biorxiv.org/content/10.64898/2026.03.09.710477v1?rss=1 Clark, M. Fujita, K. Nielsen, L. A. M. Johnson, R. T. Gu, Y. Dalton, N. D. Suur, B. E. Bergstrom, I. Adler, E. Chen, J. Quiding-Jarbrink, M. Bollano, E. Bergh, N. Sotak, M. Ehler, E. Blomgran, R. Borgeson, E. Lange, S. 2026-03-11 doi:10.64898/2026.03.09.710477 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ PD1-induced Shp2 condensation organizes inhibitory signalosomes through selective substrate partitioning ]]> https://biorxiv.org/content/10.64898/2026.03.09.710629v1?rss=1 Masubuchi, T. Wen, G. Song, X. Gaddam, K. Shao, H. Wu, C. HUI, E. 2026-03-11 doi:10.64898/2026.03.09.710629 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Spatial Landscape of Pregnancy-Associated Triple Negative Breast Cancer and Mammary Gland Involution ]]> https://biorxiv.org/content/10.64898/2026.03.09.710650v1?rss=1 Veraksa, D. Mukund, K. Frankhouser, D. Yang, L. Tomsic, J. Pillai, R. Venkatasubramani, J. Schmolze, D. Wu, X.-C. LeBlanc, M.-A. Miele, L. Ochoa, A. Seewaldt, V. Subramaniam, S. 2026-03-12 doi:10.64898/2026.03.09.710650 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ The Brain Age Gap as a Predictor of Alcohol Initiation in Adolescence ]]> https://biorxiv.org/content/10.64898/2026.03.10.710953v1?rss=1 Byrne, H. Visontay, R. Devine, E. K. Wade, N. E. Jacobus, J. Moore, A. J. Squeglia, L. M. Mewton, L. 2026-03-13 doi:10.64898/2026.03.10.710953 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Fast and accurate resolution of ecDNA sequence using Cycle-Extractor ]]> https://biorxiv.org/content/10.64898/2026.03.10.710955v1?rss=1 Faizrahnemoon, M. Luebeck, J. Hung, K. L. Rao, S. Prasad, G. Tsz-Lo Wong, I. G. Jones, M. S. Mischel, P. Y. Chang, H. Zhu, K. Bafna, V. 2026-03-13 doi:10.64898/2026.03.10.710955 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data ]]> https://biorxiv.org/content/10.64898/2026.03.11.710980v1?rss=1 Weng, Y. Moyne, O. Walker, C. Haddad, E. Lieng, C. Chin, L. Rahman, G. McDonald, D. Knight, R. Zengler, K. 2026-03-14 doi:10.64898/2026.03.11.710980 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Altered Cardiac Neural Crest Migration Patterning in a Left Atrial Ligation Model of Hypoplastic Left Heart Syndrome ]]> https://biorxiv.org/content/10.64898/2026.03.11.711140v1?rss=1 Fan, A. Porter, R. Maeng, H. Lindsey, S. E. 2026-03-14 doi:10.64898/2026.03.11.711140 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ Flipper: An advanced framework for identifyingdifferential RNA binding behavior with eCLIP data ]]> https://biorxiv.org/content/10.64898/2026.03.13.711628v1?rss=1 Flanagan, K. Xu, S. Yeo, G. W. 2026-03-15 doi:10.64898/2026.03.13.711628 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Migration of dI5 Reelin-Lmx1b-Zfhx3 and Disabled-1-Lmx1b-Zfhx3 neurons contribute to the superficial dorsal horn and lamina V ]]> https://biorxiv.org/content/10.64898/2026.03.13.707781v1?rss=1 Yvone, G. M. Chavez-Martinez, C. L. Mekonnen, M. A. Zimmer, S. Phelps, P. E. 2026-03-17 doi:10.64898/2026.03.13.707781 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ 3D vascular quantitation with application to computational modeling: a pre-clinical light sheet microscopy, high resolution ultrasound, nano-computed tomography comparison study ]]> https://biorxiv.org/content/10.64898/2026.03.13.711685v1?rss=1 Zhang, D. Lindsey, S. E. 2026-03-17 doi:10.64898/2026.03.13.711685 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Inhibitor-2 directs formation of PP1 holoenzymes through a docking motif-dependent transfer of catalytic subunits to adapters ]]> https://biorxiv.org/content/10.64898/2026.03.15.711929v1?rss=1 Varshney, N. Schlientz, A. J. Meaders, J. L. Oegema, K. Desai, A. 2026-03-17 doi:10.64898/2026.03.15.711929 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Age-related sleep changes in the human brain: insights from a large-scale thalamocortical model ]]> https://biorxiv.org/content/10.64898/2026.03.16.712170v1?rss=1 Navas Zuloaga, M. G. Purcell, S. M. Bazhenov, M. 2026-03-18 doi:10.64898/2026.03.16.712170 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ A Surfactant Cocktail Overcomes Air-Water Interface Artifacts in Single-Particle CryoEM ]]> https://biorxiv.org/content/10.64898/2026.03.17.712260v1?rss=1 Enos, S. E. Cook, B. D. Rahmani, H. Narehood, S. M. Li, Y. Kuschnerus, I. C. Redford, T. H. Dukakis, P. Ji, D. Bachochin, M. J. Grotjahn, D. J. Herzik, M. A. 2026-03-18 doi:10.64898/2026.03.17.712260 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ High specificity meets genomic flexibility in the Siphamia-Photobacterium symbiosis ]]> https://biorxiv.org/content/10.64898/2026.03.19.712928v1?rss=1 Osland, H. K. Neff, E. Gaisiner, A. Hays, D. Gould, A. L. 2026-03-19 doi:10.64898/2026.03.19.712928 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Comparative food-web analysis of bluefin tuna spawning habitats in the eastern Indian Ocean and Gulf of Mexico ]]> https://biorxiv.org/content/10.64898/2026.03.18.711569v1?rss=1 Stukel, M. R. Landry, M. R. Decima, M. Fender, C. K. Kranz, S. A. Laiz-Carrion, R. L. Malca, E. QUINTANILLA, J. M. Selph, K. E. Swalethorp, R. Yingling, N. 2026-03-20 doi:10.64898/2026.03.18.711569 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Dynamic optimization of extrachromosomal DNA copy number drives tumour evolution ]]> https://biorxiv.org/content/10.64898/2026.03.20.713026v1?rss=1 Gnanasekar, A. Zhang, S. Curtis, E. J. Tang, J. Shankar, V. Wong, I. T.-L. Yan, X. Li, R. Yang, L. M. Yao, M. A. Ventura, A. Werner, B. Chang, H. Y. Mischel, P. S. 2026-03-23 doi:10.64898/2026.03.20.713026 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Disease context dictates the cellular targets of IL-17 in inflammatory skin disease ]]> https://biorxiv.org/content/10.64898/2026.03.23.713409v1?rss=1 Cavagnero, K. J. Jo, H. Li, F. Aguilera, C. Fox, J. Kirma, J. Bogel, R. Kahlenberg, J. M. Tsoi, L. C. Gudjonsson, J. E. Gallo, R. L. 2026-03-25 doi:10.64898/2026.03.23.713409 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Alkaline phosphatase activity supports heterotrophic carbon acquisition in a coastal time series site and a representative marine bacterium ]]> https://biorxiv.org/content/10.64898/2026.03.24.713987v1?rss=1 Sachdev, E. Adams, J. C. Lanpher, K. B. Perry, S. Tostado, C. Bowman, J. S. Ingall, E. D. Diaz, J. M. 2026-03-25 doi:10.64898/2026.03.24.713987 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ NetTracer3D Enables User-Friendly Analysis of Diverse Microscopic and Medical 3D Datasets ]]> https://biorxiv.org/content/10.64898/2026.03.25.714104v1?rss=1 McLaughlin, L. Curic, M. Sharma, S. Villazon, J. Salamon, R. J. Yamaguchi, M. Sequeira-Lopez, M. L. S. Kennedy, P. R. Lyons, R. C. Shi, L. Gomez, R. A. Jain, S. 2026-03-27 doi:10.64898/2026.03.25.714104 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Pathogenic human mitochondrial tRNA variants impair RNA processing by compromising 5' leader removal ]]> https://biorxiv.org/content/10.64898/2026.03.25.714317v1?rss=1 Munozvilla, J. H. Ontiveros, A. Mishanina, T. V. 2026-03-27 doi:10.64898/2026.03.25.714317 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Inhibitory-modulatory coupling generates persistent activity during working memory ]]> https://biorxiv.org/content/10.64898/2026.03.27.714602v1?rss=1 Heintschel, M. L. Xu, J. Grover, D. 2026-03-28 doi:10.64898/2026.03.27.714602 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ A set of constitutive promoters with graded strengths for gene expression in diverse cyanobacterial strains ]]> https://biorxiv.org/content/10.64898/2026.03.25.714268v1?rss=1 Trieu, K. Bishe, B. Taton, A. Tieu, B. P. Golden, J. W. 2026-03-30 