bioRxiv Channel: University of California, San Diego https://biorxiv.org This feed contains articles for bioRxiv Channel "University of California, San Diego" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Efficient synergistic single-cell genome assembly ]]> https://biorxiv.org/content/10.1101/002972v1?rss=1 Narjes S. Movahedi Zeinab Taghavi Mallory Embree Harish Nagarajan Karsten Zengler Hamidreza Chitsaz 2014-02-24 doi:10.1101/002972 Cold Spring Harbor Laboratory Press 2014-02-24 <![CDATA[ Inhibition of protein translation by the DISC1-Boymaw fusion gene from a Scottish family with major psychiatric disorders ]]> https://biorxiv.org/content/10.1101/005710v1?rss=1 Baohu Ji Kerin Higa Minjung Kim Lynn Zhou Jared Young Mark Geyer Xianjin Zhou 2014-05-31 doi:10.1101/005710 Cold Spring Harbor Laboratory Press 2014-05-31 <![CDATA[ Boymaw, Overexpressed in Brains with Major Psychiatric Disorders, May Encode a Small Protein to Inhibit Mitochondrial Function and Protein Translation ]]> https://biorxiv.org/content/10.1101/005728v1?rss=1 Baohu Ji Minjung Kim Kerin Higa Xianjin Zhou 2014-05-31 doi:10.1101/005728 Cold Spring Harbor Laboratory Press 2014-05-31 <![CDATA[ Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele ]]> https://biorxiv.org/content/10.1101/017871v1?rss=1 Roy Ronen Glenn Tesler Ali Akbari Shay Zakov Noah A Rosenberg Vineet Bafna 2015-04-10 doi:10.1101/017871 Cold Spring Harbor Laboratory Press 2015-04-10 <![CDATA[ Selection for Intermediate Genotypes Enables a Key Innovation in Phage Lambda ]]> https://biorxiv.org/content/10.1101/018606v1?rss=1 Alita Burmeister Richard Lenski Justin Meyer 2015-04-27 doi:10.1101/018606 Cold Spring Harbor Laboratory Press 2015-04-27 <![CDATA[ Evolution of organismal stoichiometry in a 50,000-generation experiment with Escherichia coli ]]> https://biorxiv.org/content/10.1101/021360v1?rss=1 Caroline B. Turner Brian D. Wade Justin R. Meyer Richard E. Lenski 2015-06-29 doi:10.1101/021360 Cold Spring Harbor Laboratory Press 2015-06-29 <![CDATA[ SSCM: A method to analyze and predict the pathogenicity of sequence variants ]]> https://biorxiv.org/content/10.1101/021527v1?rss=1 Sharad Vikram Matthew D Rasmussen Eric A Evans Imran S Haque 2015-06-26 doi:10.1101/021527 Cold Spring Harbor Laboratory Press 2015-06-26 <![CDATA[ Remodeling of the interphase chromatin domain structures in embryonic stem cells by targeted placement of human-specific regulatory loci ]]> https://biorxiv.org/content/10.1101/022913v1?rss=1 Gennadi Glinsky 2015-07-21 doi:10.1101/022913 Cold Spring Harbor Laboratory Press 2015-07-21 <![CDATA[ Endogenous human stem cell-associated retroviruses ]]> https://biorxiv.org/content/10.1101/024273v1?rss=1 Gennadi Glinsky 2015-08-10 doi:10.1101/024273 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Effects of reference databases’ refinements on the validity of molecular definitions of 15,371 candidate human-specific regulatory sequences ]]> https://biorxiv.org/content/10.1101/026435v1?rss=1 Gennadi Glinsky 2015-09-09 doi:10.1101/026435 Cold Spring Harbor Laboratory Press 2015-09-09 <![CDATA[ Molecular stripping in the NFκB/IκB/DNA genetic regulatory network ]]> https://biorxiv.org/content/10.1101/027912v1?rss=1 Davit Potoyan Weihua Zheng Elizabeth Komives Peter Wolynes 2015-10-02 doi:10.1101/027912 Cold Spring Harbor Laboratory Press 2015-10-02 <![CDATA[ Conservation patterns’ analysis of 18,364 candidate human-specific regulatory sequences revealed two distinct pathways of the human regulatory DNA divergence ]]> https://biorxiv.org/content/10.1101/029975v1?rss=1 Gennadi Glinsky 2015-10-27 doi:10.1101/029975 Cold Spring Harbor Laboratory Press 2015-10-27 <![CDATA[ Frequency and complexity of de novo structural mutation in autism ]]> https://biorxiv.org/content/10.1101/030270v1?rss=1 William M Brandler Danny Antaki Madhusudan Gujral Amina Noor Gabriel Rosanio Timothy R Chapman Daniel J Barrera Guan Ning Lin Dheeraj Malhotra Amanda C Watts Lawrence C Wong Jasper A Estabillo Therese E Gadomski Oanh Hong Karin V Fuentes Fajardo Abhishek Bhandari Renius Owen Michael Baughn Jeffrey Yuan Terry Solomon Alexandra G Moyzis Stephan J Sanders Gail E Reiner Keith K Vaux Charles M Strom Kang Zhang Alysson R Muotri Natacha Akshoomoff Suzanne M Leal Karen Pierce Eric Courchesne Lilia M Iakoucheva Christina Corsello Jonathan Sebat 2015-10-30 doi:10.1101/030270 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Reconstitution of CO2 regulation of SLAC1 anion channel and function of CO2-permeable PIP2;1 aquaporin as carbonic anhydrase 4 interactor ]]> https://biorxiv.org/content/10.1101/030296v1?rss=1 Cun Wang Honghong Hu Xue Qin Brian Zeise Danyun Xu Wouter-Jan Rappel Walter F Boron Julian I Schroeder 2015-11-10 doi:10.1101/030296 Cold Spring Harbor Laboratory Press 2015-11-10 <![CDATA[ Analysis of protein-coding genetic variation in 60,706 humans ]]> https://biorxiv.org/content/10.1101/030338v1?rss=1 Exome Aggregation Consortium Monkol Lek Konrad Karczewski Eric Minikel Kaitlin Samocha Eric Banks Timothy Fennell Anne O'Donnell-Luria James Ware Andrew Hill Beryl Cummings Taru Tukiainen Daniel Birnbaum Jack Kosmicki Laramie Duncan Karol Estrada Fengmei Zhao James Zou Emma Pierce-Hoffman Joanne Berghout David Cooper Nicole Deflaux Mark DePristo Ron Do Jason Flannick Menachem Fromer Laura Gauthier Jackie Goldstein Namrata Gupta Daniel Howrigan Adam Kiezun Mitja Kurki Ami Levy Moonshine Pradeep Natarajan Lorena Orozco Gina Peloso Ryan Poplin Manuel Rivas Valentin Ruano-Rubio Samuel Rose Douglas 2015-10-30 doi:10.1101/030338 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Targeted mutations on 3D hub loci alter spatial interaction environment ]]> https://biorxiv.org/content/10.1101/030999v1?rss=1 Bo Ding Lina Zheng David Medovoy Wei Wang 2015-11-09 doi:10.1101/030999 Cold Spring Harbor Laboratory Press 2015-11-09 <![CDATA[ Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors ]]> https://biorxiv.org/content/10.1101/036665v1?rss=1 Yoshinao Katsu Satomi Kohno Kaori Oka Michael E Baker 2016-01-14 doi:10.1101/036665 Cold Spring Harbor Laboratory Press 2016-01-14 <![CDATA[ Best Practices in Docking and Activity Prediction ]]> https://biorxiv.org/content/10.1101/039446v1?rss=1 Manuel Rueda Ruben Abagyan 2016-02-12 doi:10.1101/039446 Cold Spring Harbor Laboratory Press 2016-02-12 <![CDATA[ Tunable bet hedging in yeast responses to osmotic stress ]]> https://biorxiv.org/content/10.1101/039982v1?rss=1 Yoshikazu Hirate Samuel Bottani Wyming Lee Pang Suzannah Rutherford 2016-02-18 doi:10.1101/039982 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ Combating Chagas Disease Through Inhibition of Tiam1, a Rho GTPase Guanine Nucleotide Exchange Factor ]]> https://biorxiv.org/content/10.1101/040121v1?rss=1 Chirag Krishna Li Xie Philip Bourne Celine DerMarderossian 2016-02-18 doi:10.1101/040121 Cold Spring Harbor Laboratory Press 2016-02-18 <![CDATA[ A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects ]]> https://biorxiv.org/content/10.1101/040493v1?rss=1 Christian Marshall Daniel Howrigan Daniele Merico Bhooma Thiruvahindrapuram Wenting Wu Douglas Greer Daniel Antaki Aniket Shetty Peter Holmans Dalila Pinto Madhusudan Gujral William Brandler Dheeraj Malholtra Zhouzhi Wang Karin Fuentes Fajarado Stephan Ripke Ingrid Agartz Esben Agerbo Margot Albus Madeline Alexander Farooq Amin Joshua Atkins Silviu Bacanu Richard Belliveau Sarah Bergen Marcelo Bertalan Elizabeth Bevilacqua Tim Bigdeli Donald Black Richard Bruggeman Nancy Buccola Randy Buckner Brendan Bulik-Sullivan William Byerley Wiepke Cahn Guiqing Cai Murray Cairns Dominique Campion Rita Ca 2016-02-23 doi:10.1101/040493 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Microarray analysis identifies malignant field signatures in biopsy samples at diagnosis predicting the likelihood of lethal disease in patients with localized Gleason 6 and 7 prostate cancer. ]]> https://biorxiv.org/content/10.1101/040519v1?rss=1 Gennadi Glinsky 2016-02-21 doi:10.1101/040519 Cold Spring Harbor Laboratory Press 2016-02-21 <![CDATA[ Hierarchical cortical transcriptome disorganization in autism ]]> https://biorxiv.org/content/10.1101/042937v1?rss=1 Michael V Lombardo Eric Courchesne Nathan E Lewis Tiziano Pramparo 2016-03-10 doi:10.1101/042937 Cold Spring Harbor Laboratory Press 2016-03-10 <![CDATA[ A method for downstream analysis of gene set enrichment results facilitates the biological interpretation of vaccine efficacy studies ]]> https://biorxiv.org/content/10.1101/043158v1?rss=1 Yan Tan Jernej Godec Felix Wu Pablo Tamayo Jill P Mesirov W Nicholas Haining 2016-04-11 doi:10.1101/043158 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Finding De novo methylated DNA motifs ]]> https://biorxiv.org/content/10.1101/043810v1?rss=1 Vu Ngo Wei Wang 2016-03-15 doi:10.1101/043810 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Testing pseudo-linear models of responses to natural scenes in primate retina ]]> https://biorxiv.org/content/10.1101/045336v1?rss=1 Alexander Heitman Nora Brackbill Martin Greschner Alexander Sher Alan M. Litke E.J. Chichilnisky 2016-03-24 doi:10.1101/045336 Cold Spring Harbor Laboratory Press 2016-03-24 <![CDATA[ Zfp423 regulates Sonic hedgehog signaling via primary cilium function ]]> https://biorxiv.org/content/10.1101/046961v1?rss=1 CHEN-JEI HONG Bruce A. Hamilton 2016-04-05 doi:10.1101/046961 Cold Spring Harbor Laboratory Press 2016-04-05 <![CDATA[ Assembly of Long Error-Prone Reads Using de Bruijn Graphs ]]> https://biorxiv.org/content/10.1101/048413v1?rss=1 Yu Lin Jeffrey Yuan Mikhail Kolmogorov Max W. Shen Pavel A. Pevzner 2016-04-13 doi:10.1101/048413 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/048942v1?rss=1 Dmitry Antipov Nolan Hartwick Max Shen Mikhail Raiko Alla Lapidus Pavel Pevzner 2016-04-15 doi:10.1101/048942 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Omics Discovery Index - Discovering and Linking Public Omics Datasets ]]> https://biorxiv.org/content/10.1101/049205v1?rss=1 Yasset Perez-Riverol Mingze Bai Felipe Leprevost Silvano Squizzato Young Mi Park Ove Kenneth Haug Adam J. Carroll Dylan Spalding Justin Paschall Mingxun Wang Noemi del-Toro Tobias Ternent Peng Zhang Nicola Buso Nuno Bandeira Eric Deutsch David S. Campbell Ronald C. Beavis Reza Salek Alexey Nesvizhskii Susanna-Assunta Sansone Christoph Steinbeck Rodrigo Lopez Juan Antonio Vizcaino Peipei Ping Henning Hermjakob 2016-04-18 doi:10.1101/049205 Cold Spring Harbor Laboratory Press 2016-04-18 <![CDATA[ Nonsinusoidal oscillations underlie pathological phase-amplitude coupling in the motor cortex in Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/049304v1?rss=1 Scott R Cole Erik J Peterson Roemer van der Meij Coralie de Hemptinne Philip A Starr Bradley Voytek 2016-04-19 doi:10.1101/049304 Cold Spring Harbor Laboratory Press 2016-04-19 <![CDATA[ Membrane tension is a key determinant of bud morphology in clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/050484v1?rss=1 Julian E. Hassinger George Oster David G. Drubin Padmini Rangamani 2016-04-27 doi:10.1101/050484 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Subiculum neurons map the current axis of travel ]]> https://biorxiv.org/content/10.1101/050641v1?rss=1 Jacob M Olson Kanyanat Tongprasearth Douglas M Nitz 2016-04-27 doi:10.1101/050641 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Reduced spatial integration in the ventral visual cortex underlies face recognition deficits in developmental prosopagnosia ]]> https://biorxiv.org/content/10.1101/051102v1?rss=1 Nathaniel Witthoft Sonia Poltoratski Mai Nguyen Golijeh Golarai Alina Liberman Karen F LaRocque Mary E Smith Kalanit Grill-Spector 2016-04-29 doi:10.1101/051102 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Separating spandrels from phenotypic targets of selection in adaptive molecular evolution ]]> https://biorxiv.org/content/10.1101/051862v1?rss=1 Stevan A Springer Michael Manhart Alexandre V Morozov 2016-05-05 doi:10.1101/051862 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Corticosteroid and progesterone transactivation of mineralocorticoid receptors from Amur sturgeon and tropical gar ]]> https://biorxiv.org/content/10.1101/053199v1?rss=1 Akira Sugimoto Kaori Oka Rui Sato Shinji Adachi Michael E. Baker Yoshinao Katsu 2016-05-13 doi:10.1101/053199 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ Transformation of Independent Oscillatory Inputs into Temporally Precise Rate Codes ]]> https://biorxiv.org/content/10.1101/054163v1?rss=1 David Tingley Andrew Alexander Laleh Quinn Andrea Chiba Douglas Nitz 2016-05-18 doi:10.1101/054163 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Scanning the Horizon: challenges and solutions for neuroimaging research ]]> https://biorxiv.org/content/10.1101/059188v1?rss=1 Russell Poldrack Chris I Baker Joke Durnez Krzysztof Gorgolewski Paul M Matthews Marcus Munafo Thomas Nichols Jean-Baptiste Poline Edward Vul Tal Yarkoni 2016-06-16 doi:10.1101/059188 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution ]]> https://biorxiv.org/content/10.1101/060756v1?rss=1 74%) of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on our previous findings, we repeated our analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support our published inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis. ]]> Tomislav Domazet-Loso Anne-Ruxanda Carvunis M. Mar Alba Matin S Sestak Robert Bakaric Rafik Neme Diethard Tautz 2016-06-26 doi:10.1101/060756 Cold Spring Harbor Laboratory Press 2016-06-26 <![CDATA[ Evaluating the diagnostic utility of applying a machine learning algorithm to diffusion tensor MRI measures in individuals with major depressive disorder ]]> https://biorxiv.org/content/10.1101/061119v1?rss=1 David M Schnyer Peter G Clasen Christopher Gonzalez Christopher G Beevers 2016-06-29 doi:10.1101/061119 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Preparatory encoding of the fine scale of human spatial attention ]]> https://biorxiv.org/content/10.1101/061259v1?rss=1 Bradley Voytek Jason Samaha Camarin E Rolle Zachery Greenberg Navdeep Gill Shai Porat Tahim Kader Sabahat Rahman Rick Malzyner Adam Gazzaley 2016-06-29 doi:10.1101/061259 Cold Spring Harbor Laboratory Press 2016-06-29 <![CDATA[ Assessment of single cell RNA-seq normalization methods ]]> https://biorxiv.org/content/10.1101/064329v1?rss=1 Bo Ding Lina Zheng Wei Wang 2016-07-17 doi:10.1101/064329 Cold Spring Harbor Laboratory Press 2016-07-17 <![CDATA[ Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/064683v1?rss=1 Michael V Lombardo Hyang Mi Moon Jennifer Su Theo D Palmer Eric Courchesne Tiziano Pramparo 2016-07-19 doi:10.1101/064683 Cold Spring Harbor Laboratory Press 2016-07-19 <![CDATA[ Mutations in EBF3 disturb transcriptional profiles and underlie a novel syndrome of intellectual disability, ataxia and facial dysmorphism ]]> https://biorxiv.org/content/10.1101/067454v1?rss=1 Frederike Leonie Harms Katta Mohan Girisha Andrew Alexander Hardigan Fanny Kortum Anju Shukla Malik Alawi Ashwin Dalal Lauren Brady Mark Tarnopolsky Lynne M. Bird Sophia Ceulemans Martina Bebin Kevin M. Bowling Susan M. Hiatt Edward J. Lose Michelle Primiano Wendy K. Chung Jane Juusola Zeynep C. Akdemir Matthew Bainbridge Wu-Lin Charng Margaret Drummond-Borg Mohammad K. Eldomery Ayman W. El-Hattab Mohammed A.M. Saleh Stephane Bezieau Benjamin Cogne Bertrand Isidor Sebastien Kury James R. Lupski Richard M. Myers Gregory M. Cooper Kerstin Kutsche 2016-08-03 doi:10.1101/067454 Cold Spring Harbor Laboratory Press 2016-08-03 <![CDATA[ Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes ]]> https://biorxiv.org/content/10.1101/072470v1?rss=1 Morgan N Price Kelly M Wetmore Robert Jordan Waters Mark Callaghan Jayashree Ray Jennifer V Kuehl Ryan A Melnyk Jacob S Lamson Yumi Suh Zuelma Esquivel Harini Sadeeshkumar Romy Chakraborty Benjamin E Rubin James Bristow Matthew J Blow Adam P Arkin Adam M Deutschbauer 2016-08-31 doi:10.1101/072470 Cold Spring Harbor Laboratory Press 2016-08-31 <![CDATA[ A living vector field reveals constraints on galactose network induction in yeast ]]> https://biorxiv.org/content/10.1101/073817v1?rss=1 Sarah R. Stockwell Scott A. Rifkin 2016-09-06 doi:10.1101/073817 Cold Spring Harbor Laboratory Press 2016-09-06 <![CDATA[ Assessing data quality in citizen science - preprint ]]> https://biorxiv.org/content/10.1101/074104v1?rss=1 Margaret Kosmala Andrea Wiggins Alexandra Swanson Brooke Simmons 2016-09-08 doi:10.1101/074104 Cold Spring Harbor Laboratory Press 2016-09-08 <![CDATA[ MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQ ]]> https://biorxiv.org/content/10.1101/074294v1?rss=1 Rongxin Fang Miao Yu Guoqiang Li Sora Chee Tristin Liu Anthony Schmitt Bing Ren 2016-09-09 doi:10.1101/074294 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Predicting binding free energies: Frontiers and benchmarks ]]> https://biorxiv.org/content/10.1101/074625v1?rss=1 David L. Mobley Michael K. Gilson 2016-09-11 doi:10.1101/074625 Cold Spring Harbor Laboratory Press 2016-09-11 <![CDATA[ A large collection of novel nematode-infecting microsporidia and their diverse interactions with C. elegans and other related nematodes ]]> https://biorxiv.org/content/10.1101/074757v1?rss=1 Gaotian Zhang Martin Sachse Marie-Christine Prevost Robert J Luallen Emily Troemel Marie-Anne Felix 2016-09-12 doi:10.1101/074757 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ Personalized genetic assessment of age associated Alzheimers disease risk ]]> https://biorxiv.org/content/10.1101/074864v1?rss=1 Rahul S. Desikan Chun Chieh Fan Yunpeng Wang Andrew J. Schork Howard J. Cabral Adrienne Cupples Wesley K. Thompson Lilah Besser Walter A. Kukull Dominic Holland Chi-Hua Chen James B. Brewer David S. Karow Karolina Kauppi Aree Witoelar Celeste M. Karch Luke W. Bonham Jennifer S. Yokoyama Howard J. Rosen Bruce L. Miller William P. Dillon David M. Wilson Christopher P. Hess Margaret Pericak-Vance Jonathan L. Haines Lindsay A. Farrer Richard Mayeux John Hardy Alison M. Goate Bradley T. Hyman Gerard D. Schellenberg Linda K. McEvoy Ole A. Andreassen Anders N. Dale 2016-09-13 doi:10.1101/074864 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset ]]> https://biorxiv.org/content/10.1101/077248v1?rss=1 Michael R. Shirts Christoph Klein Jason M. Swails Jian Yin Michael K. Gilson David L. Mobley David A. Case Ellen D. Zhong 2016-09-25 doi:10.1101/077248 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ Genome-wide profiling of heritable and de novo STR variations ]]> https://biorxiv.org/content/10.1101/077727v1?rss=1 Thomas Willems Dina Zielinski Assaf Gordon Melissa Gymrek Yaniv Erlich 2016-09-27 doi:10.1101/077727 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria ]]> https://biorxiv.org/content/10.1101/079137v1?rss=1 Kevin S Bonham Benjamin E Wolfe Rachel J Dutton 2016-10-05 doi:10.1101/079137 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP ]]> https://biorxiv.org/content/10.1101/080929v1?rss=1 Kim, D. Seo, S. W. Nam, H. Guzman, G. I. Gao, Y. Palsson, B. O. 2016-10-16 doi:10.1101/080929 Cold Spring Harbor Laboratory Press 2016-10-16 <![CDATA[ Field Potential Reflects the Balance of Synaptic Excitation and Inhibition ]]> https://biorxiv.org/content/10.1101/081125v1?rss=1 Gao, R. D. Peterson, E. J. Voytek, B. 2016-10-14 doi:10.1101/081125 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ p53 dynamically directs TFIID assembly on target gene promoters ]]> https://biorxiv.org/content/10.1101/083014v1?rss=1 Coleman, R. A. Qiao, Z. Singh, S. K. Peng, C. S. Cianfrocco, M. Zhang, Z. Song, L. Piasecka, A. Aldeborgh, H. Basishvili, G. Rice, W. Liu, W.-L. 2016-10-24 doi:10.1101/083014 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ Spatial tuning shifts increase the discriminability and fidelity of population codes in visual cortex ]]> https://biorxiv.org/content/10.1101/086892v1?rss=1 Vo, V. A. Sprague, T. Serences, J. 2016-11-10 doi:10.1101/086892 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ Modulation of Body Mass Composition using Vestibular Nerve Stimulation. ]]> https://biorxiv.org/content/10.1101/087692v1?rss=1 McGeoch, P. D. McKeown, J. Ramachandran, V. S. 2016-11-14 doi:10.1101/087692 Cold Spring Harbor Laboratory Press 2016-11-14 <![CDATA[ Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations ]]> https://biorxiv.org/content/10.1101/088815v1?rss=1 Duncan, L. Yilmaz, Z. Walters, R. Goldstein, J. Antilla, V. Bulik-Sullivan, B. Ripke, S. Adan, R. Alfredsson, L. Ando, T. Andreassen, O. Aschauer, H. Baker, J. Barrett, J. Bencko, V. Bergen, A. Berrettini, W. Birgegard, A. Boni, C. Boraska Perica, V. Brandt, H. Bughardt, R. Carlberg, L. Cassina, M. Cesta, C. Cichon, S. Clementi, M. Cohen-Woods, S. Coleman, J. Cone, R. Courtet, P. Crawford, S. Crow, S. Crowley, J. Danner, U. Davis, O. de Zaan, M. Dedoussis, G. Degortes, D. DeSocio, J. Dick, D. Dikeos, D. Dina, C. Ding, B. Dmitrzak-Weglarz, M. Docampo 2016-11-25 doi:10.1101/088815 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ A genetic risk score to guide age-specific, personalized prostate cancer screening ]]> https://biorxiv.org/content/10.1101/089383v1?rss=1 Seibert, T. M. Fan, C. C. Wang, Y. Zuber, V. Karunamuni, R. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Nielsen, S. F. Weischer, M. Bisbjerg, R. Roder, M. A. Iversen, P. Key, T. J. Travis, R. C. Neal, D. E. Donovan, J. L. Hamdy, F. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, L. Brenner, H. 2016-11-25 doi:10.1101/089383 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls ]]> https://biorxiv.org/content/10.1101/092163v1?rss=1 Buckley, A. R. Standish, K. A. Bhutani, K. Ideker, T. Harismendy, O. Carter, H. Schork, N. J. 2016-12-07 doi:10.1101/092163 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Incorporating the Rate of Transcriptional Change Improves Construction of Transcription Factor Regulatory Networks ]]> https://biorxiv.org/content/10.1101/093807v1?rss=1 Desai, J. Sartor, R. C. Lawas, L. M. Jagadish SV, K. Doherty, C. J. 2016-12-24 doi:10.1101/093807 Cold Spring Harbor Laboratory Press 2016-12-24 <![CDATA[ A Data Citation Roadmap for Scholarly Data Repositories ]]> https://biorxiv.org/content/10.1101/097196v1?rss=1 Fenner, M. Crosas, M. Grethe, J. Kennedy, D. Hermjakob, H. Rocca-Serra, P. Berjon, R. Karcher, S. Martone, M. Clark, T. 2016-12-28 doi:10.1101/097196 Cold Spring Harbor Laboratory Press 2016-12-28 <![CDATA[ Polymer dynamics of Alp7A reveals two ‘critical’ concentrations that govern dynamically unstable actin-like proteins ]]> https://biorxiv.org/content/10.1101/098954v1?rss=1 Petek, N. A. Derman, A. I. Royal, J. A. Pogliano, J. Mullins, D. 2017-01-10 doi:10.1101/098954 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ Comprehensive characterization of neutrophil genome topology ]]> https://biorxiv.org/content/10.1101/100198v1?rss=1 Zhu, Y. Gong, K. Denholtz, M. Chandra, V. Kamps, M. P. Alber, F. Murre, C. 2017-01-15 doi:10.1101/100198 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Uniform Resolution of Compact Identifiers for Biomedical Data ]]> https://biorxiv.org/content/10.1101/101279v1?rss=1 Wimalaratne, S. Juty, N. Kunze, J. Janee, G. McMurry, J. A. Beard, N. Jimenez, R. Grethe, J. Hermjakob, H. Clark, T. 2017-01-18 doi:10.1101/101279 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Paternally inherited noncoding structural variants contribute to autism ]]> https://biorxiv.org/content/10.1101/102327v1?rss=1 Brandler, W. M. Antaki, D. Gujral, M. Kleiber, M. L. Maile, M. S. Hong, O. Chapman, T. R. Tan, S. Tandon, P. Pang, T. Tang, S. C. Vaux, K. K. Yang, Y. Harrington, E. Juul, S. Turner, D. J. Kingsmore, S. F. Gleeson, J. G. Kakaradov, B. Telenti, A. Venter, J. C. Corominas, R. Cormand, B. Rueda, I. Messer, K. S. Nievergelt, C. M. Arranz, M. J. Courchesne, E. Pierce, K. Muotri, A. R. Iakoucheva, L. M. Hervas, A. Corsello, C. Sebat, J. 2017-03-29 doi:10.1101/102327 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ A toolkit for tissue-specific protein degradation in C. elegans ]]> https://biorxiv.org/content/10.1101/104398v1?rss=1 Wang, S. Tang, N. H. Lara-Gonzalez, P. Prevo, B. Cheerambathur, D. K. Chisholm, A. D. Desai, A. Oegema, K. 2017-01-30 doi:10.1101/104398 Cold Spring Harbor Laboratory Press 2017-01-30 <![CDATA[ Preprint: Environmentally-Friendly Workflow Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking For the Discovery of Potent Anti-Viral Leads From Plants ]]> https://biorxiv.org/content/10.1101/106153v1?rss=1 nView larger version (23K):norg.highwire.dtl.DTLVardef@191802aorg.highwire.dtl.DTLVardef@1755ab8org.highwire.dtl.DTLVardef@196edf5org.highwire.dtl.DTLVardef@1e0a1e0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nothias, L.-F. Boutet-Mercey, S. Cachet, X. De La Torre, E. Laboureur, L. Gallard, J.-F. Retailleau, P. Brunelle, A. Dorrestein, P. C. Costa, J. Bedoya, L. M. Roussi, F. Leyssen, P. Alcami, J. Paolini, J. Litaudon, M. Touboul, D. 2017-02-05 doi:10.1101/106153 Cold Spring Harbor Laboratory Press 2017-02-05 <![CDATA[ Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism ]]> https://biorxiv.org/content/10.1101/107425v1?rss=1 Du, B. Zielinski, D. C. Palsson, B. O. 2017-02-09 doi:10.1101/107425 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ Modeling prediction error improves power of transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/108316v1?rss=1 Bhutani, K. Sarkar, A. Park, Y. Kellis, M. Schork, N. J. 2017-02-14 doi:10.1101/108316 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ Significance estimation for large scale untargeted metabolomics annotations ]]> https://biorxiv.org/content/10.1101/109389v1?rss=1 Scheubert, K. Hufsky, F. Petras, D. Wang, M. Nothias, L.-F. Duehrkop, K. Bandeira, N. Dorrestein, P. Boecker, S. 2017-02-17 doi:10.1101/109389 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories ]]> https://biorxiv.org/content/10.1101/113050v1?rss=1 Giraldez, M. D. Spengler, R. M. Etheridge, A. Godoy, P. M. Barczak, A. J. Srinivasan, S. De Hoff, P. L. Tanriverdi, K. Courtright, A. Lu, S. Khoory, J. Rubio, R. Baxter, D. Driedonks, T. A. P. Buermans, H. P. J. Nolte-'t Hoen, E. N. M. Jiang, H. Wang, K. Ghiran, I. Wang, Y. Van Keuren-Jensen, K. Freedman, J. E. Woodruff, P. G. Laurent, L. C. Erle, D. J. Galas, D. J. Tewari, M. 2017-05-17 doi:10.1101/113050 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ A yield-cost tradeoff governs Escherichia coli's decision between fermentation and respiration in carbon-limited growth ]]> https://biorxiv.org/content/10.1101/113183v1?rss=1 Mori, M. Marinari, E. De Martino, A. 2017-03-02 doi:10.1101/113183 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Decoys reveal the genetic and biochemical roles of redundant plant E3 ubiquitin ligases ]]> https://biorxiv.org/content/10.1101/115071v1?rss=1 Lee, C.-M. Feke, A. Adamchek, C. Webb, K. Pruneda-Paz, J. Bennett, E. J. Kay, S. A. Gendron, J. M. 2017-03-11 doi:10.1101/115071 Cold Spring Harbor Laboratory Press 2017-03-11 <![CDATA[ Optimizing Pedigrees: Using a Biasing System to Determine Likely Inheritance Systems ]]> https://biorxiv.org/content/10.1101/116160v1?rss=1 Ang, J. Y. 2017-03-15 doi:10.1101/116160 Cold Spring Harbor Laboratory Press 2017-03-15 <![CDATA[ Cysteine Proteases Of Hookworm Necator Americanus As Virulence Factors And Implications For Future Drug Design: A Bioinformatics-Based Study ]]> https://biorxiv.org/content/10.1101/116921v1?rss=1 Banerjee, A. 2017-03-17 doi:10.1101/116921 Cold Spring Harbor Laboratory Press 2017-03-17 <![CDATA[ Guiding the design of bacterial signaling interactions using a coevolutionary landscape ]]> https://biorxiv.org/content/10.1101/116947v1?rss=1 Cheng, R. R. Haglund, E. Tiee, N. Morcos, F. Levine, H. Adams, J. A. Jennings, P. A. Onuchic, J. N. 2017-03-16 doi:10.1101/116947 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Genetic Variation In Adaptability And Pleiotropy In Budding Yeast ]]> https://biorxiv.org/content/10.1101/121749v1?rss=1 Jerison, E. R. Kryazhimskiy, S. Mitchell, J. Bloom, J. S. Kruglyak, L. Desai, M. M. 2017-03-29 doi:10.1101/121749 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ The ubiquity of directional and reciprocating motion in enzymes out of equilibrium ]]> https://biorxiv.org/content/10.1101/121848v1?rss=1 Slochower, D. R. Gilson, M. K. 2017-04-19 doi:10.1101/121848 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures ]]> https://biorxiv.org/content/10.1101/122689v1?rss=1 Bradley, A. R. Rose, A. S. Pavelka, A. Valasatava, Y. Duarte, J. M. Prlic, A. Rose, P. W. 2017-04-05 doi:10.1101/122689 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Four-Sphere Head Model For EEG Signals Revisited ]]> https://biorxiv.org/content/10.1101/124875v1?rss=1 Naess, S. Chintaluri, C. Ness, T. B. Dale, A. M. Einevoll, G. T. Wojcik, D. K. 2017-04-06 doi:10.1101/124875 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ A Versatile Genetic Tool For Post-Translational Control Of Gene Expression With A Small Molecule In Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/130120v1?rss=1 Sethi, S. Wang, J. W. 2017-04-24 doi:10.1101/130120 Cold Spring Harbor Laboratory Press 2017-04-24 <![CDATA[ Evolutionarily Conserved Roles For Blood-Brain Barrier Xenobiotic Transporters In Endogenous Steroid Partitioning And Behavior ]]> https://biorxiv.org/content/10.1101/131698v1?rss=1 Hindle, S. Munji, R. Dolghih, E. Gaskins, G. Orng, S. Ishimoto, H. Soung, A. DeSalvo, M. Kitamoto, T. Keiser, M. Jacobson, M. Daneman, R. Bainton, R. 2017-04-29 doi:10.1101/131698 Cold Spring Harbor Laboratory Press 2017-04-29 <![CDATA[ Diagnostic, Infection Timing and Incidence Surveillance Applications of High Dynamic Range Chemiluminescent HIV Immuno-Assay Platforms ]]> https://biorxiv.org/content/10.1101/132332v1?rss=1 Grebe, E. Welte, A. Hall, J. Keating, S. M. Facente, S. N. Marson, K. Martin, J. N. Little, S. J. Price, M. A. Kallas, E. G. Busch, M. P. Pilcher, C. D. Murphy, G. CEPHIA, 2017-05-03 doi:10.1101/132332 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ FCS In Closed Systems And Application For Membrane Nanotubes ]]> https://biorxiv.org/content/10.1101/134742v1?rss=1 Jiang, Y. Melnykov, A. Elson, E. L. 2017-05-05 doi:10.1101/134742 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Convergence of Wnt, Growth Factor and Trimeric G protein signals on Daple ]]> https://biorxiv.org/content/10.1101/137125v1?rss=1 Aznar, N. Dunkel, Y. Sun, N. Satterfield, K. He, F. Lopez-Sanchez, I. Ghassemian, M. Sahoo, D. Kufareva, I. Ghosh, P. 2017-06-12 doi:10.1101/137125 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Mapping The Malaria Parasite Drug-Able Genome Using In Vitro Evolution And Chemogenomics ]]> https://biorxiv.org/content/10.1101/139386v1?rss=1 Cowell, A. N. Istvan, E. S. Lukens, A. K. Gomez-Lorenzo, M. G. Vanaerschot, M. Sakata-Kato, T. Flannery, E. L. Magistrado, P. Abraham, M. Lamonte, G. M. Williams, R. M. Franco, V. Arriago, I. Linares, M. Bopp, S. Corey, V. Gnadig, N. F. Coburn-Flynn, O. Reimer, C. Gupta, P. Murithi, J. M. Fuchs, O. Sasaki, E. Kim, S. W. Teng, C. Wang, L. T. Willis, P. Siegel, D. Tanaseichuk, O. Zhong, Y. Zhou, Y. Otillie, S. Gamo, F.-J. Lee, M. C. S. Goldberg, D. E. Fidock, D. A. Wirth, D. F. Winzeler, E. A. 2017-05-22 doi:10.1101/139386 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements ]]> https://biorxiv.org/content/10.1101/141028v1?rss=1 Zhou, H. Kolodner, R. Putnam, C. D. Liang, J. Li, B.-z. Tan, A. P. 2017-05-23 doi:10.1101/141028 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ Forces driving cell sorting in Hydra ]]> https://biorxiv.org/content/10.1101/142976v1?rss=1 Cochet-Escartin, O. Locke, T. T. Shi, W. H. Steele, R. E. Collins, E.-M. S. 2017-05-27 doi:10.1101/142976 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ An Intracellular Pathogen Response Pathway Promotes Proteostasis In C. elegans ]]> https://biorxiv.org/content/10.1101/145235v1?rss=1 Reddy, K. C. Dror, T. Sowa, J. N. Panek, J. Chen, K. Lim, E. S. Wang, D. Troemel, E. R. 2017-06-02 doi:10.1101/145235 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ LSD1/KDM1A Maintains Genome-wide Homeostasis of Transcriptional Enhancers ]]> https://biorxiv.org/content/10.1101/146357v1?rss=1 Agarwal, S. Garay, P. M. Porter, R. S. Brookes, E. Murata-Nakamura, Y. Macfarlan, T. S. Ren, B. Iwase, S. 2017-06-05 doi:10.1101/146357 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ Homology-based hydrogen bond information improves crystallographic structures in the PDB ]]> https://biorxiv.org/content/10.1101/147231v1?rss=1 van Beusekom, B. Touw, W. G. Tatineni, M. Somani, S. Rajagopal, G. Luo, J. Gilliland, G. L. Perrakis, A. Joosten, R. P. 2017-06-07 doi:10.1101/147231 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ PinAPL-Py: a web-service for the analysis of CRISPR-Cas9 Screens ]]> https://biorxiv.org/content/10.1101/147462v1?rss=1 Spahn, P. N. Bath, T. Weiss, R. J. Kim, J. Esko, J. D. Lewis, N. E. Harismendy, O. 2017-06-08 doi:10.1101/147462 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ Akt/PKB enhances non-canonical Wnt signals by compartmentalizing β-Catenin ]]> https://biorxiv.org/content/10.1101/149351v1?rss=1 Aznar, N. Sun, N. Dunkel, Y. Ear, J. Buschman, M. Ghosh, P. 2017-06-13 doi:10.1101/149351 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/150581v1?rss=1 Sarkar, P. Switzer, A. Peters, C. Pogliano, J. Wigneshweraraj, S. 2017-06-15 doi:10.1101/150581 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Amyloid accumulation drives proteome-wide alterations in mouse models of Alzheimers disease like pathology ]]> https://biorxiv.org/content/10.1101/150623v1?rss=1 Savas, J. N. Wang, Y.-Z. DeNardo, L. A. Martinez-Bartolome, S. McClatchy, D. B. Hark, T. J. Shanks, N. F. Cozzolino, K. A. Lavallee-Adam, M. Smukowski, S. N. Park, S. K. Kelly, J. W. Koo, E. H. Nakagawa, T. Masliah, E. Ghosh, A. Yates, J. R. 2017-06-15 doi:10.1101/150623 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Enhanced cross-modal activation of sensory cortex in mouse models of autism ]]> https://biorxiv.org/content/10.1101/150839v1?rss=1 Hattori, R. Südhof, T. C. Yamakawa, K. Hensch, T. K. 2017-08-20 doi:10.1101/150839 Cold Spring Harbor Laboratory Press 2017-08-20 <![CDATA[ Evolution of steroid specificity in human, chicken, alligator, frog and zebrafish mineralocorticoid receptors: Allosteric interactions affect steroid specificity ]]> https://biorxiv.org/content/10.1101/151233v1?rss=1 Katsu, Y. Oka, K. Baker, M. E. 2017-06-16 doi:10.1101/151233 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Proximity labeling reveals an extensive steady-state stress granule interactome and insights to neurodegeneration ]]> https://biorxiv.org/content/10.1101/152520v1?rss=1 100 previously unknown SG proteins in human cells, about 10% of which localize to SGs in a cell type- or stress type-dependent manner. Supporting a link between SG proteins and neurodegeneration, we demonstrate aberrant SG composition and subcellular distribution in iPSC-derived motor neurons from ALS patients, and identify several known and previously unidentified SG proteins that modify toxicity of mutant FUS and TDP-43 overexpression in Drosophila. We show that even in an unstressed steady-state, SG proteins form a densely-connected protein interaction network (PIN) and propose a model in which existing RNPs coalesce rapidly into microscopically visible granules that can act as gateways to pathological protein aggregation.nnHighlights O_LIAPEX proximity labeling of dynamic RNP granules identifies over 100 novel SG proteinsnC_LIO_LISG proteins form a densely-connected protein interaction network in unstressed cellsnC_LIO_LISystematic immunofluorescence analysis reveals stress- and cell type-specific SG compositionnC_LIO_LIALS motor neurons contain SGs with distinct content and subcellular distributionnC_LI ]]> Markmiller, S. Soltanieh, S. Server, K. Mak, R. Jin, W. Luo, E. Krach, F. Kankel, M. W. Sen, A. Bennett, E. J. Lecuyer, E. Yeo, G. 2017-06-20 doi:10.1101/152520 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Lis1 has two opposing modes of regulating cytoplasmic dynein ]]> https://biorxiv.org/content/10.1101/152645v1?rss=1 DeSantis, M. E. Cianfrocco, M. A. Htet, Z. M. Tran, P. T. Reck-Peterson, S. L. Leschziner, A. E. 2017-06-20 doi:10.1101/152645 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Differential roles of sleep spindles and sleep slow oscillations in memory consolidation ]]> https://biorxiv.org/content/10.1101/153007v1?rss=1 Wei, Y. Krishnan, G. P. Komarov, M. Bazhenov, M. 2017-06-21 doi:10.1101/153007 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Predator-secreted sulfolipids induce fear-like defense responses in C. elegans ]]> https://biorxiv.org/content/10.1101/153056v1?rss=1 Liu, Z. Kariya, M. J. Chute, C. D. Pribadi, A. K. Leinwand, S. G. Tong, A. Curran, K. P. Bose, N. Schroeder, F. C. Srinivasan, J. Chalasani, S. 2017-06-21 doi:10.1101/153056 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Polygenic hazard scores in preclinical Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/156331v1?rss=1 Tan, C. H. Sugrue, L. P. Broce, I. J. Tong, E. Tan, J. Hess, C. P. Dillon, W. P. Bonham, L. W. Yokoyama, J. S. Rabinovici, G. D. Rosen, H. J. Miller, B. L. Hyman, B. T. Schellenberg, G. D. Besser, L. M. Kukull, W. A. Karch, C. M. Brewer, J. B. Kauppi, K. McEvoy, L. K. Andreassen, O. A. Dale, A. M. Fan, C. C. Desikan, R. S. 2017-06-27 doi:10.1101/156331 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Immune-related genetic enrichment in frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/157875v1?rss=1 Broce, I. J. Karch, C. M. Wen, N. Fan, C. C. Wang, Y. Hong Tan, C. Kouri, N. Ross, O. A. Höglinger, G. U. Muller, U. Hardy, J. - International FTD-Genomics Consortium (IFGC), Momeni, P. Hess, C. P. Dillon, W. P. Miller, Z. A. Bonham, L. W. Rabinovici, G. D. Rosen, H. J. Schellenberg, G. D. Franke, A. Karlsen, T. H. Veldink, J. H. Ferrari, R. Yokoyama, J. S. Miller, B. L. Andreassen, O. A. Dale, A. M. Desikan, R. S. Sugrue, L. P. 2017-06-30 doi:10.1101/157875 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Positive Feedback Between Contractile Ring Myosin and Ring-Directed Cortical Flow Drives Cytokinesis ]]> https://biorxiv.org/content/10.1101/161133v1?rss=1 Khaliullin, R. Green, R. Shi, L. Berns, M. Gomez-Cavazos, J. S. Desai, A. Oegema, K. 2017-07-08 doi:10.1101/161133 Cold Spring Harbor Laboratory Press 2017-07-08 <![CDATA[ Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics ]]> https://biorxiv.org/content/10.1101/164640v1?rss=1 Bose, A. Platt, D. E. Parida, L. Paschou, P. Drineas, P. 2017-07-17 doi:10.1101/164640 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Estimating inflation in GWAS summary statistics due to variance distortion from cryptic relatedness ]]> https://biorxiv.org/content/10.1101/164939v1?rss=1 Holland, D. Fan, C.-C. Frei, O. Shadrin, A. A. Smeland, O. B. Sundar, V. S. Andreassen, O. A. Dale, A. M. 2017-07-17 doi:10.1101/164939 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Polygenic hazard score: an enrichment marker for Alzheimer’s associated amyloid and tau deposition ]]> https://biorxiv.org/content/10.1101/165373v1?rss=1 Tan, C. H. Fan, C. C. Mormino, E. C. Sugrue, L. P. Broce, I. J. Hess, C. P. Dillion, W. P. Bonham, L. W. Yokoyama, J. S. Karch, C. M. Brewer, J. B. Rabinovici, G. D. Miller, B. L. Schellenberg, G. D. Kauppi, K. Feldman, H. A. Holland, D. McEvoy, L. K. Hyman, B. T. Andreassen, O. A. Dale, A. M. Desikan, R. S. 2017-07-18 doi:10.1101/165373 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ ssbio: A Python Framework for Structural Systems Biology ]]> https://biorxiv.org/content/10.1101/165506v1?rss=1 Mih, N. Brunk, E. Chen, K. Catoiu, E. Sastry, A. Kavvas, E. Monk, J. M. Zhang, Z. Palsson, B. O. 2017-07-18 doi:10.1101/165506 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Systematic mapping of chromatin state landscapes during mouse development ]]> https://biorxiv.org/content/10.1101/166652v1?rss=1 Gorkin, D. Barozzi, I. Zhang, Y. Lee, A. Y. Lee, B. Zhao, Y. Wildberg, A. Ding, B. Zhang, B. Wang, M. Strattan, J. S. Davidson, J. M. Qiu, Y. Afzal, V. Akiyama, J. A. Plajzer-Frick, I. Pickle, C. S. Kato, M. Garvin, T. H. Pham, Q. T. Harrington, A. N. Mannion, B. J. Lee, E. A. Fukuda-Yuzawa, Y. He, Y. Preissl, S. Chee, S. Williams, B. A. Trout, D. Amrhein, H. Yang, H. Cherry, J. M. Shen, Y. Ecker, J. R. Wang, W. Dickel, D. E. Visel, A. Pennacchio, L. A. Ren, B. 2017-07-21 doi:10.1101/166652 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Temporal expression divergence of network modules ]]> https://biorxiv.org/content/10.1101/167734v1?rss=1 Park, Y. Kang, T.-H. Friedmann, T. Bader, J. 2017-07-24 doi:10.1101/167734 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Category learning biases sensory representations in visual cortex. ]]> https://biorxiv.org/content/10.1101/170845v1?rss=1 Ester, E. F. Sprague, T. C. Serences, J. T. 2017-08-01 doi:10.1101/170845 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ Role of KCC2-Dependent Potassium Efflux in 4-Aminopyridine-Induced Epileptiform Synchronization ]]> https://biorxiv.org/content/10.1101/171488v1?rss=1 Gonzalez, O. C. Shiri, Z. Krishnan, G. P. Myers, T. L. Williams, S. Avoli, M. Bazhenov, M. 2017-08-03 doi:10.1101/171488 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ Dissociable components of the reward circuit are involved in appraisal versus choice ]]> https://biorxiv.org/content/10.1101/172320v1?rss=1 Shenhav, A. Karmarkar, U. R. 2017-08-03 doi:10.1101/172320 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ The antibody repertoire of colorectal cancer ]]> https://biorxiv.org/content/10.1101/176768v1?rss=1 Cha, S. W. Bonissone, S. Na, S. Pevzner, P. A. Bafna, V. 2017-08-15 doi:10.1101/176768 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ When conflict cannot be avoided: executive control dominates early selective sensory modulations during cognitive conflict ]]> https://biorxiv.org/content/10.1101/177394v1?rss=1 Itthipuripat, S. Deering, S. Serences, J. 2017-08-17 doi:10.1101/177394 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Building a genome browser with GIVE ]]> https://biorxiv.org/content/10.1101/177832v1?rss=1 Cao, X. Zheng, A. Zhong, S. 2017-08-18 doi:10.1101/177832 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid ]]> https://biorxiv.org/content/10.1101/179127v1?rss=1 Ponce-de-Leon, M. Tamarit, D. Calle-Espinosa, J. Mori, M. Latorre, A. Montero, F. Pereto, J. 2017-08-21 doi:10.1101/179127 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ A neural algorithm for a fundamental computing problem ]]> https://biorxiv.org/content/10.1101/180471v1?rss=1 Dasgupta, S. Stevens, C. F. Navlakha, S. 2017-08-25 doi:10.1101/180471 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments ]]> https://biorxiv.org/content/10.1101/180646v1?rss=1 130 PTM sites in Escherichia coli to unravel how PTMs regulate cell metabolism and fitness in response to environmental changes, such as the glucose-acetate diauxie. Using a new metabolic modeling approach, we found a significant fraction of post-translationally modified enzymes are predicted to control shifts in pathway usage following evolutionarily-important environmental changes. Genetic screens using Multiplex Automated Genome Engineering confirmed that these PTMs impact cellular fitness, especially under dynamically changing environments. Finally, mechanisms of how individual PTMs impact protein function were detailed using molecular dynamics simulations and enzyme assays for enolase, transaldolase, and serine hydroxymethyltransferase. Thus, by integrating whole-cell data and pathway modeling with detailed biochemical analysis, we unraveled how individual PTMs regulate enzymes, pathways, and phenotypes to adapt to sudden environmental changes. ]]> Brunk, E. Chang, R. L. Xia, J. Hefzi, H. Yurkovich, J. T. Kim, D. Buckmiller, E. Wang, H. Yang, C. Palsson, B. O. Church, G. Lewis, N. E. 2017-08-25 doi:10.1101/180646 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ CXCR4 involvement in neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/181693v1?rss=1 Bonham, L Karch, C Fan, C Tan, C Geier, E Wang, Y Wen, N Broce, I Li, Y Barkovich, M Ferrari, R Hardy, J Momeni, P Höeglinger, G Müller, U Hess, C Sugrue, L Dillon, W Schellenberg, G Miller, B Andreassen, O Dale, A Barkovich, A Yokoyama, J Desikan, R 2017-08-29 doi:10.1101/181693 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Functional characterization of 3D-protein structures informed by human genetic diversity ]]> https://biorxiv.org/content/10.1101/182287v1?rss=1 Hicks, M. Bartha, I. di Iulio, J. Abagyan, R. Venter, J. C. Telenti, A. 2017-08-29 doi:10.1101/182287 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection ]]> https://biorxiv.org/content/10.1101/183764v1?rss=1 LaMonte, G. Orjuela-Sanchez, P. Wang, L. Li, S. Swann, J. Cowell, A. Zou, B. Y. Abdel- Haleem Mohamed, A. Villa-Galarce, Z. Moreno, M. Tong-Rios, C. Vinetz, J. Lewis, N. Winzeler, E. A. 2017-10-02 doi:10.1101/183764 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Reversal of molecular pathology by RNA-targeting Cas9 in a myotonic dystrophy mouse model ]]> https://biorxiv.org/content/10.1101/184408v1?rss=1 Batra, R. Nelles, D. A. Krach, F. Thomas, J. D. Snjader, L. Blue, S. M. Aigner, S. Swanson, M. S. Yeo, G. W. 2017-09-04 doi:10.1101/184408 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Alpha oscillations control cortical gain by modulating excitatory-inhibitory background activity. ]]> https://biorxiv.org/content/10.1101/185074v1?rss=1 Peterson, E. J. Voytek, B. 2017-09-07 doi:10.1101/185074 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Origin of Slow Spontaneous Resting-State Neuronal Fluctuations in Brain Networks ]]> https://biorxiv.org/content/10.1101/186098v1?rss=1 Krishnan, G. P. Gonzalez, O. C. Bazhenov, M. 2017-09-07 doi:10.1101/186098 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci ]]> https://biorxiv.org/content/10.1101/190892v1?rss=1 Thurner, M. van de Bunt, M. Gaulton, K. Barrett, A. Bennett, A. J. Torres, J. M. Nylander, V. Mahajan, A. Bell, C. G. Lowe, R. Beck, S. Rakyan, V. K. Gloyn, A. L. McCarthy, M. I. 2017-09-19 doi:10.1101/190892 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Multi-platform discovery of haplotype-resolved structural variation in human genomes ]]> https://biorxiv.org/content/10.1101/193144v1?rss=1 Chaisson, M. J. P. Sanders, A. D. Zhao, X. Malhotra, A. Porubsky, D. Rausch, T. Gardner, E. J. Rodriguez, O. Guo, L. Collins, R. L. Fan, X. Wen, J. Handsaker, R. E. Fairley, S. Kronenberg, Z. N. Kong, X. Hormozdiari, F. Lee, D. Wenger, A. M. Hastie, A. Antaki, D. Audano, P. Brand, H. Cantsilieris, S. Cao, H. Cerveira, E. Chen, C. Chen, X. Chin, C.-S. Chong, Z. Chuang, N. T. Church, D. M. Clarke, L. Farrell, A. Flores, J. Galeev, T. David, G. Gujral, M. Guryev, V. Haynes-Heaton, W. Korlach, J. Kumar, S. Kwon, J. Y. Lee, J. E. Lee, J. Lee, W.-P. Lee, 2017-09-23 doi:10.1101/193144 Cold Spring Harbor Laboratory Press 2017-09-23 <![CDATA[ CYK-4 functions independently of its centralspindlin partner ZEN-4 to cellularize oocytes in germline syncytia ]]> https://biorxiv.org/content/10.1101/196279v1?rss=1 Lee, K.-Y. Green, R. A. Gutierrez, E. Gomez-Cavazos, J. S. Kolotuev, I. Wang, S. Desai, A. Groisman, A. Oegema, K. 2017-09-29 doi:10.1101/196279 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Mapping Cortical Brain Asymmetry in 17,141 Healthy Individuals Worldwide via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/196634v1?rss=1 Kong, X.-Z. Mathias, S. Guadalupe, T. Abe, C. Agartz, I. Akudjedu, T. N. Aleman, A. Alhusaini, S. Allen, N. B. Ames, D. Andreassen, O. A. Armstrong, N. J. Bergo, F. Bastin, M. E. Batalla, A. Bauer, J. Baune, B. Baur, R. Biederman, J. Blaine, S. K. Boedhoe, P. Boen, E. Bose, A. Bralten, J. Brandeis, D. Brem, S. Brodaty, H. Bröhl, H. Buitelaar, J. Bürger, C. Bülow, R. Calhoun, V. Calvo, A. Canales-Rodriguez, E. J. Canive, J. M. Cannon, D. M. Caparelli, E. C. Castellanos, F. X. Cavalleri, G. L. Cendes, F. Chaim-Avancini, T. M. Chant 2017-10-01 doi:10.1101/196634 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Evolving building blocks of rhythm: How human cognition creates music via cultural transmission ]]> https://biorxiv.org/content/10.1101/198390v1?rss=1 Ravignani, A. Thompson, B. Grossi, T. Delgado, T. Kirby, S. 2017-10-04 doi:10.1101/198390 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Revisiting microbe-metabolite interactions: doing better than random ]]> https://biorxiv.org/content/10.1101/2019.12.10.871905v1?rss=1 Morton, J. McDonald, D. Aksenov, A. Nothias-Scaglia, L.-F. Foulds, J. Quinn, R. A. Badri, M. Swenson, T. Van Goethem, M. Northen, T. Vazquez-Baeza, Y. Wang, M. Bokulich, N. Watters, A. Song, S. J. Bonneau, R. Dorrestein, P. Knight, R. 2019-12-16 doi:10.1101/2019.12.10.871905 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants ]]> https://biorxiv.org/content/10.1101/2019.12.11.873398v1?rss=1 Luo, C. Liu, H. Xie, F. Armand, E. J. Siletti, K. Bakken, T. Fang, R. Doyle, W. I. Hodge, R. D. Hu, L. Wang, B.-A. Zhang, Z. Preissl, S. Lee, D.-S. Zhou, J. Niu, S.-Y. Castanon, R. Bartlett, A. Rivkin, A. Wang, X. Lucero, J. Nery, J. R. Davis, D. A. Mash, D. C. Dixon, J. R. Linnarsson, S. Lein, E. Behrens, M. M. Ren, B. Mukamel, E. A. Ecker, J. R. 2019-12-12 doi:10.1101/2019.12.11.873398 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ High-throughput screening of the ReFRAME library identifies potential drug repurposing candidates for Trypanosoma cruzi ]]> https://biorxiv.org/content/10.1101/2019.12.11.873711v1?rss=1 Bernatchez, J. A. Chen, E. Hull, M. V. McNamara, C. W. McKerrow, J. H. Siqueira-Neto, J. L. 2019-12-16 doi:10.1101/2019.12.11.873711 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Voluntary and involuntary orienting of attention elicit similar lateralized changes in alpha activity and slow potential shifts over visual cortex ]]> https://biorxiv.org/content/10.1101/2019.12.12.874818v1?rss=1 Keefe, J. M. Stoermer, V. S. 2019-12-13 doi:10.1101/2019.12.12.874818 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Polycomb-mediated repression compensates for loss of postnatal DNA methylation in excitatory neurons ]]> https://biorxiv.org/content/10.1101/2019.12.20.883694v1?rss=1 Li, J. Pinto-Duarte, A. Zander, M. Lai, C.-Y. Osteen, J. Fang, L. Luo, C. Lucero, J. D. Gomez-Castanon, R. Nery, J. R. Silva-Garcia, I. Pang, Y. Sejnowski, T. J. Powell, S. B. Ecker, J. R. Mukamel, E. A. Behrens, M. M. 2019-12-20 doi:10.1101/2019.12.20.883694 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ HIV Care Prioritization using Phylogenetic Branch Length ]]> https://biorxiv.org/content/10.1101/2019.12.20.885202v1?rss=1 Moshiri, N. Smith, D. M. Mirarab, S. 2019-12-23 doi:10.1101/2019.12.20.885202 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats ]]> https://biorxiv.org/content/10.1101/2019.12.23.887158v1?rss=1 Mikheenko, A. Bzikadze, A. V. Gurevich, A. Miga, K. H. Pevzner, P. A. 2019-12-23 doi:10.1101/2019.12.23.887158 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Reclassification of SLC22 Transporters: Analysis of OAT, OCT, OCTN, and other Family Members Reveals 8 Functional Subgroups ]]> https://biorxiv.org/content/10.1101/2019.12.23.887299v1?rss=1 Engelhart, D. C. Granados, J. Nigam, S. K. Shi, D. Saier, M. H. Baker, M. E. 2019-12-26 doi:10.1101/2019.12.23.887299 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Parkinson's Disease-linked LRRK2 structure and model for microtubule interaction ]]> https://biorxiv.org/content/10.1101/2020.01.06.895367v1?rss=1 Deniston, C. K. Salogiannis, J. Mathea, S. Snead, D. M. Lahiri, I. Donosa, O. Watanabe, R. Böhning, J. Shiau, A. K. Knapp, S. Villa, E. Reck-Peterson, S. L. Leschziner, A. E. 2020-01-06 doi:10.1101/2020.01.06.895367 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ The Latent Genetic Structure of Impulsivity and its Relation to Internalizing Psychopathology ]]> https://biorxiv.org/content/10.1101/2020.01.07.897231v1?rss=1 Gustavson, D. E. Friedman, N. P. Fontanillas, P. Elson, S. L. the 23andMe Research Team, Palmer, A. A. Sanchez-Roige, S. 2020-01-08 doi:10.1101/2020.01.07.897231 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit ]]> https://biorxiv.org/content/10.1101/2020.01.10.902312v1?rss=1 Tenner, B. Getz, M. Ross, B. Ohadi, D. Bohrer, C. H. Greenwald, E. Mehta, S. Xiao, J. Rangamani, P. Zhang, J. 2020-01-11 doi:10.1101/2020.01.10.902312 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Electrophysiological Frequency Band Ratio Measures Conflate Periodic and Aperiodic Neural Activity ]]> https://biorxiv.org/content/10.1101/2020.01.11.900977v1?rss=1 Donoghue, T. Dominguez, J. Voytek, B. 2020-01-11 doi:10.1101/2020.01.11.900977 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS. ]]> https://biorxiv.org/content/10.1101/2020.01.13.905091v1?rss=1 Aksenov, A. Laponogov, I. Zhang, Z. Doran, S. Belluomo, I. Veselkov, D. Bittremieux, W. Nothias, L. F. Nothias-Esposito, M. Maloney, K. N. Misra, B. B. Melnik, A. V. Jones, K. L. Dorrestein, K. Panitchpakdi, M. Ernst, M. van der Hooft, J. J. J. Gonzalez, M. Carazzone, C. Amézquita, A. Callewaert, C. Morton, J. Quinn, R. A. Bouslimani, A. Albarracin Orio, A. Petras, D. Smania, A. M. Couvillion, S. P. Burnet, M. C. Nicora, C. D. Zink, E. Metz, T. O. Artaev, V. Humston-Fulmer, E. Gregor, R. Meijler, M. M. Mizrahi, I. Eyal, S. Anderson, B. Dutton, R. J. 2020-01-14 doi:10.1101/2020.01.13.905091 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus ]]> https://biorxiv.org/content/10.1101/2020.01.16.909333v1?rss=1 Ma, J. Do, M. Le Gros, M. A. Peskin, C. S. Larabell, C. A. Mori, Y. Isaacson, S. A. 2020-01-17 doi:10.1101/2020.01.16.909333 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Mechanical Instability of Adherens Junctions Overrides Intrinsic Quiescence of Hair Follicle Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.01.17.909937v1?rss=1 Biswas, R. Banerjee, A. Lembo, S. Zhao, Z. Lakshmanan, V. Nakasaki, M. Kutyavin, V. Wright, G. Palakodeti, D. Ross, R. Jamora, C. Vasioukhin, V. Yan, J. Raghavan, S. 2020-01-17 doi:10.1101/2020.01.17.909937 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Lipid Sponge Droplets as Programmable Synthetic Organelles ]]> https://biorxiv.org/content/10.1101/2020.01.20.913350v1?rss=1 Bhattacharya, A. Niederholtmeyer, H. Podolsky, K. A. Bhattacharya, R. Song, J.-J. Brea, R. J. Tsai, C.-H. Sinha, S. K. Devaraj, N. K. 2020-01-21 doi:10.1101/2020.01.20.913350 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ AmpliconReconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer ]]> https://biorxiv.org/content/10.1101/2020.01.22.916031v1?rss=1 150kb) with next-generation sequencing (NGS) to resolve fCNAs at single-nucleotide resolution. AR uses an NGS-derived breakpoint graph alongside OM scaffolds to produce high-fidelity reconstructions. After validating performance by extensive simulations, we used AR to reconstruct fCNAs in seven cancer cell lines to reveal the complex architecture of ecDNA, breakage-fusion-bridge cycles, and other complex rearrangements. By distinguishing between chromosomal and extrachromosomal origins, and by reconstructing the rearrangement signatures associated with a given fCNAs generative mechanism, AR enables a more thorough understanding of the origins of fCNAs, and their functional consequences. ]]> Luebeck, J. Coruh, C. Dehkordi, S. R. Lange, J. T. Turner, K. M. Deshpande, V. Pai, D. A. Zhang, C. Rajkumar, U. Law, J. A. Mischel, P. S. Bafna, V. 2020-01-23 doi:10.1101/2020.01.22.916031 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Systematically gap-filling the genome-scale model of CHO cells ]]> https://biorxiv.org/content/10.1101/2020.01.27.921296v1?rss=1 Fouladiha, H. Marashi, S.-A. Li, S. Vaziri, B. Lewis, N. E. 2020-01-27 doi:10.1101/2020.01.27.921296 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function ]]> https://biorxiv.org/content/10.1101/2020.01.30.925917v1?rss=1 Shen, Z. Hoeksema, M. Ouyang, Z. Benner, C. Glass, C. 2020-01-31 doi:10.1101/2020.01.30.925917 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A single-cell RNAseq atlas of the pathogenic stage of Schistosoma mansoni identifies a key regulator of blood feeding ]]> https://biorxiv.org/content/10.1101/2020.02.03.932004v1?rss=1 Wendt, G. Zhao, L. Chen, R. Lu, C. O'Donoghue, A. J. Caffrey, C. R. Collins, J. 2020-02-03 doi:10.1101/2020.02.03.932004 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53 ]]> https://biorxiv.org/content/10.1101/2020.02.04.933192v1?rss=1 Moosmueller, C. Tralie, C. J. Kooshkbaghi, M. Belkhatir, Z. Pouryahya, M. Reyes, J. Deasy, J. O. Tannenbaum, A. R. Kevrekidis, I. G. 2020-02-04 doi:10.1101/2020.02.04.933192 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Structure-function analysis of the maize bulliform cell cuticle and its role in dehydration and leaf rolling ]]> https://biorxiv.org/content/10.1101/2020.02.06.937011v1?rss=1 Matschi, S. Vasquez, M. F. Bourgault, R. Steinbach, P. Chamness, J. Kaczmar, N. Gore, M. A. Molina, I. Smith, L. G. 2020-02-07 doi:10.1101/2020.02.06.937011 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator ]]> https://biorxiv.org/content/10.1101/2020.02.13.948422v1?rss=1 Bergstrom, E. N. Barnes, M. Martincorena, I. Alexandrov, L. B. 2020-02-14 doi:10.1101/2020.02.13.948422 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Fluid and crystallised intelligence are associated with distinct regionalisation patterns of cortical morphology ]]> https://biorxiv.org/content/10.1101/2020.02.13.948596v1?rss=1 Palmer, C. E. Zhao, W. Loughnan, R. J. Fan, C.-C. Thompson, W. K. Dale, A. M. Jernigan, T. L. 2020-02-14 doi:10.1101/2020.02.13.948596 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans. ]]> https://biorxiv.org/content/10.1101/2020.02.18.955245v1?rss=1 How, J. J. Navlakha, S. Chalasani, S. H. 2020-02-19 doi:10.1101/2020.02.18.955245 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Novelty-seeking impairment in addiction ]]> https://biorxiv.org/content/10.1101/2020.02.19.955989v1?rss=1 Cogliati Dezza, I. Noel, X. Cleeremans, A. Yu, A. 2020-02-21 doi:10.1101/2020.02.19.955989 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Slow Axonal Transport and Presynaptic Targeting of Clathrin Packets ]]> https://biorxiv.org/content/10.1101/2020.02.20.958140v1?rss=1 Ganguly, A. Wernert, F. Phan, S. BOASSA, D. Das, U. Sharma, R. Caillol, G. Han, X. Yates, J. R. Ellisman, M. Leterrier, C. Roy, S. 2020-02-20 doi:10.1101/2020.02.20.958140 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Systematic functional analysis of Rab GTPasesreveals limits of neuronal robustness in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.02.21.959452v1?rss=1 Kohrs, F. E. Daumann, I.-M. Pavlovic, B. Jin, E. J. Lin, S.-C. Port, F. Kiral, F. R. Wolfenberg, H. Mathejczyk, T. F. Chan, C.-C. Boutros, M. Hiesinger, P. R. 2020-02-22 doi:10.1101/2020.02.21.959452 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Improved reference genome of the arboviral vector Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2020.02.28.969527v1?rss=1 Palatini, U. Masri, R. Cosme, L. V. Koren, S. Thibaud-Nissen, F. Biedler, J. K. Krsticevic, F. Johnston, S. Halbach, R. Crawford, J. E. Antoshechkin, I. Failloux, A.-B. Pischedda, E. Marconcini, M. Ghurye, J. Rhie, A. Sharma, A. Karagodin, D. A. Jentette, J. Gamez, S. Miesen, P. Caccone, A. Sharakhova, M. V. Tu, Z. Papathanos, P. A. van Rij, R. P. Akbari, O. S. Powell, J. Phillippy, A. M. Bonizzoni, M. 2020-02-28 doi:10.1101/2020.02.28.969527 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types ]]> https://biorxiv.org/content/10.1101/2020.02.29.970558v1?rss=1 Yao, Z. Liu, H. Xie, F. Fischer, S. Adkins, R. S. Aldrige, A. I. Ament, S. A. Bartlett, A. Behrens, M. M. Van den Berge, K. Bertagnolli, D. Biancalani, T. Booeshaghi, A. S. Corrada Bravo, H. Casper, T. Colantuoni, C. Crabtree, J. Creasy, H. Crichton, K. Crow, M. Dee, N. Dougherty, E. L. Doyle, W. I. Dudoit, S. Fang, R. Felix, V. Fong, O. Giglio, M. Goldy, J. Hawrylycz, M. Bezieux, H. R. d. Herb, B. R. Hertzano, R. Hou, X. Hu, Q. Huang, Z. J. Kancherla, J. Kroll, M. Lathia, K. Li, Y. E. Lucero, J. D. Luo, C. Mahurkar, A. McMillen, D. Nadaf, N. M. Ner 2020-03-02 doi:10.1101/2020.02.29.970558 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Lipid availability influences the metabolic maturation of human pluripotent stem cell-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.03.14.991927v1?rss=1 Zhang, H. Badur, M. G. Spiering, S. Divakaruni, A. Meurs, N. E. Yu, M. S. Colas, A. R. Murphy, A. N. Mercola, M. Metallo, C. M. 2020-03-15 doi:10.1101/2020.03.14.991927 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Discovering biomarkers of chemotherapy resistance using in vitro evolution in haploid human cells ]]> https://biorxiv.org/content/10.1101/2020.03.17.982181v1?rss=1 Jado, J. C. Dow, M. Fonseca, G. Carolino, K. Ideker, T. Carter, H. Winzeler, E. 2020-03-18 doi:10.1101/2020.03.17.982181 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines ]]> https://biorxiv.org/content/10.1101/2020.03.17.995290v1?rss=1 Lin, D. Yalamanchili, H. Zhang, X. Lewis, N. E. Alves, C. L. Groot, J. Arnsdorf, J. Peterson Bjorn, S. Wulff, T. Rude Voldborg, B. G. Zhou, Y. Zhang, B. 2020-03-18 doi:10.1101/2020.03.17.995290 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Nitrogen starvation and stationary phase lipophagy have distinct molecular mechanisms ]]> https://biorxiv.org/content/10.1101/2020.03.17.996082v1?rss=1 Kumar, R. Rahman, M. A. Nazarko, T. Y. 2020-03-18 doi:10.1101/2020.03.17.996082 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses ]]> https://biorxiv.org/content/10.1101/2020.03.18.997296v1?rss=1 Poudel, S. Tsunemoto, H. Seif, Y. Sastry, A. V. Szubin, R. Xu, S. Machado, H. Olson, C. Anand, A. Pogliano, J. Nizet, V. Palsson, B. 2020-03-20 doi:10.1101/2020.03.18.997296 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Transcriptome-wide profiles of circular RNA and RNA binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression ]]> https://biorxiv.org/content/10.1101/2020.03.19.997478v1?rss=1 Okholm, T. L. H. Sathe, S. Park, S. S. Kamstrup, A. B. Rasmussen, A. M. Shankar, A. Fristrup, N. Nielsen, M. M. Vang, S. Dyrskjoet, L. Aigner, S. Damgaard, C. K. Yeo, G. Pedersen, J. S. 2020-03-20 doi:10.1101/2020.03.19.997478 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Multiplexed photo-activation of mRNA with single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.03.19.999631v1?rss=1 Zhang, D. Jin, S. Piao, X. Devaraj, N. K. 2020-03-20 doi:10.1101/2020.03.19.999631 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2020.03.21.001693v1?rss=1 Kubo, N. Ishii, H. Xiong, X. Bianco, S. Meitinger, F. Hu, R. Hocker, J. D. Conte, M. Gorkin, D. Yu, M. Li, B. Dixon, J. Hu, M. Nicodemi, M. Zhao, H. Ren, B. 2020-03-23 doi:10.1101/2020.03.21.001693 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ Structural insights into assembly and function of the RSC chromatin remodeling complex ]]> https://biorxiv.org/content/10.1101/2020.03.24.006361v1?rss=1 Leschziner, A. E. Baker, R. W. Reimer, J. M. Dominguez, R. Carman, P. J. Arakawa, T. 2020-03-25 doi:10.1101/2020.03.24.006361 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ DDX5 targets tissue-specific RNAs to promote intestine tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.03.25.006668v1?rss=1 Abbasi, N. Long, T. Li, Y. Ma, E. Yee, B. A. Patel, P. R. Sayed, I. M. Varki, N. Das, S. Ghosh, P. Yeo, G. W. Huang, W. J. M. 2020-03-26 doi:10.1101/2020.03.25.006668 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Incorporation of a nucleoside analog maps genome repair sites in post-mitotic human neurons ]]> https://biorxiv.org/content/10.1101/2020.03.25.008490v1?rss=1 Reid, D. A. Reed, P. J. Schlachetzki, J. C. M. Chou, G. Chandran, S. Lu, A. T. McClain, C. A. Ooi, J. H. Jones, J. R. Linker, S. B. Tsui, E. C. Ricciardulli, A. S. Lau, S. Schafer, S. T. Horvath, S. Dixon, J. R. Hah, N. Glass, C. K. Gage, F. H. 2020-03-26 doi:10.1101/2020.03.25.008490 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Self-administration of heroin by vapor inhalation in female Wistar rats ]]> https://biorxiv.org/content/10.1101/2020.03.30.016725v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Taffe, M. A. 2020-03-31 doi:10.1101/2020.03.30.016725 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse ]]> https://biorxiv.org/content/10.1101/2020.03.31.016972v1?rss=1 Bakken, T. E. Jorstad, N. L. Hu, Q. Lake, B. B. Tian, W. Kalmbach, B. E. Crow, M. Hodge, R. D. Krienen, F. M. Sorensen, S. A. Eggermont, J. Yao, Z. Aevermann, B. D. Aldridge, A. I. Bartlett, A. Bertagnolli, D. Casper, T. Castanon, R. G. Crichton, K. Daigle, T. L. Dalley, R. Dee, N. Dembrow, N. Diep, D. Ding, S.-L. Dong, W. Fang, R. Fischer, S. Goldman, M. Goldy, J. Graybuck, L. T. Herb, B. R. Hou, X. Kancherla, J. Kroll, M. Lathia, K. Lew, B. v. Li, Y. E. Liu, C. S. Liu, H. Mahurkar, A. McMillen, D. Miller, J. A. Moussa, M. Nery, J. R. Orvis, J. Ow 2020-04-01 doi:10.1101/2020.03.31.016972 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Granadaene Photobleaching Reduces the Virulence and Increases Antimicrobial Susceptibility of Streptococcus agalactiae ]]> https://biorxiv.org/content/10.1101/2020.03.31.019372v1?rss=1 Jusuf, S. Dong, P.-T. Hui, J. Ulloa, E. R. Liu, G. Y. Cheng, J.-X. 2020-04-01 doi:10.1101/2020.03.31.019372 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain ]]> https://biorxiv.org/content/10.1101/2020.04.01.019612v1?rss=1 Zhang, Z. Zhou, J. Tan, P. Pang, Y. Rivkin, A. Kirchgessner, M. A. Williams, E. Lee, C.-T. Liu, H. Franklin, A. D. Miyazaki, P. A. Bartlett, A. Aldridge, A. Vu, M. Boggeman, L. Fitzpatrick, C. Nery, J. Castanon, R. G. Rashid, M. Jacobs, M. Ito, T. Dominguez, B. Niu, S.-Y. Smith, J. B. O'Connor, C. Lee, K.-F. Jin, X. Mukamel, E. A. Behrens, M. M. Ecker, J. R. Callaway, E. M. 2020-04-03 doi:10.1101/2020.04.01.019612 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.04.01.020792v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@c2c756org.highwire.dtl.DTLVardef@1ad1c03org.highwire.dtl.DTLVardef@a4136org.highwire.dtl.DTLVardef@13f403f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kellman, B. P. Baghdassarian, H. M. Pramparo, T. Shamie, I. Gazestani, V. H. Begzati, A. Li, S. Nalabolu, S. Murray, S. Lopez, L. Pierce, K. Courchesne, E. Lewis, N. E. 2020-04-03 doi:10.1101/2020.04.01.020792 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Rapid community-driven development of a SARS-CoV-2 tissue simulator ]]> https://biorxiv.org/content/10.1101/2020.04.02.019075v1?rss=1 Wang, Y. Heiland, R. Craig, M. Davis, C. L. Ford Versypt, A. N. Jenner, A. Ozik, J. Collier, N. Cockrell, C. Becker, A. An, G. Glazier, J. A. Narayanan, A. Smith, A. M. Macklin, P. 2020-04-05 doi:10.1101/2020.04.02.019075 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Mutational profiling of micro-dissected pre-malignant lesions from archived specimens ]]> https://biorxiv.org/content/10.1101/2020.04.05.026708v1?rss=1 Nachmanson, D. Steward, J. Yao, H. Jeong, E. O'Keefe, T. J. Hasteh, F. Jepsen, K. Hirst, G. L. Esserman, L. J. Borowsky, A. D. Harismendy, O. 2020-04-06 doi:10.1101/2020.04.05.026708 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ POMK Regulates Dystroglycan Function via LARGE-mediated Elongation of Matriglycan ]]> https://biorxiv.org/content/10.1101/2020.04.06.007948v1?rss=1 Walimbe, A. S. Yang, T. Yonekawa, T. Venzke, D. Anderson, M. E. Torelli, S. Manzur, A. Yu, L. Devereaux, M. Cuellar, M. Prouty, S. O'Campo Landa, S. Muntoni, F. Campbell, K. P. 2020-04-07 doi:10.1101/2020.04.06.007948 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Physical and mental health characteristics of adults with subjective cognitive decline: A study of 3,407 people aged 18-81 years from an MTurk-based U.S. national sample ]]> https://biorxiv.org/content/10.1101/2020.04.07.029553v1?rss=1 Van Patten, R. Nguyen, T. Mahmood, Z. Lee, E. Daly, R. Palmer, B. Wu, T.-C. Tu, X. Jeste, D. V. Twamley, E. 2020-04-07 doi:10.1101/2020.04.07.029553 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Visual function restoration in genetically blind mice via endogenous cellular reprogramming ]]> https://biorxiv.org/content/10.1101/2020.04.08.030981v1?rss=1 Fu, X. Zhu, J. Duan, Y. Li, G. Cai, H. Zheng, L. Zhang, C. Jin, Z. Fu, X.-D. Zhang, K. 2020-04-08 doi:10.1101/2020.04.08.030981 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia ]]> https://biorxiv.org/content/10.1101/2020.04.09.033555v1?rss=1 Bachireddy, P. Ennis, C. Nguyen, V. Clement, K. Gohil, S. H. Shukla, S. A. Forman, J. Barkas, N. Freeman, S. Bavli, N. Elagina, L. Leshchiner, I. Mohammad, A. W. Rassenti, L. Z. Kipps, T. J. Brown, J. R. Getz, G. A. Ho, V. T. Gnirke, A. Neuberg, D. Soiffer, R. J. Ritz, J. Alyea, E. P. Kharchenko, P. V. Wu, C. J. 2020-04-10 doi:10.1101/2020.04.09.033555 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ A New Form of Decellularized Extracellular Matrix Hydrogel for Treating Ischemic Tissue via Intravascular Infusion ]]> https://biorxiv.org/content/10.1101/2020.04.10.028076v1?rss=1 Spang, M. T. Lazerson, T. S. Bhatia, S. Corbitt, J. Sandoval, G. Luo, C. Osborn, K. G. Cabrales, P. Kwon, E. Contijoch, F. Reeves, R. R. DeMaria, A. N. Christman, K. L. 2020-04-12 doi:10.1101/2020.04.10.028076 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ Sensitivity to Monoclonal Antibody 447-52D and an Open Env Trimer Conformation Correlate Poorly with Inhibition of HIV-1 Infectivity by SERINC5 ]]> https://biorxiv.org/content/10.1101/2020.04.10.036483v1?rss=1 Angerstein, A. O. Stoneham, C. A. Ramirez, P. W. Guatelli, J. C. Vollbrecht, T. 2020-04-12 doi:10.1101/2020.04.10.036483 Cold Spring Harbor Laboratory Press 2020-04-12 <![CDATA[ An aptamer-based magnetic flow cytometer using matched filtering ]]> https://biorxiv.org/content/10.1101/2020.04.14.041210v1?rss=1 Huang, C.-C. Ray, P. Chan, M. Zhou, X. Hall, D. A. 2020-04-15 doi:10.1101/2020.04.14.041210 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ An Autophagy-Dependent Tubular Lysosomal Network Synchronizes Degradative Activity Required for Muscle Remodeling ]]> https://biorxiv.org/content/10.1101/2020.04.15.043075v1?rss=1 Murakawa, T. Kiger, A. A. Sakamaki, Y. Fukuda, M. Fujita, N. 2020-04-16 doi:10.1101/2020.04.15.043075 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Incremental language comprehension difficulty predicts activity in the language network but not the multiple demand network ]]> https://biorxiv.org/content/10.1101/2020.04.15.043844v1?rss=1 Wehbe, L. Blank, I. A. Shain, C. Futrell, R. Levy, R. von der Malsburg, T. Smith, N. Gibson, E. Fedorenko, E. 2020-04-17 doi:10.1101/2020.04.15.043844 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals ]]> https://biorxiv.org/content/10.1101/2020.04.16.044016v1?rss=1 10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment. ]]> Riva, L. Yuan, S. Yin, X. Martin-Sancho, L. Matsunaga, N. Burgstaller, S. Pache, L. De Jesus, P. Hull, M. V. Chang, M. Chan, J. F. W. Cao, J. Kwok-Man Poon, V. Herbert, K. Nguyen, T.-T. Pu, Y. Nguyen, C. Rubanov, A. Martinez-Sobrido, L. Lui, W.-C. Miorin, L. White, K. Johnson, J. R. Benner, C. Sun, R. Schultz, P. Su, A. I. Garcia-Sastre, A. Chatterjee, A. Yuen, K.-Y. Chanda, S. 2020-04-17 doi:10.1101/2020.04.16.044016 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes ]]> https://biorxiv.org/content/10.1101/2020.04.20.052068v1?rss=1 Moshiri, N. 2020-04-21 doi:10.1101/2020.04.20.052068 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Structural Basis of CD4 Downregulation by HIV-1 Nef ]]> https://biorxiv.org/content/10.1101/2020.04.21.054007v1?rss=1 Kwon, Y. Kaake, R. Echeverria, I. Suarez, M. Stoneham, C. Ramirez, P. W. Kress, J. Singh, R. Sali, A. Krogan, N. J. Guatelli, J. Jia, X. 2020-04-23 doi:10.1101/2020.04.21.054007 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development. ]]> https://biorxiv.org/content/10.1101/2020.04.24.060822v1?rss=1 Haist, J. Neumann, S. A. Al-Bassam, M. M. Lindenberg, S. Elliot, M. A. Tschowri, N. 2020-04-25 doi:10.1101/2020.04.24.060822 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. ]]> https://biorxiv.org/content/10.1101/2020.04.25.061598v1?rss=1 Ma, Q. Srivastav, S. P. Gamez, S. Feitosa-Suntheimer, F. Patterson, E. I. Johnson, R. Matson, E. Gold, A. Brackney, D. Connor, J. Colpitts, T. Hughes, G. Rasgon, J. Nolan, T. Akbari, O. S. Lau, N. 2020-04-27 doi:10.1101/2020.04.25.061598 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens ]]> https://biorxiv.org/content/10.1101/2020.04.25.061994v1?rss=1 Rajput, A. Seif, Y. Choudhary, K. S. Dalldorf, C. Poudel, S. Monk, J. Palsson, B. O. 2020-04-26 doi:10.1101/2020.04.25.061994 Cold Spring Harbor Laboratory Press 2020-04-26 <![CDATA[ What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data ]]> https://biorxiv.org/content/10.1101/2020.04.26.057943v1?rss=1 Richelle, A. Kellman, B. P. Wenzel, A. T. Chiang, A. W. T. Reagan, T. Gutierrez, J. M. Joshi, C. Li, S. Liu, J. K. Masson, H. Lee, J. Li, Z. Heirendt, L. Trefois, C. Juarez, E. F. Bath, T. Borland, D. Mesirov, J. P. Robasky, K. Lewis, N. E. 2020-04-28 doi:10.1101/2020.04.26.057943 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome ]]> https://biorxiv.org/content/10.1101/2020.04.26.062638v1?rss=1 Rychel, K. Sastry, A. V. Palsson, B. 2020-04-28 doi:10.1101/2020.04.26.062638 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures ]]> https://biorxiv.org/content/10.1101/2020.04.27.064584v1?rss=1 Ho, R. Workman, M. J. Mathkar, P. Wu, K. Kim, K. J. ORourke, J. G. Kellogg, M. Montel, V. Banuelos, M. G. Aladesuyi, O. Diaz-Garcia, S. Oheb, D. Huang, S. Khrebtukova, I. Watson, L. Ravits, J. Taylor, K. Baloh, R. H. Svendsen, C. N. 2020-04-28 doi:10.1101/2020.04.27.064584 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization ]]> https://biorxiv.org/content/10.1101/2020.04.27.065417v1?rss=1 Rodionova, I. A. Gao, Y. Sastry, A. V. Monk, J. wong, n. Szubin, R. Lim, H. Zhang, Z. Saier, M. H. Palsson, B. O. 2020-04-29 doi:10.1101/2020.04.27.065417 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ The TAT Protein Transduction Domain as an Intra-articular Drug-Delivery Technology ]]> https://biorxiv.org/content/10.1101/2020.04.28.066902v1?rss=1 Mailhiot, S. E. Thompson, M. A. Eguchi, A. Dinkel, S. Lotz, M. K. Dowdy, S. F. June, R. K. 2020-04-30 doi:10.1101/2020.04.28.066902 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Super-selective reconstruction of causal and direct connectivity with application to in-vitro iPSC neuronal networks ]]> https://biorxiv.org/content/10.1101/2020.04.28.067124v1?rss=1 Puppo, F. PrTh, D. Bang, A. Silva, G. A. 2020-04-30 doi:10.1101/2020.04.28.067124 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Determinants of Selective Fidelity in Diversity-Generating Retroelements ]]> https://biorxiv.org/content/10.1101/2020.04.29.068544v1?rss=1 Handa, S. Reyna, A. Wiryaman, T. Ghosh, P. 2020-04-30 doi:10.1101/2020.04.29.068544 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2020.04.30.069377v1?rss=1 Liu, H. Zhou, J. Tian, W. Luo, C. Bartlett, A. Aldridge, A. Lucero, J. Osteen, J. K. Nery, J. R. Chen, H. Rivkin, A. Castanon, R. G. Clock, B. Li, Y. E. Hou, X. Poirion, O. B. Preissl, S. O'Connor, C. Boggeman, L. Fitzpatrick, C. Nunn, M. Mukamel, E. A. Zhang, Z. Callaway, E. M. Ren, B. Dixon, J. R. Behrens, M. M. Ecker, J. R. 2020-04-30 doi:10.1101/2020.04.30.069377 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media ]]> https://biorxiv.org/content/10.1101/2020.04.30.070904v1?rss=1 Seif, Y. Poudel, S. Tsunemoto, H. Szubin, R. Meehan, M. J. Olson, C. Rajput, A. Alarcon, G. Lamsa, A. Dillon, N. Vrbanac, A. Sugie, J. Daesh, S. Monk, J. Dorrestein, P. Knight, R. Pogliano, J. Feist, A. Palsson, B. Nizet, V. 2020-05-01 doi:10.1101/2020.04.30.070904 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Sleep Deficits and Cannabis Use Behaviors: An Analysis of Shared Genetics Using Linkage Disequilibrium Score Regression and Polygenic Risk Prediction ]]> https://biorxiv.org/content/10.1101/2020.05.02.053983v1?rss=1 Winiger, E. A. Ellingson, J. M. Morrison, C. L. Corley, R. P. Pasman, J. A. Wall, T. L. Hopfer, C. J. Hewitt, J. K. 2020-05-03 doi:10.1101/2020.05.02.053983 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility ]]> https://biorxiv.org/content/10.1101/2020.05.04.077271v1?rss=1 Sastry, A. V. Dillon, N. Poudel, S. Hefner, Y. Xu, S. Szubin, R. Feist, A. Nizet, V. Palsson, B. 2020-05-04 doi:10.1101/2020.05.04.077271 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree ]]> https://biorxiv.org/content/10.1101/2020.05.04.077636v1?rss=1 Tripathi, A. Vazquez-Baeza, Y. Gauglitz, J. M. Wang, M. Duhrkop, K. Esposito-Nothias, M. Acharya, D. Ernst, M. van der Hooft, J. J. J. Zhu, Q. McDonald, D. Gonzalez, A. Handelsman, J. Fleischauer, M. Ludwig, M. Bocker, S. NOTHIAS, L. F. Knight, R. Dorrestein, P. C. 2020-05-05 doi:10.1101/2020.05.04.077636 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Vision does not impact walking performance in Argentine ants ]]> https://biorxiv.org/content/10.1101/2020.05.05.079582v1?rss=1 Clifton, G. Holway, D. Gravish, N. 2020-05-06 doi:10.1101/2020.05.05.079582 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media ]]> https://biorxiv.org/content/10.1101/2020.05.06.079640v1?rss=1 Rajput, A. Poudel, S. Tsunemoto, H. Meehan, M. Szubin, R. Olson, C. Seif, Y. Lamsa, A. Dillon, N. Vrbanac, A. Sugie, J. Dahesh, S. Monk, J. Dorrestein, P. Pogliano, J. Nizet, V. Feist, A. Palsson, B. O. 2020-05-07 doi:10.1101/2020.05.06.079640 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ In situ detection of protein interactions for recombinant therapeutic enzymes ]]> https://biorxiv.org/content/10.1101/2020.05.06.081885v1?rss=1 Samoudi, M. Kuo, C.-C. Robinson, C. M. Shams-Ud-Doha, K. Schinn, S.-M. Kol, S. Weiss, L. Petersen Bjorn, S. Voldborg, B. G. Rosa Campos, A. Lewis, N. E. 2020-05-07 doi:10.1101/2020.05.06.081885 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes ]]> https://biorxiv.org/content/10.1101/2020.05.07.081604v1?rss=1 Karottki, K. J. l. C. Hefzi, H. Li, S. Pedersen, L. E. Spahn, P. Ruckerbauer, D. Bort, J. H. Thomas, A. Lee, J. S. Borth, N. Lee, G. M. Kildegaard, H. F. Lewis, N. E. 2020-05-08 doi:10.1101/2020.05.07.081604 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Comment on 'Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism' ]]> https://biorxiv.org/content/10.1101/2020.05.08.084376v1?rss=1 Le Treut, G. Si, F. Li, D. Jun, S. 2020-05-10 doi:10.1101/2020.05.08.084376 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Computing temporal sequences associated with dynamic patterns on the C. elegans connectome ]]> https://biorxiv.org/content/10.1101/2020.05.08.085191v1?rss=1 George, V. K. Puppo, F. Silva, G. A. 2020-05-10 doi:10.1101/2020.05.08.085191 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Germline mutagenesis of Nasonia vitripennis through ovarian delivery of CRISPR-Cas9 ribonucleoprotein ]]> https://biorxiv.org/content/10.1101/2020.05.10.087494v1?rss=1 Chaverra-Rodriguez, D. Dalla Benetta, E. Heu, C. C. Rasgon, J. Ferree, P. M. Akbari, O. S. 2020-05-10 doi:10.1101/2020.05.10.087494 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum ]]> https://biorxiv.org/content/10.1101/2020.05.10.087585v1?rss=1 800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link a significant fraction of them to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of non-coding risk variants associated with various neurological disease and traits in humans. To facilitate the dissemination of information, we have set up a web portal (http://catlas.org/mousebrain). ]]> Li, Y. Preissl, S. Hou, X. Zhang, z. Zhang, K. Fang, R. Qiu, Y. Poirion, O. Li, B. Yan, Y. Liu, H. Wang, X. Han, J. Y. Lucero, J. Kuan, S. Gorkin, D. Nunn, M. Mukamel, E. A. Behrens, M. M. Ecker, J. R. Ren, B. 2020-05-11 doi:10.1101/2020.05.10.087585 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.05.12.090688v1?rss=1 Morshed, N. Ralvenius, W. T. Nott, A. Watson, L. A. Rodriguez, F. H. Akay, L. A. Joughin, B. A. Pao, P.-C. Penney, J. LaRocque, L. Mastroeni, D. Tsai, L.-H. White, F. M. 2020-05-14 doi:10.1101/2020.05.12.090688 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Catestatin (CST) is a key mediator of the immunoendocrine regulation of cardiovascular function ]]> https://biorxiv.org/content/10.1101/2020.05.12.092254v1?rss=1 Ying, W. Tang, K. Avolio, E. Schilling, J. M. Pasqua, T. Liu, M. A. Mahata, S. Bandyopadhyay, G. K. Das, S. Sahoo, D. Webster, N. J. Patel, H. H. Ghosh, P. Mahata, S. K. 2020-05-14 doi:10.1101/2020.05.12.092254 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Structural and Dynamic Basis of Molecular Recognition between Acyltransferase and Carrier Protein in E. coli Fatty Acid Synthesis ]]> https://biorxiv.org/content/10.1101/2020.05.15.098798v1?rss=1 Misson, L. E. Mindrebo, J. T. Davis, T. D. Patel, A. McCammon, J. A. Noel, J. P. Burkart, M. D. 2020-05-15 doi:10.1101/2020.05.15.098798 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein ]]> https://biorxiv.org/content/10.1101/2020.05.17.100685v1?rss=1 Ye, Q. West, A. M. V. Silletti, S. Corbett, K. D. 2020-05-17 doi:10.1101/2020.05.17.100685 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development ]]> https://biorxiv.org/content/10.1101/2020.05.18.101071v1?rss=1 Geusz, R. J. Wang, A. Chiou, J. Lancman, J. J. Wetton, N. Kefalopoulou, S. Wang, J. Qiu, Y. Yan, J. Aylward, A. Ren, B. Dong, P. D. S. Gaulton, K. J. Sander, M. 2020-05-19 doi:10.1101/2020.05.18.101071 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes ]]> https://biorxiv.org/content/10.1101/2020.05.19.104992v1?rss=1 Kavvas, E. Feist, A. Antoniewicz, M. R. Palsson, B. Monk, J. Ding, Y. Long, C. 2020-05-20 doi:10.1101/2020.05.19.104992 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Travelling spindles create necessary conditions for spike-timing-dependent plasticity in humans ]]> https://biorxiv.org/content/10.1101/2020.05.21.079152v1?rss=1 Dickey, C. W. Sargsyan, A. Madsen, J. R. Eskandar, E. N. Cash, S. S. Halgren, E. 2020-05-22 doi:10.1101/2020.05.21.079152 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Spatial Confidence Sets for Standardized Effect Size Images ]]> https://biorxiv.org/content/10.1101/2020.05.21.108761v1?rss=1 Bowring, A. Telschow, F. Schwartzman, A. Nichols, T. E. 2020-05-25 doi:10.1101/2020.05.21.108761 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.21.109694v1?rss=1 Gao, Y. Bang, I. Seif, Y. Nam, G. Sastry, A. V. Chen, K. Monk, J. Choudhary, K. S. Seo, S. W. Lee, E.-Y. Kim, D. Palsson, B. 2020-05-22 doi:10.1101/2020.05.21.109694 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Towards complete and error-free genome assemblies of all vertebrate species ]]> https://biorxiv.org/content/10.1101/2020.05.22.110833v1?rss=1 Rhie, A. McCarthy, S. A. Fedrigo, O. Damas, J. Formenti, G. Koren, S. Uliano-Silva, M. Chow, W. Fungtammasan, A. Gedman, G. L. Cantin, L. J. Thibaud-Nissen, F. Haggerty, L. Lee, C. Ko, B. J. Kim, J. Bista, I. Smith, M. Haase, B. Mountcastle, J. Winkler, S. Paez, S. Howard, J. Vernes, S. C. Lama, T. M. Grutzner, F. C. Warren, W. C. Balakrishnan, C. Burt, D. George, J. M. Biegler, M. Iorns, D. Digby, A. Eason, D. Edwards, T. Wilkinson, M. Turner, G. F. Meyer, A. Kautt, A. F. Franchini, P. Detrich, H. W. Svardal, H. Wagner, M. Naylor, G. J. P. Pippel, M 2020-05-23 doi:10.1101/2020.05.22.110833 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Explication of CB1 receptor contributions to the hypothermic effects of Δ9-tetrahydrocannabinol (THC) when delivered by vapor inhalation or parenteral injection in rats ]]> https://biorxiv.org/content/10.1101/2020.05.22.111468v1?rss=1 Nguyen, J. D. Creehan, K. M. Grant, Y. Vandewater, S. A. Kerr, T. M. Taffe, M. A. 2020-05-26 doi:10.1101/2020.05.22.111468 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Autism genetics perturb prenatal neurodevelopment through a hierarchy of broadly-expressed and brain-specific genes ]]> https://biorxiv.org/content/10.1101/2020.05.23.112623v1?rss=1 Gazestani, V. H. Chiang, A. W. Courchesne, E. Lewis, N. E. 2020-05-26 doi:10.1101/2020.05.23.112623 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Emergence and Propagation of Epistasis in Metabolic Networks ]]> https://biorxiv.org/content/10.1101/2020.05.24.113001v1?rss=1 Kryazhimskiy, S. 2020-05-26 doi:10.1101/2020.05.24.113001 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Variable Number Tandem Repeats mediate the expression of proximal genes ]]> https://biorxiv.org/content/10.1101/2020.05.25.114082v1?rss=1 Bakhtiari, M. Park, J. Ding, Y.-C. Shleizer-Burko, S. Neuhausen, S. L. Halldorsson, B. V. Stefansson, K. Gymrek, M. Bafna, V. 2020-05-25 doi:10.1101/2020.05.25.114082 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Neuronal timescales are functionally dynamic and shaped by cortical microarchitecture ]]> https://biorxiv.org/content/10.1101/2020.05.25.115378v1?rss=1 Gao, R. van den Brink, R. L. Pfeffer, T. Voytek, B. 2020-05-26 doi:10.1101/2020.05.25.115378 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli ]]> https://biorxiv.org/content/10.1101/2020.05.27.119784v1?rss=1 Flamholz, A. I. Dugan, E. Blikstad, C. Gleizer, S. Ben-Nissan, R. Amram, S. Antonovsky, N. Ravishankar, S. Noor, E. Bar-Even, A. Milo, R. Savage, D. 2020-05-27 doi:10.1101/2020.05.27.119784 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR) ]]> https://biorxiv.org/content/10.1101/2020.05.31.126623v1?rss=1 Kellman, B. P. Zhang, Y. Logomasini, E. Meinhardt, E. Chiang, A. W. T. Sorrentino, J. T. LIang, C. Bao, B. Zhou, Y. Akases, S. Sogabe, I. Kuoka, T. Wilson, I. B. H. Campbell, M. P. Neelamegham, S. Krambeck, F. J. Aoki-Kinoshita, K. F. Lewis, N. E. 2020-06-01 doi:10.1101/2020.05.31.126623 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Deep sncRNA-seq of the PPMI cohort to study Parkinson's disease progression ]]> https://biorxiv.org/content/10.1101/2020.06.01.127092v1?rss=1 Kern, F. Fehlmann, T. Violich, I. Alsop, E. Hutchins, E. Kahraman, M. Grammes, N. L. Guimaraes, P. Backes, C. Poston, K. Casey, B. Balling, R. Geffers, L. Krueger, R. Galasko, D. Mollenhauer, B. Meese, E. Wyss-Coray, T. Craig, D. W. Van Keuren-Jensen, K. Keller, A. 2020-06-01 doi:10.1101/2020.06.01.127092 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Evolutionarily related small viral fusogens hijack distinct but modular actin nucleation pathways to drive cell-cell fusion ]]> https://biorxiv.org/content/10.1101/2020.06.03.130740v1?rss=1 Chan, K. M. C. Arthur, A. L. Morstein, J. Jin, M. Bhat, A. Schlesinger, D. Son, S. Stevens, D. A. Drubin, D. G. Fletcher, D. A. 2020-06-04 doi:10.1101/2020.06.03.130740 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2020.06.07.138933v1?rss=1 Machado, H. Seif, Y. Sakoulas, G. Olson, C. A. Szubin, R. Palsson, B. Nizet, V. Feist, A. M. 2020-06-07 doi:10.1101/2020.06.07.138933 Cold Spring Harbor Laboratory Press 2020-06-07 <![CDATA[ Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution ]]> https://biorxiv.org/content/10.1101/2020.06.12.147033v1?rss=1 Lawson, C. L. Kryshtafovych, A. Adams, P. D. Afonine, P. Baker, M. L. Barad, B. A. Bond, P. Burnley, T. Cao, R. Cheng, J. Chojnowski, G. Cowtan, K. Dill, K. A. DiMaio, F. Farrell, D. Fraser, J. S. Herzik, M. A. Hoh, S. W. Hou, J. Hung, L.-W. Igaev, M. Joseph, A. P. Kihara, D. Kumar, D. Mittal, S. Monastyrskyy, B. Olek, M. Palmer, C. Patwardhan, A. Perez, A. Pfab, J. Pintilie, G. D. Richardson, J. S. Rosenthal, P. B. Sarkar, D. Schaefer, L. U. Schmid, M. F. Schroeder, G. F. Shekhar, M. Si, D. Singharoy, A. Terashi, G. Terwilliger, T. C. Vaiana, A. Wan 2020-06-15 doi:10.1101/2020.06.12.147033 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Adipose tissue macrophages orchestrate β cell adaptation in obesity through secreting miRNA-containing extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2020.06.12.148809v1?rss=1 Gao, H. Luo, Z. Jin, Z. Ji, Y. Ying, W. 2020-06-13 doi:10.1101/2020.06.12.148809 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Decoding of persistent multiscale structures in complex biological networks ]]> https://biorxiv.org/content/10.1101/2020.06.16.151555v1?rss=1 Zheng, F. Zhang, S. Churas, C. Pratt, D. Bahar, I. Ideker, T. 2020-06-17 doi:10.1101/2020.06.16.151555 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Machine Learning Models Identify Inhibitors of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.06.16.154765v1?rss=1 Gawriljuk, V. O. Kyaw Zin, P. P. Foil, D. H. Bernatchez, J. Beck, S. Beutler, N. Ricketts, J. Yang, L. Rogers, T. Puhl, A. C. Zorn, K. M. Lane, T. R. Godoy, A. S. Olivia, G. Siqueira-Neto, J. L. Madrid, P. Ekins, S. 2020-06-16 doi:10.1101/2020.06.16.154765 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Structural mimicry confers robustness in the cyanobacterial circadian clock ]]> https://biorxiv.org/content/10.1101/2020.06.17.158394v1?rss=1 Heisler, J. Swan, J. A. Palacios, J. G. Sancar, C. Ernst, D. C. Spangler, R. K. Bagshaw, C. R. Tripathi, S. Crosby, P. Golden, S. S. Partch, C. L. LiWang, A. 2020-06-19 doi:10.1101/2020.06.17.158394 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Reconstitution of an intact clock that generates circadian DNA binding in vitro ]]> https://biorxiv.org/content/10.1101/2020.06.18.158576v1?rss=1 Chavan, A. G. Ernst, D. C. Fang, M. Sancar, C. Partch, C. L. Golden, S. S. LiWang, A. 2020-06-19 doi:10.1101/2020.06.18.158576 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ An Analysis of SARS-CoV-2 Using ViReport ]]> https://biorxiv.org/content/10.1101/2020.06.20.163162v1?rss=1 Song, M. J. Moshiri, N. 2020-06-21 doi:10.1101/2020.06.20.163162 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ Phosphoproteomics after nitrate treatments reveal an important role for PIN2 phosphorylation in control of root system architecture. ]]> https://biorxiv.org/content/10.1101/2020.06.22.164640v1?rss=1 Vega, A. Fredes, I. O'Brien, J. Shen, Z. Otvos, K. Benkova, E. Briggs, S. Gutierrez, R. A. 2020-06-23 doi:10.1101/2020.06.22.164640 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species ]]> https://biorxiv.org/content/10.1101/2020.06.23.162792v1?rss=1 Hanna, E. M. Zhang, X. Eide, M. Fallahi, S. Furmanek, T. Yadetie, F. Zielinski, D. C. Goksoyr, A. Jonassen, I. 2020-06-24 doi:10.1101/2020.06.23.162792 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Elucidation of regulatory modes for five two-component systems in Escherichia coli reveals novel relationships ]]> https://biorxiv.org/content/10.1101/2020.06.23.168344v1?rss=1 Choudhary, K. S. Kleinmanns, J. A. Decker, K. Sastry, A. V. Gao, Y. Szubin, R. Seif, Y. Palsson, B. O. 2020-06-24 doi:10.1101/2020.06.23.168344 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Systematic evaluation of parameterization for genome-scale metabolic models of cultured mammalian cells ]]> https://biorxiv.org/content/10.1101/2020.06.24.169938v1?rss=1 Schinn, S.-M. Morrison, C. Wei, W. Zhang, L. Lewis, N. E. 2020-06-26 doi:10.1101/2020.06.24.169938 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor ]]> https://biorxiv.org/content/10.1101/2020.06.25.172403v1?rss=1 Zhao, P. Praissman, J. L. Grant, O. C. Cai, Y. Xiao, T. Rosenbalm, K. E. Aoki, K. Kellman, B. P. Bridger, R. Barouch, D. H. Brindley, M. A. Lewis, N. E. Tiemeyer, M. Chen, B. Woods, R. J. Wells, L. 2020-06-26 doi:10.1101/2020.06.25.172403 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Tissue specific muscle extracellular matrix hydrogel improves skeletal muscle regeneration in vivo over non-matched tissue source ]]> https://biorxiv.org/content/10.1101/2020.06.30.181164v1?rss=1 Ungerleider, J. L. Dzieciatkowska, M. Hansen, K. C. Christman, K. L. 2020-07-01 doi:10.1101/2020.06.30.181164 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation ]]> https://biorxiv.org/content/10.1101/2020.07.02.183459v1?rss=1 Kim, M. Harmanci, A. O. Bossuat, J.-P. Carpov, S. Cheon, J. H. Chilotti, I. Cho, W. Froelicher, D. Gama, N. Georgieva, M. Hong, S. Hubaux, J.-P. Kim, D. Lauter, K. Ma, Y. Ohno-Machado, L. Sofia, H. J. Son, Y. Song, Y. Troncoso-Pastoriza, J. R. Jiang, X. 2020-07-04 doi:10.1101/2020.07.02.183459 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Alcohol Dependence Differentially Alters Orbitofrontal Cortex Representations of Inferred Decision-Making and Outcomes ]]> https://biorxiv.org/content/10.1101/2020.07.03.186148v1?rss=1 Cazares, C. Schreiner, D. C. Gremel, C. M. 2020-07-04 doi:10.1101/2020.07.03.186148 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture ]]> https://biorxiv.org/content/10.1101/2020.07.06.185066v1?rss=1 Chia, R. Sabir, M. S. Bandres-Ciga, S. Saez-Atienzar, S. Reynolds, R. H. Gustavsson, E. Walton, R. L. Ahmed, S. Viollet, C. Ding, J. Makarious, M. B. Diez-Fairen, M. Portley, M. K. Shah, Z. Abramzon, Y. Hernandez, D. G. Blauwendraat, C. Stone, D. J. Eicher, J. Parkkinen, L. Ansorge, O. Clark, L. Honig, L. S. Marder, K. Lemstra, A. St. George-Hyslop, P. Londos, E. Morgan, K. Lashley, T. Warner, T. T. Jaunmuktane, Z. Galasko, D. Santana, I. Tienari, P. Myllykangas, L. Oinas, M. Cairns, N. J. Morris, J. C. Halliday, G. M. Van Deerlin, V. M. Trojanowski, J. 2020-07-06 doi:10.1101/2020.07.06.185066 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Repurposed Drugs Block Toxin-Driven Platelet Clearance by the Hepatic Ashwell-Morell Receptor to Clear Staphylococcus aureus Bacteremia ]]> https://biorxiv.org/content/10.1101/2020.07.06.190322v1?rss=1 Sun, J. Uchiyama, S. Olson, J. Morodomi, Y. Cornax, I. Ando, N. Kohno, Y. Kyaw, M. M. T. Aguilar, B. Haste, N. M. Kanaji, S. Kanaji, T. Rose, W. E. Sakoulas, G. Marth, J. D. Nizet, V. 2020-07-07 doi:10.1101/2020.07.06.190322 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains ]]> https://biorxiv.org/content/10.1101/2020.07.07.192526v1?rss=1 Hui Huang Quan Zhu Adam Jussila Yuanyuan Han Bogdan Bintu Colin Kern Mattia Conte Yanxiao Zhang Simona Bianco Andrea Chiariello Miao Yu Rong Hu Ivan Juric Ming Hu Mario Nicodemi Xiaowei Zhuang Bing Ren 2020-07-08 doi:10.1101/2020.07.07.192526 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Reference data based insights expand understanding of human metabolomes ]]> https://biorxiv.org/content/10.1101/2020.07.08.194159v1?rss=1 Julia M Gauglitz Wout Bittremieux Candace L Williams Kelly C Weldon Morgan W Panitchpakdi Francesca Di Ottavio Christine M Aceves Elizabeth Brown Nicole C Sikora Alan K. Jarmusch Cameron Martino Anupriya Tripathi Erfan Sayyari Justin Shaffer Roxana Coras Fernando Vargas Lindsay DeRight Goldasich Tara Schwartz MacKenzie Bryant Gregory Humphrey Abigail J. Johnson Katharina Spengler Pedro Belda-Ferre Edgar Diaz Daniel McDonald Qiyun Zhu Dominic S. Nguyen Emmanuel O. Elijah Mingxun Wang Clarisse Marotz Kate E. Sprecher Daniela Vargas-Robles Dana Withrow Gail Ackerm 2020-07-11 doi:10.1101/2020.07.08.194159 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2 ]]> https://biorxiv.org/content/10.1101/2020.07.13.198069v1?rss=1 Schmidt, S. H. Weng, J.-H. Aoto, P. C. Boassa, D. Mathea, S. Silletti, S. Hu, J. Wallbott, M. Komives, E. A. Knapp, S. Herberg, F. W. Taylor, S. S. 2020-07-14 doi:10.1101/2020.07.13.198069 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 ]]> https://biorxiv.org/content/10.1101/2020.07.14.201616v1?rss=1 Clausen, T. M. Sandoval, D. R. Spliid, C. B. Pihl, J. Painter, C. D. Thacker, B. E. Glass, C. A. Narayanan, A. Majowicz, S. A. Zhang, Y. Torres, J. L. Golden, G. J. Porell, R. Garretson, A. F. Laubach, L. Feldman, J. Yin, X. Pu, Y. Hauser, B. Caradonna, T. M. Kellman, B. P. Martino, C. Gordts, P. L. S. M. Leibel, S. L. Chanda, S. K. Schmidt, A. G. Godula, K. Jose, J. Corbett, K. D. Ward, A. B. Carlin, A. F. Esko, J. D. 2020-07-14 doi:10.1101/2020.07.14.201616 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Nef enhances HIV-1 replication and infectivity independently of SERINC3 and SERINC5 in CEM T cells ]]> https://biorxiv.org/content/10.1101/2020.07.15.205757v1?rss=1 Ramirez, P. W. Angerstein, A. A. Suarez, M. Vollbrecht, T. Wallace, J. O'Connell, R. M. Guatelli, J. 2020-07-17 doi:10.1101/2020.07.15.205757 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity ]]> https://biorxiv.org/content/10.1101/2020.07.16.206680v1?rss=1 Oliveira, A. S. Ibarra, A. A. Bermudez, I. Casalino, L. Gaieb, Z. Shoemark, D. K. Gallagher, T. Sessions, R. B. Amaro, R. E. Mulholland, A. J. 2020-07-17 doi:10.1101/2020.07.16.206680 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ The Argo: A 65,536 channel recording system for high density neural recording in vivo ]]> https://biorxiv.org/content/10.1101/2020.07.17.209403v1?rss=1 Sahasrabuddhe, K. Khan, A. A. Singh, A. P. Stern, T. M. Ng, Y. Tadic, A. Orel, P. LaReau, C. Pouzzner, D. Nishimura, K. Boergens, K. M. Shivakumar, S. Hopper, M. S. Kerr, B. Hanna, M.