bioRxiv Channel: University of Chicago https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Chicago" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Variational Inference of Population Structure in Large SNP Datasets ]]> https://biorxiv.org/content/10.1101/001073v1?rss=1 Anil Raj Matthew Stephens Jonathan K Pritchard 2013-12-02 doi:10.1101/001073 Cold Spring Harbor Laboratory Press 2013-12-02 <![CDATA[ PyRAD: assembly of de novo RADseq loci for phylogenetic analyses ]]> https://biorxiv.org/content/10.1101/001081v1?rss=1 Deren A. R. Eaton 2013-12-03 doi:10.1101/001081 Cold Spring Harbor Laboratory Press 2013-12-03 <![CDATA[ Ancient human genomes suggest three ancestral populations for present-day Europeans ]]> https://biorxiv.org/content/10.1101/001552v1?rss=1 Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H. Sudmant Joshua G. Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A. Babiker Graciela Baillet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M. 2013-12-23 doi:10.1101/001552 Cold Spring Harbor Laboratory Press 2013-12-23 <![CDATA[ Impact of RNA degradation on measurements of gene expression ]]> https://biorxiv.org/content/10.1101/002261v1?rss=1 Irene Gallego Romero Athma A. Pai Jenny Tung Yoav Gilad 2014-01-30 doi:10.1101/002261 Cold Spring Harbor Laboratory Press 2014-01-30 <![CDATA[ TCF7L2 is a master regulator of insulin production and processing ]]> https://biorxiv.org/content/10.1101/003202v1?rss=1 Yuedan Zhou Soo-Young Park Jing Su Kathleen Bailey Emilia Ottosson-Laakso Liliya Shcerbina Nikolay Oskolkov Enming Zhang Thomas Thevenin Jo?o Fadista Hedvig Bennet Petter Vikman Nils Wierup Malin Fex Johan Rung Claes Wollheim Marcelo Nobrega Erik Renstr?m Leif Groop Ola Hansson 2014-03-05 doi:10.1101/003202 Cold Spring Harbor Laboratory Press 2014-03-05 <![CDATA[ Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates ]]> https://biorxiv.org/content/10.1101/003467v1?rss=1 Xiang Zhou Carolyn Cain Marsha Myrthil Noah Lewellen Katelyn Michelini Emily Davenport Matthew Stephens Jonathan Pritchard Yoav Gilad 2014-03-19 doi:10.1101/003467 Cold Spring Harbor Laboratory Press 2014-03-19 <![CDATA[ Spatial localization of recent ancestors for admixed individuals ]]> https://biorxiv.org/content/10.1101/004713v1?rss=1 Wen-Yun Yang Alexander Platt Charleston Wen-Kai Chiang Eleazar Eskin John Novembre Bogdan Pasaniuc 2014-05-04 doi:10.1101/004713 Cold Spring Harbor Laboratory Press 2014-05-04 <![CDATA[ Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits ]]> https://biorxiv.org/content/10.1101/005892v1?rss=1 Darren Kessner John Novembre 2014-06-04 doi:10.1101/005892 Cold Spring Harbor Laboratory Press 2014-06-04 <![CDATA[ Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. ]]> https://biorxiv.org/content/10.1101/006171v1?rss=1 Nicholas E Banovich Xun Lan Graham McVicker Bryce Van de Geijn Jacob F Degner John D. Blischak Julien Roux Jonathan K. Pritchard Yoav Gilad 2014-06-11 doi:10.1101/006171 Cold Spring Harbor Laboratory Press 2014-06-11 <![CDATA[ Efficient site-specific editing of the C. elegans genome ]]> https://biorxiv.org/content/10.1101/007344v1?rss=1 Donglei Zhang Michael Glotzer 2014-07-21 doi:10.1101/007344 Cold Spring Harbor Laboratory Press 2014-07-21 <![CDATA[ The Genetic Architecture of Gene Expression Levels in Wild Baboons ]]> https://biorxiv.org/content/10.1101/008490v1?rss=1 Jenny Tung Xiang Zhou Susan C Alberts Matthew Stephens Yoav Gilad 2014-08-28 doi:10.1101/008490 Cold Spring Harbor Laboratory Press 2014-08-28 <![CDATA[ Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics ]]> https://biorxiv.org/content/10.1101/008862v1?rss=1 Irene Gallego Romero Bryan J Pavlovic Irene Hernando-Herraez Nicholas E Banovich Courtney L Kagan Jonathan E Burnett Constance H Huang Amy Mitrano Claudia I Chavarria Inbar F Ben-Nun Yingchun Li Karen Sabatini Trevor R Leonardo Mana Parast Tomas Marques-Bonet Louise C Laurent Jeanne F Loring Yoav Gilad 2014-09-06 doi:10.1101/008862 Cold Spring Harbor Laboratory Press 2014-09-06 <![CDATA[ Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage ]]> https://biorxiv.org/content/10.1101/009225v1?rss=1 Joerg Hagmann Claude Becker Jonas Müller Oliver Stegle Rhonda C Meyer Korbinian Schneeberger Joffrey Fitz Thomas Altmann Joy Bergelson Karsten Borgwardt Detlef Weigel 2014-09-16 doi:10.1101/009225 Cold Spring Harbor Laboratory Press 2014-09-16 <![CDATA[ Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci ]]> https://biorxiv.org/content/10.1101/009258v1?rss=1 Gosia Trynka Harm-Jan Westra Kamil Slowikowski Xinli Hu Han Xu Barbara E Stranger Buhm Han Soumya Raychaudhuri 2014-09-18 doi:10.1101/009258 Cold Spring Harbor Laboratory Press 2014-09-18 <![CDATA[ Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast ]]> https://biorxiv.org/content/10.1101/009472v1?rss=1 Gábor Csárdi Alexander Franks David S. Choi Eduardo M. Airoldi D. Allan Drummond 2014-09-21 doi:10.1101/009472 Cold Spring Harbor Laboratory Press 2014-09-21 <![CDATA[ WASP: allele-specific software for robust discovery of molecular quantitative trait loci ]]> https://biorxiv.org/content/10.1101/011221v1?rss=1 Bryce van de Geijn Graham McVicker Yoav Gilad Jonathan Pritchard 2014-11-07 doi:10.1101/011221 Cold Spring Harbor Laboratory Press 2014-11-07 <![CDATA[ A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians ]]> https://biorxiv.org/content/10.1101/011270v1?rss=1 15). Subsequent conditional analyses suggest that three of these (APOE, LPA and CETP) likely harbor multiple independently associated SNPs. Further, while different variants typically showed different characteristic patterns of association with combinations of subfractions, the two SNPs in CETP show strikingly similar patterns - both in our original data and in a replication cohort - consistent with a common underlying molecular mechanism. Notably, the CETP variants are very strongly associated with LDL subfractions, despite showing no association with total LDLs in our study, illustrating the potential value of the more detailed phenotypic measurements. In contrast with these strong subfraction associations, genetic association analysis of subfraction response to statins showed much weaker signals (none exceeding log10 Bayes Factor of 6). However, two SNPs (in APOE and LPA) previously-reported to be associated with LDL statin response do show some modest evidence for association in our data, and the subfraction response profiles at the LPA SNP are consistent with the LPA association, with response likely being due primarily to resistance of Lp(a) particles to statin therapy. An additional important feature of our analysis is that, unlike most previous analyses of multiple related phenotypes, we analyzed the subfractions jointly, rather than one at a time. Comparisons of our multivariate analyses with standard univariate analyses demonstrate that multivariate analyses can substantially increase power to detect associations. Software implementing our multivariate analysis methods is available at http://stephenslab.uchicago.edu/software.htmlnnAuthor SummaryLevels of plasma lipids and lipoproteins are related to risk of cardiovascular disease (CVD), and because of this, considerable attention has been devoted to genetic association analyses of lipid-related measures. In addition, motivated by the fact that statins are widely prescribed to lower plasma low density lipoprotein (LDL) cholesterol and CVD risk, and that response to statins has a genetic component, several studies have searched for genetic associations with response of lipid related phenotypes to statin treatment. Here, in 1868 individuals of European ancestry from the Pharmacogenomics and Risk of Cardiovascular Disease study, we have conducted genetic association analyses of 7 subfractions of LDLs and 3 subfractions of intermediate density lipoproteins (IDLs) measured by gradient gel electrophoresis, and their response to statin treatment. These phenotypic measurements offer higher resolution information on LDLs and IDLs than available previously. Therefore, our study provides a more detailed picture of association with the entire IDL/LDL subfraction profile than any prior genetic association studies of either lipid-related measures or their response to statin treatment. Moreover, unlike most previous analyses of multiple related measurements, we analyzed the subfractions jointly, rather than one at a time. Our results demonstrate that joint analyses of related measurements can considerably increase power to detect associations compared with conventional univariate analyses. ]]> Heejung Shim Daniel I Chasman Joshua D Smith Samia Mora Paul M Ridker Deborah A Nickerson Ronald M Krauss Matthew Stephens 2014-11-09 doi:10.1101/011270 Cold Spring Harbor Laboratory Press 2014-11-09 <![CDATA[ Visualizing spatial population structure with estimated effective migration surfaces ]]> https://biorxiv.org/content/10.1101/011809v1?rss=1 Desislava Petkova John Novembre Matthew Stephens 2014-11-26 doi:10.1101/011809 Cold Spring Harbor Laboratory Press 2014-11-26 <![CDATA[ msCentipede: Modeling heterogeneity across genomic sites improves accuracy in the inference of transcription factor binding ]]> https://biorxiv.org/content/10.1101/012013v1?rss=1 Anil Raj Heejung Shim Yoav Gilad Jonathan K Pritchard Matthew Stephens 2014-11-29 doi:10.1101/012013 Cold Spring Harbor Laboratory Press 2014-11-29 <![CDATA[ SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers ]]> https://biorxiv.org/content/10.1101/013573v1?rss=1 Natasha Bloch James M Morrow Belinda SW Chang Trevor D Price 2015-01-09 doi:10.1101/013573 Cold Spring Harbor Laboratory Press 2015-01-09 <![CDATA[ Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature ]]> https://biorxiv.org/content/10.1101/013631v1?rss=1 Samantha M Thomas Courtney Kagan Bryan J Pavlovic Jonathan Burnett Kristen Patterson Jonathan K Pritchard Yoav Gilad 2015-01-10 doi:10.1101/013631 Cold Spring Harbor Laboratory Press 2015-01-10 <![CDATA[ Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs ]]> https://biorxiv.org/content/10.1101/013888v1?rss=1 Courtney L Kagan Nicholas E Banovich Bryan J Pavlovic Kristen Patterson Irene Gallego Romero Jonathan K Pritchard Yoav Gilad 2015-01-19 doi:10.1101/013888 Cold Spring Harbor Laboratory Press 2015-01-19 <![CDATA[ Rates of karyotypic evolution in Estrildid finches differ between island and continental clades ]]> https://biorxiv.org/content/10.1101/013987v1?rss=1 Daniel M Hooper Trevor D Price 2015-01-19 doi:10.1101/013987 Cold Spring Harbor Laboratory Press 2015-01-19 <![CDATA[ Ancestry specific association mapping in admixed populations ]]> https://biorxiv.org/content/10.1101/014001v1?rss=1 Line Skotte Thorfinn Sand S Korneliussen Ida Moltke Anders Albrechtsen 2015-01-22 doi:10.1101/014001 Cold Spring Harbor Laboratory Press 2015-01-22 <![CDATA[ Evolution of Conditional Cooperativity Between HOXA11 and FOXO1 Through Allosteric Regulation ]]> https://biorxiv.org/content/10.1101/014381v1?rss=1 Mauris C. Nnamani Soumya Ganguly Vincent J. Lynch Laura S. Mizoue Yingchun Tong Heather Darling Monika Fuxreiter Jens Meiler Gunter P. Wagner 2015-01-26 doi:10.1101/014381 Cold Spring Harbor Laboratory Press 2015-01-26 <![CDATA[ Permutation Testing in the Presence of Polygenic Variation ]]> https://biorxiv.org/content/10.1101/014571v1?rss=1 Mark Abney 2015-01-29 doi:10.1101/014571 Cold Spring Harbor Laboratory Press 2015-01-29 <![CDATA[ Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells ]]> https://biorxiv.org/content/10.1101/016022v1?rss=1 Alain Pacis Ludovic Tailleux John Lambourne Vania Yotova Anne Dumaine Anne Danckaert Francesca Luca Jean-Christophe Grenier Kasper Hansen Brigitte Gicquel Miao Yu Athma Pai Jenny Tung Chuan He Tomi Pastinen Roger Pique-Regi Yoav Gilad Luis Barreiro 2015-03-04 doi:10.1101/016022 Cold Spring Harbor Laboratory Press 2015-03-04 <![CDATA[ Mycobacterial infection induces a specific human innate immune response ]]> https://biorxiv.org/content/10.1101/017483v1?rss=1 John D Blischak Ludovic Tailleux Amy Mitrano Luis B Barreiro Yoav Gilad 2015-04-03 doi:10.1101/017483 Cold Spring Harbor Laboratory Press 2015-04-03 <![CDATA[ Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic ]]> https://biorxiv.org/content/10.1101/018366v1?rss=1 Vincent Lynch Oscar C. Bedoya-Reina Aakrosh Ratan Michael Sulak Daniela I. Drautz-Moses George H. Perry Webb Miller Stephan C. Schuster 2015-04-23 doi:10.1101/018366 Cold Spring Harbor Laboratory Press 2015-04-23 <![CDATA[ Mass spectrometry-based quantitation of Her2 in gastroesophageal tumor tissue: Comparison to IHC and FISH ]]> https://biorxiv.org/content/10.1101/018747v1?rss=1 750 amol/g and sensitivity (75%) at lower-level cut-off of <450 amol/ug. We observed an equivocal-zone between 450-750 amol/ug, analogous to IHC2+, but less frequent (9-16% of cases versus 36-41%).nnSignificanceCompared to IHC, SRM-MS provided more objective and quantitative Her2 expression with excellent HER2/CEP17 FISH correlation and fewer equivocal cases. Along with the multiplex capability for other relevant oncoproteins, these results demonstrated a refined HER2 expression assay for clinical application. ]]> Daniel Catenacci Wei-Li Liao Lei Zhao Emma Whitcomb Les Henderson peng Xu Emily O'Day Sheeno Thyparambil Kathleen Bengali Jamar Uzzell Marlene Darflur Fabiola Cecchi Adele Blackler David Krisman Yung-Jue Bang John Hart Shu-Yuan Xiao Sang Mee Lee Jon Burrows Todd Hembrough 2015-04-30 doi:10.1101/018747 Cold Spring Harbor Laboratory Press 2015-04-30 <![CDATA[ PrediXcan: Trait Mapping Using Human Transcriptome Regulation ]]> https://biorxiv.org/content/10.1101/020164v1?rss=1 Eric R Gamazon Heather E Wheeler Kaanan Shah Sahar V Mozaffari Keston Aquino-Michaels Robert J Carroll Anne E Eyler Joshua C Denny Dan L Nicolae Nancy J Cox Hae Kyung Im GTEx Consortium 2015-06-17 doi:10.1101/020164 Cold Spring Harbor Laboratory Press 2015-06-17 <![CDATA[ Coevolution of male and female reproductive traits drive cascading reinforcement in Drosophila yakuba ]]> https://biorxiv.org/content/10.1101/022244v1?rss=1 Aaron A Comeault Aarti Venkat Daniel R Matute 2015-07-10 doi:10.1101/022244 Cold Spring Harbor Laboratory Press 2015-07-10 <![CDATA[ Stable recombination hotspots in birds ]]> https://biorxiv.org/content/10.1101/023101v1?rss=1 Sonal Singhal Ellen Leffler Keerthi Sannareddy Isaac Turner Oliver Venn Daniel Hooper Alva Strand Qiye Li Brian Raney Christopher Balakrishnan Simon Griffith Gil McVean Molly Przeworski 2015-07-23 doi:10.1101/023101 Cold Spring Harbor Laboratory Press 2015-07-23 <![CDATA[ Effect of Localization on the Stability of Mutualistic Ecological Networks ]]> https://biorxiv.org/content/10.1101/023275v1?rss=1 Samir Suweis Jacopo Grilli Jayanth Banavar Stefano Allesina Amos Maritan 2015-07-27 doi:10.1101/023275 Cold Spring Harbor Laboratory Press 2015-07-27 <![CDATA[ Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics ]]> https://biorxiv.org/content/10.1101/025429v1?rss=1 Yong Tao Zheng Hu Shaoping Ling Shiou-Hwie Yeh Weiwei Zhai Ke Chen Chunyan Li Yu Wang Kaile Wang Hurng-Yi Wang Eric A Hungate Kenan Onel Jiang Liu Changqing Zeng Richard R Hudson Pei-Jer Chen Xuemei Lu Chung-I Wu 2015-08-25 doi:10.1101/025429 Cold Spring Harbor Laboratory Press 2015-08-25 <![CDATA[ The regulator-executor-phenotype architecture shaped by natural selection ]]> https://biorxiv.org/content/10.1101/026443v1?rss=1 Han Chen Chung-I Wu Xionglei He 2016-03-03 doi:10.1101/026443 Cold Spring Harbor Laboratory Press 2016-03-03 <![CDATA[ Inference of complex population histories using whole-genome sequences from multiple populations ]]> https://biorxiv.org/content/10.1101/026591v1?rss=1 Matthias Steinrücken John A. Kamm Yun S. Song 2015-09-16 doi:10.1101/026591 Cold Spring Harbor Laboratory Press 2015-09-16 <![CDATA[ TP53 copy number expansion correlates with the evolution of increased body size and an enhanced DNA damage response in elephants ]]> https://biorxiv.org/content/10.1101/028522v1?rss=1 Michael Sulak Lindsey Fong Katelyn Mika Sravanthi Chigurupati Lisa Yon Nigel P. Mongan Richard D. Emes Vincent J. Lynch 2015-10-06 doi:10.1101/028522 Cold Spring Harbor Laboratory Press 2015-10-06 <![CDATA[ Trees, Population Structure, F-statistics! ]]> https://biorxiv.org/content/10.1101/028753v1?rss=1 Benjamin M Peter 2015-10-09 doi:10.1101/028753 Cold Spring Harbor Laboratory Press 2015-10-09 <![CDATA[ Reconstructing Genetic History of Siberian and Northeastern European Populations ]]> https://biorxiv.org/content/10.1101/029421v1?rss=1 Emily H.M. Wong Andrey Khrunin Larissa Nichols Dmitry Pushkarev Denis Khokhrin Dmitry Verbenko Oleg Evgrafov James Knowles John Novembre Svetlana Limborska Anton Valouev 2015-10-18 doi:10.1101/029421 Cold Spring Harbor Laboratory Press 2015-10-18 <![CDATA[ Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes ]]> https://biorxiv.org/content/10.1101/030759v1?rss=1 Silvia N Kariuki John D Blischak Shigeki Nakagome David B Witonsky Anna Di Rienzo 2015-11-06 doi:10.1101/030759 Cold Spring Harbor Laboratory Press 2015-11-06 <![CDATA[ Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling ]]> https://biorxiv.org/content/10.1101/031617v1?rss=1 Anil Raj Sidney Wang Heejung Shim Arbel Harpak Yang I Li Brett Englemann Matthew Stephens Yoav Gilad Jonathan K Pritchard 2015-11-13 doi:10.1101/031617 Cold Spring Harbor Laboratory Press 2015-11-13 <![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[ Multiscale simulations reveal key features of the proton pumping mechanism in cytochrome c oxidase ]]> https://biorxiv.org/content/10.1101/040717v1?rss=1 Ruibin Liang Jessica M J Swanson Yuxing Peng Marten Wikstrom Gregory Voth 2016-02-23 doi:10.1101/040717 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly ]]> https://biorxiv.org/content/10.1101/040741v1?rss=1 John M A Grime James F Dama Barbie K Ganser-Pornillos Cora L Woodward Grant J Jensen Mark J Yeager Gregory Voth 2016-02-23 doi:10.1101/040741 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Whole genome sequencing identifies a novel factor required for secretory granule maturation in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/042085v1?rss=1 Cassandra Kontur Santosh Kumar Xun Lan Jonathan K Pritchard Aaron P Turkewitz 2016-03-01 doi:10.1101/042085 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Bayesian large-scale multiple regression with summary statistics from genome-wide association studies ]]> https://biorxiv.org/content/10.1101/042457v1?rss=1 Xiang Zhu Matthew Stephens 2016-03-04 doi:10.1101/042457 Cold Spring Harbor Laboratory Press 2016-03-04 <![CDATA[ Can secondary contact following range expansion be distinguished from barriers to gene flow? ]]> https://biorxiv.org/content/10.1101/043398v1?rss=1 Johanna Bertl Michael G. B. Blum 2016-03-12 doi:10.1101/043398 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ Survey of the Heritability and Sparsity of Gene Expression Traits Across Human Tissues ]]> https://biorxiv.org/content/10.1101/043653v1?rss=1 Heather E Wheeler Kaanan P Shah Jonathon Brenner Tzintzuni Garcia Keston Aquino-Michaels GTEx Consortium Nancy J Cox Dan L Nicolae Hae Kyung Im 2016-03-15 doi:10.1101/043653 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Genetic predictors of gene expression associated with risk of bipolar disorder ]]> https://biorxiv.org/content/10.1101/043752v1?rss=1 Kaanan Shah Heather E Wheeler Eric R Gamazon Dan L Nicolae Nancy J Cox Hae Kyung Im 2016-03-15 doi:10.1101/043752 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Local RhoA Activation Induces Cytokinetic Furrows Independent of Spindle Position and Cell Cycle Stage ]]> https://biorxiv.org/content/10.1101/043836v1?rss=1 Elizabeth Wagner Michael Glotzer 2016-03-15 doi:10.1101/043836 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ LeafCutter: Annotation-free quantification of RNA splicing ]]> https://biorxiv.org/content/10.1101/044107v1?rss=1 Yang I Li David A Knowles Jonathan K Pritchard 2016-03-16 doi:10.1101/044107 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ Anxiolytic treatment impairs helping behavior in rats ]]> https://biorxiv.org/content/10.1101/044180v1?rss=1 Inbal Ben-Ami Bartal Haozhe Shan Nora Molasky Teresa Murray Jasper Williams Jean Decety Peggy Mason 2016-03-17 doi:10.1101/044180 Cold Spring Harbor Laboratory Press 2016-03-17 <![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[ Costs of Clock-Environment Misalignment in Individual Cyanobacterial Cells ]]> https://biorxiv.org/content/10.1101/045146v1?rss=1 Guillaume Lambert Michael J. Rust Justin Chew 2016-03-22 doi:10.1101/045146 Cold Spring Harbor Laboratory Press 2016-03-22 <![CDATA[ Integrating tissue specific mechanisms into GWAS summary results ]]> https://biorxiv.org/content/10.1101/045260v1?rss=1 Alvaro Barbeira Scott P Dickinson Jason M Torres Eric S Torstenson Jiamao Zheng Heather E Wheeler Kaanan P Shah Todd Edwards GTEx Consortium Dan Nicolae Nancy J Cox Hae Kyung Im 2016-03-23 doi:10.1101/045260 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Recent Cis-Trans Coevolution Driven by the Emergence of A Novel Gene in Drosophila ]]> https://biorxiv.org/content/10.1101/045385v1?rss=1 Benjamin H Krinsky Robert Arthur Kevin P White Manyuan Long 2016-03-23 doi:10.1101/045385 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Crossover in the dynamics of cell wall growth controls bacterial division times ]]> https://biorxiv.org/content/10.1101/047589v1?rss=1 Shiladitya Banerjee Klevin Lo Thomas Kuntz Matthew K Daddysman Aaron R Dinner Norbert F Scherer 2016-04-08 doi:10.1101/047589 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9 ]]> https://biorxiv.org/content/10.1101/048371v1?rss=1 2 s-1 upon introduction of mismatches proximal to the protospacer adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 12 base pairs in length, which prevent DNA cleavage, still allow the formation of a stable complex (off-rate < 0.006 s-1), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome editing thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading. ]]> Digvijay Singh Samuel H. Sternberg Jingyi Fei Taekjip Ha Jennifer A. Doudna 2016-04-13 doi:10.1101/048371 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Variance Adaptive Shrinkage (vash): Flexible Empirical Bayes estimation of variances ]]> https://biorxiv.org/content/10.1101/048660v1?rss=1 Mengyin Lu Matthew Stephens 2016-04-13 doi:10.1101/048660 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ The rate and effect of de novo mutations in natural populations of Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/050203v1?rss=1 Moises Exposito-Alonso Claude Becker Verena J. Schuenemann Ella Reitter Claudia Setzer Radka Slovak Benjamin Brachi Joerg Hagmann Dominik G. Grimm Chen Jiahui Wolfgang Busch Joy Bergelson Rob W. Ness Johannes Krause Hernan A. Burbano Detlef Weigel 2016-04-25 doi:10.1101/050203 Cold Spring Harbor Laboratory Press 2016-04-25 <![CDATA[ Demographic and immune-based selection shifts before and after European contact inferred from 50 ancient and modern exomes from the Northwest Coast of North America ]]> https://biorxiv.org/content/10.1101/051078v1?rss=1 John Lindo Emilia Huerta-Sanchez Shigeki Nakagome Morten Rasmussen Barbara Petzelt Joycellyn Mitchell Jerome S Cybulski Eske Willerslev Michael DeGiorgio Ripan S Malhi 2016-04-29 doi:10.1101/051078 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Serotonin-dependent kinetics of bursts of feeding underlie a graded response to food availability ]]> https://biorxiv.org/content/10.1101/051086v1?rss=1 Kyung Suk Lee Shachar Iwanir Ronen Kopito Monika Scholz David Biron Erel Levine 2016-04-29 doi:10.1101/051086 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ A scalable method for automatically measuring pharyngeal pumping in C. elegans ]]> https://biorxiv.org/content/10.1101/051243v1?rss=1 Monika Scholz Dylan J Lynch Kyung Suk Lee Erel Levine David Biron 2016-05-02 doi:10.1101/051243 Cold Spring Harbor Laboratory Press 2016-05-02 <![CDATA[ Clustering RNA-seq expression data using grade of membership models ]]> https://biorxiv.org/content/10.1101/051631v1?rss=1 Kushal K Dey Chiaowen Joyce Hsiao Matthew Stephens 2016-05-04 doi:10.1101/051631 Cold Spring Harbor Laboratory Press 2016-05-04 <![CDATA[ Local field potentials primarily reflect inhibitory neuron activity in human and monkey cortex ]]> https://biorxiv.org/content/10.1101/052282v1?rss=1 Bartosz Telenczuk Nima Dehghani Michel Le Van Quyen Sydney S Cash Eric Halgren Nicholas G Hatsopoulos Alain Destexhe 2016-05-10 doi:10.1101/052282 Cold Spring Harbor Laboratory Press 2016-05-10 <![CDATA[ Range overlap drives chromosome inversion fixation in passerine birds ]]> https://biorxiv.org/content/10.1101/053371v1?rss=1 Daniel M Hooper 2016-05-14 doi:10.1101/053371 Cold Spring Harbor Laboratory Press 2016-05-14 <![CDATA[ An improved reversibly dimerizing mutant of the FK506-binding protein FKBP ]]> https://biorxiv.org/content/10.1101/053751v1?rss=1 Juan J. Barrero Effrosyni Papanikou Jason C. Casler Kasey J. Day Benjamin S. Glick 2016-05-16 doi:10.1101/053751 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ Cerebellar learning using perturbations ]]> https://biorxiv.org/content/10.1101/053785v1?rss=1 Guy Bouvier Claudia Clopath Célian Bimbard Jean-Pierre Nadal Nicolas Brunel Vincent Hakim Boris Barbour 2016-05-16 doi:10.1101/053785 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ Genome reduction in an abundant and ubiquitous soil bacterial lineage ]]> https://biorxiv.org/content/10.1101/053942v1?rss=1 1000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant phylotype. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name Candidatus Udaeobacter copiosus. The Ca. U. copiosus genome is unusually small for soil bacteria, estimated to be only 2.81 Mbp compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic chemoorganoheterotroph with numerous amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggests that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to have identified an alternate strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment. ]]> Tess Brewer Kim Handley Paul Carini Jack Gibert Noah Fierer 2016-05-18 doi:10.1101/053942 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Large-scale trans-eQTLs affect hundreds of transcripts and mediate patterns of transcriptional co-regulation ]]> https://biorxiv.org/content/10.1101/056283v1?rss=1 Boel Brynedal JinMyung Choi Towfique Raj Robert Bjornson Barbara Stranger Benjamin Neale Benjamin Voight Chris Cotsapas 2016-05-31 doi:10.1101/056283 Cold Spring Harbor Laboratory Press 2016-05-31 <![CDATA[ An ancient fecundability-associated polymorphism switches a repressor into an enhancer of endometrial TAP2 expression ]]> https://biorxiv.org/content/10.1101/058388v1?rss=1 Katelyn M. Mika Vincent J. Lynch 2016-06-11 doi:10.1101/058388 Cold Spring Harbor Laboratory Press 2016-06-11 <![CDATA[ Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics ]]> https://biorxiv.org/content/10.1101/058750v1?rss=1 Tom O Delmont A. Murat Eren 2016-06-13 doi:10.1101/058750 Cold Spring Harbor Laboratory Press 2016-06-13 <![CDATA[ Metabolic Reconstruction and Modeling Microbial Electrosynthesis ]]> https://biorxiv.org/content/10.1101/059410v1?rss=1 Christopher Marshall Daniel Ross Kim Handley Pamela Weisenhorn Janaka Edirisinghe Christopher Henry Jack Gilbert Harold May R Sean Norman 2016-07-07 doi:10.1101/059410 Cold Spring Harbor Laboratory Press 2016-07-07 <![CDATA[ Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells ]]> https://biorxiv.org/content/10.1101/061739v1?rss=1 Sebastian Pott 2016-07-01 doi:10.1101/061739 Cold Spring Harbor Laboratory Press 2016-07-01 <![CDATA[ Host genetic variation in mucosal immunity pathways influences the upper airway microbiome ]]> https://biorxiv.org/content/10.1101/062232v1?rss=1 Catherine Igartua Emily R Davenport Yoav Gilad Dan L Nicolae Jayant Pinto Carole Ober 2016-07-05 doi:10.1101/062232 Cold Spring Harbor Laboratory Press 2016-07-05 <![CDATA[ Assocplots: a python package for static and interactive visualization of multiple-group GWAS results ]]> https://biorxiv.org/content/10.1101/062737v1?rss=1 Ekaterina A Khramtsova Barbara E. Stranger 2016-07-07 doi:10.1101/062737 Cold Spring Harbor Laboratory Press 2016-07-07 <![CDATA[ Batch effects and the effective design of single-cell gene expression studies ]]> https://biorxiv.org/content/10.1101/062919v1?rss=1 Po-Yuan Tung John D Blischak Chiaowen Hsiao David A Knowles Jonathan E Burnett Jonathan K Pritchard Yoav Gilad 2016-07-08 doi:10.1101/062919 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ The Origin of Coupled Chloride and Proton Transport in a Cl-/H+ Antiporter ]]> https://biorxiv.org/content/10.1101/064527v1?rss=1 Sangyun Lee Heather B. Mayes Jessica M. J. Swanson Gregory A Voth 2016-07-18 doi:10.1101/064527 Cold Spring Harbor Laboratory Press 2016-07-18 <![CDATA[ Population and individual effects of non-coding variants inform genetic risk factors ]]> https://biorxiv.org/content/10.1101/065144v1?rss=1 Mauro Pala Zachary Zappala Mara Marongiu Xin Li Joe R Davis Roberto Cusano Francesca Crobu Kimberly R Kukurba Frederic Reiner Riccardo Berutti Maria G Piras Antonella Mulas Magdalena Zoledziewska Michele Marongiu Fabio Busonero Andrea Maschio Maristella Steri Carlo Sidore Serena Sanna Edoardo Fiorillo Alexis Battle John Novembre Chris Jones Andrea Angius Goncalo R Abecasis David Schlessinger Francesco Cucca Stephen B Montgomery 2016-07-21 doi:10.1101/065144 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ A rodent model of social rejection ]]> https://biorxiv.org/content/10.1101/066993v1?rss=1 Haozhe Shan Inbal Ben-Ami Bartal Peggy Mason 2016-07-31 doi:10.1101/066993 Cold Spring Harbor Laboratory Press 2016-07-31 <![CDATA[ A FLIC motility assay reveals myosin-6 coordination limited by actin filament buckling ]]> https://biorxiv.org/content/10.1101/068163v1?rss=1 Agata K Krenc Jagoda J Rokicka Ronald S Rock 2016-08-06 doi:10.1101/068163 Cold Spring Harbor Laboratory Press 2016-08-06 <![CDATA[ Visualizing the Geography of Genetic Variants ]]> https://biorxiv.org/content/10.1101/068536v1?rss=1 Joseph H Marcus John Novembre 2016-08-09 doi:10.1101/068536 Cold Spring Harbor Laboratory Press 2016-08-09 <![CDATA[ Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells ]]> https://biorxiv.org/content/10.1101/068767v1?rss=1 Shalin B. Mehta Molly McQuilken Patrick La Riviere Patricia Occhipinti Amitabh Verma Rudolf Oldenbourg Amy S. Gladfelter Tomomi Tani 2016-08-11 doi:10.1101/068767 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Optogenetically controlled cargo shows full length human myosin VI integrates activation signals in vivo and in vitro ]]> https://biorxiv.org/content/10.1101/068965v1?rss=1 Alexander R French Tobin R Sosnick Ronald Rock 2016-08-11 doi:10.1101/068965 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Estimating time to the common ancestor for a beneficial allele ]]> https://biorxiv.org/content/10.1101/071241v1?rss=1 Joel Smith Graham Coop Matthew Stephens John Novembre 2016-08-24 doi:10.1101/071241 Cold Spring Harbor Laboratory Press 2016-08-24 <![CDATA[ Recent advances in the study of fine-scale population structure in humans ]]> https://biorxiv.org/content/10.1101/073221v1?rss=1 John Novembre Benjamin M Peter 2016-09-04 doi:10.1101/073221 Cold Spring Harbor Laboratory Press 2016-09-04 <![CDATA[ De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning ]]> https://biorxiv.org/content/10.1101/073825v1?rss=1 Christopher Quince Stephanie Connelly Sebastien Raguideau Johannes Alneberg Seung Gu Shin Gavin Collins A. Murat Eren 2016-09-06 doi:10.1101/073825 Cold Spring Harbor Laboratory Press 2016-09-06 <![CDATA[ Excitable RhoA dynamics drive pulsed contractions in the early C. elegans embryo. ]]> https://biorxiv.org/content/10.1101/076356v1?rss=1 François B Robin Jonathan B Michaux William M McFadden Edwin M Munro 2016-09-21 doi:10.1101/076356 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility ]]> https://biorxiv.org/content/10.1101/076794v1?rss=1 Felix Day Deborah Thompson Hannes Helgason Daniel Chasman Hilary Finucane Patrick Sulem Katherine Ruth Sean Whalen Abhishek Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn Lunetta Massimo Mangino Brumat Marco Gerorge McMahon Sarah Medland Ilja Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda Rose Katharina Schraut Ayellet Segre Albert Smith Lisette Stolk Alexander Teumer Irene Andrulis Stefania Ban 2016-09-23 doi:10.1101/076794 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Contribution of de novo non-coding mutations to autism and identification of risk genes from whole-genome sequencing of affected families ]]> https://biorxiv.org/content/10.1101/077578v1?rss=1 Yuwen Liu A. Ercument Cicek Yanyu Liang Jinchen Li Rebecca A Muhle Nicholas Knoblauch Martina Krenzer Yue Mei Yan Wang Yi Jiang Even Geller Zhongshan Li Iuliana Ionita-Laza Jinyu Wu Kun Xia James P Noonan Zhong Sheng Sun Xin He 2016-09-26 doi:10.1101/077578 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis ]]> https://biorxiv.org/content/10.1101/078683v1?rss=1 Fan Yang Jiebiao Wang the GTEx consortium Brandon L. Pierce Lin S. Chen 2016-09-30 doi:10.1101/078683 Cold Spring Harbor Laboratory Press 2016-09-30 <![CDATA[ Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence ]]> https://biorxiv.org/content/10.1101/080721v1?rss=1 Oppold, A.-M. Schmidt, H. Rose, M. Hellmann, S. L. Dolze, F. Ripp, F. Weich, B. Schmidt-Ott, U. Schmidt, E. Kofler, R. Hankeln, T. Pfenninger, M. 2016-10-13 doi:10.1101/080721 Cold Spring Harbor Laboratory Press 2016-10-13 <![CDATA[ Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape ]]> https://biorxiv.org/content/10.1101/083980v1?rss=1 Trizzino, M. Park, Y. Holsbach-Beltrame, M. Aracena, K. Mika, K. Caliskan, M. Perry, G. H. Lynch, V. J. Brown, C. D. 2016-10-27 doi:10.1101/083980 Cold Spring Harbor Laboratory Press 2016-10-27 <![CDATA[ Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill ]]> https://biorxiv.org/content/10.1101/084707v1?rss=1 Handley, K. M. Yvette, P. M. Hu, P. Tom, L. M. Mason, O. U. Andersen, G. L. Jansson, J. K. Gilbert, J. A. 2016-10-31 doi:10.1101/084707 Cold Spring Harbor Laboratory Press 2016-10-31 <![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[ Domains of methylated CAC and CG target MeCP2 to tune transcription in the brain ]]> https://biorxiv.org/content/10.1101/087577v1?rss=1 Lagger, S. Connelly, J. C. Schweikert, G. Webb, S. Selfridge, J. Ramsahoye, B. H. Yu, M. DeSousa, D. Seiser, C. He, C. Sanguinetti, G. Sowers, L. C. Walkinshaw, M. D. Bird, A. P. 2016-11-14 doi:10.1101/087577 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/087890v1?rss=1 Montefiori, L. Gonzales, L. Zhang, Z. Gilad, Y. Ober, C. Crawford, G. Nobrega, M. Sakabe, N. J. 2016-11-22 doi:10.1101/087890 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Slow and steady wins the race: encounters of myosin-5 and myosin-6 on shared actin filaments ]]> https://biorxiv.org/content/10.1101/087940v1?rss=1 Santos, A. Kalita, J. Rock, R. 2016-11-15 doi:10.1101/087940 Cold Spring Harbor Laboratory Press 2016-11-15 <![CDATA[ Eco-evolutionary theory and insect outbreaks ]]> https://biorxiv.org/content/10.1101/088047v1?rss=1 Paez, D. Dukic, V. Dushoff, J. Fleming-Davies, A. Dwyer, G. 2016-11-16 doi:10.1101/088047 Cold Spring Harbor Laboratory Press 2016-11-16 <![CDATA[ Disentangling the Effects of Weather and Densityon the Dynamics of a Fungal Pathogen ]]> https://biorxiv.org/content/10.1101/088054v1?rss=1 Kyle, C. Goldwyn, E. Dwyer, G. 2016-11-16 doi:10.1101/088054 Cold Spring Harbor Laboratory Press 2016-11-16 <![CDATA[ High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes ]]> https://biorxiv.org/content/10.1101/090993v1?rss=1 Lee, S. T. Kahn, S. A. Delmont, T. O. Hubert, N. A. Morrison, H. G. Antonopoulos, D. A. Rubin, D. T. Eren, A. M. 2016-12-02 doi:10.1101/090993 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Impact of regulatory variation across human iPSCs and differentiated cells ]]> https://biorxiv.org/content/10.1101/091660v1?rss=1 Banovich, N. E. Li, Y. I. Raj, A. Ward, M. C. Greenside, P. Calderon, D. Tung, P. Y. Burnett, J. E. Myrthil, M. Thomas, S. M. Burrows, C. K. Gallego Romero, I. Pavlovic, B. J. Kundaje, A. Pritchard, J. K. Gilad, Y. 2016-12-05 doi:10.1101/091660 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ Population history of the Sardinian people inferred from whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/092148v1?rss=1 Chiang, C. W. K. Marcus, J. H. Sidore, C. Al-Asadi, H. Zoledziewska, M. Pitzalis, M. Busonero, F. Maschio, A. Pistis, G. Steri, M. Angius, A. Lohmueller, K. E. Abecasis, G. R. Schlessinger, D. Cucca, F. Novembre, J. 2016-12-07 doi:10.1101/092148 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Fitness landscapes reveal simple strategies for steering evolution to minimize antibiotic resistance ]]> https://biorxiv.org/content/10.1101/093153v1?rss=1 Smith, M. Cobey, S. 2016-12-11 doi:10.1101/093153 Cold Spring Harbor Laboratory Press 2016-12-11 <![CDATA[ Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity ]]> https://biorxiv.org/content/10.1101/093468v1?rss=1 Lindo, J. Achilli, A. Perego, U. Archer, D. Valdiosera, C. Petzelt, B. Mitchell, J. Worl, R. Dixon, E. J. Fifield, T. Rasmussen, M. Willerslev, E. Cybulski, J. Kemp, B. DeGiorgio, M. Malhi, R. S. 2016-12-13 doi:10.1101/093468 Cold Spring Harbor Laboratory Press 2016-12-13 <![CDATA[ Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms ]]> https://biorxiv.org/content/10.1101/094656v1?rss=1 500 pairs with evidence of a causal relationships between expression and methylation (i.e., shared mechanism) with many additional pairs that we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite effects on expression and methylation, although a many affect multiple CpGs in opposite directions. Evidence of shared SNP-age interaction also supports shared mechanisms for two eQTL-mQTL pairs. This work demonstrates the pervasiveness of co-regulated expression and methylation traits in the human genome. This approach can be applied to other types of molecular QTLs to enhance our understanding of regulatory mechanisms. ]]> Pierce, B. Tong, L. Argos, M. Jasmine, F. Rakibuz-Zaman, M. Sarwar, G. Islam, M. T. Shahriar, H. Islam, T. Rahman, M. Yunus, M. Kibriya, M. G. Chen, L. S. Ahsan, H. 2016-12-15 doi:10.1101/094656 Cold Spring Harbor Laboratory Press 2016-12-15 <![CDATA[ Chlamydomonas reinhardtii formin and profilin are optimized for acute rapid actin filament assembly ]]> https://biorxiv.org/content/10.1101/096008v1?rss=1 Christensen, J. R. Glista, M. J. Mueller, D. M. Li, Y. Sees, J. A. Skau, C. T. Mets, L. J. Avasthi, P. Kovar, D. R. 2016-12-21 doi:10.1101/096008 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different-sized Fluorescent Probes ]]> https://biorxiv.org/content/10.1101/096966v1?rss=1 Lee, S. H. Jin, C. Cai, E. Ge, P. Ishitsuka, Y. Teng, K. W. Thomaz, A. A. d. Nall, D. L. Baday, M. Jeyifous, O. Demonte, D. Dundas, C. M. Park, S. Green, W. N. Selvin, P. R. 2016-12-27 doi:10.1101/096966 Cold Spring Harbor Laboratory Press 2016-12-27 <![CDATA[ Karp: Accurate and fast taxonomic classification using pseudoalignment ]]> https://biorxiv.org/content/10.1101/097949v1?rss=1 Reppell, M. Novembre, J. 2017-01-03 doi:10.1101/097949 Cold Spring Harbor Laboratory Press 2017-01-03 <![CDATA[ Higher genetic risk of schizophrenia is associated with lower cognitive performance in healthy individuals ]]> https://biorxiv.org/content/10.1101/103622v1?rss=1 Shafee, R. Nanda, P. Padmanabhan, J. L. Tandon, N. Alliey-Rodriguez, N. Keefe, R. S. E. Hill, S. K. Bishop, J. R. Clementz, B. A. Tamminga, C. A. Gershon, E. S. Pearlson, G. D. Keshavan, M. S. Sweeney, J. A. Robinson, E. B. McCarroll, S. A. 2017-01-27 doi:10.1101/103622 Cold Spring Harbor Laboratory Press 2017-01-27 <![CDATA[ Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells ]]> https://biorxiv.org/content/10.1101/104729v1?rss=1 Blischak, J. D. Tailleux, L. Myrthil, M. Charlois, C. Bergot, E. Dinh, A. Morizot, G. Cheny, O. Von Platen, C. Herrmann, J.-L. Brosch, R. Barreiro, L. B. Gilad, Y. 2017-02-03 doi:10.1101/104729 Cold Spring Harbor Laboratory Press 2017-02-03 <![CDATA[ Bursting on a two states stochastic model for gene transcription in Drosophila embryos ]]> https://biorxiv.org/content/10.1101/107979v1?rss=1 Yvinec, R. da Silva, L. G. S. Prata, G. N. Reinitz, J. Ferreira Ramos, A. 2017-02-13 doi:10.1101/107979 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Integrative cross tissue analysis of gene expression identifies novel type 2 diabetes genes ]]> https://biorxiv.org/content/10.1101/108134v1?rss=1 Torres, J. M. Barbeira, A. N. Bonazzola, R. Morris, A. P. Shah, K. P. Wheeler, H. E. Bell, G. Cox, N. J. Im, H. K. 2017-02-13 doi:10.1101/108134 Cold Spring Harbor Laboratory Press 2017-02-13 <![CDATA[ Harnessing optogenetics to probe sub-cellular mechanics ]]> https://biorxiv.org/content/10.1101/109595v1?rss=1 Oakes, P. W. Wagner, E. Brand, C. A. Probst, D. Linke, M. Schwarz, U. S. Glotzer, M. Gardel, M. L. 2017-02-17 doi:10.1101/109595 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ Genome-wide association study of asthma in individuals of African ancestry reveals novel asthma susceptibility loci ]]> https://biorxiv.org/content/10.1101/112953v1?rss=1 Daya, M. Rafaels, N. Chavan, S. Johnston, H. R. Shetty, A. Gignoux, C. R. Boorgula, M. P. Campbell, M. Maul, P. Maul, T. Vergara, C. Levin, A. M. Wojcik, G. Torgerson, D. G. Ortega, V. E. Doumatey, A. Araujo, M. I. Avila, P. C. Bleecker, E. Bustamante, C. Caraballo, L. Dunston, G. M. Faruque, M. U. Ferguson, T. Figueiredo, C. Ford, J. G. Gourraud, P.-A. Hansel, N. N. Hernandez, R. D. Herrera-Paz, E. F. Kenny, E. E. Knight-Madden, J. Kumar, R. Lange, L. A. Lange, E. M. Lizee, A. Mayorga, A. Meyers, D. Nicolae, D. L. O'Connor, T. D. Oliveira, R. R. Olopad 2017-03-02 doi:10.1101/112953 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Cell cycle entry triggers a switch between two modes of Cdc42 activation during yeast polarization ]]> https://biorxiv.org/content/10.1101/114504v1?rss=1 Witte, K. Strickland, D. Glotzer, M. 2017-03-06 doi:10.1101/114504 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ The Co-regulation Data Harvester for Tetrahymenathermophila: automated high-throughput geneannotation and functional inference in a microbialeukaryote ]]> https://biorxiv.org/content/10.1101/115816v1?rss=1 Tsypin, L. M. Turkewitz, A. P. 2017-03-10 doi:10.1101/115816 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data ]]> https://biorxiv.org/content/10.1101/118521v1?rss=1 Hutchison, A. L. Allada, R. Dinner, A. R. 2017-03-20 doi:10.1101/118521 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Correcting for Dependent P-values in Rhythm Detection ]]> https://biorxiv.org/content/10.1101/118547v1?rss=1 Hutchison, A. L. Dinner, A. R. 2017-03-20 doi:10.1101/118547 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Brucella abortus Induces A Warburg Shift In Host Metabolism That Enhances Intracellular Replication Of The Pathogen ]]> https://biorxiv.org/content/10.1101/120527v1?rss=1 Czyz, D. M. Willett, J. Crosson, S. 2017-03-25 doi:10.1101/120527 Cold Spring Harbor Laboratory Press 2017-03-25 <![CDATA[ Formin-Dependent Adhesions Are Required For Invasion By Epithelial Tissues ]]> https://biorxiv.org/content/10.1101/124297v1?rss=1 Fessenden, T. B. Beckham, Y. Perez-Neut, M. Chourasia, A. H. Macleod, K. F. Oakes, P. W. Gardel, M. L. 2017-04-06 doi:10.1101/124297 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families ]]> https://biorxiv.org/content/10.1101/127043v1?rss=1 Werling, D. M. Brand, H. An, J.-Y. Stone, M. R. Glessner, J. T. Zhu, L. Collins, R. L. Dong, S. Layer, R. M. Markenscoff-Papadimitriou, E.-C. Farrell, A. Schwartz, G. B. Currall, B. B. Dea, J. Duhn, C. Erdman, C. Gilson, M. Handsaker, R. E. Kashin, S. Klei, L. Mandell, J. D. Nowakowski, T. J. Liu, Y. Pochareddy, S. Smith, L. Walker, M. F. Wang, H. Z. Waterman, M. J. He, X. Kriegstein, A. R. Rubenstein, J. L. Sestan, N. McCarroll, S. A. Neale, B. M. Coon, H. Willsey, A. J. Buxbaum, J. D. Daly, M. J. State, M. W. Quinlan, A. Marth, G. T. Roeder, K. Devli 2017-04-13 doi:10.1101/127043 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Non-monotonic spatial structure of interneuronal correlations in prefrontal microcircuits ]]> https://biorxiv.org/content/10.1101/128249v1?rss=1 Safavi, S. Dwarakanath, A. Kapoor, V. Werner, J. Hatsopoulos, N. G. Logothetis, N. K. Panagiotaropoulos, T. I. 2017-04-19 doi:10.1101/128249 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ Host population structure and treatment frequency maintain balancing selection on drug resistance ]]> https://biorxiv.org/content/10.1101/128967v1?rss=1 Cobey, S. Baskerville, E. B. Colijn, C. Hanage, W. Fraser, C. Lipsitch, M. 2017-04-20 doi:10.1101/128967 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Conservation of single amino-acid polymorphisms in Plasmodium falciparum erythrocyte membrane protein 1 and association with severe pathophysiology ]]> https://biorxiv.org/content/10.1101/128983v1?rss=1 Zinder, D. Rorick, M. M. Tiedje, K. E. Ruybal-Pesantez, S. Day, K. P. Pascual, M. 2017-04-20 doi:10.1101/128983 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean ]]> https://biorxiv.org/content/10.1101/129791v1?rss=1 Delmont, T. O. Quince, C. Shaiber, A. Esen, O. C. Lee, S. T. M. Lucker, S. Eren, A. M. 2017-04-23 doi:10.1101/129791 Cold Spring Harbor Laboratory Press 2017-04-23 <![CDATA[ Bayesian Integrated Analysis Of Multiple Types Of Rare Variants To Infer Risk Genes For Schizophrenia And Other Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/135293v1?rss=1 0.55), but low between SCZ and the NDDs ({rho} < 0.3). In depth analysis of 288 NDD genes shows highly significant protein-protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichments, single-cell RNA-seq (scRNAseq) cell types and multi-region developmental brain RNA-seq.nnConclusionsWe have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs. We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells. ]]> Nguyen, H. T. Dobbyn, A. Huckins, L. M. Ruderfer, D. Genovese, G. Fromer, M. Xu, X. Buxbaum, J. Hultman, C. Sklar, P. Purcell, S. M. He, X. Sullivan, P. F. Stahl, E. A. 2017-05-08 doi:10.1101/135293 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ A Comparative Study Of Endoderm Differentiation In Humans And Chimpanzees ]]> https://biorxiv.org/content/10.1101/135442v1?rss=1 Blake, L. E. Thomas, S. M. Blischak, J. D. Hsiao, C. J. Chavarria, C. Myrthil, M. Gilad, Y. Pavlovic, B. J. 2017-05-09 doi:10.1101/135442 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ A Point Of No Return Leading To Death During Heat-Shock In C. elegans ]]> https://biorxiv.org/content/10.1101/135988v1?rss=1 Jovic, K. Sterken, M. G. Grilli, J. Bevers, R. P. J. Rodriguez, M. Riksen, J. A. G. Allesina, S. Kammenga, J. E. Snoek, L. B. 2017-05-16 doi:10.1101/135988 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Accumulation And Functional Architecture Of Deleterious Genetic Variants During The Extinction Of Wrangel Island Mammoths ]]> https://biorxiv.org/content/10.1101/137455v1?rss=1 Fry, E. Kim, S. K. Chigurapti, S. Mika, K. M. Ratan, A. Dammermann, A. Mitchell, B. J. Miller, W. Lynch, V. J. 2017-05-14 doi:10.1101/137455 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ Role Of Competition In The Strain Structure Of Rotavirus Under Invasion And Reassortment ]]> https://biorxiv.org/content/10.1101/137661v1?rss=1 Zinder, D. Riolo, M. A. Woods, R. J. Pascual, M. 2017-05-13 doi:10.1101/137661 Cold Spring Harbor Laboratory Press 2017-05-13 <![CDATA[ Transparency in Authors’ Contributions and Responsibilities to Promote Integrity in Scientific Publication ]]> https://biorxiv.org/content/10.1101/140228v1?rss=1 McNutt, M. Bradford, M. Drazen, J. Hanson, R. B. Howard, B. Jamieson, K. H. Kiermer, V. Magoulias, M. Marcus, E. Pope, B. K. Schekman, R. Swaminathan, S. Stang, P. Verma, I. 2017-05-20 doi:10.1101/140228 Cold Spring Harbor Laboratory Press 2017-05-20 <![CDATA[ Exact Topological Inference For Paired Brain Networks Via Persistent Homology ]]> https://biorxiv.org/content/10.1101/140533v1?rss=1 Chung, M. K. Villalta-Gil, V. Lee, H. Rathouz, P. J. Lahey, B. B. Zald, D. H. 2017-05-22 doi:10.1101/140533 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ High lumenal chloride in the lysosome is critical for lysosome function. ]]> https://biorxiv.org/content/10.1101/141788v1?rss=1 Krishnan, Y. Chakraborty, K. Leung, K. 2017-05-24 doi:10.1101/141788 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Filament Rigidity And Connectivity Tune The Deformation Modes Of Active Biopolymer Networks ]]> https://biorxiv.org/content/10.1101/141796v1?rss=1 Stam, S. Freedman, S. L. Banerjee, S. Weirich, K. L. Dinner, A. R. Gardel, M. L. 2017-05-24 doi:10.1101/141796 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Sepsis Reconsidered: Identifying Novel Metrics For Behavioral Landscape Characterization With A High-Performance Computing Implementation Of An Agent-Based Model ]]> https://biorxiv.org/content/10.1101/141804v1?rss=1 Cockrell, C. An, G. 2017-05-24 doi:10.1101/141804 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Rare non-coding variants are associated with plasma lipid traits in a founder population ]]> https://biorxiv.org/content/10.1101/141960v1?rss=1 Igartua, C. Mozaffari, S. V. Nicolae, D. Ober, C. 2017-05-24 doi:10.1101/141960 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Evaluation Of Chromatin Accessibility In Prefrontal Cortex Of Schizophrenia Cases And Controls ]]> https://biorxiv.org/content/10.1101/141986v1?rss=1 Bryois, J. Garrett, M. E. Song, L. Safi, A. Giusti-Rodriguez, P. Johnson, G. D. Demur, A. B. Fullard, J. F. Roussos, P. Sklar, P. Akbarian, S. Haroutunian, V. Stockmeier, C. A. Wray, G. A. White, K. P. Liu, C. Reddy, T. E. Ashley-Koch, A. Sullivan, P. F. Crawford, G. E. 2017-05-25 doi:10.1101/141986 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/142455v1?rss=1 Ward, M. C. Zhao, S. Luo, K. Pavlovic, B. J. Karimi, M. M. Stephens, M. Gilad, Y. 2017-05-28 doi:10.1101/142455 Cold Spring Harbor Laboratory Press 2017-05-28 <![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[ Parent of Origin Effects on Quantitative Phenotypes in a Founder Population ]]> https://biorxiv.org/content/10.1101/150185v1?rss=1 Mozaffari, S. V. DeCara, J. M. Shah, S. J. Lang, R. M. Nicolae, D. L. Ober, C. 2017-06-14 doi:10.1101/150185 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ Rapid adaptation with gene flow via a reservoir of chromosomal inversion variation? ]]> https://biorxiv.org/content/10.1101/150771v1?rss=1 He, Q. Knowles, L. L. 2017-06-15 doi:10.1101/150771 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ TET-mediated epimutagenesis of the Arabidopsis thaliana methylome ]]> https://biorxiv.org/content/10.1101/151027v1?rss=1 Ji, L. Jordan, W. T. Shi, X. Hu, L. He, C. Schmitz, R. J. 2017-06-20 doi:10.1101/151027 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Partitioning and Enhanced Self-Assembly of Actin in Polypeptide Coacervates ]]> https://biorxiv.org/content/10.1101/152025v1?rss=1 McCall, P. M. Srivastava, S. Perry, S. L. Kovar, D. R. Gardel, M. L. Tirrell, M. V. 2017-06-19 doi:10.1101/152025 Cold Spring Harbor Laboratory Press 2017-06-19 <![CDATA[ Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity ]]> https://biorxiv.org/content/10.1101/152223v1?rss=1 Xu, J. Peng, X. Chen, Y. Zhang, Y. Ma, Q. Liang, L. Carter, A. C. Lu, X. Wu, C.-I. 2017-06-19 doi:10.1101/152223 Cold Spring Harbor Laboratory Press 2017-06-19 <![CDATA[ An adder behavior in mammalian cells achieves size control by modulation of growth rate and cell cycle duration ]]> https://biorxiv.org/content/10.1101/152728v1?rss=1 Cadart, C. Monnier, S. Grilli, J. Attia, R. Terriac, E. Baum, B. Cosentino-Lagomarsino, M. Piel, M. 2017-06-20 doi:10.1101/152728 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Determining controllability of sepsis using genetic algorithms on a proxy agent-based model of systemic inflammation ]]> https://biorxiv.org/content/10.1101/153080v1?rss=1 Cockrell, C. An, G. 2017-06-21 doi:10.1101/153080 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Positional effects revealed in Illumina Methylation Array and the impact on analysis ]]> https://biorxiv.org/content/10.1101/153858v1?rss=1 Jiao, C. Zhang, C. Dai, R. Xia, Y. Wang, K. Giase, G. Chen, C. Liu, C. 2017-06-22 doi:10.1101/153858 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants ]]> https://biorxiv.org/content/10.1101/154799v1?rss=1 Nallu, S. Hill, J. Don, K. Sahagun, C. Zhang, W. Meslin, C. Snell-Rood, E. Clark, N. L. Morehouse, N. I. Bergelson, J. Wheat, C. W. Kronforst, M. R. 2017-06-23 doi:10.1101/154799 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Reflective imaging improves resolution, speed, andcollection efficiency in light sheet microscopy ]]> https://biorxiv.org/content/10.1101/154807v1?rss=1 Wu, Y. Kumar, A. Smith, C. Ardiel, E. Chandris, P. Christensen, R. Rey-Suarez, I. Guo, M. Vishwasrao, H. Chen, J. Tang, J. Upadhyaya, A. La Riviere, P. Shroff, H. 2017-06-23 doi:10.1101/154807 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Cofilin Drives Rapid Turnover and Fluidization of Entangled F-actin ]]> https://biorxiv.org/content/10.1101/156224v1?rss=1 McCall, P. M. MacKintosh, F. C. Kovar, D. R. Gardel, M. L. 2017-06-26 doi:10.1101/156224 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Habitat preference of an herbivore shapes the habitat distribution of its host plant ]]> https://biorxiv.org/content/10.1101/156240v1?rss=1 Alexandre, N. M. Humphrery, P. T. Frazier, J. Gloss, A. D. Lee, J. Affeldt, H. A. Whiteman, N. K. 2017-06-27 doi:10.1101/156240 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Patchwork of contrasting medication cultures across the USA ]]> https://biorxiv.org/content/10.1101/156281v1?rss=1 Melamed, R. D. Rzhetsky, A. 2017-06-30 doi:10.1101/156281 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Genetic variants affecting plant size and chemical defenses jointly shape herbivory in Arabidopsis ]]> https://biorxiv.org/content/10.1101/156299v1?rss=1 Gloss, A. D. Brachi, B. Feldmann, M. J. Groen, S. C. Bartoli, C. Gouzy, J. LaPlante, E. R. Meyer, C. G. Pyon, H. S. Rogan, S. C. Roux, F. Bergelson, J. Whiteman, N. K. 2017-06-27 doi:10.1101/156299 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Universal Microfluidic System for Analysis and Control of Cell Dynamics ]]> https://biorxiv.org/content/10.1101/157057v1?rss=1 Zhang, C. Tu, H.-L. Jia, G. Mukhtar, T. Taylor, V. Rzhetsky, A. Tay, S. 2017-06-28 doi:10.1101/157057 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Despite egg-adaptive mutations, the 2012-13 H3N2 influenza vaccine induced comparable antibody titers to the intended strain ]]> https://biorxiv.org/content/10.1101/158550v1?rss=1 Cobey, S. Parkhouse, K. Chambers, B. S. Ertl, H. C. Schmader, K. E. Halpin, R. A. Lin, X. Stockwell, T. B. Das, S. R. Landon, E. Tesic, V. Youngster, I. Pinsky, B. Wentworth, D. E. Hensley, S. E. Grad, Y. H. 2017-07-05 doi:10.1101/158550 Cold Spring Harbor Laboratory Press 2017-07-05 <![CDATA[ A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes ]]> https://biorxiv.org/content/10.1101/160770v1?rss=1 Zhu, X. Stephens, M. 2017-07-08 doi:10.1101/160770 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments ]]> https://biorxiv.org/content/10.1101/161638v1?rss=1 Yung, C. K. O'Connor, B. D. Yakneen, S. Zhang, J. Ellrott, K. Kleinheinz, K. Miyoshi, N. Raine, K. M. Royo, R. Saksena, G. B. Schlesner, M. Shorser, S. I. Vazquez, M. Weischenfeldt, J. Yuen, D. Butler, A. P. Davis-Dusenbery, B. N. Eils, R. Ferretti, V. Grossman, R. L. Harismendy, O. Kim, Y. Nakagawa, H. Newhouse, S. J. Torrents, D. Stein, L. D. - PCAWG Technical Working Group, 2017-07-10 doi:10.1101/161638 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ Working memory implements distinct maintenance mechanisms depending on task goals ]]> https://biorxiv.org/content/10.1101/162537v1?rss=1 Fahrenfort, J. J. van Leeuwen, J. Foster, J. Awh, E. Olivers, C. N. L. 2017-07-12 doi:10.1101/162537 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ DNA 5-Hydroxymethylcytosines from Cell-free Circulating DNA as Diagnostic Biomarkers for Human Cancers ]]> https://biorxiv.org/content/10.1101/163204v1?rss=1 Li, W. Zhang, X. Lu, X. You, L. Song, Y. Luo, Z. Zhang, J. Nie, J. Zheng, W. Xu, D. Wang, Y. Dong, Y. Yu, S. Hong, J. Shi, J. Hao, H. Luo, F. Hua, L. Wang, P. Qian, X. Yuan, F. Wei, L. Cui, M. Zhang, T. Liao, Q. Dai, M. Liu, Z. Chen, G. Meckel, K. Adhikari, S. Jia, G. Bissonnette, M. B. Zhang, X. Zhao, Y. Zhang, W. He, C. Liu, J. 2017-07-13 doi:10.1101/163204 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane ]]> https://biorxiv.org/content/10.1101/163295v1?rss=1 Pak, A. J. Grime, J. M. A. Sengupta, P. Chen, A. K. Durumeric, A. E. P. Srivastava, A. Yeager, M. Briggs, J. A. G. Lippincott-Schwartz, J. Voth, G. A. 2017-07-13 doi:10.1101/163295 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages ]]> https://biorxiv.org/content/10.1101/163741v1?rss=1 Costa Vieira, M. Zinder, D. Cobey, S. 2017-07-15 doi:10.1101/163741 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ Polygenic selection underlies evolution of human brain structure and behavioral traits ]]> https://biorxiv.org/content/10.1101/164707v1?rss=1 Beiter, E. R. Khramtsova, E. A. van der Merwe, C. Chimusa, E. R. Simonti, C. Stein, J. Thompson, P. Fisher, S. Stein, D. J. Capra, J. A. Knowles, J. A. Stranger, B. E. Davis, L. K. 2017-09-09 doi:10.1101/164707 Cold Spring Harbor Laboratory Press 2017-09-09 <![CDATA[ Multinucleotide mutations cause false inferences of positive selection ]]> https://biorxiv.org/content/10.1101/165969v1?rss=1 Venkat, A. Hahn, M. W. Thornton, J. W. 2017-07-20 doi:10.1101/165969 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Conjunction of Factors Triggering Waves of Seasonal Influenza ]]> https://biorxiv.org/content/10.1101/168476v1?rss=1 Chattopadhyay, I. Kiciman, E. Elliott, J. Shaman, J. Rzhetsky, A. 2017-07-27 doi:10.1101/168476 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Throughput Protein Simulation ]]> https://biorxiv.org/content/10.1101/169326v1?rss=1 Jumper, J. M. Freed, K. F. Sosnick, T. R. 2017-07-27 doi:10.1101/169326 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Tropomyosin and a-actinin cooperation inhibits fimbrin association with actin filament networks in fission yeast ]]> https://biorxiv.org/content/10.1101/169961v1?rss=1 Christensen, J. Homa, K. O'Connell, M. Kovar, D. R. 2017-07-28 doi:10.1101/169961 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection ]]> https://biorxiv.org/content/10.1101/170639v1?rss=1 Delmont, T. O. Kiefl, E. Kilinc, O. Esen, O. C. Uysal, I. Rappe, M. S. Giovannoni, S. Eren, A. M. 2017-07-31 doi:10.1101/170639 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Common variants of NRXN1, LRP1B and RORA are associated with increased ventricular volumes in psychosis - GWAS findings from the B-SNIP deep phenotyping study ]]> https://biorxiv.org/content/10.1101/175489v1?rss=1 Alliey-Rodriguez, N. Grey, T. A. Shafee, R. Padmanabhan, J. Tandon, N. Klinger, M. Spring, J. Coppes, L. Reis, K. Keshavan, M. S. Gage, D. McCarroll, S. Bishop, J. R. Hill, S. Reilly, J. Lencer, R. Clementz, B. Buckley, P. Meda, S. Narayanan, B. Glahn, D. Pearlson, G. Ivleva, E. Tamminga, C. Sweeney, J. Curtis, D. Keedy, S. Badner, J. Liu, C. Gershon, E. S. 2017-08-11 doi:10.1101/175489 Cold Spring Harbor Laboratory Press 2017-08-11 <![CDATA[ De novo mutations involved in post-transcriptional dysregulation contribute to six neuropsychiatric disorders ]]> https://biorxiv.org/content/10.1101/175844v1?rss=1 Mao, F. Wang, L. Liu, Q. Xiao, L. Li, X. He, X. Rao, R. C. Li, J. Dou, Y. Sun, Z. 2017-08-13 doi:10.1101/175844 Cold Spring Harbor Laboratory Press 2017-08-13 <![CDATA[ From foodwebs to gene regulatory networks (GRNs) - weak repressions by microRNAs confer system stability ]]> https://biorxiv.org/content/10.1101/176701v1?rss=1 25% of mRNAs, in agreement with observations. As predicted, extremely highly expressed genes are avoided and transcription factors are preferred by miRNAs. In conclusion, the diffuse repression by miRNAs is likely a system-level strategy for enhancing GRN stability. This stability control may be the mechanistic basis of "canalization" (i.e., developmental homeostasis within each species), sometimes hypothesized to be a main function of miRNAs. ]]> Chen, Y. Allesina, S. Shen, Y. Wu, C.-I. 2017-08-15 doi:10.1101/176701 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ Recurring infection with ecologically distinct human papillomavirus (HPV) types explains high prevalence and diversity ]]> https://biorxiv.org/content/10.1101/179341v1?rss=1 Ranjeva, S. Baskerville, E. B. Dukic, V. Villa, L. Lazcano-Ponce, E. Giuliano, A. R. Dwyer, G. Cobey, S. 2017-08-23 doi:10.1101/179341 Cold Spring Harbor Laboratory Press 2017-08-23 <![CDATA[ Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning ]]> https://biorxiv.org/content/10.1101/179531v1?rss=1 Teng, H. Hall, M. B. Duarte, T. Cao, M. D. Coin, L. 2017-08-23 doi:10.1101/179531 Cold Spring Harbor Laboratory Press 2017-08-23 <![CDATA[ Climate change will lead to pronounced shifts in the diversity of soil microbial communities ]]> https://biorxiv.org/content/10.1101/180174v1?rss=1 Ladau, J. Shi, Y. Jing, X. He, J.-S. Chen, L. Lin, X. Fierer, N. Gilbert, J. A. Pollard, K. S. Chu, H. 2017-09-01 doi:10.1101/180174 Cold Spring Harbor Laboratory Press 2017-09-01 <![CDATA[ Gene co-expression networks in whole blood implicate multiple interrelated molecular pathways in obese asthma ]]> https://biorxiv.org/content/10.1101/181651v1?rss=1 Croteau-Chonka, D. C. Chen, Z. Barnes, K. C. Barraza-Villarreal, A. Celedon, J. C. Gauderman, W. J. Gilliland, F. D. Krishnan, J. A. Liu, A. H. London, S. J. Martinez, F. D. Millstein, J. Naureckas, E. T. Nicolae, D. L. White, S. R. Ober, C. Weiss, S. T. Raby, B. A. 2017-08-29 doi:10.1101/181651 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Correction of autoimmune IL2RA mutations in primary human T cells using non-viral genome targeting ]]> https://biorxiv.org/content/10.1101/183418v1?rss=1 1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenic IL2RA mutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells. ]]> Roth, T. L. Yu, R. Shifrut, E. Hiatt, J. Li, H. Schumann, K. Tobin, V. Ferris, A. M. Chen, J. Schickel, J.-N. Pellerin, L. Carmody, D. Alkorta-Aranburu, G. Del Gaudio, D. Cho, M. Matsumoto, H. Morell, M. Mao, Y. Nguyen, D. Quadros, R. Gurumurthy, C. Smith, B. Haugwitz, M. Hughes, S. H. Weissman, J. May, A. P. Kupfer, G. Greeley, S. Bacchetta, R. Meffre, E. Roncarolo, M. G. Romberg, N. Herold, K. C. Leonetti, M. D. Marson, A. 2017-08-31 doi:10.1101/183418 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ The lamellipodium is a myosin independent mechanosensor ]]> https://biorxiv.org/content/10.1101/186437v1?rss=1 Oakes, P. W. Bidone, T. C. Beckham, Y. Skeeters, A. V. Ramirez-San Juan, G. R. Winter, S. P. Voth, G. A. Gardel, M. L. 2017-09-08 doi:10.1101/186437 Cold Spring Harbor Laboratory Press 2017-09-08 <![CDATA[ A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage ]]> https://biorxiv.org/content/10.1101/187922v1?rss=1 Vazquez, J. M. Sulak, M. Chigurupati, S. Lynch, V. J. 2017-09-12 doi:10.1101/187922 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection ]]> https://biorxiv.org/content/10.1101/188961v1?rss=1 40% of which are independent of expression QTLs for the same gene. Compared to eQTLs, isoQTLs are enriched for splice sites and untranslated regions, and depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs in stimulated cells explain a significant proportion of the disease heritability attributed to common genetic variants. At the IRF7 locus, we found alternative promoter usage in response to influenza as a possible mechanism by which DNA variants previously associated with immune-related disorders mediate disease risk. At the ERAP2 locus, we shed light on the function of the major haplotype that has been maintained under long-term balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with absence of ERAP2 expression while the minor haplotype, known to increase Crohns disease risk, is associated with high ERAP2 expression. Surprisingly, in response to influenza infection, the major haplotype results in the expression of two uncharacterized, alternatively transcribed, spliced and translated short isoforms. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in the innate immune response, and in the case of ERAP2, may confer a historical fitness advantage in response to virus. ]]> Chun, Y. J. Chen, J. Villani, A.-C. Subramaniam, M. Gate, R. E. Bhangale, T. Lee, M. N. Raj, T. Raychowdhury, R. Li, W. Rogel, N. Imboywa, S. H. Chipendo, P. I. McCabe, C. Lee, M. H. Frohlich, I. Y. Stranger, B. E. De Jager, P. L. Regev, A. Behrens, T. Hacohen, N. 2017-09-14 doi:10.1101/188961 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Pervasive contingency and entrenchment in a billion years of Hsp90 evolution ]]> https://biorxiv.org/content/10.1101/189803v1?rss=1 Starr, T. N. Flynn, J. M. Mishra, P. Bolon, D. N. A. Thornton, J. W. 2017-09-18 doi:10.1101/189803 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Effects of multiple sources of genetic drift on pathogen variation within hosts ]]> https://biorxiv.org/content/10.1101/190918v1?rss=1 Kennedy, D. Dwyer, G. 2017-09-19 doi:10.1101/190918 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ USA300 MRSA lineages persist on multiple body sites following infection ]]> https://biorxiv.org/content/10.1101/192096v1?rss=1 Read, T. D. Petit, R. A. Yin, Z. Montgomery, T. McNulty, M. C. David, M. Z. 2017-09-21 doi:10.1101/192096 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis ]]> https://biorxiv.org/content/10.1101/192724v1?rss=1 Singh, D. Wang, Y. Mallon, J. Yang, O. Fei, J. Poddar, A. Ceylan, D. Bailey, S. Ha, T. 2017-09-22 doi:10.1101/192724 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology ]]> https://biorxiv.org/content/10.1101/193573v1?rss=1 Brikell, I. Larsson, H. Lu, Y. Pettersson, E. Chen, Q. Kuja-Halkola, R. Karlsson, R. Lahey, B. B. Lichtenstein, P. Martin, J. 2017-09-26 doi:10.1101/193573 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/193797v1?rss=1 Nguyen, M. Brettin, T. Long, S. W. Olsen, R. J. Musser, J. M. Olson, R. Shukla, M. Stevens, R. L. Xia, F. Yoo, H. Davis, J. 2017-09-25 doi:10.1101/193797 Cold Spring Harbor Laboratory Press 2017-09-25 <![CDATA[ Enriched pathogen diversity under host-type heterogeneity and immune-mediated competition ]]> https://biorxiv.org/content/10.1101/195065v1?rss=1 Martinez, P. P. Woods, R. J. Pascual, M. 2017-09-27 doi:10.1101/195065 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Development of an Intrinsic Skin Sensor for Blood Glucose Level with CRISPR-mediated Genome Editing in Epidermal Stem Cells ]]> https://biorxiv.org/content/10.1101/195529v1?rss=1 Yue, J. Li, Y. Gou, X. Wu, X. 2017-09-28 doi:10.1101/195529 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Multiethnic Meta-analysis Identifies New Loci for Pulmonary Function ]]> https://biorxiv.org/content/10.1101/196048v1?rss=1 Wyss, A. B. Sofer, T. Lee, M. K. Terzikhan, N. Nguyen, J. N. Lahousse, L. Latourelle, J. C. Smith, A. V. Bartz, T. M. Feitosa, M. F. Gao, W. Ahluwalia, T. S. Tang, W. Oldmeadow, C. Duan, Q. de Jong, K. Wojczynski, M. K. Wang, X.-Q. Noordam, R. Hartwig, F. P. Jackson, V. E. Wang, T. Obeidat, M. Hobbs, B. D. Huan, T. Kichaev, G. Jin, J. Graff, M. Harris, T. B. Kalhan, R. Heckbert, S. R. Paternoster, L. Burkart, K. M. Liu, Y. Holliday, E. G. Wilson, J. G. Vonk, J. M. Sanders, J. Barr, R. G. de Mutsert, R. Baptista Menezes, A. M. Adams, H. H. H. van den Be 2017-10-05 doi:10.1101/196048 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow ]]> https://biorxiv.org/content/10.1101/196709v1?rss=1 Ozik, J. Collier, N. Wozniak, J. Macal, C. Cockrell, C. Friedman, S. Ghaffarizadeh, A. Heiland, R. An, G. Macklin, P. 2017-09-30 doi:10.1101/196709 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Genetic Analysis of Deep Phenotyping Projects in Common Disorders ]]> https://biorxiv.org/content/10.1101/197459v1?rss=1 Gershon, E. S. Pearlson, G. Keshavan, M. S. Tamminga, C. Clementz, B. Buckley, P. F. Alliey-Rodriguez, N. Liu, C. Sweeney, J. A. Keedy, S. Meda, S. Tandon, N. Shafee, R. Bishop, J. R. Ivleva, E. I. 2017-10-02 doi:10.1101/197459 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/197954v1?rss=1 He, Q. Pilosof, S. Tiedje, K. E. Ruybal-Pesantez, S. Artzy-Randrup, Y. Baskerville, E. B. Day, K. Pascual, M. 2017-10-03 doi:10.1101/197954 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Evolution-informed forecasting of seasonal influenza A (H3N2) ]]> https://biorxiv.org/content/10.1101/198168v1?rss=1 Du, X. King, A. A. Woods, R. J. Pascual, M. 2017-10-04 doi:10.1101/198168 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Attractor dynamics in networks with learning rules inferred from in vivo data ]]> https://biorxiv.org/content/10.1101/199521v1?rss=1 Pereira, U. Brunel, N. 2017-10-06 doi:10.1101/199521 Cold Spring Harbor Laboratory Press 2017-10-06 <![CDATA[ N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection ]]> https://biorxiv.org/content/10.1101/201475v1?rss=1 Hesser, C. Karijolich, J. Dominissini, D. He, C. Glaunsinger, B. A. 2017-10-11 doi:10.1101/201475 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ REPIC: A database for exploring N6-methyladenosine methylome ]]> https://biorxiv.org/content/10.1101/2019.12.11.873299v1?rss=1 Liu, S. He, C. Chen, M. 2019-12-12 doi:10.1101/2019.12.11.873299 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Islet architecture controls synchronous β cell response to glucose in the intact mouse pancreas in vivo ]]> https://biorxiv.org/content/10.1101/2019.12.11.873471v1?rss=1 Adams, M. T. Reissaus, C. A. Szulczewski, J. M. Dwulet, J. M. Lyman, M. R. Sdao, S. M. Nimkulrat, S. D. Ponik, S. M. Merrins, M. J. Benninger, R. K. P. Mirmira, R. G. Linnemann, A. K. Blum, B. 2019-12-12 doi:10.1101/2019.12.11.873471 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC ]]> https://biorxiv.org/content/10.1101/2019.12.13.874651v1?rss=1 Parrello, B. Butler, R. Chlenski, P. Pusch, G. D. Overbeek, R. 2019-12-15 doi:10.1101/2019.12.13.874651 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Tuning shape and internal structure of protein droplets via biopolymer filaments ]]> https://biorxiv.org/content/10.1101/2019.12.13.876003v1?rss=1 Scheff, D. R. Weirich, K. L. Dasbiswas, K. Patel, A. Vaikuntanathan, S. Gardel, M. L. 2019-12-13 doi:10.1101/2019.12.13.876003 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq ]]> https://biorxiv.org/content/10.1101/2019.12.17.880013v1?rss=1 Xu, J. Kudron, M. M. Victorsen, A. Gao, J. Ammouri, H. N. Navarro, F. C. P. Gevirtzman, L. Waterston, R. H. White, K. P. Reinke, V. Gerstein, M. 2019-12-18 doi:10.1101/2019.12.17.880013 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Capturing multiple timescales of adaptation to second-order statistics with generalized linear models: gain scaling and fractional differentiation ]]> https://biorxiv.org/content/10.1101/2019.12.30.891143v1?rss=1 Latimer, K. W. Fairhall, A. L. 2019-12-30 doi:10.1101/2019.12.30.891143 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Ancestral neural computations constrain the evolution of novel computations in simulated color vision networks ]]> https://biorxiv.org/content/10.1101/2019.12.30.891382v1?rss=1 Buerkle, N. P. Palmer, S. E. 2019-12-31 doi:10.1101/2019.12.30.891382 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ An antigenic diversification threshold for falciparum malaria and its control at high endemicity ]]> https://biorxiv.org/content/10.1101/2020.01.01.892406v1?rss=1 He, Q. Pascual, M. 2020-01-02 doi:10.1101/2020.01.01.892406 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Alignment of single-cell RNA-seq samples without over-correction using kernel density matching ]]> https://biorxiv.org/content/10.1101/2020.01.05.895136v1?rss=1 Chen, M. Zhan, Q. Mu, Z. Wang, L. Zheng, Z. Miao, J. Zhu, P. Li, Y. I. 2020-01-06 doi:10.1101/2020.01.05.895136 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ RNA-binding protein Syncrip regulates Starvation-Induced Hyperactivity in adult Drosophila ]]> https://biorxiv.org/content/10.1101/2020.01.07.897652v1?rss=1 Chi, W. Liu, W. Fu, W. Heckscher, E. Zhuang, X. 2020-01-08 doi:10.1101/2020.01.07.897652 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Assessment of Brain Glucose Metabolism Following Cardiac Arrest by FDG Positron Emission Tomography ]]> https://biorxiv.org/content/10.1101/2020.01.08.899252v1?rss=1 Zhang, H. J. Mitchell, S. Fang, Y.-H. Tsai, H.-M. Piao, L. Ousta, A. Leoni, L. Chen, C.-T. Sharp, W. W. 2020-01-09 doi:10.1101/2020.01.08.899252 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Suppression of Cytotoxic T Cell Functions and Decreased Levels of Tissue Resident Memory T cell During H5N1 infection ]]> https://biorxiv.org/content/10.1101/2020.01.09.901132v1?rss=1 Kandasamy, M. Furlong, K. Perez, J. T. Manicassamy, S. Manicassamy, B. 2020-01-10 doi:10.1101/2020.01.09.901132 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ PIE-FLIM measurements of two different FRET-based biosensor activities in the same living cells ]]> https://biorxiv.org/content/10.1101/2020.01.10.902213v1?rss=1 Day, R. N. Reissaus, C. A. Day, K. H. Mirmira, R. G. Dunn, K. W. Pavalko, F. 2020-01-10 doi:10.1101/2020.01.10.902213 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Within and cross species predictions of plant specialized metabolism genes using transfer learning ]]> https://biorxiv.org/content/10.1101/2020.01.13.112102v1?rss=1 Moore, B. M. Wang, P. Fan, P. Lee, A. Leong, B. Lou, Y.-L. Schenck, C. A. Sugimoto, K. Last, R. Lehti-Shiu, M. D. Barry, C. Shiu, S.-H. 2020-01-14 doi:10.1101/2020.01.13.112102 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Structure of the teneurin-latrophilin complex: Alternative splicing controls synapse specificity by a novel mechanism ]]> https://biorxiv.org/content/10.1101/2020.01.13.901090v1?rss=1 Li, J. Xie, Y. Cornelius, S. Jiang, X. Kordon, S. P. Sando, R. Pan, M. Leon, K. Sudhof, T. C. Zhao, M. Arac, D. 2020-01-14 doi:10.1101/2020.01.13.901090 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells ]]> https://biorxiv.org/content/10.1101/2020.01.13.903641v1?rss=1 Park, S. Prevost, K. Heideman, E. M. Carrier, M.-C. Reyer, M. A. Liu, W. Masse, E. Fei, J. 2020-01-14 doi:10.1101/2020.01.13.903641 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Species-specific, age-varying plant traits affect herbivore growth and survival ]]> https://biorxiv.org/content/10.1101/2020.01.14.906859v1?rss=1 Yang, L. H. Cenzer, M. L. Morgan, L. J. Hall, G. W. 2020-01-14 doi:10.1101/2020.01.14.906859 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Estimating the rate of cell type degeneration from epigenetic sequencing of cell-free DNA ]]> https://biorxiv.org/content/10.1101/2020.01.15.907022v1?rss=1 Caggiano, C. Celona, B. Garton, F. Mefford, J. A. Black, B. Lomen-Hoerth, C. Dahl, A. Zaitlen, N. 2020-01-16 doi:10.1101/2020.01.15.907022 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Impact of DNA sequences in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex ]]> https://biorxiv.org/content/10.1101/2020.01.16.909549v1?rss=1 Min, J. H. Broyde, S. Paul, D. Mu, H. Dai, Q. Tavakoli, A. He, C. 2020-01-17 doi:10.1101/2020.01.16.909549 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Endogenous itaconate is not required for particulate matter-induced NRF2 expression or inflammatory response ]]> https://biorxiv.org/content/10.1101/2020.01.19.911917v1?rss=1 Sun, K. A. Li, Y. Meliton, A. Y. Woods, P. S. Kimmig, L. M. Hamanaka, R. B. Mutlu, G. 2020-01-20 doi:10.1101/2020.01.19.911917 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Hox-dependent coordination of cardiac progenitor cell patterning and differentiation ]]> https://biorxiv.org/content/10.1101/2020.01.23.916981v1?rss=1 Stefanovic, S. Laforest, B. Desvignes, J.-P. Lescroart, F. Argiro, L. Maurel-Zaffran, C. Salgado, D. de Bono, C. Pazur, K. Theveniau-Ruissy, M. Beroud, C. Puceat, M. Gavalas, A. Kelly, R. G. Zaffran, S. 2020-01-24 doi:10.1101/2020.01.23.916981 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Metastable attractors explain the variable timing of stable behavioral action sequences ]]> https://biorxiv.org/content/10.1101/2020.01.24.919217v1?rss=1 Recanatesi, S. Pereira Obilinovic, U. Murakami, M. Mainen, Z. Mazzucato, L. 2020-01-25 doi:10.1101/2020.01.24.919217 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function ]]> https://biorxiv.org/content/10.1101/2020.01.26.920363v1?rss=1 LI, Y. Eshein, A. Virk, R. Eid, A. Wu, W. Frederick, J. VanDerway, D. Gladstein, S. Huang, K. Anthony, N. Bauer, G. Zhou, X. Agrawal, V. Pujadas, E. Chandler, J. Nguyen, T.-Q. Bleher, R. de Pablo, J. Szleifer, I. Dravid, V. P. Almassalha, L. M. Backman, V. 2020-01-27 doi:10.1101/2020.01.26.920363 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Deoxyribozyme-based Method for Site-specific Absolute Quantification of N6-methyladenosine Modification Fraction ]]> https://biorxiv.org/content/10.1101/2020.01.29.925255v1?rss=1 Bujnowska, M. Zhang, J. Dai, Q. Heideman, E. M. Fei, J. 2020-01-30 doi:10.1101/2020.01.29.925255 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Germline genetic contribution to the immune landscape of cancer ]]> https://biorxiv.org/content/10.1101/2020.01.30.926527v1?rss=1 9,000 individuals in The Cancer Genome Atlas, we investigated the association of common and rare variants with 139 well-defined immune traits. Our analysis of common variants identified 10 immune traits with significant heritability estimates, and an additional 23 with suggestive heritability, including estimates of T-cell subset abundance and interferon signaling. We performed genome-wide association on the 33 heritable traits and identified 23 genome-wide significant loci associated with at least one immune trait, including SNPs in the IFIH1 locus previously associated with several autoimmune diseases. We also found significant associations between immune traits and pathogenic or likely-pathogenic rare variants in BRCA1 and in genes functionally linked to telomere stabilization, and Wnt/Beta-catenin signaling. We conclude that germline genetic variants significantly impact the composition and functional orientation of the tumor immune microenvironment. ]]> Sayaman, R. W. Saad, M. Thorsson, V. Hendrickx, W. Roelands, J. Mokrab, Y. Farshidfar, F. Kirchhoff, T. Sweis, R. F. Bathe, O. F. Porta-Pardo, E. Campbell, M. J. Stretch, C. Hu, D. Huntsman, S. Graff, R. E. Syed, N. Radvanyi, L. Shelly, S. Wolf, D. Marincola, F. M. Ceccarelli, M. Galon, J. Ziv, E. Bedognetti, D. 2020-01-31 doi:10.1101/2020.01.30.926527 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission ]]> https://biorxiv.org/content/10.1101/2020.01.31.927327v1?rss=1 Flower, T. G. Takahashi, Y. Hudait, A. Rose, K. Tjahjono, N. Pak, A. Yokom, A. L. Liang, X. Wang, H.-G. Bouamr, F. Voth, G. A. Hurley, J. H. 2020-02-01 doi:10.1101/2020.01.31.927327 Cold Spring Harbor Laboratory Press 2020-02-01 <![CDATA[ Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.02.11.944561v1?rss=1 Olalekan, S. Xie, B. Back, R. Eckart, H. Basu, A. 2020-02-12 doi:10.1101/2020.02.11.944561 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Novel hemorrhage models of cerebral cavernous malformations ]]> https://biorxiv.org/content/10.1101/2020.02.12.944421v1?rss=1 Detter, M. R. Shenkar, R. Benavides, C. R. Neilson, C. A. Moore, T. Lightle, R. Hobson, N. Shen, L. Cao, Y. Girard, R. Zhang, D. Griffin, E. Gallione, C. J. Awad, I. A. Marchuk, D. A. 2020-02-13 doi:10.1101/2020.02.12.944421 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Functional specialization of human salivary glands and origins of proteins intrinsic to human saliva ]]> https://biorxiv.org/content/10.1101/2020.02.12.945659v1?rss=1 Saitou, M. Gaylord, E. Xu, D. Neznanova, L. Nathan, S. Grawe, A. Chang, J. Ryan, W. Ruhl, S. Knox, S. M. Gokcumen, O. 2020-02-13 doi:10.1101/2020.02.12.945659 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ The West African lungfish provides insights into the evolution of tetrapod tail regeneration ]]> https://biorxiv.org/content/10.1101/2020.02.12.946319v1?rss=1 Verissimo, K. M. Perez, L. N. Dragalzew, A. C. Senevirathne, G. Darnet, S. Mendes, W. R. Neves, C. A. dos Santos, E. M. Moraes, C. N. Shubin, N. H. Froebisch, N. B. Sousa, J. F. Schneider, I. 2020-02-13 doi:10.1101/2020.02.12.946319 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Humanisation of the zebrafish C5a receptor confers targeting by human-specific staphylococcal virulence factors. ]]> https://biorxiv.org/content/10.1101/2020.02.18.955021v1?rss=1 Buchan, K. D. van Gent, M. Prajsnar, T. K. Ogryzko, N. V. de Jong, N. Kolata, J. Foster, S. J. van Strijp, J. A. Renshaw, S. A. 2020-02-20 doi:10.1101/2020.02.18.955021 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs ]]> https://biorxiv.org/content/10.1101/2020.02.21.960005v1?rss=1 Marquez, R. Linderoth, T. P. Mejía-Vargas, D. Nielsen, R. Kronforst, M. R. Amezquita, A. 2020-02-25 doi:10.1101/2020.02.21.960005 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Nicotine exposure and neuronal activity regulate Golgi membrane dispersal and distribution ]]> https://biorxiv.org/content/10.1101/2020.02.25.965285v1?rss=1 Govind, A. P. Jeyifous, O. Russell, T. Vaasjo, L. O. Yi, Z. Weigel, A. V. Newell, L. Koranda, J. L. Singh, K. Valbuena, F. Glick, B. S. Mukherjee, J. Lippincott-Schwartz, J. Zhuang, X. Green, W. N. 2020-02-26 doi:10.1101/2020.02.25.965285 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Subphase Material Stabilizes Films of Pulmonary Surfactant ]]> https://biorxiv.org/content/10.1101/2020.02.27.968099v1?rss=1 Andreev, K. Martynowycz, M. Kuzmenko, I. Bu, W. Hall, S. B. Gidalevitz, D. 2020-02-28 doi:10.1101/2020.02.27.968099 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ RNA-protein interaction mapping via MS2 or Cas13-based APEX targeting ]]> https://biorxiv.org/content/10.1101/2020.02.27.968297v1?rss=1 Han, S. Zhao, B. S. Myers, S. A. Carr, S. A. He, C. Ting, A. Y. 2020-02-28 doi:10.1101/2020.02.27.968297 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ The within-host viral kinetics of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.02.29.965418v1?rss=1 Li, C. Jinhu, X. Liu, J. Zhou, Y. 2020-03-02 doi:10.1101/2020.02.29.965418 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Spatial organization of the kelp microbiome at micron scales ]]> https://biorxiv.org/content/10.1101/2020.03.01.972083v1?rss=1 90% of the microbial community. We show that kelp blades host a dense microbial biofilm, generally less than 20 m thick, in which disparate microbial taxa live in close contact with one another. The biofilm is spatially differentiated, with tightly clustered cells of the dominant symbiont Granulosicoccus sp. (Gammaproteobacteria) close to the kelp surface and filamentous Bacteroidetes and Alphaproteobacteria relatively more abundant near the biofilm-seawater interface. Further, a community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial community structure and cell density increased along the length of the kelp blade, from sparse microbial colonization of newly produced tissues at the meristematic base of the blade to an abundant microbial biofilm on older tissues at the blade tip. Finally, kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population, indicating that biofilms are characteristic of health and that biofilm loss may be related to the condition of the host. ImportanceThe microbial community coating the surfaces of macroalgae may play a key but underexplored role both in the biology of the macroalgal host and in the biogeochemistry of the coastal ocean. We show that photosynthetic blades of the canopy-forming kelp Nereocystis luetkeana host a complex microbial biofilm that is both dense and spatially differentiated. Microbes of different taxa are in intimate cell-to-cell contact with one another; microbial cells invade the interior of kelp cells as well as cover their external surfaces; and a subset of the surface microbiota projects into the water column. These results highlight the potential for metabolic interactions between key members of the kelp microbiome as well as between microbes and their host. The dense layer of microbes coating the surface of the kelp blade is well-positioned to mediate interactions between the host and surrounding organisms and to modulate the chemistry of the surrounding water column. ]]> Ramirez-Puebla, S. T. Weigel, B. L. Jack, L. Schlundt, C. Pfister, C. A. Mark Welch, J. L. 2020-03-03 doi:10.1101/2020.03.01.972083 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.03.02.968388v1?rss=1 Kim, Y. Jedrzejczak, R. Maltseva, N. I. Endres, M. Godzik, A. Michalska, K. Joachimiak, A. 2020-03-03 doi:10.1101/2020.03.02.968388 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy. ]]> https://biorxiv.org/content/10.1101/2020.03.02.973503v1?rss=1 Kolmann, M. A. Hughes, L. C. Hernandez, L. P. Arcila, D. Betancur-R., R. Sabaj, M. H. Lopez-Fernandez, H. Orti, G. 2020-03-04 doi:10.1101/2020.03.02.973503 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Metabolites alleviate staphylococcal bloodstream infection in a NO-dependent manner via arginase inhibition ]]> https://biorxiv.org/content/10.1101/2020.03.02.974345v1?rss=1 Pang, R. Su, Y. Zhou, H. Chen, X. 2020-03-04 doi:10.1101/2020.03.02.974345 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive inter- and intra-enhancer redundancy ]]> https://biorxiv.org/content/10.1101/2020.03.03.966796v1?rss=1 Hornblad, A. Langenfeld, K. Bastide, S. Langa-Vives, F. Spitz, F. 2020-03-03 doi:10.1101/2020.03.03.966796 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Natural bacterial assemblages in Arabidopsis thaliana tissues become more distinguishable and diverse during host development ]]> https://biorxiv.org/content/10.1101/2020.03.04.958165v1?rss=1 Beilsmith, K. R. Perisin, M. Bergelson, J. 2020-03-05 doi:10.1101/2020.03.04.958165 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Transient interactions and influence among bacteria in field-grown Arabidopsis thaliana tissues ]]> https://biorxiv.org/content/10.1101/2020.03.05.974105v1?rss=1 Beilsmith, K. R. Perisin, M. Bergelson, J. 2020-03-06 doi:10.1101/2020.03.05.974105 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Evolutionary diverse LIM domain-containing proteins bind stressed actin filaments through a conserved mechanism ]]> https://biorxiv.org/content/10.1101/2020.03.06.980649v1?rss=1 Winkelman, J. D. Anderson, C. A. Suarez, C. Kovar, D. R. Gardel, M. L. 2020-03-07 doi:10.1101/2020.03.06.980649 Cold Spring Harbor Laboratory Press 2020-03-07 <![CDATA[ Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis ]]> https://biorxiv.org/content/10.1101/2020.03.11.987412v1?rss=1 Miyoshi, J. Miyoshi, S. Delmont, T. O. Cham, C. Lee, S. T. M. Sakatani, A. Yang, K. Shan, Y. Kiefl, E. Yousef, M. Crosson, S. Sogin, M. Antonopoulos, D. A. Eren, A. M. Leone, V. Chang, E. B. 2020-03-12 doi:10.1101/2020.03.11.987412 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Rho1 activation recapitulates early gastrulation events in the ventral, but not dorsal, epithelium of Drosophila embryos ]]> https://biorxiv.org/content/10.1101/2020.03.12.989285v1?rss=1 Rich, A. Fehon, R. G. Glotzer, M. 2020-03-12 doi:10.1101/2020.03.12.989285 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Altered spike timing-dependent plasticity rules in physiological calcium ]]> https://biorxiv.org/content/10.1101/2020.03.16.993675v1?rss=1 Inglebert, Y. Aljadeff, J. Brunel, N. Debanne, D. 2020-03-17 doi:10.1101/2020.03.16.993675 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding ]]> https://biorxiv.org/content/10.1101/2020.03.16.993931v1?rss=1 Antoszewski, A. Feng, C.-J. Vani, B. Thiede, E. H. Hong, L. Weare, J. Tokmakoff, A. Dinner, A. R. 2020-03-17 doi:10.1101/2020.03.16.993931 Cold Spring Harbor Laboratory Press 2020-03-17 <![CDATA[ Dynamin-related Irgm proteins modulate LPS-induced caspase-4 activation and septic shock ]]> https://biorxiv.org/content/10.1101/2020.03.18.997460v1?rss=1 Finethy, R. Dockterman, J. Kutsch, M. Orench-Rivera, N. Wallace, G. Piro, A. Luoma, S. Haldar, A. Hwang, S. Martinez, J. Kuehn, M. Taylor, G. Coers, J. 2020-03-20 doi:10.1101/2020.03.18.997460 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance ]]> https://biorxiv.org/content/10.1101/2020.03.19.997213v1?rss=1 Barbeira, A. N. Liang, Y. Bonazzola, R. Wang, G. Wheeler, H. E. Melia, O. J. Aguet, F. The GTEx Consortium, Ardlie, K. G. Wen, X. Im, H. K. 2020-03-20 doi:10.1101/2020.03.19.997213 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ CD56 regulates human NK cell cytotoxicity through Pyk2 ]]> https://biorxiv.org/content/10.1101/2020.03.19.998427v1?rss=1 Gunesch, J. Dixon, A. L. Ebrahim, T. Berrien-Elliott, M. Tatineni, S. Kumar, T. Solloa, E. H. Fehniger, T. A. Mace, E. 2020-03-20 doi:10.1101/2020.03.19.998427 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ A microscopy-based kinetic analysis of yeast vacuolar protein sorting ]]> https://biorxiv.org/content/10.1101/2020.03.23.000257v1?rss=1 Glick, B. S. Casler, J. C. 2020-03-23 doi:10.1101/2020.03.23.000257 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ The role of islet lipid composition remodeling in regulation of beta-cell death via ADP-ribosyl-acceptor glycohydrolase ARH3 signaling in insulitis ]]> https://biorxiv.org/content/10.1101/2020.03.23.004481v1?rss=1 Nakayasu, E. S. Guney, M. Kyle, J. Sarbaugh, D. Deiter, C. Yin, R. Cui, Y. Nicora, C. Syed, F. Juan-Mateu, J. Mirmira, R. G. Evans-Molina, C. Eizirik, D. L. Webb-Robertson, B.-J. Burnum-Johnson, K. Orr, G. Laskin, J. Metz, T. O. Sussel, L. Ansong, C. 2020-03-25 doi:10.1101/2020.03.23.004481 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Temporal transcription factors determine circuit membership by altering motor neuron-to-muscle synaptic partnerships ]]> https://biorxiv.org/content/10.1101/2020.03.25.007252v1?rss=1 Heckscher, E. Meng, J. L. Carrillo, R. A. Wang, Y. 2020-03-25 doi:10.1101/2020.03.25.007252 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Demystifying "drop-outs" in single cell UMI data ]]> https://biorxiv.org/content/10.1101/2020.03.31.018911v1?rss=1 Kim, T. Zhou, X. Chen, M. 2020-04-01 doi:10.1101/2020.03.31.018911 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Evolution-based design of chorismate mutase enzymes ]]> https://biorxiv.org/content/10.1101/2020.04.01.020487v1?rss=1 Russ, W. P. Figliuzzi, M. Stocker, C. Barrat-Charlaix, P. Socolich, M. Kast, P. Hilvert, D. Monasson, R. Cocco, S. Weigt, M. Ranganathan, R. 2020-04-02 doi:10.1101/2020.04.01.020487 Cold Spring Harbor Laboratory Press 2020-04-02 <![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[ Subcellular localization of the J-protein Sis1 regulates the heat shock response ]]> https://biorxiv.org/content/10.1101/2020.04.02.022491v1?rss=1 Feder, Z. A. Ali, A. Singh, A. Krakowiak, J. Zheng, X. Bindokas, V. P. Wolfgeher, D. Kron, S. J. Pincus, D. 2020-04-03 doi:10.1101/2020.04.02.022491 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth ]]> https://biorxiv.org/content/10.1101/2020.04.06.017079v1?rss=1 Sakabe, N. Aneas, I. Knoblauch, N. Sobreira, D. R. Clark, N. Paz, C. Horth, C. Ziffra, R. Kaur, H. Liu, X. Anderson, R. Morrison, J. Cheung, V. C. Grotegut, C. Reddy, T. E. Jacobsson, B. Hallman, M. Teramo, K. Murtha, A. Kessler, J. Grobman, W. Zhang, G. Muglia, L. J. Rana, S. Lynch, V. J. Crawford, G. E. Ober, C. He, X. Nobrega, M. A. 2020-04-06 doi:10.1101/2020.04.06.017079 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ Separating measurement and expression models clarifies confusion in single cell RNA-seq analysis ]]> https://biorxiv.org/content/10.1101/2020.04.07.030007v1?rss=1 Sarkar, A. K. Stephens, M. 2020-04-08 doi:10.1101/2020.04.07.030007 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Integrating XMALab and DeepLabCut for high-throughput XROMM ]]> https://biorxiv.org/content/10.1101/2020.04.10.035949v1?rss=1 Laurence-Chasen, J. D. Manafzadeh, A. R. Hatsopoulos, N. Ross, C. Arce-McShane, F. 2020-04-13 doi:10.1101/2020.04.10.035949 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits ]]> https://biorxiv.org/content/10.1101/2020.04.12.038034v1?rss=1 Mao, T.-R. Liu, Y.-W. Meegaskumbura, M. Yang, J. Ellepola, G. Senevirathne, G. Fu, C.-H. Gross, J. B. Pie, M. R. 2020-04-13 doi:10.1101/2020.04.12.038034 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Cabozantinib unlocks efficient in vivo targeted delivery of neutrophil-loaded nanoparticles into murine prostate tumors ]]> https://biorxiv.org/content/10.1101/2020.04.13.037531v1?rss=1 Chaudagar, K. Landon-Brace, N. Solanki, A. Hieromnimon, H. M. Hegermiller, E. Li, W. Shao, Y. Wilkins, D. Bynoe, K. Li, X.-L. Clohessy, J. Ullas, S. Karp, J. Patnaik, A. 2020-04-14 doi:10.1101/2020.04.13.037531 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18 ]]> https://biorxiv.org/content/10.1101/2020.04.13.038638v1?rss=1 Urtecho, G. Campbell, D. E. Hershey, D. M. Whitaker, R. J. O'Toole, G. A. 2020-04-13 doi:10.1101/2020.04.13.038638 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Existing actin filaments orient new filament growth to provide structural memory of filament alignment during cytokinesis ]]> https://biorxiv.org/content/10.1101/2020.04.13.039586v1?rss=1 Li, Y. Munro, E. 2020-04-14 doi:10.1101/2020.04.13.039586 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Neuronal Subcompartment Classification and Merge Error Correction ]]> https://biorxiv.org/content/10.1101/2020.04.16.043398v1?rss=1 Li, H. Januszewski, M. Jain, V. Li, P. H. 2020-04-18 doi:10.1101/2020.04.16.043398 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation ]]> https://biorxiv.org/content/10.1101/2020.04.17.046896v1?rss=1 Henson, M. W. Lanclos, V. C. Pitre, D. M. Weckhorst, J. L. Lucchesi, A. M. Cheng, C. Temperton, B. Thrash, C. 2020-04-18 doi:10.1101/2020.04.17.046896 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ The crystal structure of nsp10-nsp16 heterodimer from SARS CoV-2in complex with S-adenosylmethionine ]]> https://biorxiv.org/content/10.1101/2020.04.17.047498v1?rss=1 Rosas Lemus, M. Minasov, G. Shuvalova, L. Inniss, N. L. Kiryukhina, O. Wiersum, G. Kim, Y. Jedrzejczak, R. Enders, M. Jaroszewski, L. Godzik, A. Joachimiak, A. Satchell, K. J. 2020-04-20 doi:10.1101/2020.04.17.047498 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Development of early-stage type 1 diabetes in germ-free interleukin-10 deficient mice ]]> https://biorxiv.org/content/10.1101/2020.04.18.048272v1?rss=1 6-months of age), polyuria and pancreatic lymphocytic infiltration resembling T1D lesions was observed. Approximately 50% of male and female mice above 6-months of age develop pancreatic immune cell infiltration, as compared to none in conventionally-raised and fecal microbiota transplanted (FMT) IL-10 KO counterparts. Immunofluorescence staining of islet infiltrates was positive for adaptive and innate immunological markers, including lymphoid and myeloid cell markers, which typically characterize autoimmune T1D lesions. A subset of GF IL-10 KO mice was also positive for insulin autoantibodies (IAA), but the majority of mice did not become diabetic. Our findings of early stage lymphocytic infiltrates in the pancreas and IAA in the absence of overt diabetes in GF IL-10 KO mice embody the early stages of T1D pathogenesis. As such, we propose that the presence of gut microbiota play a protective role against immune infiltration in the pancreas of genetically prone hosts. Moreover, our model provides an opportunity to better understand the role of the microbiota in the early stages of immune pathogenesis and perhaps conceive the development of microbe-mediated prophylactic strategies to treat or even prevent T1D. ]]> Bobe, A. M. Miyoshi, J. Moore, P. Devkota, S. Leone, V. Martinez, K. Theriault, B. R. Musch, M. W. Wasserfall, C. Atkinson, M. Rhodes, C. J. Chang, E. B. 2020-04-18 doi:10.1101/2020.04.18.048272 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Two decades of suspect evidence for adaptive DNA-sequence evolution - Less negative selection misconstrued as positive selection ]]> https://biorxiv.org/content/10.1101/2020.04.21.049973v1?rss=1 Chen, Q. He, Z. Feng, X. Yang, H. Shi, S. Wu, C.-I. 2020-04-23 doi:10.1101/2020.04.21.049973 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Mythical and observable trends in human sex ratio at birth ]]> https://biorxiv.org/content/10.1101/2020.04.21.054445v1?rss=1 Rzhetsky, A. Long, Y. Chen, Q. Larsson, H. 2020-04-24 doi:10.1101/2020.04.21.054445 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction ]]> https://biorxiv.org/content/10.1101/2020.04.22.050666v1?rss=1 Liang, Y. Aguet, F. Barbeira, A. N. Ardlie, K. Im, H. K. 2020-04-24 doi:10.1101/2020.04.22.050666 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies new candidate susceptibility genes for breast and ovarian cancer ]]> https://biorxiv.org/content/10.1101/2020.04.23.043653v1?rss=1 1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. Overlaying candidate causal risk variants identified by GWAS fine mapping onto expression prediction models for genes at known loci suggested that the association for 55% of these genes was driven by the underlying GWAS signal. SignificanceThe 22 new genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk. ]]> Kar, S. Considine, D. Tyrer, J. Plummer, J. Chen, S. Dezem, F. Barbeira, A. Rajagopal, P. Rosenow, W. Anton, F. Bodelon, C. Chang-Claude, J. Chenevix-Trench, G. deFazio, A. Doerk, T. Ekici, A. Ewing, A. Fountzilas, G. Goode, E. Hartman, M. Heitz, F. Hillemanns, P. Hogdall, E. Hogdall, C. Huzarski, T. Jensen, A. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kobel, M. Li, J. Liebrich, C. May, T. Olsson, H. Permuth, J. Peterlongo, P. Radice, P. Ramus, S. Riggan, M. Saloustros, E. Simard, J. Szafron, L. Thompson, C. Vierkant, R. Winha 2020-04-24 doi:10.1101/2020.04.23.043653 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Degradation of Alzheimers Amyloid-beta by a Catalytically Inactive Insulin Degrading Enzyme ]]> https://biorxiv.org/content/10.1101/2020.04.23.057505v1?rss=1 Sahoo, B. Liang, W. Tang, W.-J. Ramamoorthy, A. 2020-04-25 doi:10.1101/2020.04.23.057505 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The trajectory of discrete gating charges in a voltage-gated potassium channel ]]> https://biorxiv.org/content/10.1101/2020.04.23.058818v1?rss=1 Priest, M. F. Lee, E. E. L. Bezanilla, F. 2020-04-24 doi:10.1101/2020.04.23.058818 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Bayesian Hidden Markov modeling and model selection by Kalman filtering applied to multi-dimensional data of ion channels ]]> https://biorxiv.org/content/10.1101/2020.04.27.029207v1?rss=1 Muench, J. L. Paul, F. Schmauder, R. Benndorf, K. 2020-04-28 doi:10.1101/2020.04.27.029207 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Criterion Validity and Relationships between Alternative Hierarchical Dimensional Models of General and Specific Psychopathology ]]> https://biorxiv.org/content/10.1101/2020.04.27.064303v1?rss=1 Moore, T. M. Kaczkurkin, A. N. Durham, E. L. Jeong, H. J. McDowell, M. G. Dupont, R. M. Applegate, B. Tackett, J. L. Cardenas-Iniguez, C. Kardan, O. Akcelik, G. Stier, A. J. Rosenberg, M. D. Hedeker, D. Berman, M. G. Lahey, B. B. 2020-04-29 doi:10.1101/2020.04.27.064303 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ The phylogenetic functional conservation of Drosophila Seven-In-Absentia (SINA) E3 ligase and its two human paralogs, SIAH1 and SIAH2, in Drosophila eye development ]]> https://biorxiv.org/content/10.1101/2020.04.28.067074v1?rss=1 Van Sciver, R. E. Cao, Y. Tang, A. H. 2020-04-30 doi:10.1101/2020.04.28.067074 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Predicting Antimicrobial Resistance Using Conserved Genes ]]> https://biorxiv.org/content/10.1101/2020.04.29.068254v1?rss=1 Nguyen, M. Olson, R. Shukla, M. VanOeffelen, M. Davis, J. J. 2020-04-29 doi:10.1101/2020.04.29.068254 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Optimal prediction with resource constraints using the information bottleneck ]]> https://biorxiv.org/content/10.1101/2020.04.29.069179v1?rss=1 Sachdeva, V. Mora, T. Walczak, A. Palmer, S. E. 2020-05-01 doi:10.1101/2020.04.29.069179 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome ]]> https://biorxiv.org/content/10.1101/2020.04.29.069278v1?rss=1 Shaiber, A. Willis, A. D. Delmont, T. O. Roux, S. Chen, L.-X. Schmid, A. C. Yousef, M. Watson, A. R. Lolans, K. Esen, O. C. Lee, S. T. Downey, N. Morrison, H. G. Dewhirst, F. Mark Welch, J. L. Eren, A. M. 2020-04-30 doi:10.1101/2020.04.29.069278 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Acinetobacter baumannii NCIMB8209: A rare environmental strain displaying extensive insertion sequence-mediated genome remodeling resulting in the loss of exposed cell structures and defensive mechanisms ]]> https://biorxiv.org/content/10.1101/2020.04.30.071514v1?rss=1 Repizo, G. D. Espariz, M. Seravalle, J. L. Diaz Miloslavich, J. I. Steimbrüch, B. A. Shuman, H. A. Viale, A. M. 2020-05-02 doi:10.1101/2020.04.30.071514 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity ]]> https://biorxiv.org/content/10.1101/2020.05.01.072496v1?rss=1 Utter, D. R. Borisy, G. G. Eren, A. M. Cavanaugh, C. M. Mark Welch, J. L. 2020-05-02 doi:10.1101/2020.05.01.072496 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas ]]> https://biorxiv.org/content/10.1101/2020.05.01.072652v1?rss=1 Long, S. W. Christensen, P. A. Bernard, D. W. Davis, J. R. Shukla, M. Nguyen, M. Saavedra, M. O. Cantu, C. C. Yerramilli, P. Pruitt, L. Subedi, S. Hendrickson, H. Eskandari, G. Kumaraswami, M. McLellan, J. S. Musser, J. M. 2020-05-01 doi:10.1101/2020.05.01.072652 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6) ]]> https://biorxiv.org/content/10.1101/2020.05.01.072686v1?rss=1 Yu, A. Lee, E. M. Y. Jin, J. Voth, G. A. 2020-05-03 doi:10.1101/2020.05.01.072686 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids ]]> https://biorxiv.org/content/10.1101/2020.05.02.073320v1?rss=1 Duan, X. Han, Y. Yang, L. Nilsson, B. Wang, P. Zhang, T. Wang, X. Xu, D. Xiang, J. Z. uhl, s. Huang, Y. Chen, H. Wang, H. tenOever, B. R. Schwartz, R. E. Ho, D. D. Pan, F. C. Chen, S. Evans, T. R. 2020-05-02 doi:10.1101/2020.05.02.073320 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Examining sex-differentiated genetic effects across neuropsychiatric and behavioral traits ]]> https://biorxiv.org/content/10.1101/2020.05.04.076042v1?rss=1 Martin, J. Khramtsova, E. A. Goleva, S. B. Blokland, G. A. M. Traglia, M. Walters, R. K. Hübel, C. Coleman, J. R. I. Breen, G. Borglum, A. Demontis, D. Grove, J. Werge, T. Bralten, J. Bulik, C. Lee, P. H. Mathews, C. A. Peterson, R. E. Winham, S. J. Wray, N. R. Edenberg, H. J. Guo, W. Yao, Y. Neale, B. Faraone, S. V. Petryshen, T. L. Weiss, L. Duncan, L. Sex Differences Cross-Disorder Analysis Group of the Psychiatric Genomics Consortium, Goldstein, J. M. Smoller, J. W. Stranger, B. Davis, L. K. 2020-05-05 doi:10.1101/2020.05.04.076042 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model ]]> https://biorxiv.org/content/10.1101/2020.05.04.078022v1?rss=1 Miyoshi, J. Lee, S. T. M. Kennedy, M. Puertolas, M. Frith, M. Koval, J. C. Miyoshi, S. Antonopoulos, D. A. Leone, V. Chang, E. B. 2020-05-05 doi:10.1101/2020.05.04.078022 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids ]]> https://biorxiv.org/content/10.1101/2020.05.05.079095v1?rss=1 Han, Y. Yang, L. Duan, X. Duan, F. Nilsson-Payant, B. E. Yaron, T. M. Wang, P. Tang, X. Zhang, T. Zhao, Z. Bram, Y. Redmond, D. Houghton, S. Nguyen, D. Xu, D. Wang, X. Uhl, S. Huang, Y. Johnson, J. L. Xiang, J. Wang, H. Pan, F. C. Cantley, L. C. tenOever, B. R. Ho, D. D. Evans, T. Schwartz, R. E. Chen, H. J. Chen, S. 2020-05-05 doi:10.1101/2020.05.05.079095 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Causal Inference for Heritable Phenotypic Risk Factors Using Heterogeneous Genetic Instruments ]]> https://biorxiv.org/content/10.1101/2020.05.06.077982v1?rss=1 Wang, J. Zhao, Q. Bowden, J. Hemani, G. Smith, G. D. Small, D. Zhang, N. R. 2020-05-08 doi:10.1101/2020.05.06.077982 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function ]]> https://biorxiv.org/content/10.1101/2020.05.06.080184v1?rss=1 Li, Y. Osuma, A. Correa, E. Okebalama, M. Dao, P. Gaylord, O. Aburas, J. Islam, P. Brown, A. E. X. Kratsios, P. 2020-05-07 doi:10.1101/2020.05.06.080184 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes ]]> https://biorxiv.org/content/10.1101/2020.05.06.080945v1?rss=1 Monje-Galvan, V. Voth, G. A. 2020-05-08 doi:10.1101/2020.05.06.080945 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T ]]> https://biorxiv.org/content/10.1101/2020.05.07.082479v1?rss=1 Wang, C. Foxley, S. Ansorge, O. Bangerter-Christensen, S. Chiew, M. Leonte, A. Menke, R. A. Mollink, J. Pallebage-Gamarallage, M. Turner, M. R. Miller, K. L. Tendler, B. C. 2020-05-08 doi:10.1101/2020.05.07.082479 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Evolution and genetic basis of the plant-penetrating ovipositor, a key adaptation in the transition to herbivory within the Drosophilidae ]]> https://biorxiv.org/content/10.1101/2020.05.07.083253v1?rss=1 Pelaez, J. N. Gloss, A. N. Ray, J. F. Whiteman, N. K. 2020-05-08 doi:10.1101/2020.05.07.083253 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ The Genetic Architecture of DNA Replication Timing in Human Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.05.08.085324v1?rss=1 Ding, Q. Edwards, M. M. Hulke, M. L. Bracci, A. N. Hu, Y. Tong, Y. Zhu, X. Hsiao, J. Charvet, C. J. Ghosh, S. Handsaker, R. E. Eggan, K. Merkle, F. T. Gerhardt, J. Egli, D. Clark, A. G. Koren, A. 2020-05-10 doi:10.1101/2020.05.08.085324 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Trajectory analysis of cardiovascular phenotypes from biobank data uncovers novel genetic associations ]]> https://biorxiv.org/content/10.1101/2020.05.10.087130v1?rss=1 Pottinger, T. D. Pesce, L. L. Gacita, A. Montefiori, L. Hodge, N. Kearns, S. Salamone, I. M. Pacheco, J. A. Rasmussen-Torvik, L. J. Smith, M. E. Chisholm, R. Nobrega, M. A. McNally, E. M. Puckelwartz, M. J. 2020-05-11 doi:10.1101/2020.05.10.087130 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Meta-Align: A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads ]]> https://biorxiv.org/content/10.1101/2020.05.11.087676v1?rss=1 TOMII, K. Kumar, S. Zhi, D. Brenner, S. E. 2020-05-12 doi:10.1101/2020.05.11.087676 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Evaluation of the EUROIMMUN Anti-SARS-CoV-2 ELISA Assay for detection of IgA and IgG antibodies ]]> https://biorxiv.org/content/10.1101/2020.05.11.089862v1?rss=1 Matushek, S. Beavis, K. G. Abeleda, A. Bethel, C. Hunt, C. Gillen, S. Moran, A. Tesic, V. 2020-05-13 doi:10.1101/2020.05.11.089862 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Disrupted object-scene semantics boost scene recall but diminish object recall in drawings from memory ]]> https://biorxiv.org/content/10.1101/2020.05.12.090910v1?rss=1 Bainbridge, W. A. Kwok, W. Y. Baker, C. I. 2020-05-14 doi:10.1101/2020.05.12.090910 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes ]]> https://biorxiv.org/content/10.1101/2020.05.14.096081v1?rss=1 Michalska, K. Kim, Y. Jedrzejczak, R. Maltseva, N. I. Stols, L. Endres, M. Joachimiak, A. 2020-05-14 doi:10.1101/2020.05.14.096081 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Peptide YY: a novel Paneth cell antimicrobial peptide that maintains fungal commensalism ]]> https://biorxiv.org/content/10.1101/2020.05.15.096875v1?rss=1 Pierre, J. F. La Torre, D. Sidebottom, A. Kambal, A. Zhu, X. Tao, Y. Cham, C. M. Wang, L. Harris, K. G. Zaborina, O. Alverdy, J. C. Witchley, J. Noble, S. M. Chang, E. B. 2020-05-16 doi:10.1101/2020.05.15.096875 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ JAG1-NOTCH4 MECHANOSENSING DRIVES ATHEROSCLEROSIS ]]> https://biorxiv.org/content/10.1101/2020.05.15.097931v1?rss=1 Souilhol, C. Li, X. Canham, L. Roddie, H. Pirri, D. Tardajos Ayllon, B. Chambers, E. Dunning, M. Ariaans, M. Li, J. Fang, Y. FRAGIADAKI, M. Ridger, V. Serbanovic-Canic, J. De Val, S. Francis, S. Chico, T. J. Evans, P. 2020-05-16 doi:10.1101/2020.05.15.097931 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ The architecture of EMC reveals a path for membrane protein insertion ]]> https://biorxiv.org/content/10.1101/2020.05.15.098574v1?rss=1 O'Donnell, J. P. Phillips, B. P. Yagita, Y. Juszkiewicz, S. Wagner, A. Malinverni, D. Keenan, R. J. Miller, E. A. Hegde, R. S. 2020-05-16 doi:10.1101/2020.05.15.098574 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Quantification of proteins, protein complexes and mRNA in single cells by proximity-sequencing ]]> https://biorxiv.org/content/10.1101/2020.05.15.098780v1?rss=1 Vistain, L. Phan, H. V. Jordi, C. Chen, M. Reddy, S. T. Tay, S. 2020-05-16 doi:10.1101/2020.05.15.098780 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Seesaw Conformations of Npl4 in the Human p97 Complex and the Inhibitory Mechanism of a Disulfiram Derivative ]]> https://biorxiv.org/content/10.1101/2020.05.18.103085v1?rss=1 Pan, M. Zheng, Q. Yu, Y. Ai, H. Xie, Y. Zeng, X. Wang, C. Liu, L. Zhao, M. 2020-05-20 doi:10.1101/2020.05.18.103085 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Distributed functions of prefrontal and parietal cortices during sequential categorical decisions ]]> https://biorxiv.org/content/10.1101/2020.05.21.108910v1?rss=1 Zhou, Y. Rosen, M. C. Swaminathan, S. K. Masse, N. Zhu, O. Freedman, D. J. 2020-05-25 doi:10.1101/2020.05.21.108910 Cold Spring Harbor Laboratory Press 2020-05-25 <![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[ A three-dimensional thalamocortical dataset for characterizing brain heterogeneity ]]> https://biorxiv.org/content/10.1101/2020.05.22.111617v1?rss=1 Prasad, J. A. Balwani, A. H. Johnson, E. C. Miano, J. D. Sampathkumar, V. de Andrade, V. Fezza, K. Du, M. Vescovi, R. Jacobsen, C. Kording, K. P. Gürsoy, D. Gray-Roncal, W. Kasthuri, N. Dyer, E. L. 2020-05-25 doi:10.1101/2020.05.22.111617 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ The p150 Isoform of ADAR1 Blocks Sustained RLR signaling and Apoptosis during Influenza Virus Infection ]]> https://biorxiv.org/content/10.1101/2020.05.23.111419v1?rss=1 Vogel, O. A. Han, J. Liang, C.-y. Manicassamy, S. Perez, J. T. Manicassamy, B. 2020-05-23 doi:10.1101/2020.05.23.111419 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Proofreading through spatial gradients ]]> https://biorxiv.org/content/10.1101/2020.05.23.112664v1?rss=1 Galstyan, V. Husain, K. Xiao, F. Murugan, A. Phillips, R. 2020-05-24 doi:10.1101/2020.05.23.112664 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Scale-invariance in brain activity predicts practice effects in cognitive performance ]]> https://biorxiv.org/content/10.1101/2020.05.25.114959v1?rss=1 Kardan, O. Layden, E. A. Choe, K. W. Lyu, M. Zhang, X. Beilock, S. L. Rosenberg, M. D. Berman, M. G. 2020-05-26 doi:10.1101/2020.05.25.114959 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ A computational tool for direct inference of cell-specific expression profiles and cellular composition from bulk-tissue RNA-seq in brain disorders ]]> https://biorxiv.org/content/10.1101/2020.05.28.121483v1?rss=1 Doostparast Torshizi, A. Duan, J. Wang, K. 2020-05-31 doi:10.1101/2020.05.28.121483 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Cell type-specific proteogenomic signal diffusion for integrating multi-omics data predicts novel schizophrenia risk genes ]]> https://biorxiv.org/content/10.1101/2020.05.28.121517v1?rss=1 Doostparast Torshizi, A. Duan, J. Wang, K. 2020-05-30 doi:10.1101/2020.05.28.121517 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit ]]> https://biorxiv.org/content/10.1101/2020.05.29.124461v1?rss=1 Ding, J. Chen, A. Chung, J. Acaron Ledesma, H. Berson, D. Palmer, S. Wei, W. 2020-05-31 doi:10.1101/2020.05.29.124461 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Detecting runs of homozygosity from low-coverage ancient DNA ]]> https://biorxiv.org/content/10.1101/2020.05.31.126912v1?rss=1 Ringbauer, H. Novembre, J. Steinruecken, M. 2020-06-01 doi:10.1101/2020.05.31.126912 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Structural basis for polarized elongation of actin filaments ]]> https://biorxiv.org/content/10.1101/2020.06.02.129940v1?rss=1 Zsolnay, V. Katkar, H. H. Chou, S. Z. Pollard, T. D. Voth, G. A. 2020-06-03 doi:10.1101/2020.06.02.129940 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ NON-AVIAN DINOSAUR EGGSHELL CALCITE CONTAINS ANCIENT, ENDOGENOUS AMINO ACIDS ]]> https://biorxiv.org/content/10.1101/2020.06.02.129999v1?rss=1 Saitta, E. T. Vinther, J. Crisp, M. K. Abbott, G. D. Kaye, T. G. Pittman, M. Bull, I. Fletcher, I. Chen, X. Collins, M. J. Sakalauskaite, J. Mackie, M. Dal Bello, F. Dickinson, M. R. Stevenson, M. A. Donohoe, P. Heck, P. R. Demarchi, B. Penkman, K. E. H. 2020-06-03 doi:10.1101/2020.06.02.129999 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome ]]> https://biorxiv.org/content/10.1101/2020.06.04.134692v1?rss=1 Kennedy, A. L. Myers, K. C. Bowman, J. Gibson, C. J. Camarda, N. D. Furutani, E. M. Muscato, G. M. Klein, R. H. Ballotti, K. Liu, S. Harris, C. E. Galvin, A. Malsch, M. Dale, D. Gansner, J. M. Nakano, T. A. Bertuch, A. Vlachos, A. Lipton, J. M. Castillo, P. Connelly, J. Churpek, J. Edwards, J. R. Hijiya, N. Ho, R. H. Hofmann, I. Huang, J. N. Keel, S. Lamble, A. Lau, B. W. Norkin, M. Stieglitz, E. Stock, W. Walkovich, K. Boettcher, S. Brendel, C. Fleming, M. D. Davies, S. M. Weller, E. A. Bahl, C. Carter, S. L. Shimamura, A. Lindsley, R. C. 2020-06-05 doi:10.1101/2020.06.04.134692 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[ A robust two-sample Mendelian Randomization method integrating GWAS with multi-tissue eQTL summary statistics ]]> https://biorxiv.org/content/10.1101/2020.06.04.135541v1?rss=1 Gleason, K. J. Yang, F. Chen, L. S. 2020-06-05 doi:10.1101/2020.06.04.135541 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Limited inhibition of multiple nodes in a driver network blocks metastasis ]]> https://biorxiv.org/content/10.1101/2020.06.05.137117v1?rss=1 Yesilkanal, A. E. Yang, D. Tiwari, P. Sabino, A. U. Lee, J. Xie, X.