bioRxiv Channel: Yale University https://biorxiv.org This feed contains articles for bioRxiv Channel "Yale University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Optimizing Real Time fMRI Neurofeedback for Therapeutic Discovery and Development ]]> https://biorxiv.org/content/10.1101/003400v1?rss=1 Luke Stoeckel Kathleen A. Garrison Satrajit S Ghosh Paul Wighton Colleen A. Hanlon Jodi M. Gilman Stephanie Greer Nicholas B. Turk-Browne Megan T. deBettencourt Dustin Scheinost Cameron Craddock Todd Thompson Vanessa Calderon Clemens C. Bauer Mark George Hans C. Breiter Susan Whitfield-Gabrieli John D. Gabrieli Stephen M. LaConte Laurence M. Hirshberg Judson A. Brewer Michelle Hampson Andre Van Der Kouwe Sean Mackey Anne E Evins 2014-03-18 doi:10.1101/003400 Cold Spring Harbor Laboratory Press 2014-03-18 <![CDATA[ Arousal and locomotion make distinct contributions to cortical activity patterns and visual encoding ]]> https://biorxiv.org/content/10.1101/010751v1?rss=1 Martin Vinck Renata Batista-Brito Ulf Knoblich Jessica A Cardin 2014-10-30 doi:10.1101/010751 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes ]]> https://biorxiv.org/content/10.1101/010884v1?rss=1 Dmitri Pervouchine Sarah Djebali Alessandra Breschi Carrie A Davis Pablo Prieto Barja Alex Dobin Andrea Tanzer Julien Lagarde Chris Zaleski Lei-Hoon See Meagan Fastuca Jorg Drenkow Huaien Wang Giovanni Bussotti Baikang Pei Suganthi Balasubramanian Jean Monlong Arif Harmanci Mark Gerstein Michael A Beer Cedric Notredame Roderic Guigo Thomas R Gingeras 2014-10-30 doi:10.1101/010884 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ Structured dynamics of neural activity across developing neocortex ]]> https://biorxiv.org/content/10.1101/012237v1?rss=1 James B Ackman Hongkui Zeng Michael C Crair 2014-12-05 doi:10.1101/012237 Cold Spring Harbor Laboratory Press 2014-12-05 <![CDATA[ Evolution of Conditional Cooperativity Between HOXA11 and FOXO1 Through Allosteric Regulation ]]> https://biorxiv.org/content/10.1101/014381v1?rss=1 Mauris C. Nnamani Soumya Ganguly Vincent J. Lynch Laura S. Mizoue Yingchun Tong Heather Darling Monika Fuxreiter Jens Meiler Gunter P. Wagner 2015-01-26 doi:10.1101/014381 Cold Spring Harbor Laboratory Press 2015-01-26 <![CDATA[ Mediated pleiotropy between psychiatric disorders and autoimmune disorders revealed by integrative analysis of multiple GWAS ]]> https://biorxiv.org/content/10.1101/014530v1?rss=1 1.4 fold) of immune-related eQTL was observed in four psychiatric disorders. Genomic regions responsible for pleiotropy between psychiatric disorders and autoimmune disorders were detected. The MHC region on chromosome 6 appears to be the most important (and it was indeed previously noted (1-3) as a confluence between schizophrenia and immune disorder risk regions), with many other regions, such as cytoband 1p13.2. We also found that most alleles shared between schizophrenia and Crohns disease have the same effect direction, with similar trend found for other disorder pairs, such as bipolar-Crohns disease. Our results offer a novel birds-eye view of the genetic relationship and demonstrate strong evidence for mediated pleiotropy between psychiatric disorders and autoimmune disorders. Our findings might open new routes for prevention and treatment strategies for these disorders based on a new appreciation of the importance of immunological mechanisms in mediating risk. ]]> Qian Wang Can Yang Joel Gelernter Hongyu Zhao 2015-01-29 doi:10.1101/014530 Cold Spring Harbor Laboratory Press 2015-01-29 <![CDATA[ Introgression obscures and reveals historical relationships among the American live oaks ]]> https://biorxiv.org/content/10.1101/016238v1?rss=1 Deren Eaton Antonio Gonzalez-Rodriguez Andrew Hipp Jeannine Cavender-Bares 2015-03-17 doi:10.1101/016238 Cold Spring Harbor Laboratory Press 2015-03-17 <![CDATA[ A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data ]]> https://biorxiv.org/content/10.1101/018093v1?rss=1 Qiongshi Lu Yiming Hu Jiehuan Sun Yuwei Cheng Kei-Hoi Cheung Hongyu Zhao 2015-04-15 doi:10.1101/018093 Cold Spring Harbor Laboratory Press 2015-04-15 <![CDATA[ Reverse-correlation analysis of navigation dynamics in Drosophila larva using optogenetics ]]> https://biorxiv.org/content/10.1101/018408v1?rss=1 Luis Hernandez-Nunez Jonas Belina Mason Klein Guangwei Si Lindsey Claus John R Carlson Aravinthan D.T. Samuel 2015-04-22 doi:10.1101/018408 Cold Spring Harbor Laboratory Press 2015-04-22 <![CDATA[ Character trees from transcriptome data: origin and individuation of morphological characters and the so-called “species signal” ]]> https://biorxiv.org/content/10.1101/019380v1?rss=1 Jacob Musser Gunter Wagner 2015-05-16 doi:10.1101/019380 Cold Spring Harbor Laboratory Press 2015-05-16 <![CDATA[ GenoWAP: Post-GWAS Prioritization Through Integrated Analysis of Genomic Functional Annotation ]]> https://biorxiv.org/content/10.1101/019539v1?rss=1 Qiongshi Lu Xinwei Yao Yiming Hu Hongyu Zhao 2015-05-20 doi:10.1101/019539 Cold Spring Harbor Laboratory Press 2015-05-20 <![CDATA[ Computing the Internode Certainty and related measures from partial gene trees. ]]> https://biorxiv.org/content/10.1101/022053v1?rss=1 Kassian Kobert Leonidas Salichos Antonis Rokas Alexandros Stamatakis 2015-07-06 doi:10.1101/022053 Cold Spring Harbor Laboratory Press 2015-07-06 <![CDATA[ Genomic and gene-expression comparisons among phage-resistant type-IV pilus mutants of Pseudomonas syringae pathovar phaseolicola ]]> https://biorxiv.org/content/10.1101/025106v1?rss=1 Mark J Sistrom Derek Park Heath O'Brien Zheng Wang David Guttman Jeffrey P. Townsend Paul Turner 2015-08-20 doi:10.1101/025106 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis ]]> https://biorxiv.org/content/10.1101/025346v1?rss=1 David Ellison Andrew Mugler Matthew Brennan Sung Hoon Lee Robert Huebner Eliah Shamir Laura A Woo Joseph Kim Patrick Amar Ilya Nemenman Andrew J Ewald Andre Levchenko 2015-08-23 doi:10.1101/025346 Cold Spring Harbor Laboratory Press 2015-08-23 <![CDATA[ Revisiting inconsistency in large pharmacogenomic studies ]]> https://biorxiv.org/content/10.1101/026153v1?rss=1 Zhaleh Safikhani Mark Freeman Petr Smirnov Nehme El-Hachem Adrian She Rene Quevedo Anna Goldenberg Nicolai Juul Birkbak Christos Hatzis Leming Shi Andrew H Beck Hugo JWL Aerts John Quackenbush Benjamin Haibe-Kains 2015-09-06 doi:10.1101/026153 Cold Spring Harbor Laboratory Press 2015-09-06 <![CDATA[ Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies ]]> https://biorxiv.org/content/10.1101/028464v1?rss=1 Qiongshi Lu Ryan Lee Powles Qian Wang Beixin Julie He Hongyu Zhao 2015-10-06 doi:10.1101/028464 Cold Spring Harbor Laboratory Press 2015-10-06 <![CDATA[ The interdependent nature of multi-loci associations can be revealed by 4C-Seq ]]> https://biorxiv.org/content/10.1101/028555v1?rss=1 Tingting Jiang Ramya Raviram Pedro P Rocha Valentina Snetkova Charlotte Proudhon Sana Badri Richard Bonneau Jane A Skok Yuval Kluger 2015-10-06 doi:10.1101/028555 Cold Spring Harbor Laboratory Press 2015-10-06 <![CDATA[ Projection-specific visual feature encoding by layer 5 cortical subnetworks. ]]> https://biorxiv.org/content/10.1101/028910v1?rss=1 Gyorgy Lur Martin Vinck Lan Tang Jessica A Cardin Michael J Higley 2015-10-13 doi:10.1101/028910 Cold Spring Harbor Laboratory Press 2015-10-13 <![CDATA[ Hydraulic conductance and the maintenance of water balance in flowers ]]> https://biorxiv.org/content/10.1101/030122v1?rss=1 Adam Roddy Craig R. Brodersen Todd E. Dawson 2015-10-28 doi:10.1101/030122 Cold Spring Harbor Laboratory Press 2015-10-28 <![CDATA[ Climate and developmental plasticity: interannual variability in grapevine leaf morphology ]]> https://biorxiv.org/content/10.1101/030957v1?rss=1 5,500 leaves representing 270 grapevines of multiple Vitis species between two growing seasons. Leaves are paired one-to-one, vine-to-vine accounting for developmental context, between growing seasons. Linear Discriminant Analysis reveals shape features that specifically define growing season, regardless of species or developmental context. The shape feature, a more pronounced distal sinus, is associated with the colder, drier growing season, consistent with patterns observed in the paleorecord. We discuss the implications of such plasticity in a long-lived woody perennial, such as grapevine, with respect to the evolution and functionality of plant morphology and changes in climate. ]]> Daniel H Chitwood Susan M Rundell Darren Y Li Quaneisha L Woodford Tommy T Yu Jose R Lopez Danny Greenblatt Julie Kang Jason P Londo 2015-11-08 doi:10.1101/030957 Cold Spring Harbor Laboratory Press 2015-11-08 <![CDATA[ Multidimensional Heritability Analysis of Neuroanatomical Shape ]]> https://biorxiv.org/content/10.1101/033407v1?rss=1 Tian Ge Martin Reuter Anderson M. Winkler Avram J. Holmes Phil H. Lee Lee S. Tirrell Joshua L. Roffman Randy L. Buckner Jordan W. Smoller Mert R. Sabuncu 2015-12-01 doi:10.1101/033407 Cold Spring Harbor Laboratory Press 2015-12-01 <![CDATA[ Flexibility in motor timing constrains the topology and dynamics of pattern generator circuits ]]> https://biorxiv.org/content/10.1101/033472v1?rss=1 Cengiz Pehlevan Farhan Ali Bence P. Olveczky 2015-12-02 doi:10.1101/033472 Cold Spring Harbor Laboratory Press 2015-12-02 <![CDATA[ Ritornello: High fidelity control-free chip-seq peak calling ]]> https://biorxiv.org/content/10.1101/034090v1?rss=1 Kelly Patrick Stanton Jiaqi Jin Sherman Morton Weissman Yuval Kluger 2015-12-10 doi:10.1101/034090 Cold Spring Harbor Laboratory Press 2015-12-10 <![CDATA[ ŌvSim: a Simulation of the Population Dynamics of Mammalian Ovarian Follicles ]]> https://biorxiv.org/content/10.1101/034249v1?rss=1 Joshua Johnson Xin Chen Xiao Xu John Emerson 2015-12-29 doi:10.1101/034249 Cold Spring Harbor Laboratory Press 2015-12-29 <![CDATA[ Polygenic risk for schizophrenia is associated with social cognition across development ]]> https://biorxiv.org/content/10.1101/034512v1?rss=1 Laura Germine Elise B Robinson Jordan W Smoller Monica E Calkins Tyler M Moore Hakon Hakonarson Mark J Daly Phil H Lee Avram J Holmes Randy L Buckner Ruben C Gur Raquel E Gur 2015-12-16 doi:10.1101/034512 Cold Spring Harbor Laboratory Press 2015-12-16 <![CDATA[ AC-PCA: simultaneous dimension reduction and adjustment for confounding variation ]]> https://biorxiv.org/content/10.1101/040485v1?rss=1 Zhixiang Lin Can Yang Ying Zhu John C. Duchi Yao Fu Yong Wang Bai Jiang Mahdi Zamanighomi Xuming Xu Mingfeng Li Nenad Sestan Hongyu Zhao Wing Hung Wong 2016-02-22 doi:10.1101/040485 Cold Spring Harbor Laboratory Press 2016-02-22 <![CDATA[ A Dendritic Disinhibitory Circuit Mechanism for Pathway-Specific Gating ]]> https://biorxiv.org/content/10.1101/041673v1?rss=1 Guangyu R Yang John D Murray Xiao-Jing Wang 2016-02-28 doi:10.1101/041673 Cold Spring Harbor Laboratory Press 2016-02-28 <![CDATA[ Glycolytic enzymes localize to synapses under energy stress to support synaptic function ]]> https://biorxiv.org/content/10.1101/042002v1?rss=1 SoRi Jang Jessica C. Nelson Eric G. Bend Lucelenie Rodríguez-Laureano Felipe G. Tueros Luis Cartagenova Katherine Underwood Erik M. Jorgensen Daniel A. Colón-Ramos 2016-03-01 doi:10.1101/042002 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Three distinct velocities of elongating RNA polymerase define exons and introns ]]> https://biorxiv.org/content/10.1101/044123v1?rss=1 Qianqian Ye Yoon Jung Kim Hongyu Zhao Tae Hoon Kim 2016-03-17 doi:10.1101/044123 Cold Spring Harbor Laboratory Press 2016-03-17 <![CDATA[ Divergence of gene regulatory network linkages during specification of ectoderm and mesoderm in early development of sea urchins ]]> https://biorxiv.org/content/10.1101/044149v1?rss=1 Eric M Erkenbrack Eric H Davidson 2016-03-16 doi:10.1101/044149 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/048058v1?rss=1 David McFadden Katerina Politi Arjun Bhutkar Frances K Chen Xiaoling Song Mono Pirun Philip M Santiago Caroline Kim James T Platt Emily Lee Emily Hodges Adam P Rosebrock Roderick Bronson Nicholas D Socci Gregory Hannon Tyler Jacks Harold Varmus 2016-04-11 doi:10.1101/048058 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ The contribution of alternative splicing probability to the coding expansion of the genome ]]> https://biorxiv.org/content/10.1101/048124v1?rss=1 Fernando Carrillo Oesterreich Hugo Bowne-Anderson Jonathon Howard 2016-04-11 doi:10.1101/048124 Cold Spring Harbor Laboratory Press 2016-04-11 <![CDATA[ Assessment of pharmacogenomic agreement ]]> https://biorxiv.org/content/10.1101/048470v1?rss=1 Zhaleh Safikhani Nehme El-Hachem Rene Quevedo Petr Smirnov Anna Goldenberg Nicolai Juul Birkbak Christopher E Mason Christos Hatzis Leming Shi Hugo JWL Aerts John Quackenbush Benjamin Haibe-Kains 2016-04-13 doi:10.1101/048470 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ Localized structural frustration for evaluating the impact of sequence variants ]]> https://biorxiv.org/content/10.1101/052027v1?rss=1 Sushant Kumar Declan Clarke Mark Gerstein 2016-05-07 doi:10.1101/052027 Cold Spring Harbor Laboratory Press 2016-05-07 <![CDATA[ DeepCyTOF: Automated Cell Classification of Mass Cytometry Data by Deep Learning and Domain Adaptation ]]> https://biorxiv.org/content/10.1101/054411v1?rss=1 Huamin Li Uri Shaham Yi Yao Ruth Montgomery Yuval Kluger 2016-05-20 doi:10.1101/054411 Cold Spring Harbor Laboratory Press 2016-05-20 <![CDATA[ Large-scale trans-eQTLs affect hundreds of transcripts and mediate patterns of transcriptional co-regulation ]]> https://biorxiv.org/content/10.1101/056283v1?rss=1 Boel Brynedal JinMyung Choi Towfique Raj Robert Bjornson Barbara Stranger Benjamin Neale Benjamin Voight Chris Cotsapas 2016-05-31 doi:10.1101/056283 Cold Spring Harbor Laboratory Press 2016-05-31 <![CDATA[ Real-time Zika risk assessment in the United States ]]> https://biorxiv.org/content/10.1101/056648v1?rss=1 Lauren A Castro Spencer J Fox Xi Chen Kai Liu Steve E Bellan Nedialko B Dimitrov Alison P Galvani Lauren A Meyers 2016-06-07 doi:10.1101/056648 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ KIF1A/UNC-104 transports ATG-9 to regulate neurodevelopment and autophagy at synapses ]]> https://biorxiv.org/content/10.1101/057166v1?rss=1 Andrea K.H. Stavoe Sarah E. Hill Daniel A. Colón-Ramos 2016-06-05 doi:10.1101/057166 Cold Spring Harbor Laboratory Press 2016-06-05 <![CDATA[ Leveraging Functional Annotations in Genetic Risk Prediction for Human Complex Diseases ]]> https://biorxiv.org/content/10.1101/058768v1?rss=1 Yiming Hu Qiongshi Lu Ryan Powles Xinwei Yao Can Yang Fang Fang Xinran Xu Hongyu Zhao 2016-06-13 doi:10.1101/058768 Cold Spring Harbor Laboratory Press 2016-06-13 <![CDATA[ The Evolutionary Trade-off between Stem Cell Niche Size, Aging, and Tumorigenesis ]]> https://biorxiv.org/content/10.1101/059279v1?rss=1 Vincent L. Cannataro Scott A. McKinley Colette M. St. Mary 2016-06-15 doi:10.1101/059279 Cold Spring Harbor Laboratory Press 2016-06-15 <![CDATA[ A phenome-wide examination of neural and cognitive function ]]> https://biorxiv.org/content/10.1101/059733v1?rss=1 Russell Poldrack Eliza Congdon William Triplett Krzysztof Gorgolewski Katherine Karlsgodt Jeanette Mumford Fred Sabb Nelson Freimer Edythe London Tyrone Cannon Robert Bilder 2016-06-19 doi:10.1101/059733 Cold Spring Harbor Laboratory Press 2016-06-19 <![CDATA[ An improved genome assembly uncovers a prolific tandem repeat structure in Atlantic cod ]]> https://biorxiv.org/content/10.1101/060921v1?rss=1 Ole K Tørresen Bastiaan Star Sissel Jentoft William Brynildsen Reinar Harald Grove Jason R Miller Brian P Walenz James Knight Jenny M Ekholm Paul Peluso Rolf B Edvardsen Ave Tooming-Klunderud Morten Skage Sigbjørn Lien Kjetill S. Jakobsen Alexander J Nederbragt 2016-06-28 doi:10.1101/060921 Cold Spring Harbor Laboratory Press 2016-06-28 <![CDATA[ Rare copy number variants in NRXN1 and CNTN6 increase risk for Tourette syndrome ]]> https://biorxiv.org/content/10.1101/062471v1?rss=1 Alden Y Huang Dongmei Yu Lea K Davis Jae-Hoon Sul Fotis Tsetsos Vasily Ramensky Ivette Zelaya Eliana Marisa Ramos Lisa Osiecki Jason A Chen Lauren M McGrath Cornelia Illmann Paul Sandor Cathy L Barr Marco Grados Harvey S Singer Markus M Noethen Johannes Hebebrand Robert A King Yves Dion Guy Rouleau Cathy L Budman Christel Depienne Yulia Worbe Andreas Hartmann Kirsten R Muller-Vahl Manfred Stuhrmann Harald Aschauer Mara Stamenkovic Monika Schloegelhofer Anastasios Konstantinidis Gholson L Lyon William M McMahon Csaba Barta Zsanett Tarnok Peter Nagy James R Batterson Renata Rizzo Danielle C Cath 2016-07-08 doi:10.1101/062471 Cold Spring Harbor Laboratory Press 2016-07-08 <![CDATA[ The mitotic spindle in the one-cell C. elegans embryo is positioned with high precision and stability ]]> https://biorxiv.org/content/10.1101/063529v1?rss=1 Jacques Pecreaux Stephanie Redemann Zahraa Alayan Benjamin Mercat Sylvain Pastezeur Carlos Garzon Coral Anthony A Hyman Jonathon Howard 2016-07-17 doi:10.1101/063529 Cold Spring Harbor Laboratory Press 2016-07-17 <![CDATA[ Divisive suppression explains high-precision firing and contrast adaptation in retinal ganglion cells ]]> https://biorxiv.org/content/10.1101/064592v1?rss=1 Yuwei Cui Yanbin V. Wang Silvia J. H. Park Jonathan B. Demb Daniel A. Butts 2016-07-19 doi:10.1101/064592 Cold Spring Harbor Laboratory Press 2016-07-19 <![CDATA[ Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy ]]> https://biorxiv.org/content/10.1101/064758v1?rss=1 Sean G Byars Qinqin Huang Lesley-Ann Gray Samuli Ripatti Gad Abraham Stephen C Stearns Michael Inouye 2016-07-19 doi:10.1101/064758 Cold Spring Harbor Laboratory Press 2016-07-19 <![CDATA[ Altered hippocampal interneuron activity precedes ictal onset ]]> https://biorxiv.org/content/10.1101/064956v1?rss=1 Mitra L Miri Martin Vinck Rima Pant Jessica A Cardin 2016-07-20 doi:10.1101/064956 Cold Spring Harbor Laboratory Press 2016-07-20 <![CDATA[ Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology ]]> https://biorxiv.org/content/10.1101/065128v1?rss=1 Ed Hall Emily Bernhardt Raven Bier Mark Bradford Claudia Boot Jim Cotner Paul del Giorgio Sarah Evans Emily Graham Stuart Jones Jay Lennon Ken Locey Diana Nemergut Brooke Osborne Jenny Rocca Josh Schimel Matt Wallenstein 2016-07-21 doi:10.1101/065128 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Global population divergence and admixture of the brown rat (Rattus norvegicus) ]]> https://biorxiv.org/content/10.1101/065458v1?rss=1 Emily Puckett Jane Park Matthew Combs Michael J Blum Juliet E Bryant Adalgisa Caccone Federico Costa Eva E Deinum Alexander Esther Chelsea G Himsworth Peter D Keightley Albert Ko Ake Lundkvist Lorraine M McElhinney Serge Morand Judith Robins James Russell Tanja M Strand Olga Suarez Lisa Yon Jason Munshi-South 2016-07-23 doi:10.1101/065458 Cold Spring Harbor Laboratory Press 2016-07-23 <![CDATA[ Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior ]]> https://biorxiv.org/content/10.1101/066035v1?rss=1 Caleb N Fischer Eric P Trautman Jason M Crawford Eric V Stabb Nichole A Broderick Jo Handelsman 2016-07-27 doi:10.1101/066035 Cold Spring Harbor Laboratory Press 2016-07-27 <![CDATA[ PathScore: a web tool for identifying altered pathways in cancer data ]]> https://biorxiv.org/content/10.1101/067090v1?rss=1 Stephen G Gaffney Jeffrey P. Townsend 2016-08-01 doi:10.1101/067090 Cold Spring Harbor Laboratory Press 2016-08-01 <![CDATA[ Direct correlation between motile behavior and protein abundance in single cells ]]> https://biorxiv.org/content/10.1101/067918v1?rss=1 Yann S Dufour Sébastien Gillet Nicholas W Frankel Douglas B Weibel Thierry Emonet 2016-08-04 doi:10.1101/067918 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli ]]> https://biorxiv.org/content/10.1101/069385v1?rss=1 Michael G Napolitano Matthieu Landon Christopher J. Gregg Marc J Lajoie Lakshmi N. Govindarajan Joshua A. Mosberg Gleb Kuznetsov Daniel B. Goodman Oscar Vargas-Rodriguez Farren J. Isaacs Dieter Söll George M. Church 2016-08-14 doi:10.1101/069385 Cold Spring Harbor Laboratory Press 2016-08-14 <![CDATA[ Pervasive concerted evolution in gene expression shapes cell type transcriptomes ]]> https://biorxiv.org/content/10.1101/070060v1?rss=1 Cong Liang Jacob M. Musser Alison Cloutier Richard Prum Gunter Wagner 2016-08-17 doi:10.1101/070060 Cold Spring Harbor Laboratory Press 2016-08-17 <![CDATA[ Activity of the C. elegans egg-laying behavior circuit is controlled by competing activation and feedback inhibition ]]> https://biorxiv.org/content/10.1101/073049v1?rss=1 Kevin Collins Addys Bode Robert W. Fernandez Jessica E. Tanis Jacob Brewer Matthew Creamer Michael R. Koelle 2016-09-01 doi:10.1101/073049 Cold Spring Harbor Laboratory Press 2016-09-01 <![CDATA[ A Whole-Brain Computational Modeling Approach to Explain the Alterations in Resting-State Functional Connectivity during Progression of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/076851v1?rss=1 Murat Demirtas Carles Falcon Juan Domingo Gispert Lopez Alan Tucholka Jose Luis Molinuevo Gustavo Deco 2016-09-22 doi:10.1101/076851 Cold Spring Harbor Laboratory Press 2016-09-22 <![CDATA[ Developmental dysfunction of VIP interneurons impairs cortical circuits ]]> https://biorxiv.org/content/10.1101/077891v1?rss=1 Renata Batista-Brito Martin Vinck Katie Ferguson David Laubender Gyorgy Lur Michael Higley Jessica A Cardin 2016-09-27 doi:10.1101/077891 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/078865v1?rss=1 Qiongshi Lu Ryan L Powles Sarah Abdallah Derek Ou Qian Wang Yiming Hu Yisi Lu Wei Liu Shubhabrata Mukherjee Paul K Crane Hongyu Zhao 2016-10-02 doi:10.1101/078865 Cold Spring Harbor Laboratory Press 2016-10-02 <![CDATA[ The Healthy Brain Network Serial Scanning Initiative: A resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions. ]]> https://biorxiv.org/content/10.1101/078881v1?rss=1 David O'Connor Natan Vega Potler Meagan Kovacs Ting Xu Lei Ai John Pellman Tamara Vanderwal Lucas Parra Samantha Cohen Satrajit Ghosh Jasmine Escalera Natalie Grant-Villegas Yael Osman Anastasia Bui Richard Cameron Craddock Michael Peter Milham 2016-10-03 doi:10.1101/078881 Cold Spring Harbor Laboratory Press 2016-10-03 <![CDATA[ Methods for detecting co-mutated pathways in cancer samples to inform treatment selection ]]> https://biorxiv.org/content/10.1101/082552v1?rss=1 Jiang, T. Shaham, U. Parisi, F. Halaban, R. Safonov, A. Kluger, H. Weissman, S. Chang, J. Kluger, Y. 2016-10-22 doi:10.1101/082552 Cold Spring Harbor Laboratory Press 2016-10-22 <![CDATA[ Individual differences in functional connectivity during naturalistic viewing conditions ]]> https://biorxiv.org/content/10.1101/084665v1?rss=1 rest was preserved. These results suggest that using dynamic stimuli such as movies enhances the detection of FC patterns that are distinct at the individual level.nnHighlightsO_LIIntra- and inter-subject FC correlations are compared across rest and movies.nC_LIO_LIMovies outperformed rest in an unsupervised identification algorithm based on FC.nC_LIO_LIMovies outperform rest regardless of parcellation, scan length, or number of edges.nC_LIO_LIWatching movies enhances the detection of individual differences in FC.nC_LI ]]> Vanderwal, T. Eilbott, J. Finn, E. S. Craddock, R. C. Turnbull, A. G. Castellanos, F. X. 2016-11-02 doi:10.1101/084665 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Exploring Anti-correlated Resting State BOLD Signals Through Dynamic Functional Connectivity and Whole-brain Computational Modeling ]]> https://biorxiv.org/content/10.1101/085274v1?rss=1 Demirtas, M. Gilson, M. Murray, J. D. Popovic, D. Vieta, E. Pintor, L. Prčkovska, V. Villoslada, P. Deco, G. 2016-11-02 doi:10.1101/085274 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates ]]> https://biorxiv.org/content/10.1101/086298v1?rss=1 Budenhagen, C. Lemmon, A. R. Lemmon, E. M. Bruhl, J. Cappa, J. Clement, W. L. Donoghue, M. Edwards, E. J. Hipp, A. L. Kortyna, M. Mitchell, N. Moore, A. Prychid, C. J. Segovia-Salcedo, M. C. Simmons, M. P. Soltis, P. S. Wanke, S. Mast, A. 2016-11-08 doi:10.1101/086298 Cold Spring Harbor Laboratory Press 2016-11-08 <![CDATA[ Rapid shift in substrate utilization driven by hypothalamic Agrp neurons ]]> https://biorxiv.org/content/10.1101/086348v1?rss=1 Cavalcanti-de-Albuquerque, J. P. Zimmer, M. R. Bober, J. Dietrich, M. O. 2016-11-07 doi:10.1101/086348 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ The NDE1 Genomic Locus Affects Treatment of Psychiatric Illness through Gene Expression Changes Related to MicroRNA-484 ]]> https://biorxiv.org/content/10.1101/087007v1?rss=1 Bradshaw, N. J. Pankakoski, M. Ukkola-Vuoti, L. Zheutlin, A. B. Ortega-Alonso, A. Torniainen-Holm, M. Sinha, V. Therman, S. Paunio, T. Suvisaari, J. Lonnqvist, J. Cannon, T. D. Haukka, J. Hennah, W. 2016-11-10 doi:10.1101/087007 Cold Spring Harbor Laboratory Press 2016-11-10 <![CDATA[ HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps ]]> https://biorxiv.org/content/10.1101/088922v1?rss=1 Yan, K.-K. Yardımcı, G. G. Noble, W. S. Gerstein, M. 2016-11-21 doi:10.1101/088922 Cold Spring Harbor Laboratory Press 2016-11-21 <![CDATA[ Age and sex affect intersubject correlation of EEGthroughout development ]]> https://biorxiv.org/content/10.1101/089060v1?rss=1 Petroni, A. Cohen, S. Langer, N. Henin, S. Vanderwal, T. Milham, M. P. Parra, L. C. 2016-11-22 doi:10.1101/089060 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Constructing high-density linkage maps with MapDisto 2.0 ]]> https://biorxiv.org/content/10.1101/089177v1?rss=1 Heffelfinger, C. Fragoso, C. A. Lorieux, M. 2016-11-22 doi:10.1101/089177 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ C. elegans detect the color of pigmented food sources to guide foraging decisions. ]]> https://biorxiv.org/content/10.1101/092072v1?rss=1 Ghosh, D. D. Jin, X. Nitabach, M. 2016-12-07 doi:10.1101/092072 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ New single-molecule imaging of the eisosome BAR domain protein Pil1p reveals filament-like dynamics ]]> https://biorxiv.org/content/10.1101/092536v1?rss=1 Lacy, M. Baddeley, D. Berro, J. 2016-12-08 doi:10.1101/092536 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Universal scaling of maximum speed with body mass - Why the largest animals are not the fastest ]]> https://biorxiv.org/content/10.1101/095018v1?rss=1 Hirt, M. Jetz, W. Rall, B. C. Brose, U. 2016-12-17 doi:10.1101/095018 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Structurally distinct oligomers of islet amyloid polypeptide mediate toxic and non-toxic membrane poration ]]> https://biorxiv.org/content/10.1101/095158v1?rss=1 100-fold difference in pore size with the large pore form correlated with mitochondrial depolarization and toxicity.nC_LIO_LIA drug-like molecule distinguishes between the two oligomer classes and rescues toxicity by stabilizing non-toxic poration without displacing IAPP from the mitochondria.nC_LIO_LIThe mechanism of pore-forming oligomer assembly includes stepwise coalescence of smaller, dynamic assemblies.nC_LI ]]> Birol, M. Kumar, S. Rhoades, E. Miranker, A. D. 2016-12-18 doi:10.1101/095158 Cold Spring Harbor Laboratory Press 2016-12-18 <![CDATA[ The DOE Systems Biology Knowledgebase (KBase) ]]> https://biorxiv.org/content/10.1101/096354v1?rss=1 Arkin, A. P. Stevens, R. L. Cottingham, R. W. Maslov, S. Henry, C. S. Dehal, P. Ware, D. Perez, F. Harris, N. L. Canon, S. Sneddon, M. W. Henderson, M. L. Riehl, W. J. Gunter, D. Murphy-Olson, D. Chan, S. Kamimura, R. T. Brettin, T. S. Meyer, F. Chivian, D. Weston, D. J. Glass, E. M. Davison, B. H. Kumari, S. Allen, B. H. Baumohl, J. Best, A. A. Bowen, B. Brenner, S. E. Bun, C. C. Chandonia, J.-M. Chia, J.-M. Colasanti, R. Conrad, N. Davis, J. J. DeJongh, M. Devoid, S. Dietrich, E. Drake, M. M. Dubchak, I. Edirisinghe, J. N. Fang, G. Faria, J. P. Fryb 2016-12-22 doi:10.1101/096354 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions ]]> https://biorxiv.org/content/10.1101/097345v1?rss=1 Yan, K.-K. Gerstein, M. 2016-12-29 doi:10.1101/097345 Cold Spring Harbor Laboratory Press 2016-12-29 <![CDATA[ Your favorite color makes learning more adaptable and precise ]]> https://biorxiv.org/content/10.1101/097741v1?rss=1 Farashahi, S. Rowe, K. Aslami, Z. Lee, D. Soltani, A. 2017-01-03 doi:10.1101/097741 Cold Spring Harbor Laboratory Press 2017-01-03 <![CDATA[ Common object representations for visual production and recognition ]]> https://biorxiv.org/content/10.1101/097840v1?rss=1 Fan, J. E. Yamins, D. L. K. Turk-Browne, N. B. 2017-01-03 doi:10.1101/097840 Cold Spring Harbor Laboratory Press 2017-01-03 <![CDATA[ Potassium channels contribute to activity-dependent scaling of dendritic inhibition ]]> https://biorxiv.org/content/10.1101/098889v1?rss=1 Chang, J. T. Higley, M. J. 2017-01-06 doi:10.1101/098889 Cold Spring Harbor Laboratory Press 2017-01-06 <![CDATA[ Effects of altered excitation-inhibition balance on decision making in a cortical circuit model ]]> https://biorxiv.org/content/10.1101/100347v1?rss=1 Lam, N. H. Borduqui, T. Hallak, J. Roque, A. C. Anticevic, A. Krystal, J. H. Wang, X.-J. Murray, J. D. 2017-01-16 doi:10.1101/100347 Cold Spring Harbor Laboratory Press 2017-01-16 <![CDATA[ Genome-wide phenotypic analysis of growth, cell morphogenesis and cellcycle events in Escherichia coli. ]]> https://biorxiv.org/content/10.1101/101832v1?rss=1 nView larger version (43K):norg.highwire.dtl.DTLVardef@63d469org.highwire.dtl.DTLVardef@e7117org.highwire.dtl.DTLVardef@22a436org.highwire.dtl.DTLVardef@4b0167_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Campos, M. Dobihal, G. S. Jacobs-Wagner, C. 2017-02-27 doi:10.1101/101832 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ Challenges for Bayesian Model Selection of Dynamic Causal Models ]]> https://biorxiv.org/content/10.1101/102293v1?rss=1 van den Honert, R. Shultz, S. Johnson, M. K. McCarthy, G. 2017-01-22 doi:10.1101/102293 Cold Spring Harbor Laboratory Press 2017-01-22 <![CDATA[ Higher genetic risk of schizophrenia is associated with lower cognitive performance in healthy individuals ]]> https://biorxiv.org/content/10.1101/103622v1?rss=1 Shafee, R. Nanda, P. Padmanabhan, J. L. Tandon, N. Alliey-Rodriguez, N. Keefe, R. S. E. Hill, S. K. Bishop, J. R. Clementz, B. A. Tamminga, C. A. Gershon, E. S. Pearlson, G. D. Keshavan, M. S. Sweeney, J. A. Robinson, E. B. McCarroll, S. A. 2017-01-27 doi:10.1101/103622 Cold Spring Harbor Laboratory Press 2017-01-27 <![CDATA[ Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics ]]> https://biorxiv.org/content/10.1101/104422v1?rss=1 Hoehna, S. Landis, M. L. Huelsenbeck, J. P. 2017-01-30 doi:10.1101/104422 Cold Spring Harbor Laboratory Press 2017-01-30 <![CDATA[ Working memory and decision making in a fronto-parietal circuit model ]]> https://biorxiv.org/content/10.1101/104802v1?rss=1 Murray, J. D. Jaramillo, J. H. Wang, X.-J. 2017-02-06 doi:10.1101/104802 Cold Spring Harbor Laboratory Press 2017-02-06 <![CDATA[ Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses ]]> https://biorxiv.org/content/10.1101/105114v1?rss=1 Singhal, S. Turner, P. 2017-02-01 doi:10.1101/105114 Cold Spring Harbor Laboratory Press 2017-02-01 <![CDATA[ Determining the impact of putative loss-of-function variants in protein-coding genes ]]> https://biorxiv.org/content/10.1101/106468v1?rss=1 6,500 cancer exomes shows that pLoF variants predicted to be deleterious by ALoFT are enriched in known driver genes. ]]> Balasubramanian, S. Fu, Y. Pawashe, M. McGillivray, P. Jin, M. Liu, J. Karczewski, K. J. MacArthur, D. G. Gerstein, M. 2017-02-07 doi:10.1101/106468 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells. ]]> https://biorxiv.org/content/10.1101/107383v1?rss=1 Ira, G. Kumar, S. Peng, X. Daley, J. Yang, L. Shen, J. Nguyen, N. Bae, G. Niu, H. Peng, Y. Hsieh, H.-J. Wang, L. Rao, C. Stephan, C. Sung, P. Peng, G. 2017-02-09 doi:10.1101/107383 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans ]]> https://biorxiv.org/content/10.1101/107987v1?rss=1 Jahanshad, N. Ganjgahi, H. Bralten, J. den Braber, A. Faskowitz, J. Knodt, A. Lemaitre, H. Nir, T. Patel, B. Richie, S. Sprooten, E. van Hulzen, K. Zavaliangos-Petropulu, A. Zwiers, M. Almasy, L. Bastin, M. Bernstein, M. Blangero, J. Curran, J. Deary, I. J. de Zubicary, G. Duggirala, R. Fisher, S. Franke, B. Fox, P. Goldman, D. Haberg, A. Hariri, A. Hong, L. E. Hoogman, M. Huentelman, M. Martin, N. Martinot, J.-L. McIntosh, A. McMahon, K. Medland, S. Mitchell, B. Munoz-Maniega, S. Olvera, R. Oosterlaan, J. Peterson, C. Royle, N. Saykin, A. Schumann, G 2017-02-20 doi:10.1101/107987 Cold Spring Harbor Laboratory Press 2017-02-20 <![CDATA[ A common haplotype lowers SPI1 (PU.1) expression in myeloid cells and delays age at onset for Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/110957v1?rss=1 Huang, K.-l. Marcora, E. Pimenova, A. Di Narzo, A. Kapoor, M. Jin, S. C. Harari, O. Bertelsen, S. Fairfax, B. Czajkowski, J. Chouraki, V. Grenier-Boley, B. Bellenguez, C. Deming, Y. McKenzie, A. Raj, T. Renton, A. Budde, J. Smith, A. Fitzpatrick, A. Bis, J. DeStefano, A. Adams, H. Ikram, M. A. van der Lee, S. Del-Aguila, J. Fernandez, M. Ibanez, L. The International Genomics of Alzheimer's Project, The Alzheimer's Disease Neuroimaging Initiative, Sims, R. Escott-Price, V. Mayeux, R. Haines, J. Farrer, L. Pericak-Vance, M. Lambert, J. C. van Duijn, C. L 2017-02-26 doi:10.1101/110957 Cold Spring Harbor Laboratory Press 2017-02-26 <![CDATA[ MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/111591v1?rss=1 van Dijk, D. Nainys, J. Sharma, R. Kathail, P. Carr, A. J. Moon, K. R. Mazutis, L. Wolf, G. Krishnaswamy, S. Pe'er, D. 2017-02-25 doi:10.1101/111591 Cold Spring Harbor Laboratory Press 2017-02-25 <![CDATA[ A powerful approach to estimating annotation-stratified genetic covariance using GWAS summary statistics ]]> https://biorxiv.org/content/10.1101/114561v1?rss=1 Lu, Q. Li, B. Ou, D. Erlendsdottir, M. Powles, R. L. Jiang, T. Hu, Y. Chang, D. Jin, C. Dai, W. He, Q. Liu, Z. Mukherjee, S. Crane, P. K. Zhao, H. 2017-03-07 doi:10.1101/114561 Cold Spring Harbor Laboratory Press 2017-03-07 <![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[ Psychiatric Genomics: An Update and an Agenda ]]> https://biorxiv.org/content/10.1101/115600v1?rss=1 Sullivan, P. F. Agrawal, A. Bulik, C. Andreassen, O. A. Borglum, A. Breen, G. Cichon, S. Edenberg, H. Faraone, S. V. Gelernter, J. Mathews, C. A. Nievergelt, C. M. Smoller, J. O'Donovan, M. Psychiatric Genomics Consortium, 2017-03-10 doi:10.1101/115600 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Combining theory, model and experiment to understand how theta rhythms are generated in thehippocampus ]]> https://biorxiv.org/content/10.1101/115949v1?rss=1 Ferguson, K. Chatzikalymniou, A. Skinner, F. 2017-03-11 doi:10.1101/115949 Cold Spring Harbor Laboratory Press 2017-03-11 <![CDATA[ DEVELOPING GENE-SPECIFIC META-PREDICTOR OF VARIANT PATHOGENICITY ]]> https://biorxiv.org/content/10.1101/115956v1?rss=1 Rychkova, A. Buu, M. C. Scharfe, C. Lefterova, M. I. Odegaard, J. I. Schrijver, I. Milla, C. Bustamante, C. D. 2017-03-10 doi:10.1101/115956 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ PHATE: A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data ]]> https://biorxiv.org/content/10.1101/120378v1?rss=1 Moon, K. R. van Dijk, D. Wang, Z. Chen, W. Hirn, M. J. Coifman, R. R. Ivanova, N. B. Wolf, G. Krishnaswamy, S. 2017-03-24 doi:10.1101/120378 Cold Spring Harbor Laboratory Press 2017-03-24 <![CDATA[ Generation And Attenuation Of Variability In A Bacterial Signalling Network Revealed By Single-Cell FRET ]]> https://biorxiv.org/content/10.1101/124008v1?rss=1 Keegstra, J. Kamino, K. Anquez, F. Lazova, M. D. Emonet, T. Shimizu, T. S. 2017-04-04 doi:10.1101/124008 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ Sex Differences In 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism In Bicyclus anynana Butterfly Wing Patterns ]]> https://biorxiv.org/content/10.1101/124834v1?rss=1 Bhardwaj, S. Prudic, K. L. Bear, A. Das Gupta, M. Wasik, B. R. Tong, X. Cheong, W. F. Wenk, M. R. Monteiro, A. 2017-04-06 doi:10.1101/124834 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Evaluation of pre-analytical factors affecting plasma DNA analysis ]]> https://biorxiv.org/content/10.1101/126839v1?rss=1 Markus, H. Contente-Cuomo, T. Liang, W. S. Borad, M. J. Sivakumar, S. Gollins, S. Tran, N. L. Dhruv, H. D. Berens, M. E. Bryce, A. Sekulic, A. Ribas, A. Trent, J. M. LoRusso, P. M. Murtaza, M. 2017-04-18 doi:10.1101/126839 Cold Spring Harbor Laboratory Press 2017-04-18 <![CDATA[ Adolescent Tuning Of Association Cortex In Human Structural Brain Networks ]]> https://biorxiv.org/content/10.1101/126920v1?rss=1 Vasa, F. Seidlitz, J. Romero-Garcia, R. Whitaker, K. J. Rosenthal, G. Vertes, P. E. Shinn, M. Alexander-Bloch, A. Fonagy, P. Dolan, R. Jones, P. Goodyer, I. The NSPN Consortium, Sporns, O. Bullmore, E. T. 2017-04-12 doi:10.1101/126920 Cold Spring Harbor Laboratory Press 2017-04-12 <![CDATA[ De novo damaging coding mutations are strongly associated with obsessive-compulsive disorder and overlap with autism ]]> https://biorxiv.org/content/10.1101/127712v1?rss=1 Cappi, C. Oliphant, M. E. Peter, Z. Zai, G. Sullivan, C. A. Gupta, A. R. Hoffman, E. J. Virdee, M. Willsey, A. J. Shavitt, R. G. Miguel, E. C. Kennedy, J. L. Richter, M. A. Fernandez, T. V. 2017-09-21 doi:10.1101/127712 Cold Spring Harbor Laboratory Press 2017-09-21 <![CDATA[ Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion ]]> https://biorxiv.org/content/10.1101/134841v1?rss=1 Briggs, A. W. Goldfless, S. J. Timberlake, S. Belmont, B. J. Clouser, C. R. Koppstein, D. Sok, D. Heiden, J. V. A. Tamminen, M. V. Kleinstein, S. H. Burton, D. R. Church, G. M. Vigneault, F. 2017-05-05 doi:10.1101/134841 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition ]]> https://biorxiv.org/content/10.1101/134874v1?rss=1 Verster, A. Ross, B. Radey, M. Bao, Y. Goodman, A. Mougous, J. Borenstein, E. 2017-05-08 doi:10.1101/134874 Cold Spring Harbor Laboratory Press 2017-05-08 <![CDATA[ High Resolution Epigenomic Atlas of Early Human Craniofacial Development ]]> https://biorxiv.org/content/10.1101/135368v1?rss=1 Wilderman, A. Kron, J. VanOudenhove, J. Noonan, J. P. Cotney, J. 2017-05-10 doi:10.1101/135368 Cold Spring Harbor Laboratory Press 2017-05-10 <![CDATA[ Local-Global Parcellation of the Human Cerebral Cortex From Intrinsic Functional Connectivity MRI ]]> https://biorxiv.org/content/10.1101/135632v1?rss=1 Schaefer, A. Kong, R. Gordon, E. M. Laumann, T. O. Zuo, X.-N. Holmes, A. Eickhoff, S. B. Yeo, B. T. T. 2017-06-06 doi:10.1101/135632 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape ]]> https://biorxiv.org/content/10.1101/137554v1?rss=1 Armstrong, D. L. McGowen, M. R. Weckle, A. Pantham, P. Caravas, J. Agnew, D. Benirschke, K. Savage-Rumbaugh, S. Nevo, E. Kim, C. J. Wagner, G. P. Romero, R. Wildman, D. E. 2017-05-12 doi:10.1101/137554 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Analysis Of Interphase Node Proteins In Fission Yeast By Quantitative And Super Resolution Fluorescence Microscopy ]]> https://biorxiv.org/content/10.1101/137794v1?rss=1 Akamatsu, M. Lin, Y. Bewersdorf, J. Pollard, T. D. 2017-05-14 doi:10.1101/137794 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ Unbiased Emission Factor Estimators For Large Scale Forest Inventories: Domain Assessment Techniques ]]> https://biorxiv.org/content/10.1101/138131v1?rss=1 Birigazzi, L. Gamarra, J. G. P. Gregoire, T. G. 2017-05-16 doi:10.1101/138131 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Disrupting Pitx1 Regulatory Topology Results In Overtly Normal Limb Development ]]> https://biorxiv.org/content/10.1101/138644v1?rss=1 Sarro, R. Emera, D. Uebbing, S. Dutrow, E. V. Weatherbee, S. D. Nottoli, T. Noonan, J. P. 2017-05-16 doi:10.1101/138644 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ Dynein Pulling Forces On Ruptured Nuclei Counteract Lamin-Mediated Nuclear Envelope Repair Mechanisms In Vivo ]]> https://biorxiv.org/content/10.1101/138693v1?rss=1 Penfield, L. Wysolmerski, B. Farhadifar, R. Martinez, M. Biggs, R. Wu, H.-Y. Mauro, M. Broberg, C. Needleman, D. Bahmanyar, S. 2017-05-17 doi:10.1101/138693 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Reviving A Lost Species: The Case Of The Floreana Galapagos Giant Tortoise Chelonoidis elephantopus ]]> https://biorxiv.org/content/10.1101/143131v1?rss=1 Miller, J. Quinzin, M. C. Poulakakis, N. Gibbs, J. P. Beheregaray, L. B. Garrick, R. C. Russello, M. A. Ciofi, C. Edwards, D. L. Hunter, E. A. Tapia, W. Rueda, D. Carrion, J. Valdivieso, A. A. Caccone, A. 2017-05-27 doi:10.1101/143131 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility ]]> https://biorxiv.org/content/10.1101/143933v1?rss=1 - International Multiple Sclerosis Genetics Consorti, Patsopoulos, N. Baranzini, S. E. Santaniello, A. Shoostari, P. Cotsapas, C. Wong, G. Beecham, A. H. James, T. Replogle, J. Vlachos, I. McCabe, C. Pers, T. Brandes, A. White, C. Keenan, B. Cimpean, M. Winn, P. Panteliadis, I.-P. Robbins, A. Andlauer, T. F. M. Zarzycki, O. Dubois, B. Goris, A. Bach Sondergaard, H. Sellebjerg, F. Soelberg Sorensen, P. Ullum, H. Wegner Thoerner, L. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Berthele, A. Biberacher, V. 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Won, H. - ADHD Working Group of the Psychiatric Genomics Con, - Early Life 2017-06-03 doi:10.1101/145581 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ Clarinet (CLA-1), a novel active zone protein required for synaptic vesicle clustering and release ]]> https://biorxiv.org/content/10.1101/145789v1?rss=1 Xuan, Z. Manning, L. Nelson, J. Richmond, J. E. Colon-Ramos, D. Shen, K. Kurshan, P. T. 2017-06-03 doi:10.1101/145789 Cold Spring Harbor Laboratory Press 2017-06-03 <![CDATA[ The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C ]]> https://biorxiv.org/content/10.1101/149724v1?rss=1 Cannataro, V. L. Gaffney, S. G. Stender, C. Zhao, Z.-M. Philips, M. Greenstein, A. Townsend, J. P. 2017-06-13 doi:10.1101/149724 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Platform for rapid nanobody discovery in vitro ]]> https://biorxiv.org/content/10.1101/151043v1?rss=1 McMahon, C. Baier, A. S. Zheng, S. Pascolutti, R. Ong, J. X. Erlandson, S. C. Hilger, D. Ring, A. M. Manglik, A. Kruse, A. C. 2017-06-16 doi:10.1101/151043 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ Punctuated evolution shaped modern vertebrate diversity ]]> https://biorxiv.org/content/10.1101/151175v1?rss=1 Landis, M. Schraiber, J. G. 2017-06-18 doi:10.1101/151175 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Gaze-stabilizing central vestibular neurons project asymmetrically to extraocular motoneuron pools ]]> https://biorxiv.org/content/10.1101/151548v1?rss=1 Schoppik, D. Bianco, I. H. Prober, D. A. Douglass, A. D. Robson, D. N. Li, J. M. B. Greenwood, J. S. F. Soucy, E. Engert, F. Schier, A. F. 2017-06-18 doi:10.1101/151548 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Persistent homology demarcates a leaf morphospace ]]> https://biorxiv.org/content/10.1101/151712v1?rss=1 Li, M. An, H. Angelovici, R. Bagaza, C. Batushansky, A. Clark, L. Coneva, V. Donoghue, M. Edwards, E. Fajardo, D. Fang, H. Frank, M. Gallaher, T. Gebken, S. Hill, T. Jansky, S. Kaur, B. Klahs, P. Klein, L. Kuraparthy, V. Londo, J. Migicovsky, Z. Miller, A. Mohn, R. Myles, S. Otoni, W. Pires, J. C. Riffer, E. Schmerler, S. Spriggs, E. Topp, C. Van Deynze, A. Zhang, K. Zhu, L. Zink, B. M. Chitwood, D. H. 2017-06-20 doi:10.1101/151712 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ WDR5 stabilizes actin architecture to promote multiciliated cell formation ]]> https://biorxiv.org/content/10.1101/153361v1?rss=1 Kulkarni, S. S. Griffin, J. N. Liem, K. F. Khokha, M. K. 2017-06-21 doi:10.1101/153361 Cold Spring Harbor Laboratory Press 2017-06-21 <![CDATA[ Direct in vivo mapping of functional suppressors in glioblastoma genome ]]> https://biorxiv.org/content/10.1101/153460v1?rss=1 Chow, R. Guzman, C. Wang, G. Schmidt, F. Youngblood, M. Ye, L. Errami, Y. Dong, M. Martinez, M. Zhang, S. Renauer, P. Bilguvar, K. Gunel, M. Sharp, P. Zhang, F. Platt, R. Chen, S. 2017-06-22 doi:10.1101/153460 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Pooled AAV-CRISPR Screen with Targeted Amplicon Sequencing ]]> https://biorxiv.org/content/10.1101/153643v1?rss=1 Wang, G. Chow, R. Ye, L. Guzman, C. Dai, X. Dong, M. Zhang, F. Sharp, P. Platt, R. Chen, S. 2017-06-22 doi:10.1101/153643 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Structural brain development: a review of methodological approaches and best practices ]]> https://biorxiv.org/content/10.1101/153718v1?rss=1 Vijayakumar, N. Mills, K. L. Alexander-Bloch, A. Tamnes, C. K. Whittle, S. 2017-06-23 doi:10.1101/153718 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells ]]> https://biorxiv.org/content/10.1101/155010v1?rss=1 Roberts, A. W. Lee, B. L. Deguine, J. John, S. Shlomchik, M. Barton, G. M. 2017-06-24 doi:10.1101/155010 Cold Spring Harbor Laboratory Press 2017-06-24 <![CDATA[ Learning Edge Rewiring in EMT from Single Cell Data ]]> https://biorxiv.org/content/10.1101/155028v1?rss=1 Krishnaswamy, S. Zivanovic, N. Sharma, R. Pe'er, D. Bodenmiller, B. 2017-06-25 doi:10.1101/155028 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ Distinct contributions of three GABAergic interneuron populations to a mouse model of Rett Syndrome. ]]> https://biorxiv.org/content/10.1101/155382v1?rss=1 Mossner, J. Batista-Brito, R. Pant, R. Cardin, J. 2017-06-25 doi:10.1101/155382 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ A comprehensive portrait of cilia and ciliopathies from a CRISPR-based screen for Hedgehog signaling ]]> https://biorxiv.org/content/10.1101/156059v1?rss=1 Breslow, D. K. Hoogendoorn, S. Kopp, A. R. Morgens, D. W. Vu, B. K. Han, K. Li, A. Hess, G. T. Bassik, M. C. Chen, J. K. Nachury, M. V. 2017-06-27 doi:10.1101/156059 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing ]]> https://biorxiv.org/content/10.1101/156125v1?rss=1 Moreno-Mateos, M. A. Fernandez, J. P. Rouet, R. Lane, M. A. Vejnar, C. E. Mis, E. Khokha, M. K. Doudna, J. A. Giraldez, A. J. 2017-06-26 doi:10.1101/156125 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Integration of plasticity mechanisms within a single sensory neuron of C. elegans actuates a memory ]]> https://biorxiv.org/content/10.1101/157958v1?rss=1 Hawk, J. D. Calvo, A. C. Almoril-Porras, A. Aljobeh, A. Torruella-Suarez, M. L. Ren, I. Cook, N. Greenwood, J. Luo, L. Samuel, A. D. T. Colon-Ramos, D. 2017-06-30 doi:10.1101/157958 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Engineering post-translational proofreading to discriminate non-standard amino acids ]]> https://biorxiv.org/content/10.1101/158246v1?rss=1 Kunjapur, A. M. Stork, D. A. Kuru, E. Vargas-Rodriguez, O. Landon, M. Söll, D. Church, G. M. 2017-06-30 doi:10.1101/158246 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes ]]> https://biorxiv.org/content/10.1101/158659v1?rss=1 Thybert, D. Roller, M. Navarro, F. C. P. Fiddes, I. Streeter, I. Feig, C. Martin-Galvez, D. Kolmogorov, M. Janousek, V. Akanni, W. Aken, B. Aldridge, S. Chakrapani, V. Chow, W. Clarke, L. Cummins, C. Doran, A. Dunn, M. Goodstadt, L. Howe, K. Howell, M. Josselin, A.-A. Karn, R. C. Laukaitis, C. M. Jingtao, L. Martin, F. Muffato, M. Quail, M. A. Sisu, C. Stanke, M. Stefflova, K. Van Oosterhout, C. Veyrunes, F. Ward, B. Yang, F. Yazdanifar, G. Zadissa, A. Adams, D. Brazma, A. Gerstein, M. Paten, B. Pham, S. Keane, T. Odom, D. T. Flicek, P. 2017-07-02 doi:10.1101/158659 Cold Spring Harbor Laboratory Press 2017-07-02 <![CDATA[ Increased risk of many early-life diseases after surgical removal of adenoids and tonsils in childhood ]]> https://biorxiv.org/content/10.1101/158691v1?rss=1 Byars, S. G. Stearns, S. C. Boomsma, J. J. 2017-07-05 doi:10.1101/158691 Cold Spring Harbor Laboratory Press 2017-07-05 <![CDATA[ Cortical area and subcortical volume mediate the effect of parental education and adverse experiences on cognitive performance in youth ]]> https://biorxiv.org/content/10.1101/160424v1?rss=1 Mehta, C. M. Malins, J. G. Noble, K. G. Gruen, J. R. 2017-07-07 doi:10.1101/160424 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ Toward leveraging big data in human functional connectomics: Generalization of brain graphs across scanners, sessions, and paradigms ]]> https://biorxiv.org/content/10.1101/160440v1?rss=1 Cao, H. McEwen, S. Bearden, C. Addington, J. Goodyear, B. Cadenhead, K. Mirzakhanian, H. Cornblatt, B. Olvet, D. Mathalon, D. McGlashan, T. Perkins, D. Belger, A. Seidman, L. Thermenos, H. Tsuang, M. van Erp, T. Walker, E. Hamann, S. Woods, S. Cannon, T. 2017-07-07 doi:10.1101/160440 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium ]]> https://biorxiv.org/content/10.1101/160499v1?rss=1 Sanders, S. J. Neale, B. M. Huang, H. Werling, D. M. An, J.-Y. Dong, S. - Whole Genome Sequencing for Psychiatric Disorders, Abecasis, G. Arguello, P. A. Blangero, J. Boehnke, M. Daly, M. Eggan, K. Geschwind, D. H. Glahn, D. Goldstein, D. B. Gur, R. E. Handsaker, R. E. McCarroll, S. A. Ophoff, R. A. Palotie, A. Pato, C. Sabatti, C. State, M. W. Willsey, A. J. Hyman, S. E. Addington, A. Lehner, T. Freimer, N. B. 2017-07-07 doi:10.1101/160499 Cold Spring Harbor Laboratory Press 2017-07-07 <![CDATA[ GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes ]]> https://biorxiv.org/content/10.1101/161208v1?rss=1 Zhu, G. Deng, W. Hu, H. Ma, R. Zhang, S. Yang, J. Peng, J. Kaplan, T. Zeng, J. 2017-07-09 doi:10.1101/161208 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA and actin filaments ]]> https://biorxiv.org/content/10.1101/164319v1?rss=1 Espinoza Sanchez, S. Metskas, L. A. Chou, S. Z. Rhoades, E. Pollard, T. D. 2017-07-16 doi:10.1101/164319 Cold Spring Harbor Laboratory Press 2017-07-16 <![CDATA[ Neural network models of the tactile system develop first-order units with spatially complex receptive fields ]]> https://biorxiv.org/content/10.1101/164954v1?rss=1 Zhao, C. W. Daley, M. J. Pruszynski, J. A. 2017-07-17 doi:10.1101/164954 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Widespread sampling biases in herbaria revealed from large-scale digitization ]]> https://biorxiv.org/content/10.1101/165480v1?rss=1 Daru, B. H. Park, D. S. Primack, R. Willis, C. G. Barrington, D. S. Whitfeld, T. J. S. Seidler, T. G. Sweeney, P. W. Foster, D. R. Ellison, A. M. Davis, C. C. 2017-07-18 doi:10.1101/165480 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Predicting eye movements from deep neural network activity decoded from fMRI responses to natural scenes ]]> https://biorxiv.org/content/10.1101/166421v1?rss=1 O'Connell, T. P. Chun, M. 2017-07-21 doi:10.1101/166421 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging ]]> https://biorxiv.org/content/10.1101/166496v1?rss=1 Petrov, D. M. Gutman, B. A. Yu, S.-H. van Erp, T. G. M. Turner, J. A. Schmaal, L. Veltman, D. Wang, L. Alpert, K. Isaev, D. Zavaliangos-Petropulu, A. Ching, C. R. K. Calhoun, V. Glahn, D. Sattertwaite, T. Andreasen, O. A. Borgwardt, S. Howells, F. Groenewold, N. Voineskos, A. Radua, J. Potkin, S. G. Crespo-Facorro, B. Tordesillas-Gutierrez, D. Shen, L. Lebedeva, I. Spalletta, G. Donohoe, G. Kochunov, P. Rosa, P. G. P. James, A. Dannlowski, U. Baune, B. T. Aleman, A. Gotlib, I. H. Walter, H. Walter, M. Soares, J. C. Gur, R. C. Doan, N. T. Agartz, I. West 2017-07-21 doi:10.1101/166496 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Schizophrenia Exhibits Bi-Directional Brain-Wide Alterations in Cortico-Striato-Cerebellar Circuits ]]> https://biorxiv.org/content/10.1101/166728v1?rss=1 Ji, J. L. Diehl, C. Schleifer, C. Pearlson, G. Yang, G. Creatura, G. Krystal, J. Repovs, G. Murray, J. D. Winkler, A. Anticevic, A. 2017-07-24 doi:10.1101/166728 Cold Spring Harbor Laboratory Press 2017-07-24 <![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[ Single-molecule force spectroscopy of protein-membrane interactions ]]> https://biorxiv.org/content/10.1101/170290v1?rss=1 Ma, L. Cai, Y. Li, Y. Jiao, J. Wu, Z. O'Shaughnessy, B. Karatekin, E. De Camilli, P. Zhang, Y. 2017-07-30 doi:10.1101/170290 Cold Spring Harbor Laboratory Press 2017-07-30 <![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[ Genome downsizing, physiological novelty, and the global dominance of flowering plants ]]> https://biorxiv.org/content/10.1101/174615v1?rss=1 Simonin, K. A. Roddy, A. B. 2017-08-10 doi:10.1101/174615 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux ]]> https://biorxiv.org/content/10.1101/175133v1?rss=1 Saffer, A. Irish, V. 2017-08-10 doi:10.1101/175133 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Performance-optimized partitioning of clonotypes from high-throughput immunoglobulin repertoire sequencing data ]]> https://biorxiv.org/content/10.1101/175315v1?rss=1 Nouri, N. Kleinstein, S. H. 2017-08-11 doi:10.1101/175315 Cold Spring Harbor Laboratory Press 2017-08-11 <![CDATA[ Common variants of NRXN1, LRP1B and RORA are associated with increased ventricular volumes in psychosis - GWAS findings from the B-SNIP deep phenotyping study ]]> https://biorxiv.org/content/10.1101/175489v1?rss=1 Alliey-Rodriguez, N. Grey, T. A. Shafee, R. Padmanabhan, J. Tandon, N. Klinger, M. Spring, J. Coppes, L. Reis, K. Keshavan, M. S. Gage, D. McCarroll, S. Bishop, J. R. Hill, S. Reilly, J. Lencer, R. Clementz, B. Buckley, P. Meda, S. Narayanan, B. Glahn, D. Pearlson, G. Ivleva, E. Tamminga, C. Sweeney, J. Curtis, D. Keedy, S. Badner, J. Liu, C. Gershon, E. S. 2017-08-11 doi:10.1101/175489 Cold Spring Harbor Laboratory Press 2017-08-11 <![CDATA[ Ninety-nine independent genetic loci influencing general cognitive function include genes associated with brain health and structure (N = 280,360) ]]> https://biorxiv.org/content/10.1101/176511v1?rss=1 Davies, G. Lam, M. Harris, S. E. Trampush, J. Luciano, M. Hill, W. D. Hagenaars, S. P. Ritchie, S. J. Marioni, R. E. Fawns-Ritchie, C. Liewald, D. C. Okely, J. Ahola-Olli, A. Barnes, C. L. K. Bertram, L. Bis, J. C. Burdick, K. E. Christoforou, A. DeRosse, P. Djurovic, S. Espeseth, T. Giakoumaki, S. Giddaluru, S. Gustavson, D. E. Hayward, C. Hofer, E. Ikram, M. A. Karlsson, R. Knowles, E. Lahti, J. Leber, M. Li, S. Mather, K. A. Melle, I. Morris, D. Oldmeadow, C. Palviainen, T. Payton, A. Pazoki, R. Petrovic, K. Reynolds, C. A. Sargurupremraj, M. Scholz 2017-08-17 doi:10.1101/176511 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Large-Scale cognitive GWAS Meta-analysis Reveals Tissue-Specific Neural Expression and Potential Nootopic Drug Targets ]]> https://biorxiv.org/content/10.1101/176842v1?rss=1 Lam, M. Trampush, J. W. Yu, J. Knowles, E. Davies, G. Liewald, D. C. Starr, J. M. Djurovic, S. Melle, I. Sundet, K. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. J. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Attix, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. C. Avramopoulos, D. Hatzimanolis, A. Arking, D. E. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, T. D. London, E. Poldrack, R. A. 2017-08-16 doi:10.1101/176842 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ A minimal RNA ligand for potent RIG-I activation in living mice ]]> https://biorxiv.org/content/10.1101/178343v1?rss=1 Linehan, M. M. Dickey, T. H. Molinari, E. S. Fitzgerald, M. E. Potapova, O. Iwasaki, A. Pyle, A. M. 2017-08-19 doi:10.1101/178343 Cold Spring Harbor Laboratory Press 2017-08-19 <![CDATA[ Fast and Powerful Genome Wide Association Analysis of Dense Genetic Data with High Dimensional Imaging Phenotypes ]]> https://biorxiv.org/content/10.1101/179150v1?rss=1 Ganjgahi, H. Winkler, A. M. Glahn, D. C. Blangero, J. Donohue, B. Kochunov, P. Nichols, T. E. 2017-08-21 doi:10.1101/179150 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ Progressive reconfiguration of resting-state brain networks as psychosis develops: Preliminary results from the North American Prodrome Longitudinal Study (NAPLS) consortium ]]> https://biorxiv.org/content/10.1101/179242v1?rss=1 Cao, H. Chung, Y. McEwen, S. Bearden, C. Addington, J. Goodyear, B. Cadenhead, K. Mirzakhanian, H. Cornblatt, B. Olvet, D. Mathalon, D. McGlashan, T. Perkins, D. Belger, A. Seidman, L. Thermenos, H. Tsuang, M. van Erp, T. Walker, E. Hamann, S. Anticevic, A. Woods, S. Cannon, T. 2017-08-21 doi:10.1101/179242 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours ]]> https://biorxiv.org/content/10.1101/179705v1?rss=1 Rodriguez-Martin, B. Alvarez, E. G. Baez-Ortega, A. Demeulemeester, J. Ju, Y. S. Zamora, J. Detering, H. Li, Y. Contino, G. Dentro, S. C. Bruzos, A. L. Dueso-Barroso, A. Ardeljan, D. Tojo, M. Roberts, N. D. Blanco, M. G. Edwards, P. A. W. Weischenfeldt, J. Santamarina, M. Puiggros, M. Chong, Z. Chen, K. Lee, E. A. Wala, J. A. Raine, K. Butler, A. Waszak, S. M. Navarro, F. C. P. Schumacher, S. E. Monlong, J. Maura, F. Bolli, N. Bourque, G. Gerstein, M. Park, P. J. Berroukhim, R. Torrents, D. Korbel, J. O. Martincorena, I. Fitzgerald, R. C. Van Loo, P. Ka 2017-08-24 doi:10.1101/179705 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Seamless Multiscale Modeling of Coagulation Using Dissipative Particle Dynamics ]]> https://biorxiv.org/content/10.1101/181099v1?rss=1 Yazdani, A. Li, Z. Humphrey, J. Karniadakis, G. 2017-08-26 doi:10.1101/181099 Cold Spring Harbor Laboratory Press 2017-08-26 <![CDATA[ Local and global chromatin interactions are altered by large genomic deletions associated with human brain development ]]> https://biorxiv.org/content/10.1101/182451v1?rss=1 Zhang, Y. Zhang, X. Zhu, X. Purmann, C. Haney, M. Ward, T. Yao, J. Weissman, S. Urban, A. 2017-08-31 doi:10.1101/182451 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Water relations of Calycanthus flowers: hydraulic conductance, capacitance, and embolism resistance ]]> https://biorxiv.org/content/10.1101/182915v1?rss=1 Roddy, A. B. Simonin, K. A. McCulloh, K. A. Brodersen, C. R. Dawson, T. E. 2017-08-31 doi:10.1101/182915 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Conserving amphibians in the face of land development: integrating field experiments as a planning tool ]]> https://biorxiv.org/content/10.1101/183343v1?rss=1 Felson, A. J. 2017-08-31 doi:10.1101/183343 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ The Moran coalescent in a discrete one-dimensional spatial model ]]> https://biorxiv.org/content/10.1101/184705v1?rss=1 Shpak, M. Lu, J. Townsend, J. P. 2017-09-05 doi:10.1101/184705 Cold Spring Harbor Laboratory Press 2017-09-05 <![CDATA[ GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence ]]> https://biorxiv.org/content/10.1101/184853v1?rss=1 Savage, J. E. Jansen, P. R. Stringer, S. Watanabe, K. Bryois, J. de Leeuw, C. A. Nagel, M. Awasthi, S. Barr, P. B. Coleman, J. R. I. Grasby, K. L. Hammerschlag, A. R. Kaminski, J. Karlsson, R. Krapohl, E. Lam, M. Nygaard, M. Reynolds, C. A. Trampush, J. W. Young, H. Zabaneh, D. Hägg, S. Hansell, N. K. Karlsson, I. K. Linnarsson, S. Montgomery, G. W. Munoz-Manchado, A. B. Quinlan, E. B. Schumann, G. Skene, N. Webb, B. T. White, T. Arking, D. E. Attix, D. K. Avramopoulos, D. Bilder, R. M. Bitsios, P. Burdick, K. E. Cannon, T. D. Chiba-Falek, O. Chr 2017-09-06 doi:10.1101/184853 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Global connectivity of the frontoparietal cognitive control network is related to depression symptoms in undiagnosed individuals ]]> https://biorxiv.org/content/10.1101/185306v1?rss=1 Schultz, D. H. Ito, T. Solomyak, L. I. Chen, R. H. Mill, R. D. Kulkarni, K. R. Cole, M. W. 2017-09-06 doi:10.1101/185306 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Theory, practice, and conservation in the age of genomics: the Galapagos giant tortoise as a case study ]]> https://biorxiv.org/content/10.1101/187534v1?rss=1 20,000 genome-wide SNPs from 30 individuals from three Galapagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.nn"Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory."nn- Fred Allendorf (2017, p. 420) ]]> Gaughran, S. J. Quinzin, M. C. Miller, J. M. Garrick, R. C. Edwards, D. L. Russello, M. A. Poulakakis, N. Ciofi, C. Beheregaray, L. B. Caccone, A. 2017-09-12 doi:10.1101/187534 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Data-driven Modeling of Thrombus Size and Shape in Aortic Dissections: Role of Hemodynamics ]]> https://biorxiv.org/content/10.1101/187914v1?rss=1 Yazdani, A. Li, H. Bersi, M. Di Achille, P. Insley, J. Humphrey, J. Karniadakis, G. 2017-09-12 doi:10.1101/187914 Cold Spring Harbor Laboratory Press 2017-09-12 <![CDATA[ Dietary xenoestrogens significantly alter cellular metabolism induced by palbociclib/letrozole combination cancer therapy ]]> https://biorxiv.org/content/10.1101/188102v1?rss=1 Warth, B. Granados, A. Huan, T. Fang, M. Forsberg, E. M. Benton, H. P. Goetz, L. Johnson, C. Siuzdak, G. 2017-09-28 doi:10.1101/188102 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Measuring the reproducibility and quality of Hi-C data ]]> https://biorxiv.org/content/10.1101/188755v1?rss=1 Yardimci, G. Ozadam, H. Sauria, M. E. G. Ursu, O. Yan, K.-K. Yang, T. Chakraborty, A. Kaul, A. Lajoie, B. R. Song, F. Zhan, Y. Ay, F. Gerstein, M. Kundaje, A. Li, Q. Taylor, J. Yue, F. Dekker, J. Noble, W. S. 2017-09-14 doi:10.1101/188755 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Dynamic changes in oligomeric complexes of UPR sensors induced by misfolded proteins in the ER ]]> https://biorxiv.org/content/10.1101/189605v1?rss=1 Sundaram, A. Appathurai, S. Mariappan, M. 2017-09-15 doi:10.1101/189605 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Simultaneously measuring image features and resolution in live-cell STED images ]]> https://biorxiv.org/content/10.1101/190652v1?rss=1 Barentine, A. E. S. Schroeder, L. K. Graff, M. Baddeley, D. Bewersdorf, J. 2017-09-19 doi:10.1101/190652 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Nano-scale size holes in ER sheets provide an alternative to tubules for highly-curved membranes ]]> https://biorxiv.org/content/10.1101/191536v1?rss=1 Schroeder, L. K. Barentine, A. E. S. Schweighofer, S. Baddeley, D. Bewersdorf, J. Bahmanyar, S. 2017-09-20 doi:10.1101/191536 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Stimulus familiarity and expectation jointly modulate neural activity in the visual ventral stream ]]> https://biorxiv.org/content/10.1101/192518v1?rss=1 Manahova, M. E. Mostert, P. Kok, P. Schoffelen, J.-M. de Lange, F. P. 2017-09-22 doi:10.1101/192518 Cold Spring Harbor Laboratory Press 2017-09-22 <![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[ Non-Elastic Remodeling of the 3D Extracellular Matrix by Cell-Generated Forces ]]> https://biorxiv.org/content/10.1101/193458v1?rss=1 Malandrino, A. Mak, M. Trepat, X. Kamm, R. D. 2017-09-27 doi:10.1101/193458 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Learning naturalistic temporal structure in the posterior medial network ]]> https://biorxiv.org/content/10.1101/196287v1?rss=1 Aly, M. Chen, J. Turk-Browne, N. B. Hasson, U. 2017-10-01 doi:10.1101/196287 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ 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[ Genetic Analysis of Deep Phenotyping Projects in Common Disorders ]]> https://biorxiv.org/content/10.1101/197459v1?rss=1 Gershon, E. S. Pearlson, G. Keshavan, M. S. Tamminga, C. Clementz, B. Buckley, P. F. Alliey-Rodriguez, N. Liu, C. Sweeney, J. A. Keedy, S. Meda, S. Tandon, N. Shafee, R. Bishop, J. R. Ivleva, E. I. 2017-10-02 doi:10.1101/197459 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images ]]> https://biorxiv.org/content/10.1101/197517v1?rss=1 Khosravi, P. Kazemi, E. Imielinski, M. Elemento, O. Hajirasouliha, I. 2017-10-02 doi:10.1101/197517 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ RES complex is associated with intron definition and required for zebrafish early embryogenesis ]]> https://biorxiv.org/content/10.1101/197939v1?rss=1 Fernandez, J. Moreno-Mateos, M. Gohr, A. Chan, S. Irimia, M. Giraldez, A. 2017-10-03 doi:10.1101/197939 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Attending to what and where: Background connectivity integrates categorical and spatial attention ]]> https://biorxiv.org/content/10.1101/199190v1?rss=1 Tompary, A. Al-Aidroos, N. Turk-Browne, N. 2017-10-06 doi:10.1101/199190 Cold Spring Harbor Laboratory Press 2017-10-06 <![CDATA[ Hierarchy of transcriptomic specialization across human cortex captured by myelin map topography ]]> https://biorxiv.org/content/10.1101/199703v1?rss=1 Burt, J. B. Demirtas, M. Eckner, W. J. Navejar, N. M. Ji, J. L. Martin, W. J. Bernacchia, A. Anticevic, A. Murray, J. D. 2017-10-07 doi:10.1101/199703 Cold Spring Harbor Laboratory Press 2017-10-07 <![CDATA[ High-throughput fitness profiling of Zika virus E protein reveals different roles for N-linked glycosylation during infection of mammalian and mosquito cells ]]> https://biorxiv.org/content/10.1101/199935v1?rss=1 Gong, D. Zhang, T.-h. Zhao, D. Du, Y. Chapa, T. J. Shi, Y. Wang, L. Contreras, D. Zeng, G. Shi, P.-y. Wu, T.-T. Arumugaswami, V. Sun, R. 2017-10-08 doi:10.1101/199935 Cold Spring Harbor Laboratory Press 2017-10-08 <![CDATA[ A multi-modal approach to decomposing standard neuropsychological test performance: Symbol Search ]]> https://biorxiv.org/content/10.1101/200998v1?rss=1 Langer, N. Ho, E. J. Pedroni, A. Alexander, L. M. Marcelle, E. T. Schuster, K. Milham, M. P. Kelly, S. P. 2017-10-11 doi:10.1101/200998 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ The Human Accelerated Region HACNS1 modifies developmental gene expression in humanized mice ]]> https://biorxiv.org/content/10.1101/2019.12.11.873075v1?rss=1 Dutrow, E. V. Emera, D. Yim, K. Uebbing, S. Kocher, A. A. Krenzer, M. Nottoli, T. Burkhardt, D. B. Krishnaswamy, S. Louvi, A. Noonan, J. P. 2019-12-12 doi:10.1101/2019.12.11.873075 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts ]]> https://biorxiv.org/content/10.1101/2019.12.16.878488v1?rss=1 Gursoy, G. Brannon, C. Gerstein, M. 2019-12-17 doi:10.1101/2019.12.16.878488 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Independent Yet Synergistic Roles of Synaptotagmin-1 and Complexin in Calcium Regulated Neuronal Exocytosis ]]> https://biorxiv.org/content/10.1101/2019.12.16.878686v1?rss=1 Ramakrishnan, S. Bera, M. Coleman, J. Rothman, J. E. Krishnakumar, S. S. 2019-12-18 doi:10.1101/2019.12.16.878686 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Structural brain architectures match intrinsic functional networks and vary across domains: A study from 15000+ individuals ]]> https://biorxiv.org/content/10.1101/2019.12.17.879502v1?rss=1 Luo, N. SUI, J. Abrol, A. Turner, J. A. Damaraju, E. Fu, Z. Fan, L. Chen, J. Lin, D. Zhuo, C. Xu, Y. Glahn, D. C. Rodrigue, A. L. Banich, M. T. Pearlson, G. D. Calhoun, V. D. 2019-12-19 doi:10.1101/2019.12.17.879502 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq ]]> https://biorxiv.org/content/10.1101/2019.12.17.880013v1?rss=1 Xu, J. Kudron, M. M. Victorsen, A. Gao, J. Ammouri, H. N. Navarro, F. C. P. Gevirtzman, L. Waterston, R. H. White, K. P. Reinke, V. Gerstein, M. 2019-12-18 doi:10.1101/2019.12.17.880013 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Water lily (Nymphaea thermarum) draft genome reveals variable genomic signatures of ancient vascular cambium losses ]]> https://biorxiv.org/content/10.1101/2019.12.18.881573v1?rss=1 Povilus, R. A. DaCosta, J. M. Grassa, C. Satyaki, P. R. V. Moeglein, M. Jaenisch, J. Xi, Z. Mathews, S. Gehring, M. Davis, C. C. Friedman, W. E. 2019-12-19 doi:10.1101/2019.12.18.881573 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ UMAP does not preserve global structure any better than t-SNE when using the same initialization ]]> https://biorxiv.org/content/10.1101/2019.12.19.877522v1?rss=1 Kobak, D. Linderman, G. C. 2019-12-19 doi:10.1101/2019.12.19.877522 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Rewired signaling network in T cells expressing the chimeric antigen receptor (CAR) ]]> https://biorxiv.org/content/10.1101/2019.12.19.883496v1?rss=1 Dong, R. Libby, K. A. Blaeschke, F. Marson, A. Vale, R. D. Su, X. 2019-12-20 doi:10.1101/2019.12.19.883496 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Multiplexed imaging of nucleome architectures in single cells of mammalian tissue ]]> https://biorxiv.org/content/10.1101/2019.12.20.885277v1?rss=1 Liu, M. Lu, Y. Yang, B. Chen, Y. Radda, J. S. D. Hu, M. Katz, S. G. Wang, S. 2019-12-22 doi:10.1101/2019.12.20.885277 Cold Spring Harbor Laboratory Press 2019-12-22 <![CDATA[ A Primer on Modeling and Measurement of Signaling Outcomes Affecting Decision Making in Cells: Methods for Determining Optimal and Incorrect Outcomes in Noisy Biochemical Dynamics ]]> https://biorxiv.org/content/10.1101/2019.12.21.885491v1?rss=1 Ozen, M. Lipniacki, T. Levchenko, A. Emamian, E. S. Abdi, A. 2019-12-23 doi:10.1101/2019.12.21.885491 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Transcriptomic responses to hypoxia in endometrial and decidual stromal cells ]]> https://biorxiv.org/content/10.1101/2019.12.21.885657v1?rss=1 Rytkonen, K. T. Saloniemi, T. Mahmoudian, M. Ma, X. Perheentupa, A. Elo, L. L. Poutanen, M. Wagner, G. P. 2019-12-23 doi:10.1101/2019.12.21.885657 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Prolonged reaction times eliminate residual errors in visuomotor adaptation ]]> https://biorxiv.org/content/10.1101/2019.12.26.888941v1?rss=1 Langsdorf, L. Maresch, J. Hegele, M. McDougle, S. D. Schween, R. 2019-12-28 doi:10.1101/2019.12.26.888941 Cold Spring Harbor Laboratory Press 2019-12-28 <![CDATA[ Calcium induced calcium release in proximity to hair cell BK channels revealed by PKA activation ]]> https://biorxiv.org/content/10.1101/2019.12.30.890558v1?rss=1 Bai, J. Xue, N. Lawal, O. Nyati, A. Santos-Sacchi, J. Navaratnam, D. S. 2019-12-30 doi:10.1101/2019.12.30.890558 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models ]]> https://biorxiv.org/content/10.1101/2020.01.01.891705v1?rss=1 Griffith, D. Osborne, C. Edwards, E. Bachle, S. Beerling, D. Bond, W. Gallaher, T. Helliker, B. Lehmann, C. Leatherman, L. Nippert, J. Pau, S. Qiu, F. Riley, W. Smith, M. Strömberg, C. Taylor, L. Ungerer, M. Still, C. 2020-01-02 doi:10.1101/2020.01.01.891705 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Community lifespan, niche expansion and the evolution of interspecific cooperation ]]> https://biorxiv.org/content/10.1101/2020.01.02.893321v1?rss=1 Rodrigues, A. M. M. Estrela, S. Brown, S. P. 2020-01-03 doi:10.1101/2020.01.02.893321 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Inhibitory regulation of calcium transients in prefrontal dendritic spines is compromised by a nonsense Shank3 mutation ]]> https://biorxiv.org/content/10.1101/2020.01.07.894832v1?rss=1 Ali, F. Shao, L.-X. Gerhard, D. M. Sweasy, K. Pothula, S. Pittenger, C. Duman, R. S. Kwan, A. C. 2020-01-08 doi:10.1101/2020.01.07.894832 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Infestation dynamics between parasitic Antarctic fish leeches (Piscicolidae) and their crocodile icefish hosts (Channichthyidae) ]]> https://biorxiv.org/content/10.1101/2020.01.07.897496v1?rss=1 Parker, E. Jones, C. Arana, P. M. Alegria, N. A. Sarralde, R. Gallardo, F. Phillips, A. J. Williams, B. W. Dornburg, A. 2020-01-08 doi:10.1101/2020.01.07.897496 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Post-transcriptional Regulation is the Major Driver of microRNA Expression Variation ]]> https://biorxiv.org/content/10.1101/2020.01.07.897975v1?rss=1 Zhang, D. Tian, J. Roden, C. Lu, J. 2020-01-08 doi:10.1101/2020.01.07.897975 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Species tree disequilibrium positively misleads models of gene family evolution ]]> https://biorxiv.org/content/10.1101/2020.01.08.899518v1?rss=1 Lauterbur, M. E. Heder, S. Yohe, L. R. Davalos, L. M. 2020-01-09 doi:10.1101/2020.01.08.899518 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ NINJA: an inducible genetic model for creating neoantigens in vivo ]]> https://biorxiv.org/content/10.1101/2020.01.09.900894v1?rss=1 Damo, M. Fitzgerald, B. Lu, Y. Nader, M. William, I. Cheung, J. Connolly, K. A. Foster, G. G. Akama-Garren, E. Lee, D.-Y. Chang, G. P. Gocheva, V. Schmidt, L. M. Boileve, A. Wilson, J. H. Cui, C. Monroy, I. Gokare, P. R. Cabeceiras, P. Jacks, T. Joshi, N. S. 2020-01-09 doi:10.1101/2020.01.09.900894 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ The snowmelt niche differentiates three microbial life strategies that influence soil nitrogen availability during and after winter ]]> https://biorxiv.org/content/10.1101/2020.01.10.900621v1?rss=1 Sorensen, P. Beller, H. Bill, M. Bouskill, N. Hubbard, S. Karaoz, U. Polussa, A. Steltzer, H. Wang, S. Williams, K. Wu, Y. Brodie, E. 2020-01-10 doi:10.1101/2020.01.10.900621 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Presynaptic PTPσ organizes neurotransmitter release machinery at excitatory synapses ]]> https://biorxiv.org/content/10.1101/2020.01.10.901546v1?rss=1 Han, K. A. Lee, H.-Y. Lim, D. Shin, J. Yoon, T. H. Lee, C. Liu, X. Rhee, J.-S. Um, J. W. Choi, S. Y. Ko, J. 2020-01-10 doi:10.1101/2020.01.10.901546 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Ultra-deep sequencing differentiates patterns of skin clonogenic mutations associated with sun-exposure status ]]> https://biorxiv.org/content/10.1101/2020.01.10.902098v1?rss=1 Wei, L. Fitzgerald, M. Graham, J. Hutson, N. Zhang, C. Huang, Z. Hu, Q. Zhan, F. Xie, J. Zhang, J. Liu, S. Remenyik, E. Gellen, E. Colegio, O. R. Christensen, S. Lin, H. Bax, M. Xu, J. Huss, W. J. Foster, B. A. Paragh, G. 2020-01-11 doi:10.1101/2020.01.10.902098 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Functional variants within the 5UTR support reduced exon usage as a molecular mechanism underlying the quantitative trait gene Hnrnph1 for reduced methamphetamine sensitivity ]]> https://biorxiv.org/content/10.1101/2020.01.11.902908v1?rss=1 Ruan, Q. T. Yazdani, N. Reed, E. R. Beierle, J. A. Peterson, L. P. Luttik, K. P. Szumlinski, K. K. Johnson, W. E. Ash, P. E. A. Wolozin, B. Bryant, C. D. 2020-01-13 doi:10.1101/2020.01.11.902908 Cold Spring Harbor Laboratory Press 2020-01-13 <![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[ Dispersal limitation and fire feedbacks maintain mesic savannas in Madagascar ]]> https://biorxiv.org/content/10.1101/2020.01.14.905208v1?rss=1 Goel, N. Vleck, E. V. Aleman, J. C. Staver, A. C. 2020-01-15 doi:10.1101/2020.01.14.905208 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ SREBP1 regulates mitochondrial metabolism in oncogenic KRAS expressing NSCLC ]]> https://biorxiv.org/content/10.1101/2020.01.15.896373v1?rss=1 Ruiz, C. F. Haley, J. A. Montal, E. D. Haley, J. D. 2020-01-15 doi:10.1101/2020.01.15.896373 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Expanding the Genetic Architecture of Nicotine Dependence and its Shared Genetics with Multiple Traits: Findings from the Nicotine Dependence GenOmics (iNDiGO) Consortium ]]> https://biorxiv.org/content/10.1101/2020.01.15.898858v1?rss=1 Quach, B. C. Bray, M. J. Gaddis, N. C. Liu, M. Palviainen, T. Minica, C. C. Zellers, S. Sherva, R. Aliev, F. Nothnagel, M. Young, K. A. Marks, J. Young, H. Guo, Y. Waldrop, A. Sey, N. Landi, M. T. McNeil, D. W. Farrer, L. A. Markunas, C. A. Vink, J. Hottenga, J.-J. Iacono, W. G. Kranzler, H. R. Saccone, N. L. Neale, M. C. Madden, P. Rietschel, M. Marazita, M. L. McGue, M. Won, H. Winterer, G. Grucza, R. Dick, D. Gelernter, J. Caporaso, N. E. Baker, T. B. Boomsma, D. I. Kaprio, J. Hokanson, J. E. Vrieze, S. Bierut, L. J. Johnson, E. O. Hancock, D. B. 2020-01-15 doi:10.1101/2020.01.15.898858 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Can we predict real-time fMRI neurofeedback learning success from pre-training brain activity? ]]> https://biorxiv.org/content/10.1101/2020.01.15.906388v1?rss=1 Haugg, A. Sladky, R. Skouras, S. McDonald, A. Craddock, C. Kirschner, M. Herdener, M. Koush, Y. Papoutsi, M. Keynan, J. N. Hendler, T. Cohen Kadosh, K. Zich, C. MacInnes, J. Adcock, A. Dickerson, K. Chen, N.-K. Young, K. Bodurka, J. Yao, S. Becker, B. Auer, T. Schweizer, R. Pamplona, G. Emmert, K. Haller, S. Van De Ville, D. Blefari, M. L. Kim, D.-Y. Lee, J.-H. Marins, T. F. Megumi, F. Sorger, B. Kamp, T. Liew, S.-L. Veit, R. Spetter, M. Weiskopf, N. Scharnowski, F. 2020-01-15 doi:10.1101/2020.01.15.906388 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Pyruvate kinase controls signal strength in the insulin secretory pathway ]]> https://biorxiv.org/content/10.1101/2020.01.15.907790v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1f6503forg.highwire.dtl.DTLVardef@e9393org.highwire.dtl.DTLVardef@fab08borg.highwire.dtl.DTLVardef@5c7c55_HPS_FORMAT_FIGEXP M_FIG C_FIG The consensus model for {beta}-cell glucose sensing supports a dominant role for OxPhos. This model doesnt fully explain the observed metabolic and electrophysiologic oscillations associated with glucose-stimulated insulin secretion. Lewandowski et al. challenge this model by mechanistically connecting the anaplerotic PEP cycle to the electrically silent triggering phase, and OxPhos to the electrically active secretory phase. Here, the allosteric recruitment of pyruvate kinase directs metabolic traffic between the two cycles and identifies potential therapeutic strategies for diabetes based on pharmacologic pyruvate kinase activation. HIGHLIGHTSO_LICompartmentalized pyruvate kinase (PK) activity underlies {beta}-cell fuel sensing C_LIO_LIMembrane-associated PK closes KATP channels and controls calcium influx C_LIO_LIBy lowering ADP, PK toggles mitochondria between OxPhos and PEP biosynthesis C_LIO_LIPharmacologic PK activation increases oscillatory frequency and amplifies secretion C_LI ]]> Lewandowski, S. L. Cardone, R. L. Foster, H. R. Ho, T. Potapenko, E. Poudel, C. VanDeusen, H. R. Alves, T. C. Zhao, X. Capozzi, M. E. Jahan, I. Nunemaker, C. S. Campbell, J. E. Thomas, C. J. Kibbey, R. G. Merrins, M. J. 2020-01-15 doi:10.1101/2020.01.15.907790 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size ]]> https://biorxiv.org/content/10.1101/2020.01.16.904458v1?rss=1 Theroux-Rancourt, G. Roddy, A. B. Earles, J. M. Gilbert, M. E. Zwieniecki, M. A. Boyce, C. K. Tholen, D. McElrone, A. J. Simonin, K. A. Brodersen, C. R. 2020-01-16 doi:10.1101/2020.01.16.904458 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Exploiting evolutionary trade-offs to combat antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2020.01.20.912303v1?rss=1 Melnikov, S. V. Stevens, D. L. Fu, X. Kwok, H. S. Zhang, J.-T. Shen, Y. Sabina, J. Lee, K. Lee, H. Soll, D. 2020-01-20 doi:10.1101/2020.01.20.912303 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Absence of Sac2/INPP5F enhances the phenotype of a Parkinson's disease mutation of synaptojanin 1 ]]> https://biorxiv.org/content/10.1101/2020.01.21.914317v1?rss=1 Cao, M. Park, D. Wu, Y. De Camilli, P. 2020-01-21 doi:10.1101/2020.01.21.914317 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Natural selection maintains species despite widespread hybridization in the desert shrub Encelia ]]> https://biorxiv.org/content/10.1101/2020.01.23.917021v1?rss=1 DiVittorio, C. D. Singhal, S. Roddy, A. Zapata, F. Ackerly, D. D. Baldwin, B. G. Brodersen, C. R. Burquez, A. Fine, P. V. Padilla Flores, M. Solis, E. Morales-Villavicencio, J. Morales-Arce, D. Kyhos, D. W. 2020-01-24 doi:10.1101/2020.01.23.917021 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots ]]> https://biorxiv.org/content/10.1101/2020.01.24.917914v1?rss=1 Wear, E. E. Song, J. Zynda, G. J. Mickelson-Young, L. LeBlanc, C. Lee, T.-J. Deppong, D. O. Allen, G. C. Martienssen, R. A. Vaughn, M. W. Hanley-Bowdoin, L. Thompson, W. F. 2020-01-24 doi:10.1101/2020.01.24.917914 Cold Spring Harbor Laboratory Press 2020-01-24 <![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[ HySyn: A genetically-encoded synthetic synapse to rewire neural circuits in vivo ]]> https://biorxiv.org/content/10.1101/2020.01.27.922203v1?rss=1 Hawk, J. D. Colon-Ramos, D. 2020-01-28 doi:10.1101/2020.01.27.922203 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Hierarchical Network Model Excitatory-Inhibitory Tone Shapes Alternative Strategies for Different Degrees of Uncertainty in Multi-Attribute Decisions ]]> https://biorxiv.org/content/10.1101/2020.01.28.923649v1?rss=1 Pettine, W. W. Louie, K. Murray, J. D. Wang, X.-J. 2020-01-29 doi:10.1101/2020.01.28.923649 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Bicc1 and dicer regulate left-right patterning through posttranscriptionalcontrol of the Nodal-inhibitor dand5 ]]> https://biorxiv.org/content/10.1101/2020.01.29.924456v1?rss=1 Maerker, M. Getwan, M. Dowdle, M. E. Pelliccia, J. L. McSheene, J. C. Yartseva, V. Minegishi, K. Vick, P. Giraldez, A. Hamada, H. Burdine, R. D. Sheets, M. D. Schweickert, A. Blum, M. 2020-01-29 doi:10.1101/2020.01.29.924456 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Common default mode network dysfunction across psychopathologies: A neuroimaging meta-analysis of the n-back working memory paradigm ]]> https://biorxiv.org/content/10.1101/2020.01.30.927210v1?rss=1 Farruggia, M. Laird, A. R. Mattfeld, A. T. 2020-01-31 doi:10.1101/2020.01.30.927210 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Sorting liposomes of distinct sizes by DNA-brick assisted centrifugation ]]> https://biorxiv.org/content/10.1101/2020.02.01.930321v1?rss=1 Yang, Y. Wu, Z. Wang, L. Zhou, K. Xia, K. Xiong, Q. Xiong, Y. Melia, T. J. Karatekin, E. Gu, H. Lin, C. 2020-02-02 doi:10.1101/2020.02.01.930321 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ The hidden cost of receiving favors: A theory of indebtedness ]]> https://biorxiv.org/content/10.1101/2020.02.03.926295v1?rss=1 Gao, X. Jolly, E. Yu, H. Liu, H. Zhou, X. Chang, L. J. 2020-02-04 doi:10.1101/2020.02.03.926295 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ LIVE-PAINT: Super-Resolution Microscopy Inside Live Cells Using Reversible Peptide-Protein Interactions ]]> https://biorxiv.org/content/10.1101/2020.02.03.932228v1?rss=1 Oi, C. Gidden, Z. Holyoake, L. V. Kantelberg, O. Mochrie, S. Horrocks, M. H. Regan, L. 2020-02-04 doi:10.1101/2020.02.03.932228 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Epigenome-based Splicing Prediction using a Recurrent Neural Network ]]> https://biorxiv.org/content/10.1101/2020.02.03.932251v1?rss=1 80% precision-recall curve metric), we explored the derived weights of the latent factors, finding they highlight the importance of the asymmetric time-direction of chromatin context during transcription. Author SummaryIn humans, only about 2% of the genome is comprised of so-called coding regions and can give rise to protein products. However, the human transcriptome is much more diverse than the number of genes found in these coding regions. Each gene can give rise to multiple transcripts through a process during transcription called alternative splicing. There is a limited understanding of the regulation of splicing and the underlying splicing code that determines cell-type-specific splicing. Here, we studied epigenetic features that characterize splicing regulation in humans using a recurrent neural network model. Unlike feedforward neural networks, this method contains an internal memory state that learns from spatiotemporal patterns - like the context in language - from a sequence of genomic and epigenetic information, making it better suited for characterizing splicing. We demonstrated that our method improves the prediction of spicing outcomes compared to previous methods. Furthermore, we applied our method to 49 cell types in ENCODE to investigate splicing regulation and found that not only spatial but also temporal epigenomic context can influence splicing regulation during transcription. ]]> Lee, D. Zhang, J. Liu, J. Gerstein, M. 2020-02-03 doi:10.1101/2020.02.03.932251 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Latrophilins are essential for endothelial junctional fluid shear stress mechanotransduction ]]> https://biorxiv.org/content/10.1101/2020.02.03.932822v1?rss=1 Tanaka, K. Prendergast, A. Hintzen, J. Kumar, A. Chung, M. Koleske, A. Crawford, J. Nicoli, S. Schwartz, M. A. 2020-02-04 doi:10.1101/2020.02.03.932822 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Terrestrial conservation opportunities and inequities revealed by global multi-scale prioritization ]]> https://biorxiv.org/content/10.1101/2020.02.05.936047v1?rss=1 Rinnan, D. S. Jetz, W. 2020-02-07 doi:10.1101/2020.02.05.936047 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Direct Observation Of Vesicle Transport On The Synaptic Ribbon Provides Evidence That Vesicles Are Mobilized And Prepared Rapidly For Release ]]> https://biorxiv.org/content/10.1101/2020.02.05.936153v1?rss=1 Joselevitch, C. Zenisek, D. 2020-02-06 doi:10.1101/2020.02.05.936153 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Escherichia coli σ38 promoters use two UP elements instead of a -35 element: resolution of a paradoxand discovery that σ38 transcribes ribosomal promoters ]]> https://biorxiv.org/content/10.1101/2020.02.05.936344v1?rss=1 Franco, K. S. Sun, Z. Chen, Y. Cagliero, C. Zuo, Y. Zhou, Y. N. Kashlev, M. Jin, D. Schneider, T. D. 2020-02-06 doi:10.1101/2020.02.05.936344 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Inhibitory CD200-receptor signaling is rewired by type I interferon ]]> https://biorxiv.org/content/10.1101/2020.02.06.933739v1?rss=1 van der Vlist, M. Pascoal Ramos, M. I. van den Hoogen, L. L. Hiddingh, S. Timmerman, L. de Hond, T. A. P. Kaan, E. D. van der Kroef, M. Lebbink, R. J. Peters, F. M. A. Khoury-Hanold, W. Fritsch-Stork, R. Radstake, T. Meyaard, L. 2020-02-14 doi:10.1101/2020.02.06.933739 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Identifying Nootropic Drug Targets via Large-Scale Cognitive GWAS and Transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.02.06.934752v1?rss=1 Lam, M. Chen, C.-Y. Yan, X. Hill, D. W. Trampush, J. Yu, J. Knowles, E. Davies, G. Stahl, E. Huckins, L. Liewald, D. C. Djurovic, S. Melle, I. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. J. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Hartmann, A. M. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Koltai, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. C. Avramopoulos, D. Hatzimanolis, A. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, T 2020-02-06 doi:10.1101/2020.02.06.934752 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ A genome-wide case-only test for the detection of digenic inheritance in human exomes ]]> https://biorxiv.org/content/10.1101/2020.02.06.936922v1?rss=1 Kerner, G. Bouaziz, M. Cobat, A. Bigio, B. Timberlake, A. T. Bustamante, J. Lifton, R. P. Casanova, J.-L. Abel, L. 2020-02-07 doi:10.1101/2020.02.06.936922 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Distinct Hierarchical Alterations of Intrinsic Neural Timescales Account for Different Manifestations of Psychosis ]]> https://biorxiv.org/content/10.1101/2020.02.07.939520v1?rss=1 Wengler, K. Goldberg, A. Chahine, G. Horga, G. 2020-02-09 doi:10.1101/2020.02.07.939520 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Convergent molecular, cellular, and neural signatures of major depressive disorder ]]> https://biorxiv.org/content/10.1101/2020.02.10.942227v1?rss=1 Anderson, K. M. Collins, M. A. Kong, R. Fang, K. Li, J. He, T. Chekroud, A. M. Yeo, B. T. T. Holmes, A. J. 2020-02-11 doi:10.1101/2020.02.10.942227 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Tough Hydrogel-Based Biocontainment of Engineered Organisms for Continuous, Self-Powered Sensing and Computation ]]> https://biorxiv.org/content/10.1101/2020.02.11.941120v1?rss=1 Tang, T.-C. Tham, E. Liu, X. Yehl, K. Rovner, A. J. Yuk, H. Isaacs, F. J. Zhao, X. Lu, T. K. 2020-02-12 doi:10.1101/2020.02.11.941120 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Rapid and Efficient Co-Transcriptional Splicing Enhances Mammalian Gene Expression ]]> https://biorxiv.org/content/10.1101/2020.02.11.944595v1?rss=1 Reimer, K. A. Mimoso, C. Adelman, K. Neugebauer, K. M. 2020-02-12 doi:10.1101/2020.02.11.944595 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ How to read a baby's mind: Re-imagining fMRI for awake, behaving infants ]]> https://biorxiv.org/content/10.1101/2020.02.11.944868v1?rss=1 Ellis, C. T. Skalaban, L. J. Yates, T. S. Bejjanki, V. R. Cordova, N. I. Turk-Browne, N. B. 2020-02-12 doi:10.1101/2020.02.11.944868 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Climate and urbanization drive mosquito preference for humans ]]> https://biorxiv.org/content/10.1101/2020.02.12.939041v1?rss=1 Rose, N. H. Sylla, M. Badolo, A. Lutomiah, J. Ayala, D. Aribodor, O. B. Ibe, N. Akorli, J. Otoo, S. Mutebi, J.-P. Kriete, A. L. Ewing, E. G. Sang, R. Gloria-Soria, A. Powell, J. R. Baker, R. E. White, B. J. Crawford, J. E. McBride, C. S. 2020-02-13 doi:10.1101/2020.02.12.939041 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Macrophages transfer mitochondria to neurons to resolve inflammatory pain ]]> https://biorxiv.org/content/10.1101/2020.02.12.940445v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1048f6org.highwire.dtl.DTLVardef@1262306org.highwire.dtl.DTLVardef@c58261org.highwire.dtl.DTLVardef@f2d4a0_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Raoof, R. van der Vlist, M. Willemen, H. L. D. M. Prado, J. Versteeg, S. Vos, M. Lonkhorst, R. E. Pasterkamp, R. J. Khoury-Hanold, W. Meyaard, L. Eijkelkamp, N. 2020-02-13 doi:10.1101/2020.02.12.940445 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. ]]> https://biorxiv.org/content/10.1101/2020.02.12.944066v1?rss=1 Wells, J. N. Buschauer, R. Mackens-Kiani, T. Best, K. Kratzat, H. Berninghausen, O. Becker, T. Gilbert, W. V. Cheng, J. Beckmann, R. 2020-02-12 doi:10.1101/2020.02.12.944066 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Pharmacologic activation of the mitochondrial phosphoenolpyruvate cycleenhances islet function in vivo ]]> https://biorxiv.org/content/10.1101/2020.02.13.947630v1?rss=1 Abulizi, A. Stark, R. Cardone, R. L. Lewandowski, S. L. Zhao, X. Alves, T. C. Thomas, C. Kung, C. Wang, B. Siebel, S. Andrews, Z. B. Merrins, M. J. Kibbey, R. G. 2020-02-14 doi:10.1101/2020.02.13.947630 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape ]]> https://biorxiv.org/content/10.1101/2020.02.13.947796v1?rss=1 Mongiardino Koch, N. Thompson, J. R. 2020-02-13 doi:10.1101/2020.02.13.947796 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Glycation and Serum Albumin Infiltration Contribute to the Structural Degeneration of Bioprosthetic Heart Valves ]]> https://biorxiv.org/content/10.1101/2020.02.14.948075v1?rss=1 Frasca, A. Xue, Y. Kossar, A. P. Keeney, S. Rock, C. Zakharchenko, A. Streeter, M. Gorman, R. C. Grau, J. B. George, I. Bavaria, J. E. Krieger, A. Spiegel, D. Levy, R. J. Ferrari, G. 2020-02-15 doi:10.1101/2020.02.14.948075 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Granulocyte-Colony Stimulating Factor reduces cocaine-seeking and downregulates glutamatergic synaptic proteins in medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.02.17.949990v1?rss=1 Hofford, R. S. Euston, T. J. Wilson, R. S. Meckel, K. R. Peck, E. G. Godino, A. Landry, J. A. Calipari, E. S. Lam, T. T. Kiraly, D. D. 2020-02-18 doi:10.1101/2020.02.17.949990 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Greater male than female variability in regional brain structure across the lifespan ]]> https://biorxiv.org/content/10.1101/2020.02.17.952010v1?rss=1 Wierenga, L. M. Doucet, G. Dima, D. Agartz, I. Aghajani, M. Akudjedu, T. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. Andreassen, O. A. Anticevic, A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. Borgwardt, S. Bourque, J. den Braber, A. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. Busatto, G. Calhoun, V. Canales-Rodriguez, E. Cannon, D. Caseras, X. Chaim-Avancini, T. Ching, C. Conrod, P. Conzelmann, A. Crivello, F. Davey, C. Dickie, E. Ehrlich, S. van 't Ent, D. Fouche, J.-P. Fuentes- 2020-02-17 doi:10.1101/2020.02.17.952010 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Autonomic arousal tracks outcome salience not valence in monkeys making social decisions ]]> https://biorxiv.org/content/10.1101/2020.02.17.952986v1?rss=1 Basile, B. M. Joiner, J. A. Dal Monte, O. Fagan, N. A. Karaskiewicz, C. L. Lucas, D. R. Chang, S. W. C. Murray, E. A. 2020-02-18 doi:10.1101/2020.02.17.952986 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Synaptic and supra-synaptic organisation of the dopaminergic projection to the striatum. ]]> https://biorxiv.org/content/10.1101/2020.02.18.952978v1?rss=1 Pfeffer, M. Pronot, M. Angelo, M. F. Walle, R. Cordelieres, F. P. Levet, F. Claverol, S. Lacome, S. Petrel, M. Martin, C. Pitard, V. Desmedt-Peyrusse, V. Biederer, T. Trifilieff, P. Herzog, E. 2020-02-18 doi:10.1101/2020.02.18.952978 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ Analysis of Circulating Exosomes Reveals a Peripheral Signature of Astrocytic Pathology in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.02.18.955013v1?rss=1 Ranganathan, M. Rahman, M. GANESH, S. D'Souza, D. C. Skosnik, P. D. Radhakrishnan, R. Pathania, S. Mohanakumar, T. 2020-02-19 doi:10.1101/2020.02.18.955013 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Generative modeling of brain maps with spatial autocorrelation ]]> https://biorxiv.org/content/10.1101/2020.02.18.955054v1?rss=1 Burt, J. B. Helmer, M. Shinn, M. Anticevic, A. Murray, J. D. 2020-02-19 doi:10.1101/2020.02.18.955054 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Multiple timescales of neural dynamics and integration of task-relevant signals across cortex ]]> https://biorxiv.org/content/10.1101/2020.02.18.955427v1?rss=1 Spitmaan, M. M. Seo, H. Lee, D. Soltani, A. 2020-02-19 doi:10.1101/2020.02.18.955427 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11 ]]> https://biorxiv.org/content/10.1101/2020.02.19.956243v1?rss=1 Lynch, V. J. Wagner, G. 2020-02-20 doi:10.1101/2020.02.19.956243 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Characterizing Sleep-Wake Circadian Rhythm Consolidation in Early Childhood and Its Association with Motor Development Using Actigraphy ]]> https://biorxiv.org/content/10.1101/2020.02.20.957076v1?rss=1 Li, X. Kane, M. Zhang, Y. Sun, W. Song, Y. Dong, S. Lin, Q. Zhu, Q. Jiang, F. Zhao, H. 2020-02-20 doi:10.1101/2020.02.20.957076 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Transcriptional control of parallel-acting pathways that remove discrete presynaptic proteins in remodeling neurons ]]> https://biorxiv.org/content/10.1101/2020.02.21.959700v1?rss=1 Miller, D. M. Fleming-Miller, T. W. Cuentas-Condori, A. Manning, L. Palumbos, S. Richmond, J. E. 2020-02-24 doi:10.1101/2020.02.21.959700 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ Expecting the unexpected: the paranoid style of belief updating across species ]]> https://biorxiv.org/content/10.1101/2020.02.24.963298v1?rss=1 Reed, E. J. Uddenberg, S. Mathys, C. Taylor, J. R. Groman, S. Corlett, P. R. 2020-02-25 doi:10.1101/2020.02.24.963298 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Connectomic analysis reveals an interneuron with an integral role in the retinal circuit for night vision ]]> https://biorxiv.org/content/10.1101/2020.02.24.963868v1?rss=1 Park, S. J. H. Lieberman, E. M. Ke, J.-B. Rho, N. Ghorbani, P. Rahmani, P. Lee, H.-L. Jun, N. Y. Kim, I.-J. Briggman, K. L. Demb, J. Singer, J. H. 2020-02-25 doi:10.1101/2020.02.24.963868 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Dissimilarity-Overlap Analysis of Replicate Enrichment Communities ]]> https://biorxiv.org/content/10.1101/2020.02.26.966473v1?rss=1 Vila, J. C. C. Liu, Y.-Y. Sanchez, A. 2020-02-28 doi:10.1101/2020.02.26.966473 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Natural selection influenced the genetic architecture of brain structure, behavioral and neuropsychiatric traits ]]> https://biorxiv.org/content/10.1101/2020.02.26.966531v1?rss=1 Wendt, F. R. Pathak, G. A. Overstreet, C. Tylee, D. S. Gelernter, J. Atkinson, E. G. Polimanti, R. 2020-02-27 doi:10.1101/2020.02.26.966531 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Fast, Rate-Independent, Finite Element Implementation of a 3D Constrained Mixture Model of Soft Tissue Growth and Remodeling ]]> https://biorxiv.org/content/10.1101/2020.02.27.968768v1?rss=1 Latorre, M. Humphrey, J. D. 2020-02-28 doi:10.1101/2020.02.27.968768 Cold Spring Harbor Laboratory Press 2020-02-28 <![CDATA[ Predicting changes in protein thermostability upon point mutation with deep 3D convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.02.28.959874v1?rss=1 Li, B. Yang, Y. T. Capra, J. A. Gerstein, M. 2020-02-28 doi:10.1101/2020.02.28.959874 Cold Spring Harbor Laboratory Press 2020-02-28 <![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[ Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy ]]> https://biorxiv.org/content/10.1101/2020.02.28.969832v1?rss=1 Yang, L. Geng, T. Yang, G. Ma, J. Wang, L. Ketkar, H. Yang, D. Lin, T. Hwang, J. Zhu, S. Wang, Y. Dai, J. You, F. Cheng, G. Vella, A. Flavell, R. A. Fikrig, E. WANG, P. 2020-03-02 doi:10.1101/2020.02.28.969832 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Temporal learning among prefrontal and striatal ensembles ]]> https://biorxiv.org/content/10.1101/2020.02.28.970053v1?rss=1 Emmons, E. B. Chiuffa Tunes, G. Choi, J. Bruce, R. A. Weber, M. Kim, Y. Narayanan, N. 2020-03-02 doi:10.1101/2020.02.28.970053 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Nucleosome-constrained loop extrusion model for the origin of topologically associating domains ]]> https://biorxiv.org/content/10.1101/2020.02.29.969683v1?rss=1 Bailey, M. L. P. Surovtsev, I. V. Yan, H. Williams, J. F. Mochrie, S. King, M. C. 2020-02-29 doi:10.1101/2020.02.29.969683 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Children Developing Celiac Disease Have a Distinct and Proinflammatory Gut Microbiota in the First 5 Years of Life ]]> https://biorxiv.org/content/10.1101/2020.02.29.971242v1?rss=1 Huang, Q. Yang, Y. Tolstikov, V. Kiebish, M. A. ludvigsson, J. F. Palm, N. W. Ludvigsso, J. ALTINDIS, E. 2020-03-03 doi:10.1101/2020.02.29.971242 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ A Decoy Library Uncovers U-box E3 Ubiquitin Ligases that Regulate Flowering Time in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.03.02.973149v1?rss=1 Feke, A. Hong, J. Liu, W. Gendron, J. M. 2020-03-03 doi:10.1101/2020.03.02.973149 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Bayesian Structural Time Series for Mobile Health and Sensor Data: A Flexible Modeling Framework for Evaluating Interventions ]]> https://biorxiv.org/content/10.1101/2020.03.02.973677v1?rss=1 Liu, J. Spakowicz, D. J. Hoyd, R. Ash, G. I. Lou, S. Lee, D. Zhang, J. Presley, C. Greene, A. Papachristos, A. V. Gerstein, M. 2020-03-04 doi:10.1101/2020.03.02.973677 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Cell-type specific outcome representation in primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.03.03.971077v1?rss=1 Lavzin, M. Levy, S. Benisty, H. Dubin, U. Brosh, Z. Aeed, F. Mensh, B. Schiller, Y. Meir, R. Barak, O. Talmon, R. Hantman, A. W. Schiller, J. 2020-03-04 doi:10.1101/2020.03.03.971077 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Storing and analyzing a genome on a blockchain ]]> https://biorxiv.org/content/10.1101/2020.03.03.975334v1?rss=1 Gursoy, G. Brannon, C. Wagner, S. Gerstein, M. 2020-03-04 doi:10.1101/2020.03.03.975334 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Reprogramming progressive cells display low CAG promoter activity ]]> https://biorxiv.org/content/10.1101/2020.03.03.975664v1?rss=1 Hu, X. Wu, Q. Jian, Z. Chen, X. Hartman, A. Eastman, A. Guo, S. 2020-03-04 doi:10.1101/2020.03.03.975664 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Implementation of a pre- and in-scan system to minimize head motion in pediatric participants undergoing fMRI scans ]]> https://biorxiv.org/content/10.1101/2020.03.04.975417v1?rss=1 0.8). ConclusionResults indicate that with appropriate measures, it is possible to achieve low-motion fMRI data in younger participants undergoing a long scan protocol. ]]> Horien, C. Fontenelle, S. Joseph, K. Powell, N. Nutor, C. Fortes, D. Butler, M. Powell, K. Macris, D. Lee, K. McPartland, J. C. Volkmar, F. R. Scheinost, D. Chawarska, K. Constable, R. T. 2020-03-05 doi:10.1101/2020.03.04.975417 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24 ]]> https://biorxiv.org/content/10.1101/2020.03.04.977314v1?rss=1 Cao, X. Khitun, A. Na, Z. Phoodokmai, T. Sappakhaw, K. Olatunji, E. Uttamapinant, C. Slavoff, S. A. 2020-03-05 doi:10.1101/2020.03.04.977314 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib ]]> https://biorxiv.org/content/10.1101/2020.03.08.982785v1?rss=1 Alvarado-Cruz, I. Mahmoud, M. Khan, M. Zhao, S. Oeck, S. Meas, R. Clairmont, K. Quintana, V. Zhu, Y. Porciuncula, A. Wyatt, H. Ma, S. Shyr, Y. Kong, Y. LoRusso, P. M. Laverty, D. Nagel, Z. D. Schalper, K. A. Krauthammer, M. Sweasy, J. B. 2020-03-09 doi:10.1101/2020.03.08.982785 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Using the Price equation to detect inclusive fitness in class-structured populations ]]> https://biorxiv.org/content/10.1101/2020.03.09.982892v1?rss=1 Rodrigues, A. M. M. 2020-03-09 doi:10.1101/2020.03.09.982892 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Metabolic rules of microbial community assembly ]]> https://biorxiv.org/content/10.1101/2020.03.09.984278v1?rss=1 Estrela, S. Vila, J. C. Lu, N. Bajic, D. Rebolleda-Gomez, M. Chang, C.-Y. Sanchez, A. 2020-03-11 doi:10.1101/2020.03.09.984278 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. ]]> https://biorxiv.org/content/10.1101/2020.03.10.985549v1?rss=1 Xia, J. Venkat, A. Le Roch, K. Ay, F. Boyle, J. P. 2020-03-11 doi:10.1101/2020.03.10.985549 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Aberrant axonal pathfinding and exuberant myelination in an inducible model of neocortical heterotopia ]]> https://biorxiv.org/content/10.1101/2020.03.11.987388v1?rss=1 Li, A. M. Hill, R. A. Grutzendler, J. 2020-03-11 doi:10.1101/2020.03.11.987388 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Limited correspondence in visual representation between the human brain and convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.03.12.989376v1?rss=1 Xu, Y. Vaziri-Pashkam, M. 2020-03-14 doi:10.1101/2020.03.12.989376 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Global impact of phosphorylation on protein endurance ]]> https://biorxiv.org/content/10.1101/2020.03.12.989467v1?rss=1 Wu, C. Ba, Q. Li, W. Salovska, B. Hou, P. Mueller, T. Rosenberger, G. Gao, E. Di, Y. Liu, Y. 2020-03-13 doi:10.1101/2020.03.12.989467 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Selective gating of retinal information by arousal ]]> https://biorxiv.org/content/10.1101/2020.03.12.989913v1?rss=1 Liang, L. Fratzl, A. El Mansour, O. Reggiani, J. D. S. Chen, C. Andermann, M. L. 2020-03-14 doi:10.1101/2020.03.12.989913 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Light microscopy of proteins in their ultrastructural context ]]> https://biorxiv.org/content/10.1101/2020.03.13.989756v1?rss=1 M'Saad, O. Bewersdorf, J. 2020-03-14 doi:10.1101/2020.03.13.989756 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Self-antigen driven affinity maturation is required for pathogenic monovalent IgG4 autoantibody development ]]> https://biorxiv.org/content/10.1101/2020.03.14.988758v1?rss=1 Fichtner, M. L. Vieni, C. Redler, R. Kolich, L. Jiang, R. Takata, K. Stathopoulos, P. Suarez, P. Nowak, R. J. Burden, S. J. Ekiert, D. O'Connor, K. C. 2020-03-15 doi:10.1101/2020.03.14.988758 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ A flexible framework for simulating and fitting generalized drift-diffusion models ]]> https://biorxiv.org/content/10.1101/2020.03.14.992065v1?rss=1 Shinn, M. Lam, N. H. Murray, J. D. 2020-03-16 doi:10.1101/2020.03.14.992065 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Structural and developmental principles of neuropil assembly in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.03.15.992222v1?rss=1 Moyle, M. W. Barnes, K. M. Kuchroo, M. Gonopolskiy, A. Duncan, L. H. Sengupta, T. Shao, L. Guo, M. Santella, A. Christensen, R. Kumar, A. Wu, Y. Moon, K. R. Wolf, G. Krishnaswamy, S. Bao, Z. Shroff, H. Mohler, W. Colon-Ramos, D. A. 2020-03-15 doi:10.1101/2020.03.15.992222 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Accurate 4Pi single-molecule localization using an experimental PSF model ]]> https://biorxiv.org/content/10.1101/2020.03.18.997163v1?rss=1 Li, Y. Buglakova, E. Zhang, Y. Thevathasan, J. V. Bewersdorf, J. Ries, J. 2020-03-19 doi:10.1101/2020.03.18.997163 Cold Spring Harbor Laboratory Press 2020-03-19 <![CDATA[ A functional non-coding RNA is produced from xbp-1 mRNA ]]> https://biorxiv.org/content/10.1101/2020.03.20.000869v1?rss=1 Liu, X. Beaudoin, J.-D. Davison, C. A. Kosmaczewski, S. G. Meyer, B. I. Giraldez, A. J. Hammarlund, M. 2020-03-23 doi:10.1101/2020.03.20.000869 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ WOX9 functions antagonistic to STF and LAM1 to regulate leaf blade expansion in Medicago truncatula and Nicotiana sylvestris ]]> https://biorxiv.org/content/10.1101/2020.03.23.003715v1?rss=1 Wolabu, T. W. Wang, H. Tadesse, D. T. Zhang, F. Behzadirad, M. Tvorogova, V. E. Abdelmageed, H. Liu, Y. Chen, N. Jianghua, C. Allen, R. D. Tadege, M. 2020-03-25 doi:10.1101/2020.03.23.003715 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters ]]> https://biorxiv.org/content/10.1101/2020.03.23.004218v1?rss=1 Demir, M. Kadakia, N. Anderson, H. D. Clark, D. A. Emonet, T. 2020-03-25 doi:10.1101/2020.03.23.004218 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Hepatic NFAT signaling regulates the expression of inflammatory cytokines in cholestasis ]]> https://biorxiv.org/content/10.1101/2020.03.25.007831v1?rss=1 Cai, S.-Y. Yu, D. Soroka, C. J. Wang, J. Boyer, J. L. 2020-03-26 doi:10.1101/2020.03.25.007831 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Behavioral, physiological, and neural signatures of surprise during naturalistic sports viewing ]]> https://biorxiv.org/content/10.1101/2020.03.26.008714v1?rss=1 Antony, J. W. Hartshorne, T. H. Pomeroy, K. Gureckis, T. M. Hasson, U. McDougle, S. D. Norman, K. A. 2020-03-29 doi:10.1101/2020.03.26.008714 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions ]]> https://biorxiv.org/content/10.1101/2020.03.27.010736v1?rss=1 90%) classifications relevant to variant interpretation. We further evaluated the prioritisation of variants associated with disease and patient clinical outcomes, providing validations that are robust to potential mis-classification in gold-standard reference datasets. ResultsCardioBoost has higher discriminating power than published genome-wide variant classification tools in distinguishing between pathogenic and benign variants based on overall classification performance measures with the highest area under the Precision-Recall Curve as 91% for cardiomyopathies and as 96% for inherited arrhythmias. When assessed at high-confidence (>90%) classification thresholds, prediction accuracy is improved by at least 120% over existing tools for both cardiomyopathies and arrhythmias, with significantly improved sensitivity and specificity. Finally, CardioBoost improves prioritisation of variants significantly associated with disease, and stratifies survival of patients with cardiomyopathies, confirming biologically relevant variant classification. ConclusionsWe demonstrate that a disease-specific variant pathogenicity prediction tool outperforms state-of-the-art genome-wide tools for the classification of rare missense variants of uncertain significance for inherited cardiac conditions. To facilitate evaluation of CardioBoost, we provide pre-computed pathogenicity scores for all possible rare missense variants in genes associated with cardiomyopathies and arrhythmias (https://www.cardiodb.org/cardioboost/). Our results also highlight the need to develop and evaluate variant classification tools focused on specific diseases and clinical application contexts. Our proposed model for assessing variants in known disease genes, and the use of application-specific evaluations, is broadly applicable to improve variant interpretation across a wide range of Mendelian diseases. ]]> Zhang, X. Walsh, R. Whiffin, N. Buchan, R. Midwinter, W. Wilk, A. Govind, R. Li, N. Ahmad, M. Mazzarotto, F. Roberts, A. Theotokis, P. Mazaika, E. Allouba, M. de Marvao, A. Pua, C. J. Day, S. M. Ashley, E. Colan, S. D. Michels, M. Pereira, A. C. Jacoby, D. Ho, C. Y. Olivotto, I. Gunnarsson, G. T. Jefferies, J. Semsarian, C. Ingles, J. O'Regan, D. P. Aguib, Y. Yacoub, M. H. Cook, S. Barton, P. J. R. Bottolo, L. Ware, J. S. 2020-03-29 doi:10.1101/2020.03.27.010736 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Alignment free identification of clones in B cell receptor repertoires ]]> https://biorxiv.org/content/10.1101/2020.03.30.017384v1?rss=1 Lindenbaum, O. Nouri, N. Kluger, Y. Kleinstein, S. 2020-03-31 doi:10.1101/2020.03.30.017384 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Automated Feature Extraction from Population Wearable Device Data Identified Novel Loci Associated with Sleep and Circadian Rhythms ]]> https://biorxiv.org/content/10.1101/2020.03.31.017608v1?rss=1 Li, X. Zhao, H. 2020-04-01 doi:10.1101/2020.03.31.017608 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ Retromer forms low order oligomers on supported lipid bilayers ]]> https://biorxiv.org/content/10.1101/2020.03.31.018150v1?rss=1 Deatherage, C. L. Nikolaus, J. Karatekin, E. Burd, C. G. 2020-03-31 doi:10.1101/2020.03.31.018150 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ G2S3: a gene graph-based imputation method for single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2020.04.01.020586v1?rss=1 Wu, W. Dai, Q. Liu, Y. Yan, X. Wang, Z. 2020-04-03 doi:10.1101/2020.04.01.020586 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Local and global dichotomic dysfunction in resting and evoked functional connectivity precedes tauopathy ]]> https://biorxiv.org/content/10.1101/2020.04.03.022590v1?rss=1 Mandino, F. Yeow, L. Y. Bi, R. Lee, S. Bae, H. G. Baek, S. H. Lee, C. Y. Mohammad, H. Teoh, C. L. Lee, J. Lai, M. K. P. Jung, S. Yu, F. Olivo, M. Gigg, J. Grandjean, J. 2020-04-04 doi:10.1101/2020.04.03.022590 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Estimating the effect-size of gene dosage on cognitive ability across the coding genome ]]> https://biorxiv.org/content/10.1101/2020.04.03.024554v1?rss=1 50 kilobases in 24,092 individuals from unselected and autism cohorts with assessments of general intelligence. Statistical models used measures of intolerance to haploinsufficiency of genes included in CNVs to predict their effect-size on intelligence. Intolerant genes decrease general intelligence by 0.8 and 2.6 points of IQ when duplicated or deleted, respectively. Effect-sizes showed no heterogeneity across cohorts. Validation analyses demonstrated that models could predict CNV effect-sizes with 78% accuracy. Data on the inheritance of 27,766 CNVs showed that deletions and duplications with the same effect-size on intelligence occur de novo at the same frequency. We estimated that around 10,000 intolerant and tolerant genes negatively affect intelligence when deleted, and less than 2% have large effect-sizes. Genes encompassed in CNVs were not enriched in any GOterms but gene regulation and brain expression were GOterms overrepresented in the intolerant subgroup. Such pervasive effects on cognition may be related to emergent properties of the genome not restricted to a limited number of biological pathways. ]]> Huguet, G. Schramm, C. Douard, E. A. Tamer, P. Main, A. Monin, P. England, J. Jizi, K. Renne, T. Poirier, M. Nowak, S. Martin, C.-O. Younis, N. Knoth, I. S. Jean Louis, M. Saci, Z. Auger, M. Tihy, F. Mathonnet, G. Maftei, C. Leveille, F. Porteous, D. Davies, G. Redmond, P. Harris, S. E. Lemyre, E. Schumann, G. Bourgeron, T. Pausova, Z. Paus, T. Karama, S. Lippe, S. Deary, I. Almasy, L. Labbe, A. Glahn, D. Greenwood, C. M. Jacquemont, S. 2020-04-05 doi:10.1101/2020.04.03.024554 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Co-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells ]]> https://biorxiv.org/content/10.1101/2020.04.04.025536v1?rss=1 Munoz-Rojas, A. R. Kelsey, I. Pappalardo, J. Miller-Jensen, K. 2020-04-05 doi:10.1101/2020.04.04.025536 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.04.07.030684v1?rss=1 Chow, R. D. Chen, S. 2020-04-09 doi:10.1101/2020.04.07.030684 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Genetic determinants of EGFR-Driven Lung Cancer Growth and Therapeutic Response In Vivo ]]> https://biorxiv.org/content/10.1101/2020.04.13.036921v1?rss=1 Foggetti, G. Li, C. Cai, H. Hellyer, J. Lin, W.-Y. Ayeni, D. Hastings, K. Choi, J. Wurtz, A. Andrejka, L. Maghini, D. Rashleigh, N. Levy, S. Homer, R. Gettinger, S. Diehn, M. Wakelee, H. Petrov, D. Winslow, M. M. Politi, K. 2020-04-13 doi:10.1101/2020.04.13.036921 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ A Scaling Law Governing Branching Morphogenesis in Neuronal Dendrites ]]> https://biorxiv.org/content/10.1101/2020.04.13.039388v1?rss=1 Liao, M. Howard, J. 2020-04-13 doi:10.1101/2020.04.13.039388 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ A Live Attenuated Vaccine Model Confers Cross-Protective Immunity Against Different Species of Leptospira spp. ]]> https://biorxiv.org/content/10.1101/2020.04.13.039438v1?rss=1 300 serovars that can cause leptospirosis, providing a major public health benefit and opportunity to leverage One Health approaches. Live attenuated mutants that can boost immunity and induce protection are enticing vaccine candidates and poorly explored in the field. We evaluated a recently characterized motility-deficient mutant lacking the expression of a flagellar protein, FcpA. Although the fcpA- mutant has lost its ability to penetrate mucous membranes and cause disease, a transient bacteremia prior to clearance by the host immune response was observed. In two animal models, immunization with a single dose of the fcpA- mutant was sufficient to induce robust anti-protein antibodies response that promoted protection against infection with different Leptospira spp. species. Furthermore, characterization of the immune response identified a small repertoire of biologically relevant proteins that are highly conserved among pathogenic Leptospira species and potential correlates of cross-protective immunity. ]]> Wunder, E. Adhikarla, H. Hamond, C. Owers, K. Liang, L. Rodrigues, C. Bisht, V. Nally, J. Alt, D. Reis, M. Diggle, P. Felgner, P. Ko, A. 2020-04-14 doi:10.1101/2020.04.13.039438 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Global trends in biodiversity and ecosystem services from 1900 to 2050 ]]> https://biorxiv.org/content/10.1101/2020.04.14.031716v1?rss=1 Pereira, H. M. Schipper, A. Arneth, A. Hoskins, A. J. Krause, A. J. Purvis, A. Strassburg, B. Chaplin-Kramer, R. Poulter, B. Quesada, B. Rondinini, C. Guerra, C. A. Ware, C. Merow, C. Baisero, D. van Vuuren, D. Di Fulvio, F. Stehfest, E. Wolf, F. Hurtt, G. Havlik, P. Hirata, A. Humpenoeder, F. Kim, H. Rosa, I. M. Santos Martins, I. Hilbers, J. Janse, J. Johnson, J. A. Meijer, J. Settele, J. Takahashi, K. Chini, L. Leclere, D. Obersteiner, M. Harfoot, M. B. J. Di Marco, M. Talluto, M. Titeux, N. Ohashi, H. Leadley, P. Anthoni, P. Visconti, P. Popp, A. 2020-04-15 doi:10.1101/2020.04.14.031716 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ Acetylcholine is released in the basolateral amygdala in response to predictors of reward and enhances learning of cue-reward contingency ]]> https://biorxiv.org/content/10.1101/2020.04.14.041152v1?rss=1 Crouse, R. B. Kim, K. Batchelor, H. Kamaletdinova, R. Chan, J. Rajebhosale, P. Pittenger, S. Role, L. Talmage, D. Jing, M. Li, Y. Gao, X.-B. Mineur, Y. Picciotto, M. 2020-04-15 doi:10.1101/2020.04.14.041152 Cold Spring Harbor Laboratory Press 2020-04-15 <![CDATA[ A Shift from Value- to Saliency- Neural Encoding of Subjective Value in Combat Veterans with PTSD during Decision Making under Uncertainty ]]> https://biorxiv.org/content/10.1101/2020.04.14.041467v1?rss=1 Jia, R. Ruderman, L. Gordon, C. Ehrlich, D. Horvath, M. Mirchandani, S. DeFontes, C. Krystal, J. Harpaz-Rotem, I. Levy, I. 2020-04-16 doi:10.1101/2020.04.14.041467 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Proteomics of protein trafficking by in vivo tissue-specific labeling ]]> https://biorxiv.org/content/10.1101/2020.04.15.039933v1?rss=1 Droujinine, I. A. Wang, D. Hu, Y. Udeshi, N. D. Mu, L. Svinkina, T. Zeng, R. Branon, T. Tabatabai, A. Bosch, J. A. Asara, J. M. Ting, A. Y. Carr, S. A. Perrimon, N. 2020-04-16 doi:10.1101/2020.04.15.039933 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Identifying Neural Signatures Mediating Behavioral Symptoms and Psychosis Onset: High-Dimensional Whole Brain Functional Mediation Analysis ]]> https://biorxiv.org/content/10.1101/2020.04.15.043034v1?rss=1 Chén, O. Y. Cao, H. Phan, H. Nagels, G. Reinen, J. M. Gou, J. Qian, T. Di, J. Prince, J. Cannon, T. D. de Vos, M. 2020-04-16 doi:10.1101/2020.04.15.043034 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ TANGO1 membrane helices create a lipid diffusion barrier at curved membranes ]]> https://biorxiv.org/content/10.1101/2020.04.15.043307v1?rss=1 Raote, I. Ernst, A. M. Campelo, F. Rothman, J. E. Pincet, F. Malhotra, V. 2020-04-16 doi:10.1101/2020.04.15.043307 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Areas of global importance for terrestrial biodiversity, carbon, and water ]]> https://biorxiv.org/content/10.1101/2020.04.16.021444v1?rss=1 Jung, M. Arnell, A. De Lamo, X. Garcia-Rangel, S. Lewis, M. Mark, J. Merow, C. Miles, L. Ondo, I. Pironon, S. Ravilious, C. Rivers, M. Schepashenko, D. Tallowin, O. van Soesbergen, A. Govaerts, R. Boyle, B. L. Enquist, B. J. Feng, X. Gallagher, R. V. Maitner, B. Meiri, S. Mulligan, M. Ofer, G. Hanson, J. O. Jetz, W. Di Marco, M. McGowan, J. Rinnan, D. S. Sachs, J. D. Lesiv, M. Adams, V. M. Andrew, S. C. Burger, J. R. Hannah, L. Marquet, P. McCarthy, J. K. Morueta-Holme, N. Newman, E. A. Park, D. S. Roehrdanz, P. R. Svenning, J.-C. Violle, C. Wieringa, 2020-04-16 doi:10.1101/2020.04.16.021444 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ What makes Hemidactylus invasions successful? A case study on the island of Curacao. ]]> https://biorxiv.org/content/10.1101/2020.04.17.047209v1?rss=1 Lamb, A. D. Lippi, C. A. Watkins-Colwell, G. J. Jones, A. Warren, D. Iglesias, T. L. Brandley, M. Neagle, C. Dornburg, A. 2020-04-18 doi:10.1101/2020.04.17.047209 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells ]]> https://biorxiv.org/content/10.1101/2020.04.19.049254v1?rss=1 Muus, C. Luecken, M. D. Eraslan, G. Waghray, A. Heimberg, G. Sikkema, L. Kobayashi, Y. Vaishnav, E. D. Subramanian, A. Smillie, C. Jagadeesh, K. Duong, E. T. Fiskin, E. Torlai Triglia, E. Ansari, M. Cai, P. Lin, B. Buchanan, J. Chen, S. Shu, J. Haber, A. L. Chung, H. Montoro, D. T. Adams, T. Aliee, H. Allon, S. J. Andrusivova, Z. Angelidis, I. Ashenberg, O. Bassler, K. Becavin, C. Benhar, I. Bergenstrahle, J. Bergenstrahle, L. Bolt, L. Braun, E. Bui, L. T. Chaffin, M. Chichelnitskiy, E. Chiou, J. Conlon, T. M. Cuoco, M. S. Deprez, M. Fischer, D. S. G 2020-04-20 doi:10.1101/2020.04.19.049254 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Reduction of Nemo-like kinase increases lysosome biogenesis and ameliorates TDP-43-related neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.04.19.049395v1?rss=1 Tejwani, L. Kokubu, H. Lee, P. J. Xiang, Y. Luttik, K. Soriano, A. Yoon, J. Park, J. Ro, H. Ju, H. Liao, C. Tieze, S. Rigo, F. Jafar-Nejad, P. Lim, J. 2020-04-20 doi:10.1101/2020.04.19.049395 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain ]]> https://biorxiv.org/content/10.1101/2020.04.20.052175v1?rss=1 Kumar, S. Ellis, C. O'Connell, T. P. Chun, M. M. Turk-Browne, N. B. 2020-04-23 doi:10.1101/2020.04.20.052175 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Tonic GABAergic activity facilitates dendritic calcium signaling and short-term plasticity ]]> https://biorxiv.org/content/10.1101/2020.04.22.055137v1?rss=1 Chiu, C. Morse, T. Nani, F. Knoflach, F. Hernandez, M.-C. Jadi, M. Higley, M. 2020-04-24 doi:10.1101/2020.04.22.055137 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Dyrk1b is a key Regulatory Kinase Integrating Fgf, Shh and mTORC1 signaling in Skeletal Muscle Development and Homeostasis ]]> https://biorxiv.org/content/10.1101/2020.04.22.055947v1?rss=1 Bhat, N. Narayanan, A. Fathzadeh, M. Srivastava, A. Mani, A. 2020-04-23 doi:10.1101/2020.04.22.055947 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Cellular expression and functional roles of all 26 neurotransmitter GPCRs in the C. elegans egg-laying circuit ]]> https://biorxiv.org/content/10.1101/2020.04.23.037242v1?rss=1 Fernandez, R. W. Wei, K. Wang, E. Y. Mikalauskaite, D. Olson, A. Pepper, J. Christie, N. Kim, S. Koelle, M. R. 2020-04-24 doi:10.1101/2020.04.23.037242 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ The flagellar motor of Vibrio alginolyticus undergoes major structural remodeling during rotational switching ]]> https://biorxiv.org/content/10.1101/2020.04.24.060053v1?rss=1 Liu, J. Carroll, B. L. Nishikino, T. Guo, W. Zhu, S. Kojima, S. Homma, M. 2020-04-27 doi:10.1101/2020.04.24.060053 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ HtsRC-mediated accumulation of F-actin regulates ring canal size during Drosophila melanogaster oogenesis ]]> https://biorxiv.org/content/10.1101/2020.04.24.060186v1?rss=1 Gerdes, J. A. Mannix, K. M. Hudson, A. M. Cooley, L. 2020-04-25 doi:10.1101/2020.04.24.060186 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The Bacterial Cytoskeleton Spatially Confines Functional Membrane Microdomains ]]> https://biorxiv.org/content/10.1101/2020.04.25.060970v1?rss=1 Wagner, R. M. Setru, S. U. Machta, B. Wingreen, N. S. Lopez, D. 2020-04-25 doi:10.1101/2020.04.25.060970 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Detecting and Quantitating Low Fraction DNA Variants with Low-Depth Sequencing ]]> https://biorxiv.org/content/10.1101/2020.04.26.061747v1?rss=1 Song, P. Chen, S. X. Yan, Y. H. Pinto, A. Cheng, L. Y. Dai, P. Patel, A. A. Zhang, D. Y. 2020-04-28 doi:10.1101/2020.04.26.061747 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Serotonin depletion impairs both Pavlovian and instrumental reversal learning in healthy humans ]]> https://biorxiv.org/content/10.1101/2020.04.26.062463v1?rss=1 Kanen, J. W. Apergis-Schoute, A. M. Yellowlees, R. Arntz, F. E. van der Flier, F. E. Price, A. Cardinal, R. N. Christmas, D. M. Clark, L. Sahakian, B. J. Crockett, M. J. Robbins, T. W. 2020-04-27 doi:10.1101/2020.04.26.062463 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Decomposing complex links between the childhood environment and brain structure in school-aged youth ]]> https://biorxiv.org/content/10.1101/2020.04.28.063461v1?rss=1 Hong, S.-J. Sisk, L. Caballero, C. Mekhanik, A. Roy, A. K. Milham, M. Gee, D. G. 2020-04-30 doi:10.1101/2020.04.28.063461 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation ]]> https://biorxiv.org/content/10.1101/2020.04.28.066068v1?rss=1 Niederer, R. O. Rojas-Duran, M. F. Zinshteyn, B. Gilbert, W. V. 2020-04-30 doi:10.1101/2020.04.28.066068 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ PD-1 blockade-driven anti-tumor CD8+ T cell immunity requires XCR1+ dendritic cells ]]> https://biorxiv.org/content/10.1101/2020.04.28.066639v1?rss=1 Mao, T. Song, E. Iwasaki, A. 2020-04-30 doi:10.1101/2020.04.28.066639 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Fluorogenic probe for fast 3D whole-cell DNA-PAINT ]]> https://biorxiv.org/content/10.1101/2020.04.29.066886v1?rss=1 Chung, K. K. H. Zhang, Z. Kidd, P. Zhang, Y. Williams, N. D. Rollins, B. Yang, Y. Lin, C. Baddeley, D. Bewersdorf, J. 2020-04-30 doi:10.1101/2020.04.29.066886 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ α-Synuclein facilitates clathrin assembly in synaptic vesicle endocytosis ]]> https://biorxiv.org/content/10.1101/2020.04.29.069344v1?rss=1 Vargas, K. J. Colosi, P. L. Girardi, E. Chandra, S. S. 2020-04-30 doi:10.1101/2020.04.29.069344 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Artificially selecting microbial communities using propagule strategies ]]> https://biorxiv.org/content/10.1101/2020.05.01.066282v1?rss=1 Chang, C.-Y. Osborne, M. L. Bajic, D. Sanchez, A. 2020-05-03 doi:10.1101/2020.05.01.066282 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Identification of palmitoyl protein thioesterase 1 substrates defines roles for synaptic depalmitoylation ]]> https://biorxiv.org/content/10.1101/2020.05.02.074302v1?rss=1 100 novel PPT1 substrates at the synapse, including channels and transporters, G-protein-associated molecules, endo/exocytic components, synaptic adhesion molecules, and mitochondrial proteins. Cysteine depalmitoylation sites in transmembrane PPT1 substrates frequently participate in disulfide bonds in the mature protein. We confirmed that depalmitoylation regulates disulfide bond formation in a tertiary screen analyzing post-translational modifications. Collectively, the diverse PPT1 substrates highlight the role of PPT1 in mediating synapse functions, implicate molecular pathways in the etiology of CLN1, and advance our basic understanding of the purpose of depalmitoylation. HighlightsO_LI[~]10% of palmitoylated proteins are palmitoyl protein thioesterase 1 (PPT1) substrates C_LIO_LIUnbiased proteomic approaches identify 9 distinct classes of PPT1 substrates, including synaptic adhesion molecules and endocytic proteins C_LIO_LIProtein degradation does not require depalmitoylation by PPT1 C_LIO_LIDepalmitoylation mediates disulfide bond formation in transmembrane PPT1 substrates C_LI ]]> Gorenberg, E. L. Zhao, H. R. Bishai, J. Chou, V. Wirak, G. S. Lam, T. T. Chandra, S. S. 2020-05-03 doi:10.1101/2020.05.02.074302 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ The LINC complex transmits integrin-dependent tension to the nuclear lamina and represses epidermal differentiation ]]> https://biorxiv.org/content/10.1101/2020.05.03.075085v1?rss=1 Carley, E. Stewart, R. M. Zieman, A. Lin, S. Zubek, A. Horsley, V. King, M. C. 2020-05-04 doi:10.1101/2020.05.03.075085 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ PIWIL1 Promotes Gastric Cancer via a piRNA-Independent Mechanism ]]> https://biorxiv.org/content/10.1101/2020.05.03.075390v1?rss=1 Shi, S. Yang, Z.-Z. Liu, S. Yang, F. Lin, H. 2020-05-05 doi:10.1101/2020.05.03.075390 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Cortical Thickness Trajectories across the Lifespan: Data from 17,075 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.077834v1?rss=1 Frangou, S. Modabbernia, A. Doucet, G. E. Papachristou, E. Williams, S. C. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. 2020-05-07 doi:10.1101/2020.05.05.077834 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure ]]> https://biorxiv.org/content/10.1101/2020.05.05.078774v1?rss=1 Sun, L. Xu, K. Huang, W. Yang, Y. Tang, L. Xiong, T. Zhang, Q. C. 2020-05-07 doi:10.1101/2020.05.05.078774 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Cadherin Preserves Cohesion Across Involuting Tissues During C. elegans Neurulation ]]> https://biorxiv.org/content/10.1101/2020.05.05.079301v1?rss=1 Barnes, K. M. Fan, L. Moyle, M. W. Brittin, C. A. Xu, Y. Colon-Ramos, D. A. Santella, A. Bao, Z. 2020-05-06 doi:10.1101/2020.05.05.079301 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Subcortical Volume Trajectories across the Lifespan: Data from 18,605 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.079475v1?rss=1 Dima, D. Papachristou, E. Modabbernia, A. Doucet, G. E. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. M. Ching, C. R. Cl 2020-05-07 doi:10.1101/2020.05.05.079475 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Cryo-Electron Microscopy Visualization of a Large Insertion in the 5S ribosomal RNA of the Extremely Halophilic Archaeon Halococcus morrhuae. ]]> https://biorxiv.org/content/10.1101/2020.05.05.079889v1?rss=1 Tirumalai, M. R. Kaelber, J. T. Park, D. R. Tran, Q. Fox, G. E. 2020-05-06 doi:10.1101/2020.05.05.079889 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Different categories of fluorescent proteins result in GEVIs with similar characteristics ]]> https://biorxiv.org/content/10.1101/2020.05.06.081018v1?rss=1 Platisa, J. Han, Z. Pieribone, V. A. 2020-05-07 doi:10.1101/2020.05.06.081018 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Addressing Inaccurate Nosology in Mental Health: A Multi Label Data Cleansing Approach for Detecting Label Noise from Structural Magnetic Resonance Imaging Data in Mood and Psychosis Disorders ]]> https://biorxiv.org/content/10.1101/2020.05.06.081521v1?rss=1 Rokham, H. Pearlson, G. Abrol, A. Falakshahi, H. Plis, S. Calhoun, V. 2020-05-08 doi:10.1101/2020.05.06.081521 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ pegFinder: A pegRNA designer for CRISPR prime editing ]]> https://biorxiv.org/content/10.1101/2020.05.06.081612v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@1494188org.highwire.dtl.DTLVardef@6d80ccorg.highwire.dtl.DTLVardef@122eaf1org.highwire.dtl.DTLVardef@16e8e71_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO pegFinder: A pegRNA designer for CRISPR prime editing Schematic of the pegFinder workflow for designing CRISPR prime editing pegRNAs. The user provides the wildtype DNA sequence, and the edited DNA sequence. Optionally, the user can include the results from sgRNA designer tools to pegFinder, or specify a preselected sgRNA spacer to be used for pegRNA design. pegFinder then generates a pegRNA that can be used to engineer the desired alterations. pegFinder also reports alternative RT templates and PBS sequences of varying lengths that can be swapped into the pegRNA for downstream experimental optimization. pegFinder further reports secondary nicking sgRNAs that can increase prime editing efficiency (PE3 method). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/081612v1_figS1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@149ba2corg.highwire.dtl.DTLVardef@15da377org.highwire.dtl.DTLVardef@96fe3borg.highwire.dtl.DTLVardef@10cfee0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 1:C_FLOATNO pegFinder web interface Screenshot of the pegFinder web interface, available at http://pegfinder.sidichenlab.org. C_FIG ]]> Chow, R. D. Chen, S. 2020-05-08 doi:10.1101/2020.05.06.081612 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.05.06.081695v1?rss=1 Ravindra, N. G. Alfajaro, M. M. Gasque, V. Wei, J. Filler, R. B. Huston, N. C. Wan, H. Szigeti-Buck, K. Wang, B. Montgomery, R. R. eisenbarth, S. C. Williams, A. Pyle, A. M. Iwasaki, A. Horvath, T. L. Foxman, E. F. van Dijk, D. Wilen, C. 2020-05-07 doi:10.1101/2020.05.06.081695 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Primate-specific response of astrocytes to stroke limits peripheral macrophage infiltration ]]> https://biorxiv.org/content/10.1101/2020.05.08.083501v1?rss=1 Boghdadi, A. G. Spurrier, J. Teo, L. Li, M. Skarica, M. Cao, B. Kwan, W. Merson, T. D. Nilsson, S. K. Sestan, N. Strittmatter, S. M. Bourne, J. A. 2020-05-10 doi:10.1101/2020.05.08.083501 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits ]]> https://biorxiv.org/content/10.1101/2020.05.08.084475v1?rss=1 Zhang, Y. Lu, Q. Ye, Y. Huang, K. Liu, W. Wu, Y. Zhong, X. Li, B. Yu, Z. Travers, B. Werling, D. Li, J. J. Zhao, H. 2020-05-10 doi:10.1101/2020.05.08.084475 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Emergence and organization of adult brain function throughout child development ]]> https://biorxiv.org/content/10.1101/2020.05.09.085860v1?rss=1 Yates, T. S. Ellis, C. T. Turk-Browne, N. B. 2020-05-10 doi:10.1101/2020.05.09.085860 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Distinct large-scale networks are associated with motor and nonmotor symptoms in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2020.05.13.093724v1?rss=1 Tinaz, S. Kamel, S. Aravala, S. S. Sezgin, M. Elfil, M. Sinha, R. 2020-05-15 doi:10.1101/2020.05.13.093724 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Novel R-type Lectin Domain-Containing Cytotoxins Comprise a Family of Virulence-Modifying Proteins in Pathogenic Leptospira ]]> https://biorxiv.org/content/10.1101/2020.05.13.094169v1?rss=1 Chaurasia, R. Marroquin, A. Matthias, M. A. Vinetz, J. M. 2020-05-13 doi:10.1101/2020.05.13.094169 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications ]]> https://biorxiv.org/content/10.1101/2020.05.13.094292v1?rss=1 Levine, M. McDevitt, R. Meer, M. Perdue, K. Di Francesco, A. Meade, T. Farrell, C. Thrush, K. Wang, M. Dunn, C. Pellegrini, M. deCabo, R. Ferrucci, L. 2020-05-17 doi:10.1101/2020.05.13.094292 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ STING deficiency-associated aberrant CXCL10 expression contributes to pathogenesis of arthritogenic alphaviruses ]]> https://biorxiv.org/content/10.1101/2020.05.13.095083v1?rss=1 Lin, T. Geng, T. Harrison, A. Yang, D. Vella, A. T. Fikrig, E. Wang, P. 2020-05-15 doi:10.1101/2020.05.13.095083 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ A Molecular Mechanism for Probabilistic Bet-hedging and its Role in Viral Latency ]]> https://biorxiv.org/content/10.1101/2020.05.14.096560v1?rss=1 Chaturvedi, S. Klein, J. Vardi, N. Bolovan-Fritts, C. Wolf, M. Du, K. Mlera, L. Calvert, M. Moorman, N. J. Goodrum, F. Huang, B. Weinberger, L. S. 2020-05-15 doi:10.1101/2020.05.14.096560 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ The legacy of C4 evolution in the hydraulics of C3 and C4 grasses ]]> https://biorxiv.org/content/10.1101/2020.05.14.097030v1?rss=1 Zhou, H. Akcay, E. Edwards, E. Helliker, B. 2020-05-16 doi:10.1101/2020.05.14.097030 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Optimal reorganization of photosynthesis after the evolution of C4 ]]> https://biorxiv.org/content/10.1101/2020.05.15.098327v1?rss=1 Zhou, H. Akcay, E. Helliker, B. 2020-05-16 doi:10.1101/2020.05.15.098327 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis ]]> https://biorxiv.org/content/10.1101/2020.05.16.100057v1?rss=1 Li, X. Duncan, J. 2020-05-17 doi:10.1101/2020.05.16.100057 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Prostaglandin in the ventromedial hypothalamus regulates peripheral glucose metabolism ]]> https://biorxiv.org/content/10.1101/2020.05.18.056374v1?rss=1 Lee, M.-L. Matsunaga, H. Sugiura, Y. Hayasaka, T. Yamamoto, I. Imoto, D. Suematsu, M. Iijima, N. Kimura, K. Diano, S. Toda, C. 2020-05-20 doi:10.1101/2020.05.18.056374 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Molecular Mechanism for Rotational Switching of the Bacterial Flagellar Motor ]]> https://biorxiv.org/content/10.1101/2020.05.18.101634v1?rss=1 Chang, Y. Zhang, K. Carroll, B. Zhao, X. Charon, N. W. Norris, S. J. Motaleb, M. A. Li, C. Liu, J. 2020-05-19 doi:10.1101/2020.05.18.101634 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ ANALYSIS OF ULTRASONIC VOCALIZATIONS FROM MICE USING COMPUTER VISION AND MACHINE LEARNING ]]> https://biorxiv.org/content/10.1101/2020.05.20.105023v1?rss=1 4,000 USVs emitted by mice, VocalMat detected more than >98% of the USVs and accurately classified {approx}86% of USVs when considering the most likely label out of 11 different USV types. We then used Diffusion Maps and Manifold Alignment to analyze the probability distribution of USV classification among different experimental groups, providing a robust method to quantify and qualify the vocal repertoire of mice. Thus, VocalMat allows accurate and highly quantitative analysis of USVs, opening the opportunity for detailed and high-throughput analysis of this behavior. ]]> Fonseca, A. H. O. Santana, G. M. Bampi, S. Dietrich, M. O. 2020-05-23 doi:10.1101/2020.05.20.105023 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Decreased miR-24-3p potentiates DNA damage responses and increases susceptibility to COPD ]]> https://biorxiv.org/content/10.1101/2020.05.22.108688v1?rss=1 Nouws, J. Wan, F. Finnemore, E. Roque, W. Kim, S. Bazan, I. Li, C.-x. Skold, M. Yan, X. Neumeister, V. Britto, C. J. Bindra, R. Wheelock, A. Gomez-Villalobos, J. Kaminski, N. Lee, P. J. Sauler, M. 2020-05-25 doi:10.1101/2020.05.22.108688 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling ]]> https://biorxiv.org/content/10.1101/2020.05.27.118893v1?rss=1 Goldman-Israelow, B. Song, E. Mao, T. Lu, P. Meir, A. Liu, F. Madel Alfajaro, M. Wei, J. Dong, H. Homer, R. Ring, A. Wilen, C. B. Iwasaki, A. 2020-05-27 doi:10.1101/2020.05.27.118893 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Multicellular rosettes organize neuropil formation ]]> https://biorxiv.org/content/10.1101/2020.05.27.119750v1?rss=1 Brittin, C. A. Santella, A. Barnes, K. M. Moyle, M. W. Fan, L. Christensen, R. Kolotuev, I. Mohler, W. A. Schroff, H. Colón-Ramos, D. Bao, Z. 2020-05-28 doi:10.1101/2020.05.27.119750 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Deterioration of Glutaraldehyde Crosslinked Heterograft Biomaterials due to Advanced Glycation End Product Formation and Serum Albumin Infiltration ]]> https://biorxiv.org/content/10.1101/2020.05.28.117739v1?rss=1 Rock, C. A. Keeney, S. Zakharchenko, A. Takano, H. Spiegel, D. A. Krieger, A. M. Ferrari, G. Levy, R. J. 2020-05-29 doi:10.1101/2020.05.28.117739 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ Essential amnion signals for primate primitive streak formation resolved by scRNA map ]]> https://biorxiv.org/content/10.1101/2020.05.28.118703v1?rss=1 30,000 cells from postimplantation non-human primate embryos, we discovered that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 resulted in non-human primate embryos which did not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos displayed a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirmed a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development. ]]> Yang, R. Goedel, A. Kang, Y. Si, C. Chu, C. Zheng, Y. Chen, Z. Gruber, P. J. Xiao, Y. Zhou, C. Leung, C.-Y. Chen, Y. Fu, J. Ji, W. Lanner, F. Niu, Y. Chien, K. R. 2020-05-28 doi:10.1101/2020.05.28.118703 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Optimizing imaging conditions for photoconvertible protein mEos3.2 in live and fixed cells ]]> https://biorxiv.org/content/10.1101/2020.05.28.119735v1?rss=1 Sun, M. Hu, K. Bewersdorf, J. Pollard, T. D. 2020-05-29 doi:10.1101/2020.05.28.119735 Cold Spring Harbor Laboratory Press 2020-05-29 <![CDATA[ SCAN-ATAC Sim: a scalable and efficient method to simulate single-cell ATAC-seq from bulk-tissue experiments ]]> https://biorxiv.org/content/10.1101/2020.05.29.123638v1?rss=1 Chen, Z. Zhang, J. Liu, J. Zhang, Z. Zhu, J. Xu, M. Gerstein, M. 2020-05-30 doi:10.1101/2020.05.29.123638 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Obesity phenotypes are preserved in intestinal stem cell enteroids from morbidly obese patients ]]> https://biorxiv.org/content/10.1101/2020.05.29.123737v1?rss=1 Hasan, N. Johnson, K. Yin, J. Baetz, N. Sherman, V. Blutt, S. Estes, M. K. Kumbhari, V. Zachos, N. Kovbasnjuk, O. 2020-05-31 doi:10.1101/2020.05.29.123737 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ NIMBus: a Negative Binomial Regression based Integrative Method for Mutation Burden Analysis ]]> https://biorxiv.org/content/10.1101/2020.05.29.124149v1?rss=1 Zhang, J. Liu, J. McGillivray, P. Yi, C. Lochovsky, L. Lee, D. Gerstein, M. 2020-05-31 doi:10.1101/2020.05.29.124149 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ DiNeR: a Differential Graphical Model for analysis of co-regulation Network Rewiring ]]> https://biorxiv.org/content/10.1101/2020.05.29.124164v1?rss=1 Zhang, J. Liu, J. Lee, D. Lou, S. Chen, Z. Gursoy, G. Gerstein, M. 2020-05-30 doi:10.1101/2020.05.29.124164 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Privacy-preserving genotype imputation with fully homomorphic encryption ]]> https://biorxiv.org/content/10.1101/2020.05.29.124412v1?rss=1 Gursoy, G. Chielle, E. Maniatakos, M. Gerstein, M. 2020-05-30 doi:10.1101/2020.05.29.124412 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Escape of TLR5 Recognition by Leptospira spp: A Rationale for Atypical Endoflagella ]]> https://biorxiv.org/content/10.1101/2020.05.30.121202v1?rss=1 Holzapfel, M. Bonhomme, D. Cagliero, J. Vernel-Pauillac, F. Fanton d'Andon, M. Bortolussi, S. Fiette, L. Goarant, C. Wunder, E. Picardeau, M. Ko, A. Werling, D. Matsui, M. Gomberts Boneca, I. Werts, C. 2020-05-31 doi:10.1101/2020.05.30.121202 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Mother Brain is Wired for Social Moments ]]> https://biorxiv.org/content/10.1101/2020.05.31.125955v1?rss=1 Shimon-Raz, O. Salomon, R. Bloch, M. Aisenberg Romano, G. Hendler, T. Yeshurun, Y. Ulmer Yaniv, A. Zagoory-Sharon, O. Feldman, R. 2020-06-01 doi:10.1101/2020.05.31.125955 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ A genetic history of the pre-contact Caribbean ]]> https://biorxiv.org/content/10.1101/2020.06.01.126730v1?rss=1 Fernandes, D. M. Sirak, K. A. Ringbauer, H. Sedig, J. Rohland, N. Cheronet, O. Mah, M. Mallick, S. Olalde, I. Culleton, B. J. Adamski, N. Bernardos, R. Bravo, G. Broomandkhoshbacht, N. Callan, K. Candilio, F. Demetz, L. Duffett Carlson, K. S. Eccles, L. Freilich, S. Lawson, A. M. Mandl, K. Marzaioli, F. Oppenheimer, J. Özdogan, K. T. Schattke, C. Stewardson, K. Terrasi, F. Zalzala, F. Arredondo Antunez, C. Vento Canosa, E. Colten, R. Cucina, A. Genchi, F. Kraan, C. La Pastina, F. Lucci, M. Veloz Maggiolo, M. Marcheco-Teurel, B. Tavarez Maria, C. Martine 2020-06-01 doi:10.1101/2020.06.01.126730 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations ]]> https://biorxiv.org/content/10.1101/2020.06.01.127571v1?rss=1 Hemez, C. Clarelli, F. Palmer, A. C. Chindelevitch, L. Cohen, T. Abel zur Wiesch, P. 2020-06-01 doi:10.1101/2020.06.01.127571 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Moonstruck sleep: Synchronization of Human Sleep with the Moon Cycle under Natural Conditions ]]> https://biorxiv.org/content/10.1101/2020.06.01.128728v1?rss=1 Casiraghi, L. P. Spiousas, I. Dunster, G. McGlothlen, K. Fernandez-Duque, E. Valeggia, C. de la Iglesia, H. 2020-06-02 doi:10.1101/2020.06.01.128728 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Structural basis for polarized elongation of actin filaments ]]> https://biorxiv.org/content/10.1101/2020.06.02.129940v1?rss=1 Zsolnay, V. Katkar, H. H. Chou, S. Z. Pollard, T. D. Voth, G. A. 2020-06-03 doi:10.1101/2020.06.02.129940 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Liver-specific suppression of ANGPTL4 improves obesity-associated diabetes and mitigates atherosclerosis in mice ]]> https://biorxiv.org/content/10.1101/2020.06.02.130922v1?rss=1 Singh, A. K. Chaube, B. Canfran-Duque, A. Zhang, X. Price, N. L. Aryal, B. Sun, J. Citrin, K. M. Rotllan, N. Lee, R. Suarez, Y. Fernandez-Hernando, C. 2020-06-03 doi:10.1101/2020.06.02.130922 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi ]]> https://biorxiv.org/content/10.1101/2020.06.04.133876v1?rss=1 Lim, C. Berk, J. M. Blaise, A. Bircher, J. Koleske, A. J. Hochstrasser, M. Xiong, Y. 2020-06-04 doi:10.1101/2020.06.04.133876 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Akt is required for artery formation during embryonic vascular development ]]> https://biorxiv.org/content/10.1101/2020.06.04.134718v1?rss=1 Zhou, W. Ristori, E. He, L. Ghersi, J. J. Mehta, S. Zhang, R. Betsholtz, C. Nicoli, S. Sessa, W. C. 2020-06-05 doi:10.1101/2020.06.04.134718 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ MCL1 dependence across MDS subtypes and dual inhibition of MCL1 and BCL2 in MISTRG6 mice ]]> https://biorxiv.org/content/10.1101/2020.06.05.133090v1?rss=1 Fischer, M. A. Song, Y. Gbyli, R. Arrate, M. P. Villaume, M. T. Childress, M. A. Smith, B. N. Stricker, T. P. Halene, S. Savona, M. R. 2020-06-06 doi:10.1101/2020.06.05.133090 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Fentanyl-induced antinociception, reward, reinforcement, and withdrawal in Hnrnph1 mutant mice ]]> https://biorxiv.org/content/10.1101/2020.06.06.137158v1?rss=1 Bryant, C. D. Healy, A. F. Ruan, Q. T. Coehlo, M. A. Lustig, E. Yazdani, N. Luttik, K. P. Tran, T. Swancy, I. Brewin, L. W. Chen, M. M. Szumlinski, K. K. 2020-06-08 doi:10.1101/2020.06.06.137158 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ An In situ Collagen-HA Hydrogel System Promotes Survival and Preserves the Proangiogenic Secretion of hiPSC-derived Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2020.06.06.137968v1?rss=1 Dash, B. C. Duan, K. Kyriakides, T. R. Hsia, H. C. 2020-06-06 doi:10.1101/2020.06.06.137968 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Closed-loop fMRI neurofeedback to reduce negative attentional bias in depression ]]> https://biorxiv.org/content/10.1101/2020.06.07.137943v1?rss=1 Mennen, A. C. Turk-Browne, N. B. Wallace, G. Seok, D. Jaganjac, A. Stock, J. deBettencourt, M. T. Cohen, J. D. Norman, K. A. Sheline, Y. I. 2020-06-08 doi:10.1101/2020.06.07.137943 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ The epidemic consequences of virulence and free-living survival relationships in models of emerging outbreaks ]]> https://biorxiv.org/content/10.1101/2020.06.08.141366v1?rss=1 Gomez, L. M. Meszaros, V. A. Turner, W. C. Ogbunugafor, C. B. 2020-06-09 doi:10.1101/2020.06.08.141366 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2020.06.13.149443v1?rss=1 Gowrishankar, S. Lyons, L. Rafiq, N. M. Roczniak-Ferguson, A. De Camilli, P. Ferguson, S. 2020-06-13 doi:10.1101/2020.06.13.149443 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations ]]> https://biorxiv.org/content/10.1101/2020.06.16.146803v1?rss=1 1Mb from previously identified risk loci for the four cancers and an additional 23 lead variant-cancer associations were novel for one of the cancers. Bayesian models supported pleiotropic effects involving at least two cancers at 222/465 lead variants in 118/192 regions. Gene-level association analysis identified 13 shared susceptibility genes (P<2.6x10-6) in 13 regions not previously implicated in any of the four cancers and not uncovered by our variant-level meta-analysis. Several lead variants had opposite effects across cancers, including a cluster of such variants in the TP53 pathway. Fifty-four lead variants were associated with blood cell traits and suggested genetic overlaps with clonal hematopoiesis. Our study highlights the remarkable pervasiveness of pleiotropy across hormone-related cancers, further illuminating their shared genetic and mechanistic origins at variant- and gene-level resolution. ]]> Kar, S. P. Lindstroem, S. Hung, R. Lawrenson, K. Schmidt, M. O'Mara, T. Glubb, D. Tyrer, J. Schildkraut, J. Chang-Claude, J. Alsulimani, A. Anton, F. Beeghly-Fadiel, A. Bjorge, L. Bodelon, C. Brauch, H. Burghaus, S. Campa, D. Carney, M. Chen, Z. Daly, M. du Bois, A. Ekici, A. Ewing, A. Fasching, P. Flanagan, J. M. Gawelko, J. Giles, G. Hamilton, R. Harris, H. Heitz, F. Hildebrandt, M. Hillemanns, P. Huang, R.-Y. Imaz, L. Irmejs, A. Jakubowska, A. Jensen, A. John, E. Kannisto, P. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kleiblo 2020-06-19 doi:10.1101/2020.06.16.146803 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.06.16.155101v1?rss=1 Wei, J. Alfajaro, M. Hanna, R. DeWeirdt, P. Strine, M. Lu-Culligan, W. Zhang, S.-M. Graziano, V. Schmitz, C. Chen, J. Mankowski, M. Filler, R. Gasque, V. de Miguel, F. Chen, H. Oguntuyo, K. Y. Abriola, L. Surovtseva, Y. Orchard, R. Lee, B. Lindenbach, B. Politi, K. van Dijk, D. Simon, M. Yan, Q. Doench, J. G. Wilen, C. B. 2020-06-17 doi:10.1101/2020.06.16.155101 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Detection of SARS-CoV-2 RNA by multiplex RT-qPCR ]]> https://biorxiv.org/content/10.1101/2020.06.16.155887v1?rss=1 500 copies / reaction) of SARS-CoV-2 RNA were consistently detected by the multiplex RT-qPCR. Our novel multiplex RT-qPCR improves upon current singleplex diagnostics by saving reagents, costs, time and labor. ]]> Kudo, E. Israelow, B. Vogels, C. Lu, P. Wyllie, A. L. Tokuyama, M. Venkataraman, A. Brackney, D. E. Ott, I. Petrone, M. Earnest, R. Lapidus, S. Muenker, C. Moore, A. Casanovas-Massana, A. Yale IMPACT Research Team, Omer, S. Dela Cruz, C. Farhadian, S. Ko, A. Grubaugh, N. Iwasaki, A. 2020-06-17 doi:10.1101/2020.06.16.155887 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Cancer-specific associations of driver genes with immunotherapy outcome ]]> https://biorxiv.org/content/10.1101/2020.06.16.155895v1?rss=1 Jun, T. Qing, T. Dong, G. Signaevski, M. Hopkins, J. Frampton, G. Albacker, L. Cordon-Cardo, C. Samstein, R. Pusztai, L. Huang, K.-l. 2020-06-17 doi:10.1101/2020.06.16.155895 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ DReSS: A difference measurement based on reachability between state spaces of Boolean networks ]]> https://biorxiv.org/content/10.1101/2020.06.19.161224v1?rss=1 Yin, Z. Guo, B. Ma, S. S. Sun, Y. Mi, Z. Zheng, Z. 2020-06-20 doi:10.1101/2020.06.19.161224 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Cholinergic relay from punishment- to reward-encoding dopamine neurons signals punishment withdrawal as reward in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.06.22.165209v1?rss=1 McCurdy, L. Y. Sareen, P. Davoudian, P. Nitabach, M. 2020-06-23 doi:10.1101/2020.06.22.165209 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Tissue-specific dynamic codon redefinition in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.06.22.165522v1?rss=1 Hudson, A. M. M. Loughran, G. Szabo, N. L. Wills, N. M. Atkins, J. F. Cooley, L. 2020-06-22 doi:10.1101/2020.06.22.165522 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Molecular signaling pathways underlying schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.06.23.156653v1?rss=1 Tiihonen, J. Koskuvi, M. Lähteenvuo, M. Trontti, K. Ojansuu, I. Vaurio, O. Cannon, T. D. Lönnqvist, J. Therman, S. Suvisaari, J. Cheng, L. Tanskanen, A. Taipale, H. Lehtonen, S. Koistinaho, J. 2020-06-23 doi:10.1101/2020.06.23.156653 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ In Vivo Mechanisms of Chemotherapy-Induced Acute Follicle Loss in the Human Ovary: An Individual-Oocyte Transcriptomic Analysis from Human Ovarian Xenografts ]]> https://biorxiv.org/content/10.1101/2020.06.23.167783v1?rss=1 Titus, S. Szymanska, K. J. Musul, B. Turan, V. Taylan, E. Garcia - Milian, R. Mehta, S. Oktay, K. 2020-06-23 doi:10.1101/2020.06.23.167783 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Shared and unique brain network features predict cognition, personality and mental health in childhood ]]> https://biorxiv.org/content/10.1101/2020.06.24.168724v1?rss=1 Chen, J. Tam, A. Kebets, V. Orban, C. Ooi, L. Q. R. Marek, S. Dosenbach, N. Eickhoff, S. Bzdok, D. Holmes, A. J. Yeo, B. T. T. 2020-06-24 doi:10.1101/2020.06.24.168724 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ JIP3 links lysosome transport to regulation of multiple components of the axonal cytoskeleton ]]> https://biorxiv.org/content/10.1101/2020.06.24.169219v1?rss=1 Rafiq, N. M. Lyons, L. Gowrishankar, S. De Camilli, P. Ferguson, S. 2020-06-24 doi:10.1101/2020.06.24.169219 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Neuroinvasive potential of SARS-CoV-2 revealed in a human brain organoid model ]]> https://biorxiv.org/content/10.1101/2020.06.25.169946v1?rss=1 Song, E. Zhang, C. Israelow, B. Lu, P. Weizman, O.-E. Liu, F. Dai, Y. Szigeti-Buck, K. Yasumoto, Y. Wang, G. Heltke, J. Ng, E. Wheeler, J. Alfajaro, M. M. Fontes, B. Ravindra, N. van Dijk, D. Mane, S. Gunel, M. Ring, A. Wilen, C. B. Horvath, T. LOUVI, A. Farhadian, S. Bilguvar, K. Iwasaki, A. 2020-06-26 doi:10.1101/2020.06.25.169946 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Functional Redundancy in Local Spatial Scale Microbial Communities Suggest Stochastic Processes at an Urban Wilderness Preserve in Austin, TX, USA ]]> https://biorxiv.org/content/10.1101/2020.06.25.171660v1?rss=1 Stewart, J. D. Ontai, A. Yusoof, K. Bilinski, T. M. 2020-06-27 doi:10.1101/2020.06.25.171660 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function ]]> https://biorxiv.org/content/10.1101/2020.06.26.173096v1?rss=1 Feke, A. Gendron, J. 2020-06-26 doi:10.1101/2020.06.26.173096 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Identifying Modules of Cooperating Cancer Drivers ]]> https://biorxiv.org/content/10.1101/2020.06.29.168229v1?rss=1 Klein, M. I. Cannataro, V. L. Newman, S. Townsend, J. P. Stern, D. F. Zhao, H. 2020-06-29 doi:10.1101/2020.06.29.168229 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Loss of endothelial glucocorticoid receptor accelerates diabetic nephropathy ]]> https://biorxiv.org/content/10.1101/2020.06.29.178228v1?rss=1 Srivastava, S. P. Zhou, H. Setia, O. Dardik, A. Fernandez-Hernando, C. Goodwin, J. 2020-06-29 doi:10.1101/2020.06.29.178228 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Structure of the full SARS-CoV-2 RNA genome in infected cells ]]> https://biorxiv.org/content/10.1101/2020.06.29.178343v1?rss=1 Lan, T. C. T. Allan, M. F. Malsick, L. Khandwala, S. Nyeo, S. S. Y. Bathe, M. Griffiths, A. Rouskin, S. 2020-06-30 doi:10.1101/2020.06.29.178343 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Single-cell in vivo brain optogenetic stimulation by two-photon excitation fluorescence transfer ]]> https://biorxiv.org/content/10.1101/2020.06.29.179077v1?rss=1 Tong, L. Yuan, P. Chen, M. Chen, F. Bewersdorf, J. Zhou, J. Z. Grutzendler, J. 2020-06-30 doi:10.1101/2020.06.29.179077 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Spatial and single-cell transcriptional landscape of human cerebellar development ]]> https://biorxiv.org/content/10.1101/2020.06.30.174391v1?rss=1 Aldinger, K. A. Thomson, Z. Haldipur, P. Deng, M. Timms, A. E. Hirano, M. Santpere, G. Roco, C. Rosenberg, A. B. Lorente-Galdos, B. Gulden, F. O. O'Day, D. Overman, L. M. Lisgo, S. Alexandre, P. Sestan, N. Doherty, D. Dobyns, W. B. Seelig, G. Glass, I. A. Millen, K. J. 2020-07-01 doi:10.1101/2020.06.30.174391 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression ]]> https://biorxiv.org/content/10.1101/2020.06.30.178103v1?rss=1 Rosa-Mercado, N. A. Zimmer, J. T. Apostolidi, M. Rinehart, J. Simon, M. D. Steitz, J. A. 2020-07-02 doi:10.1101/2020.06.30.178103 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ PLCγ1 promotes phase separation of the T cell signaling clusters ]]> https://biorxiv.org/content/10.1101/2020.06.30.179630v1?rss=1 Su, X. Zeng, L. Palaia, I. Saric, A. 2020-07-01 doi:10.1101/2020.06.30.179630 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Two neuronal peptides encoded from a single transcript regulate mitochondrial function in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.01.182485v1?rss=1 Bosch, J. A. Ugur, B. Pichardo-Casas, I. Rabasco, J. Escobedo, F. Zuo, Z. Brown, B. Celniker, S. Bellen, H. J. Sinclair, D. Perrimon, N. 2020-07-02 doi:10.1101/2020.07.01.182485 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Phase separation enables heterochromatin domains to do mechanical work ]]> https://biorxiv.org/content/10.1101/2020.07.02.184127v1?rss=1 Williams, J. F. Surovtsev, I. V. Schreiner, S. M. Nguyen, H. Hu, Y. Mochrie, S. King, M. C. 2020-07-03 doi:10.1101/2020.07.02.184127 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Vascular dimorphism ensured by regulated proteoglycan dynamics favors rapid umbilical artery closure at birth ]]> https://biorxiv.org/content/10.1101/2020.07.02.184978v1?rss=1 Nandadasa, S. Szafron, J. M. Pathak, V. Murtada, S.-I. Craft, C. M. O'Donnell, A. Norvik, C. Hughes, C. Caterson, B. Domowicz, M. S. Schwartz, N. B. Tran-Lundmark, K. Veigl, M. Sedwick, D. Philipson, E. H. Humphrey, J. D. Apte, S. S. 2020-07-03 doi:10.1101/2020.07.02.184978 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Connectivity patterns of task-specific brain networks allow individual prediction of cognitive symptom dimension of schizophrenia and link to molecular architecture ]]> https://biorxiv.org/content/10.1101/2020.07.02.185124v1?rss=1 Chen, J. Mueller, V. I. Dukart, J. Hoffstaedter, F. Baker, J. T. Holmes, A. J. Vatansever, D. Nickl-Jockschat, T. Liu, X. Derntl, B. Kogler, L. Jardri, R. Gruber, O. Aleman, A. Sommer, I. E. Eickhoff, S. B. Patil, K. R. 2020-07-02 doi:10.1101/2020.07.02.185124 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly ]]> https://biorxiv.org/content/10.1101/2020.07.03.168831v1?rss=1 Zhao, X. Collins, R. L. Lee, W.-P. Weber, A. M. Jun, Y. Zhu, Q. Weisburd, B. Huang, Y. Audano, P. A. Wang, H. Walker, M. Lowther, C. Fu, J. Gerstein, M. B. Devine, S. E. Marschall, T. Korbel, J. O. Eichler, E. E. Chaisson, M. J. P. Lee, C. Mills, R. E. Brand, H. Talkowski, M. E. 2020-07-04 doi:10.1101/2020.07.03.168831 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Behavioral and neural fusion of expectation with sensation ]]> https://biorxiv.org/content/10.1101/2020.07.03.187146v1?rss=1 Panichello, M. F. Turk-Browne, N. B. 2020-07-04 doi:10.1101/2020.07.03.187146 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.07.06.188953v1?rss=1 Xiao, X. Wang, C. Chang, D. Wang, Y. Dong, X. Jiao, T. Zhao, Z. Ren, L. Dela Cruz, C. S. Sharma, L. Lei, X. Wang, J. 2020-07-06 doi:10.1101/2020.07.06.188953 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ The global and local distribution of RNA structure throughout the SARS-CoV-2 genome ]]> https://biorxiv.org/content/10.1101/2020.07.06.190660v1?rss=1 Tavares, R. d. C. A. Mahadeshwar, G. Pyle, A. M. 2020-07-07 doi:10.1101/2020.07.06.190660 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures ]]> https://biorxiv.org/content/10.1101/2020.07.08.191072v1?rss=1 Roberto Melero Carlos Oscar S. Sorzano Brent Foster José-Luis Vilas Marta Martínez Roberto Marabini Erney Ramírez-Aportela Ruben Sanchez-Garcia David Herreros Laura del Caño Patricia Losana Yunior C. Fonseca-Reyna Pablo Conesa Daniel Wrapp Pablo Chacon Jason S. McLellan Hemant D. Tagare Jose-Maria Carazo 2020-07-08 doi:10.1101/2020.07.08.191072 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Oviposition of the mosquito Aedes aegypti in forest and domestic habitats in Africa ]]> https://biorxiv.org/content/10.1101/2020.07.08.192187v1?rss=1 Siyang Xia Hany K. M. Dweck Joel Lutomiah Rosemary Sang Carolyn S. McBride Noah H. Rose Diego Ayala Jeffrey R. Powell 2020-07-09 doi:10.1101/2020.07.08.192187 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Bootstrap aggregating improves the generalizability of Connectome Predictive Modelling ]]> https://biorxiv.org/content/10.1101/2020.07.08.193664v1?rss=1 David O’Connor Evelyn M.R. Lake Dustin Scheinost R. Todd Constable 2020-07-09 doi:10.1101/2020.07.08.193664 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Solvent quality and chromosome folding in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.07.09.195560v1?rss=1 Yingjie Xiang Ivan V. Surovtsev Yunjie Chang Sander K. Govers Bradley R. Parry Jun Liu Christine Jacobs-Wagner 2020-07-09 doi:10.1101/2020.07.09.195560 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Comprehensive in-vivo secondary structure of SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms ]]> https://biorxiv.org/content/10.1101/2020.07.10.197079v1?rss=1 Nicholas C Huston Han Wan Rafael de Cesaris Araujo Tavares Craig B Wilen Anna Marie Pyle 2020-07-10 doi:10.1101/2020.07.10.197079 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Aedes aegypti SNAP and a calcium transporter ATPase influence dengue virus dissemination. ]]> https://biorxiv.org/content/10.1101/2020.07.10.198226v1?rss=1 Alejandro Marin-Lopez Junjun Jiang Yuchen Wang Yongguo Cao Tyler MacNeil Andrew K Hastings Erol Fikrig 2020-07-11 doi:10.1101/2020.07.10.198226 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Direct visualization of four diffusive LexA states controlling SOS response strength during antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2020.07.14.201889v1?rss=1 Schaerfen, L. Tisma, M. Hartmann, A. Schlierf, M. 2020-07-14 doi:10.1101/2020.07.14.201889 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids ]]> https://biorxiv.org/content/10.1101/2020.07.15.204800v1?rss=1 Talaia, G. Amick, J. Ferguson, S. 2020-07-15 doi:10.1101/2020.07.15.204800 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation ]]> https://biorxiv.org/content/10.1101/2020.07.17.209098v1?rss=1 Dong, J. LeBlanc, C. Poulet, A. Mermaz, B. Villarino, G. Webb, K. M. Joly, V. Mendez, J. Voigt, P. Jacob, Y. 2020-07-17 doi:10.1101/2020.07.17.209098 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Ecological load and balancing selection in circumboreal barnacles ]]> https://biorxiv.org/content/10.1101/2020.07.18.209569v1?rss=1 Nunez, J. C. B. Rong, S. Damian-Serrano, A. Burley, J. T. Elyanow, R. Ferranti, D. A. Neil, K. B. Glenner, H. Rosenblad, M. A. Blomberg, A. Johannesson, K. Rand, D. M. 2020-07-19 doi:10.1101/2020.07.18.209569 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ Vesicle Navigation of Microtubule Ends Distinguished by A Single Rate-Constant Model ]]> https://biorxiv.org/content/10.1101/2020.07.21.214023v1?rss=1 Gramlich, M. W. Balseiro Gomez, S. Tabei, S. M. A. Parkes, M. Yogev, S. 2020-07-21 doi:10.1101/2020.07.21.214023 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Inference and analysis of cell-cell communication using CellChat ]]> https://biorxiv.org/content/10.1101/2020.07.21.214387v1?rss=1 Jin, S. Guerrero-Juarez, C. F. Zhang, L. Chang, I. Myung, P. Plikus, M. V. Nie, Q. 2020-07-22 doi:10.1101/2020.07.21.214387 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Orally Administered Exosomes Alleviate Mouse Contact Dermatitis through Delivering miRNA-150 to Antigen-Primed Macrophages Targeted by Exosome-Surface Antibody Light Chains ]]> https://biorxiv.org/content/10.1101/2020.07.22.214866v1?rss=1 Askenase, P. W. Nazimek, K. Bryniarski, K. Ptak, W. Kormelink, T. G. 2020-07-23 doi:10.1101/2020.07.22.214866 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Decadal changes in fire frequencies shift tree communities and functional traits ]]> https://biorxiv.org/content/10.1101/2020.07.22.216226v1?rss=1 Pellegrini, A. Refsland, T. Averill, C. Terrer, C. Staver, C. Brockway, D. Caprio, A. Clatterbuck, W. Coetsee, C. Haywood, J. Hobbie, S. Hoffmann, W. Kush, J. Lewis, T. Moser, W. K. Overby, S. Patterson, W. Peay, K. G. Reich, P. Ryan, C. Sword, M. Scharenbroch, B. Schoennagel, T. Smith, G. Stephan, K. Swanston, C. Turner, M. Varner, M. Jackson, R. B. 2020-07-24 doi:10.1101/2020.07.22.216226 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Top-down engineering of complex communities by directed evolution ]]> https://biorxiv.org/content/10.1101/2020.07.24.214775v1?rss=1 Chang, C.-Y. Vila, J. C. C. Bender, M. Li, R. Mankowski, M. C. Bassette, M. Borden, J. Golfier, S. Sanchez, P. G. Waymack, R. Zhu, X. Diaz-Colunga, J. Estrela, S. Rebolleda-Gomez, M. Sanchez, A. 2020-07-25 doi:10.1101/2020.07.24.214775 Cold Spring Harbor Laboratory Press 2020-07-25 <![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[ Neural synchrony predicts children's learning of novel words ]]> https://biorxiv.org/content/10.1101/2020.07.28.216663v1?rss=1 Piazza, E. A. Cohen, A. Trach, J. Lew-Williams, C. 2020-07-28 doi:10.1101/2020.07.28.216663 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Polygenic Risk Score for Smoking is associated with Externalizing Psychopathology and Disinhibited Personality Traits but not Internalizing Psychopathology in Adolescence ]]> https://biorxiv.org/content/10.1101/2020.07.29.227405v1?rss=1 Hicks, B. M. Clark, D. A. Deak, J. D. Liu, M. Durbin, C. E. Schafer, J. D. Wilson, S. Iacono, W. G. McGue, M. Vrieze, S. 2020-07-30 doi:10.1101/2020.07.29.227405 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Polygenic Risk Scores Predict the Development of Alcohol and Nicotine Use Problems from Adolescence through Young Adulthood ]]> https://biorxiv.org/content/10.1101/2020.07.29.227439v1?rss=1 Deak, J. D. Clark, D. A. Liu, M. Durbin, C. E. Iacono, W. G. McGue, M. Vrieze, S. I. Hicks, B. M. 2020-07-30 doi:10.1101/2020.07.29.227439 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ A dynamic regulatory interface on SARS-CoV-2 RNA polymerase ]]> https://biorxiv.org/content/10.1101/2020.07.30.229187v1?rss=1 Shi, W. Chen, M. Yang, Y. Zhou, W. Chen, S. Hu, Y. Liu, B. 2020-07-30 doi:10.1101/2020.07.30.229187 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Heritability of individualized cortical network topography ]]> https://biorxiv.org/content/10.1101/2020.07.30.229427v1?rss=1 Anderson, K. M. Ge, T. Kong, R. Patrick, L. M. Spreng, R. N. Sabuncu, M. R. Yeo, B. T. T. Holmes, A. 2020-07-30 doi:10.1101/2020.07.30.229427 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Comparative study of curvature sensing mediated by F-BAR domain and an intrinsically disordered region of FBP17 ]]> https://biorxiv.org/content/10.1101/2020.07.30.230037v1?rss=1 Su, M. Zhuang, Y. Miao, X. Zeng, Y. Gao, W. Zhao, W. Wu, M. 2020-07-31 doi:10.1101/2020.07.30.230037 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Multiplexed fractionated proteomics reveals synaptic factors associated with cognitive resilience in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2020.07.31.230680v1?rss=1 Carlyle, B. C. Kandigian, S. E. Kreuzer, J. Das, S. Trombetta, B. A. Kuo, Y. Bennett, D. A. Schneider, J. A. Petyuk, V. A. Kitchen, R. R. Morris, R. Nairn, A. C. Hyman, B. T. Haas, W. Arnold, S. E. 2020-08-01 doi:10.1101/2020.07.31.230680 Cold Spring Harbor Laboratory Press 2020-08-01 <![CDATA[ Circumventing the optical diffraction limit with customized speckles ]]> https://biorxiv.org/content/10.1101/2020.07.31.230821v1?rss=1 Bender, N. Sun, M. Yilmaz, H. Bewersdorf, J. Cao, H. 2020-08-03 doi:10.1101/2020.07.31.230821 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Diversification, disparification, and hybridization in the desert shrubs Encelia ]]> https://biorxiv.org/content/10.1101/2020.07.31.230938v1?rss=1 Singhal, S. Roddy, A. DiVittorio, C. Sanchez-Amaya, A. Henriquez, C. Brodersen, C. Fehlberg, S. Zapata, F. 2020-07-31 doi:10.1101/2020.07.31.230938 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ The mammalian CLU homolog FMT controls development and behavior in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.08.01.231183v1?rss=1 Horvath, T. Ralevski, A. Apelt, F. Olas, J. Mueller-Roeber, B. Rugarli, E. Kragler, F. 2020-08-03 doi:10.1101/2020.08.01.231183 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue ]]> https://biorxiv.org/content/10.1101/2020.08.01.232496v1?rss=1 Liu, Y. Yang, M. Deng, Y. Su, G. Archibald Enninful, A. Guo, C. C. Tebaldi, T. Zhang, D. Kim, D. Bai, Z. Norris, E. Pan, A. Li, J. Xiao, Y. Halene, S. Fan, R. 2020-08-01 doi:10.1101/2020.08.01.232496 Cold Spring Harbor Laboratory Press 2020-08-01 <![CDATA[ Brain Anatomical Covariation Patterns Linked to Binge Drinking and Age at First Full Drink Prior to 21 Years ]]> https://biorxiv.org/content/10.1101/2020.08.02.232942v1?rss=1 Zhao, Y. Constable, R. T. Hien, D. Chung, T. Potenza, M. 2020-08-04 doi:10.1101/2020.08.02.232942 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Human vulnerability to cancer malignancy is enhanced by evolution of higher mesenchymal CD44 expression compared to other mammals ]]> https://biorxiv.org/content/10.1101/2020.08.03.234617v1?rss=1 Ma, X. Dighe, A. Maziarz, J. Neumann, E. Erkenbrack, E. Hei, Y.