-E. S. Edgington, R. J. McNamara, I. Fell, D. Gao, P. Babaie-Fishani, A. Veijalainen, S. Klekachev, A. V. Stuckey, A. M. Luyssaert, B. Kozai, T. D. Y. Xie, C. Gilja, V. Dierickx, B. Kong, Y. Straka, M. Sohal, H. S. Angle, M. R. 2020-07-17 doi:10.1101/2020.07.17.209403 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Biased orientation representations can be explained by experience with non-uniform training set statistics ]]> https://biorxiv.org/content/10.1101/2020.07.17.209536v1?rss=1 Henderson, M. M. Serences, J. 2020-07-18 doi:10.1101/2020.07.17.209536 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut. ]]> https://biorxiv.org/content/10.1101/2020.07.20.212498v1?rss=1 Zhi, H. Behnsen, J. Aron, A. Subramanian, V. Liu, J. Gerner, R. Petras, D. Green, K. Price, S. Camacho, J. Hillman, H. Tjokrosurjo, J. Montaldo, N. Hoover, E. Treacy-Abarca, S. Gilston, B. Skaar, E. Chazin, W. Garneau-Tsodikova, S. Lawrenz, M. Perry, R. Nuccio, S.-P. Dorrestein, P. Raffatellu, M. 2020-07-21 doi:10.1101/2020.07.20.212498 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner ]]> https://biorxiv.org/content/10.1101/2020.07.21.214932v1?rss=1 1/2 log10 increased infectivity in human cells expressing the human ACE2 protein as the viral receptor. The increased binding/fusion activity of the D614G Spike protein was corroborated in a cell fusion assay using Spike and ACE2 proteins expressed in different cells. These results are consistent with the possibility that the Spike D614G mutant increases the infectivity of SARS-CoV2. ]]> Ogawa, J. Zhu, W. Tonnu, N. Singer, O. Hunter, T. Ryan (Firth), A. L. Pao, G. M. 2020-07-22 doi:10.1101/2020.07.21.214932 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.23.217067v1?rss=1 Espin Palazon, R. Campbell, C. A. Fursova, O. Cheng, X. Snella, E. McCune, A. Li, L. Solchenberger, B. Schmid, B. Sahoo, D. Morton, M. Traver, D. 2020-07-23 doi:10.1101/2020.07.23.217067 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease ]]> https://biorxiv.org/content/10.1101/2020.07.23.218784v1?rss=1 Sztain, T. Amaro, R. E. McCammon, J. A. 2020-07-24 doi:10.1101/2020.07.23.218784 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Evolution of regulatory signatures in primate cortical neurons at cell type resolution ]]> https://biorxiv.org/content/10.1101/2020.07.24.219881v1?rss=1 Kozlenkov, A. Vermunt, M. W. Apontes, P. Li, J. Hao, K. Sherwood, C. C. Hof, P. R. Ely, J. J. Wegner, M. Mukamel, E. A. Creyghton, M. P. Koonin, E. V. Dracheva, S. 2020-07-27 doi:10.1101/2020.07.24.219881 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ E-cigarettes compromise the gut barrier and trigger gut inflammation ]]> https://biorxiv.org/content/10.1101/2020.07.29.227348v1?rss=1 90% of e-cigarette e-liquids as the source of harm. Given the ever-expanding importance of the integrity of the gut barrier for host fitness, and impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health. SIGNIFICANCEThe safety of electronic cigarettes has been questioned amidst emerging evidence that they may derail our immune system and increase our susceptibility to infections. Despite these insights, their impact on the most critical entity that separates trillions of microbes from the largest immune system in our body, i.e., the gut barrier, remains unexplored. Using a combination of mouse models, gut transcriptomics, and murine and human gut-derived organoids, here we show that chronic exposure to aerosols of electronic-cigarette disrupts the gut barrier, increases its susceptibility to bacterial infections and triggers inflammation. Given the importance of the gut barrier in the maintenance of immune homeostasis, these findings provide valuable insights into the potential long-term harmful effects of electronic cigarettes on health. ]]> Sharma, A. Lee, J. Fonseca, A. Moshensky, A. Kothari, T. Ibrahim, I. S. Ibeawuchi, S.-R. Pranadinata, R. Ear, J. Sahoo, D. Crotty-Alexander, L. Ghosh, P. Das, S. 2020-07-30 doi:10.1101/2020.07.29.227348 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein ]]> https://biorxiv.org/content/10.1101/2020.07.30.228023v1?rss=1 Lu, S. Ye, Q. Singh, D. Villa, E. Cleveland, D. W. Corbett, K. D. 2020-07-31 doi:10.1101/2020.07.30.228023 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ A genetic probe for visualizing glutamatergic synapses and vesicles by 3D electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.07.31.230995v1?rss=1 Steinkellner, T. Madany, M. Haberl, M. G. Zell, V. Li, C. Hu, J. Mackey, M. Ramachandra, R. Adams, S. Ellisman, M. H. Hnasko, T. BOASSA, D. 2020-08-03 doi:10.1101/2020.07.31.230995 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi ]]> https://biorxiv.org/content/10.1101/2020.08.02.233056v1?rss=1 Adolfi, A. Gantz, V. M. Jasinskiene, N. Lee, H.-F. Hwang, K. Bulger, E. A. Ramaiah, A. Bennett, J. B. Terradas, G. Emerson, J. J. Marshall, J. M. Bier, E. James, A. A. 2020-08-02 doi:10.1101/2020.08.02.233056 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment ]]> https://biorxiv.org/content/10.1101/2020.08.03.234146v1?rss=1 Marlow, J. Spietz, R. Kim, K.-Y. Ellisman, M. Girguis, P. Hatzenpichler, R. 2020-08-03 doi:10.1101/2020.08.03.234146 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Ventral Pallidum GABA Neurons Mediate Motivation Underlying Risky Choice ]]> https://biorxiv.org/content/10.1101/2020.08.04.221960v1?rss=1 Farrell, M. R. Esteban, J. Faget, L. Floresco, S. B. Hnasko, T. S. Mahler, S. V. 2020-08-04 doi:10.1101/2020.08.04.221960 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival ]]> https://biorxiv.org/content/10.1101/2020.08.05.238758v1?rss=1 Agelidis, A. Turturice, B. A. Suryawanshi, R. K. Yadavalli, T. Jaishankar, D. Ames, J. Hopkins, J. Koujah, L. Patil, C. D. Hadigal, S. R. Kyzar, E. J. Campeau, A. Wozniak, J. M. Gonzalez, D. J. Vlodavsky, I. Li, J.-p. Perkins, D. L. Finn, P. W. Shukla, D. 2020-08-06 doi:10.1101/2020.08.05.238758 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ White Matter Disruption in Pediatric Traumatic Brain Injury: Results from ENIGMA Pediatric msTBI ]]> https://biorxiv.org/content/10.1101/2020.08.06.237271v1?rss=1 Dennis, E. L. Caeyenberghs, K. Hoskinson, K. R. Merkley, T. L. Suskauer, S. J. Asarnow, R. F. Babikian, T. Bartnik-Olson, B. Bickart, K. Bigler, E. D. Ewing-Cobbs, L. Figaji, A. Giza, C. C. Hunsaker-Goodrich, N. J. Hodges, C. B. Hovenden, E. S. Irimia, A. Königs, M. Levin, H. S. Lindsey, H. M. Max, J. E. Newsome, M. R. Olsen, A. Ryan, N. P. Schmidt, A. T. Spruiell, M. S. Wade, B. S. Ware, A. L. Watson, C. G. Wheeler, A. L. Yeates, K. O. Zielinski, B. A. Kochunov, P. Jahanshad, N. Thompson, P. M. Tate, D. F. Wilde, E. A. 2020-08-07 doi:10.1101/2020.08.06.237271 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi ]]> https://biorxiv.org/content/10.1101/2020.08.09.229716v1?rss=1 Kalogriopoulos, N. Lopez-Sanchez, I. Lin, C. Ngo, T. Midde, K. Roy, S. Aznar, N. Murray, F. Garcia-Marcos, M. Kufareva, I. Ghassemian, M. Ghosh, P. 2020-08-10 doi:10.1101/2020.08.09.229716 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation ]]> https://biorxiv.org/content/10.1101/2020.08.10.243634v1?rss=1 Kuo, C.-C. Chiang, W.-T. Lewis, N. E. 2020-08-10 doi:10.1101/2020.08.10.243634 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Tomato spotted wilt virus benefits its thrips vector by modulating metabolic and plant defense pathways in tomato ]]> https://biorxiv.org/content/10.1101/2020.08.10.244665v1?rss=1 Nachappa, P. Challacombe, J. F. Margolies, D. C. Nechols, J. R. Whitfield, A. E. Rotenberg, D. 2020-08-11 doi:10.1101/2020.08.10.244665 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development ]]> https://biorxiv.org/content/10.1101/2020.08.10.244814v1?rss=1 Breuss, M. W. Yang, X. Antaki, D. Schlachetzki, J. C. M. Lana, A. A. Xu, X. Chai, G. Stanley, V. Song, Q. Fang Newmeyer, T. Nguyen, A. Cao, B. Nott, A. McEvoy-Venneri, J. Pasillas, M. P. Nahas, S. Van Der Kraan, L. Ding, Y. NIMH Brain Somatic Mosaicism Network, Glass, C. K. Gleeson, J. G. 2020-08-10 doi:10.1101/2020.08.10.244814 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Reelin deficiency contributes to long-term behavioral abnormalities induced by chronic adolescent exposure to Δ9-tetrahydrocannabinol in mice ]]> https://biorxiv.org/content/10.1101/2020.08.10.245449v1?rss=1 Iemolo, A. Nur, A. Montilla-Perez, P. Risbrough, V. B. Telese, F. 2020-08-13 doi:10.1101/2020.08.10.245449 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ A cohesin-independent mechanism modulates recombination activity along meiotic chromosomes ]]> https://biorxiv.org/content/10.1101/2020.08.11.247122v1?rss=1 Heldrich, J. Markowitz, T. E. Vale-Silva, L. A. Hochwagen, A. 2020-08-12 doi:10.1101/2020.08.11.247122 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning ]]> https://biorxiv.org/content/10.1101/2020.08.13.250159v1?rss=1 Rychel, K. Decker, K. Sastry, A. V. Phaneuf, P. V. Poudel, S. Palsson, B. O. 2020-08-14 doi:10.1101/2020.08.13.250159 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity ]]> https://biorxiv.org/content/10.1101/2020.08.17.238444v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@14ff1ecorg.highwire.dtl.DTLVardef@193d84corg.highwire.dtl.DTLVardef@15d6f9eorg.highwire.dtl.DTLVardef@14b16c6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. Diagram of hypothesis for bacterial mediation of SARS-CoV-2 infection through heparan sulfate (HS).It is well known that host microbes groom the mucosa where they reside. Recent investigations have shown that HS, a major component of mucosal layers, is necessary for SARS-CoV-2 infection. In this study we examine the impact of microbial modification of HS on viral attachment. C_FIG ]]> Martino, C. Kellman, B. P. Sandoval, D. R. Clausen, T. M. Marotz, C. A. Song, S. J. Wandro, S. Zaramela, L. S. Salido Benitez, R. A. Zhu, Q. Armingol, E. Vazquez-Baeza, Y. McDonald, D. Sorrentino, J. T. Taylor, B. Belda-Ferre, P. Liang, C. Zhang, Y. Schifanella, L. Klatt, N. R. Havulinna, A. S. Jousilahti, P. Huang, S. Haiminen, N. Parida, L. Kim, H.-C. Swafford, A. D. Zengler, K. Cheng, S. Inouye, M. Niiranen, T. Jain, M. Salomaa, V. Esko, J. D. Lewis, N. E. Knight, R. 2020-08-18 doi:10.1101/2020.08.17.238444 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome ]]> https://biorxiv.org/content/10.1101/2020.08.18.253443v1?rss=1 Lombardo, M. V. Eyler, L. Pramparo, T. Gazestani, V. H. Hagler, D. J. Chen, C.-H. Dale, A. M. Seidlitz, J. Bethlehem, R. A. I. Bertelsen, N. Carter Barnes, C. Lopez, L. Campbell, K. Lewis, N. E. Pierce, K. Courchesne, E. 2020-08-18 doi:10.1101/2020.08.18.253443 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Longitudinal changes in aperiodic and periodic activity in electrophysiological recordings in the first seven months of life ]]> https://biorxiv.org/content/10.1101/2020.08.18.256016v1?rss=1 Schaworonkow, N. Voytek, B. 2020-08-18 doi:10.1101/2020.08.18.256016 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Color compensation in anomalous trichromats assessed with fMRI ]]> https://biorxiv.org/content/10.1101/2020.08.18.256701v1?rss=1 Tregillus, K. E. Isherwood, Z. J. Vanston, J. E. Engel, S. A. MacLeod, D. I. A. Kuriki, I. Webster, M. A. 2020-08-19 doi:10.1101/2020.08.18.256701 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ Long-range sequential dependencies precede complex syntactic production in language acquisition ]]> https://biorxiv.org/content/10.1101/2020.08.19.256792v1?rss=1 Sainburg, T. Mai, A. Gentner, T. Q. 2020-08-20 doi:10.1101/2020.08.19.256792 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ BDNF/TrkB signaling endosomes mediate long-distance dendritic growth by activating CREB/PI3K-mTOR-dependent translation in neuronal cell bodies. ]]> https://biorxiv.org/content/10.1101/2020.08.22.262923v1?rss=1 Bronfman, F. C. Moya-Alvarado, G. 2020-08-24 doi:10.1101/2020.08.22.262923 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a healthy human microbiome ]]> https://biorxiv.org/content/10.1101/2020.08.24.265504v1?rss=1 Han, Z. Thuy-Boun, P. S. Pfeiffer, W. Vartabedian, V. F. Torkamani, A. Teijaro, J. R. Wolan, D. W. 2020-08-24 doi:10.1101/2020.08.24.265504 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Heterologous expression of cryptomaldamide in a cyanobacterial host ]]> https://biorxiv.org/content/10.1101/2020.08.26.267179v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@660caforg.highwire.dtl.DTLVardef@1cab871org.highwire.dtl.DTLVardef@130de4org.highwire.dtl.DTLVardef@f50c64_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Taton, A. Ecker, A. Diaz, B. Moss, N. A. Anderson, B. Reher, R. Leao, T. F. Simkovsky, R. Dorrestein, P. C. Gerwick, L. Gerwick, W. H. Golden, J. W. 2020-08-26 doi:10.1101/2020.08.26.267179 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Regulation of Vacuole Morphology by PIEZO Channels in Spreading Earth Moss ]]> https://biorxiv.org/content/10.1101/2020.08.27.269282v1?rss=1 Radin, I. Richardson, R. A. Weiner, E. R. Bascom, C. S. Bezanilla, M. Haswell, E. 2020-08-27 doi:10.1101/2020.08.27.269282 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Hyperbolic geometry of gene expression ]]> https://biorxiv.org/content/10.1101/2020.08.27.270264v1?rss=1 Zhou, Y. Sharpee, T. 2020-08-28 doi:10.1101/2020.08.27.270264 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates ]]> https://biorxiv.org/content/10.1101/2020.08.28.263020v1?rss=1 Geusz, R. J. Wang, A. Lam, D. K. Vinckier, N. K. Alysandratos, K.-D. Roberts, D. A. Wang, J. Kefalopoulou, S. Qiu, Y. Chiou, J. Gaulton, K. J. Ren, B. Kotton, D. N. Sander, M. 2020-08-29 doi:10.1101/2020.08.28.263020 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin ]]> https://biorxiv.org/content/10.1101/2020.08.29.273516v1?rss=1 Swanson, L. A. B. Katkar, G. D. Tam, J. Pranadinata, R. Chareddy, Y. Coates, J. E. Amandachar, M. S. Castillo, V. Olson, J. Nizet, V. Kufareva, I. Das, S. Ghosh, P. 2020-08-30 doi:10.1101/2020.08.29.273516 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ A Genome-wide CRISPR-Cas9 Screen Identifies Host Factors Essential for Optimal Plasmodium Liver Stage Development. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275867v1?rss=1 Vijayan, K. Arang, N. Wei, L. Morrison, R. Geiger, R. Parks, R. K. Lewis, A. J. Mast, F. D. Douglass, A. N. Kain, H. S. Aitchison, J. D. Johnson, J. S. Aderem, A. Kaushansky, A. 2020-09-01 doi:10.1101/2020.08.31.275867 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Coupled Control of Distal Axon Integrity and Somal Responses to Axonal Damage by the Palmitoyl Acyltransferase ZDHHC17 ]]> https://biorxiv.org/content/10.1101/2020.09.01.276287v1?rss=1 Niu, J. Sanders, S. Jeong, H.-K. Holland, S. Sun, Y. Collura, K. Hernandez, L. Huang, H. Hayden, M. R. Smith, G. Hu, Y. Jin, Y. Thomas, G. 2020-09-01 doi:10.1101/2020.09.01.276287 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Meaningful Effects in the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/2020.09.01.276451v1?rss=1 Dick, A. S. Watts, A. L. Heeringa, S. G. Lopez, D. A. Bartsch, H. Fan, C. C. Palmer, C. E. Reuter, C. Marshall, A. T. Haist, F. Hawes, S. Nichols, T. Barch, D. M. Jernigan, T. L. Garavan, H. Grant, S. Pariyadath, V. Hoffman, E. Neale, M. Paulus, M. P. Sher, K. Thompson, W. 2020-09-01 doi:10.1101/2020.09.01.276451 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types ]]> https://biorxiv.org/content/10.1101/2020.09.01.278879v1?rss=1 Gillespie, T. H. Tripathy, S. Sy, M. F. Martone, M. E. Hill, S. L. 2020-09-02 doi:10.1101/2020.09.01.278879 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration ]]> https://biorxiv.org/content/10.1101/2020.09.02.278663v1?rss=1 95% of the HMO content in human milk. Through our models, we propose candidate genes for elongation, branching, fucosylation, and sialylation of HMOs. We further explored selected enzyme activities through kinetic assay and their co-regulation through transcription factor analysis. These results provide the molecular basis of HMO biosynthesis necessary to guide progress in HMO research and application with the ultimate goal of understanding and improving infant health and development. SO_SCPLOWIGNIFICANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWWith the HMO biosynthesis network resolved, we can begin to connect genotypes with milk types and thereby connect clinical infant, child and even adult outcomes to specific HMOs and HMO modifications. Knowledge of these pathways can simplify the work of synthetic reproduction of these HMOs providing a roadmap for improving infant, child, and overall human health with the specific application of a newly limitless source of nutraceuticals for infants and people of all ages. ]]> Kellman, B. P. Richelle, A. Yang, J.-Y. E. Chapla, D. G. Chiang, A. W.-T. Najera, J. Bao, B. Koga, N. Mohammad, M. A. Bruntse, A. B. Haymond, M. W. Bode, L. Lewis, N. E. 2020-09-03 doi:10.1101/2020.09.02.278663 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations ]]> https://biorxiv.org/content/10.1101/2020.09.02.279265v1?rss=1 Rees, E. Creeth, H. Hwu, H.-G. Chen, W. J. Tsuang, M. Glatt, S. Rey, R. Kirov, G. Walters, J. Holmans, P. Owen, M. O'Donovan, M. 2020-09-02 doi:10.1101/2020.09.02.279265 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ A genome-scale metabolic network model synergizes with statistical learning to predict amino acid concentrations in Chinese Hamster Ovary cell cultures ]]> https://biorxiv.org/content/10.1101/2020.09.02.279687v1?rss=1 Schinn, S.-M. Morrison, C. Wei, W. Zhang, L. Lewis, N. E. 2020-09-03 doi:10.1101/2020.09.02.279687 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ A balance between matrix deformation and the coordination of turning events governs directed neutrophil migration in 3-D matrices ]]> https://biorxiv.org/content/10.1101/2020.09.02.868505v1?rss=1 Francois, J. Kandasamy, A. Yeh, Y.-T. Ayala, C. Meili, R. Chien, S. Lasheras, J. C. del Alamo, J. C. 2020-09-02 doi:10.1101/2020.09.02.868505 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ A vapor inhalation method for delivering heroin alters nociception, body temperature and spontaneous activity in female and male rats ]]> https://biorxiv.org/content/10.1101/2020.09.03.281857v1?rss=1 Gutierrez, A. Creehan, K. M. Taffe, M. A. 2020-09-04 doi:10.1101/2020.09.03.281857 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ The structure, function, and evolution of a complete human chromosome 8 ]]> https://biorxiv.org/content/10.1101/2020.09.08.285395v1?rss=1 Logsdon, G. A. Vollger, M. R. Hsieh, P. Mao, Y. Liskovykh, M. A. Koren, S. Nurk, S. Mercuri, L. Dishuck, P. C. Rhie, A. de Lima, L. G. Porubsky, D. Bzikadze, A. V. Kremitzki, M. Graves-Lindsay, T. A. Jain, C. Hoekzema, K. Murali, S. C. Munson, K. M. Baker, C. Sorenson, M. Lewis, A. M. Surti, U. Gerton, J. L. Larionov, V. Ventura, M. Miga, K. H. Phillippy, A. M. Eichler, E. E. 2020-09-08 doi:10.1101/2020.09.08.285395 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Protecting synapses from amyloid β-associated degeneration by manipulations of Wnt/planar cell polarity signaling ]]> https://biorxiv.org/content/10.1101/2020.09.09.273011v1?rss=1 Feng, B. Freitas, A. Tian, R. Lee, Y. R. Grewal, A. Wang, J. Zou, Y. 2020-09-09 doi:10.1101/2020.09.09.273011 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association ]]> https://biorxiv.org/content/10.1101/2020.09.11.291724v1?rss=1 287,000 candidate cis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner. ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases. ]]> Hocker, J. D. Poirion, O. B. Zhu, F. Buchanan, J. Zhang, K. Chiou, J. Wang, T.-M. Hou, X. Li, Y. E. Zhang, Y. Farah, E. Wang, A. McCulloch, A. D. Gaulton, K. J. Ren, B. Chi, N. C. Preissl, S. 2020-09-12 doi:10.1101/2020.09.11.291724 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Real-time structural motif searching in proteins using an inverted index strategy ]]> https://biorxiv.org/content/10.1101/2020.09.11.293977v1?rss=1 160,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids. Author summaryThe Protein Data Bank (PDB) provides open access to more than 160,000 three-dimensional structures of proteins, nucleic acids, and biological complexes. Similarities between PDB structures give valuable functional and evolutionary insights but such resemblance may not be evident at sequence or global structure level. Throughout the database, there are recurring structural motifs - groups of modest numbers of residues in proximity that, for example, support catalytic activity. Identification of common structural motifs can unveil subtle similarities between proteins and serve as fingerprints for configurations such as the His-Asp-Ser catalytic triad found in serine proteases or the zinc coordination site found in Zinc Finger DNA-binding domains. We present a highly efficient yet flexible strategy that allows users for the first time to search for arbitrary structural motifs across the entire PDB archive in real-time. Our approach scales favorably with the increasing number and complexity of deposited structures, and, also, has the potential to be adapted for other applications in a macromolecular context. ]]> Bittrich, S. Burley, S. K. Rose, A. S. 2020-09-12 doi:10.1101/2020.09.11.293977 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Optimizing Mitochondrial Maintenance in Extended Neuronal Projections ]]> https://biorxiv.org/content/10.1101/2020.09.11.294207v1?rss=1 Agrawal, A. Koslover, E. F. 2020-09-12 doi:10.1101/2020.09.11.294207 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Context influences how individuals with misophonia respond to sounds ]]> https://biorxiv.org/content/10.1101/2020.09.12.292391v1?rss=1 Edelstein, M. Monk, B. Ramachandran, V. S. Rouw, R. 2020-09-15 doi:10.1101/2020.09.12.292391 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Deciphering the postsynaptic calcium-mediated energy homeostasis through mitochondria-endoplasmic reticulum contact sites using systems modeling ]]> https://biorxiv.org/content/10.1101/2020.09.12.294827v1?rss=1 Leung, A. K. Ohadi, D. Pekkurnaz, G. Rangamani, P. 2020-09-13 doi:10.1101/2020.09.12.294827 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity ]]> https://biorxiv.org/content/10.1101/2020.09.13.276923v1?rss=1 Inde, Z. Yapp, C. Joshi, G. N. Spetz, J. Fraser, C. Deskin, B. Ghelfi, E. Sodhi, C. Hackam, D. Kobzik, L. Croker, B. Brownfield, D. Jia, H. Sarosiek, K. A. 2020-09-13 doi:10.1101/2020.09.13.276923 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ The flexibility of ACE2 in the context of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.09.16.300459v1?rss=1 Barros, E. P. Casalino, L. Gaieb, Z. Dommer, A. C. Wang, Y. Fallon, L. Raguette, L. Belfon, K. Simmerling, C. L. Amaro, R. E. 2020-09-16 doi:10.1101/2020.09.16.300459 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Scalable Models of Antibody Evolution and Benchmarking of Clonal Tree Reconstruction Methods ]]> https://biorxiv.org/content/10.1101/2020.09.17.302505v1?rss=1 Zhang, C. Bzikadze, A. V. Safonova, Y. Mirarab, S. 2020-09-20 doi:10.1101/2020.09.17.302505 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides ]]> https://biorxiv.org/content/10.1101/2020.09.19.304303v1?rss=1 Muntjewerff, E. M. Tang, K. Lutter, L. Christoffersson, G. Nicolasen, M. J. T. Gao, H. Katkar, G. D. Das, S. Beest, M. t. Ying, W. Ghosh, P. El Aidy, S. Oldenburg, B. van den Bogaart, G. Mahata, S. K. 2020-09-20 doi:10.1101/2020.09.19.304303 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ AI-guided discovery of the invariant host response to viral pandemics ]]> https://biorxiv.org/content/10.1101/2020.09.21.305698v1?rss=1 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them. Added value of this studyThis work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the cytokine storm mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs. Implications of all the available evidenceThe ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs. ]]> Sahoo, D. Katkar, G. D. Khandelwal, S. Behroozikhah, M. Claire, A. Castillo, V. Tindle, C. Fuller, M. Taheri, S. Rogers, T. F. Beutler, N. Ramirez, S. Rawlings, S. A. Pretorius, V. Smith, D. Burton, D. R. Alexander, L. C. Duran, J. M. Crotty, S. Dan, J. M. Das, S. Ghosh, P. 2020-09-22 doi:10.1101/2020.09.21.305698 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro ]]> https://biorxiv.org/content/10.1101/2020.09.21.307363v1?rss=1 Seirup, M. Sengupta, S. Swanson, S. McIntosh, B. E. Collins, M. Chu, L.-F. Cheng, Z. Gorkin, D. Duffin, B. Bolin, J. M. Argus, C. Stewart, R. Thomson, J. A. 2020-09-22 doi:10.1101/2020.09.21.307363 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Clinical interpretation of integrative molecular profiles to guide precision cancer medicine ]]> https://biorxiv.org/content/10.1101/2020.09.22.308833v1?rss=1 Reardon, B. Moore, N. D. Moore, N. Kofman, E. Aldubayan, S. Cheung, A. Conway, J. Elmarakeby, H. Imamovic, A. Kamran, S. C. Keenan, T. Keliher, D. Konieczkowski, D. J. Liu, D. Mouw, K. Park, J. Vokes, N. Dietlein, F. Van Allen, E. M. 2020-09-23 doi:10.1101/2020.09.22.308833 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection ]]> https://biorxiv.org/content/10.1101/2020.09.22.308965v1?rss=1 Song, G. He, W.-t. Callaghan, S. Anzanello, F. Huang, D. Ricketts, J. Torres, J. L. Beutler, N. Peng, L. Vargas, S. Cassell, J. Parren, M. Yang, L. Ignacio, C. Smith, D. M. Voss, J. E. Nemazee, D. Ward, A. B. Rogers, T. Burton, D. R. Andrabi, R. 2020-09-23 doi:10.1101/2020.09.22.308965 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Impacted Spike Frequency Adaptation Associated with Reduction of KCNQ2/3 Promotes Seizure Activity in Temporal Lobe Epilepsy ]]> https://biorxiv.org/content/10.1101/2020.09.25.313254v1?rss=1 Rong, L. R. Cheng, J. S. Shuo, T. Bei, L. Yang, L. Lei, J. Hong, N. Yi, W. Q. Di, Z. S. Jing, G. R. 2020-09-28 doi:10.1101/2020.09.25.313254 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Tissue topography steers migrating Drosophila border cells ]]> https://biorxiv.org/content/10.1101/2020.09.27.316117v1?rss=1 Dai, W. Guo, X. Cao, Y. S. Mondo, J. A. Campanale, J. P. Montell, B. J. Burrous, H. Streichan, S. Gov, N. Rappel, W.-J. Montell, D. 2020-09-28 doi:10.1101/2020.09.27.316117 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Evolution of Modularity, Interactome and Functions of GIV/Girdin (CCDC88A) from Invertebrates to Vertebrates ]]> https://biorxiv.org/content/10.1101/2020.09.28.317172v1?rss=1 Ear, J. Ali Abd El-Hafeez, A. Roy, S. Ngo, T. Rajapakse, N. Choi, J. Khandelwal, S. Ghassemian, M. McCaffrey, L. Kufareva, I. Sahoo, D. Ghosh, P. 2020-09-28 doi:10.1101/2020.09.28.317172 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Functional Landscape of SARS-CoV-2 Cellular Restriction ]]> https://biorxiv.org/content/10.1101/2020.09.29.319566v1?rss=1 Martin-Sancho, L. Lewinski, M. K. Pache, L. Stoneham, C. YIN, X. Pratt, D. Churas, C. Rosenthal, S. B. Liu, S. De Jesus, P. D. O'Neill, A. M. Gounder, A. P. Nguyen, C. Pu, Y. Oom, A. L. Miorin, L. Rodriguez-Frandsen, A. Urbanowski, M. Shaw, M. L. Chang, M. W. Benner, C. Frieman, M. Garcia-Sastre, A. Ideker, T. Hultquist, J. F. Guatelli, J. Chanda, S. 2020-09-30 doi:10.1101/2020.09.29.319566 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ History-driven modulations of population codes in early visual cortex during visual search ]]> https://biorxiv.org/content/10.1101/2020.09.30.321729v1?rss=1 Adam, K. C. S. Serences, J. T. 2020-10-02 doi:10.1101/2020.09.30.321729 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome ]]> https://biorxiv.org/content/10.1101/2020.10.01.322701v1?rss=1 Ho, B. Ryback, D. Benson, B. Torres, P. J. Quinn, R. A. Thackray, V. G. Kelley, S. T. 2020-10-01 doi:10.1101/2020.10.01.322701 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Cellular Anatomy of the Mouse Primary Motor Cortex ]]> https://biorxiv.org/content/10.1101/2020.10.02.323154v1?rss=1 Munoz-Castaneda, R. Zingg, B. Matho, K. S. Wang, Q. Chen, X. Foster, N. N. Narasimhan, A. Li, A. Hirokawa, K. E. Huo, B. Banerjee, S. Korobkova, L. Park, C. S. Park, Y.-G. Bienkowski, M. S. Chon, U. Wheeler, D. W. Li, X. Wang, Y. Kelly, K. An, X. Attili, S. M. Bowman, I. Bludova, A. Cetin, A. Ding, L. Drewes, R. D'Orazi, F. Elowsky, C. Fischer, S. Galbavy, W. Gao, L. Gillis, J. Groblewski, P. A. Gou, L. Hahn, J. D. Hatfield, J. T. Hintiryan, H. Huang, J. Kondo, H. Kuang, X. Lesnar, P. Li, X. Li, Y. Lin, M. Liu, L. Lo, D. Mizrachi, J. Mok, S. Nae 2020-10-02 doi:10.1101/2020.10.02.323154 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion ]]> https://biorxiv.org/content/10.1101/2020.10.02.323915v1?rss=1 Yu, A. Pak, A. J. He, P. Monje-Galvan, V. Casalino, L. Gaieb, Z. Dommer, A. C. Amaro, R. E. Voth, G. A. 2020-10-02 doi:10.1101/2020.10.02.323915 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Benchmarking ensemble docking methods as a scientific outreach project ]]> https://biorxiv.org/content/10.1101/2020.10.02.324343v1?rss=1 Gan, J. L. Kumar, D. Chen, C. Taylor, B. C. Jagger, B. R. Amaro, R. E. Lee, C. T. 2020-10-04 doi:10.1101/2020.10.02.324343 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Single-cell data and correlation analysis support the independent double adder model in both Escherichia coli and Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2020.10.06.315820v1?rss=1 Le Treut, G. Si, F. Li, D. Jun, S. 2020-10-08 doi:10.1101/2020.10.06.315820 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets ]]> https://biorxiv.org/content/10.1101/2020.10.06.327080v1?rss=1 Cantrell, K. Fedarko, M. W. Rahman, G. McDonald, D. Yang, Y. Zaw, T. Gonzalez, A. Janssen, S. Estaki, M. Haiminen, N. Beck, K. L. Zhu, Q. Sayyari, E. Morton, J. Tripathi, A. Gauglitz, J. M. Marotz, C. Matteson, N. L. martino, c. Sanders, J. G. Carrieri, A. P. Song, S. J. Swafford, A. D. Dorrestein, P. Andersen, K. G. PARIDA, L. Kim, H.-C. Vazquez-Baeza, Y. Knight, R. 2020-10-08 doi:10.1101/2020.10.06.327080 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Polo-like kinase 1 independently controls microtubule-nucleating capacity and size of the centrosome ]]> https://biorxiv.org/content/10.1101/2020.10.07.328740v1?rss=1 Ohta, M. Zhao, Z. Wu, D. Wang, S. Harrison, J. L. Gomez-Cavazos, J. S. Desai, A. Oegema, K. 2020-10-07 doi:10.1101/2020.10.07.328740 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen ]]> https://biorxiv.org/content/10.1101/2020.10.08.332510v1?rss=1 Van Nostrand, E. L. Barnhill, S. A. Shishkin, A. A. Nelles, D. A. Byeon, E. Nguyen, T. Wong, Y. C. E. Gianneschi, N. C. Yeo, G. W. 2020-10-09 doi:10.1101/2020.10.08.332510 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Activation of MAP3K DLK and LZK in Purkinje Cells Causes Rapid and Slow Degeneration Depending on Signaling Strength ]]> https://biorxiv.org/content/10.1101/2020.10.09.332940v1?rss=1 Jin, Y. Li, Y. Ritchie, E. M. Steinke, C. L. Qi, C. Chen, L. Zheng, B. 2020-10-09 doi:10.1101/2020.10.09.332940 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Fetal innate immunity contributes to the induction of atypical behaviors in a mouse model of maternal immune activation ]]> https://biorxiv.org/content/10.1101/2020.10.09.333815v1?rss=1 Nichols, E. K. Chuang, H.-C. Davis, M. T. Geiger, K. M. Li, R. Z. Arnold, M. L. Lin, P. M. Misra, R. Coscoy, L. Saijo, K. 2020-10-10 doi:10.1101/2020.10.09.333815 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells ]]> https://biorxiv.org/content/10.1101/2020.10.09.334045v1?rss=1 Shamie, I. S. Duttke, S. H. la Cour Karottki, K. J. Han, C. Z. Hansen, A. H. Hefzi, H. Xiong, K. Li, S. Roth, S. Tao, J. Lee, G. M. Glass, C. K. Kildegaard, H. F. Benner, C. Lewis, N. E. 2020-10-10 doi:10.1101/2020.10.09.334045 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Aberrant Epithelial Differentiation Contributes to Pathogenesis in a Murine Model of Congenital Tufting Enteropathy ]]> https://biorxiv.org/content/10.1101/2020.10.12.330522v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@6700d7org.highwire.dtl.DTLVardef@6855b9org.highwire.dtl.DTLVardef@1d41207org.highwire.dtl.DTLVardef@1eb9f05_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Das, B. Okamoto, K. Rabalais, J. Young, J. Barrett, K. E. Sivagnanam, M. 2020-10-12 doi:10.1101/2020.10.12.330522 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Cross-modal orienting of exogenous attention results in visual-cortical facilitation, not suppression ]]> https://biorxiv.org/content/10.1101/2020.10.13.338210v1?rss=1 Keefe, J. M. Pokta, E. Stoermer, V. S. 2020-10-14 doi:10.1101/2020.10.13.338210 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Targeted millisecond-scale activation of cells using non-invasive Sonogenetics ]]> https://biorxiv.org/content/10.1101/2020.10.14.338699v1?rss=1 Duque, M. Lee-Kubli, C. Tufail, Y. Magaram, U. Lopez, J. M. Edsinger, E. Vasan, A. Shiao, R. Weiss, C. Friend, J. Chalasani, S. H. 2020-10-15 doi:10.1101/2020.10.14.338699 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Temporal stability of human sperm mosaic mutations results in life-long threat of transmission to offspring ]]> https://biorxiv.org/content/10.1101/2020.10.14.339796v1?rss=1 Yang, X. Breuss, M. W. Xu, X. Antaki, D. James, K. N. Stanley, V. Ball, L. L. George, R. D. Wirth, S. A. Cao, B. Nguyen, A. McEvoy-Venneri, J. Chai, G. Nahas, S. Van Der Kraan, L. Ding, Y. Sebat, J. Gleeson, J. G. 2020-10-14 doi:10.1101/2020.10.14.339796 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Diverse viral proteases activate the NLRP1 inflammasome ]]> https://biorxiv.org/content/10.1101/2020.10.16.343426v1?rss=1 Tsu, B. V. Beierschmitt, C. Ryan, A. P. Agarwal, R. Mitchell, P. S. Daugherty, M. D. 2020-10-17 doi:10.1101/2020.10.16.343426 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules ]]> https://biorxiv.org/content/10.1101/2020.10.19.344077v1?rss=1 Shams, A. Higgins, S. A. Fellmann, C. Laughlin, T. J. Oakes, B. L. Lew, R. Lukarska, M. Arnold, M. Staahl, B. Doudna, J. A. Savage, D. 2020-10-19 doi:10.1101/2020.10.19.344077 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Markov State Models and NMR Uncover an Overlooked Allosteric Loop in p53 ]]> https://biorxiv.org/content/10.1101/2020.10.19.346023v1?rss=1 Barros, E. P. Demir, O. Soto, J. Cocco, M. J. Amaro, R. E. 2020-10-19 doi:10.1101/2020.10.19.346023 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Tracking changes in behavioural dynamics using prediction error ]]> https://biorxiv.org/content/10.1101/2020.10.19.346080v1?rss=1 Lorimer, T. Goodridge, R. Bock, A. K. Agarwal, V. Saberski, E. Sugihara, G. Rifkin, S. A. 2020-10-21 doi:10.1101/2020.10.19.346080 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Functional Connectome Fingerprinting Using Shallow Feedforward Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.10.19.346189v1?rss=1 Sarar, G. Rao, B. Liu, T. 2020-10-21 doi:10.1101/2020.10.19.346189 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Higher-order hub cells involved in feedforward motifs as critical factors in epileptic network instability ]]> https://biorxiv.org/content/10.1101/2020.10.20.340364v1?rss=1 Hadjiabadi, D. H. Lovett-Barron, M. Raikov, I. Sparks, F. Liao, Z. Baraban, S. C. Leskovec, J. Losonczy, A. Deisseroth, K. Soltesz, I. 2020-10-21 doi:10.1101/2020.10.20.340364 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity ]]> https://biorxiv.org/content/10.1101/2020.10.21.336578v1?rss=1 Stormo, A. E. D. FitzGibbon, M. Shavarebi, F. Earley, E. M. Lum, L. S. Verschueren, E. Swaney, D. L. Skibinski, G. Ravisankar, A. van Haren, J. Davis, E. J. Johnson, J. R. Von Dollen, J. Mirescu, C. Iaccarino, C. Dauer, W. T. Nichols, R. J. Wittmann, T. Cox, T. C. Finkbeiner, S. Krogan, N. J. Oakes, S. A. Hiniker, A. 2020-10-21 doi:10.1101/2020.10.21.336578 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells ]]> https://biorxiv.org/content/10.1101/2020.10.23.347534v1?rss=1 Mellott, D. Tseng, C.-T. Drelich, A. Fajtova, P. Chenna, B. C. Kostomiris, D. Hsu, J. C. Zhu, J. Taylor, Z. Tat, V. Katzfuss, A. Li, L. Giardini, M. A. Skinner, D. Hirata, K. Beck, S. Carlin, A. F. Clark, A. E. Berreta, L. Maneval, D. Frueh, F. Hurst, B. L. Wang, H. Kocurek, K. I. Raushel, F. M. O'Donoghue, A. Siqueira-Neto, J. L. Meek, T. D. McKerrow, J. H. 2020-10-24 doi:10.1101/2020.10.23.347534 Cold Spring Harbor Laboratory Press 2020-10-24 <![CDATA[ Sleep spindles coordinate corticostriatal reactivations during the emergence of automaticity ]]> https://biorxiv.org/content/10.1101/2020.10.25.354282v1?rss=1 Lemke, S. M. Ramanathan, D. S. Darevsky, D. Egert, D. G. Berke, J. Ganguly, K. 2020-10-25 doi:10.1101/2020.10.25.354282 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase ]]> https://biorxiv.org/content/10.1101/2020.10.27.356436v1?rss=1 Xia, Z. Tang, M. Zhang, H. Gimple, R. Prager, B. Tang, H. Sun, C. Liu, F. Lin, P. Mei, Y. Du, R. Rich, J. Xie, Q. 2020-10-27 doi:10.1101/2020.10.27.356436 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ BrainGENIE: The Brain Gene Expression and Network Imputation Engine ]]> https://biorxiv.org/content/10.1101/2020.10.27.356766v1?rss=1 Hess, J. L. Chen, S. Quinn, T. P. Neuropsychiatric Consortium for Analysis and Sharing of Transcriptomes, Kong, S. W. Cairns, M. Tsuang, M. Faraone, S. V. Glatt, S. J. 2020-10-27 doi:10.1101/2020.10.27.356766 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Towards Biophysically-Based Neuromorphic Computing at Scale: Markov Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission ]]> https://biorxiv.org/content/10.1101/2020.10.27.358390v1?rss=1 Wagner, M. S. Bartol, T. M. Sejnowski, T. J. Cauwenberghs, G. 2020-10-28 doi:10.1101/2020.10.27.358390 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Catestatin reduces hyperglycemia in insulin-resistant mice by redirecting glucose-6-phosphate from the gluconeogenic to the glycogenic pathway ]]> https://biorxiv.org/content/10.1101/2020.10.31.363481v1?rss=1 Bandyopadhyay, G. K. Tang, K. Webster, N. J. G. van den Bogaart, G. Mahata, S. K. 2020-11-01 doi:10.1101/2020.10.31.363481 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Associations between Early Midlife Lifestyle Behaviors, Young Adult Cognitive Reserve and Advanced Predicted Brain Age in Late Midlife ]]> https://biorxiv.org/content/10.1101/2020.11.02.362780v1?rss=1 Franz, C. E. Hatton, S. N. Elman, J. A. Warren, T. Gillespie, N. A. Whitsel, N. A. Puckett, O. K. Dale, A. M. Eyler, L. T. Fennema-Notestine, C. Hagler, D. J. Hauger, R. L. McKenzie, R. Neale, M. C. Panizzon, M. S. Pearce, R. C. Reynolds, C. R. Sanderson-Cimino, M. Toomey, R. Tu, X. Xian, H. Lyons, M. J. Kremen, W. 2020-11-03 doi:10.1101/2020.11.02.362780 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4 ]]> https://biorxiv.org/content/10.1101/2020.11.02.365742v1?rss=1 50 million SNPs and InDels provided by five inbred strains of mice on the responses of macrophages to interleukin 4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Remarkably, of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage determining and signal-dependent transcription factors driving late enhancer activation. These studies further revealed mechanisms by which non-coding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity. ]]> Hoeksema, M. A. Shen, Z. Holtman, I. R. Zheng, A. Spann, N. Cobo, I. Gymrek, M. Glass, C. K. 2020-11-03 doi:10.1101/2020.11.02.365742 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Synergistic Coding of Human Odorants in the Mosquito Brain ]]> https://biorxiv.org/content/10.1101/2020.11.02.365916v1?rss=1 Shankar, S. Tauxe, G. M. Spikol, E. D. Li, M. Akbari, O. S. Giraldo, D. McMeniman, C. J. 2020-11-04 doi:10.1101/2020.11.02.365916 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Elemental Mapping of Labeled Biological Specimens at Intermediate Energy Loss in an Energy-Filtered TEM acquired using a Direct Detection Device ]]> https://biorxiv.org/content/10.1101/2020.11.02.365940v1?rss=1 Ramachandra, R. Mackey, M. R. Hu, J. Peltier, S. T. Nguyen-Huu, X. Ellisman, M. H. Adams, S. R. 2020-11-03 doi:10.1101/2020.11.02.365940 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Protein Structural Alignments From Sequence ]]> https://biorxiv.org/content/10.1101/2020.11.03.365932v1?rss=1 Morton, J. Strauss, C. Blackwell, R. Berenberg, D. Gligorijevic, V. Bonneau, R. 2020-11-04 doi:10.1101/2020.11.03.365932 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Genetically encoded ratiometric biosensor for probing lysosomal pH in mammalian cells and C. elegans ]]> https://biorxiv.org/content/10.1101/2020.11.04.368654v1?rss=1 Chin, M. Y. Patwardhan, A. R. Ang, K.-H. Wang, A. L. Alquezar, C. Welch, M. Grabe, M. Arkin, M. R. Kao, A. W. 2020-11-04 doi:10.1101/2020.11.04.368654 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/2020.11.06.371724v1?rss=1 Overbey, E. G. Saravia-Butler, A. M. Zhang, Z. Rathi, K. S. Fogle, H. da Silveira, W. A. Barker, R. J. Bass, J. J. Beheshti, A. Berrios, D. C. Blaber, E. A. Cekanaviciute, E. Costa, H. A. Davin, L. B. Fisch, K. M. Gebre, S. G. Geniza, M. Gilbert, R. Gilroy, S. Hardiman, G. Herranz, R. Kidane, Y. H. Kruse, C. P. S. Lee, M. D. Liefeld, T. Lewis, N. G. McDonald, J. T. Meller, R. Mishra, T. Perera, I. Ray, S. Reinsch, S. Rosenthal, S. B. Strong, M. Szewczyk, N. J. Tahimic, C. G. T. Taylor, D. M. Vandenbrink, J. P. Villacampa, A. Weging, S. Wolverton, C. Wya 2020-11-10 doi:10.1101/2020.11.06.371724 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ The unfolded protein response links tumor aneuploidy to local immune dysregulation ]]> https://biorxiv.org/content/10.1101/2020.11.10.377358v1?rss=1 Xian, S. Searles, S. T. Sahani, P. Weller, T. C. Jepsen, K. Carter, H. Zanetti, M. 2020-11-11 doi:10.1101/2020.11.10.377358 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ CoaTran: Coalescent tree simulation along a transmission network ]]> https://biorxiv.org/content/10.1101/2020.11.10.377499v1?rss=1 Moshiri, N. 2020-11-11 doi:10.1101/2020.11.10.377499 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ VGLUT modulates sex differences in dopamine neuron vulnerability to age-related neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.11.11.379008v1?rss=1 Buck, S. A. Steinkellner, T. Aslanoglou, D. Villeneuve, M. Bhatte, S. H. Childers, V. C. Rubin, S. A. De Miranda, B. R. O'Leary, E. I. Neureiter, E. G. Fogle, K. J. Palladino, M. J. Logan, R. W. Glausier, J. R. Fish, K. N. Lewis, D. A. Greenamyre, J. T. Bonci, A. McCabe, B. D. Cheetham, C. E. Hnasko, T. S. Freyberg, Z. 2020-11-12 doi:10.1101/2020.11.11.379008 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection ]]> https://biorxiv.org/content/10.1101/2020.11.12.380634v1?rss=1 Sundaramoorthy, E. Ryan, A. P. Fulzele, A. Leonard, M. Daugherty, M. D. Bennett, E. J. 2020-11-12 doi:10.1101/2020.11.12.380634 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Defining the ultrastructure of the hematopoietic stem cell niche by correlative light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.11.12.380790v1?rss=1 Agarwala, S. Kim, K.-Y. Phan, S. Ju, S. Kong, Y. E. Castillon, G. A. Bushong, E. A. Ellisman, M. H. Tamplin, O. J. 2020-11-13 doi:10.1101/2020.11.12.380790 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities ]]> https://biorxiv.org/content/10.1101/2020.11.13.370387v1?rss=1 Shaffer, J. P. Marotz, C. Belda-Ferre, P. Martino, C. Wandro, S. Estaki, M. Salido, R. A. Carpenter, C. S. Zaramela, L. S. Minich, J. J. Bryant, M. B. Sanders, K. Fraraccio, S. Ackermann, G. Humphrey, G. Swafford, A. D. Miller-Montgomery, S. Knight, R. 2020-11-14 doi:10.1101/2020.11.13.370387 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.11.14.382473v1?rss=1 Yang, X. Xu, X. Breuss, M. W. Antaki, D. Ball, L. L. Chung, C. Li, C. George, R. D. Wang, Y. Bae, T. Abyzov, A. Sebat, J. Gleeson, J. G. 2020-11-16 doi:10.1101/2020.11.14.382473 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Challenges in Benchmarking Metagenomic Profilers ]]> https://biorxiv.org/content/10.1101/2020.11.14.382994v1?rss=1 Sun, Z. Huang, S. Zhang, M. Zhu, Q. Haiminen, N. Carrieri, A.-P. Vazquez-Baeza, Y. Parida, L. Kim, H.-C. Knight, R. Liu, Y.-Y. 2020-11-16 doi:10.1101/2020.11.14.382994 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ osr1 couples intermediate mesoderm cell fate with temporal dynamics of vessel progenitor cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.11.14.383141v1?rss=1 Perens, E. Diaz, J. Quesnel, A. Askary, A. Crump, G. Yelon, D. 2020-11-15 doi:10.1101/2020.11.14.383141 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Immunological memory to SARS-CoV-2 assessed for greater than six months after infection ]]> https://biorxiv.org/content/10.1101/2020.11.15.383323v1?rss=1 Dan, J. M. Mateus, J. Kato, Y. Hastie, K. M. Faliti, C. Ramirez, S. I. Frazier, A. Yu, E. D. Grifoni, A. Rawlings, S. A. Peters, B. Krammer, F. Simon, V. Saphire, E. O. Smith, D. Weiskopf, D. Sette, A. Crotty, S. 2020-11-16 doi:10.1101/2020.11.15.383323 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning ]]> https://biorxiv.org/content/10.1101/2020.11.17.385757v1?rss=1 Jiang, Y. Rensi, S. wang, s. Altman, R. B. 2020-11-20 doi:10.1101/2020.11.17.385757 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Transient genomic instability drives tumorigenesis through accelerated clonal evolution ]]> https://biorxiv.org/content/10.1101/2020.11.17.387753v1?rss=1 Shoshani, O. Bakker, B. Wang, Y. Kim, D. H. Maldonado, M. Demarest, M. A. Artates, J. Zhengyu, O. Mark, A. Wardenaar, R. Sasik, R. Spierings, D. C. Vitre, B. Fisch, K. Foijer, F. Cleveland, D. W. 2020-11-17 doi:10.1101/2020.11.17.387753 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Aberrant gliogenesis and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids ]]> https://biorxiv.org/content/10.1101/2020.11.19.387639v1?rss=1 Trudler, D. Ghatak, S. Parker, J. Talantova, M. Grabauskas, T. Noveral, S. M. Teranaka, M. Luevanos, M. Dolatabadi, N. Bakker, C. Lopez, K. Sultan, A. Chan, A. Choi, Y. Kawaguchi, R. Schork, N. Stankiewicz, P. Garcia-Bassets, I. Kozbial, P. Rosenfeld, M. G. Nakanishi, N. Geschwind, D. Chan, S. F. Ambasudhan, R. Lipton, S. A. 2020-11-19 doi:10.1101/2020.11.19.387639 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.19.390187v1?rss=1 Casalino, L. Dommer, A. C. Gaieb, Z. Barros, E. P. Sztain, T. Ahn, S.-H. Trifan, A. Brace, A. Ma, H. Lee, H. Turilli, M. Bogetti, A. Khalid, S. Chong, L. Simmerling, C. Hardy, D. Maia, J. Phillips, J. Kurth, T. Stern, A. Huang, L. McCalpain, J. Tatineni, M. Gibbs, T. Stone, J. E. Jha, S. Ramanathan, A. Amaro, R. E. 2020-11-20 doi:10.1101/2020.11.19.390187 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ MetENP/MetENPWeb: An R package and web application for metabolomics enrichment and pathway analysis in Metabolomics Workbench ]]> https://biorxiv.org/content/10.1101/2020.11.20.391912v1?rss=1 Choudhary, K. S. Fahy, E. Coakley, K. Sud, M. Maurya, M. R. Subramaniam, S. 2020-11-21 doi:10.1101/2020.11.20.391912 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Caenorhabditis elegans junctophilin has tissue-specific functions and regulates neurotransmission with extended-synaptotagmin ]]> https://biorxiv.org/content/10.1101/2020.11.20.392142v1?rss=1 Piggott, C. A. Wu, Z. Nurrish, S. Xu, S. Kaplan, J. M. Chisholm, A. D. Jin, Y. 2020-11-21 doi:10.1101/2020.11.20.392142 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ Inferring the spatial code of cell-cell interactions and communication across a whole animal body ]]> https://biorxiv.org/content/10.1101/2020.11.22.392217v1?rss=1 Armingol, E. Joshi, C. J. Baghdassarian, H. Shamie, I. Ghaddar, A. Chan, J. Her, H.-L. O'Rourke, E. J. Lewis, N. E. 2020-11-22 doi:10.1101/2020.11.22.392217 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ SEPIA: Simulation-based Evaluation of Prioritization Algorithms ]]> https://biorxiv.org/content/10.1101/2020.11.23.394890v1?rss=1 Almaraz, K. Jang, T. Lewis, M. Ngo, T. Song, M. Moshiri, N. 2020-11-24 doi:10.1101/2020.11.23.394890 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology ]]> https://biorxiv.org/content/10.1101/2020.11.24.396820v1?rss=1 Young, C. Meng, S. Moshiri, N. 2020-11-25 doi:10.1101/2020.11.24.396820 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Selective transport of fluorescent proteins into the phage nucleus ]]> https://biorxiv.org/content/10.1101/2020.11.25.398438v1?rss=1 Nguyen, K. T. Sugie, J. Khanna, K. MacKennon, E. E. Birkholz, E. A. Lee, J. Beierschmitt, C. Villa, E. Pogliano, J. 2020-11-25 doi:10.1101/2020.11.25.398438 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Recurrent dynamics of prefrontal cortex during context-dependent decision-making ]]> https://biorxiv.org/content/10.1101/2020.11.27.401539v1?rss=1 Cohen, Z. DePasquale, B. Aoi, M. C. Pillow, J. W. 2020-11-27 doi:10.1101/2020.11.27.401539 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Divergent pallidal pathways underlying distinct Parkinsonian behavioral deficits ]]> https://biorxiv.org/content/10.1101/2020.11.27.401554v1?rss=1 Lim, B. Lilascharoen, V. Wang, E. H.-J. Do, N. Pate, S. C. Tran, A. N. Wang, X.-Y. Park, Y.-G. Chung, K. 2020-11-27 doi:10.1101/2020.11.27.401554 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Multielectrode Cortical Stimulation Selectively Induces Unidirectional Wave Propagation in Biophysical/Neural Model ]]> https://biorxiv.org/content/10.1101/2020.11.28.402289v1?rss=1 Halgren, A. S. Siegel, Z. Golden, R. Bazhenov, M. 2020-11-29 doi:10.1101/2020.11.28.402289 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis ]]> https://biorxiv.org/content/10.1101/2020.11.29.400614v1?rss=1 Blair, A. Hu, R. K. Farah, E. N. Pollard, K. S. Przytycki, P. F. Kathiriya, I. S. Bruneau, B. G. 2020-11-30 doi:10.1101/2020.11.29.400614 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution ]]> https://biorxiv.org/content/10.1101/2020.11.30.405589v1?rss=1 Zhang, C. Zhao, Y. Braun, E. L. Mirarab, S. 2020-12-02 doi:10.1101/2020.11.30.405589 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Light-activated tetrazines enable live-cell spatiotemporal control of bioorthogonal reactions ]]> https://biorxiv.org/content/10.1101/2020.12.01.405423v1?rss=1 Liu, L. Zhang, D. Johnson, M. Devaraj, N. K. 2020-12-02 doi:10.1101/2020.12.01.405423 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveals a path to selective inhibitors ]]> https://biorxiv.org/content/10.1101/2020.12.01.406264v1?rss=1 Rathinaswamy, M. K. Gaieb, Z. Fleming, K. D. Borsari, C. Harris, N. J. Moeller, B. J. Wymann, M. P. Amaro, R. E. Burke, J. E. 2020-12-02 doi:10.1101/2020.12.01.406264 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq ]]> https://biorxiv.org/content/10.1101/2020.12.03.387894v1?rss=1 Benaglio, P. Newsome, J. Han, J. Y. Chiou, J. Aylward, A. Corban, S. Okino, M.-L. Kaur, J. Gorkin, D. Gaulton, K. J. 2020-12-03 doi:10.1101/2020.12.03.387894 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE2 ]]> https://biorxiv.org/content/10.1101/2020.12.04.409144v1?rss=1 Lei, Y. Zhang, J. Schiavon, C. R. He, M. Chen, L. Shen, H. Zhang, Y. Yin, Q. Cho, Y. Andrade, L. Shadel, G. S. Hepokoski, M. Lei, T. Wang, H. Zhang, J. Yuan, J. X.- J. Malhotra, A. Manor, U. Wang, S. Yuan, Z.-Y. Shyy, J. Y.-J. 2020-12-04 doi:10.1101/2020.12.04.409144 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Mechanism for differential recruitment of orbitostriatal transmission during outcomes and actions in alcohol dependence ]]> https://biorxiv.org/content/10.1101/2020.12.04.411819v1?rss=1 Gremel, C. M. Renteria, R. Cazares, C. Baltz, E. T. Schreiner, D. C. Yalcinbas, E. A. Steinkellner, T. Hnasko, T. S. 2020-12-04 doi:10.1101/2020.12.04.411819 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Cancer-specific overmethylation of histone H3 lysines is necessary for methionine addiction and malignancy ]]> https://biorxiv.org/content/10.1101/2020.12.04.412437v1?rss=1 Yamamoto, J. Inubushi, S. Han, Q. Tashiro, Y. Sun, Y. Sugisawa, N. Hamada, K. Nishino, H. Aoki, Y. Miyake, K. Matsuyama, R. Bouvet, M. Endo, I. Hoffman, R. M. 2020-12-06 doi:10.1101/2020.12.04.412437 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Hawkmoths use wingstroke-to-wingstroke frequency modulation for aerial recovery to vortex ring perturbations ]]> https://biorxiv.org/content/10.1101/2020.12.07.413781v1?rss=1 Gau, J. Gemilere, R. LDS-VIP FM subteam, Lynch, J. Gravish, N. Sponberg, S. 2020-12-08 doi:10.1101/2020.12.07.413781 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Quantifying liquid-liquid phase separation property of chromatin under physiological conditions using Hi-MS and Hi-C ]]> https://biorxiv.org/content/10.1101/2020.12.07.415489v1?rss=1 Shi, M. You, K. Hou, C. Chen, T. Liang, Z. Liu, M. Wang, J. Wei, T. Qin, J. Chen, Y. Li, T. Zhang, M. Q. 2020-12-08 doi:10.1101/2020.12.07.415489 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases ]]> https://biorxiv.org/content/10.1101/2020.12.08.416750v1?rss=1 Tarke, A. Sidney, J. Kidd, C. K. Dan, J. M. Ramirez, S. I. Yu, E. D. Mateus, J. da Silva Antunes, R. Moore, E. Rubiro, P. Methot, N. Phillips, E. J. Mallal, S. Frazier, A. Rawlings, S. Greenbaum, J. A. Peters, B. Smith, D. M. Crotty, S. Weiskopf, D. Grifoni, A. Sette, A. 2020-12-09 doi:10.1101/2020.12.08.416750 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Identification of a Novel Susceptibility Marker for SARS-CoV-2 Infection in Human Subjects and Risk Mitigation with a Clinically Approved JAK Inhibitor in Human/Mouse Cells ]]> https://biorxiv.org/content/10.1101/2020.12.09.416586v1?rss=1 Spalinger, M. R. Hai, R. Li, J. Santos, A. N. Nordgren, T. M. Tremblay, M. L. Eckmann, L. Hanson, E. Scharl, M. Wu, X. Boland, B. S. McCole, D. F. 2020-12-09 doi:10.1101/2020.12.09.416586 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Integrated scRNA-seq analysis identifies conserved transcriptomic features of mononuclear phagocytes in mouse and human atherosclerosis ]]> https://biorxiv.org/content/10.1101/2020.12.09.417535v1?rss=1 Zernecke, A. Erhard, F. Weinberger, T. Schulz, C. Ley, K. Saliba, A.-E. Cochain, C. 2020-12-10 doi:10.1101/2020.12.09.417535 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Effects of early life adversity on maternal effort and glucocorticoids in wild olive baboons ]]> https://biorxiv.org/content/10.1101/2020.12.11.418095v1?rss=1 Patterson, S. K. Hinde, K. Bond, A. B. Trumble, B. C. Strum, S. C. Silk, J. B. 2020-12-11 doi:10.1101/2020.12.11.418095 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ TCRMatch: Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors ]]> https://biorxiv.org/content/10.1101/2020.12.11.418426v1?rss=1 Chronister, W. D. Crinklaw, A. Mahajan, S. Vita, R. Kosaloglu-Yalcin, Z. Yan, Z. Greenbaum, J. A. Jessen, L. E. Nielsen, M. Christley, S. Cowell, L. G. Sette, A. Peters, B. 2020-12-11 doi:10.1101/2020.12.11.418426 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422541v1?rss=1 Ding, B. Liu, Y. Liu, Z. Zheng, L. Xu, P. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wei, W. Wang, W. 2020-12-14 doi:10.1101/2020.12.13.422541 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data ]]> https://biorxiv.org/content/10.1101/2020.12.13.422543v1?rss=1 Yu, M. Abnousi, A. Zhang, Y. Li, G. Lee, L. Chen, Z. Fang, R. Wen, J. Sun, Q. Li, Y. Ren, B. Hu, M. 2020-12-15 doi:10.1101/2020.12.13.422543 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Regulatory elements can be essential for maintaining broad chromatin organization and cell viability ]]> https://biorxiv.org/content/10.1101/2020.12.13.422554v1?rss=1 Liu, Y. Ding, B. Zheng, L. Xu, P. Liu, Z. Chen, Z. Wu, P. Zhao, Y. Pan, Q. Guo, Y. Wang, W. Wei, W. 2020-12-13 doi:10.1101/2020.12.13.422554 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Distinguishing the behavioral potencies of α-pyrrolidino-phenone cathinone stimulants ]]> https://biorxiv.org/content/10.1101/2020.12.14.422779v1?rss=1 Taffe, M. A. Nguyen, J. D. Vandewater, S. A. Grant, Y. Dickerson, T. J. 2020-12-15 doi:10.1101/2020.12.14.422779 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ FOXO1 mitigates the SMAD3/FOXL2C134W Transcriptomic Effect in a Model of Human Adult Granulosa Cell Tumor ]]> https://biorxiv.org/content/10.1101/2020.12.15.422901v1?rss=1 Secchi, C. Benaglio, P. Mulas, F. Belli, M. Stupack, D. Shimasaki, S. 2020-12-16 doi:10.1101/2020.12.15.422901 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ A Theory of Synaptic Transmission ]]> https://biorxiv.org/content/10.1101/2020.12.17.423159v1?rss=1 Wang, B. Dudko, O. 2020-12-19 doi:10.1101/2020.12.17.423159 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ Adaptive integration of self-motion and goals in posterior parietal cortex ]]> https://biorxiv.org/content/10.1101/2020.12.19.423589v1?rss=1 Alexander, A. S. Tung, J. C. Chapman, G. W. Shelley, L. E. Hasselmo, M. E. Nitz, D. A. 2020-12-20 doi:10.1101/2020.12.19.423589 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L ]]> https://biorxiv.org/content/10.1101/2020.12.23.424111v1?rss=1 Ashhurst, A. Tang, A. Fajtova, P. Yoon, M. Aggarwal, A. Stoye, A. Larance, M. Beretta, L. Drelich, A. Skinner, D. Li, L. Meek, T. McKerrow, J. Hook, V. Tseng, C.-T. Turville, S. G. Gerwick, W. O'Donoghue, A. Payne, R. J. 2020-12-25 doi:10.1101/2020.12.23.424111 Cold Spring Harbor Laboratory Press 2020-12-25 <![CDATA[ The N-terminal Tail of C. elegans CENP-A Interacts with KNL-2 and is Essential for Centromeric Chromatin Assembly ]]> https://biorxiv.org/content/10.1101/2020.12.28.424576v1?rss=1 de Groot, C. Houston, J. Davis, B. Gerson-Gurwitz, A. Monen, J. Oegema, K. Shiau, A. K. Desai, A. 2020-12-28 doi:10.1101/2020.12.28.424576 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Preventing post-surgical cardiac adhesions with a catechol-functionalized oxime hydrogel ]]> https://biorxiv.org/content/10.1101/2020.12.29.424755v1?rss=1 Fujita, M. Policastro, G. M. Burdick, A. Lam, H. T. Ungerleider, J. Braden, R. L. Huang, D. Osborn, K. Omens, J. H. Madani, M. Christman, K. 2020-12-30 doi:10.1101/2020.12.29.424755 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ An amiRNA screen uncovers redundant CBF & ERF34/35 transcription factors that differentially regulate arsenite and cadmium responses ]]> https://biorxiv.org/content/10.1101/2020.12.30.424898v1?rss=1 2,000 artificial microRNAs (amiRNAs). This library was designed to knock-down diverse combinations of homologous gene family members within sub-clades of transcription factor and transporter gene families. We identified six transformant lines showing an altered response to arsenite in root growth assays. Further characterization of an amiRNA line targeting closely homologous CBF and ERF transcription factors show that the CBF1,2 and 3 transcription factors negatively regulate arsenite sensitivity. Furthermore, the ERF34 and ERF35 transcription factors are required for cadmium resistance. Generation of CRISPR lines, higher-order T-DNA mutants, and gene expression analyses, further support our findings. These ERF transcription factors differentially regulate arsenite sensitivity and cadmium tolerance. ]]> Xie, Q. Yu, Q. Jobe, T. O. Pham, A. Ge, C. Guo, Q. Liu, J. Liu, H. Zhang, H. Zhao, Y. Xue, S. Hauser, F. Schroeder, J. I. 2021-01-02 doi:10.1101/2020.12.30.424898 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface ]]> https://biorxiv.org/content/10.1101/2020.12.31.424868v1?rss=1 Zost, S. J. Dong, J. Gilchuk, I. M. Gilchuk, P. Thornburg, N. J. Bangaru, S. Kose, N. Finn, J. A. Bombardi, R. Soto, C. Nargi, R. S. Irving, R. P. Suryadevara, N. Westover, J. B. Carnahan, R. H. Turner, H. L. Li, S. Ward, A. B. Crowe, J. E. 2021-01-03 doi:10.1101/2020.12.31.424868 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Comprehensive multi-omics study of the molecular perturbations induced by simulated diabetes on coronary artery endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.06.425584v1?rss=1 Moreno-Ulloa, A. Delgado De la Herran, H. C. Alvarez Delgado, C. Mendoza Porras, O. Carballo Castaneda, R. A. Villarreal, F. 2021-01-08 doi:10.1101/2021.01.06.425584 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Restoration of deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells ]]> https://biorxiv.org/content/10.1101/2021.01.07.425558v1?rss=1 Spahn, P. Zhang, X. Hu, Q. Hamaker, N. Hefzi, H. Li, S. Kuo, C.-C. Huang, Y. Lee, J. Ly, P. Lee, K. Lewis, N. E. 2021-01-07 doi:10.1101/2021.01.07.425558 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains ]]> https://biorxiv.org/content/10.1101/2021.01.08.426013v1?rss=1 Gao, Y. Poudel, S. Seif, Y. Shen, Z. Palsson, B. O. 2021-01-09 doi:10.1101/2021.01.08.426013 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Nucleus accumbens neurons encode initiation and vigor of reward approach behavior ]]> https://biorxiv.org/content/10.1101/2021.01.12.425739v1?rss=1 Levcik, D. Sugi, A. H. Pochapski, J. A. Baltazar, G. Pulido, L. N. Villas-Boas, C. Aguilar-Rivera, M. Fuentes-Flores, R. Nicola, S. M. Da Cunha, C. 2021-01-12 doi:10.1101/2021.01.12.425739 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ The SLIM1 transcription factor regulates arsenic sensitivity in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.01.12.426316v1?rss=1 Jobe, T. O. Yu, Q. Hauser, F. Xie, Q. Meng, Y. Maassen, T. Kopriva, S. Schroeder, J. 2021-01-13 doi:10.1101/2021.01.12.426316 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk ]]> https://biorxiv.org/content/10.1101/2021.01.13.426472v1?rss=1 Chiou, J. Geusz, R. Okino, M.-L. Han, J. Y. Miller, M. Benaglio, P. Huang, S. Korgaonkar, K. Heller, S. Kleger, A. Preissl, S. Gorkin, D. Sander, M. Gaulton, K. J. 2021-01-15 doi:10.1101/2021.01.13.426472 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent ]]> https://biorxiv.org/content/10.1101/2021.01.13.426522v1?rss=1 Waschke, L. Donoghue, T. Fiedler, L. Smith, S. Garrett, D. D. Voytek, B. Obleser, J. 2021-01-14 doi:10.1101/2021.01.13.426522 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ A triple-negative matrix-producing breast carcinoma is arrested by tumor-targeting Salmonella typhimurium A1-R in a PDOX model ]]> https://biorxiv.org/content/10.1101/2021.01.14.426747v1?rss=1 Hamada, K. Yamamoto, J. Hozumi, C. Zhao, M. Murata, T. Sugisawa, N. Sun, Y. Aoki, Y. Nishino, H. Bouvet, M. Tsunoda, T. Hoffman, R. M. 2021-01-16 doi:10.1101/2021.01.14.426747 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors ]]> https://biorxiv.org/content/10.1101/2021.01.18.427081v1?rss=1 Puppo, F. Sadegh, S. Trujillo, C. Thunemann, M. Campbell, E. Vandenberghe, M. Shan, X. Akkouh, I. A. Miller, E. W. Bloodgood, B. L. Silva, G. A. Dale, A. M. Einevoll, G. T. Djurovic, S. Andreassen, O. A. Muotri, A. R. Devor, A. 2021-01-19 doi:10.1101/2021.01.18.427081 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Alignment of biomedical data repositories with open, FAIR, citable and trustworthy principles ]]> https://biorxiv.org/content/10.1101/2021.01.19.427362v1?rss=1 Murphy, F. Bar-Sinai, M. Martone, M. E. 2021-01-20 doi:10.1101/2021.01.19.427362 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution ]]> https://biorxiv.org/content/10.1101/2021.01.27.428469v1?rss=1 1000s viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure, and enable the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit. ]]> Gallardo, C. M. Wang, S. Montiel-Garcia, D. J. Little, S. J. Smith, D. M. Routh, A. L. Torbett, B. E. 2021-01-28 doi:10.1101/2021.01.27.428469 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Phage Cocktails can Prevent the Evolution of Phage-Resistant Enterococcus ]]> https://biorxiv.org/content/10.1101/2021.01.27.428553v1?rss=1 Wandro, S. Ghatbale, P. Attai, H. Hendrickson, C. Samillano, C. Suh, J. Pride, D. T. Whiteson, K. 2021-01-28 doi:10.1101/2021.01.27.428553 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework ]]> https://biorxiv.org/content/10.1101/2021.01.28.428578v1?rss=1 Auddya, D. Zhang, X. Gulati, R. Vasan, R. Garikipati, K. Rangamani, P. Rudraraju, S. 2021-01-29 doi:10.1101/2021.01.28.428578 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.01.29.428890v1?rss=1 Berndt, A. J. Smalley, T. N. Ren, B. Badary, A. Sproles, A. Fields, F. Torres-Tiji, Y. Heredia, V. Mayfield, S. P. 2021-01-30 doi:10.1101/2021.01.29.428890 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Non cell-autonomous effect of astrocytes on cerebral cavernous malformations ]]> https://biorxiv.org/content/10.1101/2021.01.29.428891v1?rss=1 Lopez-Ramirez, M. A. A. Soliman, S. I. Hale, P. Lai, C. C. Pham, A. Estrada, E. J. McCurdy, S. Girard, R. Verma, R. Moore, T. Lightle, R. Hobson, N. Shenkar, R. Poulsen, O. Haddad, G. G. Daneman, R. Gongol, B. Sun, H. Lagarrigue, F. Awad, I. A. Ginsberg, M. 2021-02-01 doi:10.1101/2021.01.29.428891 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Complementary Maps for Location and Environmental Structure in CA1 and Subiculum ]]> https://biorxiv.org/content/10.1101/2021.02.01.428537v1?rss=1 Olson, J. M. Johnson, A. B. Chang, L. Tao, E. L. Wang, X. Nitz, D. A. 2021-02-02 doi:10.1101/2021.02.01.428537 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Potential global impact of the N501Y mutation on MHC-II presentation and immune escape ]]> https://biorxiv.org/content/10.1101/2021.02.02.429431v1?rss=1 Castro, A. Carter, H. Zanetti, M. 2021-02-03 doi:10.1101/2021.02.02.429431 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ PDE9 Inhibition Activates PPARa to Stimulate Mitochondrial Fat Metabolism and Reduce Cardiometabolic Syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.02.429442v1?rss=1 Mishra, S. Hahn, V. Sadagopan, N. Dunkerly-Eyring, B. Rodriguez, S. Sarver, D. C. Ceddia, R. P. Murphy, S. Knutsdottir, H. Jani, V. Ashok, D. Oeing, C. U. O'Rourke, B. Sharma, K. Gangoiti, J. Sears, D. D. Wong, G. W. Collins, S. Kass, D. A. 2021-02-02 doi:10.1101/2021.02.02.429442 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ The purine nucleoside phosphorylase pnp-1 regulates epithelial cell resistance to infection in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.02.03.429531v1?rss=1 Tecle, E. Chhan, C. B. Franklin, L. Underwood, R. S. Hanna-Rose, W. Troemel, E. R. 2021-02-03 doi:10.1101/2021.02.03.429531 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells ]]> https://biorxiv.org/content/10.1101/2021.02.04.429675v1?rss=1 Chen, P. Fiaux, P. Li, B. Zhang, K. Kubo, N. Jiang, S. Hu, R. Wu, S. Wang, M. Wang, W. McVicker, G. P. Mischel, P. Ren, B. 2021-02-05 doi:10.1101/2021.02.04.429675 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Derived loss of signal complexity and plasticity in a genus of weakly electric fish ]]> https://biorxiv.org/content/10.1101/2021.02.06.430027v1?rss=1 Saenz, D. E. Gu, T. Ban, Y. Winemiller, K. O. Markham, M. R. 2021-02-08 doi:10.1101/2021.02.06.430027 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data ]]> https://biorxiv.org/content/10.1101/2021.02.10.430563v1?rss=1 Bandrowski, A. Grethe, J. S. Pilko, A. Gillespie, T. H. Pine, G. Patel, B. Surles-Zeiglera, M. Martone, M. E. 2021-02-10 doi:10.1101/2021.02.10.430563 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates ]]> https://biorxiv.org/content/10.1101/2021.02.10.430696v1?rss=1 S Arunachalam, P. Walls, A. C. Golden, N. Atyeo, C. Fischinger, S. Li, C. Aye, P. Navarro, M. J. Lai, L. Edara, V. V. Roltgen, K. Rogers, K. Shirreff, L. Ferrell, D. E. Wrenn, S. Pettie, D. Kraft, J. C. Miranda, M. C. Kepl, E. Sydeman, C. Brunette, N. Murphy, M. Fiala, B. Carter, L. White, A. G. Trisal, M. Hsieh, C.-L. Russell-Lodrigue, K. Monjure, C. Dufour, J. Doyle-Meyer, L. Bohm, R. B. Maness, N. J. Roy, C. Plante, J. A. Plante, K. S. Zhu, A. Gorman, M. J. Shin, S. Shen, X. Fontenot, J. Gupta, S. O Hagan, D. T. Most, R. V. D. Rappuoli, R. Coffma 2021-02-11 doi:10.1101/2021.02.10.430696 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ What are housekeeping genes? ]]> https://biorxiv.org/content/10.1101/2021.02.14.431149v1?rss=1 Joshi, C. J. Ke, W. Drangowska-Way, A. O'Rourke, E. J. Lewis, N. E. 2021-02-16 doi:10.1101/2021.02.14.431149 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ APPLES-2: Faster and More Accurate Distance-based Phylogenetic Placement using Divide and Conquer ]]> https://biorxiv.org/content/10.1101/2021.02.14.431150v1?rss=1 Balaban, M. Roush, D. Zhu, Q. Mirarab, S. 2021-02-14 doi:10.1101/2021.02.14.431150 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ A glycan gate controls opening of the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.02.15.431212v1?rss=1 Sztain, T. E. Ahn, S.-H. Bogetti, A. T. Casalino, L. Goldsmith, J. A. McCool, R. S. Kearns, F. L. McCammon, J. A. McLellan, J. S. Chong, L. Amaro, R. E. 2021-02-16 doi:10.1101/2021.02.15.431212 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Plant trait heterosis is quantitatively associated with expression heterosis of plastid ribosomal proteins ]]> https://biorxiv.org/content/10.1101/2021.02.16.431485v1?rss=1 Birdseye, D. De Boer, L. Shen, Z. Bai, H. Zhou, P. Schmelz, E. A. Springer, N. M. Briggs, S. 2021-02-17 doi:10.1101/2021.02.16.431485 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Shared long-term and short-term memory representational formats in occipital and parietal cortex ]]> https://biorxiv.org/content/10.1101/2021.02.16.431528v1?rss=1 Vo, V. A. Sutterer, D. W. Foster, J. J. Sprague, T. C. Awh, E. Serences, J. T. 2021-02-16 doi:10.1101/2021.02.16.431528 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ A cell atlas of chromatin accessibility across 25 adult human tissues ]]> https://biorxiv.org/content/10.1101/2021.02.17.431699v1?rss=1 Zhang, K. Hocker, J. D. Miller, M. Hou, X. Chiou, J. Poirion, O. B. Qiu, Y. Li, Y. E. Gaulton, K. J. Wang, A. Preissl, S. Ren, B. 2021-02-17 doi:10.1101/2021.02.17.431699 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Pyrazinamide action is driven by the cell envelope stress response in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.02.17.431758v1?rss=1 Thiede, J. M. Dillon, N. Howe, M. D. Modlin, S. J. Aflakpui, R. Hoffner, S. Valafar, F. Minato, Y. Baughn, A. D. 2021-02-18 doi:10.1101/2021.02.17.431758 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Constructing An Adult Orofacial Premotor Atlas In Allen Mouse CCF ]]> https://biorxiv.org/content/10.1101/2021.02.18.431923v1?rss=1 Takatoh, J. Park, J. H. Lu, J. Li, S. Thompson, P. M. Han, B.-X. Zhao, S. Kleinfeld, D. Friedman, B. Wang, F. 2021-02-19 doi:10.1101/2021.02.18.431923 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Parallel Characterization of cis-Regulatory Elements for Multiple Genes UsingCRISPRpath ]]> https://biorxiv.org/content/10.1101/2021.02.19.431931v1?rss=1 Ren, X. Wang, M. Li, B. Jamieson, K. Zheng, L. Jones, I. R. Li, B. Takagi, M. A. Lee, J. Maliskova, L. Tam, T. W. Yu, M. Hu, R. Lee, L. Abnousi, A. Li, G. Li, Y. Hu, M. Ren, B. Wang, W. Shen, Y. 2021-02-19 doi:10.1101/2021.02.19.431931 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Precision Diffusion Imaging ]]> https://biorxiv.org/content/10.1101/2021.02.19.432023v1?rss=1 Seider, N. A. Adeyemo, B. Miller, R. Newbold, D. J. Hampton, J. M. Scheidter, K. M. Rutlin, J. Laumann, T. O. Roland, J. L. Montez, D. F. Van, A. N. Zheng, A. Marek, S. Kay, B. P. Bretthorst, G. L. Schlaggar, B. L. Greene, D. J. Wang, Y. Petersen, S. E. Gordon, E. M. Snyder, A. Z. Shimony, J. S. Dosenbach, N. U. 2021-02-20 doi:10.1101/2021.02.19.432023 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Bacterial Cytological Profiling Identifies Rhodanine-containing PAINS Analogs as Specific Inhibitors of E. coli Thymidylate Kinase in Vivo ]]> https://biorxiv.org/content/10.1101/2021.02.22.432404v1?rss=1 Montano, E. T. Nideffer, J. F. Sugie, J. Enustun, E. Shapiro, A. B. Tsunemoto, H. Derman, A. Pogliano, K. Pogliano, J. 2021-02-25 doi:10.1101/2021.02.22.432404 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Clinical Phage Microbiology:A suggested framework and recommendations for the in-vitro matching steps ‎of phage therapy ]]> https://biorxiv.org/content/10.1101/2021.02.23.432393v1?rss=1 Gelman, D. Yerushalmy, O. Ben-Porat, S. Rakov, C. Alkalay-Oren, S. Adler, K. Khalifa, L. Abdalrhman, M. Coppenhagen-Glazer, S. Aslam, S. Schooley, R. T. Nir-Paz, R. Hazan, R. 2021-02-23 doi:10.1101/2021.02.23.432393 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Widespread ripples synchronize human cortical activity ]]> https://biorxiv.org/content/10.1101/2021.02.23.432582v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Jiang, X. Rosen, B. Q. Kajfez, S. Stedelin, B. Shih, J. J. Ben-Haim, S. Raslan, A. M. Madsen, J. R. Eskandar, E. N. Gonzalez-Martinez, J. Cash, S. S. Halgren, E. 2021-02-24 doi:10.1101/2021.02.23.432582 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Csf1r-GCaMP5 Reporter Mice Reveal Immune Cell Communication in Vitro and in Vivo ]]> https://biorxiv.org/content/10.1101/2021.02.24.432710v1?rss=1 Taghdiri, N. Calcagno, D. M. Fu, Z. R. Huang, K. Kohler, R. H. Weissleder, R. Coleman, T. P. King, K. R. 2021-02-24 doi:10.1101/2021.02.24.432710 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq ]]> https://biorxiv.org/content/10.1101/2021.02.26.433126v1?rss=1 Massarat, A. R. Sen, A. Jaureguy, J. Tyndale, S. T. Fu, Y. Erikson, G. McVicker, G. 2021-02-27 doi:10.1101/2021.02.26.433126 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters ]]> https://biorxiv.org/content/10.1101/2021.02.26.433127v1?rss=1 Schaworonkow, N. Voytek, B. 2021-02-28 doi:10.1101/2021.02.26.433127 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Tetraspanin immunocapture phenotypes extracellular vesicles according to biofluid source but may limit identification of multiplexed cancer biomarkers ]]> https://biorxiv.org/content/10.1101/2021.03.02.433595v1?rss=1 Mizenko, R. R. Brostoff, T. Rojalin, T. Koster, H. J. Swindell, H. S. Leiserowitz, G. S. Wang, A. Carney, R. P. 2021-03-03 doi:10.1101/2021.03.02.433595 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Targeting Biofilm of MDR Providencia stuartii by Phages Using a Catheter Model ]]> https://biorxiv.org/content/10.1101/2021.03.02.433687v1?rss=1 Rakov, C. Ben-Porat, S. Alkalay-Oren, S. Yerushalmy, O. Abdalrhman, M. Gronovich, N. Huang, L. S. Pride, D. T. Coppenhagen-Glazer, S. Nir Paz, R. Hazan, R. 2021-03-03 doi:10.1101/2021.03.02.433687 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Predicting functional consequences of mutations using molecular interaction network features ]]> https://biorxiv.org/content/10.1101/2021.03.05.433991v1?rss=1 Ozturk, K. Carter, H. 2021-03-08 doi:10.1101/2021.03.05.433991 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius. ]]> https://biorxiv.org/content/10.1101/2021.03.08.432323v1?rss=1 O'Neill, A. M. Worthing, K. A. Kulkarni, N. Li, F. Nakatsuji, T. Mills, R. H. Cheng, J. Y. Gonzalez, D. J. Norris, J. M. Gallo, R. L. 2021-03-08 doi:10.1101/2021.03.08.432323 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1 ]]> https://biorxiv.org/content/10.1101/2021.03.08.434337v1?rss=1 Gandhi, S. Mitterhoff, R. Rapoport, R. Eden, S. Goren, A. Simon, I. 2021-03-08 doi:10.1101/2021.03.08.434337 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Effect of chronic JUUL aerosol inhalation on inflammatory states of the brain, lung, heart and colon in mice ]]> https://biorxiv.org/content/10.1101/2021.03.09.434442v1?rss=1 Moshensky, A. Brand, C. Alhaddad, H. Shin, J. Masso-Silva, J. A. Advani, I. Gunge, D. Sharma, A. Mehta, S. Jahan, A. Nilaad, S. Almarghalani, D. Pham, J. Perera, S. Park, K. Al-Kolla, R. Moon, H. Das, S. Byun, M. Shah, Z. Sari, Y. Heller Brown, J. Crotty Alexander, L. E. 2021-03-10 doi:10.1101/2021.03.09.434442 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Structural connectome quantifies tumor invasion and predicts survival in glioblastoma patients ]]> https://biorxiv.org/content/10.1101/2021.03.09.434656v1?rss=1 Wei, Y. Li, C. Cui, Z. Mayrand, R. C. Zou, J. Wong, A. L. K. C. Sinha, R. Matys, T. Schönlieb, C.-B. Price, S. J. 2021-03-10 doi:10.1101/2021.03.09.434656 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ The geometry of face memory ]]> https://biorxiv.org/content/10.1101/2021.03.12.435023v1?rss=1 She, L. Benna, M. K. Shi, Y. Fusi, S. Tsao, D. Y. 2021-03-12 doi:10.1101/2021.03.12.435023 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Structural Covariance Networks in Post-Traumatic Stress Disorder: A Multisite ENIGMA-PGC Study ]]> https://biorxiv.org/content/10.1101/2021.03.13.432212v1?rss=1 Rakesh, G. Sun, D. Logue, M. Clarke-Rubright, E. O Leary, B. M. Haswell, C. Xie, H. Thompson, P. Dennis, E. Jahanshad, N. Koch, S. Frijling, J. Nawijn, L. Olff, M. van Zuiden, M. Rashid, F. Zhu, X. De Bellis, M. Daniels, J. K. Sierk, A. Manthey, A. Stevens, J. S. Jovanovic, T. Stein, M. B. Shenton, M. van der Werff, S. J. A. van der Wee, N. J. A. Vermeiren, R. R. J. M. Schmahl, C. Herzog, J. Kaufman, M. L. O'Connor, L. Lebois, L. A. M. Baker, J. T. Gruber, S. A. Wolff, J. D. Wolf, E. J. Winternitz, S. Gonenc, A. Ressler, K. J. Hofmann, D. Bryant, R. A. 2021-03-16 doi:10.1101/2021.03.13.432212 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Using synthetic MR images for field map-less distortion correction ]]> https://biorxiv.org/content/10.1101/2021.03.13.435270v1?rss=1 Montez, D. F. Van, A. N. Miller, R. L. Seider, N. A. Marek, S. Zheng, A. Newbold, D. J. Scheidter, K. Feczko, E. Perrone, A. J. Miranda Dominguez, O. Earl, E. A. Kay, B. P. Jha, A. K. Sotiras, A. Laumann, T. O. Greene, D. J. Gordon, E. M. Tisdall, M. D. van der Kouwe, A. Fair, D. A. Dosenbach, N. U. F. 2021-03-15 doi:10.1101/2021.03.13.435270 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Open Data Commons for Preclinical Traumatic Brain Injury Research: Empowering Data Sharing and Big Data Analytics ]]> https://biorxiv.org/content/10.1101/2021.03.15.435178v1?rss=1 Chou, A. C. Torres-Espin, A. Huie, J. R. Krukowski, K. Lee, S. Nolan, A. Guglielmetti, C. Hawkins, B. E. Chaumeil, M. M. Manley, G. T. Beattie, M. S. Bresnahan, J. C. Martone, M. E. Grethe, J. S. Rosi, S. Ferguson, A. R. 2021-03-16 doi:10.1101/2021.03.15.435178 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Morphological principles of neuronal mitochondria ]]> https://biorxiv.org/content/10.1101/2021.03.15.435547v1?rss=1 Mendelsohn, R. Garcia, G. C. Bartol, T. M. Lee, C. T. Khandelwal, P. Liu, E. Spencer, D. J. Husar, A. Bushong, E. A. Phan, S. Perkins, G. Ellisman, M. H. Skupin, A. Sejnowski, T. J. Rangamani, P. 2021-03-16 doi:10.1101/2021.03.15.435547 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Meiotic Cas9 expression mediates genotype conversion in the male and female mouse germline ]]> https://biorxiv.org/content/10.1101/2021.03.16.435716v1?rss=1 Weitzel, A. J. Grunwald, H. A. Levina, R. Gantz, V. M. Hedrick, S. M. Bier, E. Cooper, K. L. 2021-03-17 doi:10.1101/2021.03.16.435716 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ iPSC-derived pancreatic progenitors are an optimal model system to study T2D regulatory variants active during fetal development of the pancreas ]]> https://biorxiv.org/content/10.1101/2021.03.17.435846v1?rss=1 D'Antonio-Chronowska, A. Donovan, M. K. R. Fujita, K. Salgado, B. M. Matsui, H. Arthur, T. D. Nguyen, J. P. D'Antonio, M. Frazer, K. A. 2021-03-17 doi:10.1101/2021.03.17.435846 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Proteomic Organellar Mapping Reveals Modulation of Peroxisomes by HIV-1 ]]> https://biorxiv.org/content/10.1101/2021.03.17.435902v1?rss=1 Oom, A. L. Stoneham, C. A. Lewinski, M. K. Richards, A. Wozniak, J. Gonzalez, D. Krogan, N. J. Guatelli, J. 2021-03-18 doi:10.1101/2021.03.17.435902 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ CONSULT: Accurate contamination removal using locality-sensitive hashing ]]> https://biorxiv.org/content/10.1101/2021.03.18.436035v1?rss=1 Rachtman, E. Bafna, V. Mirarab, S. 2021-03-19 doi:10.1101/2021.03.18.436035 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ EMBED: a low dimensional reconstruction of gut microbiome dynamics based on ecological normal modes ]]> https://biorxiv.org/content/10.1101/2021.03.18.436036v1?rss=1 Shahin, M. Ji, B. W. Dixit, P. D. 2021-03-19 doi:10.1101/2021.03.18.436036 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Closed-Loop Control between Two GTPase Switches makes the Secretory Functions of the Golgi Responsive to Growth Factors ]]> https://biorxiv.org/content/10.1101/2021.03.18.436048v1?rss=1 Qiao, L. Lo, I.-C. Midde, K. Aznar, N. Abd El-Hafeez, A. A. Lopez-Sanchez, I. Gupta, V. Farquhar, M. Rangamani, P. Ghosh, P. 2021-03-19 doi:10.1101/2021.03.18.436048 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ CCL28 modulates neutrophil responses and impacts the trajectory of mucosal infections ]]> https://biorxiv.org/content/10.1101/2021.03.19.436197v1?rss=1 Perez-Lopez, A. Silva, S. Dillon, N. Brandt, S. Gerner, R. Lee, M. Melchior, K. Torres-Ruiz, J. Sosa-Hernandez, V. Cervantes-Diaz, R. Perez-Fragoso, A. Romero-Ramirez, S. Gomez-Martin, D. Maravillas-Montero, J. Nuccio, S.-P. Nizet, V. Raffatellu, M. 2021-03-20 doi:10.1101/2021.03.19.436197 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Novelty-related engagement of VTA and anterior hippocampus propagate changes in cortical network plasticity at different scales ]]> https://biorxiv.org/content/10.1101/2021.03.22.436448v1?rss=1 Cowan, E. T. Fain, M. R. O'Shea, I. Ellman, L. M. Murty, V. P. 2021-03-22 doi:10.1101/2021.03.22.436448 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.03.22.436522v1?rss=1 Sandoval, D. R. Mandel Clausen, T. Nora, C. Magida, J. A. Cribbs, A. P. Denardo, A. Clark, A. E. Garretson, A. F. Coker, J. K. C. Narayanan, A. Majowicz, S. A. Philpott, M. Johansson, C. Dunford, J. E. Spliid, C. B. Golden, G. J. Payne, N. C. Tye, M. A. Nowell, C. J. Griffis, E. R. Piermatteo, A. Grunddal, K. V. Alle, T. Hauser, B. M. Feldman, J. Caradonna, T. M. Pu, Y. Yin, X. McVicar, R. N. Kwong, E. M. Tsimikas, S. Schmidt, A. G. Ballatore, C. Zengler, K. Chanda, S. K. Weiss, R. J. Downes, M. Evans, R. M. Croker, B. A. Leibel, S. L. Jose, J. Mazitsch 2021-03-23 doi:10.1101/2021.03.22.436522 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Parasitic nematode fatty acid- and retinol-binding proteins compromise host immunity by interfering with host lipid signaling pathways ]]> https://biorxiv.org/content/10.1101/2021.03.25.436866v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@48f582org.highwire.dtl.DTLVardef@1ee4292org.highwire.dtl.DTLVardef@1548248org.highwire.dtl.DTLVardef@13574d6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Parks, S. Nguyen, C. Nasrolahi, S. Juncaj, D. Lu, D. Ramaswamy, R. Dhillon, H. Buchman, A. Akbari, O. S. Yamanaka, N. Boulanger, M. J. Dillman, A. R. 2021-03-25 doi:10.1101/2021.03.25.436866 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ aPC/PAR1 confers endothelial anti-apoptotic activity via a discrete β-arrestin-2 mediated SphK1-S1PR1-Akt signaling axis ]]> https://biorxiv.org/content/10.1101/2021.03.27.437291v1?rss=1 Molinar-Inglis, O. Birch, C. A. Nicholas, D. Cisneros-Aguirre, M. Patwardhan, A. Chen, B. Grimsey, N. J. Gomez-Menzies, P. K. Lin, H. Coronel, L. J. Lawson, M. A. Patel, H. H. Trejo, J. 2021-03-27 doi:10.1101/2021.03.27.437291 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ A protective broadly cross-reactive human antibody defines a conserved site of vulnerability on beta-coronavirus spikes ]]> https://biorxiv.org/content/10.1101/2021.03.30.437769v1?rss=1 Zhou, P. Yuan, M. Song, G. Beutler, N. Shaabani, N. Huang, D. He, W.-t. Zhu, X. Callaghan, S. Yong, P. Anzanello, F. Peng, L. Ricketts, J. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Nemazee, D. Teijaro, J. R. Rogers, T. Wilson, I. A. Burton, D. R. Andrabi, R. 2021-03-31 doi:10.1101/2021.03.30.437769 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ An ammonium transporter is a non-canonical olfactory receptor for ammonia ]]> https://biorxiv.org/content/10.1101/2021.03.31.437861v1?rss=1 Vulpe, A. Kim, H. S. Ballou, S. Wu, S.-T. Grabe, V. Nava Gonzales, C. Sachse, S. Jeanne, J. M. Su, C.-Y. Menuz, K. 2021-03-31 doi:10.1101/2021.03.31.437861 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ The SPARC DRC: Building a resource for the autonomic nervous system community ]]> https://biorxiv.org/content/10.1101/2021.04.01.438136v1?rss=1 Osanlouy, M. Bandrowski, A. de Bono, B. Brooks, D. Cassara, A. M. Christie, R. Ebrahimi, N. Gillespie, T. Grethe, J. S. Guercio, L. A. Heal, M. Lin, M. Kuster, N. Martone, M. E. Neufeld, E. Nickerson, D. P. Soltani, E. G. Tappan, S. Wagenaar, J. B. Zhuang, K. Hunter, P. J. 2021-04-04 doi:10.1101/2021.04.01.438136 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN ]]> https://biorxiv.org/content/10.1101/2021.04.02.438274v1?rss=1 Moeller, N. H. Shi, K. Demir, O. Banerjee, S. Yin, L. Belica, C. Durfee, C. Amaro, R. E. Aihara, H. 2021-04-04 doi:10.1101/2021.04.02.438274 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures ]]> https://biorxiv.org/content/10.1101/2021.04.04.438427v1?rss=1 Zhu, Q. Huang, S. Gonzalez, A. McGrath, I. McDonald, D. Haiminen, N. Armstrong, G. Vazquez-Baeza, Y. Yu, J. Kuczynski, J. Sepich-Poore, G. D. Swafford, A. D. Das, P. Shaffer, J. P. Lejzerowicz, F. Belda-Ferre, P. Havulinna, A. S. Meric, G. Niiranen, T. Lahti, L. Salomaa, V. Kim, H.-C. Jain, M. Inouye, M. Gilbert, J. Knight, R. 2021-04-06 doi:10.1101/2021.04.04.438427 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser ]]> https://biorxiv.org/content/10.1101/2021.04.05.438475v1?rss=1 Petras, D. Phelan, V. V. Acharya, D. D. Allen, A. E. Aron, A. T. Bandeira, N. Belle-Oudry, D. Boecker, S. Bowen, B. P. Cummings, D. A. Deutsch, J. M. Fahy, E. Garg, N. Gregor, R. Handelsman, J. Navarro-Hoyos, M. Jarmusch, A. K. Jarmusch, S. A. Louie, K. B. Maloney, K. N. Marty, M. T. Meijler, M. M. Mizrahi, I. Molina-Santiago, C. Neve, R. L. Northen, T. R. Panitchpakdi, M. Pullman, B. Puri, A. W. Schmid, R. Subramaniam, S. Thukral, M. Vasquez-Castro, F. Dorrestein, P. C. Wang, M. 2021-04-06 doi:10.1101/2021.04.05.438475 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Sensory readout accounts for adaptation ]]> https://biorxiv.org/content/10.1101/2021.04.06.438664v1?rss=1 Sheehan, T. C. Serences, J. T. 2021-04-08 doi:10.1101/2021.04.06.438664 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Ubiquitin specific protease 1 expression and function in T cell immunity ]]> https://biorxiv.org/content/10.1101/2021.04.08.439046v1?rss=1 Omilusik, K. D. Nadjsombati, M. S. Yoshida, T. M. Shaw, L. A. Goulding, J. Goldrath, A. W. 2021-04-09 doi:10.1101/2021.04.08.439046 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ PRECISE 2.0: an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure ]]> https://biorxiv.org/content/10.1101/2021.04.08.439047v1?rss=1 Lamoureux, C. R. Decker, K. T. Sastry, A. V. McConn, J. L. Gao, Y. Palsson, B. O. 2021-04-11 doi:10.1101/2021.04.08.439047 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ NaCT (SLC13A5) facilitates citrate import and metabolism under nutrient-limited conditions ]]> https://biorxiv.org/content/10.1101/2021.04.08.439058v1?rss=1 Kumar, A. Cordes, T. Thalacker-Mercer, A. E. Pajor, A. M. Murphy, A. N. Metallo, C. M. 2021-04-10 doi:10.1101/2021.04.08.439058 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ State dependence of neural networks on past history and stimulus presentation in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.04.09.439242v1?rss=1 Cecere, Z. T. Yemini, E. Sharpee, T. O. Chalasani, S. H. 2021-04-11 doi:10.1101/2021.04.09.439242 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.12.439539v1?rss=1 Yoo, B. B. Griffiths, J. A. Thuy-Boun, P. Cantu, V. Weldon, K. Challis, C. Sweredoski, M. J. Chan, K. Y. Thron, T. M. Sharon, G. Moradian, A. Humphrey, G. Zhu, Q. Shaffer, J. Wolan, D. W. Dorrestein, P. Knight, R. Gradinaru, V. Mazmanian, S. 2021-04-13 doi:10.1101/2021.04.12.439539 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Adolescent Binge Drinking is Associated with Accelerated Decline of Gray Matter Volume ]]> https://biorxiv.org/content/10.1101/2021.04.13.439749v1?rss=1 Infante, M. A. Zhang, Y. Brumback, T. Brown, S. Colrain, I. Baker, F. Clark, D. Goldston, D. Nagel, B. Nooner, K. Zhao, Q. Pohl, K. Sullivan, E. Pfefferbaum, A. Tapert, S. Thompson, W. K. 2021-04-14 doi:10.1101/2021.04.13.439749 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Germline variants that influence the tumor immune microenvironment also drive response to immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.04.14.436660v1?rss=1 8000 tumors reveals novel cancer risk factors and targets for immunotherapy. ]]> Pagadala, M. Wu, V. H. Perez-Guijarro, E. Kim, H. Castro, A. Talwar, J. Gonzalez-Colin, C. Cao, S. Schmiedel, B. Salem, R. Morris, G. Harismendy, O. Patel, S. P. Mesirov, J. P. Zanetti, M. Day, C.-P. Fan, C. C. Thompson, W. K. Merlino, G. Gutkind, J. S. Vijayanand, P. Carter, H. 2021-04-15 doi:10.1101/2021.04.14.436660 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ A multiscale model predicts the sensitivity of Chlorella vulgaris to light and nitrogen levels in photobioreactors ]]> https://biorxiv.org/content/10.1101/2021.04.14.439858v1?rss=1 Tibocha-Bonilla, J. D. Zuniga, C. Broddrick, J. T. Zengler, K. Godoy-Silva, R. D. 2021-04-16 doi:10.1101/2021.04.14.439858 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Mindfulness Training Alters Resting-State EEG Dynamics in Novice Practitioners via Mindful Breathing and Body-scan ]]> https://biorxiv.org/content/10.1101/2021.04.16.439387v1?rss=1 Ng, H.-Y. H. Wu, C. W. Huang, F.-Y. Cheng, Y.-T. Guu, S.-F. Huang, C.-M. Hsu, C.-F. Chao, Y.-P. Jung, T.-P. Chuang, C.-H. 2021-04-16 doi:10.1101/2021.04.16.439387 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ System-level effects of CO2 and RuBisCO concentration on carbon isotope fractionation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440233v1?rss=1 Garcia, A. K. Kedzior, M. Taton, A. Li, M. Young, J. Kacar, B. 2021-04-20 doi:10.1101/2021.04.20.440233 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Chemoenzymatic Generation of Phospholipid Membranes Mediated by Type I Fatty Acid Synthase ]]> https://biorxiv.org/content/10.1101/2021.04.21.440816v1?rss=1 Devaraj, N. Burkart, M. Khanal, S. Brea Fernandez, R. J. 2021-04-22 doi:10.1101/2021.04.21.440816 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Expression of fatty acyl-CoA ligase drives one-pot de novo synthesis of membrane-bound vesicles in a cell free transcription-translation system ]]> https://biorxiv.org/content/10.1101/2021.04.22.440977v1?rss=1 Bhattacharya, A. Cho, C. J. Brea, R. J. Devaraj, N. K. 2021-04-22 doi:10.1101/2021.04.22.440977 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Rapid blood acid-base regulation by European sea bass (Dicentrarchus labrax) in response to sudden exposure to high environmental CO2 ]]> https://biorxiv.org/content/10.1101/2021.04.22.441026v1?rss=1 Montgomery, D. W. Kwan, G. T. Davison, W. G. Finlay, J. Berry, A. Simpson, S. Engelhard, G. H. Birchenough, S. N. Tresguerres, M. Wilson, R. W. 2021-04-23 doi:10.1101/2021.04.22.441026 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ RNA-CLAMP Enables Photo-activated Control of CRISPR-Cas9 Gene Editing by Site-specific Intramolecular Cross-linking of the sgRNA ]]> https://biorxiv.org/content/10.1101/2021.04.22.441030v1?rss=1 Devaraj, N. K. Zhang, D. Jin, S. Liu, L. Tota, E. Li, Z. Piao, X. 2021-04-23 doi:10.1101/2021.04.22.441030 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Generalization of Cortical Multivariate Genome-Wide Associations Within and Across Samples ]]> https://biorxiv.org/content/10.1101/2021.04.23.441215v1?rss=1 1,000 dimensionality for each). By deploying a replication method that aggregates discovered effects distributed across multiple phenotypes, termed PolyVertex Score (PVS), we demonstrate a higher replication yield and comparable replication rate of discovered loci for MOSTest (# replicated loci: 348-845, replication rate: 94-95%) in independent data when compared with the established min-P approach (# replicated loci: 31-68, replication rate: 65-80%). An out-of-sample replication of discovered loci was conducted with a sample of 8,336 individuals from the Adolescent Brain Cognitive Development(R) (ABCD) study, who are on average 50 years younger than UK Biobank individuals. We observe a higher replication yield and comparable replication rate of MOSTest compared to min-P. This finding underscores the importance of using well-powered multivariate techniques for both discovery and replication of high dimensional phenotypes in Genome-Wide Association studies. ]]> Loughnan, R. J. Shadrin, A. A. Frei, O. van der Meer, D. Zhao, W. Palmer, C. E. Thompson, W. E. Makowski, C. Jernigan, T. Andreassen, O. Fan, C. C. Dale, A. 2021-04-24 doi:10.1101/2021.04.23.441215 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ The nematode worm C. elegans chooses between bacterial foods exactly as if maximizing economic utility ]]> https://biorxiv.org/content/10.1101/2021.04.25.441352v1?rss=1 Katzen, A. Chung, H.-K. Harbaugh, W. Iacono, C. D. Jackson, N. Yu, S. Flavell, S. W. Glimcher, P. Lockery, S. 2021-04-26 doi:10.1101/2021.04.25.441352 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Subcellular Organization of Viral Particles During Maturation of Nucleus-Forming Jumbo Phage ]]> https://biorxiv.org/content/10.1101/2021.04.26.441357v1?rss=1 Chaikeeratisak, V. Khanna, K. Nguyen, K. T. Egan, M. E. Enustun, E. Armbruster, E. Pogliano, K. Villa, E. Pogliano, J. 2021-04-26 doi:10.1101/2021.04.26.441357 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Suboptimal proteome allocation during changing environments constrains bacterial response and growth recovery ]]> https://biorxiv.org/content/10.1101/2021.04.28.441780v1?rss=1 Balakrishnan, R. Hwa, T. Cremer, J. 2021-04-28 doi:10.1101/2021.04.28.441780 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Systematic morphological and morphometric analysis of identified olfactory receptor neurons in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.04.28.441861v1?rss=1 Nava Gonzales, C. McKaughan, Q. Bushong, E. A. Cauwenberghs, K. Ng, R. Madany, M. Ellisman, M. H. Su, C.