-H. Sun, S. Dann, C. Steinberg, E. Stuhlmiller, T. Frankenberger, C. Goldsmith, E. Johnson, G. L. Ramos, A. F. Rosner, M. R. 2020-06-07 doi:10.1101/2020.06.05.137117 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Closed-loop fMRI neurofeedback to reduce negative attentional bias in depression ]]> https://biorxiv.org/content/10.1101/2020.06.07.137943v1?rss=1 Mennen, A. C. Turk-Browne, N. B. Wallace, G. Seok, D. Jaganjac, A. Stock, J. deBettencourt, M. T. Cohen, J. D. Norman, K. A. Sheline, Y. I. 2020-06-08 doi:10.1101/2020.06.07.137943 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Monet: An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces ]]> https://biorxiv.org/content/10.1101/2020.06.08.140673v1?rss=1 Wagner, F. 2020-06-09 doi:10.1101/2020.06.08.140673 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Mendelian randomization identifies folliculin expression as a mediator of diabetic retinopathy. ]]> https://biorxiv.org/content/10.1101/2020.06.09.143164v1?rss=1 Skol, A. D. Jung, S. C. Sokovic, A. M. Chen, S. Fazal, S. Sosina, O. Borkar, P. P. Lin, A. Sverdlov, M. Cao, D. Swaroop, A. Bebu, I. DCCT/EDIC Study Group, Stranger, B. Grassi, M. A. 2020-06-11 doi:10.1101/2020.06.09.143164 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Membrane-mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins ]]> https://biorxiv.org/content/10.1101/2020.06.10.144527v1?rss=1 Jarin, Z. Pak, A. J. Bassereau, P. Voth, G. A. 2020-06-12 doi:10.1101/2020.06.10.144527 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Gene expression variability in human and chimpanzee populations share common determinants ]]> https://biorxiv.org/content/10.1101/2020.06.11.146142v1?rss=1 Fair, B. J. Blake, L. E. Sarkar, A. Pavlovic, B. J. Cuevas, C. Gilad, Y. 2020-06-12 doi:10.1101/2020.06.11.146142 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Myosin-driven actin-microtubule networks exhibit self-organized contractile dynamics ]]> https://biorxiv.org/content/10.1101/2020.06.11.146662v1?rss=1 Lee, G. Rust, M. J. Das, M. McGorty, R. J. Ross, J. L. Robertson-Anderson, R. M. 2020-06-12 doi:10.1101/2020.06.11.146662 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Structural and functional synaptic plasticity induced by convergent synapse loss requires co-innervation in the Drosophila neuromuscular circuit ]]> https://biorxiv.org/content/10.1101/2020.06.12.147421v1?rss=1 Wang, Y. Lobb-Rabe, M. Ashley, J. Carrillo, R. A. 2020-06-14 doi:10.1101/2020.06.12.147421 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ A C. elegans model of C9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation ]]> https://biorxiv.org/content/10.1101/2020.06.13.150029v1?rss=1 Sonobe, Y. Aburas, J. Islam, P. Gendron, T. F. Brown, A. E. X. Roos, R. P. Kratsios, P. 2020-06-15 doi:10.1101/2020.06.13.150029 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Untangling stability and gain modulation in cortical circuits with multiple interneuron classes ]]> https://biorxiv.org/content/10.1101/2020.06.15.148114v1?rss=1 Bos, H. Oswald, A.-M. Doiron, B. 2020-06-15 doi:10.1101/2020.06.15.148114 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ A neural circuit mechanism of categorical perception: top-down signaling in the primate cortex ]]> https://biorxiv.org/content/10.1101/2020.06.15.151506v1?rss=1 Min, B. Bliss, D. P. Sarma, A. Freedman, D. J. Wang, X.-J. 2020-06-15 doi:10.1101/2020.06.15.151506 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length ]]> https://biorxiv.org/content/10.1101/2020.06.15.152868v1?rss=1 Marinic, M. Mika, K. Chigurupati, S. Lynch, V. J. 2020-06-15 doi:10.1101/2020.06.15.152868 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ TMPRSS2, a SARS-CoV-2 internalization protease is downregulated in head and neck cancer patients. ]]> https://biorxiv.org/content/10.1101/2020.06.16.154211v1?rss=1 Sacconi, A. Donzelli, S. Pulito, C. Ferrero, S. Morrone, A. Rigoni, M. Pimipinelli, F. Ensoli, F. Sanguineti, G. Pellini, R. Agrawal, N. Izumchenko, E. Ciliberto, G. Gianni, A. Muti, P. Strano, S. Blandino, G. 2020-06-16 doi:10.1101/2020.06.16.154211 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ High fat diet disrupts diurnal interactions between REG3g and small intestinal gut microbes resulting in metabolic dysfunction ]]> https://biorxiv.org/content/10.1101/2020.06.17.130393v1?rss=1 Frazier, K. Kambal, A. Zale, E. A. Pierre, J. F. Hubert, N. Miyoshi, S. Miyoshi, J. Ringus, D. Harris, D. Yang, K. Cham, C. Musch, M. W. Chang, E. B. Leone, V. 2020-06-18 doi:10.1101/2020.06.17.130393 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale ]]> https://biorxiv.org/content/10.1101/2020.06.17.157396v1?rss=1 Voth, G. A. Li, C. Yue, Z. Espinoza-Fonseca, L. M. 2020-06-19 doi:10.1101/2020.06.17.157396 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics ]]> https://biorxiv.org/content/10.1101/2020.06.19.162248v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@aee3a3org.highwire.dtl.DTLVardef@1e3058forg.highwire.dtl.DTLVardef@1820aecorg.highwire.dtl.DTLVardef@9b32ae_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Watkins, L. C. DeGrado, W. F. Voth, G. A. 2020-06-20 doi:10.1101/2020.06.19.162248 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Wetland plant evolutionary history influences soil and endophyte microbial community composition ]]> https://biorxiv.org/content/10.1101/2020.06.22.165738v1?rss=1 Szubryt, M. B. Skinner, K. O'Loughlin, E. J. Koval, J. Greenwald, S. M. Owens, S. M. Kemner, K. M. Weisenhorn, P. B. 2020-06-23 doi:10.1101/2020.06.22.165738 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses ]]> https://biorxiv.org/content/10.1101/2020.06.24.169078v1?rss=1 Lloyd, G. T. Slater, G. J. 2020-06-25 doi:10.1101/2020.06.24.169078 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover ]]> https://biorxiv.org/content/10.1101/2020.06.25.171363v1?rss=1 Jarin, Z. Newhouse, J. Voth, G. A. 2020-06-29 doi:10.1101/2020.06.25.171363 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Inferring cellular trajectories from scRNA-seq using Pseudocell Tracer ]]> https://biorxiv.org/content/10.1101/2020.06.26.173179v1?rss=1 Reiman, D. Xu, H. Sonin, A. Chen, D. Singh, H. Khan, A. 2020-06-27 doi:10.1101/2020.06.26.173179 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.06.26.173872v1?rss=1 Kim, Y. Wower, J. Maltseva, N. Chang, C. Jedrzejczak, R. Wilamowski, M. Kang, S. Nicolaescu, V. Randall, G. Michalska, K. Joachimiak, A. 2020-06-26 doi:10.1101/2020.06.26.173872 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Quantitative occupancy of myriad transcription factors from one DNase experiment enables efficient comparisons across conditions ]]> https://biorxiv.org/content/10.1101/2020.06.28.171587v1?rss=1 Luo, K. Zhong, J. Safi, A. Hong, L. K. Tewari, A. K. Song, L. Reddy, T. E. Ma, L. Crawford, G. E. Hartemink, A. J. 2020-06-29 doi:10.1101/2020.06.28.171587 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ In situ humoral selection in human lupus tubulointerstitial inflammation ]]> https://biorxiv.org/content/10.1101/2020.06.29.178145v1?rss=1 Kinloch, A. J. Asano, Y. Mohsin, A. Henry, C. J. Abraham, R. Chang, A. Labno, C. Wilson, P. C. Clark, M. R. 2020-06-29 doi:10.1101/2020.06.29.178145 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses ]]> https://biorxiv.org/content/10.1101/2020.06.30.180448v1?rss=1 Vanni, C. Schechter, M. Acinas, S. Barberan, A. Buttigieg, P. L. Casamayor, E. O. Delmont, T. O. Duarte, C. M. Eren, A. M. Finn, R. Mitchell, A. Sanchez, P. Siren, K. Steinegger, M. Glöckner, F. O. Fernandez-Guerra, A. 2020-07-01 doi:10.1101/2020.06.30.180448 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Probabilistic Colocalization of Genetic Variants from Complex and Molecular Traits: Promise and Limitations ]]> https://biorxiv.org/content/10.1101/2020.07.01.182097v1?rss=1 Hukku, A. Pividori, M. Luca, F. Pique-Regi, R. Im, H. K. Wen, X. 2020-07-01 doi:10.1101/2020.07.01.182097 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Geographic patterns of human allele frequency variation: a variant-centric perspective ]]> https://biorxiv.org/content/10.1101/2020.07.01.182311v1?rss=1 Biddanda, A. Rice, D. P. Novembre, J. 2020-07-02 doi:10.1101/2020.07.01.182311 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission ]]> https://biorxiv.org/content/10.1101/2020.07.02.184481v1?rss=1 T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2. ]]> Sapoval, N. Mahmoud, M. Jochum, M. D. Liu, Y. Elworth, R. A. L. Wang, Q. Albin, D. Ogilvie, H. Lee, M. D. Villapol, S. Hernandez, K. Maljkovic Berry, I. Foox, J. Beheshti, A. Ternus, K. Aagaard, K. M. Posada, D. Mason, C. Sedlazeck, F. J. Treangen, T. J. 2020-07-02 doi:10.1101/2020.07.02.184481 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth ]]> https://biorxiv.org/content/10.1101/2020.07.02.184978v1?rss=1 Nandadasa, S. Szafron, J. M. Pathak, V. Murtada, S.-I. Craft, C. M. O'Donnell, A. Norvik, C. Hughes, C. Caterson, B. Domowicz, M. S. Schwartz, N. B. Tran-Lundmark, K. Veigl, M. Sedwick, D. Philipson, E. H. Humphrey, J. D. Apte, S. S. 2020-07-03 doi:10.1101/2020.07.02.184978 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ The transcriptional repressor Zfp125 modifies hepatic energy metabolism in response to fasting and insulin resistance ]]> https://biorxiv.org/content/10.1101/2020.07.02.185165v1?rss=1 Fernandes, G. W. Bocco, B. M. L. C. Fonseca, T. d. L. Salas-Lucia, F. Nickel, O. Russo, S. C. Gereben, B. Kettelhut, I. C. Bianco, A. C. 2020-07-02 doi:10.1101/2020.07.02.185165 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Repeated loss of variation in insect ovary morphology highlights the role of developmental constraint in life-history evolution ]]> https://biorxiv.org/content/10.1101/2020.07.07.191940v1?rss=1 Church, S. H. de Medeiros, B. A. S. Donoughe, S. Marquez Reyes, N. L. Extavour, C. G. 2020-07-07 doi:10.1101/2020.07.07.191940 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Yorkie-independent negative feedback couples Hippo pathway activation with Kibra degradation ]]> https://biorxiv.org/content/10.1101/2020.07.08.192765v1?rss=1 Sherzod A. Tokamov Ting Su Anne Ullyot Richard G. Fehon 2020-07-09 doi:10.1101/2020.07.08.192765 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Cognitive and Neural State Dynamics of Story Comprehension ]]> https://biorxiv.org/content/10.1101/2020.07.10.194647v1?rss=1 Hayoung Song Bo-yong Park Hyunjin Park Won Mok Shim 2020-07-10 doi:10.1101/2020.07.10.194647 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Pairwise Interactions in Adjuvant Combinations Dictate Immune Responses and Inform Cancer Immunotherapy Design ]]> https://biorxiv.org/content/10.1101/2020.07.11.198879v1?rss=1 Surya Pandey Adam Gruenbaum Tamara Kashanova Philipp Mertins Philippe Cluzel Nicolas Chevrier 2020-07-12 doi:10.1101/2020.07.11.198879 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Cell Type Aware analysis of RNA-seq data(CARseq) reveals difference and similarities ofthe molecular mechanisms of Schizophrenia andAutism ]]> https://biorxiv.org/content/10.1101/2020.07.13.201061v1?rss=1 Jin, C. Chen, M. Lin, D. Sun, W. 2020-07-14 doi:10.1101/2020.07.13.201061 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ PARP and PI3K inhibitor combination therapy eradicates c-MYC-driven murine prostate cancers via cGAS/STING pathway activation within tumor-associated macrophages ]]> https://biorxiv.org/content/10.1101/2020.07.17.198598v1?rss=1 Gupta, P. D. Chaudagar, K. Sharma-Saha, S. Bynoe, K. M. Maillat, L. Heiss, B. Stadler, W. Patnaik, A. 2020-07-18 doi:10.1101/2020.07.17.198598 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Actin bundle architecture and mechanics regulate myosin II force generation ]]> https://biorxiv.org/content/10.1101/2020.07.17.207415v1?rss=1 Weirich, K. L. Stam, S. Munro, E. Gardel, M. L. 2020-07-17 doi:10.1101/2020.07.17.207415 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing ]]> https://biorxiv.org/content/10.1101/2020.07.17.209346v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@e3b50borg.highwire.dtl.DTLVardef@182ebc9org.highwire.dtl.DTLVardef@45f69eorg.highwire.dtl.DTLVardef@142210f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Smith, K. L. Shuman, H. A. Findeisen, D. 2020-07-20 doi:10.1101/2020.07.17.209346 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ Gamma oscillations in primate primary visual cortex are severely attenuated by small stimulus discontinuities ]]> https://biorxiv.org/content/10.1101/2020.07.19.210922v1?rss=1 Shirhatti, V. Ravishankar, P. Ray, S. 2020-07-21 doi:10.1101/2020.07.19.210922 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2 ]]> https://biorxiv.org/content/10.1101/2020.07.19.210955v1?rss=1 Onabajo, O. O. Banday, A. R. Yan, W. Obajemu, A. Stanifer, M. L. Santer, D. M. Florez-Vargas, O. Piontkivska, H. Vargas, J. Kee, C. Tyrrell, D. L. Mendoza, J. L. Boulant, S. Prokunina-Olsson, L. 2020-07-20 doi:10.1101/2020.07.19.210955 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ Distributed Sampling-based Bayesian Inference in Coupled Neural Circuits ]]> https://biorxiv.org/content/10.1101/2020.07.20.212126v1?rss=1 Zhang, W. Lee, T. S. Doiron, B. Wu, S. 2020-07-22 doi:10.1101/2020.07.20.212126 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Impact of cell-type and context-dependent regulatory variants on human immune traits ]]> https://biorxiv.org/content/10.1101/2020.07.20.212753v1?rss=1 Mu, Z. Wei, W. Fair, B. J. Miao, J. Zhu, P. Li, Y. 2020-07-21 doi:10.1101/2020.07.20.212753 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Selection in males purges the standing genetic load on female fitness ]]> https://biorxiv.org/content/10.1101/2020.07.20.213132v1?rss=1 Grieshop, K. Maurizio, P. L. Arnqvist, G. Berger, D. 2020-07-21 doi:10.1101/2020.07.20.213132 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Motor and Sensory Cortical Processing of Neural Oscillatory Activities revealed by Human Swallowing using Intracranial Electrodes ]]> https://biorxiv.org/content/10.1101/2020.07.21.213868v1?rss=1 Hashimoto, H. Takahashi, K. Kameda, S. Yoshida, F. Maezawa, H. Oshino, S. Tani, N. Khoo, H. M. Yanagisawa, T. Yoshimine, T. Kishima, H. Hirata, M. 2020-07-21 doi:10.1101/2020.07.21.213868 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Flagellar perturbations activate adhesion through two distinct pathways in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2020.07.21.215269v1?rss=1 Hershey, D. M. Fiebig, A. Crosson, S. 2020-07-22 doi:10.1101/2020.07.21.215269 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Predicting cognitive abilities across individuals using sparse EEG connectivity ]]> https://biorxiv.org/content/10.1101/2020.07.22.216705v1?rss=1 Hakim, N. Awh, E. Vogel, E. K. Rosenberg, M. D. 2020-07-24 doi:10.1101/2020.07.22.216705 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity ]]> https://biorxiv.org/content/10.1101/2020.07.23.218339v1?rss=1 Hawash, M. B. F. Sanz-Remon, J. Grenier, J.-C. Kohn, J. Yotova, V. Johnson, Z. Lanford, R. E. Brinkworth, J. F. Barreiro, L. B. 2020-07-23 doi:10.1101/2020.07.23.218339 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Effects of individual base-pairs on in vivo target search and destruction kinetics of small RNA ]]> https://biorxiv.org/content/10.1101/2020.07.24.215095v1?rss=1 Poddar, A. Azam, M. S. Kayikcioglu, T. Bobrovskyy, M. Zhang, J. Ma, X. Labhsetwar, P. Fei, J. Singh, D. Luthey-Schulten, Z. Vanderpool, C. K. Ha, T. 2020-07-26 doi:10.1101/2020.07.24.215095 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Salient distractors induce a gradient of attentional suppression to cope with spatial and nonspatial filtering costs ]]> https://biorxiv.org/content/10.1101/2020.07.25.220947v1?rss=1 Feldmann-Wustefeld, T. Weinberger, M. Awh, E. 2020-07-26 doi:10.1101/2020.07.25.220947 Cold Spring Harbor Laboratory Press 2020-07-26 <![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[ Biochemical Patterns of Antibody Polyreactivity Revealed Through a Bioinformatics-Based Analysis of CDR Loops ]]> https://biorxiv.org/content/10.1101/2020.07.30.229013v1?rss=1 Boughter, C. T. Borowska, M. T. Guthmiller, J. J. Bendelac, A. Wilson, P. Roux, B. Adams, E. J. 2020-07-30 doi:10.1101/2020.07.30.229013 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ A collaborative resource platform for non-human primate neuroimaging ]]> https://biorxiv.org/content/10.1101/2020.07.31.230185v1?rss=1 Messinger, A. Sirmpilatze, N. Heuer, K. Loh, K. K. Mars, R. Sein, J. Xu, T. Glen, D. Jung, B. Seidlitz, J. Taylor, P. Toro, R. Garza-Villareal, E. Sponheim, C. Wang, X. Benn, A. Cagna, B. Dadarwal, R. Evrard, H. Garcia-Saldivar, P. Giavasis, S. Hartig, R. Lepage, C. Liu, C. Majka, P. Merchant, H. Milham, M. Rosa, M. Tasserie, J. Uhrig, L. Margulies, D. Klink, P. C. 2020-07-31 doi:10.1101/2020.07.31.230185 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Local adaptation contributes to gene expression divergence in maize ]]> https://biorxiv.org/content/10.1101/2020.08.01.231217v1?rss=1 Blanc, J. Kremling, K. A. G. Buckler, E. S. Josephs, E. B. 2020-08-03 doi:10.1101/2020.08.01.231217 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Dimension reduction and denoising of single-cell RNA sequencing data in the presence of observed confounding variables ]]> https://biorxiv.org/content/10.1101/2020.08.03.234765v1?rss=1 Huang, M. Zhang, Z. Zhang, N. R. 2020-08-04 doi:10.1101/2020.08.03.234765 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ An unexpected bifurcation in the Pointed transcriptional effector network contributes specificity and robustness to retinal cell fate acquisition ]]> https://biorxiv.org/content/10.1101/2020.08.03.235184v1?rss=1 Wu, C. Boisclair Lachance, J.-F. Ludwig, M. rebay, i. 2020-08-04 doi:10.1101/2020.08.03.235184 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Concerted evolution reveals co-adapted amino acid substitutions in frogs that prey on toxic toads ]]> https://biorxiv.org/content/10.1101/2020.08.04.234435v1?rss=1 Mohammadi, S. Yang, L. Harpak, A. Herrera-Alvarez, S. Rodriguez-Ordonez, M. d. P. Peng, J. Zhang, K. Storz, J. F. Dobler, S. Crawford, A. J. Andolfatto, P. 2020-08-05 doi:10.1101/2020.08.04.234435 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques ]]> https://biorxiv.org/content/10.1101/2020.08.04.237149v1?rss=1 Lepage, C. Wagstyl, K. Jung, B. Seidlitz, J. Sponheim, C. Ungerleider, L. Wang, X. Evans, A. C. Messinger, A. 2020-08-05 doi:10.1101/2020.08.04.237149 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ A comprehensive macaque fMRI pipeline and hierarchical atlas ]]> https://biorxiv.org/content/10.1101/2020.08.05.237818v1?rss=1 Jung, B. Taylor, P. A. Seidlitz, J. Sponheim, C. Perkins, P. Ungerleider, L. G. Glen, D. Messinger, A. 2020-08-06 doi:10.1101/2020.08.05.237818 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ The longitudinal stability of fMRI activation during reward processing in adolescents and young adults ]]> https://biorxiv.org/content/10.1101/2020.08.06.236596v1?rss=1 Baseline; mean ICC = 0.13 - 0.33) than contrasts of two active states (e.g., Win>Loss; mean ICC = 0.048 - 0.05). Additionally, activation in reward regions was less stable than in many non-task networks (e.g., dorsal attention), and activation in regions with greater between-subject variability showed higher stability in both samples. ConclusionsThese results show that functional neuroimaging activation to reward has modest stability over 1-2 years. Notably, results suggest that contrasts intended to map cognitive function and show robust group-level effects (i.e. Win > Loss) may be less effective in studies of individual differences and disease risk. The robustness of group-level activation should be weighed against other factors when selecting regions of interest in individual difference fMRI studies. ]]> Baranger, D. A. Lindenmuth, M. Nance, M. Guyer, A. E. Keenan, K. Hipwell, A. E. Shaw, D. S. Forbes, E. E. 2020-08-07 doi:10.1101/2020.08.06.236596 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Sex, fitness decline and recombination - Muller's ratchet vs. Ohta's ratchet ]]> https://biorxiv.org/content/10.1101/2020.08.06.240713v1?rss=1 Ruan, Y. Wang, H. Zhang, L. Wen, H. Wu, C.-I. 2020-08-07 doi:10.1101/2020.08.06.240713 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Fast and Flexible Estimation of Effective Migration Surfaces ]]> https://biorxiv.org/content/10.1101/2020.08.07.242214v1?rss=1 Marcus, J. H. Ha, W. Barber, R. F. Novembre, J. 2020-08-07 doi:10.1101/2020.08.07.242214 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Global inequity in scientific names and who they honor ]]> https://biorxiv.org/content/10.1101/2020.08.09.243238v1?rss=1 DuBay, S. Palmer, D. H. Piland, N. 2020-08-10 doi:10.1101/2020.08.09.243238 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Cell Programmed Nutrient Partitioning in the Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2020.08.10.238428v1?rss=1 Reinfeld, B. I. Madden, M. Z. Wolf, M. M. Chytil, A. Bader, J. E. Patterson, A. R. Cohen, A. S. Ali, A. Do, B. T. Lewis, C. A. Muir, A. Hongo, R. A. Young, K. L. Brown, R. E. Todd, V. M. Huffstater, T. Abraham, A. O'Neil, R. T. Wilson, M. T. Xin, F. Tantawy, M. N. Merryman, W. D. Johnson, R. W. Williams, C. S. Mason, E. F. Mason, F. M. Beckermann, K. E. Vander Heiden, M. G. Manning, H. C. Rathmell, J. C. Rathmell, W. K. 2020-08-10 doi:10.1101/2020.08.10.238428 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Regression dynamic causal modeling for resting-state fMRI ]]> https://biorxiv.org/content/10.1101/2020.08.12.247536v1?rss=1 200 areas) within minutes on standard hardware. This opens promising new avenues for connectomics. ]]> Frässle, S. Harrison, S. J. Heinzle, J. Clementz, B. A. Tamminga, C. A. Sweeney, J. A. Gershon, E. S. Keshavan, M. S. Pearlson, G. D. Powers, A. Stephan, K. E. 2020-08-13 doi:10.1101/2020.08.12.247536 Cold Spring Harbor Laboratory Press 2020-08-13 <![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[ 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[ Multiple regions of primate orofacial sensorimotor cortex encode bite force and gape ]]> https://biorxiv.org/content/10.1101/2020.08.16.252817v1?rss=1 Arce-McShane, F. Sessle, B. J. Ram, Y. Balcer, C. A. Ross, C. Hatsopoulos, N. G. 2020-08-16 doi:10.1101/2020.08.16.252817 Cold Spring Harbor Laboratory Press 2020-08-16 <![CDATA[ Deuteration improves small-molecule fluorophores ]]> https://biorxiv.org/content/10.1101/2020.08.17.250027v1?rss=1 Grimm, J. B. Xie, L. Casler, J. C. Patel, R. Tkachuk, A. N. Choi, H. Lippincott-Schwartz, J. Brown, T. A. Glick, B. S. Liu, Z. Lavis, L. D. 2020-08-17 doi:10.1101/2020.08.17.250027 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Interaction between neuronal encoding and population dynamics during categorization task switching in parietal cortex ]]> https://biorxiv.org/content/10.1101/2020.08.20.259820v1?rss=1 Mohan, K. Zhu, O. Freedman, D. J. 2020-08-22 doi:10.1101/2020.08.20.259820 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Load-Dependent Relationships between Frontal fNIRS Activity and Performance: A Data-Driven PLS Approach ]]> https://biorxiv.org/content/10.1101/2020.08.21.261438v1?rss=1 Meidenbauer, K. L. Choe, K. W. Cardenas-Iniguez, C. Huppert, T. J. Berman, M. G. 2020-08-24 doi:10.1101/2020.08.21.261438 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Frequency shapes the quality of tactile percepts evoked through electrical stimulation of the nerves ]]> https://biorxiv.org/content/10.1101/2020.08.24.263822v1?rss=1 Graczyk, E. L. Christie, B. P. He, Q. Tyler, D. J. Bensmaia, S. J. 2020-08-24 doi:10.1101/2020.08.24.263822 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Distributed Visual Category Processing Across Medial Superior Temporal and Lateral Intraparietal Cortices ]]> https://biorxiv.org/content/10.1101/2020.08.25.266791v1?rss=1 Zhou, Y. Mohan, K. Freedman, D. J. 2020-08-25 doi:10.1101/2020.08.25.266791 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Neural signatures of attentional engagement during narratives and its consequences for event memory ]]> https://biorxiv.org/content/10.1101/2020.08.26.266320v1?rss=1 Song, H. Finn, E. S. Rosenberg, M. D. 2020-08-27 doi:10.1101/2020.08.26.266320 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees ]]> https://biorxiv.org/content/10.1101/2020.08.27.270686v1?rss=1 Mittleman, B. E. Pott, S. Warland, S. Barr, K. Cuevas, C. Gilad, Y. 2020-08-27 doi:10.1101/2020.08.27.270686 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Aberrant RNA methylation triggers recruitment of an alkylation repair complex ]]> https://biorxiv.org/content/10.1101/2020.08.28.271874v1?rss=1 Brickner, J. R. Tsao, N. Rodell, R. Oyeniran, C. Lukinovic, V. Bacolla, A. Zhang, L. Soll, J. M. Casanova, A. Ganguly, A. He, C. Tainer, J. Reynoird, N. Mosammaparast, N. 2020-08-31 doi:10.1101/2020.08.28.271874 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Chance, contingency, and necessity in the experimental evolution of ancestral proteins ]]> https://biorxiv.org/content/10.1101/2020.08.29.273581v1?rss=1 Xie, V. C. Pu, J. Metzger, B. P. H. Thornton, J. W. Dickinson, B. 2020-08-29 doi:10.1101/2020.08.29.273581 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Identification of Lysine Isobutyrylation as A New Histone Modification Mark ]]> https://biorxiv.org/content/10.1101/2020.08.31.270165v1?rss=1 Zhu, Z. Han, Z. Halabelian, L. Yang, X. Ding, J. Zhang, N. Ngo, L. Song, J. Zeng, H. He, M. Zhao, Y. Arrowsmith, C. H. Luo, M. Bartlett, M. G. Zheng, Y. G. 2020-09-01 doi:10.1101/2020.08.31.270165 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro ]]> https://biorxiv.org/content/10.1101/2020.08.31.274639v1?rss=1 Drayman, N. Jones, K. A. Azizi, S.-A. Froggatt, H. M. Tan, K. Ivanova Maltseva, N. Chen, S. Nicolaescu, V. Dvorkin, S. Furlong, K. Kathayat, R. S. Firpo, M. R. Mastrodomenico, V. Bruce, E. A. Schmidt, M. M. Jedrzejczak, R. Munoz-Alia, M. A. Schuster, B. Nair, V. Botten, J. W. Brooke, C. B. Baker, S. C. Mounce, B. C. Heaton, N. S. Dickinson, B. C. Jaochimiak, A. Randall, G. Tay, S. 2020-09-01 doi:10.1101/2020.08.31.274639 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Many are called but few are chosen - Multiple clonal origins greatly elevate the functional heterogeneity of tumors ]]> https://biorxiv.org/content/10.1101/2020.09.01.277848v1?rss=1 Chen, B. Wu, X. Ruan, Y. Zhang, Y. Wen, H. Lan, P. Wu, C.-I. 2020-09-01 doi:10.1101/2020.09.01.277848 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Unique contribution of enhancer-driven and master-regulator genes to autoimmune disease revealed using functionally informed SNP-to-gene linking strategies ]]> https://biorxiv.org/content/10.1101/2020.09.02.279059v1?rss=1 2x stronger conditional signal (maximum standardized SNP annotation effect size ({tau}*) = 2.0 (s.e. 0.3) vs. 0.91 (s.e. 0.21)), and >2x stronger gene-level enrichment for approved autoimmune disease drug targets (5.3x vs. 2.1x), as compared to the recently proposed Enhancer Domain Score (EDS). In each case, using functionally informed S2G strategies to link genes to SNPs that may regulate them produced much stronger disease signals (4.1x-13x larger{tau} * values) than conventional window-based S2G strategies. We conclude that our characterizations of enhancer-related and candidate master-regulator genes identify gene sets that are important for autoimmune disease, and that combining those gene sets with functionally informed S2G strategies enables us to identify SNP annotations in which disease heritability is concentrated. ]]> Dey, K. K. Gazal, S. K. van de Geijn, B. Kim, S. S. Nasser, J. Engreitz, J. M. Price, A. 2020-09-03 doi:10.1101/2020.09.02.279059 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir ]]> https://biorxiv.org/content/10.1101/2020.09.02.279570v1?rss=1 Fellows Yates, J. A. Andrades Valtuena, A. Vagene, A. J. Cribdon, B. Velsko, I. M. Borry, M. Bravo-Lopez, M. J. Fernandez-Guerra, A. Green, E. J. Ramachandran, S. L. Heintzman, P. D. Spyrou, M. A. Hübner, A. Gancz, A. S. Hider, J. Allshouse, A. F. Warinner, C. G. 2020-09-03 doi:10.1101/2020.09.02.279570 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Tractable models of ecological assembly ]]> https://biorxiv.org/content/10.1101/2020.09.02.279943v1?rss=1 Servan, C. A. Allesina, S. 2020-09-03 doi:10.1101/2020.09.02.279943 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Effects of phylogeny on coexistence in model communities ]]> https://biorxiv.org/content/10.1101/2020.09.04.283507v1?rss=1 Servan, C. A. Capitan, J. A. Miller, Z. R. Allesina, S. 2020-09-06 doi:10.1101/2020.09.04.283507 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Metagenomics Strain Resolution on Assembly Graphs ]]> https://biorxiv.org/content/10.1101/2020.09.06.284828v1?rss=1 Quince, C. Nurk, S. Raguideau, S. James, R. S. Soyer, O. S. Summers, J. K. Limasset, A. Eren, A. M. Chikhi, R. Darling, A. E. 2020-09-07 doi:10.1101/2020.09.06.284828 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Visual speech differentially modulates beta, theta, and high gamma bands in auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.07.284455v1?rss=1 Ganesan, K. Plass, J. Beltz, A. M. Liu, Z. Grabowecky, M. Suzuki, S. Stacey, W. C. Wasade, V. S. Towle, V. L. Tao, J. X. Wu, S. Issa, N. P. Brang, D. 2020-09-07 doi:10.1101/2020.09.07.284455 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ OpenAWSEM with Open3SPN2: a fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations ]]> https://biorxiv.org/content/10.1101/2020.09.07.285759v1?rss=1 Lu, W. Bueno, C. Schafer, N. P. Moller, J. Jin, S. Chen, M. Gu, X. de Pablo, J. J. Wolynes, P. G. 2020-09-07 doi:10.1101/2020.09.07.285759 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits. ]]> https://biorxiv.org/content/10.1101/2020.09.08.287532v1?rss=1 Letelier, J. Naranjo, S. Sospedra, I. Lopez-Rios, J. Martinez-Morales, J. R. Shubin, N. Gomez-Skarmeta, J. L. 2020-09-08 doi:10.1101/2020.09.08.287532 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Controlling the flow of interruption in working memory ]]> https://biorxiv.org/content/10.1101/2020.09.08.288027v1?rss=1 Hakim, N. Feldmann-Wustefeld, T. Awh, E. Vogel, E. K. 2020-09-09 doi:10.1101/2020.09.08.288027 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Asthma-associated variants induce IL33 differential expression through a novel regulatory region ]]> https://biorxiv.org/content/10.1101/2020.09.09.290098v1?rss=1 Aneas, I. Decker, D. C. Howard, C. L. Sobreira, D. R. Sakabe, N. Blaine, K. M. Stein, M. M. Hrusch, C. L. Montefiori, L. E. Tena, J. J. Magnaye, K. M. Clay, S. M. Gern, J. E. Jackson, D. J. Altman, M. C. Naureckas, E. T. Hogarth, D. K. White, S. R. Gomez-Skarmeta, J. L. Schoetler, N. Ober, C. Sperling, A. I. Nobrega, M. A. 2020-09-11 doi:10.1101/2020.09.09.290098 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Distinct place cell dynamics in CA1 and CA3 encode experience in new contexts ]]> https://biorxiv.org/content/10.1101/2020.09.10.292177v1?rss=1 Dong, C. Sheffield, M. 2020-09-11 doi:10.1101/2020.09.10.292177 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike ]]> https://biorxiv.org/content/10.1101/2020.09.12.294066v1?rss=1 Guthmiller, J. J. Stovicek, O. Wang, J. Changrob, S. Li, L. Halfmann, P. Zheng, N.-Y. Utset, H. Stamper, C. T. Dugan, H. L. Miller, W. D. Huang, M. Dai, Y.-N. Nelson, C. A. Hall, P. D. Jansen, M. Shanmugarajah, K. Donington, J. S. Krammer, F. Fremont, D. Joachimiak, A. Kawaoka, Y. Tesic, V. Madariaga, M. L. Wilson, P. C. 2020-09-13 doi:10.1101/2020.09.12.294066 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Changing reward expectation transforms spatial encoding and retrieval in the hippocampus ]]> https://biorxiv.org/content/10.1101/2020.09.13.295469v1?rss=1 Krishnan, S. Cherian, C. Sheffield, M. 2020-09-14 doi:10.1101/2020.09.13.295469 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations ]]> https://biorxiv.org/content/10.1101/2020.09.14.296889v1?rss=1 Dogan, T. Atas, H. Joshi, V. Atakan, A. Rifaioglu, A. S. Nalbat, E. Nightingale, A. Saidi, R. Volynkin, V. Zellner, H. Cetin-Atalay, R. Martin, M. Atalay, V. 2020-09-15 doi:10.1101/2020.09.14.296889 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Sustained attention and spatial attention distinctly influence long-term memory encoding ]]> https://biorxiv.org/content/10.1101/2020.09.14.297341v1?rss=1 deBettencourt, M. T. Williams, S. D. Vogel, E. K. Awh, E. 2020-09-15 doi:10.1101/2020.09.14.297341 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle ]]> https://biorxiv.org/content/10.1101/2020.09.16.298463v1?rss=1 Carrillo, M. Pandey, S. Sanchez, J. Noda, M. Poudyal, I. Aldama, L. Malla, T. N. Claesson, E. Yuan Wahlgreen, W. Feliz, D. Srajer, V. Maj, M. Castillon, L. Iwata, S. Nango, E. Tanaka, R. Tanaka, T. Fangjia, L. Tono, K. Owada, S. Westenhoff, S. Stojkovic, E. Schmidt, M. 2020-09-16 doi:10.1101/2020.09.16.298463 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ A method to remove the influence of fixative concentration on post-mortem T2 maps using a Kinetic Tensor model ]]> https://biorxiv.org/content/10.1101/2020.09.16.299784v1?rss=1 Tendler, B. C. Qi, F. Foxley, S. Pallebage-Gamarallage, M. Menke, R. A. L. Ansorge, O. Hurley, S. A. Miller, K. L. 2020-09-17 doi:10.1101/2020.09.16.299784 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Morphological Integration and Modularity in the Hyperkinetic Feeding System of Aquatic-foraging Snakes ]]> https://biorxiv.org/content/10.1101/2020.09.16.300400v1?rss=1 Rhoda, D. Polly, P. D. Raxworthy, C. Segall, M. 2020-09-16 doi:10.1101/2020.09.16.300400 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ ESCargo: a regulatable fluorescent secretory cargo for diverse model organisms ]]> https://biorxiv.org/content/10.1101/2020.09.17.302133v1?rss=1 Casler, J. C. Zajac, A. L. Valbuena, F. M. Sparvoli, D. Jeyifous, O. Turkewitz, A. P. Horne-Badovinac, S. Green, W. N. Glick, B. S. 2020-09-18 doi:10.1101/2020.09.17.302133 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ Fixed single-cell RNA sequencing for understanding virus infection and host response ]]> https://biorxiv.org/content/10.1101/2020.09.17.302232v1?rss=1 Phan, H. V. van Gent, M. Drayman, N. Basu, A. Gack, M. Tay, S. 2020-09-17 doi:10.1101/2020.09.17.302232 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola ]]> https://biorxiv.org/content/10.1101/2020.09.22.307678v1?rss=1 Fontaine, M. C. Labbe, F. Dussert, Y. Deliere, L. Richart-Cervera, S. Giraud, T. Delmotte, F. 2020-09-22 doi:10.1101/2020.09.22.307678 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Primate neuronal connections are sparse as compared to mouse ]]> https://biorxiv.org/content/10.1101/2020.09.24.311852v1?rss=1 Wildenberg, G. A. Rosen, M. C. Lundell, J. Paukner, D. Freedman, D. J. Kasthuri, N. 2020-09-24 doi:10.1101/2020.09.24.311852 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ Disinhibitory circuitry gates associative synaptic plasticity in olfactory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.24.312686v1?rss=1 Canto-Bustos, M. Friason, F. K. E. Bassi, C. Oswald, A.-M. M. 2020-09-25 doi:10.1101/2020.09.24.312686 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Intrarenal B cells integrate in situ innate and adaptive immunity in human renal allograft rejection ]]> https://biorxiv.org/content/10.1101/2020.09.26.314377v1?rss=1 Asano, Y. Daccache, J. Jain, D. Ko, K. Kinloch, A. Veselits, M. Wolfgeher, D. Chang, A. Josephson, M. Cunningham, P. Tambur, A. Khan, A. Pillai, S. Chong, A. S. Clark, M. R. 2020-09-26 doi:10.1101/2020.09.26.314377 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Dscam1 promotes blood cell survival in Drosophila melanogaster through a dual role in blood cells and neurons ]]> https://biorxiv.org/content/10.1101/2020.09.26.314997v1?rss=1 Ouyang, D. Xiao, X. Mase, A. Li, G. Corcoran, S. Wang, F. Brueckner, K. 2020-09-26 doi:10.1101/2020.09.26.314997 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ Tethering-facilitated DNA 'opening' and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein ]]> https://biorxiv.org/content/10.1101/2020.09.28.313049v1?rss=1 Paul, D. Mu, H. Tavakoli, A. Dai, Q. Chen, X. Chakraborty, S. He, C. Ansari, A. Broyde, S. Min, J. H. 2020-09-29 doi:10.1101/2020.09.28.313049 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis ]]> https://biorxiv.org/content/10.1101/2020.09.28.316422v1?rss=1 Brandt, P. Sturzenegger Varvayanis, S. Baas, T. Bolgioni-Smith, A. Alder, J. Petrie, K. A. Dominguez, I. Brown, A. M. Stayart, C. A. Singh, H. Van Wart, A. Chow, C. S. Mathur, A. Schreiber, B. M. Fruman, D. A. Bowden, B. Holmquist, C. E. Arneman, D. Hall, J. D. Hyman, L. E. Gould, K. Chalkley, R. Brennwald, P. Layton, R. 2020-09-28 doi:10.1101/2020.09.28.316422 Cold Spring Harbor Laboratory Press 2020-09-28 <![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[ A sparse mapping of structure to function in microbial communities ]]> https://biorxiv.org/content/10.1101/2020.09.29.315713v1?rss=1 Gowda, K. Ping, D. Mani, M. Kuehn, S. 2020-09-30 doi:10.1101/2020.09.29.315713 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Cocaine causes rapid remodeling of dopaminergic axons, synapses, and mitochondria ]]> https://biorxiv.org/content/10.1101/2020.09.29.318881v1?rss=1 Wildenberg, G. A. Sorokina, A. M. Koranda, J. Monical, A. Heer, C. Sheffield, M. Zhuang, X. McGehee, D. S. Kasthuri, N. 2020-09-29 doi:10.1101/2020.09.29.318881 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ FANCD2 Alleviates Physiologic Replication Stress in Fetal Liver HSC ]]> https://biorxiv.org/content/10.1101/2020.09.30.320796v1?rss=1 Mochizuki-Kashio, M. Yoon, Y. m. Menna, T. Grompe, M. Kurre, P. 2020-10-01 doi:10.1101/2020.09.30.320796 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ High Throughput RNA Sequencing of Mice Retina Reveals Metabolic Pathways Involved in the Gut-Retinal Axis ]]> https://biorxiv.org/content/10.1101/2020.10.01.318949v1?rss=1 Nadeem, U. Skondra, D. Xie, B. Movahedan, A. D'Souza, M. Barba, H. Deng, N. Leonne, V. Chang, E. B. Sulakhe, D. 2020-10-02 doi:10.1101/2020.10.01.318949 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as substrates for proteolytic maturation. ]]> https://biorxiv.org/content/10.1101/2020.10.01.322081v1?rss=1 Tan, A. Pak, A. J. Morado, D. R. Voth, G. A. Briggs, J. A. G. 2020-10-01 doi:10.1101/2020.10.01.322081 Cold Spring Harbor Laboratory Press 2020-10-01 <![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[ Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture ]]> https://biorxiv.org/content/10.1101/2020.10.03.322354v1?rss=1 Bashirzadeh, Y. Redford, S. A. Lorpaiboon, C. Groaz, A. Litschel, T. Schwille, P. Hocky, G. M. Dinner, A. Liu, A. P. 2020-10-03 doi:10.1101/2020.10.03.322354 Cold Spring Harbor Laboratory Press 2020-10-03 <![CDATA[ Transcriptomic signatures of sex-specific nicotine sensitization and imprinting of self-administration in rats inform GWAS findings on human addiction phenotypes ]]> https://biorxiv.org/content/10.1101/2020.10.05.327155v1?rss=1 Kozlova, A. Butler, R. R. Zhang, S. Ujas, T. Zhang, H. Steidl, S. Sanders, A. R. Pang, Z. P. Vezina, P. Duan, J. 2020-10-06 doi:10.1101/2020.10.05.327155 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Multi-modal imaging of a single postmortem mouse brain over five orders of magnitude of resolution ]]> https://biorxiv.org/content/10.1101/2020.10.07.329789v1?rss=1 Foxley, S. Sampathkumar, V. De Andrade, V. Trinkle, S. Sorokina, A. Li, H. Norwood, K. La Riviere, P. Kasthuri, N. 2020-10-08 doi:10.1101/2020.10.07.329789 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Identification, Characterization, and Targeting of a Rare and Temporal Dendritic Cell State that Facilitates Adaptive Immune Responses ]]> https://biorxiv.org/content/10.1101/2020.10.08.331744v1?rss=1 Deak, P. E. Studnitzer, B. Steinhardt, R. Esser-Kahn, A. 2020-10-08 doi:10.1101/2020.10.08.331744 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ A general decoding strategy explains the relationship between behavior and correlated variability ]]> https://biorxiv.org/content/10.1101/2020.10.08.331850v1?rss=1 Ni, A. M. Huang, C. Doiron, B. Cohen, M. R. 2020-10-08 doi:10.1101/2020.10.08.331850 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ The coevolution of mammae number and litter size ]]> https://biorxiv.org/content/10.1101/2020.10.08.331983v1?rss=1 Stewart, T. A. Yoo, I. Upham, N. S. 2020-10-09 doi:10.1101/2020.10.08.331983 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Improved protein structure prediction by deep learning irrespective of co-evolution information ]]> https://biorxiv.org/content/10.1101/2020.10.12.336859v1?rss=1 0.5) for 26 out of 32 CASP13 FM (template-free-modeling) targets and L/5 long-range contacts for these targets with precision over 80%, a significant improvement over the CASP13 results. Although co-evolution analysis plays an important role in the most successful structure prediction methods, we show that when co-evolution is not used, our ResNet can still predict correct folds for 18 of the 32 CASP13 FM targets including several large ones. This marks a significant improvement over the top co-evolution-based, non-deep learning methods at CASP13, and other non-coevolution-based deep learning models, such as the popular recurrent geometric network (RGN). With only primary sequence, our ResNet can also predict correct folds for all 21 human-designed proteins we tested. In contrast, RGN predicts correct folds for only 3 human-designed proteins and zero CASP13 FM target. In addition, we find that ResNet may fare better for the human-designed proteins when trained without co-evolution information than with co-evolution. These results suggest that ResNet does not simply denoise co-evolution signals, but instead is able to learn important sequence-structure relationship from experimental structures. This has important implications on protein design and engineering especially when evolutionary information is not available. Availability: http://raptorx.uchicago.edu/ and https://github.com/j3xugit/RaptorX-3DModeling/ ]]> Xu, J. Mcpartlon, M. Li, J. 2020-10-12 doi:10.1101/2020.10.12.336859 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics ]]> https://biorxiv.org/content/10.1101/2020.10.15.341214v1?rss=1 View larger version (82K): org.highwire.dtl.DTLVardef@536fe5org.highwire.dtl.DTLVardef@1d72cc9org.highwire.dtl.DTLVardef@1bd5281org.highwire.dtl.DTLVardef@739512_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Delmont, T. O. Gaia, M. Hinsinger, D. D. Fremont, P. Fernandez Guerra, A. Eren, A. M. Vanni, C. Kourlaiev, A. d'Agata, L. Clayssen, Q. Villar, E. Labadie, K. Cruaud, C. Poulain, J. Da Silva, C. Wessner, M. Noel, B. Aury, J.-M. Coordinators, T. O. de Vargas, C. Bowler, C. Karsenti, E. Pelletier, E. Wincker, P. Jaillon, O. 2020-10-16 doi:10.1101/2020.10.15.341214 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Interaction Landscape of K29-Linked Ubiquitin Signaling Revealed by a Linkage-Specific Synthetic Antigen-Binding Fragment ]]> https://biorxiv.org/content/10.1101/2020.10.15.341719v1?rss=1 Yu, Y. Zheng, Q. Erramilli, S. K. Pan, M. Park, S. Xie, Y. Li, J. Fei, J. Kossiakoff, A. A. Liu, L. Zhao, M. 2020-10-15 doi:10.1101/2020.10.15.341719 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Behavioral and brain signatures of substance use vulnerability in childhood ]]> https://biorxiv.org/content/10.1101/2020.10.19.346403v1?rss=1 1,500), functional connectivity during rest and task conditions (resting-state; monetary incentive delay task; stop signal task; emotional n-back task) significantly predicted individual differences in risk-seeking (PC1) in held-out participants (partial correlations between predicted and observed scores controlling for motion and number of frames [rp]: 0.07-0.21). By contrast, functional connectivity was a weak predictor of familial risk factors associated with substance use (PC2) (rp: 0.03-0.06). These results demonstrate a novel approach to understanding substance use vulnerability, which--together with mechanistic perspectives--may inform strategies aimed at early identification of risk for addiction. ]]> Rapuano, K. M. Rosenberg, M. D. Maza, M. T. Dennis, N. Dorji, M. Greene, A. S. Horien, C. Scheinost, D. Constable, R. T. Casey, B. 2020-10-21 doi:10.1101/2020.10.19.346403 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations ]]> https://biorxiv.org/content/10.1101/2020.10.19.346445v1?rss=1 Khomtchouk, B. B. Vand, K. A. Nelson, C. S. Palmisano, S. Grossman, R. L. 2020-10-21 doi:10.1101/2020.10.19.346445 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The Abelson tyrosine kinase and the Nedd4-family ubiquitin ligase Suppressor of Deltex converge at the Notch PPxY motif to regulate endosomal trafficking and signaling ]]> https://biorxiv.org/content/10.1101/2020.10.20.347468v1?rss=1 Sanchez-Luege, N. Miranda-Alban, J. Sun, X. Valbuena, F. M. Glick, B. S. Rebay, I. 2020-10-23 doi:10.1101/2020.10.20.347468 Cold Spring Harbor Laboratory Press 2020-10-23 <![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[ Histone H2A ubiquitination resulting from Brap loss of function connects multiple aging hallmarks and accelerates neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.10.22.341784v1?rss=1 Guo, Y. Chomiak, A. A. Hong, Y. Lowe, C. C. Chan, W.-C. Andrade, J. Pan, H. Zhou, X. Berezovski, E. Monuki, E. S. Feng, Y. 2020-10-22 doi:10.1101/2020.10.22.341784 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Morphological and phylogeographic evidence for budding speciation: an example in hominins ]]> https://biorxiv.org/content/10.1101/2020.10.23.351114v1?rss=1 Parins-Fukuchi, C. 2020-10-23 doi:10.1101/2020.10.23.351114 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease ]]> https://biorxiv.org/content/10.1101/2020.10.26.356048v1?rss=1 Liu, G. Lee, J.-H. Parker, Z. M. Acharya, D. Chiang, J. J. van Gent, M. Riedl, W. Davis-Gardner, M. E. Wies, E. Chiang, C. Gack, M. U. 2020-10-27 doi:10.1101/2020.10.26.356048 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Codon usage bias levels predict taxonomic identity and genetic composition ]]> https://biorxiv.org/content/10.1101/2020.10.26.356295v1?rss=1 Khomtchouk, B. B. 2020-10-27 doi:10.1101/2020.10.26.356295 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ New Genes in Drosophila Quickly Evolved Essential Functions in Viability During Development ]]> https://biorxiv.org/content/10.1101/2020.10.27.357848v1?rss=1 Xia, S. VanKuren, N. W. Chen, C. Zhang, L. Kemkemer, C. Shao, Y. Jia, H. Lee, U. Advani, A. S. Gschwend, A. Vibranovski, M. Chen, S. Zhang, Y. E. Long, M. 2020-10-27 doi:10.1101/2020.10.27.357848 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Bacterial microcompartments linked to the flavin-based extracellular electron transfer drives anaerobic ethanolamine utilization in Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/2020.10.27.358424v1?rss=1 Zeng, Z. Boeren, S. Bhandula, V. Light, S. Smid, E. J. Notebaart, R. A. Abee, T. 2020-10-28 doi:10.1101/2020.10.27.358424 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes ]]> https://biorxiv.org/content/10.1101/2020.10.28.359240v1?rss=1 Ansari-Pour, N. Zheng, Y. Pitt, J. J. Dentro, S. Yoshimatsu, T. F. Sanni, A. Ajani, M. Woodard, A. Rajagopal, P. S. Fitzgerald, D. Gruber, A. J. Odetunde, A. Popoola, A. Falusi, A. G. Babalola, C. P. Ogundiran, T. Obafunwa, J. Ojengbede, O. Ibrahim, N. Barretina, J. Van Loo, P. Chen, M. White, K. P. Huo, D. Wedge, D. C. Olopade, O. I. 2020-10-28 doi:10.1101/2020.10.28.359240 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Discovering plasmids in metagenomes based on genetic architecture ]]> https://biorxiv.org/content/10.1101/2020.11.01.361691v1?rss=1 Yu, M. K. Fogarty, E. C. Eren, A. M. 2020-11-01 doi:10.1101/2020.11.01.361691 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Kinetic model of small RNA-mediated regulation suggests that a small RNA can regulate co-transcriptionally ]]> https://biorxiv.org/content/10.1101/2020.11.03.365106v1?rss=1 Reyer, M. A. Chennakesavalu, S. Heideman, E. M. Ma, X. Bujnowska, M. Hong, L. Dinner, A. R. Vanderpool, C. K. Fei, J. 2020-11-03 doi:10.1101/2020.11.03.365106 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ N6-methyladenosine modification of HIV-1 RNA evades RIG-I-mediated sensing to suppresses type-I interferon induction in monocytic cells ]]> https://biorxiv.org/content/10.1101/2020.11.04.368712v1?rss=1 Chen, S. Kumar, S. Tirumuru, N. Welch, J. L. Hu, L. He, C. Stapleton, J. T. Wu, L. 2020-11-04 doi:10.1101/2020.11.04.368712 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Phylogenomic conflict coincides with rapid morphological innovation ]]> https://biorxiv.org/content/10.1101/2020.11.04.368902v1?rss=1 Parins-Fukuchi, C. Stull, G. W. Smith, S. A. 2020-11-05 doi:10.1101/2020.11.04.368902 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding ]]> https://biorxiv.org/content/10.1101/2020.11.05.368969v1?rss=1 Wang, K. Stevens, R. Alachram, H. Li, Y. Soldatova, L. King, R. Ananiadou, S. Li, M. Christopoulou, F. Ambite, J. L. Garg, S. Hermjakob, U. Marcu, D. Sheng, E. Beissbarth, T. Wingender, E. Galstyan, A. Gao, X. Chambers, B. Khomtchouk, B. B. Evans, J. A. Rzhetsky, A. 2020-11-06 doi:10.1101/2020.11.05.368969 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Development of Targetable Multi-Drug Nanoparticles for Glioblastoma Treatment and In Vitro Evaluation in Glioblastoma Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.11.08.373696v1?rss=1 Smiley, S. B. Yun, Y. Ayyagari, P. Shannon, H. E. Pollok, K. E. Vannier, M. W. Das, S. K. Veronesi, M. C. 2020-11-09 doi:10.1101/2020.11.08.373696 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities. ]]> https://biorxiv.org/content/10.1101/2020.11.09.375451v1?rss=1 Heinken, A. Acharya, G. Ravcheev, D. A. Hertel, J. Nyga, M. Okpala, O. E. Hogan, M. Magnusdottir, S. Martinelli, F. Preciat, G. Edirisinghe, J. N. Henry, C. S. Fleming, R. M. T. Thiele, I. 2020-11-10 doi:10.1101/2020.11.09.375451 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu ]]> https://biorxiv.org/content/10.1101/2020.11.10.375675v1?rss=1 Goods, B. A. Askenase, M. H. Markarian, E. Beatty, H. E. Drake, R. Fleming, I. DeLong, J. H. Philip, N. H. Matouk, C. C. Awad, I. A. Zuccarello, M. Hanley, D. F. Love, J. C. Shalek, A. K. Sansing, L. H. 2020-11-12 doi:10.1101/2020.11.10.375675 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ 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[ Longitudinal characterization of phenotypic profile of T cells in chronic hepatitis B identifies immune markers predicting HBsAg loss ]]> https://biorxiv.org/content/10.1101/2020.11.16.382838v1?rss=1 Xiong, S. Zhu, D. Liang, B. Li, M. Pan, W. He, J. Wang, H. Kathrin, S. Ulf, D. Lu, M. Liu, D. Yang, D. Liu, J. Zheng, X. 2020-11-17 doi:10.1101/2020.11.16.382838 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Recurrent circuit based neural population codes for stimulus representation and inference ]]> https://biorxiv.org/content/10.1101/2020.11.18.389197v1?rss=1 Zhang, W. Wu, S. Josic, K. Doiron, B. 2020-11-20 doi:10.1101/2020.11.18.389197 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Metabolic profile discriminates and predicts Arabidopsis susceptibility to virus under field conditions ]]> https://biorxiv.org/content/10.1101/2020.11.21.392688v1?rss=1 Rubio, B. Fernandez, O. Cosson, P. Berton, T. Caballero, M. Roux, F. Bergelson, J. Gibon, Y. Schurdi-Levraud, V. 2020-11-22 doi:10.1101/2020.11.21.392688 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Prefrontal cortical activity predicts the extra-place field spiking of hippocampal place cells ]]> https://biorxiv.org/content/10.1101/2020.11.23.395012v1?rss=1 Yu, J. Y. Frank, L. 2020-11-24 doi:10.1101/2020.11.23.395012 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning ]]> https://biorxiv.org/content/10.1101/2020.11.26.400523v1?rss=1 Li, J. Xu, J. 2020-11-27 doi:10.1101/2020.11.26.400523 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Reframing Fouquieria splendens in its larger environmental and ecological context: Effect of topography and interspecific neighbors on ocotillo morphology and distribution ]]> https://biorxiv.org/content/10.1101/2020.11.28.397018v1?rss=1 Bernat, A. Tang, A. T. S. Steenson, A. Larsen, E. 2020-11-28 doi:10.1101/2020.11.28.397018 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ FiberAI: A Deep Learning model for automated analysis of nascent DNA Fibers ]]> https://biorxiv.org/content/10.1101/2020.11.28.397430v1?rss=1 Mohsin, A. Arnovitz, S. Khan, A. A. Gounari, F. 2020-11-28 doi:10.1101/2020.11.28.397430 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ A Neutralizing Antibody-Conjugated Photothermal Nanoparticle Captures and Inactivates SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.11.30.404624v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@44a5a8org.highwire.dtl.DTLVardef@d7bcd5org.highwire.dtl.DTLVardef@1ae6e70org.highwire.dtl.DTLVardef@d4a4f5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cai, X. Prominski, A. Lin, Y. Ankenbruck, N. Rosenberg, J. Chen, M. Shi, J. Chang, E. B. Penaloza-MacMaster, P. Tian, B. Huang, J. 2020-11-30 doi:10.1101/2020.11.30.404624 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ CXCR6 governs the retention of tissue-resident memory T cells to promote enhanced surveillance and control of ovarian cancer ]]> https://biorxiv.org/content/10.1101/2020.12.02.401729v1?rss=1 Muthuswamy, R. McGray, A. R. Battaglia, S. He, W. Miliotto, A. Eppolito, C. A. Litchy, B. D. Shrikant, P. Odunsi, K. 2020-12-02 doi:10.1101/2020.12.02.401729 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Circulating ACE2-expressing Exosomes Block SARS-CoV-2 Virus Infection as an Innate Antiviral Mechanism ]]> https://biorxiv.org/content/10.1101/2020.12.03.407031v1?rss=1 El-Shennawy, L. Hoffmann, A. D. Dashzeveg, N. K. Mehl, P. J. Yu, Z. Tokars, V. L. Nicolaescu, V. Ostiguin, C. Jia, Y. Li, L. Furlong, K. Mao, C. Wysocki, J. Batlle, D. Hope, T. J. Shen, Y. Luo, Y. Chae, Y. Zhang, H. Swaminathan, S. Randall, G. C. Demonbreun, A. R. Ison, M. G. Fang, D. Liu, H. 2020-12-04 doi:10.1101/2020.12.03.407031 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ The Impact of Digital Histopathology Batch Effect on Deep Learning Model Accuracy and Bias ]]> https://biorxiv.org/content/10.1101/2020.12.03.410845v1?rss=1 Howard, F. M. Dolezal, J. Kochanny, S. Schulte, J. Chen, H. Heij, L. Huo, D. Nanda, R. Olopade, O. I. Kather, J. Grossman, R. Pearson, A. T. 2020-12-04 doi:10.1101/2020.12.03.410845 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia ]]> https://biorxiv.org/content/10.1101/2020.12.04.411215v1?rss=1 Richter, W. F. Shah, R. N. Ruthenburg, A. J. 2020-12-04 doi:10.1101/2020.12.04.411215 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Swallowing-related neural oscillation: An intracranial EEG study ]]> https://biorxiv.org/content/10.1101/2020.12.05.412783v1?rss=1 Hashimoto, H. Takahashi, K. Kameda, S. Yoshida, F. Maezawa, H. Oshino, S. Tani, N. Khoo, H. M. Yanagisawa, T. Yoshimine, T. Kishima, H. Hirata, M. 2020-12-07 doi:10.1101/2020.12.05.412783 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis ]]> https://biorxiv.org/content/10.1101/2020.12.05.413229v1?rss=1 Suresh, B. Saminathan, A. Chakraborty, K. Cui, C. Becker, L. Krishnan, Y. 2020-12-06 doi:10.1101/2020.12.05.413229 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ NEONATAL THYROXINE ACTIVATION MODIFIES EPIGENETIC PROGRAMMING OF THE LIVER ]]> https://biorxiv.org/content/10.1101/2020.12.07.414938v1?rss=1 Fonseca, T. L. Garcia, T. Fernandes, G. W. Nair, T. M. Bianco, A. C. 2020-12-08 doi:10.1101/2020.12.07.414938 Cold Spring Harbor Laboratory Press 2020-12-08 <![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[ Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection ]]> https://biorxiv.org/content/10.1101/2020.12.21.423830v1?rss=1 Randolph, H. E. Mu, Z. Fiege, J. K. Thielen, B. K. Grenier, J.-C. Cobb, M. S. Hussin, J. G. Li, Y. I. Langlois, R. A. Barreiro, L. B. 2020-12-21 doi:10.1101/2020.12.21.423830 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Frequency-dependent competition between strains imparts resilience to perturbations in a model of Plasmodium falciparum malaria transmission. ]]> https://biorxiv.org/content/10.1101/2020.12.22.423749v1?rss=1 He, Q. Pilosof, S. Tiedje, K. E. Day, K. Pascual, M. 2020-12-22 doi:10.1101/2020.12.22.423749 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Cysteine biosynthesis is a determinant of Brucella ovis stress survival and fitness in the intracellular niche ]]> https://biorxiv.org/content/10.1101/2020.12.22.424080v1?rss=1 Varesio, L. Fiebig, A. Crosson, S. 2020-12-23 doi:10.1101/2020.12.22.424080 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ A cognitive state transformation model for task-general and task-specific subsystems of the brain connectome ]]> https://biorxiv.org/content/10.1101/2020.12.23.424176v1?rss=1 Yoo, K. Rosenberg, M. D. Kwon, Y. H. Scheinost, D. Constable, R. T. Chun, M. M. 2020-12-24 doi:10.1101/2020.12.23.424176 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Nanowires unravel a time-correlated stochastic vectorial process in cells ]]> https://biorxiv.org/content/10.1101/2020.12.24.424270v1?rss=1 Nair, V. Seebald, M. 2020-12-24 doi:10.1101/2020.12.24.424270 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions ]]> https://biorxiv.org/content/10.1101/2020.12.25.424401v1?rss=1 Liu, B. Shi, H. Rangadurai, A. Nussbaumer, F. Chu, C.-C. Erharter, K. A. Case, D. A. Kreutz, C. Al-Hashimi, H. M. 2020-12-26 doi:10.1101/2020.12.25.424401 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ Model-based Trajectory Inference for Single-Cell RNA Sequencing Using Deep Learning with a Mixture Prior ]]> https://biorxiv.org/content/10.1101/2020.12.26.424452v1?rss=1 Du, J.-H. Gao, M. Wang, J. 2020-12-30 doi:10.1101/2020.12.26.424452 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Why sensory neurons are tuned to multiple stimulus features ]]> https://biorxiv.org/content/10.1101/2020.12.29.424235v1?rss=1 Macellaio, M. V. Liu, B. Beck, J. M. Osborne, L. C. 2020-12-30 doi:10.1101/2020.12.29.424235 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Intergenerational microbial transmission in the little skate (Leucoraja erinacea) ]]> https://biorxiv.org/content/10.1101/2020.12.30.424594v1?rss=1 Mika, K. Okamoto, A. S. Shubin, N. Mark Welch, D. B. 2020-12-30 doi:10.1101/2020.12.30.424594 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Going beyond rote auditory learning: Neural patterns of generalized auditory learning ]]> https://biorxiv.org/content/10.1101/2020.12.30.424903v1?rss=1 Heald, S. L. Van Hedger, S. C. Veillette, J. Reis, K. Snyder, J. S. 2021-01-02 doi:10.1101/2020.12.30.424903 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ 12-Lipoxygenase Governs the Innate Immune Pathogenesis of Islet Inflammation and Autoimmune Diabetes ]]> https://biorxiv.org/content/10.1101/2021.01.02.424855v1?rss=1 Kulkarni, A. Pineros, A. R. Ibrahim, S. Hernandez-Perez, M. Orr, K. S. Glenn, L. Walsh, M. Nadler, J. L. Morris, M. A. Tersey, S. A. Mirmira, R. G. Anderson, R. M. 2021-01-04 doi:10.1101/2021.01.02.424855 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Dia1 Coordinates Differentiation and Cell Sorting in a Stratified Epithelium ]]> https://biorxiv.org/content/10.1101/2021.01.04.425231v1?rss=1 Harmon, R. M. Devany, J. Gardel, M. 2021-01-04 doi:10.1101/2021.01.04.425231 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Functionality of the putative surface glycoproteins of the Wuhan spiny eel influenza virus ]]> https://biorxiv.org/content/10.1101/2021.01.04.425274v1?rss=1 Arunkumar, G. A. Strohmeier, S. Li, T. Bhavsar, D. Chromikova, V. Amanat, F. Bunyatov, M. Wilson, P. C. Ellebedy, A. Boons, G.-J. Simon, V. de Vries, R. P. Krammer, F. 2021-01-04 doi:10.1101/2021.01.04.425274 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Widespread bacterial protein flavinylation in functionally distinct extracytosolic redox biochemistries ]]> https://biorxiv.org/content/10.1101/2021.01.07.425746v1?rss=1 Méheust, R. Huang, S. Rivera-Lugo, R. Banfield, J. Light, S. H. 2021-01-07 doi:10.1101/2021.01.07.425746 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs ]]> https://biorxiv.org/content/10.1101/2021.01.10.426065v1?rss=1 Chen, C. Liu, W. Guo, J. Liu, Y. Liu, X. Liu, J. Dou, X. Le, R. Huang, Y. Li, C. Yang, L. Kou, X. Zhao, Y. Wu, Y. Chen, J. Wang, H. Shen, B. Gao, Y. Gao, S. 2021-01-11 doi:10.1101/2021.01.10.426065 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Restored TDCA and Valine Levels Imitate the Effects of Bariatric Surgery ]]> https://biorxiv.org/content/10.1101/2021.01.11.425291v1?rss=1 Tullius, S. G. Quante, M. Iske, J. Heinbokel, T. Desai, B. N. Biefer, H. R. C. Nian, Y. Krenzien, F. Uehara, H. Maenosono, R. Azuma, H. Pratschke, J. Falk, C. Lo, T. Sheu, E. Tavakkoli, A. Perkins, D. Alegre, M.-L. Banks, A. S. Elkhal, A. 2021-01-12 doi:10.1101/2021.01.11.425291 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Gating current noise produced by Brownian models of a voltage sensor ]]> https://biorxiv.org/content/10.1101/2021.01.13.426543v1?rss=1 Catacuzzeno, L. Franciolini, F. Francisco, B. Eisenberg, R. 2021-01-13 doi:10.1101/2021.01.13.426543 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ SARS-CoV-2 infection reduces Krüppel-Like Factor 2 in human lung autopsy ]]> https://biorxiv.org/content/10.1101/2021.01.15.426691v1?rss=1 Lee, T.-H. Wu, D. Guzy, R. Schoettler, N. Adegunsoye, A. Mueller, J. Hussein, A. Sperling, A. Mutlu, G. M. Fang, Y. 2021-01-18 doi:10.1101/2021.01.15.426691 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Pupillometry signatures of sustained attention and working memory ]]> https://biorxiv.org/content/10.1101/2021.01.18.426969v1?rss=1 Keene, P. A. deBettencourt, M. T. Awh, E. Vogel, E. K. 2021-01-20 doi:10.1101/2021.01.18.426969 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Large lakes harbor streamlined free-living nitrifiers ]]> https://biorxiv.org/content/10.1101/2021.01.19.427344v1?rss=1 Podowski, J. C. Paver, S. F. Newton, R. J. Coleman, M. 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Mann, F. G. Lange, J. J. Seidel, C. Sanchez Alvarado, A. 2021-01-26 doi:10.1101/2021.01.24.427972 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Perceptual Weighting of V1 Spikes Revealed by Optogenetic White Noise Stimulation ]]> https://biorxiv.org/content/10.1101/2021.01.25.428138v1?rss=1 Day-Cooney, J. R. Cone, J. J. Maunsell, J. H. 2021-01-26 doi:10.1101/2021.01.25.428138 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions ]]> https://biorxiv.org/content/10.1101/2021.01.29.428868v1?rss=1 Findley, A. S. Monziani, A. Richards, A. L. Rhodes, K. Ward, M. C. Kalita, C. A. Alazizi, A. Pazokitoroudi, A. Sankararaman, S. Wen, X. Lanfear, D. E. Pique-Regi, R. Gilad, Y. Luca, F. 2021-01-31 doi:10.1101/2021.01.29.428868 Cold Spring Harbor Laboratory Press 2021-01-31 <![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[ A neuronal social trait space for first impressions in the human amygdala and hippocampus ]]> https://biorxiv.org/content/10.1101/2021.01.30.428973v1?rss=1 Cao, R. Lin, C. Li, X. Todorov, A. Brandmeir, N. Wang, S. 2021-01-30 doi:10.1101/2021.01.30.428973 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Kinesin-3 and kinesin-1 motors direct basement membrane protein secretion to a basal sub-region of the basolateral plasma membrane in epithelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.31.429062v1?rss=1 Zajac, A. L. Horne-Badovinac, S. 2021-02-01 doi:10.1101/2021.01.31.429062 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Nanotraps for the containment and clearance of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.02.01.428871v1?rss=1 Chen, M. Rosenberg, J. Cai, X. Lee, A. C. H. Shi, J. Nguyen, M. Wignakumar, T. Mirle, V. Edobor, A. J. Fung, J. Donington, J. S. Shanmugarajah, K. Chang, E. B. Randall, G. Penaloza-MacMaster, P. Tian, B. Madariaga, M. L. Huang, J. 2021-02-01 doi:10.1101/2021.02.01.428871 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning ]]> https://biorxiv.org/content/10.1101/2021.02.02.429064v1?rss=1 Lai, B. Qian, S. Zhang, H. Zhang, S. Kozlova, A. Duan, J. Xu, J. He, X. 2021-02-02 doi:10.1101/2021.02.02.429064 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Defining a Connectome-Based Predictive Model of Attentional Control in Aging ]]> https://biorxiv.org/content/10.1101/2021.02.02.429232v1?rss=1 Fountain-Zaragoza, S. Manglani, H. R. Rosenberg, M. D. Andridge, R. Prakash, R. S. 2021-02-03 doi:10.1101/2021.02.02.429232 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Redefining tumor classification and clinical stratification through a colorectal cancer single-cell atlas ]]> https://biorxiv.org/content/10.1101/2021.02.02.429256v1?rss=1 Khaliq, A. M. kurt, z. Grunvald, M. W. Erdogan, C. Turgut, S. S. Rand, T. Khare, S. Borgia, J. A. Hayden, D. M. Pappas, S. G. Govekar, H. R. Bhama, A. R. Singh, A. Jacobson, R. A. Kam, A. E. Zloza, A. Reiser, J. Catenacci, D. V. Turaga, K. Radovich, M. Thyparambil, S. Levy, M. A. Subramanian, J. Kuzel, T. M. Sadanandam, A. Hussain, A. El-Rayes, B. Salahudeen, A. Masood, A. 2021-02-03 doi:10.1101/2021.02.02.429256 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Knockdown of Dnmt1 links Gene body DNA methylation to regulation of gene expression and maternal-zygotic transition in the wasp Nasonia ]]> https://biorxiv.org/content/10.1101/2021.02.02.429402v1?rss=1 Arsala, D. Wu, X. Yi, S. V. Lynch, J. A. 2021-02-02 doi:10.1101/2021.02.02.429402 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology ]]> https://biorxiv.org/content/10.1101/2021.02.07.430149v1?rss=1 McCord, C. L. Cooper, W. J. Nash, C. M. Westneat, M. W. 2021-02-08 doi:10.1101/2021.02.07.430149 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Mechanistic insight into substrate processing and allosteric inhibition of human p97 ]]> https://biorxiv.org/content/10.1101/2021.02.08.430295v1?rss=1 Pan, M. Yu, Y. Ai, H. Zheng, Q. Xie, Y. Liu, L. Zhao, M. 2021-02-08 doi:10.1101/2021.02.08.430295 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ CCG*CGG interruptions in high penetrance SCA8 families increase RAN translation and protein toxicity ]]> https://biorxiv.org/content/10.1101/2021.02.08.430311v1?rss=1 Perez, B. A. Shorrock, H. K. Banez-Coronel, M. Laboissonniere, L. A. Reid, T. Ikeda, Y. Reddy, K. Gomez, C. M. Bird, T. Ashizawa, T. Schut, L. J. Brusco, A. Berglund, A. Hasholt, L. F. Nielsen, J. E. Subramony, S. H. Ranum, L. P. W. 2021-02-10 doi:10.1101/2021.02.08.430311 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Crystal structure of a bacterial CNNM magnesium transporter ]]> https://biorxiv.org/content/10.1101/2021.02.11.430706v1?rss=1 Chen, Y. S. Kozlov, G. Armitano, J. Moeller, B. J. Fakih, R. Rohaim, A. Roux, B. Burke, J. E. Gehring, K. 2021-02-11 doi:10.1101/2021.02.11.430706 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ A brain-based universal measure of attention: predicting task-general and task-specific attention performance and their underlying neural mechanisms from task and resting state fMRI ]]> https://biorxiv.org/content/10.1101/2021.02.13.431091v1?rss=1 Yoo, K. Rosenberg, M. D. Kwon, Y. H. Avery, E. W. Lin, Q. Scheinost, D. Constable, R. T. Chun, M. M. 2021-02-16 doi:10.1101/2021.02.13.431091 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ A tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases ]]> https://biorxiv.org/content/10.1101/2021.02.16.430825v1?rss=1 Simonovsky, E. Sharon, M. Ziv, M. Mauer, O. Hekselman, I. Jubran, J. Vinogradov, E. Argov, C. M. Basha, O. Kerber, L. Yogev, Y. Segre, A. Im, H. K. GTEx Consortium, Birk, O. Rokach, L. Yeger-Lotem, E. 2021-02-17 doi:10.1101/2021.02.16.430825 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[ Indoleamine 2,3-dioxygenase upregulates PD-1 expression on ovarian tumor infiltrating CD8+ T cells via kynurenine activation of the aryl hydrocarbon receptor ]]> https://biorxiv.org/content/10.1101/2021.02.18.431473v1?rss=1 Amobi-McCloud, A. MUTHUSWAMY, R. Battaglia, S. Yu, H. Liu, T. Wang, J. Putluri, V. Singh, P. K. Qian, F. Huang, R.-Y. Putluri, N. Takemasa, T. Lugade, A. Liu, S. Odunsi, K. 2021-02-18 doi:10.1101/2021.02.18.431473 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies ]]> https://biorxiv.org/content/10.1101/2021.02.18.431725v1?rss=1 Ofer, N. Berger, D. R. Kasthuri, N. Lichtman, J. W. Yuste, R. 2021-02-18 doi:10.1101/2021.02.18.431725 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ A Protein A based Staphylococcus aureus vaccine with improved safety ]]> https://biorxiv.org/content/10.1101/2021.02.19.432007v1?rss=1 Shi, M. Chen, X. Sun, Y. Kim, H. K. Schneewind, O. Missiakas, D. M. 2021-02-19 doi:10.1101/2021.02.19.432007 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Characterizing gene expression responses to biomechanical strain in an in vitro model of osteoarthritis ]]> https://biorxiv.org/content/10.1101/2021.02.22.432314v1?rss=1 Hung, A. Housman, G. Briscoe, E. Cuevas, C. Gilad, Y. 2021-02-22 doi:10.1101/2021.02.22.432314 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Pulsatile contractions and pattern formation in excitable active gels ]]> https://biorxiv.org/content/10.1101/2021.02.22.432369v1?rss=1 Staddon, M. F. Munro, E. Banerjee, S. 2021-02-23 doi:10.1101/2021.02.22.432369 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Targeted comodulation supports flexible and accurate decoding in V1 ]]> https://biorxiv.org/content/10.1101/2021.02.23.432351v1?rss=1 Haimerl, C. Ruff, D. A. Cohen, M. R. Savin, C. Simoncelli, E. P. 2021-02-23 doi:10.1101/2021.02.23.432351 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Chronic wireless neural population recordings with common marmosets ]]> https://biorxiv.org/content/10.1101/2021.02.25.432889v1?rss=1 Walker, J. Pirschel, F. Sundiang, M. Niekrasz, M. MacLean, J. N. Hatsopoulos, N. 2021-02-27 doi:10.1101/2021.02.25.432889 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ A public broadly neutralizing antibody class targets a membrane-proximal anchor epitope of influenza virus hemagglutinin ]]> https://biorxiv.org/content/10.1101/2021.02.25.432905v1?rss=1 Guthmiller, J. J. Han, J. Utset, H. A. Li, L. Lan, L. Y.-L. Henry, C. Stamper, C. T. Stovicek, O. Gentles, L. Dugan, H. L. Zheng, N.-Y. Richey, S. T. Tepora, M. E. Bitar, D. J. Changrob, S. Strohmeier, S. Huang, M. Garcia-Sastre, A. Nachbagauer, R. Palese, P. Bloom, J. D. Krammer, F. Coughlan, L. Ward, A. B. Wilson, P. C. 2021-02-27 doi:10.1101/2021.02.25.432905 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma. ]]> https://biorxiv.org/content/10.1101/2021.02.25.432934v1?rss=1 Pan, M. Wright, C. Chapple, R. Zubair, A. Sandhu, M. Batchelder, J. Low, J. Blankenship, K. Wang, L. Gordon, B. Archer, P. Brady, S. W. Natarajan, S. Pozsgai, M. Schuetz, J. Miller, D. Kalathur, R. chen, s. Connelly, P. Babu, M. Dyer, M. A. Pruett-Miller, S. M. Freeman, B. Chen, T. Godley, L. Blanchard, S. Stewart, E. Easton, J. Geeleher, P. 2021-02-25 doi:10.1101/2021.02.25.432934 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Asymmetric Contraction of Adherens Junctions arises through RhoA and E-cadherin feedback ]]> https://biorxiv.org/content/10.1101/2021.02.26.433093v1?rss=1 Cavanaugh, K. Staddon, M. Chmiel, T. A. Harmon, R. M. Budnar, S. Yap, A. S. Banerjee, S. Gardel, M. 2021-02-26 doi:10.1101/2021.02.26.433093 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Novel epitopes of human monoclonal antibodies targeting the influenza virus N1 neuraminidase ]]> https://biorxiv.org/content/10.1101/2021.02.26.433142v1?rss=1 Kirkpatrick Roubidoux, E. McMahon, M. Carreno, J. M. Capuano, C. Jiang, K. Simon, V. van Bakel, H. Wilson, P. Krammer, F. 2021-02-27 doi:10.1101/2021.02.26.433142 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo ]]> https://biorxiv.org/content/10.1101/2021.03.01.433447v1?rss=1 Smith, J. J. Xiao, Y. Pars, N. Martinez, M. A. Q. Moore, F. E. Q. Palmisano, N. J. Kohrman, A. Q. Delos Reyes, M. C. Adikes, R. C. Medwig-Kinney, T. N. N. Liu, S. Bracht, S. Zhang, W. Wen, K. Kratsios, P. Matus, D. Q. 2021-03-02 doi:10.1101/2021.03.01.433447 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut ]]> https://biorxiv.org/content/10.1101/2021.03.02.433653v1?rss=1 Watson, A. R. Fuessel, J. Veseli, I. DeLongchamp, J. Z. Silva, M. Trigodet, F. Lolans, K. Shaiber, A. Fogarty, E. Quince, C. Yu, M. K. Soylev, A. Morrison, H. G. Lee, S. T. M. Rubin, D. T. Jabri, B. Louie, T. Eren, A. M. 2021-03-03 doi:10.1101/2021.03.02.433653 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes ]]> https://biorxiv.org/content/10.1101/2021.03.03.433801v1?rss=1 Trigodet, F. Lolans, K. Fogarty, E. Shaiber, A. Morrison, H. Barreiro, L. Jabri, B. Eren, A. M. 2021-03-03 doi:10.1101/2021.03.03.433801 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Tissue specific targeting of DNA nanodevices in a multicellular living organism ]]> https://biorxiv.org/content/10.1101/2021.03.05.434169v1?rss=1 Krishnan, Y. Chakraborty, K. Surana, S. Martin, S. Aburas, J. Moutel, S. Perez, F. Koushika, S. P. Kratsios, P. 2021-03-06 doi:10.1101/2021.03.05.434169 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Molecular and Structural Basis of Olfactory Sensory Neuron Coalescence by Kirrel Receptors ]]> https://biorxiv.org/content/10.1101/2021.03.09.434456v1?rss=1 Wang, J. Vaddadi, N. Pak, J. S. Park, Y. Quilez, S. Roman, C. A. Dumontier, E. Thornton, J. W. Cloutier, J.-F. Özkan, E. 2021-03-09 doi:10.1101/2021.03.09.434456 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples ]]> https://biorxiv.org/content/10.1101/2021.03.09.434660v1?rss=1 Nadel, B. Oliva, M. Shou, B. L. Mitchell, K. Ma, F. Montoya, D. J. Mouton, A. Kim-Hellmuth, S. Stranger, B. Pellegrini, M. Mangul, S. 2021-03-10 doi:10.1101/2021.03.09.434660 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Ecophysiology of the cosmopolitan OM252 bacterioplankton (Gammaproteobacteria) ]]> https://biorxiv.org/content/10.1101/2021.03.09.434695v1?rss=1 Savoie, E. R. Lanclos, V. C. Henson, M. Cheng, C. Getz, E. W. Barnes, S. J. LaRowe, D. E. Rappe, M. S. Thrash, J. C. 2021-03-10 doi:10.1101/2021.03.09.434695 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response ]]> https://biorxiv.org/content/10.1101/2021.03.10.432967v1?rss=1 Nguyen, L. C. Yang, D. Nicolaescu, V. Best, T. Chen, S. Friesen, J. B. Drayman, N. Mohamed, A. Dann, C. Silva, D. Gula, H. Jones, K. A. Millis, J. M. Dickinson, B. C. Tay, S. Oakes, S. A. Pauli, G. F. Meltzer, D. O. Randall, G. Rosner, M. R. 2021-03-10 doi:10.1101/2021.03.10.432967 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.03.12.435191v1?rss=1 Hassler, L. Wysocki, J. Gelarden, I. Tomatsidou, A. Nicoleascu, V. Randall, G. Henkin, J. Yeldandi, A. Batlle, D. 2021-03-15 doi:10.1101/2021.03.12.435191 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms ]]> https://biorxiv.org/content/10.1101/2021.03.13.435279v1?rss=1 Stull, G. W. Qu, X.-J. Parins-Fukuchi, C. Yang, Y.-Y. Yang, J.-B. Yang, Z.-Y. Hu, Y. Ma, H. Soltis, P. S. Soltis, D. E. Li, D.-Z. Smith, S. A. Yi, T.-S. 2021-03-15 doi:10.1101/2021.03.13.435279 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ A signature of Neanderthal introgression on molecular mechanisms of environmental responses ]]> https://biorxiv.org/content/10.1101/2021.03.15.435179v1?rss=1 Findley, A. Zhang, X. Boye, C. Lin, Y.-L. Kalita, C. Barreiro, L. Lohmueller, K. E. Pique-Regi, R. Luca, F. 2021-03-15 doi:10.1101/2021.03.15.435179 Cold Spring Harbor Laboratory Press 2021-03-15 <![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[ An egg-derived sulfated N-Acetyllactosamine glycan is an antigenic decoy of influenza virus vaccines ]]> https://biorxiv.org/content/10.1101/2021.03.16.435673v1?rss=1 Guthmiller, J. J. Utset, H. A. Henry, C. Li, L. Zheng, N.-Y. Sun, W. Vieira, M. C. Zost, S. Huang, M. Hensley, S. E. Cobey, S. Palese, P. Wilson, P. C. 2021-03-16 doi:10.1101/2021.03.16.435673 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Actin filament alignment causes mechanical hysteresis in cross-linked networks ]]> https://biorxiv.org/content/10.1101/2021.03.16.435707v1?rss=1 Scheff, D. R. Redford, S. A. Lorpaiboon, C. Majumdar, S. Dinner, A. R. Gardel, M. L. 2021-03-17 doi:10.1101/2021.03.16.435707 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease ]]> https://biorxiv.org/content/10.1101/2021.03.17.435829v1?rss=1 Palanski, B. A. Weng, N. Zhang, L. Hilmer, A. J. Fall, L. A. Swaminathan, K. Jabri, B. Sousa, C. Fernandez-Becker, N. Q. Khosla, C. Elias, J. E. 2021-03-18 doi:10.1101/2021.03.17.435829 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Clathrin adaptors mediate two sequential pathwaysof intra-Golgi recycling ]]> https://biorxiv.org/content/10.1101/2021.03.17.435835v1?rss=1 Casler, J. C. Krahn, A. H. Pantazopoulou, A. Johnson, N. Day, K. J. Glick, B. S. 2021-03-17 doi:10.1101/2021.03.17.435835 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ ENCODING OF LIMB STATE BY SINGLE NEURONS IN THE CUNEATE NUCLEUS OF AWAKE MONKEYS ]]> https://biorxiv.org/content/10.1101/2021.03.17.435880v1?rss=1 Versteeg, C. Rosenow, J. M. Bensmaia, S. J. Miller, L. E. 2021-03-18 doi:10.1101/2021.03.17.435880 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ ODOR IDENTITY CAN BE EXTRACTED FROM THE RECIPROCAL CONNECTIVITY BETWEEN OLFACTORY BULB AND PIRIFORM CORTEX IN HUMANS ]]> https://biorxiv.org/content/10.1101/2021.03.18.436041v1?rss=1 Iravani, B. Arshamian, A. Lundqvist, M. Kay, L. M. Wilson, D. A. Lundstrom, J. N. 2021-03-19 doi:10.1101/2021.03.18.436041 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression ]]> https://biorxiv.org/content/10.1101/2021.03.24.436599v1?rss=1 Walter, S. Franke, V. Drayman, N. Wyler, E. Tay, S. Landthaler, M. Akalin, A. Ensser, A. Full, F. 2021-03-24 doi:10.1101/2021.03.24.436599 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean ]]> https://biorxiv.org/content/10.1101/2021.03.24.436778v1?rss=1 Delmont, T. O. Pierella Karlusich, J. J. Veseli, I. Fuessel, J. Eren, A. M. Foster, R. A. Bowler, C. Wincker, P. Pelletier, E. 2021-03-24 doi:10.1101/2021.03.24.436778 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Class I Histone Deacetylases (HDAC1-3) are Histone Lysine Delactylases ]]> https://biorxiv.org/content/10.1101/2021.03.24.436780v1?rss=1 Moreno-Yruela, C. Zhang, D. Wei, W. Baek, M. Gao, J. Nielsen, A. L. Bolding, J. E. Yang, L. Jameson, S. T. Wong, J. Olsen, C. A. Zhao, Y. 2021-03-24 doi:10.1101/2021.03.24.436780 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ A numerical framework for genetic hitchhiking in populations of variable size ]]> https://biorxiv.org/content/10.1101/2021.03.25.437048v1?rss=1 Friedlander, E. Steinruecken, M. 2021-03-25 doi:10.1101/2021.03.25.437048 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Parental-fetal interplay of immune genes leads to intrauterine growth restriction ]]> https://biorxiv.org/content/10.1101/2021.03.26.437292v1?rss=1 Kaur, G. Porter, C. B. M. Ashenberg, O. Lee, J. Riesenfeld, S. J. Hofree, M. Aggelakopoulou, M. Subramanian, A. Kuttikkatte, S. B. Attfield, K. E. Desel, C. A. E. Davies, J. L. Evans, H. G. Avraham-Davidi, I. Nguyen, L. T. Dionne, D. A. Neumann, A. E. Jensen, L. T. Barber, T. R. Soilleux, E. Carrington, M. McVean, G. Rozenblatt-Rosen, O. Regev, A. Fugger, L. 2021-03-28 doi:10.1101/2021.03.26.437292 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration ]]> https://biorxiv.org/content/10.1101/2021.03.29.436835v1?rss=1 Carlson, H. K. Youngblut, M. D. Redford, S. A. Williamson, A. J. Coates, J. 2021-03-29 doi:10.1101/2021.03.29.436835 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Species-specific gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection ]]> https://biorxiv.org/content/10.1101/2021.04.05.438504v1?rss=1 Huang, Y. Chen, J. Dong, C. Sosa, D. Xia, S. Ouyang, Y. Fan, C. Li, D. Mortola, E. Long, M. Bergelson, J. 2021-04-06 doi:10.1101/2021.04.05.438504 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Host Factor Rab11a is Critical for Efficient Assembly of Influenza A Virus Genomic Segments ]]> https://biorxiv.org/content/10.1101/2021.04.06.438577v1?rss=1 Han, J. Ganti, K. Sali, V. K. Twigg, C. Zhang, Y. Manivasagam, S. Liang, C.-Y. Vogel, O. A. Huang, I. Emmanuel, S. N. Plung, J. Radoshevich, L. Perez, J. T. Lowen, A. C. Manicassamy, B. 2021-04-06 doi:10.1101/2021.04.06.438577 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Activity-dependent Golgi satellite formation in dendrites reshapes the neuronal surface glycoproteome ]]> https://biorxiv.org/content/10.1101/2021.04.06.438745v1?rss=1 Govind, A. P. Jeyifous, O. Russell, T. A. Yi, Z. Weigel, A. V. Ramaprasad, A. Newell, L. Ramos, W. Valbuena, F. M. Casler, J. C. Yan, J.-Z. Glick, B. S. Swanson, G. T. Lippincott-Schwartz, J. Green, W. N. 2021-04-08 doi:10.1101/2021.04.06.438745 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Polymersomes decorated with SARS-CoV-2 spike protein receptor binding domain elicit robust humoral and cellular immunity ]]> https://biorxiv.org/content/10.1101/2021.04.08.438884v1?rss=1 Volpatti, L. R. Wallace, R. P. Cao, S. Raczy, M. Wang, R. Gray, L. T. Alpar, A. T. Briquez, P. S. Mitrousis, N. Marchell, T. M. Sasso, M. S. Nguyen, M. Mansurov, A. Budina, E. Solanki, A. Watkins, E. A. Schnorenberg, M. R. Tremain, A. C. Reda, J. W. Nicolaescu, V. Furlong, K. Dvorkin, S. Yu, S. S. Manicassamy, B. LaBelle, J. L. Tirrell, M. V. Randall, G. Kwissa, M. Swartz, M. Hubbell, J. 2021-04-08 doi:10.1101/2021.04.08.438884 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Active Cytoskeletal Composites Display Emergent Tunable Contractility and Restructuring ]]> https://biorxiv.org/content/10.1101/2021.04.08.439072v1?rss=1 Lee, G. Leech, G. Lwin, P. Michel, J. Currie, C. Rust, M. J. Ross, J. L. McGorty, R. J. Das, M. Robertson-Anderson, R. M. 2021-04-09 doi:10.1101/2021.04.08.439072 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ TBX5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development ]]> https://biorxiv.org/content/10.1101/2021.04.09.439219v1?rss=1 rankin, S. A. Steimle, J. D. Yang, X. Rydeen, A. B. Agarwal, K. Chatuverdi, P. Ikegami, K. Herriges, M. Moskowitz, I. P. Zorn, A. M. 2021-04-11 doi:10.1101/2021.04.09.439219 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Texture is encoded in precise temporal spiking patterns in primate somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2021.04.11.439354v1?rss=1 Long, K. H. Lieber, J. D. Bensmaia, S. J. 2021-04-11 doi:10.1101/2021.04.11.439354 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1 ]]> https://biorxiv.org/content/10.1101/2021.04.12.439291v1?rss=1 Pan, M. Zheng, Q. Wang, T. Liang, L. Mao, J. Zuo, C. Ding, R. Ai, H. Xie, Y. Si, D. Yu, Y. Liu, L. Zhao, M. 2021-04-12 doi:10.1101/2021.04.12.439291 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Evolving the Olfactory System with Machine Learning ]]> https://biorxiv.org/content/10.1101/2021.04.15.439917v1?rss=1 Wang, P. Y. Sun, Y. Axel, R. Abbott, L. Yang, G. R. 2021-04-16 doi:10.1101/2021.04.15.439917 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS) ]]> https://biorxiv.org/content/10.1101/2021.04.16.440202v1?rss=1 Marinov, G. K. Kim, S. H. Bagdatli, S. T. Trevino, A. E. Tycko, J. Wu, T. Bintu, L. Bassik, M. C. He, C. Kundaje, A. Greenleaf, W. J. 2021-04-17 doi:10.1101/2021.04.16.440202 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ The role of competition versus cooperation in microbial community coalescence ]]> https://biorxiv.org/content/10.1101/2021.04.18.440290v1?rss=1 Lechon Alonso, P. Clegg, T. Cook, J. Smith, T. P. Pawar, S. 2021-04-19 doi:10.1101/2021.04.18.440290 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis ]]> https://biorxiv.org/content/10.1101/2021.04.21.440804v1?rss=1 Kim, S. Voth, G. A. 2021-04-22 doi:10.1101/2021.04.21.440804 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Pre-existing chromatin accessibility and gene expression differences among naïve CD4+ T cells influence effector potential ]]> https://biorxiv.org/content/10.1101/2021.04.21.440846v1?rss=1 Rogers, D. Sood, A. Wang, H. van Beek, J. J. P. Rademaker, T. J. Artusa, P. Schneider, C. Shen, C. Wong, D. C. Lebel, M.-E. Condotta, S. A. Richer, M. J. Martins, A. J. Tsang, J. S. Barreiro, L. Francois, P. Langlais, D. Melichar, H. J. Textor, J. Mandl, J. N. 2021-04-22 doi:10.1101/2021.04.21.440846 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) ]]> https://biorxiv.org/content/10.1101/2021.04.22.436044v1?rss=1 Schatz, M. C. Philippakis, A. A. Afgan, E. Banks, E. Carey, V. J. Carroll, R. J. Culotti, A. Ellrott, K. Goecks, J. Grossman, R. L. Hall, I. Hansen, K. D. Lawson, J. Leek, J. T. O'Donnell Luria, A. Mosher, S. Morgan, M. Nekrutenko, A. O'Connor, B. D. Osborn, K. Paten, B. Patterson, C. Tan, F. J. Overby Taylor, C. Vessio, J. Waldron, L. D. Wang, T. Wuichet, K. AnVIL Team, 2021-04-23 doi:10.1101/2021.04.22.436044 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Undersampling and the inference of coevolution in proteins ]]> https://biorxiv.org/content/10.1101/2021.04.22.441025v1?rss=1 Kleeorin, Y. Russ, W. P. Rivoire, O. Ranganathan, R. 2021-04-23 doi:10.1101/2021.04.22.441025 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.04.23.441024v1?rss=1 McDonald, J. T. Enguita, F. J. Taylor, D. Bowen, R. A. Griffin, R. J. Priebe, W. Emmett, M. R. McGrath, M. Sajadi, M. Harris, A. D. Clement, J. Dybas, J. M. Aykin-Burns, N. Guarnieri, J. W. Singh, L. N. Grabham, P. Baylin, S. Yousey, A. Pearson, A. N. Corry, P. M. Saravia-Butler, A. Aunins, T. R. Nagpal, P. Meydan, C. Foox, J. Mozsary, C. Cerqueira, B. Zaksas, V. Singh, U. Wurtele, E. S. Costes, S. V. Galeano, D. Paccanaro, A. Meinig, S. L. Hagan, R. S. Bowman, N. M. UNC COVID-19 Pathobiology Consortium, Wolfgang, M. C. Altinok, S. Sapoval, N. Treangen 2021-04-23 doi:10.1101/2021.04.23.441024 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2021.04.27.441718v1?rss=1 Adams, A. A. Azam, M. S. Costliow, Z. Ma, X. Degnan, P. H. Vanderpool, C. K. 2021-04-28 doi:10.1101/2021.04.27.441718 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Using Stakeholder Insights to Enhance Engagement in PhD Professional Development ]]> https://biorxiv.org/content/10.1101/2021.04.28.440824v1?rss=1 Ramadoss, D. Bolgioni, A. F. Layton, R. L. Alder, J. L. Lundsteen, N. Stayart, C. A. Yellin, J. B. Smart, C. L. Varvayanis, S. S. 2021-04-29 doi:10.1101/2021.04.28.440824 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Librator, a platform for optimized sequence editing, design, and expression of influenza virus proteins ]]> https://biorxiv.org/content/10.1101/2021.04.29.441999v1?rss=1 Li, L. Stovicek, O. Guthmiller, J. J. Changrob, S. Fu, Y. Dugan, H. L. Stamper, C. T. Zheng, N.-Y. Huang, M. Wilson, P. C. 2021-04-29 doi:10.1101/2021.04.29.441999 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.04.29.442018v1?rss=1 Monje-Galvan, V. Voth, G. A. 2021-04-29 doi:10.1101/2021.04.29.442018 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Decitabine Reactivation of FoxM1-Dependent Endothelial Regeneration and Vascular Repair for Potential Treatment of Elderly ARDS and COVID-19 Patients ]]> https://biorxiv.org/content/10.1101/2021.04.29.442061v1?rss=1 Huang, X. Zhang, X. Machireddy, N. Mutlu, G. Fang, Y. Wu, D. Zhao, Y.-Y. 2021-04-30 doi:10.1101/2021.04.29.442061 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Diverse Hotspot Thermal Profiling Methods Detect Phosphorylation-Dependent Changes in Protein Stability ]]> https://biorxiv.org/content/10.1101/2021.05.01.441686v1?rss=1 Stein, B. D. Huang, J. X. Wu, D. Cantley, L. C. Moellering, R. E. 2021-05-01 doi:10.1101/2021.05.01.441686 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Capacity to erase gene occlusion is a defining feature distinguishing naive from primed pluripotency ]]> https://biorxiv.org/content/10.1101/2021.05.04.442547v1?rss=1 Foshay, K. M. Lee, J. H. Zhang, L. Fernandes, C. J. Wu, B. Gaetz, J. Baker, S. W. Looney, T. J. Xiang, A. P. Fan, G. Lahn, B. T. 2021-05-04 doi:10.1101/2021.05.04.442547 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Neural Representations of Food-Related Attributes in the Human Orbitofrontal Cortex in Health and Disease ]]> https://biorxiv.org/content/10.1101/2021.05.05.441818v1?rss=1 Xue, A. M. Foerde, K. Walsh, B. T. Steinglass, J. E. Shohamy, D. Bakkour, A. 2021-05-06 doi:10.1101/2021.05.05.441818 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Endothelial restoration of CAD GWAS gene PLPP3 by nanomedicine suppresses YAP/TAZ activity and reduces atherosclerosis in vivo ]]> https://biorxiv.org/content/10.1101/2021.05.06.443006v1?rss=1 Zhu, J. Yeh, C.-F. Huang, R.-T. Lee, T.-H. Shentu, T.-P. Wu, D. Yang, K.-C. Fang, Y. 2021-05-07 doi:10.1101/2021.05.06.443006 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Neuron specific ablation of eIF5A or deoxyhypusine synthase leads to impairment in development and cognitive functions in mice ]]> https://biorxiv.org/content/10.1101/2021.05.11.443636v1?rss=1 Kar, R. K. Hanner, A. S. Starost, M. F. Springer, D. Mastracci, T. L. Mirmira, R. G. Park, M. H. 2021-05-13 doi:10.1101/2021.05.11.443636 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Chaperones directly and efficiently disperse stress-triggered biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2021.05.13.444070v1?rss=1 Yoo, H. Bard, J. A. M. Pilipenko, E. Drummond, D. A. 2021-05-14 doi:10.1101/2021.05.13.444070 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Deficiency of Rho Kinase 1 (ROCK1) attenuates neutrophil NETosis and ameliorates UVB-induced skin inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.16.444366v1?rss=1 Li, M. Lyu, X. Liao, J. Werth, V. Liu, M.-L. 2021-05-17 doi:10.1101/2021.05.16.444366 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Mutational signatures of complex genomic rearrangements in human cancer ]]> https://biorxiv.org/content/10.1101/2021.05.16.444385v1?rss=1 Yang, L. Bao, L. Zhong, X. Yang, Y. 2021-05-17 doi:10.1101/2021.05.16.444385 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ "How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.05.17.443632v1?rss=1 Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Farina, S. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffman, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. E. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. Su 2021-05-17 doi:10.1101/2021.05.17.443632 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Lipid Bilayer Induces Contraction of the Denatured State Ensemble of a Helical-Bundle Membrane Protein ]]> https://biorxiv.org/content/10.1101/2021.05.17.444377v1?rss=1 Gaffney, K. Guo, R. Bridges, M. D. Chen, D. Muhammednazaar, S. Kim, M. yang, Z. Schilmiller, A. L. Faruk, N. F. Peng, X. Jones, A. D. Sun, L. Hubbell, W. L. Sosnick, T. Hong, H. 2021-05-17 doi:10.1101/2021.05.17.444377 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ The METTL5-TRMT112 N6-methyladenosine methyltransferase complex regulates metabolism and development via translation ]]> https://biorxiv.org/content/10.1101/2021.05.18.444567v1?rss=1 Sepich-Poore, C. Zheng, Z. Schmitt, E. Wen, K. Zhang, Z. S. Cui, X.-L. Dai, Q. Zhu, A. C. Zhang, L. Sanchez Castillo, A. Zhuang, X. He, C. Nachtergaele, S. 2021-05-18 doi:10.1101/2021.05.18.444567 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Cross-species identification of cancer-resistance associated genes uncovers their relevance to human cancer risk ]]> https://biorxiv.org/content/10.1101/2021.05.19.444895v1?rss=1 Nair, N. U. Cheng, K. Naddaf, L. Sharon, E. Pal, L. R. Rajagopal, P. S. Unterman, I. Aldape, K. Hannenhalli, S. Day, C.-P. Tabach, Y. Ruppin, E. 2021-05-21 doi:10.1101/2021.05.19.444895 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ VIP neurons desynchronize cortical assemblies ]]> https://biorxiv.org/content/10.1101/2021.05.20.444979v1?rss=1 Veit, J. Mossing, D. P. Adesnik, H. 2021-05-20 doi:10.1101/2021.05.20.444979 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Generation of potent cellular and humoral immunity against SARS-CoV-2 antigens via conjugation to a polymeric glyco-adjuvant ]]> https://biorxiv.org/content/10.1101/2021.05.20.445060v1?rss=1 Gray, L. T. Raczy, M. M. Briquez, P. S. Marchell, T. M. Alpar, A. T. Wallace, R. P. Volpatti, L. R. Sasso, M. S. Cao, S. Nguyen, M. Mansurov, A. Budina, E. Watkins, E. A. Solanki, A. Mitrousis, N. Reda, J. W. Yu, S. S. Tremain, A. C. Wang, R. Nicolaescu, V. Furlong, K. Dvorkin, S. Manicassamy, B. Randall, G. Wilson, D. S. Kwissa, M. Swartz, M. A. Hubbell, J. A. 2021-05-21 doi:10.1101/2021.05.20.445060 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Multiview super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2021.05.21.445200v1?rss=1 Wu, Y. Han, X. Su, Y. Glidewell, M. Daniels, J. S. Liu, J. Sengupta, T. Rey-Suarez, I. Fischer, R. Patel, A. Combs, C. Su, J. Wu, X. Christensen, R. Smith, C. Bao, L. Sun, Y. Duncan, L. H. Chen, J. Pommier, Y. Shi, Y.-B. Murphy, E. Roy, S. Upadhyaya, A. Colón-Ramos, D. La Riviere, P. Shroff, H. 2021-05-22 doi:10.1101/2021.05.21.445200 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ Inferring Population Size Histories using Coalescent Hidden Markov Models with TMRCA and Total Branch Length as Hidden States ]]> https://biorxiv.org/content/10.1101/2021.05.22.445274v1?rss=1 Upadhya, G. Steinruecken, M. 2021-05-23 doi:10.1101/2021.05.22.445274 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core ]]> https://biorxiv.org/content/10.1101/2021.05.24.445443v1?rss=1 Pak, A. J. Yu, A. Ke, Z. Briggs, J. Voth, G. A. 2021-05-24 doi:10.1101/2021.05.24.445443 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central tomaturation inhibition ]]> https://biorxiv.org/content/10.1101/2021.05.24.445455v1?rss=1 Pak, A. J. Purdy, M. D. Yeager, M. Voth, G. A. 2021-05-24 doi:10.1101/2021.05.24.445455 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity ]]> https://biorxiv.org/content/10.1101/2021.05.26.445841v1?rss=1 Catela, C. Weng, Y. Wen, K. Feng, W. Kratsios, P. 2021-05-27 doi:10.1101/2021.05.26.445841 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism ]]> https://biorxiv.org/content/10.1101/2021.05.26.445846v1?rss=1 Tejedor-Sanz, S. Stevens, E. T. Finnegan, P. Nelson, J. J. Knoessen, A. Light, S. H. Ajo-Franklin, C. M. Marco, M. L. 2021-05-26 doi:10.1101/2021.05.26.445846 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Notch controls the cell cycle to define leader versus follower identities during collective cell migration. ]]> https://biorxiv.org/content/10.1101/2021.05.27.445572v1?rss=1 Alhashem, Z. Feldner-Busztin, D. Revell, C. Alvarez-Garcillan Portillo, M. Richardson, J. Rocha, M. Gauert, A. Corbeaux, T. Prince, V. E. Bentley, K. Linker, C. 2021-05-27 doi:10.1101/2021.05.27.445572 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Metapopulations with habitat modification ]]> https://biorxiv.org/content/10.1101/2021.05.27.446046v1?rss=1 Miller, Z. R. Allesina, S. 2021-05-28 doi:10.1101/2021.05.27.446046 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Mitochondrial cyclophilin D promotes disease tolerance by licensing NK cell development and IL-22 production against influenza virus ]]> https://biorxiv.org/content/10.1101/2021.05.28.445832v1?rss=1 Downey, J. Randolph, H. E. Pernet, E. Tran, K. A. Khader, S. A. King, I. L. Barriero, L. B. Divangahi, M. 2021-05-28 doi:10.1101/2021.05.28.445832 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A connectomic study of a petascale fragment of human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2021.05.29.446289v1?rss=1 Shapson-Coe, A. Januszewski, M. Berger, D. R. Pope, A. Wu, Y. Blakely, T. Schalek, R. L. Li, P. Wang, S. Maitlin-Shepard, J. Karlupia, N. Dorkenwald, S. Sjostedt, E. Leavitt, L. Lee, D. Bailey, L. Fitzmaurice, A. Kar, R. Field, B. Wu, H. Wagner-Carena, J. Aley, D. Lau, J. Lin, Z. Wei, D. Pfister, H. Peleg, A. Jain, V. Lichtman, J. W. 2021-05-30 doi:10.1101/2021.05.29.446289 Cold Spring Harbor Laboratory Press 2021-05-30 <![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[ Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation ]]> https://biorxiv.org/content/10.1101/2021.06.03.446970v1?rss=1 Elorbany, R. Popp, J. M. Rhodes, K. Strober, B. J. Barr, K. Qi, G. Gilad, Y. M. Battle, A. 2021-06-03 doi:10.1101/2021.06.03.446970 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Lung epithelial signaling mediates early vaccine-induced CD4+ T cell activation and Mtb control ]]> https://biorxiv.org/content/10.1101/2021.06.03.446981v1?rss=1 Das, S. Marin, N. D. Esaulova, E. Ahmed, M. Swain, A. Rosa, B. A. Mitreva, M. Rangel-Moreno, J. Netea, M. Barreiro, L. B. Divangahi, M. Artyomov, M. Kaushal, D. Khader, S. A. 2021-06-03 doi:10.1101/2021.06.03.446981 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space ]]> https://biorxiv.org/content/10.1101/2021.06.07.447314v1?rss=1 Vanni, C. Schechter, M. S. Delmont, T. O. Eren, A. M. Steinegger, M. Gloeckner, F. O. Fernandez-Guerra, A. 2021-06-07 doi:10.1101/2021.06.07.447314 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Myofibroblast differentiation is governed by adhesion mechanics, and inhibition of the stress sensor Talin2 reverses lung fibrosis ]]> https://biorxiv.org/content/10.1101/2021.06.07.447403v1?rss=1 WHITE, M. J. V. Ozkan, M. Medellin, J. E. G. Hubbell, J. 2021-06-07 doi:10.1101/2021.06.07.447403 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Blocking antibodies against integrin-α3, integrin-αM, and integrin-αMβ2 de-differentiate myofibroblasts and reverse lung and kidney fibroses in a mouse model ]]> https://biorxiv.org/content/10.1101/2021.06.07.447405v1?rss=1 WHITE, M. ozkan, m. Raczy, M. Medellin, J. E. G. Koss, K. M. Alpar, A. T. Naved, B. A. Wertheim, J. Hubbell, J. A. 2021-06-07 doi:10.1101/2021.06.07.447405 Cold Spring Harbor Laboratory Press 2021-06-07 <![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[ Integrative Epigenomic and High-Throughput Functional Enhancer Profiling Reveals Determinants of Enhancer Heterogeneity in Gastric Cancer ]]> https://biorxiv.org/content/10.1101/2021.06.09.447637v1?rss=1 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. Specifically, we identified cancer-relevant genes (e.g. ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4 as a master trans-acting factor associated with GC enhancer heterogeneity. ConclusionsOur study indicates that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, and provides insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity. ]]> Sheng, T. Ho, S. W. T. Ooi, W. F. Xu, C. Xing, M. Padmanabhan, N. Huang, K. K. Ma, L. Ray, M. Guo, Y. A. Leng, S. N. Anene-Nzelu, C. G. Chang, M. M. Razavi-Mohseni, M. Beer, M. Foo, R. Tan, A. L. K. Ong, X. Jacobsen Skanderup, A. White, K. P. Jha, S. Tan, P. 2021-06-10 doi:10.1101/2021.06.09.447637 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Indigenous ancestry and admixture in the Uruguayan population ]]> https://biorxiv.org/content/10.1101/2021.06.09.447750v1?rss=1 Spangenberg, L. Fariello, M. I. Arce, D. Illanes, G. Greif, G. Shin, J.-Y. Yoo, S.-K. Seo, J.-S. Robello, C. Kim, C. Novembre, J. Sans, M. Naya, H. 2021-06-10 doi:10.1101/2021.06.09.447750 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression ]]> https://biorxiv.org/content/10.1101/2021.06.10.447922v1?rss=1 Goetz, J. Jessen, Z. F. Jacobi, A. Mani, A. Cooler, S. Greer, D. Kadri, S. Segal, J. Shekhar, K. Sanes, J. Schwartz, G. 2021-06-11 doi:10.1101/2021.06.10.447922 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Protein Domain-Based Prediction of Compound-Target Interactions and Experimental Validation on LIM Kinases ]]> https://biorxiv.org/content/10.1101/2021.06.14.448307v1?rss=1 Dogan, T. Akhan Güzelcan, E. Baumann, M. Koyas, A. Atas, H. Baxendale, I. Martin, M. Cetin-Atalay, R. 2021-06-14 doi:10.1101/2021.06.14.448307 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer ]]> https://biorxiv.org/content/10.1101/2021.06.14.448427v1?rss=1 Lim, S. A. Zhou, J. Martinko, A. J. Wang, Y.-H. Filippova, E. V. Steri, V. Wang, D. Remesh, S. G. Liu, J. Hann, B. Kossiakoff, A. A. Evans, M. J. Leung, K. K. Wells, J. A. 2021-06-15 doi:10.1101/2021.06.14.448427 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Validating marker-less pose estimation with 3D x-ray radiography ]]> https://biorxiv.org/content/10.1101/2021.06.15.448541v1?rss=1 Moore, D. D. Walker, J. D. MacLean, J. N. Hatsopoulos, N. G. 2021-06-16 doi:10.1101/2021.06.15.448541 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ The Human Tumor Atlas Network (HTAN) Breast PreCancer Atlas: A multi-omic integrative analysis of ductal carcinoma in situ with clinical outcomes ]]> https://biorxiv.org/content/10.1101/2021.06.16.448585v1?rss=1 Strand, S. H. Rivero-Gutierrez, B. Houlahan, K. E. Seoane, J. A. King, L. Risom, T. Simpson, L. A. Vennam, S. Khan, A. Cisneros, L. Hardman, T. Harmon, B. Couch, F. Gallagher, K. Kilgore, M. Rocque, G. B. DeMichele, A. King, T. McAuliffe, P. Nangia, J. Lee, J. Tseng, J. Storniolo, A. M. Thompson, A. Gupta, G. Burns, R. Veis, D. J. DeSchryver, K. Zhu, C. Matusiak, M. Wang, J. Zhu, S. X. Tappenden, J. Ding, D. Y. Zhang, D. Luo, J. Jiang, S. Varma, S. Anderson, L. Straub, C. Srivastava, S. Curtis, C. Tibshirani, R. Angelo, R. M. Hall, A. Owzar, K. Pol 2021-06-16 doi:10.1101/2021.06.16.448585 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types ]]> https://biorxiv.org/content/10.1101/2021.06.16.448714v1?rss=1 Rhodes, K. Barr, K. A. Popp, J. M. Strober, B. J. Battle, A. Gilad, Y. 2021-06-16 doi:10.1101/2021.06.16.448714 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples ]]> https://biorxiv.org/content/10.1101/2021.06.17.448867v1?rss=1 Biddanda, A. Steinrücken, M. Novembre, J. 2021-06-19 doi:10.1101/2021.06.17.448867 Cold Spring Harbor Laboratory Press 2021-06-19 <![CDATA[ Fast and powerful statistical method for context-specific QTL mapping in multi-context genomic studies ]]> https://biorxiv.org/content/10.1101/2021.06.17.448889v1?rss=1 Lu, A. Thompson, M. Gordon, M. G. Dahl, A. Ye, C. J. Zaitlen, N. Balliu, B. 2021-06-18 doi:10.1101/2021.06.17.448889 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Visual stimulation induces distinct forms of sensitization of On-Off direction-selective ganglion cell responses in the dorsal and ventral retina ]]> https://biorxiv.org/content/10.1101/2021.06.19.449131v1?rss=1 Huang, X. Kim, A. J. Acaron Ledesma, H. Ding, J. Smith, R. G. Wei, W. 2021-06-20 doi:10.1101/2021.06.19.449131 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ VEGF-A, PDGF-BB and HB-EGF engineered for promiscuous super affinity to the extracellular matrix improve wound healing in a model of type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.06.21.449313v1?rss=1 WHITE, M. J. V. Briquez, P. White, D. A. V. Hubbell, J. 2021-06-22 doi:10.1101/2021.06.21.449313 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Anti-clotting functions of lymphatics form the natural on-off switch for immune recognition by controlling the antigens and immune cells access to the lymph nodes ]]> https://biorxiv.org/content/10.1101/2021.06.22.449446v1?rss=1 Kilarski, W. W. Wachowska, M. Muchowicz, A. Mezyk-Kopec, R. Golab, J. Swartz, M. A. 2021-06-22 doi:10.1101/2021.06.22.449446 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Dopamine Neurons Evaluate Natural Fluctuations in Performance Quality ]]> https://biorxiv.org/content/10.1101/2021.06.23.449657v1?rss=1 Duffy, A. Latimer, K. W. Goldberg, J. H. Fairhall, A. L. Gadagkar, V. 2021-06-24 doi:10.1101/2021.06.23.449657 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ The Forget-Me-Not dHCP study: 7 Tesla high resolution diffusion imaging in the unfixed post-mortem neonatal brain ]]> https://biorxiv.org/content/10.1101/2021.06.24.449666v1?rss=1 Wu, W. Baxter, L. Rieger, S. W. Adams, E. Andersson, J. L. R. Andrade, M. C. Andritsou, F. Bastiani, M. Fry, R. E. Frost, R. Fitzgibbon, S. Foxley, S. Fowler, D. Gallagher, C. Howard, A. F. Hajnal, J. V. Moultrie, F. Monk, V. Porter, D. A. Papp, D. Price, A. Sallet, J. Sanders, M. Wilkinson, D. Smith, S. M. Slater, R. Miller, K. L. 2021-06-25 doi:10.1101/2021.06.24.449666 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment ]]> https://biorxiv.org/content/10.1101/2021.06.25.449981v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@371c3dorg.highwire.dtl.DTLVardef@1ee8e7org.highwire.dtl.DTLVardef@14ca731org.highwire.dtl.DTLVardef@1748ff7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Steimle, J. D. Kim, C. Nadadur, R. D. Wang, Z. Hoffmann, A. D. Hanson, E. Kweon, J. Sinha, T. Choi, K. Black, B. L. Cunningham, J. M. Ikegami, K. Moskowitz, I. P. 2021-06-25 doi:10.1101/2021.06.25.449981 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Fin Shape, Asymmetry, and Evolutionary Ecomorphology in Triggerfishes and Filefishes (Superfamily: Balistoidea) ]]> https://biorxiv.org/content/10.1101/2021.06.29.450391v1?rss=1 George, A. B. Westneat, M. W. 2021-07-01 doi:10.1101/2021.06.29.450391 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Predicting RNA splicing from DNA sequence using Pangolin ]]> https://biorxiv.org/content/10.1101/2021.07.06.451243v1?rss=1 Zeng, T. Li, Y. I. 2021-07-06 doi:10.1101/2021.07.06.451243 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces cerevisiae and Candida albicans ]]> https://biorxiv.org/content/10.1101/2021.07.06.451338v1?rss=1 Dohn, R. Xie, B. Back, R. Selewa, A. Eckart, H. Rao, R. P. Basu, A. 2021-07-07 doi:10.1101/2021.07.06.451338 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Rapid evolution of the functionally conserved gap gene giant in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.07.08.451553v1?rss=1 Chang, W. Matute, D. R. Kreitman, M. 2021-07-09 doi:10.1101/2021.07.08.451553 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Adolescent Brain Cognitive Development (ABCD) Community MRI Collection and Utilities ]]> https://biorxiv.org/content/10.1101/2021.07.09.451638v1?rss=1 Feczko, E. Conan, G. Marek, S. Tervo-Clemens, B. Cordova, M. Doyle, O. Earl, E. Perrone, A. Sturgeon, D. Klein, R. Harman, G. Kilamovich, D. Hermosillo, R. Miranda-Dominguez, O. Adebimpe, A. Bertolero, M. Cieslak, M. Covitz, S. Hendrickson, T. Juliano, A. C. Snider, K. Moore, L. A. Uriartel, J. Graham, A. M. Calabro, F. Rosenberg, M. D. Rapuano, K. M. Casey, B. Watts, R. Hagler, D. Thompson, W. K. Nichols, T. E. Hoffman, E. Luna, B. Garavan, H. Satterthwaite, T. D. Feldstein Ewing, S. Nagel, B. Dosenbach, N. U. Fair, D. A. 2021-07-11 doi:10.1101/2021.07.09.451638 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ The functional form of specialized predation dramatically affects whether Janzen-Connell effects can prevent competitive exclusion ]]> https://biorxiv.org/content/10.1101/2021.07.10.451901v1?rss=1 Smith, D. J. B. 2021-07-12 doi:10.1101/2021.07.10.451901 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Making Strides in Doctoral-Level Career Outcomes Reporting: Surveying the Landscape of Classification and Visualization Methodologies and Creating a Crosswalk Tool ]]> https://biorxiv.org/content/10.1101/2021.07.12.451657v1?rss=1 Collins, T. Ramadoss, D. Layton, R. MacDonald, J. Wheeler, R. Bankston, A. Stayart, C. A. Hao, Y. Robinson-Hamm, J. Sinche, M. Burghart, S. Carlsen-Bryan, A. Eswara, P. Krasna, H. Xu, H. Sullivan, M. 2021-07-14 doi:10.1101/2021.07.12.451657 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes) ]]> https://biorxiv.org/content/10.1101/2021.07.15.452585v1?rss=1 Cerny, D. Natale, R. 2021-07-16 doi:10.1101/2021.07.15.452585 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Epigenetic regulator genes direct lineage switching in MLL-AF4 leukaemia ]]> https://biorxiv.org/content/10.1101/2021.07.16.452676v1?rss=1 Tirtakusuma, R. Szoltysek, K. Milne, P. Grinev, V. V. Ptasinska, A. Meyer, C. Nakjang, S. Hehir-Kwa, J. Y. Williamson, D. Cauchy, P. Assi, S. A. Imperato, M. R. Vogiatzi, F. Lin, S. Wunderlich, M. Stutterheim, J. Komkov, A. Zerkalenkova, E. Evans, P. McNeill, H. Elder, A. Martinez Soria, N. Fordham, S. E. Shi, Y. Russell, L. J. Pal, D. Smith, A. Kingsbury, Z. Becq, J. Eckert, C. Haas, O. A. Carey, P. Bailey, S. Skinner, R. Miakova, N. Collin, M. Bigley, V. Haniffa, M. Marschalek, R. Harrison, C. J. Cargo, C. A. Schewe, D. Olshanskaya, Y. Thirman, M. J 2021-07-16 doi:10.1101/2021.07.16.452676 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Agonism and grooming behavior explain social status effects on physiology and gene regulation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.07.16.452731v1?rss=1 Simons, N. D. Michopoulos, V. Wilson, M. Barreiro, L. B. Tung, J. 2021-07-17 doi:10.1101/2021.07.16.452731 Cold Spring Harbor Laboratory Press 2021-07-17 <![CDATA[ Regional cytoarchitecture of the adult and developing mouse enteric nervous system ]]> https://biorxiv.org/content/10.1101/2021.07.16.452735v1?rss=1 Hamnett, R. Dershowitz, L. B. Sampathkumar, V. Wang, Z. De Andrade, V. Kasthuri, N. Druckmann, S. Kaltschmidt, J. A. 2021-07-18 doi:10.1101/2021.07.16.452735 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ Diet modifies allele-specific phenotypes in Drosophila carrying epilepsy-associated PNPO variants ]]> https://biorxiv.org/content/10.1101/2021.07.19.452889v1?rss=1 Chi, W. Iyengar, A. Fu, W. Liu, W. Berg, A. E. Wu, C.-F. Zhuang, X. 2021-07-20 doi:10.1101/2021.07.19.452889 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces ]]> https://biorxiv.org/content/10.1101/2021.07.19.452976v1?rss=1 Li, C. Voth, G. A. 2021-07-20 doi:10.1101/2021.07.19.452976 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Evolutionary tuning of a key helix drove androgen selectivity ]]> https://biorxiv.org/content/10.1101/2021.07.21.453223v1?rss=1 Okafor, C. D. Colucci, J. K. Cato, M. L. Khan, S. H. Cottrill, K. Hercules, D. Eick, G. Thornton, J. W. Ortlund, E. A. 2021-07-22 doi:10.1101/2021.07.21.453223 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Modelling the spatiotemporal spread of beneficial alleles using ancient genomes ]]> https://biorxiv.org/content/10.1101/2021.07.21.453231v1?rss=1 Muktupavela, R. A. Petr, M. Ségurel, L. Korneliussen, T. S. Novembre, J. Racimo, F. 2021-07-22 doi:10.1101/2021.07.21.453231 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion ]]> https://biorxiv.org/content/10.1101/2021.07.26.453663v1?rss=1 Krohannon, A. Srivastava, M. Rauch, S. Srivastava, R. Dickinson, B. Janga, S. C. 2021-07-27 doi:10.1101/2021.07.26.453663 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ Sensory computations in the cuneate nucleus of macaques ]]> https://biorxiv.org/content/10.1101/2021.07.28.454185v1?rss=1 Suresh, A. K. Greenspon, C. M. He, Q. Rosenow, J. M. Miller, L. E. Bensmaia, S. J. 2021-07-29 doi:10.1101/2021.07.28.454185 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ An Oscillatory Mechanism for Multi-level Storage in Short-term Memory ]]> https://biorxiv.org/content/10.1101/2021.07.29.454329v1?rss=1 Champion, K. Gozel, O. Lankow, B. Ermentrout, B. Goldman, M. 2021-07-30 doi:10.1101/2021.07.29.454329 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Large-scale dendritic spine extraction and analysis through petascale computing ]]> https://biorxiv.org/content/10.1101/2021.07.29.454371v1?rss=1 Wildenberg, G. Li, H. Badalamente, G. A. Uram, T. D. Ferrier, N. Kasthuri, N. 2021-07-30 doi:10.1101/2021.07.29.454371 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Neuronal correlates of attentional selectivity and intensity in visual area V4 are invariant of motivational context ]]> https://biorxiv.org/content/10.1101/2021.07.30.454515v1?rss=1 Ghosh, S. Maunsell, J. H. R. 2021-08-01 doi:10.1101/2021.07.30.454515 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Adult neuromarkers of sustained attention and working memory predict inter- and intra-individual differences in these processes in youth ]]> https://biorxiv.org/content/10.1101/2021.08.01.454530v1?rss=1 Kardan, O. Stier, A. J. Cardenas-Inigues, C. Pruin, J. C. Schertz, K. E. Deng, Y. Chamberlain, T. Meredith, W. J. Zhang, X. Bowman, J. E. Lakhtakia, T. Tindel, L. Avery, E. W. Lin, Q. Yoo, K. Chun, M. M. Berman, M. G. Rosenberg, M. D. 2021-08-02 doi:10.1101/2021.08.01.454530 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility ]]> https://biorxiv.org/content/10.1101/2021.08.06.455374v1?rss=1 Bavi, N. Clark, M. D. Contreras, G. F. Shen, R. Reddy, B. Milewski, W. M. Perozo, E. 2021-08-08 doi:10.1101/2021.08.06.455374 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ DAAM mediates the assembly of long-lived, treadmilling stress fibers in collectively migrating epithelial cells in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.08.07.455521v1?rss=1 Sherrard, K. Cetera, M. Horne-Badovinac, S. 2021-08-08 doi:10.1101/2021.08.07.455521 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Noncanonical Notch signals have opposing roles during cardiac development ]]> https://biorxiv.org/content/10.1101/2021.08.09.455692v1?rss=1 Miyamoto, M. Andersen, P. Sulistio, E. Liu, X. Murphy, S. Kannan, S. Nam, L. Miyamoto, W. Tampakakis, E. Hibino, N. Uosaki, H. Kwon, C. 2021-08-09 doi:10.1101/2021.08.09.455692 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Protein prediction for trait mapping in diverse populations ]]> https://biorxiv.org/content/10.1101/2021.08.11.455912v1?rss=1 Schubert, R. Geoffroy, E. Gregga, I. Mulford, A. Aguet, F. Ardlie, K. Gerszten, R. Clish, C. Van Den Berg, D. Taylor, K. Durda, P. Johnson, C. Cornell, E. Guo, X. Liu, Y. Tracy, R. Conomos, M. Laurie, C. Blackwell, T. Papanicolaou, G. Lappalainen, T. Mikhaylova, A. Thornton, T. Cho, M. Gignoux, C. Lange, L. Lange, E. Rich, S. Rotter, J. Manichaikul, A. Im, H. K. Wheeler, H. E. 2021-08-11 doi:10.1101/2021.08.11.455912 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Sub-3 Angstrom cryo-EM structure of RNA enabled by engineered homomeric self-assembly ]]> https://biorxiv.org/content/10.1101/2021.08.11.455951v1?rss=1 Liu, D. Thelot, F. A. Piccirilli, J. A. Liao, M. Yin, P. 2021-08-11 doi:10.1101/2021.08.11.455951 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Stoney vs. Histed: Quantifying the Spatial Effects of Intracortical Microstimulation ]]> https://biorxiv.org/content/10.1101/2021.08.12.456091v1?rss=1 Kumaravelu, K. Sombeck, J. Miller, L. E. Bensmaia, S. J. Grill, W. M. 2021-08-13 doi:10.1101/2021.08.12.456091 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[ Unique Characterization of Spatiotemporal Neuronal Network Activity ]]> https://biorxiv.org/content/10.1101/2021.08.16.456546v1?rss=1 Deshpande, S. S. Smith, G. van Drongelen, W. 2021-08-17 doi:10.1101/2021.08.16.456546 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Skin stem cells orchestrate de novo generation of extrathymic regulatory T cells to establish a temporary protective niche during wound healing ]]> https://biorxiv.org/content/10.1101/2021.08.16.456570v1?rss=1 Truong, C. Guo, W. Woodside, L. Gang, A. Savage, P. Infarinato, N. Stewart, K. Polak, L. Levorse, J. Pasolli, A. Dikiy, S. Rudensky, A. Fuchs, E. Miao, Y. 2021-08-17 doi:10.1101/2021.08.16.456570 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Machine learning predicts translation initiation sites in neurologic diseases with expanded repeats ]]> https://biorxiv.org/content/10.1101/2021.08.17.456657v1?rss=1 18%. The models presented here are then used to identify translation initiation sites in genes associated with a number of neurologic repeat expansion disorders. The results confirm a number of experimentally discovered sites of translation initiation upstream of the expanded repeats and predict many sites that are not yet established. ]]> Gleason, A. C. Ghadge, G. Chen, J. Sonobe, Y. Roos, R. P. 2021-08-17 doi:10.1101/2021.08.17.456657 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Molecular mechanisms underlying enhanced hemichannel function of a cataract-associated Cx50 mutant ]]> https://biorxiv.org/content/10.1101/2021.08.18.456706v1?rss=1 Tong, J.-J. Khan, U. Haddad, B. G. Minogue, P. J. Beyer, E. C. Berthoud, V. M. Reichow, S. L. Ebihara, L. 2021-08-19 doi:10.1101/2021.08.18.456706 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Ubiquitin modulates 26S proteasome conformational dynamics and promotes substrate degradation ]]> https://biorxiv.org/content/10.1101/2021.08.18.456915v1?rss=1 Jonsson, E. Htet, Z. M. Bard, J. A. M. Dong, K. C. Martin, A. 2021-08-19 doi:10.1101/2021.08.18.456915 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Selection against admixture and gene regulatory divergence in a long-term primate field study ]]> https://biorxiv.org/content/10.1101/2021.08.19.456711v1?rss=1 Vilgalys, T. P. Fogel, A. S. Mututua, R. S. Warutere, J. K. Siodi, L. Anderson, J. A. Kim, S. Y. Voyles, T. N. Robinson, J. A. Wall, J. D. Archie, E. A. Alberts, S. C. Tung, J. 2021-08-19 doi:10.1101/2021.08.19.456711 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ ReporterSeq reveals genome-wide determinants of proteasome expression ]]> https://biorxiv.org/content/10.1101/2021.08.19.456712v1?rss=1 Work, J. J. Alford, B. D. Dea, A. Ali, A. Pincus, D. Brandman, O. 2021-08-19 doi:10.1101/2021.08.19.456712 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Development of a universal nanobody-binding Fab module for fiducial-assisted cryo- EM studies of membrane proteins ]]> https://biorxiv.org/content/10.1101/2021.08.20.457137v1?rss=1 Bloch, J. S. Mukherjee, S. Kowal, J. Filippova, E. V. Niederer, M. Pardon, E. Steyaert, J. Kossiakoff, A. A. Locher, K. P. 2021-08-20 doi:10.1101/2021.08.20.457137 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ proovframe: frameshift-correction for long-read (meta)genomics ]]> https://biorxiv.org/content/10.1101/2021.08.23.457338v1?rss=1 Hackl, T. Trigodet, F. Eren, A. M. Biller, S. J. Eppley, J. M. Luo, E. Burger, A. DeLong, E. F. Fischer, M. G. 2021-08-24 doi:10.1101/2021.08.23.457338 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ A compilation of fecal microbiome shotgun metagenomics from hospitalized patients undergoing hematopoietic cell transplantation ]]> https://biorxiv.org/content/10.1101/2021.08.23.457365v1?rss=1 Yan, J. Liao, C. Taylor, B. P. Fontana, E. Amoretti, L. A. Wright, R. J. Dai, A. Waters, N. Peled, J. U. Taur, Y. Perales, M.