doi:10.64898/2026.03.25.714268 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes ]]> https://biorxiv.org/content/10.64898/2026.03.29.711974v1?rss=1 Kramer, A. M. Zhang, A. Ayala, N. de Sanctis, B. Karim, L. M. Hinrichs, A. S. Walia, S. Turakhia, Y. Corbett-Detig, R. 2026-03-30 doi:10.64898/2026.03.29.711974 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Adrβ2 in skeletal muscle cells is required for exercise-induced Pgc1α but not for metabolic benefits of exercise on diet-induced obesity ]]> https://biorxiv.org/content/10.64898/2026.03.27.714812v1?rss=1 Galvan, M. Fujitani, M. Dushime, J. Baset, S. Chen, B. Thomas, S. Castorena, C. M. Elmquist, J. K. Fujikawa, T. 2026-03-31 doi:10.64898/2026.03.27.714812 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Pan-Metabolomics Repository Mapping of the Carnitine Landscape ]]> https://biorxiv.org/content/10.64898/2026.03.27.714844v1?rss=1 Mannochio-Russo, H. Ferreira, P. C. Kvitne, K. E. Patan, A. Deleray, V. Agongo, J. Gouda, H. Goncalves Nunes, W. D. Xing, S. Zemlin, J. van Faassen, M. Reilly, E. R. Koo, I. Patterson, A. D. Tsunoda, S. M. Wang, M. Siegel, D. Burnett, L. A. Dorrestein, P. C. 2026-03-31 doi:10.64898/2026.03.27.714844 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ A NOD2-Encoded Toggle Switch Resolves the Host-Microbe Battle Over Cyclic AMP Control ]]> https://biorxiv.org/content/10.64898/2026.03.29.715116v1?rss=1 View larger version (70K): org.highwire.dtl.DTLVardef@b40beaorg.highwire.dtl.DTLVardef@7a6038org.highwire.dtl.DTLVardef@433d67org.highwire.dtl.DTLVardef@743f95_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC BlurbPathogens hijack macrophages by inducing cAMP surges that help them evade clearance. Anandachar et al. identify a host "toggle switch" in which NOD2 and G proteins compete for GIV, driving a rapid and robust surge-to-plunge transition in cAMP. This temporal switch limits tolerogenic signaling, restores microbial clearance and barrier integrity, and unveils a targetable host pathway in infection and IBD. HighlightsO_LIPathogens exploit cAMP surges in macrophages to block phagolysosomal killing of microbes C_LIO_LIGIV acts as a molecular "toggle" linking NOD2 sensing to Gi-mediated cAMP control C_LIO_LIStructural and mutagenesis studies reveal mutually exclusive binding of NOD2 and Gi to GIV C_LIO_LIPharmacogenomic perturbations pinpoint PKA, not EPAC, as the critical downstream effector C_LIO_LIOrganoid co-cultures show NOD2-GIV-PKA crosstalk safeguards microbial clearance and gut barrier integrity C_LI ]]> Anandachar, M. S. Chen, D. Perkins, K. C. Katkar, G. D. Roy, S. Espinoza, C. R. Mullick, M. Sinha, S. Nakayama, M. Salem, J. Estanol, M. Bhattacharjee, R. Zablan, K. Hsu, S.-T. Williams, S. Sun, A. Tindle, C. Yang, J. Kufareva, I. Ghosh, P. 2026-03-31 doi:10.64898/2026.03.29.715116 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Serum metabolic signatures of cognitive resilience in a longitudinal aging cohort ]]> https://biorxiv.org/content/10.64898/2026.03.29.715122v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@133b7ceorg.highwire.dtl.DTLVardef@686c5eorg.highwire.dtl.DTLVardef@1a297bcorg.highwire.dtl.DTLVardef@197d42d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Scheurink, T. A. W. Seo, J. I. David, L. C. Wang, C. X. Solis, D. Zemlin, J. Bergstrom, J. Dorrestein, P. C. Mohanty, I. Molina, A. J. A. 2026-04-01 doi:10.64898/2026.03.29.715122 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis ]]> https://biorxiv.org/content/10.64898/2026.03.31.715631v1?rss=1 Xue, J. Allaband, C. Zuffa, S. Zhou, D. Poulsen, O. Meadows, J. McDonald, D. Ambre, M. Ackermann, G. Birmingham, A. Cao, J. Mohanty, I. Dorrestein, P. C. Knight, R. Haddad, G. G. 2026-04-01 doi:10.64898/2026.03.31.715631 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Receptor-guided AAV Tropism Engineering via