-Y. 2021-04-29 doi:10.1101/2021.04.28.441861 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure ]]> https://biorxiv.org/content/10.1101/2021.04.29.441258v1?rss=1 Francis, J. M. Leistritz-Edwards, D. Dunn, A. Tarr, C. Lehman, J. Dempsey, C. Hamel, A. Rayon, V. Liu, G. Wang, Y. Wille, M. Durkin, M. Hadley, K. Sheen, A. Roscoe, B. Ng, M. Rockwell, G. Manto, M. Gienger, E. Nickerson, J. MGH COVID-19 Collection and Processing Team, Moarefi, A. Noble, M. Malia, T. Bardwell, P. D. Gordon, W. Swain, J. Skoberne, M. Sauer, K. Harris, T. Goldrath, A. W. Shalek, A. K. Coyle, A. J. Benoist, C. Pregibon, D. C. 2021-04-29 doi:10.1101/2021.04.29.441258 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ SmProt: a reliable repository with comprehensive annotation of small proteins identified from ribosome profiling ]]> https://biorxiv.org/content/10.1101/2021.04.29.441405v1?rss=1 Li, Y. Zhou, H. Chen, X. Zheng, Y. Kang, Q. Hao, D. Zhang, L. Song, T. Luo, H. Hao, Y. Chen, Y. Chen, R. Zhang, P. He, S. 2021-04-30 doi:10.1101/2021.04.29.441405 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Metabolic adaptation to progressive mitochondrial dysfunction in aging POLGD257A mice ]]> https://biorxiv.org/content/10.1101/2021.04.29.441996v1?rss=1 Lim, E. W. Handzlik, M. K. Trefts, E. Gengatharan, J. M. Shaw, R. J. Metallo, C. M. 2021-04-29 doi:10.1101/2021.04.29.441996 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ In heart failure reactivation of RNA-binding proteins drives the transcriptome into a fetal state ]]> https://biorxiv.org/content/10.1101/2021.04.30.442191v1?rss=1 D'Antonio, M. Nguyen, J. P. Arthur, T. D. Matsui, H. Donovan, M. K. R. DAntonio-Chronowska, A. Frazer, K. A. 2021-05-01 doi:10.1101/2021.04.30.442191 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Impaired T-cell and antibody immunity after COVID-19 infection in chronically immunosuppressed transplant recipients ]]> https://biorxiv.org/content/10.1101/2021.05.03.442371v1?rss=1 Ashokkumar, C. Rohan, V. Kroemer, A. H. Rao, S. Mazariegos, G. Higgs, B. W. Nadig, S. Almeda, J. Dhani, H. Khan, K. Yazigi, N. Ekong, U. Kaufman, S. Betancourt-Garcia, M. M. Mukund, K. Sethi, P. Mehrotra, S. Soltys, K. Singh, M. S. Bond, G. Khanna, A. Ningappa, M. Spishock, B. Sindhi, E. Atale, N. Saunders, M. Baliga, P. Fishbein, T. Subramaniam, S. Sindhi, R. 2021-05-04 doi:10.1101/2021.05.03.442371 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing ]]> https://biorxiv.org/content/10.1101/2021.05.04.442591v1?rss=1 Bickhart, D. M. Kolmogorov, M. Tseng, E. Portik, D. Korobeynikov, A. Tolstoganov, I. Uritskiy, G. Liachko, I. Sullivan, S. T. Shin, S. B. Zorea, A. Andreu, V. P. Panke-Buisse, K. Medema, M. H. Mizrahi, I. Pevzner, P. A. Smith, T. P. 2021-05-04 doi:10.1101/2021.05.04.442591 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Insights into the L3 to L4 developmental program through proteomics ]]> https://biorxiv.org/content/10.1101/2021.05.06.439182v1?rss=1 Bennuru, S. Meng, Z. McKerrow, J. H. Lustigman, S. Nutman, T. B. 2021-05-06 doi:10.1101/2021.05.06.439182 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Development of a Cell Surface Display System in Chlamydomonas reinhardtii ]]> https://biorxiv.org/content/10.1101/2021.05.06.442888v1?rss=1 Molino, J. V. D. Carpine, R. Gademann, K. Mayfield, S. Sieber, S. 2021-05-06 doi:10.1101/2021.05.06.442888 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells ]]> https://biorxiv.org/content/10.1101/2021.05.06.442935v1?rss=1 Mahoney, M. Damalanka, V. C. Tartell, M. Chung, D. H. Lourenco, A. L. Pwee, D. Mayer Bridwell, A. E. Hoffmann, M. Voss, J. Karmakar, P. Azouz, N. P. Klinger, A. M. Rothlauf, P. W. Thompson, C. E. Lee, M. Klampfer, L. Stallings, C. Rothenberg, M. E. Pöhlmann, S. Whelan, S. P. J. O'Donoghue, A. J. Craik, C. S. Janetka, J. W. 2021-05-06 doi:10.1101/2021.05.06.442935 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Discoidin Domain Receptor 2 regulates AT1 receptor expression in Angiotensin II-stimulated cardiac fibroblasts via fibronectin-dependent Integrin-β1 signalling ]]> https://biorxiv.org/content/10.1101/2021.05.06.442987v1?rss=1 Titus, A. S. V, H. Wang, M. Lakkatta, E. G. Kailasam, S. 2021-05-07 doi:10.1101/2021.05.06.442987 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Stochastic simulations reveal that dendritic spine morphology regulates synaptic plasticity in a deterministic manner ]]> https://biorxiv.org/content/10.1101/2021.05.06.442994v1?rss=1 Holst, M. V. Bell, M. K. Lee, C. T. Rangamani, P. 2021-05-06 doi:10.1101/2021.05.06.442994 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function ]]> https://biorxiv.org/content/10.1101/2021.05.06.443037v1?rss=1 Rajderkar, S. Barozzi, I. Zhu, Y. Hu, R. Zhang, Y. Li, B. Fukuda-Yuzawa, Y. Kelman, G. Akeza, A. Blow, M. J. Pham, Q. Harrington, A. N. Godoy, J. Meky, E. M. von Maydell, K. Novak, C. S. Plajzer-Frick, I. Afzal, V. Tran, S. Talkowski, M. E. Llyod, K. C. K. Ren, B. Dickel, D. E. Visel, A. Pennacchio, L. A. 2021-05-07 doi:10.1101/2021.05.06.443037 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Endoplasmic Reticulum morphological regulation by RTN4/NOGO modulates neuronal regeneration by slowing luminal transport ]]> https://biorxiv.org/content/10.1101/2021.05.10.441946v1?rss=1 Konno, T. Parutto, P. Bailey, D. M. D. Davi, V. Crapart, C. Awadelkareem, M. A. Hockings, C. Brown, A. Xiang, K. M. Agrawal, A. Chambers, J. E. Werp, M. V. Koning, K. Metzakopian, E. Westrate, L. Koslover, E. Avezov, E. 2021-05-10 doi:10.1101/2021.05.10.441946 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope ]]> https://biorxiv.org/content/10.1101/2021.05.10.443506v1?rss=1 Hetzer, M. W. tyagi, s. Chen, F. Huang, J. 2021-05-11 doi:10.1101/2021.05.10.443506 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Cortical ripples provide the conditions for consolidation during NREM sleep in humans ]]> https://biorxiv.org/content/10.1101/2021.05.11.443637v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Jiang, X. Rosen, B. Q. Kajfez, S. Eskandar, E. N. Gonzalez-Martinez, J. Cash, S. S. Halgren, E. 2021-05-13 doi:10.1101/2021.05.11.443637 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions ]]> https://biorxiv.org/content/10.1101/2021.05.12.443892v1?rss=1 Honda, T. Cremer, J. Mancini, L. Zhang, Z. Pilizota, T. Hwa, T. 2021-05-12 doi:10.1101/2021.05.12.443892 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach ]]> https://biorxiv.org/content/10.1101/2021.05.17.444458v1?rss=1 Sun, D. Adduru, V. R. Phillips, R. D. Bouchard, H. C. Sotiras, A. Michael, A. M. Baker, F. C. Tapert, S. F. Brown, S. A. Clark, D. B. Goldston, D. Nooner, K. B. Nagel, B. J. Thompson, W. K. De Bellis, M. Morey, R. A. 2021-05-17 doi:10.1101/2021.05.17.444458 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ A systems-guided approach to discover the intracellular target of a novel evolution-drug lead ]]> https://biorxiv.org/content/10.1101/2021.05.17.444532v1?rss=1 Chowdhury, S. Zielinski, D. C. Dalldorf, C. Rodrigues, J. V. Palsson, B. Shakhnovich, E. 2021-05-18 doi:10.1101/2021.05.17.444532 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Effects of vapor exposure to Δ9-tetrahydrocannabinol (THC) in the Maine Lobster (Homarus americanus) ]]> https://biorxiv.org/content/10.1101/2021.05.24.445508v1?rss=1 Gutierrez, A. Creehan, K. M. Turner, M. Tran, R. N. Kerr, T. M. Nguyen, J. D. Taffe, M. A. 2021-05-25 doi:10.1101/2021.05.24.445508 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Optimal dimensionality selection for independent component analysis of transcriptomic data ]]> https://biorxiv.org/content/10.1101/2021.05.26.445885v1?rss=1 McConn, J. L. Lamoureux, C. R. Poudel, S. Palsson, B. O. Sastry, A. V. 2021-05-27 doi:10.1101/2021.05.26.445885 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA ]]> https://biorxiv.org/content/10.1101/2021.05.27.445689v1?rss=1 Bergstrom, E. N. Luebeck, J.-C. Petljak, M. Bafna, V. Mischel, P. S. Harris, R. Alexandrov, L. B. 2021-05-27 doi:10.1101/2021.05.27.445689 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium ]]> https://biorxiv.org/content/10.1101/2021.05.27.445969v1?rss=1 60 established anthropometric loci in Hispanic/Latino populations at genome-wide significance--representing up to 30% of previously-reported index SNP anthropometric associations. Trans-ethnic meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our novel findings demonstrate that future studies may also benefit from leveraging differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification. ]]> Fernandez-Rhodes, L. Graff, M. Buchanan, V. L. Justice, A. E. Highland, H. M. Guo, X. Young, K. L. Adhikari, K. Allred, N. P. Below, J. E. Bradfield, J. Pereira, A. C. Glover, L. Kim, D. Lilly, A. G. Shrestha, P. Thomas, A. G. Zhang, X. Chen, M. Chiang, C. Pulit, S. Horimoto, A. Krieger, J. E. Guindo-Martinez, M. Preuss, M. Schumann, C. Smit, R. A. J. Torres-Mejia, G. Acuna-Alonzo, V. Bedoya, G. Bortolini, M.-C. Canizales-Quinteros, S. Gallo, C. Gonzalez-Jose, R. Poletti, G. Rothhammer, F. Hakonarson, H. Adler, S. G. Igo, R. Iyengar, S. Nicholas, S. B. 2021-05-29 doi:10.1101/2021.05.27.445969 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Rapid evolution of bacterial AB5 toxin B subunits independent of A subunits: sialic acid binding preferences correlate with host range and toxicity ]]> https://biorxiv.org/content/10.1101/2021.05.28.446168v1?rss=1 Khan, N. Sasmal, A. Khedri, Z. Secrest, P. Verhagen, A. Srivastava, S. Varki, N. Chen, X. Yu, H. Beddoe, T. Paton, A. W. Paton, J. C. Varki, A. 2021-05-28 doi:10.1101/2021.05.28.446168 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Pro-regenerative Extracellular Matrix Hydrogel Prevents and Mitigates Pathological Alterations of Pelvic Muscles Following Birth Injury ]]> https://biorxiv.org/content/10.1101/2021.05.28.446170v1?rss=1 Duran, P. Sesillo, F. B. Burnett, L. Menefee, S. A. Cook, M. Zazueta-Damian, G. Dzieciatkowska, M. Do, E. French, S. Shah, M. M. Sanvictores, C. Hansen, K. Shtrahman, M. Christman, K. L. Alperin, M. 2021-05-28 doi:10.1101/2021.05.28.446170 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Sialoglycan microarray encoding reveals differential sialoglycan binding of phylogenetically-related bacterial AB5 toxin B subunits ]]> https://biorxiv.org/content/10.1101/2021.05.28.446191v1?rss=1 113,000 likely linear sialyltrisaccharides in nature. Notably a biantennary N-glycan with two terminal sialyltrisaccharides could thus have >1010 potential combinations and a triantennary N-glycan with three terminal sequences, >1015 potential combinations. While all possibilities likely do not exist in nature, sialoglycans encode enormous diversity. While glycomic approaches are used to probe such diverse sialomes, naturally-occurring bacterial AB5 toxin B subunits are simpler tools to track the dynamic sialome in biological systems. Sialoglycan microarray was utilized to compare sialoglycan-recognizing bacterial toxin B subunits. Unlike the poor correlation between B subunits and species phylogeny, there is stronger correlation with Sia-epitope preferences. Further supporting this pattern, we report a B subunit (YenB) from Yersinia enterocolitica (broad host range) recognizing almost all sialoglycans in the microarray, including 4-O-acetylated-Sias not recognized by a Y. pestis orthologue (YpeB). Differential Sia-binding patterns were also observed with phylogenetically-related B subunits from Escherichia coli (SubB), Salmonella Typhi (PltB), S. Typhimurium (ArtB), extra-intestinal E.coli (EcPltB), Vibrio cholera (CtxB), and cholera family homologue of E. coli (EcxB). ]]> Sasmal, A. Khan, N. Khedri, Z. Kellman, B. P. Srivastava, S. Verhagen, A. Yu, H. Bruntse, A. B. Diaz, S. Varki, N. Beddoe, T. Paton, A. W. Paton, J. C. Chen, X. Lewis, N. E. Varki, A. 2021-05-29 doi:10.1101/2021.05.28.446191 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Development and applications of sialoglycan-recognizing probes (SGRPs) with defined specificities: exploring the dynamic mammalian sialoglycome ]]> https://biorxiv.org/content/10.1101/2021.05.28.446202v1?rss=1 Srivastava, S. Verhagen, A. Sasmal, A. Wasik, B. R. Diaz, S. Yu, H. Bensing, B. A. Khan, N. Khedri, Z. Secrest, P. Sullam, P. Varki, N. Chen, X. Parrish, C. R. Varki, A. 2021-05-28 doi:10.1101/2021.05.28.446202 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Identification of Leucinostatins from Ophiocordyceps sp. as Antiparasitic Agents Against Trypanosoma cruzi ]]> https://biorxiv.org/content/10.1101/2021.05.30.446362v1?rss=1 Bernatchez, J. A. Kil, Y.-S. Barbosa da Silva, E. Thomas, D. McCall, L.-I. Wendt, K. L. Souza, J. M. Ackermann, J. McKerrow, J. H. Cichewicz, R. H. Siqueira-Neto, J. L. 2021-05-31 doi:10.1101/2021.05.30.446362 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Molecular foundations of Precambrian uniformitarianism ]]> https://biorxiv.org/content/10.1101/2021.05.31.446354v1?rss=1 Kedzior, M. Garcia, A. K. Li, M. Taton, A. Adam, Z. R. Young, J. N. Kacar, B. 2021-05-31 doi:10.1101/2021.05.31.446354 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas ]]> https://biorxiv.org/content/10.1101/2021.05.31.446440v1?rss=1 Borner, K. Teichmann, S. A. Quardokus, E. M. Gee, J. Browne, K. Osumi-Sutherland, D. Herr, B. W. Bueckle, A. Paul, H. Haniffa, M. A. Jardine, L. Bernard, A. Ding, S.-L. Miller, J. A. Lin, S. Halushka, M. Boppana, A. Longacre, T. A. Hickey, J. Lin, Y. Valerius, M. T. He, Y. Pryhuber, G. Sun, X. Jorgensen, M. Radtke, A. Wasserfall, C. Ginty, F. Ho, J. Sunshine, J. Beuschel, R. T. Brusko, M. Lee, S. Malhotra, R. Jain, S. Weber, G. 2021-06-01 doi:10.1101/2021.05.31.446440 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ CDK12 is Necessary to Promote Epidermal Differentiation through Transcription Elongation ]]> https://biorxiv.org/content/10.1101/2021.06.01.446524v1?rss=1 Sen, G. Li, J. Tiwari, M. Chen, Y. 2021-06-01 doi:10.1101/2021.06.01.446524 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies ]]> https://biorxiv.org/content/10.1101/2021.06.01.446591v1?rss=1 Ye, Q. Lu, S. Corbett, K. D. 2021-06-01 doi:10.1101/2021.06.01.446591 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Gene regulatory networks underlying human microglia maturation ]]> https://biorxiv.org/content/10.1101/2021.06.02.446636v1?rss=1 Coufal, N. G. Glass, C. Han, C. Li, R. Z. Hansen, E. Bennett, H. Poirion, O. Buchanan, J. Challacombe, J. Fixsen, B. Trescott, S. Schlachetzki, J. Preissl, S. Wang, A. O'Connor, C. Warden, A. S. Shriram, S. Kim, R. Nguyen, C. Schafer, D. Ramirez, G. Anavim, S. A. Johnson, A. Sajti, E. Gupta, M. Ben-Haim, S. Gonda, D. D. Levy, M. L. Laurent, L. 2021-06-02 doi:10.1101/2021.06.02.446636 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein aggregates within processing bodies ]]> https://biorxiv.org/content/10.1101/2021.06.02.446820v1?rss=1 Fenix, A. M. Miyaoka, Y. Bertero, A. Blue, S. Spindler, M. J. Tan, K. K. B. Perez-Bermejo, J. A. Chan, A. H. Mayer, S. J. Nguyen, T. Russell, C. R. Lizarraga, P. Truong, A. So, P.-L. Kulkarni, A. Chetal, K. Sathe, S. Sniadecki, N. J. Yeo, G. W. Murry, C. E. Salomonis, N. 2021-06-03 doi:10.1101/2021.06.02.446820 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Spatially heterogeneous microstructural development within subcortical regions from 9-13 years ]]> https://biorxiv.org/content/10.1101/2021.06.04.446984v1?rss=1 Palmer, C. E. Pecheva, D. Iversen, J. R. Hagler, D. J. Sugrue, L. Nedelec, P. Fan, C. Thompson, W. Jernigan, T. L. Dale, A. M. 2021-06-06 doi:10.1101/2021.06.04.446984 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Microstructural development across white matter from 9-13 years ]]> https://biorxiv.org/content/10.1101/2021.06.04.447102v1?rss=1 Palmer, C. E. Pecheva, D. Iversen, J. R. Hagler, D. J. Sugrue, L. Nedelec, P. Fan, C. Thompson, W. Jernigan, T. L. Dale, A. M. 2021-06-06 doi:10.1101/2021.06.04.447102 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Behavioral effects of ethanol in the Red Swamp Crayfish(Procambarus clarkii) ]]> https://biorxiv.org/content/10.1101/2021.06.05.447220v1?rss=1 Gutierrez, A. Creehan, K. M. de Guglielmo, G. Roberts, A. J. A. Taffe, M. A. 2021-06-07 doi:10.1101/2021.06.05.447220 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Estimating the absolute number of axons connecting different cortical areas in humans with diffusion MRI ]]> https://biorxiv.org/content/10.1101/2021.06.07.447453v1?rss=1 Rosen, B. Q. Halgren, E. 2021-06-08 doi:10.1101/2021.06.07.447453 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation ]]> https://biorxiv.org/content/10.1101/2021.06.08.447518v1?rss=1 Orth, M. F. Surdez, D. Marchetto, A. Grossetete, S. Gerke, J. S. Zaidi, S. Alonso, J. Sastre, A. Baulande, S. Sill, M. Cidre-Aranaz, F. Ohmura, S. Kirchner, T. Hauck, S. M. Reischl, E. Gymrek, M. Pfister, S. M. Strauch, K. Delattre, O. Grunewald, T. G. P. 2021-06-08 doi:10.1101/2021.06.08.447518 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo ]]> https://biorxiv.org/content/10.1101/2021.06.10.447994v1?rss=1 Gao, Y. Lim, H. G. Verkler, H. Szubin, R. Quach, D. Rodionova, I. Chen, K. Yurkovich, J. Cho, B.-K. Palsson, B. O. 2021-06-11 doi:10.1101/2021.06.10.447994 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers ]]> https://biorxiv.org/content/10.1101/2021.06.11.447968v1?rss=1 Lange, J. T. Chen, C. Y. Pichugin, Y. Xie, F. Tang, J. Hung, K. L. Yost, K. E. Shi, Q. Erb, M. L. Rajkumar, U. Wu, S. Swanton, C. Liu, Z. Huang, W. Chang, H. Y. Bafna, V. Henssen, A. G. Werner, B. Mischel, P. S. 2021-06-11 doi:10.1101/2021.06.11.447968 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Structural Basis for Cytoplasmic Dynein-1 Regulation by Lis1 ]]> https://biorxiv.org/content/10.1101/2021.06.11.448119v1?rss=1 Gillies, J. P. Reimer, J. M. Karasmanis, E. P. Lahiri, I. Htet, Z. M. Leschziner, A. E. Reck-Peterson, S. L. 2021-06-11 doi:10.1101/2021.06.11.448119 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion function for retrotranslocation of ER multi-spanning membrane substrates ]]> https://biorxiv.org/content/10.1101/2021.06.15.448428v1?rss=1 Nejatfard, A. Wauer, N. Bhaduri, S. Conn, A. Gourkanti, S. Singh, N. Kuo, T. Kandel, R. R. Amaro, R. E. Neal, S. E. 2021-06-15 doi:10.1101/2021.06.15.448428 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ The predicted bZIP transcription factor ZIP-1 promotes resistance to intracellular infection in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.06.17.448850v1?rss=1 Lazetic, V. Wu, F. Cohen, L. B. Reddy, K. C. Chang, Y.-T. Gang, S. S. Bhabha, G. Troemel, E. R. 2021-06-17 doi:10.1101/2021.06.17.448850 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Stem Cell Microarrays for Assessing Growth Factor Signaling in Engineered Glycan Microenvironments ]]> https://biorxiv.org/content/10.1101/2021.06.19.448747v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@42584forg.highwire.dtl.DTLVardef@1b3defcorg.highwire.dtl.DTLVardef@1f4796borg.highwire.dtl.DTLVardef@14f6e23_HPS_FORMAT_FIGEXP M_FIG C_FIG The present study describes the integration of glycosaminoglycan-protein conjugates into a hydrogel-supported stem cell microarray platform to analyze the activity of extracellular glycans in growth factor signaling. Such platforms can enable rapid development and optimization of functional glycomaterials for stem cell-based regenerative therapies. ]]> Michalak, A. L. Trieger, G. W. Trieger, K. A. Godula, K. 2021-06-20 doi:10.1101/2021.06.19.448747 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Disruption of VGLUT1 in cholinergic medial habenula projections increases nicotine self-administration ]]> https://biorxiv.org/content/10.1101/2021.06.19.449108v1?rss=1 Souter, E. A. Chen, Y.-C. Zell, V. Lallai, V. Steinkellner, T. Conrad, W. S. Wisden, W. Harris, K. D. Fowler, C. D. Hnasko, T. S. 2021-06-20 doi:10.1101/2021.06.19.449108 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ Exploring cell surface-nanopillar interactions with 3D super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2021.06.21.449280v1?rss=1 Roy, A. R. Zhang, W. Jahed, Z. Tsai, C.-T. Cui, B. Moerner, W. E. 2021-06-22 doi:10.1101/2021.06.21.449280 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ The noncoding RNA PRANCR regulates splicing of Fibronectin-1 to control keratinocyte proliferation and migration ]]> https://biorxiv.org/content/10.1101/2021.06.22.449364v1?rss=1 Otten, A. B. Amarbayar, O. Cai, P. Cheng, B. Qu, K. Sun, B. 2021-06-22 doi:10.1101/2021.06.22.449364 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Leveraging Allele-Specific Expression for Therapeutic Response Gene Discovery in Glioblastoma. ]]> https://biorxiv.org/content/10.1101/2021.06.22.449493v1?rss=1 Sen, A. Prager, B. C. Park, D. Zhu, Z. Gimple, R. C. Bernatchez, J. A. Beck, S. Clark, A. E. Siqueira-Neto, J. L. Rich, J. N. McVicker, G. P. 2021-06-22 doi:10.1101/2021.06.22.449493 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Mice are not automatons; subjective experience in premotor circuits guides behavior ]]> https://biorxiv.org/content/10.1101/2021.06.23.449617v1?rss=1 Schreiner, D. C. Cazares, C. Renteria, R. Gremel, C. M. 2021-06-24 doi:10.1101/2021.06.23.449617 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Multivariate genome-wide association studies on the tissue compartments of human brain identify novel loci underpinning brain development and neuropsychiatric outcomes. ]]> https://biorxiv.org/content/10.1101/2021.06.24.449723v1?rss=1 Fan, C. C. Loughnan, R. Pechva, D. Chen, C.-H. Hagler, D. Thompson, W. K. van der Meer, D. Frei, O. Andreassen, O. Dale, A. M. 2021-06-24 doi:10.1101/2021.06.24.449723 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Protein Kinase C gamma Mutations Drive Spinocerebellar Ataxia Type 14 by Impairing Autoinhibition ]]> https://biorxiv.org/content/10.1101/2021.06.24.449810v1?rss=1 Pilo, C. A. Kornev, A. P. Baffi, T. R. Kunkel, M. T. Huang, L.-C. Longman, C. Kannan, N. A. Taylor, S. S. Gorrie, G. Newton, A. C. 2021-06-24 doi:10.1101/2021.06.24.449810 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Photoinactivation of Catalase Sensitizes Wide-Ranging Bacteria to ROS-Producing Agents and Immune Cells ]]> https://biorxiv.org/content/10.1101/2021.06.24.449847v1?rss=1 Dong, P.-T. Jusuf, S. Hui, J. Zhan, Y. Zhu, Y. Liu, G. Y. Cheng, J.-X. 2021-06-24 doi:10.1101/2021.06.24.449847 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.06.28.450262v1?rss=1 Serwas, D. Akamatsu, M. Moayed, A. Vegesna, K. Vasan, R. Hill, J. M. Schoeneberg, J. Davies, K. M. Rangamani, P. Drubin, D. G. 2021-06-29 doi:10.1101/2021.06.28.450262 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline ]]> https://biorxiv.org/content/10.1101/2021.06.30.450555v1?rss=1 Palmer, C. E. Sheth, C. Marshall, A. Adise, S. Baker, F. Chang, L. Clark, D. Dagher, R. Dowling, G. Gonzalez, M. Haist, F. Herting, M. Huber, R. Jernigan, T. LeBlanc, K. Lee, K. Lisdahl, K. Neigh, G. Patterson, M. Renshaw, P. Rhee, K. Tapert, S. Thompson, W. Uban, K. Sowell, E. Yurgelun-Todd, D. 2021-06-30 doi:10.1101/2021.06.30.450555 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Optimal balancing of clinical factors in large scale clinical RNA-Seq studies ]]> https://biorxiv.org/content/10.1101/2021.06.30.450639v1?rss=1 CHIANG, A. W. T. Gazestani, V. H. Altieri, M. G. Courchesne, E. Lewis, N. E. 2021-07-01 doi:10.1101/2021.06.30.450639 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection ]]> https://biorxiv.org/content/10.1101/2021.07.01.450045v1?rss=1 Yoo, R. Rychel, K. Poudel, S. Al-bulushi, T. Yuan, Y. Chauhan, S. Lamoureux, C. Palsson, B. Sastry, A. V. 2021-07-02 doi:10.1101/2021.07.01.450045 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ The Effect of a Fennel Extract on the STAT Signaling and Intestinal Barrier Function ]]> https://biorxiv.org/content/10.1101/2021.07.01.450766v1?rss=1 Rabalais, J. Kozan, P. Lu, T. Durali, N. Okamoto, K. Das, B. McGeough, M. D. Lee, J. B. Barrett, K. E. Marchelletta, R. Sivagnanam, M. 2021-07-02 doi:10.1101/2021.07.01.450766 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ A PKA Inhibitor Motif within Smoothened Controls Hedgehog Signal Transduction ]]> https://biorxiv.org/content/10.1101/2021.07.05.451193v1?rss=1 Happ, J. T. Arveseth, C. D. Bruystens, J. Bertinetti, D. Nelson, I. B. Olivieri, C. Hedeen, D. S. Zhu, J.-F. Capener, J. L. Bröckel, J. W. Vu, L. King, C. C. Ruiz-Perez, V. L. Veglia, G. Herberg, F. W. Taylor, S. S. Myers, B. R. 2021-07-06 doi:10.1101/2021.07.05.451193 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.07.05.451222v1?rss=1 He, W.-t. Yuan, M. Callaghan, S. Musharrafieh, R. Song, G. Silva, M. Beutler, N. Lee, W.-H. Yong, P. Torres, J. L. Melo, M. Zhou, P. Zhao, F. Zhu, X. Peng, L. Huang, D. Anzanello, F. Ricketts, J. Parren, M. Garcia, E. Ferguson, M. Rinaldi, W. Rawlings, S. A. Nemazee, D. Smith, D. M. Briney, B. Safonova, Y. Rogers, T. Crotty, S. Irvine, D. J. Ward, A. B. Wilson, I. A. Burton, D. R. Andrabi, R. 2021-07-06 doi:10.1101/2021.07.05.451222 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development ]]> https://biorxiv.org/content/10.1101/2021.07.06.449578v1?rss=1 Suban, S. Schwarz, R. Sendersky, E. Golden, S. S. 2021-07-06 doi:10.1101/2021.07.06.449578 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Ca2+-dependent liquid-liquid phase separation underlies intracellular Ca2+ stores. ]]> https://biorxiv.org/content/10.1101/2021.07.06.451223v1?rss=1 Mayfield, J. E. Pollak, A. J. Worby, C. A. Xu, J. C. Tandon, V. Newton, A. C. Dixon, J. E. 2021-07-06 doi:10.1101/2021.07.06.451223 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Early adaptation in a microbial community is dominated by mutualism-enhancing mutations ]]> https://biorxiv.org/content/10.1101/2021.07.07.451547v1?rss=1 Venkataram, S. Kuo, H.-Y. Hom, E. F. Y. Kryazhimskiy, S. 2021-07-09 doi:10.1101/2021.07.07.451547 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Microbiome divergence of marine gastropod species separated by the Isthmus of Panama ]]> https://biorxiv.org/content/10.1101/2021.07.08.451645v1?rss=1 Neu, A. T. Torchin, M. E. Allen, E. E. Roy, K. 2021-07-09 doi:10.1101/2021.07.08.451645 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Flexible utilization of spatial- and motor-based codes for the storage of visuo-spatial information ]]> https://biorxiv.org/content/10.1101/2021.07.08.451663v1?rss=1 Henderson, M. M. Rademaker, R. L. Serences, J. T. 2021-07-09 doi:10.1101/2021.07.08.451663 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Glycocalyx engineering with heparan sulfate mimetics attenuates Wnt activity during adipogenesis to promote glucose uptake and metabolism. ]]> https://biorxiv.org/content/10.1101/2021.07.08.451710v1?rss=1 Trieger, G. Pessentheiner, A. Purcell, S. Green, C. R. DeForest, N. Willert, K. Majithia, A. Metallo, C. Godula, K. Gordts, P. 2021-07-09 doi:10.1101/2021.07.08.451710 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2 ]]> https://biorxiv.org/content/10.1101/2021.07.11.451941v1?rss=1 Cheung, C. Y. Huang, T.-T. Chow, N. Zhang, S. Zhao, Y. Wong, C. C. Boassa, D. Phan, S. Ellisman, M. H. Yates, J. R. Xu, S. Yu, Z. Zhang, Y. Zhang, R. Ng, L. L. Ko, B. C. B. 2021-07-11 doi:10.1101/2021.07.11.451941 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ An intestinally secreted host factor limits bacterial colonization but promotes microsporidia invasion of C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.12.452088v1?rss=1 El Jarkass, H. T. Mok, C. Schertzberg, M. R. Fraser, A. G. Troemel, E. R. Reinke, A. W. 2021-07-12 doi:10.1101/2021.07.12.452088 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.07.14.452426v1?rss=1 270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n = 58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time the impact of age and antipsychotic treatment on chromatin organization. ]]> Zhu, B. Ainsworth, R. I. Wang, Z. Sierra, S. Deng, C. Callado, L. F. Meana, J. J. Wang, W. Lu, C. Gonzalez-Maeso, J. 2021-07-16 doi:10.1101/2021.07.14.452426 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Asymmetric Arp2/3-mediated actin assembly facilitates clathrin-mediated endocytosis at stalled sites in genome-edited human stem cells. ]]> https://biorxiv.org/content/10.1101/2021.07.16.452693v1?rss=1 Jin, M. Shirazinejad, C. Wang, B. Yan, A. Schöneberg, J. Upadhyayula, S. Xu, K. Drubin, D. G. 2021-07-16 doi:10.1101/2021.07.16.452693 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence ]]> https://biorxiv.org/content/10.1101/2021.07.16.452756v1?rss=1 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles. ]]> Salido, R. A. Cantu, V. J. Clark, A. E. Leibel, S. L. Foroughishafiei, A. Saha, A. Hakim, A. Nouri, A. Lastrella, A. L. Castro-Martinez, A. Plascencia, A. Kapadia, B. Xia, B. Ruiz, C. Marotz, C. Maunder, D. Lawrence, E. S. Smoot, E. W. Eisner, E. Crescini, E. S. Kohn, L. Franco Vargas, L. Chacon, M. Betty, M. Machnicki, M. Wu, M. Y. Baer, N. A. Belda-Ferre, P. DeHoff, P. Saever, P. Ostrander, R. T. Tsai, R. Sathe, S. Aigner, S. Morgan, S. C. Ngo, T. T. Barber, T. Cheung, W. Carlin, A. F. Yeo, G. W. Laurent, L. Fielding-Miller, R. Knight, R. 2021-07-20 doi:10.1101/2021.07.16.452756 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Artificial Intelligence-rationalized balanced PPARα/γ dual agonism resets the dysregulated macrophage processes in inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2021.07.18.452807v1?rss=1 Katkar, G. Sayed, I. M. Amandachar, M. Castillo, V. Vidales, E. Toobian, D. Usmani, F. F. Sawires, J. R. Leriche, G. Yang, J. Sandborn, W. J. Das, S. Sahoo, D. Ghosh, P. 2021-07-19 doi:10.1101/2021.07.18.452807 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data ]]> https://biorxiv.org/content/10.1101/2021.07.19.452699v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@8e1759org.highwire.dtl.DTLVardef@9ee7d5org.highwire.dtl.DTLVardef@866f04org.highwire.dtl.DTLVardef@1e27b29_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phaneuf, P. V. Zielinski, D. C. Yurkovich, J. T. Johnsen, J. Szubin, R. Yang, L. Kim, S. H. Schulz, S. Wu, M. Dalldorf, C. Ozdemir, E. Palsson, B. O. Feist, A. 2021-07-20 doi:10.1101/2021.07.19.452699 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ An Orally Available Cathepsin L Inhibitor Protects Lungs Against SARS-CoV-2-Induced Diffuse Alveolar Damage in African Green Monkeys ]]> https://biorxiv.org/content/10.1101/2021.07.20.453127v1?rss=1 Frueh, F. W. Maneval, D. C. Bohm, R. P. Dufour, J. P. Blair, R. V. Simpson, S. Powell, K. Aye, P. P. Golden, N. A. ROY, C. J. Spencer, S. Russell-Lodrigue, K. Plante, K. S. Plante, J. A. McKerrow, J. H. Rappaport, J. 2021-07-21 doi:10.1101/2021.07.20.453127 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ GIV/Girdin binds BRCA1 and links trimeric G-proteins to DNA damage response ]]> https://biorxiv.org/content/10.1101/2021.07.21.452842v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@3d5202org.highwire.dtl.DTLVardef@1d32d89org.highwire.dtl.DTLVardef@152a85dorg.highwire.dtl.DTLVardef@1ab9953_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINon-receptor G protein modulator, GIV/Girdin binds BRCA1 C_LIO_LIBinding occurs in both canonical and non-canonical modes C_LIO_LIGIV sequesters BRCA1 away from dsDNA breaks, suppresses HR C_LIO_LIActivation of Gi by GIV enhances Akt signals, favors NHEJ C_LI IN BRIEFIn this work, the authors show that heterotrimeric G protein signaling that is triggered by non-receptor GEF, GIV/Girdin, in response to double-stranded DNA breaks is critical for decisive signaling events which favor non-homologous end-joining (NHEJ) and inhibit homologous recombination (HR). ]]> Abd El-Hafeez, A. A. Sun, N. Chakraborty, A. Ear, J. Roy, S. Chamarthi, P. Rajapakse, N. Das, S. Luker, K. E. Hazra, T. K. Luker, G. D. Ghosh, P. 2021-07-22 doi:10.1101/2021.07.21.452842 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Characterization of cocaine addiction-like behavior in heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.22.453410v1?rss=1 500 outbred heterogeneous stock (HS) rats using an extended cocaine self-administration paradigm (6 h/daily). We analyzed individual differences in escalation of intake, progressive-ratio (PR) responding, continued use despite adverse consequences (contingent foot shocks), and irritability-like behavior during withdrawal. Principal component analysis showed that escalation of intake, progressive ratio responding, and continued use despite adverse consequences loaded onto a single factor that was distinct from irritability-like behaviors. Categorizing rats into resilient, mild, moderate, and severe addiction-like phenotypes showed that females exhibited higher addiction-like behaviors, with a lower proportion of resilient individuals compared to males. These findings suggest that, in genetically diverse rats with extended drug access, escalation of intake, continued use despite adverse consequences, and PR responding are highly correlated measures of a shared underlying construct. Furthermore, our results highlight sex differences in resilience to addiction-like behaviors. ]]> de Guglielmo, G. Carrette, L. Kallupi, M. Brennan, M. Boomhower, B. Maturin, L. Conlisk, D. Sedighim, S. Tieu, L. Pavlich, M. Martinez, A. Velarde, N. Kononoff, J. Kimbrough, A. Simpson, S. Smith, L. Shankar, K. Krook, C. Avelar, A. Schweitzer, P. Woods, L. S. Palmer, A. A. George, O. 2021-07-23 doi:10.1101/2021.07.22.453410 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Transcriptional regulatory features associated with Coccidioides immitis phase transition ]]> https://biorxiv.org/content/10.1101/2021.07.22.453417v1?rss=1 Duttke, S. H. Beyhan, S. Singh, R. Neal, S. E. Viriyakosol, S. Fierer, J. Kirkland, T. N. Stajich, J. E. Benner, C. Carlin, A. 2021-07-22 doi:10.1101/2021.07.22.453417 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Leptin protects against the development and expression of cocaine addiction-like behavior in heterogenous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.22.453426v1?rss=1 Carrette, L. L. G. Corral, C. Crook, C. Boomhower, B. Brennan, M. Ortez, C. Shankar, K. Simpson, S. Maturin, L. de Guglielmo, G. Solberg-Woods, L. Palmer, A. A. George, O. 2021-07-23 doi:10.1101/2021.07.22.453426 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Individual differences in members of Actinobacteria, Bacteroidetes, and Firmicutes is associated with resistance or vulnerability to addiction-like behaviors in heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2021.07.23.453592v1?rss=1 Simpson, S. de Guglielmo, G. Brennan, M. Maturin, L. Peters, G. Jia, H. Andrews, S. Solberg-Woods, L. Palmer, A. George, O. 2021-07-24 doi:10.1101/2021.07.23.453592 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent ]]> https://biorxiv.org/content/10.1101/2021.07.26.453919v1?rss=1 Luna, E. Parkar, S. G. Kirmiz, N. Hartel, S. Hearn, E. Hossine, M. Kurdian, A. Mendoza, C. Orr, K. Padilla, L. Ramirez, K. Salcedo, P. Serrano, E. Choudhury, B. Paulchakrabarti, M. Parker, C. T. Huynh, S. Cooper, K. Flores, G. E. 2021-07-28 doi:10.1101/2021.07.26.453919 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ An atlas of healthy and injured cell states and niches in the human kidney ]]> https://biorxiv.org/content/10.1101/2021.07.28.454201v1?rss=1 400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (n = 42) and disease (n = 42) kidneys. This has provided a high resolution cellular atlas of 100 cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations for major cell types spanning the entire kidney. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several segments. Molecular signatures of these states permitted their localization within injury neighborhoods using spatial transcriptomics, and large-scale 3D imaging analysis of [~]1.2 million neighborhoods provided linkages to active immune responses. These analyses further defined biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that were associated with a decline in kidney function during chronic kidney disease. This human kidney cell atlas, including injury cell states and neighborhoods, will be a valuable resource for future studies. ]]> Lake, B. B. Menon, R. Winfree, S. Hu, Q. Ferreira, R. M. Kalhor, K. Barwinska, D. Otto, E. A. Ferkowicz, M. Diep, D. Plongthongkum, N. Knoten, A. Urata, S. Naik, A. S. Eddy, S. Zhang, B. Wu, Y. Salamon, D. Williams, J. C. Wang, X. Balderrama, K. S. Hoover, P. Murray, E. Vijayan, A. Chen, F. Waikar, S. S. Rosas, S. Wilson, F. P. Palevsky, P. M. Kiryluk, K. Sedor, J. R. Toto, R. D. Parikh, C. Kim, E. H. Macosko, E. Z. Kharchenko, P. V. Gaut, J. P. Hodgin, J. B. Eadon, M. T. Dagher, P. C. El-Achkar, T. M. Zhang, K. Kretzler, M. Jain, S. KPMP Consortium, 2021-07-29 doi:10.1101/2021.07.28.454201 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators ]]> https://biorxiv.org/content/10.1101/2021.07.28.454220v1?rss=1 Rajput, A. Tsunemoto, H. Sastry, A. V. Szubin, R. Rychel, K. Sugie, J. Pogliano, J. Palsson, B. 2021-07-28 doi:10.1101/2021.07.28.454220 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ The timescale and magnitude of aperiodic activity decreases with cortical depth in humans, macaques and mice ]]> https://biorxiv.org/content/10.1101/2021.07.28.454235v1?rss=1 Halgren, M. Kang, R. Voytek, B. Ulbert, I. Fabo, D. Eross, L. G. Wittner, L. Madsen, J. Doyle, W. K. Devinsky, O. Halgren, E. Harnett, M. T. Cash, S. S. 2021-07-29 doi:10.1101/2021.07.28.454235 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius ]]> https://biorxiv.org/content/10.1101/2021.07.28.454237v1?rss=1 Chauhan, S. M. Poudel, S. Rychel, K. Lamoureux, C. Yoo, R. Al Bulushi, T. Yuan, Y. Palsson, B. Sastry, A. V. 2021-07-29 doi:10.1101/2021.07.28.454237 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML ]]> https://biorxiv.org/content/10.1101/2021.07.30.454489v1?rss=1 Krivdova, G. Voisin, V. Schoof, E. M. Marhon, S. A. Murison, A. J. McLeod, J. L. Gabra, M. Zeng, A. G. Van Nostrand, E. L. Aigner, S. J. Shishkin, A. A. Yee, B. A. Hermans, K. G. Trotman-Grant, A. G. Mbong, N. Kennedy, J. A. Gan, O. I. Wagenblast, E. De Carvalho, D. D. LAB, S. Minden, M. D. Bader, G. D. Yeo, G. W. Dick, J. E. Lechman, E. R. 2021-07-30 doi:10.1101/2021.07.30.454489 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ The role of muscle stem cells and fibro-adipogenic progenitors in female pelvic floor muscle regeneration following birth injury ]]> https://biorxiv.org/content/10.1101/2021.07.30.454534v1?rss=1 Boscolo Sesillo, F. Rajesh, V. Wong, M. Duran, P. Baynes, B. Laurent, L. C. Christman, K. Sacco, A. Alperin, M. 2021-07-31 doi:10.1101/2021.07.30.454534 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Mechanisms governing protective pregnancy-induced adaptions of the pelvic floor muscles in the rat pre-clinical model ]]> https://biorxiv.org/content/10.1101/2021.08.01.454675v1?rss=1 0.05). However, the myofibers remained significantly longer in load+/pregnancy hormones- compared to load- /pregnancy hormones- in coccygeus (13.33{+/-}0.94 vs 9.97{+/-}0.26 mm, P<0.0001) and pubocaudalis (21.20{+/-}0.52 vs 19.52{+/-}0.34 mm, P<0.04) and not different from load+/pregnancy hormones+ (12.82{+/-}0.30 and 22.53{+/-}0.32mm, respectively, P>0.1), indicating that sustained load induced sarcomerogenesis in these muscles. Intramuscular collagen content in load+/pregnancy hormones- group was significantly greater relative to controls in coccygeus (6.55{+/-}0.85 vs 3.11{+/-}0.47{micro}g/mg, P<0.001) and pubocaudalis (5.93{+/-}0.79 vs 3.46{+/-}0.52 {micro}g/mg, P<0.05) and not different from load+/pregnancy hormones+ (7.45{+/-}0.65 and 6.05{+/-}0.62 {micro}g/mg, respectively, P>0.5). Iliocaudalis required both mechanical and endocrine cues for sarcomerogenesis. Tibialis anterior was not affected by mechanical or endocrine alterations. Despite equivalent extent of adaptations, load-induced changes were only partially protective against sarcomere hyperelongation. ConclusionsLoad induces plasticity of the intrinsic pelvic floor muscle components that renders protection against mechanical birth injury. The protective effect, which varies between individual muscles and strain magnitudes, is further augmented by the presence of pregnancy hormones. Maximizing impact of mechanical load on pelvic floor muscles during pregnancy, such as with specialized pelvic floor muscle stretching regimens, is a potentially actionable target for augmenting pregnancy-induced adaptations to decrease birth injury in women who may otherwise have incomplete antepartum muscle adaptations. AJOG at a GlanceO_LIWhy was the study conducted? O_LITo determine the role of mechanical load, uncoupled from the hormonal milieu of pregnancy, in driving protective pregnancy-induced adaptations previously discovered in the rat pelvic floor muscles. C_LI C_LIO_LIWhat are the key findings? O_LIMechanical load, in the absence of pregnancy hormones, induces sarcomerogenesis and extracellular matrix remodeling in rat pelvic floor muscles. C_LIO_LILoad-induced adaptations are partially protective against mechanical pelvic floor muscle injury consequent to parturition-associated strains. C_LI C_LIO_LIWhat does this study add to what is already known? O_LIThe effect of sustained increased mechanical load, uncoupled from the hormonal milieu of pregnancy, on pelvic floor muscle plasticity has not been previously studied. C_LIO_LIModulating pelvic floor muscles stretch antepartum, such as with specialized pelvic floor physical therapy regimens, could be a promising approach for augmentation of protective muscle adaptations in women. C_LI C_LI ]]> Rieger, M. M. Wong, M. Burnett, L. A. Boscolo Sesillo, F. Baynes, B. Alperin, M. 2021-08-02 doi:10.1101/2021.08.01.454675 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ A vibrissa pathway that activates the limbic system ]]> https://biorxiv.org/content/10.1101/2021.08.02.454720v1?rss=1 Kleinfeld, D. Deschenes, M. Elbaz, M. Callado Perez, A. Foo, C. Zhao, S. Demers, M. 2021-08-04 doi:10.1101/2021.08.02.454720 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Near-Zero Phase-Lag Hyperscanning in a Novel Wireless EEG System ]]> https://biorxiv.org/content/10.1101/2021.08.04.454932v1?rss=1 Chuang, C.-H. Lu, S.-W. Chao, Y.-P. Peng, P.-H. Hsu, H.-C. Jung, T.-P. 2021-08-06 doi:10.1101/2021.08.04.454932 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ The genetic etiology of longitudinal measures of predicted brain ageing in a population-based sample of mid to late-age males ]]> https://biorxiv.org/content/10.1101/2021.08.04.455143v1?rss=1 Gillespie, N. A. Hatton, S. N. Hagler, D. H. Dale, A. M. Elman, J. A. McEvoy, L. K. Elyer, L. T. Fennema-Notestine, C. Logue, M. W. McKenzie, R. E. Puckett, O. K. Tu, X. M. Whitsel, N. Xian, H. Reynolds, C. A. Panizzon, M. S. Lyons, M. J. Neale, M. C. Kremen, W. S. Franz, C. 2021-08-06 doi:10.1101/2021.08.04.455143 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region ]]> https://biorxiv.org/content/10.1101/2021.08.04.455157v1?rss=1 Turakhia, Y. Thornlow, B. Hinrichs, A. S. Mcbroome, J. Ayala, N. Ye, C. De Maio, N. Haussler, D. Lanfear, R. Corbett-Detig, R. 2021-08-05 doi:10.1101/2021.08.04.455157 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Interleukin-33 coordinates a microglial phagocytic response and limits corticothalamic excitability and seizure susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.05.455250v1?rss=1 Han, R. T. Vainchtein, I. D. Schlachetzki, J. C. M. Cho, F. S. Dorman, L. C. Johung, T. Ahn, E. Barron, J. T. Inoue, H. N. Joshi, A. Molofsky, A. B. Glass, C. K. Paz, J. T. Molofsky, A. V. 2021-08-06 doi:10.1101/2021.08.05.455250 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Broad-spectrum in vitro antiviral activity of ODBG-P-RVn: an orally-available, lipid-modified monophosphate prodrug of remdesivir parent nucleoside (GS-441524) ]]> https://biorxiv.org/content/10.1101/2021.08.06.455494v1?rss=1 Lo, M. K. Shrivastava-Ranjan, P. Chatterjee, P. Flint, M. Beadle, J. R. Valiaeva, N. Schooley, R. Hostetler, K. Y. Montgomery, J. Spiropoulou, C. F. 2021-08-08 doi:10.1101/2021.08.06.455494 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Tankyrase interacts with the allosteric site of glucokinase and inhibits its glucose-sensing function in the beta cell ]]> https://biorxiv.org/content/10.1101/2021.08.08.454510v1?rss=1 Chi, N.-W. Eisemann, T. Yeh, T.-Y. J. Roy, S. Chi, T. J. Lu, S. H. Pascal, J. M. Osborn, O. 2021-08-08 doi:10.1101/2021.08.08.454510 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Safety and efficacy of a new vaginal gel, Feminilove, for the treatment of symptoms associated with vaginal dryness and vulvovaginal atrophy in women: an in vitro and in vivo study ]]> https://biorxiv.org/content/10.1101/2021.08.17.455703v1?rss=1 Gonzalez, A. Lee, R. Booshehri, L. Grady, D. Vaddi, V. Ip, C. Mitchell, C. Cheung, W. W. 2021-08-18 doi:10.1101/2021.08.17.455703 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Long-term p21 and p53 trends regulate the frequency of mitosis events and cell cycle arrest ]]> https://biorxiv.org/content/10.1101/2021.08.17.456721v1?rss=1 Tran, A. P. Tralie, C. J. Moosmüller, C. Belkhatir, Z. Reyes, J. Levine, A. J. Deasy, J. O. Tannenbaum, A. R. 2021-08-19 doi:10.1101/2021.08.17.456721 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway ]]> https://biorxiv.org/content/10.1101/2021.08.23.457403v1?rss=1 Farre, J.-C. Carolino, K. Devanneaux, L. Subramani, S. 2021-08-23 doi:10.1101/2021.08.23.457403 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.08.24.457187v1?rss=1 Lam, M. T. Y. Duttke, S. H. Odish, M. F. Le, H. D. Hansen, E. A. Nguyen, C. T. Trescott, S. Kim, R. Deota, S. Chang, M. W. Patel, A. Hepokoski, M. Alotaibi, M. Rolfsen, M. Perofsky, K. Warden, A. S. Foley, J. Ramirez, S. I. Dan, J. M. Abbott, R. Crotty, S. Crotty-Alexander, L. E. Malhotra, A. Panda, S. Benner, C. W. Coufal, N. G. 2021-08-24 doi:10.1101/2021.08.24.457187 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Amphetamine alters the Reward Positivity in humans and mice ]]> https://biorxiv.org/content/10.1101/2021.08.25.457689v1?rss=1 Cavanagh, J. F. Olguin, S. Talledo, J. Kotz, J. Roberts, B. Nungary, J. A. Sprock, J. Gregg, D. Bhakta, S. G. Light, G. A. Swerdlow, N. R. Young, J. W. Brigman, J. L. 2021-08-27 doi:10.1101/2021.08.25.457689 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Redesigning the Eterna100 for the Vienna 2 folding engine ]]> https://biorxiv.org/content/10.1101/2021.08.26.457839v1?rss=1 Koodli, R. V. Rudolfs, B. Wayment-Steele, H. K. Eterna Structure Designers, Das, R. 2021-08-28 doi:10.1101/2021.08.26.457839 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ The OPAQUE1/DISCORIDA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize ]]> https://biorxiv.org/content/10.1101/2021.08.29.458084v1?rss=1 Nan, Q. Liang, H. Mendoza, J. Liu, L. Fulzele, A. Wright, A. J. Bennett, E. J. Rasmussen, C. Facette, M. R. 2021-08-30 doi:10.1101/2021.08.29.458084 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ ZetaSuite, A Computational Method for Analyzing Multi-dimensional High-throughput Data, Reveals Genes with Opposite Roles in Cancer Dependency ]]> https://biorxiv.org/content/10.1101/2021.08.29.458095v1?rss=1 Hao, Y. Shao, C. Zhao, G. Fu, X.-D. 2021-08-30 doi:10.1101/2021.08.29.458095 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B ]]> https://biorxiv.org/content/10.1101/2021.08.30.458235v1?rss=1 McCann, J. Cristini, A. Law, E. LEE, S. Tellier, M. Carpenter, M. Beghe, C. Kim, J. Jarvis, M. C. Stefanovska, B. Temiz, N. A. Bergstrom, E. N. Salamango, D. Brown, M. Murphy, S. Alexandrov, L. Miller, K. Gromak, N. Harris, R. 2021-08-31 doi:10.1101/2021.08.30.458235 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease ]]> https://biorxiv.org/content/10.1101/2021.09.01.458619v1?rss=1 D'Antonio, M. Arthur, T. D. Nguyen, J. P. Matsui, H. D'Antonio-Chronowska, A. Frazer, K. A. 2021-09-02 doi:10.1101/2021.09.01.458619 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes ]]> https://biorxiv.org/content/10.1101/2021.09.02.458788v1?rss=1 Steinbrenner, A. D. Saldivar, E. Hodges, N. Chaparro, A. F. Schmelz, E. A. 2021-09-03 doi:10.1101/2021.09.02.458788 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Distinct stress-dependent signatures of cellular and extracellular tRNA-derived small RNAs (tDRs) ]]> https://biorxiv.org/content/10.1101/2021.09.03.458085v1?rss=1 Li, G. Manning, A. Bagi, A. Yang, X. Howard, J. Chan, P. P. Sweeney, T. Li, H. Laurent, B. D. Kontaridis, M. I. Laurent, L. C. Jensen, K. V. K. Aranki, S. F. Muehlschlegel, J. D. Kitchen, R. Lowe, T. M. Das, S. 2021-09-04 doi:10.1101/2021.09.03.458085 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population ]]> https://biorxiv.org/content/10.1101/2021.09.06.459155v1?rss=1 Parker, C. C. Philip, V. Gatti, D. M. Kasparek, S. Kreuzman, A. Kuffler, L. Mansky, B. Masneuf, S. Sharif, K. Sluys, E. Taterra, D. Taylor, W. M. Thomas, M. Polesskaya, O. Palmer, A. A. Holmes, A. Chesler, E. 2021-09-06 doi:10.1101/2021.09.06.459155 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes ]]> https://biorxiv.org/content/10.1101/2021.09.06.459165v1?rss=1 Mendes, M. Russell, A. B. 2021-09-06 doi:10.1101/2021.09.06.459165 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses ]]> https://biorxiv.org/content/10.1101/2021.09.08.459480v1?rss=1 He, W.-t. Musharrafieh, R. Song, G. Dueker, K. Callaghan, S. Yong, P. Beutler, N. Torres, J. L. Volk, R. M. Zhou, P. Yuan, M. Liu, H. Anzanello, F. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Wilson, I. A. Ward, A. B. Rogers, T. Burton, D. R. Andrabi, R. 2021-09-08 doi:10.1101/2021.09.08.459480 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Semisynthesis of functional transmembrane proteins in GUVs ]]> https://biorxiv.org/content/10.1101/2021.09.08.459519v1?rss=1 Podolsky, K. A. Masubuchi, T. Debelouchina, G. T. Hui, E. Devaraj, N. K. 2021-09-08 doi:10.1101/2021.09.08.459519 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Engineered bacteria detect tumor DNA in vivo ]]> https://biorxiv.org/content/10.1101/2021.09.10.459858v1?rss=1 Cooper, R. M. Wright, J. A. Ng, J. Q. Goyne, J. M. Suzuki, N. Lee, Y. K. Ichinose, M. Radford, G. Thomas, E. M. Vrbanac, L. Knight, R. Woods, S. L. Worthley, D. L. Hasty, J. 2021-09-11 doi:10.1101/2021.09.10.459858 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Ankfn1 vestibular defects in zebrafish require mutations in both ancestral and derived paralogs. ]]> https://biorxiv.org/content/10.1101/2021.09.11.459924v1?rss=1 Ross, K. D. Ren, J. Zhang, R. Chi, N. C. Hamilton, B. A. 2021-09-12 doi:10.1101/2021.09.11.459924 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation ]]> https://biorxiv.org/content/10.1101/2021.09.16.459846v1?rss=1 Yeh, Y.-T. Skinner, D. E. Criado-Hidalgo, E. Chen, N. S. Garcia-De Herreros, A. El-Sakary, N. Liu, L. Zhang, S. Chien, S. Lasheras, J. C. del Alamo, J. C. Caffrey, C. R. 2021-09-17 doi:10.1101/2021.09.16.459846 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ CRISPR-Cas Inhibits Natural Transformation through Altruistic Group Defense and Self-Sacrifice ]]> https://biorxiv.org/content/10.1101/2021.09.16.460680v1?rss=1 Cooper, R. M. Hasty, J. 2021-09-16 doi:10.1101/2021.09.16.460680 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ A BioID-derived proximity interactome for SARS-CoV-2 proteins ]]> https://biorxiv.org/content/10.1101/2021.09.17.460814v1?rss=1 May, D. G. Martin-Sancho, L. Anschau, V. Liu, S. Chrisopulos, R. J. Scott, K. L. Halfmann, C. T. Pena, R. D. Pratt, D. Campos, A. R. Roux, K. J. 2021-09-21 doi:10.1101/2021.09.17.460814 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Context-aware deconvolution of cell-cell communication with Tensor-cell2cell ]]> https://biorxiv.org/content/10.1101/2021.09.20.461129v1?rss=1 Armingol, E. Baghdassarian, H. Martino, C. Perez-Lopez, A. Knight, R. Lewis, N. E. 2021-09-23 doi:10.1101/2021.09.20.461129 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Origin of electroneutrality in living system ]]> https://biorxiv.org/content/10.1101/2021.09.21.461264v1?rss=1 Akbari, A. Palsson, B. O. 2021-09-24 doi:10.1101/2021.09.21.461264 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Extrasynaptic signaling enables an asymmetric juvenile motor circuit to produce a symmetric mature gait. ]]> https://biorxiv.org/content/10.1101/2021.09.21.461278v1?rss=1 Lu, Y. Ahamed, T. Mulcahy, B. Witvliet, D. Guan, S. A. Hung, W. Meng, J. Wen, Q. Samuel, A. Zhen, M. 2021-09-24 doi:10.1101/2021.09.21.461278 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ The connection between Rap1 and Talin1 in CD4+ T Lymphocytes ]]> https://biorxiv.org/content/10.1101/2021.09.22.461411v1?rss=1 Lagarrigue, F. Tan, B. Du, Q. Fan, Z. Lopez-Ramirez, M. A. Gingras, A. R. Qi, W. Sun, H. 2021-09-23 doi:10.1101/2021.09.22.461411 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Self-Administration of entactogen psychostimulants dysregulates GABA and Kappa Opioid Receptor signaling in the central nucleus of the amygdala of female Wistar rats ]]> https://biorxiv.org/content/10.1101/2021.09.24.461477v1?rss=1 Khom, S. Nguyen, J. D. Vandewater, S. A. Grant, Y. Roberto, M. Taffe, M. A. 2021-09-24 doi:10.1101/2021.09.24.461477 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Phostensin Enables Lymphocyte Integrin Activation and Population of Peripheral Lymphoid Organs ]]> https://biorxiv.org/content/10.1101/2021.09.24.461584v1?rss=1 Ginsberg, M. Sun, H. Gingras, A. Lee, H. Lagarrigue, F. Fox, J. W. Sherman, N. E. 2021-09-24 doi:10.1101/2021.09.24.461584 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Towards Understanding Comprehensive Morphometric Changes and Its Correlation with Cognition and Exposure to Fighting in Active Professional Boxers ]]> https://biorxiv.org/content/10.1101/2021.09.25.461817v1?rss=1 Mishra, V. R. Zhuang, X. Sreenivasan, K. R. Cordes, D. Ritter, A. Banks, S. Bernick, C. 2021-09-28 doi:10.1101/2021.09.25.461817 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Pre-mRNA Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the pre-mRNA Splice Site Signal ]]> https://biorxiv.org/content/10.1101/2021.09.27.462007v1?rss=1 Glasser, E. Maji, D. Biancon, G. Keedakkatt Puthenpeedikakkal, A. M. Cavender, C. Tebaldi, T. Pulvino, M. J. Jenkins, J. L. Mathews, D. H. Halene, S. Kielkopf, C. L. 2021-09-27 doi:10.1101/2021.09.27.462007 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Nanocrown electrodes for robust and scalable intracellular recordings of cardiomyocytes for cardiotoxicity screening ]]> https://biorxiv.org/content/10.1101/2021.09.28.462181v1?rss=1 99% success rates in obtaining intracellular access through electroporation, allowing reliable and simultaneous iAP recordings from up to 57 human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs). The accuracy of nanocrown electrode recordings is validated by simultaneous patch clamp recording from the same cell. Nanocrown electrodes enable prolonged iAP recording for continual monitoring of the same cells upon the sequential addition of four to five incremental drug doses. In this way, the dose-response data is self-referencing, which avoids the cell-to-cell variations inherent to hPSC-CMs. We are hopeful that this technology development is a step towards establishing an iAP screening assay for preclinical evaluation of drug-induced arrhythmogenicity. ]]> Jahed, Z. Yang, Y. Tsai, C.-T. Foster, E. P. McGuire, A. F. Yang, H. Liu, A. Forro, C. Yan, Z. Ke, X. J. Zhao, M.-T. Zheng, W. Li, X. Li, T. Pawlosky, A. Wu, J. C. Cui, B. 2021-09-30 doi:10.1101/2021.09.28.462181 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Integrated Regulation of PKA by Fast and Slow Neurotransmission in the Nucleus Accumbens Controls Plasticity and Stress Responses ]]> https://biorxiv.org/content/10.1101/2021.09.29.462408v1?rss=1 Thomas, R. Hernandez, A. Benavides, D. R. Li, W. Tan, C. Plattner, F. Chakraborti, A. Pozzo-Miller, L. Taylor, S. S. Bibb, J. A. 2021-10-01 doi:10.1101/2021.09.29.462408 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviours in the chick embryo ]]> https://biorxiv.org/content/10.1101/2021.10.03.462938v1?rss=1 Chuai, M. Serrano-Najere, G. Serra, M. Mahadavan, L. Weijer, C. J. 2021-10-03 doi:10.1101/2021.10.03.462938 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Novelty detection in early olfactory processing of the honey bee, Apis mellifera ]]> https://biorxiv.org/content/10.1101/2021.10.06.463371v1?rss=1 Lei, H. Haney, S. Jernigan, C. M. Cook, C. Guo, X. Smith, B. Bazhenov, M. 2021-10-08 doi:10.1101/2021.10.06.463371 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ The long-term effects of repeated heroin vapor inhalation during adolescence on measures of nociception and anxiety-like behavior in adult Wistar rats ]]> https://biorxiv.org/content/10.1101/2021.10.06.463404v1?rss=1 Gutierrez, A. Harvey, E. L. Creehan, K. M. Taffe, M. A. 2021-10-08 doi:10.1101/2021.10.06.463404 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Cytoplasmic dynein-1 cargo diversity is mediated by the combinatorial assembly of FTS-Hook-FHIP complexes ]]> https://biorxiv.org/content/10.1101/2021.10.07.463551v1?rss=1 Christensen, J. R. Kendrick, A. A. Troung, J. B. Aguilar-Maldonado, A. Adani, V. Dzieciatkowska, M. Reck-Peterson, S. L. 2021-10-08 doi:10.1101/2021.10.07.463551 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Disrupted intrinsic connectivity links to language and social deficits in toddlers with autism ]]> https://biorxiv.org/content/10.1101/2021.10.08.463640v1?rss=1 Xiao, Y. Wen, T. H. Kupis, L. Eyler, L. T. Goel, D. Lombardo, M. V. Pierce, K. Courchesne, E. 2021-10-09 doi:10.1101/2021.10.08.463640 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ HORmon: automated annotation of human centromeres ]]> https://biorxiv.org/content/10.1101/2021.10.12.464028v1?rss=1 Kunyavskaya, O. Dvorkina, T. Bzikadze, A. V. Alexandrov, I. Pevzner, P. A. 2021-10-12 doi:10.1101/2021.10.12.464028 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Multimodal tubulin binding by the yeast kinesin-8, Kip3, underlies its motility and depolymerization ]]> https://biorxiv.org/content/10.1101/2021.10.12.464151v1?rss=1 Arellano-Santoyo, H. Hernandez-Lopez, R. A. Stokasimov, E. Wang, R. Y. Pellman, D. Leschziner, A. E. 2021-10-13 doi:10.1101/2021.10.12.464151 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition ]]> https://biorxiv.org/content/10.1101/2021.10.14.464447v1?rss=1 Lu, S. Hu, J. Arogundade, O. A. Goginashvili, A. Vazquez-Sanchez, S. Diedrich, J. K. Gu, J. Blum, J. Oung, S. Yu, H. Ravits, J. Liu, C. Yates, J. R. Cleveland, D. W. 2021-10-15 doi:10.1101/2021.10.14.464447 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity ]]> https://biorxiv.org/content/10.1101/2021.10.15.464608v1?rss=1 Liu, H. Ling, W. Hua, X. Moon, J.-Y. Williams-Nguyen, J. S. Zhan, X. Plantinga, A. M. Zhao, N. Zhang, A. Knight, R. Qi, Q. Burk, R. D. Kaplan, R. C. Wu, M. C. 2021-10-16 doi:10.1101/2021.10.15.464608 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Diverse chemical functionalization of nucleobases within long RNAs using sulfinate salts ]]> https://biorxiv.org/content/10.1101/2021.10.19.465008v1?rss=1 Hirlinger, A. Bassi, T. G. Grayson, L. Vantourout, J. C. Toor, N. 2021-10-19 doi:10.1101/2021.10.19.465008 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound ]]> https://biorxiv.org/content/10.1101/2021.10.19.465031v1?rss=1 Kunselman, E. Minich, J. J. Horwith, M. Gilbert, J. Allen, E. 2021-10-19 doi:10.1101/2021.10.19.465031 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults ]]> https://biorxiv.org/content/10.1101/2021.10.20.465206v1?rss=1 Nguyen, J. P. iPSCORE Consortium, D'Antonio-Chronowska, A. Fujita, K. Salgado, B. M. Matsui, H. Arthur, T. D. Donovan, M. K. D'Antonio, M. Frazer, K. A. 2021-10-21 doi:10.1101/2021.10.20.465206 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ A focal adhesion kinase-YAP signaling axis drives drug tolerant persister cells and residual disease in lung cancer ]]> https://biorxiv.org/content/10.1101/2021.10.23.465573v1?rss=1 Haderk, F. Fernandez-Mendez, C. Cech, L. Yu, J. Meraz, I. M. Olivas, V. Barbosa Rabago, D. Kerr, D. L. Gomez, C. Allegakoen, D. V. Guan, J. Shah, K. N. Herrington, K. A. Gbenedio, O. M. Nanjo, S. Majidi, M. Tamaki, W. Rotow, J. K. McCoach, C. E. Riess, J. W. Gutkind, J. S. Tang, T. T. Post, L. Huang, B. Santisteban, P. Goodarzi, H. Bandyopadhyay, S. Kuo, C. J. Roose, J. P. Wu, W. Blakely, C. M. Roth, J. A. Bivona, T. G. 2021-10-24 doi:10.1101/2021.10.23.465573 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ A Cytoskeletal Vortex Drives Phage Nucleus Rotation During Jumbo Phage Replication inE. coli ]]> https://biorxiv.org/content/10.1101/2021.10.25.465362v1?rss=1 Birkholz, E. A. Laughlin, T. G. Suslov, S. Armbruster, E. Lee, J. Wittmann, J. Corbett, K. D. Villa, E. Pogliano, J. 2021-10-26 doi:10.1101/2021.10.25.465362 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies ]]> https://biorxiv.org/content/10.1101/2021.10.25.465810v1?rss=1 Vezina, B. Judd, L. M. McDougall, F. K. Boardman, W. S. Power, M. L. Hawkey, J. Brisse, S. Monk, J. M. Holt, K. E. Wyres, K. L. 2021-10-26 doi:10.1101/2021.10.25.465810 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Conditional depletion reveals temporal requirements for the oscillating transcription factor NHR-23/NR1F1 in C. elegans larval progression ]]> https://biorxiv.org/content/10.1101/2021.10.27.465992v1?rss=1 Johnson, L. C. Aguilera, J. D. Levenson, M. T. Rechtsteiner, A. D. Vo, A. A. Ragle, J. M. Ward, J. D. 2021-10-27 doi:10.1101/2021.10.27.465992 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Sex differences in migraine: A twin study ]]> https://biorxiv.org/content/10.1101/2021.10.27.466155v1?rss=1 Fitzgerald, M. C. Saelzler, U. G. Panizzon, M. S. 2021-10-28 doi:10.1101/2021.10.27.466155 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ FEMA: Fast and efficient mixed-effects algorithm for population-scale whole brain imaging data ]]> https://biorxiv.org/content/10.1101/2021.10.27.466202v1?rss=1 Fan, C. C. Palmer, C. E. Iverson, J. Pecheva, D. Thompson, W. K. Hagler, D. Jernigan, T. L. Dale, A. M. 2021-10-28 doi:10.1101/2021.10.27.466202 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Two parallel pathways are required for ultrasound-evoked behavioral changes in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.10.29.466533v1?rss=1 Magaram, U. Weiss, C. Vasan, A. Reddy, K. C. Friend, J. Chalasani, S. H. 2021-11-02 doi:10.1101/2021.10.29.466533 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Mem3DG: Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry ]]> https://biorxiv.org/content/10.1101/2021.10.30.466618v1?rss=1 Zhu, C. Lee, C. T. Rangamani, P. 2021-10-31 doi:10.1101/2021.10.30.466618 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Behavioral context affects social signal representations within single primate prefrontal cortex neurons ]]> https://biorxiv.org/content/10.1101/2021.11.01.466818v1?rss=1 Jovanovic, V. Fishbein, A. R. de la Mothe, L. Lee, K.-F. Miller, C. T. 2021-11-03 doi:10.1101/2021.11.01.466818 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Discovery of a carbonic anhydrase-Rubisco supercomplex within the alpha-carboxysome ]]> https://biorxiv.org/content/10.1101/2021.11.05.467472v1?rss=1 Blikstad, C. Dugan, E. J. Laughlin, T. G. Liu, M. D. Shoemaker, S. R. Remis, J. P. Savage, D. F. 2021-11-05 doi:10.1101/2021.11.05.467472 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations ]]> https://biorxiv.org/content/10.1101/2021.11.10.468164v1?rss=1 Hattori, R. Komiyama, T. 2021-11-13 doi:10.1101/2021.11.10.468164 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes ]]> https://biorxiv.org/content/10.1101/2021.11.11.468006v1?rss=1 Russell, B. J. Brown, S. D. Saran, A. R. Mai, I. Lingaraju, A. Siguenza, N. Maissy, E. Dantas Machado, A. C. Pinto, A. F. M. Miyamoto, Y. Richter, R. A. Ho, S. B. Eckmann, L. Hasty, J. Saghatelian, A. Knight, R. Zarrinpar, A. 2021-11-12 doi:10.1101/2021.11.11.468006 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Synchrony and idiosyncrasy in the gut microbiome of wild primates ]]> https://biorxiv.org/content/10.1101/2021.11.24.469913v1?rss=1 Bjork, J. R. Dasari, M. R. Roche, K. Grieneisen, L. Gould, T. J. Grenier, J.-C. Yotova, V. Gottel, N. Jansen, D. Gesquiere, L. R. Gordon, J. B. Learn, N. H. Wango, T. L. Mututua, R. S. Warutere, J. K. Siodi, L. i. Mukherjee, S. Barreiro, L. B. Alberts, S. C. Gilbert, J. A. Tung, J. Blekhman, R. Archie, E. 2021-11-24 doi:10.1101/2021.11.24.469913 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Evolution of Human-specific Alleles Protecting Cognitive Function of Grandmothers ]]> https://biorxiv.org/content/10.1101/2021.11.26.470088v1?rss=1 Saha, S. Khan, N. Comi, T. Verhagen, A. Sasmal, A. Diaz, S. Yu, H. Chen, X. Akey, J. M. Frank, M. Gagneux, P. Varki, A. 2021-11-26 doi:10.1101/2021.11.26.470088 Cold Spring Harbor Laboratory Press 2021-11-26 <![CDATA[ Functionalizing lipid sponge droplets with DNA ]]> https://biorxiv.org/content/10.1101/2021.11.28.470255v1?rss=1 Cho, C. Niederholtmeyer, H. Seo, H. Bhattacharya, A. Devaraj, N. K. 2021-11-28 doi:10.1101/2021.11.28.470255 Cold Spring Harbor Laboratory Press 2021-11-28 <![CDATA[ COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2021.11.28.470269v1?rss=1 1000 human lung transcriptomic datasets associated with various lung conditions using two viral pandemic signatures (ViP and sViP) and one covid lung-derived signature. Upon identifying similarities between COVID-19 and idiopathic pulmonary fibrosis (IPF), we subsequently dissected the basis for such similarity from molecular, cytopathic, and immunologic perspectives using a panel of IPF-specific gene signatures, alongside signatures of alveolar type II (AT2) cytopathies and of prognostic monocyte-driven processes that are known drivers of IPF. Transcriptome-derived findings were used to construct protein-protein interaction (PPI) network to identify the major triggers of AT2 dysfunction. Key findings were validated in hamster and human adult lung organoid (ALO) pre-clinical models of COVID-19 using immunohistochemistry and qPCR. FindingsCOVID-19 resembles IPF at a fundamental level; it recapitulates the gene expression patterns (ViP and IPF signatures), cytokine storm (IL15-centric), and the AT2 cytopathic changes, e.g., injury, DNA damage, arrest in a transient, damage-induced progenitor state, and senescence-associated secretory phenotype (SASP). These immunocytopathic features were induced in pre-clinical COVID models (ALO and hamster) and reversed with effective anti-CoV-2 therapeutics in hamsters. PPI-network analyses pinpointed ER stress as one of the shared early triggers of both diseases, and IHC studies validated the same in the lungs of deceased subjects with COVID-19 and SARS-CoV-2-challenged hamster lungs. Lungs from tg-mice, in which ER stress is induced specifically in the AT2 cells, faithfully recapitulate the host immune response and alveolar cytopathic changes that are induced by SARS-CoV-2. InterpretationLike IPF, COVID-19 may be driven by injury-induced ER stress that culminates into progenitor state arrest and SASP in AT2 cells. The ViP signatures in monocytes may be key determinants of prognosis. The insights, signatures, disease models identified here are likely to spur the development of therapies for patients with IPF and other fibrotic interstitial lung diseases. FundingThis work was supported by the National Institutes for Health grants R01-GM138385 and AI155696 and funding from the Tobacco-Related disease Research Program (R01RG3780). One Sentence SummarySevere COVID-19 triggers cellular processes seen in fibrosing Interstitial Lung Disease RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSIn its aftermath, the COVID-19 pandemic has left many survivors, almost a third of those who recovered, with a mysterious long-haul form of the disease which culminates in a fibrotic form of interstitial lung disease (post-COVID-19 ILD). Post-COVID-19 ILD remains a largely unknown entity. Currently, we lack insights into the core cytopathic features that drive this condition. Added value of this studyUsing an AI-guided approach, which involves the use of sets of gene signatures, protein-protein network analysis, and a hamster model of COVID-19, we have revealed here that COVID-19 -lung fibrosis resembles IPF, the most common form of ILD, at a fundamental level--showing similar gene expression patterns in the lungs and blood, and dysfunctional AT2 processes (ER stress, telomere instability, progenitor cell arrest, and senescence). These findings are insightful because AT2 cells are known to contain an elegant quality control network to respond to intrinsic or extrinsic stress; a failure of such quality control results in diverse cellular phenotypes, of which ER stress appears to be a point of convergence, which appears to be sufficient to drive downstream fibrotic remodeling in the lung. Implications of all the available evidenceBecause unbiased computational methods identified the shared fundamental aspects of gene expression and cellular processes between COVID-19 and IPF, the impact of our findings is likely to go beyond COVID-19 or any viral pandemic. The insights, tools (disease models, gene signatures, and biomarkers), and mechanisms identified here are likely to spur the development of therapies for patients with IPF and, other fibrotic interstitial lung diseases, all of whom have limited or no treatment options. To dissect the validated prognostic biomarkers to assess and track the risk of pulmonary fibrosis and develop therapeutics to halt fibrogenic progression. ]]> Sinha, S. Castillo, V. Espinoza, C. R. Tindle, C. Fonseca, A. G. Dan, J. M. Katkar, G. D. Das, S. Sahoo, D. Ghosh, P. 2021-11-30 doi:10.1101/2021.11.28.470269 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ MuDCoD: Multi-Subject Community Detection in Personalized Dynamic Gene Networks from Single Cell RNA Sequencing ]]> https://biorxiv.org/content/10.1101/2021.11.30.470619v1?rss=1 Sapci, A. O. B. Lu, S. Tastan, O. Keles, S. 2021-12-01 doi:10.1101/2021.11.30.470619 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches ]]> https://biorxiv.org/content/10.1101/2021.12.02.471004v1?rss=1 Thornlow, B. Ye, C. De Maio, N. McBroome, J. Hinrichs, A. S. Lanfear, R. Turakhia, Y. Corbett-Detig, R. 2021-12-03 doi:10.1101/2021.12.02.471004 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Pandemic-scale phylogenetics ]]> https://biorxiv.org/content/10.1101/2021.12.03.470766v1?rss=1 Ye, C. Thornlow, B. Kramer, A. M. McBroome, J. Hinrichs, A. S. Corbett-Detig, R. Turakhia, Y. 2021-12-06 doi:10.1101/2021.12.03.470766 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ A remote lecture series roadmap to equity, diversity, and inclusion in STEM ]]> https://biorxiv.org/content/10.1101/2021.12.05.471284v1?rss=1 Boyle, E. A. Goldberg, G. Schmok, J. C. Burgado, J. Izidro Layng, F. Grunwald, H. A. Balotin, K. M. Cuoco, M. S. Chang, K.-C. Ecklu-Mensah, G. Arakaki, A. K. S. Ahmed, N. Garcia Arceo, X. Jagannatha, P. Pekar, J. Iyer, M. DASL Alliance, Yeo, G. W. 2021-12-07 doi:10.1101/2021.12.05.471284 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung ]]> https://biorxiv.org/content/10.1101/2021.12.05.471312v1?rss=1 Gaddis, N. Fortriede, J. Guo, M. Bardes, E. E. Kouril, M. Tabar, S. Burns, K. Ardini-Poleske, M. E. Loos, S. Schnell, D. Jin, K. Iyer, B. Du, Y. Korte, J. Munshi, R. Smith, V. Herbst, A. Kitzmiller, J. A. Clair, G. C. Carson, J. Adkins, J. Morrisey, E. E. Pryhuber, G. S. Misra, R. Whitsett, J. A. Sun, X. Heathorn, T. Paten, B. Prasath, V. B. S. Xu, Y. Tickle, T. Aronow, B. J. Salomonis, N. 2021-12-06 doi:10.1101/2021.12.05.471312 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Design of M protein immunogens to elicit broadly reactive antibodies against Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2021.12.07.471543v1?rss=1 220 M types, as defined by the M protein hypervariable region (HVR), has been considered to limit its utility as a vaccine immunogen due to type-specificity in the antibody response. Surprisingly, a multi-HVR immunogen in clinical vaccine trials elicited M type cross-reactivity. The basis for this cross-reactivity is unknown but may be due in part to antibody recognition of a three-dimensional (3D) pattern conserved in many M protein HVRs that confers binding to human C4b-binding protein (C4BP). To test this hypothesis, we asked whether a single M protein immunogen carrying the 3D pattern would elicit cross-reactivity against other M types carrying the 3D pattern. We found that a 34-amino acid sequence of M2 protein bearing the 3D pattern retained full C4BP-binding capacity when fused to a coiled coil-stabilizing sequence from GCN4. This immunogen, called M2G, elicited cross-reactive antibodies against a number of M types that carry the 3D pattern but not against those that lack the 3D pattern. The M2G antiserum recognized M proteins as displayed natively on the Strep A surface, and promoted the opsonophagocytic killing of Strep A strains expressing these M proteins. As C4BP-binding is a conserved virulence trait of Strep A, targeting the 3D pattern may prove advantageous in vaccine design. ]]> Wang, K.-C. Nizet, V. Ghosh, P. 2021-12-07 doi:10.1101/2021.12.07.471543 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Vascular proteome responses precede organ dysfunction in sepsis ]]> https://biorxiv.org/content/10.1101/2021.12.07.471579v1?rss=1 Sorrentino, J. T. Golden, G. J. Morris, C. Painter, C. Nizet, V. Campos, A. R. Smith, J. W. Karlsson, C. A. Q. Malmström, J. Lewis, N. E. Esko, J. D. Gomez Toledo, A. 2021-12-09 doi:10.1101/2021.12.07.471579 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Dopamine D2Rs Coordinate Cue-Evoked Changes in Striatal Acetylcholine Levels ]]> https://biorxiv.org/content/10.1101/2021.12.08.471871v1?rss=1 Kellendonk, C. Martyniuk, K. M. Torres-Herraez, A. Rubinstein, M. Labouesse, M. A. 2021-12-11 doi:10.1101/2021.12.08.471871 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling ]]> https://biorxiv.org/content/10.1101/2021.12.10.472112v1?rss=1 Biering, S. B. Tramontini Gomes de Sousa, F. Tjang, L. V. Pahmeier, F. Ruan, R. Blanc, S. F. Patel, T. S. Worthington, C. M. Glasner, D. R. Castillo-Rojas, B. Servellita, V. Lo, N. T. Wong, M. P. Warnes, C. M. Sandoval, D. R. Clausen, T. M. Santos, Y. A. Ortega, V. Aguilar-Carreno, H. Esko, J. D. Chiu, C. Y. Pak, J. E. Beatty, P. R. Harris, E. 2021-12-13 doi:10.1101/2021.12.10.472112 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy ]]> https://biorxiv.org/content/10.1101/2021.12.14.472731v1?rss=1 Liu, M. Hernandez-Morales, A. C. Clark, J. Le, T. T. Biswas, B. Bishop-Lilly, K. A. Henry, M. S. Quinones, J. Hamilton, T. Schooley, R. Salka, S. Young, R. F. Gill, J. J. 2021-12-16 doi:10.1101/2021.12.14.472731 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Distinguishing COVID-19 infection and vaccination history by T cell reactivity ]]> https://biorxiv.org/content/10.1101/2021.12.15.472874v1?rss=1 Yu, E. D. Wang, E. Garrigan, E. Goodwin, B. Sutherland, A. Chang, J. Galvez, R. I. Mateus, J. Rawlings, S. A. Smith, D. M. Frazier, A. Weiskopf, D. Dan, J. M. Crotty, S. Grifoni, A. Sette, A. da Silva Antunes, R. 2021-12-17 doi:10.1101/2021.12.15.472874 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Neural signature of everyday function in older adults at-risk of cognitive impairment ]]> https://biorxiv.org/content/10.1101/2021.12.16.472826v1?rss=1 De Sanctis, P. Wagner, J. Molholm, S. Foxe, J. J. Blumen, H. Horsthuis, D. 2021-12-17 doi:10.1101/2021.12.16.472826 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Transcriptomes and metabolism define mouse and human MAIT cell heterogeneity ]]> https://biorxiv.org/content/10.1101/2021.12.20.473182v1?rss=1 Chandra, S. Ascui, G. Riffelmacher, T. Chawla, A. Ramirez-Suastegui, C. Castelan, V. C. Seumois, G. Simon, H. Murray, M. P. Seo, G.-Y. Premlal, A. L. R. Verstichel, G. Li, Y. Lin, C.-H. Greenbaum, J. Lamberti, J. Murthy, R. Nigro, J. Cheroutre, H. Ottensmeier, C. H. Hedrick, S. M. Lu, L.-F. Vijayanand, P. Kronenberg, M. 2021-12-21 doi:10.1101/2021.12.20.473182 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark ]]> https://biorxiv.org/content/10.1101/2021.12.20.473592v1?rss=1 Fang, X. Westh, H. Kemp, M. Ellermann-Eriksen, S. Palsson, B. O. Johansen, H. K. Monk, J. M. 2021-12-23 doi:10.1101/2021.12.20.473592 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A vascularized 3D model of the human pancreatic islet for ex vivo study of immune cell-islet interaction ]]> https://biorxiv.org/content/10.1101/2021.12.21.473744v1?rss=1 Bender, R. H. F. O'Donnell, B. T. Shergill, B. Pham, B. Q. Juat, D. J. Hatch, M. S. Shirure, V. S. Wortham, M. Nguyen-Ngoc, K.-V. Jun, Y. Gaetani, R. Christman, K. L. Teyton, L. George, S. C. Sander, M. Hughes, C. C. 2021-12-23 doi:10.1101/2021.12.21.473744 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Theta oscillations in the prefrontal-hippocampal circuit do not couple to respiration-related oscillations ]]> https://biorxiv.org/content/10.1101/2021.12.22.473834v1?rss=1 Srikanth, S. Le, D. Hu, Y. Leutgeb, J. K. Leutgeb, S. 2021-12-23 doi:10.1101/2021.12.22.473834 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.12.22.473864v1?rss=1 Rodionova, I. A. Gao, Y. Lim, H. G. Saier, M. H. Palsson, B. Monk, J. Rodionov, D. A. Szubin, R. 2021-12-23 doi:10.1101/2021.12.22.473864 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Mistimed feeding disrupts circadian rhythms of male mating behavior and female preovulatory LH surges in mice ]]> https://biorxiv.org/content/10.1101/2021.12.27.474267v1?rss=1 Kukino, A. Walbeek, T. J. Sun, L. J. Watt, A. T. Park, J. H. Kauffman, A. S. Butler, M. P. 2021-12-28 doi:10.1101/2021.12.27.474267 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Control of bacterial anti-phage signaling by a WYL domain transcription factor ]]> https://biorxiv.org/content/10.1101/2022.01.04.474952v1?rss=1 Blankenchip, C. L. Nguyen, J. V. Lau, R. K. Ye, Q. Gu, Y. Corbett, K. D. 2022-01-04 doi:10.1101/2022.01.04.474952 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.01.05.475095v1?rss=1 Santos, L. H. Kronenberger, T. Almeida, R. G. Barbosa da Silva, E. Rocha, R. E. O. Oliveira, J. C. Barreto, L. V. Skinner, D. Fajtova, P. Giardini, M. A. Woodworth, B. Bardine, C. Lourenco, A. L. Craik, C. S. Poso, A. Podust, L. M. McKerrow, J. H. Siqueira-Neto, J. L. O'Donoghue, A. J. da Silva Junior, E. N. Ferreira, R. 2022-01-05 doi:10.1101/2022.01.05.475095 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Quantifying biological carbon pump pathways with a data-constrained mechanistic model ensemble approach ]]> https://biorxiv.org/content/10.1101/2022.01.07.475464v1?rss=1 Stukel, M. R. Decima, M. Landry, M. R. 2022-01-10 doi:10.1101/2022.01.07.475464 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37 ]]> https://biorxiv.org/content/10.1101/2022.01.11.475926v1?rss=1 Kolesinski, P. Wang, K.-C. Hirose, Y. Nizet, V. Ghosh, P. 2022-01-11 doi:10.1101/2022.01.11.475926 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains ]]> https://biorxiv.org/content/10.1101/2022.01.11.475931v1?rss=1 Yuan, Y. Seif, Y. Rychel, K. Yoo, R. Chauhan, S. M. Poudel, S. Al-bulushi, T. Palsson, B. Sastry, A. V. 2022-01-11 doi:10.1101/2022.01.11.475931 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ GR-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction ]]> https://biorxiv.org/content/10.1101/2022.01.12.475507v1?rss=1 Duttke, S. Montilla-Perez, P. Chang, M. W. Li, H. Chen, H. Carrette, L. L. G. de Guglielmo, G. George, O. Palmer, A. A. Benner, C. Telese, F. 2022-01-12 doi:10.1101/2022.01.12.475507 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.01.12.475688v1?rss=1 Ye, C. Thornlow, B. Hinrichs, A. S. Torvi, D. Lanfear, R. Corbett-Detig, R. Turakhia, Y. 2022-01-13 doi:10.1101/2022.01.12.475688 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Endogenous 1-deoxysphingolipid synthesis compromises anchorage-independent growth and plasma membrane endocytosis in cancer cells ]]> https://biorxiv.org/content/10.1101/2022.01.19.476986v1?rss=1 Cordes, T. Kuna, R. S. McGregor, G. H. Khare, S. V. Gengatharan, J. Muthusamy, T. Metallo, C. M. 2022-01-22 doi:10.1101/2022.01.19.476986 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Wildlife and Marine Mammal Spatial Observatory: Observation and automated detection of Southern Right Whales in multispectral satellite imagery ]]> https://biorxiv.org/content/10.1101/2022.01.20.477141v1?rss=1 Houegnigan, L. Romero Merino, E. Vermeulen, E. Block, J. Safari, P. Moreno-Noguer, F. Nadeu, C. 2022-01-22 doi:10.1101/2022.01.20.477141 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Post-embryonic maturation of the C. elegans motor circuit ]]> https://biorxiv.org/content/10.1101/2022.01.24.477421v1?rss=1 Mulcahy, B. Witvliet, D. Mitchell, J. K. Schalek, R. Berger, D. Wu, Y. Holmyard, D. Lu, Y. Ahamed, T. Samuel, A. D. Chisholm, A. D. Lichtman, J. W. Zhen, M. 2022-01-25 doi:10.1101/2022.01.24.477421 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Mindin is essential for cutaneous fibrogenesis in a new mouse model of systemic sclerosis ]]> https://biorxiv.org/content/10.1101/2022.01.26.477822v1?rss=1 Rana, I. Kataria, S. Tan, T.-L. Hajam, E. Y. Kashyap, D. K. Saha, D. Ajnabi, J. Paul, S. Jayappa, S. Ananthan, A. S. Kumar, P. Zaarour, R. F. J, H. Samuel, R. George, R. Danda, D. Jacob, P. M. Dey, R. Perundurai, D. He, Y.-W. Varga, J. Varghese, S. Jamora, C. 2022-01-28 doi:10.1101/2022.01.26.477822 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 ]]> https://biorxiv.org/content/10.1101/2022.01.27.477154v1?rss=1 Simkovsky, R. Parnasa, R. Wang, J. Nagar, E. Zecharia, E. Suban, S. Yegorov, Y. Veltman, B. Sendersky, E. Schwarz, R. Golden, S. S. 2022-01-28 doi:10.1101/2022.01.27.477154 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Gnas ablation in CD11c+ cells prevents high-fat diet-induced obesity by elevating adipose tissue catecholamine levels and thermogenesis ]]> https://biorxiv.org/content/10.1101/2022.01.27.478070v1?rss=1 Zeng, L. Herdman, D. S. Lee, J. Tao, A. Das, M. Bertin, S. Eckmann, L. Mahata, S. K. Devulapalli, S. Patel, H. Molina, A. J. A. Osborn, O. Corr, M. Raz, E. Webster, N. J. G. 2022-01-28 doi:10.1101/2022.01.27.478070 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Interplay between rule learning and rule switching in a perceptual categorization task ]]> https://biorxiv.org/content/10.1101/2022.01.29.478330v1?rss=1 Bouchacourt, F. Tafazoli, S. Mattar, M. G. Buschman, T. J. Daw, N. D. 2022-01-30 doi:10.1101/2022.01.29.478330 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ AI-assisted Discovery of an Ethnicity-influenced Driver of Cell Transformation in Esophageal and Gastroesophageal Junction Adenocarcinomas ]]> https://biorxiv.org/content/10.1101/2022.01.30.478408v1?rss=1 Ghosh, P. Campos, V. J. Vo, D. T. Guccione, C. Goheen-Holland, V. Tindle, C. Mazzini, G. S. He, Y. Alexandrov, L. Lippman, S. M. Gurski, R. Das, S. Curtius, K. Yadlapati, R. Sahoo, D. 2022-02-01 doi:10.1101/2022.01.30.478408 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings ]]> https://biorxiv.org/content/10.1101/2022.02.01.478759v1?rss=1 Cantu, V. J. Sanders, K. Belda-Ferre, P. Salido, R. A. Tsai, R. Austin, B. Jordan, W. Asudani, M. Walster, A. Magallanes, C. G. Valentine, H. D. Majnoonian, A. Wijaya, C. Omaleki, V. Aigner, S. Baer, N. A. Betty, M. Castro-Martinez, A. Cheung, W. De Hoff, P. Eisner, E. Hakim, A. Lastrella, A. L. Lawrence, E. S. Ngo, T. T. Ostrander, R. T. Plascencia, A. Sathe, S. Smoot, E. W. Carlin, A. F. Yeo, G. W. Laurent, L. C. Manlutac, A. L. Fielding-Miller, R. Knight, R. 2022-02-03 doi:10.1101/2022.02.01.478759 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Epigenetic cell memory: The gene's inner chromatin modification circuit ]]> https://biorxiv.org/content/10.1101/2022.02.02.476953v1?rss=1 Bruno, S. Williams, R. J. Del Vecchio, D. 2022-02-03 doi:10.1101/2022.02.02.476953 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Nutrient gradients mediate creation of highly resistant layers in structured microbial populations during antibiotic exposures ]]> https://biorxiv.org/content/10.1101/2022.02.02.478895v1?rss=1 Stevanovic, M. Boukéké-Lesplulier, T. Hupe, L. Hasty, J. Bittihn, P. Schultz, D. 2022-02-03 doi:10.1101/2022.02.02.478895 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Exploring the frame effect ]]> https://biorxiv.org/content/10.1101/2022.02.10.479960v1?rss=1 Cavanagh, P. Anstis, S. Lisi, M. Wexler, M. Maechler, M. 't Hart, B. M. Shams-Ahmar, M. Saleki, S. 2022-02-10 doi:10.1101/2022.02.10.479960 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Examining clustered somatic mutations with SigProfilerClusters ]]> https://biorxiv.org/content/10.1101/2022.02.11.480117v1?rss=1 Bergstrom, E. N. Kundu, M. Tbeileh, N. Alexandrov, L. B. 2022-02-14 doi:10.1101/2022.02.11.480117 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission ]]> https://biorxiv.org/content/10.1101/2022.02.13.480251v1?rss=1 Aggarwal, A. Liu, R. Chen, Y. Ralowicz, A. J. Bergerson, S. J. Tomaska, F. Hanson, T. L. Hasseman, J. P. Reep, D. Tsegaye, G. Yao, P. Ji, X. Kloos, M. Walpita, D. Patel, R. Tilberg, P. W. Mohar, B. The GENIE Project Team, Looger, L. Marvin, J. Hoppa, M. Konnerth, A. Kleinfeld, D. Schreiter, E. R. Podgorski, K. 2022-02-15 doi:10.1101/2022.02.13.480251 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP ]]> https://biorxiv.org/content/10.1101/2022.02.13.480296v1?rss=1 Manakov, S. A. Shishkin, A. A. Yee, B. A. Shen, K. A. Cox, D. C. Park, S. S. Foster, H. M. Chapman, K. B. Yeo, G. W. Van Nostrand, E. L. 2022-02-14 doi:10.1101/2022.02.13.480296 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Nuclear Receptor 5A2 Regulation of Agrp underlies Olanzapine-induced Hyperphagia ]]> https://biorxiv.org/content/10.1101/2022.02.15.480590v1?rss=1 Zapata, R. C. Zhang, D. Libster, A. Porcu, A. Montilla-Perez, P. Zhang, Z. Correa, S. M. Telese, F. Osborn, O. 2022-02-18 doi:10.1101/2022.02.15.480590 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Substrate topology and cognate immunity modulate antibacterial toxicity of Tae cell wall hydrolases ]]> https://biorxiv.org/content/10.1101/2022.02.15.480620v1?rss=1 Radkov, A. Sapiro, A. Flores, S. Henderson, C. Saunders, H. Kim, R. Massa, S. Thompson, S. Mateusiak, C. Biboy, J. Zhao, Z. Starita, L. M. Hatleberg, W. Vollmer, W. Russell, A. B. Simorre, J.-P. Anthony-Cahill, S. Brzovic, P. Hayes, B. Chou, S. 2022-02-16 doi:10.1101/2022.02.15.480620 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ The Conserved CNOT1 Interaction Motif of Tristetraprolin Regulates ARE-mRNA Decay Independently of the p38 MAPK-MK2 Kinase Pathway ]]> https://biorxiv.org/content/10.1101/2022.02.15.480631v1?rss=1 Carreno, A. Lykke-Andersen, J. 2022-02-16 doi:10.1101/2022.02.15.480631 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Mitochondrial mRNA localization is governed by translation kinetics and spatial transport ]]> https://biorxiv.org/content/10.1101/2022.02.16.480701v1?rss=1 Arceo, X. G. Koslover, E. F. Zid, B. M. Brown, A. I. 2022-02-17 doi:10.1101/2022.02.16.480701 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Assessing base-resolution DNA mechanics on the genome scale ]]> https://biorxiv.org/content/10.1101/2022.02.16.480786v1?rss=1 Jiang, W.-j. Hu, C. Yi, X. Xu, Q. Lou, T. Wang, H. Zhou, J. Zhu, H. Li, Y. Wen, Y. Fan, R. Shen, J. Wong, C. C. Zheng, X. Wu, H.-J. 2022-02-19 doi:10.1101/2022.02.16.480786 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ An NKX-COUP-TFII genomic code for mucosal vascular addressins and organ morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.02.17.480956v1?rss=1 Dinh, t. t. Xiang, M. Rajaraman, A. Wang, Y. Salazar, N. Roper, W. Rhee, S. Brulois, K. O'Hara, E. Keifel, H. Dinh, T. Gonzalez, D. Bao, E. Red-Horse, K. Balogh, P. Gabris, F. Gaszner, B. Berta, G. Pan, J. Butcher, E. 2022-02-19 doi:10.1101/2022.02.17.480956 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using Mycobacterium tuberculosis Isolates ]]> https://biorxiv.org/content/10.1101/2022.02.18.481113v1?rss=1 Elghraoui, A. Mirarab, S. Swenson, K. M. Valafar, F. 2022-02-19 doi:10.1101/2022.02.18.481113 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees ]]> https://biorxiv.org/content/10.1101/2022.02.19.481132v1?rss=1 Zhang, C. Mirarab, S. 2022-02-20 doi:10.1101/2022.02.19.481132 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Quantitative sequence basis for the E. coli transcriptional regulatory network ]]> https://biorxiv.org/content/10.1101/2022.02.20.481200v1?rss=1 = 0.8) for 84% (57/68) of valid E. coli regulons identified from top-down analysis of RNA-seq data. We found that: 1) While regulatory motif strength is the most important sequence feature for determining regulon membership, additional features such as DNA shape substantially influence membership; 2) complex regulons involving multiple interacting regulators could be unraveled by machine learning; 3) investigating regulons where initial ML models failed revealed new regulator-specific sequence features that improved model accuracy. Finally, while regulon structure can appear to be variable across estimation methods and strains, we found that strong regulatory sequence features underlie both the genes that appear most consistently in regulons across estimation methods as well as the core regulon genes in the Fur pan-regulon. This work develops a quantitative understanding of the sequence basis of the TRN and suggests a path towards computationally-guided control of transcriptional regulation for synthetic biology applications. ]]> Qiu, S. Lamoureux, C. Akbari, A. Palsson, B. O. Zielinski, D. C. 2022-02-20 doi:10.1101/2022.02.20.481200 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Long-term learning transforms prefrontal cortex selectivity during working memory ]]> https://biorxiv.org/content/10.1101/2022.02.22.481537v1?rss=1 Miller, J. Tambini, A. Kiyonaga, A. D'Esposito, M. 2022-02-23 doi:10.1101/2022.02.22.481537 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Novel and Reported Compensatory Mutations in rpoABC Associate Specifically with Predominant Mycobacterium tuberculosis Rifampicin Resistance Marker rpoB:S450L ]]> https://biorxiv.org/content/10.1101/2022.02.22.481565v1?rss=1 Conkle-Gutierrez, D. Ramirez-Busby, S. M. Gorman, B. M. Elghraoui, A. Hoffner, S. E. Elmaraachli, W. Valafar, F. 2022-02-24 doi:10.1101/2022.02.22.481565 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation ]]> https://biorxiv.org/content/10.1101/2022.02.24.481768v1?rss=1 Oliver, A. Cavalheri, H. B. Lima, T. G. Jones, N. T. Podell, S. Zarate, D. Allen, E. Burton, R. S. Shurin, J. B. 2022-02-24 doi:10.1101/2022.02.24.481768 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2022.02.25.481990v1?rss=1 314,000 single-cell RA synovial cell atlas with 77 cell states from T, B/plasma, natural killer, myeloid, stromal, and endothelial cells. We stratified tissue samples into six distinct cell type abundance phenotypes (CTAPs) individually enriched for specific cell states. These CTAPs demonstrate the striking diversity of RA synovial inflammation, ranging from marked enrichment of T and B cells (CTAP-TB) to a congregation of specific myeloid, fibroblast, and endothelial cells largely lacking lymphocytes (CTAP-EFM). Disease-relevant cytokines, histology, and serology metrics are associated with certain CTAPs. This comprehensive RA synovial atlas and molecular, tissue-based CTAP stratification reveal new insights into RA pathology and heterogeneity, which could lead to novel targeted-treatment approaches in RA. ]]> Zhang, F. Jonsson, A. H. Nathan, A. Wei, K. Millard, N. Xiao, Q. Gutierrez-Arcelus, M. Apruzzese, W. Watts, G. F. M. Weisenfeld, D. Kang, J. B. Rumker, L. Mears, J. Slowikowski, K. Weinand, K. Orange, D. E. Rangel-Moreno, J. Geraldino-Pardilla, L. Deane, K. D. Tabechian, D. Ceponis, A. Firestein, G. S. Maybury, M. Sahbudin, I. Ben-Artzi, A. Mandelin, A. M. Nerviani, A. Rivellese, F. Pitzalis, C. Hughes, L. B. Horowitz, D. DiCarlo, E. Gravallese, E. M. Boyce, B. F. Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus 2022-02-28 doi:10.1101/2022.02.25.481990 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Multi-omic analysis along the gut-brain axis points to a functional architecture of autism ]]> https://biorxiv.org/content/10.1101/2022.02.25.482050v1?rss=1 Morton, J. T. Jin, D.-m. Mills, R. Shao, Y. Rahman, G. Harold-Berding, K. Needham, B. D. Zurita, M. F. David, M. Averina, O. Kovtun, A. Noto, A. Mussap, M. Wang, M. Frank, D. Li, E. Zhou, W. Fanos, V. Danilenko, V. Wall, D. P. Cardenas, P. A. Baldeon, M. xavier, r. j. Mazmanian, S. Knight, R. Gilbert, J. Donovan, S. Lawley, T. Carpenter, B. Bonneau, R. Taroncher-Oldenburg, G. 2022-02-26 doi:10.1101/2022.02.25.482050 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ RNA fluorescence in situ hybridization (FISH) to visualize microbial colonization and infection in the Caenorhabditis elegans intestines ]]> https://biorxiv.org/content/10.1101/2022.02.26.482129v1?rss=1 Rivera, D. Lazetic, V. Troemel, E. R. Luallen, R. J. 2022-02-28 doi:10.1101/2022.02.26.482129 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy and improves prediction ]]> https://biorxiv.org/content/10.1101/2022.02.28.481967v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@1641108org.highwire.dtl.DTLVardef@9a24eeorg.highwire.dtl.DTLVardef@1eeae99org.highwire.dtl.DTLVardef@108db7f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hindley, G. Shadrin, A. A. van der Meer, D. Parker, N. Cheng, W. O'Connell, K. S. Bahrami, S. Lin, A. Karadag, N. Holen, B. Bjella, T. Fan, C. C. Uelan, T. Djurovic, S. Smeland, O. B. Frei, O. Dale, A. Andreassen, O. 2022-03-02 doi:10.1101/2022.02.28.481967 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Temporal responses of bumblebee gustatory neurons encode sugar identity ]]> https://biorxiv.org/content/10.1101/2022.02.28.482341v1?rss=1 Parkinson, R. Kessler, S. Scott, J. Simpson, A. Bu, J. Pattrick, J. Mahdi, A. Miriyala, A. Wright, G. 2022-03-02 doi:10.1101/2022.02.28.482341 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Regulation associated modules reflect 3D genome modularity associated with chromatin activity ]]> https://biorxiv.org/content/10.1101/2022.03.02.482718v1?rss=1 Zheng, L. Wang, W. 2022-03-04 doi:10.1101/2022.03.02.482718 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease ]]> https://biorxiv.org/content/10.1101/2022.03.04.479488v1?rss=1 Zhou, P. Song, G. He, W.-t. Beutler, N. Tse, L. V. Martinez, D. R. Schafer, A. Anzanello, F. Yong, P. Peng, L. Dueker, K. Musharrafieh, R. Callaghan, S. Capozzola, T. Yuan, M. Liu, H. Limbo, O. Parren, M. Garcia, E. Rawlings, S. A. Smith, D. M. Nemazee, D. Jardine, J. G. Wilson, I. A. Safonova, Y. Rogers, T. Baric, R. S. Gralinski, L. E. Burton, D. R. Andrabi, R. 2022-03-07 doi:10.1101/2022.03.04.479488 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities ]]> https://biorxiv.org/content/10.1101/2022.03.07.483343v1?rss=1 Shaffer, J. P. Carpenter, C. S. Martino, C. P. Salido, R. A. Bryant, M. Sanders, K. Schwartz, T. Humphrey, G. Swafford, A. D. Knight, R. 2022-03-08 doi:10.1101/2022.03.07.483343 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Comparative transcriptomics of the Drosophila olfactory subsystems identifies a support cell-expressed Osiris protein required for pheromone sensing ]]> https://biorxiv.org/content/10.1101/2022.03.09.483212v1?rss=1 Scalzotto, M. Ng, R. Cruchet, S. Saina, M. Armida, J. Su, C.