-A. Siranosian, B. A. Bhatt, A. S. van den Brink, M. R. M. Pamer, E. G. Schluter, J. Xavier, J. 2021-08-24 doi:10.1101/2021.08.23.457365 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ A Scale-Free Gradient of Cognitive Resource Disruptions in Childhood Psychopathology ]]> https://biorxiv.org/content/10.1101/2021.08.24.457554v1?rss=1 Stier, A. J. Cardenas-Iniguez, C. Kardan, O. J. Moore, T. M. Meyer, F. A. C. Rosenberg, M. D. Lahey, B. B. Berman, M. G. 2021-08-26 doi:10.1101/2021.08.24.457554 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Developmental Venous Anomalies are a Genetic Primer for Cerebral Cavernous Malformations ]]> https://biorxiv.org/content/10.1101/2021.08.25.457657v1?rss=1 Snellings, D. A. Girard, R. Lightle, R. Srinath, A. Romanos, S. Li, Y. Chen, C. Ren, A. A. Kahn, M. L. Awad, I. A. Marchuk, D. A. 2021-08-26 doi:10.1101/2021.08.25.457657 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Rapid gene evolution in an ancient post-transcriptional and translationalregulatory system compensates for meiotic X chromosomal inactivation ]]> https://biorxiv.org/content/10.1101/2021.08.25.457683v1?rss=1 Xia, S. Ventura, I. M. Blaha, A. Sgromo, A. Han, S. Izaurralde, E. Long, M. 2021-08-27 doi:10.1101/2021.08.25.457683 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Friend or Foe: Hybrid proline-rich proteins determine how plants interact with and respond to beneficial and pathogenic microbes ]]> https://biorxiv.org/content/10.1101/2021.08.26.457806v1?rss=1 Banday, Z. Z. Cecchini, N. M. Scott, A. T. Hu, C. T. Filzen, R. C. Agbo, E. Greenberg, J. T. 2021-08-27 doi:10.1101/2021.08.26.457806 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ A Wide-Field Micro-Computed Tomography Detector: Micron Resolution at Half-centimeter Scale ]]> https://biorxiv.org/content/10.1101/2021.08.27.457808v1?rss=1 Yakovlev, M. A. Vanselow, D. J. Ngu, M. S. Zaino, C. R. Katz, S. R. Ding, Y. Parkinson, D. Wang, S. Y. Ang, K. C. La Riviere, P. J. Cheng, K. C. 2021-08-28 doi:10.1101/2021.08.27.457808 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Stereo-specific Lasofoxifene Derivatives Reveal the Interplay between Estrogen Receptor Alpha Stability and Antagonistic Activity in ESR1 Mutant Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/2021.08.27.457901v1?rss=1 Hosfield, D. J. Weber, S. Li, N.-S. Suavage, M. Sullivan, E. Nduwke, E. Han, R. Cush, S. Laine, M. Mader, S. C. Greene, G. L. Fanning, S. W. 2021-08-28 doi:10.1101/2021.08.27.457901 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ BiomeHorizon: visualizing microbiome time series data in R ]]> https://biorxiv.org/content/10.1101/2021.08.29.458140v1?rss=1 Fink, I. Abdill, R. J. Blekhman, R. Grieneisen, L. 2021-08-31 doi:10.1101/2021.08.29.458140 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Scale Invariance in fNIRS as a Measurement of Cognitive Load ]]> https://biorxiv.org/content/10.1101/2021.08.31.458427v1?rss=1 Zhuang, C. Meidenbauer, K. L. Kardan, O. Stier, A. J. Choe, K. W. Cardenas-Iniguez, C. Huppert, T. J. Berman, M. G. 2021-09-01 doi:10.1101/2021.08.31.458427 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ The chromatin organization of a chlorarachniophyte nucleomorph genome ]]> https://biorxiv.org/content/10.1101/2021.09.01.458626v1?rss=1 Marinov, G. K. Chen, X. J. Wu, T. He, C. Grossman, A. R. Kundaje, A. Greenleaf, W. 2021-09-02 doi:10.1101/2021.09.01.458626 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Elucidating the neural mechanisms of Learning-to-Learn ]]> https://biorxiv.org/content/10.1101/2021.09.02.455707v1?rss=1 Goudar, V. Peysakhovich, B. Freedman, D. J. Buffalo, E. A. Wang, X.-J. 2021-09-02 doi:10.1101/2021.09.02.455707 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ High lineage survivorship across the end-Devonian Mass Extinction suggested by a remarkable new Late Devonian actinopterygian ]]> https://biorxiv.org/content/10.1101/2021.09.02.458676v1?rss=1 Giles, S. Feilich, K. Pierce, S. E. Friedman, M. 2021-09-03 doi:10.1101/2021.09.02.458676 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ In lupus nephritis, specific in situ inflammatory states are associated with refractory disease and progression to renal failure ]]> https://biorxiv.org/content/10.1101/2021.09.03.458909v1?rss=1 Abraham, R. Durkee, M. S. Ai, J. Veselits, M. Casella, G. Asano, Y. Chang, A. Ko, K. Oshinsky, C. Peninger, E. Giger, M. Clark, M. R. 2021-09-04 doi:10.1101/2021.09.03.458909 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Assembly formation is stabilized by Parvalbumin neurons and accelerated by Somatostatin neurons ]]> https://biorxiv.org/content/10.1101/2021.09.06.459211v1?rss=1 Lagzi, F. Canto Bustos, M. Oswald, A.-M. Doiron, B. 2021-09-07 doi:10.1101/2021.09.06.459211 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior ]]> https://biorxiv.org/content/10.1101/2021.09.07.459301v1?rss=1 Watkins, L. C. DeGrado, W. F. Voth, G. A. 2021-09-07 doi:10.1101/2021.09.07.459301 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Digital Spatial Profiling of Collapsing Glomerulopathy ]]> https://biorxiv.org/content/10.1101/2021.09.08.459502v1?rss=1 Smith, K. D. Henriksen, K. Nicosia, R. F. Alpers, C. E. Akilesh, S. 2021-09-09 doi:10.1101/2021.09.08.459502 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Re-evaluating the role of nucleosomal bivalency in early development ]]> https://biorxiv.org/content/10.1101/2021.09.09.458948v1?rss=1 Shah, R. N. Grzybowski, A. T. Elias, J. Chen, Z. Hattori, T. Lechner, C. C. Lewis, P. W. Koide, S. Fierz, B. Ruthenburg, A. J. 2021-09-10 doi:10.1101/2021.09.09.458948 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Cortical dopamine reduces the impact of motivational biases governing automated behaviour ]]> https://biorxiv.org/content/10.1101/2021.09.09.459267v1?rss=1 Scholz, V. Hook, R. W. Rostami Kandroodi, M. Algermissen, J. Ioannidis, K. Christmas, D. Valle, S. Robbins, T. W. Grant, J. E. Chamberlain, S. R. den Ouden, H. E. M. 2021-09-10 doi:10.1101/2021.09.09.459267 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ A curved manifold orients rotational dynamics in motor cortex ]]> https://biorxiv.org/content/10.1101/2021.09.09.459647v1?rss=1 Sabatini, D. A. Kaufman, M. T. 2021-09-11 doi:10.1101/2021.09.09.459647 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter ]]> https://biorxiv.org/content/10.1101/2021.09.10.459748v1?rss=1 Li, C. Yue, Z. Newstead, S. Voth, G. A. 2021-09-10 doi:10.1101/2021.09.10.459748 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Genome-wide association mapping within a single Arabidopsis thaliana population reveals a richer genetic architecture for defensive metabolite diversity ]]> https://biorxiv.org/content/10.1101/2021.09.13.460136v1?rss=1 Gloss, A. D. Vergnol, A. Morton, T. C. Laurin, P. J. Roux, F. Bergelson, J. 2021-09-15 doi:10.1101/2021.09.13.460136 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis ]]> https://biorxiv.org/content/10.1101/2021.09.16.460328v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@1f849b6org.highwire.dtl.DTLVardef@1af655borg.highwire.dtl.DTLVardef@274baaorg.highwire.dtl.DTLVardef@1d8af02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sun, D. A. Patel, N. H. 2021-09-18 doi:10.1101/2021.09.16.460328 Cold Spring Harbor Laboratory Press 2021-09-18 <![CDATA[ Top2a promotes the development of social behavior via PRC2 and H3K27me3 ]]> https://biorxiv.org/content/10.1101/2021.09.20.461107v1?rss=1 Geng, Y. Zhang, T. Godar, S. C. Pluimer, B. R. Harrison, D. L. Nath, A. K. Yeh, J.-R. J. Drummond, I. A. Bortolato, M. Peterson, R. T. 2021-09-23 doi:10.1101/2021.09.20.461107 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Global Epigenetic Analysis Reveals H3K27 Methylation as a Mediator of Double Strand Break Repair ]]> https://biorxiv.org/content/10.1101/2021.09.20.461136v1?rss=1 Lutze, J. Wolfgeher, D. Kron, S. J. 2021-09-20 doi:10.1101/2021.09.20.461136 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Polygenic score accuracy in ancient samples: quantifying the effects of allelic turnover ]]> https://biorxiv.org/content/10.1101/2021.09.21.461259v1?rss=1 Carlson, M. O. Rice, D. P. Berg, J. J. Steinruecken, M. 2021-09-24 doi:10.1101/2021.09.21.461259 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Chromosomal instability mediates immune exclusion and response to cytotoxic chemotherapy in colorectal liver metastases ]]> https://biorxiv.org/content/10.1101/2021.09.22.459429v1?rss=1 Martinez, C. A. Spurr, L. F. Iyer, S. C. Pugh, S. A. Bridgewater, J. A. Primrose, J. N. Domingo, E. Maughan, T. S. D'Angelica, M. I. Talamonti, M. Posner, M. C. Connell, P. P. Weichselbaum, R. R. Pitroda, S. P. 2021-09-23 doi:10.1101/2021.09.22.459429 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Signatures of visuospatial information foraging during learning of complex environments ]]> https://biorxiv.org/content/10.1101/2021.09.22.461356v1?rss=1 Barack, D. L. Bakkour, A. Shohamy, D. Salzman, C. D. 2021-09-22 doi:10.1101/2021.09.22.461356 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ A different mechanism of C-type inactivation in the Kv-like KcsA mutant E71V ]]> https://biorxiv.org/content/10.1101/2021.09.22.461404v1?rss=1 Rohaim, A. Vermeulen, B. Li, J. Kummerer, F. Napoli, F. Blachowicz, L. Medeiros-Silva, J. Roux, B. Weingarth, M. 2021-09-22 doi:10.1101/2021.09.22.461404 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ The mosquito microbiome includes habitat-specific but rare symbionts ]]> https://biorxiv.org/content/10.1101/2021.09.24.461628v1?rss=1 Schrieke, H. Maignien, L. Constancias, F. Trigodet, F. Chakloute, S. Rakotoarivony, I. Marie, A. L'Ambert, G. Makoundou, P. Pages, N. Eren, A. M. Weill, M. Sicard, M. Reveillaud, J. 2021-09-24 doi:10.1101/2021.09.24.461628 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Topological insights into the neural basis of flexible behavior ]]> https://biorxiv.org/content/10.1101/2021.09.24.461717v1?rss=1 Rouse, T. C. Ni, A. M. Huang, C. Cohen, M. 2021-09-25 doi:10.1101/2021.09.24.461717 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Intraspecific variation stabilizes classic predator-prey dynamics ]]> https://biorxiv.org/content/10.1101/2021.09.27.461947v1?rss=1 Allesina, S. Miller, Z. R. Servan, C. A. M. 2021-09-28 doi:10.1101/2021.09.27.461947 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ PlasmidHostFinder: Prediction of plasmid hosts using random forest ]]> https://biorxiv.org/content/10.1101/2021.09.27.462084v1?rss=1 Aytan-Aktug, D. CLAUSEN, P. T. Szarvas, J. Munk, P. Otani, S. Nguyen, M. Davis, J. J. Lund, O. Aarestrup, F. M. 2021-09-29 doi:10.1101/2021.09.27.462084 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes ]]> https://biorxiv.org/content/10.1101/2021.09.28.462107v1?rss=1 Zaydman, M. A. Little, A. Haro, F. Aksianiuk, V. Buchser, W. DiAntonio, A. Gordon, J. I. Milbrandt, J. Raman, A. 2021-09-28 doi:10.1101/2021.09.28.462107 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Genome graphs detect human polymorphisms in active epigenomic states during influenza infection ]]> https://biorxiv.org/content/10.1101/2021.09.29.462206v1?rss=1 Groza, C. Chen, X. Pacis, A. Simon, M.-M. Pramatarova, A. Aracena, K. A. Pastinen, T. Barreiro, L. B. Bourque, G. 2021-10-01 doi:10.1101/2021.09.29.462206 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ The Daphnia carapace and the origin of novel structures ]]> https://biorxiv.org/content/10.1101/2021.09.29.462403v1?rss=1 Bruce, H. S. Patel, N. H. 2021-10-01 doi:10.1101/2021.09.29.462403 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Full genome Nobecovirus sequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade ]]> https://biorxiv.org/content/10.1101/2021.09.29.462406v1?rss=1 Kettenburg, G. Kistler, A. L. Ranaivoson, H. C. Andry, S. DeRisi, J. L. Gentles, A. Raharinosy, V. Randriambolamanantsoa, T. H. Ravelomanantsoa, N. A. F. Tato, C. M. Dussart, P. Heraud, J.-M. Brook, C. E. 2021-09-29 doi:10.1101/2021.09.29.462406 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ TES-1/Tes protects junctional actin networks under tension from self-injury during epidermal morphogenesis in the C. elegans embryo ]]> https://biorxiv.org/content/10.1101/2021.09.30.462556v1?rss=1 Lynch, A. M. Lucas, B. G. Winkelman, J. Martin, S. C. T. Block, S. D. Audhya, A. Gardel, M. L. Hardin, J. 2021-10-01 doi:10.1101/2021.09.30.462556 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Strain and crack propagation of HIV-1 capsids during uncoating ]]> https://biorxiv.org/content/10.1101/2021.09.30.462583v1?rss=1 Yu, A. Lee, E. M. Y. Briggs, J. A. G. Ganser-Pornillos, B. K. Pornillos, O. Voth, G. A. 2021-10-01 doi:10.1101/2021.09.30.462583 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model ]]> https://biorxiv.org/content/10.1101/2021.09.30.462680v1?rss=1 Housman, G. Briscoe, E. Gilad, Y. 2021-10-01 doi:10.1101/2021.09.30.462680 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Non-conserved metabolic regulation by LKB1 distinguishes human and mouse lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2021.10.01.462764v1?rss=1 Stein, B. D. Ferrarone, J. R. Gardner, E. E. Chang, J. W. Wu, D. Chen, Q. Hollstein, P. E. Yuan, M. Liang, R. J. Coukos, J. S. Sindelar, M. Ngo, B. Gross, S. S. Shaw, R. J. Asara, J. M. Moellering, R. E. Varmus, H. Cantley, L. C. 2021-10-02 doi:10.1101/2021.10.01.462764 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Molecular Basis of Urostyle Development: Genes and Gene Regulation Underlying an Evolutionary Novelty ]]> https://biorxiv.org/content/10.1101/2021.10.04.462674v1?rss=1 Senevirathne, G. Shubin, N. H. 2021-10-05 doi:10.1101/2021.10.04.462674 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Low-dimensional encoding of decisions in parietal cortex reflects long-term training history ]]> https://biorxiv.org/content/10.1101/2021.10.07.463576v1?rss=1 Latimer, K. W. Freedman, D. J. 2021-10-09 doi:10.1101/2021.10.07.463576 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Mast cell regranulation involves a metabolic switch promoted by the interaction between mTORC1 and a glucose-6-phosphate transporter ]]> https://biorxiv.org/content/10.1101/2021.10.09.463777v1?rss=1 Iskarpatyoti, J. A. Shi, J. Rathor, A. P. S. Miao, Y. Abraham, S. N. 2021-10-13 doi:10.1101/2021.10.09.463777 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action ]]> https://biorxiv.org/content/10.1101/2021.10.09.463779v1?rss=1 Trifan, A. Gorgun, D. Li, Z. Brace, A. Zvyagin, M. Ma, H. Clyde, A. R. Clark, D. A. Salim, M. Hardy, D. Burnley, T. Huang, L. McCalpin, J. Emani, M. Yoo, H. Yin, J. Tsaris, A. Subbiah, V. Liu, J. Trebesch, N. Wells, G. Mysore, V. Gibbs, T. Phillips, J. Chennubhotla, S. C. Foster, I. Stevens, R. Anandkumar, A. Vishwanath, V. Stone, J. E. Tajkhorshid, E. Harris, S. A. Ramanathan, A. 2021-10-12 doi:10.1101/2021.10.09.463779 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Population-specific patterns of toxin sequestration in monarch butterflies from around the world ]]> https://biorxiv.org/content/10.1101/2021.10.15.464593v1?rss=1 40 years--to a nearby island with intact birds. We found substantial genetic variation in sequestration ability, though no consistent sequestration advantage in sympatric combinations. One monarch population from Puerto Rico showed greatly reduced sequestration from Asclepias syriaca, likely reflecting a lack of evolutionary association with this host. Monarchs from Guam showed reduced sequestration from A. curassavica, both in a cross-island comparison and when reared under controlled conditions. Our results suggest that processes involved in toxin sequestration are subject to natural selection and may evolve in response to contemporary changes in species interactions. ]]> Freedman, M. Choquette, S.-L. Ramirez, S. Strauss, S. Hunter, M. Vannette, R. 2021-10-16 doi:10.1101/2021.10.15.464593 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Propofol modulates functional connectivity signatures of sustained attention ]]> https://biorxiv.org/content/10.1101/2021.10.15.464605v1?rss=1 Chamberlain, T. A. Rosenberg, M. D. 2021-10-16 doi:10.1101/2021.10.15.464605 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ M1 dynamics share similar inputs for initiating and correcting movement ]]> https://biorxiv.org/content/10.1101/2021.10.18.464704v1?rss=1 Malonis, P. J. Hatsopoulos, N. G. MacLean, J. N. Kaufman, M. T. 2021-10-19 doi:10.1101/2021.10.18.464704 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Profiling of Nascent Lariat Intermediates Reveals Key Genetic Determinants of the Timing of Human Co-transcriptional Splicing ]]> https://biorxiv.org/content/10.1101/2021.10.18.464728v1?rss=1 Zeng, Y. Zeng, H. Fair, B. J. Krishnamohan, A. Hou, Y. Hall, J. M. Ruthenburg, A. J. Li, Y. I. Staley, J. P. 2021-10-19 doi:10.1101/2021.10.18.464728 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Systematic expression profiling of dprs and DIPs reveals cell surface codes in Drosophila larval peripheral neurons ]]> https://biorxiv.org/content/10.1101/2021.10.20.465173v1?rss=1 Wang, Y. Lobb-Rabe, M. Ashley, J. Chatterjee, P. Bellen, H. J. Kanca, O. Carrillo, R. A. 2021-10-21 doi:10.1101/2021.10.20.465173 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Classical Mathematical Models for Prediction of Response to Chemotherapy and Immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.10.23.465549v1?rss=1 Ghaffari Laleh, N. Loeffler, C. M. L. Grajek, J. Stankova, K. Pearson, A. T. Muti, H. S. Trautwein, C. Enderling, H. Poleszczuk, J. Kather, J. N. 2021-10-24 doi:10.1101/2021.10.23.465549 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ The Atomic-Level Physiochemical Determinants of T Cell Receptor Dissociation Kinetics ]]> https://biorxiv.org/content/10.1101/2021.10.25.465739v1?rss=1 Rollins, Z. A. Huang, J. Tagkopoulos, I. Faller, R. George, S. C. 2021-10-26 doi:10.1101/2021.10.25.465739 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Transposable elements continuously remodel the regulatory landscape, transcriptome, and function of decidual stromal cells ]]> https://biorxiv.org/content/10.1101/2021.10.25.465769v1?rss=1 Mika, K. Lynch, V. J. 2021-10-26 doi:10.1101/2021.10.25.465769 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Architecture of the cytoplasmic face of the nuclear pore ]]> https://biorxiv.org/content/10.1101/2021.10.26.465790v1?rss=1 Bley, C. J. Nie, S. Mobbs, G. Petrovic, S. Gres, A. Liu, X. Mukherjee, S. Harvey, S. Huber, F. M. Lin, D. H. Brown, B. Tang, A. W. Rundlet, E. J. Correia, A. R. Chen, S. Regmi, S. G. Dasso, M. Patke, A. Palazzo, A. F. Kossiakoff, A. A. Hoelz, A. 2021-10-26 doi:10.1101/2021.10.26.465790 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Upregulated PD-1 Signaling is an Important Antagonist to Glomerular Health in Aged Kidneys ]]> https://biorxiv.org/content/10.1101/2021.10.26.466006v1?rss=1 Pippin, J. W. Kaverina, N. Wang, Y. Eng, D. Zeng, Y. Tran, U. Loretz, C. J. Chang, A. O'Connor, C. Bitzer, M. Wessely, O. Shankland, S. J. 2021-10-26 doi:10.1101/2021.10.26.466006 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response ]]> https://biorxiv.org/content/10.1101/2021.10.27.466170v1?rss=1 Chowdhary, S. Kainth, A. S. Paracha, S. Gross, D. S. Pincus, D. 2021-10-28 doi:10.1101/2021.10.27.466170 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ No robust coexistence in a canonical model of plant-soil feedbacks ]]> https://biorxiv.org/content/10.1101/2021.10.27.466177v1?rss=1 Miller, Z. R. Lechon-Alonso, P. Allesina, S. 2021-10-28 doi:10.1101/2021.10.27.466177 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology ]]> https://biorxiv.org/content/10.1101/2021.10.28.466194v1?rss=1 Earley, Z. M. Lisicka, W. Sifakis, J. J. Gamboa, R. A. Kowalczyk, A. Barlow, J. Shaw, D. G. Discepolo, V. Tan, I. L. Gona, S. Ernest, J. Matzinger, P. Barreiro, L. B. Morgun, A. Bendelac, A. Ismagilov, R. F. Shulzhenko, N. Riesenfeld, S. J. Jabri, B. 2021-10-28 doi:10.1101/2021.10.28.466194 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Computational Fontan Analysis: Preserving accuracy while expediting workflow ]]> https://biorxiv.org/content/10.1101/2021.10.28.466272v1?rss=1 Liu, X. Aslan, S. Kim, B. Warburton, L. Jackson, D. Muhuri, A. Subramanian, A. Mass, P. Cleveland, V. Loke, Y.-H. Hibino, N. Olivieri, L. Krieger, A. 2021-10-29 doi:10.1101/2021.10.28.466272 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Reproduction, seasonal morphology, and juvenile growth in three Malagasy fruit bats ]]> https://biorxiv.org/content/10.1101/2021.10.28.466299v1?rss=1 Andrianiaina, A. Andry, S. Gentles, A. Guth, S. Heraud, J.-M. Ranaivoson, H. C. Ravelomanantsoa, N. A. F. Treuer, T. Brook, C. E. 2021-10-29 doi:10.1101/2021.10.28.466299 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Natural transformation protein ComFA exhibits single-stranded DNA translocase activity ]]> https://biorxiv.org/content/10.1101/2021.10.29.466550v1?rss=1 Foster, H. R. Lin, X. Srikant, S. Cueny, R. R. Falbel, T. G. Keck, J. L. Gaudet, R. Burton, B. M. 2021-10-30 doi:10.1101/2021.10.29.466550 Cold Spring Harbor Laboratory Press 2021-10-30 <![CDATA[ AAV9-MCT8 delivery at juvenile stage ameliorates neurological and behavioral deficits in an AHDS mouse model ]]> https://biorxiv.org/content/10.1101/2021.10.31.466634v1?rss=1 Liao, X.-H. Avalos, P. Oksana, S. Ofan, R. Shilo, M. Bresee, C. Likhite, S. Vit, J.-P. Heuer, H. Kaspar, B. Kathrin, M. Dumitrescu, A. M. Refetoff, S. Svendsen, C. N. Vatine, G. D. 2021-11-02 doi:10.1101/2021.10.31.466634 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Optimized immunoglobulin knock-ins using Cas9 reveal peritoneal B cell lineage relationships in vivo ]]> https://biorxiv.org/content/10.1101/2021.10.31.466662v1?rss=1 Bendelac, A. Erickson, S. A. Zapata-Bultman, E. Degenstein, L. 2021-11-01 doi:10.1101/2021.10.31.466662 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Cas9-Assisted Biological Containment of a Genetically Engineered Human Commensal Bacterium and Genetic Elements ]]> https://biorxiv.org/content/10.1101/2021.11.03.467106v1?rss=1 Hayashi, N. Lai, Y. Mimee, M. Lu, T. K. 2021-11-03 doi:10.1101/2021.11.03.467106 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Fine-mapping from summary data with the "Sum of Single Effects" model ]]> https://biorxiv.org/content/10.1101/2021.11.03.467167v1?rss=1 Zou, Y. Carbonetto, P. Wang, G. Stephens, M. 2021-11-04 doi:10.1101/2021.11.03.467167 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Modelling liver cancer microenvironment: novel 3D culture system as a potential anti-cancer drug screening tool ]]> https://biorxiv.org/content/10.1101/2021.11.04.467266v1?rss=1 Al Hrout, A. Cervantes-Gracia, K. Chahwan, R. Amin, A. 2021-11-04 doi:10.1101/2021.11.04.467266 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Regulation of ERK2 activity by dynamic S-acylation ]]> https://biorxiv.org/content/10.1101/2021.11.05.467491v1?rss=1 Azizi, S.-A. Qiu, T. Brookes, N. Dickinson, B. C. 2021-11-05 doi:10.1101/2021.11.05.467491 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Making Common Fund data more Findable: Catalyzing a Data Ecosystem ]]> https://biorxiv.org/content/10.1101/2021.11.05.467504v1?rss=1 Charbonneau, A. L. Brady, A. Brown, C. T. Sansone, S.-A. Ma'ayan, A. Wagner, R. Carter, R. Harris, R. M. Gingrich, A. Lim, M. C. W. Munro, J. B. Clarke, D. J. B. Creasy, H. H. Rocca-Serra, P. Jeon, M. Liming, R. L. Schuler, R. E. Romano, C. Chard, K. Giglio, M. Nadendla, S. Hodges, T. K. Mandal, M. Canchi, S. Waldrop, A. White, O. 2021-11-08 doi:10.1101/2021.11.05.467504 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Oncogenic and Tumor Suppressor Functions for Lymphoid Enhancer Factor 1 in a Murine Model of T Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2021.11.08.467708v1?rss=1 Carr, T. McGregor, S. Dias, S. Verykokakis, M. Le Beau, M. M. Xue, H.-H. Bartom, E. T. Kee, B. L. 2021-11-08 doi:10.1101/2021.11.08.467708 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Epidermal Growth Factor Receptor Inhibition Prevents Caveolin-1-dependent Calcifying Extracellular Vesicle Biogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.08.467799v1?rss=1 Nik, A. B. Ng, H. H. Sun, P. Iacoviello, F. Shearing, P. R. Bertazzo, S. Mero, D. Khomtchouk, B. B. Hutcheson, J. D. 2021-11-08 doi:10.1101/2021.11.08.467799 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Prehension kinematics in humans and macaques ]]> https://biorxiv.org/content/10.1101/2021.11.09.467947v1?rss=1 Yan, Y. Sobinov, A. Bensmaia, S. J. 2021-11-11 doi:10.1101/2021.11.09.467947 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities ]]> https://biorxiv.org/content/10.1101/2021.11.11.468290v1?rss=1 Harper, L. R. Niemiller, M. L. Benito, J. Paddock, L. E. Knittle, E. Molano-Flores, B. Davis, M. A. 2021-11-12 doi:10.1101/2021.11.11.468290 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Key Factors Governing Initial Stages of Lipid Droplet Formation ]]> https://biorxiv.org/content/10.1101/2021.11.12.468423v1?rss=1 Kim, S. Li, C. Farese, R. Walther, T. C. Voth, G. A. 2021-11-13 doi:10.1101/2021.11.12.468423 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Large-scale algorithmic search identifies stiff and sloppy dimensions in synaptic architectures consistent with murine neocortical wiring ]]> https://biorxiv.org/content/10.1101/2021.11.13.468127v1?rss=1 Jabri, T. MacLean, J. N. 2021-11-15 doi:10.1101/2021.11.13.468127 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Modulation of cutaneous responses in the cuneate nucleus of macaques during active movement ]]> https://biorxiv.org/content/10.1101/2021.11.15.468735v1?rss=1 He, Q. Versteeg, C. S. Suresh, A. K. Miller, L. E. Bensmaia, S. J. 2021-11-19 doi:10.1101/2021.11.15.468735 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Clonal hematopoiesis in individuals with ANKRD26 or ETV6 germline mutations ]]> https://biorxiv.org/content/10.1101/2021.11.17.468983v1?rss=1 Drazer, M. W. Homan, C. C. Yu, K. de Andrade Silva, M. C. McNeely, K. E. Pozsgai, M. J. Acevedo, M. G. Segal, J. P. Wang, P. Feng, J. King-Smith, S. L. Kim, E. Korotev, S. Lawrence, D. M. Schreiber, A. W. Hahn, C. N. Scott, H. S. Sood, R. NISC Comparative Sequencing Program, Velloso, E. D. R. P. Brown, A. L. Liu, P. P. Godley, L. A. 2021-11-22 doi:10.1101/2021.11.17.468983 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ A Biophysical Model of Nonquantal Transmission at the Vestibular Hair Cell-Calyx Synapse: KLV currents Modulate Fast Electrical and Slow K+ potentials in the Synaptic Cleft ]]> https://biorxiv.org/content/10.1101/2021.11.18.469197v1?rss=1 Govindaraju, A. C. Quraishi, I. H. Lysakowski, A. Eatock, R. A. Raphael, R. M. 2021-11-20 doi:10.1101/2021.11.18.469197 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ The Effect of COVID-19 on the Postdoctoral Experience: a comparison of pre-pandemic and pandemic surveys. ]]> https://biorxiv.org/content/10.1101/2021.11.19.468693v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@174d7e3org.highwire.dtl.DTLVardef@9893dorg.highwire.dtl.DTLVardef@114470org.highwire.dtl.DTLVardef@1a4278f_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract of survey responses to: Why or how has your research been disrupted or not disrupted due to the pandemic? Overall, postdocs responded with feelings of loss of control as the pandemic was acting upon them and taking away their ability to complete their work. C_FIG ]]> Morin, A. Helling, B. A. Krishnan, S. Risner, L. E. Walker, N. D. Schwartz, N. B. 2021-11-21 doi:10.1101/2021.11.19.468693 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution ]]> https://biorxiv.org/content/10.1101/2021.11.21.469441v1?rss=1 Zhu, F. Grier, H. A. Tandon, R. Cai, C. Giovannucci, A. Kaufman, M. T. Pandarinath, C. 2021-11-21 doi:10.1101/2021.11.21.469441 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ Characterizing the short-latency evoked response to intracortical microstimulation across a multi-electrode array ]]> https://biorxiv.org/content/10.1101/2021.11.22.469555v1?rss=1 Sombeck, J. Heye, J. Kumaravelu, K. Goetz, S. M. Peterchev, A. V. Grill, W. M. Bensmaia, S. J. Miller, L. E. 2021-11-23 doi:10.1101/2021.11.22.469555 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Ribonucleotide Reductase Regulatory Subunit M2 as a Driver of Glioblastoma TMZ-Resistance through Modulation of dNTP Production ]]> https://biorxiv.org/content/10.1101/2021.11.23.469785v1?rss=1 Perrault, E. N. Shireman, J. M. Ali, E. S. Preddy, I. Lin, P. Park, C. Tomes, L. Zolp, A. J. Budhiraja, S. Baisiwala, S. James, C. D. Ben-Sahra, I. Pott, S. Basu, A. Ahmed, A. U. 2021-11-24 doi:10.1101/2021.11.23.469785 Cold Spring Harbor Laboratory Press 2021-11-24 <![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[ Stability criteria for the consumption and exchange of essential resources ]]> https://biorxiv.org/content/10.1101/2021.11.24.469922v1?rss=1 Gibbs, T. Zhang, Y. Miller, Z. R. O'Dwyer, J. P. 2021-11-25 doi:10.1101/2021.11.24.469922 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Listeria monocytogenes requires cellular respiration for NAD+ regeneration and pathogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.25.470024v1?rss=1 1,000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX rescued this phenotype. These studies show that NAD+ regeneration, rather than oxidative phosphorylation, represents the primary role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis. ]]> Rivera-Lugo, R. Deng, D. Anaya-Sanchez, A. Tejedor-Sanz, S. Reyes Ruiz, V. M. Smith, H. B. Titov, D. V. Sauer, J. D. Skaar, E. P. Ajo-Franklin, C. M. Portnoy, D. A. Light, S. H. 2021-11-25 doi:10.1101/2021.11.25.470024 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Epistasis is not a strong constraint on the recurrent evolution of toxin-resistant Na+,K+-ATPases among tetrapods ]]> https://biorxiv.org/content/10.1101/2021.11.29.470343v1?rss=1 Mohammadi, S. Yang, L. Herrera-Alvarez, S. Rodriguez-Ordonez, M. d. P. Zhang, K. Storz, J. Crawford, A. J. Andolfatto, P. 2021-11-29 doi:10.1101/2021.11.29.470343 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates ]]> https://biorxiv.org/content/10.1101/2021.11.29.470486v1?rss=1 Zhang, J. Wang, Z. Zhang, S. Bhalerao, M. M. Liu, Y. Zhu, D. Wang, S. 2021-12-01 doi:10.1101/2021.11.29.470486 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Spatiotemporal NF-κB dynamics encodes the position, amplitude and duration of local immune inputs ]]> https://biorxiv.org/content/10.1101/2021.11.30.470463v1?rss=1 Son, M. Frank, T. Holst-Hansen, T. Wang, A. G. Junkin, M. Kashaf, S. S. Trusina, A. Tay, S. 2021-12-01 doi:10.1101/2021.11.30.470463 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism ]]> https://biorxiv.org/content/10.1101/2021.12.01.470729v1?rss=1 Romitti, M. de Faria da Fonseca, B. Doumont, G. Gillotay, P. Tourneur, A. Eski, S. E. Van Simaeys, G. Chomette, L. Lasolle, h. Monestier, O. Figini Kasprzyk, D. Detours, V. Singh, S. P. Goldman, S. Refetoff, S. P. Costagliola, S. 2021-12-01 doi:10.1101/2021.12.01.470729 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ From the formation of embryonic appendages to the color of wings: Conserved and novel roles of aristaless1 in butterfly development ]]> https://biorxiv.org/content/10.1101/2021.12.02.470931v1?rss=1 Bayala, E. X. VanKuren, N. Massardo, D. Kronforst, M. 2021-12-03 doi:10.1101/2021.12.02.470931 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Trial-by-trial fluctuations in amygdala activity track motivational enhancement of desirable sensory evidence during perceptual decision-making ]]> https://biorxiv.org/content/10.1101/2021.12.03.471135v1?rss=1 Paterson, R. Lyu, Y. Leong, Y. C. 2021-12-06 doi:10.1101/2021.12.03.471135 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane ]]> https://biorxiv.org/content/10.1101/2021.12.05.471300v1?rss=1 Kim, S. Chung, J. Arlt, H. Pak, A. J. Farese, R. V. Walther, T. C. Voth, G. A. 2021-12-06 doi:10.1101/2021.12.05.471300 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Gap genes are involved in inviability in hybrids between Drosophila melanogaster and D. santomea ]]> https://biorxiv.org/content/10.1101/2021.12.06.471493v1?rss=1 Chang, W. Kreitman, M. Matute, D. R. 2021-12-07 doi:10.1101/2021.12.06.471493 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Molecular mechanism of claudin-15 strand flexibility ]]> https://biorxiv.org/content/10.1101/2021.12.07.471660v1?rss=1 Fuladi, S. McGuinness, S. Shen, L. Weber, C. R. Khalili-Araghi, F. 2021-12-09 doi:10.1101/2021.12.07.471660 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Structural basis for topological regulation of Tn3 resolvase ]]> https://biorxiv.org/content/10.1101/2021.12.07.471667v1?rss=1 Montano, S. P. Rowland, S.-J. Fuller, J. R. Burke, M. E. MacDonald, A. I. Boocock, M. R. Stark, W. M. Rice, P. A. 2021-12-08 doi:10.1101/2021.12.07.471667 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Trapping of Nicotinic Acetylcholine Receptor Ligands Assayed by in vitro Cellular Studies and in vivo PET Imaging ]]> https://biorxiv.org/content/10.1101/2021.12.08.471775v1?rss=1 Zhang, H. Kao, C.-M. Zammit, M. Govind, A. P. Mitchell, S. Holderman, N. Bhuiyan, M. Freifelder, R. Zhuang, X. Mukherjee, J. Chen, C.-T. Green, W. 2021-12-10 doi:10.1101/2021.12.08.471775 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Ion Transport, Selectivity, and Electronic Polarization in Fluoride Channels ]]> https://biorxiv.org/content/10.1101/2021.12.08.471811v1?rss=1 Yue, Z. Wang, Z. Voth, G. A. 2021-12-10 doi:10.1101/2021.12.08.471811 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Multiple genes in cis mediate the effects of a single chromatin accessibility variant on aberrant synaptic development and function in human neurons ]]> https://biorxiv.org/content/10.1101/2021.12.11.472229v1?rss=1 Zhang, S. Zhang, H. Forrest, M. Zhou, Y. Bagchi, V. A. Kozlova, A. Santos, M. D. Piguel, N. Dionisio, L. E. Sanders, A. R. Pang, Z. P. He, X. Penzes, P. Duan, J. 2021-12-12 doi:10.1101/2021.12.11.472229 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ The first Miocene fossils from coastal woodlands in the southern East African Rift ]]> https://biorxiv.org/content/10.1101/2021.12.16.472914v1?rss=1 Bobe, R. Aldeias, V. Alemseged, Z. Archer, W. Aumaitre, G. Bamford, M. K. Biro, D. Bourles, D. L. Braun, D. R. Capelli, C. d'Oliveira Coelho, J. Habermann, J. M. Head, J. J. Kupczik, K. Lebatard, A.-E. Luedecke, T. Macoa, A. Martinez, F. I. Mathe, J. Meira Paulo, L. Mendes, C. Pinto, M. Puschel, T. A. Tata Regala, F. Sier, M. Ferreira da Silva, M. J. Stalmans, M. Carvalho, S. 2021-12-18 doi:10.1101/2021.12.16.472914 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders ]]> https://biorxiv.org/content/10.1101/2021.12.20.472354v1?rss=1 Porubsky, D. Höps, W. Ashraf, H. Hsieh, P. Rodriguez-Martin, B. Yilmaz, F. Ebler, J. Hallast, P. Maggiolini, F. A. M. Harvey, W. T. Henning, B. Audano, P. A. Gordon, D. S. Ebert, P. Hasenfeld, P. Benito, E. Zhu, Q. Human Genome Structural Variation Consortium, Lee, C. Antonacci, F. Steinrücken, M. Beck, C. R. Sanders, A. D. Marschall, T. Eichler, E. E. Korbel, J. O. 2021-12-20 doi:10.1101/2021.12.20.472354 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ A discovery-based proteomics approach identifies protein disulfide isomerase (PDIA1) as a biomarker of β cell stress in type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.22.473924v1?rss=1 Syed, F. Singhal, D. Raedschelders, K. Krishnan, P. Bone, R. N. McLaughlin, M. R. Van Eyk, J. E. Mirmira, R. G. Yang, M.-L. Mamula, M. J. Wu, H. Liu, X. Evans-Molina, C. 2021-12-23 doi:10.1101/2021.12.22.473924 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ The cardiac lncRNA Chantico directly regulates Cxcl1 chemokine transcription ]]> https://biorxiv.org/content/10.1101/2021.12.23.474040v1?rss=1 Hall, J. M. Kainth, A. S. Rowton, M. J. Lu, E. Haddad, G. Keplinger, A. J. Scepanovic, J. Perez-Cervantes, C. Chan, S. S. K. Piccirilli, J. A. Moskowitz, I. P. Ruthenburg, A. J. 2021-12-24 doi:10.1101/2021.12.23.474040 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells ]]> https://biorxiv.org/content/10.1101/2021.12.30.474519v1?rss=1 Nguyen, L. C. Renner, D. M. Silva, D. Yang, D. Medina, K. M. Nicolaescu, V. Gula, H. Drayman, N. Valdespino, A. Mohamed, A. Dann, C. Wannemo, K. Robinson-Mailman, L. Gonzalez, A. Stock, L. Cao, M. Qiao, Z. Moellering, R. E. Tay, S. Randall, G. Beers, M. F. Rosner, M. R. Oakes, S. A. Weiss, S. R. 2021-12-30 doi:10.1101/2021.12.30.474519 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Development, Structure, and Mechanism of Synthetic Antibodies that Target Claudin and Clostridium perfringens Enterotoxin Complexes ]]> https://biorxiv.org/content/10.1101/2022.01.01.474715v1?rss=1 Orlando, B. J. Dominik, P. K. Roy, S. Ogbu, C. Erramilli, S. K. Kossiakoff, A. A. Vecchio, A. J. 2022-01-02 doi:10.1101/2022.01.01.474715 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences ]]> https://biorxiv.org/content/10.1101/2022.01.03.474815v1?rss=1 Hess, R. A. Erickson, O. A. Cole, R. B. Isaacs, J. M. Alvarez-Clare, S. Arnold, J. Augustus-Wallace, A. C. Ayoob, J. C. Berkowitz, A. Branchaw, J. L. Burgio, K. R. Cannon, C. H. Ceballos, R. M. Cohen, C. S. Coller, H. Disney, J. Doze, V. A. Eggers, M. J. Ferguson, E. L. Gray, J. J. Greenberg, J. T. Hoffmann, A. Jensen-Ryan, D. Kao, R. M. Keene, A. C. Kowalko, J. Lopez, S. A. Mathis, C. Minkara, M. Murren, C. J. Ondrechen, M. J. Ordonez, P. Osano, A. Padilla-Crespo, E. Palchoudhury, S. Qin, H. Ramirez-Lugo, J. Reithel, J. Shaw, C. A. Smith, A. Smith, R. J 2022-01-05 doi:10.1101/2022.01.03.474815 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Engineered collagen-targeting therapeutics reverse lung and kidney fibrosis in mice ]]> https://biorxiv.org/content/10.1101/2022.01.04.474747v1?rss=1 WHITE, M. J. V. Raczy, M. Budina, E. Solanki, A. Zhang, Z. J. Gray, L. T. Cao, S. Alpar, A. T. Hubbell, J. 2022-01-05 doi:10.1101/2022.01.04.474747 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Oligomerization of peripheral membrane proteins provides tunable control of cell surface polarity ]]> https://biorxiv.org/content/10.1101/2022.01.04.474999v1?rss=1 Lang, C. F. Munro, E. 2022-01-05 doi:10.1101/2022.01.04.474999 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ The diversity and functional capacity of microbes associated with coastal phototrophs ]]> https://biorxiv.org/content/10.1101/2022.01.05.475171v1?rss=1 Miranda, K. K. Weigel, B. L. Fogarty, E. Veseli, I. A. Giblin, A. Murat Eren, A. Pfister, C. A. 2022-01-07 doi:10.1101/2022.01.05.475171 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain's allostery and unfolding upon B12 and TonB binding ]]> https://biorxiv.org/content/10.1101/2022.01.07.475440v1?rss=1 Zmyslowski, A. M. Baxa, M. C. Gagnon, I. A. Sosnick, T. C. 2022-01-09 doi:10.1101/2022.01.07.475440 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Noise source importance in linear stochastic models of biological systems that grow, shrink, wander, or persist ]]> https://biorxiv.org/content/10.1101/2022.01.10.475598v1?rss=1 Strang, A. Huffmyer, W. Rollins, H. Abbott, K. C. Thomas, P. J. 2022-01-11 doi:10.1101/2022.01.10.475598 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ A single-cell atlas reveals shared and distinct immune responses and metabolism during SARS-CoV-2 and HIV-1 infections ]]> https://biorxiv.org/content/10.1101/2022.01.10.475725v1?rss=1 Pan, T. Cao, G. Tang, E. Zhao, Y. Penaloza-MacMaster, P. Fang, Y. Huang, J. 2022-01-11 doi:10.1101/2022.01.10.475725 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ OrganoID: a versatile deep learning platform for organoid image analysis ]]> https://biorxiv.org/content/10.1101/2022.01.13.476248v1?rss=1 Matthews, J. M. Schuster, B. Kashaf, S. S. Liu, P. Bilgic, M. Rzhetsky, A. Tay, S. 2022-01-16 doi:10.1101/2022.01.13.476248 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ NF-κB memory coordinates transcriptional responses to dynamic inflammatory stimuli ]]> https://biorxiv.org/content/10.1101/2022.01.14.476099v1?rss=1 Wang, A. G. Son, M. Thom, N. Tay, S. 2022-01-16 doi:10.1101/2022.01.14.476099 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation ]]> https://biorxiv.org/content/10.1101/2022.01.14.476225v1?rss=1 Nam, A. S. Dusaj, N. Izzo, F. Murali, R. Myers, R. M. Mouhieddine, T. Sotelo, J. Benbarche, S. Waarts, M. Gaiti, F. Tahri, S. Levine, R. Abdel-Wahab, O. Godley, L. A. Chaligne, R. Ghobrial, I. M. Landau, D. 2022-01-16 doi:10.1101/2022.01.14.476225 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Fat2 polarizes the WAVE complex in trans to align cell protrusions for collective migration ]]> https://biorxiv.org/content/10.1101/2022.01.17.476701v1?rss=1 Williams, A. M. Donoughe, S. Munro, E. Horne-Badovinac, S. 2022-01-20 doi:10.1101/2022.01.17.476701 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ A Population Response Model of Ensemble Coding ]]> https://biorxiv.org/content/10.1101/2022.01.19.476871v1?rss=1 Utochkin, I. S. Choi, J. Chong, S. C. 2022-01-22 doi:10.1101/2022.01.19.476871 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance ]]> https://biorxiv.org/content/10.1101/2022.01.21.477267v1?rss=1 Chen, W. Brown, J. S. He, T. Wu, W.-S. Tu, S. Weng, Z. Zhang, D. Lee, H.-C. 2022-01-22 doi:10.1101/2022.01.21.477267 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ PERSISTENT RELIEF OF MOTOR SYMPTOMS IN A PARKINSONIAN MOUSE MODEL AFTER INDUCTION OF LTD AT CORTICAL INPUTS TO INDIRECT PATHWAY STRIATAL NEURONS ]]> https://biorxiv.org/content/10.1101/2022.01.21.477283v1?rss=1 3 weeks. Consistent with LTD induction, oLTD-treated mice had reduced VGLUT1 expression in striatum and greater excitability of D2 neurons. These findings suggest that reversing aberrant corticostriatal synaptic plasticity in the indirect pathway may lead to persistent relief of PD motor symptoms. ]]> Abburi, C. Thome, J. Rodriguez, B. Zhuang, X. McGehee, D. S. 2022-01-23 doi:10.1101/2022.01.21.477283 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ A sparse set of spikes corresponding to reliable correlations is highly informative of visual stimulus on single trials ]]> https://biorxiv.org/content/10.1101/2022.01.24.477564v1?rss=1 Levy, M. Guo, J. K. MacLean, J. N. 2022-01-25 doi:10.1101/2022.01.24.477564 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Sampling-based Bayesian inference in recurrent circuits of stochastic spiking neurons ]]> https://biorxiv.org/content/10.1101/2022.01.26.477877v1?rss=1 Zhang, W. Wu, S. Josic, K. Doiron, B. 2022-01-28 doi:10.1101/2022.01.26.477877 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Blood flow modeling under LVAD physiology. From global circulation to local hemodynamics ]]> https://biorxiv.org/content/10.1101/2022.01.28.478161v1?rss=1 Blanco, P. J. Grinstein, J. Bulant, C. A. Torii, R. Bourantas, C. Lemos, P. Garcia-Garcia, H. 2022-01-28 doi:10.1101/2022.01.28.478161 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Multiphasic hepatitis B virus kinetic patterns in humanized chimeric mice can be explained via stochastic agent-based modeling of intracellular virion production cycles ]]> https://biorxiv.org/content/10.1101/2022.01.30.478385v1?rss=1 Hailegiorgis, A. Ishida, Y. Collier, N. Imamura, M. Shi, Z. Reinharz, V. Tsuge, M. Barash, D. Hiraga, N. Yokomichi, H. Tateno, C. Ozik, J. Uprichard, S. L. Chayama, K. Dahari, H. 2022-01-30 doi:10.1101/2022.01.30.478385 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus ]]> https://biorxiv.org/content/10.1101/2022.02.02.478820v1?rss=1 Spring, J. Lara, S. Khan, A. A. O'Grady, K. Wilks, J. Gurbuxani, S. Erickson, S. Fischbach, M. Jacobson, A. Chervonsky, A. Golovkina, T. 2022-02-02 doi:10.1101/2022.02.02.478820 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer ]]> https://biorxiv.org/content/10.1101/2022.02.04.479189v1?rss=1 Vandegrift, K. J. Yon, M. Surendran-Nair, M. Gontu, A. Amirthalingam, S. Nissly, R. H. Levine, N. Stuber, T. DeNicola, A. J. Boulanger, J. R. Kotschwar, N. Aucoin, S. G. Simon, R. Toal, K. Olsen, R. J. Davis, J. J. Bold, D. Gaudreault, N. N. Richt, J. A. Musser, J. M. Hudson, P. J. Kapur, V. Kuchipudi, S. V. 2022-02-07 doi:10.1101/2022.02.04.479189 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ An automated pipeline for extracting quantitative histological metrics for voxelwise MRI-histology comparisons ]]> https://biorxiv.org/content/10.1101/2022.02.10.479718v1?rss=1 Kor, D. Z. L. Jbabdi, S. Huszar, I. N. Mollink, J. Tendler, B. C. Foxley, S. Wang, C. Scott, C. Smart, A. Ansorge, O. Pallebage-Gamarallage, M. Miller, K. L. Howard, A. F. D. 2022-02-10 doi:10.1101/2022.02.10.479718 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Seeing the future: a better way to model and test for adaptive developmental plasticity ]]> https://biorxiv.org/content/10.1101/2022.02.10.479998v1?rss=1 Malani, A. Rosenbaum, S. Alberts, S. C. Archie, E. 2022-02-11 doi:10.1101/2022.02.10.479998 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ A novel Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening ]]> https://biorxiv.org/content/10.1101/2022.02.13.480282v1?rss=1 Zhou, Y. Luo, K. Chen, M. He, X. 2022-02-13 doi:10.1101/2022.02.13.480282 Cold Spring Harbor Laboratory Press 2022-02-13 <![CDATA[ Functional and effective connectivity between dorsolateral prefrontal and subgenual anterior cingulate cortex depends on the timing of transcranial magnetic stimulation relative to the phase of prefrontal alpha EEG ]]> https://biorxiv.org/content/10.1101/2022.02.14.480466v1?rss=1 Pantazatos, S. P. McIntosh, J. R. Saber, G. T. Sun, X. Doose, J. Faller, J. Lin, Y. Teves, J. B. Blankenship, A. Huffman, S. Goldman, R. I. George, M. S. Sajda, P. Brown, T. 2022-02-16 doi:10.1101/2022.02.14.480466 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Ingestible capsule for detecting labile inflammatory biomarkers in situ ]]> https://biorxiv.org/content/10.1101/2022.02.16.480562v1?rss=1 Inda, M. E. Jimenez, M. Liu, Q. Phan, N. Ahn, J. Steiger, C. Wentworth, A. Riaz, A. Zirtiloglu, T. Wong, K. Ishida, K. Fabian, N. Jenkins, J. Kuosmanen, J. Madani, W. McNally, R. Lai, Y. Mimee, M. Nadeau, P. Chandrakasan, A. Hayward, A. Traverso, G. Yazicigil, R. T. Lu, T. K. 2022-02-16 doi:10.1101/2022.02.16.480562 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Mechanism of Voltage Gating in the Voltage-Sensing Phosphatase Ci-VSP ]]> https://biorxiv.org/content/10.1101/2022.02.17.480971v1?rss=1 Shen, R. Meng, Y. Roux, B. Perozo, E. 2022-02-18 doi:10.1101/2022.02.17.480971 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2022.02.19.481089v1?rss=1 Guarnieri, J. W. Dybas, J. M. Fazelinia, H. Kim, M. S. Frere, J. Zhang, Y. Albrecht, Y. S. Murdock, D. G. Angelin, A. Singh, L. N. Weiss, S. L. Best, S. M. Lott, M. T. Cope, H. Zaksas, V. Saravia-Butler, A. Meydan, C. Foox, J. Mozsary, C. Kidane, Y. H. Priebe, W. Emmett, M. Meller, R. Singh, U. Bram, Y. tenOever, B. R. Heise, M. T. Moorman, N. J. Madden, E. A. Taft-Benz, S. A. Anderson, E. J. Sanders, W. A. Dickmander, R. J. Baxter, V. K. Baylin, S. Wurtele, E. Moraes-vieira, P. Taylor, D. Mason, C. Schisler, J. C. Schwartz, R. E. Beheshti, A. Wallace, 2022-02-22 doi:10.1101/2022.02.19.481089 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Interplay between external inputs and recurrent dynamics during movement preparation and execution in a network model of motor cortex ]]> https://biorxiv.org/content/10.1101/2022.02.19.481140v1?rss=1 Bachschmid-Romano, L. Hatsopoulos, N. Brunel, N. 2022-02-19 doi:10.1101/2022.02.19.481140 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Dynamic genetic adaptation of Bacteroides thetaiotaomicron murine gut colonization ]]> https://biorxiv.org/content/10.1101/2022.02.23.481734v1?rss=1 Zhang, M. Kennedy, M. DeLeon, O. Bissell, J. Trigodet, F. Lolans, K. Temelkova, S. Carroll, K. T. Fiebig, A. Deutschbauer, A. M. Sidebottom, A. M. Henry, C. S. Rice, P. A. Bergelson, J. Chang, E. 2022-02-24 doi:10.1101/2022.02.23.481734 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Model-free analysis in the spectral domain of postmortem mouse brain EPSI reveals inconsistencies with model-based analyses of the free induction decay ]]> https://biorxiv.org/content/10.1101/2022.02.24.481824v1?rss=1 Trinkle, S. Wildenberg, G. Kasthuri, N. La Riviere, P. Foxley, S. 2022-02-25 doi:10.1101/2022.02.24.481824 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ An apical membrane complex controls rhoptry exocytosis and invasion in Toxoplasma ]]> https://biorxiv.org/content/10.1101/2022.02.25.481937v1?rss=1 Sparvoli, D. Delabre, J. Penarete-Vargas, D. M. Kumar Mageswaran, S. Tsypin, L. M. Heckendorn, J. Theveny, L. Maynadier, M. Mendonca Cova, M. Berry-Sterkers, L. Guerin, A. Dubremetz, J.-F. Urbach, S. Striepen, B. Turkewitz, A. P. Chang, Y.-W. LEBRUN, M. 2022-02-25 doi:10.1101/2022.02.25.481937 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ A cooperative switch within the KaiC hexamer revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2022.02.27.481910v1?rss=1 Han, X. Zhang, D. Hong, L. Yu, D. Wu, Z. Yang, T. Rust, M. Tu, Y. Ouyang, Q. 2022-02-28 doi:10.1101/2022.02.27.481910 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ HIF-1α induces glycolytic reprogramming in tissue-resident alveolar macrophagesto promote survival during acute lung injury ]]> https://biorxiv.org/content/10.1101/2022.02.28.482301v1?rss=1 Woods, P. S. Kimmig, L. M. Sun, K. A. Meliton, A. Y. Shamaa, O. R. Tian, Y. Cetin-Atalay, R. Sharp, W. W. Hamanaka, R. B. Mutlu, G. M. 2022-03-01 doi:10.1101/2022.02.28.482301 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Human hippocampal responses to network stimulation vary with theta phase ]]> https://biorxiv.org/content/10.1101/2022.02.28.482345v1?rss=1 Lurie, S. M. Kragel, J. E. Schuele, S. U. Voss, J. L. 2022-03-02 doi:10.1101/2022.02.28.482345 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution ]]> https://biorxiv.org/content/10.1101/2022.03.02.482602v1?rss=1 Kiefl, E. Esen, O. C. Miller, S. E. Kroll, K. L. Willis, A. D. Rappe, M. S. Pan, T. Eren, A. M. 2022-03-02 doi:10.1101/2022.03.02.482602 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Confluence and tight junction dependence of volume regulation in epithelial tissue ]]> https://biorxiv.org/content/10.1101/2022.03.02.482689v1?rss=1 Chmiel, T. A. Gardel, M. L. 2022-03-04 doi:10.1101/2022.03.02.482689 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia) ]]> https://biorxiv.org/content/10.1101/2022.03.04.482893v1?rss=1 Edie, S. M. Collins, K. S. Jablonski, D. 2022-03-04 doi:10.1101/2022.03.04.482893 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions ]]> https://biorxiv.org/content/10.1101/2022.03.04.483020v1?rss=1 Tsai, F.-C. Henderson, J. M. Jarin, Z. Kremneva, E. Senju, Y. Pernier, J. Mikhajlov, O. Manzi, J. Kogan, K. Le Clainche, C. Voth, G. A. Lappalainen, P. Bassereau, P. 2022-03-04 doi:10.1101/2022.03.04.483020 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Design of the mammalian cone photoreceptor to Off bipolar cell synapse ]]> https://biorxiv.org/content/10.1101/2022.03.04.483056v1?rss=1 Grabner, C. Futagi, D. Shi, J. Bindokas, V. P. Kitano, K. Schwartz, E. A. DeVries, S. H. 2022-03-05 doi:10.1101/2022.03.04.483056 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ LanA (Language Atlas): A probabilistic atlas for the language network based on fMRI data from >800 individuals ]]> https://biorxiv.org/content/10.1101/2022.03.06.483177v1?rss=1 Lipkin, B. Tuckute, G. Affourtit, J. Small, H. Mineroff, Z. Kean, H. Jouravlev, O. Rakocevic, L. Pritchett, B. Siegelman, M. Hoeflin, C. Pongos, A. Blank, I. Shruhl, M. K. Ivanova, A. Shannon, S. Sathe, A. Hoffmann, M. Nieto-Castanon, A. Fedorenko, E. 2022-03-07 doi:10.1101/2022.03.06.483177 800 individuals]]> Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Complete identity of the cis-asRNA StfZ and its influence on FtsZ protein level and cell division in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.03.08.483438v1?rss=1 Anand, D. Jakkala, K. Nair, R. R. Sharan, D. Pradhan, A. Mukkayyan, N. Ajitkumar, P. 2022-03-08 doi:10.1101/2022.03.08.483438 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Activation of targetable inflammatory immune signaling is seen in Myelodysplastic Syndromes with SF3B1 mutations ]]> https://biorxiv.org/content/10.1101/2022.03.09.483595v1?rss=1 Choudhary, G. Pellagatti, A. Agianian, B. Smith, M. Bhagat, T. D. Gordon-Mitchell, S. Pandey, S. Shah, N. Aluri, S. Schwartz, L. Steeples, V. Booher, R. Ramachandra, M. Samson, M. Carbajal, M. Pradhan, K. Bowman, T. Pillai, M. M. Will, B. Wickrema, A. Shastri, A. Bradley, R. K. Martell, R. E. Steidl, U. Gavathiotis, E. Boultwood, J. Starczynowski, D. T. Verma, A. 2022-03-09 doi:10.1101/2022.03.09.483595 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ The lateral intraparietal area preferentially supports stimulus selection in directed tasks compared to undirected free behavior ]]> https://biorxiv.org/content/10.1101/2022.03.09.483625v1?rss=1 Johnston, W. J. Tetrick, S. M. Freedman, D. J. 2022-03-11 doi:10.1101/2022.03.09.483625 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ AttnPacker: An end-to-end deep learning method for rotamer-free protein side-chain packing ]]> https://biorxiv.org/content/10.1101/2022.03.11.483812v1?rss=1 McPartlon, M. Xu, J. 2022-03-14 doi:10.1101/2022.03.11.483812 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Structural insights into the regulation of acetylation-dependent genome condensation ]]> https://biorxiv.org/content/10.1101/2022.03.14.484228v1?rss=1 Ibrahim, Z. Wang, T. Destaing, O. Salvi, N. Hoghoughi, N. Rusu, A. D. Gao, J. Feletto, L. Reynoird, N. Schalch, T. Zhao, Y. Blackledge, M. Khochbin, S. Panne, D. 2022-03-14 doi:10.1101/2022.03.14.484228 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ TATTOO-seq delineates spatial and cell type-specific regulatory programs during limb patterning ]]> https://biorxiv.org/content/10.1101/2022.03.20.482385v1?rss=1 Bastide, S. Chomsky, E. Saudemont, B. Loe-Mie, Y. Schmutz, S. Novault, S. Marlow, H. Tanay, A. Spitz, F. 2022-03-20 doi:10.1101/2022.03.20.482385 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Arginine-dependent hypusination of the eukaryotic translation initiation factor (eIF)5A drives erythroid lineage differentiation ]]> https://biorxiv.org/content/10.1101/2022.03.21.485053v1?rss=1 Gonzalez-Menendez, P. Phadke, I. Olive, M. E. McGraw, K. L. Platon, J. Papoin, J. Yan, H. Daumur, M. Paul, F. Mirmira, R. Joly, A. Galtier, J. Narla, A. Cartron, G. Dardalhon, V. Zimmermann, V. S. Sitbon, M. Dever, T. E. Mohandas, N. Costa, L. d. Udeshi, N. D. Blanc, L. Kinet, S. Taylor, N. 2022-03-22 doi:10.1101/2022.03.21.485053 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ The little skate genome and the evolutionary emergence of wing-like fin appendages ]]> https://biorxiv.org/content/10.1101/2022.03.21.485123v1?rss=1 Marletaz, F. de la Calle-Mustienes, E. Acemel, R. D. Nakamura, T. Paliou, C. Naranjo, S. Martinez-Garcia, P. M. Cases, I. Sleight, V. A. Hirschberger, C. Marcet-Houben, M. Navon, D. Andrescavage, A. Skvortsova, K. Duckett, P. E. Gonzalez-Rajal, A. Bogdanovic, O. Gibcus, J. H. Yang, L. Gallardo-Fuentes, L. Sospedra, I. Lopez-Rios, J. Darbellay, F. Visel, A. Dekker, J. Shubin, N. Gabaldon, T. Tena, J. J. Lupianez, D. G. Rokhsar, D. S. Gomez-Skarmeta, J. L. 2022-03-22 doi:10.1101/2022.03.21.485123 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Cross-trait assortative mating is widespread and inflates genetic correlation estimates ]]> https://biorxiv.org/content/10.1101/2022.03.21.485215v1?rss=1 Border, R. Athanasiadis, G. Buil, A. Schork, A. Cai, N. Young, A. Werge, T. Flint, J. Kendler, K. Sankararaman, S. Dahl, A. Zaitlen, N. 2022-03-23 doi:10.1101/2022.03.21.485215 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ GASEOUS TRANSMITTER MODULATION OF HYPOGLOSSAL MOTONEURON ACTIVITY ]]> https://biorxiv.org/content/10.1101/2022.03.23.485481v1?rss=1 Browe, B. Peng, Y.-J. Nanduri, J. Prabhakar, N. Garcia, A. 2022-03-26 doi:10.1101/2022.03.23.485481 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ The actin assembly requirements of the formin Fus1 to build the fusion focus ]]> https://biorxiv.org/content/10.1101/2022.03.24.485616v1?rss=1 Billault-Chaumartin, I. Michon, L. Anderson, C. A. Yde, S. E. Suarez, C. Iwaszkiewicz, J. Zoete, V. Kovar, D. R. Martin, S. G. 2022-03-24 doi:10.1101/2022.03.24.485616 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Transcriptome-wide Analyses of Adipose Tissue in Outbred Rats Reveal Genetic Regulatory Mechanisms Relevant for Human Obesity ]]> https://biorxiv.org/content/10.1101/2022.03.24.485632v1?rss=1 Crouse, W. L. Das, S. K. Le, T. Keele, G. R. Holl, K. Seshi, O. Craddock, A. L. Sharma, N. Comeau, M. Langefeld, C. Hawkins, G. Mott, R. Valdar, W. Solberg Woods, L. 2022-03-24 doi:10.1101/2022.03.24.485632 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade ]]> https://biorxiv.org/content/10.1101/2022.03.24.485685v1?rss=1 Olson, B. Chaudagar, K. Bao, R. Sharma-Saha, S. Hong, C. Rameshbabu, S. Chen, R. Thomas, A. Patnaik, A. 2022-03-27 doi:10.1101/2022.03.24.485685 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response. ]]> https://biorxiv.org/content/10.1101/2022.03.26.485903v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@4368c9org.highwire.dtl.DTLVardef@1948201org.highwire.dtl.DTLVardef@e31fd9org.highwire.dtl.DTLVardef@1400805_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractModel of interactions among lncRNA and cognate RNA-binding proteins in SARS-CoV-2 infection. According to our model, the viral genome can establish direct interactions with three core proteins (DDX3X, UPF1 and IGF2BP2) involved in mRNA metabolism and regulation of the interferon response, which are also components of a SARS-CoV-2 lncRNA-centered regulatory network. The competition between viral RNA and lncRNAs could act as a counteracting factor for the normal function of homeostatic lncRNA-centered regulatory networks, contributing to viral progression and replication. Black arrows depict physical interactions between network components; red arrows represent functional relationships. ]]> Enguita, F. J. Leitao, A. L. McDonald, J. T. Zaksas, V. Das, S. Galeano, D. Taylor, D. Syrkin Wurtele, E. Saravia-Butler, A. Baylin, S. B. Meller, R. Porterfield, D. M. Wallace, D. C. Schisler, J. C. Mason, C. E. Beheshti, A. 2022-03-28 doi:10.1101/2022.03.26.485903 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins ]]> https://biorxiv.org/content/10.1101/2022.03.28.485852v1?rss=1 Kratochvil, H. T. Watkins, L. C. Mravic, M. Thomaston, J. L. Nicoludis, J. M. Liu, L. Voth, G. A. DeGrado, W. 2022-03-28 doi:10.1101/2022.03.28.485852 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies ]]> https://biorxiv.org/content/10.1101/2022.03.29.486265v1?rss=1 Pak, A. J. Gupta, M. Yeager, M. Voth, G. A. 2022-03-29 doi:10.1101/2022.03.29.486265 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Fear extinction is regulated by long noncoding RNA activity at the synapse ]]> https://biorxiv.org/content/10.1101/2022.03.30.486308v1?rss=1 Liau, W.-S. Zhao, Q. Bademosi, A. Gormal, R. Gong, H. Marshall, P. R. Periyakaruppiah, A. Madugalle, S. U. Zajackowski, E. L. Leighton, L. J. Ren, H. Musgrove, M. Davies, J. Rauch, S. He, C. Dickinson, B. Li, X. Wei, W. Meunier, F. A. Fernandez Moya, S. M. Kiebler, M. A. Srinivasan, B. Banerjee, S. Clark, M. Spitale, R. C. Bredy, T. W. 2022-03-31 doi:10.1101/2022.03.30.486308 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ Topographically distinct adaptive landscapes for skulls, skeletons, and size explain the dietary adaptive radiation of Carnivora (Mammalia) ]]> https://biorxiv.org/content/10.1101/2022.04.01.486739v1?rss=1 Slater, G. J. 2022-04-01 doi:10.1101/2022.04.01.486739 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ State Dependent Anionic Pore Currents Conducted by Single Countercharge Mutants in a Voltage-Sensing Phosphatase ]]> https://biorxiv.org/content/10.1101/2022.04.04.487073v1?rss=1 Shen, R. Perozo, E. Roux, B. 2022-04-06 doi:10.1101/2022.04.04.487073 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Sequential addition of neuronal stem cell temporal cohorts generates a feed-forward circuit in the Drosophila larval nerve cord ]]> https://biorxiv.org/content/10.1101/2022.04.05.487221v1?rss=1 Wang, Y.-w. Wreden, C. C. Levy, M. Marshall, Z. D. D. MacLean, J. N. Heckscher, E. S. 2022-04-06 doi:10.1101/2022.04.05.487221 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Rapid Rerouting of Myosin Traffic at the T Cell Immunological Synapse ]]> https://biorxiv.org/content/10.1101/2022.04.06.487340v1?rss=1 Maka, R. Plewa, N. Cichon, U. Krysztofiak, K. Rokicka, J. J. Rock, R. S. 2022-04-08 doi:10.1101/2022.04.06.487340 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ LILAC: Enhanced actin imaging with an optogenetic Lifeact ]]> https://biorxiv.org/content/10.1101/2022.04.07.487416v1?rss=1 Kroll, K. L. French, A. R. Sosnick, T. R. Rock, R. S. 2022-04-08 doi:10.1101/2022.04.07.487416 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Between-area communication through the lens of within-area neuronal dynamics ]]> https://biorxiv.org/content/10.1101/2022.04.11.487906v1?rss=1 Gozel, O. Doiron, B. 2022-04-11 doi:10.1101/2022.04.11.487906 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ On the interaction between Janzen-Connell effects and habitat partitioning in spatially structured environments ]]> https://biorxiv.org/content/10.1101/2022.04.11.487940v1?rss=1 Smith, D. J. B. 2022-04-12 doi:10.1101/2022.04.11.487940 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Phylogenomics and body shape morphometrics reveal recent origin and diversification in the goatfishes (Syngnatharia: Mullidae) ]]> https://biorxiv.org/content/10.1101/2022.04.12.488079v1?rss=1 Nash, C. M. Lungstrom, L. L. Hughes, L. C. Westneat, M. W. 2022-04-12 doi:10.1101/2022.04.12.488079 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Spinosaurids as 'subaqueous foragers' undermined by selective sampling and problematic statistical inference ]]> https://biorxiv.org/content/10.1101/2022.04.13.487781v1?rss=1 Myhrvold, N. P. Sereno, P. C. Baumgart, S. L. Formoso, K. K. Vidal, D. Fish, F. E. Henderson, D. M. 2022-04-14 doi:10.1101/2022.04.13.487781 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ A new chemotype of chemically tractable nonsteroidal estrogens based on a thienopyrimidine core. ]]> https://biorxiv.org/content/10.1101/2022.04.15.488344v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@4a0c18org.highwire.dtl.DTLVardef@16001f5org.highwire.dtl.DTLVardef@20a58forg.highwire.dtl.DTLVardef@1558bdf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sammeta, V. R. Norris, J. D. Artham, S. Torrice, C. D. Byemerwa, J. Joiner, C. Fanning, S. W. McDonnell, D. P. Willson, T. M. 2022-04-15 doi:10.1101/2022.04.15.488344 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ A Deep SE(3)-Equivariant Model for Learning Inverse Protein Folding ]]> https://biorxiv.org/content/10.1101/2022.04.15.488492v1?rss=1 McPartlon, m. Lai, B. Xu, J. 2022-04-16 doi:10.1101/2022.04.15.488492 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors ]]> https://biorxiv.org/content/10.1101/2022.04.21.489081v1?rss=1 Wcisel, D. J. Dornburg, A. McConnell, S. C. Hernandez, K. M. Andrade, J. de Jong, J. L. O. Litman, G. W. Yoder, J. A. 2022-04-22 doi:10.1101/2022.04.21.489081 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Inferring cell-type-specific causal gene regulatory networks during human neurogenesis ]]> https://biorxiv.org/content/10.1101/2022.04.25.488920v1?rss=1 Aygün, N. Liang, D. Crouse, W. L. Keele, G. R. Love, M. I. Stein, J. L. 2022-04-25 doi:10.1101/2022.04.25.488920 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Optimizing Oscillators for Specific Tasks Predicts Preferred Biochemical Implementations ]]> https://biorxiv.org/content/10.1101/2022.04.25.489380v1?rss=1 Agrahar, C. Rust, M. 2022-04-26 doi:10.1101/2022.04.25.489380 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Genetic and peripheral visual system changes underlie evolving butterfly mate preference ]]> https://biorxiv.org/content/10.1101/2022.04.25.489404v1?rss=1 VanKuren, N. W. Buerkle, N. P. Westerman, E. L. Im, A. K. Massardo, D. L. Lu, W. Palmer, S. E. Kronforst, M. R. 2022-04-26 doi:10.1101/2022.04.25.489404 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Sex-limited diversification of the eye in Heliconius butterflies ]]> https://biorxiv.org/content/10.1101/2022.04.25.489414v1?rss=1 Buerkle, N. P. VanKuren, N. W. Westerman, E. L. Kronforst, M. R. Palmer, S. E. 2022-04-26 doi:10.1101/2022.04.25.489414 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ The arthropod associates of 155 North American cynipid oak galls ]]> https://biorxiv.org/content/10.1101/2022.04.26.489445v1?rss=1 Ward, A. K. G. Busbee, R. W. Chen, R. A. Davis, C. K. Driscoe, A. L. Egan, S. P. Goldberg, B. A. Hood, G. R. Jones, D. Kranz, A. J. Meadley-Dunphy, S. A. Milks, A. K. Ott, J. R. Prior, K. M. Sheikh, S. I. Shzu, S. Weinersmith, K. L. Zhang, L. Zhang, Y. M. Forbes, A. A. 2022-04-27 doi:10.1101/2022.04.26.489445 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Truncated suPAR simultaneously causes kidney disease and autoimmune diabetes mellitus ]]> https://biorxiv.org/content/10.1101/2022.04.26.489589v1?rss=1 Zhu, K. Mukherjee, K. Wei, C. Hayek, S. S. Collins, A. Gu, C. Corapi, K. Altintas, M. M. Wang, Y. Sushrut, W. S. Bianco, A. C. Reiser, J. Sever, S. 2022-04-28 doi:10.1101/2022.04.26.489589 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Induction of Sis1 promotes fitness but not feedback in the heat shock response ]]> https://biorxiv.org/content/10.1101/2022.04.27.489698v1?rss=1 Garde, R. Singh, A. Ali, A. Pincus, D. 2022-04-28 doi:10.1101/2022.04.27.489698 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification ]]> https://biorxiv.org/content/10.1101/2022.04.29.490095v1?rss=1 Reilly, M. B. Tekieli, T. Cros, C. Aguilar, G. R. Lao, J. Toker, I. A. Vidal, B. Leyva-Diaz, E. Bhattacharya, A. Smith, J. J. Kovacevic, I. Gulez, B. Fernandez, R. Bradford, E. F. Ramadan, Y. H. Kratsios, P. Bao, Z. Hobert, O. 2022-05-02 doi:10.1101/2022.04.29.490095 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ The Features Underlying the Memorability of Objects ]]> https://biorxiv.org/content/10.1101/2022.04.29.490104v1?rss=1 Kramer, M. A. Bainbridge, W. A. Hebart, M. N. Baker, C. I. 2022-04-30 doi:10.1101/2022.04.29.490104 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Microbial metabolite butyrate-prodrug polymeric micelles promote gut health and treat food allergies ]]> https://biorxiv.org/content/10.1101/2022.05.01.490224v1?rss=1 Wang, R. Cao, S. Bashir, M. E. H. Hesser, L. A. Su, Y. Hong, S. M. C. Thompson, A. Culleen, E. Sabados, M. Dylla, N. P. Campbell, E. Alshaikh, A. A. Shim, H.-N. Wu, H. Bao, R. Wilson, D. S. Nagler, C. R. Hubbell, J. A. 2022-05-01 doi:10.1101/2022.05.01.490224 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Critical Mechanistic Role of Inositol Hexakisphosphate (IP6) in HIV-1 Viral Capsid Assembly ]]> https://biorxiv.org/content/10.1101/2022.05.03.490470v1?rss=1 Gupta, M. Pak, A. J. Voth, G. A. 2022-05-03 doi:10.1101/2022.05.03.490470 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ The mechanism underlying redundant functions of the YTHDF proteins ]]> https://biorxiv.org/content/10.1101/2022.05.05.490669v1?rss=1 Zou, Z. Sepich-Poore, C. Zhou, X. Wei, J. He, C. 2022-05-05 doi:10.1101/2022.05.05.490669 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism ]]> https://biorxiv.org/content/10.1101/2022.05.05.490791v1?rss=1 Feng, W. Destain, H. Smith, J. J. Kratsios, P. 2022-05-05 doi:10.1101/2022.05.05.490791 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa ]]> https://biorxiv.org/content/10.1101/2022.05.05.490807v1?rss=1 Wisniewski, A. L. Nations, J. A. Slater, G. J. 2022-05-05 doi:10.1101/2022.05.05.490807 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Rapid learning with highly localized synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2022.05.09.491102v1?rss=1 Masse, N. Y. Rosen, M. C. Tsao, D. Y. Freedman, D. J. 2022-05-10 doi:10.1101/2022.05.09.491102 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Transposable elements are associated with the variable response to influenza infection ]]> https://biorxiv.org/content/10.1101/2022.05.10.491101v1?rss=1 Chen, X. Pacis, A. S. Aracena, K. A. Gona, S. Kwan, T. Groza, C. Lin, Y. L. Sindeaux, R. H. M. Yotova, V. Pramatarova, A. Simon, M.-M. Pastinen, T. M. Barreiro, L. B. Bourque, G. 2022-05-10 doi:10.1101/2022.05.10.491101 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection ]]> https://biorxiv.org/content/10.1101/2022.05.10.491413v1?rss=1 Aracena, K. A. Lin, Y.-L. Luo, K. Pacis, A. Gona, S. Mu, Z. Yotova, V. Sindeaux, R. Pramatarova, A. Simon, M.-M. Chen, X. Groza, C. Lougheed, D. Gregoire, R. Brownlee, D. Li, Y. He, X. Bujold, D. Pastinen, T. Bourque, G. Barreiro, L. B. 2022-05-11 doi:10.1101/2022.05.10.491413 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells ]]> https://biorxiv.org/content/10.1101/2022.05.11.491531v1?rss=1 Jin, H. Ladd, N. A. Peev, A. M. Swarbrick, G. M. Cansler, M. Null, M. Boughter, C. T. McMurtrey, C. Nilsen, A. Dobos, K. M. Hildebrand, W. H. Lewinsohn, D. A. Adams, E. J. Lewinsohn, D. M. Harriff, M. 2022-05-11 doi:10.1101/2022.05.11.491531 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Reversal of lactate and PD-1-mediated macrophage immunosuppression controls growth of PTEN/p53-deficient prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.05.12.490223v1?rss=1 Chaudagar, K. Hieromnimon, H. M. Khurana, R. Labadie, B. Heirz, T. Mei, S. Hasan, R. Shafran, J. Kelley, A. Apostolov, E. Al-Eryani, G. Harvey, K. Rameshbabu, S. Loyd, M. Bynoe, K. Drovetsky, C. Solanki, A. Markiewicz, E. Zamora, M. Fan, X. Schuerer, S. Swarbrick, A. Sykes, D. Patnaik, A. 2022-05-13 doi:10.1101/2022.05.12.490223 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Modeling ecological communities when composition is manipulated experimentally ]]> https://biorxiv.org/content/10.1101/2022.05.12.491213v1?rss=1 Skwara, A. Lemos-Costa, P. Miller, Z. R. Allesina, S. 2022-05-13 doi:10.1101/2022.05.12.491213 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Stable population structure in Europe since the Iron Age, despite high mobility ]]> https://biorxiv.org/content/10.1101/2022.05.15.491973v1?rss=1 Antonio, M. L. Weiss, C. L. Gao, Z. Sawyer, S. Oberreiter, V. Moots, H. M. Spence, J. P. Cheronet, O. Zagorc, B. Praxmarer, E. Ozdogan, K. T. Demetz, L. Lucci, M. Alihodzic, T. Amrani, S. Avetisyan, P. Baillif-Ducros, C. Bedic, Z. Bertrand, A. Bilic, M. Bondioli, L. Borowka, P. Botte, E. Burmaz, J. Buzanic, D. Candilio, F. Cvetko, M. De Angelis, D. Drnic, I. Elschek, K. Fantar, M. Gaspari, A. Gasperetti, G. Genchi, F. Golubovic, S. Hukelova, Z. Jankauskas, R. Vuckovic, K. J. Jeremic, G. Kaic, I. Kazek, K. Khachatryan, H. Khudaverdyan, A. Kirchengast, 2022-05-16 doi:10.1101/2022.05.15.491973 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Foxe1 orchestrates thyroid and lung cell lineage divergence in mouse stem cell-derived organoids ]]> https://biorxiv.org/content/10.1101/2022.05.16.492074v1?rss=1 Fonseca, B. F. Barbee, C. Romitti, M. Eski, S. E. Gillotay, P. Monteyne, D. Perez-Morga, D. Refetoff, S. Singh, S. P. Costagliola, S. 2022-05-16 doi:10.1101/2022.05.16.492074 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Choice of 3D morphometric method leads to diverging interpretations of form--function relationships in the carnivoran calcaneus ]]> https://biorxiv.org/content/10.1101/2022.05.16.492149v1?rss=1 Wimberly, A. N. Natale, R. Higgins, R. Slater, G. 2022-05-17 doi:10.1101/2022.05.16.492149 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Dynamic Structure Of Motor Cortical Neuron Co-Activity Carries Behaviorally Relevant Information ]]> https://biorxiv.org/content/10.1101/2022.05.18.492501v1?rss=1 Sundiang, M. Hatsopoulos, N. MacLean, J. N. 2022-05-20 doi:10.1101/2022.05.18.492501 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ The canonical Wnt signaling pathway is not a promising therapeutic target for PNS regeneration enhancement ]]> https://biorxiv.org/content/10.1101/2022.05.19.492703v1?rss=1 Mehta, N. Vardy, M. Elbaz, B. 2022-05-20 doi:10.1101/2022.05.19.492703 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Interpreting the fossil record and the origination of birds ]]> https://biorxiv.org/content/10.1101/2022.05.19.492716v1?rss=1 Crouch, N. 2022-05-22 doi:10.1101/2022.05.19.492716 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ Unique Effects of Sedatives, Dissociatives, Psychedelics, Stimulants, and Cannabinoids on Episodic Memory: A Review and Reanalysis of Acute Drug Effects on Recollection, Familiarity, and Metamemory ]]> https://biorxiv.org/content/10.1101/2022.05.20.492842v1?rss=1 Doss, M. Samaha, J. Barrett, F. S. Griffiths, R. de Wit, H. Gallo, D. Koen, J. 2022-05-24 doi:10.1101/2022.05.20.492842 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Gut Microbes and the Liver Circadian Clock Partition Glucose and Lipid Metabolism ]]> https://biorxiv.org/content/10.1101/2022.05.24.491361v1?rss=1 Frazier, K. Manzoor, S. Carroll, K. DeLeon, O. Miyoshi, S. Miyoshi, J. St George, M. Tan, A. Izumo, M. Takahashi, J. S. Rao, M. C. Leone, V. A. Chang, E. B. 2022-05-25 doi:10.1101/2022.05.24.491361 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ The LEGO theory of the developing functional connectome ]]> https://biorxiv.org/content/10.1101/2022.05.24.493295v1?rss=1 Busch, E. L. Rapuano, K. M. Anderson, K. M. Rosenberg, M. D. Watts, R. Casey, B. Haxby, J. V. Feilong, M. 2022-05-24 doi:10.1101/2022.05.24.493295 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Spinosaurus is not an aquatic dinosaur ]]> https://biorxiv.org/content/10.1101/2022.05.25.493395v1?rss=1 Sereno, P. C. Myhrvold, N. Henderson, D. M. Fish, F. E. Vidal, D. Baumgart, S. L. Keillor, T. M. Formoso, K. K. Conroy, L. L. 2022-05-26 doi:10.1101/2022.05.25.493395 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Aurora A and cortical flows promote polarization and cytokinesis by inducing asymmetric ECT-2 accumulation ]]> https://biorxiv.org/content/10.1101/2022.05.25.493449v1?rss=1 Longhini-Aldis, K. Glotzer, M. 2022-05-25 doi:10.1101/2022.05.25.493449 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Masked inverse folding with sequence transfer for protein representation learning ]]> https://biorxiv.org/content/10.1101/2022.05.25.493516v1?rss=1 Yang, K. K. Yeh, H. Zanichelli, N. 2022-05-28 doi:10.1101/2022.05.25.493516 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Suction feeding of West African lungfish (Protopterus annectens): An XROMM analysis of jaw mechanics, cranial kinesis, and hyoid mobility. ]]> https://biorxiv.org/content/10.1101/2022.05.30.493759v1?rss=1 Gartner, S. M. Whitlow, K. R. Laurence-Chasen, J. D. Kaczmarek, E. B. Granatosky, M. C. Ross, C. F. Westneat, M. W. 2022-05-30 doi:10.1101/2022.05.30.493759 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Heavy-tailed neuronal connectivity arises from Hebbian self-organization ]]> https://biorxiv.org/content/10.1101/2022.05.30.494086v1?rss=1 Lynn, C. W. Holmes, C. M. Palmer, S. E. 2022-05-31 doi:10.1101/2022.05.30.494086 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Ensemble remodeling supports memory-updating ]]> https://biorxiv.org/content/10.1101/2022.06.02.494530v1?rss=1 Mau, W. Morales-Rodriguez, D. Dong, Z. Pennington, Z. T. Francisco, T. Baxter, M. G. Shuman, T. Cai, D. J. 2022-06-03 doi:10.1101/2022.06.02.494530 Cold Spring Harbor Laboratory Press 2022-06-03 <![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[ Exceptional fossil preservation and evolution of the ray-finned fish brain ]]> https://biorxiv.org/content/10.1101/2022.06.04.492470v1?rss=1 Figueroa, R. T. Goodvin, D. Kolmann, M. Coates, M. I. Caron, A. M. Friedman, M. Giles, S. 2022-06-05 doi:10.1101/2022.06.04.492470 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Discovery of synapse-specific RNA N6-methyladenosine readers associated with the consolidation of fear extinction memory ]]> https://biorxiv.org/content/10.1101/2022.06.07.495230v1?rss=1 Madugalle, S. U. Liau, W.-S. Zhao, Q. Li, X. Gong, H. Marshall, P. R. Periyakaruppiah, A. Zajaczkowski, E. L. Leighton, L. J. Ren, H. Musgrove, M. Davies, J. Rauch, S. He, C. Dickinson, B. Fletcher, L. Fulopova, B. Williams, S. R. Spitale, R. C. Bredy, T. W. 2022-06-09 doi:10.1101/2022.06.07.495230 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Electrophysiological Markers of Memory Consolidation in the Human Brain when Memories are Reactivated during Sleep ]]> https://biorxiv.org/content/10.1101/2022.06.08.495049v1?rss=1 Creery, J. D. Brang, D. J. Arndt, J. D. Bassard, A. M. Towle, V. L. Tao, J. X. Wu, S. Rose, S. Warnke, P. C. Issa, N. Paller, K. A. 2022-06-12 doi:10.1101/2022.06.08.495049 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Transcriptome-wide analysis suggests piRNAs preferentially recognize the coding region of mRNAs in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.06.08.495319v1?rss=1 Wu, W.-S. Brown, J. S. Shiue, S.-C. Lee, D.-E. Zhang, D. Lee, H.-C. 2022-06-10 doi:10.1101/2022.06.08.495319 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes ]]> https://biorxiv.org/content/10.1101/2022.06.08.495387v1?rss=1 McConnell, S. C. Hernandez, K. M. Andrade, J. de Jong, J. L. O. 2022-06-10 doi:10.1101/2022.06.08.495387 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2 ]]> https://biorxiv.org/content/10.1101/2022.06.10.495660v1?rss=1 Wolf, E. Z. Lento, C. Pu, J. Dickinson, B. C. Wilson, D. J. 2022-06-10 doi:10.1101/2022.06.10.495660 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster. ]]> https://biorxiv.org/content/10.1101/2022.06.11.495745v1?rss=1 Cotto, I. Vilardi, K. J. Huo, L. Fogarty, E. C. Khunjar, W. Wilson, C. De Clippeleir, H. Gilmore, K. Bailey, E. Lücker, S. J. Pinto, A. J. 2022-06-11 doi:10.1101/2022.06.11.495745 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely virus, from fruit bats in Madagascar ]]> https://biorxiv.org/content/10.1101/2022.06.12.495793v1?rss=1 Madera, S. Kistler, A. Ranaivoson, H. C. Ahyong, V. Andrianiaina, A. Andry, S. Raharinosy, V. Randriambolamanantsoa, T. H. Ravelomanantsoa, N. A. F. Tato, C. M. DeRisi, J. L. Aguilar, H. C. Lacoste, V. Dussart, P. Heraud, J.-M. Brook, C. E. L. 2022-06-15 doi:10.1101/2022.06.12.495793 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Structure of SARS-CoV-2 M protein in lipid nanodiscs ]]> https://biorxiv.org/content/10.1101/2022.06.12.495841v1?rss=1 Dolan, K. A. Dutta, M. Kern, D. M. Kotecha, A. Voth, G. A. Brohawn, S. G. 2022-06-13 doi:10.1101/2022.06.12.495841 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Seasonal plasticity in morphology and metabolism differs between migratory North American and resident Costa Rican monarch butterflies ]]> https://biorxiv.org/content/10.1101/2022.06.17.495480v1?rss=1 Tenger-Trolander, A. Julick, C. Lu, W. Green, D. A. Montooth, K. L. Kronforst, M. 2022-06-18 doi:10.1101/2022.06.17.495480 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Dispersal-behavioral plasticity within an insect-host system undergoing human-induced rapid environmental change (HIREC) ]]> https://biorxiv.org/content/10.1101/2022.06.19.496739v1?rss=1 3,500 soapberry bugs field collected from 2013 to 2020 and the flight performance of 378 total soapberry bugs tested in a flight mill during Fall 2019 and Winter 2020. Flight tests showed females and mainland natives exhibited variable flight responses mediated by mass, while males were consistent, wing-dependent flyers. However, historical specimens showed annual rises in flightless morphs for males and dwindling wing-to-body sizes for island natives since 2013. Despite uncertain future fitness consequences, plasticity could help predict mobility character and agent dispersal behavior and ultimately help identify whether recent trends signal adjustment or maladaptation to HIREC. ]]> Bernat, A. Cenzer, M. 2022-06-20 doi:10.1101/2022.06.19.496739 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress ]]> https://biorxiv.org/content/10.1101/2022.06.21.497008v1?rss=1 Saab, J. J. A. Dzierozynski, L. N. Jonker, P. B. Zhu, Z. Chen, R. N. Oh, M. Sheehan, C. Macleod, K. F. Weber, C. R. Muir, A. 2022-06-25 doi:10.1101/2022.06.21.497008 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ A gut commensal protist protects against virus-mediated loss of oral tolerance ]]> https://biorxiv.org/content/10.1101/2022.06.21.497012v1?rss=1 Siller, M. Zeng, Y. Sanchez, L. M. Brigleb, P. H. Sangani, K. A. Rana, M. Van Der Kraak, L. Pandey, S. P. Bender, M. J. Fitzgerald, B. Hedden, L. Fiske, K. Taylor, G. M. Rahman, S. A. Galipeau, H. J. Mullet, S. J. Wendell, S. G. Watkins, S. C. Bercik, P. Das, J. Meisel, M. Jabri, B. Dermody, T. S. Verdu, E. F. Hinterleitner, R. 2022-06-22 doi:10.1101/2022.06.21.497012 Cold Spring Harbor Laboratory Press 2022-06-22 <![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[ Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle ]]> https://biorxiv.org/content/10.1101/2022.06.23.497379v1?rss=1 Capovilla, G. Braakman, R. Fournier, G. Hackl, T. Schwartzman, J. A. Lu, X. Yelton, A. Longnecker, K. Soule, M. K. Thomas, E. Swarr, G. Mongera, A. Payette, J. Waldbauer, J. Kujawinski, E. B. Cordero, O. X. Chisholm, S. W. 2022-06-26 doi:10.1101/2022.06.23.497379 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki ]]> https://biorxiv.org/content/10.1101/2022.06.24.497508v1?rss=1 Schiffer, P. H. Natsidis, P. Leite, D. J. Robertson, H. Lapraz, F. Marletaz, F. Fromm, B. Baudry, L. Simpson, F. Hoye, E. Zakrzewski, A.-C. Kapli, P. Hoff, K. J. Mueller, S. Marbouty, M. Marlow, H. Copley, R. H. Sarkies, P. Telford, M. J. 2022-06-27 doi:10.1101/2022.06.24.497508 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Habitat heterogeneity, environmental feedbacks, and species coexistence across timescales ]]> https://biorxiv.org/content/10.1101/2022.06.26.497662v1?rss=1 Miller, Z. R. Allesina, S. 2022-06-29 doi:10.1101/2022.06.26.497662 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections ]]> https://biorxiv.org/content/10.1101/2022.06.27.497801v1?rss=1 Labbe, F. He, Q. Zhan, Q. Tiedje, K. E. Argyropoulos, D. C. Tan, M. H. Ghansah, A. Day, K. P. Pascual, M. 2022-06-30 doi:10.1101/2022.06.27.497801 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Algae drive convergent bacterial community assembly when nutrients are scarce ]]> https://biorxiv.org/content/10.1101/2022.06.27.497809v1?rss=1 Prabhakara, K. H. Kuehn, S. 2022-06-30 doi:10.1101/2022.06.27.497809 Cold Spring Harbor Laboratory Press 2022-06-30 <![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[ Intestinal Epithelial Heat Shock Protein 25/27 integrates host and microbial drivers of mucosal restitution following inflammatory injury ]]> https://biorxiv.org/content/10.1101/2022.06.30.498349v1?rss=1 Cham, C. M. Messer, J. S. Lake, J. M. Zhu, X. Tao, Y. He, L. Weber, C. R. Lin, F. Dai, Z. Tong, J. Temelkova, S. Rubin, D. T. Liu, C. Chang, E. B. 2022-07-02 doi:10.1101/2022.06.30.498349 Cold Spring Harbor Laboratory Press 2022-07-02 <![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[ Helping can be driven by non-affective cues in rat ]]> https://biorxiv.org/content/10.1101/2022.07.01.498150v1?rss=1 Vieira Sugano, Y. Y. Shan, H. Molasky, N. Mason, P. 2022-07-03 doi:10.1101/2022.07.01.498150 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels ]]> https://biorxiv.org/content/10.1101/2022.07.01.498513v1?rss=1 Park, Y. C. Reddy, B. Bavi, N. Perozo, E. Faraldo-Gomez, J. D. 2022-07-02 doi:10.1101/2022.07.01.498513 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Tissue confinement regulates cell growth and size in epithelia ]]> https://biorxiv.org/content/10.1101/2022.07.04.498508v1?rss=1 Devany, J. Falk, M. J. Holt, L. J. Murugan, A. Gardel, M. 2022-07-05 doi:10.1101/2022.07.04.498508 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Control of neuronal terminal differentiation through cell context-dependent CFI-1/ARID3 functions ]]> https://biorxiv.org/content/10.1101/2022.07.04.498728v1?rss=1 Li, Y. Smith, J. S. Marques, F. Osuma, A. Huang, H.-C. Kratsios, P. 2022-07-04 doi:10.1101/2022.07.04.498728 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ CryoEM Structures of the Human HIV-1 Restriction Factor SERINC3 and Function as a Lipid Transporter ]]> https://biorxiv.org/content/10.1101/2022.07.06.498924v1?rss=1 Leonhardt, S. A. Purdy, M. D. Grover, J. R. Yang, Z. Poulos, S. McIntire, W. E. Tatham, E. A. Erramilli, S. Nosol, K. Lai, K. K. Ding, S. Lu, M. Uchil, P. D. Finzi, A. D. Rein, A. Kossiakoff, A. A. Mothes, W. Yeager, M. 2022-07-06 doi:10.1101/2022.07.06.498924 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Integrating genetic and oral histories of Southwest Indian populations ]]> https://biorxiv.org/content/10.1101/2022.07.06.498959v1?rss=1 Biddanda, A. Bandyopadhyay, E. de la Fuente Castro, C. Witonsky, D. Pasupuleti, N. Fonseca, R. Freilich, S. Moots, H. M. Stanisavic, J. Willis, T. Menon, A. Mustak, M. S. Kodira, C. D. Naren, A. P. Sikdar, M. Rai, N. Raghavan, M. 2022-07-07 doi:10.1101/2022.07.06.498959 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Multimodal Prediction of Breast Cancer Recurrence Assays and Risk of Recurrence ]]> https://biorxiv.org/content/10.1101/2022.07.07.499039v1?rss=1 Howard, F. M. Dolezal, J. Kochanny, S. Khramtsova, G. Vickery, J. Srisuwananukorn, A. Woodard, A. Chen, N. Nanda, R. Perou, C. M. Olopade, O. I. Huo, D. Pearson, A. T. 2022-07-08 doi:10.1101/2022.07.07.499039 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Imputing the parental origin of the sibling's haplotype from parental phenotypes ]]> https://biorxiv.org/content/10.1101/2022.07.09.499429v1?rss=1 Liang, Y. 2022-07-11 doi:10.1101/2022.07.09.499429 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ End-to-End deep structure generative model for protein design ]]> https://biorxiv.org/content/10.1101/2022.07.09.499440v1?rss=1 Lai, B. McPartlon, m. Xu, J. 2022-07-11 doi:10.1101/2022.07.09.499440 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Obtaining polygenic transcriptome risk scores (PTRS) directly from GWAS summary statistics ]]> https://biorxiv.org/content/10.1101/2022.07.10.499509v1?rss=1 Liang, Y. 2022-07-11 doi:10.1101/2022.07.10.499509 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Homeostatic responses to hypoxia by the carotid body and adrenal medulla are based on mutual antagonism between HIF-1α and HIF-2α ]]> https://biorxiv.org/content/10.1101/2022.07.11.499380v1?rss=1 Yuan, G. Peng, Y.-J. Reddy, V. D. Makarenko, V. Nanduri, J. Khan, S. A. Garcia, J. A. Kumar, G. K. Semenza, G. L. Prabhakar, N. R. 2022-07-11 doi:10.1101/2022.07.11.499380 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Delivery of loaded MR1 Monomer Results in Efficient Ligand Exchange to Host MR1 and Subsequent MR1T cell activation ]]> https://biorxiv.org/content/10.1101/2022.07.11.499573v1?rss=1 Kulicke, C. A. Swarbrick, G. M. Ladd, N. A. Cansler, M. Null, M. Worley, A. Lemon, C. Ahmed, T. Bennett, J. Lewinsohn, D. A. Adams, E. J. Lewinsohn, D. M. Harriff, M. J. 2022-07-12 doi:10.1101/2022.07.11.499573 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ ION CHANNEL THERMODYNAMICS STUDIED WITH TEMPERATURE JUMPS MEASURED AT THE MEMBRANE ]]> https://biorxiv.org/content/10.1101/2022.07.11.499616v1?rss=1 Bassetto, C. A. Z. Pinto, B. I. Latorre, R. Bezanilla, F. 2022-07-12 doi:10.1101/2022.07.11.499616 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals ]]> https://biorxiv.org/content/10.1101/2022.07.11.499652v1?rss=1 Sohail, M. Chong, A. Y. Quinto-Cortes, C. D. Palma-Martinez, M. J. Ragsdale, A. Medina-Munoz, S. G. Barberena-Jonas, C. Delgado-Sanchez, G. Cruz-Hervert, L. P. Ferreyra-Reyes, L. Ferreira-Guerrero, E. Mongua-Rodriguez, N. Jimenez-Kaufmann, A. Moreno-Macias, H. Aguilar-Salinas, C. A. Auckland, K. Cortes, A. Acuna-Alonzo, V. Ioannidis, A. G. Gignoux, C. R. Wojcik, G. L. Fernandez-Valverde, S. L. Hill, A. V. S. Tusie-Luna, M. T. Mentzer, A. J. Novembre, J. Garcia-Garcia, L. Moreno-Estrada, A. 2022-07-13 doi:10.1101/2022.07.11.499652 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph ]]> https://biorxiv.org/content/10.1101/2022.07.13.499682v1?rss=1 Joublin-Delavat, A. Touahri, K. Morot, A. Rodrigues, S. Jesus, B. Trigodet, F. Delavat, F. 2022-07-13 doi:10.1101/2022.07.13.499682 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome ]]> https://biorxiv.org/content/10.1101/2022.07.15.500236v1?rss=1 Chitale, P. Lemenze, A. D. Fogarty, E. C. Shah, A. Grady, C. A. Odom-Mabey, A. R. Johnson, W. E. Yang, J. H. Eren, A. M. Brosch, R. Kumar, P. Alland, D. 2022-07-16 doi:10.1101/2022.07.15.500236 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Trait-specific patterns of community ecospace occupancy in an insular mammal radiation ]]> https://biorxiv.org/content/10.1101/2022.07.15.500274v1?rss=1 Nations, J. A. Kohli, B. A. Handika, H. Achmadi, A. S. Polito, M. J. Rowe, K. C. Esselstyn, J. A. 2022-07-18 doi:10.1101/2022.07.15.500274 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Frem1 activity regulated by Sonic Hedgehog signaling in the cranial neural crest mesenchyme guides midfacial morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.07.16.500318v1?rss=1 McLaughlin, M. T. Sun, M. R. Beames, T. G. Steward, A. C. Theisen, J. W. Chung, H. M. Everson, J. L. Moskowitz, I. P. Sheets, M. D. Lipinski, R. J. 2022-07-18 doi:10.1101/2022.07.16.500318 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Perfusable Apparatus For Thick-tissue Creation And Growth (patch) Of Cardiac Tissue ]]> https://biorxiv.org/content/10.1101/2022.07.18.500065v1?rss=1 Mir, A. Pitaktong, I. He, J. Y. Nurminsky, K. Dunn, T. Koljaka, S. Dunn, O. Ran, S. Rodgers, D. Wang, A. Matsushita, H. Hibino, N. Shih, W. 2022-07-19 doi:10.1101/2022.07.18.500065 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Probabilistic integration of transcriptome-wide association studies and colocalization analysis prioritizes molecular pathways of complex traits ]]> https://biorxiv.org/content/10.1101/2022.07.19.500651v1?rss=1 Okamoto, J. Wang, L. Yin, X. Luca, F. Pique-Regi, R. Helms, A. S. Im, H. K. Morrison, J. Wen, X. 2022-07-20 doi:10.1101/2022.07.19.500651 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Towards Self-Describing and FAIR Bulk Formats for Biomedical Data ]]> https://biorxiv.org/content/10.1101/2022.07.19.500678v1?rss=1 Lukowski, M. Prokhorenkov, A. Grossman, R. L. 2022-07-20 doi:10.1101/2022.07.19.500678 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Embryoid bodies facilitate comparative analysis of gene expression in humans and chimpanzees across dozens of cell types ]]> https://biorxiv.org/content/10.1101/2022.07.20.500831v1?rss=1 Barr, K. A. Rhodes, K. Gilad, Y. 2022-07-21 doi:10.1101/2022.07.20.500831 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Three-dimensional structured illumination microscopy with enhanced axial resolution ]]> https://biorxiv.org/content/10.1101/2022.07.20.500834v1?rss=1 Li, X. Wu, Y. Su, Y. Suarez, I. A. R. Matthaeus, C. Updegrove, T. B. Wei, Z. Zhang, L. Sasaki, H. Li, Y. Guo, M. Giannini, J. P. Vishwasrao, H. D. Chen, J. Lee, S.-J. J. Shao, L. Liu, H. Ramamurthi, K. S. Taraska, J. W. Upadhyaya, A. La Riviere, P. Shroff, H. 2022-07-21 doi:10.1101/2022.07.20.500834 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Cell envelope remodeling requires high concentrations of biotin during Mycobacterium abscessus model lung infection ]]> https://biorxiv.org/content/10.1101/2022.07.20.500843v1?rss=1 Sullivan, M. R. McGowen, K. Liu, Q. Akusobi, C. Young, D. C. Mayfield, J. A. Raman, S. Wolf, I. D. Moody, D. B. Aldrich, C. C. Muir, A. Rubin, E. J. 2022-07-21 doi:10.1101/2022.07.20.500843 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder ]]> https://biorxiv.org/content/10.1101/2022.07.20.500857v1?rss=1 Kordon, S. P. Dutka, P. Adamska, J. M. Bandekar, S. J. Leon, K. Adams, B. Li, J. Kossiakoff, A. A. Arac, D. 2022-07-21 doi:10.1101/2022.07.20.500857 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ TLR4 regulates proinflammatory intestinal immune responses mediated by an atopic gut microbiota ]]> https://biorxiv.org/content/10.1101/2022.07.21.501027v1?rss=1 Campbell, E. Maccio-Maretto, L. Hesser, L. A. Kemter, A. M. Canani, R. B. Nocerino, R. Paparo, L. Patry, R. T. Nagler, C. R. 2022-07-22 doi:10.1101/2022.07.21.501027 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ The chromatin landscape of the euryarchaeon Haloferax volcanii ]]> https://biorxiv.org/content/10.1101/2022.07.22.501187v1?rss=1 Marinov, G. K. Bagdatli, S. T. Wu, T. He, C. Kundaje, A. Greenleaf, W. 2022-07-22 doi:10.1101/2022.07.22.501187 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Ranking species based on sensitivity to perturbations under non-equilibrium community dynamics ]]> https://biorxiv.org/content/10.1101/2022.07.23.501258v1?rss=1 Medeiros, L. P. Allesina, S. Dakos, V. Sugihara, G. Saavedra, S. 2022-07-24 doi:10.1101/2022.07.23.501258 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ ATM and MSH2 control blunt DNA end joining in immunoglobulin class switch recombination ]]> https://biorxiv.org/content/10.1101/2022.07.28.501875v1?rss=1 Sible, E. Attaway, M. Fiorica, G. Michel, G. Chaudhuri, J. Vuong, B. Q. 2022-07-30 doi:10.1101/2022.07.28.501875 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Multidimensional topography of memory revealed from thousands of daily documented memories ]]> https://biorxiv.org/content/10.1101/2022.07.29.501921v1?rss=1 Bainbridge, W. A. Baker, C. I. 2022-08-02 doi:10.1101/2022.07.29.501921 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Structural basis for assembly and lipid-mediated gating of LRRC8A:C volume-regulated anion channels ]]> https://biorxiv.org/content/10.1101/2022.07.31.502239v1?rss=1 Kern, D. M. Bleier, J. Mukherjee, S. Hill, J. M. Kossiakoff, A. A. Isacoff, E. Y. Brohawn, S. G. 2022-08-02 doi:10.1101/2022.07.31.502239 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa ]]> https://biorxiv.org/content/10.1101/2022.08.02.502558v1?rss=1 Lanclos, V. C. Rasmussen, A. N. Kojima, C. Y. Cheng, C. Henson, M. W. Faircloth, B. C. Francis, C. A. Thrash, C. 2022-08-02 doi:10.1101/2022.08.02.502558 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing ]]> https://biorxiv.org/content/10.1101/2022.08.04.502826v1?rss=1 Lengyel, E. Li, Y. Weigert, M. Zhu, L. Eckart, H. Javellana, M. Ackroyd, S. Xiao, J. Olalekan, S. Glass, D. Iyer, S. Bilecz, A. J. Lastra, R. Chen, M. Basu, A. 2022-08-05 doi:10.1101/2022.08.04.502826 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Structural basis for lipid and copper regulation of the ABC transporter MsbA ]]> https://biorxiv.org/content/10.1101/2022.08.04.502837v1?rss=1 Lyu, J. Liu, C. Zhang, T. Schrecke, S. Elam, N. Hocberg, G. Russell, D. Zhao, M. Laganowsky, A. 2022-08-04 doi:10.1101/2022.08.04.502837 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Evaluation of an image-derived input function for kinetic modeling of nicotinic acetylcholine receptor-binding PET ligands ]]> https://biorxiv.org/content/10.1101/2022.08.05.502975v1?rss=1 Zammit, M. Kao, C.-M. Zhang, H. J. Holderman, N. Mitchell, S. Tanios, E. Zhang, V. Bhuiyan, M. Freifelder, R. Green, W. Mukherjee, J. Chen, C.-T. 2022-08-06 doi:10.1101/2022.08.05.502975 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults ]]> https://biorxiv.org/content/10.1101/2022.08.05.503008v1?rss=1 Smith, J. J. Kenny, I. W. Wolff, C. Cray, R. Kumar, A. Sherwood, D. R. Matus, D. Q. 2022-08-07 doi:10.1101/2022.08.05.503008 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Translation of dipeptide repeat proteins in C9ORF72-ALS/FTD through unique and redundant AUG initiation codons ]]> https://biorxiv.org/content/10.1101/2022.08.06.503063v1?rss=1 Sonobe, Y. Lee, S. Krishnan, G. Gu, Y. Kwon, D. Y. Gao, F.-B. Roos, R. Kratsios, P. 2022-08-07 doi:10.1101/2022.08.06.503063 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Phosphorylation at Ser65 modulates ubiquitin conformational dynamics ]]> https://biorxiv.org/content/10.1101/2022.08.09.502833v1?rss=1 Yovanno, R. A. Yu, A. Wied, T. J. Lau, A. Y. 2022-08-11 doi:10.1101/2022.08.09.502833 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ KAS-pipe2: a flexible toolkit for exploring KAS-seq and spKAS-seq data ]]> https://biorxiv.org/content/10.1101/2022.08.10.503490v1?rss=1 Lyu, R. Wu, T. Park, G. He, Y. He, C. Chen, M. 2022-08-13 doi:10.1101/2022.08.10.503490 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Microstimulation of human somatosensory cortex evokes task-dependent, spatially patterned responses in motor cortex ]]> https://biorxiv.org/content/10.1101/2022.08.10.503543v1?rss=1 Shelchkova, N. D. Downey, J. E. Greenspon, C. M. Okorokova, E. V. Sobinov, A. R. Verbaarschot, C. He, Q. Sponheim, C. Tortolani, A. F. Moore, D. D. Kaufman, M. T. Lee, R. C. Satzer, D. Gonzalez-Martinez, J. Warnke, P. C. Miller, L. E. Boninger, M. L. Gaunt, R. Collinger, J. Hatsopoulos, N. Bensmaia, S. J. 2022-08-13 doi:10.1101/2022.08.10.503543 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Tensor Image Registration Library: Automated Deformable Registration of Stand-Alone Histology Images to Whole-Brain Post-Mortem MRI Data ]]> https://biorxiv.org/content/10.1101/2022.08.11.503605v1?rss=1 Huszar, I. N. Pallebage-Gamarallage, M. Bangerter-Christensen, S. Brooks, H. Fitzgibbon, S. Foxley, S. Hiemstra, M. Howard, A. F. Jbabdi, S. Kor, D. Z. Leonte, A. Mollink, J. Smart, A. Tendler, B. C. Turner, M. R. Ansorge, O. Miller, K. L. Jenkinson, M. 2022-08-15 doi:10.1101/2022.08.11.503605 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ STAT3 signaling in B cells controls germinal center zone organization and recycling ]]> https://biorxiv.org/content/10.1101/2022.08.12.503811v1?rss=1 Fike, A. J. Chodisetti, S. B. Wright, N. E. Bricker, K. N. Domeier, P. D. Maienschein-Cline, M. Rosenfeld, A. M. Luckenbill, S. A. Weber, J. L. Choi, N. M. Luning Prak, E. T. Mandal, M. Clark, M. R. Rahman, Z. S. M. 2022-08-15 doi:10.1101/2022.08.12.503811 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Morphological Differences in Isolated Brook Trout Populations in the Desolation Wilderness of the Sierra Nevada ]]> https://biorxiv.org/content/10.1101/2022.08.15.503945v1?rss=1 Luby-Prikot, L. R. Bock, O. R. Martin, J. 2022-08-15 doi:10.1101/2022.08.15.503945 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Phenotype integration improves power and preserves specificity in biobank-based genetic studies of MDD ]]> https://biorxiv.org/content/10.1101/2022.08.15.503980v1?rss=1 Dahl, A. Thompson, M. An, U. Krebs, M. D. Appadurai, V. Border, R. Bacanu, S.-A. Werge, T. Flint, J. Schork, A. J. Sankararaman, S. Kendler, K. Cai, N. 2022-08-15 doi:10.1101/2022.08.15.503980 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Deep Learning-based Phenotype Imputation on Population-scale Biobank Data Increases Genetic Discoveries ]]> https://biorxiv.org/content/10.1101/2022.08.15.503991v1?rss=1 An, U. Pazokitoroudi, A. Alvarez, M. Huang, L. Bacanu, S. Schork, A. J. Kendler, K. Pajukanta, P. Flint, J. Zaitlen, N. Cai, N. Dahl, A. Sankararaman, S. 2022-08-15 doi:10.1101/2022.08.15.503991 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ A PATHWAY FOR T3 SIGNALING IN THE BRAIN TO IMPROVE THE VARIABLE EFFECTIVENESS OF THERAPY WITH L-T4 ]]> https://biorxiv.org/content/10.1101/2022.08.17.504300v1?rss=1 Salas-Lucia, F. Fekete, C. Sinko, R. Egri, P. Rada, K. Ruska, Y. Bocco, B. Fonseca, T. L. Gereben, B. Bianco, A. C. 2022-08-18 doi:10.1101/2022.08.17.504300 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Neural similarity between overlapping events at learning differentially affects reinstatement across the cortex ]]> https://biorxiv.org/content/10.1101/2022.08.18.504184v1?rss=1 Hebscher, M. Bainbridge, W. A. Voss, J. L. 2022-08-18 doi:10.1101/2022.08.18.504184 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage ]]> https://biorxiv.org/content/10.1101/2022.08.18.504214v1?rss=1 Robertson, H. Sebe-Pedros, A. Saudemont, B. Loe Mie, Y. Zakrzewski, A. Grau-Bove, X. Mailhe, M.-P. Schiffer, P. Telford, M. J. Marlow, H. 2022-08-18 doi:10.1101/2022.08.18.504214 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Developmental rules of primate dental evolution align microevolution with macroevolution ]]> https://biorxiv.org/content/10.1101/2022.08.19.504140v1?rss=1 Machado, F. A. Mongle, C. S. Slater, G. Penna, A. Wisniewski, A. Soffin, A. Dutra, V. Uyeda, J. C. 2022-08-19 doi:10.1101/2022.08.19.504140 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Texture Coding In Higher Order Somatosensory Cortices ]]> https://biorxiv.org/content/10.1101/2022.08.19.504511v1?rss=1 Long, K. H. Greenspon, C. M. van Driesche, A. Lieber, J. D. Bensmaia, S. J. 2022-08-22 doi:10.1101/2022.08.19.504511 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Universal gut microbial relationships in the gut microbiome of wild baboons ]]> https://biorxiv.org/content/10.1101/2022.08.20.504530v1?rss=1 Roche, K. Björk, J. R. Dasari, M. Grieneisen, L. Jansen, D. Gould, T. Gesquiere, L. Barreiro, L. Alberts, S. C. Blekhman, R. Gilbert, J. Tung, J. Mukherjee, S. Archie, E. A. 2022-08-21 doi:10.1101/2022.08.20.504530 Cold Spring Harbor Laboratory Press 2022-08-21 <![CDATA[ Identification of a cardiac glycoside exhibiting favorable brain bioavailability and potency for reducing levels of the cellular prion protein ]]> https://biorxiv.org/content/10.1101/2022.08.22.504810v1?rss=1 Eid, S. Zerbes, T. Williams, D. Wang, X. Sackmann, C. Meier, S. Dulin, N. O. Nagorny, P. Schmitt-Ulms, G. 2022-08-23 doi:10.1101/2022.08.22.504810 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Molecular Insights into the Role of Water in Early-stage Human Amylin Aggregation ]]> https://biorxiv.org/content/10.1101/2022.08.29.505769v1?rss=1 Guo, A. Z. de Pablo, J. J. 2022-08-30 doi:10.1101/2022.08.29.505769 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Structural insights into the formation of repulsive Netrin guidance complexes ]]> https://biorxiv.org/content/10.1101/2022.09.03.506478v1?rss=1 Priest, J. M. Nichols, E. L. Mendoza, J. L. Shen, K. Özkan, E. 2022-09-03 doi:10.1101/2022.09.03.506478 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid ]]> https://biorxiv.org/content/10.1101/2022.09.04.506554v1?rss=1 Li, M. Kasan, K. Saha, Z. Yoon, Y. Schmidt-Ott, U. 2022-09-05 doi:10.1101/2022.09.04.506554 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ The mitochondrial Cu+ transporter PiC2 (SLC25A3) is a target of MTF1 and contributes to the development of skeletal muscle in vitro ]]> https://biorxiv.org/content/10.1101/2022.09.05.506690v1?rss=1 McCann, C. Quinteros, M. Adelugba, I. Morgada, M. N. Castelblanco, A. R. Davis, E. Lanzirotti, A. Hainer, S. J. Vila, A. J. Navea, J. G. PADILLA-BENAVIDES, T. 2022-09-05 doi:10.1101/2022.09.05.506690 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Global remapping in granule cells and mossy cells of the mouse dentate gyrus ]]> https://biorxiv.org/content/10.1101/2022.09.06.506812v1?rss=1 Kim, S. H. GoodSmith, D. Temme, S. J. Moriya, F. Ming, G.-l. Christian, K. Song, H. Knierim, J. J. 2022-09-08 doi:10.1101/2022.09.06.506812 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Turbulent adaptive landscape shaped size evolution in modern ocean giants ]]> https://biorxiv.org/content/10.1101/2022.09.07.506945v1?rss=1 Burin, G. Park, T. James, T. D. Slater, G. Cooper, N. 2022-09-09 doi:10.1101/2022.09.07.506945 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Small RNAs activate Salmonella pathogenicity island 1 by modulating mRNA stability through the hilD mRNA 3' UTR ]]> https://biorxiv.org/content/10.1101/2022.09.07.507058v1?rss=1 Abdulla, S. Z. Kim, K. Azam, M. S. Golubeva, Y. A. Cakar, F. Slauch, J. M. Vanderpool, C. K. 2022-09-08 doi:10.1101/2022.09.07.507058 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Developmental role of macrophages modelled in human pluripotent stem cell derived intestinal tissue ]]> https://biorxiv.org/content/10.1101/2022.09.09.505715v1?rss=1 Andelfinger, G. Song, A. Sindeaux, R. H. M. Li, Y. Affia, H. Agnihotri, T. Leclerc, S. van Vliet, P. P. Colas, M. Guimond, J.-V. Patey, N. Joyal, J.-S. Haddad, E. Barreiro, L. 2022-09-10 doi:10.1101/2022.09.09.505715 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Activity-dependent post-translational regulation of palmitoylating and de-palmitoylating enzymes in the hippocampus ]]> https://biorxiv.org/content/10.1101/2022.09.12.507668v1?rss=1 Abazari, D. Wild, A. R. Qiu, T. Dickinson, B. C. Bamji, S. X. 2022-09-13 doi:10.1101/2022.09.12.507668 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Extensions of mean-field approximations for environmentally-transmitted pathogen networks ]]> https://biorxiv.org/content/10.1101/2022.09.13.507803v1?rss=1 Davies, K. Lenhart, S. Day, J. Lloyd, A. L. Lanzas, C. 2022-09-13 doi:10.1101/2022.09.13.507803 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Diversification of the Ruminant Skull Along an Evolutionary Line of Least Resistance ]]> https://biorxiv.org/content/10.1101/2022.09.13.507810v1?rss=1 Rhoda, D. Haber, A. Angielczyk, K. D. 2022-09-15 doi:10.1101/2022.09.13.507810 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ OpenPBTA: An Open Pediatric Brain Tumor Atlas ]]> https://biorxiv.org/content/10.1101/2022.09.13.507832v1?rss=1 Shapiro, J. A. Gaonkar, K. S. Savonen, C. L. Spielman, S. J. Bethell, C. J. Jin, R. Rathi, K. S. Zhu, Y. Egolf, L. E. Farrow, B. K. Miller, D. P. Yang, Y. Koganti, T. Noureen, N. Koptyra, M. P. Duong, N. Kraya, A. A. Kline, C. N. Guo, Y. Storm, P. B. Nazarian, J. Mack, S. C. Raman, P. Zheng, S. Madsen, P. J. Van Kuren, N. Robins, S. Huang, X. Waanders, A. J. Kim, J. Hanson, D. Koschmann, C. J. Diskin, S. J. Lulla, R. R. Brown, M. A. Wong, J. Mason, J. L. Scolaro, L. Kim, M. C. Xie, H. M. Rood, B. R. Cole, K. A. Margol, A. S. Vaksman, Z. Kaufman, R. 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N. 2022-09-16 doi:10.1101/2022.09.15.507455 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Cell-type-specific roles of inhibitory interneurons in the rehabilitation of auditory cortex after peripheral damage ]]> https://biorxiv.org/content/10.1101/2022.09.15.508128v1?rss=1 Kumar, M. Handy, G. Kouvaros, S. Ljungqvist Brinson, L. Bizup, B. Doiron, B. Tzounopoulos, T. 2022-09-17 doi:10.1101/2022.09.15.508128 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7 ]]> https://biorxiv.org/content/10.1101/2022.09.15.508141v1?rss=1 Wang, K. Lee, C.-W. Sui, X. Kim, S. Wang, S. Higgs, A. B. Baublis, A. J. Voth, G. A. Liao, M. Walther, T. C. Farese, R. V. 2022-09-15 doi:10.1101/2022.09.15.508141 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression ]]> https://biorxiv.org/content/10.1101/2022.09.16.508303v1?rss=1 Guet, C. C. Bruneaux, L. oikonomou, P. Aldana, M. Cluzel, P. 2022-09-17 doi:10.1101/2022.09.16.508303 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Chance and contingency in B cell evolution limit the similarity of antibody responses to infection across individuals ]]> https://biorxiv.org/content/10.1101/2022.09.16.508315v1?rss=1 Vieira, M. C. Palm, A.-K. E. Stamper, C. T. Tepora, M. E. Nguyen, K. D. Pham, T. D. Boyd, S. D. Wilson, P. C. Cobey, S. 2022-09-19 doi:10.1101/2022.09.16.508315 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans ]]> https://biorxiv.org/content/10.1101/2022.09.19.508328v1?rss=1 Locher, V. Park, S. Bunis, D. Makredes, S. Burt, T. D. Fragiadakis, G. K. Halkias, J. 2022-09-19 doi:10.1101/2022.09.19.508328 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ A multiplex platform to identify mechanisms and modulators of proteotoxicity in neurodegeneration ]]> https://biorxiv.org/content/10.1101/2022.09.19.508444v1?rss=1 Resnick, S. J. Qamar, S. S. Sheng, J. Huang, L. H. Nixon-Abell, J. Melore, S. Chung, C. W. Li, X. Wang, J. Zhang, N. Shneider, N. A. Kaminski, C. F. Ruggeri, F. S. Schierle, G. S. K. St George-Hyslop, P. Chavez, A. 2022-09-19 doi:10.1101/2022.09.19.508444 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Disentangling temporal and rate codes in primate somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2022.09.19.508566v1?rss=1 Callier, T. Gitchell, T. Harvey, M. A. Bensmaia, S. J. 2022-09-19 doi:10.1101/2022.09.19.508566 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Aortic Shape Space Topology ]]> https://biorxiv.org/content/10.1101/2022.09.19.508582v1?rss=1 Khabaz, K. Sankary, S. Yuan, K. Pugar, J. Kim, J. Kang, J. Nguyen, N. Cao, K. Pierce, N. Lee, C. J. Milner, R. Kindlmann, G. Pocivavsek, L. 2022-09-19 doi:10.1101/2022.09.19.508582 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ The logic of recurrent circuits in the primary visual cortex ]]> https://biorxiv.org/content/10.1101/2022.09.20.508739v1?rss=1 Oldenburg, I. A. Hendricks, W. D. Handy, G. Shamardani, K. Bounds, H. A. Doiron, B. Adesnik, H. 2022-09-22 doi:10.1101/2022.09.20.508739 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Conserved signaling pathways antagonize and synergize with co-opted doublesex to control development of novel mimetic butterfly wing patterns ]]> https://biorxiv.org/content/10.1101/2022.09.20.508752v1?rss=1 VanKuren, N. Doellman, M. M. Sheikh, S. I. Droguett, D. H. P. Massardo, D. Kronforst, M. 2022-09-20 doi:10.1101/2022.09.20.508752 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Carcinoma associated mesenchymal stem cells promote ovarian cancer metastasis by increasing tumor heterogeneity through direct mitochondrial transfer ]]> https://biorxiv.org/content/10.1101/2022.09.21.506345v1?rss=1 Pressimone, C. Frisbie, L. G. Dyer, E. Baruwal, R. Gorecki, G. Javed, Z. St. Croix, C. Watkins, S. C. Calderon, M. Atiua, H. I. Hempel, N. Pearson, A. T. Coffman, L. 2022-09-22 doi:10.1101/2022.09.21.506345 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Sequential Activation and Local Unfolding Control Poly(A)-Binding Protein Condensation ]]> https://biorxiv.org/content/10.1101/2022.09.21.508844v1?rss=1 Chen, R. Kahan, D. Shangguan, J. Sachleben, J. R. Riback, J. A. Drummond, D. A. Sosnick, T. 2022-09-21 doi:10.1101/2022.09.21.508844 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Intestinal helminth infection impairs oral and parenteral vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2022.09.22.508369v1?rss=1 Hardy, L. C. Kapita, C. M. Campbell, E. Hall, J. A. Urban, J. F. Belkaid, Y. Nagler, C. R. Iweala, O. I. 2022-09-23 doi:10.1101/2022.09.22.508369 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Overlapping Neural Representations for Dynamic Visual Imagery and Stationary Storage in Spatial Working Memory ]]> https://biorxiv.org/content/10.1101/2022.09.24.509255v1?rss=1 Günseli, E. Foster, J. Sutterer, D. Todorova, L. Vogel, E. K. Awh, E. 2022-09-26 doi:10.1101/2022.09.24.509255 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Investigating the ability of astrocytes to drive neural network synchrony ]]> https://biorxiv.org/content/10.1101/2022.09.26.508928v1?rss=1 Handy, G. Borisyuk, A. 2022-09-27 doi:10.1101/2022.09.26.508928 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Enhanced Complex Stability and Optimal JAK Geometry are Pivotal for a Potent Type III Interferon Response ]]> https://biorxiv.org/content/10.1101/2022.09.27.508945v1?rss=1 Aung, T. Horvath, C. M. Mendoza, J. L. 2022-09-28 doi:10.1101/2022.09.27.508945 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Adjusting for genetic confounders in transcriptome-wide association studies leads to reliable detection of causal genes ]]> https://biorxiv.org/content/10.1101/2022.09.27.509700v1?rss=1 Zhao, S. Crouse, W. Qian, S. Luo, K. Stephens, M. He, X. 2022-09-28 doi:10.1101/2022.09.27.509700 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ The TaxUMAP atlas: efficient display of large clinical microbiome data reveals ecological competition involved in protection against bacteremia ]]> https://biorxiv.org/content/10.1101/2022.09.27.509746v1?rss=1 Schluter, J. Djukovic, A. Taylor, B. P. Yan, J. Duan, C. Hussey, G. A. Liao, C. Sharma, S. Fontana, E. Amoretti, L. A. Wright, R. J. Dai, A. Peled, J. Taur, Y. Perales, M.