-Y. Liu, Y. Suhail, Y. Kshitiz, K. Levchenko, A. Wagner, G. 2020-08-03 doi:10.1101/2020.08.03.234617 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Cytidine monophosphate N-acetylneuraminic acid synthetase and solute carrier family 35 member A1 are required for reovirus binding and infection ]]> https://biorxiv.org/content/10.1101/2020.08.03.235572v1?rss=1 Urbanek, K. Sutherland, D. M. Orchard, R. C. Wilen, C. B. Knowlton, J. J. Aravamudhan, P. Taylor, G. M. Virgin, H. W. Dermody, T. S. 2020-08-04 doi:10.1101/2020.08.03.235572 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments ]]> https://biorxiv.org/content/10.1101/2020.08.06.239897v1?rss=1 Estrela, S. Sanchez-Gorostiaga, A. Vila, J. C. C. Sanchez, A. 2020-08-07 doi:10.1101/2020.08.06.239897 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Adipose tissue developmental growth constraints uncouple fat distribution from glucose metabolism in two mouse models of obesity ]]> https://biorxiv.org/content/10.1101/2020.08.07.239665v1?rss=1 Sebo, Z. Church, C. Berry, R. Rodeheffer, M. 2020-08-07 doi:10.1101/2020.08.07.239665 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Hidden population modes in social brain morphology: Its parts are more than its sum ]]> https://biorxiv.org/content/10.1101/2020.08.07.241497v1?rss=1 Kiesow, H. Spreng, R. N. Holmes, A. J. Chakravarty, M. M. Marquand, A. F. Yeo, B. T. T. Bzdok, D. 2020-08-07 doi:10.1101/2020.08.07.241497 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. ]]> https://biorxiv.org/content/10.1101/2020.08.09.243451v1?rss=1 Yuan, S. Peng, L. Park, J. J. Hu, Y. Devarkar, S. C. Dong, M. B. Wu, S. Chen, S. Lomakin, I. Xiong, Y. 2020-08-10 doi:10.1101/2020.08.09.243451 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ The intrinsically disordered protein SPE-18 promotes localized assembly of the major sperm protein in C. elegans spermatocytes ]]> https://biorxiv.org/content/10.1101/2020.08.10.244988v1?rss=1 Price, K. L. Presler, M. Uyehara, C. Shakes, D. 2020-08-10 doi:10.1101/2020.08.10.244988 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Mutant-selective Degradation by BRAF-targeting PROTACs ]]> https://biorxiv.org/content/10.1101/2020.08.10.245159v1?rss=1 Alabi, S. Jaime-Figueroa, S. Yao, Z. Gao, Y. Hines, J. Samarasinghe, K. . T. G. Vogt, L. Rosen, N. Crews, C. M. 2020-08-10 doi:10.1101/2020.08.10.245159 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Meta-matching: a simple framework to translate phenotypic predictive models from big to small data ]]> https://biorxiv.org/content/10.1101/2020.08.10.245373v1?rss=1 He, T. An, L. Feng, J. Bzdok, D. Holmes, A. J. Eickhoff, S. B. Yeo, B. T. T. 2020-08-13 doi:10.1101/2020.08.10.245373 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ A DNA-origami nuclear pore mimic reveals nuclear entry mechanisms of HIV-1 capsid ]]> https://biorxiv.org/content/10.1101/2020.08.10.245522v1?rss=1 Shen, Q. Xu, C. Jang, S. Xiong, Q. Devarkar, S. Tian, T. Bedwell, G. Tripler, T. Hu, Y. Yuan, S. Temple, J. Shi, J. Aiken, C. Engelman, A. Perilla, J. R. Lusk, C. P. Lin, C. Xiong, Y. 2020-08-11 doi:10.1101/2020.08.10.245522 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Joint Representation of Color and Shape in Convolutional Neural Networks: A Stimulus-rich Network Perspective ]]> https://biorxiv.org/content/10.1101/2020.08.11.246223v1?rss=1 Taylor, J. Xu, Y. 2020-08-12 doi:10.1101/2020.08.11.246223 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ The development of transformation tolerant visual representations differs between the human brain and convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.08.11.246934v1?rss=1 Xu, Y. Vaziri-Pashkam, M. 2020-08-12 doi:10.1101/2020.08.11.246934 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ The relative coding strength of object identity and nonidentity features in human occipito-temporal cortex and convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2020.08.11.246967v1?rss=1 Xu, Y. Vaziri-Pashkam, M. 2020-08-12 doi:10.1101/2020.08.11.246967 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Endothelial Cell Cycle State Determines Propensity for Arterial-Venous Fate ]]> https://biorxiv.org/content/10.1101/2020.08.12.246512v1?rss=1 Chavkin, N. W. Genet, G. Poulet, M. Genet, N. Marziano, C. Vasavada, H. Nelson, E. A. Kour, A. McDonnell, S. P. Huba, M. Walsh, K. Hirschi, K. K. 2020-08-12 doi:10.1101/2020.08.12.246512 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Regression dynamic causal modeling for resting-state fMRI ]]> https://biorxiv.org/content/10.1101/2020.08.12.247536v1?rss=1 200 areas) within minutes on standard hardware. This opens promising new avenues for connectomics. ]]> Frässle, S. Harrison, S. J. Heinzle, J. Clementz, B. A. Tamminga, C. A. Sweeney, J. A. Gershon, E. S. Keshavan, M. S. Pearlson, G. D. Powers, A. Stephan, K. E. 2020-08-13 doi:10.1101/2020.08.12.247536 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ KIAA1841, a novel SANT and BTB domain-containing protein, inhibits class switch recombination ]]> https://biorxiv.org/content/10.1101/2020.08.12.247809v1?rss=1 Zheng, S. Matthews, A. J. Rahman, N. Herrick-Reynolds, K. Choi, J. E. Sible, E. Ng, Y. K. Rhodes, D. Elledge, S. J. Vuong, B. Q. 2020-08-12 doi:10.1101/2020.08.12.247809 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Efferent feedback enforces bilateral coupling of spontaneous activity in the developing auditory system ]]> https://biorxiv.org/content/10.1101/2020.08.12.248799v1?rss=1 Wang, Y. Sanghvi, M. Gribizis, A. Zhang, Y. Song, L. Morley, B. Barson, D. Santos-Sacchi, J. Navaratnam, D. S. Crair, M. 2020-08-12 doi:10.1101/2020.08.12.248799 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Metaviromic identification of genetic hotspots of coronavirus pathogenicity using machine learning ]]> https://biorxiv.org/content/10.1101/2020.08.13.248575v1?rss=1 Park, J. J. Chen, S. 2020-08-14 doi:10.1101/2020.08.13.248575 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ In Silico Design of siRNAs Targeting Existing and Future Respiratory Viruses with VirusSi ]]> https://biorxiv.org/content/10.1101/2020.08.13.250076v1?rss=1 99% of SARS-CoV-2 strains, and the combination of the top four siRNAs is predicted to target all SARS-CoV-2 strains. Additionally, we develop Greedy Algorithm with Redundancy (GAR) and Similarity-weighted Greedy Algorithm with Redundancy (SGAR) to support the Mode B of VirusSi, which pre-designs siRNAs against future emerging viruses based on existing viral sequences. Time-simulations using known coronavirus genomes as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. Before-the-outbreak pre-design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Our data support the feasibility of pre-designing anti-viral siRNA therapeutics prior to viral outbreaks. We propose the development of a collection of pre-designed, safety-tested, and off-the-shelf siRNAs that could accelerate responses toward future viral diseases. ]]> Zhang, D. Lu, J. 2020-08-14 doi:10.1101/2020.08.13.250076 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Predicting identity-preserving object transformations across the human ventral visual stream ]]> https://biorxiv.org/content/10.1101/2020.08.13.250191v1?rss=1 Mocz, V. Vaziri-Pashkam, M. Xu, Y. Chun, M. 2020-08-14 doi:10.1101/2020.08.13.250191 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ A neuronal ensemble encoding adaptive choice during sensory conflict ]]> https://biorxiv.org/content/10.1101/2020.08.14.251553v1?rss=1 Sareen, P. McCurdy, L. Y. Nitabach, M. 2020-08-14 doi:10.1101/2020.08.14.251553 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Electronic cigarettes induce mitochondrial DNA damage and trigger toll-like receptor 9-mediated atherosclerosis ]]> https://biorxiv.org/content/10.1101/2020.08.15.252494v1?rss=1 Li, J. Huynh, D. L. Tang, M.-S. Simborio, H. Huang, J. Kosmider, B. Steinberg, M. B. Le, L. T. T. Pham, K. Liu, C. Wang, H. 2020-08-15 doi:10.1101/2020.08.15.252494 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Vesicle capture by discrete self-assembled clusters of membrane-bound Munc13 ]]> https://biorxiv.org/content/10.1101/2020.08.17.254821v1?rss=1 Li, F. Sundaram, V. K. Gatta, A. T. Coleman, J. Krishnakumar, S. Pincet, F. Rothman, J. E. 2020-08-17 doi:10.1101/2020.08.17.254821 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly ]]> https://biorxiv.org/content/10.1101/2020.08.19.257261v1?rss=1 Kalayanasundaram, R. V. Jin, H. Li, F. Shu, T. Coleman, J. Yang, J. Pincet, F. Zhang, Y. Krishnakumar, S. S. Rothman, J. E. 2020-08-19 doi:10.1101/2020.08.19.257261 Cold Spring Harbor Laboratory Press 2020-08-19 <![CDATA[ CD300lf conditional knockout mouse reveals strain-specific cellular tropism for murine norovirus ]]> https://biorxiv.org/content/10.1101/2020.08.19.258467v1?rss=1 Graziano, V. R. Alfajaro, M. M. Schmitz, C. Filler, R. B. Strine, M. S. Wei, J. Hsieh, L. L. Baldridge, M. T. Nice, T. J. Lee, S. Orchard, R. C. Wilen, C. B. 2020-08-21 doi:10.1101/2020.08.19.258467 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Chloride-dependent conformational changes in the GlyT1 glycine transporter ]]> https://biorxiv.org/content/10.1101/2020.08.20.259572v1?rss=1 Zhang, Y.-W. Uchendu, S. Leone, V. Bradshaw, R. T. Sangwa, N. Forrest, L. Rudnick, G. 2020-08-20 doi:10.1101/2020.08.20.259572 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Generating hard-to-obtain information from easy-to-obtain information: applications in drug discovery and clinical inference ]]> https://biorxiv.org/content/10.1101/2020.08.20.259598v1?rss=1 Amodio, M. Shung, D. Burkhardt, D. B. Wong, P. Simonov, M. Yamamoto, Y. van Dijk, D. Wilson, F. P. Iwasaki, A. Krishnaswamy, S. 2020-08-22 doi:10.1101/2020.08.20.259598 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Astrocytic Neurexin-1 Orchestrates Functional Synapse Assembly ]]> https://biorxiv.org/content/10.1101/2020.08.21.262097v1?rss=1 Trotter, J. H. Dargaei, Z. Wohr, M. Liakath-Ali, K. Raju, K. Essayan-Perez, S. Nabet, A. Liu, X. Sudhof, T. 2020-08-21 doi:10.1101/2020.08.21.262097 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny ]]> https://biorxiv.org/content/10.1101/2020.08.23.262857v1?rss=1 Li, Y. Steenwyk, J. L. Chang, Y. Wang, Y. James, T. Y. Stajich, J. E. Spatafora, J. W. Groenewald, M. Dunn, C. Hittinger, C. T. Shen, X.-X. Rokas, A. 2020-08-24 doi:10.1101/2020.08.23.262857 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Graph of graphs analysis for multiplexed data with application to imaging mass cytometry ]]> https://biorxiv.org/content/10.1101/2020.08.23.263467v1?rss=1 Lin, Y.-W. E. Shnitzer, T. Talmon, R. Villaroel-Espindola, F. Desai, S. Schalper, K. Kluger, Y. 2020-08-24 doi:10.1101/2020.08.23.263467 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Lamellar cells in Pacinian and Meissner corpuscles are touch sensors ]]> https://biorxiv.org/content/10.1101/2020.08.24.265231v1?rss=1 Nikolaev, Y. A. Feketa, V. V. Anderson, E. O. Gracheva, E. O. Bagriantsev, S. N. 2020-08-24 doi:10.1101/2020.08.24.265231 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Early developmental asymmetries in cell lineage trees in living individuals ]]> https://biorxiv.org/content/10.1101/2020.08.24.265751v1?rss=1 Fasching, L. Jang, Y. Tomasi, S. Schreiner, J. Tomasini, L. Brady, M. Bae, T. Sarangi, V. Vasmatzis, N. Wang, Y. Szekely, A. Fernandez, T. V. Leckman, J. Abyzov, A. Vaccarino, F. M. 2020-08-25 doi:10.1101/2020.08.24.265751 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ On stability of Canonical Correlation Analysis and Partial Least Squares with application to brain-behavior associations ]]> https://biorxiv.org/content/10.1101/2020.08.25.265546v1?rss=1 Helmer, M. Warrington, S. D. Mohammadi-Nejad, A.-R. Ji, J. L. Howell, A. Rosand, B. Anticevic, A. Sotiropoulos, S. N. Murray, J. D. 2020-08-25 doi:10.1101/2020.08.25.265546 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Effect of relative social rank within a social hierarchy on neural activation in response to familiar or unfamiliar social signals ]]> https://biorxiv.org/content/10.1101/2020.08.25.267278v1?rss=1 Lee, W. Dowd, H. N. Nikain, C. Dwortz, M. F. Yang, E. D. Curley, J. P. 2020-08-25 doi:10.1101/2020.08.25.267278 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Cryo-electron microscopy structures of pyrene-labeled ADP-Pi- and ADP-actin filaments ]]> https://biorxiv.org/content/10.1101/2020.08.26.268748v1?rss=1 Chou, S. Z. Pollard, T. D. 2020-08-26 doi:10.1101/2020.08.26.268748 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Imaging the Transmembrane and Transendothelial Sodium Gradients in Gliomas ]]> https://biorxiv.org/content/10.1101/2020.08.26.268839v1?rss=1 Khan, M. H. Walsh, J. J. Mihailovic, J. M. Mishra, S. K. Coman, D. Hyder, F. 2020-08-27 doi:10.1101/2020.08.26.268839 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Voltage imaging using transgenic mouse lines expressing the GEVI ArcLight in two olfactory cell types ]]> https://biorxiv.org/content/10.1101/2020.08.26.268904v1?rss=1 Platisa, J. Zeng, H. Madisen, L. Cohen, L. B. Pieribone, V. A. Storace, D. A. 2020-08-26 doi:10.1101/2020.08.26.268904 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Conserved amino acids residing outside the voltage field can shift the voltage sensitivity and increase the signal size of Ciona based GEVIs ]]> https://biorxiv.org/content/10.1101/2020.08.27.269761v1?rss=1 Sepehri, M. Cohen, L. B. Baker, B. J. 2020-08-27 doi:10.1101/2020.08.27.269761 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Single Gyroid and Inverse b.c.c. Photonic Crystals in Bird Feathers ]]> https://biorxiv.org/content/10.1101/2020.08.27.271213v1?rss=1 SARANATHAN, V. Narayanan, S. Sandy, A. R. Dufresne, E. R. Prum, R. O. 2020-08-29 doi:10.1101/2020.08.27.271213 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ A neurite-zippering mechanism, mediated by layer-specific expression of IgCAMs, regulates synaptic laminar specificity in the C. elegans nerve ring neuropil ]]> https://biorxiv.org/content/10.1101/2020.08.28.271437v1?rss=1 Sengupta, T. Koonce, N. L. Moyle, M. W. Duncan, L. H. Vazquez-Martinez, N. Han, X. Shao, L. Wu, Y. Santella, A. Fan, L. Bao, Z. Mohler, W. A. Shroff, H. Colon-Ramos, D. 2020-08-29 doi:10.1101/2020.08.28.271437 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.08.28.271957v1?rss=1 Ghahremanpour, M. M. Tirado-Rives, J. Deshmukh, M. Ippolito, J. A. Zhang, C.-H. Cabeza de Vaca, I. Liosi, M.-E. Anderson, K. S. Jorgensen, W. L. 2020-08-28 doi:10.1101/2020.08.28.271957 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics ]]> https://biorxiv.org/content/10.1101/2020.08.28.272807v1?rss=1 Benedetti, L. Marvin, J. S. Falahati, H. Guillen-Samander, A. Looger, L. L. De Camilli, P. 2020-08-30 doi:10.1101/2020.08.28.272807 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Representation of Color, Form, and their Conjunctionacross the Human Ventral Visual Pathway ]]> https://biorxiv.org/content/10.1101/2020.08.28.272815v1?rss=1 Taylor, J. Xu, Y. 2020-08-31 doi:10.1101/2020.08.28.272815 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Tissue pressure and cell traction compensate to drive robust aggregate spreading ]]> https://biorxiv.org/content/10.1101/2020.08.29.273334v1?rss=1 Yousafzai, M. S. Yadav, V. Amiri, S. Staddon, M. Tabatabai, A. P. Errami, Y. Jaspard, G. Amiri, S. Banerjee, S. Murrell, M. P. 2020-08-31 doi:10.1101/2020.08.29.273334 Cold Spring Harbor Laboratory Press 2020-08-31 <![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[ Advanced eMAGE for highly efficient combinatorial editing of a stable genome ]]> https://biorxiv.org/content/10.1101/2020.08.30.256743v1?rss=1 Liang, Z. Metzner, E. Isaacs, F. J. 2020-08-31 doi:10.1101/2020.08.30.256743 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ A deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging data ]]> https://biorxiv.org/content/10.1101/2020.08.31.272450v1?rss=1 35 hours from 298 neurons. We then developed a novel algorithm for spike inference (CASCADE) that is based on supervised deep networks, takes advantage of the ground truth database, infers absolute spike rates, and outperforms existing model-based algorithms. To optimize performance for unseen imaging data, CASCADE retrains itself by resampling ground truth data to match the respective sampling rate and noise level. As a consequence, no parameters need to be adjusted by the user. To facilitate routine application of CASCADE we developed systematic performance assessments for unseen data, we openly release all resources, and we provide a user-friendly cloud-based implementation. ]]> Rupprecht, P. Carta, S. Hoffmann, A. Echizen, M. Kitamura, K. Helmchen, F. Friedrich, R. W. 2020-09-01 doi:10.1101/2020.08.31.272450 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Peri-adolescent THC Exposure Does not Lead to Anxiety-like Behavior in Adult Mice ]]> https://biorxiv.org/content/10.1101/2020.08.31.274274v1?rss=1 Sestan-Pesa, M. Shanabrough, M. Horvath, T. L. Miletta, M. C. 2020-09-01 doi:10.1101/2020.08.31.274274 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ The relationship between microbiomes and selective regimes in the sponge genus Ircinia. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275412v1?rss=1 Kelly, J. B. Carlson, D. E. Low, J. S. Rice, T. Thacker, R. W. 2020-09-01 doi:10.1101/2020.08.31.275412 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ IL-4-induced hysteresis in naive T cell activation ]]> https://biorxiv.org/content/10.1101/2020.08.31.275842v1?rss=1 Meli, A. P. Wang, Y. de Kouchkovsky, D. A. Kong, Y. Basu, M. K. Ghosh, S. Rothlin, C. V. 2020-09-01 doi:10.1101/2020.08.31.275842 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Comparative metagenomics evidence distinct evolutionary trends of genome evolution in sponge-dwelling bacteria and their pelagic counterparts ]]> https://biorxiv.org/content/10.1101/2020.08.31.276493v1?rss=1 Kelly, J. B. Carlson, D. E. Low, J. S. Thacker, R. W. 2020-09-01 doi:10.1101/2020.08.31.276493 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Tet2 Controls Beta cells Responses to Inflammation in Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2020.09.01.278028v1?rss=1 Rui, J. Deng, S. Ponath, G. Kursawe, R. Lawlor, N. Sumida, T. Levine-Ritterman, M. Perdigoto, A. L. Stitzel, M. L. Pitt, D. L. Lu, J. Herold, K. C. 2020-09-02 doi:10.1101/2020.09.01.278028 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Synergistic activity of Nanog, Pou5f3, and Sox19b establishes chromatin accessibility and developmental competence in a context-dependent manner ]]> https://biorxiv.org/content/10.1101/2020.09.01.278796v1?rss=1 50% of active enhancers. Motif analysis revealed a network of TFs that depend on NPS for establishing chromatin accessibility, including the endodermal determinant Eomesa, whose binding we show is regulated by NPS pioneer-like activity. Finally, we demonstrated that NPS play an essential role in establishing H3K27ac and H3K18ac at enhancers and promoters, and that their function in transcriptional activation can be bypassed by targeted recruitment of histone acetyltransferases to individual genes. Altogether, our findings reveal a large network of TFs that function to establish developmental competency, many of which depend on the synergistic and highly context-dependent role of NPS in establishing chromatin accessibility and regulating histone acetylation in order to activate the genome. ]]> Miao, L. Tang, Y. Bonneau, A. R. Chan, S. H. Kojima, M. L. Pownall, M. E. Vejnar, C. E. Giraldez, A. J. 2020-09-02 doi:10.1101/2020.09.01.278796 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum ]]> https://biorxiv.org/content/10.1101/2020.09.02.279240v1?rss=1 Montalban, E. Giralt, A. Taing, L. Nakamura, Y. Martin, C. de Pins, B. Pelosi, A. Goutebroze, L. Castell, L. Wang, W. Daila Neiburga, K. Vestito, L. Nairn, A. C. Valjent, E. Herve, D. Heintz, N. Gambardella Le Novere, N. Greengard, P. Roussarie, J.-P. Girault, J.-A. 2020-09-03 doi:10.1101/2020.09.02.279240 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ A connectome-based prediction model of long-term memory ]]> https://biorxiv.org/content/10.1101/2020.09.02.279372v1?rss=1 Lin, Q. Yoo, K. Shen, X. Constable, R. T. Chun, M. M. 2020-09-03 doi:10.1101/2020.09.02.279372 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Differences in Chemo-signaling Compound-Evoked Brain Activity in Male and Female Young Adults: A Pilot Study in the Role of Sexual Dimorphism in Olfactory Chemo-Signaling ]]> https://biorxiv.org/content/10.1101/2020.09.03.280685v1?rss=1 Ottesen, T. Davis, K. C. Hobbs, L. K. Muncy, N. M. Stevens, N. M. Anderson, M. Johnson, P. Doxey, C. R. Richter, K. Wang, H. Hartley, R. Kirwan, C. B. Wisco, J. J. 2020-09-03 doi:10.1101/2020.09.03.280685 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Cis-Regulatory Differences Explaining Evolved Levels of Endometrial Invasibility in Eutherian Mammals ]]> https://biorxiv.org/content/10.1101/2020.09.04.283366v1?rss=1 Suhail, Y. Maziarz, J. D. Dighe, A. Wagner, G. Kshitiz, 2020-09-05 doi:10.1101/2020.09.04.283366 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Airway Basal Cells show a dedifferentiated KRT17high Phenotype and promote Fibrosis in Idiopathic Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2020.09.04.283408v1?rss=1 Jaeger, B. Schupp, J. C. Plappert, L. Terwolbeck, O. Kayser, G. Engelhard, P. Adams, T. S. Zweigerdt, R. Kempf, H. Lienenklaus, S. Garrels, W. Nazarenko, I. Jonigk, D. Wygrecka, M. Klatt, D. Schambach, A. Kaminski, N. Prasse, A. 2020-09-04 doi:10.1101/2020.09.04.283408 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ rab-27 acts in an intestinal secretory pathway to inhibit axon regeneration in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.09.05.283267v1?rss=1 Lin-Moore, A. T. Oyeyemi, M. J. Hammarlund, M. 2020-09-05 doi:10.1101/2020.09.05.283267 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis ]]> https://biorxiv.org/content/10.1101/2020.09.05.284430v1?rss=1 Bruna, R. E. Kendra, C. G. Groisman, E. A. Pontes, M. H. 2020-09-05 doi:10.1101/2020.09.05.284430 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Modeling the dynamic behaviors of the COPI vesicle formation regulators, the small GTPase Arf1 and its activating Sec7 guanine nucleotide exchange factor GBF1 on Golgi membranes ]]> https://biorxiv.org/content/10.1101/2020.09.06.285072v1?rss=1 Sager, G. Kawai, R. Presley, J. F. Sztul, E. 2020-09-06 doi:10.1101/2020.09.06.285072 Cold Spring Harbor Laboratory Press 2020-09-06 <![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[ The deacylase SIRT5 supports melanoma viability by regulating chromatin dynamics ]]> https://biorxiv.org/content/10.1101/2020.09.07.286526v1?rss=1 Giblin, W. Bringman-Rodenbarger, L. Kumar, S. Skinner, M. E. Guo, A. Mostafa, A. M. Azar, M. Mady, A. S. A. Chung, C. H. Kadambi, N. Melong, K.-A. Lee, H.-J. Zhang, L. Sajjakulnukit, P. Trefely, S. Varner, E. L. Iyer, S. Wang, M. Wilmott, J. S. Soyer, H. P. Sturm, R. A. Pritchard, A. L. Andea, A. Scolyer, R. A. Stark, M. S. Scott, D. A. Fullen, D. R. Bosenberg, M. W. Chandrasekaran, S. Nikolovska-Coleska, Z. Verhaegen, M. Snyder, N. W. Rivera, M. N. Osterman, A. L. Lyssiotis, C. A. Lombard, D. B. 2020-09-07 doi:10.1101/2020.09.07.286526 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Dysregulation of adipose ILC2 underlies thermogenic failure in aging ]]> https://biorxiv.org/content/10.1101/2020.09.08.288431v1?rss=1 Goldberg, E. L. Shchukina, I. Youm, Y.-H. Camell, C. D. Dlugos, T. Artyomov, M. Dixit, V. D. 2020-09-08 doi:10.1101/2020.09.08.288431 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Real-time conformational dynamics of SARS-CoV-2 spikes on virus particles ]]> https://biorxiv.org/content/10.1101/2020.09.10.286948v1?rss=1 Lu, M. Uchil, P. D. Li, W. Zheng, D. Terry, D. S. Gorman, J. Shi, W. Zhang, B. Zhou, T. Ding, S. Gasser, R. Prevost, J. Beaudoin-Bussieres, G. Anand, S. P. Laumaea, A. Grover, J. R. Lihong, L. Ho, D. D. Mascola, J. Finzi, A. Kwong, P. D. Blanchard, S. C. Mothes, W. 2020-09-10 doi:10.1101/2020.09.10.286948 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ CECR2 Drives Breast Cancer Metastasis by Suppressing Macrophage Inflammatory Responses ]]> https://biorxiv.org/content/10.1101/2020.09.10.291799v1?rss=1 Zhang, M. Liu, Z. Aoshima, K. An, Y. Aoshima, A. Chan, L. H. Lang, S. Sun, H. Rutter, S. Booth, C. J. Bossuyt, V. Morrow, J. Pusztai, L. Rimm, D. Yin, M. Yan, Q. 2020-09-10 doi:10.1101/2020.09.10.291799 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Immunologically distinct responses occur in the CNS of COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2020.09.11.293464v1?rss=1 Song, E. Chow, R. D. Jiang, R. Zamecnik, C. R. Loudermilk, R. Dai, Y. Liu, F. Geng, B. Chiarella, J. Israelow, B. Casanovas-Massana, A. Ko, A. Ring, A. Kleinstein, S. Spudich, S. Wilson, M. Iwasaki, A. Farhadian, S. F. 2020-09-12 doi:10.1101/2020.09.11.293464 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Type I Interferon Limits Viral Dissemination-Driven Clinical Heterogeneity in a Native Murine Betacoronavirus Model of COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.09.11.294231v1?rss=1 Qing, H. Sharma, L. Hilliard, B. K. Peng, X. Swaminathan, A. Tian, J. Israni-Winger, K. Zhang, C. Leao, D. Ryu, S. Habet, V. Wang, L. Tian, X. Ishibe, S. Young, L. H. Kotenko, S. Compton, S. Booth, C. J. Ring, A. M. Dixit, V. D. Wilen, C. B. Pereira, J. P. Dela Cruz, C. S. Wang, A. 2020-09-12 doi:10.1101/2020.09.11.294231 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model ]]> https://biorxiv.org/content/10.1101/2020.09.11.294363v1?rss=1 Ryu, S. Shchukina, I. Youm, Y.-H. Qing, H. Hilliard, B. K. Dlugos, T. Zhang, X. Yasumoto, Y. Booth, C. J. Fernandez-Hernando, C. Suarez, Y. Khanna, K. M. Horvath, T. Dietrich, M. O. Artyomov, M. Wang, A. Dixit, V. D. 2020-09-12 doi:10.1101/2020.09.11.294363 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ High performance machine learning models can fully automate labeling of camera trap images for ecological analyses ]]> https://biorxiv.org/content/10.1101/2020.09.12.294538v1?rss=1 Whytock, R. C. Swiezewski, J. Zwerts, J. A. Bara-Słupski, T. Koumba Pambo, A. F. Rogala, M. Bahaa-el-din, L. Boekee, K. Brittain, S. Cardoso, A. W. Henschel, P. Lehmann, D. Momboua, B. Opepa, C. K. Orbell, C. Pitman, R. T. Robinson, H. S. Abernethy, K. A. 2020-09-13 doi:10.1101/2020.09.12.294538 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Abl2:cortactin interactions regulate dendritic spine stability via control of a stable filamentous actin pool. ]]> https://biorxiv.org/content/10.1101/2020.09.12.294694v1?rss=1 Shaw, J. E. Kilander, M. B. C. Lin, Y.-C. Koleske, A. J. 2020-09-12 doi:10.1101/2020.09.12.294694 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ An associative learning account of sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2020.09.14.297143v1?rss=1 Avraham, G. Taylor, J. A. Ivry, R. B. McDougle, S. D. 2020-09-15 doi:10.1101/2020.09.14.297143 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Mapping Brain-Behavior Space Relationships Along the Psychosis Spectrum ]]> https://biorxiv.org/content/10.1101/2020.09.15.267310v1?rss=1 Ji, J. L. Helmer, M. Fonteneau, C. Burt, J. B. Tamayo, Z. Demsar, J. Adkinson, B. Savic, A. Preller, K. Moujaes, F. Vollenweider, F. X. Martin, W. Repovs, G. Murray, J. D. Anticevic, A. 2020-09-15 doi:10.1101/2020.09.15.267310 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ DMA-tudor interaction modules control the specificity of in vivo condensates ]]> https://biorxiv.org/content/10.1101/2020.09.15.297994v1?rss=1 Courchaine, E. M. Barentine, A. E. S. Straube, K. Bewersdorf, J. Neugebauer, K. M. 2020-09-16 doi:10.1101/2020.09.15.297994 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Evaluations of CRC2631 toxicity, tumor colonization, and genetic stability in the TRAMP prostate cancer model ]]> https://biorxiv.org/content/10.1101/2020.09.15.299081v1?rss=1 Kazmierczak, R. Dhagat-Mehta, B. Gulden, E. Lee, L. Ma, L. Davis-Stober, C. P. Barnett, A. A. Chabu, C. Y. 2020-09-16 doi:10.1101/2020.09.15.299081 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Circuit mechanisms of top-down attentional control in a thalamic reticular model ]]> https://biorxiv.org/content/10.1101/2020.09.16.300749v1?rss=1 Gu, Q. L. Lam, N. H. Halassa, M. M. Murray, J. D. 2020-09-17 doi:10.1101/2020.09.16.300749 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ PPP6C negatively regulates oncogenic ERK signaling through dephosphorylation of MEK ]]> https://biorxiv.org/content/10.1101/2020.09.18.303859v1?rss=1 Cho, E. Lou, H. J. Kuruvilla, L. Calderwood, D. A. Turk, B. E. E. 2020-09-19 doi:10.1101/2020.09.18.303859 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Single-cell analysis of prostaglandin E2-induced decidual cell differentiation: does extracellular 8-Br-cAMP cause artifacts? ]]> https://biorxiv.org/content/10.1101/2020.09.18.304212v1?rss=1 Stadtmauer, D. J. Wagner, G. P. 2020-09-19 doi:10.1101/2020.09.18.304212 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Understanding and Improving Word Embeddings through a Neuroscientific Lens ]]> https://biorxiv.org/content/10.1101/2020.09.18.304436v1?rss=1 Fereidooni, S. Mocz, V. Radev, D. Chun, M. 2020-09-20 doi:10.1101/2020.09.18.304436 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments ]]> https://biorxiv.org/content/10.1101/2020.09.19.304741v1?rss=1 Raaisa, R. Lathwal, S. Chubukov, V. Kibbey, R. G. Jha, A. K. 2020-09-20 doi:10.1101/2020.09.19.304741 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells ]]> https://biorxiv.org/content/10.1101/2020.09.20.305359v1?rss=1 William, N. D. Landajuela, A. Kasula, R. K. Zhou, W. Powell, J. T. Xi, Z. Isaacs, F. J. Berro, J. Toomre, D. Karatekin, E. Lin, C. 2020-09-20 doi:10.1101/2020.09.20.305359 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Large-scale characterization of sex pheromone communication systems in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.09.21.305854v1?rss=1 Khallaf, M. A. Cui, R. Weissflog, J. Svatos, A. Dweck, H. K. M. Valenzano, D. R. Hansson, B. S. Knaden, M. 2020-09-22 doi:10.1101/2020.09.21.305854 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization ]]> https://biorxiv.org/content/10.1101/2020.09.23.308239v1?rss=1 Schultz, B. T. Zaliani, A. Ebeling, C. Reinshagen, J. Bojkova, D. Lage-Rupprecht, V. Karki, R. Lukassen, S. Gadiya, Y. Ravindra, N. G. Das, S. Baksi, S. Domingo-Fernandez, D. Lentzen, M. Strivens, M. Raschka, T. Cinatl, J. DeLong, L. Gribbon, P. Geisslinger, G. Ciesek, S. van Dijk, D. Gardner, S. Tom Kodamullil, A. Froehlich, H. Peitsch, M. Jacobs, M. Hoeng, J. Eils, R. Claussen, C. Hofmann-Apitius, M. 2020-09-23 doi:10.1101/2020.09.23.308239 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Cyclooxgenase-2 is induced by SARS-CoV-2 infection but does not affect viral entry or replication ]]> https://biorxiv.org/content/10.1101/2020.09.24.312769v1?rss=1 Chen, J. S. Alfajaro, M. M. Wei, J. Chow, R. D. Filler, R. B. Eisenbarth, S. C. Wilen, C. B. 2020-09-25 doi:10.1101/2020.09.24.312769 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Requirements for FisB-mediated membrane fission during sporulation ]]> https://biorxiv.org/content/10.1101/2020.09.25.313023v1?rss=1 Landajuela, A. Braun, M. Rodrigues, C. D. A. Doan, T. Horenkamp, F. A. Andronicos, A. Shteyn, V. Williams, N. D. Lin, C. Rudner, D. Z. Karatekin, E. 2020-09-26 doi:10.1101/2020.09.25.313023 Cold Spring Harbor Laboratory Press 2020-09-26 <![CDATA[ A Probabilistic and Anisotropic Failure Metric for Ascending Thoracic Aortic Aneurysm Risk Stratification ]]> https://biorxiv.org/content/10.1101/2020.09.28.317255v1?rss=1 Liu, M. Liang, L. Zou, Q. Ismail, Y. Lou, X. Iannucci, G. Chen, E. P. Leshnower, B. G. Elefteriades, J. A. Sun, W. 2020-09-29 doi:10.1101/2020.09.28.317255 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ PYMEVisualize: an open-source tool for exploring 3D super-resolution data ]]> https://biorxiv.org/content/10.1101/2020.09.29.315671v1?rss=1 Marin, Z. Graff, M. Barentine, A. E. S. Soeller, C. Chung, K. K. H. Fuentes, L. A. Baddeley, D. 2020-09-30 doi:10.1101/2020.09.29.315671 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars ]]> https://biorxiv.org/content/10.1101/2020.09.30.320689v1?rss=1 Pincot, D. D. A. Ledda, M. Feldmann, M. Hardigan, M. A. Poorten, T. J. Runcie, D. Heffelfinger, C. Dellaporta, S. L. Cole, G. S. Knapp, S. J. 2020-10-01 doi:10.1101/2020.09.30.320689 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ The maize Aliphatic Suberin Feruloyl Transferase genes affect leaf water movement but are dispensable for bundle sheath CO2 concentration ]]> https://biorxiv.org/content/10.1101/2020.09.30.321265v1?rss=1 Mertz, R. A. Ellsworth, P. Z. Ellsworth, P. V. Tausta, S. L. von Caemmerer, S. Berg, R. H. Nelson, T. Carpita, N. C. Brutnell, T. P. Cousins, A. B. 2020-10-02 doi:10.1101/2020.09.30.321265 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ PsychRNN: An Accessible and Flexible Python Package for Training Recurrent Neural Network Models on Cognitive Tasks ]]> https://biorxiv.org/content/10.1101/2020.09.30.321752v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1541513org.highwire.dtl.DTLVardef@133c86borg.highwire.dtl.DTLVardef@aaf099org.highwire.dtl.DTLVardef@99d55b_HPS_FORMAT_FIGEXP M_FIG Example workflow for using PsychRNN. First, the task of interest is defined, and a recurrent neural network model is trained to perform the task, optionally with neurobiologically informed constraints on the network. After the network is trained, the researchers can investigate network properties including the synaptic connectivity patterns and the dynamics of neural population activity during task execution, and other studies, e.g. those on perturbations, can be explored. The dotted line shows the possible repetition of this cycle with one network, which allows investigation of training effects of task shaping, or curriculum learning, for closed-loop training of the network on a progression of tasks. C_FIG Significance StatementArtificial recurrent neural network (RNN) modeling is of increasing interest within computational, systems, and cognitive neuroscience, yet its proliferation as a computational tool within the field has been limited due to technical barriers in use of specialized deep-learning software. PsychRNN provides an accessible, flexible, and powerful framework for training RNN models on cognitive tasks. Users can define tasks and train models using the Python-based interface which enables RNN modeling studies without requiring user knowledge of deep learning software. PsychRNNs modular structure facilitates task specification and incorporation of neurobiological constraints, and supports extensibility for users with deep learning expertise. PsychRNNs framework for RNN modeling will increase accessibility and reproducibility of this approach across neuroscience subfields. ]]> Ehrlich, D. B. Stone, J. T. Brandfonbrener, D. Atanasov, A. Murray, J. D. 2020-10-01 doi:10.1101/2020.09.30.321752 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ High Throughput RNA Sequencing of Mice Retina Reveals Metabolic Pathways Involved in the Gut-Retinal Axis ]]> https://biorxiv.org/content/10.1101/2020.10.01.318949v1?rss=1 Nadeem, U. Skondra, D. Xie, B. Movahedan, A. D'Souza, M. Barba, H. Deng, N. Leonne, V. Chang, E. B. Sulakhe, D. 2020-10-02 doi:10.1101/2020.10.01.318949 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Cross-compartment signal propagation in the Mitotic Exit Network ]]> https://biorxiv.org/content/10.1101/2020.10.01.322719v1?rss=1 Zhou, X. Li, W. Liu, Y. Amon, A. 2020-10-02 doi:10.1101/2020.10.01.322719 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ A polymer gel index-matched to water enables diverse applications in fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2020.10.04.324996v1?rss=1 Han, X. Su, Y. White, H. O'Neill, K. M. Morgan, N. Y. Christensen, R. Potarazu, D. Vishwasrao, H. D. Xu, S. Sun, Y. Huang, S.-y. Moyle, M. W. Dai, Q. Pommier, Y. Giniger, E. Albrecht, D. R. Probst, R. Shroff, H. 2020-10-04 doi:10.1101/2020.10.04.324996 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ β-Amyloid peptides tailor switching behaviors of Donor-Acceptor Stenhouse Adducts ]]> https://biorxiv.org/content/10.1101/2020.10.04.325696v1?rss=1 Zheng, C. Yu, Y. Kuang, S. Zhu, B. Zhou, H. zhang, s.-q. Yang, J. Shi, L. Ran, C. 2020-10-05 doi:10.1101/2020.10.04.325696 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Hepatic FGF21 mediates tissue tolerance during bacterial inflammation by preserving cardiac function ]]> https://biorxiv.org/content/10.1101/2020.10.05.310508v1?rss=1 Huen, S. C. Wang, A. Feola, K. Desrouleaux, R. Luan, H. H. Hogg, R. Zhang, C. Zhang, Q.-J. Liu, Z.-P. Medzhitov, R. 2020-10-05 doi:10.1101/2020.10.05.310508 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Cooperation between oncogenic Ras and p53 stimulates JAK/STAT non-cell autonomously to promote Ras tumor radioresistance ]]> https://biorxiv.org/content/10.1101/2020.10.05.327098v1?rss=1 Dong, Y.-L. Valdka, G. Lu, J.-Y. J. Ahmad, V. Klein, T. J. Glazer, P. Xu, T. Chabu, C. Y. 2020-10-05 doi:10.1101/2020.10.05.327098 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Putamen volume predicts real-time fMRI neurofeedback learning success across paradigms and neurofeedback target regions ]]> https://biorxiv.org/content/10.1101/2020.10.05.327262v1?rss=1 Zhao, Z. Yao, S. Zweerings, J. Zhou, X. Zhou, F. Chen, H. Kendrick, K. M. Mathiak, K. Becker, B. 2020-10-06 doi:10.1101/2020.10.05.327262 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ To hum or not to hum: Neural transcriptome signature of courtship vocalization in a teleost fish ]]> https://biorxiv.org/content/10.1101/2020.10.05.327304v1?rss=1 Tripp, J. A. Feng, N. Y. Bass, A. 2020-10-06 doi:10.1101/2020.10.05.327304 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection ]]> https://biorxiv.org/content/10.1101/2020.10.06.327445v1?rss=1 Flynn, R. A. Belk, J. A. Qi, Y. Yasumoto, Y. Schmitz, C. O. Mumbach, M. R. Limaye, A. Wei, J. Alfajaro, M. M. Parker, K. R. Chang, H. Y. Horvath, T. L. Carette, J. E. Bertozzi, C. Wilen, C. B. Satpathy, A. T. 2020-10-06 doi:10.1101/2020.10.06.327445 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ SACSANN: identifying sequence-based determinants of chromosomal compartments ]]> https://biorxiv.org/content/10.1101/2020.10.06.328039v1?rss=1 Prost, J. A. Cameron, C. J. Blanchette, M. 2020-10-07 doi:10.1101/2020.10.06.328039 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Miro recruits VPS13D to mitochondria ]]> https://biorxiv.org/content/10.1101/2020.10.07.328906v1?rss=1 Guillen-Samander, A. Leonzino, M. De Camilli, P. 2020-10-07 doi:10.1101/2020.10.07.328906 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Evidence of hippocampal learning in human infants ]]> https://biorxiv.org/content/10.1101/2020.10.07.329862v1?rss=1 Ellis, C. T. Skalaban, L. J. Yates, T. S. Bejjanki, V. R. Córdova, N. I. Turk-Browne, N. B. 2020-10-08 doi:10.1101/2020.10.07.329862 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Comprehensive identification of somatic nucleotide variants in human brain tissue ]]> https://biorxiv.org/content/10.1101/2020.10.10.332213v1?rss=1 Wang, Y. Bae, T. Thorpe, J. Sherman, M. A. Jones, A. G. Cho, S. Daily, K. Dou, Y. Ganz, J. Galor, A. Lobon, I. Pattni, R. Rosenbluh, C. Tomasi, S. Tomasini, L. Yang, X. Zhou, B. Akbarian, S. Ball, L. L. Bizzotto, S. Emery, S. B. Doan, R. Fasching, L. Jang, Y. Juan, D. Lizano, E. Moldovan, J. B. Narurkar, R. Oetjens, M. T. Sekar, S. Shin, J. H. Soriano, E. Straub, R. E. Zhou, W. Chess, A. Gleeson, J. G. Marques-Bonet, T. Park, P. J. Peters, M. A. Pevsner, J. Walsh, C. A. Weinberger, D. R. Brain Somatic Mosaicism Network, Vaccarino, F. M. Moran, J. V 2020-10-10 doi:10.1101/2020.10.10.332213 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ DRP1 IS REQUIRED FOR AGRP NEURONAL ACTIVITY AND FEEDING ]]> https://biorxiv.org/content/10.1101/2020.10.11.335224v1?rss=1 Jin, S. Yoon, N. A. Liu, Z.-W. Horvath, T. Kim, J. D. Diano, S. 2020-10-11 doi:10.1101/2020.10.11.335224 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ Vulnerability of ARID1A deficient cancer cells to pyrimidine synthesis blockade ]]> https://biorxiv.org/content/10.1101/2020.10.12.331975v1?rss=1 Li, Z. Mi, S. Osagie, O. I. Ji, J. Yang, C.-P. H. Schwartz, M. Hui, P. Huang, G. S. 2020-10-12 doi:10.1101/2020.10.12.331975 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ A CRISPR interference platform for selective downregulation of gene expression in Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2020.10.12.335471v1?rss=1 95%) downregulation of gene expression. To facilitate studies of various genes in wild-type and genetically modified strains, we provide over 30 CRISPRi plasmids that produce distinct levels of dcas9 expression and carry different antibiotic resistance markers. Our CRISPRi platform represents a useful and efficient complement to traditional genetic and chemical methods to study gene function in B. burgdorferi. ]]> Takacs, C. N. Scott, M. Chang, Y. Kloos, Z. A. Irnov, I. Rosa, P. A. Liu, J. Jacobs-Wagner, C. 2020-10-12 doi:10.1101/2020.10.12.335471 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Targeted Degradation of Transcription Factors by TRAFTACs: Transcription Factor Targeting Chimeras ]]> https://biorxiv.org/content/10.1101/2020.10.12.336529v1?rss=1 Samarasinghe, K. Jaime-Figueroa, S. Dai, K. Hu, Z. Crews, C. M. 2020-10-12 doi:10.1101/2020.10.12.336529 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics ]]> https://biorxiv.org/content/10.1101/2020.10.12.336867v1?rss=1 Zhang, Y. Cheng, Y. Ye, Y. Jiang, W. Lu, Q. Zhao, H. 2020-10-13 doi:10.1101/2020.10.12.336867 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Spatial transcriptome sequencing of FFPE tissues at the cellular level ]]> https://biorxiv.org/content/10.1101/2020.10.13.338475v1?rss=1 1,000 genes per pixel). Spatial transcriptome of an E10.5 mouse embryo identified all major anatomical features in the brain and abdominal region. Integration with singlecell RNA-seq data for cell type identification indicated that most tissue pixels were dominated by single-cell transcriptional phenotype. Spatial mapping of adult mouse aorta, atrium, and ventricle tissues identified the spatial distribution of a variety of cell types. Spatial transcriptome sequencing of FFPE samples at cellular level may provide enormous opportunities in a wide range of biomedical research. It may allow us to exploit the huge resource of clinical tissue specimens to study human disease mechanisms and discover tissue biomarkers or therapeutic targets. ]]> Liu, Y. Enninful, A. Deng, Y. Fan, R. 2020-10-14 doi:10.1101/2020.10.13.338475 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Sculpting New Visual Concepts into the Human Brain ]]> https://biorxiv.org/content/10.1101/2020.10.14.339853v1?rss=1 Iordan, M. C. Ritvo, V. J. H. Norman, K. A. Turk-Browne, N. B. Cohen, J. D. 2020-10-15 doi:10.1101/2020.10.14.339853 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Attention recruits frontal cortex in human infants ]]> https://biorxiv.org/content/10.1101/2020.10.14.340216v1?rss=1 Ellis, C. T. Skalaban, L. J. Yates, T. S. Turk-Browne, N. B. 2020-10-15 doi:10.1101/2020.10.14.340216 Cold Spring Harbor Laboratory Press 2020-10-15 <![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[ Mitochondrial fission governed by Drp1 regulates exogenous fatty acid usage and storage ]]> https://biorxiv.org/content/10.1101/2020.10.17.343616v1?rss=1 Song, J. E. Alves, T. Stutz, B. Sestan-Pesa, M. Kilian, N. Diano, S. Kibbey, R. Horvath, T. 2020-10-17 doi:10.1101/2020.10.17.343616 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Targeted DNA Damage Repair CRISPR/Cas9 Knockout Screen Identifies Novel Classification of Poly-ADP Ribose Polymerase Inhibitors Based on Key Base Excision Repair Proteins ]]> https://biorxiv.org/content/10.1101/2020.10.18.333070v1?rss=1 Breuer, G. A. Bezney, J. Fons, N. R. Sundaram, R. K. Feng, W. Gupta, G. P. Bindra, R. S. 2020-10-18 doi:10.1101/2020.10.18.333070 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Behavioral and brain signatures of substance use vulnerability in childhood ]]> https://biorxiv.org/content/10.1101/2020.10.19.346403v1?rss=1 1,500), functional connectivity during rest and task conditions (resting-state; monetary incentive delay task; stop signal task; emotional n-back task) significantly predicted individual differences in risk-seeking (PC1) in held-out participants (partial correlations between predicted and observed scores controlling for motion and number of frames [rp]: 0.07-0.21). By contrast, functional connectivity was a weak predictor of familial risk factors associated with substance use (PC2) (rp: 0.03-0.06). These results demonstrate a novel approach to understanding substance use vulnerability, which--together with mechanistic perspectives--may inform strategies aimed at early identification of risk for addiction. ]]> Rapuano, K. M. Rosenberg, M. D. Maza, M. T. Dennis, N. Dorji, M. Greene, A. S. Horien, C. Scheinost, D. Constable, R. T. Casey, B. 2020-10-21 doi:10.1101/2020.10.19.346403 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission ]]> https://biorxiv.org/content/10.1101/2020.10.20.347427v1?rss=1 Haugh, K. A. Ladinsky, M. S. Ullah, I. Pi, R. Gilardet, A. Kumar, P. Bjorkman, P. Mothes, W. Uchil, P. D. 2020-10-20 doi:10.1101/2020.10.20.347427 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype ]]> https://biorxiv.org/content/10.1101/2020.10.21.346197v1?rss=1 Guha, R. Mathioudaki, A. Doumbo, S. Doumtabe, D. Skinner, J. Arora, G. Siddiqui, S. Li, S. Kayentao, K. Ongoiba, A. Zaugg, J. B. Traore, B. Crompton, P. D. 2020-10-21 doi:10.1101/2020.10.21.346197 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Integrated Single Cell Atlas of Endothelial Cells of the Human Lung ]]> https://biorxiv.org/content/10.1101/2020.10.21.347914v1?rss=1 Schupp, J. C. Adams, T. S. Cosme, C. Brickman Raredon, M. S. Omote, N. Poli, S. Rose, K.-A. Manning, E. Sauler, M. DeIuliis, G. Ahangari, F. Neumark, N. Yuan, Y. Habermann, A. C. Gutierrez, A. J. Bui, L. T. Meyer, K. B. Nawijn, M. C. Teichmann, S. A. Banovich, N. Kropski, J. A. Niklason, L. E. Pe'er, D. Yan, X. Homer, R. Rosas, I. O. Kaminski, N. 2020-10-22 doi:10.1101/2020.10.21.347914 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Executive modulation of brain reward systems endows goals with value ]]> https://biorxiv.org/content/10.1101/2020.10.21.348938v1?rss=1 McDougle, S. D. Ballard, I. C. Baribault, B. Bishop, S. J. Collins, A. G. E. 2020-10-22 doi:10.1101/2020.10.21.348938 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Determinants of Real-Time fMRI Neurofeedback Performance and Improvement: a Machine Learning Mega-Analysis ]]> https://biorxiv.org/content/10.1101/2020.10.21.349118v1?rss=1 Haugg, A. Renz, F. M. Nicholson, A. A. Lor, C. Goetzendorfer, S. J. Sladky, R. Skouras, S. McDonald, A. Craddock, C. Hellrung, L. Kirschner, M. Herdener, M. Koush, Y. Papoutsi, M. Keynan, J. N. Hendler, T. Cohen Kadosh, K. Zich, C. Kohl, S. H. Hallschmid, M. MacInnes, J. Adcock, R. A. Dickerson, K. Chen, N.-K. Young, K. Bodurka, J. Marxen, M. Yao, S. Becker, B. Auer, T. Schweizer, R. Pamplona, G. Lanius, R. Emmert, K. Haller, S. Van De Ville, D. Kim, D.-Y. Lee, J.-H. Marins, T. Megumi, F. Sorger, B. Kamp, T. Liew, S.-L. Veit, R. Spetter, M. Weiskopf 2020-10-22 doi:10.1101/2020.10.21.349118 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria ]]> https://biorxiv.org/content/10.1101/2020.10.21.349134v1?rss=1 Salvail, H. Balaji, A. Yu, D. Roth, A. Breaker, R. R. 2020-10-21 doi:10.1101/2020.10.21.349134 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro ]]> https://biorxiv.org/content/10.1101/2020.10.21.349225v1?rss=1 Sun, Y. Abriola, L. Surovtseva, Y. V. Lindenbach, B. D. Guo, J. U. 2020-10-21 doi:10.1101/2020.10.21.349225 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Single-cell secretion analysis reveals a dual role for IL-10 in restraining and resolving the TLR4-induced inflammatory response ]]> https://biorxiv.org/content/10.1101/2020.10.22.351254v1?rss=1 Alexander, A. F. Forbes, H. Miller-Jensen, K. 2020-10-23 doi:10.1101/2020.10.22.351254 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Patient iPSC-astrocytes show transcriptional and functional dysregulation in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.10.23.350413v1?rss=1 Koskuvi, M. Lehtonen, S. Trontti, K. Keuters, M. Wu, Y. C. Koivisto, H. Ludwig, A. Plotnikova, L. Virtanen, P. L. J. Räsänen, N. Kaipainen, S. Hyötyläinen, I. Dhungana, H. Giniatullina, R. Ojansuu, I. Vaurio, O. Cannon, T. D. Lönnqvist, J. Therman, S. Suvisaari, J. Kaprio, J. Lähteenvuo, M. Tohka, J. Giniatullin, R. Rivera, C. Hovatta, I. Tanila, H. Tiihonen, J. Koistinaho, J. 2020-10-23 doi:10.1101/2020.10.23.350413 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Shortfalls and opportunities in terrestrial vertebrate species discovery ]]> https://biorxiv.org/content/10.1101/2020.10.23.352690v1?rss=1 Moura, M. R. Jetz, W. 2020-10-25 doi:10.1101/2020.10.23.352690 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Latent Evolutionary Signatures: A General Framework for Analyzing Music and Cultural Evolution ]]> https://biorxiv.org/content/10.1101/2020.10.23.352930v1?rss=1 Warrell, J. Salichos, L. Gerstein, M. 2020-10-25 doi:10.1101/2020.10.23.352930 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Attribution of Cancer Origins to Endogenous, Exogenous, and Actionable Mutational Processes ]]> https://biorxiv.org/content/10.1101/2020.10.24.352989v1?rss=1 Cannataro, V. L. Mandell, J. D. Townsend, J. P. 2020-10-25 doi:10.1101/2020.10.24.352989 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Rooting the animal tree of life ]]> https://biorxiv.org/content/10.1101/2020.10.27.357798v1?rss=1 Li, Y. Shen, X.-X. Evans, B. Dunn, C. W. Rokas, A. 2020-10-28 doi:10.1101/2020.10.27.357798 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Compression-based Network Interpretability Schemes ]]> https://biorxiv.org/content/10.1101/2020.10.27.358226v1?rss=1 Warrell, J. Mohsen, H. Gerstein, M. 2020-10-28 doi:10.1101/2020.10.27.358226 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Rab34 GTPase mediates ciliary membrane biogenesis in the intracellular ciliogenesis pathway ]]> https://biorxiv.org/content/10.1101/2020.10.29.360891v1?rss=1 Ganga, A. K. Kennedy, M. C. Oguchi, M. E. Gray, S. D. Oliver, K. E. Knight, T. A. De La Cruz, E. M. Homma, Y. Fukuda, M. Breslow, D. K. 2020-10-29 doi:10.1101/2020.10.29.360891 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis ]]> https://biorxiv.org/content/10.1101/2020.10.29.361196v1?rss=1 Duan, D. Hanson, M. Holland, D. O. Johnson, M. E. 2020-10-29 doi:10.1101/2020.10.29.361196 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ A non-olfactory shark adenosine receptor activates CFTR with unique pharmacology and structural features ]]> https://biorxiv.org/content/10.1101/2020.11.01.363762v1?rss=1 S-PIA > CGS21680 > CPA > 2ClADO > CV1808 = DPMA > NECA) and (antagonists: DPCPX > PD115199 > 8PT > CGC > CGS15943). Structures of human ADORs permitted a high-confidence homology model of the shark A0 core which revealed unique structural features of ancestral receptors. We conclude: (1) A0 is a novel and unique adenosine receptor ancestor by functional and structural criteria; (2) A0 likely activates CFTR in vivo and this receptor activates CFTR in oocytes indicating an evolutionary coupling between ADORs and chloride secretion; and (3) A0 appears to be a non-olfactory evolutionary ancestor of all four mammalian ADOR subtypes. Significance StatementWe have cloned and characterized an ancient adenosine receptor from sharks that is unlikely to be olfactory in function. The shark receptor, which we designate as A0, has a unique pharmacological profile, characteristic structural features, and is also highly likely to be the dominant ADOR regulator of the shark ancient ortholog of the Cystic Fibrosis chloride channel, called CFTR. ]]> Bhanot, S. Hemminger, G. Aller, S. G. Forrest, J. N. 2020-11-02 doi:10.1101/2020.11.01.363762 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Defective Autophagy in Sf1 Neurons Perturbs the Metabolic Response to Fasting and Causes Mitochondrial Dysfunction ]]> https://biorxiv.org/content/10.1101/2020.11.02.348789v1?rss=1 Coupe, B. Leloup, C. Maillard, J. Penicaud, L. Horvath, T. Bouret, S. G. 2020-11-02 doi:10.1101/2020.11.02.348789 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Global and national trends in documenting and monitoring species distributions ]]> https://biorxiv.org/content/10.1101/2020.11.03.367011v1?rss=1 Oliver, R. Y. Meyer, C. Ranipeta, A. Winner, K. Jetz, W. 2020-11-05 doi:10.1101/2020.11.03.367011 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates ]]> https://biorxiv.org/content/10.1101/2020.11.04.368597v1?rss=1 Klein, A. Solinski, H. J. Malewicz, N. Ieong, H. F.-h. Shimada, S. Hartke, T. V. Wooten, M. Wu, G. Hoon, M. A. LaMotte, R. H. Ringkamp, M. 2020-11-04 doi:10.1101/2020.11.04.368597 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ In situ 3D comparison of Chlorella pyrenoidosa with nuclear-irradiated mutagenic strains by using focused ion beam milling and cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2020.11.05.369421v1?rss=1 Guo, W. Feng, L. Wang, Z. Guo, J. Park, D. Carroll, B. L. Zhang, X. Liu, J. Cheng, J. 2020-11-05 doi:10.1101/2020.11.05.369421 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu ]]> https://biorxiv.org/content/10.1101/2020.11.10.375675v1?rss=1 Goods, B. A. Askenase, M. H. Markarian, E. Beatty, H. E. Drake, R. Fleming, I. DeLong, J. H. Philip, N. H. Matouk, C. C. Awad, I. A. Zuccarello, M. Hanley, D. F. Love, J. C. Shalek, A. K. Sansing, L. H. 2020-11-12 doi:10.1101/2020.11.10.375675 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Recovering genomes and phenotypes using allele-specific gene expression ]]> https://biorxiv.org/content/10.1101/2020.11.11.377978v1?rss=1 Gursoy, G. Lu, N. Wagner, S. Gerstein, M. 2020-11-12 doi:10.1101/2020.11.11.377978 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ A Markov Random Field Model for Network-based Differential Expression Analysis of Single-cell RNA-seq Data ]]> https://biorxiv.org/content/10.1101/2020.11.11.378976v1?rss=1 Li, H. Xu, Z. Adams, T. Kaminski, N. Zhao, H. 2020-11-12 doi:10.1101/2020.11.11.378976 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ A metabolic coincidence mechanism controls winter photoperiodism in plants ]]> https://biorxiv.org/content/10.1101/2020.11.13.381426v1?rss=1 Liu, W. Feke, A. Leung, C. C. Tarte, D. Yuan, W. Vanderwall, M. Sager, G. C. Wu, X. Schear, A. Clark, D. Thines, B. C. Gendron, J. 2020-11-14 doi:10.1101/2020.11.13.381426 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Conserved prolines in the coiled coil-OB domain linkers of proteasomal ATPases facilitate eukaryotic proteasome base assembly ]]> https://biorxiv.org/content/10.1101/2020.11.13.381962v1?rss=1 Cheng, C. L. Wong, M. K. Li, Y. Hochstrasser, M. 2020-11-14 doi:10.1101/2020.11.13.381962 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease ]]> https://biorxiv.org/content/10.1101/2020.11.15.383661v1?rss=1 Kuchroo, M. Huang, J. Wong, P. Grenier, J.-C. Shung, D. Tong, A. Lucas, C. Klein, J. Burkhardt, D. Gigante, S. Godavarthi, A. Israelow, B. Mao, T. Oh, J. E. Silva, J. Takahashi, T. Odio, C. D. Casanovas-Massana, A. Fournier, J. IMPACT Team, Y. Farhadian, S. Dela Cruz, C. S. Ko, A. I. Wilson, F. P. Hussin, J. Wolf, G. Iwasaki, A. Krishnaswamy, S. 2020-11-17 doi:10.1101/2020.11.15.383661 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes ]]> https://biorxiv.org/content/10.1101/2020.11.16.384297v1?rss=1 Bass, V. L. Wong, V. C. Bullock, M. E. Gaudet, S. Miller-Jensen, K. 2020-11-17 doi:10.1101/2020.11.16.384297 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Shifting gradients of macroscale cortical organization mark the transition from childhood to adolescence ]]> https://biorxiv.org/content/10.1101/2020.11.17.385260v1?rss=1 Dong, H. Margulies, D. S. Zuo, X.-N. Holmes, A. 2020-11-17 doi:10.1101/2020.11.17.385260 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ KDM2B promotes cell viability by enhancing DNA damage response in canine hemangiosarcoma ]]> https://biorxiv.org/content/10.1101/2020.11.17.387704v1?rss=1 Gulay, K. C. M. Aoshima, K. Shibata, Y. Yasui, H. Yan, Q. Kobayashi, A. Kimura, T. 2020-11-17 doi:10.1101/2020.11.17.387704 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Proteomics on longitudinal serum samples differentiates localized and disseminated Lyme disease ]]> https://biorxiv.org/content/10.1101/2020.11.18.387993v1?rss=1 Fatou, B. Smolen, K. K. Belperron, A. A. Wurie, Z. Kleinstein, S. Montgomery, R. Levy, O. Bockenstedt, L. K. Steen, H. 2020-11-20 doi:10.1101/2020.11.18.387993 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ BoxCarmax: a high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples ]]> https://biorxiv.org/content/10.1101/2020.11.20.392043v1?rss=1 Salovska, B. Li, W. Di, Y. Liu, Y. 2020-11-21 doi:10.1101/2020.11.20.392043 Cold Spring Harbor Laboratory Press 2020-11-21 <![CDATA[ A unifying framework for quantifying and comparing n-dimensional hypervolumes ]]> https://biorxiv.org/content/10.1101/2020.11.21.392696v1?rss=1 Lu, M. Winner, K. Jetz, W. 2020-11-22 doi:10.1101/2020.11.21.392696 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.23.394171v1?rss=1 Pradhan, S. J. reddy, p. c. Smutny, M. Sharma, A. Sako, K. Oak, M. S. Shah, R. Pal, M. Deshpande, O. Tang, Y. Mishra, R. K. Deshpande, G. Giraldez, A. Sonawane, M. Heisenberg, C.-P. Galande, S. 2020-11-23 doi:10.1101/2020.11.23.394171 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ AN EPILEPSY-CAUSING MUTATION LEADS TO CO-TRANSLATIONAL MISFOLDING ]]> https://biorxiv.org/content/10.1101/2020.11.25.398222v1?rss=1 Urrutia, J. Aguado, A. Gomis-Perez, C. Muguruza-Montero, A. R. Ballesteros, O. Zhang, J. Nunez, E. Malo, C. Chung, H. J. Leonardo, A. Bergara, A. Villarroel, A. 2020-11-26 doi:10.1101/2020.11.25.398222 Cold Spring Harbor Laboratory Press 2020-11-26 <![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[ Hybrid Hyperalignment: A single high-dimensional model of shared information embedded in cortical patterns of response and functional connectivity ]]> https://biorxiv.org/content/10.1101/2020.11.25.398883v1?rss=1 Busch, E. L. Slipski, L. Feilong, M. Guntupalli, J. S. Visconti di Oleggio Castello, M. Huckins, J. F. Nastase, S. A. Gobbini, M. I. Wager, T. D. Haxby, J. V. 2020-11-27 doi:10.1101/2020.11.25.398883 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ 3D Adaptive Optical Nanoscopy for Thick Specimen Imaging at sub-50 nm Resolution ]]> https://biorxiv.org/content/10.1101/2020.11.25.398958v1?rss=1 Hao, X. Allgeyer, E. S. Antonello, J. Watters, K. Gerdes, J. A. Schroeder, L. K. Bottanelli, F. Zhao, J. Kidd, P. Lessard, M. D. Rothman, J. E. Cooley, L. Biederer, T. Booth, M. J. Bewersdorf, J. 2020-11-27 doi:10.1101/2020.11.25.398958 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Discovering a less-is-more effect to select transcription factor binding sites informative for motif inference ]]> https://biorxiv.org/content/10.1101/2020.11.29.402941v1?rss=1 Xu, J. Gao, J. Gerstein, M. 2020-11-30 doi:10.1101/2020.11.29.402941 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation. ]]> https://biorxiv.org/content/10.1101/2020.11.29.402974v1?rss=1 Thompson, A. D. Helms, A. S. Kannan, A. Job, J. Lakdawala, N. K. Wittekind, S. G. Pereira, A. Jacoby, D. L. Colan, S. D. Ashley, E. A. Saberi, S. Ware, J. S. Ingles, J. Semsarian, C. Michels, M. Mazzarotto, F. Olivotto, I. Ho, C. Y. Day, S. M. 2020-11-30 doi:10.1101/2020.11.29.402974 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Transient neuronal suppression for exploitation of new sensory evidence ]]> https://biorxiv.org/content/10.1101/2020.11.29.403089v1?rss=1 Shinn, M. Lee, D. Murray, J. D. Seo, H. 2020-11-30 doi:10.1101/2020.11.29.403089 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ The Erythropoietin Receptor Stimulates Rapid Cycling and Formation of Larger Red Cells During Mouse and Human Erythropoiesis ]]> https://biorxiv.org/content/10.1101/2020.11.30.404780v1?rss=1 Hidalgo, D. Bejder, J. Pop, R. Gellatly, K. Scalf, S. M. Eastman, A. E. Chen, J.-J. Zhu, J. L. Heuberger, J. A. A. C. Guo, S. Koury, M. J. Nordsborg, N. B. Socolovsky, M. 2020-11-30 doi:10.1101/2020.11.30.404780 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics ]]> https://biorxiv.org/content/10.1101/2020.11.30.405241v1?rss=1 Zhou, G. Zhao, H. 2020-12-02 doi:10.1101/2020.11.30.405241 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Retinotopic organization of visual cortex in human infants ]]> https://biorxiv.org/content/10.1101/2020.12.01.407437v1?rss=1 Ellis, C. T. Yates, T. S. Skalaban, L. J. Bejjanki, V. R. Arcaro, M. J. Turk-Browne, N. B. 2020-12-02 doi:10.1101/2020.12.01.407437 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Scalable production of tissue-like vascularised liver organoids from human PSCs. ]]> https://biorxiv.org/content/10.1101/2020.12.02.406835v1?rss=1 Harrison, S. P. Sillar, R. Tanaka, Y. Xiang, Y. Patterson, B. Kempf, H. Melum, E. Asrud, K. Chollet, M. E. Andersen, E. Sandset, P. M. Baumgarten, S. Bonanini, F. Kurek, D. Mathapati, S. Almaas, R. Sharma, K. Wilson, S. R. Skottvoll, F. S. Boger, I. C. Bogen, I. L. Nyman, T. A. Wu, J. J. Bezrouk, A. Cizkova, D. Mokry, J. Zweigerdt, R. Park, I.-H. Sullivan, G. J. 2020-12-02 doi:10.1101/2020.12.02.406835 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Local and distributed cortical markers of effort expenditure during sustained goal pursuit ]]> https://biorxiv.org/content/10.1101/2020.12.02.408609v1?rss=1 Patrick, L. M. Anderson, K. M. Holmes, A. 2020-12-03 doi:10.1101/2020.12.02.408609 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ A multi-task deep-learning system for predicting membrane associations and secondary structures of proteins ]]> https://biorxiv.org/content/10.1101/2020.12.02.409045v1?rss=1 LI, B. Mendenhall, J. Capra, J. A. Meiler, J. 2020-12-03 doi:10.1101/2020.12.02.409045 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Non-adaptive factors determine which equally effective regulatory motif evolves to generate pulses ]]> https://biorxiv.org/content/10.1101/2020.12.02.409151v1?rss=1 Xiong, K. Gerstein, M. Masel, J. 2020-12-03 doi:10.1101/2020.12.02.409151 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Fossils improve phylogenetic analyses of morphological characters ]]> https://biorxiv.org/content/10.1101/2020.12.03.410068v1?rss=1 Mongiardino Koch, N. Garwood, R. J. Parry, L. A. 2020-12-03 doi:10.1101/2020.12.03.410068 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ NGLY1 knockdown or pharmacological inhibition induces cellular autophagy ]]> https://biorxiv.org/content/10.1101/2020.12.05.400481v1?rss=1 Needs, S. H. Bootman, M. D. Grotzke, J. Kramer, H. B. Allman, S. A. 2020-12-06 doi:10.1101/2020.12.05.400481 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Ucp2-dependent microglia-neuronal coupling controls ventral hippocampal circuit function and anxiety-like behavior ]]> https://biorxiv.org/content/10.1101/2020.12.05.413179v1?rss=1 Horvath, T. Yasumoto, Y. Stoiljkovic, M. Kim, J. Sestan-Pesa, M. Gao, X.-B. Diano, S. 2020-12-06 doi:10.1101/2020.12.05.413179 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Repression of MUC1 promotes expansion and suppressive function of myeloid-derived suppressor cells in pancreatic ductal adenocarcinoma and breast cancer murine models. ]]> https://biorxiv.org/content/10.1101/2020.12.07.415299v1?rss=1 Sahraei, M. Das Roy, L. Bose, M. De, C. Nath, S. Mukherjee, P. 2020-12-08 doi:10.1101/2020.12.07.415299 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons ]]> https://biorxiv.org/content/10.1101/2020.12.07.415521v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@10e7ebdorg.highwire.dtl.DTLVardef@a2c26dorg.highwire.dtl.DTLVardef@18ab3aborg.highwire.dtl.DTLVardef@119cf87_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tharp, J. M. Vargas-Rodriguez, O. Schepartz, A. Söll, D. 2020-12-08 doi:10.1101/2020.12.07.415521 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Cryo-EM structures of outer-arm dynein array bound to microtubule doublet reveal a mechanism for motor coordination ]]> https://biorxiv.org/content/10.1101/2020.12.08.415687v1?rss=1 Zhang, K. Rao, Q. Wang, Y. Chai, P. Kuo, Y.-W. Han, L. Yang, R. Yang, Y. Howard, J. 2020-12-08 doi:10.1101/2020.12.08.415687 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Hidden limbs in the limbless skink Brachymeles lukbani: developmental observations ]]> https://biorxiv.org/content/10.1101/2020.12.09.418483v1?rss=1 Smith-Paredes, D. Griffith, O. Fabbri, M. Yohe, L. Blackburn, D. G. Siler, C. D. Bhullar, B.-A. S. Wagner, G. 2020-12-10 doi:10.1101/2020.12.09.418483 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Developmental loss of ErbB4 in PV interneurons disrupts state-dependent cortical circuit dynamics. ]]> https://biorxiv.org/content/10.1101/2020.12.09.418590v1?rss=1 Batista-Brito, R. Majumdar, A. Nuno, A. Vinck, M. Cardin, J. A. 2020-12-10 doi:10.1101/2020.12.09.418590 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Dual color mesoscopic imaging reveals spatiotemporally heterogeneous coordination of cholinergic and neocortical activity. ]]> https://biorxiv.org/content/10.1101/2020.12.09.418632v1?rss=1 Lohani, S. Moberly, A. H. Benisty, H. Landa, B. Jing, M. Li, Y. Higley, M. Cardin, J. A. 2020-12-11 doi:10.1101/2020.12.09.418632 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Coiled coil control of diverse EGFR functions ]]> https://biorxiv.org/content/10.1101/2020.12.10.419739v1?rss=1 Mozumdar, D. Quach, K. Doerner, A. Schepartz, A. 2020-12-11 doi:10.1101/2020.12.10.419739 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Association of Structural Variation with Cardiometabolic Traits in Finns ]]> https://biorxiv.org/content/10.1101/2020.12.13.422502v1?rss=1 Chen, L. Abel, H. J. Das, I. Larson, D. E. Ganel, L. Kanchi, K. L. Regier, A. A. Young, E. P. Kang, C. J. Scott, A. J. Chiang, C. Wang, X. Lu, S. Christ, R. Service, S. Chiang, C. W. K. Havulinna, A. S. Kuusisto, J. Boehnke, M. W. K. Laakso, M. Palotie, A. Ripatti, S. Freimer, N. B. Locke, A. E. Stitziel, N. O. Hall, I. M. 2020-12-13 doi:10.1101/2020.12.13.422502 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Translational control as a novel regulator of gradient sensing and chemotropism in yeast ]]> https://biorxiv.org/content/10.1101/2020.12.13.422562v1?rss=1 20 novel positive and negative regulators of pheromone gradient sensing, chemotropism, shmoo development, and mating. Aside from known regulators of exocytosis and endocytosis, genes involved in translational control downstream of the G-protein-regulated pheromone and filamentous growth MAPK pathways were identified. These include the Scp160 RNA-binding protein and the Asc1, Rpl12b, and Rpl19b ribosomal proteins (RPs). Importantly, we demonstrate that pheromone treatment and G (Gpa1) activation stimulate Scp160 binding to (and inhibition of) Asc1, which acts downstream of glucose-activated G (Gpa2) on the filamentous growth pathway. Moreover, we identify both Rpl12b and Rpl19b as RP paralog-specific positive regulators of translation of mating components, including Scp160. Thus, opposing MAPK pathways may converge at the level of translational control to regulate signaling output. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/422562v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@3944e1org.highwire.dtl.DTLVardef@1d9204eorg.highwire.dtl.DTLVardef@1d7e902org.highwire.dtl.DTLVardef@2bfc6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gelin-Licht, R. Conlon, P. J. Singh, R. Baez, C. Gal, L. Schuldiner, M. Levchenko, A. Gerst, J. E. 2020-12-13 doi:10.1101/2020.12.13.422562 Cold Spring Harbor Laboratory Press 2020-12-13 <![CDATA[ Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines Reveals Determinants of Proteotypes ]]> https://biorxiv.org/content/10.1101/2020.12.14.422682v1?rss=1 Gao, E. Li, W. Wu, C. Shao, W. Di, Y. Liu, Y. 2020-12-14 doi:10.1101/2020.12.14.422682 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Maladaptive oxidative stress cascade drives type I interferon hyperactivity in TNF activated macrophages promoting necrosis in murine tuberculosis granulomas ]]> https://biorxiv.org/content/10.1101/2020.12.14.422743v1?rss=1 Brownhill, E. Yabaji, S. M. Zhernovkov, V. Rukhlenko, O. S. Seidel, K. Bhattacharya, B. Chatterjee, S. Chen, H. A. Crossland, N. Bishai, W. Kholodenko, B. N. Gimelbrant, A. Kobzik, L. Kramnik, I. 2020-12-14 doi:10.1101/2020.12.14.422743 Cold Spring Harbor Laboratory Press 2020-12-14 <![CDATA[ Endothelial SIRT3 regulates myofibroblast metabolic shifts in diabetic kidneys ]]> https://biorxiv.org/content/10.1101/2020.12.15.422824v1?rss=1 Srivastava, S. P. Li, J. Takagaki, Y. Kitada, M. Goodwin, J. E. Kanasaki, K. Koya, D. 2020-12-16 doi:10.1101/2020.12.15.422824 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Molecular topography of an entire nervous system ]]> https://biorxiv.org/content/10.1101/2020.12.15.422897v1?rss=1 Taylor, S. R. Santpere, G. Weinreb, A. Barrett, A. Reilly, M. B. Xu, C. Varol, E. Oikonomou, P. Glenwinkel, L. McWhirter, R. Poff, A. Basavaraju, M. Rafi, I. Yemini, E. Cook, S. J. Abrams, A. Vidal, B. Cros, C. Tavazoie, S. Sestan, N. Hammarlund, M. Hobert, O. Miller, D. M. 2020-12-16 doi:10.1101/2020.12.15.422897 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Evaluation of hemispherical photos extracted from smartphone spherical panorama images to estimate canopy structure and forest light environment ]]> https://biorxiv.org/content/10.1101/2020.12.15.422956v1?rss=1 0.9) and are comparable to under- or over-exposing traditional HP by 1-1.5 stops. In addition to superior image quality, SSP HP requires no additional equipment or exposure settings and is likely to prove more robust to uneven lighting conditions by avoiding wide-angles lenses and exploiting HDR images. ]]> Arietta, A. Z. A. 2020-12-15 doi:10.1101/2020.12.15.422956 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Activity flow underlying abnormalities in brain activations and cognition in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.12.16.423109v1?rss=1 Hearne, L. J. Mill, R. D. Keane, B. P. Repovs, G. Anticevic, A. Cole, M. W. 2020-12-18 doi:10.1101/2020.12.16.423109 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Broad transcriptomic dysregulation across the cerebral cortex in ASD ]]> https://biorxiv.org/content/10.1101/2020.12.17.423129v1?rss=1 Haney, J. R. Wamsley, B. Chen, G. T. Parhami, S. Emani, P. S. Chang, N. Hoftman, G. D. de Alba, D. Kale, G. Ramaswami, G. Hartl, C. L. Jin, T. Wang, D. Ou, J. Wu, Y. E. Parikshak, N. N. Swarup, V. Belgard, T. G. Gerstein, M. Pasaniuc, B. Gandal, M. J. Geschwind, D. H. 2020-12-18 doi:10.1101/2020.12.17.423129 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Sex-specific Associations Between Traumatic Experiences and Resting-state Functional Connectivity in the Philadelphia Neurodevelopmental Cohort ]]> https://biorxiv.org/content/10.1101/2020.12.18.423455v1?rss=1 Wang, S. Malins, J. G. Zhang, H. Gruen, J. R. 2020-12-20 doi:10.1101/2020.12.18.423455 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Decidual cell differentiation is evolutionarily derived from fibroblast activation ]]> https://biorxiv.org/content/10.1101/2020.12.18.423527v1?rss=1 Wu, L. Stadtmauer, D. J. Maziarz, J. Wagner, G. 2020-12-20 doi:10.1101/2020.12.18.423527 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Multiple overlapping dynamic patterns of the visual sensory network in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.12.21.423535v1?rss=1 Sendi, M. S. E. Pearlson, G. D. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Calhoun, V. D. 2020-12-22 doi:10.1101/2020.12.21.423535 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ A WD40 repeat-like protein pathway connects F-BOX STRESS INDUCED (FBS) proteins to the NIGT1.1 transcriptional repressor in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2020.12.22.424016v1?rss=1 Sepulveda-Garcia, E. Fulton, E. C. Parlan, E. V. Brauning, A. A. O'Connor, L. E. Fleming, A. A. Replogle, A. J. Rocha-Sosa, M. Gendron, J. M. Thines, B. 2020-12-22 doi:10.1101/2020.12.22.424016 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ A Single Cell Gene Expression Atlas of 28 Human Livers ]]> https://biorxiv.org/content/10.1101/2020.12.23.422515v1?rss=1 Brancale, J. Vilarinho, S. 2020-12-24 doi:10.1101/2020.12.23.422515 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Neoantigen-driven B cell and CD4+ T follicular helper cell collaboration promotes robust anti-tumor CD8+ T cell responses ]]> https://biorxiv.org/content/10.1101/2020.12.23.424168v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@f31b57org.highwire.dtl.DTLVardef@881959org.highwire.dtl.DTLVardef@1385ccdorg.highwire.dtl.DTLVardef@154ba3b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cui, C. Wang, J. Chen, P.-M. Connolly, K. A. Damo, M. Fagerberg, E. Chen, S. Eisenbarth, S. C. Zhao, H. Craft, J. Joshi, N. S. 2020-12-24 doi:10.1101/2020.12.23.424168 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ A cognitive state transformation model for task-general and task-specific subsystems of the brain connectome ]]> https://biorxiv.org/content/10.1101/2020.12.23.424176v1?rss=1 Yoo, K. Rosenberg, M. D. Kwon, Y. H. Scheinost, D. Constable, R. T. Chun, M. M. 2020-12-24 doi:10.1101/2020.12.23.424176 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Disruption of nasal bacteria enhances protective immune responses to influenza A virus and SARS-CoV-2 infection in mice ]]> https://biorxiv.org/content/10.1101/2020.12.25.424300v1?rss=1 Nagai, M. Moriyama, M. Ichinohe, T. 2020-12-27 doi:10.1101/2020.12.25.424300 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Novel insights into the mode of action of 1,4-dioxane using a systems screening approach ]]> https://biorxiv.org/content/10.1101/2020.12.27.424470v1?rss=1 Vasiliou, V. Charkoftaki, G. Golla, J. P. Santos-Neto, A. Orlicky, D. J. Garcia-Milian, R. Chen, Y. Rattray, N. J. W. Cai, Y. Wang, Y. Shern, C. T. Mironova, V. Wang, Y. Johnson, C. H. Thompson, D. C. 2020-12-28 doi:10.1101/2020.12.27.424470 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9 ]]> https://biorxiv.org/content/10.1101/2020.12.28.424508v1?rss=1 Yang, S. Park, D. Manning, L. Hill, S. E. Cao, M. Xuan, Z. Gonzalez, I. Shao, L. Okeke, I. De Camilli, P. Colon-Ramos, D. 2020-12-28 doi:10.1101/2020.12.28.424508 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Reversion is most likely under high mutation supply, when compensatory mutations don't fully restore fitness costs ]]> https://biorxiv.org/content/10.1101/2020.12.28.424568v1?rss=1 Pennings, P. S. Ogbunugafor, C. B. Hershberg, R. 2020-12-28 doi:10.1101/2020.12.28.424568 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ A molecular clock controls periodically driven cell migration in confined spaces ]]> https://biorxiv.org/content/10.1101/2020.12.29.424673v1?rss=1 Lee, S. H. Hamidzadeh, A. Yousafzai, M. S. Ajeti, V. Chang, H. Murrell, M. Levchenko, A. 2020-12-30 doi:10.1101/2020.12.29.424673 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ The size of helical pitch is important for microtubule plus end dynamic instability ]]> https://biorxiv.org/content/10.1101/2020.12.29.424770v1?rss=1 Liu, C. Prahl, L. He, Y. Wang, Y. Zhu, R. Mao, Y. 2020-12-30 doi:10.1101/2020.12.29.424770 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat ]]> https://biorxiv.org/content/10.1101/2020.12.31.424977v1?rss=1 Yohe, L. R. Leiser-Miller, L. B. Kaliszewska, Z. A. Donat, P. Santana, S. E. Davalos, L. M. 2021-01-03 doi:10.1101/2020.12.31.424977 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ Aberrant Dynamic Functional Connectivity of Default Mode Network in Schizophrenia and Links to Symptom Severity ]]> https://biorxiv.org/content/10.1101/2021.01.03.425152v1?rss=1 Sendi, M. S. E. Zendehrouh, E. Ellis, C. A. Liang, Z. Fu, Z. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Miller, R. L. Pearlson, G. D. Turner, J. A. Calhoun, V. D. 2021-01-04 doi:10.1101/2021.01.03.425152 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Multi-Spatial Scale Dynamic Interactions between Functional Sources Reveal Sex-Specific Changes in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.01.04.425222v1?rss=1 Iraji, A. Faghiri, A. Fu, Z. Rachakonda, S. Kochunov, P. Belger, A. Ford, J. McEwen, S. Mathalon, D. Mueller, B. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. Van Erp, T. Calhoun, V. 2021-01-05 doi:10.1101/2021.01.04.425222 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Single Cell RNA-seq and Mass Cytometry Reveals a Novel and a Targetable Population of Macrophages in Idiopathic Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2021.01.04.425268v1?rss=1 Ayaub, E. A. Poli, S. Ng, J. Adams, T. S. Schupp, J. C. Quesada, L. Poli, F. Cosme, C. Matthew, R. Martinez, J. Liang, X. Villalba, J. Lederer, J. A. Chu, S. G. Raby, B. Washko, G. Coarfa, C. Perrella, M. A. El-Chemaly, S. Kaminski, N. Rosas, I. 2021-01-05 doi:10.1101/2021.01.04.425268 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Genome Wide Association Study in the New Haven Lexinome Project Identifies GARRE1 as a Novel Gene for Reading Performance ]]> https://biorxiv.org/content/10.1101/2021.01.05.423827v1?rss=1 Adams, A. K. Guertin, E. L. Truong, D. T. Atkinson, E. G. DeMille, M. M. C. Bosson-Heenan, J. M. Frijters, J. C. Gruen, J. R. 2021-01-05 doi:10.1101/2021.01.05.423827 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Chitinase 3-like-1 is a Therapeutic Target That Mediates the Effects of Aging in COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.01.05.425478v1?rss=1 Kamle, S. Ma, B. He, C. H. Akosman, B. Zhou, Y. Lee, C.-M. El-Deiry, W. S. Huntington, K. Liang, O. Machan, J. T. Kang, M.-J. Shin, H. J. Mizoguchi, E. Lee, C. G. Elias, J. A. 2021-01-06 doi:10.1101/2021.01.05.425478 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Integrin β3 Targeting Biomaterial Preferentially Promotes Secretion of bFGF and Proliferation of iPSC-Derived Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2021.01.06.425573v1?rss=1 Dash, B. C. Duan, K. Kyriakides, T. Hsia, H. 2021-01-06 doi:10.1101/2021.01.06.425573 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Fibronectin-mediated inflammatory signaling through integrin α5 in vascular remodeling ]]> https://biorxiv.org/content/10.1101/2021.01.06.425577v1?rss=1 Budatha, M. Zhang, J. Schwartz, M. A. 2021-01-08 doi:10.1101/2021.01.06.425577 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer. ]]> https://biorxiv.org/content/10.1101/2021.01.07.425777v1?rss=1 Cockburn, K. Annusver, K. Ganesan, S. Mesa, K. R. Kawaguchi, K. Kasper, M. Greco, V. 2021-01-07 doi:10.1101/2021.01.07.425777 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Effects of Ih and TASK-like shunting current on dendritic impedance in layer 5 pyramidal-tract neurons ]]> https://biorxiv.org/content/10.1101/2021.01.08.425962v1?rss=1 Kelley, C. Dura-Bernal, S. Neymotin, S. A. Antic, S. D. Carnevale, N. T. Migliore, M. Lytton, W. W. 2021-01-09 doi:10.1101/2021.01.08.425962 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Cortical Mechanisms of Saccadic Suppression ]]> https://biorxiv.org/content/10.1101/2021.01.09.426063v1?rss=1 Denagamage, S. Morton, M. Reynolds, J. Jadi, M. Nandy, A. 2021-01-09 doi:10.1101/2021.01.09.426063 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Distinct T cell chromatin landscapes in scleroderma subtypes ]]> https://biorxiv.org/content/10.1101/2021.01.10.426131v1?rss=1 Dou, D. R. Zhao, Y. Abe, B. Li, R. Zaba, L. C. Aren, K. Carns, M. Chung, L. S. Hinchcliff, M. Chang, H. Y. 2021-01-11 doi:10.1101/2021.01.10.426131 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Mapping the Promiscuous Binding Interface of HOX-A11 with KIX by Experimentally Guided in-silico docking ]]> https://biorxiv.org/content/10.1101/2021.01.11.426190v1?rss=1 Ganguly, S. Meiler, J. Wagner, G. P. 2021-01-11 doi:10.1101/2021.01.11.426190 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Correcting statistical bias in correlation-based kinship estimators ]]> https://biorxiv.org/content/10.1101/2021.01.13.426515v1?rss=1 Jiang, W. Zhang, X. Li, S. Song, S. Zhao, H. 2021-01-13 doi:10.1101/2021.01.13.426515 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Essential Role of Placenta Derived Interferon Stimulated Gene 20 Against ZIKA Virus Infection ]]> https://biorxiv.org/content/10.1101/2021.01.13.426624v1?rss=1 Ding, J. Aldo, P. Roberts, C. M. Stabach, P. R. Liu, H. You, Y. Qiu, X. Jeong, J. Maxwell, A. Lindenbach, B. D. Braddock, D. T. Liao, A. Gil, M. 2021-01-15 doi:10.1101/2021.01.13.426624 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Adiponectin Preserves Metabolic Fitness During Aging ]]> https://biorxiv.org/content/10.1101/2021.01.14.426678v1?rss=1 Scherer, P. E. Li, N. Zhang, Z. Zhao, S. Zhu, Y. Gliniak, C. M. Vishvanath, L. An, Y. A. Wang, M.-y. Deng, Y. Zhu, Q. Onodera, T. Oz, O. Gordillo, R. Gupta, R. K. Liu, M. Horvath, T. L. Dixit, V. D. 2021-01-15 doi:10.1101/2021.01.14.426678 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Chitinase 3-like-1 Stimulates PD-L1 and Other Immune Checkpoint Inhibitors ]]> https://biorxiv.org/content/10.1101/2021.01.15.426788v1?rss=1 Ma, B. Akosman, B. Kamle, S. Lee, C.-M. Koo, J. S. Lee, C. G. Elias, J. A. 2021-01-17 doi:10.1101/2021.01.15.426788 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Individual-Specific Areal-Level Parcellations Improve Functional Connectivity Prediction of Behavior ]]> https://biorxiv.org/content/10.1101/2021.01.16.426943v1?rss=1 Kong, R. Yang, Q. Gordon, E. Xue, A. Yan, X. Orban, C. Zuo, X.-N. Spreng, N. Ge, T. Holmes, A. Eickhoff, S. Yeo, B. T. T. 2021-01-19 doi:10.1101/2021.01.16.426943 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/2021.01.19.427286v1?rss=1 Kuchroo, M. DiStasio, M. Calapkulu, E. Ige, M. Zhang, L. Sheth, A. H. Menon, M. Xing, Y. Gigante, S. A. Huang, J. Dhodhapkar, R. M. Rieck, B. A. Wolf, G. Krishnaswamy, S. Hafler, B. P. 2021-01-20 doi:10.1101/2021.01.19.427286 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Population dynamics of the primary malaria vector Nyssorhynchus darlingi in a high transmission setting dominated by fish farming in western Amazonian Brazil ]]> https://biorxiv.org/content/10.1101/2021.01.20.427434v1?rss=1 Rufalco-Moutinho, P. Kadri, S. M. Alonso, D. P. Moreno, M. Carrasco-Escobar, G. Prussing, C. Gamboa, D. Vinetz, J. M. Mureb Sallum, M. A. Conn, J. E. Ribolla, P. E. M. 2021-01-21 doi:10.1101/2021.01.20.427434 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Adolescent social stress decrease of adult morphine-induced behavioral sensitization is dependent upon genetic background ]]> https://biorxiv.org/content/10.1101/2021.01.20.427504v1?rss=1 Kamens, H. Miller, C. Caulfield, J. Zeid, D. Horton, W. Silva, C. Sebastian, A. Albert, I. Gould, T. Fishbein, D. Grigson, P. S. Cavigelli, S. 2021-01-21 doi:10.1101/2021.01.20.427504 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Adipocyte lipolysis abrogates skin fibrosis in a Wnt/DPP4-dependent manner ]]> https://biorxiv.org/content/10.1101/2021.01.21.427497v1?rss=1 Jussila, A. R. Caves, E. Zhang, B. Kirti, S. Steele, M. Lei, V. Hamburg-Shields, E. Lydon, J. Ying, Y. Lafyatis, R. Rajagopalan, S. Horsley, V. Atit, R. P. 2021-01-21 doi:10.1101/2021.01.21.427497 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data ]]> https://biorxiv.org/content/10.1101/2021.01.21.427529v1?rss=1 Raredon, M. S. B. Yang, J. Garritano, J. Wang, M. Kushnir, D. Schupp, J. C. Adams, T. S. Greaney, A. M. Leiby, K. L. Kaminski, N. Kluger, Y. Levchenko, A. Niklason, L. E. 2021-01-21 doi:10.1101/2021.01.21.427529 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Integrated evaluation of telomerase activation and telomere maintenance across cancer cell lines ]]> https://biorxiv.org/content/10.1101/2021.01.22.426137v1?rss=1 Hu, K. Ghandi, M. Huang, F. 2021-01-24 doi:10.1101/2021.01.22.426137 Cold Spring Harbor Laboratory Press 2021-01-24 <![CDATA[ BNP facilitates NMB-mediated histaminergic itch via NPRC-NMBR crosstalk ]]> https://biorxiv.org/content/10.1101/2021.01.26.428310v1?rss=1 Meng, Q.-T. Liu, X.-Y. Liu, X.-T. Barry, D. M. Jin, H. Sun, Y. Yang, Q. Wan, L. Jin, J.-H. Shen, K.-F. Munanairi, A. Kim, R. Yin, J. Tao, A. Chen, Z. 2021-01-27 doi:10.1101/2021.01.26.428310 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ A reservoir of stem-like CD8 T cells in the tumor-draining lymph node maintains the ongoing anti-tumor immune response ]]> https://biorxiv.org/content/10.1101/2021.01.27.428467v1?rss=1 Connolly, K. A. Kuchroo, M. Venkat, A. Khatun, A. Wang, J. William, I. Hornick, N. Fitzgerald, B. Damo, M. Kasmani, M. Y. Cui, C. Fagerberg, E. Monroy, I. Hutchins, A. Cheung, J. F. Foster, G. G. Mariuzza, D. L. Zhao, H. Cui, W. Krishnaswamy, S. Joshi, N. S. 2021-01-27 doi:10.1101/2021.01.27.428467 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays ]]> https://biorxiv.org/content/10.1101/2021.01.27.428477v1?rss=1 Chen, Z. Zhang, J. Liu, J. Dai, Y. Lee, D. Min, M. R. Xu, M. Gerstein, M. 2021-01-28 doi:10.1101/2021.01.27.428477 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Single-cell immune profiling reveals the impact of antiretroviral therapy on HIV-1-induced immune dysfunction, T cell clonal expansion, and HIV-1 persistence in vivo ]]> https://biorxiv.org/content/10.1101/2021.01.27.428491v1?rss=1 Collora, J. A. Pinto-Santini, D. Pasalar, S. Ravindra, N. Ganoza, C. Lama, J. Alfaro, R. Chiarella, J. Spudich, S. van Dijk, D. Duerr, A. Ho, Y.-C. 2021-01-28 doi:10.1101/2021.01.27.428491 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Revealing the human mucinome ]]> https://biorxiv.org/content/10.1101/2021.01.27.428510v1?rss=1 Malaker, S. A. Riley, N. M. Shon, J. Pedram, K. Krishnan, V. Dorigo, O. Bertozzi, C. R. 2021-01-28 doi:10.1101/2021.01.27.428510 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Nodal modulator is required to sustain endoplasmic reticulum morphology ]]> https://biorxiv.org/content/10.1101/2021.01.28.428001v1?rss=1 Amaya, C. Cameron, C. J. Devarkar, S. C. Gerstein, M. B. Xiong, Y. Schlieker, C. 2021-01-28 doi:10.1101/2021.01.28.428001 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Fat and carbohydrate interact to potentiate food reward in healthy weight but not in overweight or obesity ]]> https://biorxiv.org/content/10.1101/2021.01.29.428845v1?rss=1 Perszyk, E. E. Hutelin, Z. Trinh, J. Kanyamibwa, A. Fromm, S. Davis, X. S. Wall, K. M. Flack, K. D. DiFeliceantonio, A. Small, D. M. 2021-02-01 doi:10.1101/2021.01.29.428845 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Proton egress pathway during the S1 to S2 transition of the Oxygen Evolving Complex ofPhotosystem II ]]> https://biorxiv.org/content/10.1101/2021.01.29.428861v1?rss=1 Kaur, D. Zhang, Y. Reiss, K. M. Mandal, M. Brudvig, G. W. Batista, V. S. Gunner, M. R. 2021-01-31 doi:10.1101/2021.01.29.428861 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Trial-to-trial variability of spiking delay activity in prefrontal cortex constrains burst-coding models of working memory ]]> https://biorxiv.org/content/10.1101/2021.01.30.428962v1?rss=1 Li, D. Constantinidis, C. Murray, J. D. 2021-02-01 doi:10.1101/2021.01.30.428962 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Transcriptomics-informed large-scale cortical model captures topography of pharmacological neuroimaging effects of LSD ]]> https://biorxiv.org/content/10.1101/2021.01.31.429016v1?rss=1 Burt, J. B. Preller, K. H. Demirtas, M. Ji, J. L. Krystal, J. H. Vollenweider, F. X. Anticevic, A. Murray, J. D. 2021-02-02 doi:10.1101/2021.01.31.429016 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Outer Hair Cell Function is Normal in βV Spectrin Knockout Mice ]]> https://biorxiv.org/content/10.1101/2021.02.01.427491v1?rss=1 Stankewich, M. C. Bai, J.-P. Stabach, P. R. Khan, S. Song, L. Morrow, J. S. Santos-Sacchi, J. Navaratnam, D. S. 2021-02-01 doi:10.1101/2021.02.01.427491 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Geometry of neural computation unifies working memory and planning ]]> https://biorxiv.org/content/10.1101/2021.02.01.429156v1?rss=1 Ehrlich, D. B. Murray, J. D. 2021-02-01 doi:10.1101/2021.02.01.429156 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement ]]> https://biorxiv.org/content/10.1101/2021.02.01.429194v1?rss=1 Barrasso, K. Chac, D. Debele, M. D. Harris, J. B. LaRocque, R. C. Midani, F. S. Qadri, F. Yan, J. Weil, A. A. Ng, W.-L. 2021-02-02 doi:10.1101/2021.02.01.429194 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Inferring time-lagged causality using the derivative of single-cell expression ]]> https://biorxiv.org/content/10.1101/2021.02.03.429525v1?rss=1 Wei, H.-H. Lu, H. Zhao, H. 2021-02-03 doi:10.1101/2021.02.03.429525 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Cancer relevance of human genes ]]> https://biorxiv.org/content/10.1101/2021.02.04.429823v1?rss=1 3-steps (n=362) removed from the nearest CCG in the STRING PPI and demonstrate that the cancer-biology related functional contribution of the genes in these different neighborhood categories decreases as their distance from the CCGs increases. ResultsGenes closer to cancer genes manifest greater connectedness in the network, show greater importance in maintaining cell viability in a broad range of cancer cells in vitro, are also under greater negative germline selection pressure in the healthy populations, and have higher somatic mutation frequency and cancer effect. ConclusionsApproximately 70% of human genes are 1 or 2 steps removed from cancer genes in protein network and show functional importance in cancer-biology. These results suggest that the universe of cancer-relevant genes extends to thousands of genes that can contribute functional effects when dysregulated. ]]> Qing, T. Mohsen, H. Cannataro, V. L. Marczyk, M. Rozenblit, M. Foldi, J. Murray, M. F. Townsend, J. P. Kluger, Y. Gerstein, M. Pusztai, L. 2021-02-06 doi:10.1101/2021.02.04.429823 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ A Network Propagation Approach to Prioritize Long Tail Genes in Cancer ]]> https://biorxiv.org/content/10.1101/2021.02.05.429983v1?rss=1 Mohsen, H. Gunasekharan, V. Qing, T. Negahban, S. Szallasi, Z. Pusztai, L. Gerstein, M. 2021-02-08 doi:10.1101/2021.02.05.429983 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2) ]]> https://biorxiv.org/content/10.1101/2021.02.06.428911v1?rss=1 Karmakar, S. Ramirez, O. Paul, K. V. Gupta, A. K. Botti, V. Mozos, I. R. d. l. Neuenkirchen, N. Ross, R. J. Neugebauer, K. M. Pillai, M. M. 2021-02-07 doi:10.1101/2021.02.06.428911 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Validation of biosignatures confirms the informative nature of fossil organic Raman spectra ]]> https://biorxiv.org/content/10.1101/2021.02.07.430162v1?rss=1 200 spectra in the studies in question, but also the utility of Raman spectroscopy, a well established method, for analysing organic materials in general. Here we test the claims by Alleon et al. (21) using direct spectral comparisons and statistical analyses. We present multiple independent lines of evidence that demonstrate the original, biologically and geologically informative nature of the Raman spectra in question. We demonstrate that the methodological approach introduced by Alleon et al. (21) is unsuitable for assessing the quality of spectra and identifying noise within them. Statistical analyses of large Raman spectral data sets provide a powerful tool in the search for compositional patterns in biomaterials and yield invaluable insights into the history of life. ]]> Wiemann, J. Briggs, D. E. G. 2021-02-08 doi:10.1101/2021.02.07.430162 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ A DNA-origami NanoTrap for studying the diffusion barriers formed by Phe-Gly-rich nucleoporins ]]> https://biorxiv.org/content/10.1101/2021.02.07.430177v1?rss=1 Shen, Q. Tian, T. Xiong, Q. Fisher, P. D. E. Xiong, Y. Melia, T. Lusk, C. P. Lin, C. 2021-02-08 doi:10.1101/2021.02.07.430177 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Comprehensive Analysis of Ubiquitously Expressed Genes in Human, From a Data-Driven Perspective ]]> https://biorxiv.org/content/10.1101/2021.02.09.430465v1?rss=1 Gu, J. Dai, J. Lu, H. Zhao, H. 2021-02-10 doi:10.1101/2021.02.09.430465 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Generalization of motor learning in psychological space ]]> https://biorxiv.org/content/10.1101/2021.02.09.430542v1?rss=1 Poh, E. Al-Fawakhiri, N. Tam, R. Taylor, J. A. McDougle, S. D. 2021-02-16 doi:10.1101/2021.02.09.430542 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Nigro-striatal dopamine activation lowers behavioral and neuronal phenotypes associated with obsessive-compulsive disorder ]]> https://biorxiv.org/content/10.1101/2021.02.11.430770v1?rss=1 Casado-Sainz, A. Gudmundsen, F. Baerentzen, S. L. Lange, D. Ringsted, A. Martinez-Tajada, I. Medina, S. Lee, H. Svarer, C. Keller, S. H. Schain, M. Kjaerby, C. Fisher, P. M. Cumming, P. Palner, M. 2021-02-11 doi:10.1101/2021.02.11.430770 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Phylogenomic subsampling and the search for phylogenetically reliable loci ]]> https://biorxiv.org/content/10.1101/2021.02.13.431075v1?rss=1 Mongiardino Koch, N. 2021-02-14 doi:10.1101/2021.02.13.431075 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ A brain-based universal measure of attention: predicting task-general and task-specific attention performance and their underlying neural mechanisms from task and resting state fMRI ]]> https://biorxiv.org/content/10.1101/2021.02.13.431091v1?rss=1 Yoo, K. Rosenberg, M. D. Kwon, Y. H. Avery, E. W. Lin, Q. Scheinost, D. Constable, R. T. Chun, M. M. 2021-02-16 doi:10.1101/2021.02.13.431091 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Suppression of Plasmodium MIF-CD74 Signaling Protects Against Severe Malaria ]]> https://biorxiv.org/content/10.1101/2021.02.14.430970v1?rss=1 Baeza Garcia, A. Siu, E. Du, X. Leng, L. Franke-Fayard, B. Janse, C. J. Howland, S. Renia, L. Lolis, E. Bucala, R. 2021-02-14 doi:10.1101/2021.02.14.430970 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Demands of visual processing hierarchy shape laminar compartmentalization of attention modulation of luminance contrast in area V4 ]]> https://biorxiv.org/content/10.1101/2021.02.15.431312v1?rss=1 Wang, X. Nandy, A. Jadi, M. 2021-02-17 doi:10.1101/2021.02.15.431312 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ The neural G protein Gαo tagged with GFP at an internal loop is functional in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.02.16.431479v1?rss=1 Kumar, S. Olson, A. C. Koelle, M. R. 2021-02-16 doi:10.1101/2021.02.16.431479 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia ]]> https://biorxiv.org/content/10.1101/2021.02.17.431423v1?rss=1 Sirak, K. A. Fernandes, D. M. Lipson, M. Mallick, S. Mah, M. Olalde, I. Ringbauer, H. Rohland, N. Hadden, C. S. Harney, E. Adamski, N. Bernardos, R. Broomandkhoshbacht, N. Callan, K. Ferry, M. Lawson, A. M. Michel, M. Oppenheimer, J. Stewardson, K. Zalzala, F. Patterson, N. Pinhasi, R. Thompson, J. C. Van Gerven, D. P. Reich, D. 2021-02-17 doi:10.1101/2021.02.17.431423 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Psilocybin induces rapid and persistent growth of dendritic spines in frontal cortex in vivo ]]> https://biorxiv.org/content/10.1101/2021.02.17.431629v1?rss=1 Shao, L.-X. Liao, C. Gregg, I. Savalia, N. Delagarza, K. Kwan, A. C. 2021-02-17 doi:10.1101/2021.02.17.431629 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Mechanical stress determines morphogenesis and cell ordering in confined bacterial biofilms ]]> https://biorxiv.org/content/10.1101/2021.02.17.431682v1?rss=1 Zhang, Q. Li, J. Nijjer, J. Lu, H. Kothari, M. Alert, R. Cohen, T. Yan, J. 2021-02-17 doi:10.1101/2021.02.17.431682 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Surface Densities Prewet a Near-Critical Membrane ]]> https://biorxiv.org/content/10.1101/2021.02.17.431700v1?rss=1 Rouches, M. Veatch, S. Machta, B. 2021-02-18 doi:10.1101/2021.02.17.431700 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Spatial modulation of individual behaviors enables collective decision-making during bacterial group migration ]]> https://biorxiv.org/content/10.1101/2021.02.17.431709v1?rss=1 Bai, Y. He, C. Long, J. Li, X. Fu, X. 2021-02-18 doi:10.1101/2021.02.17.431709 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Daily caffeinated soda intake is associated with impaired working memory and higher impulsivity in children ]]> https://biorxiv.org/content/10.1101/2021.02.17.431718v1?rss=1 Kwon, M. Kim, H. Yang, J. Hur, J. Lee, T.-H. Ahn, W.-Y. 2021-02-18 doi:10.1101/2021.02.17.431718 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Complex response of beta diversity to dispersal in meta-community models ]]> https://biorxiv.org/content/10.1101/2021.02.19.432043v1?rss=1 Lu, M. 2021-02-20 doi:10.1101/2021.02.19.432043 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ E. coli chemotaxis is information-limited ]]> https://biorxiv.org/content/10.1101/2021.02.22.432091v1?rss=1 Mattingly, H. H. Kamino, K. Machta, B. B. Emonet, T. 2021-02-22 doi:10.1101/2021.02.22.432091 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Human immunodeficiency reveals GIMAP5 as lymphocyte-specific regulator of senescence ]]> https://biorxiv.org/content/10.1101/2021.02.22.432146v1?rss=1 Park, A. Y. Leney-Greene, M. Lynberg, M. Xu, X. Zheng, L. Zhang, Y. Matthews, H. Chao, B. Morawski, A. Jiang, P. Aluri, J. Aydine, E. K. Kiykim, A. Pascall, J. Barlan, I. Sari, S. Butcher, G. Rao, V. K. Lifton, R. P. Baris, S. Ozen, A. Vilarinho, S. Su, H. Lenardo, M. J. 2021-02-23 doi:10.1101/2021.02.22.432146 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ CINS: Cell Interaction Network inference from Single cell expression data ]]> https://biorxiv.org/content/10.1101/2021.02.22.432206v1?rss=1 Yuan, Y. Cosme, C. Adams, T. S. Schupp, J. Sakamoto, K. Xylourgidis, N. Ruffalo, M. Kaminski, N. Bar-Joseph, Z. 2021-02-25 doi:10.1101/2021.02.22.432206 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ How human runners regulate footsteps on uneven terrain ]]> https://biorxiv.org/content/10.1101/2021.02.22.432238v1?rss=1 Dhawale, N. Venkadesan, M. 2021-02-22 doi:10.1101/2021.02.22.432238 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Kasugamycin is a novel chitinase 1 inhibitor with strong antifibrotic effects on pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2021.02.25.432796v1?rss=1 Lee, J.-H. Lee, C.-M. Kim, M.-O. Park, J. W. Kamle, S. Akosman, B. Herzog, E. L. Elias, J. A. Lee, C. G. 2021-02-26 doi:10.1101/2021.02.25.432796 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Exploring the interaction network of a synthetic gut bacterial community ]]> https://biorxiv.org/content/10.1101/2021.02.25.432904v1?rss=1 Weiss, A. S. Burrichter, A. G. Chakravarthy Durai Raj, A. von Strempel, A. Meng, C. Kleigrewe, K. Muench, P. C. Roessler, L. Huber, C. Eisenreich, W. Jochum, L. M. Goeing, S. Jung, K. Sanchez, A. Stecher, B. 2021-02-25 doi:10.1101/2021.02.25.432904 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Increasing central serotonin with 5-HTP disrupts the inhibition of social gaze in non-human primates ]]> https://biorxiv.org/content/10.1101/2021.02.26.431901v1?rss=1 Weinberg-Wolf, H. Fagan, N. A. Dal Monte, O. Chang, S. W. C. 2021-02-26 doi:10.1101/2021.02.26.431901 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Modeling gene x environment interactions in PTSD using glucocorticoid-induced transcriptomics in human neurons ]]> https://biorxiv.org/content/10.1101/2021.03.01.433391v1?rss=1 Breen, M. S. Rusielewicz, T. Bader, H. N. Seah, C. Xu, C. Hunter, C. J. McCarthy, B. Chattopadhyay, M. Desarnaud, F. Makotkine, I. Flory, J. D. Bierer, L. M. Staniskyte, M. NYSCF Global Array Team, Noggle, S. A. Paull, D. Brennand, K. J. Yehuda, R. 2021-03-02 doi:10.1101/2021.03.01.433391 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Title - Impact of extrinsic incubation temperature on natural selection during Zika virus infection of Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2021.03.02.433538v1?rss=1 10{degrees}C. Temperatures impact vector competence, extrinsic incubation period, and mosquito survival unimodally, with optimum occurring at some intermediate temperature. In addition, the mean and range of daily temperature fluctuations influence arbovirus perpetuation and vector competence. The impact of temperature on arbovirus genetic diversity during systemic mosquito infection, however, is poorly understood. Therefore, we determined how constant extrinsic incubation temperatures of 25{degrees}C, 28{degrees}C, 32{degrees}C, and 35{degrees}C control Zika virus (ZIKV) vector competence and population dynamics within Aedes aegypti and Aedes albopictus mosquitoes. We also examined diurnally fluctuating temperatures which more faithfully mimic field conditions in the tropics. We found that vector competence varied in a unimodal manner for constant temperatures peaking between 28{degrees}C and 32{degrees}C for both Aedes species. Transmission peaked at 10 days post-infection for Aedes aegypti and 14 days for Aedes albopictus. The effect of diurnal temperature was distinct and could not have been predicted from constant temperature-derived data. Using RNA-seq to characterize ZIKV population structure, we identified that temperature alters the selective environment in unexpected ways. During mosquito infection, constant temperatures more often elicited positive selection whereas diurnal temperatures led to strong purifying selection in both Aedes species. These findings demonstrate that temperature has multiple impacts on ZIKV biology within mosquitoes, including major effects on the selective environment within mosquitoes. Author SummaryArthropod-borne viruses (arboviruses) have emerged in recent decades due to complex factors that include increases in international travel and trade, the breakdown of public health infrastructure, land use changes, and many other factors. Climate change also has the potential to shift the geographical ranges of arthropod vectors, consequently increasing the global risk of arbovirus infection. Changing temperatures may also alter the virus-host interaction, ultimately resulting in the emergence of new viruses and virus genotypes in new areas. Therefore, we sought to characterize how temperature (both constant and fluctuating) alters the ability of Aedes aegypti and Aedes albopictus to transmit Zika virus, and how it influences virus populations within mosquitoes. We found that intermediate temperatures maximize virus transmission compared to more extreme and fluctuating temperatures. Constant temperatures increased positive selection on virus genomes, while fluctuating temperatures strengthened purifying selection. Our studies provide evidence that in addition to altering VC, temperature significantly influences the selective environment within mosquitoes. ]]> Murrieta, R. Garcia-Luna, S. M. Murrieta, D. J. Halladay, G. Young, M. C. Fauver, J. R. Gendernalik, A. Weger-Lucarelli, J. Rückert, C. Ebel, G. 2021-03-02 doi:10.1101/2021.03.02.433538 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ A CTDNEP1-lipin 1-mTOR regulatory network restricts ER membrane biogenesis to enable chromosome motions necessary for mitotic fidelity ]]> https://biorxiv.org/content/10.1101/2021.03.02.433553v1?rss=1 Merta, H. Carrasquillo Rodriguez, J. W. Anjur-Dietrich, M. I. Granade, M. E. Vitale, T. Harris, T. E. Needleman, D. J. Bahmanyar, S. 2021-03-02 doi:10.1101/2021.03.02.433553 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Focal Laser Stimulation of Fly Nociceptors Activates Distinct Axonal and Dendritic Ca2+ Signals ]]> https://biorxiv.org/content/10.1101/2021.03.04.433797v1?rss=1 Basak, R. Sutradhar, S. Howard, J. 2021-03-05 doi:10.1101/2021.03.04.433797 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ UBXN3B Restricts Viral Pathogenesis by Maintaining Hematopoietic Homeostasis ]]> https://biorxiv.org/content/10.1101/2021.03.04.433919v1?rss=1 WANG, P. Geng, T. Yang, D. Lin, T. Harrison, A. Haynes, L. Torrance, B. Wang, B. Vella, A. T. Cheng, G. Fikrig, E. Yang, L. 2021-03-04 doi:10.1101/2021.03.04.433919 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Trp53 ablation fails to prevent microcephaly in mouse pallium with impaired minor intron splicing ]]> https://biorxiv.org/content/10.1101/2021.03.05.434172v1?rss=1 White, A. K. Baumgartner, M. Lee, M. F. Drake, K. D. Aquino, G. S. Kanadia, R. 2021-03-06 doi:10.1101/2021.03.05.434172 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases ]]> https://biorxiv.org/content/10.1101/2021.03.06.434199v1?rss=1 Mandel-Brehm, C. Fichtner, M. L. Jiang, R. Winton, V. J. Vazquez, S. E. Pham, M. C. Hoehn, K. B. Kelleher, N. L. Nowak, R. J. Kleinstein, S. H. Wilson, M. R. DeRisi, J. L. OConnor, K. C. 2021-03-08 doi:10.1101/2021.03.06.434199 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ An objective-based prioritization approach to improve trophic complexity through ecological restoration ]]> https://biorxiv.org/content/10.1101/2021.03.09.434521v1?rss=1 Ladouceur, E. McGowan, J. Huber, P. Possingham, H. Scridel, D. van Klink, R. Poschlod, P. Cornelissen, J. H. C. Bonomi, C. Jimenez-Alfaro, B. 2021-03-10 doi:10.1101/2021.03.09.434521 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Single Cell Transcriptomic Landscape of Diabetic Foot Ulcers ]]> https://biorxiv.org/content/10.1101/2021.03.11.434413v1?rss=1 Theocharidis, G. Thomas, B. E. Sarkar, D. Pilcher, W. J. Dwivedi, B. Sandoval-Schaefer, T. Sirbulescu, R. F. Kafanas, A. Mezghani, I. Wang, P. Lobao, A. Vlachos, I. Dash, B. Hsia, H. C. Horsley, V. Bhasin, S. S. Veves, A. Bhasin, M. 2021-03-12 doi:10.1101/2021.03.11.434413 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Spatial Epigenome Sequencing at Tissue Scale and Cellular Level ]]> https://biorxiv.org/content/10.1101/2021.03.11.434985v1?rss=1 Deng, Y. Zhang, D. Liu, Y. Su, G. Enninful, A. Bai, Z. Fan, R. 2021-03-12 doi:10.1101/2021.03.11.434985 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Surf4 Promotes Endoplasmic Reticulum Exit of the Lysosomal Prosaposin-Progranulin Complex ]]> https://biorxiv.org/content/10.1101/2021.03.11.435014v1?rss=1 Devireddy, S. Ferguson, S. 2021-03-12 doi:10.1101/2021.03.11.435014 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Wrack enhancement of post-hurricane vegetation and geomorphological recovery in a coastal dune ]]> https://biorxiv.org/content/10.1101/2021.03.12.435051v1?rss=1 Joyce, M. A. Griffin, J. N. Crotty, S. M. Angelini, C. Cordero, O. Ortals, C. DeBattisti, D. 2021-03-12 doi:10.1101/2021.03.12.435051 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Reconstructing human early embryogenesis in vitro with pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.03.12.435175v1?rss=1 Zernicka-Goetz, M. Sozen, B. Jorgensen, V. Cui, T. Zhu, M. 2021-03-12 doi:10.1101/2021.03.12.435175 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Synaptotagmin rings as high sensitivity regulators of synaptic vesicle docking and fusion ]]> https://biorxiv.org/content/10.1101/2021.03.12.435193v1?rss=1 Zhu, J. McDargh, Z. A. Li, F. Krishnakumar, S. Rothman, J. E. O'Shaughnessy, B. 2021-03-13 doi:10.1101/2021.03.12.435193 Cold Spring Harbor Laboratory Press 2021-03-13 <![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[ Increasing stimulus similarity drives nonmonotonic representational change in hippocampus ]]> https://biorxiv.org/content/10.1101/2021.03.13.435275v1?rss=1 Wammes, J. D. Norman, K. A. Turk-Browne, N. B. 2021-03-14 doi:10.1101/2021.03.13.435275 Cold Spring Harbor Laboratory Press 2021-03-14 <![CDATA[ Structural insights into the role of Dicer-related helicase 3 in RNAi in Caenorhabditis elegans. ]]> https://biorxiv.org/content/10.1101/2021.03.14.433363v1?rss=1 Li, K. Zheng, J. Wirawan, M. Nguyen, T. M. Fedorova, O. Griffin, P. Pyle, A. M. Luo, D. 2021-03-16 doi:10.1101/2021.03.14.433363 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Phagocytic 'teeth' and myosin-II 'jaw' power target constriction during phagocytosis ]]> https://biorxiv.org/content/10.1101/2021.03.14.435346v1?rss=1 Vorselen, D. Barger, S. R. Wang, Y. Cai, W. Theriot, J. A. Gauthier, N. C. Krendel, M. 2021-03-15 doi:10.1101/2021.03.14.435346 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Anatomical and Functional Gradients Shape Dynamic Functional Connectivity in the Human Brain ]]> https://biorxiv.org/content/10.1101/2021.03.15.435361v1?rss=1 Kong, X. Kong, R. Orban, C. Wang, P. zhang, s. Anderson, K. M. Holmes, A. Murray, J. D. Deco, G. van den heuvel, m. Yeo, B. T. T. 2021-03-15 doi:10.1101/2021.03.15.435361 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Paratransgenic manipulation of tsetse miR275 alters the physiological homeostasis of the flys midgut environment ]]> https://biorxiv.org/content/10.1101/2021.03.15.435453v1?rss=1 Yang, L. Weiss, B. Williams, A. E. Aksoy, E. de Silva Orfano, A. Son, J. H. Wu, Y. Vigneron, A. Karakus, M. Aksoy, S. 2021-03-15 doi:10.1101/2021.03.15.435453 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Mapping origins of variation in neural trajectories of human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.03.17.435870v1?rss=1 Kim, S. K. Seo, S. Stein-O'Brien, G. Jaishankar, A. Ogawa, K. Micali, N. Wang, Y. Hyde, T. Kleinman, J. Voss, T. Fertig, E. Shin, J. H. Burli, R. Cross, A. J. Brandon, N. J. Weinberger, D. R. Chenoweth, J. G. Hoeppner, D. J. Sestan, N. Colantuoni, C. McKay, R. D. 2021-03-17 doi:10.1101/2021.03.17.435870 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Targeting de novo lipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer ]]> https://biorxiv.org/content/10.1101/2021.03.18.434804v1?rss=1 Bartolacci, C. Andreani, C. Dias do Vale, G. Berto, S. Melegari, M. Crouch, A. C. Baluya, D. L. Kemble, G. Hodges, K. Starrett, J. Politi, K. Starnes, S. L. Lorenzini, D. Raso, M. G. Solis Soto, L. Behrens, C. Kadara, H. Gao, B. Gerber, D. Wistuba, I. I. Minna, J. McDonald, J. Scaglioni, P. P. 2021-03-19 doi:10.1101/2021.03.18.434804 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Distinct Hypoxia-induced Translational Profiles of Embryonic and Adult-derived Macrophages ]]> https://biorxiv.org/content/10.1101/2021.03.18.435732v1?rss=1 Wilcox, N. S. Yarovinsky, T. O. Pandya, P. Ramgolam, V. S. Moro, A. Wu, Y. Nicoli, S. Hirschi, K. K. Bender, J. R. 2021-03-19 doi:10.1101/2021.03.18.435732 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Live imaging of SARS-CoV-2 infection in mice reveals neutralizing antibodies require Fc function for optimal efficacy ]]> https://biorxiv.org/content/10.1101/2021.03.22.436337v1?rss=1 Ullah, I. Prevost, J. Ladinsky, M. S. Stone, H. Lu, M. Anand, S. P. Beaudoin-Bussieres, G. Benlarbi, M. Ding, S. Gasser, R. Fink, C. Chen, Y. Tauzin, A. Goyette, G. Bourassa, C. Medjahed, H. Mack, M. Chung, K. Wilen, C. B. Dekaban, G. A. Dikeakos, J. D. Bruce, E. A. Kaufmann, D. E. Stamatatos, L. McGuire, A. Richard, J. Pazgier, M. Bjorkman, P. Mothes, W. Finzi, A. Kumar, P. Uchil, P. D. 2021-03-22 doi:10.1101/2021.03.22.436337 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Neurexin and Frizzled signaling intercept axonal-transport at microtubule minus-ends to control synapse formation ]]> https://biorxiv.org/content/10.1101/2021.03.22.436477v1?rss=1 Balseiro-Gomez, S. Yue, Y. Shao, L. Cetinkaya, S. Kuzoian, C. Verhey, K. J. Yogev, S. 2021-03-22 doi:10.1101/2021.03.22.436477 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Brain kernel: a new spatial covariance function for fMRI data ]]> https://biorxiv.org/content/10.1101/2021.03.22.436524v1?rss=1 Wu, A. Nastase, S. A. Baldassano, C. A. Turk-Browne, N. B. Norman, K. A. Engelhardt, B. E. Pillow, J. W. 2021-03-23 doi:10.1101/2021.03.22.436524 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Asymmetric structures and conformational plasticity of the uncleaved full-length human immunodeficiency virus (HIV-1) envelope glycoprotein trimer ]]> https://biorxiv.org/content/10.1101/2021.03.28.437443v1?rss=1 Zhang, S. Wang, K. Wei Li, W. Nguyen, H. T. Chen, S. Lu, M. Go, E. P. Ding, H. Steinbock, R. T. Desaire, H. Kappes, J. C. Sodroski, J. G. Mao, Y. 2021-03-29 doi:10.1101/2021.03.28.437443 Cold Spring Harbor Laboratory Press 2021-03-29 <![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[ Effective Therapy Targeting Cytochrome bc1 Prevents Babesia Erythrocytic Development and Protects from Lethal Infection ]]> https://biorxiv.org/content/10.1101/2021.03.31.438003v1?rss=1 Chiu, J. E. Renard, I. Chattopadhyay Pal, A. Singh, P. Vydyam, P. Thekkiniath, J. Kumar, M. Gihaz, S. Pou, S. Winter, R. W. Dodean, R. Nilsen, A. Riscoe, M. K. Doggett, J. S. Ben Mamoun, C. 2021-04-01 doi:10.1101/2021.03.31.438003 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ The Time Complexity of Self-Assembly ]]> https://biorxiv.org/content/10.1101/2021.04.01.437956v1?rss=1 Gartner, F. M. Graf, I. R. Frey, E. 2021-04-01 doi:10.1101/2021.04.01.437956 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Induction of Dopaminergic Neurons for Neuronal Subtype-Specific Modeling of Psychiatric Disease Risk ]]> https://biorxiv.org/content/10.1101/2021.04.01.438094v1?rss=1 Powell, S. K. O'Shea, C. Townsley, K. Prytkova, I. Dobrindt, K. Elahi, R. Iskhakova, M. Lambert, T. Valada, A. Liao, W. Ho, S.-M. Slesinger, P. A. Huckins, L. M. Akbarian, S. Brennand, K. J. 2021-04-02 doi:10.1101/2021.04.01.438094 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Deficiency of the paternally inherited gene Magel2 alters the development of separation induced vocalization in mice ]]> https://biorxiv.org/content/10.1101/2021.04.01.438102v1?rss=1 Bosque Ortiz, G. M. Santana, G. M. Dietrich, M. O. 2021-04-01 doi:10.1101/2021.04.01.438102 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Latent functional connectivity underlying multiple brain states ]]> https://biorxiv.org/content/10.1101/2021.04.05.438534v1?rss=1 McCormick, E. M. Arnemann, K. L. Ito, T. Hanson, S. J. Cole, M. W. 2021-04-06 doi:10.1101/2021.04.05.438534 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes. ]]> https://biorxiv.org/content/10.1101/2021.04.06.438626v1?rss=1 Dutton, C. L. Subalusky, A. L. Sanchez, A. S. Estrela, S. L. Lu, N. Hamilton, S. Njoroge, L. Rosi, E. J. Post, D. M. 2021-04-08 doi:10.1101/2021.04.06.438626 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Complex effects of kinase localization revealed by compartment-specific regulation of protein kinase A activity ]]> https://biorxiv.org/content/10.1101/2021.04.08.439038v1?rss=1 LaCroix, R. Lin, B. Levchenko, A. 2021-04-09 doi:10.1101/2021.04.08.439038 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis ]]> https://biorxiv.org/content/10.1101/2021.04.09.439144v1?rss=1 Son, J. H. Weiss, B. L. Schneider, D. l. Kisweda-sida, D. Gstöttenmayer, F. Opiro, R. Echodu, R. Saarman, N. Attardo, G. Onyango, M. Abdalla, A. Aksoy, S. 2021-04-09 doi:10.1101/2021.04.09.439144 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Multi-scale phenological niches in diverse Amazonian plant communities ]]> https://biorxiv.org/content/10.1101/2021.04.10.438715v1?rss=1 Pak, D. Swamy, V. Alvarez-Loayza, P. Cornejo, F. Queenborough, S. A. Metz, M. R. Terborgh, J. Valencia, R. Wright, S. J. Garwood, N. C. Lasky, J. R. 2021-04-11 doi:10.1101/2021.04.10.438715 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ SLIT2-ROBO signaling in tumor-associated microglia/macrophages drives glioblastoma immunosuppression and vascular dysmorphia ]]> https://biorxiv.org/content/10.1101/2021.04.12.438457v1?rss=1 Geraldo, L. H. Xu, Y. Jacob, L. Pibouin-Fragner, L. Rao, R. Maissa, N. Verreault, M. Lemaire, N. Knosp, C. Lesaffre, C. Daubon, T. Dejaegher, J. Solie, L. Rudewicz, J. Viel, T. Tavitian, B. De Vleeschouwer, S. Sanson, M. Bikfalvi, A. Idbaih, A. Lu, Q. R. Lima, F. Thomas, J.-L. Eichmann, A. Mathivet, T. 2021-04-12 doi:10.1101/2021.04.12.438457 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Renalase is a novel tissue and serological biomarker in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2021.04.12.439422v1?rss=1 Gao, Y. Wang, M. Guo, X. Hu, J. Chen, T.-m. Finn, S. Lacy, J. Kunstman, J. Cha, C. Bellin, M. Robert, M. Desir, G. Gorelick, F. S. 2021-04-12 doi:10.1101/2021.04.12.439422 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ The world's hotspot of linguistic and biocultural diversity under threat ]]> https://biorxiv.org/content/10.1101/2021.04.12.439439v1?rss=1 10% of the worlds languages and rich and varied biocultural knowledge, but the future of this diversity remains unclear. We measured language skills of 6,190 students speaking 392 languages (5.5% of the global total) and modelled their future trends, using individual-level variables characterizing family language use, socio-economic conditions, students skills, and language traits. This approach showed that only 58% of the students, compared to 91% of their parents, were fluent in indigenous languages, while the trends in key drivers of language skills (language use at home, proportion of mixed-language families, urbanization, students traditional skills) predicted accelerating decline of fluency, to an estimated 26% in the next generation of students. Ethnobiological knowledge declined in close parallel with language skills. Varied medicinal plant uses known to the students speaking indigenous languages are replaced by a few, mostly non-native species for the students speaking English or Tok Pisin, the national lingua franca. Most (88%) students want to teach indigenous language to their children. While crucial for keeping languages alive, this intention faces powerful external pressures as key factors (education, cash economy, road networks, urbanization) associated with language attrition are valued in contemporary society. Significance StatementAround the world, more than 7,000 languages are spoken, most of them by small populations of speakers in the tropics. Globalization puts small languages at a disadvantage, but our understanding of the drivers and rate of language loss remains incomplete. When we tested key factors causing language attrition among Papua New Guinean students speaking 392 different indigenous languages, we found an unexpectedly rapid decline in their language skills compared to their parents and predicted further acceleration of language loss in the next generation. Language attrition was accompanied by decline in the traditional knowledge of nature among the students, pointing to an uncertain future for languages and biocultural knowledge in the most linguistically diverse place on Earth. ]]> Kik, A. Adamec, M. Aikhenvald, A. Y. Bajzekova, J. Baro, N. Bowern, C. Colwell, R. K. Drozd, P. Duda, P. Ibalim, S. Jorge, L. R. Mogina, J. Ruli, B. Sam, K. Sarvasy, H. Saulei, S. Weiblen, G. D. Zrzavy, J. Novotny, V. 2021-04-12 doi:10.1101/2021.04.12.439439 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in the reef-building coral Montipora capitata ]]> https://biorxiv.org/content/10.1101/2021.04.14.439692v1?rss=1 Chille, E. E. Strand, E. Neder, M. Schmidt, V. Sherman, M. Putnam, H. M. Mass, T. 2021-04-14 doi:10.1101/2021.04.14.439692 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ A curated collection of human vaccination response signatures ]]> https://biorxiv.org/content/10.1101/2021.04.15.439017v1?rss=1 600 immune signatures from >60 published studies profiling human vaccination responses for the current release. The system will aid in building a broader understanding of the human immune response to stimuli by enabling researchers to easily access and interrogate published immune signatures. ]]> Smith, K. C. Chawla, D. G. Dhillon, B. K. Ji, Z. Vita, R. van der Leest, E. Weng, J. Tang, E. Abid, A. The Human Immunology Project Consortium (HIPC), Peters, B. Hancock, R. E. W. Floratos, A. Kleinstein, S. H. 2021-04-16 doi:10.1101/2021.04.15.439017 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ Single-cell antigen-specific activation landscape of CAR T infusion product identifies determinants of CD19 positive relapse in patients with ALL ]]> https://biorxiv.org/content/10.1101/2021.04.15.440005v1?rss=1 54 months). Proteomic profiles also revealed that the frequency of early memory T cell subsets, rather than activation or co-inhibitory signatures could distinguish CD19-positive relapse. Additionally, a deficit of type 1 helper and cytotoxic effector function and an enrichment for terminally differentiated CD8+ T cells exhibiting low cytokine polyfunctionality was associated with initial non-responders. By contrast, the single-cell transcriptomic data of unstimulated or TCR-activated CAR T cells failed to predict clinical responses. In aggregate, our results dissect the landscape of CAR-specific activation states in infusion products that can identify patients who do not develop a durable response to the therapy, and unveil the molecular mechanisms that may inform strategies to boost specific T cell function to maintain long term remission. ]]> Bai, Z. Woodhouse, S. Kim, D. Lundh, S. Sun, H. Deng, Y. Xiao, Y. Barrett, D. M. Myers, R. M. Grupp, S. A. June, C. H. J. Joseph Melenhorst, J. J. Camara, P. G. Fan, R. 2021-04-15 doi:10.1101/2021.04.15.440005 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking ]]> https://biorxiv.org/content/10.1101/2021.04.16.440205v1?rss=1 Higgins-Chen, A. T. Thrush, K. L. Wang, Y. Kuo, P.-L. Wang, M. Minteer, C. J. Moore, A. Z. Bandinelli, S. Vinkers, C. H. Vermetten, E. Rutten, B. P. F. Geuze, E. Okhuijsen-Pfeifer, C. van der Horst, M. Z. Schreiter, S. Gutwinski, S. Luykx, J. J. Ferrucci, L. Crimmins, E. M. Boks, M. P. Hagg, S. Hu-Seliger, T. T. Levine, M. E. 2021-04-19 doi:10.1101/2021.04.16.440205 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Network controllability enrichment analysis reveals that SARS-CoV-2 infection tends to target indispensable nodes of a directed human protein-protein interaction network ]]> https://biorxiv.org/content/10.1101/2021.04.18.440358v1?rss=1 Lee, H.-J. 2021-04-19 doi:10.1101/2021.04.18.440358 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Integrative molecular and clinical profiling of acral melanoma identifies LZTR1 as a key tumor promoter and therapeutic target ]]> https://biorxiv.org/content/10.1101/2021.04.20.440286v1?rss=1 Farshidfar, F. Peng, C. Levovitz, C. Knight, J. Bacchiocchi, A. Su, J. Rhrissorrakrai, K. Yin, M. Sznol, M. Ariyan, S. Clune, J. Olino, K. Parida, L. Nikolaus, J. Zhang, M. Zhao, S. Wang, Y. Huang, G. Wan, M. Li, X. Cao, J. Yan, Q. Chen, X. Newman, A. M. Halaban, R. M. 2021-04-21 doi:10.1101/2021.04.20.440286 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Decreased overall neuronal activity in a rodent model of impaired consciousness during absence seizures ]]> https://biorxiv.org/content/10.1101/2021.04.20.440390v1?rss=1 McCafferty, C. P. Gruenbaum, B. F. Tung, R. Li, J.-J. Salvino, P. Vincent, P. Kratochvil, Z. Ryu, J. H. Khalaf, A. Swift, K. Akbari, R. Islam, W. Antwi, P. Johnson, E. A. Vitkovskiy, P. Sampognaro, J. Freedman, I. Kundishora, A. J. Sanganahalli, B. G. Herman, P. Hyder, F. Crunelli, V. Depaulis, A. Blumenfeld, H. 2021-04-21 doi:10.1101/2021.04.20.440390 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Multi-omics profiling of U2AF1 mutants dissects pathogenic mechanisms affecting RNA granules in myeloid malignancies ]]> https://biorxiv.org/content/10.1101/2021.04.22.441020v1?rss=1 Biancon, G. Joshi, P. Zimmer, J. T. Hunck, T. Gao, Y. Lessard, M. D. Courchaine, E. Barentine, A. E. Machyna, M. Botti, V. Qin, A. Gbyli, R. Patel, A. Song, Y. Kiefer, L. Viero, G. Neuenkirchen, N. Lin, H. Bewersdorf, J. Simon, M. D. Neugebauer, K. M. Tebaldi, T. Halene, S. 2021-04-23 doi:10.1101/2021.04.22.441020 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Targeted, collaborative biodiversity conservation in the global ocean can benefit fisheries economies ]]> https://biorxiv.org/content/10.1101/2021.04.23.441004v1?rss=1 Rinnan, D. S. Reygondeau, G. McGowan, J. Lam, V. Sumaila, R. Ranipeta, A. Kaschner, K. Garilao, C. Cheung, W. L. Jetz, W. 2021-04-26 doi:10.1101/2021.04.23.441004 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ The 3D construction of leaves is coordinated with water use efficiency in conifers ]]> https://biorxiv.org/content/10.1101/2021.04.23.441113v1?rss=1 Trueba, S. Theroux-Rancourt, G. Earles, J. M. Buckley, T. N. Love, D. Johnson, D. M. Brodersen, C. 2021-04-23 doi:10.1101/2021.04.23.441113 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Sequential defects in cardiac lineage commitment and maturation cause hypoplastic left heart syndrome ]]> https://biorxiv.org/content/10.1101/2021.04.24.441110v1?rss=1 Krane, M. Dressen, M. Santamaria, G. My, I. Schneider, C. Dorn, T. Laue, S. Mastantuono, E. Berutti, R. Rawat, H. Gilsbach, R. Schneider, P. Lahm, H. Schwarz, S. Doppler, S. Paige, S. Puluca, N. Doll, S. Neb, I. Brade, T. Zhang, Z. Abou-Ajram, C. Northoff, B. Holdt, L. Sudhop, S. Sahara, M. Goedel, A. Dendorfer, A. Tjong, F. Rijlaarsdam, M. Cleuziou, J. Lang, N. Kupatt, C. Bezzina, C. Lange, R. Bowles, N. Mann, M. Gelb, B. Crotti, L. Hein, L. Meitinger, T. Wu, S. Sinnecker, D. Gruber, P. Laugwitz, K. L. Moretti, A. 2021-04-26 doi:10.1101/2021.04.24.441110 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ The Host Cell's Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV Envelope ]]> https://biorxiv.org/content/10.1101/2021.04.24.441266v1?rss=1 Yoon, J. Nekongo, E. E. Patrick, J. E. Phillips, A. M. Ponomarenko, A. I. Hendel, S. J. Butty, V. L. Ogbunugafor, C. B. Lin, Y.-S. Shoulders, M. D. 2021-04-24 doi:10.1101/2021.04.24.441266 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Measuring the tolerance of the genetic code to altered codon size ]]> https://biorxiv.org/content/10.1101/2021.04.26.441066v1?rss=1 DeBenedictis, E. A. Esvelt, K. M. Soll, D. 2021-04-26 doi:10.1101/2021.04.26.441066 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ Inositol Polyphosphate-5-phosphatase K (Inpp5k) enhances sprouting of corticospinal tract axons after CNS trauma. ]]> https://biorxiv.org/content/10.1101/2021.04.27.441184v1?rss=1 Kauer, S. D. Fink, K. L. Li, E. H. Evans, B. P. Golan, N. Cafferty, W. B. 2021-04-28 doi:10.1101/2021.04.27.441184 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Sustained coevolution of phage Lambda and Escherichia coli involves inner as well as outer membrane defenses and counter-defenses ]]> https://biorxiv.org/content/10.1101/2021.04.27.441663v1?rss=1 Burmeister, A. R. Sullivan, R. M. Gallie, J. Lenski, R. E. 2021-04-28 doi:10.1101/2021.04.27.441663 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Citrullination of glucokinase linked to autoimmune diabetes ]]> https://biorxiv.org/content/10.1101/2021.04.28.441829v1?rss=1 Yang, M.-L. Horstman, S. Gee, R. Guyer, P. Lam, T. Kanyo, J. Perdigoto, A. Speake, C. Greenbaum, C. J. Overbergh, L. Kibbey, R. Herold, K. C. James, E. A. Mamula, M. J. 2021-04-29 doi:10.1101/2021.04.28.441829 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes ]]> https://biorxiv.org/content/10.1101/2021.04.29.442059v1?rss=1 Shi, F. Mendrola, J. M. Sheetz, J. B. Wu, N. Sommer, A. Speer, K. F. Noordermeer, J. N. Kan, Z.-Y. Perry, K. Englander, S. W. Stayrook, S. E. Fradkin, L. G. Lemmon, M. A. 2021-04-30 doi:10.1101/2021.04.29.442059 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Activation of extrasynaptic kainate receptors drives hilar mossy cell activity ]]> https://biorxiv.org/content/10.1101/2021.05.01.442200v1?rss=1 Ramos, C. C. Lutzu, S. Yamasaki, M. Yanagawa, Y. Watanabe, M. Sakimura, K. Tomita, S. Castillo, P. E. 2021-05-01 doi:10.1101/2021.05.01.442200 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Myosins generate contractile force and maintain organization in the cytokinetic contractile ring ]]> https://biorxiv.org/content/10.1101/2021.05.02.442363v1?rss=1 McDargh, Z. A. Wang, S. Chin, H. F. Thiyagarajan, S. Karatekin, E. Pollard, T. D. O'Shaughnessy, B. 2021-05-03 doi:10.1101/2021.05.02.442363 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ A novel mouse model of focal limbic seizures that reproduces behavioral impairment associated with cortical slow wave activity ]]> https://biorxiv.org/content/10.1101/2021.05.05.442811v1?rss=1 Sieu, L.-A. Singla, S. Sharafeldin, A. Chandrasekaran, G. Valcarce-Aspegren, M. Niknahad, A. Fu, I. Doilicho, N. Gummadavelli, A. McCafferty, C. P. Crouse, R. B. Perrenoud, Q. Picciotto, M. Cardin, J. A. Blumenfeld, H. 2021-05-06 doi:10.1101/2021.05.05.442811 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Cortical granularity shapes information flow to the amygdala and its striatal targets in nonhuman primate ]]> https://biorxiv.org/content/10.1101/2021.05.06.442678v1?rss=1 McHale, A. C. Cho, Y. T. Fudge, J. L. 2021-05-06 doi:10.1101/2021.05.06.442678 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ A murine model of the human CREBRFR457Q obesity-risk variant does not influence energy or glucose homeostasis in response to nutritional stress ]]> https://biorxiv.org/content/10.1101/2021.05.06.442909v1?rss=1 Kershaw, E. E. Kanshana, J. S. Mattila, P. E. Ewing, M. C. Wood, A. N. Schoiswohl, G. Meyer, A. C. Kowalski, A. Rosenthal, S. L. Gingras, S. Kaufman, B. A. Lu, R. Weeks, D. E. McGarvey, S. T. Minster, R. L. Hawley, N. L. 2021-05-06 doi:10.1101/2021.05.06.442909 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[ Defective flow-migration coupling causes arteriovenous malformations in hereditary hemorrhagic telangiectasia ]]> https://biorxiv.org/content/10.1101/2021.05.06.442985v1?rss=1 Park, H. Furtado, J. Poulet, M. Chung, M. Yun, S. Lee, S. Sessa, W. C. Franco, C. A. Schwartz, M. A. Eichmann, A. 2021-05-06 doi:10.1101/2021.05.06.442985 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Comparing host module activation patterns and temporal dynamics in infection by influenza H1N1 viruses ]]> https://biorxiv.org/content/10.1101/2021.05.07.443162v1?rss=1 Nudelman, I. Kudrin, D. Nudelman, G. Deshpande, R. Hartmann, B. M. Kleinstein, S. H. Myers, C. L. Sealfon, S. C. Zaslavsky, E. 2021-05-09 doi:10.1101/2021.05.07.443162 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ Phosphatidylserine binding regulates TIM-3 effects on T cell receptor signaling ]]> https://biorxiv.org/content/10.1101/2021.05.07.443190v1?rss=1 Smith, C. M. Li, A. Krishnamurthy, N. Lemmon, M. A. 2021-05-08 doi:10.1101/2021.05.07.443190 Cold Spring Harbor Laboratory Press 2021-05-08 <![CDATA[ Pyruvate kinase M1 suppresses development and progression of prostate adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2021.05.09.443334v1?rss=1 Davidson, S. M. Heyman, J. E. O'Brien, J. P. Liu, A. C. Schmidt, D. R. Israelsen, W. J. Dayton, T. L. Sehgal, R. Bronson, R. Freinkman, E. Mak, H. Malstrom, S. Bellinger, G. Carracedo, A. Pandolfi, P. P. Courtney, K. D. Frangioni, J. Jha, A. DePinho, R. A. Horner, J. Thomas, C. Cantley, L. C. Loda, M. Vander Heiden, M. G. 2021-05-10 doi:10.1101/2021.05.09.443334 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Biofilm self-patterning: mechanical force landscaping drives a collective reorientation cascade ]]> https://biorxiv.org/content/10.1101/2021.05.11.440221v1?rss=1 Nijjer, J. Li, C. Zhang, Q. Lu, H. Zhang, S. Yan, J. 2021-05-11 doi:10.1101/2021.05.11.440221 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Viral shedding and transmission after natural infection and vaccination in an animal model of SARS-CoV-2 propagation ]]> https://biorxiv.org/content/10.1101/2021.05.11.443477v1?rss=1 Zeiss, C. J. Asher, J. L. Vander Wyk, B. J. Allore, H. G. Compton, S. J. 2021-05-11 doi:10.1101/2021.05.11.443477 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis ]]> https://biorxiv.org/content/10.1101/2021.05.11.443615v1?rss=1 Brereton, C. J. Yao, L. Zhou, Y. Vukmirovic, M. Bell, J. A. Ridley, R. A. Davies, E. Dean, L. S. N. Andriotis, O. G. Conforti, F. Mohammed, S. Wallis, T. Tavassoli, A. Ewing, R. Alzetani, A. Marshall, B. G. Fletcher, S. Thurner, P. J. Fabre, A. Kaminski, N. Richeldi, L. Bhaskar, A. Loxham, M. Davies, D. E. Wang, Y. Jones, M. 2021-05-12 doi:10.1101/2021.05.11.443615 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Perception of soft materials relies on physics-based object representations: Behavioral and computational evidence ]]> https://biorxiv.org/content/10.1101/2021.05.12.443806v1?rss=1 Bi, W. Shah, A. D. Wong, K. W. Scholl, B. Yildirim, I. 2021-05-13 doi:10.1101/2021.05.12.443806 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations ]]> https://biorxiv.org/content/10.1101/2021.05.12.443887v1?rss=1 Cheng, Y. Liu, M. Hu, M. Wang, S. 2021-05-13 doi:10.1101/2021.05.12.443887 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Composition and Biophysical Properties of the Sorting Platform Pods in the Shigella Type III Secretion System ]]> https://biorxiv.org/content/10.1101/2021.05.13.444006v1?rss=1 Tachiyama, S. Skaar, R. Chang, Y. Carroll, B. Muthuramalingam, M. Whittier, S. K. Barta, M. L. Picking, W. L. Liu, J. Picking, W. D. 2021-05-13 doi:10.1101/2021.05.13.444006 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Multiframe Evolving Dynamic Functional Connectivity (EVOdFNCs): A Method for Constructing and Investigating Functional Brain Motifs ]]> https://biorxiv.org/content/10.1101/2021.05.18.444678v1?rss=1 Miller, R. L. Vergara, V. M. Pearlson, G. D. Calhoun, V. D. 2021-05-20 doi:10.1101/2021.05.18.444678 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.05.19.444825v1?rss=1 Israelow, B. Mao, T. Klein, J. Song, E. Menasche, B. Omer, S. B. Iwasaki, A. 2021-05-19 doi:10.1101/2021.05.19.444825 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance ]]> https://biorxiv.org/content/10.1101/2021.05.20.444985v1?rss=1 Mohler, K. Moen, J. Rogulina, S. Rinehart, J. 2021-05-21 doi:10.1101/2021.05.20.444985 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Linking animal migration and ecosystem processes: data-driven simulation of propagule dispersal by migratory herbivores ]]> https://biorxiv.org/content/10.1101/2021.05.21.445111v1?rss=1 Somveille, M. Ellis-Soto, D. 2021-05-23 doi:10.1101/2021.05.21.445111 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ AMP-Kinase mediates regulation of glomerular volume and podocyte survival ]]> https://biorxiv.org/content/10.1101/2021.05.21.445180v1?rss=1 Banu, K. Lin, Q. Basgen, J. M. Planoutene, M. Wei, C. Reghuvaran, A. C. Garzon, F. Garcia, A. Chun, N. Cumpelik, A. Shi, H. Santaneusio, A. Zhang, W. Das, B. Salem, F. Li, L. Cantley, L. G. Ishibe, S. Kaufman, L. Lemley, K. V. Ni, Z. He, J. C. Murphy, B. Menon, M. C. 2021-05-23 doi:10.1101/2021.05.21.445180 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Multiview super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2021.05.21.445200v1?rss=1 Wu, Y. Han, X. Su, Y. Glidewell, M. Daniels, J. S. Liu, J. Sengupta, T. Rey-Suarez, I. Fischer, R. Patel, A. Combs, C. Su, J. Wu, X. Christensen, R. Smith, C. Bao, L. Sun, Y. Duncan, L. H. Chen, J. Pommier, Y. Shi, Y.-B. Murphy, E. Roy, S. Upadhyaya, A. Colón-Ramos, D. La Riviere, P. Shroff, H. 2021-05-22 doi:10.1101/2021.05.21.445200 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ The Molecular Logic Organizing the Functional Compartmentalization of Reciprocal Synapses ]]> https://biorxiv.org/content/10.1101/2021.05.24.445461v1?rss=1 Wang, C. Y. Trotter, J. H. Liakath-Ali, K. Lee, S.-j. Liu, X. Südhof, T. C. 2021-05-25 doi:10.1101/2021.05.24.445461 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Interactions between TULP3 tubby domain cargo site and ARL13B amphipathic helix promote lipidated protein transport to cilia ]]> https://biorxiv.org/content/10.1101/2021.05.25.445488v1?rss=1 Palicharla, V. R. Hwang, S.-h. Somatilaka, B. N. Badgandi, H. B. Legue, E. Tran, V. M. Woodruff, J. B. Liem, K. F. Mukhopadhyay, S. 2021-05-25 doi:10.1101/2021.05.25.445488 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ An infection-activated redox switch promotes tumor growth ]]> https://biorxiv.org/content/10.1101/2021.05.25.445662v1?rss=1 Kovalyova, Y. Bak, D. W. Gordon, E. M. Fung, C. Shuman, J. H. B. Cover, T. L. Amieva, M. R. Weerapana, E. Hatzios, S. K. 2021-05-25 doi:10.1101/2021.05.25.445662 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ The complete sequence of a human genome ]]> https://biorxiv.org/content/10.1101/2021.05.26.445798v1?rss=1 Nurk, S. Koren, S. Rhie, A. Rautiainen, M. Bzikadze, A. V. Mikheenko, A. Vollger, M. R. Altemose, N. Uralsky, L. Gershman, A. Aganezov, S. Hoyt, S. J. Diekhans, M. Logsdon, G. A. Alonge, M. Antonarakis, S. E. Borchers, M. Bouffard, G. G. Brooks, S. Y. Caldas, G. V. Cheng, H. Chin, C.-S. Chow, W. de Lima, L. G. Dishuck, P. C. Durbin, R. Dvorkina, T. Fiddes, I. T. Formenti, G. Fulton, R. S. Fungtammasan, A. Garrison, E. Grady, P. G. S. Graves-Lindsay, T. A. Hall, I. M. Hansen, N. F. Hartley, G. A. Haukness, M. Howe, K. Hunkapiller, M. W. Jain, C. Jain, M. 2021-05-27 doi:10.1101/2021.05.26.445798 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Rapid propagation of membrane tension at a presynaptic terminal ]]> https://biorxiv.org/content/10.1101/2021.05.26.445801v1?rss=1 Gomis Perez, C. Dudzinski, N. R. Rouches, M. Machta, B. Zenisek, D. Karatekin, E. 2021-05-27 doi:10.1101/2021.05.26.445801 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Physachenolide C induces complete regression of established murine melanoma tumors via apoptosis and cell cycle arrest ]]> https://biorxiv.org/content/10.1101/2021.05.27.445710v1?rss=1 Adams, A. C. Macy, A. M. Kang, P. Castro-Ochoa, K. F. Wijeratne, E. M. K. Xu, Y.-M. Liu, M. X. Charos, A. Bosenberg, M. W. Gunatilaka, A. A. L. Sertil, A. R. Hastings, K. T. 2021-05-28 doi:10.1101/2021.05.27.445710 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Pathways of forest savannization in a mesic African savanna-forest mosaic ]]> https://biorxiv.org/content/10.1101/2021.05.27.445949v1?rss=1 Beckett, H. Staver, C. Charles-Dominique, T. Bond, W. 2021-05-28 doi:10.1101/2021.05.27.445949 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Novel antibodies for the simple and efficient enrichment of native O-GlcNAc modified peptides ]]> https://biorxiv.org/content/10.1101/2021.05.28.446228v1?rss=1 Burt, R. A. Dejanovic, B. Peckham, H. J. Lee, K. A. Li, X. Ounadjela, J. R. Rao, A. Malaker, S. A. Carr, S. A. Myers, S. A. 2021-05-28 doi:10.1101/2021.05.28.446228 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ Magnetic Resonance Spectroscopy Frequency and Phase Correction Using Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2021.05.29.446254v1?rss=1 Ma, D. J. Le, H. A.-M. Ye, Y. Laine, A. F. Lieberman, J. A. Rothman, D. L. Small, S. A. Guo, J. 2021-05-30 doi:10.1101/2021.05.29.446254 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Spatial and temporal autocorrelation weave human brain networks ]]> https://biorxiv.org/content/10.1101/2021.06.01.446561v1?rss=1 Shinn, M. Hu, A. Turner, L. Noble, S. Achard, S. Anticevic, A. Scheinost, D. Constable, R. T. Lee, D. Bullmore, E. T. Murray, J. D. 2021-06-01 doi:10.1101/2021.06.01.446561 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Single-Cell Transcriptional Profiling of the Adult Corticospinal Tract Reveals Forelimb and Hindlimb Molecular Specialization ]]> https://biorxiv.org/content/10.1101/2021.06.02.446653v1?rss=1 Cafferty, W. B. Golan, N. Kauer, S. D. Ehrlich, D. B. Ravindra, N. van Dijk, D. 2021-06-03 doi:10.1101/2021.06.02.446653 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Extremely bright, near-IR emitting spontaneously blinking fluorophores enable ratiometric multicolor nanoscopy in live cells ]]> https://biorxiv.org/content/10.1101/2021.06.02.446776v1?rss=1 Tyson, J. Hu, K. Zheng, S. Kidd, P. Dadina, N. Chu, L. Toomre, D. Bewersdorf, J. Schepartz, A. 2021-06-02 doi:10.1101/2021.06.02.446776 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Computational Neuroimaging of Cognition-Emotion Interactions: Affective and Task-similar Interference Differentially Impact Working Memory ]]> https://biorxiv.org/content/10.1101/2021.06.03.446811v1?rss=1 Ji, J. L. Repovs, G. Yang, G. J. Savic, A. Murray, J. D. Anticevic, A. 2021-06-03 doi:10.1101/2021.06.03.446811 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Genetic expression of 4E-BP1 in juvenile mice alleviates mTOR-induced neuronal dysfunction and epilepsy ]]> https://biorxiv.org/content/10.1101/2021.06.04.445850v1?rss=1 Nguyen, L. H. Xu, Y. Mahadeo, T. Zhang, L. Lin, T. V. Born, H. A. Anderson, A. E. Bordey, A. 2021-06-05 doi:10.1101/2021.06.04.445850 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level ]]> https://biorxiv.org/content/10.1101/2021.06.06.447244v1?rss=1 Deng, Y. Bartosovic, M. Ma, S. Zhang, D. Liu, Y. Qin, X. Su, G. Xu, M. L. Halene, S. Craft, J. E. Castelo-Branco, G. Fan, R. 2021-06-07 doi:10.1101/2021.06.06.447244 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes ]]> https://biorxiv.org/content/10.1101/2021.06.06.447255v1?rss=1 Vicencio, J. Sanchez-Bolanos, C. Moreno-Sanchez, I. Brena, D. Kukhtar, D. Ruiz-Lopez, M. Cots-Ponjoan, M. Vejnar, C. E. Rubio, A. Rodrigo Melero, N. Carolis, C. Perez-Pulido, A. J. Giraldez, A. J. Kleinstiver, B. P. Ceron, J. Moreno-Mateos, M. A. 2021-06-06 doi:10.1101/2021.06.06.447255 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Magnetic Bead-Based Separation (MBS) of Pneumococcal Serotypes ]]> https://biorxiv.org/content/10.1101/2021.06.06.447277v1?rss=1 York, A. Mbodj, S. Yolda-Carr, D. Hislop, M. Weinberger, D. M. Wyllie, A. L. 2021-06-06 doi:10.1101/2021.06.06.447277 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ Baby-brain phenomena is a subjective experience: absence of evidence for cognitive deficit in new mothers at one-year postpartum. ]]> https://biorxiv.org/content/10.1101/2021.06.07.447303v1?rss=1 Orchard, E. R. Ward, P. G. Egan, G. F. Jamadar, S. D. 2021-06-07 doi:10.1101/2021.06.07.447303 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Complexin-1 regulated transition in the assembly of single neuronal SNARE complex ]]> https://biorxiv.org/content/10.1101/2021.06.07.447331v1?rss=1 Tongrui, H. Nan, F. Fan, G. Jiaquan, L. Ma, L. Yu-Xuan, R. 2021-06-07 doi:10.1101/2021.06.07.447331 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Brain charts for the human lifespan ]]> https://biorxiv.org/content/10.1101/2021.06.08.447489v1?rss=1 Bethlehem, R. A. I. Seidlitz, J. White, S. R. Vogel, J. W. Anderson, K. M. Adamson, C. Adler, S. Alexopoulos, G. S. Anagnostou, E. Areces-Gonzalez, A. Astle, D. E. Auyeung, B. Ayub, M. Ball, G. Baron-Cohen, S. Beare, R. Bedford, S. A. Benegal, V. Beyer, F. Bin Bae, J. Blangero, J. Blesa Cabez, M. Boardman, J. P. Borzage, M. Bosch-Bayard, J. F. Bourke, N. Calhoun, V. D. Chakravarty, M. M. Chen, C. Chertavian, C. Chetelat, G. Chong, Y. S. Cole, J. H. Corvin, A. Courchesne, E. Crivello, F. Cropley, V. L. Crosbie, J. Crossley, N. Delarue, M. Desrivieres, S. 2021-06-10 doi:10.1101/2021.06.08.447489 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling ]]> https://biorxiv.org/content/10.1101/2021.06.08.447593v1?rss=1 Hancock-Cerutti, W. F. Wu, Z. Tharkeshwar, A. K. Ferguson, S. M. Shadel, G. S. De Camilli, P. 2021-06-08 doi:10.1101/2021.06.08.447593 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Synthetic Cooling Agents in US-marketed E-cigarette Refill Liquids and Disposable E-cigarettes: Chemical Analysis and Risk Assessment. ]]> https://biorxiv.org/content/10.1101/2021.06.09.446946v1?rss=1 Jabba, S. V. Erythropel, H. C. Torres, D. G. Delgado, L. A. Anastas, P. T. Zimmerman, J. B. Jordt, S. E. 2021-06-10 doi:10.1101/2021.06.09.446946 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Myofilament Glycation in Diabetes Reduces Contractility by Inhibiting Tropomyosin Movement, is Rescued by cMyBPC Domains ]]> https://biorxiv.org/content/10.1101/2021.06.09.447778v1?rss=1 Papadaki, M. Kampaengsri, T. Barrick, S. K. Campbell, S. A. Harris, S. P. Greenberg, M. J. Kirk, J. A. 2021-06-09 doi:10.1101/2021.06.09.447778 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq ]]> https://biorxiv.org/content/10.1101/2021.06.10.447896v1?rss=1 Mudge, J. M. Ruiz-Orera, J. Prensner, J. R. Brunet, M. A. Gonzalez, J. M. Magrane, M. Martinez, T. Schulz, J. F. Yang, Y. T. Alba, M. M. Baranov, P. V. Bazzini, A. Bruford, E. Martin, M. J. Carvunis, A.-R. Chen, J. Couso, J. P. Flicek, P. Frankish, A. Gerstein, M. Hubner, N. Ingolia, N. T. Menschaert, G. Ohler, U. Roucou, X. Saghatelian, A. Weissman, J. van Heesch, S. 2021-06-10 doi:10.1101/2021.06.10.447896 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Expansion of RNA sequence diversity and RNA editing rates throughout human cortical development ]]> https://biorxiv.org/content/10.1101/2021.06.10.447947v1?rss=1 Cuddleston, R. Sloofman, L. Liang, L. Mossotto, E. Fan, X. Wang, M. Zhang, B. Wang, J. Sestan, N. Devlin, B. Roeder, K. Buxbaum, J. D. Sanders, S. Breen, M. S. 2021-06-10 doi:10.1101/2021.06.10.447947 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells ]]> https://biorxiv.org/content/10.1101/2021.06.10.447982v1?rss=1 Chen, J. S. Chow, R. D. Song, E. Mao, T. Israelow, B. Kamath, K. Bozekowski, J. Haynes, W. A. Filler, R. B. Menasche, B. L. Wei, J. Alfajaro, M. M. Song, W. Peng, L. Carter, L. Weinstein, J. S. Gowthaman, U. Chen, S. Craft, J. Shon, J. C. Iwasaki, A. Wilen, C. B. Eisenbarth, S. C. 2021-06-11 doi:10.1101/2021.06.10.447982 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ The incentive circuit: memory dynamics in the mushroom body of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.06.11.448104v1?rss=1 Gkanias, E. McCurdy, L. Y. Nitabach, M. N. Webb, B. 2021-06-11 doi:10.1101/2021.06.11.448104 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Quantifying concordant genetic effects of de novo mutations on multiple disorders ]]> https://biorxiv.org/content/10.1101/2021.06.13.448234v1?rss=1 Guo, H. Hou, L. Shi, Y. Jin, S. C. Zeng, X. Li, B. Lifton, R. Brueckner, M. Zhao, H.-y. Lu, Q. 2021-06-14 doi:10.1101/2021.06.13.448234 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Developmental plasticity in male courtship in Bicyclus anynana butterflies is driven by hormone regulation of the yellow gene ]]> https://biorxiv.org/content/10.1101/2021.06.13.448264v1?rss=1 Connahs, H. Tan, E. Dion, E. Ter, Y. Matsuoka, Y. Bear, A. Monteiro, A. 2021-06-14 doi:10.1101/2021.06.13.448264 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer ]]> https://biorxiv.org/content/10.1101/2021.06.14.448356v1?rss=1 farahmand, s. Fernandez, A. Ahmed, F. S. Rimm, D. Chuang, J. H. Reisenbichler, E. Zarringhalam, K. 2021-06-15 doi:10.1101/2021.06.14.448356 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Sexual dimorphism in a neuronal mechanism of spinal hyperexcitability across rodent and human models of pathological pain ]]> https://biorxiv.org/content/10.1101/2021.06.15.447407v1?rss=1 Dedek, A. Xu, J. Lorenzo, L.-E. Godin, A. G. Kandegedara, C. M. Glavina, G. Landrigan, J. A. Lombroso, P. J. De Koninck, Y. Tsai, E. C. Hildebrand, M. E. 2021-06-16 doi:10.1101/2021.06.15.447407 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Carbonyl Post-Translational Modification Associated with Early Onset Type 1 Diabetes Autoimmunity ]]> https://biorxiv.org/content/10.1101/2021.06.15.448522v1?rss=1 Yang, M.-L. Connolly, S. Gee, R. Lam, T. Kanyo, J. Clarke, S. G. Clarke, C. F. James, E. A. Speake, C. Evans-Molina, C. Wen, L. Herold, K. C. Mamula, M. 2021-06-15 doi:10.1101/2021.06.15.448522 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ PET-BIDS, an extension to the brain imaging data structure for positron emission tomography ]]> https://biorxiv.org/content/10.1101/2021.06.16.448390v1?rss=1 Norgaard, M. Matheson, G. J. Hansen, H. D. Thomas, A. G. Searle, G. Rizzo, G. Veronese, M. Giacomel, A. Yaqub, M. Tonietto, M. Funck, T. Gillman, A. Boniface, H. Routier, A. Dalenberg, J. R. Betthauser, T. Feingold, F. Markiewicz, C. J. Gorgolewski, K. J. Blair, R. W. Appelhoff, S. Gau, R. Salo, T. Niso, G. Pernet, C. Phillips, C. Oostenveld, R. Carson, R. E. Gallezot, J.-D. Knudsen, G. M. Innis, R. B. Ganz, M. 2021-06-17 doi:10.1101/2021.06.16.448390 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Time-resolved multivariate pattern analysis of infant EEG data ]]> https://biorxiv.org/content/10.1101/2021.06.16.448720v1?rss=1 Ashton, K. Zinszer, B. Cichy, R. Nelson, C. Aslin, R. Bayet, L. 2021-06-17 doi:10.1101/2021.06.16.448720 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice ]]> https://biorxiv.org/content/10.1101/2021.06.16.448754v1?rss=1 Mao, T. Israelow, B. Lucas, C. Vogels, C. B. F. Fedorova, O. Breban, M. I. Menasche, B. L. Dong, H. Linehan, M. Yale SARS-CoV-2 Genome Surveillance Initiative, Wilen, C. B. Landry, M. L. Grubaugh, N. D. Pyle, A. M. Iwasaki, A. 2021-06-17 doi:10.1101/2021.06.16.448754 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Neural event segmentation of continuous experience in human infants ]]> https://biorxiv.org/content/10.1101/2021.06.16.448755v1?rss=1 Yates, T. S. Skalaban, L. J. Ellis, C. T. Bracher, A. J. Baldassano, C. Turk-Browne, N. B. 2021-06-16 doi:10.1101/2021.06.16.448755 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Genetic code expansion in the engineered organism Vmax X2: High yield and exceptional fidelity ]]> https://biorxiv.org/content/10.1101/2021.06.22.449487v1?rss=1 Santiago, S. Ad, O. Shah, B. Zhang, Z. Zhang, X. Chatterjee, A. Schepartz, A. 2021-06-22 doi:10.1101/2021.06.22.449487 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Witnessing the Structural Evolution of an RNA Enzyme ]]> https://biorxiv.org/content/10.1101/2021.06.22.449496v1?rss=1 Portillo, X. Huang, Y.-T. Breaker, R. R. Horning, D. P. Joyce, G. F. 2021-06-22 doi:10.1101/2021.06.22.449496 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Moving Beyond the 'CAP' of the Iceberg: Intrinsic Connectivity Networks in fMRI are Continuously Engaging and Overlapping ]]> https://biorxiv.org/content/10.1101/2021.06.23.449485v1?rss=1 Iraji, A. Faghiri, A. Fu, Z. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. M. McEwen, S. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Chang, C. Calhoun, V. D. 2021-06-24 doi:10.1101/2021.06.23.449485 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Host-parasite coevolution promotes innovation through deformations in fitness landscapes ]]> https://biorxiv.org/content/10.1101/2021.06.25.449783v1?rss=1 Gupta, A. Zaman, L. Strobel, H. M. Gallie, J. Burmeister, A. R. Kerr, B. Tamar, E. S. Kishony, R. Meyer, J. R. 2021-06-27 doi:10.1101/2021.06.25.449783 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ Candida albicans Isolates 529L and CHN1 Exhibit Stable Colonization of the Murine Gastrointestinal Tract ]]> https://biorxiv.org/content/10.1101/2021.06.27.450080v1?rss=1 McDonough, L. Mishra, A. A. Tosini, N. Kakade, P. Penumutchu, S. Liang, S.-H. Maufrais, C. Zhai, B. Taur, Y. Belenky, P. Bennett, R. J. Hohl, T. J. Koh, A. Y. Ene, I. V. 2021-06-27 doi:10.1101/2021.06.27.450080 Cold Spring Harbor Laboratory Press 2021-06-27 <![CDATA[ Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis ]]> https://biorxiv.org/content/10.1101/2021.06.28.450252v1?rss=1 Rosser, N. Edelman, N. B. Queste, L. Nelson, M. Seixas, F. A. Dasmahapatra, K. K. Mallet, j. 2021-06-30 doi:10.1101/2021.06.28.450252 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ A gradient of force in the endocytic coat is revealed by new coiled-coil force sensors ]]> https://biorxiv.org/content/10.1101/2021.06.29.450294v1?rss=1 Ren, Y. Yang, J. Zhang, Y. Berro, J. 2021-06-30 doi:10.1101/2021.06.29.450294 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ The human RBM10 gene dually encodes a repressor of ribosome biogenesis that downregulates cell proliferation ]]> https://biorxiv.org/content/10.1101/2021.06.29.450363v1?rss=1 cao, x. Harold, C. M. Bryant, C. J. Zheng, S.-J. Khitun, A. Baserga, S. J. Slavoff, S. A. 2021-06-29 doi:10.1101/2021.06.29.450363 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ The number of cytokinesis nodes in mitotic fission yeast scales with cell volume ]]> https://biorxiv.org/content/10.1101/2021.07.02.450929v1?rss=1 Sayyad, W. A. Pollard, T. D. 2021-07-03 doi:10.1101/2021.07.02.450929 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Molecular Determinants of Complexin Clamping in Reconstituted Single-Vesicle Fusion ]]> https://biorxiv.org/content/10.1101/2021.07.05.451112v1?rss=1 Bera, M. Ramakrishnan, S. Coleman, J. Krishnakumar, S. S. Rothman, J. E. 2021-07-05 doi:10.1101/2021.07.05.451112 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Polybasic patches in both C2 domains of Synaptotagmin-1 are required for evoked neurotransmitter release ]]> https://biorxiv.org/content/10.1101/2021.07.05.451149v1?rss=1 Wu, Z. Ma, L. Courtney, N. A. Zhu, J. Zhang, Y. Chapman, E. R. Karatekin, E. 2021-07-06 doi:10.1101/2021.07.05.451149 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Shallow neural networks trained to detect collisions recover features of visual loom-selective neurons ]]> https://biorxiv.org/content/10.1101/2021.07.07.451307v1?rss=1 Zhou, B. Li, Z. Kim, S. S. Y. Lafferty, J. Clark, D. A. 2021-07-08 doi:10.1101/2021.07.07.451307 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Inside Information: Systematic within-node connectivity changes observed across tasks or groups ]]> https://biorxiv.org/content/10.1101/2021.07.07.451429v1?rss=1 Luo, W. Constable, R. T. 2021-07-09 doi:10.1101/2021.07.07.451429 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca ]]> https://biorxiv.org/content/10.1101/2021.07.07.451465v1?rss=1 Gilman, I. S. Moreno-Villena, J. J. Lewis, Z. R. Goolsby, E. W. Edwards, E. J. 2021-07-09 doi:10.1101/2021.07.07.451465 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Adolescent Brain Cognitive Development (ABCD) Community MRI Collection and Utilities ]]> https://biorxiv.org/content/10.1101/2021.07.09.451638v1?rss=1 Feczko, E. Conan, G. Marek, S. Tervo-Clemens, B. Cordova, M. Doyle, O. Earl, E. Perrone, A. Sturgeon, D. Klein, R. Harman, G. Kilamovich, D. Hermosillo, R. Miranda-Dominguez, O. Adebimpe, A. Bertolero, M. Cieslak, M. Covitz, S. Hendrickson, T. Juliano, A. C. Snider, K. Moore, L. A. Uriartel, J. Graham, A. M. Calabro, F. Rosenberg, M. D. Rapuano, K. M. Casey, B. Watts, R. Hagler, D. Thompson, W. K. Nichols, T. E. Hoffman, E. Luna, B. Garavan, H. Satterthwaite, T. D. Feldstein Ewing, S. Nagel, B. Dosenbach, N. U. Fair, D. A. 2021-07-11 doi:10.1101/2021.07.09.451638 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ The PD-1 checkpoint receptor maintains tolerance of self-reactive CD8 T cell in skin ]]> https://biorxiv.org/content/10.1101/2021.07.09.451765v1?rss=1 Damo, M. Cui, C. William, I. Hornick, N. I. Kwok, D. Clulo, K. Damsky, W. E. Leventhal, J. S. Joshi, N. S. 2021-07-10 doi:10.1101/2021.07.09.451765 Cold Spring Harbor Laboratory Press 2021-07-10 <![CDATA[ Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2 ]]> https://biorxiv.org/content/10.1101/2021.07.09.451812v1?rss=1 Prevost, J. Richard, J. Gasser, R. Ding, S. Fage, C. Anand, S. P. Adam, D. Gupta Vergara, N. Tauzin, A. Benlarbi, M. Gong, S. Y. Goyette, G. Prive, A. Moreira, S. Charest, H. Roger, M. Mothes, W. Pazgier, M. Brochiero, E. Boivin, G. Abrams, C. F. Schon, A. Finzi, A. 2021-07-09 doi:10.1101/2021.07.09.451812 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Arousal impacts distributed hubs modulating the integration of brain functional connectivity ]]> https://biorxiv.org/content/10.1101/2021.07.12.452041v1?rss=1 Lee, K. Horien, C. O'Connor, D. Garand-Sheridan, B. Tokoglu, F. Scheinost, D. Lake, E. M. Constable, R. T. 2021-07-13 doi:10.1101/2021.07.12.452041 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous ]]> https://biorxiv.org/content/10.1101/2021.07.12.452083v1?rss=1 Ghezelayagh, A. Harrington, R. C. Burress, E. D. Campbell, M. A. Buckner, J. C. Chakrabarty, P. Glass, J. R. McCraney, W. T. Unmack, P. J. Thacker, C. E. Alfaro, M. E. Friedman, S. T. Ludt, W. D. Cowman, P. F. Friedman, M. Price, S. A. Dornburg, A. Faircloth, B. C. Wainwright, P. C. Near, T. J. 2021-07-13 doi:10.1101/2021.07.12.452083 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Human placental villi immune cells help maintain homeostasis in utero ]]> https://biorxiv.org/content/10.1101/2021.07.14.452362v1?rss=1 Konnikova, L. Toothaker, J. M. Olaloye, O. McCourt, B. T. McCourt, C. C. Case, R. M. Liu, P. Yimlamai, D. Tseng, G. 2021-07-14 doi:10.1101/2021.07.14.452362 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation. ]]> https://biorxiv.org/content/10.1101/2021.07.15.452246v1?rss=1 Venzon, M. Bernard-Raichon, L. Klein, J. Axelrad, J. E. Hussey, G. A. Sullivan, A. P. Cassanovas-Massana, A. Noval, M. G. Valero-Jimenez, A. M. Gago, J. Wilder, E. Yale IMPACT Research Team, Thorpe, L. E. Littman, D. R. Dittmann, M. Stapleford, K. A. Shopsin, B. Torres, V. J. Ko, A. I. Iwasaki, A. Cadwell, K. Schluter, J. 2021-07-15 doi:10.1101/2021.07.15.452246 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Single-Molecule Manipulation of Macromolecules on Membranes Using High-Resolution Optical Tweezers ]]> https://biorxiv.org/content/10.1101/2021.07.15.452421v1?rss=1 Wang, Y. Jin, H. Zhang, Y. 2021-07-15 doi:10.1101/2021.07.15.452421 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ SnoRNA guide activities-real and ambiguous ]]> https://biorxiv.org/content/10.1101/2021.07.15.452550v1?rss=1 Deryusheva, S. Talross, G. J. Gall, J. G. 2021-07-17 doi:10.1101/2021.07.15.452550 Cold Spring Harbor Laboratory Press 2021-07-17 <![CDATA[ Cellular translational enhancer elements that recruit eukaryotic initiation factor 3 ]]> https://biorxiv.org/content/10.1101/2021.07.15.452589v1?rss=1 Koubek, J. Niederer, R. Stanciu, A. Aitken, C. E. Gilbert, W. V. 2021-07-17 doi:10.1101/2021.07.15.452589 Cold Spring Harbor Laboratory Press 2021-07-17 <![CDATA[ NDC1 is necessary for stable assembly of the nuclear pore scaffold to establish nuclear transport in early C. elegans embryos ]]> https://biorxiv.org/content/10.1101/2021.07.17.452264v1?rss=1 Mauro, M. S. Celma, G. Zimyanin, V. Gibson, K. H. Redemann, S. Bahmanyar, S. 2021-07-18 doi:10.1101/2021.07.17.452264 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ PLIGHT: A tool to assess privacy risk by inferring identifying characteristics from sparse, noisy genotypes ]]> https://biorxiv.org/content/10.1101/2021.07.18.452853v1?rss=1 Emani, P. S. Gursoy, G. Miranker, A. D. Gerstein, M. 2021-07-19 doi:10.1101/2021.07.18.452853 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells ]]> https://biorxiv.org/content/10.1101/2021.07.19.452885v1?rss=1 Rothenburger, T. Thomas, D. Schreiber, Y. Wratil, P. R. Pflantz, T. Knecht, K. Digianantonio, K. Temple, J. Schneider, C. Baldauf, H.-M. McLaughlin, K.-M. Rothweiler, F. Bilen, B. Farmand, S. Bojkova, D. Costa, R. Ferreiros, N. Geisslinger, G. Oellerich, T. Xiong, Y. Keppler, O. T. Wass, M. N. Michaelis, M. Cinatl, J. 2021-07-20 doi:10.1101/2021.07.19.452885 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ A high-throughput assay for directly monitoring nucleolar rRNA biogenesis ]]> https://biorxiv.org/content/10.1101/2021.07.19.452935v1?rss=1 Bryant, C. J. McCool, M. A. Abriola, L. Surovtseva, Y. V. Baserga, S. J. 2021-07-19 doi:10.1101/2021.07.19.452935 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record ]]> https://biorxiv.org/content/10.1101/2021.07.19.453013v1?rss=1 Mongiardino Koch, N. Thompson, J. R. Hatch, A. S. McCowin, M. F. Armstrong, F. Coppard, S. E. Aguilera, F. Bronstein, O. Kroh, A. Mooi, R. Rouse, G. 2021-07-20 doi:10.1101/2021.07.19.453013 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast ]]> https://biorxiv.org/content/10.1101/2021.07.20.453152v1?rss=1 Nickaeen, M. M. Berro, J. Pollard, T. D. Slepchenko, B. M. 2021-07-21 doi:10.1101/2021.07.20.453152 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ iPSC-derived Vascular Smooth Muscle Cells in a Fibronectin Functionalized Collagen Scaffold Augment Endothelial Cell Morphogenesis ]]> https://biorxiv.org/content/10.1101/2021.07.22.453420v1?rss=1 Duan, K. Dash, B. C. Sasson, D. Hsia, H. 2021-07-23 doi:10.1101/2021.07.22.453420 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Mutations in two SARS-CoV-2 variants of concern reflect two distinct strategies of antibody escape ]]> https://biorxiv.org/content/10.1101/2021.07.23.453327v1?rss=1 Fiedler, S. Denninger, V. Morgunov, A. S. Ilsley, A. Worth, R. Meisl, G. Xu, C. K. Piziorska, M. A. Ricci, F. Malik, A. Y. Devenish, S. R. A. Schneider, M. M. Kosmoliaptsis, V. Aguzzi, A. Iwasaki, A. Fiegler, H. Knowles, T. P. J. 2021-07-26 doi:10.1101/2021.07.23.453327 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Mitochondrial DNA variation across 56,434 individuals in gnomAD ]]> https://biorxiv.org/content/10.1101/2021.07.23.453510v1?rss=1 Laricchia, K. M. Lake, N. J. Watts, N. A. Shand, M. Haessly, A. Gauthier, L. Benjamin, D. Banks, E. Soto, J. Garimella, K. Emery, J. Genome Aggregation Database Consortium, Rehm, H. L. MacArthur, D. G. Tiao, G. Lek, M. V. Mootha, V. K. Calvo, S. E. 2021-07-23 doi:10.1101/2021.07.23.453510 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ IFITM3 regulates virus-induced inflammatory cytokine production by titrating Nogo-B orchestration of TLR responses ]]> https://biorxiv.org/content/10.1101/2021.07.23.453513v1?rss=1 Clement, M. Forbester, J. L. Marsden, M. Sabberwal, P. Wellington, D. Dimonte, S. Harcourt, K. Clare, S. Yin, Z. Nobre, L. Antrobus, R. Jin, B. Chen, M. Makvandi-Nejad, S. Lindborg, J. A. Strittmatter, S. M. Weekes, M. P. Stanton, R. j. Dong, T. Humphreys, I. 2021-07-24 doi:10.1101/2021.07.23.453513 Cold Spring Harbor Laboratory Press 2021-07-24 <![CDATA[ Counting actin in contractile rings reveals novel contributions of cofilin and type II myosins to fission yeast cytokinesis ]]> https://biorxiv.org/content/10.1101/2021.07.26.453848v1?rss=1 Chen, Q. Malla, M. Pollard, T. D. 2021-07-26 doi:10.1101/2021.07.26.453848 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Navigating a diversity of turbulent plumes is enhanced by sensing complementary temporal features of odor signals ]]> https://biorxiv.org/content/10.1101/2021.07.28.454116v1?rss=1 Jayaram, V. Kadakia, N. Emonet, T. 2021-07-28 doi:10.1101/2021.07.28.454116 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Cell-specific Bioorthogonal Tagging of Glycoproteins in Co-culture ]]> https://biorxiv.org/content/10.1101/2021.07.28.454135v1?rss=1 Cioce, A. Calle, B. Marchesi, A. Bineva-Todd, G. Flynn, H. Li, Z. Tastan, O. Y. Roustan, C. Keenan, T. Both, P. Huang, K. Parmeggiani, F. Snijders, A. P. Kjaer, S. Fascione, M. A. Flitsch, S. L. Schumann, B. 2021-07-28 doi:10.1101/2021.07.28.454135 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[ Evolution of gene expression across species and specialized zooids in Siphonophora ]]> https://biorxiv.org/content/10.1101/2021.07.30.454354v1?rss=1 Munro, C. Zapata, F. Howison, M. Siebert, S. Dunn, C. W. 2021-08-01 doi:10.1101/2021.07.30.454354 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Adult neuromarkers of sustained attention and working memory predict inter- and intra-individual differences in these processes in youth ]]> https://biorxiv.org/content/10.1101/2021.08.01.454530v1?rss=1 Kardan, O. Stier, A. J. Cardenas-Inigues, C. Pruin, J. C. Schertz, K. E. Deng, Y. Chamberlain, T. Meredith, W. J. Zhang, X. Bowman, J. E. Lakhtakia, T. Tindel, L. Avery, E. W. Lin, Q. Yoo, K. Chun, M. M. Berman, M. G. Rosenberg, M. D. 2021-08-02 doi:10.1101/2021.08.01.454530 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Coilin oligomerization and remodeling by Nopp140 reveals a hybrid assembly mechanism for Cajal bodies ]]> https://biorxiv.org/content/10.1101/2021.08.01.454609v1?rss=1 Courchaine, E. Machyna, M. Straube, K. Sauyet, S. Enright, J. Neugebauer, K. 2021-08-01 doi:10.1101/2021.08.01.454609 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern ]]> https://biorxiv.org/content/10.1101/2021.08.02.454546v1?rss=1 Mothes, W. Li, W. Chen, Y. Prevost, J. Ullah, I. Lu, M. Gong, S. Y. Tauzin, A. Gasser, R. Vezina, D. Anand, S. P. Goyette, G. Chaterjee, D. Ding, S. Tolbert, W. D. Grunst, M. W. Bo, Y. Zhang, S. Richard, J. Zhou, F. Huang, R. K. Esser, L. Zeher, A. Cote, M. Kumar, P. Sodroski, J. Xia, D. Uchil, P. D. Pazgier, M. Finzi, A. 2021-08-03 doi:10.1101/2021.08.02.454546 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Macaques preferentially attend to intermediately surprising information ]]> https://biorxiv.org/content/10.1101/2021.08.02.454786v1?rss=1 Wu, S. Blanchard, T. Meschke, E. Aslin, R. N. Hayden, B. Kidd, C. 2021-08-02 doi:10.1101/2021.08.02.454786 Cold Spring Harbor Laboratory Press 2021-08-02 <![CDATA[ Uncertainty quantification in subject-specific estimation of local vessel mechanical properties ]]> https://biorxiv.org/content/10.1101/2021.08.02.454803v1?rss=1 Rego, B. V. Weiss, D. Bersi, M. R. Humphrey, J. D. 2021-08-04 doi:10.1101/2021.08.02.454803 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics ]]> https://biorxiv.org/content/10.1101/2021.08.03.454943v1?rss=1 Choi, S. B. Munoz-LLancao, P. Manzini, M. C. Nemes, P. 2021-08-04 doi:10.1101/2021.08.03.454943 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Mnemonic content and hippocampal patterns shape judgments of time ]]> https://biorxiv.org/content/10.1101/2021.08.03.454949v1?rss=1 Sherman, B. E. DuBrow, S. Winawer, J. Davachi, L. 2021-08-04 doi:10.1101/2021.08.03.454949 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Single particle cryo-EM structure of the outer hair cell motor protein prestin ]]> https://biorxiv.org/content/10.1101/2021.08.03.454998v1?rss=1 BUtan, C. Song, Q. Bai, J.