-Y. Benton, R. 2022-03-12 doi:10.1101/2022.03.09.483212 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair ]]> https://biorxiv.org/content/10.1101/2022.03.10.483754v1?rss=1 Barr, J. Gentile, M. E. Lee, S. Kotas, M. Fernanda de Mello Costa, M. Holcomb, N. P. Jaquish, A. Palashikar, G. Matsumoto, I. Margolskee, R. Cohen, N. A. Sun, X. Vaughan, A. E. 2022-03-11 doi:10.1101/2022.03.10.483754 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ The KASH5 protein involved in meiotic chromosomal movements is a novel dynein activating adaptor ]]> https://biorxiv.org/content/10.1101/2022.03.11.483947v1?rss=1 Agrawal, R. Gillies, J. P. Zang, J. L. Zhang, J. Garrott, S. R. Shibuya, H. Nandakumar, J. DeSantis, M. E. 2022-03-12 doi:10.1101/2022.03.11.483947 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Opiate responses are controlled by interactions of Oprm1 and Fgf12 loci in the murine BXD family: Correspondence to human GWAS finding ]]> https://biorxiv.org/content/10.1101/2022.03.11.483993v1?rss=1 Lemen, P. M. Hatoum, A. S. Dickson, P. E. Mittleman, G. Agrawal, A. Reiner, B. C. Berrettini, W. Ashbrook, D. G. Gunturkun, H. Mulligan, M. K. Williams, R. W. Chen, H. 2022-03-12 doi:10.1101/2022.03.11.483993 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Mesoaccumbal glutamate neurons drive reward via glutamate release, but aversion via dopamine co-release ]]> https://biorxiv.org/content/10.1101/2022.03.17.484767v1?rss=1 Warlow, S. M. Zell, V. Hunker, A. C. Zweifel, L. Hnasko, T. S. 2022-03-18 doi:10.1101/2022.03.17.484767 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Cloning of Nine Glucocorticoid Receptor Isoforms from the Slender African lungfish (Protopterus dolloi) ]]> https://biorxiv.org/content/10.1101/2022.03.19.484994v1?rss=1 Katsu, Y. Oana, S. Lin, X. Hyodo, S. Bianchetti, L. Baker, M. E. 2022-03-20 doi:10.1101/2022.03.19.484994 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential ]]> https://biorxiv.org/content/10.1101/2022.03.25.485695v1?rss=1 Carlessi, R. Denisenko, E. Boslem, E. Koehn-Gaone, J. Main, N. Bakar, N. D. B. A. Shirolkar, G. D. Jones, M. Poppe, D. Dwyer, B. J. Jackaman, C. Tjiam, M. C. Lister, R. Karin, M. Fallowfield, J. A. Kendall, T. J. Forbes, S. J. Olynyk, J. K. Yeoh, G. Forrest, A. R. R. Ramm, G. A. Febbraio, M. A. Tirnitz-Parker, J. E. E. 2022-03-27 doi:10.1101/2022.03.25.485695 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sudden unexpected death in epilepsy is prevented by blocking postictal hypoxia ]]> https://biorxiv.org/content/10.1101/2022.03.25.485818v1?rss=1 George, A. Farrell, J. S. Colangeli, R. Wall, A. K. Gom, R. C. Kesler, M. T. de la Hoz, C. L. Perera, T. Rho, J. M. Kurrasch, D. Teskey, G. C. 2022-03-28 doi:10.1101/2022.03.25.485818 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ A spatial genome aligner for multiplexed DNA-FISH ]]> https://biorxiv.org/content/10.1101/2022.03.25.485845v1?rss=1 Jia, B. B. Jussila, A. P. Kern, J. C. Zhu, Q. Ren, B. 2022-03-27 doi:10.1101/2022.03.25.485845 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sperm mosaicism predicts transmission of de novo mutations to human blastocysts ]]> https://biorxiv.org/content/10.1101/2022.03.28.486034v1?rss=1 Yang, X. Stanley, V. McEvoy-Venneri, J. Xu, X. Morales, A. J. Gleeson, J. G. Breuss, M. W. 2022-03-28 doi:10.1101/2022.03.28.486034 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Characterization of a miniaturized ultrasound transducer customized for oral health applications ]]> https://biorxiv.org/content/10.1101/2022.03.31.486598v1?rss=1 Qi, B. Hariri, A. Khazaeinezhad, R. Fu, L. Jokerst, J. V. 2022-04-01 doi:10.1101/2022.03.31.486598 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ An untargeted metabolomics analysis of exogenous chemicals in human milk and transfer to the infant ]]> https://biorxiv.org/content/10.1101/2022.03.31.486633v1?rss=1 Thomas, S. P. Gauglitz, J. M. Tripathi, A. Vargas, F. Bertrand, K. Chambers, C. D. Kim, J. H. Dorrestein, P. C. Tsunoda, S. M. 2022-04-01 doi:10.1101/2022.03.31.486633 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity ]]> https://biorxiv.org/content/10.1101/2022.04.04.487013v1?rss=1 Anand, A. Patel, A. Chen, K. Olson, C. A. Phaneuf, P. V. Lamoureux, C. Hefner, Y. Szubin, R. Feist, A. Palsson, B. 2022-04-05 doi:10.1101/2022.04.04.487013 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.04.04.487056v1?rss=1 Catoiu, E. A. Phaneuf, P. V. Monk, J. Palsson, B. 2022-04-06 doi:10.1101/2022.04.04.487056 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2022.04.04.487074v1?rss=1 Rajput, A. Tsunemoto, H. Sastry, A. V. Szubin, R. Rychel, K. Chauhan, S. M. Pogliano, J. Palsson, B. 2022-04-06 doi:10.1101/2022.04.04.487074 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.04.05.487060v1?rss=1 Oh, C.-k. Nakamura, T. Beutler, N. Zhang, X. Pina-Crespo, J. Talantova, M. Ghatak, S. Trudler, D. Carnevale, L. N. McKercher, S. R. Bakowski, M. A. Diedrich, J. K. Roberts, A. J. Woods, A. K. Chi, V. Gupta, A. K. Rosenfeld, M. A. Kearns, F. L. Casalino, L. Shaabani, N. Liu, H. Wilson, I. A. Amaro, R. E. Burton, D. R. Yates, J. R. Becker, C. Rogers, T. F. Chatterjee, A. K. Lipton, S. A. 2022-04-05 doi:10.1101/2022.04.05.487060 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Comprehensive multiomic profiling of somatic mutations in malformations of cortical development ]]> https://biorxiv.org/content/10.1101/2022.04.07.487401v1?rss=1 Chung, C. Yang, X. Bae, T. Vong, K. I. Mittal, S. Donkels, C. Phillips, W. Marsh, A. P. L. Breuss, M. W. Ball, L. L. Garcia, C. A. B. George, R. D. Gu, J. Xu, M. Barrows, C. James, K. N. Stanley, V. Nidhiry, A. Khoury, S. Howe, G. Xu, X. Copeland, B. Antaki, D. Wang, Y. Kim, S. H. Kang, H.-C. Schulze-Bonhage, A. Haas, C. A. Urbach, H. Prinz, M. Sattar, S. Nespeca, M. Gonda, D. D. Imai, K. Takahashi, Y. Chen, R. Tsai, J.-W. Conti, V. Guerrini, R. Devinsky, O. Silva, W. A. Machado, H. R. Mathern, G. W. Abyzov, A. Baldassari, S. Boulac, S. Focal Corti 2022-04-08 doi:10.1101/2022.04.07.487401 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Reelin deficiency exacerbates cocaine-induced hyperlocomotion by enhancing neuronal activity in the dorsomedial striatum. ]]> https://biorxiv.org/content/10.1101/2022.04.12.488105v1?rss=1 de Guglielmo, G. Iemolo, A. Nur, A. Turner, A. Montilla-Perez, P. Telese, F. 2022-04-13 doi:10.1101/2022.04.12.488105 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins to promote corticospinal axon repair after injury ]]> https://biorxiv.org/content/10.1101/2022.04.14.488293v1?rss=1 Romaus-Sanjurjo, D. Saikia, J. M. Kim, H. J. Tsai, K. M. Le, G. Q. Zheng, B. 2022-04-14 doi:10.1101/2022.04.14.488293 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Molecular diversity and phenotypic pleiotropy of genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their impacts on pathophysiology of Modern Humans. ]]> https://biorxiv.org/content/10.1101/2022.04.19.488808v1?rss=1 Glinsky, G. 2022-04-19 doi:10.1101/2022.04.19.488808 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues ]]> https://biorxiv.org/content/10.1101/2022.04.25.489471v1?rss=1 Yu, M. Zemke, N. R. Chen, Z. Juric, I. Hu, R. Raviram, R. Abnousi, A. Fang, R. Zhang, Y. Gorkin, D. U. Li, Y. Zhao, Y. Lee, H. R. Schmitt, A. D. Qiu, Y. Dickel, D. E. Visel, A. Pennacchio, L. Hu, M. Ren, B. 2022-04-26 doi:10.1101/2022.04.25.489471 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Coupling of NOD2 to GIV is Required for Bacterial Sensing ]]> https://biorxiv.org/content/10.1101/2022.04.26.489574v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@139a1feorg.highwire.dtl.DTLVardef@ba5354org.highwire.dtl.DTLVardef@b4d933org.highwire.dtl.DTLVardef@11fe12e_HPS_FORMAT_FIGEXP M_FIG GRAPHIC ABSTRACT C_FIG HIGHLIGHTSO_LIGIV is a functional and direct interactor of the terminal LRR repeat of NOD2 C_LIO_LIMice lacking M[FE] GIV develop dysbiosis, protracted ileocolitis and sepsis C_LIO_LIMDP/NOD2-dependent protective host responses require GIV C_LIO_LICD-risk NOD2 1007fs variant lacking the terminal LRR#10 cannot bind GIV C_LI ]]> Katkar, G. D. Anandachar, M. S. Sinha, S. Ibeawuchi, S.-R. Espinoza, C. R. Coates, J. Malhotra, Y. S. Mullick, M. Castillo, V. Vo, D. T. Sahoo, D. Ghosh, P. 2022-04-27 doi:10.1101/2022.04.26.489574 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage ]]> https://biorxiv.org/content/10.1101/2022.04.27.489752v1?rss=1 Lau, R. K. Enustun, E. Gu, Y. Nguyen, J. V. Corbett, K. D. 2022-04-27 doi:10.1101/2022.04.27.489752 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ An auto-inhibited state of protein kinase G and implications for selective activation ]]> https://biorxiv.org/content/10.1101/2022.04.28.489861v1?rss=1 Sharma, R. Kim, J. J. Qin, L. Henning, P. Akimoto, M. VanSchouwen, B. Kaur, G. Sankaran, B. MacKenzie, K. R. Melacini, G. Casteel, D. E. Herberg, F. W. Kim, C. W. 2022-04-28 doi:10.1101/2022.04.28.489861 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Accelerated aging induced by stress in experimental murine ocular hypertension. ]]> https://biorxiv.org/content/10.1101/2022.05.01.490248v1?rss=1 Xu, Q. Rydz, C. Nguyen Huu, V. A. Rocha, L. Palomino La Torre, C. Lee, I. Cho, W. Jabari, M. Donello, J. Weinreb, R. N. Lyon, D. C. Ju, W.-K. Foik, A. Skowronska-Krawczyk, D. 2022-05-02 doi:10.1101/2022.05.01.490248 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Repeated birth injuries lead to pelvic floor muscle dysfunction and impairment in regeneration ]]> https://biorxiv.org/content/10.1101/2022.05.02.490259v1?rss=1 Duran, P. Zelus, E. French, S. Burnett, L. Christman, K. Alperin, M. 2022-05-02 doi:10.1101/2022.05.02.490259 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Neuroinflammation plays a critical role in cerebral cavernous malformation disease ]]> https://biorxiv.org/content/10.1101/2022.05.09.491214v1?rss=1 Lopez-Ramirez, M. A. Lai, C. C. Nelsen, B. Frias-Anaya, E. Gallego-Gutierrez, H. Orecchioni, M. Sun, H. Mesarwi, O. A. Ley, K. Gongol, B. 2022-05-10 doi:10.1101/2022.05.09.491214 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Liquid-like assembly of VASP drives actin polymerization and bundling ]]> https://biorxiv.org/content/10.1101/2022.05.09.491236v1?rss=1 Graham, K. D. Chandrasekaran, A. Wang, L. Ladak, A. Lafer, E. M. Rangamani, P. Stachowiak, J. C. 2022-05-10 doi:10.1101/2022.05.09.491236 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Voluntary and forced exposure to ethanol vapor produces similar escalation of alcohol drinking but differential recruitment of brain regions related to stress, habit, and reward in male rats. ]]> https://biorxiv.org/content/10.1101/2022.05.11.491572v1?rss=1 de Guglielmo, G. Simpson, S. Kimbrough, A. Conlisk, D. Baker, R. Cantor, M. Kallupi, M. George, O. 2022-05-12 doi:10.1101/2022.05.11.491572 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ Genome-wide selection inference at short tandem repeats ]]> https://biorxiv.org/content/10.1101/2022.05.12.491726v1?rss=1 Huang, B. Durvasula, A. Mousavi, N. Ziaei-Jam, H. Maksimov, M. Lohmueller, K. E. Gymrek, M. 2022-05-13 doi:10.1101/2022.05.12.491726 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ CD133+ Intercellsome Mediates Direct Cell-Cell Communication to Offset Intracellular Signaling Deficit ]]> https://biorxiv.org/content/10.1101/2022.05.16.492226v1?rss=1 Kaneko, K. Liang, Y. Liu, Q. Chen, W. S. Feng, G.-S. 2022-05-17 doi:10.1101/2022.05.16.492226 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Guided construction of single cell reference for human and mouse lung ]]> https://biorxiv.org/content/10.1101/2022.05.18.491687v1?rss=1 Guo, M. Morley, M. P. Wu, Y. Du, Y. Zhao, S. Wagner, A. Kouril, M. Jin, K. Gaddis, N. Kitzmiller, J. A. Stewart, K. Basil, M. C. Lin, S. M. Ying, Y. Babu, A. Wikenheiser-Brokamp, K. A. Mun, K. S. Naren, A. P. Lin, S. Clair, G. Adkins, J. N. Pryhuber, G. S. Misra, R. S. Aronow, B. J. Tickle, T. L. Salomonis, N. Sun, X. Morrisey, E. E. Whitsett, J. A. Xu, Y. 2022-05-20 doi:10.1101/2022.05.18.491687 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ The regulatory landscapes of human ovarian ageing ]]> https://biorxiv.org/content/10.1101/2022.05.18.492547v1?rss=1 Suh, Y. Jin, C. Wang, X. Hudgins, A. Gamliel, A. Pei, M. Kim, S. Contreras, D. Hoeijmakers, J. Campisi, J. Lobo, R. Williams, Z. Rosenfeld, M. G. 2022-05-19 doi:10.1101/2022.05.18.492547 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons ]]> https://biorxiv.org/content/10.1101/2022.05.19.492359v1?rss=1 Mitchell, J. W. Midillioglu, I. Wang, B. Han, C. Wildonger, J. 2022-05-20 doi:10.1101/2022.05.19.492359 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Scalable power analysis and effect size exploration of microbiome community differences with Evident ]]> https://biorxiv.org/content/10.1101/2022.05.19.492684v1?rss=1 Rahman, G. McDonald, D. Gonzalez, A. Vazquez-Baeza, Y. Jiang, L. Casals-Pascual, C. Peddada, S. Hakim, D. Dilmore, A. H. Nowinski, B. Knight, R. 2022-05-20 doi:10.1101/2022.05.19.492684 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology ]]> https://biorxiv.org/content/10.1101/2022.05.19.492707v1?rss=1 Coker, J. Zhalnina, K. Marotz, C. Thiruppathy, D. Tjuanta, M. D'Elia, G. Hailu, R. Mahosky, T. Rowan, M. Northen, T. Zengler, K. 2022-05-19 doi:10.1101/2022.05.19.492707 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ A GATA factor radiation in Caenorhabditis rewired the endoderm specification network ]]> https://biorxiv.org/content/10.1101/2022.05.20.492851v1?rss=1 Darragh, A. C. Rifkin, S. A. 2022-05-21 doi:10.1101/2022.05.20.492851 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Radiation and diversification of GATA-domain-containing proteins in the genus Caenorhabditis ]]> https://biorxiv.org/content/10.1101/2022.05.20.492891v1?rss=1 Darragh, A. C. Rifkin, S. A. 2022-05-21 doi:10.1101/2022.05.20.492891 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Epitranscriptomic Modification of MicroRNA Increases Atherosclerosis Susceptibility ]]> https://biorxiv.org/content/10.1101/2022.05.21.492858v1?rss=1 He, M. Dong, J. Zhang, Y. Han, S. Y. Wang, C. Gongol, B. Kang, J. Huang, H.-Y. Shyy, J. Y.-J. 2022-05-21 doi:10.1101/2022.05.21.492858 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains ]]> https://biorxiv.org/content/10.1101/2022.05.25.493525v1?rss=1 Poudel, S. Hefner, Y. Szubin, R. Sastry, A. V. Gao, Y. Nizet, V. Palsson, B. O. 2022-05-26 doi:10.1101/2022.05.25.493525 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Adipocytes reprogram carbon and nitrogen metabolism to maintain lipogenic flux in the absence of Bckdha ]]> https://biorxiv.org/content/10.1101/2022.05.27.493780v1?rss=1 Green, C. R. Wessendorf-Rodriguez, K. A. Turner, R. Hover, J. D. Murphy, A. N. Wallace, M. Metallo, C. M. 2022-05-29 doi:10.1101/2022.05.27.493780 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Topography of mutational signatures in human cancer ]]> https://biorxiv.org/content/10.1101/2022.05.29.493921v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@abf065org.highwire.dtl.DTLVardef@33ad99org.highwire.dtl.DTLVardef@ca37b6org.highwire.dtl.DTLVardef@fa7c6_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIComprehensive topography analysis of mutational signatures encompassing 82,890,857 somatic mutations in 5,120 whole-genome sequenced tumours integrated with 516 tissue-matched topographical features from the ENCODE project. C_LIO_LIThe accumulation of somatic mutations from most mutational signatures is affected by nucleosome occupancy, histone modifications, CTCF binding sites, transcribed regions, or replication strand/timing. C_LIO_LIMutational signatures with related aetiologies are consistently characterized by similar genome topographies across tissue types. C_LIO_LITopography analysis allows both separating signatures from different aetiologies and understanding the genomic specificity of clustered somatic mutations. C_LIO_LIA comprehensive online resource, disseminate through the COSMIC signatures database, that allows researchers to explore the interactions between somatic mutational processes and genome architecture within and across cancer types. C_LI ]]> Otlu-Saritas, B. Diaz-Gay, M. Vermes, I. Bergstrom, E. N. Barnes, M. Alexandrov, L. B. 2022-05-29 doi:10.1101/2022.05.29.493921 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Preparing glycomics data for robust statistical analysis with GlyCompareCT ]]> https://biorxiv.org/content/10.1101/2022.05.31.494178v1?rss=1 Zhang, Y. Sridevi, K. Bao, B. Chiang, W.-T. Sorrentino, J. T. Schinn, S.-M. Kellman, B. P. Lewis, N. E. 2022-06-01 doi:10.1101/2022.05.31.494178 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ The conserved AAA-ATPase PCH-2 distributes its regulation of meiotic prophase events by remodeling multiple meiotic HORMADs in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.05.31.494220v1?rss=1 Russo, A. E. Giacopazzi, S. Deshong, A. Menon, M. Ortiz, V. A. Ego, K. M. Corbett, K. D. Bhalla, N. 2022-05-31 doi:10.1101/2022.05.31.494220 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Lis1 binding regulates force-induced detachment of cytoplasmic dynein from microtubules ]]> https://biorxiv.org/content/10.1101/2022.06.02.494578v1?rss=1 Kusakci, E. Htet, Z. M. Gillies, J. P. Reck-Peterson, S. L. Yildiz, A. 2022-06-03 doi:10.1101/2022.06.02.494578 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ Relating neighborhood deprivation to childhood obesity in the ABCD Study(R): evidence for theories of neuroinflammation and neuronal stress ]]> https://biorxiv.org/content/10.1101/2022.06.04.494818v1?rss=1 Adise, S. Marshall, A. T. Kan, E. Gonzalez, M. Sowell, E. R. 2022-06-06 doi:10.1101/2022.06.04.494818 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Longitudinal assessment of brain structure and behavior in youth with rapid weight gain: Potential contributing causes and consequences ]]> https://biorxiv.org/content/10.1101/2022.06.04.494820v1?rss=1 38lbs); 63% of the WG group were healthy weight at 9-to-10-years-old. ResultsA five-fold cross-validated logistic elastic-net regression revealed that rapid weight gain was associated with structural variation amongst 39 brain features at 9-to-10-years-old in regions involved with executive functioning, appetitive control, and reward sensitivity. Two years later, WG youth showed differences in change over time in several of these regions and performed worse on measures of impulsivity. ConclusionsThese findings suggest that brain structure in pre-adolescence may predispose some to rapid weight gain and that weight gain itself may alter maturational brain change in regions important for food intake and impulsivity. Behavioral interventions that target inhibitory control may improve trajectories of brain maturation and facilitate healthier behaviors. ]]> Adise, S. Marshall, A. T. Hahn, S. Zhao, S. Kan, E. Rhee, K. Herting, M. M. Sowell, E. R. 2022-06-06 doi:10.1101/2022.06.04.494820 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ CryoEM Structures of the Nitrogenase Complex During Catalytic Turnover ]]> https://biorxiv.org/content/10.1101/2022.06.05.494884v1?rss=1 Rutledge, H. L. Cook, B. D. Nguyen, H. P. M. Herzik, M. A. Tezcan, F. A. 2022-06-05 doi:10.1101/2022.06.05.494884 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Modeling membrane curvature generation using mechanics and machine learning ]]> https://biorxiv.org/content/10.1101/2022.06.06.495017v1?rss=1 Malingen, S. A. Rangamani, P. 2022-06-06 doi:10.1101/2022.06.06.495017 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Distinct roles of dentate gyrus and medial entorhinal cortex inputs for phase precession and temporal correlations in hippocampal CA3 place cells ]]> https://biorxiv.org/content/10.1101/2022.06.07.491859v1?rss=1 Ahmadi, S. Sasaki, T. Sabariego, M. Leibold, C. Leutgeb, S. Leutgeb, J. K. 2022-06-09 doi:10.1101/2022.06.07.491859 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Strengthening of enterococcal biofilms by Esp ]]> https://biorxiv.org/content/10.1101/2022.06.09.495547v1?rss=1 Spiegelman, L. Bahn-Suh, A. Montano, E. Zhang, L. Hura, G. Patras, K. Kumar, A. Tezcan, A. Nizet, V. Tsutakawa, S. Ghosh, P. 2022-06-09 doi:10.1101/2022.06.09.495547 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Bento: A toolkit for subcellular analysis of spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2022.06.10.495510v1?rss=1 Mah, C. K. Ahmed, N. Lam, D. Monell, A. Kern, C. Han, Y. Cesnik, A. J. Lundberg, E. Zhu, Q. Carter, H. W. Yeo, G. W. 2022-06-13 doi:10.1101/2022.06.10.495510 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Design principles of dose-response alignment in coupled GTPase switches ]]> https://biorxiv.org/content/10.1101/2022.06.14.496184v1?rss=1 Qiao, L. Ghosh, P. Rangamani, P. 2022-06-15 doi:10.1101/2022.06.14.496184 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2022.06.15.496350v1?rss=1 Wan, Y. C. Troemel, E. R. Reinke, A. W. 2022-06-17 doi:10.1101/2022.06.15.496350 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ A Generalized Reinforcement Learning-Based Deep Neural Network (GRL-DNN) Agent Model for Diverse Cognitive Constructs ]]> https://biorxiv.org/content/10.1101/2022.06.17.496500v1?rss=1 Nair, S. S. Muddapu, V. R. C, V. Balasubramani, P. P. Mishra, J. Ramanathan, D. S. Chakravarthy, V. S. 2022-06-20 doi:10.1101/2022.06.17.496500 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ White matter and literacy: a dynamic system in flux ]]> https://biorxiv.org/content/10.1101/2022.06.21.497048v1?rss=1 Roy, E. Richie-Halford, A. Kruper, J. Narayan, M. Bloom, D. Brown, T. T. Jernigan, T. L. McCandliss, B. D. Rokem, A. Yeatman, J. D. 2022-06-25 doi:10.1101/2022.06.21.497048 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ VPS13A and VPS13C influence lipid droplet abundance ]]> https://biorxiv.org/content/10.1101/2022.06.21.497109v1?rss=1 Chen, S. Roberts, M. A. Chen, C.-Y. Markmiller, S. Wei, H.-G. Yeo, G. W. Granneman, J. G. Olzmann, J. A. Ferro-Novick, S. 2022-06-23 doi:10.1101/2022.06.21.497109 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Myeloid reprogramming by JAK inhibition enhances checkpoint blockade therapy ]]> https://biorxiv.org/content/10.1101/2022.06.24.497435v1?rss=1 Zak, J. Pratumchai, I. Marro, B. S. Marquardt, K. L. Beheshti Zavareh, R. Lairson, L. L. Oldstone, M. B. A. Varner, J. A. Bachanova, V. Teijaro, J. 2022-06-26 doi:10.1101/2022.06.24.497435 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Culture-Independent Detection and Identification of Leptospira Serovars ]]> https://biorxiv.org/content/10.1101/2022.06.24.497575v1?rss=1 200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches--such as multi-locus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test--are tedious and expensive, and require isolation of the organisms in culture media--a protracted and incredibly inefficient process-- precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay--targeting a Leptospira-unique gene encoding a putative polysaccharide flippase--that provides intra-species, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI ("rage one"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum and urine, with no detectable off-target amplification--even of the genetically related but low virulence group II pathogenic (formerly "intermediate") or non-pathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine-samples and environmental samples containing varied and complex microbial species-consortia. And holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies. ]]> Matthias, M. A. Lubar, A. Lanka Acharige, S. S. Chaiboonma, K. N. Pilau, N. N. Marroquin, A. S. Jayasundara, D. Agampodi, S. B. Vinetz, J. M. 2022-06-25 doi:10.1101/2022.06.24.497575 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice ]]> https://biorxiv.org/content/10.1101/2022.06.27.497828v1?rss=1 Abdel-Haq, R. Schlachetzki, J. C. M. Boktor, J. C. Cantu-Jungles, T. M. Thron, T. Zhang, M. Bostick, J. W. Khazaei, T. Chilakala, S. Morais, L. H. Humphrey, G. Keshavarzian, A. Katz, J. E. Thomson, M. Knight, R. Gradinaru, V. Hamaker, B. R. Glass, C. K. Mazmanian, S. K. 2022-06-30 doi:10.1101/2022.06.27.497828 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ A pals-25 gain-of-function allele triggers systemic resistance against natural pathogens of C. elegans ]]> https://biorxiv.org/content/10.1101/2022.06.28.497889v1?rss=1 Gang, S. S. Grover, M. Reddy, K. C. Raman, D. Chang, Y.-T. Ekiert, D. C. Barkoulas, M. Troemel, E. R. 2022-07-01 doi:10.1101/2022.06.28.497889 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades ]]> https://biorxiv.org/content/10.1101/2022.06.30.498375v1?rss=1 Kodera, S. M. Sharma, A. Martino, C. Dsouza, M. Grippo, M. Lutz, H. Knight, R. Gilbert, J. A. Negri, M. C. Allard, S. M. 2022-07-01 doi:10.1101/2022.06.30.498375 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Dendrite architecture determines mitochondrial distribution patterns in vivo ]]> https://biorxiv.org/content/10.1101/2022.07.01.497972v1?rss=1 Donovan, E. J. Agrawal, A. Liberman, N. Kalai, J. Chua, J. N. Koslover, E. F. Barnhart, E. L. 2022-07-03 doi:10.1101/2022.07.01.497972 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Effects of Variation in Urine Sample Storage Conditions on 16S Urogenital Microbiome Analyses ]]> https://biorxiv.org/content/10.1101/2022.07.05.498913v1?rss=1 Kumar, T. Bryant, M. Cantrell, K. Song, S. J. McDonald, D. Tubb, H. M. Farmer, S. Lukacz, E. S. Brubaker, L. Knight, R. 2022-07-06 doi:10.1101/2022.07.05.498913 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Co-opted Genes of Algal Origin Protect C. elegans against Cyanogenic Toxins ]]> https://biorxiv.org/content/10.1101/2022.07.06.498920v1?rss=1 Wang, B. Pandey, T. Long, Y. Delgado-Rodriguez, S. Daugherty, M. D. Ma, D. K. 2022-07-06 doi:10.1101/2022.07.06.498920 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS ]]> https://biorxiv.org/content/10.1101/2022.07.09.499398v1?rss=1 Johnson, J. A. I. Tsang, A. Mitchell, J. T. Davis-Marcisak, E. F. Sherman, T. Liefeld, T. Loth, M. Goff, L. Zimmerman, J. Kinny-Köster, B. Jaffee, E. Tamayo, P. Mesirov, J. Reich, M. Fertig, E. J. Stein-O'Brien, G. L. 2022-07-11 doi:10.1101/2022.07.09.499398 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Chemokine CXCL4 interactions with extracellular matrix proteoglycans mediate wide-spread non-receptor mediated immune cell recruitment ]]> https://biorxiv.org/content/10.1101/2022.07.10.499282v1?rss=1 Gray, A. L. Karlsson, R. Roberts, A. R. Ridley, A. J. Pun, N. Hughes, C. Medina-Ruiz, L. Birchenough, H. Salanga, C. Yates, E. A. Turnbull, J. E. Handel, T. M. Graham, G. Jowitt, T. A. Schiessl, I. Richter, R. P. Miller, R. L. Dyer, D. P. 2022-07-10 doi:10.1101/2022.07.10.499282 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Antiviral function and viral antagonism of the rapidly evolving dynein activating adapter NINL ]]> https://biorxiv.org/content/10.1101/2022.07.11.499552v1?rss=1 Stevens, D. A. Beierschmitt, C. Mahesula, S. Corley, M. R. Salogiannis, J. Tsu, B. V. Cao, B. Ryan, A. P. Reck-Peterson, S. L. Daugherty, M. D. 2022-07-11 doi:10.1101/2022.07.11.499552 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein ]]> https://biorxiv.org/content/10.1101/2022.07.13.498973v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@7758f8org.highwire.dtl.DTLVardef@172396aorg.highwire.dtl.DTLVardef@176612org.highwire.dtl.DTLVardef@2e320c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Frenkel, A. Zecharia, E. Gomez-Perez, D. Yegorov, Y. Sendersky, E. Jacobs, A. Benichou, J. Stierhof, Y.-D. Parnasa, R. Golden, S. S. Kemen, E. Schwarz, R. 2022-07-13 doi:10.1101/2022.07.13.498973 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Decline of intrinsic cerebrospinal fluid outflow in healthy humans with age detected by non-contrast spin-labeling MRI ]]> https://biorxiv.org/content/10.1101/2022.07.14.500033v1?rss=1 Malis, V. Bae, W. C. Yamamoto, A. McEvoy, L. K. McDonald, M. A. Miyazaki, M. 2022-07-18 doi:10.1101/2022.07.14.500033 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Integrated multi-cohort analysis of the Parkinson's disease gut metagenome ]]> https://biorxiv.org/content/10.1101/2022.07.20.500694v1?rss=1 Boktor, J. C. Sharon, G. Verhagen Metman, L. A. Hall, D. A. Engen, P. A. Zreloff, Z. Hakim, D. J. Bostick, J. W. Ousey, J. Lange, D. Humphrey, G. Ackermann, G. Carlin, M. Knight, R. Keshavarzian, A. Mazmanian, S. K. 2022-07-21 doi:10.1101/2022.07.20.500694 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays). ]]> https://biorxiv.org/content/10.1101/2022.07.21.500061v1?rss=1 Murphy, K. M. Dowd, T. Khalil, A. Char, S. N. Yang, B. Endelman, B. J. Shih, P. M. Topp, C. N. Schmelz, E. A. Zerbe, P. 2022-07-22 doi:10.1101/2022.07.21.500061 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Identification of pre-existing microbiome and metabolic vulnerabilities to escalation of oxycodone self-administration and identification of a causal role of short-chain fatty acids in addiction-like behaviors. ]]> https://biorxiv.org/content/10.1101/2022.07.23.501268v1?rss=1 Simpson, S. Kimbrough, A. Peters, G. Wellmeyer, E. Mclellan, R. Walker, N. Jia, H. Hu, S. Iyer, M. Sathish, V. Sedighim, S. Kallupi, M. Brennan, M. Maturin, L. Hughes, T. Xie, T. Espinoza, V. Carrette, L. Smith, L. C. Seaman, J. Solberg-Woods, L. Palmer, A. de Guglielmo, G. George, O. 2022-07-23 doi:10.1101/2022.07.23.501268 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness ]]> https://biorxiv.org/content/10.1101/2022.07.25.501481v1?rss=1 Keller, L. J. Nguyen, T. H. Liu, L. Lakemeyer, M. Gelsinger, D. J. Chanin, R. Ngo, N. Lum, K. M. Faucher, F. Ipock, P. Niphakis, M. Bhatt, A. S. O'Donoghue, A. j. Huang, K. Bogyo, M. 2022-07-26 doi:10.1101/2022.07.25.501481 Cold Spring Harbor Laboratory Press 2022-07-26 <![CDATA[ Epigenome-wide meta-analysis of BMI in nine population-based cohorts: examining the utility of methylation as a biomarker of BMI ]]> https://biorxiv.org/content/10.1101/2022.07.26.498234v1?rss=1 Do, W. L. Sun, D. Meeks, K. A. Dugue, P.-A. Demerath, E. W. Guan, W. Li, S. Chen, W. Milne, R. L. Adeyemo, A. Agyemang, C. Nassir, R. Manson, J. E. Shadyab, A. H. Hou, L. Horvath, S. Assimes, T. L. Bhatti, P. Jordahl, K. M. Baccarelli, A. A. Smith, A. Staimez, L. R. Stein, A. D. Whitsel, E. A. Narayan, K. M. V. Conneely, K. N. 2022-07-27 doi:10.1101/2022.07.26.498234 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Radiogenomics of C9orf72 expansion carriers reveals global transposable element de-repression and enables prediction of thalamic atrophy and clinical impairment ]]> https://biorxiv.org/content/10.1101/2022.07.28.501897v1?rss=1 Bonham, L. W. Geier, E. G. Sirkis, D. W. Leong, J. K. Ramos, E. M. Wang, Q. Karydas, A. Lee, S. E. Sturm, V. E. Sawyer, R. P. Friedberg, A. Ichida, J. K. Gitler, A. D. Sugrue, L. Cordingley, M. Bee, W. Weber, E. Kramer, J. Rankin, K. P. Rosen, H. J. Boxer, A. L. Seeley, W. W. Ravits, J. Miller, B. L. Yokoyama, J. S. 2022-07-31 doi:10.1101/2022.07.28.501897 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Breathing and Tilting: Mesoscale simulations illuminate influenza glycoprotein vulnerabilities ]]> https://biorxiv.org/content/10.1101/2022.08.02.502576v1?rss=1 Casalino, L. Seitz, C. Lederhofer, J. Tsybovsky, Y. Wilson, I. A. Kanekiyo, M. Amaro, R. E. 2022-08-03 doi:10.1101/2022.08.02.502576 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ The hologenome of Osedax frankpressi reveals the genetic interplay for the symbiotic digestion of vertebrate bone ]]> https://biorxiv.org/content/10.1101/2022.08.04.502725v1?rss=1 Moggioli, G. Panossian, B. Sun, Y. Thiel, D. Martin-Zamora, F. M. Tran, M. Clifford, A. M. Goffredi, S. K. Rimskaya-Korsakova, N. Jekelly, G. Tresguerres, M. Qian, P.-Y. Qiu, J.-W. Rouse, G. W. Henry, L. M. Martin-Duran, J. M. 2022-08-05 doi:10.1101/2022.08.04.502725 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Predicting regional somatic mutation rates using DNA motifs ]]> https://biorxiv.org/content/10.1101/2022.08.04.502732v1?rss=1 Liu, c. Wang, Z. Wang, J. Liu, C. Wang, M. Ngo, V. Wang, W. 2022-08-05 doi:10.1101/2022.08.04.502732 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Detecting boolean asymmetric relationships with a loop counting technique and its implications for analyzing heterogeneity within gene expression datasets ]]> https://biorxiv.org/content/10.1101/2022.08.04.502792v1?rss=1 Zhou, H. Rangan, A. V. Lin, W. Labra, S. R. Lipton, S. A. Schork, N. J. 2022-08-05 doi:10.1101/2022.08.04.502792 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins ]]> https://biorxiv.org/content/10.1101/2022.08.04.502797v1?rss=1 Hirose, Y. Poudel, S. Sastry, A. V. Szubin, R. Zielinski, D. C. Lim, H. G. Menon, N. D. Bergsten, H. Uchiyama, S. Hanada, T. Kawabata, S. Palsson, B. O. Nizet, V. 2022-08-04 doi:10.1101/2022.08.04.502797 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Development of Highly Selective Epoxyketone-based Plasmodium Proteasome Inhibitors with Negligible Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2022.08.06.502205v1?rss=1 Almaliti, J. Fajtova, P. Calla, J. LaMonte, G. M. Feng, M. Rocamora, F. Ottilie, S. Glukhov, E. Boura, E. Suhandynata, R. T. Momper, J. D. Gilson, M. K. Winzeler, E. A. Gerwick, W. H. O'Donoghue, A. J. 2022-08-07 doi:10.1101/2022.08.06.502205 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ The Impact of Population Stratification on the Analysis of Multimodal Neuroimaging Derived Measures ]]> https://biorxiv.org/content/10.1101/2022.08.06.503037v1?rss=1 Huang, T.-H. Fan, C. C. Thompson, W. Loughnan, R. 2022-08-11 doi:10.1101/2022.08.06.503037 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Orbitofrontal cortex populations are differentially recruited to support actions ]]> https://biorxiv.org/content/10.1101/2022.08.08.503227v1?rss=1 Cazares, C. Schreiner, D. C. Valencia, M. L. Gremel, C. M. 2022-08-09 doi:10.1101/2022.08.08.503227 Cold Spring Harbor Laboratory Press 2022-08-09 <![CDATA[ The genetic and environmental etiology of blood-based biomarkers related to the risks of Alzheimer's Disease in a population-based sample of early old age men ]]> https://biorxiv.org/content/10.1101/2022.08.09.503234v1?rss=1 Gillespie, N. A. Rissman, R. A. Elman, J. A. McKenzie, R. E. Tu, X. M. Reynolds, C. A. Lyons, M. J. Eglit, G. M. L. Neale, M. C. Franz, C. Kremen, W. S. 2022-08-11 doi:10.1101/2022.08.09.503234 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Fast, Efficient Multimodal Image Normalisation Tool (FEMINisT) for the Adolescent Brain and Cognitive Development study: the FEMINisT ABCD Atlas ]]> https://biorxiv.org/content/10.1101/2022.08.09.503395v1?rss=1 Pecheva, D. Iversen, J. R. Palmer, C. E. Watts, R. Jernigan, T. L. Hagler, D. J. Dale, A. M. 2022-08-11 doi:10.1101/2022.08.09.503395 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules ]]> https://biorxiv.org/content/10.1101/2022.08.10.503527v1?rss=1 Shaked, I. Foo, C. Liu, R. Cui, Y. Ji, X. Broggini, T. Mächler, P. Sundd, P. Devor, A. Friedman, B. Kleninfeld, D. 2022-08-13 doi:10.1101/2022.08.10.503527 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters ]]> https://biorxiv.org/content/10.1101/2022.08.10.503534v1?rss=1 Chaturvedi, S. Beutler, N. Pablo, M. Vasen, G. Chen, X. Calia, G. Buie, L. Rodick, R. Smith, D. Rogers, T. Weinberger, L. 2022-08-11 doi:10.1101/2022.08.10.503534 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ A thermodynamically-consistent model for ATP production in mitochondria ]]> https://biorxiv.org/content/10.1101/2022.08.16.500715v1?rss=1 Garcia, G. C. Bartol, T. M. Sejnowski, T. J. Rangamani, P. 2022-08-16 doi:10.1101/2022.08.16.500715 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling ]]> https://biorxiv.org/content/10.1101/2022.08.17.504291v1?rss=1 Leung, A. Rangamani, P. 2022-08-18 doi:10.1101/2022.08.17.504291 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression ]]> https://biorxiv.org/content/10.1101/2022.08.19.504467v1?rss=1 Liu, C. Wang, W. 2022-08-22 doi:10.1101/2022.08.19.504467 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Remarkable Sex-Specific Differences at Single-Cell Resolution in Neonatal Hyperoxic Lung Injury ]]> https://biorxiv.org/content/10.1101/2022.08.19.504541v1?rss=1 35000 cells isolated from the lungs of neonatal male and female C57BL/6 mice exposed to 95% FiO2 between PND1-5 (saccular stage of lung development) or normoxia and euthanized at PND7 (alveolar stage of lung development). ScRNAseq identified 22 cell clusters with distinct populations of endothelial, epithelial, mesenchymal, and immune cells. Our data identified that the distal lung vascular endothelium (composed of aerocytes and general capillary endothelial cells) is exquisitely sensitive to hyperoxia exposure with the emergence of an intermediate capillary endothelial population with both aCaP and gCaP markers. We also identified a myeloid derived suppressor cell population from the lung neutrophils. Sexual dimorphism was evident in all lung cell subpopulations but was striking among the lung immune cells. Finally, we identified that the specific intercellular communication networks and the ligand-receptor pairs that are impacted by neonatal hyperoxia exposure. ]]> Cantu Gutierrez, M. E. Cantu, A. Dong, X. Leek, C. Sajti, E. Lingappan, K. 2022-08-19 doi:10.1101/2022.08.19.504541 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.08.23.504974v1?rss=1 Kumpornsin, K. Kochakarn, T. Yeo, T. Luth, M. Pearson, R. D. Hoshizaki, J. Schindler, K. Mok, S. Park, H. Uhlemann, A.-C. Cubel, S. M. Franco, V. Gomez-Lorenzo, M. Gamo, F.-J. Winzeler, E. Fidock, D. A. Chookajorn, T. Lee, M. C. 2022-08-23 doi:10.1101/2022.08.23.504974 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ MicroRNA-218 instructs proper assembly of hippocampal networks ]]> https://biorxiv.org/content/10.1101/2022.08.24.505085v1?rss=1 Taylor, S. Kobayashi, M. Vilella, A. Tiwari, D. Zolboot, N. Hartzell, A. Girgiss, C. Abaci, Y. De Sanctis, C. Bellenchi, G. C. Darnell, R. B. Gross, C. Zoli, M. Berg, D. K. Lippi, G. 2022-08-25 doi:10.1101/2022.08.24.505085 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Interpretable Prediction of mRNA Abundance from Promoter Sequence using Contextual Regression Models ]]> https://biorxiv.org/content/10.1101/2022.08.27.505543v1?rss=1 Wang, S. Wang, W. 2022-08-29 doi:10.1101/2022.08.27.505543 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ A pharmacoproteomic landscape of organotypic intervention responses in gram-negative sepsis ]]> https://biorxiv.org/content/10.1101/2022.08.29.503941v1?rss=1 Mohanty, T. Karlsson, C. A. Q. Chao, Y. Malmstrom, E. Bratanis, E. Grentzmann, A. Morch, M. Nizet, V. Malmstrom, L. Linder, A. Shannon, O. Malmstrom, J. 2022-08-29 doi:10.1101/2022.08.29.503941 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Polycomb response elements reduce leaky expression of Cas9 under temperature-inducible Hsp70Bb promoter in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.08.29.505746v1?rss=1 Warsinger-Pepe, N. Chang, C. Desroberts, C. R. Akbari, O. S. 2022-08-29 doi:10.1101/2022.08.29.505746 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assemblyprior to nuclear dissolution ]]> https://biorxiv.org/content/10.1101/2022.09.01.505886v1?rss=1 Rocha, H. Simoes, P. A. Budrewicz, J. Lara-Gonzalez, P. Xavier de Carvalho, A. Dumont, J. Desai, A. Gassmann, R. 2022-09-02 doi:10.1101/2022.09.01.505886 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Effect of time spent on active learning on exam performance: A controlled case study on a course with different instructors but identical teaching materials ]]> https://biorxiv.org/content/10.1101/2022.09.01.506238v1?rss=1 Cen, X. Lee, R. J. Maloy, J. P. Owens, M. T. 2022-09-03 doi:10.1101/2022.09.01.506238 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Defining antigen targets to dissect vaccinia virus (VACV) and Monkeypox virus (MPXV)-specific T cell responses in humans ]]> https://biorxiv.org/content/10.1101/2022.09.06.506534v1?rss=1 Grifoni, A. Zhang, Y. Tarke, A. Sidney, J. Rubiro, P. Reina-Campos, M. Filaci, G. Dan, J. M. Scheuermann, R. H. Sette, A. 2022-09-07 doi:10.1101/2022.09.06.506534 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala ]]> https://biorxiv.org/content/10.1101/2022.09.08.506493v1?rss=1 Zhou, J. L. de Guglielmo, G. Ho, A. J. Kallupi, M. Li, H.-R. Chitre, A. S. Carrette, L. L. G. George, O. Palmer, A. A. McVicker, G. P. Telese, F. 2022-09-12 doi:10.1101/2022.09.08.506493 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ A small-molecule myosin inhibitor as a targeted multi-stage antimalarial ]]> https://biorxiv.org/content/10.1101/2022.09.09.507317v1?rss=1 50-fold selectivity against cardiac, skeletal, and smooth muscle myosins. KNX-115 inhibits the blood and liver stages of Plasmodium with an EC50 of about 100 nanomolar, with negligible liver cell toxicity. In addition, KNX-115 inhibits sporozoite cell traversal and blocks the gametocyte to oocyst conversion in the mosquito. KNX-115 displays a similar killing profile to pyrimethamine and parasites are totally killed after 96 hours of treatment. In line with its novel mechanism of action, KNX-115 is equally effective at inhibiting a panel of Plasmodium strains resistant to experimental and marketed antimalarials. In vitro evolution data likely suggests a refractory potential of KNX-115 in developing parasite resistance. ]]> Trivedi, D. V. Karabina, A. Bergnes, G. Racca, A. Wander, H. Jung, S. Mittal, N. Huijs, T. Ouchida, S. Ruijgrok, P. V. Song, D. Wittlin, S. Mukherjee, P. Chakraborty, A. Winzeler, E. A. Burrows, J. N. Laleu, B. Spudich, A. Ruppel, K. Dechering, K. Nag, S. Spudich, J. 2022-09-10 doi:10.1101/2022.09.09.507317 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Two Synaptic Convergence Motifs Define Functional Roles for Inputs to Cochlear Nucleus Bushy Cells ]]> https://biorxiv.org/content/10.1101/2022.09.10.507000v1?rss=1 Spirou, G. A. Kersting, M. Carr, S. Razzaq, B. Alves-Pinto, C. Y. Dawson, M. Ellisman, M. H. Manis, P. B. 2022-09-10 doi:10.1101/2022.09.10.507000 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Phosphorylation of Gαi shapes canonical Gα(i)βγ/GPCR signaling ]]> https://biorxiv.org/content/10.1101/2022.09.11.507491v1?rss=1 Roy, S. Silas, A. J. Ghassemian, M. Kufareva, I. Ghosh, P. 2022-09-12 doi:10.1101/2022.09.11.507491 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ TandemAligner: a new parameter-free framework for fast sequence alignment ]]> https://biorxiv.org/content/10.1101/2022.09.15.507041v1?rss=1 Bzikadze, A. V. Pevzner, P. A. 2022-09-17 doi:10.1101/2022.09.15.507041 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Cortico-cortical and hippocampo-cortical co-rippling are facilitated by thalamo-cortical spindles and upstates, but not by thalamic ripples ]]> https://biorxiv.org/content/10.1101/2022.09.15.507471v1?rss=1 Dickey, C. W. Verzhbinsky, I. A. Kajfez, S. Rosen, B. Q. Pati, S. Halgren, E. 2022-09-17 doi:10.1101/2022.09.15.507471 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Eliminating Genes for a Two Component System Increases PHB Productivity in Cupriavidus basilensis 4G11 Under PHB Suppressing, Non-Stress Conditions ]]> https://biorxiv.org/content/10.1101/2022.09.19.508597v1?rss=1 Sander, K. B. Abel, A. J. Friedline, S. Sharpless, W. Skerker, J. M. B. Deutschbauer, A. Clark, D. S. Arkin, A. P. 2022-09-20 doi:10.1101/2022.09.19.508597 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Host specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome ]]> https://biorxiv.org/content/10.1101/2022.09.21.508960v1?rss=1 Tsu, B. V. Agarwal, R. Gokhale, N. S. Kulsuptrakul, J. Ryan, A. P. Castro, L. K. Beierschmitt, C. M. Turcotte, E. A. Fay, E. J. Vance, R. E. Hyde, J. L. Savan, R. Mitchell, P. S. Daugherty, M. D. 2022-09-22 doi:10.1101/2022.09.21.508960 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation ]]> https://biorxiv.org/content/10.1101/2022.09.22.508219v1?rss=1 Ma, W. You, S. Regnier, M. McCammon, J. A. 2022-09-23 doi:10.1101/2022.09.22.508219 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms ]]> https://biorxiv.org/content/10.1101/2022.09.22.509046v1?rss=1 Bennett, H. Troutman, T. D. Zhou, E. Spann, N. J. Link, V. M. Seidman, J. S. Nickl, C. K. Abe, Y. Sakai, M. Pasillas, M. P. Marlman, J. M. Guzman, C. Hosseini, M. Schnabl, B. Glass, C. K. 2022-09-23 doi:10.1101/2022.09.22.509046 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Regulation of the Phage Lambda Viral Packaging Motor's Grip and DNA End-clamp Mechanism ]]> https://biorxiv.org/content/10.1101/2022.09.24.509349v1?rss=1 Rawson, B. Yang, Q. Catalano, C. E. Smith, D. E. 2022-09-25 doi:10.1101/2022.09.24.509349 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ RNA recoding in cephalopods tailors microtubule motor protein function ]]> https://biorxiv.org/content/10.1101/2022.09.25.509396v1?rss=1 Rangan, K. J. Reck-Peterson, S. L. 2022-09-25 doi:10.1101/2022.09.25.509396 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Ultrastructure of synaptic connectivity within sub-regions of the SCN revealed by genetically encoded EM tag and SBEM ]]> https://biorxiv.org/content/10.1101/2022.09.26.509467v1?rss=1 Calligaro, H. Shoghi, A. Chen, X. Kim, K.-Y. Liu, Y. H. Khov, B. Finander, B. Le, H. Ellisman, M. H. Panda, S. 2022-09-26 doi:10.1101/2022.09.26.509467 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3 ]]> https://biorxiv.org/content/10.1101/2022.09.26.509529v1?rss=1 Schindewolf, C. Lokugamage, K. Vu, M. Johnson, B. A. Scharton, D. Plante, J. A. Kalveram, B. K. Crocquet-Valdes, P. A. Sotcheff, S. L. Jaworski, E. Alvarado, R. E. Debbink, K. Daugherty, M. D. Weaver, S. Routh, A. L. Walker, D. H. Plante, K. S. Menachery, V. D. 2022-09-26 doi:10.1101/2022.09.26.509529 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ A di-arginine additive for dissociation of gold nanoparticle aggregates: A matrix-insensitive approach with applications in protease detection ]]> https://biorxiv.org/content/10.1101/2022.09.30.508454v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@13a6f3org.highwire.dtl.DTLVardef@35b42dorg.highwire.dtl.DTLVardef@1c8249forg.highwire.dtl.DTLVardef@dc8236_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Retout, M. Jin, Z. Mantri, Y. Borum, R. Creyer, M. Yim, W. He, T. Chang, Y.-C. Jokerst, J. 2022-10-03 doi:10.1101/2022.09.30.508454 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Optical Metabolic Imaging Uncovers Sex- and Diet-dependent Lipid Changes in Aging Drosophila Brain ]]> https://biorxiv.org/content/10.1101/2022.10.01.510416v1?rss=1 Li, Y. Chang, P. Sankaran, S. Jang, H. Nie, Y. Zeng, A. Hussain, S. Wu, J. Y. Chen, X. Shi, L. 2022-10-03 doi:10.1101/2022.10.01.510416 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Vascular tortuosity quantification as an outcome metric of the oxygen-induced retinopathy model of ischemic retinopathy ]]> https://biorxiv.org/content/10.1101/2022.10.02.510568v1?rss=1 Marra, K. V. Chen, J. S. Robles-Holmes, H. K. Miller, J. Wei, G. Ideguchi, Y. Ly, K. B. Prenner, S. Erdogmus, D. Ferrara, N. Campbell, J. P. Friedlander, M. Nudleman, E. 2022-10-04 doi:10.1101/2022.10.02.510568 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Artificial Intelligence Guided Discovery of Gastric Cancer Continuum ]]> https://biorxiv.org/content/10.1101/2022.10.05.510975v1?rss=1 Vo, D. T. Ghosh, P. Sahoo, D. 2022-10-07 doi:10.1101/2022.10.05.510975 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model ]]> https://biorxiv.org/content/10.1101/2022.10.06.511147v1?rss=1 Mai, U. Charvel, E. Mirarab, S. 2022-10-08 doi:10.1101/2022.10.06.511147 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ PLK-1 tethered on BUB-1 directs CDC-20 kinetochore recruitment to ensure timelyembryonic mitoses ]]> https://biorxiv.org/content/10.1101/2022.10.07.511323v1?rss=1 Houston, J. Ohta, M. Gomez-Cavazos, J. S. Deep, A. Corbett, K. D. Oegema, K. Lara-Gonzalez, P. Kim, T. Desai, A. 2022-10-07 doi:10.1101/2022.10.07.511323 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus ]]> https://biorxiv.org/content/10.1101/2022.10.07.511350v1?rss=1 Heffel, M. G. Zhou, J. Zhang, Y. Lee, D.-S. Hou, K. Pastor Alonso, O. Abuhanna, K. Schmitt, A. D. Li, T. Haeussler, M. Wick, B. Zhang, M. J. Xie, F. Ziffra, R. S. Mukamel, E. A. Eskin, E. Pasaniuc, B. Ecker, J. R. Dixon, J. Nowakowski, T. J. Paredes, M. F. Luo, C. 2022-10-08 doi:10.1101/2022.10.07.511350 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Structures of human cytoplasmic dynein in complex with the lissencephaly 1 protein, LIS1 ]]> https://biorxiv.org/content/10.1101/2022.10.08.511426v1?rss=1 Reimer, J. M. DeSantis, M. E. Reck-Peterson, S. L. Leschziner, A. E. 2022-10-08 doi:10.1101/2022.10.08.511426 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ TRB3 augments IL1β-TLR4 signaling by engaging Flightless-homolog 1. ]]> https://biorxiv.org/content/10.1101/2022.10.09.511391v1?rss=1 Gonuguntla, S. Humphrey, R. K. Gorantla, A. Hao, E. Jhala, U. S. 2022-10-10 doi:10.1101/2022.10.09.511391 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ MS2Prop: A machine learning model that directly predicts chemical properties from mass spectrometry data for novel compounds ]]> https://biorxiv.org/content/10.1101/2022.10.09.511482v1?rss=1 Voronov, G. Frandsen, A. Bargh, B. Healey, D. Lightheart, R. Kind, T. Dorrestein, P. C. Colluru, V. Butler, T. 2022-10-10 doi:10.1101/2022.10.09.511482 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Lis1 relieves cytoplasmic dynein-1 auto-inhibition by acting as a molecular wedge ]]> https://biorxiv.org/content/10.1101/2022.10.10.511666v1?rss=1 Karasmanis, E. P. Reimer, J. M. Kendrick, A. A. Rodriguez, J. A. Truong, J. B. Lahiri, I. Reck-Peterson, S. L. Leschziner, A. E. 2022-10-11 doi:10.1101/2022.10.10.511666 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters ]]> https://biorxiv.org/content/10.1101/2022.10.11.511793v1?rss=1 Diner, R. E. Zimmer-Faust, A. Cooksey, E. Allard, S. Kodera, S. M. Kunselman, E. Garodia, Y. Allen, A. E. Griffith, J. Gilbert, J. A. 2022-10-11 doi:10.1101/2022.10.11.511793 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Endosomal removal and disposal of dysfunctional, immunostimulatory mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2022.10.12.511955v1?rss=1 Newman, L. E. Tadepalle, N. Novak, S. W. Schiavon, C. R. Rojas, G. R. Chevez, J. A. Lemersal, I. Medina, M. Rocha, S. Towers, C. G. Grotjahn, D. A. Manor, U. Shadel, G. S. 2022-10-12 doi:10.1101/2022.10.12.511955 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Smaller total and subregional cerebellar volumes in posttraumatic stress disorder: a mega-analysis by the ENIGMA-PGC PTSD workgroup ]]> https://biorxiv.org/content/10.1101/2022.10.13.512111v1?rss=1 Huggins, A. A. Baird, C. L. Briggs, M. Laskowitz, S. Fouda, S. Haswell, C. C. Sun, D. Salminen, L. E. Jahanshad, N. Thomopoulos, S. I. Veltman, D. J. Frijling, J. L. Olff, M. van Zuiden, M. Koch, S. B. J. Nawijn, L. Wang, L. Zhu, Y. Li, G. Stein, D. J. Ipser, J. Seedat, S. du Plessis, S. van den Heuvel, L. L. Suarez-Jimenez, B. Zhu, X. Kim, Y. He, X. Zilcha-Mano, S. Lazarov, A. Neria, Y. Stevens, J. S. Ressler, K. J. Jovanovic, T. van Rooij, S. J. H. Fani, N. Hudson, A. R. Mueller, S. C. Sierk, A. Manthey, A. Walter, H. Daniels, J. K. Schmahl, C. Herz 2022-10-17 doi:10.1101/2022.10.13.512111 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Machine-guided cell-fate engineering ]]> https://biorxiv.org/content/10.1101/2022.10.14.512279v1?rss=1 Appleton, E. M. Tao, J. Fonseca, G. J. Liu, S. Glass, C. H. Church, G. M. 2022-10-14 doi:10.1101/2022.10.14.512279 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A fast-killing tyrosine amide ((S)-SW228703) with blood and liver-stage antimalarial activity associated with the Cyclic Amine Resistance Locus (PfCARL) ]]> https://biorxiv.org/content/10.1101/2022.10.16.512381v1?rss=1 Imlay, L. S. Lawong, A. K. Gahalawat, S. Kumar, A. Xing, C. Mittal, N. Wittlin, S. Churchyard, A. Niederstrasser, H. Crespo-Fernandez, B. Posner, B. Gamo, F.-J. S. Baum, J. Winzeler, E. Laleu, B. Ready, J. M. Phillips, M. A. 2022-10-17 doi:10.1101/2022.10.16.512381 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ A Computational Model for Storing Memories in the Synaptic Structures of the Brain ]]> https://biorxiv.org/content/10.1101/2022.10.21.513291v1?rss=1 George, V. K. Morar, V. N. Silva, G. A. 2022-10-22 doi:10.1101/2022.10.21.513291 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences ]]> https://biorxiv.org/content/10.1101/2022.10.21.513318v1?rss=1 Moshiri, N. 2022-10-24 doi:10.1101/2022.10.21.513318 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Localized APP pathology in the hippocampus is sufficient to result in progressive disorganization of the timing of neuronal firing patterns ]]> https://biorxiv.org/content/10.1101/2022.10.24.513188v1?rss=1 Viana da Silva, S. Haberl, M. G. Gaur, K. Patel, R. Narayan, G. Ledakis, M. Fu, M. L. Koo, E. H. Leutgeb, J. K. Leutgeb, S. 2022-10-25 doi:10.1101/2022.10.24.513188 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ The Molecular Signatures Database Revisited: Extending Support for Mouse Data ]]> https://biorxiv.org/content/10.1101/2022.10.24.513539v1?rss=1 Castanza, A. S. Recla, J. M. Eby, D. Thorvaldsdottir, H. Bult, C. J. Mesirov, J. P. 2022-10-25 doi:10.1101/2022.10.24.513539 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ EUGENe: A Python toolkit for predictive analyses of regulatory sequences ]]> https://biorxiv.org/content/10.1101/2022.10.24.513593v1?rss=1 Klie, A. Stites, H. Jores, T. Carter, H. 2022-10-26 doi:10.1101/2022.10.24.513593 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function ]]> https://biorxiv.org/content/10.1101/2022.10.24.513614v1?rss=1 Lewis, B. M. Cho, C. Y. Her, H.-L. Hunter, T. Yeo, G. W. 2022-10-26 doi:10.1101/2022.10.24.513614 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Capturing differences in the regulation of LRRK2 dynamics and conformational states by small molecule kinase inhibitors ]]> https://biorxiv.org/content/10.1101/2022.10.24.513618v1?rss=1 Weng, J.-H. Ma, W. Wu, J. Silletti, S. McCammon, J. A. Taylor, S. S. 2022-10-25 doi:10.1101/2022.10.24.513618 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response ]]> https://biorxiv.org/content/10.1101/2022.10.25.513771v1?rss=1 Chudnovskiy, A. Nakandakari-Higa, S. Castro, T. B. Cui, A. Lin, C.-H. Sade-Feldman, M. Phillips, B. K. Pae, J. Mesin, L. Bortolatto, J. Schweitzer, L. D. Pasqual, G. Lu, L.-F. Hacohen, N. Victora, G. D. 2022-10-25 doi:10.1101/2022.10.25.513771 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide ]]> https://biorxiv.org/content/10.1101/2022.10.26.513573v1?rss=1 BICCN Data Ecosytem Collaboration, Hawrylycz, M. J. Martone, M. E. Hof, P. R. Lein, E. S. Regev, A. Ascoli, G. A. A. Bjaalie, J. G. Dong, H.-W. Ghosh, S. S. Gillis, J. Hertzano, R. Haynor, D. R. Kim, Y. Liu, Y. Miller, J. A. Mitra, P. P. Mukamel, E. Osumi-Sutherland, D. Peng, H. Ray, P. L. Sanchez, R. Ropelewski, A. Scheuermann, R. H. Tan, S. Z. K. Tickle, T. Tilgner, H. Varghese, M. Wester, B. White, O. Aevermann, B. Allemang, D. Ament, S. Athey, T. L. Baker, P. M. Baker, C. Baker, K. S. Bandrowski, A. Bishwakarma, P. Carr, A. Chen, M. Choudhury, R. 2022-10-30 doi:10.1101/2022.10.26.513573 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Time of Sample Collection Critical for Microbiome Replicability ]]> https://biorxiv.org/content/10.1101/2022.10.26.513817v1?rss=1 Allaband, C. Lingaraju, A. Ramos, S. F. Kumar, T. Javaheri, H. Tiu, M. D. Machado, A. C. D. Richter, R. A. Elijah, E. Haddad, G. G. Leone, V. A. Dorrestein, P. C. Knight, R. Zarrinpar, A. 2022-10-28 doi:10.1101/2022.10.26.513817 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Low Temperature and High Hydrostatic Pressure Have Compounding Negative Effects on Marine Microbial Motility ]]> https://biorxiv.org/content/10.1101/2022.10.26.513967v1?rss=1 Mullane, K. K. Bartlett, D. H. Nishiyama, M. Kurihara, T. 2022-10-27 doi:10.1101/2022.10.26.513967 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Heritability estimation of cognitive phenotypes in the ABCD Study using mixed models ]]> https://biorxiv.org/content/10.1101/2022.10.28.512918v1?rss=1 Smith, D. M. Loughnan, R. J. Friedman, N. P. Parekh, P. Frei, O. Thompson, W. K. Andreassen, O. Neale, M. Jernigan, T. L. Dale, A. 2022-10-31 doi:10.1101/2022.10.28.512918 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Alveolar epithelial type 1 cells serve as a cell of origin for lung adenocarcinoma with distinct molecular and phenotypic presentation ]]> https://biorxiv.org/content/10.1101/2022.10.29.514334v1?rss=1 Yang, M. Shen, H. Flodby, P. Koss, M. Bassiouni, R. Liu, Y. Jashashvilli, T. Stueve, T. R. Mullen, D. J. Ryan, A. L. Carpten, J. Castaldi, A. Wallace, W. D. Zhou, B. Borok, MD, Z. Marconett, C. N. 2022-10-31 doi:10.1101/2022.10.29.514334 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Unraveling the coordinated dynamics of protein- and metabolite-mediated cell-cell communication ]]> https://biorxiv.org/content/10.1101/2022.11.02.514917v1?rss=1 Armingol, E. Larsen, R. O. Cequeira, M. Baghdassarian, H. Lewis, N. E. 2022-11-03 doi:10.1101/2022.11.02.514917 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Improving annotation propagation on molecular networks through random walks: Introducing ChemWalker ]]> https://biorxiv.org/content/10.1101/2022.11.04.514505v1?rss=1 Borelli, T. C. Arini, G. S. Feitosa, L. G. P. Dorrestein, P. C. Lopes, N. P. da Silva, R. R. 2022-11-05 doi:10.1101/2022.11.04.514505 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Methadone alters transcriptional programs associated with synapse formation in human cortical organoids ]]> https://biorxiv.org/content/10.1101/2022.11.04.515240v1?rss=1 Dwivedi, I. Zhou, D. Caldwell, A. B. Subramaniam, S. Haddad, G. G. 2022-11-05 doi:10.1101/2022.11.04.515240 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Whole-body gene expression atlas of an adult metazoan ]]> https://biorxiv.org/content/10.1101/2022.11.06.515345v1?rss=1 Ghaddar, A. Armingol, E. Huynh, C. Gevirtzman, L. Lewis, N. E. Waterston, R. O'Rourke, E. 2022-11-06 doi:10.1101/2022.11.06.515345 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Biophysical modeling of actin-mediated structural plasticity reveals mechanical adaptation in dendritic spines ]]> https://biorxiv.org/content/10.1101/2022.11.06.515372v1?rss=1 Bonilla-Quintana, M. Rangamani, P. 2022-11-06 doi:10.1101/2022.11.06.515372 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Rapid iPSC inclusionopathy models shed light on formation, consequence and molecular subtype of alpha-synuclein inclusions ]]> https://biorxiv.org/content/10.1101/2022.11.08.515615v1?rss=1 Lam, I. Ndayisaba, A. Lewis, A. J. Fu, Y. Sagredo, G. T. Zaccagnini, L. Sandoe, J. Sanz, R. L. Vahdatshoar, A. Martin, T. D. Morshed, N. Ichihashi, T. Tripathi, A. Ramalingam, N. Oettgen-Suazo, C. Bartels, T. Schabinger, M. Hallacli, E. Jiang, X. Verma, A. Tea, C. Wang, Z. Hakozaki, H. Yu, X. Hyles, K. Park, C. Theunissen, T. W. Wang, H. Jaenisch, R. Lindquist, S. Stevens, B. Stefanova, N. Wenning, G. Luk, K. C. Sanchez Pernaute, R. Gomez-Esteban, J. C. Felsky, D. Kiyota, Y. Sahni, N. Yi, S. S. Chung, C.-Y. Stahlberg, H. Ferrer, I. Schoneberg, J. Ell 2022-11-09 doi:10.1101/2022.11.08.515615 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2022.11.09.512793v1?rss=1 Kobayashi-Ishihara, M. Smutna, K. F. Alonso, F. E. Argilaguet, J. Esteve-Codina, A. Geiger, K. Genesca, M. Grau-Exposito, J. Duran-Castells, C. Rogenmoser, S. Böttcher, R. Jungfleisch, J. Oliva, B. Martinez, J. P. Li, M. David, M. Yamagishi, M. Ruiz-Riol, M. Brander, C. Tsunetsugu-Yokota, Y. Buzon, M. J. Diez, J. Meyerhans, A. 2022-11-09 doi:10.1101/2022.11.09.512793 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ A comparative atlas of single-cell chromatin accessibility in the human brain ]]> https://biorxiv.org/content/10.1101/2022.11.09.515833v1?rss=1 Li, Y. E. Preissl, S. Miller, M. Johnson, N. D. Wang, Z. Jiao, H. Zhu, C. Wang, Z. Xie, Y. Poirin, O. Kern, C. Pinto-Duarte, A. Tian, W. Siletti, K. Emerson, N. Osteen, J. Lucero, J. Lin, L. Yang, Q. Espinoza, S. Zhu, Q. Zemke, N. Yanny, A. M. Nyhus, J. Dee, N. Casper, T. Shapovalova, N. Hirschstein, D. Hodge, R. D. Linnarsson, S. Bakken, T. E. Levi, B. Keene, C. D. Shang, J. Lein, E. S. Wang, A. Behrens, M. M. Ecker, J. R. Ren, B. 2022-11-10 doi:10.1101/2022.11.09.515833 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations ]]> https://biorxiv.org/content/10.1101/2022.11.10.516058v1?rss=1 Ojha, A. A. Srivastava, A. Votapka, L. Amaro, R. E. 2022-11-12 doi:10.1101/2022.11.10.516058 Cold Spring Harbor Laboratory Press 2022-11-12 <![CDATA[ Inferring a cell's capabilities from omics data with ImmCellFie ]]> https://biorxiv.org/content/10.1101/2022.11.16.516672v1?rss=1 Masson, H. O. Borland, D. Reilly, J. Telleria, A. Shrivastava, S. Watson, M. Bustillo, L. Li, Z. Capps, L. Kellman, B. P. King, Z. A. Richelle, A. Lewis, N. E. Robasky, K. 2022-11-17 doi:10.1101/2022.11.16.516672 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cas9-mediated tagging of endogenous loci using HITAG ]]> https://biorxiv.org/content/10.1101/2022.11.16.516691v1?rss=1 Kim, J. Kratz, A. Sheng, J. Zhang, L. Singh, B. K. Chavez, A. 2022-11-17 doi:10.1101/2022.11.16.516691 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD ]]> https://biorxiv.org/content/10.1101/2022.11.17.516859v1?rss=1 Li, J. Jaiswal, M. K. Chien, J.-F. Kozlenkov, A. Zhou, P. Gardashli, M. Pregent, L. J. Engelberg-Cook, E. Dickson, D. W. Belzil, V. V. Mukamel, E. A. Dracheva, S. 2022-11-17 doi:10.1101/2022.11.17.516859 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Adult consequences of repeated nicotine vapor inhalation in adolescent rats ]]> https://biorxiv.org/content/10.1101/2022.11.17.516984v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Grant, Y. Taffe, M. A. 2022-11-18 doi:10.1101/2022.11.17.516984 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Plasmodium exoerythrocytic parasites redirect trafficking of human proteins to the parasitophorous vacuole ]]> https://biorxiv.org/content/10.1101/2022.11.22.517223v1?rss=1 Calla, J. Mittal, N. LaMonte, G. Liffner, B. Godinez-Macias, K. Carolino, K. Walker, G. T. Zou, B. Y. Paytas, E. Guerra, L. Tong-Rios, C. Campo, B. Vinetz, J. M. Gamboa, D. Raffatellu, M. Absalon, S. Winzeler, E. 2022-11-23 doi:10.1101/2022.11.22.517223 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Structure of LRRK1 and mechanisms of autoinhibition and activation ]]> https://biorxiv.org/content/10.1101/2022.11.22.517582v1?rss=1 Reimer, J. M. Dickey, A. M. Lin, Y. X. Abrisch, R. G. Mathea, S. Chatterjee, D. Fay, E. J. Daugherty, M. D. Reck-Peterson, S. L. Leschziner, A. E. 2022-11-23 doi:10.1101/2022.11.22.517582 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Cross-species analysis identifies conserved transcriptional mechanisms of neutrophil maturation ]]> https://biorxiv.org/content/10.1101/2022.11.28.518146v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@d46deaorg.highwire.dtl.DTLVardef@7c2647org.highwire.dtl.DTLVardef@b535eeorg.highwire.dtl.DTLVardef@e7dc38_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kirchberger, S. Shoeb, M. R. Lazic, D. Fischer, K. Shaw, L. E. Nogueira, F. Rifatbegovic, F. Bozsaky, E. Ladenstein, R. Bodenmiller, B. Lion, T. Traver, D. Farlik, M. Taschner-Mandl, S. Halbritter, F. Distel, M. 2022-11-28 doi:10.1101/2022.11.28.518146 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ A new theoretical framework jointly explains behavioral and neural variability across subjects performing flexible decision-making ]]> https://biorxiv.org/content/10.1101/2022.11.28.518207v1?rss=1 Pagan, M. Tang, V. D. Aoi, M. C. Pillow, J. W. Mante, V. Sussillo, D. Brody, C. D. 2022-11-28 doi:10.1101/2022.11.28.518207 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ The complete sequence of a human Y chromosome ]]> https://biorxiv.org/content/10.1101/2022.12.01.518724v1?rss=1 Rhie, A. Nurk, S. Cechova, M. Hoyt, S. J. Taylor, D. J. Altemose, N. Hook, P. W. Koren, S. Rautiainen, M. Alexandrov, I. A. Allen, J. Asri, M. Bzikadze, A. V. Chen, N.-C. Chin, C.-S. Diekhans, M. Flicek, P. Formenti, G. Fungtammasan, A. Garcia Giron, C. Garrison, E. Gershman, A. Gerton, J. Grady, P. G. Guarracino, A. Haggerty, L. Halabian, R. Hansen, N. F. Harris, R. Hartley, G. A. Harvey, W. T. Haukness, M. Heinz, J. Hourlier, T. Hubley, R. M. Hunt, S. E. Hwang, S. Jain, M. Kesharwani, R. K. Lewis, A. P. Li, H. Logsdon, G. A. Lucas, J. K. Makalowski, 2022-12-01 doi:10.1101/2022.12.01.518724 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding ]]> https://biorxiv.org/content/10.1101/2022.12.02.518910v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@167b370org.highwire.dtl.DTLVardef@135b62dorg.highwire.dtl.DTLVardef@14b5e9forg.highwire.dtl.DTLVardef@1311e84_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementA Golgi-localized molecular circuitry has been recently implicated in the orchestration of secrete-and-sense auto-/paracrine loops that impart self-sufficiency in growth signaling, a.k.a., growth signaling autonomy. Using a transdisciplinary approach, this work shows that growth signaling autonomy is uniquely induced in tumor cells that are in circulation. Circulating tumor cells (CTCs) represent a brutish and risky phase in the lifetime of tumor cells when they are exposed to the immune system and hemodynamic sheer forces, all in the setting of growth factor starvation. Cancer cells appear to rely on the autonomy circuit to survive and enhance their fitness to seed metastases. Autonomy generates the kind of eat-what-you-kill entrepreneurial spirit which minimizes the risk of CTCs dying on an otherwise risky journey. ]]> Sinha, S. Farfel, A. Luker, K. E. Sahoo, D. Parker, B. A. Yeung, K. Luker, G. D. Ghosh, P. 2022-12-05 doi:10.1101/2022.12.02.518910 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Nanoscaled discovery of a shunt rifamycin from Salinispora arenicola using a three-colour GFP-tagged Staphylococcus aureus macrophage infection assay. ]]> https://biorxiv.org/content/10.1101/2022.12.04.519019v1?rss=1 Pham, N. T. Alves, J. Sargison, F. A. Cullum, R. Wildenhain, J. Fenical, W. Butler, M. S. Mead, D. Duggan, B. M. Fitzgerald, J. R. La Clair, J. J. Auer, M. 2022-12-04 doi:10.1101/2022.12.04.519019 Cold Spring Harbor Laboratory Press 2022-12-04 <![CDATA[ Deciphering the determinants of recombinant protein yield across the human secretome ]]> https://biorxiv.org/content/10.1101/2022.12.12.520152v1?rss=1 Masson, H. O. Kuo, C.-C. Malm, M. Lundqvist, M. Sivertsson, A. Berling, A. Tegel, H. Hober, S. Uhlen, M. Grassi, L. Hatton, D. Rockberg, J. Lewis, N. E. 2022-12-14 doi:10.1101/2022.12.12.520152 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening ]]> https://biorxiv.org/content/10.1101/2022.12.13.520335v1?rss=1 Kim, S. H. Shin, S. Baek, M. Xiong, K. Karottki, K. J. l. C. Hefzi, H. Grav, L. M. Pedersen, L. E. Kildegaard, H. F. Lewis, N. E. Lee, J. S. Lee, G. M. 2022-12-14 doi:10.1101/2022.12.13.520335 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data ]]> https://biorxiv.org/content/10.1101/2022.12.16.520793v1?rss=1 Lee, L. Yu, H. Jia, B. B. Jussila, A. Zhu, C. Chen, J. Xie, L. Hafner, A. Strambio-De-Castillia, C. Boettiger, A. Ren, B. Li, Y. Hu, M. 2022-12-19 doi:10.1101/2022.12.16.520793 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ The ins and outs of membrane bending by intrinsically disordered proteins ]]> https://biorxiv.org/content/10.1101/2022.12.17.520884v1?rss=1 Yuan, F. Houser, J. Sangani, A. Wang, L. Lafer, E. Rangamani, P. Stachowiak, J. 2022-12-17 doi:10.1101/2022.12.17.520884 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.12.17.520895v1?rss=1 Wirthlin, M. E. Schmid, T. A. Elie, J. E. Zhang, X. Shvareva, V. A. Rakuljic, A. Ji, M. B. Bhat, N. S. Kaplow, I. M. Schäffer, D. E. Lawler, A. J. Annaldasula, S. Lim, B. Azim, E. Zoonomia Consortium, Meyer, W. K. Yartsev, M. M. Pfenning, A. R. 2022-12-18 doi:10.1101/2022.12.17.520895 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Greengenes2 enables a shared data universe for microbiome studies ]]> https://biorxiv.org/content/10.1101/2022.12.19.520774v1?rss=1 McDonald, D. Jiang, Y. Balaban, M. Cantrell, K. Zhu, Q. Gonzalez, A. Morton, J. T. Nicolaou, G. Parks, D. Karst, S. M. Albertsen, M. Hugenholtz, P. DeSantis, T. Mirarab, S. Knight, R. 2022-12-20 doi:10.1101/2022.12.19.520774 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study ]]> https://biorxiv.org/content/10.1101/2022.12.20.521181v1?rss=1 View larger version (65K): org.highwire.dtl.DTLVardef@1e7eadcorg.highwire.dtl.DTLVardef@ec127eorg.highwire.dtl.DTLVardef@b21f14org.highwire.dtl.DTLVardef@1690c5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tissink, E. Shadrin, A. A. van der Meer, D. Parker, N. Hindley, G. Roelfs, D. Frei, O. Fan, C. C. Nagel, M. Naerland, T. Budisteanu, M. Djurovic, S. Westlye, L. T. van den Heuvel, M. Posthuma, D. Kaufmann, T. Dale, A. M. Andreassen, O. 2022-12-20 doi:10.1101/2022.12.20.521181 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance ]]> https://biorxiv.org/content/10.1101/2022.12.20.521246v1?rss=1 View larger version (83K): org.highwire.dtl.DTLVardef@187f455org.highwire.dtl.DTLVardef@ba0798org.highwire.dtl.DTLVardef@148b175org.highwire.dtl.DTLVardef@17a8f8c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rychel, K. Tan, J. Patel, A. Lamoureux, C. Hefner, Y. Szubin, R. Johnsen, J. Mohamed, E. T. T. Phaneuf, P. V. Anand, A. Olson, C. A. Park, J. H. Sastry, A. V. Yang, L. Feist, A. M. Palsson, B. O. 2022-12-23 doi:10.1101/2022.12.20.521246 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function ]]> https://biorxiv.org/content/10.1101/2022.12.22.521485v1?rss=1 Parra-Rivas, L. A. Madhivanan, K. Wang, L. Boyer, N. P. Prakashchand, D. D. Aulston, B. D. Pizzo, D. P. Branes-Guerrero, K. Tang, Y. Das, U. Scott, D. A. Rangamani, P. Roy, S. 2022-12-23 doi:10.1101/2022.12.22.521485 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ An Activity-Based Nanosensor for Minimally-Invasive Measurement of Protease Activity in Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2022.12.26.521967v1?rss=1 Kudryashev, J. A. Madias, M. I. Kandell, R. M. Lin, Q. X. Kwon, E. J. 2022-12-27 doi:10.1101/2022.12.26.521967 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Structural damping renders the insect exoskeleton mechanically insensitive to non-sinusoidal deformations ]]> https://biorxiv.org/content/10.1101/2022.12.27.522009v1?rss=1 Wold, E. Lynch, J. Gravish, N. Sponberg, S. 2022-12-27 doi:10.1101/2022.12.27.522009 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories ]]> https://biorxiv.org/content/10.1101/2022.12.27.522024v1?rss=1 Fang, J. Castillon, G. Phan, S. McArdle, S. Hariharan, C. Ellisman, M. H. Deniz, A. A. Saphire, E. O. 2022-12-27 doi:10.1101/2022.12.27.522024 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Predicting alcohol-related memory problems in older adults: A machine learning study with multi-domain features ]]> https://biorxiv.org/content/10.1101/2022.12.30.522330v1?rss=1 Kamarajan, C. Pandey, A. K. Chorlian, D. B. Meyers, J. L. Kinreich, S. Pandey, G. Subbie Saenz de Viteri, S. Zhang, J. Kuang, W. Barr, P. B. Aliev, F. Anokhin, A. P. Plawecki, M. H. Kuperman, S. Almasy, L. Merikangas, A. Brislin, S. J. Bauer, L. Hesselbrock, V. Chan, G. Kramer, J. Lai, D. Hartz, S. Bierut, L. J. McCutcheon, V. V. Bucholz, K. K. Dick, D. M. Schuckit, M. A. Edenberg, H. J. Porjesz, B. 2023-01-02 doi:10.1101/2022.12.30.522330 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Functional pathways for metabolic network-based data analysis: the MetPath algorithm ]]> https://biorxiv.org/content/10.1101/202226v1?rss=1 Mattei, G. Zielinski, D. C. Gan, Z. Ramazzotti, M. Palsson, B. O. 2017-10-12 doi:10.1101/202226 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data ]]> https://biorxiv.org/content/10.1101/2023.01.05.522928v1?rss=1 Moshiri, N. 2023-01-06 doi:10.1101/2023.01.05.522928 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Supramolecular fibrous hydrogel augmentation of uterosacral ligament suspension for treatment of pelvic organ prolapse ]]> https://biorxiv.org/content/10.1101/2023.01.08.522930v1?rss=1 Miller, B. Wolfe, W. Gentry, J. L. Grewal, M. G. Highley, C. B. De Vita, R. Vaughan, M. H. Caliari, S. R. 2023-01-09 doi:10.1101/2023.01.08.522930 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ High-dimensional phenotyping to define the genetic basis of cellular morphology ]]> https://biorxiv.org/content/10.1101/2023.01.09.522731v1?rss=1 Tegtmeyer, M. Arora, J. Asgari, S. Cimini, B. A. Peirent, E. Liyanage, D. Way, G. P. Weisbart, E. Nathan, A. Amariuta, T. Eggan, K. Haghighi, M. McCarroll, S. A. Carpenter, A. E. Singh, S. Nehme, R. Raychaudhuri, S. 2023-01-09 doi:10.1101/2023.01.09.522731 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Low Rate Hippocampal Delay Period Activity Encodes Behavioral Experience ]]> https://biorxiv.org/content/10.1101/2023.01.09.523199v1?rss=1 Athanasiadis, M. Masserini, S. Yuan, L. Fetterhoff, D. Leutgeb, J. K. Leutgeb, S. Leibold, C. 2023-01-09 doi:10.1101/2023.01.09.523199 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes ]]> https://biorxiv.org/content/10.1101/2023.01.09.523365v1?rss=1 Singh, H. W. Creamer, K. E. Chase, A. B. Klau, L. J. Podell, S. Jensen, P. R. 2023-01-10 doi:10.1101/2023.01.09.523365 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Distinguishing response from stimulus driven history biases ]]> https://biorxiv.org/content/10.1101/2023.01.11.523637v1?rss=1 Sheehan, T. C. Serences, J. T. 2023-01-13 doi:10.1101/2023.01.11.523637 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Automated quantitative trait locus analysis (AutoQTL) ]]> https://biorxiv.org/content/10.1101/2023.01.12.523835v1?rss=1 Freda, P. J. Ghosh, A. Zhang, E. Luo, T. Chitre, A. Polesskaya, O. St. Pierre, C. L. Gao, J. Martin, C. D. Chen, H. Garcia-Martinez, A. G. Wang, T. Han, W. Ishiwari, K. Meyer, P. Lamparelli, A. King, C. P. Palmer, A. A. Li, R. Moore, J. H. 2023-01-15 doi:10.1101/2023.01.12.523835 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ The mitochondrial multi-omic response to exercise training across tissues ]]> https://biorxiv.org/content/10.1101/2023.01.13.523698v1?rss=1 Amar, D. Gay, N. R. Jimenez-Morales, D. Jean Beltran, P. M. Ramaker, M. E. Natarajan Raja, A. Zhao, B. Sun, Y. Marwaha, S. Gaul, D. Hershman, S. G. Xia, A. Lanza, I. Fernandez, F. M. Montgomery, S. B. Hevener, A. L. Ashley, E. Walsh, M. J. Sparks, L. M. Burant, C. F. Rector, R. S. Thyfault, J. Wheeler, M. T. Goodpaster, B. H. Coen, P. M. Schenk, S. Bodine, S. C. Lindholm, M. E. MoTrPAC Study Group, 2023-01-13 doi:10.1101/2023.01.13.523698 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.01.15.524171v1?rss=1 Lazetic, V. Blanchard, M. J. Bui, T. Troemel, E. R. 2023-01-18 doi:10.1101/2023.01.15.524171 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Bridging Big Data: Procedures for Combining Non-equivalent Cognitive Measures from the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/2023.01.16.524331v1?rss=1 Kennedy, E. Vadlamani, S. Lindsey, H. M. Lei, P.-W. Pugh, M. J. Adamson, M. Alda, M. Alonso-Lana, S. Ambrogi, S. Anderson, T. J. Arango, C. Asarnow, R. Avram, M. Ayesa-Arriola, R. Babikian, T. Banaj, N. Bird, L. J. Borgwardt, S. Brodtmann, A. Brosch, K. Caeyenberghs, K. Calhoun, V. D. Chiaravalloti, N. D. Cifu, D. X. Crespo-Facorro, B. Dalrymple-Alford, J. C. Dams-O'Connor, K. Dannlowski, U. Darby, D. Davenport, N. DeLuca, J. Diaz-Caneja, C. M. Disner, S. G. Dobryakova, E. Ehrlich, S. Esopenko, C. Ferrarelli, F. Frank, L. E. Franz, C. Fuentes-Claramonte, 2023-01-19 doi:10.1101/2023.01.16.524331 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Mixed Lineage Leukemia (Mll1) establishes global histone H3K4 trimethylation and stem like memory Cd8 T cell formation ]]> https://biorxiv.org/content/10.1101/2023.01.18.524461v1?rss=1 Getzler, A. J. Frederick, M. A. Diao, H. Milner, J. J. Belanger, S. Chen, R. Tsuda, S. M. Albao, D. Kim, J. Crotty, S. Goldrath, A. Pipkin, M. E. 2023-01-20 doi:10.1101/2023.01.18.524461 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures ]]> https://biorxiv.org/content/10.1101/2023.01.22.525049v1?rss=1 Kleven, H. Gillespie, T. H. Zehl, L. Dickscheid, T. Bjaalie, J. G. Martone, M. E. Leergaard, T. B. 2023-01-23 doi:10.1101/2023.01.22.525049 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Neurophysiological signatures of cortical micro-architecture ]]> https://biorxiv.org/content/10.1101/2023.01.23.525101v1?rss=1 Shafiei, G. Fulcher, B. D. Voytek, B. Satterthwaite, T. D. Baillet, S. Misic, B. 2023-01-23 doi:10.1101/2023.01.23.525101 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase ]]> https://biorxiv.org/content/10.1101/2023.01.23.525207v1?rss=1 Tota, E. M. Devaraj, N. K. 2023-01-23 doi:10.1101/2023.01.23.525207 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing ]]> https://biorxiv.org/content/10.1101/2023.01.24.525307v1?rss=1 Kleninfeld, D. Yao, P. Liu, R. Thunemann, M. Boggini, T. 2023-01-24 doi:10.1101/2023.01.24.525307 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways ]]> https://biorxiv.org/content/10.1101/2023.01.26.525555v1?rss=1 Monda, J. K. Ge, X. Hunkeler, M. Donovan, K. A. Ma, M. W. Jin, C. Y. Leonard, M. Fischer, E. S. Bennett, E. J. 2023-01-26 doi:10.1101/2023.01.26.525555 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Normative Modeling of Brain Morphometry Across the Lifespan using CentileBrain: Algorithm Benchmarking and Model Optimization ]]> https://biorxiv.org/content/10.1101/2023.01.30.523509v1?rss=1 Ge, R. Yu, Y. Qi, Y. X. Fan, Y. V. Chen, S. Gao, C. Haas, S. S. Modabbernia, A. New, F. Agartz, I. Asherson, P. Ayesa-Arriola, R. Banaj, N. Banaschewski, T. Baumeister, S. Bertolino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buckner, R. Buitelaar, J. K. Cannon, D. M. Caseras, X. Cervenka, S. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Haan, L. de Zubicaray, G. I. Di Giorgio, A. Erk, S. Fisher, S. E. Franke, B. Frodl, T. Glahn, D. C. Grotegerd, D. Gruber, O. Gruner, P. Gur, R. E. G 2023-01-31 doi:10.1101/2023.01.30.523509 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages ]]> https://biorxiv.org/content/10.1101/2023.01.30.526059v1?rss=1 Chen, H. I. Turakhia, Y. Bejerano, G. Kingsley, D. M. 2023-01-31 doi:10.1101/2023.01.30.526059 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations ]]> https://biorxiv.org/content/10.1101/2023.01.30.526328v1?rss=1 20-fold improvement in statistical power over existing methods. We then use BIRDMAn to identify antibiotic-mediated perturbations undetected by other DA methods due to subject-level heterogeneity. Finally, we demonstrate how BIRDMAn can construct state-of-the-art cancer-type classifiers using The Cancer Genome Atlas (TCGA) dataset, with substantial accuracy improvements over random forests and existing DA tools across multiple sequencing centers. Collectively, BIRDMAn extracts more informative biological signals while accounting for study-specific experimental conditions than existing approaches. ]]> Rahman, G. Morton, J. T. Martino, C. Sepich-Poore, G. D. Allaband, C. Guccione, C. Chen, Y. Hakim, D. Estaki, M. Knight, R. 2023-02-02 doi:10.1101/2023.01.30.526328 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ B3GALT6 Promotes Dormant Breast Cancer Cell Survival and Recurrence by Enabling Heparan Sulfate-Mediated FGF Signaling ]]> https://biorxiv.org/content/10.1101/2023.01.31.526529v1?rss=1 Sreekumar, A. Lu, M. Choudhury, B. Pan, T.-c. Pant, D. K. Sterner, C. J. Belka, G. K. Toriumi, T. Benz, B. Escobar-Aguirre, M. Marino, F. E. Esko, J. D. Chodosh, L. A. 2023-02-03 doi:10.1101/2023.01.31.526529 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE ]]> https://biorxiv.org/content/10.1101/2023.02.01.526488v1?rss=1 Chongsaritsinsuk, J. Steigmeyer, A. D. Mahoney, K. E. Rosenfeld, M. A. Lucas, T. M. Ince, D. Kearns, F. L. Battison, A. S. Hollenhorst, M. A. Shon, J. Tiemeyer, K. H. Attah, V. Kwon, C. Bertozzi, C. R. Ferracane, M. J. Amaro, R. E. Malaker, S. A. 2023-02-03 doi:10.1101/2023.02.01.526488 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Force transmission and SUN-KASH higher-order assembly in the LINC complex models ]]> https://biorxiv.org/content/10.1101/2023.02.02.526920v1?rss=1 Yerima, G. Domkam, N. Ornowski, J. Jahed, Z. Mofrad, M. R. K. 2023-02-03 doi:10.1101/2023.02.02.526920 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal ]]> https://biorxiv.org/content/10.1101/2023.02.03.526066v1?rss=1 Kudtarkar, P. Costanzo, M. Sun, Y. Jang, D. Koesterer, R. Mychaleckyj, J. C. Nayak, U. Onengut-Gumuscu, S. Rich, S. S. Flannick, J. A. Gaulton, K. J. Burtt, N. P. 2023-02-05 doi:10.1101/2023.02.03.526066 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ An integrated map of cell type-specific gene expression in pancreatic islets ]]> https://biorxiv.org/content/10.1101/2023.02.03.526994v1?rss=1 Elgamal, R. Kudtarkar, P. Melton, R. Mummey, H. Benaglio, P. Okino, M.-L. Gaulton, K. J. 2023-02-04 doi:10.1101/2023.02.03.526994 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue ]]> https://biorxiv.org/content/10.1101/2023.02.03.527012v1?rss=1 Many, G. M. Sanford, J. A. Sagendorf, T. J. Hou, Z. Nigro, P. Whytock, K. L. Amar, D. Caputo, T. Gay, N. R. Gaul, D. A. Hirshman, M. F. Jimenez-Morales, D. Lindholm, M. E. Muehlbauer, M. J. Vamvini, M. Bergman, B. C. Fernandez, F. M. Goodyear, L. J. Ortlund, E. A. Sparks, L. M. Xia, A. Adkins, J. N. Bodine, S. C. Newgard, C. B. Schenk, S. Study Group, T. M. 2023-02-04 doi:10.1101/2023.02.03.527012 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator ]]> https://biorxiv.org/content/10.1101/2023.02.03.527015v1?rss=1 Khandekar, A. Vangara, R. Barnes, M. Diaz-Gay, M. Abbasi, A. Bergstrom, E. N. Steele, C. D. Pillay, N. Alexandrov, L. B. 2023-02-04 doi:10.1101/2023.02.03.527015 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Curing GFP-itis in Bacteria with Base Editors: Development of a Genome Editing Science Program Implemented with High School Biology Students ]]> https://biorxiv.org/content/10.1101/2023.02.06.527367v1?rss=1 Vasquez, C. A. Evanoff, M. Ranzau, B. L. Gu, S. Deters, E. Komor, A. C. 2023-02-07 doi:10.1101/2023.02.06.527367 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Exploring the consequences of redirecting an exocytic Rab onto endocytic vesicles. ]]> https://biorxiv.org/content/10.1101/2023.02.09.527811v1?rss=1 Novick, P. J. Li, X. Liu, D. Griffis, E. 2023-02-10 doi:10.1101/2023.02.09.527811 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Generative Molecular Design and Experimental Validation of Selective Histamine H1 Inhibitors ]]> https://biorxiv.org/content/10.1101/2023.02.14.528391v1?rss=1 McLoughlin, K. S. Shi, D. Mast, J. E. Bucci, J. Williams, J. P. Jones, W. D. Miyao, D. Nam, L. Osswald, H. L. Zegelman, L. Allen, J. E. Bennion, B. J. Paulson, A. K. Abagyan, R. Head, M. S. Brase, J. M. 2023-02-16 doi:10.1101/2023.02.14.528391 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Selective loss of specific subsets of hair cell and spiral ganglion cell types in an outbred mouse model of age-related hearing loss ]]> https://biorxiv.org/content/10.1101/2023.02.15.528661v1?rss=1 Boussaty, E. C. Tedeschi, N. Novotny, M. Ninoyu, Y. Du, E. Draf, C. Zhang, Y. Scheuermann, R. H. Friedman, R. A. 2023-02-15 doi:10.1101/2023.02.15.528661 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2023.02.16.528701v1?rss=1 De Jesus, D. F. Zhang, Z. Brown, N. K. Li, X. Gaffrey, M. J. Kahraman, S. Wei, J. Hu, J. Basile, G. Xiao, L. Rana, T. M. Mathews, C. E. Powers, A. C. Atkinson, M. A. Eizirik, D. L. Dhe-Paganon, S. Parent, A. V. Qian, W.-J. He, C. Kulkarni, R. N. 2023-02-16 doi:10.1101/2023.02.16.528701 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Tracking and curating putative SARS-CoV-2 recombinants with RIVET ]]> https://biorxiv.org/content/10.1101/2023.02.17.529036v1?rss=1 Smith, K. Ye, C. Turakhia, Y. 2023-02-19 doi:10.1101/2023.02.17.529036 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Next-generation CRISPR gene-drive systems using Cas12a nuclease ]]> https://biorxiv.org/content/10.1101/2023.02.20.529271v1?rss=1 Sanz Juste, S. Okamoto, E. M. Feng, X. Del Amo, V. L. 2023-02-20 doi:10.1101/2023.02.20.529271 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Proteome allocation is linked to transcriptional regulation through a modularized transcriptome ]]> https://biorxiv.org/content/10.1101/2023.02.20.529291v1?rss=1 Patel, A. McGrosso, D. Hefner, Y. Campeau, A. Sastry, A. V. Maurya, S. Rychel, K. Gonzalez, D. J. Palsson, B. O. 2023-02-21 doi:10.1101/2023.02.20.529291 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Release of extracellular matrix components after human traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2023.02.23.529754v1?rss=1 Bambrick, M. Johnson, M. D. Esko, J. D. Choudhury, B. Gomez Toledo, A. Staley, K. J. Duhaime, A.-C. 2023-02-24 doi:10.1101/2023.02.23.529754 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Atypical Chemokine Receptor 3 'Senses' CXC Chemokine Receptor 4 Activation Through GPCR Kinase Phosphorylation ]]> https://biorxiv.org/content/10.1101/2023.02.25.530029v1?rss=1 Schafer, C. T. Chen, Q. Tesmer, J. J. G. Handel, T. M. 2023-02-26 doi:10.1101/2023.02.25.530029 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Small Molecule in situ Resin Capture - an Organism Independent Strategy for Natural Product Discovery. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530684v1?rss=1 Bogdanov, A. Salib, M. N. Chase, A. B. Hammerlindl, H. Muskat, M. N. Luedtke, S. O'Donoghue, A. J. Wu, L. F. Altschuler, S. J. Molinski, T. F. Jensen, P. R. 2023-03-03 doi:10.1101/2023.03.02.530684 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ CD4+ T cells display a spectrum of recall dynamics during re-infection with malaria parasites. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530907v1?rss=1 Lee, H. J. Moreira, M. d. L. Li, S. Williams, C. G. Skinner, O. P. Asad, S. Asatsuma, T. Bramhall, M. L. Jiang, Z. Engel, J. A. Soon, M. S. F. Straube, J. Barrera, I. Murray, E. Chen, F. Nideffer, J. F. Jagannathan, P. Haque, A. 2023-03-03 doi:10.1101/2023.03.02.530907 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Light-Guided Rabies Virus Tracing for Neural Circuit Analysis ]]> https://biorxiv.org/content/10.1101/2023.03.04.531104v1?rss=1 Zhang, S. Ma, Y. Ngamkanjanarat, W. Takahashi, S. Gibbs, D. Coleman, T. Doan, S. Kyriakakis, P. 2023-03-06 doi:10.1101/2023.03.04.531104 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Chromatin binding by HORMAD proteins regulates meiotic recombination initiation ]]> https://biorxiv.org/content/10.1101/2023.03.04.531117v1?rss=1 Milano, C. R. Ur, S. N. Gu, Y. Tromer, E. C. Zhang, J. Hochwagen, A. Corbett, K. D. 2023-03-05 doi:10.1101/2023.03.04.531117 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method ]]> https://biorxiv.org/content/10.1101/2023.03.05.531179v1?rss=1 Mikhaylov, V. Rzepka, M. Kawamura, T. Xia, Y. Chang, P. L. Zhou, S. Pham, L. Modi, N. Yao, L. Perez-Agustin, A. Pagans, S. Boles, T. C. Lei, M. Wang, Y. Garcia-Bassets, I. Chen, Z. 2023-03-06 doi:10.1101/2023.03.05.531179 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ FBP1 is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness ]]> https://biorxiv.org/content/10.1101/2023.03.05.531181v1?rss=1 Gu, L. Zhu, Y. Watari, K. Lee, M. Liu, J. Perez, S. Thai, M. Mayfield, J. Zhang, B. Rocha, K. C. e. Li, F. Kim, L. Jones, A. C. Wierzbicki, I. H. Liu, X. Newton, A. C. Kisseleva, T. Lee, J. H. Ying, W. Gonzalez, D. J. Saltiel, A. Simon, M. C. Karin, M. 2023-03-05 doi:10.1101/2023.03.05.531181 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors ]]> https://biorxiv.org/content/10.1101/2023.03.06.531398v1?rss=1 Lange, M. Granados, A. VijayKumar, S. Bragantini, J. Ancheta, S. Santhosh, S. Borja, M. Kobayashi, H. McGeever, E. Solak, A. C. Yang, B. Zhao, X. Liu, Y. Detweiler, A. Paul, S. Mekonen, H. Lao, T. Banks, R. Jacobo, A. Balla, K. Awayan, K. D'souza, S. Haase, R. Dizeux, A. Pourquie, O. Gomez-Sjoberg, R. Huber, G. Serra, M. Neff, N. Pisco, A. Royer, L. A. 2023-03-07 doi:10.1101/2023.03.06.531398 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks ]]> https://biorxiv.org/content/10.1101/2023.03.07.531453v1?rss=1 Li, H.-H. Su, M. P. Wu, S.-C. Tsou, H.-H. Chang, M.-C. Cheng, Y.-C. Tsai, K.-N. Wang, H.-W. Chen, G.-H. Tang, C.-K. Chung, P.-J. Tsai, W.-T. Huang, L.-R. Yueh, Y. A. Chen, H.-W. Pan, C.-Y. Akbari, O. Chang, H.-H. Yu, G.-Y. Marshall, J. M. CHEN, C.-H. 2023-03-07 doi:10.1101/2023.03.07.531453 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Synaptic changes in pallidostriatal circuits observed in parkinsonian model triggers abnormal beta synchrony with accurate spatio-temporal properties across the basal ganglia ]]> https://biorxiv.org/content/10.1101/2023.03.07.531640v1?rss=1 40Hz), whereas strong pallidostriatal loops drive low-{beta} (10-15Hz) oscillations. We show that pathophysiological strengthening of striatal and pallidal synapses following dopamine depletion leads to the emergence of synchronized oscillatory activity in the mid-{beta} range with spike-phase relationships between BG neuronal populations in-line with experiments. Furthermore, inhibition of GPe, contrary to STN, abolishes oscillations. Our modeling study uncovers the neural mechanisms underlying PD {beta} oscillations and may thereby guide the future development of therapeutic strategies. Significance statementIn Parkinsons disease, neural activity in subcortical nuclei called the basal ganglia displays abnormal oscillatory synchronization that constitutes an important biomarker for therapeutic effectiveness. The neural mechanisms for the generation of these oscillations remain unknown. Here, in a theoretical neuronal network model strongly constrained by anatomical and physiological data, we show that specific circuit modifications in basal ganglia connectivity during Parkinsons disease lead to the emergence of synchronized oscillatory activity in the network with properties that strongly agree with available experimental evidence. This and future theoretical investigations of the neural mechanisms underlying abnormal neuronal activity in Parkinsons disease are necessary to guide the future development of therapeutic strategies to ameliorate symptoms. ]]> Azizpour Lindi, S. Mallet, N. P. Leblois, A. 2023-03-10 doi:10.1101/2023.03.07.531640 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolopyrimidines as Potential Candidates to Treat Human African Trypanosomiasis ]]> https://biorxiv.org/content/10.1101/2023.03.11.532093v1?rss=1 Monti, L. Liu, L. J. Varricchio, C. Lucero, B. Alle, T. Yang, W. Bem-Shalom, I. Gilson, M. Brunden, K. R. Brancale, A. Caffrey, C. R. Ballatore, C. 2023-03-11 doi:10.1101/2023.03.11.532093 Cold Spring Harbor Laboratory Press 2023-03-11 <![CDATA[ A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics ]]> https://biorxiv.org/content/10.1101/2023.03.11.532245v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1edcea0org.highwire.dtl.DTLVardef@198a3c8org.highwire.dtl.DTLVardef@28d394org.highwire.dtl.DTLVardef@5a9dbb_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefThis work creates a prospectively biobanked phenotyped-genotyped Crohns disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTSO_LIProspectively biobanked CD-organoids recapitulate the disease epithelium in patients C_LIO_LIThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypes C_LIO_LIOne subtype shows impaired microbial clearance, another increased cellular senescence C_LIO_LIPhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics C_LI ]]> Tindle, C. Katkar, G. Fonseca, A. Taheri, S. Lee, J. Maity, P. Sayed, I. Ibeawuchi, S.-R. Vidales, E. Pranadinata, R. Fuller, M. Stec, D. Anandachar, M. S. Perry, K. Lee, H. Ear, J. Boland, B. Sandborn, W. Sahoo, D. Das, S. Ghosh, P. 2023-03-13 doi:10.1101/2023.03.11.532245 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ The landscape of cancer rewired GPCR signaling axes ]]> https://biorxiv.org/content/10.1101/2023.03.13.532291v1?rss=1 Raimondi, F. Arora, C. Matic, M. Rosa, N. D. O. Nemati, L. Clubb, L. Kargas, G. Vukotic, R. Licata, L. Wu, G. Gutkind, J. S. 2023-03-14 doi:10.1101/2023.03.13.532291 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome ]]> https://biorxiv.org/content/10.1101/2023.03.13.532310v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@196aefforg.highwire.dtl.DTLVardef@1bafcadorg.highwire.dtl.DTLVardef@122f502org.highwire.dtl.DTLVardef@35afd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Venkatraman, K. Lee, C. T. Garcia, G. C. Mahapatra, A. Perkins, G. Kim, K.-Y. Pasolli, H. A. Phan, S. Lippincott-Schwartz, J. Ellisman, M. Rangamani, P. Budin, I. 2023-03-15 doi:10.1101/2023.03.13.532310 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.03.16.532226v1?rss=1 Jones, A. C. Kornev, A. P. Weng, J.-H. Manning, G. C. Taylor, S. S. Newton, A. C. 2023-03-16 doi:10.1101/2023.03.16.532226 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Multiomic Analysis of Intercellular Communication through Tumor-Stroma Tunnels in Breast Cancers ]]> https://biorxiv.org/content/10.1101/2023.03.18.533175v1?rss=1 Sinha, S. Callow, B. Farfel, A. Roy, S. Chen, S. Rajendran, S. Buschhaus, J. Luker, K. E. Ghosh, P. Luker, G. D. 2023-03-21 doi:10.1101/2023.03.18.533175 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium ]]> https://biorxiv.org/content/10.1101/2023.03.18.533282v1?rss=1 Dunlap, G. S. Wagner, A. Meednu, N. Zhang, F. Jonsson, A. H. Wei, K. Sakaue, S. Nathan, A. Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (A, Bykerk, V. P. Donlin, L. T. Goodman, S. M. Firestein, G. S. Boyle, D. L. Holers, V. M. Moreland, L. W. Tabechian, D. Pitzalis, C. Filer, A. Raychaudhuri, S. Brenner, M. B. Rao, D. A. Anolik, J. 2023-03-21 doi:10.1101/2023.03.18.533282 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome Study ]]> https://biorxiv.org/content/10.1101/2023.03.21.533195v1?rss=1 Ecklu-Mensah, G. Choo-Kang, C. Maseng, M. G. Donato, S. Bovet, P. Bedu-Addo, K. Plange-Rhule, J. Forrester, T. E. Lambert, E. V. Rae, D. Luke, A. Layden, B. T. O'Keefe, S. Gilbert, J. A. Dugas, L. R. 2023-03-22 doi:10.1101/2023.03.21.533195 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition ]]> https://biorxiv.org/content/10.1101/2023.03.21.533564v1?rss=1 Lee, K. Cho, K. Morey, R. Cook-Andersen, H. 2023-03-23 doi:10.1101/2023.03.21.533564 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Unrecognized Potent Activities of Colistin Against Clinically Important mcr+ Enterobacteriaceae Revealed in Synergy with Host Immunity ]]> https://biorxiv.org/content/10.1101/2023.03.21.533661v1?rss=1 Kumaraswamy, M. Riestra, A. Flores, A. Uchiyama, S. Dahesh, S. Bondsater, G. Nilsson, V. Chang, M. Seo, H. Sakoulas, G. Nizet, V. 2023-03-21 doi:10.1101/2023.03.21.533661 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium ]]> https://biorxiv.org/content/10.1101/2023.03.21.533663v1?rss=1 Cordoza, J. L. Chen, P. Y.-T. Blaustein, L. R. Lima, S. T. Fiore, M. F. Chekan, J. R. Moore, B. S. McKinnie, S. M. K. 2023-03-21 doi:10.1101/2023.03.21.533663 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Flux exponent control predicts metabolic dynamics from network structure ]]> https://biorxiv.org/content/10.1101/2023.03.23.533708v1?rss=1 Xiao, F. Li, J. S. Doyle, J. C. 2023-03-25 doi:10.1101/2023.03.23.533708 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Kinetochore dynein is sufficient to biorient chromosomes and remodel the outer kinetochore ]]> https://biorxiv.org/content/10.1101/2023.03.23.534015v1?rss=1 Prevo, B. Cheerambathur, D. Earnshaw, W. C. Desai, A. 2023-03-24 doi:10.1101/2023.03.23.534015 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Pulmonary vein flow split effects in patient-specific simulations of left atrial flow ]]> https://biorxiv.org/content/10.1101/2023.03.24.534045v1?rss=1 Duran, E. Garcia-Villalba, M. Martinez-Legazpi, P. Gonzalo, A. McVeigh, E. Kahn, A. M. Bermejo, J. Flores, O. del Alamo, J. C. 2023-03-25 doi:10.1101/2023.03.24.534045 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Predicting phenotype to mechanotype relationships in cells based on intra-cellular signaling network ]]> https://biorxiv.org/content/10.1101/2023.03.24.534160v1?rss=1 Karabay, E. T. Turnlund, A. Grear, J. Fraley, S. I. Katira, P. 2023-03-27 doi:10.1101/2023.03.24.534160 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Scaling deep phylogenetic embedding to ultra-large reference trees: a tree-aware ensemble approach ]]> https://biorxiv.org/content/10.1101/2023.03.27.534201v1?rss=1 Jiang, Y. McDonald, D. Knight, R. Mirarab, S. 2023-03-29 doi:10.1101/2023.03.27.534201 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Tools and methods for high-throughput single-cell imaging with the mother machine ]]> https://biorxiv.org/content/10.1101/2023.03.27.534286v1?rss=1 Thiermann, R. Sandler, M. Ahir, G. Sauls, J. T. Schroeder, J. W. Brown, S. D. Le Treut, G. Si, F. Li, D. Wang, J. Jun, S. 2023-03-29 doi:10.1101/2023.03.27.534286 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Hyperconnectivity of two separate long-range cholinergic systems contributes to the reorganization of the brain functional connectivity during nicotine withdrawal in male mice ]]> https://biorxiv.org/content/10.1101/2023.03.29.534836v1?rss=1 Carrette, L. L. G. Kimbrough, A. Davoudian, P. A. Kwan, A. C. Collazo, A. George, O. 2023-03-31 doi:10.1101/2023.03.29.534836 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Role of DNA-DNA sliding friction and non-equilibrium dynamics in viral genome ejection and packaging ]]> https://biorxiv.org/content/10.1101/2023.04.03.535472v1?rss=1 Fizari, M. Keller, N. Jardine, P. J. Smith, D. E. 2023-04-05 doi:10.1101/2023.04.03.535472 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis ]]> https://biorxiv.org/content/10.1101/2023.04.04.535621v1?rss=1 Reich, M. M. Tabor, T. Liefeld, T. joshi, j. Kim, F. Thorvaldsdottir, H. Blankenberg, D. Mesirov, J. P. 2023-04-06 doi:10.1101/2023.04.04.535621 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Development of subunit selective substrates for Trichomonas vaginalis proteasome ]]> https://biorxiv.org/content/10.1101/2023.04.05.535794v1?rss=1 Fajtova, P. Hurysz, B. Miyamoto, Y. Serafim, M. Jiang, Z. Trujillo, D. F. Liu, L. J. Somani, U. Almaliti, J. Myers, S. Caffrey, C. Gerwick, W. H. Kirk, C. J. Boura, E. Eckmann, L. O'Donoghue, A. J. 2023-04-06 doi:10.1101/2023.04.05.535794 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex ]]> https://biorxiv.org/content/10.1101/2023.04.08.536119v1?rss=1 Zemke, N. R. Armand, E. J. Wang, W. Lee, S. Zhou, J. Li, Y. E. Liu, H. Tian, W. Nery, J. R. Castanon, R. G. Bartlett, A. Osteen, J. K. Li, D. Zhuo, X. Xu, V. Miller, M. Krienen, F. M. Zhang, Q. Taskin, N. Ting, J. Feng, G. McCarroll, S. A. Callaway, E. M. Wang, T. Behrens, M. Lein, E. S. Ecker, J. R. Ren, B. 2023-04-08 doi:10.1101/2023.04.08.536119 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Do perineuronal nets stabilize the engram of a synaptic circuit? ]]> https://biorxiv.org/content/10.1101/2023.04.09.536164v1?rss=1 Lev-Ram, V. Palida, S. Deerinck, T. J. Bushong, E. A. Toyoma, B. H. Perez, A. McClatchy, D. B. Prichard, D. R. Savas, J. N. Ellisman, M. H. Yates, J. R. Tsien, R. Y. 2023-04-09 doi:10.1101/2023.04.09.536164 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Diverse Gut Pathogens Exploit the Host Engulfment Pathway via a Conserved Mechanism ]]> https://biorxiv.org/content/10.1101/2023.04.09.536168v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@21dbcorg.highwire.dtl.DTLVardef@ee27ccorg.highwire.dtl.DTLVardef@176f2c4org.highwire.dtl.DTLVardef@3c55e6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Anandachar, M. S. Agyekum, B. Sinha, S. Roy, S. Ibeawuchi, S.