-A. Siranosian, B. A. Bhatt, A. S. van den Brink, M. R. M. Pamer, E. G. Xavier, J. B. 2022-09-28 doi:10.1101/2022.09.27.509746 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Combinatorial control of biofilm development by quorum-sensing and nutrient-sensing regulators. ]]> https://biorxiv.org/content/10.1101/2022.09.27.509822v1?rss=1 Chen, G. Lim, E. D. Winkelman, B. T. Winkelman, J. T. Mukherjee, S. 2022-09-28 doi:10.1101/2022.09.27.509822 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Subpopulation Codes Permit Information Modulation Across Cortical States ]]> https://biorxiv.org/content/10.1101/2022.09.28.509815v1?rss=1 Getz, M. P. Huang, C. Doiron, B. 2022-09-30 doi:10.1101/2022.09.28.509815 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Divergent expression of aristaless1 and aristaless2 is associated with embryonic appendage and pupal wing development in butterflies ]]> https://biorxiv.org/content/10.1101/2022.09.28.509918v1?rss=1 Bayala, E. X. Cisneros, I. Massardo, D. VanKuren, N. W. Kronforst, M. R. 2022-09-29 doi:10.1101/2022.09.28.509918 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Meta-analysis refinement of plasma extracellular vesicle composition identifies proplatelet basic protein as a signaling messenger in type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2022.09.28.509996v1?rss=1 Vallejo, M. C. Sarkar, S. Elliott, E. C. Henry, H. R. Huang, F. Payne, S. H. Ramanadham, S. Sims, E. K. Metz, T. O. Mirmira, R. Nakayasu, E. S. 2022-09-29 doi:10.1101/2022.09.28.509996 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps ]]> https://biorxiv.org/content/10.1101/2022.09.29.510189v1?rss=1 Nakamura, A. Meng, H. Zhao, M. Wang, F. Hou, J. Cao, R. Si, D. 2022-10-02 doi:10.1101/2022.09.29.510189 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ Locus coeruleus norepinephrine selectively controls visual attention ]]> https://biorxiv.org/content/10.1101/2022.09.30.510394v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@7966c1org.highwire.dtl.DTLVardef@49395borg.highwire.dtl.DTLVardef@154c101org.highwire.dtl.DTLVardef@14b63ce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ghosh, S. Maunsell, J. H. R. 2022-10-03 doi:10.1101/2022.09.30.510394 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics ]]> https://biorxiv.org/content/10.1101/2022.10.03.510547v1?rss=1 Nittala, P. V. K. Hohreiter, A. Linhard, E. R. Dohn, R. Mishra, S. Konda, A. Divan, R. N. S. Guha, S. Basu, A. 2022-10-05 doi:10.1101/2022.10.03.510547 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Entropic control of the free energy landscape of an archetypal biomolecular machine ]]> https://biorxiv.org/content/10.1101/2022.10.03.510626v1?rss=1 Ray, K. K. Kinz-Thompson, C. D. Fei, J. Wang, B. Lin, Q. Gonzalez, R. L. 2022-10-05 doi:10.1101/2022.10.03.510626 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ The X-factor in ART: does the use of Assisted Reproductive Technologies influence DNA methylation on the X chromosome? ]]> https://biorxiv.org/content/10.1101/2022.10.06.510603v1?rss=1 Romanowska, J. Nustad, H. E. Page, C. M. Denault, W. R. P. Bohlin, J. Lee, Y. Magnus, M. C. Haftorn, K. L. Gjerdevik, M. Novakovic, B. Saffery, R. Gjessing, H. K. Lyle, R. Magnus, P. M. Haberg, S. E. Jugessur, A. 2022-10-07 doi:10.1101/2022.10.06.510603 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A single amino acid change drives left- right asymmetry in Bilateria ]]> https://biorxiv.org/content/10.1101/2022.10.06.511172v1?rss=1 Truchado-Garcia, M. Perry, K. J. Cavodeassi, F. Kenny, N. J. Henry, J. Q. Grande, C. 2022-10-07 doi:10.1101/2022.10.06.511172 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions ]]> https://biorxiv.org/content/10.1101/2022.10.08.511420v1?rss=1 Shaw, T. R. Wisser, K. Schaffner, T. A. Gaffney, A. Machta, B. Veatch, S. L. 2022-10-08 doi:10.1101/2022.10.08.511420 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511571v1?rss=1 Zvyagin, M. T. Brace, A. Hippe, K. Deng, Y. Zhang, B. Orozco Bohorquez, C. Clyde, A. Kale, B. Perez-Rivera, D. Ma, H. Mann, C. M. Irvin, M. Pauloski, J. G. Ward, L. Hayot, V. Emani, M. Foreman, S. Xie, Z. Lin, D. Shukla, M. Nie, W. Romero, J. Dallago, C. Vahdat, A. Xiao, C. Gibbs, T. Foster, I. Davis, J. J. Papka, M. E. Brettin, T. Anandkumar, A. Vishwanath, V. Ramanathan, A. 2022-10-11 doi:10.1101/2022.10.10.511571 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Endosomal Trafficking of Two Pore K+ Efflux Channel TWIK2 to Plasmalemma Mediates NLRP3 Inflammasome Activation and Inflammatory Injury ]]> https://biorxiv.org/content/10.1101/2022.10.12.511914v1?rss=1 Di, A. Huang, L. S. Zhou, B. Toth, P. T. Krishnan, Y. Malik, A. B. 2022-10-12 doi:10.1101/2022.10.12.511914 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Export of discarded splicing intermediates requires mRNA export factors and the nuclear basket ]]> https://biorxiv.org/content/10.1101/2022.10.13.511998v1?rss=1 Zeng, Y. Staley, J. P. 2022-10-14 doi:10.1101/2022.10.13.511998 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Inhibition of Microbial Methane Oxidation by 2-Chloro-6-Methylpyridine ]]> https://biorxiv.org/content/10.1101/2022.10.13.512149v1?rss=1 20 months was observed at 10 mM. ANOSIM of weighted UniFrac distances between groups of triplicate samples supported a primary distinction of the inoculum relative to the enrichments (R=0.999) and a secondary distinction between bottles containing 2C6MP versus those without (R=0.464 [0.1 mM]; R=0.894 [1 mM]). The inoculum was dominated by members of the Proteobacteria (49.9{+/-}1.5%), and to a lesser extent by Bacteroidetes (8.8{+/-}0.2%), Acidobacteria (8.9{+/-}0.4%), and Verrucomicrobia (4.4{+/-}0.3%). In enrichments with or without 2C6MP, Proteobacteria expanded to comprise 65-70% of the total. In the absence of inhibitor, members of the Methylococcaceae and Methylophilaceae increased in relative abundance from < 0.1% of the inoculum to 8.5{+/-}1.0% and 13.4{+/-}2.3%, of the total community respectively. At both 0.1 and 1 mM concentrations of the inhibitor, the Methylococcaceae were much less abundant, representing 3.3{+/-}0.5% and 2.8{+/-}3.3% respectively. No inhibition of the Methylophilaceae was seen at the lower concentration of 2C6MP, but at the higher concentration this taxon was only 7.8{+/-}1.1% of the total. In contrast, members of the Crenotrichaceae, another group of methane oxidizers, increased in relative abundance with greater amounts of inhibitor, representing 8.6{+/-}3.6% of the total at 0.1 mM and 12.0{+/-}4.5% at 1 mM, compared to only 4.1{+/-}0.4% when no inhibitor was present. These results clearly show changes in the populations of putative aerobic methanotrophs relative to the amount of 2C6MP present. ]]> O'Loughlin, E. J. Antonopoulos, D. A. Arend, K. K. Flynn, T. M. Koval, J. C. Owens, S. M. 2022-10-14 doi:10.1101/2022.10.13.512149 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A unified model for the dynamics of ATP-independent ultrafast contraction ]]> https://biorxiv.org/content/10.1101/2022.10.14.512304v1?rss=1 Floyd, C. Molines, A. T. Lei, X. Honts, J. E. Chang, F. Elting, M. W. Vaikuntanathan, S. Dinner, A. R. Bhamla, M. S. 2022-10-16 doi:10.1101/2022.10.14.512304 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ A context-dependent switch from sensing to feeling in the primate amygdala ]]> https://biorxiv.org/content/10.1101/2022.10.15.512319v1?rss=1 Martin, A. B. Cardenas, M. A. Anderson, R. K. Bowman, A. I. Hillier, E. A. Bensmaia, S. J. Fuglevand, A. J. Gothard, K. M. 2022-10-18 doi:10.1101/2022.10.15.512319 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Nuclear speckle-localized RNAs exhibit preferential positioning and orientation ]]> https://biorxiv.org/content/10.1101/2022.10.17.512423v1?rss=1 Paul, S. Arias, M. A. Wen, L. Liao, S. E. Zhang, J. Wang, X. Regev, O. Fei, J. 2022-10-19 doi:10.1101/2022.10.17.512423 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Adipocytes reprogram glucose metabolism in cancer cells promoting metastasis ]]> https://biorxiv.org/content/10.1101/2022.10.17.512437v1?rss=1 Mukherjee, A. Bezwada, D. Zandbergen, M. Francesco Greco, F. Chiang, C.-Y. Tasdemir, M. Fahrmann, J. Grapov, D. La Frano, M. R. Vu, H. S. Newman, J. W. McDonnell, L. A. Nezi, L. Fiehn, O. DeBerardinis, R. J. Lengyel, E. 2022-10-21 doi:10.1101/2022.10.17.512437 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Prevention of thrombocytopenia and thrombosis in heparin-induced thrombocytopenia (HIT) using deglycosylated KKO: A novel therapeutic? ]]> https://biorxiv.org/content/10.1101/2022.10.19.512755v1?rss=1 Sarkar, A. Khandelwal, S. Kim, H. Gruel, Y. Rollin, J. Wool, G. D. Arepally, G. M. Cines, D. B. Rauova, L. Poncz, M. 2022-10-19 doi:10.1101/2022.10.19.512755 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Neuronal birthdate reveals topography in a vestibular brainstem circuit for gaze stabilization ]]> https://biorxiv.org/content/10.1101/2022.10.21.513243v1?rss=1 Goldblatt, D. Huang, S. Greaney, M. R. Hamling, K. R. Voleti, V. Perez-Campos, C. Patel, K. B. Li, W. Hillman, E. M. C. Bagnall, M. W. Schoppik, D. 2022-10-22 doi:10.1101/2022.10.21.513243 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ TGF-β promotes the postselection thymic development and peripheral function of interferon-γ-producing iNKT cells ]]> https://biorxiv.org/content/10.1101/2022.10.23.513409v1?rss=1 Morgan, R. C. Frank, C. Greger, M. Sigvardsson, M. Bartom, E. T. Kee, B. L. 2022-10-23 doi:10.1101/2022.10.23.513409 Cold Spring Harbor Laboratory Press 2022-10-23 <![CDATA[ A general approach to discover conformational epitope-directed binders for selective inhibition of protein proteolytic activation ]]> https://biorxiv.org/content/10.1101/2022.10.24.513434v1?rss=1 Zhou, J. 2022-10-25 doi:10.1101/2022.10.24.513434 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Identification of dendritic cell-T cell interactions driving immune responses to food ]]> https://biorxiv.org/content/10.1101/2022.10.26.513772v1?rss=1 Canesso, M. C. C. Castro, T. B. Nakandakari-Higa, S. Lockhart, A. Esterhazy, D. Reis, B. S. Victora, G. D. Mucida, D. 2022-10-27 doi:10.1101/2022.10.26.513772 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ A multi-enhancer hub at the Ets1 locus controls T cell differentiation and allergic inflammation through 3D genome topology ]]> https://biorxiv.org/content/10.1101/2022.10.28.514213v1?rss=1 Chandra, A. Yoon, S. Michieletto, M. Goldman, N. Ferrari, E. Fasolino, M. Joannas, L. Kee, B. Henao-Mejia, J. Vahedi, G. 2022-10-28 doi:10.1101/2022.10.28.514213 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ In-vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2022.10.31.514397v1?rss=1 DeBerardinis, R. J. Kaushik, A. Burroughs, L. K. Tarangelo, A. Ragavan, M. Wu, C.-Y. Li, X. Ahumada, K. Tcheuyap, V. T. Saatchi, F. Do, Q. Yong, C. Rosales, T. Stevens, C. Rao, A. D. Faubert, B. Pachnis, P. Zacharias, L. G. Vu, H. Cai, F. Mathews, T. P. Slusher, B. S. P. Kapur, P. Sun, X. Merritt, M. Brugarolas, J. Zhang, Y. Chiang, J.-C. Genovese, G. 2022-11-01 doi:10.1101/2022.10.31.514397 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ e-cone and d-cone singularities drive submucosal collagen fiber remodeling in intestinal anastomotic surgery ]]> https://biorxiv.org/content/10.1101/2022.10.31.514540v1?rss=1 Fleischer, B. Nguyen, N. Pal, A. Khabaz, K. Tsamis, A. Efrati, E. Witten, T. Alverdy, J. Pocivavsek, L. 2022-11-01 doi:10.1101/2022.10.31.514540 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct omicron SARS-CoV-2 subvariants ]]> https://biorxiv.org/content/10.1101/2022.10.31.514592v1?rss=1 Changrob, S. Halfmann, P. J. Liu, H. Torres, J. L. McGrath, J. J. C. Ozorowski, G. Li, L. Kuroda, M. Maemura, T. Huang, M. Wilbanks, D. G. Zheng, N.-Y. Turner, H. L. Erickson, S. A. Fu, Y. Singh, G. Krammer, F. Sather, D. N. Ward, A. B. Wilson, I. A. Kawaoka, Y. Wilson, P. C. 2022-11-01 doi:10.1101/2022.10.31.514592 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ P bodies coat germ granules to promote transgenerational gene silencing in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.11.01.514641v1?rss=1 Du, Z. Shi, K. Brown, J. S. He, T. Wu, W.-S. Zhang, Y. Lee, H.-C. Zhang, D. 2022-11-02 doi:10.1101/2022.11.01.514641 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Learning low-dimensional generalizable naturalfeatures from retina using a U-net ]]> https://biorxiv.org/content/10.1101/2022.11.02.514893v1?rss=1 Wang, S. Hoshal, B. de Laittre, E. Marre, O. Berry, M. J. Palmer, S. 2022-11-03 doi:10.1101/2022.11.02.514893 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Tropomyosin Cdc8 acetylation enhances binding to expressed S. pombe actin but does not promote differential association with fission yeast formins ]]> https://biorxiv.org/content/10.1101/2022.11.03.514925v1?rss=1 Tang, Q. Pollard, L. Homa, K. E. Kovar, D. R. Trybus, K. M. 2022-11-04 doi:10.1101/2022.11.03.514925 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[ Distinct energy-coupling factor transporter subunits enable flavin acquisition and extracytosolic trafficking for extracellular electron transfer in Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/2022.11.04.515267v1?rss=1 Rivera-Lugo, R. Huang, S. Lee, F. Meheust, R. Iavarone, A. T. Sidebottom, A. M. Oldfield, E. Portnoy, D. A. Light, S. H. 2022-11-07 doi:10.1101/2022.11.04.515267 Cold Spring Harbor Laboratory Press 2022-11-07 <![CDATA[ Large-scale neural dynamics in a shared low-dimensional state space reflect cognitive and attentional dynamics ]]> https://biorxiv.org/content/10.1101/2022.11.05.515307v1?rss=1 Song, H. Shim, W. M. Rosenberg, M. D. 2022-11-05 doi:10.1101/2022.11.05.515307 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ A mathematical theory for the mechanics of three-dimensional cellular aggregates reveals the mechanical atlas for Ascidian embryogenesis ]]> https://biorxiv.org/content/10.1101/2022.11.05.515310v1?rss=1 Liu, S. Lemaire, P. Munro, E. Mani, M. 2022-11-06 doi:10.1101/2022.11.05.515310 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Volumetric microscopy of CD9 and CD63 reveals distinct subpopulations and novel structures of extracellular vesicle in situ in triple negative breast cancer cells ]]> https://biorxiv.org/content/10.1101/2022.11.08.515679v1?rss=1 White, E. D. Walker, N. D. Yi, H. Dinner, A. R. Scherer, N. F. Rosner, M. R. 2022-11-08 doi:10.1101/2022.11.08.515679 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates ]]> https://biorxiv.org/content/10.1101/2022.11.09.515856v1?rss=1 Ali, A. Garde, R. Schaffer, O. C. Bard, J. A. M. Husain, K. Keyport Kik, S. Davis, K. A. Luengo-Woods, S. Drummond, D. A. Squires, A. H. Pincus, D. 2022-11-10 doi:10.1101/2022.11.09.515856 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Trans-eQTL mapping in gene sets identifies network effects of genetic variants ]]> https://biorxiv.org/content/10.1101/2022.11.11.516189v1?rss=1 Wang, L. Babushkin, N. Liu, Z. Liu, X. 2022-11-11 doi:10.1101/2022.11.11.516189 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ In silico network-based screening reveals candidates for endothelial dysfunction therapy ]]> https://biorxiv.org/content/10.1101/2022.11.17.516953v1?rss=1 Pinheiro-de-Sousa, I. Giudice, G. Fonseca-Alaniz, M. H. Modestia, S. M. Mattioli, S. V. Fang, Y. Petsalaki, E. Krieger, J. E. 2022-11-18 doi:10.1101/2022.11.17.516953 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ HAPPY: A deep learning pipeline for mapping cell-to-tissue graphs across placenta histology whole slide images ]]> https://biorxiv.org/content/10.1101/2022.11.21.517353v1?rss=1 Vanea, C. Dzigurski, J. Rukins, V. Dodi, O. Siigur, S. Salumae, L. Meir, K. Parks, W. T. Hochner-Celnikier, D. Fraser, A. Hochner, H. Laisk, T. Ernst, L. M. Lindgren, C. M. Nellaker, C. 2022-11-24 doi:10.1101/2022.11.21.517353 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes ]]> https://biorxiv.org/content/10.1101/2022.11.22.517471v1?rss=1 Morgante, F. Carbonetto, P. Wang, G. Zou, Y. Sarkar, A. Stephens, M. 2022-11-23 doi:10.1101/2022.11.22.517471 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Centromere-associated retroelement evolution in Drosophila melanogaster reveals an underlying conflict ]]> https://biorxiv.org/content/10.1101/2022.11.25.518008v1?rss=1 Hemmer, L. W. Negm, S. Geng, X. Courret, C. Navarro-Dominguez, B. Speece, I. Wei, X. Altidor, E. Chaffer, J. Sproul, J. S. Larracuente, A. M. 2022-11-26 doi:10.1101/2022.11.25.518008 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Proteomic Analysis Defines the Interactome of Telomerase in the Protozoan Parasite, Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2022.11.27.518122v1?rss=1 Davis, J. A. Reyes, A. V. Nitika, Saha, A. Wolfgeher, D. J. Xu, S.-L. Truman, A. Li, B. Chakrabarti, K. 2022-11-28 doi:10.1101/2022.11.27.518122 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Selection-driven trait loss in independently evolved cavefish populations ]]> https://biorxiv.org/content/10.1101/2022.11.28.518185v1?rss=1 Moran, R. L. Richards, E. J. Ornelas-Garcia, C. P. Gross, J. B. Donny, A. Wiese, J. Keene, A. C. Kowalko, J. E. Rohner, N. McGaugh, S. E. 2022-11-28 doi:10.1101/2022.11.28.518185 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Factorizing polygenic epistasis improves prediction and uncovers biological pathways in complex traits ]]> https://biorxiv.org/content/10.1101/2022.11.29.518075v1?rss=1 Tang, D. Freudenberg, J. Dahl, A. 2022-11-30 doi:10.1101/2022.11.29.518075 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Unclearing Microscopy ]]> https://biorxiv.org/content/10.1101/2022.11.29.518361v1?rss=1 8,000 volumetrically and opaquing their bulk with light-scattering molecules of sufficient density, cell microstructure can now be discerned with a contrast visible to the unaided eye. We further inspect uncleared samples with transmitted light microscopy modalities and prove that 3D ultrastructural features, previously accessible only with super-resolution fluorescence or electron microscopy methods, can now be visualized with simple magnification optics alone. ]]> M'Saad, O. Shribak, M. Bewersdorf, J. 2022-12-02 doi:10.1101/2022.11.29.518361 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ FMRP phosphorylation modulates neuronal translation through YTHDF1 ]]> https://biorxiv.org/content/10.1101/2022.11.29.518448v1?rss=1 Zou, Z. Wei, J. Chen, Y. Kang, Y. Shi, H. Yang, F. Chen, S. Zhou, Y. Sepich-Poore, C. Zhuang, X. Zhou, X. Jiang, H. Wen, Z. Jin, P. Luo, C. He, C. 2022-11-30 doi:10.1101/2022.11.29.518448 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ The Role of the 3-Dimensional Genome in New Gene Evolution ]]> https://biorxiv.org/content/10.1101/2022.11.30.518413v1?rss=1 Lee, U. Arsala, D. Xia, S. Ali, M. Sobreira, D. Eres, I. Zhou, Q. Long, M. 2022-12-01 doi:10.1101/2022.11.30.518413 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ New gene evolution with subcellular expression patterns detected in PacBio-sequenced genomes of Drosophila genus ]]> https://biorxiv.org/content/10.1101/2022.11.30.518489v1?rss=1 Dong, C. Zhang, L. Xia, S. Sosa, D. Arsala, D. Long, M. 2022-12-02 doi:10.1101/2022.11.30.518489 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ ythdf2(ch200) and its role in development of the early zebrafish embryo ]]> https://biorxiv.org/content/10.1101/2022.12.02.516060v1?rss=1 Beadell, A. V. 2022-12-05 doi:10.1101/2022.12.02.516060 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses. ]]> https://biorxiv.org/content/10.1101/2022.12.02.518889v1?rss=1 Lucaci, A. G. Zehr, J. D. Kosakovsky Pond, S. L. 2022-12-03 doi:10.1101/2022.12.02.518889 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Superiority of intranasal over systemic administration of bioengineered soluble ACE2 for survival and brain protection against SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.12.05.519032v1?rss=1 Hassler, L. Wysocki, J. Ahrendsen, J. T. Ye, M. Gelarden, I. Nicolaescu, V. Tomatsidou, A. Gula, H. Cianfarini, C. Khurram, N. Kanwar, Y. Singer, B. D. Randall, G. Missiakas, D. M. Henkin, J. Batlle, D. 2022-12-06 doi:10.1101/2022.12.05.519032 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Redundant representations are required to disambiguate simultaneously presented complex stimuli ]]> https://biorxiv.org/content/10.1101/2022.12.07.519040v1?rss=1 Johnston, W. J. Freedman, D. J. 2022-12-07 doi:10.1101/2022.12.07.519040 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Emergence of counting in the brains of 3- to 5-year-old children ]]> https://biorxiv.org/content/10.1101/2022.12.13.520249v1?rss=1 Kersey, A. J. Aulet, L. S. Cantlon, J. F. 2022-12-13 doi:10.1101/2022.12.13.520249 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Merging short and stranded long reads improves transcript assembly ]]> https://biorxiv.org/content/10.1101/2022.12.13.520317v1?rss=1 Kainth, A. S. Haddad, G. A. Hall, J. M. Ruthenburg, A. J. 2022-12-15 doi:10.1101/2022.12.13.520317 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Analysis of gene expression heterogeneity reveals therapeutic targets and novel regulators of metastasis ]]> https://biorxiv.org/content/10.1101/2022.12.16.520816v1?rss=1 Yang, D. Dann, C. Valdespino, A. Robinson-Mailman, L. Henn, M. Chen, M. Balazsi, G. Rosner, M. R. 2022-12-19 doi:10.1101/2022.12.16.520816 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Dynamics of activation in the voltage-sensing domain of Ci-VSP ]]> https://biorxiv.org/content/10.1101/2022.12.19.521128v1?rss=1 Dinner, A. R. Roux, B. Shen, R. Guo, S. C. 2022-12-20 doi:10.1101/2022.12.19.521128 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Children Develop Adult-Like Visual Sensitivity to Image Memorability by the Age of Four ]]> https://biorxiv.org/content/10.1101/2022.12.20.520853v1?rss=1 Guo, X. Bainbridge, W. A. 2022-12-22 doi:10.1101/2022.12.20.520853 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Deep learning-enabled design of synthetic orthologs of a signaling protein ]]> https://biorxiv.org/content/10.1101/2022.12.21.521443v1?rss=1 Lian, X. Praljak, N. Subramanian, S. Wasinger, S. Ranganathan, R. Ferguson, A. L. 2022-12-21 doi:10.1101/2022.12.21.521443 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models ]]> https://biorxiv.org/content/10.1101/2022.12.22.521678v1?rss=1 Strober, B. J. Tayeb, K. Popp, J. Qi, G. Gordon, M. G. Perez, R. Ye, C. J. Battle, A. 2022-12-23 doi:10.1101/2022.12.22.521678 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Comparing scientific abstracts generated by ChatGPT to original abstracts using an artificial intelligence output detector, plagiarism detector, and blinded human reviewers ]]> https://biorxiv.org/content/10.1101/2022.12.23.521610v1?rss=1 Gao, C. A. Howard, F. M. Markov, N. S. Dyer, E. C. Ramesh, S. Luo, Y. Pearson, A. T. 2022-12-27 doi:10.1101/2022.12.23.521610 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Spatial Evolution of Information Dynamics in the Primary Motor Cortex During Reach ]]> https://biorxiv.org/content/10.1101/2022.12.23.521792v1?rss=1 Liang, W. Papadourakis, V. Hatsopoulos, N. 2022-12-23 doi:10.1101/2022.12.23.521792 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Exceptionally versatile respiratory metabolisms drive metabolite production by diverse gut bacteria ]]> https://biorxiv.org/content/10.1101/2022.12.26.521950v1?rss=1 Little, A. S. Younker, I. T. Schechter, M. S. Meheust, R. Stemczynski, J. Scorza, K. Nol Bernardino, P. Mullowney, M. W. Sharan, D. Waligurski, E. Smith, R. Ramanswamy, R. Leiter, W. Moran, D. McMillin, M. Odenwald, M. A. Iavarone, A. T. Sidebottom, A. M. Sundararajan, A. Pamer, E. G. Eren, A. M. Light, S. H. 2022-12-27 doi:10.1101/2022.12.26.521950 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Androgen-mediated TGFβ expression suppresses anti-tumor neutrophil response in bone metastatic prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.12.30.522329v1?rss=1 Cook, L. M. Alsamraae, M. Costanzo-Garvey, D. Teply, B. Sommerville, G. Herbert, Z. Morrissey, C. Abdalla, M. Y. Fallet, R. W. Kielian, T. Jensen-Smith, H. deOliveira, E. I. Chen, K. Bettencourt, I. Wang, J. M. Keeley, T. Yu, F. 2022-12-31 doi:10.1101/2022.12.30.522329 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ Dietary Restriction Impacts Peripheral Circadian Clock Output Important for Longevity in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.01.04.522718v1?rss=1 Hwangbo, D.-S. Kwon, Y.-J. Iwanaszko, M. Jiang, P. Abbasi, L. Wright, N. Alli, S. Hutchison, A. L. Dinner, A. Braun, R. Allada, R. 2023-01-04 doi:10.1101/2023.01.04.522718 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Establishing a causal role for left ventrolateral prefrontal cortex in value-directed memory encoding with high-definition transcranial direct current stimulation ]]> https://biorxiv.org/content/10.1101/2023.01.04.522746v1?rss=1 Han, L. T. Cohen, M. S. He, L. K. Green, L. M. Knowlton, B. J. Castel, A. D. Rissman, J. 2023-01-04 doi:10.1101/2023.01.04.522746 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Leveraging family data to design Mendelian Randomization that is provably robust to population stratification ]]> https://biorxiv.org/content/10.1101/2023.01.05.522936v1?rss=1 LaPierre, N. Fu, B. Turnbull, S. Eskin, E. Sankararaman, S. 2023-01-06 doi:10.1101/2023.01.05.522936 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Passive endocytosis in protocells enables nutrient transport bypassing permeability limits ]]> https://biorxiv.org/content/10.1101/2023.01.07.522792v1?rss=1 Zhang, S. J. Anees, P. Krishnan, Y. Fai, T. G. Szostak, J. W. Wang, A. 2023-01-07 doi:10.1101/2023.01.07.522792 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Imbalanced gut microbiota predicts and drives the progression of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model ]]> https://biorxiv.org/content/10.1101/2023.01.09.523249v1?rss=1 Fei, N. Miyoshi, S. Hermanson, J. B. Miyoshi, J. Xie, B. DeLeon, O. Hawkins, M. Charlton, W. D'Souza, M. Hart, J. Sulakhe, D. Martinez-Guryn, K. B. Chang, E. B. Charlton, M. R. Leone, V. A. 2023-01-09 doi:10.1101/2023.01.09.523249 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ HYENA detects non-coding genes activated by distal enhancers in cancer ]]> https://biorxiv.org/content/10.1101/2023.01.09.523321v1?rss=1 Yesilkanal, A. E. Yu, A. Thakur, A. Wang, F. Wu, X. Muir, A. He, X. Spitz, F. Yang, L. 2023-01-10 doi:10.1101/2023.01.09.523321 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Retroviral infection and commensal bacteria dependently alter the metabolomic profile in a sterile organ ]]> https://biorxiv.org/content/10.1101/2023.01.10.523497v1?rss=1 Spring, J. Beilinson, V. DeFelice, B. C. Sanchez, J. M. Fischbach, M. Chervonsky, A. Golovkina, T. 2023-01-11 doi:10.1101/2023.01.10.523497 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Axial regionalization in Tiktaalik roseae and the origin of quadrupedal locomotion ]]> https://biorxiv.org/content/10.1101/2023.01.11.523301v1?rss=1 Stewart, T. A. Lemberg, J. B. Hillan, E. Magallanes, I. Daeschler, E. B. Shubin, N. H. 2023-01-13 doi:10.1101/2023.01.11.523301 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile ]]> https://biorxiv.org/content/10.1101/2023.01.12.523823v1?rss=1 Dong, Q. Lin, H. Allen, M.-M. Garneau, J. R. Sia, J. K. Smith, R. C. Haro, F. McMillen, T. Pope, R. L. Metcalfe, C. Burgo, V. Woodson, C. Dylla, N. Kohout, C. Sundararajan, A. Snitkin, E. S. Young, V. B. Fortier, L.-C. Kamboj, M. Pamer, E. G. 2023-01-12 doi:10.1101/2023.01.12.523823 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Testing the accuracy of species distribution models based on community science data ]]> https://biorxiv.org/content/10.1101/2023.01.13.523331v1?rss=1 Velde, M. Cooper, J. C. Garrod, H. 2023-01-16 doi:10.1101/2023.01.13.523331 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ Genome-wide CRISPR screen reveals genetic modifiers of Ca2+-mediated cell death ]]> https://biorxiv.org/content/10.1101/2023.01.13.523980v1?rss=1 Reyes Gaido, O. E. Schole, K. L. Anderson, M. E. Luczak, E. D. 2023-01-14 doi:10.1101/2023.01.13.523980 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Specificity Guides Interpretation: On H3K4 Methylation at Enhancers and Broad Promoters ]]> https://biorxiv.org/content/10.1101/2023.01.16.524067v1?rss=1 Shah, R. N. Ruthenburg, A. J. 2023-01-17 doi:10.1101/2023.01.16.524067 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Experimental Tests of the Virtual Circular Genome Model for Non-enzymatic RNA Replication ]]> https://biorxiv.org/content/10.1101/2023.01.16.524303v1?rss=1 Ding, D. Zhou, L. Mittal, S. Szostak, J. W. 2023-01-18 doi:10.1101/2023.01.16.524303 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome ]]> https://biorxiv.org/content/10.1101/2023.01.16.524325v1?rss=1 Feng, X. Cui, X. Zhang, L.-S. Ye, C. Wang, P. Zhong, Y. Zheng, Z. He, C. 2023-01-17 doi:10.1101/2023.01.16.524325 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Predicting Protein-encoding Gene Content in Escherichia coli Genomes ]]> https://biorxiv.org/content/10.1101/2023.01.17.524402v1?rss=1 Nguyen, M. Elmore, Z. Ihle, C. Moen, F. S. Slater, A. D. Turner, B. N. Parrello, B. Best, A. A. Davis, J. J. 2023-01-19 doi:10.1101/2023.01.17.524402 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Primate superior colliculus is engaged in abstract higher-order cognition ]]> https://biorxiv.org/content/10.1101/2023.01.17.524416v1?rss=1 Peysakhovich, B. Tetrick, S. M. Silva, A. A. Li, S. Zhu, O. Ibos, G. Johnston, W. J. Freedman, D. J. 2023-01-18 doi:10.1101/2023.01.17.524416 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Sensitized piRNA reporter identifies multiple RNA processing factors involved in piRNA-mediated gene silencing ]]> https://biorxiv.org/content/10.1101/2023.01.22.525052v1?rss=1 Brown, J. S. Zhang, D. Chen, W. Lee, H.-C. 2023-01-22 doi:10.1101/2023.01.22.525052 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Fungal zoospores show contrasting swimming patterns specific to phylum and cytology ]]> https://biorxiv.org/content/10.1101/2023.01.22.525074v1?rss=1 Galindo, L. J. Richards, T. A. Nirody, J. A. 2023-01-22 doi:10.1101/2023.01.22.525074 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ MHC class II antigen presentation by intestinal epithelial cells fine-tunes bacteria-reactive CD4 T cell responses ]]> https://biorxiv.org/content/10.1101/2023.01.23.525150v1?rss=1 Heuberger, C. Janney, A. Ilott, N. Bertocchi, A. Pott, S. Gu, Y. Pohin, M. Friedrich, M. Mann, E. Pearson, C. Powrie, F. Pott, J. Thornton, E. E. Maloy, K. J. 2023-01-23 doi:10.1101/2023.01.23.525150 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes ]]> https://biorxiv.org/content/10.1101/2023.01.23.525212v1?rss=1 Mandal, M. Maienschein-Cline, M. Hu, Y. Mohsin, A. Veselits, M. L. Wright, N. E. Okoreeh, M. K. Yoon, Y. m. Veselits, J. Georgopoulos, K. Clark, M. 2023-01-23 doi:10.1101/2023.01.23.525212 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Rhythmically bursting songbird vocomotor neurons are organized into multiple sequences, suggesting a network/intrinsic properties model encoding song and error, not time ]]> https://biorxiv.org/content/10.1101/2023.01.23.525213v1?rss=1 Fetterman, G. C. Margoliash, D. 2023-01-23 doi:10.1101/2023.01.23.525213 Cold Spring Harbor Laboratory Press 2023-01-23 <![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[ Increments in Visual Motion Coherence are More Readily Detected than Decrements ]]> https://biorxiv.org/content/10.1101/2023.01.25.525590v1?rss=1 Wei, L. Mitchell, A. O. Maunsell, J. H. R. 2023-01-26 doi:10.1101/2023.01.25.525590 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny ]]> https://biorxiv.org/content/10.1101/2023.01.25.525612v1?rss=1 Cerny, D. Simonoff, A. L. 2023-01-26 doi:10.1101/2023.01.25.525612 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Senescence of cortical neurons following persistent DNA double-strand breaks induces cerebrovascular lesions ]]> https://biorxiv.org/content/10.1101/2023.01.26.525738v1?rss=1 Feng, Y. Kopsidas, C. A. Lowe, C. C. Zhang, J. Zhou, X. Kang, W. 2023-01-27 doi:10.1101/2023.01.26.525738 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Analysis of National Institutes of Health Grant K99 to R00 Transitions from 2007 to 2022 ]]> https://biorxiv.org/content/10.1101/2023.01.26.525751v1?rss=1 Tyrrell, D. J. 2023-01-27 doi:10.1101/2023.01.26.525751 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Protracted morphine withdrawal corresponds with sex-specific alterations to motivated behavior and mesoaccumbal subcircuit dopamine cell plasticity ]]> https://biorxiv.org/content/10.1101/2023.01.29.526129v1?rss=1 Gomez, D. M. Kahl, T. Brettingen, E. Hearing, M. 2023-01-31 doi:10.1101/2023.01.29.526129 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling Cyanobacterial Mat ]]> https://biorxiv.org/content/10.1101/2023.01.30.526236v1?rss=1 Grim, S. L. Stuart, D. G. Aron, P. Levin, N. E. Kinsman-Costello, L. E. Waldbauer, J. E. Dick, G. J. 2023-01-30 doi:10.1101/2023.01.30.526236 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Organism-Wide Analysis of Sepsis Reveals Mechanisms of Systemic Inflammation ]]> https://biorxiv.org/content/10.1101/2023.01.30.526342v1?rss=1 Takahama, M. Patil, A. Johnson, K. Cipurko, D. Miki, Y. Taketomi, Y. Carbonetto, P. Plaster, M. Richey, G. Pandey, S. Cheronis, K. Ueda, T. Gruenbaum, A. Dudek, S. Stephens, M. Murakami, M. Chevrier, N. 2023-02-02 doi:10.1101/2023.01.30.526342 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Three-dimensional spatial quantitative analysis of cardiac lymphatics in the mouse heart ]]> https://biorxiv.org/content/10.1101/2023.02.01.526338v1?rss=1 Phillips, E. H. Bindokas, V. P. Jung, D. Teamer, J. Kitajewski, J. K. Solaro, R. J. Wolska, B. M. Lee, S. S.-Y. 2023-02-03 doi:10.1101/2023.02.01.526338 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ The double-drift illusion biases the marmoset oculomotor system ]]> https://biorxiv.org/content/10.1101/2023.02.02.526908v1?rss=1 Dotson, N. M. Davis, Z. W. Salisbury, J. M. Palmer, S. E. Cavanagh, P. Reynolds, J. 2023-02-03 doi:10.1101/2023.02.02.526908 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Cancer relevance of circulating antibodies against LINE-1 antigens in humans ]]> https://biorxiv.org/content/10.1101/2023.02.03.526997v1?rss=1 3,000 individuals with or without cancer, we observed significantly higher IgG titers against L1-encoded ORF1p and ORF2p in patients with lung, pancreatic, ovarian, esophageal, and liver cancers compared to healthy individuals. Remarkably, elevated levels of anti-ORF1p-reactive IgG were observed in cancer patients with disease stages 1 and 2, indicating that immune response to L1 antigens can occur at early phases of carcinogenesis. We conclude that the antibody response against L1 antigens could contribute to the diagnosis and determination of immunoreactivity of tumors among cancer types that frequently escape early detection. ]]> Vylegzhanina, A. Bespalov, I. Novototskaya-Vlasova, K. Hall, B. Gleiberman, A. Yu, H. Leontieva, O. Leonova, K. Kurnasov, O. Osterman, A. Dy, G. Komissarov, A. Vasilieva, E. Gehlhausen, J. Iwasaki, A. Ambrosone, C. Tsuji, T. Matsuzaki, J. Odunsi, K. Andrianova, E. Gudkov, A. V. 2023-02-05 doi:10.1101/2023.02.03.526997 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ RNA conformation and metal ion coordination in the nonenzymatic primer extension reaction center ]]> https://biorxiv.org/content/10.1101/2023.02.03.527041v1?rss=1 Mittal, S. Nisler, C. Szostak, J. W. 2023-02-04 doi:10.1101/2023.02.03.527041 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Coronary Artery Disease risk variant dampens the expression of CALCRL by reducing HSF binding to shear stress responsive enhancer in endothelial cells ]]> https://biorxiv.org/content/10.1101/2023.02.08.527795v1?rss=1 Selvarajan, I. Li, J. Pölönen, P. Örd, T. Öunap, K. Ravindran, A. Mäklin, K. Toropainen, A. Stolze, L. White, S. J. Romanoski, C. E. Heinäniemi, M. Fang, Y. Kaikkonen, M. U. 2023-02-13 doi:10.1101/2023.02.08.527795 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Multivariate adaptive shrinkage improves cross-population transcriptome prediction for transcriptome-wide association studies in underrepresented populations ]]> https://biorxiv.org/content/10.1101/2023.02.09.527747v1?rss=1 Araujo, D. S. Nguyen, C. Hu, X. Mikhaylova, A. V. Gignoux, C. Ardlie, K. G. Taylor, K. D. Durda, P. Liu, Y. Papanicolaou, G. Cho, M. H. Rich, S. S. Rotter, J. I. NHLBI TOPMed Consortium, Im, H. K. Manichaikul, A. W. Wheeler, H. E. 2023-02-09 doi:10.1101/2023.02.09.527747 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Decoding the content of working memory in school-aged children ]]> https://biorxiv.org/content/10.1101/2023.02.10.527990v1?rss=1 Turoman, N. Fiave, P. A. Zahnd, C. deBettencourt, M. T. Vergauwe, E. 2023-02-12 doi:10.1101/2023.02.10.527990 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures ]]> https://biorxiv.org/content/10.1101/2023.02.14.528493v1?rss=1 Barnett, K. R. Mobley, R. J. Diedrich, J. D. Bergeron, B. P. Bhattarai, K. R. Yang, W. Crews, K. R. Manring, C. S. Jabbour, E. Paietta, E. Litzow, M. R. Kornblau, S. M. Stock, W. Inaba, H. Jeha, S. Pui, C.-H. Mullighan, C. G. Relling, M. V. Yang, J. J. Evans, W. E. Savic, D. 2023-02-15 doi:10.1101/2023.02.14.528493 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ The Development of Synapses in Mouse and Macaque Primary Sensory Cortices ]]> https://biorxiv.org/content/10.1101/2023.02.15.528564v1?rss=1 Wildenberg, G. A. Li, H. Kasthuri, N. 2023-02-15 doi:10.1101/2023.02.15.528564 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ A novel triptolide analog downregulates NF-κB and induces mitochondrial apoptosis pathways in human pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.02.15.528599v1?rss=1 Tian, Q. Zhang, P. Wang, Y. Si, Y. Yin, D. Weber, C. R. Fishel, M. Pollok, K. E. Qiu, B. Xiao, F. Chong, A. 2023-02-15 doi:10.1101/2023.02.15.528599 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Pervasive, conserved secondary structure in highly charged protein regions ]]> https://biorxiv.org/content/10.1101/2023.02.15.528637v1?rss=1 40% charged residues), which are routinely presumed to be disordered. Using recent advances in structure prediction and experimental structures, we show that roughly 40% of these regions form well-structured helices. Features often used to predict disorder--high charge density, low hydrophobicity, low sequence complexity, and evolutionarily varying length--are also compatible with solvated, variable-length helices. We show that a simple composition classifier predicts the existence of structure far better than well-established heuristics based on charge and hydropathy. We show that helical structure is more prevalent than previously appreciated in highly charged regions of diverse proteomes and characterize the conservation of highly charged regions. Our results underscore the importance of integrating, rather than choosing between, structure- and disorder-based approaches. ]]> Triandafillou, C. G. Pan, R. W. Dinner, A. R. Drummond, D. A. 2023-02-15 doi:10.1101/2023.02.15.528637 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ The response time paradox in functional magnetic resonance imaging analyses ]]> https://biorxiv.org/content/10.1101/2023.02.15.528677v1?rss=1 Mumford, J. A. Bissett, P. G. Jones, H. M. Shim, S. Rios, J. A. H. Poldrack, R. A. 2023-02-15 doi:10.1101/2023.02.15.528677 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[ Biomimetic multi-channel microstimulation of somatosensory cortex conveys high resolution force feedback for bionic hands ]]> https://biorxiv.org/content/10.1101/2023.02.18.528972v1?rss=1 Greenspon, C. M. Valle, G. Hobbs, T. Verbaarschot, C. Callier, T. Schelchkova, N. Sobinov, A. Jordan, P. Weiss, J. M. Fitzgerald, E. Prasad, D. van Driesche, A. Lee, R. Satzer, D. Gonzalez-Martinez, J. Warnke, P. Miller, L. E. Boninger, M. Collinger, J. Gaunt, R. Hatsopoulos, N. Downey, J. E. Bensmaia, S. J. 2023-02-18 doi:10.1101/2023.02.18.528972 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Ulinastatin Ameliorates Cardiac Ischemia/Reperfusion Injury via Inhibiting the tissue kallikrein-kinin system ]]> https://biorxiv.org/content/10.1101/2023.02.21.529463v1?rss=1 Ran, X. Ruan, H. Li, S.-s. Wu, R. Luo, A. Zhang, Q. 2023-02-26 doi:10.1101/2023.02.21.529463 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct ]]> https://biorxiv.org/content/10.1101/2023.02.22.529538v1?rss=1 Getz, E. W. Lanclos, V. C. Kojima, C. Y. Cheng, C. Henson, M. W. Schon, M. E. Ettema, T. J. Faircloth, B. C. Thrash, J. C. 2023-02-22 doi:10.1101/2023.02.22.529538 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2023.02.24.529987v1?rss=1 Chen, M. Dahl, A. 2023-02-27 doi:10.1101/2023.02.24.529987 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Screening in serum-derived medium reveals differential response to compounds targeting metabolism ]]> https://biorxiv.org/content/10.1101/2023.02.25.529972v1?rss=1 Abbott, K. L. Ali, A. Casalena, D. Do, B. T. Ferreira, R. Cheah, J. H. Soule, C. K. Deik, A. Kunchok, T. Schmidt, D. R. Renner, S. Honeder, S. E. Wu, M. Chan, S. H. Tseyang, T. Greaves, D. Hsu, P. P. Ng, C. W. Zhang, C. J. Farsidjani, A. Gramatikov, I. M. T. Matheson, N. J. Lewis, C. A. Clish, C. B. Rees, M. G. Roth, J. A. Griner, L. M. Muir, A. Auld, D. S. Vander Heiden, M. G. 2023-02-27 doi:10.1101/2023.02.25.529972 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ The Kinase Module of the Mediator regulates cell cycle re-entry and transcriptional response following DNA damage ]]> https://biorxiv.org/content/10.1101/2023.02.26.530133v1?rss=1 Memisoglu, G. Bohn, S. Krogan, N. Haber, J. E. Ruthenburg, A. J. 2023-02-26 doi:10.1101/2023.02.26.530133 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Permutation-based group sequential analyses for cognitive neuroscience ]]> https://biorxiv.org/content/10.1101/2023.02.27.530244v1?rss=1 Veillette, J. P. Ho, L. Nusbaum, H. C. 2023-02-28 doi:10.1101/2023.02.27.530244 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Folding of Prestin's Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility ]]> https://biorxiv.org/content/10.1101/2023.02.27.530320v1?rss=1 Lin, X. Haller, P. Bavi, N. Faruk, N. Perozo, E. Sosnick, T. 2023-02-28 doi:10.1101/2023.02.27.530320 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Fat2 polarizes Lar and Sema5c to coordinate the motility of collectively migrating epithelial cells ]]> https://biorxiv.org/content/10.1101/2023.02.28.530349v1?rss=1 Williams, A. M. Horne-Badovinac, S. 2023-03-01 doi:10.1101/2023.02.28.530349 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression ]]> https://biorxiv.org/content/10.1101/2023.03.02.529724v1?rss=1 Hasselluhn, M. C. Decker-Farrell, A. R. Vlahos, L. Thomas, D. H. Curiel-Garcia, A. Maurer, H. C. Wasko, U. N. Tomassoni, L. Sastra, S. A. Palermo, C. F. Dalton, T. C. Ma, A. Li, F. Tolosa, E. J. Hibshoosh, H. Muir, A. Fernandez-Zapico, M. E. Califano, A. Olive, K. P. 2023-03-02 doi:10.1101/2023.03.02.529724 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Neuronal wiring receptors Dprs and DIPs are GPI anchored and this modification contributes to their cell surface organization ]]> https://biorxiv.org/content/10.1101/2023.03.02.530872v1?rss=1 Lobb-Rabe, M. Nawrocka, W. I. Carrillo, R. A. Özkan, E. 2023-03-02 doi:10.1101/2023.03.02.530872 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Interpreting structure in sequence count data with differential expression analysis allowing for grades of membership ]]> https://biorxiv.org/content/10.1101/2023.03.03.531029v1?rss=1 Carbonetto, P. Luo, K. Sarkar, A. Hung, A. Tayeb, K. Pott, S. Stephens, M. 2023-03-06 doi:10.1101/2023.03.03.531029 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Antigenic strain diversity explains different biogeographic patterns of invasion and maintenance of anti-malarial drug resistance ]]> https://biorxiv.org/content/10.1101/2023.03.06.531320v1?rss=1 He, Q. Chaillet, J. K. Labbe, F. 2023-03-07 doi:10.1101/2023.03.06.531320 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Orthogonal coupling of a 3D cytoskeletal scaffold coordinates cell morphogenesis and maintains tissue organization in the Drosophila pupal retina ]]> https://biorxiv.org/content/10.1101/2023.03.06.531386v1?rss=1 Sun, X. Decker, J. Sanchez-Luege, N. REBAY, I. 2023-03-07 doi:10.1101/2023.03.06.531386 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Neutrophil efferocytosis reprograms mitochondrial metabolism to switch alveolar macrophages to a pro-resolution phenotype at the cost of bacterial control ]]> https://biorxiv.org/content/10.1101/2023.03.07.528464v1?rss=1 Better, J. Wetstein, M. Estiri, M. Malainou, C. Ferrero, M. Langelage, M. Kuznetsova, I. Vazquez-Armendariz, I. Kimmig, L. Mansouri, S. Savai, R. Wilhelm, J. Alexopoulos, I. Sommer, N. Herold, S. Matt, U. 2023-03-07 doi:10.1101/2023.03.07.528464 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Testing for differences in polygenic scores in the presence of confounding ]]> https://biorxiv.org/content/10.1101/2023.03.12.532301v1?rss=1 Blanc, J. Berg, J. J. 2023-03-12 doi:10.1101/2023.03.12.532301 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ A Novel HIF-2α/ARNT Signaling Pathway Protects Against Microvascular Dysfunction and heart failure After Myocardial Infarction ]]> https://biorxiv.org/content/10.1101/2023.03.12.532316v1?rss=1 Ullah, K. Ai, L. Li, Y. Liu, L. Zhang, Q. Pan, K. Humayun, Z. Sitikov, A. Su, Q. Zhao, Q. Sharp, W. W. Fang, Y. Wu, D. Liao, J. K. Wu, R. 2023-03-14 doi:10.1101/2023.03.12.532316 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Fast or slow? Clock readout sets internal periods ]]> https://biorxiv.org/content/10.1101/2023.03.17.533212v1?rss=1 Palmer, S. E. Holmes, C. M. 2023-03-21 doi:10.1101/2023.03.17.533212 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ A Consequence of Immature Breathing induces Persistent Changes in Hippocampal Synaptic Plasticity and Behavior: A Role of Pro-Oxidant State and NMDA Receptor Imbalance ]]> https://biorxiv.org/content/10.1101/2023.03.21.533692v1?rss=1 Arias-Cavieres, A. Garcia, A. 2023-03-21 doi:10.1101/2023.03.21.533692 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ BIBSNet: A Deep Learning Baby Image Brain Segmentation Network for MRI Scans ]]> https://biorxiv.org/content/10.1101/2023.03.22.533696v1?rss=1 Hendrickson, T. J. Reiners, P. Moore, L. A. Perrone, A. J. Alexopoulos, D. Lee, E. G. Styner, M. Kardan, O. Chamberlain, T. A. Mummaneni, A. Caldas, H. A. Bower, B. Stoyell, S. Martin, T. Sung, S. Fair, E. Uriarte-Lopez, J. Rueter, A. R. Rosenberg, M. D. Smyser, C. D. Elison, J. T. Graham, A. Fair, D. A. Feczko, E. 2023-03-24 doi:10.1101/2023.03.22.533696 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Latent transcriptional programs reveal histology-encoded tumor features spanning tissue origins ]]> https://biorxiv.org/content/10.1101/2023.03.22.533810v1?rss=1 Hieromnimon, H. M. Dolezal, J. Doytcheva, K. Howard, F. M. Kochanny, S. Zhang, Z. Grossman, R. L. Tanager, K. Wang, C. Kather, J. N. Izumchenko, E. Cipriani, N. A. Fertig, E. J. Pearson, A. T. Riesenfeld, S. J. 2023-03-24 doi:10.1101/2023.03.22.533810 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Coexistence of many species under a random competition-colonization trade-off ]]> https://biorxiv.org/content/10.1101/2023.03.23.533867v1?rss=1 Miller, Z. R. Clenet, M. Della Libera, K. Massol, F. Allesina, S. 2023-03-25 doi:10.1101/2023.03.23.533867 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Glycopolymer-conjugated antigens as an inverse vaccine platform prevent anaphylaxis in a pre-clinical model of food allergy ]]> https://biorxiv.org/content/10.1101/2023.03.23.534004v1?rss=1 Cao, S. Maulloo, C. D. Raczy, M. M. Sabados, M. Slezak, A. J. Nguyen, M. Solanki, A. Wallace, R. P. Shim, H.-N. Wilson, D. S. Hubbell, J. A. 2023-03-25 doi:10.1101/2023.03.23.534004 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Environmental modulators of algae-bacteria interactions at scale ]]> https://biorxiv.org/content/10.1101/2023.03.23.534036v1?rss=1 100,000 communities across [~]525 environmental conditions with varying pH, carbon availability and phosphorous availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that dependance of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. By leveraging a high-throughput platform, our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions. ]]> Gopalakrishnappa, C. Li, Z. Kuehn, S. 2023-03-24 doi:10.1101/2023.03.23.534036 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Learning the functional landscape of microbial communities ]]> https://biorxiv.org/content/10.1101/2023.03.24.534159v1?rss=1 Skwara, A. Gowda, K. Yousef, M. Diaz-Colunga, J. Raman, A. S. Sanchez, A. Tikhonov, M. Kuehn, S. 2023-03-25 doi:10.1101/2023.03.24.534159 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut ]]> https://biorxiv.org/content/10.1101/2023.03.25.534219v1?rss=1 Fogarty, E. C. Schechter, M. S. Lolans, K. Sheahan, M. L. Veseli, I. Moore, R. Kiefl, E. Moody, T. Rice, P. A. Yu, M. K. Mimee, M. Chang, E. B. McLellan, S. L. Willis, A. D. Comstock, L. E. Eren, A. M. 2023-03-25 doi:10.1101/2023.03.25.534219 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Exploring the effects of ecological parameters on the spatial structure of genetic tree sequences ]]> https://biorxiv.org/content/10.1101/2023.03.27.534388v1?rss=1 Ianni-Ravn, M. K. Petr, M. Racimo, F. 2023-03-29 doi:10.1101/2023.03.27.534388 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Direct Thalamic Inputs to Hippocampal CA1 Transmit a Signal That Suppresses Ongoing Contextual Fear Memory Retrieval ]]> https://biorxiv.org/content/10.1101/2023.03.27.534420v1?rss=1 Ratigan, H. C. Krishnan, S. Smith, S. Sheffield, M. E. J. 2023-03-27 doi:10.1101/2023.03.27.534420 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Multiple climbing fiber innervation of mature Purkinje cells with distinct dendritic subfields ]]> https://biorxiv.org/content/10.1101/2023.03.27.534425v1?rss=1 Busch, S. E. Hansel, C. 2023-03-28 doi:10.1101/2023.03.27.534425 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ A transthalamic pathway is crucial for stimulus feature selectivity in higher order cortex ]]> https://biorxiv.org/content/10.1101/2023.03.30.533323v1?rss=1 Mo, C. McKinnon, C. Makitani, M. Sherman, S. M. 2023-03-31 doi:10.1101/2023.03.30.533323 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota ]]> https://biorxiv.org/content/10.1101/2023.03.31.535104v1?rss=1 Carasso, S. Zaatry, R. Hajjo, H. Kadosh-Kariti, D. Ben-Assa, N. Naddaf, R. Mandelbaum, N. Pressman, S. Chowers, Y. Gefen, T. Jeffrey, K. L. Jofre, J. Coyne, M. J. Comstock, L. E. Sharon, I. Geva-Zatorsky, N. 2023-04-01 doi:10.1101/2023.03.31.535104 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ Deep Learning for Flexible and Site-Specific Protein Docking and Design ]]> https://biorxiv.org/content/10.1101/2023.04.01.535079v1?rss=1 McPartlon, M. Xu, J. 2023-04-02 doi:10.1101/2023.04.01.535079 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ The adhesion GPCRs CELSR1-3 and LPHN3 engage G proteins via distinct activation mechanisms ]]> https://biorxiv.org/content/10.1101/2023.04.02.535287v1?rss=1 Bui, D. L. H. Roach, A. Li, J. Bandekar, S. J. Orput, E. Raghavan, R. Arac, D. Sando, R. 2023-04-03 doi:10.1101/2023.04.02.535287 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Dopamine D1 and NMDA receptor co-regulation of protein translation in cultured nucleus accumbens neurons ]]> https://biorxiv.org/content/10.1101/2023.04.02.535293v1?rss=1 Zimbelman, A. R. Wong, B. Murray, C. H. Wolf, M. E. Stefanik, M. T. 2023-04-02 doi:10.1101/2023.04.02.535293 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ SFyNCS detects oncogenic fusions involving non-coding sequences in cancer ]]> https://biorxiv.org/content/10.1101/2023.04.03.535462v1?rss=1 Zhong, X. Luan, J. Yu, A. Lee-Hassett, A. Miao, Y. Yang, L. 2023-04-06 doi:10.1101/2023.04.03.535462 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Reply to Barton et al: signatures of natural selection during the Black Death ]]> https://biorxiv.org/content/10.1101/2023.04.06.535944v1?rss=1 Vilgalys, T. P. Klunk, J. Demeure, C. E. Cheng, X. Shiratori, M. Madej, J. Beau, R. Elli, D. Patino, M. I. Redfern, R. DeWitte, S. N. Gamble, J. Boldsen, J. L. Carmichael, A. Varlik, N. Eaton, K. Grenier, J.-C. Golding, G. B. Devault, A. Rouillard, J.-M. Yotova, V. Sindeaux, R. Ye, C. J. Bikaran, M. Dumaine, A. Brinkworth, J. F. Missiakas, D. Rouleau, G. A. Steinrücken, M. Pizarro-Cerda, J. Poinar, H. Barreiro, L. B. 2023-04-07 doi:10.1101/2023.04.06.535944 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Synthetically mannosylated antigens induce antigen-specific humoral tolerance and reduce anti-drug antibody responses to immunogenic biologics ]]> https://biorxiv.org/content/10.1101/2023.04.07.534593v1?rss=1 Wallace, R. P. Refvik, K. C. Antane, J. T. Brünggel, K. Tremain, A. C. Raczy, M. R. Alpar, A. T. Nguyen, M. Solanki, A. Slezak, A. J. Watkins, E. A. Lauterbach, A. L. Wilson, D. S. Hubbell, J. A. 2023-04-07 doi:10.1101/2023.04.07.534593 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Glial Draper signaling triggers cross-neuron plasticity in bystander neurons after neuronal cell death ]]> https://biorxiv.org/content/10.1101/2023.04.09.536190v1?rss=1 Wang, Y. Zhang, R. Huang, S. Valverde, P. T.-T. Lobb-Rabe, M. Ashley, J. Venkatasubramanian, L. Carrillo, R. A. 2023-04-10 doi:10.1101/2023.04.09.536190 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs ]]> https://biorxiv.org/content/10.1101/2023.04.10.536266v1?rss=1 Ashwood, B. Jones, M. S. Radakovic, A. Khanna, S. Lee, Y. Sachleben, J. R. Szostak, J. W. Ferguson, A. L. Tokmakoff, A. 2023-04-10 doi:10.1101/2023.04.10.536266 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides ]]> https://biorxiv.org/content/10.1101/2023.04.12.536642v1?rss=1 Ding, D. Zhang, S. J. Szostak, J. W. 2023-04-12 doi:10.1101/2023.04.12.536642 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model ]]> https://biorxiv.org/content/10.1101/2023.04.14.536893v1?rss=1 3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type. ]]> Zou, Y. Carbonetto, P. Xie, D. Wang, G. Stephens, M. 2023-04-14 doi:10.1101/2023.04.14.536893 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Limited Diffusion of Scientific Knowledge Forecasts Collapse ]]> https://biorxiv.org/content/10.1101/2023.04.15.536986v1?rss=1 Kang, D. Danziger, R. S. Rehman, J. Evans, J. A. 2023-04-17 doi:10.1101/2023.04.15.536986 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Growth Hormone Accelerates Recovery From Acetaminophen-Induced Murine Liver Injury ]]> https://biorxiv.org/content/10.1101/2023.04.17.537197v1?rss=1 Everton, E. del Rio Moreno, M. Villacorta-Martin, C. Singh Bawa, P. Lindstrom-Vautrin, J. Muramatsu, H. Rizvi, F. Smith, A. R. Tam, Y. Pardi, N. Kineman, R. Waxman, D. J. Gouon-Evans, V. 2023-04-18 doi:10.1101/2023.04.17.537197 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Normalization in mouse primary visual cortex ]]> https://biorxiv.org/content/10.1101/2023.04.18.537260v1?rss=1 Zayyad, Z. A. Maunsell, J. H. MacLean, J. N. 2023-04-18 doi:10.1101/2023.04.18.537260 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Epistasis facilitates functional evolution in an ancient transcription factor ]]> https://biorxiv.org/content/10.1101/2023.04.19.537271v1?rss=1 Metzger, B. P. Park, Y. Starr, T. N. Thornton, J. W. 2023-04-20 doi:10.1101/2023.04.19.537271 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Validating a low-cost, open-source, locally manufactured workstation and computational pipeline for automated histopathology evaluation using deep learning ]]> https://biorxiv.org/content/10.1101/2023.04.19.537544v1?rss=1 Choudhury, D. Dolezal, J. Dyer, E. Kochanny, S. Ramesh, S. Howard, F. M. Margalus, J. R. Schroeder, A. Schulte, J. J. Garassino, M. C. Kather, J. N. Pearson, A. T. 2023-04-21 doi:10.1101/2023.04.19.537544 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ A core Nrf2 gene set defined through comprehensive transcriptomic analysis predicts drug resistance and poor multi-cancer prognosis ]]> https://biorxiv.org/content/10.1101/2023.04.20.537691v1?rss=1 Luo, G. Kumar, H. Alridge, K. Rieger, S. Jiang, E. Chan, E. R. Soliman, A. Mahdi, H. Letterio, J. J. 2023-04-21 doi:10.1101/2023.04.20.537691 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Tbx5 maintains atrial identity by regulating an atrial enhancer network ]]> https://biorxiv.org/content/10.1101/2023.04.21.537535v1?rss=1 Sweat, M. E. Cao, Y. Zhang, X. Burnicka-Turek, O. Perez-Cervantes, C. Akerberg, B. N. Ma, Q. Wakimoto, H. Gorham, J. M. Song, M. K. Trembley, M. A. Wang, P. Lu, F. Gianeselli, M. Prondzynski, M. Bortolin, R. H. Seidman, J. G. Seidman, C. Moskowitz, I. P. Pu, W. T. 2023-04-22 doi:10.1101/2023.04.21.537535 Cold Spring Harbor Laboratory Press 2023-04-22 <![CDATA[ A spatially resolved single cell genomic atlas of the adult human breast ]]> https://biorxiv.org/content/10.1101/2023.04.22.537946v1?rss=1 Kumar, T. Nee, K. Wei, R. He, S. Nguyen, Q. Bai, S. Blake, K. Pein, M. Gong, Y. Sei, E. Hu, M. Casasent, A. Thennavan, A. Li, J. Tran, T. Chen, K. Nilges, B. Kashikar, N. Braubach, O. Cheikh, B. Nikulina, N. Chen, H. Teshome, M. Menegaz, B. Javaid, H. Nagi, C. Montalvan, J. Lev, T. Tifrea, D. Edwards, R. Lin, E. Parajuli, R. Hanson, S. Winocour, S. Thompson, A. Lim, B. Lawson, D. Kessenbrock, K. Navin, N. 2023-04-24 doi:10.1101/2023.04.22.537946 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ ProtWave-VAE: Integrating autoregressive sampling with latent-based inference for data-driven protein design ]]> https://biorxiv.org/content/10.1101/2023.04.23.537971v1?rss=1 Praljak, N. Lian, X. Ranganathan, R. Ferguson, A. 2023-04-23 doi:10.1101/2023.04.23.537971 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Loss of thymocyte competition underlies the tumor suppressive functions of the E2a transcription factor in T lymphocyte acute lymphoblastic leukemia. ]]> https://biorxiv.org/content/10.1101/2023.04.23.537993v1?rss=1 Parriott, G. Hegermiller, E. Morman, R. E. Frank, C. Saygin, C. Stock, W. Bartom, E. T. Kee, B. L. 2023-04-25 doi:10.1101/2023.04.23.537993 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease ]]> https://biorxiv.org/content/10.1101/2023.04.24.538091v1?rss=1 Upadhyay, V. Yoon, Y. m. Vazquez, S. E. Velez, T. E. Jones, K. D. Lee, C. T. Law, C. S. Wolters, P. J. Lee, S. Yang, M. M. Farrand, E. Noth, I. Strek, M. E. Anderson, M. DeRisi, J. Sperling, A. I. Shum, A. K. 2023-04-24 doi:10.1101/2023.04.24.538091 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ The mechanics of correlated variability in segregated cortical excitatory subnetworks ]]> https://biorxiv.org/content/10.1101/2023.04.25.538323v1?rss=1 Negron, A. Getz, M. P. Handy, G. Doiron, B. 2023-04-27 doi:10.1101/2023.04.25.538323 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ 5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma. ]]> https://biorxiv.org/content/10.1101/2023.04.27.538309v1?rss=1 Chennakesavalu, M. Moore, K. Chaves, G. Veeravalli, S. Terhaar, R. Wu, T. Lyu, R. Chlenski, A. He, C. Piunti, A. Applebaum, M. A. 2023-04-28 doi:10.1101/2023.04.27.538309 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ A Mechanistic Reinterpretation of Fast Inactivation in Voltage-Gated Na+ Channels ]]> https://biorxiv.org/content/10.1101/2023.04.27.538555v1?rss=1 Liu, Y. Pinto, B. I. Bassetto, C. Z. Bezanilla, F. 2023-04-28 doi:10.1101/2023.04.27.538555 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Seryl-butyrate: a prodrug that enhances butyrate's oral bioavailability and suppresses autoimmune arthritis and experimental autoimmune encephalomyelitis ]]> https://biorxiv.org/content/10.1101/2023.04.28.538720v1?rss=1 Cao, S. Budina, E. Raczy, M. M. Solanki, A. Nguyen, M. Hultgren, K. Ang, P. Reda, J. W. Shores, L. S. Pillai, I. Wallace, R. P. Dhar, A. Watkins, E. Hubbell, J. A. 2023-04-29 doi:10.1101/2023.04.28.538720 Cold Spring Harbor Laboratory Press 2023-04-29 <![CDATA[ Neighborhood air pollution is negatively associated with neurocognitive maturation in early adolescence ]]> https://biorxiv.org/content/10.1101/2023.04.28.538763v1?rss=1 Kardan, O. Sereeyothin, C. Schertz, K. E. Angstadt, M. Weigard, A. Berman, M. G. Rosenberg, M. D. 2023-05-02 doi:10.1101/2023.04.28.538763 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ Structural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development ]]> https://biorxiv.org/content/10.1101/2023.05.04.539414v1?rss=1 Rosas, G. C. Li, J. Smith, J. J. Cheng, S. Baltrusaitis, E. Nawrocka, W. Zhao, M. Kratsios, P. Arac, D. Ozkan, E. 2023-05-04 doi:10.1101/2023.05.04.539414 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Diving dinosaurs? Caveats on the use of bone compactness and pFDA for inferring lifestyle ]]> https://biorxiv.org/content/10.1101/2023.05.04.539484v1?rss=1 Myhrvold, N. P. Sereno, P. C. Baumgart, S. L. Vidal, D. Fish, F. E. Henderson, D. M. Saitta, E. T. 2023-05-07 doi:10.1101/2023.05.04.539484 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Illusion of agency over involuntary muscle movements reveals temporal dynamics of neural activity underlying self-agency judgments ]]> https://biorxiv.org/content/10.1101/2023.05.06.539706v1?rss=1 Veillette, J. P. Lopes, P. Nusbaum, H. C. 2023-05-08 doi:10.1101/2023.05.06.539706 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Conformation-specific synthetic antibodies discriminate multiple functional states of the ion channel CorA ]]> https://biorxiv.org/content/10.1101/2023.05.07.539746v1?rss=1 Erramilli, S. K. Dominik, P. K. Deneka, D. Tokarz, P. P. Kim, S. S. Reddy, B. G. Skrobek, B. M. Dalmas, O. Perozo, E. Kossiakoff, A. A. 2023-05-07 doi:10.1101/2023.05.07.539746 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ SHORT-TERM CALORIC RESTRICTION IN MICE PROMOTES RESOLUTION OF ATHEROSCLEROSIS, WHILE WEIGHT REGAIN ACCELERATES ITS PROGRESSION ]]> https://biorxiv.org/content/10.1101/2023.05.07.539777v1?rss=1 60% will regain their lost weight. This weight cycling is associated with elevated risk of cardiovascular disease, relative to never having lost weight. How weight loss/regain directly influence atherosclerotic inflammation is unknown. Thus, we studied short-term caloric restriction (stCR) in obese hypercholesterolemic mice, without confounding effects from changes in diet composition. Weight loss was found to promote atherosclerosis resolution independent of plasma cholesterol. From single-cell RNA-sequencing and subsequent mechanistic studies, this can be partly attributed to a unique subset of macrophages accumulating with stCR in epididymal adipose tissue (eWAT) and atherosclerotic plaques. These macrophages, distinguished by high expression of Fcgr4, help to clear necrotic cores in atherosclerotic plaques. Conversely, weight regain (WR) following stCR accelerated atherosclerosis progression with disappearance of Fcgr4+ macrophages from eWAT and plaques. Furthermore, WR caused reprogramming of immune progenitors, sustaining hyper-inflammatory responsiveness. In summary, we have developed a model to investigate the inflammatory effects of weight cycling on atherosclerosis and the interplay between adipose tissue, bone marrow, and plaques. The findings suggest potential approaches to promote atherosclerotic plaque resolution in obesity and weight cycling through induction of Fcgr4+ macrophages and inhibition of immune progenitor reprogramming. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/539777v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@c6e857org.highwire.dtl.DTLVardef@bfd443org.highwire.dtl.DTLVardef@88973org.highwire.dtl.DTLVardef@78198f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Scolaro, B. Brown, E. J. Krautter, F. Petitjean, M. Donahoe, C. Pena, S. Garabedian, M. L. Nikain, C. A. Laskou, M. Tufanli, O. Hannemann, C. Aouadi, M. Weinstock, A. Fisher, E. 2023-05-08 doi:10.1101/2023.05.07.539777 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Sinogram Domain Angular Upsampling of Sparse-View Micro-CT with Dense Residual Hierarchical Transformer and Noise-Aware Loss ]]> https://biorxiv.org/content/10.1101/2023.05.09.540072v1?rss=1 Adishesha, A. S. Vanselow, D. J. La Riviere, P. Cheng, K. C. Huang, S. X. 2023-05-12 doi:10.1101/2023.05.09.540072 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Microbes with higher metabolic independence are enriched in human gut microbiomes under stress ]]> https://biorxiv.org/content/10.1101/2023.05.10.540289v1?rss=1 Veseli, I. Chen, Y. T. Schechter, M. S. Vanni, C. Fogarty, E. C. Watson, A. R. Jabri, B. A. Blekhman, R. Willis, A. D. Yu, M. K. Fernandez-Guerra, A. Fussel, J. Eren, A. M. 2023-05-15 doi:10.1101/2023.05.10.540289 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Multi-omics analysis of a Bacteroides fragilis isolate from an ulcerative colitis patient defines genetic determinants of fitness in bile ]]> https://biorxiv.org/content/10.1101/2023.05.11.540287v1?rss=1 50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of {approx}50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile. ImportanceThe Gram-negative bacterium, Bacteroides fragilis, is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation. ]]> Fiebig, A. Schnizlein, M. Pena-Rivera, S. Trigodet, F. Dubey, A. Hennessy, M. Basu, A. Pott, S. Dalal, S. Rubin, D. Sogin, M. Eren, A. M. Chang, E. Crosson, S. 2023-05-11 doi:10.1101/2023.05.11.540287 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Electron transport inhibition increases cellular dependence on purine transport and salvage ]]> https://biorxiv.org/content/10.1101/2023.05.11.540429v1?rss=1 Wu, Z. Bezwada, D. Harris, R. C. Pan, C. Nguyen, P. T. Faubert, B. Cai, L. Cai, F. Vu, H. S. Chen, H. Martin-Sandoval, M. Do, D. Gu, W. Zhang, Y. Ko, B. Brooks, B. Kelekar, S. Zhang, Y. Zacharias, L. G. Oaxaca, K. C. Mathews, T. P. Garcia-Bermudez, J. Ni, M. DeBerardinis, R. J. 2023-05-11 doi:10.1101/2023.05.11.540429 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Structural snapshots of hyaluronan formation reveal principles of length control and secretion ]]> https://biorxiv.org/content/10.1101/2023.05.11.540447v1?rss=1 Gorniak, I. Stephens, Z. Erramilli, S. Gawda, T. Kossiakoff, A. Zimmer, J. 2023-05-12 doi:10.1101/2023.05.11.540447 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Prolonged DNA Damage Checkpoint Arrest Requires Constant Renewal and the Spindle Assembly Checkpoint ]]> https://biorxiv.org/content/10.1101/2023.05.15.540538v1?rss=1 Zhou, F. Y. Waterman, D. P. Caban-Penix, S. Eapen, V. V. Haber, J. E. 2023-05-15 doi:10.1101/2023.05.15.540538 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Direct detection of deformation modes on varying length scales in active biopolymer networks ]]> https://biorxiv.org/content/10.1101/2023.05.15.540780v1?rss=1 Stam, S. Gardel, M. L. Weirich, K. 2023-05-16 doi:10.1101/2023.05.15.540780 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ A Recombinant Antibody For Tracking Murine Gammaherpesvirus 68 Uracil DNA Glycosylase Expression. ]]> https://biorxiv.org/content/10.1101/2023.05.17.541089v1?rss=1 Mu, Y. Plummer, J. B. Zelazowska, M. A. Paul, S. Dong, Q. Chen, Z. Krug, L. T. McBride, K. M. 2023-05-18 doi:10.1101/2023.05.17.541089 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Microsecond dynamics control the HIV-1 envelope conformation ]]> https://biorxiv.org/content/10.1101/2023.05.17.541130v1?rss=1 Bennett, A. L. Edwards, R. J. Kosheleva, I. Saunders, C. Bililign, Y. Williams, A. Manosouri, K. Saunders, K. O. Haynes, B. F. Acharya, P. Henderson, R. 2023-05-18 doi:10.1101/2023.05.17.541130 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Emerging Activity Patterns and Synaptogenesis in Dissociated Hippocampal Cultures ]]> https://biorxiv.org/content/10.1101/2023.05.18.541345v1?rss=1 Van Drongelen, W. 2023-05-18 doi:10.1101/2023.05.18.541345 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ DNA methylation-environment interactions in the human genome ]]> https://biorxiv.org/content/10.1101/2023.05.19.541437v1?rss=1 Johnston, R. A. Aracena, K. A. Barreiro, L. B. Lea, A. J. Tung, J. 2023-05-19 doi:10.1101/2023.05.19.541437 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Imputation Efficacy Across Global Human Populations ]]> https://biorxiv.org/content/10.1101/2023.05.22.541241v1?rss=1 Cahoon, J. L. Rui, X. Tang, E. Simons, C. Langie, J. Chen, M. Lo, Y.-C. Chiang, C. W. K. 2023-05-24 doi:10.1101/2023.05.22.541241 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Nighthawk: acoustic monitoring of nocturnal bird migration in the Americas ]]> https://biorxiv.org/content/10.1101/2023.05.22.541336v1?rss=1 Van Doren, B. M. Farnsworth, A. Stone, K. Osterhaus, D. M. Drucker, J. Van Horn, G. 2023-05-23 doi:10.1101/2023.05.22.541336 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter ]]> https://biorxiv.org/content/10.1101/2023.05.22.541801v1?rss=1 Levin-Konigsberg, R. Mitra, K. Nigam, A. Spees, K. Hivare, P. Liu, K. Kundaje, A. Krishnan, Y. Bassik, M. 2023-05-22 doi:10.1101/2023.05.22.541801 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Suppression of tumor cell lactate-generating signaling pathways eradicates murine PTEN/p53-deficient aggressive-variant prostate cancer via macrophage phagocytosis ]]> https://biorxiv.org/content/10.1101/2023.05.23.540590v1?rss=1 Chaudagar, K. K. Hieromnimon, H. Kelley, A. Labadie, B. Shafran, J. Rameshbabu, S. Drovetsky, C. Bynoe, K. Solanki, A. Markiewicz, E. Fan, X. Loda, M. Patnaik, A. 2023-05-23 doi:10.1101/2023.05.23.540590 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae ]]> https://biorxiv.org/content/10.1101/2023.05.23.541939v1?rss=1 Yakovlev, M. A. Liang, K. Zaino, C. R. Vanselow, D. J. Sugarman, A. L. Lin, A. Y. La Riviere, P. J. Zheng, Y. Silverman, J. D. Liechty, J. C. Huang, S. X. Cheng, K. C. 2023-05-24 doi:10.1101/2023.05.23.541939 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ m6A mRNA Methylation in Brown Adipose Tissue Regulates Systemic Insulin Sensitivity via an Inter-Organ Prostaglandin Signaling Axis ]]> https://biorxiv.org/content/10.1101/2023.05.26.542169v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@16b3393org.highwire.dtl.DTLVardef@1072ae3org.highwire.dtl.DTLVardef@190a6d7org.highwire.dtl.DTLVardef@1b98bce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xiao, L. De Jesus, D. F. Ju, C.-W. Wei, J.-B. Hu, J. DiStefano-Forti, A. Tsuji, T. Cero, C. Mannisto, V. Manninen, S. M. Wei, S.-Y. Ijaduola, O. Blueher, M. Cypess, A. M. Pihlajamaki, J. Tseng, Y.-H. He, C. Kulkarni, R. N. 2023-05-26 doi:10.1101/2023.05.26.542169 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Influence of Fast-Spiking Prefrontal Neurons on Working Memory Behavior ]]> https://biorxiv.org/content/10.1101/2023.05.28.542641v1?rss=1 Chung, S. Mozumder, R. Li, S. Constantinidis, C. 2023-05-30 doi:10.1101/2023.05.28.542641 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ HMGB1 acts as an agent of host defense at the gut mucosal barrier ]]> https://biorxiv.org/content/10.1101/2023.05.30.542477v1?rss=1 Overstreet, A.-M. C. Anderson, B. Burge, M. Zhu, X. Tao, Y. Cham, C. Michaud, B. Horam, S. Sangwan, N. Dwidar, M. Liu, X. Santos, A. Finney, C. Dai, Z. Leone, V. Messer, J. S. 2023-05-30 doi:10.1101/2023.05.30.542477 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ System Neglect and the Neurocomputational Substrates for Over- and Underreactions to Change ]]> https://biorxiv.org/content/10.1101/2023.05.30.542806v1?rss=1 Wang, M.-C. Wu, G. Wu, S.-W. 2023-05-31 doi:10.1101/2023.05.30.542806 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Closed ecosystems extract energy through self-organized nutrient cycles ]]> https://biorxiv.org/content/10.1101/2023.05.30.542875v1?rss=1 Goyal, A. Flamholz, A. I. Petroff, A. P. Murugan, A. 2023-06-01 doi:10.1101/2023.05.30.542875 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Contributions of early and mid-level visual cortex to high-level object categorization ]]> https://biorxiv.org/content/10.1101/2023.05.31.541514v1?rss=1 Kramer, L. E. Konkle, T. Chen, Y.-C. Long, B. Cohen, M. R. 2023-06-01 doi:10.1101/2023.05.31.541514 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Genomic patterns in the global soil microbiome emerge from microbial interactions ]]> https://biorxiv.org/content/10.1101/2023.05.31.542950v1?rss=1 Crocker, K. Chakraverti-Wuerthwein, M. Li, Z. Mani, M. Gowda, K. Kuehn, S. 2023-06-01 doi:10.1101/2023.05.31.542950 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Resolving conformational changes that mediate a two-step catalytic mechanism in a model enzyme ]]> https://biorxiv.org/content/10.1101/2023.06.02.543507v1?rss=1 Greisman, J. B. Dalton, K. M. Brookner, D. E. Klureza, M. A. Sheehan, C. J. Kim, I.-S. Henning, R. W. Russi, S. Hekstra, D. R. 2023-06-03 doi:10.1101/2023.06.02.543507 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ The impact of common variants on gene expression in the human brain: from RNA to protein to schizophrenia risk ]]> https://biorxiv.org/content/10.1101/2023.06.04.543603v1?rss=1 Liang, Q. Jiang, Y. Shieh, A. W. Zhou, D. Chen, R. Wang, F. Xu, M. Wang, X. Pinto, D. Wang, Y. Cheng, L. Vadukapuram, R. Zhang, C. Grennan, K. Giase, G. The PsychENCODE Consortium, White, K. P. Peng, J. Li, B. Liu, C. Chen, C. Wang, S. H. 2023-06-05 doi:10.1101/2023.06.04.543603 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Apical polarity and actomyosin dynamics regulate Hippo signaling by controlling Kibra subcellular localization ]]> https://biorxiv.org/content/10.1101/2023.06.05.543736v1?rss=1 Tokamov, S. A. Nouri, N. Rich, A. Buiter, S. Glotzer, M. Fehon, R. G. 2023-06-06 doi:10.1101/2023.06.05.543736 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Anoctamin-1 is induced by TGF-beta and contributes to lung myofibroblast differentiation ]]> https://biorxiv.org/content/10.1101/2023.06.07.544093v1?rss=1 Reed, E. B. Orbeta, S. Sitikov, A. Levitan, I. Mutlu, G. M. Mongin, A. A. Dulin, N. O. 2023-06-07 doi:10.1101/2023.06.07.544093 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Limiting Pool and Actin Architecture Controls Myosin Cluster Sizes in Adherent Cells ]]> https://biorxiv.org/content/10.1101/2023.06.07.544121v1?rss=1 Chou, W.-h. Molaei, M. Wu, H. Oakes, P. W. Beach, J. Gardel, M. 2023-06-07 doi:10.1101/2023.06.07.544121 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ A 2-million-year-old microbial and viral communities from the Kap Kobenhavn Formation in North Greenland ]]> https://biorxiv.org/content/10.1101/2023.06.10.544454v1?rss=1 Fernandez-Guerra, A. Borrel, G. Delmont, T. O. Elberling, B. Eren, A. M. Gribaldo, S. Jochheim, A. Henriksen, R. A. Hinrichs, K.-U. Korneliussen, T. S. Krupovic, M. Larsen, N. K. Perez-Laso, R. Pedersen, M. W. Pedersen, V. K. Sand, K. K. Sikora, M. Steinegger, M. Veseli, I. A. Wörmer, L. Zhao, L. Zure, M. Kjaer, K. H. Willerslev, E. 2023-06-10 doi:10.1101/2023.06.10.544454 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation ]]> https://biorxiv.org/content/10.1101/2023.06.11.543863v1?rss=1 Ousalem, F. Singh, S. Bailey, N. A. Wong, K.-H. Zhu, L. Neky, M. J. Sibindi, C. Fei, J. Gonzalez, R. L. Boël, G. Hunt, J. F. 2023-06-12 doi:10.1101/2023.06.11.543863 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Cryo-EM structures of a synthetic antibody against 22 kDa claudin-4 reveal its complex with Clostridium perfringens enterotoxin ]]> https://biorxiv.org/content/10.1101/2023.06.12.544689v1?rss=1 Erramilli, S. K. Dominik, P. K. Ogbu, C. P. Kossiakoff, A. A. Vecchio, A. J. 2023-06-12 doi:10.1101/2023.06.12.544689 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Dissection and Integration of Bursty TranscriptionalDynamics for Complex Systems ]]> https://biorxiv.org/content/10.1101/2023.06.13.544828v1?rss=1 Gao, C. F. Vaikuntanathan, S. Riesenfeld, S. 2023-06-13 doi:10.1101/2023.06.13.544828 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ WFIKKN2 is a bifunctional axon guidance cue that signals through divergent DCC family receptors ]]> https://biorxiv.org/content/10.1101/2023.06.15.544950v1?rss=1 Nickerson, K. R. Tom, I. Cortes, E. Abolafia, J. R. Özkan, E. Gonzalez, L. C. Jaworski, A. 2023-06-15 doi:10.1101/2023.06.15.544950 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ β Cell microRNAs Function as Molecular Hubs of Type 1 Diabetes Pathogenesis and as Biomarkers of Diabetes Risk ]]> https://biorxiv.org/content/10.1101/2023.06.15.545170v1?rss=1 Syed, F. Krishnan, P. Chang, G. Langlais, S. R. Hati, S. Yamada, K. Lam, A. K. Talware, S. Liu, X. Sardar, R. Liu, J. Mirmira, R. G. Evans-Molina, C. 2023-06-15 doi:10.1101/2023.06.15.545170 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications ]]> https://biorxiv.org/content/10.1101/2023.06.18.545436v1?rss=1 Wang, Y. Zhang, L. Zhang, W. Gao, B. Ye, C. Dai, Q. Wang, K. Luo, M. Pan, T. He, C. 2023-06-18 doi:10.1101/2023.06.18.545436 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Cortical tension regulates Hippo signaling via Par-1-mediated Kibra degradation ]]> https://biorxiv.org/content/10.1101/2023.06.18.545491v1?rss=1 Tokamov, S. A. Buiter, S. Ullyot, A. Scepanovic, G. Williams, A. M. Fernandez-Gonzalez, R. Horne-Badovinac, S. Fehon, R. G. 2023-06-18 doi:10.1101/2023.06.18.545491 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Place field precision during an episode predicts place field fate across episodes ]]> https://biorxiv.org/content/10.1101/2023.06.18.545503v1?rss=1 Chiu, Y. Dong, C. Krishnan, S. Sheffield, M. M. E. 2023-06-21 doi:10.1101/2023.06.18.545503 Cold Spring Harbor Laboratory Press 2023-06-21 <![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[ Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment ]]> https://biorxiv.org/content/10.1101/2023.06.22.544406v1?rss=1 Rowdo, F. P. M. Xiao, G. Khramtsova, G. F. Nguyen, J. Olopade, O. Martini, R. Stonaker, B. Boateng, R. Oppong, J. K. Adjei, E. K. Awuah, B. Kyei, I. Aitpillah, F. S. Adinku, M. O. Ankomah, K. Osei-Bonsu, E. B. Gyan, K. K. Altorki, N. K. Cheng, E. Ginter, P. S. Hoda, S. Newman, L. Elemento, O. Davis, M. B. Martin, M. L. Bargonetti, J. 2023-06-22 doi:10.1101/2023.06.22.544406 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ High performers demonstrate greater neural synchrony than low performers across behavioral domains ]]> https://biorxiv.org/content/10.1101/2023.06.22.546173v1?rss=1 Chamberlain, T. A. Corriveau, A. Song, H. Kwon, Y. H. Yoo, K. Chun, M. Rosenberg, M. D. 2023-06-26 doi:10.1101/2023.06.22.546173 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Flagellar switch inverted repeat sequence variation impacts Clostridioides difficile RT027/MLST1 virulence. ]]> https://biorxiv.org/content/10.1101/2023.06.22.546185v1?rss=1 99% ON or OFF). Taken together, our results reveal that phenotypic heterogeneity in flagellar gene expression may contribute to the variable disease severity observed in C. difficile patients. ]]> Nhu, N. T. Q. Lin, H. Sia, J. K. Snitkin, E. S. Young, V. B. Kamboj, M. Pamer, E. G. Rice, P. A. Dong, Q. 2023-06-23 doi:10.1101/2023.06.22.546185 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Tessellation Of Artificial Touch Via Microstimulation Of Human Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/2023.06.23.545425v1?rss=1 Greenspon, C. M. Shelchkova, N. D. Valle, G. Hobbs, T. Berger-Wolf, E. I. Hutchison, B. C. Dogruoz, E. Jordan, P. M. Verbarschott, C. Callier, T. Sobinov, A. Okorokova, E. V. Prasad, D. He, Q. Liu, F. Miller, J. P. Lee, R. C. Satzer, D. Gonzalez-Martinez, J. Warnke, P. Miller, L. E. Boninger, M. L. Ajiboye, B. B. Graczyk, E. L. Downey, J. E. Collinger, J. Hatsopoulos, N. Gaunt, R. Bensmaia, S. J. 2023-06-26 doi:10.1101/2023.06.23.545425 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Data-driven discovery of innate immunomodulators via machine learning-guided high throughput screening ]]> https://biorxiv.org/content/10.1101/2023.06.26.546393v1?rss=1 Tang, Y. Kim, J. Y. IP, C. K. Bahmani, A. Chen, Q. Rosenberger, M. G. Esser-Kahn, A. P. Ferguson, A. L. 2023-06-28 doi:10.1101/2023.06.26.546393 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ T-cell inflammation is prognostic of survival in patients with high-risk neuroblastoma enriched for an adrenergic signature ]]> https://biorxiv.org/content/10.1101/2023.06.26.546541v1?rss=1 Kaufman, M. E. Vayani, O. R. Moore, K. Chlenski, A. Wu, T. Chaves, G. Lee, S. M. Desai, A. V. He, C. Cohn, S. L. Applebaum, M. A. 2023-06-28 doi:10.1101/2023.06.26.546541 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Cracked actin filaments as mechanosensitive receptors ]]> https://biorxiv.org/content/10.1101/2023.06.26.546553v1?rss=1 Zsolnay, V. Gardel, M. L. Kovar, D. R. Voth, G. A. 2023-06-28 doi:10.1101/2023.06.26.546553 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Pushed to the edge: hundreds of myosin 10s pack into filopodia and could cause traffic jams on actin ]]> https://biorxiv.org/content/10.1101/2023.06.26.546598v1?rss=1 Shangguan, J. Rock, R. S. 2023-06-26 doi:10.1101/2023.06.26.546598 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power ]]> https://biorxiv.org/content/10.1101/2023.06.28.546921v1?rss=1 LaPierre, N. Pimentel, H. 2023-06-30 doi:10.1101/2023.06.28.546921 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Statistical prediction of microbial metabolic traits from genomes ]]> https://biorxiv.org/content/10.1101/2023.06.30.547261v1?rss=1 Li, Z. Selim, A. Kuehn, S. 2023-07-02 doi:10.1101/2023.06.30.547261 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Edge-based general linear models capture high-frequency fluctuations in attention ]]> https://biorxiv.org/content/10.1101/2023.07.06.547966v1?rss=1 Jones, H. M. Yoo, K. Chun, M. M. Rosenberg, M. D. 2023-07-10 doi:10.1101/2023.07.06.547966 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Engineered Antigen-Binding Fragments for Enhanced Crystallisation of Antibody:Antigen Complexes ]]> https://biorxiv.org/content/10.1101/2023.07.06.548021v1?rss=1 Bruce, H. A. Singer, A. U. Filippova, E. V. Blazer, L. L. Adams, J. J. Enderle, L. Ben-David, M. Radley, E. H. Mao, D. Y. Pau, V. Orlicky, S. Sicheri, F. Kourinov, I. Atwell, S. Kossiakoff, A. A. Sidhu, S. S. 2023-07-06 doi:10.1101/2023.07.06.548021 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Functional Protein Dynamics in a Crystal ]]> https://biorxiv.org/content/10.1101/2023.07.06.548023v1?rss=1 Klyshko, E. Kim, J. S.-H. McGough, L. Valeeva, V. Lee, E. Ranganathan, R. Rauscher, S. 2023-07-07 doi:10.1101/2023.07.06.548023 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1 ]]> https://biorxiv.org/content/10.1101/2023.07.10.548240v1?rss=1 Mondal, R. Mandal, M. Lahiri, T. 2023-07-11 doi:10.1101/2023.07.10.548240 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Hostile attribution bias shapes neural synchrony in the left ventromedial prefrontal cortexduring ambiguous social narratives ]]> https://biorxiv.org/content/10.1101/2023.07.11.548407v1?rss=1 Lyu, Y. Su, Z. Neumann, D. Meidenbauer, K. L. Leong, Y. C. 2023-07-12 doi:10.1101/2023.07.11.548407 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Multi-monoubiquitination controls VASP-mediated actin dynamics ]]> https://biorxiv.org/content/10.1101/2023.07.16.549237v1?rss=1 McCormick, L. E. Suarez, C. Herring, L. E. Cannon, K. S. Kovar, D. R. Brown, N. G. Gupton, S. L. 2023-07-17 doi:10.1101/2023.07.16.549237 Cold Spring Harbor Laboratory Press 2023-07-17 <![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[ Mathematical Model Predicts Tumor Control Patterns Induced by Fast and Slow CTL Killing Mechanisms ]]> https://biorxiv.org/content/10.1101/2023.07.19.548738v1?rss=1 Wang, Y. Bergman, D. Trujillo, E. Pearson, A. T. Sweis, R. F. Jackson, T. L. 2023-07-20 doi:10.1101/2023.07.19.548738 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth ]]> https://biorxiv.org/content/10.1101/2023.07.19.549370v1?rss=1 Johnson, K. E. Heisel, T. Fields, D. A. Isganaitis, E. Jacobs, K. M. Knights, D. Lock, E. F. Rudolph, M. C. Gale, C. A. Schleiss, M. R. Albert, F. W. Demerath, E. W. Blekhman, R. 2023-07-19 doi:10.1101/2023.07.19.549370 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Multiple objects evoke fluctuating responses in several regions of the visual pathway ]]> https://biorxiv.org/content/10.1101/2023.07.19.549668v1?rss=1 Schmehl, M. N. Caruso, V. C. Chen, Y. Jun, N. Y. Willett, S. M. Mohl, J. T. Ruff, D. A. Cohen, M. R. Ebihara, A. Freiwald, W. Tokdar, S. T. Groh, J. M. 2023-07-19 doi:10.1101/2023.07.19.549668 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum ]]> https://biorxiv.org/content/10.1101/2023.07.19.549760v1?rss=1 Lin, T.-F. Busch, S. E. Hansel, C. 2023-07-21 doi:10.1101/2023.07.19.549760 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ An oxadiazole-based compound potentiates anti- tuberculosis treatment by increasing host resistance via zinc poisoning ]]> https://biorxiv.org/content/10.1101/2023.07.21.549986v1?rss=1 Maure, A. Lawaree, E. Fiorentino, F. Pawlik, A. Gona, S. Giraud-Gatineau, A. Eldridge, M. J. G. Danckaert, A. Hardy, D. Frigui, W. Keck, C. Aulner, N. Mai, A. Hamon, M. Barreiro, L. B. Brodin, P. Brosch, R. Rotili, D. Tailleux, L. 2023-07-21 doi:10.1101/2023.07.21.549986 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity ]]> https://biorxiv.org/content/10.1101/2023.07.21.550072v1?rss=1 McIntire, E. Barr, K. A. Gilad, Y. 2023-07-22 doi:10.1101/2023.07.21.550072 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics ]]> https://biorxiv.org/content/10.1101/2023.07.22.550182v1?rss=1 Ashwood, B. Jones, M. S. Lee, Y. Sachleben, J. R. Ferguson, A. L. Tokmakoff, A. 2023-07-25 doi:10.1101/2023.07.22.550182 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Evaluating steroid hormone receptor interactions using the live-cell NanoBRET proximity assay ]]> https://biorxiv.org/content/10.1101/2023.07.25.550078v1?rss=1 Huggins, R. J. Hosfield, D. Ishag-Osman, A. Lee, K. Ton-That, E. Greene, G. L. 2023-07-26 doi:10.1101/2023.07.25.550078 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Computational prediction of protein interactions on single cells by proximity sequencing ]]> https://biorxiv.org/content/10.1101/2023.07.27.550388v1?rss=1 Xia, J. Phan, H. V. Vistain, L. Chen, M. Khan, A. A. Tay, S. 2023-07-30 doi:10.1101/2023.07.27.550388 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Functional and anatomical connectivity predict brain stimulation's mnemonic effects ]]> https://biorxiv.org/content/10.1101/2023.07.27.550851v1?rss=1 Ezzyat, Y. Kragel, J. E. Solomon, E. A. Lega, B. C. Aronson, J. P. Jobst, B. C. Gross, R. E. Sperling, M. R. Worrell, G. A. Sheth, S. A. Wanda, P. A. Rizzuto, D. S. Kahana, M. J. 2023-07-29 doi:10.1101/2023.07.27.550851 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ An adaptive biomolecular condensation response is conserved across environmentally divergent species ]]> https://biorxiv.org/content/10.1101/2023.07.28.551061v1?rss=1 Keyport Kik, S. Christopher, D. Glauninger, H. Wong Hickernell, C. Bard, J. A. M. Ford, M. Sosnick, T. R. Drummond, D. A. 2023-07-29 doi:10.1101/2023.07.28.551061 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons ]]> https://biorxiv.org/content/10.1101/2023.08.01.551489v1?rss=1 Lin, W. Wall, J. Li, G. Newman, D. VandeBerg, J. Yang, Y. Abney, M. Olivier, M. Gilad, Y. Cox, L. A. 2023-08-03 doi:10.1101/2023.08.01.551489 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme uptake ]]> https://biorxiv.org/content/10.1101/2023.08.01.551527v1?rss=1 Knejski, P. P. Erramilli, S. K. Kossiakoff, A. A. 2023-08-01 doi:10.1101/2023.08.01.551527 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ EpiVar Browser: advanced exploration of epigenomics data under controlled access ]]> https://biorxiv.org/content/10.1101/2023.08.03.551309v1?rss=1 Lougheed, D. R. Liu, H. Aracena, K. A. Gregoire, R. Pacis, A. Pastinen, T. Barreiro, L. B. Joly, Y. Bujold, D. Bourque, G. 2023-08-05 doi:10.1101/2023.08.03.551309 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ m6A mRNA Methylation Regulates Early Pancreatic β-Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2023.08.03.551675v1?rss=1 Kahraman, S. De Jesus, D. F. Wei, J. Brown, N. K. Zou, Z. Hu, J. He, C. Kulkarni, R. N. 2023-08-03 doi:10.1101/2023.08.03.551675 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Mechanism of Phosphate Release from Actin Filaments ]]> https://biorxiv.org/content/10.1101/2023.08.03.551904v1?rss=1 Wang, Y. Zsolnay, V. Pollard, T. D. Voth, G. A. 2023-08-05 doi:10.1101/2023.08.03.551904 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Oligomerization and feedback on membrane recruitment stabilize PAR-3 asymmetries in C. elegans zygotes. ]]> https://biorxiv.org/content/10.1101/2023.08.04.552031v1?rss=1 Lang, C. F. Anneken, A. Munro, E. 2023-08-04 doi:10.1101/2023.08.04.552031 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes ]]> https://biorxiv.org/content/10.1101/2023.08.04.552048v1?rss=1 Smith, J. J. Taylor, S. R. Blum, J. A. Gitler, A. Miller, D. M. Kratsios, P. 2023-08-06 doi:10.1101/2023.08.04.552048 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ HIV-1 Capsid Shape, Orientation, and Entropic Elasticity Regulate Translocationinto the Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2023.08.05.552137v1?rss=1 Hudait, A. Voth, G. A. 2023-08-06 doi:10.1101/2023.08.05.552137 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ TMEM165 acts as a proton-activated Ca2+ importer in lysosomes ]]> https://biorxiv.org/content/10.1101/2023.08.08.552438v1?rss=1 Zajac, M. Mukherjee, S. Anees, P. Oettinger, D. Henn, K. Srikumar, J. Zou, J. Saminathan, A. Krishnan, Y. 2023-08-09 doi:10.1101/2023.08.08.552438 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Stimulus invariant aspects of the retinal code drive discriminability of natural scenes ]]> https://biorxiv.org/content/10.1101/2023.08.08.552526v1?rss=1 Hoshal, B. Holmes, C. M. Bojanek, K. Salisbury, J. M. Berry, M. J. Marre, O. Palmer, S. 2023-08-12 doi:10.1101/2023.08.08.552526 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Photolipid excitation triggers depolarizing optocapacitive currents and action potentials ]]> https://biorxiv.org/content/10.1101/2023.08.11.552849v1?rss=1 Bassetto, C. A. Z. Pfeffermann, J. Yadav, R. Strassgschwandtner, S. Glasnov, T. Bezanilla, F. Pohl, P. 2023-08-14 doi:10.1101/2023.08.11.552849 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Volumetric imaging of an intact organism by a distributed molecular network ]]> https://biorxiv.org/content/10.1101/2023.08.11.553025v1?rss=1 Weinstein, J. A. Qian, N. 2023-08-14 doi:10.1101/2023.08.11.553025 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group ]]> https://biorxiv.org/content/10.1101/2023.08.13.553086v1?rss=1 Flynn, J. M. Ahmed-Braimah, Y. H. Long, M. Wing, R. A. Clark, A. G. 2023-08-14 doi:10.1101/2023.08.13.553086 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition ]]> https://biorxiv.org/content/10.1101/2023.08.15.553436v1?rss=1 Liu, Y. Carbonetto, P. Willwerscheid, J. Oakes, S. A. Macleod, K. F. Stephens, M. 2023-08-17 doi:10.1101/2023.08.15.553436 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Molecular dynamics analyses of CLDN15 pore size and charge selectivity ]]> https://biorxiv.org/content/10.1101/2023.08.16.553400v1?rss=1 McGuinness, S. Li, P. Li, Y. Fuladi, S. Konar, S. Bafghi, S. S. Sidahmed, M. Li, Y. Shen, L. Khalili-Araghi, F. Weber, C. R. 2023-08-17 doi:10.1101/2023.08.16.553400 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding ]]> https://biorxiv.org/content/10.1101/2023.08.16.553549v1?rss=1 Banerjee, P. Voth, G. A. 2023-08-16 doi:10.1101/2023.08.16.553549 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ The minimum intervention principle of optimal control relates the uncontrolled manifold to muscle synergies ]]> https://biorxiv.org/content/10.1101/2023.08.18.553939v1?rss=1 Sharma, N. 2023-08-21 doi:10.1101/2023.08.18.553939 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Injectable butyrate-prodrug micelles induce long-acting immune modulation and suppress autoimmune arthritis in mice ]]> https://biorxiv.org/content/10.1101/2023.08.20.554028v1?rss=1 Cao, S. Budina, E. Wang, R. Sabados, M. Solanki, A. Nguyen, M. Hultgren, K. Dhar, A. Hubbell, J. 2023-08-21 doi:10.1101/2023.08.20.554028 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Spectral decomposition unlocks ascidian morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.22.554368v1?rss=1 Dokmegang, J. Faure, E. Lemaire, P. Munro, E. Mani, M. 2023-08-23 doi:10.1101/2023.08.22.554368 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Temporal weighting of cortical and subcortical spikes reveals stimulus dependent differences in their contributions to behavior. ]]> https://biorxiv.org/content/10.1101/2023.08.23.554473v1?rss=1 Cone, J. J. Mitchell, A. O. Parker, R. K. Maunsell, J. H. 2023-08-24 doi:10.1101/2023.08.23.554473 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Ligand-induced segregation from large cell-surface phosphatases is a critical step in γδ TCR triggering ]]> https://biorxiv.org/content/10.1101/2023.08.23.554524v1?rss=1 Li, F. Roy, S. Niculcea, J. Gould, K. Adams, E. J. van der Merwe, P. A. Choudhuri, K. 2023-08-24 doi:10.1101/2023.08.23.554524 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiota ]]> https://biorxiv.org/content/10.1101/2023.08.25.553775v1?rss=1 Sheahan, M. L. Coyne, M. J. Flores, K. Garcia-Bayona, L. Chatzidaki-Livanis, M. Sundararajan, A. Holst, A. Q. Barquera, B. Comstock, L. E. 2023-08-26 doi:10.1101/2023.08.25.553775 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[ The cGAS-STING pathway is dispensable in a mouse model of LMNA-cardiomyopathy despite nuclear envelope rupture ]]> https://biorxiv.org/content/10.1101/2023.08.28.555134v1?rss=1 En, A. Bogireddi, H. Thomas, B. Stutzman, A. Ikegami, S. LaForest, B. Almakki, O. Pytel, P. Moskowitz, I. P. Ikegami, K. 2023-08-28 doi:10.1101/2023.08.28.555134 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Task success in trained spiking neuronal network models coincides with emergence of cross-stimulus-modulated inhibition ]]> https://biorxiv.org/content/10.1101/2023.08.29.555334v1?rss=1 Zhu, Y. Smith, C. M. B. Tang, M. Scherr, F. MacLean, J. N. 2023-08-31 doi:10.1101/2023.08.29.555334 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression ]]> https://biorxiv.org/content/10.1101/2023.08.29.555401v1?rss=1 Ross, M. O. Xie, Y. Owyang, R. C. Ye, C. Zbihley, O. N. P. Lyu, R. Wu, T. Wang, P. Karginova, O. Olopade, O. I. Zhao, M. He, C. 2023-08-29 doi:10.1101/2023.08.29.555401 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma ]]> https://biorxiv.org/content/10.1101/2023.08.30.554943v1?rss=1 Vayani, O. R. Kaufman, M. E. Moore, K. Chennakesavalu, M. Terhaar, R. Chaves, G. Chlenski, A. He, C. Cohn, S. L. Applebaum, M. A. 2023-09-01 doi:10.1101/2023.08.30.554943 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Claudin-2 limits pancreatitis development through regulating tight junction-controlled pancreatic ductal transport ]]> https://biorxiv.org/content/10.1101/2023.09.01.555960v1?rss=1 Kesaraju, S. Li, Y. Tracy, M. Wannemo, K. Kainov, J. Rana, N. Sidahmed, M. Hyoju, S. Smith, L. Matthews, J. Khalili-Araghi, F. Rana, M. Oakes, S. Shen, L. Weber, C. 2023-09-05 doi:10.1101/2023.09.01.555960 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ HCN channels sense temperature and determine heart rate responses to heat ]]> https://biorxiv.org/content/10.1101/2023.09.02.556046v1?rss=1 Wu, Y. Wang, Q. Granger, J. Reyes Gaido, O. E. Aguilar, E. N. Ludwig, A. Moroni, A. Bianchet, M. A. Anderson, M. E. 2023-09-03 doi:10.1101/2023.09.02.556046 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ The simplicity of protein sequence-function relationships ]]> https://biorxiv.org/content/10.1101/2023.09.02.556057v1?rss=1 92% in every case). Only a tiny fraction of genotypes are strongly affected by third- or higher-order epistasis. Genetic architecture is also sparse: the number of terms required to explain the vast majority of variance is smaller than the number of genotypes by many orders of magnitude. The sequence-function relationship in most proteins is therefore far simpler than previously thought, opening the way for new and tractable approaches to characterize it. ]]> Park, Y. Metzger, B. P. H. Thornton, J. W. 2023-09-05 doi:10.1101/2023.09.02.556057 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Protein coopted from a phage restriction system dictates orthogonal cell division plane selection in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.09.03.556088v1?rss=1 Ramos-Leon, F. Anjuwon-Foster, B. R. Anantharaman, V. Ferreira, C. N. Ibrahim, A. M. Tai, C.-H. Missiakas, D. M. Camberg, J. Aravind, L. Ramamurthi, K. S. 2023-09-03 doi:10.1101/2023.09.03.556088 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Phylogeny structures species' interactions in experimental ecological communities ]]> https://biorxiv.org/content/10.1101/2023.09.04.556236v1?rss=1 Lemos-Costa, P. Miller, Z. R. Allesina, S. 2023-09-06 doi:10.1101/2023.09.04.556236 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Backmapping with Mapping and Isomeric Information ]]> https://biorxiv.org/content/10.1101/2023.09.05.556379v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@5704aforg.highwire.dtl.DTLVardef@f4bdf6org.highwire.dtl.DTLVardef@1e362feorg.highwire.dtl.DTLVardef@1781ade_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kim, S. 2023-09-06 doi:10.1101/2023.09.05.556379 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Photoemission electron microscopy for connectomics ]]> https://biorxiv.org/content/10.1101/2023.09.05.556423v1?rss=1 Boergens, K. M. Wildenberg, G. Li, R. Lambert, L. Moradi, A. Stam, G. Tromp, R. van der Molen, S. J. King, S. B. Kasthuri, N. 2023-09-06 doi:10.1101/2023.09.05.556423 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, and gall morphospace ]]> https://biorxiv.org/content/10.1101/2023.09.07.556376v1?rss=1 Ward, A. Zhang, Y. M. Brown, G. E. Hippee, A. C. Prior, K. M. Rollins, S. Sierra, N. Sheikh, S. I. Tribull, C. M. Forbes, A. A. 2023-09-07 doi:10.1101/2023.09.07.556376 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Structure and dynamics of the contractile vacuole complex in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/2023.09.13.557576v1?rss=1 Cheng, C.-Y. Romero, D. P. Zoltner, M. Yao, M.-C. Turkewitz, A. 2023-09-14 doi:10.1101/2023.09.13.557576 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Cryptic splicing mediates genetic and therapeutic perturbation of human gene expression levels ]]> https://biorxiv.org/content/10.1101/2023.09.13.557588v1?rss=1 Fair, B. J. Abad, C. B. Zhao, J. Lozano, S. Reilly, A. K. Staley, J. P. Wang, J. Li, Y. I. 2023-09-16 doi:10.1101/2023.09.13.557588 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes ]]> https://biorxiv.org/content/10.1101/2023.09.15.557899v1?rss=1 Dutta, M. Su, Y. Voth, G. A. Stahelin, R. V. 2023-09-15 doi:10.1101/2023.09.15.557899 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ PD-1 Mediated Regulation of Unique Activated CD8+ T Cells by NK Cells in the Submandibular Gland ]]> https://biorxiv.org/content/10.1101/2023.09.15.557930v1?rss=1 Brossay, L. Borys, S. M. Reilly, S. P. Magill, I. Zemmour, D. 2023-09-17 doi:10.1101/2023.09.15.557930 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Structure-Activity Relationship Studies of Novel Gut-derived Lantibiotics Against Human Gut Commensals ]]> https://biorxiv.org/content/10.1101/2023.09.15.557961v1?rss=1 Zhang, Z. J. Wu, C. Dorantes, D. Pappas, T. Sundararajan, A. Lin, H. Pamer, E. G. van der Donk, W. A. 2023-09-17 doi:10.1101/2023.09.15.557961 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ A Novel Quantitative Metric Based on a Complete and Unique Characterization of Neural Network Activity: 4D Shannon`s Entropy ]]> https://biorxiv.org/content/10.1101/2023.09.15.557974v1?rss=1 Deshpande, S. S. van Drongelen, W. 2023-09-15 doi:10.1101/2023.09.15.557974 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Androgen blockade primes NLRP3 in macrophages to induce tumor phagocytosis ]]> https://biorxiv.org/content/10.1101/2023.09.15.557996v1?rss=1 Chaudagar, K. K. Srikrishnan, R. Mei, S. Hirz, T. Hu, Y.-M. Argulian, A. Labadie, B. Desai, K. Grimaldo, S. Kahramangil, D. Nair, R. D Souza, S. Zhou, D. Li, M. Doughan, F. Chen, R. Shafran, J. Loyd, M. Xia, Z. Sykes, D. B. Moran, A. E. Patnaik, A. 2023-09-17 doi:10.1101/2023.09.15.557996 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases ]]> https://biorxiv.org/content/10.1101/2023.09.20.558301v1?rss=1 Zhao, A. Y. Unterman, A. Abu Hussein, N. Sharma, P. Flint, J. Yan, X. Adams, T. S. Justet, A. Sumida, T. S. Zhao, J. Schupp, J. C. Raredon, M. S. B. Ahangari, F. C. Zhang, Y. Buendia-Roldan, I. Adegunsoye, A. Sperling, A. I. Prasse, A. Ryu, C. Herzog, E. Selman, M. Pardo, A. Kaminski, N. 2023-09-22 doi:10.1101/2023.09.20.558301 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Automated customization of large-scale spiking network models to neuronal population activity ]]> https://biorxiv.org/content/10.1101/2023.09.21.558920v1?rss=1 Wu, S. Huang, C. Snyder, A. Smith, M. A. Doiron, B. Yu, B. 2023-09-22 doi:10.1101/2023.09.21.558920 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Cooperative Membrane Binding of HIV-1 Matrix Proteins ]]> https://biorxiv.org/content/10.1101/2023.09.22.559012v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@c4380corg.highwire.dtl.DTLVardef@3bbc05org.highwire.dtl.DTLVardef@1b50f42org.highwire.dtl.DTLVardef@1fccd7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Banerjee, P. Monje-Galvan, V. Voth, G. A. 2023-09-24 doi:10.1101/2023.09.22.559012 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Microbially-catalyzed conjugation of GABA and tyramine to bile acids ]]> https://biorxiv.org/content/10.1101/2023.09.25.559407v1?rss=1 Mullowney, M. Fiebig, A. Schnizlein, M. McMillin, M. Koval, J. Rubin, D. Dalal, S. Sogin, M. Chang, E. Sidebottom, A. Crosson, S. 2023-09-25 doi:10.1101/2023.09.25.559407 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Transient States During Oligonucleotides Hybridization: Insights from Annealing Kinetics of Mismatches and Bulges ]]> https://biorxiv.org/content/10.1101/2023.09.27.559754v1?rss=1 Todisco, M. Ding, D. Szostak, J. W. 2023-09-28 doi:10.1101/2023.09.27.559754 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Cognitive tasks, anatomical MRI, and functional MRI data evaluating the construct of self-regulation ]]> https://biorxiv.org/content/10.1101/2023.09.27.559869v1?rss=1 Bissett, P. G. Eisenberg, I. W. Shim, S. Rios, J. A. H. Jones, H. M. Hagen, M. P. Enkavi, A. Z. Li, J. K. Mumford, J. A. MacKinnon, D. P. Marsch, L. A. Poldrack, R. 2023-09-29 doi:10.1101/2023.09.27.559869 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Modeling the Evolution of Populations with Multiple Killer Meiotic Drivers ]]> https://biorxiv.org/content/10.1101/2023.09.28.560003v1?rss=1 Hernandez, J. F. L. Rubinstein, B. Y. Unckless, R. L. Zanders, S. E. 2023-10-01 doi:10.1101/2023.09.28.560003 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ The near-normal viability of heterozygote for a lethalenhancer allele suggests a route for cis-regulatory evolution. ]]> https://biorxiv.org/content/10.1101/2023.09.30.560335v1?rss=1 Ludwig, M. Z. 2023-10-01 doi:10.1101/2023.09.30.560335 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation ]]> https://biorxiv.org/content/10.1101/2023.10.01.560363v1?rss=1 Banerjee, P. Qu, K. Briggs, J. A. G. Voth, G. A. 2023-10-01 doi:10.1101/2023.10.01.560363 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ A Method For Estimating The Cholesterol Affinity Of Integral Membrane Proteins From Experimental Data ]]> https://biorxiv.org/content/10.1101/2023.10.03.560595v1?rss=1 Steck, T. L. Tabei, A. Lange, Y. 2023-10-03 doi:10.1101/2023.10.03.560595 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Structural and molecular basis of choline uptake into the brain by FLVCR2 ]]> https://biorxiv.org/content/10.1101/2023.10.05.561059v1?rss=1 Cater, R. J. Mukherjee, D. Gil Iturbe, E. Erramilli, S. K. Chen, T. Koo, K. Santander, N. G. Reckers, A. R. Kloss, B. Gawda, T. Choy, B. C. Zhang, Z. Clarke, O. B. Yee, S. W. Kossiakoff, A. K. Quick, M. Arnold, T. Mancia, F. 2023-10-05 doi:10.1101/2023.10.05.561059 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Suppression of the Integrated Stress Response in Islet β Cells Decreases Risk of Autoimmune Diabetes ]]> https://biorxiv.org/content/10.1101/2023.10.06.561126v1?rss=1 Muralidharan, C. Huang, F. Enriquez, J. R. Wang, J. E. Nelson, J. B. Nargis, T. May, S. C. Chakraborty, A. Figatner, K. T. Navitskaya, S. Anderson, C. M. Calvo, V. Surguladze, D. Mulvihill, M. J. Yi, X. Sarkar, S. Oakes, S. A. Webb-Robertson, B.-J. M. Eizirik, D. L. Nakayasu, E. S. Stokes, M. E. Tersey, S. A. Mirmira, R. G. 2023-10-06 doi:10.1101/2023.10.06.561126 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ FORMATION OF MALIGNANT, METASTATIC SMALL CELL LUNG CANCERS THROUGH OVERPRODUCTION OF cMYC PROTEIN IN TP53 AND RB1 DEPLETED PULMONARY NEUROENDOCRINE CELLS DERIVED FROM HUMAN EMBRYONIC STEM CELLS ]]> https://biorxiv.org/content/10.1101/2023.10.06.561244v1?rss=1 Chen, H. Gardner, E. E. Shah, Y. Zhang, K. Thakur, A. Zhang, C. Elemento, O. Varmus, H. 2023-10-10 doi:10.1101/2023.10.06.561244 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Exploring the tumor micro-environment in ovarian cancer histotypes and tumor sites ]]> https://biorxiv.org/content/10.1101/2023.10.07.561344v1?rss=1 Xie, B. Olalekan, S. BACK, R. Ashitey, N. A. A. A. Basu, A. 2023-10-10 doi:10.1101/2023.10.07.561344 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES ]]> https://biorxiv.org/content/10.1101/2023.10.08.561395v1?rss=1 Guarnieri, J. W. Topper, M. Beigel, K. Haltoom, J. A. Chadburn, A. Frere, J. An, J. Cope, H. Borczuk, A. Sinha, S. Lim, C. Kim, J. Park, J. Meydan, C. Foox, J. Mozsary, C. Bram, Y. Richard, S. Epsi, N. Agan, B. Chenoweth, J. Simons, M. Tribble, D. Burgess, T. Dalgard, C. L. Heise, M. T. Moorman, N. Baxter, V. Madden, E. A. Taft-Benz, S. Anderson, E. Sanders, W. A. Dickmander, R. J. Widjaja, G. A. Janssen, K. Lie, T. Murdock, D. G. Angelin, A. Albrecht, Y. E. S. Olali, A. Dybas, J. M. Priebe, W. Emmett, M. R. Best, S. Johnson, M. K. Trovao, N. S. Cl 2023-10-09 doi:10.1101/2023.10.08.561395 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Integration of 168,000 samples reveals global patterns of the human gut microbiome ]]> https://biorxiv.org/content/10.1101/2023.10.11.560955v1?rss=1 Abdill, R. J. Graham, S. P. Rubinetti, V. Albert, F. W. Greene, C. S. Davis, S. Blekhman, R. 2023-10-11 doi:10.1101/2023.10.11.560955 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Microbiota may affect the tumor type but not overall tumor development in two models of heritable cancer ]]> https://biorxiv.org/content/10.1101/2023.10.11.561890v1?rss=1 Spring, J. Gurbuxani, S. Golovkina, T. 2023-10-12 doi:10.1101/2023.10.11.561890 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection ]]> https://biorxiv.org/content/10.1101/2023.10.12.562101v1?rss=1 Cheng, X. Steinruecken, M. 2023-10-17 doi:10.1101/2023.10.12.562101 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Ovarian Cancer Cells ]]> https://biorxiv.org/content/10.1101/2023.10.13.562273v1?rss=1 Challa, S. Nandu, T. Kim, H. B. Gong, A. Renshaw, C. W. Li, W.-C. Tan, X. Camacho, C. V. Chen, J. Kraus, W. L. 2023-10-14 doi:10.1101/2023.10.13.562273 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit ]]> https://biorxiv.org/content/10.1101/2023.10.15.562341v1?rss=1 Carrillo, R. A. Wang, Y. Salazar, R. Simonetta, L. Sorrentino, V. Gatton, T. J. Wu, B. Vecsey, C. G. 2023-10-17 doi:10.1101/2023.10.15.562341 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2023.10.15.562439v1?rss=1 Guo, M. Wu, Y. Su, Y. Qian, S. Krueger, E. Christensen, R. Kroeschell, G. Bui, J. Chaw, M. Zhang, L. Liu, J. Hou, X. Han, X. Ma, X. Zhovmer, A. Combs, C. Moyle, M. Yemini, E. Liu, H. Liu, Z. La Riviere, P. Colon-Ramos, D. Shroff, H. 2023-10-18 doi:10.1101/2023.10.15.562439 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ BTSP, not STDP, Drives Shifts in Hippocampal Representations During Familiarization ]]> https://biorxiv.org/content/10.1101/2023.10.17.562791v1?rss=1 Madar, A. D. Dong, C. Sheffield, M. 2023-10-17 doi:10.1101/2023.10.17.562791 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ On the problem of inflation in transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/2023.10.17.562831v1?rss=1 Liang, Y. Nyasimi, F. Im, H. K. 2023-10-20 doi:10.1101/2023.10.17.562831 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ A dynamic scale-mixture model of motion in natural scenes ]]> https://biorxiv.org/content/10.1101/2023.10.19.563101v1?rss=1 Salisbury, J. M. Palmer, S. E. 2023-10-23 doi:10.1101/2023.10.19.563101 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Divergent spike mutations impact the activation of the fusion core in Delta and Omicronvariants of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.10.19.563184v1?rss=1 Dutta, M. Voth, G. A. 2023-10-20 doi:10.1101/2023.10.19.563184 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ A Pipeline for a Primate Projectome: mapping every individual myelinated axon across the whole brain ]]> https://biorxiv.org/content/10.1101/2023.10.23.563679v1?rss=1 Wildenberg, G. A. Boergens, K. M. Nikitin, V. Deriy, A. De Carlo, F. De Andrade, V. Xiao, X. Kasthuri, N. 2023-10-24 doi:10.1101/2023.10.23.563679 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ RELAXING SELECTIVE PRESSURES ON DEVELOPMENTALLY COMPLEX INTEGUMENTARY STRUCTURES: FEATHER VANE SYMMETRY EVOLVES IN ADDITION TO BODY MASS AND WING LENGTH AFTER FLIGHT LOSS IN RECENT BIRDS ]]> https://biorxiv.org/content/10.1101/2023.10.24.563691v1?rss=1 Saitta, E. T. Carden, L. E. Mitchell, J. S. Makovicky, P. J. 2023-10-27 doi:10.1101/2023.10.24.563691 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Detection, characterization, and phylogenetic analysis of a near-whole genome sequence of a novel astrovirus in an endemic Malagasy fruit bat, Rousettus madagascariensis ]]> https://biorxiv.org/content/10.1101/2023.10.27.564436v1?rss=1 Horigan, S. Kistler, A. L. Ranaivoson, H. C. Andrianiaina, A. Andry, S. Kettenburg, G. Raharinosy, V. Randriambolamanantsoa, T. H. Tato, C. Lacoste, V. Heraud, J.-M. Dussart, P. Brook, C. E. 2023-11-01 doi:10.1101/2023.10.27.564436 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Social buffering switches fear to safety encoding by oxytocin recruitment of central amygdala "buffer neurons" ]]> https://biorxiv.org/content/10.1101/2023.10.29.563530v1?rss=1 Hegoburu, C. Tang, Y. Niu, R. Ghosh, S. Triana del Rio, R. Salgado, I. Abatis, m. Caseiro, D. A. M. grundschober, c. STOOP, R. 2023-10-30 doi:10.1101/2023.10.29.563530 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases ]]> https://biorxiv.org/content/10.1101/2023.10.29.564605v1?rss=1 Shan, Y. Lake, J. Cham, C. M. Zhu, M. Kaur, D. Ringus, D. Fei, N. Weber, C. R. Spedale, M. Theriault, B. Dalal, S. Rubin, D. T. Fiebig, A. Crosson, S. Lolans, K. Comstock, L. Eren, A. M. Basu, A. Pott, S. Sogin, M. Liu, C. Chang, E. B. 2023-10-29 doi:10.1101/2023.10.29.564605 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness ]]> https://biorxiv.org/content/10.1101/2023.10.30.564779v1?rss=1 Battistini, C. Kenny, H. A. Nieddu, V. Melocchi, V. Decio, A. Gatto, A. Ghioni, M. Porta, F. M. Giavazzi, R. Colombo, N. Bianchi, F. Lengyel, E. Cavallaro, U. 2023-11-02 doi:10.1101/2023.10.30.564779 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Structural determinants of pure antiestrogenicity ]]> https://biorxiv.org/content/10.1101/2023.10.31.564979v1?rss=1 Marine, D. Shaikh, F. El Ezzy, M. Thiombane, K. Weber, S. Poupart, J. Mendoza-Sanchez, R. Gao, Z. Gleason, J. Schuetz, D. A. Greene, G. Marinier, A. Fanning, S. W. MADER, S. 2023-11-02 doi:10.1101/2023.10.31.564979 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Autophagy regulates tumor growth and metastasis ]]> https://biorxiv.org/content/10.1101/2023.10.31.564991v1?rss=1 Qiang, L. Zhao, B. Ming, M. Wang, N. He, T.-C. Hwang, S. Thorburn, A. He, Y.-Y. 2023-11-03 doi:10.1101/2023.10.31.564991 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Climate-Change Driven Decline of an Insect Pathogen Increases the Risk of Defoliation by a Forest Pest Insect ]]> https://biorxiv.org/content/10.1101/2023.11.01.564627v1?rss=1 Liu, J. Kyle, C. Wang, J. Kotamarthi, R. Koval, W. Dwyer, G. 2023-11-02 doi:10.1101/2023.11.01.564627 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ The Host-specific Microbiota is Required for Diet-Specific Metabolic Homeostasis ]]> https://biorxiv.org/content/10.1101/2023.11.05.565654v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@16a864org.highwire.dtl.DTLVardef@1894996org.highwire.dtl.DTLVardef@3e5429org.highwire.dtl.DTLVardef@77bfb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fei, N. Xie, B. Long, T. J. StGeorge, M. Tan, A. Manzoor, S. Sidebottom, A. M. Melanie Spedale, M. Betty R Theriault, B. R. Dinanath Sulakhe, D. S. B., E. B. 2023-11-06 doi:10.1101/2023.11.05.565654 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ A paradoxical population structure of var DBLα types in Africa ]]> https://biorxiv.org/content/10.1101/2023.11.05.565723v1?rss=1 Tan, M. H. Tiedje, K. E. Feng, Q. Zhan, Q. Pascual, M. Shim, H. S. Chan, Y.-b. Day, K. P. 2023-11-07 doi:10.1101/2023.11.05.565723 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective ]]> https://biorxiv.org/content/10.1101/2023.11.06.565293v1?rss=1 Peona, V. Martelossi, J. Almojil, D. Bocharkina, J. Brännström, I. Brown, M. Cang, A. Carrasco-Valenzuela, T. DeVries, J. Doellman, M. Elsner, D. Espindola-Hernandez, P. Friis, G. Gaspar, B. Zagorski, D. Hałakuc, P. Ivanovska, B. Laumer, C. Lehmann, R. Bostjancic, L. L. Mashoodh, R. Mazzoleni, S. Mouton, A. Janke, M. N. Pei, Y. Potente, G. Provataris, P. Pardos-Blas, J. R. Raut, R. Sbaffi, T. Schwarz, F. Stapley, J. Stevens, L. Sultana, N. Symonova, R. Tahami, M. S. Urzi, A. Yang, H. Yusuf, A. Pecoraro, C. Suh, A. 2023-11-07 doi:10.1101/2023.11.06.565293 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ VPS8D, a CORVET subunit, is required to maintain the contractile vacuole complex in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/2023.11.07.566071v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@b652c6org.highwire.dtl.DTLVardef@1f456f7org.highwire.dtl.DTLVardef@79ab8dorg.highwire.dtl.DTLVardef@1edbf74_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cheng, C.-Y. Hernandez, J. Turkewitz, A. 2023-11-08 doi:10.1101/2023.11.07.566071 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Mitochondrial One-Carbon Metabolism is Required for TGF-β-Induced Glycine Synthesis and Collagen Protein Production ]]> https://biorxiv.org/content/10.1101/2023.11.07.566074v1?rss=1 Meliton, A. Y. Cetin-Atalay, R. Tian, Y. Szafran, J. C. Shin, K. W. D. Cho, T. Sun, K. A. Woods, P. S. Shamaa, O. R. Chen, B. Muir, A. Mutlu, G. M. Hamanaka, R. B. 2023-11-07 doi:10.1101/2023.11.07.566074 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Microbiota-dependent early life programming of gastrointestinal motility ]]> https://biorxiv.org/content/10.1101/2023.11.08.566304v1?rss=1 Frith, M. E. Kashyap, P. C. Linden, D. R. Theriault, B. Chang, E. B. 2023-11-13 doi:10.1101/2023.11.08.566304 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Human organoid modeling of congenital malformations caused by RFX6 mutations reveal an essential role for this transcription factor in establishing and maintaining duodenal identity upstream of PDX1 ]]> https://biorxiv.org/content/10.1101/2023.11.09.566480v1?rss=1 Wells, J. M. Sanchez, G. Rankin, S. A. Paul, E. McCauley, H. A. Kechele, D. Enriquez, J. Jones, N.-H. Greeley, S. A. Letourneau-Friedberg, L. Zorn, A. A. Krishnamurthy, M. 2023-11-11 doi:10.1101/2023.11.09.566480 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Modifications in the T arm of tRNA globally determine tRNA maturation, function and cellular fitness ]]> https://biorxiv.org/content/10.1101/2023.11.11.566336v1?rss=1 Schultz, S. K. Katanski, C. D. Halucha, M. Pena, N. Fahlman, R. P. Pan, T. Kothe, U. 2023-11-11 doi:10.1101/2023.11.11.566336 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Causal interpretations of family GWAS in the presence of heterogeneous effects ]]> https://biorxiv.org/content/10.1101/2023.11.13.566950v1?rss=1 Veller, C. Przeworski, M. Coop, G. 2023-11-16 doi:10.1101/2023.11.13.566950 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Dynamic Functional Connectivity Encodes Generalizable Representations of Emotional Arousal But Not Valence ]]> https://biorxiv.org/content/10.1101/2023.11.14.566767v1?rss=1 Ke, J. Song, H. Bai, Z. Rosenberg, M. D. Leong, Y. C. 2023-11-16 doi:10.1101/2023.11.14.566767 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. ]]> https://biorxiv.org/content/10.1101/2023.11.14.567139v1?rss=1 Chen, J. Arsala, D. Xia, S. Atlas, J. Sosa, D. Guzzetta, A. Dong, C. Shen, B. Cheng, J. Zhang, Y. Long, M. 2023-11-15 doi:10.1101/2023.11.14.567139 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Thermodynamic framework for nonequilibrium self-assembly of branched actin networks ]]> https://biorxiv.org/content/10.1101/2023.11.19.567734v1?rss=1 Rennert, E. Vaikuntanathan, S. 2023-11-19 doi:10.1101/2023.11.19.567734 Cold Spring Harbor Laboratory Press 2023-11-19 <![CDATA[ Correlated evolution of beak and braincase morphology is present only in select bird clades ]]> https://biorxiv.org/content/10.1101/2023.11.19.567761v1?rss=1 Xu, X. Natale, R. 2023-11-20 doi:10.1101/2023.11.19.567761 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ The potassium channel subunit KV1.8 (Kcna10) is essential for the distinctive outwardly rectifying conductances of type I and II vestibular hair cells ]]> https://biorxiv.org/content/10.1101/2023.11.21.563853v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1409188org.highwire.dtl.DTLVardef@12aaa0org.highwire.dtl.DTLVardef@18000e0org.highwire.dtl.DTLVardef@b995c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Martin, H. R. Lysakowski, A. Eatock, R. A. 2023-11-22 doi:10.1101/2023.11.21.563853 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ The endogenous Mtv8 locus and the immunoglobulin repertoire ]]> https://biorxiv.org/content/10.1101/2023.11.24.567955v1?rss=1 Beilinson, H. A. Erickson, S. A. Golovkina, T. V. 2023-11-25 doi:10.1101/2023.11.24.567955 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Reference-Free Germline Immunoglobulin Allele Discovery from B CellReceptor Sequencing Data ]]> https://biorxiv.org/content/10.1101/2023.11.25.568681v1?rss=1 Cvijovic, I. Jerison, E. R. Quake, S. R. 2023-11-26 doi:10.1101/2023.11.25.568681 Cold Spring Harbor Laboratory Press 2023-11-26 <![CDATA[ The integration of tactile and proprioceptive signals to achieve haptic object perception ]]> https://biorxiv.org/content/10.1101/2023.11.27.568836v1?rss=1 Dogruoz, R. E. Shelchkova, N. S. Sheets, D. E. Greenspon, C. M. Bensmaia, S. J. 2023-11-27 doi:10.1101/2023.11.27.568836 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ TRIBAL: Tree Inference of B cell Clonal Lineages ]]> https://biorxiv.org/content/10.1101/2023.11.27.568874v1?rss=1 Weber, L. L. Reiman, D. Roddur, M. S. Qi, Y. L. El-Kebir, M. Khan, A. A. 2023-11-27 doi:10.1101/2023.11.27.568874 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ Signaling ligand heterogeneities in the peduncle complex of the cephalopod mollusc Octopus bimaculoides ]]> https://biorxiv.org/content/10.1101/2023.11.27.568875v1?rss=1 Wang, Z. Y. Ragsdale, C. W. 2023-11-27 doi:10.1101/2023.11.27.568875 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ ChemXTree: A Tree-enhanced Classification Approach to Small-molecule Drug Discovery ]]> https://biorxiv.org/content/10.1101/2023.11.28.568989v1?rss=1 Xu, Y. Liu, X. Ge, J. Xia, W. Ju, C.