-p. Tan, W. Navaratnam, D. S. Santos-Sacchi, J. 2021-08-05 doi:10.1101/2021.08.03.454998 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Pupil correlates of decision variables in mice playing a competitive mixed-strategy game ]]> https://biorxiv.org/content/10.1101/2021.08.05.455292v1?rss=1 Wang, H. Ortega, H. K. Atilgan, H. Murphy, C. E. Kwan, A. C. 2021-08-06 doi:10.1101/2021.08.05.455292 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Data science competition for cross-site delineation and classification of individual trees from airborne remote sensing data ]]> https://biorxiv.org/content/10.1101/2021.08.06.453503v1?rss=1 Graves, S. J. Marconi, S. Stewart, D. Harmon, I. Weinstein, B. G. Kanazawa, Y. Scholl, V. M. Joseph, M. B. McClinchy, J. Browne, L. Sullivan, M. K. Estrada-Villegas, S. Tusa, E. Wang, D. Z. Singh, A. Bohlman, S. A. Zare, A. White, E. P. 2021-08-09 doi:10.1101/2021.08.06.453503 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Lung injury induces alveolar type 2 cell hypertrophy and polyploidy with implications for repair and regeneration ]]> https://biorxiv.org/content/10.1101/2021.08.10.455833v1?rss=1 Weng, A. Maciel-Herrerias, M. Watanabe, S. J. Flozak, A. S. Welch, L. Aillon, R. P. Grant, R. Han, S. Dada, L. HInchcliff, M. Misharin, A. Budinger, G. S. Gottardi, C. J. 2021-08-10 doi:10.1101/2021.08.10.455833 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Typhoid toxin sorting and exocytic transport from Salmonella Typhi infected cells ]]> https://biorxiv.org/content/10.1101/2021.08.10.455839v1?rss=1 Chang, S.-J. Lin, Y.-Y. Lara-Tejero, M. Galan, J. E. 2021-08-10 doi:10.1101/2021.08.10.455839 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ The impact of evolutionary processes in shaping the genetics of complex traits in East Asia and Europe: a specific contribution from Denisovan and Neanderthal introgression ]]> https://biorxiv.org/content/10.1101/2021.08.12.456138v1?rss=1 Koller, D. Wendt, F. R. Pathak, G. De Lillo, A. De Angelis, F. Cabrera Mendoza, B. Tucci, S. Polimanti, R. 2021-08-13 doi:10.1101/2021.08.12.456138 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Learning from the path not taken: Sensory prediction errors are sufficient for implicit adaptation of withheld movements ]]> https://biorxiv.org/content/10.1101/2021.08.12.456140v1?rss=1 Kim, O. A. Forrence, A. D. McDougle, S. D. 2021-08-13 doi:10.1101/2021.08.12.456140 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq ]]> https://biorxiv.org/content/10.1101/2021.08.13.456236v1?rss=1 Kavita, K. Zhang, A. Tai, C.-H. Majdalani, N. Storz, G. Gottesman, S. 2021-08-13 doi:10.1101/2021.08.13.456236 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Host cell amplification of nutritional stress contributes to persistence in Chlamydia trachomatis ]]> https://biorxiv.org/content/10.1101/2021.08.14.456350v1?rss=1 Pokorzynski, N. D. CARABEO, R. 2021-08-15 doi:10.1101/2021.08.14.456350 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Rapid fluctuations in functional connectivity of cortical networks encode spontaneous behavior ]]> https://biorxiv.org/content/10.1101/2021.08.15.456390v1?rss=1 Benisty, H. Moberly, A. H. Lohani, S. Barson, D. Coifman, R. R. Mishne, G. Cardin, J. A. Higley, M. J. 2021-08-15 doi:10.1101/2021.08.15.456390 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.17.456253v1?rss=1 Griffin, K. N. Li, H. Walters, B. W. Wang, H. Kaya, C. B. Kanyo, J. Lam, T. Cox, A. L. Chung, J.-J. Lesch, B. J. 2021-08-17 doi:10.1101/2021.08.17.456253 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Estimating genetic correlation jointly using individual-level and summary-level GWAS data ]]> https://biorxiv.org/content/10.1101/2021.08.18.456908v1?rss=1 Zhang, Y. Cheng, Y. Ye, Y. Jiang, W. Lu, Q. Zhao, H. 2021-08-19 doi:10.1101/2021.08.18.456908 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Connectomic features underlying diverse synaptic connection strengths and subcellular computation ]]> https://biorxiv.org/content/10.1101/2021.08.19.456845v1?rss=1 Liu, T. X. Davoudian, P. A. Lizbinski, K. M. Jeanne, J. M. 2021-08-19 doi:10.1101/2021.08.19.456845 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ MEKK3-TGFβ crosstalk regulates inward arterial remodeling ]]> https://biorxiv.org/content/10.1101/2021.08.19.456893v1?rss=1 Deng, H. Xu, Y. Hu, X. Zhuang, Z. W. Chang, Y. Wang, Y. Ntokou, A. Schwartz, M. A. Su, B. Simons, M. 2021-08-19 doi:10.1101/2021.08.19.456893 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ The active zone protein Clarinet regulates ATG-9 trafficking at synapses and presynaptic autophagy ]]> https://biorxiv.org/content/10.1101/2021.08.19.457026v1?rss=1 Xuan, Z. Yang, S. Hill, S. E. Clark, B. Manning, L. Colon-Ramos, D. 2021-08-19 doi:10.1101/2021.08.19.457026 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors ]]> https://biorxiv.org/content/10.1101/2021.08.20.457142v1?rss=1 Shi, G. Torres Robles, J. Song, C. Salichos, L. Lou, H. J. Gerstein, M. Turk, B. E. 2021-08-20 doi:10.1101/2021.08.20.457142 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Reconstructing hunter-gatherer planet Earthusing machine-learning ]]> https://biorxiv.org/content/10.1101/2021.08.21.457222v1?rss=1 Hamilton, M. J. Walker, R. S. Buchanan, B. Blasi, D. E. Bowern, C. 2021-08-24 doi:10.1101/2021.08.21.457222 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Ergodic patterns of cell state transitions underlie the reproducibility of embryonic development ]]> https://biorxiv.org/content/10.1101/2021.08.23.457360v1?rss=1 Holley, S. Genuth, M. Kojima, Y. Jülich, D. Kiryu, H. 2021-08-26 doi:10.1101/2021.08.23.457360 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Characterization of the flagellar collar reveals structural plasticity essential for spirochete motility ]]> https://biorxiv.org/content/10.1101/2021.08.23.457452v1?rss=1 Chang, Y. Xu, H. MOTALEB, M. A. Liu, J. 2021-08-24 doi:10.1101/2021.08.23.457452 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Innate and adaptive immunity to transfused allogenic red blood cells in mice requires MyD88 ]]> https://biorxiv.org/content/10.1101/2021.08.24.457332v1?rss=1 Soldatenko, A. Hoyt, L. R. Xu, L. Calabro, S. Lewis, S. M. Gallman, A. E. Hudson, K. E. Stowell, S. R. Luckey, C. J. Zimring, J. C. Liu, D. Santhanakrishnan, M. Hendrickson, J. E. Eisenbarth, S. C. 2021-08-25 doi:10.1101/2021.08.24.457332 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Long-term precision editing of neural circuits using engineered gap junction hemichannels ]]> https://biorxiv.org/content/10.1101/2021.08.24.457429v1?rss=1 Ransey, E. Chesnov, K. Wisdom, E. Bowman, R. Rodriguez, T. Adamson, E. Thomas, G. Almoril-Porras, A. Schwennesen, H. Colon-Ramos, D. Hultman, R. Bursac, N. Dzirasa, K. 2021-08-27 doi:10.1101/2021.08.24.457429 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Reading Modality Modifies Reading Network: Insights from Neural basis of Braille in Proficient Blind Readers ]]> https://biorxiv.org/content/10.1101/2021.08.24.457544v1?rss=1 Tian, M. Saccone, E. J. Kim, J. S. Kanjlia, S. Bedny, M. 2021-08-25 doi:10.1101/2021.08.24.457544 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ A hierarchical GBP network promotes cytosolic LPS recognition and sepsis ]]> https://biorxiv.org/content/10.1101/2021.08.25.457662v1?rss=1 MacMicking, J. D. Park, E. Kim, B. Kumar, P. Tretina, K. Maminska, A. Philbrick, W. M. Flavell, R. 2021-08-26 doi:10.1101/2021.08.25.457662 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Single-cell foundations of live social gaze interaction in the prefrontal cortex and amygdala ]]> https://biorxiv.org/content/10.1101/2021.08.25.457686v1?rss=1 Dal Monte, O. Fan, S. Fagan, N. Chu, C.-C. Zhou, M. Putnam, P. Nair, A. Chang, S. W. C. 2021-08-25 doi:10.1101/2021.08.25.457686 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Cryo-ET of a human GBP coatomer governing cell-autonomous innate immunity to infection ]]> https://biorxiv.org/content/10.1101/2021.08.26.457804v1?rss=1 MacMicking, J. D. Zhu, S. Bradfield, C. J. Maminska, A. Park, E. Kim, B. Kumar, P. Huang, S. Zhang, Y. Bewersdorf, J. 2021-08-27 doi:10.1101/2021.08.26.457804 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ Peer teaching as bioinformatics training strategy: incentives, challenges, and benefits. ]]> https://biorxiv.org/content/10.1101/2021.08.26.457832v1?rss=1 Rahman, N.-T. Meyer, C. Thakral, D. Cai, W. L. Garcia-Milian, R. Chen, A. T. Obaid, R. 2021-08-30 doi:10.1101/2021.08.26.457832 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ Policy-relevant indicators for invasive alien species assessment and reporting ]]> https://biorxiv.org/content/10.1101/2021.08.26.457851v1?rss=1 McGeoch, M. A. Arle, E. Belmaker, J. Buba, Y. Clarke, D. A. Essl, F. Garcia-Berthou, E. Groom, Q. Henriksen, M. V. Jetz, W. Kuhn, I. Lenzner, B. Meyer, C. Pagad, S. Pili, A. Roige, M. Seebens, H. Tingley, R. Vicente, J. R. Wilson, J. R. Winter, M. 2021-08-30 doi:10.1101/2021.08.26.457851 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ LyTS: A Lysosome Localized Complex of TMEM192 and STK11IP ]]> https://biorxiv.org/content/10.1101/2021.08.27.457973v1?rss=1 Angarola, B. Froehlich, F. Ferguson, S. M. 2021-08-28 doi:10.1101/2021.08.27.457973 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Large-scale differences in functional organization of left- and right-handed individuals using whole-brain, data-driven analysis of connectivity ]]> https://biorxiv.org/content/10.1101/2021.08.28.458027v1?rss=1 Tejavibulya, L. Peterson, H. Greene, A. S. Gao, S. Rolison, M. Noble, S. Scheinost, D. 2021-08-30 doi:10.1101/2021.08.28.458027 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ Systems analysis of the familial cardiomyopathy signaling network ]]> https://biorxiv.org/content/10.1101/2021.08.28.458032v1?rss=1 Khalilimeybodi, A. McCulloch, A. Omens, J. Saucerman, J. J. 2021-08-28 doi:10.1101/2021.08.28.458032 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ ATM phosphorylates PP2A subunit A resulting in nuclearexport and spatiotemporal regulation of the DNA damageresponse ]]> https://biorxiv.org/content/10.1101/2021.08.29.458108v1?rss=1 Sule, A. Golding, S. E. Farhan, S. F. Watson, J. Ahmed, M. H. Kellogg, G. E. Bernas, T. Koebley, S. Reed, J. C. Povirk, L. F. Valerie, K. 2021-08-29 doi:10.1101/2021.08.29.458108 Cold Spring Harbor Laboratory Press 2021-08-29 <![CDATA[ The information signature of diverging lineages ]]> https://biorxiv.org/content/10.1101/2021.08.30.458276v1?rss=1 Moore, D. G. Morales, M. Walker, S. I. Dolby, G. A. 2021-09-01 doi:10.1101/2021.08.30.458276 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Secretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production ]]> https://biorxiv.org/content/10.1101/2021.09.01.458573v1?rss=1 Kang, Y.-A. Paik, H. Zhang, S. Y. Chen, J. Warr, M. R. Fan, R. Passegue, E. 2021-09-02 doi:10.1101/2021.09.01.458573 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Batch Effects are Causal Effects: Applications in Human Connectomics ]]> https://biorxiv.org/content/10.1101/2021.09.03.458920v1?rss=1 Bridgeford, E. W. Powell, M. Kiar, G. Lawrence, R. Caffo, B. Milham, M. Vogelstein, J. T. 2021-09-06 doi:10.1101/2021.09.03.458920 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Robust de novo design of protein binding proteins from target structural information alone ]]> https://biorxiv.org/content/10.1101/2021.09.04.459002v1?rss=1 Cao, L. Coventry, B. Goreshnik, I. Huang, B. Park, J. S. Jude, K. M. Markovic, I. Kadam, R. U. Verschueren, K. H. G. Verstraete, K. Walsh, S. T. R. Bennett, N. Phal, A. Yang, A. Kozodoy, L. DeWitt, M. Picton, L. Miller, L. Strauch, E.-M. Halabiya, S. Hammerson, B. Yang, W. Benard, S. Stewart, L. Wilson, I. A. Ruohola-Baker, H. Schlessinger, J. Lee, S. Savvides, S. N. Garcia, K. C. N. Baker, D. 2021-09-05 doi:10.1101/2021.09.04.459002 Cold Spring Harbor Laboratory Press 2021-09-05 <![CDATA[ Ecological constraints on highly evolvable olfactory receptor genes and morphology ]]> https://biorxiv.org/content/10.1101/2021.09.06.459178v1?rss=1 Yohe, L. R. Fabbri, M. Lee, D. Davies, K. Yohe, T. P. Sanchez, M. K. Rengifo, E. Hall, R. Mutumi, G. Hedrick, B. P. Sadier, A. A. Simmons, N. B. Sears, K. E. Dumont, E. Rossiter, S. Bhullar, B.-A. Davalos, L. 2021-09-06 doi:10.1101/2021.09.06.459178 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Symbiotic bacterial community of Drosophila melanogaster changes with nutritional modifications of the diet but can alleviate negative effects on larval phenotypes ]]> https://biorxiv.org/content/10.1101/2021.09.07.458894v1?rss=1 Bombin, A. Cunneely, O. Bombin, S. Eickman, K. Ruesy, A. Cowan, R. Myers, A. Su, M. Mosley, J. D. Ferguson, J. Reed, L. K. 2021-09-07 doi:10.1101/2021.09.07.458894 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.09.07.459322v1?rss=1 Liu, S. Won, H. Clarke, D. Matoba, N. Khullar, S. Mu, Y. Wang, D. Gerstein, M. 2021-09-07 doi:10.1101/2021.09.07.459322 Cold Spring Harbor Laboratory Press 2021-09-07 <![CDATA[ An anti-SARS-CoV-2 non-neutralizing antibody with Fc-effector function defines a new NTD epitope and delays neuroinvasion and death in K18-hACE2 mice ]]> https://biorxiv.org/content/10.1101/2021.09.08.459408v1?rss=1 Beaudoin-Bussieres, G. Chen, Y. Ullah, I. Prevost, J. Tolbert, W. D. Symmes, K. Ding, S. Benlarbi, M. Gong, S. Y. Tauzin, A. Gasser, R. Chatterjee, D. Vezina, D. Goyette, G. Richard, J. Zhou, F. Stamatatos, L. McGuire, A. T. Charest, H. Roger, M. Pozharski, E. Kumar, P. Mothes, W. Uchil, P. D. Pazgier, M. Finzi, A. 2021-09-08 doi:10.1101/2021.09.08.459408 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ A redox cycle with complex II promotes sulfide quinone oxidoreductase dependent H2S oxidation ]]> https://biorxiv.org/content/10.1101/2021.09.08.459449v1?rss=1 Kumar, R. Landry, A. P. Guha, A. Vitvitsky, V. Lee, H.-J. Seike, K. Reddy, P. Lyssiotis, C. A. Banerjee, R. 2021-09-08 doi:10.1101/2021.09.08.459449 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes ]]> https://biorxiv.org/content/10.1101/2021.09.08.459464v1?rss=1 Pawlica, P. Yario, T. White, S. Wang, J. Moss, W. Hui, P. Vinetz, J. M. Steitz, J. A. 2021-09-08 doi:10.1101/2021.09.08.459464 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Multi-omic Characterization of Pancreatic Cancer-Associated Macrophage Polarization Reveals Deregulated Metabolic Programs Driven by the GMCSF-PI3K Pathway ]]> https://biorxiv.org/content/10.1101/2021.09.10.459752v1?rss=1 Boyer, S. M. Lee, H.-J. Steele, N. Zhang, L. Sajjakulnukit, P. Andren, A. Ward, M. H. Basrur, V. Zhang, Y. Nesvizhskii, A. Pasca di Magliano, M. Halbrook, C. J. Lyssiotis, C. A. 2021-09-11 doi:10.1101/2021.09.10.459752 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ SILAC phosphoproteomics reveals unique signaling circuits in CAR-T cells and the inhibition of B cell-activating phosphorylation in target cells ]]> https://biorxiv.org/content/10.1101/2021.09.10.459784v1?rss=1 Griffith, A. A. Callahan, K. P. King, N. G. Xiao, Q. Su, X. Salomon, A. R. 2021-09-10 doi:10.1101/2021.09.10.459784 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Canonical retinotopic shifts under an inverse force field explain predictive remapping ]]> https://biorxiv.org/content/10.1101/2021.09.10.459799v1?rss=1 Adeyefa-Olasupo, I. Xiao, Z. Nandy, A. S. 2021-09-11 doi:10.1101/2021.09.10.459799 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production ]]> https://biorxiv.org/content/10.1101/2021.09.10.459864v1?rss=1 Noch, E. K. Palma, L. Yim, I. Barnett, D. Walsh, A. Bhinder, B. Benedetti, E. Krumsiek, J. Gurvitch, J. Khwaja, S. Elemento, O. Cantley, L. 2021-09-11 doi:10.1101/2021.09.10.459864 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Activation of the CaMKII-Sarm1-ASK1 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria ]]> https://biorxiv.org/content/10.1101/2021.09.12.459970v1?rss=1 Ding, C. Wu, Y. Dabas, H. Hammarlund, M. 2021-09-12 doi:10.1101/2021.09.12.459970 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ Critical Pressure of Intramural Delamination in Aortic Dissection ]]> https://biorxiv.org/content/10.1101/2021.09.12.459981v1?rss=1 Ban, E. Cavinato, C. Humphrey, J. D. 2021-09-15 doi:10.1101/2021.09.12.459981 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ The Lyme Disease agent co-opts adiponectin receptor-mediated signaling in its arthropod vector ]]> https://biorxiv.org/content/10.1101/2021.09.13.460039v1?rss=1 Tang, X. cao, y. Arora, G. Hwang, J. Sajid, A. Brown, C. Mehta, S. Marin-Lopez, A. Chuang, Y.-M. Wu, M.-J. Ma, H. Pal, U. Narasimhan, S. Fikrig, E. 2021-09-15 doi:10.1101/2021.09.13.460039 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Cell-based and cell-free firefly luciferase complementation assay to quantify Human Immunodeficiency Virus type 1 Rev-Rev interaction ]]> https://biorxiv.org/content/10.1101/2021.09.13.460071v1?rss=1 Hansen, T. Baris, J. Zhao, M. Sutton, R. 2021-09-13 doi:10.1101/2021.09.13.460071 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Glycosaminoglycans Modulate Long-Range Mechanical Communication Between Cells in Collagen Networks ]]> https://biorxiv.org/content/10.1101/2021.09.13.460122v1?rss=1 Chen, X. Chen, D. Ban, E. Janmey, P. A. Wells, R. G. Shenoy, V. B. 2021-09-14 doi:10.1101/2021.09.13.460122 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ ProtAnno, an Automated Cell Type Annotation Tool for Single Cell Proteomics Data that Integrates Information from Multiple Reference Sources ]]> https://biorxiv.org/content/10.1101/2021.09.13.460162v1?rss=1 Deng, W. Zhu, B. Park, S. Sumida, T. S. Unterman, A. Hafler, D. A. Cruz, C. S. D. Kaminski, N. Lucas, C. L. Zhao, H.-y. 2021-09-13 doi:10.1101/2021.09.13.460162 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9 ]]> https://biorxiv.org/content/10.1101/2021.09.14.460226v1?rss=1 Palermo, G. Nierzwicki, L. East, K. W. Morzan, U. N. Arantes, P. R. Lisi, G. P. Batista, V. S. 2021-09-14 doi:10.1101/2021.09.14.460226 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ The individuality of shape asymmetries of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2021.09.14.460242v1?rss=1 Chen, Y.-C. Arnatkeviciute, A. McTavish, E. Pang, J. Suo, C. Fornito, A. Aquino, K. M. The Alzheimer's Disease Neuroimaging Initiative, 2021-09-15 doi:10.1101/2021.09.14.460242 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers ]]> https://biorxiv.org/content/10.1101/2021.09.14.460319v1?rss=1 Grant, A. Xicola, R. M. Nguyen, V. T. Lim, J. Thorne, C. Salhia, B. Llor, X. Ellis, N. Padi, M. 2021-09-16 doi:10.1101/2021.09.14.460319 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Inhibition of sodium conductance by cannabigerol contributes to a reduction of neuronal dorsal root ganglion excitability ]]> https://biorxiv.org/content/10.1101/2021.09.14.460359v1?rss=1 Ghovanloo, M.-R. Estacion, M. zhao, P. Dib-Hajj, S. Waxman, S. G. 2021-09-16 doi:10.1101/2021.09.14.460359 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ The Physiological Landscape and Specificity of Antibody Repertoires ]]> https://biorxiv.org/content/10.1101/2021.09.15.460420v1?rss=1 Csepregi, L. Hoehn, K. B. Neumeier, D. Taft, J. M. Friedensohn, S. Weber, C. R. Kummer, A. Sesterhenn, F. Correia, B. E. Reddy, S. T. 2021-09-17 doi:10.1101/2021.09.15.460420 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ m6A modifications regulate intestinal immunity and rotavirus infection ]]> https://biorxiv.org/content/10.1101/2021.09.17.460776v1?rss=1 Zhu, S. Wang, A. Wang, J. Tao, W. Ding, S. Flavell, R. A. Tong, J. Hou, G. Gao, J. Zhang, G. Li, R. Ren, X. Wang, D. Zhang, K. Pan, W. Li, H. Qian, C. 2021-09-17 doi:10.1101/2021.09.17.460776 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Non-linear Archetypal Analysis of Single-cell RNA-seq Data by Deep Autoencoders ]]> https://biorxiv.org/content/10.1101/2021.09.17.460824v1?rss=1 Wang, Y. Zhao, H. 2021-09-20 doi:10.1101/2021.09.17.460824 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Sexually dimorphic interplay between anxiety-related phenotype and fear memory extinction ]]> https://biorxiv.org/content/10.1101/2021.09.17.460842v1?rss=1 Bonilla, M. I. Lee, H.-L. Kim, I.-J. Rudenko, A. 2021-09-20 doi:10.1101/2021.09.17.460842 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ A mechanism for migrating bacterial populations to non-genetically adapt to new environments ]]> https://biorxiv.org/content/10.1101/2021.09.21.461202v1?rss=1 Mattingly, H. H. Emonet, T. 2021-09-22 doi:10.1101/2021.09.21.461202 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Selective Microautophagy of Proteasomes is Initiated by ESCRT-0 and Is Promoted by Proteasome Ubiquitylation ]]> https://biorxiv.org/content/10.1101/2021.09.21.461272v1?rss=1 Li, J. Hochstrasser, M. 2021-09-22 doi:10.1101/2021.09.21.461272 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Single shot detector application for image disease localization ]]> https://biorxiv.org/content/10.1101/2021.09.21.461307v1?rss=1 pawar, s. Stanam, A. Chopade, R. 2021-09-24 doi:10.1101/2021.09.21.461307 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ A Comparison of Methods to Harmonize Cortical Thickness Measurements Across Scanners and Sites ]]> https://biorxiv.org/content/10.1101/2021.09.22.461242v1?rss=1 Sun, D. Rakesh, G. Clarke-Rubright, E. K. Haswell, C. C. Logue, M. O'Leary, B. M. Cotton, A. S. Xie, H. Dennis, E. L. Jahanshad, N. Salminen, L. E. Thomopolous, S. I. Rashid, F. Ching, C. R. K. Koch, S. B. J. Frijling, J. L. Nawijn, L. van Zuiden, M. Zhu, X. Suarez-Jimenez, B. Sierk, A. Walter, H. Manthey, A. Stevens, J. S. Fani, N. van Rooij, S. J. H. Stein, M. Bomyea, J. Koerte, I. K. Choi, K. van der Werff, S. J. A. Vermeiren, R. R. J. M. Herzog, J. Lebois, L. A. M. Baker, J. T. Ressler, K. J. Olson, E. A. Straube, T. Korgaonkar, M. S. Andrew, E. Zhu, 2021-09-24 doi:10.1101/2021.09.22.461242 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2021.09.22.461331v1?rss=1 Begik, O. Liu, H. Delgado-Tejedor, A. Kontur, C. Giraldez, A. J. Beaudoin, J.-D. Mattick, J. S. Novoa, E. M. 2021-09-22 doi:10.1101/2021.09.22.461331 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Leveling up: improving power in fMRI by moving beyond cluster-level inference ]]> https://biorxiv.org/content/10.1101/2021.09.23.461354v1?rss=1 Noble, S. Mejia, M. Zalesky, A. Scheinost, D. 2021-09-24 doi:10.1101/2021.09.23.461354 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ The mutation effect reaction norm (MERN) highlights environmentally dependent mutation effects and genetic interactions ]]> https://biorxiv.org/content/10.1101/2021.09.23.461533v1?rss=1 Ogbunugafor, C. B. 2021-09-24 doi:10.1101/2021.09.23.461533 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Cancer missense mutations in the BRC repeats of BRCA2 protein disrupt RAD51 binding and activity leading to chemotherapeutic sensitivity ]]> https://biorxiv.org/content/10.1101/2021.09.24.461749v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@1e5e3c6org.highwire.dtl.DTLVardef@1cd0e60org.highwire.dtl.DTLVardef@16adf4corg.highwire.dtl.DTLVardef@16a0089_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jimenez-Sainz, J. Mathew, J. Garbarino, J. Eder, J. P. Jensen, R. B. 2021-09-25 doi:10.1101/2021.09.24.461749 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ An innate immune activation state prior to vaccination predicts responsiveness to multiple vaccines ]]> https://biorxiv.org/content/10.1101/2021.09.26.461847v1?rss=1 Fourati, S. Tomalin, L. E. Mule, M. P. Chawla, D. G. Gerritsen, B. Rychkov, D. Henrich, E. Miller, H. E. Hagan, T. Diray-Arce, J. Dunn, P. The Human Immunology Project Consortium (HIPC), Levy, O. Gottardo, R. Sarwal, M. Tsang, J. Suarez-Farinas, M. Pulendran, B. Sekaly, R.-P. Kleinstein, S. H. 2021-09-26 doi:10.1101/2021.09.26.461847 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Interactions of cytosolic termini of the Jen1 monocarboxylate transporter are critical for trafficking, transport activity and endocytosis ]]> https://biorxiv.org/content/10.1101/2021.09.27.461913v1?rss=1 Barata Antunes, C. Talaia, G. Broutzakis, G. Ribas, D. De Beule, P. Casal, M. Stefan, C. J. Diallinas, G. Paiva, S. 2021-09-28 doi:10.1101/2021.09.27.461913 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Viral replication in human macrophages enhances an inflammatory cascade and interferon driven chronic COVID-19 in humanized mice. ]]> https://biorxiv.org/content/10.1101/2021.09.27.461948v1?rss=1 Sefik, E. Qu, R. Kaffe, E. Zhao, J. Junqueira, C. Mirza, H. Brewer, R. Han, A. Steach, H. Israelow, B. Chen, Y. G. Halene, S. Iwasaki, A. Meffre, E. Nussenzweig, M. Lieberman, J. Wilen, C. B. Kluger, Y. Flavell, R. A. 2021-09-27 doi:10.1101/2021.09.27.461948 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Reovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis ]]> https://biorxiv.org/content/10.1101/2021.09.27.462002v1?rss=1 Ortega Gonzalez, P. Taylor, G. M. Jangra, R. Tenorio Vela, R. Fernandez de Castro Martin, I. Mainou, B. Orchard, R. Wilen, C. B. Brigleb, P. A. Sojati, J. Chandran, K. Risco, C. Dermody, T. S. 2021-09-28 doi:10.1101/2021.09.27.462002 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[ Mutational signature profiling classifies subtypes of clinically different mismatch repair deficient tumors with a differential immunogenic response potential ]]> https://biorxiv.org/content/10.1101/2021.09.28.460630v1?rss=1 Giner-Calabuig, M. De Leon, S. Wang, J. Fehlmann, T. Ukaegbu, C. Gibson, J. Alustiza Fernandez, M. Pico, M.-D. Alenda, C. Herraiz, M. Carrillo-Palau, M. Salces, I. Reyes, J. Ortega, S. P. Obrador, A. Cecchini, M. Syngal, S. Stoffel, E. Ellis, N. A. Sweasy, J. Jover, R. Llor, X. Xicola, R. M. 2021-09-29 doi:10.1101/2021.09.28.460630 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Data-driven approaches for genetic characterization of SARS-CoV-2 lineages ]]> https://biorxiv.org/content/10.1101/2021.09.28.462270v1?rss=1 Mostefai, F. Gamache, I. Huang, J. N'Guessan, A. Pelletier, J. Pesaranghader, A. Hamelin, D. Murall, C. L. Poujol, R. Grenier, J.-C. Smith, M. Caron, E. Craig, M. Shapiro, J. Wolf, G. Krishnaswamy, S. Hussin, J. 2021-09-29 doi:10.1101/2021.09.28.462270 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons ]]> https://biorxiv.org/content/10.1101/2021.09.29.462281v1?rss=1 SARANGI, V. Jang, Y. Suvakov, M. Bae, T. Fasching, L. Sekar, S. Tomasini, L. Mariani, J. Vaccarino, F. M. Abyzov, A. 2021-09-30 doi:10.1101/2021.09.29.462281 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Odor motion sensing enables complex plume navigation ]]> https://biorxiv.org/content/10.1101/2021.09.29.462473v1?rss=1 Kadakia, N. Demir, M. Michaelis, B. T. Reidenbach, M. A. Clark, D. A. Emonet, T. 2021-10-01 doi:10.1101/2021.09.29.462473 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Brain networks in human conscious visual perception ]]> https://biorxiv.org/content/10.1101/2021.10.04.462661v1?rss=1 Kronemer, S. I. Aksen, M. Ding, J. Ryu, J. H. Xin, Q. Ding, Z. Prince, J. S. Kwon, H. Khalaf, A. Forman, S. Jin, D. Wang, K. Chen, K. Hu, C. Agarwal, A. Saberski, E. Wafa, S. M. A. Morgan, O. P. Wu, J. Christison-Lagay, K. L. Hasulak, N. Morrell, M. Urban, A. Constable, R. T. Pitts, M. Richardson, R. M. Crowley, M. J. Blumenfeld, H. 2021-10-05 doi:10.1101/2021.10.04.462661 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Non-coding function for mRNAs in Focal Adhesion Architecture and Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2021.10.04.463097v1?rss=1 Boraas, L. Hu, M. Thornton, L. Vejnar, C. Zhen, G. Giraldez, A. Mayr, C. Wang, S. Nicoli, S. 2021-10-04 doi:10.1101/2021.10.04.463097 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Evidence of individual differences in motives for nicotine seeking in classical nicotine self-administration and associated outcomes of varenicline administration ]]> https://biorxiv.org/content/10.1101/2021.10.05.463198v1?rss=1 Deroche-Gamonet, V. Garcia-Rivas, V. Fiancette, J.-F. Tostain, J. De Maio, G. Wiart, J.-F. Gaulier, J.-M. 2021-10-07 doi:10.1101/2021.10.05.463198 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Genetic patterns in Montipora capitata across an environmental mosaic in Kaneohe Bay ]]> https://biorxiv.org/content/10.1101/2021.10.07.463582v1?rss=1 Caruso, C. Rocha de Souza, M. Ruiz-Jones, L. Conetta, D. Hancock, J. Hobbs, C. Hobbs, C. Kahkejian, V. Kitchen, R. Marin, C. Monismith, S. Madin, J. Gates, R. D. Drury, C. 2021-10-09 doi:10.1101/2021.10.07.463582 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ BDNF signaling in Hebbian and Stentian structural plasticity in the developing visual system ]]> https://biorxiv.org/content/10.1101/2021.10.07.463583v1?rss=1 Kutsarova, E. Schohl, A. Munz, M. Wang, A. Zhang, Y. Y. Bilash, O. M. Ruthazer, E. S. 2021-10-09 doi:10.1101/2021.10.07.463583 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Age-related change in task-evoked amygdala-prefrontal circuitry: a multiverse approach with an accelerated longitudinal cohort aged 4-22 years ]]> https://biorxiv.org/content/10.1101/2021.10.08.463601v1?rss=1 Bloom, P. A. VanTieghem, M. Gabard-Durnam, L. Gee, D. G. Flannery, J. Caldera, C. Goff, B. Telzer, E. H. Humphreys, K. L. Fareri, D. S. Shapiro, M. Algharazi, S. Bolger, N. Aly, M. Tottenham, N. 2021-10-09 doi:10.1101/2021.10.08.463601 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Membrane fission during bacterial spore development requires DNA-driven cellular inflation ]]> https://biorxiv.org/content/10.1101/2021.10.08.463650v1?rss=1 Landajuela, A. Braun, M. Martinez-Calvo, A. Rodrigues, C. D. A. Doan, T. Rudner, D. Z. Wingreen, N. S. Karatekin, E. 2021-10-08 doi:10.1101/2021.10.08.463650 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ SARS-CoV-2 variants exhibit increased kinetic stability of open spike conformations as an evolutionary strategy ]]> https://biorxiv.org/content/10.1101/2021.10.11.463956v1?rss=1 Yang, Z. Han, Y. Ding, S. Finzi, A. Mothes, W. Lu, M. 2021-10-12 doi:10.1101/2021.10.11.463956 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Dynamic metabolic network modeling of a mammalian cell cycle using time-course multi-omics data ]]> https://biorxiv.org/content/10.1101/2021.10.11.464012v1?rss=1 Lee, H.-J. Shen, F. Eames, A. Jedrychowski, M. P. Chandrasekaran, S. 2021-10-13 doi:10.1101/2021.10.11.464012 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Tissue-wide coordination of calcium signaling regulates the epithelial stem cell pool during homeostasis ]]> https://biorxiv.org/content/10.1101/2021.10.12.464066v1?rss=1 Moore, J. L. Gao, F. Matte-Martone, C. Du, S. Lathrop, E. Ganesan, S. Shao, L. Bhaskar, D. Cox, A. Hendry, C. E. Rieck, B. A. Krishnaswamy, S. Greco, V. 2021-10-13 doi:10.1101/2021.10.12.464066 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Dual polarity voltage imaging reveals subthreshold dynamics and concurrent spiking patterns of multiple neuron-types ]]> https://biorxiv.org/content/10.1101/2021.10.13.463730v1?rss=1 50 neurons per field-of-view in awake mice and [~]30-min continuous imaging in flies. Using dual-polarity multiplexed imaging, we uncovered behavioral state-dependent interactions between distinct neocortical subclasses, as well as contributions to hippocampal field potentials from non-overlapping projection neuronal ensembles. By combining three mutually compatible indicators, we demonstrate concurrent triple-population voltage imaging. Our approach will empower investigations of the dynamic interplay between neuronal subclasses at single-spike resolution. One Sentence SummaryA new suite of voltage sensors enables simultaneous cellular-resolution activity imaging from multiple, targeted neuron-types in awake animals. ]]> Kannan, M. Vasan, G. Haziza, S. Huang, C. Chrapkiewicz, R. Luo, J. Cardin, J. A. Schnitzer, M. J. Pieribone, V. A. 2021-10-15 doi:10.1101/2021.10.13.463730 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Visual space curves before eye movements ]]> https://biorxiv.org/content/10.1101/2021.10.13.464140v1?rss=1 Adeyefa-Olasupo, I.-E. 2021-10-15 doi:10.1101/2021.10.13.464140 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Dynamic Instability of Dendrite Tips Generates the Highly Branched Morphologies of Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2021.10.13.464245v1?rss=1 Shree, S. Sutradhar, S. Trottier, O. Tu, Y. Liang, X. Howard, J. 2021-10-14 doi:10.1101/2021.10.13.464245 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Oxidative stress induces inflammation of lens cells and triggers immune surveillance of ocular tissues ]]> https://biorxiv.org/content/10.1101/2021.10.16.464542v1?rss=1 Thompson, B. Davidson, E. A. Chen, Y. Orlicky, D. J. Thompson, D. C. Vasiliou, V. 2021-10-16 doi:10.1101/2021.10.16.464542 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs ]]> https://biorxiv.org/content/10.1101/2021.10.18.464293v1?rss=1 Bredeson, J. V. Mudd, A. B. Medina-Ruiz, S. Mitros, T. Smith, O. K. Miller, K. E. Lyons, J. B. Batra, S. S. Park, J. Berkoff, K. C. Plott, C. Grimwood, J. Schmutz, J. Aguirre-Figueroa, G. Khokha, M. K. Lane, M. Philipp, I. Laslo, M. Hanken, J. Kerdivel, G. Buisine, N. Sachs, L. M. Buchholz, D. R. Kwon, T. Smith-Parker, H. Gridi-Papp, M. Ryan, M. J. Denton, R. D. Malone, J. H. Wallingford, J. B. Straight, A. F. Heald, R. Hockemeyer, D. Harland, R. M. Rokhsar, D. S. 2021-10-18 doi:10.1101/2021.10.18.464293 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ Remembering the pattern: A longitudinal case study on statistical learning in spatial navigation and memory consolidation ]]> https://biorxiv.org/content/10.1101/2021.10.18.464818v1?rss=1 Graves, K. N. Sherman, B. E. Huberdeau, D. Damisah, E. Quraishi, I. H. Turk-Browne, N. B. 2021-10-19 doi:10.1101/2021.10.18.464818 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Language experience shapes music processing across 40 tonal, pitch-accented, and non-tonal languages ]]> https://biorxiv.org/content/10.1101/2021.10.18.464888v1?rss=1 Liu, J. Hilton, C. B. Bergelson, E. Mehr, S. A. 2021-10-20 doi:10.1101/2021.10.18.464888 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Differential effects of Wnt-β-catenin signaling in Purkinje cells and Bergmann glia in SCA1 ]]> https://biorxiv.org/content/10.1101/2021.10.21.465333v1?rss=1 Luttik, K. P. Tejwani, L. Ju, H. Driessen, T. Smeets, C. Lim, J. 2021-10-21 doi:10.1101/2021.10.21.465333 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ DOT1L bridges transcription and heterochromatin formation at pericentromeres ]]> https://biorxiv.org/content/10.1101/2021.10.21.465349v1?rss=1 Malla, A. B. Yu, H. Kadimi, S. Lam, T. Cox, A. L. Smith, Z. D. Lesch, B. J. 2021-10-21 doi:10.1101/2021.10.21.465349 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Developmental Dynamics of RNA Translation in the Human Brain ]]> https://biorxiv.org/content/10.1101/2021.10.22.465170v1?rss=1 Duffy, E. E. Finander, B. Choi, G. Carter, A. C. Pritisanac, I. Alam, A. Luria, V. Karger, A. Phu, W. Sherman, M. A. Assad, E. G. Khitun, A. Crouch, E. E. Ganesh, S. Berger, B. Sestan, N. O'Donnell-Luria, A. Huang, E. J. Griffith, E. C. Forman-Kay, J. D. Moses, A. Kalish, B. T. Greenberg, M. E. 2021-10-23 doi:10.1101/2021.10.22.465170 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ RAGE antagonist peptide mitigates AGE-mediated endothelial hyperpermeability and accumulation of glycoxidation products in human ascending aortas and in a murine model of aortic aneurysm ]]> https://biorxiv.org/content/10.1101/2021.10.22.465199v1?rss=1 5.5 cm in tricuspid aortic valve patients. Aortopathies are associated with altered wall stress and stiffness as well as endothelial cell dysfunction and synthetic vascular smooth muscle cell (VSMC) phenotype. We reported that these mechanisms are mediated by glycoxidation products [Reactive oxygen species (ROS) and Advance Glycation End products (AGE)]. This study addresses the role of glycoxidation on endothelial function and AGE-mediated aortic stiffness. Hypothesis and aimsHere we investigate how circulating glycation products infiltrate the aortic wall via AGE-mediated endothelial hyperpermeability and contribute to both VSMC synthetic phenotype and extracellular matrix (ECM) remodeling in vivo and ex vivo. We also study how RAGE antagonist peptide (RAP) can rescue the effect of AGEs in vitro and in vivo in eNOS-/- vs WT mice. Methods and resultsHuman ascending aortas (n=30) were analyzed for AGE, ROS, and ECM markers. In vitro glycation was obtained by treating VSMC or human and murine aortas with glyoxal. Endothelial permeability was measured under glycation treatment. Vascular stiffness was measured by a pressure myograph comparing wild-type mice {+/-} glyoxal. eNOS-/- mice, a model of increased endothelial permeability, were treated for 28 days with hyperlipidemic diet {+/-} Angiotensin II (1000ng/kg/min) with or without anti-glycation treatment (RAP 20mg/kg). Echo data of aortic diameter were collected. Murine vascular stiffness was measured by a pressure myograph (n=5/group). Glycoxidation products were detected in all human aortas independently of aortic diameter, with stronger accumulation on the lumen and the adventitia layer. AGEs increased endothelial permeability, induce synthetic phenotypic switch in human VSMCs, and inhibit cell migration. RAP pre-treatment rescue the effect of glyoxal on endothelial cells. Ex vivo glycation treatment of murine arteries impacted on ECM and increased stiffness. Aortic stiffness was higher in eNOS-/- vs WT mice. Ang II-mediated aortopathies results in aortic dilation, and AGE/ROS accumulation, which is rescued by RAGE antagonist peptide treatment of eNOS-/- mice. ConclusionsGlycoxidation reaction mediate EC permeability, VSMCs phenotype, and ECM remodeling leading to dysfunctional microstructure of the ascending aorta, altered vascular stiffness and increasing aortic susceptibility to dilation and rupture. Moreover, we show that RAP can mitigate AGE-mediated endothelial hyper-permeability in vitro and impact on ascending aneurysm in vivo ]]> Camillo, C. Abramov, A. Allen, P. M. Castillero, E. Roberts, E. Xue, Y. Frasca, A. Moreno, V. Kurade, M. Robinson, K. Spiegel, D. LaPar, D. Grau, J. B. Assoian, R. Bavaria, J. E. Takayama, H. Ferrari, G. 2021-10-24 doi:10.1101/2021.10.22.465199 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ The Wolbachia CinB Nuclease is Sufficient for Induction of Cytoplasmic Incompatibility ]]> https://biorxiv.org/content/10.1101/2021.10.22.465375v1?rss=1 Sun, G. Zhang, M. Chen, H. Hochstrasser, M. 2021-10-23 doi:10.1101/2021.10.22.465375 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1 ]]> https://biorxiv.org/content/10.1101/2021.10.22.465444v1?rss=1 Tejwani, L. Ravindra, N. G. Nguyen, B. Luttik, K. Lee, C. Gionco, J. Kim, K. Yoon, J. Haidery, F. Ro, H. Ni, L. Orr, H. Ranum, L. Shakkottai, V. Faust, P. L. van Dijk, D. Lim, J. 2021-10-24 doi:10.1101/2021.10.22.465444 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Activity-dependent endoplasmic reticulum Ca2+ uptake depends on Kv2.1-mediated endoplasmic reticulum/plasma membrane junctions to promote synaptic transmission ]]> https://biorxiv.org/content/10.1101/2021.10.23.465516v1?rss=1 Panzera, L. C. Johnson, B. Cho, I. H. Tamkun, M. M. Hoppa, M. B. 2021-10-23 doi:10.1101/2021.10.23.465516 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Ultra-cheap and scalable epigenetic age predictions with TIME-Seq ]]> https://biorxiv.org/content/10.1101/2021.10.25.465725v1?rss=1 Griffin, P. T. Kane, A. E. Trapp, A. Li, J. McNamara, M. S. Meer, M. V. MacArthur, M. R. Mitchell, S. J. Mueller, A. L. Carmody, C. Vera, D. L. Kerepesi, C. Noren Hooten, N. Mitchell, J. R. Evans, M. K. Gladyshev, V. N. Sinclair, D. A. 2021-10-28 doi:10.1101/2021.10.25.465725 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ MLF2 modulates phase separated nuclear envelope condensates that provoke dual proteotoxicity ]]> https://biorxiv.org/content/10.1101/2021.10.26.465916v1?rss=1 Prophet, S. M. Rampello, A. J. Niescier, R. F. Shaw, J. E. Koleske, A. J. Schlieker, C. 2021-10-27 doi:10.1101/2021.10.26.465916 Cold Spring Harbor Laboratory Press 2021-10-27 <![CDATA[ Cell wall damage reveals spatial flexibility in peptidoglycan synthesis and a non-redundant role for RodA in mycobacteria ]]> https://biorxiv.org/content/10.1101/2021.10.26.465981v1?rss=1 Melzer, E. S. Kado, T. Garcia-Heredia, A. Gupta, K. R. Meniche, X. Morita, Y. S. Sassetti, C. M. Rego, E. H. M. Siegrist, M. S. 2021-10-26 doi:10.1101/2021.10.26.465981 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Long-term effects of network-based fMRI neurofeedback training for sustained attention ]]> https://biorxiv.org/content/10.1101/2021.10.27.465722v1?rss=1 Pamplona, G. S. P. Heldner, J. Langner, R. Koush, Y. Michels, L. Ionta, S. Garrido Salmon, C. E. Scharnowski, F. 2021-10-28 doi:10.1101/2021.10.27.465722 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Causal Haplotype Block Identification in Plant Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/2021.10.28.466332v1?rss=1 Wu, X. Jiang, W. Fragoso, C. Huang, J. Zhou, G. Zhao, H.-y. Dellaporta, S. 2021-10-29 doi:10.1101/2021.10.28.466332 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Optimized immunoglobulin knock-ins using Cas9 reveal peritoneal B cell lineage relationships in vivo ]]> https://biorxiv.org/content/10.1101/2021.10.31.466662v1?rss=1 Bendelac, A. Erickson, S. A. Zapata-Bultman, E. Degenstein, L. 2021-11-01 doi:10.1101/2021.10.31.466662 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ More than a feeling: scalp EEG and eye correlates of conscious tactile perception ]]> https://biorxiv.org/content/10.1101/2021.10.31.466706v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@e4e7fforg.highwire.dtl.DTLVardef@3b3ed0org.highwire.dtl.DTLVardef@198d517org.highwire.dtl.DTLVardef@cddef3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA novel tactile perceptual threshold task yields robust behavioral results C_LIO_LIEvent-related potentials differ according to perception status C_LIO_LIP300 is observed in both perceived and not perceived trials C_LIO_LIBlink rate, pupil diameter, and microsaccades differ across trial conditions C_LI ]]> Gusso, M. M. Christison-Lagay, K. L. Zuckerman, D. Chandrasekaran, G. Kronemer, S. I. Ding, J. Z. Freedman, N. C. Nohama, P. Blumenfeld, H. 2021-11-03 doi:10.1101/2021.10.31.466706 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Manipulating neural dynamics to tune motion detection ]]> https://biorxiv.org/content/10.1101/2021.11.02.466844v1?rss=1 Gonzalez-Suarez, A. D. Zavatone-Veth, J. A. Chen, J. Matulis, C. Badwan, B. Clark, D. A. 2021-11-03 doi:10.1101/2021.11.02.466844 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ SHIP164 is a Chorein Motif Containing Lipid Transport Protein that Controls Membrane Dynamics and Traffic at the Endosome-Golgi Interface. ]]> https://biorxiv.org/content/10.1101/2021.11.04.467353v1?rss=1 Hanna, M. G. Suen, P. Wu, Y. Reinisch, K. M. De Camilli, P. 2021-11-04 doi:10.1101/2021.11.04.467353 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ The Immune Signatures Data Resource: A compendium of systems vaccinology datasets ]]> https://biorxiv.org/content/10.1101/2021.11.05.465336v1?rss=1 Diray-Arce, J. Miller, H. E. R. Henrich, E. Gerritsen, B. Mule, M. P. Fourati, S. Gygi, J. Hagan, T. Tomalin, L. Rychov, D. Kazmin, D. Chawla, D. G. Meng, H. Dunn, P. Campbell, J. The Human Immunology Project Consortium (HIPC), Sarwal, M. Tsang, J. Levy, O. Pulendran, B. Sekaly, R.-P. Floratos, A. Gottardo, R. Kleinstein, S. Suarez-Farinas, M. 2021-11-08 doi:10.1101/2021.11.05.465336 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ The IPF fibroblastic focus is an active collagen biosynthesis factory embedded in a distinct extracellular matrix ]]> https://biorxiv.org/content/10.1101/2021.11.06.467549v1?rss=1 Herrera, J. A. Dingle, L. Montero, M. A. Shah, R. Venkateswaran, R. V. Blaikley, J. F. Lawless, C. Schwartz, M. A. 2021-11-06 doi:10.1101/2021.11.06.467549 Cold Spring Harbor Laboratory Press 2021-11-06 <![CDATA[ Oxytocinergic modulation of stress-associated amygdala-hippocampus pathways in humans is specially mediated by serotonergic mechanisms ]]> https://biorxiv.org/content/10.1101/2021.11.06.467580v1?rss=1 Lan, C. Liu, C. Li, K. Zhao, Z. Ma, Y. Yang, J. Scheele, D. Yao, S. Kendrick, K. Becker, B. 2021-11-08 doi:10.1101/2021.11.06.467580 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ An interactome landscape of SARS-CoV-2 virus-human protein-protein interactions by protein sequence-based multi-label classifiers ]]> https://biorxiv.org/content/10.1101/2021.11.07.467640v1?rss=1 80,000 virus-host PPIs along with evidence scores for multi-level evidence prediction, which is distinct from predicting binary interactions in previous studies. Our multi-label classifiers are based on 5 evidence levels binned from evidence scores. Our best model of XGBoost achieves 74% AUC and 68% accuracy on average in 10-fold cross validation. The most important amino acids are cysteine and histidine. In addition, our model predicts experimental PPIs with higher accuracy than text mining-based PPIs by 4% despite their smaller data size by more than 6-fold. We then predict evidence levels of [~]2,000 SARS-CoV-2 virus-human PPIs from public experimental proteomics data. Interactions with SARS-CoV-2 Nsp7b show high evidence. We also predict evidence levels of all pairwise PPIs of [~]550,000 between the SARS-CoV-2 and human proteomes to provide a draft virus-host interactome landscape for SARS-CoV-2 infection in humans in a comprehensive and unbiased way in silico. Most human proteins from 140 highest evidence predictions interact with SARS-CoV-2 Nsp7, Nsp1, and ORF14, with significant enrichment in the top 2 pathways of vascular smooth muscle contraction (CALD1, NPR2, CALML3) and Myc targets (CBX3, PES1). Our prediction also suggests that histone H2A components are targeted by multiple SARS-CoV-2 proteins. ]]> Lee, H.-J. 2021-11-08 doi:10.1101/2021.11.07.467640 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ AWGAN: A Powerful Batch Correction Model for scRNA-seq Data ]]> https://biorxiv.org/content/10.1101/2021.11.08.467781v1?rss=1 Liu, T. Wang, Y. Zhao, H.-y. 2021-11-10 doi:10.1101/2021.11.08.467781 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2021.11.10.467836v1?rss=1 Papadas, A. Deb, G. Officer, A. Cicala, A. Hope, C. Emmerich, P. Wiesner, J. Pagenkopf, A. Matkowskyj, K. Deming, D. A. Politi, K. Abrams, S. Harismendy, O. Asimakopoulos, F. 2021-11-13 doi:10.1101/2021.11.10.467836 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Real-time alerts from AI-enabled camera traps using the Iridium satellite network: a case-study in Gabon, Central Africa ]]> https://biorxiv.org/content/10.1101/2021.11.10.468078v1?rss=1 Whytock, R. C. Suijten, T. van Deursen, T. Swiezewski, J. Mermiaghe, H. Madamba, N. Moukoumou, N. Zwerts, J. A. Koumba Pambo, A. F. Bahaa-el-din, L. Brittain, S. Cardoso, A. W. Henschel, P. Lehmann, D. Momboua, B. R. Makaga, L. Orbell, C. White, L. J. Iponga, D. M. Abernethy, K. A. 2021-11-13 doi:10.1101/2021.11.10.468078 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ A Multi-Omics and Bioenergetics Longitudinal Aging Dataset in Primary Human Fibroblasts with Mitochondrial Perturbations ]]> https://biorxiv.org/content/10.1101/2021.11.12.468448v1?rss=1 Sturm, G. Monzel, A. S. Karan, K. R. Michelson, J. Ware, S. A. Cardenas, A. Lin, J. Bris, C. Santhanam, B. Murphy, M. P. Levine, M. E. Horvath, S. Belsky, D. W. Wang, S. Procaccio, V. Kaufman, B. A. Hirano, M. Picard, M. 2021-11-13 doi:10.1101/2021.11.12.468448 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Brain state and cortical layer-specific mechanisms underlying perception at threshold ]]> https://biorxiv.org/content/10.1101/2021.11.16.468866v1?rss=1 Morton, M. P. Denagamage, S. Blume, I. J. Reynolds, J. H. Jadi, M. P. Nandy, A. S. 2021-11-18 doi:10.1101/2021.11.16.468866 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Morpholino-mediated knockdown of the brain mineralocorticoid receptor affects glucocorticoid signaling and neuroplasticity in wild ocellated wrasse (Symphodus ocellatus) ]]> https://biorxiv.org/content/10.1101/2021.11.17.468986v1?rss=1 Nugent, B. M. Stiver, K. A. Han, J. Kindsvater, H. K. Marsh-Rollo, S. E. Hofmann, H. A. Alonzo, S. H. 2021-11-19 doi:10.1101/2021.11.17.468986 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ A Biophysical Model of Nonquantal Transmission at the Vestibular Hair Cell-Calyx Synapse: KLV currents Modulate Fast Electrical and Slow K+ potentials in the Synaptic Cleft ]]> https://biorxiv.org/content/10.1101/2021.11.18.469197v1?rss=1 Govindaraju, A. C. Quraishi, I. H. Lysakowski, A. Eatock, R. A. Raphael, R. M. 2021-11-20 doi:10.1101/2021.11.18.469197 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Competition for endothelial cell polarity drives vascular morphogenesis ]]> https://biorxiv.org/content/10.1101/2021.11.23.469704v1?rss=1 Barbacena, P. Dominguez-Cejudo, M. Fonseca, C. G. Gomez-Gonzalez, M. Faure, L. M. Zarkada, G. Pena, A. A. Pezzarossa, A. Ramalho, D. Giarratano, Y. Ouarne, M. Barata, D. Fortunato, I. Misikova, L. H. Mauldin, I. Carvalho, Y. Trepat, X. Roca-Cusachs, P. Eichmann, A. Bernabeu, M. O. Franco, C. 2021-11-23 doi:10.1101/2021.11.23.469704 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ LRRC15 is an inhibitory receptor blocking SARS-CoV-2 spike-mediated entry in trans ]]> https://biorxiv.org/content/10.1101/2021.11.23.469714v1?rss=1 Song, J. Chow, R. D. Pena-Hernandez, M. Zhang, L. Loeb, S. A. So, E.-Y. Liang, O. D. Wilen, C. B. Lee, S. 2021-11-24 doi:10.1101/2021.11.23.469714 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities ]]> https://biorxiv.org/content/10.1101/2021.11.24.469776v1?rss=1 Chen, Y. Sun, L. Ullah, I. Beaudoin-Bussieres, G. Anand, S. P. Hederman, A. P. Tolbert, W. D. Sherburn, R. Nguyen, D. N. Marchitto, L. Ding, S. Wu, D. Luo, Y. Gottumukkala, S. Moran, S. Kumar, P. Piszczek, G. Mothes, W. Ackerman, M. E. Finzi, A. E. Uchil, P. D. Gonzalez, F. J. Pazgier, M. 2021-11-24 doi:10.1101/2021.11.24.469776 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Spatial resolution of an integrated C4+CAM photosynthetic metabolism ]]> https://biorxiv.org/content/10.1101/2021.11.25.470062v1?rss=1 Moreno-Villena, J. J. Zhou, H. Gilman, I. S. Tausta, S. L. Cheung, C. Y. M. 2021-11-26 doi:10.1101/2021.11.25.470062 Cold Spring Harbor Laboratory Press 2021-11-26 <![CDATA[ NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects ]]> https://biorxiv.org/content/10.1101/2021.11.26.470128v1?rss=1 Dubos, T. Poulet, A. Thomson, G. Pery, E. Chausse, F. Tatout, C. Desset, S. van Wolfswinkel, J. C. Jacob, Y. 2021-11-27 doi:10.1101/2021.11.26.470128 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ OxPhos Dysfunction Causes Hypermetabolism and Reduces Lifespan in Cells and in Patients with Mitochondrial Diseases ]]> https://biorxiv.org/content/10.1101/2021.11.29.470428v1?rss=1 Sturm, G. Karan, K. R. Santhanham, B. S. Taivassalo, T. Bris, C. Duplaga, S. A. Cross, M. Towheed, A. Higgins-Chen, A. T. McManus, M. J. Cardenas, A. Lin, J. Epel, E. S. Rahman, S. Vissing, J. Grassi, B. Levine, M. Horvath, S. Haller, R. G. Lenaers, G. Wallace, D. C. Tavazoie, S. Procaccio, V. Kaufman, B. A. Seifert, E. Hirano, M. Monzel, A. Picard, M. 2021-11-30 doi:10.1101/2021.11.29.470428 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Multi-task representations in human cortex transform along a sensory-to-motor hierarchy ]]> https://biorxiv.org/content/10.1101/2021.11.29.470432v1?rss=1 Ito, T. Murray, J. D. 2021-11-30 doi:10.1101/2021.11.29.470432 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Ubiquitination drives COPI priming and Golgi SNARE localization ]]> https://biorxiv.org/content/10.1101/2021.11.29.470439v1?rss=1 Date, S. S. Xu, P. Hepowit, N. L. Diab, N. S. Best, J. Xie, B. Du, J. Strieter, E. R. Jackson, L. P. MacGurn, J. A. Graham, T. R. 2021-11-29 doi:10.1101/2021.11.29.470439 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ T cell receptor repertoire signatures associated with COVID-19 severity ]]> https://biorxiv.org/content/10.1101/2021.11.30.470640v1?rss=1 Park, J. Lee, K. Lam, S. Chen, S. 2021-12-02 doi:10.1101/2021.11.30.470640 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ The evolution of ovary-specific gene expression in Hawaiian Drosophilidae ]]> https://biorxiv.org/content/10.1101/2021.11.30.470652v1?rss=1 Church, S. H. Munro, C. Dunn, C. Extavour, C. G. 2021-12-01 doi:10.1101/2021.11.30.470652 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Ligand-induced changes in dynamics mediate long-range allostery in the lac repressor ]]> https://biorxiv.org/content/10.1101/2021.11.30.470682v1?rss=1 Glasgow, A. Hobbs, H. T. Perry, Z. R. Marqusee, S. Kortemme, T. 2021-12-01 doi:10.1101/2021.11.30.470682 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Babesia duncani as a model organism to study the development, virulence and drug susceptibility of intraerythrocytic parasites in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2021.12.01.470698v1?rss=1 Mamoun, C. Pal, A. C. Renard, I. Singh, P. Vydyam, P. Chiu, J. E. Pou, S. W. Winter, R. Dodean, R. Frueh, L. Nilsen, A. C. Riscoe, M. K. Doggett, J. S. 2021-12-01 doi:10.1101/2021.12.01.470698 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ A versatile new ubiquitin detection and purification tool derived from a bacterial deubiquitylase ]]> https://biorxiv.org/content/10.1101/2021.12.02.470885v1?rss=1 Zhang, M. Berk, J. M. Mehrtash, A. B. Kanyo, J. Hochstrasser, M. 2021-12-02 doi:10.1101/2021.12.02.470885 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Systems immune profiling of variant-specific vaccination against SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.12.02.471028v1?rss=1 Peng, L. Park, J. Fang, Z. Zhou, X. Dong, M. Xiong, Q. Lin, C. Chen, S. 2021-12-03 doi:10.1101/2021.12.02.471028 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ LINE-1 activation in the cerebellum drives ataxia ]]> https://biorxiv.org/content/10.1101/2021.12.03.471151v1?rss=1 Takahashi, T. Kudo, E. Song, E. Carvalho, F. Yasumoto, Y. Kong, Y. Park, A. Stoiljkovic, M. Gao, X.-B. Shanabrough, M. Szigeti-Buck, K. Liu, Z.-W. Zhang, Y. Sulkowski, P. Glazer, P. Kaczmarek, L. Horvath, T. Iwasaki, A. 2021-12-03 doi:10.1101/2021.12.03.471151 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Finger stability in precision grips ]]> https://biorxiv.org/content/10.1101/2021.12.04.470276v1?rss=1 Sharma, N. Venkadesan, M. 2021-12-06 doi:10.1101/2021.12.04.470276 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Constructing a multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and co-infecting microbes ]]> https://biorxiv.org/content/10.1101/2021.12.05.471290v1?rss=1 Lou, S. Li, T. Gerstein, M. 2021-12-07 doi:10.1101/2021.12.05.471290 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Neuron-like function of the nephron central command ]]> https://biorxiv.org/content/10.1101/2021.12.06.471478v1?rss=1 Gyarmati, G. Shroff, U. N. Riquier-Brison, A. Stocker, S. D. Izuhara, A. Deepak, S. Chen, Y. Biemesderfer, D. James, A. Minichiello, L. Zlokovic, B. V. Peti-Peterdi, J. 2021-12-07 doi:10.1101/2021.12.06.471478 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Impaired LAIR-1-mediated immune control due to collagen degradation in fibrosis ]]> https://biorxiv.org/content/10.1101/2021.12.07.471103v1?rss=1 Carvalheiro, T. Marut, W. Pascoal Ramos, M. I. Garcia, S. Fleury, D. Affandi, A. J. Meijers, A. S. Giovannone, B. Tieland, R. G. Elshof, E. Ottria, A. Cossu, M. Meizlish, M. L. Veenendaal, T. Ramanujam, M. Moreno-Garcia, M. E. Klumperman, J. Liv, N. Radstake, T. R. D. J. Meyaard, L. 2021-12-07 doi:10.1101/2021.12.07.471103 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination ]]> https://biorxiv.org/content/10.1101/2021.12.07.471539v1?rss=1 Lu-Culligan, A. Tabachnikova, A. Tokuyama, M. Lee, H. J. Lucas, C. Silva Monteiro, V. Muenker, M. C. Mohanty, S. Huang, J. Kang, I. Dela Cruz, C. Farhadian, S. Campbell, M. Yildirim, I. Shaw, A. Ko, A. Omer, S. Iwasaki, A. 2021-12-08 doi:10.1101/2021.12.07.471539 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Predicting the Toxicity of Druggable Proteins to Human Tissues ]]> https://biorxiv.org/content/10.1101/2021.12.07.471637v1?rss=1 Hao, Y. Thangaraj, P. Tatonetti, N. 2021-12-09 doi:10.1101/2021.12.07.471637 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ CXCL8/CXCR2 signaling mediates bone marrow fibrosis and represents a therapeutic target in myelofibrosis ]]> https://biorxiv.org/content/10.1101/2021.12.08.471791v1?rss=1 Dunbar, A. Kim, D. Lu, M. Farina, M. Yang, J. L. Park, Y. Gobbo, F. Verachi, P. Martelli, F. Karzai, A. Xiao, W. Xia, L. Elmansy, N. Kleppe, M. Chen, Z. Xiao, Y. McGovern, E. Snyder, J. Krishnan, A. Hill, C. Cordner, K. Zouak, A. Salama, M. Yohai, J. Tucker, E. Chen, J. Zhou, J. McConnell, T. Koche, R. Rampal, R. Migliaccio, A. R. Fan, R. Levine, R. Hoffman, R. 2021-12-10 doi:10.1101/2021.12.08.471791 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Minor intron splicing efficiency increases with the development of lethal prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.12.09.471104v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@1c1c296org.highwire.dtl.DTLVardef@1ce1416org.highwire.dtl.DTLVardef@88d842org.highwire.dtl.DTLVardef@2ddf96_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Augspach, A. Drake, K. Roma, L. Qian, E. Lee, S. R. Clarke, D. Kumar, S. Jaquet, M. Gallon, J. Bolis, M. Triscott, J. Galvan, J. A. Chen, Y. Thalmann, G. Kruithof-de Julio, M. Theurillat, J.-P. P. Wuchty, S. Gerstein, M. Piscuoglio, S. Kanadia, R. Rubin, M. A. 2021-12-10 doi:10.1101/2021.12.09.471104 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Macroevolutionary dynamics of climatic niche space ]]> https://biorxiv.org/content/10.1101/2021.12.09.471977v1?rss=1 Quintero, I. Suchard, M. A. Jetz, W. 2021-12-09 doi:10.1101/2021.12.09.471977 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Neural mechanisms to exploit positional geometry for collision avoidance ]]> https://biorxiv.org/content/10.1101/2021.12.11.472218v1?rss=1 Tanaka, R. Clark, D. A. 2021-12-13 doi:10.1101/2021.12.11.472218 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size. ]]> https://biorxiv.org/content/10.1101/2021.12.12.472293v1?rss=1 Miao, R. Chun, H. Gomes, A. C. Choi, J. Pereira, J. 2021-12-12 doi:10.1101/2021.12.12.472293 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ A Precision Medicine Approach to Metabolic Therapy for Breast Cancer in Mice ]]> https://biorxiv.org/content/10.1101/2021.12.15.472809v1?rss=1 Akingbesote, N. D. Norman, A. Zhu, W. Halberstam, A. A. Zhang, X. Foldi, J. R. Lustberg, M. B. Perry, R. J. 2021-12-16 doi:10.1101/2021.12.15.472809 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Social evolution of shared biofilm matrix components ]]> https://biorxiv.org/content/10.1101/2021.12.16.472970v1?rss=1 Tai, J.-S. B. Mukherjee, S. Nero, T. Olson, R. Tithof, J. Nadell, C. D. Yan, J. 2021-12-17 doi:10.1101/2021.12.16.472970 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ SMAD4 and TGFβ are architects of inverse genetic programs during fate-determination of antiviral memory CD8 T cells ]]> https://biorxiv.org/content/10.1101/2021.12.16.472993v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@5ac140org.highwire.dtl.DTLVardef@455a2aorg.highwire.dtl.DTLVardef@1227d96org.highwire.dtl.DTLVardef@16336b9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chandiran, K. Suarez-Ramirez, J. Hu, Y. Ugur, Z. Jellison, E. R. low, J.-S. McDonald, B. Kaech, S. M. Cauley, L. S. 2021-12-16 doi:10.1101/2021.12.16.472993 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Lonafarnib improves cardiovascular function and survival in a mouse model of Hutchinson-Gilford Progeria Syndrome ]]> https://biorxiv.org/content/10.1101/2021.12.17.473197v1?rss=1 Murtada, S.-I. Mikush, N. Wang, M. Ren, P. Kawamura, Y. Ramachandra, A. B. Braddock, D. T. Tellides, G. Gordon, L. B. Humphrey, J. D. 2021-12-19 doi:10.1101/2021.12.17.473197 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ OligoTRAFTACs: A Generalizable Method for Transcription Factor Degradation ]]> https://biorxiv.org/content/10.1101/2021.12.20.473482v1?rss=1 Samarasinghe, K. T. G. An, E. Genuth, M. Chu, L. Holley, S. Crews, C. M. M. 2021-12-21 doi:10.1101/2021.12.20.473482 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Targeting RTN4/NoGo-Receptor reduces levels of ALS protein ataxin-2 ]]> https://biorxiv.org/content/10.1101/2021.12.20.473562v1?rss=1 Rodriguez, C. M. Bechek, S. C. Jones, G. L. Nakayama, L. Akiyama, T. Kim, G. Solow-Cordero, D. E. Strittmatter, S. M. Gitler, A. D. 2021-12-21 doi:10.1101/2021.12.20.473562 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ ANTAGONISM OF SAXITOXIN AND TETRODOTOXIN BLOCK BY INTERNAL MONOVALENT CATIONS IN SQUID AXON ]]> https://biorxiv.org/content/10.1101/2021.12.21.473550v1?rss=1 Oxford, G. S. Forscher, P. Wagoner, P. K. Adams, D. J. 2021-12-22 doi:10.1101/2021.12.21.473550 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ CSNet: Estimating cell-type-specific gene co-expression networks from bulk gene expression data ]]> https://biorxiv.org/content/10.1101/2021.12.21.473558v1?rss=1 Su, C. Zhang, J. Zhao, H. 2021-12-23 doi:10.1101/2021.12.21.473558 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion ]]> https://biorxiv.org/content/10.1101/2021.12.21.473680v1?rss=1 Onuchic, L. Padovano, V. Schena, G. Rajendran, V. Dong, K. Gresko, N. P. Shi, X. Shen, H. Somlo, S. Caplan, M. J. 2021-12-23 doi:10.1101/2021.12.21.473680 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617 ]]> https://biorxiv.org/content/10.1101/2021.12.21.473733v1?rss=1 Peng, L. Hu, Y. Mankowski, M. Ren, P. Chen, R. Wei, J. Zhao, M. Li, T. Tripler, T. Ye, L. Chow, R. Fang, Z. Wu, C. Dong, M. Cook, M. Wang, G. Clark, P. Nelson, B. Klein, D. Sutton, R. Diamond, M. Wilen, C. Xiong, Y. Chen, S. 2021-12-24 doi:10.1101/2021.12.21.473733 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Liquid-liquid phase separation facilitates the biogenesis of secretory storage granules ]]> https://biorxiv.org/content/10.1101/2021.12.22.472607v1?rss=1 PARCHURE, A. Tian, M. Boyer, C. K. Bearrows, S. C. Rohli, K. E. Zhang, J. Ramazanov, B. R. Wang, Y. Stephens, S. von Blume, J. 2021-12-23 doi:10.1101/2021.12.22.472607 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ A discovery-based proteomics approach identifies protein disulfide isomerase (PDIA1) as a biomarker of β cell stress in type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.22.473924v1?rss=1 Syed, F. Singhal, D. Raedschelders, K. Krishnan, P. Bone, R. N. McLaughlin, M. R. Van Eyk, J. E. Mirmira, R. G. Yang, M.-L. Mamula, M. J. Wu, H. Liu, X. Evans-Molina, C. 2021-12-23 doi:10.1101/2021.12.22.473924 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ PTHrP Induces STAT5 Activation, Secretory Differentiation and Mammary Tumor Progression ]]> https://biorxiv.org/content/10.1101/2021.12.28.473846v1?rss=1 Grinman, D. Y. Boras-Granic, K. Takyar, F. M. Dann, P. Hens, J. R. Marmol, C. Lee, J. Choi, J. Chodosh, L. A. Garcia Sola, M. E. Wysolmerski, J. J. 2021-12-28 doi:10.1101/2021.12.28.473846 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Diversity of microglial transcriptional responses during opioid exposure and neuropathic pain ]]> https://biorxiv.org/content/10.1101/2021.12.29.473853v1?rss=1 Sypek, E. I. Collins, H. Y. McCallum, W. M. Bourdillon, A. T. Bohlen, C. J. Scherrer, G. 2021-12-29 doi:10.1101/2021.12.29.473853 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Rheology of crossbridge ensembles ]]> https://biorxiv.org/content/10.1101/2021.12.29.474482v1?rss=1 Nguyen, K. D. Venkadesan, M. 2021-12-30 doi:10.1101/2021.12.29.474482 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Properties and proximity proteomics of synaptopodin provide insight into the molecular organization of the spine apparatus of dendritic spines ]]> https://biorxiv.org/content/10.1101/2021.12.30.474557v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@197d23borg.highwire.dtl.DTLVardef@6b60eeorg.highwire.dtl.DTLVardef@1a8ce67org.highwire.dtl.DTLVardef@186cd0a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Falahati, H. Wu, Y. Feuerer, V. De Camilli, P. 2021-12-30 doi:10.1101/2021.12.30.474557 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Efficient simulation of 3D reaction-diffusion in models of neurons and networks ]]> https://biorxiv.org/content/10.1101/2022.01.01.474683v1?rss=1 McDougal, R. A. Conte, C. Eggleston, L. Newton, A. J. H. Galijasevic, H. 2022-01-02 doi:10.1101/2022.01.01.474683 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Phase tracking algorithms detect both real and imaginary components of outer hair cell nonlinear membrane capacitance that exhibits dielectric loss. ]]> https://biorxiv.org/content/10.1101/2022.01.01.474702v1?rss=1 Santos-Sacchi, J. 2022-01-02 doi:10.1101/2022.01.01.474702 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ Counting fluorescently labeled proteins in tissues in the spinning disk microscope using single-molecule calibrations ]]> https://biorxiv.org/content/10.1101/2022.01.02.474734v1?rss=1 Liao, M. Kuo, Y.-W. Howard, J. 2022-01-02 doi:10.1101/2022.01.02.474734 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron ]]> https://biorxiv.org/content/10.1101/2022.01.04.474803v1?rss=1 Yuan, T. Z. Lucas, C. Monteiro, V. S. Iwasaki, A. Yang, M. L. Nepita, H. F. Lujan Hernandez, A. G. Taft, J. M. Frei, L. Reddy, S. T. Weber, C. Malobisky, K. P. Mesquita, R. Sato, A. 2022-01-04 doi:10.1101/2022.01.04.474803 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Theoretical model of efficient phagocytosis driven by curved membrane proteins and active cytoskeleton forces ]]> https://biorxiv.org/content/10.1101/2022.01.04.474893v1?rss=1 Sadhu, R. K. Barger, S. R. Penic, S. Iglic, A. Krendel, M. Gauthier, N. Gov, N. 2022-01-05 doi:10.1101/2022.01.04.474893 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in In Vitro, In Vivo and Ex Vivo Models of Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2022.01.04.474955v1?rss=1 Ahangari, F. Becker, C. Foster, D. G. Chioccioli, M. Nelson, M. Beke, K. wang, X. Readhead, B. Meador, C. Correll, K. Lili, L. Roybal, H. M. Rose, K.-A. Ding, S. Barnthaler, T. Briones, N. Deluliis, G. Schupp, J. C. Li, Q. Omote, N. Aschner, Y. Kopf, K. W. Magnusson, B. Hicks, R. Backmark, A. Cousens, L. P. Dudley, J. T. Kaminski, N. Downey, G. P. 2022-01-05 doi:10.1101/2022.01.04.474955 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland ]]> https://biorxiv.org/content/10.1101/2022.01.05.475069v1?rss=1 Hou, H. Chan, C. Yuki, K. E. Sokolowski, D. Roy, A. Qu, R. Uuskula-Reimand, L. Faykoo-Martinez, M. Hudson, M. Corre, C. Goldenberg, A. Zhang, Z. Palmert, M. R. Wilson, M. D. 2022-01-06 doi:10.1101/2022.01.05.475069 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Molecular Mechanism of Hyperactivation Conferred by a Truncated TRPA1 Disease Mutant Suggests New Gating Insights ]]> https://biorxiv.org/content/10.1101/2022.01.05.475133v1?rss=1 Bali, A. Schaefer, S. P. Trier, I. Zhang, A. L. Kabeche, L. Paulsen, C. E. 2022-01-05 doi:10.1101/2022.01.05.475133 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Defining the dynamics of naive CD4 and CD8 T cells across the mouse lifespan ]]> https://biorxiv.org/content/10.1101/2022.01.07.475400v1?rss=1 Rane, S. Hogan, T. Lee, E. Seddon, B. Yates, A. 2022-01-08 doi:10.1101/2022.01.07.475400 Cold Spring Harbor Laboratory Press 2022-01-08 <![CDATA[ Experimenter sex modulates mouse biobehavioural and pharmacological responses ]]> https://biorxiv.org/content/10.1101/2022.01.09.475572v1?rss=1 Georgiou, P. Zanos, P. Mou, T.-C. M. An, X. Gerhard, D. M. Dryanovski, D. I. Potter, L. E. Highland, J. N. Jenne, C. E. Stewart, B. W. Pultorak, K. Yuan, P. Powels, C. F. Lovett, J. Pereira, E. F. R. Clark, S. M. Tonelli, L. H. Moaddel, R. F. R. Zarate, C. A. Duman, R. S. Thompson, S. M. Gould, T. D. 2022-01-11 doi:10.1101/2022.01.09.475572 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Recognition of HIV-1 capsid licenses innate immune response to viral infection ]]> https://biorxiv.org/content/10.1101/2022.01.10.472699v1?rss=1 yoh, s. M. Mamede, J. Lau, D. Ahn, N. Sanchez, M. T. Temple, J. Tuckwell, A. Fuchs, N. V. Cianci, G. Riva, L. Curry, H. Yin, X. Gambut, S. Simons, L. M. Hultquist, J. F. Koenig, R. Xiong, Y. Garcia-Sastre, A. BÖcking, T. Hope, T. J. Chanda, S. 2022-01-10 doi:10.1101/2022.01.10.472699 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ 40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds. ]]> https://biorxiv.org/content/10.1101/2022.01.11.475364v1?rss=1 Benito, J. Chen, A. Wilson, L. E. Bhullar, B.-A. S. Burnham, D. Field, D. J. 2022-01-12 doi:10.1101/2022.01.11.475364 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae) ]]> https://biorxiv.org/content/10.1101/2022.01.11.475856v1?rss=1 Dornburg, A. Zapfe, K. Williams, R. Alfaro, M. Morris, R. Adachi, H. Flores, J. Santini, F. Near, T. Frederich, B. 2022-01-12 doi:10.1101/2022.01.11.475856 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Optimal control methods for nonlinear parameter estimation in biophysical neuron models ]]> https://biorxiv.org/content/10.1101/2022.01.11.475951v1?rss=1 Kadakia, N. 2022-01-12 doi:10.1101/2022.01.11.475951 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Emergence of Heartbeat Frailty in Advanced Age: Perspectives from Life-Long EKG Recordings in Mice ]]> https://biorxiv.org/content/10.1101/2022.01.12.475659v1?rss=1 Moen, J. M. Morrell, C. H. Ahmet, I. Matt, M. G. Davoodi, M. Petr, M. Charles, S. deCabo, R. Yaniv, Y. Lakatta, E. G. 2022-01-12 doi:10.1101/2022.01.12.475659 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Epigenetic dysregulation from chromosomal transit in micronuclei ]]> https://biorxiv.org/content/10.1101/2022.01.12.475944v1?rss=1 Agustinus, A. Raviram, R. Dameracharla, B. Luebeck, J. Stransky, S. Scipioni, L. Myers, R. DiBona, M. Duran, M. Weigelt, B. Yomtoubian, S. Toufektchan, E. Mischel, P. Mittal, V. Shah, S. Maciejowski, J. Gratton, E. Ly, P. Bakhoum, M. Landau, D. Bafna, V. Sidoli, S. David, Y. Bakhoum, S. F. 2022-01-12 doi:10.1101/2022.01.12.475944 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Endothelial Nitric Oxide Synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation ]]> https://biorxiv.org/content/10.1101/2022.01.13.476234v1?rss=1 Lee, M. Y. Rahman, N.-T. Sessa, B. 2022-01-16 doi:10.1101/2022.01.13.476234 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Quantitative Models of Lipid Transfer and Membrane Contact Formation ]]> https://biorxiv.org/content/10.1101/2022.01.17.476625v1?rss=1 Zhang, Y. Ge, J. Bian, X. Kumar, A. 2022-01-18 doi:10.1101/2022.01.17.476625 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time ]]> https://biorxiv.org/content/10.1101/2022.01.17.476649v1?rss=1 Corcoran, E. T. LeBlanc, C. Arias Tsang, M. Sarkiss, A. Hu, Y. Pedmale, U. V. Jacob, Y. 2022-01-18 doi:10.1101/2022.01.17.476649 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Microenvironmental sensing by fibroblasts controls macrophage population size ]]> https://biorxiv.org/content/10.1101/2022.01.18.476683v1?rss=1 Zhou, X. Franklin, R. A. Adler, M. Carter, T. S. Condiff, E. Adams, T. S. Pope, S. D. Philip, N. H. Meizlish, M. L. Kaminski, N. S. Medzhitov, R. 2022-01-21 doi:10.1101/2022.01.18.476683 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Bone marrow age dictates clonality of smooth muscle-derived cells in the atherosclerotic plaque ]]> https://biorxiv.org/content/10.1101/2022.01.18.476756v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@12f7090org.highwire.dtl.DTLVardef@186ff92org.highwire.dtl.DTLVardef@1f4da69org.highwire.dtl.DTLVardef@2f509c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kabir, I. Zhang, X. Dave, J. Chakraborty, R. Qu, R. Chandran, R. R. Ntokou, A. Aryal, B. Rotllan, N. Garcia-Milian, R. Hwa, J. Klugar, Y. Martin, K. A. Fernandez-Hernando, C. Greif, D. M. 2022-01-21 doi:10.1101/2022.01.18.476756 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis ]]> https://biorxiv.org/content/10.1101/2022.01.20.477132v1?rss=1 Alfaro-Murillo, J. A. Townsend, J. P. 2022-01-22 doi:10.1101/2022.01.20.477132 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Multi-curve fitting and tubulin-lattice signal removal for structure determination of large microtubule-based motors ]]> https://biorxiv.org/content/10.1101/2022.01.22.477366v1?rss=1 Chai, P. Rao, Q. Zhang, K. 2022-01-23 doi:10.1101/2022.01.22.477366 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES ]]> https://biorxiv.org/content/10.1101/2022.01.23.477401v1?rss=1 Raredon, M. S. B. Yang, J. Kothapalli, N. Kaminski, N. Niklason, L. E. Kluger, Y. 2022-01-24 doi:10.1101/2022.01.23.477401 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Cryo-EM structure of an active central apparatus ]]> https://biorxiv.org/content/10.1101/2022.01.23.477438v1?rss=1 Han, L. Rao, Q. Yang, R. Wang, Y. Chai, P. Xiong, Y. Zhang, K. 2022-01-24 doi:10.1101/2022.01.23.477438 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Hijacking Methyl Reader proteins for Nuclear-Specific Protein Degradation ]]> https://biorxiv.org/content/10.1101/2022.01.24.477424v1?rss=1 Nalawansha, D. A. Li, K. Hines, J. Crews, C. M. 2022-01-27 doi:10.1101/2022.01.24.477424 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Dynamic observation of 2H labeled compounds in the human brain with 1H versus 2H magnetic resonance spectroscopy at 9.4T ]]> https://biorxiv.org/content/10.1101/2022.01.24.477582v1?rss=1 Ruhm, L. Ziegs, T. Wright, A. M. Mathy, C. S. Murali-Manohar, S. Dorst, J. Avdievich, N. Henning, A. 2022-01-27 doi:10.1101/2022.01.24.477582 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ Modeling the longitudinal changes of ancestry diversity in the Million Veteran Program ]]> https://biorxiv.org/content/10.1101/2022.01.24.477583v1?rss=1 Wendt, F. R. Pathak, G. A. Vahey, J. Qin, X. Koller, D. Cabrera-Mendoza, B. Haeny, A. Harrington, K. M. Rajeevan, N. Duong, L. M. Levey, D. F. De Angelis, F. De Lillo, A. Bigdeli, T. B. Pyarajan, S. VA Million Veteran Program, Gaziano, J. M. Gelernter, J. Aslan, M. Provenzale, D. Helmer, D. A. Hauser, E. R. Polimanti, R. Department of Veteran Affairs Cooperative Study Program (#2006), 2022-01-25 doi:10.1101/2022.01.24.477583 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Unadjuvanted intranasal spike vaccine booster elicits robust protective mucosal immunity against sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2022.01.24.477597v1?rss=1 Mao, T. Goldman-Israelow, B. Suberi, A. Zhou, L. reschke, m. pena-hernandez, M. Dong, H. Homer, R. Saltzman, M. Iwasaki, A. 2022-01-26 doi:10.1101/2022.01.24.477597 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Cannabidiol increases gramicidin current in human embryonic kidney cells: An observational study ]]> https://biorxiv.org/content/10.1101/2022.01.24.477627v1?rss=1 Ghovanloo, M. R. Goodchild, S. J. Ruben, P. 2022-01-25 doi:10.1101/2022.01.24.477627 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Face processing in the infant brain after pandemic lockdown ]]> https://biorxiv.org/content/10.1101/2022.01.26.477758v1?rss=1 Repeat), whereas post-lockdown infants showed the opposite (Repeat>Novel), often referred to as repetition enhancement. These findings provide speculative evidence that altered visual experience during the lockdown, or other correlated environmental changes, may have affected face processing in the infant brain. ]]> Yates, T. S. Ellis, C. T. Turk-Browne, N. B. 2022-01-28 doi:10.1101/2022.01.26.477758 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Interaction of the Proline-Rich Domain of Fission Yeast WASp (Ws1p1) with Actin Filaments ]]> https://biorxiv.org/content/10.1101/2022.01.26.477833v1?rss=1 Pollard, T. D. Rosenbloom, A. D. 2022-01-26 doi:10.1101/2022.01.26.477833 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Geographical and ecological drivers of coexistence dynamics in squamate reptiles ]]> https://biorxiv.org/content/10.1101/2022.01.27.478006v1?rss=1 Alencar, L. Quental, T. 2022-01-28 doi:10.1101/2022.01.27.478006 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ In vivo correction of cystic fibrosis mediated by PNA nanoparticles ]]> https://biorxiv.org/content/10.1101/2022.01.28.478191v1?rss=1 Piotrowski-Daspit, A. S. Barone, C. Lin, C.-Y. Deng, Y. Wu, D. Binns, T. C. Xu, E. Ricciardi, A. S. Putman, R. Nguyen, R. Gupta, A. Fan, R. Glazer, P. Saltzman, W. M. Egan, M. E. 2022-01-28 doi:10.1101/2022.01.28.478191 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection ]]> https://biorxiv.org/content/10.1101/2022.01.29.478335v1?rss=1 Greaney, A. M. Raredon, M. S. B. Kochugaeva, M. P. Niklason, L. E. Levchenko, A. 2022-01-31 doi:10.1101/2022.01.29.478335 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Anti-seed PNAs targeting multiple oncomiRs for brain tumor therapy ]]> https://biorxiv.org/content/10.1101/2022.01.31.478549v1?rss=1 120 days). RNA sequencing analysis revealed the role of vascular endothelial growth factor A (VEGFA) and integrin beta 8 (ITGB8), direct targets of both miR-10b and miR-21, in mediating the tumor growth. Hence, we established that BNPs loaded with anti-seed s{gamma}PNAs targeting multiple oncomiRs is a promising approach to improve the treatment of GBM, with a potential to personalize treatment based on tumor specific oncomiRs. SummaryO_ST_ABSTargeting oncomiRs 21 and 10b to improve GBM survivalC_ST_ABSGlioblastoma (GBM) is an aggressive malignant disorder with high recurrence rates and poor survival. Here, we aimed to simultaneously inhibit two aberrant oncomiRs--miR 21 and miR 10b--which have been previously associated with GBM invasiveness and progression. We synthesized short, gamma-modified peptide nucleic acids (s{gamma}PNA) targeted to the miR seed regions and loaded the s{gamma}PNAs into bioadhesive nanoparticles (BNPs). When the s{gamma}PNA-BNPs were added to cultured tumor cells, we observed significant reduction of target oncomiRs and increase of apoptosis in vitro. When delivered in vivo by convection-enhanced delivery, s{gamma}PNA BNPs dramatically increased the survival in two orthotopic (intracranial) mouse models of GBM. Moreover, the combination of s{gamma}PNA BNPs with temozolomide (TMZ) increased the survival of mice with GBM beyond the planned endpoint (120 days) with significant improvements in histopathology. The proposed strategy of s{gamma}PNA BNP with TMZ provides an alternative, promising approach for treatment of GBM. ]]> Wang, Y. Malik, S. Suh, H.-W. Xiao, Y. Deng, Y. Fan, R. Huttner, A. Bindra, R. S. Saltzman, W. M. Bahal, R. 2022-02-01 doi:10.1101/2022.01.31.478549 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Identifying inputs to visual projection neurons in Drosophila lobula by analyzing connectomic data ]]> https://biorxiv.org/content/10.1101/2022.02.02.478876v1?rss=1 Tanaka, R. Clark, D. A. 2022-02-02 doi:10.1101/2022.02.02.478876 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Antibody affinity and concentration of convalescent sera provide context for reduced SARS-CoV-2 Omicron spike affinity of therapeutic antibodies ]]> https://biorxiv.org/content/10.1101/2022.02.03.478946v1?rss=1 Fiedler, S. Devenish, S. R. A. Morgunov, A. S. Ilsley, A. Ricci, F. Emmenegger, M. Kosmoliaptsis, V. Theel, E. S. Mills, J. R. Sholukh, A. M. Aguzzi, A. A. A. Iwasaki, A. Lynn, A. K. Knowles, T. P. J. 2022-02-04 doi:10.1101/2022.02.03.478946 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Physiological causes and biogeographic consequences of thermal optima in the hypoxia tolerance of marine ectotherms ]]> https://biorxiv.org/content/10.1101/2022.02.03.478967v1?rss=1 Endress, M.-G. A. Boag, T. H. Burford, B. P. Penn, J. L. Sperling, E. A. Deutsch, C. A. 2022-02-05 doi:10.1101/2022.02.03.478967 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ VE607 Stabilizes SARS-CoV-2 Spike In the "RBD-up" Conformation and Inhibits Viral Entry ]]> https://biorxiv.org/content/10.1101/2022.02.03.479007v1?rss=1 Ding, S. Gong, S. Y. Grover, J. Mohammadjavad, M. Chen, Y. Vezina, D. Beaudoin-Bussieres, G. Verma, V. T. Goyette, G. Richard, J. Yang, D. Smith, A. B. Pazgier, M. Cote, M. Abrams, C. Mothes, W. Finzi, A. Baron, C. 2022-02-04 doi:10.1101/2022.02.03.479007 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Endothelial beta-arrestins Regulate Mechanotransduction by the Type II Bone Morphogenetic Protein Receptor in Primary Cilia ]]> https://biorxiv.org/content/10.1101/2022.02.04.479175v1?rss=1 Park, S. Ma, Z. Zarkada, G. Papangeli, I. Paluri, S. Nazo, N. Xiong, X. Rivera-Molina, F. Toomre, D. Rajagopal, S. Chun, H. J. 2022-02-05 doi:10.1101/2022.02.04.479175 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Dopamine transporter and synaptic vesicle sorting defects initiate auxilin-linked Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2022.02.04.479203v1?rss=1 Vidyadhara, D. J. Somayaji, M. Wade, N. Yücel, B. Zhao, H. Shashaank, N. Ribaudo, J. Gupta, J. Lam, T. T. Sames, D. Greene, L. E. Sulzer, D. L. Chandra, S. S. 2022-02-06 doi:10.1101/2022.02.04.479203 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects ]]> https://biorxiv.org/content/10.1101/2022.02.07.479293v1?rss=1 Liu, Y. Wang, N. Adams, T. S. Schupp, J. C. Wu, W. McDonough, J. E. Chupp, G. L. Kaminski, N. Wang, Z. Yan, X. 2022-02-10 doi:10.1101/2022.02.07.479293 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Identification of functional Spo0A residues critical for sporulation in Clostridioides difficile ]]> https://biorxiv.org/content/10.1101/2022.02.07.479450v1?rss=1 DiCandia, M. A. Edwards, A. N. Jones, J. B. Swaim, G. L. Mills, B. D. McBride, S. M. 2022-02-07 doi:10.1101/2022.02.07.479450 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ ACh signaling modulates activity of the GABAergic signaling network in the basolateral amygdala and behavior in stress-relevant paradigms. ]]> https://biorxiv.org/content/10.1101/2022.02.08.479551v1?rss=1 Mineur, Y. Mose, T. N. Lefoli Maibom, K. Pittenger, S. Soares, A. R. Wu, H. Huang, Y. Picciotto, M. 2022-02-08 doi:10.1101/2022.02.08.479551 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ CD36 homologs determine microbial resistance to the Lyme disease spirochete ]]> https://biorxiv.org/content/10.1101/2022.02.09.479763v1?rss=1 O'Neal, A. J. Singh, N. Forrest, I. S. Rolandelli, A. Wang, X. Shaw, D. K. Young, B. D. Narasimhan, S. Dutta, S. Snyder, G. A. Marnin, L. Butler, L. R. Samaddar, S. Mendes, M. T. Paz, F. E. C. Valencia, L. M. Sundberg, E. J. Fikrig, E. Pal, U. Weber, D. J. Do, R. Pedra, J. H. F. 2022-02-10 doi:10.1101/2022.02.09.479763 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Inactivation of Nphp2 in renal epithelial cells drives infantile nephronophthisis like phenotypes in mouse ]]> https://biorxiv.org/content/10.1101/2022.02.10.479981v1?rss=1 Li, Y. Xu, W. Makova, S. Brueckner, M. Sun, Z. 2022-02-10 doi:10.1101/2022.02.10.479981 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ PP1 inhibitor-2 promotes PP1γ positive regulation of synaptic transmission ]]> https://biorxiv.org/content/10.1101/2022.02.10.480004v1?rss=1 Foley, K. Altimimi, H. Hou, H. Zhang, Y. McKee, C. Papasergi-Scott, M. M. Yang, H. Mayer, A. Ward, N. MacLean, D. M. Nairn, A. C. Stellwagen, D. Xia, H. 2022-02-11 doi:10.1101/2022.02.10.480004 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Clock Work: Deconstructing the Epigenetic Clock Signals in Aging, Disease, and Reprogramming ]]> https://biorxiv.org/content/10.1101/2022.02.13.480245v1?rss=1 Levine, M. Higgins-Chen, A. T. Thrush, K. Minteer, C. J. Niimi, P. 2022-02-15 doi:10.1101/2022.02.13.480245 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Diversity begets diversity under microbial niche construction ]]> https://biorxiv.org/content/10.1101/2022.02.13.480281v1?rss=1 Estrela, S. Diaz-Colunga, J. Vila, J. C. C. Sanchez-Gorostiaga, A. Sanchez, A. 2022-02-15 doi:10.1101/2022.02.13.480281 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Single-cell transcriptomic and proteomic analysis of Parkinson's disease Brains ]]> https://biorxiv.org/content/10.1101/2022.02.14.480397v1?rss=1 Zhu, B. Park, J.-M. Coffey, S. Hsu, I.-U. Lam, T. T. Gopal, P. P. Ginsberg, S. D. Wang, J. Su, C. Zhao, H. Hafler, D. A. Chandra, S. Zhang, L. 2022-02-14 doi:10.1101/2022.02.14.480397 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Dissociable roles of theta and alpha in sub-second and supra-second time reproduction:An investigation of their links to depression and anxiety ]]> https://biorxiv.org/content/10.1101/2022.02.14.480446v1?rss=1 Liang, M. Lomayesva, S. Isham, E. 2022-02-16 doi:10.1101/2022.02.14.480446 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ SARS-CoV-2 Omicron-specific mRNA vaccine induces potent and broad antibody responses in vivo ]]> https://biorxiv.org/content/10.1101/2022.02.14.480449v1?rss=1 40-fold reduction in neutralization potency against Omicron variant than that against WT two weeks post second dose, which further reduced to background level >3 months post second dose. As a booster shot for two-dose WT mRNA vaccinated mice, a single dose of either a homologous booster with WT LNP-mRNA or a heterologous booster with Omicron LNP-mRNA restored the waning antibody response against Omicron, with over 40-fold increase at two weeks post injection as compared to right before booster. Interestingly, the heterologous Omicron LNP-mRNA booster elicited neutralizing titers 10-20 fold higher than the homologous WT booster against the Omicron variant, with comparable titers against the Delta variant. All three types of vaccination, including Omicron mRNA alone, WT mRNA homologous booster, and Omicron heterologous booster, elicited broad binding antibody responses against SARS-CoV-2 WA-1, Beta, and Delta variants, as well as other Betacoronavirus species such as SARS-CoV, but not Middle East respiratory syndrome coronavirus (MERS-CoV). These data provided direct proof-of-concept assessments of an Omicron-specific mRNA vaccination in vivo, both alone and as a heterologous booster to the existing widely-used WT mRNA vaccine form. ]]> Fang, Z. Peng, L. Lin, Q. Ren, P. Suzuki, K. Xiong, Q. Clark, P. Lin, C. Chen, S. 2022-02-15 doi:10.1101/2022.02.14.480449 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Comparative evaluation of glomerular morphometric techniques reveals differential technical artefacts between FSGS and normal glomeruli ]]> https://biorxiv.org/content/10.1101/2022.02.15.480420v1?rss=1 Basgen, J. M. Reghuvaran, A. C. Lin, Q. Banu, K. Shi, H. Pell, J. DiRito, J. Tietjen, G. T. Perincheri, S. Moledina, D. G. Wilson, F. P. Menon, M. C. 2022-02-18 doi:10.1101/2022.02.15.480420 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ scDVF: Data-driven Single-cell Transcriptomic Deep Velocity Field Learning with Neural Ordinary Differential Equations ]]> https://biorxiv.org/content/10.1101/2022.02.15.480564v1?rss=1 Chen, Z. King, W. C. Gerstein, M. Zhang, J. 2022-02-19 doi:10.1101/2022.02.15.480564 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Contribution of individual excitatory synapses on dendritic spines to electrical signaling ]]> https://biorxiv.org/content/10.1101/2022.02.15.480607v1?rss=1 Weng, J.-Y. Ceballos, C. Zecevic, D. 2022-02-17 doi:10.1101/2022.02.15.480607 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay ]]> https://biorxiv.org/content/10.1101/2022.02.17.480814v1?rss=1 Thoreen, C. van den Elzen, A. Watson, M. 2022-02-18 doi:10.1101/2022.02.17.480814 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ Distributed network processes account for the majority of variance in localized visual category selectivity ]]> https://biorxiv.org/content/10.1101/2022.02.19.481103v1?rss=1 Cocuzza, C. V. Sanchez-Romero, R. Ito, T. Mill, R. D. Keane, B. P. Cole, M. W. 2022-02-22 doi:10.1101/2022.02.19.481103 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ When Vibrios Take Flight: A Meta-analysis of Pathogenic Vibrios Species in Wild and Domestic Birds ]]> https://biorxiv.org/content/10.1101/2022.02.19.481111v1?rss=1 Ayala, A. J. Ogbunugafor, C. B. 2022-02-20 doi:10.1101/2022.02.19.481111 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Structural and Functional Characterization of Novel Phosphotyrosine Phosphatase Protein from Drosophila Melanogaster (Pupal Retina) ]]> https://biorxiv.org/content/10.1101/2022.02.19.481152v1?rss=1 Naz, R. Iqbal, A. Saeed, A. Khan, A. Shutaywi, M. VRINCEANU, N. Cioca, A. L. 2022-02-20 doi:10.1101/2022.02.19.481152 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ HIV-1 Vpu restricts Fc-mediated effector functions in vivo ]]> https://biorxiv.org/content/10.1101/2022.02.21.481308v1?rss=1 Prevost, J. Anand, S. P. Rajashekar, J. K. Richard, J. Goyette, G. Medjahed, H. Gendron-Lepage, G. Chen, H.-C. Chen, Y. Horwitz, J. A. Grunst, M. W. Zolla-Pazner, S. Haynes, B. F. Burton, D. R. Flavell, R. A. Kirchhoff, F. Hahn, B. H. Smith, A. B. Pazgier, M. Nussenzweig, M. C. Kumar, P. Finzi, A. 2022-02-22 doi:10.1101/2022.02.21.481308 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ 3D bioprinting of an implantable xeno-free vascularized human skin graft ]]> https://biorxiv.org/content/10.1101/2022.02.21.481363v1?rss=1 Baltazar, T. Jiang, B. Moncayo, A. Merola, J. Albanna, M. Z. Saltzman, W. M. Pober, J. S. 2022-02-22 doi:10.1101/2022.02.21.481363 Cold Spring Harbor Laboratory Press 2022-02-22 <![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[ Chronic Glucocorticoid Stress Reveals Increased Energy Expenditure and Accelerated Aging as Cellular Features of Allostatic Load ]]> https://biorxiv.org/content/10.1101/2022.02.22.481548v1?rss=1 Bobba-Alves, N. Sturm, G. Lin, J. Ware, S. A. Karan, K. R. Monzel, A. S. Bris, C. Procaccio, V. Lenaers, G. Higgins-Chen, A. Levine, M. Horvath, S. Santhanam, B. S. Kaufman, B. A. Hirano, M. Epel, E. S. Picard, M. 2022-02-23 doi:10.1101/2022.02.22.481548 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Distinct glycerophospholipids potentiate Gsα-activated adenylyl cyclase activity ]]> https://biorxiv.org/content/10.1101/2022.02.23.481604v1?rss=1 Seth, A. Landau, M. Shevchenko, A. Traikov, S. Schultz, A. Elsabbagh, S. Schultz, J. E. 2022-02-24 doi:10.1101/2022.02.23.481604 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Hypoconnectivity between anterior insula and amygdala in neonates with familial history of autism ]]> https://biorxiv.org/content/10.1101/2022.02.24.481850v1?rss=1 Scheinost, D. Chang, J. Lacadie, C. Brennan-Wydra, E. Foster, R. Boxberger, A. Macari, S. Vernetti, A. Constable, R. T. Ment, L. R. Chawarska, K. 2022-02-27 doi:10.1101/2022.02.24.481850 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Human neutrophil development and functionality are enabled in a humanized mouse model ]]> https://biorxiv.org/content/10.1101/2022.02.25.481352v1?rss=1 Zheng, Y. Sefik, E. Astle, J. Solis, A. G. Oz, H. H. Jackson, R. Bruscia, E. M. Halene, S. Shan, L. Flavell, R. A. 2022-02-25 doi:10.1101/2022.02.25.481352 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ In utero delivery of miRNA induces epigenetic alterations and corrects pulmonary pathology in congenital diaphragmatic hernia ]]> https://biorxiv.org/content/10.1101/2022.02.27.482144v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@3531caorg.highwire.dtl.DTLVardef@57ff5aorg.highwire.dtl.DTLVardef@13d6ee9org.highwire.dtl.DTLVardef@3cb3d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Stitelman, D. Ullrich, S. Yung, N. Bauer-Pisani, T. Maassel, N. Guerra, M. E. Freedman-Weiss, M. Ahle, S. Ricciardi, A. Sauler, M. Saltzman, W. M. Piotrowski-Daspit, A. 2022-03-01 doi:10.1101/2022.02.27.482144 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Aging the Brain: Multi-Region Methylation Principal Component Based Clock in the Context of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.02.28.481849v1?rss=1 Thrush, K. L. Bennett, D. A. Gaiteri, C. Horvath, S. van Dyck, C. H. Higgins-Chen, A. T. Levine, M. E. 2022-03-03 doi:10.1101/2022.02.28.481849 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Orthogonal synthetases for polyketide precursors ]]> https://biorxiv.org/content/10.1101/2022.02.28.482149v1?rss=1 Schepartz, A. Fricke, R. Swenson, C. Roe, L. T. Hamlish, N. Ad, O. Smaga, S. Gee, C. L. 2022-03-01 doi:10.1101/2022.02.28.482149 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Connexin 43-mediated Neurovascular Interactions Regulate Neurogenesis in the Adult Brain Subventricular Zone ]]> https://biorxiv.org/content/10.1101/2022.02.28.482353v1?rss=1 Genet, N. Genet, G. Fang, J. S. Chavkin, N. W. Vasavada, H. H. Goldberg, J. S. Acharya, B. R. Bhatt, N. Baker, K. McDonnell, S. Huba, M. R. Ma, G. Eichmann, A. Thomas, J. L. ffrench-constant, C. Hirschi, K. K. 2022-03-01 doi:10.1101/2022.02.28.482353 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Hedgehog signaling is non-cell autonomously activated in the cystic kidney of Arl13b mutant mice ]]> https://biorxiv.org/content/10.1101/2022.02.28.482403v1?rss=1 Hsieh, C.-L. Jerman, S. J. Sun, Z. 2022-03-01 doi:10.1101/2022.02.28.482403 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Synergistic effect of mutations in the Parkinson's disease-linked proteins synaptojanin 1 and auxilin ]]> https://biorxiv.org/content/10.1101/2022.02.28.482419v1?rss=1 Ng, X. Y. Wu, Y. Lin, Y. Yaqoob, S. M. Greene, L. E. De Camilli, P. Cao, M. 2022-03-02 doi:10.1101/2022.02.28.482419 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Insights of the role of estrogen in obesity from two models of ERα deletion ]]> https://biorxiv.org/content/10.1101/2022.03.01.482291v1?rss=1 Saavedra-Pena, R. D. Taylor, N. Rodeheffer, M. S. 2022-03-03 doi:10.1101/2022.03.01.482291 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Single cell atlas of the neonatal small intestine with necrotizing enterocolitis ]]> https://biorxiv.org/content/10.1101/2022.03.01.482508v1?rss=1 Egozi, A. Olaloye, O. Werner, L. Silva, T. McCourt, B. Pierce, R. An, X. Wang, F. Chen, K. Pober, J. Shouval, D. Itzkovitz, S. Konnikova, L. 2022-03-02 doi:10.1101/2022.03.01.482508 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing ]]> https://biorxiv.org/content/10.1101/2022.03.01.482553v1?rss=1 Buhagiar, A. F. McCool, M. A. Bryant, C. J. Abriola, L. Surovtseva, Y. V. Baserga, S. J. 2022-03-01 doi:10.1101/2022.03.01.482553 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Double knockout CRISPR screen in cancer resistance to T cell cytotoxicity ]]> https://biorxiv.org/content/10.1101/2022.03.01.482556v1?rss=1 Park, J. Codina, A. Ye, L. Lam, S. Guo, J. Clark, P. Zhou, X. Peng, L. Chen, S. 2022-03-02 doi:10.1101/2022.03.01.482556 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Amplification of Olfactory Signals by Anoctamin 9 is Essential for Mammalian Olfaction: a Risk Factor for the Covid-19-associated Anosmia ]]> https://biorxiv.org/content/10.1101/2022.03.02.482745v1?rss=1 Kim, H. Kim, H. Nguyen, L. T. Ha, T. Lim, S. Kim, K. Kim, S. H. Han, K. Hyeon, S. J. Ryu, H. Park, Y. S. Kim, S. H. Kim, I.-B. Hong, G.-S. Lee, S. E. Choi, Y. Cohen, L. B. Oh, U. 2022-03-03 doi:10.1101/2022.03.02.482745 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Modernizing the NEURON Simulator for Sustainability, Portability, and Performance ]]> https://biorxiv.org/content/10.1101/2022.03.03.482816v1?rss=1 Awile, O. Kumbhar, P. Cornu, N. Dura-Bernal, S. King, J. G. Lupton, O. Magkanaris, I. McDougal, R. A. Newton, A. J. H. Pereira, F. Savulescu, A. Carnevale, N. T. Lytton, W. W. Hines, M. L. Schürmann, F. 2022-03-04 doi:10.1101/2022.03.03.482816 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Stress promotes RNA G-quadruplex folding in human cells ]]> https://biorxiv.org/content/10.1101/2022.03.03.482884v1?rss=1 Kharel, P. Fay, M. Manasova, E. Anderson, P. Kurkin, A. Guo, J. Ivanov, P. 2022-03-03 doi:10.1101/2022.03.03.482884 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Structural basis of flagellar filament asymmetry and supercoil templating by Leptospira spirochete sheath proteins ]]> https://biorxiv.org/content/10.1101/2022.03.03.482903v1?rss=1 Brady, M. R. San Martin, F. Debs, G. E. Gibson, K. H. Rodriguez, A. Duran, R. Wunder, E. Ko, A. Buschiazzo, A. Sindelar, C. V. 2022-03-03 doi:10.1101/2022.03.03.482903 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ Neural representations of vicarious rewards are linked to interoception and prosocial behaviour ]]> https://biorxiv.org/content/10.1101/2022.03.04.482889v1?rss=1 Contreras-Huerta, L. S. Coll, M.-P. Bird, G. Yu, H. Prosser, A. Lockwood, P. L. Murphy, J. Crockett, M. J. Apps, M. A. J. 2022-03-05 doi:10.1101/2022.03.04.482889 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Incorporating the image formation process into deep learning improves network performance in deconvolution applications ]]> https://biorxiv.org/content/10.1101/2022.03.05.483139v1?rss=1 Li, Y. Su, Y. Guo, M. Han, X. Liu, J. Vishwasrao, H. Li, X. Christensen, R. Sengupta, T. Moyle, M. Chen, J. Usdin, T. B. Colon-Ramos, D. Liu, H. Wu, Y. Shroff, H. 2022-03-06 doi:10.1101/2022.03.05.483139 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ Automated assembly of high-quality diploid human reference genomes ]]> https://biorxiv.org/content/10.1101/2022.03.06.483034v1?rss=1 Jarvis, E. D. Formenti, G. Rhie, A. Guarracino, A. Yang, C. Wood, J. Tracey, A. Thibaud-Nissen, F. Vollger, M. R. Porubsky, D. Cheng, H. Asri, M. Logsdon, G. A. Carnevali, P. Chaisson, M. Chin, C.-S. Cody, S. Collins, J. Ebert, P. Escalona, M. Fedrigo, O. Fulton, R. S. Fulton, L. L. Garg, S. Ghurye, J. Green, E. Hall, I. M. Harvey, W. H. Hasenfeld, P. Hastie, A. Haukness, M. Jain, M. Kirsche, M. Kolmogorov, M. Korbel, J. O. Koren, S. Korlach, J. Lee, J. Li, D. Lindsay, T. Lucas, J. Luo, F. Marschall, T. McDaniel, J. Nie, F. Olsen, H. E. Olson, N. 2022-03-06 doi:10.1101/2022.03.06.483034 Cold Spring Harbor Laboratory Press 2022-03-06 <![CDATA[ In situ architecture of the lipid transport protein VPS13C at ER-lysosomes membrane contacts ]]> https://biorxiv.org/content/10.1101/2022.03.08.482579v1?rss=1 Cai, S. Wu, Y. Guillen-Samander, A. Hancock-Cerutti, W. F. Liu, J. De Camilli, P. 2022-03-08 doi:10.1101/2022.03.08.482579 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Comparison of individualized behavioral predictions across anatomical, diffusion and functional connectivity MRI ]]> https://biorxiv.org/content/10.1101/2022.03.08.483564v1?rss=1 Ooi, L. Q. R. Chen, J. Zhang, S. Kong, R. Tam, A. Li, J. Dhamala, E. Zhou, J. H. Holmes, A. Yeo, B. T. T. 2022-03-10 doi:10.1101/2022.03.08.483564 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Activation of targetable inflammatory immune signaling is seen in Myelodysplastic Syndromes with SF3B1 mutations ]]> https://biorxiv.org/content/10.1101/2022.03.09.483595v1?rss=1 Choudhary, G. Pellagatti, A. Agianian, B. Smith, M. Bhagat, T. D. Gordon-Mitchell, S. Pandey, S. Shah, N. Aluri, S. Schwartz, L. Steeples, V. Booher, R. Ramachandra, M. Samson, M. Carbajal, M. Pradhan, K. Bowman, T. Pillai, M. M. Will, B. Wickrema, A. Shastri, A. Bradley, R. K. Martell, R. E. Steidl, U. Gavathiotis, E. Boultwood, J. Starczynowski, D. T. Verma, A. 2022-03-09 doi:10.1101/2022.03.09.483595 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ Structural and biochemical insights into lipid transport by VPS13 proteins. ]]> https://biorxiv.org/content/10.1101/2022.03.11.484024v1?rss=1 Adlakha, J. Hong, Z. Li, P. Reinisch, k. M. 2022-03-12 doi:10.1101/2022.03.11.484024 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ In vitro engineering of the lung alveolus ]]> https://biorxiv.org/content/10.1101/2022.03.13.484143v1?rss=1 Leiby, K. L. Yuan, Y. Ng, R. Raredon, M. S. B. Adams, T. S. Baevova, P. Hirschi, K. K. Campbell, S. G. Kaminski, N. Herzog, E. L. Niklason, L. E. 2022-03-14 doi:10.1101/2022.03.13.484143 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Temporal dynamics of competition between statistical learning and episodic memory in intracranial recordings of human visual cortex ]]> https://biorxiv.org/content/10.1101/2022.03.14.484293v1?rss=1 Sherman, B. E. Graves, K. N. Huberdeau, D. M. Quraishi, I. H. Damisah, E. C. Turk-Browne, N. B. 2022-03-16 doi:10.1101/2022.03.14.484293 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Proportional intracranial volume correction differentially biases behavioral predictions across neuroanatomical features and populations ]]> https://biorxiv.org/content/10.1101/2022.03.15.483970v1?rss=1 Dhamala, E. Ooi, L. Q. R. Chen, J. Kong, R. Anderson, K. Chin, R. Yeo, B. T. T. Holmes, A. 2022-03-17 doi:10.1101/2022.03.15.483970 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Growth inhibition of Akkermansia muciniphila by a secreted pathobiont sialidase ]]> https://biorxiv.org/content/10.1101/2022.03.15.484512v1?rss=1 van Muijlwijk, G. H. Bröring, E. van Mierlo, G. Jansen, P. W. Vermeulen, M. Aerts, P. C. van Putten, J. P. Palm, N. W. de Zoete, M. R. 2022-03-15 doi:10.1101/2022.03.15.484512 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ A systematic comparison of current bioinformatic tools for glycoproteomics data ]]> https://biorxiv.org/content/10.1101/2022.03.15.484528v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@17c371forg.highwire.dtl.DTLVardef@70532org.highwire.dtl.DTLVardef@e640b7org.highwire.dtl.DTLVardef@a2bb26_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rangel-Angarita, V. Mahoney, K. E. Ince, D. Malaker, S. A. 2022-03-18 doi:10.1101/2022.03.15.484528 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Potent and specific human monoclonal antibodies against SARS-CoV-2 Omicron variant by rapid mRNA immunization of humanized mice ]]> https://biorxiv.org/content/10.1101/2022.03.17.484817v1?rss=1 Ren, P. Peng, L. Fang, Z. Suzuki, K. Renauer, P. A. Lin, Q. Bai, M. Yang, L. Li, T. Clark, P. Klein, D. Chen, S. 2022-03-18 doi:10.1101/2022.03.17.484817 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Shared and distinct brain regions targeted for immediate early gene expression by ketamine and psilocybin ]]> https://biorxiv.org/content/10.1101/2022.03.18.484437v1?rss=1 Davoudian, P. A. Shao, L.-X. Kwan, A. C. 2022-03-20 doi:10.1101/2022.03.18.484437 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ ASD modelling in organoids reveals imbalance of excitatory cortical neuron subtypes during early neurogenesis ]]> https://biorxiv.org/content/10.1101/2022.03.19.484988v1?rss=1 Jourdon, A. Wu, F. Mariani, J. Capauto, D. Norton, S. Tomasini, L. Amiri, A. Suvakov, M. Schreiner, J. Jang, Y. Nguyen, C. K. Cummings, E. M. Han, G. Powell, K. Szekely, A. McPartland, J. C. Pelphrey, K. Chawarska, K. Ventola, P. Abyzov, A. Vaccarino, F. M. 2022-03-20 doi:10.1101/2022.03.19.484988 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Stroke disconnectome decodes reading networks ]]> https://biorxiv.org/content/10.1101/2022.03.20.485029v1?rss=1 Forkel, S. J. Labache, L. Nachev, P. Thiebaut de Schotten, M. Hesling, I. 2022-03-21 doi:10.1101/2022.03.20.485029 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Regulation of EGF-stimulated activation of the PI-3K/AKT pathway by exocyst-mediated exocytosis ]]> https://biorxiv.org/content/10.1101/2022.03.21.485168v1?rss=1 An, S. Anneken, A. Xi, Z. Choi, C. Schlessinger, J. Toomre, D. 2022-03-21 doi:10.1101/2022.03.21.485168 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2022.03.21.485199v1?rss=1 Ravi, A. Gainor, J. F. Arniella, M. B. Holton, M. Freeman, S. S. Stewart, C. Leshchiner, I. Kim, J. Akiyama, Y. Griffin, A. T. Vokes, N. I. Sakhi, M. Kamesan, V. Rizvi, H. Ricciuti, B. Forde, P. M. Anagnostou, V. Reiss, J. W. Gibbons, D. L. Pennell, N. A. Velcheti, V. Digumarthy, S. R. Mino-Kenudson, M. Califano, A. Heymach, J. V. Herbst, R. S. Brahmer, J. R. Schalper, K. A. Velculescu, V. E. Henick, B. S. Rizvi, N. Janne, P. A. Awad, M. M. Chow, A. Greenbaum, B. D. Luksza, M. Shaw, A. T. Wolchok, J. Hacohen, N. Getz, G. Hellmann, M. D. 2022-03-23 doi:10.1101/2022.03.21.485199 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Inhalable polymer nanoparticles for versatile mRNA delivery and mucosal vaccination ]]> https://biorxiv.org/content/10.1101/2022.03.22.485401v1?rss=1 Suberi, A. Grun, M. K. Mao, T. Goldman-Israelow, B. Reschke, M. Grundler, J. Akhtar, L. Lee, T. Shin, K. Piotrowski-Daspit, A. S. Homer, R. Iwasaki, A. Suh, H. W. Saltzman, W. M. 2022-03-23 doi:10.1101/2022.03.22.485401 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2 ]]> https://biorxiv.org/content/10.1101/2022.03.22.485418v1?rss=1 Fang, Z. Peng, L. Lin, Q. Zhou, L. Yang, L. Feng, Y. Ren, P. Renauer, P. A. Park, J. J. Zhou, X. Wilen, C. B. Chen, S. 2022-03-23 doi:10.1101/2022.03.22.485418 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ HALO: A software tool for real-time head alignment in the MR scanner ]]> https://biorxiv.org/content/10.1101/2022.03.23.485491v1?rss=1 Zhao, Z. Galiana, G. Zillo, C. Camarro, T. Qiu, M. Papademetris, X. Hampson, M. 2022-03-27 doi:10.1101/2022.03.23.485491 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Transcriptome of epibiont Saccharibacteria Nanosynbacter lyticus strain TM7x during establishment of symbiosis ]]> https://biorxiv.org/content/10.1101/2022.03.25.485537v1?rss=1 Hendrickson, E. L. Batbileg, B. Kristopher, K. A. Lamont, E. I. Cen, L. Chang, Y. Liu, J. Shi, W. He, X. McLean, J. S. 2022-03-26 doi:10.1101/2022.03.25.485537 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Localized and Distributed Representations of Person Knowledge for Faces ]]> https://biorxiv.org/content/10.1101/2022.03.27.485948v1?rss=1 Shehzad, Z. Taylor, J. McCarthy, G. 2022-03-28 doi:10.1101/2022.03.27.485948 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Local 5-HT signal bi-directionally regulates the coincidence time window of associative learning ]]> https://biorxiv.org/content/10.1101/2022.03.27.485970v1?rss=1 Zeng, J. Li, X. Zhangren, Z. Lv, M. Wang, Y. Tan, K. Xia, X. Wan, J. Jing, M. Yang, Y. Li, Y. Li, Y. 2022-03-27 doi:10.1101/2022.03.27.485970 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ The force required to remove tubulin from the microtubule lattice ]]> https://biorxiv.org/content/10.1101/2022.03.28.486117v1?rss=1 Kuo, Y.-W. Mahamdeh, M. S. S. Tuna, Y. Howard, J. 2022-03-29 doi:10.1101/2022.03.28.486117 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Glia-neuron coupling via a bipartite sialylation pathway promotes neural transmission and stress tolerance in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.03.29.486211v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@15b8de3org.highwire.dtl.DTLVardef@1c037e8org.highwire.dtl.DTLVardef@9674bborg.highwire.dtl.DTLVardef@1c9c010_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Scott, H. Novikov, B. Ugur, B. Allen, B. Mertsalov, I. Monagas-Valentin, P. Koff, M. Baas Robinson, S. Aoki, K. Veizaj, R. Lefeber, D. Tiemeyer, M. Bellen, H. J. Panin, V. 2022-03-29 doi:10.1101/2022.03.29.486211 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Optimal inference of molecular interactions in live FRET imaging ]]> https://biorxiv.org/content/10.1101/2022.03.29.486267v1?rss=1 Kamino, K. Kadakia, N. Aoki, K. Shimizu, T. S. Emonet, T. 2022-03-30 doi:10.1101/2022.03.29.486267 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Convergent impact of schizophrenia risk genes ]]> https://biorxiv.org/content/10.1101/2022.03.29.486286v1?rss=1 Townsley, K. G. Li, A. Deans, P. M. Fullard, J. F. Yu, A. Cartwright, S. Zhang, W. Wang, M. Voloudakis, G. Girdhar, K. Stahl, E. Akbarian, S. Zhang, B. Roussos, P. Huckins, L. M. Brennand, K. J. 2022-03-30 doi:10.1101/2022.03.29.486286 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ A partnership of the lipid scramblase XK and of the lipid transfer protein VPS13A at the plasma membrane ]]> https://biorxiv.org/content/10.1101/2022.03.30.486314v1?rss=1 Guillen-Samander, A. Wu, Y. Pineda, S. S. Garcia, F. J. Eisen, J. N. Leonzino, M. Ugur, B. Kellis, M. Heiman, M. De Camilli, P. 2022-03-30 doi:10.1101/2022.03.30.486314 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation ]]> https://biorxiv.org/content/10.1101/2022.03.30.486357v1?rss=1 Yan, Q. Chen, J. F.-Y. Cai, W. Chen, H. Wingrove, E. Kurley, S. Chan, L. H. Zhang, M. Arnal-Estape, A. Zhao, M. Balabaki, A. Li, W. Yu, X. Dou, Y. Liu, Y. Jin, J. Westbrook, T. F. Nguyen, D. 2022-03-30 doi:10.1101/2022.03.30.486357 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Constitutive, calcium-independent endoplasmic reticulum-plasma membrane contact site oscillations and its implications in store-operated calcium entry ]]> https://biorxiv.org/content/10.1101/2022.03.30.486443v1?rss=1 Xiong, D. Tong, C. Yang, Y. Yong, J. Wu, M. 2022-03-30 doi:10.1101/2022.03.30.486443 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences ]]> https://biorxiv.org/content/10.1101/2022.03.30.486449v1?rss=1 Gurun, B. Horton, W. Murugan, D. Zhu, B. Leyshock, P. Kumar, S. Byrne, K. T. Vonderheide, R. H. Margolin, A. A. Mori, M. Spellman, P. T. Coussens, L. M. Speed, T. P. 2022-04-01 doi:10.1101/2022.03.30.486449 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ OTTERS: A powerful TWAS framework leveraging summary-level reference data ]]> https://biorxiv.org/content/10.1101/2022.03.30.486451v1?rss=1 Dai, Q. Zhou, G. Zhao, H. Vosa, U. Franke, L. Battle, A. Teumer, A. Lehtimaki, T. Raitakari, O. Esko, T. eQTLGen Consortium, Epstein, M. P. Yang, J. 2022-04-01 doi:10.1101/2022.03.30.486451 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Human iPSC-Vascular Smooth Muscle Cell Spheroids Demonstrate Size-dependent Alterations in Cellular Viability and Secretory Function ]]> https://biorxiv.org/content/10.1101/2022.03.31.486610v1?rss=1 Islam, S. Parker, J. Dash, B. C. Hsia, H. 2022-04-01 doi:10.1101/2022.03.31.486610 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping ]]> https://biorxiv.org/content/10.1101/2022.04.01.486788v1?rss=1 Liu, Y. Distasio, M. Su, G. Asashima, H. Enninful, A. Qin, X. Deng, Y. Bordignon, P. Cassano, M. Tomayko, M. Xu, M. L. Halene, S. Craft, J. E. Hafler, D. A. Fan, R. 2022-04-02 doi:10.1101/2022.04.01.486788 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Pathogenic variants of sphingomyelin synthase SMS2 disrupt lipid landscapes in the secretory pathway ]]> https://biorxiv.org/content/10.1101/2022.04.02.486804v1?rss=1 Sokoya, T. Parolek, J. Foged, M. M. Danylchuk, D. I. Bozan, M. Sarkar, B. Hilderink, A. Philippi, M. Botto, L. D. Terhal, P. A. Maekitie, O. Piehler, J. Kim, Y. Burd, C. G. Klymchenko, A. S. Maeda, K. Holthuis, J. C. M. 2022-04-03 doi:10.1101/2022.04.02.486804 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Computational design and construction of an Escherichia coli strain engineered to produce a non-standard amino acid ]]> https://biorxiv.org/content/10.1101/2022.04.02.486821v1?rss=1 Zomorrodi, A. R. Hemez, C. Arranz-Gibert, P. Wu, T. Isaacs, F. J. Segre, D. 2022-04-02 doi:10.1101/2022.04.02.486821 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ All-optical visualization of specific molecules in the ultrastructural context of brain tissue ]]> https://biorxiv.org/content/10.1101/2022.04.04.486901v1?rss=1 M'Saad, O. Kasula, R. Kondratiuk, I. Kidd, P. Falahati, H. Gentile, J. E. Niescier, R. F. Watters, K. Sterner, R. C. Lee, S. Liu, X. De Camilli, P. Rothman, J. E. Koleske, A. J. Biederer, T. Bewersdorf, J. 2022-04-05 doi:10.1101/2022.04.04.486901 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons. ]]> https://biorxiv.org/content/10.1101/2022.04.05.487209v1?rss=1 Barrett, A. Varol, E. Weinreb, A. Taylor, S. R. McWhirter, R. Cros, C. Basavaraju, M. Poff, A. Tipps, J. A. Majeed, M. Vidal, B. Wang, C. Yemini, E. Bayer, E. A. Sun, H. Hobert, O. Miller, D. M. Hammarlund, M. 2022-04-08 doi:10.1101/2022.04.05.487209 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Platelet response to influenza vaccination reflects effects of aging ]]> https://biorxiv.org/content/10.1101/2022.04.06.487196v1?rss=1 Konstorum, A. Mohanty, S. Zhao, Y. Melillo, A. Vander Wyk, B. Nelson, A. Tsang, S. Blevins, T. P. Belshe, R. B. Chawla, D. G. Rondina, M. T. Montgomery, R. R. Allore, H. G. Kleinstein, S. H. Shaw, A. C. 2022-04-09 doi:10.1101/2022.04.06.487196 Cold Spring Harbor Laboratory Press 2022-04-09 <![CDATA[ Structural insights into sodium/iodide symporter (NIS) substrate binding and specificity ]]> https://biorxiv.org/content/10.1101/2022.04.07.487502v1?rss=1 Ravera, S. Nicola, J. P. Salazar de Simone, G. Sigworth, F. J. Karakas, E. Amzel, L. M. Bianchet, M. A. Carrasco, N. 2022-04-08 doi:10.1101/2022.04.07.487502 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Dyslexia associated gene, KIAA0319, regulates cell cycle during human neuroepithelium development ]]> https://biorxiv.org/content/10.1101/2022.04.07.487504v1?rss=1 Paniagua, S. Cakir, B. Hu, Y. Kiral, F. R. Tanaka, Y. Xiang, Y. Patterson, B. Gruen, J. R. Park, I.-H. 2022-04-08 doi:10.1101/2022.04.07.487504 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Periodic Environmental Disturbance Drives Repeated Ecomorphological Diversification in an Adaptive Radiation of Antarctic Fishes ]]> https://biorxiv.org/content/10.1101/2022.04.08.487509v1?rss=1 Parker, E. Zapfe, K. L. Yadav, J. Frederich, B. Jones, C. D. Economo, E. P. Federman, S. Near, T. J. Dornburg, A. 2022-04-10 doi:10.1101/2022.04.08.487509 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.04.08.487666v1?rss=1 Cotter, K. A. Shah, S. R. Paramo, M. I. Lou, S. Yao, L. Rubin, P. D. Chen, Y. Gerstein, M. Rubin, M. Yu, H. 2022-04-10 doi:10.1101/2022.04.08.487666 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Multimodal single cell data integration challenge: results and lessons learned ]]> https://biorxiv.org/content/10.1101/2022.04.11.487796v1?rss=1 Lance, C. Luecken, M. D. Burkhardt, D. B. Cannoodt, R. Rautenstrauch, P. Laddach, A. C. Ubingazhibov, A. Cao, Z.-J. Deng, K. Khan, S. Liu, Q. Russkikh, N. Ryazantsev, G. Ohler, U. NeurIPS 2021 Multimodal data integration competition participants, Pisco, A. O. Bloom, J. M. Krishnaswamy, S. Theis, F. J. 2022-04-12 doi:10.1101/2022.04.11.487796 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Systematic generation and imaging of tandem repeats reveal multivalent base-pairing as a major determinant of RNA aggregation ]]> https://biorxiv.org/content/10.1101/2022.04.11.487960v1?rss=1 Isiktas, A. U. Eshov, A. Yang, S. Guo, J. U. 2022-04-12 doi:10.1101/2022.04.11.487960 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Defining tertiary sulci in lateral prefrontal cortex in chimpanzees using human predictions ]]> https://biorxiv.org/content/10.1101/2022.04.12.488091v1?rss=1 Hathaway, C. Voorhies, W. I. Sathishkumar, N. Mittal, C. Yao, J. K. Miller, J. A. Parker, B. Weiner, K. S. 2022-04-13 doi:10.1101/2022.04.12.488091 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Reduced ventral attention network connectivity is linked to the accelerated maturation of adult-like cortical organization in childhood ]]> https://biorxiv.org/content/10.1101/2022.04.12.488101v1?rss=1 Dong, H. Holmes, A. Zuo, X.-N. 2022-04-13 doi:10.1101/2022.04.12.488101 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Peptidergic signaling controls the dynamics of sickness behavior in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.04.16.488560v1?rss=1 Marquina-Solis, J. Vandewyver, E. Hawk, J. Colon-Ramos, D. Beets, I. Bargmann, C. 2022-04-17 doi:10.1101/2022.04.16.488560 Cold Spring Harbor Laboratory Press 2022-04-17 <![CDATA[ US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes ]]> https://biorxiv.org/content/10.1101/2022.04.18.488565v1?rss=1 ZHANG, C. Shine, M. Pyle, A. M. Zhang, Y. 2022-04-18 doi:10.1101/2022.04.18.488565 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Predicting A/B compartments from histone modifications using deep learning ]]> https://biorxiv.org/content/10.1101/2022.04.19.488754v1?rss=1 Zheng, S. Thakkar, N. Harris, H. L. Zhang, M. Liu, S. Gerstein, M. Aiden, E. L. Rowley, J. Noble, W. S. Gursoy, G. Singh, R. 2022-04-19 doi:10.1101/2022.04.19.488754 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Global and gene-specific translational regulation in Escherichia coli across different conditions ]]> https://biorxiv.org/content/10.1101/2022.04.19.488838v1?rss=1 Zhang, D. Li, S. H.-J. King, C. G. Wingreen, N. S. Gitai, Z. Li, Z. 2022-04-21 doi:10.1101/2022.04.19.488838 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ The Global Register of Introduced and Invasive Species: Country Compendium ]]> https://biorxiv.org/content/10.1101/2022.04.19.488841v1?rss=1 McGeoch, M. A. Pagad, S. Bisset, S. Genovesi, P. Groom, Q. Hirsch, T. Jetz, W. Ranipeta, A. Schigel, D. Sica, Y. V. 2022-04-20 doi:10.1101/2022.04.19.488841 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses ]]> https://biorxiv.org/content/10.1101/2022.04.20.488939v1?rss=1 Hagan, T. Gerristen, B. Tomalin, L. E. Fourati, S. Mule, M. P. Chawla, D. G. Rychkov, D. Henrich, E. Miller, H. E. Diray-Arce, J. Dunn, P. Lee, A. The Human Immunology Project Consortium (HIPC), Levy, O. Gottardo, R. Sarwal, M. M. Tsang, J. Suarez-Farinas, M. Sekaly, R.-P. Kleinstein, S. Pulendran, B. 2022-04-26 doi:10.1101/2022.04.20.488939 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Breakpoint models shown no evidence of thresholds in recreational response to increasing wildfire smoke in the American West ]]> https://biorxiv.org/content/10.1101/2022.04.21.489032v1?rss=1 Clark, M. Killion, A. Williamson, M. A. Hillis, V. 2022-04-21 doi:10.1101/2022.04.21.489032 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ CLASP2 stabilizes GDP-associated terminal tubulins to prevent microtubule catastrophe ]]> https://biorxiv.org/content/10.1101/2022.04.25.489454v1?rss=1 Luo, W. Demidov, V. Shen, Q. Hugo, G. Chakraborty, M. Maiorov, A. Ataullakhanov, F. Lin, C. Maiato, H. Grishchuk, E. 2022-04-25 doi:10.1101/2022.04.25.489454 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Functional genomics analysis identifies impairment of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome. ]]> https://biorxiv.org/content/10.1101/2022.04.26.489616v1?rss=1 Thomson, E. Tran, M. Robevska, G. Ayers, K. Gopalakrishnan Bhaskaran, P. Haan, E. Cereghini, S. Vash-Margita, A. Margetts, M. Hensley, A. Nguyen, Q. Sinclair, A. Koopman, P. Pelosi, E. 2022-04-27 doi:10.1101/2022.04.26.489616 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ StandardRat: A multi-center consensus protocol to enhance functional connectivity specificity in the rat brain ]]> https://biorxiv.org/content/10.1101/2022.04.27.489658v1?rss=1 Grandjean, J. Desrosiers-Gregoire, G. Anckaerts, C. Angeles-Valdez, D. Ayad, F. Barriere, D. A. Blockx, I. Bortel, A. B. Broadwater, M. Cardoso, B. M. Celestine, M. Chavez-Negrete, J. E. Choi, S. Christiaen, E. Clavijo, P. Colon-Perez, L. Cramer, S. Daniele, T. Dempsey, E. Diao, Y. Doelemeyer, A. Dopfel, D. Dvorakova, L. Falfan-Melgoza, C. Fernandes, F. F. Fowler, C. F. Fuentes-Ibanez, A. Garin, C. Gelderman, E. Golden, C. E. Guo, C. C. Henckens, M. J. Hennessy, L. A. Herman, P. Hofwijks, N. Horien, C. Ionescu, T. M. Jones, J. Kaesser, J. Kim, E. Lambers 2022-04-28 doi:10.1101/2022.04.27.489658 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ A Neuropeptidergic Signaling Pathway for Olfactory Gain Modulation ]]> https://biorxiv.org/content/10.1101/2022.04.27.489804v1?rss=1 Sizemore, T. R. Jonaitis, J. Dacks, A. M. 2022-04-28 doi:10.1101/2022.04.27.489804 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Covalent Docking and Molecular Dynamics Simulations Reveal the Specificity-Shifting Mutations Ala237Arg and Ala237Lys in TEM Beta-Lactamase ]]> https://biorxiv.org/content/10.1101/2022.04.29.490038v1?rss=1 Monteiro da Silva, G. Yang, J. Leang, B. Huang, J. Weinreich, D. Rubenstein, B. M. 2022-05-01 doi:10.1101/2022.04.29.490038 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Robust associations between white matter microstructure and general intelligence ]]> https://biorxiv.org/content/10.1101/2022.05.02.490274v1?rss=1 Stammen, C. Fraenz, C. Grazioplene, R. G. Schlüter, C. Merhof, V. Johnson, W. Güntürkün, O. DeYoung, C. G. Genc, E. 2022-05-04 doi:10.1101/2022.05.02.490274 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Actuating tension-loaded DNA clamps drives membrane tubulation ]]> https://biorxiv.org/content/10.1101/2022.05.02.490361v1?rss=1 Liu, L. Xiong, Q. Xie, C. Pincet, F. Lin, C. 2022-05-03 doi:10.1101/2022.05.02.490361 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription ]]> https://biorxiv.org/content/10.1101/2022.05.03.490387v1?rss=1 Bullock, M. E. Moreno-Martinez, N. Miller-Jensen, K. 2022-05-03 doi:10.1101/2022.05.03.490387 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Temporal PHATE: A multi-view manifold learningmethod for brain state trajectories ]]> https://biorxiv.org/content/10.1101/2022.05.03.490534v1?rss=1 Busch, E. L. Huang, J. Benz, A. Wallenstein, T. Lajoie, G. Wolf, G. Krishnaswamy, S. Turk-Browne, N. B. 2022-05-04 doi:10.1101/2022.05.03.490534 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ SARS-CoV-2 variants do not evolve to promote further escape from MHC-I recognition ]]> https://biorxiv.org/content/10.1101/2022.05.04.490614v1?rss=1 Moriyama, M. Lucas, C. Monteiro, V. S. Iwasaki, A. 2022-05-04 doi:10.1101/2022.05.04.490614 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Inflammatory stress signaling via NF-kB alters accessible cholesterol to upregulate SREBP2 transcriptional activity in endothelial cells ]]> https://biorxiv.org/content/10.1101/2022.05.05.490737v1?rss=1 Sessa, W. C. Fowler, J. W. M. Zhang, R. Tao, B. Boutagy, N. E. 2022-05-05 doi:10.1101/2022.05.05.490737 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Sinking a giant: quantitative macroevolutionary comparative methods debunk qualitative assumptions ]]> https://biorxiv.org/content/10.1101/2022.05.05.490811v1?rss=1 Fabbri, M. Navalon, G. Benson, R. B. Pol, D. O'Connor, J. Bhullar, B.-A. S. Erickson, G. Norell, M. A. Orkney, A. Lamanna, M. C. Zouhri, S. Becker, J. Dal Sasso, C. Bindellini, G. Maganuco, S. Auditore, M. Ibrahim, N. 2022-05-06 doi:10.1101/2022.05.05.490811 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ A Multidimensional Approach to Understanding the Emergence of Sex Differences in Internalizing Symptoms in Adolescence ]]> https://biorxiv.org/content/10.1101/2022.05.05.490817v1?rss=1 Serio, B. Kohler, R. Ye, F. Lichenstein, S. D. Yip, S. W. 2022-05-05 doi:10.1101/2022.05.05.490817 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Spontaneously produced lysogenic phages are an important component of the soybean Bradyrhizobium mobilome ]]> https://biorxiv.org/content/10.1101/2022.05.06.490963v1?rss=1 Joglekar, P. Ferrell, B. D. Jarvis, T. Haramoto, K. Place, N. Dums, J. T. Polson, S. W. Wommack, K. E. Fuhrmann, J. J. 2022-05-09 doi:10.1101/2022.05.06.490963 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Simultaneous and sequential multi-species coronavirus vaccination ]]> https://biorxiv.org/content/10.1101/2022.05.07.491038v1?rss=1 Peng, L. Fang, Z. Renauer, P. A. McNamara, A. Park, J. J. Lin, Q. Zhou, X. Dong, M. B. Zhu, B. Zhao, H. Wilen, C. B. Chen, S. 2022-05-08 doi:10.1101/2022.05.07.491038 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Scaled-expansion of the membrane associated cytoskeleton requires conserved kinesin adaptors ]]> https://biorxiv.org/content/10.1101/2022.05.09.491207v1?rss=1 Glomb, O. Swaim, G. LLancao, P. M. Lovejoy, C. Sutradhar, S. Park, J. Wu, Y. Hammarlund, M. Howard, J. Ferguson, S. Yogev, S. 2022-05-09 doi:10.1101/2022.05.09.491207 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Modeling ecological communities when composition is manipulated experimentally ]]> https://biorxiv.org/content/10.1101/2022.05.12.491213v1?rss=1 Skwara, A. Lemos-Costa, P. Miller, Z. R. Allesina, S. 2022-05-13 doi:10.1101/2022.05.12.491213 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission ]]> https://biorxiv.org/content/10.1101/2022.05.13.491776v1?rss=1 Stern, S. Zhang, L. Wang, M. Wright, R. Cordeiro, D. Peles, D. Hang, Y. Mendes, A. P. Baul, T. Roth, J. Coorapati, S. Boks, M. Pol, H. H. Brennand, K. J. Rethelyi, J. M. Kahn, R. S. Marchetto, M. C. Gage, F. H. 2022-05-13 doi:10.1101/2022.05.13.491776 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Flexible perceptual encoding by discrete gamma events ]]> https://biorxiv.org/content/10.1101/2022.05.13.491832v1?rss=1 Perrenoud, Q. Fonseca, A. H. d. O. Airhart, A. Bonanno, J. Mao, R. Cardin, J. A. 2022-05-13 doi:10.1101/2022.05.13.491832 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Neuroinflammation in neuronopathic Gaucher disease: Role of microglia and NK cells ]]> https://biorxiv.org/content/10.1101/2022.05.13.491834v1?rss=1 Mistry, P. Boddupalli, C. S. Belinsky, G. Gans, J. Teeple, E. Nguyen, T.-H. Mehta, S. Guo, L. Kramer, M. Ruan, J. Wang, H. Davison, M. DJ, V. Zhang, B. Klinger, K. Nair, S. 2022-05-16 doi:10.1101/2022.05.13.491834 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Population genomics of a threespine stickleback tapeworm in Vancouver Island ]]> https://biorxiv.org/content/10.1101/2022.05.15.491937v1?rss=1 Shim, K. C. Weber, J. N. Hernadez, C. A. Bolnick, D. I. 2022-05-16 doi:10.1101/2022.05.15.491937 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Gray Matter Volumetric Correlates of Attention Deficit and Hyperactivity Traits in Emerging Adolescents ]]> https://biorxiv.org/content/10.1101/2022.05.16.492088v1?rss=1 Li, C. S. Chen, Y. Ide, J. S. 2022-05-16 doi:10.1101/2022.05.16.492088 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ Evolution and diversification dynamics of butterflies ]]> https://biorxiv.org/content/10.1101/2022.05.17.491528v1?rss=1 Kawahara, A. Y. Storer, C. Carvalho, A. P. S. Plotkin, D. M. Condamine, F. Braga, M. P. Ellis, E. A. St Laurent, R. A. Li, X. Barve, V. Cai, L. Earl, C. Frandsen, P. B. Owens, H. L. Valencia-Montoya, W. A. Aduse-Poku, K. Toussaint, E. F. A. Dexter, K. M. Doleck, T. Markee, A. Messcher, R. Nguyen, Y.-L. Badon, J. A. T. Benitez, H. A. Braby, M. F. Buenavente, P. A. C. Chan, W.-P. Collins, S. C. Childers, R. A. R. Dankowicz, E. Eastwood, R. Fric, Z. F. Gott, R. Hall, J. P. W. Hallwachs, W. Hardy, N. B. Sipe, R. L. H. Heath, A. Hinolan, J. D. Homziak, N. T. 2022-05-19 doi:10.1101/2022.05.17.491528 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Clonally selected lines after CRISPR/Cas editing are not isogenic ]]> https://biorxiv.org/content/10.1101/2022.05.17.492193v1?rss=1 Panda, A. Suvakov, M. Mariani, J. Drucker, K. L. Park, Y. H. Jang, Y. Kollmeyer, T. M. Sarkar, G. Bae, T. Kim, J. J. Yoon, W. H. Jenkins, R. B. Vaccarino, F. M. Abyzov, A. 2022-05-17 doi:10.1101/2022.05.17.492193 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression ]]> https://biorxiv.org/content/10.1101/2022.05.17.492198v1?rss=1 Arshad, N. Laurent-Rolle, M. Ahmed, W. S. Hsu, J. C.-C. Mitchell, S. M. Pawlak, J. Sengupta, D. Biswas, K. H. Cresswell, P. 2022-05-17 doi:10.1101/2022.05.17.492198 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death during Mammary Gland Involution ]]> https://biorxiv.org/content/10.1101/2022.05.17.492309v1?rss=1 JEONG, J. Lee, J. Talaia, G. Kim, W. Song, J. Yoo, K. Gonzalez, D. Athonvarangkul, D. Shin, J. Dann, P. Haberman, A. Kim, L. K. Ferguson, S. Choi, J. Wysolmerski, J. 2022-05-17 doi:10.1101/2022.05.17.492309 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action ]]> https://biorxiv.org/content/10.1101/2022.05.17.492313v1?rss=1 Gumbs, R. Gray, C. L. Bohm, M. Burfield, I. J. Couchman, O. R. Faith, D. P. Forest, F. Hoffmann, M. Isaac, N. J. B. Jetz, W. Mace, G. M. Mooers, A. O. Safi, K. Scott, O. Steel, M. Tucker, C. M. Pearse, W. D. Owen, N. R. Rosindell, J. 2022-05-19 doi:10.1101/2022.05.17.492313 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Microglia maintain homeostatic conditions in the developing rostral migratory stream. ]]> https://biorxiv.org/content/10.1101/2022.05.17.492317v1?rss=1 Meller, S. J. Sanchez, E. M. H. Martin-Lopez, E. Liberia, T. GREER, C. A. 2022-05-19 doi:10.1101/2022.05.17.492317 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Actin limits egg aneuploidies associated with female reproductive aging. ]]> https://biorxiv.org/content/10.1101/2022.05.18.491967v1?rss=1 Mogessie, B. Dunkley, S. 2022-05-18 doi:10.1101/2022.05.18.491967 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Design of a mucin-selective protease for targeted degradation of cancer-associated mucins ]]> https://biorxiv.org/content/10.1101/2022.05.20.492748v1?rss=1 Pedram, K. Shon, D. J. Tender, G. S. Mantuano, N. R. Northey, J. J. Metcalf, K. J. Wisnovsky, S. P. Riley, N. M. Forcina, G. C. Malaker, S. A. Kuo, A. George, B. M. Miller, C. L. Casey, K. M. Vilches-Moure, J. G. Weaver, V. M. Laubli, H. Bertozzi, C. R. 2022-05-20 doi:10.1101/2022.05.20.492748 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Emergent coexistence in multispecies microbial communities ]]> https://biorxiv.org/content/10.1101/2022.05.20.492860v1?rss=1 Chang, C.-Y. Bajic, D. Vila, J. C. C. Estrela, S. Sanchez, A. 2022-05-20 doi:10.1101/2022.05.20.492860 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Tissue-specific modifier alleles determine Mertk loss-of-function traits ]]> https://biorxiv.org/content/10.1101/2022.05.23.493101v1?rss=1 Akalu, Y. T. Mercau, M. E. Ansems, M. Wagage, S. Hughes, L. D. Nevin, J. Alberto, E. J. Liu, X. E. He, L.-Z. Alvarado, D. Keler, T. Kong, Y. Philbrick, W. M. Finnemann, S. C. Iavarone, A. Lasorella, A. Rothlin, C. V. Ghosh, S. 2022-05-23 doi:10.1101/2022.05.23.493101 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ The LEGO theory of the developing functional connectome ]]> https://biorxiv.org/content/10.1101/2022.05.24.493295v1?rss=1 Busch, E. L. Rapuano, K. M. Anderson, K. M. Rosenberg, M. D. Watts, R. Casey, B. Haxby, J. V. Feilong, M. 2022-05-24 doi:10.1101/2022.05.24.493295 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ A preprocessing and functional connectivity analysis pipeline for mesoscale calcium imaging ]]> https://biorxiv.org/content/10.1101/2022.05.24.493310v1?rss=1 O'Connor, D. Mandino, F. Shen, X. Horien, C. Ge, X. Herman, P. Crair, M. Papademetris, X. Lake, E. M. Constable, R. T. 2022-05-25 doi:10.1101/2022.05.24.493310 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Change point estimation by the mouse medial frontal cortex during probabilistic reward learning ]]> https://biorxiv.org/content/10.1101/2022.05.26.493245v1?rss=1 Atilgan, H. Murphy, C. E. Wang, H. Ortega, H. K. Pinto, L. Kwan, A. C. 2022-05-29 doi:10.1101/2022.05.26.493245 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ A dual role for CRTH2 in acute lung injury ]]> https://biorxiv.org/content/10.1101/2022.05.29.493897v1?rss=1 Jung, E. Cohen, A. J. Howell, R. Cosme, C. Tsang, D. Ristic, N. Dela Cruz, C. S. Spiegel, D. Chupp, G. L. Gautam, S. 2022-05-29 doi:10.1101/2022.05.29.493897 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Developmental transitions coordinate assembly of the Coxiella burnetii Dot/Icm type IV secretion system ]]> https://biorxiv.org/content/10.1101/2022.05.29.493899v1?rss=1 Park, D. Steiner, S. Shao, M. Roy, C. Liu, J. 2022-05-29 doi:10.1101/2022.05.29.493899 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues ]]> https://biorxiv.org/content/10.1101/2022.05.31.493925v1?rss=1 The COVID Tissue Atlas Consortium, Granados, A. A. Bucher, S. Agrawal, A. Song, H. Chen, A. T. Peng, T. Neff, N. Pisco, A. O. Huang, F. Wang, B. 2022-05-31 doi:10.1101/2022.05.31.493925 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Recapitulating Human Ovarian Aging Using Random Walks ]]> https://biorxiv.org/content/10.1101/2022.05.31.494088v1?rss=1 Johnson, J. Emerson, J. Lawley, S. D. 2022-06-01 doi:10.1101/2022.05.31.494088 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Normalizing need not be the norm: count-based math for analyzing single-cell data ]]> https://biorxiv.org/content/10.1101/2022.06.01.494334v1?rss=1 Church, S. H. Mah, J. L. Wagner, G. Dunn, C. 2022-06-02 doi:10.1101/2022.06.01.494334 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Olfactory decoding is positively associated with ad libitum food intake in sated humans ]]> https://biorxiv.org/content/10.1101/2022.06.01.494392v1?rss=1 Perszyk, E. E. Davis, X. S. Small, D. M. 2022-06-02 doi:10.1101/2022.06.01.494392 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Evolutionarily conserved midbody reorganization precedes ring canal formation during gametogenesis ]]> https://biorxiv.org/content/10.1101/2022.06.03.494691v1?rss=1 Price, K. L. Tharakan, D. M. Cooley, L. 2022-06-04 doi:10.1101/2022.06.03.494691 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ QuNex -- An Integrative Platform forReproducible Neuroimaging Analytics ]]> https://biorxiv.org/content/10.1101/2022.06.03.494750v1?rss=1 Ji, J. L. Demsar, J. Fonteneau, C. Tamayo, Z. Pan, L. Kraljic, A. Matkovic, A. Purg, N. Helmer, M. Warrington, S. Sotiropoulos, S. Harms, M. Murray, J. D. Anticevic, A. Repovs, G. 2022-06-05 doi:10.1101/2022.06.03.494750 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Dose-dependent nuclear delivery and transcriptional repression with a cell-penetrant MeCP2 ]]> https://biorxiv.org/content/10.1101/2022.06.03.494754v1?rss=1 Zhang, X. Zoltek, M. Mozumdar, D. Schepartz, A. 2022-06-04 doi:10.1101/2022.06.03.494754 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Proteotype Co-evolution and Diversity in Mammals ]]> https://biorxiv.org/content/10.1101/2022.06.08.495293v1?rss=1 Ba, Q. Hei, Y. Dighe, A. Li, W. Maziarz, J. Pak, I. Wang, S. Wagner, G. Liu, Y. 2022-06-10 doi:10.1101/2022.06.08.495293 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Early adversity changes the economic conditions of structural brain network organisation ]]> https://biorxiv.org/content/10.1101/2022.06.08.495303v1?rss=1 Carozza, S. Holmes, J. Vertes, P. E. Bullmore, E. Arefin, T. Pugliese, A. Zhang, J. Kaffman, A. Akarca, D. Astle, D. 2022-06-10 doi:10.1101/2022.06.08.495303 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Orphan genes are clustered with allorecognition loci and may be involved in incompatibility and speciation in Neurospora ]]> https://biorxiv.org/content/10.1101/2022.06.10.495464v1?rss=1 Wang, Z. Wang, Y. Kasuga, T. Lopez-Giraldez, F. Zhang, Y. Zhang, Z. Diaz, R. Dong, C. Sil, A. Trail, F. Yarden, O. Townsend, J. P. 2022-06-12 doi:10.1101/2022.06.10.495464 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice ]]> https://biorxiv.org/content/10.1101/2022.06.10.495677v1?rss=1 Ullah, I. Beaudoin-Bussieres, G. Symmes, K. Cloutier, M. Ducas, E. Tauzin, A. Laumaea, A. Begin, P. Mothes, W. Bazin, R. Finzi, A. Uchil, P. D. 2022-06-12 doi:10.1101/2022.06.10.495677 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Conserved reward-mediated, reinforcement-learning mechanisms in Pavlovian and instrumental tasks ]]> https://biorxiv.org/content/10.1101/2022.06.12.495805v1?rss=1 Moin Afshar, N. Cinotti, F. Martin, D. A. Khamassi, M. A. Calu, D. J. Taylor, J. R. Groman, S. M. 2022-06-16 doi:10.1101/2022.06.12.495805 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Integrative deep learning analysis improves colon adenocarcinoma patient stratification at risk for mortality ]]> https://biorxiv.org/content/10.1101/2022.06.13.495227v1?rss=1 5years, N=25) patients (AUC=0.81{+/-}0.08, 5year survival p-value=2.13e-25, 5year relative risk=5.09{+/-}0.05) though such models are less effective at predicting OS for moderate risk (3years Zhou, J. Foroughi pour, A. Deirawan, H. Daaboul, F. Aung, T. Beydoun, R. Ahmed, F. S. Chuang, J. H. 2022-06-16 doi:10.1101/2022.06.13.495227 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Structure-based Discovery of Conformationally Selective Inhibitors of the Serotonin Transporter ]]> https://biorxiv.org/content/10.1101/2022.06.13.495991v1?rss=1 Singh, I. Seth, A. Billesbolle, C. B. Braz, J. Rodriguiz, R. M. Roy, K. Bekele, B. Craik, V. Huang, X.-P. Boytsov, D. Lak, P. O'Donnell, H. R. Sandtner, W. R. Roth, B. L. Basbaum, A. Wetsel, W. C. Manglik, A. Shoichet, B. K. Rudnick, G. 2022-06-13 doi:10.1101/2022.06.13.495991 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Evolving copy number gains promote tumor expansion and bolster mutational diversification ]]> https://biorxiv.org/content/10.1101/2022.06.14.495959v1?rss=1 Wang, Z. Xia, Y. Mills, L. T. Nikolakopoulos, A. N. Maeser, N. Sheltzer, J. M. Sun, R. 2022-06-17 doi:10.1101/2022.06.14.495959 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Synaptic vesicle proteins and ATG9A self-organize in distinct vesicle phases within synapsin condensates ]]> https://biorxiv.org/content/10.1101/2022.06.14.496103v1?rss=1 Park, D. Wu, Y. Baublis, A. De Camilli, P. 2022-06-15 doi:10.1101/2022.06.14.496103 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Inhibition of Fas Receptor Endocytosis Sensitizes Cancer Cells to Fas-induced Apoptosis ]]> https://biorxiv.org/content/10.1101/2022.06.14.496195v1?rss=1 Kural, M. Djakbarova, U. Cakir, B. Tanaka, Y. Madraki, Y. Qian, H. Park, J. Sewanan, L. Kural, C. Niklason, L. 2022-06-17 doi:10.1101/2022.06.14.496195 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Molecular evolution of IRG1 shapes itaconate production in metazoans and alleviates the 'double-edged dilemma' of innate immune defense ]]> https://biorxiv.org/content/10.1101/2022.06.17.496652v1?rss=1 Szeligowski, R. Miros, F. Saez, A. DeCiucis, M. Wagner, G. Shen, H. 2022-06-19 doi:10.1101/2022.06.17.496652 Cold Spring Harbor Laboratory Press 2022-06-19 <![CDATA[ Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast ]]> https://biorxiv.org/content/10.1101/2022.06.20.496808v1?rss=1 Sultana, S. Abdullah, M. Li, J. Hochstrasser, M. Kachroo, A. H. 2022-06-21 doi:10.1101/2022.06.20.496808 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Abl2 mediates microtubule nucleation and repair via tubulin co-condensation. ]]> https://biorxiv.org/content/10.1101/2022.06.21.496973v1?rss=1 Lyu, W. Duan, D. Wu, K. Wu, C. Xiong, Y. Koleske, A. J. 2022-06-21 doi:10.1101/2022.06.21.496973 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ Emergent ecosystem functions follow simple quantitative rules ]]> https://biorxiv.org/content/10.1101/2022.06.21.496987v1?rss=1 Diaz-Colunga, J. Skwara, A. Vila, J. C. C. Bajic, D. Sanchez, A. 2022-06-26 doi:10.1101/2022.06.21.496987 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Compensatory aortic remodeling in Marfan syndrome protects against sexually dimorphic rupture during a BAPN challenge ]]> https://biorxiv.org/content/10.1101/2022.06.21.497029v1?rss=1 Weiss, D. Rego, B. V. Cavinato, C. Li, D. S. Kawamura, Y. Emuna, N. Humphrey, J. D. 2022-06-24 doi:10.1101/2022.06.21.497029 Cold Spring Harbor Laboratory Press 2022-06-24 <![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[ Intrinsic Neural Timescales in Autism Spectrum Disorder and Schizophrenia. A Replication and Direct Comparison Study ]]> https://biorxiv.org/content/10.1101/2022.06.26.497652v1?rss=1 Uscatescu, L. C. Kronbichler, M. Yuerekli, S. S. Kronbichler, L. Calhoun, V. Corbera, S. Bell, M. Pelphrey, K. Pearlson, G. Assaf, M. 2022-06-29 doi:10.1101/2022.06.26.497652 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Extravascular spaces are reservoirs of antigenic diversity in Trypanosoma brucei infection ]]> https://biorxiv.org/content/10.1101/2022.06.27.497797v1?rss=1 Beaver, A. Crilly, N. P. Hakim, J. Zhang, B. Bobb, B. Rijo-Ferreira, F. Figueiredo, L. M. Mugnier, M. R. 2022-06-27 doi:10.1101/2022.06.27.497797 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Identification and Mechanistic Basis of non-ACE2 Blocking Neutralizing Antibodies from COVID-19 Patients with Deep RNA Sequencing and Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/2022.06.29.498206v1?rss=1 100 million reads) of peripheral blood as a diagnostic tool for predicting the severity of the disease and as a means to pinpoint specific compensatory NAb treatments. Clinical data were prospectively collected at multiple time points during ICU admission, and amino acid sequences for the NAb CDR3 segments were identified. Patients who survived severe COVID-19 had significantly more of a Class 3 antibody (C135) to SARS-CoV-2 compared to non-survivors (16,315 reads vs 1,412 reads, p=0.02). In addition to highlighting the utility of RNA sequencing in revealing unique NAb profiles in COVID-19 patients with different outcomes, we provided a physical basis for our findings via atomistic modeling combined with molecular dynamics simulations. We established the interactions of the Class 3 NAb C135 with the SARS-CoV-2 spike protein, proposing a mechanistic basis for inhibition via multiple conformations that can effectively prevent ACE2 from binding to the spike protein, despite C135 not directly blocking the ACE2 binding motif. Overall, we demonstrate that deep RNA sequencing combined with structural modeling offers the new potential to identify and understand novel therapeutic(s) NAbs in individuals lacking certain immune responses due to their poor endogenous production. Our results suggest a possible window of opportunity for administration of such NAbs when their full sequence becomes available. A method involving rapid deep RNA sequencing of patients infected with SARS-CoV-2 or its variants at the earliest infection time could help to develop personalized treatments using the identified specific NAbs. ]]> Fredericks, A. M. East, K. W. Shi, Y. Liu, J. Maschietto, F. Ayala, A. Cioffi, W. G. Cohen, M. Fairbrother, W. G. Lefort, C. T. Nau, G. J. Levy, M. M. Wang, J. Batista, V. S. Lisi, G. P. Monaghan, S. F. 2022-06-30 doi:10.1101/2022.06.29.498206 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Rhythmic information sampling in the brain during visual recognition ]]> https://biorxiv.org/content/10.1101/2022.06.30.498324v1?rss=1 Caplette, L. Jerbi, K. Gosselin, F. 2022-07-02 doi:10.1101/2022.06.30.498324 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Single-Cell Multi-Modal GAN (scMMGAN) reveals spatial patterns in single-cell data from triple negative breast cancer ]]> https://biorxiv.org/content/10.1101/2022.07.04.498732v1?rss=1 Amodio, M. Youlten, S. E. Venkat, A. Chaffer, C. San Juan, B. P. Krishnaswamy, S. 2022-07-04 doi:10.1101/2022.07.04.498732 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ Polyploidy, regular patterning of genome copies, and unusual control of DNA partitioning in the Lyme disease spirochete ]]> https://biorxiv.org/content/10.1101/2022.07.05.498848v1?rss=1 Takacs, C. N. Wachter, J. Xiang, Y. Karaboja, X. Zhongqing, R. Scott, M. Stoner, M. R. Irnov, I. Jannetty, N. Rosa, P. A. Wang, X. Jacobs-Wagner, C. 2022-07-05 doi:10.1101/2022.07.05.498848 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ A membrane sensing mechanism couples local lipid metabolism to protein degradation at the inner nuclear membrane ]]> https://biorxiv.org/content/10.1101/2022.07.06.498903v1?rss=1 Lee, S. Merta, H. Rodriguez, J. W. C. Bahmanyar, S. 2022-07-06 doi:10.1101/2022.07.06.498903 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ CryoEM Structures of the Human HIV-1 Restriction Factor SERINC3 and Function as a Lipid Transporter ]]> https://biorxiv.org/content/10.1101/2022.07.06.498924v1?rss=1 Leonhardt, S. A. Purdy, M. D. Grover, J. R. Yang, Z. Poulos, S. McIntire, W. E. Tatham, E. A. Erramilli, S. Nosol, K. Lai, K. K. Ding, S. Lu, M. Uchil, P. D. Finzi, A. D. Rein, A. Kossiakoff, A. A. Mothes, W. Yeager, M. 2022-07-06 doi:10.1101/2022.07.06.498924 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Estimating the prevalence of LAMA2 congenital muscular dystrophy using population genetic databases ]]> https://biorxiv.org/content/10.1101/2022.07.06.499037v1?rss=1 Lake, N. J. Phua, J. Liu, W. Moors, T. Axon, S. Lek, M. 2022-07-10 doi:10.1101/2022.07.06.499037 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Deep Phosphoproteomic Elucidation of Metformin-Signaling in Heterogenous Colorectal Cancer Cells ]]> https://biorxiv.org/content/10.1101/2022.07.07.499038v1?rss=1 Salovska, B. Gao, E. Mueller-Dott, S. Li, W. Dugourd, A. Rosenberger, G. Saez-Rodriguez, J. Liu, Y. 2022-07-08 doi:10.1101/2022.07.07.499038 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ The age of reason: Functional brain network development during childhood ]]> https://biorxiv.org/content/10.1101/2022.07.07.499176v1?rss=1 Tooley, U. A. Park, A. T. Leonard, J. A. Boroshok, A. L. McDermott, C. L. Tisdall, D. Bassett, D. S. Mackey, A. P. 2022-07-09 doi:10.1101/2022.07.07.499176 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Mitoguardin-2 is a lipid transporter and its lipid transfer ability is required for function ]]> https://biorxiv.org/content/10.1101/2022.07.08.499339v1?rss=1 Hong, Z. Adlakha, J. Guinn, E. Giska, F. Gupta, K. Melia, T. Reinisch, K. M. 2022-07-09 doi:10.1101/2022.07.08.499339 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Evaluating the Reliability of AlphaFold 2 for Unknown Complex Structures with Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.07.08.499384v1?rss=1 Xiong, H. Han, L. Wang, Y. Chai, P. 2022-07-10 doi:10.1101/2022.07.08.499384 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Gene Trajectory Inference for Single-cell Data by Optimal Transport Metrics ]]> https://biorxiv.org/content/10.1101/2022.07.08.499404v1?rss=1 Qu, R. Cheng, X. Myung, P. Sefik, E. Flavell, R. Kluger, Y. 2022-07-10 doi:10.1101/2022.07.08.499404 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ A Draft Human Pangenome Reference ]]> https://biorxiv.org/content/10.1101/2022.07.09.499321v1?rss=1 Liao, W.-W. Asri, M. Ebler, J. Doerr, D. Haukness, M. Hickey, G. Lu, S. Lucas, J. K. Monlong, J. Abel, H. J. Buonaiuto, S. Chang, X. H. Cheng, H. Chu, J. Colonna, V. Eizenga, J. M. Feng, X. Fischer, C. Fulton, R. S. Garg, S. Groza, C. Guarracino, A. Harvey, W. T. Heumos, S. Howe, K. Jain, M. Lu, T.-Y. Markello, C. Martin, F. J. Mitchell, M. W. Munson, K. M. Mwaniki, M. N. Novak, A. M. Olsen, H. E. Pesout, T. Porubsky, D. Prins, P. Sibbesen, J. A. Tomlinson, C. Villani, F. Vollger, M. R. Human Pangenome Reference Consortium, Bourque, G. Chaisson, M. 2022-07-09 doi:10.1101/2022.07.09.499321 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Insights from Incorporating Quantum Computing into Drug Design Workflows ]]> https://biorxiv.org/content/10.1101/2022.07.11.499644v1?rss=1 Lau, B. Emani, P. S. Chapman, J. Yao, L. Lam, T. Merrill, P. Warrell, J. Gerstein, M. B. Lam, H. 2022-07-12 doi:10.1101/2022.07.11.499644 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ Sugar sensation and mechanosensation in the egg-laying preference shift of Drosophila suzukii ]]> https://biorxiv.org/content/10.1101/2022.07.13.499915v1?rss=1 Wang, W. Dweck, H. K. M. Talross, G. J. S. Zaidi, A. Gendron, J. M. Carlson, J. R. 2022-07-14 doi:10.1101/2022.07.13.499915 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ R methylCIPHER: A Methylation Clock Investigational Package for Hypothesis-Driven Evaluation & Research ]]> https://biorxiv.org/content/10.1101/2022.07.13.499978v1?rss=1 Thrush, K. Higgins-Chen, A. T. Liu, Z. Levine, M. 2022-07-16 doi:10.1101/2022.07.13.499978 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Diverse strategies for tracking seasonal environmental niches at hemispheric scale ]]> https://biorxiv.org/content/10.1101/2022.07.15.500241v1?rss=1 Cohen, J. Jetz, W. 2022-07-18 doi:10.1101/2022.07.15.500241 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Automated and manual segmentation of the hippocampus in human infants ]]> https://biorxiv.org/content/10.1101/2022.07.17.500316v1?rss=1 Fel, J. T. Ellis, C. T. Turk-Browne, N. B. 2022-07-18 doi:10.1101/2022.07.17.500316 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Group 3 Innate Lymphoid Cells are regulated by WASP in a microbiota-dependent manner ]]> https://biorxiv.org/content/10.1101/2022.07.19.500438v1?rss=1 Biswas, A. Redhu, N. S. Nandy, A. Kang, Y. H. Field, M. Kelly, R. Konnikova, L. Goettel, J. Tsou, A. Horwitz, B. Snapper, S. 2022-07-20 doi:10.1101/2022.07.19.500438 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron subvariants BA.2, BA.2.12.1 and BA.5 ]]> https://biorxiv.org/content/10.1101/2022.07.19.500616v1?rss=1 Fang, Z. Chen, S. 2022-07-19 doi:10.1101/2022.07.19.500616 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Cross Atlas Remapping via Optimal Transport (CAROT): Creating connectomes for any atlas when raw data is not available ]]> https://biorxiv.org/content/10.1101/2022.07.19.500642v1?rss=1 Dadashkarimi, J. Karbasi, A. Scheinost, D. 2022-07-20 doi:10.1101/2022.07.19.500642 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Comprehensive analysis of platelet glycoprotein Ibα glycosylation. ]]> https://biorxiv.org/content/10.1101/2022.07.19.500646v1?rss=1 Hollenhorst, M. A. Tiemeyer, K. H. Mahoney, K. E. Aoki, K. Ishihara, M. Lowery, S. C. Rangel-Angarita, V. Bertozzi, C. R. Malaker, S. A. 2022-07-20 doi:10.1101/2022.07.19.500646 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference ]]> https://biorxiv.org/content/10.1101/2022.07.20.500802v1?rss=1 Meng, X. Navoly, G. Giannakopoulou, O. DL, D. Koller, D. Pathak, G. Koen, N. Lin, K. Renteria, M. Feng, Y. Gaziano, J. M. Stein, D. Zar, H. Campbell, M. van Heel, D. Trivedi, B. Finer, S. McQuillin, A. Bass, N. Chundru, V. K. Martin, H. Huang, Q. Q. Valkovskaya, M. Kuo, P.-H. Chen, H.-C. Tsai, S.-J. Liu, Y.-L. Kendler, K. Peterson, R. Cai, N. Fang, Y. Sen, S. Scott, L. Burmeister, M. Loos, R. Preuss, M. Actkins, K. Davis, L. Uddin, M. Wani, A. Wildman, D. Ursano, R. Kessler, R. Kanai, M. Okada, Y. Sakaue, S. Rabinowitz, J. Maher, B. Uhl, G. Eato 2022-07-21 doi:10.1101/2022.07.20.500802 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Three-dimensional structured illumination microscopy with enhanced axial resolution ]]> https://biorxiv.org/content/10.1101/2022.07.20.500834v1?rss=1 Li, X. Wu, Y. Su, Y. Suarez, I. A. R. Matthaeus, C. Updegrove, T. B. Wei, Z. Zhang, L. Sasaki, H. Li, Y. Guo, M. Giannini, J. P. Vishwasrao, H. D. Chen, J. Lee, S.-J. J. Shao, L. Liu, H. Ramamurthi, K. S. Taraska, J. W. Upadhyaya, A. La Riviere, P. Shroff, H. 2022-07-21 doi:10.1101/2022.07.20.500834 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Sex differences in default mode network connectivity in healthy aging adults ]]> https://biorxiv.org/content/10.1101/2022.07.21.500964v1?rss=1 Ficek-Tani, B. Horien, C. Ju, S. Li, N. Lacadie, C. Shen, X. Scheinost, D. Constable, R. T. Fredericks, C. A. 2022-07-22 doi:10.1101/2022.07.21.500964 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Shared and distinct neural activity during anticipation and outcome of win and loss: A meta-analysis of the monetary incentive delay task ]]> https://biorxiv.org/content/10.1101/2022.07.21.500974v1?rss=1 Chen, Y. Chaudhary, S. Li, C.-s. R. 2022-07-22 doi:10.1101/2022.07.21.500974 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Global change drivers and the risk of infectious disease ]]> https://biorxiv.org/content/10.1101/2022.07.21.501013v1?rss=1 Mahon, M. B. Sack, A. Aleuy, O. A. Barbera, C. Brown, E. Buelow, H. Civitello, D. J. Cohen, J. M. de Wit, L. Forstchen, M. Halliday, F. W. Heffernan, P. Knutie, S. Korotasz, A. Larson, J. G. Rumschlag, S. L. Selland, E. Shepack, A. Vincent, N. Rohr, J. R. 2022-07-22 doi:10.1101/2022.07.21.501013 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Human Brain Development: a cross-sectional and longitudinal study integrating multiple neuromorphological features ]]> https://biorxiv.org/content/10.1101/2022.07.21.501018v1?rss=1 Kalantar Hormozi, H. Patel, R. Dai, A. Ziolkowski, J. Dong, H. Holmes, A. Raznahan, A. Devenyi, G. Chakravarty, M. 2022-07-22 doi:10.1101/2022.07.21.501018 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling ]]> https://biorxiv.org/content/10.1101/2022.07.21.501031v1?rss=1 Hackstein, P. C. Spitzer, J. Symeonidis, K. Horvatic, H. Bedke, T. Steglich, B. Assmus, L. Odainic, A. Kessler, N. Klein, S. Beyer, M. Schmithausen, R. Latz, E. Kurts, C. Trebicka, J. Flavell, R. Garbi, N. Roers, A. Huber, S. Schmidt, S. Knolle, P. Abdullah, Z. 2022-07-22 doi:10.1101/2022.07.21.501031 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells ]]> https://biorxiv.org/content/10.1101/2022.07.21.501032v1?rss=1 Tornini, V. A. Lee, H.-J. Miao, L. Tang, Y. Dube, S. E. Gerson, T. Schmidt, V. J. Du, K. Kuchroo, M. Kroll, F. Vejnar, C. E. Bazzini, A. A. Krishnaswamy, S. Rihel, J. Giraldez, A. 2022-07-22 doi:10.1101/2022.07.21.501032 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Adaptive phototaxis of Chlamydomonas and the evolutionary transition to multicellularity in Volvocine green algae ]]> https://biorxiv.org/content/10.1101/2022.07.24.500296v1?rss=1 Leptos, K. C. Chioccioli, M. Furlan, S. Pesci, A. I. Goldstein, R. E. 2022-07-24 doi:10.1101/2022.07.24.500296 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Hidden species diversity in a living fossil vertebrate ]]> https://biorxiv.org/content/10.1101/2022.07.25.500718v1?rss=1 Brownstein, C. D. Kim, D. Orr, O. D. Hogue, G. M. Tracy, B. H. Pugh, M. W. Singer, R. Myles-McBurney, C. Mollish, J. M. Simmons, J. W. David, S. R. Watkins-Colwell, G. Hoffman, E. A. Near, T. J. 2022-07-27 doi:10.1101/2022.07.25.500718 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Ketamine selectively changes outcome valuation in a biased matching pennies task ]]> https://biorxiv.org/content/10.1101/2022.07.25.501468v1?rss=1 Oemisch, M. Seo, H. 2022-07-27 doi:10.1101/2022.07.25.501468 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut ]]> https://biorxiv.org/content/10.1101/2022.07.26.501624v1?rss=1 Bara, A. M. Chen, L. Ma, C. Underwood, J. Moreci, R. S. Sumigray, K. Sun, T. Diao, Y. Verzi, M. Lechler, T. 2022-07-28 doi:10.1101/2022.07.26.501624 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain ]]> https://biorxiv.org/content/10.1101/2022.07.27.501708v1?rss=1 Chen, Y. Prevost, J. Ullah, I. Romero, H. Lisi, V. Tolbert, W. D. Grover, J. R. Ding, S. Gong, S. Y. Beaudoin-Bussieres, G. Gasser, R. Benlarbi, M. Vezina, D. Anand, S. P. Chatterjee, D. Goyette, G. Grunst, M. W. Yang, Z. Bo, Y. Zhou, F. Beland, K. Bai, X. Zeher, A. R. Huang, R. K. Nguyen, D. N. Sherburn, R. Wu, D. Piszczek, G. Pare, B. Matthies, D. Xia, D. Richard, J. Kumar, P. Mothes, W. Cote, M. Uchil, P. D. Lavallee, V.-P. Smith, M. A. Pazgier, M. Haddad, E. Finzi, A. 2022-07-28 doi:10.1101/2022.07.27.501708 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Dynamic microtubules slow down during their shrinkage phase ]]> https://biorxiv.org/content/10.1101/2022.07.27.501773v1?rss=1 Luchniak, A. Kuo, Y.-W. McGuinness, C. Sutradhar, S. Orbach, R. Mahamdeh, M. S. S. Howard, J. 2022-07-28 doi:10.1101/2022.07.27.501773 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Assessment of mosquito longevity, fecundity, and dengue virus titer following exposure to plasma from a host with Type 2 diabetes mellitus - a pilot study ]]> https://biorxiv.org/content/10.1101/2022.07.28.501853v1?rss=1 Smartt, C. T. Kendziorski, N. Chen, T.-Y. Farless, S. 2022-07-31 doi:10.1101/2022.07.28.501853 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ Neural patterns differentiate traumatic from sad autobiographical memories in PTSD ]]> https://biorxiv.org/content/10.1101/2022.07.30.502151v1?rss=1 Perl, O. Duek, O. Kulkarni, K. R. Kelmendi, B. Amen, S. Gordon, C. Krystal, J. H. Levy, I. Harpaz-Rotem, I. Schiller, D. 2022-08-02 doi:10.1101/2022.07.30.502151 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Causal identification of single-cell experimental perturbation effects with CINEMA-OT ]]> https://biorxiv.org/content/10.1101/2022.07.31.502173v1?rss=1 Dong, M. Wang, B. Wei, J. Frey, A. Ouerghi, F. Foxman, E. F. Ishizuka, J. J. Dhodapkar, R. M. van Dijk, D. 2022-08-01 doi:10.1101/2022.07.31.502173 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Appetitive and aversive cue reactivities differentiate biotypes of alcohol drinkers ]]> https://biorxiv.org/content/10.1101/2022.07.31.502197v1?rss=1 Chen, Y. Li, C.-S. R. 2022-08-02 doi:10.1101/2022.07.31.502197 Cold Spring Harbor Laboratory Press 2022-08-02 <![CDATA[ Mutational screens highlight glycosylation as a modulator of CSF3R activity ]]> https://biorxiv.org/content/10.1101/2022.08.01.502088v1?rss=1 Hollander, M. J. Malaker, S. A. Perez, I. Maxson, J. E. Cochran, J. R. Bertozzi, C. R. 2022-08-01 doi:10.1101/2022.08.01.502088 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Heme Hopping Falls Short: What Explains Anti-Arrhenius Conductivity in a Multi-heme Cytochrome Nanowire? ]]> https://biorxiv.org/content/10.1101/2022.08.01.502099v1?rss=1 Guberman-Pfeffer, M. J. 2022-08-03 doi:10.1101/2022.08.01.502099 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Serum response factor reduces gene expression noise and confers cell state stability ]]> https://biorxiv.org/content/10.1101/2022.08.04.502808v1?rss=1 Zhang, J. Hu, X. Wu, Q. Guo, S. 2022-08-05 doi:10.1101/2022.08.04.502808 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Filming space-time changes of gene expression with expressyouRcell ]]> https://biorxiv.org/content/10.1101/2022.08.04.502810v1?rss=1 Paganin, M. Tebaldi, T. Lauria, F. Viero, G. 2022-08-06 doi:10.1101/2022.08.04.502810 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Warm blood meal increases digestion rate and milk protein production to maximize reproductive output for the tsetse fly, Glossina morsitans ]]> https://biorxiv.org/content/10.1101/2022.08.07.501667v1?rss=1 Benoit, J. Lahondere, C. Attardo, G. M. Michalkova, V. Oyen, K. Xiao, Y. Aksoy, S. 2022-08-07 doi:10.1101/2022.08.07.501667 Cold Spring Harbor Laboratory Press 2022-08-07 <![CDATA[ There is no fundamental trade-off between prediction accuracy and feature importance reliability ]]> https://biorxiv.org/content/10.1101/2022.08.08.503167v1?rss=1 Chen, J. Ooi, L. Q. R. Li, J. Asplund, C. L. Eickhoff, S. B. Bzdok, D. Holmes, A. J. Yeo, B. T. T. 2022-08-11 doi:10.1101/2022.08.08.503167 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Sex differences in early and term placenta are conserved in adult tissues ]]> https://biorxiv.org/content/10.1101/2022.08.08.503197v1?rss=1 Olney, K. C. Plaisier, S. B. Phung, T. N. Silasi, M. Perley, L. O'Bryan, J. Ramirez, L. Kliman, H. J. Wilson, M. A. 2022-08-08 doi:10.1101/2022.08.08.503197 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ FGF21 Counteracts Alcohol Intoxication by Activating Noradrenergic Neurons ]]> https://biorxiv.org/content/10.1101/2022.08.09.502667v1?rss=1 Choi, M. Schneeberger, M. Fan, W. Bugde, A. Gautron, L. Vale, K. Zhang, Y. Friedman, J. M. Mangelsdorf, D. J. Kliewer, S. A. 2022-08-11 doi:10.1101/2022.08.09.502667 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[ Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages ]]> https://biorxiv.org/content/10.1101/2022.08.09.503414v1?rss=1 Ren, P. Hu, Y. Peng, L. Yang, L. Suzuki, K. Fang, Z. Bai, M. Zhou, L. Feng, Y. Xiong, Y. Chen, S. 2022-08-10 doi:10.1101/2022.08.09.503414 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Membrane remodeling properties of the Parkinson's disease protein LRRK2 ]]> https://biorxiv.org/content/10.1101/2022.08.10.503505v1?rss=1 Wang, X. Wu, Y. Cai, S. Ge, J. Shao, L. De Camilli, P. 2022-08-10 doi:10.1101/2022.08.10.503505 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ The addiction-susceptibility TaqIA/Ankyrin repeat and kinase domain containing 1 kinase (ANKK1) controls reward and metabolism through dopamine receptor type 2 (DR2)-expressing neurons ]]> https://biorxiv.org/content/10.1101/2022.08.12.503577v1?rss=1 Montalban, E. Walle, R. Castel, J. Ansoult, A. Hassouna, R. Foppen, E. Fang, X. Hutelin, Z. Mickus, S. Perszyk, E. E. Petitbon, A. Berthelet, J. Rodrigues-Lima, F. Cebrian-Serrano, A. Gangarossa, G. Martin, C. Trifileff, P. Bosch-Bouju, C. Small, D. M. Luquet, S. H. 2022-08-15 doi:10.1101/2022.08.12.503577 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ SIC50: Determination of IC50 by an optimized Sobel operator and a vision transformer ]]> https://biorxiv.org/content/10.1101/2022.08.12.503661v1?rss=1 Wang, Y. Zhang, W. Yip, H. Qu, C. Hu, H. Chen, X. Lee, T. Yang, X. Yang, B. Kumar, P. Lee, S. Y. Casimiro, J. Zhang, J. Lam, K. S. Wang, A. 2022-08-15 doi:10.1101/2022.08.12.503661 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome ]]> https://biorxiv.org/content/10.1101/2022.08.15.503927v1?rss=1 Zimmermann-Kogadeeva, M. Bencivenga-Barry, N. A. Zimmermann, M. Bork, P. Goodman, A. 2022-08-15 doi:10.1101/2022.08.15.503927 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ ATG9 vesicles comprise the seed membrane of mammalian autophagosomes ]]> https://biorxiv.org/content/10.1101/2022.08.16.504143v1?rss=1 Olivas, T. J. Wu, Y. Yu, S. Luan, L. Choi, P. Nag, S. De Camilli, P. Gupta, K. Melia, T. J. 2022-08-16 doi:10.1101/2022.08.16.504143 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Fibronectin-integrin α5 signaling promotes thoracic aortic aneurysm in a mouse model of Marfan syndrome ]]> https://biorxiv.org/content/10.1101/2022.08.16.504169v1?rss=1 chen, m. Cavinato, C. Hansen, J. Tanaka, K. ren, p. Hassab, A. li, d. s. Joshuao, E. Tellides, G. Iyengar, R. Humphrey, J. D. Schwartz, M. 2022-08-16 doi:10.1101/2022.08.16.504169 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Deriving Schwann Cells from hPSCs Enables Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy ]]> https://biorxiv.org/content/10.1101/2022.08.16.504209v1?rss=1 Majd, H. Amin, S. Ghazizadeh, Z. Cesiulis, A. Arroyo, E. Lankford, K. Farahvashi, S. Chemel, A. K. Okoye, M. Scantlen, M. D. Tchieu, J. Calder, E. L. LeRouzic, V. Arab, A. Goodarzi, H. Pasternak, G. Kocsis, J. D. Chen, S. Studer, L. Fattahi, F. 2022-08-17 doi:10.1101/2022.08.16.504209 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ The olfactory bulb carries out concentration invariance calculations by itself and does it very quickly. ]]> https://biorxiv.org/content/10.1101/2022.08.17.504274v1?rss=1 Choi, Y. Cohen, L. B. 2022-08-18 doi:10.1101/2022.08.17.504274 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Autologous humanized PDX modeling for immuno-oncology recapitulates the human tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.08.19.503502v1?rss=1 Chiorazzi, M. Martinek, J. Krasnick, B. Zheng, Y. Robbins, K. J. Qu, R. Kaufmann, G. Skidmore, Z. Henze, L. A. Brosecke, F. Adonyi, A. Zhao, J. Shan, L. Sefik, E. Mudd, J. Bi, Y. Goedegebuure, S. P. Griffith, M. Griffith, O. Oyedeji, A. Fertuzinhos, S. Garcia-Milian, R. Boffa, D. Detterbeck, F. Dhanasopon, A. Blasberg, J. Judson, B. Gettinger, S. Politi, K. Kluger, Y. Palucka, A. K. Fields, R. Flavell, R. A. 2022-08-19 doi:10.1101/2022.08.19.503502 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ Alpha-synuclein pathology and reduced neurogenesis in the olfactory system affect olfaction in a mouse model of Parkinsons disease ]]> https://biorxiv.org/content/10.1101/2022.08.19.504562v1?rss=1 Martin-Lopez, E. GREER, C. A. Chandra, S. D J, V. Liberia, T. Meller, S. J. Harmon, L. E. Hsu, R. M. Han, K. Yucel, B. 2022-08-22 doi:10.1101/2022.08.19.504562 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases ]]> https://biorxiv.org/content/10.1101/2022.08.23.505039v1?rss=1 Torres Robles, J. Shi, G. Turk, B. E. 2022-08-24 doi:10.1101/2022.08.23.505039 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Targeting keratin 17-mediated reprogramming of de novo pyrimidine biosynthesis to overcome chemoresistance in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2022.08.24.504873v1?rss=1 Pan, C.