-R. Gementera, H. Amamoto, A. Katkar, G. D. Ghosh, P. 2023-04-09 doi:10.1101/2023.04.09.536168 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack ]]> https://biorxiv.org/content/10.1101/2023.04.10.536170v1?rss=1 Nobori, T. Monell, A. Lee, T. A. Zhou, J. Nery, J. R. Ecker, J. R. 2023-04-10 doi:10.1101/2023.04.10.536170 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Spatial proteomics of human diabetic kidney disease, from health to class III ]]> https://biorxiv.org/content/10.1101/2023.04.12.534028v1?rss=1 Kondo, A. McGrady, M. Nallapothula, D. Ali, H. Trevino, A. E. Lam, A. Preska, R. D'Angio, H. B. Wu, Z. Lopez, L. N. Badhesha, H. K. Vargas, C. R. Ramesh, A. Wiegley, N. Han, S. S. Dall'Era, M. Jen, K.-Y. Mayer, A. Afkarian, M. 2023-04-12 doi:10.1101/2023.04.12.534028 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Automatic Discovery of Cognitive Strategies with Tiny Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/2023.04.12.536629v1?rss=1 Ji-An, L. Benna, M. K. Mattar, M. G. 2023-04-13 doi:10.1101/2023.04.12.536629 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Building functional circuits in multispecies brains. ]]> https://biorxiv.org/content/10.1101/2023.04.13.536815v1?rss=1 Throesch, B. Imtiaz, M. K. Munoz-Castaneda, R. Sakurai, M. James, K. N. Rodriguez, A. Martin, G. S. Lippi, G. Kuprianov, S. Wu, Z. Osten, P. Belmonte, J. C. I. Wu, J. Baldwin, K. K. 2023-04-15 doi:10.1101/2023.04.13.536815 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae ]]> https://biorxiv.org/content/10.1101/2023.04.15.537036v1?rss=1 Morrill, S. R. Saha, S. Varki, A. P. Lewis, W. G. Ram, S. Lewis, A. L. 2023-04-15 doi:10.1101/2023.04.15.537036 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain ]]> https://biorxiv.org/content/10.1101/2023.04.16.536509v1?rss=1 Liu, H. Zeng, Q. Zhou, J. Bartlett, A. Wang, B.-A. Berube, P. Tian, W. Kenworthy, M. Altshul, J. Nery, J. R. Chen, H. Castanon, R. G. Zu, S. Li, Y. E. Lucero, J. Osteen, J. K. Pinto-Duarte, A. Lee, J. Rink, J. Cho, S. Emerson, N. Nunn, M. O'Connor, C. Yao, Z. Tasic, B. Smith, K. A. Zeng, H. Luo, C. Dixon, J. R. Ren, B. Behrens, M. M. Ecker, J. R. 2023-04-18 doi:10.1101/2023.04.16.536509 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Incongruence between transcriptional and vascular pathophysiological cell states ]]> https://biorxiv.org/content/10.1101/2023.04.16.537057v1?rss=1 Fernandez-Chacon, M. Muhleder, S. Regano, A. Garcia-Ortega, L. Torroja, C. Lytvyn, M. Sanchez-Munoz, M. S. Casquero-Garcia, V. Camafeita, E. Vazquez, J. Benguria, A. Dopazo, A. Sanchez-Cabo, F. Carter, H. Benedito, R. 2023-04-17 doi:10.1101/2023.04.16.537057 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Distinct blood CD3+ CD14+ T Cell-Monocyte complexes harbor HIV and are dynamic, glucose-dependent, and increased in individuals with glucose intolerance ]]> https://biorxiv.org/content/10.1101/2023.04.24.538020v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@fdc324org.highwire.dtl.DTLVardef@168fc4org.highwire.dtl.DTLVardef@138a9a0org.highwire.dtl.DTLVardef@1087108_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICirculating CD3+ CD14+ T cell-monocyte complexes are higher in individuals with diabetes. C_LIO_LICD3+ CD14+ T cell-monocytes complexes comprise a heterogenous group of functional and dynamic cell-cell interactions. C_LIO_LIThe proportion of CD3+ CD14+ T cell-monocyte complexes is positively associated with fasting blood glucose and negatively with plasma IL-10 levels and CD4+ T regulatory cells. C_LIO_LICD3+ CD14+ T cell-monocyte complexes are metabolically flexible and can utilize both glycolysis and oxidative phosphorylation for their energy requirements. C_LIO_LIIn persons with treated HIV, CD3+ CD14+ T cell-monocytes have more detectable HIV DNA than circulating CD4+ T cells alone. C_LI ]]> Wanjalla, C. N. Simmons, J. Oakes, J. Zhang, X. Nochowivz, C. Priest, S. Bailin, S. S. Watten, C. M. Mashayekhi, M. Beasley, H. K. Wang, J. Meenderink, L. M. Sheng, Q. Stolze, J. Gangula, R. Chopra, A. Gabriel, C. L. Temu, T. Pakala, S. Wilfong, E. M. Gianella, S. Phillips, E. J. Harrison, D. G. Hinton, A. Kalams, S. A. Mallal, S. A. Koethe, J. R. 2023-04-26 doi:10.1101/2023.04.24.538020 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution ]]> https://biorxiv.org/content/10.1101/2023.04.26.538152v1?rss=1 Epstein, H. E. Brown, T. Akinrinade, A. O. McMinds, R. Pollock, F. J. Sonett, D. Smith, S. Bourne, D. G. Carpenter, C. S. Knight, R. Willis, B. L. Medina, M. Lamb, J. B. Thurber, R. V. Zaneveld, J. R. 2023-04-26 doi:10.1101/2023.04.26.538152 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ TorsinA is essential for the timing and localization of neuronal nuclear pore complex biogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.26.538491v1?rss=1 Kim, S. Phan, S. Shaw, T. R. Ellisman, M. H. Veatch, S. L. Barmada, S. J. Pappas, S. S. Dauer, W. T. 2023-04-27 doi:10.1101/2023.04.26.538491 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols ]]> https://biorxiv.org/content/10.1101/2023.04.28.538741v1?rss=1 Forry, S. P. Servetas, S. L. Kralj, J. G. Soh, K. Hadjithomas, M. Carlin, M. de Amorim, M. G. Bartelli, T. F. Bustamante, J. P. Cassol, I. Chalita, M. Dias-Neto, E. Gohl, D. Kazantseva, J. Menzel, P. Moda, B. S. Neuberger-Castillo, L. Nunes, D. Peralta, R. D. Saliou, A. Schwarzer, R. Takenaka, I. K. T. M. Wang, J. Knight, R. Jackson, S. A. 2023-04-28 doi:10.1101/2023.04.28.538741 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by L. iners regardless of HPV status ]]> https://biorxiv.org/content/10.1101/2023.05.05.539619v1?rss=1 Vargas Robles, D. Romaguera, J. Alvarado-Velez, I. Tosado-Rodriguez, E. Dominicci-Maura, A. Sanchez, M. Wiggin, K. Martinez-Ferrer, M. Gilbert, J. A. Forney, L. J. Godoy-Vitorino, F. 2023-05-09 doi:10.1101/2023.05.05.539619 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Robust identification of perturbed cell types in single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.05.06.539326v1?rss=1 Nicol, P. B. Paulson, D. Qian, G. Liu, X. S. Irizarry, R. A. Sahu, A. D. 2023-05-08 doi:10.1101/2023.05.06.539326 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Optogenetic inhibition of Gα signalling alters and regulates circuit functionality and early circuit formation ]]> https://biorxiv.org/content/10.1101/2023.05.06.539674v1?rss=1 Lockyer, J. L. Reading, A. Vicenzi, S. Delandre, C. Marshall, O. J. Gasperini, R. Foa, L. Lin, J. Y.-l. 2023-05-08 doi:10.1101/2023.05.06.539674 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ The subiculum encodes environmental geometry ]]> https://biorxiv.org/content/10.1101/2023.05.07.539721v1?rss=1 Sun, Y. Nitz, D. A. Xu, X. Giocomo, L. M. 2023-05-07 doi:10.1101/2023.05.07.539721 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Molecular signatures associated with successful implantation of the human blastocyst ]]> https://biorxiv.org/content/10.1101/2023.05.09.539763v1?rss=1 Cook-Andersen, H. Chousal, J. N. Srinivasan, S. Lee, K. To, C. Cho, K. Zhang, W. Yeo, A. L. Garzo, V. G. Parast, M. M. Laurent, L. C. 2023-05-09 doi:10.1101/2023.05.09.539763 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection ]]> https://biorxiv.org/content/10.1101/2023.05.10.540184v1?rss=1 Bajpe, H. Rychel, K. Lamoureux, C. Sastry, A. V. Palsson, B. O. 2023-05-10 doi:10.1101/2023.05.10.540184 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Generalized fear following acute stress is caused by change in co-transmitter identity of serotonergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.10.540268v1?rss=1 Li, H.-q. L. Jiang, W. Ling, L. Gupta, V. Chen, C. Pratelli, M. Godavarthi, S. K. Spitzer, N. C. 2023-05-11 doi:10.1101/2023.05.10.540268 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.05.16.541025v1?rss=1 Rodionova, I. A. Lim, H. Rodionov, D. A. Hutchison, Y. Dalldorf, C. Gao, Y. Monk, J. Palsson, B. O. 2023-05-16 doi:10.1101/2023.05.16.541025 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family ]]> https://biorxiv.org/content/10.1101/2023.05.16.541042v1?rss=1 Rajput, A. Chauhan, S. M. Mohite, O. S. Hyun, J. C. Ardalani, O. Jahn, L. J. Sommer, M. O. Palsson, B. O. 2023-05-16 doi:10.1101/2023.05.16.541042 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Deep learning and host variable embedding augment microbiome-based simultaneous detection of multiple diseases ]]> https://biorxiv.org/content/10.1101/2023.05.16.541058v1?rss=1 Wu, S. Li, Z. Chen, Y. Zhang, M. Sun, Y. Xing, J. Zhao, F. Huang, S. Knight, R. Su, X. 2023-05-18 doi:10.1101/2023.05.16.541058 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Identification of the bacteriophage nucleus protein interaction network ]]> https://biorxiv.org/content/10.1101/2023.05.18.541317v1?rss=1 Enustun, E. Deep, A. Gu, Y. Nguyen, K. T. Chaikeeratisak, V. Armbruster, E. Ghassemian, M. Villa, E. Pogliano, J. Corbett, K. D. 2023-05-18 doi:10.1101/2023.05.18.541317 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Unsupervised Machine Learning Identifies Chromatin Accessibility Regulatory Networks that Define Cell State Transitions in Pluripotency ]]> https://biorxiv.org/content/10.1101/2023.05.20.541447v1?rss=1 Arthur, T. D. Nguyen, J. P. D'Antonio-Chronowska, A. Matsui, H. Silva, N. Joshua, I. N. iPSCORE Consortium, Young Greenwald, W. W. D'Antonio, M. Pera, M. F. Frazer, K. A. 2023-05-22 doi:10.1101/2023.05.20.541447 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Do cortical co-ripples bind lines, letters, words, meanings, strategy and action in reading? ]]> https://biorxiv.org/content/10.1101/2023.05.20.541597v1?rss=1 12cm), especially when many areas were co-rippling. General co-activation, indexed by non-oscillatory high gamma, was mainly confined to early latencies in fusiform and earlier visual areas, preceding co-ripples. These findings suggest that widespread synchronous co-ripples may assist the integration of multiple cortical areas for sustained periods during cognition. One Sentence SummaryWidespread visual, wordform, semantic, executive and response areas phase-lock at 90Hz during integrative semantic processing. ]]> Garrett, J. C. Verzhbinsky, I. A. Kaestner, E. Carlson, C. Doyle, W. K. Devinsky, O. Thesen, T. Halgren, E. 2023-05-22 doi:10.1101/2023.05.20.541597 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ A pancreatic cancer mouse model with human immunity ]]> https://biorxiv.org/content/10.1101/2023.05.24.542127v1?rss=1 Miyamura, N. Suzuki, K. Friedman, R. A. Floratos, A. Kunisada, Y. Masuda, K. Lowy, A. M. Tsuji, M. Sugahara, K. N. 2023-05-24 doi:10.1101/2023.05.24.542127 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Projectome-defined subtypes and modular intra-hypothalamic subnetworks of peptidergic neurons ]]> https://biorxiv.org/content/10.1101/2023.05.25.542241v1?rss=1 Jiao, Z. Gao, T. Wang, X. Zhang, W. Biglari, N. Boxer, E. E. Steuernagel, L. Ding, X. Yu, Z. Li, M. Hao, M. Zhou, H. Cao, X. Li, S. Jiang, T. Qi, J. Jia, X. Feng, Z. Ren, B. Chen, Y. Shi, X. Wang, D. Wang, X. Han, L. Liang, Y. Wang, C. Li, E. Hu, Y. Tao, Z. Li, H. Xiang, Y. Xu, M. Chang, H.-C. Zhang, Y. Xu, H.-t. Yan, J. Li, A. Luo, Q. Stoop, R. Sternson, S. Bruning, J. C. Poo, M.-m. Anderson, D. J. Gong, H. Sun, Y. Xu, X.-H. 2023-05-25 doi:10.1101/2023.05.25.542241 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Glaucoma-associated Optineurin mutations increase transmitophagy in a vertebrate optic nerve ]]> https://biorxiv.org/content/10.1101/2023.05.26.542507v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@c1d3d4org.highwire.dtl.DTLVardef@13a33e6org.highwire.dtl.DTLVardef@2544beorg.highwire.dtl.DTLVardef@c456a5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jeong, Y. Davis, c.-h. Muscarella, A. Deshpande, V. Kim, K.-Y. Ellisman, M. Marsh-Armstrong, N. 2023-05-30 doi:10.1101/2023.05.26.542507 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses ]]> https://biorxiv.org/content/10.1101/2023.05.26.542519v1?rss=1 Zhao, J. Chen, K. Palsson, B. O. Yang, L. 2023-05-26 doi:10.1101/2023.05.26.542519 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species ]]> https://biorxiv.org/content/10.1101/2023.05.26.542542v1?rss=1 Hyun, J. C. Monk, J. M. Szubin, R. Hefner, Y. Palsson, B. 2023-05-28 doi:10.1101/2023.05.26.542542 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Replication initiation in bacteria: precision control based on protein counting ]]> https://biorxiv.org/content/10.1101/2023.05.26.542547v1?rss=1 Fu, H. Xiao, F. Jun, S. 2023-05-27 doi:10.1101/2023.05.26.542547 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization ]]> https://biorxiv.org/content/10.1101/2023.05.28.542535v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@553e82org.highwire.dtl.DTLVardef@7add7dorg.highwire.dtl.DTLVardef@637549org.highwire.dtl.DTLVardef@1a9236a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Phan, T. M. Kim, Y. C. Debelouchina, G. Mittal, J. 2023-05-30 doi:10.1101/2023.05.28.542535 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Emergence of Darwinian evolution in Bayesian collectives ]]> https://biorxiv.org/content/10.1101/2023.05.29.542733v1?rss=1 Csillag, M. Giaffar, H. Szathmary, E. Czegel, D. 2023-06-01 doi:10.1101/2023.05.29.542733 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Efficient multi-fidelity computation of blood coagulation under flow ]]> https://biorxiv.org/content/10.1101/2023.05.29.542763v1?rss=1 Guerrero-Hurtado, M. Garcia-Villalba, M. Gonzalo, A. Martinez-Legazpi, P. Kahn, A. M. McVeigh, E. Bermejo, J. del Alamo, J. C. Flores, O. 2023-06-01 doi:10.1101/2023.05.29.542763 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.05.30.542936v1?rss=1 Castillon, G. A. Phan, S. Hu, J. Boassa, D. Adams, S. R. Ellisman, M. H. 2023-05-31 doi:10.1101/2023.05.30.542936 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Cell motility modes are selected by the interplay of mechanosensitive adhesion and membrane tension ]]> https://biorxiv.org/content/10.1101/2023.05.31.543156v1?rss=1 Chen, Y. Saintillan, D. Rangamani, P. 2023-06-01 doi:10.1101/2023.05.31.543156 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ A novel method for tracking nitrogen kinetics in vivo and ex vivo using radioactive nitrogen-13 gas and Positron Emission Tomography ]]> https://biorxiv.org/content/10.1101/2023.06.01.543280v1?rss=1 Ashworth, E. Ogawa, R. Vera, D. R. Lindholm, P. 2023-06-05 doi:10.1101/2023.06.01.543280 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ A Boltzmann model predicts glycan structures from lectin binding ]]> https://biorxiv.org/content/10.1101/2023.06.03.543532v1?rss=1 Yom, A. CHIANG, W.-T. Lewis, N. 2023-06-06 doi:10.1101/2023.06.03.543532 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Activation of the TRIF pathway and downstream targets results in the development of precancerous lesions during infection with Helicobacter. ]]> https://biorxiv.org/content/10.1101/2023.06.04.543598v1?rss=1 Bali, P. Lozano-Pope, I. Hernandez, J. Estrada, M. V. Corr, M. Turner, M. A. Bouvet, M. Benner, C. Obonyo, M. 2023-06-06 doi:10.1101/2023.06.04.543598 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Engineering cell and nuclear morphology on nano topography by contact-free protein micropatterning ]]> https://biorxiv.org/content/10.1101/2023.06.05.543791v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1b3a13dorg.highwire.dtl.DTLVardef@1edbdaorg.highwire.dtl.DTLVardef@1f3e40corg.highwire.dtl.DTLVardef@100d6fc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sarikhani, E. Pushpa Meganathan, D. Rahmani, K. Tsai, C.-T. Marquez-Serrano, A. Li, X. Santoro, F. Cui, B. Hyldgaard Klausen, L. Jahed, Z. 2023-06-07 doi:10.1101/2023.06.05.543791 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle ]]> https://biorxiv.org/content/10.1101/2023.06.06.542650v1?rss=1 Birnbaum, S. K. Cohen, J. D. Belfi, A. Murray, J. I. Adams, J. R. G. Chisholm, A. D. Sundaram, M. V. 2023-06-07 doi:10.1101/2023.06.06.542650 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ The chromatin landscape of healthy and injured cell types in the human kidney ]]> https://biorxiv.org/content/10.1101/2023.06.07.543965v1?rss=1 Gisch, D. L. Brennan, M. Lake, B. B. Basta, J. Keller, M. Melo Ferreira, R. Akilesh, S. Ghag, R. Lu, C. Cheng, Y.-H. Collins, K. S. Parikh, S. V. Rovin, B. H. Robbins, L. Conklin, K. Y. Diep, D. Zhang, B. Knoten, A. Barwinska, D. Asghari, M. Sabo, A. R. Ferkowicz, M. J. Sutton, T. A. Kelly, K. J. De Boer, I. H. Rosas, S. E. Kiryluk, K. Hodgin, J. B. Alakwaa, F. Jefferson, N. Gaut, J. P. Gehlenborg, N. Phillips, C. L. El-Achkar, T. M. Dagher, P. C. Hato, T. Zhang, K. Himmelfarb, J. Kretzler, M. Mollah, S. Kidney Precision Medicine Project, Jain, S. Ra 2023-06-10 doi:10.1101/2023.06.07.543965 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Large-scale map of RNA binding protein interactomes across the mRNA life-cycle ]]> https://biorxiv.org/content/10.1101/2023.06.08.544225v1?rss=1 Rothamel, K. Street, L. Brannan, K. Jin, W. Rhine, K. Al-Azzam, N. Wolin, E. Bokor, B. Abdou, A. Doron-Mandel, E. W. Kim, J. Ma, Y. Ahdout, J. Dong, K. Madrigel, A. Mujumba, M. Jovanovic, M. Yeo, G. W. 2023-06-08 doi:10.1101/2023.06.08.544225 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration. ]]> https://biorxiv.org/content/10.1101/2023.06.12.544338v1?rss=1 Correia, J. C. Jannig, P. R. Gosztyla, M. L. Cervenka, I. Ducommun, S. Praestholm, S. M. Dumont, K. D. Liu, Z. Liang, Q. Edsgard, D. Emanuelsson, O. Gregorevic, P. Westerblad, H. Venckunas, T. Brazaitis, M. Kamandulis, S. Lanner, J. T. Yeo, G. W. Ruas, J. L. 2023-06-13 doi:10.1101/2023.06.12.544338 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ High-Resolution Characterization of Human Brain Cortex with High-Fidelity Spatial Transcriptomic Slides (HiFi-Slides) ]]> https://biorxiv.org/content/10.1101/2023.06.12.544625v1?rss=1 Xu, T. Zhu, E. Zhang, C. Calandrelli, R. Lin, P. Zhong, S. 2023-06-13 doi:10.1101/2023.06.12.544625 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration ]]> https://biorxiv.org/content/10.1101/2023.06.16.545370v1?rss=1 Liefeld, T. Huang, E. Wenzel, A. T. Yoshimoto, K. Sharma, A. K. Sicklick, J. K. Mesirov, J. P. Reich, M. M. 2023-06-18 doi:10.1101/2023.06.16.545370 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Nyctinastic leaf folding mimic reduces herbivory by Chromacris trogon grasshoppers (Orthoptera:Romaleidae) ]]> https://biorxiv.org/content/10.1101/2023.06.16.545391v1?rss=1 Bell, A. B. 2023-06-18 doi:10.1101/2023.06.16.545391 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Spatiotemporal Control of Genomics and Epigenomics by Ultrasound ]]> https://biorxiv.org/content/10.1101/2023.06.21.544125v1?rss=1 Wu, Y. Huang, Z. Liu, Y. Yoon, C.-W. Sun, K. Situ, Y. Ho, P. Yuan, Z. Zhu, L. Eyquem, J. Zhao, Y. Liu, T. Kwong, G. A. Chien, S. Wang, Y. 2023-06-23 doi:10.1101/2023.06.21.544125 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Liquid-like condensates mediate competition between actin branching and bundling ]]> https://biorxiv.org/content/10.1101/2023.06.23.546267v1?rss=1 Graham, K. Chandrasekaran, A. Wang, L. Yang, N. Lafer, E. M. Rangamani, P. Stachowiak, J. C. 2023-06-26 doi:10.1101/2023.06.23.546267 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Luminal transport rates through intact endoplasmic reticulum limit the magnitude of localized Ca2+ signals ]]> https://biorxiv.org/content/10.1101/2023.06.23.546357v1?rss=1 Crapart, C. Scott, Z. C. Konno, T. Sharma, A. Bailey, D. M. Avezov, E. Koslover, E. F. 2023-06-26 doi:10.1101/2023.06.23.546357 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ CaBLAM! A high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase ]]> https://biorxiv.org/content/10.1101/2023.06.25.546478v1?rss=1 Lambert, G. G. Crespo, E. L. Murphy, J. Boassa, D. Luong, S. Hu, J. Sprecher, B. Tree, M. O. Orcutt, R. Heydari, D. Bell, A. B. Torreblanca Zanca, A. Hakimi, A. Lipscombe, D. Moore, C. I. Hochgeschwender, U. Shaner, N. C. 2023-06-26 doi:10.1101/2023.06.25.546478 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Cell Type- and Tissue-specific Enhancers in Craniofacial Development ]]> https://biorxiv.org/content/10.1101/2023.06.26.546603v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@7595a9org.highwire.dtl.DTLVardef@1b48b81org.highwire.dtl.DTLVardef@32fe86org.highwire.dtl.DTLVardef@1e41fed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rajderkar, S. S. Paraiso, K. Amaral, M. L. Kosicki, M. Cook, L. Darbellay, F. Spurrell, C. Osterwalder, M. Zhu, Y. Wu, H. Afzal, S. Y. Blow, M. Kelman, G. Barozzi, I. Fukuda-Yuzawa, Y. Akiyama, J. A. Afzal, V. Tran, S. Plajzer-Frick, I. Novak, C. S. Kato, M. Hunter, R. D. von Maydell, K. Wang, A. Lin, L. Preissl, S. Lisgo, S. Ren, B. Dickel, D. E. Pennacchio, L. A. Visel, A. 2023-06-26 doi:10.1101/2023.06.26.546603 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain ]]> https://biorxiv.org/content/10.1101/2023.06.28.546457v1?rss=1 Luo, Z. Wen, X. Zhao, W. Nguyen, T. Wan, X. Richard, J. L. C. Zhong, S. 2023-06-29 doi:10.1101/2023.06.28.546457 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2023.07.03.547507v1?rss=1 Inamo, J. Keegan, J. Griffith, A. Ghosh, T. Horisberger, A. Howard, K. Pulford, J. Murzin, E. Hancock, B. Jonsson, A. H. Seifert, J. Feser, M. L. Norris, J. M. Cao, Y. Apruzzese, W. Bridges, S. L. Bykerk, V. Goodman, S. Donlin, L. Firestein, G. S. Perlman, H. Bathon, J. M. Hughes, L. B. Tabechian, D. Filer, A. Pitzalis, C. H. Anolik, J. Moreland, L. Guthridge, J. M. James, J. A. Brenner, M. B. Raychaudhuri, S. Sparks, J. A. The Accelerating Medicines Partnership RA/SLE Network, Holers, V. M. Deane, K. D. Lederer, J. A. Rao, D. A. Zhang, F. 2023-07-04 doi:10.1101/2023.07.03.547507 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Covalent macrocyclic proteasome inhibitors mitigate resistance in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2023.07.03.547579v1?rss=1 Bennett, J. M. Ward, K. E. Muir, R. Kabeche, S. Yoo, E. Yeo, T. Lam, G. Berger, G. Faucher, F. F. Lin, G. Gerwick, W. H. Yeh, E. Fidock, D. A. Bogyo, M. 2023-07-03 doi:10.1101/2023.07.03.547579 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Exposure to constant artificial light alters honey bee sleep rhythms and disrupts sleep ]]> https://biorxiv.org/content/10.1101/2023.07.03.547605v1?rss=1 Kim, A. Y. Velazquez, A. Saavedra, B. Smarr, B. Nieh, J. C. 2023-07-04 doi:10.1101/2023.07.03.547605 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Epigenetic Germline Variants Predict Cancer Prognosis and Risk and Distribute Uniquely in Topologically Associating Domains ]]> https://biorxiv.org/content/10.1101/2023.07.04.547722v1?rss=1 Goudarzi, S. Pagadala, M. Klie, A. Talwar, J. Carter, H. 2023-07-07 doi:10.1101/2023.07.04.547722 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ A conserved antigen induces respiratory Th17-mediated serotype-independent protection against pneumococcal superinfection ]]> https://biorxiv.org/content/10.1101/2023.07.07.548156v1?rss=1 Liu, X. Van Maele, L. Matarazzo, L. Soulard, D. Alves Duarte da Silva, V. de Bakker, V. Denereaz, J. Bock, F. P. Taschner, M. Gruber, S. Nizet, V. Sirard, J.-C. Veening, J.-W. 2023-07-07 doi:10.1101/2023.07.07.548156 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment ]]> https://biorxiv.org/content/10.1101/2023.07.10.548264v1?rss=1 Diaz-Gay, M. Vangara, R. Barnes, M. Wang, X. Islam, S. M. A. Vermes, I. Narasimman, N. B. Yang, T. Jiang, Z. Moody, S. Senkin, S. Brennan, P. Stratton, M. Alexandrov, L. B. 2023-07-11 doi:10.1101/2023.07.10.548264 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.07.10.548468v1?rss=1 Kim, J. Y. Yang, J. E. Mitchell, J. W. English, L. A. Yang, S. Z. Tenpas, T. Dent, E. W. Wildonger, J. Wright, E. R. 2023-07-11 doi:10.1101/2023.07.10.548468 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Systems Age: A single blood methylation test to quantify aging heterogeneity across 11 physiological systems ]]> https://biorxiv.org/content/10.1101/2023.07.13.548904v1?rss=1 Sehgal, R. Meer, M. Shadyab, A. H. Casanova, R. Manson, J. E. Bhatti, P. Crimmins, E. M. Assimes, T. L. Whitsel, E. A. Higgins-Chen, A. T. Levine, M. 2023-07-17 doi:10.1101/2023.07.13.548904 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection ]]> https://biorxiv.org/content/10.1101/2023.07.14.548955v1?rss=1 Aiyer, S. Baldwin, P. R. Tan, S. M. Shan, Z. Oh, J. Mehrani, A. Bowman, M. E. Louie, G. Passos, D. O. Đorđevic-Marquardt, S. Mietzsch, M. Hull, J. A. Hoshika, S. Barad, B. A. Grotjahn, D. McKenna, R. Agbandje-Mckenna, M. Benner, S. A. Noel, J. P. Wang, D. Tan, Y. Z. Lyumkis, D. 2023-07-15 doi:10.1101/2023.07.14.548955 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Glycan-specific IgM is critical for human immunity to Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.07.14.548956v1?rss=1 Hendriks, A. M. Kerkman, P. F. Varkila, M. R. Haitsma-Mulier, J. L. Ali, S. ten Doesschate, T. van der Vaart, T. W. de Haas, C. J. C. Aerts, P. C. Cremer, O. L. Bonten, M. J. Nizet, V. Liu, G. Y. Codee, J. D. C. Rooijakkers, S. H. van Strijp, J. A. van Sorge, N. M. 2023-07-14 doi:10.1101/2023.07.14.548956 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ The MEK-ERK signaling pathway promotes maintenance of cardiac chamber identity ]]> https://biorxiv.org/content/10.1101/2023.07.17.549343v1?rss=1 Yao, Y. Yelon, D. 2023-07-19 doi:10.1101/2023.07.17.549343 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Contrasting roles of different mismatch repair proteins in basal-like breast cancer ]]> https://biorxiv.org/content/10.1101/2023.07.20.549745v1?rss=1 Mo, J. Borcherding, N. Jo, S. Tithi, T. I. Cho, E. Cash, C. E. Honda, M. Ahmed, K. K. kolb, R. Weigel, R. Spies, M. Zhang, W. 2023-07-22 doi:10.1101/2023.07.20.549745 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Membrane mechanics dictate axonal morphology and function ]]> https://biorxiv.org/content/10.1101/2023.07.20.549958v1?rss=1 Griswold, J. M. Bonilla-Quintana, M. Pepper, R. Lee, C. T. Raychaudhuri, S. Ma, S. Gan, Q. Syed, S. Zhu, C. Bell, M. Suga, M. Yamaguchi, Y. Chereau, R. Nagerl, V. Knott, G. W. Rangamani, P. Watanabe, S. 2023-07-21 doi:10.1101/2023.07.20.549958 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ Altered Fhod3 Expression Involved in Progressive High-Frequency Hearing Loss via Dysregulation of Actin Polymerization Stoichiometry in The Cuticular Plate ]]> https://biorxiv.org/content/10.1101/2023.07.20.549974v1?rss=1 Boussaty, E. C. Ninoyu, Y. Andrade, L. Li, Q. Ohyama, T. Wahlin, K. J. Manor, U. Friedman, R. A. 2023-07-25 doi:10.1101/2023.07.20.549974 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia ]]> https://biorxiv.org/content/10.1101/2023.07.21.549930v1?rss=1 Haney, M. Palovics, R. Munson, C. Long, C. Johansson, P. Yip, O. Dong, W. Rawat, E. West, E. Schlachetzki, J. Tsai, A. P.-Y. Guldner, I. Lamichhane, B. Smith, A. Schaum, N. Calcuttawala, K. Shin, A. Wang, Y.-H. Wang, C. Koutsodendris, N. Serrano, G. E. Beach, T. Reiman, E. M. Glass, C. Abu-Remaileh, M. M. Enejder, A. Huang, Y. Wyss-Coray, T. 2023-07-25 doi:10.1101/2023.07.21.549930 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction ]]> https://biorxiv.org/content/10.1101/2023.07.26.550757v1?rss=1 Poudel, S. Hyun, J. C. Hefner, Y. Monk, J. Nizet, V. Palsson, B. O. 2023-07-29 doi:10.1101/2023.07.26.550757 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework ]]> https://biorxiv.org/content/10.1101/2023.07.26.550768v1?rss=1 Liang, C. Murray, S. Li, Y. Lee, R. Low, A. Sasaki, S. Chiang, W.-T. Lin, W.-J. Mathews, J. Barnes, W. Lewis, N. E. 2023-07-28 doi:10.1101/2023.07.26.550768 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus ]]> https://biorxiv.org/content/10.1101/2023.07.27.550855v1?rss=1 Liang, Z. Gilbreath, C. Liu, W. Wang, Y. Zhang, M. Q. Zhang, D.-E. Wu, S. Fu, X.-D. 2023-07-27 doi:10.1101/2023.07.27.550855 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Sex, gender diversity, and brain structure in children ages 9 to 11 years old ]]> https://biorxiv.org/content/10.1101/2023.07.28.551036v1?rss=1 Torgerson, C. Ahmadi, H. Choupan, J. Fan, C. C. Blosnich, J. R. Herting, M. 2023-07-29 doi:10.1101/2023.07.28.551036 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Transformation of value signaling in a striatopallidal circuit ]]> https://biorxiv.org/content/10.1101/2023.08.01.551547v1?rss=1 Lee, D. Liu, L. Root, C. M. 2023-08-03 doi:10.1101/2023.08.01.551547 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ An AI-assisted Investigation of Tumor-Associated Macrophages and their Polarization in Colorectal Cancer ]]> https://biorxiv.org/content/10.1101/2023.08.01.551559v1?rss=1 Dadlani, E. Dash, T. Sahoo, D. 2023-08-03 doi:10.1101/2023.08.01.551559 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ scMD: cell type deconvolution using single-cell DNA methylation references ]]> https://biorxiv.org/content/10.1101/2023.08.03.551733v1?rss=1 Cai, M. Zhou, J. McKennan, C. Wang, J. 2023-08-06 doi:10.1101/2023.08.03.551733 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.04.551992v1?rss=1 Quiroz, E. J. Kim, S. Gautam, L. K. Borok, Z. Kintner, C. Ryan, A. L. 2023-08-04 doi:10.1101/2023.08.04.551992 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes ]]> https://biorxiv.org/content/10.1101/2023.08.04.552006v1?rss=1 Goodheart, J. A. Rio, R. A. Taraporevala, N. F. Fiorenza, R. A. Barnes, S. R. Morrill, K. Jacob, M. A. C. Whitesel, C. Masterson, P. Batzel, G. O. Johnston, H. T. Ramirez, M. D. Katz, P. S. Lyons, D. 2023-08-06 doi:10.1101/2023.08.04.552006 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Analysis of 8839 pan-primate retroviral LTR elements with regulatory functions during human embryogenesis reveals their global impacts on evolution of Modern Humans. ]]> https://biorxiv.org/content/10.1101/2023.08.06.552206v1?rss=1 Glinsky, G. 2023-08-07 doi:10.1101/2023.08.06.552206 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Rats Chasing the Dragon: A new heroin inhalation method ]]> https://biorxiv.org/content/10.1101/2023.08.09.552712v1?rss=1 Gutierrez, A. Taffe, M. A. 2023-08-14 doi:10.1101/2023.08.09.552712 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains ]]> https://biorxiv.org/content/10.1101/2023.08.10.552793v1?rss=1 Gu, Y. Li, H. Deep, A. Enustun, E. Zhang, D. Corbett, K. D. 2023-08-10 doi:10.1101/2023.08.10.552793 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ A fluorescent sex-sorting technique for insects with the demonstration in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.08.11.553026v1?rss=1 Liu, J. Rayes, D. Akbari, O. 2023-08-14 doi:10.1101/2023.08.11.553026 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Estimating the Total Variance Explained by Whole-Brain Imaging for Zero-inflated Outcomes ]]> https://biorxiv.org/content/10.1101/2023.08.14.553270v1?rss=1 Ren, J. Loughnan, R. J. Xu, B. Thompson, W. K. Fan, C. C. 2023-08-16 doi:10.1101/2023.08.14.553270 Cold Spring Harbor Laboratory Press 2023-08-16 <![CDATA[ Co-Occurrence Network Analysis Reveals The Alterations Of The Skin Microbiome And Metabolome In Atopic Dermatitis Patients ]]> https://biorxiv.org/content/10.1101/2023.08.17.553735v1?rss=1 Portal Gomes, P. W. Mannochio-Russo, H. Mao, J. Zhao, H. N. Tipton, C. D. Ancira, J. Dorrestein, P. C. Li, M. 2023-08-18 doi:10.1101/2023.08.17.553735 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Identification of human skin microbiome odorants that manipulate mosquito landing behavior - towards engineering a repellent skin flora ]]> https://biorxiv.org/content/10.1101/2023.08.19.553996v1?rss=1 Coutinho-Abreu, I. V. Jamshidi, O. Raban, R. Atabakhsh, K. Merriman, J. A. Fischbach, M. A. Akbari, O. S. 2023-08-21 doi:10.1101/2023.08.19.553996 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Acquired stress resilience through bacteria-to-nematode horizontal gene transfer ]]> https://biorxiv.org/content/10.1101/2023.08.20.554039v1?rss=1 Pandey, T. Kalluraya, C. Wang, B. Xu, T. Huang, X. Guang, S. Daugherty, M. D. Ma, D. K. 2023-08-21 doi:10.1101/2023.08.20.554039 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Correlating stress reduction and eye movement patterns in a world famous Kyoto Japanese garden ]]> https://biorxiv.org/content/10.1101/2023.08.21.554170v1?rss=1 Goto, S. Takase, H. Yamaguchi, K. Tamoki, K. Sun, M. Koga, A. Tiankai, L. Poy, I. Herrup, K. 2023-08-23 doi:10.1101/2023.08.21.554170 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ ]]> https://biorxiv.org/content/10.1101/2023.08.21.554211v1?rss=1 Tao, A. J. Jiang, J. Gadbois, G. E. Goyal, P. Boyle, B. T. Mumby, E. J. Myers, S. A. English, J. G. Ferguson, F. M. 2023-08-25 doi:10.1101/2023.08.21.554211 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ A data-driven approach for timescale decomposition of biochemical reaction networks ]]> https://biorxiv.org/content/10.1101/2023.08.21.554230v1?rss=1 Akbari, A. Haiman, Z. B. Palsson, B. O. 2023-08-25 doi:10.1101/2023.08.21.554230 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Impairment of the SKN-1A/NRF1 proteasome surveillance pathway triggers tissue-specific protective immune responses against distinct natural pathogens in C. elegans. ]]> https://biorxiv.org/content/10.1101/2023.08.22.554255v1?rss=1 Grover, M. Gang, S. S. Troemel, E. Barkoulas, M. 2023-08-23 doi:10.1101/2023.08.22.554255 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ A simple solid media assay for detection of synergy between bacteriophages and antibiotics ]]> https://biorxiv.org/content/10.1101/2023.08.23.554535v1?rss=1 Khong, E. Oh, J. Jiminez, J. M. Liu, R. Dunham, S. J. B. Monsibais, A. Rhoads, A. Ghatbale, P. Garcia, A. Cobian-Güemes, A. G. Blanc, A. Chiu, M. Kuo, P. Proost, M. Kline, A. Aslam, S. Schooley, R. Whiteson, K. Fraley, S. Pride, D. T. 2023-08-25 doi:10.1101/2023.08.23.554535 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ S-Nitrosylation of CRTC1 in Alzheimer's disease impairs CREB-dependent gene expression induced by neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.08.25.554320v1?rss=1 Zhang, X. Vlkolinsky, R. Wu, C. Dolatabadi, N. Scott, H. Prikhodko, O. Blanco, M. Lang, N. Pina-Crespo, J. Nakamura, T. Roberto, M. Lipton, S. A. 2023-08-27 doi:10.1101/2023.08.25.554320 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Fe-TAMLs as a new class of small molecule peroxidase probes for correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/2023.08.25.554352v1?rss=1 Adams, S. R. Mackey, M. R. Ramachandra, R. Deerinck, T. J. Castillon, G. A. Phan, S. Hu, J. Boassa, D. Ngo, J. T. Ellisman, M. H. 2023-08-26 doi:10.1101/2023.08.25.554352 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris ]]> https://biorxiv.org/content/10.1101/2023.08.27.555018v1?rss=1 Leavitt, W. D. Waldbauer, J. Venceslau, S. S. Sim, M. S. Zhang, L. Boidi, F. J. Plummer, S. Diaz, J. M. Pereira, I. A. C. Bradley, A. S. 2023-08-27 doi:10.1101/2023.08.27.555018 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene GUT fecal stabilization ]]> https://biorxiv.org/content/10.1101/2023.08.29.555241v1?rss=1 Isokaanta, H. Pinto da Silva, L. Karu, N. Kallonen, T. Aatsinki, A. K. Hankemeier, T. Schimmel, L. Diaz, E. Hyotylainen, T. Dorrestein, P. C. Knight, R. Oresic, M. Daouk, R. K. Dickens, A. M. Lamichhane, S. 2023-08-29 doi:10.1101/2023.08.29.555241 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2023.08.30.555359v1?rss=1 Yang, X. Jones, I. R. Chen, P. B. Yang, H. Ren, X. Zheng, L. Li, B. Li, Y. E. Sun, Q. Wen, J. Beaman, C. Cui, X. Li, Y. Wang, W. Hu, M. Ren, B. Shen, Y. 2023-08-30 doi:10.1101/2023.08.30.555359 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Network effects of traumatic brain injury: from infra slow to high frequency oscillations ]]> https://biorxiv.org/content/10.1101/2023.08.31.555809v1?rss=1 Marsh, B. Huang, M. Bazhenov, M. 2023-09-03 doi:10.1101/2023.08.31.555809 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Protein Kinase Structure and Dynamics: Role of the αC-β4 Loop ]]> https://biorxiv.org/content/10.1101/2023.08.31.555822v1?rss=1 Wu, J. Jonniya, N. A. Hirakis, S. P. Olivieri, C. Veglia, G. Kornev, A. P. Taylor, S. S. 2023-09-01 doi:10.1101/2023.08.31.555822 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Inhibition of Parkinsons Disease-related LRRK2 by type-I and type-II kinase inhibitors: activity and structures ]]> https://biorxiv.org/content/10.1101/2023.09.07.556689v1?rss=1 Leschziner, A. E. Sanz Murillo, M. Suarez, A. V. Dederer, V. Chatterjee, D. Louro, J. A. Knapp, S. Mathea, S. 2023-09-09 doi:10.1101/2023.09.07.556689 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Elf1 promotes Rad26 interaction with lesion-arrested Pol II for transcription-coupled repair ]]> https://biorxiv.org/content/10.1101/2023.09.08.556893v1?rss=1 Sarsam, R. Xu, J. Lahiri, I. Gong, W. Oh, J. Zhou, Z. Chong, J. Hao, N. Li, S. Wang, D. Leschziner, A. E. 2023-09-10 doi:10.1101/2023.09.08.556893 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure ]]> https://biorxiv.org/content/10.1101/2023.09.08.556894v1?rss=1 Yoon, J. Zhang, Y. M. Her, C. Grant, R. A. Ponomarenko, A. M. Ackermann, B. E. Debelouchina, G. Shoulders, M. D. 2023-09-12 doi:10.1101/2023.09.08.556894 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Adult consequences of repeated nicotine and Δ9-tetrahydrocannabinol (THC) vapor inhalation in adolescent rats ]]> https://biorxiv.org/content/10.1101/2023.09.08.556932v1?rss=1 Gutierrez, A. Creehan, K. M. Grant, Y. Taffe, M. A. 2023-09-14 doi:10.1101/2023.09.08.556932 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Distinct 3D contacts and phenotypic consequences of adjacent non-coding loci in the epigenetically quiescent regions ]]> https://biorxiv.org/content/10.1101/2023.09.11.557110v1?rss=1 Wu, P. Wang, W. 2023-09-13 doi:10.1101/2023.09.11.557110 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis ]]> https://biorxiv.org/content/10.1101/2023.09.11.557221v1?rss=1 Ren, B. Zhang, K. Zemke, N. Armand, E. 2023-09-15 doi:10.1101/2023.09.11.557221 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Categorization dynamically alters representations in human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.11.557257v1?rss=1 Henderson, M. M. Serences, J. T. Rungratsameetaweemana, N. 2023-09-13 doi:10.1101/2023.09.11.557257 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks ]]> https://biorxiv.org/content/10.1101/2023.09.13.557626v1?rss=1 Gopalakrishnan, S. Johnson, W. Gomez, M. A. V. Icten, E. Tat, J. Lay, F. Diep, J. Gomez, N. Stevens, J. Schlegel, F. Rolandi, P. Kontoravdi, C. Lewis, N. E. 2023-09-17 doi:10.1101/2023.09.13.557626 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Reinstatement of CDX2 as a differentiation therapy for colorectal cancers ]]> https://biorxiv.org/content/10.1101/2023.09.13.557628v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@16eeb1eorg.highwire.dtl.DTLVardef@10e308borg.highwire.dtl.DTLVardef@9512f0org.highwire.dtl.DTLVardef@10e74eb_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIn this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk. HighlightsO_LIAn ML framework (CANDiT) identifies target for differentiation therapy for CRCs C_LIO_LITherapy induces crypt differentiation and CSC-specific cytotoxicity C_LIO_LICDX2-low state predicts therapeutic response; restoration improves prognosis C_LIO_LITherapy dismantles stemness via reactivation of stress polarity signaling C_LI ]]> Sinha, S. Alcantara, J. Perry, K. Castillo, V. Espinoza, C. R. Taheri, S. Vidales, E. Tindle, C. Adel, A. Amirfakhri, S. Sawires, J. R. Yang, J. Bouvet, M. Sahoo, D. Ghosh, P. 2023-09-17 doi:10.1101/2023.09.13.557628 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2023.09.13.557637v1?rss=1 Crits-Christoph, A. Levy, J. I. Pekar, J. Goldstein, S. A. Singh, R. Hensel, Z. Gangavarapu, K. Rogers, M. B. Moshiri, N. Garry, R. f. Holmes, E. C. Koopmans, M. P. G. Lemey, P. Popescu, S. Rambaut, A. Robertson, D. L. Suchard, M. A. Wertheim, J. Rasmussen, A. L. Andersen, K. G. Worobey, M. Debarre, F. 2023-09-14 doi:10.1101/2023.09.13.557637 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling ]]> https://biorxiv.org/content/10.1101/2023.09.13.557646v1?rss=1 Gopalakrishnan, S. Johnson, W. Valderrama-Gomez, M. A. Icten, E. Tat, J. Ingram, M. Shek, C. F. Chan, P. K. Schlegel, F. Rolandi, P. Kontoravdi, C. Lewis, N. E. 2023-09-17 doi:10.1101/2023.09.13.557646 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Machine assisted annotation in neuroanatomy ]]> https://biorxiv.org/content/10.1101/2023.09.13.557658v1?rss=1 Qian, K. Kleinfeld, D. Friedman, B. Freund, Y. 2023-09-14 doi:10.1101/2023.09.13.557658 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA ]]> https://biorxiv.org/content/10.1101/2023.09.14.557527v1?rss=1 Okholm, T. L. H. Kamstrup, A. B. Nielsen, M. M. Hollensen, A. K. Graversgaard, M. L. Kristensen, L. S. Vang, S. Park, S. S. Yeo, G. W. Dyrskjot, L. Kjems, J. Pedersen, J. S. Damgaard, C. K. 2023-09-14 doi:10.1101/2023.09.14.557527 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Cold Storage and Cryopreservation Methods for Spermatozoa of the Sea Urchin, Lytechinus pictus . ]]> https://biorxiv.org/content/10.1101/2023.09.14.557644v1?rss=1 90% development and producing larvae that successfully undergo metamorphosis to juvenile sea urchins. Sperm of these two species can be frozen and thawed at least twice and still give rise to larvae that undergo metamorphosis. Main PointsO_LISperm can maintain fertilizing capacity ex vivo for 5-10 weeks when stored at 0{degrees}C. C_LIO_LIWhen freezing in liquid nitrogen no stepwise addition of cryoprotectant, or stepwise drop in temperature are required. C_LIO_LIA standard fertilization assay is presented to score cleavage stage sea urchin embryos produced by cryopreserved sperm. C_LIO_LISperm frozen and thawed more than once can produce larvae. C_LI ]]> Vacquier, V. Hamdoun, A. 2023-09-15 doi:10.1101/2023.09.14.557644 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Generating Novel Leads for Drug Discovery using LLMs with Logical Feedback ]]> https://biorxiv.org/content/10.1101/2023.09.14.557698v1?rss=1 Brahmavar, S. B. Srinivasan, A. Dash, T. Krishnan, S. R. Vig, L. Roy, A. Aduri, R. 2023-09-17 doi:10.1101/2023.09.14.557698 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Structural and dynamic changes in P-Rex1 upon activation by PIP3 and inhibition by IP4 ]]> https://biorxiv.org/content/10.1101/2023.09.15.557836v1?rss=1 Ravala, S. K. Adame-Garcia, S. R. Li, S. Chen, C.-L. Cianfrocco, M. A. Gutkind, J. S. Cash, J. N. Tesmer, J. J. G. 2023-09-16 doi:10.1101/2023.09.15.557836 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Variability in the phytoplankton response to upwelling across an iron limitation mosaic within the California Current System ]]> https://biorxiv.org/content/10.1101/2023.09.22.558967v1?rss=1 Lin, Y. Torano, O. Whitehouse, L. Pierce, E. Till, C. P. Hurst, M. Freiberger, R. Mellett, T. Maldonado, M. T. Guo, J. Sutton, M. Zeitz, D. Marchetti, A. 2023-09-23 doi:10.1101/2023.09.22.558967 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A phage nucleus-associated RNA-binding protein is required for jumbo phage infection ]]> https://biorxiv.org/content/10.1101/2023.09.22.559000v1?rss=1 Enustun, E. Armbruster, E. G. Lee, J. Zhang, S. Yee, B. A. Gu, Y. Deep, A. Naritomi, J. T. Liang, Q. Aigner, S. Adler, B. A. Cress, B. F. Doudna, J. A. Chaikeeratisak, V. Cleveland, D. W. Ghassemian, M. Yeo, G. W. Pogliano, J. Corbett, K. D. 2023-09-22 doi:10.1101/2023.09.22.559000 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Next-generation genetic sexing strain establishment in the agricultural pest Ceratitis capitata ]]> https://biorxiv.org/content/10.1101/2023.09.29.560088v1?rss=1 Davydova, S. Liu, J. Kandul, N. P. Braswell, W. E. Akbari, O. S. Meccariello, A. 2023-10-01 doi:10.1101/2023.09.29.560088 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ Light-induced trapping of endogenous proteins reveals spatiotemporal roles of microtubule and kinesin-1 in dendrite patterning of Drosophila sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.09.30.560303v1?rss=1 Xu, Y. Wang, B. Bush, I. Saunders, H. A. Wildonger, J. Han, C. 2023-10-02 doi:10.1101/2023.09.30.560303 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ A mobile intron facilitates interference competition between co-infecting viruses ]]> https://biorxiv.org/content/10.1101/2023.09.30.560319v1?rss=1 Birkholz, E. A. Morgan, C. J. Laughlin, T. G. Lau, R. K. Prichard, A. Rangarajan, S. Meza, G. N. Lee, J. Armbruster, E. G. Suslov, S. Pogliano, K. Meyer, J. R. Villa, E. Corbett, K. D. Pogliano, J. 2023-09-30 doi:10.1101/2023.09.30.560319 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.10.02.560584v1?rss=1 Buck, S. A. Rubin, S. A. Kunkhyen, T. Treiber, C. D. Xue, X. Fenno, L. E. Mabry, S. J. Sundar, V. R. Yang, Z. Shah, D. Ketchesin, K. D. Becker-Krail, D. D. Vasylieva, I. Smith, M. C. Weisel, F. J. Wang, W. Erickson-Oberg, M. Q. O'Leary, E. I. Aravind, E. Ramakrishnan, C. Kim, Y. S. Wu, Y. Quick, M. Coleman, J. A. MacDonald, W. A. Elbakri, R. De Miranda, B. R. Palladino, M. J. McCabe, B. D. Fish, K. N. Seney, M. L. Rayport, S. Mingote, S. Deisseroth, K. Hnasko, T. S. Awatramani, R. Watson, A. M. Waddell, S. Cheetham, C. E. Logan, R. W. Freyberg, Z. 2023-10-03 doi:10.1101/2023.10.02.560584 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ CASTER: Direct species tree inference from whole-genome alignments ]]> https://biorxiv.org/content/10.1101/2023.10.04.560884v1?rss=1 Zhang, C. Nielsen, R. Mirarab, S. 2023-10-06 doi:10.1101/2023.10.04.560884 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Structure-Function Coupling in Highly Sampled Individual Brains ]]> https://biorxiv.org/content/10.1101/2023.10.04.560909v1?rss=1 Rajesh, A. Seider, N. A. Newbold, D. J. Adeyemo, B. Marek, S. Greene, D. J. Snyder, A. Z. Shimony, J. S. Laumann, T. O. Dosenbach, N. U. F. Gordon, E. M. 2023-10-05 doi:10.1101/2023.10.04.560909 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model ]]> https://biorxiv.org/content/10.1101/2023.10.06.560776v1?rss=1 Bottom-Tanzer, S. Corella, S. Meyer, J. Sommer, M. Bolanos, L. Murphy, T. Quinones, S. Heiney, S. Shtrahman, M. Whalen, M. Oren, R. Higley, M. J. Cardin, J. A. Noubary, F. Armbruster, M. Dulla, C. 2023-10-06 doi:10.1101/2023.10.06.560776 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Encoding extracellular modification of artificial cell membranes using engineered self-translocating proteins ]]> https://biorxiv.org/content/10.1101/2023.10.06.561148v1?rss=1 Harjung, A. Fracassi, A. Devaraj, N. 2023-10-06 doi:10.1101/2023.10.06.561148 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Changes in electrophysiological aperiodic activity during cognitive control in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2023.10.09.561166v1?rss=1 Monchy, N. Modolo, J. Houvenaghel, J.-F. Voytek, B. Duprez, J. 2023-10-10 doi:10.1101/2023.10.09.561166 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Inputs to the locus coeruleus from the periaqueductal gray and rostroventral medulla shape opioid-mediated descending pain modulation ]]> https://biorxiv.org/content/10.1101/2023.10.10.561768v1?rss=1 Lubejko, S. T. Livrizzi, G. Patel, J. Yung, J. Yaksh, T. L. Banghart, M. R. 2023-10-10 doi:10.1101/2023.10.10.561768 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Environment-driven trends in fish larval abundance predict fishery recruitment in two temperature reef congeners: mechanisms and implications for management ]]> https://biorxiv.org/content/10.1101/2023.10.11.561723v1?rss=1 Mason, E. T. J. Thompson, A. R. Semmens, B. X. 2023-10-16 doi:10.1101/2023.10.11.561723 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Hidden evolutionary constraints dictate the retention of coronavirus accessory genes ]]> https://biorxiv.org/content/10.1101/2023.10.12.561935v1?rss=1 Goldstein, S. A. Feeley, T. M. Babler, K. M. Hilbert, Z. A. Downhour, D. M. Moshiri, N. Elde, N. C. 2023-10-14 doi:10.1101/2023.10.12.561935 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Metabolic bypass rescues aberrant S-nitrosylation-induced TCA cycle inhibition and synapse loss in Alzheimer's disease human neurons ]]> https://biorxiv.org/content/10.1101/2023.10.12.562118v1?rss=1 Andreyev, A. Y. Yang, H. Doulias, P.-T. Dolatabadi, N. Zhang, X. Luevanos, M. Blanco, M. Baal, C. Putra, I. Nakamura, T. Ischiropoulos, H. Tannenbaum, S. R. Lipton, S. A. 2023-10-17 doi:10.1101/2023.10.12.562118 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Long chain monomethyl branched-chain fatty acid levels in human milk vary with gestational weight gain ]]> https://biorxiv.org/content/10.1101/2023.10.13.561203v1?rss=1 O'Sullivan, A. Brady, E. Lafferty, L. O'Shea, F. O'Regan, Z. Meurs, N. Baldini, M. Gengatharan, J. Metallo, C. M. Wallace, M. 2023-10-17 doi:10.1101/2023.10.13.561203 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Resting-state is not enough: alpha and mu rhythms change shape across development, but lack diagnostic sensitivity ]]> https://biorxiv.org/content/10.1101/2023.10.13.562301v1?rss=1 Bender, A. Voytek, B. Schaworonkow, N. 2023-10-17 doi:10.1101/2023.10.13.562301 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Emergent effects of synaptic connectivity on cortical sleep slow wave amplitude, density and propagation in a large-scale thalamocortical network model of the human brain ]]> https://biorxiv.org/content/10.1101/2023.10.15.562408v1?rss=1 Marsh, B. Zuloaga, M. G. N. Rosen, B. Q. Sokolov, Y. Delanois, J. E. Gonzalez, O. C. Krishnan, G. P. Halgren, E. Bazhenov, M. 2023-10-17 doi:10.1101/2023.10.15.562408 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ GRAMD2+ alveolar type I cell plasticity facilitates cell state transitions in organoid culture ]]> https://biorxiv.org/content/10.1101/2023.10.17.560801v1?rss=1 Shen, H. Chen, W. Liu, Y. Castaldi, A. Castillo, J. Horie, M. Flodby, P. Sundar, S. Li, C. Ji, Y. Minoo, P. Marconett, C. N. Zhou, B. Borok, Z. 2023-10-18 doi:10.1101/2023.10.17.560801 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia ]]> https://biorxiv.org/content/10.1101/2023.10.17.562767v1?rss=1 Fricker, A. D. Padilla, L. Luna, E. Choudhury, B. Hughes, E. R. Panzetta, M. E. Valdivia, R. Flores, G. E. 2023-10-17 doi:10.1101/2023.10.17.562767 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Eukaryotic chemotaxis under periodic stimulation shows temporal gradient dependence ]]> https://biorxiv.org/content/10.1101/2023.10.17.562804v1?rss=1 Karmakar, R. Karanam, A. R. Tang, M.-H. Rappel, W.-J. 2023-10-19 doi:10.1101/2023.10.17.562804 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement ]]> https://biorxiv.org/content/10.1101/2023.10.23.563531v1?rss=1 Handa, S. Biswas, T. Chakraborty, J. Paul, B. G. Ghosh, P. 2023-10-23 doi:10.1101/2023.10.23.563531 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain ]]> https://biorxiv.org/content/10.1101/2023.10.24.563814v1?rss=1 Chung, C. Yang, X. Hevner, R. Kennedy, K. Vong, K. L. Liu, Y. Patel, A. Nedunuri, R. Barton, S. T. Barrows, C. Stanley, V. Mittal, S. Breuss, M. W. Schlachetzki, J. C. M. Gleeson, J. G. 2023-10-25 doi:10.1101/2023.10.24.563814 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens ]]> https://biorxiv.org/content/10.1101/2023.10.24.563841v1?rss=1 Nuqui, X. Casalino, L. Zhou, L. Shehata, M. Wang, A. Tse, A. L. Ojha, A. Kearns, F. L. Rosenfeld, M. A. Miller, E. H. Acreman, C. M. Ahn, S.-H. Chandran, K. McLellan, J. S. Amaro, R. E. 2023-10-25 doi:10.1101/2023.10.24.563841 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Oxycodone Self-Administration in Female Rats is Enhanced by Δ9-tetrahydrocannabinol, but not by Cannabidiol, in a Progressive Ratio Procedure ]]> https://biorxiv.org/content/10.1101/2023.10.26.564282v1?rss=1 Nguyen, J. D. Grant, Y. Yang, C. Gutierrez, A. Taffe, M. A. 2023-10-31 doi:10.1101/2023.10.26.564282 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Benchmarking of small and large variants across tandem repeats ]]> https://biorxiv.org/content/10.1101/2023.10.29.564632v1?rss=1 English, A. Dolzhenko, E. Ziaei-Jam, H. Olson, N. D. Mckenzie, S. De Coster, W. Park, J. Gu, B. Wagner, J. Eberle, M. Gymrek, M. Chaisson, M. Zook, J. M. Sedlazeck, F. J. 2023-11-01 doi:10.1101/2023.10.29.564632 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Brain Injury Knowledge Ontology (BIKO) for traumatic brain injury: Formalizing concepts and methods used in translational traumatic brain injury research. ]]> https://biorxiv.org/content/10.1101/2023.10.29.564650v1?rss=1 Surles-Zeigler, M. Sincomb, T. Dixon, C. E. Imam, F. Gillespie, T. H. Grethe, J. S. Ferguson, A. R. Martone, M. E. 2023-11-01 doi:10.1101/2023.10.29.564650 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ The Generation and Propagation of the Human Alpha Rhythm ]]> https://biorxiv.org/content/10.1101/202564v1?rss=1 Halgren, M. Devinsky, O. Doyle, W. K. Bastuji, H. Rey, M. Mak-McCully, R. Chauvel, P. Ulbert, I. Fabo, D. Wittner, L. Heit, G. Eskandar, E. Mandell, A. Cash, S. S. 2017-11-18 doi:10.1101/202564 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Simulating human sleep spindle MEG and EEG from ion channel and circuit level dynamics ]]> https://biorxiv.org/content/10.1101/202606v1?rss=1 Rosen, B. Q. Krishnan, G. Sanda, P. Komarov, M. Sejnowski, T. Rulkov, N. Bazhenov, M. Halgren, E. 2017-10-13 doi:10.1101/202606 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Alpha-band oscillations track the retrieval of precise spatial representations from long-term memory ]]> https://biorxiv.org/content/10.1101/207860v1?rss=1 Sutterer, D. W. Foster, J. J. Serences, J. T. Vogel, E. K. Awh, E. 2018-02-18 doi:10.1101/207860 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Quantification of autism recurrence risk by direct assessment of paternal sperm mosaicism ]]> https://biorxiv.org/content/10.1101/208165v1?rss=1 90x) whole genome sequencing of four paternal sperm samples, which detected 12/355 transmitted de novo single nucleotide variants that were mosaic above 2% AF, and more than two dozen additional, non-transmitted mosaic variants in paternal sperm. Our results demonstrate that germline mosaicism is an underestimated phenomenon, which has important implications for clinical practice and in understanding the basis of human disease. Genetic analysis of sperm can assess individualized recurrence risk following the birth of a child with a de novo disease, as well as the risk in any male planning to have children. ]]> Breuss, M. Kleiber, M. George, R. D. Antaki, D. James, K. N. Ball, L. L. Hong, O. Garcia, C. A. B. Musaev, D. Nguyen, A. McEvoy-Venneri, J. Knox, R. Sticca, E. Devinsky, O. Gymrek, M. Sebat, J. Gleeson, J. G. 2017-10-24 doi:10.1101/208165 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Id proteins suppress E2A-driven innate-like T cell development prior to TCR selection ]]> https://biorxiv.org/content/10.1101/208728v1?rss=1 Roy, S. Moore, A. J. Love, C. Reddy, A. Rajagopalan, D. Dave, S. S. Li, L. Murre, C. Zhuang, Y. 2017-10-25 doi:10.1101/208728 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Sequence Transfer Learning for Neural Decoding ]]> https://biorxiv.org/content/10.1101/210732v1?rss=1 Elango, V. Patel, A. N. Miller, K. J. Gilja, V. 2017-10-29 doi:10.1101/210732 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data ]]> https://biorxiv.org/content/10.1101/210997v1?rss=1 Liu, C. Wang, W. 2017-10-29 doi:10.1101/210997 Cold Spring Harbor Laboratory Press 2017-10-29 <![CDATA[ Quantitative proteomic analysis of auxin signaling during seedling development ]]> https://biorxiv.org/content/10.1101/211532v1?rss=1 Kelley, D. Shen, Z. Walley, J. W. Chapman, E. J. Briggs, S. P. Estelle, M. 2017-10-30 doi:10.1101/211532 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Processive movement of actin by biased polymerization: a new paradigm of axonal transport ]]> https://biorxiv.org/content/10.1101/212449v1?rss=1 Chakrabarty, N. Dubey, P. Tang, Y. Ganguly, A. Ladt, K. Leterrier, C. Jung, P. Roy, S. 2017-11-01 doi:10.1101/212449 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction ]]> https://biorxiv.org/content/10.1101/212639v1?rss=1 1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. ]]> Herbert, Z. T. Kershner, J. P. Butty, V. L. Thimmapuram, J. Choudhari, S. Alekseyev, Y. O. Fan, J. Podnar, J. W. Wilcox, E. Gipson, J. Gillaspy, A. Jepsen, K. BonDurant, S. S. Morris, K. Berkeley, M. LeClerc, A. Simpson, S. D. Sommerville, G. Grimmett, L. Adams, M. Levine, S. S. 2017-11-01 doi:10.1101/212639 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Selective Recruitment of Cortical Neurons by Electrical Stimulation ]]> https://biorxiv.org/content/10.1101/213017v1?rss=1 Komarov, M. Malerba, P. Nunez, P. Halgren, E. Bazhenov, M. 2017-11-02 doi:10.1101/213017 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ A linear-time algorithm to sample the dual-birth model ]]> https://biorxiv.org/content/10.1101/226423v1?rss=1 Moshiri, N. 2017-11-28 doi:10.1101/226423 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ Catalytic potential and disturbance rejection of glycolytic kinases in the human red blood cell ]]> https://biorxiv.org/content/10.1101/227058v1?rss=1 Yurkovich, J. T. Alcantar, M. A. Haiman, Z. B. Palsson, B. O. 2017-11-30 doi:10.1101/227058 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ RIFRAF: a frame-resolving consensus algorithm ]]> https://biorxiv.org/content/10.1101/227520v1?rss=1 Eren, K. Murrell, B. 2017-12-03 doi:10.1101/227520 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Multi-scale model of the proteomic and metabolic consequences of reactive oxygen species ]]> https://biorxiv.org/content/10.1101/227892v1?rss=1 Yang, L. Mih, N. Yurkovich, J. T. Park, J. H. Seo, S. Kim, D. Monk, J. M. Lloyd, C. J. Tan, J. Gao, Y. Broddrick, J. T. Chen, K. Heckmann, D. Feist, A. M. Palsson, B. O. 2017-12-02 doi:10.1101/227892 Cold Spring Harbor Laboratory Press 2017-12-02 <![CDATA[ Assembly-free and alignment-free sample identification using genome skims ]]> https://biorxiv.org/content/10.1101/230409v1?rss=1 Sarmashghi, S. Bohmann, K. Gilbert, M. T. P. Bafna, V. Mirarab, S. 2017-12-08 doi:10.1101/230409 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons ]]> https://biorxiv.org/content/10.1101/230474v1?rss=1 Eren, K. Weaver, S. Ketteringham, R. Valentyn, M. Laird Smith, M. Kumar, V. Mohan, S. Kosakovsky Pond, S. L. Murrell, B. 2017-12-07 doi:10.1101/230474 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ Integrated analysis of anatomical and electrophysiological human intracranial data ]]> https://biorxiv.org/content/10.1101/230912v1?rss=1 Stolk, A. Griffin, S. van der Meij, R. Dewar, C. Saez, I. Lin, J. J. Piantoni, G. Schoffelen, J.-M. Knight, R. T. Oostenveld, R. 2017-12-08 doi:10.1101/230912 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Genome wide association study of behavioral, physiological and gene expression traits in a multigenerational mouse intercross ]]> https://biorxiv.org/content/10.1101/230920v1?rss=1 Gonzales, N. M. Seo, J. Hernandez-Cordero, A. I. St. Pierre, C. L. Gregory, J. S. Distler, M. G. Abney, M. Canzar, S. Lionikas, A. Palmer, A. A. 2017-12-08 doi:10.1101/230920 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Study of the mitotic chromatin shows involvement of histone modifications in bookmarking and reveals nucleosome deposition patterns ]]> https://biorxiv.org/content/10.1101/233056v1?rss=1 Javasky, E. Shamir, I. Gandhi, S. Egri, S. Sandler, O. Kaplan, N. Jaffe, J. D. Goren, A. Simon, I. 2017-12-12 doi:10.1101/233056 Cold Spring Harbor Laboratory Press 2017-12-12 <![CDATA[ The Anorexia Nervosa Genetics Initiative: Overview and Methods ]]> https://biorxiv.org/content/10.1101/234013v1?rss=1 Thornton, L. M. Munn-Chernoff, M. A. Baker, J. H. Jureus, A. Parker, R. Henders, A. K. Larsen, J. T. Petersen, L. Watson, H. J. Yilmaz, Z. Kirk, K. M. Gordon, S. Leppa, V. M. Martin, F. C. Whiteman, D. C. Olsen, C. M. Werge, T. Pedersen, N. L. Kaye, W. Bergen, A. W. Halmi, K. A. Strober, M. Kaplan, A. S. Woodside, D. B. Mitchell, J. Johnson, C. L. Brandt, H. Crawford, S. Horwood, L. J. Boden, J. M. Pearson, J. F. Duncan, L. E. Grove, J. Mattheisen, M. Jordan, J. Kennedy, M. A. Birgegard, A. Lichtenstein, P. Norring, C. Wade, T. D. Montgomery, G. Martin, 2017-12-15 doi:10.1101/234013 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Bivariate Gaussian Mixture Model of GWAS (BGMG)quantifies polygenic overlap between complex traitsbeyond genetic correlation ]]> https://biorxiv.org/content/10.1101/240275v1?rss=1 Frei, O. Holland, D. Smeland, O. B. Shadrin, A. A. Fan, C. C. Witoelar, A. Wang, Y. Djurovic, S. Thompson, W. Andreassen, O. A. Dale, A. M. 2017-12-27 doi:10.1101/240275 Cold Spring Harbor Laboratory Press 2017-12-27 <![CDATA[ IMPROVEMENTS TO BAYESIAN GENE ACTIVITY STATE ESTIMATION FROM GENOME-WIDE TRANSCRIPTOMICS DATA ]]> https://biorxiv.org/content/10.1101/241000v1?rss=1 Disselkoen, C. Hekman, N. Gilbert, B. Benson, S. Anderson, M. DeJongh, M. Best, A. Tintle, N. 2017-12-29 doi:10.1101/241000 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ Viral gain-of-function experiments uncover residues under diversifying selection in nature ]]> https://biorxiv.org/content/10.1101/242495v1?rss=1 Maddamsetti, R. Johnson, D. T. Spielman, S. J. Petrie, K. L. Marks, D. S. Meyer, J. R. 2018-01-03 doi:10.1101/242495 Cold Spring Harbor Laboratory Press 2018-01-03 <![CDATA[ Assembly of Long Error-Prone Reads Using Repeat Graphs ]]> https://biorxiv.org/content/10.1101/247148v1?rss=1 Kolmogorov, M. Yuan, J. Lin, Y. Pevzner, P. 2018-01-12 doi:10.1101/247148 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ Characterizing concentration-dependent neural dynamics of 4-aminopyridine-induced epileptiform activity ]]> https://biorxiv.org/content/10.1101/252726v1?rss=1 Myers, T. L. Gonzalez, O. C. Stein, J. B. Bazhenov, M. 2018-01-24 doi:10.1101/252726 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Beyond synthetic lethality: multiple gene interaction types play a key functional role in cancer ]]> https://biorxiv.org/content/10.1101/253120v1?rss=1 Magen, A. Das, A. Sang Lee, J. Sharmin, M. Lugo, A. Gutkind, S. Ruppin, E. Hannenhalli, S. 2018-01-24 doi:10.1101/253120 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Sex-specific impact of prenatal androgens on intrinsic functional connectivity between social brain default mode subsystems ]]> https://biorxiv.org/content/10.1101/253310v1?rss=1 Lombardo, M. V. Auyeung, B. Pramparo, T. Quartier, A. Courraud, J. Holt, R. J. Waldman, J. Ruigrok, A. Mooney, N. Lai, M.-C. Kundu, P. Bullmore, E. T. Mandel, J.-L. Piton, A. Baron-Cohen, S. 2018-01-25 doi:10.1101/253310 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish ]]> https://biorxiv.org/content/10.1101/254854v1?rss=1 Brennan, R. S. Healy, T. M. Bryant, H. J. La, M. V. Schulte, P. M. Whitehead, A. 2018-01-27 doi:10.1101/254854 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ Social behavior and anxiety contribute to nicotine self-administration in adolescent outbred rats ]]> https://biorxiv.org/content/10.1101/257097v1?rss=1 Wang, T. Han, W. Chitre, A. Polesskaya, O. Solberg Woods, L. C. Palmer, A. A. Chen, H. 2018-01-30 doi:10.1101/257097 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Trans-ancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/257311v1?rss=1 Walters, R. K. Adams, M. J. Adkins, A. E. Aliev, F. Bacanu, S.-A. Batzler, A. Bertelsen, S. Biernacka, J. Bigdeli, T. B. Chen, L.-S. Clarke, T.-K. Chou, Y.-L. Degenhardt, F. Docherty, A. R. Fontanillas, P. Foo, J. Fox, L. Frank, J. Giegling, I. Gordon, S. Hack, L. -, Hartz, S. M. Heilmann-Heimbach, S. Herms, S. Hodgkinson, C. Hoffmann, P. Hottenga, J.-J. Kennedy, M. A. Alanne-Kinnunen, M. Konte, B. Lahti, J. Lahti-Pulkkinen, M. Ligthart, L. Loukola, A.-M. Maher, B. S. Mbarek, H. McIntosh, A. M. McQueen, M. B. Milaneschi, Y. Palviainen, T. Pearson, J. 2018-03-10 doi:10.1101/257311 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation ]]> https://biorxiv.org/content/10.1101/258194v1?rss=1 Arora, K. Corbett, K. D. 2018-02-01 doi:10.1101/258194 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Local Cortical Activity Of Distant Brain Areas Can Time-Lock To The Respiratory Rhythm In The Freely Behaving Rat ]]> https://biorxiv.org/content/10.1101/259457v1?rss=1 Rojas-Libano, D. Wimmer del Solar, J. Aguilar, M. Montefusco-Siegmund, R. Maldonado, P. E. 2018-02-04 doi:10.1101/259457 Cold Spring Harbor Laboratory Press 2018-02-04 <![CDATA[ Theta bursts precede, and spindles follow, cortical and thalamic downstates in human NREM sleep ]]> https://biorxiv.org/content/10.1101/260786v1?rss=1 Gonzalez, C. E. Mak-McCully, R. Cash, S. Chauvel, P. Bastuji, H. Rey, M. Halgren, E. 2018-02-06 doi:10.1101/260786 Cold Spring Harbor Laboratory Press 2018-02-06 <![CDATA[ ClusterPicker-II: Massively scalable transmission clustering using phylogenetic trees ]]> https://biorxiv.org/content/10.1101/261354v1?rss=1 Moshiri, A. N. 2018-02-07 doi:10.1101/261354 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues ]]> https://biorxiv.org/content/10.1101/261594v1?rss=1 Tsang, T. K. Bushong, E. A. Boassa, D. Hu, J. Romoli, B. Phan, S. Dulcis, D. Su, C.-Y. Ellisman, M. H. 2018-02-07 doi:10.1101/261594 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP pathways in macrophages ]]> https://biorxiv.org/content/10.1101/263434v1?rss=1 Muse, E. D. Yu, S. Edillor, C. R. Tao, J. Spann, N. J. Troutman, T. D. Seidman, J. S. Henke, A. Roland, J. T. Ozeki, K. A. McDonald, J. G. Bahadorani, J. Tsimikas, S. Grossman, T. R. Tremblay, M. S. Glass, C. K. 2018-02-11 doi:10.1101/263434 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ Transcriptional Activation of a Cartilaginous Fish (Elephant Shark, Callorhinchus milii) Mineralocorticoid Receptor by Corticosteroids, Progestins and Spironolactone ]]> https://biorxiv.org/content/10.1101/265348v1?rss=1 Katsu, Y. Kohno, S. Oka, K. Lin, X. Otake, S. Pillai, N. E. Takagi, W. Hyodo, S. Venkatesh, B. Baker, M. E. 2018-02-13 doi:10.1101/265348 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ MARGE: Mutation Analysis for Regulatory Genomic Elements ]]> https://biorxiv.org/content/10.1101/268839v1?rss=1 Link, V. M. Romanoski, C. E. Metzler, D. Glass, C. K. 2018-02-21 doi:10.1101/268839 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing ]]> https://biorxiv.org/content/10.1101/273433v1?rss=1 Ganem, N. S. Ben-Asher, N. Manning, A. C. Deffit, S. N. Washburn, M. C. Wheeler, E. C. Yeo, G. W. Ben-Naim Zgayer, O. Mantsur, E. Hundley, H. A. Lamm, A. T. 2018-02-28 doi:10.1101/273433 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Strong Episodic Selection for Natural Competence for Transformation Due to Host-Pathogen Dynamics ]]> https://biorxiv.org/content/10.1101/275651v1?rss=1 Palmer, N. D. Cartwright, R. A. 2018-03-03 doi:10.1101/275651 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures ]]> https://biorxiv.org/content/10.1101/277277v1?rss=1 Choudhary, K. S. Mih, N. Monk, J. Kavvas, E. Yurkovich, J. T. Sakoulas, G. Palsson, B. O. 2018-03-06 doi:10.1101/277277 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA ]]> https://biorxiv.org/content/10.1101/283812v1?rss=1 Welkie, D. G. Rubin, B. E. Chang, Y.-G. Diamond, S. Rifkin, S. A. LiWang, A. Golden, S. S. 2018-03-17 doi:10.1101/283812 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Nuisance Effects and the Limitations of Nuisance Regression in Dynamic Functional Connectivity fMRI ]]> https://biorxiv.org/content/10.1101/285239v1?rss=1 Nalci, A. Rao, B. D. Liu, T. T. 2018-03-21 doi:10.1101/285239 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Changes in the genetic requirements for microbial interactions with increasing community complexity ]]> https://biorxiv.org/content/10.1101/290353v1?rss=1 Morin, M. Pierce, E. C. Dutton, R. J. 2018-03-28 doi:10.1101/290353 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Development of a joint evolutionary model for the genome and the epigenome ]]> https://biorxiv.org/content/10.1101/293076v1?rss=1 Lu, J. Cao, X. Zhong, S. 2018-04-02 doi:10.1101/293076 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ An inter-chromosomal transcription hub activates the unfolded protein response in plasma cells ]]> https://biorxiv.org/content/10.1101/295915v1?rss=1 Bortnick, A. He, Z. Aubrey, M. Chandra, V. Denholtz, M. Chen, K. Lin, Y. C. Murre, C. 2018-04-06 doi:10.1101/295915 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences ]]> https://biorxiv.org/content/10.1101/297267v1?rss=1 Moshiri, N. Ragonnet-Cronin, M. Wertheim, J. O. Mirarab, S. 2018-04-07 doi:10.1101/297267 Cold Spring Harbor Laboratory Press 2018-04-07 <![CDATA[ Parameterizing neural power spectra ]]> https://biorxiv.org/content/10.1101/299859v1?rss=1 Haller, M. Donoghue, T. Peterson, E. Varma, P. Sebastian, P. Gao, R. Noto, T. Knight, R. T. Shestyuk, A. Voytek, B. 2018-04-11 doi:10.1101/299859 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome ]]> https://biorxiv.org/content/10.1101/300483v1?rss=1 Chen, W. Yan, Z. Li, S. Huang, N. Huang, X. Zhang, J. Zhong, S. 2018-04-12 doi:10.1101/300483 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Assessing key decisions for transcriptomic data integration in biochemical networks ]]> https://biorxiv.org/content/10.1101/301945v1?rss=1 Richelle, A. Joshi, C. Lewis, N. E. 2018-04-16 doi:10.1101/301945 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Cycle-by-cycle analysis of neural oscillations ]]> https://biorxiv.org/content/10.1101/302000v1?rss=1 Cole, S. R. Voytek, B. 2018-04-16 doi:10.1101/302000 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ Development and validation of a phenotypic high-content imaging assay for assessing the antiviral activity of small-molecule inhibitors targeting the Zika virus ]]> https://biorxiv.org/content/10.1101/302927v1?rss=1 Bernatchez, J. A. Yang, Z. Coste, M. Li, J. Beck, S. Liu, Y. Clark, A. E. Zhu, Z. Luna, L. A. Sohl, C. Purse, B. W. Li, R. Siqueira-Neto, J. L. 2018-04-17 doi:10.1101/302927 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ A novel sialylation site on Neisseria gonorrhoeae lipooligosaccharide links heptose II lactose expression with pathogenicity ]]> https://biorxiv.org/content/10.1101/302968v1?rss=1 Ram, S. Gulati, S. Lewis, L. A. Chakraborti, S. Zheng, B. DeOliveira, R. B. Reed, G. W. Cox, A. D. Li, J. St. Michael, F. Stupak, J. Su, X.-H. Saha, S. Landig, C. S. Varki, A. RICE, P. A. 2018-04-17 doi:10.1101/302968 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Movement-related activity dominates cortex during sensory-guided decision making ]]> https://biorxiv.org/content/10.1101/308288v1?rss=1 Musall, S. Kaufman, M. T. Gluf, S. Churchland, A. 2018-04-25 doi:10.1101/308288 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Enzyme promiscuity shapes evolutionary innovation and optimization ]]> https://biorxiv.org/content/10.1101/310946v1?rss=1 Guzman, G. I. Sandberg, T. E. LaCroix, R. A. Nyerges, A. Papp, H. de Raad, M. King, Z. A. Northen, T. R. Notebaart, R. A. Pal, C. Palsson, B. O. Papp, B. Feist, A. M. 2018-05-03 doi:10.1101/310946 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Mechanistic Origins of Dynamic Instability in Filaments from the Phage Tubulin, PhuZ ]]> https://biorxiv.org/content/10.1101/311498v1?rss=1 Zehr, E. A. Rohu, A. Liu, Y. Verba, K. A. Pogliano, J. Grigorieff, N. Agard, D. A. 2018-04-30 doi:10.1101/311498 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Two Isoforms of the Guanine Nucleotide Exchange Factor, Daple/CCDC88C Cooperate as Tumor Suppressors ]]> https://biorxiv.org/content/10.1101/312934v1?rss=1 Dunkel, Y. Ear, J. Mittal, Y. Lim, B. Liu, L. Holda, M. Nitsche, U. Barbazan, J. Goel, A. Janssen, K.-P. Aznar, N. Ghosh, P. 2018-05-02 doi:10.1101/312934 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria ]]> https://biorxiv.org/content/10.1101/315499v1?rss=1 Peters, J. M. Koo, B.-M. Patino, R. Heussler, G. E. Hearne, C. C. Inclan, Y. Hawkins, J. S. Lu, C. H. S. Harden, M. M. Osadnik, H. Peters, J. E. Engel, J. N. Dutton, R. J. Grossman, A. D. Gross, C. A. Rosenberg, O. S. 2018-05-05 doi:10.1101/315499 Cold Spring Harbor Laboratory Press 2018-05-05 <![CDATA[ Spatial gene-by-environment mapping for schizophrenia reveals locale of upbringing effects beyond urban-rural differences ]]> https://biorxiv.org/content/10.1101/315820v1?rss=1 Fan, C. C. McGrath, J. J. Appadurai, V. Buil, A. Gandal, M. J. Schork, A. J. Mortensen, P. B. Agerbo, E. Geschwind, S. A. Geschwind, D. Werge, T. Thompson, W. K. Pedersen, C. B. 2018-05-11 doi:10.1101/315820 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics ]]> https://biorxiv.org/content/10.1101/318972v1?rss=1 Heckmann, D. Zielinski, D. C. Palsson, B. O. 2018-05-10 doi:10.1101/318972 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Links between environment, diet, and the hunter-gatherer microbiome ]]> https://biorxiv.org/content/10.1101/319673v1?rss=1 Fragiadakis, G. K. Smits, S. A. Sonnenburg, E. D. Van Treuren, W. Reid, G. Knight, R. Manjurano, A. Changalucha, J. Dominguez-Bello, M. G. Leach, J. Sonnenburg, J. L. 2018-05-15 doi:10.1101/319673 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution ]]> https://biorxiv.org/content/10.1101/320747v1?rss=1 Phaneuf, P. V. Gosting, D. Palsson, B. Feist, A. 2018-05-15 doi:10.1101/320747 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ The Repertoire of Mutational Signatures in Human Cancer ]]> https://biorxiv.org/content/10.1101/322859v1?rss=1 Alexandrov, L. Kim, J. Haradhvala, N. J. Huang, M. N. Ng, A. W. T. Boot, A. Covington, K. R. Gordenin, D. A. Bergstrom, E. Lopez-Bigas, N. Klimczak, L. J. McPherson, J. R. Morganella, S. Sabarinathan, R. Wheeler, D. A. Mustonen, V. Getz, G. Rozen, S. G. Stratton, M. R. PCAWG Mutational Signatures Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net, 2018-05-15 doi:10.1101/322859 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ TreeSwift: a massively scalable Python package for trees ]]> https://biorxiv.org/content/10.1101/325522v1?rss=1 Moshiri, N. 2018-05-18 doi:10.1101/325522 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Hyperactive Rac1 drives MAPK-independent proliferation in melanoma by assembly of a mechanosensitive dendritic actin network ]]> https://biorxiv.org/content/10.1101/326710v1?rss=1 Mohan, A. S. Dean, K. M. Kasitinon, S. Y. Isogai, T. Siruvallur Murali, V. Han, S. J. Roudot, P. Groisman, A. Welf, E. Danuser, G. 2018-05-22 doi:10.1101/326710 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Relevance of coral geometry in the outcomes of the coral-algal benthic war ]]> https://biorxiv.org/content/10.1101/327031v1?rss=1 George, E. E. Mullinix, J. Meng, F. Bailey, B. Edwards, C. Felts, B. Haas, A. Hartmann, A. C. Mueller, B. Nulton, J. Roach, T. N. F. Salamon, P. Silveira, C. B. Vermeij, M. J. A. Rohwer, F. L. Luque, A. 2018-05-24 doi:10.1101/327031 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Impact of MMP-2 and MMP-9 activation on wound healing, tumor growth and RACPP cleavage ]]> https://biorxiv.org/content/10.1101/327791v1?rss=1 Ellies, L. G. Hingorani, D. V. Lippert, C. N. Crisp, J. L. Savariar, E. N. Hasselmann, J. P. C. Kuo, C. P. C. Nguyen, Q. T. Tsien, R. Y. Whitney, M. A. 2018-05-21 doi:10.1101/327791 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Using global t-SNE to preserve inter-cluster data structure ]]> https://biorxiv.org/content/10.1101/331611v1?rss=1 Zhou, Y. Sharpee, T. 2018-05-25 doi:10.1101/331611 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Using deep whole genome sequence, transcriptome and epigenome data to characterize the mutational burden of induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/334870v1?rss=1 D'Antonio, M. Benaglio, P. Jakubosky, D. A. Greenwald, W. W. Matsui, H. Donovan, M. K. R. Li, H. Smith, E. N. D'Antonio-Chronowska, A. Frazer, K. A. 2018-05-30 doi:10.1101/334870 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ PI(4,5)P2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding ]]> https://biorxiv.org/content/10.1101/341248v1?rss=1 Johnson, K. A. Budicini, M. R. Urata, S. Bhattarai, N. Gerstman, B. S. Chapagain, P. P. Li, S. Stahelin, R. V. 2018-06-07 doi:10.1101/341248 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 ]]> https://biorxiv.org/content/10.1101/343913v1?rss=1 Gao, Y. Yurkovich, J. T. Seo, S. W. Kabimoldayev, I. Drager, A. Chen, K. Sastry, A. V. Fang, X. Mih, N. Yang, L. Eichner, J. Cho, B.-K. Kim, D. Palsson, B. O. 2018-06-11 doi:10.1101/343913 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ The Evolution of White Matter Microstructural Changes After Mild Traumatic Brain Injury: A Longitudinal DTI and NODDI Study ]]> https://biorxiv.org/content/10.1101/345629v1?rss=1 Palacios, E. Owen, J. P. Yuh, E. L. Wang, M. B. Vassar, M. J. Ferguson, A. R. Diaz-Arrastia, R. Giacino, J. T. Okonkwo, D. O. Robertson, C. S. Stein, M. B. Temkin, N. Jain, S. McCrea, M. Mac Donald, C. L. Manley, G. T. Mukherjee, P. TRACK-TBI Investigators, 2018-06-14 doi:10.1101/345629 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Prognostic Relevance of CCDC88C (Daple) Transcripts in the Peripheral Blood of Patients with Malignant Melanoma ]]> https://biorxiv.org/content/10.1101/346551v1?rss=1 Dunkel, Y. Reid, A. Ear, J. Aznar, N. Millward, M. Gray, E. Pearce, R. Ziman, M. Ghosh, P. 2018-06-13 doi:10.1101/346551 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages ]]> https://biorxiv.org/content/10.1101/347716v1?rss=1 Gauglitz, J. M. Aceves, C. M. Aksenov, A. A. Aleti, G. Almaliti, J. Bouslimani, A. Brown, E. A. Campeau, A. Caraballo-Rodriguez, A. M. Chaar, R. da Silva, R. R. Demko, A. M. Di Ottavio, F. Elijah, E. Ernst, M. Ferguson, L. P. Holmes, X. van der Hooft, J. J. J. Jarmusch, A. K. Jiang, L. Kang, K. B. Koester, I. Kwan, B. Ni, B. Li, J. Li, Y. Melnik, A. V. Molina-Santiago, C. Oom, A. L. Panitchpakdi, M. W. Petras, D. Quinn, R. Sikora, N. C. Spengler, K. Teke, B. Tripathi, A. Ul-Hasan, S. Vargas, F. Vrbanac, A. Vu, A. Q. Wang, S. C. Weldon, K. Wilson, K. W 2018-06-15 doi:10.1101/347716 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite ]]> https://biorxiv.org/content/10.1101/350991v1?rss=1 Lieven, C. Beber, M. E. Olivier, B. G. Bergmann, F. T. Babaei, P. Bartell, J. A. Blank, L. M. Chauhan, S. Correia, K. Diener, C. Dräger, A. Ebert, B. E. Edirisinghe, J. N. Fleming, R. M. T. Garcia-Jimenez, B. van Helvoirt, W. Henry, C. Hermjakob, H. Herrgard, M. J. Kim, H. U. King, Z. Koehorst, J. J. Klamt, S. Klipp, E. Lakshmanan, M. Le Novere, N. Lee, D.-Y. Lee, S. Y. Lee, S. Lewis, N. E. Ma, H. Machado, D. Mahadevan, R. Maia, P. Mardinoglu, A. Medlock, G. L. Monk, J. Nielsen, J. Nielsen, L. K. Nogales, J. Nookaew, I. Resendis, O. Palsson, B. 2018-06-21 doi:10.1101/350991 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry ]]> https://biorxiv.org/content/10.1101/351130v1?rss=1 Zhang, F. Wei, K. Slowikowski, K. Fonseka, C. Y. Rao, D. A. Kelly, S. Goodman, S. M. Tabechian, D. Hughes, L. B. Salomon-Escoto, K. Watts, G. F. M. Apruzzese, W. Lieb, D. J. Boyle, D. L. Mandelin, A. M. Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Boyce, B. F. DiCarlo, E. Gravallese, E. M. Gregersen, P. K. Moreland, L. Firestein, G. S. Hacohen, N. Nusbaum, C. Lederer, J. A. Perlman, H. Pitzalis, C. Filer, A. Holers, V. M. Bykerk, V. P. Donlin, L. T. Anolik, J. H. Brenner, M. B. Raychaudhuri, S. 2018-06-20 doi:10.1101/351130 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion ]]> https://biorxiv.org/content/10.1101/351387v1?rss=1 25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology. ]]> Gutierrez, J. M. Feizi, A. Li, S. Kallehauge, T. B. Hefzi, H. Grav, L. M. Ley, D. Hizal, D. B. Betenbaugh, M. J. Voldborg, B. Kildegaard, H. F. Lee, G. M. Palsson, B. O. Nielsen, J. Lewis, N. 2018-06-20 doi:10.1101/351387 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Allele-specific NKX2-5 binding underlies multiple genetic associations with human EKG traits ]]> https://biorxiv.org/content/10.1101/351411v1?rss=1 Benaglio, P. D'Antonio-Chronowska, A. Greenwald, W. W. DeBoever, C. Li, H. Drees, F. Singhal, S. Matsui, H. D'Antonio, M. Smith, E. N. Frazer, K. A. 2018-06-20 doi:10.1101/351411 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Communication and quorum sensing in non-living mimics of eukaryotic cells ]]> https://biorxiv.org/content/10.1101/352666v1?rss=1 Niederholtmeyer, H. Chaggan, C. Devaraj, N. K. 2018-06-20 doi:10.1101/352666 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION ]]> https://biorxiv.org/content/10.1101/352674v1?rss=1 Justice, A. E. Karaderi, T. Highland, H. M. Young, K. L. Graff, M. Lu, Y. Turcot, V. Auer, P. L. Fine, R. S. Guo, X. Schurmann, C. Lempradl, A. Marouli, E. Mahajan, A. Winkler, T. W. Locke, A. E. Medina-Gomez, C. Esko, T. Vedantam, S. Giri, A. Lo, K. S. Alfred, T. Mudgal, P. Ng, M. C. Heard-Costa, N. C. Feitosa, M. F. Manning, A. K. Willems, S. M. Sivapalaratnam, S. Abecasis, G. Alam, D. S. Allison, M. Amouyel, P. Arzumanyan, Z. Balkau, B. Bastarache, L. Bergmann, S. Bielak, L. F. Blüher, M. Boehnke, M. Boeing, H. Boerwinkle, E. Böger, 2018-06-30 doi:10.1101/352674 Cold Spring Harbor Laboratory Press 2018-06-30 <![CDATA[ CDeep3M - Plug-and-Play cloud based deep learning for image segmentation of light, electron and X-ray microscopy ]]> https://biorxiv.org/content/10.1101/353425v1?rss=1 Haberl, M. Churas, C. Tindall, L. Boassa, D. Phan, S. Bushong, E. A. Madany, M. Akay, R. Deerinck, T. J. Peltier, S. T. Ellisman, M. H. 2018-06-21 doi:10.1101/353425 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ TP53 mutations promote immunogenic activity in breast cancer ]]> https://biorxiv.org/content/10.1101/354779v1?rss=1 Liu, Z. Jiang, Z. Gao, Y. Wang, L. Chen, C. Wang, X. 2018-06-24 doi:10.1101/354779 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ Evidence that recurrent Group A streptococcus tonsillitis is animmunosusceptibility disease involving antibody deficiency and aberrant Tfh cells ]]> https://biorxiv.org/content/10.1101/356741v1?rss=1 Dan, J. M. Havenar-Daughton, C. Kendric, K. Kaushik, K. Rosales, S. Anderson, E. LaRock, C. Vijayanand, P. Seumois, G. Layfield, D. Cutress, R. Ottensmeier, C. Lindestam Arlehamn, C. Sette, A. Nizet, V. Bothwell, M. Brigger, M. Crotty, S. 2018-06-27 doi:10.1101/356741 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans ]]> https://biorxiv.org/content/10.1101/357756v1?rss=1 Reddy, K. C. Dror, T. Underwood, R. S. Osman, G. A. Desjardins, C. A. Cuomo, C. A. Barkoulas, M. Troemel, E. R. 2018-06-28 doi:10.1101/357756 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Peak p-values and false discovery rate inference in neuroimaging ]]> https://biorxiv.org/content/10.1101/358051v1?rss=1 Schwartzman, A. Telschow, F. 2018-06-28 doi:10.1101/358051 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Breakdown of spatial coding and neural synchronization in epilepsy ]]> https://biorxiv.org/content/10.1101/358580v1?rss=1 Shuman, T. Aharoni, D. Cai, D. J. Lee, C. R. Chavlis, S. Taxidis, J. Flores, S. E. Cheng, K. Javaherian, M. Kaba, C. C. Shtrahman, M. Kakhurin, K. I. Masmanidis, S. Khakh, B. S. Poirazi, P. Silva, A. J. Golshani, P. 2018-06-29 doi:10.1101/358580 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ VPAC1 couples with TRPV4 channel to promote calcium-dependent gastric cancer progression ]]> https://biorxiv.org/content/10.1101/360404v1?rss=1 Tang, B. Wu, J. Zhu, M. X. Sun, X. Liu, J. Xie, R. Dong, T. X. Xiao, Y. Carethers, J. M. Yang, S.-M. Dong, H. 2018-07-02 doi:10.1101/360404 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ Beauty-in-averageness and its contextual modulations: A Bayesian statistical account ]]> https://biorxiv.org/content/10.1101/360651v1?rss=1 Ryali, C. Yu, A. J. 2018-07-04 doi:10.1101/360651 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Computational modeling of social face perception in humans: Leveraging the active appearance model ]]> https://biorxiv.org/content/10.1101/360776v1?rss=1 Guan, J. Ryali, C. Yu, A. J. 2018-07-03 doi:10.1101/360776 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Ad-Seq, a genome-wide DNA-adduct profiling assay ]]> https://biorxiv.org/content/10.1101/364794v1?rss=1 Harismendy, O. Howell, S. 2018-07-08 doi:10.1101/364794 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria ]]> https://biorxiv.org/content/10.1101/367797v1?rss=1 Ortega, F. E. Koslover, E. F. Theriot, J. A. 2018-07-12 doi:10.1101/367797 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Dorsal Premotor Contributions to Auditory Rhythm Perception: Causal Transcranial Magnetic Stimulation Studies of Interval, Tempo, and Phase ]]> https://biorxiv.org/content/10.1101/368597v1?rss=1 Ross, J. M. Iversen, J. R. Balasubramaniam, R. R. 2018-07-13 doi:10.1101/368597 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Overview of the SAMPL6 host-guest binding affinity prediction challenge ]]> https://biorxiv.org/content/10.1101/371724v1?rss=1 Rizzi, A. Murkli, S. McNeill, J. N. Yao, W. Sullivan, M. Gilson, M. K. Chiu, M. W. Isaacs, L. Gibb, B. C. Mobley, D. L. Chodera, J. D. 2018-07-19 doi:10.1101/371724 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Spatial Control of Neuronal Metabolism Through Glucose-Mediated Mitochondrial Transport Regulation ]]> https://biorxiv.org/content/10.1101/372284v1?rss=1 Agrawal, A. Pekkurnaz, G. Koslover, E. F. 2018-07-18 doi:10.1101/372284 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Co-occurring genetic alterations in the RAS pathway promote resistance to MET inhibitor treatment in non-small cell lung cancer with a MET exon 14 skipping mutation ]]> https://biorxiv.org/content/10.1101/374181v1?rss=1 Rotow, J. K. Gui, P. Wu, W. Raymond, V. M. Lanman, R. B. Kaye, F. J. Peled, N. Fece de la Cruz, F. Nadres, B. Corcoran, R. B. Yeh, I. Bastian, B. C. Starostik, P. Newsom, K. Olivas, V. R. Wolff, A. M. Fraser, J. S. Collisson, E. A. McCoach, C. E. Blakely, C. M. Bivona, T. G. 2018-07-22 doi:10.1101/374181 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ A conserved mechanism for meiotic chromosome organization through self-assembly of a filamentous chromosome axis core ]]> https://biorxiv.org/content/10.1101/375220v1?rss=1 West, A. M. V. Rosenberg, S. C. Ur, S. N. Lehmer, M. K. Ye, Q. Hagemann, G. Caballero, I. Uson, I. Herzog, F. Corbett, K. D. 2018-07-24 doi:10.1101/375220 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ A nonlinear simulation framework supports adjusting for age when analyzing BrainAGE. ]]> https://biorxiv.org/content/10.1101/377648v1?rss=1 Le, T. T. Kuplicki, R. McKinney, B. A. Yeh, H.-w. Thompson, W. K. Tulsa 1000 Investigators, Paulus, M. P. 2018-07-26 doi:10.1101/377648 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Episodic Memory Can Replace Active Storage in Visual Working Memory ]]> https://biorxiv.org/content/10.1101/381848v1?rss=1 Schurgin, M. W. Cunningham, C. A. Egeth, H. E. Brady, T. F. 2018-08-01 doi:10.1101/381848 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ TreeN93: a non-parametric distance-based method for inferring viral transmission clusters ]]> https://biorxiv.org/content/10.1101/383190v1?rss=1 Moshiri, N. 2018-08-02 doi:10.1101/383190 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Long-read amplicon denoising ]]> https://biorxiv.org/content/10.1101/383794v1?rss=1 Kumar, V. Vollbrecht, T. Chernyshev, M. Mohan, S. Hanst, B. Bavafa, N. Lorenzo, A. Ketteringham, R. Eren, K. Golden, M. Oliveira, M. F. Murrell, B. 2018-08-03 doi:10.1101/383794 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions ]]> https://biorxiv.org/content/10.1101/384099v1?rss=1 Richelle, A. Chiang, A. W. T. Kuo, C.-C. Lewis, N. E. 2018-08-03 doi:10.1101/384099 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive ]]> https://biorxiv.org/content/10.1101/386441v1?rss=1 1000 TB data worth of raw sequence data) into a single unified dataset of allelic read counts for nearly 300,000 variants of biomedical relevance curated by NCBI dbSNP, where germline variants were detected in a median of 912 sequencing runs, and somatic variants were detected in a median of 4,876 sequencing runs, suggesting that this dataset facilitates identification of sequencing runs that harbor variants of interest. Allelic read counts obtained using a targeted alignment were very similar to read counts obtained from whole genome alignment. Analyzing allelic read count data for matched DNA and RNA samples from tumors, we find that RNA-seq can also recover variants identified by WXS, suggesting that reprocessed allelic read counts can support variant detection across different library strategies in SRA. This study provides a rich database of known human variants across SRA samples that can support future meta-analyses of human sequence variation. ]]> Tsui, B. Y. Dow, M. Skola, D. Carter, H. 2018-08-07 doi:10.1101/386441 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Human pluripotent stem cell-derived brain pericyte-like cells induce blood-brain barrier properties ]]> https://biorxiv.org/content/10.1101/387100v1?rss=1 Stebbins, M. J. Gastfriend, B. D. Canfield, S. G. Lee, M.-S. Richards, D. Faubion, M. G. Li, W.-J. Daneman, R. Palecek, S. P. Shusta, E. V. 2018-08-07 doi:10.1101/387100 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Human frontoparietal cortex represents behaviorally-relevant target status during invariant object recognition ]]> https://biorxiv.org/content/10.1101/387498v1?rss=1 Henderson, M. M. Serences, J. 2018-08-09 doi:10.1101/387498 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Reconciling fMRI and EEG indices of attentional modulations in human visual cortex ]]> https://biorxiv.org/content/10.1101/391193v1?rss=1 Itthipuripat, S. Sprague, T. Serences, J. 2018-08-13 doi:10.1101/391193 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA ]]> https://biorxiv.org/content/10.1101/396275v1?rss=1 Yang, E.-W. Bahn, J. H. Hsiao, E. Y.-H. Tan, B. X. Sun, Y. Fu, T. Zhou, B. Van Nostrand, E. L. Pratt, G. A. Freese, P. Wei, X. Quinones-Valdez, G. Urban, A. E. Graveley, B. R. Burge, C. B. Yeo, G. W. Xiao, X. 2018-08-20 doi:10.1101/396275 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ The genetic architecture of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/399402v1?rss=1 Grasby, K. L. Jahanshad, N. Painter, J. N. Colodro-Conde, L. Bralten, J. Hibar, D. P. Lind, P. A. Pizzagalli, F. Ching, C. R. McMahon, M. A. Shatokhina, N. Zsembik, L. C. P. Agartz, I. Alhusaini, S. Almeida, M. A. Alnaes, D. Amlien, I. K. Andersson, M. Ard, T. Armstrong, N. J. Ashley-Koch, A. Bernard, M. Brouwer, R. M. Buimer, E. E. Bülow, R. Bürger, C. Cannon, D. M. Chakravarty, M. Chen, Q. Cheung, J. W. Couvy-Duchesne, B. Dale, A. M. Dalvie, S. de Araujo, T. K. de Zubicaray, G. I. de Zwarte, S. M. den Braber, A. Doan, N. T. Dohm, K. Ehrlich, S. Engel 2018-09-03 doi:10.1101/399402 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Planar cell polarity pathway and development of the human visual cortex ]]> https://biorxiv.org/content/10.1101/404558v1?rss=1 Shin, J. Ma, S. Hofer, E. Patel, Y. Roshchupkin, G. Sousa, A. M. Jian, X. Gottesmann, R. Mosley, T. H. Fornage, M. Saba, Y. Pirpamer, L. Schmidt, R. Schmidt, H. Mazoyer, B. Carrion-Castillo, A. Bis, J. Li, S. Yang, Q. Luciano, M. Karama, S. Lewis, L. Bastin, M. Harris, M. A. Deary, I. Wardlaw, J. M. Scholz, M. Loeffler, M. Witte, V. Beyer, F. Villringer, A. Adams, H. H. Ikrum, M. A. Kremen, W. S. Gillespie, N. A. Sestan, N. Pausova, Z. Seshadri, S. Paus, T. 2018-08-31 doi:10.1101/404558 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Social integration predicts mitochondrial DNA copy number in rhesus macaques ]]> https://biorxiv.org/content/10.1101/408849v1?rss=1 Debray, R. Snyder-Mackler, N. Kohn, J. Wilson, M. Barreiro, L. Tung, J. 2018-09-06 doi:10.1101/408849 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Genetic Determinants of Cortical Structure (Thickness, Surface Area and Volumes) among Disease Free Adults in the CHARGE Consortium ]]> https://biorxiv.org/content/10.1101/409649v1?rss=1 Hofer, E. Roshchupkin, G. V. Adams, H. Knol, M. Lin, H. Li, S. Zare, H. Ahmad, S. Armstrong, N. Satizabal, C. Bernard, M. Bis, J. Gillespie, N. Luciano, M. Mishra, A. Scholz, M. Teumer, A. Xia, R. Jian, X. Mosley, T. Saba, Y. Pirpamer, L. Seiler, S. Becker, J. Carmichael, O. Rotter, J. Psaty, B. Lopez, O. Amin, N. Lee, S. Yang, Q. Himali, J. Maillard, P. Beiser, A. DeCarli, C. Karama, S. Lewis, L. Bastin, M. Harris, M. Deary, I. Witte, V. Beyer, F. Loeffler, M. Mather, K. Schofield, P. Thalamuthu, A. Kwok, J. Wright, M. Ames, D. Trollor, J. Jia 2018-09-09 doi:10.1101/409649 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments ]]> https://biorxiv.org/content/10.1101/411835v1?rss=1 Juric, I. Yu, M. Abnousi, A. Raviram, R. Fang, R. Zhao, Y. Zhang, Y. Yang, Y. Li, Y. Ren, B. Hu, M. 2018-09-08 doi:10.1101/411835 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism ]]> https://biorxiv.org/content/10.1101/414912v1?rss=1 Cheng, C. O'brien, E. J. McCloskey, D. Utrilla, J. Olson, C. LaCroix, R. A. Sandberg, T. E. Feist, A. M. Palsson, B. O. King, Z. A. 2018-09-12 doi:10.1101/414912 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Active protein neddylation or ubiquitylation is dispensable for stress granule dynamics ]]> https://biorxiv.org/content/10.1101/418848v1?rss=1 Markmiller, S. Fulzele, A. Higgins, R. Yeo, G. Bennett, E. J. 2018-09-15 doi:10.1101/418848 Cold Spring Harbor Laboratory Press 2018-09-15 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Split-miniSOG for detecting and localizing intracellular protein-protein interactions: application to correlated light and electron microscopy ]]> https://biorxiv.org/content/10.1101/423566v1?rss=1 BOASSA, D. Lemieux, S. P. Lev-Ram, V. Hu, J. Xiong, Q. Phan, S. Mackey, M. Ramachandra, R. Adams, S. R. Tsien, R. Y. Ellisman, M. H. Ngo, J. T. 2018-09-21 doi:10.1101/423566 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity ]]> https://biorxiv.org/content/10.1101/423590v1?rss=1 Chiang, A. W. T. Li, S. Kellman, B. P. Chattopadhyay, G. Zhang, Y. Kuo, C.