MATCH ]]> https://biorxiv.org/content/10.64898/2026.03.31.715691v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@445506org.highwire.dtl.DTLVardef@2a2e4aorg.highwire.dtl.DTLVardef@1450fd9org.highwire.dtl.DTLVardef@1137d8b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Graham, N. Kumar, S. Rainaldi, J. Yang, S. Portell, A. Santoso, B. Mali, P. 2026-04-01 doi:10.64898/2026.03.31.715691 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome ]]> https://biorxiv.org/content/10.64898/2026.03.31.715750v1?rss=1 Kvitne, K. Zuffa, S. Charron-Lamoureux, V. Patan, A. Agongo, J. Cai, J. Deleray, V. El Abiead, Y. Xing, S. Zemlin, J. Thomas, S. Nelson, M. Gant, A. Ghadishah, A. Lam, A. Ho, B. Momper, J. Suhandynata, R. Bertrand, K. Knight, R. Chambers, C. Dorrestein, P. Tsunoda, S. 2026-04-01 doi:10.64898/2026.03.31.715750 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Functional genomics reveals mediators of beta cell survival in ER stress and type 2 diabetes risk ]]> https://biorxiv.org/content/10.64898/2026.03.30.715154v1?rss=1 Okino, M.-L. Zhu, H. Corban, S. Benaglio, P. Djulamsah, J. OMahony, B. Vanderstel, K. Elgamal, R. Miller, M. Wang, A. Sander, M. Gaulton, K. J. 2026-04-02 doi:10.64898/2026.03.30.715154 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Coupling between sterol and sphingolipid structure in ordered membrane domains ]]> https://biorxiv.org/content/10.64898/2026.04.01.715929v1?rss=1 Juarez-Contreras, I. Kim, H. Budin, I. 2026-04-02 doi:10.64898/2026.04.01.715929 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Left atrial flow and thrombosis risk from 4D CT contrast dynamics by physics-informed neural network and indicator dilution theory ]]> https://biorxiv.org/content/10.64898/2026.03.31.715623v1?rss=1 Maidu, B. Gonzalo, A. Guerrero-Hurtado, M. Bargellini, C. Martinez-Legazpi, P. Bermejo, J. Contijoch, F. Flores, O. Garcia-Villalba, M. McVeigh, E. Kahn, A. del Alamo, J. C. 2026-04-03 doi:10.64898/2026.03.31.715623 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Top-down regulation of ingestive behavior fragmentation ]]> https://biorxiv.org/content/10.64898/2026.03.31.715709v1?rss=1 Qi, T. Krull, C. Leung, V. H. Mardare, V. Yang, D. Lal, N. Ma, J. Wang, S. Shen, H. Zhang, A. Zhao, B. Heydari Seradj, S. Korotkova, T. Kennedy, A. Ye, L. 2026-04-03 doi:10.64898/2026.03.31.715709 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Fatty acid scavenging enables cancer escape from KRAS inhibition ]]> https://biorxiv.org/content/10.64898/2026.04.01.715565v1?rss=1 Yuan, Z. Lin, B. Wang, C. Miao, Y. Zhang, D. Meng, Z. Wang, G. Lowy, A. M. Karin, M. Yang, F. Sun, B. Su, H. 2026-04-03 doi:10.64898/2026.04.01.715565 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Nonlinear associations between body mass index and brain microstructure across adolescence in the ABCD Study ]]> https://biorxiv.org/content/10.64898/2026.04.02.716201v1?rss=1 Rigby, A. Pecheva, D. Parekh, P. Smith, D. M. Becker, A. Linkersdoerfer, J. Watts, R. Loughnan, R. Hagler, D. J. Makowski, C. Jernigan, T. L. Dale, A. M. 2026-04-04 doi:10.64898/2026.04.02.716201 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Stress-Induced PTBP1 Reprograms Neuronal Function and Activates Cellular Senescence ]]> https://biorxiv.org/content/10.64898/2026.04.03.711742v1?rss=1 Priyanka, P. Gamliel, A. Taylor, H. Ohgi, K. A. Rosenfeld, M. G. 2026-04-04 doi:10.64898/2026.04.03.711742 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Expanding the scope of redox-balance growth coupling techniques with a carbon cofeeding strategy ]]> https://biorxiv.org/content/10.64898/2026.04.01.713023v1?rss=1 Cowan, A. E. Cawthon, B. Hillers, M. Perea, S. Grabovac, M. Stanton, A. Saleh, S. Gin, J. Chen, Y. Petzold, C. J. Keasling, J. D. 2026-04-05 doi:10.64898/2026.04.01.713023 Cold Spring Harbor Laboratory Press 2026-04-05