-H. Chaika, N. Tseng, R. Siraj, M. A. Chen, B. Donnelly, K. L. Horowitz, M. Leiton, C. V. Chowdhury, S. Roa-Pena, L. Oblein, L. Marchenko, N. Singh, P. K. Shroyer, K. R. Escobar-Hoyos, L. F. 2022-08-26 doi:10.1101/2022.08.24.504873 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ spARC Recovers Human Glioma Spatial SignalingNetworks with Graph Filtering ]]> https://biorxiv.org/content/10.1101/2022.08.24.505139v1?rss=1 Kuchroo, M. Miyagishima, D. Steach, H. Godavarthi, A. Takeo, Y. Duy, P. Q. Barak, T. Erson-Omay, E. Z. Youlten, S. E. Mishra-Gorur, K. Moliterno, J. McGuone, D. Gunel, M. Krishnaswamy, S. 2022-08-26 doi:10.1101/2022.08.24.505139 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Bringing language to dynamic brain states: the default network dominates neural responses to evolving movie stories ]]> https://biorxiv.org/content/10.1101/2022.08.24.505147v1?rss=1 53,000 brain image time points watching Forrest Gump, we could show that distinct dynamic brain states capture unique semantic facets along the unfolding movie narrative. The spatiotemporal dynamics of brain states explicitly captured subject-level responses throughout the brain network hierarchy. Across all analyses, the default network was most intimately linked to semantic information integration, and this neural system switched online for longest durations during movie watching. Further, we identified and described two mechanisms of how the default network liaises dynamically with microanatomically defined subregion partners: the amygdala and the hippocampus. Our study thus unlocks the potential of natural language processing to explore neural processes in everyday life situations that engage key aspects of conscious awareness. ]]> Yang, E. Milisav, F. Kopal, J. Holmes, A. Mitsis, G. D. Misic, B. Finn, E. S. Bzdok, D. 2022-08-24 doi:10.1101/2022.08.24.505147 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ A genome-wide atlas of recurrent repeat expansions in human cancer ]]> https://biorxiv.org/content/10.1101/2022.08.24.505159v1?rss=1 Erwin, G. S. Gursoy, G. Al-Abri, R. Suriyaprakash, A. Dolzhenko, E. Zhu, K. Hoerner, C. R. White, S. M. Ramirez, L. Vadlakonda, A. Vadlakonda, A. von Kraut, K. Park, J. Brannon, C. M. Sumano, D. A. Kirtikar, R. A. Erwin, A. A. Metzner, T. J. Yuen, R. K. C. Fan, A. C. Leppert, J. T. Eberle, M. A. Gerstein, M. Snyder, M. P. 2022-08-24 doi:10.1101/2022.08.24.505159 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ An Aedes aegypti seryl-tRNA synthetase paralog controls bacteroidetes growth in the midgut ]]> https://biorxiv.org/content/10.1101/2022.08.25.505225v1?rss=1 Silveira, G. d. O. Talyuli, O. A. C. Walter-Nuno, A. B. Crnkovic, A. Gandara, A. C. P. Gaviraghi, A. Bottino-Rojas, V. Söll, D. Polycarpo, C. 2022-08-25 doi:10.1101/2022.08.25.505225 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Fighting isn't sexy in lekking Greater Sage-grouse (Centrocercus urophasianus) ]]> https://biorxiv.org/content/10.1101/2022.08.26.505294v1?rss=1 Snow, S. S. Patricelli, G. L. Butts, C. T. Krakauer, A. H. Perry, A. C. Logsdon, R. Prum, R. O. 2022-08-26 doi:10.1101/2022.08.26.505294 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Three-dimensional imaging of vascular development in the mouse epididymis: a prerequisite to better understand the post-testicular immune context of spermatozoa ]]> https://biorxiv.org/content/10.1101/2022.08.26.505406v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@307802org.highwire.dtl.DTLVardef@170c07org.highwire.dtl.DTLVardef@116b006org.highwire.dtl.DTLVardef@7e7f66_HPS_FORMAT_FIGEXP M_FIG Summary of the expansion of the conventional and hybrid lymphatic vasculature during postnatal development of the murine epididymis. C_FIG ]]> Damon-Soubeyrand, C. Bongiovanni, A. Chorfa, A. Goubely, C. Pirot, N. Pardanaud, L. Piboin-Fragner, L. Vachias, C. Bravard, S. Guiton, R. Thomas, J.-L. Saez, F. Kocer, A. Tardivel, M. Drevet, J. R. Henry-Berger, J. 2022-08-28 doi:10.1101/2022.08.26.505406 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Disassembly of embryonic keratin filaments promotes pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2022.08.27.504988v1?rss=1 Kawalerski, R. R. Torrente Goncalves, M. Pan, C.-H. Tseng, R. Roa-Pena, L. Leiton, C. V. Torre-Healy, L. A. Boyle, T. Chowdhury, S. Snider, N. T. Shroyer, K. R. Escobar-Hoyos, L. F. 2022-08-28 doi:10.1101/2022.08.27.504988 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Dear-DIAXMBD: deep autoencoder for data-independent acquisition proteomics ]]> https://biorxiv.org/content/10.1101/2022.08.27.505516v1?rss=1 He, Q. Zhong, C. Li, X. Guo, H. Li, Y. Gao, M. Yu, R. Liu, X. Zhang, F. Guo, T. Guo, D. Ye, F. Shuai, J. Han, J. 2022-08-29 doi:10.1101/2022.08.27.505516 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome ]]> https://biorxiv.org/content/10.1101/2022.08.28.505582v1?rss=1 Zhou, H. Arapoglou, T. Li, X. Li, Z. Zheng, X. Moore, J. E. Asok, A. Kumar, S. Blue, E. E. Buyske, S. Cox, N. Felsenfeld, A. Gerstein, M. Kenny, E. Li, B. Matise, T. Philippakis, A. Rehm, H. Sofia, H. J. Neale, B. Snyder, G. Weng, Z. Sunyaev, S. Lin, X. 2022-08-29 doi:10.1101/2022.08.28.505582 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Human XIRP1 is a macrophage podosome protein utilized by Listeria for actin-based motility ]]> https://biorxiv.org/content/10.1101/2022.08.28.505595v1?rss=1 Urbano, R. Park, E.-S. Tretina, K. Tunaru, A. Gaudet, R. G. Hu, X. Wang, D.-Z. MacMicking, J. D. 2022-08-28 doi:10.1101/2022.08.28.505595 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ Activation of ERK by altered RNA splicing in cancer ]]> https://biorxiv.org/content/10.1101/2022.08.31.505957v1?rss=1 Zhang, Y. Siraj, M. A. Chakraborty, P. Tseng, R. Ku, L.-T. Das, S. Dey, A. Dwivedi, S. K. D. Rao, G. Zhang, M. Yang, D. Hossen, M. N. Ding, W.-Q. Fung, K.-M. Bhattacharya, R. Escobar-Hoyos, L. Mukherjee, P. 2022-09-02 doi:10.1101/2022.08.31.505957 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity ]]> https://biorxiv.org/content/10.1101/2022.08.31.506117v1?rss=1 Kim, D. Biancon, G. Bai, Z. VanOudenhove, J. Liu, Y. Kothari, S. Gowda, L. Kwan, J. M. Buitrago-Pocasangre, N. C. Lele, N. Asashima, H. Racke, M. K. Wilson, J. E. Givens, T. S. Tomayko, M. M. Schulz, W. L. Longbrake, E. E. Hafler, D. A. Halene, S. Fan, R. 2022-09-02 doi:10.1101/2022.08.31.506117 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Dectin-1 Stimulation Promotes a Distinct Inflammatory Signature in the Setting of HIV-infection and Aging ]]> https://biorxiv.org/content/10.1101/2022.09.01.505710v1?rss=1 Kumar, A. Wang, J. Zhou, H. Radcliffe, C. Vander Wyk, B. Allore, H. Tsang, S. Barakat, L. Mohanty, S. Zhao, H.-y. Shaw, A. Zapata, H. 2022-09-02 doi:10.1101/2022.09.01.505710 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Sensory uncertainty punctuates motor learning independently of movement error when both feedforward and feedback control processes are engaged ]]> https://biorxiv.org/content/10.1101/2022.09.01.506147v1?rss=1 Hewitson, C. L. Kaplan, D. M. Crossley, M. 2022-09-03 doi:10.1101/2022.09.01.506147 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Differential kinetic analysis using nucleotide recoding RNA-seq and bakR ]]> https://biorxiv.org/content/10.1101/2022.09.02.505697v1?rss=1 Vock, I. W. Simon, M. 2022-09-05 doi:10.1101/2022.09.02.505697 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites ]]> https://biorxiv.org/content/10.1101/2022.09.03.505525v1?rss=1 Obara, C. J. Nixon-Abell, J. Moore, A. S. Riccio, F. Hoffman, D. P. Shtengel, G. Xu, C. S. Schaefer, K. Pasolli, H. A. Masson, J.-B. Hess, H. F. Calderon, C. P. Blackstone, C. Lippincott-Schwartz, J. 2022-09-03 doi:10.1101/2022.09.03.505525 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Canonical and Replicable Multi-Scale Intrinsic Connectivity Networks in 100k+ Resting-State fMRI Datasets ]]> https://biorxiv.org/content/10.1101/2022.09.03.506487v1?rss=1 Iraji, A. Fu, Z. Faghiri, A. Duda, M. Chen, J. Rachakonda, S. DeRamus, T. P. Kochunov, P. Adhikari, B. M. Belger, A. Ford, J. Mathalon, D. H. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Van Erp, T. G. M. Bustillo, J. R. Yang, K. Ishizuka, K. Sawa, A. Hutchison, K. Osuch, E. A. Theberge, J. Abbott, C. Mueller, B. A. Zhi, D. Zhuo, C. Liu, S. Xu, Y. Salman, M. Liu, J. Du, Y. SUI, J. Adali, T. Calhoun, V. 2022-09-05 doi:10.1101/2022.09.03.506487 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ A novel cancer-associated cassette exon in TLN1 alters Talin 1 mechanosensitivity ]]> https://biorxiv.org/content/10.1101/2022.09.06.506802v1?rss=1 Gallego-Paez, L. M. Edwards, W. J. S. Guo, Y. Chanduri, M. Koorman, T. Lee, C.-Y. Grexa, N. Derksen, P. W. B. Yan, J. Schwartz, M. A. Mauer, J. Goult, B. T. 2022-09-06 doi:10.1101/2022.09.06.506802 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Cryo-EM analyses of wild-type and oncogenic KIT mutants reveal structural oncogenic plasticity and a novel Achilles heel for therapeutic intervention ]]> https://biorxiv.org/content/10.1101/2022.09.08.506998v1?rss=1 Krimmer, S. G. Bertoletti, N. Suzuki, Y. Katic, L. Mohanty, J. Shu, S. Lee, S. Lax, I. Mi, W. Schlessinger, J. 2022-09-08 doi:10.1101/2022.09.08.506998 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ When good species have porous boundaries: weak reproductive isolation and extensive gene flow between Mimulus glaucescens and M. guttatus in northern California ]]> https://biorxiv.org/content/10.1101/2022.09.08.507212v1?rss=1 Coughlan, J. M. Habecker, N. Bergmann, J. P. Ewald, J. Ivey, C. 2022-09-10 doi:10.1101/2022.09.08.507212 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ A dynamic template complex mediates Munc18-chaperoned SNARE assembly ]]> https://biorxiv.org/content/10.1101/2022.09.09.507208v1?rss=1 Yang, J. Jin, H. Liu, Y. Guo, Y. Zhang, Y. 2022-09-09 doi:10.1101/2022.09.09.507208 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes ]]> https://biorxiv.org/content/10.1101/2022.09.09.507331v1?rss=1 Rose, N. H. Badolo, A. Sylla, M. Akorli, J. Otoo, S. Gloria-Soria, A. Powell, J. R. White, B. J. Crawford, J. E. McBride, C. S. 2022-09-13 doi:10.1101/2022.09.09.507331 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Treatment with anti-inflammatory viral serpin modulates immuno-thrombotic responses and improves outcomes in SARS-CoV-2 infected mice ]]> https://biorxiv.org/content/10.1101/2022.09.09.507363v1?rss=1 Zhang, L. Li, Y. H. Kibler, K. Kraberger, S. Varsani, A. Turk, J. Elmadbouly, N. Aliskevich, E. Spaccarelli, L. Estifanos, B. Enow, J. Zanetti, I. R. Saldevar, N. Lim, E. Browder, K. Wilson, A. Juan, F. A. Pinteric, A. Garg, A. Gisriel, S. Jacobs, B. Karr, T. L. Florsheim, E. B. Kumar, V. Wallen, J. Rahman, M. McFadden, D. G. Hogue, B. Lucas, A. R. 2022-09-11 doi:10.1101/2022.09.09.507363 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ Subthreshold serotonin signals combined by the G proteins Gαq and Gαs activate the C. elegans egg-laying muscles ]]> https://biorxiv.org/content/10.1101/2022.09.12.507489v1?rss=1 Olson, A. C. Butt, A. M. Christie, N. T. M. Shelar, A. Koelle, M. R. 2022-09-13 doi:10.1101/2022.09.12.507489 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Neutrophils regulate ITPR2 levels in epithelia by direct injection of elastase ]]> https://biorxiv.org/content/10.1101/2022.09.13.506588v1?rss=1 Ogino, N. Leite, M. F. Kruglov, E. Asashima, H. Hafler, D. A. Ehrlich, B. E. Nathanson, M. 2022-09-14 doi:10.1101/2022.09.13.506588 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Loss of H3.1K27me1 in Arabidopsis confers resistance to Geminivirus by sequestering DNA repair proteins onto rDNA and defense-related genes ]]> https://biorxiv.org/content/10.1101/2022.09.13.507805v1?rss=1 Wang, Z. Gonzalez, C. M. C. Zhao, C. Tong, C.-Y. Li, C. Liu, Z. Xie, K. Zhu, J. Wu, Z. Peng, X. Jacob, Y. Michaels, S. D. Jacobsen, S. E. Zhang, X. 2022-09-15 doi:10.1101/2022.09.13.507805 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses ]]> https://biorxiv.org/content/10.1101/2022.09.13.507833v1?rss=1 Strine, M. S. Cai, W. L. Wei, J. Alfajaro, M. M. Filler, R. B. Biering, S. B. Sarnik, S. Patil, A. Cervantes, K. S. Collings, C. K. DeWeirdt, P. C. Hanna, R. E. Schofield, K. Hulme, C. Konermann, S. Doench, J. G. Hsu, P. D. Kadoch, C. Yan, Q. Wilen, C. B. 2022-09-14 doi:10.1101/2022.09.13.507833 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Deficiency of Heterogeneous Nuclear Ribonucleoprotein U leads to delayed neurogenesis ]]> https://biorxiv.org/content/10.1101/2022.09.14.507275v1?rss=1 Mastropasqua, F. Oksanen, M. Soldini, C. Alatar, S. Arora, A. Ballarino, R. Molinari, M. Agostini, F. Poulet, A. Watts, M. E. Rabkina, I. Becker, M. Li, D. Anderlid, B.-M. Isaksson, J. Remnelius, K. L. Moslem, M. Jacob, Y. Falk, A. Crosetto, N. Bienko, M. Santini, E. Borgkvist, A. Bölte, S. Tammimies, K. 2022-09-17 doi:10.1101/2022.09.14.507275 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Perception and Memory Retrieval States are Reflected in Distributed Patterns of Background Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2022.09.14.507854v1?rss=1 Li, Y. P. Wang, Y. Turk-Browne, N. B. Kuhl, B. A. Hutchinson, J. B. 2022-09-17 doi:10.1101/2022.09.14.507854 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome ]]> https://biorxiv.org/content/10.1101/2022.09.14.507975v1?rss=1 Minteer, C. J. Thrush, K. Niimi, P. Rozowsky, J. Liu, J. Frank, M. McCabe, T. Hofstatter, E. Rozenblit, M. Pusztai, L. Beckman, K. Gerstein, M. Levine, M. E. 2022-09-17 doi:10.1101/2022.09.14.507975 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation ]]> https://biorxiv.org/content/10.1101/2022.09.14.507992v1?rss=1 Xin, T. Gallini, S. Gonzalez, D. Gonzalez, L. E. Regot, S. Greco, V. 2022-09-17 doi:10.1101/2022.09.14.507992 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Contribute to the Mutational Trajectory in Variants of Concern ]]> https://biorxiv.org/content/10.1101/2022.09.15.508093v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@71b54eorg.highwire.dtl.DTLVardef@1361b4aorg.highwire.dtl.DTLVardef@139bdd9org.highwire.dtl.DTLVardef@1df192b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gonzalez-Rodriguez, E. Zol-Hanlon, M. Bineva-Todd, G. Marchesi, A. Skehel, M. Mahoney, K. Roustan, C. Borg, A. Di Vagno, L. Kjaer, S. Wrobel, A. G. Benton, D. J. Nawrath, P. Flitsch, S. L. Joshi, D. Gonzalez-Ramirez, A. M. Wilkinson, K. A. Wilkinson, R. J. Hurtado-Guerrero, R. Malaker, S. A. Schumann, B. 2022-09-15 doi:10.1101/2022.09.15.508093 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Inflammation-mediated Upregulation of VCAM-1 but not KIM-1 during Acute Kidney Injury to Chronic Kidney Disease Transition ]]> https://biorxiv.org/content/10.1101/2022.09.15.508151v1?rss=1 Melchinger, I. Guo, K. Guo, J. Xu, L. 2022-09-17 doi:10.1101/2022.09.15.508151 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Microbiota-stimulated Interleukin-22 regulates brain neurons and protects against stress-induced anxiety ]]> https://biorxiv.org/content/10.1101/2022.09.16.508224v1?rss=1 Ilanges, A. Xia, M. Lu, J. Chen, L. Shiao, R. Wang, C. Feng, R. Jin, Z. Yi, H. Qi, Q. Li, J. Schneeberger, M. Lu, B. Friedman, J. M. Yu, X. 2022-09-19 doi:10.1101/2022.09.16.508224 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Representing cells as sentences enables natural-language processing for single-cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.09.18.508438v1?rss=1 Dhodapkar, R. M. 2022-09-19 doi:10.1101/2022.09.18.508438 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ A neuron that regulates locomotion makes a potential sensory cilium lying over the C. elegans egg-laying apparatus ]]> https://biorxiv.org/content/10.1101/2022.09.19.508547v1?rss=1 Koelle, M. R. Christie, N. T. M. 2022-09-19 doi:10.1101/2022.09.19.508547 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut ]]> https://biorxiv.org/content/10.1101/2022.09.22.508973v1?rss=1 or < 2-fold) in the presence of high heme [219 heme-induced genes (HIGs) and 217 heme-repressed genes (HRGs)]. HIGs were enriched in Gene Ontology (GO) terms related to regulation of a variety of biological functions, including gene expression and metabolic processes. We observed that 11 out of 13 Sgm genes that were heme regulated in vitro were similarly regulated in bacteria that resided within tsetses midgut 24 hr (high heme environment) and 96 hr (low heme environment) after the flies had consumed a blood meal. We used intron mutagenesis to make insertion mutations in 12 Sgm HIGs and observed no significant change in growth in vitro in any of the mutant strains in high versus low heme conditions. However, Sgm strains that carried mutations in genes encoding a putative undefined phosphotransferase sugar (PTS) system component (SG2427), fucose transporter (SG0182), bacterioferritin (SG2280), and a DNA-binding protein (SGP1-0002) presented growth and/or survival defects in tsetse midguts as compared to normal Sgm. These findings suggest that the uptake up of sugars and storage of iron represent strategies that Sgm employs to successfully reside within the high heme environment of its tsetse hosts midgut. Our results are of epidemiological relevance, as many hematophagous arthropods house gut-associated bacteria that mediate their hosts competency as a vector of disease-causing pathogens. Author summaryTsetse flies feed exclusively on vertebrate blood. This nutrient source contains large quantities of heme, which can be toxic to the flys associated microorganisms. We investigated the genetic mechanisms that underlie the ability of the bacterial endosymbiont, Sodalis glossinidius, to successfully reside within tsetses heme-rich midgut. Exposure of cultured S. glossinidius to high levels of heme induced changes in the expression of genes that encode proteins involved in transcription, replication and repair of DNA, inorganic ion transport, and carbohydrate transport and metabolism processes. Changes in the expression of several of these same S. glossinidius genes also occurred within tsetses midgut following exposure to a blood meal. S. glossinidius genetically engineered to present mutations in several of these heme regulated genes were unable to successfully colonize tsetses gut. Our results provide insight into how bacteria that live in the gut of blood feeding arthropods mitigate the toxic effects of excessive heme. This information is of epidemiological relevance, as many of these bacteria influence their hosts ability to transmit disease pathogens that cause disease in humans and domesticated animals. ]]> Weiss, B. L. Runyen-Janecky, L. J. Scheutzow, J. Farsin, R. Cabo, L. F. Kuhn, K. M. Amador, R. D'Souza, S. J. Vigneron, A. Wall, K. E. 2022-09-22 doi:10.1101/2022.09.22.508973 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.09.22.509123v1?rss=1 Zhou, T. Gilliam, N. J. Li, S. Spaudau, S. Osborn, R. Anderson, C. S. Mariani, T. J. Thakar, J. Dewhurst, S. Mathews, D. H. Huang, L. Sun, Y. 2022-09-23 doi:10.1101/2022.09.22.509123 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Assembly and architecture of the type III secretion sorting platform ]]> https://biorxiv.org/content/10.1101/2022.09.23.509200v1?rss=1 Soto, J. E. Galan, J. E. Lara-Tejero, M. 2022-09-24 doi:10.1101/2022.09.23.509200 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin-beta receptor signaling ]]> https://biorxiv.org/content/10.1101/2022.09.23.509256v1?rss=1 Feng, X. Sun, R. Lee, M. Chen, X. Guo, S. Geng, H. Müschen, M. Choi, J. Pereira, J. P. 2022-09-28 doi:10.1101/2022.09.23.509256 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Cell-type specific deletions of Neuroligin 2 reveal a vital role of synaptic excitation-inhibition balance ]]> https://biorxiv.org/content/10.1101/2022.09.23.509267v1?rss=1 Longley, C. M. Xu, X. Messier, J. E. Cai, Z.-L. Park, J. W. Chen, H. Reznik, D. L. Jadi, M. P. Xue, M. 2022-09-24 doi:10.1101/2022.09.23.509267 Cold Spring Harbor Laboratory Press 2022-09-24 <![CDATA[ The maternal brain is more flexible and responsive at rest: effective connectivity of the parental caregiving network in postpartum mothers ]]> https://biorxiv.org/content/10.1101/2022.09.26.509524v1?rss=1 Orchard, E. R. Voigt, K. Chopra, S. Thapa Rana, T. Ward, P. G. Egan, G. F. Jamadar, S. D. 2022-09-28 doi:10.1101/2022.09.26.509524 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ The enrichment of self-domestication and neural crest function loci in the heritability of neurodevelopmental disorders is not independent of genomic regulatory functions ]]> https://biorxiv.org/content/10.1101/2022.09.26.509526v1?rss=1 Koller, D. Benitez-Burraco, A. Polimanti, R. 2022-09-27 doi:10.1101/2022.09.26.509526 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ ATR protects centromere identity by promoting DAXX association with PML nuclear bodies ]]> https://biorxiv.org/content/10.1101/2022.09.26.509554v1?rss=1 Trier, I. Joo, Y. K. Black, E. Kabeche, L. 2022-09-26 doi:10.1101/2022.09.26.509554 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Widespread sympatry in a species-rich clade of marine fishes (Carangoidei) ]]> https://biorxiv.org/content/10.1101/2022.09.26.509594v1?rss=1 Glass, J. R. Harrington, R. C. Cowman, P. F. Faircloth, B. C. Near, T. J. 2022-09-27 doi:10.1101/2022.09.26.509594 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Trends in self-citation rates in neuroscience literature ]]> https://biorxiv.org/content/10.1101/2022.09.27.509533v1?rss=1 Rosenblatt, M. Mehta, S. Peterson, H. Dadashkarimi, J. Rodriguez, R. X. Foster, M. L. Adkinson, B. D. Liang, Q. Kimble, V. M. Ye, J. McCusker, M. C. Farruggia, M. C. Rolison, M. Westwater, M. L. Jiang, R. Noble, S. Scheinost, D. 2022-09-28 doi:10.1101/2022.09.27.509533 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Developmental trajectories of the default mode, executive control, and salience networks from the third trimester through the newborn period ]]> https://biorxiv.org/content/10.1101/2022.09.27.509687v1?rss=1 Scheinost, D. Chang, J. Brennan-Wydra, E. Lacadie, C. Constable, R. T. Chawarska, K. Ment, L. R. 2022-09-28 doi:10.1101/2022.09.27.509687 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Cell type-independent profiling of interactions between intracellular pathogens and the human phosphoproteome ]]> https://biorxiv.org/content/10.1101/2022.09.27.509702v1?rss=1 Mohler, K. Moen, J. Rogulina, S. Rinehart, J. 2022-09-28 doi:10.1101/2022.09.27.509702 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Multi-scale observations of mangrove blue carbon fluxes; the NASA Carbon Monitoring System BlueFlux field campaign ]]> https://biorxiv.org/content/10.1101/2022.09.27.509753v1?rss=1 Poulter, B. Adams, F. Amaral, C. Barenblitt, A. Campbell, A. Charles, S. Cuesta, R. Delaria, E. Doughty, C. Fatoyinbo, T. Gewirtzman, J. Hanisco, T. Hull, M. Kawa, R. Hannun, R. Lagomasino, D. Lait, L. Malone, S. Newman, P. Raymond, P. Rosentreter, J. Thomas, N. Wolfe, G. Xiong, L. Ying, Q. Zhang, Z. 2022-09-28 doi:10.1101/2022.09.27.509753 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments ]]> https://biorxiv.org/content/10.1101/2022.09.28.509840v1?rss=1 Sehdev, A. Jayaram, V. Kadakia, N. Brown, E. Emonet, T. 2022-09-28 doi:10.1101/2022.09.28.509840 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Decoupled spectral tuning and eye size diversification patterns in an Antarctic adaptive radiation ]]> https://biorxiv.org/content/10.1101/2022.09.28.509872v1?rss=1 Yoder, E. B. Parker, C. E. Tew, A. Jones, C. D. Dornburg, A. 2022-09-28 doi:10.1101/2022.09.28.509872 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Wildflower phenological escape differs by continent and spring temperature ]]> https://biorxiv.org/content/10.1101/2022.09.28.509910v1?rss=1 Lee, B. R. Miller, T. Rosche, C. Yang, Y. Heberling, J. M. Kuebbing, S. E. Primack, R. B. 2022-09-30 doi:10.1101/2022.09.28.509910 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium ]]> https://biorxiv.org/content/10.1101/2022.09.28.509963v1?rss=1 Ghersi, J. J. Baldissera, g. Hintzen, J. Luff, S. A. Cheng, S. Xia, I. F. Sturgeon, C. M. Nicoli, S. 2022-09-30 doi:10.1101/2022.09.28.509963 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Altered CD8+ T cell associated aging gene signature in the peripheral blood of patients with Alzheimer's disease. ]]> https://biorxiv.org/content/10.1101/2022.09.29.510171v1?rss=1 Young, J. J. Park, H.-J. Kim, M. Par-Young, J. Bartlett, H. H. Kim, H. S. Shin, M. S. Unlu, S. Bucala, R. J. Van Dyck, C. H. Allore, H. G. Mecca, A. P. You, S. Kang, I. 2022-10-03 doi:10.1101/2022.09.29.510171 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ Spatial proteomics and iPSC modeling uncover mechanisms of axonal pathology in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.09.30.510408v1?rss=1 Cai, Y. Kanyo, J. Wilson, R. Mansuri, M. S. Cardozo, P. L. Goshay, D. Tian, Z. Braker, A. Trinh, H. K. Lam, T. Brennand, K. Nairn, A. C. Grutzendler, J. 2022-10-03 doi:10.1101/2022.09.30.510408 Cold Spring Harbor Laboratory Press 2022-10-03 <![CDATA[ The cellular states and fates of shed intestinal cells ]]> https://biorxiv.org/content/10.1101/2022.10.03.510592v1?rss=1 Bahar Halpern, K. Biram, A. Egozi, A. Korem Kohanim, Y. Shulman, Z. Itzkovitz, S. 2022-10-04 doi:10.1101/2022.10.03.510592 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Ultrasonic measures of prestin (SLC26a5) charge movements in membrane patches. ]]> https://biorxiv.org/content/10.1101/2022.10.03.510610v1?rss=1 Santos-Sacchi, J. Bai, J.-P. Navaratnam, D. S. 2022-10-05 doi:10.1101/2022.10.03.510610 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A graph-matching based metric of functional connectome distance between pairs of individuals varies with their ages, cognitive performances and familial relationships. ]]> https://biorxiv.org/content/10.1101/2022.10.03.510660v1?rss=1 Bukhari, S. H. U. F. Su, C. Dhamala, E. Gu, Z. Jamison, K. Kuceyeski, A. 2022-10-06 doi:10.1101/2022.10.03.510660 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Three transcriptional axes underpin anatomy, development, and disorders of the human cortex ]]> https://biorxiv.org/content/10.1101/2022.10.05.510582v1?rss=1 Dear, R. Seidlitz, J. Markello, R. D. Arnatkeviciute, A. Anderson, K. M. Bethlehem, R. A. I. Lifespan Brain Chart Consortium, Wagstyl, K. Bullmore, E. T. Raznahan, A. Vertes, P. 2022-10-06 doi:10.1101/2022.10.05.510582 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Diverse photoperiodic gene expression patterns are likely mediated by distinct transcriptional systems in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.10.05.510993v1?rss=1 Gendron, J. M. Leung, C. C. Tarte, D. A. Oliver, L. S. 2022-10-10 doi:10.1101/2022.10.05.510993 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ GESIAP: A Versatile Genetically Encoded Sensor-based Image Analysis Program ]]> https://biorxiv.org/content/10.1101/2022.10.05.511006v1?rss=1 Zheng, W. S. Zhang, Y. Zhu, R. E. Zhang, P. Gupta, S. Huang, L. Sahoo, D. Guo, K. Glover, M. E. Vadodaria, K. C. Li, M. Qian, T. Jing, M. Feng, J. Wan, J. Borden, P. M. Podgorski, K. Ali, F. Kwan, A. C. Gan, L. Lin, L. Gage, F. H. Venton, B. J. Marvin, J. S. Clinton, S. M. Zhang, M. Looger, L. Li, Y. Zhu, J. J. 2022-10-07 doi:10.1101/2022.10.05.511006 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Benchmarking Automated Cell Type Annotation Tools for Single-cell ATAC-seq Data ]]> https://biorxiv.org/content/10.1101/2022.10.05.511014v1?rss=1 Wang, Y. Sun, X. Zhao, H. 2022-10-10 doi:10.1101/2022.10.05.511014 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Chemico-genetic Analysis of Native Autism Proteomes Reveals Shared Biology Predictive of Functional Modifiers ]]> https://biorxiv.org/content/10.1101/2022.10.06.511211v1?rss=1 Gao, Y. Trn, M. Shonai, D. Zhao, J. Soderblom, E. J. Garcia-moreno, S. A. Gersbach, C. A. Wetsel, W. C. Dawson, G. Velmeshev, D. Jiang, Y.-h. Sloofman, L. Buxbaum, J. Soderling, S. H. 2022-10-07 doi:10.1101/2022.10.06.511211 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo ]]> https://biorxiv.org/content/10.1101/2022.10.07.511316v1?rss=1 May, D. Yun, S. Gonzalez, D. Park, S. Chen, Y. Lathrop, E. Cai, B. Xin, T. Zhao, H.-y. Wang, S. Gonzalez, L. E. Cockburn, K. Greco, V. 2022-10-07 doi:10.1101/2022.10.07.511316 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Tissue-Specific and Interorgan Metabolic Reprogramming Maintains Tolerance to Sepsis ]]> https://biorxiv.org/content/10.1101/2022.10.08.511411v1?rss=1 10% body weight loss, >50% reductions in oxygen consumption and carbon dioxide production, and near full suppression of voluntary activity for the 48 hours following sepsis as compared to sham-operated controls. We found increased correlations in the metabolome between liver, kidney, and spleen, with drastic loss of correlations between the heart and quadriceps metabolome and all other organs, pointing to a shared metabolic signature within vital abdominal organs, and unique metabolic signatures for skeletal and cardiac muscle during sepsis. A lowered GSH:GSSG and elevated AMP:ATP ratio in the liver underlie the significant upregulation of isotopically labeled glutamines contribution to TCA anaplerosis and glutamine-derived glutathione biosynthesis; meanwhile, the skeletal muscle and spleen were the only organs where glutamines contribution to the TCA cycle was significantly suppressed. These results highlight tissue-specific mitochondrial reprogramming, rather than global mitochondrial dysfunction, as a mechanistic consequence of sepsis. Using a multi-omic approach, we demonstrate a model by which sepsis-induced proteolysis fuels the livers production of anaplerotic substrates and the antioxidant glutathione to sustain tolerance to sepsis. ]]> Leitner, B. P. Lee, W. D. Zhu, W. Zhang, X. Gaspar, R. C. Li, Z. Rabinowitz, J. D. Perry, R. J. 2022-10-08 doi:10.1101/2022.10.08.511411 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Inflammation Of The Retinal Pigment Epithelium Drives Early-Onset Photoreceptor Degeneration In Mertk-Associated Retinitis Pigmentosa ]]> https://biorxiv.org/content/10.1101/2022.10.08.511415v1?rss=1 Mercau, M. E. Akalu, Y. T. Mazzoni, F. Gyimesi, G. Alberto, E. J. Kong, Y. Hafler, B. Finnemann, S. C. Rothlin, C. V. Ghosh, S. 2022-10-08 doi:10.1101/2022.10.08.511415 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions ]]> https://biorxiv.org/content/10.1101/2022.10.08.511420v1?rss=1 Shaw, T. R. Wisser, K. Schaffner, T. A. Gaffney, A. Machta, B. Veatch, S. L. 2022-10-08 doi:10.1101/2022.10.08.511420 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ 7q11.23 CNV alters protein synthesis and REST-mediated neuronal intrinsic excitability ]]> https://biorxiv.org/content/10.1101/2022.10.10.511483v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@1b0fa99org.highwire.dtl.DTLVardef@146624org.highwire.dtl.DTLVardef@13dc89aorg.highwire.dtl.DTLVardef@13d098f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mihailovich, M. Germain, P.-L. Shyti, R. Pozzi, D. Noberini, R. Liu, Y. Aprile, D. Tenderini, E. Troglio, F. Trattaro, S. Fabris, S. Ciptasari, U. Rigoli, M. T. Caporale, N. D Agostino, G. Vitriolo, A. Capocefalo, D. Skaros, A. Franchini, A. Ricciardi, S. Biunno, I. Neri, A. Kasri, N. N. Bonaldi, T. Aebersold, R. Matteoli, M. Testa, G. 2022-10-10 doi:10.1101/2022.10.10.511483 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ OPTIMIZED NEURON TRACING USING POST HOC REANALYSIS ]]> https://biorxiv.org/content/10.1101/2022.10.10.511642v1?rss=1 Azzouz, S. Walker, L. A. Doerner, A. Geisel, K. Rodriguez-Rivera, A. K. Li, Y. Roossien, D. H. Cai, D. 2022-10-13 doi:10.1101/2022.10.10.511642 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Prefrontal norepinephrine represents a threat prediction error under uncertainty ]]> https://biorxiv.org/content/10.1101/2022.10.13.511463v1?rss=1 Basu, A. Yang, J.-h. Yu, A. L. Glaeser-Khan, S. Feng, J. Krystal, J. H. Li, Y. Kaye, A. P. 2022-10-17 doi:10.1101/2022.10.13.511463 Cold Spring Harbor Laboratory Press 2022-10-17 <![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[ Declining autozygosity over time: an exploration in over 1 million individuals from three diverse cohorts ]]> https://biorxiv.org/content/10.1101/2022.10.13.512166v1?rss=1 Colbert, S. M. Wendt, F. R. Pathak, G. Helmer, D. A. Hauser, E. Keller, M. C. Polimanti, R. Johnson, E. C. 2022-10-17 doi:10.1101/2022.10.13.512166 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Identifying dynamic reproducible brain states using a predictive modelling approach ]]> https://biorxiv.org/content/10.1101/2022.10.14.512147v1?rss=1 O'Connor, D. Horien, C. Mandino, F. Constable, R. T. 2022-10-18 doi:10.1101/2022.10.14.512147 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Neural signatures of second language proficiency in narrative processing. ]]> https://biorxiv.org/content/10.1101/2022.10.14.512249v1?rss=1 Zhang, R. Wang, J. Lin, H. Turk-Browne, N. B. Cai, Q. 2022-10-17 doi:10.1101/2022.10.14.512249 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ A drug's most potent target is not necessarily the source of its anti-cancer activity ]]> https://biorxiv.org/content/10.1101/2022.10.16.512438v1?rss=1 30-fold higher concentrations than it inhibits p38. Finally, while deletion of the gene encoding p38 has no effect on ralimetinib sensitivity, expression of the EGFR-T790M gatekeeper mutation confers resistance to ralimetinib treatment. These findings suggest that future clinical trials involving ralimetinib could incorporate EGFR mutation status as a biomarker to identify sensitive patients. Moreover, our results demonstrate that a compounds anti-cancer effects should not necessarily be attributed to the protein that it inhibits most strongly, and instead, comprehensive cellular and genetic profiling is required to understand a drugs mechanism-of-action. ]]> Bhattacharjee, D. Bakar, J. Sausville, E. L. Mendelson, B. E. Long, K. Smith, J. C. Sheltzer, J. M. 2022-10-16 doi:10.1101/2022.10.16.512438 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ 7SK methylation Promotes Transcriptional Activity upon Growth Factor Stimulation ]]> https://biorxiv.org/content/10.1101/2022.10.17.512631v1?rss=1 Alarcon, C. R. Perez-Pepe, M. Desotell, A. W. Li, H. Li, W. Han, B. Lin, Q. Klein, D. E. Liu, Y. Goodarzi, H. 2022-10-18 doi:10.1101/2022.10.17.512631 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program ]]> https://biorxiv.org/content/10.1101/2022.10.18.512710v1?rss=1 Cheng, Y. Dao, C. Zhou, H. Li, B. Kember, R. L. Toikumo, S. Zhao, H. Gelernter, J. Kranzler, H. R. Justice, A. Xu, K. 2022-10-21 doi:10.1101/2022.10.18.512710 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ MLL1 regulates cytokine-driven cell migration and metastasis ]]> https://biorxiv.org/content/10.1101/2022.10.18.512715v1?rss=1 Nair, P. R. Danilova, L. Gomez-de-Mariscal, E. Kim, D. Fan, R. Munoz-Barrutia, A. Fertig, E. J. Wirtz, D. 2022-10-19 doi:10.1101/2022.10.18.512715 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Cancer-Associated Fibroblasts Regulate Patient-Derived Organoid Drug Responses ]]> https://biorxiv.org/content/10.1101/2022.10.19.512668v1?rss=1 2,500 colorectal cancer (CRC) PDOs and cancer-associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment-specific drug responses in thousands of single-cell datasets, we developed Trellis -- a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is patient-specific. We found drug-induced apoptosis does not correlate with genotype or clinical staging but does align with cell-intrinsic PTM signaling in PDOs. CAFs protect chemosensitive PDOs by shifting cancer cells into a slow-cycling cell-state and CAF chemoprotection can be reversed by inhibiting YAP. HighlightsO_LI>2,500 single-cell PTM signaling, DNA-damage, cell-cycle, and apoptosis responses from drug-treated PDOs and CAFs. C_LIO_LITrellis: hierarchical tree-based treatment effect method for single-cell screening analysis. C_LIO_LIPDOs have patient-specific drug responses that align with cell-intrinsic PTM signaling states. C_LIO_LICAFs chemoprotect PDOs by altering PDO cell-state via YAP signaling. C_LI ]]> Ramos Zapatero, M. Tong, A. Sufi, J. Vlckova, P. Cardoso Rodriguez, F. Nattress, C. Qin, X. Hochhauser, D. Krishnaswamy, S. Tape, C. J. 2022-10-21 doi:10.1101/2022.10.19.512668 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Long-term, super-resolution HIDE imaging of the inner mitochondrial membrane in live cells with a cell-permeant lipid probe ]]> https://biorxiv.org/content/10.1101/2022.10.19.512772v1?rss=1 Zheng, S. Dadina, N. Mozumdar, D. Lesiak, L. Martinez, K. Miller, E. Schepartz, A. 2022-10-19 doi:10.1101/2022.10.19.512772 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Improving fine-mapping by modeling infinitesimal effects ]]> https://biorxiv.org/content/10.1101/2022.10.21.513123v1?rss=1 Cui, R. Elzur, R. A. Kanai, M. Ulirsch, J. C. Weissbrod, O. Daly, M. Neale, B. Fan, Z. Finucane, H. K. 2022-10-24 doi:10.1101/2022.10.21.513123 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Forest bird decline and community change over 19 years in long-isolated South Asian tropical rainforest fragments ]]> https://biorxiv.org/content/10.1101/2022.10.22.513365v1?rss=1 Surendra, A. Raman, T. R. S. 2022-10-24 doi:10.1101/2022.10.22.513365 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Mechanotransduction events at the physiological site of touch detection ]]> https://biorxiv.org/content/10.1101/2022.10.23.513402v1?rss=1 Gracheva, E. O. Ziolkowski, L. H. Bagriantsev, S. N. 2022-10-24 doi:10.1101/2022.10.23.513402 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Spatially controlled microtubule nucleation and organization from crosslinker MAP65 condensates ]]> https://biorxiv.org/content/10.1101/2022.10.23.513406v1?rss=1 Sahu, S. Chauhan, P. Lumen, E. Moody, K. Peddireddy, K. Mani, N. Subramanian, R. Robertson-Anderson, R. M. Wolfe, A. Ross, J. L. 2022-10-23 doi:10.1101/2022.10.23.513406 Cold Spring Harbor Laboratory Press 2022-10-23 <![CDATA[ Oncogenic context shapes the fitness landscape of tumor suppression ]]> https://biorxiv.org/content/10.1101/2022.10.24.511787v1?rss=1 Blair, L. M. Juan, J. M. Sebastian, L. Tran, V. B. Nie, W. Wall, G. D. Gerceker, M. Lai, I. K. Apilado, E. A. Grenot, G. Amar, D. Foggetti, G. Do Carmo, M. Ugur, Z. Deng, D. Chenchik, A. Paz Zafra, M. Dow, L. E. Politi, K. MacQuitty, J. J. Petrov, D. A. Winslow, M. M. Rosen, M. J. Winters, I. P. 2022-10-26 doi:10.1101/2022.10.24.511787 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Helicobacter pylori FlgV forms a flagellar motor ring structure required for optimal motility ]]> https://biorxiv.org/content/10.1101/2022.10.24.513468v1?rss=1 Hoover, T. R. Botting, J. M. Tachiyama, S. Gibson, K. H. Liu, J. Starai, V. J. 2022-10-25 doi:10.1101/2022.10.24.513468 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ A SNP affects Wnt4 expression in endometrial stroma, with antagonistic implications for pregnancy, endometriosis and reproductive cancers ]]> https://biorxiv.org/content/10.1101/2022.10.25.513653v1?rss=1 Pavlicev, M. McDonough-Godlstein, C. Moset Zupan, A. Muglia, L. Hu, Y.-C. Kong, F. Monangi, N. Dagdas, G. Zupancic, N. Maziarz, J. Sinner, D. Wagner, G. Muglia, L. 2022-10-26 doi:10.1101/2022.10.25.513653 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Homotopic local-global parcellation of the human cerebral cortex from resting-state functional connectivity ]]> https://biorxiv.org/content/10.1101/2022.10.25.513788v1?rss=1 Yan, X. Kong, R. Xue, A. Yang, Q. Orban, C. An, L. Holmes, A. J. Qian, X. Chen, J. Zuo, X.-N. Zhou, J. H. Fortier, M. V. Tan, A. P. Gluckman, P. Chong, Y. S. Meaney, M. Bzdok, D. Eickhoff, S. B. Yeo, B. T. T. 2022-10-27 doi:10.1101/2022.10.25.513788 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Stochastic Spatiotemporal Simulation of a General Reaction System ]]> https://biorxiv.org/content/10.1101/2022.10.26.512711v1?rss=1 Loza, A. J. Sherman, M. S. 2022-10-28 doi:10.1101/2022.10.26.512711 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Statistical analysis supports pervasive RNA subcellular localization and alternative 3' UTR regulation ]]> https://biorxiv.org/content/10.1101/2022.10.26.513902v1?rss=1 Bierman, R. Salzman, J. 2022-10-27 doi:10.1101/2022.10.26.513902 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ KDM6A/UTX promotes spermatogenic gene expression across generations but is dispensable for male fertility ]]> https://biorxiv.org/content/10.1101/2022.10.27.513976v1?rss=1 Walters, B. W. Rainsford, S. R. Dias, N. Huang, X. de Rooij, D. G. Lesch, B. J. 2022-10-27 doi:10.1101/2022.10.27.513976 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Linking Choroid Plexus Enlargement with Plasma Analyte and Structural Phenotypes in Clinical High Risk for Psychosis: A Multisite Neuroimaging Study ]]> https://biorxiv.org/content/10.1101/2022.10.28.514160v1?rss=1 Bannai, D. Reuter, M. Hegde, R. Hoang, D. Adhan, I. Gandu, S. Pong, S. Zeng, A. Raymond, N. Zeng, V. Chung, Y. He, G. Sun, D. van Erp, T. G. M. Addington, J. Bearden, C. E. Cadenhead, K. Cornblatt, B. Mathalon, D. H. McGlashan, T. Jeffries, C. Stone, W. Tsuang, M. Walker, E. Woods, S. W. Cannon, T. D. Perkins, D. Keshavan, M. Lizano, P. 2022-10-30 doi:10.1101/2022.10.28.514160 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Spatiotemporal coordination of stem cell behavior following alveolar injury ]]> https://biorxiv.org/content/10.1101/2022.10.28.514255v1?rss=1 Chioccioli, M. Magruder, S. McDonough, J. E. Nouws, J. Gonzalez, D. Borriello, L. Traub, B. Ye, X. Hendry, C. E. Entenberg, D. Kaminski, N. Krishnaswamy, S. Sauler, M. 2022-10-30 doi:10.1101/2022.10.28.514255 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ Prefrontal allopregnanolone mediates the adverse effects of acute stress in a mouse model of tic pathophysiology ]]> https://biorxiv.org/content/10.1101/2022.10.29.514372v1?rss=1 Cadeddu, R. Van Zandt, M. Odeh, K. Anderson, C. J. Flanagan, D. Nordkild, P. Pittenger, C. J. Bortolato, M. 2022-10-31 doi:10.1101/2022.10.29.514372 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ The neuropeptidergic connectome of C. elegans ]]> https://biorxiv.org/content/10.1101/2022.10.30.514396v1?rss=1 Sanchez, L. R. Watteyne, J. Sun, H. Fernandez, R. Taylor, S. Weinreb, A. Hammarlund, M. Miller, D. Hobert, O. Beets, I. Vertes, P. Schafer, W. 2022-10-31 doi:10.1101/2022.10.30.514396 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ RSV-induced Expanded Ciliated Cells Contribute to Bronchial Wall Thickening ]]> https://biorxiv.org/content/10.1101/2022.10.31.514471v1?rss=1 Talukdar, S. N. Osan, J. Ryan, K. Grove, B. Perley, D. Kumar, B. D. Yang, S. Dallman, S. Hollingsworth, L. Bailey, K. L. Mehedi, M. 2022-11-01 doi:10.1101/2022.10.31.514471 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Automated community ecology using deep learning: a case study of planktonic foraminifera ]]> https://biorxiv.org/content/10.1101/2022.10.31.514514v1?rss=1 Hsiang, A. Y. Hull, P. M. 2022-11-01 doi:10.1101/2022.10.31.514514 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Ketamine induces multiple individually distinct whole-brain functional connectivity signatures ]]> https://biorxiv.org/content/10.1101/2022.11.01.514692v1?rss=1 Moujaes, F. Ji, J. L. Rahmati, M. Burt, J. Schleifer, C. H. Adkinson, B. Savic, A. Santamauro, N. Tamayo, Z. Diehl, C. Kolobaric, A. Flynn, M. Rieser, N. M. Fonteneau, C. Camarro, T. Xu, J. Cho, Y. Repovs, G. Fineberg, S. Morgan, P. Seifritz, E. Vollenweider, F. X. Krystal, J. Murray, J. D. Preller, K. H. Anticevic, A. 2022-11-01 doi:10.1101/2022.11.01.514692 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Environmental modulation of global epistasis is governed by effective genetic interactions ]]> https://biorxiv.org/content/10.1101/2022.11.02.514859v1?rss=1 Diaz-Colunga, J. Sanchez, A. Ogbunugafor, C. B. 2022-11-03 doi:10.1101/2022.11.02.514859 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ 5-MeO-DMT modifies innate behaviors and promotes structural neural plasticity in mice ]]> https://biorxiv.org/content/10.1101/2022.11.03.515044v1?rss=1 Jefferson, S. J. Gregg, I. Dibbs, M. Liao, C. Wu, H. Davoudian, P. A. Sprouse, J. S. Sherwood, A. M. Kaye, A. P. Pittenger, C. Kwan, A. C. 2022-11-03 doi:10.1101/2022.11.03.515044 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ The Cousa objective: a long working distance air objective for multiphoton imaging in vivo ]]> https://biorxiv.org/content/10.1101/2022.11.06.515343v1?rss=1 4 mm2 field-of-view with submicron lateral resolution, and is compatible with commonly used multiphoton imaging systems. We share the full optical prescription, and report performance including in vivo 2-photon and 3-photon imaging in a range of species and preparations. ]]> Yu, C.-H. Yu, Y. Adsit, L. M. Chang, J. T. Barchini, J. Moberly, A. H. Benisty, H. Kim, J. Ricci, A. J. Fitzpatrick, D. Cardin, J. A. Higley, M. Smith, G. B. Nielsen, K. J. Smith, I. T. Smith, S. L. 2022-11-06 doi:10.1101/2022.11.06.515343 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Microtubule binding-induced allostery promotes LIS1 dissociation from dynein prior to cargo transport ]]> https://biorxiv.org/content/10.1101/2022.11.08.515461v1?rss=1 Ton, W. D. Wang, Y. Chai, P. Beauchamp-Perez, C. Flint, N. T. Lammers, L. G. Xiong, H. Zhang, K. Markus, S. M. 2022-11-08 doi:10.1101/2022.11.08.515461 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Human Nucleolar Protein 7 (NOL7) is required for pre-rRNA transcription and pre-18S rRNA processing ]]> https://biorxiv.org/content/10.1101/2022.11.08.515626v1?rss=1 McCool, M. A. Bryant, C. J. Huang, H. Ogawa, L. M. Farley-Barnes, K. I. Sondalle, S. B. Abriola, L. Surovtseva, Y. V. Baserga, S. J. 2022-11-08 doi:10.1101/2022.11.08.515626 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty ]]> https://biorxiv.org/content/10.1101/2022.11.14.516371v1?rss=1 Farmer, R. Apps, R. Quiel, J. Sellers, B. Cheung, F. Chen, J. Mukherjee, A. McGuire, P. Tsang, J. S. 2022-11-16 doi:10.1101/2022.11.14.516371 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Social Curiosity in Monkeys ]]> https://biorxiv.org/content/10.1101/2022.11.15.516657v1?rss=1 Joiner, J. A. Nair, A. R. Fagan, N. A. Chang, S. W. C. 2022-11-15 doi:10.1101/2022.11.15.516657 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Emergence of division of labor in tissues through cell interactions and spatial cues ]]> https://biorxiv.org/content/10.1101/2022.11.16.516540v1?rss=1 Adler, M. Moriel, N. Goeva, A. Avraham-Davidi, I. Mages, S. Adams, T. S. Kaminski, N. Macosko, E. Z. Regev, A. Medzhitov, R. Nitzan, M. 2022-11-17 doi:10.1101/2022.11.16.516540 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ The Cul5 E3 Ligase Complex Is a Key Negative Feedback Regulator of TCR/IL2 Signaling and Anti-Tumor Activity in CD8+ T Cells ]]> https://biorxiv.org/content/10.1101/2022.11.16.516824v1?rss=1 Liao, X. Li, W. Li, A. Rajendran, B. K. Ren, J. Zhou, H. Calderwood, D. Turk, B. Tang, W. Liu, Y. Wu, D. 2022-11-17 doi:10.1101/2022.11.16.516824 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ SARS-CoV-2 exposure in Norwegian rats (Rattus norvegicus) from New York City ]]> https://biorxiv.org/content/10.1101/2022.11.18.517156v1?rss=1 Wang, Y. Lenoch, J. Kohler, D. DeLiberto, T. Tang, C. Li, T. Tao, Y. Guan, M. Compton, S. Zeiss, C. J. Hang, J. Wan, X.-F. 2022-11-21 doi:10.1101/2022.11.18.517156 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Maximum Classifier Discrepancy Generative Adversarial Network for Jointly Harmonizing Scanner Effects and Improving Reproducibility of Downstream Tasks ]]> https://biorxiv.org/content/10.1101/2022.11.19.517154v1?rss=1 Yan, W. Fu, Z. Jiang, R. Sui, J. Calhoun, V. 2022-11-22 doi:10.1101/2022.11.19.517154 Cold Spring Harbor Laboratory Press 2022-11-22 <![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[ Large-scale signal and noise correlations configure multi-task coding in human brain networks ]]> https://biorxiv.org/content/10.1101/2022.11.23.517699v1?rss=1 Ito, T. Murray, J. D. 2022-11-24 doi:10.1101/2022.11.23.517699 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Fast actin disassembly and fimbrin mechanosensitivity support rapid turnover during clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/2022.11.25.517735v1?rss=1 Mousavi, S. I. Lacy, M. M. Li, X. Berro, J. 2022-11-25 doi:10.1101/2022.11.25.517735 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Reconceptualizing beta diversity: a hypervolume geometric approach ]]> https://biorxiv.org/content/10.1101/2022.11.27.518099v1?rss=1 Song, C. Lu, M. Bennett, J. R. Gilbert, B. Fortin, M.-J. Gonzalez, A. 2022-11-28 doi:10.1101/2022.11.27.518099 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Unclearing Microscopy ]]> https://biorxiv.org/content/10.1101/2022.11.29.518361v1?rss=1 8,000 volumetrically and opaquing their bulk with light-scattering molecules of sufficient density, cell microstructure can now be discerned with a contrast visible to the unaided eye. We further inspect uncleared samples with transmitted light microscopy modalities and prove that 3D ultrastructural features, previously accessible only with super-resolution fluorescence or electron microscopy methods, can now be visualized with simple magnification optics alone. ]]> M'Saad, O. Shribak, M. Bewersdorf, J. 2022-12-02 doi:10.1101/2022.11.29.518361 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Individual Decision-Making Underlying the Tragedy of the Commons ]]> https://biorxiv.org/content/10.1101/2022.11.29.518377v1?rss=1 Chawla, M. Piva, M. Ahmed, S. Jia, R. Levy, I. Chang, S. W. C. 2022-11-29 doi:10.1101/2022.11.29.518377 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Polyvalent mRNA vaccination elicited potent immune response to monkeypox surface antigens ]]> https://biorxiv.org/content/10.1101/2022.11.29.518427v1?rss=1 Fang, Z. Renauer, P. A. Suzuki, K. Chen, S. 2022-11-29 doi:10.1101/2022.11.29.518427 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ The Role of the 3-Dimensional Genome in New Gene Evolution ]]> https://biorxiv.org/content/10.1101/2022.11.30.518413v1?rss=1 Lee, U. Arsala, D. Xia, S. Ali, M. Sobreira, D. Eres, I. Zhou, Q. Long, M. 2022-12-01 doi:10.1101/2022.11.30.518413 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Changes in gut microbiome composition drive fentanyl intake and striatal proteomic changes ]]> https://biorxiv.org/content/10.1101/2022.11.30.518531v1?rss=1 Hofford, R. S. Meckel, K. R. Wang, W. Kim, M. Godino, A. Lam, T. T. Kiraly, D. 2022-12-01 doi:10.1101/2022.11.30.518531 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ An Autoimmune Transcriptional Circuit Driving Foxp3+ Regulatory T cell Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.12.02.518871v1?rss=1 Hafler, D. A. Sumida, T. S. Lincoln, M. R. He, L. Park, Y. Ota, M. Stillwell, H. A. Leissa, G. A. Fujio, K. Kulminski, A. Epstein, C. B. Bernstein, B. E. Kellis, M. 2022-12-03 doi:10.1101/2022.12.02.518871 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma ]]> https://biorxiv.org/content/10.1101/2022.12.03.518966v1?rss=1 Obacz, J. Nibhani, R. Adams, T. S. Schupp, J. C. Valer, J. A. Veale, N. Aresu, G. Coonar, A. S. Peryt, A. Biffi, G. Kaminski, N. Francies, H. E. Rassl, D. Garnett, M. Rintoul, R. C. Marciniak, S. J. 2022-12-05 doi:10.1101/2022.12.03.518966 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell ]]> https://biorxiv.org/content/10.1101/2022.12.05.519090v1?rss=1 Liu, Z. Liu, T. Sun, W. Zhao, Y. Wang, X. 2022-12-08 doi:10.1101/2022.12.05.519090 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ The build-up of the present-day tropical diversity of tetrapods ]]> https://biorxiv.org/content/10.1101/2022.12.05.519156v1?rss=1 Quintero, I. Landis, M. J. Jetz, W. MORLON, H. 2022-12-08 doi:10.1101/2022.12.05.519156 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification ]]> https://biorxiv.org/content/10.1101/2022.12.07.519534v1?rss=1 Kang, T.-Y. Bocci, F. Nie, Q. Onuchic, J. N. Levchenko, A. 2022-12-12 doi:10.1101/2022.12.07.519534 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Regulation of Nuclear Transcription by Mitochondrial RNA ]]> https://biorxiv.org/content/10.1101/2022.12.10.519922v1?rss=1 Sriram, K. Qi, Z. Yuan, D. Malhi, N. K. Liu, X. Calandrelli, R. Luo, Y. Jin, S. Shi, J. Salas, M. Dang, R. Armstrong, B. Priceman, S. J. Wang, P. Liao, J. Natarajan, R. Zhong, S. Chen, Z. B. 2022-12-11 doi:10.1101/2022.12.10.519922 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ SpaGFT is a graph Fourier transform for tissue module identification from spatially resolved transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.12.10.519929v1?rss=1 Chang, Y. Liu, J. Ma, A. Li, Z. Liu, B. Ma, Q. 2022-12-13 doi:10.1101/2022.12.10.519929 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes ]]> https://biorxiv.org/content/10.1101/2022.12.12.519811v1?rss=1 MacGuigan, D. J. Krabbenhoft, T. J. Harrington, R. C. Wainwright, D. K. Backenstose, N. J. C. Near, T. J. 2022-12-14 doi:10.1101/2022.12.12.519811 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. C 2022-12-13 doi:10.1101/2022.12.12.519838 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Evaluation of a scalable approach to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells ]]> https://biorxiv.org/content/10.1101/2022.12.13.520148v1?rss=1 Dillard, L. J. Rosenow, W. T. Calabrese, G. M. Mesner, L. D. Al-Barghouthi, B. M. Abood, A. Farber, E. A. Onengut-Gumuscu, S. Tommasini, S. M. Horowitz, M. A. Rosen, C. J. Yao, L. Qin, L. Farber, C. R. 2022-12-14 doi:10.1101/2022.12.13.520148 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Cell-type-specific co-expression inference from single cell RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/2022.12.13.520181v1?rss=1 Su, C. Xu, Z. Shan, X. Cai, B. Zhao, H. Zhang, J. 2022-12-15 doi:10.1101/2022.12.13.520181 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Robust hierarchically organized whole-brain patterns of dysconnectivity in schizophrenia spectrum disorders observed after Personalized Intrinsic Network Topography ]]> https://biorxiv.org/content/10.1101/2022.12.13.520333v1?rss=1 Dickie, E. W. Shahab, S. Hawco, C. Miranda, D. Herman, G. Argyelan, M. Ji, J. L. W. Jeyachandra, J. Anticevic, A. Malhotra, A. K. Voineskos, A. N. 2022-12-15 doi:10.1101/2022.12.13.520333 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Transcriptional Responses of Cancer Cells to Heat Shock-Inducing Stimuli Involve Amplification of Robust HSF1 Binding ]]> https://biorxiv.org/content/10.1101/2022.12.14.519647v1?rss=1 Ghosh Dastidar, S. De Kumar, B. Lauckner, B. Parrello, D. Perley, D. Vlasenok, M. Tyagi, A. Koney-Kwaku Koney, N. Abbas, A. Nechaev, S. 2022-12-15 doi:10.1101/2022.12.14.519647 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Atypical language network lateralization is reflected throughout the macroscale functional organization of cortex ]]> https://biorxiv.org/content/10.1101/2022.12.14.520417v1?rss=1 Labache, L. Ge, T. Yeo, B. T. T. Holmes, A. J. 2022-12-15 doi:10.1101/2022.12.14.520417 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Predictability of the community-function landscape in wine yeast ecosystems ]]> https://biorxiv.org/content/10.1101/2022.12.15.520418v1?rss=1 Ruiz, J. de Celis, M. Diaz-Colunga, J. Vila, J. C. C. Benitez-Dominguez, B. VICENTE, J. Santos, A. Sanchez, A. Belda, I. 2022-12-16 doi:10.1101/2022.12.15.520418 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Quantifying constraint in human mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/2022.12.16.520778v1?rss=1 Lake, N. J. Liu, W. Battle, S. L. Laricchia, K. M. Tiao, G. Compton, A. G. Cowie, S. Christodoulou, J. Thorburn, D. R. Zhao, H. Arking, D. E. Sunyaev, S. R. Lek, M. 2022-12-19 doi:10.1101/2022.12.16.520778 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ A phylogenetic approach to studying the roles of within-host evolution and between-host transmission of resistance for clinical Escherichia coli infections ]]> https://biorxiv.org/content/10.1101/2022.12.16.520823v1?rss=1 Van Nouhuijs, F. Arakkal Antony, M. Orcales, F. Gozashti, L. Roy, S. W. Ogbunugafor, C. B. Pennings, P. S. 2022-12-19 doi:10.1101/2022.12.16.520823 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ NeuroDecodeR: A package for neural decoding analyses in R ]]> https://biorxiv.org/content/10.1101/2022.12.17.520811v1?rss=1 Meyers, E. M. 2022-12-20 doi:10.1101/2022.12.17.520811 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ LRRK2 Suppresses Lysosome Degradative Activity in Macrophages and Microglia via Transcription Factor E3 Inhibition ]]> https://biorxiv.org/content/10.1101/2022.12.17.520834v1?rss=1 Yadavalli, N. Ferguson, S. 2022-12-18 doi:10.1101/2022.12.17.520834 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Brain-based predictions of psychiatric illness-linked behaviors across the sexes ]]> https://biorxiv.org/content/10.1101/2022.12.18.520947v1?rss=1 Dhamala, E. Ooi, L. Q. R. Chen, J. Ricard, J. A. Berkeley, E. Chopra, S. Qu, Y. Lawhead, C. Yeo, B. T. T. Holmes, A. 2022-12-19 doi:10.1101/2022.12.18.520947 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Calcium flux through ER-TGN contact sites facilitates cargo export ]]> https://biorxiv.org/content/10.1101/2022.12.19.521097v1?rss=1 Ramazanov, B. R. Di Martino, R. Kumar, A. PARCHURE, A. Kim, Y. Griesbeck, O. Schwartz, M. A. Luini, A. von Blume, J. 2022-12-19 doi:10.1101/2022.12.19.521097 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Friction patterns guide actin network contraction ]]> https://biorxiv.org/content/10.1101/2022.12.21.521384v1?rss=1 Colin, A. Orhant-Prioux, M. Guerin, C. Savinov, M. Scarfone, I. Roux, A. De La Cruz, E. M. Mogilner, A. Thery, M. Blanchoin, L. 2022-12-22 doi:10.1101/2022.12.21.521384 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 locus mismatches associated with long-term renal transplant survival ]]> https://biorxiv.org/content/10.1101/2022.12.21.521481v1?rss=1 Sun, Z. Zhang, Z. Banu, K. Gibson, I. Colvin, R. Yi, Z. Zhang, W. Kumar, B. D. Pell, J. Djamali, A. Gallon, L. O Connell, P. He, C. Pober, J. Heeger, P. Menon, M. C. 2022-12-22 doi:10.1101/2022.12.21.521481 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Cx26 heterozygous mutations cause hyperacusis-like hearing sensitivity enhancement and increase susceptibility to noise ]]> https://biorxiv.org/content/10.1101/2022.12.23.521807v1?rss=1 50% of nonsyndromic hearing loss. Its recessive hetero-mutation carriers, who have no deafness, occupy [~]10-20% of the general population. Here, we report an unexpected finding that these heterozygote carriers have hearing over-sensitivity and active cochlear amplification increased. Mouse models show that Cx26 hetero-deletion reduced endocochlear potential (EP) generation in the cochlear lateral wall and caused outer hair cell electromotor protein prestin compensatively upregulated to increase active cochlear amplification and hearing sensitivity. The increase of active cochlear amplification also increased sensitivity to noise; exposure of daily-level noise could cause Cx26+/- mice permanent hearing threshold shift leading to hearing loss. This study demonstrate that Cx26 recessive heterozygous mutations are not harmless for hearing as previously considered and can cause hyperacusis-like hearing over-sensitivity. The data also indicate that GJB2 hetero-mutation carriers are vulnerable to noise and should avoid noise exposure in daily-life. TeaserCx26 hetero-mutations are not harmless and can cause hearing over-sensitivity and increase susceptibility to noise. ]]> Liu, L.-M. Liang, C. Chen, J. Fang, S. Zhao, H.-B. 2022-12-23 doi:10.1101/2022.12.23.521807 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Asymmetric HIV-1 envelope trimers bound to one and two CD4 molecules are intermediates during membrane binding ]]> https://biorxiv.org/content/10.1101/2022.12.23.521843v1?rss=1 Li, W. Nand, E. Qin, Z. Grunst, M. W. Grover, J. R. Bess, J. W. Lifson, J. D. Zwick, M. B. Tagare, H. D. Uchil, P. D. Mothes, W. 2022-12-24 doi:10.1101/2022.12.23.521843 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ Reduced progranulin increases tau and alpha-synuclein inclusions and alters phenotypes of tauopathy mice via glucocerebrosidase ]]> https://biorxiv.org/content/10.1101/2022.12.25.521308v1?rss=1 Takahashi, H. Bhagwagar, S. Nies, S. H. Chiasseu, M. T. Wang, G. Mackenzie, I. R. Strittmatter, S. M. 2022-12-25 doi:10.1101/2022.12.25.521308 Cold Spring Harbor Laboratory Press 2022-12-25 <![CDATA[ A new framework for metabolic connectivity mapping using bolus FDG PET and kinetic modelling ]]> https://biorxiv.org/content/10.1101/2022.12.27.522050v1?rss=1 Volpi, T. Vallini, G. Silvestri, E. De Francisci, M. Durbin, T. Corbetta, M. Lee, J. J. Vlassenko, A. G. Goyal, M. S. Bertoldo, A. 2022-12-30 doi:10.1101/2022.12.27.522050 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Systemic effects of melanoma-secreted MIDKINE in the inhibition of dendritic cell differentiation and function ]]> https://biorxiv.org/content/10.1101/2022.12.28.521901v1?rss=1 Catena, X. Contreras, M. Cerezo-Wallis, D. Larrea, N. J. Olmeda, D. Calvo, G. G. Mucientes, C. Oterino, S. Soengas, M. S. 2022-12-31 doi:10.1101/2022.12.28.521901 Cold Spring Harbor Laboratory Press 2022-12-31 <![CDATA[ BRCA2 chaperones RAD51 to single molecules of RPA-coated ssDNA ]]> https://biorxiv.org/content/10.1101/2022.12.28.522061v1?rss=1 Bell, J. C. Dombrowski, C. C. Plank, J. L. Jensen, R. B. Kowalczykowski, S. C. 2022-12-29 doi:10.1101/2022.12.28.522061 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ The C. elegans Anchor Cell Transcriptome: Ribosome Biogenesis Drives Cell Invasion through Basement Membrane ]]> https://biorxiv.org/content/10.1101/2022.12.28.522136v1?rss=1 Costa, D. S. Kenny-Ganzert, I. W. Chi, Q. Park, K. Kelley, L. C. Garde, A. Matus, D. Q. Park, J. Yogev, S. Goldstein, B. Gibney, T. V. Pani, A. M. Sherwood, D. R. 2022-12-29 doi:10.1101/2022.12.28.522136 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Circuit to target approach defines an autocrine myofibroblast loop that drives cardiac fibrosis ]]> https://biorxiv.org/content/10.1101/2023.01.01.522422v1?rss=1 Miyara, S. Adler, M. Bassat, E. Divinsky, Y. Umansky, K. B. Elkahal, J. Genzelinakh, A. Kain, D. Lendengolts, D. Shalit, T. Gershovits, M. Shakked, A. Zhang, L. Wang, J. Kimchi, D. M. Baehr, A. Sarig, R. Kupatt, C. Tanaka, E. M. Medzhitov, R. Mayo, A. Alon, U. Tzahor, E. 2023-01-03 doi:10.1101/2023.01.01.522422 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Regulated Induced Proximity Targeting Chimeras (RIPTACs): a Novel Heterobifunctional Small Molecule Therapeutic Strategy for Killing Cancer Cells Selectively ]]> https://biorxiv.org/content/10.1101/2023.01.01.522436v1?rss=1 Raina, K. Forbes, C. D. Stronk, R. Rappi, J. P. Eastman, K. J. Gerritz, S. W. Yu, X. Li, H. Bhardwaj, A. Forgione, M. Hundt, A. King, M. P. Posner, Z. M. Denny, A. McGovern, A. Puleo, D. E. Garvin, E. Chenard, R. Zaware, N. Mousseau, I. J. Macaluso, J. Martin, M. Bassoli, K. Jones, K. Garcia, M. Howard, K. Smith, L. M. Chen, J. M. De Leon, C. A. Hines, J. Kayser-Bricker, K. J. Crews, C. M. 2023-01-02 doi:10.1101/2023.01.01.522436 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Pan-genome study underling the extent of genomic variation of invasive Streptococcus pneumoniae in Malawi ]]> https://biorxiv.org/content/10.1101/2023.01.02.522535v1?rss=1 Iranzadeh, A. Alisoltani, A. Kiran, A. Breiman, R. Chaguza, C. Peno, C. French, N. Cornick, J. E. Everett, D. B. Mulder, N. 2023-01-03 doi:10.1101/2023.01.02.522535 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories ]]> https://biorxiv.org/content/10.1101/2023.01.04.522730v1?rss=1 Piovani, L. Leite, D. J. Yanez-Guerra, L. A. Simpson, F. Musser, J. M. Salvador-Martinez, I. A. Marletaz, F. Jekely, G. Telford, M. J. 2023-01-04 doi:10.1101/2023.01.04.522730 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Drosophila integrates visual evidence and counterevidence in self motion estimation ]]> https://biorxiv.org/content/10.1101/2023.01.04.522814v1?rss=1 Tanaka, R. Zhou, B. Agrochao, M. Badwan, B. A. Au, B. Matos, N. C. B. Clark, D. A. 2023-01-05 doi:10.1101/2023.01.04.522814 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ When Geometric Deep Learning Meets Pretrained Protein Language Models ]]> https://biorxiv.org/content/10.1101/2023.01.05.522958v1?rss=1 Wu, F. Radev, D. Xu, J. 2023-01-06 doi:10.1101/2023.01.05.522958 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Long timescale anti-directional rotation in Drosophila optomotor behavior ]]> https://biorxiv.org/content/10.1101/2023.01.06.523055v1?rss=1 Mano, O. Choi, M. Tanaka, R. Creamer, M. S. Castelo Branco Matos, N. Shomar, J. Badwan, B. A. Clandinin, T. R. Clark, D. A. 2023-01-07 doi:10.1101/2023.01.06.523055 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Ex Vivo Biomechanical Characterization of Umbilical Vessels: Possible Shunts in Congenital Heart Palliation ]]> https://biorxiv.org/content/10.1101/2023.01.07.523118v1?rss=1 Murtada, S.-I. Ramachandra, A. B. Humphrey, J. D. 2023-01-08 doi:10.1101/2023.01.07.523118 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry ]]> https://biorxiv.org/content/10.1101/2023.01.09.523326v1?rss=1 Bai, N. Adeshina, Y. Bychkov, I. Xia, Y. Gowthaman, R. Miller, S. A. Gupta, A. K. Johnson, D. K. Lan, L. Golemis, E. A. Makhov, P. B. Xu, L. Pillai, M. M. Boumber, Y. Karanicolas, J. 2023-01-10 doi:10.1101/2023.01.09.523326 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Oncogene-like addiction to aneuploidy in human cancers ]]> https://biorxiv.org/content/10.1101/2023.01.09.523344v1?rss=1 Girish, V. Lakhani, A. A. Scaduto, C. M. Thompson, S. L. Brown, L. M. Hagenson, R. A. Sausville, E. L. Mendelson, B. E. Lukow, D. A. Yuan, M. L. Kandikuppa, P. K. Stevens, E. C. Lee, S. N. Salovska, B. Li, W. Smith, J. C. Taylor, A. M. Martienssen, R. A. Liu, Y. Sun, R. Sheltzer, J. M. 2023-01-10 doi:10.1101/2023.01.09.523344 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Physical mechanisms of red blood cell splenic filtration ]]> https://biorxiv.org/content/10.1101/2023.01.10.523245v1?rss=1 Moreau, A. Yaya, F. Lu, H. Surendranath, A. Charrier, A. Dehapiot, B. Helfer, E. Viallat, A. Peng, Z. 2023-01-10 doi:10.1101/2023.01.10.523245 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Smooth Muscle Cell Death Drives an Osteochondrogenic Phenotype and Severe Proximal Vascular Disease in Progeria ]]> https://biorxiv.org/content/10.1101/2023.01.10.523266v1?rss=1 Murtada, S.-I. Kawamura, Y. Cavinato, C. Wang, M. Ramachandra, A. B. Spronck, B. Tellides, G. Humphrey, J. 2023-01-11 doi:10.1101/2023.01.10.523266 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Identification of Cell-Type Specific Alternative Transcripts in the Multicellular Alga Volvox carteri ]]> https://biorxiv.org/content/10.1101/2023.01.10.523483v1?rss=1 Balasubramanian, R. N. Umen, J. G. 2023-01-12 doi:10.1101/2023.01.10.523483 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Online abstraction during statistical learning revealed by neural entrainment from intracranial recordings ]]> https://biorxiv.org/content/10.1101/2023.01.11.523605v1?rss=1 Sherman, B. E. Aljishi, A. Graves, K. N. Quraishi, I. H. Sivaraju, A. Damisah, E. C. Turk-Browne, N. B. 2023-01-12 doi:10.1101/2023.01.11.523605 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Class switching is differentially regulated in RBC alloimmunization and vaccination ]]> https://biorxiv.org/content/10.1101/2023.01.11.523608v1?rss=1 Prakash, A. Medved, J. Arneja, A. Niebuhr, C. Li, A. N. Tarrah, S. Boscia, A. R. Burnett, E. D. Singh, A. Salazar, J. E. Xu, W. Santhanakrishnan, M. Hendrickson, J. E. Luckey, C. J. 2023-01-12 doi:10.1101/2023.01.11.523608 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ End Binding protein 1 promotes specific motor-cargo association in the cell body prior to axonal delivery of Dense Core Vesicles ]]> https://biorxiv.org/content/10.1101/2023.01.12.523768v1?rss=1 Park, J. Miller, K. G. De Camilli, P. Yogev, S. 2023-01-12 doi:10.1101/2023.01.12.523768 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ The neural activity of auditory conscious perception ]]> https://biorxiv.org/content/10.1101/2023.01.12.523829v1?rss=1 Christison-Lagay, K. L. Freedman, N. C. Micek, C. Khalaf, A. Kronemer, S. I. Gusso, M. M. Kim, L. Forman, S. Ding, J. Aksen, M. Abdel-Aty, A. Kwon, H. Markowitz, N. Yeagle, E. Espinal, E. Herrero, J. Bickel, S. Young, J. Mehta, A. Wu, K. Gerrard, J. Damisah, E. Spencer, D. Blumenfeld, H. 2023-01-13 doi:10.1101/2023.01.12.523829 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.13.523996v1?rss=1 Aranda-Diaz, A. Willis, L. Nguyen, T. H. Ho, P.-Y. Vila, J. Thomsen, T. Chavez, T. Yan, R. Yu, F. B. Neff, N. Sanchez, A. Estrela, S. Huang, K. 2023-01-14 doi:10.1101/2023.01.13.523996 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Using a Topic Model to Map and Analyze a Large Curriculum ]]> https://biorxiv.org/content/10.1101/2023.01.14.524073v1?rss=1 Takizawa, P. 2023-01-17 doi:10.1101/2023.01.14.524073 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ LDL Receptor-Related Protein 5 is a Selective Transporter for Unesterified Polyunsaturated Fatty Acids ]]> https://biorxiv.org/content/10.1101/2023.01.16.524146v1?rss=1 Tang, W. Luan, Y. Yuan, Q. Li, A. Chen, S. Menacherry, S. Young, L. Wu, D. D. 2023-01-17 doi:10.1101/2023.01.16.524146 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Apoptosis recognition receptors regulate skin tissue repair in mice ]]> https://biorxiv.org/content/10.1101/2023.01.17.523241v1?rss=1 Justynski, O. Bridges, K. Krause, W. Forni, M. F. Phan, Q. Sandoval-Schaefer, T. Driskell, R. Miller-Jensen, K. Horsley, V. 2023-01-17 doi:10.1101/2023.01.17.523241 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Metacognitive Judgments during Visuomotor Learning Reflect the Integration of Error History ]]> https://biorxiv.org/content/10.1101/2023.01.17.524436v1?rss=1 Hewitson, C. L. McDougle, S. Al-Fawakhiri, N. 2023-01-20 doi:10.1101/2023.01.17.524436 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ A deep generative model of the SARS-CoV-2 spike protein predicts future variants ]]> https://biorxiv.org/content/10.1101/2023.01.17.524472v1?rss=1 Dhodapkar, R. M. 2023-01-18 doi:10.1101/2023.01.17.524472 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Hepatocyte-specific miR-33 deletion attenuates NAFLD-NASH-HCC progression ]]> https://biorxiv.org/content/10.1101/2023.01.18.523503v1?rss=1 FERNANDEZ TUSSY, P. Sun, J. Cardelo, M. P. Price, N. L. Goedeke, L. Xirouchaki, C. E. Yang, X. Pastor-Rojo, O. Bennett, A. M. Tiganis, T. Suarez, Y. Fernandez-Hernando, C. 2023-01-20 doi:10.1101/2023.01.18.523503 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Immune sensing of food allergens promotes aversive behaviour ]]> https://biorxiv.org/content/10.1101/2023.01.19.524823v1?rss=1 Florsheim, E. B. Bachtel, N. D. Cullen, J. Costa Lima, B. G. Godazgar, M. Zhang, C. Carvalho, F. Gautier, G. Launay, P. Wang, A. Dietrich, M. O. Medzhitov, R. 2023-01-21 doi:10.1101/2023.01.19.524823 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires ]]> https://biorxiv.org/content/10.1101/2023.01.21.525004v1?rss=1 Guberman-Pfeffer, M. J. 2023-01-22 doi:10.1101/2023.01.21.525004 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Netrin-1 binding to Unc5B regulates Blood-Retina Barrier integrity ]]> https://biorxiv.org/content/10.1101/2023.01.21.525006v1?rss=1 Furtado, J. Geraldo, L. H. Leser, F. S. Poulet, M. Park, H. Pibouin-Fragner, L. Eichmann, A. Boye, K. 2023-01-21 doi:10.1101/2023.01.21.525006 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Adult-specific Reelin expression alters striatal neuronal organization. Implications for neuropsychiatric disorders. ]]> https://biorxiv.org/content/10.1101/2023.01.21.525025v1?rss=1 Pardo, M. Gregorio, S. Montalban, E. Pujadas, L. Elias-Tersa, A. Masachs, N. Vilchez-Acosta, A. Parent, A. Auladell, C. Girault, J. A. Vila, M. Nairn, A. C. Manso, Y. Soriano, E. 2023-01-22 doi:10.1101/2023.01.21.525025 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Pulmonary Alveolar Cell Death Induced by LPS and Coronavirus ]]> https://biorxiv.org/content/10.1101/2023.01.23.524390v1?rss=1 Yuan, Q. Luan, Y. Rajendran, B. K. Compton, S. Tang, W. Wu, D. 2023-01-23 doi:10.1101/2023.01.23.524390 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting ]]> https://biorxiv.org/content/10.1101/2023.01.23.525275v1?rss=1 Wei, L.-H. Sun, Y. Guo, J. U. 2023-01-24 doi:10.1101/2023.01.23.525275 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Static and dynamic functional connectomes represent largely similar information ]]> https://biorxiv.org/content/10.1101/2023.01.24.525348v1?rss=1 Matkovic, A. Anticevic, A. Murray, J. D. Repovs, G. 2023-01-24 doi:10.1101/2023.01.24.525348 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ The memory of pathogenic IgE is contained within CD23+IgG1+ memory B cells poised to switch to IgE in food allergy ]]> https://biorxiv.org/content/10.1101/2023.01.25.525506v1?rss=1 Ota, M. Hoehn, K. Ota, T. Aranda, C. Friedman, S. Braga, W. Malbari, A. Kleinstein, S. Sicherer, S. Curotto de Lafaille, M. 2023-01-25 doi:10.1101/2023.01.25.525506 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ SPEAR: a Sparse Supervised Bayesian Factor Model for Multi-omic Integration ]]> https://biorxiv.org/content/10.1101/2023.01.25.525545v1?rss=1 Gygi, J. P. Konstorum, A. Pawar, S. Kleinstein, S. H. Guan, L. 2023-01-26 doi:10.1101/2023.01.25.525545 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ ]]> https://biorxiv.org/content/10.1101/2023.01.26.525608v1?rss=1 Fuentes, L. A. Marin, Z. Tyson, J. Baddeley, D. Bewersdorf, J. 2023-01-27 doi:10.1101/2023.01.26.525608 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ SeqPanther: Sequence manipulation and mutation statistics toolset ]]> https://biorxiv.org/content/10.1101/2023.01.26.525629v1?rss=1 San, J. E. Wyke, S. V. Tegally, H. Wilkinson, E. Eche, S. Kanzi, A. Oliveira, T. d. Kiran, A. E. 2023-01-27 doi:10.1101/2023.01.26.525629 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ PP1β opposes classic PP1 function, inhibiting spine maturation and promoting LTP ]]> https://biorxiv.org/content/10.1101/2023.01.26.525737v1?rss=1 Foley, K. McKee, C. Ganguly, A. Barnett, D. Ward, N. Mayer, A. Zhang, Y. Nairn, A. Xia, H. 2023-01-27 doi:10.1101/2023.01.26.525737 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Extracting nanoscale morphology from localizations ]]> https://biorxiv.org/content/10.1101/2023.01.26.525798v1?rss=1 Marin, Z. Fuentes, L. A. Bewersdorf, J. Baddeley, D. 2023-01-27 doi:10.1101/2023.01.26.525798 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Loss of WNT5 Proteins Reprograms Neutrophils in the Spleen to Provide Protection for DSS-Induced Colitis ]]> https://biorxiv.org/content/10.1101/2023.01.28.526056v1?rss=1 Luan, Y. Hu, J. Wang, Q. Li, W. Wang, X. Qu, R. Rajendran, B. K. Zhou, H. Liu, P. Shi, Y. Liu, Y. Lu, J. Tang, W. Wu, D. 2023-01-30 doi:10.1101/2023.01.28.526056 Cold Spring Harbor Laboratory Press 2023-01-30 <![CDATA[ Spectro-temporal acoustical markers differentiate speech from song across cultures ]]> https://biorxiv.org/content/10.1101/2023.01.29.526133v1?rss=1 Albouy, P. Mehr, S. A. Hoyer, R. S. Ginzburg, J. Zatorre, R. J. 2023-01-29 doi:10.1101/2023.01.29.526133 Cold Spring Harbor Laboratory Press 2023-01-29 <![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[ Structures of Arabidopsis thaliana MDL Proteins and Synergistic Effects with the Cytokine MIF on Human Receptors ]]> https://biorxiv.org/content/10.1101/2023.01.30.525655v1?rss=1 Spiller, L. Ramu, M. Leissing, F. Basquin, J. Bourilhon, P. Sinitski, D. Brandhofer, M. Levecque, S. C. Sabelleck, B. Feederle, R. Flatley, A. Panstruga, R. Bernhagen, J. Lolis, E. 2023-01-31 doi:10.1101/2023.01.30.525655 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Ataxin-2 polyglutamine expansions aberrantly sequester TDP-43, drive ribonucleoprotein condensate transport dysfunction and suppress local translation ]]> https://biorxiv.org/content/10.1101/2023.01.30.526372v1?rss=1 Wijegunawardana, D. Vishal, S. S. Venkatesh, N. Gopal, P. P. 2023-01-31 doi:10.1101/2023.01.30.526372 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ High-content image-based CRISPR screening reveals regulators of 3D genome architectures ]]> https://biorxiv.org/content/10.1101/2023.01.31.525983v1?rss=1 Hu, M. Yang, B. Jensen, T. B. Radda, J. S. D. Cheng, Y. Jin, S. Wang, S. 2023-02-01 doi:10.1101/2023.01.31.525983 Cold Spring Harbor Laboratory Press 2023-02-01 <![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[ On the money and right on target: How robust are reward and task success effects on implicit motor adaptation? ]]> https://biorxiv.org/content/10.1101/2023.02.01.526533v1?rss=1 Al-Fawakhiri, N. Ma, A. Taylor, J. A. Kim, O. A. 2023-02-03 doi:10.1101/2023.02.01.526533 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ EphrinA4/EphA4 controls blood pressure via arterial sympathetic innervation ]]> https://biorxiv.org/content/10.1101/2023.02.03.526852v1?rss=1 SIMONNET, E. MARTIN, S. VILAR, J. ROY-VESSIERES, E. TAIB, S. MONCEAU, V. Pardanaud, L. BOUBY, N. Eichmann, A. SILVESTRE, J.-S. HENRION, D. BRUNET, I. V. 2023-02-04 doi:10.1101/2023.02.03.526852 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Cancer relevance of circulating antibodies against LINE-1 antigens in humans ]]> https://biorxiv.org/content/10.1101/2023.02.03.526997v1?rss=1 3,000 individuals with or without cancer, we observed significantly higher IgG titers against L1-encoded ORF1p and ORF2p in patients with lung, pancreatic, ovarian, esophageal, and liver cancers compared to healthy individuals. Remarkably, elevated levels of anti-ORF1p-reactive IgG were observed in cancer patients with disease stages 1 and 2, indicating that immune response to L1 antigens can occur at early phases of carcinogenesis. We conclude that the antibody response against L1 antigens could contribute to the diagnosis and determination of immunoreactivity of tumors among cancer types that frequently escape early detection. ]]> Vylegzhanina, A. Bespalov, I. Novototskaya-Vlasova, K. Hall, B. Gleiberman, A. Yu, H. Leontieva, O. Leonova, K. Kurnasov, O. Osterman, A. Dy, G. Komissarov, A. Vasilieva, E. Gehlhausen, J. Iwasaki, A. Ambrosone, C. Tsuji, T. Matsuzaki, J. Odunsi, K. Andrianova, E. Gudkov, A. V. 2023-02-05 doi:10.1101/2023.02.03.526997 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ State-dependent modulation of dependencies in a laminar cortical circuit ]]> https://biorxiv.org/content/10.1101/2023.02.04.527119v1?rss=1 Das, A. Sheffield, A. G. Nandy, A. S. Jadi, M. P. 2023-02-05 doi:10.1101/2023.02.04.527119 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Origin and Development of the Claustrum in Rhesus Macaque ]]> https://biorxiv.org/content/10.1101/2023.02.06.527286v1?rss=1 Li, H. Duque, A. Rakic, P. 2023-02-06 doi:10.1101/2023.02.06.527286 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Odor imagery but not perception drives risk for food cue reactivity and increased adiposity ]]> https://biorxiv.org/content/10.1101/2023.02.06.527292v1?rss=1 Perszyk, E. E. Davis, X. S. Djordjevic, J. Jones-Gotman, M. Trinh, J. Hutelin, Z. Veldhuizen, M. G. Koban, L. Wager, T. D. Kober, H. Small, D. M. 2023-02-08 doi:10.1101/2023.02.06.527292 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ A fast, robust method for quantitative assessment of collagen fibril architecture from transmission electron micrographs ]]> https://biorxiv.org/content/10.1101/2023.02.06.527383v1?rss=1 Rego, B. V. Weiss, D. Humphrey, J. D. 2023-02-07 doi:10.1101/2023.02.06.527383 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Stacking multiple optimal transport policies to map functional connectomes ]]> https://biorxiv.org/content/10.1101/2023.02.06.527388v1?rss=1 Dadashkarimi, J. Rosenblatt, M. Karbasi, A. Scheinost, D. 2023-02-07 doi:10.1101/2023.02.06.527388 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Counterintuitive effect of antiviral therapy on influenza A-SARS-CoV-2 coinfection due to viral interference ]]> https://biorxiv.org/content/10.1101/2023.02.07.527372v1?rss=1 Cheemarla, N. R. Mihaylova, V. T. Watkins, T. A. Foxman, E. F. 2023-02-08 doi:10.1101/2023.02.07.527372 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Subdural CMOS optical probe (SCOPe) for bidirectional neural interfacing ]]> https://biorxiv.org/content/10.1101/2023.02.07.527500v1?rss=1 Pollmann, E. H. Yin, H. Uguz, I. Dubey, A. Wingel, K. E. Choi, J. S. Moazeni, S. Gilhotra, Y. Pavlovsky, V. A. Banees, A. A. Boominathan, V. Robinson, J. Veeraraghavan, A. Pieribone, V. A. Pesaran, B. Shepard, K. L. 2023-02-08 doi:10.1101/2023.02.07.527500 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Assessing changes in global fire regimes ]]> https://biorxiv.org/content/10.1101/2023.02.07.527551v1?rss=1 Sayedi, S. S. Global group of fire experts, 2023-02-08 doi:10.1101/2023.02.07.527551 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Sensory diversity and precise adaptation enable independent bet-hedging strategies for multiple signals at the same time ]]> https://biorxiv.org/content/10.1101/2023.02.08.527720v1?rss=1 Moore, J. P. Kamino, K. Kottou, R. Shimizu, T. S. Emonet, T. 2023-02-09 doi:10.1101/2023.02.08.527720 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Hippocampal mechanisms support cortisol-induced memory enhancements ]]> https://biorxiv.org/content/10.1101/2023.02.08.527745v1?rss=1 Sherman, B. E. Harris, B. B. Turk-Browne, N. B. Sinha, R. Goldfarb, E. V. 2023-02-09 doi:10.1101/2023.02.08.527745 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Parallel mechanisms detect different photoperiods to independently control seasonal flowering and growth in plants ]]> https://biorxiv.org/content/10.1101/2023.02.10.528016v1?rss=1 Wang, Q. Liu, W. Leung, C. C. Tarte, D. A. Gendron, J. 2023-02-13 doi:10.1101/2023.02.10.528016 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ cGAS-activating lupus autoantibody for cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.02.11.527649v1?rss=1 Chen, X. Tang, X. Cuffari, B. J. Tang, C. Gao, X. Noble, P. W. Young, M. R. Turk, O. M. Shirali, A. Gera, J. Nishimura, R. N. Zhou, J. Hansen, J. E. 2023-02-12 doi:10.1101/2023.02.11.527649 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ IN SITU IMAGING OF RETINAL CALCIUM DYNAMICS IN AWAKE ANIMALS ]]> https://biorxiv.org/content/10.1101/2023.02.11.528145v1?rss=1 Wang, Y. Su, A. Jin, J. Barson, D. Crair, M. 2023-02-12 doi:10.1101/2023.02.11.528145 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Measuring chondrocyte viability of articular cartilage based on label-free two-photon microscopy and deep learning image analysis ]]> https://biorxiv.org/content/10.1101/2023.02.13.527931v1?rss=1 Fan, H. Xu, P. Chen, X. Li, Y. Hsu, J. Le, M. Zhang, Z. Ye, E. Gao, B. Ye, T. 2023-02-14 doi:10.1101/2023.02.13.527931 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Disease-causing Slack potassium channel mutations produce opposite effects on excitability of excitatory and inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2023.02.14.528229v1?rss=1 Wu, J. Quraishi, I. H. Zhang, Y. Bromwich, M. Kaczmarek, L. K. 2023-02-14 doi:10.1101/2023.02.14.528229 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex ]]> https://biorxiv.org/content/10.1101/2023.02.15.528663v1?rss=1 Deng, C. Whalen, S. Steyert, M. Ziffra, R. Przytycki, P. F. Inoue, F. Pereira, D. A. Capauto, D. Norton, S. Vaccarino, F. M. Pollen, A. A. Nowakowski, T. J. Ahituv, N. A. Pollard, K. S. 2023-02-15 doi:10.1101/2023.02.15.528663 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging ]]> https://biorxiv.org/content/10.1101/2023.02.15.528714v1?rss=1 Occean, J. R. Yang, N. Sun, Y. Dawkins, M. S. Munk, R. Belair, C. Dar, S. Anerillas, C. Wang, L. Shi, C. Dunn, C. Bernier, M. Price, N. L. Kim, J. S. Cui, C.-Y. Fan, J. Bhattacharyya, M. De, S. Maragkakis, M. Cabo, R. d. Sidoli, S. Sen, P. 2023-02-15 doi:10.1101/2023.02.15.528714 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Functional networks in the infant brain during sleep and wake states ]]> https://biorxiv.org/content/10.1101/2023.02.15.528718v1?rss=1 Yates, T. S. Ellis, C. T. Turk-Browne, N. B. 2023-02-15 doi:10.1101/2023.02.15.528718 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis ]]> https://biorxiv.org/content/10.1101/2023.02.15.528736v1?rss=1 Rosenberger, G. Li, W. Turunen, M. He, J. Subramaniam, P. S. Pampou, S. Griffin, A. T. Karan, C. Kerwin, P. Murray, D. Honig, B. Liu, Y. Califano, A. 2023-02-16 doi:10.1101/2023.02.15.528736 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Transcriptional heterogeneity in diabetic foot wounds ]]> https://biorxiv.org/content/10.1101/2023.02.16.528839v1?rss=1 Sandoval-Schaefer, T. Phan, Q. Dash, B. Prassinos, A. Duan, K. Gazes, M. I. Vyce, S. D. Hsai, H. C. Driskell, R. Horsley, V. 2023-02-18 doi:10.1101/2023.02.16.528839 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Discovery of novel microRNA regulators of ribosome biogenesis ]]> https://biorxiv.org/content/10.1101/2023.02.17.526327v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1449771org.highwire.dtl.DTLVardef@329602org.highwire.dtl.DTLVardef@1168c97org.highwire.dtl.DTLVardef@1684da9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bryant, C. J. McCool, M. A. Rosado-Gonzalez, G. T. Abriola, L. Surovtseva, Y. V. Baserga, S. J. 2023-02-17 doi:10.1101/2023.02.17.526327 Cold Spring Harbor Laboratory Press 2023-02-17 <![CDATA[ Determination of oligomeric organization of membrane proteins from native membranes at nanoscale-spatial and single-molecule resolution ]]> https://biorxiv.org/content/10.1101/2023.02.19.529138v1?rss=1 Walker, G. Brown, C. Ge, X. Kumar, S. Muzumdar, M. D. Gupta, K. Bhattacharyya, M. 2023-02-21 doi:10.1101/2023.02.19.529138 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ The cytidine deaminase APOBEC3A is required for large ribosomal subunit biogenesis ]]> https://biorxiv.org/content/10.1101/2023.02.20.529126v1?rss=1 McCool, M. A. Bryant, C. J. Abriola, L. Surovtseva, Y. V. Baserga, S. J. 2023-02-20 doi:10.1101/2023.02.20.529126 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Ketamine Effects on Energy Metabolism, Functional Connectivity and Working Memory in Healthy Humans ]]> https://biorxiv.org/content/10.1101/2023.02.21.529425v1?rss=1 Driesen, N. R. Herman, P. Rowland, M. A. Thompson, G. Qiu, M. He, G. Fineberg, S. K. Barron, D. S. Helgeson, L. Lacadie, C. Chow, R. Gueorguieva, R. Straun, T.-C. Krystal, J. H. Hyder, F. 2023-02-22 doi:10.1101/2023.02.21.529425 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Cellular protection from H2O2 toxicity by Fv-Hsp70 and mutants of Fv-Hsp70. Protection via catalase and gamma-glutamyl cysteine synthase. ]]> https://biorxiv.org/content/10.1101/2023.02.22.529417v1?rss=1 Hino, C. Chan, G. Jordaan, G. Chang, S. S. Saunders, J. Bashir, M. T. Hansen, J. E. Gera, J. Weisbart, R. H. Nishimura, R. N. 2023-02-22 doi:10.1101/2023.02.22.529417 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ A compact regulatory RNA element in human Hsp70 mRNA ]]> https://biorxiv.org/content/10.1101/2023.02.22.529618v1?rss=1 Wang, W. Liu, F. Pyle, A. M. 2023-02-23 doi:10.1101/2023.02.22.529618 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Synthetic Cooling Agent in Oral Nicotine Pouch Products Marketed as "Flavor Ban Approved" ]]> https://biorxiv.org/content/10.1101/2023.02.23.529797v1?rss=1 Jabba, S. V. Erythropel, H. C. Woodrow, J. G. Anastas, P. T. O'Malley, S. Krishnan-sarin, S. Zimmerman, J. B. Jordt, S. E. 2023-02-24 doi:10.1101/2023.02.23.529797 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape ]]> https://biorxiv.org/content/10.1101/2023.02.25.530019v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@dc6d22org.highwire.dtl.DTLVardef@180f36borg.highwire.dtl.DTLVardef@ed341forg.highwire.dtl.DTLVardef@f8dfb2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Boddu, P. C. Gupta, A. K. Roy, R. De La Pena Avalos, B. Olazabal Herrero, A. Neuenkirchen, N. Zimmer, J. Chandhok, N. S. King, D. Nannya, Y. Ogawa, S. Lin, H. Simon, M. Dray, E. Kupfer, G. Verma, A. K. Neugebauer, K. M. Pillai, M. M. 2023-02-26 doi:10.1101/2023.02.25.530019 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ LRRC23 loss-of-function impairs radial spoke 3 head assembly and causes defective sperm motility underlying male infertility ]]> https://biorxiv.org/content/10.1101/2023.02.25.530050v1?rss=1 Hwang, J. Y. Chai, P. Nawaz, S. Choi, J. Lopez-Giraldez, F. Hussain, S. Bilguvar, K. Mane, S. Lifton, R. P. Ahmad, W. Zhang, K. Chung, J.-J. 2023-02-26 doi:10.1101/2023.02.25.530050 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Continuous, long-term crawling behavior characterized by a robotic transport system ]]> https://biorxiv.org/content/10.1101/2023.02.27.530235v1?rss=1 Yu, J. Dancausse, S. Paz, M. Faderin, T. Gaviria, M. Shomar, J. W. Zucker, D. Venkatachalam, V. Klein, M. 2023-02-28 doi:10.1101/2023.02.27.530235 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Topology recapitulates ontogeny of dendritic arbors ]]> https://biorxiv.org/content/10.1101/2023.02.27.530331v1?rss=1 Liao, M. Bird, A. D. Cuntz, H. Howard, J. 2023-03-01 doi:10.1101/2023.02.27.530331 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Identification of efflux substrates using a riboswitch-based reporter in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2023.02.27.530370v1?rss=1 Urdaneta-Paez, V. Hamchand, R. Anthony, K. G. Crawford, J. Sutherland, A. G. Kazmierczak, B. I. 2023-02-28 doi:10.1101/2023.02.27.530370 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ The Giant Clam Photosymbiosis is a Physically Optimal Photoconversion System for the Most Intense Sunlight on Earth ]]> https://biorxiv.org/content/10.1101/2023.02.28.530416v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@52764borg.highwire.dtl.DTLVardef@1d453d6org.highwire.dtl.DTLVardef@cc461dorg.highwire.dtl.DTLVardef@10f32f2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Holt, A. L. Rehm, L. Sweeney, A. M. 2023-03-01 doi:10.1101/2023.02.28.530416 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Representing Multiple Visual Objects in the Human Brain and Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2023.02.28.530472v1?rss=1 Mocz, V. Jeong, S. Chun, M. Xu, Y. 2023-03-01 doi:10.1101/2023.02.28.530472 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations ]]> https://biorxiv.org/content/10.1101/2023.02.28.530478v1?rss=1 Yan, H. Talty, R. Jain, A. Cai, Y. Zheng, J. Shen, X. Muca, E. Paty, P. Bosenburg, M. Khan, S. Johnson, C. 2023-03-01 doi:10.1101/2023.02.28.530478 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics ]]> https://biorxiv.org/content/10.1101/2023.02.28.530526v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@10e7728org.highwire.dtl.DTLVardef@b1078aorg.highwire.dtl.DTLVardef@65f874org.highwire.dtl.DTLVardef@9ab0e8_HPS_FORMAT_FIGEXP M_FIG C_FIG Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions. ]]> Ao, Y. Grover, J. R. Han, Y. Zhong, G. Qin, W. Ghimire, D. Haque, M. A. Bhattacharjee, R. Zhang, B. Arthos, J. Lemke, E. A. Kwong, P. D. Lu, M. 2023-03-01 doi:10.1101/2023.02.28.530526 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome ]]> https://biorxiv.org/content/10.1101/2023.03.01.530696v1?rss=1 Becker-Krail, D. Ketchesin, K. D. D. Xue, X. Wilson, R. Lam, T. T. Williams, K. Nairn, A. Tseng, G. Logan, R. W. 2023-03-02 doi:10.1101/2023.03.01.530696 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ SifA SUMOylation governs Salmonella intracellular survival via modulation of lysosomal function ]]> https://biorxiv.org/content/10.1101/2023.03.02.530793v1?rss=1 Srikanth, C. V. Chandrasekhar, H. Mohapatra, G. Singh, M. Rana, S. Kaur, N. Sharma, S. Tuli, A. Das, P. 2023-03-03 doi:10.1101/2023.03.02.530793 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Human Vascularized Bile Duct-on-a Chip: A multi-cellular micro-physiological system for studying Primary Sclerosing Cholangitis ]]> https://biorxiv.org/content/10.1101/2023.03.02.530888v1?rss=1 Du, Y. Gupta, K. Waisbourd-Zinman, O. Har-Zahav, A. Soroka, C. J. Boyer, J. L. Llewellyn, J. Liu, C. Naji, A. Polacheck, W. J. Wells, R. G. 2023-03-03 doi:10.1101/2023.03.02.530888 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Animal-vectored nutrient flows across resource gradients influence the nature of local and meta-ecosystem functioning ]]> https://biorxiv.org/content/10.1101/2023.03.03.530982v1?rss=1 Rizzuto, M. Leroux, S. J. Schmitz, O. J. Vander Wal, E. Wiersma, Y. F. Heckford, T. R. 2023-03-06 doi:10.1101/2023.03.03.530982 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Interaction Between HCN and Slack Channels Regulates mPFC Pyramidal Cell Excitability and Working Memory ]]> https://biorxiv.org/content/10.1101/2023.03.04.529157v1?rss=1 Wu, J. El-Hassar, L. Datta, D. Thomas, M. Zhang, Y. Jenkins, D. P. DeLuca, N. J. Chatterjee, M. Gribkoff, V. K. Arnsten, A. F. T. Kaczmarek, L. K. 2023-03-05 doi:10.1101/2023.03.04.529157 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ A phylogeny-informed characterization of global tetrapod traits addresses data gaps and biases ]]> https://biorxiv.org/content/10.1101/2023.03.04.531098v1?rss=1 Moura, M. R. Ceron, K. Guedes, J. J. M. Sica, Y. V. Catenazzi, A. Werneck, F. Toledo, L. F. Jetz, W. 2023-03-06 doi:10.1101/2023.03.04.531098 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Induction of T-DNA amplification by retrotransposon-derived sequences ]]> https://biorxiv.org/content/10.1101/2023.03.05.531200v1?rss=1 Dickinson, L. Yuan, W. LeBlanc, C. Thomson, G. Wang, S. Jacob, Y. 2023-03-07 doi:10.1101/2023.03.05.531200 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Operant training for highly palatable food alters translating mRNA in nucleus accumbens D2 neurons and reveals a modulatory role of Neurochondrin ]]> https://biorxiv.org/content/10.1101/2023.03.07.531496v1?rss=1 Montalban, E. Giralt, A. Taing, L. Nakamura, Y. Pelosi, A. Brown, M. de Pins, B. Valjent, E. Martin, M. Nairn, A. C. Greengard, P. Flajolet, M. Herve, D. Gambardella, N. Roussarie, J.-P. Girault, J.-A. 2023-03-09 doi:10.1101/2023.03.07.531496 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ The ability to sense the environment is heterogeneously distributed in cell populations ]]> https://biorxiv.org/content/10.1101/2023.03.07.531554v1?rss=1 Goetz, A. Akl, H. Dixit, P. D. 2023-03-10 doi:10.1101/2023.03.07.531554 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer ]]> https://biorxiv.org/content/10.1101/2023.03.12.532274v1?rss=1 Panda, A. Giska, F. Duncan, A. L. Welch, A. J. Brown, C. McAllister, R. Parameswaran, H. Goder, J. N. D. Coleman, J. Ramakrishnan, S. Pincet, F. Guan, L. Krishnakumar, S. Rothman, J. E. Gupta, K. 2023-03-12 doi:10.1101/2023.03.12.532274 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling ]]> https://biorxiv.org/content/10.1101/2023.03.13.532151v1?rss=1 Lee, J. Robinson, M. E. Sun, R. Kume, K. Ma, N. Cosgun, K. N. Chan, L. N. Leveille, E. Geng, H. Vykunta, V. S. Shy, B. R. Marson, A. Katz, S. G. Chen, J. Paietta, E. Meffre, E. Nagarajan, V. Mueschen, M. 2023-03-15 doi:10.1101/2023.03.13.532151 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Targeted engagement of β-catenin-Ikaros complexes in refractory B-cell malignancies ]]> https://biorxiv.org/content/10.1101/2023.03.13.532152v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1b70e4dorg.highwire.dtl.DTLVardef@10bfcc8org.highwire.dtl.DTLVardef@b10eorg.highwire.dtl.DTLVardef@1683a3e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIAbundant nuclear {beta}-catenin C_LIO_LI{beta}-catenin pairs with TCF7 factors for transcriptional activation of MYC C_LIO_LIB-cells rely on efficient degradation of {beta}-catenin by GSK3{beta} C_LIO_LIB-cell-specific expression of Ikaros factors C_LI Unique vulnerability in B-cell tumors: O_LIGSK3{beta}-inhibitors induce nuclear accumulation of {beta}-catenin. C_LIO_LI{beta}-catenin pairs with B-cell-specific Ikaros factors for transcriptional repression of MYC C_LI ]]> Cosgun, K. N. Jumaa, H. Robinson, M. E. Liang, X. Xiao, G. Chan, L. N. Lee, J. Kume, K. Leveille, E. Fonseca-Arce, D. Khanduja, D. Ng, H. L. Feldhahn, N. Song, J. Chan, W. C. Chen, J. Taketo, M. M. Kothari, S. Davids, M. S. Schjerven, H. Jellusova, J. Mueschen, M. 2023-03-15 doi:10.1101/2023.03.13.532152 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data ]]> https://biorxiv.org/content/10.1101/2023.03.13.532468v1?rss=1 Dai, R. Chu, T. Zhang, M. Wang, X. Jourdon, A. Wu, F. Mariani, J. Vaccarino, F. M. Lee, D. Fullard, J. F. Hoffman, G. E. Roussos, P. Wang, Y. Wang, X. Pinto, D. Wang, S. Zhang, C. Chen, C. LIU, C. 2023-03-15 doi:10.1101/2023.03.13.532468 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beauty composite system ]]> https://biorxiv.org/content/10.1101/2023.03.14.532651v1?rss=1 Ye, L. Lam, S. Z. Yang, L. Suzuki, K. Zou, Y. Lin, Q. Zhang, Y. Clark, P. Peng, L. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532651 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Perturbomics of tumor-infiltrating NK cells ]]> https://biorxiv.org/content/10.1101/2023.03.14.532653v1?rss=1 Peng, L. Renauer, P. A. Ye, L. Yang, L. Park, J. J. Chow, R. D. Zhang, Y. Lin, Q. Bai, M. Sanchez, A. Zhang, Y. Lam, S. Z. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532653 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ CTLA-4 tail fusion enhances CAR-T anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2023.03.14.532655v1?rss=1 Zhou, X. Cao, H. Fang, S.-Y. Chow, R. D. Tang, K. Majety, M. Bai, M. Dong, M. B. Renauer, P. A. Shang, X. Suzuki, K. Levchenko, A. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532655 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Cas12a/Cpf1 knock-in mice enable efficient multiplexed immune cell engineering ]]> https://biorxiv.org/content/10.1101/2023.03.14.532657v1?rss=1 Dong, M. B. Tang, K. Zhou, X. Shen, J. Chen, K. Kim, H. R. Zhou, J. Cao, H. Vandenbulcke, E. Zhang, Y. Chow, R. D. Du, A. Suzuki, K. Fang, S.-Y. Majety, M. Dai, X. Chen, S. 2023-03-14 doi:10.1101/2023.03.14.532657 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function ]]> https://biorxiv.org/content/10.1101/2023.03.14.532663v1?rss=1 Renauer, P. A. Park, J. J. Bai, M. Acosta, A. Lee, W.-H. Lin, G. H. Zhang, Y. Dai, X. Wang, G. Errami, Y. Wu, T. Clark, P. Ye, L. Yang, Q. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532663 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ VIP interneurons regulate cortical size tuning and visual perception ]]> https://biorxiv.org/content/10.1101/2023.03.14.532664v1?rss=1 Ferguson, K. A. Salameh, J. Alba, C. Selwyn, H. Barnes, C. Lohani, S. Cardin, J. A. 2023-03-14 doi:10.1101/2023.03.14.532664 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Rational design of immune gene therapy combinations via in vivo CRISPR activation screen of tumor microenvironment modulators ]]> https://biorxiv.org/content/10.1101/2023.03.14.532665v1?rss=1 Wang, G. Zhang, F. Chow, R. D. He, E. Zhu, L. Han, Q. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532665 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies ]]> https://biorxiv.org/content/10.1101/2023.03.14.532666v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@151f6eforg.highwire.dtl.DTLVardef@2ae877org.highwire.dtl.DTLVardef@103e0d1org.highwire.dtl.DTLVardef@19cd695_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Edman, N. I. Redler, R. L. Phal, A. Schlichthaerle, T. Srivatsan, S. R. Etemadi, A. An, S. Favor, A. Ehnes, D. Li, Z. Praetorius, F. Gordon, M. Yang, W. Coventry, B. Hicks, D. R. Cao, L. Bethel, N. Heine, P. Murray, A. N. Gerben, S. Carter, L. Miranda, M. Negahdari, B. Lee, S. Trapnell, C. Stewart, L. Ekiert, D. C. Schlessinger, J. Shendure, J. Bhabha, G. Ruohola-Baker, H. Baker, D. 2023-03-15 doi:10.1101/2023.03.14.532666 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Multiplexed repression of immunosuppressive genes as combinatorial cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.03.14.532668v1?rss=1 Zhang, F. Wang, G. Chow, R. D. He, E. Majety, M. Zhang, Y. Chen, S. 2023-03-15 doi:10.1101/2023.03.14.532668 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Hypothalamic thyroid hormone deficiency underlies reversible anorexia in a mammalian hibernator ]]> https://biorxiv.org/content/10.1101/2023.03.15.532843v1?rss=1 Mohr, S. M. Pra, R. D. Platt, M. P. Feketa, V. V. Shanabrough, M. Varela, L. Kristant, A. Cao, H. Merriman, D. K. Horvath, T. L. Bagriantsev, S. N. Gracheva, E. O. 2023-03-16 doi:10.1101/2023.03.15.532843 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Breaking the C. elegans invasion/proliferation dichotomy ]]> https://biorxiv.org/content/10.1101/2023.03.16.533034v1?rss=1 Martinez, M. A. Q. Zhao, C. Moore, F. E. Q. Yee, C. S. Zhang, W. Shen, K. Martin, B. L. Matus, D. Q. 2023-03-18 doi:10.1101/2023.03.16.533034 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Abnormal weather drives disease outbreaks in wild and agricultural plants ]]> https://biorxiv.org/content/10.1101/2023.03.17.533130v1?rss=1 Kirk, D. Cohen, J. Nguyen, V. Childs, M. L. Farner, J. E. Davies, T. J. Flory, S. L. Rohr, J. R. O'Connor, M. I. Mordecai, E. A. 2023-03-20 doi:10.1101/2023.03.17.533130 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 ]]> https://biorxiv.org/content/10.1101/2023.03.17.533220v1?rss=1 Abini-Agbomson, S. Gretarsson, K. Shih, R. M. Hsieh, L. Lou, T. De Ioannes, P. Vasilyev, N. Lee, R. Wang, M. Simon, M. Armache, J.-P. Nudler, E. Narlikar, G. Liu, S. Lu, C. Armache, K.-J. 2023-03-18 doi:10.1101/2023.03.17.533220 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ TREM2 and APOE do not modulate phagocytic clearance of dying cells in the live mammalian brain ]]> https://biorxiv.org/content/10.1101/2023.03.17.533222v1?rss=1 Damisah, E. Rai, A. Hill, R. A. Tong, L. Grutzendler, J. 2023-03-18 doi:10.1101/2023.03.17.533222 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations ]]> https://biorxiv.org/content/10.1101/2023.03.18.532837v1?rss=1 Zhao, S. Mekbib, K. Y. van der Ent, M. A. Allington, G. Prendergast, A. Chau, J. E. Smith, H. Shohfi, J. Ocken, J. Duran, D. Furey, C. G. Le, H. T. Duy, P. Q. Reeves, B. C. Zhang, J. Nelson-Williams, C. Chen, D. Li, B. Nottoli, T. Bai, S. Rolle, M. Zeng, X. Dong, W. Fu, P.-Y. Wang, Y.-C. Mane, S. Piwowarczyk, P. Fehnel, K. P. See, A. P. Iskandar, B. J. Aagaard-Kienitz, B. Kundishora, A. J. DeSpenza, T. Greenberg, A. B. W. Kidanemariam, S. M. Prendergast, A. Johnston, J. M. Jackson, E. Storm, P. B. Lang, S.-S. Butler, W. E. Carter, B. S. Chapman, P. St 2023-03-22 doi:10.1101/2023.03.18.532837 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Dual impact of PTEN mutation on CSF dynamics and cortical networks via the dysregulation of neural precursors and their interneuron descendants ]]> https://biorxiv.org/content/10.1101/2023.03.18.533275v1?rss=1 DeSpenza, T. Kiziltug, E. Allington, G. Barson, D. O'Connor, D. Robert, S. M. Mekbib, K. Y. Nanda, P. Greenberg, A. Singh, A. Duy, P. Q. Mandino, F. Zhao, S. Lynn, A. Reeves, B. C. Marlier, A. Getz, S. A. Nelson-Williams, C. Shimelis, H. Zhang, J. Walsh, L. K. Wang, W. Smith, H. OuYang, A. Deniz, E. Lake, E. Jin, S. C. Luikart, B. W. Kahle, K. T. 2023-03-19 doi:10.1101/2023.03.18.533275 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Neuronal phase shifts differ for excitation vs. inhibition: a computer modeling study ]]> https://biorxiv.org/content/10.1101/2023.03.20.533519v1?rss=1 Kelley, C. Antic, S. D. Carnevale, N. T. Kubie, J. L. Lytton, W. 2023-03-21 doi:10.1101/2023.03.20.533519 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Loss of endothelial glucocorticoid receptor accelerates organ fibrosis in db/db mice ]]> https://biorxiv.org/content/10.1101/2023.03.20.533532v1?rss=1 Srivastava, S. P. Goodwin, J. 2023-03-23 doi:10.1101/2023.03.20.533532 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Overexpressed Malat1 Drives Metastasis through Inflammatory Reprogramming of Lung Adenocarcinoma Microenvironment ]]> https://biorxiv.org/content/10.1101/2023.03.20.533534v1?rss=1 Martinez-Terroba, E. de Miguel, F. J. Li, V. Robles-Oteiza, C. Politi, K. Zamudio, J. R. Dimitrova, N. 2023-03-23 doi:10.1101/2023.03.20.533534 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Cell-type specific EWAS identifies genes involved in HIV pathogenesis andoncogenesis among people with chronic HIV infection ]]> https://biorxiv.org/content/10.1101/2023.03.21.533691v1?rss=1 Zhang, X. Hu, Y. Vandenhoudt, R. E. Yan, C. Marconi, V. C. Cohen, M. H. Justice, A. C. Aouizerat, B. E. Xu, K. 2023-03-24 doi:10.1101/2023.03.21.533691 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Sequence independent activity of a predicted long disordered segment of the human papillomavirus L2 capsid protein during virus entry ]]> https://biorxiv.org/content/10.1101/2023.03.21.533711v1?rss=1 Oh, C. Buckley, P. Choi, J. Hierro, A. DiMaio, D. 2023-03-22 doi:10.1101/2023.03.21.533711 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Capturing Spatiotemporal Signaling Patterns in Cellular Data with Geometric Scattering Trajectory Homology ]]> https://biorxiv.org/content/10.1101/2023.03.22.533807v1?rss=1 Bhaskar, D. Moore, J. L. Gao, F. Rieck, B. Khasawneh, F. Munch, E. Greco, V. Krishnaswamy, S. 2023-03-24 doi:10.1101/2023.03.22.533807 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Modeling, dissecting, and subtyping of E-Cadherin inactivation-associated diffuse-type gastric adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.03.23.533976v1?rss=1 Zou, G. Huang, Y. Zhang, S. Ko, K.-P. Kim, B. J. Zhang, J. Pizzi, M. P. Jun, S. Niu, N. Wang, H. Song, S. Ajani, J. A. Park, J.-I. 2023-03-25 doi:10.1101/2023.03.23.533976 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ MPL36, a major plasminogen (PLG) receptor in pathogenic Leptospira, has an essential role during infection ]]> https://biorxiv.org/content/10.1101/2023.03.24.534066v1?rss=1 Zhu, W. Passalia, F. Hamond, C. Abe, C. Ko, A. Barbosa, A. Wunder, E. 2023-03-25 doi:10.1101/2023.03.24.534066 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Learning the functional landscape of microbial communities ]]> https://biorxiv.org/content/10.1101/2023.03.24.534159v1?rss=1 Skwara, A. Gowda, K. Yousef, M. Diaz-Colunga, J. Raman, A. S. Sanchez, A. Tikhonov, M. Kuehn, S. 2023-03-25 doi:10.1101/2023.03.24.534159 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Lipoarabinomannan regulates septation in Mycobacterium smegmatis ]]> https://biorxiv.org/content/10.1101/2023.03.26.534150v1?rss=1 Sparks, I. L. Nijjer, J. Yan, J. Morita, Y. S. 2023-03-26 doi:10.1101/2023.03.26.534150 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ PyTorch-FEA: Autograd-enabled Finite Element Analysis Methods with Applications for Biomechanical Analysis of Human Aorta ]]> https://biorxiv.org/content/10.1101/2023.03.27.533816v1?rss=1 Liang, L. Liu, M. Elefteriades, J. Sun, W. 2023-03-28 doi:10.1101/2023.03.27.533816 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport ]]> https://biorxiv.org/content/10.1101/2023.03.28.534644v1?rss=1 Tong, A. Kuchroo, M. Gupta, S. Venkat, A. Perez San Juan, B. Rangel, L. Zhu, B. Lock, J. G. Chaffer, C. Krishnaswamy, S. 2023-03-29 doi:10.1101/2023.03.28.534644 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[ Nucleolar structure connects with global nuclear organization ]]> https://biorxiv.org/content/10.1101/2023.03.30.534966v1?rss=1 Wang, C. Ma, H. Baserga, S. Pederson, T. Huang, S. 2023-03-31 doi:10.1101/2023.03.30.534966 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia ]]> https://biorxiv.org/content/10.1101/2023.03.30.534980v1?rss=1 Castaneda, D. C. Jangra, S. Yurieva, M. Martinek, J. Callender, M. Coxe, M. Choi, A. Diego, J. G.-B. Lin, J. Wu, T.-C. Marches, F. Chaussabel, D. Yu, P. Salner, A. Aucello, G. Koff, J. Hudson, B. Church, S. E. Gorman, K. Anguiano, E. Garcia-Sastre, A. Williams, A. Schotsaert, M. Palucka, K. 2023-03-31 doi:10.1101/2023.03.30.534980 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Spatial and seasonal variation in thermal sensitivity within North American bird species ]]> https://biorxiv.org/content/10.1101/2023.03.31.535105v1?rss=1 Cohen, J. Fink, D. Zuckerberg, B. 2023-04-03 doi:10.1101/2023.03.31.535105 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Differentiation and Integration of Competing Memories: A Neural Network Model ]]> https://biorxiv.org/content/10.1101/2023.04.02.535239v1?rss=1 Ritvo, V. J. H. Nguyen, A. Turk-Browne, N. B. Norman, K. A. 2023-04-03 doi:10.1101/2023.04.02.535239 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ Synergistic Integration of Deep Neural Networks and Finite Element Method with Applications for Biomechanical Analysis of Human Aorta ]]> https://biorxiv.org/content/10.1101/2023.04.03.535423v1?rss=1 Liang, L. Liu, M. Elefteriades, J. Sun, W. 2023-04-05 doi:10.1101/2023.04.03.535423 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using In vitro Platform for Improving Insulin Therapy ]]> https://biorxiv.org/content/10.1101/2023.04.03.535481v1?rss=1 Thoduvayil, S. Weerakkody, J. S. Topper, M. Bera, M. Coleman, J. Li, X. Mariappan, M. Ramakrishnan, S. 2023-04-04 doi:10.1101/2023.04.03.535481 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Whole-genome sequencing confirms multiple species of Galapagos giant tortoises ]]> https://biorxiv.org/content/10.1101/2023.04.05.535692v1?rss=1 Gaughran, S. J. Gray, R. Jones, M. Fusco, N. Ochoa, A. Miller, J. M. Poulakakis, N. de Queiroz, K. Caccone, A. Jensen, E. L. 2023-04-05 doi:10.1101/2023.04.05.535692 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ 3D architecture and a bi-cellular mechanism of touch detection in mechanosensory corpuscle ]]> https://biorxiv.org/content/10.1101/2023.04.05.535701v1?rss=1 Nikolaev, Y. A. Ziolkowski, L. H. Pang, S. Li, W.-P. Feketa, V. V. Xu, C. S. Gracheva, E. O. Bagriantsev, S. N. 2023-04-06 doi:10.1101/2023.04.05.535701 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Detailed Social Network Interactions and Gut Microbiome Strain-Sharing Within Isolated Honduras Villages ]]> https://biorxiv.org/content/10.1101/2023.04.06.535875v1?rss=1 Pullman, J. Beghini, F. Alexander, M. Vishnempet Shridhar, S. Prinster, D. Brito, I. L. Christakis, N. A. 2023-04-07 doi:10.1101/2023.04.06.535875 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Structured memory representations develop at multiple time scales in hippocampal-cortical networks ]]> https://biorxiv.org/content/10.1101/2023.04.06.535935v1?rss=1 Tambini, A. Miller, J. Ehlert, L. Kiyonaga, A. D'Esposito, M. 2023-04-07 doi:10.1101/2023.04.06.535935 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications ]]> https://biorxiv.org/content/10.1101/2023.04.08.536116v1?rss=1 Guerrero, R. F. Dorji, T. Harris, R. M. Shoulders, M. D. Ogbunugafor, C. B. 2023-04-08 doi:10.1101/2023.04.08.536116 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance ]]> https://biorxiv.org/content/10.1101/2023.04.09.535490v1?rss=1 Ogbunugafor, C. B. Guerrero, R. F. Shakhnovich, E. I. Shoulders, M. D. 2023-04-09 doi:10.1101/2023.04.09.535490 Cold Spring Harbor Laboratory Press 2023-04-09 <![CDATA[ Distinct interactions stabilize EGFR dimers and higher-order oligomers in cell membranes ]]> https://biorxiv.org/content/10.1101/2023.04.10.536273v1?rss=1 Mudumbi, K. C. Burns, E. A. Schodt, D. J. Petrova, Z. O. Kiyatkin, A. Kim, L. W. Mangiacapre, E. M. Ortiz-Caraveo, I. Ortiz, H. R. Hu, C. Ashtekar, K. D. Lidke, K. A. Lidke, D. Lemmon, M. A. 2023-04-10 doi:10.1101/2023.04.10.536273 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ How individual P. aeruginosa cells with diverse stator distributions collectively form a heterogeneous macroscopic swarming population ]]> https://biorxiv.org/content/10.1101/2023.04.10.536285v1?rss=1 de Anda, J. Kuchma, S. Webster, S. S. Boromand, A. Lewis, K. A. Lee, C. Contreras, M. Medeiros Pereira, V. F. Hogan, D. A. O'Hern, C. O'Toole, G. A. Wong, G. C. L. 2023-04-10 doi:10.1101/2023.04.10.536285 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Astrovirus replication is dependent on induction of double membrane vesicles through a PI3K-dependent, LC3-independent pathway ]]> https://biorxiv.org/content/10.1101/2023.04.11.536492v1?rss=1 Bub, T. Hargest, V. Tan, S. Smith, M. Vazquez-Pagan, A. Flerlage, T. Brigleb, P. H. Meliopoulos, V. A. Lindenbach, B. D. Cortez, V. Crawford, J. C. Schultz-Cherry, S. 2023-04-12 doi:10.1101/2023.04.11.536492 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ DNA-targeting and cell-penetrating antibody-drug conjugate ]]> https://biorxiv.org/content/10.1101/2023.04.12.536500v1?rss=1 Shirali, A. Dubljevic, V. Cao, F. Nishimura, R. N. Ebens, A. Campbell, J. A. Hansen, J. E. 2023-04-13 doi:10.1101/2023.04.12.536500 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ FGF-21 Conducts a Liver-Brain-Kidney Axis to Promote Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.12.536558v1?rss=1 Li, Z. Zhang, X. Zhu, W. Zhang, C. Sadak, K. Halberstam, A. A. Brown, J. R. Perry, C. J. Bunn, A. Braun, D. A. Adeniran, A. Lee, S. Wang, A. Perry, R. J. 2023-04-13 doi:10.1101/2023.04.12.536558 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ There and back again: when and how the world's richest snake family (Dipsadidae) dispersed and speciated across the Neotropical region ]]> https://biorxiv.org/content/10.1101/2023.04.15.535132v1?rss=1 Serrano, F. C. Pontes-Nogueira, M. Sawaya, R. J. Alencar, L. Nogueira, C. Grazziotin, F. G. 2023-04-16 doi:10.1101/2023.04.15.535132 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ Loss of presenilin-1 in smooth muscle cells ameliorates elastin aortopathy ]]> https://biorxiv.org/content/10.1101/2023.04.15.536809v1?rss=1 Saito, J. Dave, J. M. Lau, F. D. Greif, D. M. 2023-04-15 doi:10.1101/2023.04.15.536809 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories ]]> https://biorxiv.org/content/10.1101/2023.04.15.536945v1?rss=1 Cudone, E. Lower, A. McDougal, R. A. 2023-04-16 doi:10.1101/2023.04.15.536945 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ EGFR+ lung adenocarcinomas coopt alveolar macrophage metabolism and function to support EGFR signaling and growth ]]> https://biorxiv.org/content/10.1101/2023.04.15.536974v1?rss=1 Kuhlmann-Hogan, A. Cordes, T. Xu, Z. Traina, K. Robles-Oteiza, C. Ayeni, D. Kwong, E. M. Levy, S. Nobari, M. Cheng, G. Z. Shaw, R. J. Leibel, S. L. Metallo, C. Politi, K. Kaech, S. M. 2023-04-17 doi:10.1101/2023.04.15.536974 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Myosin Light Chain Dephosphorylation by PPP1R12C Promotes Atrial Hypocontractility in Atrial Fibrillation ]]> https://biorxiv.org/content/10.1101/2023.04.19.537590v1?rss=1 40% reduction in MLC2a phosphorylation (P=1.4x10-6, n=12,12 in each group). PPP1R12C-PP1c binding and PPP1R12C-MLC2a binding were significantly increased in AF (P=2.9x10-2 and 6.7x10-3 respectively, n=8,8 in each group). In vitro studies utilizing drug BDP5290, which inhibits T560-PPP1R12C phosphorylation, demonstrated increased PPP1R12C binding with both PP1c and MLC2a, and dephosphorylation of MLC2a. Lenti-12C mice demonstrated a 150% increase in LA size versus controls (P=5.0x10-6, n=12,8,12), with reduced atrial strain and atrial ejection fraction. Pacing-induced AF in Lenti-12C mice was significantly higher than controls (P=1.8x10-2 and 4.1x10-2 respectively, n= 6,6,5). ConclusionsAF patients exhibit increased levels of PPP1R12C protein compared to controls. PPP1R12C overexpression in mice increases PP1c targeting to MLC2a and causes MLC2a dephosphorylation, which reduces atrial contractility and increases AF inducibility. These findings suggest that PP1 regulation of sarcomere function at MLC2a is a key determinant of atrial contractility in AF. ]]> McCauley, M. D. Perike, S. Gonzalez-Gonzalez, F. J. Abu-Taha, I. Damen, F. Lizama, K. S. Aboonabi, A. Capote, A. E. Aguilar-Torres, Y. Levin, B. Han, Z. Sridhar, A. Grand, J. Martin, J. Akar, J. G. Warren, C. M. Solaro, R. J. Ong, S.-G. Darbar, D. Goergen, C. J. Wolska, B. M. Dobrev, D. Wehrens, X. H. 2023-04-20 doi:10.1101/2023.04.19.537590 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ The architecture of metabolic networks constrains the evolution of microbial resource hierarchies ]]> https://biorxiv.org/content/10.1101/2023.04.21.537789v1?rss=1 Takano, S. Vila, J. C. C. Miyazaki, R. Sanchez, A. Bajic, D. 2023-04-21 doi:10.1101/2023.04.21.537789 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ A Nanoparticle RIG-I Agonist for Cancer Immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.04.25.537919v1?rss=1 Wang-Bishop, L. Wehbe, M. Pastora, L. E. Yang, J. Garland, K. M. Becker, K. W. Carson, C. S. Gibson-Corley, K. N. Ulkoski, D. Krishnamurthy, V. Fedorova, O. Richmond, A. Pyle, A. M. Wilson, J. T. 2023-04-25 doi:10.1101/2023.04.25.537919 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Statistical learning in epilepsy: Behavioral, anatomical, and causal mechanisms in the human brain ]]> https://biorxiv.org/content/10.1101/2023.04.25.538321v1?rss=1 Aljishi, A. Sherman, B. E. Huberdeau, D. M. Obaid, S. Sivaraju, A. Turk-Browne, N. B. Damisah, E. C. 2023-04-28 doi:10.1101/2023.04.25.538321 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly ]]> https://biorxiv.org/content/10.1101/2023.04.26.538436v1?rss=1 Webster, T. H. Vannan, A. Pinto, B. J. Denbrock, G. Morales, M. Dolby, G. A. Fiddes, I. T. DeNardo, D. F. Wilson, M. A. 2023-04-28 doi:10.1101/2023.04.26.538436 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Analyzing bivariate cross-trait genetic architecture in GWAS summary statistics with the BIGA cloud computing platform ]]> https://biorxiv.org/content/10.1101/2023.04.28.538585v1?rss=1 Li, Y. Xue, F. Li, B. Yang, Y. Fan, Z. Shu, J. Wang, X. Lin, J. Copana, C. Zhao, B. 2023-05-01 doi:10.1101/2023.04.28.538585 Cold Spring Harbor Laboratory Press 2023-05-01 <![CDATA[ Phenomenological modeling reveals the emergent simplicity of host-associated microbiomes ]]> https://biorxiv.org/content/10.1101/2023.04.28.538625v1?rss=1 Plata, G. D. Krishnamurthy, M. Herron, L. Dixit, P. D. 2023-04-29 doi:10.1101/2023.04.28.538625 Cold Spring Harbor Laboratory Press 2023-04-29 <![CDATA[ Fight not flight: parasites drive the bacterial evolution of resistance, not avoidance ]]> https://biorxiv.org/content/10.1101/2023.04.29.538831v1?rss=1 Blazanin, M. Moore, J. P. Olsen, S. Travisano, M. 2023-04-30 doi:10.1101/2023.04.29.538831 Cold Spring Harbor Laboratory Press 2023-04-30 <![CDATA[ gcplyr: an R package for microbial growth curve data analysis ]]> https://biorxiv.org/content/10.1101/2023.04.30.538883v1?rss=1 Blazanin, M. 2023-04-30 doi:10.1101/2023.04.30.538883 Cold Spring Harbor Laboratory Press 2023-04-30 <![CDATA[ Widespread Receptive Field Remapping in Early Visual Cortex ]]> https://biorxiv.org/content/10.1101/2023.05.01.539001v1?rss=1 Denagamage, S. Morton, M. P. Nandy, A. 2023-05-02 doi:10.1101/2023.05.01.539001 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer ]]> https://biorxiv.org/content/10.1101/2023.05.05.539577v1?rss=1 Lu, L. Zhang, Q. Shen, X. Zhen, P. Marin, A. Garcia-Milian, R. Roper, J. Khan, S. A. Johnson, C. 2023-05-05 doi:10.1101/2023.05.05.539577 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ IL-10 constrains sphingolipid metabolism via fatty acid desaturation to limit inflammation ]]> https://biorxiv.org/content/10.1101/2023.05.07.539780v1?rss=1 York, A. G. Skadow, M. H. Qu, R. G. Oh, J. Mowel, W. K. Brewer, J. R. Kaffe, E. Williams, K. J. Kluger, Y. Crawford, J. M. Smale, S. M. Bensinger, S. J. Flavell, R. A. 2023-05-08 doi:10.1101/2023.05.07.539780 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ MscS is a critical component for osmotic survival of Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2023.05.08.539864v1?rss=1 Ramsey, K. Britt, M. Maramba, J. Ushijima, B. Moller, E. Anishkin, A. Hase, C. Sukharev, S. 2023-05-09 doi:10.1101/2023.05.08.539864 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Focal vs Diffuse: Mechanisms of attention mediated performance enhancement in a hierarchical model of the visual system ]]> https://biorxiv.org/content/10.1101/2023.05.09.540022v1?rss=1 Wang, X. Jadi, M. 2023-05-09 doi:10.1101/2023.05.09.540022 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ CpG island turnover events predict evolutionary changes in enhancer activity ]]> https://biorxiv.org/content/10.1101/2023.05.09.540063v1?rss=1 Kocher, A. A. Dutrow, E. V. Uebbing, S. Yim, K. M. Larios, M. F. R. Baumgartner, M. Nottoli, T. Noonan, J. P. 2023-05-09 doi:10.1101/2023.05.09.540063 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans Germ Line ]]> https://biorxiv.org/content/10.1101/2023.05.10.540274v1?rss=1 Sanchez, N. Gonzalez, L. E. Reinke, V. 2023-05-12 doi:10.1101/2023.05.10.540274 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Distribution and dynamics of chromatin states in the C. elegans germ line ]]> https://biorxiv.org/content/10.1101/2023.05.11.540452v1?rss=1 Mazzetto, M. Gonzalez, L. E. Sanchez, N. Reinke, V. 2023-05-14 doi:10.1101/2023.05.11.540452 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Cryo-EM structures of both ends of the actin filament explain why the barbed end elongates faster than the pointed end ]]> https://biorxiv.org/content/10.1101/2023.05.12.540494v1?rss=1 Chou, S. Z. Pollard, T. D. 2023-05-12 doi:10.1101/2023.05.12.540494 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores ]]> https://biorxiv.org/content/10.1101/2023.05.12.540511v1?rss=1 Ahuja, N. Cao, X. Schultz, D. T. Picciani, N. Lord, A. Shao, S. Burdick, D. R. Haddock, S. H. D. Li, Y. Dunn, C. W. 2023-05-14 doi:10.1101/2023.05.12.540511 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Beyond rhythm - A framework for understanding the frequency spectrum of neural activity ]]> https://biorxiv.org/content/10.1101/2023.05.12.540559v1?rss=1 Perrenoud, Q. Cardin, J. A. 2023-05-12 doi:10.1101/2023.05.12.540559 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Hierarchical gradient of timescales in the mammalian forebrain ]]> https://biorxiv.org/content/10.1101/2023.05.12.540610v1?rss=1 Song, M. Shin, E. J. Seo, H. Soltani, A. Steinmetz, N. A. Lee, D. Jung, M. W. Paik, S.-B. 2023-05-13 doi:10.1101/2023.05.12.540610 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ REPIC -- an ensemble learning methodology for cryo-EM particle picking ]]> https://biorxiv.org/content/10.1101/2023.05.13.540636v1?rss=1 Cameron, C. J. Seager, S. J. Sigworth, F. J. Tagare, H. D. Gerstein, M. B. 2023-05-14 doi:10.1101/2023.05.13.540636 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity ]]> https://biorxiv.org/content/10.1101/2023.05.15.540865v1?rss=1 Reese, F. Williams, B. Balderrama-Gutierrez, G. Wyman, D. Celik, M. H. Rebboah, E. Rezaie, N. Trout, D. Razavi-Mohseni, M. Jiang, Y. Borsari, B. Morabito, S. Liang, H. Y. McGill, C. J. Rahmanian, S. Sakr, J. Jiang, S. Zeng, W. Carvalho, K. Weimer, A. K. Dionne, L. A. McShane, A. Bedi, K. Elhajjajy, S. I. Upchurch, S. Jou, J. Youngworth, I. Gabdank, I. Sud, P. Jolanki, O. Strattan, J. S. Kagda, M. S. Snyder, M. P. Hitz, B. C. Moore, J. E. Weng, Z. Bennett, D. Reinholdt, L. Ljungman, M. Beer, M. A. Gerstein, M. B. Pachter, L. Guigo, R. Wold, B. J. Mort 2023-05-16 doi:10.1101/2023.05.15.540865 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Synthetic Cooling Agent and Candy Flavors in California-marketed "non-Menthol" Cigarettes ]]> https://biorxiv.org/content/10.1101/2023.05.15.540890v1?rss=1 Jabba, S. V. Erythropel, H. C. Anastas, P. Zimmerman, J. B. Jordt, S. E. 2023-05-18 doi:10.1101/2023.05.15.540890 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Unraveling cellular complexity with unlimited multiplexed super-resolution imaging ]]> https://biorxiv.org/content/10.1101/2023.05.17.541061v1?rss=1 Schueder, F. Rivera-Molina, F. Su, M. Kidd, P. Rothman, J. E. Toomre, D. Bewersdorf, J. 2023-05-18 doi:10.1101/2023.05.17.541061 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data ]]> https://biorxiv.org/content/10.1101/2023.05.18.541372v1?rss=1 Mah, J. L. Dunn, C. 2023-05-19 doi:10.1101/2023.05.18.541372 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ The role of serotonin and of perceived social differences in infering the motivation of others ]]> https://biorxiv.org/content/10.1101/2023.05.20.541280v1?rss=1 Moutoussis, M. Barnby, J. M. Durant, A. Croal, M. Rutledge, R. Mason, L. 2023-05-22 doi:10.1101/2023.05.20.541280 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Distinct brain network features predict internalizing and externalizing traits in children and adults ]]> https://biorxiv.org/content/10.1101/2023.05.20.541490v1?rss=1 Qu, Y. L. Chen, J. Tam, A. Ooi, L. Q. R. Dhamala, E. Cocuzza, C. Lawhead, C. Yeo, B. T. T. Holmes, A. 2023-05-21 doi:10.1101/2023.05.20.541490 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Focusing attention in human working memory and long-term memory: benefits through dissociable processes ]]> https://biorxiv.org/content/10.1101/2023.05.20.541594v1?rss=1 Gong, D. Draschkow, D. Nobre, A. C. 2023-05-21 doi:10.1101/2023.05.20.541594 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Stem cells tightly regulate dead cell clearance to maintain tissue fitness ]]> https://biorxiv.org/content/10.1101/2023.05.22.541773v1?rss=1 Stewart, K. S. Gonzales, K. A. Yuan, S. Tierney, M. T. Bonny, A. R. Yang, Y. Infarinato, N. R. Cowley, C. J. Levorse, J. M. Pasolli, H. A. Ghosh, S. Rothlin, C. V. Fuchs, E. 2023-05-22 doi:10.1101/2023.05.22.541773 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Periodicity, Mixed-Mode Oscillations, and Multiple Timescale in a Phosphoinositide-Rho GTPase Network ]]> https://biorxiv.org/content/10.1101/2023.05.22.541800v1?rss=1 Tong, C. S. Wu, M. 2023-05-22 doi:10.1101/2023.05.22.541800 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Sex Differences in Human Music Perception are Negligible ]]> https://biorxiv.org/content/10.1101/2023.05.23.541970v1?rss=1 Bertolo, M. Müllensiefen, D. Peretz, I. Woolley, S. C. Sakata, J. Mehr, S. 2023-05-24 doi:10.1101/2023.05.23.541970 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry ]]> https://biorxiv.org/content/10.1101/2023.05.24.542133v1?rss=1 Zimmer, J. T. Vock, I. W. Schofield, J. A. Kiefer, L. Moon, M. H. Simon, M. D. 2023-05-24 doi:10.1101/2023.05.24.542133 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT ]]> https://biorxiv.org/content/10.1101/2023.05.25.542276v1?rss=1 Araujo Tavares, R. d. C. Mahadeshwar, G. Wan, H. Pyle, A. M. 2023-05-25 doi:10.1101/2023.05.25.542276 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Adolescent gulls have the opportunity for social development at breeding colonies ]]> https://biorxiv.org/content/10.1101/2023.05.26.542504v1?rss=1 Taylor, L. U. 2023-05-29 doi:10.1101/2023.05.26.542504 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ False positive glycopeptide identification via in-FAIMS fragmentation ]]> https://biorxiv.org/content/10.1101/2023.05.28.542648v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@d94300org.highwire.dtl.DTLVardef@1bdc6dforg.highwire.dtl.DTLVardef@4b8ea8org.highwire.dtl.DTLVardef@82beed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rangel-Angarita, V. Mahoney, K. E. Kwon, C. Sarker, R. Lucas, T. M. Malaker, S. A. 2023-05-28 doi:10.1101/2023.05.28.542648 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Detection of interactions between genetic marker sets and environment in a genome-wide study of hypertension ]]> https://biorxiv.org/content/10.1101/2023.05.28.542666v1?rss=1 Shen, L. Amei, A. Liu, B. Liu, Y. Xu, G. Oh, E. C. Wang, Z. 2023-05-30 doi:10.1101/2023.05.28.542666 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Transformer with Convolution and Graph-Node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image ]]> https://biorxiv.org/content/10.1101/2023.05.28.542669v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@1c6a4dforg.highwire.dtl.DTLVardef@7266d4org.highwire.dtl.DTLVardef@bcfd0aorg.highwire.dtl.DTLVardef@188d452_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Xiao, X. Kong, Y. Wang, Z. Lu, H. 2023-05-30 doi:10.1101/2023.05.28.542669 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ VEGF-C promotes brain-derived fluid drainage, confers neuroprotection, and improves stroke outcomes ]]> https://biorxiv.org/content/10.1101/2023.05.30.542708v1?rss=1 Simoes Braga Boisserand, L. Bouchart, J. Geraldo, L. H. M. Lee, S. Sanganahalli Ganganna, B. Parent, M. Zhang, S. Xue, Y. Skarica, M. Guegan, J. Li, M. Liu, X. Poulet, M. Askanase, M. Osherov, A. Spajer, M. El Kamouh, M.-R. Eichmann, A. Alitalo, K. K. Zhou, J. Sestan, N. Sansing, L. Benveniste, H. Hyder, F. thomas, j.-l. 2023-05-30 doi:10.1101/2023.05.30.542708 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Prefrontal Cortex Astroglia Modulate Anhedonia-like Behavior ]]> https://biorxiv.org/content/10.1101/2023.05.31.542974v1?rss=1 Codeluppi, S. A.-M. Xu, M. Bansal, Y. Lepack, A. E. Duric, V. Chow, M. Muir, J. Bagot, R. C. Licznerski, P. Wilber, S. L. Sanacora, G. Sibille, E. Duman, R. Pittenger, C. Banasr, M. 2023-06-03 doi:10.1101/2023.05.31.542974 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Combinatorial Regimens Augment Drug Monotherapy for SARS-CoV-2 Clearance in Mice ]]> https://biorxiv.org/content/10.1101/2023.05.31.543159v1?rss=1 Ullah, I. Escudie, F. Scandale, I. Gilani, Z. Gendron-Lepage, G. Gaudette, F. Mowbray, C. Fraisse, L. Bazin, R. Finzi, A. Mothes, W. Kumar, P. Chatelain, E. Uchil, P. D. 2023-06-01 doi:10.1101/2023.05.31.543159 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model ]]> https://biorxiv.org/content/10.1101/2023.06.01.543315v1?rss=1 Phan, T. V. Mattingly, H. H. Vo, L. Marvin, J. S. Looger, L. L. Emonet, T. 2023-06-05 doi:10.1101/2023.06.01.543315 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Finetuning ERK activity enables most somatic cells to reprogram into pluripotency ]]> https://biorxiv.org/content/10.1101/2023.06.02.543427v1?rss=1 Wu, Q. Zhang, J. Hu, X. Mafra de Faria, B. Scalf, S. M. Karatepe, K. Roy, A. L. Guo, S. 2023-06-03 doi:10.1101/2023.06.02.543427 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Functionally and metabolically divergent melanoma-associated macrophages originate from common bone-marrow precursors ]]> https://biorxiv.org/content/10.1101/2023.06.02.543515v1?rss=1 Pizzurro, G. A. Bridges, K. Jiang, X. Vidyarthi, A. Miller-Jensen, K. Colegio, O. R. 2023-06-05 doi:10.1101/2023.06.02.543515 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Actin and microtubules position stress granules ]]> https://biorxiv.org/content/10.1101/2023.06.04.543599v1?rss=1 Boeddeker, T. J. Rusch, A. Leeners, K. Murrell, M. P. Dufresne, E. R. 2023-06-04 doi:10.1101/2023.06.04.543599 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Novel Roles for Diacylglycerol in Synaptic Vesicle Priming and Release Revealed by Complete Reconstitution of Core Protein Machinery ]]> https://biorxiv.org/content/10.1101/2023.06.05.543781v1?rss=1 Sundaram, R. V. K. Chatterjee, A. Bera, M. Grushin, K. Panda, A. Li, F. Coleman, J. Ramakrishnan, S. Ernst, A. Gupta, K. Rothman, J. E. Krishnakumar, S. S. 2023-06-07 doi:10.1101/2023.06.05.543781 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression ]]> https://biorxiv.org/content/10.1101/2023.06.06.543780v1?rss=1 Cao, D. Zhong, L. Hemalatha, A. Bergmann, J. Cox, A. L. Greco, V. Sozen, B. 2023-06-07 doi:10.1101/2023.06.06.543780 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Spatiotemporal organization of prefrontal norepinephrine influences neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.06.09.544191v1?rss=1 Glaeser-Khan, S. Savalia, N. K. Cressy, J. Feng, J. Li, Y. Kwan, A. C. Kaye, A. P. 2023-06-13 doi:10.1101/2023.06.09.544191 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ The effects of data leakage on neuroimaging predictive models ]]> https://biorxiv.org/content/10.1101/2023.06.09.544383v1?rss=1 Rosenblatt, M. Tejavibulya, L. Jiang, R. Noble, S. Scheinost, D. 2023-06-11 doi:10.1101/2023.06.09.544383 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ Rescuing missing data in connectome-based predictive modeling ]]> https://biorxiv.org/content/10.1101/2023.06.09.544392v1?rss=1 Liang, Q. Jiang, R. Adkinson, B. D. Rosenblatt, M. Mehta, S. Foster, M. L. Dong, S. You, C. Negahban, S. Zhou, H. H. Chang, J. Scheinost, D. 2023-06-11 doi:10.1101/2023.06.09.544392 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in M. smegmatis ]]> https://biorxiv.org/content/10.1101/2023.06.12.544663v1?rss=1 Ng, W. L. Park, J. H. Rego, E. H. 2023-06-12 doi:10.1101/2023.06.12.544663 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Lysinoalanine crosslinking is a conserved post-translational modification in the spirochete flagellar hook ]]> https://biorxiv.org/content/10.1101/2023.06.13.544825v1?rss=1 Lynch, M. J. Deshpande, M. Kyrniyati, K. Zhang, K. James, M. Miller, M. Zhang, S. Passalia, F. J. Wunder, E. A. Charon, N. W. Li, C. Crane, B. R. 2023-06-13 doi:10.1101/2023.06.13.544825 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Endocrine pancreas-specific Gclc gene deletion causes a severe diabetes phenotype ]]> https://biorxiv.org/content/10.1101/2023.06.13.544855v1?rss=1 Davidson, E. A. Chen, Y. Singh, S. Orlicky, D. J. Thompson, B. Wang, Y. Charkoftaki, G. Furnary, T. Cardone, R. Kibbey, R. G. Shearn, C. T. Nebert, D. W. Thompson, D. C. Vasiliou, V. 2023-06-14 doi:10.1101/2023.06.13.544855 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Temporal segmentation and 'look ahead' simulation: Physical events structure visual perception of intuitive physics ]]> https://biorxiv.org/content/10.1101/2023.06.14.544968v1?rss=1 Yates, T. S. Yasuda, S. Yildirim, I. 2023-06-15 doi:10.1101/2023.06.14.544968 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering ]]> https://biorxiv.org/content/10.1101/2023.06.15.545118v1?rss=1 Hislop, J. J. Alavi, A. Song, Q. Schoenberger, R. L. Keshavarz F., K. LeGraw, R. Velazquez, J. J. Mokhtari, T. Taheri, M. N. Rytel, M. de Sousa Lopes, S. M. C. Watkins, S. C. Stolz, D. B. Kiani, S. Sozen, B. Bar-Joseph, Z. Ebrahimkhani, M. 2023-06-15 doi:10.1101/2023.06.15.545118 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Non-coding sequence variation reveals fragility within interleukin 2 feedback circuitry and shapes autoimmune disease risk ]]> https://biorxiv.org/content/10.1101/2023.06.17.545426v1?rss=1 Simeonov, D. R. Park, K. Cortez, J. T. Young, A. Li, Z. Nguyen, V. Umhoefer, J. Indart, A. C. Woo, J. Anderson, M. S. Tsang, J. S. Germain, R. N. Wong, H. S. Marson, A. 2023-06-18 doi:10.1101/2023.06.17.545426 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Evolutionary innovations in germline biology of placental mammals revealed by transcriptomics of first wave spermatogenesis in opossum ]]> https://biorxiv.org/content/10.1101/2023.06.17.545442v1?rss=1 Marshall, K. L. Stadtmauer, D. J. Maziarz, J. Wagner, G. Lesch, B. J. 2023-06-20 doi:10.1101/2023.06.17.545442 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ The extension of mammalian pregnancy required taming inflammation; independent evolution of extended placentation in the tammar wallaby ]]> https://biorxiv.org/content/10.1101/2023.06.18.545206v1?rss=1 Dudley, J. S. Renfree, M. B. Wagner, G. P. Griffith, O. W. 2023-06-21 doi:10.1101/2023.06.18.545206 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Metagenomics for pathogen detection during a wildlife mortality event in songbirds ]]> https://biorxiv.org/content/10.1101/2023.06.20.545358v1?rss=1 Mwakibete, L. Greening, S. S. Kalantar, K. Ahyong, V. Anis, E. Miller, E. A. Needle, D. B. Oglesbee, M. Thomas, W. K. Sevigny, J. L. Gordon, L. M. Nemeth, N. M. Ogbunugafor, C. B. Ayala, A. J. Faith, S. A. Neff, N. Detweiler, A. M. Baillargeon, T. Tanguay, S. Simpson, S. D. Murphy, L. A. Ellis, J. C. Tato, C. M. Gagne, R. B. 2023-06-23 doi:10.1101/2023.06.20.545358 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Tomosyns attenuate SNARE assembly and synaptic depression by binding to VAMP2-containing template complexes ]]> https://biorxiv.org/content/10.1101/2023.06.20.545669v1?rss=1 Meijer, M. Ottl, M. Yang, J. Subkhangulova, A. Kumar, A. Groffen, A. J. van Weering, J. R. T. Zhang, Y. Verhage, M. 2023-06-23 doi:10.1101/2023.06.20.545669 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity ]]> https://biorxiv.org/content/10.1101/2023.06.21.545145v1?rss=1 Wang, M. Patsenker, J. Li, H. Kluger, Y. Kleinstein, S. 2023-06-23 doi:10.1101/2023.06.21.545145 Cold Spring Harbor Laboratory Press 2023-06-23 <![CDATA[ Stimulus-Specific Modulation is Enabled by Differential Serotonin Receptor Expression ]]> https://biorxiv.org/content/10.1101/2023.06.21.546011v1?rss=1 Jonaitis, J. Mazri, M. F. E. B. Sizemore, T. R. Ralston, J. D. Salman, F. Fletcher, E. J. Matheny, D. E. Ramachandra, K. L. Dacks, A. M. 2023-06-21 doi:10.1101/2023.06.21.546011 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Hippocampal Codes for Real-World Human Navigation ]]> https://biorxiv.org/content/10.1101/2023.06.22.545396v1?rss=1 Graves, K. N. Letrou, A. Gray, T. E. Quraishi, I. H. Turk-Browne, N. B. 2023-06-22 doi:10.1101/2023.06.22.545396 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ GDF15 is a Critical Renostat in the Defense Against Hypoglycemia ]]> https://biorxiv.org/content/10.1101/2023.06.22.546095v1?rss=1 Li, Z. Zhang, X. Zhu, W. Xu, Q. Yu, C. Zhao, Q. Siebel, S. Zhang, C. Costa Lima, B. G. Li, X. Israni-Winger, K. Nasiri, A. R. Caplan, M. J. Chang, R. B. Wang, A. Belfort de Aguiar, R. Hwang, J. J. Perry, R. J. 2023-06-25 doi:10.1101/2023.06.22.546095 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Maternal regulation of the vertebrate oocyte-to-egg transition ]]> https://biorxiv.org/content/10.1101/2023.06.22.546137v1?rss=1 Fuentes, R. Marlow, F. Abrams, E. Zhang, H. Kobayashi, M. Gupta, T. Kapp, L. DiNardo, Z. Montecinos-Franjola, F. Vought, W. Vejnar, C. Giraldez, A. E. Mullins, M. C. 2023-06-22 doi:10.1101/2023.06.22.546137 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ High performers demonstrate greater neural synchrony than low performers across behavioral domains ]]> https://biorxiv.org/content/10.1101/2023.06.22.546173v1?rss=1 Chamberlain, T. A. Corriveau, A. Song, H. Kwon, Y. H. Yoo, K. Chun, M. Rosenberg, M. D. 2023-06-26 doi:10.1101/2023.06.22.546173 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data ]]> https://biorxiv.org/content/10.1101/2023.06.23.546284v1?rss=1 Bryce-Smith, S. Burri, D. Gazzara, M. R. Herrmann, C. J. Danecka, W. Fitzsimmons, C. M. Wan, Y. K. Zhuang, F. Fansler, M. M. Fernandez, J. M. Ferret, M. Gonzalez-Uriarte, A. Haynes, S. Herdman, C. Kanitz, A. Katsantoni, M. Marini, F. McDonnel, E. Nicolet, B. Poon, C.-L. Rot, G. Schärfen, L. Wu, P.-J. Yoon, Y. Barash, Y. Zavolan, M. 2023-06-26 doi:10.1101/2023.06.23.546284 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Population encoding of stimulus features along the visual hierarchy ]]> https://biorxiv.org/content/10.1101/2023.06.27.545450v1?rss=1 Dyballa, L. Rudzite, A. M. Hoseini, M. S. Thapa, M. Stryker, M. P. Field, G. D. Zucker, S. W. 2023-06-27 doi:10.1101/2023.06.27.545450 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program ]]> https://biorxiv.org/content/10.1101/2023.06.28.545586v1?rss=1 Meizlish, M. L. Kimura, Y. Pope, S. D. Matta, R. Kim, C. Philip, N. Meyaard, L. Gonzalez, A. Medzhitov, R. 2023-06-30 doi:10.1101/2023.06.28.545586 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Fiber alignment in 3D collagen networks as a biophysical marker for cell contractility ]]> https://biorxiv.org/content/10.1101/2023.06.28.546896v1?rss=1 Boehringer, D. Bauer, A. Moravec, I. Bischof, L. Kah, D. Mark, C. Grundy, T. J. Goerlach, E. O'Neill, G. M. Budday, S. Strissel, P. Strick, R. Malandrino, A. Gerum, R. Mak, M. Rausch, M. Fabry, B. 2023-06-29 doi:10.1101/2023.06.28.546896 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Human Th17- and IgG3-associated autoimmunity induced by a translocating gut pathobiont ]]> https://biorxiv.org/content/10.1101/2023.06.29.546430v1?rss=1 Gronke, K. Nguyen, M. Santamaria de Souza, N. Schumacher, J. Yang, Y. Sonnert, N. D. Leopold, S. Martin, A. Hallet, R. Richter, K. Schubert, D. Daniel, G. M. Dylus, D. Forkel, M. Manfredo Vieira, S. Schwinge, D. Schramm, C. Lassen, K. G. Piali, L. Palm, N. W. Bieniossek, C. Kriegel, M. A. 2023-07-01 doi:10.1101/2023.06.29.546430 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Theoretical validation of growth curves for quantifying phage-bacteria interactions ]]> https://biorxiv.org/content/10.1101/2023.06.29.546975v1?rss=1 Blazanin, M. Vasen, E. Jolis, C. V. An, W. Turner, P. 2023-06-29 doi:10.1101/2023.06.29.546975 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ BeeDC: An R package and globally synthesised and flagged bee occurrence dataset ]]> https://biorxiv.org/content/10.1101/2023.06.30.547152v1?rss=1 18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation. ]]> Dorey, J. B. Fischer, E. E. Chesshire, P. R. Nava-Bolanos, A. OReilly, R. L. Bossert, S. Collins, S. M. Lichtenberg, E. M. Tucker, E. M. Smith-Pardo, A. Falcon-Brindis, A. Guevara, D. A. Ribeiro, B. de Pedro, D. Pickering, J. James, K.-L. Parys, K. A. McCabe, L. M. Rogan, M. S. Minckley, R. L. Velazco, S. J. E. Griswold, T. Zarrillo, T. A. Jetz, W. Sica, Y. V. Orr, M. C. Guzman, L. M. Ascher, J. A. Hughes, A. C. Cobb, N. S. 2023-07-02 doi:10.1101/2023.06.30.547152 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail ]]> https://biorxiv.org/content/10.1101/2023.06.30.547189v1?rss=1 Sexton, J. A. Potchernikov, T. Sepulveda, G. C. Cao, W. Lou, H. J. Boggon, T. J. De La Cruz, E. M. Turk, B. E. 2023-06-30 doi:10.1101/2023.06.30.547189 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Imaging proteins sensitive to direct fusions using transient peptide-peptide interactions ]]> https://biorxiv.org/content/10.1101/2023.07.01.547312v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@ce1d9borg.highwire.dtl.DTLVardef@1f9b5c8org.highwire.dtl.DTLVardef@10d92ccorg.highwire.dtl.DTLVardef@20ad5d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gidden, Z. Oi, C. Johnston, E. Bhaskar, H. Rosser, S. Mochrie, S. G. J. Horrocks, M. H. Regan, L. 2023-07-02 doi:10.1101/2023.07.01.547312 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ The Cellular Underpinnings of the Human Cortical Connectome ]]> https://biorxiv.org/content/10.1101/2023.07.05.547828v1?rss=1 Zhang, X.-H. Anderson, K. M. Dong, H.-M. Chopra, S. Dhamala, E. Emani, P. S. Margulies, D. Holmes, A. J. 2023-07-06 doi:10.1101/2023.07.05.547828 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Synaptophysin Chaperones the Assembly of 12 SNAREpins under each Ready-Release Vesicle ]]> https://biorxiv.org/content/10.1101/2023.07.05.547834v1?rss=1 Bera, M. Radhakrishnan, A. Coleman, J. Kalyana Sundaram, R. V. Ramakrishnan, S. Pincet, F. Rothman, J. E. 2023-07-06 doi:10.1101/2023.07.05.547834 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Alterations in grey matter structure linked to frequency-specific cortico-subcortical connectivity in schizophrenia via multimodal data fusion ]]> https://biorxiv.org/content/10.1101/2023.07.05.547840v1?rss=1 Duda, M. Faghiri, A. Belger, A. Bustillo, J. R. Ford, J. M. Mathalon, D. H. Mueller, B. A. Pearlson, G. D. Potkin, S. G. Preda, A. Sui, J. Van Erp, T. G. M. Calhoun, V. D. 2023-07-06 doi:10.1101/2023.07.05.547840 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Augmented Super-Resolution Radial Fluctuations (aSRRF) Pushing the Limits of Structured Illumination Microscopy ]]> https://biorxiv.org/content/10.1101/2023.07.05.547885v1?rss=1 Zhang, H. Wang, J. Jin, L. Zhu, Y. Guo, Y. Zhang, M. Zhang, Y. Wang, Z. Su, Y. Wu, Y. Ji, B. Toomre, D. Liu, X. Xu, Y. 2023-07-06 doi:10.1101/2023.07.05.547885 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Edge-based general linear models capture high-frequency fluctuations in attention ]]> https://biorxiv.org/content/10.1101/2023.07.06.547966v1?rss=1 Jones, H. M. Yoo, K. Chun, M. M. Rosenberg, M. D. 2023-07-10 doi:10.1101/2023.07.06.547966 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Nuclear envelope assembly relies on CHMP-7 in the absence of BAF-LEM-mediated hole closure ]]> https://biorxiv.org/content/10.1101/2023.07.06.547980v1?rss=1 Barger, S. R. Penfield, L. Bahmanyar, S. 2023-07-07 doi:10.1101/2023.07.06.547980 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Individual differences in spatial working memory strategies differentially reflected in the engagement of control and default brain networks ]]> https://biorxiv.org/content/10.1101/2023.07.07.548112v1?rss=1 Purg, N. Rahmati, M. Cho, Y. T. Slana Ozimic, A. Kraljic, A. Murray, J. D. Anticevic, A. Repovs, G. 2023-07-07 doi:10.1101/2023.07.07.548112 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Experimental and Phylogenetic Evidence for Correlated Gene Expression Evolution between Dermal and Endometrial Fibroblasts: implications for the evolution of cancer malignancy ]]> https://biorxiv.org/content/10.1101/2023.07.08.548194v1?rss=1 Dighe, A. Maziarz, J. IbrahimHashim, A. Gatenby, R. Kshitiz, Levchenko, A. Wagner, G. P. 2023-07-09 doi:10.1101/2023.07.08.548194 Cold Spring Harbor Laboratory Press 2023-07-09 <![CDATA[ A novel naive Bayes approach to identifying grooming behaviors in the force-plate actometric platform ]]> https://biorxiv.org/content/10.1101/2023.07.08.548198v1?rss=1 Anderson, C. J. Cadeddu, R. Anderson, D. N. Huxford, J. A. VanLuik, E. R. Odeh, K. Pittenger, C. Pulst, S. M. Bortolato, M. 2023-07-10 doi:10.1101/2023.07.08.548198 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ DNA Recognition and Induced Genome Modification by a Hydroxymethyl-γ Tail-Clamp Peptide Nucleic Acid ]]> https://biorxiv.org/content/10.1101/2023.07.08.548209v1?rss=1 Oyaghire, S. N. Quijano, E. Perera, D. R. Mandl, H. K. Saltzman, W. M. Bahal, R. Glazer, P. M. 2023-07-09 doi:10.1101/2023.07.08.548209 Cold Spring Harbor Laboratory Press 2023-07-09 <![CDATA[ MKP1 promotes nonalcoholic steatohepatitis by suppressing AMPK activity through LKB1 nuclear retention ]]> https://biorxiv.org/content/10.1101/2023.07.10.548263v1?rss=1 Qiu, B. Lawan, A. Xirouchaki, C. E. Yi, J.-S. Robert, M. Zhang, L. Brown, W. Fernandez-Hernando, C. Yang, X. Bennett, A. M. 2023-07-11 doi:10.1101/2023.07.10.548263 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Beyond the Visual Word Form Area: Characterizing a hierarchical, distributed and bilateral network for visual word processing ]]> https://biorxiv.org/content/10.1101/2023.07.11.548613v1?rss=1 Vin, R. Blauch, N. M. Plaut, D. Behrmann, M. 2023-07-12 doi:10.1101/2023.07.11.548613 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Using Saturation Mutagenesis-Reinforced Functional Assays (SMuRF) to improve the variant interpretation for alpha-dystroglycan glycosylation enzymes ]]> https://biorxiv.org/content/10.1101/2023.07.12.548370v1?rss=1 Ma, K. Ng, K. K. Huang, S. Lake, N. J. Xu, J. Ge, L. Woodman, K. G. Koczwara, K. E. Lek, A. Lek, M. 2023-07-12 doi:10.1101/2023.07.12.548370 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Polarized localization of kinesin-1 and RIC-7 drives axonal mitochondria anterograde transport ]]> https://biorxiv.org/content/10.1101/2023.07.12.548706v1?rss=1 Wu, Y. Ding, C. Weinreb, A. Manning, L. Swaim, G. Yogev, S. Colon-Ramos, D. Hammarlund, M. 2023-07-12 doi:10.1101/2023.07.12.548706 Cold Spring Harbor Laboratory Press 2023-07-12 <![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[ Two successive oligomeric Munc13 assemblies scaffold vesicle docking and SNARE assembly to support neurotransmitter release ]]> https://biorxiv.org/content/10.1101/2023.07.14.549017v1?rss=1 Bera, M. Grushin, K. Kalyana Sundaram, V. Shahanoor, Z. Chatterjee, A. Radhakrishnan, A. Lee, S. Padmanarayana, M. Coleman, J. Pincet, F. Rothman, J. E. Dittman, J. S. 2023-07-16 doi:10.1101/2023.07.14.549017 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Rewiring the carbon cycle: a theoretical framework for animal-driven ecosystem carbon sequestration ]]> https://biorxiv.org/content/10.1101/2023.07.14.549071v1?rss=1 Rizzuto, M. Leroux, S. J. Schmitz, O. J. 2023-07-15 doi:10.1101/2023.07.14.549071 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Integrating ecosystem and contaminant models to predict the effects of ecosystem fluxes on contaminant dynamics ]]> https://biorxiv.org/content/10.1101/2023.07.15.549171v1?rss=1 McLeod, A. Leroux, S. Rizzuto, M. Leibold, M. A. Schiesari, L. C. 2023-07-16 doi:10.1101/2023.07.15.549171 Cold Spring Harbor Laboratory Press 2023-07-16 <![CDATA[ Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes ]]> https://biorxiv.org/content/10.1101/2023.07.17.549339v1?rss=1 Powell, S. Liao, W. O'Shea, C. Kammourh, S. Ghorbani, S. Rigat, R. Elahi, R. Deans, P. M. Le, D. Agarwal, P. Seow, W. Q. Wang, K. C. Akbarian, S. Brennand, K. 2023-07-19 doi:10.1101/2023.07.17.549339 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and its Links to Genetic Risk ]]> https://biorxiv.org/content/10.1101/2023.07.18.548880v1?rss=1 Iraji, A. Chen, J. Lewis, N. Fu, Z. Agcaoglu, O. Kochunov, P. Adhikari, B. M. Mathalon, D. H. Pearlson, G. D. Macciardi, F. Preda, A. van Erp, T. G. M. Bustillo, J. R. Diaz-Caneja, C. M. Andres-Camazon, P. Dhamala, M. Adali, T. Calhoun, V. D. 2023-07-19 doi:10.1101/2023.07.18.548880 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Evidence of an optimal error rate for motor skill learning ]]> https://biorxiv.org/content/10.1101/2023.07.19.549705v1?rss=1 Al-Fawakhiri, N. Kayani, S. McDougle, S. D. 2023-07-19 doi:10.1101/2023.07.19.549705 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Spatial patterns of within-thalamus anatomical connectivity vary across the cortical hierarchy in humans and macaques ]]> https://biorxiv.org/content/10.1101/2023.07.22.550168v1?rss=1 Howell, A. M. Warrington, S. Fonteneau, C. Cho, Y. Sotiropoulos, S. Murray, J. D. Anticevic, A. 2023-07-25 doi:10.1101/2023.07.22.550168 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ A genome-wide single-cell 3D genome atlas of lung cancer progression ]]> https://biorxiv.org/content/10.1101/2023.07.23.550157v1?rss=1 Liu, M. Jin, S. Agabiti, S. S. Jensen, T. B. Yang, T. Radda, J. S. D. Ruiz, C. F. Baldissera, G. Muzumdar, M. D. Wang, S. 2023-07-24 doi:10.1101/2023.07.23.550157 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Collective dynamics of formin and microtubule and its crosstalk mediated by FHDC1 ]]> https://biorxiv.org/content/10.1101/2023.07.25.550329v1?rss=1 Tong, C. S. Su, M. Sun, H. Chua, X. L. Guo, S. Ramaraj, R. S. Lee, A. G. Ong, N. W. P. Miao, Y. Wu, M. 2023-07-25 doi:10.1101/2023.07.25.550329 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Predictive microbial community changes across a temperature gradient ]]> https://biorxiv.org/content/10.1101/2023.07.28.550899v1?rss=1 Sun, X. Folmar, J. Favier, A. Pyenson, N. Sanchez, A. Rebolleda-Gomez, M. 2023-07-30 doi:10.1101/2023.07.28.550899 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Assessing the impact of binary land cover variables on species distribution models: A North Americanstudy on water birds ]]> https://biorxiv.org/content/10.1101/2023.07.31.551237v1?rss=1 Gabor, L. Cohen, J. Jetz, W. 2023-08-02 doi:10.1101/2023.07.31.551237 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Metabolomic changes associated with acquired resistance to Ixodes scapularis ]]> https://biorxiv.org/content/10.1101/2023.07.31.551287v1?rss=1 Cui, Y. Matias, J. Tang, X. Cibichakravarthy, B. DePonte, K. Wu, M.-J. Fikrig, E. 2023-07-31 doi:10.1101/2023.07.31.551287 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires ]]> https://biorxiv.org/content/10.1101/2023.08.01.549754v1?rss=1 Schoelmerich, M. C. Ly, L. West-Roberts, J. Shi, L.-D. Shen, C. Malvankar, N. Taib, N. Gribaldo, S. Woodcroft, B. J. Al-Shayeb, B. Dai, X. Mozsary, C. Hickey, S. He, C. Beaulaurier, J. A. Juul, S. Sachdeva, R. Banfield, J. 2023-08-01 doi:10.1101/2023.08.01.549754 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Anopheles gambiae mosGILT regulates innate immune genes and zpg expression ]]> https://biorxiv.org/content/10.1101/2023.08.01.551536v1?rss=1 Arora, G. Tang, X. Cui, Y. Yang, J. Chuang, Y.-M. Joshi, J. Sajid, A. Dong, Y. Cresswell, P. Dimopoulos, G. Fikrig, E. 2023-08-02 doi:10.1101/2023.08.01.551536 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Antibody gene features associated with binding and functional activity in vaccine-derived human mAbs targeting malaria parasites ]]> https://biorxiv.org/content/10.1101/2023.08.01.551554v1?rss=1 Coelho, C. Marquez, S. Tentokam, B. T. Berhe, A. Miura, k. Long, C. Healy, S. Sagara, I. Kleinstein, S. Duffy, P. 2023-08-03 doi:10.1101/2023.08.01.551554 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Specific configurations of electrical synapses filter sensory information to drive choices in behavior ]]> https://biorxiv.org/content/10.1101/2023.08.01.551556v1?rss=1 Almoril-Porras, A. Calvo, A. Niu, L.-G. Beagan, J. Hawk, J. D. Aljobeh, A. Wisdom, E. Ren, I. Diaz-Garcia, M. Wang, Z.-W. Colon-Ramos, D. 2023-08-03 doi:10.1101/2023.08.01.551556 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Comparative pathogenesis of two lineages of Powassan virus reveals differing routes of neuroinvasion leading to distinct clinical outcome, neuropathology and inflammation ]]> https://biorxiv.org/content/10.1101/2023.08.01.551588v1?rss=1 Reynolds, E. Hart, C. Nelson, J. Marzullo, B. Esterly, A. Paine, D. Crooker, J. Massa, P. Thangamani, S. 2023-08-02 doi:10.1101/2023.08.01.551588 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Differences Between Human and Non-Human Primate Theory of Mind: Evidence from Computational Modeling ]]> https://biorxiv.org/content/10.1101/2023.08.02.551487v1?rss=1 Berke, M. Horschler, D. Jara-Ettinger, J. Santos, L. 2023-08-03 doi:10.1101/2023.08.02.551487 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response ]]> https://biorxiv.org/content/10.1101/2023.08.02.551666v1?rss=1 Ruperti, F. Becher, I. Stokkermans, A. Wang, L. Marschlich, N. Potel, C. Maus, E. Stein, F. Drotleff, B. Schippers, K. J. Nickel, M. Prevedel, R. Musser, J. M. Savitski, M. M. Arendt, D. 2023-08-02 doi:10.1101/2023.08.02.551666 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Social context and the evolution of delayed reproduction in birds ]]> https://biorxiv.org/content/10.1101/2023.08.02.551693v1?rss=1 Taylor, L. U. Prum, R. O. 2023-08-03 doi:10.1101/2023.08.02.551693 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ MHC-B Diversity and Signs of Respiratory Illness in Wild, East African Chimpanzees (Pan troglodytes schweinfurthii) ]]> https://biorxiv.org/content/10.1101/2023.08.02.551731v1?rss=1 Phillips, S. R. 2023-08-05 doi:10.1101/2023.08.02.551731 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Molecular pharmacology of selective NaV1.6 and dual NaV1.6 and NaV1.2 channel inhibitors that suppress excitatory neuronal activity ex vivo ]]> https://biorxiv.org/content/10.1101/2023.08.03.551643v1?rss=1 100 fold against NaV1.1 channels that are dominant in inhibitory cells. This profile will enable pharmacological dissection of the physiological roles of NaV1.2 and NaV1.6 and help to define the role of each channel in disease states. These compounds bind to and stabilize the inactivated-state of the channels, demonstrate higher potency with longer residency times, and slower off-rates than carbamazepine and phenytoin. These compounds possess cellular selectivity ex vivo in inhibiting action potential firing in cortical excitatory pyramidal neurons, whilst sparing fast spiking inhibitory interneurons. XPC-5462 also suppresses epileptiform activity in an ex vivo brain slice seizure model. This class of compounds provides a unique approach for treating neuronal excitability disorders by selectively down-regulating excitatory circuits. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/551643v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@70750corg.highwire.dtl.DTLVardef@114756aorg.highwire.dtl.DTLVardef@289009org.highwire.dtl.DTLVardef@1086e23_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Goodchild, S. J. Shuart, N. G. Williams, A. D. Ye, W. Parrish, R. R. Soriano, M. Thouta, S. Mezeyova, J. Waldbrook, M. Dean, R. A. Focken, T. Ghovanloo, M.-R. Ruben, P. C. Scott, F. Cohen, C. J. Empfield, J. R. Johnson, J. 2023-08-05 doi:10.1101/2023.08.03.551643 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Highly conserved, positively charged tandem repeats mediate multimerization of ice nucleation proteins ]]> https://biorxiv.org/content/10.1101/2023.08.03.551873v1?rss=1 Hansen, T. Lee, J. C. Reicher, N. Ovadia, G. Guo, S. Guo, W. Liu, J. Braslavsky, I. Rudich, Y. Davies, P. L. 2023-08-03 doi:10.1101/2023.08.03.551873 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Mechanism of Phosphate Release from Actin Filaments ]]> https://biorxiv.org/content/10.1101/2023.08.03.551904v1?rss=1 Wang, Y. Zsolnay, V. Pollard, T. D. Voth, G. A. 2023-08-05 doi:10.1101/2023.08.03.551904 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria ]]> https://biorxiv.org/content/10.1101/2023.08.04.551995v1?rss=1 Qin, W. Wei, S. P. Zheng, Y. Choi, E. Li, X. Johnston, J. Wan, X. Abrahamson, B. Flinkstrom, Z. Wang, B. Li, H. Hou, L. Tao, Q. Chlouber, W. W. Sun, X. Wells, M. Ngo, L. Hunt, K. A. Urakawa, H. Tao, X. Wang, D. Pan, C. Weber, P. K. Jiang, J. Zhou, J. Zhang, Y. Stahl, D. A. Ward, B. B. Mayali, X. Martens-Habbena, W. Winkler, M. 2023-08-04 doi:10.1101/2023.08.04.551995 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Dynamic clustering of genomics cohorts beyond race, ethnicity--and ancestry ]]> https://biorxiv.org/content/10.1101/2023.08.04.552035v1?rss=1 Mohsen, H. Blenman, K. Emani, P. S. Morris, Q. Carrot-Zhang, J. Pusztai, L. 2023-08-07 doi:10.1101/2023.08.04.552035 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ HEARTSVG: a fast and accurate method for spatially variable gene identification in large-scale spatial transcriptomic data ]]> https://biorxiv.org/content/10.1101/2023.08.06.552154v1?rss=1 Yuan, X. Ma, Y. Gao, R. Cui, S. Fa, B. Wang, Y. Ma, S. Wei, T. Ma, S. S. Yu, Z. 2023-08-07 doi:10.1101/2023.08.06.552154 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.08.07.552269v1?rss=1 Townsend, J. P. Gaughran, S. Hassler, H. B. Fisk, J. N. Nagib, M. Wu, Y. Wang, Y. Wang, Z. Galvani, A. P. Dornburg, A. 2023-08-07 doi:10.1101/2023.08.07.552269 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Discovery of a Well-Folded Protein Interaction Hub Within the Human Long Non-Coding RNA NORAD ]]> https://biorxiv.org/content/10.1101/2023.08.07.552337v1?rss=1 Kumar, A. Wan, H. Perry, Z. Patel, S. Araujo Tavares, R. d. C. Pyle, A. M. 2023-08-07 doi:10.1101/2023.08.07.552337 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ Early Deprivation Impairs Perforant Pathway Connectivity and Contextual Memory in Adolescent Male Mice ]]> https://biorxiv.org/content/10.1101/2023.08.08.552517v1?rss=1 Islam, R. White, J. D. Arefin, T. M. Mehta, S. Liu, X. Polis, B. Giuliano, L. Ahmed, S. Bowers, C. Zhang, J. Kaffman, A. 2023-08-13 doi:10.1101/2023.08.08.552517 Cold Spring Harbor Laboratory Press 2023-08-13 <![CDATA[ Erythroid differentiation dependent interaction of VPS13A with XK at the plasma membrane of K562 cells ]]> https://biorxiv.org/content/10.1101/2023.08.09.552634v1?rss=1 Amos, C. Xu, P. De Camilli, P. 2023-08-10 doi:10.1101/2023.08.09.552634 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia ]]> https://biorxiv.org/content/10.1101/2023.08.10.552443v1?rss=1 Brunson, K. Witt, K. E. Monge, S. Williams, S. Peede, D. Odsuren, D. Bukhchuluun, D. Cameron, A. Szpak, P. Amartuvshin, C. Honeychurch, W. Wright, J. Pleuger, S. Erdene, M. Tumen, D. Rogers, L. Khatanbaatar, D. Batdalai, B. Galdan, G. Janz, L. 2023-08-10 doi:10.1101/2023.08.10.552443 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ The mTOR pathway genes mTOR, Rheb, Depdc5, Pten, and Tsc1 have convergent and divergent impacts on cortical neuron development and function ]]> https://biorxiv.org/content/10.1101/2023.08.11.553034v1?rss=1 Nguyen, L. H. Xu, Y. Bordey, A. 2023-08-12 doi:10.1101/2023.08.11.553034 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ PARG inhibition induces nuclear aggregation of PARylated PARP1 ]]> https://biorxiv.org/content/10.1101/2023.08.12.553088v1?rss=1 Paradkar, S. Purcell, J. Cui, A. Friedman, S. Sundaram, R. Jensen, R. B. Bindra, R. S. 2023-08-15 doi:10.1101/2023.08.12.553088 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids ]]> https://biorxiv.org/content/10.1101/2023.08.14.553170v1?rss=1 Capauto, D. Wang, Y. Wu, F. Norton, S. Mariani, J. Inoue, F. Crawford, G. E. Ahituv, N. Abyzov, A. Vaccarino, F. M. 2023-08-14 doi:10.1101/2023.08.14.553170 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ ATG2A-mediated bridge-like lipid transport regulates lipid droplet accumulation ]]> https://biorxiv.org/content/10.1101/2023.08.14.553257v1?rss=1 Korfhage, J. L. Wan, N. Elhan, H. Kauffman, L. Pineda, M. J. Fuller, D. M. Thiam, A. R. Reinisch, K. Melia, T. 2023-08-14 doi:10.1101/2023.08.14.553257 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Geometry of anisotropic contextual interactions in the visual cortex places fundamental limits on spatial vision ]]> https://biorxiv.org/content/10.1101/2023.08.15.553380v1?rss=1 Morton, M. P. Denagamage, S. Hudson, N. V. Nandy, A. S. 2023-08-17 doi:10.1101/2023.08.15.553380 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Effect of Tokenization on Transformers for Biological Sequences ]]> https://biorxiv.org/content/10.1101/2023.08.15.553415v1?rss=1 Dotan, E. Jaschek, G. Pupko, T. Belinkov, Y. 2023-08-17 doi:10.1101/2023.08.15.553415 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Situating the parietal memory network in the context of multiple parallel distributed networks using high-resolution functional connectivity ]]> https://biorxiv.org/content/10.1101/2023.08.16.553585v1?rss=1 Kwon, Y. H. Salvo, J. J. Anderson, N. Holubecki, A. M. Lakshman, M. Yoo, K. Kay, K. Gratton, C. Braga, R. M. 2023-08-17 doi:10.1101/2023.08.16.553585 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Phenotypic lags influence rapid evolution throughout a drought cycle ]]> https://biorxiv.org/content/10.1101/2023.08.18.553905v1?rss=1 Branch, H. A. Anstett, D. N. Angert, A. L. 2023-08-21 doi:10.1101/2023.08.18.553905 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone ]]> https://biorxiv.org/content/10.1101/2023.08.19.553966v1?rss=1 Norton, E. S. Whaley, L. A. Jones, V. K. Brooks, M. M. Russo, M. N. Morderer, D. Jessen, E. Schiapparelli, P. Ramos-Fresnedo, A. Zarco, N. Carrano, A. Rossoll, W. Asmann, Y. W. Lam, T. T. Chaichana, K. L. Anastasiadis, P. Z. Quinones-Hinojosa, A. Guerrero-Cazares, H. 2023-08-21 doi:10.1101/2023.08.19.553966 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Interactions between temperature and nutrients determine the population dynamics of primary producers ]]> https://biorxiv.org/content/10.1101/2023.08.22.554290v1?rss=1 Bieg, C. Vasseur, D. 2023-08-23 doi:10.1101/2023.08.22.554290 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Movies reveal the fine-grained organization of infant visual cortex ]]> https://biorxiv.org/content/10.1101/2023.08.22.554318v1?rss=1 Ellis, C. T. Yates, T. S. Arcaro, M. J. Turk-Browne, N. B. 2023-08-23 doi:10.1101/2023.08.22.554318 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Single Cell Measurements and Modeling and Computation of Decision Making Errors in a Molecular Signaling System with Two Output Molecules ]]> https://biorxiv.org/content/10.1101/2023.08.22.554323v1?rss=1 Emadi, A. Lipniacki, T. Levchenko, A. Abdi, A. 2023-08-23 doi:10.1101/2023.08.22.554323 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Role of toll-like receptor 2 during infection of Leptospira spp.: A systematic review. ]]> https://biorxiv.org/content/10.1101/2023.08.23.554396v1?rss=1 Kappagoda, C. Senavirathna, I. Agampodi, S. 2023-08-24 doi:10.1101/2023.08.23.554396 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling ]]> https://biorxiv.org/content/10.1101/2023.08.23.554490v1?rss=1 Mühlenbeck, H. Tsutsui, Y. Lemmon, M. Bender, K. W. Zipfel, C. 2023-08-25 doi:10.1101/2023.08.23.554490 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Spatiotemporal dynamics of cytokines expression dictate fetal liver hematopoiesis. ]]> https://biorxiv.org/content/10.1101/2023.08.24.554612v1?rss=1 Peixoto, M. M. Soares-da-Silva, F. Bonnet, V. Ronteix, G. Santos, R. F. Mailhe, M.-P. Feng, X. Pereira, J. Azzoni, E. Anselmi, G. de Bruijn, M. Baroud, C. Pinto-do-O, P. Cumano, A. 2023-08-25 doi:10.1101/2023.08.24.554612 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ A hybrid machine learning and regression method for cell type deconvolution of spatial barcoding-based transcriptomic data ]]> https://biorxiv.org/content/10.1101/2023.08.24.554722v1?rss=1 Liu, Y. Li, N. Qi, J. Xu, G. Zhao, J. Wang, N. Huang, X. Jiang, W. Justet, A. Adams, T. S. Homer, R. Amei, A. Rosas, I. Kaminski, N. Wang, Z. Yan, X. 2023-08-26 doi:10.1101/2023.08.24.554722 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity ]]> https://biorxiv.org/content/10.1101/2023.08.25.554311v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@157c28aorg.highwire.dtl.DTLVardef@a4ff05org.highwire.dtl.DTLVardef@62caa0org.highwire.dtl.DTLVardef@1e4ce92_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Flores, M. Ly, C. Ho, E. Ceberio, N. Felix, K. Thorner, H. M. Guardado, M. Paunovich, M. Godek, C. Kalaydjian, C. Rohlfs, R. 2023-08-27 doi:10.1101/2023.08.25.554311 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Local and dynamic regulation of neuronal glycolysis in vivo ]]> https://biorxiv.org/content/10.1101/2023.08.25.554774v1?rss=1 Wolfe, A. D. Koberstein, J. N. Smith, C. B. Stewart, M. L. Hammarlund, M. Hyman, A. A. Stork, P. J. S. Goodman, R. H. Colon-Ramos, D. A. 2023-08-26 doi:10.1101/2023.08.25.554774 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Glycolytic Metabolon Assembly on Mitochondria via Hexokinase O-GlcNAcylation Promotes Metabolic Efficiency ]]> https://biorxiv.org/content/10.1101/2023.08.26.554955v1?rss=1 Wang, H. Vant, J. Wu, Y. Sanchez, R. Micou, M. L. Zhang, A. Luczak, V. Yu, S. B. Jabbo, M. Yoon, S. Abushawish, A. A. Ghassemian, M. Griffis, E. Hammarlund, M. Singharoy, A. Pekkurnaz, G. 2023-08-27 doi:10.1101/2023.08.26.554955 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ SIMVI reveals intrinsic and spatial-induced states in spatial omics data ]]> https://biorxiv.org/content/10.1101/2023.08.28.554970v1?rss=1 Dong, M. Kluger, H. Fan, R. Kluger, Y. 2023-08-30 doi:10.1101/2023.08.28.554970 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ PKC modulator bryostatin-1 therapeutically targets CNS innate immunity to attenuate neuroinflammation and promote remyelination ]]> https://biorxiv.org/content/10.1101/2023.08.28.555084v1?rss=1 Gharibani, P. Abramson, E. Shanmukha, S. Smith, M. D. Godfrey, W. H. Lee, J. J. Hu, J. Baydyuk, M. Dorion, M.