-W. Zhang, H. Zhang, J. Z. H. 2023-11-29 doi:10.1101/2023.11.28.568989 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Effects of transient, persistent, and resurgent sodium currents on excitability and spike regularity in vestibular ganglion neurons ]]> https://biorxiv.org/content/10.1101/2023.11.28.569044v1?rss=1 Baeza Loya, S. Eatock, R. A. 2023-11-29 doi:10.1101/2023.11.28.569044 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ BCG vaccination impacts the epigenetic landscape of progenitor cells in human bone marrow ]]> https://biorxiv.org/content/10.1101/2023.11.28.569076v1?rss=1 0.8) with the IL-1{beta} secretion capacity of paired PBMCs upon secondary immune challenge. Overall, our findings shed light on BCG vaccinations profound and lasting effects on HSPCs and its influence on innate immune responses. ]]> Sun, S. J. Aguirre-Gamboa, R. de Bree, C. J. Sanz, J. Dumaine, A. Joosten, L. A. Divangahi, M. Netea, M. Barreiro, L. B. 2023-11-28 doi:10.1101/2023.11.28.569076 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during behavior and learning ]]> https://biorxiv.org/content/10.1101/2023.11.29.569214v1?rss=1 Heer, C. M. Sheffield, M. E. J. 2023-11-30 doi:10.1101/2023.11.29.569214 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Diagnostic images for mild cognitive impairment reveal biomarker status and abnormal scene processing ]]> https://biorxiv.org/content/10.1101/2023.11.30.569265v1?rss=1 Bai, Y. Peters, O. Freiesleben, S. D. Fenski, F. Priller, J. Spruth, E. J. Schneider, A. Fliessbach, K. Wiltfang, J. Bartels, C. Rostamzadeh, A. Glanz, W. Teipel, S. Kilimann, I. Laske, C. Munk, M. H. Spottke, A. Roy-Kluth, N. Brosseron, F. Wagner, M. Frommann, I. Luesebrink, F. Ramirez, A. Dechent, P. Hetzer, S. Scheffler, K. Yakupov, R. Jessen, F. Duezel, E. Bainbridge, W. A. 2023-12-02 doi:10.1101/2023.11.30.569265 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Brain network dynamics predict moments of surprise across contexts ]]> https://biorxiv.org/content/10.1101/2023.12.01.569271v1?rss=1 Zhang, Z. Rosenberg, M. D. 2023-12-04 doi:10.1101/2023.12.01.569271 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ A female-biased gene expression signature of dominance in cooperatively breeding meerkats ]]> https://biorxiv.org/content/10.1101/2023.12.01.569325v1?rss=1 Campbell, C. R. Manser, M. Shiratori, M. Williams, K. Barreiro, L. Clutton-Brock, T. H. Tung, J. 2023-12-03 doi:10.1101/2023.12.01.569325 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Single cell dissection of developmental origins and transcriptional heterogeneity in B-cell acute lymphoblastic leukemia ]]> https://biorxiv.org/content/10.1101/2023.12.04.569954v1?rss=1 Iacobucci, I. Zeng, A. G. X. Gao, Q. Garcia-Prat, L. Baviskar, P. Shah, S. Murison, A. J. Voisin, V. Chan-Seng-Yue, M. Cheng, C. Qu, C. Bailey, C. Lear, M. Witkowski, M. Zhou, X. Zaldivar Peraza, A. Gangwani, K. Advani, A. Luger, S. M. Litzow, M. R. Rowe, J. M. Paietta, E. M. Stock, W. Dick, J. E. Mullighan, C. G. 2023-12-09 doi:10.1101/2023.12.04.569954 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ An evolution-based framework for describing human gut bacteria ]]> https://biorxiv.org/content/10.1101/2023.12.04.569969v1?rss=1 7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary history. One Sentence SummaryDescribing bacterial strains in the human gut by a statistical model that captures their evolutionary history provides insight into their biology. ]]> Doran, B. A. Chen, R. Y. Giba, H. Behera, V. Barat, B. Sundararajan, A. Lin, H. Sidebottom, A. Pamer, E. G. Raman, A. 2023-12-05 doi:10.1101/2023.12.04.569969 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/2023.12.04.570014v1?rss=1 Coley, A. K. Lu, C. Pankaj, A. Emmett, M. J. Lang, E. R. Song, Y. Xu, K. H. Xu, N. Patel, B. K. Chougule, A. Nieman, L. T. Aryee, M. Ferrone, C. R. Deshpande, V. Franses, J. W. Ting, D. T. 2023-12-05 doi:10.1101/2023.12.04.570014 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Cue-Invariant Geometric Structure of the Population Codes in Macaque V1 and V2 ]]> https://biorxiv.org/content/10.1101/2023.12.05.570110v1?rss=1 Massot, C. Zhang, X. Wang, Z. Rockwell, H. Papandreou, G. Yuille, A. Lee, T.-S. 2023-12-07 doi:10.1101/2023.12.05.570110 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes ]]> https://biorxiv.org/content/10.1101/2023.12.08.570583v1?rss=1 Paukner, D. Wildenberg, G. A. Badalamente, G. S. Littlewood, P. B. Kronforst, M. R. Palmer, S. E. Kasthuri, N. 2023-12-08 doi:10.1101/2023.12.08.570583 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning ]]> https://biorxiv.org/content/10.1101/2023.12.08.570839v1?rss=1 Song, S. Mohsin, E. Zhang, R. Kuznetsov, A. Shen, L. Grossman, R. L. Weber, C. R. Khan, A. A. 2023-12-10 doi:10.1101/2023.12.08.570839 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity ]]> https://biorxiv.org/content/10.1101/2023.12.09.569604v1?rss=1 Nakano, Y. Gamper, H. McGuigan, H. Maharjan, S. Sun, Z. Krishnan, K. Yigit, E. Li, N.-S. Piccirilli, J. A. Kleiner, R. E. Nichols, N. Hou, Y.-M. 2023-12-09 doi:10.1101/2023.12.09.569604 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology ]]> https://biorxiv.org/content/10.1101/2023.12.09.569632v1?rss=1 Maharjan, S. Gamper, H. Yamaki, Y. Henley, R. Y. Sheng, N. Suzuki, T. Suzuki, T. Piccirilli, J. A. Wanunu, M. Seifert, E. Wallace, D. C. Hou, Y.-M. 2023-12-10 doi:10.1101/2023.12.09.569632 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits ]]> https://biorxiv.org/content/10.1101/2023.12.12.571316v1?rss=1 Pazokitoroudi, A. Dahl, A. Zaitlen, N. Rosset, S. Sankararaman, S. 2023-12-13 doi:10.1101/2023.12.12.571316 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.12.13.571566v1?rss=1 Benitz, S. Steep, A. Nasser, M. Preall, J. Mahajan, U. M. McQuithey, H. Loveless, I. Davis, E. T. Wen, H.-J. Long, D. W. Metzler, T. Zwernik, S. Louw, M. Rempinski, D. Salas-Escabillas, D. Brender, S. Song, L. Huang, L. Zhang, Z. Steele, N. Regel, I. Bednar, F. Crawford, H. C. 2023-12-14 doi:10.1101/2023.12.13.571566 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Potassium dependent structural changes in the selectivity filter of HERG potassium channels ]]> https://biorxiv.org/content/10.1101/2023.12.14.571769v1?rss=1 Lau, C. H. Flood, E. Hunter, M. J. Williams-Noonan, B. J. Corbett, K. M. Ng, C.-A. Bouwer, J. C. Stewart, A. G. Perozo, E. Allen, T. W. Vandenberg, J. I. 2023-12-15 doi:10.1101/2023.12.14.571769 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Cardiac afferent signals can facilitate visual dominance in binocular rivalry ]]> https://biorxiv.org/content/10.1101/2023.12.16.571868v1?rss=1 Veillette, J. P. Gao, F. Nusbaum, H. C. 2023-12-16 doi:10.1101/2023.12.16.571868 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ JASPER: fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression ]]> https://biorxiv.org/content/10.1101/2023.12.18.571948v1?rss=1 Mbatchou, J. McPeek, M. S. 2023-12-19 doi:10.1101/2023.12.18.571948 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Learning Image Memorability with Feedback-Based Training ]]> https://biorxiv.org/content/10.1101/2023.12.18.572187v1?rss=1 Revsine, C. Bainbridge, W. A. 2023-12-19 doi:10.1101/2023.12.18.572187 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Phase diversity-based wavefront sensing for fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2023.12.19.572369v1?rss=1 100-fold faster than comparable methods (corresponding to wavefront sensing on the ~100 ms scale), and sensing and subsequent correction of severe aberrations (RMS wavefront distortion exceeding {lambda}/2), restoring diffraction-limited imaging on extended biological samples. ]]> Johnson, C. Guo, M. Schneider, M. C. Su, Y. Khuon, S. C. Reiser, N. Wu, Y. La Riviere, P. J. Shroff, H. 2023-12-19 doi:10.1101/2023.12.19.572369 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ New Insights into the Conformational Activation of Full-Length Integrin ]]> https://biorxiv.org/content/10.1101/203661v1?rss=1 Bidone, T. C. Polley, A. Durumeric, A. E. P. Driscoll, T. Iwamoto, D. Calderwood, D. Schwartz, M. A. Voth, G. A. 2017-10-15 doi:10.1101/203661 Cold Spring Harbor Laboratory Press 2017-10-15 <![CDATA[ Cooperative recruitment of Yan to paired high affinity ETS sites organizes repression to confer specificity and robustness to cardiac cell fate specification ]]> https://biorxiv.org/content/10.1101/205724v1?rss=1 Boisclair Lachance, J.-F. Webber, J. L. Rebay, I. 2017-10-18 doi:10.1101/205724 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Vulnerabilities of transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/206961v1?rss=1 Wainberg, M. Sinnott-Armstrong, N. Knowles, D. Golan, D. Ermel, R. Ruusalepp, A. Quertermous, T. Hao, K. Bjorkegren, J. L. M. Rivas, M. A. Kundaje, A. 2017-10-20 doi:10.1101/206961 Cold Spring Harbor Laboratory Press 2017-10-20 <![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[ Energy demand and the context-dependent effects of genetic interactions ]]> https://biorxiv.org/content/10.1101/209510v1?rss=1 Hoekstra, L. A. Julick, C. R. Mika, K. M. Montooth, K. L. 2017-10-26 doi:10.1101/209510 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Predicting Global Forest Reforestation Potential ]]> https://biorxiv.org/content/10.1101/210062v1?rss=1 Crowther, T. W. Glick, H. B. Maynard, D. S. Ashley-Cantello, W. Evans, T. Routh, D. 2017-11-04 doi:10.1101/210062 Cold Spring Harbor Laboratory Press 2017-11-04 <![CDATA[ An evolutionary switch in the specificity of an endosomal CORVET tether underlies formation of regulated secretory vesicles in the ciliate Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/210328v1?rss=1 Sparvoli, D. Richardson, E. Osakada, H. Lan, X. Iwamoto, M. Bowman, G. R. Kontur, C. Bourland, W. A. Lynn, D. H. Pritchard, J. K. Haraguchi, T. Dacks, J. B. Turkewitz, A. P. 2017-10-27 doi:10.1101/210328 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Heritable plant phenotypes track light and herbivory levels at fine spatial scales ]]> https://biorxiv.org/content/10.1101/210765v1?rss=1 Humphrey, P. Gloss, A. D. Frazier, J. Nelson-Dittrich, A. C. Faries, S. Whiteman, N. K. 2017-10-29 doi:10.1101/210765 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes ]]> https://biorxiv.org/content/10.1101/212381v1?rss=1 Knowles, D. A. Burrows, C. K. Blischak, J. D. Patterson, K. M. Ober, C. Pritchard, J. K. Gilad, Y. 2017-11-01 doi:10.1101/212381 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival ]]> https://biorxiv.org/content/10.1101/212902v1?rss=1 Tien, M. Z. Fiebig, A. Crosson, S. 2017-11-01 doi:10.1101/212902 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage ]]> https://biorxiv.org/content/10.1101/214908v1?rss=1 Wong, J. B. Hewitt, S. L. Heltemes-Harris, L. M. Mandal, M. Johnson, K. Rajewsky, K. Koralov, S. B. Clark, M. R. Farrar, M. A. Skok, J. A. 2017-11-13 doi:10.1101/214908 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Panaconda: Application of pan-synteny graph models to genome content analysis ]]> https://biorxiv.org/content/10.1101/215988v1?rss=1 Warren, A. S. Davis, J. J. Wattam, A. R. Machi, D. Setubal, J. C. Heath, L. 2017-11-08 doi:10.1101/215988 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Sex differences in the genetic architecture of obsessive-compulsive disorder ]]> https://biorxiv.org/content/10.1101/219170v1?rss=1 Khramtsova, E. A. Heldman, R. Derks, E. M. Yu, D. TS/OCD Psychiatric Genomics Disorders Workgroup, Davis, L. K. Stranger, B. E. 2017-11-21 doi:10.1101/219170 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Causal gene inference by multivariate mediation analysis in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/219428v1?rss=1 Park, Y. Sarkar, A. He, L. Davilla-Velderrain, J. De Jager, P. L. Kellis, M. 2017-11-14 doi:10.1101/219428 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ Gene expression imputation across multiple brain regions reveals schizophrenia risk throughout development. ]]> https://biorxiv.org/content/10.1101/222596v1?rss=1 Huckins, L. M. Dobbyn, A. Ruderfer, D. Hoffman, G. Wang, W. Pardinas, A. F. Rajagopal, V. M. Als, T. D. Hoang, H. T. Girdhar, K. Boocock, J. Roussos, P. Fromer, M. Kramer, R. Domenici, E. Gamazon, E. Purcell, S. CommonMind Consortium, Schizophrenia Working Group of the Psychiatric Gen, iPSYCH-GEMS Schizophrenia Working Group, Demontis, D. Borglum, A. Walters, J. O'Donovan, M. Sullivan, P. F. Owen, M. Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Sklar, P. Stahl, E. A. 2017-11-21 doi:10.1101/222596 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Transcriptomic Imputation of Bipolar Disorder and Bipolar subtypes reveals 29 novel associated genes ]]> https://biorxiv.org/content/10.1101/222786v1?rss=1 Huckins, L. Dobbyn, A. McFadden, W. Wang, W. Ruderfer, D. Hoffman, G. Rajagopal, V. Nguyen, H. T. Roussos, P. Fromer, M. Kramer, R. Domenici, E. Gamazon, E. CommonMind Consortium, Bipolar Disorder Working Group of the Psychiatric, iPSYCH Consortium, Demontis, D. Borglum, A. Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Sklar, P. Stahl, E. A. 2017-11-21 doi:10.1101/222786 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Experimental evidence that female rhesus macaques (Macaca mulatta) perceive variation in male facial masculinity ]]> https://biorxiv.org/content/10.1101/222810v1?rss=1 Rosenfield, K. A. Semple, S. Georgiev, A. V. Maestripieri, D. HIgham, J. P. Dubuc, C. 2017-11-21 doi:10.1101/222810 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal ]]> https://biorxiv.org/content/10.1101/223081v1?rss=1 Jeong, C. Witonsky, D. B. Basnyat, B. Neupane, M. Beall, C. M. Childs, G. Craig, S. R. Novembre, J. Di Rienzo, A. 2017-11-23 doi:10.1101/223081 Cold Spring Harbor Laboratory Press 2017-11-23 <![CDATA[ Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings ]]> https://biorxiv.org/content/10.1101/224147v1?rss=1 Stewart, T. A. Liang, C. Cotney, J. Noonan, J. P. Sanger, T. Wagner, G. 2017-12-05 doi:10.1101/224147 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Neuronal resonance in the theta (4-10 Hz) frequency range is modulated by dynamic changes in the input resistance ]]> https://biorxiv.org/content/10.1101/224253v1?rss=1 Vera, J. Pereira, U. Reynaert, B. Bacigalupo, J. Sanhueza, M. 2017-11-23 doi:10.1101/224253 Cold Spring Harbor Laboratory Press 2017-11-23 <![CDATA[ A new sequence logo plot to highlight enrichment and depletion ]]> https://biorxiv.org/content/10.1101/226597v1?rss=1 Dey, K. K. Xie, D. Stephens, M. 2017-11-29 doi:10.1101/226597 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes ]]> https://biorxiv.org/content/10.1101/226936v1?rss=1 Lee, Y. C. G. Ventura, I. M. Rice, G. R. Chen, D.-Y. Long, M. 2017-11-30 doi:10.1101/226936 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Gene regulatory network rewiring by an adaptively evolving microRNA cluster in Drosophila ]]> https://biorxiv.org/content/10.1101/227314v1?rss=1 Lyu, Y. Liufu, Z. Xiao, J. Chen, Y. Wu, C.-I. Tang, T. 2017-11-30 doi:10.1101/227314 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans ]]> https://biorxiv.org/content/10.1101/227660v1?rss=1 Steinrücken, M. Spence, J. P. Kamm, J. A. Wieczorek, E. Song, Y. S. 2017-12-01 doi:10.1101/227660 Cold Spring Harbor Laboratory Press 2017-12-01 <![CDATA[ NuMA is a negative regulator of 53BP1 in DNA double-strand break repair ]]> https://biorxiv.org/content/10.1101/230706v1?rss=1 Salvador-Moreno, N. Liu, J. Haas, K. Parker, L. Chakraborty, C. Kron, S. Hodges, K. Miller, L. Robinson, P. Lelievre, S. Vidi, P.-A. 2017-12-07 doi:10.1101/230706 Cold Spring Harbor Laboratory Press 2017-12-07 <![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[ Female mate choice is a reproductive isolating barrier in Heliconius butterflies ]]> https://biorxiv.org/content/10.1101/233270v1?rss=1 Southcott, L. Kronforst, M. 2017-12-12 doi:10.1101/233270 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ Genetic landscapes reveal how human genetic diversity aligns with geography ]]> https://biorxiv.org/content/10.1101/233486v1?rss=1 Peter, B. M. Petkova, D. Novembre, J. 2017-12-13 doi:10.1101/233486 Cold Spring Harbor Laboratory Press 2017-12-13 <![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[ Pharmacological manipulation of olfactory bulb granule cell excitability modulates beta oscillations: Testing a model ]]> https://biorxiv.org/content/10.1101/234625v1?rss=1 Osinski, B. Kim, A. Xiao, W. Mehta, N. M. Kay, L. M. 2017-12-15 doi:10.1101/234625 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons ]]> https://biorxiv.org/content/10.1101/238345v1?rss=1 Dechery, J. B. MacLean, J. N. 2017-12-21 doi:10.1101/238345 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Conditioning nausea in a laboratory setting: A pilot study ]]> https://biorxiv.org/content/10.1101/243121v1?rss=1 Van Hedger, K. Cavallo, J. S. Ruiz, N. A. de Wit, H. 2018-01-05 doi:10.1101/243121 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake ]]> https://biorxiv.org/content/10.1101/244657v1?rss=1 Han, M. Dsouza, M. Zhou, C. Li, H. Zhang, J. Chen, C. Yao, Q. Zhong, C. Zhou, H. Gilbert, J. A. Wang, Z. Ning, K. 2018-01-08 doi:10.1101/244657 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ An ancient fecundability-associated polymorphism creates a new GATA2 binding site in a distal enhancer of HLA-F ]]> https://biorxiv.org/content/10.1101/245043v1?rss=1 Mika, K. M. Li, X. DeMayo, F. J. Lynch, V. J. 2018-01-08 doi:10.1101/245043 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Septal Secretion of Protein A in Staphylococcus aureus Requires SecA and Lipoteichoic Acid Synthesis ]]> https://biorxiv.org/content/10.1101/245522v1?rss=1 Yu, W. Missiakas, D. M. Schneewind, O. 2018-01-09 doi:10.1101/245522 Cold Spring Harbor Laboratory Press 2018-01-09 <![CDATA[ Genetic architecture of gene expression traits across diverse populations ]]> https://biorxiv.org/content/10.1101/245761v1?rss=1 0.86 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at .nnAuthor summaryMost genome-wide association studies (GWAS) have been conducted in populations of European ancestry leading to a disparity in understanding the genetics of complex traits between populations. For many complex traits, gene regulation is critical, given the consistent enrichment of regulatory variants among trait-associated variants. However, it is still unknown how the effects of these key variants differ across populations. We used data from MESA to study the underlying genetic architecture of gene expression by optimizing gene expression prediction within and across diverse populations. The populations with genotype and gene expression data available are from individuals with African American (AFA, n=233), Hispanic (HIS, n=352), and European (CAU, n=578) ancestry. After calculating the prediction performance, we found that there are many genes that were well predicted in one population are poorly predicted in another. We further show that a training set with ancestry similar to the test set resulted in better gene expression predictions, demonstrating the need to incorporate diverse populations in genomic studies. Our gene expression prediction models and performance statistics are publicly available to facilitate future transcriptome mapping studies in diverse populations. ]]> Mogil, L. S. Andaleon, A. Badalamenti, A. Dickinson, S. P. Guo, X. Rotter, J. I. Johnson, W. C. Im, H. K. Liu, Y. Wheeler, H. E. 2018-01-10 doi:10.1101/245761 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Insights into circovirus host range from the genomic fossil record. ]]> https://biorxiv.org/content/10.1101/246777v1?rss=1 Dennis, T. P. W. Flynn, P. J. De Souza, W. M. Singer, J. B. Moreau, C. Wilson, S. J. Gifford, R. J. 2018-03-08 doi:10.1101/246777 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells ]]> https://biorxiv.org/content/10.1101/247429v1?rss=1 Murmann, A. E. Gao, Q. Q. Putzbach, W. Patel, M. Bartom, E. T. Law, C. Bridgeman, B. Chen, S. McMahon, K. M. Thaxton, C. S. Peter, M. E. 2018-01-12 doi:10.1101/247429 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Human local adaptation of the TRPM8 cold receptor along a latitudinal cline ]]> https://biorxiv.org/content/10.1101/251033v1?rss=1 Key, F. M. Abdul-Aziz, M. A. Mundry, R. Peter, B. Sekar, A. D Amato, M. Dennis, M. Y. Schmidt, J. M. Andres, A. M. 2018-01-19 doi:10.1101/251033 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ Molecular control of gene expression by Brucella BaaR, an IclR-family repressor ]]> https://biorxiv.org/content/10.1101/251942v1?rss=1 Herrou, J. Czyc, D. M. Fiebig, A. Willett, J. W. Kim, Y. Wu, R. Babnigg, G. Crosson, S. 2018-01-22 doi:10.1101/251942 Cold Spring Harbor Laboratory Press 2018-01-22 <![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[ N6-methyladenosine Binding Proteins Negatively Regulate HIV-1 Infectivity and Viral Production ]]> https://biorxiv.org/content/10.1101/257410v1?rss=1 Lu, W. Tirumuru, N. Koneru, P. C. Liu, C. Kvaratskhelia, M. He, C. Wu, L. 2018-01-31 doi:10.1101/257410 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ BDQC: a general-purpose analytics tool for domain-blind validation of Big Data ]]> https://biorxiv.org/content/10.1101/258822v1?rss=1 Deutsch, E. Kramer, R. Ames, J. Bauman, A. Campbell, D. S. Chard, K. Clark, K. D'Arcy, M. Dinov, I. Donovan, R. Foster, I. Heavner, B. D. Hood, L. E. Kesselman, C. Madduri, R. Mi, H. Muruganujan, A. Pa, J. Price, N. D. Robinson, M. Sepehrband, F. Toga, A. W. Van Horn, J. D. Zhao, L. Glusman, G. 2018-02-02 doi:10.1101/258822 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a vaccine ]]> https://biorxiv.org/content/10.1101/258871v1?rss=1 Cai, F. Y. Fussell, T. Cobey, S. E. Lipsitch, M. 2018-02-05 doi:10.1101/258871 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Laminin heparin-binding peptides promiscuously bind growth factors and enhance diabetic wound healing ]]> https://biorxiv.org/content/10.1101/259481v1?rss=1 Ishihara, J. Ishihara, A. Fukunaga, K. Briquez, P. S. Hubbell, J. A. 2018-02-05 doi:10.1101/259481 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ Genome-wide study identifies 611 loci associated with risk tolerance and risky behaviors ]]> https://biorxiv.org/content/10.1101/261081v1?rss=1 Karlsson Linner, R. Biroli, P. Kong, E. Meddens, S. F. W. Wedow, R. Fontana, M. A. Lebreton, M. Abdellaoui, A. Hammerschlag, A. R. Nivard, M. G. Okbay, A. Rietveld, C. A. Timshel, P. N. Tino, S. P. Trzaskowski, M. de Vlaming, R. Zünd, C. L. Bao, Y. Buzdugan, L. Caplin, A. H. Chen, C.-Y. Eibich, P. Fontanillas, P. Gonzalez, J. R. Joshi, P. K. Karhunen, V. Kleinman, A. Levin, R. Z. Lill, C. M. Meddens, G. A. Muntane, G. Sanchez-Roige, S. van Rooij, F. J. Taskesen, E. Wu, Y. Zhang, F. 23andMe Research Team, eQTLgen Consortium, International Cannab 2018-02-08 doi:10.1101/261081 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ An Escherichia coli nitrogen starvation response is important for mutualistic coexistence with Rhodopseudomonas palustris ]]> https://biorxiv.org/content/10.1101/262139v1?rss=1 McCully, A. L. Behringer, M. G. Gliessman, J. R. Pilipenko, E. V. Mazny, J. L. Lynch, M. Drummond, D. A. McKinlay, J. B. 2018-02-08 doi:10.1101/262139 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ The variability of song variability in wild and domesticated zebra finches Taeniopygia guttata ]]> https://biorxiv.org/content/10.1101/263913v1?rss=1 Lansverk, A. L. London, S. E. Griffith, S. C. Clayton, D. F. Balakrishnan, C. N. 2018-02-11 doi:10.1101/263913 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ Identifying tissues implicated in Anorexia Nervosa using Transcriptomic Imputation ]]> https://biorxiv.org/content/10.1101/265017v1?rss=1 Huckins, L. M. Dobbyn, A. McFadden, W. Ruderfer, D. Wang, W. Gamazon, E. R. Leppa, V. Eating Disorders working group of the Psychiatric Genomics Consortium (PGC-ED), Devlin, B. Sieberts, S. K. Cox, N. Im, H. K. Breen, G. Sklar, P. Bulik, C. Stahl, E. A. 2018-02-14 doi:10.1101/265017 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Reproducible big data science: A case study in continuous FAIRness ]]> https://biorxiv.org/content/10.1101/268755v1?rss=1 Madduri, R. K. Chard, K. D'Arcy, M. Jung, S. C. Rodriguez, A. Sulakhe, D. Deutsch, E. W. Funk, C. Heavner, B. Richards, M. Shannon, P. Dinov, I. Glusman, G. Price, N. Van Horn, J. D. Kesselman, C. Toga, A. W. Foster, I. 2018-02-27 doi:10.1101/268755 Cold Spring Harbor Laboratory Press 2018-02-27 <![CDATA[ Interhemispheric Integration for Complex Behaviors, Absent the Corpus Callosum in Normal Ontogeny ]]> https://biorxiv.org/content/10.1101/271072v1?rss=1 Layden, E. A. Schertz, K. E. London, S. E. Berman, M. G. 2018-02-25 doi:10.1101/271072 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes ]]> https://biorxiv.org/content/10.1101/271650v1?rss=1 Engelmann, B. W. Hsiao, C. J. Blischak, J. D. Fourne, Y. Ford, M. Gilad, Y. 2018-02-26 doi:10.1101/271650 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ SoS Notebook: An Interactive Multi-Language Data Analysis Environment ]]> https://biorxiv.org/content/10.1101/274001v1?rss=1 Peng, B. Wang, G. Ma, J. Leong, M. C. Wakefield, C. Chiu, Y. Di, D. Weinstein, J. N. 2018-03-02 doi:10.1101/274001 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ Different inhibitory interneuron cell classes make distinct contributions to visual perception ]]> https://biorxiv.org/content/10.1101/275172v1?rss=1 Cone, J. J. Scantlen, M. D. Histed, M. H. Maunsell, J. H. R. 2018-03-02 doi:10.1101/275172 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans ]]> https://biorxiv.org/content/10.1101/276030v1?rss=1 0.05), the association between Tshared and ({Delta}LTL)2 (P=0.002) was stronger than the association between {phi} and ({Delta}LTL)2 (P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2 despite telomere "reprogramming" during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2 attributable to direction transmission. ]]> Delgado, D. A. Zhang, C. Demanelis, K. Chen, L. S. Gao, J. Roy, S. Shinkle, J. Sabarinathan, M. Argos, M. Tong, L. Ahmed, A. Islam, T. Rakibuz-Zaman, M. Sarwar, G. Shahriar, H. Rahman, M. Yanus, M. Doherty, J. A. Jasmine, F. Kibriya, M. G. Ahsan, H. Pierce, B. L. 2018-03-05 doi:10.1101/276030 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Tuning molecular motor transport through cytoskeletal filament network organization ]]> https://biorxiv.org/content/10.1101/277947v1?rss=1 Scholz, M. Weirich, K. L. Gardel, M. L. Dinner, A. R. 2018-03-07 doi:10.1101/277947 Cold Spring Harbor Laboratory Press 2018-03-07 <![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[ Flexible Learning-Free Segmentation and Reconstruction for Sparse Neuronal Circuit Tracing ]]> https://biorxiv.org/content/10.1101/278515v1?rss=1 Shahbazi, A. Kinnison, J. Vescovi, R. Du, M. Hill, R. Jösch, M. Takeno, M. Zeng, H. da Costa, N. M. Grutzendler, J. Kasthuri, N. Scheirer, W. J. 2018-03-08 doi:10.1101/278515 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Evaluation of Caulobacter crescentus strain fitness at the genomic scale during growth in natural freshwater ]]> https://biorxiv.org/content/10.1101/279711v1?rss=1 Hentchel, K. L. Reyes Ruiz, L. M. Fiebig, A. Curtis, P. D. Coleman, M. L. Crosson, S. 2018-03-10 doi:10.1101/279711 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Harnessing Empirical Bayes and Mendelian Segregation for Genotyping Autopolyploids from Messy Sequencing Data ]]> https://biorxiv.org/content/10.1101/281550v1?rss=1 Gerard, D. Ferrao, L. F. V. Garcia, A. A. F. Stephens, M. 2018-03-16 doi:10.1101/281550 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Sex differences in gene expression in response to ischemia in the human myocardium ]]> https://biorxiv.org/content/10.1101/282350v1?rss=1 Stone, G. Choi, A. Oliva, M. Gorham, J. Heydarpour, M. Seidman, C. E. Seidman, J. G. Aranki, S. F. Body, S. C. Carey, V. J. Raby, B. A. Stranger, B. E. Muehlschlegel, J. D. 2018-03-31 doi:10.1101/282350 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Adipose fin development and its relation to the evolutionary origins of median fins ]]> https://biorxiv.org/content/10.1101/283432v1?rss=1 Stewart, T. Ho, R. Hale, M. A. 2018-03-16 doi:10.1101/283432 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ 6mer Seed Toxicity Determines Strand Selection in miRNAs ]]> https://biorxiv.org/content/10.1101/284406v1?rss=1 80% of the 6mer seed in the most toxic siRNAs. These 6mer seed containing siRNAs exert their toxicity by targeting survival genes which contain GC-rich 3UTRs. The master tumor suppressor miRNA miR-34a was found to be toxic through such a G-rich 6mer seed suggesting that certain tumor suppressive miRNAs use a toxic 6mer seed to kill cancer cells. An analysis of all mature miRNAs suggests that most miRNAs evolved to avoid guanine at the 5' end of the 6mer seed sequence of the predominantly expressed arm. In contrast, for many tumor suppressive miRNAs the predominant arm contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells. ]]> Gao, Q. Q. Putzbach, W. E. Murmann, A. E. Chen, S. Ambrosini, G. Peter, J. M. Bartom, E. T. Peter, M. 2018-03-18 doi:10.1101/284406 Cold Spring Harbor Laboratory Press 2018-03-18 <![CDATA[ Using biological control data to understand host-pathogen dynamics ]]> https://biorxiv.org/content/10.1101/285080v1?rss=1 Mihaljevic, J. R. Polivka, K. M. Mehmel, C. J. Li, C. Dukic, V. Dwyer, G. 2018-03-19 doi:10.1101/285080 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Hierarchy, Morphology, and Adaptive Radiation: a Test of Osborn’s Law in the Carnivora ]]> https://biorxiv.org/content/10.1101/285700v1?rss=1 Slater, G. J. Friscia, A. R. 2018-03-20 doi:10.1101/285700 Cold Spring Harbor Laboratory Press 2018-03-20 <![CDATA[ A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues ]]> https://biorxiv.org/content/10.1101/289942v1?rss=1 Pavlovic, B. J. Blake, L. E. Roux, J. Chavarria, C. Gilad, Y. 2018-03-27 doi:10.1101/289942 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Large-Scale Genome-Wide Meta Analysis of Polycystic Ovary Syndrome Suggests Shared Genetic Architecture for Different Diagnosis Criteria. ]]> https://biorxiv.org/content/10.1101/290502v1?rss=1 Day, F. Karaderi, T. Jones, M. R. Meun, C. He, C. Drong, A. Kraft, P. Lin, N. Huang, H. Broer, L. Magi, R. Saxena, R. Laisk-Podar, T. Urbanek, M. Hayes, G. M. Thorleifsson, G. Fernandez-Tajes, J. Mahajan, A. Mullin, B. H. Stuckey, B. G. A. Spector, T. D. Wilson, S. G. Goodarzi, M. O. Davis, L. Obermeyer-Pietsch, B. Uitterlinden, A. G. Anttila, V. Neale, B. M. Jarvelin, M.-R. Fauser, B. Kowalska, I. Visser, J. A. Anderson, M. Ong, K. Stener-Victorin, E. Ehrmann, D. Legro, R. S. Salumets, A. McCarthy, M. I. Morin-Papunen, L. Thorsteinsdottir, U. Stefansso 2018-03-28 doi:10.1101/290502 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Entropic Forces Drive Clustering and Spatial Localization of Influenza A M2 During Viral Budding ]]> https://biorxiv.org/content/10.1101/291120v1?rss=1 Madsen, J. J. Grime, J. M. A. Rossman, J. S. Voth, G. A. 2018-03-28 doi:10.1101/291120 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Integrating Predicted Transcriptome From Multiple Tissues Improves Association Detection ]]> https://biorxiv.org/content/10.1101/292649v1?rss=1 Barbeira, A. N. Pividori, M. D. Zheng, J. Wheeler, H. E. Nicolae, D. L. Im, H. K. 2018-03-31 doi:10.1101/292649 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/296608v1?rss=1 Reyfman, P. A. Walter, J. M. Joshi, N. Anekalla, K. R. McQuattie-Pimentel, A. C. Chiu, S. Fernandez, R. Akbarpour, M. Chen, C.-I. Ren, Z. Verma, R. Abdala-Valencia, H. Nam, K. Chi, M. Han, S. Gonzalez-Gonzalez, F. J. Soberanes, S. Watanabe, S. Williams, K. J. N. Flozak, A. S. Nicholson, T. T. Morgan, V. K. Hrusch, C. L. Guzy, R. D. Bonham, C. A. Sperling, A. I. Bag, R. Hamanaka, R. B. Mutlu, G. M. Yeldandi, A. V. Marshall, S. A. Shilatifard, A. Amaral, L. A. N. Perlman, H. Sznajder, J. I. Winter, D. R. Hinchcliff, M. Argento, A. C. Gillespie, C. T. Dematt 2018-04-06 doi:10.1101/296608 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Circuit mechanisms for the maintenance and manipulation of information in working memory ]]> https://biorxiv.org/content/10.1101/305714v1?rss=1 Masse, N. Y. Yang, G. R. Song, H. F. Wang, X.-J. Freedman, D. J. 2018-04-22 doi:10.1101/305714 Cold Spring Harbor Laboratory Press 2018-04-22 <![CDATA[ The SERM/SERD Bazedoxifene Disrupts ESR1 Helix 12 to Overcome Acquired Hormone Resistance in Breast Cancer Cells ]]> https://biorxiv.org/content/10.1101/306472v1?rss=1 Fanning, S. W. Jeselsohn, R. Dharmarajan, V. Mayne, C. G. Karimi, M. Buchwalter, G. Houtman, R. Toy, W. Fowler, C. E. Laine, M. Carlson, K. E. Martin, T. A. Nowak, J. Nwachukwu, J. C. Hosfield, D. J. Chandarlapaty, S. Tajkhorshid, E. Nettles, K. W. Griffin, P. R. Shen, Y. Katzenellenbogen, J. A. Brown, M. Greene, G. L. 2018-04-23 doi:10.1101/306472 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Intrinsic Excitability Increase in Cerebellar Purkinje Cells Following Delay Eyeblink Conditioning in Mice ]]> https://biorxiv.org/content/10.1101/306639v1?rss=1 Titley, H. K. Watkins, G. V. Lin, C. Weiss, C. McCarthy, M. Disterhoft, J. F. Hansel, C. 2018-04-23 doi:10.1101/306639 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Reverse Engineered Virtual Patient Populations as Surrogates for Real Patient-Level Data ]]> https://biorxiv.org/content/10.1101/308403v1?rss=1 Alenghat, F. J. 2018-04-25 doi:10.1101/308403 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation ]]> https://biorxiv.org/content/10.1101/310920v1?rss=1 Fei, Q. Yu, Y. Liu, L. Zhang, Y. Baldrich, P. Dai, Q. Chen, X. Meyers, B. 2018-04-30 doi:10.1101/310920 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Gating Mechanisms during Actin Filament Elongation by Formins ]]> https://biorxiv.org/content/10.1101/311431v1?rss=1 Aydin, F. Courtemanche, N. Pollard, T. D. Voth, G. A. 2018-04-30 doi:10.1101/311431 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Regulation of the error-prone DNA polymerase polκ by oncogenic signaling and its contribution to drug resistance ]]> https://biorxiv.org/content/10.1101/316729v1?rss=1 Temprine, K. Langdon, E. M. Mehta, K. Clapp, A. White, R. M. 2018-05-11 doi:10.1101/316729 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ PLK1 plays dual roles in centralspindlin regulation during cytokinesis ]]> https://biorxiv.org/content/10.1101/317388v1?rss=1 Adriaans, I. E. Basant, A. Ponsioen, B. Glotzer, M. Lens, S. 2018-05-08 doi:10.1101/317388 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. ]]> https://biorxiv.org/content/10.1101/319236v1?rss=1 David, M. M. Tataru, C. Daniels, J. Schwartz, J. Keating, J. Hampton-Marcell, J. Gottel, N. Gilbert, J. A. Wall, D. P. 2018-05-10 doi:10.1101/319236 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Insights into the cooperative nature of ATP hydrolysis in actin filaments ]]> https://biorxiv.org/content/10.1101/319558v1?rss=1 Katkar, H. H. Davtyan, A. Durumeric, A. E. P. Hocky, G. M. Schramm, A. C. De La Cruz, E. M. Voth, G. A. 2018-05-10 doi:10.1101/319558 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Monocyte and Macrophage Subtypes as Paired Cell Biomarkers for Coronary Artery Disease ]]> https://biorxiv.org/content/10.1101/323287v1?rss=1 Arnold, K. A. Blair, J. E. Paul, J. D. Shah, A. P. Nathan, S. Alenghat, F. 2018-05-16 doi:10.1101/323287 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Absolute pitch can be learned by some adults ]]> https://biorxiv.org/content/10.1101/325050v1?rss=1 Van Hedger, S. C. Heald, S. L. M. Nusbaum, H. C. 2018-05-17 doi:10.1101/325050 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Inference and visualization of DNA damage patterns using a grade of membership model ]]> https://biorxiv.org/content/10.1101/327684v1?rss=1 Al-Asadi, H. Dey, K. Novembre, J. Stephens, M. 2018-05-21 doi:10.1101/327684 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach ]]> https://biorxiv.org/content/10.1101/327718v1?rss=1 de Anda-Jauregui, G. Espinal-Enriquez, J. Hur, J. Alcala-Corona, S. A. Ruiz-Azuara, L. Hernandez-Lemus, E. 2018-05-21 doi:10.1101/327718 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design ]]> https://biorxiv.org/content/10.1101/328559v1?rss=1 Handel, A. Li, Y. McKay, B. Pawelek, K. Zarnitsyna, V. Antia, R. 2018-05-22 doi:10.1101/328559 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Transcriptional Network Analysis on Brains Reveals a Potential Regulatory Role of PPP1R3F in Autism Spectrum Disorders ]]> https://biorxiv.org/content/10.1101/330449v1?rss=1 Doostparast Torshizi, A. Duan, J. Wang, K. 2018-05-25 doi:10.1101/330449 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Age-specific differences in the dynamics of protective immunity to influenza ]]> https://biorxiv.org/content/10.1101/330720v1?rss=1 Ranjeva, S. Subramanian, R. Fang, V. J. Leung, G. M. Ip, D. K. M. Perera, R. A. P. M. Peiris, J. S. M. Cowling, B. J. Cobey, S. 2018-05-25 doi:10.1101/330720 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Quasi-neutral molecular evolution -- When positive and negative selection cancel out ]]> https://biorxiv.org/content/10.1101/330811v1?rss=1 Chen, B. Shi, Z. Chen, Q. Shibata, D. Wen, H. Wu, C.-I. 2018-05-25 doi:10.1101/330811 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/333617v1?rss=1 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy number states, a considerable fraction of the events involves multiple chromosomes as well as additional structural alterations. In addition to non-homologous end-joining, we detect signatures of replicative processes and templated insertions. Chromothripsis contributes to oncogene amplification as well as to inactivation of genes such as mismatch-repair related genes. These findings show that chromothripsis is a major process driving genome evolution in human cancer. ]]> Cortes-Ciriano, I. Lee, J.-K. Xi, R. Jain, D. Jung, Y. L. Yang, L. Gordenin, D. Klimczak, L. J. Zhang, C.-Z. Pellman, D. S. Park, P. J. PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, 2018-05-30 doi:10.1101/333617 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Depolymerized lamins link nuclear envelope breakdown to mitotic transcriptional quiescence ]]> https://biorxiv.org/content/10.1101/334110v1?rss=1 Ikegami, K. Secchia, S. Lieb, J. D. Moskowitz, I. P. 2018-05-30 doi:10.1101/334110 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Speciation with gene flow via cycles of isolation and migration: Insights from multiple mangrove taxa ]]> https://biorxiv.org/content/10.1101/335166v1?rss=1 1) species after n cycles.nnSignificance statementMechanisms of species formation have always been a conundrum. Speciation between populations that are fully geographically isolated, or allopatric speciation, has been the standard solution in the last 50 years. Complete geographical isolation with no possibility of gene flow, however, is often untenable and is inefficient in generating the enormous biodiversity. By studying mangroves on the Indo-Malayan coasts, a global hotspot of coastal biodiversity, we were able to combine genomic data with geographical records on the Indo-Pacific barrier that separates Pacific and Indian Ocean coasts. We discovered a novel mechanism of speciation, that we call mixing-isolation-mixing (MIM) cycles. By permitting intermittent gene flow during speciation, MIM can potentially generate species at an exponential rate, thus combining speciation and biodiversity in a unified framework. ]]> He, Z. Li, X. Yang, M. Wang, X. Zhong, C. Duke, N. C. Shi, S. Wu, C.-I. 2018-05-31 doi:10.1101/335166 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Force localization modes in dynamic epithelial colonies ]]> https://biorxiv.org/content/10.1101/336164v1?rss=1 Schaumann, E. N. Staddon, M. F. Gardel, M. L. Banerjee, S. 2018-05-31 doi:10.1101/336164 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors ]]> https://biorxiv.org/content/10.1101/338897v1?rss=1 Romero Calvo, I. Weber, C. R. Ray, M. Brown, M. A. Kirby, K. J. Nandi, R. K. Long, T. M. Sparrow, S. M. Ugolkov, A. V. Qiang, W. Zhang, Y. Brunetti, T. M. Kindler, H. L. Segal, J. P. Rzhetsky, A. Mazar, A. P. Buschmann, M. M. Weichselbaum, R. R. Rogin, K. K. White, K. P. 2018-06-04 doi:10.1101/338897 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Associations between Afrotropical bats, parasites, and microbial symbionts ]]> https://biorxiv.org/content/10.1101/340109v1?rss=1 Lutz, H. L. Jackson, E. W. Webala, P. W. Babyesiza, W. S. Kerbis Peterhans, J. C. Demos, T. C. Patterson, B. D. Gilbert, J. A. 2018-06-07 doi:10.1101/340109 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ A promoter interaction map for cardiovascular disease genetics ]]> https://biorxiv.org/content/10.1101/340869v1?rss=1 Montefiori, L. E. Sobreira, D. R. Sakabe, N. J. Aneas, I. Joslin, A. C. Hansen, G. T. Bozek, G. Moskowitz, I. P. McNally, E. M. Nobrega, M. A. 2018-06-08 doi:10.1101/340869 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Multiple optic gland signaling pathways implicated in octopus maternal behaviors and death ]]> https://biorxiv.org/content/10.1101/340984v1?rss=1 Wang, Z. Y. Ragsdale, C. W. 2018-06-07 doi:10.1101/340984 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Identification of Novel Common Breast Cancer Risk Variants in Latinas at the 6q25 Locus ]]> https://biorxiv.org/content/10.1101/343806v1?rss=1 Hoffman, J. Fejerman, L. Hu, D. Hunstman, S. Li, M. John, E. Torres-Mejia, G. Kushi, L. Ding, Y. C. Weitzel, J. Neuhausen, S. Lott, P. COLUMBUS Consortium, Echeverry, M. Carvajal-Carmona, L. Burchard, E. Eng, C. Long, J. Zheng, W. Olopade, O. Huo, D. Haiman, C. Ziv, E. 2018-06-11 doi:10.1101/343806 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Parent of origin gene expression in a founder population identifies two new imprinted genes at known imprinted regions ]]> https://biorxiv.org/content/10.1101/344457v1?rss=1 Mozaffari, S. V. Stein, M. M. Magnaye, K. M. Nicolae, D. L. Ober, C. 2018-06-11 doi:10.1101/344457 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Coherent feedforward regulation of gene expression by Caulobacter σT and GsrN during hyperosmotic stress ]]> https://biorxiv.org/content/10.1101/344820v1?rss=1 Tien, M. Z. Stein, B. J. Crosson, S. 2018-06-12 doi:10.1101/344820 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Recombination between co-infecting herpesviruses occurs where replication compartments coales ]]> https://biorxiv.org/content/10.1101/345918v1?rss=1 Tomer, E. Cohen, E. M. Drayman, N. Afriaat, A. Weitzman, M. D. Zaritsky, A. Kobiler, O. 2018-06-13 doi:10.1101/345918 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems ]]> https://biorxiv.org/content/10.1101/347021v1?rss=1 Paver, S. Muratore, D. J. Newton, R. J. Coleman, M. 2018-06-14 doi:10.1101/347021 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Dissecting the neural focus of attention reveals distinct processes for spatial attention and object-based storage in visual working memory ]]> https://biorxiv.org/content/10.1101/347518v1?rss=1 Hakim, N. Adam, K. C. S. Gunseli, E. Awh, E. Vogel, E. K. 2018-06-15 doi:10.1101/347518 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Mechanisms of gene death in the Red Queen race revealed by the analysis of de novo microRNAs ]]> https://biorxiv.org/content/10.1101/349217v1?rss=1 Lu, G.-A. Zhao, Y. Lan, A. Liufu, Z. Wen, H. Tang, T. Xu, J. Wu, C.-I. 2018-06-17 doi:10.1101/349217 Cold Spring Harbor Laboratory Press 2018-06-17 <![CDATA[ Two-step binding kinetics of tRNAGly by the glyQS T-box riboswitch and its regulation by T-box structural elements ]]> https://biorxiv.org/content/10.1101/350413v1?rss=1 Zhang, J. Chetnani, B. Cormack, E. D. Liu, W. Mondragon, A. Fei, J. 2018-06-19 doi:10.1101/350413 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Brain Connectivity Tracks Effects of Chemotherapy Separately from Behavioral Measures ]]> https://biorxiv.org/content/10.1101/352690v1?rss=1 Kardan, O. Reuter-Lorenz, P. A. Peltier, S. Churchill, N. W. Jung, M. Misic, B. Askren, M. K. Cimprich, B. Berman, M. G. 2018-06-21 doi:10.1101/352690 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Critical transitions in malaria transmission models are consistently generated by superinfection ]]> https://biorxiv.org/content/10.1101/355420v1?rss=1 alonso, d. Pascual, M. Dobson, A. 2018-06-26 doi:10.1101/355420 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey ]]> https://biorxiv.org/content/10.1101/355511v1?rss=1 McConnell, S. C. Westerman, E. L. Pierre, J. F. Heckler, E. J. Schwartz, N. B. 2018-06-26 doi:10.1101/355511 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ Neurofeedback helps to reveal a relationship between context reinstatement and memory retrieval ]]> https://biorxiv.org/content/10.1101/355727v1?rss=1 deBettencourt, M. T. Turk-Browne, N. B. Norman, K. A. 2018-06-29 doi:10.1101/355727 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ RPA resolves conflicting activities of accessory proteins during reconstitution of Dmc1-mediated meiotic recombination ]]> https://biorxiv.org/content/10.1101/356592v1?rss=1 Chan, Y.-L. Zhang, A. Weissman, B. P. Bishop, D. K. 2018-06-27 doi:10.1101/356592 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Quantification of genetic components of population differentiation in UK Biobank traits reveals signals of polygenic selection ]]> https://biorxiv.org/content/10.1101/357483v1?rss=1 Liu, X. Price, A. L. Loh, P.-R. O'Connor, L. J. Gazal, S. Schoech, A. Maier, R. M. Patterson, N. 2018-06-27 doi:10.1101/357483 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in Genomic Sequencing Studies ]]> https://biorxiv.org/content/10.1101/359265v1?rss=1 Sun, S. Zhu, J. Mozaffari, S. Ober, C. Chen, M. Zhou, X. 2018-06-29 doi:10.1101/359265 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Non-enzymatic roles of human RAD51 at stalled replication forks ]]> https://biorxiv.org/content/10.1101/359380v1?rss=1 Mason, J. Chan, Y.-L. Weichselbaum, R. W. Bishop, D. K. 2018-06-29 doi:10.1101/359380 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ A total synthetic approach to CRISPR/Cas9 genome editing and homology directed repair ]]> https://biorxiv.org/content/10.1101/359984v1?rss=1 DiNapoli, S. E. Martinez-McFaline, R. Gribbin, C. K. Balgobin, C. A. Nelson, I. Leonard, A. Mailhiot, D. Kao, C. McDonnell, S. de Jong, J. L. O. Houvras, Y. 2018-07-01 doi:10.1101/359984 Cold Spring Harbor Laboratory Press 2018-07-01 <![CDATA[ The ATPase activity of E. coli RecA prevents accumulation of toxic complexes formed by erroneous binding to undamaged double strand DNA ]]> https://biorxiv.org/content/10.1101/361097v1?rss=1 Gataulin, D. V. Carey, J. N. Li, J. Shah, P. Grubb, J. Bishop, D. K. 2018-07-03 doi:10.1101/361097 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/365049v1?rss=1 Snyder-Mackler, N. Sanz, J. Kohn, J. N. Voyles, T. N. Pique-Regi, R. Wilson, M. E. Barreiro, L. B. Tung, J. 2018-07-09 doi:10.1101/365049 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Estimating recent migration and population size surfaces ]]> https://biorxiv.org/content/10.1101/365536v1?rss=1 Al-Asadi, H. Petkova, D. Stephens, M. Novembre, J. 2018-07-09 doi:10.1101/365536 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Model-based analysis of positive selection significantly expands the list of cancer driver genes, including RNA methyltransferases ]]> https://biorxiv.org/content/10.1101/366823v1?rss=1 Zhao, S. Liu, J. Nanga, P. Liu, Y. Cicek, E. Knoblauch, N. He, C. Stephens, M. He, X. 2018-07-12 doi:10.1101/366823 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Cancer eQTLs can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity ]]> https://biorxiv.org/content/10.1101/366922v1?rss=1 Geeleher, P. Nath, A. Wang, F. Zhang, Z. Barbeira, A. N. Fessler, J. Grossman, R. L. Seoighe, C. Huang, R. S. 2018-07-10 doi:10.1101/366922 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ CorShrink : Empirical Bayes shrinkage estimation of correlations, with applications ]]> https://biorxiv.org/content/10.1101/368316v1?rss=1 dey, k. K. Stephens, M. 2018-07-13 doi:10.1101/368316 Cold Spring Harbor Laboratory Press 2018-07-13 <![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[ Metabolically activated macrophages in mammary adipose tissue link obesity to triple-negative breast cancer ]]> https://biorxiv.org/content/10.1101/370627v1?rss=1 Tiwari, P. Blank, A. Cui, C. Schoenfelt, K. Zhou, G. Xu, Y. Shah, A. Khan, S. Rosner, M. R. Becker, L. 2018-07-17 doi:10.1101/370627 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ Applying Inter-rater Reliability to Improve Consistency in Classifying PhD Career Outcomes ]]> https://biorxiv.org/content/10.1101/370783v1?rss=1 Stayart, C. A. Brandt, P. Brown, A. Hutto, T. Layton, R. Petrie, K. A. Flores-Kim, E. N. Pena, C. G. Fuhrmann, C. N. Monsalve, G. C. 2018-07-19 doi:10.1101/370783 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ The structural basis for activation of voltage sensor domains in an ion channel TPC1 ]]> https://biorxiv.org/content/10.1101/373860v1?rss=1 Kintzer, A. F. Green, E. Dominik, P. Bridges, M. Armache, J.-p. Deneka, D. Kim, S. Hubbell, W. Kossiakoff, A. Cheng, Y. Stroud, R. 2018-07-21 doi:10.1101/373860 Cold Spring Harbor Laboratory Press 2018-07-21 <![CDATA[ Tumor extracellular vesicles are required for tumor-associated macrophage programming ]]> https://biorxiv.org/content/10.1101/375022v1?rss=1 Rabe, D. C. Rustandy, F. D. Lee, J. Rosner, M. R. 2018-07-23 doi:10.1101/375022 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein. ]]> https://biorxiv.org/content/10.1101/376632v1?rss=1 Riback, J. A. Bowman, M. A. Zmyslowski, A. M. Plaxco, K. W. Clark, P. L. Sosnick, T. R. 2018-07-28 doi:10.1101/376632 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ A genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics ]]> https://biorxiv.org/content/10.1101/377549v1?rss=1 Krause, M. D. Huang, R.-T. Wu, D. Shentu, T.-P. Harrison, D. L. Whalen, M. B. Stolze, L. K. Di Rienzo, A. Moskowitz, I. P. Civelek, M. Romanoski, C. E. Fang, Y. 2018-07-25 doi:10.1101/377549 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella ]]> https://biorxiv.org/content/10.1101/380782v1?rss=1 Nguyen, M. Long, S. W. McDermott, P. F. Olsen, R. J. Olson, R. Stevens, R. L. Tyson, G. H. Zhao, S. Davis, J. J. 2018-07-31 doi:10.1101/380782 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ The genetic prehistory of the Andean highlands 7,000 Years BP though European contact ]]> https://biorxiv.org/content/10.1101/381905v1?rss=1 Lindo, J. Haas, R. Hofman, C. Apata, M. Moraga, M. Verdugo, R. Watson, J. T. Llave, C. Witonsky, D. Pacheco, E. Villena, M. Soria, R. Beall, C. Warinner, C. Novembre, J. Aldenderfer, M. Di Rienzo, A. 2018-07-31 doi:10.1101/381905 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Static kinks or flexible hinges: conformational distributions of bent DNA bound to integration host factor mapped by fluorescence lifetime measurements ]]> https://biorxiv.org/content/10.1101/382655v1?rss=1 Connolly, M. Arra, A. Zvoda, V. Steinbach, P. J. Rice, P. A. Ansari, A. 2018-08-02 doi:10.1101/382655 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Item-specific delay activity demonstrates concurrent storage of multiple items in working memory ]]> https://biorxiv.org/content/10.1101/382879v1?rss=1 Sutterer, D. W. Foster, J. J. Adam, K. C. S. Vogel, E. K. Awh, E. 2018-08-01 doi:10.1101/382879 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Inter-species differences in response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees ]]> https://biorxiv.org/content/10.1101/382895v1?rss=1 Ward, M. C. Gilad, Y. 2018-08-02 doi:10.1101/382895 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin ]]> https://biorxiv.org/content/10.1101/386961v1?rss=1 Harker, A. J. Katkar, H. H. Bidone, T. C. Aydin, F. Voth, G. A. Applewhite, D. A. Kovar, D. R. 2018-08-07 doi:10.1101/386961 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[ Homing and egg discrimination in the Western Slimy Salamander, Plethodon albagula (Caudata: Plethodontidae) ]]> https://biorxiv.org/content/10.1101/388249v1?rss=1 Jordan, R. Milanovich, J. R. McCallum, M. Trauth, S. E. 2018-08-09 doi:10.1101/388249 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Latent Structure of Risk Perception ]]> https://biorxiv.org/content/10.1101/389890v1?rss=1 Pabon, E. MacKillop, J. Palmer, A. de Wit, H. 2018-08-10 doi:10.1101/389890 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Expected patterns of local ancestry in a hybrid zone ]]> https://biorxiv.org/content/10.1101/389924v1?rss=1 Smith, J. Payseur, B. Novembre, J. 2018-08-11 doi:10.1101/389924 Cold Spring Harbor Laboratory Press 2018-08-11 <![CDATA[ Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography ]]> https://biorxiv.org/content/10.1101/392381v1?rss=1 Ding, Y. Vanselow, D. J. Yakovlev, M. A. Katz, S. R. Lin, A. Y. Clark, D. P. Vargas, P. Xin, X. Copper, J. E. Canfield, V. A. Ang, K. C. Wang, Y. Xiao, X. De Carlo, F. van Rossum, D. B. La Riviere, P. Cheng, K. C. 2018-08-25 doi:10.1101/392381 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ Total lung capacity without plethysmography ]]> https://biorxiv.org/content/10.1101/395160v1?rss=1 Adam, O. Cohen, I. Yip, W.-k. Shiner, R. J. Calverley, P. Peles, Z. LaPrad, A. Dagan, Y. J. Brown, R. J. Solway, J. J. Fredberg, J. J. 2018-08-30 doi:10.1101/395160 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ GBAT: a gene-based association method for robust trans-gene regulation detection ]]> https://biorxiv.org/content/10.1101/395970v1?rss=1 Liu, X. Mefford, J. A. Dahl, A. Subramaniam, M. Battle, A. Price, A. L. Zaitlen, N. 2018-08-20 doi:10.1101/395970 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Relaxed constraint and thermal desensitization of the cold-sensing ion channel TRPM8 in mammoths ]]> https://biorxiv.org/content/10.1101/397356v1?rss=1 Chigurapati, S. Miller, W. Lynch, V. J. 2018-08-22 doi:10.1101/397356 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ TCF7L2 Regulation of GATA6-dependent and -Independent Vascular Smooth Muscle Cell Plasticity and Intimal Hyperplasia ]]> https://biorxiv.org/content/10.1101/397851v1?rss=1 Mani, A. Srivastava, R. Xie, Y. Li, N. Bhat, N. Hong, L. Esteghamat, S. Adeniran, A. Geirsson, A. Zhang, J. Ge, G. Nobrega, M. Martin, K. A. Rolyan, H. 2018-08-22 doi:10.1101/397851 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Gut microbial features can predict host phenotype response to protein deficiency ]]> https://biorxiv.org/content/10.1101/398248v1?rss=1 Navarro, G. Sharma, A. Dugas, L. R. Forrester, T. Gilbert, J. A. Layden, B. T. 2018-08-22 doi:10.1101/398248 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Kinpute: Using identity by descent to improve genotype imputation ]]> https://biorxiv.org/content/10.1101/399147v1?rss=1 Abney, M. El Sherbiny, A. 2018-08-23 doi:10.1101/399147 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Hemagglutinin stalk-reactive antibodies interfere with influenza virus neuraminidase activity by steric hindrance ]]> https://biorxiv.org/content/10.1101/400036v1?rss=1 Chen, Y.-Q. Lan, L. Y.-L. Huang, M. Henry, C. Wilson, P. C. 2018-08-25 doi:10.1101/400036 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ Self-organizing motors divide active liquid droplets ]]> https://biorxiv.org/content/10.1101/403121v1?rss=1 Weirich, K. L. Dasbiswas, K. Witten, T. A. Vaikuntanathan, S. Gardel, M. L. 2018-08-29 doi:10.1101/403121 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/406546v1?rss=1 Pilosof, S. He, Q. Tiedje, K. E. Ruybal-Pesantez, S. Day, K. Pascual, M. 2018-09-03 doi:10.1101/406546 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ mTADA: a framework for analyzing de novo mutations in multiple traits ]]> https://biorxiv.org/content/10.1101/406868v1?rss=1 13,000 trios for six disorders: schizophrenia (SCZ), autism spectrum disorder (ASD), developmental disorders (DD), intellectual disability (ID), epilepsy (EPI), and congenital heart disease (CHD). We report the proportion of overlapping risk genes and the specific risk genes shared for each pair of disorders. A total of 153 genes were found to be shared in at least one pair of disorders. The largest percentages of shared risk genes were observed for pairs of DD, ID, ASD, and CHD (>20%) whereas SCZ, CHD, and EPI did not show strong overlaps In risk gene set between them. Furthermore, mTADA identified additional SCZ, EPI and CHD risk genes through integration with DD de novo mutation data. For CHD, using DD information, 31 risk genes with posterior probabilities > 0.8 were identified, and 20 of these 31 genes were not in the list of known CHD genes. We find evidence that most significant CHD risk genes are strongly expressed in prenatal stages of the human genes. Finally, we validated our findings for CHD and EPI in independent cohorts comprising 1241 CHD trios, 226 CHD singletons and 197 EPI trios. Multiple novel risk genes identified by mTADA also had de novo mutations in these independent data sets. The joint analysis method introduced here, mTADA, is able to identify risk genes shared by two traits as well as additional risk genes not found through single-trait analysis only. A number of risk genes reported by mTADA are identified only through joint analysis, specifically when ASD, DD, or ID are one of the two traits examined. This suggests that novel genes for the trait or a new trait might converge to a core gene list of the three traits. ]]> Nguyen, H. T. Dobbyn, A. Buxbaum, J. Pinto, D. Purcell, S. M. Sullivan, P. F. He, X. Stahl, E. A. 2018-09-03 doi:10.1101/406868 Cold Spring Harbor Laboratory Press 2018-09-03 <![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[ Information content of downwelling skylight for non-imaging visual systems ]]> https://biorxiv.org/content/10.1101/408989v1?rss=1 Thiermann, R. Sweeney, A. Murugan, A. 2018-09-07 doi:10.1101/408989 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ The contribution of psychiatric risk alleles to a general liability to psychopathology in early life ]]> https://biorxiv.org/content/10.1101/409540v1?rss=1 Riglin, L. Thapar, A. K. Leppert, B. Martin, J. Richards, A. Anney, R. Davey Smith, G. Tilling, K. Stergiakouli, E. Lahey, B. B. O'Donovan, M. C. Collishaw, S. Thapar, A. 2018-09-12 doi:10.1101/409540 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Genome-Wide Control of Population Structure and Relatedness in Genetic Association Studies via Linear Mixed Models with Orthogonally Partitioned Structure ]]> https://biorxiv.org/content/10.1101/409953v1?rss=1 Conomos, M. P. Reiner, A. P. McPeek, M. S. Thornton, T. A. 2018-09-07 doi:10.1101/409953 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Prioritizing risk genes for neurodevelopmental disorders using pathway information ]]> https://biorxiv.org/content/10.1101/410100v1?rss=1 0.95), 6 of which replicate in an independent whole-genome sequencing study. In addition, 30/40 genes are novel genes. We found that epilepsy genes had high protein-protein interaction (PPI) network connectivity, and show specific expression during human brain development. Some of the top prioritized EPI genes were connected to a PPI subnetwork of immune genes and show specific expression in prenatal microglia. We also identified multiple enriched drug-target gene sets for EPI which included immunostimulants as well as known antiepileptics. Immune biology was supported specifically by case-control variants from familial epilepsies rather than do novo mutations in generalized encephalitic epilepsy. ]]> Nguyen, H. T. Dobbyn, A. Charney, A. Bryois, J. Skene, N. G. Huckins, L. M. Wang, W. Ruderfer, D. M. Xu, X. Fromer, M. Purcell, S. M. Verhage, M. Smit, A. B. Hjerling-Leffler, J. Buxbaum, J. Pinto, D. He, X. Sullivan, P. F. Stahl, E. A. 2018-09-09 doi:10.1101/410100 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Influenza incidence prediction for the United States: an update for the 2018-2019 season ]]> https://biorxiv.org/content/10.1101/411348v1?rss=1 Du, X. Peng, Y. Liu, M. Pascual, M. 2018-09-07 doi:10.1101/411348 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America ]]> https://biorxiv.org/content/10.1101/414623v1?rss=1 Silliman, K. 2018-09-11 doi:10.1101/414623 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ Transient intracellular acidification regulates the core transcriptional heat shock response ]]> https://biorxiv.org/content/10.1101/414706v1?rss=1 Triandafillou, C. G. Katanski, C. D. Dinner, A. R. Drummond, D. A. 2018-09-12 doi:10.1101/414706 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Unsupervised learning of persistent and sequential activity ]]> https://biorxiv.org/content/10.1101/414813v1?rss=1 Pereira, U. Brunel, N. 2018-09-12 doi:10.1101/414813 Cold Spring Harbor Laboratory Press 2018-09-12 <![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[ Aβ Fibrils Can Act as Aqueous Pores: a Molecular Dynamics Study ]]> https://biorxiv.org/content/10.1101/418137v1?rss=1 Haddadian, E. J. Natesh, S. Sachleben, J. R. Sosnick, T. R. Freed, K. Meredith, S. C. 2018-09-14 doi:10.1101/418137 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Discovery and characterization of variance QTLs in human induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/424192v1?rss=1 Sarkar, A. K. Tung, P.-Y. Blischak, J. D. Burnett, J. E. Li, Y. I. Stephens, M. Gilad, Y. 2018-09-23 doi:10.1101/424192 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Transsynaptic interactions between IgSF proteins DIP-α and Dpr10 are required for motor neuron targeting specificity in Drosophila ]]> https://biorxiv.org/content/10.1101/424416v1?rss=1 Ashley, J. Sorrentino, V. Nagarkar-Jaiswal, S. Tan, L. Xu, S. Xiao, Q. Zinn, K. Carrillo, R. A. 2018-09-21 doi:10.1101/424416 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Deeply conserved susceptibility in a multi-host, multi-parasite system ]]> https://biorxiv.org/content/10.1101/424549v1?rss=1 Barrow, L. N. McNew, S. M. Mitchell, N. Galen, S. C. Lutz, H. L. Skeen, H. Valqui, T. Weckstein, J. D. Witt, C. C. 2018-09-26 doi:10.1101/424549 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ 5-Hydroxymethylcytosines from Circulating Cell-free DNA as Diagnostic and Prognostic Markers for Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/424978v1?rss=1 Cai, J. Chen, L. Zhang, Z. Zhang, X. Lu, X. Liu, W. Shi, G. Ge, Y. Gao, P. Yang, Y. Ke, A. Xiao, L. Dong, R. Zhu, Y. Yang, X. Wang, J. Zhu, T. Yang, D. Huang, X. Sui, C. Qiu, S. Shen, F. Sun, H. Zhou, W. Zhou, J. Nie, J. Zhang, X. Chiu, B. C.-H. Lau, W. Y. He, C. Wang, H. Zhang, W. Fan, J. 2018-09-23 doi:10.1101/424978 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Trans effects on gene expression can drive omnigenic inheritance ]]> https://biorxiv.org/content/10.1101/425108v1?rss=1 Liu, X. Li, Y. I. Pritchard, J. K. 2018-09-24 doi:10.1101/425108 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Differential expression and homotypic enrichment of a classic Cadherin directs tissue-level contractile asymmetry during neural tube closure ]]> https://biorxiv.org/content/10.1101/425165v1?rss=1 Hashimoto, H. Munro, E. M. 2018-09-26 doi:10.1101/425165 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Novel 5-Hydroxymethylcytosine Markers for Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/425983v1?rss=1 850,000 CpG sites) in 17 pairs of tumor/adjacent tissue samples from US patients.nnRESULTSWe demonstrated distinctive distributions of 5hmC in tissues, and substantial differences between tumor and adjacent tissues, suggesting their diagnostic/prognostic value of for PaC.nnCONCLUSIONThis study established the potential of 5hmC as a novel epigenetic biomarker for PaC. ]]> Zeng, C. Zhang, Z. Wang, J. Chiu, B. C.-H. Hou, L. Zhang, W. 2018-09-25 doi:10.1101/425983 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Gata4 drives Hh-signaling for second heart field migration and outflow tract development ]]> https://biorxiv.org/content/10.1101/427336v1?rss=1 Liu, J. Cheng, H. Xiang, M. Zhou, L. Zhang, K. Moskowitz, I. P. Xie, L. 2018-09-25 doi:10.1101/427336 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Shared and distinct genetic risk factors for childhood onset and adult onset asthma ]]> https://biorxiv.org/content/10.1101/427427v1?rss=1 Pividori, M. Schoettler, N. Nicolae, D. L. Ober, C. Im, H. K. 2018-09-26 doi:10.1101/427427 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Untangling the dynamics of persistence and colonization in microbial communities ]]> https://biorxiv.org/content/10.1101/427542v1?rss=1 Ranjeva, S. L. Mihaljevic, J. R. Joseph, M. B. Giuliano, A. R. Dwyer, G. 2018-09-26 doi:10.1101/427542 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Transcriptional initiation and mechanically driven self-propagation of a tissue contractile wave during axis elongation ]]> https://biorxiv.org/content/10.1101/430512v1?rss=1 Bailles, A. Collinet, C. Philippe, J.-M. Lenne, P.-F. Munro, E. Lecuit, T. 2018-09-29 doi:10.1101/430512 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Discrete stepping and nonlinear ramping dynamics underlie spiking responses of LIP neurons during decision-making ]]> https://biorxiv.org/content/10.1101/433458v1?rss=1 Zoltowski, D. M. Latimer, K. W. Yates, J. L. Huk, A. C. Pillow, J. W. 2018-10-02 doi:10.1101/433458 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[ Existence and implications of population variance structure ]]> https://biorxiv.org/content/10.1101/439661v1?rss=1 Musharoff, S. Park, D. S. Dahl, A. Galanter, J. M. Liu, X. Huntsman, S. Eng, C. Burchard, E. G. Ayroles, J. F. Zaitlen, N. 2018-10-11 doi:10.1101/439661 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ A simple microbiome in esophagus and gills of the European common cuttlefish, Sepia officinalis ]]> https://biorxiv.org/content/10.1101/440677v1?rss=1 Lutz, H. L. Ramirez-Puebla, T. Abbo, L. Schlundt, C. Sjaarda, A. K. Durand, A. Hanlon, R. T. Gilbert, J. Mark Welch, J. L. 2018-10-11 doi:10.1101/440677 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus ]]> https://biorxiv.org/content/10.1101/442541v1?rss=1 Crosson, S. Herrou, J. Willett, J. Fiebig, A. Varesio, L. Czyz, D. Cheng, J. Ultee, E. Briegel, A. Bigelow, L. Babnigg, G. Kim, Y. 2018-10-13 doi:10.1101/442541 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Microbial and Metabolic Succession on Common Building Materials Under High Humidity Conditions ]]> https://biorxiv.org/content/10.1101/444521v1?rss=1 Lax, S. Cardona, C. Zhao, D. Winton, V. J. Goodney, G. Gao, P. Gottel, N. Hartmann, E. M. Henry, C. Thomas, P. M. Kelley, S. T. Stephens, B. Gilbert, J. A. 2018-10-17 doi:10.1101/444521 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Cytoarchitecture and Layer Estimation in High-Resolution Neuroanatomical Images ]]> https://biorxiv.org/content/10.1101/445742v1?rss=1 LaGrow, T. J. Moore, M. G. Prasad, J. A. Webber, A. Davenport, M. A. Dyer, E. L. 2018-10-17 doi:10.1101/445742 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Functional Morphology of Endurance Swimming Performance and Gait Transition Strategies in Balistoid Fishes ]]> https://biorxiv.org/content/10.1101/446526v1?rss=1 George, A. B. Westneat, M. W. 2018-10-17 doi:10.1101/446526 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ A genome-wide analysis of adhesion in Caulobacter crescentus identifies new regulatory and biosynthetic components for holdfast assembly ]]> https://biorxiv.org/content/10.1101/446781v1?rss=1 Hershey, D. M. Fiebig, A. Crosson, S. 2018-10-18 doi:10.1101/446781 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis ]]> https://biorxiv.org/content/10.1101/447367v1?rss=1 Vosa, U. Claringbould, A. Westra, H.-J. Bonder, M. J. Deelen, P. Zeng, B. Kirsten, H. Saha, A. Kreuzhuber, R. Kasela, S. Pervjakova, N. Alvaes, I. Fave, M.-J. Agbessi, M. Christiansen, M. Jansen, R. Seppälä, I. Tong, L. Teumer, A. Schramm, K. Hemani, G. Verlouw, J. Yaghootkar, H. Sönmez, R. Andrew, A. A. Kukushkina, V. Kalnapenkis, A. Rüeger, S. Porcu, E. Kronberg-Guzman, J. Kettunen, J. Powell, J. Lee, B. Zhang, F. Arindrarto, W. Beutner, F. BIOS Consortium, Brugge, H. i2QTL Consortium, Dmitrieva, J. Elansary, M. Fairfax, B. P. Georges, M. He 2018-10-19 doi:10.1101/447367 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Cyclical environments drive variation in life history strategies: a general theory of cyclical phenology ]]> https://biorxiv.org/content/10.1101/450387v1?rss=1 Park, J. S. 2018-10-23 doi:10.1101/450387 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ High-dimensional representation of texture in the somatosensory cortex of primates ]]> https://biorxiv.org/content/10.1101/451187v1?rss=1 Lieber, J. D. Bensmaia, S. 2018-10-23 doi:10.1101/451187 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Permutation methods for assessing significance in binary trait association mapping with structured samples ]]> https://biorxiv.org/content/10.1101/451377v1?rss=1 Mbatchou, J. Abney, M. McPeek, M. S. 2018-10-24 doi:10.1101/451377 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Ddx3x regulates B-cell development and light chain recombination in mice ]]> https://biorxiv.org/content/10.1101/452086v1?rss=1 Liu, K. Tuazon, J. Karmele, E. Krishnamurthy, D. Perlot, T. Foong-Sobis, M. Karns, R. Mandal, M. Reynaud, D. Scofield, R. H. Penninger, J. Harley, J. Waggoner, S. 2018-10-25 doi:10.1101/452086 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Activation of dopamine receptor 2 (DRD2) prompts transcriptomic and metabolic plasticity in glioblastoma ]]> https://biorxiv.org/content/10.1101/454389v1?rss=1 Caragher, S. P. Shireman, J. M. Huang, M. Miska, J. Baisiwala, S. Park, C. Saathoff, M. Warnke, L. Xiao, T. Lesniak, M. S. James, C. D. Meltzer, H. Tryba, A. K. Ahmed, A. U. 2018-11-09 doi:10.1101/454389 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ An ancient role for Collier/Olf/Ebf (COE)-type transcription factors in axial motor neuron development ]]> https://biorxiv.org/content/10.1101/454926v1?rss=1 Catela, C. Correa, E. Aburas, J. Croci, L. Consalez, G. Kratsios, P. 2018-10-27 doi:10.1101/454926 Cold Spring Harbor Laboratory Press 2018-10-27 <![CDATA[ A diallel of the mouse Collaborative Cross founders reveals strong strain-specific maternal effects on litter size ]]> https://biorxiv.org/content/10.1101/458877v1?rss=1 Shorter, J. R. Maurizio, P. L. Bell, T. A. Shaw, G. D. Miller, D. R. Gooch, T. J. Spence, J. S. McMillan, L. Valdar, W. Pardo-Manuel de Villena, F. 2018-10-31 doi:10.1101/458877 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ White Matter Microstructure Correlates of General and Specific Second-Order Factors of Psychopathology ]]> https://biorxiv.org/content/10.1101/459396v1?rss=1 Hinton, K. E. Lahey, B. B. Villalta-Gil, V. Meyer, F. A. C. Burgess, L. L. Chodes, L. K. Applegate, B. Van Hulle, C. A. Landman, B. A. Zald, D. H. 2018-11-01 doi:10.1101/459396 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Does batrachotoxin autoresistance co-evolve with toxicity in Phyllobates poison-dart frogs? ]]> https://biorxiv.org/content/10.1101/460865v1?rss=1 Marquez, R. Ramirez-Castaneda, V. Amezquita, A. 2018-11-03 doi:10.1101/460865 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ Rapid Geometric Feature Signaling In The Spiking Activity Of A Complete Population Of Tactile Nerve Fibers ]]> https://biorxiv.org/content/10.1101/461095v1?rss=1 Delhaye, B. P. Xia, X. Bensmaia, S. J. 2018-11-03 doi:10.1101/461095 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra ]]> https://biorxiv.org/content/10.1101/461517v1?rss=1 Rice, D. P. Novembre, J. Desai, M. M. 2018-11-03 doi:10.1101/461517 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ A new family of neural wiring receptors across bilaterians defined by phylogenetic, biochemical and structural evidence ]]> https://biorxiv.org/content/10.1101/462036v1?rss=1 Cheng, S. Park, Y. Kurleto, J. D. Jeon, M. Zinn, K. Thornton, J. W. Özkan, E. 2018-11-05 doi:10.1101/462036 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ The spermidine acetyltransferase SpeG regulates transcription of the small RNA RprA ]]> https://biorxiv.org/content/10.1101/462937v1?rss=1 Hu, L. I. Filippova, E. V. Dang, J. Pshenychnyi, S. Ruan, J. Kiryukhina, O. Anderson, W. F. Kuhn, M. L. Wolfe, A. 2018-11-05 doi:10.1101/462937 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Proprioceptive neurons of larval Drosophila melanogaster show direction selective activity requiring the mechanosensory channel TMC. ]]> https://biorxiv.org/content/10.1101/463216v1?rss=1 He, L. Gulyanon, S. Mihovilovic Skanata, M. Karagyozov, D. Heckscher, E. Krieg, M. Tschekpenakis, G. Gershow, M. Tracey, D. 2018-11-09 doi:10.1101/463216 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ The association between weight at birth and breast cancer risk revisited using Mendelian randomisation ]]> https://biorxiv.org/content/10.1101/464115v1?rss=1 Kar, S. P. Andrulis, I. L. Brenner, H. Burgess, S. Chang-Claude, J. Considine, D. Doerk, T. Evans, D. G. R. Gago-Dominguez, M. Giles, G. G. Hartman, M. Huo, D. Kaaks, R. Li, J. Lophatananon, A. Margolin, S. Milne, R. L. Muir, K. R. Olsson, H. Punie, K. Radice, P. Simard, J. Tamimi, R. M. Van Nieuwenhuysen, E. Wendt, C. Wei, Z. Pharoah, P. D. P. 2018-11-09 doi:10.1101/464115 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ The association between low-density lipoprotein cholesterol predicted by HMGCR genetic variants and breast cancer risk may be mediated by body mass index ]]> https://biorxiv.org/content/10.1101/464446v1?rss=1 Kar, S. P. Brenner, H. Giles, G. G. Huo, D. Milne, R. L. Rennert, G. Simard, J. Zheng, W. Burgess, S. Pharoah, P. D. P. 2018-11-09 doi:10.1101/464446 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Genomic architecture and introgression shape a butterfly radiation ]]> https://biorxiv.org/content/10.1101/466292v1?rss=1 Edelman, N. B. Frandsen, P. Miyagi, M. Clavijo, B. J. Davey, J. Dikow, R. Garcia Accinelli, G. Van Belleghem, S. Patterson, N. J. Neafsey, D. E. Challis, R. J. Kumar, S. Moreira, G. Salazar, C. Chouteau, M. Counterman, B. Papa, R. Blaxter, M. Reed, R. D. Dasmahapatra, K. Kronforst, M. Joron, M. Jiggins, C. D. McMillan, W. O. Di-Palma, F. Blumberg, A. J. Wakeley, J. Jaffe, D. Mallet, J. 2018-11-08 doi:10.1101/466292 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/466631v1?rss=1 Gallego Romero, I. Gopalakrishnan, S. Gilad, Y. 2018-11-09 doi:10.1101/466631 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Phenome-wide investigation of health outcomes associated with genetic predisposition to loneliness ]]> https://biorxiv.org/content/10.1101/468835v1?rss=1 Abdellaoui, A. Sanchez-Roige, S. Sealock, J. Treur, J. L. Dennis, J. Fontanillas, P. Elson, S. The 23andme Research Team, Nivard, M. G. Ip, H. F. van der Zee, M. Baselmans, B. Hottenga, J. J. Willemsen, G. Mosing, M. Yu, L. Pedersen, N. L. Amin, N. van Duijn, C. M. Szilagyi, I. Tiemeier, H. Neumann, A. Verweij, K. Cacioppo, S. Cacioppo, J. T. Davis, L. K. Palmer, A. A. Boomsma, D. I. 2018-11-14 doi:10.1101/468835 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Mechanism of Mycolactone Toxin Membrane Permeation: Atomistic vs Coarse-Grained MARTINI Simulations ]]> https://biorxiv.org/content/10.1101/470807v1?rss=1 Aydin, F. Sun, R. Swanson, J. M. J. 2018-11-14 doi:10.1101/470807 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits ]]> https://biorxiv.org/content/10.1101/471748v1?rss=1 Wheeler, H. E. Ploch, S. Barbeira, A. N. Bonazzola, R. Siahpirani, A. F. Saha, A. Battle, A. Roy, S. Im, H. K. 2018-11-19 doi:10.1101/471748 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Insect egg size and shape evolve with ecology, not developmental rate ]]> https://biorxiv.org/content/10.1101/471946v1?rss=1 Church, S. H. Donoughe, S. de Medeiros, B. A. S. Extavour, C. G. 2018-11-29 doi:10.1101/471946 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ A database of egg size and shape from more than 6,700 insect species ]]> https://biorxiv.org/content/10.1101/471953v1?rss=1 Church, S. H. Donoughe, S. de Medeiros, B. A. D. Extavour, C. G. 2018-11-19 doi:10.1101/471953 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability ]]> https://biorxiv.org/content/10.1101/474684v1?rss=1 van de Geijn, B. Finucane, H. Gazal, S. Hormozdiari, F. Amariuta, T. Liu, X. Gusev, A. Loh, P.-R. Reshef, Y. Kichaev, G. Raychauduri, S. Price, A. 2018-11-20 doi:10.1101/474684 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates ]]> https://biorxiv.org/content/10.1101/474841v1?rss=1 Eres, I. E. Luo, K. Hsiao, C. J. Blake, L. E. Gilad, Y. 2018-11-20 doi:10.1101/474841 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ T cells instruct dendritic cells to produce inflammasome independent IL-1β causing systemic inflammation ]]> https://biorxiv.org/content/10.1101/475517v1?rss=1 Jain, A. Irizarry-Caro, R. A. Chawla, A. S. Philip, N. H. Carroll, K. R. Katz, J. Oberst, A. Chervonsky, A. Pasare, C. 2018-11-26 doi:10.1101/475517 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Ecological networks: Pursuing the shortest path, however narrow and crooked ]]> https://biorxiv.org/content/10.1101/475715v1?rss=1 Costa, A. Martin Gonzalez, A. M. Guizien, K. Doglioli, A. M. Gomez, J. M. Petrenko, A. Allesina, S. 2018-11-27 doi:10.1101/475715 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Size, shape and structure of insect wings ]]> https://biorxiv.org/content/10.1101/478768v1?rss=1 Salcedo, M. K. Hoffmann, J. Donoughe, S. Mahadevan, L. 2018-11-26 doi:10.1101/478768 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/content/10.1101/484113v1?rss=1 Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. Grove, J. Klei, L. Stevens, C. Reichert, J. Mulhern, M. Artomov, M. Gerges, S. Sheppard, B. Xu, X. Bhaduri, A. Norman, U. Brand, H. Schwartz, G. Nguyen, R. Guerrero, E. Dias, C. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Natural selection contributed to immunological differences between human hunter-gatherers and agriculturalists ]]> https://biorxiv.org/content/10.1101/487207v1?rss=1 Harrison, G. F. Sanz, J. Boulais, J. Mina, M. J. Grenier, J.-C. Leng, Y. Dumaine, A. Yotova, V. Bergey, C. M. Elledge, S. J. Schurr, E. Quintana-Murci, L. Perry, G. H. Barreiro, L. B. 2018-12-04 doi:10.1101/487207 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ A comparison of gene expression and DNA methylation patterns across tissues and species ]]> https://biorxiv.org/content/10.1101/487413v1?rss=1 Blake, L. E. Roux, J. Hernando-Herraez, I. Banovich, N. E. Garcia Perez, R. Hsiao, C. J. Eres, I. Chavarria, C. Marques-Bonet, T. Gilad, Y. 2018-12-04 doi:10.1101/487413 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape of human ovarian cancer via a multi-omics integrative analysis ]]> https://biorxiv.org/content/10.1101/488833v1?rss=1 Song, X. Ji, J. Gleason, K. J. Martignetti, J. A. Chen, L. S. Wang, P. 2018-12-06 doi:10.1101/488833 Cold Spring Harbor Laboratory Press 2018-12-06 <![CDATA[ Immune potentiator for increased safety and improved protection of vaccines by NF-kB modulation ]]> https://biorxiv.org/content/10.1101/489732v1?rss=1 Moser, B. A. Steinhardt, R. C. Escalante-Buendia, Y. Bolt, D. A. Barker, K. M. Yoo, S. McGonnigal, B. G. Esser-Kahn, A. P. 2018-12-10 doi:10.1101/489732 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Uncovering the role admixture in health disparity: characterization of hepatocyte gene expression and DNA methylation in African-Americans ]]> https://biorxiv.org/content/10.1101/491225v1?rss=1 Park, S. C. De, T. Xu, Y. Zhoug, Y. Smithberger, E. Alarcon, C. Perera, M. 2018-12-09 doi:10.1101/491225 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Quantification of microenvironmental metabolites in murine cancer models reveals determinants of tumor nutrient availability ]]> https://biorxiv.org/content/10.1101/492652v1?rss=1 118 metabolites in plasma and tumor interstitial fluid, the extracellular fluid that perfuses tumors. Comparison of nutrient levels in tumor interstitial fluid and plasma revealed that the nutrients available to tumors differ from those present in circulation. Further, by comparing interstitial fluid nutrient levels between autochthonous and transplant models of murine pancreatic and lung adenocarcinoma, we found that tumor type, anatomical location and animal diet affect local nutrient availability. These data provide a comprehensive characterization of the nutrients present in the tumor microenvironment of widely used models of lung and pancreatic cancer and identify factors that influence metabolite levels in tumors.nnImpact StatementNutrient availability is an important tumor microenvironmental factor that impacts cancer cell biology; we developed methods to measure nutrients available to tumor cells and characterized factors that influence tumor nutrient availability. ]]> Sullivan, M. R. Danai, L. V. Lewis, C. A. Chan, S. H. Gui, D. Y. Kunchok, T. Dennstedt, E. A. Vander Heiden, M. G. Muir, A. 2018-12-10 doi:10.1101/492652 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Mechanical and kinetic factors drive sorting of F-actin crosslinkers on bundles ]]> https://biorxiv.org/content/10.1101/493841v1?rss=1 Freedman, S. L. Suarez, C. Winkelman, J. D. Kovar, D. R. Voth, G. A. Dinner, A. R. Hocky, G. M. 2018-12-11 doi:10.1101/493841 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Imputation of single-cell gene expression with an autoencoder neural network ]]> https://biorxiv.org/content/10.1101/504977v1?rss=1 Badsha, M. B. Li, R. Liu, B. Li, Y. I. Xian, M. Banovich, N. E. Fu, A. Q. 2018-12-29 doi:10.1101/504977 Cold Spring Harbor Laboratory Press 2018-12-29 <![CDATA[ WDR76 promotes MLL-rearranged leukemia via selective recognition of 5-hydroxymethylcytosine in DNA ]]> https://biorxiv.org/content/10.1101/511394v1?rss=1 Malecek, K. E. Weng, H. Sullivan, M. A. Kokontis, C. Y. Werner, M. S. Chen, J. Ruthenburg, A. J. 2019-01-03 doi:10.1101/511394 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types ]]> https://biorxiv.org/content/10.1101/513598v1?rss=1 Nadadur, R. D. Perez-Cervantes, C. Lonfat, N. Smith, L. A. Hughes, A. E. O. Wang, S. Corbo, J. C. Cepko, C. L. Moskowitz, I. P. 2019-01-07 doi:10.1101/513598 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ RegSNPs-Intron: A Computational Framework For Prioritizing Intronic Single Nucleotide Variants in Human Genetic Disease ]]> https://biorxiv.org/content/10.1101/515171v1?rss=1 Lin, H. Hargreaves, K. A. Li, R. Reiter, J. L. Mort, M. Cooper, D. N. Zhou, Y. Eadon, M. T. Dolan, M. E. Ipe, J. Skaar, T. Liu, Y. 2019-01-09 doi:10.1101/515171 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes ]]> https://biorxiv.org/content/10.1101/521054v1?rss=1 Fachal, L. Aschard, H. Beesley, J. Barnes, D. Allen, J. Kar, S. Pooley, K. Dennis, J. Michailidou, K. Turman, C. Soucy, P. Lemacon, A. Lush, M. Tyrer, J. Ghoussaini, M. Moradi Marjaneh, M. Jiang, X. Agata, S. Aittomaki, K. Alonso, M. R. Andrulis, I. Anton-Culver, H. Antonenkova, N. Arason, A. Arndt, V. Aronson, K. Arun, B. Auber, B. Auer, P. Azzollini, J. Balmana, J. Barkardottir, R. Barrowdale, D. Beeghly-Fadiel, A. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Blot, W. Bogdanova, N. Bojesen, S. Bolla, M. Bonanni, B. Borg, A. B 2019-01-15 doi:10.1101/521054 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ A DNA-based voltmeter for organelles ]]> https://biorxiv.org/content/10.1101/523019v1?rss=1 Saminathan, A. Devany, J. Pillai, K. S. Veetil, A. T. Schwake, M. Krishnan, Y. 2019-01-16 doi:10.1101/523019 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[ The role of Caulobacter cell surface structures in colonization of the air-liquid interface ]]> https://biorxiv.org/content/10.1101/524058v1?rss=1 Fiebig, A. 2019-01-18 doi:10.1101/524058 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Identifying Genomic Islands with Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/525030v1?rss=1 Assaf, R. Xia, F. Stevens, R. 2019-01-20 doi:10.1101/525030 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis ]]> https://biorxiv.org/content/10.1101/526848v1?rss=1 Hsiao, C. J. Tung, P. Blischak, J. D. Burnett, J. Barr, K. Dey, K. K. Stephens, M. Gilad, Y. 2019-02-03 doi:10.1101/526848 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth ]]> https://biorxiv.org/content/10.1101/527036v1?rss=1 He, Y. Chang, Y. Bao, L. Yu, M. Li, R. Niu, J. Fan, G. Song, W. Seim, I. Qin, Y. Li, X. Liu, J. Kong, X. Peng, M. Sun, M. Wang, M. Qu, J. Wang, X. Liu, X. Wu, X. Zhao, X. Wang, X. Zhao, Y. Guo, J. Liu, Y. Liu, K. Wang, Y. Zhang, H. Liu, L. Wang, M. Yu, H. Wang, X. Cheng, J. Wang, Z. Xu, X. Wang, J. Yang, H. Lee, S. M.-Y. Liu, X. Zhang, Q. Qi, J. 2019-01-22 doi:10.1101/527036 Cold Spring Harbor Laboratory Press 2019-01-22 <![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[ Loss of CIC promotes mitotic dysregulation and chromosome segregation defects ]]> https://biorxiv.org/content/10.1101/533323v1?rss=1 Chittaranjan, S. Song, J. Chan, S. Y. Lee, S. D. Ahmad, S. T. Brothers, W. Corbett, R. D. Gagliardi, A. Lum, A. Moradian, A. Pleasance, S. Coope, R. Cairncross, J. G. Yip, S. Laks, E. Aparicio, S. A. Chan, J. A. Hughes, C. S. Morin, G. B. LeBlanc, V. G. Marra, M. A. 2019-01-29 doi:10.1101/533323 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Genetically Increased Telomere Length and Aging-related Physical and Cognitive Traits in the UK Biobank ]]> https://biorxiv.org/content/10.1101/538124v1?rss=1 50 aging-related traits from UKB and restricted to unrelated participants of British ancestry (n=337,522). We estimated GI-TL as a linear combination of nine TL-associated SNPs, each weighted by its previously-reported association with leukocyte TL. Regression models were used to assess the associations between GI-TL and each trait. We obtained MR estimates using the two-sample inverse variance weighted (IVW) approach. ResultsWe identified 5 age-related traits associated with GI-TL (Bonferroni-corrected threshold p<0.001): pulse pressure (PP) (p=5.2x10-14), systolic blood pressure (SBP) (p=2.9x10-15), diastolic blood pressure (DBP) (p=5.5x10-6), forced expiratory volume (FEV1) (p= p=0.0001), and forced vital capacity (FVC) (p=3.8x10-6). Under MR assumptions, one standard deviation increase in TL ([~]1200 base pairs) increased PP, SBP, and DBP by 1.5, 2.3, and 0.8 mmHg, respectively, while FEV1 and FVC increased by 34.7 and 52.2 mL, respectively. The observed associations appear unlikely to be due to selection bias based on analyses including inverse probability weights and analyses of simulated data. ConclusionsThese findings suggest that longer TL increases pulmonary function and blood pressure traits. Further research is necessary to evaluate TL in cardiovascular and pulmonary age-related decline. KEY MESSAGESO_LITelomere length (TL) is a potential biomarker and cause of aging, however, the causal relationship between TL and aging-related traits has not been thoroughly examined using a Mendelian randomization (MR) approach. C_LIO_LIWe evaluated genetically increased TL (GI-TL) and its association with over 50 aging-related traits in the UK Biobank cohort using regression models and MR approaches. C_LIO_LIPulmonary function (FEV1 and FVC) and blood pressure (SBP, DBP, and PP) traits were positively associated with GI-TL in the expected and unexpected direction, respectively. C_LIO_LIUsing inverse probability weights to account for the non-representativeness of the UKB, our observed associations for GI-TL with blood pressure traits and pulmonary function persisted. C_LIO_LIUsing simulated data to examine study selection as a potential source of collider bias, we concluded that selection bias was unlikely to explain the observed associations. C_LI ]]> Demanelis, K. Tong, L. Pierce, B. L. 2019-02-01 doi:10.1101/538124 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Multiscale model of integrin adhesion assembly ]]> https://biorxiv.org/content/10.1101/542266v1?rss=1 Bidone, T. C. Skeeters, A. V. Oakes, P. W. Voth, G. A. 2019-02-06 doi:10.1101/542266 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Horizontal transfer of prokaryotic cytolethal distending toxin B genes to eukaryotes ]]> https://biorxiv.org/content/10.1101/544197v1?rss=1 40 million years ago and encode a protein that retains ancestral DNase activity. This phage-derived toxin has been domesticated by diverse insects and we hypothesize that it is used as a defensive weapon against parasitoid wasps. One Sentence SummaryWe report horizontal transfer of the gene cytolethal distending toxin B, which encodes a DNase, into eukaryotic genomes from bacteriophage. SignificanceCytolethal distending toxins (CDTs) are secreted by diverse pathogenic bacterial species to kill animal cells. The cdtB subunit enters cell nuclei, damaging the DNA and leading to mitotic arrest and apoptosis. In the pea aphid, a bacterial endosymbiont provides protection against wasp attack, possibly via cdtB. We discovered that this same endosymbiont-encoded lineage of cdtB was transferred to the genomes of Diptera and Hemiptera species and retains ancestral DNase activity. This is the first report of cdtB outside of bacteria or phages. A toxin that first evolved to kill eukaryotic cells has been co-opted by insects, potentially to their benefit. ]]> Verster, K. I. Wisecaver, J. H. Duncan, R. P. Karageorgi, M. Gloss, A. D. Armstrong, E. Price, D. K. Menon, A. R. Ali, Z. M. Whiteman, N. K. 2019-02-08 doi:10.1101/544197 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Quantifying the impact of genetically regulated expression on complex traits and diseases ]]> https://biorxiv.org/content/10.1101/546580v1?rss=1 Cai, M. Chen, L. Liu, J. Yang, C. 2019-02-11 doi:10.1101/546580 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ A dataset to explore kinase control of environmental stress responsive transcription ]]> https://biorxiv.org/content/10.1101/547356v1?rss=1 Mace, K. Krakowiak, J. El-Samad, H. Pincus, D. 2019-02-12 doi:10.1101/547356 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Propagating patterns of activity across motor cortex facilitate movement initiation ]]> https://biorxiv.org/content/10.1101/549568v1?rss=1 Balasubramanian, K. Papadourakis, V. Liang, W. Takahashi, K. Best, M. D. Suminski, A. J. Hatsopoulos, N. G. 2019-02-14 doi:10.1101/549568 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Brucella EipB is periplasmic β-spiral protein required for envelope stress resistance and infection ]]> https://biorxiv.org/content/10.1101/551135v1?rss=1 Herrou, J. Willett, J. Fiebig, A. Czyz, D. Cheng, J. Ultee, E. Briegel, A. Bigelow, L. Babnigg, G. Kim, Y. Crosson, S. 2019-02-16 doi:10.1101/551135 Cold Spring Harbor Laboratory Press 2019-02-16 <![CDATA[ Social history and exposure to pathogen signals modulate social status effects on gene regulation in rhesus macaques ]]> https://biorxiv.org/content/10.1101/552356v1?rss=1 Sanz, J. Maurizio, P. L. Snyder-Mackler, N. Simons, N. D. Voyles, T. Kohn, J. Michopoulos, V. Wilson, M. Tung, J. Barreiro, L. B. 2019-02-18 doi:10.1101/552356 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Regulation of bacterial surface attachment by a network of sensory transduction proteins ]]> https://biorxiv.org/content/10.1101/554154v1?rss=1 Reyes Ruiz, L. M. Fiebig, A. Crosson, S. 2019-02-18 doi:10.1101/554154 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Varying crosslinking motifs drive the mesoscale mechanics of actin-microtubule composites ]]> https://biorxiv.org/content/10.1101/554584v1?rss=1 Ricketts, S. N. Francis, M. L. Farhadi, L. Rust, M. J. Das, M. Ross, J. L. Robertson-Anderson, R. M. 2019-02-19 doi:10.1101/554584 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ The Effects of Mutations are Modified by Genetic Background in Mice ]]> https://biorxiv.org/content/10.1101/555383v1?rss=1 Rau, C. D. Gonzales, N. M. Park, D. Palmer, A. A. Lusis, A. J. Zaitlen, N. 2019-02-19 doi:10.1101/555383 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ How prolonged expression of Hunchback, a temporal transcription factor, re-wires locomotor circuits ]]> https://biorxiv.org/content/10.1101/556209v1?rss=1 Heckscher, E. Meng, J. L. Marshall, Z. D. Lobb-Rabe, M. 2019-02-20 doi:10.1101/556209 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Feeding kinematics and morphology of the alligator gar (Atractosteus spatula, Lacepede, 1803) ]]> https://biorxiv.org/content/10.1101/561993v1?rss=1 Lemberg, J. B. Shubin, N. H. Westneat, M. W. 2019-02-27 doi:10.1101/561993 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Signatures of divergent antimalarial treatment responses in peripheral blood from infants and adults in Malawi ]]> https://biorxiv.org/content/10.1101/564757v1?rss=1 18 years old), we assessed blood cytokine levels and characterized monocyte and dendritic cell frequencies at two timepoints: acute infection, and four weeks post antimalarial treatment. We modeled the effects of age group, sex, and timepoint, and evaluated the role of these factors on infection and treatment outcomes. ResultsRegardless of treatment timepoint, in our population age was significantly associated with overall blood hemoglobin, which was higher in adults, and plasma nitric oxide, IL-10, and TNF- levels, which were higher in infants. We found a significant effect of age on the hemoglobin treatment response, whereby after treatment, levels increased in infants and decreased in adults. Furthermore, we observed significant age-specific effects on treatment response for overall parasite load, IFN-{gamma} and IL-12(p40), and these effects were sex-dependent. We uncovered significant age effects on the overall levels and treatment response of myeloid dendritic cell frequencies. In addition, within each age group, we found continuous age effects on gametocyte levels (Pfs16), TNF-, and nitric oxide. ConclusionsIn a clinical study of infants and adults experiencing natural malaria infection and receiving antimalarial treatment, we identified age-specific signatures of infection and treatment responses in peripheral blood. We describe host markers that may indicate, and potentially mediate, differential post-treatment outcomes for malaria in infants versus adults. ]]> Maurizio, P. L. Fuseini, H. Tegha, G. Hosseinipour, M. De Paris, K. 2019-03-01 doi:10.1101/564757 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Supercharged Assembly: A Broad-Spectrum Mechanism of Action for Drugs that Undermine Controlled HIV-1 Viral Capsid Formation ]]> https://biorxiv.org/content/10.1101/565515v1?rss=1 Pak, A. J. Grime, J. M. A. Yu, A. Voth, G. A. 2019-03-01 doi:10.1101/565515 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations ]]> https://biorxiv.org/content/10.1101/566489v1?rss=1 Drayman, N. Patel, P. Vistain, L. Tay, S. 2019-03-05 doi:10.1101/566489 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Postural representations of the hand in primate sensorimotor cortex ]]> https://biorxiv.org/content/10.1101/566539v1?rss=1 Goodman, J. M. Tabot, G. A. Lee, A. S. Suresh, A. K. Rajan, A. T. Hatsopoulos, N. G. Bensmaia, S. J. 2019-03-05 doi:10.1101/566539 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Complex polymorphic genetic architecture underlies trans-regulatory variation among strains of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/566653v1?rss=1 Metzger, B. P. H. Wittkopp, P. J. 2019-03-04 doi:10.1101/566653 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Single-cell RNA-seq reveals spatially restricted multicellular fibrotic niches during lung fibrosis ]]> https://biorxiv.org/content/10.1101/569855v1?rss=1 Joshi, N. Watanabe, S. Verma, R. Jablonski, R. P. Chen, C.-I. Cheresh, P. Reyfman, P. A. McQuattie-Pimentel, A. C. Sichizya, L. Flozak, A. S. Gottardi, C. J. Cuda, C. M. Perlman, H. Jain, M. Kamp, D. W. Budinger, G. S. Misharin, A. V. 2019-03-06 doi:10.1101/569855 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Fractionation of impulsive and compulsive trans-diagnostic phenotypes and their longitudinal associations ]]> https://biorxiv.org/content/10.1101/570218v1?rss=1 Chamberlain, S. R. Tiego, J. Fontenelle, L. Hook, R. Segrave, R. Hauser, T. Dolan, R. Goodyer, I. Bullmore, E. Grant, J. Yucel, M. 2019-03-06 doi:10.1101/570218 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Evolutionary patterns of the chimerical retrogenes in Oryza ]]> https://biorxiv.org/content/10.1101/573501v1?rss=1 Zhou, Y. Song, H. Xiao, J. Zhang, Q. Long, M. Zhang, C. 2019-03-11 doi:10.1101/573501 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Cultured pluripotent planarian stem cells retain potency and express proteins from exogenously introduced mRNAs ]]> https://biorxiv.org/content/10.1101/573725v1?rss=1 Sanchez Alvarado, A. Lei, K. McKinney, S. A. Ross, E. J. Lee, H.-C. 2019-03-12 doi:10.1101/573725 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Single-base mapping of m6A by an antibody-independent method ]]> https://biorxiv.org/content/10.1101/575555v1?rss=1 Zhang, Z. Chen, L.-Q. Zhao, Y.-L. Yang, C.-G. Roundtree, I. A. Zhang, Z. Ren, J. Xie, W. He, C. Luo, G.-Z. 2019-03-13 doi:10.1101/575555 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Nonlinear mixed selectivity supports reliable neural computation ]]> https://biorxiv.org/content/10.1101/577288v1?rss=1 Johnston, W. J. Palmer, S. E. Freedman, D. J. 2019-03-14 doi:10.1101/577288 Cold Spring Harbor Laboratory Press 2019-03-14 <![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[ Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits ]]> https://biorxiv.org/content/10.1101/579581v1?rss=1 Gleason, K. J. Yang, F. Pierce, B. He, X. Chen, L. S. 2019-03-16 doi:10.1101/579581 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Pyridox(am)ine 5’-phosphate oxidase deficiency induces seizures in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/580050v1?rss=1 A missense mutation in sgll - the Drosophila homolog of human PNPO (hPNPO) and found mutant (sgll95) flies exhibiting a lethal phenotype on a diet devoid of VB6. Here we report the establishment of both sgll95 and ubiquitous sgll knockdown (KD) flies as valid animal models of PNPO-deficiency-induced epilepsy. Both sgll95 and sgll KD flies exhibit spontaneous seizures before they die. Electrophysiological recordings reveal that seizures caused by PNPO deficiency have characteristics similar to that in flies treated with GABA antagonist picrotoxin. Both seizures and lethality are associated with low PLP levels and can be rescued by ubiquitous expression of wild-type sgll or hPNPO, suggesting the functional conservation of the PNPO enzyme between humans and flies. Results from cell type-specific sgll KD further demonstrate that PNPO in the brain is necessary for seizure prevention and survival. Our establishment of the first animal model of PNPO deficiency will lead to better understanding of VB6 biology, the PNPO gene and its mutations discovered in patients, and can be a cost-effective system to test therapeutic strategies. ]]> Chi, W. Iyengar, A. Albersen, M. Bosma, M. Verhoeven-Duif, N. M. Wu, C.-F. Zhuang, X. 2019-03-16 doi:10.1101/580050 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Vps34/PIK3C3 deletion in thyroid impairs thyroid hormonogenesis and autophagic flux ]]> https://biorxiv.org/content/10.1101/580142v1?rss=1 Grieco, G. Wang, T. Delcorte, O. Janssens, V. Spourquet, C. Strickaert, A. Gaide-Chevronnay, H. Liao, X.-H. Bilanges, B. Refetoff, S. Vanhaesebroeck, B. Maenhaut, C. Courtoy, P. Pierreux, C. 2019-03-16 doi:10.1101/580142 Cold Spring Harbor Laboratory Press 2019-03-16 <![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[ Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective ]]> https://biorxiv.org/content/10.1101/583104v1?rss=1 Marcus, J. H. Posth, C. Ringbauer, H. Lai, L. Skeates, R. Sidore, C. Beckett, J. Furtwängler, A. Olivieri, A. Chiang, C. Al-Asadi, H. Dey, K. Joseph, T. A. Der Sarkissian, C. Radzeviciute, R. Gradoli, M. G. Haak, W. Reich, D. Schlessinger, D. Cucca, F. Krause, J. Novembre, J. 2019-03-21 doi:10.1101/583104 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Local climate and social inequality drive spatio-temporal variation in malaria risk across a complex urban landscape ]]> https://biorxiv.org/content/10.1101/583880v1?rss=1 Santos-Vega, M. Lowe, R. Anselin, L. Desai, V. Vaishnav, K. G. Naik, A. Pascual, M. 2019-03-21 doi:10.1101/583880 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Visual area V4 encodes history dependent attentional effort and single-trial perceptual detection ]]> https://biorxiv.org/content/10.1101/584409v1?rss=1 Ghosh, S. Maunsell, J. H. R. 2019-03-21 doi:10.1101/584409 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation ]]> https://biorxiv.org/content/10.1101/585901v1?rss=1 Selewa, A. Dohn, R. Eckart, H. Lozano, S. Xie, B. Gauchat, E. Elorbany, R. Rhodes, K. Burnett, J. Gilad, Y. Pott, S. Basu, A. 2019-03-22 doi:10.1101/585901 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ The mechanisms of dynamin-actin interaction ]]> https://biorxiv.org/content/10.1101/586461v1?rss=1 Zhang, R. Gerassimov, N. Lee, D. M. Jimah, J. R. Kim, S. Luvsanjav, D. Winkelman, J. Mettlen, M. Abrams, M. E. Kalia, R. Keene, P. Pandey, P. Ravaux, B. Kim, J. H. Ditlev, J. A. Zhang, G. Rosen, M. K. Frost, A. Alto, N. M. Gardel, M. Schmid, S. L. Hinshaw, J. E. Chen, E. H. 2019-03-25 doi:10.1101/586461 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Multivariate Genome-wide Association Analyses Reveal the Genetic Basis of Seed Fatty Acid Composition in Oat (Avena sativa L.) ]]> https://biorxiv.org/content/10.1101/589952v1?rss=1 Carlson, M. O. Montilla-Bascon, G. Hoekenga, O. A. Tinker, N. A. Poland, J. Baseggio, M. Sorrells, M. Jannink, J.-L. Gore, M. A. Yeats, T. H. 2019-03-29 doi:10.1101/589952 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ NatB modulates Rb mutant cell death and tumor growth by regulating EGFR/MAPK signaling through the N-end rule pathways ]]> https://biorxiv.org/content/10.1101/590349v1?rss=1 Sheng, Z. Du, W. 2019-03-26 doi:10.1101/590349 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Oriented basement membrane fibrils provide a memory for F-actin planar polarization via the Dystrophin-Dystroglycan complex during tissue elongation ]]> https://biorxiv.org/content/10.1101/591628v1?rss=1 Cerqueira Campos, F. Alegot, H. Dennis, C. Fritsch, C. Isabella, A. Pouchin, P. Bardot, O. Horne-Badovinac, S. Mirouse, V. 2019-03-30 doi:10.1101/591628 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Multi-omics co-localization with genome-wide association studies reveals context-specific mechanisms of asthma risk variants ]]> https://biorxiv.org/content/10.1101/593558v1?rss=1 Soliai, M. Kato, A. Stanhope, C. T. Norton, J. E. Naughton, K. A. Klinger, A. I. Kern, R. C. Tan, B. K. Schleimer, R. P. Nicolae, D. L. Pinto, J. M. Ober, C. 2019-03-29 doi:10.1101/593558 Cold Spring Harbor Laboratory Press 2019-03-29 <![CDATA[ The human microbiota is associated with cardiometabolic risk across the epidemiologic transition ]]> https://biorxiv.org/content/10.1101/595934v1?rss=1 Fei, N. Bernabe, B. P. Lie, L. Baghdan, D. Bedu-Addo, K. Plange-Rhule, J. Forrester, T. E. Lambert, E. V. Bovet, P. Gottel, N. Riesen, W. Korte, W. Kliethermes, S. A. K. A. Luke, A. T. Layden, B. T. Gilbert, J. A. Dugas, L. R. 2019-04-01 doi:10.1101/595934 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ A role for Hypoxia Inducible Factor 1a (HIF1a) in intermittent hypoxia-dependent changes in spatial memory and synaptic plasticity ]]> https://biorxiv.org/content/10.1101/595975v1?rss=1 Arias-Cavieres, A. Khuu, M. A. Nwakudu, C. U. Barnard, J. E. Dalgin, G. Garcia, A. J. 2019-04-02 doi:10.1101/595975 Cold Spring Harbor Laboratory Press 2019-04-02 <![CDATA[ Predicting coexistence in experimental ecologicalcommunities ]]> https://biorxiv.org/content/10.1101/598326v1?rss=1 Maynard, D. S. Miller, Z. R. Allesina, S. 2019-04-04 doi:10.1101/598326 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Long-term intrahost evolution of methicillin-resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage ]]> https://biorxiv.org/content/10.1101/599431v1?rss=1 Azarian, T. Ridgway, J. P. Yin, Z. David, M. 2019-04-04 doi:10.1101/599431 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Composition of the holdfast polysaccharide from Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/602995v1?rss=1 Hershey, D. M. Porfirio, S. Heiss, C. Jaehrig, B. Azadi, P. Fiebig, A. Crosson, S. 2019-04-09 doi:10.1101/602995 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ RhoA mediates epithelial cell shape changes via mechanosensitive endocytosis ]]> https://biorxiv.org/content/10.1101/605485v1?rss=1 Cavanaugh, K. E. Staddon, M. F. Munro, E. Banerjee, S. Gardel, M. L. 2019-04-10 doi:10.1101/605485 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Deep learning for cancer type classification ]]> https://biorxiv.org/content/10.1101/612762v1?rss=1 Zeng, Z. Mao, C. Vo, A. Nugent, J. O. Khan, S. A. Clare, S. E. Luo, Y. 2019-04-17 doi:10.1101/612762 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ Somatic Genetic Aberrations in Benign Breast Disease and the Risk of Subsequent Breast Cancer ]]> https://biorxiv.org/content/10.1101/613505v1?rss=1 Zeng, Z. Vo, A. Li, X. Shidfar, A. Saldana, P. Xuei, X. Luo, Y. Khan, S. A. Clare, S. E. 2019-04-18 doi:10.1101/613505 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Biological Structure and Function Emerge from Scaling Unsupervised Learning to 250 Million Protein Sequences ]]> https://biorxiv.org/content/10.1101/622803v1?rss=1 Rives, A. Goyal, S. Meier, J. Guo, D. Ott, M. Zitnick, C. L. Ma, J. Fergus, R. 2019-04-29 doi:10.1101/622803 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Does deliberation really need more effort than intuition? A test using event-related brain potential ]]> https://biorxiv.org/content/10.1101/628446v1?rss=1 Zeng, J. Tang, D.-l. Yu, J. Zhang, Q. Nusbaum, H. 2019-05-07 doi:10.1101/628446 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Tubewell use protects against rotavirus infection during the monsoons in an urban setting ]]> https://biorxiv.org/content/10.1101/630855v1?rss=1 Martinez, P. P. Mahmud, A. S. Yunus, M. Faruque, A. S. G. Ahmed, T. Pascual, M. Buckee, C. 2019-05-10 doi:10.1101/630855 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Predicting neurodevelopmental outcomes in children with perinatal HIV using a novel machine learning algorithm ]]> https://biorxiv.org/content/10.1101/632273v1?rss=1 90%). Dynamic change indices and interactions between mental health and biological indices emerged as key predictors.nnConclusionMachine learning-based regression defined a unique explanatory model of neurocognitive outcomes among children with pHIV. The predictive algorithm included a combination of HIV, physical health, and mental health indices extracted from readily available clinical measures. Studies are needed to explore the clinical relevance of the data-driven explanatory model, including potential to inform targeted interventions aimed at modifiable risk factors. ]]> Paul, R. Mellins, C. Robbins, R. Kerr, S. Malee, K. Sophonphan, J. Jahanshad, N. Auripibul, L. Thongpibul, K. Kosalaraksa, P. Kanjanavanit, S. Ngampiyaskul, C. Luesomboon, W. Wongsawat, J. Vonthanak, S. Chettra, K. Suwanlerk, T. Valcour, V. Balla, L. Salminen, L. Preston, R. Garcia, P. Ananworanich, J. Puthanakit, T. 2019-05-09 doi:10.1101/632273 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Quantifying genetic regulatory variation in human populations improves transcriptome analysis in rare disease patients ]]> https://biorxiv.org/content/10.1101/632794v1?rss=1 Mohammadi, P. Castel, S. E. Cummings, B. B. Einson, J. Sousa, C. Hoffman, P. Donkervoort, S. Mohassel, P. Foley, R. Wheeler, H. E. Im, H. K. Bonnemann, C. G. MacArthur, D. G. Lappalainen, T. 2019-05-09 doi:10.1101/632794 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ A platform for semi-automated voluntary training of common marmosets for behavioral neuroscience ]]> https://biorxiv.org/content/10.1101/635334v1?rss=1 Walker, J. D. Pirschel, F. Gidmark, N. MacLean, J. N. Hatsopouolos, N. G. 2019-05-11 doi:10.1101/635334 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ Recurrent interactions can explain the variance in single trial responses ]]> https://biorxiv.org/content/10.1101/635359v1?rss=1 Kotekal, S. MacLean, J. N. 2019-05-11 doi:10.1101/635359 Cold Spring Harbor Laboratory Press 2019-05-11 <![CDATA[ Bayesian multivariate reanalysis of large genetic studies identifies many new associations ]]> https://biorxiv.org/content/10.1101/638882v1?rss=1 400 additional associations. Our method makes use of univariate GWAS summary statistics and is available as a software package, thus making it accessible to other researchers interested in conducting the same analyses. We also show, using studies that have multiple releases, that our new associations have high rates of replication. Overall, we argue multivariate approaches in GWAS should no longer be overlooked and how, often, there is low-hanging fruit in the form of new associations by running these methods on data already collected. ]]> Turchin, M. C. Stephens, M. 2019-05-16 doi:10.1101/638882 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light ]]> https://biorxiv.org/content/10.1101/641647v1?rss=1 nView larger version (19K):norg.highwire.dtl.DTLVardef@65ed9borg.highwire.dtl.DTLVardef@1d25e65org.highwire.dtl.DTLVardef@333ff9org.highwire.dtl.DTLVardef@ad2cf4_HPS_FORMAT_FIGEXP M_FIG C_FIG ABBREVIATED SUMMARYGeneral stress response (GSR) systems protect bacteria from a diverse range of physical and chemical stressors. We have developed Erythrobacter litoralis as a new genetic model to study GSR in Alphaproteobacteria and show that three HWE-family histidine kinases collectively regulate GSR transcription via {sigma}EcfG. Visible light is a GSR regulatory signal in E. litoralis, and LovK is a blue-light photosensor kinase that functions as a dark activated GSR regulator. ]]> Fiebig, A. Varesio, L. M. Alejandro Navarreto, X. Crosson, S. 2019-05-19 doi:10.1101/641647 Cold Spring Harbor Laboratory Press 2019-05-19 <![CDATA[ A terminal selector prevents a Hox transcriptional switch to safeguard motor neuron identity throughout life ]]> https://biorxiv.org/content/10.1101/643320v1?rss=1 Feng, W. Li, Y. Dao, P. Aburas, J. Islam, P. Elbaz, B. Kolarzyk, A. Brown, A. E. X. Kratsios, P. 2019-05-20 doi:10.1101/643320 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids ]]> https://biorxiv.org/content/10.1101/644062v1?rss=1 Turner, N. Mikalauskaite, D. Barone, K. Flaherty, K. Senevirathne, G. Adachi, N. Shubin, N. Nakamura, T. 2019-05-21 doi:10.1101/644062 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Sympatric and allopatric differentiation delineate population structure in a free-living terrestrial bacterium ]]> https://biorxiv.org/content/10.1101/644468v1?rss=1 Chase, A. B. Arevalo, P. Brodie, E. L. Polz, M. F. Karaoz, U. Martiny, J. B. H. 2019-05-30 doi:10.1101/644468 Cold Spring Harbor Laboratory Press 2019-05-30 <![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[ Emergence of an invariant representation of texture in primate somatosensory cortex ]]> https://biorxiv.org/content/10.1101/646042v1?rss=1 Lieber, J. D. Bensmaia, S. 2019-05-24 doi:10.1101/646042 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Chromatin-enriched RNAs mark active and repressive cis-regulation: an analysis of nuclear RNA-seq ]]> https://biorxiv.org/content/10.1101/646950v1?rss=1 Sun, X. Wang, Z. Perez-Cervantes, C. H. Ruthenburg, A. Moskowitz, I. H. Gribskov, M. Yang, X. 2019-05-22 doi:10.1101/646950 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ Accelerating iterative deconvolution and multiview fusion by orders of magnitude ]]> https://biorxiv.org/content/10.1101/647370v1?rss=1 Guo, M. Li, Y. Su, Y. Lambert, T. Nogare, D. D. Moyle, M. W. Duncan, L. H. Ikegami, R. Santella, A. Rey-Suarez, I. Green, D. Chen, J. Vishwasrao, H. Ganesan, S. Waters, J. C. Annunziata, C. M. Hafner, M. Mohler, W. A. Chitnis, A. B. Upadhyaya, A. Usdin, T. B. Bao, Z. Colon-Ramos, D. Riviere, P. L. Liu, H. Wu, Y. Shroff, H. 2019-05-23 doi:10.1101/647370 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Mechanosensitive junction remodelling promotes robust epithelial morphogenesis ]]> https://biorxiv.org/content/10.1101/648980v1?rss=1 Staddon, M. F. Cavanaugh, K. E. Munro, E. M. Gardel, M. L. Banerjee, S. 2019-05-24 doi:10.1101/648980 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Inhibitory cell populations depend on age, sex, and prior experience across a neural network for Critical Period learning ]]> https://biorxiv.org/content/10.1101/650051v1?rss=1 Gogola, J. V. Gores, E. O. London, S. E. 2019-06-04 doi:10.1101/650051 Cold Spring Harbor Laboratory Press 2019-06-04 <![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[ A mutant form of Dmc1 that bypasses the requirement for accessory protein Mei5-Sae3 reveals independent activities of Mei5-Sae3 and Rad51 in Dmc1 filament stability ]]> https://biorxiv.org/content/10.1101/652636v1?rss=1 Bishop, D. K. Reitz, D. Grubb, J. 2019-05-29 doi:10.1101/652636 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Agent-based modeling of persons who inject drugs in metropolitan Chicago suggests that re-treatment with antivirals of persons who are re-infected with Hep C is critical to achieve the WHO incidence reduction objective by 2030 ]]> https://biorxiv.org/content/10.1101/653196v1?rss=1 7.5% per year and high (90%) adherence, 75%, 19%, 5% and <2% of PWID will require 1, 2, 3, and 4 treatment courses with overall DAA cost of $325 million to achieve the WHO goal in metropolitan Chicago. We estimate a 28% increase in the overall DAA cost under low adherence (70%) compared to high adherence (90%). ConclusionsModeling results predict the frequency of DAA retreatment needed to achieve the WHO goal and underscore the importance of retreatment of HCV re-infections. ]]> Tatara, E. GUTFRAIND, A. COLLIER, N. COTLER, S. MAJOR, M. BOODRAM, B. Ozik, J. DAHARI, H. 2019-05-31 doi:10.1101/653196 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Restored tactile sensation improves neuroprosthetic arm control ]]> https://biorxiv.org/content/10.1101/653428v1?rss=1 Flesher, S. N. Downey, J. E. Weiss, J. M. Hughes, C. L. Herrera, A. J. Tyler-Kabara, E. C. Boninger, M. L. Collinger, J. L. Gaunt, R. A. 2019-05-31 doi:10.1101/653428 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Fully Interpretable Deep Learning Model of Transcriptional Control ]]> https://biorxiv.org/content/10.1101/655639v1?rss=1 Liu, Y. Barr, K. Reinitz, J. 2019-05-31 doi:10.1101/655639 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Functional connectivity strength within the auditory forebrain is altered by song learning and predicts song stereotypy in developing male zebra finches ]]> https://biorxiv.org/content/10.1101/657825v1?rss=1 Layden, E. A. Schertz, K. E. Berman, M. G. London, S. E. 2019-06-02 doi:10.1101/657825 Cold Spring Harbor Laboratory Press 2019-06-02 <![CDATA[ Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43 acts on the catalytic snRNA U6 ]]> https://biorxiv.org/content/10.1101/659029v1?rss=1 Toroney, R. Nielsen, K. H. Staley, J. P. 2019-06-04 doi:10.1101/659029 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[ THE FREQUENCY OF CORTICAL MICROSTIMULATION SHAPES ARTIFICIAL TOUCH ]]> https://biorxiv.org/content/10.1101/659516v1?rss=1 Callier, T. Brantly, N. W. Caravelli, A. Bensmaia, S. J. 2019-06-04 doi:10.1101/659516 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Transcriptome dynamics predict thermotolerance in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/661652v1?rss=1 Jovic, K. Grilli, J. L. Sterken, M. L. Riksen, J. A. Snoek, B. L. Allesina, S. Kammenga, J. 2019-06-06 doi:10.1101/661652 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ NeuronUnit: A package for data-driven validation of neuron models using SciUnit ]]> https://biorxiv.org/content/10.1101/665331v1?rss=1 Gerkin, R. C. Birgiolas, J. Jarvis, R. J. Omar, C. Crook, S. M. 2019-06-09 doi:10.1101/665331 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ Use of a mechanistic growth model in fish habitat restoration: juvenile Chinook salmon and steelhead as a test case ]]> https://biorxiv.org/content/10.1101/665588v1?rss=1 Polivka, C. M. Mihaljevic, J. R. Dwyer, G. 2019-06-10 doi:10.1101/665588 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ NEURAL POPULATION DYNAMICS IN MOTOR CORTEX ARE DIFFERENT FOR REACH AND GRASP ]]> https://biorxiv.org/content/10.1101/667196v1?rss=1 Suresh, A. K. Goodman, J. M. Okorokova, E. V. Kaufman, M. T. Hatsopoulos, N. G. Bensmaia, S. J. 2019-06-11 doi:10.1101/667196 Cold Spring Harbor Laboratory Press 2019-06-11 <![CDATA[ Adopting tipping-point theory to transcriptome profiles unravels disease regulatory trajectory ]]> https://biorxiv.org/content/10.1101/668442v1?rss=1 Yang, X. H. Wang, Z. Griggs, D. An, Q. Tang, F. Cunningham, J. 2019-06-12 doi:10.1101/668442 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin ]]> https://biorxiv.org/content/10.1101/670497v1?rss=1 Lee, J. M. Eguia, R. Zost, S. J. Choudhary, S. Wilson, P. C. Bedford, T. Stevens-Ayers, T. Boeckh, M. Hurt, A. Lakdawala, S. S. Hensley, S. E. Bloom, J. D. 2019-06-13 doi:10.1101/670497 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Trevolver: simulating non-reversible DNA sequence evolution in trinucleotide context on a bifurcating tree ]]> https://biorxiv.org/content/10.1101/672717v1?rss=1 Nelson, C. W. Fu, Y.