-C. Gutierrez, J. M. Ghazi, F. Schmeisser, H. Menard, P. Petersen Bjorn, S. Voldborg, B. G. Rosenberg, A. S. Puig, M. Lewis, N. E. 2018-09-21 doi:10.1101/423590 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ A Cortico- Basal Ganglia Model for choosing an optimal rehabilitation strategy in Hemiparetic Stroke ]]> https://biorxiv.org/content/10.1101/423863v1?rss=1 Chakravarthy, S. Muralidharan, V. Narayanamurthy, R. Jayakumar, S. Elango, S. 2018-09-21 doi:10.1101/423863 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ A Sparse Unreliable Distributed Code Underlies the Limits of Behavioral Discrimination ]]> https://biorxiv.org/content/10.1101/424713v1?rss=1 Sriram, B. Cruz-Martin, A. Li, L. Reinagel, P. Ghosh, A. 2018-09-23 doi:10.1101/424713 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Repeated Δ9-tetrahydrocannabinol (THC) vapor inhalation during adolescence: Sex differences inacute thermoregulatory tolerance and in feeding during adulthood ]]> https://biorxiv.org/content/10.1101/426064v1?rss=1 Nguyen, J. D. Creehan, K. M. Kerr, T. M. Taffe, M. A. 2018-09-25 doi:10.1101/426064 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Visualizing metabolic network dynamics through time-series metabolomics data ]]> https://biorxiv.org/content/10.1101/426106v1?rss=1 Buchweitz, L. F. Yurkovich, J. T. Blessing, C. Kohler, V. Schwarzkopf, F. King, Z. A. Yang, L. Johannsson, F. Sigurjonsson, O. Rolfsson, O. Heinrich, J. Draeger, A. 2018-09-26 doi:10.1101/426106 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Asymmetric ephaptic inhibition between compartmentalized olfactory receptor neurons ]]> https://biorxiv.org/content/10.1101/427252v1?rss=1 Zhang, Y. Tsang, T. K. Bushong, E. A. Chu, L.-A. Chiang, A.-S. Ellisman, M. H. Reingruber, J. Su, C.-Y. 2018-09-25 doi:10.1101/427252 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Extracellular matrix components are required to protect Bacillus subtilis colonies from T6SS-dependent Pseudomonas invasion and modulate co-colonization of plant ]]> https://biorxiv.org/content/10.1101/429001v1?rss=1 Molina-Santiago, C. Pearson, J. R. Navarro, Y. Berlanga-Clavero, M. V. Caraballo-Rodriguez, A. M. Petras, D. Cazorla, F. M. de Vicente, A. Dorrestein, P. C. Romero, D. 2018-10-05 doi:10.1101/429001 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance ]]> https://biorxiv.org/content/10.1101/432666v1?rss=1 Cirelli, K. M. Carnathan, D. G. Nogal, B. Rodriguez, O. L. Martin, J. T. Upadhyay, A. A. Enemuo, C. A. Gebru, E. H. Choe, Y. Viviano, F. Nakao, C. Pauthner, M. Reiss, S. Cottrell, C. A. Bastidas, R. Gibson, W. Wolabaugh, A. N. Melo, M. B. Cosette, B. Kuman, V. Patel, N. Tokatlian, T. Menis, S. Kulp, D. W. Burton, D. R. Murrell, B. Bosinger, S. E. Schief, W. R. Ward, A. B. Watson, C. T. Silvestri, G. Irvine, D. J. Crotty, S. 2018-10-01 doi:10.1101/432666 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores ]]> https://biorxiv.org/content/10.1101/432906v1?rss=1 Rabiee, M. Mirarab, S. 2018-10-02 doi:10.1101/432906 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ TCR-pMHC bond length controls TCR ligand discrimination ]]> https://biorxiv.org/content/10.1101/433938v1?rss=1 Sasmal, D. K. Feng, W. Roy, S. Leung, P. He, Y. Cai, C. Cao, G. Lian, H. Qin, J. Hui, E. Schreiber, H. Adams, E. Huang, J. 2018-10-03 doi:10.1101/433938 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Multi-allele species reconstruction using ASTRAL ]]> https://biorxiv.org/content/10.1101/439489v1?rss=1 Rabiee, M. Sayyari, E. Mirarab, S. 2018-10-11 doi:10.1101/439489 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Measuring the average power of neural oscillations ]]> https://biorxiv.org/content/10.1101/441626v1?rss=1 40 hours of human M/EEG and ECoG, we show that in all cases it is not.nC_LIO_LIThis effect is demonstrated in simple simulation of an event-related task.nC_LIO_LIOverinflated power estimates are reduced via log-transformation or median power.nC_LI ]]> Izhikevich, L. Gao, R. Peterson, E. Voytek, B. 2018-10-13 doi:10.1101/441626 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Cell Mechanics at the Rear Act To Steer the Direction of Cell Migration ]]> https://biorxiv.org/content/10.1101/443408v1?rss=1 Allen, G. M. Lee, K. C. Barnhart, E. L. Tsuchida, M. A. Wilson, C. A. Gutierrez, E. Groisman, A. Mogilner, A. Theriot, J. A. 2018-10-15 doi:10.1101/443408 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Comparative genetic architectures of schizophrenia in East Asian and European populations ]]> https://biorxiv.org/content/10.1101/445874v1?rss=1 Lam, M. Chen, C.-Y. Li, Z. Martin, A. Bryois, J. Ma, X. Gaspar, H. Ikeda, M. Benyamin, B. Brown, B. Liu, R. Zhou, W. Huan, L. Kamatani, Y. Kim, S.-W. Kubo, M. Kusumawardhani, A. Liu, C.-M. Ma, H. Periyasamy, S. Takahashi, A. Wang, Q. Xu, Z. Yu, H. Zhu, F. Psychiatric Genomics Consortium - Schizophrenia Working Group, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and Netherland (GREAT-CN), Chen, W. Faraone, S. Glatt, S. He, L. Hyman, S. Hwu, H.-G. Li, T. McCarroll, S. Neale, B. Sklar, P. Wildenauer, D. Yu, X. Zh 2018-10-17 doi:10.1101/445874 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ The RNA-binding protein AATF coordinates rRNA maturation ]]> https://biorxiv.org/content/10.1101/446260v1?rss=1 Kaiser, R. Ignarski, M. Van Nostrand, E. L. Frese, C. Jain, M. Cukoski, S. Heinen, H. Schaechter, M. Bunte, K. Frommolt, P. Keller, P. Helm, M. Bohl, K. Höhne, M. Schermer, B. Benzing, T. Höpker, K. Dieterich, C. Yeo, G. W. Mueller, R.-U. Fabretti, F. 2018-10-17 doi:10.1101/446260 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network ]]> https://biorxiv.org/content/10.1101/446666v1?rss=1 Hu, J. Li, Y. Hao, Y. Zheng, T. Parada, G. Wu, H. Lin, S. Wang, S. Zhao, X. Goldman, R. Cai, S. Guo, M. 2018-10-17 doi:10.1101/446666 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Homogenization of capillary flow and oxygenation in deeper cortical layers correlates with increased oxygen extraction ]]> https://biorxiv.org/content/10.1101/450932v1?rss=1 Li, B. Esipova, T. V. Sencan, I. Kılıc, K. Fu, B. Desjardins, M. Moeini, M. Kura, S. Yaseen, M. A. Lesage, F. Ostergaard, L. Devor, A. Boas, D. A. Vinogradov, S. A. Sakadzic, S. 2018-10-23 doi:10.1101/450932 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic β-cell function ]]> https://biorxiv.org/content/10.1101/451542v1?rss=1 Wortham, M. Benthuysen, J. R. Wallace, M. Savas, J. N. Mulas, F. Divakaruni, A. S. Liu, F. Albert, V. Taylor, B. L. Sui, Y. Saez, E. Murphy, A. N. Yates, J. R. Metallo, C. M. Sander, M. 2018-10-24 doi:10.1101/451542 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Hippocampal theta bursting and waveform shape reflect CA1 spiking patterns ]]> https://biorxiv.org/content/10.1101/452987v1?rss=1 Cole, S. R. Voytek, B. 2018-10-25 doi:10.1101/452987 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Heritability and genetic variance of dementia with Lewy bodies ]]> https://biorxiv.org/content/10.1101/454249v1?rss=1 Guerreiro, R. Escott-Price, V. Hernandez, D. Kun-Rodrigues, C. Ross, O. Orme, T. Neto, J. L. Carmona, S. Dehghani, N. Eicher, J. D. Shepherd, C. Parkkinen, L. Darwent, L. Heckman, M. G. Scholz, S. Troncoso, J. Pletnikova, O. Dawson, T. Rosenthal, L. Ansorge, O. Clarimon, J. Lleo, A. Morenas-Rodriguez, E. Clark, L. Honig, L. Marder, K. Lemstra, A. Rogaeva, E. St. George-Hyslop, P. Londos, E. Zetterberg, H. Barber, I. Braae, A. Brown, K. Morgan, K. Troakes, C. Al-Sarraj, S. Lashley, T. Holton, J. Compta, Y. Van Deerlin, V. Serrano, G. Beach, T. Lesage, 2018-10-26 doi:10.1101/454249 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells ]]> https://biorxiv.org/content/10.1101/456491v1?rss=1 HIGASHIJIMA, Y. MATSUI, Y. SHIMAMURA, T. TSUTSUMI, S. NAKAKI, R. ABE, Y. LINK, V. M. OSAKA, M. YOSHIDA, M. WATANABE, R. TANAKA, T. TAGUCHI, A. MIURA, M. INOUE, T. NANGAKU, M. KIMURA, H. FURUKAWA, T. ABURATANI, H. WADA, Y. GLASS, C. K. KANKI, Y. 2018-11-11 doi:10.1101/456491 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ The Molecular Basis of Monopolin Recruitment to the Kinetochore ]]> https://biorxiv.org/content/10.1101/456798v1?rss=1 Plowman, R. Singh, N. Duro, E. Payan, A. Corbett, K. D. Marston, A. L. 2018-10-30 doi:10.1101/456798 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Image processing and analysis methods for the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/457739v1?rss=1 Hagler, D. J. Hatton, S. N. Makowski, C. Cornejo, M. D. Fair, D. A. Dick, A. S. Sutherland, M. T. Casey, B. J. Barch, D. M. Harms, M. P. Watts, R. Bjork, J. M. Garavan, H. P. Hilmer, L. Pung, C. J. Sicat, C. S. Kuperman, J. Bartsch, H. Xue, F. Heitzeg, M. M. Laird, A. R. Trinh, T. T. Gonzalez, R. Tapert, S. F. Riedel, M. C. Squeglia, L. M. Hyde, L. W. Rosenberg, M. D. Earl, E. A. Howlett, K. D. Baker, F. C. Soules, M. Diaz, J. Ruiz de Leon, O. Thompson, W. K. Neale, M. C. Herting, M. Sowell, E. R. Alvarez, R. P. Hawes, S. W. Sanchez, M. Bodurka, J. Bre 2018-11-04 doi:10.1101/457739 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Intermittent abstinence potentiates oxycodone self-administration under extended access conditions and alters brain reward sensitivity ]]> https://biorxiv.org/content/10.1101/460048v1?rss=1 Nguyen, J. Grant, Y. Taffe, M. 2018-11-02 doi:10.1101/460048 Cold Spring Harbor Laboratory Press 2018-11-02 <![CDATA[ Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae ]]> https://biorxiv.org/content/10.1101/463620v1?rss=1 Kang, K. B. Ernst, M. van der Hooft, J. J. J. da Silva, R. R. Park, J. Medema, M. H. Sung, S. H. Dorrestein, P. C. 2018-11-07 doi:10.1101/463620 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements ]]> https://biorxiv.org/content/10.1101/468181v1?rss=1 Li, S. Cha, S. W. Heffner, K. Hizal, D. B. Bowen, M. Chaerkady, R. Cole, R. Tejwani, V. Kaushik, P. Henry, M. Meleady, P. Sharfstein, S. Betenbaugh, M. Bafna, V. Lewis, N. 2018-11-12 doi:10.1101/468181 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model ]]> https://biorxiv.org/content/10.1101/472688v1?rss=1 Torres, P. Ho, B. Arroyo, P. Sau, L. Chen, A. Kelley, S. Thackray, V. 2018-11-19 doi:10.1101/472688 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Modulation of RNA-dependent interactions in stress granules prevents persistent TDP-43 accumulation in ALS/FTD ]]> https://biorxiv.org/content/10.1101/474577v1?rss=1 Fang, M. Y. Markmiller, S. Dowdle, W. E. Vu, A. Q. Bushway, P. J. Ding, S. Mercola, M. M. Lewcock, J. W. Yeo, G. 2018-11-20 doi:10.1101/474577 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Reconstitution of eukaryotic chromosomes and manipulation of DNA N6-methyladenine alters chromatin and gene expression ]]> https://biorxiv.org/content/10.1101/475384v1?rss=1 Beh, L. Y. Debelouchina, G. T. Clay, D. M. Thompson, R. E. Lindblad, K. A. Hutton, E. R. Bracht, J. R. Sebra, R. P. Muir, T. W. Landweber, L. F. 2018-11-20 doi:10.1101/475384 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state ]]> https://biorxiv.org/content/10.1101/481283v1?rss=1 Stamenova, E. K. Durand, N. Dudchenko, O. Shamim, M. S. Huang, S.-C. Jiang, Y. Bochkov, I. D. Rao, S. S. P. Lander, E. S. Gnirke, A. Aiden, E. L. 2018-11-29 doi:10.1101/481283 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Mechanism of action of methotrexate against Zika virus ]]> https://biorxiv.org/content/10.1101/481440v1?rss=1 Beck, S. Bernatchez, J. A. Zhu, Z. Oliveira, M. F. Smith, D. M. Siqueira-Neto, J. L. 2018-11-29 doi:10.1101/481440 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Mutations In PIK3C2A Cause Syndromic Short Stature, Skeletal Abnormalities, and Cataracts Associated With Ciliary Dysfunction ]]> https://biorxiv.org/content/10.1101/488411v1?rss=1 Tiosano, D. Baris Feldman, H. Chen, A. Hitzert, M. M. Schueler, M. Gulluni, F. Wiesener, A. Bergua, A. Mory, A. Copeland, B. Gleeson, J. G. Rump, P. van Meer, H. Sival, D. A. Haucke, V. Kriwinsky, J. Knaup, K. X. Reis, A. Hauer, N. N. Hirsch, E. Roepman, R. Pfundt, R. Thiel, C. T. Wiesener, M. S. Aslanyan, M. G. Buchner, D. A. 2018-12-07 doi:10.1101/488411 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Rapid screening of engineered microbial therapies in a 3-D multicellular model ]]> https://biorxiv.org/content/10.1101/491159v1?rss=1 Harimoto, T. Singer, Z. Velazquez, O. Zhang, J. Castro, S. Hinchliffe, T. Mather, W. Danino, T. 2018-12-10 doi:10.1101/491159 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers ]]> https://biorxiv.org/content/10.1101/491845v1?rss=1 Fan, S. Tang, J. Li, N. Zhao, Y. Ai, R. Zhang, K. Wang, M. Du, W. Wang, W. 2018-12-18 doi:10.1101/491845 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Schizophrenia risk conferred by protein-coding de novo mutations ]]> https://biorxiv.org/content/10.1101/495036v1?rss=1 Howrigan, D. Rose, S. A. Samocha, K. E. Fromer, M. Cerrato, F. Chen, W. J. Churchhouse, C. Chambert, K. Chandler, S. D. Daly, M. J. Dumont, A. Genovese, G. Hwu, H.-G. Laird, N. Kosmicki, J. A. Moran, J. Roe, C. Singh, T. Wang, S.-H. Faraone, S. Glatt, S. McCarroll, S. Tsuang, M. Neale, B. 2018-12-13 doi:10.1101/495036 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ The molecular architecture of engulfment during Bacillus subtilis sporulation ]]> https://biorxiv.org/content/10.1101/498220v1?rss=1 Khanna, K. Lopez-Garrido, J. Zhao, Z. Watanabe, R. Yuan, Y. Pogliano, K. Villa, E. 2018-12-16 doi:10.1101/498220 Cold Spring Harbor Laboratory Press 2018-12-16 <![CDATA[ Beyond SNP Heritability: Polygenicity and Discoverability of Phenotypes Estimated with a Univariate Gaussian Mixture Model ]]> https://biorxiv.org/content/10.1101/498550v1?rss=1 1%. We apply the model to diverse phenotypes and validate the implementation with simulations. We find model polygenicities ranging from [~=] 2 x 10-5 to [~=] 4 x 10-3, with discoverabilities similarly ranging over two orders of magnitude. A power analysis allows us to estimate the proportions of phenotypic variance explained additively by causal SNPs at current sample sizes, and map out sample sizes required to explain larger portions of additive SNP heritability. The model also allows for estimating residual inflation. ]]> Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Sundar, V. S. Thompson, P. Andreassen, O. A. Dale, A. M. 2018-12-17 doi:10.1101/498550 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Structures of the PKA RIα holoenzyme with the FLHCC driver J-PKAcα or wild type PKAcα ]]> https://biorxiv.org/content/10.1101/505347v1?rss=1 Cao, B. Lu, T.-W. Martinez Fiesco, J. Tomasini, M. Fan, L. Simon, S. Taylor, S. Zhang, P. 2018-12-22 doi:10.1101/505347 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ Cryo-EM Structure of OSCA1.2 from Oryza sativa: Mechanical basis of hyperosmolality-gating in Plants ]]> https://biorxiv.org/content/10.1101/505453v1?rss=1 Maity, K. Heumann, J. McGrath, A. P. Kopcho, N. J. Hsu, P.-K. Lee, C.-W. Mapes, J. H. Garza, D. Krishnan, S. Morgan, G. P. Medrano-Soto, A. Hendargo, K. J. Klose, T. Rees, S. D. Saier, M. H. Pineros, M. Komives, E. A. Schroeder, J. I. Chang, G. Stowell, M. H. B. 2018-12-30 doi:10.1101/505453 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Partitioning the genetic architecture of amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/505693v1?rss=1 3 million people. We found strong genetic enrichment between ALS and a number of disparate traits including frontotemporal dementia, coronary artery disease, C-reactive protein, celiac disease and memory function. Beyond C9ORF72, we detected novel genetic signal within numerous loci including GIPC1, ELMO1 and COL16A and confirmed previously reported variants, such as ATXN2, KIF5A, UNC13A and MOBP. We found that ALS variants form a small-world co-expression network characterized by highly inter-connected hub genes. This network clustered into smaller sub-networks, each associated with a unique function. Altered gene expression of several sub-networks and hubs was over-represented in neuropathological samples from ALS patients and SOD1 G93A mice. Our collective findings indicate that the genetic architecture of ALS can be partitioned into distinct components where some genes are highly important for developing disease. These findings have implications for stratification and enrichment strategies for ALS clinical trials. ]]> Broce, I. J. Fan, C. C. Olney, N. T. Lomen-Hoerth, C. Finkbeiner, S. Atassi, N. Cudkowicz, M. E. Yokoyama, J. S. Kao, A. Dillon, W. P. Glastonbury, C. M. Hess, C. P. van Rheenen, W. Veldink, J. H. Al-Chalabi, A. Andreassen, O. A. Dale, A. M. Seeley, W. W. Sugrue, L. P. Karch, C. M. Miller, B. L. Desikan, R. S. 2018-12-23 doi:10.1101/505693 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ Cooperation of dominant oncogenes with regulatory germline variants shapes clinical outcomes in childhood cancer ]]> https://biorxiv.org/content/10.1101/506659v1?rss=1 Musa, J. Cidre-Aranaz, F. Aynaud, M.-M. Orth, M. F. Mirabeau, O. Varon, M. Grossetete, S. Surdez, D. Ohmura, S. Gerke, J. S. Marchetto, A. Dallmayer, M. Baldauf, M. C. Gartlgruber, M. Westermann, F. Stein, S. Hoelting, T. L. B. Knott, M. Sannino, G. Li, J. Romero-Perez, L. Hartmann, W. Dirksen, U. Gymrek, M. Anderson, N. D. Shlien, A. Rotblat, B. Kirchner, T. Delattre, O. Grunewald, T. G. P. 2018-12-27 doi:10.1101/506659 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Evolutionary loss of foot muscle during development with characteristics of atrophy and no evidence of cell death ]]> https://biorxiv.org/content/10.1101/512590v1?rss=1 Tran, M. P. Tsutsumi, R. Erberich, J. M. Chen, K. D. Flores, M. D. Cooper, K. L. 2019-01-06 doi:10.1101/512590 Cold Spring Harbor Laboratory Press 2019-01-06 <![CDATA[ Visual-olfactory integration in the human disease vector mosquito, Aedes aegypti ]]> https://biorxiv.org/content/10.1101/512996v1?rss=1 Vinauger, C. Van Breugel, F. Locke, L. Tobin, K. Dickinson, M. Fairhall, A. Akbari, O. Riffell, J. 2019-01-07 doi:10.1101/512996 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B ]]> https://biorxiv.org/content/10.1101/513366v1?rss=1 Shi, K. Demir, O. Carpenter, M. A. Banerjee, S. Harki, D. A. Amaro, R. E. Harris, R. S. Aihara, H. 2019-01-07 doi:10.1101/513366 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Geometric control of frequency modulation of cAMP oscillations due to Ca2+-bursts in dendritic spines ]]> https://biorxiv.org/content/10.1101/520643v1?rss=1 Ohadi, D. Rangamani, P. 2019-01-15 doi:10.1101/520643 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines ]]> https://biorxiv.org/content/10.1101/521740v1?rss=1 Ohadi, D. Schmitt, D. L. Calabrese, B. Halpain, S. Zhang, J. Rangamani, P. 2019-01-16 doi:10.1101/521740 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Global phylogeography and ancient evolution of the widespread human gut virus crAssphage ]]> https://biorxiv.org/content/10.1101/527796v1?rss=1 Edwards, R. Vega, A. Norman, H. Ohaeri, M. C. Levi, K. Dinsdale, E. Cinek, O. Aziz, R. McNair, K. Barr, J. Bibby, K. Brouns, S. Cazares, A. de Jonge, P. A. Desnues, C. Diaz-Munoz, S. Fineran, P. Kurilshikov, A. Lavigne, R. Mazankova, K. McCarthy, D. Nobrega, F. Reyes, A. Tapia, G. Trefault, N. Tyakht, A. Vinuesa, P. Wagemans, J. Zhernakova, A. Aarestrup, F. Ahmadov, G. Alassaf, A. Anton, J. Asangba, A. Billings, E. Cantu, A. Carlton, J. Cazares Lopez, D. Cho, G.-S. Condeff, T. Cortes, P. Cranfield, M. Cuevas, D. De la Iglesia, R. Decewicz, P. Doane, 2019-01-26 doi:10.1101/527796 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Planning Face, Hand, and Leg Movements: Anatomical Constraints on Preparatory Inhibition. ]]> https://biorxiv.org/content/10.1101/529107v1?rss=1 Labruna, L. Tischler, C. Cazares, C. Greenhouse, I. Duque, J. Lebon, F. Ivry, R. B. 2019-01-26 doi:10.1101/529107 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage ]]> https://biorxiv.org/content/10.1101/530204v1?rss=1 Li, Z.-R. Li, J. Cai, W. Lai, J. McKinnie, S. Zhang, W.-P. Moore, B. Zhang, W. Qian, P.-Y. 2019-01-24 doi:10.1101/530204 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Activity of Selected Nucleoside Analogue ProTides against Zika Virus in Human Neural Stem Cells ]]> https://biorxiv.org/content/10.1101/533497v1?rss=1 Bernatchez, J. A. Coste, M. Beck, S. Wells, G. A. Luna, L. A. Clark, A. E. Zhu, Z. Sohl, C. D. Purse, B. W. Siqueira-Neto, J. L. 2019-01-29 doi:10.1101/533497 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Characteristics of Beta Waveform Shape in Parkinson's Disease Detected with Scalp Electroencephalography ]]> https://biorxiv.org/content/10.1101/534396v1?rss=1 Jackson, N. Cole, S. C. Voytek, B. Swann, N. C. 2019-01-29 doi:10.1101/534396 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs ]]> https://biorxiv.org/content/10.1101/534479v1?rss=1 Lee, C. T. Laughlin, J. G. Angliviel de La Beaumelle, N. Amaro, R. McCammon, J. A. Ramamoorthi, R. Holst, M. J. Rangamani, P. 2019-01-29 doi:10.1101/534479 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Occupation and Parkinson disease in Women's Health Initiative Observational Study ]]> https://biorxiv.org/content/10.1101/535732v1?rss=1 Burstyn, I. LaCroix, A. Z. Litvan, I. Wallace, R. B. Checkoway, H. 2019-02-01 doi:10.1101/535732 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids ]]> https://biorxiv.org/content/10.1101/538421v1?rss=1 Huang, Q. Chan, K. Y. Tobey, I. G. Chan, Y. A. Poterba, T. Boutros, C. L. Balazs, A. B. Daneman, R. Bloom, J. M. Seed, C. Deverman, B. E. 2019-02-01 doi:10.1101/538421 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ DLITE: Dynamic Local Intercellular Tension Estimation ]]> https://biorxiv.org/content/10.1101/541144v1?rss=1 Vasan, R. Maleckar, M. M. Williams, C. D. Rangamani, P. 2019-02-05 doi:10.1101/541144 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Age and sex-dependent patterns of gut microbial diversity in human adults ]]> https://biorxiv.org/content/10.1101/544270v1?rss=1 de la Cuesta-Zuluaga, J. Kelley, S. T. Chen, Y. Esobar, J. S. Mueller, N. T. Ley, R. E. McDonald, D. Huang, S. Swafford, A. D. Knight, R. Thackray, V. 2019-02-08 doi:10.1101/544270 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Implementations of the chemical structural and compositional similarity metric in R and Python ]]> https://biorxiv.org/content/10.1101/546150v1?rss=1 Brejnrod, A. D. Ernst, M. Dworzynski, P. Rasmussen, L. B. Dorrestein, P. van der Hooft, J. Arumugam, M. 2019-02-11 doi:10.1101/546150 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes ]]> https://biorxiv.org/content/10.1101/549816v1?rss=1 Thompson, L. R. Haroon, M. F. Shibl, A. A. Cahill, M. J. Ngugi, D. K. Williams, G. J. Morton, J. Knight, R. Goodwin, K. D. Stingl, U. 2019-02-14 doi:10.1101/549816 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Flower-like patterns in multi-species biofilms ]]> https://biorxiv.org/content/10.1101/550996v1?rss=1 Xiong, L. Cao, Y. Cooper, R. Rappel, W.-J. Hasty, J. Tsimring, L. 2019-02-15 doi:10.1101/550996 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ EpiAlignment: alignment with both DNA sequence and epigenomic data ]]> https://biorxiv.org/content/10.1101/562199v1?rss=1 Lu, J. Cao, X. Zhong, S. 2019-02-27 doi:10.1101/562199 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ The laminar profile of sleep spindles in humans ]]> https://biorxiv.org/content/10.1101/563221v1?rss=1 Ujma, P. P. Hajnal, B. Bodizs, R. Gombos, F. Eross, L. Wittner, L. Halgren, E. Cash, S. Ulbert, I. Fabo, D. 2019-02-28 doi:10.1101/563221 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease ]]> https://biorxiv.org/content/10.1101/564161v1?rss=1 D'Antonio, M. Reyna, J. D'Antonio-Chronowska, A. Bonder, M.-J. Jakubosky, D. Matsui, H. Smith, E. N. Stegle, O. Nariai, N. Frazer, K. A. 2019-02-28 doi:10.1101/564161 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing ]]> https://biorxiv.org/content/10.1101/564443v1?rss=1 Edge, P. Bansal, V. 2019-03-01 doi:10.1101/564443 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Heterozygous variants in KMT2E cause a spectrum of neurodevelopmental disorders and epilepsy ]]> https://biorxiv.org/content/10.1101/566091v1?rss=1 O'Donnell-Luria, A. H. Pais, L. S. Faundes, V. Wood, J. C. Sveden, A. Luria, V. Abou Jamra, R. Accogli, A. Amburgey, K. Anderlid, B.-M. Azzarello-Burri, S. Basinger, A. A. Bianchini, C. Bird, L. M. Buchert, R. Carre, W. Ceulemans, S. Charles, P. Cox, H. Culliton, L. Curro, A. Deciphering Developmental Disorders (DDD) Study, Demurger, F. Dowling, J. J. Duban-Bedu, B. Dubourg, C. Escobar, L. F. Ferrarini, A. Haack, T. B. Hashim, M. Heide, S. Helbig, K. L. Helbig, I. Heredia, R. Heron, D. Isidor, B. Jonasson, A. R. Joset, P. Keren, B. Kok, F. Kroes, H. Y 2019-03-05 doi:10.1101/566091 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ The Tangent copy-number inference pipeline for cancer genome analyses ]]> https://biorxiv.org/content/10.1101/566505v1?rss=1 Tabak, B. Saksena, G. Oh, C. Gao, G. F. Hill Meyers, B. Reich, M. Schumacher, S. E. Westlake, L. C. Berger, A. C. Carter, S. L. Cherniack, A. D. Meyerson, M. Beroukhim, R. Getz, G. 2019-03-05 doi:10.1101/566505 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Interaction of Hippocampal Ripples and Cortical Slow Waves Leads to Coordinated Large-Scale Sleep Rhythm ]]> https://biorxiv.org/content/10.1101/568881v1?rss=1 Sanda, P. Malerba, P. Jiang, X. Krishnan, G. Cash, S. Halgren, E. Bazhenov, M. 2019-03-05 doi:10.1101/568881 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Can sleep protect memories from catastrophic forgetting? ]]> https://biorxiv.org/content/10.1101/569038v1?rss=1 Gonzalez, O. C. Sokolov, Y. Krishnan, G. Bazhenov, M. 2019-03-07 doi:10.1101/569038 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Identification of DNA motifs that regulate DNA methylation ]]> https://biorxiv.org/content/10.1101/573352v1?rss=1 Wang, M. Zhang, K. Ngo, V. Liu, C. Fan, S. Whitaker, J. W. Chen, Y. Ai, R. Chen, Z. Wang, J. Zheng, L. Wang, W. 2019-03-11 doi:10.1101/573352 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia ]]> https://biorxiv.org/content/10.1101/574509v1?rss=1 Tam, O. Rozhkov, N. V. Shaw, R. Kim, D. Hubbard, I. Fennessey, S. Propp, N. The NYGC ALS Consortium, Fagegaltier, D. Ostrow, L. W. Phatnani, H. Ravits, J. Dubnau, J. Gale Hammell, M. 2019-03-11 doi:10.1101/574509 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Quantifying and understanding well-to-well contamination in microbiome research ]]> https://biorxiv.org/content/10.1101/577718v1?rss=1 Minich, J. J. Sanders, J. Amir, A. Humphrey, G. Gilbert, J. A. Knight, R. 2019-03-14 doi:10.1101/577718 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Multiple memory tests in midlife improve prediction of mild cognitive impairment ]]> https://biorxiv.org/content/10.1101/584193v1?rss=1 Gustavson, D. E. Sanderson-Cimino, M. Elman, J. A. Franz, C. E. Panizzon, M. S. Jak, A. J. Reynolds, C. A. Lyons, M. J. Kremen, W. S. 2019-03-21 doi:10.1101/584193 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ A newly defined cullin-RING ubiquitin ligase promotes thermotolerance as part of the Intracellular Pathogen Response in C. elegans ]]> https://biorxiv.org/content/10.1101/586834v1?rss=1 Panek, J. Reddy, K. C. Luallen, R. J. Fulzele, A. Bennett, E. J. Troemel, E. R. 2019-03-23 doi:10.1101/586834 Cold Spring Harbor Laboratory Press 2019-03-23 <![CDATA[ Progressive recruitment of distal MEC-4 channels determines touch response strength in C. elegans ]]> https://biorxiv.org/content/10.1101/587014v1?rss=1 Katta, S. Sanzeni, A. Vergassola, M. Goodman, M. B. 2019-03-24 doi:10.1101/587014 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Recovery of trait heritability from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/588020v1?rss=1 Wainschtein, P. Jain, D. P. Yengo, L. Zheng, Z. TOPMed Anthropometry Working Group, Trans-Omics for Precision Medicine Consortium, Cupples, L. A. Shadyab, A. H. McKnight, B. Shoemaker, B. M. Mitchell, B. D. Psaty, B. M. Kooperberg, C. Roden, D. Darbar, D. Arnett, D. K. Regan, E. A. Boerwinkle, E. Rotter, J. I. Allison, M. A. McDonald, M.-L. N. Chung, M. K. Smith, N. L. Ellinor, P. T. Vasan, R. S. Mathias, R. A. Rich, S. S. Heckbert, S. R. Redline, S. Guo, X. Chen, Y.-D. I. Liu, C.-T. Andrade, M. d. Yanek, L. R. Albert, C. M. Hernandez, R. D. McGarvey, S. 2019-03-25 doi:10.1101/588020 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Predicting primary production in the southern California Current Ecosystem from chlorophyll, nutrient concentrations, and irradiance ]]> https://biorxiv.org/content/10.1101/590240v1?rss=1 Stukel, M. Goericke, R. Landry, M. R. 2019-03-28 doi:10.1101/590240 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ A conserved acidic cluster motif in SERINC5 confers resistance to antagonism by HIV-1 Nef ]]> https://biorxiv.org/content/10.1101/590646v1?rss=1 Stoneham, C. Ramirez, P. W. Singh, R. Suarez, M. Debray, A. Lim, C. Jia, X. Xiong, Y. Guatelli, J. 2019-03-27 doi:10.1101/590646 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Resting networks and personality predict attack speed in social spiders ]]> https://biorxiv.org/content/10.1101/591453v1?rss=1 Hunt, E. R. Mi, B. Geremew, R. Fernandez, C. Wong, B. M. Pruitt, J. N. Pinter-Wollman, N. 2019-03-28 doi:10.1101/591453 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Common DNA sequence variation influences 3-dimensional conformation of the human genome ]]> https://biorxiv.org/content/10.1101/592741v1?rss=1 Gorkin, D. Qiu, Y. Hu, M. Fletez-Brant, K. Liu, T. Schmitt, A. Noor, A. Chiou, J. Gaulton, K. Sebat, J. Li, Y. Hansen, K. Ren, B. 2019-03-30 doi:10.1101/592741 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome ]]> https://biorxiv.org/content/10.1101/594010v1?rss=1 Claesen, J. Spagnolo, J. B. Flores Ramos, S. Kurita, K. L. Byrd, A. L. Aksenov, A. A. Melnik, A. V. Wong, W. R. Wang, S. Hernandez, R. D. Donia, M. S. Dorrestein, P. C. Kong, H. H. Segre, J. A. Linington, R. G. Fischbach, M. A. Lemon, K. P. 2019-03-30 doi:10.1101/594010 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ StanDep: capturing transcriptomic variability improves context-specific metabolic models ]]> https://biorxiv.org/content/10.1101/594861v1?rss=1 Joshi, C. J. Schinn, S.-M. Richelle, A. Shamie, I. O'Rourke, E. J. Lewis, N. 2019-04-01 doi:10.1101/594861 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ Nuisance effects in inter-scan functional connectivity estimates before and after nuisance regression ]]> https://biorxiv.org/content/10.1101/603183v1?rss=1 Nalci, A. Luo, W. Liu, T. T. 2019-04-09 doi:10.1101/603183 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects ]]> https://biorxiv.org/content/10.1101/604371v1?rss=1 Young Greenwald, W. W. D'Antonio-Chronowska, A. Benaglio, P. Matsui, H. Smith, E. N. D'Antonio, M. Frazer, K. A. 2019-04-09 doi:10.1101/604371 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ Confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations ]]> https://biorxiv.org/content/10.1101/607267v1?rss=1 Sanchez C., H. M. Bennett, J. B. Wu, S. L. Rasic, G. Akbari, O. S. Marshall, J. M. 2019-04-12 doi:10.1101/607267 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Motto: Representing motifs in consensus sequences with minimum information loss ]]> https://biorxiv.org/content/10.1101/607408v1?rss=1 Wang, M. Wang, D. Zhang, K. Ngo, V. Fan, S. Wang, W. 2019-04-13 doi:10.1101/607408 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Methods for the generation of heritable germline mutations in the disease vector Culex quinquefasciatus using CRISPR/Cas9. ]]> https://biorxiv.org/content/10.1101/609206v1?rss=1 Li, M. Li, T. Liu, N. Raban, R. Wang, X. Akbari, O. 2019-04-16 doi:10.1101/609206 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ Activation of a Protein Kinase Via Asymmetric Allosteric Coupling of Structurally Conserved Signaling Modules ]]> https://biorxiv.org/content/10.1101/611772v1?rss=1 Hao, Y. England, J. P. Belluci, L. Paci, E. Hodges, H. C. Taylor, S. S. Maillard, R. A. 2019-04-18 doi:10.1101/611772 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Sex-dependent polygenic effects on the clinical progressions of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/613893v1?rss=1 Fan, C. C. Banks, S. J. Thompson, W. K. Chen, C.-H. McEvoy, L. K. Tan, C. H. Kukull, W. Bennett, D. A. Farrer, L. A. Mayeux, R. Schellenberg, G. D. Andreassen, O. A. Desikan, R. Dale, A. M. 2019-04-18 doi:10.1101/613893 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Fast and Accurate Clustering of Single Cell Epigenomes Reveals Cis-Regulatory Elements in Rare Cell Types ]]> https://biorxiv.org/content/10.1101/615179v1?rss=1 Fang, R. Preissl, S. Hou, X. Lucero, J. Wang, X. Motamedi, A. Shiau, A. K. Mukamel, E. A. Zhang, Y. Behrens, M. M. Ecker, J. Ren, B. 2019-04-22 doi:10.1101/615179 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ Homeostatic mechanisms may shape the type and duration of oscillatory modulation. ]]> https://biorxiv.org/content/10.1101/615450v1?rss=1 Peterson, E. J. Voytek, B. 2019-04-22 doi:10.1101/615450 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ Catestatin improves insulin sensitivity in diet-induced obese mice: in vivo and in silico validation ]]> https://biorxiv.org/content/10.1101/615997v1?rss=1 Mahata, S. K. Dasgupta, A. Bandyopadhyay, K. Ray, I. Bandyopadhyay, G. K. Chowdhury, N. De, R. K. 2019-04-22 doi:10.1101/615997 Cold Spring Harbor Laboratory Press 2019-04-22 <![CDATA[ A network of microRNAs acts to promote cell cycle exit and differentiation of human pancreatic endocrine cells ]]> https://biorxiv.org/content/10.1101/618330v1?rss=1 Jin, W. Mulas, F. Gaertner, B. Sui, Y. Wang, J. Zeng, C. Vinckier, N. Wang, A. Nguyen-Ngoc, K.-V. Chiou, J. Kaestner, K. H. Frazer, K. Carrano, A. C. Shih, H.-P. Sander, M. 2019-04-25 doi:10.1101/618330 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ A genetic hazard score to personalize prostate cancer screening, applied to population data ]]> https://biorxiv.org/content/10.1101/619718v1?rss=1 Huynh-Le, M.-P. Fan, C. C. Karunamuni, R. Walsh, E. I. Turner, E. L. Lane, J. A. Martin, R. M. Neal, D. E. Donovan, J. L. Hamdy, F. C. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Key, T. J. Travis, R. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Thibodeau, S. N. McDonnell, S. K. Schaid, D. J. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, 2019-04-26 doi:10.1101/619718 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ The Escherichia coli Transcriptome Consists of Independently Regulated Modules ]]> https://biorxiv.org/content/10.1101/620799v1?rss=1 Sastry, A. V. Gao, Y. Szubin, R. Hefner, Y. Xu, S. Kim, D. Choudhary, K. S. Yang, L. King, Z. A. Palsson, B. O. 2019-04-29 doi:10.1101/620799 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences ]]> https://biorxiv.org/content/10.1101/621532v1?rss=1 Vakirlis, N. Acar, O. Hsu, B. Castilho Coelho, N. Van Oss, S. B. Wacholder, A. Medetgul-Ernar, K. Ianotta, J. McLysaght, A. Camacho, C. J. O'Donnell, A. F. Ideker, T. Carvunis, A.-R. 2019-04-29 doi:10.1101/621532 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Pupillary dilation responses as a midlife indicator of risk for Alzheimer’s Disease: Association with Alzheimer’s disease polygenic risk ]]> https://biorxiv.org/content/10.1101/624767v1?rss=1 Kremen, W. Panizzon, M. Elman, J. A. Granholm, E. Andreassen, O. A. Dale, A. Gillespie, N. Gustavson, D. E. Logue, M. Lyons, M. Neale, M. Reynolds, C. Whitsel, N. Franz, C. 2019-05-02 doi:10.1101/624767 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Single-cell chromatin accessibility analysis of mammary gland development reveals cell state transcriptional regulators and cellular lineage relationships ]]> https://biorxiv.org/content/10.1101/624957v1?rss=1 Chung, C.-Y. Ma, Z. Dravis, C. Preissl, S. Poirion, O. Luna, G. Hou, X. Giraddi, R. R. Ren, B. Wahl, G. M. 2019-05-02 doi:10.1101/624957 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Mammalian gene expression variability is explained by underlying cell state ]]> https://biorxiv.org/content/10.1101/626424v1?rss=1 Foreman, R. Wollman, R. 2019-05-03 doi:10.1101/626424 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Spatial Confidence Sets for Raw Effect Size Images ]]> https://biorxiv.org/content/10.1101/631473v1?rss=1 Bowring, A. Telschow, F. Schwartzman, A. Nichols, T. 2019-05-08 doi:10.1101/631473 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Polygenic Score of Intelligence is More Predictive of Crystallized than Fluid Performance Among Children ]]> https://biorxiv.org/content/10.1101/637512v1?rss=1 Loughnan, R. Palmer, C. E. Thompson, W. K. Dale, A. M. Jernigan, T. L. Fan, C. C. 2019-05-15 doi:10.1101/637512 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ metaFlye: scalable long-read metagenome assembly using repeat graphs ]]> https://biorxiv.org/content/10.1101/637637v1?rss=1 Kolmogorov, M. Rayko, M. Yuan, J. Polevikov, E. Pevzner, P. 2019-05-15 doi:10.1101/637637 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier ]]> https://biorxiv.org/content/10.1101/641506v1?rss=1 Chen, Z. Gabizon, R. Bustamante, C. Yao, T. Lee, A. Diaz-Celis, C. Koslover, E. F. Brown, A. I. Song, A. 2019-05-17 doi:10.1101/641506 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Inverted encoding models estimate sensible channel responses for sensible models ]]> https://biorxiv.org/content/10.1101/642710v1?rss=1 Sprague, T. C. Boynton, G. M. Serences, J. 2019-05-21 doi:10.1101/642710 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ The olfactory basis of orchid pollination by mosquitoes ]]> https://biorxiv.org/content/10.1101/643510v1?rss=1 Lahondere, C. Vinauger, C. Okubo, R. Wolff, G. Akbari, O. Riffell, J. 2019-05-27 doi:10.1101/643510 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Mitochondrial morphology provides a mechanism for energy buffering at synapses ]]> https://biorxiv.org/content/10.1101/643551v1?rss=1 Garcia, G. C. Bartol, T. M. Phan, S. Bushong, E. A. Perkins, G. Sejnowski, T. J. Ellisman, M. H. Skupin, A. 2019-05-20 doi:10.1101/643551 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Human iPSC gene signatures and X chromosome dosage impact response to WNT inhibition and cardiac differentiation fate ]]> https://biorxiv.org/content/10.1101/644633v1?rss=1 D'Antonio-Chronowska, A. Donovan, M. K. R. Benaglio, P. Young Greenwald, W. W. W. Ward, M. C. Matsui, H. Fujita, K. Hashem, S. Soncin, F. Parast, M. Adler, E. Smith, E. N. D'Antonio, M. Frazer, K. A. 2019-05-24 doi:10.1101/644633 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Plasticity of cell migration resulting from mechanochemical coupling ]]> https://biorxiv.org/content/10.1101/644880v1?rss=1 Cao, Y. Ghabache, E. Rappel, W.-J. 2019-05-21 doi:10.1101/644880 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences ]]> https://biorxiv.org/content/10.1101/645762v1?rss=1 Godoy, P. M. Barczak, A. J. DeHoff, P. Srinivasan, S. Das, S. Erle, D. J. Laurent, L. C. 2019-05-24 doi:10.1101/645762 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ PHLPP1 Counter-regulates STAT1-mediated Inflammatory Signaling ]]> https://biorxiv.org/content/10.1101/647883v1?rss=1 Cohen Katsenelson, K. Stender, J. D. Kawashima, A. T. Lorden, G. Uchiyama, S. Nizet, V. Glass, C. K. Newton, A. C. 2019-05-24 doi:10.1101/647883 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Age dependence of modern clinical risk groups for localized prostate cancer -- a population-based study ]]> https://biorxiv.org/content/10.1101/648519v1?rss=1 Huynh-Le, M.-P. Myklebust, T. A. Feng, C. Karunamuni, R. Johannesen, T. B. Dale, A. M. Andreassen, O. A. Seibert, T. M. 2019-05-24 doi:10.1101/648519 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ On the impact of biomass composition in constraint-based flux analysis ]]> https://biorxiv.org/content/10.1101/652040v1?rss=1 Lakshmanan, M. Long, S. Ang, K. S. Lewis, N. E. Lee, D.-Y. 2019-05-28 doi:10.1101/652040 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Tyr1 phosphorylation promotes the phosphorylation of Ser2 on the C-terminal domain of RNA polymerase II by P-TEFb ]]> https://biorxiv.org/content/10.1101/652214v1?rss=1 Zhang, Y. Mayfield, J. E. Irani, S. Escobar, E. E. Zhang, Z. Burkholder, N. T. Robinson, M. R. Mehaffey, M. R. Sipe, S. N. Yang, W. Prescott, N. A. Kathuria, K. Liu, Z. Brodbelt, J. 2019-05-28 doi:10.1101/652214 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events ]]> https://biorxiv.org/content/10.1101/653097v1?rss=1 Bergstrom, E. N. Huang, M. N. Mahto, U. Barnes, M. Stratton, M. R. Rozen, S. G. Alexandrov, L. B. 2019-05-29 doi:10.1101/653097 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Ventral Pallidum is Essential for Cocaine Reinstatement After Voluntary Abstinence ]]> https://biorxiv.org/content/10.1101/653741v1?rss=1 Farrell, M. R. Ruiz, C. M. Castillo, E. Faget, L. Khanbijian, C. Liu, S. Schoch, H. Rojas, G. Hnasko, T. S. Mahler, S. V. 2019-05-30 doi:10.1101/653741 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in IGH-CRLF2 patients ]]> https://biorxiv.org/content/10.1101/654418v1?rss=1 Badri, S. Carella, B. Lhoumaud, P. Castro, D. M. Raviram, R. Watters, A. Bonneau, R. M. Skok, J. A. 2019-05-31 doi:10.1101/654418 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids ]]> https://biorxiv.org/content/10.1101/654756v1?rss=1 Quinn, R. A. Vrbanac, A. Melnik, A. V. Patras, K. A. Christy, M. Nelson, A. T. Aksenov, A. A. Tripathi, A. Humphrey, G. da Silva, R. Bussell, R. Thron, T. Wang, M. Vargas, F. Gauglitz, J. Meehan, M. J. Poulsen, O. Boland, B. S. Chang, J. T. Sandborn, W. J. Lim, M. Garg, N. Lumeng, J. Kazmierczak, B. I. Jain, R. Egan, M. Rhee, K. E. Haddad, G. G. Siegel, D. Mazmanian, S. Nizet, V. Knight, R. Dorrestein, P. C. 2019-06-03 doi:10.1101/654756 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ The cohesin loader NIPBL interacts with pre-ribosomal RNA and treacle to regulate ribosomal RNA synthesis ]]> https://biorxiv.org/content/10.1101/658492v1?rss=1 Kong, X. Chen, Y.-Y. Lin, J. Flowers, E. Van Nostrand, E. Blue, S. Chau, J. Ma, C. I.-H. Mohr, I. Thai, R. Yao, C. Ball, A. Chien, R. Kawauchi, S. Santos, R. Calof, A. Lander, A. Shi, Y. Okuwaki, M. Yeo, G. W. Yokomori, K. 2019-06-03 doi:10.1101/658492 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Vapor inhalation of cannabidiol (CBD) in rats ]]> https://biorxiv.org/content/10.1101/659250v1?rss=1 Javadi-Paydar, M. Creehan, K. M. Kerr, T. M. Taffe, M. A. 2019-06-04 doi:10.1101/659250 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Behavioral and neural signatures of working memory in childhood ]]> https://biorxiv.org/content/10.1101/659409v1?rss=1 Rosenberg, M. D. Martinez, S. A. Rapuano, K. M. Conley, M. I. Cohen, A. O. Cornejo, M. D. Hagler, D. J. Anderson, K. M. Wager, T. D. Feczko, E. Earl, E. Fair, D. A. Barch, D. M. Watts, R. Casey, B. 2019-06-06 doi:10.1101/659409 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Semantic Fluency Predicts Six-Year Progression to Mild Cognitive Impairment in Middle-Aged Men ]]> https://biorxiv.org/content/10.1101/659417v1?rss=1 Gustavson, D. E. Elman, J. A. Panizzon, M. S. Franz, C. E. Zuber, J. Sanderson-Cimino, M. Reynolds, C. A. Jacobson, K. C. Xian, H. Jak, A. J. Toomey, R. Lyons, M. J. Kremen, W. A. 2019-06-04 doi:10.1101/659417 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Small-molecule control of super-Mendelian inheritance in gene drives ]]> https://biorxiv.org/content/10.1101/665620v1?rss=1 nView larger version (15K):norg.highwire.dtl.DTLVardef@1aa8522org.highwire.dtl.DTLVardef@a99c8org.highwire.dtl.DTLVardef@1f63636org.highwire.dtl.DTLVardef@1613408_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Lopez Del Amo, V. Leger, B. S. Cox, K. J. Gill, S. Bishop, A. L. Scanlon, G. D. Walker, J. A. Gantz, V. M. Choudhary, A. 2019-06-14 doi:10.1101/665620 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Stimulation augments spike sequence replay and memory consolidation during slow-wave sleep ]]> https://biorxiv.org/content/10.1101/670091v1?rss=1 Wei, Y. Krishnan, G. Marshall, L. Martinetz, T. BAZHENOV, M. 2019-06-13 doi:10.1101/670091 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction ]]> https://biorxiv.org/content/10.1101/672485v1?rss=1 Vasan, R. Rudraraju, S. Akamatsu, M. Garikipati, K. Rangamani, P. 2019-06-15 doi:10.1101/672485 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ Higher fitness yeast genotypes are less robust to deleterious mutations ]]> https://biorxiv.org/content/10.1101/675314v1?rss=1 Johnson, M. S. Martsul, A. Kryazhimskiy, S. Desai, M. M. 2019-06-20 doi:10.1101/675314 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ The Molecular and Microbial Microenvironments in Chronically Diseased Lungs ]]> https://biorxiv.org/content/10.1101/676148v1?rss=1 Garg, N. Melnik, A. V. Vasquez-Baeza, Y. Aksenov, A. Hyde, E. R. McAvoy, A. C. Wang, M. da Silva, R. Protsyuk, I. Wu, J. V. Bouslimani, A. Lim, Y. W. Luzzatto-Knaan, T. Comstock, W. Quinn, R. A. Wong, R. Humphrey, G. Ackermann, G. Spivey, T. Brouha, S. S. Bandeira, N. Lin, G. Y. Rohwer, F. Conrad, D. Alexandrov, T. Dorrestein, P. C. Knight, R. 2019-06-19 doi:10.1101/676148 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Altered White Matter Microstructural Organization in Post-Traumatic Stress Disorder across 3,049 Adults: Results from the PGC-ENIGMA PTSD Consortium ]]> https://biorxiv.org/content/10.1101/677153v1?rss=1 Dennis, E. Disner, S. E. Fani, N. Salminen, L. E. Logue, M. Clarke-Rubright, E. K. Haswell, C. C. Averill, C. Baugh, L. A. Bomyea, J. Bruce, S. E. Cha, J. Choi, K. Davenport, N. D. Densmore, M. du Plessis, S. Forster, G. L. Frijling, J. L. Gonenc, A. Gruber, S. Grupe, D. W. Guenette, J. P. Hayes, J. Hofmann, D. Ipser, J. Jovanovic, T. Kelly, S. Kennis, M. Kinzel, P. Koch, S. B. Koerte, I. Koopowitz, S. Korgaonkar, M. Krystal, J. Lebois, L. A. Li, G. Magnotta, V. A. Manthey, A. May, G. J. Menefee, D. S. Nawijn, L. Nelson, S. M. Neufeld, R. W. Nitschke, 2019-06-20 doi:10.1101/677153 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Aequorea victoria’s secrets ]]> https://biorxiv.org/content/10.1101/677344v1?rss=1 Lambert, G. G. Depernet, H. Gotthard, G. Schultz, D. T. Navizet, l. Lambert, T. Bindels, D. S. Levesque, V. Nero Moffatt, J. N. Salih, A. Royant, A. Shaner, N. C. 2019-06-19 doi:10.1101/677344 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/678797v1?rss=1 Akamatsu, M. Vasan, R. Serwas, D. Ferrin, M. Rangamani, P. Drubin, D. G. 2019-06-21 doi:10.1101/678797 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ A receptor for herbivore-associated molecular patterns mediates plant immunity ]]> https://biorxiv.org/content/10.1101/679803v1?rss=1 Steinbrenner, A. D. Munoz-Amatriain, M. Venegas, J. M. A. Lo, S. Shi, D. Holton, N. Zipfel, C. Abagyan, R. Huffaker, A. Close, T. J. Schmelz, E. A. 2019-06-22 doi:10.1101/679803 Cold Spring Harbor Laboratory Press 2019-06-22 <![CDATA[ Impact of insertion sequences on convergent evolution of Shigella species ]]> https://biorxiv.org/content/10.1101/680777v1?rss=1 Hawkey, J. Monk, J. M. Billman-Jacobe, H. Palsson, B. Holt, K. E. 2019-06-24 doi:10.1101/680777 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities ]]> https://biorxiv.org/content/10.1101/683367v1?rss=1 Armstrong, N. J. Mather, K. A. Sargurupremraj, M. Knol, M. J. Malik, R. Satizabal, C. L. Yanek, L. R. Wen, W. Gudnason, V. Dueker, N. D. Elliott, L. T. Hofer, E. Jahanshad, N. Li, S. Logue, M. A. Luciano, M. Scholz, M. Smith, A. V. Trompet, S. S. Vojinovic, D. Xia, R. Alfaro-Almagro, F. Ames, D. Amin, N. Amouyel, P. Beiser, A. S. Brodaty, H. Deary, I. J. Fennema-Notestine, C. Gampawar, P. G. Gottesman, R. F. Griffanti, L. Jack, C. R. Jenkinson, M. Jiang, J. Kral, B. G. Kwok, J. B. Lampe, L. Liewald, D. C. Maillard, P. Marchini, J. Bastin, M. E. Mazoyer 2019-06-27 doi:10.1101/683367 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses ]]> https://biorxiv.org/content/10.1101/685008v1?rss=1 Lee, J. Zhang, J. Chung, Y.-J. Kim, J. H. Kook, C. M. Gonzalez-Navajas, J. M. Herdman, D. S. Nürnberg, B. Insel, P. Corr, M. Tao, A. Yasuda, K. Rifkin, I. R. Broide, D. H. Sciammas, R. Webster, N. J. G. Raz, E. 2019-06-28 doi:10.1101/685008 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Convergent metatarsal fusion in jerboas and chickens is mediated by similarities and differences in the patterns of osteoblast and osteoclast activities ]]> https://biorxiv.org/content/10.1101/688036v1?rss=1 Gutierrez, H. L. Tsutsumi, R. Moore, T. Y. Cooper, K. L. 2019-07-01 doi:10.1101/688036 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Isolation of muscle stem cells from rat skeletal muscles ]]> https://biorxiv.org/content/10.1101/690776v1?rss=1 Boscolo Sesillo, F. Wong, M. Cortez, A. Alperin, M. 2019-07-03 doi:10.1101/690776 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Correcting for sparsity and non-independence in glycomic data through a system biology framework ]]> https://biorxiv.org/content/10.1101/693507v1?rss=1 Bao, B. Kellman, B. P. Chiang, A. W. T. York, A. K. Mohammad, M. A. Haymond, M. W. Bode, L. Lewis, N. E. 2019-07-05 doi:10.1101/693507 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ HORMA domain proteins and a Pch2-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity ]]> https://biorxiv.org/content/10.1101/694695v1?rss=1 Ye, Q. Lau, R. K. Mathews, I. T. Watrous, J. D. Azimi, C. S. Jain, M. Corbett, K. D. 2019-07-06 doi:10.1101/694695 Cold Spring Harbor Laboratory Press 2019-07-06 <![CDATA[ Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity ]]> https://biorxiv.org/content/10.1101/694703v1?rss=1 Lau, R. K. Ye, Q. Patel, L. Berg, K. R. Mathews, I. T. Watrous, J. D. Whiteley, A. T. Lowey, B. Mekalanos, J. J. Kranzusch, P. J. Jain, M. Corbett, K. 2019-07-07 doi:10.1101/694703 Cold Spring Harbor Laboratory Press 2019-07-07 <![CDATA[ Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders - findings from a Danish population-based study ]]> https://biorxiv.org/content/10.1101/699462v1?rss=1 Liu, X. Nudel, R. Thompson, W. K. Appadurai, V. Schork, A. J. Buil, A. Rasmussen, S. Allesoee, R. L. Werge, T. Mors, O. Boerglum, A. D. Hougaard, D. M. Mortensen, P. B. Nordentoft, M. Benros, M. E. 2019-07-11 doi:10.1101/699462 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex ]]> https://biorxiv.org/content/10.1101/701532v1?rss=1 Partlow, E. A. Baker, R. W. Beacham, G. M. Chappie, J. S. Leschziner, A. E. Hollopeter, G. 2019-07-13 doi:10.1101/701532 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Improved identification and differentiation from epileptiform activity of human hippocampal sharpwave-ripples during NREM sleep ]]> https://biorxiv.org/content/10.1101/702894v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Cash, S. S. S. Chauvel, P. Gale, J. Halgren, E. 2019-07-15 doi:10.1101/702894 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Coordination of human hippocampal sharpwave-ripples during NREM sleep with cortical theta bursts, spindles, downstates and upstates ]]> https://biorxiv.org/content/10.1101/702928v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Halgren, E. 2019-07-15 doi:10.1101/702928 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Posterior hippocampal spindle-ripples co-occur with neocortical theta-bursts and down-upstates, and phase-lock with parietal spindles during NREM sleep in humans ]]> https://biorxiv.org/content/10.1101/702936v1?rss=1 Jiang, X. Gonzalez-Martinez, J. Halgren, E. 2019-07-15 doi:10.1101/702936 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ The potential for gas-free measurements of absolute oxygen metabolism during both baseline and activation states in the human brain ]]> https://biorxiv.org/content/10.1101/705186v1?rss=1 Liu, E. Y. Guo, J. Simon, A. B. Haist, F. Dubowitz, D. J. Buxton, R. B. 2019-07-16 doi:10.1101/705186 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Linkage Disequilibrium and Heterozygosity Modulate the Genetic Architecture of Human Complex Phenotypes: Evidence of Natural Selection from GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/705285v1?rss=1 Holland, D. Frei, O. Desikan, R. Fan, C. C. Shadrin, A. Smeland, O. Andreassen, O. A. Dale, A. 2019-07-16 doi:10.1101/705285 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ The C. elegans RIG-I homolog drh-1 mediates the Intracellular Pathogen Response upon viral infection ]]> https://biorxiv.org/content/10.1101/707141v1?rss=1 Sowa, J. N. Jiang, H. Somasundaram, L. Xu, G. Wang, D. Troemel, E. 2019-07-18 doi:10.1101/707141 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks ]]> https://biorxiv.org/content/10.1101/709683v1?rss=1 Zhang, H. B. Kim, M. Chuang, J. H. Ruan, Y. 2019-07-20 doi:10.1101/709683 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ TMEM16F phospholipid scramblase mediates trophoblast fusion and placental development ]]> https://biorxiv.org/content/10.1101/711473v1?rss=1 Yang, H. Zhang, Y. Le, T. Grabau, R. Mohseni, Z. Kim, H. Natale, D. R. Feng, L. Pan, H. 2019-07-24 doi:10.1101/711473 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats using Deep Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/713198v1?rss=1 Jakubosky, D. Smith, E. N. D'Antonio, M. Bonder, M. J. Young Greenwald, W. W. Matsui, H. D'Antonio-Chronowska, A. i2QTL Consortium, HipSci Consortium, Stegle, O. Montgomery, S. B. DeBoever, C. Frazer, K. A. 2019-07-24 doi:10.1101/713198 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ ALS Motor Neurons Exhibit Hallmark Metabolic Defects That Are Rescued by Nicotinamide and SIRT3 Activation ]]> https://biorxiv.org/content/10.1101/713651v1?rss=1 Hor, J.-H. Mohamad Santosa, M. Lim, V. J. W. Ho, B. X. Taylor, A. Khong, Z. J. Ravits, J. Fan, Y. Liou, Y.-C. Soh, B.-S. Ng, S.-Y. 2019-08-02 doi:10.1101/713651 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Structural variant classes and short tandem repeats differentially impact gene expression and complex traits ]]> https://biorxiv.org/content/10.1101/714477v1?rss=1 Jakubosky, D. D'Antonio, M. Bonder, M. J. Smail, C. Donovan, M. K. R. Young Greenwald, W. W. D'Antonio-Chronowska, A. Matsui, H. i2QTL Consortium, Stegle, O. Smith, E. N. Montgomery, S. B. DeBoever, C. Frazer, K. A. 2019-07-25 doi:10.1101/714477 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signalling. ]]> https://biorxiv.org/content/10.1101/716647v1?rss=1 Vinckier, N. K. Patel, N. A. Wang, A. Wang, J. Shih, H.-P. Wang, J. Jhala, U. S. Rosenfeld, M. G. Benner, C. Sander, M. 2019-08-01 doi:10.1101/716647 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Skeletal Muscle mTORC1 Activation Increases Energy Expenditure and Reduces Longevity in Mice ]]> https://biorxiv.org/content/10.1101/720540v1?rss=1 Stephenson, E. J. Redd, J. R. Snyder, D. Tran, Q. T. Lu, B. Peloquin, M. J. Mulcahy, M. C. Harvey, I. Fisher, K. Han, J. C. Qi, N. Saltiel, A. R. Bridges, D. 2019-07-31 doi:10.1101/720540 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Predictive coding account of action perception: Evidence from effective connectivity in the Action Observation Network ]]> https://biorxiv.org/content/10.1101/722298v1?rss=1 Urgen, B. A. Saygin, A. P. 2019-08-01 doi:10.1101/722298 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ In vivo lineage conversion of vertebrate muscle into early endoderm-like cells ]]> https://biorxiv.org/content/10.1101/722967v1?rss=1 Campbell, C. Lancman, J. J. Espin-Palazon, R. Matalonga, J. He, J. Graves, A. Zeng, X.-X. I. Huisken, J. Traver, D. Dong, P. D. S. 2019-08-09 doi:10.1101/722967 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Relating visual production and recognition of objects in human visual cortex ]]> https://biorxiv.org/content/10.1101/724294v1?rss=1 Fan, J. Wammes, J. Gunn, J. Yamins, D. Norman, K. Turk-Browne, N. 2019-08-03 doi:10.1101/724294 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast ]]> https://biorxiv.org/content/10.1101/724617v1?rss=1 Jerison, E. R. Nguyen Ba, A. N. Desai, M. M. Kryazhimskiy, S. 2019-08-03 doi:10.1101/724617 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Laccase-mediated catalyzed fluorescent reporter deposition for live cell imaging ]]> https://biorxiv.org/content/10.1101/731539v1?rss=1 Cisneros, B. T. Devaraj, N. K. 2019-08-10 doi:10.1101/731539 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Variations in Brain Morphometry Among Healthy Preschoolers Born Very Preterm ]]> https://biorxiv.org/content/10.1101/734277v1?rss=1 Hasler, H. M. Brown, T. T. Akshoomoff, N. 2019-08-13 doi:10.1101/734277 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Movement abilities and brain development in preschoolers born very preterm ]]> https://biorxiv.org/content/10.1101/734319v1?rss=1 Hasler, H. M. Fuller, M. G. Vaucher, Y. E. Brown, T. T. Stiles, J. Dale, A. M. Jernigan, T. L. Akshoomoff, N. 2019-08-13 doi:10.1101/734319 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Formation of talin-vinculin pre-complexes dictates maturation of nascent adhesions by accelerated force transmission and vinculin recruitment ]]> https://biorxiv.org/content/10.1101/735183v1?rss=1 Han, S. J. Dean, K. Whitewood, A. J. Bachir, A. Guttierrez, E. Groisman, A. Horwitz, A. R. Goult, B. T. Danuser, G. 2019-08-14 doi:10.1101/735183 Cold Spring Harbor Laboratory Press 2019-08-14 <![CDATA[ Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway ]]> https://biorxiv.org/content/10.1101/735894v1?rss=1 LaMonte, G. M. Marapana, D. S. Gnadig, N. Ottilie, S. Luth, M. R. Worgall, T. S. Rocamora, F. Goldgof, G. M. Mohunlal, R. Kumar, T. R. S. Thompson, J. K. Vigil, E. Yang, J. Hutson, D. Johnson, T. Huang, J. Williams, R. M. Zou, B. Y. Cheung, A. L. Kumar, P. Egan, T. J. Lee, M. C. S. Siegel, D. Cowman, A. F. Fidock, D. A. Winzeler, E. A. 2019-08-15 doi:10.1101/735894 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Telomere-to-telomere assembly of a complete human X chromosome ]]> https://biorxiv.org/content/10.1101/735928v1?rss=1 Miga, K. H. Koren, S. Rhie, A. Vollger, M. R. Gershman, A. Bzikadze, A. Brooks, S. Howe, E. Porubsky, D. Logsdon, G. A. Schneider, V. A. Potapova, T. Wood, J. Chow, W. Armstrong, J. Fredrickson, J. Pak, E. Tigyi, K. Kremitzki, M. Markovic, C. Maduro, V. Dutra, A. Bouffard, G. G. Chang, A. M. Hansen, N. F. Thibaud-Nissen, F. Schmitt, A. D. Belton, J.-M. Selvaraj, S. Dennis, M. Y. Soto, D. C. Sahasrabudhe, R. Kaya, G. Quick, J. Loman, N. J. Holmes, N. Loose, M. Surti, U. Risques, R. a. Lindsay, T. A. G. Fulton, R. Hall, I. Paten, B. Howe, K. Timp, W. 2019-08-16 doi:10.1101/735928 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Dynamic regulation of immunity through post-translational control of defense transcript splicing ]]> https://biorxiv.org/content/10.1101/736249v1?rss=1 Dressano, K. Weckwerth, P. Poretsky, E. Takahashi, Y. Villarreal, C. Shen, Z. Schroeder, J. Briggs, S. Huffaker, A. 2019-08-15 doi:10.1101/736249 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Hippocampal subfield volumes are uniquely affected in PTSD and depression: International analysis of 31 cohorts from the PGC-ENIGMA PTSD Working Group ]]> https://biorxiv.org/content/10.1101/739094v1?rss=1 Salminen, L. E. Sämann, P. G. Zheng, Y. Dennis, E. L. Clarke, E. K. Jahanshad, N. Iglesias, J. E. Whelan, C. D. Bruce, S. E. Hayes, J. P. Seedat, S. Averill, C. L. Baugh, L. A. Bomyea, J. Bright, J. Buckle, C. J. Choi, K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. du Plessis, S. Elman, J. A. Fani, N. Forster, G. L. Franz, C. E. Frijling, J. L. Gonenc, A. Gruber, S. A. Grupe, D. W. Guenette, J. P. Haswell, C. C. Hofmann, D. Hollifield, M. Hosseini, B. Hudson, A. R. Ipser, J. Jovanovic, T. Kennedy-Krage, A. Kennis, M. King, A. Kinzel, P. 2019-08-21 doi:10.1101/739094 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems ]]> https://biorxiv.org/content/10.1101/740530v1?rss=1 Lim, B. J. Ackermann, B. E. Debelouchina, G. T. 2019-08-27 doi:10.1101/740530 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ Trading Genome Vulnerability for Stable Genetic Inheritance: Active Retrotransposons Help Maintain Pericentromeric Heterochromatin Required for Faithful Cell Division ]]> https://biorxiv.org/content/10.1101/740753v1?rss=1 Hao, Y. Wang, D. Wu, S. Li, X. Shao, C. Zhang, P. Chen, J.-Y. Lim, D.-H. Fu, X.-D. He, S. Chen, R. 2019-08-20 doi:10.1101/740753 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Nutrient regulation of the islet epigenome controls adaptive insulin secretion ]]> https://biorxiv.org/content/10.1101/742403v1?rss=1 Wortham, M. Liu, F. Fleischman, J. Y. Wallace, M. Mulas, F. Vinckier, N. K. Harrington, A. R. Cross, B. R. Chiou, J. Patel, N. A. Sui, Y. Jhala, U. S. Shirihai, O. S. Huising, M. O. Gaulton, K. J. Metallo, C. M. Sander, M. 2019-08-21 doi:10.1101/742403 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Pharmacological inhibition of the heart of glass (HEG1)-Krev interaction trapped protein 1 (KRIT1) protein complex increases Kruppel-like Factors 4 and 2 (KLF4/2) expression in endothelial cells ]]> https://biorxiv.org/content/10.1101/744821v1?rss=1 Lopez-Ramirez, M. A. Haynes, M. K. Hale, P. Oukoloff, K. Bautista, M. Gongol, B. Shyy, J. Y. Ballatore, C. Sklar, L. A. Gingras, A. R. 2019-08-23 doi:10.1101/744821 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Evolution of resistance in vitro reveals a novel mechanism of artemisinin activity in Toxoplasma gondii. ]]> https://biorxiv.org/content/10.1101/746065v1?rss=1 Rozenberg, A. Luth, M. R. Behnke, M. Winzeler, E. Sibley, L. D. 2019-08-24 doi:10.1101/746065 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Enzyme-free synthesis of natural phospholipids in water ]]> https://biorxiv.org/content/10.1101/746156v1?rss=1 Liu, L. Zou, Y. Bhattacharya, A. Zhang, D. Lang, S. Q. Houk, K. N. Devaraj, N. K. 2019-08-24 doi:10.1101/746156 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Polygenic Prediction of Substance Use Disorders in Clinical and Population Samples ]]> https://biorxiv.org/content/10.1101/748038v1?rss=1 Barr, P. B. Ksinan, A. Su, J. Johnson, E. C. Meyers, J. L. Wetherill, L. Latvala, A. Aleive, F. Chan, G. Kuperman, S. Nurnberger, J. Kamarajan, C. Anokhin, A. Agrawal, A. Rose, R. J. Edenberg, H. J. Schuckit, M. Kaprio, J. Dick, D. M. 2019-08-30 doi:10.1101/748038 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance ]]> https://biorxiv.org/content/10.1101/749887v1?rss=1 Tan, J. Olson, C. A. Park, J. H. Sastry, A. V. Phaneuf, P. Yang, L. Szubin, R. Hefner, Y. Feist, A. M. Palsson, B. O. 2019-08-29 doi:10.1101/749887 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data ]]> https://biorxiv.org/content/10.1101/750471v1?rss=1 Jarmusch, A. K. Wang, M. Aceves, C. M. Advani, R. S. Aguire, S. Aksenov, A. A. Aleti, G. Aron, A. T. Bauermeister, A. Bolleddu, S. Bouslimani, A. Caraballo-Rodriguez, A. M. Chaar, R. Coras, R. Elijah, E. O. Ernst, M. Gauglitz, J. M. Gentry, E. C. Husband, M. Jarmusch, S. A. Jones, K. L. Kamenik, Z. Le Gouellec, A. Lu, A. McCall, L.-I. McPhail, K. L. Meehan, M. J. Melnik, A. V. Menezes, R. C. Montoya-Giraldo, Y. A. Nguyen, N. H. Nothias, L. F. Nothias-Esposito, M. Panitchpakdi, M. Petras, D. Quinn, R. Sikora, N. van der Hooft, J. J. J. Vargas, F. Vrbanac, 2019-08-29 doi:10.1101/750471 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production ]]> https://biorxiv.org/content/10.1101/751347v1?rss=1 Fouladiha, H. Marashi, S.-A. Torkashvand, F. Mahboudi, F. Lewis, N. Vaziri, B. 2019-09-01 doi:10.1101/751347 Cold Spring Harbor Laboratory Press 2019-09-01 <![CDATA[ Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion ]]> https://biorxiv.org/content/10.1101/754002v1?rss=1 Saxena, A. Sharma, V. Tran, M. P. Gutierrez, H. L. Erberich, J. M. Birmingham, A. Hiller, M. Cooper, K. L. 2019-08-31 doi:10.1101/754002 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Factors that influence the thymic selection of CD8αα intraepithelial lymphocytes ]]> https://biorxiv.org/content/10.1101/761601v1?rss=1 Kurd, N. S. Hoover, A. Yoon, J. Weist, B. M. Robey, E. A. 2019-09-12 doi:10.1101/761601 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Cross-Sectional and Longitudinal Validation of Serum Neurofilament Light Chain (NfL) as a Biomarker of Parkinson’s Disease Progression ]]> https://biorxiv.org/content/10.1101/762237v1?rss=1 Mollenhauer, B. Dakna, D. Liu, T.-Y. Galasko, D. Foroud, T. Zetterberg, H. Schade, S. Gera, R. Wang, W. Gao, F. Kruse, N. Frasier, M. Chahine, L. Coffey, C. S. Singleton, A. B. Simuni, T. Weintraub, D. Seibyl, J. Toga, A. W. Tanner, C. M. Kieburtz, K. Marek, K. Siderowf, A. Cedarbaum, J. M. Hutten, S. J. Trenkwalder, C. Graham, D. 2019-09-11 doi:10.1101/762237 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Network-based clustering for drug sensitivity prediction in cancer cell lines ]]> https://biorxiv.org/content/10.1101/764043v1?rss=1 Pouryahya, M. Oh, J. H. Mathews, J. C. Belkhatir, Z. Moosmuller, C. Deasy, J. O. Tannenbaum, A. R. 2019-09-18 doi:10.1101/764043 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Interferon stimulated genes mark pathogenic cells of the emergency myelopoietic response to sterile tissue injury in mice and humans ]]> https://biorxiv.org/content/10.1101/765404v1?rss=1 Ng, R. Calcagno, D. M. Toomu, A. Huang, K. Aguirre, A. Daniels, L. Fu, Z. King, K. 2019-09-11 doi:10.1101/765404 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries ]]> https://biorxiv.org/content/10.1101/765453v1?rss=1 Lee, C. T. Laughlin, J. G. Moody, J. B. Amaro, R. E. McCammon, J. A. Holst, M. J. Rangamani, P. 2019-09-11 doi:10.1101/765453 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Beyond the ecology of fear: non-lethal effects of predators are strong whereas those of parasites are diverse ]]> https://biorxiv.org/content/10.1101/766477v1?rss=1 Daversa, D. R. Hechinger, R. F. Madin, E. Fenton, A. 2019-09-18 doi:10.1101/766477 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Understanding the role of urban design in disease spreading ]]> https://biorxiv.org/content/10.1101/766667v1?rss=1 Brizuela, N. G. Garcia-Chan, N. Gutierrez Pulido, H. Chowell, G. 2019-09-12 doi:10.1101/766667 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Making the MOSTest of imaging genetics ]]> https://biorxiv.org/content/10.1101/767905v1?rss=1 van der Meer, D. Frei, O. Kaufmann, T. Shadrin, A. A. Devor, A. Smeland, O. B. Thompson, W. Fan, C. C. Holland, D. Westlye, L. T. Andreassen, O. A. Dale, A. 2019-09-14 doi:10.1101/767905 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ A Pairwise Distance Distribution Correction (DDC) algorithm for blinking-free super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/768051v1?rss=1 Bohrer, C. H. Yang, X. Weng, X. Tenner, B. Ross, B. Mcquillen, R. Zhang, J. Roberts, E. Xiao, J. 2019-09-12 doi:10.1101/768051 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Reliability of Mismatch Negativity Event-Related Potentials in a Multisite, Traveling Subjects Study ]]> https://biorxiv.org/content/10.1101/768408v1?rss=1 0.5). Reliability of MMN amplitude was greater than latency, and reliability with mastoid referencing significantly outperformed nose-referencing.nnConclusionsEEG preprocessing methods have a significant impact on the reliability of MMN amplitude. Within site MMN reliability can be excellent, consistent with prior single site studies.nnSignificanceWith standardized data collection and ERP processing, MMN can be reliably obtained in multisite studies, providing larger samples sizes within rare patient groups. ]]> Roach, B. Carrion, R. E. Hamilton, H. K. Bachman, P. Belger, A. Duncan, E. Johannesen, J. Light, G. A. Niznikiewicz, M. Addington, J. Bearden, C. E. Cadenhead, K. S. Cannon, T. D. Cornblatt, B. A. McGlashan, T. H. Perkins, D. O. Seidman, L. J. Tsuang, M. Walker, E. F. Woods, S. W. Mathalon, D. H. 2019-09-18 doi:10.1101/768408 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ centroFlye: Assembling Centromeres with Long Error-Prone Reads ]]> https://biorxiv.org/content/10.1101/772103v1?rss=1 Bzikadze, A. V. Pevzner, P. A. 2019-09-16 doi:10.1101/772103 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Annotation-Informed Causal Mixture Modeling (AI-MiXeR) reveals phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories ]]> https://biorxiv.org/content/10.1101/772202v1?rss=1 Shadrin, A. A. Frei, O. Smeland, O. B. Bettella, F. O`Connell, K. S. Gani, O. Bahrami, S. Uggen, T. K. E. Djurovic, S. Holland, D. Andreassen, O. A. Dale, A. M. 2019-09-16 doi:10.1101/772202 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Secondary Motor Cortex Transforms Spatial Information into Planned Action During Navigation ]]> https://biorxiv.org/content/10.1101/776765v1?rss=1 Olson, J. M. Li, J. Montgomery, S. E. Nitz, D. A. 2019-09-20 doi:10.1101/776765 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk association ]]> https://biorxiv.org/content/10.1101/778183v1?rss=1 Nott, A. Holtman, I. R. Coufal, N. G. Schlachetzki, J. C. M. Yu, M. Hu, R. Han, C. Z. Pena, M. Xiao, J. Wu, Y. Keuelen, Z. Pasillas, M. P. O'Connor, C. Schafer, S. T. Shen, Z. Rissman, R. A. Brewer, J. B. Gosselin, D. Gonda, D. D. Levy, M. L. Rosenfeld, M. G. McVicker, G. P. Gage, F. H. Ren, B. Glass, C. K. 2019-09-22 doi:10.1101/778183 Cold Spring Harbor Laboratory Press 2019-09-22 <![CDATA[ Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses ]]> https://biorxiv.org/content/10.1101/778605v1?rss=1 Zhang, H. Ahearn, T. Lecarpentier, J. Barnes, D. Beesley, J. Qi, G. Jiang, X. O'Mara, T. A. Zhao, N. Bolla, M. K. Dunning, A. M. Dennis, J. Wang, Q. Abu Ful, Z. Aittomaki, K. Andrulis, I. L. Anton-Culver, H. Arndt, V. Aronson, K. J. Arun, B. K. Auer, P. L. Azzollini, J. Barrowdale, D. Becher, H. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Bogdanova, N. V. Bojesen, S. E. Bonanni, B. Bondavalli, D. Borg, A. Brauch, H. Brenner, H. Briceno, I. Broeks, A. Brucker, S. Y. Bruning, T. Burwinkel, B. Buys, S. 2019-09-24 doi:10.1101/778605 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets ]]> https://biorxiv.org/content/10.1101/781328v1?rss=1 Mohite, O. S. Lloyd, C. J. Monk, J. M. Weber, T. Palsson, B. O. 2019-09-25 doi:10.1101/781328 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Systematic assessment of regulatory effects of human disease variants in pluripotent cells ]]> https://biorxiv.org/content/10.1101/784967v1?rss=1 Bonder, M. J. Smail, C. Gloudemans, M. J. Fresard, L. Jakubosky, D. D'Antonio, M. Li, X. Ferraro, N. M. Carcamo-Orive, I. Mirauta, B. Seaton, D. D. Cai, N. Horta, D. HipSci Consortium, iPSCORE Consortium, GENESiPS Consortium, PhLiPS Consortium, Smith, E. N. Frazer, K. A. Montgomery, S. B. Stegle, O. 2019-09-28 doi:10.1101/784967 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract ]]> https://biorxiv.org/content/10.1101/787358v1?rss=1 Sidhwani, P. Boezio, G. L. M. Yang, H. Chi, N. C. Roman, B. L. Stainier, D. Y. R. Yelon, D. 2019-09-30 doi:10.1101/787358 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ c-di-AMP hydrolysis by a novel type of phosphodiesterase promotes differentiation of multicellular bacteria ]]> https://biorxiv.org/content/10.1101/789354v1?rss=1 Latoscha, A. Drexler, D. J. Al-Bassam, M. M. Kaever, V. Findlay, K. C. Witte, G. Tschowri, N. 2019-10-01 doi:10.1101/789354 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs ]]> https://biorxiv.org/content/10.1101/790063v1?rss=1 Gauglitz, J. M. Morton, J. T. Tripathi, A. Hansen, S. Gaffney, M. Carpenter, C. Weldon, K. C. Shah, R. Parampil, A. Fidgett, A. Swafford, A. D. Knight, R. Dorrestein, P. C. 2019-10-02 doi:10.1101/790063 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Regional dynamics of fractal dimension of the LV endocardium from cine CT images ]]> https://biorxiv.org/content/10.1101/791731v1?rss=1 Manohar, A. Rossini, L. Colvert, G. Vigneault, D. M. Contijoch, F. Chen, M. Y. del Alamo, J. C. McVeigh, E. R. 2019-10-03 doi:10.1101/791731 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations ]]> https://biorxiv.org/content/10.1101/795005v1?rss=1 Rizzi, A. Jensen, T. Slochower, D. R. Aldeghi, M. Gapsys, V. Ntekoumes, D. Bosisio, S. Papadourakis, M. Henriksen, N. M. de Groot, B. L. Cournia, Z. Dickson, A. Michel, J. Gilson, M. K. Shirts, M. R. Mobley, D. L. Chodera, J. D. 2019-10-07 doi:10.1101/795005 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Vaping nicotine-containing electronic cigarettes produces addiction-like behaviors and cardiopulmonary abnormalities in rats ]]> https://biorxiv.org/content/10.1101/797084v1?rss=1 Smith, L. C. Kallupi, M. Tieu, L. Jaquish, A. Barr, J. Su, Y. Velarde, N. Sedighim, S. Klodnicki, M. Carrette, L. L. G. Sun, X. de Guglielmo, G. George, O. 2019-10-08 doi:10.1101/797084 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ The maize heterotrimeric G-protein β subunit controls shoot meristem development and immune responses. ]]> https://biorxiv.org/content/10.1101/797985v1?rss=1 Wu, Q. Xu, F. Liu, L. Char, S. N. Ding, Y. Schmelz, E. A. Yang, B. Jackson, D. 2019-10-08 doi:10.1101/797985 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ The effects of modified sialic acids on mucus and erythrocytes on influenza A virus HA and NA functions ]]> https://biorxiv.org/content/10.1101/800300v1?rss=1 Barnard, K. N. Alford-Lawrence, B. K. Buchholz, D. W. Wasik, B. R. LaClair, J. R. Yu, H. Honce, R. Ruhl, S. Pajic, P. Daugherity, E. K. Chen, X. Schultz-Cherry, S. Aguilar, H. C. Varki, A. Parrish, C. R. 2019-10-10 doi:10.1101/800300 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure ]]> https://biorxiv.org/content/10.1101/804401v1?rss=1 Vargas, F. Weldon, K. C. Sikora, N. Wang, M. Zhang, Z. Gentry, E. C. Panitchpakdi, M. W. Caraballo, M. Dorrestein, P. C. Jarmusch, A. K. 2019-10-15 doi:10.1101/804401 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ A simple mass-action model predicts protein timecourses from mRNA trajectories during a dynamic response in two strains of S. cerevisiae ]]> https://biorxiv.org/content/10.1101/805846v1?rss=1 Kuo, S. Egertson, J. Merrihew, G. MacCoss, M. J. Pollard, D. Rifkin, S. A. 2019-10-16 doi:10.1101/805846 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. ]]> https://biorxiv.org/content/10.1101/807008v1?rss=1 Van Nostrand, E. L. Pratt, G. A. Yee, B. A. Wheeler, E. C. Blue, S. M. Mueller, J. Park, S. S. Garcia, K. E. Gelboin-Burkhart, C. Nguyen, T. B. Rabano, I. Stanton, R. Sundararaman, B. Wang, R. Fu, X.-D. Graveley, B. R. Yeo, G. W. 2019-10-16 doi:10.1101/807008 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program ]]> https://biorxiv.org/content/10.1101/808568v1?rss=1 Denholtz, M. Zhu, Y. Doehrmann, S. He, Z. Lu, H. Isoda, T. Nizet, V. Murre, C. 2019-10-17 doi:10.1101/808568 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Structural Brain Imaging Studies Offer Clues about the Effects of the Shared Genetic Etiology among Neuropsychiatric Disorders ]]> https://biorxiv.org/content/10.1101/809582v1?rss=1 Radonjic, N. V. Hess, J. L. Rovira, P. Andreassen, O. Buitelaar, J. K. Ching, C. R. K. Franke, B. Hoogman, M. Jahanshad, N. McDonald, C. Schmaal, L. Sisodiya, S. M. Stein, D. J. van den Heuvel, O. A. van Erp, T. G. M. van Rooij, D. Veltman, D. J. Thompson, P. Faraone, S. V. 2019-10-17 doi:10.1101/809582 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ The γH2AX Peak in the S Phase After UV Irradiation Corresponds to the sites of DNA Replication and not DNA Damage ]]> https://biorxiv.org/content/10.1101/810689v1?rss=1 Dhuppar, S. Roy, S. Mazumder, A. 2019-10-21 doi:10.1101/810689 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ The polyvertex score (PVS): a whole-brain phenotypic prediction framework for neuroimaging studies ]]> https://biorxiv.org/content/10.1101/813915v1?rss=1 Zhao, W. Palmer, C. E. Thompson, W. K. Jernigan, T. L. Dale, A. M. Fan, C. C. 2019-10-22 doi:10.1101/813915 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Genetic and clinical analyses of psychosis spectrum symptoms in a large multi-ethnic youth cohort reveal significant link with ADHD. ]]> https://biorxiv.org/content/10.1101/814087v1?rss=1 Olde Loohuis, L. M. Mennigen, E. Ori, A. P. S. Perkins, D. Robinson, E. Addington, J. Cadenhead, K. S. Cornblatt, B. A. Mathalon, D. H. McGlashan, T. H. Seidman, L. J. Keshavan, M. Stone, W. Tsuang, M. T. Walker, E. F. Woods, S. W. Cannon, T. D. Gur, R. C. Gur, R. E. Bearden, C. E. Ophoff, R. A. 2019-10-22 doi:10.1101/814087 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Determining the association between cortical morphology and cognition in 10,145 children from the Adolescent Brain and Cognitive Development (ABCD) study using the MOSTest ]]> https://biorxiv.org/content/10.1101/816025v1?rss=1 Palmer, C. E. Zhao, W. E. Loughnan, R. J. Fan, C. C. Thompson, W. K. Jernigan, T. L. Dale, A. M. 2019-10-23 doi:10.1101/816025 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ The circadian clock and darkness control natural competence in cyanobacteria ]]> https://biorxiv.org/content/10.1101/822627v1?rss=1 Taton, A. Erikson, C. Yang, Y. Rubin, B. E. Rifkin, S. A. Golden, J. W. Golden, S. S. 2019-10-30 doi:10.1101/822627 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ N-terminal domain Increases Activation of Elephant Shark Glucocorticoid and Mineralocorticoid Receptors ]]> https://biorxiv.org/content/10.1101/822718v1?rss=1 Katsu, Y. Shariful, I. M. Lin, X. Takagi, W. Urushitani, H. Kohno, S. Hyodo, S. Baker, M. E. 2019-10-29 doi:10.1101/822718 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation ]]> https://biorxiv.org/content/10.1101/823096v1?rss=1 Hahn, W. C. Kim, J. W. Berrios, C. Kim, M. Schade, A. E. Adelmant, G. Yeerna, H. Damato, E. Iniguez, A. B. Swanson, S. K. Florens, L. Washburn, M. P. Stegmaier, K. Gray, N. S. Tamayo, P. Gjoerup, O. Marto, J. A. DeCaprio, J. 2019-10-29 doi:10.1101/823096 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds ]]> https://biorxiv.org/content/10.1101/824888v1?rss=1 Aron, A. T. Petras, D. Schmid, R. Gauglitz, J. M. Buttel, I. Antelo, L. Zhi, H. Saak, C. C. Malarney, K. P. Thines, E. Dutton, R. J. Raffatellu, M. Dorrestein, P. C. 2019-10-30 doi:10.1101/824888 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters ]]> https://biorxiv.org/content/10.1101/831941v1?rss=1 Rachtman, E. Balaban, M. Bafna, V. Mirarab, S. 2019-11-05 doi:10.1101/831941 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Resolving intrinsic ambiguities of the fMRI signal in the human brain ]]> https://biorxiv.org/content/10.1101/833681v1?rss=1 Liu, E. Y. Haist, F. Shin, D. D. Buxton, R. B. 2019-11-07 doi:10.1101/833681 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression and drug response ]]> https://biorxiv.org/content/10.1101/835918v1?rss=1 Zhang, P. Kitchen-Smith, I. Xiong, L. Stracquadanio, G. Brown, K. Richter, P. Wallace, M. Bond, E. Sahgal, N. Moore, S. Nornes, S. De Val, S. Surakhy, M. Sims, D. Wang, X. Bell, D. A. Zeron-Medina, J. Jiang, Y. Ryan, A. Selfe, J. Shipley, J. Kar, S. Pharoah, P. Loveday, C. Jansen, R. Grochola, L. F. Palles, C. Protheroe, A. Millar, V. Ebner, D. Pagadala, M. Blagden, S. P. Maughan, T. Domingo, E. Tomlinson, I. Turnbull, C. Carter, H. Bond, G. 2019-11-09 doi:10.1101/835918 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Co-Increasing Neuronal Noise and Beta Power in the Developing Brain ]]> https://biorxiv.org/content/10.1101/839258v1?rss=1 He, W. Donoghue, T. Sowman, P. F. Seymour, R. A. Brock, J. Crain, S. Voytek, B. Hillebrand, A. 2019-11-12 doi:10.1101/839258 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy ]]> https://biorxiv.org/content/10.1101/840520v1?rss=1 Oliver, A. LaMere, B. Weihe, C. Wandro, S. Lindsay, K. Wadhwa, P. Mills, D. Pride, D. T. Fiehn, O. Northen, T. de Raad, M. Li, H. Martiny, J. B. H. Lynch, S. Whiteson, K. 2019-11-13 doi:10.1101/840520 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Anthropomorphic left ventricular mesh phantom: a framework to investigate the accuracy of SQUEEZ using Coherent Point Drift for the detection of regional wall motion abnormalities ]]> https://biorxiv.org/content/10.1101/840595v1?rss=1 Manohar, A. Colvert, G. M. Schluchter, A. Contijoch, F. J. McVeigh, E. R. 2019-11-13 doi:10.1101/840595 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Predictive Coding Models for Pain Perception ]]> https://biorxiv.org/content/10.1101/843284v1?rss=1 Song, Y. Yao, M. Kemprecos, H. byrne, a. Xiao, Z. Zhang, Q. Singh, A. Wang, J. Chen, Z. S. 2019-11-18 doi:10.1101/843284 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Fluorescence correlation spectroscopy and photon count histograms in small domains. Part I: General theory ]]> https://biorxiv.org/content/10.1101/847129v1?rss=1 Elson, E. L. Jiang, Y. Xu, B. Melnykov, A. Genin, G. M. 2019-11-20 doi:10.1101/847129 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Antagonistic odor interactions in olfactory sensory neurons are widespread in freely breathing mice ]]> https://biorxiv.org/content/10.1101/847525v1?rss=1 Zak, J. D. Reddy, G. Vergassola, M. Murthy, V. N. 2019-11-20 doi:10.1101/847525 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Human-specific regulatory features of brain development manifest staggering breadth of associations with physiological processes and pathological conditions of H. sapiens ]]> https://biorxiv.org/content/10.1101/848762v1?rss=1 Glinsky, G. 2019-11-20 doi:10.1101/848762 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Economic, social, and physiological resilience predict brain structure and cognitive performance in 9 - 10-year-old children ]]> https://biorxiv.org/content/10.1101/852988v1?rss=1 Gonzalez, M. R. Palmer, C. E. Uban, K. A. Jernigan, T. L. Thompson, W. K. Sowell, E. R. 2019-11-25 doi:10.1101/852988 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Sub-2 A Resolution Structure Determination Using Single-Particle Cryo-EM at 200 keV ]]> https://biorxiv.org/content/10.1101/855643v1?rss=1 Wu, M. Lander, G. C. Herzik, M. A. 2019-11-26 doi:10.1101/855643 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Systematic analyses of factors required for adhesion of Salmonella enterica serovar Typhimurium to corn salad (Valerianella locusta) ]]> https://biorxiv.org/content/10.1101/855726v1?rss=1 Hensel, M. Elpers, L. Kretzschmar, J. Nuccio, S.-P. Bäumler, A. J. 2019-11-27 doi:10.1101/855726 Cold Spring Harbor Laboratory Press 2019-11-27 <![CDATA[ Identifying Brain Network Topology Changes in Task Processes and Psychiatric Disorders ]]> https://biorxiv.org/content/10.1101/866855v1?rss=1 Rezaeinia, P. Fairley, K. Pal, P. Meyer, F. Carter, R. M. 2019-12-06 doi:10.1101/866855 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Quantifying the polygenic architecture of the human cerebral cortex: Extensive genetic overlap between cortical thickness and surface area ]]> https://biorxiv.org/content/10.1101/868307v1?rss=1 van der Meer, D. Frei, O. Kaufmann, T. Chen, C.-H. Thompson, W. K. O'Connell, K. S. Monereo Sanchez, J. Linden, D. E. Westlye, L. T. Dale, A. M. Andreassen, O. A. 2019-12-06 doi:10.1101/868307 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Cognitive Functions Mediate the Effect of Preterm Birth on Mathematics Skills in Young Children ]]> https://biorxiv.org/content/10.1101/868547v1?rss=1 Adrian, J. A. Bakeman, R. Akshoomoff, N. Haist, F. 2019-12-08 doi:10.1101/868547 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ SODA: Multi-locus species delimitation using quartet frequencies ]]> https://biorxiv.org/content/10.1101/869396v1?rss=1 Rabiee, M. Mirarab, S. 2019-12-09 doi:10.1101/869396 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ GIV/Girdin and Exo70 Constitute the Core of the Mammalian Polarized Exocytic Machinery ]]> https://biorxiv.org/content/10.1101/870071v1?rss=1 Rohena, C. Rajapakse, N. Lo, I.-C. Novick, P. Sahoo, D. Ghosh, P. 2019-12-09 doi:10.1101/870071 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ GIV-Kindlin interaction is required for Kindlin-Mediated Integrin Recognition and Activation ]]> https://biorxiv.org/content/10.1101/870113v1?rss=1 Rohena, C. Kalogriopoulos, N. Rajapakse, N. Roy, S. Lopez-Sanchez, I. Ablack, J. Sahoo, D. Ghosh, P. 2019-12-10 doi:10.1101/870113 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Latent space visualization, characterization, and generation of diverse vocal communication signals ]]> https://biorxiv.org/content/10.1101/870311v1?rss=1 Sainburg, T. Thielk, M. Gentner, T. Q. 2019-12-11 doi:10.1101/870311 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites ]]> https://biorxiv.org/content/10.1101/870949v1?rss=1 Xu, F. Jimenez-Gonzalez, A. Einarsson, E. Astvaldsson, A. Peirasmaki, D. Eckmann, L. Andersson, J. O. Svärd, S. G. Jerlström-Hultqvist, J. 2019-12-10 doi:10.1101/870949 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Inference of Gorilla demographic and selective history from whole genome sequence data ]]> https://biorxiv.org/content/10.1101/009191v1?rss=1 Kimberly F. McManus Joanna L. Kelley Shiya Song Krishna Veeramah August E. Woerner Laurie S. Stevison Oliver A. Ryder Great Ape Genome Project Jeffrey M. Kidd Jeffrey D. Wall Carlos D. Bustamante Michael F. Hammer 2014-09-17 doi:10.1101/009191 Cold Spring Harbor Laboratory Press 2014-09-17 <![CDATA[ Abnormal X Chromosome Inactivation in Females with Major Psychiatric Disorders ]]> https://biorxiv.org/content/10.1101/009555v1?rss=1 Baohu Ji Kerin K Higa John Kelsoe Xianjin Zhou 2014-09-23 doi:10.1101/009555 Cold Spring Harbor Laboratory Press 2014-09-23 <![CDATA[ On the scope and limitations of baker’s yeast as a model organism for studying human tissue-specific pathways ]]> https://biorxiv.org/content/10.1101/011858v1?rss=1 Shahin Mohammadi Baharak Saberidokht Shankar Subramaniam Ananth Grama 2014-11-26 doi:10.1101/011858 Cold Spring Harbor Laboratory Press 2014-11-26 <![CDATA[ Identification of an Arabidopsis Aminotransferase that Facilitates Tryptophan and Auxin Homeostasis ]]> https://biorxiv.org/content/10.1101/013821v1?rss=1 Michael Pieck Youxi Yuan Jason Godfrey Christopher Fisher Sanda Zolj Nicholas Thomas Connie Wu Julian Ramos Norman Lee Jennifer Normanly John Celenza 2015-01-16 doi:10.1101/013821 Cold Spring Harbor Laboratory Press 2015-01-16 <![CDATA[ Restoration of Sp4 in forebrain GABAergic neurons rescues hypersensitivity to ketamine in Sp4 hypomorphic mice ]]> https://biorxiv.org/content/10.1101/015677v1?rss=1 Kerin K Higa Baohu Ji Mahalah R Buell Risbrough B Victoria Susan B Powell Jared W Young Mark A Geyer Xianjin Zhou 2015-02-26 doi:10.1101/015677 Cold Spring Harbor Laboratory Press 2015-02-26 <![CDATA[ The C. elegans ephrin EFN-4 functions non-cell autonomously with heparan sulfate proteoglycans to promote axon outgrowth and branching ]]> https://biorxiv.org/content/10.1101/022756v1?rss=1 Alicia A Schwieterman Alyse N Steves Vivian Yee Cory J Donelson Aaron Pital Taylor Voyles Austin M Howard Danielle E Ereddia Kelsie S Effrein Jonathan L McMurry Brian D Ackley Andrew D Chisholm Martin L Hudson 2015-07-17 doi:10.1101/022756 Cold Spring Harbor Laboratory Press 2015-07-17 <![CDATA[ Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis ]]> https://biorxiv.org/content/10.1101/026948v1?rss=1 Jean Fan Neeraj Salathia Rui Liu Gwen Kaeser Yun Yung Joseph L Herman Fiona Kaper Jian-Bing Fan Kun Zhang Jerold Chun Peter Kharchenko 2015-09-16 doi:10.1101/026948 Cold Spring Harbor Laboratory Press 2015-09-16 <![CDATA[ Balanced Oscillatory Coupling Improves Information Flow ]]> https://biorxiv.org/content/10.1101/030304v1?rss=1 Erik J Peterson Bradley Voytek 2015-10-30 doi:10.1101/030304 Cold Spring Harbor Laboratory Press 2015-10-30 <![CDATA[ Resources for the comprehensive discovery of functional RNA elements ]]> https://biorxiv.org/content/10.1101/030486v1?rss=1 Balaji Sundararaman Lijun Zhan Steven Blue Rebecca Stanton Keri Elkins Sara Olson Xintao Wei Eric L Van Nostrand Stephanie C Huelga Brendan M Smalec Xiaofeng Wang Eurie L Hong Jean M Davidson Eric Lecuyer Brenton R Graveley Gene W Yeo 2015-11-03 doi:10.1101/030486 Cold Spring Harbor Laboratory Press 2015-11-03 <![CDATA[ Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/032474v1?rss=1 Dominic Holland Yunpeng Wang Wesley K Thompson Andrew Schork Chi-Hua Chen Min-Tzu Lo Aree Witoelar Thomas Werge Michael O'Donovan Ole A Andreassen Anders Dale 2015-11-21 doi:10.1101/032474 Cold Spring Harbor Laboratory Press 2015-11-21 <![CDATA[ Peroxisomes move by hitchhiking on early endosomes using the novel linker protein PxdA ]]> https://biorxiv.org/content/10.1101/034231v1?rss=1 John Salogiannis Martin J. Egan Samara L. Reck-Peterson 2015-12-11 doi:10.1101/034231 Cold Spring Harbor Laboratory Press 2015-12-11 <![CDATA[ The Arabidopsis Auxin F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram ]]> https://biorxiv.org/content/10.1101/034652v1?rss=1 Michael J Prigge Kathleen Greenham Yi Zhang Aaron Santner Cristina Castillejo Ronan C O'Malley Joseph R Ecker Mark Estelle 2015-12-17 doi:10.1101/034652 Cold Spring Harbor Laboratory Press 2015-12-17 <![CDATA[ Systematic identification of cooperation between DNA binding proteins in 3D space ]]> https://biorxiv.org/content/10.1101/036145v1?rss=1 Kai Zhang Nan Li Wei Wang 2016-01-07 doi:10.1101/036145 Cold Spring Harbor Laboratory Press 2016-01-07 <![CDATA[ Gene Expression Signatures of Sporadic ALS Motor Neuron Populations ]]> https://biorxiv.org/content/10.1101/038448v1?rss=1 Ranjan Batra Kasey Hutt Anthony Vu Stuart J Rabin Michael W Baughn Ryan T Libby Shawn Hoon John Ravits Gene W Yeo 2016-02-01 doi:10.1101/038448 Cold Spring Harbor Laboratory Press 2016-02-01 <![CDATA[ Rigidity of silicone substrates controls cell spreading and stem cell differentiation ]]> https://biorxiv.org/content/10.1101/040048v1?rss=1 25 kPa, have been classified as soft (adipogenic) [2,3], medium rigidity (myogenic)1, and hard (osteogenic) [1], respectively. In most studies, the soft substrates are hydrogels, and variations in their elastic moduli are usually accompanied by variations in the dry mass and porosity. The paradigm of the effect of substrate rigidity on the cellular functions has been challenged by Trappmann et al. [4], who claimed that cell spreading and differentiation on hydrogel substrates depend not on the elastic moduli of the substrates, but rather on their porosity, which affects the density of adhesion points between the substrate surface and the extracellular matrix (ECM) coating on it. This claim has been rebutted by Wen at al. [3], who have used hydrogel substrates with different porosities but identical elastic moduli to show that it is the elastic modulus rather than the porosity that is key to the effect of the substrate on cell spreading and differentiation. Both publications agree, however, that there is no appreciable effect of the substrate rigidity on either cell spreading or differentiation, if the substrate is made of a silicone gel rather than a hydrogel. This conclusion appears to contradict the findings of several other groups, who reported that when cells are plated on an array of flexible silicone microposts, their spreading and differentiation depend on the rigidity of the substrate [5], and that when cell are plated on silicone gels, their differentiation depends on the gel rigidity [6]. To resolve this contradiction, we used soft, medium, and hard silicone gel substrates with elastic moduli of 0.5, 16, and 64 kPa, respectively, (Fig.1) to perform experiments similar to those reported in Refs.4 and 3, testing the dependence of differentiation and spreading of MSCs and of spreading of fibroblasts and keratinocytes on the substrate rigidity. ]]> Grigory Vertelov Edgar Gutierrez Sin-Ae Lee Edward Ronan Alex Groisman Eugene Tkachenko 2016-02-19 doi:10.1101/040048 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/044412v1?rss=1 9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ~2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, p = 5.87x10-9; odds ratio = 1.12) and markers within ERBB2 (rs2517959, p = 4.53x10-9; odds ratio = 1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS. ]]> Liping Hou Sarah E Bergen Nirmala Akula Jie Song Christina M Hultman Mikael Landen Mazda Adli Martin Alda Raffaella Ardau Barbara Arias Jean-Michel Aubry Lena Backlund Judith A Badner Thomas B Barrett Michael Bauer Bernhard T Baune Frank Bellivier Antonio Benabarre Susanne Bengesser Wade H Berrettini Abesh Kumar Bhattacharjee Joanna M Biernacka Armin Birner Cinnamon S Bloss Clara Brichant-Petitjean Elise T Bui William Byerley Pablo Cervantes Caterina Chillotti Sven Cichon Francesc Colom William Coryell David W Craig Cristiana Cruceanu Piotr M Czerski Tony Davis Alexandre Dayer Franziska Degenh 2016-03-22 doi:10.1101/044412 Cold Spring Harbor Laboratory Press 2016-03-22 <![CDATA[ Control of Transposon-mediated Activation of the glpFK Operon of Escherichia coli by two DNA binding Proteins ]]> https://biorxiv.org/content/10.1101/046649v1?rss=1 Zhongge Zhang Milton H. Saier 2016-03-31 doi:10.1101/046649 Cold Spring Harbor Laboratory Press 2016-03-31 <![CDATA[ Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/047720v1?rss=1 Robert J Luallen Aaron W Reinke Linda Tong Michael R Botts Marie-Anne Felix Emily R Troemel 2016-04-08 doi:10.1101/047720 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Immune DNA signature of T-cell infiltration in breast tumor exomes ]]> https://biorxiv.org/content/10.1101/047753v1?rss=1 Eric Levy Rachel Marty Valentina Garate-Calderon Brian Woo Michelle Dow Ricardo Armisen Hannah Carter Olivier Harismendy 2016-04-08 doi:10.1101/047753 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ Rapid hyperosmotic-induced Ca2+ responses in Arabidopsis thaliana exhibit sensory potentiation and establish involvement of plastidial KEA transporters ]]> https://biorxiv.org/content/10.1101/048330v1?rss=1 Aaron Benjamin Stephan Eric Yang Hans-Henning Kunz Julian I. Schroeder 2016-04-13 doi:10.1101/048330 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Paradoxical signaling regulates structural plasticity in dendritic spines ]]> https://biorxiv.org/content/10.1101/050492v1?rss=1 Padmini Rangamani Michael G. Levy Shahid M. Khan George Oster 2016-04-27 doi:10.1101/050492 Cold Spring Harbor Laboratory Press 2016-04-27 <![CDATA[ Shear-induced nitric oxide production by endothelial cells ]]> https://biorxiv.org/content/10.1101/051946v1?rss=1 Krishna Sriram Justin G. Laughlin Padmini Rangamani Daniel M. Tartakovsky 2016-05-05 doi:10.1101/051946 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Detection of human adaptation during the past 2,000 years ]]> https://biorxiv.org/content/10.1101/052084v1?rss=1 Yair Field Evan A Boyle Natalie Telis Ziyue Gao Kyle J Gaulton David Golan Loic Yengo Ghislain Rocheleau Philippe Froguel Mark I McCarthy Jonathan K Pritchard 2016-05-07 doi:10.1101/052084 Cold Spring Harbor Laboratory Press 2016-05-07 <![CDATA[ Cell-to-cell spread of microsporidia causes C. elegans organs to form syncytia ]]> https://biorxiv.org/content/10.1101/053181v1?rss=1 Keir M Balla Robert J Luallen Malina A Bakowski Emily R Troemel 2016-05-13 doi:10.1101/053181 Cold Spring Harbor Laboratory Press 2016-05-13 <![CDATA[ Harnessing Molecular Motors for Nanoscale Pulldown in Live Cells ]]> https://biorxiv.org/content/10.1101/053744v1?rss=1 Jonathan E Bird Melanie Barzik Meghan Drummond Daniel C Sutton Spencer M Goodman Eva L Morozko Stacey M Cole Jennifer Skidmore Diana Syam Elizabeth A Wilson Tracy Fitzgerald Atteeq U Rehman Donna M Martin Erich T Boger Inna A Belyantseva Thomas B Friedman 2016-06-07 doi:10.1101/053744 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ Rapidly evolving homing CRISPR barcodes ]]> https://biorxiv.org/content/10.1101/055863v1?rss=1 Reza Kalhor Prashant Mali George M Church 2016-05-27 doi:10.1101/055863 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ Fungal Induced Protein Hyperacetylation Identified by Acetylome Profiling ]]> https://biorxiv.org/content/10.1101/057174v1?rss=1 Justin W Walley Zhouxin Shen Maxwell R McReynolds Steven P Briggs 2016-06-05 doi:10.1101/057174 Cold Spring Harbor Laboratory Press 2016-06-05 <![CDATA[ Distinct Cellular States Determine Calcium Signaling Response ]]> https://biorxiv.org/content/10.1101/059287v1?rss=1 Jason Yao Roy Wollman 2016-06-16 doi:10.1101/059287 Cold Spring Harbor Laboratory Press 2016-06-16 <![CDATA[ Williams Syndrome-Specific Neuroarchitectural Profile and Its Associations with Cognitive Features ]]> https://biorxiv.org/content/10.1101/060764v1?rss=1 Chun Chieh Fan Timothy T. Brown Hauke Bartsch Joshua M. Kuperman Donald J. Hagler Andrew Schork Eric Halgren Anders Dale 2016-06-26 doi:10.1101/060764 Cold Spring Harbor Laboratory Press 2016-06-26 <![CDATA[ Metabolic complementation in bacterial communities: necessary conditions and optimality ]]> https://biorxiv.org/content/10.1101/064121v1?rss=1 Matteo Mori Miguel Ponce-de-Leon Juli Pereto Francisco Montero Montero 2016-07-15 doi:10.1101/064121 Cold Spring Harbor Laboratory Press 2016-07-15 <![CDATA[ An introduction to linear stability analysis for deciphering spatial patterns in signaling networks ]]> https://biorxiv.org/content/10.1101/065474v1?rss=1 Jasmine Nirody Padmini Rangamani 2016-07-23 doi:10.1101/065474 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Chaotic propagation of spatial cytoskeletal instability modulates integrity of podocyte foot processes ]]> https://biorxiv.org/content/10.1101/065839v1?rss=1 Cibele V Falkenberg Evren U Azeloglu Mark Stothers Thomas J Deerinck Yibang Chen John C He Mark H. Ellisman James C. Hone Ravi Iyengar Leslie M. Loew 2016-07-26 doi:10.1101/065839 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion ]]> https://biorxiv.org/content/10.1101/066944v1?rss=1 Zachary Andrew King Edward J O'Brien Adam M Feist Bernhard O Palsson 2016-08-01 doi:10.1101/066944 Cold Spring Harbor Laboratory Press 2016-08-01 <![CDATA[ ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions ]]> https://biorxiv.org/content/10.1101/069021v1?rss=1 Haythem Latif Stephen Federowicz Ali Ebrahim Janna Tarasova Richard Szubin Jose Utrilla Karsten Zengler Bernhard Palsson 2016-08-11 doi:10.1101/069021 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Pulsatile lipid vesicles under osmotic stress ]]> https://biorxiv.org/content/10.1101/070342v1?rss=1 Morgan Chabanon James C.S. Ho Bo Liedberg Atul N. Parikh Padmini Rangamani 2016-08-18 doi:10.1101/070342 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ A new foreperiod effect on single-trial phase coherence.