-F. Deng, X. Guo, Y. Hwang, S. Huang, J. K. Calabresi, P. A. Kornberg, M. D. Kim, P. M. 2023-08-29 doi:10.1101/2023.08.28.555084 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ A systems vaccinology resource to develop and test computational models of immunity ]]> https://biorxiv.org/content/10.1101/2023.08.28.555193v1?rss=1 Shinde, P. Soldevila, F. Reyna, J. Aoki, M. Rasmussen, M. Willemsen, L. Kojima, M. Ha, B. Greenbaum, J. A. Overton, J. A. Guzman-Orozco, H. Nili, S. Orfield, S. Gygi, J. P. Antunes, R. d. S. Sette, A. Grant, B. J. Olsen, L. R. Konstorum, A. Guan, L. Ay, F. Kleinstein, S. H. Peters, B. 2023-08-29 doi:10.1101/2023.08.28.555193 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Toxoplasma gondii actin filaments are tuned for rapid disassembly and turnover ]]> https://biorxiv.org/content/10.1101/2023.08.29.555340v1?rss=1 Hvorecny, K. L. Sladewski, T. E. De La Cruz, E. M. Kollman, J. M. Heaslip, A. T. 2023-08-30 doi:10.1101/2023.08.29.555340 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Social learning of a challenging two-step action sequence fulfils key criteria of cumulative culture in an insect ]]> https://biorxiv.org/content/10.1101/2023.08.29.555358v1?rss=1 Bridges, A. D. Royka, A. Wilson, T. Chittka, L. 2023-08-31 doi:10.1101/2023.08.29.555358 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Loss of finger control complexity and intrusion of flexor biases are dissociable in finger individuation impairment after stroke ]]> https://biorxiv.org/content/10.1101/2023.08.29.555444v1?rss=1 Xu, J. Ma, T. Kumar, S. Olds, K. Brown, J. Carducci, J. Forrence, A. Krakauer, J. W. 2023-08-31 doi:10.1101/2023.08.29.555444 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53 ]]> https://biorxiv.org/content/10.1101/2023.08.31.555625v1?rss=1 Lee, J. D. Menasche, B. L. Mavrikaki, M. Uyemura, M. M. Hong, S. M. Kozlova, N. Wei, J. Alfajaro, M. M. Filler, R. Muller, A. Saxena, T. Posey, R. R. Cheung, P. Muranen, T. Heng, J. Paulo, J. A. Wilen, C. B. Slack, F. J. 2023-09-01 doi:10.1101/2023.08.31.555625 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Community ecology of phages on a clonal bacterial host ]]> https://biorxiv.org/content/10.1101/2023.09.01.555216v1?rss=1 Pyenson, N. C. Leeks, A. Nweke, O. Goldford, J. Turner, P. Foster, K. R. Sanchez, A. 2023-09-01 doi:10.1101/2023.09.01.555216 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ The Effects of Aging on Rod Bipolar Cell Ribbon Synapses ]]> https://biorxiv.org/content/10.1101/2023.09.01.555825v1?rss=1 Shrestha, A. P. Rameshkumar, N. Boff, J. M. Rajmanna, R. Chandrasegaran, T. Zenisek, D. Vaithianathan, T. 2023-09-05 doi:10.1101/2023.09.01.555825 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Lipid scrambling is a general feature of protein insertases ]]> https://biorxiv.org/content/10.1101/2023.09.01.555937v1?rss=1 Li, D. Rocha Roa, C. Schilling, M. A. Reinisch, K. Vanni, S. 2023-09-01 doi:10.1101/2023.09.01.555937 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Mechanosensing through talin 1 contributes to tissue mechanical homeostasis ]]> https://biorxiv.org/content/10.1101/2023.09.03.556084v1?rss=1 Chanduri, M. V. Kumar, A. Weiss, D. Emuna, N. Barsukov, I. Shi, M. Tanaka, K. Wang, X. Datye, A. Kanyo, J. Collin, F. Lam, T. Schwarz, U. D. Bai, S. Nottoli, T. Goult, B. T. Humphrey, J. T. Schwartz, M. A. 2023-09-05 doi:10.1101/2023.09.03.556084 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Normative Birth Weight Variation is Associated with White Matter Connectivity in Full-Term Neonates ]]> https://biorxiv.org/content/10.1101/2023.09.05.556390v1?rss=1 2.5 kg and <4.5 kg) and white matter connectivity in full-term neonates. Further, the main objective includes testing associations between normative birth weight variation and cognitive and language developmental scores at 18 months, and if white matter connectivity that is related to birth weight variation is further associated with cognitive language development. We hypothesized, greater normative birth weight would be associated with higher white matter connectivity controlling for gestational age, particularly in thalamic, inferior frontal, and middle temporal connectivity. Further, we predicted greater connectivity for these tracts would be associated with higher scores for cognitive (thalamic) and language development (inferior and middle temporal) at 18 months of age. DesignThe study was an observational longitudinal design of data from the Developing Human Connectome Project (dHCP). Birth weight was measured at the birth of the child, white matter connectivity was measured as neonates (mean=40.07 weeks, SD=1.14), and cognitive/language outcomes were measured at 18 months of age. SettingThe dHCP data was collected at the Evelina Newborn Imaging Centre, Evalina London Childrens Hospital between 2015 and 2019. ParticipantsA sub-sample of the full dHCP was tested. These participants were full-term neonates with birth weight variation in the normative range (> 2.5 kg and < 4.5 kg). Participants also had to have usable diffusion-weighted imaging data as neonates and cognitive/language developmental assessments collected at 18 months (n=323). Exposure(s)The study participants were all born at full-term and in the normative birth weight range. Main Outcome(s) and Measure(s)The study had two main outcomes: white matter connectivity at the neonatal timepoint and cognitive/language developmental scores at 18 months. White matter connectivity was calculated from diffusion-weighted data for the whole-brain. Cognitive/language developmental scores were measured using the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) at 18 months. ResultsUsing a Network-Based Statistic (NBS) approach, we found widespread associations between normative birth weight variation and white matter connectivity in full-term neonates, primarily in the positive direction for the right middle occipital gyrus and left supplementary motor area. Conclusions and RelevanceWhile investigations have been focused on the extreme ends of the birth weight spectrum, we find evidence that there is a robust association between birth weight and white matter connectivity even within the normative birth weight range. As normative birth weight variation and regions of white matter associated with birth weight were further associated with language development scores at 18 months, our results suggest the birth weight to white matter pathway may be an underlying pathway between birth weights association with language development. Key PointsO_ST_ABSQuestionC_ST_ABSAre variations in normative birth weight associated with white matter connectivity and cognitive/language outcomes in infancy? FindingsGreater normative birth weight is associated with greater white matter organization across a widespread network of connections in the neonatal brain. Greater white matter organization in this network for neonates has a positive prospective with expressive language development at 18 months of age. MeaningEven variations within the normative birth weight range have robust associations with early white matter development and can be prospectively linked to language development. ]]> Dufford, A. J. Dai, W. Scheinost, D. 2023-09-05 doi:10.1101/2023.09.05.556390 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Enhancer-driven regulatory network of forebrain human development provides insights into autism ]]> https://biorxiv.org/content/10.1101/2023.09.06.555206v1?rss=1 Vaccarino, F. M. Jourdon, A. Mariani, J. Wu, F. Capauto, D. Norton, S. Tomasini, L. Amiri, A. Schreiner, J. Nguyen, C. K. Nolan, N. Szekely, A. McPartland, J. C. Pelphrey, K. Chawarska, K. Ventola, P. Abyzov, A. 2023-09-08 doi:10.1101/2023.09.06.555206 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ MetFinder: a neural network-based tool for automated quantitation of metastatic burden in histological sections from animal models ]]> https://biorxiv.org/content/10.1101/2023.09.07.555360v1?rss=1 Karz, A. Coudray, N. Bayraktar, E. Galbraith, K. Jour, G. Shadaloey, A. A. S. Eskow, N. Rubanov, A. Navarro, M. Moubarak, R. Baptiste, G. Levinson, G. Mezzano, V. Alu, M. Loomis, C. Lima, D. Rubens, A. Jilaveanu, L. Tsirigos, A. Hernando, E. 2023-09-08 doi:10.1101/2023.09.07.555360 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Evaluating the Utilities of Large Language Models in Single-cell Data Analysis ]]> https://biorxiv.org/content/10.1101/2023.09.08.555192v1?rss=1 Liu, T. Li, K. Wang, Y. Li, H. Zhao, H. 2023-09-08 doi:10.1101/2023.09.08.555192 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Clustering of cortical dynein regulates the mechanics of spindle orientation in human mitotic cells ]]> https://biorxiv.org/content/10.1101/2023.09.11.557210v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@56e8daorg.highwire.dtl.DTLVardef@1d16449org.highwire.dtl.DTLVardef@f3006org.highwire.dtl.DTLVardef@119f6aa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Anjur-Dietrich, M. Hererra, V. G. Farhadifar, R. Wu, H.-Y. Merta, H. Bahmanyar, S. Shelley, M. Needleman, D. 2023-09-12 doi:10.1101/2023.09.11.557210 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Predicting photosynthetic pathway from anatomy using machine learning ]]> https://biorxiv.org/content/10.1101/2023.09.11.557216v1?rss=1 Gilman, I. S. Heyduk, K. Maya-Lastra, C. A. Hancock, L. P. Edwards, E. J. 2023-09-15 doi:10.1101/2023.09.11.557216 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior ]]> https://biorxiv.org/content/10.1101/2023.09.11.557249v1?rss=1 Kochersberger, A. Torkashvand, M. M. Lee, D. Baskoylu, S. Sengupta, T. Koonce, N. Emerson, C. Patel, N. V. Colon-Ramos, D. Flavell, S. W. Horvitz, H. R. Venkatachalam, V. Hammarlund, M. 2023-09-14 doi:10.1101/2023.09.11.557249 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Cell2Sentence: Teaching Large Language Models the Language of Biology ]]> https://biorxiv.org/content/10.1101/2023.09.11.557287v1?rss=1 Levine, D. Rizvi, S. A. Levy, S. Pallikkavaliyaveetil MohammedSheriff, N. Wu, R. Zhang, Z. Fonseca, A. Chen, X. Ghadermarzi, S. Dhodapkar, R. M. van Dijk, D. 2023-09-14 doi:10.1101/2023.09.11.557287 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Seasonal migration alters energetic trade-off optimization and shapes life history. ]]> https://biorxiv.org/content/10.1101/2023.09.12.557441v1?rss=1 Pierce, A. K. Yanco, S. W. Wunder, M. B. 2023-09-15 doi:10.1101/2023.09.12.557441 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ BrainLM: A foundation model for brain activity recordings ]]> https://biorxiv.org/content/10.1101/2023.09.12.557460v1?rss=1 Ortega Caro, J. Oliveira Fonseca, A. H. Averill, C. Rizvi, S. A. Rosati, M. Cross, J. L. Mittal, P. Zappala, E. Levine, D. Dhodapkar, R. M. Abdallah, C. G. van Dijk, D. 2023-09-13 doi:10.1101/2023.09.12.557460 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Rat Wetness Response: Sensory Cues, Behavior & Fur-based Drying ]]> https://biorxiv.org/content/10.1101/2023.09.13.557175v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@ea8b80org.highwire.dtl.DTLVardef@6ca3d9org.highwire.dtl.DTLVardef@78fccdorg.highwire.dtl.DTLVardef@11d0c83_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Triumph Attah, A. Negron-Moreno, P. Amigo-Duran, M. Zhang, L. Kenngott, M. Brecht, M. Clemens, A. M. 2023-09-13 doi:10.1101/2023.09.13.557175 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Competition and Synergy of Arp2/3 and Formins in Nucleating Actin Waves ]]> https://biorxiv.org/content/10.1101/2023.09.13.557508v1?rss=1 Chua, X. L. Tong, C. S. Xu, X. J. Su, M. Xiao, S. Wu, X. Wu, M. 2023-09-13 doi:10.1101/2023.09.13.557508 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Lysosomal TMEM106B interacts with galactosylceramidase to regulate myelin lipid metabolism ]]> https://biorxiv.org/content/10.1101/2023.09.14.557804v1?rss=1 Takahashi, H. Perez-Canams, A. Ye, H. Han, X. Strittmatter, S. M. 2023-09-14 doi:10.1101/2023.09.14.557804 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Sensory neuron population expansion enhances odour tracking through relaxed projection neuron adaptation ]]> https://biorxiv.org/content/10.1101/2023.09.15.556782v1?rss=1 Takagi, S. Abuin, L. Stupski, S. D. Arguello, J. R. Prieto-Godino, L. L. Stern, D. L. Cruchet, S. Alvarez-Ocana, R. Wienecke, C. F. R. van Breugel, F. Auer, T. O. Benton, R. 2023-09-15 doi:10.1101/2023.09.15.556782 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Neural correlates of visual object recognition in rats ]]> https://biorxiv.org/content/10.1101/2023.09.17.555183v1?rss=1 Rhee, J. Y. Echavarria, C. Soucy, E. Greenwood, J. Masis, J. A. Cox, D. D. 2023-09-17 doi:10.1101/2023.09.17.555183 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Human brain state dynamics reflect individual neuro-phenotypes ]]> https://biorxiv.org/content/10.1101/2023.09.18.557763v1?rss=1 Lee, K. Ji, J. L. Fonteneau, C. Berkovitch, L. Rahmati, M. Pan, L. Repovs, G. Krystal, J. H. Murray, J. D. Anticevic, A. 2023-09-19 doi:10.1101/2023.09.18.557763 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ The circadian clock regulates PIF3 protein stability in parallel to red light ]]> https://biorxiv.org/content/10.1101/2023.09.18.558326v1?rss=1 Liu, W. Lowrey, H. Leung, C. C. Adamchek, C. Du, J. He, J. Chen, M. Gendron, J. M. 2023-09-18 doi:10.1101/2023.09.18.558326 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition ]]> https://biorxiv.org/content/10.1101/2023.09.19.558325v1?rss=1 Cheng, Y.-C. Zhang, Y. Tripathi, S. BV, H. Jolly, M. K. Schiebinger, G. Levine, H. McDonald, T. O. Michor, F. 2023-09-22 doi:10.1101/2023.09.19.558325 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions ]]> https://biorxiv.org/content/10.1101/2023.09.19.558525v1?rss=1 Sivadas, A. McDonald, E. F. Shuster, S. O. Davis, C. M. Plate, L. 2023-09-20 doi:10.1101/2023.09.19.558525 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases ]]> https://biorxiv.org/content/10.1101/2023.09.20.558301v1?rss=1 Zhao, A. Y. Unterman, A. Abu Hussein, N. Sharma, P. Flint, J. Yan, X. Adams, T. S. Justet, A. Sumida, T. S. Zhao, J. Schupp, J. C. Raredon, M. S. B. Ahangari, F. C. Zhang, Y. Buendia-Roldan, I. Adegunsoye, A. Sperling, A. I. Prasse, A. Ryu, C. Herzog, E. Selman, M. Pardo, A. Kaminski, N. 2023-09-22 doi:10.1101/2023.09.20.558301 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Bayesian analysis of resting-state temporal low-γ power in children with phonemic decoding deficits and certain comorbidities ]]> https://biorxiv.org/content/10.1101/2023.09.20.558564v1?rss=1 Lasnick, O. H. M. Hancock, R. Hoeft, F. 2023-09-22 doi:10.1101/2023.09.20.558564 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Independent Influences of Movement Distance and Visual Distance on Fitts' Law ]]> https://biorxiv.org/content/10.1101/2023.09.20.558709v1?rss=1 Al-Fawakhiri, N. McDougle, S. 2023-09-22 doi:10.1101/2023.09.20.558709 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Chitinase 3-like-1 (CHI3L1) in the Pathogenesis of Epidermal Growth Factor Receptor Mutant Non-Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2023.09.21.558861v1?rss=1 Kamle, S. Ma, B. Schor, G. Bailey, M. Pham, B. Cho, I. Khan, H. Azzoli, C. Hofstetter, M. Lee, C.-M. Herbst, R. Politi, K. Lee, C. G. Elias, J. A. 2023-09-23 doi:10.1101/2023.09.21.558861 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Estimating multimodal brain variability in schizophreniaspectrum disorders: A worldwide ENIGMA study ]]> https://biorxiv.org/content/10.1101/2023.09.22.559032v1?rss=1 Omlor, W. Rabe, F. Fuchs, S. Cecere, G. Homan, S. Surbeck, W. Kallen, N. Georgiadis, F. Seifritz, E. Weickert, T. Bruggemann, J. Weickert, C. Potkin, S. Hashimoto, R. Sim, K. Rootes-Murdy, K. Quide, Y. Houenou, J. Banaj, N. Vecchio, D. Piras, F. Spalletta, G. Salvador, R. Rodrigue, A. Pearlson, G. Glahn, D. Tomecek, D. Kirschner, M. Kochunov, P. Fan, F.-M. Andreassen, O. Westlye, L. T. A. Berthet, P. Calhoun, V. Howells, F. M. Uhlmann, A. Stein, D. Iasevoli, F. van Erp, T. Turner, J. Homan, P. 2023-09-23 doi:10.1101/2023.09.22.559032 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Acetylcholine signaling in the medial prefrontal cortex mediates the ability to learn an active avoidance response following learned helplessness training ]]> https://biorxiv.org/content/10.1101/2023.09.23.559126v1?rss=1 Abdulla, Z. I. Mineur, Y. S. Crouse, R. B. Etherington, I. M. Yousuf, H. Na, J. J. Picciotto, M. R. 2023-09-23 doi:10.1101/2023.09.23.559126 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A 3D Printed Ventilated Perfused Lung Model Platform to Dissect the Lung's Response to Viral Infection in the Presence of Respiration ]]> https://biorxiv.org/content/10.1101/2023.09.24.559194v1?rss=1 Derman, I. D. Alioglu, M. A. Banerjee, D. Holton, S. E. Klunk, D. N. Nagamine, M. Rizvi, S. H. A. Mikacenic, C. Celik, N. Castaneda, D. C. Prajakta, W. Chen, P. Schotsaert, M. Peeples, M. E. Palucka, K. Koff, J. Ozbolat, I. T. 2023-09-24 doi:10.1101/2023.09.24.559194 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain ]]> https://biorxiv.org/content/10.1101/2023.09.25.558837v1?rss=1 Small, G. I. Federova, O. Olinares, P. D. B. Chandanani, J. Banerjee, A. Choi, Y. J. Molina, H. Chait, B. Darst, S. A. Campbell, E. A. 2023-09-26 doi:10.1101/2023.09.25.558837 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Hidden HCN channels permit pathway-specific synaptic amplification in L2/3 pyramidal neurons ]]> https://biorxiv.org/content/10.1101/2023.09.25.559198v1?rss=1 Olah, V. J. Wu, J. Kaczmarek, L. K. Rowan, M. J. 2023-09-26 doi:10.1101/2023.09.25.559198 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Neural circuit mechanisms underlying context-specific halting in Drosophila. ]]> https://biorxiv.org/content/10.1101/2023.09.25.559438v1?rss=1 Sapkal, N. Mancini, N. Kumar, D. S. Spiller, N. Murakami, K. Vitelli, G. Bargeron, B. Maier, K. Eichler, K. Jefferis, G. S. X. E. Shiu, P. Sterne, G. R. Bidaye, S. S. 2023-09-27 doi:10.1101/2023.09.25.559438 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ HI-FISH: WHOLE BRAIN IN SITU MAPPING OF NEURONAL ACTIVATION IN DROSOPHILA DURING SOCIAL BEHAVIORS AND OPTOGENETIC STIMULATION ]]> https://biorxiv.org/content/10.1101/2023.09.28.560045v1?rss=1 Anderson, D. J. Chiu, H. V. Watanabe, K. 2023-09-29 doi:10.1101/2023.09.28.560045 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB ]]> https://biorxiv.org/content/10.1101/2023.09.29.560128v1?rss=1 Munir, M. Embry, A. Doench, J. G. Heaton, N. Wilen, C. B. Orchard, R. 2023-09-29 doi:10.1101/2023.09.29.560128 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser ]]> https://biorxiv.org/content/10.1101/2023.09.29.560187v1?rss=1 Jensen, C. G. Sumner, J. A. Kleinstein, S. H. Hoehn, K. B. 2023-10-02 doi:10.1101/2023.09.29.560187 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles ]]> https://biorxiv.org/content/10.1101/2023.09.30.560294v1?rss=1 Chang, D. Gupta, V. K. Hur, B. Cobo-Lopez, S. Cunningham, K. Y. Han, N. Lee, I. Kronzer, V. L. Teigen, L. Karnatovskaia, L. Longbrake, E. E. Davis, J. M. Nelson, H. Sung, J. 2023-10-02 doi:10.1101/2023.09.30.560294 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ IDR-induced CAR condensation improves the cytotoxicity of CAR-Ts against low-antigen cancers ]]> https://biorxiv.org/content/10.1101/2023.10.02.560460v1?rss=1 Zhang, X. Xiao, Q. Zeng, L. Hashmi, F. Su, X. 2023-10-03 doi:10.1101/2023.10.02.560460 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life ]]> https://biorxiv.org/content/10.1101/2023.10.02.560517v1?rss=1 1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family. ]]> Kim, B. Y. Gellert, H. R. Church, S. H. Suvorov, A. Anderson, S. S. Barmina, O. Beskid, S. G. Comeault, A. A. Crown, K. N. Diamond, S. E. Dorus, S. Fujichika, T. Hemker, J. A. Hrcek, J. Kankare, M. Katoh, T. Magnacca, K. N. Martin, R. A. Matsunaga, T. Medeiros, M. J. Miller, D. E. Pitnick, S. Simoni, S. Steenwinkel, T. E. Schiffer, M. Syed, Z. A. Takahashi, A. Wei, K. H.-C. Yokoyama, T. Eisen, M. B. Kopp, A. Matute, D. Obbard, D. J. O'Grady, P. M. Price, D. K. Toda, M. J. Werner, T. Petrov, D. A. 2023-10-02 doi:10.1101/2023.10.02.560517 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance ]]> https://biorxiv.org/content/10.1101/2023.10.02.560611v1?rss=1 Wang, N. Zhu, B. Allnutt, M. A. Grijalva, R. M. Zhao, H. Chandra, S. S. 2023-10-03 doi:10.1101/2023.10.02.560611 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Retrosplenial inputs drive diverse visual representations in the medial entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2023.10.03.560642v1?rss=1 Dubanet, O. Higley, M. J. 2023-10-04 doi:10.1101/2023.10.03.560642 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Backbone extension acyl rearrangements enable cellular synthesis of proteins with internal β2-peptide linkages ]]> https://biorxiv.org/content/10.1101/2023.10.03.560714v1?rss=1 Schepartz, A. Roe, L. Schissel, C. K. Dover, T. L. Shah, B. Hamlish, N. X. Zheng, S. Dilworth, D. A. Wong, N. Zhang, Z. Chatterjee, A. Francis, M. B. Miller, S. J. 2023-10-03 doi:10.1101/2023.10.03.560714 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Oleic acid differentially affects de novo lipogenesis in adipocytes and hepatocytes ]]> https://biorxiv.org/content/10.1101/2023.10.04.560581v1?rss=1 Castillo, H. B. Shuster, S. O. Tarekegn, L. H. Davis, C. M. 2023-10-06 doi:10.1101/2023.10.04.560581 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Dissecting glial scar formation by spatial point pattern and topological data analysis ]]> https://biorxiv.org/content/10.1101/2023.10.04.560910v1?rss=1 Manrique-Castano, D. ElAli, A. Bhaskar, D. 2023-10-06 doi:10.1101/2023.10.04.560910 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease ]]> https://biorxiv.org/content/10.1101/2023.10.04.560924v1?rss=1 Chandran, R. R. Adams, T. Kabir, I. Gallardo, E. Kaminski, N. Gomperts, B. Greif, D. 2023-10-06 doi:10.1101/2023.10.04.560924 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion. ]]> https://biorxiv.org/content/10.1101/2023.10.05.560890v1?rss=1 Yuan, T. Yan, H. Li, K. C. Surovtsev, I. V. King, M. C. Mochrie, S. G. J. 2023-10-06 doi:10.1101/2023.10.05.560890 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ A Confounder Controlled Machine Learning Approach: Group Analysis and Classification of Schizophrenia and Alzheimer's Disease using Resting-State Functional Network Connectivity ]]> https://biorxiv.org/content/10.1101/2023.10.05.561035v1?rss=1 Hassanzadeh, R. Abrol, A. Pearlson, G. Turner, J. A. Calhoun, V. D. 2023-10-06 doi:10.1101/2023.10.05.561035 Cold Spring Harbor Laboratory Press 2023-10-06 <![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[ The Hierarchy of Psychedelic Effects: Three Systematic Reviews and Meta-Analyses ]]> https://biorxiv.org/content/10.1101/2023.10.06.561183v1?rss=1 Shinozuka, K. Jerotic, K. Mediano, P. A. M. Zhao, A. T. Preller, K. H. Carhart-Harris, R. L. Kringelbach, M. L. 2023-10-07 doi:10.1101/2023.10.06.561183 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Biomechanical stress analysis of Type-A aortic dissection at pre-dissection, post-dissection, and post-repair states ]]> https://biorxiv.org/content/10.1101/2023.10.06.561307v1?rss=1 Sun, C. Qin, T. Kalyanasundaram, A. Elefteriades, J. Sun, W. Liang, L. 2023-10-07 doi:10.1101/2023.10.06.561307 Cold Spring Harbor Laboratory Press 2023-10-07 <![CDATA[ Mast-Cell Expressed Membrane Protein-1 (MCEMP1) is expressed in classical monocytes and alveolar macrophages in Idiopathic Pulmonary Fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ dependent manner. ]]> https://biorxiv.org/content/10.1101/2023.10.07.561349v1?rss=1 Perrot, C. Y. Karampitsakos, T. Unterman, A. Adams, T. Marlin, K. Arsenault, A. Zhao, A. Kaminski, N. Katlaps, G. Patel, K. Bandyopadhyay, D. Herazo-Maya, J. D. 2023-10-13 doi:10.1101/2023.10.07.561349 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Transthalamic input to higher-order cortex selectively conveys state information ]]> https://biorxiv.org/content/10.1101/2023.10.08.561424v1?rss=1 Neske, G. Cardin, J. A. 2023-10-10 doi:10.1101/2023.10.08.561424 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Volumetric Compression Shifts Rho GTPase Balance and Induces Mechanobiological Cell State Transition ]]> https://biorxiv.org/content/10.1101/2023.10.08.561452v1?rss=1 Gong, X. Nguyen, R. Chen, Z. Zhang, X. Mak, M. 2023-10-10 doi:10.1101/2023.10.08.561452 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Adaptation to volumetric compression drives hepatoblastoma cells to an apoptosis-resistant and invasive phenotype ]]> https://biorxiv.org/content/10.1101/2023.10.08.561453v1?rss=1 Gong, X. Ogino, N. Leite, M. F. Chen, Z. Liu, R. Kruglov, E. Flores, K. Cabral, A. Mendes, G. M. M. Ehrlich, B. E. Mak, M. 2023-10-10 doi:10.1101/2023.10.08.561453 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Instant Assembly of Collagen for Scaffolding, Tissue Engineering, and Bioprinting ]]> https://biorxiv.org/content/10.1101/2023.10.08.561456v1?rss=1 Gong, X. Wen, Z. Liang, Z. Xiao, H. Lee, S. Wright, T. Nguyen, R. Y. Rossello, A. Mak, M. 2023-10-10 doi:10.1101/2023.10.08.561456 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Intraspecific plant-soil feedbacks vary under field conditions among species in a tropical tree community ]]> https://biorxiv.org/content/10.1101/2023.10.09.561486v1?rss=1 Eck, J. L. Hernandez Hassan, L. Comita, L. S. 2023-10-10 doi:10.1101/2023.10.09.561486 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Triple-action inhibitory mechanism of allosteric TYK2-specific inhibitors ]]> https://biorxiv.org/content/10.1101/2023.10.09.561507v1?rss=1 Wang, J. Batista, V. S. Bunick, C. G. 2023-10-09 doi:10.1101/2023.10.09.561507 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage ]]> https://biorxiv.org/content/10.1101/2023.10.12.562096v1?rss=1 Carrasquillo Rodriguez, J. W. Uche, O. Gao, S. Lee, S. Airola, M. V. Bahmanyar, S. 2023-10-13 doi:10.1101/2023.10.12.562096 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Parkinsonism Sac domain mutation in Synaptojanin-1 affects ciliary properties in iPSC-derived dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.10.12.562142v1?rss=1 Mohd Rafiq, N. Fujise, K. Rosenfeld, M. Xu, P. Wu, Y. De Camilli, P. 2023-10-13 doi:10.1101/2023.10.12.562142 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2023.10.15.562439v1?rss=1 Guo, M. Wu, Y. Su, Y. Qian, S. Krueger, E. Christensen, R. Kroeschell, G. Bui, J. Chaw, M. Zhang, L. Liu, J. Hou, X. Han, X. Ma, X. Zhovmer, A. Combs, C. Moyle, M. Yemini, E. Liu, H. Liu, Z. La Riviere, P. Colon-Ramos, D. Shroff, H. 2023-10-18 doi:10.1101/2023.10.15.562439 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Reliability of dynamic causal modelling of resting state magnetoencephalography ]]> https://biorxiv.org/content/10.1101/2023.10.16.562379v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@135c964org.highwire.dtl.DTLVardef@38e4a7org.highwire.dtl.DTLVardef@12bc358org.highwire.dtl.DTLVardef@25f110_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jafarian, A. Assem, M. K. Ece Kocagoncu, E. Lanskey, J. H. Williams, R. Cheng, Y.-J. Quinn, A. J. Pitt, J. Raymont, V. Lowe, S. Lowe, S. Singh, K. D. Woolrich, M. W. Nobre, A. C. Henson, R. N. Friston, K. Rowe, J. 2023-10-19 doi:10.1101/2023.10.16.562379 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Instability in computational models of vascular smooth muscle cell contraction ]]> https://biorxiv.org/content/10.1101/2023.10.16.562505v1?rss=1 Giudici, A. Szafron, J. M. Ramachandra, A. B. Spronck, B. 2023-10-18 doi:10.1101/2023.10.16.562505 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Detecting time-varying genetic effects in Alzheimer's disease using a longitudinal GWAS model ]]> https://biorxiv.org/content/10.1101/2023.10.17.562756v1?rss=1 Zhuang, X. Xu, G. Amei, A. Cordes, D. Wang, Z. Oh, E. 2023-10-17 doi:10.1101/2023.10.17.562756 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Dynamic decoding of VEGF signaling and coordinated control of multiple phenotypes by the Src-TEM4-YAP pathway ]]> https://biorxiv.org/content/10.1101/2023.10.19.562360v1?rss=1 Lee, S. H. Kang, T.-Y. Levchenko, A. 2023-10-20 doi:10.1101/2023.10.19.562360 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Critical reproductive behaviors in Scaled Quail and Northern Bobwhite are affected by thermal variability and mean temperature ]]> https://biorxiv.org/content/10.1101/2023.10.20.563339v1?rss=1 Kirkpatrick, W. Sauer, E. Carroll, R. Cohen, J. DuRant, S. 2023-10-23 doi:10.1101/2023.10.20.563339 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ A mechanical circuit in End4p coordinates force transmission during clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/2023.10.23.563344v1?rss=1 Ren, Y. Yang, J. Fujita, B. Zhang, Y. Berro, J. 2023-10-23 doi:10.1101/2023.10.23.563344 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling ]]> https://biorxiv.org/content/10.1101/2023.10.24.563764v1?rss=1 Deng, H. Rukhlenko, O. S. Joshi, D. Hu, X. Junk, P. Tuliakova, A. Kholodenko, B. N. Schwartz, M. A. 2023-10-25 doi:10.1101/2023.10.24.563764 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Power and reproducibility in the external validation of brain-phenotype predictions ]]> https://biorxiv.org/content/10.1101/2023.10.25.563971v1?rss=1 Rosenblatt, M. Tejavibulya, L. Camp, C. C. Jiang, R. Westwater, M. L. Noble, S. Scheinost, D. 2023-10-30 doi:10.1101/2023.10.25.563971 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Metabolic similarity and the predictability of microbial community assembly ]]> https://biorxiv.org/content/10.1101/2023.10.25.564019v1?rss=1 Vila, J. C. C. Goldford, J. Estrela, S. Bajic, D. Sanchez-Gorostiaga, A. Damian-Serrano, A. Lu, N. Marsland, R. Rebolleda-Gomez, M. Mehta, P. Sanchez, A. 2023-10-28 doi:10.1101/2023.10.25.564019 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Continental species distribution and biodiversity predictions depend on modeling grain ]]> https://biorxiv.org/content/10.1101/2023.10.25.564051v1?rss=1 Cohen, J. Jetz, W. 2023-10-29 doi:10.1101/2023.10.25.564051 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Impact of Memory T Cells on SARS-COV-2 Vaccine Response in Hematopoietic Stem Cell Transplant ]]> https://biorxiv.org/content/10.1101/2023.10.26.564259v1?rss=1 VanOudenhove, J. J. Liu, Y. Nelakanti, R. Kim, D. Busarello, E. Tijaro Ovalle, N. Qi, Z. Mamillapalli, P. Siddon, A. Bai, Z. Axtmayer, A. Corso, C. Kothari, S. Foss, F. Isufi, I. Tebaldi, T. Gowda, L. Fan, R. Seropian, S. Halene, S. 2023-10-27 doi:10.1101/2023.10.26.564259 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Leveraging genetic correlations and multiple populations to improve genetic risk prediction for non-European populations ]]> https://biorxiv.org/content/10.1101/2023.10.29.564615v1?rss=1 Xu, L. Zhou, G. Guan, L. Zhao, H. 2023-11-01 doi:10.1101/2023.10.29.564615 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Glucose Challenge Uncovers Temporal Fungibility of Metabolic Homeostasis Throughout the Day ]]> https://biorxiv.org/content/10.1101/2023.10.30.564837v1?rss=1 Malik, D. M. Rhoades, S. D. Zhang, S. L. Sengupta, A. Barber, A. Haynes, P. Arnadottir, E. S. Pack, A. Kibbey, R. G. Sehgal, A. Weljie, A. M. 2023-11-02 doi:10.1101/2023.10.30.564837 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A STING-CASM-GABARAP Pathway Activates LRRK2 at Lysosomes ]]> https://biorxiv.org/content/10.1101/2023.10.31.564602v1?rss=1 Bentley-DeSousa, A. Ferguson, S. 2023-11-01 doi:10.1101/2023.10.31.564602 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Auxetic patch material exhibits systolic thickening and restores pump function in a finite element model of acute myocardial infarction repair ]]> https://biorxiv.org/content/10.1101/2023.11.02.565400v1?rss=1 Borrello, J. Zheng, Z. Estrada, A. C. Costa, K. D. 2023-11-04 doi:10.1101/2023.11.02.565400 Cold Spring Harbor Laboratory Press 2023-11-04 <![CDATA[ Mutation of NOTCH1 is selected within normal esophageal tissues, yet leads to selective epistasis suppressive of further evolution into cancer ]]> https://biorxiv.org/content/10.1101/2023.11.03.565535v1?rss=1 Glasmacher, K. A. Cannataro, V. L. Mandell, J. D. Jackson, M. Fisk, J. N. Townsend, J. P. 2023-11-05 doi:10.1101/2023.11.03.565535 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Male-male interactions shape mate selection in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.11.03.565582v1?rss=1 Hindmarsh Sten, T. Li, R. Hollunder, F. Eleazer, S. Ruta, V. 2023-11-05 doi:10.1101/2023.11.03.565582 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Towards Choice Engineering ]]> https://biorxiv.org/content/10.1101/2023.11.04.565653v1?rss=1 Dan, O. Plonsky, O. Loewenstein, Y. 2023-11-06 doi:10.1101/2023.11.04.565653 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Contexts facilitate dynamic value encoding in the mesolimbic dopamine system ]]> https://biorxiv.org/content/10.1101/2023.11.05.565687v1?rss=1 Fraser, K. M. Collins, V. L. Wolff, A. R. Ottenheimer, D. J. Bornhoft, K. N. Pat, F. Chen, B. J. Janak, P. H. Saunders, B. T. 2023-11-05 doi:10.1101/2023.11.05.565687 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ A vasopressin circuit that modulates sex-specific social interest and anxiety-like behavior in mice ]]> https://biorxiv.org/content/10.1101/2023.11.06.564847v1?rss=1 Rigney, N. Campos-Lira, E. Kirchner, M. K. Wei, W. Belkasim, S. Beaumont, R. Singh, S. Sterm, J. E. de Vries, G. J. Petrulis, A. 2023-11-07 doi:10.1101/2023.11.06.564847 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis ]]> https://biorxiv.org/content/10.1101/2023.11.06.565855v1?rss=1 Shi, X. DeCiucis, M. Grabinska, K. A. Kanyo, J. Liu, A. Lam, T. Shen, H. 2023-11-06 doi:10.1101/2023.11.06.565855 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Nanoscale imaging of pT217-tau in aged rhesus macaque entorhinal and dorsolateral prefrontal cortex: Evidence of interneuronal trafficking and early-stage neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.11.07.566046v1?rss=1 Datta, D. Perone, I. Wijegunawardana, D. Liang, F. Morozov, Y. M. Arellano, J. Duque, A. Xie, Z. van Dyck, C. H. Arnsten, A. F. 2023-11-10 doi:10.1101/2023.11.07.566046 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Renal Angptl4 is a key fibrogenic molecule in progressive diabetic kidney disease ]]> https://biorxiv.org/content/10.1101/2023.11.08.565844v1?rss=1 Srivastava, S. P. Zhou, H. Shenoi, R. Morris, M. Goedeke, L. Rajendran, B. K. Setia, O. Aryal, B. Kanasaki, K. Koya, D. Dardik, A. Bell, T. Fernandez-Hernando, C. Shulman, G. Goodwin, J. E. 2023-11-09 doi:10.1101/2023.11.08.565844 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ NaP-TRAP, a novel massively parallel reporter assay to quantify translation control. ]]> https://biorxiv.org/content/10.1101/2023.11.09.566434v1?rss=1 Strayer, E. C. Krishna, S. Lee, H. Vejnar, C. Beaudoin, J.-D. Giraldez, A. J. 2023-11-09 doi:10.1101/2023.11.09.566434 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Acetylcholine promotes directionally biased glutamatergic retinal waves ]]> https://biorxiv.org/content/10.1101/2023.11.10.566639v1?rss=1 Zhang, K. Su, A. Wang, Y. Crair, M. C. 2023-11-15 doi:10.1101/2023.11.10.566639 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states ]]> https://biorxiv.org/content/10.1101/2023.11.11.566161v1?rss=1 Dong, M. Kluger, Y. 2023-11-15 doi:10.1101/2023.11.11.566161 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Multivariate links between the developmental timing of adversity exposure and white matter tract integrity in adulthood ]]> https://biorxiv.org/content/10.1101/2023.11.12.566271v1?rss=1 Sisk, L. M. Keding, T. J. Cohodes, E. M. McCauley, S. Pierre, J. C. Odriozola, P. Kribakaran, S. Haberman, J. T. Zacharek, S. J. Hodges, H. R. Caballero, C. Gold, G. Huang, A. Y. Talton, A. Gee, D. G. 2023-11-13 doi:10.1101/2023.11.12.566271 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ LMD: Multiscale Marker Identification in Single-cell RNA-seq Data ]]> https://biorxiv.org/content/10.1101/2023.11.12.566780v1?rss=1 Li, R. Qu, R. Parisi, F. Strino, F. Cheng, X. Kluger, Y. 2023-11-13 doi:10.1101/2023.11.12.566780 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2023.11.13.566870v1?rss=1 Singh, A. K. Sessa, B. 2023-11-15 doi:10.1101/2023.11.13.566870 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD ]]> https://biorxiv.org/content/10.1101/2023.11.13.566896v1?rss=1 Yang, S. Wijegunawardana, D. Sheth, U. Veire, A. Salgado, J. M. S. Agrawal, M. Zhou, J. Pereira, J. D. Gendron, T. F. Guo, J. U. 2023-11-14 doi:10.1101/2023.11.13.566896 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ A Method for Sampling the Living Wood Microbiome ]]> https://biorxiv.org/content/10.1101/2023.11.14.567064v1?rss=1 Arnold, W. Gewirtzman, J. Raymond, P. A. Bradford, M. Butler, C. Peccia, J. 2023-11-15 doi:10.1101/2023.11.14.567064 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein function in vivo. ]]> https://biorxiv.org/content/10.1101/2023.11.15.567075v1?rss=1 Boswell, C. W. Hoppe, C. Sherrard, A. Miao, L. Kojima, M. L. Krishna, S. Musaev, D. Zhao, N. Stasevich, T. J. Giraldez, A. J. 2023-11-17 doi:10.1101/2023.11.15.567075 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ The human Toll-like receptor 2 (TLR2) response during pathogenic Leptospira infection ]]> https://biorxiv.org/content/10.1101/2023.11.16.567338v1?rss=1 Kappagoda, C. Senavirathna, I. Jayasundara, D. Warnasekara, J. Srimantha, S. De Silva, F. Agampodi, S. 2023-11-17 doi:10.1101/2023.11.16.567338 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A shared spatial topography links the functional connectome correlates of cocaine use disorder and dopamine D2/3 receptor densities ]]> https://biorxiv.org/content/10.1101/2023.11.17.567591v1?rss=1 Ricard, J. A. Labache, L. Segal, A. Dhamala, E. Cocuzza, C. V. Jones, G. Yip, S. Chopra, S. Holmes, A. J. 2023-11-20 doi:10.1101/2023.11.17.567591 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.11.20.567573v1?rss=1 Miles, J. Lozano, G. L. Rajendhran, J. Stabb, E. V. Handelsman, J. Broderick, N. A. 2023-11-21 doi:10.1101/2023.11.20.567573 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology ]]> https://biorxiv.org/content/10.1101/2023.11.20.567952v1?rss=1 Gao, S. Rodriguez, J. W. C. Bahmanyar, S. Airola, M. V. 2023-11-20 doi:10.1101/2023.11.20.567952 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus ]]> https://biorxiv.org/content/10.1101/2023.11.21.568070v1?rss=1 Crawford, J. E. Beebe, N. Bonizzoni, M. Caputo, B. Carter, B. H. Chen, C.-H. Cosme, L. De Marco, C. M. della Torre, A. Estallo, E. L. Guo, X. Liu, W.-L. Maringer, K. Mains, J. Maynard, A. Mogi, M. Livdahl, T. Rose, N. H. Scarafia, P. Y. Severson, D. Stein, M. Surendran, S. N. Tuno, N. Wahid, I. Wang, X. Xu, J. Yan, G. Yee, D. Armbruster, P. A. Caccone, A. White, B. 2023-11-22 doi:10.1101/2023.11.21.568070 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ ERK Activation by BRAFV600E suppresses mesenchymal migration and tumorigenesis by inhibiting RAC1. ]]> https://biorxiv.org/content/10.1101/2023.11.21.568071v1?rss=1 gadal, s. Boyer, J. A. Roy, S. F. Outmezguine, N. A. Sharma, M. Li, H. Fan, N. Chan, E. Romin, Y. Barlas, A. Chang, Q. Pancholi, P. Timaul, N. M. Overholtzer, M. Yaeger, R. Todorova, K. M. Stanchina, E. d. Bosenberg, M. Rosen, N. 2023-11-21 doi:10.1101/2023.11.21.568071 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Leveraging a large language model to predict protein phase transition: a physical, multiscale and interpretable approach ]]> https://biorxiv.org/content/10.1101/2023.11.21.568125v1?rss=1 Frank, M. Ni, P. Jensen, M. Gerstein, M. B. 2023-11-22 doi:10.1101/2023.11.21.568125 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. ]]> https://biorxiv.org/content/10.1101/2023.11.21.568162v1?rss=1 Chahine, Z. M. Abel, S. Hollin, T. Chung, J. H. Barnes, G. L. Daub, M. E. Renard, I. Choi, J. Y. Vydyam, P. Chattopadhyay Pal, A. Argomaniz, M. Banks, C. kirkwood, J. Saraf, A. Camino Diaz, I. Castaneda-Casado, P. Cuevas-Martin, M. De Mercado-Arnanz, J. Fernandez Alvaro, E. Garcia-Perez, A. Ibarz-Ferrer, N. Viera-Morilla, S. Prudhomme, J. Joyner, C. J. Bei, A. Florens, L. Ben Mamoun, C. Vanderwal, C. Le Roch, K. G. 2023-11-22 doi:10.1101/2023.11.21.568162 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Focal adhesion-derived liquid-liquid phase separations regulate mRNA translation ]]> https://biorxiv.org/content/10.1101/2023.11.22.568289v1?rss=1 Kumar, A. Schwartz, M. A. 2023-11-22 doi:10.1101/2023.11.22.568289 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information ]]> https://biorxiv.org/content/10.1101/2023.11.22.568329v1?rss=1 Dong, Z. Jiang, W. Li, H. Dewan, A. T. Zhao, H. 2023-11-23 doi:10.1101/2023.11.22.568329 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Epigenetic and transcriptional regulation of the human angiotensinogen gene by high salt ]]> https://biorxiv.org/content/10.1101/2023.11.22.568343v1?rss=1 Perla, S. Kumar, A. 2023-11-23 doi:10.1101/2023.11.22.568343 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ The endogenous Mtv8 locus and the immunoglobulin repertoire ]]> https://biorxiv.org/content/10.1101/2023.11.24.567955v1?rss=1 Beilinson, H. A. Erickson, S. A. Golovkina, T. V. 2023-11-25 doi:10.1101/2023.11.24.567955 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ MolLM: Integrating 3D and 2D Molecular Representations with Biomedical Text via a Unified Pre-trained Language Model ]]> https://biorxiv.org/content/10.1101/2023.11.25.568656v1?rss=1 Tang, X. Tran, A. Tan, J. Gerstein, M. 2023-11-25 doi:10.1101/2023.11.25.568656 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Mapping the gene space at single-cell resolution with gene signal pattern analysis ]]> https://biorxiv.org/content/10.1101/2023.11.26.568492v1?rss=1 Venkat, A. Leone, S. Youlten, S. E. Fagerberg, E. Attanasio, J. Joshi, N. S. Perlmutter, M. Krishnaswamy, S. 2023-11-27 doi:10.1101/2023.11.26.568492 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ The integration of tactile and proprioceptive signals to achieve haptic object perception ]]> https://biorxiv.org/content/10.1101/2023.11.27.568836v1?rss=1 Dogruoz, R. E. Shelchkova, N. S. Sheets, D. E. Greenspon, C. M. Bensmaia, S. J. 2023-11-27 doi:10.1101/2023.11.27.568836 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ The contribution of diverse and stable functional connectivity edges to brain-behavior associations ]]> https://biorxiv.org/content/10.1101/2023.11.27.568848v1?rss=1 Matkovic, A. Murray, J. D. Anticevic, A. Repovs, G. 2023-11-28 doi:10.1101/2023.11.27.568848 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ A Bayesian Approach to Correcting the Attenuation Bias of Regression Using Polygenic Risk Score ]]> https://biorxiv.org/content/10.1101/2023.11.27.568907v1?rss=1 Zhou, G. Qie, X. Zhao, H. 2023-11-28 doi:10.1101/2023.11.27.568907 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Frontal cortex norepinephrine, serotonin, and dopamine dynamics in an innate fear-reward behavioral model ]]> https://biorxiv.org/content/10.1101/2023.11.27.568929v1?rss=1 Yang, J.-h. Basu, A. Liu, R.-J. Staszko, S. M. Yu, A. L. Rondeau, J. Glaeser-Khan, S. Li, Y. Che, A. Kaye, A. P. 2023-11-28 doi:10.1101/2023.11.27.568929 Cold Spring Harbor Laboratory Press 2023-11-28 <![CDATA[ Context versus aiming in motor learning when both feedforward and feedback control processes are engaged ]]> https://biorxiv.org/content/10.1101/2023.11.28.569130v1?rss=1 Crossley, M. J. Hewitson, C. L. Kaplan, D. M. 2023-11-30 doi:10.1101/2023.11.28.569130 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Sensory uncertainty influences motor learning differently in blocked versus interleaved trial contexts when both feedforward and feedback processes are engaged ]]> https://biorxiv.org/content/10.1101/2023.11.28.569131v1?rss=1 Crossley, M. J. Hewitson, C. L. Kaplan, D. M. 2023-11-30 doi:10.1101/2023.11.28.569131 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Spartin-mediated lipid transfer facilitates lipid droplet turnover ]]> https://biorxiv.org/content/10.1101/2023.11.29.569220v1?rss=1 Wan, N. Hong, Z. Parson, M. A. Korfhage, J. L. Burke, J. E. Melia, T. Reinisch, K. 2023-11-29 doi:10.1101/2023.11.29.569220 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Association between recovering from tempo perturbations and reading measurements. ]]> https://biorxiv.org/content/10.1101/2023.11.30.569275v1?rss=1 Wei, Y. Hancock, R. 2023-12-03 doi:10.1101/2023.11.30.569275 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Network-level encoding of local neurotransmitters in cortical astrocytes ]]> https://biorxiv.org/content/10.1101/2023.12.01.568932v1?rss=1 Cahill, M. K. Collard, M. Tse, V. Reitman, M. E. Etchenique, R. Kirst, C. Poskanzer, K. E. 2023-12-04 doi:10.1101/2023.12.01.568932 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Inducing representational change in the hippocampus through real-time neurofeedback ]]> https://biorxiv.org/content/10.1101/2023.12.01.569487v1?rss=1 Peng, K. Wammes, J. D. Nguyen, A. Iordan, M. C. Norman, K. A. Turk-Browne, N. B. 2023-12-04 doi:10.1101/2023.12.01.569487 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria ]]> https://biorxiv.org/content/10.1101/2023.12.01.569614v1?rss=1 Gwin, C. M. Gupta, K. R. Lu, Y. Shao, L. Rego, E. H. 2023-12-02 doi:10.1101/2023.12.01.569614 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis ]]> https://biorxiv.org/content/10.1101/2023.12.01.569622v1?rss=1 Cheng, S. Xia, I. F. Wanner, R. Abello, J. Stratman, A. N. Nicoli, S. 2023-12-02 doi:10.1101/2023.12.01.569622 Cold Spring Harbor Laboratory Press 2023-12-02 <![CDATA[ When Age Tips the Balance: a Dual Mechanism Affecting Hemispheric Specialization for Language ]]> https://biorxiv.org/content/10.1101/2023.12.04.569978v1?rss=1 Roger, E. Labache, L. Hamlin, N. Kruse, J. Baciu, M. Doucet, G. E. 2023-12-05 doi:10.1101/2023.12.04.569978 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Geometric experience sculpts the development and dynamics of hippocampal sequential cell assemblies ]]> https://biorxiv.org/content/10.1101/2023.12.04.570026v1?rss=1 Farooq, U. Dragoi, G. 2023-12-06 doi:10.1101/2023.12.04.570026 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Multilayer meta-matching: translating phenotypic prediction models from multiple datasets to small data ]]> https://biorxiv.org/content/10.1101/2023.12.05.569848v1?rss=1 Chen, P. An, L. Wulan, N. Zhang, C. Zhang, S. Ooi, L. Q. R. Kong, R. Chen, J. Wu, J. Chopra, S. Bzdok, D. Eickhoff, S. B. Holmes, A. Yeo, B. T. T. 2023-12-07 doi:10.1101/2023.12.05.569848 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning ]]> https://biorxiv.org/content/10.1101/2023.12.05.570153v1?rss=1 Steach, H. R. Viswanath, S. He, Y. Zhang, X. Ivanova, N. Hirn, M. Perlmutter, M. Krishnaswamy, S. 2023-12-07 doi:10.1101/2023.12.05.570153 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Transposition, duplication, and divergence of the telomerase RNA underlies the Mimulus telomere evolution ]]> https://biorxiv.org/content/10.1101/2023.12.06.568249v1?rss=1 Kumawat, S. Martinez, I. Logeswaran, D. Chen, H. Coughlan, J. Chen, J. Yuan, Y.-w. Sobel, J. Choi, J. Y. 2023-12-07 doi:10.1101/2023.12.06.568249 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Wind speed affects the rate and kinetics of stomatal conductance ]]> https://biorxiv.org/content/10.1101/2023.12.06.569782v1?rss=1 Shapira, O. Hochberg, U. McAdam, S. Azoulay-Shemer, T. Brodersen, C. R. Holbrook, N. M. Zait, Y. 2023-12-14 doi:10.1101/2023.12.06.569782 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts ]]> https://biorxiv.org/content/10.1101/2023.12.06.570396v1?rss=1 Johnson, B. Iuliano, M. Lam, T. Biederer, T. De Camilli, P. 2023-12-06 doi:10.1101/2023.12.06.570396 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis ]]> https://biorxiv.org/content/10.1101/2023.12.07.569910v1?rss=1 Liu, T. Chen, T. Zheng, W. Luo, X. Zhao, H. 2023-12-08 doi:10.1101/2023.12.07.569910 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Bridge-like lipid transfer protein family member 2 suppresses ciliogenesis ]]> https://biorxiv.org/content/10.1101/2023.12.07.570614v1?rss=1 Parolek, J. Burd, C. G. 2023-12-12 doi:10.1101/2023.12.07.570614 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ RluA is the major mRNA pseudouridine synthase in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.12.08.570740v1?rss=1 Schaening Burgos, C. Li, G.-W. Gilbert, W. V. 2023-12-12 doi:10.1101/2023.12.08.570740 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Vitamin B5 Metabolism is Essential for Vacuolar and Mitochondrial Integrity and Xenobiotic Detoxification in Fungi ]]> https://biorxiv.org/content/10.1101/2023.12.10.571002v1?rss=1 Choi, J.-Y. Gihaz, S. Munshi, M. Singh, P. Vydyam, P. Hamel, P. Adams, E. M. Fuller, K. Ben Mamoun, C. 2023-12-11 doi:10.1101/2023.12.10.571002 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development ]]> https://biorxiv.org/content/10.1101/2023.12.11.570452v1?rss=1 Cao, X. Ma, T. Fan, R. Yuan, G.-C. 2023-12-12 doi:10.1101/2023.12.11.570452 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Stochastic Epigenetic Mutations: Reliable Detection and Cardiovascular Associations ]]> https://biorxiv.org/content/10.1101/2023.12.12.571149v1?rss=1 Markov, Y. Levine, M. Higgins-Chen, A. T. 2023-12-13 doi:10.1101/2023.12.12.571149 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ Role of Ribeye PXDLS/T-binding cleft in normal synaptic ribbon function ]]> https://biorxiv.org/content/10.1101/2023.12.12.571266v1?rss=1 Zhu, J. Lv, C. Henry, D. Viviano, S. Santos-Sacchi, J. Matthews, G. Zenisek, D. 2023-12-12 doi:10.1101/2023.12.12.571266 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Differential developmental blueprints of organ-intrinsic nervous systems ]]> https://biorxiv.org/content/10.1101/2023.12.12.571306v1?rss=1 Hsu, I.-U. Lin, Y. Guo, Y. Xu, Q. J. Shao, Y. Wang, R. L. Yin, D. Zhao, J. Young, L. H. Zhao, H. Zhang, L. Chang, R. B. 2023-12-13 doi:10.1101/2023.12.12.571306 Cold Spring Harbor Laboratory Press 2023-12-13 <![CDATA[ Aerosolized α1 adrenoreceptor antagonism does not affect experimentally induced lung fibrosis in animal models ]]> https://biorxiv.org/content/10.1101/2023.12.12.571378v1?rss=1 Ghincea, A. Perry, C. Liu, A. McGovern, J. Sheeline, Y. Peng, X. Y. Genta, I. Barnthaler, T. Herzog, E. Sun, H. 2023-12-14 doi:10.1101/2023.12.12.571378 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ chronODE: A framework to integrate time-series multi-omics data based on ordinary differential equations combined with machine learning ]]> https://biorxiv.org/content/10.1101/2023.12.13.571513v1?rss=1 Borsari, B. Frank, M. Wattenberg, E. S. Xu, K. Liu, S. X. Yu, X. Gerstein, M. 2023-12-14 doi:10.1101/2023.12.13.571513 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Isolation and Lipidomic Profiling of Neuronal Lipid Droplets: Unveiling the Lipid Landscape for insights into Neurodegenerative Disorders ]]> https://biorxiv.org/content/10.1101/2023.12.13.571527v1?rss=1 Kumar, M. Knapp, J. Gupta, K. Ryan, T. A. 2023-12-14 doi:10.1101/2023.12.13.571527 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors ]]> https://biorxiv.org/content/10.1101/2023.12.13.571595v1?rss=1 Johnston, A. C. Alicea, G. M. Lee, C. C. Patel, P. V. Hanna, E. A. Vaz, E. Forjaz, A. Wan, Z. Nair, P. R. Lim, Y. Chen, T. Du, W. Kim, D. Nichakawade, T. D. Rebecca, V. W. Bonifant, C. L. Fan, R. Kiemen, A. L. Wu, P.-H. Wirtz, D. 2023-12-14 doi:10.1101/2023.12.13.571595 Cold Spring Harbor Laboratory Press 2023-12-14 <![CDATA[ HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination ]]> https://biorxiv.org/content/10.1101/2023.12.14.571747v1?rss=1 Haji-Seyed-Javadi, R. Koyen, A. E. Rath, S. K. Madden, M. Z. Hou, Y. Song, B. S. Kenney, A. M. Lan, L. Yao, B. Yu, D. S. 2023-12-15 doi:10.1101/2023.12.14.571747 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Synergistic Effects of Sulopenem in Combination with Cefuroxime or Durlobactam against Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2023.12.15.571879v1?rss=1 Dousa, K. M. Shin, E. Kurz, S. G. Plummer, M. Nantongo, M. Bethel, C. R. Taracila, M. A. Nguyen, D. C. Kreiswith, B. N. Daley, C. L. Remy, K. E. Holland, S. Bonomo, R. A. 2023-12-15 doi:10.1101/2023.12.15.571879 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Lysosomal TBK1 Responds to Amino Acid Availability to Relieve Rab7-Dependent mTORC1 Inhibition ]]> https://biorxiv.org/content/10.1101/2023.12.16.571979v1?rss=1 Talaia, G. Bentley-DeSousa, A. Ferguson, S. 2023-12-17 doi:10.1101/2023.12.16.571979 Cold Spring Harbor Laboratory Press 2023-12-17 <![CDATA[ Macrophages control pathological interferon responses during viral respiratory infection ]]> https://biorxiv.org/content/10.1101/2023.12.16.572019v1?rss=1 Hoagland, D. A. Rodriguez-Morales, P. Mann, A. O. Yu, S. Lai, A. Baez Vazquez, A. Pope, S. D. Lim, J. Li, S. Zhang, X. Li, M. O. Medzhitov, R. Franklin, R. A. 2023-12-17 doi:10.1101/2023.12.16.572019 Cold Spring Harbor Laboratory Press 2023-12-17 <![CDATA[ Bayesian Hidden Mark Interaction Model forDetecting Spatially Variable Genes inImaging-Based Spatially ResolvedTranscriptomics Data ]]> https://biorxiv.org/content/10.1101/2023.12.17.572071v1?rss=1 Yang, J. Jiang, X. Jin, K. W. Shin, S. Li, Q. 2023-12-17 doi:10.1101/2023.12.17.572071 Cold Spring Harbor Laboratory Press 2023-12-17 <![CDATA[ VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1 ]]> https://biorxiv.org/content/10.1101/2023.12.18.572081v1?rss=1 Ugur, B. Schueder, F. Shin, J. Hanna, M. G. Wu, Y. Leonzino, M. Su, M. McAdow, A. R. Wilson, C. A. Postlethwait, J. Solnica-Krezel, L. Bewersdorf, J. De Camilli, P. 2023-12-18 doi:10.1101/2023.12.18.572081 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention ]]> https://biorxiv.org/content/10.1101/2023.12.18.572176v1?rss=1 Fan, S. Dal Monte, O. Nair, A. Fagan, N. A. Chang, S. W. C. 2023-12-18 doi:10.1101/2023.12.18.572176 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence ]]> https://biorxiv.org/content/10.1101/2023.12.18.572198v1?rss=1 Chowdhury, N. B. Pokorzynski, N. D. Rucks, E. A. Ouellette, S. P. CARABEO, R. Saha, R. 2023-12-18 doi:10.1101/2023.12.18.572198 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ DDHD2 is necessary for activity-driven fatty acid fueling of nerve terminal function ]]> https://biorxiv.org/content/10.1101/2023.12.18.572201v1?rss=1 Kumar, M. Wu, Y. Knapp, J. Park, D. Gupta, K. De Camilli, P. Ryan, T. A. 2023-12-18 doi:10.1101/2023.12.18.572201 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Optimized mucin-selective enrichment strategy to probe the mucinome ]]> https://biorxiv.org/content/10.1101/2023.12.18.572204v1?rss=1 Mahoney, K. E. Chang, V. Lucas, T. M. Maruszko, K. Malaker, S. A. 2023-12-18 doi:10.1101/2023.12.18.572204 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ The molecular basis of sugar detection by an insect taste receptor ]]> https://biorxiv.org/content/10.1101/2023.12.18.572227v1?rss=1 Gomes, J. V. T. Singh-Bhagania, S. Cenci, M. Cordon, C. C. Singh, M. Butterwick, J. A. 2023-12-18 doi:10.1101/2023.12.18.572227 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2023.12.20.572522v1?rss=1 Li, Z. Di Vagno, L. Ni Cheallaigh, A. Sammon, D. Briggs, D. C. Chung, N. Chang, V. Mahoney, K. E. Cioce, A. Murphy, L. D. Chen, Y.-H. Narimatsu, Y. Miller, R. L. Willems, L. I. Malaker, S. A. Miller, G. J. Hohenester, E. Schumann, B. 2023-12-20 doi:10.1101/2023.12.20.572522 Cold Spring Harbor Laboratory Press 2023-12-20 <![CDATA[ DHCR24-mediated sterol homeostasis during spermatogenesis is required for sperm mitochondrial sheath formation and impacts male fertility over time ]]> https://biorxiv.org/content/10.1101/2023.12.21.572851v1?rss=1 Relovska, S. Wang, H. Zhang, X. Fernandez-Tussy, P. Jeong, K. Choi, J. Suarez, Y. McDonald, J. Fernandez-Hernando, C. Chung, J.-J. 2023-12-22 doi:10.1101/2023.12.21.572851 Cold Spring Harbor Laboratory Press 2023-12-22 <![CDATA[ Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization ]]> https://biorxiv.org/content/10.1101/2023.12.21.572903v1?rss=1 Guo, E. Chou, S. Z. Lara-Tejero, M. Galan, J. E. 2023-12-22 doi:10.1101/2023.12.21.572903 Cold Spring Harbor Laboratory Press 2023-12-22 <![CDATA[ Investigating the impact of whole genome duplication on transposable element evolution in ray-finned fishes ]]> https://biorxiv.org/content/10.1101/2023.12.22.572151v1?rss=1 Mallik, R. Wcisel, D. J. Yoder, J. A. Near, T. J. Dornburg, A. 2023-12-23 doi:10.1101/2023.12.22.572151 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Homological landscape of human brain functional sub-circuits ]]> https://biorxiv.org/content/10.1101/2023.12.22.573062v1?rss=1 Duong-Tran, D. Kaufmann, R. Chen, J. Wang, X. Garai, S. Xu, F. Bao, J. Amico, E. Kaplan, A. D. Petri, G. Goni, J. Zhao, Y. Shen, L. 2023-12-23 doi:10.1101/2023.12.22.573062 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Common genetic variation impacts molecular stress response in the brain ]]> https://biorxiv.org/content/10.1101/2023.12.27.573459v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@1e07fa9org.highwire.dtl.DTLVardef@1dd530forg.highwire.dtl.DTLVardef@17822a5org.highwire.dtl.DTLVardef@2a889f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Seah, C. Singer, R. Deans, P. M. Bader, H. Rusielewicz, T. Hicks, E. M. Young, H. Cote, A. Townsley, K. Xu, C. Hunter, C. J. McCarthy, B. Goldberg, J. Dobariya, S. Holtzherimer, P. E. Young, K. A. NYSCF Global Stem Cell Array Team, Traumatic Stress Brain Research Group, Noggle, S. A. Krystal, J. H. Paull, D. Girgenti, M. J. Yehuda, R. Brennand, K. Huckins, L. 2023-12-28 doi:10.1101/2023.12.27.573459 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Molecular identification of wide-field amacrine cells in mouse retina that encode stimulus orientation ]]> https://biorxiv.org/content/10.1101/2023.12.28.573580v1?rss=1 60 amacrine cell types, molecular identities and specialized functional attributes remain elusive. Here, we developed an intersectional genetic strategy to target a group of wide-field amacrine cells (WACs) in mouse retina that co-express the transcription factor Bhlhe22 and the Kappa Opioid Receptor (KOR; B/K WACs). B/K WACs feature straight, unbranched dendrites spanning over 0.5 mm ([~]15{degrees} visual angle) and produce non-spiking responses to either light increments or decrements. Two-photon dendritic population imaging reveals Ca2+ signals tuned to the physical orientations of B/K WAC dendrites, signifying a robust structure-function alignment. B/K WACs establish divergent connections with multiple retinal neurons, including unexpected connections with non-orientation-tuned ganglion cells and bipolar cells. Our work sets the stage for future comprehensive investigations of the most enigmatic group of retinal neurons: WACs. ]]> Park, S. J. Lei, W. Pisano, J. Orpia, A. Minehart, J. Pottackal, J. Hanke-Gogokhia, C. Zapadka, T. Clarkson-Paredes, C. Popratiloff, A. Ross, S. E. Singer, J. H. Demb, J. 2023-12-29 doi:10.1101/2023.12.28.573580 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Identification of the potassium binding site in serotonin transporter SERT ]]> https://biorxiv.org/content/10.1101/2023.12.29.573628v1?rss=1 Hellsberg, E. Boytsov, D. Chen, Q. Niello, M. Freissmuth, M. Rudnick, G. Zhang, Y.-W. Sandtner, W. Forrest, L. R. 2023-12-29 doi:10.1101/2023.12.29.573628 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Solid tumor growth depends on an intricate equilibrium of malignant cell states ]]> https://biorxiv.org/content/10.1101/2023.12.30.573100v1?rss=1 Torborg, S. R. Grbovic-Huezo, O. Singhal, A. Holm, M. Wu, K. Han, X. Ho, Y.-J. Haglund, C. Mitchell, M. J. Lowe, S. W. Dow, L. E. Pitter, K. L. Sanchez-Rivera, F. J. Levchenko, A. Tammela, T. 2023-12-30 doi:10.1101/2023.12.30.573100 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ SORBET: Automated cell-neighborhood analysis of spatial transcriptomics or proteomics for interpretable sample classification via GNN ]]> https://biorxiv.org/content/10.1101/2023.12.30.573739v1?rss=1 Shimonov, S. Cunningham, J. Talmon, R. Aizenbud, L. Desai, S. Rimm, D. Schalper, K. Kluger, H. Kluger, Y. 2024-01-02 doi:10.1101/2023.12.30.573739 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ Transoceanic pathogen circulation in the age of sail and steam ]]> https://biorxiv.org/content/10.1101/2024.01.01.573813v1?rss=1 Blackmore, E. N. Lloyd-Smith, J. O. 2024-01-02 doi:10.1101/2024.01.01.573813 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ Rare genetic variation in Fibronectin 1 (FN1) protects against APOEe4 in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.01.02.573895v1?rss=1 Bhattarai, P. Gunasekaran, T. I. Reyes-Dumeyer, D. Juelich, D. Tayran, H. Yilmaz, E. Flaherty, D. Rafael, L. Martin, M. Diones, R. Patricia, R. Ertekin-Taner, N. Teich, A. F. Dennis, D. W. Scott, H. Mayeux, R. Kizil, C. Vardarajan, B. N. 2024-01-02 doi:10.1101/2024.01.02.573895 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ Non-genetic adaptation by collective migration ]]> https://biorxiv.org/content/10.1101/2024.01.02.573956v1?rss=1 Vo, L. Avgidis, F. Mattingly, H. Balasubramanian, R. Shimizu, T. S. Kazmierczak, B. I. Emonet, T. 2024-01-03 doi:10.1101/2024.01.02.573956 Cold Spring Harbor Laboratory Press 2024-01-03 <![CDATA[ Synaptic Proteomes of Cortical Interneuron Classes Revealed by Antibody Directed Proximity Labeling. ]]> https://biorxiv.org/content/10.1101/2024.01.03.574066v1?rss=1 Battison, A. S. Liddle, J. Sumsky, S. O'Connell, C. Balsbaugh, J. LoTurco, J. 2024-01-04 doi:10.1101/2024.01.03.574066 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ Spatial characterization of interface dermatitis in cutaneous lupus reveals novel chemokine ligand-receptor pairs that drive disease ]]> https://biorxiv.org/content/10.1101/2024.01.05.574422v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@1e86dbeorg.highwire.dtl.DTLVardef@7d0208org.highwire.dtl.DTLVardef@1108aa8org.highwire.dtl.DTLVardef@ff255f_HPS_FORMAT_FIGEXP M_FIG C_FIG Model of chemokine systems governing recruitment of immune cell subsets to form interface dermatitis in cutaneous lupus. A. Summary of fresh tissue blister biopsy studies demonstrating increases in HLADR+ cells in nonlesional lupus biopsies as assessed by flow cytometry, and increased CXCL6 and CCL8 as assessed by 96 plex immunoassay. Lesional lupus biopsies also demonstrated significant increases in T cells and CXCL9/10/11 production. B. Model of chemokine-directed formation of interface dermatitis in cutaneous lupus. 1. Whole transcriptome atlas (WTA) digital spatial profiling (DSP) revealed increased AIM2 in keratinocytes proximal to inflammation, which is reported to be induced by environmental triggers including UV light and toxins. We also noted increased Caspase 8 (Casp8) and IL18 at the protein level, which can be induced downstream of AIM2. Chemokines including CXCL6 and CCL8 can be induced downstream of IL18, explaining how CCL8 and CXCL6 might be induced. 2. Recruitment of myeloid cell first responders by CCL8 and CXCL6. CD14+CD16+ myeloid cells, which were recently described in nonlesional lupus skin, express CXCR1 and migrate towards CXCL6, whereas CD14+CD16-myeloid cells express more CCR2 and migrate towards CCL8. 3. The CXCR3 ligands CXCL9/10/11 are expressed by keratinocytes, but more strongly in CD45+ immune cell and T cell regions of interest (ROIs). 4. T cells express CXCR3 and migrate towards CXCL9 and to a greater extent CXCL11. 5. The recruited HLADR+ myeloid populations and T cells contribute to formation of interface dermatitis. Thus, we propose a model in which keratinocyte/myeloid crosstalk can reinforce chemokine systems to optimally recruit lymphocytes and other immune cells to form interface dermatitis. Created with Biorender.com. Plain language summaryLupus skin rashes arise during flares, after exposure to medications or sunlight, or in response to other triggers of inflammation. To understand how white blood cells enter the skin to cause these rashes, we used new technologies to look at proteins that attract them into the skin. We found proteins that are expressed by skin cells in lesions that can recruit specific types of white blood cells that are thought to be the initiators of skin rashes. Once in the skin, these and other white blood cells can make additional proteins that bring in more and more cells. We hope that our findings will be used to test new topical treatments for lupus and other autoimmune skin rashes. ]]> Shakiba, S. Haddadi, N.-S. Afshari, K. Lubov, J. E. Raef, H. S. Li, R. Yildiz-Altay, U. Daga, M. Refat, M. A. Kim, E. Galindo de Laflin, J. Akabane, A. Sherman, S. MacDonald, E. Strassner, J. P. Zhang, L. Leon, M. Baer, C. E. Dresser, K. Liang, Y. Whitley, J. B. Skopelja-Gardner, S. Harris, J. E. Deng, A. Vesely, M. D. Rashighi, M. Richmond, J. M. 2024-01-06 doi:10.1101/2024.01.05.574422 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ Heterozygosity for neurodevelopmental disorder-associated TRIO variants yields distinct deficits in behavior, neuronal development, and synaptic transmission in mice ]]> https://biorxiv.org/content/10.1101/2024.01.05.574442v1?rss=1 Ishchenko, Y. Jeng, A. T. Feng, S. Nottoli, T. Manriquez-Rodriguez, C. Nguyen, K. Carrizales, M. G. Vitarelli, M. J. Corcoran, E. E. Greer, C. A. Myers, S. A. Koleske, A. J. 2024-01-06 doi:10.1101/2024.01.05.574442 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration ]]> https://biorxiv.org/content/10.1101/2024.01.07.574469v1?rss=1 Obata, T. Mizoguchi, S. Greaney, A. M. Adams, T. S. Yuan, Y. Edelstein, S. Leiby, K. L. Rivero, R. Wang, N. Kim, H. Yang, J. Schupp, J. C. Stitelman, D. Tsuchiya, T. Levchenko, A. Kaminski, N. Niklason, L. E. Raredon, M. S. B. 2024-01-08 doi:10.1101/2024.01.07.574469 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Effect of Pressure on the Conformational Landscape of Human γD-crystallin from Replica Exchange Molecular Dynamics Simulations ]]> https://biorxiv.org/content/10.1101/2024.01.07.574493v1?rss=1 Kacirani, A. Uralcan, B. Domingues, T. S. Haji-Akbari, A. 2024-01-07 doi:10.1101/2024.01.07.574493 Cold Spring Harbor Laboratory Press 2024-01-07 <![CDATA[ Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow ]]> https://biorxiv.org/content/10.1101/2024.01.08.574656v1?rss=1 Zhang, Y. Lin, C. 2024-01-08 doi:10.1101/2024.01.08.574656 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice ]]> https://biorxiv.org/content/10.1101/2024.01.09.574855v1?rss=1 Zamba-Campero, M. Soliman, D. Yu, H. Lasseter, A. G. Chang, Y.-Y. Liu, J. Aravind, L. Jewett, M. W. Storz, G. Adams, P. P. 2024-01-09 doi:10.1101/2024.01.09.574855 Cold Spring Harbor Laboratory Press 2024-01-09 <![CDATA[ Growth-induced collective bending and kinetic trapping of cytoskeletal filaments ]]> https://biorxiv.org/content/10.1101/2024.01.09.574885v1?rss=1 Banerjee, D. S. Freedman, S. L. Murrell, M. P. Banerjee, S. 2024-01-10 doi:10.1101/2024.01.09.574885 Cold Spring Harbor Laboratory Press 2024-01-10 <![CDATA[ Generative modeling of biological shapes and images using a probabilistic α-shape sampler ]]> https://biorxiv.org/content/10.1101/2024.01.09.574919v1?rss=1 Winn-Nunez, E. T. Witt, H. Bhaskar, D. Huang, R. Y. Reichner, J. S. Wong, I. Y. Crawford, L. 2024-01-11 doi:10.1101/2024.01.09.574919 Cold Spring Harbor Laboratory Press 2024-01-11 <![CDATA[ Reproductive innovation enabled radiation in the deep sea during an ecological crisis ]]> https://biorxiv.org/content/10.1101/2024.01.12.575380v1?rss=1 Brownstein, C. Zapfe, K. Lott, S. Harrington, R. C. Ghezelayagh, A. Dornburg, A. Near, T. J. 2024-01-15 doi:10.1101/2024.01.12.575380 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.01.14.575614v1?rss=1 Verma, N. Renauer, P. A. Dong, C. Xin, S. Lin, Q. Zhang, F. Glazer, P. M. Chen, S. 2024-01-15 doi:10.1101/2024.01.14.575614 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability ]]> https://biorxiv.org/content/10.1101/2024.01.15.575733v1?rss=1 Dalton, G. D. Siecinski, S. K. Nikolova, V. D. Cofer, G. P. Hornburg, K. Qi, Y. Johnson, G. A. Jiang, Y.-H. Moy, S. S. Gregory, S. G. 2024-01-16 doi:10.1101/2024.01.15.575733 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing ]]> https://biorxiv.org/content/10.1101/2024.01.16.575234v1?rss=1 Shen, X. Chen, C. Wang, Y. Zheng, W. Zheng, J. Jones, A. Zhu, B. Zhang, H. Lyons, C. Rijal, A. Mobley, J. Cao, G. Liu, K. Winn, R. Dickinson, A. J. G. Zhang, K. Wang, H. 2024-01-16 doi:10.1101/2024.01.16.575234 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Gamma protocadherins in vascular endothelial cells inhibit Klf2/4 to promote atherosclerosis ]]> https://biorxiv.org/content/10.1101/2024.01.16.575958v1?rss=1 Joshi, D. Coon, B. G. Chakraborty, R. Deng, H. Fernandez Tussy, P. Meredith, E. Traylor, J. G. Orr, A. W. Fernandez-Hernando, C. Schwartz, M. A. 2024-01-17 doi:10.1101/2024.01.16.575958 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework ]]> https://biorxiv.org/content/10.1101/2024.01.18.576147v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@e39504org.highwire.dtl.DTLVardef@14c52aforg.highwire.dtl.DTLVardef@1c87664org.highwire.dtl.DTLVardef@1d4d78b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gabernet, G. Marquez, S. Bjornson, R. Peltzer, A. Meng, H. Aron, E. Lee, N. Y. Jensen, C. Ladd, D. Hanssen, F. Heumos, S. nf-core community, Yaari, G. Kowarik, M. C. Nahnsen, S. Kleinstein, S. H. 2024-01-20 doi:10.1101/2024.01.18.576147 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Binding profiles for 954 Drosophila and C. elegans transcription factors revealtissue specific regulatory relationships ]]> https://biorxiv.org/content/10.1101/2024.01.18.576242v1?rss=1 Kudron, M. Gewirtzman, L. Victorsen, A. Lear, B. C. Gao, J. Xu, J. Samanta, S. Frink, E. Tran-Pearson, A. Huynh, C. Vafeados, D. Hammonds, A. FIsher, W. Wall, M. Wesseling, G. Hernandez, V. Lin, Z. Kasparian, M. White, K. P. Allada, R. Gerstein, M. Hillier, L. Celniker, S. E. Reinke, V. Waterston, R. H. 2024-01-20 doi:10.1101/2024.01.18.576242 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ A Variational Graph Partitioning Approach to Modeling Protein Liquid-liquid Phase Separation ]]> https://biorxiv.org/content/10.1101/2024.01.20.576375v1?rss=1 Wang, G. Warrell, J. Zheng, S. Gerstein, M. 2024-01-23 doi:10.1101/2024.01.20.576375 Cold Spring Harbor Laboratory Press 2024-01-23 <![CDATA[ An unconventional regulatory circuitry involving Aurora B controls anaphase onset and error-free chromosome segregation in trypanosomes ]]> https://biorxiv.org/content/10.1101/2024.01.20.576407v1?rss=1 Ballmer, D. Lou, H. J. Ishii, M. Turk, B. E. Akiyoshi, B. 2024-01-20 doi:10.1101/2024.01.20.576407 Cold Spring Harbor Laboratory Press 2024-01-20 <![CDATA[ Frontal noradrenergic and cholinergic transients exhibit distinct spatiotemporal dynamics during competitive decision-making ]]> https://biorxiv.org/content/10.1101/2024.01.23.576893v1?rss=1 Wang, H. Ortega, H. K. Kelly, E. B. Indajang, J. Feng, J. Li, Y. Kwan, A. C. 2024-01-24 doi:10.1101/2024.01.23.576893 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Brain-phenotype predictions can survive across diverse real-world data ]]> https://biorxiv.org/content/10.1101/2024.01.23.576916v1?rss=1 Adkinson, B. D. Rosenblatt, M. Dadashkarimi, J. Tejavibulya, L. Jiang, R. Noble, S. Scheinost, D. 2024-01-24 doi:10.1101/2024.01.23.576916 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Dissociable neural signals for reward and emotion prediction errors ]]> https://biorxiv.org/content/10.1101/2024.01.24.577042v1?rss=1 Heffner, J. Frömer, R. Nassar, M. FeldmanHall, O. 2024-01-25 doi:10.1101/2024.01.24.577042 Cold Spring Harbor Laboratory Press 2024-01-25 <![CDATA[ Proximity labeling proteomics reveals Kv1.3 potassium channel immune interactors in microglia. ]]> https://biorxiv.org/content/10.1101/2024.01.29.577122v1?rss=1 Bowen, C. A. Nguyen, H. M. Lin, Y. Bagchi, P. Natu, A. Espinosa-Garcia, C. Werner, E. Kumar, P. Tobin, B. Wood, L. B. Faundez, V. Wulff, H. Seyfried, N. Rangaraju, S. 2024-01-30 doi:10.1101/2024.01.29.577122 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ Chloride binding and cholesterol effects on high frequency complex nonlinear capacitance (cNLC) in the mouse outer hair cell: experiment and molecular dynamics ]]> https://biorxiv.org/content/10.1101/2024.01.29.577264v1?rss=1 Bai, J.-P. Zhang, C. Renigunta, V. Oliver, D. Navaratnam, D. S. Beckstein, O. Santos-Sacchi, J. 2024-01-31 doi:10.1101/2024.01.29.577264 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ The human claustrum tracks slow waves during sleep ]]> https://biorxiv.org/content/10.1101/2024.01.29.577851v1?rss=1 Lamsam, L. Liang, M. Gu, B. Sun, G. Hirsch, L. J. Pittenger, C. Kaye, A. P. Krystal, J. H. Damisah, E. 2024-01-30 doi:10.1101/2024.01.29.577851 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links ]]> https://biorxiv.org/content/10.1101/2024.01.30.576698v1?rss=1 N point mutations that partially recapitulate the mutation signature associated with colibactin exposure in vivo. Taken together, our work provides a biochemical framework for understanding how cells tolerate a naturally-occurring and clinically-relevant ICL. ]]> Altshuller, M. He, X. MacKrell, E. J. Wernke, K. M. Wang, J. W. H. Selles-Baiget, S. Wang, T.-Y. Chou, T.-F. Duxin, J. P. Balskus, E. P. Herzon, S. B. Semlow, D. 2024-01-30 doi:10.1101/2024.01.30.576698 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ A framework for reconstructing ancient food webs using functional trait data ]]> https://biorxiv.org/content/10.1101/2024.01.30.578036v1?rss=1 Shaw, J. O. Dunhill, A. M. Beckerman, A. P. Dunne, J. A. Hull, P. M. 2024-01-30 doi:10.1101/2024.01.30.578036 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ A novel microporous biomaterial vaccine platform for long-lasting antibody mediated immunity against viral infection. ]]> https://biorxiv.org/content/10.1101/2024.01.30.578038v1?rss=1 Mayer, D. P. Nelson, M. Andriyanova, D. Antao, O. Q. Chen, J. S. Scumpia, P. O. Weaver, W. M. Deshayes, S. Weinstein, J. S. 2024-01-31 doi:10.1101/2024.01.30.578038 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ Systematic characterization of protein structural features of alternative splicing isoforms using AlphaFold 2 ]]> https://biorxiv.org/content/10.1101/2024.01.30.578053v1?rss=1 Yang, Y. Xie, Y. Li, Z. Diala, C. Ali, M. Li, R. Xu, Y. Wu, A. Kim, P. Hosseini, S.-R. Bi, E. Zhao, H. Zheng, W. J. 2024-02-01 doi:10.1101/2024.01.30.578053 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ Evolutionary innovation in conserved regulatory elements across the mammalian tree of life ]]> https://biorxiv.org/content/10.1101/2024.01.31.578197v1?rss=1 Uebbing, S. Kocher, A. A. Baumgartner, M. Ji, Y. Bai, S. Xing, X. Nottoli, T. Noonan, J. P. 2024-01-31 doi:10.1101/2024.01.31.578197 Cold Spring Harbor Laboratory Press 2024-01-31 <![CDATA[ Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease ]]> https://biorxiv.org/content/10.1101/2024.02.01.577565v1?rss=1 Zhou, X. Shen, X. Johnson, J. Spakowicz, D. Agnello, M. Zhou, W. Avina, M. Honkala, A. Chleilat, F. Chen, S. J. Cha, K. Leopold, S. Zhu, C. Chen, L. Lyu, L. Hornburg, D. Wu, S. Zhang, X. Jiang, C. Jiang, L. jiang, l. Jian, R. Brooks, A. W. Wang, M. Contrepois, K. Gao, P. Schussler-Fiorenza Rose, S. M. Tran, T. D. B. Nguyen, H. Celli, A. Hong, B.-Y. Bautista, E. J. Dorsett, Y. Kavathas, P. zhou, y. Sodergren, E. Weinstock, G. M. Snyder, M. P. 2024-02-01 doi:10.1101/2024.02.01.577565 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ A Comprehensive Benchmarking Study on Computational Tools for Cross-omics Label Transfer from Single-cell RNA to ATAC Data ]]> https://biorxiv.org/content/10.1101/2024.02.01.578507v1?rss=1 Wang, Y. Zhao, H. 2024-02-07 doi:10.1101/2024.02.01.578507 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ A Novel, Open-Source Virtual Reality Platform for Dendritic Spine Analysis ]]> https://biorxiv.org/content/10.1101/2024.02.02.578597v1?rss=1 Reimer, M. L. Kauer, S. D. Benson, C. A. King, J. F. Patwa, S. Feng, S. Estacion, M. A. Bangalore, L. Waxman, S. Tan, A. M. 2024-02-07 doi:10.1101/2024.02.02.578597 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ μSim: A goal-driven framework for elucidating the neural control of movement through musculoskeletal modeling ]]> https://biorxiv.org/content/10.1101/2024.02.02.578628v1?rss=1 Almani, M. N. Lazzari, J. Chacon, A. Saxena, S. 2024-02-04 doi:10.1101/2024.02.02.578628 Cold Spring Harbor Laboratory Press 2024-02-04 <![CDATA[ Brain and grammar: revealing electrophysiological basic structures with competing statistical models ]]> https://biorxiv.org/content/10.1101/2024.02.06.579088v1?rss=1 Cometa, A. Battaglini, C. Artoni, F. Greco, M. Frank, R. Repetto, C. Bottoni, F. Cappa, S. F. Micera, S. Ricciardi, E. Moro, A. 2024-02-06 doi:10.1101/2024.02.06.579088 Cold Spring Harbor Laboratory Press 2024-02-06 <![CDATA[ Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines ]]> https://biorxiv.org/content/10.1101/2024.02.06.579115v1?rss=1 Zamora, P. F. Reidy, T. G. Armbruster, C. R. Sun, M. Van Tyne, D. Turner, P. E. Koff, J. L. Bomberger, J. M. 2024-02-06 doi:10.1101/2024.02.06.579115 Cold Spring Harbor Laboratory Press 2024-02-06 <![CDATA[ Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues ]]> https://biorxiv.org/content/10.1101/2024.02.06.579143v1?rss=1 Bai, Z. Zhang, D. Gao, Y. Tao, B. Bao, S. Enninful, A. Zhang, D. Su, G. Tian, X. Zhang, N. Xiao, Y. Liu, Y. Gerstein, M. Li, M. Xing, Y. Lu, J. Xu, M. L. Fan, R. 2024-02-08 doi:10.1101/2024.02.06.579143 Cold Spring Harbor Laboratory Press 2024-02-08 <![CDATA[ Systematic Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2024.02.07.576204v1?rss=1 Wei, J. Moon, J. Yasumizu, Y. Zhang, L. Radassi, K. Buitrago-Pocasangre, N. Deerhake, M. E. Strauli, N. Chan, A. Herman, A. Pedotte, R. Raposo, C. Tackenberg, B. Yim, I. Pappalardo, J. Longbrake, E. E. Sumida, T. S. Axisa, P.-P. Hafler, D. A. 2024-02-09 doi:10.1101/2024.02.07.576204 Cold Spring Harbor Laboratory Press 2024-02-09 <![CDATA[ Neuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators ]]> https://biorxiv.org/content/10.1101/2024.02.07.579306v1?rss=1 Malone, T. J. Wu, J. Zhang, Y. Licznerski, P. Chen, R. Nahiyan, S. Pedram, M. Jonas, E. A. Kaczmarek, L. K. 2024-02-07 doi:10.1101/2024.02.07.579306 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Congenital T cell activation impairs transitional to follicular B cell maturation in humans ]]> https://biorxiv.org/content/10.1101/2024.02.08.579495v1?rss=1 Allard-Chamard, H. Hillier, K. Ramseier, M. L. Bertocchi, A. Kaneko, N. Premo, K. Lam, T. Yuen, G. Karpel, M. Mahajan, V. S. Tsekeri, C. Vencic, J. Crotty, R. Sharda, A. Barmettler, S. Westermann-Clark, E. Walter, J. E. Ghebremichael, M. Shalek, A. K. Farmer, J. R. Pillai, S. 2024-02-11 doi:10.1101/2024.02.08.579495 Cold Spring Harbor Laboratory Press 2024-02-11 <![CDATA[ Key unprotected areas for carnivore conservation in Mexico ]]> https://biorxiv.org/content/10.1101/2024.02.10.579669v1?rss=1 Gonzalez, G. I. Harris, N. C. 2024-02-12 doi:10.1101/2024.02.10.579669 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ A proteome-wide quantitative guide for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs ]]> https://biorxiv.org/content/10.1101/2024.02.10.579775v1?rss=1 Brown, C. Ghosh, S. McAllister, R. Kumar, M. Walker, G. Sun, E. Aman, T. Panda, A. Kumar, S. Li, W. V. Coleman, J. Liu, Y. Rothman, J. E. Bhattacharyya, M. Gupta, K. 2024-02-12 doi:10.1101/2024.02.10.579775 Cold Spring Harbor Laboratory Press 2024-02-12 <![CDATA[ Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations ]]> https://biorxiv.org/content/10.1101/2024.02.13.580158v1?rss=1 Kobren, S. N. Moldovan, M. A. Reimers, R. Traviglia, D. Li, X. Barnum, D. Veit, A. Willett, J. Berselli, M. Ronchetti, W. Sherwood, R. Krier, J. Kohane, I. S. Undiagnosed Diseases Network, Sunyaev, S. R. 2024-02-16 doi:10.1101/2024.02.13.580158 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Atlas for the Lateralized Visuospatial Attention Networks (ALANs): Insights from fMRI and Network Analyses ]]> https://biorxiv.org/content/10.1101/2024.02.13.580164v1?rss=1 Labache, L. Petit, L. Joliot, M. Zago, L. 2024-02-14 doi:10.1101/2024.02.13.580164 Cold Spring Harbor Laboratory Press 2024-02-14 <![CDATA[ Neural dynamics of shifting attention between perception and working-memory contents ]]> https://biorxiv.org/content/10.1101/2024.02.14.580280v1?rss=1 Gresch, D. Boettcher, S. E. P. van Ede, F. Nobre, A. C. 2024-02-15 doi:10.1101/2024.02.14.580280 Cold Spring Harbor Laboratory Press 2024-02-15 <![CDATA[ Transient Impairment in Microglial Function Causes Sex-Specific Deficits in Synaptic and Hippocampal Function in Mice Exposed to Early Adversity ]]> https://biorxiv.org/content/10.1101/2024.02.14.580284v1?rss=1 Ahmed, S. Polis, B. Jamwal, S. Sanganahalli, B. G. MacDowell Kaswan, Z. Islam, R. Kim, D. Bowers, C. Giuliano, L. Biederer, T. Hyder, F. Kaffman, A. 2024-02-15 doi:10.1101/2024.02.14.580284 Cold Spring Harbor Laboratory Press 2024-02-15 <![CDATA[ Brain substates induced by DMT relate to sympathetic output and meaningfulness of the experience ]]> https://biorxiv.org/content/10.1101/2024.02.14.580356v1?rss=1 Pasquini, L. Simon, A. Gallen, C. Kettner, H. Roseman, L. Gazzaley, A. Carhart-Harris, R. Timmermann, C. 2024-02-19 doi:10.1101/2024.02.14.580356 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation ]]> https://biorxiv.org/content/10.1101/2024.02.14.580360v1?rss=1 Machado, L. F. M. Galan, J. E. 2024-02-14 doi:10.1101/2024.02.14.580360 Cold Spring Harbor Laboratory Press 2024-02-14 <![CDATA[ Brain-handedness associations depend on how and when handedness is measured ]]> https://biorxiv.org/content/10.1101/2024.02.15.580563v1?rss=1 Tejavibulya, L. Horien, C. Fredricks, C. Ficek-Tani, B. Westwater, M. L. Scheinost, D. 2024-02-15 doi:10.1101/2024.02.15.580563 Cold Spring Harbor Laboratory Press 2024-02-15 <![CDATA[ Development of a Marmoset Apparatus for Automated Pulling (MarmoAAP) to Study Cooperative Behaviors ]]> https://biorxiv.org/content/10.1101/2024.02.16.579531v1?rss=1 Meisner, O. C. Fagan, N. A. Greenwood, J. Jadi, M. Nandy, A. S. Chang, S. W. C. 2024-02-18 doi:10.1101/2024.02.16.579531 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ MRI economics: Balancing sample size and scan duration in brain wide association studies ]]> https://biorxiv.org/content/10.1101/2024.02.16.580448v1?rss=1 Ooi, L. Q. R. Orban, C. Nichols, T. Zhang, S. Tan, T. W. K. Kong, R. Marek, S. Dosenbach, N. U. F. Laumann, T. O. Gordon, E. M. Zhou, J. H. Bzdok, D. Eickhoff, S. B. Holmes, A. J. Yeo, B. T. T. 2024-02-18 doi:10.1101/2024.02.16.580448 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Discovery and characterization of chromosomal inversions in the arboviral vector mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2024.02.16.580682v1?rss=1 Liang, J. Rose, N. H. Brusentsov, I. I. Lukyanchikova, V. Karagodin, D. A. Feng, Y. Yurchenko, A. A. Sylla, M. Lutomiah, J. Badolo, A. Aribodor, O. B. Ayala, D. Acosta, C. G. Alto, B. W. Ahmad, N. W. Tu, Z. Gloria-Soria, A. Black, W. C. Powell, J. Sharakhov, I. V. McBride, C. S. Sharakhova, M. V. 2024-02-18 doi:10.1101/2024.02.16.580682 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Automated 3D analysis of social head-gaze behaviors in freely moving marmosets ]]> https://biorxiv.org/content/10.1101/2024.02.16.580693v1?rss=1 Xing, F. Sheffield, A. G. Jadi, M. P. Chang, S. W. C. Nandy, A. S. 2024-02-18 doi:10.1101/2024.02.16.580693 Cold Spring Harbor Laboratory Press 2024-02-18 <![CDATA[ Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions ]]> https://biorxiv.org/content/10.1101/2024.02.16.580719v1?rss=1 Lee, P. J. Soares, A. R. Sun, Y. Fai, C. Picciotto, M. Guo, J. U. 2024-02-17 doi:10.1101/2024.02.16.580719 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ Polygenic risk for depression and resting state functional connectivity of subgenual anterior cingulate cortex in young adults ]]> https://biorxiv.org/content/10.1101/2024.02.18.580883v1?rss=1 Chen, Y. Li, H.-T. Luo, X. Li, G. Ide, J. S. Li, C.-S. R. 2024-02-21 doi:10.1101/2024.02.18.580883 Cold Spring Harbor Laboratory Press 2024-02-21 <![CDATA[ Activation of Macrophages by Extracellular Vesicles Derived from Babesia-infected Red Blood Cells ]]> https://biorxiv.org/content/10.1101/2024.02.19.581030v1?rss=1 Hagos, B. Brasov, I. Branscome, H. Kashanchi, F. Ben Mamoun, C. Molestina, R. E. 2024-02-19 doi:10.1101/2024.02.19.581030 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ Personalized circuit modeling captures variation in cortical functional connectivity ]]> https://biorxiv.org/content/10.1101/2024.02.19.581085v1?rss=1 Cooper, R. A. Demirtas, M. Burt, J. B. Howell, A. M. Ji, J. L. Repovs, G. Sotiropoulos, S. Anticevic, A. Murray, J. D. 2024-02-20 doi:10.1101/2024.02.19.581085 Cold Spring Harbor Laboratory Press 2024-02-20 <![CDATA[ Optic nerve injury impairs intrinsic mechanisms underlying electrical activity in a resilient retinal ganglion cell ]]> https://biorxiv.org/content/10.1101/2024.02.20.581201v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@33df78org.highwire.dtl.DTLVardef@1945f2forg.highwire.dtl.DTLVardef@1f52745org.highwire.dtl.DTLVardef@1e5367b_HPS_FORMAT_FIGEXP M_FIG Schematic view of the effects of axon injury (optic nerve crush) on the physiology of an sustained ON-Alpha (AlphaONS) retinal ganglion cell. These cells are highly resilient to axon injury and survive for several weeks while other retinal ganglion cell types perish. At one week after injury, the AlphaONS RGC has diminished spontaneous and light-evoked action potential firing. Reduced firing depends not on changes in synaptic inputs but rather on reductions in intrinsic excitability. Reduced excitability is explained by a Ca2+-dependent mechanism and by a reduction in sodium channel density and function. C_FIG Key Points Summary1) Retinal ganglion cell (RGC) types show diverse rates of survival after axon injury. 2) A resilient RGC type maintains its synaptic inputs one week post-injury. 3) The resilient RGC type shows diminished firing and reduced expression of axon initial segment (AIS) genes following injury 4) Activity deficits arise from intrinsic dysfunction (Na+ channels, intracellular Ca2+), not from loss of excitation or enhanced inhibition. ]]> Zapadka, T. E. Tran, N. M. Demb, J. B. 2024-02-23 doi:10.1101/2024.02.20.581201 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Genetic polymorphisms of Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3) gene in African American kidney transplant recipients are associated with post-transplant graft failure ]]> https://biorxiv.org/content/10.1101/2024.02.21.581383v1?rss=1 Sun, Z. Yi, Z. Wei, C. Wang, W. Cravedi, P. Tedla, F. Ward, S. C. Azeloglu, E. Schrider, D. R. Li, Y. Ali, S. Ren, T. Liu, S. Liang, D. Fu, J. Liu, T. Li, H. Xi, C. Vy, T. H. Mosoyan, G. Sun, Q. Kumar, A. Zhang, Z. Farouk, S. Campbell, K. Ochando, J. Lee, K. Coca, S. Xiang, J. Connolly, P. Gallon, L. Colvin, R. Menon, M. Nadkarni, G. He, J. C. Kraft, M. Jiang, X. Zhang, X. Zhang, W. Chen, S.-h. Heeger, P. Zhang, W. 2024-02-23 doi:10.1101/2024.02.21.581383 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Spatial context non-uniformly modulates inter-laminar communication in the primary visual cortex ]]> https://biorxiv.org/content/10.1101/2024.02.21.581417v1?rss=1 Xu, X. Morton, M. P. Hudson, N. Nandy, A. Jadi, M. P. 2024-02-23 doi:10.1101/2024.02.21.581417 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Large-scale characterization of cell niches in spatial atlases using bio-inspired graph learning ]]> https://biorxiv.org/content/10.1101/2024.02.21.581428v1?rss=1 Birk, S. Bonafonte-Pardas, I. Feriz, A. M. Boxall, A. Agirre, E. Memi, F. Maguza, A. Fan, R. Castelo-Branco, G. Bayraktar, O. Theis, F. J. Talavera-Lopez, C. Lotfollahi, M. 2024-02-23 doi:10.1101/2024.02.21.581428 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Synaptic vesicle characterization of iPSC-derived dopaminergic neurons provides insight into distinct secretory vesicle pools ]]> https://biorxiv.org/content/10.1101/2024.02.22.581435v1?rss=1 Fujise, K. Rosenfeld, M. Rafiq, N. M. 2024-02-24 doi:10.1101/2024.02.22.581435 Cold Spring Harbor Laboratory Press 2024-02-24 <![CDATA[ Intervertebral disc cells from human back pain subjects exhibit TNFR1-mediated senescence and lack TNFR2-modulated repair capacity ]]> https://biorxiv.org/content/10.1101/2024.02.22.581620v1?rss=1 Gansau, J. Grossi, E. Rodriguez, L. Wang, M. Laudier, D. Chaudhary, S. Hecht, A. Fu, W. Sebra, R. Liu, C. Iatridis, J. C. 2024-02-25 doi:10.1101/2024.02.22.581620 Cold Spring Harbor Laboratory Press 2024-02-25 <![CDATA[ Multi-ancestry tandem repeat association study of hair color using exome-wide sequencing ]]> https://biorxiv.org/content/10.1101/2024.02.24.581865v1?rss=1 Fazzari, V. Moo-Choy, A. Panoyan, M. A. Abbatangelo, C. L. Polimanti, R. Novroski, N. M. Wendt, F. R. 2024-02-28 doi:10.1101/2024.02.24.581865 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ β-amino acids reduce ternary complex stability and alter the translation elongation mechanism ]]> https://biorxiv.org/content/10.1101/2024.02.24.581891v1?rss=1 Cruz Navarrete, F. A. Griffin, W. C. Chan, Y.-C. Martin, M. I. Alejo, J. L. Natchiar, S. K. Knudson, I. Altman, R. B. Schepartz, A. Miller, S. J. Blanchard, S. C. 2024-02-25 doi:10.1101/2024.02.24.581891 Cold Spring Harbor Laboratory Press 2024-02-25 <![CDATA[ Interneuron loss and microglia activation by transcriptome analyses in the basal ganglia of Tourette syndrome ]]> https://biorxiv.org/content/10.1101/2024.02.28.582504v1?rss=1 Wang, Y. Fasching, L. Wu, F. Huttner, A. Berretta, S. Roberts, R. Leckman, J. F. Abyzov, A. Vaccarino, F. M. 2024-02-28 doi:10.1101/2024.02.28.582504 Cold Spring Harbor Laboratory Press 2024-02-28 <![CDATA[ Quantitative profiling of human translation initiation reveals regulatory elements that potently affect endogenous and therapeutically modified mRNAs ]]> https://biorxiv.org/content/10.1101/2024.02.28.582532v1?rss=1 30,000 human 5' UTRs reveals a 250-fold range of translation output C_LIO_LISystematic mutagenesis demonstrates the causality of short (3-6nt) regulatory elements C_LIO_LIN1-methylpseudouridine alters translation initiation in a sequence-specific manner C_LIO_LIOptimal modified 5' UTRs outperform those in the current class of mRNA vaccines C_LI ]]> Lewis, C. J. T. Xie, L. Bhandarkar, S. Jin, D. Abdallah, K. S. Draycott, A. S. Chen, Y. Thoreen, C. C. Gilbert, W. V. 2024-03-03 doi:10.1101/2024.02.28.582532 Cold Spring Harbor Laboratory Press 2024-03-03 <![CDATA[ Choices to landscapes: Mechanisms of animal movement scale to landscape patterns ]]> https://biorxiv.org/content/10.1101/2024.02.28.582548v1?rss=1 Rogers, W. Yanco, S. Jetz, W. 2024-03-03 doi:10.1101/2024.02.28.582548 Cold Spring Harbor Laboratory Press 2024-03-03 <![CDATA[ Neural coding in gustatory cortex reflects consumption decisions: Evidence from conditioned taste aversion ]]> https://biorxiv.org/content/10.1101/2024.02.28.582584v1?rss=1 Raymond, M. A. Chapman, I. F. Staszko, S. M. Fletcher, M. L. Boughter, J. D. 2024-03-03 doi:10.1101/2024.02.28.582584 Cold Spring Harbor Laboratory Press 2024-03-03 <![CDATA[ Sexual dimorphism in the distribution and density of regulatory interneurons in the striatum ]]> https://biorxiv.org/content/10.1101/2024.02.29.582798v1?rss=1 Van Zandt, M. Flanagan, D. Pittenger, C. 2024-03-04 doi:10.1101/2024.02.29.582798 Cold Spring Harbor Laboratory Press 2024-03-04 <![CDATA[ Manifold Learning Uncovers Nonlinear Interactions between the Adolescent Brain and the Social Environment in Predicting Mental Health Problems ]]> https://biorxiv.org/content/10.1101/2024.02.29.582854v1?rss=1 Busch, E. L. Conley, M. I. Baskin-Sommers, A. 2024-03-06 doi:10.1101/2024.02.29.582854 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ CRISPR-Cas9 editing efficiency in fission yeast is not limited by homology search and is improved by combining gap-repair with fluoride selection ]]> https://biorxiv.org/content/10.1101/2024.03.01.582946v1?rss=1 Fernandez, R. Berro, J. 2024-03-02 doi:10.1101/2024.03.01.582946 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Damage sensing through TLR9 Promotes Viral Clearance and Recovery During Influenza Infection ]]> https://biorxiv.org/content/10.1101/2024.03.04.583378v1?rss=1 Kim, J. Yuan, Y. Agaronyan, K. Zhao, A. Wang, V. D. Gupta, G. Essayas, H. Kaminski, A. McGovern, J. Yu, S. Woo, S. Lee, C. J. Saleh, T. Hu, B. Sun, Y. Ishikawa, G. Bain, W. Evankovich, J. Herzog, E. Dela Cruz, C. S. Ryu, C. Sharma, L. 2024-03-06 doi:10.1101/2024.03.04.583378 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Developmental trajectory of cortical somatostatin interneuron function ]]> https://biorxiv.org/content/10.1101/2024.03.05.583539v1?rss=1 Wang, A. Ferguson, K. A. Gupta, J. Higley, M. J. Cardin, J. A. 2024-03-07 doi:10.1101/2024.03.05.583539 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion ]]> https://biorxiv.org/content/10.1101/2024.03.08.584053v1?rss=1 Busarello, E. Biancon, G. Lauria, F. Ibnat, Z. Ramirez, C. Tome, G. Aass, K. R. VanOudenhove, J. J. Standal, T. Viero, G. Halene, S. Tebaldi, T. 2024-03-12 doi:10.1101/2024.03.08.584053 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Evolutionary integration of the geography and pacing of the annual cycle in migratory birds ]]> https://biorxiv.org/content/10.1101/2024.03.08.584102v1?rss=1 Winger, B. M. La Sorte, F. A. Hack, M. D. Pegan, T. M. 2024-03-12 doi:10.1101/2024.03.08.584102 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584115v1?rss=1 Black, E. M. Ramirez Parrado, C. A. Trier, I. Li, W. V. Joo, Y. K. Pichurin, J. Liu, Y. Kabeche, L. 2024-03-12 doi:10.1101/2024.03.08.584115 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Human mobility and malaria risk in peri-urban and rural communities in the Peruvian Amazon ]]> https://biorxiv.org/content/10.1101/2024.03.11.584373v1?rss=1 Gomez, J. Grosso, A. Guzman-Guzman, M. Garcia Castillo, S. Castro, M. C. Torres, K. Vinetz, J. M. Gamboa, D. 2024-03-11 doi:10.1101/2024.03.11.584373 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Adaptation to visual sparsity enhances responses to infrequent stimuli ]]> https://biorxiv.org/content/10.1101/2024.03.12.584626v1?rss=1 Gou, T. Matulis, C. A. Clark, D. A. 2024-03-14 doi:10.1101/2024.03.12.584626 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Physical basis for the interaction between Drosophila ROS1 and the GPCR BOSS ]]> https://biorxiv.org/content/10.1101/2024.03.13.584817v1?rss=1 Zhang, J. Tsutsui, Y. Li, H. Li, T. Wang, Y. Klein, D. E. 2024-03-14 doi:10.1101/2024.03.13.584817 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors ]]> https://biorxiv.org/content/10.1101/2024.03.14.584949v1?rss=1 Wagner, S. Malmsheimer, S. Grin, I. Bohn, E. Franz-Wachtel, M. Macek, B. Sahr, T. Smollich, F. Chetrit, D. Meir, A. Roy, C. Buchrieser, C. 2024-03-14 doi:10.1101/2024.03.14.584949 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq ]]> https://biorxiv.org/content/10.1101/2024.03.14.585066v1?rss=1 Gaynor-Gillett, S. C. Cheng, L. Shi, M. Liu, J. Wang, G. Spector, M. Flaherty, M. Wall, M. Hwang, A. Gu, M. Chen, Z. Chen, Y. PsychENCODE Consortium, Moran, J. R. Zhang, J. Lee, D. Gerstein, M. Geschwind, D. White, K. P. 2024-03-18 doi:10.1101/2024.03.14.585066 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ High-fidelity enhanced AsCas12a knock-in mice for efficient multiplexed gene editing, disease modeling and orthogonal immunogenetics ]]> https://biorxiv.org/content/10.1101/2024.03.14.585126v1?rss=1 Tang, K. Zhou, X. Fang, S.-Y. Vandenbulcke, E. Du, A. Shen, J. Cao, H. Zhou, J. Chen, K. Xin, S. Zhou, L. Lin, S. H. Majety, M. Ling, X. Lam, S. Z. Chow, R. Bai, S. Nottoli, T. Booth, C. Liu, C. Dong, M. B. Chen, S. 2024-03-16 doi:10.1101/2024.03.14.585126 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Dendritic Cell - Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis ]]> https://biorxiv.org/content/10.1101/2024.03.15.584457v1?rss=1 Carter, H. Medina Costa, R. Bame, M. Gilchrist, T. Emch, C. Adams, T. Linderholm, A. Oldham, J. M. Noth, I. Kaminski, N. Moore, B. B. Gurczynski, S. J. 2024-03-17 doi:10.1101/2024.03.15.584457 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease ]]> https://biorxiv.org/content/10.1101/2024.03.17.585403v1?rss=1 Fleck, K. Luria, V. Garag, N. Karger, A. Hunter, T. Marten, D. Phu, W. Nam, K.-M. Sestan, N. O'Donnell-Luria, A. H. Erceg, J. 2024-03-17 doi:10.1101/2024.03.17.585403 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes ]]> https://biorxiv.org/content/10.1101/2024.03.18.585480v1?rss=1 Lu, X. Ni, P. Suarez-Meade, P. Yu, M. Forrest, E. N. Wang, G. Wang, Y. Quinones-Hinojosa, A. Gerstein, M. Jiang, Y.-h. 2024-03-19 doi:10.1101/2024.03.18.585480 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Single-cell genomics and regulatory networks for 388 human brains ]]> https://biorxiv.org/content/10.1101/2024.03.18.585576v1?rss=1 2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Emani, P. S. Liu, J. J. Clarke, D. Jensen, M. Warrell, J. Gupta, C. Meng, R. Lee, C. Y. Xu, S. Dursun, C. Lou, S. Chen, Y. Chu, Z. Galeev, T. Hwang, A. Li, Y. Ni, P. Zhou, X. PsychENCODE Consortium, Bakken, T. E. Bendl, J. Bicks, L. Chatterjee, T. Cheng, L. Cheng, Y. Dai, Y. Duan, Z. Flaherty, M. Fullard, J. F. Gancz, M. Garrido-Martin, D. Gaynor-Gillett, S. Grundman, J. Hawken, N. Henry, E. Hoffman, G. E. Huang, A. Jiang, Y. Jin, T. Jorstad, N. L. Kawaguchi, R. Khullar, S. Liu, J. Liu, J. Liu, S. Ma, S. Margolis, M. Mazariegos, S. Moore, J. M 2024-03-19 doi:10.1101/2024.03.18.585576 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ The RNA-dependent interactions of phosphatidylinositol 4,5-bisphosphate with intrinsically disordered proteins contribute to nuclear compartmentalization. ]]> https://biorxiv.org/content/10.1101/2024.03.19.585734v1?rss=1 Sztacho, M. Cervenka, J. Salovska, B. Antiga, L. Hoboth, P. Hozak, P. 2024-03-19 doi:10.1101/2024.03.19.585734 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ The Evolutionary Origins and Ancestral Features of Septins ]]> https://biorxiv.org/content/10.1101/2024.03.25.586683v1?rss=1 Delic, S. Shuman, B. Lee, S. Bahmanyar, S. Momany, M. Onishi, M. 2024-03-27 doi:10.1101/2024.03.25.586683 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ A Comprehensive Model of Blood Flow Restriction in the Post-surgical Rat ]]> https://biorxiv.org/content/10.1101/2024.03.27.586962v1?rss=1 Fosam, A. Nakandakari, S. C. B. R. Ohashi, Y. Bai, H. O'Connell, J. Raines, A. Chavez Miranda, I. Dardik, A. Allen, C. Perry, R. J. 2024-03-29 doi:10.1101/2024.03.27.586962 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ The Neural Basis of Attentional Blink as a Selective Control Mechanism in Conscious Perception ]]> https://biorxiv.org/content/10.1101/2024.03.30.587354v1?rss=1 Xin, Q. Forman, S. Christison-Lagay, K. Micek, C. Kronemer, S. Aksen, M. Grobois, L. Contreras Ramirez, V. Khalaf, A. Jin, D. Aerts, S. Chun, M. Crowley, M. Blumenfeld, H. 2024-03-30 doi:10.1101/2024.03.30.587354 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Dissecting Reactive Astrocyte Responses: Lineage Tracing and Morphology-based Clustering ]]> https://biorxiv.org/content/10.1101/2024.04.01.587565v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1899db6org.highwire.dtl.DTLVardef@1d152fcorg.highwire.dtl.DTLVardef@19f4754org.highwire.dtl.DTLVardef@3f853_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Brain damage triggers diverse cellular and molecular events, with astrocytes playing a crucial role in activating local neuroprotective and reparative signaling within damaged neuronal circuits. Here, we investigated reactive astrocytes using a multidimensional approach to categorize their responses into different subtypes based on morphology using the StarTrack lineage tracer, single-cell imaging reconstruction and multivariate data analysis. Our findings revealed three profiles of reactive astrocyte responses affecting cell size- and shape-related morphological parameters: "moderate," "strong," and "very strong". We also explored the heterogeneity in astrocyte reactivity, with a particular emphasis in the spatial and clonal distribution. Our research highlights the importance of the relationships between the different astrocyte subpopulations with their reactive responses, showing an enrichment of protoplasmic and fibrous astrocytes within the "strong" and "very strong" subtypes. Overall, our study contributes to a better understanding of astrocyte heterogeneity in response to an injury. By elucidating the diverse reactive responses among astrocyte subpopulations, we pave the way for future research aimed at uncovering novel therapeutic targets for mitigating the effects of brain damage and promoting neural repair. ]]> Delgado-Garcia, L. M. OJALVO-SANZ, A. C. Nakamura, T. K. E. Martin-Lopez, E. Porcionatto, M. Lopez-Mascaraque, L. 2024-04-02 doi:10.1101/2024.04.01.587565 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ High-resolution In-situ Structures of Mammalian Mitochondrial Respiratory Supercomplexes in Reaction within Native Mitochondria ]]> https://biorxiv.org/content/10.1101/2024.04.02.587796v1?rss=1 Zheng, W. Chai, P. Zhu, J. Zhang, K. 2024-04-03 doi:10.1101/2024.04.02.587796 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ A disease-associated PPP2R3C-MAP3K1 phospho-regulatory module controls centrosome function ]]> https://biorxiv.org/content/10.1101/2024.04.02.587836v1?rss=1 Ganga, A. K. Sweeney, L. K. Rubio-Ramos, A. Bishop, C. S. Hamel, V. Guichard, P. Breslow, D. K. 2024-04-03 doi:10.1101/2024.04.02.587836 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Unique functional neuroimaging signatures of genetic versus clinical high risk for psychosis ]]> https://biorxiv.org/content/10.1101/2024.04.03.587988v1?rss=1 Schleifer, C. H. Chang, S. E. Amir, C. M. O'Hora, K. P. Fung, H. Kang, J. W. D. Kushan-Wells, L. Daly, E. Di Fabio, F. Frascarelli, M. Gudbrandsen, M. Kates, W. R. Murphy, D. Addington, J. Anticevic, A. Cadenhead, K. S. Cannon, T. D. Cornblatt, B. A. Keshavan, M. Mathalon, D. H. Perkins, D. O. Stone, W. Walker, E. Woods, S. W. Uddin, L. Q. Kumar, K. Hoftman, G. D. Bearden, C. E. 2024-04-05 doi:10.1101/2024.04.03.587988 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition ]]> https://biorxiv.org/content/10.1101/2024.04.05.588255v1?rss=1 Zhang, Y. Wang, Z. Jiang, Y. Littler, D. R. Gerstein, M. Purcell, A. W. Rossjohn, J. Ou, H.-Y. Song, J. 2024-04-07 doi:10.1101/2024.04.05.588255 Cold Spring Harbor Laboratory Press 2024-04-07 <![CDATA[ Connectome caricatures: removing large-amplitude co-activation patterns in resting-state fMRI emphasizes individual differences ]]> https://biorxiv.org/content/10.1101/2024.04.08.588578v1?rss=1 Rodriguez, R. X. Noble, S. Camp, C. C. Scheinost, D. 2024-04-11 doi:10.1101/2024.04.08.588578 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ BAITSAO: Building A Foundation Model for Drug Synergy Analysis Powered by Language Models ]]> https://biorxiv.org/content/10.1101/2024.04.08.588634v1?rss=1 Liu, T. Chu, T. Luo, X. Zhao, H. 2024-04-12 doi:10.1101/2024.04.08.588634 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Sex differences in oxycodone-taking behaviors are linked to disruptions in reward-guided, decision-making functions ]]> https://biorxiv.org/content/10.1101/2024.04.09.587443v1?rss=1 LaRocco, K. Villiamma, P. Russell, M. Hill, J. DiLeone, R. Groman, S. 2024-04-11 doi:10.1101/2024.04.09.587443 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Metabolite accumulation from oral NMN supplementation drives aging-specific kidney inflammation ]]> https://biorxiv.org/content/10.1101/2024.04.09.588624v1?rss=1 Saleh, T. A. Whitson, J. A. Keiser, P. Prasad, P. Jenkins, B. C. Sodeinde, T. Mann, C. Rabinovitch, P. S. McReynolds, M. R. Sweetwyne, M. T. 2024-04-13 doi:10.1101/2024.04.09.588624 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Age-Invariant Genes: Multi-Tissue Identification and Characterization of Murine Reference Genes ]]> https://biorxiv.org/content/10.1101/2024.04.09.588721v1?rss=1 Gonzalez, J. T. Thrush, K. Meer, M. V. Levine, M. E. Higgins-Chen, A. T. 2024-04-13 doi:10.1101/2024.04.09.588721 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Meta-analysis: a quantitative model of adult neurogenesis in the rodent hippocampus ]]> https://biorxiv.org/content/10.1101/2024.04.09.588728v1?rss=1 Arellano, J. I. Rakic, P. 2024-04-13 doi:10.1101/2024.04.09.588728 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Multiple pathways for licensing human replication origins ]]> https://biorxiv.org/content/10.1101/2024.04.10.588796v1?rss=1 Yang, R. Hunker, O. Wise, M. Bleichert, F. 2024-04-10 doi:10.1101/2024.04.10.588796 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Epigenetic Remodeling in Human Coronary Artery Smooth Muscle Cell Phenotypic Switching ]]> https://biorxiv.org/content/10.1101/2024.04.11.589030v1?rss=1 Chakraborty, R. Schulz, V. P. Lezon-Geyda, K. Dave, J. M. Martin, K. A. Gallagher, P. G. 2024-04-14 doi:10.1101/2024.04.11.589030 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ TAM receptors control actomyosin dynamics in osteoclasts via RHOA-COFILIN-MYOSIN II signaling ]]> https://biorxiv.org/content/10.1101/2024.04.12.589232v1?rss=1 Engelmann, J. Zarrer, J. Schmerder, M. J. Mess, C. Ragipoglu, D. Riecken, K. Burstyn-Cohen, T. Alberto, E. Ghosh, S. Rothlin, C. V. Pantel, K. Bokemeyer, C. Hesse, E. Taipaleenmaeki, H. Loges, S. Ben-Batalla, I. 2024-04-14 doi:10.1101/2024.04.12.589232 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties ]]> https://biorxiv.org/content/10.1101/2024.04.12.589235v1?rss=1 Shin, J. H. Park, J. Lim, J. Jeong, J. Dinesh, R. K. Maher, S. E. Hong, J. Y. Wysolmerski, J. Choi, J. Bothwell, A. L. M. 2024-04-15 doi:10.1101/2024.04.12.589235 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Comparing the impact of contextual associations and statistical regularities in visual search and attention orienting ]]> https://biorxiv.org/content/10.1101/2024.04.12.589295v1?rss=1 Sefranek, M. Zokaei, N. Draschkow, D. Nobre, A. C. 2024-04-15 doi:10.1101/2024.04.12.589295 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer ]]> https://biorxiv.org/content/10.1101/2024.04.16.589460v1?rss=1 Jeong, J. Lee, J. Lim, J. Shin, J. Yoo, K. Kim, J. Tanaka, Y. Tae, H. S. Kim, L. K. Park, I.-H. Wysolmerski, J. choi, j. 2024-04-20 doi:10.1101/2024.04.16.589460 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes ]]> https://biorxiv.org/content/10.1101/2024.04.16.589618v1?rss=1 50 kilobases in 258k individuals from 6 general population cohorts with assessments of general cognitive abilities. We performed a CNV-GWAS and functional burden analyses, which tested 6502 gene-sets defined by tissue and cell-type transcriptomics as well as gene ontology disrupted by all rare coding CNVs. CNV-GWAS identified a novel duplication at 2q12.3 associated with higher performance in cognitive ability. Among the 864 gene-sets associated with cognitive ability, only 11% showed significant effects for both deletions and duplication. Accordingly, we systematically observed negative correlations between deletion and duplication effect sizes across all levels of biological observations. We quantified the preferential effects of deletions versus duplication using tagDS, a new normalized metric. Cognitive ability was preferentially affected by cortical, presynaptic, and negative-regulation gene-sets when duplicated. In contrast, preferential effects of deletions were observed for subcortical, post-synaptic, and positive-regulation gene-sets. A large proportion of gene-sets assigned to non-brain organs were associated with cognitive ability due to low tissue specificity genes, which were associated with higher sensitive to haploinsufficiency. Overall, most biological functions associated with cognitive ability are divided into those sensitive to either deletion or duplications. ]]> Huguet, G. Renne, T. Poulain, C. Dubuc, A. Kumar, K. Kazem, S. Engchuan, W. B. Shanta, O. Douard, E. Proulx, C. Jean-Louis, M. Saci, Z. Mollon, J. Schultz, L. M. Knowles, E. E. Cox, S. R. Porteous, D. Davies, G. Redmond, P. Harris, S. E. Schumann, G. Dumas, G. Labbe, A. Pausova, Z. Paus, T. Scherer, S. W. Sebat, J. Almasy, L. Glahn, D. C. Jacquemont, S. 2024-04-17 doi:10.1101/2024.04.16.589618 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Atp1a2 and Kcnj9 are candidate genes underlying oxycodone behavioral sensitivity and withdrawal in C57BL/6 substrains ]]> https://biorxiv.org/content/10.1101/2024.04.16.589731v1?rss=1 Goldberg, L. R. Baskin, B. M. Adla, Y. Beierle, J. A. Kelliher, J. C. Yao, E. J. Kirkpatrick, S. L. Reed, E. R. Jenkins, D. F. Luong, A. M. Luttik, K. P. Scotellaro, J. A. Drescher, T. A. Crotts, S. B. Yazdani, N. Ferris, M. T. R. Johnson, W. E. Mulligan, M. K. Bryant, C. D. 2024-04-17 doi:10.1101/2024.04.16.589731 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Ectopic Reconstitution of a Spine-Apparatus Like Structure Provides Insight into Mechanisms Underlying Its Formation ]]> https://biorxiv.org/content/10.1101/2024.04.16.589782v1?rss=1 Falahati, H. Wu, Y. De Camilli, P. 2024-04-16 doi:10.1101/2024.04.16.589782 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Enhancements in squid retinal responses to change of polarizations in a caustic shallow water ]]> https://biorxiv.org/content/10.1101/2024.04.17.589948v1?rss=1 Cai, J. Nikonov, S. Sweeney, A. M. 2024-04-20 doi:10.1101/2024.04.17.589948 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli ]]> https://biorxiv.org/content/10.1101/2024.04.19.590186v1?rss=1 Thappeta, Y. Canas-Duarte, S. J. Kallem, T. Fragasso, A. Xiang, Y. Gray, W. Lee, C. Cegelski, L. Jacobs-Wagner, C. 2024-04-20 doi:10.1101/2024.04.19.590186 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ SqueakOut: Autoencoder-based segmentation of mouse ultrasonic vocalizations ]]> https://biorxiv.org/content/10.1101/2024.04.19.590368v1?rss=1 Santana, G. M. Dietrich, M. O. 2024-04-23 doi:10.1101/2024.04.19.590368 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Rapid, simultaneous increases in the effective sizes of adaptively divergent yellow perch (Perca flavescens) populations ]]> https://biorxiv.org/content/10.1101/2024.04.21.590447v1?rss=1 Yin, X. Schraidt, C. Sparks, M. Euclide, P. Hoyt, T. Ruetz, C. Höök, T. Christie, M. 2024-04-25 doi:10.1101/2024.04.21.590447 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Time-resolved function of cell polarity kinases PRKCZ and PRKCI in CNS myelination ]]> https://biorxiv.org/content/10.1101/2024.04.22.589759v1?rss=1 Mercau, M. E. Hackbarth, R.-M. Liu, X. Wang, H. Zhang, L. Basu, M. K. Rothlin, C. V. Ghosh, S. 2024-04-23 doi:10.1101/2024.04.22.589759 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Sex differences in the functional network underpinnings of psychotic-like experiences in children ]]> https://biorxiv.org/content/10.1101/2024.04.22.590660v1?rss=1 Dhamala, E. Chopra, S. Ooi, L. Q. R. Rubio, J. M. Yeo, B. T. T. Malhotra, A. K. Holmes, A. J. 2024-04-23 doi:10.1101/2024.04.22.590660 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ CTHRC1+ Fibroblasts and SPP1+ Macrophages Synergistically Contribute to Pro-Tumorigenic Tumor Microenvironment in Pancreatic Ductal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.04.23.590663v1?rss=1 Li, E. Cheung, H. C. Ma, S. 2024-04-26 doi:10.1101/2024.04.23.590663 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Brain age prediction and deviations from normative trajectories in the neonatal connectome ]]> https://biorxiv.org/content/10.1101/2024.04.23.590811v1?rss=1 Sun, H. Mehta, S. Khaitova, M. Cheng, B. Hao, X. Spann, M. Scheinost, D. 2024-04-25 doi:10.1101/2024.04.23.590811 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Insulin signaling accelerates the anterograde movement of Rab4 vesicles in axons through Klp98a/KIF16B recruitment via Vps34-PI3Kinase ]]> https://biorxiv.org/content/10.1101/2024.04.24.590898v1?rss=1 Singh, K. Das, S. Sutradhar, S. Howard, J. Ray, K. 2024-04-24 doi:10.1101/2024.04.24.590898 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Perturbation-Specific Transcriptional Mapping facilitates unbiased target elucidation of antibiotics ]]> https://biorxiv.org/content/10.1101/2024.04.25.590978v1?rss=1 Romano, K. P. Bagnall, J. Warrier, T. Sullivan, J. Ferrara, K. Orzechowski, M. Nguyen, P. Raines, K. Livny, J. Shoresh, N. Hung, D. 2024-04-28 doi:10.1101/2024.04.25.590978 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ LSD flattens the hierarchy of directed information flow in fast whole-brain dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.25.591130v1?rss=1 Shinozuka, K. Tewarie, P. Luppi, A. Lynn, C. Roseman, L. Muthukumaraswamy, S. D. Nutt, D. J. Carhart-Harris, R. Deco, G. Kringelbach, M. L. 2024-04-28 doi:10.1101/2024.04.25.591130 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission ]]> https://biorxiv.org/content/10.1101/2024.04.26.591283v1?rss=1 Sobkowiak, B. Cudahy, P. Chitwood, M. H. Clark, T. G. Colijn, C. Grandjean, L. Walter, K. S. Crudu, V. Cohen, T. 2024-04-29 doi:10.1101/2024.04.26.591283 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Divergent short-term plasticity creates parallel pathways for computation and behavior in an olfactory circuit ]]> https://biorxiv.org/content/10.1101/2024.04.29.591740v1?rss=1 Kim, H. S. Jeanne, J. M. 2024-05-01 doi:10.1101/2024.04.29.591740 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Polymer Collapse and Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition ]]> https://biorxiv.org/content/10.1101/2024.04.29.591767v1?rss=1 Rouches, M. N. Machta, B. B. 2024-04-30 doi:10.1101/2024.04.29.591767 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing ]]> https://biorxiv.org/content/10.1101/2024.04.29.591790v1?rss=1 ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses. Key pointsO_LIWe provide a protocol for MASTR-seq: Multiplexed Analysis of Short Tandem Repeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. C_LIO_LIMASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease. C_LIO_LIMASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell. C_LI ]]> Chandradoss, K. R. Su, C. Malachowski, T. Boya, R. Ryu, H.-S. Brennand, K. Phillips-Cremins, J. E. 2024-05-02 doi:10.1101/2024.04.29.591790 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis ]]> https://biorxiv.org/content/10.1101/2024.04.30.591719v1?rss=1 Gleiberman, A. Invernizzi, R. Molyneaux, P. L. Wu, B. G. Lipinski, Y. Kugler, M. Segal, L. N. Sakamachi, Y. Wiley, E. Solis, A. Johnson, C. G. Meng, X. Malphurs, J. Papas, B. Mehta, S. Trempus, C. S. Thomas, S. Y. Li, J.-L. Zhou, L. karmaus, P. W. Fessler, M. B. Garantziotis, S. Randall, T. Hussain, S. Gudkov, A. V. McGrath, J. A. Walts, A. Yang, I. V. Schwartz, D. A. Lipinski, J. H. O'Dwyer, D. N. Gibson, K. Kass, D. J. Zhang, Y. Kaminski, N. 2024-04-30 doi:10.1101/2024.04.30.591719 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Receptors Determine Lytic Phage Host Range in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2024.04.30.591980v1?rss=1 Mueller, D. M. Pourtois, J. Kim, K. M. Targ, B. McBride, R. Bollyky, P. 2024-05-01 doi:10.1101/2024.04.30.591980 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Comparative single cell analysis reveals complex patterns of cell type and cell signaling innovations at the fetal-maternal interface ]]> https://biorxiv.org/content/10.1101/2024.05.01.591945v1?rss=1 Stadtmauer, D. J. Basanta, S. Maziarz, J. D. Cole, A. G. Dagdas, G. Smith, G. R. van Breukelen, F. Pavlicev, M. Wagner, G. P. 2024-05-02 doi:10.1101/2024.05.01.591945 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ CD4 downregulation precedes Env expression and protects HIV-1-infected cells from ADCC mediated by non-neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2024.05.01.592003v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@1c34d91org.highwire.dtl.DTLVardef@11975c0org.highwire.dtl.DTLVardef@81b5beorg.highwire.dtl.DTLVardef@1c2e0b2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Richard, J. Sannier, G. Zhu, L. Prevost, J. Marchitto, L. Benlarbi, M. Beaudoin-Bussieres, G. Sun, Y. Hongil, K. Chatterjee, D. A. Medjahed, H. Bourassa, C. Delgado, G.-G. Dube, M. Kirchhoff, F. Hahn, B. H. Kumar, P. Kaufmann, D. E. Finzi, A. 2024-05-02 doi:10.1101/2024.05.01.592003 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Cryo-EM Reveals the Mechanochemical Cycle of Reactive Full-length Human Dynein-1 ]]> https://biorxiv.org/content/10.1101/2024.05.01.592044v1?rss=1 Chai, P. Yang, J. Geohring, I. C. Markus, S. M. Wang, Y. Zhang, K. 2024-05-01 doi:10.1101/2024.05.01.592044 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Strengths and limitations of using participatory science data to characterize a wildlife mass mortality event ]]> https://biorxiv.org/content/10.1101/2024.05.02.592273v1?rss=1 Taylor, L. U. Barychka, T. McKeon, S. Bartolotta, N. Avery-Gomm, S. 2024-05-05 doi:10.1101/2024.05.02.592273 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues ]]> https://biorxiv.org/content/10.1101/2024.05.02.592275v1?rss=1 Rodriguez, C. Pan, D. Natan, R. G. Mohr, M. A. Miao, M. Chen, X. Northen, T. R. Vogel, J. P. Ji, N. 2024-05-05 doi:10.1101/2024.05.02.592275 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses ]]> https://biorxiv.org/content/10.1101/2024.05.03.591923v1?rss=1 Cormier, T. Barychka, T. Beaumont, M. Burt, T. V. English, M. D. Giacinti, J. A. Giroux, J.-F. Guillemette, M. Hargan, K. E. A. Jones, M. Lair, S. Lang, A. S. Lepage, C. Montevecchi, W. A. Rahman, I. Rail, J.-F. Robertson, G. J. Ronconi, R. A. Seyer, Y. Taylor, L. U. Ward, C. R. E. Wight, J. Wilhelm, S. I. Avery-Gomm, S. 2024-05-06 doi:10.1101/2024.05.03.591923 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Expert Panel Curation of 31 Genes in Relation to Limb Girdle Muscular Dystrophy ]]> https://biorxiv.org/content/10.1101/2024.05.03.592369v1?rss=1 2 years of age with progressive proximal weakness, elevated serum creatine kinase levels and dystrophic features on muscle biopsy. Advances in massively parallel sequencing have led to a surge in genes linked to LGMD. MethodsThe ClinGen Muscular Dystrophies and Myopathies gene curation expert panel (MDM GCEP, formerly Limb Girdle Muscular Dystrophy GCEP) convened to evaluate the strength of evidence supporting gene-disease relationships (GDR) using the ClinGen gene-disease clinical validity framework to evaluate 31 genes implicated in LGMD. ResultsThe GDR was exclusively LGMD for 17 genes, whereas an additional 14 genes were related to a broader phenotype encompassing congenital weakness. Four genes (CAPN3, COL6A1, COL6A2, COL6A3) were split into two separate disease entities, based on each displaying both dominant and recessive inheritance patterns, resulting in curation of 35 GDRs. Of these, 30 (86%) were classified as Definitive, 4 (11%) as Moderate and 1 (3%) as Limited. Two genes, POMGNT1 and DAG1, though definitively related to myopathy, currently have insufficient evidence to support a relationship specifically with LGMD. ConclusionsThe expert-reviewed assertions on the clinical validity of genes implicated in LGMDs form an invaluable resource for clinicians and molecular geneticists. We encourage the global neuromuscular community to publish case-level data that help clarify disputed or novel LGMD associations. ]]> Mohan, S. McNulty, S. Thaxton, C. Elnagheeb, M. Owens, E. Flowers, M. Nunnery, T. Self, A. Palus, B. Gorokhova, S. Kennedy, A. Niu, Z. Johari, M. Baneye Maiga, A. Macalalad, K. Clause, A. R. Beckmann, J. S. Bronicki, L. Cooper, S. T. Ganesh, V. S. Kang, P. B. Kesari, A. Lek, M. Levy, J. Rufibach, L. Savarese, M. Spencer, M. J. Straub, V. Tasca, G. Weihl, C. C. 2024-05-06 doi:10.1101/2024.05.03.592369 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Protective role of parenthood on age-related brain function in mid- to late-life ]]> https://biorxiv.org/content/10.1101/2024.05.03.592382v1?rss=1 Orchard, E. R. Chopra, S. Ooi, L. Q. R. Chen, P. An, L. Jamadar, S. D. Yeo, B. T. T. Rutherford, H. J. V. Holmes, A. J. 2024-05-04 doi:10.1101/2024.05.03.592382 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Does standard adjustment for genomic population structure capture direct genetic effects? ]]> https://biorxiv.org/content/10.1101/2024.05.03.592431v1?rss=1 Sotoudeh, R. Trejo, S. Harpak, A. Conley, D. 2024-05-06 doi:10.1101/2024.05.03.592431 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Changes in Cerebrospinal Fluid Proteins across the Spectrum of Untreated and Treated Chronic HIV-1 Infection ]]> https://biorxiv.org/content/10.1101/2024.05.03.592451v1?rss=1 Hu, Z. Cinque, P. Dravid, A. Hagberg, L. Yilmaz, A. Zetterberg, H. Fuchs, D. Gostner, J. Blennow, K. Spudich, S. Kincer, L. Zhou, S. Joseph, S. B. Swanstrom, R. Price, R. W. Gisslen, M. 2024-05-05 doi:10.1101/2024.05.03.592451 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Functional dissection of complex and molecular trait variants at single nucleotide resolution ]]> https://biorxiv.org/content/10.1101/2024.05.05.592437v1?rss=1 Siraj, L. Castro, R. I. Dewey, H. Kales, S. Nguyen, T. T. L. Kanai, M. Berenzy, D. Mouri, K. Wang, Q. McCaw, Z. R. Gosai, S. J. Aguet, F. Cui, R. Vockley, C. M. Lareau, C. A. Okada, Y. Gusev, A. Jones, T. R. Lander, E. S. Sabeti, P. C. Finucane, H. K. Reilly, S. K. Ulirsch, J. C. Tewhey, R. 2024-05-06 doi:10.1101/2024.05.05.592437 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Energy partitioning in the cell cortex ]]> https://biorxiv.org/content/10.1101/2024.05.06.592707v1?rss=1 Chen, S. Seara, D. Michaud, A. Kim, S. Bement, W. Murrell, M. 2024-05-09 doi:10.1101/2024.05.06.592707 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes ]]> https://biorxiv.org/content/10.1101/2024.05.06.592768v1?rss=1 Luebeck, J. Huang, E. Kim, F. Liefeld, T. Dameracharla, B. Ahuja, R. Schreyer, D. Prasad, G. Adamaszek, M. Kenkre, R. Agashe, T. Torvi, D. Tabor, T. Giurgiu, M. Kim, S. Kim, H. Bailey, P. Verhaak, R. G. W. Deshpande, V. B. Reich, M. M. Mischel, P. S. Mesirov, J. Bafna, V. 2024-05-10 doi:10.1101/2024.05.06.592768 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Timing Matters: Lessons from Perinatal Neurogenesis in the Olfactory Bulb ]]> https://biorxiv.org/content/10.1101/2024.05.06.592776v1?rss=1 Liberia, T. Han, K. Meller, S. Martin-Lopez, E. Greer, C. 2024-05-07 doi:10.1101/2024.05.06.592776 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Simultaneous Prediction of Functional States and Types of cis-regulatory Modules Reveals Their Prevalent Dual Uses as Enhancers and Silencers ]]> https://biorxiv.org/content/10.1101/2024.05.07.592879v1?rss=1 Yuan, S. Ni, P. Su, Z. 2024-05-10 doi:10.1101/2024.05.07.592879 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred C. elegans mutation accumulation lines ]]> https://biorxiv.org/content/10.1101/2024.05.08.593038v1?rss=1 Crombie, T. A. Rajaei, M. Saxena, A. S. Johnson, L. M. Saber, S. Tanny, R. E. Ponciano, J. M. Andersen, E. C. Zhou, J. Baer, C. F. 2024-05-10 doi:10.1101/2024.05.08.593038 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Environment by environment interactions (ExE) differ across genetic backgrounds (ExExG) ]]> https://biorxiv.org/content/10.1101/2024.05.08.593194v1?rss=1 Schmidlin, K. Ogbunugafor, C. B. Geiler-Samerotte, K. 2024-05-10 doi:10.1101/2024.05.08.593194 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ An unbiased method to partition diverse neuronal responses into functional ensembles reveals interpretable population dynamics during innate social behavior ]]> https://biorxiv.org/content/10.1101/2024.05.08.593229v1?rss=1 Lin, A. Akafia, C. Dal Monte, O. Fan, S. Fagan, N. Putnam, P. Tye, K. M. Chang, S. Ba, D. Allsop, A. S. 2024-05-09 doi:10.1101/2024.05.08.593229 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ Channel width modulates the permeability of DNA origami based nuclear pore mimics ]]> https://biorxiv.org/content/10.1101/2024.05.09.593438v1?rss=1 Feng, Q. Saladin, M. Wu, C. Cao, E. Zheng, W. Zhang, A. Bhardwaj, P. Li, X. Shen, Q. Kapinos, L. E. Mariappan, M. Lusk, C. P. Xiong, Y. Lim, R. Y. H. Lin, C. 2024-05-12 doi:10.1101/2024.05.09.593438 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Control of Inflammatory Response by Tissue Microenvironment ]]> https://biorxiv.org/content/10.1101/2024.05.10.592432v1?rss=1 Wu, Z. Pope, S. D. Ahmed, N. S. Leung, D. L. Hajjar, S. Yue, Q. Anand, D. M. Kopp, E. B. Okin, D. Ma, W. Kagan, J. C. Hargreaves, D. C. Medzhitov, R. Zhou, X. 2024-05-14 doi:10.1101/2024.05.10.592432 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Connecting the Dots: Approaching a Standardized Nomenclature for Molecular Connectivity Combining Data and Literature ]]> https://biorxiv.org/content/10.1101/2024.05.10.593490v1?rss=1 Reed, M. B. Cocchi, L. Knudsen, G. M. Sander, C. Gryglewski, G. Chen, J. Volpi, T. Fisher, P. Khattar, N. Silberbauer, L. R. Murgas, M. Godbersen, G. M. Nics, L. Walter, M. Hacker, M. Hammers, A. Ogden, T. R. Mann, J. J. Biswal, B. Rosen, B. Carson, R. Price, J. Lanzenberger, R. Hahn, A. 2024-05-10 doi:10.1101/2024.05.10.593490 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Two retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity ]]> https://biorxiv.org/content/10.1101/2024.05.11.592987v1?rss=1 Wood, T. W. P. Henriques, W. S. Cullen, H. B. Romero, M. Blengini, C. S. Sarathy, S. Sorkin, J. Bekele, H. Jin, C. Kim, S. Chemiakine, A. Khondker, R. Isola, J. V. V. Stout, M. Gennarino, V. A. Mogessie, B. Jain, D. Schindler, K. Suh, Y. Wiedenheft, B. Berchowitz, L. E. 2024-05-14 doi:10.1101/2024.05.11.592987 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease ]]> https://biorxiv.org/content/10.1101/2024.05.11.593693v1?rss=1 West, P. VanPortfliet, J. J. Lei, Y. Martinez, C. G. Wong, J. Pflug, K. Sitcheran, R. Kneeland, S. Murray, S. McGuire, P. Cannon, C. 2024-05-14 doi:10.1101/2024.05.11.593693 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity ]]> https://biorxiv.org/content/10.1101/2024.05.11.593705v1?rss=1 Venkat, A. Youlten, S. E. Perez San Juan, B. Purcell, C. Amodio, M. Burkhardt, D. B. Benz, A. Holst, J. McCool, C. Mollbrink, A. Lundeberg, J. van Dijk, D. Goldstein, L. D. Kummerfeld, S. Krishnaswamy, S. Chaffer, C. L. 2024-05-14 doi:10.1101/2024.05.11.593705 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT ]]> https://biorxiv.org/content/10.1101/2024.05.12.593740v1?rss=1 Ong, Q. Lim, L. T. R. Goh, C. Liao, Y. Chan, S. E. Lim, C. J. Y. Kam, V. Yap, J. Tseng, T. Desrouleaux, R. Wang, L. C. Ler, S. G. Lim, S. L. Kim, S. Sobota, R. M. Bennett, A. M. Han, W. Yang, X. 2024-05-14 doi:10.1101/2024.05.12.593740 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Novel cell states arise in embryonic cells devoid of key reprogramming factors ]]> https://biorxiv.org/content/10.1101/2024.05.13.593729v1?rss=1 Youlten, S. E. Miao, L. Hoppe, C. Boswell, C. W. Musaev, D. Abdelmessih, M. Krishnaswamy, S. Tornini, V. A. Giraldez, A. J. 2024-05-14 doi:10.1101/2024.05.13.593729 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction ]]> https://biorxiv.org/content/10.1101/2024.05.13.593807v1?rss=1 Wang, M. Patsenker, J. Li, H. Kluger, Y. Kleinstein, S. H. 2024-05-13 doi:10.1101/2024.05.13.593807 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ IL-4 Licenses B Cell Activation Through Cholesterol Synthesis ]]> https://biorxiv.org/content/10.1101/2024.05.13.593964v1?rss=1 Steach, H. R. York, A. G. Skadow, M. H. Chen, S. Zhao, J. Williams, K. J. Zhou, Q. Hsieh, W.-Y. Brewer, J. R. Qu, R. Shyer, J. A. Harman, C. Sefik, E. Mowell, W. K. Bailis, W. Cui, C. Kluger, Y. Bensinger, S. J. Craft, J. Flavell, R. 2024-05-15 doi:10.1101/2024.05.13.593964 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Birds affected by a 2021 avian mortality event are strongly associated with supplemental feeding and ground foraging behaviors ]]> https://biorxiv.org/content/10.1101/2024.05.14.593614v1?rss=1 Yala, A. J. Baillargeon, T. Gordon, L. Greening, S. Mwakibete, L. Sevigny, J. Shearn-Bochsler, V. Burrell, C. Casey, C. Driscoll, C. Klein, P. Lewis, N. Murphy, L. Poppenga, R. Thomas, K. Yabsley, M. Gagne, R. B. Nemeth, N. Tato, C. Needle, D. Ogbunugafor, C. B. 2024-05-15 doi:10.1101/2024.05.14.593614 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Endocardial primary cilia and blood flow are required for regulation of EndoMT during endocardial cushion development ]]> https://biorxiv.org/content/10.1101/2024.05.15.594405v1?rss=1 Berg, K. Gorham, J. Lundt, F. Seidman, J. Brueckner, M. 2024-05-16 doi:10.1101/2024.05.15.594405 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Cortico-amygdala synaptic structural abnormalities produced by templated aggregation of α-synuclein ]]> https://biorxiv.org/content/10.1101/2024.05.15.594419v1?rss=1 Gcwensa, N. Z. Russell, D. L. Long, K. Y. Brzozowski, C. F. Liu, X. Gamble, K. L. Cowell, R. M. Volpicelli-Daley, L. 2024-05-15 doi:10.1101/2024.05.15.594419 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ DeepVID v2: Self-Supervised Denoising with Decoupled Spatiotemporal Enhancement for Low-Photon Voltage Imaging ]]> https://biorxiv.org/content/10.1101/2024.05.16.594448v1?rss=1 Liu, C. Lu, J. Wu, Y. Ye, X. Ahrens, A. M. Platisa, J. Pieribone, V. A. Chen, J. L. Tian, L. 2024-05-16 doi:10.1101/2024.05.16.594448 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Differential modulation of sensory response dynamics by cilia structure and intraflagellar transport within and across chemosensory neurons ]]> https://biorxiv.org/content/10.1101/2024.05.16.594529v1?rss=1 Philbrook, A. ODonnell, M. Grunenkovaite, L. Sengupta, P. 2024-05-16 doi:10.1101/2024.05.16.594529 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Alternative splicing across the C. elegans nervous system ]]> https://biorxiv.org/content/10.1101/2024.05.16.594567v1?rss=1 Weinreb, A. Varol, E. Barrett, A. McWhirter, R. M. Taylor, S. R. Courtney, I. Basavaraju, M. Poff, A. Tipps, J. A. Collings, B. The CeNGEN Consortium, Krishnaswamy, S. Miller, D. M. Hammarlund, M. 2024-05-16 doi:10.1101/2024.05.16.594567 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Harmonising distributed tree inventory datasets across India can fill critical gaps in tropical ecology ]]> https://biorxiv.org/content/10.1101/2024.05.18.594774v1?rss=1 Anujan, K. Mohanbabu, N. Gopal, A. Surendra, A. Krishnan, A. Jayanth, A. Nair, T. Ongole, S. Sankaran, M. 2024-05-21 doi:10.1101/2024.05.18.594774 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Sympathetic neuron-derived NPY protects from obesity by sustaining the mural progenitors of thermogenic adipocytes. ]]> https://biorxiv.org/content/10.1101/2024.05.18.594804v1?rss=1 Zhu, Y. Yao, L. Gallo-Ferraz, A. L. Bombassaro, B. Simoes, M. R. Abe, I. Chen, J. Sarker, G. Ciccarelli, A. Zhou, L. Lee, C. Martinez-Sanchez, N. Dustin, M. Anderson, K. Zhan, C. Horvath, T. Velloso, L. Kajimura, S. Domingos, A. I. 2024-05-21 doi:10.1101/2024.05.18.594804 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Specification of human regional brain lineages using orthogonal gradients of WNT and SHH in organoids ]]> https://biorxiv.org/content/10.1101/2024.05.18.594828v1?rss=1 Scuderi, S. Kang, T.-Y. Jourdon, A. Yang, L. Wu, F. Nelson, A. Anderson, G. M. Mariani, J. SARANGI, V. Abyzov, A. Levchenko, A. Vaccarino, F. M. 2024-05-19 doi:10.1101/2024.05.18.594828 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ Ultra-stable insulin-glucagon fusion protein exploits an endogenous hepatic switch to mitigate hypoglycemic risk ]]> https://biorxiv.org/content/10.1101/2024.05.20.594997v1?rss=1 Varas, N. Grabowski, R. Jarosinski, M. A. Tai, N. Herzog, R. I. Ismail-Beigi, F. Yang, Y. Cherrington, A. D. Weiss, M. A. 2024-05-21 doi:10.1101/2024.05.20.594997 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Sexual dimorphism in histamine regulation of striatal dopamine ]]> https://biorxiv.org/content/10.1101/2024.05.20.595049v1?rss=1 Van Zandt, M. Pittenger, C. 2024-05-20 doi:10.1101/2024.05.20.595049 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines ]]> https://biorxiv.org/content/10.1101/2024.05.21.589311v1?rss=1 Clark, T. W. Mohan, J. Schaffer, L. V. Obernier, K. Al Manir, S. Churas, C. P. Dailamy, A. Doctor, Y. Forget, A. Hansen, J. N. Hu, M. Levinson, M. A. Marquez, C. Nourreddine, S. Niestroy, J. Pratt, D. Qian, G. Thaker, S. Belisle-Pipon, J.-C. Brandt, C. Chen, J. Ding, Y. Fodeh, S. Krogan, N. Lundberg, E. Mali, P. Payne-Foster, P. Ratcliffe, S. J. Ravitsky, V. Sali, A. Schulz, W. Ideker, T. 2024-05-24 doi:10.1101/2024.05.21.589311 Cold Spring Harbor Laboratory Press 2024-05-24 <![CDATA[ Rab6a enables BICD2/dynein-mediated trafficking of human papillomavirus from the trans-Golgi network during virus entry ]]> https://biorxiv.org/content/10.1101/2024.05.21.595194v1?rss=1 Choi, J. Speckhart, K. Tsai, B. DiMaio, D. 2024-05-21 doi:10.1101/2024.05.21.595194 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Functional roles of neural aPKCs in mouse brain development and survival ]]> https://biorxiv.org/content/10.1101/2024.05.22.595312v1?rss=1 El Ellam, A. Alberto, E. J. Mercau, M. E. Pramio, D. T. Bhat, K. M. Philbrick, W. M. Schechtman, D. Rothlin, C. V. Ghosh, S. 2024-05-23 doi:10.1101/2024.05.22.595312 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ CosGeneGate Selects Multi-functional and Credible Biomarkers for Single-cell Analysis ]]> https://biorxiv.org/content/10.1101/2024.05.22.595428v1?rss=1 Liu, T. Long, W. Cao, Z. Wang, Y. He, C. H. Zhang, L. Strittmatter, S. M. Zhao, H. 2024-05-26 doi:10.1101/2024.05.22.595428 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Classification of psychedelic drugs based on brain-wide imaging of cellular c-Fos expression ]]> https://biorxiv.org/content/10.1101/2024.05.23.590306v1?rss=1 95% accuracy. We used Shapley additive explanation to pinpoint the brain regions driving the machine learning predictions. Our results support a novel approach for characterizing and validating psychoactive drugs with psychedelic properties. ]]> Aboharb, F. Davoudian, P. A. Shao, L.-X. Liao, C. Rzepka, G. N. Wojtasiewicz, C. Dibbs, M. Rondeau, J. Sherwood, A. M. Kaye, A. P. Kwan, A. C. 2024-05-26 doi:10.1101/2024.05.23.590306 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ TIF1γ regulates stability of T regulatory cells during inflammation ]]> https://biorxiv.org/content/10.1101/2024.05.23.595623v1?rss=1 Contreras-Castillo, E. Zambrano-Romero, J. D. Perez-Vazquez, D. Garcia-Patino, M. G. Tapia-Urzua, G. Candelario-Martinez, A. Ramos-Balderas, J. L. Licona-Limon, I. I. Madera-Salcedo, I. K. Rosetti-Scuitto, F. Crispin-Acuna, J. C. Noriega-Lopez, L. Nava, P. Recillas-Targa, F. Kaartinen, V. Henao-Mejia, J. Flavell, R. Limon, P. L. 2024-05-28 doi:10.1101/2024.05.23.595623 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Multimodal identification of the mouse brain using simultaneous Ca2+ imaging and fMRI ]]> https://biorxiv.org/content/10.1101/2024.05.24.594620v1?rss=1 Mandino, F. Horien, C. Shen, X. Desrosier-Gregoire, G. Luo, W. Markicevic, M. Constable, R. T. Papademetris, X. Chakravarty, M. Betzel, R. Lake, E. M. 2024-05-26 doi:10.1101/2024.05.24.594620 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ N-Methyl-D-aspartate receptor hypofunction causes recurrent and transient failures of perceptual inference ]]> https://biorxiv.org/content/10.1101/2024.05.24.595590v1?rss=1 Weilnhammer, V. Rothkirch, M. Yilmaz, D. Fritsch, M. Ptasczynski, L. E. Reichenbach, K. Roediger, L. Corlett, P. Sterzer, P. 2024-05-24 doi:10.1101/2024.05.24.595590 Cold Spring Harbor Laboratory Press 2024-05-24 <![CDATA[ Epidermal Growth Factor Receptor Regulates Beclin-1 in Hyperoxia ]]> https://biorxiv.org/content/10.1101/2024.05.24.595621v1?rss=1 Harris, Z. Korde, A. Khoury, J. Manning, E. Stanley, G. Sun, Y. Hu, B. Shin, H. J. Joerns, J. Clark, B. Placek, L. Unutmaz, D. Chun, H. Sharma, L. Sauler, M. Rajagopalan, G. Zhang, X. Wang, H. Kang, M.-J. Koff, J. 2024-05-27 doi:10.1101/2024.05.24.595621 Cold Spring Harbor Laboratory Press 2024-05-27 <![CDATA[ The hyperphosphorylation of SARS-CoV-2s nucleocapsid protein by GSK-3 involves a complex and redundant priming mechanism ]]> https://biorxiv.org/content/10.1101/2024.05.25.595913v1?rss=1 Chen, S. He, Z. Kanyo, J. Lam, T. Ha, G. Lindenbach, B. D. D. Ha, Y. 2024-05-27 doi:10.1101/2024.05.25.595913 Cold Spring Harbor Laboratory Press 2024-05-27 <![CDATA[ Homomorphic Encryption: An Application to Polygenic Risk Scores ]]> https://biorxiv.org/content/10.1101/2024.05.26.595961v1?rss=1 Knight, E. Li, J. Jensen, M. Yolou, I. Kockan, C. Gerstein, M. 2024-05-28 doi:10.1101/2024.05.26.595961 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ Bifurcation enhances temporal information encoding in the olfactory periphery ]]> https://biorxiv.org/content/10.1101/2024.05.27.596086v1?rss=1 Choi, K. Rosenbluth, W. Graf, I. R. Kadakia, N. Emonet, T. 2024-05-31 doi:10.1101/2024.05.27.596086 Cold Spring Harbor Laboratory Press 2024-05-31 <![CDATA[ Periodic ER-plasma membrane junctions support long-range Ca2+ signal integration in dendrites ]]> https://biorxiv.org/content/10.1101/2024.05.27.596121v1?rss=1 Benedetti, L. Fan, R. Weigel, A. V. Moore, A. S. Houlihan, P. R. Kittisopikul, M. Park, G. Petruncio, A. Hubbard, P. M. Pang, S. Xu, C. S. Hess, H. Saalfeld, S. Rangaraju, V. Clapham, D. E. De Camilli, P. Ryan, T. A. Lippincott-Schwartz, J. 2024-05-31 doi:10.1101/2024.05.27.596121 Cold Spring Harbor Laboratory Press 2024-05-31 <![CDATA[ The Latent Aging of Cells ]]> https://biorxiv.org/content/10.1101/2024.05.28.596284v1?rss=1 Niimi, P. Gould, V. Thrush-Evensen, K. Levine, M. E. 2024-05-30 doi:10.1101/2024.05.28.596284 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Lattice ultrasensitivity produces large gain in E. coli chemosensing ]]> https://biorxiv.org/content/10.1101/2024.05.28.596300v1?rss=1 Sherry, D. M. Graf, I. R. Bryant, S. J. Emonet, T. Machta, B. M. 2024-06-01 doi:10.1101/2024.05.28.596300 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Overlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles ]]> https://biorxiv.org/content/10.1101/2024.05.29.596401v1?rss=1 Park, D. Fujise, K. Wu, Y. Lujan, R. Del Olmo-Cabrera, S. Wesseling, J. De Camilli, P. 2024-05-31 doi:10.1101/2024.05.29.596401 Cold Spring Harbor Laboratory Press 2024-05-31 <![CDATA[ A diverse and distinct microbiome inside living trees ]]> https://biorxiv.org/content/10.1101/2024.05.30.596553v1?rss=1 Arnold, W. Gewirtzman, J. Raymond, P. A. Duguid, M. Brodersen, C. R. Brown, C. Norbraten, N. Wood, Q. T. V. Bradford, M. A. Peccia, J. 2024-06-02 doi:10.1101/2024.05.30.596553 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer ]]> https://biorxiv.org/content/10.1101/2024.05.31.596845v1?rss=1 Wong, E. W. P. Sahin, M. Yang, R. Lee, U. Zhan, Y. A. Misra, R. Tomas, F. Alomran, N. Polyzos, A. Lee, C. J. Trieu, T. Fundichely, A. M. Wiesner, T. Rosowicz, A. Cheng, S. Liu, C. L. Lallo, M. Merghoub, T. Hamard, P.-J. Koche, R. Khurana, E. Apostolou, E. Zheng, D. Chen, Y. Leslie, C. S. Chi, P. 2024-06-06 doi:10.1101/2024.05.31.596845 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Predicting Spatially Resolved Gene Expression via Tissue Morphology using Adaptive Spatial GNNs ]]> https://biorxiv.org/content/10.1101/2024.06.02.596505v1?rss=1 Song, T. Cosatto, E. Wang, G. Kuang, R. Gerstein, M. Min, M. R. Warrell, J. 2024-06-03 doi:10.1101/2024.06.02.596505 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Medial amygdalar tau is associated with anxiety symptoms in preclinical Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.06.03.597160v1?rss=1 Li, J. S. Tun, S. M. Ficek-Tani, B. Xu, W. Wang, S. Horien, C. Toyonaga, T. Nuli, S. S. Zeiss, C. J. Powers, A. R. Zhao, Y. Mormino, E. C. Fredericks, C. A. 2024-06-03 doi:10.1101/2024.06.03.597160 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Quantifying Contributions from TopologicalCycles in the Brain Network towards Cognition ]]> https://biorxiv.org/content/10.1101/2024.06.03.597217v1?rss=1 Garai, S. Vo, S. Blank, L. Xu, F. Chen, J. Duong-Tran, D. Zhao, Y. Shen, L. 2024-06-04 doi:10.1101/2024.06.03.597217 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Geographic redistributions are insufficient to mitigate the erosion of species environmental niches ]]> https://biorxiv.org/content/10.1101/2024.06.04.596070v1?rss=1 Cohen, J. Jetz, W. 2024-06-04 doi:10.1101/2024.06.04.596070 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Prevention and treatment of noise-induced hearing loss and cochlear synapse degeneration by potassium channel blockers in vivo ]]> https://biorxiv.org/content/10.1101/2024.06.04.597382v1?rss=1 Zhao, H.-B. Liu, L.-M. Mei, L. Quinonez, A. T. Roberts, R. A. Lu, X. 2024-06-06 doi:10.1101/2024.06.04.597382 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Data rescue in high-motion youth cohorts for robust and reproducible brain-behavior relationships ]]> https://biorxiv.org/content/10.1101/2024.06.04.597447v1?rss=1 Ramduny, J. Vanderwal, T. Kelly, C. 2024-06-06 doi:10.1101/2024.06.04.597447 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Role of microglia in stress-induced alcohol intake in female and male mice ]]> https://biorxiv.org/content/10.1101/2024.06.05.597614v1?rss=1 Soares, A. Garcia-Rivas, V. Fai, C. Thomas, M. Zheng, X. Picciotto, M. Mineur, Y. 2024-06-06 doi:10.1101/2024.06.05.597614 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ The inactive X chromosome drives sex differences in microglial inflammatory activity in human glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.06.06.597433v1?rss=1 Tharp, M. E. Han, C. Z. Balak, C. D. Fitzpatrick, C. O'Connor, C. Preissl, S. Buchanan, J. Nott, A. Escoubet, L. Mavrommatis, K. Gupta, M. Schwartz, M. S. U, H. S. Jones, P. S. Levy, M. L. Gonda, D. D. Ben-Haim, S. Ciacci, J. Barba, D. Khalessi, A. Coufal, N. G. Chen, C. C. Glass, C. K. Page, D. C. 2024-06-06 doi:10.1101/2024.06.06.597433 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ A DNA-based molecular clamp for probing protein interactions and structure under force. ]]> https://biorxiv.org/content/10.1101/2024.06.06.597759v1?rss=1 Chung, M. Zhou, K. Powell, J. Lin, C. Schwartz, M. A. 2024-06-06 doi:10.1101/2024.06.06.597759 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares ]]> https://biorxiv.org/content/10.1101/2024.06.07.597819v1?rss=1 Mattessich, M. Reyna, J. Aron, E. Ay, F. Kilmer, M. Kleinstein, S. H. Konstorum, A. 2024-06-10 doi:10.1101/2024.06.07.597819 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Broken time reversal symmetry in visual motion detection ]]> https://biorxiv.org/content/10.1101/2024.06.08.598068v1?rss=1 Wu, N. Zhou, B. Agrochao, M. Clark, D. A. 2024-06-10 doi:10.1101/2024.06.08.598068 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Lysosome damage triggers acute formation of ER to lysosomes membrane tethers mediated by the bridge-like lipid transport protein VPS13C ]]> https://biorxiv.org/content/10.1101/2024.06.08.598070v1?rss=1 Wang, X. Xu, P. Bentley-DeSousa, A. Hancock-Cerutti, W. Cai, S. Johnson, B. T. Tonelli, F. Talaia, G. Alessi, D. R. Ferguson, S. M. De Camilli, P. 2024-06-08 doi:10.1101/2024.06.08.598070 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM ]]> https://biorxiv.org/content/10.1101/2024.06.10.598346v1?rss=1 Renganathan, B. Moore, A. S. Yeo, W.-H. Petruncio, A. Ackerman, D. Wiegel, A. The CellMap Team, Pasolli, H. A. Xu, C. S. Hess, H. F. Serpinskaya, A. S. Zhang, H. F. Lippincott-Schwartz, J. Gelfand, V. I. 2024-06-10 doi:10.1101/2024.06.10.598346 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Latrophilin-2 mediates fluid shear stress mechanotransduction at endothelial junctions ]]> https://biorxiv.org/content/10.1101/2024.06.13.598386v1?rss=1 Tanaka, K. Chen, M. Prendergast, A. Zhuang, Z. Nasiri, A. Joshi, D. Hintzen, J. Chung, M. Kumar, A. Mani, A. Koleske, A. Crawford, J. Nicoli, S. Schwartz, M. A. 2024-06-14 doi:10.1101/2024.06.13.598386 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Children Who Develop Celiac Disease Exhibit Distinct Metabolic Pathways Among Their Gut Microbiota Years Before Diagnosis ]]> https://biorxiv.org/content/10.1101/2024.06.13.598929v1?rss=1 Kelley, K. Dogru, D. Huang, Q. Yang, Y. Palm, N. Ludvigsson, J. ALTINDIS, E. 2024-06-14 doi:10.1101/2024.06.13.598929 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ A Discard-and-Restart MD algorithm for the sampling of realistic protein transition states and enhance structure-based drug discovery ]]> https://biorxiv.org/content/10.1101/2024.06.14.598892v1?rss=1 Ianeselli, A. Howard, J. Gerstein, M. 2024-06-17 doi:10.1101/2024.06.14.598892 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.06.14.598925v1?rss=1 Mato-Blanco, X. Kim, S.-K. Jourdon, A. Ma, S. Tebbenkamp, A. T. N. Liu, F. Duque, A. Vaccarino, F. M. Sestan, N. Colantuoni, C. Rakic, P. Santpere, G. Micali, N. 2024-06-14 doi:10.1101/2024.06.14.598925 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Dopamine D1 receptor expression in dlPFC inhibitory parvalbumin neurons may contribute to higher visuospatial distractibility in marmosets versus macaques ]]> https://biorxiv.org/content/10.1101/2024.06.15.599163v1?rss=1 Joyce, M. K. P. Ivanov, T. G. Krienen, F. Mitchell, J. Ma, S. Inoue, W. Nandy, A. P. Datta, D. Duque, A. Arellano, J. I. Gupta, R. Gonzalez-Burgos, G. Lewis, D. A. Sestan, N. McCarroll, S. A. Martinez-Trujillo, J. C. Froudist-Walsh, S. Arnsten, A. F. 2024-06-16 doi:10.1101/2024.06.15.599163 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2024.06.17.599411v1?rss=1 Chandran, R. R. Vijayaraj, P. Garcia-Milian, R. King, J. Castillo, K. Chen, L. Kwon, Y. Williams, S. Rickabaugh, T. Langerman, J. Choi, W. Sen, C. Lever, J. E. P. Li, Q. Pavelkov, N. Plosa, E. Rowe, S. M. Plath, K. Clair, G. Gomperts, B. 2024-06-22 doi:10.1101/2024.06.17.599411 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline ]]> https://biorxiv.org/content/10.1101/2024.06.18.599438v1?rss=1 Jang, Y. Tomasini, L. Bae, T. Szekely, A. Vaccarino, F. M. Abyzov, A. 2024-06-22 doi:10.1101/2024.06.18.599438 Cold Spring Harbor Laboratory Press 2024-06-22 <![CDATA[ Activation of NLRP3 inflammasome/pyroptosis by protease inhibitor atazanavir at high concentrations is mediated through mitochondrial dysfunction ]]> https://biorxiv.org/content/10.1101/2024.06.18.599585v1?rss=1 Zhou, L. Cosme, M. E. Li, M. Eduafo, V. Amakye, D. Paintsil, E. 2024-06-19 doi:10.1101/2024.06.18.599585 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Optimized Biomechanical Design of a Pulsatile Fontan Conduit for Congenital Heart Palliation ]]> https://biorxiv.org/content/10.1101/2024.06.19.599796v1?rss=1 Emuna, N. Marsden, A. L. Humphrey, J. 2024-06-23 doi:10.1101/2024.06.19.599796 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Nonlinear compliance of NompC gating spring and its implication in mechanotransduction ]]> https://biorxiv.org/content/10.1101/2024.06.20.599842v1?rss=1 Wang, Y. Jin, P. Kumar, A. Jan, L. Cheng, Y. Jan, Y.-N. Zhang, Y. 2024-06-24 doi:10.1101/2024.06.20.599842 Cold Spring Harbor Laboratory Press 2024-06-24 <![CDATA[ MICOS Complex Loss Governs Age-Associated Murine Mitochondrial Architecture and Metabolism in the Liver, While Sam50 Dictates Diet Changes ]]> https://biorxiv.org/content/10.1101/2024.06.20.599846v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@1cdd61corg.highwire.dtl.DTLVardef@a3fb74org.highwire.dtl.DTLVardef@1d1ad36org.highwire.dtl.DTLVardef@c2e55f_HPS_FORMAT_FIGEXP M_FIG C_FIG Liver aging causes metabolic, lipidomic, and mitochondrial structural alterations, reflecting age-dependent losses in the MICOS complex. Key components of the MICOS complex (MIC60, CHCHD3 and CHCHD6) are illustrated. ]]> Vue, Z. Murphy, A. C. Le, H. Neikirk, K. Lopez, E. G. Marshall, A. G. Mungai, M. Jenkins, B. C. Vang, L. Ezedimma, M. Manus, S. A. Whiteside, A. Forni, M. F. Harris, C. Crabtree, A. Albritton, C. F. Jamison, S. Demirci, M. Prasad, P. Oliver, A. Actkins, K. Shao, J. Zaganjor, E. Scudese, E. Rodriguez, B. I. Koh, A. Rabago, I. Moore, J. Nguyen, D. Aftab, M. Kirk, B. Li, Y. Wandira, N. Ahmad, T. Saleem, M. Kadam, A. A. Katti, P. Koh, H.-J. Evans, C. Koo, Y. D. Wang, E. Smith, Q. Tomar, D. Williams, C. R. Sweetwyne, M. T. Quintana, A. Phillips, M. A. 2024-06-25 doi:10.1101/2024.06.20.599846 Cold Spring Harbor Laboratory Press 2024-06-25 <![CDATA[ Using fingerprinting as a testbed for strategies to improve reproducibility of functional connectivity ]]> https://biorxiv.org/content/10.1101/2024.06.21.599225v1?rss=1 Ramduny, J. Vanderwal, T. Kelly, C. 2024-06-25 doi:10.1101/2024.06.21.599225 Cold Spring Harbor Laboratory Press 2024-06-25 <![CDATA[ Increasing the representation of minoritized youth for inclusive and reproducible brain-behavior associations ]]> https://biorxiv.org/content/10.1101/2024.06.22.600221v1?rss=1 Ramduny, J. Uddin, L. Q. Vanderwal, T. Feczko, E. Fair, D. A. Kelly, C. Baskin-Sommers, A. 2024-06-28 doi:10.1101/2024.06.22.600221 Cold Spring Harbor Laboratory Press 2024-06-28 <![CDATA[ Taking stock of selective logging in the Andaman Islands, India: recent & legacy effects of timber extraction, assisted natural regeneration and a revamped working plan ]]> https://biorxiv.org/content/10.1101/2024.06.23.600264v1?rss=1 Surendra, A. Sridhar, V. Osuri, A. M. Ratnam, J. 2024-06-27 doi:10.1101/2024.06.23.600264 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Reduced accrual of mineral-associated organic matter after two years of enhanced rock weathering in cropland soils, though no net losses of soil organic carbon ]]> https://biorxiv.org/content/10.1101/2024.06.23.600278v1?rss=1 Sokol, N. W. Sohng, J. Moreland, K. Slessarev, E. Goertzen, H. Schmidt, R. Samaddar, S. Holzer, I. Almaraz, M. Geoghegan, E. Houlton, B. Montanez, I. Pett-Ridge, J. Scow, K. 2024-06-27 doi:10.1101/2024.06.23.600278 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ A machine learning and drug repurposing approach to target ferroptosis in colorectal cancer stratified by sex and KRAS ]]> https://biorxiv.org/content/10.1101/2024.06.24.600340v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1607205org.highwire.dtl.DTLVardef@ddab12org.highwire.dtl.DTLVardef@10a3885org.highwire.dtl.DTLVardef@4cc4d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yan, H. Shen, X. Yao, Y. Khan, S. Ma, S. JOHNSON, C. 2024-06-28 doi:10.1101/2024.06.24.600340 Cold Spring Harbor Laboratory Press 2024-06-28 <![CDATA[ MAPK Phosphatase-5 is required for TGF-β signaling through a JNK-dependent pathway ]]> https://biorxiv.org/content/10.1101/2024.06.27.600976v1?rss=1 Dorry, S. J. Perla, S. Bennett, A. M. 2024-06-27 doi:10.1101/2024.06.27.600976 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Transpirational water loss from flowers is low but unregulated ]]> https://biorxiv.org/content/10.1101/2024.06.28.600864v1?rss=1 Roddy, A. Schreel, J. Paiva, D. Qin, N. Jiang, G.-F. Brodersen, C. R. Simonin, K. 2024-07-02 doi:10.1101/2024.06.28.600864 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ NREM sleep brain networks modulate cognitive recovery from sleep deprivation ]]> https://biorxiv.org/content/10.1101/2024.06.28.601285v1?rss=1 Lee, K. Wang, Y. Cross, N. Jegou, A. Razavipour, F. Pomares, F. B. Perrault, A. A. Nguyen, A. Aydin, U. Uji, M. Abdallah, C. Anticevic, A. Frauscher, B. Benali, H. Dang-vu, T. T. Grova, C. 2024-07-02 doi:10.1101/2024.06.28.601285 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock ]]> https://biorxiv.org/content/10.1101/2024.06.29.601336v1?rss=1 Mohsen, J. J. Mohsen, M. G. Jiang, K. Landajuela, A. Quinto, L. Isaacs, F. J. Karatekin, E. Slavoff, S. A. 2024-06-29 doi:10.1101/2024.06.29.601336 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ SPACEc: A Streamlined, Interactive Python Workflow for Multiplexed Image Processing and Analysis ]]> https://biorxiv.org/content/10.1101/2024.06.29.601349v1?rss=1 Tan, Y. Kempchen, T. N. Becker, M. Haist, M. Feyaerts, D. Xiao, Y. Su, G. Rech, A. J. Fan, R. Hickey, J. W. Nolan, G. P. 2024-07-02 doi:10.1101/2024.06.29.601349 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions ]]> https://biorxiv.org/content/10.1101/2024.06.30.601407v1?rss=1 188,000 NSCs, we identified a set of HAR perturbations with convergent transcriptional effects on gene networks involved in NSC apicobasal polarity, a cellular process whose precise regulation is critical to the developmental emergence of basal radial glia (bRG), a progenitor population that is expanded in humans. Across multiple HAR perturbations, we found convergent dysregulation of specific apicobasal polarity and adherens junction regulators, including PARD3, ABI2, SETD2, and PCM1. We found that the repression of one candidate from the screen, HAR181, as well as its target gene CADM1, disrupted apical PARD3 localization and NSC rosette formation. Our findings reveal interconnected roles for HARs in NSC biology and cortical development and link specific HARs to processes implicated in human cortical expansion. ]]> Noble, M. A. Ji, Y. Yim, K. M. Yang, J. W. Morales, M. Abu-Shamma, R. Pal, A. Poulsen, R. Baumgartner, M. Noonan, J. P. 2024-07-01 doi:10.1101/2024.06.30.601407 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ Sphingosine kinase 1 is integral for elastin deficiency-induced arterial hypermuscularization ]]> https://biorxiv.org/content/10.1101/2024.07.01.601150v1?rss=1 Saito, J. Dave, J. M. Gallardo-Vara, E. Kabir, I. Tellides, G. Riemer, R. K. Urban, Z. Hla, T. Greif, D. M. 2024-07-03 doi:10.1101/2024.07.01.601150 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Dynamic functional connectivity correlates of trait mindfulness in early adolescence ]]> https://biorxiv.org/content/10.1101/2024.07.01.601544v1?rss=1 Treves, I. N. Marusak, H. A. Decker, A. Kucyi, A. Hubbard, N. A. Bauer, C. C. C. Leonard, J. Grotzinger, H. Giebler, M. A. Camacho Torres, Y. Imhof, A. Romeo, R. Calhoun, V. Gabrieli, J. D. E. 2024-07-04 doi:10.1101/2024.07.01.601544 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ APCCdh1-mediated degradation of Cdh1 is necessary for faithful meiotic chromosome segregation in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.07.01.601619v1?rss=1 Ostapenko, D. Solomon, M. J. 2024-07-03 doi:10.1101/2024.07.01.601619 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Visualizing the translation landscape in human cells at high resolution ]]> https://biorxiv.org/content/10.1101/2024.07.02.601723v1?rss=1 Zheng, W. Zhang, Y. Wang, J. Wang, S. Chai, P. Bailey, E. J. Guo, w. Devarkar, S. C. Wu, S. Lin, J. Zhang, K. Liu, J. Lomakin, I. B. Xiong, Y. 2024-07-05 doi:10.1101/2024.07.02.601723 Cold Spring Harbor Laboratory Press 2024-07-05 <![CDATA[ Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs ]]> https://biorxiv.org/content/10.1101/2024.07.02.601809v1?rss=1 Dong, C. Zhang, F. He, E. Ren, P. Verma, N. Zhu, X. Feng, D. Zhao, H. Chen, S. 2024-07-04 doi:10.1101/2024.07.02.601809 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Drugging Disordered Proteins by Conformational Selection to Inform Therapeutic Intervention ]]> https://biorxiv.org/content/10.1101/2024.07.03.601611v1?rss=1 Levine, Z. A. Bogin, B. A. 2024-07-06 doi:10.1101/2024.07.03.601611 Cold Spring Harbor Laboratory Press 2024-07-06 <![CDATA[ Pathophysiology of hypereosinophilia-associated heart disease ]]> https://biorxiv.org/content/10.1101/2024.07.03.601845v1?rss=1 Sunusi, U. Ziegelmeyer, B. Osuji, I. Medvedovic, M. Todd, H. Abou-Khalil, J. Zimmermann, N. 2024-07-05 doi:10.1101/2024.07.03.601845 Cold Spring Harbor Laboratory Press 2024-07-05 <![CDATA[ Quantification and site-specific analysis of co-occupied N- and O-glycopeptides ]]> https://biorxiv.org/content/10.1101/2024.07.06.602348v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@b14908org.highwire.dtl.DTLVardef@131e812org.highwire.dtl.DTLVardef@17b07cborg.highwire.dtl.DTLVardef@3cb199_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chongsaritsinsuk, J. Rangel-Angarita, V. Mahoney, K. E. Lucas, T. M. Enny, O. M. Katemauswa, M. Malaker, S. A. 2024-07-07 doi:10.1101/2024.07.06.602348 Cold Spring Harbor Laboratory Press 2024-07-07 <![CDATA[ FapR regulates HssRS-mediated heme homeostasis in Bacillus anthracis ]]> https://biorxiv.org/content/10.1101/2024.07.08.602573v1?rss=1 Skaar, E. P. Pi, H. Carlin, S. M. Beavers, W. N. Hillebrand, G. H. Krystofiak, E. S. Stauff, D. L. 2024-07-08 doi:10.1101/2024.07.08.602573 Cold Spring Harbor Laboratory Press 2024-07-08 <![CDATA[ E. coli do not count single molecules ]]> https://biorxiv.org/content/10.1101/2024.07.09.602750v1?rss=1 Mattingly, H. H. Kamino, K. Kottou, R. Ong, J. Emonet, T. Machta, B. B. 2024-07-13 doi:10.1101/2024.07.09.602750 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation ]]> https://biorxiv.org/content/10.1101/2024.07.09.602754v1?rss=1 Kantroo, P. Wagner, G. Machta, B. 2024-07-13 doi:10.1101/2024.07.09.602754 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Dynamic stress- and inflammatory-based regulation of psychiatric risk loci in human neurons ]]> https://biorxiv.org/content/10.1101/2024.07.09.602755v1?rss=1 Retallick-Townsley, K. G. Lee, S. Cartwright, S. Cohen, S. Sen, A. Jia, M. Young, H. Dobbyn, L. Deans, M. Fernandez-Garcia, M. Huckins, L. M. Brennand, K. J. 2024-07-09 doi:10.1101/2024.07.09.602755 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Relaxed selection can speed the evolution of complex adaptations ]]> https://biorxiv.org/content/10.1101/2024.07.09.602773v1?rss=1 Draghi, J. A. Ogbunugafor, C. B. Zaman, L. Parsons, T. 2024-07-09 doi:10.1101/2024.07.09.602773 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Global genomics of the man-o'-war (Physalia) reveal biodiversity at the ocean surface ]]> https://biorxiv.org/content/10.1101/2024.07.10.602499v1?rss=1 Church, S. H. Abedon, R. B. Ahuja, N. Anthony, C. J. Ramirez, D. A. Rojas, L. M. Albinsson, M. E. Alvarez Trasobares, I. Bergemann, R. E. Bogdanovic, O. Burdick, D. R. Cunha, T. J. Damian-Serrano, A. D'Elia, G. Dion, K. Doyle, T. K. Goncalves, J. M. Gonzalez Rajal, A. Haddock, S. H. D. Helm, R. R. Le Gouvello, D. Lewis, Z. R. Magalhaes, B. I. M. M. Manko, M. K. de Mendoza, A. Moura, C. J. Nel, R. Perelman, J. N. Prieto, L. Munro, C. Oguchi, K. Pitt, K. A. Schaeffer, A. Schmidt, A. L. Sellanes, J. Wilson, N. G. Yamamoto, G. Lazo-Wasem, E. Simon, C. Decker, 2024-07-10 doi:10.1101/2024.07.10.602499 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Langerhans cells regulate immunity in adulthood by regulating postnatal dermal lymphatic development ]]> https://biorxiv.org/content/10.1101/2024.07.12.603312v1?rss=1 Sim, J. H. Bell, R. Feng, Z. Chyou, S. Shipman, W. Kataru, R. Ivashkiv, L. Mehrara, B. Lu, T. 2024-07-16 doi:10.1101/2024.07.12.603312 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Beyond Static Models: The Dynamic Interplay of Facial Emotions and Attentional Scope ]]> https://biorxiv.org/content/10.1101/2024.07.15.603432v1?rss=1 Hu, K. He, S. Li, Q. Li, C.-S. 2024-07-16 doi:10.1101/2024.07.15.603432 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ A second wave of Notch signaling diversifies the intestinal secretory lineage ]]> https://biorxiv.org/content/10.1101/2024.07.15.603542v1?rss=1 Zagoren, E. Dias, N. Smith, Z. D. Ameen, N. A. Sumigray, K. 2024-07-16 doi:10.1101/2024.07.15.603542 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ High-motility pro-tumorigenic monocytes drive macrophage enrichment in the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.07.16.603739v1?rss=1 Du, W. Zhou, B. Forjaz, A. Shin, S. M. Wu, F. Crawford, A. J. Nair, P. R. Johnston, A. C. West-Foyle, H. Tang, A. Kim, D. Fan, R. Kiemen, A. L. Wu, P.-H. Phillip, J. M. Ho, W. J. Sanin, D. E. Wirtz, D. 2024-07-18 doi:10.1101/2024.07.16.603739 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Hair cells in the cochlea must tune resonant modes to the edge of instability without destabilizing collective modes ]]> https://biorxiv.org/content/10.1101/2024.07.19.604330v1?rss=1 Momi, A. S. Abbott, M. C. Rubinfien, J. Machta, B. B. Graf, I. R. 2024-07-23 doi:10.1101/2024.07.19.604330 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference ]]> https://biorxiv.org/content/10.1101/2024.07.23.604154v1?rss=1 Dingeldein, L. Silva-Sanchez, D. Evans, L. D'Imprima, E. Grigorieff, N. Covino, R. Cossio, P. 2024-07-24 doi:10.1101/2024.07.23.604154 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Site-specific metabolic labeling reveals proteome-wide phospho-dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.23.604744v1?rss=1 Alevra, M. Correa Marrero, M. Kluever, V. Mandad, S. Hemandhar-Kumar, N. Pan, K.-T. van Gerwen, J. Glowacki, S. K. Wildhagen, H. Ischebeck, T. Liu, Y. RIzzoli, S. O. Urlaub, H. Beltrao, P. Fornasiero, E. F. 2024-07-24 doi:10.1101/2024.07.23.604744 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Sequencing 1206 genomes reveals origin and movement of Aedes aegypti driving increased dengue risk ]]> https://biorxiv.org/content/10.1101/2024.07.23.604830v1?rss=1 Crawford, J. E. Balcazar, D. Redmond, S. Rose, N. H. Youd, H. A. Lucas, E. R. Sudirman Made Ali, R. Al-Nazawi, A. M. Badolo, A. CHEN, C.-H. Cosme, L. V. Henke, J. A. Hung, K. Y. Kluh, S. Liu, W. -L. Maringer, K. Micieli, M. V. Pless, E. Sombie, A. R. Surendran, S. N. Wahid, I. Armbruster, P. A. Weetman, D. McBride, C. S. Gloria-Soria, A. Powell, J. R. White, B. J. 2024-07-24 doi:10.1101/2024.07.23.604830 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Evolutionarily divergent Mycobacterium tuberculosis CTP synthase filaments are under selective pressure ]]> https://biorxiv.org/content/10.1101/2024.07.25.605180v1?rss=1 Lynch, E. M. Lu, Y. Park, J. H. Shao, L. Kollman, J. M. Rego, E. H. 2024-07-25 doi:10.1101/2024.07.25.605180 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ Proliferative arrest induces neuron differentiation and innate immune responses in control and Creutzfeldt-Jakob Disease agent infected rat septal neurons ]]> https://biorxiv.org/content/10.1101/2024.07.26.605349v1?rss=1 pagano, n. aguilar, g. Garcia-Milian, R. manuelidis, l. 2024-07-29 doi:10.1101/2024.07.26.605349 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ AutoMorFi: Automated Whole-image Morphometry in Fiji/ImageJ for Diverse Image Analysis Needs ]]> https://biorxiv.org/content/10.1101/2024.07.26.605357v1?rss=1 Bouadi, O. Yao, C. Zeng, J. Beason, D. Inda, N. Malone, Z. Yoshihara, J. Manjally, A. V. Johnson, C. Cherry, J. Chen, C.-Y. Huang, T.-C. Popovic, B. Henley, M. Liu, G. Kharitonova, E. Zeldich, E. Aichelman, H. Davies, S. W. Walentek, P. Tian, Y. Man, H. Ozsen, E. Harder, K. Gilmore, T. D. Pitt, D. Tay, T. L. 2024-07-27 doi:10.1101/2024.07.26.605357 Cold Spring Harbor Laboratory Press 2024-07-27 <![CDATA[ Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping ]]> https://biorxiv.org/content/10.1101/2024.07.28.605493v1?rss=1 Zhang, D. Rubio Rodriguez-Kirby, L. A. Lin, Y. Song, M. Wang, L. Wang, L. Kanatani, S. Jimenez-Beristain, T. Dang, Y. Zhong, M. Kukanja, P. Wang, S. Chen, X. L. Gao, F. Wang, D. Hang, X. Lou, X. Liu, Y. Chen, J. Sestan, N. Uhlen, P. Kriegstein, A. Zhao, H. Castelo-Branco, G. Fan, R. 2024-07-28 doi:10.1101/2024.07.28.605493 Cold Spring Harbor Laboratory Press 2024-07-28 <![CDATA[ Perceived and observed biases within scientific communities: a case study in movement ecology ]]> https://biorxiv.org/content/10.1101/2024.07.29.605602v1?rss=1 Shaw, A. K. Fouda, L. Mezzini, S. Kim, D. Chatterjee, N. Wolfson, D. Abrahms, B. Attias, N. Beardsworth, C. E. Beltran, R. Binning, S. A. Blincow, K. M. Chan, Y.-C. Fronhofer, E. A. Hegemann, A. Hurme, E. R. Iannarilli, F. Kellner, J. B. McCoy, K. D. Rafiq, K. Saastamoinen, M. Sequeira, A. M. M. Serota, M. W. Sumasgutner, P. Tao, Y. Torstenson, M. Yanco, S. W. Beck, K. B. Bertram, M. G. Beumer, L. T. Bradaric, M. Clermont, J. Ellis-Soto, D. Faltusova, M. Fieberg, J. Hall, R. J. Kolzsch, A. Lai, S. Lee-Cruz, L. Loretto, M.-C. Loveridge, A. Michelangeli, 2024-08-02 doi:10.1101/2024.07.29.605602 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Effects of ketamine on GABAergic and glutamatergic activity in the mPFC: biphasic recruitment of GABA function in antidepressant-like responses ]]> https://biorxiv.org/content/10.1101/2024.07.29.605610v1?rss=1 60 min), in parallel with a transient increase in excitation/inhibition levels (10 min) and lasting enhancement of glutamatergic activity (30-120 min). Previous administration of ketamine enhanced GABA neuron activity during the sucrose splash test (SUST) and novelty suppressed feeding test (NSFT), 24 h and 72 h post-treatment, respectively. Chemogenetic inhibition of GABA interneurons during the surge of GABAergic activity (phase 2), or immediately before the SUST or NSFT, occluded ketamines behavioral actions. These results indicate that time-dependent modulation of GABAergic activity is required for the sustained antidepressant-like responses induced by ketamine, suggesting that approaches to enhance GABAergic plasticity and function are promising therapeutic targets for antidepressant development. ]]> V Fogaca, M. Daher, F. Picciotto, M. 2024-07-30 doi:10.1101/2024.07.29.605610 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Topological mixing and irreversibility in animal chromosome evolution ]]> https://biorxiv.org/content/10.1101/2024.07.29.605683v1?rss=1 Schultz, D. T. Blümel, A. Destanovic, D. Sarigol, F. Simakov, O. 2024-07-30 doi:10.1101/2024.07.29.605683 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Comparative lifespan and healthspan of nonhuman primate species common to biomedical research ]]> https://biorxiv.org/content/10.1101/2024.07.31.606010v1?rss=1 Huber, H. F. Ainsworth, H. C. Quillen, E. E. Salmon, A. Ross, C. Azhar, A. D. Bales, K. Basso, M. A. Coleman, K. Colman, R. Darusman, H. S. Hopkins, B. Hotchkiss, C. E. Jorgensen, M. J. Kavanagh, K. Li, C. Mattison, J. A. Nathanielsz, P. W. Saputro, S. Scorpio, D. G. Sosa, P.