-X. Li, W.-H. 2019-06-18 doi:10.1101/672717 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ DNA damage response clamp loader Rad24(Rad17) and Mec1(ATR) kinase have distinct functions in regulating meiotic crossovers ]]> https://biorxiv.org/content/10.1101/674507v1?rss=1 Shinohara, A. Shinohara, M. Bishop, D. K. 2019-06-18 doi:10.1101/674507 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans ]]> https://biorxiv.org/content/10.1101/675272v1?rss=1 Zost, S. J. Lee, J. Gumina, M. E. Parkhouse, K. Henry, C. Wilson, P. C. Bloom, J. D. Hensley, S. E. 2019-06-19 doi:10.1101/675272 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance. ]]> https://biorxiv.org/content/10.1101/675561v1?rss=1 Sevillano, M. C. Dai, Z. Calus, S. T. Bautista de los Santos, Q. M. Eren, A. M. Ijaz, U. Z. van der Wielen, P. W. J. J. Pinto, A. 2019-06-20 doi:10.1101/675561 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ An in silico analysis of robust but fragile gene regulation links enhancer length to robustness ]]> https://biorxiv.org/content/10.1101/677641v1?rss=1 Barr, K. A. Reinitz, J. Radulescu, O. 2019-06-21 doi:10.1101/677641 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Texture-Elicited Vibrations Stretch Or Contract Systematically Depending On Scanning Speed ]]> https://biorxiv.org/content/10.1101/680322v1?rss=1 Greenspon, C. McLellan, K. Lieber, J. D. Bensmaia, S. J. 2019-06-23 doi:10.1101/680322 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Mendelian randomization accounting for horizontal and correlated pleiotropic effects using genome-wide summary statistics. ]]> https://biorxiv.org/content/10.1101/682237v1?rss=1 Morrison, J. Knoblauch, N. Marcus, J. Stephens, M. He, X. 2019-06-26 doi:10.1101/682237 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Phosphorylated Lamin A targets active enhancers and is associated with abnormal transcriptional activation in progeria ]]> https://biorxiv.org/content/10.1101/682260v1?rss=1 Ikegami, K. Secchia, S. Lieb, J. D. Moskowitz, I. P. 2019-06-26 doi:10.1101/682260 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Deep learning reveals hidden variables underlying NF-κB activation in single cells ]]> https://biorxiv.org/content/10.1101/687848v1?rss=1 Patel, P. Drayman, N. Liu, P. Bilgic, M. Tay, S. 2019-07-01 doi:10.1101/687848 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Metal bridge in S4 segment supports helix transition in Shaker channel ]]> https://biorxiv.org/content/10.1101/689620v1?rss=1 Bassetto, C. A. Z. Carvalho-de-Souza, J. L. Bezanilla, F. 2019-07-02 doi:10.1101/689620 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Deep learning detects virus presence in cancer histology ]]> https://biorxiv.org/content/10.1101/690206v1?rss=1 Kather, J. N. Schulte, J. Grabsch, H. I. Loeffler, C. Muti, H. S. Dolezal, J. Srisuwananukorn, A. Agrawal, N. Kochanny, S. von Stillfried, S. Boor, P. Yoshikawa, T. Jaeger, D. Trautwein, C. Bankhead, P. Cipriani, N. A. Luedde, T. Pearson, A. T. 2019-07-05 doi:10.1101/690206 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ The role of lipoprotein subfractions in coronary artery disease: A Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/691089v1?rss=1 Zhao, Q. Wang, J. Miao, Z. Zhang, N. R. Hennessy, S. Small, D. S. Rader, D. J. 2019-07-03 doi:10.1101/691089 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Evolutionary dynamics of abundant 7 bp satellites in the genome of Drosophila virilis ]]> https://biorxiv.org/content/10.1101/693077v1?rss=1 40% of its genome composed of a few related 7 bp satellites. Here we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the highly abundant satellite family arose from a related satellite in the branch leading to the virilis phylad 4.5 - 11 million years ago before exploding in abundance in some species of the clade. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. By analyzing multiple strains of D. virilis, we saw that one centromere-proximal satellite is increasing in abundance along a geographical gradient while the other is contracting in an anti-correlated manner, suggesting ongoing conflicts at the centromere. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes like selection, meiotic drive, and constraints on satellite sequence and abundance. ]]> Flynn, J. M. Long, M. Wing, R. A. Clark, A. G. 2019-07-04 doi:10.1101/693077 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Population genetics of the highly polymorphic RPP8 gene family ]]> https://biorxiv.org/content/10.1101/694240v1?rss=1 MacQueen, A. H. Tian, D. Chang, W. Holub, E. Kreitman, M. Bergelson, J. 2019-07-08 doi:10.1101/694240 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Unexpected Complexity Of Everyday Manual Behaviors ]]> https://biorxiv.org/content/10.1101/694778v1?rss=1 Yan, Y. Goodman, J. M. Bensmaia, S. J. 2019-07-08 doi:10.1101/694778 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ STARRPeaker: Uniform processing and accurate identification of whole human STARR-seq active regions ]]> https://biorxiv.org/content/10.1101/694869v1?rss=1 Lee, D. Shi, M. Moran, J. Wall, M. Zhang, J. Liu, J. Fitzgerald, D. Kyono, Y. Ma, L. White, K. P. Gerstein, M. 2019-07-08 doi:10.1101/694869 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Promoter-specific dynamics of TATA-binding protein association with the human genome ]]> https://biorxiv.org/content/10.1101/696369v1?rss=1 Hasegawa, Y. Lieb, J. D. Struhl, K. 2019-07-08 doi:10.1101/696369 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Multiple timescales account for adaptive responses across sensory cortices ]]> https://biorxiv.org/content/10.1101/700062v1?rss=1 Latimer, K. Barbera, D. Sokoletsky, M. Awwad, B. Katz, Y. Nelken, I. Lampl, I. Fairhall, A. Priebe, N. J. 2019-07-14 doi:10.1101/700062 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Cryptic genetic variation underpins rapid adaptation to ocean acidification ]]> https://biorxiv.org/content/10.1101/700526v1?rss=1 Bitter, M. C. Kapsenberg, L. Gattuso, J.-P. Pfister, C. A. 2019-07-14 doi:10.1101/700526 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ SINATRA: A Sub-Image Analysis Pipeline for Selecting Features that Differentiate Classes of 3D Shapes ]]> https://biorxiv.org/content/10.1101/701391v1?rss=1 Wang, B. Sudijono, T. Kirveslahti, H. Gao, T. Boyer, D. M. Mukherjee, S. Crawford, L. 2019-07-14 doi:10.1101/701391 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area ]]> https://biorxiv.org/content/10.1101/703793v1?rss=1 Tilot, A. L. Khramtsova, E. A. Grasby, K. Jahanshad, N. Painter, J. Colodro Conde, L. Bralten, J. Hibar, D. P. Lind, P. Liu, S. Brotman, S. M. Thompson, P. M. Medland, S. E. Macciardi, F. Stranger, B. E. Davis, L. K. Fisher, S. E. Stein, J. 2019-07-16 doi:10.1101/703793 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Adult dentate gyrus neurogenesis: A functional model ]]> https://biorxiv.org/content/10.1101/704791v1?rss=1 Gozel, O. Gerstner, W. 2019-07-16 doi:10.1101/704791 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Towards a state-space geometry of neural responses to natural scenes: A steady-state approach ]]> https://biorxiv.org/content/10.1101/705376v1?rss=1 Hansen, B. Field, D. J. Greene, M. R. Olson, C. Miskovic, V. 2019-07-16 doi:10.1101/705376 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ An integrative ENCODE resource for cancer genomics ]]> https://biorxiv.org/content/10.1101/706424v1?rss=1 Zhang, J. Lee, D. Dhiman, V. Jiang, P. Xu, J. McGillivray, P. Yang, H. Liu, J. Meyerson, W. Clarke, D. Gu, M. Li, S. Lou, S. Xu, J. Lochovsky, L. Ung, M. Ma, L. Yu, S. Cao, Q. Harmanci, A. Yan, K.-K. Sethi, A. Gursoy, G. Schoenberg, M. R. Rozowsky, J. Warrell, J. Emani, P. Yang, Y. T. Galeev, T. Kong, X. Liu, S. Li, X. Krishnan, J. Feng, Y. Rivera-Mulia, J. C. Adrian, J. Broach, J. R. Bolt, M. Moran, J. Fitzgerald, D. Dileep, V. Liu, T. Mei, S. Sasaki, T. Trevilla-Garcia, C. Wang, S. Wang, Y. Zang, C. Wang, D. Klein, R. Snyder, M. Gilbert, D. 2019-07-18 doi:10.1101/706424 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Non-apoptotic caspase-dependent regulation of enteroblast quiescence in Drosophila ]]> https://biorxiv.org/content/10.1101/707380v1?rss=1 Baena Lopez, L. A. Arthurton, L. Nahotko, D. A. Alonso, J. 2019-07-20 doi:10.1101/707380 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Transposable elements have contributed human regulatory regions that are activated upon bacterial infection ]]> https://biorxiv.org/content/10.1101/707612v1?rss=1 Bogdan, L. Barreiro, L. Bourque, G. 2019-07-20 doi:10.1101/707612 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Overlapping attentional networks yield divergent behavioral predictions across tasks: Neuromarkers for diffuse and focused attention? ]]> https://biorxiv.org/content/10.1101/713339v1?rss=1 Wu, E. X. W. Liaw, G. J. Goh, R. Z. Chia, T. T. Y. Chee, A. M. J. Obana, T. Rosenberg, M. D. Yeo, B. T. T. Asplund, C. L. 2019-07-24 doi:10.1101/713339 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Perturbing neural representations of working memory with task-irrelevant interruption ]]> https://biorxiv.org/content/10.1101/716613v1?rss=1 Hakim, N. Feldmann-Wustefeld, T. Awh, E. Vogel, E. 2019-07-26 doi:10.1101/716613 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ The Aging Microenvironment Shapes Alveolar Macrophage Identity in Aging ]]> https://biorxiv.org/content/10.1101/717033v1?rss=1 McQuattie-Pimentel, A. C. Ren, Z. Joshi, N. Watanabe, S. Stoeger, T. Chi, M. Lu, Z. Sichizya, L. Piseaux, R. Chen, C.-I. Soberanes, S. Reyfman, P. A. Walter, J. M. Anekalla, K. R. Davis, J. M. Helmin, K. A. Runyan, C. E. Abdala-Valencia, H. Nam, K. Meliton, A. Y. Winter, D. R. Morimoto, R. I. Mutlu, G. M. Bharat, A. Gottardi, C. J. Perlman, H. Ridge, K. M. Chandel, N. S. Sznajder, J. I. Balch, W. E. Singer, B. D. Misharin, A. V. Budinger, G. S. 2019-07-28 doi:10.1101/717033 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ A carbonic anhydrase pseudogene sensitizes select Brucella lineages to low CO2 partial pressure ]]> https://biorxiv.org/content/10.1101/721597v1?rss=1 Varesio, L. M. Willet, J. W. Fiebig, A. Crosson, S. 2019-08-01 doi:10.1101/721597 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ In-silico definition of the Drosophila melanogaster matrisome ]]> https://biorxiv.org/content/10.1101/722868v1?rss=1 Davis, M. N. Horne-Badovinac, S. Naba, A. 2019-08-02 doi:10.1101/722868 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Cytochrome P450 26b1-mediated specification of vestibular striola and central zones is required for transient responses in linear acceleration ]]> https://biorxiv.org/content/10.1101/726232v1?rss=1 Ono, K. Keller, J. Ramirez, O. L. Garrido, A. G. Zobeiri, O. Chang, V. Vijayakumar, S. Ayiotis, A. Duester, G. Santina, C. C. D. Jones, S. M. Cullen, K. Eatock, R. A. Wu, D. K. 2019-08-06 doi:10.1101/726232 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Multivariate analysis of EEG activity indexes contingent and non-contingent attentional capture ]]> https://biorxiv.org/content/10.1101/734004v1?rss=1 156 ms), while alpha power revealed sustained spatial selection in the cued locations at a later moment in the trial (>250 ms). Moreover, while raw EEG showed stronger capture by contingent cues during this early time window, the advantage for contingent cues arose during a later time window in alpha band activity. Thus, our findings suggest that raw EEG activity and alpha-band power tap into distinct neural processes that index movements of covert spatial attention. Both signals provide clear neural evidence that both contingent and non-contingent cues can capture attention, and that this process is robustly shaped by the target-defining properties in the current block of trials. ]]> Munneke, J. Fahrenfort, J. J. Sutterer, D. Theeuwes, J. Awh, E. 2019-08-20 doi:10.1101/734004 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ A Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation ]]> https://biorxiv.org/content/10.1101/736322v1?rss=1 Guzzetta, A. Koska, M. Rowton, M. Kweon, J. Hidalgo, H. Eckart, H. Back, R. Lozano, S. Moon, A. M. Basu, A. Bressan, M. Pott, S. Moskowitz, I. P. 2019-08-16 doi:10.1101/736322 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Capturing medical practice with indication embeddings ]]> https://biorxiv.org/content/10.1101/737049v1?rss=1 Melamed, R. D. 2019-08-15 doi:10.1101/737049 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Diversification of CORVET tethers facilitates transport complexity in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/737247v1?rss=1 Sparvoli, D. Zoltner, M. Field, M. Turkewitz, A. 2019-08-16 doi:10.1101/737247 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Mice Lacking FXR Are Susceptible to Liver Ischemia-Reperfusion Injury ]]> https://biorxiv.org/content/10.1101/739839v1?rss=1 Li, Y. Xu, R. Rao, P. K. Gomes, C. K. Moran, E. R. Puchowicz, M. Chang, E. B. Yin, D. P. Pierre, J. F. 2019-08-19 doi:10.1101/739839 Cold Spring Harbor Laboratory Press 2019-08-19 <![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[ MACF1 Facilitates SMAD7 Nuclear Translocation to Drive Bone Formation in Mice ]]> https://biorxiv.org/content/10.1101/743930v1?rss=1 Zhao, F. Ma, X. Qiu, W. Wang, P. Zhang, R. Chen, Z. Su, P. Zhang, Y. Li, D. Ma, J. Yang, C. Chen, L. Ying, C. Tian, Y. Hu, L. Li, Y. Zhang, G. Wu, X. Qian, A. 2019-08-25 doi:10.1101/743930 Cold Spring Harbor Laboratory Press 2019-08-25 <![CDATA[ Input dose differentiation by NF-κB ]]> https://biorxiv.org/content/10.1101/752394v1?rss=1 Son, M. Wang, A. Tu, H.-L. Metzig, M. O. Patel, P. Husain, K. Lin, J. Murugan, A. Hoffmann, A. Tay, S. 2019-09-04 doi:10.1101/752394 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Manner of death and demographic effects on microbial community composition in organs of the human cadaver ]]> https://biorxiv.org/content/10.1101/752576v1?rss=1 Lutz, H. L. Vangelatos, A. L. Gottel, N. Speed, E. Osculati, A. Visona, S. Finley, S. J. Tuomisto, S. Karhunen, P. J. Gilbert, J. A. Javan, G. T. 2019-08-31 doi:10.1101/752576 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Derivation of endometrial gland organoids from term post-partum placenta ]]> https://biorxiv.org/content/10.1101/753780v1?rss=1 Marinic, M. Lynch, V. J. 2019-08-31 doi:10.1101/753780 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Impaired carotid body hypoxic sensing in mice deficient in olfactory receptor 78 ]]> https://biorxiv.org/content/10.1101/757120v1?rss=1 Peng, Y.-J. Gridina, A. Nanduri, J. Fox, A. Prabhakar, N. R. 2019-09-04 doi:10.1101/757120 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection ]]> https://biorxiv.org/content/10.1101/758201v1?rss=1 Lopez, P. Girardi, E. Mounce, B. C. Weiss, A. Chane-Woon-Ming, B. Messmer, M. Kaukinen, P. Kopp, A. Bortolamiol-Becet, D. Fendri, A. Vignuzzi, M. Brino, L. Pfeffer, S. 2019-09-05 doi:10.1101/758201 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies ]]> https://biorxiv.org/content/10.1101/759969v1?rss=1 Watterson, W. Tanyeri, M. Watson, A. Cham, C. Shan, Y. Chang, E. B. Eren, M. Tay, S. 2019-09-06 doi:10.1101/759969 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery ]]> https://biorxiv.org/content/10.1101/760256v1?rss=1 Chen, W. Hu, Y. Lang, C. Brown, J. S. Song, X. Munro, E. Bennett, K. Zhang, D. Lee, H.-C. 2019-09-06 doi:10.1101/760256 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Urban birdsongs: higher minimum song frequency of an urban colonist persists in a common garden experiment ]]> https://biorxiv.org/content/10.1101/761734v1?rss=1 Reichard, D. G. Atwell, J. W. Pandit, M. M. Cardoso, G. C. Price, T. D. Ketterson, E. D. 2019-09-08 doi:10.1101/761734 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Systemic Infection Facilitates Transmission of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/765339v1?rss=1 Bachta, K. E. R. Allen, J. P. Cheung, B. H. Chiu, C.-H. Hauser, A. R. 2019-09-12 doi:10.1101/765339 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities ]]> https://biorxiv.org/content/10.1101/765685v1?rss=1 Nieves-Colon, M. A. Pestle, W. J. Reynolds, A. W. Llamas, B. de la Fuente, C. Fowler, K. Skerry, K. Crespo-Torres, E. Bustamante, C. D. Stone, A. C. 2019-09-12 doi:10.1101/765685 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Evolution of herbivory remodels a Drosophila genome ]]> https://biorxiv.org/content/10.1101/767160v1?rss=1 400 million years ago (mya) spurred the diversification of plant-feeding (herbivorous) insects and triggered an ongoing chemical co-evolutionary arms race. Because ancestors of most herbivorous insects first colonized plants >200 mya, the sands of time have buried evidence of how their genomes changed with their diet. We leveraged the serendipitous intersection of two genetic model systems: a close relative of yeast-feeding fruit fly (Drosophila melanogaster), the "wasabi fly" (Scaptomyza flava), that evolved to consume mustard plants including Arabidopsis thaliana. The yeast-to-mustard dietary transition remodeled the flys gene repertoire for sensing and detoxifying chemicals. Although many genes were lost, some underwent duplications that encode the most efficient detoxifying enzymes against mustard oils known from animals. ]]> Gloss, A. D. Nelson Dittrich, A. C. Lapoint, R. T. Goldman Huertas, B. Verster, K. I. Pelaez, J. L. Nelson, A. D. L. Aguilar, J. Armstrong, E. Charboneau, J. L. M. Groen, S. C. Hembry, D. H. Ochoa, C. J. O'Connor, T. K. Prost, S. Suzuki, H. C. Zaaijer, S. Nabity, P. D. Whiteman, N. K. 2019-09-12 doi:10.1101/767160 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Straightforward clustering of single-cell RNA-Seq data with t-SNE and DBSCAN ]]> https://biorxiv.org/content/10.1101/770388v1?rss=1 Wagner, F. 2019-09-16 doi:10.1101/770388 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Haplotype-based inference of the distribution of fitness effects ]]> https://biorxiv.org/content/10.1101/770966v1?rss=1 Ortega-Del Vecchyo, D. Lohmueller, K. E. Novembre, J. 2019-09-16 doi:10.1101/770966 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Club cell TRPV4 as a damage sensor driving lung allergic inflammation ]]> https://biorxiv.org/content/10.1101/773382v1?rss=1 nView larger version (24K):norg.highwire.dtl.DTLVardef@c03f95org.highwire.dtl.DTLVardef@18e54b6org.highwire.dtl.DTLVardef@15ba395org.highwire.dtl.DTLVardef@1509e5c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wiesner, D. L. Merkhofer, R. M. Ober, C. L. Kujoth, G. C. Gern, J. E. Brockman Schneider, R. Evans, M. D. Jackson, D. J. Warner, T. F. Jarjour, N. Esnault, S. J. Feldman, M. B. Freeman, M. J. Mou, H. Vyas, J. Klein, B. S. 2019-09-19 doi:10.1101/773382 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ GSDMA drives the most replicated association with asthma in naïve CD4+ T cells ]]> https://biorxiv.org/content/10.1101/774760v1?rss=1 Madore, A.-M. Pain, L. Boucher-Lafleur, A.-M. Meloche, J. Morin, A. Simon, M.-M. Ge, B. Kwan, T. Cheung, W. A. Pastinen, T. Laprise, C. 2019-09-19 doi:10.1101/774760 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Cyclic transitions between higher order motifs underlie sustained activity in asynchronous sparse recurrent networks ]]> https://biorxiv.org/content/10.1101/777219v1?rss=1 Bojanek, K. Zhu, Y. MacLean, J. 2019-09-20 doi:10.1101/777219 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Understanding artificial mouse-microbiome heterogeneity and six actionable themes to increase study power ]]> https://biorxiv.org/content/10.1101/778043v1?rss=1 Basson, A. R. LaSalla, A. Lam, G. Kulpins, D. Moen, E. L. Sundrud, M. Miyoshi, J. Ilic, S. Theriault, B. R. Cominelli, F. Rodriguez-Palacios, A. 2019-09-25 doi:10.1101/778043 Cold Spring Harbor Laboratory Press 2019-09-25 <![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[ 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[ A streamlined mass spectrometry-based proteomics workflow forlarge scale FFPE tissue analysis ]]> https://biorxiv.org/content/10.1101/779009v1?rss=1 15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner. ]]> Coscia, F. Doll, S. Bech, J. M. Mund, A. Lengyel, E. Lindebjerg, J. Madsen, G. I. Moreira, J. M. A. Mann, M. 2019-09-23 doi:10.1101/779009 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Coronavirus Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages ]]> https://biorxiv.org/content/10.1101/782409v1?rss=1 Deng, X. Volk, A. Chen, Y. Kesely, K. R. Hackbart, M. Mettelman, R. C. OBrien, A. Mesecar, A. D. Baker, S. 2019-09-25 doi:10.1101/782409 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ P2X1 selective antagonists block HIV-1 infection through inhibition of envelope conformation-dependent fusion ]]> https://biorxiv.org/content/10.1101/783464v1?rss=1 Soare, A. Y. Malik, H. S. Durham, N. Freeman, T. L. Alvarez, R. A. Patel, F. Satija, N. Upadhyay, C. Hioe, C. E. Chen, B. K. Swartz, T. H. 2019-09-26 doi:10.1101/783464 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs ]]> https://biorxiv.org/content/10.1101/785584v1?rss=1 He, Y. Chhetri, S. B. Arvanitis, M. Srinivasan, K. Aguet, F. Ardlie, K. G. Barbeira, A. N. Bonazzola, R. Im, H. K. GTEx Consortium, Brown, C. D. Battle, A. 2019-10-06 doi:10.1101/785584 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Diverse transcriptomic signatures across human tissues identify functional rare genetic variation ]]> https://biorxiv.org/content/10.1101/786053v1?rss=1 Ferraro, N. M. Strober, B. J. Einson, J. Li, X. Aguet, F. Barbeira, A. N. Castel, S. E. Davis, J. R. Hilliard, A. T. Kotis, B. Park, Y. Scott, A. J. Smail, C. Tsang, E. K. Ardlie, K. G. Assimes, T. L. Hall, I. Im, H. K. GTEx Consortium, Lappalainen, T. Mohammadi, P. Montgomery, S. B. Battle, A. 2019-10-03 doi:10.1101/786053 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ A new formalism for perceptual classification with normative inference of internal criteria ]]> https://biorxiv.org/content/10.1101/787424v1?rss=1 Lee, H. Lee, H.-J. Choe, K. W. Lee, S.-H. 2019-09-30 doi:10.1101/787424 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ The GTEx Consortium atlas of genetic regulatory effects across human tissues ]]> https://biorxiv.org/content/10.1101/787903v1?rss=1 Aguet, F. Barbeira, A. N. Bonazzola, R. Brown, A. Castel, S. E. Jo, B. Kasela, S. Kim-Hellmuth, S. Liang, Y. Oliva, M. Parsana, P. E. Flynn, E. Fresard, L. Gaamzon, E. R. Hamel, A. R. He, Y. Hormozdiari, F. Mohammadi, P. Munoz-Aguirre, M. Park, Y. Saha, A. Segrc, A. V. Strober, B. J. Wen, X. Wucher, V. Das, S. Garrido-Martin, D. Gay, N. R. Handsaker, R. E. Hoffman, P. J. Kashin, S. Kwong, A. Li, X. MacArthur, D. Rouhana, J. M. Stephens, M. Todres, E. Vinuela, A. Wang, G. Zou, Y. The GTEx Consortium, Brown, C. D. Cox, N. Dermitzakis, E. Engelhardt, 2019-10-03 doi:10.1101/787903 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Uniform Genomic Data Analysis in the NCI Genomic Data Commons ]]> https://biorxiv.org/content/10.1101/788919v1?rss=1 Zhang, Z. Hernandez, K. Savage, J. Li, S. Miller, D. Agrawal, S. Ortuno, F. Staudt, L. Heath, A. Grossman, R. L. 2019-10-01 doi:10.1101/788919 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser ]]> https://biorxiv.org/content/10.1101/789305v1?rss=1 Claesson, E. Yuan Wahlgren, W. Takala, H. Pandey, S. Castillon, L. Kuznetsova, V. Henry, L. Carrillo, M. Panman, M. Kubel, J. Nanekar, R. Isaksson, L. Nimmrich, A. Cellini, A. Morozov, D. Maj, M. Kurttila, M. Bosman, R. Nango, E. Tanaka, R. Tanaka, T. Fangjia, L. Iwata, S. Owada, S. Moffat, K. Groenhof, G. Stojkovic, E. Ihalainen, J. Schmidt, M. Westenhoff, S. 2019-10-01 doi:10.1101/789305 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Prevalence of RFC1-Mediated Spinocerebellar Ataxia in a United States Ataxia Cohort ]]> https://biorxiv.org/content/10.1101/790006v1?rss=1 Syriani, D. A. Wong, D. De Gusmao, C. M. Andani, S. Mao, Y. Glotzer, G. Lockhart, P. Hassin-Baer, S. Khurana, V. Das, S. Gomez, C. M. Perlman, S. Fogel, B. 2019-10-01 doi:10.1101/790006 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Long non-coding RNA gene regulation and trait associations across human tissues ]]> https://biorxiv.org/content/10.1101/793091v1?rss=1 de Goede, O. M. Ferraro, N. M. Nachun, D. C. Rao, A. Aguet, F. Barbeira, A. N. Castel, S. E. Kim-Hellmuth, S. Park, Y. Scott, A. J. Strober, B. J. GTEx Consortium, Brown, C. D. Wen, X. Hall, I. M. Battle, A. Lappalainen, T. Im, H. K. Ardlie, K. G. Quertermous, T. Kirkegaard, K. Montgomery, S. B. 2019-10-04 doi:10.1101/793091 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Determinants of telomere length across human tissues ]]> https://biorxiv.org/content/10.1101/793406v1?rss=1 20 tissue types and 952 individuals from the Genotype-Tissue Expression (GTEx) Project. We describe differences across tissue types, positive correlation among tissue types, and associations with age and ancestry. We show that genetic variation impacts TL in multiple tissue types, and that TL can mediate the effect of age on gene expression. Our results provide the foundational knowledge regarding TL in healthy tissues that is needed to interpret epidemiological studies of TL and human health.nnONE SENTENCE SUMMARYTelomere length varies by tissue type but is generally correlated among tissue types (positively) and with age (negatively). ]]> Demanelis, K. Jasmine, F. Chen, L. S. Chernoff, M. Tong, L. Shinkle, J. Sabarinathan, M. Lin, H. Ramirez, E. Oliva, M. Kim-Hellmuth, S. Stranger, B. E. Ardlie, K. G. Aguet, F. Ahsan, H. GTEx Consortium, Doherty, J. Kibriya, M. G. Pierce, B. L. 2019-10-07 doi:10.1101/793406 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage ]]> https://biorxiv.org/content/10.1101/799569v1?rss=1 Marinic, M. Lynch, V. J. 2019-10-09 doi:10.1101/799569 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ CCmed: cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits ]]> https://biorxiv.org/content/10.1101/803106v1?rss=1 Yang, F. Gleason, K. J. Wang, J. The GTEx Consortium, Duan, J. He, X. Pierce, B. L. Chen, L. S. 2019-10-13 doi:10.1101/803106 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Cell division Rate Controls Cell Shape Remodeling in Epithelia ]]> https://biorxiv.org/content/10.1101/804294v1?rss=1 Devany, J. Sussman, D. M. Manning, M. L. Gardel, M. L. 2019-10-14 doi:10.1101/804294 Cold Spring Harbor Laboratory Press 2019-10-14 <![CDATA[ Structural basis for adhesion G protein-coupled receptor Gpr126 function ]]> https://biorxiv.org/content/10.1101/805515v1?rss=1 Leon, K. Cunningham, R. Riback, J. Feldman, E. Li, J. Sosnick, T. Zhao, M. Monk, K. Arac, D. 2019-10-17 doi:10.1101/805515 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Cell type specific genetic regulation of gene expression across human tissues ]]> https://biorxiv.org/content/10.1101/806117v1?rss=1 Kim-Hellmuth, S. Aguet, F. Oliva, M. Munoz-Aguirre, M. Wucher, V. Kasela, S. Castel, S. E. Hamel, A. Vinuela, A. Roberts, A. L. Mangul, S. Wen, X. Wang, G. Barbeira, A. Garrido-Martin, D. Nadel, B. Zou, Y. Bonazzola, R. Quan, J. Brown, A. Martinez-Perez, A. Soria, J. M. Getz, G. Dermitzakis, E. Small, K. S. Stephens, M. Xi, H. S. Im, H. K. Guigo, R. Segre, A. Stranger, B. Ardlie, K. Lappalainen, T. 2019-10-16 doi:10.1101/806117 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis ]]> https://biorxiv.org/content/10.1101/808295v1?rss=1 Chen, Y. Quick, C. Yu, K. Barbeira, A. The GTEx Consortium, Luca, F. Pique-Regi, R. Im, H. K. Wen, X. 2019-10-17 doi:10.1101/808295 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Accurate and Complete Genomes from Metagenomes ]]> https://biorxiv.org/content/10.1101/808410v1?rss=1 Chen, L.-X. Anantharaman, K. Shaiber, A. Eren, A. M. Banfield, J. F. 2019-10-17 doi:10.1101/808410 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Liver cells and PBMC secrete Tumor-suppressive Plasma Extracellular Vesicles in Melanoma patients ]]> https://biorxiv.org/content/10.1101/809301v1?rss=1 Baur, A. S. Lee, J.-H. Eberhardt, M. Blume, K. Vera-Gonzalez, J. 2019-10-23 doi:10.1101/809301 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ A photostable monomeric superfolder GFP ]]> https://biorxiv.org/content/10.1101/811588v1?rss=1 Valbuena, F. Fitzgerald, I. Strack, R. L. Andruska, N. Smith, L. Glick, B. S. 2019-10-20 doi:10.1101/811588 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Phenylpropionc acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity ]]> https://biorxiv.org/content/10.1101/811984v1?rss=1 Cho, S. Won, K.-J. Yang, X. Leone, V. Chang, E. B. Chung, E. Park, J.-S. Lee, H. Jeong, H. 2019-10-21 doi:10.1101/811984 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Integrating enhancer RNA signatures with diverse omics data identifies characteristics of transcription initiation in pancreatic islets ]]> https://biorxiv.org/content/10.1101/812552v1?rss=1 Varshney, A. Kyono, Y. Elangovan, V. R. Wang, C. Erdos, M. R. Narisu, N. Albanus, R. D. O. Orchard, P. Stitzel, M. L. Collins, F. S. Kitzman, J. O. Parker, S. C. J. 2019-10-21 doi:10.1101/812552 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Systematic identification of A-to-I editing associated regulators from multiple human cancers ]]> https://biorxiv.org/content/10.1101/812610v1?rss=1 Gu, T. Fu, A. Q. Bolt, M. J. Zhao, X. 2019-10-21 doi:10.1101/812610 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans ]]> https://biorxiv.org/content/10.1101/813642v1?rss=1 Stutzman, A. V. Beilinson, V. Liang, A. Ikegami, K. 2019-10-22 doi:10.1101/813642 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Axonal gap junctions in the fly visual system enable fast prediction for evasive flight maneuvers ]]> https://biorxiv.org/content/10.1101/814319v1?rss=1 Wang, S. Borst, A. Segev, I. Palmer, S. 2019-10-22 doi:10.1101/814319 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits ]]> https://biorxiv.org/content/10.1101/814350v1?rss=1 Barbeira, A. N. Bonazzola, R. Gamazon, E. R. Liang, Y. Park, Y. Kim-Hellmuth, S. Wang, G. Jiang, Z. Zhou, D. Hormozdiari, F. Liu, B. Rao, A. Hamel, A. R. Pividori, M. D. Aguet, F. GTEx GWAS Working Group, Bastarache, L. Jordan, D. M. Verbanck, M. Do, R. GTEx Consortium, Stephens, M. Ardlie, K. McCarthy, M. Montgomery, S. B. Segre, A. Brown, C. D. Lappalainen, T. Wen, X. Im, H. K. 2019-10-22 doi:10.1101/814350 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Silicon Nanowires for Intracellular Optical Interrogation with Sub-Cellular Resolution ]]> https://biorxiv.org/content/10.1101/825489v1?rss=1 Rotenberg, M. Y. Elbaz, B. Nair, V. Schaumann, E. N. Yamamoto, N. Matino, L. Santoro, F. Tian, B. 2019-10-31 doi:10.1101/825489 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Modeling adaptive therapy in non-muscle invasive bladder cancer ]]> https://biorxiv.org/content/10.1101/826438v1?rss=1 Ferrall-Fairbanks, M. C. Kimmel, G. J. Black, M. Bravo, R. Deac, O. Martinez, P. Myers, M. Nazari, F. Osojnik, A. Subramanian, H. Viossat, Y. Whiting, F. Li, R. Mann, K. M. Altrock, P. M. 2019-11-06 doi:10.1101/826438 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants ]]> https://biorxiv.org/content/10.1101/827048v1?rss=1 Zhang, S. Zhang, H. Qiao, M. Zhou, Y. Zhao, S. Kozlova, A. Shi, J. Sanders, A. R. Wang, G. Sengupta, S. West, S. Streit, M. Cowan, C. A. Chen, M. Pang, Z. Gejman, P. V. He, X. Duan, J. 2019-11-01 doi:10.1101/827048 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ A Bayesian method for rare variant analysis using functional annotations and its application to Autism ]]> https://biorxiv.org/content/10.1101/828061v1?rss=1 Han, S. Knoblauch, N. Wang, G. Zhao, S. Liu, Y. Xie, Y. Sheng, W. Nguyen, H. T. He, X. 2019-11-01 doi:10.1101/828061 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere ]]> https://biorxiv.org/content/10.1101/828814v1?rss=1 Karasov, T. L. Neumann, M. Duque-Jaramillo, A. Kersten, S. Bezrukov, I. Schroeppel, B. Symeonidi, E. Lundberg, D. S. Regalado, J. Shirsekar, G. Bergelson, J. Weigel, D. 2019-11-02 doi:10.1101/828814 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Disinfection exhibits systematic impacts on the drinking water microbiome. ]]> https://biorxiv.org/content/10.1101/828970v1?rss=1 Dai, Z. Sevillano, M. C. Calus, S. T. Bautista-de los Santos, Q. M. Eren, A. M. van der Wielen, P. W. J. J. Ijaz, U. Z. Pinto, A. J. 2019-11-02 doi:10.1101/828970 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Variation in the life history strategy of cells underlies tumor’s functional diversity ]]> https://biorxiv.org/content/10.1101/829135v1?rss=1 Lu, X. Li, T. Liu, J. Feng, J. Liu, Z. Liu, S. Zhang, M. Zhang, Y. Hou, Y. Wu, D. Li, C. Chen, Y.-B. Wu, C.-I. Chen, H. 2019-11-04 doi:10.1101/829135 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ RNA-binding protein altered expression and mislocalization in multiple sclerosis ]]> https://biorxiv.org/content/10.1101/829457v1?rss=1 Masaki, K. Sonobe, Y. Ghadge, G. Pytel, P. Lepine, P. Pernin, F. Cui, Q.-L. Antel, J. P. Zandee, S. Prat, A. Roos, R. P. 2019-11-05 doi:10.1101/829457 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ DRAMS: A Tool to Detect and Re-Align Mixed-up Samples for Integrative Studies of Multi-omics Data ]]> https://biorxiv.org/content/10.1101/831537v1?rss=1 Jiang, Y. Giase, G. Grennan, K. Shieh, A. W. Xia, Y. Han, L. Wang, Q. Wei, Q. Chen, R. Liu, S. White, K. P. Chen, C. Li, B. Liu, C. 2019-11-06 doi:10.1101/831537 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ PhenomeXcan: Mapping the genome to the phenome through the transcriptome ]]> https://biorxiv.org/content/10.1101/833210v1?rss=1 0.1). We successfully replicate associations from PheWAS Catalog (AUC=0.61) and OMIM (AUC=0.64). We provide examples of (a) finding novel and underreported genome-to-phenome associations, (b) exploring complex gene-trait clusters within PhenomeXcan, (c) studying phenome-to-phenome relationships between common and rare diseases via further integration of PhenomeXcan with ClinVar, and (d) evaluating potential therapeutic targets. PhenomeXcan (phenomexcan.org) broadens access to complex genomic and transcriptomic data and empowers translational researchers. One-Sentence SummaryPhenomeXcan is a gene-based resource of gene-trait associations with biological context that supports translational research. ]]> Pividori, M. Rajagopal, P. S. Barbeira, A. N. Liang, Y. Melia, O. Bastarache, L. Park, Y. The GTEx Consortium, Wen, X. Im, H. K. 2019-11-06 doi:10.1101/833210 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Photoproximity profiling of protein-protein interactions in cells ]]> https://biorxiv.org/content/10.1101/833384v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@5319bborg.highwire.dtl.DTLVardef@1be7ea0org.highwire.dtl.DTLVardef@16b51d6org.highwire.dtl.DTLVardef@c9d400_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> McCutcheon, D. C. Lee, G. Carlos, A. J. Montgomery, J. E. Moellering, R. E. 2019-11-17 doi:10.1101/833384 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Pan-cancer image-based detection of clinically actionable genetic alterations ]]> https://biorxiv.org/content/10.1101/833756v1?rss=1 Kather, J. N. Heij, L. R. Grabsch, H. I. Kooreman, L. F. Loeffler, C. Echle, A. Krause, J. Muti, H. S. Niehues, J. M. Sommer, K. A. Bankhead, P. Schulte, J. J. Cipriani, N. A. Ortiz-Bruechle, N. Patnaik, A. Srisuwananukorn, A. Brenner, H. Hoffmeister, M. Van den Brandt, P. A. Jaeger, D. Trautwein, C. Pearson, A. T. Luedde, T. 2019-11-08 doi:10.1101/833756 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Bayesian Modeling Reveals Ultrasensitivity Underlying Metabolic Compensation in the Cyanobacterial Circadian Clock ]]> https://biorxiv.org/content/10.1101/835280v1?rss=1 Hong, L. Lavrentovich, D. O. Chavan, A. Leypunskiy, E. Li, E. Matthews, C. LiWang, A. Rust, M. J. Dinner, A. R. 2019-11-08 doi:10.1101/835280 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Accelerating functional gene discovery in osteoarthritis ]]> https://biorxiv.org/content/10.1101/836221v1?rss=1 Butterfield, N. C. Curry, K. F. Steinberg, J. Dewhurst, H. Komla-Ebri, D. Mannan, N. S. Adoum, A.-T. Leitch, V. D. Logan, J. G. Waung, J. A. Ghirardello, E. Southam, L. Youlten, S. E. Wilkinson, J. M. McAninch, E. A. Vancollie, V. E. Kussy, F. White, J. K. Adams, D. J. Lelliott, C. J. Jacques, R. Bianco, A. C. Boyde, A. Zeggini, E. Croucher, P. I. Williams, G. R. Bassett, J. H. D. 2019-11-10 doi:10.1101/836221 Cold Spring Harbor Laboratory Press 2019-11-10 <![CDATA[ Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx ]]> https://biorxiv.org/content/10.1101/836825v1?rss=1 0.7), providing a resource to enhance functional follow-up.nnConclusionsWe provide a local ancestry map for admixed individuals in the final GTEx release and describe the impact of ancestry and admixture on gene expression, eQTLs, and GWAS colocalization. While the majority of results are concordant between local and global ancestry-based adjustments, we identify distinct advantages and disadvantages to each approach. ]]> Gay, N. R. Gloudemans, M. Antonio, M. L. L. Balliu, B. Park, Y. Martin, A. R. Musharoff, S. Rao, A. Aguet, F. Barbeira, A. Bonazzola, R. Hormozdiari, F. GTEx Consortium, Ardlie, K. G. Brown, C. D. Im, H. K. Lappalainen, T. Wen, X. Montgomery, S. B. 2019-11-09 doi:10.1101/836825 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Covert spatial attention speeds target individuation ]]> https://biorxiv.org/content/10.1101/838557v1?rss=1 Foster, J. J. Bsales, E. M. Awh, E. 2019-11-12 doi:10.1101/838557 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ 6mer seed toxicity in viral microRNAs ]]> https://biorxiv.org/content/10.1101/838979v1?rss=1 Murmann, A. E. Bartom, E. T. Schipma, M. J. Vilker, J. Chen, S. Peter, M. E. 2019-11-12 doi:10.1101/838979 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Targeted complement inhibition at synapses prevents microglial synaptic engulfment and synapse loss in demyelinating disease ]]> https://biorxiv.org/content/10.1101/841601v1?rss=1 Werneburg, S. Jung, J. Kunjamma, R. B. Ha, S.-K. Luciano, N. J. Willis, C. M. Gao, G. Crocker, S. J. Popko, B. Reich, D. S. Schafer, D. P. 2019-11-15 doi:10.1101/841601 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Distinct representational structure and spatial distribution for visual encoding and recall ]]> https://biorxiv.org/content/10.1101/842120v1?rss=1 Bainbridge, W. A. Hall, E. H. Baker, C. I. 2019-11-14 doi:10.1101/842120 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ A precision medicine approach uncovers a unique signature of neutrophils in patients with brushite kidney stones ]]> https://biorxiv.org/content/10.1101/844142v1?rss=1 Makki, M. S. Winfree, S. Lingeman, J. E. Witzmann, F. A. Worcester, E. M. Krambeck, A. Coe, F. Evan, A. P. Bledsoe, S. Bergsland, K. Khochare, S. Barwinska, D. Willliams, J. C. El-Achkar, T. M. 2019-11-16 doi:10.1101/844142 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ A comparison of humans and baboons suggests germline mutation rates do not track cell divisions ]]> https://biorxiv.org/content/10.1101/844910v1?rss=1 Wu, F. L. Strand, A. Ober, C. Wall, J. D. Moorjani, P. Przeworski, M. 2019-11-16 doi:10.1101/844910 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Alternative polyadenylation mediates genetic regulation of gene expression ]]> https://biorxiv.org/content/10.1101/845966v1?rss=1 Mittleman, B. E. Pott, S. Warland, S. Zheng, T. Laur, M. Gilad, Y. Li, Y. 2019-11-17 doi:10.1101/845966 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Tensor Image Registration Library: Automated Non-Linear Registration of Sparsely Sampled Histological Specimens to Post-Mortem MRI of the Whole Human Brain ]]> https://biorxiv.org/content/10.1101/849570v1?rss=1 Huszar, I. N. Pallebage-Gamarallage, M. Foxley, S. Tendler, B. C. Leonte, A. Hiemstra, M. Mollink, J. Smart, A. Bangerter-Christensen, S. Brooks, H. Turner, M. R. Ansorge, O. Miller, K. L. Jenkinson, M. 2019-11-26 doi:10.1101/849570 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification ]]> https://biorxiv.org/content/10.1101/850800v1?rss=1 Pilosof, S. Alcala-Corona, S. A. Wang, T. Kim, T. Maslov, S. Whitaker, R. J. Pascual, M. 2019-11-22 doi:10.1101/850800 Cold Spring Harbor Laboratory Press 2019-11-22 <![CDATA[ Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq ]]> https://biorxiv.org/content/10.1101/852038v1?rss=1 1,000 nt), and often overlap those of adjacent transcripts. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. By capturing the 5 ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle resulting in an updated view of the P. falciparum transcriptome. ]]> Chappell, L. Ross, P. Orchard, L. Otto, T. D. Berriman, M. Rayner, J. C. Llinas, M. 2019-11-26 doi:10.1101/852038 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ CORE GREML: Estimating covariance between random effects in linear mixed models for genomic analyses of complex traits ]]> https://biorxiv.org/content/10.1101/853515v1?rss=1 Zhou, X. Im, H. K. Lee, S. H. 2019-11-25 doi:10.1101/853515 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Skap2 Regulates Atherosclerosis through Macrophage Polarization and Efferocytosis ]]> https://biorxiv.org/content/10.1101/857649v1?rss=1 Hyatt, D. Schroeder, A. E. Bhatnagar, A. Golan, D. E. Swanson, K. D. Alenghat, F. J. 2019-12-02 doi:10.1101/857649 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Identifying Operons with Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/860221v1?rss=1 Assaf, R. Xia, F. Stevens, R. 2019-12-01 doi:10.1101/860221 Cold Spring Harbor Laboratory Press 2019-12-01 <![CDATA[ Use of multi-flip angle measurements to account for transmit inhomogeneity and non-Gaussian diffusion in DW-SSFP ]]> https://biorxiv.org/content/10.1101/861880v1?rss=1 Tendler, B. C. Foxley, S. Hernandez-Fernandez, M. Cottaar, M. Scott, C. Ansorge, O. Miller, K. Jbabdi, S. 2019-12-02 doi:10.1101/861880 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Mice preferentially use increases in cerebral cortex spike rates to detect changes in visual stimuli ]]> https://biorxiv.org/content/10.1101/865410v1?rss=1 Cone, J. J. Bade, M. L. Masse, N. Y. Page, E. A. Freedman, D. J. Maunsell, J. H. 2019-12-04 doi:10.1101/865410 Cold Spring Harbor Laboratory Press 2019-12-04 <![CDATA[ Quantifying Aphantasia through drawing: Those without visual imagery show deficits in object but not spatial memory ]]> https://biorxiv.org/content/10.1101/865576v1?rss=1 Bainbridge, W. A. Pounder, Z. Eardley, A. F. Baker, C. I. 2019-12-05 doi:10.1101/865576 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Competition between kinesin-1 and myosin-V define Drosophila posterior determination ]]> https://biorxiv.org/content/10.1101/866467v1?rss=1 Lu, W. Lakonishok, M. Liu, R. Billington, N. Rich, A. Glotzer, M. Sellers, J. R. Gelfand, V. I. 2019-12-05 doi:10.1101/866467 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ RADAR: Differential analysis of MeRIP-seq data with a random effect model ]]> https://biorxiv.org/content/10.1101/867903v1?rss=1 Zhang, Z. Zhan, Q. Eckert, M. Zhu, A. Chryplewicz, A. De Jesus, D. F. Ren, D. Kulkarni, R. N. Lengyel, E. He, C. Chen, M. 2019-12-06 doi:10.1101/867903 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Antibiotic degradation by commensal microbes shields pathogens ]]> https://biorxiv.org/content/10.1101/870931v1?rss=1 Gjonbalaj, M. Keith, J. W. Do, M. Hohl, T. Pamer, E. Becattini, S. 2019-12-10 doi:10.1101/870931 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Pragmatic Language Processing in the Adolescent Brain ]]> https://biorxiv.org/content/10.1101/871343v1?rss=1 Asaridou, S. S. Demir-Lira, E. Udden, J. S. Goldin-Meadow, S. Small, S. L. 2019-12-11 doi:10.1101/871343 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ A simple model-based approach to inferring and visualizing cancer mutation signatures ]]> https://biorxiv.org/content/10.1101/019901v1?rss=1 A mutations are frequent in lung caners whereas C > T and CC > TT mutations are frequent in skin cancers. Each mutation signature may be associated with a specific kind of carcinogen, such as tobacco smoke or ultraviolet light. Identifying mutation signatures therefore has the potential to identify new carcinogens, and yield new insights into the mechanisms and causes of cancer,nnIn this paper, we introduce new statistical tools for tackling this important problem. These tools provide more robust and interpretable mutation signatures compared to previous approaches, as we demonstrate by applying them to large-scale cancer genomic data. ]]> Yuichi Shiraishi Georg Tremmel Satoru Miyano Matthew Stephens 2015-05-27 doi:10.1101/019901 Cold Spring Harbor Laboratory Press 2015-05-27 <![CDATA[ False Discovery Rates: A New Deal. ]]> https://biorxiv.org/content/10.1101/038216v1?rss=1 Matthew Stephens 2016-01-29 doi:10.1101/038216 Cold Spring Harbor Laboratory Press 2016-01-29 <![CDATA[ SNP-based heritability estimation: measurement noise, population stratification and stability ]]> https://biorxiv.org/content/10.1101/040055v1?rss=1 Eric R Gamazon Danny S Park 2016-02-18 doi:10.1101/040055 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Architectures of a lipid transport systems for the bacterial outer membrane ]]> https://biorxiv.org/content/10.1101/064360v1?rss=1 Damian C Ekiert Gira Bhabha Garrett Greenan Sergey Ovchinnikov Jeffery S Cox Ronald D Vale 2016-07-18 doi:10.1101/064360 Cold Spring Harbor Laboratory Press 2016-07-18 <![CDATA[ Distinct cAMP signaling modalities mediate behavioral flexibility and consolidation of social status in Drosophila aggression. ]]> https://biorxiv.org/content/10.1101/089979v1?rss=1 Chouhan, N. S. Mohan, K. Ghose, A. 2016-11-27 doi:10.1101/089979 Cold Spring Harbor Laboratory Press 2016-11-27 <![CDATA[ The DOE Systems Biology Knowledgebase (KBase) ]]> https://biorxiv.org/content/10.1101/096354v1?rss=1 Arkin, A. P. Stevens, R. L. Cottingham, R. W. Maslov, S. Henry, C. S. Dehal, P. Ware, D. Perez, F. Harris, N. L. Canon, S. Sneddon, M. W. Henderson, M. L. Riehl, W. J. Gunter, D. Murphy-Olson, D. Chan, S. Kamimura, R. T. Brettin, T. S. Meyer, F. Chivian, D. Weston, D. J. Glass, E. M. Davison, B. H. Kumari, S. Allen, B. H. Baumohl, J. Best, A. A. Bowen, B. Brenner, S. E. Bun, C. C. Chandonia, J.-M. Chia, J.-M. Colasanti, R. Conrad, N. Davis, J. J. DeJongh, M. Devoid, S. Dietrich, E. Drake, M. M. Dubchak, I. Edirisinghe, J. N. Fang, G. Faria, J. P. Fryb 2016-12-22 doi:10.1101/096354 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions ]]> https://biorxiv.org/content/10.1101/096552v1?rss=1 Urbut, S. M. Wang, G. Stephens, M. 2016-12-24 doi:10.1101/096552 Cold Spring Harbor Laboratory Press 2016-12-24 <![CDATA[ DroNc-Seq: Deciphering cell types in human archived brain tissues by massively-parallel single nucleus RNA-seq ]]> https://biorxiv.org/content/10.1101/115196v1?rss=1 Habib, N. Basu, A. Avraham-Davidi, I. Burks, T. Choudhury, S. R. Aguet, F. Gelfand, E. Ardlie, K. Weitz, D. A. Rozenblatt-Rosen, O. Zhang, F. Regev, A. 2017-03-09 doi:10.1101/115196 Cold Spring Harbor Laboratory Press 2017-03-09 <![CDATA[ Effects of mutation and selection on plasticity of TDH3 promoter activity in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/173344v1?rss=1 Duveau, F. Yuan, D. C. Metzger, B. P. H. Hodgins-Davis, A. Wittkopp, P. J. 2017-08-08 doi:10.1101/173344 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ ebony affects pigmentation divergence and cuticular hydrocarbons in Drosophila americana and D. novamexicana ]]> https://biorxiv.org/content/10.1101/2020.03.05.977009v1?rss=1 Lamb, A. M. Wang, Z. Simmer, P. Chung, H. Wittkopp, P. J. 2020-03-06 doi:10.1101/2020.03.05.977009 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Cell-free styrene biosynthesis at high titers ]]> https://biorxiv.org/content/10.1101/2020.03.05.979302v1?rss=1 Grubbe, W. S. Rasor, B. J. Kruger, A. Jewett, M. C. Karim, A. S. 2020-03-06 doi:10.1101/2020.03.05.979302 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Enhancer and Promoter Usage in the Normal and Failed Human Heart ]]> https://biorxiv.org/content/10.1101/2020.03.17.988790v1?rss=1 Gacita, A. M. Dellefave-Castillo, L. Page, P. G. T. Barefield, D. Y. Wasserstrom, A. Puckelwartz, M. J. Nobrega, M. A. McNally, E. M. 2020-03-19 doi:10.1101/2020.03.17.988790 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.03.28.012823v1?rss=1 Ward, M. C. Banovich, N. E. Sarkar, A. Stephens, M. Gilad, Y. 2020-03-29 doi:10.1101/2020.03.28.012823 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ The Sec63/BiP complex suppresses higher-order oligomerization and RNase activity of IRE1α during ER stress ]]> https://biorxiv.org/content/10.1101/2020.04.03.024356v1?rss=1 Li, X. Sun, S. Appathurai, S. Sundaram, A. Plumb, R. Mariappan, M. 2020-04-04 doi:10.1101/2020.04.03.024356 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ iPSC-derived hepatocytes from patients with nonalcoholic fatty liver disease display a disease-specific gene expression profile ]]> https://biorxiv.org/content/10.1101/2020.04.20.052001v1?rss=1 Duwaerts, C. C. Her, C. L. Phillips, N. J. Willenbring, H. Mattis, A. N. Maher, J. J. 2020-04-22 doi:10.1101/2020.04.20.052001 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Larval zebrafish respond to the alarm pheromone Schreckstoff by immobility and a change in brain state ]]> https://biorxiv.org/content/10.1101/2020.04.23.054734v1?rss=1 Jesuthasan, S. J. Krishnan, S. Cheng, R.-K. Mathuru, A. 2020-04-25 doi:10.1101/2020.04.23.054734 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ FGF signaling regulates development through combinatorial transduction pathways and by modulating cellular adhesion ]]> https://biorxiv.org/content/10.1101/2020.05.13.093252v1?rss=1 Ray, A. Mazot, P. Brewer, J. R. Catela, C. Soriano, P. 2020-05-14 doi:10.1101/2020.05.13.093252 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Precise detection of Acrs in prokaryotes using only six features ]]> https://biorxiv.org/content/10.1101/2020.05.23.112011v1?rss=1 Dong, C. Pu, D.-K. Ma, C. Wang, X. Wen, Q.-F. Zeng, Z. Guo, F.-B. 2020-05-26 doi:10.1101/2020.05.23.112011 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Molecular Basis of Far-red Sensing in Cyanobacteriochrome ]]> https://biorxiv.org/content/10.1101/2020.06.02.130930v1?rss=1 Bandara, S. Rockwell, N. C. Zeng, X. Ren, Z. Wang, C. Shin, H. Martin, S. Moreno, M. Lagarias, J. C. Yang, X. 2020-06-03 doi:10.1101/2020.06.02.130930 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Gene Expression Imputation with Generative Adversarial Imputation Nets ]]> https://biorxiv.org/content/10.1101/2020.06.09.141689v1?rss=1 Vinas Torne, R. Azevedo, T. Gamazon, E. Lio, P. 2020-06-10 doi:10.1101/2020.06.09.141689 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Genetic architecture of host proteins interacting with SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.01.182709v1?rss=1 Pietzner, M. Wheeler, E. Carrasco-Zanini, J. Raffler, J. Kerrison, N. D. Oerton, E. Auyeung, V. P. W. Luan, J. Finan, C. Casas, J. P. Ostroff, R. Williams, S. A. Kastenmüller, G. Ralser, M. Gamazon, E. G. Wareham, N. J. Hingorani, A. D. Langenberg, C. 2020-07-01 doi:10.1101/2020.07.01.182709 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Publicly available hiPSC lines with extreme polygenic risk scores for modeling schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.07.04.185348v1?rss=1 Rehbach, K. Zhang, H. Das, D. Sara Abdollahi, S. Prorok, T. Ghosh, S. Weintraub, S. Genovese, G. Powell, S. Lund, A. Akbarian, S. Eggan, K. McCarroll, S. A. Duan, J. Avramopoulos, D. Brennand, K. J. 2020-07-04 doi:10.1101/2020.07.04.185348 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors ]]> https://biorxiv.org/content/10.1101/2020.08.06.240192v1?rss=1 Osipiuk, J. Azizi, S.-A. Dvorkin, S. Endres, M. Jedrzejczak, R. Jones, K. A. Kathayat, R. S. Lisnyak, V. G. Maki, S. L. Kang, S. Kim, Y. Nicolaescu, V. Taylor, C. A. Tesar, C. Zhang, Y.-A. Zhou, Z. Randall, G. Michalska, K. Snyder, S. A. Dickinson, B. C. Joachimiak, A. 2020-08-06 doi:10.1101/2020.08.06.240192 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ GHB confers neuroprotection by stabilizing the CaMKIIα hub domain ]]> https://biorxiv.org/content/10.1101/2020.09.28.310474v1?rss=1 Leurs, U. Klein, A. B. McSpadden, E. D. Griem-Krey, N. Solbak, S. M. Houlton, J. Villumsen, I. S. Vogensen, S. B. Hamborg, L. Gauger, S. J. Palmelund, L. B. Larsen, A. S. G. Shehata, M. A. Kelstrup, C. D. Olsen, J. V. Bach, A. Burnie, R. O. Kerr, D. S. Gowing, E. K. Teurlings, S. M. W. Chi, C. C. Gee, C. L. Frolund, B. Kornum, B. R. van Woerden, G. M. Clausen, R. P. Kuriyan, J. Clarkson, A. N. Wellendorph, P. 2020-09-28 doi:10.1101/2020.09.28.310474 Cold Spring Harbor Laboratory Press 2020-09-28 <![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[ Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation ]]> https://biorxiv.org/content/10.1101/2020.10.15.341503v1?rss=1 Coe, A. Biller, S. Thomas, E. Boulias, K. Bliem, C. Arellano, A. Dooley, K. Rasmussen, A. N. LeGault, K. O'Keefe, T. J. Greer, E. L. Chisholm, S. W. 2020-10-15 doi:10.1101/2020.10.15.341503 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Human antigen-specific memory natural killer cell responses develop against HIV-1 and influenza virus and are dependent on MHC-E restriction ]]> https://biorxiv.org/content/10.1101/2020.11.09.374348v1?rss=1 Jost, S. Lucar, O. Yoder, T. Kroll, K. Sugawara, S. Smith, S. Jones, R. Tweet, G. Werner, A. Tomezsko, P. J. Dugan, H. L. Ghofrani, J. Altfeld, M. Grundhoff, A. Muller-Trutwin, M. Goepfert, P. Reeves, R. K. 2020-11-10 doi:10.1101/2020.11.09.374348 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Quantification of Brucella abortus population structure in a natural host ]]> https://biorxiv.org/content/10.1101/2020.11.12.380766v1?rss=1 Fiebig, A. Vrentas, C. E. Le, T. M. Huebner, M. Boggiatto, P. M. Olsen, S. C. Crosson, S. 2020-11-13 doi:10.1101/2020.11.12.380766 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Peptide Ancestry Informative Markers in Uterine Neoplasms from Women of European, African and Asian Ancestry ]]> https://biorxiv.org/content/10.1101/2020.11.23.380337v1?rss=1 260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms. ]]> Bateman, N. W. Tarney, C. Abulez, T. Hood, B. L. Conrads, K. Zhou, M. Soltis, A. R. Teng, P.-i. Jackson, A. Tian, C. Dalgard, C. Wilkerson, M. Kessler, M. Shriver, C. D. Hu, H. Cote, M. Parker, G. J. Segars, J. Al-Hendy, A. Risinger, J. Darcy, K. Casablanca, Y. George, M. L. Conrads, T. P. O'Connor, T. D. 2020-11-23 doi:10.1101/2020.11.23.380337 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Highly multiplexed quantitative phosphosite assay for biology and preclinical studies ]]> https://biorxiv.org/content/10.1101/2020.12.08.415281v1?rss=1 Keshishian, H. McDonald, E. R. Melanson, R. Porter, D. A. Mundth, F. Krug, K. Wallace, L. Forestier, D. Rabasha, B. Marlow, S. E. Jane-Valbuena, J. Todres, E. Specht, H. Golji, J. Kuhn, E. Burgess, M. MacMullan, M. Satpathy, S. Mani, D. R. Gillette, M. Clauser, K. Rejtar, T. Wang, K. Garraway, L. A. Sellers, W. R. Carr, S. A. 2020-12-09 doi:10.1101/2020.12.08.415281 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ A protease-initiated model of wound detection ]]> https://biorxiv.org/content/10.1101/2020.12.08.415554v1?rss=1 O'Connor, J. T. Stevens, A. C. Shannon, E. K. Akbar, F. B. LaFever, K. S. Narayanan, N. Hutson, M. S. Page-McCaw, A. 2020-12-09 doi:10.1101/2020.12.08.415554 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Genetic variation among wMel strains of Wolbachia pipientis differentially rescues a bag of marbles partial loss of function mutant in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.01.15.426050v1?rss=1 Bubnell, J. E. Ulbing, C. K. Fernandez Begne, P. Aquadro, C. F. 2021-01-17 doi:10.1101/2021.01.15.426050 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Mechanisms Driving Genome Reduction of a Novel Roseobacter Lineage Showing Vitamin B12 Auxotrophy ]]> https://biorxiv.org/content/10.1101/2021.01.15.426902v1?rss=1 4 Mbp). These taxonomic minorities are phylogenetically diverse but form a Pelagic Roseobacter Cluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novel Roseobacter lineage which we named CHUG. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members were globally distributed and active in marine environments. CHUG members possess some of the smallest genomes (~2.52 Mb) among all known roseobacters, but they do not exhibit canonical features of genome streamlining like higher coding density or fewer paralogues and pseudogenes compared to their sister lineages. While CHUG members are clustered with traditional PRC members at the genome content level, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their gene expression levels are correlated with chlorophyll a concentration across the global samples. Moreover, CHUG members cannot synthesize vitamin B12, a key metabolite made by most roseobacters but not by many phytoplankton species and thus thought to mediate the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection is likely an important driver of genome reduction in CHUG. ]]> Feng, X. Chu, X. Qian, Y. Henson, M. W. Lanclos, V. C. Qin, F. Zhao, Y. Thrash, C. Luo, H. 2021-01-16 doi:10.1101/2021.01.15.426902 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ CometChip Enables Parallel Analysis of Multiple DNA Repair Activities ]]> https://biorxiv.org/content/10.1101/2021.01.19.427336v1?rss=1 Ge, J. Ngo, L. P. Kaushal, S. Tay, I. J. Thadhani, E. Kay, J. E. Mazzucato, P. Chow, D. N. Fessler, J. L. Weingeist, D. M. Sobol, R. W. Samson, L. D. Floyd, S. R. Engelward, B. P. 2021-01-20 doi:10.1101/2021.01.19.427336 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Induction of a colitogenic phenotype in Th1 cells depends on IL-23R signaling ]]> https://biorxiv.org/content/10.1101/2021.01.24.426445v1?rss=1 Pawlak, M. DeTomaso, D. Meyer zu Horste, G. Lee, Y. Nyman, J. Dionne, D. Wang, C. Wallrapp, A. Burkett, P. R. Riesenfeld, S. J. Anderson, A. C. Regev, A. Xavier, R. J. Yosef, N. Kuchroo, V. K. 2021-01-26 doi:10.1101/2021.01.24.426445 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Interpretable prioritization of splice variants in diagnostic next-generation sequencing ]]> https://biorxiv.org/content/10.1101/2021.01.28.428499v1?rss=1 Danis, D. Jacobsen, J. O. B. Carmody, L. Gargano, M. A. McMurry, J. A. Hegde, A. Haendel, M. A. Valentini, G. Smedley, D. Robinson, P. N. 2021-01-28 doi:10.1101/2021.01.28.428499 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures ]]> https://biorxiv.org/content/10.1101/2021.02.13.431008v1?rss=1 Shen, Z. Ratia, K. Cooper, L. Kong, D. Lee, H. Kwon, Y. Li, Y. Alqarni, S. Huang, F. Dubrovskyi, O. Rong, L. Thatcher, G. R. XIONG, R. 2021-02-15 doi:10.1101/2021.02.13.431008 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2021.02.22.432283v1?rss=1 Duveau, F. Vande Zande, P. Metzger, B. P. H. Diaz, C. J. Walker, E. A. Tryban, S. Siddiq, M. A. Yang, B. Wittkopp, P. J. 2021-02-22 doi:10.1101/2021.02.22.432283 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Re-evaluating rhythmic attentional switching: Spurious oscillations from shuffling-in-time ]]> https://biorxiv.org/content/10.1101/2021.05.07.443101v1?rss=1 Brookshire, G. 2021-05-09 doi:10.1101/2021.05.07.443101 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Zones of Cellular Damage Around Pulsed-Laser Wounds ]]> https://biorxiv.org/content/10.1101/2021.05.28.446116v1?rss=1 O'Connor, J. Akbar, F. B. Hutson, M. S. Page-McCaw, A. 2021-05-28 doi:10.1101/2021.05.28.446116 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Adaptive shifts underlie the divergence in wing morphology in bombycoid moths ]]> https://biorxiv.org/content/10.1101/2021.06.23.449655v1?rss=1 Aiello, B. R. Tan, M. Bin Sikandar, U. Alvey, A. J. Bhinderwala, B. Kimball, K. Barber, J. Hamilton, C. A. Kawahara, A. Y. Sponberg, S. 2021-06-24 doi:10.1101/2021.06.23.449655 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Functional divergence of the bag of marbles gene in the Drosophila melanogaster species group ]]> https://biorxiv.org/content/10.1101/2021.06.25.449946v1?rss=1 Bubnell, J. E. Ulbing, C. K. Fernandez Begne, P. Aquadro, C. F. 2021-06-25 doi:10.1101/2021.06.25.449946 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Cellular and behavioral effects of altered NaV1.2 sodium channel ion permeability in Scn2aK1422E mice ]]> https://biorxiv.org/content/10.1101/2021.07.19.452930v1?rss=1 Echevarria-Cooper, D. M. Hawkins, N. A. Misra, S. N. Huffman, A. Thaxton, T. Thompson, C. H. Ben-Shalom, R. Nelson, A. D. Lipkin, A. M. George, A. L. Bender, K. J. Kearney, J. A. 2021-07-19 doi:10.1101/2021.07.19.452930 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Repair of Noise-Induced Damage to Stereocilia F-actin Cores is Facilitated by XIRP2 ]]> https://biorxiv.org/content/10.1101/2021.08.10.455815v1?rss=1 Wagner, E. L. Im, J.-S. Nakahata, M. I. Imbery, T. E. Li, S. Chen, D. B. Noy, Y. Archer, D. W. Xu, W. Hashisaki, G. T. Avraham, K. B. Shin, J.-B. 2021-08-10 doi:10.1101/2021.08.10.455815 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Mapping of genotype-by-environment interactions in phenology identifies two cues for flowering in switchgrass (Panicum virgatum) ]]> https://biorxiv.org/content/10.1101/2021.08.19.456975v1?rss=1 MacQueen, A. H. Zhang, L. Bonette, J. Boe, A. R. Fay, P. A. Fritschi, F. B. Lowry, D. B. Mitchell, R. B. Rouquette, F. M. Wu, Y. Juenger, T. E. 2021-08-19 doi:10.1101/2021.08.19.456975 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges ]]> https://biorxiv.org/content/10.1101/2021.08.26.457769v1?rss=1 Clark, C. M. Hernandez, A. Mullowney, M. W. Fitz-Henley, J. Li, E. Romanowski, S. B. Pronzato, R. Manconi, R. Murphy, B. T. 2021-08-26 doi:10.1101/2021.08.26.457769 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The role of antigen recognition in the γδ T cell response at the controlled stage of M. tuberculosis infection. ]]> https://biorxiv.org/content/10.1101/2021.09.14.460324v1?rss=1 Roy Chowdhury, R. Valainis, J. R. Kask, O. Ohanyan, M. Sun, M. Huang, H. Dubey, M. von Boehmer, L. Sola, E. Huang, X. Nguyen, P. K. Scriba, T. Davis, M. M. Bendall, S. C. Chien, Y.-h. 2021-09-15 doi:10.1101/2021.09.14.460324 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy ]]> https://biorxiv.org/content/10.1101/2021.09.27.461980v1?rss=1 Mika, K. Whittington, C. M. McAllan, B. M. Lynch, V. J. 2021-09-27 doi:10.1101/2021.09.27.461980 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Ormyrus labotus Walker (Hymenoptera: Ormyridae): another generalist that should not be a generalist is not a generalist ]]> https://biorxiv.org/content/10.1101/2021.10.26.465982v1?rss=1 Sheikh, S. I. Ward, A. K. G. Zhang, Y. M. Davis, C. K. Zhang, L. Egan, S. P. Forbes, A. A. 2021-10-28 doi:10.1101/2021.10.26.465982 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution ]]> https://biorxiv.org/content/10.1101/2021.12.23.474023v1?rss=1 Panibe, J. P. Wang, L. Lee, Y.-C. Wang, C.-S. Li, W.-H. 2021-12-24 doi:10.1101/2021.12.23.474023 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Loss-of-function of OTUD7A in the schizophrenia-associated 15q13.3 deletion impairs synapse development and function in human neurons ]]> https://biorxiv.org/content/10.1101/2022.01.06.473910v1?rss=1 Kozlova, A. Zhang, S. Kotlar, A. V. Jamison, B. Zhang, H. Shi, S. Forrest, M. P. McDaid, J. Cutler, D. J. Epstein, M. P. Zwick, M. E. Pang, Z. P. Sanders, A. R. Warren, S. T. Gejman, P. V. Mulle, J. G. Duan, J. 2022-01-07 doi:10.1101/2022.01.06.473910 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ A bivalent EBV vaccine induces neutralizing antibodies that block B and epithelial cell infection and confer immunity in humanized mice ]]> https://biorxiv.org/content/10.1101/2022.01.18.476774v1?rss=1 Wei, C.-J. Bu, W. Nguyen, L. A. Batchelor, J. D. Kim, J. Pittaluga, S. Fuller, J. R. Nguyen, H. Chou, T.-H. Cohen, J. Nabel, G. J. 2022-01-20 doi:10.1101/2022.01.18.476774 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Tyrosine phosphorylation of mitofusin 2 regulates endoplasmic reticulum-mitochondria tethering ]]> https://biorxiv.org/content/10.1101/2022.02.21.481295v1?rss=1 Zhang, P. Ford, K. Sung, J. H. Moeller, J. Suzuki, Y. Polina, I. Tachibana, T. Kusakari, Y. Cypress, M. W. Chaput, I. Drenkova, K. Landherr, M. Adaniya, S. M. Mishra, J. Mende, U. Jhun, B. S. O-Uchi, J. 2022-02-21 doi:10.1101/2022.02.21.481295 Cold Spring Harbor Laboratory Press 2022-02-21 <![CDATA[ DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse ]]> https://biorxiv.org/content/10.1101/2022.03.24.485667v1?rss=1 Zhou, W. Hinoue, T. Barnes, B. Mitchell, O. Iqbal, W. Lee, S. M. Foy, K. K. Lee, K.-H. Moyer, E. J. VanderArk, A. Koeman, J. M. Ding, W. Kalkat, M. Spix, N. J. Eagleson, B. Pospisilik, J. A. Szabo, P. E. Bartolomei, M. S. Schaaf, N. A. V. Kang, L. Wiseman, A. K. Jones, P. A. Krawczyk, C. M. Adams, M. Porecha, R. Chen, B. H. Shen, H. Laird, P. W. 2022-03-27 doi:10.1101/2022.03.24.485667 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Manipulating the 3D organization of the largest synthetic yeast chromosome ]]> https://biorxiv.org/content/10.1101/2022.04.09.487066v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@18bf586org.highwire.dtl.DTLVardef@1a471d5org.highwire.dtl.DTLVardef@12d7690org.highwire.dtl.DTLVardef@1c32510_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDe novo synthesis of the largest eukaryotic chromosome, synIV C_LIO_LISynIV shows similar 3D structure to wild-type IV, despite thousands of changes made to it C_LIO_LI"Inside-out" repositioning of synIV in nucleus shows minor transcriptional changes C_LIO_LIMultipoint tethering synIV to inner nuclear membrane represses transcription of whole chromosome C_LI ]]> Zhang, W. Stefanita, L. L. Yamashita, H. Shen, M. J. Mitchell, L. A. Kurasawa, H. Haase, M. A. B. Sun, X. Jiang, Q. Lauer, S. L. McCulloch, L. H. Zhao, Y. Ichikawa, D. Easo, N. Lin, S. J. Fanfani, V. Camellato, B. R. Zhu, Y. Cai, J. Xu, Z. Sacasa, M. Accardo, R. Ahn, J. Y. Annadanam, S. Brammer Basta, L. A. Bello, N. Cai, L. Cerritos, S. Cornwell, M. D'Amato, A. Hacker, M. Hersey, K. Kennedy, E. Kianercy, A. Kim, D. Lim, H. S. McCutcheon, G. McGirr, K. Meaney, N. Meyer, L. Moyer, A. Nimer, M. Sabbatini, C. Scheifele, L. Shores, L. Silvestrone, C. S 2022-04-10 doi:10.1101/2022.04.09.487066 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2022.04.26.489564v1?rss=1 Dubose, C. O. Daum, J. R. Sansam, C. L. Gorbsky, G. J. 2022-04-27 doi:10.1101/2022.04.26.489564 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ NPC1 confers metabolic flexibility in Triple Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.05.05.490674v1?rss=1 O'Neill, K. I. Kuo, L.-W. Williams, M. M. Lind, H. T. Crump, L. S. Hammond, N. G. Spoelstra, N. S. Caino, M. C. Richer, J. K. 2022-05-05 doi:10.1101/2022.05.05.490674 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death during Mammary Gland Involution ]]> https://biorxiv.org/content/10.1101/2022.05.17.492309v1?rss=1 JEONG, J. Lee, J. Talaia, G. Kim, W. Song, J. Yoo, K. Gonzalez, D. Athonvarangkul, D. Shin, J. Dann, P. Haberman, A. Kim, L. K. Ferguson, S. Choi, J. Wysolmerski, J. 2022-05-17 doi:10.1101/2022.05.17.492309 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ A single closed head injury in mice induces chronic, progressive white matter atrophy and increased phospho-tau expressing oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2022.05.19.492705v1?rss=1 Havlicek, D. F. Furhang, R. Nikulina, E. Smith-Salzberg, B. Lawless, S. Severin, S. A. Mallaboeva, S. Nayab, F. Seifert, A. C. Crary, J. F. Bergold, P. 2022-05-20 doi:10.1101/2022.05.19.492705 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Drosophila embryos spatially sort their nutrient stores to facilitate their utilization ]]> https://biorxiv.org/content/10.1101/2022.05.20.492771v1?rss=1 Kilwein, M. D. Johnson, M. R. Thomalla, J. M. Mahowald, A. Welte, M. A. 2022-05-20 doi:10.1101/2022.05.20.492771 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Definition of a saxitoxin (STX) binding code enables discovery and characterization of the Anuran saxiphilin family ]]> https://biorxiv.org/content/10.1101/2022.06.09.495489v1?rss=1 Chen, Z. Zakrzewska, S. Hajare, H. S. Alvarez-Buylla, A. Abderemane-Ali, F. Bogan, M. Ramirez, D. O'Connell, L. A. Du Bois, J. Minor, D. L. 2022-06-10 doi:10.1101/2022.06.09.495489 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Gene expression as phenotype - Many small-step changes leading to little long-term phenotypic evolution ]]> https://biorxiv.org/content/10.1101/2022.06.24.497468v1?rss=1 Lin, P. Lu, G.-A. Liufu, Z.-Q. Zhao, Y. Ruan, Y.-S. Wu, C.-I. Wen, H.-J. 2022-06-28 doi:10.1101/2022.06.24.497468 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Multiplexed and millimeter-scale superresolution imaging of cells and tissue sections via prism-illumination and microfluidics-enhanced DNA-PAINT ]]> https://biorxiv.org/content/10.1101/2022.08.07.503091v1?rss=1 Rames, M. J. Kenison, J. Heineck, D. Civitci, F. Szczepaniak, M. Tao, K. Zheng, T. Shangguan, J. Esener, S. Nan, X. 2022-08-07 doi:10.1101/2022.08.07.503091 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast ]]> https://biorxiv.org/content/10.1101/2022.08.26.505417v1?rss=1 Bhattacharjee, R. Hall, A. Mangione, M. C. Igarashi, M. G. Roberts-Galbraith, R. H. Chen, J.-S. Vavylonis, D. Gould, K. 2022-08-26 doi:10.1101/2022.08.26.505417 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Structural insights into pore dynamics of human Pannexin isoforms ]]> https://biorxiv.org/content/10.1101/2022.09.09.507385v1?rss=1 Hussain, N. Apotikar, A. Pidathala, S. Mukherjee, S. Burada, A. P. Sikdar, S. K. Kutti, V. R. Penmatsa, A. 2022-09-10 doi:10.1101/2022.09.09.507385 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Small-molecule ketone esters treat brain network abnormalities in an Alzheimer's disease mouse model ]]> https://biorxiv.org/content/10.1101/2022.09.24.509337v1?rss=1 Newman, J. C. Ma, K. Kroll, F. Higgins, E. Ulrich, S. Palop, J. J. Verdin, E. 2022-09-26 doi:10.1101/2022.09.24.509337 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Inflammation drives age-induced loss of tissue resident macrophages ]]> https://biorxiv.org/content/10.1101/2022.10.02.510513v1?rss=1 Ade, K. Coronilla, J. S. Obino, D. Weinberger, T. Kaiser, C. Mella, S. Chen, C. Katsimpardi, L. Werts, C. Dardenne, P. Lallemand, Y. Gomez-Perdiguero, E. 2022-10-05 doi:10.1101/2022.10.02.510513 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Celiac dysbiosis does not transcend geographic boundaries ]]> https://biorxiv.org/content/10.1101/2022.10.02.510531v1?rss=1 Colgan, J. J. Burns, M. B. 2022-10-05 doi:10.1101/2022.10.02.510531 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Revaluation of old data with new techniques reveals novel insights into the celiac microbiome ]]> https://biorxiv.org/content/10.1101/2022.10.05.510990v1?rss=1 Colgan, J. J. Burns, M. B. 2022-10-07 doi:10.1101/2022.10.05.510990 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations ]]> https://biorxiv.org/content/10.1101/2022.10.21.513306v1?rss=1 chen, j. Zhong, J. He, X. Jakovlic, I. Zhang, Y. Yang, H. Chen, Y. Yang, G. Fan, C. Shen, B. 2022-10-22 doi:10.1101/2022.10.21.513306 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation ]]> https://biorxiv.org/content/10.1101/2022.12.01.518658v1?rss=1 2-fold higher recurrence rate compared to inversions in the rest of the human genome. Ampliconic sequences associated with these inversions further show differing mutation rates that are sequence context-dependent and some ampliconic genes show evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, the Yq12, is composed of alternating arrays of DYZ1 and DYZ2 repeat units that show extensive variation in the number, size and distribution of these arrays, but retain a 1:1 copy number ratio of the monomer repeats, consistent with the notion that functional or evolutionary forces are acting on this chromosomal region. Finally, our data suggests that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kbp distal to the currently established boundary. The availability of sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of specific traits with Y-chromosomal variants and garnering novel insights into the evolution and function of complex regions of the human genome. ]]> Hallast, P. Ebert, P. Loftus, M. Yilmaz, F. Audano, P. A. Logsdon, G. A. Bonder, M. J. Zhou, W. Hoeps, W. Kim, K. Li, C. Dishuck, P. C. Porubsky, D. Tsetsos, F. Kwon, J. Y. Zhu, Q. Munson, K. M. Hasenfeld, P. Harvey, W. T. Lewis, A. P. Kordosky, J. Hoekzema, K. (HGSVC), T. H. G. S. V. C. Korbel, J. O. Tyler-Smith, C. Eichler, E. E. Shi, X. Beck, C. R. Marschall, T. Konkel, M. K. Lee, C. 2022-12-01 doi:10.1101/2022.12.01.518658 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Mobile genetic element-encoded putative DNA primases composed of A-family polymerase - SSB pairs ]]> https://biorxiv.org/content/10.1101/2022.12.02.518924v1?rss=1 Rice, P. 2022-12-02 doi:10.1101/2022.12.02.518924 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Is niche divergence more likely in parapatry? A test in Sclerurus mexicanus sensu lato (Aves: Furnariidae) ]]> https://biorxiv.org/content/10.1101/2022.12.06.519370v1?rss=1 Cooper, J. C. Barragan Diaz, D. 2022-12-10 doi:10.1101/2022.12.06.519370 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Spin-coupled electron densities of iron-sulfur cluster imaged by in situ serial Laue diffraction ]]> https://biorxiv.org/content/10.1101/2023.01.09.523341v1?rss=1 Ren, Z. Zhang, F. Kang, W. Wang, C. Shin, H. Zeng, X. Gunawardana, S. Bowatte, K. Krauss, N. Lamparter, T. Yang, X. 2023-01-10 doi:10.1101/2023.01.09.523341 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ In situ architecture of Opa1-dependent mitochondrial cristae remodeling ]]> https://biorxiv.org/content/10.1101/2023.01.16.524176v1?rss=1 Fry, M. Y. Navarro, P. P. Qin, X. Inde, Z. Ananda, V. Y. Lugo, C. M. Hakim, P. Luce, B. E. Ge, Y. McDonald, J. L. Ali, I. Ha, L. L. Kleinstiver, B. P. Chan, D. C. Sarosiek, K. Chao, L. H. 2023-01-18 doi:10.1101/2023.01.16.524176 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Ultrastructural identification and molecular characterization of two new parabasalid species that naturally colonize laboratory mice, Tritrichomonas musculus and Tritrichomonas casperi ]]> https://biorxiv.org/content/10.1101/2023.01.20.524969v1?rss=1 Tuzla, L. Alves-Ferreira, E. V. C. Kennard, A. Shehata, C. Schwartz, C. Grigg, M. E. 2023-01-21 doi:10.1101/2023.01.20.524969 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ SIRT2 inhibition protects against cardiac hypertrophy and heart failure ]]> https://biorxiv.org/content/10.1101/2023.01.25.525524v1?rss=1 Yang, X. Chang, H.-C. Tatekoshi, Y. Balibegloo, M. Wu, R. Chen, C. Sato, T. Shapiro, J. S. Ardehali, H. 2023-01-25 doi:10.1101/2023.01.25.525524 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Phenelzine-based probes reveal Secernin-3 is involved in thermal nociception ]]> https://biorxiv.org/content/10.1101/2023.02.02.526866v1?rss=1 Bustin, K. A. Shishikura, K. Chen, I. Lin, Z. McNight, N. Chang, Y. Wang, X. Pei, L. Lin, J. J. Arellano, E. Morton, P. D. Gregus, A. M. Buczynski, M. W. Matthews, M. L. 2023-02-03 doi:10.1101/2023.02.02.526866 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ RNA-catalyzed RNA Ligation within Prebiotically Plausible Model Protocells ]]> https://biorxiv.org/content/10.1101/2023.02.09.527907v1?rss=1 DasGupta, S. Zhang, S. J. Smela, M. P. Szostak, J. W. 2023-02-09 doi:10.1101/2023.02.09.527907 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations ]]> https://biorxiv.org/content/10.1101/2023.02.23.529575v1?rss=1 Garcia, J. H. Akins, E. A. Jain, S. Wolf, K. J. Zhang, J. Choudhary, N. Lad, M. Shukla, P. Gill, S. Carson, W. Carette, L. Zheng, A. Kumar, S. Aghi, M. K. 2023-02-24 doi:10.1101/2023.02.23.529575 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[ Continuous, long-term crawling behavior characterized by a robotic transport system ]]> https://biorxiv.org/content/10.1101/2023.02.27.530235v1?rss=1 Yu, J. Dancausse, S. Paz, M. Faderin, T. Gaviria, M. Shomar, J. W. Zucker, D. Venkatachalam, V. Klein, M. 2023-02-28 doi:10.1101/2023.02.27.530235 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ A Systems Serology Approach to the Investigation of Infection-Induced Antibody Responses and Protection in Trachoma ]]> https://biorxiv.org/content/10.1101/2023.03.01.530575v1?rss=1 Barton, A. Rosenkrands, I. Pickering, H. Faal, N. Harte, A. Joof, H. Makalo, P. Ragonnet, M. Weinreich Olsen, A. Bailey, R. L. Mabey, D. C. Follmann, F. Dietrich, J. Holland, M. J. 2023-03-02 doi:10.1101/2023.03.01.530575 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Plasticity in parental behavior and vasopressin: Responses to co-parenting, pup age, and an acute stressor are experience-dependent ]]> https://biorxiv.org/content/10.1101/2023.03.01.530631v1?rss=1 Hiura, L. C. Lazaro, V. Ophir, A. G. 2023-03-02 doi:10.1101/2023.03.01.530631 Cold Spring Harbor Laboratory Press 2023-03-02 <![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[ Mitigation of membrane morphology defects explain stability and orientational specificity of CLC dimers ]]> https://biorxiv.org/content/10.1101/2023.03.16.533024v1?rss=1 Ozturk, T. N. Bernhardt, N. Schwartz, N. Chadda, R. Robertson, J. L. Faraldo-Gomez, J. 2023-03-20 doi:10.1101/2023.03.16.533024 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Real Time In vivo Analysis of Pancreatic Beta-cell Autophagic Flux Reveals Impairment Before Onset of Autoimmune Diabetes ]]> https://biorxiv.org/content/10.1101/2023.05.23.541935v1?rss=1 Melnyk, O. Muralidharan, C. Duffett, B. Novak, A. N. Perez-Aviles, G. Martinez, M. M. Crowder, J. J. Linnemann, A. K. 2023-05-23 doi:10.1101/2023.05.23.541935 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity ]]> https://biorxiv.org/content/10.1101/2023.06.22.546190v1?rss=1 Joglekar, P. Conlan, S. Lee-Lin, S.-Q. Deming, C. Kashaf, S. S. Thomas, P. Kong, H. H. Segre, J. 2023-06-23 doi:10.1101/2023.06.22.546190 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Shape-changing electrode array for minimally invasive large-scale intracranial brain activity mapping ]]> https://biorxiv.org/content/10.1101/2023.06.29.547140v1?rss=1 Wei, S. Jiang, A. Sun, H. Zhu, J. Liu, X. Xu, Z. Zhang, J. Jia, S. Shang, Y. Fu, X. Li, G. Wang, P. Xia, Z. Jiang, T. Cao, A. Duan, X. 2023-07-02 doi:10.1101/2023.06.29.547140 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide sp2O, N, C and sp3C Unified Atoms with Naphthalene sp2C Atoms in Water ]]> https://biorxiv.org/content/10.1101/2023.07.12.548600v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1683bb4org.highwire.dtl.DTLVardef@27db75org.highwire.dtl.DTLVardef@b915ccorg.highwire.dtl.DTLVardef@1461b04_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zytkiewicz, E. Shkel, I. A. Cheng, X. Rupanya, A. McClure, K. Karim, R. Yang, S. Yang, F. Record, T. 2023-07-12 doi:10.1101/2023.07.12.548600 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Re-education of myeloid immune cells to reduce regulatory T cell expansion and impede breast cancer progression ]]> https://biorxiv.org/content/10.1101/2023.08.14.553229v1?rss=1 Gamage, H. E. V. Shahoei, S. H. Albright, S. T. Wang, Y. Smith, A. J. Farmer, R. Fink, E. C. Jacquin, E. Weisser, E. Bautista, R. O. Henn, M. A. Schane, C. P. Nelczyk, A. T. Ma, L. Das Gupta, A. Bendre, S. V. Nguyen, T. Tiwari, S. Krawczynska, N. He, S. Tjoanda, E. Chen, H. Sverdlov, M. Gann, P. H. Boidot, R. Vegran, F. Fanning, S. W. Apetoh, L. Hergenrother, P. J. Nelson, E. R. 2023-08-14 doi:10.1101/2023.08.14.553229 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Shared and distinct neural signatures of feature and spatial attention ]]> https://biorxiv.org/content/10.1101/2023.08.20.554014v1?rss=1 Yang, A. Tian, J. Wang, W. Liu, J. Zhou, L. Zhou, K. 2023-08-21 doi:10.1101/2023.08.20.554014 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Metabolic trade-offs can reverse the resource-diversityrelationship ]]> https://biorxiv.org/content/10.1101/2023.08.28.555123v1?rss=1 Miller, Z. R. O'Dwyer, J. P. 2023-08-29 doi:10.1101/2023.08.28.555123 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Deletion of FAT1 in hybrid EMT cells stimulates the migration of neighboring non-mutant cells through secretion of extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2023.09.06.556588v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@104063eorg.highwire.dtl.DTLVardef@135f9fforg.highwire.dtl.DTLVardef@b0052eorg.highwire.dtl.DTLVardef@243864_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure:C_FLOATNO Schematic showing how FAT1 deletion stimulates the migration of neighboring non mutant cells. FAT1 KO cells secrete extracellular vesicles that carry factors that promote migration of non-mutant control cells, possibly through relaxation of traction forces in the recipient cells. C_FIG ]]> Geay, J. Seetharaman, S. Vianay, B. Gelin, M. Fresnoy, O. Blanchoin, L. Thery, M. 2023-09-06 doi:10.1101/2023.09.06.556588 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Neurotransmitter signaling specifies sweat gland stem cell fate through SLN-mediated intracellular calcium regulation ]]> https://biorxiv.org/content/10.1101/2023.09.10.557066v1?rss=1 Remark, J. Tong, J. Lin, M. J. Concepcion, A. R. Mareedu, S. Babu, G. J. Feske, S. Lu, C. P.-j. 2023-09-13 doi:10.1101/2023.09.10.557066 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Selectivity to acoustic features of human speech in the auditory cortex of the mouse ]]> https://biorxiv.org/content/10.1101/2023.09.20.558699v1?rss=1 Mohn, J. L. Baese-Berk, M. Jaramillo, S. L. 2023-09-21 doi:10.1101/2023.09.20.558699 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Cytogenetic resource enables mechanistic resolution of changing trends in human pluripotent stem cell aberrations linked to feeder-free culture ]]> https://biorxiv.org/content/10.1101/2023.09.21.558777v1?rss=1 Stavish, D. Price, C. J. Gelezauskaite, G. Leonhard, K. A. Taapken, S. M. McIntire, E. M. Laing, O. James, B. M. Riley, J. J. Zerbib, J. Baker, D. Harding, A. L. Jestice, L. H. Eleveld, T. F. Gillis, A. J. M. Hillenius, S. Looijenga, L. H. J. Gokhale, P. J. Ben-David, U. J. Ludwig, T. Barbaric, I. 2023-09-21 doi:10.1101/2023.09.21.558777 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Adaptive Functions of Structural Variants in Human Brain Development ]]> https://biorxiv.org/content/10.1101/2023.09.25.558917v1?rss=1 Ding, W. Li, X. Zhang, J. Ji, M. Zhang, M. Zhong, X. Cao, Y. Liu, X. Li, C. Xiao, C. Wang, J. Li, T. Yu, Q. Mo, F. Zhang, B. Qi, J. Yang, J.-C. Qi, J. Tian, L. Xu, X. Peng, Q. Zhou, W.-Z. Liu, Z. Fu, A. Zhang, X. Zhang, J.-j. Sun, Y. Hu, B. An, N. A. Zhang, L. Li, C.-Y. 2023-09-26 doi:10.1101/2023.09.25.558917 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ A Drug-Free Pathogen Capture and Neutralizing Nasal Spray to Prevent Emerging Respiratory Infections ]]> https://biorxiv.org/content/10.1101/2023.10.02.560602v1?rss=1 99.99%. In mice, PCANS showed nasal retention for at least 8 h and was safe for daily administration. A single prophylactic dose of PCANS protected mice against supra-lethal dosages of a mouse-adapted H1N1 Influenza virus (PR8), reduced lung viral titer by >99.99%, improved survival, and suppressed pathological manifestations. Together, our data suggest PCANS as a promising daily-use prophylactic approach against current and emerging respiratory infections. ]]> Joseph, J. Baby, H. M. Quintero, J. R. Kenney, D. Mebratu, Y. Bhatia, E. Shah, P. Swain, K. Kaur, S. Li, X. L. Mwangi, J. Snapper, O. Nair, R. Agus, E. Ranganathan, S. Kage, J. Gao, J. Luo, J. N. Yu, A. Douam, F. Tesfaigzi, Y. Karp, J. Joshi, N. 2023-10-03 doi:10.1101/2023.10.02.560602 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Cue-specific neuronal ensembles span intermittent rate coding of working memory ]]> https://biorxiv.org/content/10.1101/2023.10.06.561121v1?rss=1 Panichello, M. F. Jonikaitis, D. Oh, J. Zhu, S. Trepka, E. B. Moore, T. 2023-10-06 doi:10.1101/2023.10.06.561121 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ The genetic basis of novel trait gain in walking fish ]]> https://biorxiv.org/content/10.1101/2023.10.14.562356v1?rss=1 Herbert, A. L. Allard, C. A. McCoy, M. J. Wucherpfennig, J. I. Krueger, S. P. Chen, H. I. Gourlay, A. N. Jackson, K. D. Abbo, L. A. Bennett, S. H. Sears, J. D. Rhyne, A. L. Bellono, N. W. Kingsley, D. M. 2023-10-14 doi:10.1101/2023.10.14.562356 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan ]]> https://biorxiv.org/content/10.1101/2023.10.18.562852v1?rss=1 Bomba-Warczak, E. K. Velez, K. M. Zhou, L. T. Guillermier, C. Edassery, S. Steinhauser, M. Savas, J. N. Elizabeth Duncan, F. 2023-10-20 doi:10.1101/2023.10.18.562852 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Novel gut probiotic engages microbiota for recovery and pathobiont clearance while preventing inflammation ]]> https://biorxiv.org/content/10.1101/2023.11.14.566997v1?rss=1 Cabral, V. Oliveira, R. A. Correia, M. B. Pedro, M. F. Ubeda, C. Xavier, K. B. 2023-11-15 doi:10.1101/2023.11.14.566997 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Virus specificity and nucleoporin requirements for MX2 activity are affected by GTPase function and capsid-CypA interactions ]]> https://biorxiv.org/content/10.1101/2023.11.16.567336v1?rss=1 Bailey, L. Goli, R. Flick, H. Huang, S.-W. Zhang, R. Kvaratskhelia, M. Kane, M. 2023-11-16 doi:10.1101/2023.11.16.567336 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Inferring amino acid interactions underlying protein function ]]> https://biorxiv.org/content/10.1101/215368v1?rss=1 Salinas, V. H. Ranganathan, R. 2017-11-07 doi:10.1101/215368 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Motor selection dynamics in FEF explain the reaction time variance of saccades to single targets ]]> https://biorxiv.org/content/10.1101/221218v1?rss=1 Hauser, C. K. Zhu, D. Stanford, T. R. Salinas, E. 2017-11-17 doi:10.1101/221218 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Prioritizing Parkinson’s Disease genes using population-scale transcriptomic data ]]> https://biorxiv.org/content/10.1101/231001v1?rss=1 Li, Y. I. Wong, G. Humphrey, J. Raj, T. 2017-12-08 doi:10.1101/231001 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ A hypermorphic Nfkbid allele represents an Idd7 locus gene contributing to impaired thymic deletion of autoreactive diabetogenic CD8+ T-cells in NOD mice. ]]> https://biorxiv.org/content/10.1101/249094v1?rss=1 Presa, M. Racine, J. J. Lamont, D. Dwyer, J. Ratiu, J. Sarsani, V. K. Chen, Y.-G. Geurts, A. Schmitz, I. Stearns, T. Allocco, J. Chapman, H. D. Serreze, D. V. 2018-01-22 doi:10.1101/249094 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system in Streptococcus mutans competence ]]> https://biorxiv.org/content/10.1101/263210v1?rss=1 Son, M. Kaspar, J. R. Ahn, S.-J. Burne, R. A. Hagen, S. J. 2018-02-12 doi:10.1101/263210 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Tolerogenic transcriptome landscape in CD8+ T lymphocytes after exposure to erythrocyte-targeted antigens ]]> https://biorxiv.org/content/10.1101/278457v1?rss=1 Grimm, A. Gobet, C. Diaceri, G. Quaglia-Thermes, X. Hubbell, J. 2018-03-08 doi:10.1101/278457 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Fitness effects of altering gene expression noise in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/294603v1?rss=1 Duveau, F. Hodgins-Davis, A. Metzger, B. P. H. Yang, B. Tryban, S. Walker, E. A. Lybrook, P. Wittkopp, P. J. 2018-04-03 doi:10.1101/294603 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT ]]> https://biorxiv.org/content/10.1101/301267v1?rss=1 Harvey, S. Xu, Y. Lin, X. Gao, X. D. Qiu, Y. Ahn, J. Xiao, X. Cheng, C. 2018-04-13 doi:10.1101/301267 Cold Spring Harbor Laboratory Press 2018-04-13 <![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[ Reassortment, positive selection, and the inter-segmental patterns of divergence and polymorphism in influenza virus H3N2 ]]> https://biorxiv.org/content/10.1101/360941v1?rss=1 Kim, K. Park, Y. Kim, Y. 2018-07-02 doi:10.1101/360941 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ It takes a dimer to tango: Oligomeric small heat-shock proteins dissociate to capture substrate ]]> https://biorxiv.org/content/10.1101/369454v1?rss=1 Santhanagopalan, I. Degiacomi, M. T. Shepherd, D. A. Hochberg, G. K. A. Benesch, J. L. P. Vierling, E. 2018-07-14 doi:10.1101/369454 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ How to make a rodent giant: Genomic basis and tradeoffs of gigantism in the capybara, the world’s largest rodent ]]> https://biorxiv.org/content/10.1101/424606v1?rss=1 Herrera-Alvarez, S. Karlsson, E. Ryder, O. A. Lindblad-Toh, K. Crawford, A. J. 2018-09-23 doi:10.1101/424606 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Evolution in small steps - A nearly-universal rule of negative selection on codons ]]> https://biorxiv.org/content/10.1101/510735v1?rss=1 0.8) only when the genes are under predominant negative selection. Nevertheless, since most genes in most taxa are strongly constrained by negative selection, {Delta}U would appear to be a nearly-universal measure of codon evolution. In conclusion, the driving force of the small-step evolution at the codon level is negative selection. The unanswered question of whether positive selection may, or may not, follow the small-step rule will be addressed in a companion study (Chen, et al. 2019). ]]> Chen, Q. Lan, A. Shen, X. Wu, C.-I. 2019-01-03 doi:10.1101/510735 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Molecular evolution in large steps - Codon substitutions under positive selection ]]> https://biorxiv.org/content/10.1101/510958v1?rss=1 Chen, Q. He, Z. Lan, A. Wen, H. Wu, C.-I. 2019-01-03 doi:10.1101/510958 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Intrinsic temporal tuning of neurons in the optic tectum is shaped by multisensory experience ]]> https://biorxiv.org/content/10.1101/540898v1?rss=1 Busch, S. E. Khakhalin, A. S. 2019-02-07 doi:10.1101/540898 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Highly Efficient Repair of the ΔF508 Mutation in Airway Stem Cells of Cystic Fibrosis Patients with Functional Rescue of the Differentiated Epithelia ]]> https://biorxiv.org/content/10.1101/561183v1?rss=1 Vaidyanathan, S. Salahudeen, A. A. Sellers, Z. M. Bravo, D. T. Choi, S. S. Batish, A. Le, W. De La O, S. Kaushik, M. P. Galper, N. Lee, C. M. Bao, G. Chang, E. H. Wine, J. J. Milla, C. E. Desai, T. J. Nayak, J. V. Kuo, C. J. Porteus, M. H. 2019-02-26 doi:10.1101/561183 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Learning-accelerated Discovery of Immune-Tumour Interactions ]]> https://biorxiv.org/content/10.1101/573972v1?rss=1 Ozik, J. Collier, N. Heiland, R. Macklin, P. 2019-03-11 doi:10.1101/573972 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ TeoNAM: a nested association mapping population for domestication and agronomic trait analysis in maize ]]> https://biorxiv.org/content/10.1101/647461v1?rss=1 Chen, Q. Yang, C. J. York, A. M. Xue, W. Daskalska, L. L. DeValk, C. A. Krueger, K. W. Lawton, S. B. Spiegelberg, B. G. Schnell, J. M. Neumeyer, M. A. Perry, J. S. Peterson, A. C. Kim, B. Bergstrom, L. Yang, L. Barber, I. C. Tian, F. Doebley, J. F. 2019-05-24 doi:10.1101/647461 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design ]]> https://biorxiv.org/content/10.1101/685768v1?rss=1 Karim, A. S. Dudley, Q. M. Juminaga, A. Yuan, Y. Crowe, S. A. Heggestad, J. T. Abdalla, T. Grubbe, W. Rasor, B. Coar, D. Torculas, M. Krein, M. Liew, F. Quattlebaum, A. Jensen, R. O. Stuart, J. Simpson, S. D. Köpke, M. Jewett, M. C. 2019-06-28 doi:10.1101/685768 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Pathogenic and uncertain genetic variants have clinical cardiac correlates in diverse biobank participants ]]> https://biorxiv.org/content/10.1101/716662v1?rss=1 Pottinger, T. D. Puckelwartz, M. J. Pesce, L. L. Robinson, A. Kearns, S. Pacheco, J. A. Rasmussen-Torvik, L. J. Smith, M. E. Chisholm, R. McNally, E. M. 2019-07-28 doi:10.1101/716662 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ In utero estrogenic endocrine disruption alters the stroma to increase extracellular matrix density and mammary gland stiffness. ]]> https://biorxiv.org/content/10.1101/749044v1?rss=1 Wormsbaecher, C. Hindman, A. R. Avendano, A. Cortes, M. Bushman, A. Onua, L. Kovalchin, C. E. Murphy, A. R. Helber, H. L. Shapiro, A. Voytovitch, K. Kuang, X. Song, J. W. Burd, C. J. 2019-08-30 doi:10.1101/749044 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ nkx3.2 mutant zebrafish accommodate the jaw joint loss through a phenocopy of the head shapes of Paleozoic agnathans ]]> https://biorxiv.org/content/10.1101/776351v1?rss=1 Miyashita, T. Baddam, P. Smeeton, J. Oel, A. P. Natarajan, N. Gordon, B. Palmer, R. Crump, G. Graf, D. Allison, W. T. 2019-09-19 doi:10.1101/776351 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Monocyte reconstitution and gut microbiota composition after hematopoietic stem cell transplantation ]]> https://biorxiv.org/content/10.1101/777268v1?rss=1 Morjaria, S. Zhang, A. W. Kim, S. Peled, J. U. Becattini, S. Littmann, E. R. Pamer, E. G. Perales, M.-A. Abt, M. C. 2019-09-20 doi:10.1101/777268 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Chromatin information content landscapes inform transcription factor and DNA interactions ]]> https://biorxiv.org/content/10.1101/777532v1?rss=1 D'Oliveira Albanus, R. Kyono, Y. Hensley, J. Varshney, A. Orchard, P. Kitzman, J. O. Parker, S. C. J. 2019-09-23 doi:10.1101/777532 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Membrane stiffness is a key determinant of E coli MscS channel mechanosensitivity ]]> https://biorxiv.org/content/10.1101/790501v1?rss=1 Xue, F. Cox, C. D. Bavi, N. Rohde, P. R. Nakayama, Y. Martinac, B. 2019-10-04 doi:10.1101/790501 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ MetAP2 inhibition reduces food intake and body weight in a ciliopathy mouse model of obesity ]]> https://biorxiv.org/content/10.1101/800151v1?rss=1 Pottorf, T. S. Fagan, M. Burkey, B. Cho, D. J. Vath, J. E. Tran, P. V. 2019-10-13 doi:10.1101/800151 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Phenotypic clustering reveals distinct subtypes of polycystic ovary syndrome with novel genetic associations ]]> https://biorxiv.org/content/10.1101/814210v1?rss=1 Dapas, M. Lin, F. T. J. Nadkarni, G. N. Sisk, R. Legro, R. S. Urbanek, M. Hayes, M. G. Dunaif, A. 2019-10-22 doi:10.1101/814210 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Gene Expression Networks in the Drosophila Genetic Reference Panel ]]> https://biorxiv.org/content/10.1101/816579v1?rss=1 Everett, L. J. Huang, W. Zhou, S. Carbone, M. A. Lyman, R. Arya, G. Geisz, M. S. Ma, J. Morgante, F. St. Armour, G. Turlapati, L. Anholt, R. R. H. Mackay, T. F. C. 2019-10-24 doi:10.1101/816579 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Leveraging multiple layers of data to predict Drosophila complex traits ]]> https://biorxiv.org/content/10.1101/824896v1?rss=1 Morgante, F. Huang, W. Sorensen, P. Maltecca, C. Mackay, T. 2019-10-30 doi:10.1101/824896 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Experience shapes initial exploration for non-generalizable spatial learning ]]> https://biorxiv.org/content/10.1101/2023.12.26.573368v1?rss=1 Awh, M. P. Latimer, K. W. Zhou, N. Leveroni, Z. M. Stephens, Z. M. Yu, J. Y. 2023-12-27 doi:10.1101/2023.12.26.573368 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Mfn2 and Opa1 ]]> https://biorxiv.org/content/10.1101/2023.12.29.573615v1?rss=1 Boopathy, S. Lugo, C. M. Luce, B. E. McDonald, J. L. Hakim, P. Ponce, J. Ueberheide, B. Chao, L. H. 2023-12-29 doi:10.1101/2023.12.29.573615 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Structural Basis of Voltage-Dependent Gating in BK Channels and Its Coupling to the Calcium Sensor ]]> https://biorxiv.org/content/10.1101/2023.12.29.573674v1?rss=1 Contreras, G. F. Shen, R. Latorre, R. Perozo, E. 2023-12-30 doi:10.1101/2023.12.29.573674 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ Exposure and resistance to lantibiotics impact microbiota composition and function ]]> https://biorxiv.org/content/10.1101/2023.12.30.573728v1?rss=1 Zhang, Z. J. Cole, C. Lin, H. Wu, C. Haro, F. McSpadden, E. van der Donk, W. Pamer, E. G. 2023-12-30 doi:10.1101/2023.12.30.573728 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ A novel classification framework for genome-wide association study of whole brain MRI images using deep learning ]]> https://biorxiv.org/content/10.1101/2024.01.11.575251v1?rss=1 Yu, S. Wu, J. Shao, Y. Qiu, D. Qin, Z. Alzheimer's Disease Neuroimaging Initiative, 2024-01-14 doi:10.1101/2024.01.11.575251 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Integrative genomic analysis identifies unique immune environments associated with immunotherapy response in diffuse large B cell lymphoma ]]> https://biorxiv.org/content/10.1101/2024.01.17.576100v1?rss=1 Tumuluru, S. Godfrey, J. K. Cooper, A. Yu, J. Chen, X. MacNabb, B. W. Venkataraman, G. Zha, Y. Pelzer, B. Song, J. Duns, G. Bolen, C. Penuel, E. Postovalova, E. Kotlov, N. Bagaev, A. Fowler, N. Smith, S. M. Steidl, C. Kline, J. 2024-01-22 doi:10.1101/2024.01.17.576100 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Constraints on the Emergence of RNA through Non-Templated Primer Extension with Mixtures of Potentially Prebiotic Nucleotides ]]> https://biorxiv.org/content/10.1101/2024.01.21.576316v1?rss=1 Jia, X. Zhang, S. J. Zhou, L. Szostak, J. W. 2024-01-22 doi:10.1101/2024.01.21.576316 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Structure of hepatitis B/D antiviral drug Bulevirtide bound to its receptor protein NTCP ]]> https://biorxiv.org/content/10.1101/2024.01.22.576510v1?rss=1 Liu, H. Zakrzewicz, D. Nosol, K. Irobalieva, R. N. Mukherjee, S. Bang-Soerensen, R. Goldmann, N. Kunz, S. Rossi, L. Kossiakoff, A. A. Urban, S. Glebe, D. Geyer, J. Locher, K. P. 2024-01-22 doi:10.1101/2024.01.22.576510 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP ]]> https://biorxiv.org/content/10.1101/2024.01.25.577236v1?rss=1 Valbuena, F. M. Krahn, A. H. Tokamov, S. A. Greene, A. C. Fehon, R. G. Glick, B. S. 2024-01-26 doi:10.1101/2024.01.25.577236 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Epitranscriptomic Reader YTHDF2 Regulates SEK1(MAP2K4)-JNK-cJUN Inflammatory Signaling in Astrocytes during Neurotoxic Stress ]]> https://biorxiv.org/content/10.1101/2024.01.26.577106v1?rss=1 Malovic, E. Ealy, A. Hsu, P. J. Sarkar, S. Miller, C. Rokad, D. Goeser, C. Hartman, A. K. Zhu, A. Palanisamy, B. Zenitsky, G. Jin, H. Anantharam, V. Kanthasamy, A. He, C. Kanthasamy, A. 2024-01-26 doi:10.1101/2024.01.26.577106 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Structure of the extracellular region of the adhesion GPCR CELSR1 reveals a compact module which regulates G protein-coupling ]]> https://biorxiv.org/content/10.1101/2024.01.26.577439v1?rss=1 Bandekar, S. J. Garbett, K. Kordon, S. P. Dintzner, E. Shearer, T. Sando, R. Arac, D. 2024-01-27 doi:10.1101/2024.01.26.577439 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ A critical role for Pol II CTD phosphorylation in heterochromatic gene activation ]]> https://biorxiv.org/content/10.1101/2024.01.26.577526v1?rss=1 Kainth, A. S. Zhang, H. Gross, D. S. 2024-01-27 doi:10.1101/2024.01.26.577526 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Molecular and computational studies of ADGRG6 reveal its extracellular CUB domain as a key regulator of cAMP signaling ]]> https://biorxiv.org/content/10.1101/2024.02.16.580607v1?rss=1 Dintzner, E. Bandekar, S. J. Leon, K. Arac, D. 2024-02-16 doi:10.1101/2024.02.16.580607 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Nanogap Solid-State Single-Molecule Detection at Mars, Europa, and Microgravity Conditions ]]> https://biorxiv.org/content/10.1101/2024.02.29.582359v1?rss=1 Ramirez-Colon, J. L. Johnson, E. Duzdevich, D. Lee, S. Soderblom, J. Zuber, M. T. Taniguchi, M. Ohshiro, T. Komoto, Y. Carr, C. E. 2024-03-02 doi:10.1101/2024.02.29.582359 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq ]]> https://biorxiv.org/content/10.1101/2024.02.29.582869v1?rss=1 Lyu, R. Gao, Y. Wu, T. Ye, C. Wang, P. He, C. 2024-03-02 doi:10.1101/2024.02.29.582869 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ LDL-Binding IL-10 Reduces Vascular Inflammation in Atherosclerotic Mice ]]> https://biorxiv.org/content/10.1101/2024.03.04.582839v1?rss=1 Volpatti, L. R. Norton de Matos, S. Borjas, G. Reda, J. Watkins, E. A. Zhou, Z. Nguyen, M. Solanki, A. Fang, Y. Hubbell, J. A. 2024-03-06 doi:10.1101/2024.03.04.582839 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Task interference as a neuronal basis for the cost of cognitive flexibility ]]> https://biorxiv.org/content/10.1101/2024.03.04.583375v1?rss=1 Xue, C. Markman, S. K. Chen, R. Kramer, L. E. Cohen, M. R. 2024-03-06 doi:10.1101/2024.03.04.583375 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues ]]> https://biorxiv.org/content/10.1101/2024.03.07.583776v1?rss=1 Shin, T. W. Wang, H. Zhang, C. An, B. Lu, Y. Zhang, E. Lu, X. Karagiannis, E. Kang, J. S. Emenari, A. Symvoulidis, P. Asano, S. Lin, L. Costa, E. IMAXT Grand Challenge Consortium, Marblestone, A. H. Kasthuri, N. Tsai, L.-H. Boyden, E. 2024-03-08 doi:10.1101/2024.03.07.583776 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution ]]> https://biorxiv.org/content/10.1101/2024.03.08.584156v1?rss=1 Zhang, Z. J. Cole, C. G. Coyne, M. Lin, H. Dylla, N. Smith, R. C. Waligurski, E. Ramaswamy, R. Woodson, C. Burgo, V. Little, J. Moran, D. Rose, A. McMillin, M. Mcspadden, E. Sundararajan, A. Sidebottom, A. Pamer, E. G. Comstock, L. E. 2024-03-09 doi:10.1101/2024.03.08.584156 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains ]]> https://biorxiv.org/content/10.1101/2024.03.08.584176v1?rss=1 Loes, A. N. Tarabi, R. A. L. Huddleston, J. Touyon, L. Wong, S. S. Cheng, S. M. Leung, N. H. Hannon, W. W. Bedford, T. Cobey, S. Cowling, B. J. Bloom, J. D. 2024-03-09 doi:10.1101/2024.03.08.584176 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM) ]]> https://biorxiv.org/content/10.1101/2024.03.09.584243v1?rss=1 Chandler, T. Guo, M. Su, Y. Chen, J. Wu, Y. Liu, J. Agashe, A. Fischer, R. S. Mehta, S. B. Kumar, A. Baskin, T. I. Jamouille, V. Liu, H. Swaminathan, V. Nain, A. Oldenbourg, R. La Riviere, P. Shroff, H. 2024-03-12 doi:10.1101/2024.03.09.584243 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Pf bacteriophages hinder sputum antibiotic diffusion via electrostatic binding ]]> https://biorxiv.org/content/10.1101/2024.03.10.584330v1?rss=1 Chen, Q. Cai, P. Chang, T. H. W. Burgener, E. Kratochvil, M. J. Gupta, A. Hargil, A. Secor, P. R. Nielsen, J. E. Barron, A. E. Milla, C. Heilshorn, S. C. Spakowitz, A. J. Bollyky, P. L. 2024-03-10 doi:10.1101/2024.03.10.584330 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Adaptive landscapes unveil the complex evolutionary path to mammalian forelimb function and posture ]]> https://biorxiv.org/content/10.1101/2024.03.12.584484v1?rss=1 Brocklehurst, R. J. Mercado, M. Angielczyk, K. D. Pierce, S. E. 2024-03-13 doi:10.1101/2024.03.12.584484 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Mutability and hypermutation antagonize immunoglobulin codon optimality ]]> https://biorxiv.org/content/10.1101/2024.03.13.584690v1?rss=1 McGrath, J. J. Park, J. Troxell, C. A. Chervin, J. C. Li, L. Kent, J. R. Changrob, S. Fu, Y. Huang, M. Zheng, N.-Y. Wilbanks, G. D. Nelson, S. A. Sun, J. Inghirami, G. Madariaga, M. L. L. Georgiou, G. Wilson, P. C. 2024-03-14 doi:10.1101/2024.03.13.584690 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer ]]> https://biorxiv.org/content/10.1101/2024.03.13.584918v1?rss=1 Huang, S. Meheust, R. Barquera, B. Light, S. H. 2024-03-14 doi:10.1101/2024.03.13.584918 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Convergence of inputs from the basal ganglia with layer 5 of motor cortex and cerebellum in mouse motor thalamus ]]> https://biorxiv.org/content/10.1101/2024.03.14.584958v1?rss=1 Koster, K. P. Sherman, M. 2024-03-14 doi:10.1101/2024.03.14.584958 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Data Imbalance in Drug Response Prediction - Multi-Objective Optimization Approach in Deep Learning Setting ]]> https://biorxiv.org/content/10.1101/2024.03.14.585074v1?rss=1 Narykov, O. Zhu, Y. Brettin, T. Evrard, Y. A. Partin, A. Xia, F. Shukla, M. Vasanthakumari, P. Doroshow, J. H. Stevens, R. L. 2024-03-15 doi:10.1101/2024.03.14.585074 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Functional phases encode the response of the soil microbiome to environmental change ]]> https://biorxiv.org/content/10.1101/2024.03.15.584851v1?rss=1 1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrientlimiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change. ]]> Lee, K. K. Liu, S. Crocker, K. Huggins, D. R. Tikhonov, M. Mani, M. Kuehn, S. 2024-03-17 doi:10.1101/2024.03.15.584851 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Engineered Flt3L Drives Tolerogenic State to Attenuate Anti-drug Antibody Responses ]]> https://biorxiv.org/content/10.1101/2024.03.21.586168v1?rss=1 Alpar, A. T. Wallace, R. P. Refvik, K. C. Gomes, S. Solanki, A. Gray, L. T. Slezak, A. J. Lauterbach, A. L. Hesser, L. A. Cao, S. Medellin, J. E. G. Robinson, L. G. Hubbell, J. A. 2024-03-27 doi:10.1101/2024.03.21.586168 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Novel non-immunogenic trained immunity inducing small molecule with improved anti-tumor properties ]]> https://biorxiv.org/content/10.1101/2024.03.22.585780v1?rss=1 Ajit, J. Knight, H. R. Chen, Q. Solanki, A. Shen, J. Esser-Kahn, A. P. 2024-03-27 doi:10.1101/2024.03.22.585780 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Generative Adversarial Networks Accurately Reconstruct Pan-Cancer Histology from Pathologic, Genomic, and Radiographic Latent Features ]]> https://biorxiv.org/content/10.1101/2024.03.22.586306v1?rss=1 Howard, F. M. Hieromnimon, H. Ramesh, S. Dolezal, J. Kochanny, S. Zhang, Q. Feiger, B. Peterson, J. Fan, C. Perou, C. Vickery, J. M. Sullivan, M. Cole, K. Khramtsova, G. Pearson, A. T. 2024-03-25 doi:10.1101/2024.03.22.586306 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Accelerated dimensionality reduction of single -cell RNA sequencing data with fastglmpca ]]> https://biorxiv.org/content/10.1101/2024.03.23.586420v1?rss=1 Weine, E. Carbonetto, P. Stephens, M. 2024-03-27 doi:10.1101/2024.03.23.586420 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The repercussions of timing in the invasion of synthetic bacterial communities ]]> https://biorxiv.org/content/10.1101/2024.03.24.586461v1?rss=1 Dooley, K. D. Bergelson, J. 2024-03-27 doi:10.1101/2024.03.24.586461 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Higher amplitudes of visual networks are associated with trait but not state- depression. ]]> https://biorxiv.org/content/10.1101/2024.03.25.584801v1?rss=1 Zhang, W. Dutt, R. Lew, D. Barch, D. M. Bijsterbosch, J. D. 2024-03-27 doi:10.1101/2024.03.25.584801 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function ]]> https://biorxiv.org/content/10.1101/2024.03.26.586740v1?rss=1 Ono, K. Jarysta, A. Hughes, N. Jukic, A. Chang, V. H. H. Deans, M. R. Eatock, R. A. Cullen, K. E. Kindt, K. S. Tarchini, B. 2024-03-29 doi:10.1101/2024.03.26.586740 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits. ]]> https://biorxiv.org/content/10.1101/2024.03.28.587202v1?rss=1 Okamoto, J. Yin, X. Ryan, B. Chiou, J. Luca, F. Pique-Regi, R. Im, H. K. Morrison, J. Burant, C. Fauman, E. Laakso, M. Boehnke, M. Wen, X. 2024-03-31 doi:10.1101/2024.03.28.587202 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ SMARCA2 and SMARCA4 participate in DNA damage repair ]]> https://biorxiv.org/content/10.1101/2024.03.28.587286v1?rss=1 Wu, D. Yu, L. 2024-03-29 doi:10.1101/2024.03.28.587286 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ DO BIRDS SHOW UNIQUE MACROEVOLUTIONARY PATTERNS OF SEXUAL SIZE DIMORPHISM COMPARED TO OTHER AMNIOTES? ]]> https://biorxiv.org/content/10.1101/2024.04.01.587589v1?rss=1 Saitta, E. T. 2024-04-02 doi:10.1101/2024.04.01.587589 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ RosetteArray Platform for Quantitative High-Throughput Screening of Human Neurodevelopmental Risk ]]> https://biorxiv.org/content/10.1101/2024.04.01.587605v1?rss=1 Lundin, B. F. Knight, G. T. Fedorchak, N. J. Krucki, K. Iyer, N. Maher, J. E. Izban, N. R. Roberts, A. Cicero, M. R. Robinson, J. F. Iskandar, B. J. Willett, R. Ashton, R. S. 2024-04-02 doi:10.1101/2024.04.01.587605 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Perceptual Resolution of Ambiguity: Can Tuned, Divisive Normalization Account for both Interocular Similarity Grouping and Difference Enhancement ]]> https://biorxiv.org/content/10.1101/2024.04.01.587646v1?rss=1 Peiso, J. R. Palmer, S. E. Shevell, S. K. 2024-04-02 doi:10.1101/2024.04.01.587646 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Evolutionary origin of synovial joints ]]> https://biorxiv.org/content/10.1101/2024.04.02.587820v1?rss=1 Sharma, N. Haridy, Y. Shubin, N. 2024-04-03 doi:10.1101/2024.04.02.587820 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Variable orthogonality of RDF-large serine integrase interactions within the phiC31 family ]]> https://biorxiv.org/content/10.1101/2024.04.03.587898v1?rss=1 MacDonald, A. I. Baksh, A. Holland, A. Shin, H. Rice, P. Stark, M. W. Olorunniji, F. J. 2024-04-03 doi:10.1101/2024.04.03.587898 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Positive Selection on Rare Variants Underlying the Cold Adaptation of Wild Boar ]]> https://biorxiv.org/content/10.1101/2024.04.07.588424v1?rss=1 Chen, J. Jakovlic, I. Sablin, M. Xia, S. Xu, z. Guo, Y. Kuang, R. Zhong, J. Jia, Y. Thi, T. N. T. Yang, H. Ma, H. Sprem, N. Liu, D. Zhao, Y. Zhao, S. 2024-04-10 doi:10.1101/2024.04.07.588424 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Synergistic innate immune activation and anti-tumor immunity through combined STING and TLR4 stimulation ]]> https://biorxiv.org/content/10.1101/2024.04.08.588610v1?rss=1 Higgs, E. F. Gajewski, T. F. 2024-04-12 doi:10.1101/2024.04.08.588610 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Sex differences in oxycodone-taking behaviors are linked to disruptions in reward-guided, decision-making functions ]]> https://biorxiv.org/content/10.1101/2024.04.09.587443v1?rss=1 LaRocco, K. Villiamma, P. Russell, M. Hill, J. DiLeone, R. Groman, S. 2024-04-11 doi:10.1101/2024.04.09.587443 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole- to triphosphate-activation ]]> https://biorxiv.org/content/10.1101/2024.04.11.588910v1?rss=1 DasGupta, S. Weiss, Z. Nisler, C. Szostak, J. W. 2024-04-11 doi:10.1101/2024.04.11.588910 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ β-glucan induced trained immunity enhances antibody levels in a vaccination model in mice ]]> https://biorxiv.org/content/10.1101/2024.04.11.588932v1?rss=1 Ajit, J. Chen, Q. Ung, T. Rosenberger, M. G. Kim, J. Solanki, A. Shen, J. Esser-Kahn, A. P. 2024-04-17 doi:10.1101/2024.04.11.588932 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Chk2 homologue Mek1 limits Exo1-dependent DNA end resection during meiotic recombination in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.04.12.589255v1?rss=1 Bishop, D. K. 2024-04-12 doi:10.1101/2024.04.12.589255 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends ]]> https://biorxiv.org/content/10.1101/2024.04.13.589350v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@8b11d3org.highwire.dtl.DTLVardef@3f55c6org.highwire.dtl.DTLVardef@185703org.highwire.dtl.DTLVardef@1f8a9e8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Todisco, M. Radakovic, A. Szostak, J. 2024-04-13 doi:10.1101/2024.04.13.589350 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts ]]> https://biorxiv.org/content/10.1101/2024.04.15.589678v1?rss=1 Glauninger, H. Bard, J. A. M. Wong Hickernell, C. J. Airoldi, E. M. Li, W. Singer, R. H. Paul, S. Fei, J. Sosnick, T. R. Wallace, E. W. J. Drummond, D. A. 2024-04-16 doi:10.1101/2024.04.15.589678 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Proinflammatory stress activates neutral sphingomyelinase 2 based generation of a ceramide-enriched β cell EV subpopulation ]]> https://biorxiv.org/content/10.1101/2024.04.17.589943v1?rss=1 Xu, J. Harris Kawano, A. Enriquez, J. R. Mirmira, R. G. Sims, E. K. 2024-04-18 doi:10.1101/2024.04.17.589943 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models ]]> https://biorxiv.org/content/10.1101/2024.04.17.589997v1?rss=1 Nguyen, V. T. D. Nguyen, N. Hy, T. S. 2024-04-20 doi:10.1101/2024.04.17.589997 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Dependence of Contextual Modulation in Macaque V1 on Interlaminar Signal Flow ]]> https://biorxiv.org/content/10.1101/2024.04.18.590176v1?rss=1 Zhu, S. Oh, Y. J. Trepka, E. B. Chen, X. Moore, T. 2024-04-21 doi:10.1101/2024.04.18.590176 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Information theory for data-driven model reduction in physics and biology ]]> https://biorxiv.org/content/10.1101/2024.04.19.590281v1?rss=1 Schmitt, M. S. Koch-Janusz, M. Fruchart, M. Seara, D. S. Rust, M. Vitelli, V. 2024-04-25 doi:10.1101/2024.04.19.590281 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Minimally and vaguely informative priors to combat practical parameter non-identifiability of hidden Markov models exemplified by ion channel data ]]> https://biorxiv.org/content/10.1101/2024.04.20.590387v1?rss=1 Münch, J. L. Schmauder, R. Paul, F. Habeck, M. 2024-04-25 doi:10.1101/2024.04.20.590387 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ A unified theory for predicting pathogen mutual invasibility and co-circulation ]]> https://biorxiv.org/content/10.1101/2024.04.22.590623v1?rss=1 Park, S. W. Cobey, S. Metcalf, J. Levine, J. Grenfell, B. 2024-04-24 doi:10.1101/2024.04.22.590623 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Testing frameworks for early life effects: the developmental constraints and adaptive responsehypotheses do not explain key fertility outcomes in wild female baboons ]]> https://biorxiv.org/content/10.1101/2024.04.23.590627v1?rss=1 Rosenbaum, S. Malani, A. Lea, A. J. Tung, J. Alberts, S. C. Archie, E. A. 2024-04-28 doi:10.1101/2024.04.23.590627 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Interferon-sensitized hematopoietic progenitors dynamically alter organismal immunity ]]> https://biorxiv.org/content/10.1101/2024.04.24.590828v1?rss=1 Guillamot, M. Subudhi, I. Paraskevopoulou, V. Prystupa, A. Sidhu, I. Yeaton, A. Laskou, M. Hannemann, C. Donahoe, C. Wiseman, D. Aifantis, I. Naik, S. Weinstock, A. 2024-04-28 doi:10.1101/2024.04.24.590828 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ PROSTATE CELL HETEROGENEITY AND CXCL17 UPREGULATION IN MOUSE STEROID HORMONE IMBALANCE ]]> https://biorxiv.org/content/10.1101/2024.04.24.590980v1?rss=1 Silver, S. V. Tucker, K. J. Vickman, R. E. Lanman, N. A. Semmes, O. J. Alvarez, N. S. Popovics, P. 2024-04-28 doi:10.1101/2024.04.24.590980 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function ]]> https://biorxiv.org/content/10.1101/2024.04.25.591154v1?rss=1 Wright, N. E. Kennedy, D. E. Ai, J. Veselits, M. L. Attaway, M. Yoon, Y. m. Durkee, M. S. Veselits, J. Maienschein-Cline, M. Mandal, M. Clark, M. R. 2024-04-28 doi:10.1101/2024.04.25.591154 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations ]]> https://biorxiv.org/content/10.1101/2024.04.29.590671v1?rss=1 Garcia-Bayona, L. Said, N. Coyne, M. J. Flores, K. Elmekki, N. M. Sheahan, M. Camacho, A. G. Hutt, K. Yildiz, F. H. Kovacs, A. T. Waldor, M. K. Comstock, L. E. 2024-04-29 doi:10.1101/2024.04.29.590671 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Reduction of Neuroinflammation and Seizures in a Mouse Model of CLN1 Batten Disease using the Small Molecule Enzyme Mimetic, N-Tert-Butyl Hydroxylamine. ]]> https://biorxiv.org/content/10.1101/2024.05.01.591955v1?rss=1 Fyke, Z. Johansson, R. Scott, A. I. Wiley, D. Chelsky, D. Zak, J. D. Al Nakouzi, N. Koster, K. P. Yoshii, A. 2024-05-01 doi:10.1101/2024.05.01.591955 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures ]]> https://biorxiv.org/content/10.1101/2024.05.02.592174v1?rss=1 Popp, J. M. Rhodes, K. Jangi, R. Li, M. Barr, K. A. Tayeb, K. Battle, A. Gilad, Y. 2024-05-03 doi:10.1101/2024.05.02.592174 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Cysteine Rich Intestinal Protein 2 is a copper-Responsive regulator of skeletal muscle differentiation. ]]> https://biorxiv.org/content/10.1101/2024.05.03.592485v1?rss=1 Verdejo-Torres, O. Klein, D. C. Novoa-Aponte, L. Carrazco-Carrillo, J. Bonilla-Pinto, D. Rivera, A. Fitisemanu, F. M. Jimenez-Gonzalez, M. Flinn, L. Pezacki, A. T. Lanzirotti, A. Ortiz-Frade, L. A. Chang, C. Navea, J. G. Blaby-Haas, C. Hainer, S. J. PADILLA-BENAVIDES, T. 2024-05-05 doi:10.1101/2024.05.03.592485 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Energy partitioning in the cell cortex ]]> https://biorxiv.org/content/10.1101/2024.05.06.592707v1?rss=1 Chen, S. Seara, D. Michaud, A. Kim, S. Bement, W. Murrell, M. 2024-05-09 doi:10.1101/2024.05.06.592707 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Protection against Clostridioides difficile disease by a naturally avirulent C. difficile strain ]]> https://biorxiv.org/content/10.1101/2024.05.06.592814v1?rss=1 Dong, Q. Harper, S. McSpadden, E. Son, S. S. Allen, M.