\\ Part I: existence and relevance ]]> https://biorxiv.org/content/10.1101/072371v1?rss=1 Joaquin Rapela Marissa Westerfield Jeanne Townsend Scott Makeig 2016-08-30 doi:10.1101/072371 Cold Spring Harbor Laboratory Press 2016-08-30 <![CDATA[ Hand2 Inhibits Kidney Specification While Promoting Vein Formation Within the Posterior Mesoderm ]]> https://biorxiv.org/content/10.1101/075036v1?rss=1 Elliot A. Perens Zayra V. Garavito-Aguilar Gina P. Guio-Vega Karen T. Pena Yocheved L. Schindler Deborah Yelon 2016-09-13 doi:10.1101/075036 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ PDGF signaling directs cardiomyocyte movement toward the midline during heart tube assembly ]]> https://biorxiv.org/content/10.1101/076703v1?rss=1 Joshua Bloomekatz Reena Singh Owen W.J. Prall Ariel C. Dunn Megan Vaughan Chin-San Loo Richard P. Harvey Deborah Yelon 2016-09-21 doi:10.1101/076703 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Change-point detection without needing to detect change-points? ]]> https://biorxiv.org/content/10.1101/077719v1?rss=1 Chaitanya K Ryali Angela J Yu 2016-09-27 doi:10.1101/077719 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ CLEAR: Composition of Likelihoods for Evolve And Resequence Experiments ]]> https://biorxiv.org/content/10.1101/080085v1?rss=1 Arya Iranmehr Ali Akbari Christian Schlötterer Vineet Bafna 2016-10-10 doi:10.1101/080085 Cold Spring Harbor Laboratory Press 2016-10-10 <![CDATA[ Complete coverage of space favors modularity of the grid system in the brain ]]> https://biorxiv.org/content/10.1101/081356v1?rss=1 Sanzeni, A. Balasubramanian, V. Tiana, G. Vergassola, M. 2016-10-16 doi:10.1101/081356 Cold Spring Harbor Laboratory Press 2016-10-16 <![CDATA[ Deconstructing cell size control into physiological modules in Escherichia coli ]]> https://biorxiv.org/content/10.1101/081422v1?rss=1 Si, F. Li, D. Cox, S. E. Sauls, J. T. Azizi, O. Schwartz, A. B. Erickstad, M. J. Jun, Y. Li, X. Jun, S. 2016-10-17 doi:10.1101/081422 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ The human functional genome defined by genetic diversity ]]> https://biorxiv.org/content/10.1101/082362v1?rss=1 di Iulio, J. Bartha, I. Wong, E. Yu, H.-C. Hicks, M. Shah, N. Lavrenko, V. Kirkness, E. Fabani, M. Yang, D. Jung, I. Biggs, W. Ren, B. Venter, J. C. Telenti, A. 2016-10-21 doi:10.1101/082362 Cold Spring Harbor Laboratory Press 2016-10-21 <![CDATA[ Single cell analysis of lincRNA expression during human blastocyst differentiation identifies TERT (+) multi-lineage precursor cells ]]> https://biorxiv.org/content/10.1101/084087v1?rss=1 Durruthy-Durruthy, J. Wossidlo, M. Sebastiano, V. Glinsky, G. 2016-10-28 doi:10.1101/084087 Cold Spring Harbor Laboratory Press 2016-10-28 <![CDATA[ Feature-coding transitions to conjunction-coding with progression through human visual cortex ]]> https://biorxiv.org/content/10.1101/085381v1?rss=1 Cowell, R. A. Serences, J. T. 2016-11-03 doi:10.1101/085381 Cold Spring Harbor Laboratory Press 2016-11-03 <![CDATA[ Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals ]]> https://biorxiv.org/content/10.1101/086504v1?rss=1 Boehme, U. Otto, T. D. Cotton, J. Steinbiss, S. Sanders, M. Oyola, S. O. Nicot, A. Gandon, S. Patra, K. P. Herd, C. Bushell, E. Modrzynska, K. K. Billker, O. Vinetz, J. M. Rivero, A. Newbold, C. I. Berriman, M. 2016-11-08 doi:10.1101/086504 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ T cell co-stimulatory receptor CD28 is a primary target for PD-1-mediated inhibition ]]> https://biorxiv.org/content/10.1101/086652v1?rss=1 Hui, E. Cheung, J. Zhu, J. Su, X. Taylor, M. J. Wallweber, H. A. Sasmal, D. K. Huang, J. Kim, J. M. Mellman, I. Vale, R. D. 2016-11-09 doi:10.1101/086652 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Natural Genetic Variation Modifies Gene Expression Dynamics at the Protein Level During Pheromone Response in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/090480v1?rss=1 Pollard, D. A. Asamoto, C. K. Rahnamoun, H. Abendroth, A. S. Lee, S. R. Rifkin, S. A. 2016-11-29 doi:10.1101/090480 Cold Spring Harbor Laboratory Press 2016-11-29 <![CDATA[ Non-linear tradeoffs allow cooperation to evolve from Prisoner’s Dilemma to Snow Drift ]]> https://biorxiv.org/content/10.1101/091041v1?rss=1 Chao, L. Elena, S. 2016-12-06 doi:10.1101/091041 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ Splice Expression Variation Analysis (SEVA) for Differential Gene Isoform Usage in Cancer ]]> https://biorxiv.org/content/10.1101/091637v1?rss=1 Afsari, B. Guo, T. Considine, M. Florea, L. Kelly, D. Flam, E. Ha, P. Geman, D. Ochs, M. F. Califano, J. A. Gaykalova, D. A. Favorov, A. V. Fertig, E. J. 2016-12-05 doi:10.1101/091637 Cold Spring Harbor Laboratory Press 2016-12-05 <![CDATA[ A framework to interpret short tandem repeat variation in humans ]]> https://biorxiv.org/content/10.1101/092734v1?rss=1 Gymrek, M. Willems, T. Erlich, Y. Reich, D. E. 2016-12-09 doi:10.1101/092734 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ DataMed: Finding useful data across multiple biomedical data repositories ]]> https://biorxiv.org/content/10.1101/094888v1?rss=1 Ohno-Machado, L. Sansone, S.-A. Alter, G. Fore, I. Grethe, J. Xu, H. Gonzalez-Beltran, A. Rocca-Serra, P. Soysal, E. Zong, N. Kim, H.-e. bioCADDIE Consortium, 2016-12-17 doi:10.1101/094888 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Blood flow directs arterial-venous remodeling through Notch activation and endothelial cell migration ]]> https://biorxiv.org/content/10.1101/095307v1?rss=1 Weijts, B. Gutierrez, E. Saikin, S. K. Ablooglu, A. J. Traver, D. Groisman, A. Tkachenko, E. 2016-12-19 doi:10.1101/095307 Cold Spring Harbor Laboratory Press 2016-12-19 <![CDATA[ In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase ]]> https://biorxiv.org/content/10.1101/097600v1?rss=1 Carbone, C. B. Kern, N. Fernandes, R. A. Hui, E. Su, X. Garcia, K. C. Vale, R. 2016-12-31 doi:10.1101/097600 Cold Spring Harbor Laboratory Press 2016-12-31 <![CDATA[ Evolution of the Mineralocorticoid Receptor: Sequence, Structure and Function ]]> https://biorxiv.org/content/10.1101/098921v1?rss=1 Baker, M. E. Katsu, Y. 2017-01-06 doi:10.1101/098921 Cold Spring Harbor Laboratory Press 2017-01-06 <![CDATA[ A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information ]]> https://biorxiv.org/content/10.1101/100305v1?rss=1 Luo, Y. Zhao, X. Zhou, J. Yang, J. Zhang, Y. Kuang, W. Peng, J. Chen, L. Zeng, J. 2017-01-13 doi:10.1101/100305 Cold Spring Harbor Laboratory Press 2017-01-13 <![CDATA[ Spatially periodic activation patterns of retrosplenial cortex encode route sub-spaces and distance travelled ]]> https://biorxiv.org/content/10.1101/100537v1?rss=1 Alexander, A. S. Nitz, D. A. 2017-01-15 doi:10.1101/100537 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Multi-generational silencing dynamics control cell aging ]]> https://biorxiv.org/content/10.1101/102210v1?rss=1 Li, Y. Jin, M. O'Laughlin, R. Tsimring, L. S. Pillus, L. Hasty, J. Hao, N. 2017-01-22 doi:10.1101/102210 Cold Spring Harbor Laboratory Press 2017-01-22 <![CDATA[ COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression ]]> https://biorxiv.org/content/10.1101/106559v1?rss=1 Lloyd, C. J. Ebrahim, A. Yang, L. King, Z. A. Catoiu, E. O'Brien, E. J. Liu, J. K. Palsson, B. O. 2017-02-07 doi:10.1101/106559 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Multi-tissue polygenic models for transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/107623v1?rss=1 Park, Y. Sarkar, A. K. Bhutani, K. Kellis, M. 2017-02-10 doi:10.1101/107623 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers ]]> https://biorxiv.org/content/10.1101/110239v1?rss=1 Yan, J. Chen, S.-A. A. Local, A. Liu, T. Qiu, Y. Lee, A.-Y. Jung, I. Preissl, S. Rivera, C. M. Wang, C. Ishii, H. Fang, R. Ye, Z. Ge, K. Hu, M. Ren, B. 2017-02-21 doi:10.1101/110239 Cold Spring Harbor Laboratory Press 2017-02-21 <![CDATA[ SV2: Accurate Structural Variation Genotyping and De Novo Mutation Detection ]]> https://biorxiv.org/content/10.1101/113498v1?rss=1 Antaki, D. Brandler, W. M. Sebat, J. 2017-03-03 doi:10.1101/113498 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data ]]> https://biorxiv.org/content/10.1101/117812v1?rss=1 McMurry, J. Juty, N. Blomberg, N. Burdett, A. Conlin, T. Conte, N. Courtot, M. Deck, J. Dumontier, M. Fellows, D. Gonzalez-Beltran, A. Gormanns, P. Grethe, J. Hastings, J. Hermjakob, H. Heriche, J.-K. Ison, J. Jimenez, R. Jupp, S. Kunze, J. Laibe, C. Le Novere, N. Malone, J. R. Martin, M.-J. McEntyre, J. Morris, C. Muilu, J. Mueller, W. Rocca-Serra, P. Sansone, S.-A. Sariyar, M. Snoep, J. Stanford, N. J. Soiland-Reyes, S. Swainston, N. Washington, N. Williams, A. Wimalaratne, S. Winfree, L. Wolstencroft, K. Goble, C. Mungall, C. Haendel, M. Parkinson, 2017-03-20 doi:10.1101/117812 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/118737v1?rss=1 Kubo, N. Ishii, H. Gorkin, D. Meitinger, F. Xiong, X. Fang, R. Liu, T. Ye, Z. Li, B. Dixon, J. Desai, A. Zhao, H. Ren, B. 2017-03-20 doi:10.1101/118737 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields ]]> https://biorxiv.org/content/10.1101/125229v1?rss=1 Shao, M. Ma, J. Wang, S. 2017-04-07 doi:10.1101/125229 Cold Spring Harbor Laboratory Press 2017-04-07 <![CDATA[ Predicting Protein Binding Affinity With Word EmbeddingsAnd Recurrent Neural Networks ]]> https://biorxiv.org/content/10.1101/128223v1?rss=1 Mazzaferro, C. 2017-04-18 doi:10.1101/128223 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Integrative Single-Cell Analysis By Transcriptional And Epigenetic States In Human Adult Brain ]]> https://biorxiv.org/content/10.1101/128520v1?rss=1 Lake, B. Cheng, S. Sos, B. Fan, J. Yung, Y. Kaeser, G. Duong, T. Gao, D. Chun, J. Kharchenko, P. Zhang, K. 2017-04-19 doi:10.1101/128520 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ Estimating Degree Of Polygenicity, Causal Effect Size Variance, And Confounding Bias In GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/133132v1?rss=1 Holland, D. Fan, C.-C. Frei, O. Shadrin, A. A. Smeland, O. B. Sundar, V. S. ENIGMA, Andreassen, O. A. Dale, A. M. 2017-05-24 doi:10.1101/133132 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ BugBase Predicts Organism Level Microbiome Phenotypes ]]> https://biorxiv.org/content/10.1101/133462v1?rss=1 Ward, T. Larson, J. Meulemans, J. Hillmann, B. Lynch, J. Sidiropoulos, D. Spear, J. Caporaso, G. Blekhman, R. Knight, R. Fink, R. Knights, D. 2017-05-02 doi:10.1101/133462 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Precision Medicine Screening Using Whole Genome Sequencing And Advanced Imaging To Identify Disease Risk In Adults ]]> https://biorxiv.org/content/10.1101/133538v1?rss=1 Perkins, B. A. Caskey, C. T. Brar, P. Dec, E. Karow, D. Kahn, A. Hou, C. Shah, N. Boeldt, D. Coughlin, E. Hands, G. Lavrenko, V. Yu, J. Procko, A. Appis, J. Dale, A. M. Guo, L. Jonsson, T. J. Wittmann, B. M. Bartha, I. Ramakrishnan, S. Bernal, A. Brewer, J. Brewerton, S. Biggs, W. H. Turpaz, Y. Telenti, A. Venter, J. C. 2017-05-03 doi:10.1101/133538 Cold Spring Harbor Laboratory Press 2017-05-03 <![CDATA[ MutPred2: inferring the molecular and phenotypic impact of amino acid variants ]]> https://biorxiv.org/content/10.1101/134981v1?rss=1 Pejaver, V. Urresti, J. Lugo-Martinez, J. Pagel, K. A. Lin, G. N. Nam, H.-J. Mort, M. Cooper, D. N. Sebat, J. Iakoucheva, L. M. Mooney, S. D. Radivojac, P. 2017-05-09 doi:10.1101/134981 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells ]]> https://biorxiv.org/content/10.1101/135384v1?rss=1 Chu, W. K. Edge, P. Lee, H. S. Bansal, V. Bafna, V. Huang, X. Zhang, K. 2017-05-08 doi:10.1101/135384 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ Untangling The Gene-Epigenome Networks: Timing Of Epigenetic Regulation Of Gene Expression In Acquired Cetuximab Resistance ]]> https://biorxiv.org/content/10.1101/136564v1?rss=1 Stein-O'Brien, G. Kagohara, L. T. Li, S. Thakar, M. Ranaweera, R. Ozawa, H. Cheng, H. Considine, M. Favorov, A. Danilova, L. Califano, J. Izumchenko, E. Gaykalova, D. A. Chung, C. H. Fertig, E. J. 2017-05-10 doi:10.1101/136564 Cold Spring Harbor Laboratory Press 2017-05-10 <![CDATA[ Gaussian Curvature Directs The Distribution Of Spontaneous Curvature On Bilayer Membrane Necks ]]> https://biorxiv.org/content/10.1101/137091v1?rss=1 Chabanon, M. Rangamani, P. 2017-05-12 doi:10.1101/137091 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness ]]> https://biorxiv.org/content/10.1101/139121v1?rss=1 Nogales, J. Gudmundsson, S. Duque, E. Ramos, J. L. Palsson, B. O. 2017-05-19 doi:10.1101/139121 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ The Human Cytoplasmic Dynein Interactome Reveals Novel Activators Of Motility ]]> https://biorxiv.org/content/10.1101/143743v1?rss=1 Redwine, W. B. DeSantis, M. E. Hollyer, I. Htet, Z. M. Tran, P. T. Swanson, S. K. Florens, L. Washburn, M. P. Reck-Peterson, S. L. 2017-05-30 doi:10.1101/143743 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Genetics of the Research Domain Criteria (RDoC): genome-wide association study of delay discounting ]]> https://biorxiv.org/content/10.1101/146936v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - The 23andMe Research Team, Pandit, A. Schmidt, E. Forster, J. Abecasis, G. R. Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-07 doi:10.1101/146936 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Genome-wide association study of Alcohol Use Disorder Identification Test (AUDIT) scores in 20,328 research participants of European ancestry ]]> https://biorxiv.org/content/10.1101/147397v1?rss=1 Sanchez-Roige, S. Fontanillas, P. Elson, S. L. - the 23andMe Research Team, Gray, J. C. de Wit, H. Davis, L. K. MacKillop, J. Palmer, A. A. 2017-06-15 doi:10.1101/147397 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals ]]> https://biorxiv.org/content/10.1101/149781v1?rss=1 Getz, M. Swanson, L. Sahoo, D. Ghosh, P. Rangamani, P. 2017-06-13 doi:10.1101/149781 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ The role of traction in membrane curvature generation ]]> https://biorxiv.org/content/10.1101/157313v1?rss=1 Alimohamadi, H. Vasan, R. Hassinger, J. E. Stachowiak, J. Rangamani, P. 2017-06-29 doi:10.1101/157313 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ Single nucleus analysis of the chromatin landscape in mouse forebrain development ]]> https://biorxiv.org/content/10.1101/159137v1?rss=1 Preissl, S. Fang, R. Zhao, Y. Raviram, R. Zhang, Y. Sos, B. C. Huang, H. Gorkin, D. U. Afzal, V. Dickel, D. E. Kuan, S. Visel, A. Pennacchio, L. A. Zhang, K. Ren, B. 2017-07-04 doi:10.1101/159137 Cold Spring Harbor Laboratory Press 2017-07-04 <![CDATA[ Common Piezo1 allele in African populations causes xerocytosis and attenuates Plasmodium infection ]]> https://biorxiv.org/content/10.1101/159830v1?rss=1 Ma, S. Cahalan, S. Lohia, R. LaMonte, G. Zeng, W. Murthy, S. Paytas, E. Grubaugh, N. D. Gamini, R. Berry, L. Lukacs, V. Whitwam, T. Loud, M. Su, A. I. Andersen, K. G. Winzeler, E. A. Honore, E. Wengelnik, K. Patapoutian, A. 2017-07-06 doi:10.1101/159830 Cold Spring Harbor Laboratory Press 2017-07-06 <![CDATA[ Rapid and scalable preparation of bacterial lysates for cell-free gene expression ]]> https://biorxiv.org/content/10.1101/162768v1?rss=1 Didovyk, A. Tonooka, T. Tsimring, L. Hasty, J. 2017-07-12 doi:10.1101/162768 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Defining the synaptic mechanisms that tune CA3-CA1 reactivation during sharp-wave ripples. ]]> https://biorxiv.org/content/10.1101/164699v1?rss=1 Malerba, P. Jones, M. W. Bazhenov, M. 2017-07-18 doi:10.1101/164699 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus ]]> https://biorxiv.org/content/10.1101/166744v1?rss=1 He, Y. Hariharan, M. Gorkin, D. U. Dickel, D. E. Luo, C. Castanon, R. G. Nery, J. R. Lee, A. Y. Williams, B. A. Trout, D. Amrhein, H. Fang, R. Chen, H. Li, B. Visel, A. Pennacchio, L. Ren, B. Ecker, J. 2017-07-21 doi:10.1101/166744 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Systems-level identification of transcription factors critical for mouse embryonic development ]]> https://biorxiv.org/content/10.1101/167197v1?rss=1 Zhang, K. Wang, M. Zhao, Y. Wang, W. 2017-07-21 doi:10.1101/167197 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Genomewide association study identifies 30 loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/173062v1?rss=1 Stahl, E. Forstner, A. McQuillin, A. Ripke, S. Ophoff, R. Scott, L. Cichon, S. Andreassen, O. A. Sklar, P. Kelsoe, J. Breen, G. 2017-08-07 doi:10.1101/173062 Cold Spring Harbor Laboratory Press 2017-08-07 <![CDATA[ Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide ]]> https://biorxiv.org/content/10.1101/173831v1?rss=1 Satizabal, C. L. Adams, H. H. H. Hibar, D. P. White, C. C. Stein, J. L. Scholz, M. Sargurupremraj, M. Jahanshad, N. Smith, A. V. Bis, J. C. Jian, X. Luciano, M. Hofer, E. Teumer, A. van der Lee, S. J. Yang, J. Yanek, L. R. Lee, T. V. Li, S. Hu, Y. Koh, J. Y. Eicher, J. D. Desrivieres, S. Arias-Vasquez, A. Chauhan, G. Athanasiu, L. Renteria, M. E. Kim, S. Hohn, D. Armstrong, N. J. Chen, Q. Holmes, A. J. den Braber, A. Kloszewska, I. Andersson, M. Espeseth, T. Grimm, O. Abramovic, L. Alhusaini, S. Milaneschi, Y. Papmeyer, M. Axelsson, T. Ehrlich, S. Roi 2017-08-28 doi:10.1101/173831 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms ]]> https://biorxiv.org/content/10.1101/176024v1?rss=1 Rastogi, A. Maheswari, U. Dorrell, R. G. Maumus, F. Rocha Jimenez Vieira, F. Kustka, A. McCarthy, J. Allen, A. E. Kersey, P. Bowler, C. Tirichine, L. 2017-08-14 doi:10.1101/176024 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Ligand-regulated entry into the HRD ERAD pathway: The dark side of allostery ]]> https://biorxiv.org/content/10.1101/177311v1?rss=1 Wangeline, M. A. Hampton, R. Y. 2017-08-18 doi:10.1101/177311 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A Large-Scale Binding and Functional Map of Human RNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/179648v1?rss=1 Van Nostrand, E. L. Freese, P. Pratt, G. A. Wang, X. Wei, X. Blue, S. M. Dominguez, D. Cody, N. A. L. Olson, S. Sundararaman, B. Xiao, R. Zhan, L. Bazile, C. Benoit Bouvrette, L. P. Chen, J. Duff, M. O. Garcia, K. Gelboin-Burkhart, C. Hochman, A. Lambert, N. J. Li, H. Nguyen, T. B. Palden, T. Rabano, I. Sathe, S. Stanton, R. Louie, A. L. Aigner, S. Bergalet, J. Zhou, B. Su, A. Wang, R. Yee, B. A. Fu, X.-D. Lecuyer, E. Burge, C. B. Graveley, B. Yeo, G. W. 2017-08-23 doi:10.1101/179648 Cold Spring Harbor Laboratory Press 2017-08-23 <![CDATA[ Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility ]]> https://biorxiv.org/content/10.1101/182576v1?rss=1 Grotjahn, D. A. Chowdhury, S. Xu, Y. McKenney, R. J. Schroer, T. Lander, G. 2017-08-31 doi:10.1101/182576 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor ]]> https://biorxiv.org/content/10.1101/182964v1?rss=1 Doshi, R. McGrath, A. P. Pineros, M. A. Szewczyk, P. Garza, D. M. Kochian, L. V. Chang, G. 2017-08-31 doi:10.1101/182964 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ A neural decoder for learned vocal behavior ]]> https://biorxiv.org/content/10.1101/193987v1?rss=1 Arneodo, E. Chen, S. Gilja, V. Gentner, T. Q. 2017-09-26 doi:10.1101/193987 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ A distributed algorithm to maintain and repair the trail networks of arboreal ants ]]> https://biorxiv.org/content/10.1101/194480v1?rss=1 Chandrasekhar, A. Gordon, D. M. Navlakha, S. 2017-09-27 doi:10.1101/194480 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Thalamocortical and Intracortical Laminar Connectivity Determines Sleep Spindle Properties ]]> https://biorxiv.org/content/10.1101/195552v1?rss=1 Krishnan, G. P. Rosen, B. Q. Chen, J.-Y. Muller, L. Sejnowski, T. J. Cash, S. S. Halgren, E. Bazhenov, M. 2017-09-28 doi:10.1101/195552 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Coupling of autonomic and central events during sleep boosts declarative memory consolidation ]]> https://biorxiv.org/content/10.1101/195586v1?rss=1 Naji, M. Krishnan, G. McDevitt, E. A. Bazhenov, M. Mednick, S. C. 2017-09-28 doi:10.1101/195586 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Dissociable signatures of visual salience and behavioral relevance across attentional priority maps in human cortex ]]> https://biorxiv.org/content/10.1101/196642v1?rss=1 Sprague, T. Itthipuripat, S. Vo, V. Serences, J. T. 2017-10-02 doi:10.1101/196642 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Cell surface vimentin is involved in matrix stiffness-dependent infection of endothelial cells by Listeria monocytogenes ]]> https://biorxiv.org/content/10.1101/198739v1?rss=1 Bastounis, E. E. Yeh, Y.-T. Theriot, J. A. 2017-10-05 doi:10.1101/198739 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Computational model of brainstem circuit for state dependent control of hypoglossal motoneurons ]]> https://biorxiv.org/content/10.1101/199117v1?rss=1 Naji, M. Komarov, M. Krishnan, G. Malhotra, A. Powell, F. Rukhadze, I. Fenik, V. Bazhenov, M. 2017-10-05 doi:10.1101/199117 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Is N-Hacking Ever OK? 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Subramanian, S. Vo, J. Wang, F. Wartchow, C. Uehara, T. 2019-12-15 doi:10.1101/2019.12.14.850305 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Visualizing 'omic feature rankings and log-ratios using Qurro ]]> https://biorxiv.org/content/10.1101/2019.12.17.880047v1?rss=1 Fedarko, M. W. Martino, C. Morton, J. T. Gonzalez, A. Rahman, G. Marotz, C. A. Minich, J. J. Allen, E. E. Knight, R. 2019-12-18 doi:10.1101/2019.12.17.880047 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Implications of TP53 Allelic State for Genome Stability, Clinical Presentation and Outcomes in Myelodysplastic Syndromes ]]> https://biorxiv.org/content/10.1101/2019.12.19.868844v1?rss=1 Bernard, E. Nannya, Y. Hasserjian, R. P. Devlin, S. M. Tuechler, H. Medina-Martinez, J. S. Yoshizato, T. Shiozawa, Y. Saiki, R. Malcovati, L. Levine, M. F. Arango, J. E. Zhou, Y. Sole, F. Cargo, C. A. Haase, D. Creignou, M. Germing, U. Zhang, Y. Gundem, G. Sarian, A. van de Loosdrecht, A. A. Jadersten, M. Tobiasson, M. Kosmider, O. Follo, M. Y. Thol, F. Pinheiro, R. F. Santini, V. Kotsianidis, I. Boultwood, J. Santos, F. P. S. Schanz, J. Kasahara, S. Ishikawa, T. Tsurumi, H. Takaori-Kondo, A. Kiguchi, T. Polprasert, C. Bennett, J. M. Klimek, V. M. Savon 2019-12-19 doi:10.1101/2019.12.19.868844 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling ]]> https://biorxiv.org/content/10.1101/2019.12.19.882985v1?rss=1 DelGiorno, K. E. Chung, C.-Y. Maurer, H. C. Weiser Novak, S. Giraddi, R. R. Wang, D. Naeem, R. F. Fang, L. Andrade, L. R. Lytle, N. K. Ali, W. H. Tsui, C. Gubbala, V. B. Ridinger-Saison, M. Ohmoto, M. O'Connor, C. Erikson, G. Shokhirev, M. N. Urade, Y. Matsumoto, I. Vavinskaya, V. Singh, P. K. Manor, U. Olive, K. P. Wahl, G. 2019-12-20 doi:10.1101/2019.12.19.882985 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA Epilepsy study ]]> https://biorxiv.org/content/10.1101/2019.12.19.883405v1?rss=1 Hatton, S. N. Huynh, K. H. Bonilha, L. Abela, E. Alhusaini, S. Altmann, A. N. Alvim, M. K. Balachandra, A. R. Bargallo, N. Bartolini, E. Bender, B. Bernasconi, A. Bernasconi, N. Bernhardt, B. Caldairou, B. Caligiuri, M. E. Carr, S. J. Cavalleri, G. L. Cendes, F. Concha, L. Davoodi-Bojd, E. Desmond, P. M. Devinsky, O. Doherty, C. P. Domin, M. Duncan, J. S. Niels, N. K. Foley, S. F. Gambardella, A. Gleichgerrcht, E. Hamandi, K. Ishikawa, A. Keller, S. S. Kochunov, P. V. Kotikalapudi, R. Kreilkamp, B. A. Kwan, P. Labate, A. Langner, S. Lenge, M. Liu, M. Lu 2019-12-20 doi:10.1101/2019.12.19.883405 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Empirical dynamic modeling reveals ecological drivers of dengue dynamics ]]> https://biorxiv.org/content/10.1101/2019.12.20.883363v1?rss=1 Nova, N. Deyle, E. R. Shocket, M. MacDonald, A. J. Childs, M. Rypdal, M. Sugihara, G. Mordecai, E. A. 2019-12-20 doi:10.1101/2019.12.20.883363 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Log Transformation Improves Dating of Phylogenies ]]> https://biorxiv.org/content/10.1101/2019.12.20.885582v1?rss=1 Mai, U. Mirarab, S. 2019-12-21 doi:10.1101/2019.12.20.885582 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Sequestration of Methane by Symbiotic Deep-Sea Annelids: Ancient and Future Implications of Redefining the Seep Influence ]]> https://biorxiv.org/content/10.1101/2019.12.23.887653v1?rss=1 Goffredi, S. K. Tilic, E. Mullin, S. W. Dawson, K. S. Keller, A. Lee, R. Wu, F. Levin, L. A. Rouse, G. W. Cordes, E. Orphan, V. J. 2019-12-27 doi:10.1101/2019.12.23.887653 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ A Novel Chloroplast Super-Complex Consisting of the ATP Synthase and Photosystem I Reaction Center ]]> https://biorxiv.org/content/10.1101/2019.12.25.888495v1?rss=1 Bhaduri, S. Singh, S. K. Cohn, W. Hasan, S. S. Whitelegge, J. P. Cramer, W. A. 2019-12-27 doi:10.1101/2019.12.25.888495 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ The String Decomposition Problem and its Applications to Centromere Assembly ]]> https://biorxiv.org/content/10.1101/2019.12.26.888685v1?rss=1 Dvorkina, T. Bzikadze, A. V. Pevzner, P. A. 2019-12-26 doi:10.1101/2019.12.26.888685 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ A Molecular Pathway for Arterial-Specific Association of Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2019.12.27.889782v1?rss=1 Stratman, A. N. Burns, M. C. Farrelly, O. M. Davis, A. E. Li, W. Pham, V. N. Castranova, D. Yano, J. J. Goddard, L. M. Nguyen, O. Venero Galanternik, M. Bolan, T. J. Kahn, M. L. Mukouyama, Y. Weinstein, B. M. 2019-12-28 doi:10.1101/2019.12.27.889782 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Dual role of auxin in regulating plant defense and bacterial virulence gene expression during Pseudomonas syringae PtoDC3000 pathogenesis. ]]> https://biorxiv.org/content/10.1101/2019.12.29.881581v1?rss=1 Djami-Tchatchou, A. T. Harrison, G. A. Harper, C. P. Wang, R. Prigge, M. J. Estelle, M. Kunkel, B. N. 2019-12-30 doi:10.1101/2019.12.29.881581 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Sequence, Structure and Context Preferences of Human RNA Binding Proteins ]]> https://biorxiv.org/content/10.1101/201996v1?rss=1 Dominguez, D. Freese, P. Alexis, M. S. Su, A. Hochman, M. Palden, T. Bazile, C. Lambert, N. J. Van Nostrand, E. L. Pratt, G. A. Yeo, G. W. Graveley, B. Burge, C. B. 2017-10-12 doi:10.1101/201996 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ DNA damage induced during mitosis undergoes DNA repair synthesis ]]> https://biorxiv.org/content/10.1101/2020.01.03.893784v1?rss=1 Gomez Godinez, V. Kabbara, S. Cohen, S. Sherman, A. Wu, T. Kong, X. Maravillas-Montero, J. L. Shi, Z. Preece, D. Yokomori, K. Berns, M. 2020-01-03 doi:10.1101/2020.01.03.893784 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ A qualitative difference in decision-making of rats vs. humans explained by quantitative differences in behavioral variability ]]> https://biorxiv.org/content/10.1101/2020.01.05.895268v1?rss=1 Nguyen, Q. N. Reinagel, P. 2020-01-06 doi:10.1101/2020.01.05.895268 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Lipid-specific labeling of enveloped viruses with quantum dots for single-virus tracking ]]> https://biorxiv.org/content/10.1101/2020.01.06.895805v1?rss=1 Zhang, L.-J. Wang, S. Xia, L. Lv, C. Tang, H.-W. Xiao, G. Pang, D.-W. 2020-01-06 doi:10.1101/2020.01.06.895805 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance ]]> https://biorxiv.org/content/10.1101/2020.01.06.896316v1?rss=1 Gaidarenko, O. Mills, D. W. Vernet, M. Hildebrand, M. 2020-01-07 doi:10.1101/2020.01.06.896316 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling ]]> https://biorxiv.org/content/10.1101/2020.01.06.896365v1?rss=1 Johnson, J. R. Crosby, D. C. Hultquist, J. F. Li, D. Marlett, J. Swann, J. Hüttenhain, R. Verschueren, E. Johnson, T. L. Newton, B. W. Shales, M. Beltrao, P. Frankel, A. D. Marson, A. Fregoso, O. I. Young, J. A. Krogan, N. J. 2020-01-07 doi:10.1101/2020.01.06.896365 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Regulation of HDAC2-PDX1 by RNF125 defines pancreatic cancer development ]]> https://biorxiv.org/content/10.1101/2020.01.06.896555v1?rss=1 Hasnis, E. Kim, H. Verma, S. Feng, Y. Almog, R. Matsliah, S. Vavinskaya, V. Alelbaum, R. Ben-Ishay, O. Tuveson, D. Sears, R. Ronai, Z. A. 2020-01-07 doi:10.1101/2020.01.06.896555 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Long-term warming weakens stabilizing effects of biodiversity in aquatic ecosystems ]]> https://biorxiv.org/content/10.1101/2020.01.06.896746v1?rss=1 Chang, C.-W. Ye, H. Miki, T. Deyle, E. R. Souissi, S. Anneville, O. Adrian, R. Chiang, Y.-R. Ichise, S. Kumagai, M. Matsuzaki, S.-i. S. Shiah, F.-K. Wu, J.-T. Hsieh, C.-h. Sugihara, G. 2020-01-07 doi:10.1101/2020.01.06.896746 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication ]]> https://biorxiv.org/content/10.1101/2020.01.07.897082v1?rss=1 Badouin, H. Velt, A. Gindraud, F. Flutre, T. Dumas, V. Vautrin, S. Marande, W. Corbi, J. Sallet, E. Ganofsky, J. Santoni, S. Guyot, D. Ricciardelli, E. Jepsen, K. Kafer, J. Berges, H. Duchene, E. Picard, F. Hugueney, P. Tavares, R. Bacilieri, R. Rustenholz, C. Marais, G. A. 2020-01-08 doi:10.1101/2020.01.07.897082 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Enhanced triacylglycerol (TAG) and protein accumulation in transgenic diatom Thalassiosira pseudonana with altered photosynthetic pigmentation ]]> https://biorxiv.org/content/10.1101/2020.01.07.897850v1?rss=1 Gaidarenko, O. Yee, D. P. Hildebrand, M. 2020-01-08 doi:10.1101/2020.01.07.897850 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ UDP-glucose dehydrogenase Ugd in E. coli is activated by Gmd and RffD, is inhibited by CheY, and regulates swarming ]]> https://biorxiv.org/content/10.1101/2020.01.08.899336v1?rss=1 Rodionova, I. A. Zhang, Z. Aboulwafa, M. Saier, M. H. 2020-01-09 doi:10.1101/2020.01.08.899336 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity ]]> https://biorxiv.org/content/10.1101/2020.01.10.900951v1?rss=1 Ngo, T. Stephens, B. S. Gustavsson, M. Holden, L. G. Abagyan, R. Handel, T. M. Kufareva, I. 2020-01-11 doi:10.1101/2020.01.10.900951 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Transport Phenomena in Fluid Films with Curvature Elasticity ]]> https://biorxiv.org/content/10.1101/2020.01.14.906917v1?rss=1 Mahapatra, A. Saintillan, D. Rangamani, P. 2020-01-15 doi:10.1101/2020.01.14.906917 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods. ]]> https://biorxiv.org/content/10.1101/2020.01.15.908111v1?rss=1 Menke, J. Roelandse, M. Ozyurt, B. I. Martone, M. E. Bandrowski, A. E. 2020-01-18 doi:10.1101/2020.01.15.908111 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ mosaicFlye: Resolving long mosaic repeats using long error-prone reads ]]> https://biorxiv.org/content/10.1101/2020.01.15.908285v1?rss=1 Bankevich, A. Pevzner, P. 2020-01-16 doi:10.1101/2020.01.15.908285 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning ]]> https://biorxiv.org/content/10.1101/2020.01.16.909861v1?rss=1 Gao, C. Welch, J. D. 2020-01-17 doi:10.1101/2020.01.16.909861 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ AAV Ablates Neurogenesis in the Adult Murine Hippocampus ]]> https://biorxiv.org/content/10.1101/2020.01.18.911362v1?rss=1 Johnston, S. T. Parylak, S. L. Kim, S. Mac, N. Lim, C. Gallina, I. Bloyd, C. Newberry, A. Saavedra, C. Novák, O. Goncalves, J. T. Gage, F. H. Shtrahman, M. 2020-01-19 doi:10.1101/2020.01.18.911362 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ The effect of statistical normalisation on network propagation scores ]]> https://biorxiv.org/content/10.1101/2020.01.20.911842v1?rss=1 Picart-Armada, S. Thompson, W. K. Buil, A. Perera-Lluna, A. 2020-01-20 doi:10.1101/2020.01.20.911842 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Functional anatomy of the full length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis ]]> https://biorxiv.org/content/10.1101/2020.01.21.913772v1?rss=1 Stephens, B. S. Ngo, T. Kufareva, I. Handel, T. M. 2020-01-21 doi:10.1101/2020.01.21.913772 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Wnt signaling determines body axis polarity in regenerating Hydra tissue ]]> https://biorxiv.org/content/10.1101/2020.01.22.915702v1?rss=1 Wang, R. Steele, R. Collins, E.-M. 2020-01-23 doi:10.1101/2020.01.22.915702 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Giant magnetoresistive biosensors for real-time quantitative detection of protease activity ]]> https://biorxiv.org/content/10.1101/2020.01.26.917476v1?rss=1 Adem, S. Jain, S. Sveiven, M. Zhou, X. O'Donoghue, A. J. Hall, D. A. 2020-01-27 doi:10.1101/2020.01.26.917476 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Transcriptomic Organization of Human Posttraumatic Stress Disorder ]]> https://biorxiv.org/content/10.1101/2020.01.27.921403v1?rss=1 Girgenti, M. J. Wang, J. Ji, D. Cruz, D. Traumatic Stress Brain Research Study Group, The Million Veteran Program, Stein, M. B. Gelernter, J. Young, K. A. Huber, B. R. Williamson, D. E. Friedman, M. J. Krystal, J. H. Zhao, H.-y. Duman, R. S. 2020-01-28 doi:10.1101/2020.01.27.921403 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway ]]> https://biorxiv.org/content/10.1101/2020.01.28.924217v1?rss=1 Allemann, M. N. Allen, E. E. 2020-01-29 doi:10.1101/2020.01.28.924217 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Early detection of biomarkers for circulating tumor cells in Bone marrow and Peripheral blood in a fast-progressing gastric cancer model. ]]> https://biorxiv.org/content/10.1101/2020.01.29.925727v1?rss=1 Bali, P. Lozano-Pope, I. Pachow, C. Obonyo, M. 2020-01-30 doi:10.1101/2020.01.29.925727 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2020.01.31.929117v1?rss=1 Bamberger, T. C. Pankow, S. Martinez-Bartolome, S. Ma, M. Diedrich, J. K. Rissman, R. A. Yates, J. R. 2020-02-02 doi:10.1101/2020.01.31.929117 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Fast transport of RNA granules by direct interactions with KIF5A/KLC1 motors prevents axon degeneration ]]> https://biorxiv.org/content/10.1101/2020.02.02.931204v1?rss=1 Segal, R. A. Seo, H.-S. Adelmant, G. Walensky, L. Marto, J. A. Dhe-Paganon, S. Fukuda, Y. Pazyra-Murphy, M. F. Tasdemir-Yilmaz, O. E. Li, Y. Rose, L. Yeoh, Z. C. Vangos, N. E. Geffken, E. A. Bird, G. H. 2020-02-03 doi:10.1101/2020.02.02.931204 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Zebrafish Kit ligands cooperate with erythropoietin to promote erythroid cell expansion ]]> https://biorxiv.org/content/10.1101/2020.02.03.931634v1?rss=1 Oltova, J. Svoboda, O. Svatonova, P. Kolar, M. Bartunek, P. 2020-02-03 doi:10.1101/2020.02.03.931634 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Regulation of peroxisome and lipid droplet hitchhiking by PxdA and the DipA phosphatase ]]> https://biorxiv.org/content/10.1101/2020.02.03.932616v1?rss=1 Salogiannis, J. Christensen, J. R. Aguilar-Maldonado, A. Shukla, N. Reck-Peterson, S. L. 2020-02-04 doi:10.1101/2020.02.03.932616 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Twist, Snail, and Sox9 form an allosterically regulated complex, the EMTosome, on a bipartite E-box site. ]]> https://biorxiv.org/content/10.1101/2020.02.03.932962v1?rss=1 McCracken, D. Peng, H. P. Ayyanathan, K. Jiang, Y. L. Welsh, S. Yang, J. Kennedy, E. Rauscher, F. J. Gardini, A. Rauscher, F. J. 2020-02-05 doi:10.1101/2020.02.03.932962 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Microstructural meal pattern analysis reveals that nicotine is a potent anti-anorectic drug despite producing long-term anorexigenic effects ]]> https://biorxiv.org/content/10.1101/2020.02.04.934414v1?rss=1 Shankar, K. Ambroggi, F. George, O. 2020-02-05 doi:10.1101/2020.02.04.934414 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Telomere length heterogeneity in ALT cells is maintained by PML-dependent localization of the BTR complex to telomeres ]]> https://biorxiv.org/content/10.1101/2020.02.07.938753v1?rss=1 Loe, T. K. Li, J. Zhang, Y. Azeroglu, B. Boddy, M. N. Lazzerini Denchi, E. 2020-02-07 doi:10.1101/2020.02.07.938753 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance ]]> https://biorxiv.org/content/10.1101/2020.02.07.938894v1?rss=1 Rapaport, F. Boisson, B. Gregor, A. Beziat, V. Boisson-Dupuis, S. Bustamante, J. Jouanguy, E. Puel, A. Rosain, J. Zhang, Q. Zhang, S.-Y. Gleeson, J. Quintana-Murci, L. Casanova, J.-L. Abel, L. Patin, E. 2020-02-08 doi:10.1101/2020.02.07.938894 Cold Spring Harbor Laboratory Press 2020-02-08 <![CDATA[ Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling ]]> https://biorxiv.org/content/10.1101/2020.02.07.939256v1?rss=1 Amar, M. Pramod, A. B. Herrera, V. M. Yu, N.-K. Qiu, L. R. Zhang, P. Moran-Losada, P. Trujillo, C. A. Ellegood, J. Urresti, J. Chau, K. Diedrich, J. Chen, J. Gutierrez, J. Sebat, J. Ramanathan, D. Lerch, J. P. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-02-12 doi:10.1101/2020.02.07.939256 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Strong inhibitory signaling underlies stable temporal dynamics and working memory in spiking neural networks ]]> https://biorxiv.org/content/10.1101/2020.02.11.944751v1?rss=1 Kim, R. Sejnowski, T. J. 2020-02-12 doi:10.1101/2020.02.11.944751 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Antagonistic roles of NOT1 paralogues in the timing of gene expression in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2020.02.12.945477v1?rss=1 Liu, Y. Rai, R. Lei, Z. Zhang, C. Rocamora, F. Featherstone, M. Bozdech, Z. 2020-02-12 doi:10.1101/2020.02.12.945477 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome ]]> https://biorxiv.org/content/10.1101/2020.02.16.951699v1?rss=1 Lee, J. S. Nair, N. U. Chapman, L. M. Sinha, S. Wang, K. Cha, H. Rubin, E. Berger, R. Lazar, V. Kurzrock, R. Gilbert, M. R. Hannenhalli, S. S. Lee, S.-H. Aldape, K. Ruppin, E. 2020-02-17 doi:10.1101/2020.02.16.951699 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ IRE1? regulates macrophage polarization, PD-L1 expression and tumor survival ]]> https://biorxiv.org/content/10.1101/2020.02.17.952457v1?rss=1 Zanetti, M. Batista, A. T. Rodvold, J. Xian, S. Searles, S. T. Lew, A. Iwawaki, T. Almanza, G. Weller, T. C. Lin, J. Jepsen, K. Carter, H. 2020-02-17 doi:10.1101/2020.02.17.952457 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Acoustogenetic Control of CAR T Cells via Focused Ultrasound ]]> https://biorxiv.org/content/10.1101/2020.02.18.955005v1?rss=1 WU, Y. Liu, Y. Huang, Z. Wang, X. Jin, Z. Li, J. Limsakul, P. Zhu, L. Allen, M. Pan, Y. Bussell, R. Jacobson, A. Liu, T. Chien, S. Wang, Y. 2020-02-19 doi:10.1101/2020.02.18.955005 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Commensal oral Rothia mucilaginosa produces enterobactin - a metal chelating siderophore ]]> https://biorxiv.org/content/10.1101/2020.02.20.956391v1?rss=1 Uranga, C. Arroyo, P. Duggan, B. M. Gerwick, W. H. Edlund, A. 2020-02-20 doi:10.1101/2020.02.20.956391 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ B cells expressing authentic naive human VRC01-class BCRs can be primed and recruited to germinal centers in multiple independent mouse models ]]> https://biorxiv.org/content/10.1101/2020.02.24.963629v1?rss=1 Huang, D. Abbott, R. K. Havenar-Daughton, C. Skog, P. Al-Kolla, R. Groschel, B. Blane, T. Menis, S. Tran, J. T. Thinnes, T. C. Volpi, S. A. Pintea, M. Voss, J. E. Phelps, N. Tingle, R. Rodriguez, A. R. Martin, G. S. Kupryianov, S. Schief, W. R. Nemazee, D. Crotty, S. 2020-02-26 doi:10.1101/2020.02.24.963629 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Deep neural networks identify context-specific determinants of transcription factor binding affinity ]]> https://biorxiv.org/content/10.1101/2020.02.26.965343v1?rss=1 Zheng, A. Lamkin, M. Wu, C. Su, H. Gymrek, M. 2020-02-27 doi:10.1101/2020.02.26.965343 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans ]]> https://biorxiv.org/content/10.1101/2020.02.26.966747v1?rss=1 Wilmanski, T. Diener, C. Rappaport, N. Patwardhan, S. Wiedrick, J. Lapidus, J. Earls, J. C. Zimmer, A. Glusman, G. Robinson, M. Yurkovich, J. T. Kado, D. M. Cauley, J. A. Zmuda, J. Lane, N. E. Magis, A. T. Lovejoy, J. C. Gibbons, S. M. Hood, L. Orwoll, E. S. Price, N. D. 2020-02-28 doi:10.1101/2020.02.26.966747 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ TP53 abnormalities correlate with immune infiltration and are associated with response to flotetuzumab, an investigational immunotherapy, in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2020.02.28.961391v1?rss=1 Lai, C. Vadakekolathu, J. Reeder, S. Church, S. E. Hood, T. Aldoss, I. Godwin, J. Wieduwilt, M. J. Arellano, M. Muth, J. Ravandi, F. Sweet, K. Altmann, H. Foulds, G. A. Stolzel, F. Middeke, J. M. Ciciarello, M. Curti, A. Valk, P. J. M. Lowenberg, B. Bornhauser, M. DiPersio, J. F. Davidson-Moncada, J. K. Rutella, S. 2020-02-28 doi:10.1101/2020.02.28.961391 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation ]]> https://biorxiv.org/content/10.1101/2020.03.01.955443v1?rss=1 Arneson, A. Felsheim, B. Chien, J. Ernst, J. 2020-03-02 doi:10.1101/2020.03.01.955443 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Molecular determinants and heterogeneity of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2020.03.02.973578v1?rss=1 Kurd, N. He, Z. Milner, J. Omilusik, K. Louis, T. Tsai, M. Widjaja, C. Kanbar, J. Olvera, J. Tysl, T. Quezada, L. Boland, B. Huang, W. Murre, C. Goldrath, A. Yeo, G. Chang, J. 2020-03-04 doi:10.1101/2020.03.02.973578 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition ]]> https://biorxiv.org/content/10.1101/2020.03.03.968750v1?rss=1 Stopfer, L. E. Mesfin, J. M. Joughin, B. A. Lauffenburger, D. A. White, F. 2020-03-04 doi:10.1101/2020.03.03.968750 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ The contribution of de novo tandem repeat mutations to autism spectrum disorders ]]> https://biorxiv.org/content/10.1101/2020.03.04.974170v1?rss=1 Mitra, I. Mousavi, N. Ma, N. Lamkin, M. Yanicky, R. Shleizer-Burko, S. Gymrek, M. 2020-03-05 doi:10.1101/2020.03.04.974170 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Genetic elucidation of complex biochemical traits mediating maize innate immunity ]]> https://biorxiv.org/content/10.1101/2020.03.04.977355v1?rss=1 Ding, Y. Weckwerth, P. R. Poretsky, E. Murphy, K. M. Sims, J. Saldivar, E. Christensen, S. A. Char, S. N. Yang, B. Tong, A.-d. Shen, Z. Kremling, K. Buckler, E. S. Kono, T. J. Y. Nelson, D. R. Bohlmann, J. Bakker, M. G. Vaughan, M. M. Khalil, A. S. Betsiashvili, M. Briggs, S. Zerbe, P. Schmelz, E. A. Huffaker, A. 2020-03-05 doi:10.1101/2020.03.04.977355 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Functional delineation of tissue-resident CD8 T cell heterogeneity during infection and cancer ]]> https://biorxiv.org/content/10.1101/2020.03.05.979146v1?rss=1 Milner, J. J. Toma, C. He, Z. Kurd, N. S. Nguyen, Q. P. McDonald, B. Quezada, L. Widjaja, C. E. Witherden, D. A. Crowl, J. T. Yeo, G. W. Chang, J. T. Omilusik, K. D. Goldrath, A. W. 2020-03-06 doi:10.1101/2020.03.05.979146 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ One-Day Construction Of Multiplex Arrays to Harness Natural CRISPR Systems ]]> https://biorxiv.org/content/10.1101/2020.03.06.981316v1?rss=1 Cooper, R. M. Hasty, J. 2020-03-08 doi:10.1101/2020.03.06.981316 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Evidence for a biological source of widespread, reproducible nighttime oxygen spikes in tropical reef ecosystems has implications for coral health ]]> https://biorxiv.org/content/10.1101/2020.03.08.982645v1?rss=1 Calhoun, S. K. Haas, A. F. Takeshita, Y. Johnson, M. D. Fox, M. D. Kelly, E. L. A. Mueller, B. Vermeij, M. J. A. Kelly, L. W. Nelson, C. E. Price, N. N. Roach, T. N. F. Rohwer, F. Smith, J. E. 2020-03-09 doi:10.1101/2020.03.08.982645 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Combined membrane potential imaging and connectome of behavioral circuits in an annelid worm ]]> https://biorxiv.org/content/10.1101/2020.03.09.984013v1?rss=1 Ashaber, M. Tomina, Y. Kassraian-Fard, P. Bushong, E. A. Kristan, W. B. Ellisman, M. H. Wagenaar, D. A. 2020-03-10 doi:10.1101/2020.03.09.984013 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ ZNF423 orthologs are highly constrained in vertebrates but show domain-level plasticity across invertebrate lineages ]]> https://biorxiv.org/content/10.1101/2020.03.09.984518v1?rss=1 Hamilton, B. A. 2020-03-11 doi:10.1101/2020.03.09.984518 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Gamma activity accelerates during prefrontal development ]]> https://biorxiv.org/content/10.1101/2020.03.10.986281v1?rss=1 Bitzenhofer, S. H. Poepplau, J. A. Hanganu-Opatz, I. L. 2020-03-11 doi:10.1101/2020.03.10.986281 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research ]]> https://biorxiv.org/content/10.1101/2020.03.12.989400v1?rss=1 Sigmon, J. S. Blanchard, M. Baric, R. S. Bell, T. A. Brennan, J. Brockmann, G. A. Burks, A. W. Calabrese, M. Caron, K. M. Cheney, R. E. Ciavatta, D. Conlon, F. Darr, D. B. Faber, J. Franklin, C. Gershon, T. R. Gralinski, L. E. Gu, B. Gaines, C. H. Hagan, R. S. Heimsath, E. G. Heise, M. T. Hock, P. Ideraabdullah, F. Jennette, J. C. Kafri, T. Kashfeen, A. Kelada, S. N. P. Kulis, M. Kumar, V. Linnertz, C. L. Livraghi-Butrico, A. Lloyd, K. Loeser, R. Lutz, C. M. Lynch, R. M. Magnuson, T. Matsushima, G. K. McMullan, R. Miller, D. Mohlke, K. L. Moy, S. S. Mu 2020-03-14 doi:10.1101/2020.03.12.989400 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Maturational trajectories of white matter microstructure underlying the right presupplementary motor area reflect individual improvements in motor response cancellation in children and adolescents ]]> https://biorxiv.org/content/10.1101/2020.03.13.990507v1?rss=1 Madsen, K. S. Johansen, L. B. Thompson, W. K. Siebner, H. R. Jernigan, T. L. Baare, W. F. 2020-03-15 doi:10.1101/2020.03.13.990507 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Distinctive Gene and Protein Characteristics of Extremely Piezophilic Colwellia ]]> https://biorxiv.org/content/10.1101/2020.03.15.992594v1?rss=1 Peoples, L. M. Kyaw, T. S. Ugalde, J. U. Mullane, K. K. Chastain, R. A. Yayanos, A. A. Kusube, M. Methe, B. A. Bartlett, D. H. 2020-03-15 doi:10.1101/2020.03.15.992594 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Importance of polymorphic SNPs, short tandem repeats and structural variants for differential gene expression among inbred C57BL/6 and C57BL/10 substrains ]]> https://biorxiv.org/content/10.1101/2020.03.16.993683v1?rss=1 Mortazavi, M. Ren, Y. Saini, S. Antaki, D. Pierre, C. S. Williams, A. Sebat, J. Gymrek, M. Palmer, A. A. 2020-03-18 doi:10.1101/2020.03.16.993683 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ TRTools: a toolkit for genome-wide analysis of tandem repeats ]]> https://biorxiv.org/content/10.1101/2020.03.17.996033v1?rss=1 Mousavi, N. Margoliash, J. Pusarla, N. Saini, S. Yanicky, R. Gymrek, M. 2020-03-18 doi:10.1101/2020.03.17.996033 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners ]]> https://biorxiv.org/content/10.1101/2020.03.19.999193v1?rss=1 Pierce, E. C. Morin, M. Little, J. C. Liu, R. B. Tannous, J. Keller, N. P. Wolfe, B. E. Sanchez, L. M. Dutton, R. J. 2020-03-20 doi:10.1101/2020.03.19.999193 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth ]]> https://biorxiv.org/content/10.1101/2020.03.23.003236v1?rss=1 Lloyd, C. J. Monk, J. Ebrahim, A. Yang, L. Palsson, B. 2020-03-23 doi:10.1101/2020.03.23.003236 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning ]]> https://biorxiv.org/content/10.1101/2020.03.25.008664v1?rss=1 Gur, D. Bain, E. J. Johnson, K. Aman, A. J. Pasoili, A. Flynn, J. D. Allen, M. C. Deheyn, D. D. Lee, J. C. Lippincott-Schwartz, J. Parichy, D. M. 2020-03-25 doi:10.1101/2020.03.25.008664 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli ]]> https://biorxiv.org/content/10.1101/2020.03.28.985986v1?rss=1 Yu, H. Lu, S. Gasior, K. Singh, D. Tapia, O. Vazquez-Sanchez, S. Toprani, D. Beccari, M. Yates, J. R. Da Cruz, S. Newby, J. Larfaga, M. Gladfelter, A. Villa, E. Cleveland, D. W. 2020-03-29 doi:10.1101/2020.03.28.985986 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into an N-prenyltransferase ]]> https://biorxiv.org/content/10.1101/2020.03.31.014811v1?rss=1 Chekan, J. R. McKinnie, S. M. K. Noel, J. P. Moore, B. S. 2020-04-01 doi:10.1101/2020.03.31.014811 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ A common analgesic enhances the anti-tumour activity of 5-aza-2'-deoxycytidine through induction of oxidative stress ]]> https://biorxiv.org/content/10.1101/2020.03.31.017947v1?rss=1 Gleneadie, H. J. Baker, A. H. Batis, N. Bryant, J. Jiang, Y. Clokie, S. J. Mehanna, H. Garcia, P. Gendoo, D. M. Roberts, S. Molinolo, A. Gutkind, S. Scheven, B. A. Cooper, P. R. Khanim, F. Wiench, M. 2020-04-01 doi:10.1101/2020.03.31.017947 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Bedscales: A non-contact adherence-independent multi-person sensor for longitudinal physiologic monitoring in the home bed ]]> https://biorxiv.org/content/10.1101/2020.03.31.018523v1?rss=1 Harrington, N. Wei, Z. Hernandez-Pacheco, B. Biu, Q. DeYoung, P. N. Duwaik, B. Desai, A. S. Bhatt, D. L. Owens, R. L. Coleman, T. P. King, K. R. 2020-04-01 doi:10.1101/2020.03.31.018523 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated ]]> https://biorxiv.org/content/10.1101/2020.04.02.021535v1?rss=1 30-bp decrease using CRISPR/Cas9 mutagenesis. These findings provide implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation. ]]> Shen, Z. Tao, J. Fonseca, G. J. Glass, C. K. 2020-04-03 doi:10.1101/2020.04.02.021535 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ ZNF423 patient variants, truncations, and in-frame deletions in mice define an allele-dependent range of midline brain abnormalities ]]> https://biorxiv.org/content/10.1101/2020.04.04.024562v1?rss=1 Deshpande, O. Lara, R. Z. Zhang, O. R. Concepcion, D. Hamilton, B. A. 2020-04-05 doi:10.1101/2020.04.04.024562 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Therapeutic Reversal of Chemically Induced Parkinson Disease by Converting Astrocytes into Nigral Neurons ]]> https://biorxiv.org/content/10.1101/2020.04.06.028084v1?rss=1 Fu, X.-D. 2020-04-07 doi:10.1101/2020.04.06.028084 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila ]]> https://biorxiv.org/content/10.1101/2020.04.08.032177v1?rss=1 Hinzke, T. Kleiner, M. Meister, M. Schlueter, R. Hentschker, C. Pane-Farre, J. Hildebrandt, P. Felbeck, H. Sievert, S. M. Bonn, F. Voelker, U. Becher, D. Schweder, T. Markert, S. 2020-04-09 doi:10.1101/2020.04.08.032177 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2020.04.12.037580v1?rss=1 Wang, A. Chiou, J. A. Poirion, O. B. Buchanan, J. Valdez, M. J. Verheyden, J. M. Hou, X. Guo, M. Newsome, J. M. Kudtarkar, P. Faddah, D. A. Zhang, K. Young, R. E. Barr, J. Misra, R. Huyck, H. Rogers, L. Poole, C. Whitsett, J. A. Pryhuber, G. Xu, Y. Gaulton, K. J. Preissl, S. Sun, X. NHLBI LungMap Consortium, 2020-04-14 doi:10.1101/2020.04.12.037580 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ ISG15 drives immune pathology and respiratory failure during viral infection ]]> https://biorxiv.org/content/10.1101/2020.04.13.039321v1?rss=1 Shaabani, N. Zak, J. Johnson, J. L. Huang, Z. Nguyen, N. Lazar, D. C. Vartabedian, V. F. Honke, N. Prinz, M. Knobeloch, K.-P. Arimoto, K.-i. Zhang, D.-E. Catz, S. D. Teijaro, J. R. 2020-04-14 doi:10.1101/2020.04.13.039321 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry ]]> https://biorxiv.org/content/10.1101/2020.04.14.041459v1?rss=1 Kim, S. Y. Jin, W. Sood, A. Montgomery, D. W. Grant, O. C. Fuster, M. M. Fu, L. Dordick, J. S. Woods, R. J. Zhang, F. Linhardt, R. J. 2020-04-15 doi:10.1101/2020.04.14.041459 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Automated docking refinement and virtual compound screening with absolute binding free energy calculations ]]> https://biorxiv.org/content/10.1101/2020.04.15.043240v1?rss=1 Heinzelmann, G. Gilson, M. K. 2020-04-16 doi:10.1101/2020.04.15.043240 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization ]]> https://biorxiv.org/content/10.1101/2020.04.16.044255v1?rss=1 Mortensen, M. S. Rasmussen, M. A. Stokholm, J. Brejnrod, A. D. Balle, C. Thorsen, J. Krogfelt, K. A. Bisgaard, H. Sorensen, S. J. 2020-04-17 doi:10.1101/2020.04.16.044255 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Weight Sensitivity of Temporal SNR Metrics in multi-echo fMRI ]]> https://biorxiv.org/content/10.1101/2020.04.20.049460v1?rss=1 Liu, T. Li, B. Chen, C. Fernandez, B. Yang, B. Banerjee, S. 2020-04-23 doi:10.1101/2020.04.20.049460 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Determining the Depth Limit of Bioluminescent Sources in Scattering Media ]]> https://biorxiv.org/content/10.1101/2020.04.21.044982v1?rss=1 Raghuram, A. Ye, F. Adams, J. K. Shaner, N. Robinson, J. Veeraraghavan, A. 2020-04-23 doi:10.1101/2020.04.21.044982 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ G protein-regulated endocytic trafficking of adenylyl cyclase type 9 ]]> https://biorxiv.org/content/10.1101/2020.04.23.057026v1?rss=1 Lazar, A. M. Irannejad, R. Baldwin, T. A. Sundaram, A. B. Gutkind, J. S. Inoue, A. Dessauer, C. W. Von Zastrow, M. 2020-04-25 doi:10.1101/2020.04.23.057026 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Dynamics of Brain Structure and its Genetic Architecture over the Lifespan ]]> https://biorxiv.org/content/10.1101/2020.04.24.031138v1?rss=1 Brouwer, R. M. Klein, M. Grasby, K. L. Schnack, H. G. Jahanshad, N. Teeuw, J. Thomopoulos, S. I. Sprooten, E. Franz, C. E. Gogtay, N. Kremen, W. Panizzon, M. S. Olde Loohuis, L. M. Whelan, C. D. Aghajani, M. Alloza, C. Alnaes, D. Artiges, E. Ayesa-Arriola, R. Barker, G. J. Blok, E. Boen, E. Breukelaar, I. A. Bright, J. K. Buimer, E. E. Bülow, R. Cannon, D. M. Ciufolini, S. Crossley, N. A. Damatac, C. G. Dazzan, P. de Mol, C. L. de Zwarte, S. M. Desrivieres, S. Diaz-Caneja, C. M. Doan, N. T. Dohm, K. Fröhner, J. H. Goltermann, J. Grigis, A. Grotegerd, D 2020-04-27 doi:10.1101/2020.04.24.031138 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Regulatory interactions between Vax1, Pax6, and miR-7 regionalize the lateral Ventricular-Subventricular Zone during post-natal Olfactory Bulb neurogenesis in mice ]]> https://biorxiv.org/content/10.1101/2020.04.24.059428v1?rss=1 Core, N. Erni, A. Mellon, P. L. Hoffmann, H. M. Beclin, C. Cremer, H. 2020-04-25 doi:10.1101/2020.04.24.059428 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ A transcriptional regulatory atlas of coronavirus infection of human cells ]]> https://biorxiv.org/content/10.1101/2020.04.24.059527v1?rss=1 Ochsner, S. A. McKenna, N. 2020-04-25 doi:10.1101/2020.04.24.059527 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Matrix factorization recovers consistent regulatory signals from disparate datasets ]]> https://biorxiv.org/content/10.1101/2020.04.26.061978v1?rss=1 Sastry, A. V. Hu, A. Heckmann, D. Poudel, S. Kavvas, E. Palsson, B. O. 2020-04-27 doi:10.1101/2020.04.26.061978 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Inhibition of the NLRP3 inflammasome prevents ovarian aging ]]> https://biorxiv.org/content/10.1101/2020.04.26.062646v1?rss=1 Navarro-Pando, J. M. Alcocer-Gomez, E. Castejon-Vega, B. Muntane, J. Wang, C. Hoffman, H. M. Sanz, A. Mbalaviele, G. Ryffel, B. Cordero, M. D. 2020-04-28 doi:10.1101/2020.04.26.062646 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Expanding magnetic organelle biogenesis in the domain Bacteria ]]> https://biorxiv.org/content/10.1101/2020.04.27.061960v1?rss=1 Lin, W. Zhang, W. Paterson, G. A. Zhu, Q. Zhao, X. Knight, R. Bazylinski, D. A. Roberts, A. P. Pan, Y. 2020-04-28 doi:10.1101/2020.04.27.061960 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells ]]> https://biorxiv.org/content/10.1101/2020.04.27.065227v1?rss=1 Panwar, B. Schmiedel, B. J. Liang, S. White, B. Rodriquez, E. Kalunian, K. McKnight, A. J. Soloff, R. Seumois, G. Vijayanand, P. Ay, F. 2020-04-29 doi:10.1101/2020.04.27.065227 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.04.28.062679v1?rss=1 View larger version (96K): org.highwire.dtl.DTLVardef@10715caorg.highwire.dtl.DTLVardef@27af76org.highwire.dtl.DTLVardef@17083a6org.highwire.dtl.DTLVardef@1d31f9f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIExtensive lncRNA translation and microprotein production during human pancreas development C_LIO_LIA small-scale loss-of-function screen shows most translated lncRNAs are dispensable C_LIO_LILINC00261 is highly translated and regulates endocrine cell differentiation C_LIO_LIDeleting LINC00261s evolutionary young microproteins reveals no essential roles C_LI ]]> Gaertner, B. van Heesch, S. Schneider-Lunitz, V. Schulz, J. F. Witte, F. Blachut, S. Nguyen, S. Wong, R. Matta, I. Hubner, N. Sander, M. 2020-04-29 doi:10.1101/2020.04.28.062679 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Representative diatom and coccolithophore species exhibit divergent responses throughout simulated upwelling cycles ]]> https://biorxiv.org/content/10.1101/2020.04.30.071480v1?rss=1 Lampe, R. H. Hernandez, G. Lin, Y. Y. Marchetti, A. 2020-05-01 doi:10.1101/2020.04.30.071480 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ An integrated genomics approach towards deciphering human genome codes shaping HIV-1 proviral transcription and fate ]]> https://biorxiv.org/content/10.1101/2020.05.01.072231v1?rss=1 Ruess, H. Lee, J. Guzman, C. Malladi, V. D'Orso, I. 2020-05-02 doi:10.1101/2020.05.01.072231 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake. ]]> https://biorxiv.org/content/10.1101/2020.05.03.074617v1?rss=1 Rodionova, I. A. Rodionov, D. A. Gao, Y. Yoo, R. Sastry, A. Saier, M. Palsson, B. O. 2020-05-03 doi:10.1101/2020.05.03.074617 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) ]]> https://biorxiv.org/content/10.1101/2020.05.03.075499v1?rss=1 Robinson, J. T. Thorvaldsdottir, H. Turner, D. Mesirov, J. P. 2020-05-05 doi:10.1101/2020.05.03.075499 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability ]]> https://biorxiv.org/content/10.1101/2020.05.04.074443v1?rss=1 Parisian, A. D. Koga, T. Miki, S. Johann, P. D. Kool, M. Crawford, J. R. Furnari, F. 2020-05-05 doi:10.1101/2020.05.04.074443 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Interhemispheric callosal projections enforce response fidelity and frequency tuning in auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.05.05.079012v1?rss=1 Slater, B. J. Isaacson, J. S. 2020-05-06 doi:10.1101/2020.05.05.079012 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Nucleoid openness profiling links bacterial genome structure to phenotype ]]> https://biorxiv.org/content/10.1101/2020.05.07.082990v1?rss=1 Al-Bassam, M. M. Moyne, O. Chapin, N. Zengler, K. 2020-05-07 doi:10.1101/2020.05.07.082990 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Interactive MS/MS Visualization with the Metabolomics Spectrum Resolver Web Service ]]> https://biorxiv.org/content/10.1101/2020.05.09.086066v1?rss=1 Wang, M. Rogers, S. Bittremieux, W. Chen, C. Dorrestein, P. C. Schymanski, E. L. Schulze, T. Neumann, S. Meier, R. 2020-05-10 doi:10.1101/2020.05.09.086066 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Ion Identity Molecular Networking in the GNPS Environment ]]> https://biorxiv.org/content/10.1101/2020.05.11.088948v1?rss=1 Schmid, R. Petras, D. Nothias, L.-F. Wang, M. Aron, A. T. Jagels, A. Tsugawa, H. Rainer, J. Garcia-Aloy, M. Duehrkop, K. Korf, A. Pluskal, T. Kamenik, Z. Jarmusch, A. K. Caraballo-Rodriguez, A. M. Weldon, K. Nothias-Esposito, M. Aksenov, A. A. Bauermeister, A. Albarracin-Orio, A. Grundmann, C. O. Vargas, F. Koester, I. Gauglitz, J. M. Gentry, E. C. Hoevelmann, Y. Kalinina, S. A. Pendergraft, M. A. Panitchpakdi, M. W. Tehan, R. Le Gouellec, A. Aleti, G. Mannochio Russo, H. Arndt, B. Huebner, F. Hayen, H. Zhi, H. Raffatellu, M. Prather, K. A. Aluwihare, L. 2020-05-13 doi:10.1101/2020.05.11.088948 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Strain-dependent modifier genes determine survival in Zfp423 mice ]]> https://biorxiv.org/content/10.1101/2020.05.12.091629v1?rss=1 Alcaraz, W. A. Liu, Z. Valdes, P. Chen, E. Valdovino Gonzalez, A. G. Wade, S. Wong, C. Kim, E. Chen, H.-H. M. Concepcion, D. Hamilton, B. A. 2020-05-13 doi:10.1101/2020.05.12.091629 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Sensitivity to food and cocaine cues are independent traits in a large sample of heterogeneous stock rats. ]]> https://biorxiv.org/content/10.1101/2020.05.13.066944v1?rss=1 King, C. P. Tripi, J. A. Hughson, A. R. Hovarth, A. P. Lamparelii, A. C. Holl, K. L. Chitre, A. S. Polesskaya, O. Richards, J. B. Solberg-Woods, L. C. Palmer, A. A. Robinson, T. E. Flagel, S. B. Meyer, P. J. 2020-05-14 doi:10.1101/2020.05.13.066944 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ I ncreased accuracy of signaling by hyperbolic odorant mixtures in a beneficial insect-plant relationship ]]> https://biorxiv.org/content/10.1101/2020.05.13.093864v1?rss=1 Ghaninia, M. Knauer, A. C. Schiestl, F. Sharpee, T. O. Smith, B. H. 2020-05-14 doi:10.1101/2020.05.13.093864 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Metabolite profiling of experimental cutaneous leishmaniasis lesions demonstrates significant perturbations in tissue phospholipids ]]> https://biorxiv.org/content/10.1101/2020.05.13.094649v1?rss=1 McCall, L.-I. Parab, A. McKerrow, J. Dorrestein, P. C. Thomas, D. Lostracco-Johnson, S. de Siquiera-Neto, J. L. 2020-05-15 doi:10.1101/2020.05.13.094649 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence ]]> https://biorxiv.org/content/10.1101/2020.05.14.096305v1?rss=1 Traver, D. Sahai, P. Pouget, C. Svoboda, O. 2020-05-15 doi:10.1101/2020.05.14.096305 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Mapping Cognitive Brain Functions at Scale ]]> https://biorxiv.org/content/10.1101/2020.05.14.097014v1?rss=1 Balasubramani, P. P. Ojeda, A. Maric, V. Le, H. Grennan, G. Alim, F. Zafar-Khan, M. Diaz-Delgado, J. Silveira, S. Ramanathan, D. Mishra, J. 2020-05-16 doi:10.1101/2020.05.14.097014 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ PI3Kγ inhibition suppresses microglia/TAM accumulation in glioblastoma microenvironment to promote exceptional temozolomide response ]]> https://biorxiv.org/content/10.1101/2020.05.14.097121v1?rss=1 Li, J. Kaneda, M. M. Ma, J. Li, M. Patel, K. Koga, T. Sarver, A. L. Furnari, F. Xu, B. Dhawan, S. Ning, J. Zhu, H. Wu, A. You, G. Jiang, T. Venteichera, A. S. Rich, J. N. Glass, C. K. Varner, J. A. Chen, C. C. 2020-05-16 doi:10.1101/2020.05.14.097121 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2020.05.15.038679v1?rss=1 Aylward, A. Okino, M.-L. Benaglio, P. Chiou, J. Beebe, E. Padilla, J. A. Diep, S. Gaulton, K. J. 2020-05-16 doi:10.1101/2020.05.15.038679 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ A characterization of the electrophysiological, morphological and input domains of vasoactive intestinal peptide (VIP) interneurons in the medial entorhinal cortex (MEC) ]]> https://biorxiv.org/content/10.1101/2020.05.15.097972v1?rss=1 Badrinarayanan, S. Manseau, F. Lim, B. K. Williams, S. Brandon, M. P. 2020-05-16 doi:10.1101/2020.05.15.097972 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes ]]> https://biorxiv.org/content/10.1101/2020.05.17.095000v1?rss=1 Brouwer, S. Barnett, T. C. Ly, D. Kasper, K. J. De Oliveira, D. M. Rivera-Hernandez, T. Cork, A. J. McIntyre, L. Jespersen, M. G. Richter, J. Schulz, B. L. Dougan, G. Nizet, V. Yuen, K.-Y. You, Y. McCormick, J. K. Sanderson-Smith, M. L. Davies, M. R. Walker, M. J. 2020-05-17 doi:10.1101/2020.05.17.095000 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Role of Inflammasome-independent Activation of IL-1β by the Pseudomonas aeruginosa Protease LasB ]]> https://biorxiv.org/content/10.1101/2020.05.18.101303v1?rss=1 Sun, J. LaRock, D. Skowronski, E. Kimmey, J. M. Olson, J. Jiang, Z. O'Donoghue, A. Nizet, V. LaRock, C. 2020-05-19 doi:10.1101/2020.05.18.101303 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Human Hair Graying is Naturally Reversible and Linked to Stress ]]> https://biorxiv.org/content/10.1101/2020.05.18.101964v1?rss=1 Rosenberg, A. Rausser, S. Ren, J. Mosharov, E. Sturm, G. M. Ogden, R. T. Patel, P. Soni, R. K. Lacefield, C. Paus, R. Picard, M. 2020-05-19 doi:10.1101/2020.05.18.101964 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Cell cycle-gated feedback control mediates desensitization to interferon stimulation ]]> https://biorxiv.org/content/10.1101/2020.05.18.103101v1?rss=1 Mudla, A. Jiang, Y. Arimoto, K.-i. Xu, B. Rajesh, A. Ryan, A. P. Wang, W. Daugherty, M. D. Zhang, D.-E. Hao, N. 2020-05-20 doi:10.1101/2020.05.18.103101 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions ]]> https://biorxiv.org/content/10.1101/2020.05.19.079962v1?rss=1 Dillon, N. A. Seif, Y. Tsunemoto, H. Poudel, S. Meehan, M. Szubin, R. Olson, C. Rajput, A. Alarcon, G. Lamsa, A. Vrbanac, A. Sugie, J. Dahesh, S. Monk, J. Dorrestein, P. Knight, R. Feist, A. Pogliano, J. Palsson, B. Nizet, V. 2020-05-20 doi:10.1101/2020.05.19.079962 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment ]]> https://biorxiv.org/content/10.1101/2020.05.19.105270v1?rss=1 Minich, J. J. Power, C. Melanson, M. Knight, R. Webber, C. Rough, K. Bott, N. J. Nowak, B. Allen, E. 2020-05-20 doi:10.1101/2020.05.19.105270 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Development of follicular dendritic cells in lymph nodes depends on retinoic acid mediated signaling ]]> https://biorxiv.org/content/10.1101/2020.05.20.106385v1?rss=1 Koning, J. J. Rajaraman, A. Reijmers, R. M. Konijn, T. Pan, J. Ware, C. F. Butcher, E. C. Mebius, R. E. 2020-05-21 doi:10.1101/2020.05.20.106385 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ On the effectiveness of small, discriminatively pre-trained language representation models for biomedical text mining ]]> https://biorxiv.org/content/10.1101/2020.05.20.107003v1?rss=1 Ozyurt, I. B. 2020-05-23 doi:10.1101/2020.05.20.107003 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ The emergence of SARS-CoV-2 in Europe and the US ]]> https://biorxiv.org/content/10.1101/2020.05.21.109322v1?rss=1 Worobey, M. Pekar, J. Larsen, B. B. Nelson, M. I. Hill, V. Joy, J. B. Rambaut, A. Suchard, M. A. Wertheim, J. O. Lemey, P. 2020-05-23 doi:10.1101/2020.05.21.109322 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Membrane bending by protein phase separation ]]> https://biorxiv.org/content/10.1101/2020.05.21.109751v1?rss=1 Yuan, F. Alimohamadi, H. Bakka, B. Trementozzi, A. N. Fawzi, N. L. Rangamani, P. Stachowiak, J. C. 2020-05-22 doi:10.1101/2020.05.21.109751 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Identification and physiological significance of temporal NFκB signaling codewords deployed by macrophages to classify immune threats ]]> https://biorxiv.org/content/10.1101/2020.05.23.112862v1?rss=1 Taylor, B. Adelaja, A. Liu, Y. Luecke, S. Hoffmann, A. 2020-05-26 doi:10.1101/2020.05.23.112862 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Hidden features of the malaria vectormosquito, Anopheles stephensi ,revealed by a high-quality referencegenome ]]> https://biorxiv.org/content/10.1101/2020.05.24.113019v1?rss=1 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively through male development and adulthood, suggesting an important role throughout male development. ConclusionCollectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate development of genetic control strategies of malaria transmission. ]]> Chakraborty, M. Ramaiah, A. Adolfi, A. Halas, P. Kaduskar, B. Ngo, L. T. Jayaprasad, S. Paul, K. Whadgar, S. Srinivasan, S. Subramani, S. Bier, E. James, A. Emerson, J. J. 2020-05-24 doi:10.1101/2020.05.24.113019 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ The gene cortex controls scale colour identity in Heliconius ]]> https://biorxiv.org/content/10.1101/2020.05.26.116533v1?rss=1 Livraghi, L. Hanly, J. J. Loh, L. S. Ren, A. Warren, I. A. Concha, C. Wright, C. Walker, J. M. Foley, J. Arenas-Castro, H. Brenes, L. R. Martin, A. McMillan, W. O. Jiggins, C. D. 2020-05-29 doi:10.1101/2020.05.26.116533 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ An improved CRISPR/dCas9 interference tool for neuronal gene suppression ]]> https://biorxiv.org/content/10.1101/2020.05.26.116822v1?rss=1 Duke, C. G. Bach, S. V. Revanna, J. S. Sultan, F. A. Southern, N. T. Davis, M. N. Gallus, N. V. N. Bauman, A. J. Phillips, R. A. Day, J. J. 2020-05-27 doi:10.1101/2020.05.26.116822 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Local sensitivity analysis of the 'Membrane shape equation'derived from the Helfrich energy ]]> https://biorxiv.org/content/10.1101/2020.05.26.117275v1?rss=1 Rangamani, P. Behzadan, A. Holst, M. 2020-05-28 doi:10.1101/2020.05.26.117275 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Plasmin cascade mediates thrombolytic events in SARS-CoV-2 infection via complement and platelet-activating systems ]]> https://biorxiv.org/content/10.1101/2020.05.28.120162v1?rss=1 Mukund, K. Mathee, K. Subramaniam, S. 2020-05-29 doi:10.1101/2020.05.28.120162 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Antineoplastic kinase inhibitors: a new class of potent anti-amoebic compounds ]]> https://biorxiv.org/content/10.1101/2020.05.28.120923v1?rss=1 Sauvey, C. Ehrenkaufer, G. Shi, D. Debnath, A. Abagyan, R. 2020-05-28 doi:10.1101/2020.05.28.120923 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Sofosbuvir protects human brain organoids against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.05.30.125856v1?rss=1 Mesci, P. Macia, A. Saleh, A. Martin-Sancho, L. YIN, X. Snethlage, C. Avansini, S. Chanda, S. Muotri, A. 2020-05-31 doi:10.1101/2020.05.30.125856 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.05.31.122085v1?rss=1 Busby, K. N. Fulzele, A. Zhang, D. Bennett, E. J. Devaraj, N. K. 2020-05-31 doi:10.1101/2020.05.31.122085 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Leveraging non-structural data to predict structures of protein-ligand complexes ]]> https://biorxiv.org/content/10.1101/2020.06.01.128181v1?rss=1 Paggi, J. M. Belk, J. A. Hollingsworth, S. A. Villanueva, N. Powers, A. S. Clark, M. J. Chemparathy, A. G. Tynan, J. E. Lau, T. K. Sunahara, R. K. Dror, R. O. 2020-06-02 doi:10.1101/2020.06.01.128181 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Sustained attention and vigilance deficits associated with HIV and a history of methamphetamine dependence ]]> https://biorxiv.org/content/10.1101/2020.06.03.132522v1?rss=1 Pocuca, N. Young, J. W. MacQueen, D. A. Letendre, S. Heaton, R. K. Geyer, M. A. Perry, W. Grant, I. Minassian, A. Translational Methamphetamine AIDS Research Center (TMARC), 2020-06-04 doi:10.1101/2020.06.03.132522 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Neural divergence and convergence for interoceptive and somatosensory attention and detection ]]> https://biorxiv.org/content/10.1101/2020.06.04.134288v1?rss=1 Herman, A. M. Palmer, C. E. Azevedo, R. Tsakiris, M. 2020-06-05 doi:10.1101/2020.06.04.134288 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Multivariate analysis reveals a generalizable human electrophysiological signature of working memory load ]]> https://biorxiv.org/content/10.1101/2020.06.04.135053v1?rss=1 250,000 trials), we demonstrate that multivariate analysis of EEG voltage topography provides a sensitive index of the number of items stored in WM that generalizes to novel human observers. Moreover, multivariate load detection ("mvLoad") can provide robust information at the single-trial level, exceeding the sensitivity of extant univariate approaches. We show that this method tracks WM load in a manner that is (1) independent of the spatial position of the memoranda, (2) precise enough to differentiate item-by-item increments in the number of stored items, (3) generalizable across distinct tasks and stimulus displays and (4) correlated with individual differences in WM behavior. Thus, this approach provides a powerful complement to univariate analytic approaches, enabling temporally-resolved tracking of online memory storage in humans. ]]> Adam, K. C. S. Vogel, E. K. Awh, E. 2020-06-05 doi:10.1101/2020.06.04.135053 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box ]]> https://biorxiv.org/content/10.1101/2020.06.05.133405v1?rss=1 Reader, J. van der Watt, M. E. Taylor, D. Le Manach, C. Mittal, N. Ottilie, S. Theron, A. Moyo, P. Erlank, E. Nardini, L. Venter, N. Lauterbach, S. Bezuidenhout, B. Horatscheck, A. van Heerden, A. Boyle, G. A. Calvo, D. Mancama, D. Coetzer, T. L. Winzeler, E. A. Duffy, J. Koekemoer, L. L. Basarab, G. Chibale, K. Birkholtz, L.-M. 2020-06-05 doi:10.1101/2020.06.05.133405 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways ]]> https://biorxiv.org/content/10.1101/2020.06.08.140079v1?rss=1 Serbyn, N. Bagdiul, I. Michel, A. H. Suhandynata, R. T. Zhou, H. Kornmann, B. Stutz, F. 2020-06-09 doi:10.1101/2020.06.08.140079 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ DYNC1LI2 regulates localization of the chaperone-mediated autophagy-receptor LAMP2A and improves cellular homeostasis in cystinosis ]]> https://biorxiv.org/content/10.1101/2020.06.09.142349v1?rss=1 Rahman, F. Johnson, J. L. Zhang, J. He, J. Cherqui, S. Catz, S. D. 2020-06-10 doi:10.1101/2020.06.09.142349 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Both HIV Infection and Conditional Tat Expression Decrease Prepulse Inhibition with Further Impairment by Methamphetamine History in Humans ]]> https://biorxiv.org/content/10.1101/2020.06.11.130666v1?rss=1 Walter, T. Young, J. Milienne-Petiot, M. Deben, D. S. Heaton, R. Letendre, S. Grelotti, D. Perry, W. Grant, I. Minassian, A. 2020-06-12 doi:10.1101/2020.06.11.130666 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein ]]> https://biorxiv.org/content/10.1101/2020.06.11.146522v1?rss=1 Casalino, L. Gaieb, Z. Dommer, A. C. Harbison, A. M. Fogarty, C. A. Barros, E. P. Taylor, B. C. Fadda, E. Amaro, R. E. 2020-06-11 doi:10.1101/2020.06.11.146522 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Hybrid analysis reveals how DNA sequence governs genomic location and DNA contacts of bacterial chromatin H-NS filaments ]]> https://biorxiv.org/content/10.1101/2020.06.11.146589v1?rss=1 Shen, B. A. Hustmyer, C. M. Roston, D. Wolfe, M. B. Jessen, E. D. Landick, R. 2020-06-12 doi:10.1101/2020.06.11.146589 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Co-Occurrence of Enzyme Domains Guides the Discovery of an Oxazolone Synthetase ]]> https://biorxiv.org/content/10.1101/2020.06.11.147165v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@20cb16org.highwire.dtl.DTLVardef@f54df0org.highwire.dtl.DTLVardef@cffa51org.highwire.dtl.DTLVardef@3b085d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> de Rond, T. Asay, J. E. Moore, B. S. 2020-06-12 doi:10.1101/2020.06.11.147165 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Learning the synaptic and intrinsic membrane dynamics underlying working memory in spiking neural network models ]]> https://biorxiv.org/content/10.1101/2020.06.11.147405v1?rss=1 Li, Y. Kim, R. Sejnowski, T. J. 2020-06-12 doi:10.1101/2020.06.11.147405 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ DNA glycosylase NEIL2 prevents Fusobacterium-mediated inflammation and DNA damage in colonic epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.06.11.147454v1?rss=1 Sayed, I. Chakraborty, A. Ali, A. Sharma, A. Sahan, A. Sahoo, D. Ghosh, P. Hazra, T. Das, S. 2020-06-12 doi:10.1101/2020.06.11.147454 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ The genetic organization of subcortical volumetric change is stable throughout the lifespan ]]> https://biorxiv.org/content/10.1101/2020.06.12.143834v1?rss=1 Fjell, A. Grydeland, H. Wang, Y. Amlien, I. K. Bartres-Faz, D. Brandmaier, A. Duzel, S. Elman, J. Franz, C. Haberg, A. Kietzmann, T. C. Kievit, R. A. Kremen, W. Krogsrud, S. K. Kuhn, S. A. Lindenberger, U. Macia, D. Mowinckel, A. M. Nyberg, L. Panizzon, M. Sole-Padulles, C. Sorensen, O. Westerhausen, R. Walhovd, K. B. 2020-06-12 doi:10.1101/2020.06.12.143834 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ PP2A:B56 Regulates Meiotic Chromosome Segregation in C. elegans Oocytes ]]> https://biorxiv.org/content/10.1101/2020.06.12.148254v1?rss=1 Bel Borja, L. Soubigou, F. Taylor, S. J. P. Fraguas Bringas, C. Budrewicz, J. Lara-Gonzalez, P. Sorensen-Turpin, C. G. Bembenek, J. N. Cheerambathur, D. K. Pelisch, F. 2020-06-13 doi:10.1101/2020.06.12.148254 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE ]]> https://biorxiv.org/content/10.1101/2020.06.15.134403v1?rss=1 Bickler, S. W. Cauvi, D. M. Fisch, K. M. Prieto, J. M. Gaidry, A. D. Thangarajah, H. Lazar, D. Ignacio, R. Gerstmann, D. R. Ryan, A. F. Bickler, P. E. De Maio, A. 2020-06-16 doi:10.1101/2020.06.15.134403 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Resident macrophages establish and control lipid stores via PDGFcc production ]]> https://biorxiv.org/content/10.1101/2020.06.15.152397v1?rss=1 Cox, N. Crozet, L. Holtman, I. R. Loyher, P.-L. Lazarov, T. Mass, E. Stanley, R. Glass, C. K. Geissmann, F. 2020-06-15 doi:10.1101/2020.06.15.152397 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals ]]> https://biorxiv.org/content/10.1101/2020.06.15.152546v1?rss=1 Celinskis, D. Friedman, N. Koksharov, M. Murphy, J. Gomez-Ramirez, M. Borton, D. Shaner, N. Hochgeschwender, U. Lipscombe, D. Moore, C. 2020-06-16 doi:10.1101/2020.06.15.152546 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Photoperiod-Induced Neurotransmitter Switching in the Circadian Pacemaker Regulates Hypothalamic Dopamine Expression ]]> https://biorxiv.org/content/10.1101/2020.06.16.155440v1?rss=1 Porcu, A. Booreddy, S. Welsh, D. K. Dulcis, D. 2020-06-17 doi:10.1101/2020.06.16.155440 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Differential covariance: A new method to estimate functional connectivity in fMRI ]]> https://biorxiv.org/content/10.1101/2020.06.16.155630v1?rss=1 lin, w. Chen, Y. Bukhari, Q. Krishnan, G. Bazhenov, M. Sejnowski, T. J. 2020-06-17 doi:10.1101/2020.06.16.155630 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Molecular mode of action of an Acyl Protein thioesterase ]]> https://biorxiv.org/content/10.1101/2020.06.18.157545v1?rss=1 Abrami, L. Audagnotto, M. Ho, S. Marcaida, M. J. Mesquita, F. Anward, M. Sandoz, P. A. Fonti, G. Pojer, F. Dal Peraro, M. van der Goot, F. G. 2020-06-19 doi:10.1101/2020.06.18.157545 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Mapping cell structure across scales by fusing protein images and interactions ]]> https://biorxiv.org/content/10.1101/2020.06.21.163709v1?rss=1 Qin, Y. Winsnes, C. F. Huttlin, E. L. Zheng, F. Ouyang, W. Park, J. Pitea, A. Kreisberg, J. F. Gygi, S. P. Harper, J. W. Ma, J. Lundberg, E. Ideker, T. 2020-06-22 doi:10.1101/2020.06.21.163709 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals ]]> https://biorxiv.org/content/10.1101/2020.06.22.164533v1?rss=1 Montano, E. T. Nideffer, J. F. Brumage, L. Erb, M. Derman, A. I. Davis, J. P. Estrada, E. Fu, S. Le, D. Vuppala, A. Tran, C. Luterstein, E. Lakkaraju, S. Panchagnula, S. Ren, C. Doan, J. Tran, S. Soriano, J. Fujita, Y. Gutala, P. Fujii, Q. Lee, M. Bui, A. Villarreal, C. Shing, S. R. Kim, S. Freeman, D. Racha, V. Ho, A. Kumar, P. Falah, K. Dawson, T. Enustun, E. Prichard, A. Gomez, A. Khanna, K. Trigg, S. Pogliano, K. Pogliano, J. 2020-06-22 doi:10.1101/2020.06.22.164533 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ A whole-cortex probabilistic diffusion tractography connectome ]]> https://biorxiv.org/content/10.1101/2020.06.22.166041v1?rss=1 Rosen, B. Q. Halgren, E. 2020-06-23 doi:10.1101/2020.06.22.166041 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ A Live-Cell Assay for the Detection of pre-microRNA-Protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.06.23.167734v1?rss=1 Rosenblum, S. L. Lorenz, D. A. Garner, A. L. 2020-06-24 doi:10.1101/2020.06.23.167734 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2. ]]> https://biorxiv.org/content/10.1101/2020.06.23.167791v1?rss=1 Krishnan, S. Krishnan, G. P. 2020-06-24 doi:10.1101/2020.06.23.167791 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ A Simple Procedure for Bacterial Expression and Purification of the Fragile X Protein Family ]]> https://biorxiv.org/content/10.1101/2020.06.24.169243v1?rss=1 Edwards, M. M. Xu, M. Joseph, S. 2020-06-26 doi:10.1101/2020.06.24.169243 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ The Human Fragile X Mental Retardation Protein Inhibits the Elongation Step of Translation through its RGG and C-terminal domains ]]> https://biorxiv.org/content/10.1101/2020.06.25.171967v1?rss=1 Athar, Y. M. Joseph, S. 2020-06-27 doi:10.1101/2020.06.25.171967 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism ]]> https://biorxiv.org/content/10.1101/2020.06.25.172262v1?rss=1 Urresti, J. Zhang, P. Moran-Losada, P. Yu, N.-K. Negraes, P. D. Trujillo, C. A. Antaki, D. Amar, M. Chau, K. Pramod, A. B. Diedrich, J. Tejwani, L. Romero, S. Sebat, J. Yates, J. R. Muotri, A. R. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.25.172262 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Genetics of human gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2020.06.26.173724v1?rss=1 Kurilshikov, A. Medina-Gomez, C. Bacigalupe, R. Radjabzadeh, D. Wang, J. Demirkan, A. Le Roy, C. I. Raygoza Garay, J. A. Finnicum, C. Liu, X. Zhernakova, D. Bonder, M. J. Hansen, T. H. Frost, F. Ruhlemann, M. C. Turpin, W. Moon, J.-Y. Kim, H.-N. Lull, K. Barkan, E. Shah, S. A. Fornage, M. Szopinska-Tokov, J. Wallen, Z. Borisevich, D. Agreus, L. Andreasson, A. Bang, C. Bedrani, L. Bell, J. T. Bisgaard, H. Boehnke, M. Boomsma, D. I. Burk, R. D. Claringbould, A. Croitoru, K. Davies, G. Van Duijn, C. Duijts, L. Falony, G. Fu, J. van der Graaf, A. Hansen, T 2020-06-28 doi:10.1101/2020.06.26.173724 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ The N-terminus of GPR37L1 is proteolytically processed by matrix metalloproteases ]]> https://biorxiv.org/content/10.1101/2020.06.27.174847v1?rss=1 Coleman, J. L. J. Ngo, T. Smythe, R. E. Cleave, A. J. Jones, N. M. Graham, R. M. Smith, N. J. 2020-06-28 doi:10.1101/2020.06.27.174847 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Isoform transcriptome of developing human brain provides new insights into autism risk variants ]]> https://biorxiv.org/content/10.1101/2020.06.27.175489v1?rss=1 Chau, K. Zhang, P. Urresti, J. Amar, M. Pramod, A. B. Thomas, A. Corominas, R. Lin, G. N. Iakoucheva, L. M. 2020-06-27 doi:10.1101/2020.06.27.175489 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ A Small Molecule Fluorogenic Probe for the Detection of Sphingosine in Living Cells ]]> https://biorxiv.org/content/10.1101/2020.06.27.175661v1?rss=1 Rudd, A. K. Mittal, N. Lim, E. W. Metallo, C. M. Devaraj, N. K. 2020-06-29 doi:10.1101/2020.06.27.175661 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Spatial metabolomics identifies localized chemical changes in heart tissue during chronic cardiac Chagas disease ]]> https://biorxiv.org/content/10.1101/2020.06.29.178038v1?rss=1 Dean, D. A. Gautham, Siqueira-Neto, J. L. McKerrow, J. H. Dorrestein, P. C. McCall, L.-I. 2020-06-29 doi:10.1101/2020.06.29.178038 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Local Field Potentials in a Pre-motor Region Predict Learned Vocal Sequences ]]> https://biorxiv.org/content/10.1101/2020.06.30.179861v1?rss=1 Brown, D. E. Chavez, J. I. Nguyen, D. H. Kadwory, A. Voytek, B. Arneodo, E. Gentner, T. Q. Gilja, V. 2020-06-30 doi:10.1101/2020.06.30.179861 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Biophysical modeling of the neural origin of EEG and MEG signals ]]> https://biorxiv.org/content/10.1101/2020.07.01.181875v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@47f029org.highwire.dtl.DTLVardef@e8244dorg.highwire.dtl.DTLVardef@a765c1org.highwire.dtl.DTLVardef@96550_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICurrent dipoles are computed from biophysically detailed simulated neuron and network activity C_LIO_LIExtracted current dipoles allow for accurate computation of EEG and MEG signals in simplified and detailed head models C_LIO_LICurrent-diplole approximation generally not suitable for accurate calculations of ECoG signals C_LIO_LIMethod provides biophysics-based link between detailed neural activity and systems-level signals C_LI ]]> Naess, S. Halnes, G. Hagen, E. Hagler, D. J. Dale, A. Einevoll, G. T. Ness, T. V. 2020-07-04 doi:10.1101/2020.07.01.181875 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Phosphoregulation of HORMA domain protein HIM-3 promotes asymmetric synaptonemal complex disassembly in meiotic prophase in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.07.01.182063v1?rss=1 Sato-Carlton, A. Nakamura-Tabuchi, C. Li, X. Boog, H. Lehmer, M. K. Rosenberg, S. C. Barroso, C. Martinez-Perez, E. Corbett, K. D. Carlton, P. M. 2020-07-01 doi:10.1101/2020.07.01.182063 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Development of a Synthetic Poxvirus-Based SARS-CoV-2 Vaccine ]]> https://biorxiv.org/content/10.1101/2020.07.01.183236v1?rss=1 Chiuppesi, F. Werner, M. S. Contreras, H. Nguyen, H. V. Martinez, J. Park, S. Nguyen, J. Kha, M. Iniguez, A. Zhou, Q. Kaltcheva, T. Levytskyy, R. Ebelt, N. D. Kang, T. H. Wu, X. Rogers, T. Manuel, E. R. Shostak, Y. Diamond, D. J. Wussow, F. 2020-07-02 doi:10.1101/2020.07.01.183236 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Title: Acetylcholine regulates pulmonary inflammation and facilitates the transition from active immunity to tissue repair during respiratory viral infection ]]> https://biorxiv.org/content/10.1101/2020.07.02.184226v1?rss=1 Horkowitz, A. P. Schwartz, A. V. Alvarez, C. A. Herrera, E. B. Thoman, M. L. Chatfield, D. A. Osborn, K. G. Feuer, R. George, U. Z. Phillips, J. A. 2020-07-02 doi:10.1101/2020.07.02.184226 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Heart Snapshot: a broadly validated smartphone measure of VO2max for collection of real world data ]]> https://biorxiv.org/content/10.1101/2020.07.02.185314v1?rss=1 Webster, D. E. Tummalacherla, M. Higgins, M. Wing, D. Ashley, E. Kelly, V. E. McConnell, M. V. Muse, E. D. Olgin, J. Mangravite, L. Godino, J. Kellen, M. Omberg, L. 2020-07-04 doi:10.1101/2020.07.02.185314 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota ]]> https://biorxiv.org/content/10.1101/2020.07.06.190181v1?rss=1 Aranda-Diaz, A. Ng, K. Thomsen, T. Real-Ramirez, I. Dahan, D. Dittmar, S. Gutierrez Gonzalez, C. Chavez, T. Vasquez, K. S. Nguyen, T. H. Yu, F. B. Higginbottom, S. K. Neff, N. Elias, J. E. Sonnenburg, J. L. Huang, K. C. 2020-07-06 doi:10.1101/2020.07.06.190181 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Activity Mapping the Acyl Carrier Protein - Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis ]]> https://biorxiv.org/content/10.1101/2020.07.09.196451v1?rss=1 Jeffrey T Mindrebo Laetitia Estelle Misson Mindrebo Caitlin Johnson Joseph P. Noel Michael Burkart 2020-07-10 doi:10.1101/2020.07.09.196451 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Temperature triggers provide quantitative predictions of multi-species fish spawning peaks ]]> https://biorxiv.org/content/10.1101/2020.07.10.196923v1?rss=1 0.97) between a single event in daily sea surface temperatures each spring, and peak fish egg abundance measurements the following summer, in 7 years of approximately weekly fish egg abundance data collected at Scripps Pier in La Jolla California. Even more surprising is that this event-based result persists despite the large and variable number of fish species involved (up to 46), and the large and variable time interval between trigger and response (up to ~3 months). To mitigate against potential over-fitting, we make a true out-of-sample prediction for the peak summer egg abundance that will be observed at Scripps Pier this year. ]]> Emma S. Choi Erik Saberski Tom Lorimer Cameron Smith Unduwap Kandage-don Ronald S. Burton George Sugihara 2020-07-10 doi:10.1101/2020.07.10.196923 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Wide phenotypic spectrum of human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations ]]> https://biorxiv.org/content/10.1101/2020.07.12.189621v1?rss=1 Rebecca SF Mok Wen-Bo Zhang Taimoor I Sheikh Isabella R Fernandes Leah C DeJong Matthew R Hildebrandt Marat Mufteev Deivid C Rodrigues Wei Wei Alina Piekna Jiajie Liu Alysson R Muotri John B Vincent Michael W Salter James Ellis 2020-07-12 doi:10.1101/2020.07.12.189621 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Tobacco, but not nicotine and flavor-less electronic cigarettes, induces ACE2 and immune dysregulation ]]> https://biorxiv.org/content/10.1101/2020.07.13.198630v1?rss=1 Lee, A. C. Chakladar, J. Li, W. T. Chen, C. Chang, E. Y. Wang-Rodriguez, J. Ongkeko, W. M. 2020-07-13 doi:10.1101/2020.07.13.198630 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Cigarette Smoke and Nicotine-Containing E-cigarette Vapor Downregulate Lung WWOX Expression Which is Associated with Increased Severity of Murine ARDS ]]> https://biorxiv.org/content/10.1101/2020.07.13.200832v1?rss=1 Zeng, Z. Chen, W. Moshensky, A. Khan, R. Alexander, L. C. Ware, L. B. Aldaz, C. M. Jacobson, J. R. Dudek, S. M. Natarajan, V. Machado, R. F. Singla, S. 2020-07-13 doi:10.1101/2020.07.13.200832 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Acidosis, Zinc and HMGB1 in Sepsis: A Common Connection Involving Sialoglycan Recognition ]]> https://biorxiv.org/content/10.1101/2020.07.15.198010v1?rss=1 Siddiqui, S. S. Dhar, C. Sundaramurthy, V. Sasmal, A. Yu, H. Bandala-Sanchez, E. Li, M. Zhang, X. Chen, X. Harrison, L. C. Xu, D. Varki, A. 2020-07-15 doi:10.1101/2020.07.15.198010 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications ]]> https://biorxiv.org/content/10.1101/2020.07.15.202929v1?rss=1 Prodanov, T. Bansal, V. 2020-07-16 doi:10.1101/2020.07.15.202929 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Delineation of a molecularly distinct terminally differentiated memory CD8 T cell population ]]> https://biorxiv.org/content/10.1101/2020.07.17.207266v1?rss=1 Milner, J. Nguyen, H. Omilusik, K. Reina-Campos, M. Tsai, M. Toma, C. Delpoux, A. D. Boland, B. Hedrick, S. M. Chang, J. T. Goldrath, A. W. 2020-07-17 doi:10.1101/2020.07.17.207266 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Aβ-induced synaptic injury is mediated by presynaptic expression of amyloid precursor protein (APP) in hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2020.07.18.210344v1?rss=1 Vicario-Orri, E. Kasuga, K. Tyan, S.-H. Chiang, K. Viana da Silva, S. Bushong, E. A. DeLoach, K. Ling, I.-F. Luo, L. Ellisman, M. H. Leutgeb, S. Koo, E. H. 2020-07-20 doi:10.1101/2020.07.18.210344 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ Unique contributions of sensory discrimination and gamma synchronization deficits to cognitive, clinical, and psychosocial functional impairments in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.07.19.211193v1?rss=1 Koshiyama, D. Miyakoshi, M. Thomas, M. L. Joshi, Y. B. Molina, J. L. Tanaka-Koshiyama, K. Sprock, J. Braff, D. L. Swerdlow, N. R. Light, G. A. 2020-07-21 doi:10.1101/2020.07.19.211193 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Tractography-Pathology Correlations in Traumatic Brain Injury: A TRACK-TBI Study ]]> https://biorxiv.org/content/10.1101/2020.07.20.209668v1?rss=1 Nolan, A. L. Petersen, C. Iacono, D. Mac Donald, C. L. Mukherjee, P. van der Kouwe, A. Jain, S. Stevens, A. Diamond, B. R. Wang, R. Markowitz, A. J. Fischl, B. Perl, D. P. Manley, G. T. Keene, C. D. Diaz-Arrastia, R. Edlow, B. L. the TRACK-TBI Investigators, 2020-07-22 doi:10.1101/2020.07.20.209668 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Unique genomic features of crAss-like phages, the dominant component of the human gut virome ]]> https://biorxiv.org/content/10.1101/2020.07.20.212944v1?rss=1 Yutin, N. Benler, S. Shmakov, S. A. Wolf, Y. I. Tolstoy, I. Rayko, M. Antipov, D. Pevzner, P. A. Koonin, E. V. 2020-07-20 doi:10.1101/2020.07.20.212944 Cold Spring Harbor Laboratory Press 2020-07-20 <![CDATA[ A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease ]]> https://biorxiv.org/content/10.1101/2020.07.21.214874v1?rss=1 Alexanian, M. Przytycki, P. F. Micheletti, R. Padmanabhan, A. Ye, L. Travers, J. G. Gonzalez Teran, B. Duan, Q. Ranade, S. S. Felix, F. Linares-Saldana, R. Huang, Y. Andreoletti, G. Yang, J. Ivey, K. N. Jain, R. McKinsey, T. A. Rosenfeld, M. G. Gifford, C. Pollard, K. S. Haldar, S. M. Srivastava, D. 2020-07-22 doi:10.1101/2020.07.21.214874 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ ABCB-mediated auxin transport in outer root tissues regulates lateral root spacing in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.07.22.206300v1?rss=1 CHEN, J. Hu, Y. Hao, P. Zhang, Y. Roth, O. Njo, M. Sterck, L. Hu, Y. Zhao, Y. Geisler, M. Shani, E. Beeckman, T. Vanneste, S. 2020-07-22 doi:10.1101/2020.07.22.206300 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Asymmetric localization of the cell division machinery during Bacillus subtilis sporulation ]]> https://biorxiv.org/content/10.1101/2020.07.22.216184v1?rss=1 Khanna, K. Lopez-Garrido, J. Sugie, J. Pogliano, K. Villa, E. 2020-07-22 doi:10.1101/2020.07.22.216184 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project ]]> https://biorxiv.org/content/10.1101/2020.07.23.216507v1?rss=1 Hansen, J. Sealfon, R. Menon, R. Eadon, M. T. Lake, B. B. Steck, B. Dobi, D. Parikh, S. Sidgel, T. K. Alexandrov, T. Schroeder, A. Otto, E. A. Anderton, C. R. Barwinska, D. Zheng, G. Rose, M. P. Shapiro, J. P. Velickovic, D. Pamreddy, A. Winfree, S. He, Y. de Boer, I. H. Hodgin, J. B. Nair, A. Sharma, K. Sarwal, M. Zhang, K. Himmelfarb, J. Laszik, Z. Rovin, B. Dagher, P. C. He, J. C. El-Achkar, T. M. Jain, S. Troyanskaya, O. G. Kretzler, M. Iyengar, R. Azeloglu, E. U. 2020-07-24 doi:10.1101/2020.07.23.216507 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Benchmarking challenging small variants with linked and long reads ]]> https://biorxiv.org/content/10.1101/2020.07.24.212712v1?rss=1 Wagner, J. Olson, N. D. Harris, L. Khan, Z. Farek, J. Mahmoud, M. Stankovic, A. Kovacevic, V. Wenger, A. M. Rowell, W. J. Xiao, C. Yoo, B. Miller, N. Rosenfeld, J. A. Ni, B. Zarate, S. Kirsche, M. Aganezov, S. Schatz, M. Narzisi, G. Byrska-Bishop, M. Clarke, W. Evani, U. S. Markello, C. Shafin, K. Zhou, X. Sidow, A. Bansal, V. Martinez Barrio, A. Fiddes, I. T. Fungtammasan, A. Chin, C.