-M. Vallender, E. J. Wang, Y. Zeiss, C. J. Shively, C. A. Cox, L. A. 2024-08-01 doi:10.1101/2024.07.31.606010 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Unraveling the Neural Landscape of Mental Disorders using Double Functional Independent Primitives (dFIPs) ]]> https://biorxiv.org/content/10.1101/2024.08.01.606076v1?rss=1 Soleimani, N. Iraji, A. Pearlson, G. D. Preda, A. Calhoun, V. 2024-08-02 doi:10.1101/2024.08.01.606076 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ The Paleozoic assembly of the holocephalian body plan far preceded post-Cretaceous radiations into the ocean depths ]]> https://biorxiv.org/content/10.1101/2024.08.01.606185v1?rss=1 1000 m) ocean waters after the Cretaceous-Paleogene mass extinction, contrasting with the hypothesis that this ecosystem has acted as a refugium of ancient cartilaginous fishes. These invasions were decoupled from the evolution of key features of the holocephalian body plan, including crushing dentition, a single frontal clasper, and holostylic jaw suspension, in the Paleozoic Era, and considerably postdated the appearance of the living familes by 150 million years ago during a major period of biotic turnover in oceans termed the Mesozoic Marine Revolution. These results clarify the origins of living holocephalians as the recent diversification of a single surviving clade among numerous Paleozoic lineages. ]]> Brownstein, C. D. Near, T. J. Dearden, R. P. 2024-08-05 doi:10.1101/2024.08.01.606185 Cold Spring Harbor Laboratory Press 2024-08-05 <![CDATA[ CHRONIC LUNG INFLAMMATION LEADS TO MYELOID SKEWING OF HEMATOPOIETIC STEM CELLS IN A CYSTIC FIBROSIS MOUSE MODEL ]]> https://biorxiv.org/content/10.1101/2024.08.02.606400v1?rss=1 Braga, C. L. Isler Mancuso, R. Thompson, E. N. Öz, H. H. Gudneppanavar, R. Zhang, P.-X. Huang, P. Murray, T. Egan, M. Krause, D. S. Bruscia, E. M. 2024-08-06 doi:10.1101/2024.08.02.606400 Cold Spring Harbor Laboratory Press 2024-08-06 <![CDATA[ Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma ]]> https://biorxiv.org/content/10.1101/2024.08.02.606432v1?rss=1 Goetz, A. Shanahan, F. Brooks, L. Lin, E. Mroue, R. Dela Cruz, D. Hunsaker, T. Czech, B. Dixit, P. Segal, U. Martin, S. Foster, S. A. Gerosa, L. 2024-08-06 doi:10.1101/2024.08.02.606432 Cold Spring Harbor Laboratory Press 2024-08-06 <![CDATA[ Humans use local spectrotemporal correlations to detect rising and falling pitch ]]> https://biorxiv.org/content/10.1101/2024.08.03.606481v1?rss=1 Vaziri, P. A. McDougle, S. D. Clark, D. A. 2024-08-03 doi:10.1101/2024.08.03.606481 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ ERBB2/HOXB13 co-amplification with interstitial deletion of BRCA1 defines a unique subset of breast cancers ]]> https://biorxiv.org/content/10.1101/2024.08.04.605361v1?rss=1 Mitsiades, I. R. Onozato, M. Iafrate, A. J. Hicks, D. Sgroi, D. C. Rheinbay, E. 2024-08-07 doi:10.1101/2024.08.04.605361 Cold Spring Harbor Laboratory Press 2024-08-07 <![CDATA[ Pertpy: an end-to-end framework for perturbation analysis ]]> https://biorxiv.org/content/10.1101/2024.08.04.606516v1?rss=1 Heumos, L. Ji, Y. May, L. Green, T. Zhang, X. Wu, X. Ostner, J. Peidli, S. Schumacher, A. Hrovatin, K. Mueller, M. Chong, F. Sturm, G. Tejada, A. Dann, E. Dong, M. Bahrami, M. Gold, I. Rybakov, S. Namsaraeva, A. Moinfar, A. A. Zheng, Z. Roellin, E. Mekki, I. Sander, C. Lotfollahi, M. Schiller, H. B. Theis, F. J. 2024-08-07 doi:10.1101/2024.08.04.606516 Cold Spring Harbor Laboratory Press 2024-08-07 <![CDATA[ Multiscale heterogeneity of white matter morphometry in psychiatric disorders ]]> https://biorxiv.org/content/10.1101/2024.08.04.606523v1?rss=1 Segal, A. Smith, R. E. Chopra, S. Oldham, S. Parkes, L. Aquino, K. M. Kia, S. M. Wolfers, T. Franke, B. Hoogman, M. Beckmann, C. F. Westlye, L. T. Andreassen, O. A. Zaleskey, A. Ben, H. J. Davey, C. G. Soriano-Mas, C. Cardoner, N. Tiego, J. Yucel, M. Braganza, L. Suo, C. Berk, M. Cotton, S. Bellgrove, M. A. Marquand, A. F. Fornito, A. 2024-08-06 doi:10.1101/2024.08.04.606523 Cold Spring Harbor Laboratory Press 2024-08-06 <![CDATA[ Mfn2 induces NCLX-mediated calcium release from mitochondria. ]]> https://biorxiv.org/content/10.1101/2024.08.05.606704v1?rss=1 Kolitsida, P. Saha, A. Caliri, A. W. Assali, E. Riera, A. M. Itskanov, S. Magana, C. S. Stork, B. Shirihai, O. S. Sekler, I. Koehler, C. M. van der Bliek, A. M. 2024-08-06 doi:10.1101/2024.08.05.606704 Cold Spring Harbor Laboratory Press 2024-08-06 <![CDATA[ Cysteine depletion triggers adipose tissue thermogenesis and weight-loss. ]]> https://biorxiv.org/content/10.1101/2024.08.06.606880v1?rss=1 Lee, A. Orliaguet, L. Youm, Y.-H. Maeda, R. Dlugos, T. Lei, Y. Coman, D. Shchukina, I. Andhey, P. S. Smith, S. R. Ravussin, E. Stadler, K. Hyder, F. Artyomov, M. N. Sugiura, Y. Dixit, V. D. 2024-08-08 doi:10.1101/2024.08.06.606880 Cold Spring Harbor Laboratory Press 2024-08-08 <![CDATA[ Unifying regulatory motifs in endocrine circuits ]]> https://biorxiv.org/content/10.1101/2024.08.06.606903v1?rss=1 Raz, M. Glass, D. S. Milo, T. Kohanim, Y. K. karin, O. Tendler, A. Mayo, A. Alon, U. 2024-08-08 doi:10.1101/2024.08.06.606903 Cold Spring Harbor Laboratory Press 2024-08-08 <![CDATA[ Coevolving Residues Distant from the Ligand Binding Site are Involved in GAF Domain Function ]]> https://biorxiv.org/content/10.1101/2024.08.07.605472v1?rss=1 Ahmed, W. S. Geethakumari, A. M. Sultana, A. Tiwari, A. Altamash, T. Arshad, N. Visweswariah, S. S. Biswas, K. H. 2024-08-07 doi:10.1101/2024.08.07.605472 Cold Spring Harbor Laboratory Press 2024-08-07 <![CDATA[ Structure and function of the human apoptotic scramblase Xkr4 ]]> https://biorxiv.org/content/10.1101/2024.08.07.607004v1?rss=1 Accardi, A. Chakraborty, S. Feng, Z. Lee, S. Alvarenga, O. E. Panda, A. Bruni, R. Khelashvili, G. Gupta, K. 2024-08-09 doi:10.1101/2024.08.07.607004 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ Confidence and insight into working memories are shaped by attention and recent performance ]]> https://biorxiv.org/content/10.1101/2024.08.09.607293v1?rss=1 Chekroud, S. R. Nobre, A. C. Kolling, N. 2024-08-09 doi:10.1101/2024.08.09.607293 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ The Performance and Potential of Deep Learning for Predicting Species Distributions ]]> https://biorxiv.org/content/10.1101/2024.08.09.607358v1?rss=1 Kellenberger, B. A. Winner, K. Jetz, W. 2024-08-09 doi:10.1101/2024.08.09.607358 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ Transcriptional analysis of efferocytosis in mouse skin wounds ]]> https://biorxiv.org/content/10.1101/2024.08.12.607219v1?rss=1 Krause, W. S. W. King, D. Horsley, V. 2024-08-13 doi:10.1101/2024.08.12.607219 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating ]]> https://biorxiv.org/content/10.1101/2024.08.12.607667v1?rss=1 Liu, P. Pan, Y. Chang, H.-C. Fang, Y. Xue, X. Zou, J. Toothaker, J. M. Olaloye, O. Santiago, E. G. McCourt, B. Mitsialis, V. Presicce, P. Kallapur, S. G. Snapper, S. B. Liu, J.-J. Tseng, G. Konnikova, L. Liu, S. 2024-08-15 doi:10.1101/2024.08.12.607667 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Single-cell analysis identifies distinct CD4+ T cells associated with the pathobiology of pediatric obesity-related asthma ]]> https://biorxiv.org/content/10.1101/2024.08.13.607447v1?rss=1 Thompson, D. Wabara, Y. Duran, S. Reichenbach, A. Chen, L. Collado, K. Yon, C. Greally, J. M. Rastogi, D. 2024-08-16 doi:10.1101/2024.08.13.607447 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Audiomotor prediction errors drive speech adaptation even in the absence of overt movement ]]> https://biorxiv.org/content/10.1101/2024.08.13.607718v1?rss=1 Parrell, B. Naber, C. Kim, O. A. Niziolek, C. A. McDougle, S. D. 2024-08-16 doi:10.1101/2024.08.13.607718 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Vesiculation pathways in clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/2024.08.13.607731v1?rss=1 Wang, X. Berro, J. Ma, R. 2024-08-13 doi:10.1101/2024.08.13.607731 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Axonal mitochondria regulate gentle touch response through control of axonal actin dynamics ]]> https://biorxiv.org/content/10.1101/2024.08.13.607780v1?rss=1 Hegde, S. Modi, S. Deih, E. W. Glomb, O. V. Yogev, S. Hoerndli, F. Koushika, S. P. 2024-08-13 doi:10.1101/2024.08.13.607780 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data ]]> https://biorxiv.org/content/10.1101/2024.08.13.607784v1?rss=1 Simmons, S. K. Adiconis, X. Haywood, N. Parker, J. Lin, Z. Liao, Z. Tuncali, I. Al'Khafaji, A. Shin, A. Jagadeesh, K. Gosik, K. Gatzen, M. Smith, J. T. El Kodsi, D. N. Kuras, Y. Baecher-Allan, C. Serrano, G. E. Beach, T. G. Garimella, K. Rozenblatt-Rosen, O. Regev, A. Dong, X. Scherzer, C. Levin, J. Z. 2024-08-16 doi:10.1101/2024.08.13.607784 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ alpha-Actinin-3 deficiency protects from the effects of acute cold exposure through altered skeletal muscle Ca2+ and OXPHOS signaling. ]]> https://biorxiv.org/content/10.1101/2024.08.14.605938v1?rss=1 Houweling, P. J. Tiong, C. F. Kiriaev, L. Diaz-Pena, R. Albers, P. K. Wood, H. Wyckelsma, V. Stait, T. Venckunas, T. Valenzuela, P. Castillo-Garcia, A. Brazaitis, M. Berman, Y. Seto, J. T. Westerblad, H. Lek, M. Thorburn, D. Lucia, A. Head, S. North, K. N. 2024-08-15 doi:10.1101/2024.08.14.605938 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Neural mechanisms of awareness of action ]]> https://biorxiv.org/content/10.1101/2024.08.15.608153v1?rss=1 Jin, D. S. Agdali, O. Yadav, T. Kronemer, S. I. Kunkler, S. Majumder, S. Khurana, M. McCusker, M. C. Fu, I. Khalaf, A. Christison-Lagay, K. L. Aerts, S. L. Xin, Q. Li, J.-J. McGill, S. H. Crowley, M. J. Blumenfeld, H. 2024-08-19 doi:10.1101/2024.08.15.608153 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Electron tomography visualization of HIV-1 virions trapped by fusion inhibitors to host cells in infected tissues ]]> https://biorxiv.org/content/10.1101/2024.08.19.608557v1?rss=1 Bjorkman, P. J. Ladinsky, M. S. Zhu, L. Ullah, I. Uchil, P. D. Kumar, P. Kay, M. S. 2024-08-19 doi:10.1101/2024.08.19.608557 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus ]]> https://biorxiv.org/content/10.1101/2024.08.19.608685v1?rss=1 Yang, Y. Yan, J. Olson, R. Jiang, X. 2024-08-20 doi:10.1101/2024.08.19.608685 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ An in vivo screen identifies NAT10 as a master regulator of brain metastasis ]]> https://biorxiv.org/content/10.1101/2024.08.20.608711v1?rss=1 Chen, J. F. Xu, P. Cai, W. L. Chen, H. Wingrove, E. Li, W. Biancon, G. Zhang, M. Balabaki, A. Krop, E. D. Zhang, Y. Yin, M. Tebaldi, T. Meier, J. L. Westbrook, T. F. Halene, S. Liu, Y. Nguyen, D. Yan, Q. 2024-08-21 doi:10.1101/2024.08.20.608711 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ In utero human intestine contains maternally derived bacterial metabolites ]]> https://biorxiv.org/content/10.1101/2024.08.20.608888v1?rss=1 Wang, W. Gu, W. Schweitzer, R. Koren, O. Khatib, S. Tseng, G. Konnikova, L. 2024-08-21 doi:10.1101/2024.08.20.608888 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Spatial and morphological organization of mitochondria across a connectome ]]> https://biorxiv.org/content/10.1101/2024.08.21.608912v1?rss=1 Sager, G. Pallasdies, F. C. Gowers, R. Ravikumar, S. Wu, E. Colon-Ramos, D. Schreiber, S. Clark, D. A. 2024-08-21 doi:10.1101/2024.08.21.608912 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Investigation of pair-wise single-cell interactions by statistically interpreting spatial cell state correlation learned by self-supervised graph inductive bias transformer ]]> https://biorxiv.org/content/10.1101/2024.08.21.608964v1?rss=1 Xiao, X. 2024-08-22 doi:10.1101/2024.08.21.608964 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Zfp263 is a transcriptional checkpoint of neutrophil development ]]> https://biorxiv.org/content/10.1101/2024.08.22.609132v1?rss=1 Devaprasad, A. Ai, Z. Mukherjee, A. K. Panczel, A. Khoyratty, T. Ballesteros, I. Rubio-Ponce, A. Grinsven, E. v. Wang, L. Gomez, J. S. Eames, H. L. Hidalgo, A. Mocsai, A. Udalova, I. A. 2024-08-22 doi:10.1101/2024.08.22.609132 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Regulation of angiogenesis by signal sequence-derived peptides ]]> https://biorxiv.org/content/10.1101/2024.08.22.609269v1?rss=1 Ghim, M. Wei, L. Jung, J.-J. The, E. Kukreja, G. Neishabouri, A. Ahmad, A. Raza, M. Z. Golbazi, A. Hedayatyanfard, K. Nie, L. Zhang, J. Sadeghi, M. M. 2024-08-23 doi:10.1101/2024.08.22.609269 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Structural and functional dissection of the Pacinian corpuscle reveals an active role of the inner core in touch detection ]]> https://biorxiv.org/content/10.1101/2024.08.24.609509v1?rss=1 Ziolkowski, L. H. Nikolaev, Y. A. Chikamoto, A. Oda, M. Feketa, V. V. Monedero-Alonso, D. Ardasheva, S. A. Bae, S. S. Xu, C. S. Pang, S. Gracheva, E. O. Bagriantsev, S. N. 2024-08-26 doi:10.1101/2024.08.24.609509 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ VISTA Uncovers Missing Gene Expression and Spatial-induced Information for Spatial Transcriptomic Data Analysis ]]> https://biorxiv.org/content/10.1101/2024.08.26.609718v1?rss=1 Liu, T. Lin, Y. Luo, X. Sun, Y. Zhao, H. 2024-08-27 doi:10.1101/2024.08.26.609718 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ Prewetting couples membrane and protein phase transitions to greatly enhance coexistence in models and cells. ]]> https://biorxiv.org/content/10.1101/2024.08.26.609758v1?rss=1 Bagheri, Y. Rouches, M. Machta, B. Veatch, S. L. 2024-08-27 doi:10.1101/2024.08.26.609758 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ Vibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-dispersal activity against Vibrio Polysaccharide (VPS) ]]> https://biorxiv.org/content/10.1101/2024.08.27.609776v1?rss=1 Weeresekera, R. Moreau, A. Huang, X. Nam, K.-M. Hinbest, A. Huynh, Y. Liu, X. Ashwood, C. Pepi, L. E. Cegelski, L. Yan, J. Olson, R. 2024-08-27 doi:10.1101/2024.08.27.609776 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ Modeling Decision-Making Under Uncertainty with Qualitative Outcomes ]]> https://biorxiv.org/content/10.1101/2024.08.27.609831v1?rss=1 Korem, N. Duek, O. Jia, R. Wertheimer, E. Metviner, S. Grubb, M. Levy, I. 2024-08-28 doi:10.1101/2024.08.27.609831 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC ]]> https://biorxiv.org/content/10.1101/2024.08.27.609961v1?rss=1 Richard, J. Grunst, M. W. Niu, L. Diaz-Salinas, M. A. Tolbert, W. D. Marchitto, L. Zhou, F. Bourassa, C. Yang, D. Chiu, T.-J. Chen, H.-C. Benlarbi, M. Beaudoin-Bussieres, G. Gottumukkala, S. Li, W. Dionne, K. Belanger, E. Chatterjee, D. Medjahed, H. Hendrickson, W. A. Sodroski, J. Lang, Z. C. Morton, A. J. Huang, R. K. Matthies, D. Smith, A. B. Mothes, W. Munro, J. Pazgier, M. Finzi, A. 2024-08-27 doi:10.1101/2024.08.27.609961 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks ]]> https://biorxiv.org/content/10.1101/2024.08.27.609993v1?rss=1 Koonce, N. L. Emerson, S. E. Bhaskar, D. Kuchroo, M. Moyle, M. W. Arroyo-Morales, P. Martinez, N. V. Krishnaswamy, S. Mohler, W. Colon-Ramos, D. 2024-08-27 doi:10.1101/2024.08.27.609993 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ Gain-of-function study reveals the pleiotropic roles of serine protease HtrA in Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2024.08.28.610130v1?rss=1 Zhang, K. Sze, C. W. Zhao, H. Liu, J. Li, C. 2024-08-28 doi:10.1101/2024.08.28.610130 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Role of AMPK in Atrial Metabolic Homeostasis and Substrate Preference ]]> https://biorxiv.org/content/10.1101/2024.08.29.608789v1?rss=1 Toksoy, Z. Ma, Y. Goedeke, L. Li, W. V. Hu, X. Wu, X. Cacheux, M. Liu, Y. Akar, F. G. Shulman, G. I. Young, L. H. 2024-08-30 doi:10.1101/2024.08.29.608789 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ The C2 domain augments Ras GTPase Activating Protein catalytic activity ]]> https://biorxiv.org/content/10.1101/2024.08.29.609784v1?rss=1 Paul, M. E. Chen, D. Vish, K. J. Lartey, N. L. Hughes, E. Freeman, Z. T. Saunders, T. Stiegler, A. L. King, P. D. Boggon, T. J. 2024-08-29 doi:10.1101/2024.08.29.609784 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Genomically recoded Escherichia coli with optimized functional phenotypes ]]> https://biorxiv.org/content/10.1101/2024.08.29.610322v1?rss=1 Isaacs, F. Hemez, C. Mohler, K. Radford, F. Moen, J. Rinehart, J. 2024-08-29 doi:10.1101/2024.08.29.610322 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ A Phylogenetic Model of Established and Enabled Biome Shifts ]]> https://biorxiv.org/content/10.1101/2024.08.30.610561v1?rss=1 McHugh, S. W. Donoghue, M. Landis, M. J. 2024-09-02 doi:10.1101/2024.08.30.610561 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Systemic in utero gene editing as a treatment for cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2024.09.04.611031v1?rss=1 Ricciardi, A. S. Barone, C. Putman, R. Quijano, E. Gupta, A. Nguyen, R. Mandl, H. Piotrowski-Daspit, A. S. Lopez-Giraldez, F. Luks, V. Freedman-Weiss, M. R. Farrelly, J. S. Ahle, S. Glazer, P. M. Saltzman, W. M. Stitelman, D. H. Egan, M. E. 2024-09-08 doi:10.1101/2024.09.04.611031 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Widespread Associations between Behavioral Metrics and Brain Microstructure in ASD ]]> https://biorxiv.org/content/10.1101/2024.09.04.611183v1?rss=1 Ressa, H. Newman, B. T. Jacokes, Z. McPartland, J. Kleinhans, N. M. Druzgal, T. J. Pelphrey, K. A. Van Horn, J. D. the GENDAAR Research Consortium, 2024-09-06 doi:10.1101/2024.09.04.611183 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes ]]> https://biorxiv.org/content/10.1101/2024.09.04.611290v1?rss=1 Shinde, P. Willemsen, L. Anderson, M. Aoki, M. Basu, S. Burel, J. G. Cheng, P. Dastidar, S. G. Dunleavy, A. Einav, T. Forschmiedt, J. Fourati, S. Garcia, J. Gibson, W. Greenbaum, J. A. Guan, L. Guan, W. Gygi, J. P. Ha, B. Hou, J. Hsiao, J. Huang, Y. Jansen, R. Kakoty, B. Kang, Z. Kobie, J. J. Kojima, M. Konstorum, A. Lee, J. Lewis, S. A. Li, A. Lock, E. F. Mahita, J. Mendes, M. Meng, H. Neher, A. Nili, S. Orfield, S. Overton, J. Pai, N. Parker, C. Qian, B. Rasmussen, M. Reyna, J. Richardson, E. Safo, S. Sorenson, J. Srinivasan, A. Thrupp, N. Tip 2024-09-08 doi:10.1101/2024.09.04.611290 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ A trans-synaptic IgLON adhesion molecular complex directly contacts and clusters a nicotinic receptor ]]> https://biorxiv.org/content/10.1101/2024.09.05.611427v1?rss=1 Mialon, M. Patrash, L. Weinreb, A. Ozkan, E. Bessereau, J.-L. Pinan-Lucarre, B. 2024-09-10 doi:10.1101/2024.09.05.611427 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Dynamic and structural insights into allosteric regulation on MKP5 a dual-specificity phosphatase ]]> https://biorxiv.org/content/10.1101/2024.09.05.611520v1?rss=1 Skeens, E. Maschietto, F. Ramu, M. Shillingford, S. Lolis, E. J. Batista, V. S. Bennett, A. M. Lisi, G. P. 2024-09-05 doi:10.1101/2024.09.05.611520 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Variation in moment-to-moment brain state engagement changes across development and contributes to individual differences in executive function ]]> https://biorxiv.org/content/10.1101/2024.09.06.611627v1?rss=1 3000). SEV developmental trajectories stabilize around mid-adolescence, with timing varying by sex and brain state. SEV successfully predicts executive function (EF) in youths from an independent dataset. Worse EF is further linked to alterations in SEV development. These converging findings suggest SEV changes over development, allowing individuals to flexibly recruit various brain states to meet evolving needs. ]]> Ye, J. Tejavibulya, L. Dai, W. Cope, L. M. Hardee, J. E. Heitzeg, M. M. Lichenstein, S. Yip, S. W. Banaschewski, T. Baker, G. J. Bokde, A. L. W. Brühl, R. Desrivieres, S. Flor, H. Gowland, P. Grigis, A. Heinz, A. Martinot, J.-L. Martinot, M.-L. P. Artiges, E. Nees, F. Orfanos, D. P. Poustka, L. Hohmann, S. Holz, N. Baeuchl, C. Smolka, M. N. Vaidya, N. Walter, H. Whelan, R. Schumann, G. Garavan, H. Chaarani, B. Gee, D. G. Baskin-Sommers, A. Casey, B. IMAGEN consortium, Scheinost, D. 2024-09-11 doi:10.1101/2024.09.06.611627 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Nodal Modulator (NOMO) is a force-bearing transmembrane protein required for muscle differentiation ]]> https://biorxiv.org/content/10.1101/2024.09.06.611727v1?rss=1 Naughton, B. Devarkar, S. C. Mallik, S. Oxendine, S. Junnarkar, S. Ren, Y. Todorow, V. Berro, J. Kirstein, J. Xiong, Y. Schlieker, C. 2024-09-07 doi:10.1101/2024.09.06.611727 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ A Nerve-Fibroblast Axis in Mammalian Lung Fibrosis ]]> https://biorxiv.org/content/10.1101/2024.09.09.611003v1?rss=1 Ishikawa, G. Peng, X. McGovern, J. Ghincea, A. Woo, S. Okuno, D. Yu, S. Lee, C. J. Liu, A. Saber, T. Hu, B. Sun, Y. Sun, H. Jumaily, K. A. Feghali-Bostwick, C. Sumida, T. S. Sauler, M. Ryu, C. Herzog, E. L. 2024-09-09 doi:10.1101/2024.09.09.611003 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon ]]> https://biorxiv.org/content/10.1101/2024.09.09.611954v1?rss=1 Cabrera-Sosa, L. Safarpour, M. Kattenberg, J. H. Ramirez, R. Vinetz, J. M. Rosanas-Urgell, A. Gamboa, D. Delgado-Ratto, C. 2024-09-09 doi:10.1101/2024.09.09.611954 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ High-quality peptide evidence for annotating non-canonical open reading frames as human proteins ]]> https://biorxiv.org/content/10.1101/2024.09.09.612016v1?rss=1 Deutsch, E. W. Kok, L. W. Mudge, J. M. Ruiz-Orera, J. Fierro-Monti, I. Sun, Z. Abelin, J. G. Alba, M. M. Aspden, J. L. Bazzini, A. A. Bruford, E. Brunet, M. A. Calviello, L. Carr, S. A. Carvunis, A.-R. Chothani, S. Clauwaert, J. Dean, K. Faridi, P. Frankish, A. Hubner, N. Ingolia, N. Magrane, M. Martin, M. J. Martinez, T. F. Menschaert, G. Ohler, U. Orchard, S. Rackham, O. Roucou, X. Slavoff, S. A. Valen, E. Wacholder, A. C. Weissman, J. S. Wu, W. Xie, Z. Choudhary, J. Bassani-Sternberg, M. Vizcaino, J. A. Ternette, N. Moritz, R. L. Prensner, J. van He 2024-09-09 doi:10.1101/2024.09.09.612016 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ The myokine FGF21 associates with enhanced survival in ALS and mitigates stress-induced cytotoxicity ]]> https://biorxiv.org/content/10.1101/2024.09.11.611693v1?rss=1 Guha, A. Si, Y. Smith, R. Kazamel, M. Jiang, N. Smith, K. A. Thalacker-Mercer, A. Singh, B. K. Ho, R. Anadrabi, S. Pereira, J. D. T. D. S. Salgado, J. S. Agrawal, M. Velic, E. H. King, P. H. 2024-09-14 doi:10.1101/2024.09.11.611693 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin ]]> https://biorxiv.org/content/10.1101/2024.09.12.612526v1?rss=1 Menon, V. Garcia-Ruiz, A. Neveu, S. Cartmel, B. Ferrucci, L. M. Palmatier, M. Ko, C. Tsai, K. Y. Nakamura, M. Kim, S. R. Girardi, M. Kornacker, K. Brash, D. 2024-09-16 doi:10.1101/2024.09.12.612526 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1 ]]> https://biorxiv.org/content/10.1101/2024.09.12.612660v1?rss=1 Tsemperouli, M. Kumar Cheppali, S. Rivera Molina, F. Chetrit, D. Landajuela, A. Toomre, D. Karatekin, E. 2024-09-12 doi:10.1101/2024.09.12.612660 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Stabilization of fluctuating population dynamics via the evolution of dormancy ]]> https://biorxiv.org/content/10.1101/2024.09.12.612663v1?rss=1 Miller, Z. R. Vasseur, D. A. Hull, P. M. 2024-09-17 doi:10.1101/2024.09.12.612663 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Transdiagnostic Symptom Domains are Associated with Head Motion During Multimodal Imaging in Children ]]> https://biorxiv.org/content/10.1101/2024.09.13.612668v1?rss=1 Hercules, K. Liu, Z. Wei, J. Venegas, G. Ciocca, O. Dyer, A. Lee, G. Santini-Bishop, S. Shappell, H. Gee, D. G. Sukhodolsky, D. G. Ibrahim, K. 2024-09-16 doi:10.1101/2024.09.13.612668 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Cytoplasmic ribosomes hitchhike on mitochondria to dendrites ]]> https://biorxiv.org/content/10.1101/2024.09.13.612863v1?rss=1 Renken, C. J. Kim, S. Wu, Y. Hammarlund, M. Yogev, S. 2024-09-13 doi:10.1101/2024.09.13.612863 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ A workflow for microclimate sensor networks: integrating geographic tools, statistics, and local knowledge ]]> https://biorxiv.org/content/10.1101/2024.09.13.612939v1?rss=1 Klinges, D. H. Lembrechts, J. Van de Vondel, S. Greenlee, E. Hayles-Cotton, K. Senior, R. 2024-09-19 doi:10.1101/2024.09.13.612939 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Filter bank common spatial pattern and envelope-based features in multimodal EEG-fTCD brain-computer interfaces ]]> https://biorxiv.org/content/10.1101/2024.09.15.613144v1?rss=1 Khalaf, A. Essam, A.-A. Ibrahim, A. Zanqour, A. El-Saqa, M. Mohamed, S. Anwar, A. Eldeib, A. Akcakaya, M. 2024-09-19 doi:10.1101/2024.09.15.613144 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Rapid adaptation to a globally introduced virulent pathogen in a keystone species ]]> https://biorxiv.org/content/10.1101/2024.09.16.613142v1?rss=1 95% mortality during epizootics. Recently, survival from plague has been documented in a small number of black-tailed prairie dogs (C. ludovicianus) in natural populations in Colorado (USA). We performed whole-genome sequencing on 7 individuals from 3 colonies that survived infection with plague and 7 individuals from the same colonies that likely died during a plague epizootic. Using genome-wide association tests, FST outlier tests, and other inferences of selection, we detected SNPs on 5 scaffolds that were strongly associated with survivorship from plague in the wild. Some genes associated with these scaffolds also differ in humans that survived versus died in the plague pandemic in London, UK, suggesting conservation of gene function across taxonomically diverse lineages. Understanding the genetic basis of immunity can enable genetically-informed management actions such as targeted relocation to protect prairie dogs and the species that rely on them. More generally, understanding how rapid adaptation to pathogens occurs can help us predict the time frame and spatial scale at which adaptation may occur, during which other interventions are needed. Significance StatementEmerging infectious diseases are one of the foremost threats to global biodiversity, causing extinctions and population crashes on all continents. Introduced pathogens can exert strong selection on hosts for the evolution of tolerance or resistance, yet these evolutionary events are rare and it remains challenging to identify and sample both immune and susceptible individuals during an epizootic. This study leverages one of the only documented examples of prairie dogs surviving infection from introduced sylvatic plague in nature and compares their genomes to those of individuals that perished. We find strong signatures of selection in a small number of immune and non-immune genes, one of which has been implicated in survival from plague in humans. These findings suggest that adaptation to novel pathogens may occur via a combination of conserved genes and the co-opting of genes outside of classical immune pathways. Finally, it provides evidence that in native species with sufficient standing genetic variation, there is potential for adaptation to introduced pathogens. ]]> Cassin-Sackett, L. Tsuchiya, M. T. N. Dikow, R. B. 2024-09-20 doi:10.1101/2024.09.16.613142 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors ]]> https://biorxiv.org/content/10.1101/2024.09.16.613227v1?rss=1 Guo, S. Karatepe, K. Mafra de Faria, B. zhang, j. Chen, X. Pinto, H. Fyodorov, D. Sefik, E. Willcockson, M. Flavell, R. Skoultchi, A. I. 2024-09-16 doi:10.1101/2024.09.16.613227 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Glycosite Mapping and in situ Mass Spectrometry Imaging of MUC2 Glycopeptides via On-slide Digestion with Mucinase StcE ]]> https://biorxiv.org/content/10.1101/2024.09.16.613285v1?rss=1 Lowery, S. C. Tran, I. P. Grimsley, G. Stubler, R. Mahoney, K. E. Lucas, T. M. Charkoftaki, G. Santos-Neto, A. Varki, N. Vasiliou, V. Drake, R. R. Malaker, S. A. 2024-09-20 doi:10.1101/2024.09.16.613285 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment ]]> https://biorxiv.org/content/10.1101/2024.09.16.613301v1?rss=1 Dokmai, N. Zhu, K. Sahinalp, S. C. Cho, H. 2024-09-20 doi:10.1101/2024.09.16.613301 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Shared subcortical arousal systems across sensory modalities during transient modulation of attention ]]> https://biorxiv.org/content/10.1101/2024.09.16.613316v1?rss=1 Khalaf, A. Lopez, E. Li, J. Horn, A. Edlow, B. Blumenfeld, H. 2024-09-16 doi:10.1101/2024.09.16.613316 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ RalB uncoupled exocyst mediates endothelial Weibel-Palade body exocytosis ]]> https://biorxiv.org/content/10.1101/2024.09.16.613344v1?rss=1 Yang, M. Boye-Doe, A. Abosabie, S. A. S. Barr, A. M. Mendez, L. M. Sharda, A. V. 2024-09-16 doi:10.1101/2024.09.16.613344 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates ]]> https://biorxiv.org/content/10.1101/2024.09.17.613401v1?rss=1 Senavirathna, I. Jayasundara, D. Warnasekara, J. Agampodi, S. B. Putz, E. J. Nally, J. E. Bayles, D. O. Chaurasia, R. Vinetz, J. M. 2024-09-17 doi:10.1101/2024.09.17.613401 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Optical photothermal infrared imaging using metabolic probes in biological systems ]]> https://biorxiv.org/content/10.1101/2024.09.19.613881v1?rss=1 Shuster, S. O. Curtis, A. E. Davis, C. M. 2024-09-22 doi:10.1101/2024.09.19.613881 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS ]]> https://biorxiv.org/content/10.1101/2024.09.19.613975v1?rss=1 Xu, J. Zhu, K. Cai, J. Kockan, C. Dokmai, N. Cho, H. Woodruff, D. Sahinalp, C. 2024-09-24 doi:10.1101/2024.09.19.613975 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ hiPSC-derived astrocytes from individuals with schizophrenia promote alterations in phagocytosis and chemotaxis of microglial-like cells ]]> https://biorxiv.org/content/10.1101/2024.09.20.614161v1?rss=1 Cardozo, P. L. Lee, C.-Y. Lacerda, J. P. S. Fahel, J. S. Trindade, P. Vitoria, G. Chicaybam, L. Cordeiro, R. C. de Faria, I. J. S. Silva, N. C. Todjro, Y. M. H. Maciel, J. C. d. P. Bonamino, M. H. Vieira, L. B. Cruz, B. F. Nicolato, R. Brennand, K. J. Rehen, S. K. Ribeiro, F. M. 2024-09-21 doi:10.1101/2024.09.20.614161 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Postnatal Enrichment Corrects Deficits in Perineuronal Net Formation and Reversal Learning in Adult Mice Exposed to Early Adversity ]]> https://biorxiv.org/content/10.1101/2024.09.21.614236v1?rss=1 Jamwal, S. Islam, R. MacDowell Kaswan, Z. Bowers, C. Giuliano, L. Kaffman, A. 2024-09-23 doi:10.1101/2024.09.21.614236 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Assessment of the relationship between synaptic density and metabotropic glutamate receptors in early Alzheimer's disease: a multi-tracer PET study ]]> https://biorxiv.org/content/10.1101/2024.09.21.614277v1?rss=1 Salardini, E. O'Dell, R. S. Tchorz, E. Nabulsi, N. B. Huang, Y. Carson, R. E. van Dyck, C. H. Mecca, A. P. 2024-09-24 doi:10.1101/2024.09.21.614277 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Effects of age on resting-state cortical networks ]]> https://biorxiv.org/content/10.1101/2024.09.23.614004v1?rss=1 Gohil, C. Kohl, O. Pitt, J. van Es, M. W. J. Quinn, A. J. Vidaurre, D. Turner, M. R. Nobre, A. C. Woolrich, M. W. 2024-09-24 doi:10.1101/2024.09.23.614004 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources ]]> https://biorxiv.org/content/10.1101/2024.09.23.614539v1?rss=1 Zhao, J. Zhang, X. Wang, G. Lin, Y. Liu, T. Chang, R. Zhao, H. 2024-09-25 doi:10.1101/2024.09.23.614539 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Complex genetic variation in nearly complete human genomes ]]> https://biorxiv.org/content/10.1101/2024.09.24.614721v1?rss=1 Logsdon, G. A. Ebert, P. Audano, P. A. Loftus, M. Porubsky, D. Ebler, J. Yilmaz, F. Hallast, P. Prodanov, T. Yoo, D. Paisie, C. A. Harvey, W. T. Zhao, X. Martino, G. V. Henglin, M. Munson, K. M. Rabbani, K. Chin, C.-S. Gu, B. Ashraf, H. Austine-Orimoloye, O. Balachandran, P. Bonder, M. J. Cheng, H. Chong, Z. Crabtree, J. Gerstein, M. Guethlein, L. A. Hasenfeld, P. Hickey, G. Hoekzema, K. Hunt, S. E. Jensen, M. Jiang, Y. Koren, S. Kwon, Y. Li, C. Li, H. Li, J. Norman, P. J. Oshima, K. K. Paten, B. Phillippy, A. M. Pollock, N. R. Rausch, T. Rautiainen 2024-09-25 doi:10.1101/2024.09.24.614721 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination ]]> https://biorxiv.org/content/10.1101/2024.09.24.614732v1?rss=1 Wu, L. Yadavalli, A. D. Rodrigues, G. Xu, D. Pintado-Urbanc, A. Simon, M. Wu, W. Nussenzweig, A. Schatz, D. 2024-09-26 doi:10.1101/2024.09.24.614732 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Location-biased β-arrestin conformations direct GPCR signaling ]]> https://biorxiv.org/content/10.1101/2024.09.24.614742v1?rss=1 Pham, U. Chundi, A. Stepniewski, T. M. Darbha, S. Eiger, D. S. Gazula, S. Gardner, J. Hicks, C. Selent, J. Rajagopal, S. 2024-09-26 doi:10.1101/2024.09.24.614742 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Disruption of the Social Visual Pathway in Autism Spectrum Disorder ]]> https://biorxiv.org/content/10.1101/2024.09.24.614813v1?rss=1 Li, C. Park, H. Awasthi, J. Rolison, M. Li, M. Scheinost, D. Chawarska, K. Hampson, M. 2024-09-25 doi:10.1101/2024.09.24.614813 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Cataloguing the postnatal small intestinal transcriptome during the period of susceptibility to necrotizing enterocolitis ]]> https://biorxiv.org/content/10.1101/2024.09.25.612672v1?rss=1 Oliveria, L. F. S. Wu, Y.-S. Dasuri, V. S. Harrington, A. W. Olaloye, O. Goldsmith, J. D. Breault, D. T. Konnikova, L. O'Connell, A. E. 2024-09-28 doi:10.1101/2024.09.25.612672 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Identification of Human Pathways Acting on Nuclear Non-Coding RNAs Using the Mirror Forward Genetic Approach ]]> https://biorxiv.org/content/10.1101/2024.09.26.615073v1?rss=1 Che, R. Panah, M. Mirani, B. Knowles, K. Ostapovich, A. Majumdar, D. Chen, X. DeSimone, J. White, W. Noonan, M. Luo, H. Alexandrov, A. 2024-09-27 doi:10.1101/2024.09.26.615073 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Weak, specific chemical interactions dictate barnase stability in diverse cellular environments ]]> https://biorxiv.org/content/10.1101/2024.09.26.615174v1?rss=1 Tahir, U. Davis, C. M. 2024-09-27 doi:10.1101/2024.09.26.615174 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Hypothalamic connectivities and self-evaluated aggression in young adults ]]> https://biorxiv.org/content/10.1101/2024.09.26.615292v1?rss=1 Yao, Y. J. Chen, Y. Li, C.-S. R. 2024-09-27 doi:10.1101/2024.09.26.615292 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Refined Myocardium Segmentation from CT Using a Hybrid-Fusion Transformer ]]> https://biorxiv.org/content/10.1101/2024.09.27.615510v1?rss=1 Qin, S. Xing, F. Cho, J. Park, J. Liu, X. Rouhollahi, A. Bou Farhat, E. J. Javadikasgari, H. Sabe, A. Nezami, F. R. Woo, J. Aganj, I. 2024-09-30 doi:10.1101/2024.09.27.615510 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM ]]> https://biorxiv.org/content/10.1101/2024.09.28.615015v1?rss=1 Hanna, M. G. Rodriguez Cruz, H. O. Fujise, K. Zhuoning, L. Monetti, M. De Camilli, P. 2024-09-28 doi:10.1101/2024.09.28.615015 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ The first complete 3D reconstruction and morphofunctional mapping of an insect eye ]]> https://biorxiv.org/content/10.1101/2024.09.30.615804v1?rss=1 Makarova, A. A. Chua, N. J. Diakova, A. V. Desyatirkina, I. A. Gunn, P. Pang, S. Xu, C. S. Hess, H. F. Chklovskii, D. B. Polilov, A. A. 2024-10-01 doi:10.1101/2024.09.30.615804 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Clade Distillation for Genome-wide Association Studies ]]> https://biorxiv.org/content/10.1101/2024.09.30.615852v1?rss=1 Christ, R. Wang, X. Aslett, L. J. M. Steinsaltz, D. Hall, I. 2024-10-01 doi:10.1101/2024.09.30.615852 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Subendothelial Calcification Increases Surface Roughness and Promotes Lipid Deposition into the Arterial Wall ]]> https://biorxiv.org/content/10.1101/2024.09.30.615966v1?rss=1 Kosciuszek, N. D. Petrosian, D. Voleti, N. Dave, P. Kelly, I. Moussouros, D. Davidov, J. Mararenko, A. Borges, K. Nasruddin, S. A. Padalkar, M. Plummer, M. Millan, J. L. Carka, D. Beatty, B. L. Savinova, O. V. 2024-10-02 doi:10.1101/2024.09.30.615966 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes ]]> https://biorxiv.org/content/10.1101/2024.09.30.615987v1?rss=1 Brownstein, C. D. Dornburg, A. Near, T. J. 2024-10-02 doi:10.1101/2024.09.30.615987 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Tunable ligand discrimination via kinetic sorting ]]> https://biorxiv.org/content/10.1101/2024.10.01.615884v1?rss=1 Dixit, P. D. Goetz, A. Madsen, R. R. 2024-10-02 doi:10.1101/2024.10.01.615884 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ scMODAL: A general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links ]]> https://biorxiv.org/content/10.1101/2024.10.01.616142v1?rss=1 Wang, G. Zhao, J. Lin, Y. Liu, T. Zhao, Y. Zhao, H. 2024-10-03 doi:10.1101/2024.10.01.616142 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Stable primary brain cell cultures from zebrafish reveal hyperproliferation of non-neuronal cells from scn1lab mutants ]]> https://biorxiv.org/content/10.1101/2024.10.01.616210v1?rss=1 Odierna, L. Stednitz, S. Pruitt, A. Arnold, J. Hoffman, E. J. Scott, E. 2024-10-03 doi:10.1101/2024.10.01.616210 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Mosaic integration of spatial multi-omics with SpaMosaic ]]> https://biorxiv.org/content/10.1101/2024.10.02.616189v1?rss=1 Yan, X. Li, M. Ang, K. S. Olst, L. v. Edwards, A. Watson, T. Zheng, R. Fan, R. Gate, D. Chen, J. 2024-10-03 doi:10.1101/2024.10.02.616189 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Engineered Whole Lungs for Tissue Biology ]]> https://biorxiv.org/content/10.1101/2024.10.02.616240v1?rss=1 Greaney, A. M. Raredon, M. S. B. Obata, T. Wang, J. Adams, T. S. Schupp, J. C. Mizoguchi, S. Edelstein, S. Yuan, Y. Baevova, P. Wang, N. Engler, A. Leiby, K. Tsuchiya, T. Homer, R. Kaminski, N. Langer, R. Niklason, L. Medzhitov, R. 2024-10-03 doi:10.1101/2024.10.02.616240 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon ]]> https://biorxiv.org/content/10.1101/2024.10.02.616241v1?rss=1 Kubica, J. Korsak, S. Clerkin, A. B. Kouril, D. Schirman, D. Yadavalli, A. D. Banecki, K. Kadlof, M. Busby, B. Plewczynski, D. 2024-10-03 doi:10.1101/2024.10.02.616241 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A 3D Image Segmentation Study of U-Net on CT Images of the Human Aorta with Morphologically Diverse Anatomy ]]> https://biorxiv.org/content/10.1101/2024.10.02.616348v1?rss=1 Chen, J. Qian, L. Wang, P. Sun, C. Qin, T. Kalyanasundaram, A. Zafar, M. Elefteriades, J. Sun, W. Liang, L. 2024-10-03 doi:10.1101/2024.10.02.616348 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Cell cycle regulation of polymerase theta mediated end-joining underlies its sensitivity to loss of BLM-DNA2 ]]> https://biorxiv.org/content/10.1101/2024.10.03.616590v1?rss=1 McBrine, C. P. Jensen, R. B. King, M. C. 2024-10-04 doi:10.1101/2024.10.03.616590 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments ]]> https://biorxiv.org/content/10.1101/2024.10.04.616591v1?rss=1 Walker, L. A. Lee, W. J. Duan, B. Weatherspoon, M. Li, Y. Shen, F. Y. Cheng, M.-C. Niu, X. Eggerd, J. Xie, B. Cheng, J. H. P. Xu, H. Zhong, X.-X. Jiang, H. Cui, M. Yan, Y. Cai, D. 2024-10-04 doi:10.1101/2024.10.04.616591 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Coupled Solvent Dynamics and Protein Dynamics Help Drive Functional Differences in Exon-19 Deletion Mutants in the Epidermal Growth Factor Receptor (EGFR/ErbB1/HER1) Kinase Domain ]]> https://biorxiv.org/content/10.1101/2024.10.04.616731v1?rss=1 Patil, K. Ashtekar, K. D. Tsutsui, Y. Dhabal, D. Suresh, K. Lemmon, M. A. Radhakrishnan, R. 2024-10-06 doi:10.1101/2024.10.04.616731 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ The brain's "dark energy" puzzle upgraded: FDG uptake, delivery and phosphorylation, and their coupling with resting-state brain activity ]]> https://biorxiv.org/content/10.1101/2024.10.05.615717v1?rss=1 Volpi, T. Lee, J. J. Vlassenko, A. G. Goyal, M. S. Corbetta, M. Bertoldo, A. 2024-10-07 doi:10.1101/2024.10.05.615717 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Decision analysis shows scientific and economic value of community-based monitoring in Madagascar ]]> https://biorxiv.org/content/10.1101/2024.10.06.616891v1?rss=1 Soifer, L. Klinges, D. H. Randriamiharisoa, L. Scheffers, B. 2024-10-06 doi:10.1101/2024.10.06.616891 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Revising transcriptome assemblies with phylogenetic information in Agalma1.0 ]]> https://biorxiv.org/content/10.1101/202416v1?rss=1 Guang, A. Howison, M. Zapata, F. Lawrence, C. E. Dunn, C. 2017-10-12 doi:10.1101/202416 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ The correspondence problem: which brain maps are significantly similar? ]]> https://biorxiv.org/content/10.1101/203083v1?rss=1 Alexander-Bloch, A. Vandekar, S. N. Shinohara, R. T. Liu, S. Satterthwaite, T. D. Glahn, D. C. Raznahan, A. 2017-10-13 doi:10.1101/203083 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ New Insights into the Conformational Activation of Full-Length Integrin ]]> https://biorxiv.org/content/10.1101/203661v1?rss=1 Bidone, T. C. Polley, A. Durumeric, A. E. P. Driscoll, T. Iwamoto, D. Calderwood, D. Schwartz, M. A. Voth, G. A. 2017-10-15 doi:10.1101/203661 Cold Spring Harbor Laboratory Press 2017-10-15 <![CDATA[ Emergent Simplicity in Microbial Community Assembly ]]> https://biorxiv.org/content/10.1101/205831v1?rss=1 Goldford, J. E. Lu, N. Bajic, D. Estrela, S. Tikhonov, M. Sanchez-Gorostiaga, A. Segre, D. Mehta, P. Sanchez, A. 2017-10-19 doi:10.1101/205831 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Normative Brain Size Variation and the Remodeling of Brain Shape in Humans ]]> https://biorxiv.org/content/10.1101/205930v1?rss=1 Reardon, P. K. Vandekar, S. N. Liu, S. Patel, R. Park, M. T. M. Alexander-Bloch, A. Seidlitz, J. Clasen, L. S. Blumenthal, J. D. Giedd, J. N. Gur, R. C. Gur, R. E. Lerch, J. P. Chakravarty, M. M. Satterthwaite, T. D. Shinohara, R. T. Raznahan, A. 2017-10-19 doi:10.1101/205930 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Mapping the human brain’s cortical-subcortical functional network organization ]]> https://biorxiv.org/content/10.1101/206292v1?rss=1 Spronk, M. Ji, J. L. Kulkarni, K. Repovs, G. Anticevic, A. Cole, M. W. 2017-10-19 doi:10.1101/206292 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Germline determinants of the somatic mutation landscape in 2,642 cancer genomes ]]> https://biorxiv.org/content/10.1101/208330v1?rss=1 T mutagenesis at CpG dinucleotides, a ubiquitous mutational process acting across tissues. Analysis of somatic structural variation exposed complex rearrangement patterns, involving cycles of templated insertions and tandem duplications, in BRCA1-deficient tumours. Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer types. We further inferred over a hundred polymorphic L1/LINE elements with somatic retrotransposition activity in cancer. Our study highlights the major impact of rare and common germline variants on mutational landscapes in cancer. ]]> Waszak, S. M. Tiao, G. Zhu, B. Rausch, T. Muyas, F. Rodriguez-Martin, B. Rabionet, R. Yakneen, S. Escaramis, G. Li, Y. Saini, N. Roberts, S. A. Demidov, G. M. Pitkanen, E. Delaneau, O. Heredia-Genestar, J. M. Weischenfeldt, J. Shringarpure, S. S. Chen, J. Nakagawa, H. Alexandrov, L. B. Drechsel, O. Dursi, L. J. Segre, A. V. Garrison, E. Erkek, S. Habermann, N. Urban, L. Khurana, E. Cafferkey, A. Hayashi, S. Imoto, S. Aaltonen, L. A. Alvarez, E. G. Baez-Ortega, A. Bailey, M. Bosio, M. Bruzos, A. L. Buchhalter, I. Bustamante, C. D. Calabrese, C. DiBiase, 2017-11-01 doi:10.1101/208330 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ The SAM domain of mouse SAMHD1 is critical for its activation and regulation ]]> https://biorxiv.org/content/10.1101/208363v1?rss=1 Buzovetsky, O. Tang, C. Knecht, K. Antonucci, J. M. Wu, L. Ji, X. Xiong, Y. 2017-10-24 doi:10.1101/208363 Cold Spring Harbor Laboratory Press 2017-10-24 <![CDATA[ Hydraulic constraints of reproduction do not explain sexual dimorphism in the genus Leucadendron (Proteaceae) ]]> https://biorxiv.org/content/10.1101/209460v1?rss=1 Roddy, A. van Blerk, J. J. Midgley, J. J. West, A. G. 2017-10-28 doi:10.1101/209460 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors ]]> https://biorxiv.org/content/10.1101/209478v1?rss=1 Manheimer, K. B. Patel, N. Richter, F. Gorham, J. Tai, A. C. Homsy, J. Boskovski, M. T. Parfenov, M. Goldmuntz, E. Chung, W. K. Brueckner, M. Tristani-Firouzi, M. Srivastava, D. Seidman, J. G. Seidman, C. E. Gelb, B. D. Sharp, A. J. 2017-10-26 doi:10.1101/209478 Cold Spring Harbor Laboratory Press 2017-10-26 <![CDATA[ Predicting Global Forest Reforestation Potential ]]> https://biorxiv.org/content/10.1101/210062v1?rss=1 Crowther, T. W. Glick, H. B. Maynard, D. S. Ashley-Cantello, W. Evans, T. Routh, D. 2017-11-04 doi:10.1101/210062 Cold Spring Harbor Laboratory Press 2017-11-04 <![CDATA[ An evolutionary switch in the specificity of an endosomal CORVET tether underlies formation of regulated secretory vesicles in the ciliate Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/210328v1?rss=1 Sparvoli, D. Richardson, E. Osakada, H. Lan, X. Iwamoto, M. Bowman, G. R. Kontur, C. Bourland, W. A. Lynn, D. H. Pritchard, J. K. Haraguchi, T. Dacks, J. B. Turkewitz, A. P. 2017-10-27 doi:10.1101/210328 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Combinatorial effect of promoter activity, mRNA degradation and site-specific transcriptional pausing in modulating protein expression noise ]]> https://biorxiv.org/content/10.1101/210401v1?rss=1 Kim, S. Jacobs-Wagner, C. 2017-10-27 doi:10.1101/210401 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Dark selection for JAK/STAT-inhibitor resistance in chronic myelomonocytic leukemia ]]> https://biorxiv.org/content/10.1101/211151v1?rss=1 Kaznatcheev, A. Grimes, D. R. Vander Velde, R. Cannataro, V. L. Baratchart, E. Dhawan, A. Liu, L. Myroshnychenko, D. Taylor-King, J. P. Yoon, N. Padron, E. Marusyk, A. Basanta, D. 2017-10-30 doi:10.1101/211151 Cold Spring Harbor Laboratory Press 2017-10-30 <![CDATA[ Controlling for Intra-Subject and Inter-Subject Variability in Individual-Specific Cortical Network Parcellations ]]> https://biorxiv.org/content/10.1101/213041v1?rss=1 Kong, R. Li, J. Sun, N. Sabuncu, M. R. Schaefer, A. Zuo, X.-N. Holmes, A. Eickhoff, S. B. Yeo, B. T. T. 2017-11-02 doi:10.1101/213041 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks ]]> https://biorxiv.org/content/10.1101/213405v1?rss=1 Leland, B. A. Chen, A. B. Zhao, A. Y. Wharton, R. C. King, M. C. 2017-11-03 doi:10.1101/213405 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ Genome-wide analysis yields new loci associating with aortic valve stenosis ]]> https://biorxiv.org/content/10.1101/213595v1?rss=1 Helgadottir, A. Thorleifsson, G. Gretarsdottir, S. Stefansson, O. A. Tragante, V. Thorolfsdottir, R. B. Jonsdottir, I. Bjornsson, T. Steinthorsdottir, V. Verweij, N. Nielsen, J. B. Zhou, W. Folkersen, L. Martinsson, A. Heydarpour, M. Prakash, S. Oskarsson, G. Gudbjartsson, T. Geirsson, A. Olafsson, I. Sigurdsson, E. L. Almgren, P. Melander, O. Franco-Cereceda, A. Hamsten, A. Fritsche, L. Lin, M. Yang, B. Hornsby, W. Guo, D. Brummett, C. M. Abecasis, G. Mathis, M. Milewicz, D. Body, S. C. Eriksson, P. Willer, C. J. Hveem, K. Newton-Cheh, C. Smith, J. G. D 2017-11-03 doi:10.1101/213595 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ Eye movement-related confounds in neural decoding of visual working memory representations ]]> https://biorxiv.org/content/10.1101/215509v1?rss=1 Mostert, P. Albers, A. M. Brinkman, L. Todorova, L. Kok, P. de Lange, F. P. 2017-11-20 doi:10.1101/215509 Cold Spring Harbor Laboratory Press 2017-11-20 <![CDATA[ The Impact of 2017 ACC/AHA Guidelines on the Prevalence of Hypertension and Eligibility for Anti-Hypertensive Therapy in the United States and China ]]> https://biorxiv.org/content/10.1101/218859v1?rss=1 Khera, R. Lu, Y. Saxena, A. Nasir, K. Krumholz, H. M. 2017-11-13 doi:10.1101/218859 Cold Spring Harbor Laboratory Press 2017-11-13 <![CDATA[ Changes in global brain connectivity in LSD-induced altered states of consciousness are attributable to the 5-HT2A receptor ]]> https://biorxiv.org/content/10.1101/219956v1?rss=1 Preller, K. H. Burt, J. B. Ji, J. L. Schleifer, C. Adkinson, B. Staempfli, P. Repovs, G. Krystal, J. H. Murray, J. D. Vollenweider, F. X. Anticevic, A. 2017-11-15 doi:10.1101/219956 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ Evidence for, and Metabolic Consequences of, a Cardiac Mitochondrial KNa1.2 Channel ]]> https://biorxiv.org/content/10.1101/223321v1?rss=1 Smith, C. O. Wang, Y. T. Nadtochiy, S. M. Miller, J. H. Jonas, E. A. Dirksen, R. T. Nehrke, K. Brookes, P. S. 2017-11-21 doi:10.1101/223321 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Regulatory mechanisms are revealed by the distribution of transcription initiation times in single microbial cells ]]> https://biorxiv.org/content/10.1101/223552v1?rss=1 Choubey, S. Kondev, J. Sanchez, A. 2017-11-22 doi:10.1101/223552 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings ]]> https://biorxiv.org/content/10.1101/224147v1?rss=1 Stewart, T. A. Liang, C. Cotney, J. Noonan, J. P. Sanger, T. Wagner, G. 2017-12-05 doi:10.1101/224147 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ The paradoxical sustainability of periodic migration and habitat destruction ]]> https://biorxiv.org/content/10.1101/226589v1?rss=1 Tan, Z. X. Cheong, K. H. 2017-11-29 doi:10.1101/226589 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Reciprocal Disruptions in Thalamic and Hippocampal Resting-State Functional Connectivity in Youth with 22q11.2 Deletions ]]> https://biorxiv.org/content/10.1101/226951v1?rss=1 Schleifer, C. H. Lin, A. Kushan, L. Ji, J. L. Yang, G. Bearden, C. E. Anticevic, A. 2017-11-29 doi:10.1101/226951 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Sex-specific genome-wide association study in glioma identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21 ]]> https://biorxiv.org/content/10.1101/229112v1?rss=1 Ostrom, Q. T. Kinnersley, B. Wrensch, M. R. Eckel-Passow, J. E. Armstrong, G. Rice, T. Chen, Y. Wiencke, J. K. McCoy, L. S. Hansen, H. M. Amos, C. I. Bernstein, J. L. Claus, E. B. Il'yasova, D. Johansen, C. Lachance, D. H. Lai, R. K. Merrell, R. T. Olson, S. H. Sadetzki, S. Schildkraut, J. M. Shete, S. Rubin, J. B. Lathia, J. D. Berens, M. E. Andersson, U. Rajaraman, P. Chanock, S. J. Linet, M. S. Wang, Z. Yeager, M. Houlston, R. S. Jenkins, R. B. Melin, B. Bondy, M. L. Barnholtz-Sloan, J. S. 2017-12-18 doi:10.1101/229112 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Effect sizes of somatic mutations in cancer ]]> https://biorxiv.org/content/10.1101/229724v1?rss=1 Cannataro, V. L. Gaffney, S. G. Townsend, J. P. 2017-12-06 doi:10.1101/229724 Cold Spring Harbor Laboratory Press 2017-12-06 <![CDATA[ Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events ]]> https://biorxiv.org/content/10.1101/230334v1?rss=1 Herzel, L. Straube, K. Neugebauer, K. M. 2017-12-18 doi:10.1101/230334 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Trait-level paranoia shapes inter-subject synchrony in brain activity during an ambiguous social narrative ]]> https://biorxiv.org/content/10.1101/231738v1?rss=1 Finn, E. S. Corlett, P. R. Chen, G. Bandettini, P. A. Constable, R. T. 2017-12-13 doi:10.1101/231738 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Genome-wide association analysis of lifetime cannabis use (N=184,765) identifies new risk loci, genetic overlap with mental health, and a causal influence of schizophrenia on cannabis use ]]> https://biorxiv.org/content/10.1101/234294v1?rss=1 Pasman, J. A. Verweij, K. J. H. Gerring, Z. Stringer, S. Sanchez-Roige, S. Treur, J. L. Abdellaoui, A. Nivard, M. G. Baselmans, B. M. L. Ong, J.-S. Ip, H. F. van der Zee, M. D. Bartels, M. Day, F. R. Fontanillas, P. Elson, S. L. the 23andMe Research Team, de Wit, H. Davis, L. K. MacKillop, J. International Cannabis Consortium, Derringer, J. L. Branje, S. J. T. Hartman, C. A. Heath, A. C. van Lier, P. A. C. Madden, P. A. F. Magi, R. Meeus, W. Montgomery, G. W. Oldehinkel, A. J. Pausova, Z. Ramos-Quiroga, J. A. Paus, T. Ribases, M. Kaprio, J. Boks, M. P. M 2018-01-08 doi:10.1101/234294 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Sex-specific gene and pathway modeling of inherited glioma risk ]]> https://biorxiv.org/content/10.1101/235408v1?rss=1 Ostrom, Q. T. Coleman, W. Huang, W. Rubin, J. B. Lathia, J. D. Berens, M. E. Speyer, G. Liao, P. Wrensch, M. R. Eckel-Passow, J. E. Armstrong, G. Rice, T. Wiencke, J. K. McCoy, L. S. Hansen, H. M. Amos, C. I. Bernstein, J. L. Claus, E. B. Il'yasova, D. Johansen, C. Lachance, D. H. Lai, R. K. Merrell, R. T. Olson, S. H. Sadetzki, S. Schildkraut, J. M. Shete, S. Houlston, R. S. Jenkins, R. B. Andersson, U. Rajaraman, P. Chanock, S. J. Linet, M. S. Wang, Z. Yeager, M. Melin, B. Bondy, M. L. Barnholtz-Sloan, J. S. 2017-12-18 doi:10.1101/235408 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies. ]]> https://biorxiv.org/content/10.1101/235481v1?rss=1 Ziegler, S. J. Liu, C. Landau, M. Buzovetsky, O. Desimmie, B. A. Zhao, Q. Sasaki, T. Burdick, R. C. Pathak, V. K. Anderson, K. S. Xiong, Y. 2017-12-16 doi:10.1101/235481 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci ]]> https://biorxiv.org/content/10.1101/235838v1?rss=1 Lilue, J. Doran, A. G. Fiddes, I. T. Abrudan, M. Armstrong, J. Bennett, R. Chow, W. Collins, J. Czechanski, A. Danecek, P. Diekhans, M. Dolle, D.-D. Dunn, M. Durbin, R. Earl, D. Ferguson-Smith, A. Flicek, P. Flint, J. Frankish, A. Fu, B. Gerstein, M. Gilbert, J. Goodstadt, L. Harrow, J. Howe, K. Kolmogorov, M. Koenig, S. Lelliott, C. Loveland, J. Mott, R. Muir, P. Navarro, F. Odom, D. Park, N. Pelan, S. Phan, S. K. Quail, M. Reinholdt, L. Romoth, L. Shirley, L. Sisu, C. Sjoberg-Herrera, M. Stanke, M. Steward, C. Thomas, M. Threadgold, G. Thybert, D 2018-02-12 doi:10.1101/235838 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Importance of homo-dimerization of Fanconi-associated nuclease 1 in DNA flap cleavage ]]> https://biorxiv.org/content/10.1101/236208v1?rss=1 Rao, T. Longerich, S. Zhao, W. Aihara, H. Sung, P. Xiong, Y. 2017-12-18 doi:10.1101/236208 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Exploring Single-Cell Data with Multitasking Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/237065v1?rss=1 Amodio, M. Srinivasan, K. van Dijk, D. Mohsen, H. Yim, K. Muhle, R. Moon, K. R. Kaech, S. Sowell, R. Montgomery, R. Noonan, J. Wolf, G. Krishnaswamy, S. 2017-12-19 doi:10.1101/237065 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes ]]> https://biorxiv.org/content/10.1101/237313v1?rss=1 2,500 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We developed a statistically rigorous strategy for combining significance levels from multiple driver discovery methods and demonstrate that the integrated results overcome limitations of individual methods. We combined this strategy with careful filtering and applied it to protein-coding genes, promoters, untranslated regions (UTRs), distal enhancers and non-coding RNAs. These analyses redefine the landscape of non-coding driver mutations in cancer genomes, confirming a few previously reported elements and raising doubts about others, while identifying novel candidate elements across 27 cancer types. Novel recurrent events were found in the promoters or 5UTRs of TP53, RFTN1, RNF34, and MTG2, in the 3UTRs of NFKBIZ and TOB1, and in the non-coding RNA RMRP. We provide evidence that the previously reported non-coding RNAs NEAT1 and MALAT1 may be subject to a localized mutational process. Perhaps the most striking finding is the relative paucity of point mutations driving cancer in non-coding genes and regulatory elements. Though we have limited power to discover infrequent non-coding drivers in individual cohorts, combined analysis of promoters of known cancer genes show little excess of mutations beyond TERT. ]]> Rheinbay, E. Nielsen, M. M. Abascal, F. Tiao, G. Hornshoj, H. Hess, J. M. Pedersen, R. I. I. Feuerbach, L. Sabarinathan, R. Madsen, H. T. KIM, J. Mularoni, L. Shuai, S. Lanzos Camaioni, A. A. Herrmann, C. Maruvka, Y. E. Shen, C. Amin, S. B. Bertl, J. Dhingra, P. Diamanti, K. Gonzalez-Perez, A. Guo, Q. Haradhvala, N. J. Isaev, K. Juul, M. Komorowski, J. kumar, s. Lee, D. Lochovsky, L. Liu, E. M. M. Pich, O. tamborero, d. Umer, H. M. Uusküla-Reimand, L. Wadelius, C. Wadi, L. Zhang, J. Boroevich, K. A. Carlevaro-Fita, J. Chakravarty, D. Chan, C. W. 2017-12-23 doi:10.1101/237313 Cold Spring Harbor Laboratory Press 2017-12-23 <![CDATA[ Structural organization and energy storage in crosslinked actin-assemblies ]]> https://biorxiv.org/content/10.1101/237412v1?rss=1 Ma, R. Berro, J. 2017-12-20 doi:10.1101/237412 Cold Spring Harbor Laboratory Press 2017-12-20 <![CDATA[ Individual connectomes are unique and stable in the developing brain from adolescence to young adulthood. ]]> https://biorxiv.org/content/10.1101/238113v1?rss=1 Horien, C. Shen, X. Scheinost, D. Constable, R. T. 2017-12-22 doi:10.1101/238113 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control ]]> https://biorxiv.org/content/10.1101/240747v1?rss=1 Matthews, B. J. Dudchenko, O. Kingan, S. Koren, S. Antoshechkin, I. Crawford, J. E. Glassford, W. J. Herre, M. Redmond, S. N. Rose, N. H. Weedall, G. D. Wu, Y. Batra, S. S. Brito-Sierra, C. A. Buckingham, S. D. Campbell, C. L. Chan, S. Cox, E. Evans, B. R. Fansiri, T. Filipovic, I. Fontaine, A. Gloria-Soria, A. Hall, R. Joardar, V. S. Jones, A. K. Kay, R. G. G. Kodali, V. Lee, J. Lycett, G. J. Mitchell, S. N. Muehling, J. Murphy, M. R. Omer, A. Partridge, F. A. Peluso, P. Aiden, A. P. Ramasamy, V. Rasic, G. Roy, S. Saavedra-Rodriguez, K. Sharan, S. Sha 2017-12-29 doi:10.1101/240747 Cold Spring Harbor Laboratory Press 2017-12-29 <![CDATA[ The mammalian decidual cell evolved from a cellular stress response ]]> https://biorxiv.org/content/10.1101/246397v1?rss=1 Erkenbrack, E. M. Maziarz, J. D. Griffith, O. W. Liang, C. Chavan, A. R. Wagner, G. P. 2018-01-15 doi:10.1101/246397 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Stimulus prediction in the hippocampus ]]> https://biorxiv.org/content/10.1101/246843v1?rss=1 Kok, P. Turk-Browne, N. B. 2018-01-11 doi:10.1101/246843 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Whole Genome Sequencing and Rare Variant Analysis in Essential Tremor Families ]]> https://biorxiv.org/content/10.1101/248443v1?rss=1 A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 (family D), which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). This work has identified candidate genes and pathways for ET that can now be prioritized for functional studies. ]]> Odgerel, Z. Hernandez, N. Park, J. Ottman, R. Louis, E. Clark, L. 2018-01-16 doi:10.1101/248443 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ Microbiota-independent antiviral protection conferred by aminoglycoside antibiotics ]]> https://biorxiv.org/content/10.1101/248617v1?rss=1 Gopinath, S. Kim, M. V. Rakib, T. Wong, P. W. van Zandt, M. Barry, N. A. Kaisho, T. Goodman, A. L. Iwasaki, A. 2018-01-16 doi:10.1101/248617 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution ]]> https://biorxiv.org/content/10.1101/251116v1?rss=1 Munro, C. Siebert, S. Zapata, F. Howison, M. Damian-Serrano, A. Church, S. H. Goetz, F. E. Pugh, P. R. Haddock, S. H. D. Dunn, C. W. 2018-01-20 doi:10.1101/251116 Cold Spring Harbor Laboratory Press 2018-01-20 <![CDATA[ Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity ]]> https://biorxiv.org/content/10.1101/253195v1?rss=1 Shi, W. Ng, C. K. Y. Lim, R. S. Jiang, T. Kumar, S. Li, X. Wali, V. B. Piscuoglio, S. Gerstein, M. B. Chagpar, A. B. Weigelt, B. Pusztai, L. Reis-Filho, J. S. Hatzis, C. 2018-01-24 doi:10.1101/253195 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Tumor regression mediated by oncogene withdrawal or erlotinib stimulates infiltration ofinflammatory immune cells in EGFR mutant lung tumors ]]> https://biorxiv.org/content/10.1101/254847v1?rss=1 Ayeni, D. Miller, B. Kuhlmann, A. Ho, P.-C. Robles-Oteiza, C. Gaefele, M. Levy, S. de Miguel, F. Perry, C. Guan, T. Zelterman, D. Homer, R. Liu, Z. Kaech, S. Politi, K. 2018-01-27 doi:10.1101/254847 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ Rehydration rates and the prevalence of xylem-hydration of flowers ]]> https://biorxiv.org/content/10.1101/255042v1?rss=1 Roddy, A. Brodersen, C. 2018-01-27 doi:10.1101/255042 Cold Spring Harbor Laboratory Press 2018-01-27 <![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[ Dissection of the microProtein miP1 floral repressor complex in Arabidopsis ]]> https://biorxiv.org/content/10.1101/258228v1?rss=1 Rodrigues, V. L. Dolde, U. Straub, D. Eguen, T. Botterweg-Paredes, E. Sun, B. Hong, S. Graeff, M. Li, M.-W. Gendron, J. Wenkel, S. 2018-02-01 doi:10.1101/258228 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ A novel surfactant protein is associated with extrapulmonary respiration in lungless salamanders ]]> https://biorxiv.org/content/10.1101/261412v1?rss=1 Lewis, Z. R. Dorantes, J. A. Hanken, J. 2018-02-07 doi:10.1101/261412 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ A Highly Efficient and Faithful MDS Patient-Derived Xenotransplantation Model for Pre-Clinical Studies ]]> https://biorxiv.org/content/10.1101/265082v1?rss=1 Song, Y. Rongvaux, A. Taylor, A. Jiang, T. Tebaldi, T. Balasubramanian, K. Bagale, A. Terzi, Y. K. Gbyli, R. Wang, X. Zhao, J. Podoltsev, N. Xu, M. Neparidze, N. Wong, E. Torres, R. Bruscia, E. M. Kluger, Y. Manz, M. G. Flavell, R. A. Halene, S. 2018-02-14 doi:10.1101/265082 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Feature Specific Prediction Errors and Surprise across Macaque Fronto-Striatal Circuits during Attention and Learning ]]> https://biorxiv.org/content/10.1101/266205v1?rss=1 Oemisch, M. Westendorff, S. Azimi, M. Hassani, S. A. Ardid, S. Tiesinga, P. Womelsdorf, T. 2018-02-15 doi:10.1101/266205 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum ]]> https://biorxiv.org/content/10.1101/270298v1?rss=1 Kim, W. Miguel-Rojas, C. Wang, J. Townsend, J. P. Trail, F. 2018-02-23 doi:10.1101/270298 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Do pneumococcal conjugate vaccines (PCVs) reduce childhood pneumonia mortality? An assessment across socioeconomic groups in Brazil ]]> https://biorxiv.org/content/10.1101/270637v1?rss=1 Schuck-Paim, C. Taylor, R. M. Alonso, W. J. Weinberger, D. M. Simonsen, L. 2018-02-24 doi:10.1101/270637 Cold Spring Harbor Laboratory Press 2018-02-24 <![CDATA[ SAMHD1 Impairs HIV-1 Gene Expression and Reactivation of Viral Latency in CD4+ T-cells ]]> https://biorxiv.org/content/10.1101/270843v1?rss=1 Antonucci, J. M. Kim, S. H. St. Gelais, C. Bonifati, S. Buzovetsky, O. Knecht, K. Duchon, A. A. Xiong, Y. Musier-Forsyth, K. M. Wu, L. 2018-02-23 doi:10.1101/270843 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose ]]> https://biorxiv.org/content/10.1101/271916v1?rss=1 Bartoli, K. M. Schaening, C. Carlile, T. Gilbert, W. V. 2018-02-26 doi:10.1101/271916 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Label-free high-speed wide-field imaging of single microtubules using interference reflection microscopy ]]> https://biorxiv.org/content/10.1101/273086v1?rss=1 Mahamdeh, M. Simmert, S. Luchniak, A. Schaeffer, E. Howard, J. 2018-03-06 doi:10.1101/273086 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ mRNA structure dynamics identifies the embryonic RNA regulome ]]> https://biorxiv.org/content/10.1101/274290v1?rss=1 Beaudoin, J.-D. Novoa, E. M. Vejnar, C. E. Yartseva, V. Takacs, C. Kellis, M. Giraldez, A. J. 2018-03-01 doi:10.1101/274290 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Channelrhodopsin variants engage distinct patterns of network activity ]]> https://biorxiv.org/content/10.1101/275644v1?rss=1 Jun, N. Y. Cardin, J. A. 2018-03-03 doi:10.1101/275644 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ YES1 amplification: a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics ]]> https://biorxiv.org/content/10.1101/275974v1?rss=1 Fan, P.-D. Narzisi, G. Jayaprakash, A. D. Venturini, E. Robine, N. Smibert, P. Germer, S. Yu, H. A. Jordan, E. J. Paik, P. K. Janjigian, Y. Y. Chaft, J. E. Wang, L. Jungbluth, A. A. Middha, S. Spraggon, L. Qiao, H. Lovly, C. M. Kris, M. G. Riely, G. J. Politi, K. Varmus, H. Ladanyi, M. 2018-03-16 doi:10.1101/275974 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Flexible Learning-Free Segmentation and Reconstruction for Sparse Neuronal Circuit Tracing ]]> https://biorxiv.org/content/10.1101/278515v1?rss=1 Shahbazi, A. Kinnison, J. Vescovi, R. Du, M. Hill, R. Jösch, M. Takeno, M. Zeng, H. da Costa, N. M. Grutzendler, J. Kasthuri, N. Scheirer, W. J. 2018-03-08 doi:10.1101/278515 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Presurgical language fMRI: Current technical practices in epilepsy surgical planning ]]> https://biorxiv.org/content/10.1101/279117v1?rss=1 Benjamin, C. F. A. Dhingra, I. Li, A. Blumenfeld, H. Alkawadri, R. Bickel, S. Helmstaedter, C. Meletti, S. Bronen, R. A. Warfield, S. K. Peters, J. M. Reutens, D. Polczynska, M. M. Hirsch, L. J. Spencer, D. D. 2018-03-08 doi:10.1101/279117 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences ]]> https://biorxiv.org/content/10.1101/280446v1?rss=1 Kumar, S. Warrell, J. Li, S. McGillivray, P. Meyerson, W. Salichos, L. Harmanci, A. Martinez-Fundichely, A. Chan, C. W. Y. Nielsen, M. Lochovsky, L. Zhang, Y. Li, X. Pedersen, J. S. Herrmann, C. Getz, G. Khurana, E. Gerstein, M. PCAWG Drivers and Functional Interpretation Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, 2018-03-12 doi:10.1101/280446 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Cohesiveness in microbial community coalescence ]]> https://biorxiv.org/content/10.1101/282723v1?rss=1 Lu, N. Sanchez-Gorostiaga, A. Tikhonov, M. Sanchez, A. 2018-03-15 doi:10.1101/282723 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ Structural elements required for coupling ion and substrate transport in the neurotransmitter transporter homolog LeuT. ]]> https://biorxiv.org/content/10.1101/283176v1?rss=1 Zhang, Y.-W. Tavoulari, S. Sinning, S. Aleksandrova, A. Forrest, L. R. Rudnick, G. 2018-03-15 doi:10.1101/283176 Cold Spring Harbor Laboratory Press 2018-03-15 <![CDATA[ A statistical framework for cross-tissue transcriptome-wide association analysis ]]> https://biorxiv.org/content/10.1101/286013v1?rss=1 Hu, Y. Li, M. Lu, Q. Weng, H. Wang, J. Zekavat, S. M. Yu, Z. Li, B. Muchnik, S. Shi, Y. Kunkle, B. W. Mukherjee, S. Natarajan, P. Naj, A. Kuzma, A. Zhao, Y. Crane, P. K. Alzheimer's Disease Genetics Consortium, Zhao, H. 2018-03-21 doi:10.1101/286013 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Distinct Functional Connectivity Mode during Viewing Natural Scenes Revealed by Principal Component Analysis ]]> https://biorxiv.org/content/10.1101/286484v1?rss=1 Demirtas, M. Ponce-Alvarez, A. Gilson, M. Hagmann, P. Mantini, D. Betti, V. Romani, G. L. Friston, K. Corbetta, M. Deco, G. 2018-03-21 doi:10.1101/286484 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Low frequency and rare coding variation contributes to multiple sclerosis risk ]]> https://biorxiv.org/content/10.1101/286617v1?rss=1 230 identified by genome-wide association studies (Patsopoulos et al., 2017). Multiple strands of evidence suggest that the majority of the remaining heritability is also due to the additive effects of individual variants, rather than epistatic interactions between these variants, or mutations exclusive to individual families. Here, we show in 68,379 cases and controls that as much as 5% of this heritability is explained by low-frequency variation in gene coding sequence. We identify four novel genes driving MS risk independently of common variant signals, which highlight a key role for regulatory T cell homeostasis and regulation, IFN{gamma} biology and NF{kappa}B signaling in MS pathogenesis. As low-frequency variants do not show substantial linkage disequilibrium with other variants, and as coding variants are more interpretable and experimentally tractable than non-coding variation, our discoveries constitute a rich resource for dissecting the pathobiology of MS. ]]> International Multiple Sclerosis Genetics Consortium, Mitrovic, M. Patsopoulos, N. Beecham, A. Dankowski, T. Goris, A. Dubois, B. Dhooghe, M.-B. Lemmens, R. Van Damme, P. Fitzgerald, K. Bach Sondergaard, H. Sellebjerg, F. Sorensen, P. S. Ullum, H. Wegner Thoerner, L. Werge, T. Saarela, J. Cournu-Rebeix, I. Damotte, V. Fontaine, B. Guillot-Noel, L. Lathrop, M. Vukusik, S. Gourraud, P.-A. Andlauer, T. Pongratz, V. Buck, D. Gasperi, C. Graetz, C. Bayas, A. Heesen, C. Kumpfel, T. Linker, R. Paul, F. Stangel, M. Tackenberg, B. Then Bergh, F. Warnke, C. Wiend 2018-03-23 doi:10.1101/286617 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Phosphoserine acidic cluster motifs in the cytoplasmic domains of transmembrane proteins bind distinct basic regions on the μ subunits of clathrin adaptor protein complexes ]]> https://biorxiv.org/content/10.1101/286633v1?rss=1 Singh, R. Stoneham, C. Lim, C. jia, X. Guenaga, J. Wyatt, R. Wertheim, J. o. Xiong, Y. Guatelli, J. 2018-03-21 doi:10.1101/286633 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Retrograde Transport and ATG-4.2-Mediated Maturation Cooperate to Remove Autophagosomes from the Synapse ]]> https://biorxiv.org/content/10.1101/287144v1?rss=1 Hill, S. E. Colon-Ramos, D. 2018-03-22 doi:10.1101/287144 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ A Polygenic Score for Higher Educational Attainment is Associated with Larger Brains ]]> https://biorxiv.org/content/10.1101/287490v1?rss=1 Elliott, M. L. Belsky, D. W. Anderson, K. Corcoran, D. L. Ge, T. Knodt, A. Prinz, J. A. Sugden, K. Williams, B. Ireland, D. Poulton, R. Caspi, A. Holmes, A. Moffitt, T. Hariri, A. R. 2018-03-23 doi:10.1101/287490 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Structural insights into the conformational plasticity of the full-length trimeric HIV-1 envelope glycoprotein precursor ]]> https://biorxiv.org/content/10.1101/288472v1?rss=1 Zhang, S. Wang, W. L. Chen, S. Lu, M. Go, E. P. Steinbock, R. T. Ding, H. Desaire, H. Kappes, J. C. Sodroski, J. G. Mao, Y. 2018-03-25 doi:10.1101/288472 Cold Spring Harbor Laboratory Press 2018-03-25 <![CDATA[ The functional brain organization of an individual predicts measures of social abilities in autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/290320v1?rss=1 Lake, E. M. R. Finn, E. S. Noble, S. M. Vanderwal, T. Shen, X. Rosenberg, M. D. Spann, M. N. Chun, M. M. Scheinost, D. Constable, R. T. 2018-03-28 doi:10.1101/290320 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition ]]> https://biorxiv.org/content/10.1101/292441v1?rss=1 Vejnar, C. E. Abdel Messih, M. Takacs, C. M. Yartseva, V. Oikonomou, P. Christiano, R. Stoeckius, M. Lau, S. Lee, M. T. Beaudoin, J.-D. Darwich-Codore, H. Walther, T. C. Tavazoie, S. Cifuentes, D. Giraldez, A. J. 2018-03-30 doi:10.1101/292441 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Beta diversity patterns derived from island biogeography theory ]]> https://biorxiv.org/content/10.1101/292490v1?rss=1 Lu, M. Vasseur, D. Jetz, W. 2018-03-30 doi:10.1101/292490 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ On the deformability of an empirical fitness landscape by microbial evolution ]]> https://biorxiv.org/content/10.1101/293407v1?rss=1 Bajic, D. Vila, J. C. C. Blount, Z. D. Sanchez, A. 2018-04-02 doi:10.1101/293407 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration ]]> https://biorxiv.org/content/10.1101/295196v1?rss=1 Fu, X. Kato, S. Long, J. Mattingly, H. H. He, C. Vural, D. C. Zucker, S. W. Emonet, T. 2018-04-05 doi:10.1101/295196 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Pathological Oxidation of PTPN12 Underlies ABL1 Phosphorylation in HLRCC ]]> https://biorxiv.org/content/10.1101/296194v1?rss=1 10X. Applying q-oxPTPome to FH-deficient cell models shows that multiple PTPs are either highly oxidized (including PTPN12) or overexpressed. In general, highly oxidized PTPs were those that have relatively high sensitivity to exogenous H2O2. Most PTP oxidation in FH-deficient cells is reversible, although nearly 40% of PTPN13 is oxidized irreversibly to the sulfonic acid state. Using "substrate-trapping mutants", we mapped PTPs to their putative substrates, and found that only PTPN12 could target ABL1. Furthermore, knockdown experiments identify PTPN12 as the major ABL1 phosphatase in HLRCC. Overall, our results show that ROS-induced PTPN12 oxidation accounts for ABL1 phosphorylation in HLRCC-associated PRCC, reveal a novel mechanism for inactivating a tumor suppressor gene product, and establish a direct link between pathological PTP oxidation and neoplastic disease. ]]> Xu, Y. Taylor, P. Andrade, J. Ueberheide, B. Shuch, B. Glazer, P. M. Bindra, R. S. Moran, M. F. Linehan, M. Neel, B. G. 2018-04-06 doi:10.1101/296194 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1 ]]> https://biorxiv.org/content/10.1101/296624v1?rss=1 Knecht, K. M. Buzovetsky, O. Schneider, C. Thomas, D. Srikanth, V. Tofoleanu, F. Reiss, K. Ferreiros, N. Geisslinger, G. Batista, V. S. Ji, X. Cinatl, J. Keppler, O. T. Xiong, Y. 2018-04-06 doi:10.1101/296624 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Morphofunctional deficits in the cerebral cortex of NeuroD2 mutant mice are associated with autism/schizophrenia-like behaviors ]]> https://biorxiv.org/content/10.1101/296889v1?rss=1 Bugeon, S. Lafi, S. Beurrier, C. Sahu, S. Runge, K. Schaller, F. Loubat, A. Mathieu, R. Herault, L. Gaillard, S. Cahuc, M. Pallesi-Pocachard, E. Montheil, A. Bosio, A. Represa, A. Cardoso, C. Cremer, H. de Chevigny, A. 2018-04-12 doi:10.1101/296889 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Combination of tenofovir and emtricitabine with efavirenz does not moderate inhibitory effect of efavirenz on mitochondrial function and cholesterol biosynthesis in human T lymphoblastoid cell line ]]> https://biorxiv.org/content/10.1101/297044v1?rss=1 Li, M. Sopeyin, A. Paintsil, E. 2018-04-07 doi:10.1101/297044 Cold Spring Harbor Laboratory Press 2018-04-07 <![CDATA[ Model testing for distinctive functional connectivity gradients with resting-state fMRI data ]]> https://biorxiv.org/content/10.1101/298752v1?rss=1 O'Rawe, J. F. Ide, J. S. Leung, H.-C. 2018-04-11 doi:10.1101/298752 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty ]]> https://biorxiv.org/content/10.1101/301887v1?rss=1 Landis, M. J. Freyman, W. A. Baldwin, B. G. 2018-04-17 doi:10.1101/301887 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ In situ structures of periplasmic flagella reveal a distinct cytoplasmic ATPase complex in Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/303222v1?rss=1 Liu, J. Qin, Z. Manne, A. Yu, Z. Yerke, A. Lees, K. Motaleb, M. A. Tu, J. Norris, S. J. Lin, T. Li, C. 2018-04-17 doi:10.1101/303222 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Motor nuclei innervating eye muscles spared in mouse model of SOD1-linked ALS ]]> https://biorxiv.org/content/10.1101/304857v1?rss=1 Thomas, E. V. Nagy, M. Fenton, W. A. Horwich, A. L. 2018-04-20 doi:10.1101/304857 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ The Amyloid Precursor-like Protein APL-1 Regulates Axon Regeneration ]]> https://biorxiv.org/content/10.1101/305284v1?rss=1 Zeng, L. El Bejjani, R. Hammarlund, M. 2018-04-20 doi:10.1101/305284 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Differential valuation and learning from social and non-social cues in Borderline Personality Disorder ]]> https://biorxiv.org/content/10.1101/305938v1?rss=1 Fineberg, S. K. Leavitt, J. Stahl, D. S. Kronemer, S. Landry, C. Alexander-Bloch, A. Hunt, L. Corlett, P. 2018-04-22 doi:10.1101/305938 Cold Spring Harbor Laboratory Press 2018-04-22 <![CDATA[ DNA polymerase β fingers movement revealed by single-molecule FRET suggests a partially closed conformation as a fidelity checkpoint ]]> https://biorxiv.org/content/10.1101/306175v1?rss=1 Fijen, C. Mahmoud, M. Kaup, R. Towle-Weicksel, J. Sweasy, J. Hohlbein, J. 2018-04-22 doi:10.1101/306175 Cold Spring Harbor Laboratory Press 2018-04-22 <![CDATA[ Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results ]]> https://biorxiv.org/content/10.1101/307421v1?rss=1 Liu, Y. Mi, Y. Mueller, T. Kreibich, S. Williams, E. G. Van Drogen, A. Borel, C. Germain, P.-L. Frank, M. Bludau, I. Mehnert, M. Seifert, M. Emmenlauer, M. Sorg, I. Bezrukov, F. Bena, F. S. Zhou, H. Dehio, C. Testa, G. Saez-Rodriguez, J. Antonarakis, S. E. Hardt, W.-D. Aebersold, R. 2018-04-30 doi:10.1101/307421 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Supporting global biodiversity assessment through high-resolution macroecological modelling: Methodological underpinnings of the BILBI framework ]]> https://biorxiv.org/content/10.1101/309377v1?rss=1 Hoskins, A. J. Harwood, T. D. Ware, C. Williams, K. J. Perry, J. J. Ota, N. Croft, J. R. Yeates, D. K. Jetz, W. Golebiewski, M. Purvis, A. Ferrier, S. 2018-05-02 doi:10.1101/309377 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides ]]> https://biorxiv.org/content/10.1101/309534v1?rss=1 Chou, S. Z. Pollard, T. D. 2018-04-27 doi:10.1101/309534 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ Gating Mechanisms during Actin Filament Elongation by Formins ]]> https://biorxiv.org/content/10.1101/311431v1?rss=1 Aydin, F. Courtemanche, N. Pollard, T. D. Voth, G. A. 2018-04-30 doi:10.1101/311431 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Large-scale experimental removal of non-native slider turtles has unexpected consequences on basking behavior for both conspecifics and a native, threatened turtle ]]> https://biorxiv.org/content/10.1101/312173v1?rss=1 LAMBERT, M. R. McKenzie, J. Screen, R. Clause, A. Johnson, B. Mount, G. Shaffer, H. B. Pauly, G. 2018-05-02 doi:10.1101/312173 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Structural basis for transfer RNA mimicry by a bacterial Y RNA ]]> https://biorxiv.org/content/10.1101/312249v1?rss=1 Wang, W. Chen, X. Wolin, S. L. Xiong, Y. 2018-05-02 doi:10.1101/312249 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Automated cellular structure extraction in biological images with applications to calcium imaging data ]]> https://biorxiv.org/content/10.1101/313981v1?rss=1 Mishne, G. Coifman, R. R. Lavzin, M. Schiller, J. 2018-05-03 doi:10.1101/313981 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ The ubiquitin ligase CRL3Kelch targets HtsRC to organize the Drosophila ring canal cytoskeleton ]]> https://biorxiv.org/content/10.1101/315077v1?rss=1 Hudson, A. M. Mannix, K. M. Gerdes, J. A. Kottemann, M. C. Cooley, L. 2018-05-04 doi:10.1101/315077 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Amazon Mechanical Turk as a platform for borderline personality disorder research ]]> https://biorxiv.org/content/10.1101/316356v1?rss=1 Collison, K. L. Lesser, R. E. Stahl, D. S. Robinson, E. Miller, J. Lynam, D. Fineberg, S. 2018-05-08 doi:10.1101/316356 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Insights into the cooperative nature of ATP hydrolysis in actin filaments ]]> https://biorxiv.org/content/10.1101/319558v1?rss=1 Katkar, H. H. Davtyan, A. Durumeric, A. E. P. Hocky, G. M. Schramm, A. C. De La Cruz, E. M. Voth, G. A. 2018-05-10 doi:10.1101/319558 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Serotonin and neuropeptides are both released by the HSN command neuron to initiate C. elegans egg laying ]]> https://biorxiv.org/content/10.1101/323857v1?rss=1 Brewer, J. Collins, K. Koelle, M. 2018-05-16 doi:10.1101/323857 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Presence of midline cilia supersedes the expression of Lefty1 in forming the midline barrier during the establishment of left-right asymmetry ]]> https://biorxiv.org/content/10.1101/324533v1?rss=1 Shylo, N. A. Ramrattan, D. A. Weatherbee, S. D. 2018-05-17 doi:10.1101/324533 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ A whole-brain and cross-diagnostic perspective on functional brain network dysfunction ]]> https://biorxiv.org/content/10.1101/326728v1?rss=1 Spronk, M. Kulkarni, K. Ji, J. L. Keane, B. Anticevic, A. Cole, M. W. 2018-05-21 doi:10.1101/326728 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Genetic compensation is triggered by mutant mRNA degradation ]]> https://biorxiv.org/content/10.1101/328153v1?rss=1 El-Brolosy, M. Rossi, A. Kontarakis, Z. Kuenne, C. Guenther, S. Fukuda, N. Takacs, C. Lai, S.-L. Fukuda, R. Gerri, C. Kikhi, K. Giraldez, A. Stainier, D. Y. R. 2018-05-22 doi:10.1101/328153 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease ]]> https://biorxiv.org/content/10.1101/329151v1?rss=1 Mäkeläinen, S. Godia, M. Hellsand, M. Viluma, A. Hahn, D. Makdoumi, K. Zeiss, C. J. Mellersh, C. Ricketts, S. L. Narfström, K. Hallböök, F. Ekesten, B. Andersson, G. Bergström, T. F. 2018-05-25 doi:10.1101/329151 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Optimization of Experiment Design for Mass Spectrometric Isotopic Labeling Kinetics ]]> https://biorxiv.org/content/10.1101/331520v1?rss=1 Lathwal, S. Raaisa, R. Alves, T. C. Kibbey, R. G. Jha, A. K. Mason, G. F. 2018-05-27 doi:10.1101/331520 Cold Spring Harbor Laboratory Press 2018-05-27 <![CDATA[ Ancestral resurrection reveals mechanisms of kinase regulatory evolution ]]> https://biorxiv.org/content/10.1101/331637v1?rss=1 Sang, D. Pinglay, S. Vatansever, S. Lou, H. J. Turk, B. E. Gumus, Z. H. Holt, L. J. 2018-05-25 doi:10.1101/331637 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ A genetically-encoded fluorescent sensor enables rapid and specific detection of dopamine in flies, fish, and mice ]]> https://biorxiv.org/content/10.1101/332528v1?rss=1 Sun, F. Zeng, J. Jing, M. Zhou, J. Feng, J. Owen, S. F. Luo, Y. Li, F. Yamaguchi, T. Yong, Z. Gao, Y. Peng, W. Wang, L. Zhang, S. Du, J. Lin, D. Xu, M. Kreitzer, A. C. Cui, G. Li, Y. 2018-05-31 doi:10.1101/332528 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ High-order interactions dominate the functional landscape of microbial consortia ]]> https://biorxiv.org/content/10.1101/333534v1?rss=1 Sanchez-Gorostiaga, A. Bajic, D. Osborne, M. L. Poyatos, J. F. Sanchez, A. 2018-05-29 doi:10.1101/333534 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ Available energy fluxes drive a phase transition in the diversity, stability, and functional structure of microbial communities ]]> https://biorxiv.org/content/10.1101/335893v1?rss=1 Marsland, R. Cui, W. Goldford, J. E. Sanchez, A. Korolev, K. Mehta, P. 2018-05-31 doi:10.1101/335893 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Fold-change detection of NF-κB at target genes with different transcript outputs ]]> https://biorxiv.org/content/10.1101/339697v1?rss=1 Wong, V. C. Ramji, R. Gaudet, S. Miller-Jensen, K. 2018-06-05 doi:10.1101/339697 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Ketamine disrupts neuromodulatory control of glutamatergic synaptic transmission. ]]> https://biorxiv.org/content/10.1101/341172v1?rss=1 Lur, G. Higley, M. 2018-06-07 doi:10.1101/341172 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ Hierarchical heterogeneity across human cortex shapes large-scale neural dynamics ]]> https://biorxiv.org/content/10.1101/341966v1?rss=1 Demirtas, M. Burt, J. B. Helmer, M. Ji, J. L. Adkinson, B. D. Glasser, M. F. Van Essen, D. C. Sotiropoulos, S. N. Anticevic, A. Murray, J. D. 2018-06-08 doi:10.1101/341966 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ 14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface ]]> https://biorxiv.org/content/10.1101/342659v1?rss=1 Karlberg, T. Hornyak, P. Pinto, A. F. Milanova, S. Ebrahimi, M. Lindberg, M. Pullen, N. Nordstrom, A. Loverli, E. Caraballo, R. Wong, E. V. Nareoja, K. Thorsell, A.-G. Elofsson, M. De La Cruz, E. M. Bjorkegren, C. Schuler, H. 2018-06-08 doi:10.1101/342659 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Conditions for optimal mechanical power generation by a bundle of growing actin filaments ]]> https://biorxiv.org/content/10.1101/344671v1?rss=1 Martiel, J.-L. Michelot, A. Boujema-Paterski, R. Blanchoin, L. Berro, J. 2018-06-12 doi:10.1101/344671 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Aberrant Information Transfer Interferes with Functional Axon Regeneration ]]> https://biorxiv.org/content/10.1101/347427v1?rss=1 Ding, C. Hammarlund, M. 2018-06-14 doi:10.1101/347427 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ GABARAP Like-1 enrichment on membranes: Direct observation of trans-homo-oligomerization between membranes and curvature-dependent partitioning into membrane tubules. ]]> https://biorxiv.org/content/10.1101/348730v1?rss=1 Motta, I. Nguyen, N. Gardavot, H. Richerson, D. Pincet, F. Melia, T. 2018-06-17 doi:10.1101/348730 Cold Spring Harbor Laboratory Press 2018-06-17 <![CDATA[ Determining the Hierarchical Architecture of the Human Brain Using Subject-Level Clustering of Functional Networks ]]> https://biorxiv.org/content/10.1101/350462v1?rss=1 Akiki, T. J. Abdallah, C. G. 2018-06-19 doi:10.1101/350462 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Antioxidant Gene Expression in Vocal Hindbrain of a Teleost Fish ]]> https://biorxiv.org/content/10.1101/354977v1?rss=1 Liao, C. Feng, N. Y. Bass, A. H. 2018-06-26 doi:10.1101/354977 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ MBIR: A Cryo-electron Tomography 3D Reconstruction Method that Effectively Minimizes Missing Wedge Artifacts and Restores Missing Information ]]> https://biorxiv.org/content/10.1101/355529v1?rss=1 Yan, R. Venkatakrishnan, S. V. Liu, J. Bouman, C. A. Jiang, W. 2018-06-25 doi:10.1101/355529 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Neurofeedback helps to reveal a relationship between context reinstatement and memory retrieval ]]> https://biorxiv.org/content/10.1101/355727v1?rss=1 deBettencourt, M. T. Turk-Browne, N. B. Norman, K. A. 2018-06-29 doi:10.1101/355727 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Nemo-like kinase regulates Progranulin levels in the brain through the microglial endocytosis-lysosomal pathway ]]> https://biorxiv.org/content/10.1101/358010v1?rss=1 Dong, T. Kokubu, H. Driessen, T. M. Tejwani, L. Lim, J. 2018-06-28 doi:10.1101/358010 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ APC/CCdh1-mediated degradation of Cdh1 during meiosis in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/358655v1?rss=1 Ostapenko, D. Solomon, M. J. 2018-06-28 doi:10.1101/358655 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ The Vibrio H-ring facilitates the outer membrane penetration of polar-sheathed flagellum ]]> https://biorxiv.org/content/10.1101/358820v1?rss=1 Liu, J. Zhu, S. Nishikino, T. Kojima, S. Homma, M. 2018-06-29 doi:10.1101/358820 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Visualization of the type III secretion mediated Salmonella-host cell interface using cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/359166v1?rss=1 Liu, J. Park, D. Lara-Tejero, M. Galan, J. E. Li, W. Waxham, M. N. Hu, B. 2018-06-29 doi:10.1101/359166 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis ]]> https://biorxiv.org/content/10.1101/359521v1?rss=1 Moro, A. Driscoll, T. Armero, W. Boraas, L. C. Kasper, D. Baeyens, N. Jouy, C. Mallikarjun, V. Swift, J. Ahn, S. J. Lee, D. Zhang, J. Gu, M. Gerstein, M. Schwartz, M. Nicoli, S. 2018-07-03 doi:10.1101/359521 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Antisense lncRNA transcription drives stochastic Protocadherin α promoter choice ]]> https://biorxiv.org/content/10.1101/360206v1?rss=1 Canzio, D. Nwakeze, C. Horta, A. Rajkumar, S. Coffey, E. Duffy, E. Duffie, R. Simon, M. Lomvardas, S. Maniatis, T. 2018-07-01 doi:10.1101/360206 Cold Spring Harbor Laboratory Press 2018-07-01 <![CDATA[ Nearly all new protein-coding predictions in the CHESS database are not protein-coding ]]> https://biorxiv.org/content/10.1101/360602v1?rss=1 Jungreis, I. Tress, M. L. Mudge, J. Sisu, C. Hunt, T. Johnson, R. Uszczynska-Ratajczak, B. Lagarde, J. Wright, J. Muir, P. Gerstein, M. Guigo, R. Kellis, M. Frankish, A. Flicek, P. The GENCODE Consortium, 2018-07-02 doi:10.1101/360602 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ DNMT3A-NPM1 mutated acute myeloid leukaemia shows sensitivity to a PARP1 inhibitor combined with daunorubicin in an in vitro model ]]> https://biorxiv.org/content/10.1101/362103v1?rss=1 Gafencu, G. A. Pileczki, V. Jurj, A. Magdo, L. Selicean, C. Ola, R. Ghiaur, G. Berindan-Neagoe, I. Tomuleasa, C. 2018-07-05 doi:10.1101/362103 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Characterization of fluorescent proteins, promoters, and selectable markers for applications in the Lyme disease spirochete Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/363390v1?rss=1 Takacs, C. N. Scott, M. Jacobs-Wagner, C. 2018-07-06 doi:10.1101/363390 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Covariation analysis with improved parameters reveals conservation in lncRNA structures ]]> https://biorxiv.org/content/10.1101/364109v1?rss=1 Tavares, R. C. A. Pyle, A. M. Somarowthu, S. 2018-07-06 doi:10.1101/364109 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ The Biological Basis of Mathematical Beauty ]]> https://biorxiv.org/content/10.1101/367185v1?rss=1 Zeki, S. Chen, O. Y. Romaya, J. P. 2018-07-11 doi:10.1101/367185 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Expansion of a core regulon in specialized metabolism by mobile genetic elements promotes chemical diversity in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/368340v1?rss=1 Barco, B. Kim, Y. Clay, N. K. 2018-07-13 doi:10.1101/368340 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Brd4 and P300 regulate zygotic genome activation through histone acetylation ]]> https://biorxiv.org/content/10.1101/369231v1?rss=1 Chan, S. H. Tang, Y. Miao, L. Darwich-Codore, H. Vejnar, C. E. Beaudoin, J.-D. Musaev, D. Fernandez, J. P. Moreno-Mateos, M. A. Giraldez, A. J. 2018-07-13 doi:10.1101/369231 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ The landscape of S100B+ and HLA-DR+ dendritic cell subsets in tonsils at the single cell level via high-parameter mapping ]]> https://biorxiv.org/content/10.1101/369983v1?rss=1 40 markers) immunofluorescent approach, cell type-specific image segmentation and the use of bioinformatics platforms. Through this deep phenotypic and spatial examination, classic cDC1, cDC2, pDC subsets have been further refined and a novel subset of DC co-expressing IRF4 and IRF8 identified. Based on unique tissue locations within the tonsil, and close interactions with T cells (cDC1) or B cells (cDC2), DC subsets can be further subdivided by correlative phenotypic changes associated with these interactions. In addition, monocytes and macrophages expressing HLA-DR or S100AB are identified and localized in the tissue. This study thus provides a whole tissue in situ catalog of human DC subsets and their cellular interactions within spatially defined niches. ]]> Bolognesi, M. M. Bosisio, F. M. Manzoni, M. Schapiro, D. Tagliabue, R. Faretta, M. Parravicini, C. Haberman, A. M. Cattoretti, G. 2018-07-16 doi:10.1101/369983 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ The Subtype Specificity of Genetic Loci Associated with Stroke in 16,664 cases and 32,792 controls ]]> https://biorxiv.org/content/10.1101/371153v1?rss=1 Traylor, M. Anderson, C. Rutten-Jacobs, L. Falcone, G. Comeau, M. Ay, H. Sudlow, C. Xu, H. Mitchell, B. Cole, J. Rexrode, K. Jimenez-Conde, J. Schmidt, R. Grewal, R. Sacco, R. Ribases, M. Rundek, T. Rosand, J. Dichgans, M. Lee, J.-M. Langefeld, C. Kittner, S. Markus, H. Woo, D. Malik, R. 2018-07-20 doi:10.1101/371153 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ A simple and effective method to isolate germ nuclei from C. elegans for genomic assays. ]]> https://biorxiv.org/content/10.1101/371351v1?rss=1 Han, M. Wei, G. McManus, C. E. Reinke, V. 2018-07-17 doi:10.1101/371351 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ Systems analysis by mass cytometry identifies susceptibility of latent HIV-infected T cells to targeting of p38 and mTOR pathways ]]> https://biorxiv.org/content/10.1101/371922v1?rss=1 Fong, L. E. Bass, V. L. Spudich, S. Miller-Jensen, K. 2018-07-19 doi:10.1101/371922 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ State-specific individualized functional networks form a predictive signature of brain state ]]> https://biorxiv.org/content/10.1101/372110v1?rss=1 Salehi, M. Karbasi, A. Barron, D. S. Scheinost, D. Constable, R. T. 2018-07-19 doi:10.1101/372110 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast ]]> https://biorxiv.org/content/10.1101/372706v1?rss=1 Epstein, A. E. Espinoza Sanchez, S. V. Pollard, T. D. 2018-07-19 doi:10.1101/372706 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ The prokaryotic SPHINX 1.8 REP protein is tissue-specific and expressed in human germline cells ]]> https://biorxiv.org/content/10.1101/373803v1?rss=1 Manuelidis, L. 2018-07-20 doi:10.1101/373803 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins ]]> https://biorxiv.org/content/10.1101/374926v1?rss=1 Steinauer, A. LaRochelle, J. Wissner, R. Berry, S. Schepartz, A. 2018-07-23 doi:10.1101/374926 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Altered trajectories in the dynamical repertoire of functional network states under psilocybin ]]> https://biorxiv.org/content/10.1101/376491v1?rss=1 Lord, L.-D. Expert, P. Atasoy, S. Roseman, L. Rapuano, K. Lambiotte, R. Nutt, D. J. Deco, G. Carhart-Harris, R. Kringelbach, M. L. Cabral, J. 2018-07-25 doi:10.1101/376491 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ The Drosophila Cortactin Binding Protein 2 homolog, Nausicaa, regulates lamellipodial actin dynamics in a Cortactin-dependent manner. ]]> https://biorxiv.org/content/10.1101/376665v1?rss=1 O'Connell, M. E. Sridharan, D. Driscoll, T. Krishnamurthy, I. Perry, W. G. Applewhite, D. A. 2018-07-24 doi:10.1101/376665 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Evaluation of InSeq to Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization ]]> https://biorxiv.org/content/10.1101/377168v1?rss=1 Sivakumar, R. Ranjani, J. Vishnu, U. S. Jayashree, S. Lozano, G. L. Miles, J. Broderick, N. Guan, C. Gunasekaran, P. Handelsman, J. Rajendhran, J. 2018-07-25 doi:10.1101/377168 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales ]]> https://biorxiv.org/content/10.1101/377358v1?rss=1 Musser, J. M. Wagner, G. P. Liang, C. Stabile, F. A. Cloutier, A. Baker, A. J. Prum, R. O. 2018-07-25 doi:10.1101/377358 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Perceptual grouping in the cocktail party: contributions of voice-feature continuity ]]> https://biorxiv.org/content/10.1101/379545v1?rss=1 Kreitewolf, J. Mathias, S. R. Trapeau, R. Obleser, J. Schönwiesner, M. 2018-07-30 doi:10.1101/379545 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Batch Effect Removal via Batch-Free Encoding ]]> https://biorxiv.org/content/10.1101/380816v1?rss=1 Shaham, U. 2018-07-31 doi:10.1101/380816 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: The case of hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/381467v1?rss=1 Walsh, R. Mazzarotto, F. Whiffin, N. Buchan, R. Midwinter, W. Wilk, A. Li, N. Felkin, L. Ingold, N. Govind, R. Ahmad, M. Mazaika, E. Allouba, M. Zhang, X. de Marvao, A. Day, S. M. Ashley, E. Colan, S. D. Michels, M. Pereira, A. C. Jacoby, D. Ho, C. Y. Thomson, K. L. Watkins, H. Barton, P. J. Olivotto, I. Cook, S. A. Ware, J. S. 2018-07-31 doi:10.1101/381467 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Alcohol-responsive genes identified in human iPSC-derived neural cultures ]]> https://biorxiv.org/content/10.1101/381673v1?rss=1 Jensen, K. Lieberman, R. Kranzler, H. Gelernter, J. Covault, J. 2018-07-31 doi:10.1101/381673 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Lesion Attributes Segmentation for Melanoma Detection with Deep Learning ]]> https://biorxiv.org/content/10.1101/381855v1?rss=1 Chen, E. Z. Dong, X. Wu, J. Jiang, H. Li, X. Rong, R. 2018-07-31 doi:10.1101/381855 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Skin Lesion Classification Via Combining Deep Learning Features and Clinical Criteria Representations ]]> https://biorxiv.org/content/10.1101/382010v1?rss=1 Li, X. Wu, J. Jiang, H. Chen, E. Z. Dong, X. Rong, R. 2018-08-01 doi:10.1101/382010 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Exploring the prediction of emotional valence and pharmacologic effect across fMRI studies of antidepressants. ]]> https://biorxiv.org/content/10.1101/382408v1?rss=1 Barron, D. S. Salehi, M. Browning, M. Harmer, C. Constable, R. Duff, E. 2018-08-01 doi:10.1101/382408 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Skin Lesion Segmentation with Improved C-UNet Networks ]]> https://biorxiv.org/content/10.1101/382549v1?rss=1 Jiang, H. Rong, R. Wu, J. Li, X. Dong, X. Chen, E. Z. 2018-08-01 doi:10.1101/382549 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Synapse-selective control of cortical maturation and plasticity engages an interneuron-autonomous synaptic switch ]]> https://biorxiv.org/content/10.1101/382614v1?rss=1 Ribic, A. Crair, M. Biederer, T. 2018-08-01 doi:10.1101/382614 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Individual differences in dopamine are associated with reward discounting in clinical groups but not in healthy adults ]]> https://biorxiv.org/content/10.1101/383810v1?rss=1 Castrellon, J. J. Seaman, K. L. Crawford, J. L. Young, J. S. Smith, C. T. Dang, L. C. Hsu, M. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2018-08-02 doi:10.1101/383810 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Novel allosteric mechanism of p53 activation by small molecules for targeted anticancer therapy ]]> https://biorxiv.org/content/10.1101/384248v1?rss=1 Zawacka-Pankau, J. Grinkevich, V. V. Burmakin, M. Vema, A. Ridderstrale, K. Issaeva, N. Andreotti, V. Dickinson, E. R. Hedstrom, E. Spinnler, C. Inga, A. Larsson, L.-G. Karlen, A. Tarasova, O. Poroikov, V. Lavrenov, S. Preobrazhenskaya, M. Wilhelm, M. Barran, P. E. Okorokov, A. L. Selivanova, G. 2018-08-03 doi:10.1101/384248 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation ]]> https://biorxiv.org/content/10.1101/385237v1?rss=1 Sethi, A. Gu, M. Gumusgoz, E. Chan, L. Yan, K.-K. Rozowsky, J. S. Barozzi, I. Afzal, V. Akiyama, J. Plajzer-Frick, I. Yan, C. Pickle, C. Kato, M. Garvin, T. Pham, Q. Harrington, A. Mannion, B. Lee, E. Fukuda-Yuzawa, Y. Visel, A. Dickle, D. E. Yip, K. Sutton, R. Pennacchio, L. A. Gerstein, M. 2018-08-05 doi:10.1101/385237 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history ]]> https://biorxiv.org/content/10.1101/386656v1?rss=1 Sisu, C. Muir, P. Frankish, A. Fiddes, I. Diekhans, M. Thybert, D. Odom, D. Flicek, P. Keane, T. Hubbard, T. Harrow, J. Gerstein, M. 2018-08-07 doi:10.1101/386656 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Nuclear TARBP2 drives oncogenic dysregulation of RNA splicing and decay ]]> https://biorxiv.org/content/10.1101/389213v1?rss=1 Fish, L. Nguyen, H. C. B. Zhang, S. Hochman, M. Dill, B. D. Molina, H. Najafabadi, H. S. Alarcon, C. Goodarzi, H. 2018-08-17 doi:10.1101/389213 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Variants in regulatory elements of PDE4D associate with Major Mental Illness in the Finnish population ]]> https://biorxiv.org/content/10.1101/390518v1?rss=1 Hennah, W. Sinha, V. Vuoti, L.-U. Ortega-Alonso, A. Torniainen-Holm, M. Therman, S. Tuulio-Henriksson, A. Jylhä, P. Kaprio, J. Hovatta, I. Isometsä, E. Cannon, T. D. Lonnqvist, J. Paunio, T. Suvisaari, J. 2018-08-13 doi:10.1101/390518 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Spatial dynamics of brain functional domains: A new avenue to study time-varying brain function ]]> https://biorxiv.org/content/10.1101/391094v1?rss=1 Iraji, A. Fu, Z. Damarajua, E. Belger, A. Ford, J. M. McEwen, S. Mathalon, D. H. Mueller, B. A. Pearlson, G. D. Potkin, S. G. Preda, A. Turner, J. A. Vaidya, J. G. van Erp, T. G. M. Calhoun, V. D. 2018-08-13 doi:10.1101/391094 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Multimodal gradients across mouse cortex ]]> https://biorxiv.org/content/10.1101/393215v1?rss=1 Fulcher, B. D. Murray, J. D. Zerbi, V. Wang, X.-J. 2018-08-16 doi:10.1101/393215 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ A Data-driven Individual-based Model of Infectious Disease in Livestock Operation: A Validation Study for Paratuberculosis ]]> https://biorxiv.org/content/10.1101/394569v1?rss=1 Al-Mamun, M. A. Smith, R. L. Nigsch, A. Schukken, Y. H. Grohn, Y. T. 2018-08-17 doi:10.1101/394569 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Robust Automated Assessment of Human Blastocyst Quality using Deep Learning ]]> https://biorxiv.org/content/10.1101/394882v1?rss=1 Khosravi, P. Kazemi, E. Zhan, Q. Toschi, M. E. Malmsten, J. Hickman, C. Meseguer, M. Rosenwaks, Z. Elemento, O. Zaninovic, N. Hajirasouliha, I. 2018-08-20 doi:10.1101/394882 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole genome sequencing studies ]]> https://biorxiv.org/content/10.1101/395046v1?rss=1 Chen, H. Huffman, J. E. Brody, J. A. Wang, C. Lee, S. Li, Z. Gogarten, S. M. Sofer, T. Bielak, L. F. Bis, J. C. Blangero, J. Bowler, R. P. Cade, B. E. Cho, M. H. Correa, A. Curran, J. E. de Vries, P. S. Glahn, D. C. Guo, X. Johnson, A. D. Kardia, S. Kooperberg, C. Lewis, J. P. Liu, X. Mathias, R. A. Mitchell, B. D. O'Connell, J. R. Peyser, P. A. Post, W. S. Reiner, A. P. Rich, S. S. Rotter, J. I. Silverman, E. K. Smith, J. A. Vasan, R. S. Wilson, J. G. Yanek, L. R. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Hematology and Hemos 2018-08-20 doi:10.1101/395046 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Investigating functional brain network integrity using a traditional and novel diagnostic system for neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/396317v1?rss=1 Dajani, D. R. Burrows, C. A. Odriozola, P. Baez, A. Nebel, M. B. Mostofsky, S. H. Uddin, L. Q. 2018-08-22 doi:10.1101/396317 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Zero-preserving imputation of scRNA-seq data using low-rank approximation ]]> https://biorxiv.org/content/10.1101/397588v1?rss=1 Linderman, G. C. Zhao, J. Kluger, Y. 2018-08-22 doi:10.1101/397588 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Two lytic bacteriophages that depend on the Escherichia coli multi-drug efflux gene tolC and differentially affect bacterial growth and selection ]]> https://biorxiv.org/content/10.1101/397695v1?rss=1 Burmeister, A. R. Bender, R. G. Fortier, A. Lessing, A. J. Chan, B. K. Turner, P. E. 2018-08-22 doi:10.1101/397695 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ TCF7L2 Regulation of GATA6-dependent and -Independent Vascular Smooth Muscle Cell Plasticity and Intimal Hyperplasia ]]> https://biorxiv.org/content/10.1101/397851v1?rss=1 Mani, A. Srivastava, R. Xie, Y. Li, N. Bhat, N. Hong, L. Esteghamat, S. Adeniran, A. Geirsson, A. Zhang, J. Ge, G. Nobrega, M. Martin, K. A. Rolyan, H. 2018-08-22 doi:10.1101/397851 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ Group Based Trajectory Analysis of Cognitive Outcomes in Children with Perinatal HIV ]]> https://biorxiv.org/content/10.1101/398339v1?rss=1 8 years, OR: 2.72; p 0.01) and report lower household income level (OR: 0.33-0.42; p<0.005). Neither CD4 nadir nor treatment arm was associated with cognitive trajectory status.nnConclusionOur study reflects the benefit of using group based trajectory modeling to classify the heterogeneity in cognitive outcomes of children with pHIV. Children were described as belonging to three distinct subgroups determined at study onset alluding to the fact that cognitive outcomes are likely to be determined at an early age with little variability over time in children with pHIV. Demographic variables, including older age at presentation and household income, were associated with low scoring cognitive trajectories, whereas HIV related variables were not. These findings mirror other studies and demonstrate the impact of socioeconomic factors on cognitive development in children with pHIV. ]]> Patel, P. Apornpong, T. Kerr, S. J. Puthanakit, T. Thongpibul, K. Kosalaraksa, P. Ounchanum, P. Kanhanavanit, S. Ngampiyaskul, C. Penhsun, L. Chettra, K. Spudich, S. Ananworanich, J. Luesonboon, W. Mellins, C. Malee, K. Paul, R. The PREDICT Resilience Study, 2018-08-23 doi:10.1101/398339 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Catalytic promiscuity potentiated the divergence of new cytochrome P450 enzyme functions in cyanogenic defense metabolism ]]> https://biorxiv.org/content/10.1101/398503v1?rss=1 Barco, B. Zipperer, L. Clay, N. K. 2018-08-29 doi:10.1101/398503 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Data quality reporting: good practice for transparentestimates from forest and land cover surveys ]]> https://biorxiv.org/content/10.1101/399055v1?rss=1 Birigazzi, L. Gregoire, T. G. Finegold, Y. Condor Goled, R. D. Sandker, M. Donegan, E. Gamarra, J. G. P. 2018-08-23 doi:10.1101/399055 Cold Spring Harbor Laboratory Press 2018-08-23 <![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[ Ex vivo dynamics of human glioblastoma cells in a microvasculature-on-a-chip system correlates with tumor heterogeneity and subtypes ]]> https://biorxiv.org/content/10.1101/400739v1?rss=1 Xiao, Y. Kim, D. Dura, B. Zhang, K. Yan, R. Li, H. Han, E. Ip, J. Zou, P. Liu, J. Chen, A. T. Vortmeyer, A. O. Zhou, J. Fan, R. 2018-09-03 doi:10.1101/400739 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Evaluation of RNA-seq normalization methods using challenging datasets ]]> https://biorxiv.org/content/10.1101/401679v1?rss=1 Uebbing, S. 2018-08-27 doi:10.1101/401679 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Deep Learning for Quality Control of Subcortical Brain 3D Shape Models ]]> https://biorxiv.org/content/10.1101/402255v1?rss=1 Petrov, D. Gutman, B. A. Kuznetsov, E. van Erp, T. G. M. Turner, J. A. Schmaal, L. Veltman, D. Wang, L. Alpert, K. Isaev, D. Zavaliangos-Petropolu, A. Ching, C. R. K. Calhoun, V. Glahn, D. Satterthwaite, T. D. Andreassen, O. A. Borgwardt, S. Howells, F. Groenewold, N. Voineskos, A. Radua, J. Potkin, S. G. Crespo-Favorro, B. Tordesillas-Gutirrez, D. Shen, L. Lebedeva, I. Spalletta, G. Donohoe, G. Kochunov, P. Rosa, P. G. P. James, A. Dannlowski, U. Baune, B. T. Aleman, A. Gotlib, I. H. Walter, H. Walter, M. Soarez, J. C. Ehrlich, S. Gur, R. C. Doan, N. T. 2018-08-28 doi:10.1101/402255 Cold Spring Harbor Laboratory Press 2018-08-28 <![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[ α-Synuclein binds extracellular complex N-linked glycans ]]> https://biorxiv.org/content/10.1101/407247v1?rss=1 Birol, M. Wojcik, S. P. Miranker, A. D. Rhoades, E. 2018-09-03 doi:10.1101/407247 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Genome-wide association studies in Samoans give insight into the genetic etiology of fasting serum lipid levels. ]]> https://biorxiv.org/content/10.1101/411546v1?rss=1 Carlson, J. Weeks, D. Hawley, N. L. Sun, G. Chen, H. Naseri, T. Reupena, M. S. Deka, R. McGarvey, S. T. Minster, R. L. 2018-09-08 doi:10.1101/411546 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Evidence of causal effect of major depression on alcohol dependence: Findings from the Psychiatric Genomics Consortium ]]> https://biorxiv.org/content/10.1101/412098v1?rss=1 Polimanti, R. Peterson, R. E. Ong, J. S. Macgregor, S. Edwards, A. Clarke, T.-K. Frank, J. Gerring, Z. Gillespie, N. A. Lind, P. A. Maes, H. H. Martin, N. G. Mbarek, H. Medland, S. E. Streit, F. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Substance Use Disorder Working Group of the Psychiatric Genomics Consortium, 23andMe Research Team, Agrawal, A. Edenberg, H. J. Kendler, K. S. Lewis, C. M. Sullivan, P. F. Wray, N. R. Gelernter, J. Derks, E. M. 2018-09-09 doi:10.1101/412098 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Critical role of miR-10b in BRafV600E dependent anchorage independent growth and invasion of melanoma cells ]]> https://biorxiv.org/content/10.1101/413476v1?rss=1 Datar, I. Kalpana, G. de la Serna, I. Trumbly, R. Choi, J. Yeung, K. C. 2018-09-10 doi:10.1101/413476 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Munc18-1 catalyzes neuronal SNARE assembly by templating SNARE association ]]> https://biorxiv.org/content/10.1101/413724v1?rss=1 Jiao, J. He, M. Port, S. A. Baker, R. W. Xu, Y. Qu, H. Xiong, Y. Wang, Y. Jin, H. Eisemann, T. J. Hughson, F. M. Zhang, Y. 2018-09-10 doi:10.1101/413724 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ The spatial chronnectome reveals a dynamic interplay between functional segregation and integration ]]> https://biorxiv.org/content/10.1101/427450v1?rss=1 Iraji, A. DeRamus, T. Lewis, N. Yaesoubi, M. Stephen, J. M. Erhardt, E. Belger, A. Ford, J. McEwen, S. Mathalon, D. Mueller, B. Pearlson, G. Potkin, S. Preda, A. Turner, J. Vaidya, J. van Erp, T. Calhoun, V. 2018-09-25 doi:10.1101/427450 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Evolution of embryo implantation was enabled by the origin of decidual cells in eutherian mammals ]]> https://biorxiv.org/content/10.1101/429571v1?rss=1 Chavan, A. R. Griffith, O. W. Stadtmauer, D. Maziarz, J. Pavlicev, M. Fishman, R. Koren, L. Romero, R. Wagner, G. P. 2018-09-27 doi:10.1101/429571 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Enhanced population coding for rewarded choices in the medial frontal cortex of the mouse ]]> https://biorxiv.org/content/10.1101/429852v1?rss=1 Siniscalchi, M. J. Wang, H. Kwan, A. C. 2018-09-28 doi:10.1101/429852 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ A phylogenomic resolution of the sea urchin tree of life ]]> https://biorxiv.org/content/10.1101/430595v1?rss=1 Mongiardino Koch, N. Coppard, S. E. Lessios, H. A. Briggs, D. E. Mooi, R. Rouse, G. W. 2018-09-29 doi:10.1101/430595 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Model colibactins exhibit human cell genotoxicity in the absence of host bacteria ]]> https://biorxiv.org/content/10.1101/431098v1?rss=1 Shine, E. E. Xue, M. Patel, J. R. Healy, A. R. Surovtseva, Y. V. Herzon, S. Crawford, J. M. 2018-09-29 doi:10.1101/431098 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Single-cell microRNA/mRNA co-sequencing reveals non-genetic heterogeneity and novel regulatory mechanisms ]]> https://biorxiv.org/content/10.1101/431213v1?rss=1 Wang, N. Zheng, J. Chen, Z. Liu, Y. Dura, B. Kwak, M. Xavier-Ferrucio, J. Lu, Y.-C. Zhang, M. Roden, C. Cheng, J. Krauss, D. Ding, Y. Fan, R. Lu, J. 2018-09-30 doi:10.1101/431213 Cold Spring Harbor Laboratory Press 2018-09-30 <![CDATA[ There is no single functional atlas even for a single individual: Parcellation of the human brain is state dependent ]]> https://biorxiv.org/content/10.1101/431833v1?rss=1 Salehi, M. Greene, A. S. Karbasi, A. Shen, X. Scheinost, D. Constable, R. T. 2018-10-01 doi:10.1101/431833 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Membrane-cytoskeleton mechanical feedback mediated by myosin-I controls phagocytic efficiency ]]> https://biorxiv.org/content/10.1101/433631v1?rss=1 Barger, S. R. Reilly, N. S. Shutova, M. S. Li, Q. Maiuri, P. Mooseker, M. S. Flavell, R. A. Svitkina, T. Oakes, P. W. Krendel, M. Gauthier, N. 2018-10-02 doi:10.1101/433631 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ RNA polymerases display collaborative and antagonistic group behaviors over long distances through DNA supercoiling ]]> https://biorxiv.org/content/10.1101/433698v1?rss=1 Kim, S. Beltran, B. Irnov, I. Jacobs-Wagner, C. 2018-10-02 doi:10.1101/433698 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Innate Immune Priming by cGAS as a Preparatory Countermeasure Against RNA Virus Infection ]]> https://biorxiv.org/content/10.1101/434027v1?rss=1 Parker, M. T. Gopinath, S. Perez, C. E. Linehan, M. M. Crawford, J. Iwasaki, A. Lindenbach, B. D. 2018-10-03 doi:10.1101/434027 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Single-cell integrative analysis of CAR-T cell activation reveals a predominantly TH1/TH2 mixed response independent of differentiation ]]> https://biorxiv.org/content/10.1101/435693v1?rss=1 Xhangolli, I. Dura, B. Lee, G. Kim, D. Fan, R. Fan, R. 2018-10-04 doi:10.1101/435693 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Classical-contextual interactions in V1 may rely on dendritic computations ]]> https://biorxiv.org/content/10.1101/436956v1?rss=1 JIN, L. Behabadi, B. F. Jadi, M. P. Ramachandra, C. A. Mel, B. W. 2018-10-07 doi:10.1101/436956 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Cytoskeletal tension actively sustains the T cell immunological synapse ]]> https://biorxiv.org/content/10.1101/437236v1?rss=1 Kumari, S. Mak, M. Poh, Y. Tohme, M. Watson, N. Melo, M. Janssen, E. Dustin, M. Geha, R. Irvine, D. 2018-10-08 doi:10.1101/437236 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Distinct waking states for strong evoked responses in primary visual cortex and optimal visual detection performance ]]> https://biorxiv.org/content/10.1101/437681v1?rss=1 Neske, G. T. McCormick, D. A. 2018-10-08 doi:10.1101/437681 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Heterotrimeric G-proteins in unfolded protein response mediate plant growth-defense tradeoffs upstream of steroid and immune signaling ]]> https://biorxiv.org/content/10.1101/438135v1?rss=1 Miller, J. C. Lawrence, S. A. Ceserani, T. Beakes, C. L. Clay, N. K. 2018-10-08 doi:10.1101/438135 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer ]]> https://biorxiv.org/content/10.1101/438531v1?rss=1 Lio, C.-W. J. Shukla, V. Samaniego-Castruita, D. Gonzalez-Avalos, E. Chakraborty, A. Yue, X. Schatz, D. G. Ay, F. Rao, A. 2018-10-08 doi:10.1101/438531 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ MxB restricts HIV-1 by targeting the tri-hexamer interface of the viral capsid ]]> https://biorxiv.org/content/10.1101/444067v1?rss=1 Smaga, S. S. Xu, C. Summers, B. J. Digianantonio, K. M. Perilla, J. R. Xiong, Y. 2018-10-15 doi:10.1101/444067 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Using long-read sequencing to detect imprinted DNA methylation ]]> https://biorxiv.org/content/10.1101/445924v1?rss=1 Gigante, S. Gouil, Q. Lucattini, A. Keniry, A. Beck, T. Tinning, M. Gordon, L. Woodruff, C. Speed, T. P. Blewitt, M. Ritchie, M. 2018-10-17 doi:10.1101/445924 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Nitrogen addition has minimal effect in Wyoming big sagebrush (Artemisia tridentata) communities ]]> https://biorxiv.org/content/10.1101/446294v1?rss=1 Beltz, C. W. Mobley, M. L. Burke, I. C. 2018-10-17 doi:10.1101/446294 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Focusing on what matters: Modulation of the human hippocampus by relational attention ]]> https://biorxiv.org/content/10.1101/446443v1?rss=1 Cordova, N. I. Turk-Browne, N. B. Aly, M. 2018-10-18 doi:10.1101/446443 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ scFTD-seq: freeze-thaw lysis based, portable approach toward high-quality distributed single-cell 3 mRNA profiling ]]> https://biorxiv.org/content/10.1101/447524v1?rss=1 Dura, B. Choi, J.-Y. Zhang, K. Damsky, W. Thakral, D. Bosenberg, M. Craft, J. Fan, R. 2018-10-19 doi:10.1101/447524 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Genomic variants concurrently listed in a somatic and a germline mutation database have implications for disease-variant discovery and genomic privacy ]]> https://biorxiv.org/content/10.1101/450239v1?rss=1 T]G, C->A, etc.) have correlated mutation rates in the germline and soma. Matched-normal read depth analysis suggests that an appreciable fraction of this excess may also derive from germline contamination of somatic samples.nnConclusionOverall, our results highlight the commonalities in substitution patterns between the germline and soma. The universality of some aspects of human mutation rates offers insight into the potential molecular mechanisms of human mutation. The highlighted similarities between somatic and germline mutation rates also lay the groundwork for future studies that distinguish disease-causing variants from a genomic background informed by both somatic and germline variant data. Moreover, our results also indicate that the depth of matched normal sequencing necessary to ensure genomic privacy of donors of somatic samples may be higher than previously appreciated. Furthermore, the fact that we were able to explain such a high portion of recurrent variants using known determinants of mutation rates is evidence that the genomics community has already discovered the most important predictors of mutation rates for single nucleotide variants. ]]> Meyerson, W. Gerstein, M. B. 2018-10-22 doi:10.1101/450239 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ The dynamic and structural properties of axonemal tubulins support the high length stability of cilia ]]> https://biorxiv.org/content/10.1101/451351v1?rss=1 Orbach, R. Howard, J. 2018-10-24 doi:10.1101/451351 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ The Heterotaxy Gene, CCDC11, is Essential for Cytokinesis and Cell-Cell Adhesion Via RhoA Regulation ]]> https://biorxiv.org/content/10.1101/452631v1?rss=1 Kulkarni, S. S. Stephenson, R. Amalraj, S. Betleja, E. Moresco, J. J. Yates, J. R. Mahjoub, M. R. Miller, A. Khokha, M. 2018-10-24 doi:10.1101/452631 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Dopamine modulation of prefrontal cortex activity is manifold and operates at multiple temporal and spatial scales ]]> https://biorxiv.org/content/10.1101/452862v1?rss=1 Lohani, S. Martig, A. K. Deisseroth, K. Witten, I. Moghaddam, B. 2018-10-25 doi:10.1101/452862 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ SV40 polyomavirus activates the Ras-MAPK signaling pathway for vacuolization, cell death, and virus release ]]> https://biorxiv.org/content/10.1101/454850v1?rss=1 Motamedi, N. Sewald, X. Luo, Y. Mothes, W. DiMaio, D. 2018-10-28 doi:10.1101/454850 Cold Spring Harbor Laboratory Press 2018-10-28 <![CDATA[ Embedding the single-cell sample manifold to reveal insights into cancer pathogenesis and disease heterogeneity ]]> https://biorxiv.org/content/10.1101/455436v1?rss=1 Chen, W. S. Zivanovic, N. van Dijk, D. Wolf, G. Bodenmiller, B. Krishnaswamy, S. 2018-10-29 doi:10.1101/455436 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ Genome wide association study of hippocampal subfield volume in PTSD cases and trauma-exposed controls ]]> https://biorxiv.org/content/10.1101/456988v1?rss=1 Morey, R. A. Garrett, M. E. Stevens, J. S. Clarke, E. Haswell, C. C. van Rooij, S. J. H. Fani, N. Lori, A. VA Mid-Atlantic MIRECC Workgroup, Marx, C. E. Beckham, J. C. McCarthy, G. Hauser, M. A. Ashley-Koch, A. E. 2018-10-30 doi:10.1101/456988 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[ Limitations of Topological Data Analysis for event-related fMRI ]]> https://biorxiv.org/content/10.1101/457747v1?rss=1 Ellis, C. T. Lesnick, M. Henselman-Petrusek, G. Keller, B. Cohen, J. D. 2018-10-31 doi:10.1101/457747 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Human APOBEC3G prevents emergence of infectious endogenous retrovirus in mice ]]> https://biorxiv.org/content/10.1101/457937v1?rss=1 Treger, R. Tokuyama, M. Dong, H. Ross, S. R. Kong, Y. Iwasaki, A. 2018-10-31 doi:10.1101/457937 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Multiscale causal network models of Alzheimer’s disease identify VGF as a key regulator of disease ]]> https://biorxiv.org/content/10.1101/458430v1?rss=1 Beckmann, N. D. Lin, W.-J. Wang, M. Cohain, A. T. Wang, P. Ma, W. Wang, Y.-C. Jiang, C. Audrain, M. Comella, P. Hariharan, S. P. Belbin, G. M. Levey, A. I. Seyfried, N. T. Dammer, E. B. Duong, D. Lah, J. J. Haure-Mirande, J.-V. Shackleton, B. Charney, A. W. Kenny, E. Zhu, J. Haroutunian, V. Katsel, P. Gandy, S. Tu, Z. Ehrlich, M. Zhang, B. Salton, S. R. Schadt, E. E. 2018-11-04 doi:10.1101/458430 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways ]]> https://biorxiv.org/content/10.1101/458562v1?rss=1 Nievergelt, C. M. Maihofer, A. X. Klengel, T. Atkinson, E. G. Chen, C.-Y. Choi, K. W. Coleman, J. R. I. Dalvie, S. Duncan, L. E. Logue, M. W. Provost, A. Ratanatharathorn, A. Stein, M. B. Torres, K. Aiello, A. E. Almli, L. M. Amstadter, A. B. Andersen, S. B. Andreassen, O. A. Arbisi, P. A. Ashley-Koch, A. E. Austin, S. B. Avdibegovic, E. Babic, D. Baekvad-Hansen, M. Baker, D. G. Beckham, J. C. Bierut, L. J. Bisson, J. I. Boks, M. P. Bolger, E. A. Borglum, A. D. Bradley, B. Brashear, M. Breen, G. Bryant, R. A. Bustamante, A. C. Bybjerg-Grauholm, J. Calabres 2018-11-01 doi:10.1101/458562 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ NetPyNE: a tool for data-driven multiscale modeling of brain circuits ]]> https://biorxiv.org/content/10.1101/461137v1?rss=1 Dura-Bernal, S. Suter, B. Gleeson, P. Cantarelli, M. Quintana, A. Rodriguez, F. Kedziora, D. J. Chadderdon, G. L. Kerr, C. C. Neymotin, S. A. McDougal, R. Hines, M. Shepherd, G. M. Lytton, W. W. 2018-11-03 doi:10.1101/461137 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ Skin inflammation driven by differentiation of quiescent tissue-resident ILCs into a spectrum of pathogenic effectors ]]> https://biorxiv.org/content/10.1101/461228v1?rss=1 Bielecki, P. Riesenfled, S. J. Kowalczyk, M. S. Amezcua Vesely, M. C. Kroehling, L. Yaghoubi, P. Dionne, D. Jarret, A. Steach, H. R. McGee, H. M. Porter, C. B. M. Licona-Limon, P. Bailis, W. Jackson, R. Gagliani, N. Locksley, R. M. Regev, A. Flavell, R. A. 2018-11-11 doi:10.1101/461228 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Hydraulic traits are more diverse in flowers than in leaves ]]> https://biorxiv.org/content/10.1101/461244v1?rss=1 Roddy, A. Jiang, G.-F. Cao, K. Simonin, K. Brodersen, C. 2018-11-03 doi:10.1101/461244 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ The spermidine acetyltransferase SpeG regulates transcription of the small RNA RprA ]]> https://biorxiv.org/content/10.1101/462937v1?rss=1 Hu, L. I. Filippova, E. V. Dang, J. Pshenychnyi, S. Ruan, J. Kiryukhina, O. Anderson, W. F. Kuhn, M. L. Wolfe, A. 2018-11-05 doi:10.1101/462937 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Phylogeny of the Australian Solanum dioicum group using seven nuclear genes: testing Symons fruit and seed dispersal hypotheses ]]> https://biorxiv.org/content/10.1101/462945v1?rss=1 Martine, C. T. Jordon-Thaden, I. E. McDonnell, A. J. Cantley, J. T. Hayes, D. S. Roche, M. D. Frawley, E. S. Gilman, I. S. Tank, D. C. 2018-11-05 doi:10.1101/462945 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Spanning spatiotemporal scales with simultaneous mesoscopic Ca2+ imaging and functional MRI ]]> https://biorxiv.org/content/10.1101/464305v1?rss=1 Lake, E. M. Ge, X. Shen, X. Herman, P. Hyder, F. Cardin, J. A. Higley, M. J. Scheinost, D. Papademetris, X. Crair, M. C. Constable, R. T. 2018-11-06 doi:10.1101/464305 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ The innate immune DNA sensor cGAS is a negative regulator of DNA repair hence promotes genome instability and cell death ]]> https://biorxiv.org/content/10.1101/465401v1?rss=1 Jiang, H. Panda, S. Xue, X. Liang, F. Sung, P. Gekara, N. O. 2018-11-08 doi:10.1101/465401 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ A stable, high refractive index, switching buffer for super-resolution imaging ]]> https://biorxiv.org/content/10.1101/465492v1?rss=1 Hartwich, T. M. Chung, K. K. Schroeder, L. Bewersdorf, J. Soeller, C. Baddeley, D. 2018-11-08 doi:10.1101/465492 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ ImmuneRegulation: A web-based tool for identifying human immune regulatory elements ]]> https://biorxiv.org/content/10.1101/468124v1?rss=1 Kalayci, S. Esai Selvan, M. Ramos, I. Cotsapas, C. Montgomery, R. R. Poland, G. Pulendran, B. Tsang, J. Klein, R. J. Gumus, Z. H. 2018-11-11 doi:10.1101/468124 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits ]]> https://biorxiv.org/content/10.1101/468348v1?rss=1 Barson, D. Hamodi, A. S. Shen, X. Lur, G. Constable, R. T. Cardin, J. Crair, M. Higley, M. 2018-11-11 doi:10.1101/468348 Cold Spring Harbor Laboratory Press 2018-11-11 <![CDATA[ Genetic loss of the ubiquitin ligase RNF126, an AID interacting partner and modifier, affects strand targeting during somatic hypermutation of antibody genes ]]> https://biorxiv.org/content/10.1101/469775v1?rss=1 C bias; strickingly, loss of RNF126 was also associated with tandem indels within the variable region (JH4 intron) but only a slight increase in the types of chromosomal translocations that are characteristic of deregulated AID. Conversely, these findings suggest that mono-ubiquitination of AID, likely in situ, is necessary for the proper removal of the protein from the non-transcribed strand, thus producing both optimal patterns of SHM and also limiting the number of indels within the target locus. ]]> Economos, N. G. Delker, R. K. Stavropoulos, P. Papavasiliou, F. N. 2018-11-14 doi:10.1101/469775 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Colonization of the tsetse fly midgut with commensal Enterobacter inhibits trypanosome infection establishment ]]> https://biorxiv.org/content/10.1101/472373v1?rss=1 Weiss, B. L. Maltz, M. A. Vigneron, A. Wu, Y. Walter, K. O'Neill, M. B. Wang, J. Aksoy, S. 2018-11-16 doi:10.1101/472373 Cold Spring Harbor Laboratory Press 2018-11-16 <![CDATA[ A Novel Melatonergic Signature Predicts Reccurence Risk and Therapeutic Response in Breast Cancer Patients ]]> https://biorxiv.org/content/10.1101/472753v1?rss=1 Nguyen, M. N. Tran, H. Q. Luu, P. L. Than, V. T. Clarke, D. Lam, H. N. Nguyen, D. T. Le, K. V. T. Nguyen, T. V. Le, M. T. Hoang, T. X. Duy, P. Q. Tran, H. T. 2018-11-17 doi:10.1101/472753 Cold Spring Harbor Laboratory Press 2018-11-17 <![CDATA[ Do Deep Neural Networks Outperform Kernel Regression for Functional Connectivity Prediction of Behavior? ]]> https://biorxiv.org/content/10.1101/473603v1?rss=1 He, T. Kong, R. Holmes, A. Nguyen, M. Sabuncu, M. Eickhoff, S. B. Bzdok, D. Feng, J. Yeo, B. T. T. 2018-11-19 doi:10.1101/473603 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins ]]> https://biorxiv.org/content/10.1101/474072v1?rss=1 Zhang, J. Liu, J. Lee, D. Feng, J.-J. Lochovsky, L. Lou, S. Rutenberg-Schoenberg, M. Gerstein, M. 2018-11-19 doi:10.1101/474072 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding ]]> https://biorxiv.org/content/10.1101/475103v1?rss=1 Kadakia, N. Emonet, T. 2018-11-21 doi:10.1101/475103 Cold Spring Harbor Laboratory Press 2018-11-21 <![CDATA[ Dispersal increases the resilience of tropical savanna and forest distributions ]]> https://biorxiv.org/content/10.1101/476184v1?rss=1 Goel, N. Guttal, V. Levin, S. Staver, C. 2018-11-27 doi:10.1101/476184 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Historical contingency shapes adaptive radiation in Antarctic fishes ]]> https://biorxiv.org/content/10.1101/478842v1?rss=1 250,000 loci across 46 species to examine hypotheses concerning the origin and diversification of key traits in the adaptive radiation of Antarctic notothenioid fishes. Contrary to expectations of adaptive evolution, we show that notothenioids experienced a punctuated burst of genomic diversification and evolved key skeletal modifications before the onset of polar conditions in the Southern Ocean. We show that diversifying selection in pathways associated with human skeletal dysplasias facilitates ecologically important variation in buoyancy among Antarctic notothenioid species, and demonstrate the sufficiency of altered trip11, col1a2 and col1a1 function in zebrafish (Danio rerio) to phenocopy skeletal reduction in Antarctic notothenioids. Rather than adaptation being driven by the cooling of the Antarctic (6), our results highlight the role of exaptation and historical contingency in shaping the adaptive radiation of notothenioids. Understanding the historical and environmental context for the origin of key traits in adaptive radiations provides context in forecasting the effects of climate change on the stability and evolvability of natural populations. ]]> Daane, J. M. Dornburg, A. Smits, P. MacGuigan, D. J. Hawkins, M. B. Near, T. J. Detrich, H. W. Harris, M. P. 2018-11-26 doi:10.1101/478842 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Nucleoid size scaling and intracellular organization of translation across bacteria ]]> https://biorxiv.org/content/10.1101/479840v1?rss=1 Gray, W. T. Govers, S. K. Xiang, Y. Parry, B. R. Campos, M. Kim, S. Jacobs-Wagner, C. 2018-11-28 doi:10.1101/479840 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ The transcriptional landscape of cortical interneurons underlies in-vivo brain function and schizophrenia risk ]]> https://biorxiv.org/content/10.1101/481036v1?rss=1 Anderson, K. M. Collins, M. A. Chin, R. Ge, T. Rosenberg, M. D. Holmes, A. J. 2018-11-29 doi:10.1101/481036 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Non-cell-autonomous promotion of pluripotency induction mediated by YAP ]]> https://biorxiv.org/content/10.1101/481127v1?rss=1 Hartman, A. Hu, X. Chen, X. Eastman, A. E. Yang, C. Guo, S. 2018-11-28 doi:10.1101/481127 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner ]]> https://biorxiv.org/content/10.1101/482992v1?rss=1 Lou, S. Cotter, K. A. Li, T. Liang, J. Mohsen, H. Liu, J. Zhang, J. Cohen, S. Xu, J. Yu, H. Rubin, M. Gerstein, M. 2018-11-29 doi:10.1101/482992 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Hippocampal-neocortical interactions sharpen over time for predictive actions ]]> https://biorxiv.org/content/10.1101/483115v1?rss=1 Hindy, N. C. Avery, E. W. Turk-Browne, N. B. 2018-11-30 doi:10.1101/483115 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ MLL-AF9 Initiates Transformation From Fast-Proliferating Myeloid Progenitors ]]> https://biorxiv.org/content/10.1101/484220v1?rss=1 Chen, X. Hartman, A. Hu, X. Eastman, A. E. Wang, X. Zhong, M. Guo, S. 2018-11-30 doi:10.1101/484220 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ ciftify: A framework for surface-based analysis of legacy MR acquisitions ]]> https://biorxiv.org/content/10.1101/484428v1?rss=1 Dickie, E. W. Anticevic, A. Smith, D. E. Coalson, T. S. Manogaran, M. Calarco, N. Viviano, J. D. Glasser, M. F. Van Essen, D. C. Voineskos, A. N. 2018-12-03 doi:10.1101/484428 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ The lupus susceptibility locus Sgp3 encodes the suppressor of endogenous retrovirus expression SNERV ]]> https://biorxiv.org/content/10.1101/487231v1?rss=1 Treger, R. S. Pope, S. D. Kong, Y. Tokuyama, M. Taura, M. Iwasaki, A. 2018-12-04 doi:10.1101/487231 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Functional connectomics of affective and psychotic pathology ]]> https://biorxiv.org/content/10.1101/489377v1?rss=1 Baker, J. T. Dillon, D. G. Patrick, L. M. Roffman, J. L. Brady, R. O. Pizzagalli, D. A. Ongur, D. Holmes, A. 2018-12-07 doi:10.1101/489377 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1 ]]> https://biorxiv.org/content/10.1101/490763v1?rss=1 Mehnert, M. Li, W. Wu, C. Salovska, B. Liu, Y. 2018-12-09 doi:10.1101/490763 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Perception is shaped along the (L+M)/S axis (and possibly confused with a memory color effect) ]]> https://biorxiv.org/content/10.1101/490888v1?rss=1 Adeyefa-Olasupo, I.-E. 2018-12-13 doi:10.1101/490888 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Virus-like vesicles expressing multiple antigens for immunotherapy of chronic hepatitis B ]]> https://biorxiv.org/content/10.1101/491985v1?rss=1 Yarovinsky, T. O. Mason, S. W. Menon, M. Krady, M. M. Haslip, M. Madina, B. R. Moshkani, S. Chiale, C. Chattopadhyay Pal, A. Almassian, B. Rose, J. K. Robek, M. D. Nakaar, V. 2018-12-10 doi:10.1101/491985 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ The Dot/Icm-translocated effector LegC4 potentiates cytokine-mediated restriction of Legionella within accidental hosts. ]]> https://biorxiv.org/content/10.1101/493197v1?rss=1 Ngwaga, T. Hydock, A. J. Ganesan, S. Shames, S. R. 2018-12-11 doi:10.1101/493197 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells ]]> https://biorxiv.org/content/10.1101/494252v1?rss=1 Eastman, A. E. Chen, X. Hu, X. Hartman, A. A. Pearlman Morales, A. M. Yang, C. Lu, J. Kueh, H. Y. Guo, S. 2018-12-11 doi:10.1101/494252 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Reliability of the correlative triad among aging, dopamine D2-like receptor availability, and cognition ]]> https://biorxiv.org/content/10.1101/494765v1?rss=1 Juarez, E. J. Castrellon, J. J. Green, M. A. Crawford, J. L. Seaman, K. L. Smith, C. T. Dang, L. C. Matuskey, D. Morris, E. D. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2018-12-13 doi:10.1101/494765 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Introducing THOR, a model microbiome for genetic dissection of community behavior ]]> https://biorxiv.org/content/10.1101/499715v1?rss=1 Lozano, G. L. Bravo, J. I. Garavito Diago, M. F. Park, H. B. Hurley, A. Peterson, S. B. Stabb, E. V. Crawford, J. M. Broderick, N. A. Handelsman, J. 2018-12-19 doi:10.1101/499715 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system ]]> https://biorxiv.org/content/10.1101/499731v1?rss=1 Lozano, G. L. Park, H. B. Bravo, J. I. Armstrong, E. A. Denu, J. M. Stabb, E. V. Broderick, N. A. Crawford, J. M. Handelsman, J. 2018-12-19 doi:10.1101/499731 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Rapamycin, an Immunosuppressant and mTORC1 Inhibitor, Triples the antidepressant Response Rate of Ketamine at 2 Weeks Following Treatment: A double-blind, placebo-controlled, cross-over, randomized clinical trial ]]> https://biorxiv.org/content/10.1101/500959v1?rss=1 Abdallah, C. Averill, L. A. Gueorguieva, R. Goktas, S. Purohit, P. Ranganathan, M. D'Souza, D. C. Formica, R. Southwick, S. M. Duman, R. S. Sanacora, G. Krystal, J. 2018-12-19 doi:10.1101/500959 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Decoys provide a scalable platform for the genetic analysis of plant E3 ubiquitin ligases that regulate circadian clock function ]]> https://biorxiv.org/content/10.1101/501965v1?rss=1 Feke, A. Liu, W. Hong, J. Li, M.-W. Lee, C.-M. Zhou, E. Gendron, J. 2018-12-20 doi:10.1101/501965 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Reduced Salience and Enhanced Central Executive Connectivity Following PTSD Treatment ]]> https://biorxiv.org/content/10.1101/501973v1?rss=1 Abdallah, C. Averill, C. Ramage, A. Averill, L. Alkin, E. Krystal, J. Roache, J. Resick, P. Young-McCaughan, S. Peterson, A. Fox, P. 2018-12-19 doi:10.1101/501973 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Dual language experience enhances neural activation variability during an fMRI reading and language task ]]> https://biorxiv.org/content/10.1101/502625v1?rss=1 Malins, J. G. D'Silva, H. Luk, G. Hernandez, A. E. Frost, S. J. Pugh, K. R. Mencl, W. E. Mehta, C. Bosson-Heenan, J. Gruen, J. R. 2018-12-20 doi:10.1101/502625 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Estimating prevalence for limb-girdle muscular dystrophy based on public sequencing databases ]]> https://biorxiv.org/content/10.1101/502708v1?rss=1 Liu, W. Pajusalu, S. Lake, N. Zhou, G. Williams, B. Rufibach, L. Lek, M. 2018-12-21 doi:10.1101/502708 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Economic status mediates the relationship between educational attainment and posttraumatic stress disorder: a multivariable Mendelian randomization study ]]> https://biorxiv.org/content/10.1101/503300v1?rss=1 0.05). MR analysis indicated that EdAtt has negative causal effects on PTSD (beta=-0.23, p=0.004). Investigating potential mediators of the EdAtt-PTSD relationship, we observed that propensity for trauma exposure and risk-taking behaviors are risk factors for PTSD independently from EdAtt (beta = 0.36, p = 2.57x10-5 and beta = 0.76, p = 6.75x10-4, respectively), while income fully mediates the causal effect of EdAtt on PSTD (MR: Income - beta = -0.18, p =0.001; EdAtt - beta =-0.23, p=0.004; multivariable MR: Income - beta = -0.32, p = 0.017; EdAtt - beta = -0.04, p = 0.786).nnConclusionsWe report novel findings based on large-scale datasets regarding the relationship between educational attainment and PTSD, supporting the role of economic status as the key mediator in the causal relationship observed.nnWhat is already known on this topicThere is a well-established negative association of educational attainment and other traits related to cognitive ability with posttraumatic stress disorders (PTSD). However, the findings of these previous studies support various possible causal explanations: 1) individuals with high educational attainment are more resilient with respect to developing PTSD, 2) PTSD negatively impacts cognitive ability, or 3) PTSD and educational attainment share some underlying determinants, including relevant molecular mechanisms.nnA key obstacle to disentangling the complex association between educational attainment and PTSD is reverse causation, i.e. the situation in which the outcome precedes and causes the exposure instead of the other way around.nnWhat this study addsWe conducted a causal-inference investigation based on large-scale information from the investigation of more than one million individuals. Our main assumption is that genetic information can strongly minimize the bias of reverse causation, because genetic variants are determined at conception and do not change throughout life.nnOur findings indicate 1) the effect of traits related to educational attainment on PTSD, 2) no reverse effect of PTSD on educational attainment, and 3) economic status mediates the relationship between educational attainment and PTSD, independently from the brain mechanisms related to educational attainment. ]]> Polimanti, R. Ratanatharathorn, A. Maihofer, A. X. Choi, K. W. Stein, M. B. Morey, R. A. Logue, M. W. Nievergelt, C. Stein, D. J. Koenen, K. C. Gelernter, J. the Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup, 2018-12-21 doi:10.1101/503300 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Affective flexibility without perceptual awareness ]]> https://biorxiv.org/content/10.1101/505545v1?rss=1 Homan, P. Lau, H. L. Levy, I. Raio, C. M. Bach, D. R. Carmel, D. Schiller, D. 2018-12-25 doi:10.1101/505545 Cold Spring Harbor Laboratory Press 2018-12-25 <![CDATA[ Increased hippocampal GABAergic inhibition after long-term high-intensity sound exposure ]]> https://biorxiv.org/content/10.1101/507004v1?rss=1 Cunha, A. S. de Deus, J. l. Ceballos, C. C. Leao, R. M. 2018-12-27 doi:10.1101/507004 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Leveraging protein dynamics to identify cancer mutational hotspots in 3D-structures ]]> https://biorxiv.org/content/10.1101/508788v1?rss=1 Kumar, S. Clarke, D. Gerstein, M. 2018-12-31 doi:10.1101/508788 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Multiplexed, sequential secretion analysis of the same single cells reveals distinct effector response dynamics dependent on the initial basal state ]]> https://biorxiv.org/content/10.1101/511238v1?rss=1 Chen, Z. Lu, Y. Zhang, K. Xiao, Y. Lu, J. Fan, R. 2019-01-03 doi:10.1101/511238 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Structure and function of a 9.6 megadalton bacterial iron storage compartment ]]> https://biorxiv.org/content/10.1101/511345v1?rss=1 Giessen, T. W. Orlando, B. J. Verdegaal, A. A. Chambers, M. G. Gardener, J. Bell, D. C. Birrane, G. Liao, M. Silver, P. A. 2019-01-03 doi:10.1101/511345 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Active cargo positioning in antiparallel transport networks ]]> https://biorxiv.org/content/10.1101/512863v1?rss=1 Richard, M. Blanch-Mercader, C. Ennomani, H. Cao, W. De La Cruz, E. Joanny, J.-F. Jülicher, F. Blanchoin, L. Martin, P. 2019-01-06 doi:10.1101/512863 Cold Spring Harbor Laboratory Press 2019-01-06 <![CDATA[ Minimal membrane interactions conferred by Rheb C-terminal farnesylation are essential for mTORC1 activation ]]> https://biorxiv.org/content/10.1101/513473v1?rss=1 Ferguson, S. M. Angarola, B. 2019-01-07 doi:10.1101/513473 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ WNT/β-CATENIN modulates the axial identity of ES derived human neural crest ]]> https://biorxiv.org/content/10.1101/514570v1?rss=1 Gomez, G. A. Prasad, M. S. Wong, M. Charney, R. M. Shelar, P. Sandhu, N. Hackland, J. Hernandez, J. C. Leung, A. W. Garcia-Castro, M. I. 2019-01-08 doi:10.1101/514570 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ Comprehensive substrate specificity profiling of the human nek kinome reveals unexpected signaling outputs ]]> https://biorxiv.org/content/10.1101/515221v1?rss=1 van de Kooij, B. Creixell, P. van Vlimmeren, A. Joughin, B. Miller, C. J. Haider, N. Linding, R. Stambolic, V. Turk, B. E. Yaffe, M. B. 2019-01-08 doi:10.1101/515221 Cold Spring Harbor Laboratory Press 2019-01-08 <![CDATA[ Genomewide Analyses of Psychological Resilience in US Army Soldiers ]]> https://biorxiv.org/content/10.1101/516716v1?rss=1 Stein, M. Choi, K. W. Jain, S. Campbell-Sills, L. Chen, C.-Y. Gelernter, J. He, F. Heeringa, S. G. Maihofer, A. X. Nievergelt, C. M. Nock, M. K. Ripke, S. Sun, X. Kessler, R. C. Smoller, J. W. Ursano, R. J. 2019-01-20 doi:10.1101/516716 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions ]]> https://biorxiv.org/content/10.1101/516864v1?rss=1 Mahmoudabadi, G. Homyk, K. Catching, A. Foley, H. Tadmor, A. Mahmoudabadi, A. Cheung, A. Phillips, R. 2019-01-10 doi:10.1101/516864 Cold Spring Harbor Laboratory Press 2019-01-10 <![CDATA[ Simulation of the mechanics of actin assembly during endocytosis in yeast ]]> https://biorxiv.org/content/10.1101/518423v1?rss=1 Nickaeen, M. Berro, J. Pollard, T. D. Slepchenko, B. M. 2019-01-11 doi:10.1101/518423 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways ]]> https://biorxiv.org/content/10.1101/519967v1?rss=1 Lam, M. Hill, W. D. Trampush, J. W. Yu, J. Knowles, E. Davies, G. Stahl, E. Huckins, L. Liewald, D. C. Djurovic, S. Melle, I. Sundet, K. Christoforou, A. Reinvang, I. DeRosse, P. Lundervold, A. Steen, V. M. Espeseth, T. Raikkonen, K. Widen, E. Palotie, A. Eriksson, J. G. Giegling, I. Konte, B. Hartmann, A. M. Roussos, P. Giakoumaki, S. Burdick, K. E. Payton, A. Ollier, W. Chiba-Falek, O. Attix, D. K. Need, A. C. Cirulli, E. T. Voineskos, A. N. Stefanis, N. Avramopoulos, D. Hatzimanolis, A. Arking, D. E. Smyrnis, N. Bilder, R. M. Freimer, N. A. Cannon, 2019-01-20 doi:10.1101/519967 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ O-GlcNAc transferase suppresses necroptosis and liver fibrosis ]]> https://biorxiv.org/content/10.1101/519975v1?rss=1 Zhang, B. Li, M.-D. Yin, R. Liu, Y. Yang, Y. Mitchell-Richards, K. A. Nam, J. H. Li, R. Wang, L. Iwakiri, Y. Chung, D. Robert, M. E. Ehrlich, B. E. Bennett, A. M. Yu, J. Nathanson, M. Yang, X. 2019-01-14 doi:10.1101/519975 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Observing the origins of human brain development: Automated processing of fetal fMRI ]]> https://biorxiv.org/content/10.1101/525386v1?rss=1 Rutherford, S. Sturmfels, P. Angstadt, M. Hect, J. Wiens, J. van den Heuval, M. I. Scheinost, D. Thomason, M. Sripada, C. 2019-01-21 doi:10.1101/525386 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals ]]> https://biorxiv.org/content/10.1101/525683v1?rss=1 Epi25 Collaborative, Feng, Y.-C. A. Howrigan, D. P. Abbott, L. E. Tashman, K. Cerrato, F. Singh, T. Heyne, H. Byrnes, A. Churchhouse, C. Lal, D. Heinzen, E. L. Cavalleri, G. L. Hakonarson, H. Helbig, I. Krause, R. May, P. Weckhuysen, S. Petrovski, S. Kamalakaran, S. Sisodiya, S. M. Cossette, P. Cotsapas, C. De Jonghe, P. Dixon-Salazar, T. Guerrini, R. Kwan, P. Marson, A. G. Stewart, R. Depondt, C. Dlugos, D. J. Scheffer, I. E. Striano, P. Freyer, C. McKenna, K. Regan, B. M. Bellows, S. T. Leu, C. Bennett, C. A. Johns, E. M. C. Macdonald, A. Shilling, 2019-01-21 doi:10.1101/525683 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Genome-wide Association Study of Alcohol Consumption and Use Disorder in Multiple Populations (N = 274,424) ]]> https://biorxiv.org/content/10.1101/527929v1?rss=1 Kranzler, H. Zhou, H. Kember, R. Smith, R. V. Justice, A. Damrauer, S. Tsao, P. S. Klarin, D. Rader, D. J. Cheng, Z. Tate, J. P. Becker, W. C. Concato, J. Xu, K. Polimanti, R. Zhao, H. Gelernter, J. 2019-01-25 doi:10.1101/527929 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Genome wide meta-analysis identifies genomic relationships, novel loci, and pleiotropic mechanisms across eight psychiatric disorders. ]]> https://biorxiv.org/content/10.1101/528117v1?rss=1 Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee, P. H. Anttila, V. Won, H. Feng, Y.-C. A. Rosenthal, J. Zhu, Z. Tucker-Drob, E. M. Nivard, M. G. Grotzinger, A. D. Posthuma, D. Wang, M. M.- J. Yu, D. Stahl, E. Walters, R. K. Anney, R. J. L. Duncan, L. E. Belangero, S. Luykx, J. Kranzler, H. Keski-Rahkonen, A. Cook, E. H. Kirov, G. Coppola, G. Kaprio, J. Zai, C. C. Hoekstra, P. J. Banaschewski, T. Rohde, L. A. PGC Attention Deficit Hyperactivity Disorder Group, PGC Autism Spectrum Disorder Group, PGC Bipolar Disorder Group, PGC Eating Diso 2019-01-26 doi:10.1101/528117 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ The Evolution of Placental Invasion and Cancer Metastasis are Causally Linked ]]> https://biorxiv.org/content/10.1101/528646v1?rss=1 Gupta, K. Afzal, J. Maziarz, J. D. Hamidzadeh, A. Liang, C. Erkenbrack, E. M. Nam, H. Haeger, J.-D. Pfarrer, C. Hoang, T. Ott, T. Spencer, T. Pavlicev, M. Antczak, D. Levchenko, A. Wagner, G. P. 2019-01-23 doi:10.1101/528646 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Leveraging tissue specific gene expression regulation to identify genes associated with complex diseases ]]> https://biorxiv.org/content/10.1101/529297v1?rss=1 0.99) pLI scores compared to other methods. When T-GEN was applied to late-onset Alzheimers disease, we identified 96 genes located at 15 loci, including two novel loci not implicated in previous GWAS. We further replicated 50 genes in an independent GWAS, including one of the two novel loci. Author summaryTWAS-like methods have been widely applied to understand disease etiology using eQTL data and GWAS results. However, it is still challenging to discriminate the true disease-associated genes from those in strong LD with true genes, which is largely due to the misidentification of eQTLs. Here we introduce a novel statistical method named T-GEN to identify disease-associated genes considering epigenetic information. Compared to current TWAS methods, T-GEN can not only identify eQTLs with higher CADD scores and function potentials in gene-expression imputation models, but also identify more disease-associated genes across 207 traits and more genes with high (>0.99) pLI scores. Applying T-GEN in late-onset Alzheimers disease identified 96 genes at 15 loci with two novel loci. Among 96 identified genes, 50 genes were further replicated in an independent GWAS. ]]> Liu, W. Li, M. Zhang, W. Zhou, G. Wu, X. Wang, J. Zhao, H. 2019-01-23 doi:10.1101/529297 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Facilitating open-science with realistic fMRI simulation: validation and application ]]> https://biorxiv.org/content/10.1101/532424v1?rss=1 Ellis, C. Baldassano, C. Schapiro, A. C. Cai, M. B. Cohen, J. 2019-01-28 doi:10.1101/532424 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Enhancing experimental signals in single-cell RNA-sequencing data using graph signal processing ]]> https://biorxiv.org/content/10.1101/532846v1?rss=1 Burkhardt, D. B. Stanley, J. S. Perdigoto, A. L. Gigante, S. A. Herold, K. C. Wolf, G. Giraldez, A. van Dijk, D. Krishnaswamy, S. 2019-01-28 doi:10.1101/532846 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ A physiological approach to the ecology and evolution of flowers ]]> https://biorxiv.org/content/10.1101/539668v1?rss=1 Roddy, A. 2019-02-07 doi:10.1101/539668 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Reproducible Risk Loci and Psychiatric Comorbidities in Anxiety: Results from ~200,000 Million Veteran Program Participants ]]> https://biorxiv.org/content/10.1101/540245v1?rss=1 Levey, D. F. Gelernter, J. Polimanti, R. Zhou, H. Cheng, Z. Aslan, M. Quaden, R. Concato, J. Radhakrishnan, K. Bryois, J. Sullivan, P. F. the Million Veteran Program, Stein, M. 2019-02-05 doi:10.1101/540245 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Machine-learning to Improve Prediction of Mortality following Acute Myocardial Infarction: An Assessment in the NCDR-Chest Pain-Myocardial Infarction Registry ]]> https://biorxiv.org/content/10.1101/540369v1?rss=1 Khera, R. Haimovich, J. Hurley, N. McNamara, R. Spertus, J. A. Desai, N. Masoudi, F. A. Huang, C. Normand, S.-L. Mortazavi, B. J. Krumholz, H. M. 2019-02-05 doi:10.1101/540369 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Layer 5 circuits in V1 differentially control visuomotor behavior ]]> https://biorxiv.org/content/10.1101/540807v1?rss=1 Tang, L. Higley, M. J. 2019-02-05 doi:10.1101/540807 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Fingerprinting Adiposity and Metabolic Function in the Brains of Overweight and Obese Humans ]]> https://biorxiv.org/content/10.1101/540997v1?rss=1 Farruggia, M. C. van Kooten, M. J. Burke, M. V. Scheinost, D. Constable, R. T. Small, D. M. 2019-02-05 doi:10.1101/540997 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Relationships between depressive symptoms and brain responses during emotional movie viewing emerge in adolescence ]]> https://biorxiv.org/content/10.1101/542720v1?rss=1 Gruskin, D. C. Rosenberg, M. D. Holmes, A. J. 2019-02-06 doi:10.1101/542720 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Proximity labeling reveals novel interactomes in live Drosophila tissue ]]> https://biorxiv.org/content/10.1101/542795v1?rss=1 Mannix, K. M. Starble, R. M. Kaufman, R. S. Cooley, L. 2019-02-06 doi:10.1101/542795 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Whole Brain Polarity Regime Dynamics are Significantly Disrupted in Schizophrenia and Correlate Strongly with Network Connectivity Measures ]]> https://biorxiv.org/content/10.1101/543751v1?rss=1 Miller, R. Pearlson, G. Calhoun, V. 2019-02-08 doi:10.1101/543751 Cold Spring Harbor Laboratory Press 2019-02-08 <![CDATA[ Metabolome-Wide Mendelian Randomization Analysis of Emotional and Behavioral Responses to Traumatic Stress ]]> https://biorxiv.org/content/10.1101/545442v1?rss=1 Muniz Carvalho, C. Wendt, F. R. Stein, D. J. Stein, M. B. Gelernter, J. Belangero, S. I. Polimanti, R. 2019-02-10 doi:10.1101/545442 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Reclamation is not the primary determinant of soil recovery from oil and gas development in Wyoming sagebrush systems ]]> https://biorxiv.org/content/10.1101/546804v1?rss=1 Rottler, C. Burke, I. C. Lauenroth, W. K. 2019-02-11 doi:10.1101/546804 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ The kinetics of nucleotide binding to isolated Chlamydomonas axonemes using UV-TIRF microscopy ]]> https://biorxiv.org/content/10.1101/547091v1?rss=1 Feofilova, M. Mahamdeh, M. S. S. Howard, J. 2019-02-11 doi:10.1101/547091 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Global Signal Regression Strengthens Association between Resting-State Functional Connectivity and Behavior ]]> https://biorxiv.org/content/10.1101/548644v1?rss=1 Li, J. Kong, R. Liegeois, R. Orban, C. Tan, Y. Sun, N. Holmes, A. J. Sabuncu, M. R. Ge, T. Yeo, B. T. T. 2019-02-13 doi:10.1101/548644 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Unmatched level of molecular convergence among deeply divergent complex multicellular fungi ]]> https://biorxiv.org/content/10.1101/549758v1?rss=1 650 million years of divergence, the same genes have repeatedly been co-opted for the development of complex multicellularity in the two largest clades of fungi--the Ascomycota and Basidiomycota. Co-opted genes have undergone duplications in both clades, resulting in >81% convergence across shared multicellularity-related families. This convergence is coupled with a rich repertoire of multicellularity-related genes in ancestors that predate complex multicellular fungi, suggesting that the coding capacity of early fungal genomes was well suited for the repeated evolution of complex multicellularity. Our work suggests that evolution may be predictable not only when organisms are closely related or are under similar selection pressures, but also if the genome biases the potential evolutionary trajectories organisms can take, even across large phylogenetic distances. ]]> Merenyi, Z. Prasanna, A. N. Zheng, W. Kovacs, K. Hegedus, B. Balint, B. Papp, B. Townsend, J. P. Nagy, L. G. 2019-02-14 doi:10.1101/549758 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Altered brain function in anorexia nervosa and bulimia nervosa: A hierarchical series of task-based fMRI meta-analyses ]]> https://biorxiv.org/content/10.1101/550301v1?rss=1 Liu, B. Liu, J. Ju, Y. Wang, M. Liu, T. Zhang, Y. Li, L. Potenza, M. Barron, D. S. 2019-02-14 doi:10.1101/550301 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ In situ structures of periplasmic flagella in Borrelia reveals conformational changes essential for flagellar rotation ]]> https://biorxiv.org/content/10.1101/553289v1?rss=1 Liu, J. Chang, Y. Moon, K. Zhao, X. Norris, S. J. Motaleb, M. A. 2019-02-18 doi:10.1101/553289 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Short-term consumption of sucralose with, but not without, carbohydrate impairs neural and metabolic sensitivity to sugar ]]> https://biorxiv.org/content/10.1101/557801v1?rss=1 Dalenberg, J. R. Patel, B. P. Denis, R. Veldhuizen, M. G. Nakamura, Y. Vinke, P. C. Luquet, S. Small, D. M. 2019-02-22 doi:10.1101/557801 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination ]]> https://biorxiv.org/content/10.1101/558825v1?rss=1 Hoehn, K. B. Vander Heiden, J. A. Zhou, J. Q. Lunter, G. Pybus, O. G. Kleinstein, S. 2019-02-24 doi:10.1101/558825 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro ]]> https://biorxiv.org/content/10.1101/558841v1?rss=1 Kosyakova, N. Kao, D. D. Lopez-Giraldez, F. Spindler, S. Graham, M. James, K. J. Shin, J. W. Liu, X. Tietjen, G. T. Pober, J. S. Chang, W. G. 2019-02-22 doi:10.1101/558841 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Mechanics of membrane internalization against osmotic pressure: boundary conditions make a difference ]]> https://biorxiv.org/content/10.1101/558890v1?rss=1 MA, R. Berro, J. 2019-02-22 doi:10.1101/558890 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Pleiotropic requirements for human TDP-43 in the regulation of cell and organelle homeostasis ]]> https://biorxiv.org/content/10.1101/560144v1?rss=1 Ferguson, S. M. Roczniak-Ferguson, A. 2019-02-25 doi:10.1101/560144 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions ]]> https://biorxiv.org/content/10.1101/560912v1?rss=1 Quintero, I. Landis, M. J. 2019-02-25 doi:10.1101/560912 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Effects of age, BMI and sex on the glial cell marker TSPO - a multicentre PBR28 HRRT PET study ]]> https://biorxiv.org/content/10.1101/564831v1?rss=1 Tuisku, J. Plaven-Sigray, P. Gaiser, E. C. Airas, L. Al-Abdulrasul, H. Bruck, A. Carson, R. E. Chen, M.-K. Cosgrove, K. P. Ekblad, L. Esterlis, I. Farde, L. Forsberg, A. Halldin, C. Helin, S. Kosek, E. Lekander, M. Lindgren, N. Marjamaki, P. Rissanen, E. Sucksdorff, M. Varrone, A. HRRT [11C]PBR28 study group, Rinne, J. Matuskey, D. Cervenka, S. 2019-03-01 doi:10.1101/564831 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Dosing regimen of gentamicin and the effect of antenatal steroids on clearance in preterm infants ]]> https://biorxiv.org/content/10.1101/566125v1?rss=1 48 hours from January 2005 to June 2007. Serum gentamicin peak and trough concentrations were determined, and PK/PD profiles calculated using standard noncompartmental methods.nnResult122 (63%) infants received ODD and 73 (37%) received q18h regimen. Desired gentamicin peak (5 to 12 mcg/mL) and trough (<2 mcg/mL) concentrations were achieved in 80% (95%CI, 72-86) on ODD vs. 47% (95%CI, 36-58) on q18h (p<0.001). Target drug exposure (AUC >72 mcg/mL/hr) was achieved in 73% (89/122) of infants on ODD vs. 22% (16/73) on q18h (p < 0.001). GentCL was significantly lower in those who receive antenatal steroid (37+/-8 mL/kg/hr vs. 42+/-13 mL/kg/hr, p=0.04) but not affected by postnatal indomethacin treatment (p>0.86).nnConclusionPK/PD profile of gentamicin is improved by ODD in preterm infants. GentCl was significantly less in infants exposed to antenatal steroids but not in those treated with indomethacin. ]]> Santos, R. P. Chang, Y. Oliveira, C. R. Adams-Huet, B. Gard, J. Sanchez, P. J. 2019-03-20 doi:10.1101/566125 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Modulation of Flagellar Rotation in Surface-Attached Bacteria: A Circuit for Rapid Surface-Sensing ]]> https://biorxiv.org/content/10.1101/567438v1?rss=1 Schniederberend, M. Johnston, J. F. Shine, E. E. Shen, C. Jain, R. Emonet, T. Kazmierczak, B. 2019-03-04 doi:10.1101/567438 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Risk of differential cancer types over age in families with Li-Fraumeni syndrome: a validation study using multi-center cohorts ]]> https://biorxiv.org/content/10.1101/567727v1?rss=1 Shin, S. J. Dodd, E. Peng, G. Bojadzieva, J. Chen, J. Amos, C. Mai, P. L. Savage, S. A. Ballinger, M. L. Thomas, D. M. yuan, Y. Strong, L. C. Wang, W. 2019-03-05 doi:10.1101/567727 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Content-based dissociation of hippocampal involvement in prediction ]]> https://biorxiv.org/content/10.1101/568303v1?rss=1 Kok, P. Rait, L. I. Turk-Browne, N. B. 2019-03-05 doi:10.1101/568303 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Structure elucidation of colibactin. ]]> https://biorxiv.org/content/10.1101/574053v1?rss=1 Xue, M. Kim, C. S. Healy, A. R. Wernke, K. W. Wang, Z. Frischling, M. C. Shine, E. E. Wang, W. Herzon, S. B. Crawford, J. M. 2019-03-12 doi:10.1101/574053 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Structural Basis for the Clamping and Ca2+ Activation of SNARE-mediated Fusion by Synaptotagmin ]]> https://biorxiv.org/content/10.1101/574632v1?rss=1 Grushin, K. Wang, J. Coleman, J. Rothman, J. E. Sindelar, C. E. Krishnakumar, S. S. 2019-03-12 doi:10.1101/574632 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Impact of Direct Acting Antivirals on Survival in Patients with Chronic Hepatitis C and Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.1101/575670v1?rss=1 Kamp, W. M. Sellers, C. M. Stein, S. M. Lim, J. K. Kim, H. S. 2019-03-12 doi:10.1101/575670 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Gender differences in attitudes toward death among Chinese university students: A survey in hunan and Heilongjiang province ]]> https://biorxiv.org/content/10.1101/578955v1?rss=1 Wang, Y. Tang, S. Hu, X. Qin, C. Ma, L. Li, Y. Khoshnood, K. Sun, M. 2019-03-16 doi:10.1101/578955 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Transverse sinus injections: A novel method for whole-brain vector-driven gene delivery ]]> https://biorxiv.org/content/10.1101/579730v1?rss=1 Hamodi, A. S. Martinez Sabino, A. Fitzgerald, N. D. Crair, M. C. 2019-03-16 doi:10.1101/579730 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ A Drosophila model of neuronal ceroid lipofuscinosis CLN4 reveals a hypermorphic gain of function mechanism ]]> https://biorxiv.org/content/10.1101/579771v1?rss=1 Imler, E. Pyon, J. S. Kindelay, S. Zhang, Y.-q. Chandra, S. S. Zinsmaier, K. E. 2019-03-15 doi:10.1101/579771 Cold Spring Harbor Laboratory Press 2019-03-15 <![CDATA[ Ring canals permit extensive cytoplasm sharing among germline cells independent of fusomes in Drosophila testes ]]> https://biorxiv.org/content/10.1101/581702v1?rss=1 Kaufman, R. S. Price, K. L. Mannix, K. Ayers, K. Hudson, A. M. Cooley, L. 2019-03-18 doi:10.1101/581702 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Breast cancer classification based on proteotypes obtained by SWATH mass spectrometry ]]> https://biorxiv.org/content/10.1101/583443v1?rss=1 0.67), general correlation did not exceed R=0.29, indicating the value of protein-level measurements of biomarkers and disease-regulated genes. Overall, our data shows how large-scale protein-level measurements by next-generation proteomics can lead to improved patient stratification for precision medicine. ]]> Bouchal, P. Schubert, O. T. Faktor, J. Capkova, L. Imrichova, H. Zoufalova, K. Paralova, V. Hrstka, R. Liu, Y. Ebhardt, H. A. Budinska, E. Nenutil, R. Aebersold, R. 2019-03-26 doi:10.1101/583443 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Functional diversification enabled grassy biomes to fill global climate space ]]> https://biorxiv.org/content/10.1101/583625v1?rss=1 50% of the ground layer is covered by grasses) occupy almost every part of Earths vegetated climate space, characterising over 40% of the land surface. Major evolutionary lineages of grasses have specialised in different environments, but species from only three grass lineages occupy 88% of the land area of grassy vegetation, segregating along gradients of temperature, rainfall and fire. The environment occupied by each lineage is associated with unique plant trait combinations, including C3 and C4 photosynthesis, maximum plant height, and adaptations to fire and aridity. There is no single global climatic limit where C4 grasses replace C3 grasses. Instead this ecological transition varies biogeographically, with continental disjunctions arising through contrasting evolutionary histories.nnSignificance statementWorldviews of vegetation generally focus on trees and forests but grasses characterize the ground layer over 40% of the Earths vegetated land surface. This omission is important because grasses transform surface-atmosphere exchanges, biodiversity and disturbance regimes. We looked beneath the trees to produce the first global map of grass-dominated biomes. Grassy biomes occur in virtually every climate on Earth. However, three lineages of grasses are much more successful than others, characterizing 88% of the land area of grassy biomes. Each of these grass lineages evolved ecological specializations related to aridity, freezing and fire. Recognizing the extent and causes of grass dominance beneath trees is important because grassy vegetation plays vital roles in the dynamics of our biosphere and human wellbeing. ]]> Lehmann, C. Griffith, D. Simpson, K. Anderson, M. Archibald, S. Beerling, D. Bond, W. Denton, E. Edwards, E. Forrestel, E. Fox, D. Georges, D. Hoffmann, W. Kluyver, T. Mucina, L. Pau, S. Ratnam, J. Salamin, N. Santini, B. Smith, M. Spriggs, E. Westley, R. Still, C. Stromberg, C. Osborne, C. 2019-03-21 doi:10.1101/583625 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Statistical learning shapes neural sequence representations ]]> https://biorxiv.org/content/10.1101/583856v1?rss=1 Henin, S. Turk-Browne, N. Friedman, D. Liu, A. Dugan, P. Flinker, A. Doyle, W. Devinsky, O. Melloni, L. 2019-03-21 doi:10.1101/583856 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress ]]> https://biorxiv.org/content/10.1101/586305v1?rss=1 Grey, M. J. Cloots, E. Simpson, M. S. LeDuc, N. Serebrenik, Y. De Luca, H. De Sutter, D. Luong, P. Thiagarajah, J. R. Paton, A. W. Paton, J. C. Seeliger, M. Eyckerman, S. Janssens, S. Lencer, W. I. 2019-03-23 doi:10.1101/586305 Cold Spring Harbor Laboratory Press 2019-03-23 <![CDATA[ A chemical counterpunch: Chromobacterium violaceum ATCC31532 produces violacein in response to translation-inhibiting antibiotics ]]> https://biorxiv.org/content/10.1101/589192v1?rss=1 Lozano, G. L. Guan, C. Cao, Y. Borlee, B. R. Broderick, N. A. Stabb, E. V. Handelsman, J. 2019-03-27 doi:10.1101/589192 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Effect of READ1 on latent profiles of reading disability and comorbid attention and language learning disability subtypes ]]> https://biorxiv.org/content/10.1101/589226v1?rss=1 Li, M. Truong, D. DeMille, M. Malins, J. Lovett, M. Bosson-Heenan, J. Gruen, J. R. Frijters, J. 2019-03-27 doi:10.1101/589226 Cold Spring Harbor Laboratory Press 2019-03-27 <![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[ Spatio-temporal distribution of Spiroplasma infections in the tsetse fly (Glossina fuscipes fuscipes) in northern Uganda ]]> https://biorxiv.org/content/10.1101/591321v1?rss=1 Schneider, D. I. Saarman, N. Onyango, M. G. Hyseni, C. Opiro, R. Echodu, R. O'Neill, M. Bloch, D. Vigneron, A. Johnson, T. J. Dion, K. Weiss, B. L. Opiyo, E. Caccone, A. Aksoy, S. 2019-03-28 doi:10.1101/591321 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ High-Speed Automatic Characterization of Rare Events in Flow Cytometric Data ]]> https://biorxiv.org/content/10.1101/591644v1?rss=1 Qi, Y. Fang, Y. Sinclair, D. R. Guo, S. Alberich-Jorda, M. Lu, J. Tenen, D. G. Kharas, M. G. Pyne, S. 2019-03-30 doi:10.1101/591644 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Quantification of biomolecular dynamics inside real and synthetic nuclear pore complexes using time-resolved atomic force microscopy ]]> https://biorxiv.org/content/10.1101/592303v1?rss=1 Stanley, G. J. Akpinar, B. Shen, Q. Ellis Fisher, P. D. Lusk, C. P. Lin, C. Hoogenboom, B. 2019-03-28 doi:10.1101/592303 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Prokaryotic SPHINX sequences are conserved in mammalian brain and participate in neurodegeneration ]]> https://biorxiv.org/content/10.1101/593954v1?rss=1 Manuelidis, L. Szigeti-Buck, K. 2019-03-30 doi:10.1101/593954 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Synaptotagmin 1 oligomers clamp and regulate different modes of neurotransmitter release ]]> https://biorxiv.org/content/10.1101/594051v1?rss=1 Tagliatti, E. Bello, O. D. Mendonca, P. R. F. Kotzadimitriou, D. Nicholson, E. Coleman, J. Timofeeva, Y. Rothman, J. Krishnakumar, S. Volynski, K. 2019-03-30 doi:10.1101/594051 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Limiting-stress-elimination hypothesis: approach to increase savanna cowpea productivity by stress reduction ]]> https://biorxiv.org/content/10.1101/594754v1?rss=1 Atta-Boateng, A. Berlyn, G. 2019-03-31 doi:10.1101/594754 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Molecular Dynamics Analysis of Mg2+-dependent Cleavage of a Pistol Ribozyme Reveals a Fail-safe Secondary Ion for Catalysis ]]> https://biorxiv.org/content/10.1101/596270v1?rss=1 Roy, R. N. Joseph, N. N. Steitz, T. A. 2019-04-02 doi:10.1101/596270 Cold Spring Harbor Laboratory Press 2019-04-02 <![CDATA[ A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer ]]> https://biorxiv.org/content/10.1101/600130v1?rss=1 Lee, B. H. Kelly, G. Bradford, S. Davila, M. Guo, X. V. Amir, E.