-M. Lin, H. Smith, R. C. Metcalfe, C. Burgo, V. Woodson, C. Sundararajan, A. Rose, A. McMillin, M. Moran, D. Little, J. Mullowney, M. W. Sidebottom, A. M. Shen, A. Fortier, L.-C. Pamer, E. G. 2024-05-07 doi:10.1101/2024.05.06.592814 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Eubacterium rectale detoxification mechanism increases resilience of the gut environment ]]> https://biorxiv.org/content/10.1101/2024.05.09.593360v1?rss=1 Richie, T. G. Wiechman, H. Ingold, C. Heeren, L. Kamke, A. Pogranichniy, S. Monk, K. Summers, T. Ran, Q. Sarkar, S. Plattner, B. L. Sidebottom, A. M. Chang, E. Lee, S. T. M. 2024-05-09 doi:10.1101/2024.05.09.593360 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ A novel expectation-maximization approach to infer general diploid selection from time-series genetic data ]]> https://biorxiv.org/content/10.1101/2024.05.10.593575v1?rss=1 Fine, A. G. Steinruecken, M. 2024-05-14 doi:10.1101/2024.05.10.593575 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Functional brain networks predicting sustained attention are not specific to perceptual modality ]]> https://biorxiv.org/content/10.1101/2024.05.15.594382v1?rss=1 Corriveau, A. Ke, J. Terashima, H. Kondo, H. M. Rosenberg, M. D. 2024-05-16 doi:10.1101/2024.05.15.594382 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix ]]> https://biorxiv.org/content/10.1101/2024.05.15.594415v1?rss=1 Manghrani, A. Rangadurai, A. K. Szekely, O. Liu, B. Guseva, S. Al-Hashimi, H. 2024-05-15 doi:10.1101/2024.05.15.594415 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Impact of microchannel width on axons for brain-on-chip applications ]]> https://biorxiv.org/content/10.1101/2024.05.16.594497v1?rss=1 Vulic, K. Amos, G. Ruff, T. Kasm, R. Ihle, S. J. Kuchler, J. Voros, J. Weaver, S. 2024-05-16 doi:10.1101/2024.05.16.594497 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ A Mechanically Resilient Soft Hydrogel Improves Drug Delivery for Treating Post-Traumatic Osteoarthritis in Physically Active Joints ]]> https://biorxiv.org/content/10.1101/2024.05.16.594611v1?rss=1 Joshi, N. Yan, J. Dang, M. Slaughter, K. Wang, Y. Wu, D. Ung, T. Pandya, V. Chen, M. X. Kaur, S. Bhagchandani, S. Alfassam, H. Joseph, J. Gao, J. Dewani, M. Yip, R. C. S. Weldon, E. Shah, P. Shukla, C. Sherman, N. Luo, J. N. Conway, T. Elickhoff, J. P. Botelho, L. Alhasan, A. Karp, J. Ermann, J. 2024-05-21 doi:10.1101/2024.05.16.594611 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Protein Structure Inspired Drug Discovery ]]> https://biorxiv.org/content/10.1101/2024.05.17.594634v1?rss=1 Qiao, F. Binkowski, A. Broughan, I. Chen, W. Natarajan, A. Schiltz, G. Scheidt, K. Anderson, W. Bergan, R. 2024-05-20 doi:10.1101/2024.05.17.594634 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Bursts from the past: Intrinsic properties link a network model to zebra finch song ]]> https://biorxiv.org/content/10.1101/2024.05.18.594825v1?rss=1 Medina, N. Margoliash, D. 2024-05-19 doi:10.1101/2024.05.18.594825 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ Temperature-Dependent Fold-Switching Mechanism of the Circadian Clock Protein KaiB ]]> https://biorxiv.org/content/10.1101/2024.05.21.594594v1?rss=1 Liwang, A. Dinner, A. Sosnick, T. Wang, L.-P. Partch, C. L. Zhang, N. Sood, D. Guo, S. Chen, N. Baxa, M. Chavan, A. Hong, L. Antoszewski, A. Marianchuk, T. Peng, X. Xiao, Y. Dey, S. 2024-05-21 doi:10.1101/2024.05.21.594594 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Sex differences in olfactory behavior and neurophysiology in Long Evans Rats ]]> https://biorxiv.org/content/10.1101/2024.05.21.595192v1?rss=1 Maheshwar, K. V. Stuart, A. E. Kay, L. M. 2024-05-22 doi:10.1101/2024.05.21.595192 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals ]]> https://biorxiv.org/content/10.1101/2024.05.22.595209v1?rss=1 McNulty, P. Wu, R. Yamaguchi, A. Heckscher, E. H. Haas, A. Nwankpa, A. Skanata, M. M. Gershow, M. H. 2024-05-26 doi:10.1101/2024.05.22.595209 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Critical role of Gα12 and Gα13 proteins in TGF-β-induced myofibroblast differentiation. ]]> https://biorxiv.org/content/10.1101/2024.05.29.596473v1?rss=1 Reed, E. B. Sitikov, A. Hamanaka, R. B. Cetin-Atalay, R. Mutlu, G. M. Mongin, A. A. Dulin, N. O. 2024-05-30 doi:10.1101/2024.05.29.596473 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Neuronal segmentation in cephalopod arms ]]> https://biorxiv.org/content/10.1101/2024.05.29.596333v1?rss=1 Olson, C. S. Schulz, N. G. Ragsdale, C. W. 2024-06-01 doi:10.1101/2024.05.29.596333 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Beyond variability: a novel gene expression stability metric to unveil homeostasis and regulation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596283v1?rss=1 Chen, M. 2024-06-02 doi:10.1101/2024.05.28.596283 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ The curses of performing differential expression analysis using single-cell data ]]> https://biorxiv.org/content/10.1101/2024.05.28.596315v1?rss=1 Wu, C.-H. Zhou, X. Chen, M. 2024-06-02 doi:10.1101/2024.05.28.596315 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ A Patient-Specific Morphoelastic Growth Model of Aortic Dissection Evolution ]]> https://biorxiv.org/content/10.1101/2024.05.28.596335v1?rss=1 Khabaz, K. Kim, J. Milner, R. Nguyen, N. Pocivavsek, L. 2024-06-02 doi:10.1101/2024.05.28.596335 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs) ]]> https://biorxiv.org/content/10.1101/2024.05.29.596366v1?rss=1 Zhang, L. Deng, T. Liufu, Z. Liu, X. Chen, B. Hu, Z. Liu, C. Lv, X. Wen, H.-J. Wu, C.-I. 2024-06-02 doi:10.1101/2024.05.29.596366 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ On the discovered Cancer Driving Nucleotides (CDNs)-Distributions across genes, cancer types and patients ]]> https://biorxiv.org/content/10.1101/2024.05.29.596367v1?rss=1 5-fold) fall on non-canonical than canonical cancer driving genes (CDGs). Most undiscovered CDNs are expected to be on unknown CDGs. iii) CDNs tend to be more widely shared among cancer types than canonical CDGs, mainly because of the higher resolution at the nucleotide than the whole-gene level. iv) Most important, among the 50[~]100 coding region mutations carried by a cancer patient, 5[~]8 CDNs are expected but only 0[~]2 CDNs have been identified at present. This low level of identification has hampered functional test and gene targeted therapy. We show that, by expanding the sample size to 105, most CDNs can be identified. Full CDN identification will then facilitate the design of patient-specific targeting against multiple CDN-harboring genes. ]]> Zhang, L. Deng, T. Liufu, Z. Chen, X. Wu, S. Liu, X. Shi, C. Chen, B. Hu, Z. Cai, Q. Lv, X. Liu, C. Li, M. Wen, H.-J. Wu, C.-I. 2024-06-02 doi:10.1101/2024.05.29.596367 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Enhanced Treatment Efficiency of Holmium:YAG Laser Lithotripsy by Using PEDOT:PSS Nanofluid ]]> https://biorxiv.org/content/10.1101/2024.06.01.596977v1?rss=1 Fan, Q. Chen, J. Anees, F. Dominguez, J. Chen, T.-H. Payne, C. Zhong, P. Hsu, P.-C. 2024-06-03 doi:10.1101/2024.06.01.596977 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Rapid evolution of fine-scale recombination during domestication ]]> https://biorxiv.org/content/10.1101/2024.06.05.597134v1?rss=1 Liu, Z.-X. Li, M. Si, S. Chen, J. Hu, L.-R. Peng, M.-S. Yin, T.-T. Esmailizadeh, A. Zhang, C. Qu, L. Lu, X.-M. Han, J.-L. Zhang, Y.-p. Wang, M.-S. 2024-06-06 doi:10.1101/2024.06.05.597134 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Infiltrating lipid-rich macrophage subpopulations identified as a regulator of increasing prostate size in human benign prostatic hyperplasia ]]> https://biorxiv.org/content/10.1101/2024.06.07.597992v1?rss=1 90 grams) and 10 small (<40 grams) human prostates was conducted. Macrophage subpopulations were defined using marker genes. BPH macrophages do not distinctly categorize into M1 and M2 phenotypes. Instead, macrophages with neither polarization signature preferentially accumulate in large versus small prostates. Specifically, macrophage subpopulations with altered lipid metabolism pathways, demarcated by TREM2 and MARCO expression, significantly accumulate with increased prostate volume. TREM2+ and MARCO+ macrophage abundance positively correlates with patient body mass index and urinary symptom scores. TREM2+ macrophages have significantly higher neutral lipid than TREM2- macrophages from BPH tissues. Lipid-rich macrophages were observed to localize within the stroma in BPH tissues. In vitro studies indicate that lipid-loaded macrophages increase prostate epithelial and stromal cell proliferation compared to control macrophages. These data define two new BPH immune subpopulations, TREM2+ and MARCO+ macrophages, and suggest that lipid-rich macrophages may exacerbate lower urinary tract symptoms in patients with large prostates. Further investigation is needed to evaluate the therapeutic benefit of targeting these cells in BPH. ]]> Lanman, N. A. Meco, E. Fitchev, P. Kolliegbo, A. K. Broman, M. M. Filipovich, Y. Kothandaraman, H. Cresswell, G. M. Talaty, P. Antoniak, M. Brumer, S. Glaser, A. P. Higgins, A. M. Helfand, B. T. Franco, O. E. Crawford, S. E. Ratliff, T. L. Hayward, S. W. Vickman, R. E. 2024-06-10 doi:10.1101/2024.06.07.597992 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Interpretation of two-sample Mendelian randomization for binary exposures and outcome ]]> https://biorxiv.org/content/10.1101/2024.06.09.598150v1?rss=1 Wu, Z. Wang, J. 2024-06-11 doi:10.1101/2024.06.09.598150 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Suppression of T cell function by phosphoethanolamine, a metabolite enriched in tumor interstitial fluid ]]> https://biorxiv.org/content/10.1101/2024.06.10.598334v1?rss=1 Wang, Y. Wilfahrt, D. Cai, C. Lontos, K. Cameron, B. Xie, B. Peralta, R. M. AminiTabrizi, R. Shah, H. Rivadeneira, D. B. Muir, A. Delgoffe, G. M. 2024-06-12 doi:10.1101/2024.06.10.598334 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ ATF4 and mTOR regulate metabolic reprogramming in TGF-β-treated lung fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.06.12.598694v1?rss=1 Shin, K. W. D. Atalay, M. V. Cetin-Atalay, R. O'Leary, E. M. Glass, M. E. Szafran, J. C. H. Woods, P. S. Meliton, A. Y. Shamaa, O. R. Tian, Y. Mutlu, G. M. Hamanaka, R. B. 2024-06-13 doi:10.1101/2024.06.12.598694 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Acetylation of the yeast Hsp40 chaperone protein Ydj1 fine-tunes proteostasis and translational fidelity ]]> https://biorxiv.org/content/10.1101/2024.06.13.598777v1?rss=1 Omkar, S. Shrader, C. Hoskins, J. R. Kline, J. T. Mitchem, M. M. Nitika, Fornelli, L. Wickner, S. Truman, A. W. 2024-06-14 doi:10.1101/2024.06.13.598777 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Conditional frequency spectra as a tool for studying selection on complex traits in biobanks ]]> https://biorxiv.org/content/10.1101/2024.06.15.599126v1?rss=1 Patel, R. A. Weiss, C. L. Zhu, H. Mostafavi, H. Simons, Y. B. Spence, J. P. Pritchard, J. K. 2024-06-17 doi:10.1101/2024.06.15.599126 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Elasticity and Thermal Stability are Key Determinants of Hearing Rescue by Mini-Protocadherin-15 Proteins ]]> https://biorxiv.org/content/10.1101/2024.06.16.599132v1?rss=1 De-la-Torre, P. Wen, H. Brower, J. Martinez-Perez, K. Narui, Y. Yeh, F. Hale, E. Ivanchenko, M. V. Corey, D. P. Sotomayor, M. Indzhykulian, A. A. 2024-06-17 doi:10.1101/2024.06.16.599132 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Mechanosensitive FHL2 tunes endothelial function ]]> https://biorxiv.org/content/10.1101/2024.06.16.599227v1?rss=1 Seetharaman, S. Devany, J. Kim, H. R. van Bodegraven, E. J. Chmiel, T. Tzu-Pin, S. Chou, W.-h. Fang, Y. Gardel, M. 2024-06-17 doi:10.1101/2024.06.16.599227 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity ]]> https://biorxiv.org/content/10.1101/2024.06.21.599965v1?rss=1 Saba, J. Flores, K. Marshall, B. A. Engstrom, M. D. Peng, Y. Garje, A. S. Comstock, L. Landick, R. 2024-06-21 doi:10.1101/2024.06.21.599965 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ Lectins and polysaccharide EPS I have flow-responsive roles in the attachment and biofilm mechanics of plant pathogenic Ralstonia ]]> https://biorxiv.org/content/10.1101/2024.06.21.599993v1?rss=1 Carter, M. D. Tran, T. M. Cope-Arguello, M. Weinstein, S. Li, H. Hendrich, C. G. Prom, J. L. Li, J. Chu, L. T. Bui, L. Manikantan, H. Lowe-Power, T. Allen, C. 2024-06-21 doi:10.1101/2024.06.21.599993 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ Structural Insights into the Roles of PARP4 and NAD+ in the Human Vault Cage ]]> https://biorxiv.org/content/10.1101/2024.06.27.601040v1?rss=1 Lodwick, J. E. Shen, R. Erramilli, S. K. Xie, Y. Roganowicz, K. Kossiakoff, A. A. Zhao, M. 2024-06-27 doi:10.1101/2024.06.27.601040 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Whole Tissue Imaging of Cellular Boundaries at Sub-Micron Resolutions for Automatic Cell Segmentation: Applications in Epithelial Bending of Ectodermal Appendages ]]> https://biorxiv.org/content/10.1101/2024.06.26.600880v1?rss=1 Norris, S. C. P. Hu, J. K. Shubin, N. H. 2024-06-30 doi:10.1101/2024.06.26.600880 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ Uridine Phosphorylase-1 supports metastasis of mammary cancer by altering immune and extracellular matrix landscapes of the lung ]]> https://biorxiv.org/content/10.1101/2024.07.02.601676v1?rss=1 Whyte, D. Vande Voorde, J. Sumpton, D. Dhayade, S. Dornier, E. Moore, M. Novo, D. Peters, J. Wiesheu, R. Mackey, J. B. McFarlane, A. J. Fercoq, F. Fisher, S. Dehesa Caballero, C. Gilroy, K. Redmond, K. L. Mitchell, L. E. Anderson, E. Thomson, G. Dzierozynski, L. N. Apiz Saab, J. J. Lewis, C. A. Muir, A. Halbrook, C. J. Strathdee, D. Jackstadt, R. Nixon, C. Dunne, P. Steele, C. W. Carlin, L. M. Macpherson, I. R. Roberts, E. W. Coffelt, S. B. Blyth, K. Sansom, O. J. Norman, J. C. Clarke, C. J. 2024-07-04 doi:10.1101/2024.07.02.601676 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Methamphetamine-induced adaptation of learning rate dynamics depend on baseline performance. ]]> https://biorxiv.org/content/10.1101/2024.07.04.602054v1?rss=1 Kirschner, H. Molla, H. M. Nassar, M. R. de Wit, H. Ullsperger, M. 2024-07-08 doi:10.1101/2024.07.04.602054 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways ]]> https://biorxiv.org/content/10.1101/2024.07.08.602367v1?rss=1 Nawrocka, W. I. Cheng, S. Hao, B. Rosen, M. Cortes, E. Baltrusaitis, E. Aziz, Z. Kovacs, I. A. Özkan, E. 2024-07-08 doi:10.1101/2024.07.08.602367 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ Objective Markers of Sustained Attention Fluctuate Independently of Mind-Wandering Reports ]]> https://biorxiv.org/content/10.1101/2024.07.08.602532v1?rss=1 Chidharom, M. Bonnefond, A. Vogel, E. K. Rosenberg, M. D. 2024-07-11 doi:10.1101/2024.07.08.602532 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Robust coexistence in ecological competitive communities ]]> https://biorxiv.org/content/10.1101/2024.07.10.602979v1?rss=1 Lechon-Alonso, P. Kundu, S. Lemos-Costa, P. Allesina, S. 2024-07-16 doi:10.1101/2024.07.10.602979 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Context-dependent roles for autophagy in myeloid cells in tumor progression ]]> https://biorxiv.org/content/10.1101/2024.07.12.603292v1?rss=1 Choi, J. Park, G. Lee, S. S.-Y. Dominici, E. Becker, L. Macleod, K. F. KRON, S. J. Hwang, S. 2024-07-16 doi:10.1101/2024.07.12.603292 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Ancient tree-topologies and gene-flow processes among human lineages in Africa ]]> https://biorxiv.org/content/10.1101/2024.07.15.603519v1?rss=1 Breton, G. Sjodin, P. Zervakis, P. I. Laurent, R. Froment, A. Sjostrand, A. E. Hewlett, B. S. Barreiro, L. B. Perry, G. H. Soodyall, H. Heyer, E. Schlebusch, C. M. Jakobsson, M. Verdu, P. 2024-07-16 doi:10.1101/2024.07.15.603519 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson's Disease associated protein. ]]> https://biorxiv.org/content/10.1101/2024.07.18.603797v1?rss=1 Ackloo, S. Arrowsmith, C. H. Ban, F. Barden, C. J. Beck, H. Beranek, J. Berenger, F. Bolotokova, A. Bret, G. Breznik, M. Carosati, E. Chau, I. Chen, Y. Cherkasov, A. Della Corte, D. Denzinger, K. Dong, A. Draga, S. Dunn, I. Edfeldt, K. Edwards, A. Eguida, M. Eisenhuth, P. Friedrich, L. Fuerll, A. Gardiner, S. Gentile, F. Ghiabi, P. Gibson, E. Glavatskikh, M. Gorgulla, C. Guenther, J. Gunnarsson, A. Guseve, F. Gutkin, E. Hillisch, A. Hoffer, L. Hogner, A. Irwin, J. J. Isayev, O. Ivanova, A. Jacquemard, C. Jarrett, A. J. Jensen, J. H. Kireev, D. Klebe 2024-07-18 doi:10.1101/2024.07.18.603797 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Analysis of mixtures of birds and insects in weather radar data ]]> https://biorxiv.org/content/10.1101/2024.07.17.601450v1?rss=1 Shi, X. Drucker, J. Chapman, J. Sanchez-Herrera, M. Dokter, A. M. 2024-07-19 doi:10.1101/2024.07.17.601450 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ In-Silico Analyses of Molecular Force Sensors for Mechanical Characterization of Biological Systems ]]> https://biorxiv.org/content/10.1101/2024.07.17.603923v1?rss=1 Lopez, D. M. Castro, C. E. Sotomayor, M. 2024-07-22 doi:10.1101/2024.07.17.603923 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Dynamic regulation of H2A.Zub and H3K27me3 by ambient temperature in plant cell fate determination ]]> https://biorxiv.org/content/10.1101/2024.07.18.604029v1?rss=1 Zhu, K. Zhao, L. Lu, F. Lin, X. He, C. Wagner, D. Xiao, J. 2024-07-22 doi:10.1101/2024.07.18.604029 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ FhlA is a Formate Binding Protein ]]> https://biorxiv.org/content/10.1101/2024.07.24.604796v1?rss=1 Al Fardan, A. A. Koestler, B. J. 2024-07-24 doi:10.1101/2024.07.24.604796 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Overlapping Cortical Substrate of Biomechanical Control and Subjective Agency ]]> https://biorxiv.org/content/10.1101/2024.07.24.604976v1?rss=1 Veillette, J. P. Chao, A. F. Nith, R. Lopes, P. Nusbaum, H. C. 2024-07-24 doi:10.1101/2024.07.24.604976 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Imperfect symmetry facilitated the evolution of specificity and high-order stoichiometry in vertebrate hemoglobin ]]> https://biorxiv.org/content/10.1101/2024.07.24.604985v1?rss=1 Cortez-Romero, C. R. Lyu, J. Pillai, A. Laganowsky, A. Thornton, J. W. 2024-07-24 doi:10.1101/2024.07.24.604985 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Illuminating microbial mat assembly: Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms ]]> https://biorxiv.org/content/10.1101/2024.07.24.605005v1?rss=1 Bunbury, F. Rivas, C. Calatrava, V. Malkovskiy, A. Joubert, L.-M. Parvate, A. Evans, J. E. Grossman, A. R. Bhaya, D. 2024-07-25 doi:10.1101/2024.07.24.605005 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Activation of the influenza B M2 proton channel (BM2) ]]> https://biorxiv.org/content/10.1101/2024.07.26.605324v1?rss=1 Yue, Z. Wu, J. Teng, D. Wang, Z. Voth, G. A. 2024-07-26 doi:10.1101/2024.07.26.605324 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ 12-Lipoxygenase Inhibition Suppresses Islet Immune and Inflammatory Responses and Delays Autoimmune Diabetes in Human Gene Replacement Mice ]]> https://biorxiv.org/content/10.1101/2024.07.28.604986v1?rss=1 Nargis, T. Muralidharan, C. Enriquez, J. R. Wang, J. E. Kaylan, K. Chakraborty, A. Pratuagntham, S. Figatner, K. Nelson, J. B. May, S. C. Nadler, J. L. Boxer, M. B. Maloney, D. J. Tersey, S. A. Mirmira, R. G. 2024-07-28 doi:10.1101/2024.07.28.604986 Cold Spring Harbor Laboratory Press 2024-07-28 <![CDATA[ Scaling and Merging Time-Resolved Laue Data with Variational Inference ]]> https://biorxiv.org/content/10.1101/2024.07.30.605871v1?rss=1 Zielinski, K. A. Dolamore, C. Wang, H. K. Henning, R. W. Wilson, M. A. Pollack, L. Srajer, V. Hekstra, D. R. Dalton, K. M. 2024-07-31 doi:10.1101/2024.07.30.605871 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ How different immersive environments affect intracortical brain computer interfaces ]]> https://biorxiv.org/content/10.1101/2024.07.30.605911v1?rss=1 Tortolani, A. F. Kunigk, N. G. Sobinov, A. R. Boninger, M. L. Bensmaia, S. J. Collinger, J. L. Hatsopoulos, N. G. Downey, J. E. 2024-07-31 doi:10.1101/2024.07.30.605911 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ What the Average Really Means: Dissociating Effect Size and Effect Prevalence using p-curve Mixtures ]]> https://biorxiv.org/content/10.1101/2024.07.31.606048v1?rss=1 Veillette, J. P. Nusbaum, H. C. 2024-08-01 doi:10.1101/2024.07.31.606048 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ YTHDF1 mediates translational control by m6A mRNA methylation in adaptation to environmental challenges ]]> https://biorxiv.org/content/10.1101/2024.08.07.607063v1?rss=1 Shi, Z. Wen, K. Zou, Z. Fu, W. Guo, K. Sammudin, N. H. Ruan, X. Sullere, S. Wang, S. Zhang, X. Thinakaran, G. He, C. Zhuang, X. 2024-08-12 doi:10.1101/2024.08.07.607063 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Interplay between the cyclophilin homology domain of RANBP2 and MX2 regulates HIV-1 capsid dependencies on nucleoporins ]]> https://biorxiv.org/content/10.1101/2024.08.12.607676v1?rss=1 Flick, H. Venbakkam, A. Singh, P. K. Layish, B. Huang, S.-W. K. Radhakrishnan, R. Kvaratskhelia, M. Engelman, A. N. Kane, M. 2024-08-12 doi:10.1101/2024.08.12.607676 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Phylogenetic analysis of Centralspindlin and Ect2 provides mechanistic insights into the emergence of Metazoa and multicellularity ]]> https://biorxiv.org/content/10.1101/2024.08.16.607330v1?rss=1 Glotzer, M. 2024-08-17 doi:10.1101/2024.08.16.607330 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Neural Mechanisms of Feedback Processing and Behavioral Adaptation during Neurofeedback Training ]]> https://biorxiv.org/content/10.1101/2024.08.19.608543v1?rss=1 Pamplona, G. S. P. Zweerings, J. Lor, C. S. deErney, L. Roecher, E. Taebi, A. Hellrung, L. Amano, K. Scheinost, D. Krause, F. Rosenberg, M. D. Ionta, S. Brem, S. Hermans, E. Mathiak, K. Scharnowski, F. 2024-08-19 doi:10.1101/2024.08.19.608543 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Stabilizing selection generates selection against introgressed DNA ]]> https://biorxiv.org/content/10.1101/2024.08.20.608860v1?rss=1 Veller, C. Simons, Y. 2024-08-20 doi:10.1101/2024.08.20.608860 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Large serine integrases utilise scavenged phage proteins as directionality cofactors ]]> https://biorxiv.org/content/10.1101/2024.08.21.608926v1?rss=1 Alsaleh, A. Pena Reyes, T. Baksh, A. Taiwo-Aiyerin, O. T. Holland, A. Pigli, Y. Z. Rice, P. A. Olorunniji, F. J. 2024-08-21 doi:10.1101/2024.08.21.608926 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Quantifying the seasonal reproductive cycle in three species of Malagasy fruit bats with implications for pathogen and population dynamics ]]> https://biorxiv.org/content/10.1101/2024.08.21.608949v1?rss=1 Cornelius Ruhs, E. Kettenburg, G. Andrianiaina, A. Andry, S. Ranaivoson, H. C. Grewe, F. Brook, C. E. 2024-08-22 doi:10.1101/2024.08.21.608949 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Transmembrane channel-like 4 and 5 proteins at microvillar tips are potential ion channels and lipid scramblases ]]> https://biorxiv.org/content/10.1101/2024.08.22.609173v1?rss=1 Ebrahim, S. Ballesteros, A. Zheng, W. S. Mukherjee, S. Hu, G. Weng, W.-H. Montgomery, J. W. Agyemang, Y. Cui, R. Sun, W. Krystofiak, E. Foster, M. P. Sotomayor, M. Kachar, B. 2024-08-23 doi:10.1101/2024.08.22.609173 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Optimizing real-time phase detection in diverse rhythmic biological signals for phase-specificneuromodulation ]]> https://biorxiv.org/content/10.1101/2024.08.24.609522v1?rss=1 Liufu, M. Leveroni, Z. M. Shridhar, S. Zhou, N. Yu, J. Y. 2024-08-26 doi:10.1101/2024.08.24.609522 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ GageTracker: a tool for dating gene age by micro- and macro-synteny with high speed and accuracy ]]> https://biorxiv.org/content/10.1101/2024.08.28.610050v1?rss=1 Fang, C. Dong, C. Wang, C. Xiong, F. Lu, S. Fang, W. Li, T. Gan, X. Yang, L. Zeng, H. He, S. 2024-08-29 doi:10.1101/2024.08.28.610050 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to millisecond protein folding ]]> https://biorxiv.org/content/10.1101/2024.08.28.610178v1?rss=1 3-fold in estimating the folding rate constant. Our efforts are a significant step forward in the unsupervised learning of slow coordinates during rare event sampling. ]]> Leung, J. Frazee, N. Brace, A. Ramanathan, A. Chong, L. 2024-08-30 doi:10.1101/2024.08.28.610178 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Coordinated Tbx3 / Tbx5 transcriptional control of the adult ventricular conduction system ]]> https://biorxiv.org/content/10.1101/2024.08.29.610377v1?rss=1 Burnicka-Turek, O. Trampel, K. A. Laforest, B. Broman, M. T. Khan, Z. Rytkin, E. Li, B. Schaffer, E. Gadek, M. Shen, K. M. Efimov, I. R. Moskowitz, I. P. 2024-08-30 doi:10.1101/2024.08.29.610377 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology ]]> https://biorxiv.org/content/10.1101/2024.08.30.610485v1?rss=1 Sangani, K. A. Parker, M. E. Anderson, H. D. Chen, L. Pandey, S. P. Pierre, J. F. Meisel, M. Riesenfeld, S. J. Hinterleitner, R. Jabri, B. 2024-08-30 doi:10.1101/2024.08.30.610485 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ β-Glucan Reprograms Neutrophils to Induce Disease Tolerance Against Influenza A Virus ]]> https://biorxiv.org/content/10.1101/2024.09.02.610822v1?rss=1 Khan, N. Chevre, R. Sun, S. J. Sadeghi, M. Pernet, E. Herrero, A. Grant, A. Downey, J. Barreiro, L. B. Yipp, B. G. Soehnlein, O. Divangahi, M. 2024-09-03 doi:10.1101/2024.09.02.610822 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ A type 1 immune-stromal cell network mediates disease tolerance and barrier protection against intestinal infection ]]> https://biorxiv.org/content/10.1101/2024.09.04.611190v1?rss=1 Westfall, S. Gentile, M. E. Olsen, T. M. Karo-Atar, D. Bogza, A. Roestel, F. Pardy, R. Mandato, G. Fontes, G. Herbert, D. Melichar, H. J. Abadie, V. Richer, M. Vinh, D. C. Koenig, J. F. Harrison, O. J. Divangahi, M. J. Weis, S. Gregorieff, A. King, I. L. 2024-09-08 doi:10.1101/2024.09.04.611190 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Mast cells promote pathology and susceptibility in tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.09.04.611333v1?rss=1 Gupta, A. Taneja, V. Rangel-Moreno, J. Abhimanyu, A. Ahmed, M. Naqvi, N. Chauhan, K. S. de Leon, D. T.-P. Ramirez-Martinez, G. Jimenez-Alvarez, L. Luna-Rivero, C. Zuniga, J. Kaushal, D. Khader, S. 2024-09-10 doi:10.1101/2024.09.04.611333 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ A trans-synaptic IgLON adhesion molecular complex directly contacts and clusters a nicotinic receptor ]]> https://biorxiv.org/content/10.1101/2024.09.05.611427v1?rss=1 Mialon, M. Patrash, L. Weinreb, A. Ozkan, E. Bessereau, J.-L. Pinan-Lucarre, B. 2024-09-10 doi:10.1101/2024.09.05.611427 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex ]]> https://biorxiv.org/content/10.1101/2024.09.09.612108v1?rss=1 Ruan, X. Hu, K. Yang, Y. Yang, R. Tseng, E. Kang, B. Kauffman, A. Zhong, R. Zhang, X. 2024-09-10 doi:10.1101/2024.09.09.612108 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Non-allometric expansion and enhanced compartmentalization of Purkinje cell dendrites in the human cerebellum ]]> https://biorxiv.org/content/10.1101/2024.09.09.612113v1?rss=1 Busch, S. E. Hansel, C. 2024-09-10 doi:10.1101/2024.09.09.612113 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ A circular engineered sortase for interrogating histone H3 in chromatin ]]> https://biorxiv.org/content/10.1101/2024.09.10.612318v1?rss=1 Whedon, S. D. Lee, K. Wang, Z. A. Zahn, E. Lu, C. Abeywardana, M. Y. Fairall, L. Nam, E. Dubois-Coyne, S. De Ioannes, P. Sheng, X. Andrei, A. Lundberg, E. Jiang, J. Armache, K.-J. D. Zhao, Y. Schwabe, J. W. R. Wu, M. Garcia, B. Cole, P. A. 2024-09-10 doi:10.1101/2024.09.10.612318 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Early Life Neuroimaging: The Generalizability of Cortical Area Parcellations Across Development ]]> https://biorxiv.org/content/10.1101/2024.09.09.612056v1?rss=1 Tu, J. Myers, M. Li, W. Li, J. Wang, X. Dierker, D. Day, T. Snyder, A. Z. Latham, A. Kenley, J. K. Sobolewski, C. M. Wang, Y. Labonte, A. K. Feczko, E. Kardan, O. Moore, L. A. Sylvester, C. M. Fair, D. A. Elison, J. T. Warner, B. B. Barch, D. M. Rogers, C. E. Luby, J. L. Smyser, C. D. Gordon, E. M. Laumann, T. O. Eggebrecht, A. T. Wheelock, M. D. 2024-09-11 doi:10.1101/2024.09.09.612056 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health ]]> https://biorxiv.org/content/10.1101/2024.09.13.612812v1?rss=1 Kubra, S. Sun, M. Dion, W. Catak, A. Luong, H. Wang, H. Pan, Y. Liu, J.-J. Ponna, A. Sipula, I. Jurczak, M. J. Liu, S. Zhu, B. 2024-09-13 doi:10.1101/2024.09.13.612812 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Biofabrication of Small Vascular Graft with Acellular Human Amniotic Membrane: A Proof-of-Concept Study in Pig ]]> https://biorxiv.org/content/10.1101/2024.09.11.612466v1?rss=1 Aung, O. Rossi, P. Dyer, M. Stellpflug, A. Zhai, Y. Kenneth, A. Wang, X. Chang, J. Chen, Y. Tefft, B. J. Wu, R. Gu, L. Wang, B. 2024-09-15 doi:10.1101/2024.09.11.612466 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Cryo-EM Structure of Phospholipase Cϵ Defines N-terminal Domains and their Roles in Activity ]]> https://biorxiv.org/content/10.1101/2024.09.11.612521v1?rss=1 Samassekou, K. Garland-Kuntz, E. E. Ohri, V. Fisher, I. J. Erramilli, S. K. Muralidharan, K. Bogdan, L. M. Gick, A. M. Kossiakoff, A. A. Lyon, A. M. 2024-09-15 doi:10.1101/2024.09.11.612521 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Bird Name-a-thon: Categorizing English bird names using crowdsourcing ]]> https://biorxiv.org/content/10.1101/2024.09.13.612884v1?rss=1 Morrison, E. S. Pandolfi, G. P. Aguillon, S. M. Ali, J. R. Archard, O. Baldassarre, D. T. Baquero, I. Bennett, K. F. P. Bonney, K. M. Bryant, R. Catanach, R. M. Catanach, T. A. Chavoshan, I. Davis, S. N. Goodman, B. D. Gulson-Castillo, E. R. Hack, M. Hudon, J. Leighton, G. M. Long, K. M. Ma, Z. McCoy, D. E. McLaughlin, J. F. Rueda Moreno, G. Mota, T. M. Noguchi, L. Nwigwe, U. Pegan, T. Provost, K. Rasband, S. A. Salter, J. F. Silvernail, L. C. Simard, J. A. Skeen, H. R. Soto-Patino, J. Suh, Y. H. Wang, Q. Warshauer, M. E. Yan, S. Zalinski, B. Zhao, Z. S 2024-09-16 doi:10.1101/2024.09.13.612884 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ A mosaic of whole-body representations in human motor cortex ]]> https://biorxiv.org/content/10.1101/2024.09.14.613041v1?rss=1 Deo, D. R. Okorokova, E. V. Pritchard, A. L. Hahn, N. V. Card, N. S. Nason-Tomaszewski, S. R. Jude, J. Hosman, T. Choi, E. Y. Qiu, D. Meng, Y. Wairagkar, M. Nicolas, C. Kamdar, F. B. Iacobacci, C. Acosta, A. Hochberg, L. R. Cash, S. S. Williams, Z. M. Rubin, D. B. Brandman, D. M. Stavisky, S. D. AuYong, N. Pandarinath, C. Downey, J. E. Bensmaia, S. J. Henderson, J. M. Willett, F. R. 2024-09-16 doi:10.1101/2024.09.14.613041 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Structural insights into terminal arabinosylation biosynthesis of the mycobacterial cell wall arabinan ]]> https://biorxiv.org/content/10.1101/2024.09.17.613533v1?rss=1 Liu, Y. Brown, C. M. Erramilli, S. Su, Y.-C. Tseng, P.-S. Wang, Y.-J. Duong, N. H. Tokarz, P. Kloss, B. Han, C.-R. Chen, H.-Y. Rodrigues, J. Archer, M. Lowary, T. L. Kossiakoff, A. A. Stansfeld, P. J. Nygaard, R. Mancia, F. 2024-09-18 doi:10.1101/2024.09.17.613533 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE ]]> https://biorxiv.org/content/10.1101/2024.09.17.613550v1?rss=1 Liu, Y. Brown, C. M. Borges, N. Nobre, R. N. Erramilli, S. Dufrisne, M. B. Kloss, B. Giacometti, S. Esteves, A. M. Timoteo, C. G. Tokarz, P. Cater, R. Morita, Y. S. Kossiakoff, A. A. Santos, H. Stansfeld, P. J. Nygaard, R. Mancia, F. 2024-09-18 doi:10.1101/2024.09.17.613550 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Molecular Magnetic Resonance Imaging of Dysregulated Zinc Secretion Detects Early Pancreatic Ductal Adenocarcinoma Lesions and Response to KRASG12D Inhibitor Treatment ]]> https://biorxiv.org/content/10.1101/2024.09.15.613145v1?rss=1 Jordan, V. C. Sojoodi, M. Moloudi, F. Pagan, P. G. Jin, M. Pantazopoulos, P. French, E. Weigand-Whittier, J. Rotile, N. Tavallai, M. Hallin, J. Ramsay, I. Gale, E. M. Barrett, S. Bardeesy, N. Qadan, M. Tanabe, K. Caravan, P. 2024-09-19 doi:10.1101/2024.09.15.613145 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans ]]> https://biorxiv.org/content/10.1101/2024.09.18.613595v1?rss=1 Ludin, A. Stirtz, G. L. Tal, A. Nirmal, A. J. Besson, N. Jones, S. M. Pfaff, K. L. Manos, M. Liu, S. Barrera, I. Gong, Q. Rodrigues, C. P. Sahu, A. Jerison, E. Alessi, J. V. Ricciuti, B. Richardson, D. S. Weiss, J. D. Moreau, H. M. Stanhope, M. E. Afeyan, A. B. Sefton, J. McCall, W. D. Formato, E. Yang, S. Zhou, Y. Hoytema van Konijnenburg, D. P. Cole, H. L. Cordova, M. Deng, L. Rajadhyaksha, M. Quake, S. R. Awad, M. M. Chen, F. Sorger, P. K. Hodi, F. S. Rodig, S. J. Murphy, G. F. Zon, L. I. 2024-09-19 doi:10.1101/2024.09.18.613595 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Beta cell extracellular vesicle PD-L1 as a novel regulator of CD8+ T cell activity and biomarker during the evolution of Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2024.09.18.613649v1?rss=1 Rao, C. Cater, D. T. Roy, S. Xu, J. Olivera, A. D. G. Evans-Molina, C. Eizirik, D. L. Piganelli, J. D. Mirmira, R. Sims, E. K. 2024-09-19 doi:10.1101/2024.09.18.613649 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Response to "Protein sequence landscapes are not so simple: on reference-free versus reference-based inference" ]]> https://biorxiv.org/content/10.1101/2024.09.17.613512v1?rss=1 Park, Y. Metzger, B. P. H. Thornton, J. W. 2024-09-20 doi:10.1101/2024.09.17.613512 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ The evolution, diversity, and genetic architecture of sex in waterhemp (Amaranthus tuberculatus) ]]> https://biorxiv.org/content/10.1101/2024.09.17.613486v1?rss=1 Kreiner, J. M. Todesco, M. Bercovich, N. Gong, Y. Elphinstone, C. Tranel, P. J. Rieseberg, L. H. Wright, S. I. 2024-09-21 doi:10.1101/2024.09.17.613486 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer ]]> https://biorxiv.org/content/10.1101/2024.09.18.613588v1?rss=1 Carlos, A. J. Yang, D. Thomas, D. M. Huang, S. Harter, K. I. Moellering, R. E. 2024-09-22 doi:10.1101/2024.09.18.613588 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ The TMRCA of general genealogies in populations of variable size ]]> https://biorxiv.org/content/10.1101/2024.09.19.613917v1?rss=1 Wemces, A. H. Penaloza, L. Steinruecken, M. Siri-Jegousse, A. 2024-09-24 doi:10.1101/2024.09.19.613917 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Dynamic responses of human lung innate and adaptive immune cells highlight the roles of genes at asthma risk loci ]]> https://biorxiv.org/content/10.1101/2024.09.20.614132v1?rss=1 Tian, F. Decker, D. C. Sperling, A. I. Schoettler, N. 2024-09-24 doi:10.1101/2024.09.20.614132 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Efficacy and limitations of combined A2.CAR Treg and anti-CD154 therapy in a mouse model of haplo-mismatched heart transplantation ]]> https://biorxiv.org/content/10.1101/2024.09.20.614149v1?rss=1 Durgam, S. S. Rosado sanchez, I. Yin, D. Speck, M. Mojibian, M. Sayin, I. Hynes, G. Alegre, M.-L. Levings, M. K. Chong, A. S. 2024-09-24 doi:10.1101/2024.09.20.614149 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Intranasal immunization with CPAF combined with cyclic-di-AMP induces a memory CD4 T cell response and reduces bacterial burden following intravaginal infection with Chlamydia muridarum ]]> https://biorxiv.org/content/10.1101/2024.09.20.614154v1?rss=1 Poston, T. B. Girardi, J. Kim, M. Zwarycz, P. Polson, A. G. Yount, K. S. Hanlan, C. Jaras Salas, I. Lammert, S. M. Arroyo, D. Bruno, T. Wu, M. Rozzelle, J. Fairman, J. Esser-Kahn, A. P. Darville, T. 2024-09-24 doi:10.1101/2024.09.20.614154 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Navigating Memorability Landscapes: Hyperbolic Geometry Reveals Hierarchical Structures in Object Concept Memory ]]> https://biorxiv.org/content/10.1101/2024.09.22.614329v1?rss=1 Lee, F. M. Berman, M. G. Stier, A. J. Bainbridge, W. A. 2024-09-24 doi:10.1101/2024.09.22.614329 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Plasticity in the pectoral fin skeleton is induced by altered foraging regime in a South American cichlid ]]> https://biorxiv.org/content/10.1101/2024.09.24.614498v1?rss=1 Gilbert, M. Kwiatkowski, A. J. Woodburn, C. M. Piggott, S. N. Haridy, Y. Aiello, B. R. Albertson, R. C. Stewart, T. A. 2024-09-24 doi:10.1101/2024.09.24.614498 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Mitochondrial oxidation of the carbohydrate fuel driven by pyruvate dehydrogenase robustly enhances stemness of older and geriatric Intestinal Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.09.23.614374v1?rss=1 Ahmed, S. Awwad, A. Eddy, N. Weber, G. Shahid, Z. Sethi, Z. Labampa, J. Murphy, R. Roth, E. W. Gustafson, K. Shah, H. Sundaresan, S. 2024-09-25 doi:10.1101/2024.09.23.614374 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ The Neural Underpinnings of Aphantasia: A Case Study of Identical Twins ]]> https://biorxiv.org/content/10.1101/2024.09.23.614521v1?rss=1 Megla, E. Prasad, D. Bainbridge, W. A. 2024-09-26 doi:10.1101/2024.09.23.614521 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ ADENYLATE CYCLASE 3 MEDIATES CAROTID BODY ACTIVATION AND AUTONOMIC DYSFUNCTION IN A SLEEP APNEA MODEL ]]> https://biorxiv.org/content/10.1101/2024.09.24.614747v1?rss=1 Peng, Y.-J. Nanduri, J. Wang, N. Su, X. Hildreth, M. PRABHAKAR, N. 2024-09-26 doi:10.1101/2024.09.24.614747 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder ]]> https://biorxiv.org/content/10.1101/2024.09.29.615714v1?rss=1 Zhang, H. Wetherington, M. T. Ko, H. FitzGerald, C. E. Nirody, J. A. 2024-09-30 doi:10.1101/2024.09.29.615714 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Effects of Host-Tree Foliage on Polymorphism in an Insect Pathogen ]]> https://biorxiv.org/content/10.1101/2024.09.29.615698v1?rss=1 Freedman, A. S. Huang, A. Dixon, K. Polivka, C. M. Dwyer, G. 2024-10-01 doi:10.1101/2024.09.29.615698 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations ]]> https://biorxiv.org/content/10.1101/2024.10.02.616147v1?rss=1 Feczko, E. J. Stoyell, S. M. Moore, L. A. Alexopoulos, D. Bagonis, M. Barrett, K. Bower, B. Cavender, A. Chamberlain, T. A. Conan, G. Day, T. K. Goradia, D. Graham, A. Heisler-Roman, L. Hendrickson, T. J. Houghton, A. Kardan, O. Kiffmeyer, E. A. Lee, E. G. Lundquist, J. T. Lucena, C. Martin, T. Mummaneni, A. Myricks, M. Narnur, P. Perrone, A. J. Reiners, P. Rueter, A. R. Saw, H. Styner, M. Sung, S. Tiklasky, B. Wisnowski, J. L. Yacoub, E. Zimmermann, B. Smyser, C. D. Rosenberg, M. D. Fair, D. A. Elison, J. T. 2024-10-03 doi:10.1101/2024.10.02.616147 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Protein-protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits ]]> https://biorxiv.org/content/10.1101/2024.10.02.616321v1?rss=1 Li, J. Li, Y. I. Liu, X. 2024-10-03 doi:10.1101/2024.10.02.616321 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Disruption of riboflavin biosynthesis in mycobacteria establishes 5-amino-6-D-ribitylaminouracil (5-A-RU) as key precursor of MAIT cell agonists ]]> https://biorxiv.org/content/10.1101/2024.10.03.616430v1?rss=1 Chengalroyen, M. D. Oketade, N. Worley, A. Lucas, M. Ramirez, L. N. Raphela, M. L. Swarbrick, G. Warner, D. F. Lewinsohn, D. Mehaffy, C. Adams, E. J. Hildebrand, W. Dobos, K. M. Mizrahi, V. Lewinsohn, D. 2024-10-04 doi:10.1101/2024.10.03.616430 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ A preprocessing toolbox for 2-photon subcellular calcium imaging ]]> https://biorxiv.org/content/10.1101/2024.10.04.616737v1?rss=1 Jiang, A. Zhao, C. Sheffield, M. 2024-10-05 doi:10.1101/2024.10.04.616737 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis ]]> https://biorxiv.org/content/10.1101/2024.10.06.616878v1?rss=1 Rodriguez-Horta, E. Strahan, J. Dinner, A. Barton, J. P. 2024-10-07 doi:10.1101/2024.10.06.616878 Cold Spring Harbor Laboratory Press 2024-10-07 <![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[ Catabolism of extracellular glutathione supplies amino acids to support tumor growth ]]> https://biorxiv.org/content/10.1101/2024.10.10.617667v1?rss=1 Hecht, F. Zocchi, M. Tuttle, E. T. Ward, N. P. Smith, B. Kang, Y. P. Cazarin, J. Soares, Z. G. Ozgurses, M. E. Zhao, H. Sheehan, C. Alimohammadi, F. Munger, L. D. Trivedi, D. Asantewaa, G. Blick-Nitko, S. K. Zoeller, J. J. Chen, Y. Vasiliou, V. Turner, B. M. Muir, A. Coloff, J. L. Munger, J. DeNicola, G. M. Harris, I. S. 2024-10-11 doi:10.1101/2024.10.10.617667 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ An atlas of conserved transcription factor binding sites reveals the cell type-resolved gene regulatory landscape of flowering plants ]]> https://biorxiv.org/content/10.1101/2024.10.08.617089v1?rss=1 Baumgart, L. A. Morales-Cruz, A. Greenblum, S. I. Wang, P. Zhang, Y. Yang, L. Chen, C. Dilworth, D. J. Garretson, A. C. Grosjean, N. He, G. Savage, E. Yoshinaga, Y. Blaby, I. K. Daum, C. G. O'Malley, R. C. 2024-10-12 doi:10.1101/2024.10.08.617089 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Analysis of the dynamics of a complex, multipathway reaction: Insulin dimer dissociation ]]> https://biorxiv.org/content/10.1101/2024.10.08.617297v1?rss=1 Jeong, K. Guo, S. C. Allaw, S. Dinner, A. R. 2024-10-12 doi:10.1101/2024.10.08.617297 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ The Xenopus respiratory system reveals common tetrapod mechanisms for growth, regeneration and healing ]]> https://biorxiv.org/content/10.1101/2024.10.10.617686v1?rss=1 Perry, S. K. Shaidani, N.-I. Horb, M. Shubin, N. H. 2024-10-12 doi:10.1101/2024.10.10.617686 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Changes in cortical grasp-related activity before and after object contact ]]> https://biorxiv.org/content/10.1101/2024.10.11.617909v1?rss=1 Yan, Y. Sobinov, A. R. Goodman, J. M. Okorokova, E. V. Miller, L. E. Bensmaia, S. J. 2024-10-12 doi:10.1101/2024.10.11.617909 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation ]]> https://biorxiv.org/content/10.1101/2024.10.10.617682v1?rss=1 Wu, J. Dasetty, S. Beckett, D. Wang, Y. Xue, W. Skora, T. Bidone, T. C. Ferguson, A. L. Voth, G. A. 2024-10-13 doi:10.1101/2024.10.10.617682 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Active RNA synthesis patterns nuclear condensates ]]> https://biorxiv.org/content/10.1101/2024.10.12.614958v1?rss=1 Banani, S. F. Goychuk, A. Natarajan, P. Zheng, M. M. Dall'Agnese, G. Henninger, J. E. Kardar, M. Young, R. A. Chakraborty, A. K. 2024-10-13 doi:10.1101/2024.10.12.614958 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ HIF-1α regulates mitochondrial function in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages ]]> https://biorxiv.org/content/10.1101/2024.10.14.618294v1?rss=1 Woods, P. S. Cetin-Atalay, R. Meliton, A. Y. Sun, K. A. Shamaa, O. R. Shin, K. W. D. Tian, Y. Haugen, B. Hamanaka, R. B. Mutlu, G. M. 2024-10-15 doi:10.1101/2024.10.14.618294 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Multiplexed single-cell imaging reveals diverging subpopulations with distinct senescence phenotypes during long-term senescence induction. ]]> https://biorxiv.org/content/10.1101/2024.10.14.618296v1?rss=1 Sessions, G. A. Loops, M. V. Diekman, B. O. Purvis, J. E. 2024-10-15 doi:10.1101/2024.10.14.618296 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Direct and indirect selection in a proofreading polymerase ]]> https://biorxiv.org/content/10.1101/2024.10.14.618309v1?rss=1 Husain, K. Sachdeva, V. Ravasio, R. Peruzzo, M. Liu, W. Good, B. H. Murugan, A. 2024-10-15 doi:10.1101/2024.10.14.618309 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges ]]> https://biorxiv.org/content/10.1101/2024.10.14.618236v1?rss=1 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders. ]]> Hegde, S. Akhter, S. Tang, Z. Qi, C. Yu, C. Lewicka, A. Liu, Y. Koirala, K. Reibarkh, M. Battaile, K. P. Cooper, A. Lovell, S. Holmstrom, E. D. Wang, X. Piccirilli, J. A. Gao, Q. Miao, Y. Wang, J. 2024-10-17 doi:10.1101/2024.10.14.618236 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Simple models of non-random mating and environmental transmission bias standard human genetics statistical methods ]]> https://biorxiv.org/content/10.1101/2024.10.16.618755v1?rss=1 Border, R. Wang, J. Caggiano, C. Sankararaman, S. Schork, A. J. Turley, P. Young, A. S. Benjamin, D. J. Dahl, A. W. Zaitlen, N. 2024-10-18 doi:10.1101/2024.10.16.618755 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Optical blur affects differently ON and OFF visual pathways ]]> https://biorxiv.org/content/10.1101/2024.10.17.618707v1?rss=1 View larger version (96K): org.highwire.dtl.DTLVardef@9161eorg.highwire.dtl.DTLVardef@8b11beorg.highwire.dtl.DTLVardef@39e5bdorg.highwire.dtl.DTLVardef@119fd42_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pons, C. Mazade, R. Jin, J. Dul, M. Alonso, J. M. 2024-10-21 doi:10.1101/2024.10.17.618707 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Conserved principles of spatial biology define tumor heterogeneity and response to immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.10.18.619136v1?rss=1 Behera, V. Giba, H. Pen, U.-Y. Di Lello, A. Doran, B. A. Esposito, A. Pezeshk, A. Bestvina, C. Kline, J. Garassino, M. Raman, A. 2024-10-22 doi:10.1101/2024.10.18.619136 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases ]]> https://biorxiv.org/content/10.1101/2024.10.18.619139v1?rss=1 Zhou, Y. Komnick, M. R. Sepulveda, F. Liu, G. Nieves-Ortiz, E. Meador, K. Ndatabaye, O. Fatkhullina, A. Wu-Woods, N. Naydenkov, P. M. Kent, J. Christiansen, N. Madariaga, M. L. Witkowski, P. Ismagilov, R. F. Esterhazy, D. 2024-10-22 doi:10.1101/2024.10.18.619139 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Correlating Disordered Activation Domain Ensembles with Gene Expression Levels ]]> https://biorxiv.org/content/10.1101/2024.10.19.619222v1?rss=1 Flores, E. Camacho, A. Cuevas-Zepeda, E. McCoy, M. B. Yu, F. Staller, M. V. Sukenik, S. 2024-10-22 doi:10.1101/2024.10.19.619222 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Mosaic of Somatic Mutations in the Ancient and Still-Living Aspen Clone, Pando ]]> https://biorxiv.org/content/10.1101/2024.10.19.619233v1?rss=1 Pineau, R. Mock, K. E. Morris, J. L. Kraklow, V. Brunelle, A. Pageot, A. Ratcliff, W. C. Gompert, Z. 2024-10-22 doi:10.1101/2024.10.19.619233 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Executive control can query hidden human memories ]]> https://biorxiv.org/content/10.1101/2024.10.22.619676v1?rss=1 Zhao, C. Fukuda, K. Woodman, G. F. 2024-10-22 doi:10.1101/2024.10.22.619676 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Multigenerational Proteolytic Inactivation of Restriction Upon Subtle Genomic Hypomethylation ]]> https://biorxiv.org/content/10.1101/2024.10.21.619520v1?rss=1 Shmidov, E. Villani, A. Mendoza, S. D. Avihu, E. Lebenthal-Loinger, I. Karako-Lampert, S. Shoshani, S. Ye, C. Wang, Y. Yan, H. Tang, W. Bondy-Denomy, J. Banin, E. 2024-10-23 doi:10.1101/2024.10.21.619520 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Structural Basis for Voltage Gating and Dalfampridine Binding in the Shaker Potassium Channel Revealed by Closed-State Model ]]> https://biorxiv.org/content/10.1101/2024.10.22.619486v1?rss=1 Pinto-Anwandter, B. I. 2024-10-25 doi:10.1101/2024.10.22.619486 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Organic opto-nanobiointerface enables multiscale biomodulation ]]> https://biorxiv.org/content/10.1101/2024.10.23.619813v1?rss=1 Mueller, C. Zhang, Y. Meng, L. Kalatanova, A. Madsen, J. G. Klompmaker, K. K. Jakobsen, T. S. Joergensen, A. C. Askou, A. L. Huang, G. Li, W. Davidsen, R. S. Bek, T. Hatzakis, N. S. Corydon, T. J. Leinonen, H. O. Tian, B. Dong, M. Chen, M. 2024-10-25 doi:10.1101/2024.10.23.619813 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ribozyme ]]> https://biorxiv.org/content/10.1101/2024.10.26.620442v1?rss=1 Radakovic, A. Todisco, M. Mishra, A. Szostak, J. W. 2024-10-28 doi:10.1101/2024.10.26.620442 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Probabilistic Fine-mapping of Putative Causal Genes ]]> https://biorxiv.org/content/10.1101/2024.10.27.620482v1?rss=1 Okamoto, J. Yin, X. Ryan, B. Chiou, J. Luca, F. Pique-Regi, R. Im, H. K. Morrison, J. Burant, C. Fauman, E. Laakso, M. Boehnke, M. Wen, X. 2024-10-29 doi:10.1101/2024.10.27.620482 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[ Fragment-based development of small molecule inhibitors targeting Mycobacterium tuberculosis cholesterol metabolism ]]> https://biorxiv.org/content/10.1101/2024.10.28.620643v1?rss=1 Kavanagh, M. E. McLean, K. J. Gilbert, S. H. Amadi, C. Snee, M. Tunnicliffe, R. B. Arora, K. Boshoff, H. Fanourakis, A. Rebello-Lopez, M. J. Ortega-Muro, F. Levy, C. Munro, A. W. Leys, D. Abell, C. Coyne, A. G. 2024-10-31 doi:10.1101/2024.10.28.620643 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Hypoxia induces extensive protein and proteolytic remodeling of the cell surface in pancreatic adenocarcinoma (PDAC) cell lines ]]> https://biorxiv.org/content/10.1101/2024.10.30.621099v1?rss=1 Lui, I. Schaefer, K. Kirkemo, L. Zhou, J. Perera, R. M. Leung, K. K. Wells, J. A. 2024-11-02 doi:10.1101/2024.10.30.621099 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ Counterfactual Diffusion Models for Mechanistic Explainability of Artificial Intelligence Models in Pathology ]]> https://biorxiv.org/content/10.1101/2024.10.29.620913v1?rss=1 Zigutyte, L. Lenz, T. Han, T. Hewitt, K. J. Reitsam, N. G. Foersch, S. Carrero, Z. Unger, M. Pearson, A. T. Truhn, D. Kather, J. N. 2024-11-03 doi:10.1101/2024.10.29.620913 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[ Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly ]]> https://biorxiv.org/content/10.1101/2024.11.04.620124v1?rss=1 Dutta, M. Dolan, K. A. Amiar, S. Bass, E. J. Sultana, R. Voth, G. A. Stahelin, R. V. Brohawn, S. G. 2024-11-05 doi:10.1101/2024.11.04.620124 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ Fishnet mesh of centrin-Sfi1 drives ultrafast calcium-activated contraction of the giant cell Spirostomum ambiguum ]]> https://biorxiv.org/content/10.1101/2024.11.07.622534v1?rss=1 Lannan, J. Floyd, C. Xu, L. X. Yan, C. Marshall, W. F. Vaikuntanathan, S. Dinner, A. R. Honts, J. E. Bhamla, S. Elting, M. W. 2024-11-08 doi:10.1101/2024.11.07.622534 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images ]]> https://biorxiv.org/content/10.1101/2024.11.10.622859v1?rss=1 Wu, E. Bieniosek, M. Wu, Z. Thakkar, N. Charville, G. W. Makky, A. Schürch, C. Huyghe, J. R. Peters, U. Li, C. I. Li, L. Giba, H. Behera, V. Raman, A. Trevino, A. E. Mayer, A. T. Zou, J. 2024-11-11 doi:10.1101/2024.11.10.622859 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Biophysical Basis of Paracellular Barrier Modulation by a Pan-Claudin-Binding Molecule ]]> https://biorxiv.org/content/10.1101/2024.11.10.622873v1?rss=1 Ogbu, C. P. Mandriota, A. M. Liu, X. de las Alas, M. Kapoor, S. Choudhury, J. Kossiakoff, A. A. Duffey, M. E. Vecchio, A. J. 2024-11-11 doi:10.1101/2024.11.10.622873 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Natural Language Prompts Guide the Design of Novel Functional Protein Sequences ]]> https://biorxiv.org/content/10.1101/2024.11.11.622734v1?rss=1 Praljak, N. Yeh, H. Moore, M. Socolich, M. Ranganathan, R. Ferguson, A. L. 2024-11-11 doi:10.1101/2024.11.11.622734 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle ]]> https://biorxiv.org/content/10.1101/2024.11.11.623012v1?rss=1 Nap, R. J. Gonzalez, P. C. Coraor, A. E. Virk, R. K. A. de Pablo, J. J. Backman, V. Szleifer, I. 2024-11-12 doi:10.1101/2024.11.11.623012 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Semaphorin 4A maintains functional diversity of the hematopoietic stem cell pool ]]> https://biorxiv.org/content/10.1101/2024.11.12.622506v1?rss=1 Toghani, D. Gupte, S. Zeng, S. Mahammadov, E. Crosse, E. Seyedhassantehrani, N. Burns, C. Gravano, D. Radtke, S. Kiem, H.-P. Rodriguez, S. Carlesso, N. Pradeep, A. Georgiades, A. Lucas, F. Wilson, N. K. Kinston, S. J. Gottgens, B. Zong, L. Beerman, I. Park, B. Janssens, D. Jones, D. Toghani, A. Nerlov, C. Pietras, E. C. Mesnieres, M. Maes, C. Kumanogoh, A. Worzfeld, T. Cheong, J.-G. Josefowicz, S. Z. Kharchenko, P. Scadden, D. Scialdone, A. Spencer, J. A. Silberstein, L. 2024-11-13 doi:10.1101/2024.11.12.622506 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ scPrediXcan integrates advances in deep learning and single-cell data into a powerful cell-type-specific transcriptome-wide association study framework ]]> https://biorxiv.org/content/10.1101/2024.11.11.623049v1?rss=1 Zhou, Y. Adeluwa, T. Zhu, L. Salazar, S. Sumner, S. Kim, H. Gona, S. Nyasimi, F. Kulkarni, R. Powell, J. Madduri, R. Liu, B. Chen, M. Im, H. K. 2024-11-14 doi:10.1101/2024.11.11.623049 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ A highly conserved sRNA downregulates multiple genes, including a sigma54 transcriptional activator, in the virulence mode of Bordetella pertussis ]]> https://biorxiv.org/content/10.1101/2024.11.19.624354v1?rss=1 Sim, M. Nguyen, J. Skopova, K. Yoo, K. Tai, C.-H. Knipling, L. Chen, Q. Kim, D. Nolan, S. Elaksher, R. Majdalani, N. Lorenzi, H. Stibitz, S. Moon, K. Hinton, D. M. 2024-11-19 doi:10.1101/2024.11.19.624354 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Organization of the apical extracellular matrix during tubular organ formation ]]> https://biorxiv.org/content/10.1101/2024.11.20.624565v1?rss=1 Woodward, J. L. Matthew, J. Vishwakarma, V. Xiao, Y. Chung, S. 2024-11-21 doi:10.1101/2024.11.20.624565 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Sub-therapeutic Concentrations of Antibiotics Induce Prophage-driven Superinfection Exclusion and Fitness Cost in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2024.11.20.624585v1?rss=1 Bucher, M. J. Puente, C. P. Sehdev, N. Czyz, D. M. 2024-11-21 doi:10.1101/2024.11.20.624585 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport ]]> https://biorxiv.org/content/10.1101/2024.11.21.624706v1?rss=1 Brousseau, M. Teng, D. Thomas, N. Voth, G. A. Henzler-Wildman, K. A. 2024-11-22 doi:10.1101/2024.11.21.624706 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Visual speech enhances auditory onset timing and envelope tracking through distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2024.11.23.624953v1?rss=1 Cao, C. Z. Stacey, W. C. Wasade, V. S. Towle, V. L. Tao, J. X. Wu, S. Issa, N. P. Brang, D. J. 2024-11-24 doi:10.1101/2024.11.23.624953 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ Impacts of urbanization on the health of American Robins (Turdus migratorus) in Chicagoland ]]> https://biorxiv.org/content/10.1101/2024.11.24.625046v1?rss=1 Riccardi, A. Douglass, K. R. Jackson, V. S. Dehnert, G. K. Herbst, H. Grewe, F. Walker, M. Magle, S. Murray, M. H. Adams, H. Brook, C. E. Cornelius Ruhs, E. 2024-11-25 doi:10.1101/2024.11.24.625046 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality. ]]> https://biorxiv.org/content/10.1101/2024.11.26.625482v1?rss=1 Krishnan, S. Dong, C. Ratigan, H. Morales-Rodriguez, D. Cherian, C. Sheffield, M. 2024-11-27 doi:10.1101/2024.11.26.625482 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Stereoselectivity of Aminoacyl-RNA Loop-closing Ligation ]]> https://biorxiv.org/content/10.1101/2024.11.26.625528v1?rss=1 Kim, S. Todisco, M. Radakovic, A. Szostak, J. W. 2024-11-27 doi:10.1101/2024.11.26.625528 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Molecular characterization of the archaic HLA-B*73:01 allele reveals presentation of a unique peptidome and skewed engagement by KIR2DL2 ]]> https://biorxiv.org/content/10.1101/2024.11.25.625330v1?rss=1 Ross, P. Hilton, H. G. Lodwick, J. Slezak, T. Guethlein, L. A. McMurtrey, C. P. Han, A. S. Nielsen, M. Yong, D. Dulberger, C. L. Nolan, K. T. Roy, S. Castro, C. D. Hildebrand, W. H. Zhao, M. Kossiakoff, A. Parham, P. Adams, E. J. 2024-11-28 doi:10.1101/2024.11.25.625330 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology ]]> https://biorxiv.org/content/10.1101/2024.11.26.625329v1?rss=1 Sokolowski, D. J. Miclaus, M. Nater, A. Faykoo-Martinez, M. Hoekzema, K. Zuzarte, P. Monis, S. Alvi, S. A. Erdmann, J. Erdmann, A. L. Kumaragurubaran, R. Bayerl, J. Yoo, D. Karimpour, N. Ungerleider, K. Hou, H. Fergal, M. Hourlier, T. Clarke, Z. A. Lischer, H. E. Leordean, D. V. Jiang, Y. Pugh, T. J. Smith, E. S. J. Haggerty, L. Laird, D. J. Lilue, J. Holmes, M. M. Eichler, E. E. Bruggmann, R. Simpson, J. T. Balmus, G. Wilson, M. D. 2024-11-28 doi:10.1101/2024.11.26.625329 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Chromatin Structures from Integrated AI and Polymer Physics Model ]]> https://biorxiv.org/content/10.1101/2024.11.27.624905v1?rss=1 Schultz, E. R. Kyhl, S. Willett, R. de Pablo, J. J. 2024-11-29 doi:10.1101/2024.11.27.624905 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Study design and the sampling of deleterious rare variants in biobank-scale datasets ]]> https://biorxiv.org/content/10.1101/2024.12.02.626424v1?rss=1 Steiner, M. C. Rice, D. P. Biddanda, A. Ianni-Ravn, M. K. Porras, C. Novembre, J. 2024-12-02 doi:10.1101/2024.12.02.626424 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2024.12.03.626676v1?rss=1 Randolph, H. E. Aguirre-Gamboa, R. Brunet-Ratnasingham, E. Nakanishi, T. Locher, V. Ketter, E. Brandolino, C. Larochelle, C. Prat, A. Arbour, N. Dumaine, A. Finzi, A. Durand, M. Richards, J. B. Kaufmann, D. E. Barreiro, L. B. 2024-12-04 doi:10.1101/2024.12.03.626676 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Bayesian Least-Squares Supertrees (BLeSS): flexible inference of large time-calibrated phylogenies ]]> https://biorxiv.org/content/10.1101/2024.11.29.625936v1?rss=1 Cerny, D. Slater, G. J. 2024-12-05 doi:10.1101/2024.11.29.625936 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Kinetic Implications of IP6 Anion Binding on the Molecular Switch of the HIV-1 Capsid Assembly ]]> https://biorxiv.org/content/10.1101/2024.12.05.627050v1?rss=1 Gupta, M. Hudait, A. Yeager, M. Voth, G. A. 2024-12-06 doi:10.1101/2024.12.05.627050 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ A new universal chimeric-antigen receptor (CAR)- fragment antibody binder (FAB) split system for cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.12.05.627079v1?rss=1 Arina, A. Arauz, E. Warzecha, K. Masoumi, E. Saaf, A. Widlo, L. Slezak, T. Zieminska, A. Dudek, K. Schaefer, Z. P. Lecka, M. Usatyuk, S. Weichselbaum, R. R. Kossiakoff, A. A. 2024-12-10 doi:10.1101/2024.12.05.627079 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Inkube: An all-in-one solution for neuron culturing, electrophysiology, and fluidic exchange ]]> https://biorxiv.org/content/10.1101/2024.12.06.627248v1?rss=1 Maurer, B. Fassbind, S. Ruff, T. Duru, J. Spacone, G. Rodde, T. Voros, J. Ihle, S. J. 2024-12-11 doi:10.1101/2024.12.06.627248 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Specificity, length, and luck: How genes are prioritized by rare and common variant association studies ]]> https://biorxiv.org/content/10.1101/2024.12.12.628073v1?rss=1 Spence, J. P. Mostafavi, H. Ota, M. Milind, N. Gjorgjieva, T. Smith, C. J. Simons, Y. B. Sella, G. Pritchard, J. K. 2024-12-16 doi:10.1101/2024.12.12.628073 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ The first comorbidity networks in companion dogs in the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.12.18.629088v1?rss=1 Fang, A. Kumar, L. Creevy, K. E. Promislow, D. E. L. Ma, J. 2024-12-20 doi:10.1101/2024.12.18.629088 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Image Processing in the Acute to Chronic Pain Signatures (A2CPS) Project ]]> https://biorxiv.org/content/10.1101/2024.12.19.627509v1?rss=1 Sadil, P. Arfanakis, K. Bhuiyan, E. H. Caffo, B. Calhoun, V. D. Clauw, D. J. DeLano, M. C. Ford, J. C. Gattu, R. Guo, X. Harris, R. E. Ichesco, E. Johnson, M. A. Jung, H. Kahn, A. B. Kaplan, C. M. Leloudas, N. Lindquist, M. A. Luo, Q. Mulderink, T. A. Peltier, S. J. Prasad, P. V. Sica, C. Urrutia, J. Vance, C. G. Wager, T. D. Xuan, Y. Zhou, X. J. Zhou, Y. Shu, D. C. The Acute to Chronic Pain Signatures Consortium, 2024-12-20 doi:10.1101/2024.12.19.627509 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Neuronal activation in the axolotl brain promotes spinal cord regeneration ]]> https://biorxiv.org/content/10.1101/2024.12.19.629459v1?rss=1 Walker, S. Yu, K. Burgess, S. M. Echeverri, K. 2024-12-20 doi:10.1101/2024.12.19.629459 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Distinct Microbiomes Underlie Divergent Responses of Methane Emissions from Diverse Wetland soils to Oxygen Shifts ]]> https://biorxiv.org/content/10.1101/2024.12.19.629461v1?rss=1 Reji, L. Zhang, X. Duan, J. 2024-12-20 doi:10.1101/2024.12.19.629461 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The natural variability of a dexterous motor skill is stably encoded in the cortex of freely behaving mice ]]> https://biorxiv.org/content/10.1101/2024.12.20.629771v1?rss=1 de Laittre, E. A. MacLean, J. N. 2024-12-21 doi:10.1101/2024.12.20.629771 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Robustness of ancestral sequence reconstruction to among-site evolutionary heterogeneity and epistasis ]]> https://biorxiv.org/content/10.1101/2024.12.20.629812v1?rss=1 Muniz-Trejo, R. Park, Y. Thornton, J. W. 2024-12-21 doi:10.1101/2024.12.20.629812 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Engineered biological neural networks as basic logic operators ]]> https://biorxiv.org/content/10.1101/2024.12.23.630065v1?rss=1 Küchler, J. Vulic, K. Yao, H. Valmaggia, C. Ihle, S. J. Weaver, S. Vörös, J. 2024-12-23 doi:10.1101/2024.12.23.630065 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk ]]> https://biorxiv.org/content/10.1101/2024.12.24.630179v1?rss=1 Gonzalez, F. L. Ranaivoson, H. C. Andrianiaina, A. Andry, S. Raharinosy, V. Randriambolamanantsoa, T. H. Lacoste, V. Dussart, P. Heraud, J.-M. Brook, C. E. 2024-12-24 doi:10.1101/2024.12.24.630179 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Glycerol-3-phosphate activates ChREBP, FGF21 transcription and lipogenesis in Citrin Deficiency ]]> https://biorxiv.org/content/10.1101/2024.12.27.630525v1?rss=1 Tiwari, V. Jin, B. Sun, O. Lopez Gonzalez, E. D. J. Chen, M.-H. Wu, X. Shah, H. Zhang, A. Herman, M. A. Spracklen, C. N. Goodman, R. P. Brenner, C. 2024-12-27 doi:10.1101/2024.12.27.630525 Cold Spring Harbor Laboratory Press 2024-12-27 <![CDATA[ Characterization and modulation of human insulin degrading enzyme conformational dynamics to control enzyme activity ]]> https://biorxiv.org/content/10.1101/2024.12.30.630732v1?rss=1 Mancl, J. M. Liang, w. G. bayhi, N. L. Wei, H. Carragher, B. Potter, C. S. Tang, W.-J. 2024-12-30 doi:10.1101/2024.12.30.630732 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax ]]> https://biorxiv.org/content/10.1101/2024.12.31.630814v1?rss=1 Villano, D. J. Prahlad, M. Singhal, A. Sanbonmatsu, K. Y. Landweber, L. F. 2025-01-02 doi:10.1101/2024.12.31.630814 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Molecular basis for the activation of Pseudomonas aeruginosa MsbA by Zn2+ ]]> https://biorxiv.org/content/10.1101/2024.12.31.630943v1?rss=1 Lyu, J. Bahramimoghaddam, H. Zhang, T. Yadav, G. Zhao, M. Russell, D. Laganowsky, A. 2025-01-02 doi:10.1101/2024.12.31.630943 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Picornaviridae and Caliciviridae diversity in Madagascar fruit bats is driven by cross-continental genetic exchange ]]> https://biorxiv.org/content/10.1101/2024.12.31.630946v1?rss=1 Kettenburg, G. Ranaivoson, H. C. Andrianiaina, A. Andry, S. Henry, A. R. Davis, R. L. Laboune, F. Longtine, E. R. Godbole, S. Horigan, S. Ruhs, E. C. Raharinosy, V. Randriambolamanantsoa, T. H. Lacoste, V. Heraud, J.-M. Dussart, P. Douek, D. C. Brook, C. E. 2025-01-02 doi:10.1101/2024.12.31.630946 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Single-base m6A epitranscriptomics reveals novel HIV-1 host interaction targets in primary CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2024.12.31.630958v1?rss=1 Huang, S. Zhao, Y. Phillips, S. Wilms, B. He, C. Wu, L. 2025-01-02 doi:10.1101/2024.12.31.630958 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Structural basis of directionality control in large serine integrases ]]> https://biorxiv.org/content/10.1101/2025.01.03.631226v1?rss=1 Shin, H. Pigli, Y. Pena Reyes, T. Fuller, J. R. Olorunniji, F. J. Rice, P. 2025-01-03 doi:10.1101/2025.01.03.631226 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Linking neural population formatting to function ]]> https://biorxiv.org/content/10.1101/2025.01.03.631242v1?rss=1 Ruff, D. A. Markman, S. K. Kim, J. Z. Cohen, M. R. 2025-01-04 doi:10.1101/2025.01.03.631242 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ High-throughput protein binder discovery by rapid in vivo selection ]]> https://biorxiv.org/content/10.1101/2025.01.06.631531v1?rss=1 Styles, M. J. Pixley, J. A. Wei, T. Basile, C. Lu, S. Dickinson, B. C. 2025-01-06 doi:10.1101/2025.01.06.631531 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC) ]]> https://biorxiv.org/content/10.1101/2025.01.07.631731v1?rss=1 Monsen, P. J. Bommi, P. V. Grigorescu, A. A. Lauing, K. L. Mao, Y. Berardi, P. Zhai, L. Ojo, O. Penco-Campillo, M. Koch, T. Egozi, M. Jha, S. V. Dunne, S. F. Jiang, H. Song, G. Zhang, F. Kregel, S. Vaziri-Gohar, A. Fanning, S. Sanchez-Gomez, P. Allen, J. M. Yamini, B. Lukas, R. V. Wainwright, D. A. Schiltz, G. E. 2025-01-08 doi:10.1101/2025.01.07.631731 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Inferring resource competition in microbial communities from time series ]]> https://biorxiv.org/content/10.1101/2025.01.08.631910v1?rss=1 Chen, X. Crocker, K. Kuehn, S. Walczak, A. M. Mora, T. 2025-01-12 doi:10.1101/2025.01.08.631910 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Noise Correlations in Balanced Networks with Unreliable Synapses ]]> https://biorxiv.org/content/10.1101/2025.01.09.632185v1?rss=1 Leone, M. J. Huang, C. Doiron, B. 2025-01-13 doi:10.1101/2025.01.09.632185 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ 12-Lipoxygenase inhibition improves glucose homeostasis and obesity-associated inflammation in human gene replacement mice ]]> https://biorxiv.org/content/10.1101/2025.01.10.632274v1?rss=1 Kaylan, K. B. Nargis, T. Figatner, K. Wang, J. E. Pratuangtham, S. Chakraborty, A. Casimiro, I. Nadler, J. L. Boxer, M. B. Maloney, D. J. Anderson, R. M. Mirmira, R. Tersey, S. A. 2025-01-13 doi:10.1101/2025.01.10.632274 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Microscopic Control of Cortical Flows in Polarized C. elegans Zygotes ]]> https://biorxiv.org/content/10.1101/2025.01.12.632635v1?rss=1 White, E. Li, Y. Kadzik, R. Qiu, Y. Dinner, A. Munro, E. 2025-01-13 doi:10.1101/2025.01.12.632635 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Causal Spike Timing Dependent Plasticity Prevents Assembly Fusion in Recurrent Networks ]]> https://biorxiv.org/content/10.1101/2025.01.14.633085v1?rss=1 Yang, X. Doiron, B. 2025-01-15 doi:10.1101/2025.01.14.633085 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Diversity and seasonality of ectoparasite burden on two species of Madagascar fruit bat, Eidolon dupreanum and Rousettus madagascariensis ]]> https://biorxiv.org/content/10.1101/2025.01.20.633693v1?rss=1 Andrianiaina, A. F. Andry, S. Kettenburg, G. F. Ranaivoson, H. C. Lacoste, V. Dussart, P. Heraud, J.-M. Laverty, T. M. Guth, S. Young, K. I. Andrianarimisa, A. Brook, C. E. 2025-01-22 doi:10.1101/2025.01.20.633693 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Contribution of DNA breathing to physical interactions with transcription factors ]]> https://biorxiv.org/content/10.1101/2025.01.20.633840v1?rss=1 60 TFs, we found that the propensity of DNA forming bubbles near motifs is often associated with binding affinity of DNA sequence. Interestingly the patterns of these associations seem to vary with TFs. Altogether, our results highlighted the potential of DNA breathing in influencing TF-DNA interactions. ]]> Butt, W. A. Lai, B. Chiu, T.-P. Bhattarai, M. Qian, S. Bishop, A. R. Duan, J. Alexandrov, B. S. Rohs, R. He, X. 2025-01-22 doi:10.1101/2025.01.20.633840 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION ]]> https://biorxiv.org/content/10.1101/2025.01.21.634169v1?rss=1 Veselits, M. McLean, K. C. Wright, N. E. Veselits, J. Okoreeh, M. Maienschein-Cline, M. Mandal, M. Clark, M. R. 2025-01-23 doi:10.1101/2025.01.21.634169 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Nucleoporins shape germ granule architecture and balance small RNA silencing pathways ]]> https://biorxiv.org/content/10.1101/2025.01.23.634177v1?rss=1 Shi, K. Zhang, Y. Du, Z. Liu, S. C. Fan, X. Lee, H.-C. Zhang, D. 2025-01-25 doi:10.1101/2025.01.23.634177 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network ]]> https://biorxiv.org/content/10.1101/2025.01.24.634581v1?rss=1 Lax, C. Baumgart, L. A. Tahiri, G. Nicolas-Munoz, N. Zhang, Y. Blaby, I. K. O'Malley, R. C. Ng, V. Navarro, E. Grigoriev, I. V. Nicolas, F. E. Garre, V. 2025-01-27 doi:10.1101/2025.01.24.634581 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Histopathologic Evaluation and Single-Cell Spatial Transcriptomics of the Colon Reveal Cellular and Molecular Abnormalities Linked to J-Pouch Failure in Patients with Inflammatory Bowel Disease. ]]> https://biorxiv.org/content/10.1101/2025.01.27.635092v1?rss=1 Olivas, A. O. D. Ngai, P. C. M. Schahrer, E. Olortegui, K. S. Cursio, J. F. Akiyama, S. Chang, E. B. Shen, L. Umanskiy, K. Rubin, D. T. Zemmour, D. Weber, C. R. 2025-01-28 doi:10.1101/2025.01.27.635092 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Ancient biases in phenotype production drove the functional evolution of a protein family ]]> https://biorxiv.org/content/10.1101/2025.01.28.635160v1?rss=1 Herrera-Alvarez, S. Patton, J. E. J. Thornton, J. W. 2025-01-29 doi:10.1101/2025.01.28.635160 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Receptor Allostery Promotes Context-Specific Sonic Hedgehog Signaling During Embryonic Development ]]> https://biorxiv.org/content/10.1101/2025.01.28.635336v1?rss=1 Ansari, S. S. Dillard, M. A. Ghonim, M. Zhang, Y. Stewart, D. P. Canac, R. Moskowitz, I. P. Wright, W. C. Daly, C. A. Pruett-Miller, S. M. Steinberg, J. Wang, Y.-D. Chen, T. Thomas, P. Bridges, J. P. Ogden, S. K. 2025-01-29 doi:10.1101/2025.01.28.635336 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Microbial functional guilds respond cohesively to rapidly fluctuating environments ]]> https://biorxiv.org/content/10.1101/2025.01.30.635766v1?rss=1 Crocker, K. A. Skwara, A. A. Kannan, R. Murugan, A. Kuehn, S. 2025-01-30 doi:10.1101/2025.01.30.635766 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Spatially-structured inflammatory response in the presence of a uniform stimulus ]]> https://biorxiv.org/content/10.1101/2025.01.28.635318v1?rss=1 Jerison, E. R. Quake, S. R. Romeo, N. 2025-01-31 doi:10.1101/2025.01.28.635318 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Dietary macronutrients modulate the proteome of brown adipose tissue in males and their female offspring ]]> https://biorxiv.org/content/10.1101/2025.02.01.636065v1?rss=1 50% of the proteome was affected by macronutrient composition, with distinct clusters of proteins that responded in similar ways. We identified two clusters with inverse patterns that correlated with BAT mass. Notably, UCP1 was reduced on low fat diets that promoted increased BAT mass, while there were increased levels of proteins involved in protein turnover on those same diets. The same diets also led to a reduction in proteins involved in purine biosynthesis (often UCP1 inhibitors). We did not find any effects of paternal diet on the BAT proteome in sons, but paternal protein intake negatively affected basigin expression in daughters - a protein that regulates UCP1 transcription. Our results highlight that dietary macronutrient composition in males remodels the protein expression landscape of BAT, and pre-conceptionally reprograms BAT expression profiles of female offspring. ]]> Macartney, E. L. Senior, A. Crean, A. J. Small, L. Pulpitel, T. Nobrega, M. A. Barres, R. 2025-02-02 doi:10.1101/2025.02.01.636065 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ A Litmus Test for Confounding in Polygenic Scores ]]> https://biorxiv.org/content/10.1101/2025.02.01.635985v1?rss=1 Smith, S. P. Smith, O. S. Mostafavi, H. Peng, D. Berg, J. J. Edge, M. D. Harpak, A. 2025-02-04 doi:10.1101/2025.02.01.635985 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Deciphering DNA's sequence-dependent structure and deformability with normalizing flows ]]> https://biorxiv.org/content/10.1101/2025.02.01.636041v1?rss=1 Liebl, K. 2025-02-06 doi:10.1101/2025.02.01.636041 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ LRRC8A-containing anion channels promote glioblastoma proliferation via a WNK1/mTORC2-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2025.02.02.636139v1?rss=1 Fidaleo, A. M. Bach, M. D. Orbeta, S. Abdullaev, I. F. Martino, N. Adam, A. P. Boulos, M. A. Dulin, N. O. Paul, A. R. Kuo, Y.-H. Mongin, A. A. 2025-02-06 doi:10.1101/2025.02.02.636139 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Genomic Insights into the Demographic History and Local Adaptation of Wild Boars Across Eurasia ]]> https://biorxiv.org/content/10.1101/2025.02.05.636574v1?rss=1 Wang, Z. Li, Z. Huang, T. Chen, J. Xu, P. Qiao, R. Yin, H. Song, C. Zhang, D. Liu, D. Zhao, S. Groenen, M. Madsen, O. Zhang, Y. Bai, L. Li, K. 2025-02-07 doi:10.1101/2025.02.05.636574 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Modeling of hepatitis B virus infection spread in primary human hepatocytes ]]> https://biorxiv.org/content/10.1101/2025.02.05.636596v1?rss=1 Shi, Z. Tsuge, M. Collier, N. Takeuchi, Y. Uchida, T. Rutter, C. Teraoka, Y. Uprichard, S. L. Ishida, Y. Tateno, C. Ozik, J. Dahari, H. Chayama, K. 2025-02-07 doi:10.1101/2025.02.05.636596 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ NMR Spectroscopy for the Validation of AlphaFold2 Structures ]]> https://biorxiv.org/content/10.1101/2025.02.04.636507v1?rss=1 Sachleben, J. R. Williams, J. L. Gagnon, I. A. 2025-02-08 doi:10.1101/2025.02.04.636507 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Disruption of transthalamic circuitry from primary visual cortex impairs visual discrimination in mice ]]> https://biorxiv.org/content/10.1101/2025.02.07.637190v1?rss=1 McKinnon, C. Mo, C. Sherman, S. M. 2025-02-08 doi:10.1101/2025.02.07.637190 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ CDKN2ALow cancer cells outcompete macrophages for microenvironmental zinc to drive immunotherapy resistance ]]> https://biorxiv.org/content/10.1101/2025.02.08.637227v1?rss=1 Buj, R. Cole, A. R. Danielson, J. Xu, J. Hurd, D. Kishore, A. Kedziora, K. M. Chen, J. Yang, B. Barras, D. Uboveja, A. Amalric, A. Apiz, J. J. Wickramasinghe, J. Tangudu, N. K. Levasseur, E. Wang, H. Minasyan, A. Dadey, R. E. Sharrow, A. C. Vendetti, F. P. Rivadeneira, D. B. Bakkenist, C. J. Delgoffe, G. M. Hempel, N. Snyder, N. W. Bao, R. Soloff, A. C. Kirkwood, J. M. Dangaj Laniti, D. Kossenkov, A. V. Muir, A. Das, J. Davar, D. Mesaros, C. Aird, K. M. 2025-02-08 doi:10.1101/2025.02.08.637227 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Calcium channel-coupled transcription factors facilitate direct nuclear signaling ]]> https://biorxiv.org/content/10.1101/2025.02.09.637126v1?rss=1 Rao, E. R. Thaxton, T. Gama, E. Godfrey, J. Wei, C. Lin, Q. Li, Y. Pastor, D. P. H. Hansel, C. Du, X. Gomez, C. M. 2025-02-10 doi:10.1101/2025.02.09.637126 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data ]]> https://biorxiv.org/content/10.1101/2025.02.10.637323v1?rss=1 Ashesh, A. Carrara, F. Zubarev, I. Galinova, V. Croft, M. Pezzotti, M. Gong, D. Casagrande, F. Colombo, E. Giussani, S. Restelli, E. Cammarota, E. Battagliotti, J. M. Klena, N. Di Sante, M. Pigino, G. Taverna, E. Harschnitz, O. Maghelli, N. Scherer, N. F. Dalle Nogare, D. E. Dechamps, J. Pasqualini, F. Jug, F. 2025-02-11 doi:10.1101/2025.02.10.637323 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Molecular and morphological circuitry of the octopus sucker ganglion ]]> https://biorxiv.org/content/10.1101/2025.02.10.637560v1?rss=1 Olson, C. S. Moorjani, A. Ragsdale, C. W. 2025-02-11 doi:10.1101/2025.02.10.637560 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ Development of the zebrafish anterior lateral line system is influenced by underlying cranial neural crest ]]> https://biorxiv.org/content/10.1101/2025.02.11.637483v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@ce9c43org.highwire.dtl.DTLVardef@7511e5org.highwire.dtl.DTLVardef@1e9e208org.highwire.dtl.DTLVardef@1f6af7d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Venkataraman, V. McGrory, N. H. Christiansen, T. J. Navajas Acedo, J. Coates, M. I. Prince, V. E. 2025-02-11 doi:10.1101/2025.02.11.637483 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ A dendritic guidance receptor functions in both ligand dependent and independent modes ]]> https://biorxiv.org/content/10.1101/2025.02.11.637350v1?rss=1 Reddy, A. R. Machera, S. J. Cook, Z. T. Ozkan, E. Shen, K. 2025-02-12 doi:10.1101/2025.02.11.637350 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.02.11.637768v1?rss=1 20 {micro}m) are irregularly and randomly organized, while neuron pairs that are extremely close (< 20 {micro}m) have strongly correlated orientation tuning, indicating a narrow yet strong spatially clustered organization of orientation preference, which we term micro-clustered organization. Exploring a circuit-based model of recurrently coupled mouse V1 we derived two key predictions for the micro-cluster: spatially localized recurrent connections over a comparable narrow spatial scale, and common relative spatial spreads of balanced excitation and inhibition in the network over broad spatial scales. These predictions are validated by both anatomical and optogenetic-based physiological circuit mapping experiments. Altogether, our work takes an important step in building a circuit-based theory of visual processing in mouse V1 over spatial scales that are often ignored, yet contain powerful synaptic interactions. ]]> Yu, P. Yang, Y. Gozel, O. Oldenburg, I. Dipoppa, M. Rossi, F. Miller, K. Adesnik, H. Ji, N. Doiron, B. 2025-02-13 doi:10.1101/2025.02.11.637768 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Analysis of crosslinking sites suggests C. elegnas PIWI Argonaute exhibits flexible conformations for target recognition ]]> https://biorxiv.org/content/10.1101/2025.02.14.638322v1?rss=1 Wu, W.-S. Lee, D.-E. Chung, C.-J. Lu, S.-Y. Brown, J. S. Zhang, D. Lee, H.-C. 2025-02-15 doi:10.1101/2025.02.14.638322 Cold Spring Harbor Laboratory Press 2025-02-15 <![CDATA[ Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders ]]> https://biorxiv.org/content/10.1101/2025.02.17.638682v1?rss=1 Liang, L. Zhang, S. Wang, Z. Zhang, H. Li, C. Duhe, A. C. Sun, X. Zhong, X. Kozlova, A. Jamison, B. Wood, W. G. Pang, Z. P. Sanders, A. R. He, X. Duan, J. 2025-02-18 doi:10.1101/2025.02.17.638682 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ Mouse sensorimotor cortex reflects complex kinematic details during reaching and grasping ]]> https://biorxiv.org/content/10.1101/2025.02.19.639049v1?rss=1 Grier, H. Salimian, S. Kaufman, M. 2025-02-24 doi:10.1101/2025.02.19.639049 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences ]]> https://biorxiv.org/content/10.1101/2025.02.24.639989v1?rss=1 Santangelo, B. E. Caufield, J. H. Reese, J. Kliegr, T. Hunter, L. E. Lozupone, C. A. Hegde, H. Joachimiak, M. P. 2025-02-28 doi:10.1101/2025.02.24.639989 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Succinate dehydrogenase activity supports de novo purine synthesis ]]> https://biorxiv.org/content/10.1101/2025.02.26.640389v1?rss=1 Nengroo, M. A. Klein, A. T. Carr, H. S. Vidal-Cruchez, O. Sahu, U. McGrail, D. J. Sahni, N. Gao, P. Asara, J. M. Shah, H. Mendillo, M. L. Ben-Sahra, I. 2025-03-01 doi:10.1101/2025.02.26.640389 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Repulsive interactions instruct synaptic partner matching in an olfactory circuit ]]> https://biorxiv.org/content/10.1101/2025.03.01.640985v1?rss=1 Li, Z. Lyu, C. Xu, C. Hu, Y. Luginbuhl, D. J. Caspi-Lebovic, A. B. Priest, J. M. Özkan, E. Luo, L. 2025-03-02 doi:10.1101/2025.03.01.640985 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ A shared gene but distinct dynamics regulate mimicry polymorphisms in closely related species ]]> https://biorxiv.org/content/10.1101/2025.03.03.641230v1?rss=1 Sheikh, S. I. Doellman, M. M. VanKuren, N. W. Hall, P. Kronforst, M. R. 2025-03-04 doi:10.1101/2025.03.03.641230 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ On ARGs, pedigrees, and genetic relatedness matrices ]]> https://biorxiv.org/content/10.1101/2025.03.03.641310v1?rss=1 Lehmann, B. Lee, H. Anderson-Trocme, L. Kelleher, J. Gorjanc, G. Ralph, P. L. 2025-03-05 doi:10.1101/2025.03.03.641310 Cold Spring Harbor Laboratory Press 2025-03-05 <![CDATA[ FACED 2.0 enables large-scale voltage and calcium imaging in vivo ]]> https://biorxiv.org/content/10.1101/2025.03.06.641784v1?rss=1 Zhong, J. Natan, R. G. Zhang, Q. Wong, J. S. J. Miehl, C. Bose, K. Lu, X. St-Pierre, F. Guo, S. Doiron, B. Tsia, K. K. Ji, N. 2025-03-10 doi:10.1101/2025.03.06.641784 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Two-Stage CD8+ CAR T-Cell Differentiation in Patients with Large B-Cell Lymphoma ]]> https://biorxiv.org/content/10.1101/2025.03.05.641715v1?rss=1 Cao, G. Hu, Y. Pan, T. Tang, E. Asby, N. Althaus, T. Wan, J. Riedell, P. Bishop, M. Kline, J. Huang, J. 2025-03-11 doi:10.1101/2025.03.05.641715 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Light-induced reversible assembly and actuation in ultrafast Ca2+-driven chemomechanical protein networks ]]> https://biorxiv.org/content/10.1101/2025.03.03.641304v1?rss=1 Lei, X. Floyd, C. Ferrer, L. C. Chakrabortty, T. Chandrasekharan, N. Dinner, A. Coyle, S. M. Honts, J. Bhamla, S. 2025-03-12 doi:10.1101/2025.03.03.641304 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe-Virus Coevolutionary System ]]> https://biorxiv.org/content/10.1101/2025.03.09.642151v1?rss=1 Liaghat, A. Guillemet, M. Whitaker, R. Gandon, S. Pascual, M. 2025-03-13 doi:10.1101/2025.03.09.642151 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis ]]> https://biorxiv.org/content/10.1101/2025.03.10.642426v1?rss=1 Jonker, P. B. Sadullozoda, M. Cognet, G. Saab, J. J. A. Sokol, K. H. Wu, V. X. Kumari, D. Sheehan, C. Ozgurses, M. E. Agovino, D. Croley, G. Patel, S. A. Bock-Hughes, A. Macleod, K. F. Shah, H. Coloff, J. L. Lien, E. C. Muir, A. 2025-03-13 doi:10.1101/2025.03.10.642426 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Functional interaction of hybrid extracellular vesicle-liposome nanoparticles with target cells: absence of toxicity ]]> https://biorxiv.org/content/10.1101/2025.03.11.642711v1?rss=1 Riazanski, V. Purvina, L. Cavinato, L. Sui, Z. Sun, L. Nelson, D. J. 2025-03-13 doi:10.1101/2025.03.11.642711 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Cortical reinstatement of causally related events sparks narrative insights by updating neural representation patterns ]]> https://biorxiv.org/content/10.1101/2025.03.12.642853v1?rss=1 Song, H. Ke, J. Madhogarhia, R. Leong, Y. C. Rosenberg, M. D. 2025-03-13 doi:10.1101/2025.03.12.642853 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Preserving predictive information under biologically plausible compression ]]> https://biorxiv.org/content/10.1101/2025.03.12.642864v1?rss=1 Durian, S. C. L. Bojanek, K. Marre, O. Palmer, S. E. 2025-03-13 doi:10.1101/2025.03.12.642864 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Emotional arousal enhances narrative memories through functional integration of large-scale brain networks ]]> https://biorxiv.org/content/10.1101/2025.03.13.643125v1?rss=1 Park, J. S. Gollapudi, K. Ke, J. Nau, M. Pappas, I. Leong, Y. C. 2025-03-13 doi:10.1101/2025.03.13.643125 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Tissue Engineering Applications for Novel Integrated and Mobile Perfusion System ]]> https://biorxiv.org/content/10.1101/2025.03.12.642925v1?rss=1 Zhu, A. Jain, T. Reid, E. Siddiqi, U. Mir, A. Dunne, O. Hibino, N. 2025-03-14 doi:10.1101/2025.03.12.642925 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition ]]> https://biorxiv.org/content/10.1101/2025.03.14.643063v1?rss=1 A:T driver mutations in KRAS plus short subclonal diversification. LUAD in never smokers showed early occurrence of copy number alterations and EGFR mutations associated with SBS5 and SBS40a mutational signatures. Tumors harboring EGFR mutations exhibited long latency, particularly in females of European-ancestry (EU_N). In EU_N, EGFR mutations preceded the occurrence of other driver genes, including TP53 and RBM10. Tumors from Asian never smokers showed a short clonal evolution and presented with heterogeneous repetitive patterns for the inferred mutational order. Importantly, we found that the mutational signature ID2 is a marker of a previously unrecognized mechanism for LUAD evolution. Tumors with ID2 showed short latency and high L1 retrotransposon activity linked to L1 promoter demethylation. These tumors exhibited an aggressive phenotype, characterized by increased genomic instability, elevated hypoxia scores, low burden of neoantigens, propensity to develop metastasis, and poor overall survival. Re-activated L1 retrotransposition-induced mutagenesis can contribute to the origin of the mutational signature ID2, including through the regulation of the transcriptional factor ZNF695, a member of the KZFP family. The complex nature of LUAD evolution creates both challenges and opportunities for screening and treatment plans. ]]> Zhang, T. Zhao, W. Wirth, C. Diaz-Gay, M. Yin, J. Cecati, M. Marchegiani, F. Hoang, P. H. Leduc, C. Baine, M. K. Travis, W. D. Sholl, L. M. Joubert, P. Sang, J. McElderry, J. P. Klein, A. Khandekar, A. Hartman, C. Rosenbaum, J. Colon-Matos, F. J. Miraftab, M. Saha, M. Lee, O. W. Jones, K. M. Caporaso, N. E. Wong, M. P. Leung, K. C. Hsiung, C. A. Chen, C.-Y. Homer, R. Yang, S.-R. Pesatori, A. C. Consonni, D. Yang, L. Zhu, B. Edell, E. S. Santamaria, J. M. Schabath, M. B. Yendamuri, S. S. Manczuk, M. Lissowska, J. Swiatkowska, B. Mukeria, A. Shangina, O 2025-03-16 doi:10.1101/2025.03.14.643063 Cold Spring Harbor Laboratory Press 2025-03-16 <![CDATA[ DiCE: Differential Centrality-Ensemble Analysis Based on Gene Expression Profiles and Protein-Protein Interaction Network ]]> https://biorxiv.org/content/10.1101/2025.03.14.638654v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@1ce9b81org.highwire.dtl.DTLVardef@14352e1org.highwire.dtl.DTLVardef@f63caeorg.highwire.dtl.DTLVardef@a0086_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pashaei, E. Liu, S. Li, K. Zang, Y. Yang, L. Lautenschlaeger, T. Huang, J. Lu, X. Wan, J. 2025-03-17 doi:10.1101/2025.03.14.638654 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Interleaving asynchronous and synchronous activity in balanced cortical networks with short-term synaptic depression ]]> https://biorxiv.org/content/10.1101/2025.03.13.643074v1?rss=1 Dunworth, J. Xu, Y. Graupner, M. Ermentrout, B. Reyes, A. D. Doiron, B. 2025-03-18 doi:10.1101/2025.03.13.643074 Cold Spring Harbor Laboratory Press 2025-03-18 <![CDATA[ Nonenzymatic RNA copying with a potentially primordial genetic alphabet ]]> https://biorxiv.org/content/10.1101/2025.03.19.644114v1?rss=1 Fang, Z. Jia, X. Xing, Y. Szostak, J. W. 2025-03-19 doi:10.1101/2025.03.19.644114 Cold Spring Harbor Laboratory Press 2025-03-19 <![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[ A novel membrane contact site in vestibular hair cells ]]> https://biorxiv.org/content/10.1101/2025.03.21.644540v1?rss=1 Brouilly, N. Pujol, N. Richard, F. Cazevieille, C. Stone, J. S. Eatock, R. A. Pujol, R. 2025-03-24 doi:10.1101/2025.03.21.644540 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Excitability and travelling waves in renewable active matter ]]> https://biorxiv.org/content/10.1101/2025.03.25.645200v1?rss=1 M, A. Dhanuka, A. Banerjee, D. S. Rao, M. 2025-03-27 doi:10.1101/2025.03.25.645200 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design ]]> https://biorxiv.org/content/10.1101/2025.03.28.645802v1?rss=1 Yousef, M. Lee, K. K. Tang, J. Charisopoulos, V. Willett, R. Kuehn, S. 2025-03-28 doi:10.1101/2025.03.28.645802 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ The PXBAR-domain protein SNX9 selectively sequesters PI(3,4)P2 lipid and protects it from hydrolysis at the plasma membrane ]]> https://biorxiv.org/content/10.1101/2025.03.26.645564v1?rss=1 Beiter, J. Sung, C.-J. Lin, S.-S. DeVuono, N. Arumugam, S. Manzi, J. Bertin, A. Bassereau, P. Liu, Y.-W. Voth, G. A. Tsai, F.-C. 2025-03-29 doi:10.1101/2025.03.26.645564 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Epithelia mediate inflammation with myeloid cells in Crohn's disease patients under treatment ]]> https://biorxiv.org/content/10.1101/2025.03.26.645552v1?rss=1 50% of the patients experiencing relapses marked by inflammation. Our cellular atlas (380,000 cells) of the terminal ileum (TI) and ascending colon (AC) mucosa from 46 CD and non-IBD donors across various clinical condition, decipher disease heterogeneity for CD relapse and refractory inflammation. We identified an inflammatory cascade mediated by follicle-associated enterocytes in the inflamed TI involving pro-inflammatory macrophage M1 that remained unresolved by given biologic treatments. Spatial transcriptomic validation confirmed this epithelial-immune crosstalk. In contrast, interactions between colonocytes, FAP+ stroma and innate immune cells were were the unresolved cascade in AC driving inflammation. In addition, we propose a transcript-based scoring method to quantify inflammation activity that can be used to compare inflammation levels across patients, with the overall aim to help disease stratification. ]]> Zhou, R. Xie, B. Liu, J. Zhao, Y. Koval, J. Cham, C. Pekow, J. Weber, C. Chang, E. Basu, A. 2025-03-31 doi:10.1101/2025.03.26.645552 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ The BK channel-NS1619 agonist complex reveals molecular insights on allosteric activation gating ]]> https://biorxiv.org/content/10.1101/2025.03.27.645783v1?rss=1 Gonzalez-Sanabria, N. Contreras, G. F. Rojas, M. Duarte, Y. Gonzalez-Nilo, F. D. Perozo, E. Latorre, R. 2025-04-01 doi:10.1101/2025.03.27.645783 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Sirtuin 2 controls global protein synthesis by regulating Rheb-GTPase ]]> https://biorxiv.org/content/10.1101/2025.03.31.646364v1?rss=1 Shrama, A. Zi, Y. Pandit, A. S. Jha, K. Sinha, V. K. Ravi, V. Ghosh, S. Nagesh, D. Shivanaiah, B. Khan, D. Prabhashankar, A. B. Sumi, T. S. Raghu, S. Srivastava, A. Singh, M. Lin, H. Sundaresan, N. R. 2025-04-01 doi:10.1101/2025.03.31.646364 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ SIRT2 Mediates Integrated Stress Response by Deacetylating and Stabilizing 4EBP1 to Suppress Translation ]]> https://biorxiv.org/content/10.1101/2025.03.31.646365v1?rss=1 Zi, Y. Wang, M. Hou, D. Cerione, R. A. Lin, H. 2025-04-01 doi:10.1101/2025.03.31.646365 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Overnutrition directly impairs thyroid hormone biosynthesis and utilization, causing hypothyroidism, despite remarkable thyroidal adaptations ]]> https://biorxiv.org/content/10.1101/2025.03.31.645596v1?rss=1 Rampy, J. Torres-Manzo, A. P. Hoffsmith, K. Loberg, M. A. Sheng, Q. Salas-Lucia, F. Bianco, A. C. Arrojo e Drigo, R. Wang, H. Weiss, V. L. Carrasco, N. 2025-04-02 doi:10.1101/2025.03.31.645596 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Neuronal modulation of the superior colliculus associated with visual spatial attention represents perceptual sensitivity, independent of perceptual decision and motor biases ]]> https://biorxiv.org/content/10.1101/2025.04.01.646682v1?rss=1 Ghosh, S. Maunsell, J. H. 2025-04-03 doi:10.1101/2025.04.01.646682 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Epidermal Resident Memory T Cell Fitness Requires Antigen Encounter in the Skin ]]> https://biorxiv.org/content/10.1101/2025.03.31.646438v1?rss=1 Weiss, E. S. Hirai, T. Li, H. Liu, A. Baker, S. Magill, I. Gillis, J. Zhang, Y. R. Ramcke, T. Kurihara, K. The ImmGen Consortium OpenSource T cell Project, Masopust, D. Anandasabapathy, N. Singh, H. Zemmour, D. Mackay, L. K. Kaplan, D. H. 2025-04-05 doi:10.1101/2025.03.31.646438 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Teeth Outside the Jaw: Evolution and Development of the Toothed Head Clasper in Chimaeras ]]> https://biorxiv.org/content/10.1101/2025.04.04.647311v1?rss=1 Cohen, K. E. Fraser, G. J. Coates, M. I. 2025-04-05 doi:10.1101/2025.04.04.647311 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Invasion blurs the biphasic mosaic, amplifies the 'wicked problem' through impacts on avian distributions in montane habitats. ]]> https://biorxiv.org/content/10.1101/2025.04.03.646526v1?rss=1 Jobin, V. Harikrishnan, C. P. Lele, A. Joshi, V. Chanda, R. Lawrence, S. Aravind, P. S. Mubeen, M. Joseph, M. R. Subash, M. Nandini, R. Das, A. Jathanna, D. Robin, V. 2025-04-06 doi:10.1101/2025.04.03.646526 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Tumor-Initiating Cells Fine-tune the Plasticity of Neutrophils to Sculpt a Protective Niche ]]> https://biorxiv.org/content/10.1101/2025.04.04.647324v1?rss=1 Guo, W. Luan, J. Huang, X. Leon, D. Good, J. Nicholson, B. Izumchenko, E. Rosenberg, A. J. Agrawal, N. Bertacchi, B. Bolotin, D. Gunzer, M. Ballesteros, I. Hidalgo, A. Miao, Y. P. 2025-04-09 doi:10.1101/2025.04.04.647324 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ N-Terminal Deleted Isoforms of E3 Ligase RNF220 (Isoform 4) Are Ubiquitously Expressed and Required for Mouse Muscle Differentiation. ]]> https://biorxiv.org/content/10.1101/2025.04.07.647521v1?rss=1 Choi, S. Wolfgeher, D. J. Kim, J. Go, Y.-H. Cha, H.-J. Bae, G.-U. Kron, S. J. Kim, W.-Y. 2025-04-09 doi:10.1101/2025.04.07.647521 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing ]]> https://biorxiv.org/content/10.1101/2025.04.07.647663v1?rss=1 Huberman, L. B. Wu, V. W. Kowbel, D. J. Lee, J. Daum, C. Singan, V. R. Grigoriev, I. V. O'Malley, R. C. Glass, L. 2025-04-09 doi:10.1101/2025.04.07.647663 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ The precision of hippocampal representations predicts incremental value-learning across the adult lifespan ]]> https://biorxiv.org/content/10.1101/2025.04.08.647815v1?rss=1 vanGeen, C. Lempert, K. M. Cohen, M. MacNear, K. A. Reckers, F. M. Zaneski, L. Kable, J. W. Wolk, D. 2025-04-09 doi:10.1101/2025.04.08.647815 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Small non-coding RNAs encapsulating mammalian cells fuel innate immunity ]]> https://biorxiv.org/content/10.1101/2025.04.07.647669v1?rss=1 hu, l. Jiang, X. Xu, C. Yang, E. Xu, D. Peng, Y. Han, X. Si, J. Shao, Q. Liu, Z. Chen, Q. He, W. He, S. Xu, Y. He, C. Huang, X. 2025-04-10 doi:10.1101/2025.04.07.647669 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Robust detection of specific epistasis using rank statistics ]]> https://biorxiv.org/content/10.1101/2025.04.08.647864v1?rss=1 Carlson, M. O. Andrews, B. L. Simons, Y. B. 2025-04-10 doi:10.1101/2025.04.08.647864 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ THE FUNCTION AND EVOLUTION OF STEGOSAUR OSTEODERMS AND HYPOTHESIZED SEXUAL DIMORPHISM IN HESPEROSAURUS ]]> https://biorxiv.org/content/10.1101/2025.04.10.648273v1?rss=1 Saitta, E. T. Bonhomme, V. Lukens, M. Vidal, D. Longrich, N. R. Richmond, D. R. Stockdale, M. T. 2025-04-16 doi:10.1101/2025.04.10.648273 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Microglial Fructose Metabolism Is Essential for Glioblastoma Growth ]]> https://biorxiv.org/content/10.1101/2025.04.12.646414v1?rss=1 Billingham, L. K. Delay, S. L. Tripathi, S. Olson, I. E. Zilinger, K. Subbiah, J. Wang, Z. Sadagopan, N. S. Chia, T.-Y. Najem, H. Cognet, G. Katz, J. L. Vazquez-Cervantes, G. I. Wang, S. Wan, H. Murphy, A. R. Lipshutz, A. B. Duffy, J. T. Valyasnikova, I. V. Zhang, P. Heiland, D. H. Ahmed, A. U. Lee-Chang, C. Heimberger, A. B. Perry, J. S. Muir, A. Chandel, N. S. Miska, J. 2025-04-18 doi:10.1101/2025.04.12.646414 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Cerebellum instructs plasticity in the mouse primary somatosensory cortex ]]> https://biorxiv.org/content/10.1101/2025.04.18.649578v1?rss=1 Silbaugh, A. Koster, K. P. Hansel, C. 2025-04-21 doi:10.1101/2025.04.18.649578 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories ]]> https://biorxiv.org/content/10.1101/2025.04.21.649824v1?rss=1 Grimm, S. L. Jangid, R. Bartolomei, M. S. Dolinoy, D. C. Aylor, D. L. Mutlu, G. M. Biswal, S. Zhang, B. Wang, T. TaRGET II Consortium, Coarfa, C. Walker, C. L. 2025-04-22 doi:10.1101/2025.04.21.649824 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Azurify integrates cancer genomics with machine learning to classify the clinical significance of somatic variants ]]> https://biorxiv.org/content/10.1101/2025.04.18.649588v1?rss=1 Bigdeli, A. Chandrashekar, D. S. Chitturi, A. Rushton, C. Mackinnon, A. C. Segal, J. Harada, S. Sacan, A. Faryabi, R. B. 2025-04-23 doi:10.1101/2025.04.18.649588 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ The Effects of Antidepressants on the Hippocampus: A Meta-Analysis of Public Transcriptional Profiling Data ]]> https://biorxiv.org/content/10.1101/2025.04.21.648805v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@8b41b1org.highwire.dtl.DTLVardef@85d600org.highwire.dtl.DTLVardef@a4bc1eorg.highwire.dtl.DTLVardef@13a8723_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Geoghegan, E. M. Hagenauer, M. H. Hernandez, E. Espinoza, S. Flandreau, E. I. Nguyen, P. T. Bhuiyan, M. R. Mensch, S. Watson, S. J. Akil, H. 2025-04-23 doi:10.1101/2025.04.21.648805 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Mechanistic insights and clinical implications of cross-reactive anti-prophage antibodies and bacterial heteroresistance on phage therapeutic failure ]]> https://biorxiv.org/content/10.1101/2025.04.22.650118v1?rss=1 Gordillo Altamirano, F. L. Subedi, D. Beiers, M. Bucher, M. J. Dahlman, S. Patel, D. M. Parker, M. Korneev, D. Pragastis, K. Wisniewski, J. Rees, C. Ramshaw, H. Khan, S. Gardiner, B. Hammerschlag, Y. Keating, D. Kotsimbos, T. Hawkey, J. Barr, J. J. Peleg, A. Y. 2025-04-23 doi:10.1101/2025.04.22.650118 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ MotorBench: A Cryo-Electron Tomography Dataset of Bacterial Flagellar Motors for Testing Detection Algorithms ]]> https://biorxiv.org/content/10.1101/2025.04.23.650258v1?rss=1 Owens, C. B. Morse, B. S. Darley, A. J. Hart, T. J. Webb, R. Maggi, S. Jensen, G. J. Ward, M. M. Reade, W. C. Kaplan, M. Hart, G. L. W. 2025-04-23 doi:10.1101/2025.04.23.650258 Cold Spring Harbor Laboratory Press 2025-04-23 <![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[ Emergence of coordinated cell division during the evolution of multicellularity ]]> https://biorxiv.org/content/10.1101/2025.04.23.650085v1?rss=1 Cedeno Perez, L. F. Pineau, R. Day, T. C. Ratcliff, W. C. Conlin, P. L. 2025-04-24 doi:10.1101/2025.04.23.650085 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Short-term gonadal cultures are sufficient for germline transmission in a songbird ]]> https://biorxiv.org/content/10.1101/2025.04.25.650428v1?rss=1 Biegler, M. T. Harter, E. Sidhu, A. V. Szialta, C. Durham, G. Tchernichovski, L. Collier, P. Luo, J.-D. Wang, W. MacIsaac, R. Belay, K. Carroll, T. Keyte, A. L. Jarvis, E. D. 2025-04-29 doi:10.1101/2025.04.25.650428 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Immune Pressure is Key to Understanding Observed Patterns of Respiratory Virus Evolution in Prolonged Infections ]]> https://biorxiv.org/content/10.1101/2025.04.28.651059v1?rss=1 Coats, A. Wang, Y. R. Koelle, K. 2025-04-30 doi:10.1101/2025.04.28.651059 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Chromatix: a differentiable, GPU-accelerated wave-optics library ]]> https://biorxiv.org/content/10.1101/2025.04.29.651152v1?rss=1 Deb, D. Both, G.-J. Bezzam, E. Kohli, A. Yang, S. Chaware, A. Allier, C. Cai, C. Anderberg, G. Eybposh, M. H. Schneider, M. C. Heintzmann, R. Rivera-Sanchez, F. A. Simmerer, C. Meng, G. Tormes-Vaquerano, J. Han, S. Shanmugavel, S. C. Maruvada, T. Yang, X. Kim, Y. Diederich, B. Joo, C. Waller, L. Durr, N. J. Pegard, N. C. La Riviere, P. J. Horstmeyer, R. Chowdhury, S. Turaga, S. C. 2025-05-02 doi:10.1101/2025.04.29.651152 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Disease-associated loci share properties with response eQTLs under common environmental exposures ]]> https://biorxiv.org/content/10.1101/2025.04.30.651602v1?rss=1 Lin, W. Li, M. Allen, O. Burnett, J. Popp, J. M. Stephens, M. Battle, A. Gilad, Y. 2025-05-04 doi:10.1101/2025.04.30.651602 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ A ribozyme ligase that requires a 3' terminal phosphate on its RNA substrate ]]> https://biorxiv.org/content/10.1101/2025.05.06.652512v1?rss=1 Biswas, A. Weiss, Z. Szostak, J. W. DasGupta, S. 2025-05-08 doi:10.1101/2025.05.06.652512 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Intracellular Delivery of Bone Nanoparticles to Mitigate Irradiation-Induced Damage in Bone Marrow Mesenchymal Stem Cells ]]> https://biorxiv.org/content/10.1101/2025.05.05.652269v1?rss=1 Wang, B. Ma, X. Nguyen, C. Stellpflug, A. Li, S. Han, L. Frei, A. Himburg, H. Gu, L. Dong, P. Wang, S. Mak, M. Wu, R. 2025-05-09 doi:10.1101/2025.05.05.652269 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Formation of chromosomal rearrangements in Saccharomyces cerevisiae diploids through regionally-biased non-allelic homologous recombination ]]> https://biorxiv.org/content/10.1101/2025.05.08.650247v1?rss=1 Merriman, S. A. Chapman, M. J. Stewart, J. A. Schmelzer, C. D. Sharif, R. S. Hemmerlein, M. J. Puccia, C. M. de Mattos, G. M. Wienke, M. A. Cornelio, D. A. Dilsaver, M. Watson, R. A. Argueso, J. L. 2025-05-10 doi:10.1101/2025.05.08.650247 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ RNA Helicase A promotes small RNA biogenesis and sorting in germ cells ]]> https://biorxiv.org/content/10.1101/2025.05.11.653140v1?rss=1 Gaylord, O. Brown, J. S. Wu, W.-S. Lee, H.-C. 2025-05-11 doi:10.1101/2025.05.11.653140 Cold Spring Harbor Laboratory Press 2025-05-11 <![CDATA[ Population-Level Activity Dissociates Preparatory Overt from Covert Attention ]]> https://biorxiv.org/content/10.1101/2025.05.07.652629v1?rss=1 Koevoet, D. Voet, V. Jones, H. M. Awh, E. Strauch, C. Van der Stigchel, S. 2025-05-12 doi:10.1101/2025.05.07.652629 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Predicting Neural Activity from Connectome Embedding Spaces ]]> https://biorxiv.org/content/10.1101/2025.05.09.653224v1?rss=1 Zhang, Z. Zhang, H. Mihalas, S. 2025-05-14 doi:10.1101/2025.05.09.653224 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Advanced eTAM-seq enables high-fidelity, low-input N6-methyladenosine profiling in human cells and embryonic mouse tissues ]]> https://biorxiv.org/content/10.1101/2025.05.11.653357v1?rss=1 51% of A sites in all expressed genes with moderate sequencing depth (60 million uniquely mapped reads) and delivers robust performance with as little as 10 ng of total RNA ([~]500 cells). With eTAM-seq-v2, we delineate the m6A landscape across six human cell lines and seven embryonic mouse tissues. While uncovering broadly conserved m6A patterns, we reveal that most neighboring m6A sites are independently deposited at the single-molecule level. Moving forward, we envision that eTAM-seq-v2 will enable researchers to survey m6A in diverse biological contexts and uncover new insights into its regulatory roles. ]]> He, E. M. Wu, Y. Ye, C. Zeng, T.-B. He, C. Tang, W. 2025-05-15 doi:10.1101/2025.05.11.653357 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Rainbow Nucleus Charts Dynamic Interactome of Membrane-less Organelles ]]> https://biorxiv.org/content/10.1101/2025.05.14.654140v1?rss=1 Ye, S. Benhamou Goldfajn, N. So, C. L. Inoue, T. Cai, D. 2025-05-15 doi:10.1101/2025.05.14.654140 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Low-Strength Type I Interferon Signaling Promotes CAR T-Cell Treatment Efficacy ]]> https://biorxiv.org/content/10.1101/2025.05.13.653878v1?rss=1 Tang, E. Hu, Y. Cao, G. Asby, N. W. Nguyen, D.-T. Aboelella, N. S. Ruiz, H. Zhao, Y. Xie, L. Chen, X. Bishop, M. R. Riedell, P. A. LaBelle, J. L. Kline, J. P. Huang, J. 2025-05-17 doi:10.1101/2025.05.13.653878 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Mutation-selection-drift balance models of complex diseases ]]> https://biorxiv.org/content/10.1101/2025.05.18.654722v1?rss=1 Berg, J. J. Li, X. Riall, K. Hayward, L. Sella, G. 2025-05-18 doi:10.1101/2025.05.18.654722 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Interlocked transcription factor feedback loops maintain and restore touch sensation ]]> https://biorxiv.org/content/10.1101/2025.05.15.654349v1?rss=1 Marques, F. Chen, Y. Destain, H. Marinelli, M. Kratsios, P. 2025-05-20 doi:10.1101/2025.05.15.654349 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Accounting for uncertainty in residual variances improves calibration of the Sum of Single Effects model for small sample sizes ]]> https://biorxiv.org/content/10.1101/2025.05.16.654543v1?rss=1 Denault, W. R. P. Carbonetto, P. Li, R. Consortium, T. A. s. D. F. G. Wang, G. Stephens, M. 2025-05-21 doi:10.1101/2025.05.16.654543 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Prediction of αIIbβ3 integrin structures along its minimum free energy activation pathway ]]> https://biorxiv.org/content/10.1101/2025.05.16.654557v1?rss=1 Dasetty, S. Coffman, R. E. Bidone, T. C. Ferguson, A. L. 2025-05-21 doi:10.1101/2025.05.16.654557 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Methamphetamine modulates functional connectivity signatures of sustained attention and arousal ]]> https://biorxiv.org/content/10.1101/2025.05.20.655181v1?rss=1 Lyu, Y. Corriveau, A. Molla, H. de Wit, H. Rosenberg, M. D. 2025-05-21 doi:10.1101/2025.05.20.655181 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Mechanisms of Output Gating for visual working memory ]]> https://biorxiv.org/content/10.1101/2025.05.22.655454v1?rss=1 Zhao, C. Adekoya, T. Horwitz, S. Awh, E. Vogel, E. K. 2025-05-22 doi:10.1101/2025.05.22.655454 Cold Spring Harbor Laboratory Press 2025-05-22 <![CDATA[ Life-history trade-offs explain local adaptation in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2025.05.18.654693v1?rss=1 Brachi, B. Filiault, D. Pisupati, R. Dahan, T. Igolkina, A. Anastasio, A. Box, M. S. Duncan, S. Karasov, T. Kerdaffrec, E. Merwin, L. Morton, T. Nizhynska, V. Novikova, P. Y. Rabanal, F. A. Tsuchimatsu, T. Sall, T. Dean, C. Holm, S. Bergelson, J. Nordborg, M. 2025-05-23 doi:10.1101/2025.05.18.654693 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Molecular Basis of Sodium Channel Inactivation ]]> https://biorxiv.org/content/10.1101/2025.05.22.655422v1?rss=1 Liu, Y. Galpin, J. Ahern, C. A. Bezanilla, F. 2025-05-23 doi:10.1101/2025.05.22.655422 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ When good guides go bad: empirical evaluation of all unique Cas9 targets in E. coli reveal widespread functionality and rules for gRNA biological design ]]> https://biorxiv.org/content/10.1101/2025.05.23.651106v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@1038ddcorg.highwire.dtl.DTLVardef@566e37org.highwire.dtl.DTLVardef@5df6b2org.highwire.dtl.DTLVardef@ef453c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phillips, E. K. Harrison, R. Charles, S. Klingeman, D. M. Wiser, T. Eckert, C. A. Alexander, W. G. 2025-05-23 doi:10.1101/2025.05.23.651106 Cold Spring Harbor Laboratory Press 2025-05-23 <![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[ On the Curvature and Relaxation of Microtubule Plus-endTips ]]> https://biorxiv.org/content/10.1101/2025.05.23.655844v1?rss=1 Skora, T. Wu, J. Beckett, D. Xue, W. Voth, G. A. Bidone, T. C. 2025-05-26 doi:10.1101/2025.05.23.655844 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Mechanosensitive Endothelial METTL7A Regulates Internal m7G mRNA Methylation and Protects Against Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.05.22.655328v1?rss=1 Shentu, T.-P. Wu, T. Zhou, Z. Yeh, C.-F. Zhu, J. Li, J. Miao, B. A. Lee, T.-H. Zhang, L. Huang, R.-T. Harrison, D. Hodonsky, C. J. Auguste, G. Husain, A. Tirrell, M. V. Miller, C. L. Dickinson, B. Yang, K.-C. Fang, Y. 2025-05-27 doi:10.1101/2025.05.22.655328 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Ketone Bodies-mediated Cysteine Modifications Discovered by Chemical Proteomics ]]> https://biorxiv.org/content/10.1101/2025.05.25.655943v1?rss=1 Zhou, Y.-F. Zhang, L. Niu, Z. L. WANG, X. Hunt, R. Zhao, Y. Sharifi, N. Wang, Z. A. 2025-05-28 doi:10.1101/2025.05.25.655943 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ RNA localization to nuclear speckles follows splicing logic ]]> https://biorxiv.org/content/10.1101/2025.05.28.656493v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@1efbb02org.highwire.dtl.DTLVardef@1deb7aaorg.highwire.dtl.DTLVardef@ec1ec2org.highwire.dtl.DTLVardef@1d78b72_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Wen, L. Arias, M. A. Fan, X. Paul, S. Liao, S. E. Sobczyk, M. Regev, O. Fei, J. 2025-05-28 doi:10.1101/2025.05.28.656493 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States ]]> https://biorxiv.org/content/10.1101/2025.05.28.656658v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@3ae1e6org.highwire.dtl.DTLVardef@1c4c535org.highwire.dtl.DTLVardef@16f3627org.highwire.dtl.DTLVardef@4c3f47_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ghaby, K. Roux, B. 2025-05-29 doi:10.1101/2025.05.28.656658 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Fine-Resolution Asymmetric Migration Estimation ]]> https://biorxiv.org/content/10.1101/2025.05.29.656894v1?rss=1 Shen, H. Novembre, J. 2025-05-30 doi:10.1101/2025.05.29.656894 Cold Spring Harbor Laboratory Press 2025-05-30 <![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[ A dendritic cell population responsible for transglutaminase 2-mediated gluten antigen presentation in celiac disease ]]> https://biorxiv.org/content/10.1101/2025.06.02.657527v1?rss=1 Yang, F.-C. Besser, H. A. Chun, H. R. Albertelli, M. A. Fernandez-Becker, N. Q. Jabri, B. Khosla, C. 2025-06-05 doi:10.1101/2025.06.02.657527 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Tissue-like compression stiffening in biopolymer networks induced by aggregated and irregularly shaped inclusions ]]> https://biorxiv.org/content/10.1101/2025.06.02.657447v1?rss=1 Shi, X. Shivers, J. L. MacKintosh, F. C. Janmey, P. A. 2025-06-06 doi:10.1101/2025.06.02.657447 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ CrossFilt: A Cross-species Filtering Tool that Eliminates Alignment Bias in Comparative Genomics Studies ]]> https://biorxiv.org/content/10.1101/2025.06.05.654938v1?rss=1 Barr, K. A. Gilad, Y. 2025-06-06 doi:10.1101/2025.06.05.654938 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[ Structural insights into wiring specificity in the neuromuscular system through the Beat-Side complex ]]> https://biorxiv.org/content/10.1101/2025.06.05.656487v1?rss=1 Priest, J. M. Zhang, R. Olechwier, A. M. Caspi-Lebovic, A. B. Ashley, J. Aher, V. Carrillo, R. A. Özkan, E. 2025-06-09 doi:10.1101/2025.06.05.656487 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Improved chromatin QTL mapping with CACTI ]]> https://biorxiv.org/content/10.1101/2025.06.06.657866v1?rss=1 Wang, L. Liu, X. 2025-06-10 doi:10.1101/2025.06.06.657866 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Shouldering the challenge of deciphering avian palate evolution ]]> https://biorxiv.org/content/10.1101/2025.06.10.658509v1?rss=1 Benito, J. Kuo, P.