-S. Sedlazeck, F. J. Carroll, A. Salit, M. Zook, J. M. Genome in a Bottle Consortium, 2020-07-25 doi:10.1101/2020.07.24.212712 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Synapsin-caveolin-1 mitigates cognitive deficits and neurodegeneration in Alzheimer's disease mice ]]> https://biorxiv.org/content/10.1101/2020.07.24.220129v1?rss=1 Wang, S. Leem, J. Podvin, S. Hook, V. Kleschevnikov, N. Savchenko, P. Dhanani, M. Zhou, K. Kelly, I. Zhang, T. Miyanohara, A. Kleschevnikov, A. Wagner, S. Trojanowski, J. Roth, D. Patel, H. Patel, P. Head, B. P. 2020-07-25 doi:10.1101/2020.07.24.220129 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ A Novel CD206 Targeting Peptide Inhibits Bleomycin Induced Pulmonary Fibrosis in Mice ]]> https://biorxiv.org/content/10.1101/2020.07.27.218115v1?rss=1 Gheberemedhin, A. Salam, A. B. Adu-Addai, B. Noonan, S. Stratton, R. Ahmed, M. S. U. khantwal, C. Martin, G. Huixian, L. Andrews, C. Balasubramanyam, K. Udo, R. Henry, L. Jaynes, J. Yates, C. 2020-07-29 doi:10.1101/2020.07.27.218115 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ The ABCD Stop Signal Data: Response to Bissett et al. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223057v1?rss=1 Garavan, H. Hahn, S. Chaarani, B. Juliano, A. Allgaier, N. Yuan, D. K. Weigard, A. Orr, C. Watts, R. Wager, T. Ruiz de Leon, O. Hagler, D. Potter, A. 2020-07-28 doi:10.1101/2020.07.27.223057 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ ABO genetic variation in Neanderthals and Denisovans ]]> https://biorxiv.org/content/10.1101/2020.07.27.223628v1?rss=1 Fox, K. Huerta-Sanchez, E. Villanea, F. A. 2020-07-27 doi:10.1101/2020.07.27.223628 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ RNA-binding protein RBM3 negatively regulates innate lymphoid cells (ILCs) and lung inflammation ]]> https://biorxiv.org/content/10.1101/2020.07.27.223958v1?rss=1 Doherty, T. 2020-07-28 doi:10.1101/2020.07.27.223958 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Insights into the catalytic properties of the mitochondrial rhomboid protease PARL ]]> https://biorxiv.org/content/10.1101/2020.07.27.224220v1?rss=1 Lysyk, L. Brassard, R. Arutyunova, E. Siebert, V. Jiang, Z. Takyi, E. Morrison, M. Young, H. S. Lemberg, M. K. O'Donoghue, A. J. Lemieux, M. J. 2020-07-29 doi:10.1101/2020.07.27.224220 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Understanding the Human Brain using Brain Organoids and a Structure-Function Theory ]]> https://biorxiv.org/content/10.1101/2020.07.28.225631v1?rss=1 Silva, G. A. Muotri, A. R. White, C. 2020-07-28 doi:10.1101/2020.07.28.225631 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Plankton food webs of the Gulf of Mexico spawning grounds of Atlantic Bluefin tuna ]]> https://biorxiv.org/content/10.1101/2020.07.29.227116v1?rss=1 80% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). In contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <4% of net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on calanoid copepods and other suspension-feeding zooplankton that in turn derive much of their nutrition from diatoms and mixotrophic flagellates. This allows ABT larvae to maintain a comparatively low trophic level ([~]4.0 for pre-flexion larvae; [~]4.2 for post-flexion larvae) that increases trophic transfer from phytoplankton to larval fish. ]]> Stukel, M. R. Gerard, T. Kelly, T. B. Knapp, A. N. Laiz-Carrion, R. Lamkin, J. Landry, M. R. Malca, E. Selph, K. E. Shiroza, A. Shropshire, T. A. Swalethorp, R. R. 2020-07-30 doi:10.1101/2020.07.29.227116 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Spatial attention enhances the spatial selectivity of population codes during the first wave of visual processing ]]> https://biorxiv.org/content/10.1101/2020.07.30.228981v1?rss=1 Foster, J. J. Thyer, W. Wennberg, J. W. Awh, E. 2020-07-31 doi:10.1101/2020.07.30.228981 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ MOLECULAR DETERMINANTS OF THE ENDOCYTIC PROTEIN EPSIN CONTROLLING ITS LOCALIZATION AND FUNCTION IN CANCER CELL MIGRATION AND INVASION ]]> https://biorxiv.org/content/10.1101/2020.07.30.229195v1?rss=1 Madhivanan, K. Cao, L. Staiger, C. J. Aguilar, R. C. 2020-07-30 doi:10.1101/2020.07.30.229195 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics ]]> https://biorxiv.org/content/10.1101/2020.07.31.230334v1?rss=1 Haiman, Z. B. Zielinski, D. C. Koike, Y. Yurkovich, J. T. Palsson, B. O. 2020-07-31 doi:10.1101/2020.07.31.230334 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Injectable Myocardial Matrix Hydrogel Mitigates Negative Left Ventricular Remodeling in a Chronic Myocardial Infarction Model ]]> https://biorxiv.org/content/10.1101/2020.07.31.231449v1?rss=1 Diaz, M. D. Tran, E. Wassenaar, J. Spang, M. Gaetani, R. Luo, C. Braden, R. Hill, R. C. Hansen, K. C. DeMaria, A. N. Christman, K. 2020-08-02 doi:10.1101/2020.07.31.231449 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Myocardial matrix material supports a proliferative microenvironment for cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.07.31.231845v1?rss=1 Wang, R. M. Cattaneo, P. Luo, C. Camboa, N. Braden, R. Christman, K. Evans, S. 2020-08-02 doi:10.1101/2020.07.31.231845 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Mast Cells Contribute to the Immunomodulatory Effect of the Biomaterial Microenvironment in a Gender Specific Manner ]]> https://biorxiv.org/content/10.1101/2020.07.31.231852v1?rss=1 Wang, R. M. Ungerleider, J. Kawakami, Y. Kawakami, Y. Kawakami, T. Christman, K. 2020-08-02 doi:10.1101/2020.07.31.231852 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ NPC1-mTORC1 signaling Couples Cholesterol Sensing to Organelle Homeostasis and is a Targetable Pathway in Niemann-Pick type C ]]> https://biorxiv.org/content/10.1101/2020.08.02.233254v1?rss=1 Davis, O. B. Shin, H. R. Lim, C.-Y. Wu, E. Y. Kukurugya, M. Maher, C. F. Perera, R. M. Ordonez, P. Zoncu, R. 2020-08-02 doi:10.1101/2020.08.02.233254 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Specific OCRL1 patient mutations differentially impact Lowe Syndrome cellular phenotypes ]]> https://biorxiv.org/content/10.1101/2020.08.04.236612v1?rss=1 Ramadesikan, S. Skiba, L. Lee, J. Madhivanan, K. Sarkar, D. De La Fuente, A. Hanna, C. B. Hazbun, T. Kihara, D. Aguilar, R. C. 2020-08-05 doi:10.1101/2020.08.04.236612 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Paranode stability requires UNC5B expression by oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2020.08.06.234906v1?rss=1 de Faria, O. Nakamura, D. S. Clemot, S. Kim, D. Mocanu, M. V. Pilgram, R. Bin, J. M. Wong, E. W. Shmuel, A. Sadikot, A. Ackerman, S. L. Kennedy, T. E. 2020-08-07 doi:10.1101/2020.08.06.234906 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Identification of the keystone species in non-alcoholic fatty liver disease by causal inference and dynamic intervention modeling ]]> https://biorxiv.org/content/10.1101/2020.08.06.240655v1?rss=1 Wu, D. Jiao, N. Zhu, R. Zhang, Y. Gao, W. Fang, S. Li, Y. Cheng, S. Tian, C. Lan, P. Loomba, R. Zhu, L. 2020-08-07 doi:10.1101/2020.08.06.240655 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Influenza A virus NS1 protein binds as a dimer to the RNA-free PABP1 but not to the PABP1-Poly(A) RNA Complex ]]> https://biorxiv.org/content/10.1101/2020.08.10.245225v1?rss=1 de Rozieres, C. M. Joseph, S. 2020-08-10 doi:10.1101/2020.08.10.245225 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase ]]> https://biorxiv.org/content/10.1101/2020.08.12.248690v1?rss=1 Seitz, C. Casalino, L. Konecny, R. Huber, G. Amaro, R. E. McCammon, J. A. 2020-08-12 doi:10.1101/2020.08.12.248690 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Learned adaptive multiphoton illumination microscopy ]]> https://biorxiv.org/content/10.1101/2020.08.14.251314v1?rss=1 Pinkard, H. Baghdassarian, H. Mujal, A. Roberts, E. Hu, K. H. Friedman, D. H. Malenica, I. Shagam, T. Fries, A. Corbin, K. Krummel, M. F. Waller, L. 2020-08-15 doi:10.1101/2020.08.14.251314 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Abortive Intussusceptive Angiogenesis Causes Multi-Cavernous Vascular Malformations ]]> https://biorxiv.org/content/10.1101/2020.08.14.251744v1?rss=1 Li, W. Tran, V. Shaked, I. Xue, B. Moore, T. Lightle, R. Kleinfeld, D. Awad, I. A. Ginsberg, M. 2020-08-14 doi:10.1101/2020.08.14.251744 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD ]]> https://biorxiv.org/content/10.1101/2020.08.14.251876v1?rss=1 Jiao, N. Loomba, R. Yang, Z.-H. Wu, D. Fang, S. Bettencourt, R. Lan, P. Zhu, R. Zhu, L. 2020-08-14 doi:10.1101/2020.08.14.251876 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.17.253955v1?rss=1 Kim, H. Ding, Y.-H. Lu, S. Zuo, M.-Q. Conte, D. Dong, M.-Q. Mello, C. 2020-08-17 doi:10.1101/2020.08.17.253955 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Extracellular matrix and cyclic stretch alter fetal cardiomyocyte proliferation and maturation in a rodent model of heart hypoplasia ]]> https://biorxiv.org/content/10.1101/2020.08.17.254334v1?rss=1 Watson, M. C. Williams, C. Wang, R. M. Perreault, L. R. Sullivan, K. E. Stoppel, W. L. Black, L. D. 2020-08-18 doi:10.1101/2020.08.17.254334 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors ]]> https://biorxiv.org/content/10.1101/2020.08.19.257352v1?rss=1 Hunkeler, M. Jin, C. Y. Ma, M. W. Overwijn, D. Monda, J. K. Bennett, E. J. Fischer, E. S. 2020-08-19 doi:10.1101/2020.08.19.257352 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ An autonomous, but INSIG-modulated, role for the Sterol Sensing Domain in mallostery-regulated ERAD of yeast HMG-CoA reductase ]]> https://biorxiv.org/content/10.1101/2020.08.20.260133v1?rss=1 Wangeline, M. A. Hampton, R. Y. 2020-08-21 doi:10.1101/2020.08.20.260133 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ A home and rescue gene drive forces its inheritance stably persisting in populations ]]> https://biorxiv.org/content/10.1101/2020.08.21.261610v1?rss=1 Kandul, N. P. Liu, J. Bennett, J. B. Marshall, J. M. Akbari, O. 2020-08-23 doi:10.1101/2020.08.21.261610 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Functional validation of a finding from a mouse genome-wide association study demonstrates that a mutant allele of Azi2 alters sensitivity to methamphetamine ]]> https://biorxiv.org/content/10.1101/2020.08.22.262709v1?rss=1 Zhou, X. Barkley-Levenson, A. Montilla-Perez, P. Telese, F. Palmer, A. A. 2020-08-22 doi:10.1101/2020.08.22.262709 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Developmental stage-specific changes in protein synthesis differentially sensitize hematopoietic stem cells and erythroid progenitors to impaired ribosome biogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.22.262816v1?rss=1 Magee, J. A. Signer, R. A. J. 2020-08-23 doi:10.1101/2020.08.22.262816 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ Assessment of research ethics education offerings of pharmacy master programs: a qualitative content analysis ]]> https://biorxiv.org/content/10.1101/2020.08.25.266023v1?rss=1 Ahmed, W. S. Nebeker, C. 2020-08-25 doi:10.1101/2020.08.25.266023 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ The population genetics of pleiotropy, and the evolution of collateral resistance and sensitivity in bacteria ]]> https://biorxiv.org/content/10.1101/2020.08.25.267484v1?rss=1 Ardell, S. M. Kryazhimskiy, S. 2020-08-25 doi:10.1101/2020.08.25.267484 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Rethinking Remdesivir: Synthesis of Lipid Prodrugs that Substantially Enhance Anti-Coronavirus Activity ]]> https://biorxiv.org/content/10.1101/2020.08.26.269159v1?rss=1 Schooley, R. T. Carlin, A. F. Beadle, J. R. Valiaeva, N. Zhang, X.-Q. Garretson, A. F. Smith, V. I. Murphy, J. A. Hostetler, K. Y. 2020-08-27 doi:10.1101/2020.08.26.269159 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ PIEZO ion channel is required for root mechanotransduction in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2020.08.27.270355v1?rss=1 Patapoutian, A. Mousavi, S. A. R. Dubin, A. E. Zeng, W.-Z. Coombs, A. M. Do, K. Ghadiri, D. A. Zhao, Y. Ge, C. 2020-08-28 doi:10.1101/2020.08.27.270355 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Neural vulnerability and hurricane-related media predict posttraumatic stress in youth ]]> https://biorxiv.org/content/10.1101/2020.08.27.271056v1?rss=1 Dick, A. S. Silva, K. Gonzalez, R. Sutherland, M. T. Laird, A. R. Thompson, W. K. Tapert, S. F. Squeglia, L. M. Gray, K. M. Nixon, S. J. Cottler, L. B. La Greca, A. M. Gurwitch, R. H. Comer, J. S. 2020-08-29 doi:10.1101/2020.08.27.271056 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors ]]> https://biorxiv.org/content/10.1101/2020.08.28.270454v1?rss=1 Hong, L. Ko, C. S. Kang, S. E. Pruneda-Paz, J. L. Roeder, A. H. K. 2020-08-30 doi:10.1101/2020.08.28.270454 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ De Novo Mutation in an Enhancer of EBF3 in simplex autism ]]> https://biorxiv.org/content/10.1101/2020.08.28.270751v1?rss=1 Padhi, E. M. Hayeck, T. J. Mannion, B. Chatterjee, S. Byrska-Bishop, M. Musunuri, R. Narzisi, G. Abhyankar, A. Cheng, Z. Hunter, R. D. Akiyama, J. Fries, L. E. Ng, J. Stong, N. Allen, A. S. Dickel, D. E. Bernier, R. A. Gorkin, D. U. Pennacchio, L. A. Zody, M. C. Turner, T. N. 2020-08-28 doi:10.1101/2020.08.28.270751 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing ]]> https://biorxiv.org/content/10.1101/2020.08.29.273565v1?rss=1 Martinez, N. M. Gilbert, W. V. Yeo, G. W. Su, A. Schaening, C. Burns, M. C. Nussbacher, J. K. Sathe, S. 2020-08-31 doi:10.1101/2020.08.29.273565 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275602v1?rss=1 Adam, K. Chang, L. Rangan, N. Serences, J. 2020-09-01 doi:10.1101/2020.08.31.275602 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Stability analysis of a signaling circuit with dual species of GTPase switches ]]> https://biorxiv.org/content/10.1101/2020.08.31.276311v1?rss=1 Stolerman, L. M. Ghosh, P. Rangamani, P. 2020-08-31 doi:10.1101/2020.08.31.276311 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Single-vessel cerebral blood flow fMRI to map blood velocity by phase-contrast imaging ]]> https://biorxiv.org/content/10.1101/2020.09.03.280636v1?rss=1 Chen, X. Jiang, Y. Choi, S. Pohmann, R. Scheffler, K. Kleninfeld, D. Yu, X. 2020-09-03 doi:10.1101/2020.09.03.280636 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis ]]> https://biorxiv.org/content/10.1101/2020.09.03.281675v1?rss=1 Terrey, M. Adamson, S. I. Gibson, A. L. Deng, T. Ishimura, R. Chuang, J. H. Ackerman, S. L. 2020-09-04 doi:10.1101/2020.09.03.281675 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Inherently confinable split-drive systems in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.09.03.282079v1?rss=1 Terradas, G. Buchman, A. B. Bennett, J. B. Shriner, I. Marshall, J. M. Akbari, O. S. Bier, E. 2020-09-03 doi:10.1101/2020.09.03.282079 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Differential gene expression reflects larval development and survival of monarch butterflies on different milkweed hosts ]]> https://biorxiv.org/content/10.1101/2020.09.05.284489v1?rss=1 Gonzalez-De-la-Rosa, P. M. Ramirez Loustalot-Laclette, M. Abreu-Goodger, C. Markow, T. A. 2020-09-06 doi:10.1101/2020.09.05.284489 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects ]]> https://biorxiv.org/content/10.1101/2020.09.06.285056v1?rss=1 Larkin, A. A. Garcia, C. A. Brock, M. L. Lee, J. A. Garcia, N. Ustick, L. J. Barbero, L. Carter, B. R. Sonnerup, R. E. Talley, L. Tarran, G. A. Volkov, D. L. Martiny, A. C. 2020-09-08 doi:10.1101/2020.09.06.285056 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.09.06.285387v1?rss=1 Fan, X. Masamsetti, V. P. Sun, J. Q. J. Engholm-Keller, K. Osteil, P. Studdert, J. Graham, M. E. Fossat, N. Tam, P. P. L. 2020-09-07 doi:10.1101/2020.09.06.285387 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Direct observation of RAG recombinase recruitment to chromatin and the IgH locus in live pro-B cells ]]> https://biorxiv.org/content/10.1101/2020.09.07.286484v1?rss=1 Lovely, G. A. Braikia, F.-Z. Singh, A. K. Schatz, D. Murre, C. Liu, Z. Sen, R. 2020-09-07 doi:10.1101/2020.09.07.286484 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity ]]> https://biorxiv.org/content/10.1101/2020.09.08.288233v1?rss=1 1000 fold more specific RNA editing. Taken together, we anticipate this comprehensive deaminase engineering will enable broader utility of the ADAR toolset for RNA biotechnology and therapeutic applications. ]]> Katrekar, D. Palmer, N. Xiang, Y. Saha, A. Meluzzi, D. Mali, P. 2020-09-09 doi:10.1101/2020.09.08.288233 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Mechanical principles governing the shapes of dendritic spines ]]> https://biorxiv.org/content/10.1101/2020.09.09.290650v1?rss=1 Alimohamadi, H. Bell, M. Halpain, S. Rangamani, P. 2020-09-10 doi:10.1101/2020.09.09.290650 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement ]]> https://biorxiv.org/content/10.1101/2020.09.09.290668v1?rss=1 Boyle, E. A. Becker, W. R. Bai, H. B. Chen, J. S. Doudna, J. A. Greenleaf, W. J. 2020-09-10 doi:10.1101/2020.09.09.290668 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Gene exchange networks define species-like units in marine prokaryotes ]]> https://biorxiv.org/content/10.1101/2020.09.10.291518v1?rss=1 12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes. ]]> Stepanauskas, R. Brown, J. M. Mai, U. Bezuidt, O. Pachiadaki, M. Brown, J. Biller, S. Berube, P. M. Record, N. R. Mirarab, S. 2020-09-10 doi:10.1101/2020.09.10.291518 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Orphan G protein-coupled receptor, GPR37L1: pharmacological toolbox empty once again ]]> https://biorxiv.org/content/10.1101/2020.09.11.290486v1?rss=1 Ngo, T. Wilkins, B. P. So, S. S. Keov, P. Chahal, K. K. Finch, A. M. Coleman, J. L. J. Kufareva, I. Smith, N. J. 2020-09-11 doi:10.1101/2020.09.11.290486 Cold Spring Harbor Laboratory Press 2020-09-11 <![CDATA[ Selective activation of FZD7 promotes mesendodermal differentiation of human pluripotent stem cells. ]]> https://biorxiv.org/content/10.1101/2020.09.14.297028v1?rss=1 Gumber, D. Do, M. Suresh Kumar, N. Wu, C. C. N. Carson, D. Gaasterland, T. Willert, K. 2020-09-14 doi:10.1101/2020.09.14.297028 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ Optimal transcriptional regulation of cellular responses to sudden environmental shifts ]]> https://biorxiv.org/content/10.1101/2020.09.14.297317v1?rss=1 Schultz, D. Tsimring, L. S. 2020-09-15 doi:10.1101/2020.09.14.297317 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits ]]> https://biorxiv.org/content/10.1101/2020.09.16.300152v1?rss=1 Ward, S. Riley, C. Carey, E. M. Nguyen, J. Esener, S. Nimmerjahn, A. Sirbuly, D. J. 2020-09-17 doi:10.1101/2020.09.16.300152 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ The organization and developmental establishment ofcortical interneuron presynaptic circuits ]]> https://biorxiv.org/content/10.1101/2020.09.17.302117v1?rss=1 Pouchelon, G. Bollmann, Y. Fisher, E. Agba, C. K. Xu, Q. Ritola, K. D. Mirow, A. M. Kim, S. Cossart, R. Fishell, G. 2020-09-17 doi:10.1101/2020.09.17.302117 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ A De Novo Genome Assembly, Gene Annotation, And Expression Atlas For The Monarch Butterfly Danaus plexippus ]]> https://biorxiv.org/content/10.1101/2020.09.19.304162v1?rss=1 Ranz, J. M. Gonzalez, P. Clifton, B. Nazario, N. Hernandez-Cervantes, P. Palma-Martinez, M. Valdivia, D. Jimenez-Kaufman, A. Lu, M. Markow, T. A. Abreu-Goodger, C. 2020-09-20 doi:10.1101/2020.09.19.304162 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Altered lipid metabolism marks glioblastoma stem and non-stem cells in separate tumor niches ]]> https://biorxiv.org/content/10.1101/2020.09.20.304964v1?rss=1 Shakya, S. Gromovsky, A. Hale, J. Knudsen, A. Prager, B. Wallace, L. Penalva, L. O. Ivanova, P. Brown, H. A. Kristensen, B. Rich, J. Lathia, J. Brown, J. M. Hubert, C. G. 2020-09-20 doi:10.1101/2020.09.20.304964 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Multivariate GWAS elucidates the genetic architecture of alcohol consumption and misuse, corrects biases, and reveals novel associations with disease ]]> https://biorxiv.org/content/10.1101/2020.09.21.304196v1?rss=1 Mallard, T. T. Savage, J. E. Johnson, E. C. Huang, Y. Edwards, A. C. Hottenga, J. J. Grotzinger, A. D. Gustavson, D. E. Jennings, M. V. Anokhin, A. Dick, D. M. Edenberg, H. J. Kramer, J. R. Lai, D. Meyers, J. L. Pandey, A. K. Harden, K. P. Nivard, M. G. de Geus, E. J. Boomsma, D. I. Agrawal, A. Davis, L. K. Clarke, T.-K. Palmer, A. A. Sanchez-Roige, S. 2020-09-22 doi:10.1101/2020.09.21.304196 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna ]]> https://biorxiv.org/content/10.1101/2020.09.21.307181v1?rss=1 Ho, E. K. H. Bellis, E. S. Calkins, J. Adrion, J. R. Latta, L. C. Schaack, S. 2020-09-21 doi:10.1101/2020.09.21.307181 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia ]]> https://biorxiv.org/content/10.1101/2020.09.22.307728v1?rss=1 Karmeinski, D. Meusemann, K. Goodheart, J. A. Schroedl, M. Martynov, A. Korshunova, T. Wägele, H. Donath, A. 2020-09-23 doi:10.1101/2020.09.22.307728 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ RNA adenosine deaminase ADAR2 modulates T helper 17 cell effector function ]]> https://biorxiv.org/content/10.1101/2020.09.22.308221v1?rss=1 Ma, S. Cho, B. S. Li, Y. Abbasi, N. Yee, B. A. Sun, G. Luo, C. Chang, J. T. Zhou, B. Fu, X.-d. Yeo, G. W. Huang, W. J. M. 2020-09-22 doi:10.1101/2020.09.22.308221 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Functional Organization for Color Appearance Mechanisms in Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2020.09.22.309054v1?rss=1 Li, P. Garg, A. K. Zhang, L. A. Rashid, M. S. Callaway, E. M. 2020-09-23 doi:10.1101/2020.09.22.309054 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Resolving atomic site interactions of the Y. pestis outer membrane protein Ail with human serum in the bacterial cell envelope ]]> https://biorxiv.org/content/10.1101/2020.09.23.310672v1?rss=1 Kent, J. E. Fujimoto, L. M. Shn, K. Singh, C. Yao, Y. Park, S. Opella, S. J. Plano, G. V. Marassi, F. M. 2020-09-23 doi:10.1101/2020.09.23.310672 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ The quantitative metabolome is shaped by abiotic constraints ]]> https://biorxiv.org/content/10.1101/2020.09.26.315135v1?rss=1 Akbari, A. Yurkovich, J. T. Zielinski, D. C. Palsson, B. O. 2020-09-27 doi:10.1101/2020.09.26.315135 Cold Spring Harbor Laboratory Press 2020-09-27 <![CDATA[ THAP1 Modulates Oligodendrocyte Maturationby Regulating ECM Degradation in Lysosomes ]]> https://biorxiv.org/content/10.1101/2020.09.27.316133v1?rss=1 Yellajoshyula, D. Pappas, S. S. Rogers, A. Choudhury, B. Cookson, M. Reed, X. Shakkottai, V. Giger, R. Dauer, W. T. 2020-09-28 doi:10.1101/2020.09.27.316133 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Boolean Implication Analysis Improves Prediction Accuracy of In Silico Gene Reporting of Retinal Cell Types ]]> https://biorxiv.org/content/10.1101/2020.09.28.317313v1?rss=1 Subramanian, R. Sahoo, D. 2020-10-01 doi:10.1101/2020.09.28.317313 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities ]]> https://biorxiv.org/content/10.1101/2020.09.28.317438v1?rss=1 Pena Montenegro, T. D. Kleindienst, S. Allen, A. E. Eren, A. M. McCrow, J. Sanchez Calderon, J. D. Arnold, J. Joye, S. B. 2020-09-28 doi:10.1101/2020.09.28.317438 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate Promiscuity ]]> https://biorxiv.org/content/10.1101/2020.10.01.322594v1?rss=1 Bielinski, V. A. Brunson, J. K. Ghosh, A. Moosburner, M. A. Garza, E. A. Fussy, Z. Bai, J. McKinnie, S. M. K. Moore, B. Allen, A. E. Almo, S. C. Dupont, C. L. 2020-10-02 doi:10.1101/2020.10.01.322594 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Modulating the Blood-Brain Barrier by Light Stimulation of Molecular-Targeted Nanoparticles ]]> https://biorxiv.org/content/10.1101/2020.10.05.326843v1?rss=1 Li, X. Vemireddy, V. Cai, Q. Xiong, H. Kang, P. Li, X. Giannotta, M. Hayenga, H. Pan, E. Sirsi, S. Mateo, C. Kleinfeld, D. Greene, C. Campbell, M. Dejana, E. Bachoo, R. Qin, Z. 2020-10-07 doi:10.1101/2020.10.05.326843 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors ]]> https://biorxiv.org/content/10.1101/2020.10.06.323634v1?rss=1 Mor, M. Werbner, M. Alter, J. Safra, M. Chomsky, E. Hada-Neeman, S. Polonsky, K. Nowell, C. Clark, A. Roitburd-Berman, A. Ben-Shalom, N. Navon, M. Rafael, D. Sharim, H. Kiner, E. Griffis, E. Gershoni, J. M. Kobiler, O. Leibel, S. L. Zimhony, O. Carlin, A. F. Yaari, G. Dassau, M. Gal-Tanamy, M. Hagin, D. Croker, B. A. Freund, N. 2020-10-06 doi:10.1101/2020.10.06.323634 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Antinociceptive, hypothermic, and appetitive effects of vaped and injected Δ9-tetrahydrocannabinol (THC) in rats: exposure and dose-effect comparisons by strain and sex ]]> https://biorxiv.org/content/10.1101/2020.10.06.327312v1?rss=1 Moore, C. F. Davis, C. M. Harvey, E. L. Taffe, M. A. Weerts, E. M. 2020-10-08 doi:10.1101/2020.10.06.327312 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ FARCI: Fast and Robust Connectome Inference ]]> https://biorxiv.org/content/10.1101/2020.10.07.330175v1?rss=1 Meamardoost, S. Bhattacharya, M. Hwang, E. Komiyama, T. Mewes, C. K. Wang, L. Zhang, Y. Gunawan, R. 2020-10-08 doi:10.1101/2020.10.07.330175 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Thousands of previously unknown phages discovered in whole-community human gut metagenomes ]]> https://biorxiv.org/content/10.1101/2020.10.07.330464v1?rss=1 Benler, S. Yutin, N. Antipov, D. Raykov, M. Shmakov, S. A. Gussow, A. B. Pevzner, P. A. Koonin, E. V. 2020-10-07 doi:10.1101/2020.10.07.330464 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Neural network dynamics underlying gamma synchronization deficits in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.10.07.330498v1?rss=1 Koshiyama, D. Miyakoshi, M. Joshi, Y. Molina, J. Tanaka-Koshiyama, K. Sprock, J. Braff, D. Swerdlow, N. Light, G. 2020-10-09 doi:10.1101/2020.10.07.330498 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Intercellular telomere transfer extends T cell lifespan ]]> https://biorxiv.org/content/10.1101/2020.10.09.331918v1?rss=1 Vaz, B. Vuotto, C. Valvo, S. D'Ambra, C. Esposito, F. M. Chiurchiu, V. Devine, O. Sanchez, M. Borsellino, G. Gilroy, D. Akbar, A. Dustin, M. Karin, M. Lanna, A. 2020-10-09 doi:10.1101/2020.10.09.331918 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP ]]> https://biorxiv.org/content/10.1101/2020.10.11.335273v1?rss=1 Sahin, M. Wong, W. Zhan, Y. Van Deynze, K. Koche, R. Leslie, C. S. 2020-10-11 doi:10.1101/2020.10.11.335273 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ Expansion of gamma-butyrolactone signaling molecule biosynthesis to phosphotriester natural products ]]> https://biorxiv.org/content/10.1101/2020.10.11.335315v1?rss=1 Kudo, Y. Awakawa, T. Du, Y.-L. Jordan, P. A. Creamer, K. E. Jensen, P. R. Linington, R. G. Ryan, K. S. Moore, B. S. 2020-10-11 doi:10.1101/2020.10.11.335315 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ ELOVL2 is required for robust visual function in zebrafish ]]> https://biorxiv.org/content/10.1101/2020.10.13.336974v1?rss=1 Dasyani, M. Gao, F. Xu, Q. Van Fossan, D. Zhang, E. Pinto, A. F. M. Saghatelian, A. Skowronska-Krawczyk, D. Chao, D. L. 2020-10-13 doi:10.1101/2020.10.13.336974 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling ]]> https://biorxiv.org/content/10.1101/2020.10.14.340349v1?rss=1 Scott, K. Fraley, S. Rangamani, P. 2020-10-15 doi:10.1101/2020.10.14.340349 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Microbiome signatures in a fast and slow progressing gastric cancer murine model and their contribution to gastric carcinogenesis ]]> https://biorxiv.org/content/10.1101/2020.10.15.341701v1?rss=1 Bali, P. Coker, J. Pope, I. L. Zengler, K. Obonyo, M. 2020-10-15 doi:10.1101/2020.10.15.341701 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signaling-molecule diversity ]]> https://biorxiv.org/content/10.1101/2020.10.16.342204v1?rss=1 Creamer, K. E. Kudo, Y. Moore, B. S. Jensen, P. R. 2020-10-16 doi:10.1101/2020.10.16.342204 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Multivariate genomic analysis of 1.5 million people identifies genes related to addiction, antisocial behavior, and health ]]> https://biorxiv.org/content/10.1101/2020.10.16.342501v1?rss=1 Karlsson Linner, R. Mallard, T. T. Barr, P. B. Sanchez-Roige, S. Madole, J. W. Driver, M. N. Poore, H. E. Grotzinger, A. D. Tielbeek, J. J. Johnson, E. C. Liu, M. Zhou, H. Kember, R. Pasman, J. A. Verweij, K. J. H. Liu, D. Vrieze, S. Kranzler, H. Gelernter, J. Mullan Harris, K. Tucker-Drob, E. M. Waldman, I. D. Palmer, A. A. Harden, K. P. Koellinger, P. D. Dick, D. M. 2020-10-16 doi:10.1101/2020.10.16.342501 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.10.17.344002v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@1d1507aorg.highwire.dtl.DTLVardef@faa17forg.highwire.dtl.DTLVardef@80ceb1org.highwire.dtl.DTLVardef@81d61c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHuman lung organoids with mixed proximodistal epithelia are created C_LIO_LIProximal airway cells are critical for viral infectivity C_LIO_LIDistal alveolar cells are important for emulating host response C_LIO_LIBoth are required for the overzealous response in severe COVID-19 C_LI IN BRIEFAn integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19. ]]> Tindle, C. Fuller, M. Fonseca, A. Taheri, S. Ibeawuchi, S.-R. Beutler, N. Claire, A. Castillo, V. Hernandez, M. Russo, H. Duran, J. Crotty Alexander, L. E. Tipps, A. Lin, G. Thistlethwaite, P. A. Chattopadhyay, R. Rogers, T. F. Sahoo, D. Ghosh, P. Das, S. 2020-10-18 doi:10.1101/2020.10.17.344002 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Real-Time Observation of Structure and Dynamics during the Liquid-to-Solid Transition of FUS LC ]]> https://biorxiv.org/content/10.1101/2020.10.19.345710v1?rss=1 Berkeley, R. F. Kashefi, M. Debelouchina, G. T. 2020-10-19 doi:10.1101/2020.10.19.345710 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Cyclic-di-GMP induces STING-dependent ILC2 to ILC1 shift during innate type 2 lung inflammation ]]> https://biorxiv.org/content/10.1101/2020.10.19.345850v1?rss=1 Cavagnero, K. J. Doherty, T. A. Badrani, J. H. Naji, L. H. Lacasa, L. D. Strohm, A. N. Amadeo, M. B. Leng, A. S. 2020-10-19 doi:10.1101/2020.10.19.345850 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ Circadian benefits of exercise training reflect metabolic and structural flexibility ]]> https://biorxiv.org/content/10.1101/2020.10.19.346015v1?rss=1 Duglan, D. Casanova Vallve, N. Vaughan, M. E. Handzlik, M. K. Fan, W. Yu, R. Liddle, C. Downes, M. Chan, A. B. Pariollaud, M. Afetian, M. E. Metallo, C. Evans, R. Lamia, K. A. 2020-10-21 doi:10.1101/2020.10.19.346015 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis ]]> https://biorxiv.org/content/10.1101/2020.10.20.347138v1?rss=1 Gong, S. Kirmizialtin, S. Chang, A. Mayfield, J. E. Zhang, Y. Johnson, K. A. 2020-10-20 doi:10.1101/2020.10.20.347138 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Evaluation of pigmentation gene knock-outs by CRISPR as potential targets for the genetic engineering of Culex quinquefasciatus ]]> https://biorxiv.org/content/10.1101/2020.10.21.349704v1?rss=1 Feng, X. Kambic, L. Nishimoto, J. H. Reed, F. A. Denton, J. A. Sutton, J. T. Gantz, V. M. 2020-10-22 doi:10.1101/2020.10.21.349704 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Multivariate genome-wide association study identifies 1735 unique genetic loci associated with cortical morphology. ]]> https://biorxiv.org/content/10.1101/2020.10.22.350298v1?rss=1 Shadrin, A. A. Kaufmann, T. van der Meer, D. Palmer, C. E. Makowski, C. Loughnan, R. J. Jernigan, T. L. Seibert, T. M. Hagler, D. J. Smeland, O. B. Chu, Y. Lin, A. Cheng, W. Hindley, G. Thompson, W. K. Fan, C. C. Holland, D. Westlye, L. T. Frei, O. Andreassen, O. A. Dale, A. M. 2020-10-23 doi:10.1101/2020.10.22.350298 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Distributed Phase Oscillatory Excitation Efficiently Produces Attractors Using Spike Timing Dependent Plasticity ]]> https://biorxiv.org/content/10.1101/2020.10.22.351379v1?rss=1 Wong, E. C. 2020-10-23 doi:10.1101/2020.10.22.351379 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA targets sites promotes commitment of mammalian nephron progenitor cells ]]> https://biorxiv.org/content/10.1101/2020.10.26.356410v1?rss=1 Guo, Q. Kim, A. D. Li, B. Ransick, A. Bugacov, H. Chen, X. Lindstrom, N. O. Brown, A. Oxburgh, L. Ren, B. McMahon, A. P. 2020-10-27 doi:10.1101/2020.10.26.356410 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Using a betting game to reveal the rich nature of visual working memories ]]> https://biorxiv.org/content/10.1101/2020.10.28.357442v1?rss=1 Jabar, S. B. Sreenivasan, K. K. Lentzou, S. Kanabar, A. Brady, T. F. Fougnie, D. 2020-10-30 doi:10.1101/2020.10.28.357442 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Neural basis of opioid-induced respiratory depression and its rescue ]]> https://biorxiv.org/content/10.1101/2020.10.28.359893v1?rss=1 Liu, S. Kim, D.-I. Oh, T. G. Pao, G. M. Kim, J. H. Palmiter, R. D. Banghart, M. M. Lee, K.-F. Evans, R. M. Han, S. 2020-10-29 doi:10.1101/2020.10.28.359893 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Optogenetic interrogation of the role of striatal patches in habit formation and inhibition of striatal dopamine ]]> https://biorxiv.org/content/10.1101/2020.10.29.359265v1?rss=1 Nadel, J. A. Pawelko, S. S. Scott, J. R. McLaughlin, R. Fox, M. Hollon, N. G. Howard, C. D. 2020-10-29 doi:10.1101/2020.10.29.359265 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Infant functional connectivity fingerprints predict long-term language and pre-literacy outcomes ]]> https://biorxiv.org/content/10.1101/2020.10.29.360081v1?rss=1 Yu, X. Ferradal, S. Sliva, D. D. Dunstan, J. Carruthers, C. Sanfilippo, J. Zuk, J. Zollei, L. Boyd, E. Gagoski, B. Grant, E. P. Gaab, N. 2020-10-29 doi:10.1101/2020.10.29.360081 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Unsupervised Learning of Brain State Dynamics during Emotion Imagery using High-Density EEG ]]> https://biorxiv.org/content/10.1101/2020.10.29.361394v1?rss=1 Hsu, S.-H. Lin, Y. Onton, J. Jung, T.-P. Makeig, S. 2020-10-30 doi:10.1101/2020.10.29.361394 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing ]]> https://biorxiv.org/content/10.1101/2020.10.31.337758v1?rss=1 Gupta, A. Peng, S. Leung, C. Y. Borin, J. M. Weitz, J. Meyer, J. R. 2020-11-01 doi:10.1101/2020.10.31.337758 Cold Spring Harbor Laboratory Press 2020-11-01 <![CDATA[ Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance ]]> https://biorxiv.org/content/10.1101/2020.11.02.365361v1?rss=1 Borin, J. M. Avrani, S. Barrick, J. E. Petrie, K. L. Meyer, J. R. 2020-11-02 doi:10.1101/2020.11.02.365361 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ With Childhood Hemispherectomy, One Hemisphere Can Support--But is Suboptimal for--Word and Face Recognition ]]> https://biorxiv.org/content/10.1101/2020.11.06.371823v1?rss=1 Granovetter, M. C. Ettensohn, L. Behrmann, M. 2020-11-08 doi:10.1101/2020.11.06.371823 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ A plant lipocalin is required for retinal-mediated de novo root organogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.09.375444v1?rss=1 Dickinson, A. J. Zhang, J. Luciano, M. Schnermann, M. Dinneny, J. R. Benfey, P. N. 2020-11-10 doi:10.1101/2020.11.09.375444 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ A scale-free, fully connected global transition network underlies known microbiome diversity ]]> https://biorxiv.org/content/10.1101/2020.11.11.376103v1?rss=1 Jing, G. Zhang, Y. Liu, L. Wang, Z. Sun, Z. Knight, R. Su, X. Xu, J. 2020-11-11 doi:10.1101/2020.11.11.376103 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Polygenic transcriptome risk scores improve portability of polygenic risk scores across ancestries ]]> https://biorxiv.org/content/10.1101/2020.11.12.373647v1?rss=1 Liang, Y. Pividori, M. Manichaikul, A. Palmer, A. A. Cox, N. J. Wheeler, H. E. Im, H. K. 2020-11-13 doi:10.1101/2020.11.12.373647 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ MUNIn (Multiple cell-type UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple cell types ]]> https://biorxiv.org/content/10.1101/2020.11.12.380782v1?rss=1 Liu, W. Abnousi, A. Zhang, Q. Li, Y. Hu, M. Yang, Y. 2020-11-13 doi:10.1101/2020.11.12.380782 Cold Spring Harbor Laboratory Press 2020-11-13 <![CDATA[ Lipid-specific protein oligomerization is regulated by two interfaces in Marburg virus matrix protein VP40 ]]> https://biorxiv.org/content/10.1101/2020.11.13.381350v1?rss=1 Amiar, S. Husby, M. L. Wijesinghe, K. J. Angel, S. Bhattarai, N. Gerstman, B. S. Chapagain, P. P. Li, S. Stahelin, R. V. 2020-11-14 doi:10.1101/2020.11.13.381350 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ The ant fungus garden acts as an external digestive system ]]> https://biorxiv.org/content/10.1101/2020.11.18.389361v1?rss=1 Caraballo-Rodriguez, A. M. Pucket, S. P. Kyle, K. E. Petras, D. da Silva, R. R. Nothias, L.-F. Ernst, M. van der Hooft, J. J. J. Tripathi, A. Wang, M. Balunas, M. J. Klassen, J. L. Dorrestein, P. C. 2020-11-20 doi:10.1101/2020.11.18.389361 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Genetic and pharmacological manipulations of glyoxalase 1 mediate ethanol withdrawal seizure susceptibility in mice ]]> https://biorxiv.org/content/10.1101/2020.11.19.389452v1?rss=1 Barkley-Levenson, A. M. Lee, A. Palmer, A. A. 2020-11-19 doi:10.1101/2020.11.19.389452 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ EcDNA hubs drive cooperative intermolecular oncogene expression ]]> https://biorxiv.org/content/10.1101/2020.11.19.390278v1?rss=1 Hung, K. L. Yost, K. E. Xie, L. Wu, S. Lange, J. T. Duffy, C. V. Kraft, K. Tang, J. Shi, Q. Rose, J. C. Corces, M. R. Granja, J. M. Li, R. Rajkumar, U. Tjian, R. Bafna, V. Mischel, P. S. Liu, Z. Chang, H. Y. 2020-11-20 doi:10.1101/2020.11.19.390278 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A Cre-dependent CRISPR/dCas9 activation system for gene expression regulation in neurons ]]> https://biorxiv.org/content/10.1101/2020.11.20.391987v1?rss=1 Carullo, N. V. N. Revanna, J. S. Tuscher, J. J. Bauman, A. J. Day, J. J. 2020-11-20 doi:10.1101/2020.11.20.391987 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Timing the SARS-CoV-2 Index Case in Hubei Province ]]> https://biorxiv.org/content/10.1101/2020.11.20.392126v1?rss=1 Pekar, J. Worobey, M. Moshiri, N. Scheffler, K. Wertheim, J. O. 2020-11-24 doi:10.1101/2020.11.20.392126 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Inhibition of Biofilm Formation by Modified Oxylipins from the Shipworm Symbiont Teredinibacter turnerae ]]> https://biorxiv.org/content/10.1101/2020.11.22.393314v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@145f68org.highwire.dtl.DTLVardef@183df5borg.highwire.dtl.DTLVardef@bcdb6corg.highwire.dtl.DTLVardef@e9b9e3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lacerna, N. M. Ramones, C. M. V. Robes, J. M. D. Picart, M. R. D. Tun, J. O. Miller, B. W. Haygood, M. G. Schmidt, E. W. Salvador-Reyes, L. Concepcion, G. P. 2020-11-22 doi:10.1101/2020.11.22.393314 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome ]]> https://biorxiv.org/content/10.1101/2020.11.22.393546v1?rss=1 Markaki, Y. Chong, J. G. Luong, C. Tan, S. Y. X. Wang, Y. Jacobson, E. C. Maestrini, D. Dror, I. Mistry, B. A. Schoeneberg, J. Banerjee, A. Guttman, M. Chou, T. Plath, K. 2020-11-23 doi:10.1101/2020.11.22.393546 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ The anti-inflammatory peptide Catestatin blocks chemotaxis ]]> https://biorxiv.org/content/10.1101/2020.11.23.393934v1?rss=1 Muntjewerff, E. M. Parv, K. Mahata, S. K. Phillipson, M. Christoffersson, G. van den Bogaart, G. 2020-11-24 doi:10.1101/2020.11.23.393934 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ The Drosophila Baramicin polypeptide gene protects against fungal infection ]]> https://biorxiv.org/content/10.1101/2020.11.23.394148v1?rss=1 Hanson, M. A. Cohen, L. B. Marra, A. Iatsenko, I. Wasserman, S. A. Lemaitre, B. 2020-11-23 doi:10.1101/2020.11.23.394148 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Competition-based screening secures the evolutionary stability of a defensive microbiome ]]> https://biorxiv.org/content/10.1101/2020.11.24.395384v1?rss=1 Worsley, S. F. Innocent, T. M. Holmes, N. A. Al-Bassam, M. M. Wilkinson, B. Murrell, J. C. Boomsma, J. J. Yu, D. W. Hutchings, M. I. 2020-11-24 doi:10.1101/2020.11.24.395384 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Non-linear manifold learning in fMRI uncovers a low-dimensional space of brain dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.25.398693v1?rss=1 Gao, S. Mishne, G. Scheinost, D. 2020-11-27 doi:10.1101/2020.11.25.398693 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Augmenter of Liver Regeneration Regulates Cellular Iron by Modulating Mitochondrial Transport of ATP-Binding Cassette B8 ]]> https://biorxiv.org/content/10.1101/2020.11.30.403295v1?rss=1 Ardehali, H. Chang, H.-C. Shapiro, J. S. Jiang, X. Senyei, G. Sato, T. Sawicki, K. 2020-11-30 doi:10.1101/2020.11.30.403295 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ 3D Genome Contributes to Protein-Protein Interactome ]]> https://biorxiv.org/content/10.1101/2020.11.30.404517v1?rss=1 Shi, Y. Cao, S. Zhang, M. Su, X. Guo, Z. Wang, J. Liu, T. Shi, H. He, G. 2020-12-01 doi:10.1101/2020.11.30.404517 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. ]]> https://biorxiv.org/content/10.1101/2020.12.01.404483v1?rss=1 Ho, J. S. Y. Mok, B. W.-Y. Campisi, L. Jordan, T. Yildiz, S. Parameswaran, S. Wayman, J. A. Gaudreault, N. N. Meekins, D. A. Indran, S. V. Morozov, I. Trujillo, J. D. Fstkchyan, Y. S. Rathnasinghe, R. Zhu, Z. Zheng, S. Zhao, N. White, K. Ray-Jones, H. Malysheva, V. Thiecke, M. J. Lau, S.-Y. Liu, H. Zhang, A. J. Lee, A. C.-Y. Liu, W.-C. Aydillo, T. Melo, B. S. Guccione, E. Sebra, R. Shum, E. Bakker, J. Kaufman, D. A. Moreira, A. Carossino, M. Balasuriya, U. B. R. Byun, M. Miraldi, E. R. Albrecht, R. A. Schotsaert, M. Garcia-Sastre, A. Chanda, S. K. Jeya 2020-12-01 doi:10.1101/2020.12.01.404483 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ AlphaTracker: A Multi-Animal Tracking and Behavioral Analysis Tool ]]> https://biorxiv.org/content/10.1101/2020.12.04.405159v1?rss=1 Chen, Z. Zhang, R. Zhang, Y. E. Fang, H.-S. Zhou, H. Rock, R. R. Bal, A. Padilla-Coreano, N. Keyes, L. Tye, K. M. Lu, C. 2020-12-06 doi:10.1101/2020.12.04.405159 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Light-harvesting in mesophotic corals is powered by a spatially efficient photosymbiotic system between coral host and microalgae ]]> https://biorxiv.org/content/10.1101/2020.12.04.411496v1?rss=1 Kramer, N. Tamir, R. Ben-Zvi, O. Jacques, S. L. Loya, Y. Wangpraseurt, D. 2020-12-06 doi:10.1101/2020.12.04.411496 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Is it all in our head? When subjective beliefs about receiving an intervention are better predictors of experimental results than the intervention itself ]]> https://biorxiv.org/content/10.1101/2020.12.06.411850v1?rss=1 Fassi, L. Cohen Kadosh, R. 2020-12-07 doi:10.1101/2020.12.06.411850 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Universal Spectrum Identifier for mass spectra ]]> https://biorxiv.org/content/10.1101/2020.12.07.415539v1?rss=1 Deutsch, E. W. Perez-Riverol, Y. Carver, J. Kawano, S. Mendoza, L. Van Den Bossche, T. Gabriels, R. Binz, P.-A. Pullman, B. Sun, Z. Shofstahl, J. Bittremieux, W. Mak, T. Klein, J. Zhu, Y. Lam, H. Vizcaino, J. A. Bandeira, N. 2020-12-09 doi:10.1101/2020.12.07.415539 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Mechanisms for Communicating in a Marmoset "Cocktail Party" ]]> https://biorxiv.org/content/10.1101/2020.12.08.416693v1?rss=1 Jovanovic, V. Miller, C. T. 2020-12-09 doi:10.1101/2020.12.08.416693 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors ]]> https://biorxiv.org/content/10.1101/2020.12.10.416495v1?rss=1 Sam, P. Calzada, E. Acoba, M. G. Zhao, T. Watanabe, Y. Nejatfard, A. Trinidad, J. Shutt, T. Neal, S. E. Claypool, S. M. 2020-12-11 doi:10.1101/2020.12.10.416495 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Assembling Long Accurate Reads Using de Bruijn Graphs ]]> https://biorxiv.org/content/10.1101/2020.12.10.420448v1?rss=1 Bankevich, A. Bzikadze, A. V. Kolmogorov, M. Pevzner, P. 2020-12-11 doi:10.1101/2020.12.10.420448 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor ]]> https://biorxiv.org/content/10.1101/2020.12.13.422570v1?rss=1 Islam, S. M. A. Wu, Y. Diaz-Gay, M. Bergstrom, E. N. He, Y. Barnes, M. Vella, M. Wang, J. Teague, J. W. Clapham, P. Moody, S. Senkin, S. Li, Y. R. Riva, L. Zhang, T. Gruber, A. J. Vangara, R. Steele, C. D. Otlu, B. Khandekar, A. Abbasi, A. Humphreys, L. Syulyukina, N. Brady, S. W. Alexandrov, B. S. Pillay, N. Zhang, J. Adams, D. J. Marticorena, I. Wedge, D. C. Landi, M. T. Brennan, P. Stratton, M. R. Rozen, S. G. Alexandrov, L. B. 2020-12-13 doi:10.1101/2020.12.13.422570 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response ]]> https://biorxiv.org/content/10.1101/2020.12.14.422616v1?rss=1 Mishra, H. K. Ying, N. M. Luis, A. Wei, H. Nguyen, M. Nakhla, T. Vandenburgh, S. Alda, M. Berrettini, W. H. Brennand, K. J. Calabrese, J. R. Coryell, W. H. Frye, M. A. Gage, F. H. Gershon, E. S. McInnis, M. G. Nievergelt, C. M. Nurnberger, J. I. Shilling, P. D. Oedegaard, K. J. Zandi, P. P. The Pharmacogenomics of Bipolar Disorder Study, Kelsoe, J. R. Welsh, D. K. McCarthy, M. J. 2020-12-15 doi:10.1101/2020.12.14.422616 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A CRISPR endonuclease gene drive reveals two distinct mechanisms of inheritance bias ]]> https://biorxiv.org/content/10.1101/2020.12.15.421271v1?rss=1 Verkuijl, S. A. N. Gonzalez, E. Ang, J. X. D. Li, M. Kandul, N. P. Anderson, M. Akbari, O. S. Bonsall, M. Alphey, L. 2020-12-15 doi:10.1101/2020.12.15.421271 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Wild-type FUS corrects ALS-like disease induced by cytoplasmic mutant FUS through autoregulation. ]]> https://biorxiv.org/content/10.1101/2020.12.16.423060v1?rss=1 Sanjuan-Ruiz, I. Govea-Perez, N. McAlonis-Downes, M. Dieterle, S. Megat, S. Dirrig-Grosch, S. Picchiarelli, G. Piol, D. Zhu, Q. Myers, B. D. Lee, C.-Z. Cleveland, D. W. Lagier-Tourenne, C. Da Cruz, S. Dupuis, L. 2020-12-16 doi:10.1101/2020.12.16.423060 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Alternative splicing of GluN1 gates glycine-primed internalization of NMDA receptors ]]> https://biorxiv.org/content/10.1101/2020.12.18.423454v1?rss=1 Li, H. Rajani, V. Han, L. Chung, D. Cooke, J. Sengar, A. Salter, M. 2020-12-20 doi:10.1101/2020.12.18.423454 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Complex evolutionary dynamics govern the diversity and distribution of biosynthetic gene clusters and their encoded specialized metabolites ]]> https://biorxiv.org/content/10.1101/2020.12.19.423547v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@aef190org.highwire.dtl.DTLVardef@17536baorg.highwire.dtl.DTLVardef@5bf336org.highwire.dtl.DTLVardef@bc7d2f_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TEXTBOXSIGNIFICANCENatural products are traditionally exploited for their pharmaceutical potential; yet what is often overlooked is that the evolution of the biosynthetic gene clusters (BGCs) encoding these small molecules likely affects the diversification of the produced compounds and implicitly has an impact on the compounds activities and ecological functions. And while the prevailing dogma in natural product research attributes frequent and widespread horizontal gene transfer (HGT) as an integral driver of BGC evolution, we find that the majority of BGC diversity derives from processes of vertical descent, with HGT events being rare. This understanding can facilitate informed biosynthetic predictions to identify novel natural products, in addition to uncovering how these specialized metabolites contribute to the environmental distribution of microbes. C_TEXTBOX ]]> Chase, A. B. Sweeney, D. Muskat, M. N. Guillen-Matus, D. Jensen, P. R. 2020-12-20 doi:10.1101/2020.12.19.423547 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ The ENIGMA Toolbox: Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets ]]> https://biorxiv.org/content/10.1101/2020.12.21.423838v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@183a3f3org.highwire.dtl.DTLVardef@180d368org.highwire.dtl.DTLVardef@b752a3org.highwire.dtl.DTLVardef@1928c53_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lariviere, S. Paquola, C. Park, B.-y. Royer, J. Wang, Y. Benkarim, O. Vos de Wael, R. Valk, S. L. Thomopoulos, S. I. Kirschner, M. ENIGMA Consortium, Sisodiya, S. McDonald, C. Thompson, P. M. Bernhardt, B. 2020-12-22 doi:10.1101/2020.12.21.423838 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Selective Targeting of Ras Mutant Cancers via a New Small Molecule ]]> https://biorxiv.org/content/10.1101/2020.12.23.423300v1?rss=1 Tolani, B. Celli, A. Yao, Y. Tan, Y. Z. Fetter, R. Liem, C. R. de Smith, A. J. Vasanthakumar, T. Bisignano, P. Seiple, I. B. Rubinstein, J. L. Jost, M. Weissman, J. S. 2020-12-23 doi:10.1101/2020.12.23.423300 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Retracing the Evolutionary Trajectory of Adenine Base Editors Using Theoretical Approaches ]]> https://biorxiv.org/content/10.1101/2020.12.24.424366v1?rss=1 Rallapalli, K. L. Ranzau, B. L. Ganapathy, K. R. Komor, A. C. Lab, P. 2020-12-24 doi:10.1101/2020.12.24.424366 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ MHC-II constrains the natural neutralizing antibody response to the SARS-CoV-2 spike RBM in humans ]]> https://biorxiv.org/content/10.1101/2020.12.26.424449v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@d332ccorg.highwire.dtl.DTLVardef@1ac1a95org.highwire.dtl.DTLVardef@5688dorg.highwire.dtl.DTLVardef@1133d83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Castro, A. Ozturk, K. Zanetti, M. Carter, H. 2020-12-28 doi:10.1101/2020.12.26.424449 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma ]]> https://biorxiv.org/content/10.1101/2020.12.28.424451v1?rss=1 Andreano, E. Piccini, G. Licastro, D. Casalino, L. Johnson, N. V. Paciello, I. Dal Monego, S. Pantano, E. Manganaro, N. Manenti, A. Manna, R. Casa, E. Hyseni, I. Benincasa, L. Montomoli, E. Amaro, R. E. McLellan, J. S. Rappuoli, R. 2020-12-28 doi:10.1101/2020.12.28.424451 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Heterologous expression of methylxanthine synthesis enzymes in mammalian cells and their use as reporter proteins ]]> https://biorxiv.org/content/10.1101/2020.12.29.424659v1?rss=1 Cisneros, B. Devaraj, N. 2020-12-29 doi:10.1101/2020.12.29.424659 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ The structural basis for Ulp2 recruitment to the kinetochore ]]> https://biorxiv.org/content/10.1101/2020.12.30.424835v1?rss=1 Quan, Y. Hinshaw, S. M. Wang, P.-C. Harrison, S. C. Zhou, H. 2021-01-01 doi:10.1101/2020.12.30.424835 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing ]]> https://biorxiv.org/content/10.1101/2020.12.31.425022v1?rss=1 Rustici, G. Williams, E. Barzine, M. Brazma, A. Bumgarner, R. Chierici, M. Furlanello, C. Greger, L. Jurman, G. Miller, M. Ouellette, B. F. F. Quackenbush, J. Reich, M. Stoeckert, C. J. Taylor, R. C. Trutane, S. C. Weller, J. Wilhelm, B. Winegarden, N. 2021-01-03 doi:10.1101/2020.12.31.425022 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Histone H3K4me3 and H3K9me3 are super over-methylated in soft tissue sarcoma compared to normal muscle in patient-derived xenograft (PDX) mouse models: an indicator of cancer methionine addiction ]]> https://biorxiv.org/content/10.1101/2021.01.01.425040v1?rss=1 Aoki, Y. Hoffman, R. M. Nishida, K. Endo, I. Bouvet, M. Tashiro, Y. Inubushi, S. Hamada, K. Tome, Y. Yamamoto, J. 2021-01-05 doi:10.1101/2021.01.01.425040 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Comberons from single cell transcriptomics in endothelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.04.425317v1?rss=1 Domanskyi, S. Hakansson, A. Meng, M. Graff Zivin, J. S. Piermarocchi, C. Paternostro, G. Ferrara, N. 2021-01-05 doi:10.1101/2021.01.04.425317 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Simultaneous readout of multiple FRET pairs using photochromism ]]> https://biorxiv.org/content/10.1101/2021.01.06.425528v1?rss=1 Roebroek, T. Vandenberg, W. Sipieter, F. Hugelier, S. Stove, C. Zhang, J. Dedecker, P. 2021-01-06 doi:10.1101/2021.01.06.425528 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Microglial Neuropilin-1 trans-regulates oligodendrocyte expansion during development and remyelination ]]> https://biorxiv.org/content/10.1101/2021.01.07.425796v1?rss=1 Sherafat, A. Pfeiffer, F. Reiss, A. Wood, W. M. Nishiyama, A. 2021-01-07 doi:10.1101/2021.01.07.425796 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Unveiling unexpected complexity and multipotentiality of early heart fields ]]> https://biorxiv.org/content/10.1101/2021.01.08.425950v1?rss=1 Zhang, Q. Carlin, D. Zhu, F. Cattaneo, P. Ideker, T. Evans, S. Bloomekatz, J. Chi, N. C. 2021-01-09 doi:10.1101/2021.01.08.425950 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Interhemispheric connectivity endures across species: An allometric expose on the corpuscallosum ]]> https://biorxiv.org/content/10.1101/2021.01.10.426155v1?rss=1 Cipollini, B. Cottrell, G. W. 2021-01-11 doi:10.1101/2021.01.10.426155 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence ]]> https://biorxiv.org/content/10.1101/2021.01.11.426172v1?rss=1 Molina-Santiago, C. Vela-Corcia, D. Petras, D. Diaz-Martinez, L. Perez-Lorente, A. Sopena-Torres, S. Pearson, J. R. Caraballo-Rodriguez, A. M. Dorrestein, P. de Vicente, A. romero, d. 2021-01-11 doi:10.1101/2021.01.11.426172 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs ]]> https://biorxiv.org/content/10.1101/2021.01.12.426286v1?rss=1 Katrekar, D. Yen, J. Xiang, Y. Saha, A. Meluzzi, D. Savva, Y. Mali, P. 2021-01-13 doi:10.1101/2021.01.12.426286 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution ]]> https://biorxiv.org/content/10.1101/2021.01.12.426373v1?rss=1 Vrancken, B. Dellicour, S. Smith, D. M. Chaillon, A. 2021-01-13 doi:10.1101/2021.01.12.426373 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision ]]> https://biorxiv.org/content/10.1101/2021.01.13.426552v1?rss=1 Yu, L. Myers, G. Ku, C.-J. Schneider, E. Wang, Y. Singh, S. Jearawiriyapaisarn, N. White, A. Moriguchi, T. Khoriaty, R. Yamamoto, M. Rosenfeld, M. G. Pedron, J. Bushweller, J. H. Lim, K.-C. Engel, J. D. 2021-01-14 doi:10.1101/2021.01.13.426552 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ The genetic architecture of human cortical folding ]]> https://biorxiv.org/content/10.1101/2021.01.13.426555v1?rss=1 van der Meer, D. Kaufmann, T. Shadrin, A. A. Makowski, C. Frei, O. Roelfs, D. Monereo Sanchez, J. Linden, D. E. Rokicki, J. de Leeuw, C. Thompson, W. K. Loughnan, R. J. Fan, C. C. Thompson, P. M. Westlye, L. T. Andreassen, O. A. Dale, A. M. 2021-01-13 doi:10.1101/2021.01.13.426555 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion ]]> https://biorxiv.org/content/10.1101/2021.01.13.426627v1?rss=1 Schalk, F. Gostincar, C. Kreuzenbeck, N. B. Schantz-Conlon, B. Sommerwerk, E. Rabe, P. Burkhardt, I. Krüger, T. Kniemeyer, O. Brakhage, A. A. Gunde-Cimerman, N. De Beer, W. Z. Dickschat, J. S. Poulsen, M. Beemelmanns, C. 2021-01-15 doi:10.1101/2021.01.13.426627 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Dynamic molecular epidemiology reveals lineage-associated single-nucleotide variants that alter RNA structure in Chikungunya virus ]]> https://biorxiv.org/content/10.1101/2021.01.17.427002v1?rss=1 Spicher, T. Delitz, M. de Bernardi Schneider, A. Wolfinger, M. T. 2021-01-17 doi:10.1101/2021.01.17.427002 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Histone Deacetylase 2 (HDAC2) influences maturation and mitochondrial dynamics in human induced pluripotent stem cell derived neurons. ]]> https://biorxiv.org/content/10.1101/2021.01.18.427156v1?rss=1 Frankowski, H. Yeboah, F. Berry, B. Kinoshita, C. Lee, M. Evitts, K. Davis, J. Kinoshita, Y. Morrison, R. S. Young, J. E. 2021-01-18 doi:10.1101/2021.01.18.427156 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Generation and characterization of a laforin nanobody inhibitor ]]> https://biorxiv.org/content/10.1101/2021.01.20.426524v1?rss=1 Simmons, Z. R. Sharma, S. Wayne, J. Li, S. Vander Kooi, C. W. Gentry, M. S. 2021-01-20 doi:10.1101/2021.01.20.426524 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Regulation by Progestins, Corticosteroids and RU486 of Activation of Elephant Shark and Human Progesterone Receptors: An Evolutionary Perspective ]]> https://biorxiv.org/content/10.1101/2021.01.20.427507v1?rss=1 Lin, X. Takagi, W. T. Hyodo, S. Ijiri, S. Katsu, Y. K. Baker, M. E. 2021-01-21 doi:10.1101/2021.01.20.427507 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ DEPP: Deep Learning Enables Extending Species Trees using Single Genes ]]> https://biorxiv.org/content/10.1101/2021.01.22.427808v1?rss=1 Jiang, Y. Balaban, M. Zhu, Q. Mirarab, S. 2021-01-24 doi:10.1101/2021.01.22.427808 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology ]]> https://biorxiv.org/content/10.1101/2021.01.25.428167v1?rss=1 Terrey, M. Adamson, S. I. Chuang, J. H. Ackerman, S. L. 2021-01-25 doi:10.1101/2021.01.25.428167 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Discovery of an IKK2 Site that Allosterically Controls Its Activation ]]> https://biorxiv.org/content/10.1101/2021.01.27.428502v1?rss=1 Hotchkiss, S. J. Mulero, M. C. Chan, G. J. Biswas, T. Polley, S. Ohn, C. Konduri, S. Demir, O. Amaro, R. E. Ghosh, G. 2021-01-27 doi:10.1101/2021.01.27.428502 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT ]]> https://biorxiv.org/content/10.1101/2021.01.28.428636v1?rss=1 Sarmashghi, S. Balaban, M. Rachtman, E. Touri, B. Mirarab, S. Bafna, V. 2021-01-29 doi:10.1101/2021.01.28.428636 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Somatic mutational profiles and germline polygenic risk scores in human cancer ]]> https://biorxiv.org/content/10.1101/2021.01.28.428663v1?rss=1 Liu, Y. Gusev, A. Heng, Y. J. Alexandrov, L. B. Kraft, P. 2021-01-30 doi:10.1101/2021.01.28.428663 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Non-Canonical Projections from Ventral CA1 and Subicular Complex to CA3 Augments the Feedforward Hippocampal Trisynaptic Pathway ]]> https://biorxiv.org/content/10.1101/2021.02.01.429124v1?rss=1 Lin, X. Amarlraj, M. Blanton, C. Avila, B. Todd, H. Nitz, D. Xu, X. 2021-02-01 doi:10.1101/2021.02.01.429124 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ A modular platform for engineering function ofnatural and synthetic biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2021.02.03.429226v1?rss=1 Lasker, K. Boeynaems, S. Lam, V. Stainton, E. Jacquemyn, M. Daelemans, D. Villa, E. Holehouse, A. S. Gitler, A. Shapiro, L. 2021-02-03 doi:10.1101/2021.02.03.429226 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Pre-mutagenic and mutagenic changes imprinted on the genomes of mammalian cells after irradiation with a nail polish dryer ]]> https://biorxiv.org/content/10.1101/2021.02.03.429605v1?rss=1 A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of mammalian cells. These results have far-reaching implications in regard to public health and to preventing skin cancer due to consumer-based exposure to ultraviolet light from artificial sources. ]]> Zhivagui, M. Valenzuela, N. Yeh, Y.-Y. Dai, J. He, Y. Alexandrov, L. B. 2021-02-03 doi:10.1101/2021.02.03.429605 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ High fiber, whole foods dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids ]]> https://biorxiv.org/content/10.1101/2021.02.04.429869v1?rss=1 Oliver, A. Chase, A. B. Weihe, C. Orchanian, S. B. Riedel, S. F. Hendrickson, C. Lay, M. Massimelli Sewall, J. Martiny, J. B. Whiteson, K. 2021-02-05 doi:10.1101/2021.02.04.429869 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Large-scale tandem mass spectrum clustering using fast nearest neighbor searching ]]> https://biorxiv.org/content/10.1101/2021.02.05.429957v1?rss=1 Bittremieux, W. Laukens, K. Noble, W. S. Dorrestein, P. C. 2021-02-08 doi:10.1101/2021.02.05.429957 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ The role of IL-1 in adipose browning and muscle wasting in CKD-associated cachexia ]]> https://biorxiv.org/content/10.1101/2021.02.05.429984v1?rss=1 Cheung, W. W. Zheng, R. Hao, S. Wang, Z. Gonzalez, A. Zhou, P. Hoffman, H. M. Mak, R. H. 2021-02-07 doi:10.1101/2021.02.05.429984 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Targeting interleukin-1 for reversing fat browning and muscle wasting in infantile nephropathic cystinosis ]]> https://biorxiv.org/content/10.1101/2021.02.05.429989v1?rss=1 Cheung, W. W. Hao, S. Zheng, R. Wang, Z. Gonzalez, A. Zhou, P. Hoffman, H. M. Mak, R. H. 2021-02-07 doi:10.1101/2021.02.05.429989 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility ]]> https://biorxiv.org/content/10.1101/2021.02.05.429998v1?rss=1 Zou, J. Gopalakrishnan, S. Parker, C. C. Nicod, J. Mott, R. Cai, N. Lionikas, A. Davies, R. W. Palmer, A. A. Flint, J. 2021-02-07 doi:10.1101/2021.02.05.429998 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Methylomic alteration in peripheral blood lymphocytes of prodromal stage and first-episode Chinese Han schizophrenia patients ]]> https://biorxiv.org/content/10.1101/2021.02.07.430160v1?rss=1 Liu, Y. Lang, B. Smith, R. C. Wang, G. Wang, J. Liu, Y. Jin, H. Lyu, H. Davis, J. M. Guidotti, A. R. Zhao, J. Wu, R. 2021-02-09 doi:10.1101/2021.02.07.430160 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ A Human 3D neural assembloid model for SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.02.09.430349v1?rss=1 Gleeson, J. G. Wang, L. Sievert, D. Clark, A. E. Federman, H. Gastfriend, B. D. Shusta, E. Palecek, S. Carlin, A. Clark, A. E. 2021-02-09 doi:10.1101/2021.02.09.430349 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Catestatin regulates the colonic mucus layer in inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2021.02.09.430377v1?rss=1 Muntjewerff, E. Lutter, L. Tang, K. Kea-te Lindert, M. Fransen, J. Oldenburg, B. Mahata, S. K. van den Bogaart, G. 2021-02-10 doi:10.1101/2021.02.09.430377 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Customized de novo mutation detection for any variant calling pipeline: SynthDNM ]]> https://biorxiv.org/content/10.1101/2021.02.10.427198v1?rss=1 Lian, A. Guevara, J. Xia, K. Sebat, J. 2021-02-10 doi:10.1101/2021.02.10.427198 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Optimized CRISPR tools and site-directed transgenesis in Culex quinquefasciatus mosquitoes for gene drive development. ]]> https://biorxiv.org/content/10.1101/2021.02.10.430702v1?rss=1 Feng, X. Lopez Del Amo, V. Mameli, E. Lee, M. Bishop, A. L. Perrimon, N. Gantz, V. M. 2021-02-11 doi:10.1101/2021.02.10.430702 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Structure and mechanistic analyses of the gating mechanism of elongating ketosynthases ]]> https://biorxiv.org/content/10.1101/2021.02.13.431092v1?rss=1 Mindrebo, J. T. Chen, A. Kim, W. E. Re, R. N. Davis, T. D. Noel, J. P. Burkart, M. D. 2021-02-14 doi:10.1101/2021.02.13.431092 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape ]]> https://biorxiv.org/content/10.1101/2021.02.14.431043v1?rss=1 West, A. P. Barnes, C. O. Yang, Z. Bjorkman, P. J. 2021-02-15 doi:10.1101/2021.02.14.431043 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ The APOBEC3A deaminase drives episodic mutagenesis in cancer cells ]]> https://biorxiv.org/content/10.1101/2021.02.14.431145v1?rss=1 Petljak, M. Chu, K. Dananberg, A. Bergstrom, E. N. von Morgen, P. Alexandrov, L. Stratton, M. R. Maciejowski, J. 2021-02-14 doi:10.1101/2021.02.14.431145 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Dynamic association of IκBα to chromatin is regulated by acetylation and cleavage of histone H4 ]]> https://biorxiv.org/content/10.1101/2021.02.15.431217v1?rss=1 Espinosa, L. Bertran, J. Alvarez-Villanueva, D. Floor, M. Mulero, M. C. Vert, A. Guillen, Y. Arce, S. Batlle-Morera, L. Villa-Freixa, J. Ghosh, G. Bigas, A. Marruecos, L. 2021-02-16 doi:10.1101/2021.02.15.431217 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Nicotine-mediated recruitment of GABAergic neurons to a dopaminergic phenotype attenuates motor deficits in alpha-synuclein Parkinson's model. ]]> https://biorxiv.org/content/10.1101/2021.02.15.431290v1?rss=1 Lai, I.-C. Romoli, B. Keisler, M. Manfredsson, F. Powell, S. B. Dulcis, D. 2021-02-16 doi:10.1101/2021.02.15.431290 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Defining the Yeast Resistome through in vitro Evolution and Whole Genome Sequencing ]]> https://biorxiv.org/content/10.1101/2021.02.17.430112v1?rss=1 Ottilie, S. Luth, M. R. Hellemann, E. Goldgof, G. M. Vigil, E. Kumar, P. Cheung, A. L. Song, M. Godinez-Macias, K. P. Carolino, K. Yang, J. Lopez, G. Abraham, M. Tarsio, M. LeBlanc, E. Whitesell, L. Schenken, J. Gunawan, F. Patel, R. Smith, J. Love, M. S. Williams, R. M. McNamara, C. W. Gerwick, W. H. Ideker, T. Suzuki, Y. Wirth, D. F. Lukens, A. K. Kane, P. M. Cowen, L. E. Durrant, J. D. Winzeler, E. A. 2021-02-17 doi:10.1101/2021.02.17.430112 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Invariant Differential Expression Analysis Reveals Mechanism of Cancer Resistance to Cell Cycle Inhibitors ]]> https://biorxiv.org/content/10.1101/2021.02.17.431607v1?rss=1 Chatterjee, A. Pandey, S. Danda, R. Kumar R, R. S, M. Khetan, V. Rishi, P. S, R. Elchuri, S. V. Sahoo, D. 2021-02-17 doi:10.1101/2021.02.17.431607 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ A photoswitchable GPCR-based opsin for presynaptic silencing ]]> https://biorxiv.org/content/10.1101/2021.02.19.432008v1?rss=1 Copits, B. A. O'Neill, P. R. Gowrishankar, R. Yoo, J. J. Meshik, X. Parker, K. E. Spangler, S. M. Vasquez, A. M. Elerding, A. J. Stander, M. C. Kalyanaraman, V. Vogt, S. K. Samineni, V. K. Gautam, N. Sunahara, R. K. Gereau, R. W. Bruchas, M. R. 2021-02-20 doi:10.1101/2021.02.19.432008 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor ]]> https://biorxiv.org/content/10.1101/2021.02.22.432252v1?rss=1 Stoneham, C. A. Langer, S. De Jesus, P. Wozniak, J. Lapek, J. Deerinck, T. Thor, A. Pache, L. Chanda, S. Gonzalez, D. Ellisman, M. Guatelli, J. 2021-02-22 doi:10.1101/2021.02.22.432252 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees. ]]> https://biorxiv.org/content/10.1101/2021.02.27.433180v1?rss=1 Tarke, A. Sidney, J. Methot, N. Zhang, Y. Dan, J. M. Goodwin, B. Rubiro, P. Sutherland, A. da Silva Antunes, R. Fraizer, A. Rawlings, S. A. Smith, D. M. Peters, B. Scheuermann, R. H. Weiskopf, D. Crotty, S. Grifoni, A. Sette, A. 2021-03-01 doi:10.1101/2021.02.27.433180 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques ]]> https://biorxiv.org/content/10.1101/2021.02.27.433211v1?rss=1 800 genera detected across the five sites. Additionally, 39 genera were only detected using CD approaches revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in the delineation of sediment communities. This study provides important baseline data describing shallow water sediment microbial communities and evidence that standard cultivation techniques may be more effective than previously recognized. Originality-Significance StatementMarine sediments host some of the most diverse microbial communities on the planet. While these communities are critical for global nutrient cycling, the oceanic food web, and the maintenance of ecosystem dynamics, they remain poorly studied. Studies that have assessed sediment communities typically use culture-independent approaches, which have known biases and can miss ecologically important taxa. Here we describe microbial diversity in marine sediments using both culture-dependent and culture-independent approaches. Our culturing approach, sequencing communities as opposed to individual colonies, revealed an additional 39 genera that were not detected with culture-independent methods. Additionally, we cultured numerous, as-yet undescribed species, suggesting that traditional culturing practices can be more efficient than commonly thought. Moreover, our results indicate rare taxa play an important role in distinguishing microbial communities at different sites, thus highlighting the importance of deep sequencing and incorporating culture-dependent approaches for diversity assessments. ]]> Demko, A. M. Patin, N. V. Jensen, P. R. 2021-02-28 doi:10.1101/2021.02.27.433211 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning ]]> https://biorxiv.org/content/10.1101/2021.03.01.431313v1?rss=1 1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource. ]]> Greenwald, N. F. Miller, G. Moen, E. Kong, A. Kagel, A. Fullaway, C. C. McIntosh, B. J. Leow, K. Schwartz, M. S. Dougherty, T. Pavelchek, C. Cui, S. Camplisson, I. Bar-Tal, O. Singh, J. Fong, M. Chaudhry, G. Abraham, Z. Moseley, J. Warshawsky, S. Soon, E. Greenbaum, S. Risom, T. Hollmann, T. Keren, L. Graf, W. Angelo, M. Van Valen, D. 2021-03-02 doi:10.1101/2021.03.01.431313 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Taxon-specific phytoplankton growth, nutrient utilization, and light limitation in the oligotrophic Gulf of Mexico ]]> https://biorxiv.org/content/10.1101/2021.03.01.433426v1?rss=1 Yingling, N. Kelly, T. B. Shropshire, T. A. Landry, M. R. Selph, K. E. Knapp, A. N. Kranz, S. A. Stukel, M. R. 2021-03-02 doi:10.1101/2021.03.01.433426 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ When is it Worth Working for Water? A Utility Maximization Theory ]]> https://biorxiv.org/content/10.1101/2021.03.01.433467v1?rss=1 Reinagel, P. 2021-03-02 doi:10.1101/2021.03.01.433467 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naive human B cells ]]> https://biorxiv.org/content/10.1101/2021.03.01.433480v1?rss=1 Lee, J. H. Toy, L. Kos, J. T. Safonova, Y. Schief, W. R. Watson, C. T. Havenar-Daughton, C. Crotty, S. 2021-03-02 doi:10.1101/2021.03.01.433480 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Synthetic algal-bacteria consortia for space-efficient microalgal growth in a simple hydrogel system ]]> https://biorxiv.org/content/10.1101/2021.03.01.433490v1?rss=1 Martin, N. Bernat, T. Dinasquet, J. Stofko, A. Damon, A. Deheyn, D. Azam, F. Smith, J. Davey, M. P. Smith, A. G. Vignolini, S. Wangpraseurt, D. 2021-03-02 doi:10.1101/2021.03.01.433490 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Blockade of SARS-CoV-2 infection in-vitro by highly potent PI3K-α/mTOR/BRD4 inhibitor ]]> https://biorxiv.org/content/10.1101/2021.03.02.433604v1?rss=1 Acharya, A. Pandey, K. Thurman, M. Challagundla, K. B. Vann, K. R. Kutateladze, T. G. Morales, G. A. Durden, D. L. Byrareddy, S. N. 2021-03-03 doi:10.1101/2021.03.02.433604 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Slow, heterogeneous NFκB single molecule conformational dynamics and implications for function ]]> https://biorxiv.org/content/10.1101/2021.03.02.433616v1?rss=1 Chen, W. Liu, W. Wolynes, P. G. Komives, E. A. 2021-03-02 doi:10.1101/2021.03.02.433616 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Probiotic bacteria and bile acid profile are modulated by prebiotic diet and associate with facilitated diurnal clock/sleep realignment after chronic disruption of rhythms ]]> https://biorxiv.org/content/10.1101/2021.03.03.433775v1?rss=1 Thompson, R. S. Gaffney, M. K. Hopkins, S. Kelley, T. Gonzalez, A. Bowers, S. J. Vitaterna, M. H. Turek, F. W. Foxx, C. L. Lowry, C. A. Vargas, F. Dorrestein, P. C. Wright, K. P. Knight, R. Fleshner, M. 2021-03-04 doi:10.1101/2021.03.03.433775 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ BoolSim, a Graphical Interface for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling ]]> https://biorxiv.org/content/10.1101/2021.03.05.434139v1?rss=1 Karanam, A. R. He, D. Hsu, P.-K. Schulze, S. Dubeaux, G. Karmakar, R. Schroeder, J. Rappel, W.-J. 2021-03-07 doi:10.1101/2021.03.05.434139 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Nanoscale organization of Actin Filaments in the Red Blood Cell Membrane Skeleton ]]> https://biorxiv.org/content/10.1101/2021.03.07.434292v1?rss=1 Nowak, R. B. Alimohamadi, H. Pestonjamasp, K. Rangamani, P. Fowler, V. M. 2021-03-08 doi:10.1101/2021.03.07.434292 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ A novel nitrogen concentrating mechanism in the coral-algae symbiosome ]]> https://biorxiv.org/content/10.1101/2021.03.08.434475v1?rss=1 Thies, A. Quijada-Rodriguez, A. R. Zhouyao, H. Weihrauch, D. Tresguerres, M. 2021-03-09 doi:10.1101/2021.03.08.434475 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas ]]> https://biorxiv.org/content/10.1101/2021.03.09.434648v1?rss=1 Parekh, U. McDonald, D. Dailamy, A. Wu, Y. Cordes, T. Zhang, K. Tipps, A. Metallo, C. Mali, P. 2021-03-09 doi:10.1101/2021.03.09.434648 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Bayesian Multivariate Growth Mixture Modeling of Longitudinal Data: An Application to Alzheimer's Disease Study ]]> https://biorxiv.org/content/10.1101/2021.03.10.434854v1?rss=1 Lin, W. Donohue, M. C. Insel, P. Schwartzman, A. Thompson, W. K. 2021-03-12 doi:10.1101/2021.03.10.434854 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ A wild-derived antimutator drives germline mutation spectrum differences in a genetically diverse murine family ]]> https://biorxiv.org/content/10.1101/2021.03.12.435196v1?rss=1 A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily due to the activity of a C>A-dominated mutational signature known as SBS18. The B and D QTL haplotypes encode different alleles of the DNA repair gene Mutyh, which underlies the heritable colorectal cancer syndrome in which SBS18 was first identified. The B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species. ]]> Sasani, T. A. Ashbrook, D. G. Lu, L. Palmer, A. A. Williams, R. W. Pritchard, J. K. Harris, K. 2021-03-13 doi:10.1101/2021.03.12.435196 Cold Spring Harbor Laboratory Press 2021-03-13 <![CDATA[ Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. ]]> https://biorxiv.org/content/10.1101/2021.03.15.435499v1?rss=1 Blazie, S. M. Takayanagi-Kiya, S. McCulloch, K. M. Jin, Y. 2021-03-16 doi:10.1101/2021.03.15.435499 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Targeting Glioblastoma Signaling and Metabolism with A Re-Purposed Brain-Penetrant Drug ]]> https://biorxiv.org/content/10.1101/2021.03.16.435487v1?rss=1 Bi, J. Khan, A. Tang, J. Wu, S. Zhang, W. Gimple, R. C. Koga, T. Armando, A. M. Miki, S. Yang, H. Prager, B. Curtis, E. J. Wainwright, D. A. Furnari, F. B. Rich, J. N. Cloughesy, T. F. Quehenberger, O. Kornblum, H. I. Rzhetsky, A. Cravatt, B. F. Mischel, P. S. 2021-03-17 doi:10.1101/2021.03.16.435487 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ MLL3/MLL4 Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.17.435905v1?rss=1 Kubo, N. Hu, R. Ye, Z. Ren, B. 2021-03-18 doi:10.1101/2021.03.17.435905 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Assigning confidence to structural annotations from mass spectra with COSMIC ]]> https://biorxiv.org/content/10.1101/2021.03.18.435634v1?rss=1 Hoffmann, M. A. Nothias, L.-F. Ludwig, M. Fleischauer, M. Gentry, E. C. Witting, M. Dorrestein, P. C. Dührkop, K. Böcker, S. 2021-03-19 doi:10.1101/2021.03.18.435634 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Kawasaki Disease patient stratification and pathway analysis based on host transcriptomic and proteomic profiles ]]> https://biorxiv.org/content/10.1101/2021.03.18.435948v1?rss=1 Jackson, H. Menikou, S. Hamilton, S. McArdle, A. Shimizu, C. Galassini, R. Huang, H. Kim, J. Tremoulet, A. de Jonge, M. Kuijpers, T. W. Wright, V. Burns, J. Casals-Pascual, C. Herberg, J. Levin, M. Kaforou, M. The PERFORM Consortium, 2021-03-19 doi:10.1101/2021.03.18.435948 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Transcription Factor NF-κB Unravels Nucleosomes ]]> https://biorxiv.org/content/10.1101/2021.03.18.436050v1?rss=1 Stormberg, T. Filliaux, S. Baughman, H. Komives, E. Lyubchenko, Y. L. 2021-03-18 doi:10.1101/2021.03.18.436050 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ The Human Milk Oligosaccharide 3-Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice. ]]> https://biorxiv.org/content/10.1101/2021.03.19.433472v1?rss=1 Pessentheiner, A. R. Spann, N. J. Autran, C. A. Ramms, B. Chiang, A. W. T. Grunddal, K. V. Wang, Y. Quach, A. Booshehri, L. M. Hammond, A. Tognaccini, C. Latasiewicz, J. Witztum, j. L. Hoffman, H. M. Lewis, N. E. Glass, C. K. Bode, L. Gordts, P. L. S. M. 2021-03-20 doi:10.1101/2021.03.19.433472 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics ]]> https://biorxiv.org/content/10.1101/2021.03.19.436193v1?rss=1 Wu, Y. Lake, B. Sos, B. Chen, S. Duong, T. E. Yun, Y. C. Dong, W. Limaye, S. Chun, J. Zhang, K. 2021-03-19 doi:10.1101/2021.03.19.436193 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Proteome plasticity in response to persistent environmental change ]]> https://biorxiv.org/content/10.1101/2021.03.22.436511v1?rss=1 Domnauer, M. Zheng, F. Li, L. Zhang, Y. Chang, C. E. Unruh, J. Conkright-Fincham, J. McCroskey, S. Florens, L. Zhang, Y. Seidel, C. Fong, B. Schilling, B. Sharma, R. Ramanathan, A. Si, K. Zhou, C. 2021-03-22 doi:10.1101/2021.03.22.436511 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Genes identified in rodent studies of alcohol intake are enriched for heritability of human substance use ]]> https://biorxiv.org/content/10.1101/2021.03.22.436527v1?rss=1 Huggett, S. B. Johnson, E. C. Hatoum, A. S. Lai, D. Bubier, J. A. Chesler, E. C. Agrawal, A. A. Palmer, A. Edenberg, H. J. Palmer, R. H. C. 2021-03-23 doi:10.1101/2021.03.22.436527 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes ]]> https://biorxiv.org/content/10.1101/2021.03.24.436806v1?rss=1 Hempel, T. del Razo, M. J. Lee, C. T. Taylor, B. C. Amaro, R. E. Noe, F. 2021-03-25 doi:10.1101/2021.03.24.436806 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ An empirical pipeline for personalized diagnosis of Lafora disease mutations ]]> https://biorxiv.org/content/10.1101/2021.03.26.437206v1?rss=1 Brewer, M. K. Machio-Castello, M. Viana, R. Wayne, J. L. Kuchtova, A. Simmons, Z. R. Sternbach, S. Li, S. Garcia-Gimeno, M. A. Serratosa, J. Sanz, P. Vander Kooi, C. W. Gentry, M. S. 2021-03-26 doi:10.1101/2021.03.26.437206 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Single-Cell Transcriptomic Analysis of Livers During NLRP3 Inflammasome Activation Reveals a Novel Immune Niche ]]> https://biorxiv.org/content/10.1101/2021.03.31.437725v1?rss=1 Calcagno, D. M. Chu, A. Gaul, S. Taghdiri, N. Toomu, A. Leszczynska, A. Kaufmann, B. Wree, A. Geisler, L. Hoffman, H. M. Feldstein, A. E. King, K. R. 2021-03-31 doi:10.1101/2021.03.31.437725 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Acetylated α-tubulin residue K394 regulates microtubule stability to shape the growth of axon terminals ]]> https://biorxiv.org/content/10.1101/2021.04.01.438108v1?rss=1 Saunders, H. A. J. Johnson-Schlitz, D. M. Jenkins, B. V. Volkert, P. J. Yang, S. Z. Wildonger, J. 2021-04-02 doi:10.1101/2021.04.01.438108 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Anatomy and Development of the Pectoral Fin Vascular Network in the Zebrafish ]]> https://biorxiv.org/content/10.1101/2021.04.02.437283v1?rss=1 Paulissen, S. Castranova, D. M. Krispin, S. Burns, M. C. Weinstein, B. M. 2021-04-02 doi:10.1101/2021.04.02.437283 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers ]]> https://biorxiv.org/content/10.1101/2021.04.02.438263v1?rss=1 Mahapatra, A. Saintillan, D. Rangamani, P. 2021-04-04 doi:10.1101/2021.04.02.438263 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ THEM6-mediated lipid remodelling sustains stress resistance in cancer ]]> https://biorxiv.org/content/10.1101/2021.04.04.438378v1?rss=1 Blomme, A. Peter, C. Mui, E. Rodriguez Blanco, G. Mason, L. M. Jamieson, L. E. McGregor, G. H. Lilla, S. Ntala, C. Patel, R. Thiry, M. Kung, S. H. Ford, C. A. Rushworth, L. K. McGarry, D. J. Mason, S. Repiscak, P. Nixon, C. Salji, M. J. Markert, E. MacKay, G. M. Kamphorst, J. J. Graham, D. Faulds, K. Fazli, L. Gleave, M. E. Avezov, E. Edwards, J. Yin, H. Sumpton, D. Blyth, K. Close, P. Murphy, D. J. Zanivan, S. R. Leung, H. Y. 2021-04-04 doi:10.1101/2021.04.04.438378 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Cell-type specific circadian bioluminescence rhythms recorded from Dbp reporter mice reveal circadian oscillator misalignment ]]> https://biorxiv.org/content/10.1101/2021.04.04.438413v1?rss=1 Smith, C. B. van der Vinne, V. McCartney, E. Stowie, A. C. Leise, T. L. Martin-Burgos, B. Molyneux, P. C. Garbutt, L. A. Brodsky, M. H. Davidson, A. J. Harrington, M. E. Dallmann, R. Weaver, D. R. 2021-04-05 doi:10.1101/2021.04.04.438413 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity ]]> https://biorxiv.org/content/10.1101/2021.04.06.438579v1?rss=1 DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5 position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. Author SummaryThe novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein. ]]> Park, S. H. Siddiqi, H. Castro, D. De Angelis, A. Oom, A. L. Stoneham, C. Lewinski, M. Clark, A. Croker, B. Carlin, A. Guatelli, J. Opella, S. J. 2021-04-06 doi:10.1101/2021.04.06.438579 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ An AI-guided invariant signature places MIS-C with Kawasaki disease in a continuum of host immune responses ]]> https://biorxiv.org/content/10.1101/2021.04.11.439347v1?rss=1 Sahoo, D. Dattatray, G. Shimizu, C. Kim, J. Khandelwal, S. Tremoulet, A. H. Kanegaye, J. Bocchini, J. Das, S. Burns, J. C. Ghosh, P. Pediatric Emergency Medicine Kawasaki Disease Research Group, 2021-04-12 doi:10.1101/2021.04.11.439347 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Vacuole phase-partitioning boosts mitochondria activity and cell lifespan through an inter-organelle lipid pipeline ]]> https://biorxiv.org/content/10.1101/2021.04.11.439383v1?rss=1 Seo, A. Y. Sarkleti, F. Budin, I. Chang, C.-L. King, C. R. Kohlwein, S.-D. Sengupta, P. Lippincott-Schwartz, J. 2021-04-12 doi:10.1101/2021.04.11.439383 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Human Fronto-Striatal Connectivity is Organized into Discrete Functional Subnetworks ]]> https://biorxiv.org/content/10.1101/2021.04.12.439415v1?rss=1 Gordon, E. M. Laumann, T. O. Marek, S. Newbold, D. J. Hampton, J. M. Seider, N. A. Montez, D. F. Nielsen, A. M. Van, A. N. Zheng, A. Miller, R. Siegel, J. S. Kay, B. P. Snyder, A. Z. Greene, D. J. Schlaggar, B. L. Petersen, S. Nelson, S. M. Dosenbach, N. 2021-04-12 doi:10.1101/2021.04.12.439415 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Underwater dual-magnification imaging for automated lake plankton monitoring ]]> https://biorxiv.org/content/10.1101/2021.04.14.439767v1?rss=1 Merz, E. Kozakiewicz, T. Reyes, M. Ebi, C. Isles, P. Baity Jesi, M. Roberts, P. L. D. Jaffe, J. S. Dennis, S. Hardeman, R. Stevens, N. Lorimer, T. Pomati, F. 2021-04-14 doi:10.1101/2021.04.14.439767 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity ]]> https://biorxiv.org/content/10.1101/2021.04.14.439786v1?rss=1 Zhou, B. Stueve, T. R. Mihalakakos, E. Miao, L. Mullen, D. J. Wang, Y. Liu, Y. Luo, J. Tran, E. Siegmund, K. D. Lynch, S. K. Ryan, A. L. Offringa, I. A. Borok, Z. Marconett, C. N. 2021-04-15 doi:10.1101/2021.04.14.439786 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Monosodium Urate Crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response ]]> https://biorxiv.org/content/10.1101/2021.04.14.439881v1?rss=1 Cobo, I. Cheng, A. Saich, J. Coras, R. Torres, A. Lana, A. J. Schlachetzki, J. Bryan, R. Terkeltaub, R. Lopez, E. Glass, C. K. Guma, M. 2021-04-14 doi:10.1101/2021.04.14.439881 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome ]]> https://biorxiv.org/content/10.1101/2021.04.16.440249v1?rss=1 Flores Ramos, S. Brugger, S. D. Fernandez Escapa, I. Skeete, C. A. Cotton, S. L. Eslami, S. M. Gao, W. Bomar, L. Tran, T. H. Jones, D. S. Minot, S. Roberts, R. J. Johnston, C. D. Lemon, K. P. 2021-04-18 doi:10.1101/2021.04.16.440249 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses ]]> https://biorxiv.org/content/10.1101/2021.04.17.440161v1?rss=1 Lucas, T. M. Gupta, C. Altman, M. O. Sanchez, E. Naticchia, M. R. Gagneux, P. Singharoy, A. Godula, K. 2021-04-17 doi:10.1101/2021.04.17.440161 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440649v1?rss=1 Garshott, D. M. An, H. Sundaramoorthy, E. Leonard, M. Vicary, A. Harper, J. W. Bennett, E. J. 2021-04-21 doi:10.1101/2021.04.20.440649 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.04.20.440657v1?rss=1 Tewari, A. K. Cheung, A. T. M. Crowdis, J. Conway, J. R. Camp, S. Y. Wankowicz, S. A. Livitz, D. G. Park, J. Lis, R. T. Boosma-Moody, A. He, M. X. AlDubayan, S. H. Zhang, Z. McKay, R. R. Leshchiner, I. Brown, M. Balk, S. Getz, G. Taplin, M.-E. Van Allen, E. 2021-04-21 doi:10.1101/2021.04.20.440657 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Chronic Presence of Blood Circulating Anti-NMDAR1 Autoantibodies Impairs Cognitive Function in Mice ]]> https://biorxiv.org/content/10.1101/2021.04.22.440976v1?rss=1 Zhou, X. Yue, W. Caldwell, S. Risbrough, V. Powell, S. 2021-04-22 doi:10.1101/2021.04.22.440976 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Convergent, functionally independent signaling by mu and delta opioid receptors in hippocampal parvalbumin interneurons ]]> https://biorxiv.org/content/10.1101/2021.04.23.441199v1?rss=1 He, X. J. Patel, J. Weiss, C. E. Ma, X. Bloodgood, B. L. Banghart, M. R. 2021-04-24 doi:10.1101/2021.04.23.441199 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants ]]> https://biorxiv.org/content/10.1101/2021.04.24.438478v1?rss=1 Yan, C. Nayar, N. Zhao, H. Rhee, K. Lumeng, J. 2021-04-24 doi:10.1101/2021.04.24.438478 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Entropy Regularized Deconvolution of Cellular Cryo-Transmission Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2021.04.26.441469v1?rss=1 Croxford, M. Elbaum, M. Arigovindan, M. Kam, Z. Agard, D. A. Villa, E. Sedat, J. 2021-04-26 doi:10.1101/2021.04.26.441469 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Understanding double descent through the lens of principal component regression ]]> https://biorxiv.org/content/10.1101/2021.04.26.441538v1?rss=1 Lind, C. H. Yu, A. J. 2021-04-27 doi:10.1101/2021.04.26.441538 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ THC modifies the impact of heroin delivered by vapor inhalation in rats ]]> https://biorxiv.org/content/10.1101/2021.04.26.441541v1?rss=1 Gutierrez, A. Nguyen, J. D. Creehan, K. M. Javadi-Paydar, M. Grant, Y. Taffe, M. A. 2021-04-27 doi:10.1101/2021.04.26.441541 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Red blood cells protect oxygen transport with adrenergic sodium-proton exchangers in hypoxic and hypercapnic white seabass ]]> https://biorxiv.org/content/10.1101/2021.04.28.441819v1?rss=1 Harter, T. S. Clifford, A. M. Tresguerres, M. 2021-04-28 doi:10.1101/2021.04.28.441819 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Signatures of copy number alterations in human cancer ]]> https://biorxiv.org/content/10.1101/2021.04.30.441940v1?rss=1 Steele, C. D. Abbasi, A. Islam, A. S. M. Khandekar, A. Haase, K. Hames, S. Tarabichi, M. Lesluyes, T. Flanagan, A. M. Mertens, F. Van Loo, P. Alexandrov, L. B. Pillay, N. 2021-04-30 doi:10.1101/2021.04.30.441940 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression ]]> https://biorxiv.org/content/10.1101/2021.04.30.442101v1?rss=1 Rissman, R. A. Grundman, J. Spencer, B. Sarsoza, F. 2021-04-30 doi:10.1101/2021.04.30.442101 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Repeated administration of 2-hydroxypropyl-β-cyclodextrin (HPβCD) attenuates the chronic inflammatory response to experimental stroke ]]> https://biorxiv.org/content/10.1101/2021.05.03.442388v1?rss=1 Becktel, D. A. Zbesko, J. C. Frye, J. B. Chung, A. G. Hayes, M. Calderon, K. Grover, J. W. Li, A. Garcia, F. G. Tavera-Garcia, M. A. Schnellmann, R. G. Wu, H.-J. J. Nguyen, T.-V. V. Doyle, K. P. 2021-05-03 doi:10.1101/2021.05.03.442388 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Mapping the Central and Peripheral Projections of Lung Innervating Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2021.05.05.442702v1?rss=1 Su, Y. Barr, J. Jaquish, A. Xu, J. Verheyden, J. M. Sun, X. 2021-05-05 doi:10.1101/2021.05.05.442702 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Cecropins contribute to Drosophila host defense against fungal and Gram-negative bacterial infection ]]> https://biorxiv.org/content/10.1101/2021.05.06.442783v1?rss=1 Carboni, A. Hanson, M. A. Lindsay, S. A. Wasserman, S. A. Lemaitre, B. 2021-05-06 doi:10.1101/2021.05.06.442783 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Capturing the nature of events and event context using Hierarchical Event Descriptors (HED) ]]> https://biorxiv.org/content/10.1101/2021.05.06.442841v1?rss=1 Robbins, K. A. Truong, D. Appelhoff, S. Delorme, A. Makeig, S. 2021-05-07 doi:10.1101/2021.05.06.442841 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ GIV/Girdin, a Non-receptor Modulator for Gαi/s, Regulates Spatiotemporal Signaling during Sperm Capacitation and is Required for Male Fertility ]]> https://biorxiv.org/content/10.1101/2021.05.06.442927v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@f4901forg.highwire.dtl.DTLVardef@2211dforg.highwire.dtl.DTLVardef@c37ff5org.highwire.dtl.DTLVardef@105eed7_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGIV is highly expressed in spermatozoa, and is required for male fertility C_LIO_LIGIV is rapidly phosphoregulated during sperm capacitation C_LIO_LIIt enhances tyrosine-based signals in sperm tail, enhances motility C_LIO_LIIt suppresses cAMP in the sperm head, inhibits premature acrosome exocytosis C_LI ]]> Reynoso, S. Castillo, V. Katkar, G. D. Lopez-Sanchez, I. Taheri, S. Espinoza, C. R. Rohena, C. Sahoo, D. Gagneux, P. Ghosh, P. 2021-05-06 doi:10.1101/2021.05.06.442927 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ SPT6 loss Permits the Transdifferentiation of Keratinocytes into anIntestinal Fate that Recapitulates Barretts Metaplasia ]]> https://biorxiv.org/content/10.1101/2021.05.06.442930v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@8ce08aorg.highwire.dtl.DTLVardef@e98c83org.highwire.dtl.DTLVardef@107f521org.highwire.dtl.DTLVardef@16e7523_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIKeratinocytes transdifferentiate into the gut lineage upon depletion of SPT6 C_LIO_LISuch transdifferentiation recapitulates Barretts metaplasia, not the healthy gut C_LIO_LIAcid downregulates SPT6, which derails the expression and functions of TP63 C_LIO_LISuch downregulation precedes the metaplasia-dysplasia-neoplasia cascade C_LI ]]> Vo, D. Fuller, M. R. Tindle, C. Anandachar, M. Das, S. Sahoo, D. Ghosh, P. 2021-05-06 doi:10.1101/2021.05.06.442930 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Accuracy in near-perfect virus phylogenies ]]> https://biorxiv.org/content/10.1101/2021.05.06.442951v1?rss=1 Wertheim, J. O. Steel, M. Sanderson, M. J. 2021-05-06 doi:10.1101/2021.05.06.442951 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Endothelial Unc5B controls blood-brain barrier integrity ]]> https://biorxiv.org/content/10.1101/2021.05.06.442974v1?rss=1 Boye, K. Geraldo, L. H. M. furtado, J. Pibouin-fragner, L. Poulet, M. Kim, D. Nelson, B. Xu, Y. Jacob, L. Maissa, N. Tavitian, B. Agalliu, D. Claesson-Welsh, L. Ackerman, S. Eichmann, A. 2021-05-06 doi:10.1101/2021.05.06.442974 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Glycocalyx crowding with synthetic mucin mimetics strengthens interactions between soluble and virus-associated lectins and cell surface glycan receptors ]]> https://biorxiv.org/content/10.1101/2021.05.07.443169v1?rss=1 Honigfort, D. J. Altman, M. O. Gagneux, P. Godula, K. 2021-05-07 doi:10.1101/2021.05.07.443169 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ ]]> https://biorxiv.org/content/10.1101/2021.05.11.443641v1?rss=1 Nachmanson, D. Officer, A. Mori, H. Gordon, J. Evans, M. F. Steward, J. Yao, H. O'Keefe, T. Hasteh, F. Stein, G. S. Jepsen, K. Weaver, D. L. Hirst, G. Sprague, B. L. Esserman, L. J. Borowsky, A. D. Stein, J. L. Harismendy, O. 2021-05-12 doi:10.1101/2021.05.11.443641 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Serine 182 on RORγt regulates T helper 17 and regulatory T cell functions to resolve inflammation ]]> https://biorxiv.org/content/10.1101/2021.05.14.444071v1?rss=1 Ma, S. Patel, S. Chen, N. Patel, P. R. Cho, B. S. Chang, J. T. Huang, W. J. M. 2021-05-16 doi:10.1101/2021.05.14.444071 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Distinct features of brain perivascular fibroblasts and mural cells revealed by in vivo two-photon imaging ]]> https://biorxiv.org/content/10.1101/2021.05.14.444194v1?rss=1 Bonney, S. K. Sullivan, L. T. Cherry, T. J. Daneman, R. Shih, A. Y. 2021-05-17 doi:10.1101/2021.05.14.444194 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Pan-ErbB inhibition protects from SARS-CoV-2 replication, inflammation, and injury ]]> https://biorxiv.org/content/10.1101/2021.05.15.444128v1?rss=1 Saul, S. Karim, M. Huang, P. T. Ghita, L. Chiu, W. Kumar, S. Bhalla, N. Leyssen, P. Cohen, C. A. Huie, K. E. Tindle, C. Sahoo, M. K. Sibai, M. Pinsky, B. A. Das, S. Ghosh, P. Dye, J. Solow-Cordero, D. E. Jin, J. Jochmans, D. Neyts, J. Narayanan, A. De Jonghe, S. Einav, S. 2021-05-16 doi:10.1101/2021.05.15.444128 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ The autophagy initiating kinase ULK1 is required for pancreatic cancer cell growth and survival ]]> https://biorxiv.org/content/10.1101/2021.05.15.444304v1?rss=1 Shaw, R. J. Brun, S. N. Lumibao, J. Limpert, A. Ren, H. Ianniciello, A. Cosford, N. Tiriac, H. Downes, M. Evans, R. Engle, D. D. 2021-05-17 doi:10.1101/2021.05.15.444304 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Feral and managed honey bees, Apis mellifera (Hymenoptera: Apidae), in southern California have similar levels of viral pathogens ]]> https://biorxiv.org/content/10.1101/2021.05.17.444546v1?rss=1 Geffre, A. C. Travis, D. Kohn, J. Nieh, J. 2021-05-18 doi:10.1101/2021.05.17.444546 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Subcellular localization of PKA catalytic subunits provides a basis for their distinct functions in the retina ]]> https://biorxiv.org/content/10.1101/2021.05.17.444584v1?rss=1 Roa, J. N. Ma, Y. Mikulski, Z. Xu, Q. Ilouz, R. Taylor, S. S. Skowronska-Krawczyk, D. 2021-05-18 doi:10.1101/2021.05.17.444584 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Detection of Small Fiber Neuronal Activity with Optically Pumped Magnetometers ]]> https://biorxiv.org/content/10.1101/2021.05.18.444539v1?rss=1 Bu, Y. Borna, A. Schwindt, P.