-a. D. Thrash, E. M. Solga, M. Lannigan, J. Sellers, B. Candia, J. Tsang, J. Montgomery, R. Tamaki, S. Sigdel, T. Sarwal, M. Lanier, L. Tian, Y. Kim, C. Hinz, D. Peters, B. Sette, A. Rahman, A. 2019-04-05 doi:10.1101/600130 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ YAP controls cell migration and invasion through a Rho-GTPase switch ]]> https://biorxiv.org/content/10.1101/602052v1?rss=1 Shah, S. R. Tippens, N. D. Park, J. Mohyeldin, A. Wang, S. Vela, G. Martinez-Gutierrez, J. C. Margolis, S. S. Schmidt, S. Xia, S. Levchenko, A. Quinones-Hinojosa, A. 2019-04-08 doi:10.1101/602052 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ N-Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/602912v1?rss=1 Kasper, D. Wu, Y. Mandl, H. K. Salina, K. Ghersi, J. Hintzen, J. Armerp, W. He, Z. Heindel, D. W. Park, E. J. Sessa, W. Mahal, L. Hirschi, K. Nicoli, S. 2019-04-09 doi:10.1101/602912 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ 3D Multicolor Nanoscopy at 10,000 Cells a Day ]]> https://biorxiv.org/content/10.1101/606954v1?rss=1 Barentine, A. E. S. Lin, Y. Liu, M. Kidd, P. Balduf, L. Grace, M. R. Wang, S. Bewersdorf, J. Baddeley, D. 2019-04-12 doi:10.1101/606954 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Aging induces Nlrp3 inflammasome dependent adipose B cell expansion to impair metabolic homeostasis ]]> https://biorxiv.org/content/10.1101/607192v1?rss=1 Camell, C. D. Lee, A. Günther, P. Goldberg, E. L. Spadaro, O. Youm, Y.-H. Bartke, A. Hubbard, G. B. Ikeno, Y. Ruddle, N. H. Schultz, J. L. Dixit, V. D. 2019-04-13 doi:10.1101/607192 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Phylogenetic and Spatial Distribution of Evolutionary Isolation and Threat in Turtles and Crocodilians (Non-Avian Archosauromorphs) ]]> https://biorxiv.org/content/10.1101/607796v1?rss=1 Colston, T. J. Kulkarni, P. Jetz, W. Pyron, R. A. 2019-04-13 doi:10.1101/607796 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Targeted sequence capture outperforms RNA-Seq and degenerate-primer PCR cloning for sequencing the largest mammalian multi-gene family ]]> https://biorxiv.org/content/10.1101/607994v1?rss=1 400 intact OR genes, more than double the number based on original estimates. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomic ORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all putative receptors in the genome. Therefore, variation among assemblies was caused by low coverage of some receptors, rather than high rates of assembly error. Given this variability, we caution against using the counts of number of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes. ]]> Yohe, L. R. Davies, K. T. Simmons, N. B. Sears, K. E. Dumont, E. Rossiter, S. J. Davalos, L. 2019-04-13 doi:10.1101/607994 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ Pericytes enable effective angiogenesis in the presence of pro inflammatory signals ]]> https://biorxiv.org/content/10.1101/608059v1?rss=1 Kang, T.-Y. Bocci, F. Jolly, M. K. Levine, H. Onuchic, J. N. Levchenko, A. 2019-04-13 doi:10.1101/608059 Cold Spring Harbor Laboratory Press 2019-04-13 <![CDATA[ A programmable DNA-origami platform for studying protein-mediated lipid transfer between bilayers ]]> https://biorxiv.org/content/10.1101/610212v1?rss=1 Bian, X. Zhang, Z. De Camilli, P. Lin, C. 2019-04-15 doi:10.1101/610212 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ GIGANTEA recruits deubiquitylases, UBP12 and UBP13, to regulate accumulation of the ZTL photoreceptor complex ]]> https://biorxiv.org/content/10.1101/611533v1?rss=1 Lee, C.-m. Li, M. W. Feke, A. Saffer, A. M. Liu, W. Gendron, J. M. 2019-04-18 doi:10.1101/611533 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Retinal and callosal activity-dependent chandelier cell elimination shapes binocularity in primary visual cortex ]]> https://biorxiv.org/content/10.1101/612358v1?rss=1 Wang, B.-S. Bernardez Sarria, M. S. He, M. Crair, M. C. Huang, Z. J. 2019-04-18 doi:10.1101/612358 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Nanoscale subcellular architecture revealed by multicolor 3D salvaged fluorescence imaging ]]> https://biorxiv.org/content/10.1101/613174v1?rss=1 Zhang, Y. Schroeder, L. K. Lessard, M. D. Kidd, P. Chung, J. Song, Y. Benedetti, L. Li, Y. Ries, J. De Camilli, P. Rothman, J. E. Baddeley, D. Bewersdorf, J. 2019-04-18 doi:10.1101/613174 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Crosslinking actin networks produces compressive force ]]> https://biorxiv.org/content/10.1101/614453v1?rss=1 Ma, R. Berro, J. 2019-04-19 doi:10.1101/614453 Cold Spring Harbor Laboratory Press 2019-04-19 <![CDATA[ Lowe Syndrome-linked endocytic adaptors direct membrane cycling kinetics with OCRL in Dictyostelium discoideum. ]]> https://biorxiv.org/content/10.1101/616664v1?rss=1 Luscher, A. Fröhlich, F. Barisch, C. Littlewood, C. Metcalfe, J. Leuba, F. Palma, A. Pirruccello, M. Cesareni, G. Stagi, M. Walther, T. C. Soldati, T. De Camilli, P. Swan, L. E. 2019-04-24 doi:10.1101/616664 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Single-molecule turnover dynamics of actin and membrane coat proteins in clathrin-mediated endocytosis ]]> https://biorxiv.org/content/10.1101/617746v1?rss=1 Lacy, M. M. Baddeley, D. Berro, J. 2019-04-24 doi:10.1101/617746 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ The scaling of genome size and cell size limits maximum rates of photosynthesis with implications for ecological strategies ]]> https://biorxiv.org/content/10.1101/619585v1?rss=1 Roddy, A. Theroux-Rancourt, G. Abbo, T. Brodersen, C. R. Jensen, B. M. Jiang, G.-F. Thompson, R. A. Kuebbing, S. E. Simonin, K. A. 2019-04-26 doi:10.1101/619585 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ N-WASP regulates the mobility of the B cell receptor and co-receptors during signaling activation ]]> https://biorxiv.org/content/10.1101/619627v1?rss=1 Rey-Suarez, I. Wheatley, B. Koo, P. Shu, Z. Mochrie, S. Song, W. Shroff, H. Upadhyaya, A. 2019-04-26 doi:10.1101/619627 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Functional genomics of the stable fly, Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control ]]> https://biorxiv.org/content/10.1101/623009v1?rss=1 Olafson, P. U. Aksoy, S. Attardo, G. M. Buckmeier, G. Chen, X. Coates, C. J. Davis, M. Dykema, J. T. Emrich, S. J. Friedrich, M. Holmes, C. J. Ioannidis, P. Jansen, E. N. Jennings, E. C. Lawson, D. Martinson, E. O. Maslen, G. L. Meisel, R. P. Murphy, T. D. Nayduch, D. Nelson, D. R. Oyen, K. J. Raszick, T. J. Ribeiro, J. M. C. Robertson, H. M. Rosendale, A. J. Sackton, T. B. Swiger, S. L. Sze, S.-H. Tarone, A. M. Taylor, D. B. Warren, W. C. Waterhouse, R. M. Weirauch, M. T. Werren, J. H. Wilson, R. K. Zdobnov, E. M. Benoit, J. B. 2019-05-02 doi:10.1101/623009 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ C9orf72 dipeptide repeats inhibit UPF1-mediated RNA decay independent of stress granule formation ]]> https://biorxiv.org/content/10.1101/623769v1?rss=1 Sun, Y. Eshov, A. Guo, J. U. 2019-04-30 doi:10.1101/623769 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ The neuronal calcium sensor Synaptotagmin-1 and SNARE proteins cooperate to dilate fusion pores mechanically ]]> https://biorxiv.org/content/10.1101/623827v1?rss=1 Wu, Z. Dharan, N. Thiyagarajan, S. O'Shaughnessy, B. Karatekin, E. 2019-04-30 doi:10.1101/623827 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Alternate subunit assembly diversifies the function of a bacterial toxin ]]> https://biorxiv.org/content/10.1101/624130v1?rss=1 Galan, J. E. Fowler, C. Stack, G. Xiao, X. Lara-Tejero, M. 2019-04-30 doi:10.1101/624130 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Multi-Scale, Patient-Specific Computational Flow Dynamics Models Predict Formation of Neointimal Hyperplasia in Saphenous Vein Grafts ]]> https://biorxiv.org/content/10.1101/624312v1?rss=1 Donadoni, F. Diaz, V. Pichardo-Almarza, C. Homer-Vanniasinkam, S. Dardik, A. 2019-05-03 doi:10.1101/624312 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ 3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples ]]> https://biorxiv.org/content/10.1101/626887v1?rss=1 Lin, R. Lutz, T. Clowsley, A. H. Baddeley, D. Soeller, C. 2019-05-03 doi:10.1101/626887 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ Induced illusory body ownership in Borderline Personality Disorder ]]> https://biorxiv.org/content/10.1101/628131v1?rss=1 HC, F = 11.94 p = 0.001), and condition (synchronous > asynchronous, F(1,43) = 22.80, p < 0.001). There was a group x condition interaction for proprioceptive drift (F(1,43) = 6.48, p = 0.015) such that people with BPD maintained illusion susceptibility in the asynchronous condition. Borderline symptom severity correlated with illusion strength within the BPD group, and this effect was specific to affective symptoms (r = 0.48, p < 0.01). Across all participants, trait psychoticism correlated with illusion strength (r = 0.44, p < 0.01).nnConclusionPeople with BPD are more susceptible to illusory body ownership than controls. This is consistent with the clinical literature describing aberrant physical and emotional experience of self in BPD. A predictive-coding framework holds promise to develop testable mechanistic hypotheses for disrupted bodily self in BPD.nnHighlightsO_LIThe rubber hand illusion (RHI) allows measurement of self-disturbance.nC_LIO_LIPeople with BPD had greater illusion susceptibility and this correlated with affective symptoms.nC_LIO_LIInteroception stabilizes representations of body ownership, and is impaired in BPD.nC_LIO_LIIllusion strength correlates with psychotic traits across levels of psychopathology.nC_LIO_LIPredictive coding frameworks can probe mechanisms of impaired body ownership in psychopathology.nC_LI ]]> Neustadter, E. S. Fineberg, S. K. Leavitt, J. Carr, M. M. Corlett, P. R. 2019-05-05 doi:10.1101/628131 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use ]]> https://biorxiv.org/content/10.1101/628180v1?rss=1 Wu, W. Wang, Z. Xu, K. Zhang, X. Amei, A. Gelernter, J. Zhao, H. Justice, A. C. Wang, Z. 2019-05-17 doi:10.1101/628180 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Corticostriatal stimulation compensates for medial frontal inactivation during interval timing ]]> https://biorxiv.org/content/10.1101/628263v1?rss=1 Emmons, E. B. Kennedy, M. Kim, Y. Narayanan, N. S. 2019-05-05 doi:10.1101/628263 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness ]]> https://biorxiv.org/content/10.1101/628669v1?rss=1 Song, R. Acar, M. 2019-05-05 doi:10.1101/628669 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Quantitative insights into age-associated DNA-repair inefficiency in single cells ]]> https://biorxiv.org/content/10.1101/628909v1?rss=1 Young, T. Z. Liu, P. Acar, M. 2019-05-07 doi:10.1101/628909 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Inhibition of GMP synthesis extends yeast replicative lifespan ]]> https://biorxiv.org/content/10.1101/629428v1?rss=1 Sarnoski, E. A. Liu, P. Urbonaite, G. Olmez, T. T. Young, T. Z. Song, R. Acar, M. 2019-05-07 doi:10.1101/629428 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ High risk glioblastoma cells revealed by machine learning and single cell signaling profiles ]]> https://biorxiv.org/content/10.1101/632208v1?rss=1 Leelatian, N. Sinnaeve, J. Mistry, A. M. Barone, S. M. Diggins, K. E. Greenplate, A. R. Weaver, K. D. Thompson, R. C. Chambless, L. B. Mobley, B. C. Ihrie, R. A. Irish, J. M. 2019-05-10 doi:10.1101/632208 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Sphingolipid production by gut Bacteroidetes regulates glucose homeostasis ]]> https://biorxiv.org/content/10.1101/632877v1?rss=1 Johnson, E. L. Heaver, S. L. Waters, J. L. Kim, B. I. Bretin, A. Goodman, A. L. Gewirtz, A. T. Worgall, T. S. Ley, R. E. 2019-05-09 doi:10.1101/632877 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS ]]> https://biorxiv.org/content/10.1101/633479v1?rss=1 Heusel, M. Frank, M. Koehler, M. Amon, S. Frommelt, F. Rosenberger, G. Bludau, I. Aulakh, S. Linder, M. I. Liu, Y. Collins, B. C. Matthias, G. Ulrike, K. Aebersold, R. 2019-05-09 doi:10.1101/633479 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Discovery of an essential mycobacterial polar growth factor involved in cell envelope integrity and LM/LAM transport ]]> https://biorxiv.org/content/10.1101/633768v1?rss=1 Gupta, K. R. Rahlwes, K. C. Wang, C. Liu, J. Morita, Y. S. Rego, E. H. 2019-05-09 doi:10.1101/633768 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Quantitative Models of Phage-Antibiotics Combination Therapy ]]> https://biorxiv.org/content/10.1101/633784v1?rss=1 Rodriguez-Gonzalez, R. A. Leung, C. Y. Chan, B. K. Turner, P. E. Weitz, J. S. 2019-05-10 doi:10.1101/633784 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ The Connectivity Index: An Effective Metric for Grading Epileptogenicity ]]> https://biorxiv.org/content/10.1101/635664v1?rss=1 Yan, Q. Gaspard, N. Zaveri, H. P. Blumenfeld, H. Hirsch, L. J. Spencer, D. D. Alkawadri, R. 2019-05-12 doi:10.1101/635664 Cold Spring Harbor Laboratory Press 2019-05-12 <![CDATA[ The Glycolytic Protein Phosphofructokinase Dynamically Relocalizes into Subcellular Compartments with Liquid-like Properties in vivo ]]> https://biorxiv.org/content/10.1101/636449v1?rss=1 Jang, S. Xuan, Z. Lagoy, R. C. Jawerth, L. M. Gonzalez, I. Singh, M. Prashad, S. Kim, H. S. Patel, A. Albrecht, D. R. Hyman, A. A. Colon-Ramos, D. 2019-05-13 doi:10.1101/636449 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Diversification in evolutionary arenas -- assessment and synthesis ]]> https://biorxiv.org/content/10.1101/636803v1?rss=1 Nürk, N. M. Linder, H. P. Onstein, R. E. Larcombe, M. Hughes, C. E. Pineiro Fernandez, L. Schlüter, P. M. Valente, L. M. Beierkuhnlein, C. Cutts, V. Donoghue, M. J. Edwards, E. J. Field, R. Flantua, S. G. A. Higgins, S. I. Jentsch, A. Liede-Schumann, S. Pirie, M. D. 2019-05-16 doi:10.1101/636803 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ A microwell cell capture device reveals variable response to dobutamine in isolated cardiomyocytes ]]> https://biorxiv.org/content/10.1101/636852v1?rss=1 Clark, J. A. Weiss, J. D. Campbell, S. 2019-05-15 doi:10.1101/636852 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Somatosensory-Motor Dysconnectivity Spans Multiple Transdiagnostic Dimensions of Psychopathology ]]> https://biorxiv.org/content/10.1101/637827v1?rss=1 Kebets, V. Holmes, A. J. Orban, C. Tang, S. Li, J. Sun, N. Kong, R. Poldrack, R. A. Yeo, B. T. T. 2019-05-15 doi:10.1101/637827 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Task-Based Functional Connectomes Predict Cognitive Phenotypes Across Psychiatric Disease ]]> https://biorxiv.org/content/10.1101/638825v1?rss=1 Barron, D. S. Gao, S. Dadashkarimi, J. Greene, A. S. Spann, M. N. Noble, S. Lake, E. Krystal, J. H. Constable, R. T. Scheinost, D. 2019-05-16 doi:10.1101/638825 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ When will the cancer start? Elucidating the correlations between cancer initiation times and lifetime cancer risks ]]> https://biorxiv.org/content/10.1101/640284v1?rss=1 Teimouri, H. Kochugaeva, M. Kolomeisky, A. B. 2019-05-17 doi:10.1101/640284 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Specialized medial prefrontal-amygdala coordination in prosocial and antisocial decision-making ]]> https://biorxiv.org/content/10.1101/640292v1?rss=1 dal monte, o. Chu, C.-C. J. Fagan, N. A. Chang, S. W. C. 2019-05-17 doi:10.1101/640292 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ The effect of APOE genotype and streamline density volume, on hippocampal CA1 down-regulation: a real-time fMRI virtual reality neurofeedback study ]]> https://biorxiv.org/content/10.1101/643577v1?rss=1 Skouras, S. Torner, J. Anderson, P. Koush, Y. Falcon, C. Minguillon, C. Fauria, K. Alpiste, F. Gispert, J. D. Molinuevo, J. L. ALFA Study, 2019-05-21 doi:10.1101/643577 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ An omnidirectional visualization model of personalized gene regulatory networks ]]> https://biorxiv.org/content/10.1101/644070v1?rss=1 Chen, C. Jiang, L. Wang, M. Wang, Y. Shen, B. Liu, Z. Wang, Z. Hou, W. Berceli, S. Wu, R. 2019-05-21 doi:10.1101/644070 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Morphology and development of the Portuguese man of war, Physalia physalis ]]> https://biorxiv.org/content/10.1101/645465v1?rss=1 Munro, C. Vue, Z. Behringer, R. R. Dunn, C. W. 2019-05-27 doi:10.1101/645465 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ PRE-BORDER GENE FOXB1 REGULATES THE DIFFERENTIATION TIMING AND AUTONOMIC NEURONAL POTENTIAL OF HUMAN NEURAL CREST CELLS ]]> https://biorxiv.org/content/10.1101/646026v1?rss=1 Leung, A. W. Lopez-Giraldez, F. Broton, C. Lin, K. Prasad, M. S. Hernandez, J. C. Xiao, A. Garcia-Castro, M. I. 2019-06-03 doi:10.1101/646026 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients ]]> https://biorxiv.org/content/10.1101/646976v1?rss=1 Lou, S. Li, T. spakowicz, D. Chupp, G. L. Gerstein, M. B. 2019-05-22 doi:10.1101/646976 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ Two-color nanoscopy of organelles for extended times with HIDE probes ]]> https://biorxiv.org/content/10.1101/647065v1?rss=1 Chu, L. Tyson, J. Shaw, J. E. Rivera-Molina, F. Koleske, A. J. Schepartz, A. Toomre, D. 2019-05-22 doi:10.1101/647065 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ Deconstructing higher-order interactions in the microbiota: A theoretical examination ]]> https://biorxiv.org/content/10.1101/647156v1?rss=1 Yitbarek, S. Guittar, J. L. Knutie, S. A. Ogbunugafor, C. B. 2019-05-24 doi:10.1101/647156 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Accelerating iterative deconvolution and multiview fusion by orders of magnitude ]]> https://biorxiv.org/content/10.1101/647370v1?rss=1 Guo, M. Li, Y. Su, Y. Lambert, T. Nogare, D. D. Moyle, M. W. Duncan, L. H. Ikegami, R. Santella, A. Rey-Suarez, I. Green, D. Chen, J. Vishwasrao, H. Ganesan, S. Waters, J. C. Annunziata, C. M. Hafner, M. Mohler, W. A. Chitnis, A. B. Upadhyaya, A. Usdin, T. B. Bao, Z. Colon-Ramos, D. Riviere, P. L. Liu, H. Wu, Y. Shroff, H. 2019-05-23 doi:10.1101/647370 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis ]]> https://biorxiv.org/content/10.1101/648279v1?rss=1 Lewandowski, J. P. Lee, J. C. Hwang, T. Sunwoo, H. Goldstein, J. M. Groff, A. F. Chang, N. Mallard, W. Williams, A. Henao-Meija, J. Flavell, R. A. Lee, J. T. Gerhardinger, C. Wagers, A. J. Rinn, J. L. 2019-05-24 doi:10.1101/648279 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements ]]> https://biorxiv.org/content/10.1101/648667v1?rss=1 Navarro, F. Hoops, J. Bellfy, L. Cerveira, E. Zhu, Q. Zhang, C. Lee, C. Gerstein, M. 2019-05-24 doi:10.1101/648667 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ The Evolution of Siphonophore Tentilla as Specialized Tools for Prey Capture ]]> https://biorxiv.org/content/10.1101/653345v1?rss=1 Damian-Serrano, A. Haddock, S. H. D. Dunn, C. W. 2019-06-12 doi:10.1101/653345 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Distinct effects of amyloid and tau deposition on eigenvector centrality during hippocampal down-regulation: a real-time fMRI virtual reality closed-loop neurofeedback study with CSF biomarkers ]]> https://biorxiv.org/content/10.1101/654426v1?rss=1 Skouras, S. Torner, J. Andersson, P. Koush, Y. Falcon, C. Minguillon, C. Fauria, K. Alpiste, F. Blennow, K. Zetterberg, H. Gispert, J. D. Molinuevo, J. L. Alfa Study, 2019-05-31 doi:10.1101/654426 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[ Rainfall and other meteorological factors as drivers of urban transmission of leptospirosis ]]> https://biorxiv.org/content/10.1101/658872v1?rss=1 Costa, F. Cunha, M. Ribeiro, G. S. Carvalho, M. S. Reis, R. B. Nery, N. Pischel, L. Gouveia, E. Santos, A. Queiroz, A. Wunder, E. Reis, M. Diggle, P. Ko, A. 2019-06-04 doi:10.1101/658872 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Molecular pathway analysis indicates a distinct metabolic and immune phenotype in women with right-sided colon cancer ]]> https://biorxiv.org/content/10.1101/659151v1?rss=1 Johnson, C. Sun, Y. Mironova, V. Chen, Y. Lundh, E. P. F. Zhang, Q. Cai, Y. Vasiliou, V. Zhang, Y. Garcia-Milian, R. Khan, S. A. 2019-06-04 doi:10.1101/659151 Cold Spring Harbor Laboratory Press 2019-06-04 <![CDATA[ Ketamine disinhibits dendrites and enhances calcium signals in prefrontal dendritic spines ]]> https://biorxiv.org/content/10.1101/659292v1?rss=1 Ali, F. Gerhard, D. M. Sweasy, K. Pothula, S. Pittenger, C. Duman, R. S. Kwan, A. C. 2019-06-03 doi:10.1101/659292 Cold Spring Harbor Laboratory Press 2019-06-03 <![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[ A computational model for learning from repeated trauma ]]> https://biorxiv.org/content/10.1101/659425v1?rss=1 Kaye, A. P. Kwan, A. C. Ressler, K. J. Krystal, J. H. 2019-06-10 doi:10.1101/659425 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics ]]> https://biorxiv.org/content/10.1101/660613v1?rss=1 nView larger version (64K):norg.highwire.dtl.DTLVardef@13429c5org.highwire.dtl.DTLVardef@1a2493borg.highwire.dtl.DTLVardef@175e120org.highwire.dtl.DTLVardef@f1852_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> East, K. W. Newton, J. C. Morzan, U. N. Acharya, A. Skeens, E. Jogl, G. Batista, V. S. Palermo, G. Lisi, G. P. 2019-06-05 doi:10.1101/660613 Cold Spring Harbor Laboratory Press 2019-06-05 <![CDATA[ Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia ]]> https://biorxiv.org/content/10.1101/660779v1?rss=1 Zhu, X. Zhou, B. Pattni, R. Gleason, K. Tan, C. Kalinowski, A. Sloan, S. Fiston-Lavier, A.-S. Mariani, J. Abyzov, A. Petrov, D. Vogel, H. Moran, J. V. Vaccarino, F. M. Tamminga, C. Levinson, D. Urban, A. E. 2019-06-06 doi:10.1101/660779 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Microenvironmental adaptations drive obesity-associated pancreatic cancer ]]> https://biorxiv.org/content/10.1101/663583v1?rss=1 Chung, K. M. Singh, J. Lawres, L. Dorans, K. J. Robbins, R. Bhutkar, A. Babic, A. Vayrynen, S. A. Dias Costa, A. Nowak, J. A. Chang, D. T. Dunne, R. F. Hezel, A. F. Koong, A. C. Wilhelm, J. J. Bellin, M. D. Nylander, V. Gloyn, A. L. McCarthy, M. I. Wolpin, B. M. Jacks, T. Fuchs, C. S. Muzumdar, M. D. 2019-06-21 doi:10.1101/663583 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships ]]> https://biorxiv.org/content/10.1101/665760v1?rss=1 Zhou, J. Q. Kleinstein, S. H. 2019-06-10 doi:10.1101/665760 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Spatial distribution of epibionts on olive ridley sea turtles at Playa Ostional, Costa Rica ]]> https://biorxiv.org/content/10.1101/669523v1?rss=1 Robinson, N. J. Lazo-Wasem, E. Butler, B. Lazo-Wasem, E. Zardus, J. Pinou, T. 2019-06-12 doi:10.1101/669523 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ PQLC2 signals lysosomal cationic amino acid abundance to the C9orf72 complex ]]> https://biorxiv.org/content/10.1101/670034v1?rss=1 Amick, J. Tharkeshwar, A. K. Talaia, G. Ferguson, S. M. 2019-06-13 doi:10.1101/670034 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Interpretable Multimodality Embedding of Cerebral Cortex Using Attention Graph Network for Identifying Bipolar Disorder ]]> https://biorxiv.org/content/10.1101/671339v1?rss=1 Yang, H. Li, X. Wu, Y. Li, S. Lu, S. Duncan, J. S. Gee, J. C. Gu, S. 2019-06-14 doi:10.1101/671339 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus ]]> https://biorxiv.org/content/10.1101/671966v1?rss=1 Melnikov, S. V. Kwok, H. S. Manakongtreecheep, K. van den Elzen, A. Thoreen, C. C. Soll, D. 2019-06-14 doi:10.1101/671966 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Functions of ventral visual cortex after bilateral hippocampal loss ]]> https://biorxiv.org/content/10.1101/673228v1?rss=1 Kim, J. G. Gregory, E. Landau, B. McCloskey, M. Turk-Browne, N. B. Kastner, S. 2019-06-18 doi:10.1101/673228 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Identifying Combinations of Cancer Drivers in Individual Patients. ]]> https://biorxiv.org/content/10.1101/674234v1?rss=1 Klein, M. I. Cannataro, V. L. Townsend, J. P. Stern, D. F. Zhao, H. 2019-06-19 doi:10.1101/674234 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ A DNA Methylation Fingerprint of Cellular Senescence ]]> https://biorxiv.org/content/10.1101/674580v1?rss=1 Levine, M. E. Leung, D. Minteer, C. Gonzalez, J. 2019-06-21 doi:10.1101/674580 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution ]]> https://biorxiv.org/content/10.1101/675017v1?rss=1 Braga, M. P. Landis, M. J. Nylin, S. Janz, N. Ronquist, F. 2019-06-18 doi:10.1101/675017 Cold Spring Harbor Laboratory Press 2019-06-18 <![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[ Dolosigranulum pigrum cooperation and competition in human nasal microbiota ]]> https://biorxiv.org/content/10.1101/678698v1?rss=1 Brugger, S. D. Eslami, S. M. Pettigrew, M. M. Fernandez Escapa, I. Henke, M. M. Kong, Y. Lemon, K. P. 2019-06-21 doi:10.1101/678698 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Fibronectin receptor integrin α5β1 regulates assembly of PP2A complexes through PDE4D: modulation of vascular inflammation and atherosclerosis ]]> https://biorxiv.org/content/10.1101/680728v1?rss=1 Yun, S. Hu, R. Schwaemmle, M. E. Scherer, A. N. Zhuang, Z. Koleske, A. J. Pallas, D. C. Schwartz, M. A. 2019-06-24 doi:10.1101/680728 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Translatomic database of cortical astroglia across male and female mouse development reveals two distinct developmental phenotypes ]]> https://biorxiv.org/content/10.1101/681684v1?rss=1 Rurak, G. M. Simard, S. Van Geel, A. Stead, J. Woodside, B. Coppola, G. Salmaso, N. 2019-06-24 doi:10.1101/681684 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Guilty by association: How group-based (collective) guilt arises in the brain ]]> https://biorxiv.org/content/10.1101/683730v1?rss=1 Li, Z. Yu, H. Zhou, Y. Kalenscher, T. Zhou, X. 2019-06-27 doi:10.1101/683730 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ FAAH, SLC6A4, and BDNF variants are not associated with psychosocial stress and mental health outcomes in a population of Syrian refugee youth ]]> https://biorxiv.org/content/10.1101/685636v1?rss=1 Clukay, C. J. Matarazzo, A. Dajani, R. Hadfield, K. Panter-Brick, C. Mulligan, C. J. 2019-06-27 doi:10.1101/685636 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ NMDAR-dependent emergence of behavioral representation in primary visual cortex ]]> https://biorxiv.org/content/10.1101/688366v1?rss=1 Puscian, A. Benisty, H. Higley, M. J. 2019-07-01 doi:10.1101/688366 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ A missense variant in CREBRF is associated with taller stature in Samoans ]]> https://biorxiv.org/content/10.1101/690586v1?rss=1 Carlson, J. C. Rosenthal, S. L. Russell, E. M. Hawley, N. L. Sun, G. Cheng, H. Naseri, T. Reupena, M. S. Tuitele, J. Deka, R. McGarvey, S. T. Weeks, D. E. Minster, R. L. 2019-07-02 doi:10.1101/690586 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Activation of Smad 2/3 signaling by low shear stress mediates artery inward remodeling ]]> https://biorxiv.org/content/10.1101/691980v1?rss=1 Min, E. Baeyens, N. Hu, R. Zhuang, Z. Chen, M. Huang, B. Zarkada, G. Acheampong, A. McEntee, K. Simons, M. Eichmann, A. Schwartz, M. 2019-07-05 doi:10.1101/691980 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Individual Variation in Control Network Topography Supports Executive Function in Youth ]]> https://biorxiv.org/content/10.1101/694489v1?rss=1 Cui, Z. Li, H. Xia, C. H. Larsen, B. Adebimpe, A. Baum, G. L. Cieslak, M. Gur, R. E. Gur, R. C. Moore, T. M. Oathes, D. J. Alexander-Bloch, A. F. Raznahan, A. Roalf, D. R. Shinohara, R. T. Wolf, D. H. Davatzikos, C. Bassett, D. S. Fair, D. A. Fan, Y. Satterthwaite, T. D. 2019-07-08 doi:10.1101/694489 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ STARRPeaker: Uniform processing and accurate identification of whole human STARR-seq active regions ]]> https://biorxiv.org/content/10.1101/694869v1?rss=1 Lee, D. Shi, M. Moran, J. Wall, M. Zhang, J. Liu, J. Fitzgerald, D. Kyono, Y. Ma, L. White, K. P. Gerstein, M. 2019-07-08 doi:10.1101/694869 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Zero-shot neural decoding of visual categories withoutprior exemplars ]]> https://biorxiv.org/content/10.1101/700344v1?rss=1 O'Connell, T. Chun, M. M. Kreiman, G. 2019-07-14 doi:10.1101/700344 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Functional connectivity predicts changes in attention over minutes, days, and months ]]> https://biorxiv.org/content/10.1101/700476v1?rss=1 Rosenberg, M. D. Scheinost, D. Greene, A. S. Avery, E. W. Kwon, Y. H. Finn, E. S. Ramani, R. Qiu, M. Constable, R. T. Chun, M. M. 2019-07-14 doi:10.1101/700476 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Hierarchical and dynamic regulation of defense-responsive specialized metabolism by WRKY and MYB transcription factors. ]]> https://biorxiv.org/content/10.1101/700583v1?rss=1 Barco, B. Clay, N. 2019-07-12 doi:10.1101/700583 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Gclc deletion in surface-ectoderm tissues induces microphthalmia ]]> https://biorxiv.org/content/10.1101/700591v1?rss=1 Thompson, B. Chen, Y. Philippe, J. Anderson, D. Prakash, J. G. Davidson, E. Apostolopoulos, N. Schey, K. Katsanis, N. Orlicky, D. J. Thompson, D. Vasiliou, V. 2019-07-13 doi:10.1101/700591 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ Robust latent-variable interpretation of in vivo regression models by nested resampling ]]> https://biorxiv.org/content/10.1101/703470v1?rss=1 Caulk, A. W. Janes, K. A. 2019-07-16 doi:10.1101/703470 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Blastula stage specification of avian neural crest ]]> https://biorxiv.org/content/10.1101/705731v1?rss=1 Prasad, M. Uribe-Querol, E. Marquez, J. Vadasz, S. Yardley, N. Shelar, P. Charney, R. Garcia-Castro, M. I. 2019-07-17 doi:10.1101/705731 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ An integrative ENCODE resource for cancer genomics ]]> https://biorxiv.org/content/10.1101/706424v1?rss=1 Zhang, J. Lee, D. Dhiman, V. Jiang, P. Xu, J. McGillivray, P. Yang, H. Liu, J. Meyerson, W. Clarke, D. Gu, M. Li, S. Lou, S. Xu, J. Lochovsky, L. Ung, M. Ma, L. Yu, S. Cao, Q. Harmanci, A. Yan, K.-K. Sethi, A. Gursoy, G. Schoenberg, M. R. Rozowsky, J. Warrell, J. Emani, P. Yang, Y. T. Galeev, T. Kong, X. Liu, S. Li, X. Krishnan, J. Feng, Y. Rivera-Mulia, J. C. Adrian, J. Broach, J. R. Bolt, M. Moran, J. Fitzgerald, D. Dileep, V. Liu, T. Mei, S. Sasaki, T. Trevilla-Garcia, C. Wang, S. Wang, Y. Zang, C. Wang, D. Klein, R. Snyder, M. Gilbert, D. 2019-07-18 doi:10.1101/706424 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Functional community assembly and turnover along elevation and latitude ]]> https://biorxiv.org/content/10.1101/706523v1?rss=1 Jarzyna, M. A. Quintero, I. Jetz, W. 2019-07-18 doi:10.1101/706523 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ High-resolution view of the type III secretion export apparatus in situ reveals membrane remodeling and a secretion pathway ]]> https://biorxiv.org/content/10.1101/709592v1?rss=1 Butan, C. Lara-Tejero, M. Li, W. Liu, J. Galan, J. 2019-07-21 doi:10.1101/709592 Cold Spring Harbor Laboratory Press 2019-07-21 <![CDATA[ Movement and performance predict widespread cortical activity in a visual detection task ]]> https://biorxiv.org/content/10.1101/709642v1?rss=1 Salkoff, D. Zagha, E. McCarthy, E. McCormick, D. A. 2019-07-22 doi:10.1101/709642 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Principles of Cell Circuits for Tissue Repair and Fibrosis ]]> https://biorxiv.org/content/10.1101/710012v1?rss=1 Adler, M. Mayo, A. Zhou, X. Franklin, R. Meizlish, M. Medzhitov, R. Kallenberger, S. Alon, U. 2019-07-24 doi:10.1101/710012 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ A catalog of cis-regulatory mutations in 12 major cancer types ]]> https://biorxiv.org/content/10.1101/710103v1?rss=1 Cheng, Z. Vermeulen, M. Rollins-Green, M. DeVeale, B. Babak, T. 2019-07-22 doi:10.1101/710103 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Molecular correlates of topiramate and GRIK1 rs2832407 genotype in pluripotent stem cell-derived neural cultures ]]> https://biorxiv.org/content/10.1101/710343v1?rss=1 Lieberman, R. Jensen, K. P. Clinton, K. Levine, E. S. Kranzler, H. R. Covault, J. 2019-07-22 doi:10.1101/710343 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome ]]> https://biorxiv.org/content/10.1101/711184v1?rss=1 Alharatani, R. Vervari, A. Beleza-Meireles, A. Ji, W. Mis, E. Patterson, Q. Griffin, J. Bhujel, N. Chang, C. Dixit, A. Konstantino, M. Healy, C. Hannan, S. Neo, N. Cash, A. Li, D. Bhoj, E. Zackai, E. Cleaver, R. Baralle, D. McEntagart, M. Newbury-Ecob, R. Scott, R. Hurst, J. Au, P. Y. B. Hosey, M. T. Marciano, D. Khokha, M. Lakhani, S. Liu, K. 2019-07-27 doi:10.1101/711184 Cold Spring Harbor Laboratory Press 2019-07-27 <![CDATA[ Detecting regions of differential abundance betweenscRNA-Seq datasets ]]> https://biorxiv.org/content/10.1101/711929v1?rss=1 Zhao, J. Jaffe, A. Cheng, X. Flavell, R. Kluger, Y. 2019-07-23 doi:10.1101/711929 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes ]]> https://biorxiv.org/content/10.1101/713081v1?rss=1 Berv, J. S. Campagna, L. Feo, T. J. Castro-Astor, I. Ribas, C. C. Prum, R. O. Lovette, I. 2019-07-24 doi:10.1101/713081 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ The Kinesin-5 Tail Domain Directly Modulates the Mechanochemical Cycle of the Motor for Anti-Parallel Microtubule Sliding ]]> https://biorxiv.org/content/10.1101/713909v1?rss=1 Bodrug, T. Wilson-Kubalek, E. Nithianantham, S. Thompson, A. F. Alfieri, A. Gaska, I. Major, J. Debs, G. Inagaki, S. Gutierrez, P. Gheber, L. McKenney, R. Sindelar, C. Milligan, R. Stumpff, J. Rosenfeld, S. Forth, S. T. Al-Bassam, J. 2019-07-25 doi:10.1101/713909 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Pan-cancer classifications of tumor histological images using deep learning ]]> https://biorxiv.org/content/10.1101/715656v1?rss=1 Noorbakhsh, J. Farahmand, S. Soltanieh-ha, M. Namburi, S. Zarringhalam, K. Chuang, J. H. 2019-07-26 doi:10.1101/715656 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Genomic Influences on Self-Reported Childhood Maltreatment ]]> https://biorxiv.org/content/10.1101/717314v1?rss=1 Dalvie, S. Maihofer, A. X. Coleman, J. R. Bradley, B. Breen, G. Brick, L. A. Chen, C.-Y. Choi, K. W. Duncan, L. E. Guffanti, G. Haas, M. Harnal, S. Liberzon, I. Nugent, N. R. Provost, A. C. Ressler, K. J. Torres, K. Amstadter, A. B. Austin, S. B. Baker, D. G. Bolger, E. A. Bryant, R. A. Calabrese, J. R. Delahanty, D. L. Farrer, L. A. Feeny, N. C. Flory, J. D. Forbes, D. Galea, S. Gautam, A. Gelernter, J. Hammamieh, R. Jett, M. Junglen, A. G. Kaufman, M. L. Kessler, R. C. Khan, A. Kranzler, H. R. Lebois, L. A. Marmar, C. Mavissakalian, M. R. McFarlane, A 2019-07-28 doi:10.1101/717314 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Neural signatures of model-free learning when avoiding harm to self and other ]]> https://biorxiv.org/content/10.1101/718106v1?rss=1 Lockwood, P. Klein-Flugge, M. Abdurahman, A. Crockett, M. 2019-07-29 doi:10.1101/718106 Cold Spring Harbor Laboratory Press 2019-07-29 <![CDATA[ Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults ]]> https://biorxiv.org/content/10.1101/719203v1?rss=1 Avey, S. Mohanty, S. Chawla, D. G. Meng, H. Bandaranayake, T. Ueda, I. Zapata, H. J. Park, K. Blevins, T. P. Tsang, S. Belshe, R. B. Kaech, S. M. Shaw, A. C. Kleinstein, S. 2019-08-01 doi:10.1101/719203 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Tolerance to NADH/NAD+ imbalance anticipates aging and anti-aging interventions ]]> https://biorxiv.org/content/10.1101/719401v1?rss=1 Alonso-Lavin, A. J. Bajic, D. Poyatos, J. F. 2019-07-31 doi:10.1101/719401 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production ]]> https://biorxiv.org/content/10.1101/723221v1?rss=1 Wu, N. Sun, H. Zhao, X. Chen, L. Qi, Y. Han, Y. Liu, X.-n. Gao, C. Wang, Q. He, L. Niu, X. Liu, Z. Li, H. Zeng, Y. A. Roulis, M. Liu, D. Yang, Z. Zhou, B. Flavell, R. Su, B. 2019-08-07 doi:10.1101/723221 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts ]]> https://biorxiv.org/content/10.1101/723742v1?rss=1 Gumbs, R. Gray, C. L. Bohm, M. Hoffmann, M. Grenyer, R. Jetz, W. Meiri, S. Roll, U. Owen, N. R. Rosindell, J. 2019-08-02 doi:10.1101/723742 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses ]]> https://biorxiv.org/content/10.1101/723882v1?rss=1 Mongiardino Koch, N. Parry, L. A. 2019-08-05 doi:10.1101/723882 Cold Spring Harbor Laboratory Press 2019-08-05 <![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[ Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species, Yucca gloriosa ]]> https://biorxiv.org/content/10.1101/726737v1?rss=1 Heyduk, K. Ray, J. N. Leebens-Mack, J. 2019-08-06 doi:10.1101/726737 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Genetic Background Dominates Fibrotic Aortic Remodeling During Angiotensin-Induced Hypertension in Mice ]]> https://biorxiv.org/content/10.1101/727800v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@e9f1d9org.highwire.dtl.DTLVardef@104e221org.highwire.dtl.DTLVardef@19a00bforg.highwire.dtl.DTLVardef@1a70cd5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Spronck, B. Caulk, A. W. Ramachandra, A. B. Murtada, S.-I. Rojas, A. He, C.-S. Bersi, M. R. Tellides, G. Humphrey, J. D. 2019-08-15 doi:10.1101/727800 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify candidate risk genes and biological pathways ]]> https://biorxiv.org/content/10.1101/730952v1?rss=1 Fernandez, T. V. Williams, Z. P. Kline, T. Rajendran, S. Augustine, F. Wright, N. Sullivan, C. A. W. Olfson, E. Abdallah, S. B. Liu, W. Hoffman, E. J. Gupta, A. R. Singer, H. S. 2019-08-13 doi:10.1101/730952 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ PIWI-piRNA pathway-mediated transposable element repression in Hydra somatic stem cells ]]> https://biorxiv.org/content/10.1101/731695v1?rss=1 Teefy, B. B. Siebert, S. Cazet, J. F. Lin, H. Juliano, C. E. 2019-08-10 doi:10.1101/731695 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Peculiar cases of a \"sleeping\" brain in alert cancer patients ]]> https://biorxiv.org/content/10.1101/732230v1?rss=1 Benveniste, H. Vaska, P. Franceschi, D. Salerno, M. Rizwan, S. Lee, H. Logan, J. Rothman, D. Lazebnik, Y. Volkow, N. D. Bilfinger, T. V. 2019-08-13 doi:10.1101/732230 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ CHD8 regulates the balance between proliferation and differentiation of human iPSCs in neural development ]]> https://biorxiv.org/content/10.1101/732693v1?rss=1 Liu, W. Dong, W. Hoffman, E. J. Fernandez, T. V. Gupta, A. R. 2019-08-13 doi:10.1101/732693 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Controlling and measuring dynamic odorant stimuli in the laboratory ]]> https://biorxiv.org/content/10.1101/733055v1?rss=1 Gorur-Shandilya, S. Martelli, C. Demir, M. Emonet, T. 2019-09-06 doi:10.1101/733055 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Early post-zygotic mutations contribute to congenital heart disease ]]> https://biorxiv.org/content/10.1101/733105v1?rss=1 Hsieh, A. Morton, S. U. Willcox, J. A. Gorham, J. M. Tai, A. C. Qi, H. DePalma, S. McKean, D. Griffin, E. Manheimer, K. B. Bernstein, D. Kim, R. W. Newburger, J. W. Porter, G. A. Srivastava, D. Tristani-Firouzi, M. Brueckner, M. Lifton, R. P. Goldmuntz, E. Gelb, B. D. Chung, W. K. Seidman, C. Seidman, J. G. Shen, Y. 2019-08-13 doi:10.1101/733105 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Direct comparison of clathrin-mediated endocytosis in budding and fission yeast reveals conserved and evolvable features ]]> https://biorxiv.org/content/10.1101/733543v1?rss=1 Sun, Y. Schoeneberg, J. Chen, S. Jiang, T. Kaplan, C. Xu, K. Pollard, T. Drubin, D. G. 2019-08-13 doi:10.1101/733543 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Defects in the assembly of ribosomes selected for β-amino acid incorporation ]]> https://biorxiv.org/content/10.1101/733584v1?rss=1 Ward, F. R. Watson, Z. L. Ad, O. Schepartz, A. Cate, J. H. D. 2019-08-13 doi:10.1101/733584 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ ADAMTS-family protease MIG-17 regulates synaptic allometry by modifying the extracellular matrix and modulating glia morphology during growth ]]> https://biorxiv.org/content/10.1101/734830v1?rss=1 Ji, T. Wang, K. Fan, J. Huang, J. Wang, M. Dong, X. Shi, Y. Manning, L. Zhang, X. Shao, Z. Colon-Ramos, D. A. 2019-08-16 doi:10.1101/734830 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development ]]> https://biorxiv.org/content/10.1101/735969v1?rss=1 He, M. Wu, B. Le, D. D. Ye, W. Sinclair, A. W. Padovano, V. Chen, Y. Li, K. Sit, R. Tan, M. Caplan, M. J. Neff, N. Jan, Y. N. Darmanis, S. Jan, L. Y. 2019-08-15 doi:10.1101/735969 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing ]]> https://biorxiv.org/content/10.1101/737577v1?rss=1 90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes. Notably, neuropeptide-related genes are often differentially expressed between subtypes of the given neuron class which points to distinct functional characteristics. All of these data are publicly available at our website (http://www.cengen.org) and can be interrogated at the web application SCeNGEA (https://cengen.shinyapps.io/SCeNGEA). We expect that this gene expression catalog will spur the goal of delineating the underlying mechanisms that define the developmental lineage, detailed anatomy, synaptic connectivity and function of each type of C. elegans neuron. ]]> Taylor, S. R. Santpere, G. Reilly, M. Glenwinkel, L. Poff, A. McWhirter, R. Xu, C. Weinreb, A. Basavaraju, M. Cook, S. J. Barrett, A. Abrams, A. Vidal, B. Cros, C. Rafi, I. Sestan, N. Hammarlund, M. Hobert, O. Miller, D. M. 2019-08-16 doi:10.1101/737577 Cold Spring Harbor Laboratory Press 2019-08-16 <![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[ SVFX: a machine-learning framework to quantify the pathogenicity of structural variants ]]> https://biorxiv.org/content/10.1101/739474v1?rss=1 kumar, s. Harmanci, A. Vytheeswaran, J. Gerstein, M. 2019-08-19 doi:10.1101/739474 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Evolutionary rescue is determined by differential selection on demographic rates and density dependence. ]]> https://biorxiv.org/content/10.1101/740365v1?rss=1 Vinton, A. C. Vasseur, D. A. 2019-08-20 doi:10.1101/740365 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Human Neocortical Neurosolver (HNN): A new software tool for interpreting the cellular and network origin of human MEG/EEG data ]]> https://biorxiv.org/content/10.1101/740597v1?rss=1 Neymotin, S. A. Daniels, D. S. Caldwell, B. McDougal, R. A. Carnevale, N. T. Moore, C. I. Hines, M. L. Hamalainen, M. Jones, S. R. 2019-08-20 doi:10.1101/740597 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Dysregulation of Sterol Regulatory Element-Binding Protein 2 Gene in HIV Treatment-Experienced Individuals ]]> https://biorxiv.org/content/10.1101/742486v1?rss=1 Sopeyin, A. Zhou, L. Li, M. Barakat, L. Paintsil, E. 2019-08-21 doi:10.1101/742486 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Environmental sensing in dynamic quorum responses ]]> https://biorxiv.org/content/10.1101/745091v1?rss=1 Chu, E. K. Groisman, A. Levchenko, A. 2019-09-05 doi:10.1101/745091 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Longitudinal bioluminescent imaging of HIV-1 infection during antiretroviral therapy and treatment interruption in humanized mice ]]> https://biorxiv.org/content/10.1101/745125v1?rss=1 Ventura, J. D. Beloor, J. Allen, E. J. Zhang, T. Haugh, K. Uchil, P. Ochsenbauer, C. Kieffer, C. Kumar, P. Hope, T. J. Mothes, W. 2019-08-24 doi:10.1101/745125 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/746222v1?rss=1 Nackenoff, A. G. Hohman, T. J. Neuner, S. M. Akers, C. S. Weitzel, N. C. Shostak, A. Ferguson, S. Bennett, D. A. Schneider, J. A. Jefferson, A. L. Kaczorowski, C. C. Schrag, M. S. 2019-08-24 doi:10.1101/746222 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Generating Templates and Growth Charts for School-Aged Brain Development ]]> https://biorxiv.org/content/10.1101/747352v1?rss=1 Dong, H.-M. Castellanos, F. X. Yang, N. Zhang, Z. He, Y. Zhang, L. Xu, T. Holmes, A. Yeo, B. T. T. Chen, F. Wang, B. Beckmann, C. F. White, T. H. Sporns, O. Qiu, J. Feng, T. Chen, A. Liu, X. Chen, X. Weng, X. Milham, M. Zuo, X.-N. 2019-08-28 doi:10.1101/747352 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Accelerating Inflammation Resolution to Counteract Chemical Cutaneous Injury ]]> https://biorxiv.org/content/10.1101/749184v1?rss=1 Achanta, S. Chintagari, N. R. Balakrishna, S. Liu, B. Jordt, S. E. 2019-08-29 doi:10.1101/749184 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms ]]> https://biorxiv.org/content/10.1101/749366v1?rss=1 Tretina, K. Pelle, R. Orvis, J. Gotia, H. T. Ifeonu, O. O. Kumari, P. Palmateer, N. C. Iqbal, S. B. Fry, L. Nene, V. M. Daubenberger, C. Bishop, R. P. Silva, J. C. 2019-08-31 doi:10.1101/749366 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ AMPK regulates ESCRT-dependent microautophagy of proteasomes concomitant with proteasome storage granule assembly during glucose starvation ]]> https://biorxiv.org/content/10.1101/751420v1?rss=1 Li, J. Breker, M. Graham, M. Schuldiner, M. Hochstrasser, M. 2019-08-29 doi:10.1101/751420 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis ]]> https://biorxiv.org/content/10.1101/751909v1?rss=1 Uyhazi, K. E. Yang, Y. Liu, N. Qi, H. Huang, X. A. Mak, W. Weatherbee, S. D. Song, X. Lin, H. 2019-08-30 doi:10.1101/751909 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Predicted effects of severing enzymes on the length distribution and total mass of microtubules ]]> https://biorxiv.org/content/10.1101/752006v1?rss=1 Kuo, Y.-W. Howard, J. Trottier, O. 2019-08-30 doi:10.1101/752006 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Estimating growth patterns and driver effects in tumor evolution from individual samples ]]> https://biorxiv.org/content/10.1101/753871v1?rss=1 Salichos, L. Meyerson, W. U. Warrell, J. Gerstein, M. 2019-09-02 doi:10.1101/753871 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Local regulation of lipid synthesis controls ER sheet insertion into nuclear envelope holes to complete nuclear closure ]]> https://biorxiv.org/content/10.1101/757013v1?rss=1 Penfield, L. Shankar, R. Szentgyörgyi, E. Laffitte, A. Mauro, M. Audhya, A. Müller-Reicher, T. Bahmanyar, S. 2019-09-04 doi:10.1101/757013 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide ]]> https://biorxiv.org/content/10.1101/757401v1?rss=1 Allen, B. L. Quach, K. Levandowski, C. B. Rubin, J. D. Read, T. Dowell, R. D. Schepartz, A. Taatjes, D. J. 2019-09-04 doi:10.1101/757401 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ In silico hippocampal modeling for multi-target pharmacotherapy in schizophrenia ]]> https://biorxiv.org/content/10.1101/758466v1?rss=1 Sherif, M. Neymotin, S. A. Lytton, W. W. 2019-09-05 doi:10.1101/758466 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ A limited role for autophagy during arbovirus infection of mosquito cells ]]> https://biorxiv.org/content/10.1101/760728v1?rss=1 Brackney, D. E. Correa, M. A. 2019-09-06 doi:10.1101/760728 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Genomic Characterization of Posttraumatic Stress Disorder in a Large US Military Veteran Sample ]]> https://biorxiv.org/content/10.1101/764001v1?rss=1 Stein, M. B. Levey, D. F. Cheng, Z. Wendt, F. R. Harrington, K. Cho, K. Quaden, R. Radhakrishnan, K. Girgenti, M. J. Ho, Y.-L. A. Posner, D. PTSD Working Group of the Psychiatric Genomics Consortium, Traumatic Stress Brain Research Study Group, VA Million Veteran Program, VA Cooperative Studies Program, Aslan, M. Duman, R. S. Zhao, H. Polimanti, R. Concato, J. Gelernter, J. 2019-09-10 doi:10.1101/764001 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium ]]> https://biorxiv.org/content/10.1101/765065v1?rss=1 360,000) found association of this variant with propensity to use dietary supplements (p=1.68x10-8). With respect to the same OE phenotype in the gene-based analysis, we identified SDCCAG8 (z=4.69, p=10-6), which was previously associated with educational attainment, risk-taking behaviors, and schizophrenia. In addition, rs201123820 showed a genome-wide significant difference between OD cases and unexposed controls (z=5.55, p=2.9x10-8) and a significant association with musculoskeletal disorders in the UK Biobank (p=4.88x10-7). A polygenic risk score (PRS) based on a GWAS of risk-tolerance (N=466,571) was positively associated with OD (OD cases vs. unexposed controls, p=8.1x10-5; OD cases vs. exposed controls, p=0.054) and OE (exposed controls vs. unexposed controls, p=3.6x10-5). A PRS based on a GWAS of neuroticism (N=390,278) was positively associated with OD (OD cases vs. unexposed controls, p=3.2x10-5; OD cases vs. exposed controls, p=0.002) but not with OE (p=0.671). Our analyses highlight the difference between dependence and exposure and the importance of considering the definition of controls (exposed vs. unexposed) in studies of addiction. ]]> Polimanti, R. Psychiatric Genomics Consortium Substance Use Disorder Workgroup, Edenberg, H. J. Agrawal, A. Gelernter, J. 2019-09-11 doi:10.1101/765065 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients ]]> https://biorxiv.org/content/10.1101/765297v1?rss=1 Spakowicz, D. Lou, S. Barron, B. Li, T. Gomez, J. Liu, Q. Grant, N. Yan, X. Weinstock, G. Chupp, G. L. Gerstein, M. 2019-09-11 doi:10.1101/765297 Cold Spring Harbor Laboratory Press 2019-09-11 <![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[ Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community ]]> https://biorxiv.org/content/10.1101/772475v1?rss=1 Bono, L. M. Orton, R. J. Peredo, E. L. Morrison, H. G. Sistrom, M. J. Simmons, S. Turner, P. 2019-09-18 doi:10.1101/772475 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Increasing demand for plasma membrane contributes to the energetic cost of early zebrafish embryogenesis. ]]> https://biorxiv.org/content/10.1101/775114v1?rss=1 Rodenfels, J. Sartori, P. Golfier, S. Nagendra, K. Neugebauer, K. Howard, J. 2019-09-18 doi:10.1101/775114 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data ]]> https://biorxiv.org/content/10.1101/775338v1?rss=1 Gursoy, G. Navarro, F. C. Gerstein, M. 2019-09-19 doi:10.1101/775338 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Antibody against envelope protein from human endogenous retrovirus activates neutrophils in systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/776468v1?rss=1 Tokuyama, M. Gunn, B. M. Venkataraman, A. Kong, Y. M. Kang, I. Townsend, M. Costenbader, K. Alter, G. Iwasaki, A. 2019-09-20 doi:10.1101/776468 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids ]]> https://biorxiv.org/content/10.1101/776690v1?rss=1 Ye, J. J. Bian, X. Lim, J. Medzhitov, R. 2019-09-20 doi:10.1101/776690 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Signaling Diversity Enabled by Rap1-Regulated Plasma Membrane ERK with Distinct Temporal Dynamics ]]> https://biorxiv.org/content/10.1101/781716v1?rss=1 Keyes, J. Ganesan, A. Molinar-Inglis, O. Hamidzadeh, A. Ling, M. Trejo, J. Levchenko, A. Zhang, J. 2019-09-25 doi:10.1101/781716 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors ]]> https://biorxiv.org/content/10.1101/782896v1?rss=1 Hurley, K. Ding, J. Villacorta-Martin, C. Herriges, M. J. Jacob, A. Vedaie, M. Alysandratos, K. D. Sun, Y. L. Lin, C. Werder, R. B. Wilson, A. A. Mithal, A. Mostoslavsky, G. Caballero, I. S. Guttentag, S. H. Ahangari, F. Kaminski, N. Rodriguez- Fraticelli, A. Camargo, F. Bar-Joseph, Z. Kotton, D. 2019-09-26 doi:10.1101/782896 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Patchy, incomplete, and heterogeneous X-inactivation in the human placenta ]]> https://biorxiv.org/content/10.1101/785105v1?rss=1 Phung, T. N. Olney, K. C. Kliman, H. J. Wilson, M. A. 2019-09-28 doi:10.1101/785105 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny ]]> https://biorxiv.org/content/10.1101/786087v1?rss=1 Luque, J. Allison, W. T. Bracken-Grissom, H. D. Jenkins, K. M. Palmer, A. R. Porter, M. L. Wolfe, J. M. 2019-10-07 doi:10.1101/786087 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Discovery of novel Defense Regulated WD40-repeat proteins DRW1/2 and their roles in plant immunity ]]> https://biorxiv.org/content/10.1101/786848v1?rss=1 Miller, J. C. Clay, N. K. Barco, B. 2019-09-30 doi:10.1101/786848 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue ]]> https://biorxiv.org/content/10.1101/788992v1?rss=1 View larger version (77K): org.highwire.dtl.DTLVardef@41d937org.highwire.dtl.DTLVardef@11bdc46org.highwire.dtl.DTLVardef@1aa143org.highwire.dtl.DTLVardef@51755c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Liu, Y. Yang, M. Deng, Y. Su, G. Guo, C. C. Zhang, D. Kim, D. Bai, Z. Xiao, Y. Fan, R. 2019-10-01 doi:10.1101/788992 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ 3D super-resolution deep-tissue imaging in living mice ]]> https://biorxiv.org/content/10.1101/790212v1?rss=1 Velasco, M. G. M. Zhang, M. Antonello, J. Yuan, P. Allgeyer, E. S. May, D. M'Saad, O. Kidd, P. Barentine, A. E. S. Greco, V. Grutzendler, J. Booth, M. J. Bewersdorf, J. 2019-10-02 doi:10.1101/790212 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Paradoxical Aortic Stiffening and Subsequent Cardiac Dysfunction in Hutchinson-Gilford Progeria Syndrome ]]> https://biorxiv.org/content/10.1101/790477v1?rss=1 Murtada, S.-I. Kawamura, Y. Caulk, A. W. Ahmadzadeh, H. Mikush, N. Zimmerman, K. Kavanagh, D. Weiss, D. Latorre, M. Zhuang, Z. W. Shadel, G. S. Braddock, D. T. Humphrey, J. D. 2019-10-02 doi:10.1101/790477 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Automated analysis of sleep in adult C. elegans with closed-loop assessment of state-dependent neural activity ]]> https://biorxiv.org/content/10.1101/791764v1?rss=1 Lawler, D. E. Chew, Y. L. Hawk, J. D. Aljobeh, A. Schafer, W. Albrecht, D. R. 2019-10-03 doi:10.1101/791764 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/793463v1?rss=1 Zhang, Y. Liang, K. Liu, M. Li, Y. Ge, H. Zhao, H. 2019-10-04 doi:10.1101/793463 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Evolutionary analyses guide selection of model systems to investigate proto-oncogene function in ALK and LTK ]]> https://biorxiv.org/content/10.1101/795468v1?rss=1 Wang, Z. Dornburg, A. Wang, J. Elizabeth, M. Lopez-Giraldez, F. Townsend, J. P. 2019-10-07 doi:10.1101/795468 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/799189v1?rss=1 Zheng, X. Huang, Y. Zou, X. 2019-10-09 doi:10.1101/799189 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Wikidata as a FAIR knowledge graph for the life sciences ]]> https://biorxiv.org/content/10.1101/799684v1?rss=1 Waagmeester, A. Stupp, G. Burgstaller-Muehlbacher, S. Good, B. M. Griffith, M. Griffith, O. Hanspers, K. Hermjakob, H. Hybiske, K. Keating, S. M. Manske, M. Mayers, M. Mitraka, E. Pico, A. R. Putman, T. Riutta, A. Queralt-Rosinach, N. Schriml, L. M. Slenter, D. Tsueng, G. Tu, R. Willighagen, E. Wu, C. Su, A. I. 2019-10-21 doi:10.1101/799684 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum ]]> https://biorxiv.org/content/10.1101/811067v1?rss=1 Landis, M. J. Eaton, D. A. R. Clement, W. L. Park, B. Spriggs, E. L. Sweeney, P. W. Edwards, E. J. Donoghue, M. J. 2019-10-21 doi:10.1101/811067 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Orexin signaling in GABAergic lateral habenula neurons modulates aggressive behavior ]]> https://biorxiv.org/content/10.1101/811265v1?rss=1 Flanigan, M. Aleyasin, H. Li, L. Burnett, C. J. Chan, K. LeClair, K. Lucas, E. Matikainen-Ankney, B. Janssen, W. Takahashi, A. Menard, C. Pfau, M. Golden, S. Bouchard, S. Calipari, E. S. Nestler, E. J. DiLeone, R. Yamanaka, A. Huntley, G. Clem, R. Russo, S. 2019-10-21 doi:10.1101/811265 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Discovery of the prickle patterning on the stem of rose and the mathematical model of the pattern. ]]> https://biorxiv.org/content/10.1101/811281v1?rss=1 Amikura, K. Ito, H. 2019-10-28 doi:10.1101/811281 Cold Spring Harbor Laboratory Press 2019-10-28 <![CDATA[ Correlates of non-random patterns of capsule switching in pneumococcus ]]> https://biorxiv.org/content/10.1101/811406v1?rss=1 90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood.nnMethodsWe used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity.nnResultsA number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule.nnConclusionsCertain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics. ]]> Joshi, S. Al-Mamun, M. A. Weinberger, D. M. 2019-10-21 doi:10.1101/811406 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ PhyB induces intron retention and uORF-mediated translational inhibition of PIF3 ]]> https://biorxiv.org/content/10.1101/813840v1?rss=1 Dong, J. Chen, H. Deng, X. W. Irish, V. F. Wei, N. 2019-10-21 doi:10.1101/813840 Cold Spring Harbor Laboratory Press 2019-10-21 <![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[ A Sensitive Yellow Fever Virus Entry Reporter Identifies Valosin-Containing Protein (VCP/p97) as an Essential Host Factor for Flavivirus Uncoating ]]> https://biorxiv.org/content/10.1101/814764v1?rss=1 Ramanathan, H. N. Zhang, S. Douam, F. Chang, J. Yang, P. L. Ploss, A. Lindenbach, B. D. 2019-10-22 doi:10.1101/814764 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Digitally Deconstructing Leaves in 3D Using X-ray Microcomputed Tomography and Machine Learning ]]> https://biorxiv.org/content/10.1101/814954v1?rss=1 1500 in the full leaf scan, it achieves >90% accuracy in background and tissue segmentation. ConclusionOverall, this 3D segmentation and quantification pipeline can reduce one of the major barriers to using microCT imaging in high-throughput plant phenotyping. ]]> Theroux-Rancourt, G. Jenkins, M. R. Brodersen, C. R. McElrone, A. Forrestel, E. J. Earles, J. M. 2019-10-23 doi:10.1101/814954 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ High-phytate/low-calcium diet is a risk factor for crystal nephropathies, renal phosphate wasting, and bone loss ]]> https://biorxiv.org/content/10.1101/816512v1?rss=1 Kim, O.-H. Booth, C. J. Choi, H. S. Lee, J. Kang, J. Hur, J. Choi, H. J. Kim, H. Auh, J.-H. Cha, J.-Y. Lee, Y. J. Lee, C. S. Choi, C. Yang, J.-y. Im, S.-S. Lee, D. H. Cho, S. W. Kim, Y.-B. Park, K. S. Park, Y. J. Oh, B.-C. 2019-10-29 doi:10.1101/816512 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Cumulative effects of social stress on reward-guided actions and prefrontal cortical activity ]]> https://biorxiv.org/content/10.1101/817361v1?rss=1 Barthas, F. Hu, M. Y. Siniscalchi, M. J. Ali, F. Mineur, Y. S. Picciotto, M. R. Kwan, A. C. 2019-10-25 doi:10.1101/817361 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Regulation of FXR1 by alternative splicing is required for muscle development and controls liquid-like condensates in muscle cells ]]> https://biorxiv.org/content/10.1101/818476v1?rss=1 Smith, J. A. Curry, E. G. Blue, R. E. Roden, C. Dundon, S. E. R. Rodriguez-Vargas, A. Jordan, D. C. Chen, X. Lyons, S. M. Crutchley, J. Anderson, P. Horb, M. E. Gladfelter, A. S. Giudice, J. 2019-10-24 doi:10.1101/818476 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Establishing Rod-Shape from Spherical, Peptidoglycan-Deficient Bacterial Spores ]]> https://biorxiv.org/content/10.1101/818641v1?rss=1 Zhang, H. Mulholland, G. A. Seef, S. Zhu, S. Liu, J. Mignot, T. Nan, B. 2019-10-25 doi:10.1101/818641 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ SECAT: Quantifying differential protein-protein interaction states by network-centric analysis ]]> https://biorxiv.org/content/10.1101/819755v1?rss=1 Rosenberger, G. Heusel, M. Bludau, I. Collins, B. C. Martelli, C. Williams, E. Xue, P. Liu, Y. Aebersold, R. Califano, A. 2019-10-25 doi:10.1101/819755 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Torsin ATPases are required to complete nuclear pore complex biogenesis in interphase ]]> https://biorxiv.org/content/10.1101/821835v1?rss=1 Rampello, A. J. Laudermilch, E. Vishnoi, N. Prohet, S. M. Shao, L. Zhao, C. Lusk, C. P. Schlieker, C. 2019-10-29 doi:10.1101/821835 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ A role for keratins in supporting mitochondrial organization and function in skin keratinocytes ]]> https://biorxiv.org/content/10.1101/822403v1?rss=1 Steen, K. Chen, D. Wang, F. Majumdar, R. Chen, S. Kumar, S. Lombard, D. B. Weigert, R. Parent, C. A. Coulombe, P. A. 2019-10-30 doi:10.1101/822403 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Valuing Carbon Stocks across a Tropical Lagoon after Accounting for Black and Inorganic Carbon: Bulk Density Proxies for monitoring ]]> https://biorxiv.org/content/10.1101/824490v1?rss=1 Gallagher, J. B. B. Chew, S. T. Madin, J. Thorhaug, A. 2019-11-06 doi:10.1101/824490 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ A circuit mechanism for irrationalities in decision-making and NMDA receptor hypofunction: behaviour, computational modelling, and pharmacology ]]> https://biorxiv.org/content/10.1101/826214v1?rss=1 Cavanagh, S. E. Lam, N. H. Murray, J. D. Hunt, L. T. Kennerley, S. W. 2019-10-31 doi:10.1101/826214 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Resolvin D-series regulates Phospholipase D both during inflammation and resolution by modulating phagocyte functions ]]> https://biorxiv.org/content/10.1101/827295v1?rss=1 Ganesan, R. Henkels, K. M. Shah, K. Rosa, X. D. Libreros, S. Cheemarla, N. R. Serhan, C. N. Cambronero, J. G. 2019-11-02 doi:10.1101/827295 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Identification of a novel tedizolid resistance mutation in rpoB of methicillin-resistant Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/827501v1?rss=1 Shen, T. Penewit, K. Waalkes, A. Xu, L. Salipante, S. Nath, A. Werth, B. J. 2019-11-01 doi:10.1101/827501 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements ]]> https://biorxiv.org/content/10.1101/827857v1?rss=1 Henderson, R. Lu, M. Zhou, Y. Mu, Z. Parks, R. Han, Q. Hsu, A. L. Carter, E. Blanchard, S. C. Edwards, R. Wiehe, K. Saunders, K. O. Borgnia, M. J. Bartesaghi, A. Mothes, W. Haynes, B. F. Acharya, P. Alam, S. M. 2019-11-02 doi:10.1101/827857 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Local Glutamate-Mediated Dendritic Plateau Potentials Change the State of the Cortical Pyramidal Neuron ]]> https://biorxiv.org/content/10.1101/828582v1?rss=1 Gao, P. P. Graham, J. W. Zhou, W.-L. L. Jang, J. Angulo, S. Dura-Bernal, S. Hines, M. Lytton, W. W. Antic, S. D. 2019-11-02 doi:10.1101/828582 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ The olfactory bulb contributes to the adaptation of odor responses: the input-output transformation ]]> https://biorxiv.org/content/10.1101/829531v1?rss=1 Storace, D. A. Cohen, L. B. 2019-11-04 doi:10.1101/829531 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Cyclic and Multilevel Causation in Evolutionary Processes ]]> https://biorxiv.org/content/10.1101/830422v1?rss=1 Warrell, J. Gerstein, M. 2019-11-04 doi:10.1101/830422 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Transcriptional reprogramming in fused cells is triggered by plasma-membrane diminution ]]> https://biorxiv.org/content/10.1101/832378v1?rss=1 Feliciano, D. Espinosa-Medina, I. Weigel, A. Milano, K. M. Tang, Z. Lee, T. Kliman, H. J. Guller, S. M. Ott, C. M. Lippincott-Schwartz, J. 2019-11-06 doi:10.1101/832378 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Modeling phylogenetic biome shifts on a planet with a past ]]> https://biorxiv.org/content/10.1101/832527v1?rss=1 Landis, M. J. Edwards, E. J. Donoghue, M. J. 2019-11-07 doi:10.1101/832527 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Molecular Evolution of the Sex Peptide Network in Drosophila ]]> https://biorxiv.org/content/10.1101/833939v1?rss=1 McGeary, M. K. Findlay, G. D. 2019-11-16 doi:10.1101/833939 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ A minimal synaptic model for direction selective neurons in Drosophila ]]> https://biorxiv.org/content/10.1101/833970v1?rss=1 Zavatone-Veth, J. Badwan, B. Clark, D. 2019-11-07 doi:10.1101/833970 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Within Visit Test-Retest Reliability of EEG Profiles in Children with Autism Spectrum Disorder and Typical Development ]]> https://biorxiv.org/content/10.1101/834697v1?rss=1 Levin, A. R. Naples, A. Scheffler, A. W. Webb, S. J. Shic, F. Sugar, C. A. Murias, M. Bernier, R. A. Chawarska, K. Dawson, G. Faja, S. Jeste, S. Nelson, C. A. McPartland, J. C. Senturk, D. Autism Biomarkers Consortium for Clinical Trials, 2019-11-20 doi:10.1101/834697 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ microRNA seedless sites attenuate strong-seed-site-mediated target repression ]]> https://biorxiv.org/content/10.1101/837682v1?rss=1 70% of transcriptomic datasets examined, in which specific miRNAs are experimentally increased or decreased. The attenuation effect is confirmed by 3UTR reporter assays and mediated through base-pairing between miRNA and seedless sites. Furthermore, this seedless-site-based attenuation effect could affect seed sites of the same miRNA or another miRNA, thus partially explaining the variability in target suppression and miRNA-mediated gene upregulation. Our findings reveal an unexpected principle of miRNA-mediated gene regulation, and could impact the understanding of many miRNA-regulated biological processes. ]]> Wang, X. Tian, J. Cui, P. Mastriano, S. Zhang, D. Zhao, H. Lu, H. Ding, Y. Lu, J. 2019-11-11 doi:10.1101/837682 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Division of labor in metabolic regulation by transcription, translation, acetylation and phosphorylation ]]> https://biorxiv.org/content/10.1101/838243v1?rss=1 0.8). Our model uncovered enzymes regulated by phosphorylation during a mammalian cell-cycle, which we validate using phosphoproteomics. Interpreting the machine-learning model using game-theory uncovered enzyme properties including network connectivity, essentiality, and condition-specific factors such as maximum flux that differentiate regulation by phosphorylation from acetylation. The conserved and predictable partitioning of metabolic regulation identified here between these PTMs can enable rational engineering of regulatory circuits. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/838243v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1bf290org.highwire.dtl.DTLVardef@d1fd3borg.highwire.dtl.DTLVardef@4852ddorg.highwire.dtl.DTLVardef@383bb9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chandrasekaran, S. 2019-11-11 doi:10.1101/838243 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ A big-data approach to understanding metabolic rate and response to obesity in laboratory mice ]]> https://biorxiv.org/content/10.1101/839076v1?rss=1 Corrigan, J. K. Ramachandran, D. He, Y. Palmer, C. Jurczak, M. J. Li, B. Friedline, R. H. Kim, J. K. Ramsey, J. J. Lantier, L. McGuinness, O. P. Banks, A. S. Mouse Metabolic Phenotyping Center Energy Balance Working Group, 2019-11-12 doi:10.1101/839076 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ LESSeq: Local event-based analysis of alternative splicing using RNA-Seq data ]]> https://biorxiv.org/content/10.1101/841494v1?rss=1 Leng, J. Cameron, C. J. Oh, S. Khurana, E. Noonan, J. P. Gerstein, M. B. 2019-11-14 doi:10.1101/841494 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Astral Microtubules Regulate Formation of the Cytokinetic Cleavage Furrow in Fission Yeast ]]> https://biorxiv.org/content/10.1101/843110v1?rss=1 Dundon, S. E. Pollard, T. D. 2019-11-14 doi:10.1101/843110 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ The C-terminal tail guides assembly and degradation of membrane proteins ]]> https://biorxiv.org/content/10.1101/843326v1?rss=1 Sun, S. Mariappan, M. 2019-11-15 doi:10.1101/843326 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Functional connectome analyses reveal a highly optimized human olfactory network ]]> https://biorxiv.org/content/10.1101/843532v1?rss=1 Arnold, T. C. You, Y. Ding, M. Zuo, X.-N. de Araujo, I. E. Li, W. 2019-11-16 doi:10.1101/843532 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin ]]> https://biorxiv.org/content/10.1101/843714v1?rss=1 Vonica, A. Bhat, N. Phan, K. Guo, J. Iancu, L. Weber, J. Karger, A. Cain, J. W. Wang, E. C. E. DeStefano, G. O'Donnell-Luria, A. Christiano, A. M. Riley, B. Butler, S. Luria, V. 2019-11-15 doi:10.1101/843714 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Recombination, variance in genetic relatedness, and selection against introgressed DNA ]]> https://biorxiv.org/content/10.1101/846147v1?rss=1 Veller, C. Edelman, N. B. Muralidhar, P. Nowak, M. A. 2019-11-18 doi:10.1101/846147 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ An asymmetric sheath controls flagellar supercoiling and motility in the Leptospira spirochete ]]> https://biorxiv.org/content/10.1101/847533v1?rss=1 Sindelar, C. V. Buschiazzo, A. Ko, A. Gibson, K. H. Trajtenberg, F. Brady, M. Wunder, E. San Martin, F. Mechaly, A. E. Shang, Z. Liu, J. Picardeau, M. 2019-11-21 doi:10.1101/847533 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Mechanisms of high-intensity sound exposure on inhibiting hippocampal long-term potentiation: role of brain-derived neurotrophic factor ]]> https://biorxiv.org/content/10.1101/850214v1?rss=1 de Deus, J. L. Amorim, M. R. Ribeiro, A. B. Barcellos-Filho, P. G. Ceballos, C. C. Branco, L. G. Cunha, A. S. Leao, R. M. 2019-11-21 doi:10.1101/850214 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Neurocognitive mechanisms of social inferences in typical and autistic adolescents ]]> https://biorxiv.org/content/10.1101/850552v1?rss=1 Rosenblau, G. Korn, C. W. Dutton, A. Lee, D. Pelphrey, K. 2019-11-21 doi:10.1101/850552 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Learning not to remember: How predicting the future impairs encoding of the present ]]> https://biorxiv.org/content/10.1101/851147v1?rss=1 Sherman, B. E. Turk-Browne, N. B. 2019-11-21 doi:10.1101/851147 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Emergent honeycomb topology of the leaf spongy mesophyll ]]> https://biorxiv.org/content/10.1101/852459v1?rss=1 Borsuk, A. Roddy, A. Theroux-Rancourt, G. Brodersen, C. 2019-11-25 doi:10.1101/852459 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Ectopic HCN4 expression drives mTOR-dependent epilepsy ]]> https://biorxiv.org/content/10.1101/853820v1?rss=1 Hsieh, L. Wen, J. Nguyen, L. Zhang, L. Torres-Reveron, J. Spencer, D. Bordey, A. 2019-11-24 doi:10.1101/853820 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ RIPK3 inhibition prevents KRAS mutant p53 deficient lung tumor progression by impeding MDSCs ]]> https://biorxiv.org/content/10.1101/853978v1?rss=1 Jayakumar, A. 2019-11-25 doi:10.1101/853978 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Mate discrimination among subspecies through a conserved olfactory pathway ]]> https://biorxiv.org/content/10.1101/854364v1?rss=1 Khallaf, M. A. Auer, T. O. Grabe, V. Depetris-Chauvin, A. Ammagarahalli, B. Zhang, D.-D. Lavista-Llanos, S. Kaftan, F. Weissflog, J. Matzkin, L. M. Rollmann, S. Loefstedt, C. Svatos, A. Dweck, H. K. Sachse, S. Benton, R. Hansson, B. S. Knaden, M. 2019-11-25 doi:10.1101/854364 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ White Matter Microstructure and its Relation to Clinical Features of Obsessive-Compulsive Disorder: Findings from the ENIGMA OCD Working Group ]]> https://biorxiv.org/content/10.1101/855916v1?rss=1 Piras, F. Piras, F. Abe, Y. Agarwal, S. M. Anticevic, A. Ameis, S. Arnold, P. Bargallo, N. Batistuzzo, M. Benedetti, F. Beucke, J. C. Boedhoe, P. S. W. Bollettini, I. Brem, S. Calvo, A. Cho, K. I. K. Dallaspezia, S. Dickie, E. Adam, B. Fan, S. Fouche, J. P. Gruner, P. Gursel, D. A. Hauser, T. U. Hirano, Y. Hoexter, M. Q. Iorio, M. James, A. Reddy, J. Kaufmann, C. Koch, K. Kochunov, P. Kwon, J. S. Lazaro, L. Lochner, C. Marsh, R. Nakagawa, A. Nakamae, T. Narayanaswamy, J. C. Sakai, Y. Shimizu, E. Simon, D. Simpson, H. B. Soreni, N. Stampfli, P. Stern 2019-11-30 doi:10.1101/855916 Cold Spring Harbor Laboratory Press 2019-11-30 <![CDATA[ CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus ]]> https://biorxiv.org/content/10.1101/859025v1?rss=1 Graziano, V. Walker, F. C. Kennedy, E. A. Wei, J. Ettayebi, K. Simoes, M. Filler, R. Hassan, E. Hsieh, L. L. Kolawole, A. O. Wobus, C. Lindesmith, L. C. Baric, R. S. Estes, M. Orchard, R. C. Baldridge, M. T. Wilen, C. 2019-11-28 doi:10.1101/859025 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ The Fusiform Gyrus Processes Faces Relative to an Overall Face Average and a Person Average ]]> https://biorxiv.org/content/10.1101/861625v1?rss=1 Shehzad, Z. Byeon, E. McCarthy, G. 2019-12-02 doi:10.1101/861625 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ TopicNet: a framework for measuring transcriptional regulatory network change ]]> https://biorxiv.org/content/10.1101/862177v1?rss=1 Lou, S. Li, T. Kong, X. Zhang, J. Liu, J. Lee, D. Gerstein, M. 2019-12-02 doi:10.1101/862177 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ Characterizing the tolerance of phage therapy candidate OMKO1 to environmental stress ]]> https://biorxiv.org/content/10.1101/864025v1?rss=1 Blazanin, M. Lam, W. T. Turner, P. 2019-12-03 doi:10.1101/864025 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Confluence of timing and reward biases in perceptual decision-making dynamics ]]> https://biorxiv.org/content/10.1101/865501v1?rss=1 Shinn, M. Ehrlich, D. Lee, D. Murray, J. D. Seo, H. 2019-12-05 doi:10.1101/865501 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Phage steering of antibiotic-resistance evolution in the bacterial pathogen Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/868661v1?rss=1 Gurney, J. Pradier, L. Griffin, J. S. Gougat-Barbera, C. Chan, B. K. Turner, P. E. Kaltz, O. Hochberg, M. E. 2019-12-10 doi:10.1101/868661 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Mitotic spindle disassembly in human cells relies on CRIPT-bearing hierarchical redox signals ]]> https://biorxiv.org/content/10.1101/869123v1?rss=1 Cai, C. Li, H. 2019-12-08 doi:10.1101/869123 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Depurination of colibactin-derived interstrand cross-links. ]]> https://biorxiv.org/content/10.1101/869313v1?rss=1 Xue, M. Wernke, K. Herzon, S. 2019-12-10 doi:10.1101/869313 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ How tasks change whole-brain functional organization to reveal brain-phenotype relationships ]]> https://biorxiv.org/content/10.1101/870287v1?rss=1 Greene, A. S. Gao, S. Noble, S. Scheinost, D. Constable, T. 2019-12-10 doi:10.1101/870287 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation ]]> https://biorxiv.org/content/10.1101/017277v1?rss=1 Jinmyung Choi Parisa Shooshtari Kaitlin E Samocha Mark J Daly Chris Cotsapas 2015-03-29 doi:10.1101/017277 Cold Spring Harbor Laboratory Press 2015-03-29 <![CDATA[ Genomic variant calling: Flexible tools and a diagnostic data set ]]> https://biorxiv.org/content/10.1101/027227v1?rss=1 Michael Lawrence Melanie A Huntley Eric Stawiski Art Owen Thomas D Wu Leonard D Goldstein Yi Cao Jeremiah Degenhardt Jason Young Joseph Guillory Sherry Heldens Marlena Jackson Somasekar Seshagiri Robert Gentleman 2015-09-18 doi:10.1101/027227 Cold Spring Harbor Laboratory Press 2015-09-18 <![CDATA[ Winners curse correction and variable thresholding improve performance of polygenic risk modeling based on summary-level data from genome-wide association studies ]]> https://biorxiv.org/content/10.1101/034082v1?rss=1 Jianxin Shi JuHyun Park Jubao Duan Sonja Berndt Winton Moy William Wheeler Xing Hua Debra Silverman Montserrat Garcia-Closas Chao Agnes Hsiung Jonine D. Figueroa Victoria K. Cortessis Nuria Malats Margaret R. Karagas Paolo Vineis I-Shou Chang Dongxin Lin Baosen Zhou Adeline Seow Keitaro Matsuo Yun-Chul Hong Neil E. Caporaso Brian Wolpin Eric Jacobs Gloria Petersen Donghui Li Harvey Risch Alan R. Sanders Li Hsu Robert E. Schoen Hermann Brenner Rachael Stolzenberg-Solomon Pablo Gejman Qing Lan Nathaniel Rothman Laufey T. Amundadottir Alison P. Klein Maria Teresa Landi Douglas F. Levinson Stephen 2016-01-10 doi:10.1101/034082 Cold Spring Harbor Laboratory Press 2016-01-10 <![CDATA[ Whole genome sequencing identifies a novel factor required for secretory granule maturation in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/042085v1?rss=1 Cassandra Kontur Santosh Kumar Xun Lan Jonathan K Pritchard Aaron P Turkewitz 2016-03-01 doi:10.1101/042085 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Insights into telomerase action from high-throughput sequencing of S. pombe telomeres ]]> https://biorxiv.org/content/10.1101/047837v1?rss=1 Henrietta W Bennett Na Liu Yan Hu Megan C King 2016-04-09 doi:10.1101/047837 Cold Spring Harbor Laboratory Press 2016-04-09 <![CDATA[ Analysis of shared heritability in common disorders of the brain ]]> https://biorxiv.org/content/10.1101/048991v1?rss=1 Verneri Anttila Brendan Bulik-Sullivan Hilary Kiyo Finucane Jose Bras Laramie Duncan Valentina Escott-Price Guido Falcone Padhraig Gormley Rainer Malik Nikolaos Patsopoulos Stephan Ripke Raymond Walters Zhi Wei Dongmei Yu Phil Lee IGAP consortium IHGC consortium ILAE Consortium on Complex Epilepsies IMSGC consortium IPDGC consortium METASTROKE and ICH Studies of the ISGC ADHD Working Group of the PGC Anorexia Nervosa Working Group of the PGC ASD Working Group of the PGC Bipolar Disorders Working Group of the PGC Major Depressive Disorder Working Group of the PGC OCD and TS Working Group of the 2016-04-16 doi:10.1101/048991 Cold Spring Harbor Laboratory Press 2016-04-16 <![CDATA[ Chm7 and Heh1 form a nuclear envelope subdomain for nuclear pore complex quality control ]]> https://biorxiv.org/content/10.1101/049148v1?rss=1 Brant M Webster David J Thaller Jens Jaeger Sarah E Ochmann C. Patrick Lusk 2016-04-18 doi:10.1101/049148 Cold Spring Harbor Laboratory Press 2016-04-18 <![CDATA[ Goggatomy: a Method for Opening Small Cuticular Compartments in Arthropods for Physiological Experiments ]]> https://biorxiv.org/content/10.1101/053298v1?rss=1 Alan R Kay Davide Raccuglia Jon Scholte Elena Loukianova Christopher A Barwacz Steven A Armstrong C Allan Guymon Michael N Nitabach Daniel F Eberl 2016-05-18 doi:10.1101/053298 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Feedforward and feedback frequency-dependent interactions in a large-scale laminar network of the primate cortex ]]> https://biorxiv.org/content/10.1101/065854v1?rss=1 Jorge F Mejias John D Murray Henry Kennedy Xiao-Jing Wang 2016-07-26 doi:10.1101/065854 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ High-resolution phenotypic landscape of the RNA Polymerase II trigger loop ]]> https://biorxiv.org/content/10.1101/068726v1?rss=1 Chenxi Qiu Olivia C. Erinne Jui Dave Ping Cui Huiyan Jin Nandhini Muthukrishnan Leung K. Tang Sabareesh Ganesh Babu Kenny C. Lam Paul J. Vandeventer Ralf Strohner Jan Van den Brulle Sing-Hoi Sze Craig D. Kaplan 2016-08-14 doi:10.1101/068726 Cold Spring Harbor Laboratory Press 2016-08-14 <![CDATA[ mTORC1 controls cytoplasmic crowding by regulating ribosome concentration ]]> https://biorxiv.org/content/10.1101/073866v1?rss=1 Delarue, M. Brittingham, G. Surovtsev, I. Kennedy, K. J. Gutierrez, I. Chung, J. Groves, J. T. Jacobs-Wagner, C. Holt, L. J. 2017-02-16 doi:10.1101/073866 Cold Spring Harbor Laboratory Press 2017-02-16 <![CDATA[ Adipocyte JAK2 mediates hepatic insulin sensitivity and the diabetogenic action of Growth Hormone ]]> https://biorxiv.org/content/10.1101/076265v1?rss=1 Kevin Corbit Joao Paulo G. Camporez Jennifer L Tran Camella G Wilson Rachel J Perry Gerald Schulman Michael J Jurczak Ethan Weiss 2016-09-20 doi:10.1101/076265 Cold Spring Harbor Laboratory Press 2016-09-20 <![CDATA[ Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences ]]> https://biorxiv.org/content/10.1101/078832v1?rss=1 Alexander Bucksch Acheampong Atta-Boateng Akomian Fortune Azihou Mathilde Balduzzi Dorjsuren Battogtokh Aly Baumgartner Brad Binder Siobhan Braybrook Cynthia Chang Viktoriya Coneva Thomas DeWitt Alexander Fletcher Malia Gehan Diego Hernan Diaz Martinez Lilan Hong Anjali Iyer-Pascuzzi Laura Klein Samuel Leiboff Mao Li Jonathan Lynch Alexis Maizel Julin Maloof RJ Cody Markelz Ciera Martinez Laura Miller Washington Mio Wojtek Palubicki Hendrik Poorter Christophe Pradal Charles Price Eetu Puttonen John Reese Ruben Rellan-Alvarez Edgar Spalding Erin Sparks Chris Topp Joseph Williams Daniel Chitwood 2016-10-04 doi:10.1101/078832 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ The Drosophila pheromone Z4-11Al is encoded together with habitat olfactory cues and mediates species-specific communication ]]> https://biorxiv.org/content/10.1101/083071v1?rss=1 Lebreton, S. Borrero-Echeverry, F. Gonzalez, F. Solum, M. Wallin, E. Hedenstroem, E. Hansson, B. S. Gustavsson, A.-L. Bengtsson, M. Birgersson, G. Walker, W. B. Dweck, H. Becher, P. G. Witzgall, P. 2016-10-25 doi:10.1101/083071 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ Neural precursors of decisions that matter--an ERP study of deliberate and arbitrary choice ]]> https://biorxiv.org/content/10.1101/097626v1?rss=1 Maoz, U. Yaffe, G. Koch, C. Mudrik, L. 2017-01-01 doi:10.1101/097626 Cold Spring Harbor Laboratory Press 2017-01-01 <![CDATA[ Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway ]]> https://biorxiv.org/content/10.1101/101154v1?rss=1 He, B. Z. Zhou, X. O'Shea, E. 2017-01-18 doi:10.1101/101154 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ microCT-Based Skeletal Phenomics in Zebrafish Reveals Virtues of Deep Phenotyping at the Whole-Organism Scale ]]> https://biorxiv.org/content/10.1101/105569v1?rss=1 Hur, M. Gistelinck, C. A. Huber, P. Lee, J. Thompson, M. H. Monstad-Rios, A. T. Watson, C. J. McMenamin, S. K. Willaert, A. Parichy, D. M. Coucke, P. Kwon, R. Y. 2017-02-14 doi:10.1101/105569 Cold Spring Harbor Laboratory Press 2017-02-14 <![CDATA[ Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families ]]> https://biorxiv.org/content/10.1101/127043v1?rss=1 Werling, D. M. Brand, H. An, J.-Y. Stone, M. R. Glessner, J. T. Zhu, L. Collins, R. L. Dong, S. Layer, R. M. Markenscoff-Papadimitriou, E.-C. Farrell, A. Schwartz, G. B. Currall, B. B. Dea, J. Duhn, C. Erdman, C. Gilson, M. Handsaker, R. E. Kashin, S. Klei, L. Mandell, J. D. Nowakowski, T. J. Liu, Y. Pochareddy, S. Smith, L. Walker, M. F. Wang, H. Z. Waterman, M. J. He, X. Kriegstein, A. R. Rubenstein, J. L. Sestan, N. McCarroll, S. A. Neale, B. M. Coon, H. Willsey, A. J. Buxbaum, J. D. Daly, M. J. State, M. W. Quinlan, A. Marth, G. T. Roeder, K. Devli 2017-04-13 doi:10.1101/127043 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Reversal of cardiac and skeletal manifestations of Duchenne muscular dystrophy by cardiosphere-derived cells and their exosomes in mdx dystrophic mice and in human Duchenne cardiomyocytes ]]> https://biorxiv.org/content/10.1101/128900v1?rss=1 Aminzadeh, M. A. Rogers, R. G. Gouin, K. Fournier, M. Tobin, R. E. Guan, X. Childers, M. K. Andres, A. M. Taylor, D. J. Ibrahim, A. Ding, X.-m. Torrente, A. Goldhaber, J. I. Victor, R. A. Gottlieb, R. A. Lewis, M. Marban, E. 2017-04-20 doi:10.1101/128900 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Purification Of The Mammalian NgBR/hCIT cis-Prenyltransferase Complex: IdentificationOf A Conserved Carboxyterminal RxG Motif Crucial For Enzymatic Activity ]]> https://biorxiv.org/content/10.1101/139675v1?rss=1 Grabinska, K. A. Edani, B. H. Park, E. J. Kraehling, J. R. Sessa, B. 2017-05-18 doi:10.1101/139675 Cold Spring Harbor Laboratory Press 2017-05-18 <![CDATA[ Unique belowground ecological strategies of subtropical and tropical plant species expand the root trait space ]]> https://biorxiv.org/content/10.1101/2024.10.06.616893v1?rss=1 Guerrero Ramirez, N. R. Weemstra, M. Addo-Danso, S. D. Andersen, K. Arnaud, M. Cordeiro, A. L. Cusack, D. F. Kotowska, M. M. Lee, M. Y. Leroy, C. Lugli, L. F. Pierick, K. Smith-Martin, C. M. Toro, L. Umana, M. N. Valverde-Barrantes, O. J. Wong, M. Fortunel, C. 2024-10-10 doi:10.1101/2024.10.06.616893 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ The role of GPR87 in Pulmonary Fibrosis ]]> https://biorxiv.org/content/10.1101/2024.10.10.617569v1?rss=1 Khoury, J. Ahangari, F. Adams, T. Justet, A. Manning, E. McDonough, J. E. Barnthaler, T. Anderson, S. Nikola, F. Beermann, M. L. Gomez, J. L. Kaminski, N. 2024-10-11 doi:10.1101/2024.10.10.617569 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Catabolism of extracellular glutathione supplies amino acids to support tumor growth ]]> https://biorxiv.org/content/10.1101/2024.10.10.617667v1?rss=1 Hecht, F. Zocchi, M. Tuttle, E. T. Ward, N. P. Smith, B. Kang, Y. P. Cazarin, J. Soares, Z. G. Ozgurses, M. E. Zhao, H. Sheehan, C. Alimohammadi, F. Munger, L. D. Trivedi, D. Asantewaa, G. Blick-Nitko, S. K. Zoeller, J. J. Chen, Y. Vasiliou, V. Turner, B. M. Muir, A. Coloff, J. L. Munger, J. DeNicola, G. M. Harris, I. S. 2024-10-11 doi:10.1101/2024.10.10.617667 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ RAD51 Paralogs and RAD51 Paralog Complexes BCDX2 and CX3 Interact with BRCA2 ]]> https://biorxiv.org/content/10.1101/2024.10.10.617680v1?rss=1 Thrasher, J. G. Fagunloye, A. A. G. Justiniano, F. S. Bernstein, K. A. Jensen, R. B. 2024-10-11 doi:10.1101/2024.10.10.617680 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ An atypical E3 ligase safeguards the ribosome during nutrient stress ]]> https://biorxiv.org/content/10.1101/2024.10.10.617692v1?rss=1 Douglas, T. Zhang, J. Wu, Z. Abdallah, K. McReynolds, M. Gilbert, W. V. Iwai, K. Peng, J. Young, L. H. Crews, C. M. 2024-10-11 doi:10.1101/2024.10.10.617692 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Intranasal hemagglutinin protein boosters induce robust mucosal immunity and cross-protection against influenza A viral challenge ]]> https://biorxiv.org/content/10.1101/2024.10.10.616291v1?rss=1 Moriyama, M. Rodrigues, G. Wang, J. Hudak, A. Dong, H. Homer, R. J. Weissman, D. Ma, S. Iwasaki, A. 2024-10-12 doi:10.1101/2024.10.10.616291 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ ExoSloNano: Multi-Modal Nanogold Tags for identi-fication of Macromolecules in Live Cells & Cryo-Electron Tomograms ]]> https://biorxiv.org/content/10.1101/2024.10.12.617288v1?rss=1 Young, L. N. Sherrard, A. Zhou, H. Shaikh, F. Hutchings, J. Riggi, M. Rosen, M. K. Giraldez, A. Villa, E. 2024-10-13 doi:10.1101/2024.10.12.617288 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation ]]> https://biorxiv.org/content/10.1101/2024.10.12.618004v1?rss=1 Gonzalez-Hurtado, E. Leveau, C. Li, K. Qu, R. Mishra, M. Goldberg, E. L. Sidorov, S. Yeung, S. T. Khairallah, C. Gonzalez, D. Shepard, T. M. Camell, C. Artyomov, M. N. Kluger, Y. Khanna, K. M. Dixit, V. D. 2024-10-13 doi:10.1101/2024.10.12.618004 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Amyloid-beta, alpha-synuclein and tau aggregated co-pathologies enhance neuropathology and neuroinflammation ]]> https://biorxiv.org/content/10.1101/2024.10.13.618101v1?rss=1 Webster, J. M. Stone, W. J. Yang, Y.-T. Miller, A. T. Childers, G. M. Corbin-Stein, N. J. Mudium, N. Molina, J. Won, W.-J. Sandoval, I. M. Tyrrell, D. J. Manfredsson, F. P. Kordower, J. H. Harms, A. S. 2024-10-13 doi:10.1101/2024.10.13.618101 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Critical role for the TGF-β1/mTORC1 signalling axis in defining the transcriptional identity of CTHRC1+ pathologic fibroblasts ]]> https://biorxiv.org/content/10.1101/2024.10.12.617979v1?rss=1 Wilson, J.-A. A. M. Walters, R. Guillotin, D. Kaminski, N. Parolo, S. Plate, M. Chambers, R. C. 2024-10-14 doi:10.1101/2024.10.12.617979 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Caging of membrane-to-cortex attachment proteins can trigger cellular symmetry breaking ]]> https://biorxiv.org/content/10.1101/2024.10.14.618153v1?rss=1 Dar, S. Moreno, R. T. Palaia, I. Gopalan, A. B. Sun, Z. G. Strauss, L. Springer, R. Belmonte, J. M. Foster, S. K. Murrell, M. Ejsing, C. S. Saric, A. Leptin, M. Diz-Munoz, A. 2024-10-14 doi:10.1101/2024.10.14.618153 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Wild Florida Mottled Ducks demonstrate strong heterogeneity in their humoral innate immune response ]]> https://biorxiv.org/content/10.1101/2024.10.12.617993v1?rss=1 Ayala, A. J. Cheng, M. Hellinger, T. A. McBride, K. M. Webb, J. Fanning, A. Snyder, P. Ferragamo, M. Garcia, S. C. Sterner, N. Bischoff, K. L. Moreno, S.-A. Ogbunugafor, C. B. 2024-10-15 doi:10.1101/2024.10.12.617993 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Diversity of ancestral brainstem noradrenergic neurons across species and multiple biological factors ]]> https://biorxiv.org/content/10.1101/2024.10.14.618224v1?rss=1 Kelberman, M. A. Rodberg, E. Arabzadeh, E. Bair-Marshall, C. J. Berridge, C. W. Berrocoso, E. Breton-Provencher, V. Chandler, D. J. Che, A. Davy, O. Devilbiss, D. M. Downs, A. M. Drummond, G. Dvorkin, R. Fazlali, Z. Froemke, R. C. Glennon, E. Gold, J. I. Ito, H. Jiang, X. Johansen, J. P. Kaye, A. P. Kim, J. R. Kuo, C.-c. Liu, R.-j. Liu, Y. Llorca-Torralba, M. McCall, J. G. McElligott, Z. A. McKinney, A. M. Miguelez, C. Min, M.-Y. Nowlan, A. C. Omrani, M. Pickering, A. E. Poe, G. R. Ranjbar-Slamloo, Y. Razquin, J. Rodenkirch, C. Sales, A. C. Satyasambit, 2024-10-16 doi:10.1101/2024.10.14.618224 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Information transfer from spatial to social distance in rats: implications for the role of the posterior parietal cortex in spatial-social integration ]]> https://biorxiv.org/content/10.1101/2024.10.14.618305v1?rss=1 Wise, T. B. Templer, V. L. Burwell, R. D. 2024-10-16 doi:10.1101/2024.10.14.618305 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ ATP-gated P2x7 receptor is a major channel type at type II auditory nerves and required for hearing sensitivity efferent controlling and noise protection ]]> https://biorxiv.org/content/10.1101/2024.10.14.618333v1?rss=1 Liang, C. Zhai, T.-Y. Fang, S. Chen, J. Liu, L.-M. Yu, N. Zhao, H.-B. 2024-10-16 doi:10.1101/2024.10.14.618333 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Individual variation in the functional lateralization of human ventral temporal cortex: Local competition and long-range coupling ]]> https://biorxiv.org/content/10.1101/2024.10.15.618268v1?rss=1 Blauch, N. M. Plaut, D. C. Vin, R. Behrmann, M. 2024-10-16 doi:10.1101/2024.10.15.618268 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite ]]> https://biorxiv.org/content/10.1101/2024.10.14.617411v1?rss=1 Vock, I. Mabin, J. Machyna, M. Zhang, A. Hogg, J. R. Simon, M. D. 2024-10-17 doi:10.1101/2024.10.14.617411 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ EGFR and tyrosine kinase inhibitor interactions probed by hydrogen-deuterium exchange and mass spectrometry (HDX-MS) ]]> https://biorxiv.org/content/10.1101/2024.10.14.618277v1?rss=1 Ashtekar, K. D. Lemmon, M. A. Tsutsui, Y. 2024-10-17 doi:10.1101/2024.10.14.618277 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ ISWI chromatin remodeler SMARCA5 is essential for meiotic gene expression and male fertility in mammals ]]> https://biorxiv.org/content/10.1101/2024.10.14.618292v1?rss=1 Kataruka, S. Malla, A. B. Rainsford, S. R. Lesch, B. J. 2024-10-17 doi:10.1101/2024.10.14.618292 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions ]]> https://biorxiv.org/content/10.1101/2024.10.15.618303v1?rss=1 Li, W. Dasgupta, A. Yang, K. Wang, S. Hemandhar-Kumar, N. Yarbro, J. M. Hu, Z. Salovska, B. Fornasiero, E. F. Peng, J. Liu, Y. 2024-10-17 doi:10.1101/2024.10.15.618303 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ 14C-age of carbon used to grow fine roots reflects tree carbon status ]]> https://biorxiv.org/content/10.1101/2024.10.15.618388v1?rss=1 Hilman, B. Solly, E. F. Hagedorn, F. Kuhlmann, I. Herrera-Ramirez, D. Trumbore, S. 2024-10-17 doi:10.1101/2024.10.15.618388 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ White Matter Microstructural Alterations in Autism Localized with Bundle Analytics ]]> https://biorxiv.org/content/10.1101/2024.10.16.618731v1?rss=1 Kim, G. S. Chandio, B. Q. Benavidez, S. M. Thompson, P. M. Lawrence, K. E. 2024-10-17 doi:10.1101/2024.10.16.618731 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Connectome-based Predictive Models of General and Specific Cognitive Control ]]> https://biorxiv.org/content/10.1101/2024.10.21.619468v1?rss=1 Qu, S. Qu, Y. L. Yoo, K. Chun, M. M. 2024-10-22 doi:10.1101/2024.10.21.619468 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson's disease and Dementia with Lewy bodies ]]> https://biorxiv.org/content/10.1101/2024.10.23.619548v1?rss=1 Vidyadhara, D. J. Backstrom, D. Chakraborty, R. Ruan, J. Park, J.-M. Mistry, P. K. Chandra, S. S. 2024-10-23 doi:10.1101/2024.10.23.619548 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Decoding the transcriptomic signatures of psychological trauma in human cortex and amygdala ]]> https://biorxiv.org/content/10.1101/2024.10.23.619681v1?rss=1 Hicks, E. M. Seah, C. Deans, M. Lee, S. Johnston, K. J. Cote, A. Ciarcia, J. Chakka, A. Collier, L. Holtzheimer, P. Young, K. A. Traumatic Stress Brain Research Group, Brennand, K. Nestler, E. J. Girgenti, M. J. Huckins, L. M. 2024-10-23 doi:10.1101/2024.10.23.619681 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Alternative transcripts recode human genes to express overlapping, frameshifted microproteins ]]> https://biorxiv.org/content/10.1101/2024.10.22.619581v1?rss=1 Su, H. Katz, S. G. Slavoff, S. A. 2024-10-25 doi:10.1101/2024.10.22.619581 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Partially characterized topology guides reliable anchor-free scRNA integration ]]> https://biorxiv.org/content/10.1101/2024.10.22.619682v1?rss=1 He, C. Filippidis, P. Kleinstein, S. Guan, L. 2024-10-25 doi:10.1101/2024.10.22.619682 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ When to Trust Epigenetic Clocks: Avoiding False Positives in Aging Interventions. ]]> https://biorxiv.org/content/10.1101/2024.10.22.619720v1?rss=1 Borrus, D. S. Sehgal, R. Armstrong, J. F. Kasamoto, J. Gonzalez, J. Higgins-Chen, A. T. 2024-10-25 doi:10.1101/2024.10.22.619720 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Abl kinases regulate FGF signaling independent of Crk phosphorylation to prevent Peters anomaly ]]> https://biorxiv.org/content/10.1101/2024.10.24.619064v1?rss=1 Wu, H. Mao, Y. Wang, Q. Yu, H. Bouaziz, M. Makrides, N. Koleske, A. J. Radice, G. Zhang, X. 2024-10-26 doi:10.1101/2024.10.24.619064 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Testing the Tests: Using Connectome-Based Predictive Models to Reveal the Systems Standardized Tests and Clinical Symptoms Are Reflecting ]]> https://biorxiv.org/content/10.1101/2024.10.24.619737v1?rss=1 Samardzija, A. Shen, X. Luo, W. Greene, A. S. Mehta, S. Tokoglu, F. Arora, J. Woods, S. Katz, R. Sanacora, G. Srihari, V. H. Scheinost, D. Constable, R. T. 2024-10-26 doi:10.1101/2024.10.24.619737 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Encoding manifolds constructed from grating responses organize responses to natural scenes in cortical visual areas ]]> https://biorxiv.org/content/10.1101/2024.10.24.620089v1?rss=1 Dyballa, L. Field, G. D. Stryker, M. P. Zucker, S. W. 2024-10-26 doi:10.1101/2024.10.24.620089 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Shared and unique lifetime stressor characteristics and brain networks predict adolescent anxiety and depression ]]> https://biorxiv.org/content/10.1101/2024.10.25.620373v1?rss=1 Qu, Y. Chopra, S. Qu, S. Cocuzza, C. V. Labache, L. Bauer, C. C. C. Morfini, F. Whitfield-Gabrieli, S. Slavich, G. M. Joormann, J. Holmes, A. J. 2024-10-26 doi:10.1101/2024.10.25.620373 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ DNAm aging biomarkers are responsive: Insights from 51 longevity interventional studies in humans ]]> https://biorxiv.org/content/10.1101/2024.10.22.619522v1?rss=1 Sehgal, R. Borrus, D. Kasamato, J. Armstrong, J. F. Gonzalez, J. Markov, Y. Priyanka, A. Smith, R. Carreras, N. Dwaraka, V. B. DNA aging biomarkers community, Longevity interventional studies community, Higgins-Chen, A. 2024-10-27 doi:10.1101/2024.10.22.619522 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Motor Clustering Enhances Kinesin-driven Vesicle Transport ]]> https://biorxiv.org/content/10.1101/2024.10.23.619892v1?rss=1 Jiang, R. Feng, Q. Nong, D. Kang, Y. J. Sept, D. Hancock, W. O. 2024-10-27 doi:10.1101/2024.10.23.619892 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ CpGPT: a Foundation Model for DNA Methylation ]]> https://biorxiv.org/content/10.1101/2024.10.24.619766v1?rss=1 de Lima Camillo, L. P. Sehgal, R. Armstrong, J. Higgins-Chen, A. T. Horvath, S. Wang, B. 2024-10-29 doi:10.1101/2024.10.24.619766 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Differential gene expression analysis identifies a group of defensin like peptides from Solanum chacoense ovules with in vitro pollen tube attraction activity ]]> https://biorxiv.org/content/10.1101/2024.10.25.620243v1?rss=1 Liu, Y. Joly, V. Sabar, M. Matton, D. P. Morse, D. 2024-10-29 doi:10.1101/2024.10.25.620243 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DNA nanodevice for analysis of force-activated protein extension and interactions ]]> https://biorxiv.org/content/10.1101/2024.10.25.620262v1?rss=1 Zhou, K. Chung, M. Cheng, J. Powell, J. T. Liu, J. Xiong, Y. Schwartz, M. A. Lin, C. 2024-10-29 doi:10.1101/2024.10.25.620262 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Dynamic Mechanism for Subtype Selectivity of Endocannabinoids ]]> https://biorxiv.org/content/10.1101/2024.10.25.620304v1?rss=1 Dutta, S. Zhao, L. Y. Shukla, D. 2024-10-29 doi:10.1101/2024.10.25.620304 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Ice and air: Visualisation of freeze-thaw embolism and freezing spread in young L. tulipifera leaves ]]> https://biorxiv.org/content/10.1101/2024.10.26.620221v1?rss=1 Johnson, K. M. Scherer, M. Gerber, D. Style, R. W. Dufresne, E. R. Brodersen, C. R. 2024-10-29 doi:10.1101/2024.10.26.620221 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency ]]> https://biorxiv.org/content/10.1101/2024.10.26.620318v1?rss=1 Koehnke, T. Karigane, D. Hilgart, E. Fan, A. C. Kayamori, K. Miyauchi, M. Collins, C. T. Suchy, F. P. Rangavajhula, A. Feng, Y. Nakauchi, Y. Martinez-Montes, E. Fowler, J. Loh, K. M. Nakauchi, H. Koldobskiy, M. A. Feinberg, A. P. Majeti, R. 2024-10-29 doi:10.1101/2024.10.26.620318 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2024.10.27.620507v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@116edb1org.highwire.dtl.DTLVardef@4f010corg.highwire.dtl.DTLVardef@cde718org.highwire.dtl.DTLVardef@1ff0841_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Label-free indicators of diabetic nephropathies. C_FIG ]]> Fung, A. A. Li, Z. Boote, C. Markov, P. P. Jain, S. A. Shi, L. 2024-10-29 doi:10.1101/2024.10.27.620507 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Identification of a large cohort of Enterobacter jumbo phages with broad host ranges across pathogenic Gammaproteobacteria ]]> https://biorxiv.org/content/10.1101/2024.10.29.620934v1?rss=1 Kanhirun, N. Blanc, A. Aindow, A. You, M. Antani, J. D. Ghatbale, P. Leonard, J. Garcia, A. G. Nghiem, K. Whiteson, K. Schooley, R. Turner, P. Pogliano, J. Guemes, A. G. C. Pride, D. T. 2024-10-29 doi:10.1101/2024.10.29.620934 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Mapping intratumoral myeloid-T cell interactomes at single-cell resolution reveals targets for overcoming checkpoint inhibitor resistance ]]> https://biorxiv.org/content/10.1101/2024.10.28.620093v1?rss=1 Bridges, K. Pizzurro, G. A. Baysoy, A. Baskaran, J. P. Xu, Z. Mathew, V. Tripple, V. LaPorte, M. Park, K. Damsky, W. Kluger, H. Fan, R. Kaech, S. M. Bosenberg, M. W. Miller-Jensen, K. 2024-10-31 doi:10.1101/2024.10.28.620093 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Small-molecule modulators of lipid raft stability and protein-raft partitioning ]]> https://biorxiv.org/content/10.1101/2024.10.28.620521v1?rss=1 Stefanski, K. M. Huang, H. Luu, D. D. Hutchison, J. M. Saksena, N. Fisch, A. J. Hasaka, T. P. Bauer, J. A. Kenworthy, A. K. Van Horn, W. D. Sanders, C. 2024-10-31 doi:10.1101/2024.10.28.620521 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance ]]> https://biorxiv.org/content/10.1101/2024.10.28.620709v1?rss=1 Salovska, B. Li, W. Bernhardt, O. M. Germain, P.-L. Gandhi, T. Reiter, L. Liu, Y. 2024-10-31 doi:10.1101/2024.10.28.620709 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ Systemic inhibition of de novo purine biosynthesis prevents weight gain and improves metabolic health by increasing thermogenesis and decreasing food intake ]]> https://biorxiv.org/content/10.1101/2024.10.28.620705v1?rss=1 Myers, J. W. Park, W. Y. Eddie, A. M. Shinde, A. B. Prasad, P. Murphy, A. C. Leonard, M. Z. Pinette, J. A. Rampy, J. J. Montufar, C. Shaikh, Z. Hickman, T. T. Reynolds, G. N. Winn, N. C. Lantier, L. Peck, S. H. Coate, K. C. Stein, R. W. Carrasco, N. Calipari, E. S. McReynolds, M. R. Zaganjor, E. 2024-11-01 doi:10.1101/2024.10.28.620705 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus ]]> https://biorxiv.org/content/10.1101/2024.10.31.621351v1?rss=1 Duffy, E. E. Traunmüller, L. Liu, H. Sanalidou, S. Assad, E. G. Sun, S. Pajarillo, N. S. Niu, N. Griffith, E. C. Greenberg, M. E. 2024-11-01 doi:10.1101/2024.10.31.621351 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Nanophysiology Approach Revealed Diversity in Calcium Microdomains in Zebrafish Retinal Bipolar Ribbon Synapses ]]> https://biorxiv.org/content/10.1101/2024.11.01.617078v1?rss=1 Rameshkumar, N. Shrestha, A. P. Boff, J. M. Hoon, M. Matveev, V. Zenisek, D. Vaithianathan, T. 2024-11-01 doi:10.1101/2024.11.01.617078 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ New Insights Into The Melanin Structure Of Lomentospora prolificans ]]> https://biorxiv.org/content/10.1101/2024.11.01.621558v1?rss=1 Liporagi Lopes, L. Chrissian, C. Kacirani, A. Camacho, E. Stark, R. E. Casadevall, A. 2024-11-01 doi:10.1101/2024.11.01.621558 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Structure and evolution of Photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis ]]> https://biorxiv.org/content/10.1101/2024.10.31.621444v1?rss=1 Jiang, H.-W. Gisriel, C. J. Cardona, T. Flesher, D. A. Brudvig, G. W. Ho, M.-Y. 2024-11-02 doi:10.1101/2024.10.31.621444 Cold Spring Harbor Laboratory Press 2024-11-02 <![CDATA[ BC-Design: A Biochemistry-Aware Framework for High-Precision Inverse Protein Folding ]]> https://biorxiv.org/content/10.1101/2024.10.28.620755v1?rss=1 Tang, X. Ye, X. Wu, F. Shao, Y. Fang, Y. Chen, S. Xu, D. Gerstein, M. 2024-11-03 doi:10.1101/2024.10.28.620755 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ The role of REM sleep in neural differentiation of memories in the hippocampus ]]> https://biorxiv.org/content/10.1101/2024.11.01.621588v1?rss=1 McDevitt, E. A. Kim, G. Turk-Browne, N. B. Norman, K. A. 2024-11-03 doi:10.1101/2024.11.01.621588 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Pyramidal cell types and 5-HT2A receptors are essential for psilocybin's lasting drug action ]]> https://biorxiv.org/content/10.1101/2024.11.02.621692v1?rss=1 Shao, L.-X. Liao, C. Davoudian, P. A. Savalia, N. K. Jiang, Q. Wojtasiewicz, C. Tan, D. Nothnagel, J. D. Liu, R.-J. Woodburn, S. C. Bilash, O. M. Kim, H. Che, A. Kwan, A. C. 2024-11-03 doi:10.1101/2024.11.02.621692 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Mechanical load conditions the spectrin network to `run-on' proteolysis and promotes early onset neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.11.04.621798v1?rss=1 Malaiwong, N. Dahse, A.-K. Lin, L. Das, R. Porta-de-la-Riva, M. Scholz, N. Krieg, M. 2024-11-04 doi:10.1101/2024.11.04.621798 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Aging drives a program of DNA methylation decay in plant organs ]]> https://biorxiv.org/content/10.1101/2024.11.04.621941v1?rss=1 Dai, D. Chen, K. Tao, J. Williams, B. P. 2024-11-05 doi:10.1101/2024.11.04.621941 Cold Spring Harbor Laboratory Press 2024-11-05 <![CDATA[ A high-quality genome of the mass-blooming desert plant Cistanthe longiscapa and its photosynthetic behavior related to drought and life history ]]> https://biorxiv.org/content/10.1101/2024.11.06.622337v1?rss=1 Chomentowska, A. Raimondeau, P. Wei, L. Jose, E. G. D. Dauerman, S. G. Davis, V. Z. Moreira-Munoz, A. Peralta, I. E. Edwards, E. J. 2024-11-07 doi:10.1101/2024.11.06.622337 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ Recurrent Connectivity Shapes Spatial Coding in Hippocampal CA3 Subregions ]]> https://biorxiv.org/content/10.1101/2024.11.07.622379v1?rss=1 Kong, E. Zabeh, E. Liao, Z. Mihaila, T. S. Peterka, D. S. Wilson, C. Santhirasegaran, C. Losonczy, A. Geiller, T. 2024-11-07 doi:10.1101/2024.11.07.622379 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ ENaC contributes to macrophage dysfunction in cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2024.11.06.622340v1?rss=1 Moran, J. Pugh, C. Brown, N. Thomas, A. Zhang, S. McCauley, E. Cephas, A. Shrestha, C. Partida-Sanchez, S. Bai, S. Bruscia, E. M. Kopp, B. 2024-11-08 doi:10.1101/2024.11.06.622340 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Deep Multimodal Representations and Classification of First-Episode Psychosis via Live Face Processing ]]> https://biorxiv.org/content/10.1101/2024.11.07.622469v1?rss=1 Singh, R. Zhang, Y. Bhaskar, D. Srihari, V. Tek, C. Zhang, X. Noah, J. A. Krishnaswamy, S. Hirsch, J. 2024-11-08 doi:10.1101/2024.11.07.622469 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ The development of aperiodic neural activity in the human brain ]]> https://biorxiv.org/content/10.1101/2024.11.08.622714v1?rss=1 Cross, Z. R. Gray, S. M. Dede, A. J. O. Rivera, Y. M. Yin, Q. Vahidi, P. Rau, E. M. B. Cyr, C. Holubecki, A. M. Asano, E. Lin, J. J. McManus, O. K. Sattar, S. Saez, I. Girgis, F. King-Stephens, D. Weber, P. B. Laxer, K. D. Schuele, S. U. Rosenow, J. M. Wu, J. Y. Kam, S. K. Raskin, J. S. Chang, E. F. Shaikhouni, A. Brunner, P. Roland, J. L. Braga, R. M. Knight, R. T. Ofen, N. Johnson, E. L. 2024-11-09 doi:10.1101/2024.11.08.622714 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus ]]> https://biorxiv.org/content/10.1101/2024.11.07.622523v1?rss=1 Enninful, A. Zhang, Z. Klymyshyn, D. Zong, H. Bai, Z. Farzad, N. Su, G. Baysoy, A. Nam, J. Yang, M. Lu, Y. Zhang, N. Braubach, O. Xu, M. L. Ma, Z. Fan, R. 2024-11-11 doi:10.1101/2024.11.07.622523 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Inferring Cell-Type-Specific Co-Expressed Genes from Single Cell Data ]]> https://biorxiv.org/content/10.1101/2024.11.08.622700v1?rss=1 Shan, X. Zhao, H. 2024-11-11 doi:10.1101/2024.11.08.622700 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Inhibition of serine and arginine-rich splicing factor 3 induces epidermal differentiation and decreases cutaneous squamous cell carcinoma risk ]]> https://biorxiv.org/content/10.1101/2024.11.07.622551v1?rss=1 Donohue, I. M. He, H. Nguyen, A. Hui, G. Muralidharan, J. Pike, W. C. Jackson, M. L. Ko, C. Srivastava, A. Lee, C. S. 2024-11-12 doi:10.1101/2024.11.07.622551 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Master regulators governing protein abundance across ten human cancer types ]]> https://biorxiv.org/content/10.1101/2024.11.11.619147v1?rss=1 Wang, Z. Wojciechowicz, M. Rosen, J. Elmas, A. Song, W.-M. Liu, Y. Huang, K.-l. 2024-11-12 doi:10.1101/2024.11.11.619147 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Surface remodeling and inversion of cell-matrix interactions underlies community recognition and dispersal in Vibrio cholerae biofilms ]]> https://biorxiv.org/content/10.1101/2024.11.11.623042v1?rss=1 Moreau, A. P. Nguyen, D. T. Hinbest, A. Zamora, A. Weerasekera, R. Matej, K. Zhou, X. Sanchez, S. Rodriguez-Brenes, I. A. Tai, J.-S. B. Nadell, C. D. Ng, W.-L. Gordon, V. D. Komarova, N. L. Olson, R. Li, Y. Yan, J. 2024-11-12 doi:10.1101/2024.11.11.623042 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Dynamic metabolic modeling of ATP allocation during viral infection ]]> https://biorxiv.org/content/10.1101/2024.11.12.623198v1?rss=1 Lu, A. Dukovski, I. Segre, D. 2024-11-13 doi:10.1101/2024.11.12.623198 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Boosting GPT Models for Genomics Analysis: Generating Trusted Genetic Variant Annotations and Interpretations through RAG and fine-tuning ]]> https://biorxiv.org/content/10.1101/2024.11.12.623275v1?rss=1 Lu, S. Cosgun, E. 2024-11-15 doi:10.1101/2024.11.12.623275 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides ]]> https://biorxiv.org/content/10.1101/2024.11.13.623061v1?rss=1 Kabonick, S. G. Verma, K. Modesto, J. L. Pearce, V. H. Winokur, K. M. Groisman, E. A. Townsend, G. E. 2024-11-15 doi:10.1101/2024.11.13.623061 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ High fitness paths can connect proteins with low sequence overlap ]]> https://biorxiv.org/content/10.1101/2024.11.13.623265v1?rss=1 Kantroo, P. Wagner, G. P. Machta, B. B. 2024-11-15 doi:10.1101/2024.11.13.623265 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Parameters for sensing lipid loosening at the inner nuclear membrane by amphipathic helices ]]> https://biorxiv.org/content/10.1101/2024.11.14.623600v1?rss=1 Lee, S. Le Roux, A.-L. Mors, M. Vanni, S. Roca-Cusachs, P. Bahmanyar, S. 2024-11-15 doi:10.1101/2024.11.14.623600 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Individual brain activity patterns during task are predicted by distinct resting-state networks that may reflect local neurobiological features ]]> https://biorxiv.org/content/10.1101/2024.11.13.621472v1?rss=1 Scholz, R. Benn, R. A. Shevchenko, V. Klatzmann, U. Wei, W. Alberti, F. Chiou, R. Zhang, X.-H. Leech, R. Smallwood, J. Margulies, D. S. 2024-11-17 doi:10.1101/2024.11.13.621472 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion ]]> https://biorxiv.org/content/10.1101/2024.11.16.623947v1?rss=1 Tegtmeyer, M. Liyanage, D. Han, Y. Hebert, K. Pei, R. Way, G. P. Ryder, P. V. Hawes, D. Tromans-Coia, C. Cimini, B. A. Carpenter, A. E. Singh, S. Nehme, R. 2024-11-17 doi:10.1101/2024.11.16.623947 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Chromosome engineering to restore euploidy in cells harboring a complex rearrangement of chromosome 8 ]]> https://biorxiv.org/content/10.1101/2024.11.17.624023v1?rss=1 Lee, S. N. Qiao, L. Thompson, S. L. Hagenson, R. A. Davoli, T. Sheltzer, J. M. 2024-11-17 doi:10.1101/2024.11.17.624023 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT ]]> https://biorxiv.org/content/10.1101/2024.11.18.624106v1?rss=1 Baysoy, A. Tian, X. Zhang, F. Renauer, P. Bai, Z. Shi, H. Li, H. Tao, B. Yang, M. Enninful, A. Gao, F. Wang, G. Zhang, W. Tran, T. Patterson, N. H. Bao, S. Dong, C. Xin, S. Zhong, M. Rankin, S. Guy, C. Wang, Y. Connelly, J. P. Pruett-Miller, S. M. Chi, H. Chen, S. Fan, R. 2024-11-19 doi:10.1101/2024.11.18.624106 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Mood impacts confidence through biased learning of reward likelihood ]]> https://biorxiv.org/content/10.1101/2024.11.18.624111v1?rss=1 Mason, L. Woelk, S. Eldar, E. Rutledge, R. 2024-11-19 doi:10.1101/2024.11.18.624111 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Extracellular domains of CATSPERε are essential for CatSper assembly during development and activity modulation in sperm capacitation ]]> https://biorxiv.org/content/10.1101/2024.11.18.624146v1?rss=1 Hwang, J. Y. Wang, H. Clouser, G. Oh, J.-N. Finnegan, S. F. Skakkebaek, N. E. Chung, J.-J. 2024-11-19 doi:10.1101/2024.11.18.624146 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Endothelial Rho kinase controls blood vessel integrity and angiogenesis ]]> https://biorxiv.org/content/10.1101/2024.11.19.624343v1?rss=1 Lange, M. Francis, C. Furtado, J. Kim, Y.-B. Liao, J. K. Eichmann, A. 2024-11-19 doi:10.1101/2024.11.19.624343 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ A highly conserved sRNA downregulates multiple genes, including a sigma54 transcriptional activator, in the virulence mode of Bordetella pertussis ]]> https://biorxiv.org/content/10.1101/2024.11.19.624354v1?rss=1 Sim, M. Nguyen, J. Skopova, K. Yoo, K. Tai, C.-H. Knipling, L. Chen, Q. Kim, D. Nolan, S. Elaksher, R. Majdalani, N. Lorenzi, H. Stibitz, S. Moon, K. Hinton, D. M. 2024-11-19 doi:10.1101/2024.11.19.624354 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states ]]> https://biorxiv.org/content/10.1101/2024.11.18.624166v1?rss=1 Liu, T. De Brouwer, E. Kuo, T. Diamant, N. Missarova, A. Wang, H. Hao, M. Bravo, H. C. Scalia, G. Regev, A. Heimberg, G. 2024-11-20 doi:10.1101/2024.11.18.624166 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Recurrent hyper-motif circuits in developmental programs ]]> https://biorxiv.org/content/10.1101/2024.11.20.624466v1?rss=1 Adler, M. Medzhitov, R. 2024-11-20 doi:10.1101/2024.11.20.624466 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Beyond Integration: SuperGLUE Facilitates Explainable Training Framework for Multi-modal Data Analysis ]]> https://biorxiv.org/content/10.1101/2024.11.19.624293v1?rss=1 Liu, T. Zhao, J. Zhao, H. 2024-11-21 doi:10.1101/2024.11.19.624293 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ RobustCell: A Model Attack-Defense Framework for Robust Transcriptomic Data Analysis ]]> https://biorxiv.org/content/10.1101/2024.11.19.624294v1?rss=1 Liu, T. Luo, X. Xiao, Y. Zhao, H. 2024-11-21 doi:10.1101/2024.11.19.624294 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Genetic Characterization of the Cell Types of in Developing Feathers, and the Evolution of Feather Complexity ]]> https://biorxiv.org/content/10.1101/2024.11.21.624532v1?rss=1 Limber, C. Wagner, G. Prum, R. O. 2024-11-21 doi:10.1101/2024.11.21.624532 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Improving antibody-mediated protection against HSV infection by eliminating interactions with the viral Fc receptor gE/gI ]]> https://biorxiv.org/content/10.1101/2024.11.20.624598v1?rss=1 Slein, M. D. Backes, I. M. Kelkar, N. S. Garland, C. R. Khanwalkar, U. S. Sholukh, A. M. Johnston, C. M. Leib, D. A. Ackerman, M. E. 2024-11-22 doi:10.1101/2024.11.20.624598 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ The Impact of Acute Endurance Exercise on Alternative Splicing in Skeletal Muscle ]]> https://biorxiv.org/content/10.1101/2024.11.21.624690v1?rss=1 Ahn, A. Kim, J. J. Slusher, A. L. Ying, J. Y. Zhang, E. Y. Ludlow, A. T. 2024-11-22 doi:10.1101/2024.11.21.624690 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Buprenorphine Induces Human Fetal Membrane Sterile Inflammation ]]> https://biorxiv.org/content/10.1101/2024.11.22.624850v1?rss=1 Lynn, T. Kelleher, M. E. Georges, H. M. McCauley, E. M. Logan, R. Yonkers, K. A. Abrahams, V. M. 2024-11-22 doi:10.1101/2024.11.22.624850 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Shroom3-Rock interaction and profibrotic function: Resolving mechanism of an intronic CKD risk allele. ]]> https://biorxiv.org/content/10.1101/2024.11.22.624409v1?rss=1 Reghuvaran, A. C. Kumar, A. Lin, Q. Rajeevan, N. Sun, Z. Shi, H. Barsotti, G. Tanvir, E. M. Pell, J. F. Perincheri, S. Wei, C. Planoutene, M. Eichmann, A. Mas, V. Zhang, W. Das, B. Cantley, L. G. Xu, L. He, J. C. Menon, M. 2024-11-23 doi:10.1101/2024.11.22.624409 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Receptor polarization through localized activity and global sensitization ]]> https://biorxiv.org/content/10.1101/2024.11.22.624862v1?rss=1 Goetz, A. Dixit, P. D. 2024-11-23 doi:10.1101/2024.11.22.624862 Cold Spring Harbor Laboratory Press 2024-11-23 <![CDATA[ Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping ]]> https://biorxiv.org/content/10.1101/2024.11.22.624784v1?rss=1 Wang, K. Nie, Y. Maguire, C. Syphurs, C. Sheen, H. Karoly, M. Lapp, L. Gygi, J. P. Jayavelu, N. D. Patel, R. K. Hoch, A. IMPACC Network, Corry, D. Kheradmand, F. McComsey, G. A. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Messer, W. B. David, M. M. Nadeau, K. C. Kraft, M. Bime, C. Schaenman, J. Erle, D. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Hafler, D. A. Shaw, A. C. Rahman, A. Hough, C. L. Geng, L. N. Ozonoff, A. Haddad, E. K. Reed, E. F. Bakel, H. v. Kim-Schulze, S. H. Krammer, F. Wilson, M. Eckalbar, W. Bosinger, 2024-11-25 doi:10.1101/2024.11.22.624784 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Dysregulated airway epithelial antiviral immunity in Down Syndrome impairs type III IFN response and amplifies airway inflammation during RSV infection. ]]> https://biorxiv.org/content/10.1101/2024.11.22.624921v1?rss=1 Chorvinsky, E. Bhattacharya, S. Bera, B. S. Welham, A. L. Hussain Ismat, K. Lawlor, C. M. Preciado, D. Gomez Villalobos, J. Morizono, H. Pillai, D. Gutierrez, M. J. Jaiswal, J. Nino, G. 2024-11-25 doi:10.1101/2024.11.22.624921 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Rigosertib reverses hypertrophic cardiomyopathy in RAF1-associated Noonan syndrome ]]> https://biorxiv.org/content/10.1101/2024.11.25.623865v1?rss=1 Legler, L. Xu, B. Keshavarz Shirazi, T. Kurzum, S. Marchetti, K. Kessinger, C. W. Vredenburg, I. Sun, Y. Dinenno, F. A. Bohler, D. Aleman, A. Rodriguez, N. A. Ng, S. Gao, S. Wang, A. Suarez-Farinas, M. Lin, H.-M. Das, T. Ocorr, K. Cagan, R. L. Gelb, B. D. Kontaridis, M. I. 2024-11-25 doi:10.1101/2024.11.25.623865 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Embryonically generated interneurons (EGINs) exhibit a distinctive developmental program and lamination in the olfactory bulb ]]> https://biorxiv.org/content/10.1101/2024.11.25.625264v1?rss=1 Spence, N. J. Martin-Lopez, E. Han, K. Lefevre, M. Lange, N. W. Brennan, B. GREER, C. A. 2024-11-25 doi:10.1101/2024.11.25.625264 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Ecological associations of the coastal marsh periwinkle snail Littoraria irrorata: field and laboratory evidence of vegetation habitat preferences ]]> https://biorxiv.org/content/10.1101/2024.11.24.625093v1?rss=1 Klinges, D. H. Martin, C. Roberts, B. 2024-11-26 doi:10.1101/2024.11.24.625093 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ An abundance of aliC and aliD genes were identified in saliva using a novel multiplex qPCR to characterize group II non-encapsulated pneumococci with improved specificity ]]> https://biorxiv.org/content/10.1101/2024.11.26.624535v1?rss=1 Laxton, C. S. Toekiran, F. L. Lin, T.-Y. Lomeda, B. D. Hislop, M. Keller, L. Allicock, O. M. Wyllie, A. L. 2024-11-27 doi:10.1101/2024.11.26.624535 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Coral restoration is only practical when local human pressure levels are low ]]> https://biorxiv.org/content/10.1101/2024.11.26.622858v1?rss=1 Brookson, C. B. Greiner, A. 2024-11-28 doi:10.1101/2024.11.26.622858 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ PIEZO1 overexpression in hereditary hemorrhagic telangiectasia arteriovenous malformations ]]> https://biorxiv.org/content/10.1101/2024.11.27.625696v1?rss=1 Park, H. Lee, S. Furtado, J. Robinson, M. Schwartz, M. Young, L. H. Eichmann, A. 2024-11-28 doi:10.1101/2024.11.27.625696 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Circuit mechanisms underlying sexually dimorphic outcomes of early life stress ]]> https://biorxiv.org/content/10.1101/2024.11.27.625736v1?rss=1 Jiang, C. Ruiz-Sanchez, I. Mei, C. Pittenger, C. 2024-11-28 doi:10.1101/2024.11.27.625736 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ A multi-level formalism to capture the characteristics of hybrid phenotypes in Epithelial-Mesenchymal Plasticity ]]> https://biorxiv.org/content/10.1101/2024.11.26.625479v1?rss=1 Hari, K. Tripathi, S. Anand, V. Jolly, M. K. Levine, H. 2024-12-02 doi:10.1101/2024.11.26.625479 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Tobacco smoke alters the landscape of mutation, selection, and epistasis in lung adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.11.27.625765v1?rss=1 Dasari, K. Alfaro-Murillo, J. A. Townsend, J. P. 2024-12-02 doi:10.1101/2024.11.27.625765 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Early exposure to Western diet exacerbates visual outcomes in female mice. ]]> https://biorxiv.org/content/10.1101/2024.11.27.625688v1?rss=1 Meseguer, D. Furtado, J. Zapadka, T. Rodriguez, A. Na, D. Grajales, J. Demb, J. Eichmann, A. E. Schneeberger, M. 2024-12-03 doi:10.1101/2024.11.27.625688 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Cell-sheet shape transformation by internally-driven, oriented forces ]]> https://biorxiv.org/content/10.1101/2024.11.28.625908v1?rss=1 Huang, J. Chen, J. Luo, Y. 2024-12-03 doi:10.1101/2024.11.28.625908 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction ]]> https://biorxiv.org/content/10.1101/2024.11.29.626072v1?rss=1 Nasser, J. Nam, K.-M. Gunawardena, J. 2024-12-03 doi:10.1101/2024.11.29.626072 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Beta cells are essential drivers of pancreatic ductal adenocarcinoma development ]]> https://biorxiv.org/content/10.1101/2024.11.29.626079v1?rss=1 Garcia, C. C. Venkat, A. McQuaid, D. C. Agabiti, S. S. Tong, A. Cardone, R. L. Starble, R. Sogunro, A. Jacox, J. B. Ruiz, C. F. Kibbey, R. Krishnaswamy, S. Muzumdar, M. D. 2024-12-03 doi:10.1101/2024.11.29.626079 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ OST Catalytic Subunit Redundancy Enables Therapeutic Targeting of N-Glycosylation ]]> https://biorxiv.org/content/10.1101/2024.12.03.626593v1?rss=1 Baro, M. Lee, H. Kelley, V. Lou, R. Phoomak, C. Politi, K. Zeiss, C. J. Van Zandt, M. Contessa, J. N. 2024-12-05 doi:10.1101/2024.12.03.626593 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ CHD4 Interacts With TBX5 to Maintain the Gene Regulatory Network of Postnatal Atrial Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2024.12.04.626894v1?rss=1 Sweat, M. E. Shi, W. Keating, E. M. Ponek, A. Li, J. Ma, Q. Park, C. Trembley, M. A. Wang, Y. Bezzerides, V. J. Conlon, F. J. Pu, W. T. 2024-12-05 doi:10.1101/2024.12.04.626894 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ E-box independent chromatin recruitment turns MYOD into a transcriptional repressor ]]> https://biorxiv.org/content/10.1101/2024.12.05.627024v1?rss=1 Nicoletti, C. Massenet, J. Pintado-Urbanc, A. P. Connor, L. J. Nicolau, M. Sundar, S. Xu, M. Schmitt, A. Zhang, W. Fang, Z. Chan, T. C. I. Tapscott, S. J. Cheung, T. H. Simon, M. D. Caputo, L. Puri, P. L. 2024-12-05 doi:10.1101/2024.12.05.627024 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ The capsule and genetic background, rather than specific loci, strongly influence pneumococcal growth kinetics ]]> https://biorxiv.org/content/10.1101/2024.12.05.627025v1?rss=1 Chaguza, C. Arends, D. W. Lo, S. W. Putri, I. H. York, A. Lees, J. A. Wyllie, A. L. Weinberger, D. M. Bentley, S. D. de Jonge, M. I. Cremers, A. J. H. 2024-12-05 doi:10.1101/2024.12.05.627025 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ GM-CSF engages multiple signaling pathways to enhance pro-inflammatory cytokine responses in human monocytes during Legionella infection ]]> https://biorxiv.org/content/10.1101/2024.12.05.627084v1?rss=1 Vazquez Marrero, V. R. Dresler, M. Haggadone, M. D. Lu, A. Shin, S. 2024-12-10 doi:10.1101/2024.12.05.627084 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Chemical perturbations impacting histone acetylation governcolorectal cancer differentiation ]]> https://biorxiv.org/content/10.1101/2024.12.06.626451v1?rss=1 Likasitwatanakul, P. Li, Z. Doan, P. Spisak, S. Akhouri, K. R. Liu, Q. Liow, P. Lee, S. E. Chen, D. Bala, P. Sahgal, P. Aitymbayev, D. Thalappillil, J. S. Papanastasiou, M. Hawkins, W. Carr, S. A. Park, H. Cleary, J. M. Qi, J. Sethi, N. S. 2024-12-10 doi:10.1101/2024.12.06.626451 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Scaling ecological niches from individuals to populations and beyond ]]> https://biorxiv.org/content/10.1101/2024.12.06.627157v1?rss=1 Lu, M. Yanco, S. Carlson, B. Winner, K. Cohen, J. Ellis Soto, D. Sharma, S. Rogers, W. Jetz, W. 2024-12-11 doi:10.1101/2024.12.06.627157 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Single-nucleus RNA sequencing of human periventricular white matter in vascular dementia ]]> https://biorxiv.org/content/10.1101/2024.12.06.627202v1?rss=1 Diaz-Perez, S. DeLong, J. H. Rivier, C. A. Lee, C.-Y. Askenase, M. H. Zhu, B. Zhang, L. Brennand, K. J. Martins, A. J. Sansing, L. H. 2024-12-11 doi:10.1101/2024.12.06.627202 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ GEMS: A Generalizable GNN Framework For Protein-Ligand Binding Affinity Prediction Through Robust Data Filtering and Language Model Integration ]]> https://biorxiv.org/content/10.1101/2024.12.09.627482v1?rss=1 Graber, D. Stockinger, P. Meyer, F. Mishra, S. Horn, C. Buller, R. M. U. 2024-12-11 doi:10.1101/2024.12.09.627482 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability ]]> https://biorxiv.org/content/10.1101/2024.12.09.627617v1?rss=1 Yuan, W. Huang, Y.-C. LeBlanc, C. Poulet, A. Valsakumar, D. van Wolfswinkel, J. C. Voigt, P. Jacob, Y. 2024-12-11 doi:10.1101/2024.12.09.627617 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ PathOmCLIP: Connecting tumor histology with spatial gene expression via locally enhanced contrastive learning of Pathology and Single-cell foundation model ]]> https://biorxiv.org/content/10.1101/2024.12.10.627865v1?rss=1 Lee, Y. Liu, X. Hao, M. Liu, T. Regev, A. 2024-12-11 doi:10.1101/2024.12.10.627865 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Variant Set Distillation ]]> https://biorxiv.org/content/10.1101/2024.12.06.627210v1?rss=1 Christ, R. Kang, C. J. Aslett, L. Lam, D. Savitski, M. F. Stitziel, N. O. Steinsaltz, D. Hall, I. 2024-12-12 doi:10.1101/2024.12.06.627210 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Alteration of skin fibroblast steady state contributes to healing outcomes ]]> https://biorxiv.org/content/10.1101/2024.12.06.627278v1?rss=1 Huang, Y. Wang, N. Xing, H. Tian, J. Zhang, D. Gao, D. Hsia, H. C.-h. Lu, J. Raredon, M. S. B. Kyriakides, T. 2024-12-12 doi:10.1101/2024.12.06.627278 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Calmodulin binding is required for calcium mediated TRPA1 desensitization ]]> https://biorxiv.org/content/10.1101/2024.12.11.627969v1?rss=1 Sanders, J. H. Taiwo, K. M. Adekanye, G. A. Bali, A. P. Zhang, Y. Paulsen, C. 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Su, X. 2024-12-18 doi:10.1101/2024.12.17.628879 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Pyruvate Kinase Directly Generates GTP in Glycolysis, Supporting Growth and Contributing to Guanosine Toxicity ]]> https://biorxiv.org/content/10.1101/2024.12.17.629031v1?rss=1 She, F. Liu, K. Anderson, B. Fung, K. C. Amador-Noguez, D. Wang, J. D. 2024-12-18 doi:10.1101/2024.12.17.629031 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury ]]> https://biorxiv.org/content/10.1101/2024.12.16.628787v1?rss=1 Yuan, Y. Sharma, L. Tang, W. Yoon, Y. kirk, S. Raredon, M. S. B. Ahangari, F. Khoury, J. Qian, H. Luan, Y. Yuan, Q. Chen, L. Ke, Y. Birukov, K. Simons, M. Wu, D. Niklason, L. E. Kaminski, N. 2024-12-20 doi:10.1101/2024.12.16.628787 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ BACH2-driven tissue resident memory programs promote HIV-1 persistence ]]> https://biorxiv.org/content/10.1101/2024.12.16.628794v1?rss=1 Wei, Y. Ma, H. K. Wang, M. E. Papasavvas, E. Konnikova, L. Tebas, P. Morgenstern, R. Montaner, L. J. Ho, Y.-C. 2024-12-20 doi:10.1101/2024.12.16.628794 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ CSF1R-CAR T cells induce CSF1R signalling and promote cancer cell growth ]]> https://biorxiv.org/content/10.1101/2024.12.17.629028v1?rss=1 Callahan, A. Zhang, X. Wang, A. Mojumdar, A. Zeng, L. Su, X. Salomon, A. R. 2024-12-20 doi:10.1101/2024.12.17.629028 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures ]]> https://biorxiv.org/content/10.1101/2024.12.18.629229v1?rss=1 Li, H. Pham, M. C. Teng, J. O'Connor, K. C. Noviello, C. M. Hibbs, R. E. 2024-12-20 doi:10.1101/2024.12.18.629229 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Visualizing Functional Network Connectivity Differences Using an Explainable Machine-learning Method ]]> https://biorxiv.org/content/10.1101/2024.12.18.629283v1?rss=1 Sendi, M. S. E. Itkyal, V. S. Edwards-Swart, S. J. Chun, J. Y. Mathalon, D. H. Ford, J. M. Preda, A. van Erp, T. G. M. Pearlson, G. D. Turner, J. A. Calhoun, V. D. 2024-12-20 doi:10.1101/2024.12.18.629283 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Ongoing loss of viable neurons for weeks after mild perinatal hypoxia-ischemia ]]> https://biorxiv.org/content/10.1101/2024.12.19.629457v1?rss=1 McNally, M. Lau, L. A. Granak, S. Hike, D. Liu, X. Yu, X. Donahue, R. Chibnik, L. Ortiz, J. Che, A. Northington, F. Staley, K. J. 2024-12-20 doi:10.1101/2024.12.19.629457 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment ]]> https://biorxiv.org/content/10.1101/2024.12.19.629497v1?rss=1 Kyro, G. W. Smaldone, A. M. Shee, Y. Xu, C. Batista, V. S. 2024-12-20 doi:10.1101/2024.12.19.629497 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens ]]> https://biorxiv.org/content/10.1101/2024.12.19.629550v1?rss=1 Kalinich, C. C. Gonzalez, F. L. Omaston, A. Breban, M. I. Distefano, I. Leon, C. Sheen, P. Zimic, M. Coronel, J. Tan, G. Crudu, V. Ciobanu, N. Codreanu, A. Solano, W. Raez, J. Allicock, O. M. Chaguza, C. Wyllie, A. L. Brandt, M. Weinberger, D. M. Sobkowiak, B. Cohen, T. Grandjean, L. Grubaugh, N. D. Redmond, S. N. 2024-12-20 doi:10.1101/2024.12.19.629550 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Order matters: Autocorrelation of temperature dictates extinction risk in populations with nonlinear thermal performance ]]> https://biorxiv.org/content/10.1101/2024.12.19.629491v1?rss=1 Robey, A. J. Vasseur, D. A. 2024-12-22 doi:10.1101/2024.12.19.629491 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk ]]> https://biorxiv.org/content/10.1101/2024.12.24.630179v1?rss=1 Gonzalez, F. L. Ranaivoson, H. C. Andrianiaina, A. Andry, S. Raharinosy, V. Randriambolamanantsoa, T. H. Lacoste, V. Dussart, P. Heraud, J.-M. Brook, C. E. 2024-12-24 doi:10.1101/2024.12.24.630179 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Single-Cell Temporal Atlas of Myeloid Cells in the Live Haemorrhagic Brain ]]> https://biorxiv.org/content/10.1101/2024.12.24.630187v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@ff4fa0org.highwire.dtl.DTLVardef@1c4cc5borg.highwire.dtl.DTLVardef@1449761org.highwire.dtl.DTLVardef@2e7ea6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kawamura, Y. Johnson, C. DeLong, J. de Lima Camillo, L. P. Takahashi, M. Beatty, H. E. Herbert, R. Cord, B. J. Matouk, C. Askenase, M. Sansing, L. H. 2024-12-24 doi:10.1101/2024.12.24.630187 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing ]]> https://biorxiv.org/content/10.1101/2024.12.24.630263v1?rss=1 Dehghannasiri, R. Kokot, M. Starr, A. L. Maziarz, J. Gordon, T. Tan, S. Y. Wang, P. L. Voskoboynik, A. Musser, J. M. Deorowicz, S. Salzman, J. 2024-12-24 doi:10.1101/2024.12.24.630263 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Visual circuitry for distance estimation in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.12.25.630346v1?rss=1 Shomar, J. Wu, E. Au, B. Maier, K. Zhou, B. Matos, N. Sager, G. C. Santana, G. Tanaka, R. Gish, C. Clark, D. A. 2024-12-26 doi:10.1101/2024.12.25.630346 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation ]]> https://biorxiv.org/content/10.1101/2024.12.26.629296v1?rss=1 Moore, J. E. Pratt, H. E. Fan, K. Phalke, N. Fisher, J. Elhajjajy, S. I. Andrews, G. Gao, M. Shedd, N. Fu, Y. Lacadie, M. C. Meza, J. Ganna, M. Choudhury, E. Swofford, R. Farrell, N. P. Pampari, A. Ramalingam, V. Reese, F. Borsari, B. Yu, X. Wattenberg, E. S. Ruiz-Romero, M. Razavi-Mohseni, M. Xu, J. Galeev, T. Beer, M. A. Guigo, R. Gerstein, M. Engreitz, J. M. Ljungman, M. Reddy, T. E. Snyder, M. Epstein, C. B. Gaskell, E. Bernstein, B. E. Dickel, D. E. Visel, A. Pennacchio, L. A. Mortazavi, A. Kundaje, A. Weng, Z. 2024-12-26 doi:10.1101/2024.12.26.629296 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ A nucleotide code governs Lis1's ability to relieve dynein autoinhibition ]]> https://biorxiv.org/content/10.1101/2024.12.30.630615v1?rss=1 Geohring, I. C. Chai, P. Iyer, B. R. Ton, W. D. Yang, J. Ide, A. H. George, S. C. Bagri, J. S. Baird, S. V. Zhang, K. Markus, S. M. 2024-12-30 doi:10.1101/2024.12.30.630615 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Nde1 Promotes Lis1 Binding to Full-Length Autoinhibited Human Dynein-1 ]]> https://biorxiv.org/content/10.1101/2024.12.30.630764v1?rss=1 Yang, J. Zhao, Y. Chai, P. Yildiz, A. Zhang, K. 2024-12-30 doi:10.1101/2024.12.30.630764 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Molecular basis for the assembly of the dynein transport machinery on microtubules ]]> https://biorxiv.org/content/10.1101/2024.12.30.630772v1?rss=1 Rao, Q. Chai, P. Zhang, K. 2024-12-30 doi:10.1101/2024.12.30.630772 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Brief disruption of the microbiome has age-dependent effects on morphine reward and gene expression in the medial prefrontal cortex of adolescent and adult mice ]]> https://biorxiv.org/content/10.1101/2025.01.02.631117v1?rss=1 Hofford, R. S. Sens, J. P. Shipman, A. L. Kimble, V. M. Coric, C. Meckel, K. R. Kiraly, D. 2025-01-02 doi:10.1101/2025.01.02.631117 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Divergent endothelial mechanisms drive arteriovenous malformations in Alk1 and Smad4 loss-of-function ]]> https://biorxiv.org/content/10.1101/2025.01.03.631070v1?rss=1 Oppenheim, O. Giese, W. Park, H. Baumann, E. Ivanov, A. Beule, D. Eichmann, A. Gerhardt, H. 2025-01-03 doi:10.1101/2025.01.03.631070 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Three-dimensional quantitative characterization of Coxiella burnetii infection using focused ion beam-scanning electron microscopy ]]> https://biorxiv.org/content/10.1101/2025.01.03.631259v1?rss=1 Botting, J. Steiner, S. Graham, M. Liu, X. Roy, C. R. Liu, J. 2025-01-04 doi:10.1101/2025.01.03.631259 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Transcriptional Integration of Meiotic Prophase I Progression and Early Oocyte Differentiation ]]> https://biorxiv.org/content/10.1101/2025.01.06.631470v1?rss=1 Abt, K. M. Bartholomew, M. A. Nixon, A. N. Richman, H. E. Gura, M. A. Seymour, K. A. Freiman, R. N. 2025-01-06 doi:10.1101/2025.01.06.631470 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Optogenetic control of Protein Kinase C-epsilon activity reveals its intrinsic signaling properties with spatiotemporal resolution ]]> https://biorxiv.org/content/10.1101/2025.01.06.631444v1?rss=1 Ong, Q. Lim, C. J. Y. Liao, Y. Ng, J. T.-Y. Lim, L. T. R. Koh, S. X. Y. Chan, S. E. Lee, P. Y. Y. Lim, H. Ye, C. R. Wang, L. C. Ler, S. G. Sobota, R. M. Tan, Y. S. I. Shulman, G. Yang, X. Han, W. 2025-01-08 doi:10.1101/2025.01.06.631444 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Coordination of distinct sources of excitatory inputs enhances motion selectivity in the mouse visual thalamus ]]> https://biorxiv.org/content/10.1101/2025.01.08.631826v1?rss=1 Fei, Y. Luh, M. Ontiri, A. Ghauri, D. Hu, W. Liang, L. 2025-01-09 doi:10.1101/2025.01.08.631826 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ Deficiency of Shank3 in the Nucleus Accumbens Reveals a Loss of Social-Specific Motivation ]]> https://biorxiv.org/content/10.1101/2025.01.08.631742v1?rss=1 Folkes, O. M. Donahue, M. Wang, S. E. Oo, N. X. Wang, X. Negron-Moreno, P. N. Jiang, Y.-H. 2025-01-10 doi:10.1101/2025.01.08.631742 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci ]]> https://biorxiv.org/content/10.1101/2025.01.08.631787v1?rss=1 Mimoso, C. A. Vlaming, H. de Wagenaar, N. P. Adelman, K. 2025-01-10 doi:10.1101/2025.01.08.631787 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ High resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory ]]> https://biorxiv.org/content/10.1101/2025.01.10.632429v1?rss=1 Chavali, S. S. Carman, P. J. Shuman, H. Ostap, E. M. Sindelar, C. V. 2025-01-12 doi:10.1101/2025.01.10.632429 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Giant KASH proteins and ribosomes synergistically establish cytoplasmic biophysical properties in vivo ]]> https://biorxiv.org/content/10.1101/2025.01.10.632479v1?rss=1 Ding, X. Hao, H. Elnatan, D. Alinaya, P. N. Kalra, S. Kaur, A. Kumari, S. J. Holt, L. J. Luxton, G. G. Starr, D. A. 2025-01-12 doi:10.1101/2025.01.10.632479 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ A temporal coordination between Nodal and Wnt signalling governs the emergence of the mammalian body plan ]]> https://biorxiv.org/content/10.1101/2025.01.11.632562v1?rss=1 Dias, A. Pascual-Mas, P. Torregrosa-Cortes, G. McNamara, H. M. Wehmeyer, A. E. Arnold, S. J. Martinez Arias, A. 2025-01-12 doi:10.1101/2025.01.11.632562 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Golgi-associated nuclear import receptor importin-7 targets HPV from the Golgi to the nucleus to promote infection ]]> https://biorxiv.org/content/10.1101/2025.01.08.631933v1?rss=1 Woo, T.-T. Takeo, Y. Harwood, M. C. Houck, E. T. DiMaio, D. Tsai, B. 2025-01-13 doi:10.1101/2025.01.08.631933 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Fibroblast contractility drives network reorganization and epithelial proliferation in intestinal polyposis ]]> https://biorxiv.org/content/10.1101/2025.01.08.632004v1?rss=1 Li, M.-L. Wang, Y. Figetakis, M. Gonzalez, D. Jin, J. McDonald, E. S. Ameen, N. A. Sumigray, K. 2025-01-13 doi:10.1101/2025.01.08.632004 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Rapid evolution of Wolbachia in cherry fruit flies ]]> https://biorxiv.org/content/10.1101/2025.01.13.632697v1?rss=1 Bruzzese, D. J. Schuler, H. Yee, W. L. Holzschuh, A. Feder, J. L. 2025-01-13 doi:10.1101/2025.01.13.632697 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Genetic background sets the trajectory of cancer evolution ]]> https://biorxiv.org/content/10.1101/2025.01.13.632787v1?rss=1 Aitken, S. J. Connor, F. Feig, C. Rayner, T. F. Lukk, M. Luft, J. Aitken, S. Arnedo-Pac, C. Hayes, J. F. Nicholson, M. D. Sundaram, V. Verburg, J. C. Connelly, J. Anderson, C. J. Behm, M. Campbell, S. Daunesse, M. Ewing, A. Kaiser, V. B. Kentepozidou, E. Pich, O. Redmond, A. M. Santoyo-Lopez, J. Sentis, I. Talmane, L. Liver Cancer Evolution Consortium, Flicek, P. Lopez-Bigas, N. Semple, C. A. Taylor, M. S. Odom, D. T. 2025-01-15 doi:10.1101/2025.01.13.632787 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ spEMO: Exploring the Capacity of Foundation Models for Analyzing Spatial Multi-Omic Data ]]> https://biorxiv.org/content/10.1101/2025.01.13.632818v1?rss=1 Liu, T. Huang, T. Ying, R. Zhao, H. 2025-01-17 doi:10.1101/2025.01.13.632818 Cold Spring Harbor Laboratory Press 2025-01-17 <![CDATA[ Identification of novel Kv1.3 channel-interacting proteins using proximity labelling in T-cells ]]> https://biorxiv.org/content/10.1101/2025.01.16.633279v1?rss=1 Kour, D. Bowen, C. A. Srivastava, U. Nguyen, H. M. Kumari, R. Kumar, P. Brandelli, A. D. Bitarafan, S. Tobin, B. R. Wood, L. B. Seyfried, N. Wulff, H. Rangaraju, S. 2025-01-18 doi:10.1101/2025.01.16.633279 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ Genetically encoded mechano-sensors with versatile readouts and compact size ]]> https://biorxiv.org/content/10.1101/2025.01.16.633409v1?rss=1 Ren, Y. Yang, J. Saito, T. Glomb, O. Mousavi, S. I. Naughton, B. de Fontnouvelle, C. Fujita, B. Schlieker, C. Yogev, S. Zhang, Y. Berro, J. 2025-01-18 doi:10.1101/2025.01.16.633409 Cold Spring Harbor Laboratory Press 2025-01-18 <![CDATA[ Transfusion of allogenic murine HOD red blood cells preferentially induces low-affinity, short-lived IgG antibodies that are germinal center independent ]]> https://biorxiv.org/content/10.1101/2025.01.16.633377v1?rss=1 Medved, J. Arneja, A. Moscovich, T. C. Shah, N. Muppidi, R. J. Burnett, E. D. Boscia, A. R. Hester, B. N. Maram, J. Raghavan, R. Ireland, S. A. Berberian, M. B. Stern-Green, E. A. Kodali, A. S. Niebuhr, C. S. Salazar, J. E. Santhanakrishnan, M. Hudson, K. E. Zimring, J. C. Hendrickson, J. E. Luckey, C. J. 2025-01-21 doi:10.1101/2025.01.16.633377 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ The Binary Cellular Biology of Human Growth I Quantifying the Creation and Growth of the Body and its Parts ]]> https://biorxiv.org/content/10.1101/2025.01.22.634248v1?rss=1 Chodrow, P. Su, J. Lee, D. He, N. De Man, R. Tiwari, A. Mannherz, W. Citi, L. Gupta, R. Gu, Z. Cantonwine, D. E. McElrath, T. F. Tiemeier, H. Michaelson, J. S. 2025-01-22 doi:10.1101/2025.01.22.634248 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Development of a floxed Gabbr2 gene allows for widespread conditional disruption of GABBR2 and recapitulates the phenotype of germline Gabbr2 knockout mice ]]> https://biorxiv.org/content/10.1101/2025.01.23.634473v1?rss=1 Hens, J. R. Brown, S. Licznerski, P. Suarez, J. Jonas, E. Wysolmerski, J. 2025-01-23 doi:10.1101/2025.01.23.634473 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ DMEM and EMEM are suitable surrogate media to mimic host environment and expand leptospiral pathogenesis studies using in vitro tools ]]> https://biorxiv.org/content/10.1101/2025.01.22.634353v1?rss=1 Garcia, L. Lin, Z. Culos, S. Muenker, M. C. Johnson, E. E. Wang, Z. Lopez-Giraldez, F. Giraud-Gatineau, A. Jackson, A. Picardeau, M. Goodlett, D. R. Townsend, J. P. Petrosova, H. Wunder, E. A. 2025-01-24 doi:10.1101/2025.01.22.634353 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ UNICORN: Towards Universal Cellular Expression Prediction with an Explainable Multi-Task Learning Framework ]]> https://biorxiv.org/content/10.1101/2025.01.22.634371v1?rss=1 Liu, T. Huang, T. Lin, Y. Ying, R. Zhao, H. 2025-01-25 doi:10.1101/2025.01.22.634371 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Unraveling Dengue Serotype 3 Transmission in Brazil: Evidence for Multiple Introductions of the 3III_B.3.2 Lineage ]]> https://biorxiv.org/content/10.1101/2025.01.23.634513v1?rss=1 Pereira, J. S. Slavov, S. N. Brcko, I. C. Ribeiro, G. de Souza, V. C. Ribeiro, I. S. de Lima, I. T. T. Borges, G. A. L. Furtado, K. C. d. L. Chagas, S. M. d. S. da Costa, P. M. S. S. B. Adelino, T. Iani, F. C. d. M. Alcantara, L. C. J. Hill, V. Grubaugh, N. D. Sampaio, S. C. Sabbaga, M. C. Giovanetti, M. Lima, A. R. J. 2025-01-26 doi:10.1101/2025.01.23.634513 Cold Spring Harbor Laboratory Press 2025-01-26 <![CDATA[ APOE-ϵ4-induced Fibronectin at the blood-brain barrier is a conserved pathological mediator of disrupted astrocyte-endothelia interaction in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.01.24.634732v1?rss=1 View larger version (70K): org.highwire.dtl.DTLVardef@1efff03org.highwire.dtl.DTLVardef@14f40cdorg.highwire.dtl.DTLVardef@27743aorg.highwire.dtl.DTLVardef@3fa9a9_HPS_FORMAT_FIGEXP M_FIG C_FIG Accessibility textThis image illustrates the effects of different APOE isoforms (ApoE-{varepsilon}3 and ApoE-{varepsilon}4) on blood-brain barrier (BBB) integrity, focusing on the molecular interactions between astrocytes and endothelial cells. This figure emphasizes the detrimental effects of ApoE-{varepsilon}4 on BBB integrity via fibronectin accumulation and altered signaling pathways. The top section provides a schematic overview of the blood-brain barrier, highlighting astrocytes, endothelial cells, and their interface. The left panel represents the ApoE-{varepsilon}3 condition: Normal fibronectin (FN1) levels support healthy interactions between astrocytes and endothelial cells. Growth factors, including VEGFA, HBEGF, and IGF1, maintain BBB integrity through their respective receptors (VEGFR and EGFR). Green arrows indicate activation of these signaling pathways. The right panel depicts the ApoE-{varepsilon}4 condition: Elevated fibronectin (FN1) disrupts astrocyte-endothelium interactions. FN1 binds integrins and activates focal adhesion kinase (FAK), inhibiting VEGFA, which is required for endothelial HBEGF that in turn activates IGF1 signaling. Red symbols indicate inhibition of HBEGF, VEGFA, and IGF1 pathways, leading to BBB dysfunction. HighlightsAPOE-{varepsilon}4 drives fibronectin deposition in Alzheimers, disrupting astrocyte-endothelia interactions. APOE-{varepsilon}4 and fibronectin co-localize, forming aggregates at blood-brain barrier (BBB). Fibronectin alters the signaling between VEGF, IGF1, and HBEGF impairing BBB function. Reducing fibronectin restores BBB integrity and offsets APOE-{varepsilon}4 pathology. ]]> Bhattarai, P. Yilmaz, E. Cakir, E. O. Yuceer Korkmaz, H. Lee, A. J. Ma, Y. Celikkaya, H. Cosacak, M. I. Haage, V. Wang, X. Nelson, N. Lin, W. Zhang, Y. Nuriel, T. Juelich, D. Is, O. Scott, H. de Jager, P. Fisher, E. Tubessing, K. Teich, A. F. Bertucci, T. Temple, S. Ertekin-Taner, N. Vardarajan, B. N. Mayeux, R. Kizil, C. 2025-01-27 doi:10.1101/2025.01.24.634732 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow ]]> https://biorxiv.org/content/10.1101/2025.01.24.634814v1?rss=1 Zhang, D. Chu, Z. Huo, Y. Bai, Z. Fan, R. Lu, J. Gerstein, M. 2025-01-27 doi:10.1101/2025.01.24.634814 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Epigenetic priming promotes acquisition of tyrosine kinase inhibitor resistance and oncogene amplification in human lung cancer ]]> https://biorxiv.org/content/10.1101/2025.01.26.634826v1?rss=1 Starble, R. Sun, E. G. Gbyli, R. Radda, J. Lu, J. Jensen, T. B. Sun, N. Khudaverdyan, N. Hu, B. Melnick, M. A. Zhao, S. Roper, N. Wang, G. G. Song, J. Politi, K. Wang, S. Xiao, A. 2025-01-27 doi:10.1101/2025.01.26.634826 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons ]]> https://biorxiv.org/content/10.1101/2025.01.26.634951v1?rss=1 Barrett, A. Varol, E. Weinreb, A. Taylor, S. R. McWhirter, R. M. Cros, C. C. Vidal, B. Basaravaju, M. Poff, A. Tipps, J. A. Majeed, M. Wang, C. Bayer, E. A. Reilly, M. B. Yemini, E. Sun, H. Hobert, O. Miller, D. M. Hammarlund, M. 2025-01-27 doi:10.1101/2025.01.26.634951 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Microbial functional guilds respond cohesively to rapidly fluctuating environments ]]> https://biorxiv.org/content/10.1101/2025.01.30.635766v1?rss=1 Crocker, K. A. Skwara, A. A. Kannan, R. Murugan, A. Kuehn, S. 2025-01-30 doi:10.1101/2025.01.30.635766 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling ]]> https://biorxiv.org/content/10.1101/2025.01.29.635500v1?rss=1 Ramelow, C. C. Dammer, E. B. Xiao, H. Cheng, L. Kumar, P. Espinosa-Garcia, C. Sampson, M. M. Nelson, R. S. Malepati, S. Kour, D. Kumari, R. Guo, Q. Bagchi, P. Duong, D. M. Seyfried, N. T. Sloan, S. A. Rangaraju, S. 2025-02-01 doi:10.1101/2025.01.29.635500 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding ]]> https://biorxiv.org/content/10.1101/2025.01.30.635736v1?rss=1 Westbrook, J. W. Malukiewicz, J. Sreedasyam, A. Jenkins, J. W. Zhang, Q. Lakoba, V. Fitzsimmons, S. F. Van Clief, J. Collins, K. Hoy, S. Stark, C. Grabowski, L. Jenkins, E. Saielli, T. Jarrett, B. T. Wigfield, L. Kerwien, L. M. Wilbur, C. Sandercock, A. Craddock, J. H. Zannini, P. Kerio, S. Zhebentyayeva, T. Fan, S. Thomas, A. Abbott, A. Nelson, C. D. Xia, X. Williams, M. Boston, L. Plott, C. Carle, F. Swatt, J. Ostroff, J. Jeffers, S. Mckeever, K. Smith, E. Ellis, T. J. James, J. B. Sisco, P. Newhouse, A. E. Carlson, E. Powell, W. A. Hebard, F. V. 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Trail, F. 2025-02-03 doi:10.1101/2025.02.03.636182 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Targeted ubiquitination of NaV1.8 reduces sensory neuronal excitability ]]> https://biorxiv.org/content/10.1101/2025.02.04.636451v1?rss=1 Tyagi, S. Ghovanloo, M.-R. Alsaloum, M. Effraim, P. Higerd-Rusli, G. P. Dib-Hajj, F. Zhao, P. Liu, S. Waxman, S. G. Dib-Hajj, S. D. 2025-02-04 doi:10.1101/2025.02.04.636451 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ NoisyFlow: Differentially Private Optimal Transport Using Neural Networks for Secure Biomedical Data Sharing ]]> https://biorxiv.org/content/10.1101/2025.01.31.635830v1?rss=1 Li, Y. Khandekar, N. Wang, S. Khanna, V. Sanker, J. Gerstein, M. 2025-02-05 doi:10.1101/2025.01.31.635830 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Hepatic Arterial Flow-Induced Portal Tract Fibrosis in Portal Hypertension: The Role of VCAM-1 and Osteopontin-Expressing Macrophages ]]> https://biorxiv.org/content/10.1101/2025.01.31.634947v1?rss=1 Ma, R. Gong, L. Dong, C. Utsumi, T. Qi, J. Zhuang, Z. Zhang, X. Yang, Y. McConnell, M. J. Huang, H.-C. Iwakiri, Y. 2025-02-06 doi:10.1101/2025.01.31.634947 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Tumor-associated stroma shapes the spatial tumor immune microenvironment of primary Ewing sarcomas ]]> https://biorxiv.org/content/10.1101/2025.01.31.635996v1?rss=1 Kuo, C. Giannikou, K. Wang, N. Warren, M. Goodspeed, A. Shillingford, N. Hayashi, M. Raredon, M. S. B. Amatruda, J. 2025-02-06 doi:10.1101/2025.01.31.635996 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Cutaneous lupus features specialized stromal niches and altered retroelement expression ]]> https://biorxiv.org/content/10.1101/2025.02.01.636053v1?rss=1 Gehlhausen, J. R. Kong, Y. Baker, E. Ramachandran, S. Koumpouras, F. Ko, C. Vesely, M. Little, A. Damsky, W. King, B. Iwasaki, A. 2025-02-06 doi:10.1101/2025.02.01.636053 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Knockoff procedure improves causal gene identifications in conditional transcriptome-wide association studies ]]> https://biorxiv.org/content/10.1101/2025.02.05.636660v1?rss=1 Zhang, X. Wang, L. Zhao, J. Zhao, H. 2025-02-08 doi:10.1101/2025.02.05.636660 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions ]]> https://biorxiv.org/content/10.1101/2025.02.05.636707v1?rss=1 Yang, J. Agrawal, K. Stanley, J. S. Li, R. Jacobs, N. Wang, H. Lu, C. Qu, R. Clarke, D. Chen, Y. Jiang, Y. Bai, D. Zheng, S. Fox, H. Ho, Y.-C. Huttner, A. Gerstein, M. Kluger, Y. Zhang, L. Spudich, S. 2025-02-08 doi:10.1101/2025.02.05.636707 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses ]]> https://biorxiv.org/content/10.1101/2025.02.06.636817v1?rss=1 House, C. Huang, Z. Shankar, K. N. Young, S. J. Roberts, M. E. Diamond, S. L. Tomaiuolo, M. Stalker, T. J. Lu, L. Sinno, T. 2025-02-08 doi:10.1101/2025.02.06.636817 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ PI(3)P signaling regulates endosomal flux underlying developmental synaptic remodeling via Rab4 ]]> https://biorxiv.org/content/10.1101/2025.02.07.636819v1?rss=1 Singh, K. Das, S. Rai, D. Sutradhar, S. Sarkar, A. Howard, J. Ray, K. 2025-02-08 doi:10.1101/2025.02.07.636819 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Multiple interactions mediate the localization of BLTP2 at ER-PM contacts to control plasma membrane dynamics ]]> https://biorxiv.org/content/10.1101/2025.02.07.637094v1?rss=1 Dai, A. Xu, P. Amos, C. Fujise, K. Wu, Y. Yang, H. Eisen, J. N. Guillen-Samander, A. De Camilli, P. 2025-02-08 doi:10.1101/2025.02.07.637094 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Interplay between cytokine and FGF2 signaling in induction of entosis and vasculogenic mimicry response in glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.02.09.637275v1?rss=1 Kang, T.-Y. Park, J. Dincer, A. Baskaran, J. Ren, C. Scuderi, S. Yang, L. McGuone, D. Miller-Jensen, K. Gunel, J. M. Gunel, M. Levchenko, A. 2025-02-10 doi:10.1101/2025.02.09.637275 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Wildlife trade drives animal-to-human pathogen transmission over 40 years ]]> https://biorxiv.org/content/10.1101/2025.02.09.637309v1?rss=1 Gippet, J. M. W. Carlson, C. J. Klaftenberger, T. Schweizer, M. Bertelsmeier, C. 2025-02-10 doi:10.1101/2025.02.09.637309 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ A lateralized pathway for associating nutrients with flavors ]]> https://biorxiv.org/content/10.1101/2025.02.09.637334v1?rss=1 Grove, J. C. R. Li, Q. Backes, H. Kuzmanovic, B. Choi, J. Ubadiah, V. Qiu, L. Zhang, J. Liu, Z. Small, D. M. Tittgemeyer, M. Knight, Z. A. 2025-02-10 doi:10.1101/2025.02.09.637334 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Ketamine Alters Tuning of Neural and Behavioral Spatial Working Memory Precision ]]> https://biorxiv.org/content/10.1101/2025.02.10.637233v1?rss=1 Rahmati, M. Moujaes, F. Suljic, N. P. Ji, J. L. Berkovitch, L. Lee, K. Fonteneau, C. Schleifer, C. H. Adkinson, B. D. Savic, A. Santamauro, N. Tamayo, Z. Diehl, C. Kolobaric, A. Flynn, M. Camarro, T. Curtis, C. E. Repovs, G. Fineberg, S. K. Morgan, P. T. Preller, K. H. Krystal, J. H. Murray, J. D. Cho, Y. T. Anticevic, A. 2025-02-12 doi:10.1101/2025.02.10.637233 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Geometric Protein Optimization ]]> https://biorxiv.org/content/10.1101/2025.02.10.637504v1?rss=1 Horn, C. Wirtz, D. 2025-02-12 doi:10.1101/2025.02.10.637504 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis ]]> https://biorxiv.org/content/10.1101/2025.02.11.636632v1?rss=1 Christian, L. Yilmaz, H. Ruwisch, J. Giercke, L. Seeliger, B. Kamp, J.-C. Bayraktar, S. Ewen, R. Graalmann, T. Fuge, J. Greer, M. Ius, F. Welte, T. Hohlfeld, J. M. Hoeper, M. M. Gottlieb, J. Kaminski, N. Prasse, A. Jonigk, D. Li, Y. Falk, C. Neubert, L. Schupp, J. C. 2025-02-12 doi:10.1101/2025.02.11.636632 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Identifying Neurobiological Psychosis Biotypes Using Multi-Scale Functional Network Connectivity and its Latent Independent Subspace ]]> https://biorxiv.org/content/10.1101/2025.02.11.637551v1?rss=1 Ballem, R. Camazon, P. A. Jensen, K. M. Bajracharya, P. Diaz-Caneja, C. M. Bustillo, J. R. Turner, J. A. Pearlson, G. D. Chen, J. Calhoun, V. Iraji, A. 2025-02-12 doi:10.1101/2025.02.11.637551 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Axonal Mechanotransduction Drives Cytoskeletal Responses to Physiological Mechanical Forces ]]> https://biorxiv.org/content/10.1101/2025.02.11.637689v1?rss=1 Swaim, G. L. Glomb, O. Xie, Y. Emerson, C. Li, Z. Beaudet, D. Hendricks, A. G. Yogev, S. 2025-02-12 doi:10.1101/2025.02.11.637689 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ HKU5 bat merbecoviruses use divergent mechanisms to engage bat and mink ACE2 as entry receptors ]]> https://biorxiv.org/content/10.1101/2025.02.12.637862v1?rss=1 Alfajaro, M. M. Keeler, E. L. Li, N. Cantanzaro, N. J. Teng, I.-T. Zhao, Z. Grunst, M. W. Yount, B. Schaefer, A. Wang, D. Kim, A. Synowiec, A. Pena-Hernandez, M. A. Arinola, R. Kaur, R. Menasche, B. L. Wei, J. Russell, G. A. Huck, J. Song, J. Ring, A. Iwasaki, A. Jangra, R. K. Lee, S. Martinez, D. R. Mothes, W. Uchil, P. D. Doench, J. G. Spaulding, A. Baric, R. S. Serebryannyy, L. Tsybovsky, Y. Zhou, T. Doueck, D. Wilen, C. B. 2025-02-13 doi:10.1101/2025.02.12.637862 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Identification of a multi-omics factor predictive of long COVID in the IMPACC study ]]> https://biorxiv.org/content/10.1101/2025.02.12.637926v1?rss=1 500 hospitalized COVID-19 patients in the IMPACC cohort to identify a multi-omics "recovery factor". IMPACC participants who experienced LC had lower recovery factor scores compared to participants without LC. Biologic characterization revealed increased levels of plasma proteins associated with inflammation, elevated transcriptional signatures of heme metabolism, and decreased androgenic steroids in LC patients. The recovery factor was also associated with altered circulating immune cell frequencies. Notably, recovery factor scores were predictive of LC occurrence in patients as early as hospital admission, irrespective of acute disease severity. Thus, the recovery factor identifies patients at risk of LC early after SARS-CoV-2 infection and reveals LC biomarkers and potential treatment targets. ]]> Gabernet, G. Maciuch, J. Gygi, J. P. Moore, J. F. Hoch, A. Syphurs, C. Chu, T. Jayavelu, N. D. Corry, D. B. Kheradmand, F. Baden, L. R. Sekaly, R.-P. McComsey, G. A. Haddad, E. K. Cairns, C. B. Rouphael, N. Fernandez-Sesma, A. Simon, V. Metcalf, J. P. Agudelo Higuita, N. I. Hough, C. L. Messer, W. B. Davis, M. M. Nadeau, K. C. Pulendran, B. Kraft, M. Bime, C. Reed, E. F. Schaenman, J. Erle, D. J. Calfee, C. S. Atkinson, M. A. Brackenridge, S. C. Melamed, E. Shaw, A. C. Hafler, D. A. Ozonoff, A. Bosinger, S. E. Eckalbar, W. Maecker, H. T. Kim-Schulze, S. 2025-02-14 doi:10.1101/2025.02.12.637926 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Autism-associated ASPM variant causes macrocephaly and social-cognitive deficits in mice ]]> https://biorxiv.org/content/10.1101/2025.02.17.638753v1?rss=1 Singh, S. Kim, H. Ecevitoglu, A. Chasse, R. Ludko, A. M. Sanganahalli, B. Gangasandra, V. Park, S. R. Yee, S.-P. Grady, J. Salamone, J. Fitch, R. H. Spellman, T. Hyder, F. Bae, B.-I. 2025-02-19 doi:10.1101/2025.02.17.638753 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ The architecture, assembly, and evolution of a complex flagellar motor ]]> https://biorxiv.org/content/10.1101/2025.02.19.638559v1?rss=1 Feng, X. Tachiyama, S. He, J. Zhu, S. Zhao, H. Botting, J. M. Liu, Y. Chen, Y. Hua, C. Lara-Tejero, M. Baker, M. A. Gao, X. Liu, J. Gao, B. 2025-02-19 doi:10.1101/2025.02.19.638559 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ The Legionella pneumophila type IVb secretion system effector BinA subverts amino acid transport to sensitize TORC1 signaling in macrophages ]]> https://biorxiv.org/content/10.1101/2025.02.20.639245v1?rss=1 Circu, M. Castore, R. Latimer, B. Shames, S. Roy, C. Dragoi, A.-M. Ivanov, S. S. 2025-02-20 doi:10.1101/2025.02.20.639245 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ PLK4 inhibition as a strategy to enhance non-small cell lung cancer radiosensitivity ]]> https://biorxiv.org/content/10.1101/2025.02.19.638860v1?rss=1 Dominguez-Vigil, I. G. Banik, K. Baro, M. Contessa, J. N. Hayman, T. J. 2025-02-23 doi:10.1101/2025.02.19.638860 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment ]]> https://biorxiv.org/content/10.1101/2025.02.19.639069v1?rss=1 Wacholder, A. Deutsch, E. W. Kok, L. W. van Dinter, J. T. Lee, J. Wright, J. C. Leblanc, S. Jayatissa, A. H. Jiang, K. Arefiev, I. Cao, K. Bourassa, F. Trifiro, F.-A. Bassani-Sternberg, M. Baranov, P. V. Bogaert, A. Chothani, S. Fierro-Monti, I. Fijalkowska, D. Gevaert, K. Hubner, N. Mudge, J. M. Ruiz-Orera, J. Schulz, J. Vizcaino, J. A. Prensner, J. R. Brunet, M. A. Martinez, T. F. Slavoff, S. A. Roucou, X. Chaudhary, J. S. van Heesch, S. Moritz, R. L. Carvunis, A.-R. 2025-02-23 doi:10.1101/2025.02.19.639069 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Loss of JAK1 Function Causes G2/M Cell Cycle Defects Vulnerable to Kif18a Inhibition ]]> https://biorxiv.org/content/10.1101/2025.02.19.638911v1?rss=1 Kelley, V. M. Serrano, M. B. Gasperi, W. Ader, N. Lea, H. Lee, H. Phoomak, C. Kabeche, L. King, M. C. Contessa, J. 2025-02-24 doi:10.1101/2025.02.19.638911 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation ]]> https://biorxiv.org/content/10.1101/2025.02.19.638991v1?rss=1 Mayday, M. Y. Biancon, G. Wei, M. Ramirez, C. Moratti, I. Pintado-Urbanc, A. P. Wang, L. Espinosa, J. A. Simon, M. D. Ofir-Rosenfeld, Y. Rausch, O. Tebaldi, T. Halene, S. Krause, D. S. 2025-02-24 doi:10.1101/2025.02.19.638991 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ The neuron-intrinsic membrane skeleton is required for motor neuron integrity throughout lifespan ]]> https://biorxiv.org/content/10.1101/2025.02.23.639536v1?rss=1 Davison, C. A. Garcia, D. Feng, C. Hao, H. Jorgensen, E. M. Hammarlund, M. 2025-02-24 doi:10.1101/2025.02.23.639536 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Endogenously generated Dutch-type Aβ nonfibrillar aggregates dysregulate presynaptic neurotransmission in the absence of detectable inflammation ]]> https://biorxiv.org/content/10.1101/2025.02.25.639746v1?rss=1 Castranio, E. L. Varghese, M. Argyrousi, E. K. Tripathi, K. Soderbergh, L. Bresnahan, E. Lerner, D. Garretti, F. Zhang, H. van de Loo, J. Stimpson, C. Talty, R. Glabe, C. Levy, E. Wang, M. Ivkov, M. Zhang, B. Lannfelt, L. Guerin, B. Lubell, W. Rahimipour, S. Dickstein, D. L. Gandy, S. E. Arancio, O. Ehrlich, M. E. 2025-02-26 doi:10.1101/2025.02.25.639746 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Molecular grammars of intrinsically disordered regions that span the human proteome ]]> https://biorxiv.org/content/10.1101/2025.02.27.640591v1?rss=1 Ruff, K. M. King, M. R. Ying, A. W. Liu, V. Pant, A. Lieberman, W. E. Shinn, M. K. su, x. Kadoch, C. Pappu, R. V. 2025-02-28 doi:10.1101/2025.02.27.640591 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics ]]> https://biorxiv.org/content/10.1101/2025.02.26.640468v1?rss=1 Liu, T. Zhang, X. Ying, R. Zhao, H. 2025-03-02 doi:10.1101/2025.02.26.640468 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Coarse-grained chromatin dynamics by trackingmultiple similarly labeled gene loci ]]> https://biorxiv.org/content/10.1101/2025.02.27.640402v1?rss=1 Mader, A. Rodriguez, A. I. Yuan, T. Surovtsev, I. V. King, M. C. Mochrie, S. G. J. 2025-03-02 doi:10.1101/2025.02.27.640402 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Spatial and molecular insights into microglial roles in cerebellar aging ]]> https://biorxiv.org/content/10.1101/2025.03.01.640978v1?rss=1 Tsai, A. P. Henze, D. E. Ramirez Lopez, E. Haberberger, J. Dong, C. Lu, N. Atkins, M. Costa, E. K. Farinas, A. Oh, H. Moran-Losada, P. Le Guen, Y. Isakova, A. Quake, S. R. Wyss-Coray, T. 2025-03-02 doi:10.1101/2025.03.01.640978 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge. ]]> https://biorxiv.org/content/10.1101/2025.02.27.640393v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@1012e67org.highwire.dtl.DTLVardef@8d99d7org.highwire.dtl.DTLVardef@6f21b9org.highwire.dtl.DTLVardef@f23fd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Type locality locations for species-rank mammal taxa described from 1 January 2000 to 15 August 2024. Map gray-scale country coloration represents the total number of currently valid species type localities found per country described within this period. Colored dots represent the exact georeferenced type locality of all currently valid species (red circles) and names currently considered synonyms and subspecies (blue diamonds) in MDD2. Most coordinates were generated from the original description of each name when included directly in publication, while others were georeferenced using GeoLocate or WikiMedia GeoHack place coordinates when not included in the original description publication. The georeferenced localities were mapped and both programmatically and visually vetted for accuracy. Latitude and longitude in decimal degrees is included for each of the names mapped here in the MDD2 synonym list, Supplementary Data SD2. C_FIG ]]> Burgin, C. J. Zijlstra, J. S. Becker, M. A. Handika, H. Alston, J. M. Widness, J. Liphardt, S. Huckaby, D. G. Upham, N. S. 2025-03-03 doi:10.1101/2025.02.27.640393 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Distinct representations of an anxiogenic environment in different cell types of the ventral hippocampus ]]> https://biorxiv.org/content/10.1101/2025.03.07.641976v1?rss=1 Berry, J. E. Jimenez, J. Chang, W.-l. Ogbu, K. M. Manfred, N. Tegang, K. Fusi, S. Hen, R. Lacefield, C. 2025-03-10 doi:10.1101/2025.03.07.641976 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Leveraging cell-type specificity and similarity improves single-cell eQTL fine-mapping ]]> https://biorxiv.org/content/10.1101/2025.03.05.641709v1?rss=1 Lin, C. Lin, Y. Li, W. Xu, L. Zhang, X. Zhao, H. 2025-03-11 doi:10.1101/2025.03.05.641709 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ spVelo: RNA velocity inference for multi-batch spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.03.06.641905v1?rss=1 Long, W. Liu, T. Xue, L. Zhao, H. 2025-03-11 doi:10.1101/2025.03.06.641905 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue ]]> https://biorxiv.org/content/10.1101/2025.03.06.641951v1?rss=1 Cheng, Y. Dang, S. Zhang, Y. Chen, Y. Yu, R. Liu, M. Jin, S. Han, A. Katz, S. Wang, S. 2025-03-11 doi:10.1101/2025.03.06.641951 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Comparison of oviposition and adult trapping to monitor wMel introgression for Wolbachia-based vector control ]]> https://biorxiv.org/content/10.1101/2025.03.10.642347v1?rss=1 Nelson, E. Pereira, T. N. Ribeiro, E. M. d. C. Mafra e Silva, B. D. Camillo, C. Rodrigues da Costa, T. Teixeira, M. M. Ko, A. I. Cummings, D. A. Moreira, L. A. 2025-03-13 doi:10.1101/2025.03.10.642347 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Cortical reinstatement of causally related events sparks narrative insights by updating neural representation patterns ]]> https://biorxiv.org/content/10.1101/2025.03.12.642853v1?rss=1 Song, H. Ke, J. Madhogarhia, R. Leong, Y. C. Rosenberg, M. D. 2025-03-13 doi:10.1101/2025.03.12.642853 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Overlooked features lead to divergent neurobiological interpretations of brain-based machine learning biomarkers ]]> https://biorxiv.org/content/10.1101/2025.03.12.642878v1?rss=1 Adkinson, B. D. Rosenblatt, M. Sun, H. Dadashkarimi, J. Tejavibulya, L. Horien, C. Westwater, M. L. Noble, S. Scheinost, D. 2025-03-13 doi:10.1101/2025.03.12.642878 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Emotional arousal enhances narrative memories through functional integration of large-scale brain networks ]]> https://biorxiv.org/content/10.1101/2025.03.13.643125v1?rss=1 Park, J. S. Gollapudi, K. Ke, J. Nau, M. Pappas, I. Leong, Y. C. 2025-03-13 doi:10.1101/2025.03.13.643125 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR ]]> https://biorxiv.org/content/10.1101/2025.03.12.642874v1?rss=1 Mabin, J. W. Vock, I. W. Machyna, M. Haque, N. Thakran, P. Zhang, A. Rai, G. Leibler, I. N.