-C. Torres, C. R. Navalon, G. Plateau, O. Clark, A. D. Steell, E. M. Field, D. J. 2025-06-13 doi:10.1101/2025.06.10.658509 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain ]]> https://biorxiv.org/content/10.1101/2025.06.10.658982v1?rss=1 180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. ]]> Petkova, M. D. Januszewski, M. Blakely, T. Herrera, K. J. Schuhknecht, G. F. P. Tiller, R. Choi, J. Schalek, R. L. Boulanger-Weil, J. Peleg, A. Wu, Y. Wang, S. Troidl, J. Kumar Vohra, S. Wei, D. Lin, Z. Bahl, A. Tapia, J. C. Iyer, N. Miller, Z. T. Hebert, K. B. Pavarino, E. C. Taylor, M. Deng, Z. Stingl, M. Hockling, D. Hebling, A. Wang, R. C. Zhang, L. L. Dvorak, S. Faik, Z. King, K. I. Goel, P. Wagner-Carena, J. Aley, D. Chalyshkan, S. Contreas, D. Li, X. Muthukumar, A. V. Vernaglia, M. S. Tapia Carrasco, T. Melnychuck, S. Yan, T. Dalal, A. DiMarti 2025-06-15 doi:10.1101/2025.06.10.658982 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ DCPS modulates TDP-43 mediated neurodegeneration through P-body regulation ]]> https://biorxiv.org/content/10.1101/2025.06.13.659508v1?rss=1 Ye, Y. Zhang, Z. Yu, X. Zhu, C. Wright, N. Asbury, J. Huang, Y. Wang, W. Gomez-Isaza, L. Troncoso, J. He, C. Sun, S. 2025-06-15 doi:10.1101/2025.06.13.659508 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Susceptible host dynamics explain pathogen resilience to perturbations ]]> https://biorxiv.org/content/10.1101/2025.06.13.659551v1?rss=1 Park, S. W. Nielsen, B. F. Howerton, E. Grenfell, B. Cobey, S. 2025-06-16 doi:10.1101/2025.06.13.659551 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Magnimaribacterales marine bacteria genetically partition across the nearshore to open-ocean in the tropical Pacific Ocean ]]> https://biorxiv.org/content/10.1101/2025.06.17.660167v1?rss=1 Ramfelt, O. Tucker, S. J. Freel, K. C. Eren, A. M. Rappe, M. S. 2025-06-17 doi:10.1101/2025.06.17.660167 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Immune pathways and perinatal environmental exposures contribute to epigenetic gestational age prediction and acceleration ]]> https://biorxiv.org/content/10.1101/2025.06.13.659090v1?rss=1 Eapen, A. A. Loveless, I. M. Pan, M. Liang, X. Straughen, J. Cassidy-Bushrow, A. Sitarik, A. R. Simmerman, N. Thompson, E. E. Kottyan, L. Ober, C. Johnson, C. C. Zoratti, E. Levin, A. M. 2025-06-18 doi:10.1101/2025.06.13.659090 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Host- and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression ]]> https://biorxiv.org/content/10.1101/2025.06.18.660398v1?rss=1 Arif, S. J. Hoffman, K. M. Flynn, J. M. Wiggen, T. D. Lucas, S. K. Villarreal, A. R. Gilbertsen, A. J. Dunitz, J. M. Hunter, R. C. 2025-06-19 doi:10.1101/2025.06.18.660398 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Conservation and lability within the structure of mandibular integration in "old endemic" Australian rodents ]]> https://biorxiv.org/content/10.1101/2025.06.17.660249v1?rss=1 Ng, R. Y. 2025-06-22 doi:10.1101/2025.06.17.660249 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Humans Optimally Integrate Cutaneous and Proprioceptive Cues In Haptic Size Perception ]]> https://biorxiv.org/content/10.1101/2025.06.24.661403v1?rss=1 Allen, K. S. Goldreich, D. 2025-06-25 doi:10.1101/2025.06.24.661403 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Evolutionary trade-offs between functional and immune selection shape multigene families in pathogens ]]> https://biorxiv.org/content/10.1101/2025.06.24.661038v1?rss=1 Zhan, Q. Pascual, M. He, Q. 2025-06-27 doi:10.1101/2025.06.24.661038 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ 5-azacytosine induces cytotoxicity via 5-methylcytosine depletion on chromatin-associated RNA in leukemia ]]> https://biorxiv.org/content/10.1101/2025.06.24.661348v1?rss=1 Gao, B. Li, Y. Zhao, L. Zou, Z. Ma, X. Hong, J. Xiang, J. Dou, X. Yang, F.-C. Xu, M. He, C. 2025-06-27 doi:10.1101/2025.06.24.661348 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Fluctuation structure predicts genome-wide perturbation outcomes ]]> https://biorxiv.org/content/10.1101/2025.06.27.661814v1?rss=1 Kuznets-Speck, B. Schwartz, L. Sun, H. Melzer, M. E. Kumari, N. Haley, B. Prashnani, E. Vaikuntanathan, S. Goyal, Y. 2025-07-01 doi:10.1101/2025.06.27.661814 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ Groove architecture controls lipid scrambling in simulations of protein and model systems ]]> https://biorxiv.org/content/10.1101/2025.06.27.662058v1?rss=1 Smith, H. E. Harrison-Rawn, T. Zheng, W. Ballesteros, A. Sotomayor, M. 2025-07-01 doi:10.1101/2025.06.27.662058 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ Multi-season analysis reveals hundreds of drought-responsive genes in sorghum ]]> https://biorxiv.org/content/10.1101/2025.06.27.662006v1?rss=1 Cole, B. Zhang, W. Shi, J. Wang, H. Baker, C. Varoquaux, N. Hollingsworth, J. Hutmacher, R. Dahlberg, J. Pierroz, G. Barry, K. W. Singan, V. Yoshinaga, Y. Daum, C. Zane, M. Blow, M. OMalley, R. Shu, S. Jenkins, J. W. Lovell, J. T. Schmutz, J. Taylor, J. W. Coleman-Derr, D. Visel, A. Lemaux, P. G. Purdom, E. Vogel, J. P. 2025-07-02 doi:10.1101/2025.06.27.662006 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ A global genetic interaction map of a human cell reveals conserved principles of genetic networks ]]> https://biorxiv.org/content/10.1101/2025.06.30.662193v1?rss=1 Billmann, M. Costanzo, M. Zhang, X. Hassan, A. Z. Rahman, M. Brown, K. R. Chan, K. S. Tong, A. H. Pons, C. Ward, H. N. Ross, C. van Leeuwen, J. Aregger, M. Lawson, K. A. Mair, B. Roth, A. F. Sen, N. E. Forster, D. T. Tan, G. Merro, P. Masud, S. N. Lee, Y. Aguilera-Uribe, M. Usaj, M. Almeida, S. M. Aulakh, K. Bhojoo, U. Birkadze, S. Budijono, N. Cai, X. Caumanns, J. J. Chandrashekhar, M. Chang, D. Clinie, R. Dasgupta, K. Drazic, A. Rojas Echenique, J. I. Gacesa, R. Granda Farias, A. Habsid, A. Horecka, I. Kantautas, K. Ji, F. Kim, D.-K. Lee, S. Y. Li 2025-07-02 doi:10.1101/2025.06.30.662193 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Proteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes ]]> https://biorxiv.org/content/10.1101/2025.07.01.662686v1?rss=1 Abdelghany, S. Helmkampf, M. Schechter, M. S. Veseli, I. A. Leray, M. Eren, A. M. Puebla, O. 2025-07-02 doi:10.1101/2025.07.01.662686 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ TMC1 and TMC2 are cholesterol-dependent scramblases that regulate membrane homeostasis in auditory hair cells ]]> https://biorxiv.org/content/10.1101/2025.07.03.663083v1?rss=1 Lee, H. Park, Y. C. Wen, H. Smith, H. E. Balaraman, J. Cui, R. Sotomayor, M. Ballesteros, A. 2025-07-04 doi:10.1101/2025.07.03.663083 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production ]]> https://biorxiv.org/content/10.1101/2025.07.02.662322v1?rss=1 Lin, J. Hu, Y. Pial, T. H. Goodier, K. D. Yu, D. Guise, M. Brailsford, P. Choi-Ali, M. Li, S. Zhu, Y. Ma, J. Cheng, L. Lu, X. Korinetz, N. Wang, J. Curk, T. Mao, H.-Q. 2025-07-05 doi:10.1101/2025.07.02.662322 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies ]]> https://biorxiv.org/content/10.1101/2025.07.03.662938v1?rss=1 Paez, E. Kergoat, G. J. Chazot, N. Benmesbah, M. Briscoe, A. D. Finkbeiner, S. D. Freitas, A. V. L. Guralnick, R. P. Hill, R. I. Kronforst, M. R. Moraes Magaldi, L. Mullen, S. P. Nakamura, I. Owens, H. L. Wahlberg, N. Woodbury, M. Elias, M. Willmott, K. R. 2025-07-07 doi:10.1101/2025.07.03.662938 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Historical Contingency Shapes Toxin Resistance in a Specialist Avian Predator ]]> https://biorxiv.org/content/10.1101/2025.07.04.662692v1?rss=1 Mohammadi, S. Pradhan, S. Hoffmann, F. G. Herrera-Alvarez, S. Deng, Y. Eacock, A. Dobler, S. Storz, J. F. Rowland, H. M. 2025-07-07 doi:10.1101/2025.07.04.662692 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Comparative ScRNA-Seq Profiling of Antigen-Specific CD4+ T cells in Semi-Allogeneic Transplantation and Pregnancy Reveals Intersecting Signatures of Rejection and Tolerance ]]> https://biorxiv.org/content/10.1101/2025.07.06.663404v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@1b30a86org.highwire.dtl.DTLVardef@17820cforg.highwire.dtl.DTLVardef@1b1fbeaorg.highwire.dtl.DTLVardef@11ff17_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Andrade, M. S. Hynes, G. Suran, Z. Yin, D. Alegre, M.-L. Sage, P. T. Chong, A. S. 2025-07-10 doi:10.1101/2025.07.06.663404 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development ]]> https://biorxiv.org/content/10.1101/2025.07.07.663558v1?rss=1 Iyyappan, R. Niu, Y. Ming, H. Pajdzik, K. Rakestraw, N. R. Jain, P. K. He, C. Zong, C. Jiang, Z. 2025-07-10 doi:10.1101/2025.07.07.663558 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Contributions from Long-Term Memory Explain Superior Visual Working Memory Performance with Meaningful Objects ]]> https://biorxiv.org/content/10.1101/2025.07.07.663569v1?rss=1 PARK, H.-B. Awh, E. 2025-07-10 doi:10.1101/2025.07.07.663569 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking ]]> https://biorxiv.org/content/10.1101/2025.07.09.659702v1?rss=1 Bosch, J. A. Beltran, P. M. J. Cavers, C. LaGraff, J. T. Melanson, R. Singh, A. Chen, W. Hu, Y. Tattikota, S. G. Liu, Y. Hashmi, Y. Asara, J. M. Branon, T. Ting, A. Y. Carr, S. A. Perrimon, N. 2025-07-11 doi:10.1101/2025.07.09.659702 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ From Concrete to Canopy: Illuminating Moth Biodiversity in New York City's Urban Jungle ]]> https://biorxiv.org/content/10.1101/2025.07.11.663976v1?rss=1 Linsk, S. Thonis, A. Winchell, K. 2025-07-15 doi:10.1101/2025.07.11.663976 Cold Spring Harbor Laboratory Press 2025-07-15 <![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[ Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes ]]> https://biorxiv.org/content/10.1101/2025.07.17.663733v1?rss=1 Dang, H. Edwards, C. E. Kato, T. Reidel, B. Meganck, R. M. Esther, C. R. Ehre, C. Fulcher, M. L. Bailey, A. B. Cooley, M. R. Mikami, Y. Asakura, T. Hawkins, P. E. Saito, M. Meyers, J. L. Konopka, K. Gerayeli, F. V. Park, H. Y. Sin, D. D. Livraghi-Butrico, A. Okuda, K. Pickles, R. J. Klein, S. L. Randell, S. H. O'Neal, W. K. Baric, R. S. Boucher, R. C. 2025-07-17 doi:10.1101/2025.07.17.663733 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Modeling habitat suitability for insect pollinators in New York City: Two decades of change ]]> https://biorxiv.org/content/10.1101/2025.07.13.664483v1?rss=1 Linsk, S. Winchell, K. M. Thonis, A. 2025-07-18 doi:10.1101/2025.07.13.664483 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ CDK8 Inhibition Releases the Muscle Differentiation Block in Fusion-driven Alveolar Rhabdomyosarcoma ]]> https://biorxiv.org/content/10.1101/2025.07.14.663986v1?rss=1 Zhang, S. Engel, K. Fahs, A. Malone, C. Ross, K. Just, M. Guedes, B. Granum, D. Oristian, K. M. Kovach, A. Alexe, G. Digiovanni, G. Barbar, L. Bentley, R. Cerda-Smith, C. Le Roux, O. Mendes, E. Zimmerman, S. P. Rees, M. Roth, J. Shern, J. F. Wood, K. C. Counter, C. M. Linardic, C. M. Stegmaier, K. 2025-07-18 doi:10.1101/2025.07.14.663986 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ The geometry of G x E: how scaling and endogenous treatment effects shape interaction direction ]]> https://biorxiv.org/content/10.1101/2025.07.15.664999v1?rss=1 Sadowski, M. Dahl, A. W. Zaitlen, N. Border, R. 2025-07-18 doi:10.1101/2025.07.15.664999 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ SOX2 utilizes FOXA1 as a heteromeric transcriptional partner to drive proliferation in therapy-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.07.18.664790v1?rss=1 Phoenix, J. T. Budreika, A. Schmeck, D. A. Kostlan, R. J. Ferrari, M. G. Young, K. S. Rogers, C. S. Deegan, C. D. Bergom, H. E. Boytim, E. Brown, R. M. Bienko, M. W. Walewicz, J. A. Bhagi, S. K. Ellis, L. Antonarakis, E. S. Drake, J. M. Bawa, P. S. Vellky, J. E. Williams, A. Reizine, N. M. Rennhack, J. P. Fanning, S. W. Hwang, J. H. Szmulewitz, R. Z. Vander Griend, D. J. Kregel, S. 2025-07-19 doi:10.1101/2025.07.18.664790 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ Gut microbes mediate the synergistic effects of dietary cholesterol and saturated fat in driving fibrosing MASH ]]> https://biorxiv.org/content/10.1101/2025.07.16.665145v1?rss=1 Hermanson, J. B. Tolba, S. Gazi, M. A. Chrisler, E. Kaur, M. Sidebottom, A. M. Liu, Y. Martinez-Boggio, G. Lucas, L. Amador-Noguez, D. Rey, F. E. Leone, V. A. 2025-07-21 doi:10.1101/2025.07.16.665145 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Endothelial Nucleoporin93 (Nup93) Maintains Vascular Function via Sun1-Dependent Regulation of RhoA-eNOS Signaling ]]> https://biorxiv.org/content/10.1101/2025.07.18.664980v1?rss=1 Nguyen, T. D. Khan, Y. Z. Hossen, F. Makim, R. Banks, J. M. Michalkiewicz, J. Winek, M. A. Moraes, L. Lee, J. C. Phillips, S. A. Lee, M. Y. 2025-07-21 doi:10.1101/2025.07.18.664980 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Changes in habitat connectivity for range-restricted birds reflect patterns of woodland invasion ]]> https://biorxiv.org/content/10.1101/2025.07.18.665495v1?rss=1 Jain, A. Arvind, C. V, J. Lele, A. V.V., R. 2025-07-23 doi:10.1101/2025.07.18.665495 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Assembly-based computations through contextual dendritic gating of plasticity ]]> https://biorxiv.org/content/10.1101/2025.07.22.666089v1?rss=1 Onasch, S. Miehl, C. Miekus, M. M. Gjorgjieva, J. 2025-07-24 doi:10.1101/2025.07.22.666089 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Neuronal normalization in monkey MT is an intensity-weighted average ]]> https://biorxiv.org/content/10.1101/2025.07.21.665985v1?rss=1 Cherian, C. Maunsell, J. H. 2025-07-25 doi:10.1101/2025.07.21.665985 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ The Role of Primate-Specific Genes and Network Dynamics in Cancer Evolution ]]> https://biorxiv.org/content/10.1101/2025.07.23.666306v1?rss=1 Dong, C. Su, Y.-W. Liao, Z. Xu, Q. Guo, H.-X. Chen, J. Wei, W. Xia, S. Cheng, Z. Zhang, C. Guo, F.-B. 2025-07-27 doi:10.1101/2025.07.23.666306 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Regulatory Plasticity and Metabolic Trade-offs Drive Adaptive Evolution of Alternative Flagellar Configurations in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.07.29.667523v1?rss=1 Migueles-Lozano, A. Asp, M. Rocha, S. T. Li, J. Fanouraki, G. Sun, A. D. Zhang, L. Waldbauer, J. R. Hong, J. Shrivastava, A. Yan, J. Mukherjee, S. 2025-07-29 doi:10.1101/2025.07.29.667523 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Actin network heterogeneity tunes activator-inhibitor dynamics at the cell cortex ]]> https://biorxiv.org/content/10.1101/2025.07.28.667299v1?rss=1 Maxian, O. Dinner, A. Munro, E. 2025-07-30 doi:10.1101/2025.07.28.667299 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Dual Mechanisms for Heterogeneous Responses of Inspiratory Neurons to Noradrenergic Modulation ]]> https://biorxiv.org/content/10.1101/2025.07.25.666713v1?rss=1 Venkatakrishnan, S. Tryba, A. K. Garcia, A. Wang, Y. 2025-07-31 doi:10.1101/2025.07.25.666713 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Neural components underlying successful free recall are specific to episodic memory ]]> https://biorxiv.org/content/10.1101/2025.07.25.666835v1?rss=1 DeHaan, R. D. Ezzyat, Y. Randazzo, M. J. Rao, A. M. Papanastassiou, A. M. Geller, A. S. Lega, B. C. Aronson, J. P. Gross, R. E. Jobst, B. C. Zaghloul, K. A. Worrell, G. A. Sheth, S. A. Sperling, M. R. Kahana, M. J. 2025-07-31 doi:10.1101/2025.07.25.666835 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Overcoming distortion in multidimensional predictive representation ]]> https://biorxiv.org/content/10.1101/2025.07.29.667463v1?rss=1 Prentis, E. Bakkour, A. 2025-07-31 doi:10.1101/2025.07.29.667463 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Distributed control circuits across a brain-and-cord connectome ]]> https://biorxiv.org/content/10.1101/2025.07.31.667571v1?rss=1 Bates, A. S. Phelps, J. S. Kim, M. Yang, H. H. Matsliah, A. Ajabi, Z. Perlman, E. Delgado, K. M. Osman, M. A. M. Salmon, C. K. Gager, J. Silverman, B. Renauld, S. Collie, M. F. Fan, J. Pacheco, D. A. Zhao, Y. Patel, J. Zhang, W. Serratosa Capdevilla, L. Roberts, R. J. Munnelly, E. J. Griggs, N. Langley, H. Moya-Llamas, B. Maloney, R. T. Yu, S.-c. Sterling, A. R. Sorek, M. Kruk, K. Serafetinidis, N. Dhawan, S. Stuerner, T. Klemm, F. Brooks, P. Lesser, E. Jones, J. M. Pierce-Lundgren, S. E. Lee, S.-Y. Luo, Y. Cook, A. P. McKim, T. H. Kophs, E. C. Falt, 2025-08-01 doi:10.1101/2025.07.31.667571 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource ]]> https://biorxiv.org/content/10.1101/2025.07.28.667191v1?rss=1 Zhang, B. A. Miao, B. Fu, S. Coarfa, C. Kumar, R. Kuntala, P. K. Park, B. Colacino, J. A. Svobada, L. K. Shao, W. Xing, X. Li, D. Liu, S. Hamanaka, R. B. Lalancette, C. Sartor, M. A. Krapp, C. Crawford, G. E. Patisaul, H. B. Wiltshire, T. Aylor, D. L. Biswal, S. Mutlu, G. M. Rajagopalan, S. Tang, W.-Y. Dolinoy, D. C. Wang, T. Bartolomei, M. S. Walker, C. L. Grimm, S. L. Ruiz-Echartea, E. Katz, T. Jangid, R. 2025-08-02 doi:10.1101/2025.07.28.667191 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Angulin-1/LSR inhibition transiently disrupts the blood-tumor barrier to enhance doxil permeability and impair malignant glioma progression ]]> https://biorxiv.org/content/10.1101/2025.07.31.667901v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@b1b46corg.highwire.dtl.DTLVardef@bc552dorg.highwire.dtl.DTLVardef@7c1a74org.highwire.dtl.DTLVardef@1ace101_HPS_FORMAT_FIGEXP M_FIG C_FIG Angubindin-1 targets both bicellular tight junctions and the tricellular tight junction protein, Angulin-1/LSR, in brain endothelial and glioma cells leading to transient disruption of the blood-tumor barrier (BTB) and inhibition of P-glycoprotein towards enhanced Doxil penetration and reduced tumor burden. ]]> Ferguson, D. Kwak, M. Lim, S. Cesair, M. Mills, J. Dalmage, M. Jones, J. Tarasov, S. Dyba, M. Robey, R. W. Yang, Y. Simpson, S. Karim, B. Butcher, D. Gartrell, R. Gottesman, M. Jackson, S. 2025-08-02 doi:10.1101/2025.07.31.667901 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Brr2p-mediated unwinding of U4/U6 is promoted by a mutually exclusive intra-molecular stem loop in U4 and involves destabilization of the 5' stem-loop of U4 ]]> https://biorxiv.org/content/10.1101/2025.08.01.667943v1?rss=1 Nielsen, K. H. Das, A. Staley, J. P. 2025-08-02 doi:10.1101/2025.08.01.667943 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Targeting intracranial electrical stimulation to network regions defined within individuals causes network-level effects ]]> https://biorxiv.org/content/10.1101/2025.07.31.667730v1?rss=1 Cyr, C. Holubecki, A. M. Shi, L. Lakshman, M. Salvo, J. J. Anderson, N. L. Kragel, J. E. Lurie, S. M. Voss, J. Kokkinos, V. Rosenow, J. Schuele, S. U. Johnson, E. L. Zelano, C. Braga, R. M. 2025-08-03 doi:10.1101/2025.07.31.667730 Cold Spring Harbor Laboratory Press 2025-08-03 <![CDATA[ Evidence for the major role of PH4EFB in the prolyl 4-hydroxylation of Drosophila collagen IV ]]> https://biorxiv.org/content/10.1101/2025.08.05.668786v1?rss=1 Ishikawa, Y. Toups, M. A. Elkrewi, M. Zajac, A. L. Horne-Badovinac, S. Matsubayashi, Y. 2025-08-06 doi:10.1101/2025.08.05.668786 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Cytoplasmic Abundant Heat-Soluble Proteins from Tardigrades Protect Synthetic Cells Under Stress ]]> https://biorxiv.org/content/10.1101/2025.08.07.669088v1?rss=1 Xi, Y. Mao, J. Chen, S. J. Moghimianavval, H. Lee, Y. J. Huang, A. J. Zhou, D. Xu, A. Fu, K. Adera, S. Ferguson, A. L. Liu, A. P. 2025-08-07 doi:10.1101/2025.08.07.669088 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Advancing Target Discovery Through Disease-Specific Integration of Multi-Modal Target Identification Models and Comprehensive Target Benchmarking System ]]> https://biorxiv.org/content/10.1101/2025.08.06.668866v1?rss=1 Leung, H. Duan, C. Gou, W. Chen, J. Xin, Y. Zheng, Z. Naumov, V. Gennert, D. Zhang, M. Aliper, A. Ren, F. Izumchenko, E. Pun, F. W. Zhavoronkov, A. 2025-08-08 doi:10.1101/2025.08.06.668866 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Cold exposure induces the constitutively active thermogenic receptor, GPR3, via ERRα and ERRγ ]]> https://biorxiv.org/content/10.1101/2025.08.09.669357v1?rss=1 Sveidahl Johansen, O. McIntyre, R. L. Rahbani, J. Scholtes, C. Lagarde, D. M. Tandio, D. Linde Basse, A. Giguere, V. Kazak, L. Gerhart-Hines, Z. 2025-08-09 doi:10.1101/2025.08.09.669357 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone ]]> https://biorxiv.org/content/10.1101/2025.08.08.669436v1?rss=1 Vilgalys, T. P. Anderson, J. A. Fogel, A. S. Lin, D. Archie, E. A. Alberts, S. C. Tung, J. 2025-08-10 doi:10.1101/2025.08.08.669436 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ A Cell-Autonomous Role for the Vitamin B6 Metabolism Gene PNPO in Drosophila GABAergic Neurons ]]> https://biorxiv.org/content/10.1101/2025.08.07.669010v1?rss=1 Fu, W. Landaverde, S. Zhuang, X. Iyengar, A. 2025-08-11 doi:10.1101/2025.08.07.669010 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Dehydration promotes intracellular lipid synthesis and accumulation ]]> https://biorxiv.org/content/10.1101/2025.08.07.669190v1?rss=1 Carty, J. S. Selvasingh, J. Zuchowski, Y. Nam, H.-J. Penalva, C. Nanayakkara, G. Jennings, E. Q. Voss, K. Adame, E. T. Tossberg, J. Yap, W. S. Melzer, M. Viquez, O. McCall, A. S. Piotrowski, E. R. Bessho, R. Cao, S. Leaptrot, K. Schrimpe-Rutledge, A. C. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Trapani, J. B. Cottam, M. A. Wan, M. Shrivastava, D. Delker, D. A. Wilson, M. H. Hassenour, C. M. Lantier, L. Chernova, I. Young, J. D. Haase, V. H. Medina, J.-P. V. Kosma, D. K. Kim, P. Cartailler, J. P. Zhang, M. Zent, R. Harris,, R. C. Watts, J. A. Terker, 2025-08-11 doi:10.1101/2025.08.07.669190 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Mental Imagery abilities affect visual working memory performance: evidence from aphantasic participants ]]> https://biorxiv.org/content/10.1101/2025.08.08.669378v1?rss=1 Zhao, C. Vogel, E. K. Bainbridge, W. A. 2025-08-12 doi:10.1101/2025.08.08.669378 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Geometry of neural dynamics along the cortical attractor landscape reflects changes in attention ]]> https://biorxiv.org/content/10.1101/2025.08.08.669432v1?rss=1 Song, H. Chen, R. Botch, T. L. Braver, T. S. Rosenberg, M. D. Zacks, J. M. Ching, S. 2025-08-12 doi:10.1101/2025.08.08.669432 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Generalized brain-state modeling with KenazLBM ]]> https://biorxiv.org/content/10.1101/2025.08.10.669538v1?rss=1 Johnson, G. W. Makhoul, G. Doss, D. Hidalgo, B. Cai, L. Liao, E. Paulo, D. Reda, A. Withers, C. P. Cavender, A. Qian, H. Obiri-Yeboah, D. Mensah-Brown, K. Kerezoudis, P. Baker, M. Jensen, M. Reddy, S. Roberson, S. W. Crudele, A. Naftel, R. Hermes, D. Hawkes, M. Kremen, V. Bydon, M. Ali, R. Lee, K. Lanzino, G. Bick, S. Van Gompel, J. Constantinidis, C. Morgan, V. Marsh, R. Zadeh, G. Worrell, G. Miller, K. Englot, D. 2025-08-12 doi:10.1101/2025.08.10.669538 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example ]]> https://biorxiv.org/content/10.1101/2025.08.11.669737v1?rss=1 Iyer, S. S. Hermana, K. M. Wang, Y. Pollard, T. D. Voth, G. A. 2025-08-13 doi:10.1101/2025.08.11.669737 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Mechanism for oil-phase separation by the lipid droplet assembly complex ]]> https://biorxiv.org/content/10.1101/2025.08.12.669882v1?rss=1 Malia, P. C. Kim, S. Ambaw, Y. Voth, G. A. Walther, T. C. Farese, R. 2025-08-13 doi:10.1101/2025.08.12.669882 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Tau-Driven Coordination of Microtubule-Actin Crosstalk in Cell-Sized Vesicles ]]> https://biorxiv.org/content/10.1101/2025.08.12.669979v1?rss=1 Akter, M. Shivers, J. L. Ding, L. Dinner, A. R. Liu, A. P. 2025-08-13 doi:10.1101/2025.08.12.669979 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Mechanistic Insights into Lenacapavir-Induced Off-Pathway HIV-1 Capsid Assembly ]]> https://biorxiv.org/content/10.1101/2025.08.13.670175v1?rss=1 Gupta, M. Waltmann, C. Renner, N. Wang, Y. James, L. Jacques, D. A. Bocking, T. Voth, G. A. 2025-08-13 doi:10.1101/2025.08.13.670175 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Metalog: curated and harmonised contextual data for global metagenomics samples ]]> https://biorxiv.org/content/10.1101/2025.08.14.670324v1?rss=1 Kuhn, M. Schmidt, T. S. B. Ferretti, P. Glazek, A. Robbani, M. Akanni, W. Fullam, A. Schudoma, C. Cetin, E. Hassan, M. Noack, K. Schwarz, A. Thielemann, R. Thomas, L. von Stetten, M. Alves, R. Iyappan, A. Kartal, E. Kel, I. Keller, M. I. Maistrenko, O. Mankowski, A. Nishijima, S. Podlesny, D. Schiller, J. Schulz, S. Van Rossum, T. Bork, P. 2025-08-14 doi:10.1101/2025.08.14.670324 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus) ]]> https://biorxiv.org/content/10.1101/2025.08.12.667688v1?rss=1 Cespedes Arias, L. Cuervo, A. M. Cadena, C. D. Bonaccorso, E. Witt, C. Lovette, I. Campagna, L. 2025-08-15 doi:10.1101/2025.08.12.667688 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics ]]> https://biorxiv.org/content/10.1101/2025.08.12.669906v1?rss=1 Arias, L. C. Bennett, K. F. P. Campagna, L. Wood, A. W. Bonaccorso, E. Cuervo, A. M. Cadena, C. D. Lovette, I. J. Toews, D. P. L. 2025-08-15 doi:10.1101/2025.08.12.669906 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Spatial proteomics reveals mechanisms of cell-intrinsic tryptophan metabolism controlling ovarian cancer survival ]]> https://biorxiv.org/content/10.1101/2025.08.14.670277v1?rss=1 Xu, T. T. Metousis, A. Kainacher, L. Zhang, X. Steigenberger, B. Madden, K. G. Schweitzer, L. C. Duteil, C. Rossini, S. Lengyel, E. Obermayr, E. Shulman, Z. Nordmann, T. M. Lindberg, E. L. Mann, M. Murray, P. J. 2025-08-18 doi:10.1101/2025.08.14.670277 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Antagonism by the Type VI secretion system of Bacteroides fragilis is controlled by a TetR family regulator and released small molecule ]]> https://biorxiv.org/content/10.1101/2025.08.20.671311v1?rss=1 Tuzlak, L. Pappas, T. E. Coyne, M. J. Sheahan, M. L. Burgo, V. Rice, P. A. Comstock, L. E. 2025-08-20 doi:10.1101/2025.08.20.671311 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ SEAHORSE: A Serendipity Engine Assaying Heterogeneous Omics-Related Sampling Experiments ]]> https://biorxiv.org/content/10.1101/2025.08.15.670514v1?rss=1 Quackenbush, A. Kolluri, J. Biju, R. Nhong, S. DeConti, D. Quackenbush, J. Saha, E. 2025-08-21 doi:10.1101/2025.08.15.670514 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Ceramide-induced Endoplasmic Reticulum Stress as a Targetable Vulnerability in Endocrine Therapy-Resistant Breast Cancer ]]> https://biorxiv.org/content/10.1101/2025.08.18.670862v1?rss=1 Pal, P. Chitkara, S. Sarpey, G. K. Alani, F. Zhao, H. Ata, M. Qu, J. Schiff, R. Tonetti, D. Greene, G. L. Frasor, J. Atilla, G. E. Coloff, J. L. 2025-08-22 doi:10.1101/2025.08.18.670862 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Mechanistic basis of dynamic and heterogeneous divisive normalization in visual cortex ]]> https://biorxiv.org/content/10.1101/2025.08.19.671076v1?rss=1 Rockwell, H. MacLean, J. N. 2025-08-24 doi:10.1101/2025.08.19.671076 Cold Spring Harbor Laboratory Press 2025-08-24 <![CDATA[ Sequencing of distinct wing behaviors during Drosophila courtship ]]> https://biorxiv.org/content/10.1101/2025.08.21.671456v1?rss=1 Li, X. Thieringer, K. Gao, Y. Murthy, M. 2025-08-25 doi:10.1101/2025.08.21.671456 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ HP1B and H3K9me3 Regulate Olfactory Receptor Choice and Transcriptional Identity ]]> https://biorxiv.org/content/10.1101/2025.08.21.671605v1?rss=1 Escamilla-del-Arenal, M. Duffie, R. Shayya, H. Loconte, V. Ekman, A. Street, L. A. Horta, A. Canzio, D. Monahan, K. Larabell, C. A. Jovanovic, M. Lomvardas, S. 2025-08-25 doi:10.1101/2025.08.21.671605 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ BCL6 in T cells promotes type 1 diabetes by redirecting fates of insulin-autoreactive B lymphocytes ]]> https://biorxiv.org/content/10.1101/2025.08.25.671997v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@bf0daforg.highwire.dtl.DTLVardef@11b95fdorg.highwire.dtl.DTLVardef@141ccaorg.highwire.dtl.DTLVardef@6e4100_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Clark, L. M. McAninch, J. C. McNitt, D. H. Padgett, M. L. Jenkins, T. W. Bass, L. E. Nichols, C. M. Rathmell, J. C. Bonami, R. H. 2025-08-28 doi:10.1101/2025.08.25.671997 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods ]]> https://biorxiv.org/content/10.1101/2025.08.29.672809v1?rss=1 Rogers, T. F. Stock, J. Schulz, N. G. Yalcin, G. Rencken, S. D. Weissenbacher, A. Clarence, T. Schultz, D. T. Ragsdale, C. W. Albertin, C. B. Simakov, O. 2025-08-29 doi:10.1101/2025.08.29.672809 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ In situ architecture of the endosymbiont Wolbachia pipientis ]]> https://biorxiv.org/content/10.1101/2025.08.29.673095v1?rss=1 Pujhari, S. Heebner, J. Raumann, E. Zhong, T. Rasgon, J. L. Swulius, M. T. Shaffer, C. L. Kaplan, M. 2025-08-29 doi:10.1101/2025.08.29.673095 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Functional rather than anatomic connectivity predicts seizure propagation in a multi-node model of focal neocortical epilepsy ]]> https://biorxiv.org/content/10.1101/2025.08.26.672408v1?rss=1 Niemeyer, J. E. Zhan, F. Pons, C. Schwartz, T. H. 2025-08-31 doi:10.1101/2025.08.26.672408 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Sex chromosome turnover and mitonuclear conflict drive reproductive isolation ]]> https://biorxiv.org/content/10.1101/2025.08.29.673102v1?rss=1 Moran, R. L. Radcliffe, W. V. Dye, M. Kim, D. Muralidhar, P. L. 2025-09-04 doi:10.1101/2025.08.29.673102 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[ A neural network with episodic memory learns causal relationships between narrative events ]]> https://biorxiv.org/content/10.1101/2025.09.01.673596v1?rss=1 Song, H. Lu, Q. Nguyen, T. T. Chen, J. Leong, Y. C. Rosenberg, M. D. Ching, S. Zacks, J. M. 2025-09-05 doi:10.1101/2025.09.01.673596 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Tuning the gate and the gear: The LRRC26 (γ1) subunit modulates intrinsic gating and voltage-sensor coupling of the BK channel ]]> https://biorxiv.org/content/10.1101/2025.09.04.674290v1?rss=1 Echeverria, F. Fernandez, M. Pena-Pichicoi, A. Castillo, J. P. Carrasquel-Ursulaez, W. Alvarez, O. Latorre, R. 2025-09-06 doi:10.1101/2025.09.04.674290 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Complementary regulation of memory flexibility and stabilization by dentate gyrus granule cells and mossy cells ]]> https://biorxiv.org/content/10.1101/2025.09.05.674488v1?rss=1 GoodSmith, D. Carson, W. H. Sheffield, M. E. 2025-09-06 doi:10.1101/2025.09.05.674488 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Query Augmented Generation (QAG) from the Genomic DataCommons for Accurate Variant Statistics ]]> https://biorxiv.org/content/10.1101/2025.09.02.673797v1?rss=1 Venkat, A. Wysocki, W. P. Lukowski, M. Song, S. Subramanyam, A. Zhang, Z. Grossman, R. L. 2025-09-07 doi:10.1101/2025.09.02.673797 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.09.04.673818v1?rss=1 Sheehan, C. Hu, L. Cognet, G. Croley, G. Nguyen, T. T. Thomas-Toth, A. Agovino, D. Jonker, P. B. Sadullozoda, M. Ziolkowski, L. M. Martin, J. K. Beutel, A. K. Dano, R. Khan, M. A. Halbrook, C. J. Macleod, K. F. Weber, C. R. LaBelle, J. L. Muir, A. 2025-09-08 doi:10.1101/2025.09.04.673818 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ MiR-34a deficiency enhances nucleic acid sensing and type I IFN signaling in a mouse model of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.09.05.674298v1?rss=1 Yang, J. Tsourdinis, G. E. Holas, C. Maienschein-Cline, M. Lalonde, R. Fukuchi, K. 2025-09-09 doi:10.1101/2025.09.05.674298 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[ METTL3-mediated m6A modification of DNMT1 enhances ovarian cancer progression ]]> https://biorxiv.org/content/10.1101/2025.09.10.675425v1?rss=1 Kumari, K. Perez-Nunez, I. Noguera, A. Pluvinet, R. Peula, C. Patthey, A. Khan, G. N. Pajdzik, K. Roman, A. Dassi, E. He, C. Lundin, E. Esteller, M. Celia-Terrassa, T. Aguilo, F. 2025-09-12 doi:10.1101/2025.09.10.675425 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization ]]> https://biorxiv.org/content/10.1101/2025.09.12.675697v1?rss=1 Yasuma-Mitobe, K. Liao, C. Nemeth, T. Byrne, K. Bilipps, A. Ramos, R. J. J. F. Salinas, C. N. Chan, E. Perissinoto, M. Sidebottom, A. M. Plitas, G. Butler, G. Cross, J. R. Pamer, E. G. Gacser, A. Xavier, J. B. Hohl, T. M. 2025-09-12 doi:10.1101/2025.09.12.675697 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Sequential sampling from memory underlies perceptual decisions unyoked from actions ]]> https://biorxiv.org/content/10.1101/2025.09.10.675475v1?rss=1 Sharma, P. Shadlen, M. Shushruth, S. 2025-09-13 doi:10.1101/2025.09.10.675475 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts ]]> https://biorxiv.org/content/10.1101/2025.09.15.676277v1?rss=1 Tucker, S. J. Fuessel, J. Freel, K. C. Kiefl, E. Freel, E. B. Ramfelt, O. Sullivan, C. E. S. Gajigan, A. P. Mochimaru, H. Rocha de Souza, M. Quinn, M. Ratum, C. Tran, L. L. Sobczyk, M. Miller, S. E. Trigodet, F. Lolans, K. Morrison, H. G. Fallon, B. Huettel, B. Pan, T. Rappe, M. S. Eren, A. M. 2025-09-15 doi:10.1101/2025.09.15.676277 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ ALM enables contextual decision-making via dynamic reconfiguration of local circuits ]]> https://biorxiv.org/content/10.1101/2025.09.11.675319v1?rss=1 Shen, J. Rungratsameetaweemana, N. Sharma, P. Peterka, D. S. Wu, H. Z. Shadlen, M. N. 2025-09-16 doi:10.1101/2025.09.11.675319 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Rapid Adaptation to Road Salts in a Freshwater Microbial Eukaryote ]]> https://biorxiv.org/content/10.1101/2025.09.11.675700v1?rss=1 Zufall, R. Pereda, N. Plum, K. Rothschild, E. 2025-09-16 doi:10.1101/2025.09.11.675700 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[ Insular Traveling Waves Link Distributed Neural Dynamics to Human Memory Performance ]]> https://biorxiv.org/content/10.1101/2025.09.15.676376v1?rss=1 Das, A. Wu, C. Sheth, S. Jacobs, J. 2025-09-17 doi:10.1101/2025.09.15.676376 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Structural Heterogeneity of the Membrane-Interacting Region of the HIV-1 Envelope Glycoprotein ]]> https://biorxiv.org/content/10.1101/2025.09.16.676619v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@1ca7fc0org.highwire.dtl.DTLVardef@1894c82org.highwire.dtl.DTLVardef@fe22fcorg.highwire.dtl.DTLVardef@aaf7ee_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Majumder, A. Voth, G. A. 2025-09-17 doi:10.1101/2025.09.16.676619 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Biochemical characterizations of Pontocerebellar Hypoplasia linked mutations of Target of Egr1 (TOE1) reveal impacts on thermal stability, ribonuclease activity, and oligomerization ]]> https://biorxiv.org/content/10.1101/2025.09.18.672001v1?rss=1 Hayne, C. K. Zavala, L. Sobien, M. 2025-09-18 doi:10.1101/2025.09.18.672001 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation ]]> https://biorxiv.org/content/10.1101/2025.09.17.676724v1?rss=1 Dalkiran, A. Rifaioglu, A. S. Cetin-Atalay, R. Acar, A. C. Dogan, T. Atalay, V. M. 2025-09-19 doi:10.1101/2025.09.17.676724 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Adaptations in Plasmodium tubulin determine unique microtubule architectures, mechanics and drug susceptibility ]]> https://biorxiv.org/content/10.1101/2025.09.17.676853v1?rss=1 Bangera, M. Wu, J. Beckett, D. Fachet, D. Ferreira, J. L. Voth, G. A. Reber, S. Moores, C. A. 2025-09-19 doi:10.1101/2025.09.17.676853 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Discovering flexible codes for prediction across timescales in the retina ]]> https://biorxiv.org/content/10.1101/2025.09.19.677348v1?rss=1 Bojanek, K. Lefebvre, B. Salisbury, J. M. Marre, O. Palmer, S. 2025-09-19 doi:10.1101/2025.09.19.677348 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Quantitative system drift ]]> https://biorxiv.org/content/10.1101/2025.09.17.676933v1?rss=1 Veller, C. Muralidhar, P. 2025-09-20 doi:10.1101/2025.09.17.676933 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Network dynamics underlying activity-timescale differences between cortical regions ]]> https://biorxiv.org/content/10.1101/2025.09.19.677442v1?rss=1 Canton-Josh, J. E. Ackert-Smith, L. Costa, R. M. Pinto, L. 2025-09-20 doi:10.1101/2025.09.19.677442 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Discovery of circulating cell-free DNA 5hmC biomarkers for peritoneal metastasis in colorectal and appendiceal cancer ]]> https://biorxiv.org/content/10.1101/2025.09.18.676945v1?rss=1 Malina, Y. F. Gao, L. Dhiman, A. West-Szymanski, D. C. Berger, Y. Cui, X.-L. Zhang, Z. Rivas, M. Dougherty, U. Ye, C. Kwesi, A. Deng, Z. Reddy, B. Witmer, H. D. D. Hsu, P. J. He, C. Zhang, W. Bissonnette, M. Turaga, K. 2025-09-21 doi:10.1101/2025.09.18.676945 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ COPI-dependent intra-Golgi recycling at an intermediate stageof cisternal maturation ]]> https://biorxiv.org/content/10.1101/2025.09.20.677526v1?rss=1 Krahn, A. H. Pantazopoulou, A. Austin, J. Johnson, N. Lee-Smith, C. F. Glick, B. S. 2025-09-21 doi:10.1101/2025.09.20.677526 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Spatially organized lymphocytic microenvironments in high grade primary prostate tumors ]]> https://biorxiv.org/content/10.1101/2025.09.21.677465v1?rss=1 Amiryousefi, A. Wala, J. Lin, J.-R. Labadie, B. W. Atmakuri, A. Maliga, Z. Toye, E. Chaudagar, K. Torcasso, M. S. Coy, S. Fanelli, G. N. Kobs, B. Socciarelli, F. Gagne, A. Van Allen, E. Patnaik, A. Sorger, P. K. 2025-09-21 doi:10.1101/2025.09.21.677465 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Nutrient availability-driven changes in extracellular matrix biochemical and mechanical properties regulate pancreatic cancer cell biology ]]> https://biorxiv.org/content/10.1101/2025.09.21.677637v1?rss=1 Turan, K. Guillard, J. Storl-Desmond, M. R. Lin, S. Huang, Y.-C. Forti, K. M. Schwoerer, S. 2025-09-21 doi:10.1101/2025.09.21.677637 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes ]]> https://biorxiv.org/content/10.1101/2025.09.22.677704v1?rss=1 McCafferty, C. L. Hoogerbrugge, G. Papoulas, O. Schwartz, E. A. Ritchey, S. Taylor, D. W. Brilot, A. F. Marcotte, E. M. 2025-09-22 doi:10.1101/2025.09.22.677704 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Neuronal signatures of successful one-shot memory in mid-level visual cortex ]]> https://biorxiv.org/content/10.1101/2025.09.22.677855v1?rss=1 DiRisio, G. F. Xue, C. Cohen, M. R. 2025-09-22 doi:10.1101/2025.09.22.677855 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target ]]> https://biorxiv.org/content/10.1101/2025.09.23.678089v1?rss=1 Mogol, A. N. Yoo, J. Y. Eve, A. A. Goel, M. Dutton, D. J. Schane, C. P. Lam, A. Dutta, D. Barnick, B. Erdogan, E. D. Nelson, E. R. Grosse-Perdekamp, M. Madak-Erdogan, Z. 2025-09-23 doi:10.1101/2025.09.23.678089 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Potentiating CAR-T bystander killing by enhanced Fas/FasL signaling mitigates antigen escape in heterogeneous tumors ]]> https://biorxiv.org/content/10.1101/2025.09.22.677496v1?rss=1 20%) to define how Fas/FasL-dependent bystander killing contributes to tumor clearance. Across patient cohorts, Fas expression predicted survival after CD19 CAR-T therapy, particularly in CD19-low disease. In both murine and human systems, Fas-dependent bystander killing required Ag stimulation and cell contact, operated within a defined therapeutic window, and could eradicate large fractions of Ag- tumors in vivo. Pharmacologic potentiation with inhibitor of apoptosis protein antagonists or genetic stabilization of CAR-T membrane-bound FasL enhanced bystander killing but simultaneously induced CD4 T cell fratricide, which was rescued by CAR-T Fas knockout. Importantly, Fas sensitization also enabled bispecific antibody-redirected T cells to mediate bystander killing in resistant tumors. Finally, targeting tumor-associated macrophages triggered Fas-dependent clearance of neighboring tumor cells. These findings establish Fas-mediated bystander killing as a generalizable and therapeutically actionable axis to prevent Ag escape and broaden the scope of targeted T cell therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/677496v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@11bedorg.highwire.dtl.DTLVardef@d09d07org.highwire.dtl.DTLVardef@1f53c1dorg.highwire.dtl.DTLVardef@13d96f9_HPS_FORMAT_FIGEXP M_FIG C_FIG Fas-mediated bystander killing can be potentiated by IAP inhibition and FasL stabilization, and further improved by decoupling CD4 T cell fratricide via Fas knockout. Schematic representation of CAR-T bystander killing across three mechanistic states. Left (Baseline): Antigen-positive (CD19) tumor cells activate CAR-T cells, leading to FasL-mediated cytotoxicity of neighboring antigen-negative (CD19-) tumor cells via membrane-bound FasL. Limited FasL expression and ADAM10-mediated shedding constrain bystander killing, and CD4 T cells are largely spared. Middle (Potentiated): Enhancing Fas signaling through IAP inhibition (IAPi), increasing FasL expression, and reducing FasL shedding result in improved bystander killing but also increased CD4 T cell fratricide. Right (Potentiated & Decoupled): Combining IAPi with FasL stabilization and CAR-T Fas knockout (FasKO) augments bystander killing while eliminating CD4 T cell fratricide. ]]> Lin, M. J. Chorazeczewski, J. K. Pantsulaia, G. Coooper, A. Sohn, M. Reci, S. Mateus-Tique, J. Hirsh, N. H. Xie, X. Odak, I. Dutta, R. Charytonowicz, D. Upadhyay, R. Brown, B. D. Huse, M. Kline, J. Brody, J. D. 2025-09-24 doi:10.1101/2025.09.22.677496 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2025.09.23.678164v1?rss=1 Liu, J. Chandler, T. Li, Y. Agashe, A. Wei, M. Su, Y. Wu, Y. Baskin, T. I. Jaumouille, V. Chen, J. Xu, P. Ye, H. Zhu, W. Fischer, R. S. Swaminathan, V. Nain, A. S. Mehta, S. B. La Riviere, P. J. Shroff, H. Liu, H. Guo, M. 2025-09-25 doi:10.1101/2025.09.23.678164 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Decoding Distraction From the Human Brain: A Unique Neural Signature Beyond Failures of Selective Attention and Control ]]> https://biorxiv.org/content/10.1101/2025.09.24.678372v1?rss=1 Chidharom, M. Jones, H. M. Rosenberg, M. D. Vogel, E. K. 2025-09-25 doi:10.1101/2025.09.24.678372 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding ]]> https://biorxiv.org/content/10.1101/2025.09.24.678334v1?rss=1 Keplinger, A. J. Srinivasan, P. A. Christensen, S. M. Suarez, C. Ruthenburg, A. J. 2025-09-26 doi:10.1101/2025.09.24.678334 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ GluN2A-mediated currents and calcium signal in human iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2025.09.26.678211v1?rss=1 Escamilla, S. Aviles-Granados, C. Andres-Peralta, F. V-Paternain, A. Cortes-Gomez, M.-A. Zetterberg, H. de la Pena, E. Salas-Lucia, F. Saez-Valero, J. Cuchillo-Ibanez, I. 2025-09-27 doi:10.1101/2025.09.26.678211 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Dual Membrane-spanning Anti-Sigma 2 Controls OMV biogenesis and Colonization Fitness in Bacteroides thetaiotaomicron ]]> https://biorxiv.org/content/10.1101/2025.09.27.678952v1?rss=1 Pardue, E. J. Zhong, T. Scott, N. E. Jana, B. Beatty, W. Ortiz-Marquez, J. C. Kaplan, M. Jackson-Litteken, C. Feldman, M. F. 2025-09-27 doi:10.1101/2025.09.27.678952 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.09.28.674326v1?rss=1 Chortis, V. Silva-Borges, K. Yao, C.-H. Ribeiro, C. Nagano, L. F. Berber, M. Prete, A. Najdekr, L. Klontzas, M. E. Jankevics, A. Vendramini, P. Kremer, J. L. Kelley, L. Raveenthiraraj, S. Tsagarakis, S. Macech, M. Pupovac, I. D. Papathomas, T. G. Haykir, B. Winder, C. L. Quinkler, M. Dennedy, M. C. Ueland, G. A. Beuschlein, F. Tabarin, A. Fassnacht, M. Taylor, A. E. Kastelan, D. Ambroziak, U. Vassiliadi, D. A. Kiseljak-Vassiliades, K. Bancos, I. Carlone, D. L. Dunn, W. B. Arlt, W. Haigis, M. C. Breault, D. T. 2025-09-30 doi:10.1101/2025.09.28.674326 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ LINE1 RNA dysregulation impairs chromatin accessibility in C9ORF72- and TDP-43-linked ALS/FTD ]]> https://biorxiv.org/content/10.1101/2025.09.30.679260v1?rss=1 Li, Y. Dou, X. Xiao, Y. Zhang, Z. Ye, Y. Wright, N. Chang, K. Liu, C. Troncoso, J. C. He, C. Sun, S. 2025-10-02 doi:10.1101/2025.09.30.679260 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Neural activity profiles reveal overlapping, intermingled subpopulations spanning area borders in mouse sensorimotor cortex ]]> https://biorxiv.org/content/10.1101/2025.10.02.680044v1?rss=1 39,000 layer 2/3 neurons). We characterized each neurons trial-averaged peri-event activity with interpretable metrics and mapped these response properties across areas, revealing large-scale spatial structure. Neuronal response profiles often shifted abruptly at anatomical borders: motor areas showed sharper tuning and more linear relationships with target location, whereas somatosensory areas displayed more heterogeneous response patterns. Neural response properties also differed according to somatotopic representation. Nonlinear dimensionality reduction of the neural feature matrix revealed that areas varied in their average response profiles, but that areas did not have well-separated feature distributions; instead, each area contained subpopulations. Neurons in each subpopulation had characteristic response profiles and were distributed across multiple cortical areas. The spatial distributions of the subpopulations overlapped, with neurons from different subpopulations salt-and-pepper intermingled in the overlap zones. Together, these results describe novel activity structure across sensorimotor cortex and identify several distinct but spatially-overlapping subpopulations with characteristic activity patterns during reach-to-grasp behavior. ]]> Salimian, S. Grier, H. Kaufman, M. T. 2025-10-03 doi:10.1101/2025.10.02.680044 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya ]]> https://biorxiv.org/content/10.1101/2025.10.03.680086v1?rss=1 Southworth, C. A. Winans, J. C. Gordon, J. B. Learn, N. H. Wilber, W. A. Andreadis, C. Andreasen, G. Arandjelovic, M. Campbell, C. R. Chege, M. N. Creighton, M. J. A. Cromer, C. M. Debray, R. Dickson, C. C. Ferretti, P. George, E. M. Gesquiere, L. R. He, S. Hey, L. Jefferson, E. E. Kulahci, I. G. Lerch, B. A. Nonnamaker, L. Rivas-Gonzalez, I. Tuliozi, B. Webb, S. E. Alberts, S. C. Archie, E. A. Tung, J. 2025-10-03 doi:10.1101/2025.10.03.680086 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ The genomic response to drought across spatiotemporal scales in Amaranthus tuberculatus ]]> https://biorxiv.org/content/10.1101/2025.10.02.679894v1?rss=1 Pineau, R. Bercovich, N. Rieseberg, L. H. Kreiner, J. M. 2025-10-04 doi:10.1101/2025.10.02.679894 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Accurate determination of the preferred aggregation number of a micelle-encapsulated membrane protein dimer ]]> https://biorxiv.org/content/10.1101/2025.10.02.679921v1?rss=1 Harris, J. Pantelopulos, G. A. Straub, J. E. 2025-10-04 doi:10.1101/2025.10.02.679921 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ The G Protein-Coupled Receptor GPR31 Promotes Pro-inflammatory Responses in Pancreatic Islets and Macrophages ]]> https://biorxiv.org/content/10.1101/2025.10.02.680021v1?rss=1 Kaylan, K. B. Checkcinco, C. Enriquez, J. R. Nargis, T. Elliot, E. Puente, A. A. Wang, J. E. Walsh, M. Nelson, J. Kulkarni, A. Muralidharan, C. May, S. C. Anderson, R. M. Mirmira, R. Tersey, S. A. 2025-10-04 doi:10.1101/2025.10.02.680021 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Membrane Remodeling by the Collective Action of Caveolin-1 ]]> https://biorxiv.org/content/10.1101/2025.10.03.680304v1?rss=1 Liebl, K. Voth, G. A. 2025-10-04 doi:10.1101/2025.10.03.680304 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Therapeutic remodeling of the tuberculosis granuloma with 1-methyl-D-tryptophan enhances CD8+ T cell-macrophage interactions ]]> https://biorxiv.org/content/10.1101/2025.10.02.680083v1?rss=1 McCaffrey, E. F. Delmastro, A. C. Singh, B. Devi, A. Golden, N. A. Khader, S. A. Angelo, M. Kaushal, D. Mehra, S. 2025-10-07 doi:10.1101/2025.10.02.680083 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag ]]> https://biorxiv.org/content/10.1101/2025.10.06.680180v1?rss=1 Liao, Y. Zhou, W. Jiang, M.-Z. Yu, K. Wang, Z. J. Drummond, T. Ding, M. Zhao, Y. Pino, I. Taverna, S. D. Ji, H. Zhu, H. 2025-10-07 doi:10.1101/2025.10.06.680180 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Islet-intrinsic sex differences in inflammatory signaling contribute to autoimmune diabetes susceptibility ]]> https://biorxiv.org/content/10.1101/2025.10.06.680429v1?rss=1 Webster, K. L. Puente, A. A. Enriquez, J. R. Sarkar, S. Nakayasu, E. S. Webb-Robertson, B.-J. M. Bramer, L. M. Figatner, K. Pratuangtham, S. Wu, W. Evans-Molina, C. Tse, H. M. Roy, S. Piganelli, J. D. Hammes, S. R. Tersey, S. A. Mirmira, R. G. 2025-10-07 doi:10.1101/2025.10.06.680429 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Maternal SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven 2-cell totipotency transcriptional program in the mouse embryo ]]> https://biorxiv.org/content/10.1101/2025.10.07.680892v1?rss=1 Zeng, T.-B. Fu, Z. Majewski, M. F. Liao, J. Adams, M. Szabo, P. E. 2025-10-09 doi:10.1101/2025.10.07.680892 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Distinct contributions of anterior and posterior orbitofrontal cortex to outcome-guided behavior ]]> https://biorxiv.org/content/10.1101/2025.10.08.681180v1?rss=1 Liu, Q. Porter, D. Damra, H. Zhao, Y. Voss, J. L. Schoenbaum, G. Kahnt, T. 2025-10-09 doi:10.1101/2025.10.08.681180 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Phylogenetic relationships and the evolution of fin and body shape in the surgeonfishes ]]> https://biorxiv.org/content/10.1101/2025.10.09.680739v1?rss=1 Lungstrom, L. L. Farjo, M. Isdonas, R. George, A. B. Westneat, M. W. 2025-10-10 doi:10.1101/2025.10.09.680739 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA ]]> https://biorxiv.org/content/10.1101/2025.10.09.681456v1?rss=1 He, C. Dai, Q. Baldwin, T. Lyu, R. Daniels, B. Ye, C. Cao, C. Zhu, C. Fan, D. Lin, L. Liu, Y. Wang, Y. 2025-10-10 doi:10.1101/2025.10.09.681456 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ When migration leaves a clean trace: Decoupling migration from coalescence in the Structured Serial Coalescent ]]> https://biorxiv.org/content/10.1101/2025.10.10.681523v1?rss=1 Shen, H. Novembre, J. 2025-10-10 doi:10.1101/2025.10.10.681523 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Geometric Tuning of Cytokine Receptor Association Modulates Synthetic Agonist Signaling ]]> https://biorxiv.org/content/10.1101/2025.10.12.681819v1?rss=1 Exposit, M. Abedi, M. Krishnakumar, A. Jain, S. Yu, T.-Y. Hercus, T. R. Mathew, D. Gray-Gaillard, S. Chen, Z. Grubbe, W. S. Favor, A. Kan, W. L. Schlichthaerle, T. Chen, W. Parker, M. W. Mendoza, J. L. Lopez, A. F. Wherry, E. J. Baker, D. 2025-10-13 doi:10.1101/2025.10.12.681819 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites ]]> https://biorxiv.org/content/10.1101/2025.10.13.659964v1?rss=1 Bose, M. L. Tovar, A. Kyono, Y. Varshney, A. Kitzman, J. O. Parker, S. C. 2025-10-14 doi:10.1101/2025.10.13.659964 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Contrasting evolutionary outcomes in a human life history trait which is heritable and under consistent unbiased directional selection ]]> https://biorxiv.org/content/10.1101/2025.10.13.682154v1?rss=1 Mawass, W. Milot, E. 2025-10-14 doi:10.1101/2025.10.13.682154 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Mapping the diverse topologies of protein-protein interaction fitness landscapes ]]> https://biorxiv.org/content/10.1101/2025.10.14.682342v1?rss=1 1,300 independent selections of various library sizes and compositions of a randomized small protein to identify binders to a panel of 96 distinct target proteins. For successful selections, we discovered reproducible fitness landscapes that group into a few, target-specific, clusters. Each cluster defines a minimal binding motif whose frequency is inversely proportional to the number of specified amino acids ([~]2-8) and determines selection success, which is quantifiable by the density of binders to the target within a theoretical sequence space. We leverage these data to develop a supervised contrastive learning approach that discriminates binders from non-binders and demonstrates generalization beyond a threshold amount of data. Together, this framework renders PPI landscapes measurable and predictive, accelerating de novo binder discovery and optimization. ]]> Dickinson, B. C. Lu, S. S. Styles, M. J. Gao, C. F. Nandy, A. Basile, C. Pixley, J. A. Tao, S. Dinner, A. R. Vaikuntanathan, S. 2025-10-14 doi:10.1101/2025.10.14.682342 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Ampyrone (4-Aminoantipyrine) is a Direct Agonist of Human Tyrosinase and Potential Therapeutic for Oculocutaneous Albinism and Disorders of Hypopigmentation. ]]> https://biorxiv.org/content/10.1101/2025.10.13.682036v1?rss=1 Dolinska, M. Wang, Y. Coussens, N. Kalaskar, V. Eraslan, Z. Grondin, S. Bonica, J. Toay, S. Hall, M. Shen, M. Boxer, M. Chen, Q. Gross, S. Attarwala, N. Jittayasothorn, Y. Alur, R. Shukla, D. Kee, R. Deyoung, C. Sha, C. Adams, D. Loftus, S. K. Cogliati, T. Sergeev, Y. V. Zippin, J. H. Brooks, B. 2025-10-15 doi:10.1101/2025.10.13.682036 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Psychological stress and social support are associated with opposing single-cell pro-inflammatory gene regulatory mechanisms in adults ]]> https://biorxiv.org/content/10.1101/2025.10.14.682318v1?rss=1 Ranjbaran, A. Kalita, C. Wei, J. Davis, K. M. Bruinsma, J. Mair-Meijers, H. Garlicki, G. Alazizi, A. Petriello, M. Jiang, Y. Zilioli, S. Pique-Regi, R. Luca, F. 2025-10-15 doi:10.1101/2025.10.14.682318 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.10.14.682328v1?rss=1 Lee, D. Abu-Shihab, Y. Plas, K. Nicolet, D. Mrozek, K. Routbort, M. J. Patel, K. P. Walker, C. J. Buss, J. Stiff, A. R. Laganson, A. DiNardo, C. D. Daver, N. G. Kadia, T. M. Ravandi, F. Carroll, A. J. Kolitz, J. E. Powell, B. L. Blum, W. G. Baer, M. R. Marcucci, G. Uy, G. L. Stock, W. Stone, R. M. Medeiros, L. J. Byrd, J. C. Blachly, J. S. Bowman, R. L. Tyner, J. Loghavi, S. Eisfeld, A.-K. Miles, L. A. 2025-10-15 doi:10.1101/2025.10.14.682328 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Minimal Perturbation of Activation Loop Dynamics Rewires KinaseSignaling ]]> https://biorxiv.org/content/10.1101/2025.10.15.682502v1?rss=1 Jain, P. Yehorova, D. Febri, R. R. Clifton, B. E. Demkiv, A. Uechi, G.-i. Robinson, M. Kamerlin, S. C. L. Okada, M. Imamoto, A. Laurino, P. 2025-10-15 doi:10.1101/2025.10.15.682502 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[ Spatial and semantic memory reorganize a hippocampal long-axis gradient ]]> https://biorxiv.org/content/10.1101/2025.10.15.682651v1?rss=1 Jordan, A. G. Voss, J. L. Kragel, J. E. 2025-10-15 doi:10.1101/2025.10.15.682651 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ 3' Nucleotide Asymmetry Directs miRNA Strand Selection ]]> https://biorxiv.org/content/10.1101/2025.10.15.682714v1?rss=1 Medley, J. C. Kurosu Moriya, S. Ouyang, H. Crawshaw, H. Zhang, S. Y. Panzade, G. Sydzyik, W. J. Sydzyik, J. T. Bhandari, M. Hammell, C. M. Zinovyeva, A. 2025-10-16 doi:10.1101/2025.10.15.682714 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[ The impacts of almond pollination on honeybee viral dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.17.678657v1?rss=1 Sokolov, N. A. Northrup, G. R. Wilfert, L. Boots, M. 2025-10-17 doi:10.1101/2025.10.17.678657 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes ]]> https://biorxiv.org/content/10.1101/2025.10.17.683178v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1ea3e5forg.highwire.dtl.DTLVardef@1a4e999org.highwire.dtl.DTLVardef@1e468c3org.highwire.dtl.DTLVardef@99e04e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chakraborty, P. Carlos, A. Thomas, T. Ghaby, K. Fathi, S. Sharma, M. Nguyen, N. K. Farmwald, M. Blachowicz, L. Yu, S. Pillai, K. Roux, B. Moellering, R. E. 2025-10-18 doi:10.1101/2025.10.17.683178 Cold Spring Harbor Laboratory Press 2025-10-18 <![CDATA[ Spatially-resolved Photoproximity Profiling of MYC Identifies a MYC-BAF Liability in Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.10.17.683176v1?rss=1 Carlos, A. Huang, S. Yang, D. E. Swenson, C. Chakraborty, P. Yu, S. Fu, J. Stein, B. Moellering, R. 2025-10-19 doi:10.1101/2025.10.17.683176 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Coarse-graining reveals collective predictive information in a sensory population ]]> https://biorxiv.org/content/10.1101/2025.10.18.683195v1?rss=1 Kline, A. G. Koch-Janusz, M. Walczak, A. M. Mora, T. Palmer, S. E. 2025-10-19 doi:10.1101/2025.10.18.683195 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ CD8 T cells mediate immunosurveillance for neoantigen+ epithelial stem cells in the colon ]]> https://biorxiv.org/content/10.1101/2025.10.19.683142v1?rss=1 Buck, J. Iyer, N. R. Fagerberg, E. Micevic, G. He, J. St. Denis, K. Shah, V. Blackburn, H. N. Venkatesan, S. Attanasio, J. Hunt, B. G. Dalrymple, A. Konnikova, L. Beyaz, S. Damo, M. Booth, C. J. Connolly, K. A. Joshi, N. S. 2025-10-19 doi:10.1101/2025.10.19.683142 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Transcriptomic and protein analysis of human cortex reveals genes and pathways linked to NPTX2 disruption in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.10.17.683150v1?rss=1 Lao, Y. Xiao, M.-F. Ji, S. Piras, I. S. Bonfitto, A. Song, S. Aldabergenova, A. Na, C.-H. Sloan, J. Trejo, A. Geula, C. Rogalski, E. J. Kawas, C. H. Corrada, M. M. Serrano, G. E. Beach, T. G. Troncoso, J. C. Huentelman, M. J. Barnes, C. A. Worley, P. F. Colantuoni, C. 2025-10-20 doi:10.1101/2025.10.17.683150 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ The effect of environmental enrichment on whole-brain gene expression in an imperiled fish ]]> https://biorxiv.org/content/10.1101/2025.10.18.683224v1?rss=1 Kopack, C. J. Moran, R. L. Broder, E. D. McDonald, C. A. Fetherman, E. R. Hoke, K. L. Angeloni, L. M. 2025-10-20 doi:10.1101/2025.10.18.683224 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Transcriptomic profiling of the middle temporal gyrus reveals differential glial/neuronal dysregulation across Alzheimer disease and aging. ]]> https://biorxiv.org/content/10.1101/2025.10.19.683343v1?rss=1 Piras, I. S. Bonfitto, A. Song, S. Aldabergenova, A. Sloan, J. Trejo, A. Troncoso, J. Geula, C. Rogalski, E. J. Kawas, C. H. Corrada, M. Beach, T. G. Serrano, G. E. Worley, P. F. Barnes, C. A. Huentelman, M. J. 2025-10-20 doi:10.1101/2025.10.19.683343 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ A human brain network specialized for abstract formal reasoning ]]> https://biorxiv.org/content/10.1101/2025.10.21.683445v1?rss=1 Kean, H. H. Fung, A. Ohams, C. Chen, J. Rule, J. Tenenbaum, J. B. Piantadosi, S. T. Fedorenko, E. 2025-10-22 doi:10.1101/2025.10.21.683445 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Xeno-free human iPSC-derived prostate organoid platform for multilineage differentiation and genetic manipulation ]]> https://biorxiv.org/content/10.1101/2025.10.21.683654v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1cc13eborg.highwire.dtl.DTLVardef@12fe2a4org.highwire.dtl.DTLVardef@c89d64org.highwire.dtl.DTLVardef@d541e0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shaikh, N. Teasdale, M. Walker, L. J. Wilson, L. Howarth, R. Saleem, S. Hepburn, A. C. Nelson, R. Elizondo, A. C. Hussain, R. Coxhead, J. Gaughan, L. Scott, E. Robson, C. Simons, B. Hayward, S. W. Strand, D. W. Heer, R. Buskin, A. 2025-10-22 doi:10.1101/2025.10.21.683654 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ A unique neural signature of long-term memory encoding from EEG inter-electrode correlation ]]> https://biorxiv.org/content/10.1101/2025.10.21.683799v1?rss=1 Zhao, C. Vogel, E. K. Rosenberg, M. D. 2025-10-23 doi:10.1101/2025.10.21.683799 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Acyl-protein thioesterase 1 (LYPLA1) activity promotes the growth of MDA-MB-468 triple-negative breast cancer cells. ]]> https://biorxiv.org/content/10.1101/2025.10.22.683516v1?rss=1 Salsaa, M. Tavasoli, M. Zein, H. S. Pani, S. Kathayat, R. S. Dickinson, B. C. Fairn, G. D. 2025-10-23 doi:10.1101/2025.10.22.683516 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Environmental stress amplifies competitive asymmetry and drives divergent hybrid zone outcomes ]]> https://biorxiv.org/content/10.1101/2025.10.23.684133v1?rss=1 Johnson, B. E. Adkins, C. Black, T. N. Dye, M. Mendoza, I. Moran, R. L. 2025-10-23 doi:10.1101/2025.10.23.684133 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Host transcriptional responses to gut microbiome variation arising from urbanism ]]> https://biorxiv.org/content/10.1101/2025.10.26.683539v1?rss=1 Arif, S. Nirmalan, S. Alazizi, A. Mair-Meijers, H. Agyei, A. Afihene, M. Asibey, S. Awuku, Y. Duah, A. Plymoth, A. Nartey, Y. Roberts, L. Valles, K. Ibrahim, F. Lim, Y. Pin, T. M. Onyekwere, C. Rusine, J. Mwikarago, I. Alm, E. Poyet, M. Groussin, M. Luca, F. Blekhman, R. 2025-10-26 doi:10.1101/2025.10.26.683539 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Accurate processing of ultra-short immune signals by singlemacrophages ]]> https://biorxiv.org/content/10.1101/2025.10.26.684377v1?rss=1 Mercado-Vasquez, G. Vizzard, J. Celiker, B. Xia, J. Wang, A. Padhi, A. Tay, S. 2025-10-26 doi:10.1101/2025.10.26.684377 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Mapping Functional Dynamics Hotspots for Protein Engineering with NMR Peak Intensity Analysis ]]> https://biorxiv.org/content/10.1101/2025.10.26.684639v1?rss=1 Damry, A. M. Hunt, S. E. Legault, S. Thompson, M. C. Goto, N. K. Chica, R. A. 2025-10-26 doi:10.1101/2025.10.26.684639 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ PRSformer: Disease Prediction from Million-Scale Individual Genotypes ]]> https://biorxiv.org/content/10.1101/2025.10.26.684578v1?rss=1 106 individuals) with ultra-high-dimensional features (L > 105 genotypes). Current methods, often linear and reliant on summary statistics, fail to capture complex genetic interactions and discard valuable individual-level information. We introduce PRSformer, a scalable deep learning architecture designed for end-to-end, multitask disease prediction directly from million-scale individual genotypes. PRSformer employs neighborhood attention, achieving linear O(L) complexity per layer, making Transformers tractable for genome-scale inputs. Crucially, PRSformer utilizes a stacking of these efficient attention layers, progressively increasing the effective receptive field to model local dependencies (e.g., within linkage disequilibrium blocks) before integrating information across wider genomic regions. This design, tailored for genomics, allows PRSformer to learn complex, potentially non-linear and long-range interactions directly from raw genotypes. We demonstrate PRSformers effectiveness using a unique large private cohort (N {approx} 5M) for predicting 18 autoimmune and inflammatory conditions using L {approx} 140k variants. PRSformer significantly outperforms highly optimized linear models trained on the same individual-level data and state-of-the-art summary-statistic-based methods (LDPred2) derived from the same cohort, quantifying the benefits of non-linear modeling and multitask learning at scale. Furthermore, experiments reveal that the advantage of non-linearity emerges primarily at large sample sizes (N > 1M), and that a multi-ancestry trained model improves generalization, establishing PRSformer as a new framework for deep learning in population-scale genomics. ]]> Dibaeinia, P. German, C. Shringarpure, S. Auton, A. Khan, A. A. 2025-10-27 doi:10.1101/2025.10.26.684578 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Learning-Dependent Shift from Right to Left CA3 Input Dominance Shapes the Evolution of Right CA1 Spatial Maps ]]> https://biorxiv.org/content/10.1101/2025.10.26.684700v1?rss=1 Jiang, A. GoodSmith, D. Ramirez-Matias, J. Tortolani, A. Sheffield, M. 2025-10-27 doi:10.1101/2025.10.26.684700 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Spatial proximity sequencing maps developmental dynamics in the germinal center ]]> https://biorxiv.org/content/10.1101/2025.10.27.684659v1?rss=1 WANG, H. XIA, J. RAHMAN, P. M. S. M. KEISHAM, B. PADHI, A. DENG, Y. LI, Y. VISTAIN, L. KIM, S. VASQUEZ, G. M. KHAN, A. CLARK, M. Tay, S. 2025-10-28 doi:10.1101/2025.10.27.684659 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ A brain-wide, trial- and time-dependent deterministic drive for self-initiated action decisions ]]> https://biorxiv.org/content/10.1101/2025.10.28.685235v1?rss=1 Elbaz, M. A. Butterer, K. Glaser, J. Miri, A. 2025-10-30 doi:10.1101/2025.10.28.685235 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Behavioural and neuronal insights into multisensory combination of unpracticed cues. ]]> https://biorxiv.org/content/10.1101/2025.10.29.685323v1?rss=1 Allen, K. S. Ruff, D. A. Cohen, M. R. 2025-10-30 doi:10.1101/2025.10.29.685323 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Type VIIb secretion system recruits a dedicated cell wall hydrolase EssH to enable effector secretion by Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2025.10.30.685510v1?rss=1 Agyen, R. Powell, I. McNair, M. Missiakas, D. Bobrovskyy, M. 2025-10-30 doi:10.1101/2025.10.30.685510 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Meta-analyses reveal no clear demographic consequences of phenological change across taxa ]]> https://biorxiv.org/content/10.1101/2025.10.29.685396v1?rss=1 Godtfredsen, E. B. CaraDonna, P. Foxx, A. J. Bain, J. A. Connolly, B. J. Dawdy, K. M. Doucet, A. M. Fitzgerald, J. L. Kirschke, G. E. Ogilvie, J. E. Rigby, C. C. Scholl, J. P. Sandacz, D. J. Rosa, S. Zink, A. C. Iler, A. M. 2025-10-31 doi:10.1101/2025.10.29.685396 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Massively multiplexed microfluidics maps combinatorial andsequential antibiotic responses in 3D ]]> https://biorxiv.org/content/10.1101/2025.10.30.684665v1?rss=1 JEONG, Y. MERCADO VASQUEZ, G. PADHI, A. DENG, Y. PRAKASH, M. MATTHEWS, J. OZCAN, S. TOPRAK, E. Tay, S. 2025-10-31 doi:10.1101/2025.10.30.684665 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Dynamic translocation of Inside-Out proteins to the cell surface underlies cellular adaptation to cancer-induced stress ]]> https://biorxiv.org/content/10.1101/2025.10.30.685532v1?rss=1 Slezak, T. O'Leary, K. M. Guevara Avella, T. Musial, N. Li, J. Andrzejczak, A. Scott, E. F. Anh Le, D. Kossiakoff, A. A. 2025-10-31 doi:10.1101/2025.10.30.685532 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Structural Mechanism of Prestin-Membrane Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2025.10.31.685930v1?rss=1 Bavi, N. Haller, P. Homma, K. Lin, X. Milewski, W. Zhao, M. Sosnick, T. Perozo, E. 2025-11-01 doi:10.1101/2025.10.31.685930 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Zwitterionic hydrogel designs for conducting polymers enable bioelectronics with suppressed foreign body response ]]> https://biorxiv.org/content/10.1101/2025.10.31.683260v1?rss=1 Wai, S. Kang, S. Li, N. Dai, Y. Lavoie, T. Strzalka, J. Sutyak, S. Weires, M. Fu, T. Wang, J. Stevens, K. C. Li, R. Hubbell, J. A. Tirrell, M. V. Wang, S. 2025-11-03 doi:10.1101/2025.10.31.683260 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence ]]> https://biorxiv.org/content/10.1101/2025.11.03.686283v1?rss=1 Chitale, P. Ocke, E. Odom, A. R. Fan, H. Henoch, A. Vasco, K. Fogarty, E. C. Grady, C. Lemenze, A. D. Kumar, P. Manning, S. Eren, A. M. Johnson, W. E. Alland, D. 2025-11-03 doi:10.1101/2025.11.03.686283 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies ]]> https://biorxiv.org/content/10.1101/2025.11.01.685815v1?rss=1 Ging-Jehli, N. R. Rac-Lubashevsky, R. Bera, K. Roberts, A. Loder, A. Boudewyn, M. A. Carter, C. S. Erickson, M. A. Gold, J. M. Luck, S. J. Ragland, J. D. Yonelinas, A. P. MacDonald, A. W. Barch, D. M. Frank, M. J. 2025-11-04 doi:10.1101/2025.11.01.685815 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance ]]> https://biorxiv.org/content/10.1101/2025.11.03.685478v1?rss=1 Zou, M. Tian, F. Zheng, W. Jiang, M. Zhang, S. Liu, X. Ma, C. Zhao, M. Dai, L. Li, C. Wang, S. 2025-11-04 doi:10.1101/2025.11.03.685478 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Hidden Spirals Reveal Neurocomputational Mechanisms of Traveling Waves in Human Memory ]]> https://biorxiv.org/content/10.1101/2025.11.03.686225v1?rss=1 Das, A. Zhang, J. Zabeh, E. Ermentrout, B. Jacobs, J. 2025-11-04 doi:10.1101/2025.11.03.686225 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Neural Dynamics Underlying Repeated Learning of Visual Image Sequences ]]> https://biorxiv.org/content/10.1101/2025.11.04.686589v1?rss=1 Zhao, C. Kim, A. Campos, L. Vogel, E. K. 2025-11-05 doi:10.1101/2025.11.04.686589 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ On the Mechanism of Ezrin Activation ]]> https://biorxiv.org/content/10.1101/2025.11.07.687285v1?rss=1 Vasiliauskas, D. Beiter, J. Iyer, S. S. Lombardo, A. T. Mendoza, M. C. Voth, G. A. 2025-11-07 doi:10.1101/2025.11.07.687285 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Stress granules and protein aggregates reveal intracellular resource competition ]]> https://biorxiv.org/content/10.1101/2025.11.08.687377v1?rss=1 Buchholz, H. E. Martin, S. A. Dorweiler, J. E. Prosser, D. C. Sontag, E. M. Manogaran, A. L. 2025-11-10 doi:10.1101/2025.11.08.687377 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Neural recordings of continuous speech reveal robust signatures of prediction in second language learners of English ]]> https://biorxiv.org/content/10.1101/2025.11.10.684289v1?rss=1 Thorburn, C. A. Karunathilake, I. M. D. Dixon, L. N. Lau, E. Simon, J. Z. 2025-11-10 doi:10.1101/2025.11.10.684289 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B ]]> https://biorxiv.org/content/10.1101/2025.11.10.687577v1?rss=1 Liu, X. Bilger, A. Lee, D. Argyris, P. Chen, J. Ward-Shaw, E. Barreto Duran, E. Lin, Y.-H. Durfee, C. Chun, S. H. Ibrahim, M. Proehl, J. Allen, Y. Lambert, P. F. Harris, R. S. 2025-11-10 doi:10.1101/2025.11.10.687577 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Parsing auditory neural code into maximum-entropy packets ]]> https://biorxiv.org/content/10.1101/2025.11.09.687481v1?rss=1 Zhang, H. Nelken, I. Sharpee, T. 2025-11-11 doi:10.1101/2025.11.09.687481 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Spinal cord regeneration deploys cell-type specific developmental and non-developmental strategies to restore neuron diversity ]]> https://biorxiv.org/content/10.1101/2025.11.10.687703v1?rss=1 Angell Swearer, A. Perkowski, S. B. Husain, I. Figueiredo, T. A. McCartney, M. Wills, A. E. 2025-11-12 doi:10.1101/2025.11.10.687703 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis ]]> https://biorxiv.org/content/10.1101/2025.11.10.687731v1?rss=1 Kuppers, D. Arora, S. Wladyka, C. Ge, R. Liu, S. Peng, Y. Su, R. Wilhite, A. Chen, J. He, C. Hsieh, A. Paddison, P. 2025-11-12 doi:10.1101/2025.11.10.687731 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins ]]> https://biorxiv.org/content/10.1101/2025.11.12.688084v1?rss=1 Dutta, M. Voth, G. A. 2025-11-12 doi:10.1101/2025.11.12.688084 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1Restriction Factor ]]> https://biorxiv.org/content/10.1101/2025.11.13.688349v1?rss=1 Banerjee, P. Yeager, M. A. Voth, G. A. 2025-11-13 doi:10.1101/2025.11.13.688349 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ The Closed State of the Shaker Potassium Channel and the Mechanism of Voltage Activation ]]> https://biorxiv.org/content/10.1101/2025.11.13.687653v1?rss=1 Agrawal, R. Uriarte, R. M. Anwandter, B. P. Thomas, T. Blachowicz, L. Koh, Y. Bezanila, F. Perozo, E. Roux, B. 2025-11-14 doi:10.1101/2025.11.13.687653 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ DETERMINATION OF THE TRANSBILAYER DISTRIBUTION OF PLASMA MEMBRANE CHOLESTEROL ]]> https://biorxiv.org/content/10.1101/2025.11.13.687888v1?rss=1 Steck, T. L. Lange, Y. 2025-11-14 doi:10.1101/2025.11.13.687888 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Repeat Opioid Use Modulates Microglia Activity and Amyloid Beta Clearance in a Mouse Model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.11.14.688256v1?rss=1 Gogola, J. V. Wee, S. W. S. Garcia, A. J. 2025-11-16 doi:10.1101/2025.11.14.688256 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Deep Learning for Cognitive Task Presence Prediction from Dynamic Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2025.11.14.688561v1?rss=1 Chen, K. Torabi, M. Jian, J. Yang, A. Poline, J.-B. 2025-11-16 doi:10.1101/2025.11.14.688561 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling ]]> https://biorxiv.org/content/10.1101/2025.11.18.686377v1?rss=1 Kumar, S. Jung, H. A. Walker, G. Rana, J. K. Fu, R. Hong, M. T. Malerba, F. Kumar, J. Navratna, V. Jung, W. Miller, S. J. Kruckenhauser, L. M. Capsoni, S. Hafler, B. P. Cattaneo, A. Krishnan, Y. Mosalaganti, S. Bhattacharyya, M. 2025-11-18 doi:10.1101/2025.11.18.686377 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ A nucleic acid labeling chemistry reveals surface DNA on exosomes ]]> https://biorxiv.org/content/10.1101/2025.11.18.689134v1?rss=1 Boskovic, F. Dutta Gupta, P. Zhang, J. Krishnan, Y. Szostak, J. W. 2025-11-19 doi:10.1101/2025.11.18.689134 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Single-nucleotide resolution mapping of m6A of zebrafish mRNAs in early embryonic development links m6A modifications to the maternal-to-zygotic transition ]]> https://biorxiv.org/content/10.1101/2025.11.19.688951v1?rss=1 4-fold decrease in m6A levels from 256-cell to 50% epiboly, clearly linking this methylation to zebrafish maternal-to-zygotic transition. We highlight that differential methylation between developmental stages was observed in transcripts associated with mRNA metabolism, translational processing, and organ development. ]]> Wardale, A. Peng, Y. Ge, R. Jorgensen, T. E. Johansen, S. D. He, C. Babiak, I. 2025-11-19 doi:10.1101/2025.11.19.688951 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders ]]> https://biorxiv.org/content/10.1101/2025.11.19.689279v1?rss=1 100-fold higher affinity than the highly related KRAS isoform, and (2) discovery of epitope-specific binders that either target or avoid the LIR interaction region of LC3B. PANCS-spec-Binders enables rapid identification of binders with defined specificity within days. SIGNIFICANCEAffinity reagents, termed "binders", are essential tools in research and therapeutic development. Binders generally require high specificity either at the selectivity level (binding only the target protein, but not related proteins) or at the epitope level (binding only at a specific surface on the target rather than another). While methods to discover binders in general have progressed, identifying binders with defined specificity features often requires extensive secondary screening and frequently results in failure. Here, we adapt our recently developed binder discovery platform to solve these two selectivity problems. By rapidly screening billions of variants, we can direct specificity between highly related proteins, direct binding to a specific epitope, and, because of the fidelity of our selections, identify binders that specifically avoid a defined epitope. ]]> Pixley, J. A. Styles, M. J. Aphicho, K. Endres, M. Gade, P. Michalska, K. Joachimiak, A. Dickinson, B. C. 2025-11-19 doi:10.1101/2025.11.19.689279 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ Progesterone receptors drive advanced breast cancer phenotypes including circulating tumor- and stem-like cell expansion in the context of ESR1 mutation ]]> https://biorxiv.org/content/10.1101/2025.11.20.689560v1?rss=1 Truong, T. Gillis, N. E. Dwyer, A. R. Huggins, R. J. Hagen, K. M. Posani, S. H. Temiz, N. A. Perez Kerkvliet, C. Piepgras, E. M. Ostrander, J. H. Greene, G. L. Lange, C. A. 2025-11-21 doi:10.1101/2025.11.20.689560 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Multiple longitudinal tracts in the cephalopod arm sensorimotor system ]]> https://biorxiv.org/content/10.1101/2025.11.20.689621v1?rss=1 Olson, C. S. Ragsdale, C. W. 2025-11-22 doi:10.1101/2025.11.20.689621 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution ]]> https://biorxiv.org/content/10.1101/2025.11.24.689867v1?rss=1 Sosa, D. Sobczyk, M. Chen, J.-H. Xia, S. Pan, T. Long, M. 2025-11-24 doi:10.1101/2025.11.24.689867 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Learning the mechanism of collective microbial function via random community-media pairing ]]> https://biorxiv.org/content/10.1101/2025.11.25.690499v1?rss=1 Wang, L. Kuehn, S. Tikhonov, M. 2025-11-27 doi:10.1101/2025.11.25.690499 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ A cholinergic mechanism orchestrating task-dependent computation across the cortex ]]> https://biorxiv.org/content/10.1101/2025.11.26.690825v1?rss=1 Luo, J. K. Tan, J. Myhre, E. Salvino, P. Hark, A. Pinto, L. 2025-11-27 doi:10.1101/2025.11.26.690825 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain. ]]> https://biorxiv.org/content/10.1101/2025.11.25.690439v1?rss=1 Liu, A. De Jager, P. L. Bennett, D. The Alzheimer's Disease Functional Genomics Consortium, Wang, G. Denault, W. R. P. 2025-11-28 doi:10.1101/2025.11.25.690439 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Composite biomaterials of polyelectrolyte complex micelle nanoparticles in hyaluronic acid gels enable local, targeted miR-92a inhibition and enhanced angiogenesis in diabetic wound repair ]]> https://biorxiv.org/content/10.1101/2025.11.25.690510v1?rss=1 Xi, B. J. Wang, S. Alpar, A. T. Hubbell, J. A. Fang, Y. Tirrell, M. V. 2025-11-28 doi:10.1101/2025.11.25.690510 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction ]]> https://biorxiv.org/content/10.1101/2025.11.25.690514v1?rss=1 McCreight, A. Cho, Y. Li, R. Nachun, D. Gan, H.-Y. Carbonetto, P. Stephens, M. Denault, W. R. Wang, G. 2025-11-28 doi:10.1101/2025.11.25.690514 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Interpretable Thermodynamic Score-based Classification of Relaxation Excursions ]]> https://biorxiv.org/content/10.1101/2025.11.26.690838v1?rss=1 Kuznets-Speck, B. Jung, J. Pholraksa, P. Zhong, A. Schwartz, L. Prashnani, E. Vaikuntanathan, S. Goyal, Y. 2025-12-01 doi:10.1101/2025.11.26.690838 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow ]]> https://biorxiv.org/content/10.64898/2025.11.30.691458v1?rss=1 Srinivasan, H. Yuan, R. Cong, Q. Zhou, J. 2025-12-02 doi:10.64898/2025.11.30.691458 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Exploring the Evolution of the Cariogenic Oral Pathobiont Streptococcus mutans Using Ancient DNA ]]> https://biorxiv.org/content/10.64898/2025.12.02.691581v1?rss=1 Michel, M. Valuena, A. A. Akar, M. Alonso-Fernandez, C. Calmet, M. A. Andreadaki-Vlazaki, M. Jimenez, G. A. Banffy, E. Barquera, R. Barreto-Romero, M. Fuello, P. B. Bedford, S. Belinkskiy, A. B. Berezina, N. Boyadzhiev, K. Boyadzhiev, Y. Buzhilova, A. Cappuccini, L. Huamani, J. E. C. Beltran, E. C. Clark, G. Daubaras, M. Ibanez, P. d. M. Bonilla, M. D.-Z. Dobes, M. Dresely, V. Erdal, Y. S. Ernee, M. Ferraz, T. Figuti, L. Farre, J. F. Flexner, J. L. Friederich, S. Gaffney, D. Atienzar, G. G. Pena, R. G. Gomez-Valdes, J. A. Gradoli, M. G. Guardia i Llorens, 2025-12-04 doi:10.64898/2025.12.02.691581 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Quantifying the susceptibility of polygenic scores to ancestry stratification ]]> https://biorxiv.org/content/10.64898/2025.12.04.692430v1?rss=1 Blanc, J. Mawass, W. Berg, J. J. 2025-12-04 doi:10.64898/2025.12.04.692430 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Ovarian Hormones and Obesity Drive Th17-mediated Airway Inflammation through Estrogen Receptor Signaling ]]> https://biorxiv.org/content/10.64898/2025.12.02.691857v1?rss=1 Henriquez-Pilier, E. Cephus, J.-Y. Kuehnle, S. N. Tannous, E. Tomasello, A. McKernan, K. E. Peebles, R. S. Cahill, K. N. Rathmell, J. C. Newcomb, D. C. 2025-12-05 doi:10.64898/2025.12.02.691857 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression ]]> https://biorxiv.org/content/10.64898/2025.12.02.691870v1?rss=1 Zhou, Y. D. Wang, P. Schaffer, E. Komnick, M. R. Brown, H. Taylor, G. M. Fiske, K. Sheehan, C. Dermody, T. Muir, A. Esterhazy, D. 2025-12-05 doi:10.64898/2025.12.02.691870 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Exosome secretion is required for sonic hedgehog dispersal and signal gradient formation in the embryonic limb mesenchyme ]]> https://biorxiv.org/content/10.64898/2025.12.05.692671v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@76b266org.highwire.dtl.DTLVardef@ba5b4borg.highwire.dtl.DTLVardef@bf9d67org.highwire.dtl.DTLVardef@1f6d699_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Corcoran, S. Fisher, J. Sanders, T. A. Munro, E. 2025-12-09 doi:10.64898/2025.12.05.692671 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis ]]> https://biorxiv.org/content/10.64898/2025.12.08.693020v1?rss=1 Sadeghi, M. Khan, N. Chen, Y. Jurado, L. F. Sinha, A. Couto, K. Vong, I. Locher, V. Tran, K. A. Bolori Hanafi, S. Thurairajah, B. Shiri, T. J. Ghanem, N. Kaufmann, E. Ming Low, J. Amin, Z. Maurice, C. Kolter, J. Xia, J. Knip, M. Xavier, R. Netea, M. G. King, I. L. Barreiro, L. Thanabalasuriar, A. Singhal, A. Divangahi, M. 2025-12-11 doi:10.64898/2025.12.08.693020 Cold Spring Harbor Laboratory Press 2025-12-11 <![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[ Organelles harbour pH gradients ]]> https://biorxiv.org/content/10.64898/2025.12.12.694065v1?rss=1 Lee, S. Chakraborty, S. Kim, S. Ali, A. Mitra, K. Zajac, M. Brown, A. Pincus, D. Krishnan, Y. 2025-12-16 doi:10.64898/2025.12.12.694065 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Nanopore-based profiling of PEGylation in nucleic acid therapeutics ]]> https://biorxiv.org/content/10.64898/2025.12.15.694309v1?rss=1 Patino Guillen, G. Schmidt, T. T. Baumberg, J. J. Szostak, J. W. Keyser, U. F. Boskovic, F. 2025-12-17 doi:10.64898/2025.12.15.694309 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Parallel Selection for Longevity in Mammals and Birds ]]> https://biorxiv.org/content/10.64898/2025.12.16.694703v1?rss=1 Zhang, W. B. Kronforst, M. R. 2025-12-17 doi:10.64898/2025.12.16.694703 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Conformation-specific Antibody Deciphers K27-linked Ubiquitination in Chaperone-Mediated Proteostasis ]]> https://biorxiv.org/content/10.64898/2025.12.18.695067v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@113b980org.highwire.dtl.DTLVardef@1f7c1a0org.highwire.dtl.DTLVardef@c91656org.highwire.dtl.DTLVardef@1d9a507_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Han, C. Weng, Y. Zheng, Q. Qu, Q. Erramilli, S. K. Su, Z. Duan, Y. Han, Y. Zhai, X. Kossiakoff, A. A. Pan, M. Zhao, M. Liu, L. Yu, Y. 2025-12-18 doi:10.64898/2025.12.18.695067 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Tirzepatide Synergizes with Leptin on Weight Loss and Restoring Metabolic Homeostasis in Diet-induced Obesity Model ]]> https://biorxiv.org/content/10.64898/2025.12.18.695152v1?rss=1 Sun, X. Yin, Y. Song, M. Droz, B. A. Lin, Y. Beaty, K. N. Zhou, B. Roh, H. C. Wilson, J. M. Cain, P. F. Samms, R. J. Sheets, P. L. Ai, M. Ren, H. 2025-12-23 doi:10.64898/2025.12.18.695152 Cold Spring Harbor Laboratory Press 2025-12-23 <![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[ Routing of task-relevant information in mouse PPC during continuousvisuomotor control ]]> https://biorxiv.org/content/10.64898/2025.12.22.696069v1?rss=1 Ravishankar, P. Grier, H. Kaufman, M. T. 2025-12-24 doi:10.64898/2025.12.22.696069 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Influence of phosphate activation chemistry on the selection of the primordial genetic alphabet ]]> https://biorxiv.org/content/10.64898/2025.12.23.696203v1?rss=1 Boskovic, F. Zhang, J. Swatiputra, A. A. Szostak, J. W. 2025-12-25 doi:10.64898/2025.12.23.696203 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ PBX-dependent and independent Hox programs establish and maintain motor neuron terminal Identity ]]> https://biorxiv.org/content/10.64898/2025.12.24.696347v1?rss=1 Prahlad, M. Feng, W. Bat-Erdene, O. Chen, Y. Kratsios, P. 2025-12-26 doi:10.64898/2025.12.24.696347 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons ]]> https://biorxiv.org/content/10.64898/2025.12.26.696633v1?rss=1 Escamilla-del-Arenal, M. Tang, L. C. Kodra, A. Shayya, H. J. Ugurbil, A. C. Stathi, O. Keskin, A. Horta, A. Pulupa, J. M. Ye, J. Jovanovic, M. Lomvardas, S. Duffie, R. 2025-12-27 doi:10.64898/2025.12.26.696633 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Trainable computation in molecular networks ]]> https://biorxiv.org/content/10.64898/2025.12.28.696421v1?rss=1 Trifonova, K. Falk, M. J. Rouches, M. Vaikuntanathan, S. Elowitz, M. B. Murugan, A. 2025-12-30 doi:10.64898/2025.12.28.696421 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[ Development and application of nbLIBRA-seq for high-throughput discovery of antigen-specific nanobodies ]]> https://biorxiv.org/content/10.64898/2025.12.30.697047v1?rss=1 Leonard, S. E. Wasdin, P. T. Webb, K. E. Amlashi, P. B. Rathmell, J. C. Spiller, B. W. Wadzinski, B. E. Georgiev, I. S. Voss, K. 2025-12-31 doi:10.64898/2025.12.30.697047 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Perturbing H-NS function reveals roles in restricting virulence heterogeneity and pathogen adaptation ]]> https://biorxiv.org/content/10.64898/2026.01.01.697318v1?rss=1 McLelland, L. Karki, D. Spratt, M. Burt, M. Zhao, J. Lane, K. 2026-01-02 doi:10.64898/2026.01.01.697318 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Long-range neural pathways for octopus chemotactile processing revealed from periphery-to-brain by centimeter-field microCT ]]> https://biorxiv.org/content/10.64898/2026.01.02.697341v1?rss=1 Vanselow, D. J. Sugarman, A. L. Northover, D. Senft, S. Zaino, C. R. Yakovlev, M. A. Christ, J. M. Silverman, J. Chung, W.-S. La Riviere, P. Hanlon, R. T. Cheng, K. C. Ang, K. C. Ngu, M. S. 2026-01-02 doi:10.64898/2026.01.02.697341 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ An Insoluble De Novo Protein Enables Survival of E. coli by Co-precipitating with a Gene Repressor ]]> https://biorxiv.org/content/10.64898/2026.01.02.697383v1?rss=1 Liao, G. Tao, S. Dessau, J. L. Bann, Y. Hecht, M. H. 2026-01-02 doi:10.64898/2026.01.02.697383 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Trait anxiety is associated with idiosyncratic neural event boundaries during naturalistic movie-watching ]]> https://biorxiv.org/content/10.64898/2026.01.03.697513v1?rss=1 Liu, A. T. H. Chen, J. Park, J. S. Kim, H. Leong, Y. C. 2026-01-04 doi:10.64898/2026.01.03.697513 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1 ]]> https://biorxiv.org/content/10.64898/2026.01.06.697917v1?rss=1 Shen, K. Su, R. Ji, Y. Zhang, W. Liu, X. Chai, X. Wang, J. Liu, B. Li, A. Wu, H. Wang, T. Zhou, X. Jiang, Z. Zhu, H. H. Dong, L. Zhu, Y. Dong, B. Pan, J. Wang, Q. Xue, W. 2026-01-07 doi:10.64898/2026.01.06.697917 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Convergence of Cortical and Thalamic Origins of Free Behavior Modulation of Mouse Primary Visual Cortex ]]> https://biorxiv.org/content/10.64898/2026.01.07.698022v1?rss=1 Yu, P. Yoon, H. Y. A. Yang, Y. Xu, Y. Gozel, O. Tian, G. J. Ji, N. Doiron, B. 2026-01-08 doi:10.64898/2026.01.07.698022 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Indomethacin exerts both cyclooxygenase inhibition-dependent and independent mechanisms to enhance chemo-immunotherapy in mice ]]> https://biorxiv.org/content/10.64898/2026.01.07.698231v1?rss=1 Okoko, O. D. Aboelella, N. S. Ye, Y. Wang, X. Simon, S. E. Gazi, M. Y. Victor J. Enriquez Castro, V. J. Kehinde-Ige, M. Brandle, C. Lv, D. Wolff, D. Hedrick, C. C. Piazza, G. Shi, H. Zhou, G. 2026-01-08 doi:10.64898/2026.01.07.698231 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Dual-mode ClfA-targeting DARPin biologics protect against diverse methicillin-resistant Staphylococcus aureus strains ]]> https://biorxiv.org/content/10.64898/2026.01.09.698026v1?rss=1 Chockalingam, K. Banerjee, B. Zeng, Y. Miao, S. Bryant, J. Missiakas, D. Chen, Z. 2026-01-09 doi:10.64898/2026.01.09.698026 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Predictability of Sleep Slow Oscillation Emergence and Spatial Extent from Pre-Onset Neural Dynamics ]]> https://biorxiv.org/content/10.64898/2026.01.09.698723v1?rss=1 95% accuracy in distinguishing SOs from surrogate events and differentiated Global from Frontal SOs with [~]83% multiclass accuracy, showing further sensitivity improvements when delta power was included. These findings demonstrate that isolated SOs are preceded by structured network dynamics that are tied to their spatial extent. Thus, theta activity can be used to predict SO occurrence and might be leveraged in closed-loop neuromodulation. ]]> Alipour, M. Drongelen, W. v. Malerba, P. Voss, J. Satzer, D. 2026-01-12 doi:10.64898/2026.01.09.698723 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ CRANBERRY: An RNA Dynamics Model with Sugar Puckering and Noncanonical Base Pairing ]]> https://biorxiv.org/content/10.64898/2026.01.12.699131v1?rss=1 Wu, Y. Alessandri, R. Coraor, A. E. Peng, X. Zubieta, P. F. Liebl, K. Trinh, K. Sosnick, T. de Pablo, J. J. 2026-01-13 doi:10.64898/2026.01.12.699131 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Enhancing Predictive Accuracy in Immunotherapy Models through Data Integration and Parameter Identifiability ]]> https://biorxiv.org/content/10.64898/2026.01.12.699041v1?rss=1 Wang, Y. Bergman, D. R. Trujillo, E. Ziblat, A. Fernald, A. A. Li, L. Pearson, A. T. Sweis, R. F. Jackson, T. L. 2026-01-14 doi:10.64898/2026.01.12.699041 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Deep learning-guided design of cell type-specific AAV promoters ]]> https://biorxiv.org/content/10.64898/2026.01.13.699371v1?rss=1 Wang, S. K. Deng, B. Nair, S. Ren, X. Li, J. Tijerina, J. Prakhar, P. Luo, Z. Nnebe, C. Kim, S. H. Zhou, Y. Shah, S. H. Davis, A. Mahajan, R. Qiao, Y. Zhou, Y. Zhang, J. Xue, Y. Goldberg, J. L. Wei, W. Kundaje, A. Chang, H. Y. Wang, S. 2026-01-14 doi:10.64898/2026.01.13.699371 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ The geometry of context-dependent biased decisions during learning ]]> https://biorxiv.org/content/10.64898/2026.01.14.699497v1?rss=1 Nogueira, R. Esteki, S. Fusi, S. Kiani, R. 2026-01-15 doi:10.64898/2026.01.14.699497 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ High-dimensional spatial proteomics and novel machine learning pipeline identifies disease specific renal damage states ]]> https://biorxiv.org/content/10.64898/2026.01.14.699505v1?rss=1 Cao, T. P. Durkee, M. S. Ai, J. Hara, S. Andrade, M. S. Chang, A. Casella, G. Chong, A. S. Giger, M. L. Clark, M. R. 2026-01-15 doi:10.64898/2026.01.14.699505 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Macrophage immunosenescence prolongs intraocular inflammation in aged mice via impaired induction of regulatory T cells ]]> https://biorxiv.org/content/10.64898/2026.01.15.697975v1?rss=1 Yamamoto, T. Hase, K. Lin, J. B. Yamaguchi, S. Misawa, N. Li, J. Kato, K. Terao, R. Sohn, B. S. Du, D. Yoshida, M. Pfeifer, C. W. Lee, T. J. Colasanti, J. Santeford, A. Walsh, J. T. Apte, R. S. 2026-01-20 doi:10.64898/2026.01.15.697975 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ General moment closure for the neutral two-locus Wright-Fisher dynamics ]]> https://biorxiv.org/content/10.64898/2026.01.16.700021v1?rss=1 Kundagrami, R. Yetter, S. Steinruecken, M. 2026-01-20 doi:10.64898/2026.01.16.700021 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Choice of phenotype scale is critical in biobank-based GxE tests ]]> https://biorxiv.org/content/10.64898/2026.01.20.694695v1?rss=1 Costantino, M. Fonseca, R. Liu, Z. Huang, Z. Sankararaman, S. Mathieson, I. Dahl, A. 2026-01-21 doi:10.64898/2026.01.20.694695 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Site-specific integration of transposon via engineered piggyBac transposase ]]> https://biorxiv.org/content/10.64898/2026.01.20.700476v1?rss=1 Xu, N. Han, L. Hu, X. Fang, Y. Wu, L. Wang, X. Tu, H. Cong, W. Sun, K. Jin, Y. Wu, X. 2026-01-21 doi:10.64898/2026.01.20.700476 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Phylogenomics and biogeography of the parrot genus Pyrrhura with implications for systematics and conservation ]]> https://biorxiv.org/content/10.64898/2026.01.21.700815v1?rss=1 Morin-Lagos, J. G. Hains, T. Cerca, J. Wink, M. Pirro, S. Miyaki, C. Y. Hackett, S. J. Bates, J. Martin, M. D. 2026-01-23 doi:10.64898/2026.01.21.700815 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Distinct trajectories of urbanization shape the human gut microbiome across South Asia ]]> https://biorxiv.org/content/10.64898/2026.01.22.701183v1?rss=1 Ramachandran, S. L. Pasupuleti, N. Abdill, R. J. Adikari, G. Ahlawat, B. Blekhman, R. Burgo, V. Davenport, E. R. Dwivedi, A. Gupta, S. Ijinu, T. P. Jamir, T. Karu, R. Kaushik, A. Komarabathini, J. M. Laithangpuii, Lalzarliana, J. Norbu, T. Pautu, T. Pawar, K. Raman, A. S. Ramaswamy, R. Ranasinghe, R. Rashmi, Sasidharan, S. P. Satheesh, T. Shaji, S. Shapiro, J. W. Singh, E. Singson, V. Sundararajan, A. Tennekoon, K. H. Tetso, D. Urban Aragon, J. A. Welikala, A. H. J. Yhome, R. R. Rai, N. Raghavan, M. 2026-01-23 doi:10.64898/2026.01.22.701183 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Polymer-lipid hybrid nanoparticle enhances mRNA delivery and T cell-mediated immunity ]]> https://biorxiv.org/content/10.64898/2026.01.22.701138v1?rss=1 Cai, X. Chen, M. Cao, G. Asby, N. Elli, D. Gula, H. Nicolaescu, V. Nguyen, D.-T. Huang, X. Dangi, T. Solanki, A. Woessner, S. Zhang, W. Tang, E. Volpatti, L. Wallace, R. Pan, T. Nguyen, M. Chen, Q. Geng, Z. Sagar, R. Esser-Khan, A. Penaloza-MacMaster, P. Missiakas, D. Huang, J. 2026-01-24 doi:10.64898/2026.01.22.701138 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ PySteMoDA: An Open Source Python Package for the Analysis of Steered Molecular Dynamics Simulations Data ]]> https://biorxiv.org/content/10.64898/2026.01.26.699872v1?rss=1 Mesbah, I. Klaus, C. Sotomayor, M. Sumbul, F. Rico, F. 2026-01-28 doi:10.64898/2026.01.26.699872 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer ]]> https://biorxiv.org/content/10.64898/2026.01.26.700635v1?rss=1 Della Libera, K. S. Adamowicz, E. M. Muehlbauer, A. Priya, S. Alazizi, A. Luca, F. Blekhman, R. 2026-01-28 doi:10.64898/2026.01.26.700635 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Ancient human genomes from Ladakh reveal Tibetan, South Asian, and Central Asian admixture over the last three millennia ]]> https://biorxiv.org/content/10.64898/2026.01.26.701789v1?rss=1 Rai, N. Ahlawat, B. Dwivedi, A. Gupta, S. Konar, S. Bandyopadhyay, E. Urban Aragon, J. A. Witonsky, D. Rajpal, R. Garg, P. Rashmi, Vuppulury, C. Baghel, P. S. Agrawal, S. Spalzin, S. Ldawa Thsangspa, T. Raghavan, M. 2026-01-28 doi:10.64898/2026.01.26.701789 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ The fossil record of siliceous sponge spicules can be taken at face value ]]> https://biorxiv.org/content/10.64898/2026.01.27.702024v1?rss=1 Cui, S. Y. Mizrahi, N. S. Rahman, S. Nichols, S. A. Karim, T. S. Simpson, C. 2026-01-30 doi:10.64898/2026.01.27.702024 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ IL-6R blockade with tocilizumab disrupts pericyte-and tumor cell-driven IL-6/STAT3 signaling, enhancing docetaxel efficacy in ER+ breast cancer ]]> https://biorxiv.org/content/10.64898/2026.01.29.702661v1?rss=1 Przanowska, R. K. Gomez-Villa, J. Liu, V. J. Antonides-Jensen, N. Visvabharathy, L. Alverdy, J. C. Hernandez, S. L. Yee, S. S. 2026-01-30 doi:10.64898/2026.01.29.702661 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Hydration-Controlled Proton Transport in Respiratory Complex I ]]> https://biorxiv.org/content/10.64898/2026.01.29.702666v1?rss=1 Choi, J. H. Voth, G. A. 2026-01-30 doi:10.64898/2026.01.29.702666 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Optimality with room to vary: stiff and sloppy modes in a sensory population ]]> https://biorxiv.org/content/10.64898/2026.01.30.702802v1?rss=1 Bojanek, K. Marre, O. Palmer, S. 2026-02-02 doi:10.64898/2026.01.30.702802 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ immgenT Treg: A Reference Landscape of Regulatory T Cell States in Mice ]]> https://biorxiv.org/content/10.64898/2026.01.30.702856v1?rss=1 Freuchet, A. Mehrotra, N. Magill, I. Casey, O. Chi, X. Zhang, S. Imianowski, C. J. Huh, J. Vignali, D. A. A. Benoist, C. Zemmour, D. immgenT Project, 2026-02-02 doi:10.64898/2026.01.30.702856 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse ]]> https://biorxiv.org/content/10.64898/2026.01.30.702892v1?rss=1 Magill, I. Casey, O. Mallah, D. Panigrahi, S. S. Zhou, L. Barreiro del Rio, O. Bangs, D. J. Bee, G. C. W. Borys, S. Choi, J. Ergen, C. Ferraj, E. Fiusco, M. Freuchet, A. Galletti, G. Globig, A.-M. Heim, T. Imianowski, C. Lai, R. Liang, Z. Lebron Figueroa, A. Lucas, E. D. Merkenschlager, J. Osum, K. Reilly, S. Shinkawa, T. Thefaine, C. E. Weiss, E. S. Yang, L. Zhang, S. Zorzetto-Fernandes, A. L. Croteau, J. D. Alegre, M.-L. Behar, S. M. Bosselut, R. Brossay, L. Cadwell, K. Chervonsky, A. Gapin, L. Hamilton, S. E. Huh, J. R. Iliev, I. Jabri, B. Jameson, 2026-02-02 doi:10.64898/2026.01.30.702892 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ The αβTCR repertoire at scale in the immgenT dataset ]]> https://biorxiv.org/content/10.64898/2026.01.30.702900v1?rss=1 Croze, M. Yang, L. Candeias, S. Magill, I. Casey, O. Piekarsa, V. Vijaykumar, B. Giudicelli, V. Kossida, S. Zemmour, D. Benoist, C. Project, i. 2026-02-02 doi:10.64898/2026.01.30.702900 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Histotripsy-initiated immune response synergizes with chemotherapy in a neuroblastoma murine model ]]> https://biorxiv.org/content/10.64898/2026.01.30.702878v1?rss=1 Antonides-Jensen, N. Singh, M. Xue, Y. Flores-Guzman, F. Wu, L. L. Yee, S. S. Gomez-Villa, J. Hall, T. L. Applebaum, M. A. Bader, K. B. Hernandez, S. L. 2026-02-03 doi:10.64898/2026.01.30.702878 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Cave evolution on repeat: reuse of the same genomic regions across lineages but not across traits in Astyanax mexicanus ]]> https://biorxiv.org/content/10.64898/2026.01.31.703033v1?rss=1 Richards, E. J. Moran, R. L. Wiese, J. O'Gorman, M. Hutton, P. Rastogi, A. North, O. W. Manning, A. E. Roback, E. Y. Kowalko, J. E. Rohner, N. Keene, A. C. McGaugh, S. E. 2026-02-03 doi:10.64898/2026.01.31.703033 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Distinct neural modes carry information about grasp force and phase in the sensorimotor cortex ]]> https://biorxiv.org/content/10.64898/2026.02.01.702680v1?rss=1 Blumenthal, G. H. Dekleva, B. M. Gontier, C. Gonzalez, I. C. Gonzalez-Martinez, J. A. Yu, B. M. Batista, A. P. Sobinov, A. R. Miller, L. E. Gaunt, R. A. Boninger, M. L. Chase, S. M. Collinger, J. L. 2026-02-03 doi:10.64898/2026.02.01.702680 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ m6A-dependent microRNA binding to chromatin-associated RNA for transcriptional activation ]]> https://biorxiv.org/content/10.64898/2026.02.02.703428v1?rss=1 Zhong, Y. Zheng, L. Li, J. Liu, C. Wei, J. Ye, C. Dou, X. Liu, B. Barbosa, E. Yang, F. Pitroda, S. Chen, M. Weichselbaum, R. He, C. 2026-02-03 doi:10.64898/2026.02.02.703428 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Diverse Microbial Exposure Enhances CD8+ T Cell Effector Memory Output and Function ]]> https://biorxiv.org/content/10.64898/2026.02.02.703037v1?rss=1 Thefaine, C. E. Lucas, E. D. Block, K. E. Pierson, M. Dehm, E. Huggins, M. Casey, O. W. Zemmour, D. Jameson, S. C. Hamilton, S. E. 2026-02-04 doi:10.64898/2026.02.02.703037 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[ Virtual Cells Need Context, Not Just Scale ]]> https://biorxiv.org/content/10.64898/2026.02.04.703804v1?rss=1 Dibaeinia, P. Babu, S. Knudson, M. ElSheikh, A. Wen, Y. Liu, H. Perera, J. Khan, A. A. 2026-02-09 doi:10.64898/2026.02.04.703804 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Assessing extracellular vesicle proteins as predictive biomarkers for developing type 1 diabetes ]]> https://biorxiv.org/content/10.64898/2026.02.06.703600v1?rss=1 Dakup, P. P. Bramer, L. Schepmoes, A. Diaz Ludovico, I. Flores, J. Mirmira, R. Webb-Robertson, B.-J. Metz, T. O. Sims, E. K. Nakayasu, E. S. 2026-02-09 doi:10.64898/2026.02.06.703600 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Noradrenergic neuromodulation produces a NMDAR-dependent network state of respiratory rhythmogenesis in the preBotzinger Complex ]]> https://biorxiv.org/content/10.64898/2026.02.11.705209v1?rss=1 Tryba, A. K. Viemari, J.-C. Wang, Y. Garcia, A. 2026-02-14 doi:10.64898/2026.02.11.705209 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Integrating AI and causal genetics to prioritize therapeutic targets for aging and age-related diseases ]]> https://biorxiv.org/content/10.64898/2026.02.13.705676v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@b94af7org.highwire.dtl.DTLVardef@e89e80org.highwire.dtl.DTLVardef@1fde804org.highwire.dtl.DTLVardef@8b817b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Leung, G. H. D. Chen, J. Ergun, I. A. Izumchenko, E. Aliper, A. Ren, F. Pun, F. W. Zhavoronkov, A. 2026-02-16 doi:10.64898/2026.02.13.705676 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Assessing positive selection in centromere-associated kinetochore proteins across Metazoan groups. ]]> https://biorxiv.org/content/10.64898/2026.02.13.705784v1?rss=1 Healey, H. M. Gomez, L. E. Sheikh, S. I. Camel, B. R. Forbes, A. A. Sterner, K. N. Beck, E. A. 2026-02-18 doi:10.64898/2026.02.13.705784 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Cryo-electron tomography reveals paracellular claudin-15 pores at the tight junction ]]> https://biorxiv.org/content/10.64898/2026.02.19.706806v1?rss=1 Demchenko, E. McGuinness, S. Wood, S. Kainov, J. Pappas, V. Austin, J. Khalili-Araghi, F. Shen, L. Weber, C. R. Hyatt, D. 2026-02-20 doi:10.64898/2026.02.19.706806 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Subdomains of Endophilin-NBAR Can Synergistically Drive Membrane Remodeling and Facilitate Controlled Membrane Scission ]]> https://biorxiv.org/content/10.64898/2026.02.19.706845v1?rss=1 Beiter, J. R. Tsai, F.-C. Bassereau, P. Voth, G. A. 2026-02-20 doi:10.64898/2026.02.19.706845 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Role of staphylococcal EzrA as a molecular organizer of cell division ]]> https://biorxiv.org/content/10.64898/2026.02.20.707072v1?rss=1 Azam, M. S. Pius, T. Missiakas, D. M. 2026-02-21 doi:10.64898/2026.02.20.707072 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ The Kaposi's sarcoma-associated herpesvirus viral genome packaging accessory factor ORF68 forms cytoplasmic puncta dependent on the viral tyrosine kinase ]]> https://biorxiv.org/content/10.64898/2026.02.23.707506v1?rss=1 Gelles-Watnick, S. Liu, D. Cerezo-Matias, M. A. Liu, J. Ospina, G. Schafer, A. Kabeche, L. Cristea, I. M. Didychuk, A. L. 2026-02-23 doi:10.64898/2026.02.23.707506 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines ]]> https://biorxiv.org/content/10.64898/2026.02.23.707528v1?rss=1 Loes, A. N. Tarabi, R. A. Li, S. H. Atkinson, R. K. Huddleston, J. Kikawa, C. Griffths, T. Drapeau, E. M. Wong, S.-S. Cheng, S. M. Leung, N. H. Cobey, S. Cowling, B. J. Bedford, T. Hensley, S. E. Bloom, J. D. 2026-02-23 doi:10.64898/2026.02.23.707528 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ The gene ivory:mir-193 controls scale type differentiation in Heliconius butterflies ]]> https://biorxiv.org/content/10.64898/2026.02.24.707831v1?rss=1 Hanly, J. J. Camino, L. Loh, L. S. Livraghi, L. Gilbert, L. E. Wray, G. A. Martin, A. McMillan, W. O. Holder, J. C. Calderon-Onate, P. Stroh, E. D. Wagh, P. R. Arias, C. F. Ruiz-Moreira, J. Zhao, L. 2026-02-26 doi:10.64898/2026.02.24.707831 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Sex-specific Genetic Regulatory Effects in Chickens ]]> https://biorxiv.org/content/10.64898/2026.02.26.708179v1?rss=1 Zhang, H. Lin, B. Xi, Y. Zhu, D. Peng, C. Tu, J. Liu, H. GUAN, D. Ouyang, Q. Liu, B. Fan, C. Song, Z. Meng, X. Li, H. Zheng, W. Zhu, X. An, B. Li, Z. Wang, Y. Lu, J. Wang, M. Teng, J. Lu, X. Cui, L. Li, B. Guo, S. Song, Z. Xie, K. Li, Y. Madsen, O. Ionita-Laza, I. Wright, D. Godia, M. Xiang, R. Wang, X. Hao, D. Zhang, Q. Yin, Y. Yi, G. Wang, Z. Zhou, C. Wang, Y. Sun, C. Hu, X. Yang, N. Darrington, C. Hsu, S.-H. Zhao, X. Zhou, H. van der Wijst, M. Zeng, J. Liu, L. Shi, S. Hou, Y. Zhao, G. Zhao, P. Fang, L. He, X. 2026-02-28 doi:10.64898/2026.02.26.708179 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ AI-Guided CRISPR Screen Accelerates Discovery of New Drug Targets ]]> https://biorxiv.org/content/10.64898/2026.02.26.708368v1?rss=1 Zhao, C. Shih, M. Ahmed, S. Song, S. Lennon, A. Mayes, J. M. Fan, M. J. Lo, P.-Y. Perera, J. Tutar, A. Kang, A. Warren, E. McClure, R. Khan, A. A. Kelley, S. O. Abdrabou, A. M. 2026-02-28 doi:10.64898/2026.02.26.708368 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation ]]> https://biorxiv.org/content/10.64898/2026.02.27.708613v1?rss=1 Thapa, C. Oh, E. K. Sirkin, D. Lahey, J. Diaz de Leon Guerrerro, S. McCarroll, A. Gowda, P. Zhang, H. Barishman, A. Peyton, L. Zhang, S. Pollak, R. M. Hart, R. P. Pato, C. N. Kreimer, A. Mulle, J. G. Sanders, A. R. Pang, Z. Duan, J. 2026-03-01 doi:10.64898/2026.02.27.708613 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ The emergence of the language system in the toddler brain ]]> https://biorxiv.org/content/10.64898/2026.02.26.707550v1?rss=1 Olson, H. A. Chen, E. M. Osumah, C. J. Du, H. Fedorenko, E. Saxe, R. 2026-03-02 doi:10.64898/2026.02.26.707550 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Core circadian clock genes control molecular and behavioral circatidal rhythms in Parhyale hawaiensis ]]> https://biorxiv.org/content/10.64898/2026.02.27.708297v1?rss=1 Louis, V. Bellido, Z. Helfenbein, A. Rosenthal, J. J. C. Emery, P. 2026-03-02 doi:10.64898/2026.02.27.708297 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Model selection in ADMIXTURE can be inconsistent: proof of the K=2 phenomenon ]]> https://biorxiv.org/content/10.64898/2026.02.27.708651v1?rss=1 Do, D. Terhorst, J. 2026-03-02 doi:10.64898/2026.02.27.708651 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Membrane localisation and checkpoint blockade enhance xenoantigen delivery to redirect pre-existing immunity against tumours ]]> https://biorxiv.org/content/10.64898/2026.03.01.708859v1?rss=1 Briquez, P. S. Hauert, S. Zhou, F. Sidiskis, J. Saxena, A. Goldberger, Z. Chang, K. Kling, C. Koehler, N. Fichtner-Feigl, S. Hubbell, J. A. Jumaa, H. 2026-03-03 doi:10.64898/2026.03.01.708859 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Intestinal intraepithelial lymphocyte migration and tissue homeostasis are dictated by Gα13 ]]> https://biorxiv.org/content/10.64898/2026.03.01.708910v1?rss=1 Earley, Z. M. Rao, A. Knopper, K. Peng, F. Qiu, L. Jo, N. Lisicka, W. Taglinao, H. An, J. Xu, Y. Yang, L. V. Liu, D. Looney, M. R. Cyster, J. G. 2026-03-03 doi:10.64898/2026.03.01.708910 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Learning functional groups in complex microbiomes ]]> https://biorxiv.org/content/10.64898/2026.03.03.709366v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@1f76c74org.highwire.dtl.DTLVardef@f13bdcorg.highwire.dtl.DTLVardef@19107c6org.highwire.dtl.DTLVardef@9558f7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO An integrated ML and experimental pipeline to discover functional groups and their dynamics in complex microbiomes and beyond. (a) First, our Soft Clustering Function Informed (SCiFI) algorithm identifies functional groups directly from species abundances data using neural networks. Crucially, the learned functional groups are informed by a chosen community function. (b) Descriptions of the system in terms of the original high-dimensional abundances of individual species are prohibitively complex (left). By contrast, a description in terms of the few functional groups identified by SCiFI leads to a simple structure-function map (right). (c) Next, the identified groups can be directly input as variables into predictive mathematical models for the dynamics of the community. (d) The last step of our pipeline relies on the identified groups comprising only a small number of species. This sparsity enables targeted experiments that interrogate isolated species (e.g. with whole-genome sequencing or phenotyping) shedding light on the mechanistic underpinnings of the structure-function map with potential applications beyond microbiomes, from gene expression to neuronal activity. C_FIG ]]> Schmitt, M. S. Lee, K. Bunbury, F. Landsittel, J. A. Vitelli, V. Kuehn, S. 2026-03-03 doi:10.64898/2026.03.03.709366 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Hormone signaling and immune programs define differential endocrine responsiveness in high-risk breast tissue ]]> https://biorxiv.org/content/10.64898/2026.03.02.709108v1?rss=1 Goldhammer, N. Bont, M. Warhadpande, S. Choi, M. Cedano, J. Greenwood, H. Ye, J. Schwartz, C. Alvarado, M. Ewing, C. Goodwin, K. Mukhtar, R. Wong, J. Abe, S. Chandler, J. Jackson, J. Olopade, O. Campbell, M. Lam, A. Park, C. Vertido, A. van 't Veer, L. Hylton, N. Esserman, L. Rosenbluth, J. 2026-03-04 doi:10.64898/2026.03.02.709108 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Preventing Disease Emergence Following Eradication: Application to Mpox ]]> https://biorxiv.org/content/10.64898/2026.03.03.709287v1?rss=1 Hirst, C. Deichmann, J. Saha, A. Longini, I. Handel, A. Lipsitch, M. Weissman, D. Antia, R. 2026-03-04 doi:10.64898/2026.03.03.709287 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Consistent EMG encoding during reach and grasp by neurons in motor cortex ]]> https://biorxiv.org/content/10.64898/2026.03.02.709159v1?rss=1 Ciucci, C. Ma, X. Rizzoglio, F. Gasper, E. Sobinov, A. R. Miller, L. E. 2026-03-05 doi:10.64898/2026.03.02.709159 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Network pharmacology-based discovery and experimental validation of novel drug repurposing candidates in Alzheimer's Disease ]]> https://biorxiv.org/content/10.64898/2026.03.05.709917v1?rss=1 Jones, A. Loeffler, T. Wu, E. Varma, V. R. Im, H. K. Thambisetty, M. 2026-03-09 doi:10.64898/2026.03.05.709917 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Placental prostaglandin signaling disrupts barrier integrity and relays an acute inflammatory signal to the fetus. ]]> https://biorxiv.org/content/10.64898/2026.03.11.706681v1?rss=1 Horackova, H. Zhao, Q. Faulkner, S. Alvarez, J. Akiz, C. Liu, Y. Crosthwait, J. Dai, W. Santoyo, D. Pham-Chang, D. Bhinderwala, N. Tagliaferro, T. Wallace, W. Walia, S. Martinovic, J. Baldauf, C. Montagne, A. Bonnin, A. 2026-03-12 doi:10.64898/2026.03.11.706681 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Differential chromatin looping regulated by two GA-binding transcription factors creates an X-specific chromatin environment for dosage compensation ]]> https://biorxiv.org/content/10.64898/2026.03.12.711449v1?rss=1 Aguilera, J. L. Cortez, K. Segarra Alonzo, L. C. Aldana, M. Aragon Vasquez, A. Gray, C. Woodman-Sousa, M. Grive, K. J. Ray, M. Larschan, E. 2026-03-14 doi:10.64898/2026.03.12.711449 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ A Deep Quantitative Proteome Turnover Platform for Human iPSC-derived Neurons ]]> https://biorxiv.org/content/10.64898/2026.03.14.711828v1?rss=1 Hao, L. Frankenfield, A. M. Shih, J. Zhang, T. Ni, J. Mazli, W. N. A. b. Lo, E. Liu, Y. Wang, J. 2026-03-16 doi:10.64898/2026.03.14.711828 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Individuals with Intermittent Explosive Disorder Exhibit Idiosyncratic Neural Responses during Social-emotional Processing ]]> https://biorxiv.org/content/10.64898/2026.03.13.711681v1?rss=1 Chen, J. Keedy, S. Coccaro, E. Leong, Y. C. 2026-03-17 doi:10.64898/2026.03.13.711681 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ A holistic survey of small mammal diversity across an iconic Madrean Sky Island (Santa Catalina Mountains, Arizona, USA) ]]> https://biorxiv.org/content/10.64898/2026.03.15.711934v1?rss=1 Rowsey, D. M. Smith, S. M. Zamora Chavez, L. J. Rivera, D. C. Hess, S. C. Jones, M. F. Bucci, M. E. Mohammadian, S. Alston, J. M. Baez, J. R. Vargas, K. L. Upham, N. S. 2026-03-18 doi:10.64898/2026.03.15.711934 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Sequential experience reshapes population representations in visual cortex ]]> https://biorxiv.org/content/10.64898/2026.03.18.712658v1?rss=1 Kramer, L. E. Cohen, M. R. 2026-03-20 doi:10.64898/2026.03.18.712658 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ A Spatially Structured Spiking Network Model of Beta Traveling Waves and Their Attenuation in Motor Cortex ]]> https://biorxiv.org/content/10.64898/2026.03.18.712701v1?rss=1 Bachschmid-Romano, L. Hatsopoulos, N. Brunel, N. 2026-03-20 doi:10.64898/2026.03.18.712701 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing ]]> https://biorxiv.org/content/10.64898/2026.03.19.709872v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@f7ada7org.highwire.dtl.DTLVardef@a9bab8org.highwire.dtl.DTLVardef@121b695org.highwire.dtl.DTLVardef@5a1dea_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ruiz, E. O. Neyra, K. Lopez, D. Chen, R.-W. Paramasamy, D. Bizjak, Q. Halley, P. D. Wei, Y. Sotomayor, M. Poirier, M. G. Mathur, D. Castro, C. E. Pfeifer, W. G. 2026-03-23 doi:10.64898/2026.03.19.709872 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Overlap in neural representations of coordinated wrist and finger movements in human motor cortex ]]> https://biorxiv.org/content/10.64898/2026.03.19.712976v1?rss=1 Emonds, A. M. Okorokova, E. V. Blumenthal, G. H. Collinger, J. L. Bensmaia, S. J. Miller, L. E. Downey, J. E. Sobinov, A. R. 2026-03-23 doi:10.64898/2026.03.19.712976 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Capping protein regulates the balance of assembly among diverse actin networks in C. elegans zygotes ]]> https://biorxiv.org/content/10.64898/2026.03.23.713757v1?rss=1 Yde, S. E. Suarez, C. Ray, S. Zaidel-Bar, R. Kadzik, R. S. Munro, E. Kovar, D. R. 2026-03-24 doi:10.64898/2026.03.23.713757 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Genetic architectures of brain-related traits are shaped by strong selective constraints ]]> https://biorxiv.org/content/10.64898/2026.03.22.713538v1?rss=1 Zhu, H. Simons, Y. B. Spence, J. P. Sella, G. Pritchard, J. K. 2026-03-25 doi:10.64898/2026.03.22.713538 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Spike-in probe-enhanced single-cell RNA-seq reveals post-infusion transcriptomic remodeling of "prime-and-kill" synNotch-CAR-T cells ]]> https://biorxiv.org/content/10.64898/2026.03.26.713760v1?rss=1 Nejo, T. Watchmaker, P. B. Simic, M. S. Yamamichi, A. Lakshmanachetty, S. Zhao, A. Lu, J. Gallus, M. Benway, H. L. Zhu, R. Almeida, R. Lim, W. A. Okada, H. 2026-03-29 doi:10.64898/2026.03.26.713760 Cold Spring Harbor Laboratory Press 2026-03-29 <![CDATA[ BCAR: A fast and general barcode-sequence mapper for correcting sequencing errors ]]> https://biorxiv.org/content/10.64898/2026.03.27.714882v1?rss=1 Andrews, B. Ranganathan, R. 2026-03-31 doi:10.64898/2026.03.27.714882 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ A Neural Population Code for Value in Human Orbitofrontal Cortex. ]]> https://biorxiv.org/content/10.64898/2026.03.28.715037v1?rss=1 Le Bouc, R. de Hollander, G. 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