-M. Inglese, J. Simon, M. D. Hogg, J. R. 2025-03-14 doi:10.1101/2025.03.12.642874 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Tissue Engineering Applications for Novel Integrated and Mobile Perfusion System ]]> https://biorxiv.org/content/10.1101/2025.03.12.642925v1?rss=1 Zhu, A. Jain, T. Reid, E. Siddiqi, U. Mir, A. Dunne, O. Hibino, N. 2025-03-14 doi:10.1101/2025.03.12.642925 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Auditory Perception Induces Cortical and Thalamic Event-Related Desynchronization in the Mouse ]]> https://biorxiv.org/content/10.1101/2025.03.21.644604v1?rss=1 McGill, S. H. Xin, Q. Yadav, T. Zhao, C. W. Paszkowski, P. Darby, F. Guha, M. Nguyen, T. Jin, D. S. Nir, Y. Liu, J. Sieu, L.-A. Blumenfeld, H. 2025-03-22 doi:10.1101/2025.03.21.644604 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ H3K4me3 instructs transcription at intergenic active regulatory elements ]]> https://biorxiv.org/content/10.1101/2025.03.21.644682v1?rss=1 Yu, H. Zhang, Y. Liao, Z. Walters, B. W. Lesch, B. J. 2025-03-22 doi:10.1101/2025.03.21.644682 Cold Spring Harbor Laboratory Press 2025-03-22 <![CDATA[ AMULETY: A Python package to embed adaptive immune receptor sequences ]]> https://biorxiv.org/content/10.1101/2025.03.21.644583v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1c0bafaorg.highwire.dtl.DTLVardef@337816org.highwire.dtl.DTLVardef@111136forg.highwire.dtl.DTLVardef@1300dc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, M. Kluger, Y. Kleinstein, S. Gabernet, G. 2025-03-25 doi:10.1101/2025.03.21.644583 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ ATG2A engages Rab1a and ARFGAP1 positive membranes during autophagosome biogenesis ]]> https://biorxiv.org/content/10.1101/2025.03.24.645038v1?rss=1 Fuller, D. M. Wu, Y. Schueder, F. Rasool, B. Nag, S. Korfhage, J. L. Garcia-Milian, R. Melnyk, K. D. Bewersdorf, J. De Camilli, P. Melia, T. 2025-03-25 doi:10.1101/2025.03.24.645038 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Rare Jackpot Individuals Drive Rapid Adaptation in Threespine Stickleback ]]> https://biorxiv.org/content/10.1101/2025.03.25.642177v1?rss=1 Kwakye, A. Reid, K. Wund, M. A. Heins, D. C. Bell, M. A. Veeramah, K. R. 2025-03-26 doi:10.1101/2025.03.25.642177 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Long-term editing of brain circuits in mice using an engineered electrical synapse ]]> https://biorxiv.org/content/10.1101/2025.03.25.645291v1?rss=1 Ransey, E. Thomas, G. Wisdom, E. Almoril-Porras, A. Bowman, R. Adamson, E. Walder-Christensen, K. K. White, J. A. Hughes, D. N. Schwennesen, H. Ferguson, C. Tye, K. Mague, S. D. Niu, L.-G. Wang, Z.-W. Colon-Ramos, D. Hultman, R. Bursac, N. Dzirasa, K. 2025-03-26 doi:10.1101/2025.03.25.645291 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ CFTR function in alveolar type 1 cells drives lung liquid secretion and host defense ]]> https://biorxiv.org/content/10.1101/2025.03.25.645303v1?rss=1 Suthakaran, S. Homami, S. Chavez, D. Tang, S. Moore, S. K. L. Sussman, C. Zhang, J. Britto, C. J. Prince, A. May, A. J. Kathiriya, J. J. Hook, J. L. 2025-03-26 doi:10.1101/2025.03.25.645303 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Characterization of gut microbiomes in rural Honduras reveals novel species and associations with human genetic variation ]]> https://biorxiv.org/content/10.1101/2025.03.25.645309v1?rss=1 Beghini, F. Brito, I. L. Gerstein, M. Christakis, N. A. 2025-03-26 doi:10.1101/2025.03.25.645309 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Growth charts of infant visual neurodevelopment generalize across global contexts ]]> https://biorxiv.org/content/10.1101/2025.03.25.645314v1?rss=1 Margolis, E. T. Camp, C. Sobrino, A. C. Polanczyk, G. V. Fatori, D. Khula South Africa Team, Germina Team, LABS Team, GABA Team, 1kD EEG Working Group, 1kD Machine Learning Working Group, Cornelissen, L. Berde, C. B. Hensch, T. K. Nelson, C. A. Shephard, E. Donald, K. A. Scheinost, D. Gabard-Durnam, L. J. 2025-03-26 doi:10.1101/2025.03.25.645314 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase ]]> https://biorxiv.org/content/10.1101/2025.03.26.645524v1?rss=1 130 {degrees}C (>8 {degrees}C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme, and showcase the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/645524v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@186bfccorg.highwire.dtl.DTLVardef@19a265borg.highwire.dtl.DTLVardef@14c526corg.highwire.dtl.DTLVardef@1b75920_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yehorova, D. Alansson, N. Shen, R. Denson, J. M. Robinson, M. Risso, V. A. Molina, N. R. Loria, J. P. Gaucher, E. Sanchez-Ruiz, J. M. Hengge, A. C. Johnson, S. Kamerlin, S. C. L. 2025-03-26 doi:10.1101/2025.03.26.645524 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Androgen Deprivation-Induced TET2 Activation Fuels Prostate Cancer Progression via Epigenetic Priming and Slow-Cycling Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.03.26.645495v1?rss=1 Li, L. Cheng, S. Xu, Y. Deng, S. Mu, P. Yu, X. 2025-03-29 doi:10.1101/2025.03.26.645495 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Asymmetric phosphoinositide lipid bilayers generated by spontaneous lipid insertion ]]> https://biorxiv.org/content/10.1101/2025.03.26.645509v1?rss=1 Guerin, G. Nguyen, T. L. A. Manzi, J. Le Clainche, C. Heuvingh, J. Rodriguez, N. Cribier, S. Berro, J. Tsai, F.-C. 2025-03-30 doi:10.1101/2025.03.26.645509 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Generative World Models to compute protein folding pathways ]]> https://biorxiv.org/content/10.1101/2025.03.26.645554v1?rss=1 Ianeselli, A. Im, J. Cavallin, E. Gerstein, M. 2025-03-30 doi:10.1101/2025.03.26.645554 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ TARP γ-8 is a target of ethanol that regulates self-administration and relapse in mice ]]> https://biorxiv.org/content/10.1101/2025.03.27.645788v1?rss=1 Faccidomo, S. Hoffman, J. L. Lee, J. Whindleton, C. M. Kim, M. Taylor, S. Kim, A. Richter, C. Seiters, H. Bryant, J. Chang, A. Smith, E. Agoglia, A. E. Tomita, S. Herman, M. A. Hodge, C. W. 2025-04-01 doi:10.1101/2025.03.27.645788 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Overnutrition directly impairs thyroid hormone biosynthesis and utilization, causing hypothyroidism, despite remarkable thyroidal adaptations ]]> https://biorxiv.org/content/10.1101/2025.03.31.645596v1?rss=1 Rampy, J. Torres-Manzo, A. P. Hoffsmith, K. Loberg, M. A. Sheng, Q. Salas-Lucia, F. Bianco, A. C. Arrojo e Drigo, R. Wang, H. Weiss, V. L. Carrasco, N. 2025-04-02 doi:10.1101/2025.03.31.645596 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Accelerated learning of a noninvasive human brain-computer interface via manifold geometry ]]> https://biorxiv.org/content/10.1101/2025.03.29.646109v1?rss=1 Busch, E. L. Fincke, E. C. Lajoie, G. Krishnaswamy, S. Turk-Browne, N. B. 2025-04-03 doi:10.1101/2025.03.29.646109 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Adolescents with major depression featured by sensory-association subtyping show divergent information dynamics and streams ]]> https://biorxiv.org/content/10.1101/2025.03.29.646114v1?rss=1 Liu, X. Wan, B. Zhang, X. Liu, L. Long, S. Ge, R. Cui, R. Wen, X. Yang, G. Gao, Y. 2025-04-03 doi:10.1101/2025.03.29.646114 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Promotion of new expression of connexin gene Cx46 (GJA3) in the cochlea after Cx26 (GJB2) deficiency ]]> https://biorxiv.org/content/10.1101/2025.03.30.646179v1?rss=1 Zhai, T.-Y. Chen, J. Kong, Y. Liang, C. Zhao, H.-B. 2025-04-03 doi:10.1101/2025.03.30.646179 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Fly navigational responses to odor motion and gradient cues are tuned to plume statistics ]]> https://biorxiv.org/content/10.1101/2025.03.31.646361v1?rss=1 Brudner, S. Zhou, B. Jayaram, V. Santana, G. M. Clark, D. Emonet, T. 2025-04-03 doi:10.1101/2025.03.31.646361 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Neural signatures of flexible temporal orienting under spatial and motor uncertainty ]]> https://biorxiv.org/content/10.1101/2025.04.03.646700v1?rss=1 Gao, Y. Echeverria-Altuna, I. Boettcher, S. E. P. Nobre, A. C. 2025-04-03 doi:10.1101/2025.04.03.646700 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Associations between fluid biomarkers and PET imaging (UCB-J) of synaptic pathology in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.03.31.646290v1?rss=1 Nilsson, J. Mecca, A. Ashton, N. J. Salardini, E. Odell, R. Carson, R. Benedet, A. Blennow, K. Zetterberg, H. Van Dyck, C. Brinkmalm, A. 2025-04-05 doi:10.1101/2025.03.31.646290 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Incorporating special interests to investigate the language system in autism: A feasibility pilot fMRI study ]]> https://biorxiv.org/content/10.1101/2025.04.04.647117v1?rss=1 Olson, H. A. Johnson, K. T. Nishith, S. Gabrieli, J. D. E. D'Mello, A. M. 2025-04-05 doi:10.1101/2025.04.04.647117 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Implementation of an adaptive-optics assisted isoSTED nanoscope ]]> https://biorxiv.org/content/10.1101/2025.04.02.645322v1?rss=1 Li, Y. Lee, D. Allgeyer, E. S. Schroeder, L. K. Tu, S. Bewersdorf, J. Hao, X. 2025-04-06 doi:10.1101/2025.04.02.645322 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Diet-induced phospholipid remodeling dictates ferroptosis sensitivity and tumorigenesis in the pancreas ]]> https://biorxiv.org/content/10.1101/2025.04.04.645324v1?rss=1 Ruiz, C. F. Ge, X. McDonnell, R. Agabiti, S. S. McQuaid, D. C. Tang, A. Kharwa, M. Goodell, J. Saavedra-Pena, R. d. M. Wing, A. Li, G. Pinto Medicine, N. Robert, M. E. Varshney, R. R. Rudolph, M. C. Gorelick, F. S. Wysolmerski, J. J. Canals, D. Haley, J. Rodeheffer, M. S. Muzumdar, M. D. 2025-04-06 doi:10.1101/2025.04.04.645324 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ PERADIGM: Phenotype Embedding Similarity-based Rare Disease Gene Mapping ]]> https://biorxiv.org/content/10.1101/2025.04.01.646670v1?rss=1 Zheng, W. Xie, Y. Gu, J. Li, H. Somlo, S. Besse, W. Zhao, H. 2025-04-07 doi:10.1101/2025.04.01.646670 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Leukemia Inhibitory Factor as a late-stage treatment for delayed white matter loss in concussive head injury ]]> https://biorxiv.org/content/10.1101/2025.04.07.647435v1?rss=1 D'Mello, V. d. Mihailovic, J. Ali, S. Sanganahalli, B. G. Coman, D. Hyder, F. Fernando, M. Mampilly, A. Kannurpatti, S. S. Levison, S. W. 2025-04-07 doi:10.1101/2025.04.07.647435 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Th1 cells express Tfh effector molecules and associate with B cells at the T-B borderfollowing viral infection ]]> https://biorxiv.org/content/10.1101/2025.04.02.646697v1?rss=1 Chen, J. S. Tierney, A. L. Ojo, O. A. Chow, R. D. Song, E. Mao, T. Israelow, B. Weinstein, J. S. Williams, A. Wilen, C. B. Eisenbarth, S. C. 2025-04-08 doi:10.1101/2025.04.02.646697 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Autism-associated Scn2a haploinsufficiency disrupts in vivo dendritic signaling and impairs flexible decision-making ]]> https://biorxiv.org/content/10.1101/2025.04.08.647866v1?rss=1 Wu, H. Shen, L. Indajang, J. Savalia, N. K. Johnson, T. G. Qu, J. Bender, K. J. Kwan, A. C. 2025-04-09 doi:10.1101/2025.04.08.647866 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Bactofilins are essential spatial organizers of peptidoglycan insertion in the Lyme disease spirochete Borrelia burgdorferi ]]> https://biorxiv.org/content/10.1101/2025.04.09.647816v1?rss=1 Zinck, C. B. Carracoi, V. Kloos, Z. A. Wachter, J. Schwartz, C. Stewart, P. E. Jacobs-Wagner, C. Rosa, P. A. Takacs, C. N. 2025-04-09 doi:10.1101/2025.04.09.647816 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Integrative Single-Cell RNA and ATAC Sequencing Reveals the Impact of Chronic Cigarette Smoking on Lung Epithelial Responses to Influenza and Hyperoxia ]]> https://biorxiv.org/content/10.1101/2025.04.06.647429v1?rss=1 Cha, P.-C. Zou, Z. Nouws, J. Dela Cruz, C. Sharma, L. K. Yan, X. Sauler, M. 2025-04-10 doi:10.1101/2025.04.06.647429 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion ]]> https://biorxiv.org/content/10.1101/2025.04.07.647587v1?rss=1 Suhail, Y. Du, W. Afzal, J. Wagner, G. Kshitiz, 2025-04-11 doi:10.1101/2025.04.07.647587 Cold Spring Harbor Laboratory Press 2025-04-11 <![CDATA[ Genetic variants linked to neurodevelopmental disorders within the β3-β4 loop of the TRIO PH2 domain release autoinhibition of GEF2 activity. ]]> https://biorxiv.org/content/10.1101/2025.04.14.648796v1?rss=1 Carrizales, M. G. Boulton, A. Koleske, A. J. 2025-04-14 doi:10.1101/2025.04.14.648796 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Nuclear and cytosolic J-domain proteins provide synergistic control of Hsf1 at distinct phases of the heat shock response ]]> https://biorxiv.org/content/10.1101/2025.04.14.648540v1?rss=1 Ruger-Herreros, C. Svoboda, L. Male, G. Srivastava, A. Höpfner, M. Jetzinger, K. Koubek, J. Kramer, G. den Brave, F. Mogk, A. Gross, D. S. Bukau, B. 2025-04-16 doi:10.1101/2025.04.14.648540 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Efficient near telomere-to-telomere assembly of Nanopore Simplex reads ]]> https://biorxiv.org/content/10.1101/2025.04.14.648685v1?rss=1 Cheng, H. Qu, H. McKenzie, S. Lawrence, K. R. Windsor, R. Vella, M. Park, P. J. Li, H. 2025-04-17 doi:10.1101/2025.04.14.648685 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Scaling Large Language Models for Next-Generation Single-Cell Analysis ]]> https://biorxiv.org/content/10.1101/2025.04.14.648850v1?rss=1 Rizvi, S. A. Levine, D. Patel, A. Zhang, S. Wang, E. He, S. Zhang, D. Tang, C. Lyu, Z. Darji, R. Li, M. Sun, E. Jeong, D. Zhao, L. Kwan, J. Braun, D. Hafler, B. Ishizuka, J. Dhodapkar, R. Chung, H. Azizi, S. Perozzi, B. van Dijk, D. 2025-04-17 doi:10.1101/2025.04.14.648850 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Microglial Fructose Metabolism Is Essential for Glioblastoma Growth ]]> https://biorxiv.org/content/10.1101/2025.04.12.646414v1?rss=1 Billingham, L. K. Delay, S. L. Tripathi, S. Olson, I. E. Zilinger, K. Subbiah, J. Wang, Z. Sadagopan, N. S. Chia, T.-Y. Najem, H. Cognet, G. Katz, J. L. Vazquez-Cervantes, G. I. Wang, S. Wan, H. Murphy, A. R. Lipshutz, A. B. Duffy, J. T. Valyasnikova, I. V. Zhang, P. Heiland, D. H. Ahmed, A. U. Lee-Chang, C. Heimberger, A. B. Perry, J. S. Muir, A. Chandel, N. S. Miska, J. 2025-04-18 doi:10.1101/2025.04.12.646414 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ The LINC complex component Kms1 and CENP-B protein Cbp1 cooperate to enforce faithful homology-directed DNA repair at the nuclear periphery in S. pombe ]]> https://biorxiv.org/content/10.1101/2025.04.12.648544v1?rss=1 Laffitte, A. Lin, D. Tian, Y. J. Liu, N. Lusk, C. P. Mochrie, S. King, M. C. 2025-04-18 doi:10.1101/2025.04.12.648544 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays ]]> https://biorxiv.org/content/10.1101/2025.04.16.648420v1?rss=1 Butts, J. C. Rong, S. Gosai, S. J. Castro, R. I. Noon, M. Adeniran, K. Ghosh, R. Sabeti, P. C. Tewhey, R. Reilly, S. K. 2025-04-18 doi:10.1101/2025.04.16.648420 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Personalized Brain Morphometric Feature as a Transdiagnostic Predictor of Psychopathology: Insights from Dual Systems Models ]]> https://biorxiv.org/content/10.1101/2025.04.14.644899v1?rss=1 Kang, M. Song, K.-r. Zhang, J.-l. Xu, L. Zhang, Y. Zhao, Z. Deng, H. Fang, X. Potenza, M. N. Zhang, J. 2025-04-19 doi:10.1101/2025.04.14.644899 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Feature-temporal predictions dynamically modulate performance, feature-based attentional capture, and motor response activity during visual search ]]> https://biorxiv.org/content/10.1101/2025.04.18.649503v1?rss=1 Williams, G. C. Nobre, A. C. Boettcher, S. E. P. 2025-04-19 doi:10.1101/2025.04.18.649503 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Updated neuronal numbers of the rat hippocampal formation: redesigning the hippocampal model. ]]> https://biorxiv.org/content/10.1101/2025.04.16.649153v1?rss=1 Arellano, J. I. Rakic, P. 2025-04-21 doi:10.1101/2025.04.16.649153 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Single-Cell Pharmacogenomic Landscapes of Epigenetic Therapy in Gastric Cancer ]]> https://biorxiv.org/content/10.1101/2025.04.16.649236v1?rss=1 200 GC-related genes across 4 distinct epigenetic drug classes in multiple gastric lines. We captured 17.7 million pharmocogenomic expression interactions in 625,866 cells representing baseline and post-therapeutic molecular phenotypes. This single-cell pharmacogenomic compendium confirmed previously known gene-driven molecular phenotypes, elucidated poorly characterized genes, and uncovered novel gene dosage-molecular phenotype relationships. Molecular phenotypes in post-therapeutic surviving cells revealed diverse gene perturbation-associated pathways causing convergent drug resistance (EMT plasticity, cell cycle alterations, metabolic reprogramming), highlighting combinatorial strategies for restoring sensitivity. Mapping of in vitro molecular phenotypes to primary human GCs imparted prognostic information and insights into spatial heterogeneity. Comparative analysis of gene perturbations across therapies and lines revealed both conserved and context-specific molecular alterations. Our results illustrate how Perturb-seq approaches can systematically map diverse cancer-associated molecular phenotypes across multiple gene/drug/cell line interactions, yielding translational insights. ]]> Xu, C. Ma, H. Sheng, T. Lee, M. H. Abdul Ghani, S. A. B. Perlaza-Jimenez, L. Huang, K. K. Lim, S. K. Srivastava, S. Ong, X. Tay, S. T. Ho, S. W. T. Tan, A. L. K. Zhu, F. Nasca, V. Randon, G. Ashktorab, H. Cheng, A. S.-L. Jeyasekharan, A. D. Li, S. Teh, M. Sundar, R. Powell, D. R. Rosenbluh, J. Pietrantonio, F. Yong, W. P. So, J. B.-Y. Tan, P. 2025-04-21 doi:10.1101/2025.04.16.649236 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Cryptovaranoides is not a squamate ]]> https://biorxiv.org/content/10.1101/2025.04.18.649532v1?rss=1 Caldwell, M. W. Brownstein, C. D. Meyer, D. L. Scarpetta, S. G. Lee, M. S. Y. Simoes, T. R. 2025-04-23 doi:10.1101/2025.04.18.649532 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Pan-cancer Analysis Identified Ectopic RUNX1T1 Associated with Lineage Plasticity ]]> https://biorxiv.org/content/10.1101/2025.04.18.649575v1?rss=1 Jiang, Y. Cheng, S. Kim, I. Y. Deng, S. Mu, P. 2025-04-23 doi:10.1101/2025.04.18.649575 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images ]]> https://biorxiv.org/content/10.1101/2025.04.19.649665v1?rss=1 Huang, T. Liu, T. Babadi, M. Ying, R. Jin, W. 2025-04-24 doi:10.1101/2025.04.19.649665 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Behavioral deficits and exacerbated hemodynamics during lifespan of a mouse model of late onset Alzheimer's disease expressing humanized APOEϵ4 and Trem2*R47H ]]> https://biorxiv.org/content/10.1101/2025.04.20.649712v1?rss=1 izydorczak, M. Oumov, M. Udhwani, M. V. Fostok, F. Coronas-Samano, G. Sanganahalli, B. G. Herman, P. Hyder, F. Verhagen, J. V. 2025-04-24 doi:10.1101/2025.04.20.649712 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver ]]> https://biorxiv.org/content/10.1101/2025.04.22.649812v1?rss=1 Montagna, C. Albert, O. Sun, S. Lin, J.-R. Lee, M. Chan, C. Maslov, A. Y. Ellerby, L. Huttner, A. Zhang, Z. Vijg, J. V. 2025-04-24 doi:10.1101/2025.04.22.649812 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Multispecies coexistence emerges from pairwise exclusions in communities with competitive hierarchy ]]> https://biorxiv.org/content/10.1101/2025.04.22.649899v1?rss=1 Miller, Z. R. Max, D. 2025-04-24 doi:10.1101/2025.04.22.649899 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Anks3 mediates cilia dependent polycystin signaling and is essential for adult kidney homeostasis ]]> https://biorxiv.org/content/10.1101/2025.04.22.649832v1?rss=1 Wei, Z. Rehman, M. Gu, J. Lerner, G. Dong, K. Roy, K. Cordido, A. Cai, Y. Tian, X. Tham, M. S. Kanyo, J. Lam, T. T. Zhao, H. Somlo, S. 2025-04-29 doi:10.1101/2025.04.22.649832 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Functional Dissection of the Zdhhc5-GOLGA7 Protein Palmitoylation Complex ]]> https://biorxiv.org/content/10.1101/2025.04.28.651057v1?rss=1 Kahlson, M. A. Ritho, J. Gomez, J. V. Wang, H. Butterwick, J. Dixon, S. J. 2025-04-29 doi:10.1101/2025.04.28.651057 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Myo1e/f at the podosome base regulate podosome dynamics and promote macrophage migration ]]> https://biorxiv.org/content/10.1101/2025.04.28.651090v1?rss=1 Cervero, P. Barger, S. R. Verdys, P. Herzog, R. Paul, T. Palmieri, M. Poincloux, R. Linder, S. Krendel, M. 2025-04-29 doi:10.1101/2025.04.28.651090 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Forecasting Extinction Risk using Thermal Performance Curves and Population Dynamic Modeling ]]> https://biorxiv.org/content/10.1101/2025.04.27.650737v1?rss=1 Vasseur, D. A. Bieg, C. Kummel, M. Robey, A. J. 2025-04-30 doi:10.1101/2025.04.27.650737 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Joint Modeling of Effect Sizes for Two Correlated Traits: Characterizing Trait Properties to Enhance Polygenic Risk Prediction ]]> https://biorxiv.org/content/10.1101/2025.04.28.650892v1?rss=1 zhang, c. Zhou, G. Chen, T. Zhao, H. 2025-05-01 doi:10.1101/2025.04.28.650892 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Chromatix: a differentiable, GPU-accelerated wave-optics library ]]> https://biorxiv.org/content/10.1101/2025.04.29.651152v1?rss=1 Deb, D. Both, G.-J. Bezzam, E. Kohli, A. Yang, S. Chaware, A. Allier, C. Cai, C. Anderberg, G. Eybposh, M. H. Schneider, M. C. Heintzmann, R. Rivera-Sanchez, F. A. Simmerer, C. Meng, G. Tormes-Vaquerano, J. Han, S. Shanmugavel, S. C. Maruvada, T. Yang, X. Kim, Y. Diederich, B. Joo, C. Waller, L. Durr, N. J. Pegard, N. C. La Riviere, P. J. Horstmeyer, R. Chowdhury, S. Turaga, S. C. 2025-05-02 doi:10.1101/2025.04.29.651152 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Epithelial-Immune-Stromal Interactions Define Divergent Repair and Fibrosis Pathways After Acute Kidney Injury in Human Renal Transplants ]]> https://biorxiv.org/content/10.1101/2025.04.30.651080v1?rss=1 Azim, S. Rousselle, T. Zubair, H. Shetty, A. C. Archer, K. J. Marshall, J. Rajabi, A. Lara, C. Mustofa, S. Drachenberg, C. Bromberg, J. Menon, M. Maluf, D. G. Akalin, E. Mas, V. R. 2025-05-02 doi:10.1101/2025.04.30.651080 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ LRP10 promotes trafficking of progranulin and prosaposin to lysosomes ]]> https://biorxiv.org/content/10.1101/2025.05.02.651888v1?rss=1 Filippini, F. Devireddy, S. Ferguson, S. 2025-05-03 doi:10.1101/2025.05.02.651888 Cold Spring Harbor Laboratory Press 2025-05-03 <![CDATA[ A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores ]]> https://biorxiv.org/content/10.1101/2025.05.01.651713v1?rss=1 Ahuja, N. Schultz, D. T. Destanovic, D. Church, S. H. Picciani, N. Munro, C. Kon-Nanjo, K. Kon, T. Manko, M. K. Shi, W. Haddock, S. H. D. Simakov, O. Dunn, C. W. 2025-05-07 doi:10.1101/2025.05.01.651713 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Diverse and Flexible Strategies Enable Successful Cooperation in Marmoset Dyads ]]> https://biorxiv.org/content/10.1101/2025.05.06.652115v1?rss=1 Meisner, O. C. Shi, W. Nair, A. Nandy, G. Jadi, M. P. Nandy, A. S. Chang, S. W. C. 2025-05-07 doi:10.1101/2025.05.06.652115 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Conserved and lineage-restricted gene regulatory programs modulate developmental cnidocyte specification in Nematostella vectensis. ]]> https://biorxiv.org/content/10.1101/2025.05.08.652877v1?rss=1 Danladi, B. Al-Shaer, L. Havrilak, J. A. Faltine-Gonzalez, D. Z. Jia, K. Forwood, W. Dubuc, T. Musser, J. Layden, M. J. 2025-05-09 doi:10.1101/2025.05.08.652877 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Evolutionary consequences of bacterial resistance to a flagellotropic phage ]]> https://biorxiv.org/content/10.1101/2025.05.06.652435v1?rss=1 Antani, J. D. Theroux, A. Emonet, T. Turner, P. E. 2025-05-10 doi:10.1101/2025.05.06.652435 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Prevalence, Production and the Role of Staphylococcus aureus Superantigens in Cystic Fibrosis Lung Disease. ]]> https://biorxiv.org/content/10.1101/2025.05.07.652658v1?rss=1 Sun, Y. Hu, B. Chhabra, S. Tolentino, J. Suzuki, N. Natarajan, J. Harris, Z. Stanley, G. Bianco, C. Planet, P. J. Sherchand, S. P. Adhikari, R. Aman, J. Zhang, X. Koff, J. L. Rajagopalan, G. 2025-05-12 doi:10.1101/2025.05.07.652658 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Nickel binding to a split ATCUN motif in c-Src SH3 domain facilitates crystallization ]]> https://biorxiv.org/content/10.1101/2025.05.08.652639v1?rss=1 Calicdan, X. Fisher, O. S. Ha, B. H. Boggon, T. J. Stiegler, A. L. 2025-05-13 doi:10.1101/2025.05.08.652639 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice ]]> https://biorxiv.org/content/10.1101/2025.05.09.653147v1?rss=1 Xu, P. Mancuso, R. I. Leonzino, M. Zeiss, C. J. Krause, D. S. De Camilli, P. 2025-05-13 doi:10.1101/2025.05.09.653147 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Explainable Machine Learning Identifies Dosage Compensation Factors in Aneuploid Human Cancer Cells ]]> https://biorxiv.org/content/10.1101/2025.05.12.653427v1?rss=1 Heller, E. M. Barthel, K. Raschle, M. Schukken, K. Sheltzer, J. Storchova, Z. 2025-05-13 doi:10.1101/2025.05.12.653427 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ TidyMass2: Advancing LC-MS Untargeted Metabolomics Through Metabolite Origin Inference and Metabolic Feature-based Functional Module Analysis ]]> https://biorxiv.org/content/10.1101/2025.05.09.652992v1?rss=1 Wang, X. Liu, Y. Jiang, C. Huang, Z. Yan, H. Wong, S. Johnson, C. Zhang, J. Ge, Y. Zhang, F. Lai, R. Gao, P. Zhang, X. Shen, X. 2025-05-14 doi:10.1101/2025.05.09.652992 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ A Notch signal required for a morphological novelty in Drosophila has antecedent functions in genital disc eversion ]]> https://biorxiv.org/content/10.1101/2025.05.09.653167v1?rss=1 Shodja, D. N. Glassford, W. J. Rice, G. R. Smith, S. J. Rebeiz, M. 2025-05-14 doi:10.1101/2025.05.09.653167 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Spatial epigenomic niches underlie glioblastoma cell state plasticity ]]> https://biorxiv.org/content/10.1101/2025.05.09.653178v1?rss=1 Kint, S. Younes, S. T. Bao, S. Long, G. Wouters, D. Stephenson, E. Lou, X. Zhong, M. Zhang, D. Su, G. Enninful, A. Yang, M. Chen, H.-M. Ellestad, K. Anderson, C. Moliterno, J. Kelly, J. Chan, J. A. Sifrim, A. Zhou, J. Nikolic, A. Fan, R. Gallo, M. 2025-05-14 doi:10.1101/2025.05.09.653178 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Opposing Modulation of EEG Aperiodic Component by Ketamine and Thiopental: Implications for the Noninvasive Assessment of Cortical E/I Balance in Humans ]]> https://biorxiv.org/content/10.1101/2025.05.12.653580v1?rss=1 Cortes-Briones, J. Urrutia-Gandolfo, J. Estevez, P. Sengupta, A. Basilico, M. Skosnik, P. Limoncelli, D. D'Souza, D. C. Petrakis, I. Krystal, J. 2025-05-14 doi:10.1101/2025.05.12.653580 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Mechanisms of force transmission on cytokinesis Formin Cdc12 in fission yeast revealed by coiled-coil force sensors ]]> https://biorxiv.org/content/10.1101/2025.05.14.653946v1?rss=1 Saito, T. Ren, Y. Berro, J. 2025-05-14 doi:10.1101/2025.05.14.653946 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ African Cichlid Lake Radiations Recapitulate Riverine Axial Morphologies Through Repeated Exploration of Morphospace ]]> https://biorxiv.org/content/10.1101/2025.05.13.653847v1?rss=1 Bucklow, C. V. Ribeiro, E. D. Ronco, F. Vranken, N. Oliver, M. K. Salzburger, W. Stiassny, M. Benson, R. Verd, B. 2025-05-15 doi:10.1101/2025.05.13.653847 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Interplay between SpaO variants shapes the architecture of the Salmonella type III secretion sorting platform ]]> https://biorxiv.org/content/10.1101/2025.05.15.654217v1?rss=1 Soto, J. E. Wang, T. Galan, J. E. Lara-Tejero, M. 2025-05-15 doi:10.1101/2025.05.15.654217 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Interferon-β paracrine signaling mediates synergy between TLR3 and TRIF-independent TLR pathways ]]> https://biorxiv.org/content/10.1101/2025.05.13.653801v1?rss=1 Rocha, E. I. S. Samo, K. Miller-Jensen, K. 2025-05-17 doi:10.1101/2025.05.13.653801 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ Efficacy of DNA Methyltransferase Inhibitor Immune Priming Therapy in Combination with PD-1 Inhibitors to Treat High-Risk Pediatric Brain Tumors ]]> https://biorxiv.org/content/10.1101/2025.05.14.654106v1?rss=1 Mishra, D. K. Morris, S. M. Popovski, D. Girard, E. J. Bondoc, A. Kumar, S. S. Andrade, A. F. Zhu, X. Yao, F. Brusniak, M.-Y. Umaru, B. Crotty, E. E. Brasel, K. Pakiam, F. Russo, C. Zeinieh, M. Biery, M. C. Coxon, M. Conti, H. Clarke, M. Lu, M. Rutka, J. Llivichuzhca-Loja, D. Konnikova, L. Fouladi, M. Jabado, N. Huang, A. Olson, J. M. Drissi, R. 2025-05-18 doi:10.1101/2025.05.14.654106 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Desmoplakin loss leads to PKC-dependent insertion of series sarcomeres and contractile dysfunction in cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2025.05.15.654389v1?rss=1 Gokhan, I. Li, X. Sendek, J. M. Mora Pagan, A. J. Akar, F. G. Campbell, S. G. 2025-05-19 doi:10.1101/2025.05.15.654389 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Robust inference and widespread genetic correlates from a large-scale genetic association study of human personality ]]> https://biorxiv.org/content/10.1101/2025.05.16.648988v1?rss=1 Schwaba, T. Clapp Sullivan, M. L. Akingbuwa, W. A. Ilves, K. Tanksley, P. T. Williams, C. M. Dragostinov, Y. Liao, W. Ackerman, L. S. Fealy, J. C. M. Hemani, G. de la Fuente, J. Gupta, P. Stein, M. B. Gelernter, J. Levey, D. F. Vosa, U. Ausmees, L. Realo, A. Estonian Biobank Research Team, Vaht, M. Allik, J. Esko, T. Mottus, R. Vainik, U. Jonsdottir, G. A. Thorleifsson, G. Gunnarsson, A. F. Bjornsdottir, G. Thorgeirsson, T. E. Steffansson, H. Stefansson, K. Cheesman, R. Qin, Q. Corfield, E. C. Ask, H. Ask Torvik, F. Ystrom, E. Tesli, M. Boomsma, D. I. 2025-05-20 doi:10.1101/2025.05.16.648988 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Multiplexed Molecularly-Specific SWCNT Cytokine Sensing is Enabled and Enhanced by Amine-Functionalized DNA Aqueous Two-Phase Extraction ]]> https://biorxiv.org/content/10.1101/2025.05.16.654499v1?rss=1 Ryan, A. Parveen, S. Cohen, Z. Israel, A. Williams, R. M. 2025-05-21 doi:10.1101/2025.05.16.654499 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons ]]> https://biorxiv.org/content/10.1101/2025.05.20.652233v1?rss=1 Li, Z. Kaur, N. Santpere, G. Muchnik, S. K. Sindhu, S. K. Qi, C. Shibata, M. Clement, O. Klaric, T. S. Martin, X. d. Luria, V. Cho, H. Li, M. Shibata, A. Tebbenkamp, A. T. N. Ma, S. Han, W. Kim, S. K. Pochareddy, S. Phan, D. Q. Xing, X. Bao, Y. Xu, X. Gladwyn-Ng, I. E. Cullen, H. D. Paolino, A. Fenlon, L. R. Kozulin, P. Suarez, R. Risgaard, R. D. Gulden, F. O. Karger, A. Suzuki, I. K. Hirata, T. Gobeske, K. T. Richards, L. J. Sousa, A. M. M. Heng, J. I. Sestan, N. 2025-05-21 doi:10.1101/2025.05.20.652233 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Shared and distinct cortical mechanisms for working memory and decision-making. ]]> https://biorxiv.org/content/10.1101/2025.05.21.655340v1?rss=1 Seo, H. Lee, D. Murray, S. K. 2025-05-21 doi:10.1101/2025.05.21.655340 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ High-throughput iNaturalist image analysis reveals flower color divergence in Monarda fistulosa ]]> https://biorxiv.org/content/10.1101/2025.05.21.655392v1?rss=1 McKenzie, P. F. Church, S. H. Hopkins, R. 2025-05-26 doi:10.1101/2025.05.21.655392 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Unveiling functional-metabolic synergy in the healthy brain: multivariate integration of dynamic FDG-PET and resting-state fMRI ]]> https://biorxiv.org/content/10.1101/2025.05.21.655345v1?rss=1 Tarricone, C. Vallini, G. Baron, G. Silvestri, E. Volpi, T. Vlassenko, A. G. Goyal, M. S. Bertoldo, A. 2025-05-27 doi:10.1101/2025.05.21.655345 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Drought reduces formation, but enhances persistence, of mineral-associated organic matter in a grassland soil ]]> https://biorxiv.org/content/10.1101/2025.05.23.655838v1?rss=1 Sokol, N. Foley, M. Blazewicz, S. J. Didonato, N. Estera-Molina, K. Firestone, M. K. Greenlon, A. Hungate, B. A. Kew, W. Pasa-Tolic, L. Slessarev, E. Pett-Ridge, J. 2025-05-28 doi:10.1101/2025.05.23.655838 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Brain network dynamics reflect psychiatric illness status and transdiagnostic symptom profiles across health and disease ]]> https://biorxiv.org/content/10.1101/2025.05.23.655864v1?rss=1 Cocuzza, C. V. Chopra, S. Segal, A. Labache, L. Chin, R. Joss, K. Holmes, A. J. 2025-05-28 doi:10.1101/2025.05.23.655864 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease ]]> https://biorxiv.org/content/10.1101/2025.05.24.655962v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@178b77dorg.highwire.dtl.DTLVardef@569226org.highwire.dtl.DTLVardef@1951281org.highwire.dtl.DTLVardef@1f1e046_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPersistent expansion of diverse alloreactive T cell clones is a hallmark of severe GVHD C_LIO_LIDecompTCR reveals dynamic clonal expansion programs linked to GVHD severity and clinical outcome C_LIO_LICD8+ T cell clones exhibit phenotypic plasticity in vivo across intestinal tissue compartments in GVHD C_LIO_LIHigh-resolution spatial profiling shows CD8+ effector T cells localize near intestinal stem cell niches and drive epithelial injury in GVHD C_LI ]]> Shi, L. Uzuni, A. Wang, X. K. Pressler, M. Harle, D. W. Chakrabarti, S. Macedo, R. Belay, K. Gordillo, C. A. Raps, E. Zhang, J. Y. A. Nazaret, A. Fan, J. L. Jin, Y. Shen, X. Fuller, J. S. Azad, T. Huang, J. Chainani, P. Abrams, J. A. Del Portillo, A. Mapara, M. Y. Alhamar, M. Sykes, M. McFaline-Figueroa, J. Azizi, E. Reshef, R. 2025-05-28 doi:10.1101/2025.05.24.655962 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ Microglial SWELL1 Deficiency Drives Male-Specific Seizure Vulnerability but Paradoxical Neuroprotection through Impaired Phagocytosis ]]> https://biorxiv.org/content/10.1101/2025.05.26.656163v1?rss=1 Barath, A. S. Dheer, A. Dale, E. Goche, F. Nguyen, T. T. L. Montier, L. Akter, M. Peshoff, M. Qi, F. Umpierre, A. D. Bosco, D. B. Haruwaka, K. Sah, R. Wu, L.-J. 2025-05-29 doi:10.1101/2025.05.26.656163 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Notch as a Driver of Lineage Plasticity and Therapeutic Target in Enzalutamide-Resistant Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.05.26.656166v1?rss=1 Jiang, Y. Cheng, S. Li, L. Fraidenburg, M. Kim, I. Y. Deng, S. Mu, P. 2025-05-29 doi:10.1101/2025.05.26.656166 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Chemotaxis of branched cells in complex environments ]]> https://biorxiv.org/content/10.1101/2025.05.27.656457v1?rss=1 Liu, J. Ron, J. E. Rinaldi, G. Williantarra, I. Georgantzoglou, A. de Vries, I. Sixt, M. Sarris, M. Gov, N. 2025-05-29 doi:10.1101/2025.05.27.656457 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ AURKA inhibition amplifies DNA replication stress to foster WEE1 kinase dependency and synergistic antitumor effects with WEE1 inhibition in cancers ]]> https://biorxiv.org/content/10.1101/2025.05.28.656693v1?rss=1 Lee, J. W. Shi, J. Barrantes, J. Chaurasia, P. Kim, S. Cruz-Gomez, S. Yang, C. Gu, J. Zhao, H. Zhao, D. Schiff, B. Roche, A. Perry, E. B. Townsend, J. P. Kupfer, G. M. Politi, K. Golemis, E. Burtness, B. 2025-05-29 doi:10.1101/2025.05.28.656693 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ A PDZ-RapGEF promotes synaptic development in C. elegans through a Rap/Rac signaling pathway ]]> https://biorxiv.org/content/10.1101/2025.05.27.656318v1?rss=1 Lamb, R. Scales, M. Watkins, J. Werner, M. Cherra, S. J. 2025-05-30 doi:10.1101/2025.05.27.656318 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Using Fiji as a simplified tool for assessing alveolar chord length and septal thickness in neonatal pulmonary disease research ]]> https://biorxiv.org/content/10.1101/2025.05.29.656796v1?rss=1 Das, P. Martini, E. Aloudat, O. Tran, E. Rajendran, D. T. Agarwal, B. Homer, R. J. Bhandari, V. 2025-05-30 doi:10.1101/2025.05.29.656796 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire ]]> https://biorxiv.org/content/10.1101/2025.05.28.656470v1?rss=1 70% of light chain genes in the repertoire, directly impacting the amino acids of expressed light chain transcripts, including complementarity determining region domains. The genomic locations of usage - associated variants in both intergenic and coding regions indicated that IG polymorphisms modulate gene usage via diverse mechanisms, likely including the modulation of V(D)J recombination, heavy and light chain pairing biases, and transcription/translation. Finally, relative to IGL, IGK was characterized by more extensive linkage disequilibrium and genetic co-regulation of gene usage, illuminating differential regulatory and evolutionary features between the two light chain loci. These results firmly establish the critical contribution of IG light chain polymorphism in Ab repertoire diversity, with important implications for investigating Ab responses in health and disease. ]]> Engelbrecht, E. Rodriguez, O. L. Lees, W. Vanwinkle, Z. Shields, K. Schultze, S. Gibson, W. S. Smith, D. R. Jana, U. Saha, S. Peres, A. Yaari, G. Smith, M. L. Watson, C. T. 2025-06-01 doi:10.1101/2025.05.28.656470 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Basal forebrain volume is associated with cortical amyloid burden in cognitively unimpaired older adults at varying genetic risk for Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2025.05.28.656557v1?rss=1 Cho, G. Kelly, K. Toyonaga, T. Carson, R. E. Miner, B. Van Dyck, C. Mecca, A. P. O'Dell, R. 2025-06-01 doi:10.1101/2025.05.28.656557 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types ]]> https://biorxiv.org/content/10.1101/2025.05.31.657191v1?rss=1 Chen, H. Shu, J. Mudappathi, R. Li, E. Wang, P. Bergsagel, L. Yang, P. Sun, Z. Zhao, L. Shi, C. Townsend, J. P. Maley, C. Liu, L. 2025-06-03 doi:10.1101/2025.05.31.657191 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Postnatal Pulmonary Artery Development from Transcript to Tissue ]]> https://biorxiv.org/content/10.1101/2025.06.03.657639v1?rss=1 Schwarz, E. L. Ramachandra, A. B. Yeung, N. Manning, E. P. Weiss, D. Humphrey, J. D. 2025-06-06 doi:10.1101/2025.06.03.657639 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ A high-throughput, image-based assay to assess drug sensitivity of Acanthamoeba castellanii cysts. ]]> https://biorxiv.org/content/10.1101/2025.06.06.658337v1?rss=1 Flynn, C. A. Harmez, A. Colon-Rios, R. Flynn, W. F. Kazmierczak, B. I. 2025-06-06 doi:10.1101/2025.06.06.658337 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Examining the Role of Extrachromosomal DNA in 1,216 Lung Cancers ]]> https://biorxiv.org/content/10.1101/2025.06.03.657117v1?rss=1 Khandekar, A. Hoang, P. H. Luebeck, J. Diaz-Gay, M. Zhao, W. McElderry, J. P. Hartman, C. Miraftab, M. Lee, O. W. Barnao, K. M. Bergstrom, E. N. Yang, Y. Nowak, M. A. Rothman, N. Homer, R. Yang, S.-R. Lan, Q. Wedge, D. C. Yang, L. Chanock, S. J. Zhang, T. Alexandrov, L. B. Landi, M. T. 2025-06-07 doi:10.1101/2025.06.03.657117 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Dual inhibition of EGFR and PI3Kinase signaling in EGFR amplified triple negative breast cancer cells induces apoptosis and reduces tumor growth ]]> https://biorxiv.org/content/10.1101/2025.06.03.657674v1?rss=1 Wisniewski, D. J. Voeller, D. Addissie, Y. A. Deshmukh, S. K. Wangsa, D. Wangsa, D. Heselmeyer-Haddad, K. Wu, S. Lustberg, M. B. Sledge, G. W. Lipkowitz, S. 2025-06-07 doi:10.1101/2025.06.03.657674 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Single-cell imaging reveals spontaneous phenotypic sorting and bet-hedging in developing biofilms ]]> https://biorxiv.org/content/10.1101/2025.06.03.657734v1?rss=1 Tai, J.-S. B. Nam, K.-M. Li, C. Nijjer, J. Zhang, S. Waters, C. M. Yan, J. 2025-06-07 doi:10.1101/2025.06.03.657734 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma ]]> https://biorxiv.org/content/10.1101/2025.06.04.657841v1?rss=1 Xu, X. Liu, X. Dollar, J. Liu, X. Jasani, N. Posorske, B. Sriramareddy, S. N. Jarajapu, V. Kuznetsoff, J. N. Sinard, J. Bennett, R. L. Licht, J. Smalley, K. Harbour, J. W. Yu, X. Karreth, F. A. 2025-06-07 doi:10.1101/2025.06.04.657841 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ TITAN-RNA: A hybrid-capture sequencing panel detects known and unknown Flaviviridae for diagnostics and vector surveillance ]]> https://biorxiv.org/content/10.1101/2025.06.08.658352v1?rss=1 Murrell, C. M. Sabaawy, A. Wang, X. Hashimoto, N. Ceres, K. Sun, Y. Zehr, J. D. Lehane, A. Mader, E. Bailey, N. Lilly, M. V. Plimpton, L. Reboul, G. Brown, J. J. Sams, K. L. Singh, L. Seiz, E. Bourgikos, E. Vogels, C. B. F. Ciota, A. Schnurr, V. Grenier, J. K. Berthet, X. Bento, A. I. Harrington, L. C. Diuk-Wasser, M. Olarte-Castillo, X. Goodman, L. B. 2025-06-08 doi:10.1101/2025.06.08.658352 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ A Tunable Pulmonary Organoid Model Demonstrates Compositionally Driven Epithelial Plasticity and Immune Polarization ]]> https://biorxiv.org/content/10.1101/2025.06.05.658120v1?rss=1 Edelstein, S. E. Mizoguchi, S. Gracia, M. T. Wang, N. Lee, V. Kim, H. Haynes, C. Danelski, C. Tsuchiya, T. Sauler, M. Raredon, M. S. B. 2025-06-09 doi:10.1101/2025.06.05.658120 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ JIP4 deficiency causes a novel lysosome storage disease arising from impaired cystine efflux ]]> https://biorxiv.org/content/10.1101/2025.06.06.657909v1?rss=1 Nassar, L. M. Shi, x. Roczniak-Ferguson, A. Shen, H. Ferguson, S. M. 2025-06-09 doi:10.1101/2025.06.06.657909 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Canonical nuclear envelope protein emerin regulates structure and integrity of the erythrocyte plasma membrane ]]> https://biorxiv.org/content/10.1101/2025.06.06.658339v1?rss=1 O'Brien, B. Oliver, J. Thompson, E. N. Mayday, M. Y. Mancuso, R. Jha, A. Kwan, J. Bonne, G. Ben Yaou, R. Leturcq, F. Bai, S. Nottoli, T. Hwa, J. Krause, D. S. Gallagher, P. G. Gu, S. X. Martin, K. A. 2025-06-09 doi:10.1101/2025.06.06.658339 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ G1 and G2 ApolipoproteinL1 modulate macrophage inflammation and lipid accumulation through the polyamine pathway ]]> https://biorxiv.org/content/10.1101/2025.06.06.658371v1?rss=1 Liu, E. Wright, M. Kearney, A. O. Caza, T. Yang, J. Y. Garcia, V. Dadi, A. O. Ishibe, S. Chandel, N. S. Zhang, H. Benjamin Thorp, E. Lin, J. 2025-06-09 doi:10.1101/2025.06.06.658371 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Alveolar epithelial cell plasticity and injury memory in human pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.06.10.658504v1?rss=1 Adams, T. S. Schupp, J. C. Balayev, A. Khoury, J. Justet, A. Nikola, F. Laurens, D. S. J. Garcia, J. C. Zapata-Ortega, M. Panayiotis, B. V. McDonough, J. E. Ahangari, F. Koenigshoff, M. Ding, J. Homer, R. J. Rosas, I. O. Yan, X. Vanaudenaerde, B. M. Wuyts, W. A. Kaminski, N. 2025-06-10 doi:10.1101/2025.06.10.658504 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ The Susceptibility of Airborne SARS-CoV-2 to Far-UVC Irradiation ]]> https://biorxiv.org/content/10.1101/2025.06.09.658611v1?rss=1 Angel, D. M. Luhung, I. Santos Guedes de Sa, K. Peccia, J. 2025-06-11 doi:10.1101/2025.06.09.658611 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ NDR kinase SAX-1 controls dendrite branch-specific elimination during neuronal remodeling in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.06.09.658633v1?rss=1 Figueroa-Delgado, P. V. Yogev, S. 2025-06-12 doi:10.1101/2025.06.09.658633 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ A single-cell fixed RNA profiling of liver fibrosis progression and regression reveals SEMA4D and LMCD1 as key mediators of fibrogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.12.657772v1?rss=1 Pham, D. M. Thuy, L. T. T. Hoang, H. Nguyen, H. T. Pham, A. T. Ikenaga, H. Fuji, H. Yuasa, H. Matsubara, T. Vu, H. T. Yi, C. Yamagishi, R. Ohtani, N. Oikawa, D. Tokunaga, F. Kisseleva, T. Brenner, D. Iwakiri, Y. Sancho, J. G. Kawada, N. 2025-06-12 doi:10.1101/2025.06.12.657772 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Proximal Pulmonary Artery Stiffening as a Biomarker of Cardiopulmonary Aging ]]> https://biorxiv.org/content/10.1101/2025.06.10.658632v1?rss=1 De Man, R. Cai, Z. Doddaballapur, P. Guerrera, N. Lin, L. Justet, A. Abu Hussein, N. S. Cavinato, C. Raredon, M. S. B. Heerdt, P. Singh, I. Yan, X. Kang, M.-J. Bruns, D. R. Lee, P. J. Tellides, G. Humphrey, J. Kaminski, N. Ramachandra, A. B. Manning, E. P. 2025-06-15 doi:10.1101/2025.06.10.658632 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain ]]> https://biorxiv.org/content/10.1101/2025.06.10.658982v1?rss=1 180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. ]]> Petkova, M. D. Januszewski, M. Blakely, T. Herrera, K. J. Schuhknecht, G. F. P. Tiller, R. Choi, J. Schalek, R. L. Boulanger-Weil, J. Peleg, A. Wu, Y. Wang, S. Troidl, J. Kumar Vohra, S. Wei, D. Lin, Z. Bahl, A. Tapia, J. C. Iyer, N. Miller, Z. T. Hebert, K. B. Pavarino, E. C. Taylor, M. Deng, Z. Stingl, M. Hockling, D. Hebling, A. Wang, R. C. Zhang, L. L. Dvorak, S. Faik, Z. King, K. I. Goel, P. Wagner-Carena, J. Aley, D. Chalyshkan, S. Contreas, D. Li, X. Muthukumar, A. V. Vernaglia, M. S. Tapia Carrasco, T. Melnychuck, S. Yan, T. Dalal, A. DiMarti 2025-06-15 doi:10.1101/2025.06.10.658982 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Transient AMPK activation by nutrient stress of high fat diet preserves cardiac electrophysiological stability and protects against arrhythmias ]]> https://biorxiv.org/content/10.1101/2025.06.11.658631v1?rss=1 Rudokas, M. W. McKay, M. Wu, X. Granger, J. M. Williams, Y. Bogner, M. Kang, T. Seyfried, A. Toksoy, Z. Cacheux, M. Young, L. H. Akar, F. G. 2025-06-15 doi:10.1101/2025.06.11.658631 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Characterization of neuronal ensembles in a model of dual reward conditioned place preference ]]> https://biorxiv.org/content/10.1101/2025.06.11.659163v1?rss=1 Flom, L. T. Sandum, K. Hodgins, S. Johnson-Noya, S. Crouse, J. Zhang, Z. Bobadilla, A. C. 2025-06-15 doi:10.1101/2025.06.11.659163 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Two Specialized Intrinsic Cardiac Neuron Types Safeguard Heart Homeostasis and Stress Resilience ]]> https://biorxiv.org/content/10.1101/2025.06.13.659555v1?rss=1 Xu, Q. J. Applegate, M. C. Hsu, I.-U. Kogan, R. P. Hafez, O. A. Wang, R. L. Rios Coronado, P. E. Young, L. H. Zeng, X. Zhang, L. Chang, R. 2025-06-15 doi:10.1101/2025.06.13.659555 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Erratic Maternal Care Induces Avoidant-Like Attachment Deficits in a Mouse Model of Early Life Adversity ]]> https://biorxiv.org/content/10.1101/2025.06.13.659607v1?rss=1 MacDowell Kaswan, Z. Bowers, C. Teplyakov, I. Munoz-Martin, J. Ahmed, S. Kaffman, L. Giuliano, L. Dietrich, M. O. Kaffman, A. 2025-06-15 doi:10.1101/2025.06.13.659607 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Predicting Disease-Specific Histone Modifications and Functional Effects of Non-coding Variants by Leveraging DNA Language Models ]]> https://biorxiv.org/content/10.1101/2025.06.15.659749v1?rss=1 Wang, X. Pan, T. Chen, S. Webb, G. Jiang, Y. Rozowsky, J. Gerstein, M. Song, J. 2025-06-17 doi:10.1101/2025.06.15.659749 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ In-depth analysis of the tear fluid glycoproteome reveals diverse lacritin glycosylation and spliceoforms ]]> https://biorxiv.org/content/10.1101/2025.06.13.659589v1?rss=1 Chang, V. Mahoney, K. E. Lian, I. Chen, R. Chung, N. Paaske Utheim, T. Karlsson, N. G. Malaker, S. A. 2025-06-18 doi:10.1101/2025.06.13.659589 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories ]]> https://biorxiv.org/content/10.1101/2025.06.17.659820v1?rss=1 Sun, L. Qin, W. Liang, X. Wang, C. Men, W. Duan, Y. Fan, X.-R. Cai, Q. Qiu, S. Wang, M. Gong, Q. Tian, Y. Liang, P. Liu, Z. Zhang, X. Song, H. Ye, Z. Zhang, P. Dong, Q. Tao, S. Zhu, W. Zhang, J. Xie, F. Feng, J. Zhang, J. Liu, C. Qian, Q. Zhang, B. Meng, M. Hu, L. Gao, J.-H. Jiang, T. Zhu, X. Zhang, Y. Liu, L. Liu, H. Liao, W. Wang, D. Wang, H. Guo, T. Dai, Z. Lui, S. Xu, K. Li, L. Xie, P. Feng, C. Cui, G. Wu, J. Yin, X. Ding, G. Xian, J. Zhao, L. Lu, J. Liu, Z. Han, Y. Yuan, Z. Zhang, X. Si, T. Zhou, F. Bi, Y. Wu, D. Gao, F. Wang, 2025-06-18 doi:10.1101/2025.06.17.659820 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Almost Free Enhancement of Multi-Population PRS: From Data-Fission to Pseudo-GWAS Subsampling ]]> https://biorxiv.org/content/10.1101/2025.06.16.659952v1?rss=1 Xu, L. Dong, Y. Zeng, X. Bian, Z. Zhou, G. Guan, L. Zhao, H. 2025-06-20 doi:10.1101/2025.06.16.659952 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Single cell transcriptomics in a treatment-segregated cohort exposes a STAT3-regulated therapeutic gap in idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.06.16.659944v1?rss=1 McKenna, N. Ochsner, S. A. Cohen, A. W. Cala-Garcia, J. Echartea, M. E. Grimm, S. L. Poli, F. Castillo, R. C. Zuluaga, J. D. Poli, S. Adams, T. S. Pineda, R. Moss, B. Ryter, S. Pillich, R. T. Villalba, J. Kato, K. Hecker, L. Celada, L. J. Sauler, M. Koenigshoff, M. Kaminski, N. Raby, B. Agarwal, S. K. Tsoyi, K. Coarfa, C. Rosas, I. 2025-06-21 doi:10.1101/2025.06.16.659944 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Parallel emergence of perisomatic inhibition and ripples in the developing hippocampal circuit ]]> https://biorxiv.org/content/10.1101/2025.06.17.660075v1?rss=1 Da Silva, A. F. G. Dubanet, O. Rouault, H. Leinekugel, X. 2025-06-21 doi:10.1101/2025.06.17.660075 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Growth Arrest of Thoracic Aortic Aneurysms in Aging Marfan Mice ]]> https://biorxiv.org/content/10.1101/2025.06.18.660413v1?rss=1 Weiss, D. Means, C. Mays, G. Yeung, N. Cavinato, C. Manning, E. Lam, T. T. Humphrey, J. 2025-06-24 doi:10.1101/2025.06.18.660413 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Phosphoinositide 3-kinase regulates wild-type RAS signaling to confer resistance to KRAS inhibition ]]> https://biorxiv.org/content/10.1101/2025.06.20.660715v1?rss=1 90% of pancreatic ductal adenocarcinomas (PDAC) on oncogenic KRAS mutations, resistance to KRAS inhibition remains a serious obstacle. We show here that phosphoinositide 3-kinase (PI3K) plays a major role in this resistance through upstream activation of wild-type RAS signaling - beyond its known KRAS effector function. Combining proximity labeling, CRISPR screens, live-cell imaging, and functional assays we found that PI3K orchestrates phosphoinositide-mediated GAB1 recruitment to the plasma membrane, nucleating assembly of RAS signaling complexes that activate mitogen-activated protein kinase (MAPK) in an EGFR/SHP2/SOS1-dependent manner. We further demonstrate that inhibiting PI3K enhances sensitivity to mutant-specific KRAS inhibitors in PDAC cells, including cells with clinically identified PIK3CA mutations. Our findings refine RAS-PI3K signaling paradigms, reveal that PI3K-driven wild-type RAS activation drives resistance to KRAS inhibition, and illuminate new avenues for augmenting KRAS-targeted therapies in PDAC. ]]> Ge, X. Singh, J. Li, W. Markham, C. S. Ruiz, C. F. Bhattacharyya, M. Liu, Y. Muzumdar, M. D. 2025-06-25 doi:10.1101/2025.06.20.660715 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Biological point-light displays scanning by the principal eyes of a jumping spider ]]> https://biorxiv.org/content/10.1101/2025.06.23.661007v1?rss=1 De Agro, M. Winsor, A. Walsh, W. Shamble, P. S. Jakob, E. 2025-06-25 doi:10.1101/2025.06.23.661007 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Scanning for Representation: A Scoping Review of Racial and Ethnic Diversity in MRI Studies of the Maternal Brain ]]> https://biorxiv.org/content/10.1101/2025.06.20.660240v1?rss=1 Orchard, E. R. Murray, C. L. Wall, K. M. Levy, J. C. P. Shin, J. Y. Gaebler, C. G. Hart-Derrick, V. R. Ayala, K. Adodo, A. Day, M. J. Funaro, M. C. Guan, K. Parker, T. C. Ricard, J. A. Penner, F. Yatziv, T. Rutherford, H. J. V. 2025-06-26 doi:10.1101/2025.06.20.660240 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Stiffness sensing fuels matrix-driven metabolic reboot for kidney repair and regeneration ]]> https://biorxiv.org/content/10.1101/2025.06.22.660927v1?rss=1 Gui, Y. Wang, Y. Li, W. Liu, J.-J. Zheng, K. Li, J. Shaffer, H. Jones, C. Mallari, S. Yu, Y. Liu, S. Liu, Y. Zhou, D. 2025-06-26 doi:10.1101/2025.06.22.660927 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ CellSpliceNet: Interpretable Multimodal Modeling ofAlternative Splicing Across Neurons in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.06.22.660966v1?rss=1 Afrasiyabi, A. Kovalic, J. Liu, C. Castro, E. Weinreb, A. Varol, E. Miller, D. Hammarlund, M. Krishnaswamy, S. 2025-06-26 doi:10.1101/2025.06.22.660966 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ EVscope: A Comprehensive Bioinformatics Pipeline for Accurate and Robust Analysis of Total RNA Sequencing from Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2025.06.24.660984v1?rss=1 Zhao, Y. Chintalapudi, H. Xu, Z. Liu, W. Hu, Y. Grassin, E. Song, M. Hong, S. Lee, L. P. Dong, X. 2025-06-27 doi:10.1101/2025.06.24.660984 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Functional Inputs to the Subgenual Cingulate Cortex Distinguish Neurotypical Individuals with Severe and Mild Depressive Problems: Granger Causality and Clustering Analyses ]]> https://biorxiv.org/content/10.1101/2025.06.25.661556v1?rss=1 Li, H.-T. Chen, Y. Chaudhary, S. Ide, J. S. Li, C.-S. R. 2025-06-27 doi:10.1101/2025.06.25.661556 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Competing Programs Shape Cortical Sensorimotor-Association Axis Development ]]> https://biorxiv.org/content/10.1101/2025.06.26.660775v1?rss=1 Tsyporin, J. Zhang, M. Qi, C. Segal, A. Finn, T. Kim, H. Choi, S.-H. Li, X. Bandiera, S. Pavlovic, I. Kim, S. K. K. Shibata, A. Onishi, K. Zhang, Z. Hammarlund, E. Su, G. Salla, N. Kachko, J. Hawley, C. Li, S. Doyle, D. Z. Peng, X. Nottoli, T. Ruiz-Reig, N. Tissir, F. Nakagawa, Y. Herzog, E. Ma, S. Gobeske, K. Pattabiraman, K. Shimogori, T. Duque, A. Fornito, A. Huang, H. Shibata, M. Chen, B. Sestan, N. 2025-06-27 doi:10.1101/2025.06.26.660775 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Dynamics and Regulation of mRNA Cap Recognition by Human eIF4F ]]> https://biorxiv.org/content/10.1101/2025.06.26.660926v1?rss=1 Hong, H. Guevara, M. G. Li, S. Liu, Y. Huang, A. N. Lin, E. Neal, A. Xu, D. Hai, R. Zandi, R. O'Leary, S. E. 2025-06-27 doi:10.1101/2025.06.26.660926 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut ]]> https://biorxiv.org/content/10.1101/2025.06.28.662088v1?rss=1 Peng, D. Marrogi, E. Nelson, E. Liu, Q. Rinvee, T. A. de Vries, L. E. Thornburg, K. Singh, N. Shaw, W. R. Catteruccia, F. 2025-06-29 doi:10.1101/2025.06.28.662088 Cold Spring Harbor Laboratory Press 2025-06-29 <![CDATA[ Red Blood Cell Transfusion is a Non-Canonical Immune Stimulus Characterized by the Suboptimal Induction of CD4+ T Cell Help ]]> https://biorxiv.org/content/10.1101/2025.06.26.661795v1?rss=1 Medved, J. Arneja, A. Shah, N. Hester, B. N. Burnett, E. D. Boscia, A. R. Moscovich, T. C. Swain, W. R. Kodali, A. S. Chandler, A. Thorkelsdottir, G. A. Schwartzschild, C. J. W. Muppidi, R. J. Cherkaoui, I. Strand, J. M. Trubetskoy, M. Stern-Green, E. A. Tarrah, S. N. Li, A. Niebuhr, C. S. Salazar, J. E. Sannthanakrishnan, M. Zimring, J. C. Gorham, J. D. Hudson, K. E. Hendrickson, J. E. Luckey, C. J. 2025-06-30 doi:10.1101/2025.06.26.661795 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology ]]> https://biorxiv.org/content/10.1101/2025.06.27.661875v1?rss=1 Mukherjee, S. Patiyal, S. Pal, L. R. Chang, T. Biswas, S. Dhruba, S. R. Stemmer, A. Singh, A. Yousefi-Rad, A. Chen, T.-H. Wang, B. Marino, D. Shon, W. Yuan, Y. Faries, M. Hamid, O. Reckamp, K. Waissengrin, B. Ornelas, B. Chu, P.-Y. Boudjadi, S. Ley, L. Akbulut, D. Ahmar, N. E. Signoretti, S. Braun, D. A. Joo, H. Kim, H. Osipov, A. Figlin, R. A. Bar, J. Barshack, I. Day, C.-P. Sargsyan, K. Apolo, A. B. Aldape, K. Yang, M.-H. Atkins, M. B. Ronai, Z. A. Hoang, D.-T. Ruppin, E. 2025-06-30 doi:10.1101/2025.06.27.661875 Cold Spring Harbor Laboratory Press 2025-06-30 <![CDATA[ AMPK alters proteasome phosphorylation status and prevents persistent proteasome condensates ]]> https://biorxiv.org/content/10.1101/2025.07.01.662652v1?rss=1 Li, J. Butcher, C. VanderVen, K. Hochstrasser, M. 2025-07-02 doi:10.1101/2025.07.01.662652 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Latrophilin mediates flow activation of Notch to control vascular endothelial phenotype and atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.07.01.662676v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@11e055forg.highwire.dtl.DTLVardef@1f2a5acorg.highwire.dtl.DTLVardef@15af06aorg.highwire.dtl.DTLVardef@15dd97d_HPS_FORMAT_FIGEXP M_FIG Latrophilin-Notch axis to suppress vascular inflammation C_FIG ]]> Tanaka, K. Chen, M. Chanduri, M. V. Zhang, H. Fernandez-Hernando, C. Schwartz, M. A. 2025-07-02 doi:10.1101/2025.07.01.662676 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ High-fat diet ablates an insulin-responsive pool of GLUT4 glucose transporters in skeletal muscle ]]> https://biorxiv.org/content/10.1101/2025.06.29.662135v1?rss=1 Hu, Y. Brown, S. N. Nasiri, A. Li, D. T. Wang, H. Cartee, G. D. Shulman, G. I. Bogan, J. S. 2025-07-03 doi:10.1101/2025.06.29.662135 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Latrophilin-2 Orchestrates Endothelial Flow-Mediated Smad1/5 Activation via Endoglin and Shank3 ]]> https://biorxiv.org/content/10.1101/2025.06.30.662394v1?rss=1 Tanaka, K. Chanduri, M. V. Chen, M. Prendergast, A. Mani, A. Schwartz, M. A. 2025-07-03 doi:10.1101/2025.06.30.662394 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Epidermal Stem Cells Control Periderm Injury Repair via Matrix-Driven Specialization of Intercellular Junctions ]]> https://biorxiv.org/content/10.1101/2025.07.02.662640v1?rss=1 He, H. M. Boraas, L. C. Bell, J. M. Gong, X. Iannaccone, S. L. Wen, Z. Carson, M. Mak, M. Sumigray, K. Nicoli, S. 2025-07-03 doi:10.1101/2025.07.02.662640 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Phase Separation Oppositely Modulates G-quadruplex and i-Motif DNA Folding in the Nuclei of Living Cells ]]> https://biorxiv.org/content/10.1101/2025.06.30.661982v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@e76eedorg.highwire.dtl.DTLVardef@23aefforg.highwire.dtl.DTLVardef@b6117aorg.highwire.dtl.DTLVardef@135736a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Patel, B. Hoang, C. Yoo, H. Davis, C. 2025-07-04 doi:10.1101/2025.06.30.661982 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Low and high frequency signatures of impaired consciousness in temporal lobe seizures ]]> https://biorxiv.org/content/10.1101/2025.07.01.662627v1?rss=1 Yadav, T. Litvinov, B. P. Culler, G. W. Kumar, A. Khalaf, A. Song, Y. Brinkmann, B. H. Joseph, B. Ahmad, Z. Gunawardane, N. Ramirez, V. C. Quraishi, I. H. START Clinical Trial Research Consortium, Jobst, B. C. Worrell, G. Blumenfeld, H. 2025-07-04 doi:10.1101/2025.07.01.662627 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Prenatal cannabis smoke exposure alters placental development in a murine model of pregnancy ]]> https://biorxiv.org/content/10.1101/2025.06.28.662155v1?rss=1 Podinic, T. Sunil, M. MacAndrew, A. Monaco, C. Lee, G. Lockington, C. Lucas, A.-M. Tomy, T. Kasinska, J. Jamshed, L. Holloway, A. Petrik, J. Tomy, G. Ratcliffe, E. Raha, S. 2025-07-05 doi:10.1101/2025.06.28.662155 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ An expanded reference catalog of translated open reading frames for biomedical research ]]> https://biorxiv.org/content/10.1101/2025.07.03.662928v1?rss=1 Chothani, S. Ruiz-Orera, J. Tierney, J. A. S. Clauwaert, J. Deutsch, E. W. Alba, M. M. Aspden, J. L. Baranov, P. V. Bazzini, A. A. Bruford, E. A. Brunet, M. A. Cardon, T. Carvunis, A.-R. Casola, C. Choudhary, J. S. Dean, K. Faridi, P. Fierro-Monti, I. Fournier, I. Frankish, A. Gerstein, M. Hubner, N. Jiang, Y. Kellis, M. Kok, L. W. Martinez, T. F. Menschaert, G. Ni, P. Orchard, S. Roucou, X. Rozowsky, J. Salzet, M. Siragusa, M. Slavoff, S. Swirski, M. I. Valen, E. Vizcaino, J. A. Wacholder, A. Wu, W. Xie, Z. Yang, Y. T. Moritz, R. L. Mudge, J. van Hee 2025-07-07 doi:10.1101/2025.07.03.662928 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Inclusion of the ζ-chain drives phosphotyrosine signalling in CD19-CAR T cells ]]> https://biorxiv.org/content/10.1101/2025.07.04.663030v1?rss=1 Callahan, A. Puterbaugh, R. Z. Ro, T. Zhang, X. Su, X. Salomon, A. 2025-07-07 doi:10.1101/2025.07.04.663030 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis ]]> https://biorxiv.org/content/10.1101/2025.07.06.663336v1?rss=1 Ruwisch, J. Cazes, A. Leiber, L. M. Borie, R. Neubert, L. Christian, L. De Montpreville, V. T. Szmul, A. Moussa, F. Verleden, S. Gaedcke, S. Hegermann, J. Fuge, J. Ballmaier, M. Kamp, J. C. Greer, M. Braubach, P. Werlein, C. Ius, F. Graalmann, T. Aburahma, K. de Sadaleer, L. Egashira, R. Ackermann, M. Yamda, D. Hoeper, M. Falk, C. Gottlieb, J. Schiller, H. Vanaudenaerde, B. Seeliger, B. Debray, M.-P. Bernaudin, J. F. Knudsen, L. Bergot, E. Jacob, J. Mal, H. Jonigk, D. Dettmer, S. Mordant, P. Prasse, A. Fadel, E. Wuyts, W. Crestani, B. Kaminski, N. J 2025-07-08 doi:10.1101/2025.07.06.663336 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis ]]> https://biorxiv.org/content/10.1101/2025.07.08.662037v1?rss=1 Schroer, H. W. Beghini, F. Garay, J. A. R. Christakis, N. A. Bosch, D. E. 2025-07-08 doi:10.1101/2025.07.08.662037 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ T cell protrusions enable fast, localised initiation of CAR signalling ]]> https://biorxiv.org/content/10.1101/2025.07.08.662959v1?rss=1 Rodilla-Ramirez, C. Carai, G. Fox, E. Zehtabian, A. Adam, H. Dallio, K. Ewers, H. Su, X. Bottanelli, F. 2025-07-09 doi:10.1101/2025.07.08.662959 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ EED Maintains the Small Cell Lung Cancer Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation ]]> https://biorxiv.org/content/10.1101/2025.07.07.663486v1?rss=1 Li, Y. Laimon, Y. N. Cho, H. Vivero, M. De Oliveira, G. R. Delcea, A. Savla, V. Chen, Y. Durmaz, Y. T. Qiu, X. Kukreja, S. Li, R. El Zarif, T. Lu, W. Van Orden, M. Berchuck, J. E. Bronson, R. T. Li, S. Ji, H. Politi, K. Freedman, M. L. Long, H. W. Signoretti, S. Oser, M. G. 2025-07-10 doi:10.1101/2025.07.07.663486 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ A yeast model reveals the SMAD3 nuclear import mechanism ]]> https://biorxiv.org/content/10.1101/2025.07.09.663975v1?rss=1 Gonzalez, D. P. Emokpae, M. C. Lusk, C. P. Khokha, M. K. 2025-07-11 doi:10.1101/2025.07.09.663975 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Macropinocytosis inhibition attenuates pro-fibrotic responses in lung fibroblasts and pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/2025.07.09.663937v1?rss=1 Rosas, I. McDowell-Sanchez, A. Sanchez, S. Cala-Garcia, J. Cohen, A. W. Echartea, M. Ochsner, S. A. Kraushaar, D. Celada, L. J. Sun, D. Polverino, F. Coarfa, C. McKenna, N. Tsoyi, K. 2025-07-14 doi:10.1101/2025.07.09.663937 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas ]]> https://biorxiv.org/content/10.1101/2025.07.11.664189v1?rss=1 20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy. ]]> Chowdhury, T. Tesileanu, C. M. S. Kocakavuk, E. Johnson, K. C. Lee, J. Erson-Omay, Z. Heo, C. Aldape, K. Amin, S. B. Anderson, K. J. Ashley, D. M. Barnholtz-Sloan, J. S. Brat, D. J. Brodbelt, A. R. Castro, A. V. Claus, E. B. Connelly, J. M. Costello, J. Datta, I. Elliott, C. Finocchiaro, G. French, P. J. Gan, H. K. Garofano, L. Ghospurkar, P. L. Golebiewska, A. Gundla, P. S. Hermes, B. Hong, C. Hoogstrate, Y. Horbinski, C. Huse, J. T. Iavarone, A. Karadag, C. Khasraw, M. Kouwenhoven, M. C. LaViolette, P. S. Li, K. Lowman, A. McCortney, K. Moon, H.-E. Na 2025-07-15 doi:10.1101/2025.07.11.664189 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Conformations and sequence determinants in the lipid binding of an adhesive peptide derived from Vibrio cholerae biofilm ]]> https://biorxiv.org/content/10.1101/2025.07.14.664771v1?rss=1 Huang, X. Prasad, R. Saluja, S. Yang, Y. Yan, Q. Shuster, S. O. Olson, R. Lin, C. Davis, C. M. Jiang, X. Zhou, H.-X. Yan, J. 2025-07-15 doi:10.1101/2025.07.14.664771 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Gut microbiota of dogs with cancer receiving anti-EGFR/HER2 immunization reveals potential biomarkers of patient survival ]]> https://biorxiv.org/content/10.1101/2025.07.13.663784v1?rss=1 Rodrigues, R. R. Karumuru, V. Nuss, S. Elliott, M. Shriver, I. Chao, C.-M. Doyle, H. A. Tripp, C. Mamula, M. J. Dzutsev, A. Morgun, A. Shulzhenko, N. 2025-07-16 doi:10.1101/2025.07.13.663784 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Dual Inhibition of CDK4/6 and mTORC1 Establishes a Preclinical Strategy for Translocation Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2025.07.11.663903v1?rss=1 Gupta, S. Khanna, P. Saad, E. Saliby, R. M. AbuHammad, S. Li, J. Li, B. Konda, P. Ahmad, U. A. Sadagopan, A. Xu, Q. Bakouny, Z. Xu, W. Srinivasan, R. Choueiri, T. K. Viswanathan, S. R. 2025-07-17 doi:10.1101/2025.07.11.663903 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ METTL3 promotes cell cycle progression via activation of transcriptional elongation. ]]> https://biorxiv.org/content/10.1101/2025.07.12.664541v1?rss=1 Alarcon, C. 2025-07-17 doi:10.1101/2025.07.12.664541 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Diet context gates AgRP neuron involvement in Semaglutide-induced weight loss ]]> https://biorxiv.org/content/10.1101/2025.07.13.664597v1?rss=1 d'Avila, M. Collado-Perez, R. Liu, Z. Horvath, T. 2025-07-17 doi:10.1101/2025.07.13.664597 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ A T-cell Intrinsic Role for APOL1 Risk Alleles in Allograft Rejection ]]> https://biorxiv.org/content/10.1101/2025.07.14.664793v1?rss=1 Pell, J. Tanvir, E. M. Sun, Z. Chernova, I. Reghuvaran, A. Nagata, S. Guerra, M. Choi, J. Chaar, S. A. Mizuno, H. Dong, K. Tian, X. Ishibe, R. Franchin, B. Cravedi, P. Kumar, A. Barsotti, G. Shi, H. Kumar, B. D. Song, W. He, C. Pober, J. S. Somlo, S. Gibson, I. W. Popik, W. Zhang, Z. Craft, J. Azzi, J. Murakami, N. Ishibe, S. Heeger, P. Menon, M. C. 2025-07-18 doi:10.1101/2025.07.14.664793 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ QOBRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design ]]> https://biorxiv.org/content/10.1101/2025.07.15.665010v1?rss=1 Yu, Y. Calcagno, F. Li, H. Batista, V. S. 2025-07-18 doi:10.1101/2025.07.15.665010 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ A live tumor fragment platform to assess immunotherapy response in core needle biopsies while addressing challenges of tumor heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.07.18.663728v1?rss=1 Ramasubramanian, T. S. Adstamongkonkul, P. Scribano, C. Johnson, C. Caenepeel, S. Hrycyniak, L. Vedder, L. C. Dana, N. Baltes, C. Browning, T. Chen, Y.-I. Dietz, T. Flietner, E. Kaplewski, N. Kellner, A. Korrer, M. Liu, C. Marhefke, N. McDonnell, P. Nasreen, A. Pope, V. Prasad, A. Richardson, J. Schneider, S. Schultz, M. Sood, C. Sunil, A. von Euw, E. Wait, E. Wargowski, E. Advani, P. Broome, B. Bruckbauer, A. Godwin, A. Kokabi, N. Martin, R. Robaina, M. Toia, G. Routh, J. Friedl, A. Eliceiri, K. Szulczewski, M. Johnson, S. Oliner, J. Galon, J. Capi 2025-07-18 doi:10.1101/2025.07.18.663728 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Constraints and tunability of antigen-agnostic memory durability ]]> https://biorxiv.org/content/10.1101/2025.07.18.663399v1?rss=1 Tripathi, S. Liu, C. Lau, W. W. Sparks, R. Tsang, J. S. 2025-07-19 doi:10.1101/2025.07.18.663399 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ mGluR4-Npdc1 complex mediates α-synuclein fibril-induced neurodegeneration ]]> https://biorxiv.org/content/10.1101/2025.07.16.665194v1?rss=1 Perez-Canamas, A. Chen, M. Almandoz-Gil, L. Khan, N. Tang, S. J. Ho, A. Gunther, E. C. Strittmatter, S. M. 2025-07-21 doi:10.1101/2025.07.16.665194 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Structural brain correlates of poor reading comprehension ]]> https://biorxiv.org/content/10.1101/2025.07.23.666369v1?rss=1 Mahaffy, K. E. Koirala, N. Kleinman, D. Landi, N. 2025-07-24 doi:10.1101/2025.07.23.666369 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Context-Dependent Fitness Outcomes of Helping in the Cooperatively-Breeding Florida Scrub-Jay (Aphelocoma coerulescens) ]]> https://biorxiv.org/content/10.1101/2025.07.21.666021v1?rss=1 Summers, J. Jones, B. S. C. L. Cosgrove, E. J. Bakley, T. D. Barve, S. Bowman, R. Fitzpatrick, J. W. Chen, N. 2025-07-25 doi:10.1101/2025.07.21.666021 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Copy number variation facilitates rapid toggling between ecological strategies ]]> https://biorxiv.org/content/10.1101/2025.07.22.666191v1?rss=1 Abdul-Rahman, F. Gresham, D. 2025-07-26 doi:10.1101/2025.07.22.666191 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Consensus DNA Inhibits p53 Aggregation but Fails to Rescue Mutants ]]> https://biorxiv.org/content/10.1101/2025.07.24.665437v1?rss=1 Steinsaltz, M. Gomes, G.-N. W. Levine, Z. A. 2025-07-26 doi:10.1101/2025.07.24.665437 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ FGF13 regulates cardiomyocyte impulse propagation via Cx43 trafficking independent of voltage-gated sodium channels ]]> https://biorxiv.org/content/10.1101/2025.07.23.666473v1?rss=1 Das, L. T. Malvezzi, M. Gade, A. R. Matsui, M. McKay, M. Wei, E. Q. Kushner, J. Chen, B.-X. Zelich, M. Mazdisnian, K. DiStefano, I. Roybal, D. D. Yang, L. Stoll, L. Lo, J. C. Kalocsay, M. Akar, F. G. Marx, S. O. Pitt, G. S. 2025-07-27 doi:10.1101/2025.07.23.666473 Cold Spring Harbor Laboratory Press 2025-07-27 <![CDATA[ Metrics for studying the porous void space of packed particles ]]> https://biorxiv.org/content/10.1101/2025.07.23.666315v1?rss=1 Riley, L. Lee, E. C. Cheng, P. Adrianzen Alvarez, D. Segura, T. 2025-07-28 doi:10.1101/2025.07.23.666315 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Oscillatory signal decoding within the ERK cascade ]]> https://biorxiv.org/content/10.1101/2025.07.24.666680v1?rss=1 Ganesan, A. Lee, H. N. Tenner, B. Mehta, S. Levchenko, A. Zhang, J. 2025-07-28 doi:10.1101/2025.07.24.666680 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Distinct Roles of CaMKII in Synaptic Vesicle Dynamics at Zebrafish Retinal Rod Bipolar Ribbon Synapses ]]> https://biorxiv.org/content/10.1101/2025.07.27.667036v1?rss=1 Boff, J. M. Rameshkumar, N. Khamrai, M. Seetharaman, J. Olmos-Carrenno, C. L. Chudasama, N. Yoshimatsu, T. Zenisek, D. Tavalin, S. J. Vaithianathan, T. 2025-07-28 doi:10.1101/2025.07.27.667036 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Compositionality of social gaze in the prefrontal-amygdala circuits ]]> https://biorxiv.org/content/10.1101/2025.07.28.667161v1?rss=1 Qi, G. Dal Monte, O. Fan, S. Chang, S. W. C. 2025-07-29 doi:10.1101/2025.07.28.667161 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Regulatory Plasticity and Metabolic Trade-offs Drive Adaptive Evolution of Alternative Flagellar Configurations in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.07.29.667523v1?rss=1 Migueles-Lozano, A. Asp, M. Rocha, S. T. Li, J. Fanouraki, G. Sun, A. D. Zhang, L. Waldbauer, J. R. Hong, J. Shrivastava, A. Yan, J. Mukherjee, S. 2025-07-29 doi:10.1101/2025.07.29.667523 Cold Spring Harbor Laboratory Press 2025-07-29 <![CDATA[ Antibodies targeting HSV glycoprotein B require effector functions to protect neonatal mice ]]> https://biorxiv.org/content/10.1101/2025.07.25.666806v1?rss=1 Slein, M. D. Jimenez, L. M. Backes, I. M. Turnbaugh, E. M. Garland, C. R. MacDonald, S. W. Balazs, A. B. Leib, D. A. Ackerman, M. E. 2025-07-30 doi:10.1101/2025.07.25.666806 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Scalable automated segmentation quantifies mitochondrial proteins and morphology at the nanoscale ]]> https://biorxiv.org/content/10.1101/2025.07.28.667278v1?rss=1 Tian, Y. Sauer, A. Dmitrieva, M. Han, H. Mekbib, H. T. Bao, Y. Guo, X. Chen, T.-m. Safirstein, R. Desir, G. Rittscher, J. Bewersdorf, J. 2025-07-30 doi:10.1101/2025.07.28.667278 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Glucose Metabolism echoes Long-Range Temporal Correlations in the Human Brain ]]> https://biorxiv.org/content/10.1101/2025.07.29.667370v1?rss=1 Facca, M. Ridolfo, A. Celli, M. Tarricone, C. Mazzonetto, I. Volpi, T. Vlassenko, A. G. Goyal, M. S. Corbetta, M. Bertoldo, A. 2025-07-30 doi:10.1101/2025.07.29.667370 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Psilocybin Prolongs the Neurovascular Coupling Response in Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.07.25.666803v1?rss=1 Zirkel, R. T. Isaacson, M. Liao, C. Yi, M. Yamaguchi, K. Rivera, D. Kuceyeski, A. Nishimura, N. Kwan, A. C. Schaffer, C. B. 2025-07-31 doi:10.1101/2025.07.25.666803 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ NAPRT expression and epigenetic regulation in pediatric rhabdomyosarcoma as a potential biomarker for NAMPT inhibition ]]> https://biorxiv.org/content/10.1101/2025.07.28.667284v1?rss=1 Kim, A. Bhardwaj, P. Heer, C. D. Zhao, S. J. Lucas, K. N. Noronha, K. J. Friedman, S. Morotti, R. Sundaram, R. K. Rehman, S. Bhatt, D. Dela Cruz, F. S. Feinberg, T. Ramakrishnan, S. Xue, W. Barkauskas, D. A. Hall, D. Shern, J. F. Barr, F. G. Yi, J.-S. Spurrier, J. Yu, A. Brenner, C. Heske, C. M. Vasquez, J. C. 2025-07-31 doi:10.1101/2025.07.28.667284 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages ]]> https://biorxiv.org/content/10.1101/2025.07.29.667423v1?rss=1 Gaeta, I. M. Du, S. Villeneuve, C. Gonzalez, D. G. Matte-Martone, C. Ganesan, S. Simpson, D. Moore, J. L. Kam, C. Y. Gallini, S. Wei, H. Bertillot, F. Zeuschner, D. Gonzalez, L. E. Sumigray, K. Wickstrom, S. A. Greco, V. 2025-07-31 doi:10.1101/2025.07.29.667423 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Detecting Nuclear Pore Complex assembly in living cells ]]> https://biorxiv.org/content/10.1101/2025.07.30.667432v1?rss=1 Veldsink, A. C. Fischer, J. S. Terpstra, H. M. Mannino, P. de Lange, E. M. Hell, S. van Benthem, K. J. Saba, L. J. Steen, A. Vlijm, R. Heinemann, M. Weis, K. Lusk, C. P. Veenhoff, L. M. 2025-07-31 doi:10.1101/2025.07.30.667432 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species ]]> https://biorxiv.org/content/10.1101/2025.07.28.667252v1?rss=1 Teixeira, M. Souque, C. Worby, C. J. Commins, N. Smith, J. T. Miklos, A. M. Abeel, T. Earl, A. M. Manson, A. L. 2025-08-01 doi:10.1101/2025.07.28.667252 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ miR-146a-3p packaged in small extracellular vesicles triggers fetal membrane inflammation in response to viral dsRNA through activation of Toll-like Receptor 7 and 8 ]]> https://biorxiv.org/content/10.1101/2025.07.29.667498v1?rss=1 Georges, H. M. Fischer, A. C. Casanova, P. Abrahams, V. M. 2025-08-01 doi:10.1101/2025.07.29.667498 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Temporal autocorrelation increases temperature-driven extinction risk by clustering stressful conditions ]]> https://biorxiv.org/content/10.1101/2025.07.29.667527v1?rss=1 Robey, A. J. Kummel, M. T. Vasseur, D. A. 2025-08-01 doi:10.1101/2025.07.29.667527 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Imagined Speech Reconstruction with 3D Neural Metabolism and Large Language Model Integration ]]> https://biorxiv.org/content/10.1101/2025.07.30.667805v1?rss=1 Rajagopal, G. Chaudhari, A. Larocco, J. Xue, J. Zachariah, E. Varanasi, S. Rothman, D. 2025-08-01 doi:10.1101/2025.07.30.667805 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Robust and replicable effects of ageing on resting state brain electrophysiology measured with MEG. ]]> https://biorxiv.org/content/10.1101/2025.08.01.668093v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@97954dorg.highwire.dtl.DTLVardef@1cb1776org.highwire.dtl.DTLVardef@717101org.highwire.dtl.DTLVardef@1b224fd_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThere is a strong effect of ageing across the adult lifespan on neuronal oscillations across a range of frequencies and spatial locations. C_LIO_LIThe effect is replicable across multiple open-access datasets. C_LIO_LIThe effect is robust to a range of sources of inter-subject variability. C_LIO_LIThe age effect has heterogeneous effect size across space and frequency with implications for future study planning. C_LI ]]> Quinn, A. J. Pitt, J. Kohl, O. Gohil, C. van Es, M. W. J. Nobre, A. C. Woolrich, M. W. 2025-08-01 doi:10.1101/2025.08.01.668093 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy ]]> https://biorxiv.org/content/10.1101/2025.07.31.667872v1?rss=1 Lee, K. Negi, H. Chen, X. Atallah-Yunes, K. Truslow, S. Castelino, R. Guest, M. Ciancone, A. Tarasov, S. Chari, R. Walters, K. O'Reilly, F. 2025-08-02 doi:10.1101/2025.07.31.667872 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Bioactive Enhanced Adjuvant Chemokine Oligonucleotide Nanoparticles (BEACONs) for Mucosal Vaccination Against Genital Herpes ]]> https://biorxiv.org/content/10.1101/2025.07.31.667899v1?rss=1 Bhagchandani, S. H. Ehrenzeller, S. Pires, I. S. Chaudhary, N. Booth, C. J. Guedes de Sa, K. S. Kwon, D.-i. Li, S. Olszowka, A. Hudak, A. Fischer, S. Bayarri-Olmos, R. Iwasaki, A. 2025-08-02 doi:10.1101/2025.07.31.667899 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Exoproteome of calorie-restricted humans identifies complement deactivation as an immunometabolic checkpoint reducing inflammaging ]]> https://biorxiv.org/content/10.1101/2025.08.04.668533v1?rss=1 Mishra, M. Kim, H.-H. Youm, Y.-H. Gonzalez-Hurtado, E. Zaitsev, K. Dlugos, T. Shchukina, I. Gliniak, C. Ravussin, E. Mohanty, S. Shaw, A. C. Scherer, P. E. Artyomov, M. N. Dixit, V. D. 2025-08-06 doi:10.1101/2025.08.04.668533 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ In Vivo Evolution of Monoclonal Antibody CR3022 to Achieve Cross-Neutralization of SARS-CoV-2 and Implications for Vaccine Strategies Against SARS-Related Viruses ]]> https://biorxiv.org/content/10.1101/2025.08.05.666673v1?rss=1 Fu, Y. Feng, Z. Erickson, S. A. Halfmann, P. J. Li, L. Chervin, J. C. Troxell, C. A. Sun, J. Yasuhara, A. Changrob, S. Huang, M. Zheng, N.-Y. Yuan, M. Kawaoka, Y. Wilson, I. A. Wilson, P. 2025-08-06 doi:10.1101/2025.08.05.666673 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding ]]> https://biorxiv.org/content/10.1101/2025.08.05.668705v1?rss=1 Xu, L. Zheng, W. Hu, J. Lin, Y. Zhao, J. Wang, G. Liu, T. Zhao, H. 2025-08-07 doi:10.1101/2025.08.05.668705 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ A Scalable Toolkit for Modeling 3D Surface-based Brain Geometry ]]> https://biorxiv.org/content/10.1101/2025.08.06.668521v1?rss=1 Im, Y. Nabulsi, L. Kang, M. J. Y. Thomopoulos, S. I. Zuluaga, A. M. D. Dale, A. M. Karuk, A. Giorgio, A. D. Mwangi, B. Gutman, B. Overs, B. Jaramillo, C. L. McDonald, C. Stein, D. Cannon, D. M. Glahn, D. Hidalgo-Mazzei, D. Pecheva, D. Grotegerd, D. Pomarol-Clotet, E. Vieta, E. Olie, E. Cherto, E. V. Sambataro, F. Howells, F. Scheffler, F. Busatto, G. Anmella, G. Zunta-Soares, G. B. Roberts, G. Temmingh, H. Gotlib, I. Agartz, I. Soares, J. C. Karantonis, J. A. Prisciandaro, J. Fullerton, J. M. Radua, J. Savitz, J. Houenou, J. Sim, K. Harada, K. Berger, 2025-08-09 doi:10.1101/2025.08.06.668521 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Pan-ASLM: a high-resolution and large-field-of-view light sheet microscope for Expansion Microscopy ]]> https://biorxiv.org/content/10.1101/2025.08.06.668765v1?rss=1 Mekbib, H. T. Andersen, L. P. Zhang, S. Gulcicek, J. Tian, Y. Ross, J. R. Lessard, M. D. Bewersdorf, J. 2025-08-09 doi:10.1101/2025.08.06.668765 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ AgRP Neuronal Suppression by Spontaneous Movement Encodes Exercise Reinforcement ]]> https://biorxiv.org/content/10.1101/2025.08.06.668910v1?rss=1 Yoshida, J. Suematsu, N. Soma, S. Levy, I. Horvath, T. 2025-08-09 doi:10.1101/2025.08.06.668910 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Causal Dynamics of Social Gaze in Primate Prefrontal-Amygdala Networks Revealed by Dynamic Bayesian Modeling ]]> https://biorxiv.org/content/10.1101/2025.08.08.669405v1?rss=1 Xing, F. Fan, S. Dal Monte, O. Jadi, M. Chang, S. Nandy, A. 2025-08-10 doi:10.1101/2025.08.08.669405 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease ]]> https://biorxiv.org/content/10.1101/2025.08.07.669006v1?rss=1 Markov, N. S. Esposito, A. J. Senkow, K. J. Schleck, M. J. Cusick, L. Yu, Z. Sokolenko, Y. V. Diaz, E. Jonasson, E. Swaminathan, S. Lu, Z. Nafikova, R. A. Fenske, S. Bunyan, E. G. Perez-Leonor, X. G. Abdala-Valencia, H. Flozak, A. S. Joshi, N. Argento, C. A. Malsin, E. S. Reyfman, P. A. Puchalski, J. T. Gulati, M. Carns, M. Aren, K. Cooper, P. R. Field, N. S. Mohsin, S. Shawabkeh, M. Soriano, A. Gundersheimer, A. N. Goldberg, I. A. Damore, B. Peltekian, A. K. Agrawal, A. Cheung, C. Perez, S. Teaw, S. Williams, A. Page, N. Kujawski, S. E. Odell, W. Gune 2025-08-11 doi:10.1101/2025.08.07.669006 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Dehydration promotes intracellular lipid synthesis and accumulation ]]> https://biorxiv.org/content/10.1101/2025.08.07.669190v1?rss=1 Carty, J. S. Selvasingh, J. Zuchowski, Y. Nam, H.-J. Penalva, C. Nanayakkara, G. Jennings, E. Q. Voss, K. Adame, E. T. Tossberg, J. Yap, W. S. Melzer, M. Viquez, O. McCall, A. S. Piotrowski, E. R. Bessho, R. Cao, S. Leaptrot, K. Schrimpe-Rutledge, A. C. Codreanu, S. G. Sherrod, S. D. McLean, J. A. Trapani, J. B. Cottam, M. A. Wan, M. Shrivastava, D. Delker, D. A. Wilson, M. H. Hassenour, C. M. Lantier, L. Chernova, I. Young, J. D. Haase, V. H. Medina, J.-P. V. Kosma, D. K. Kim, P. Cartailler, J. P. Zhang, M. Zent, R. Harris,, R. C. Watts, J. A. Terker, 2025-08-11 doi:10.1101/2025.08.07.669190 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Inflammation increases the penetrance of behavioral impairment in Shank3 haploinsufficiency mice -- can it explain the behavioral regression in Autism? ]]> https://biorxiv.org/content/10.1101/2025.08.07.669241v1?rss=1 Qiao, S.-N. Wang, S. E. Kim, K.-Y. Jo, S. Jiang, Y.-H. 2025-08-11 doi:10.1101/2025.08.07.669241 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ The fibrocystin C-terminal domain inhibits Src/STAT3 signal induced cystogenesis of kidney epithelia. ]]> https://biorxiv.org/content/10.1101/2025.08.08.669180v1?rss=1 Hassan, F. Hahnenstein, S. T. Kraus, A. Buchholz, B. Mukenhirn, M. Honigmann, A. Dafinger, C. Liebau, M. C. Pokrant, T. Faix, J. Grund, A. Haffner, D. Ziegler, W. H. 2025-08-11 doi:10.1101/2025.08.08.669180 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ A scalable approach for tissue microarray profiling using spatial single cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.08.08.669400v1?rss=1 Arnedo-Pac, C. Heffer, J. Golotiuk, M. Piskorz, A. M. Aitken, S. J. 2025-08-12 doi:10.1101/2025.08.08.669400 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ LIPTER, a cardiomyocyte-enriched long noncoding RNA, controls cardiac cytoskeletal maturation and is regulated by a cardiomyocyte-specific enhancer. ]]> https://biorxiv.org/content/10.1101/2025.08.10.669544v1?rss=1 Nzelu, G. A. Lee, M. Koslowski, S. Zheng, W. Benzaki, M. Mak, M. Xiao, W. Tan, L. W. Dashi, A. Zhu, Y. Fawaz, T. Ng, K. Pham, D. LeBlanc, F. Lettre, G. Hussin, J. Foo, R. 2025-08-12 doi:10.1101/2025.08.10.669544 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ B Cell Tolerance and BCR Signaling Dysregulation in NF155-Mediated Autoimmune Nodopathies ]]> https://biorxiv.org/content/10.1101/2025.08.10.669569v1?rss=1 Roy, B. Obaid, A. H. Wang, Z. Kovacs, K. G. Ohashi, S. Kalayci, F. N. C. Joo, D. Masi, G. Coppola, C. Das, S. Hernandez, A. L. Martin-Aguilar, L. Lleixa, C. Querol, L. Nowak, R. J. O'Connor, K. C. 2025-08-12 doi:10.1101/2025.08.10.669569 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ The Microglial TREM2 Receptor Programs Hippocampal Development in a Mouse Model of Childhood Deprivation ]]> https://biorxiv.org/content/10.1101/2025.08.11.669425v1?rss=1 Ahmed, S. Bowers, C. Munoz-Martin, J. Jamwal, S. Sanganahalli, B. G. Giuliano, L. MacDowell Kaswan, Z. A. Hyder, F. Yang, X. W. Kaffman, A. 2025-08-12 doi:10.1101/2025.08.11.669425 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example ]]> https://biorxiv.org/content/10.1101/2025.08.11.669737v1?rss=1 Iyer, S. S. Hermana, K. M. Wang, Y. Pollard, T. D. Voth, G. A. 2025-08-13 doi:10.1101/2025.08.11.669737 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Lysine lactylation regulates ATF4-mediated stress responses under glucose starvation in canine hemangiosarcoma ]]> https://biorxiv.org/content/10.1101/2025.08.12.669864v1?rss=1 Suzuki, T. Heishima, K. Yamazaki, J. Yamazaki, M. Kinoshita, R. Kim, S. Hosoya, K. Okamatsu-Ogura, Y. Sasaki, M. Xu, P. Kimura, T. Yan, Q. Aoshima, K. 2025-08-13 doi:10.1101/2025.08.12.669864 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ The Cephalopod Reflectin Domain Specifically Chelates Cu(I), Inducing Assembly ]]> https://biorxiv.org/content/10.1101/2025.08.12.669908v1?rss=1 Rajkumar Kammath, A. Altan, I. Sweeney, A. 2025-08-13 doi:10.1101/2025.08.12.669908 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.08.13.670097v1?rss=1 Chitwood, M. H. Rancu, I. Song, Y. Potter, B. Chew, Y. T. Ciobanu, N. Crudu, V. Colijn, C. Cohen, T. Sobkowiak, B. 2025-08-13 doi:10.1101/2025.08.13.670097 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials ]]> https://biorxiv.org/content/10.1101/2025.08.12.669946v1?rss=1 Chen, H. Joseph, P. V. Coughlan, J. M. 2025-08-15 doi:10.1101/2025.08.12.669946 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Introgression and Parental Conflict Underlie Repeated Occurrences of Postzygotic Isolation ]]> https://biorxiv.org/content/10.1101/2025.08.12.669975v1?rss=1 Frayer, M. E. Soliman, H. K. Schwarz, P. F. Coughlan, J. M. 2025-08-15 doi:10.1101/2025.08.12.669975 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Distributed theta networks support the control of working memory: Evidence from scalp and intracranial EEG ]]> https://biorxiv.org/content/10.1101/2025.08.14.670214v1?rss=1 Shi, L. Chattopadhyay, K. Gray, S. M. Yarbrough, J. B. King-Stephens, D. Saez, I. Girgis, F. Shaikhouni, A. Schuele, S. U. Rosenow, J. M. Asano, E. Kim-McManus, O. Sattar, S. Knight, R. T. Johnson, E. L. 2025-08-15 doi:10.1101/2025.08.14.670214 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Fetal inflammatory signals regulate maternal investment in a pregnant marsupial ]]> https://biorxiv.org/content/10.1101/2025.08.16.669780v1?rss=1 Stadtmauer, D. J. Maziarz, J. D. Griffith, O. W. Wagner, G. 2025-08-17 doi:10.1101/2025.08.16.669780 Cold Spring Harbor Laboratory Press 2025-08-17 <![CDATA[ A Toolkit for In Vivo Mapping and Modulating Neurotransmission at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.08.18.670838v1?rss=1 Cuentas-Condori, A. Chanaba-Lopez, P. Thomas, M. Feng, L. Wolfe, A. Agoba, P. Schwartz, M. L. Brown, M. Ebert, M. Jorgensen, E. Bargmann, C. I. Colon-Ramos, D. A. 2025-08-18 doi:10.1101/2025.08.18.670838 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Deep Learning for Molecular and Genomic Characterization of Lung Cancer in Never-Smokers Using Hematoxylin and Eosin-Stained Images ]]> https://biorxiv.org/content/10.1101/2025.08.14.670178v1?rss=1 Saha, M. Tran, T.-V.-T. Bhawsar, P. M. Zhang, T. Zhao, W. Hoang, P. H. Mutreja, K. Lawrence, S. M. Rothman, N. Lan, Q. Homer, R. Baine, M. K. Sholl, L. M. Joubert, P. Leduc, C. Travis, W. D. Chanock, S. J. Shi, J. Yang, S.-R. Almeida, J. S. Landi, M. T. 2025-08-19 doi:10.1101/2025.08.14.670178 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Depression symptoms enhance goal-directed behavior underuncertainty ]]> https://biorxiv.org/content/10.1101/2025.08.14.670362v1?rss=1 Liang, S. Russek, E. M. Rutledge, R. Wimmer, G. E. 2025-08-19 doi:10.1101/2025.08.14.670362 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Renalase activates mitochondrial leak metabolism in response to cellular stress and to repair damage after injury ]]> https://biorxiv.org/content/10.1101/2025.08.19.671117v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@96ea7eorg.highwire.dtl.DTLVardef@1fcffbaorg.highwire.dtl.DTLVardef@f946cdorg.highwire.dtl.DTLVardef@197498a_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Guo, X. Chen, R. Shugrue, C. Shang, F.-F. Milian, R. G. Moller, H. Licznerski, P. Chen, T.-m. Kibbey, R. M Saad, O. Tian, Y. Bewersdorf, J. Giordano, F. Gorelick, F. S. Safirstein, R. Jonas, E. A. Desir, G. V. 2025-08-20 doi:10.1101/2025.08.19.671117 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines ]]> https://biorxiv.org/content/10.1101/2025.08.19.671151v1?rss=1 Vock, I. W. Tang, D. Giraldez, A. Simon, M. 2025-08-21 doi:10.1101/2025.08.19.671151 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Texas 2-Step: A new Model for YcgR::c-di-GMP Action at the Flagellar Motor ]]> https://biorxiv.org/content/10.1101/2025.08.21.671521v1?rss=1 Bhattarai, N. Guo, W. Partridge, J. D. Harshey, R. M. 2025-08-21 doi:10.1101/2025.08.21.671521 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Intestinal catabolism of dietary fructose promotes obesity and insulin resistance via ileal lacteal remodeling ]]> https://biorxiv.org/content/10.1101/2025.08.18.670963v1?rss=1 Lopez, M. L. Kang, T. Espeleta, A. Rubtsova, V. I. Baek, J. Songcuan, J. Moyer, E. M. Kim, J. Song, W.-S. Jung, S. D'Sa, N. Anica, A. Tran, E. Chun, Y. Choi, W. Jang, K.-H. Kelly, M. E. Tamburini, I. J. Alam, Y. H. Le, J. Ramirez, C. B. Kataru, R. P. Hong, S. P. Nicholas, D. A. Xue, K. S. Lee, G. Bae, H. Jang, C. 2025-08-22 doi:10.1101/2025.08.18.670963 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Regulatory features determine the evolutionary fate of laterally acquired genes in plants ]]> https://biorxiv.org/content/10.1101/2025.08.22.671697v1?rss=1 Collins, C. F. Alston, B. J. Hibdige, S. G. Raimondeau, P. Baker, E. Sotelo, G. Papadopulos, A. S. Christin, P. A. Pereira, L. Dunning, L. T. 2025-08-26 doi:10.1101/2025.08.22.671697 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Uncovering Developmental Lineages from Single-cell Data with Contrastive Poincare Maps ]]> https://biorxiv.org/content/10.1101/2025.08.22.671789v1?rss=1 Bhasker, N. Chung, H. Boucherie, L. Kim, V. Speidel, S. Weber, M. 2025-08-27 doi:10.1101/2025.08.22.671789 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Drought drives reversible disengagement of root-mycorrhizal symbiosis ]]> https://biorxiv.org/content/10.1101/2025.08.25.671999v1?rss=1 Akmakjian, G. Z. Nozue, K. Nakayama, H. Borowsky, A. T. Morris, A. M. Baker, K. Canto-Pastor, A. Paszkowski, U. Sinha, N. Brady, S. Bailey-Serres, J. 2025-08-27 doi:10.1101/2025.08.25.671999 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Subtyping psychotic disorders using a data-driven approach reveals divergent cortical and cellular signatures ]]> https://biorxiv.org/content/10.1101/2025.08.26.672411v1?rss=1 Hill, L. D. Zhang, X.-H. Rogers, B. P. Huang, A. S. Fox, V. Feola, B. Heckers, S. Holmes, A. J. Woodward, N. D. 2025-08-27 doi:10.1101/2025.08.26.672411 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Vibrio cholerae adhesin-derived peptide mediates strong pull-off forces in aqueous high ionic strength environments ]]> https://biorxiv.org/content/10.1101/2025.08.25.672170v1?rss=1 1 {micro}m), as compared to milliQ (Hz {approx} 100-500 nm) water and DMSO (Hz {approx} 100 nm), resulting in heterogeneous peptide film thicknesses. This letter concludes with a comparison to the pull-off forces of mussel foot protein-inspired peptides reported in the literature. ]]> Ahmed, S. T. Zhai, S. Huang, X. Saluja, S. Adewole, A. Ioffe, A. Merg, A. Yan, J. Andresen Eguiluz, R. C. 2025-08-29 doi:10.1101/2025.08.25.672170 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a non-canonical DNA binding mode to promote viral late gene transcription ]]> https://biorxiv.org/content/10.1101/2025.08.25.672222v1?rss=1 Llacsahuanga Allcca, L. E. Didychuk, A. L. Rodriguez-Vargas, A. Glaunsinger, B. 2025-08-29 doi:10.1101/2025.08.25.672222 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ SPINK3-sperm interaction determines a stable sperm subpopulation with intact CatSper channel ]]> https://biorxiv.org/content/10.1101/2025.08.26.672324v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@164c737org.highwire.dtl.DTLVardef@1531499org.highwire.dtl.DTLVardef@16d7abaorg.highwire.dtl.DTLVardef@945453_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nicolli, A. R. Huang, X. Zalazar, L. Stival, C. Demare, G. Romarowski, A. Buffone, M. G. Krapf, D. Chung, J.-j. Cesari, A. 2025-08-29 doi:10.1101/2025.08.26.672324 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ A conserved electron transport chain sensitizes Bacteroides to a pore-forming type VI secretion toxin ]]> https://biorxiv.org/content/10.1101/2025.08.29.672963v1?rss=1 Ratner, H. K. Duong, B. D. Miao, P. Bertolli, S. Shen, B. A. Mitchell, U. Gallagher, L. A. Radey, M. Peterson, S. B. Mougous, J. 2025-08-29 doi:10.1101/2025.08.29.672963 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Matrix metalloproteinase-3 promotes arteriovenous fistula failure by regulating FAK-AKT signaling ]]> https://biorxiv.org/content/10.1101/2025.08.27.672378v1?rss=1 Xie, Y. Zhang, W. Thaxton, C. Jin, Y. Yatsula, B. Bai, H. Davis, S. Exsted, T. Dardik, A. Guzman, R. J. Cai, Y. 2025-08-30 doi:10.1101/2025.08.27.672378 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma ]]> https://biorxiv.org/content/10.1101/2025.08.28.672849v1?rss=1 Konda, P. Weiss, C. N. Cui, Y. Matar, S. Wang, J. Nabil, Y. L. Deodhar, R. Li, J. Horst, J. Camp, S. Y. Sheshdeh, A. B. Hecht, J. L. Einstein, D. J. Rustagi, Y. Nag, A. Thorner, A. R. Zhang, C.-Z. Van Allen, E. M. Signoretti, S. Choueiri, T. Viswanathan, S. R. 2025-09-01 doi:10.1101/2025.08.28.672849 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Utilization of Arabidopsis E3 ubiquitin decoys high-throughput yeast screen platform to dissect the ubiquitin-mediated circadian clock regulation ]]> https://biorxiv.org/content/10.1101/2025.08.31.673341v1?rss=1 Tu, Y.-T. Chen, C.-A. Gendron, J. Lee, C.-M. 2025-09-01 doi:10.1101/2025.08.31.673341 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Endosymbiont hijacking of acylcarnitines regulates insect vector fecundity by suppressing the viability of stored sperm ]]> https://biorxiv.org/content/10.1101/2025.09.02.673677v1?rss=1 Weiss, B. L. Gstöttenmayer, F. Awuoche, E. Smallenberger, G. Attardo, G. Scolari, F. Koch, R. Bruzzese, D. J. Echodu, R. Opiro, R. Malacrida, A. Abd-Alla, A. Aksoy, S. 2025-09-02 doi:10.1101/2025.09.02.673677 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Systematic identification of oscillatory gene expression in single cell types ]]> https://biorxiv.org/content/10.1101/2025.09.02.673125v1?rss=1 5,000 genes. While many oscillatory genes relate to cuticle production, each cell type expresses largely distinct genes, suggesting that cuticle production is a patchwork of cell-type-specific programs. Finally, we derive a potential set of regulatory transcription factors that can explain coordinated oscillatory gene expression and find that shared upstream factors likely control gene timing across cell types. Together, our results suggest that shared regulators control cell-type-specific oscillatory gene expression, including in previously overlooked cell types such as glia. ]]> Weinreb, A. Basavaraju, M. Hammarlund, M. Heiman, M. G. 2025-09-05 doi:10.1101/2025.09.02.673125 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ VANGL2 shapes the mouse heart tube from adjacent epithelia and without planar polarity ]]> https://biorxiv.org/content/10.1101/2025.09.05.674213v1?rss=1 Palmquist-Gomes, P. Letort, G. Hegde, A. U. Perez-Pomares, J. M. Meilhac, S. M. 2025-09-05 doi:10.1101/2025.09.05.674213 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Comprehensive analysis of pseudogene expression in human and macaque brains compared with other tissues ]]> https://biorxiv.org/content/10.1101/2025.09.02.673826v1?rss=1 Jiang, Y. Yang, Y. T. Sisu, C. He, T. Won, H. Gerstein, M. 2025-09-06 doi:10.1101/2025.09.02.673826 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ HuD controls widespread RNA stability to drive neuronal activity-dependent responses ]]> https://biorxiv.org/content/10.1101/2025.09.05.674581v1?rss=1 Duffy, E. E. Patop, I. Kalaora, S. Assad, E. G. Koren, S. A. Traunmüller, L. Krüttner, S. Pajarillo, N. S. Finander, B. Barsdale, Z. Macias, M. M. Feng, M. Y. Paulo, J. A. Griffith, E. C. Kalish, B. T. Gygi, S. P. Churchman, L. S. Greenberg, M. E. 2025-09-06 doi:10.1101/2025.09.05.674581 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ The human cerebellum encodes temporally sensitive reinforcement learning signals ]]> https://biorxiv.org/content/10.1101/2025.09.06.674658v1?rss=1 Trach, J. E. Ou, Y. McDougle, S. D. 2025-09-07 doi:10.1101/2025.09.06.674658 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Decoupling between activation time and steady-state level in input-output responses ]]> https://biorxiv.org/content/10.1101/2025.09.03.673941v1?rss=1 Ravanelli, G. Nam, K. M. Gunawardena, J. Corral, R. M. 2025-09-08 doi:10.1101/2025.09.03.673941 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Effect of pharmacokinetically-relevant ivermectin concentrations on survivorship and fecundity of Anopheles coluzzii and Aedes aegypti in Burkina Faso: a laboratory experimental study ]]> https://biorxiv.org/content/10.1101/2025.09.04.674356v1?rss=1 0.05). Additionally, in An. coluzzii, IVM significantly reduced both egg laying and egg development (p<0.0001 and p<0.001, respectively), whereas no significant impact on fecundity was observed in Ae. aegypti (all p>0.80). ConclusionIvermectin concentrations typically achieved in human plasma during mass drug administration campaigns were sufficient to significantly reduce both survival and fecundity of wild type An. coluzzii, but had no measurable effect on recently colonized Ae. aegypti. These findings highlight the species-specific efficacy of ivermectin and support its potential role in integrated vector control strategies targeting malaria vectors in Africa. ]]> SOUGUE, E. Ouedraogo, C. O. W. Some, F. A. Pugh, G. Sagna, A. B. Dah, S. R. Bagayogo, S. Ouedraogo, R. T. Ndiaye, M. Parikh, S. Niang, E. H. M. Foy, B. D. Dabire, R. K. 2025-09-08 doi:10.1101/2025.09.04.674356 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ An Experimental Study of Social Signaling through Delayed Plumage Maturation in a Colony-Nesting Seabird ]]> https://biorxiv.org/content/10.1101/2025.09.05.674431v1?rss=1 Hill, M. M. Dobney, S. L. Fanburg, L. K. Mennill, D. J. Taylor, L. U. 2025-09-08 doi:10.1101/2025.09.05.674431 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Machine Learning Models Based on Histological Images from Healthy Donors Identify ImageQTLs and Predict Chronological Age ]]> https://biorxiv.org/content/10.1101/2025.09.04.674328v1?rss=1 Meng, R. Zhu, W. Z. Cameron, C. C. Ni, P. Zhou, X. Ulammandakh, T. Gerstein, M. 2025-09-09 doi:10.1101/2025.09.04.674328 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Human-specific features of the cerebellum and ZP2-regulated synapse development ]]> https://biorxiv.org/content/10.1101/2025.09.08.674970v1?rss=1 Kim, S.-K. Cherskov, A. Sindhwani, A. Choi, S.-H. Kim, H. Li, M.-L. Zhang, M. Mato-Blanco, X. Liu, Y. Micali, N. Young, D. M. Estacion, M. Zhang, Y. Ruiz-Jimenez, J. M. Nadkarni, A. Luria, V. Sindhu, S. K. Chatterjee, I. Shibata, A. Liang, D. Cho, H. Park, S. Spajic, A. Kovner, R. Glavan, M. Chen, R. J. Risgaard, R. D. Li, X. Pochareddy, S. Karger, A. Huttner, A. Morozov, Y. M. Daadi, E. W. Colantuoni, C. Gobeske, K. T. Ely, J. J. Hof, P. R. Daadi, M. M. Sherwood, C. C. Duque, A. Ma, S. Sousa, A. M. M. Waxman, S. Rakic, P. Santpere, G. Sanders, S. J 2025-09-09 doi:10.1101/2025.09.08.674970 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Insulin resistance alters cortical inhibitory neurons and microglia to exacerbate Alzheimer knock-in mouse phenotypes ]]> https://biorxiv.org/content/10.1101/2025.09.05.674487v1?rss=1 Nicholson, L. Tang, S. J. Karra, T. Abouletta, H. Strittmatter, S. M. 2025-09-11 doi:10.1101/2025.09.05.674487 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2025.09.11.675340v1?rss=1 Sullivan, J. R. Ferrara, K. Barrick, R. Romano, K. P. Warrier, T. Hung, D. T. 2025-09-11 doi:10.1101/2025.09.11.675340 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Deconvoluting Metabolomic Flux in Living Cells with Real-time 13C J-coupling-edited Proton High-Resolution Magic Angle Spinning (HRMAS) NMR ]]> https://biorxiv.org/content/10.1101/2025.09.07.674640v1?rss=1 Biswas, R. G. Zhang, E. Pavao, A. Bry, L. Cheng, L. L. 2025-09-12 doi:10.1101/2025.09.07.674640 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ PGRP-LA regulates peritrophic matrix synthesis and influences trypanosome infection outcomes in tsetse flies ]]> https://biorxiv.org/content/10.1101/2025.09.08.674804v1?rss=1 Vigneron, A. Weiss, B. L. Feng, Y. Wang, J. Awuoche, E. Nguyen, H. Orfano, A. Yang, L. Aksoy, E. Aksoy, S. 2025-09-12 doi:10.1101/2025.09.08.674804 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma ]]> https://biorxiv.org/content/10.1101/2025.09.09.675071v1?rss=1 Hamon, P. Park, M. D. Le Berichel, J. Cohen, M. Soong, B. Y. Buckup, M. Hennequin, C. Lindblad, K. E. Mattiuz, R. Figueiredo, I. Tabachnikova, A. Dawson, T. D'souza, D. Troncoso, L. Ioannou, G. Price, C. Fernandez, N. Giladi, A. Barboy, O. Zhao, Z. Ozbey, S. Cappuyns, S. Reid, A. Hamel, S. Kim, J. Donne, R. Chang, C. Marvin, R. Stefanos, H. Chung, G. Merand, R. Halasz, L. Hegde, S. Guerin, L. M. Ni, M. Wei, Y. Atwal, G. Lansky, A. Jamal, H. Yi, N. Chin, T. James, N. Malissen, N. Desland, F. Lavin, Y. Ward, S. C. Fiel, M. I. Brody, R. Dekervel, J. 2025-09-12 doi:10.1101/2025.09.09.675071 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Dissecting the unique self-assembly landscape of the HIV-2 capsid protein ]]> https://biorxiv.org/content/10.1101/2025.09.10.675445v1?rss=1 Cook, M. Bhardwaj, P. Lozano, F. Freniere, C. Malonis, R. J. Xiong, Y. 2025-09-12 doi:10.1101/2025.09.10.675445 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Evaluating the Contribution of Genome 3D Folding to Variation in Human Height Using Machine Learning ]]> https://biorxiv.org/content/10.1101/2025.09.09.675195v1?rss=1 Gu, W. Gilbertson, E. Baranzini, S. E. Salem, R. Capra, J. A. 2025-09-15 doi:10.1101/2025.09.09.675195 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ MAP65-1/PRC1 reinforces microtubules through nucleation ]]> https://biorxiv.org/content/10.1101/2025.09.14.676082v1?rss=1 Romeiro Motta, M. Grisam, C. Gruenewald, M. Koenig, B. Meissner, L. Niese, L. Diez, S. Hamant, O. Schaedel, L. 2025-09-15 doi:10.1101/2025.09.14.676082 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ N6-methyladenosine promotes temozolomide resistance through non-canonical regulation of mRNA stability in glioblastoma cells ]]> https://biorxiv.org/content/10.1101/2025.09.14.676126v1?rss=1 Dangelmaier, E. A. Fang, D. Htet, K. S. Harry, N. S. Pascoe, R. Yang, J. W. Wang, C. D. Nachtergaele, S. 2025-09-15 doi:10.1101/2025.09.14.676126 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Multitasking Recurrent Networks Utilize CompositionalStrategies for Control of Movement ]]> https://biorxiv.org/content/10.1101/2025.09.10.675375v1?rss=1 Lazzari, J. Saxena, S. 2025-09-16 doi:10.1101/2025.09.10.675375 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Epigenomic Heterogeneity of Non-Functional Pancreatic Neuroendocrine Tumors Uncovered by Single nucleus and Spatial ATAC Profiling ]]> https://biorxiv.org/content/10.1101/2025.09.11.675640v1?rss=1 Wang, D. Di, x. Gao, f. Li, g. Lin, l. He, s. Zhang, d. Xu, j. Jin, y. Liang, y. Cecchini, m. Lacy, j. Kunstman, j. Kunz, p. Du, j. Liu, Y. 2025-09-16 doi:10.1101/2025.09.11.675640 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Lateral septal inhibition of nucleus basalis through direct and indirect pathways in focal limbic seizures ]]> https://biorxiv.org/content/10.1101/2025.09.17.676820v1?rss=1 Liu, J. Sieu, L.-A. Shi, I. Doan, V. Liu, S. Sun, C. Brodovskaya, A. Kapur, J. Cardin, J. A. Blumenfeld, H. 2025-09-17 doi:10.1101/2025.09.17.676820 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ A Dual-Action Mechanism to Prevent OX40 Signaling: The Structural Basis for the Differentiated Antagonist STAR-0310 ]]> https://biorxiv.org/content/10.1101/2025.09.16.676329v1?rss=1 Biris, N. Zhao, C. Macoin, J. Fuller, J. R. Blauvelt, A. Chovatiya, R. Bunick, C. G. 2025-09-19 doi:10.1101/2025.09.16.676329 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Noradrenergic inputs to the basolateral amygdala have bidirectional effects on coping behavior and neuronal activity in mice ]]> https://biorxiv.org/content/10.1101/2025.09.18.677150v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1b642a7org.highwire.dtl.DTLVardef@d20eedorg.highwire.dtl.DTLVardef@d22aa7org.highwire.dtl.DTLVardef@1ee4291_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBLA NE levels signal behavioral transitions between coping responses to stress C_LIO_LILow-frequency stimulation of BLA NE terminals inhibits passive coping and BLA cFos C_LIO_LIHigh-frequency stimulation of BLA NE terminals promotes passive coping and BLA cFos C_LIO_LIBehavioral effects are similar across sexes, but cFos alterations are male- specific C_LI ]]> Soares, A. R. Fai, C. Mineur, Y. S. Picciotto, M. R. 2025-09-19 doi:10.1101/2025.09.18.677150 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Metabolic Trajectories During Surgical Stress in Patients Undergoing Cardiac Surgery ]]> https://biorxiv.org/content/10.1101/2025.09.16.676529v1?rss=1 Ku, D. Bartelt, J. Feeley, J. Perez-Guzman, M. C. Guerrero-Arroyo, L. Abraham, A. Kollipara, S. Gonzalez, N. Usman, S. Huneault, H. E. Corujo-Rodriguez, A. Davis, G. M. Kibbey, R. G. Jones, D. P. Ziegler, T. R. Halkos, M. Quyyumi, A. A. Smith, M. R. Li, J. Pasquel, F. J. 2025-09-20 doi:10.1101/2025.09.16.676529 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues ]]> https://biorxiv.org/content/10.1101/2025.09.17.675534v1?rss=1 Salla, M. Obermayer, B. Cotta, M. Friebel, E. Campo-Garcia, J. Charalambous, G. Bueno, R. J. Lieu, D. Dabek, P. Helmuth, A. Tellides, G. Assi, R. Bankov, K. Lodrini, M. Deubzer, H. Chung, H. Beule, D. Radbruch, H. Capper, D. Heppner, F. Starossom, S. C. Lareau, C. Liu, I. Ludwig, L. S. 2025-09-20 doi:10.1101/2025.09.17.675534 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Discovery of circulating cell-free DNA 5hmC biomarkers for peritoneal metastasis in colorectal and appendiceal cancer ]]> https://biorxiv.org/content/10.1101/2025.09.18.676945v1?rss=1 Malina, Y. F. Gao, L. Dhiman, A. West-Szymanski, D. C. Berger, Y. Cui, X.-L. Zhang, Z. Rivas, M. Dougherty, U. Ye, C. Kwesi, A. Deng, Z. Reddy, B. Witmer, H. D. D. Hsu, P. J. He, C. Zhang, W. Bissonnette, M. Turaga, K. 2025-09-21 doi:10.1101/2025.09.18.676945 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Lower Airway Dysbiosis in NTM+ Bronchiectasis is Associated with NET-Predominant Severe Phenotypes ]]> https://biorxiv.org/content/10.1101/2025.09.18.677189v1?rss=1 Singh, S. Darawshy, F. Erlandson, K. Narayana, J. Li, Q. Li, Y. Atandi, I. Krolikowski, K. Patel, S. Collazo, D. Mac Aogain, M. Gilmour, A. Long, M. Chang, M. Hoque, A. Schluger, R. Kumar, S. Chung, C. Wong, K. Porter, G. Feng, Y. Czachor, A. McCormick, C. Clementi, E. Kyeremateng, Y. Lukovnikova, A. Harris, D. Gomez, S. Kain, T. Kocak, I. Singh, R. Rodriguez, C. Kwok, B. Barnett, C. Kugler, M. Weiden, M. D. Nelson, N. Natalini, J. G. Luglio, D. Desvignes, L. Gautam, S. McGuire, E. Gordon, T. Sulaiman, S. M. I. Tsay, J.-C. Basavaraj, A. Wu, B. G. 2025-09-21 doi:10.1101/2025.09.18.677189 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Dynamics of Macrophage Polarization Reveal Unique Phenotypes During Mouse Postpartum Uterine Remodeling ]]> https://biorxiv.org/content/10.1101/2025.09.19.676950v1?rss=1 Chaves Rivera, M. N. Bell, S. Solomon, A. Kliman, H. Tal, A. Tal, R. 2025-09-21 doi:10.1101/2025.09.19.676950 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy ]]> https://biorxiv.org/content/10.1101/2025.09.19.677400v1?rss=1 View larger version (44K): org.highwire.dtl.DTLVardef@101b333org.highwire.dtl.DTLVardef@9be92corg.highwire.dtl.DTLVardef@1e95c88org.highwire.dtl.DTLVardef@1b9eeee_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sipple, M. T. Hamazaki, S. Todorow, V. Cisco, L. A. Lupia, K. M. Heil, C. S. Meinke, P. Thornton, C. A. Lueck, J. D. 2025-09-21 doi:10.1101/2025.09.19.677400 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Fetal and maternal immune cells exhibit tandem maturation across gestation and dysregulation in preterm birth ]]> https://biorxiv.org/content/10.1101/2025.09.20.677440v1?rss=1 Rice, T. A. Cao, Y. Bichmann, L. Snisky, T. S. Singh, S. Gu, W. Yimlamai, D. Radda, J. S. D. Wang, S. Tsang, J. S. Megli, C. Konnikova, L. 2025-09-21 doi:10.1101/2025.09.20.677440 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations ]]> https://biorxiv.org/content/10.1101/2025.09.20.677549v1?rss=1 Boev, N. Gerstein, M. Kumar, S. 2025-09-21 doi:10.1101/2025.09.20.677549 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ 3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors ]]> https://biorxiv.org/content/10.1101/2025.09.21.677628v1?rss=1 Forjaz, A. Queiroga, V. Li, Y. Hernandez, A. Crawford, A. Qin, X. Zhong, M. Tsapatsis, M. Joshi, S. Kramer, D. Nizet, O. Bea, H. Li, Y. Qin, S. O Flynn, R. Yang, M. Pratt, B. Wu, F. Gensbigler, P. Blecher, M. Wu, P.-H. Kagohara, L. T. Shih, I. M. Zwicker, D. Atkinson, M. A. Shi, L. Fan, R. Kiemen, A. L. Wirtz, D. 2025-09-21 doi:10.1101/2025.09.21.677628 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Engineering Spatial Control of Bacterial Organelles ]]> https://biorxiv.org/content/10.1101/2025.09.22.677801v1?rss=1 Hoang, Y. Jadhav, P. V. Trettel, D. Dow, R. E. Kwon, S. Matej, K. Byrne, J. A. Azaldegui, C. A. Giessen, T. W. Pi, H. Mosalaganti, S. Vecchiarelli, A. G. 2025-09-22 doi:10.1101/2025.09.22.677801 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Spiroplasma impairs testes gene expression in Glossina fuscipes fuscipes ]]> https://biorxiv.org/content/10.1101/2025.09.23.678099v1?rss=1 Piccinno, R. Fiorenza, G. Lescai, F. Carpanzano, S. Gstottenmayer, F. Dera, K.-s. M. Croce, A. C. de Beer, C. J. Santorsola, M. Gasperi, G. Forneris, F. Abd-Alla, A. M. M. Aksoy, S. Malacrida, A. R. 2025-09-25 doi:10.1101/2025.09.23.678099 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Exploring endothelial cell environments across organs in spatially resolved omics data ]]> https://biorxiv.org/content/10.1101/2025.09.23.678129v1?rss=1 Jain, Y. Jepson, J. Chen, R. Maier, E. Herr, B. W. Puig-Barbe, A. Quardokus, E. M. Qaurooni, D. Yapp, C. Ewing, S. L. Enninful, A. Farzad, N. Bueckle, A. Easter, Q. T. Matuck, B. Zhu, C. Monte, E. M. Purkerson, J. M. Jehrio, M. Misra, R. S. Fan, R. Ginty, F. Karunamurthy, A. Fan, J. Campbell-Thompson, M. Pryhuber, G. S. Byrd, K. M. Hickey, J. W. Börner, K. 2025-09-25 doi:10.1101/2025.09.23.678129 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Non-integrating direct reprogramming generates therapeutic endothelial cells with sustained vascular regeneration capacity enhanced by nanomatrix delivery ]]> https://biorxiv.org/content/10.1101/2025.09.24.678308v1?rss=1 Lee, S. Chen, D. Tanaka, Y. Bae, S. Li, H. J. Jang, E. Y. Chan, E. Park, I.-H. Jun, H.-W. Park, C. Yoon, Y.-s. 2025-09-25 doi:10.1101/2025.09.24.678308 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ The NMDAR positive allosteric modulator NYX-783 selectively blocks opioid withdrawal conditioned place aversion in mice. ]]> https://biorxiv.org/content/10.1101/2025.09.25.678598v1?rss=1 Trinko, J. R. Foscue, E. P. Diaz, D. M. Thompson, S. L. Malison, R. T. Sinha, R. Taylor, J. R. DiLeone, R. J. 2025-09-25 doi:10.1101/2025.09.25.678598 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Evolution of the rate, spectrum, and fitness effects of mutation under minimal selection in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.09.24.678306v1?rss=1 Saber, S. Rifat, M. M. I. Rahimi, F. Snyder, M. Singh, A. Eickwort, B. Newhall, Y. Rajaei, M. Saxena, A. S. Tanny, R. Katju, V. Andersen, E. C. Zhou, J. Baer, C. F. 2025-09-26 doi:10.1101/2025.09.24.678306 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability ]]> https://biorxiv.org/content/10.1101/2025.09.25.678633v1?rss=1 Rosenberger, G. Xue, P. Bludau, I. Martelli, C. Williams, E. Collins, B. C. Califano, A. Liu, Y. Aebersold, R. 2025-09-26 doi:10.1101/2025.09.25.678633 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Structures redefine the mechanism of action for tetracyclines ]]> https://biorxiv.org/content/10.1101/2025.09.25.678686v1?rss=1 Devarkar, S. C. Lomakin, I. B. Wang, J. Grada, A. Bunick, C. G. 2025-09-26 doi:10.1101/2025.09.25.678686 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Somatic evolution of prostate cancer: mutation, selection, and epistasis across disease stages ]]> https://biorxiv.org/content/10.1101/2025.09.25.678387v1?rss=1 Rajaei, M. Yang, A. Glasmacher, K. A. Cross, C. N. Fisk, N. Perry, E. B. Mandell, J. D. Gaffney, S. G. Yamaguchi, T. N. Livingstone, J. Costa, J. Humphrey, P. Cannataro, V. L. Boutros, P. C. Townsend, J. P. 2025-09-28 doi:10.1101/2025.09.25.678387 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Beta bursts mediate amygdala gating of hippocampal emotional encoding ]]> https://biorxiv.org/content/10.1101/2025.09.26.678792v1?rss=1 Zhou, Y. Huang, Y. Pittaro, G. Zareian, B. Aljishi, A. Toro, A. Zibly, Z. Obaid, S. Sivaraju, A. Harpaz-Rotem, I. Kaye, A. P. Krystal, J. Sheth, K. Gu, X. Pittenger, C. Damisah, E. 2025-09-28 doi:10.1101/2025.09.26.678792 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ ALDH2 Deficiency Drives Proliferative Mammary Morphogenesis and Epithelial Cell Stemness via Oxidative Stress and Estrogen Receptor Activation ]]> https://biorxiv.org/content/10.1101/2025.09.25.678642v1?rss=1 Ma, Z. Parris, A. B. Lester, M. Gissendanner, D. Vasiliou, V. Yang, X. 2025-09-29 doi:10.1101/2025.09.25.678642 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Prediction in Pediatric AML ]]> https://biorxiv.org/content/10.1101/2025.09.25.678688v1?rss=1 NajafPanah, M. J. Stevens, A. M. Krueger, M. J. Rochette, M. Sandhu, S. Kim, L. Chiu, H.-S. Epps, J. Somvanshi, S. Zorman, B. Martinez, M. R. Rapsomaniki, M. Unger, S. Becher, B. Yi, J. S. Man, T.-K. Redell, M. S. Sumazin, P. 2025-09-29 doi:10.1101/2025.09.25.678688 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts ]]> https://biorxiv.org/content/10.1101/2025.09.26.678416v1?rss=1 Stein, Y. Freund, O. Borsekofsky, S. Cohn-Schwartz, D. Levy, L. Ofek, E. Spitzer, A. Adams, T. S. Schupp, J. C. Kaminski, N. Bar-Shai, A. Unterman, A. 2025-09-29 doi:10.1101/2025.09.26.678416 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2025.09.28.679043v1?rss=1 Daron, J. Lecuyer, A. Ma, L. Marzooghi, P. Breban, M. I. Kryrylos, P. Donovan-Banfield, I. Redmond, S. N. LAMBRECHTS, L. 2025-09-30 doi:10.1101/2025.09.28.679043 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ MDR1 promotes CD8 T cell persistence in tumors and protects against cytotoxic chemotherapy ]]> https://biorxiv.org/content/10.1101/2025.09.28.679049v1?rss=1 Brown, L. A. Erwin, M. M. Favret, N. R. McDavid, C. N. Roetman, J. J. Ewell, Z. D. Wolf, M. M. Murray, K. A. Smithwick, J. E. Goemann, M. A. Philip, M. 2025-09-30 doi:10.1101/2025.09.28.679049 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Tree microbiomes and methane emissions in upland forests ]]> https://biorxiv.org/content/10.1101/2025.09.30.679632v1?rss=1 Gewirtzman, J. Arnold, W. Taylor, M. Burrows, H. Merenstein, C. Woodbury, D. Whitlock, N. Kraut, K. Gonzalez, L. Brodersen, C. R. Duguid, M. Raymond, P. A. Peccia, J. Bradford, M. A. 2025-09-30 doi:10.1101/2025.09.30.679632 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Smooth Muscle Cell-Specific TGFβ2 Protects Against Thoracic Aortic Aneurysm and Dissection in Mice ]]> https://biorxiv.org/content/10.1101/2025.10.01.679917v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@1ef41d3org.highwire.dtl.DTLVardef@ca8feborg.highwire.dtl.DTLVardef@aebce4org.highwire.dtl.DTLVardef@1f3599b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Azhar, M. Gebere, M. G. Chakrabarti, M. Azhar, A. Wang, X. Vyavahare, N. R. Johnson, J. 2025-10-03 doi:10.1101/2025.10.01.679917 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ scGPD: single-cell informed gene panel design for targeted spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.10.02.680117v1?rss=1 Guo, Y. Zhao, J. Chang, R. B. Zhao, H. 2025-10-03 doi:10.1101/2025.10.02.680117 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Common-specific edge-centric connectome across Four Episodes in Bipolar Disorder ]]> https://biorxiv.org/content/10.1101/2025.10.03.680275v1?rss=1 Liu, X. Wang, S. Yu, Q. Zhang, X. Liu, L. Gao, Y. 2025-10-03 doi:10.1101/2025.10.03.680275 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Clinically observed RASA1 missense mutants exhibit diverse RasGAP protein behaviors ]]> https://biorxiv.org/content/10.1101/2025.10.03.680326v1?rss=1 Paul, M. E. Delelegne, R. B. Chau, J. E. Boggon, T. J. 2025-10-04 doi:10.1101/2025.10.03.680326 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Neuroinflammatory Stress Preferentially Impacts Synaptic MAPK Signaling and Mitochondria in Excitatory Neurons ]]> https://biorxiv.org/content/10.1101/2025.10.03.680087v1?rss=1 1000 proteins, consistent with neuron-specific biotinylation, also confirmed by immunofluorescence microscopy. Camk2a-specific synaptic proteome revealed molecular signatures related to mitochondrial function, synaptic transmission, protein translation. LPS-treated mice displayed body weight loss and neuroinflammation, characterized by glial activation, increased pro-inflammatory cytokine levels and upregulated expression of Alzheimers disease (AD)-related microglial genes. LPS-induced neuroinflammation exerted distinct effects on the synaptic proteome, including increased mitochondrial and reduced cytoskeletal-synaptic proteins, while suppressed synaptic MAPK signaling. Importantly, these changes were not observed at the whole neuron level, indicating unique vulnerability of the synapse to neuroinflammation. In line with synapse proteomic and signaling changes, LPS altered the ultrastructure of asymmetric synapses, suggesting dysregulation of excitatory neurotransmission. Co-expression network analysis of Camk2a neuronal proteins further resolved mitochondria- and synapse-specific protein modules, some of which were neuroinflammation-dependent. Neuroinflammation increased levels of a mitochondria-enriched module, and decreased levels of a pre-synaptic vesicle module, without impacting a post-synaptic membrane module. LPS-dependent mitochondrial and LPS-independent post-synaptic modules in mouse neurons mapped to post-mortem human AD brain proteomic modules which were decreased in cases with AD dementia and positively correlated to cognitive function, including pro-resilience markers for AD. ConclusionOur findings using native-state proteomics of Camk2a neurons combined with synaptosome enrichment identify proteome-level mechanisms of early synaptic vulnerability to neuroinflammation relevant to AD. ]]> Espinosa-Garcia, C. Srivastava, U. Kumar, P. Kour, D. Malepati, S. Tobin, B. Xiao, H. Sunna, S. Bowen, C. A. Cheng, L. Bagchi, P. Duong, D. M. Whitworth, T. J. Liu, X. Seyfried, N. Wood, L. B. Faundez, V. Rangaraju, S. 2025-10-05 doi:10.1101/2025.10.03.680087 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Protamine lacunae preserve the paternal chromatin landscape in sperm ]]> https://biorxiv.org/content/10.1101/2025.10.03.680364v1?rss=1 Tullius, T. W. Heuer, R. A. Bohaczuk, S. C. Mallory, B. Dubocanin, D. Ranchalis, J. Ayaz, A. Mason, C. Seli, E. Phillippy, A. M. Stergachis, A. Lesch, B. J. 2025-10-05 doi:10.1101/2025.10.03.680364 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Plant-soil feedback persists beyond host death to shape density-dependent plant competition ]]> https://biorxiv.org/content/10.1101/2025.10.04.680482v1?rss=1 Huang, C.-L. Wan, J. Wei, S. Chang-Yang, C.-H. Ke, P.-J. 2025-10-06 doi:10.1101/2025.10.04.680482 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function ]]> https://biorxiv.org/content/10.1101/2025.10.05.680386v1?rss=1 Allain, V. Rothrock, A. G. Bernard, P.-L. Nyberg, W. A. Talbot, A. Muldoon, J. J. Chung, J.-Y. To, A. Chang, C. R. Kimmerly, G. R. Liu, C. Tsao, T. Mortazavi, Y. Seo, J. Li, Z. Shemesh, A. Schmidt, R. Ward, C. C. Marson, A. Lanier, L. L. Aguilar, O. A. Eyquem, J. 2025-10-06 doi:10.1101/2025.10.05.680386 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Epigenetic characterization of pseudogenes across human tissues ]]> https://biorxiv.org/content/10.1101/2025.10.05.680540v1?rss=1 Jiang, Y. Borsari, B. Gerstein, M. 2025-10-06 doi:10.1101/2025.10.05.680540 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics studies ]]> https://biorxiv.org/content/10.1101/2025.10.06.680672v1?rss=1 Ma, W. Hou, S. Shang, L. Lu, J. Zhou, X. 2025-10-06 doi:10.1101/2025.10.06.680672 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ CardioWAS Pathway-Based RNA-Seq and Genome Integration Platform for CVD Omics-Wide Associations ]]> https://biorxiv.org/content/10.1101/2025.10.06.679779v1?rss=1 Singh, Y. Sharma, N. Raghuvanshi, K. Kwan, J. Jha, A. 2025-10-07 doi:10.1101/2025.10.06.679779 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Behavioral unresponsiveness and impaired auditory event-related potentials in the anterior insula during rat absence seizures ]]> https://biorxiv.org/content/10.1101/2025.10.06.680740v1?rss=1 Sumsky, S. Ashmeade, R. Liu, J. Zheng, Y. Chopra, S. Gruenbaum, B. F. McCafferty, C. P. Blumenfeld, H. 2025-10-07 doi:10.1101/2025.10.06.680740 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ RUNX1T1-HDAC Reprogramming of the HOX Code Signaling Drives a Targetable Pan-Cancer Lineage Plasticity ]]> https://biorxiv.org/content/10.1101/2025.10.07.681000v1?rss=1 Mu, P. Jiang, Y. Cheng, S. Zhang, C. Y. Jin, X. Xu, Y. Kim, I. Y. 2025-10-08 doi:10.1101/2025.10.07.681000 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Engineering substrate selectivity in the human sodium/iodide symporter (NIS) ]]> https://biorxiv.org/content/10.1101/2025.10.07.681042v1?rss=1 Llorente-Esteban, A. Sabbineni, H. Hoffsmith, K. Manville, R. W. Lopez-Gonzalez, D. Reyna-Neyra, A. Leyva, A. Abbott, G. W. Bianchet, M. A. Carrasco, N. 2025-10-08 doi:10.1101/2025.10.07.681042 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ African Green Monkeys Respond to Synthetic AB Oligomers with Persistent Alzheimers-like Activation ]]> https://biorxiv.org/content/10.1101/2025.10.08.678256v1?rss=1 Brown, B. Li, X. Grasty, M. R. Lopez, I. Dzigurski, S. Geradi, M. Lawrence, M. Elsworth, J. Lawrence, M. Weed, M. Gursoy, G. Miranker, A. D. 2025-10-08 doi:10.1101/2025.10.08.678256 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Thermodynamic principles govern evolutionary tradeoffs by regulating allostery ]]> https://biorxiv.org/content/10.1101/2025.10.08.680613v1?rss=1 Muthahari, Y. A. Aditama, R. Providaki, M. Tsirigotaki, A. Sarafoglou, C. Xu, R. Krishnamurthy, S. Hertadi, R. Kokkinidis, M. Hui, C. Laurino, P. Pozidis, C. Gouridis, G. 2025-10-08 doi:10.1101/2025.10.08.680613 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Climate-driven specialisation in plant-pollinator networks peaks outside the tropics ]]> https://biorxiv.org/content/10.1101/2025.10.08.680666v1?rss=1 3,400 networks, >110,000 interactions), we show that the latitudinal specialisation gradient (LSG) exists, but it is non-linear, hemispherically asymmetric, and strongly taxon-dependent. Network-level and pollinator specialisation were lowest in the tropics and peaked at northern mid-latitudes, whereas plants tended to become more specialised toward higher latitudes. Climate consistently outperformed latitude, species richness, and environmental productivity as a predictor of these patterns. Specialisation declined with increasing temperature, rose with moderate rainfall before declining at the wettest sites, and increased with temperature seasonality, but plants and pollinators responded differently to these drivers. Functional groups diverged strongly: ectothermic insects were most specialised in cooler, seasonal climates, while birds showed weaker links to latitude but reduced specialisation in wetter regions. These findings demonstrate that climate, rather than latitude or species richness, structures global variation in specialisation. Because warmer and less seasonal climates promote generalisation, climate change is likely to disrupt the most specialised pollination systems, unevenly across taxa and regions, with important consequences for biodiversity and ecosystem stability. ]]> Sakhalkar, S. P. Blüthgen, N. Burkle, L. A. CaraDonna, P. Dalsgaard, B. Dormann, C. F. Kaiser-Bunbury, C. N. Knight, T. M. Ollerton, J. Resasco, J. Schleuning, M. Vazquez, D. P. Afagwu, R. N. Alarcon, R. Amorim, F. W. Amorim, M. D. Anyz, D. Arroyo-Correa, B. Artamendi, M. Atalay, Z. Bain, J. A. Baldock, K. C. R. Ballantyne, G. Ballarin, C. S. Balmaki, B. Bartos, M. Belavadi, V. Biella, P. Bjorkman, A. D. Borges, J. P. R. Bosch, J. Bosenbecker, C. Boyer, S. Burghardt, K. T. Cardona, E. Casia, Q. Castagna, A. M. T. Celep, F. Chiste, M. N. Clough, Y. Cook, 2025-10-08 doi:10.1101/2025.10.08.680666 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ A Unifying Mechanism for Shared Splicing Aberrations in Splicing Factor Mutant Cancers ]]> https://biorxiv.org/content/10.1101/2025.10.08.679601v1?rss=1 Boddu, P. C. Roy, R. Hutter, S. Baumgartner, F. Li, W. Todisco, G. Ficara, F. Della Porta, M. G. Liu, Y. Haferlach, T. Pillai, M. 2025-10-09 doi:10.1101/2025.10.08.679601 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Mechanical stretch disrupts calcium dynamics and redistributes Piezo1 in human astrocytes ]]> https://biorxiv.org/content/10.1101/2025.10.08.681038v1?rss=1 Shiravi, S. Chakka, A. Xiao, X. Garcia, M. F. Yufa, A. Mitevska, A. Seah, C. Huckins, L. M. Brennand, K. Finan, J. D. 2025-10-09 doi:10.1101/2025.10.08.681038 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ The GLP-1R Agonist Semaglutide Reduces Motivated Running and Alters Dopamine Dynamics in the Nucleus Accumbens ]]> https://biorxiv.org/content/10.1101/2025.10.08.681212v1?rss=1 Foscue, E. Trinko, J. R. Jimenez, J. L. Kong, E. Thompson, S. Stankewich, K. Corstens, A. Serlie, M. Taylor, J. DiLeone, R. 2025-10-09 doi:10.1101/2025.10.08.681212 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Sexual dimorphism in the complete connectome of the Drosophila male central nervous system ]]> https://biorxiv.org/content/10.1101/2025.10.09.680999v1?rss=1 Berg, S. Beckett, I. R. Costa, M. Schlegel, P. Januszewski, M. Marin, E. C. Nern, A. Preibisch, S. Qiu, W. Takemura, S.-y. Fragniere, A. M. C. Champion, A. S. Adjavon, D.-Y. Cook, M. Gkantia, M. Hayworth, K. J. Huang, G. B. Kampf, F. Katz, W. T. Lu, Z. Ordish, C. Paterson, T. Stuerner, T. Trautman, E. T. Whittle, C. R. Burnett, L. E. Hoeller, J. Li, F. Loesche, F. Morris, B. J. Pietzsch, T. Pleijzier, M. W. Silva, V. Yin, Y. Ali, I. Badalamente, G. Bates, A. S. Bogovic, J. Brooks, P. Cachero, S. Canino, B. S. Chaisrisawatsuk, B. Clements, J. Crowe, A. 2025-10-09 doi:10.1101/2025.10.09.680999 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ TET CpG sequence context specific DNA demeth-ylation shapes progression of IDH-mutant gliomas ]]> https://biorxiv.org/content/10.1101/2025.10.09.681314v1?rss=1 Hoogstrate, Y. Ghisai, S. A. van Hijfte, L. Head, R. de Heer, I. Padovan, M. de Wit, M. Vallentgoed, W. R. Dipasquale, A. Wijnenga, M. M. J. Weenink, B. Luning, R. Maas, S. L. N. Brzobohata, A. Weller, M. Weiss, T. Mair, M. J. Berghoff, A. S. Woehrer, A. Jeltsch, A. Koekkoek, J. A. F. Hazelbag, H. M. Kouwehoven, M. C. M. Kim, Y. Westerman, B. A. Ylstra, B. Niers, J. M. Johnson, K. C. Verhaak, R. G. W. Varn, F. S. Khasraw, M. van den Bent, M. J. Wesseling, P. French, P. J. 2025-10-10 doi:10.1101/2025.10.09.681314 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ A Physically-Realistic Simulator and Cosine-Based Decoder for MERFISH Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.10.09.681318v1?rss=1 Tsui, J. Adam, N. Choi, W. Liu, L. Y. Flores, C. Ansari, S. Kong, E. Thapliyal, Y. Lee, H. Haider, S. Von Riedemann, I. O'Flanagan, C. IMAXT Cancer Grand Challenges Consortium, Aparicio, S. Roth, A. 2025-10-10 doi:10.1101/2025.10.09.681318 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Larp1 supports brain growth and spatial memory via post-transcriptional control of the translation machinery ]]> https://biorxiv.org/content/10.1101/2025.10.09.681478v1?rss=1 Williams, M. S. Watson, M. Thoreen, C. C. 2025-10-10 doi:10.1101/2025.10.09.681478 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Phylogenomic analyses of the diverse desert-alpine plant lineage Cistantheae ]]> https://biorxiv.org/content/10.1101/2025.10.10.680062v1?rss=1 Chomentowska, A. Dauerman, S. G. Heaphy, N. Gaspar, L. Molina, P. M. Guilliams, C. M. Ogburn, R. M. Hancock, L. P. Holtum, J. A. Moreira-Munoz, A. Arakaki, M. Sweeney, P. W. Peralta, I. E. Edwards, E. J. 2025-10-13 doi:10.1101/2025.10.10.680062 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Interruption of rat absence seizures by auditory stimulation ]]> https://biorxiv.org/content/10.1101/2025.10.10.681637v1?rss=1 McCafferty, C. P. Zheng, X. Tung, R. Gruenbaum, B. F. Blumenfeld, H. 2025-10-13 doi:10.1101/2025.10.10.681637 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Distinct Filament Conformation for Receptor-Bound Amyloid-β from Alzheimers Disease Brain ]]> https://biorxiv.org/content/10.1101/2025.10.10.681740v1?rss=1 Kostylev, M. A. Butan, C. Carmen, G. P. Liu, Y. Gopal, P. Strittmatter, S. M. 2025-10-13 doi:10.1101/2025.10.10.681740 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Axon Regeneration and Functional Recovery after Spinal Cord Injury is Enhanced by Allele-Specific ApoE Neuronal Action through LRP8 ]]> https://biorxiv.org/content/10.1101/2025.10.10.681747v1?rss=1 Kannan, R. Wang, X. Nicholson, L. Lin, N. Z. Howard, E. M. Basu, A. Ingabire, I. Sekine, Y. Strittmatter, S. M. 2025-10-13 doi:10.1101/2025.10.10.681747 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Imaging Cellular Metabolic Rewiring with SuMMIT-SRS ]]> https://biorxiv.org/content/10.1101/2025.10.10.681769v1?rss=1 Li, Y. Li, Z. Li, Y. Rhine, K. Ranamukhaarachchi, S. Qin, S. Jang, H. Villazon, J. Bai, Z. Fraley, S. I. Yeo, G. W. Fan, R. Shi, L. 2025-10-13 doi:10.1101/2025.10.10.681769 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Coordinated and compartmentalized functions of CAII and CAIV establish a dual pH-regulatory mechanism essential for sperm maturation and capacitation ]]> https://biorxiv.org/content/10.1101/2025.10.13.681600v1?rss=1 Wiesehoefer, C. Gardner, C. C. Stoskus, A. Battistone, M. A. Wennemuth, G. Chung, J.-J. 2025-10-14 doi:10.1101/2025.10.13.681600 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Mosaic pattern: lung functional heterogeneity at the alveolus level ]]> https://biorxiv.org/content/10.1101/2025.10.13.682072v1?rss=1 Grifno, G. N. Kahvecioglu, H. A. LeBourdais, R. Travnik, V. Banerji, R. Wangsrikhun, W. Shi, L. Bozal, S. B. Suh, H. Raslan, A. A. Batgidis, A. Kang, B. Deng, F. Dalton, C. Tsao, A. Castle, L. Regan, K. Kobayter, A. Vannini, M. Rashidian, M. Hao, L. Ligresti, G. Mizgerd, J. P. Longest, W. Hindle, M. Saltzman, W. M. Butler, J. P. Suki, B. Nia, H. T. 2025-10-14 doi:10.1101/2025.10.13.682072 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Extreme weather risk shrinks range size estimates and alters biodiversity predictions ]]> https://biorxiv.org/content/10.1101/2025.10.13.682097v1?rss=1 Cohen, J. Ellis-Soto, D. La Sorte, F. Sharma, S. Jetz, W. 2025-10-14 doi:10.1101/2025.10.13.682097 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Slow Intrinsic Oscillations in the Ventrolateral Preoptic nucleus ]]> https://biorxiv.org/content/10.1101/2025.10.13.682168v1?rss=1 Perrenoud, Q. Ribot, J. Geoffroy, H. Gallopin, T. Rouach, N. Rancillac, A. 2025-10-14 doi:10.1101/2025.10.13.682168 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Biological versus Technical Reliability of Epigenetic Clocks and Implications for Disease Prognosis and Intervention Response ]]> https://biorxiv.org/content/10.1101/2025.10.13.682176v1?rss=1 0.75 for biological reliability. Importantly, technical reproducibility did not predict biological reliability; clocks that were technically robust often proved biologically unreliable. We further demonstrated that reliability directly constrains downstream applications. Clocks with higher ICCs produced more stable prognostic associations with cognitive decline and more consistent responsiveness to a vegan diet intervention, whereas unreliable clocks yielded highly variable or spurious effects. Together, these findings reveal that technical reliability is not enough: biological reliability remains a critical limitation for many DNA methylation clocks that constrains their utility, and our work provides a roadmap for prioritizing next-generation clocks most suited for clinical translation. ]]> Sehgal, R. Borrus, D. Gonzalez, J. T. Markov, Y. ADNI, Higgins-Chen, A. T. 2025-10-14 doi:10.1101/2025.10.13.682176 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Tubulin autoregulation factors SCAPER and TTC5 recruit γ-tubulin to non-centrosomal MTOCs for neuronal microtubule nucleation and axon regeneration ]]> https://biorxiv.org/content/10.1101/2025.10.13.682208v1?rss=1 XIE, Y. Comincini, A. Feng, C. Davison, C. A. Hammarlund, M. Bartolini, F. Yogev, S. 2025-10-15 doi:10.1101/2025.10.13.682208 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Optimized reference region and the effect on test-retest reliability and detection of Parkinson's disease with UCB-J. ]]> https://biorxiv.org/content/10.1101/2025.10.15.682460v1?rss=1 Khattar, N. Matuskey, D. Gallezot, J.-D. Naganawa, M. Holmes, S. E. Sadabad, F. E. Esterlis, I. van Dyck, C. H. Mecca, A. P. D'Souza, D. C. Nabulsi, N. B. Finnema, S. J. Huang, Y. Carson, R. E. Toyonaga, T. 2025-10-15 doi:10.1101/2025.10.15.682460 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Multi-scale neural networks enhance species distribution modelling across predictors and taxonomic groups ]]> https://biorxiv.org/content/10.1101/2025.10.15.682577v1?rss=1 van Tiel, N. Zbinden, R. Vanalli, C. Kellenberger, B. Pellissier, L. Tuia, D. 2025-10-15 doi:10.1101/2025.10.15.682577 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Spatial and semantic memory reorganize a hippocampal long-axis gradient ]]> https://biorxiv.org/content/10.1101/2025.10.15.682651v1?rss=1 Jordan, A. G. Voss, J. L. Kragel, J. E. 2025-10-15 doi:10.1101/2025.10.15.682651 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Beyond the Genotype: A Multi-Omic Analysis of APOEe4's Role in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.10.16.682426v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1477a2forg.highwire.dtl.DTLVardef@1a6d173org.highwire.dtl.DTLVardef@1010821org.highwire.dtl.DTLVardef@bcde3a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Markov, Y. Priyanka, A. Xu, L. Wang, W. Thrush-Evensen, K. Gonzalez, J. T. Borrus, D. Kasamoto, J. Sehgal, R. Zou, G. Armstrong, J. Carlyle, B. C. Horvath, S. Bennett, D. A. Zhao, H. van Dyck, C. Lam, T. T. Levine, M. E. Higgins-Chen, A. T. 2025-10-16 doi:10.1101/2025.10.16.682426 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ A multicenter spatial transcriptomics atlas of human tuberculosis and non-tuberculous mycobacterial disease ]]> https://biorxiv.org/content/10.1101/2025.10.17.683002v1?rss=1 Jiang, X. Christian, L. Xi, Y. Zhou, L. Ahmed, A. Zheng, X. Unen, N. V. Neubert, L. Dietrich, J. Kamp, J. C. Kayser, M. Kuehnel, M. Hohlfeld, J. Slevogt, H. Hoeper, M. M. Kaminski, N. Welte, T. Fuge, J. Ringshausen, F. C. Homer, R. J. Jonigk, D. D. Xu, C.-J. Schupp, J. C. Li, Y. 2025-10-17 doi:10.1101/2025.10.17.683002 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ TranslAGE: A Comprehensive Platform for Systematic Validation of Epigenetic Aging Biomarkers ]]> https://biorxiv.org/content/10.1101/2025.10.16.682960v1?rss=1 42,000 total samples. Users can explore these data through interactive dashboards that evaluate four fundamental performance domains: Stability, Treatment response, Associations, and Risk, collectively forming the STAR framework. Stability quantifies robustness to multiple types of technical and biological noise. Treatment response measures biomarker sensitivity to aging interventions and environmental exposures. Associations capture cross-sectional relationships with age, demographics, disease, and other phenotypes, and Risk assesses predictive power for future functional decline, morbidity and mortality. The STAR framework unifies these test metrics into a single composite scoring system that enables researchers to identify, benchmark, and validate biomarkers best suited to their scientific or clinical applications. TranslAGE will be continually updated, with rapid scaling by adding datasets, biomarkers, or analyses. By providing harmonized datasets, precomputed biomarker scores, and interactive data tools, TranslAGE establishes the first standardized, reproducible framework for benchmarking epigenetic aging biomarkers across populations, and accelerates the translation toward clinical use. ]]> Borrus, D. S. Sehgal, R. Armstrong, J. F. Gonzalez, J. T. Zou, G. Kasamoto, J. Markov, Y. Lasky-Su, J. Higgins-Chen, A. 2025-10-19 doi:10.1101/2025.10.16.682960 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ CD8 T cells mediate immunosurveillance for neoantigen+ epithelial stem cells in the colon ]]> https://biorxiv.org/content/10.1101/2025.10.19.683142v1?rss=1 Buck, J. Iyer, N. R. Fagerberg, E. Micevic, G. He, J. St. Denis, K. Shah, V. Blackburn, H. N. Venkatesan, S. Attanasio, J. Hunt, B. G. Dalrymple, A. Konnikova, L. Beyaz, S. Damo, M. Booth, C. J. Connolly, K. A. Joshi, N. S. 2025-10-19 doi:10.1101/2025.10.19.683142 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomic. ]]> https://biorxiv.org/content/10.1101/2025.10.19.683341v1?rss=1 Bolognesi, M. M. Dall'Olio, L. Mandelli, G. E. Lorenzi, L. Bosisio, F. M. Haberman, A. M. Bhagat, G. Borghesi, S. Faretta, M. Castellani, G. CATTORETTI, G. 2025-10-20 doi:10.1101/2025.10.19.683341 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ A high-coverage genome from a 200,000-year-old Denisovan ]]> https://biorxiv.org/content/10.1101/2025.10.20.683404v1?rss=1 Peyregne, S. Massilani, D. Swiel, Y. Boyle, M. J. Iasi, L. N. M. Suemer, A. P. Bossoms Mesa, A. de Filippo, C. Viola, B. Essel, E. Nagel, S. Richter, J. Weihmann, A. Schellbach, B. Zeberg, H. Visagie, J. Kozlikin, M. B. Shunkov, M. V. Derevianko, A. P. Pruefer, K. Peter, B. M. Meyer, M. Paabo, S. Kelso, J. 2025-10-20 doi:10.1101/2025.10.20.683404 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ ATR promotes genome instability via CENP-A eviction from centromeres under replication stress ]]> https://biorxiv.org/content/10.1101/2025.10.20.683416v1?rss=1 Ostapenko, D. Li, H. Trier, I. Shamby, R. Zagoren, E. Bacerra Sabrebra, C. Sumigray, K. Kabeche, L. 2025-10-20 doi:10.1101/2025.10.20.683416 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Mechanisms Driving Thoracic Aortic Aneurysm Stability ]]> https://biorxiv.org/content/10.1101/2025.10.20.683467v1?rss=1 Schwarz, E. L. Li, D. S. Means, C. W. Assi, R. Humphrey, J. D. 2025-10-21 doi:10.1101/2025.10.20.683467 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Coordination of local and global responses in individual mouse thalamic local interneurons ]]> https://biorxiv.org/content/10.1101/2025.10.20.683501v1?rss=1 Wang, K. Hu, W. Fei, Y. Li, C. Liu, C. Ontiri, A. Zhang, D. Chen, Y. Luh, M. Liang, L. 2025-10-21 doi:10.1101/2025.10.20.683501 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Nuclear receptor-neurotransmitter coupling links behavior to metabolic state ]]> https://biorxiv.org/content/10.1101/2025.10.20.683577v1?rss=1 Malaiwong, P. Schroeder, A. F. Brown, T. Wrobel, C. J. Dasgupta, M. Malaiwong, N. Schroeder, F. C. O'Donnell, M. P. 2025-10-21 doi:10.1101/2025.10.20.683577 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Quantifying the impact of genetic mutations on enhancer dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.21.683558v1?rss=1 Das, M. Banerjee, D. Hossain, A. Jensen, M. Mogre, S. Sun, J. Mao, J. Glick, A. B. Salis, H. Girirajan, S. 2025-10-22 doi:10.1101/2025.10.21.683558 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Sleep deprivation constrains dynamic configurations of integrated and segregated brain states impacting cognitive performance ]]> https://biorxiv.org/content/10.1101/2025.10.21.683658v1?rss=1 Cross, N. Borgetto, F. Uji, M. Jegou, A. Nguyen, A. Lee, K. Aydin, U. Perrault, A. Dang-Vu, T. T. Grova, C. 2025-10-22 doi:10.1101/2025.10.21.683658 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Astrocytic PIEZO activation by heartbeat sound promotes extracellular matrix and maturation in human brain organoids ]]> https://biorxiv.org/content/10.1101/2025.10.21.683816v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1ba3159org.highwire.dtl.DTLVardef@fdd741org.highwire.dtl.DTLVardef@13ef417org.highwire.dtl.DTLVardef@b3064_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ferreira-Oliveira, A. Rambow, F. Rambow-Makhzami, S. Nikolaev, Y. A. Novak, A. Shevchuk, O. Voss, H. L. Engel, D. R. Schult, P. A. Pillath-Eilers, M. Kaltwasser, B. Brockmeier, U. Kleinschnitz, C. Hermann, D. M. Dzyubenko, E. 2025-10-22 doi:10.1101/2025.10.21.683816 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Is the whole more than the sum of its parts? Considering global and local features of the connectome improves prediction of individuals and phenotype ]]> https://biorxiv.org/content/10.1101/2025.10.22.683965v1?rss=1 Riley, S. Cheng, A. Wang, Y.-W. Shen, X. Zhao, Y. Holmes, A. Constable, R. T. Yip, S. W. 2025-10-23 doi:10.1101/2025.10.22.683965 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Canonical decision computations underlie behavioral and neural signatures of cooperation in primates ]]> https://biorxiv.org/content/10.1101/2025.10.22.683999v1?rss=1 Shi, W. Meisner, O. C. Jadi, M. P. Chang, S. W. C. Nandy, A. S. 2025-10-23 doi:10.1101/2025.10.22.683999 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Effect of prescribing and deprescribing oxycodone on pain and function in a mouse model of osteoarthritis: impact of polypharmacy and sex on response ]]> https://biorxiv.org/content/10.1101/2025.10.22.684045v1?rss=1 Mach, J. Blaker, C. Winters, B. Otsu, Y. Clarke, E. Allore, H. Vander Wyk, B. Winardi, K. Peel, R. Gregson, C. Assareh, N. Kourieh, M. Hilmer, S. N. 2025-10-23 doi:10.1101/2025.10.22.684045 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ UFMylation of 14-3-3ϵ coordinates MAVS signaling complex assembly to promote antiviral innate immune induction ]]> https://biorxiv.org/content/10.1101/2025.10.21.683613v1?rss=1 Gutierrez, I. V. Park, M. Sar, L. Rodriguez, R. E. Schmidt, H. M. Snider, D. L. Torres, G. Scaglione, K. M. Horner, S. M. 2025-10-24 doi:10.1101/2025.10.21.683613 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX ]]> https://biorxiv.org/content/10.1101/2025.10.23.682564v1?rss=1 O'Brien, M. Silva-Sanchez, D. Woollard, G. Je, K. Hanson, S. M. Needleman, D. J. Cossio, P. Thiede, E. Astore, M. A. 2025-10-24 doi:10.1101/2025.10.23.682564 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ PIWIL3-piRNA Pathway Is Essential for Rabbit Oogenesis and Embryogenesis via Broad Regulation of the Transcriptome and Proteome ]]> https://biorxiv.org/content/10.1101/2025.10.23.684072v1?rss=1 Gong, Y. Li, L. Qian, Y. Lu, T. Zhang, Z. Jiang, L. Liu, G. Cui, M. Li, S. Li, Z. Shi, S. Lin, H. 2025-10-24 doi:10.1101/2025.10.23.684072 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Adipose-mimetic granular hydrogels uncover biophysical cues driving breast cancer invasion ]]> https://biorxiv.org/content/10.1101/2025.10.23.684224v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@d3ce0org.highwire.dtl.DTLVardef@117abb1org.highwire.dtl.DTLVardef@10917faorg.highwire.dtl.DTLVardef@55f3e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Polyacrylamide bead granular hydrogels recapitulate adipose tissue structure and alter cancer cell invasion in a stiffness-dependent manner. The invasion of primary breast cancer cells through mammary adipose is influenced by the heterogeneous mechanical properties of native stromal components, namely adipocytes and extracellular matrix (left). Customizable granular hydrogels provide insight into the physical regulation of breast cancer progression by mimicking adipose tissue extracellular matrix structure (collagen I, i.) and stromal cell mechanics (polyacrylamide bead, ii.), whereby the inclusion of soft beads and/or dilute matrix promotes cancer cell migration compared to stiffer hydrogels (right). C_FIG ]]> Knode, B. K. Beeghly, G. F. Schutrum, B. E. Wang, D. Zheng, Y. Battistella, A. Goswami, R. Eom, C.-Y. Bozec, A. Guck, J. Nishimura, N. Girardo, S. O'Hern, C. Fischbach, C. 2025-10-24 doi:10.1101/2025.10.23.684224 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Multi-Class Classification of Cannabis and Alcohol Use Disorder: Identifying Common and Substance-Specific Neural Circuits. ]]> https://biorxiv.org/content/10.1101/2025.10.24.684424v1?rss=1 Kato, A. Kulkarni, K. R. Das, N. R. Heflin, M. Fiore, V. G. Filbey, F. M. Gu, X. 2025-10-26 doi:10.1101/2025.10.24.684424 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Stress drives the hippocampus to prioritize statistical prediction over episodic encoding ]]> https://biorxiv.org/content/10.1101/2025.10.25.683838v1?rss=1 Zhou, I. Bai, Z. Huang, Y. Wijaya, E. G. Sherman, B. E. Turk-Browne, N. B. Goldfarb, E. V. 2025-10-26 doi:10.1101/2025.10.25.683838 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ In Silico Post-screening of Anti-polymerization Agents to Treat Sickle Cell Disease ]]> https://biorxiv.org/content/10.1101/2025.10.25.684554v1?rss=1 Qian, Y. Daryakenari, N. A. Hallow, M. Lu, L. Buffet, P. A. Dao, M. Li, H. Karniadakis, G. E. 2025-10-26 doi:10.1101/2025.10.25.684554 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Seventy-five Years of Systematic Biology: Looking Back, Moving Forward ]]> https://biorxiv.org/content/10.1101/2025.10.21.683502v1?rss=1 Landis, M. J. Donoghue, M. J. 2025-10-27 doi:10.1101/2025.10.21.683502 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ A simple circuit to sustain intact tumor microenvironments for complex drug interrogations ]]> https://biorxiv.org/content/10.1101/2025.10.26.684624v1?rss=1 Sarvestani, A. L. Ruff, S. M. Remmert, K. Teke, M. Verbus, E. Saif, A. Garmendia-Cedillos, M. Rossi, A. Rainey, A. Nomie, K. Sinha, S. Wach, M. M. Ryan, C. Gregory, S. N. Desai, P. Panda, A. K. Smith, E. C. Ayabe, R. McDonald, J. D. Gupta, S. Pu, T. Khan, T. M. Lambdin, J. Luberice, K. Lux, S. C. Hong, H. Alexander, I. Akmal, S. R. Reman, S. Xiao, S. Ho, J. Burke, J. Hannah, C. E. Livanova, A. Tyshevich, A. Kurpe, S. Kravets, A. Salem, B. Vibe, D. Tkachukv, A. Belozerova, A. Sarachakov, A. Barykin, E. Kushnarev, V. Postovalova, E. Bagaev, A. Kedei, 2025-10-27 doi:10.1101/2025.10.26.684624 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ A major histocompatibility complex (MHC) class II molecule that binds the same viral pathogen peptide with both nonamer and decamer core sequences for presentation to T cells ]]> https://biorxiv.org/content/10.1101/2025.10.27.684722v1?rss=1 Goryanin, A. Cook, A. G. Behboudi, S. Kaufman, J. Halabi, S. 2025-10-27 doi:10.1101/2025.10.27.684722 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ CRISPR-engineered deletion of POGZ alters transcription factor binding at promoters of genes involved in synaptic signaling ]]> https://biorxiv.org/content/10.1101/2025.10.27.684870v1?rss=1 Oliveira, M. M. Liu, Y. Erdin, S. Gao, D. Bhavsar, R. Mohajeri, K. O'Keefe, K. Boone, P. M. Xavier, G. Liao, C. Li, A. Yadav, R. Salani, M. Lucente, D. Currall, B. de Esch, C. E. F. Tai, D. J. C. Ruderfer, D. Brennand, K. J. Gusella, J. F. Talkowski, M. E. 2025-10-27 doi:10.1101/2025.10.27.684870 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Longitudinal, simultaneous wide-field fluorescent Ca2+ imaging and fMRI in awake mice ]]> https://biorxiv.org/content/10.1101/2025.10.27.684863v1?rss=1 Mandino, F. Kang, T. Shen, X. Horien, C. Papademetris, X. Strittmatter, S. M. Lake, E. M. 2025-10-28 doi:10.1101/2025.10.27.684863 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Universal phylogenetic inertia in body temperature evolution across endothermic and ectothermic tetrapods. ]]> https://biorxiv.org/content/10.1101/2025.10.27.684885v1?rss=1 Tarimo, E. White, E. Bodensteiner, B. Munoz, M. Waldron, B. UYEDA, J. 2025-10-28 doi:10.1101/2025.10.27.684885 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ Single cell whole genome and transcriptome sequencing links somatic mutations to cell identity and ancestry ]]> https://biorxiv.org/content/10.1101/2025.10.28.685157v1?rss=1 Natu, A. Dehankar, M. K. Pattni, R. Suvakov, M. Olisov, D. Tomasini, L. Jang, Y. Huang, Y. Benito-Garragori, E. Hasenfeld, P. Korbel, J. Urban, A. E. Abyzov, A. Vaccarino, F. M. 2025-10-29 doi:10.1101/2025.10.28.685157 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Two-Step Mechanism of Bruton's Tyrosine Kinase MembraneRecruitment and Activation ]]> https://biorxiv.org/content/10.1101/2025.10.28.685231v1?rss=1 McAllister, R. Stiegler, A. Chari, K. Chari, M. Bhattacharyya, M. Gupta, K. 2025-10-30 doi:10.1101/2025.10.28.685231 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Spatial analysis reveals the cellular microenvironments and mechanisms of inflammation and kidney injury in acute interstitial nephritis ]]> https://biorxiv.org/content/10.1101/2025.10.29.684811v1?rss=1 Baker, M. L. Kakade, V. R. Budiman, T. Weiss, M. Cunningham, J. M. Sadarangani, S. Lerner, G. Moeckel, G. Rosenberg, A. Z. Parikh, C. R. Kluger, Y. Moledina, D. G. Cantley, L. G. 2025-10-30 doi:10.1101/2025.10.29.684811 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Development of Collagenous Filaments with Tuneable Mechanical Properties Using a 3D Bioprinter and Molecular Crowding ]]> https://biorxiv.org/content/10.1101/2025.10.29.684883v1?rss=1 Rossello-Martinez, A. Liang, Z. Zhou, Z. Gong, X. Nguyen, R. Jordan, S. N. Mak, M. 2025-10-30 doi:10.1101/2025.10.29.684883 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ The LINC complex and microtubule motors regulate the number and position of nuclei in the subperineurial glial cells of the Drosophila blood-brain barrier ]]> https://biorxiv.org/content/10.1101/2025.10.29.685339v1?rss=1 Annes, O. R. Schmitt, A. Akinremi, D. B. Koskas, D. Qiu, Y. Jewell, H. DaCosta, J. M. Folker, E. 2025-10-30 doi:10.1101/2025.10.29.685339 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Acetoacetate suppresses colon cancer via an MR1-MAIT axis ]]> https://biorxiv.org/content/10.1101/2025.10.29.685375v1?rss=1 Clay, S. L. El Tekle, G. Rashan, E. H. Fonseca-Pereira, D. Shin, Y.-H. Andreeva, N. Nakatsu, G. Lobo, A. F. Chen, S. P. Bae, S. Michaud, M. Glickman, J. N. Clardy, J. Vander Heiden, M. Garrett, W. 2025-10-30 doi:10.1101/2025.10.29.685375 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Engineered orthogonal translation systems from metagenomic libraries expand the genetic code ]]> https://biorxiv.org/content/10.1101/2025.10.30.685624v1?rss=1 200 tRNAs, test >1,250 combinations of aaRS:tRNA pairs, and identify the AP1 TrpRS:tRNATrpUCA as an orthogonal pair that natively encodes tryptophan at the UGA codon. We demonstrate that the AP1 TrpRS:tRNATrpUCA is highly active in cell-free and cellular contexts. We then use Ochre, a genomically recoded Escherichia coli strain that lacks UAG and UGA codons, to engineer an AP1 TrpRS variant capable of 5-hydroxytryptophan incorporation at an open UGA codon. We anticipate that our strategy of integrating metagenomic bioprospecting with cell-free screening and cell-based engineering will accelerate the discovery and optimization of orthogonal translation systems for genetic code expansion. ]]> Seki, K. Nguyen, M. T. A. Penev, P. I. Isaacs, F. J. Banfield, J. F. Jewett, M. C. 2025-10-30 doi:10.1101/2025.10.30.685624 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ MHC-I diversity enables rapid adaptation during viral pandemic in wild rabbit populations ]]> https://biorxiv.org/content/10.1101/2025.10.30.685367v1?rss=1 Zhang, Y. Day, J. P. Lirintzi, M. Ji, J. Tregaskes, C. Carneiro, M. Alves, J. M. Strive, T. Kaufman, J. Jiggins, F. M. 2025-10-31 doi:10.1101/2025.10.30.685367 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Planar cell polarity aligns epithelial migration to coordinate tissue architecture and functional zonation ]]> https://biorxiv.org/content/10.1101/2025.10.30.685585v1?rss=1 Lee, R. F. Oluwatade, D. Sumigray, K. 2025-10-31 doi:10.1101/2025.10.30.685585 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Protein-protein interaction networks can be highly sensitive to the membrane phase transition ]]> https://biorxiv.org/content/10.1101/2025.10.30.685611v1?rss=1 Schaffner, T. A. Machta, B. B. 2025-10-31 doi:10.1101/2025.10.30.685611 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm ]]> https://biorxiv.org/content/10.1101/2025.10.30.685666v1?rss=1 Oel, A. P. Cros, C. C. D. R. Pan, L. Buglakova, E. Haury Parra, S. Santangeli, L. Gerber, T. Papalopoulos, N. Martinez Vergara, H. Puga, D. Disela, V. Lara, N. Bertucci, P. Y. Witte, V. Kilic, A. B. Quintana Urzainqui, I. Acevedo, J. M. Musser, J. Kreshuk, A. Arendt, D. 2025-10-31 doi:10.1101/2025.10.30.685666 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Decay in transcriptional information flow is a hallmark of cellular aging ]]> https://biorxiv.org/content/10.1101/2025.10.30.685689v1?rss=1 Emison, B. Lynn, C. W. Mugler, A. Ambrosio, F. Dixit, P. D. 2025-10-31 doi:10.1101/2025.10.30.685689 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Precocial ancestry of placental mammals ]]> https://biorxiv.org/content/10.1101/2025.10.30.685703v1?rss=1 Chavan, A. R. Pavlicev, M. Wagner, G. P. 2025-10-31 doi:10.1101/2025.10.30.685703 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Structural basis of HSV-1 DNA replication origin-binding protein UL9 ]]> https://biorxiv.org/content/10.1101/2025.10.31.685793v1?rss=1 Huang, C. Wu, H. Song, J. Zhang, X. Ma, J. 2025-10-31 doi:10.1101/2025.10.31.685793 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ A chromatin-associated pool of Aurora A controls kinetochore-microtubule attachments to ensure chromosome biorientation ]]> https://biorxiv.org/content/10.1101/2025.10.31.685952v1?rss=1 Meaders, J. L. Rodriguez, A. A. Variyar, S. Park, S. Cirulli, A. E. Oegema, K. Corbett, K. D. Desai, A. 2025-11-01 doi:10.1101/2025.10.31.685952 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ A comprehensive view of somatic mosaicism by single-cell DNA analysis ]]> https://biorxiv.org/content/10.1101/2025.10.31.685648v1?rss=1 Luquette, L. J. Coorens, T. H. H. Natu, A. Suvakov, M. Caplin, A. Jun, M. S. Mo, A. Pelt, J. Anderson, L. Berselli, M. Bhamidipati, S. Blanchard, T. Brew, J. Chun, H.-J. E. Chun, H. Dehankar, M. K. Feng, W. C. Furatero, R. Grochowski, C. M. Ho, E. Jang, Y. Kottapalli, K. Leonard, M. K. Lim, N. S. Lindsay, T. Nicholson, S. Raimondi, I. Runnels, A. Scharlee, C. Shin, J. Veit, A. D. VonDran, M. Wang, Y. Yuan, D. J. Zhao, Y. Bell, T. J. Ardlie, K. Doddapaneni, H. Fulton, R. Germer, S. Landau, D. Oh, J. W. Park, P. J. Vaccarino, F. M. Walsh, C. A. Abyzov 2025-11-03 doi:10.1101/2025.10.31.685648 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Spatial Transcriptomics Identify T Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis ]]> https://biorxiv.org/content/10.1101/2025.10.31.685702v1?rss=1 Qin, Q. A. Ostendorf, L. Wells, S. L. Gao, C. Tran, M. Alikhan, F. M. Zhang, X. Chewcharat, A. Rider, R. S. Prell, S. A. Chowdhury, R. B. Weins, A. Shah, S. I. Mistry, K. Bowman, T. Villani, A.-C. LeBoeuf, N. Selamet, U. Ravi, K. S. Sharon, E. Leaf, D. E. Moledina, D. G. Sise, M. E. De Vlaminck, I. Rao, D. A. Wei, K. Gupta, S. 2025-11-03 doi:10.1101/2025.10.31.685702 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Niche dimensionality drives microbial community structure ]]> https://biorxiv.org/content/10.1101/2025.11.02.686095v1?rss=1 Srinivasan, K. Plata, G. Dixit, P. D. 2025-11-03 doi:10.1101/2025.11.02.686095 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Evaluating the potential of cross-species neutralization of anti-PfCyRPA and anti-PfRIPR Monoclonal Antibodies ]]> https://biorxiv.org/content/10.1101/2025.11.03.682341v1?rss=1 Guerra, N. Hagadorn, K. A. Nair, M. Thiam, L. G. Williams, B. G. McHugh, K. Pipini, D. Healer, J. Masendycz, P. Cowman, A. F. Draper, S. J. Bei, A. K. 2025-11-04 doi:10.1101/2025.11.03.682341 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib ]]> https://biorxiv.org/content/10.1101/2025.11.04.686193v1?rss=1 Podszywalow-Bartnicka, P. Shine, M. Lin, J. Neugebauer, K. M. 2025-11-05 doi:10.1101/2025.11.04.686193 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology ]]> https://biorxiv.org/content/10.1101/2025.11.04.686570v1?rss=1 Zhan, L. Yu, D. Ivankovic, F. Niarchou, M. Domenech-Salgado, L. Barr, C. L. Benarroch, F. Budman, C. L. Cath, D. C. Freimer, N. B. Garrido, H. Grados, M. A. Gross-Tsur, V. Herrera-Amighetti, L. King, R. A. Kurlan, R. Leckman, J. F. Lyon, G. J. McMahon, W. M. Pauls, D. L. Pollak, Y. Robertson, M. M. Romero, R. Rouleau, G. A. Sandor, P. Singer, H. S. Giusti-Rodriguez, P. Davis, L. K. Mathews, C. A. Scharf, J. M. Ophoff, R. A. 2025-11-05 doi:10.1101/2025.11.04.686570 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Lipid lowering alone fails to limit atherosclerosis progression and neutrophilic inflammation in middle-aged mice ]]> https://biorxiv.org/content/10.1101/2025.11.04.686598v1?rss=1 Gannon, O. J. Rahtes, A. Bonin, J. Salfate del Rio, I. Partridge, J. Khan, S. Nobles, A. Covert, G. Bahr, A. Ramos, R. B. MacNamara, K. C. Fredman, G. 2025-11-05 doi:10.1101/2025.11.04.686598 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Global distribution patterns of an ocean-surface dwelling animal are associated with organismal mirror asymmetry ]]> https://biorxiv.org/content/10.1101/2025.11.04.686608v1?rss=1 Iwanicki, T. Maximenko, N. Dunn, C. Church, S. H. Goodwin, D. S. Helm, R. R. 2025-11-06 doi:10.1101/2025.11.04.686608 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.11.04.686660v1?rss=1 Perets, E. A. Spies, J. A. Cheong, J. H. Shi, L. Asamoto, D. K. Holehouse, A. S. Kim, J. E. Min, W. Neu, J. Yan, E. C. Y. 2025-11-06 doi:10.1101/2025.11.04.686660 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ Geographic distribution of the Birmingham Darter Etheostoma birminghamense ]]> https://biorxiv.org/content/10.1101/2025.11.05.686853v1?rss=1 Brownstein, C. D. Andriotis, K. Haynes, C. B. Sturm, N. D. Kuhajda, B. R. Near, T. J. 2025-11-07 doi:10.1101/2025.11.05.686853 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Control of gene output by intron RNA structure ]]> https://biorxiv.org/content/10.1101/2025.11.08.687378v1?rss=1 Schärfen, L. Bech, P. Podszywałow-Bartnicka, P. Neugebauer, K. M. 2025-11-09 doi:10.1101/2025.11.08.687378 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Sensory processing reformats odor coding around valence and dynamics ]]> https://biorxiv.org/content/10.1101/2025.11.08.687380v1?rss=1 Lizbinski, K. Ellison, K. J. Sancer, G. Mao, H. X. Jeanne, J. M. 2025-11-09 doi:10.1101/2025.11.08.687380 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Electrophysiological profiling of exocytosis during early-stage development of the zebrafish lateral line ]]> https://biorxiv.org/content/10.1101/2025.11.07.686968v1?rss=1 Wang, J. Karatekin, E. Zenisek, D. 2025-11-10 doi:10.1101/2025.11.07.686968 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Region-specific proteomic analysis of aging rhesus macaques following chronic glutamate-carboxypeptidase-II (GCPII) inhibition elucidates potential treatment strategies for sporadic Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.11.07.687004v1?rss=1 2,400 proteins across experimental conditions, and label-free quantification revealed region-specific differential expression patterns paralleling known vulnerability gradients in sAD. Gene ontology enrichment of vulnerable regions implicated pathways governing protein deneddylation, amyloid and tau-associated processes, synaptic plasticity, mitochondrial homeostasis, and oxidative stress, revealing putative targets for therapeutic intervention in sAD. These findings demonstrate that GCPII inhibition engages distinct, region-selective molecular programs in the aging primate cortex, consistent with the protection of circuits most vulnerable to sAD. By mapping the proteomic shifts that occur with treatment, we reveal molecular signatures that not only serve as candidate biomarkers but also highlight novel mechanistic pathways contributing to calcium-driven degeneration in sAD. As such, more focused investigations into these pathways of therapeutic interest are warranted, in addition to the analysis of key post-translational modifications and their potential roles in sAD. ]]> Steigmeyer, A. D. Battison, A. S. Liebman, I. R. van Dyck, C. H. Slusher, B. S. Arnsten, A. F. Malaker, S. A. Datta, D. 2025-11-10 doi:10.1101/2025.11.07.687004 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research ]]> https://biorxiv.org/content/10.1101/2025.11.08.687330v1?rss=1 Demsar, J. Kraljic, A. Matkovic, A. Brege, S. Pan, L. Tamayo, Z. Fonteneau, C. Helmer, M. Ji, J. L. Anticevic, A. Korponay, C. Salavrakos, M. Glasser, M. F. Nickerson, L. D. Cho, Y. T. Repovs, G. 2025-11-10 doi:10.1101/2025.11.08.687330 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Spatial Partitioning of Core Glycolysis Enables Tissue-Specific Metabolic Programs In Vivo ]]> https://biorxiv.org/content/10.1101/2025.11.09.687253v1?rss=1 Gonzalez, I. J. Wolfe, A. D. Clark, B. Hanna, M. Sun, Q. Ravikumar, S. Tsives, A. Emerson, S. E. Siebel, S. Kibbey, R. Colon-Ramos, D. 2025-11-10 doi:10.1101/2025.11.09.687253 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ PKMζ-PKC{iota}/{lambda} double-knockout reveals the atypical PKCs are crucial for hippocampal late-LTP and spatial long-term memory ]]> https://biorxiv.org/content/10.1101/2025.11.10.687514v1?rss=1 Tsokas, P. Hsieh, C. Grau-Perales, A. Kwok, L. Rodriguez-Valencia, L. M. Cano, D. A. Allen, K. D. Smith, H. J. H. Kubayeva, S. Wei, B. J. Sabzanov, S. Flores-Obando, R. E. Ghosh, S. Bergold, P. J. Cottrell, J. E. Fenton, A. A. Sacktor, T. C. 2025-11-11 doi:10.1101/2025.11.10.687514 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Learning-dependent cholinergic plasticity reconfigures cortical circuit dynamics. ]]> https://biorxiv.org/content/10.1101/2025.11.10.687664v1?rss=1 Moberly, A. Cardin, J. A. Higley, M. 2025-11-11 doi:10.1101/2025.11.10.687664 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C. ]]> https://biorxiv.org/content/10.1101/2025.11.10.687702v1?rss=1 Li, D. Wang, X. Hu, B. Hao, H. Hamill, S. Li, Y. Chen, G. De Camilli, P. Reinisch, K. 2025-11-11 doi:10.1101/2025.11.10.687702 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC organoids ]]> https://biorxiv.org/content/10.1101/2025.11.11.687875v1?rss=1 Cao, L. Fan, Y. Ghorbani, S. Mariani, J. Zhang, Y. Fernando, M. B. Bendl, J. Fullard, J. Ramos, S. I. Mead, E. A. Deikus, G. Beaumont, K. G. Sebra, R. Tsankova, N. Roussos, P. Brennand, K. J. Fang, G. 2025-11-12 doi:10.1101/2025.11.11.687875 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Niche partitioning by resource size in the gut microbiome ]]> https://biorxiv.org/content/10.1101/2025.11.13.688124v1?rss=1 Moreno-Gamez, S. Anderson, B. W. Vercelli, G. T. Altmann, F. Goodman, A. L. Cordero, O. X. 2025-11-13 doi:10.1101/2025.11.13.688124 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases ]]> https://biorxiv.org/content/10.1101/2025.11.13.683933v1?rss=1 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI ]]> Wu, J. Athavale, D. Balch, C. Zhao, J. Zou, G. Fan, Y. Zhang, Y. Zhao, J. Ghelfi, M. Pompetti, A. Calendo, G. Scott, A. Shao, S. Yao, X. Pizzi, M. P. Vellano, C. Khazak, V. Zhang, S. Yap, T. A. Dhar, S. S. Sundar, R. Spitz, F. Grana, G. Ajani, J. A. Song, S. 2025-11-14 doi:10.1101/2025.11.13.683933 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Brain-wide Genome Editing via STEP-RNPs for Treatment of Angelman Syndrome ]]> https://biorxiv.org/content/10.1101/2025.11.13.684643v1?rss=1 Lu, X. Xie, Y. Bao, Y. Yu, J. Wang, Z. Fan, J. Sheu, W. C. Long, G. Tu, Z. Tong, J. Manquen, G. Li, Y. Katta, V. Chow, R. Chen, B. Meng, Z. Ma, Y.-h. Qiu, C. Chen, S. Tsai, S. Kumar, B. D. Hendry, C. E. Jiang, Y.-h. Zhou, J. 2025-11-14 doi:10.1101/2025.11.13.684643 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS ]]> https://biorxiv.org/content/10.1101/2025.11.13.688350v1?rss=1 Sariipek, N. E. Safina, K. R. Lu, W. S. Li, S. Janes, J. T. Van Orden, M. Livak, K. J. Heaton, H. Ho, V. T. Koreth, J. Luskin, M. R. Griffin, G. K. Garcia, J. S. Lindsley, R. C. Cutler, C. Soiffer, R. J. Ritz, J. Wu, C. J. Antin, J. H. Lane, A. A. Gooptu, M. Galen, P. v. 2025-11-14 doi:10.1101/2025.11.13.688350 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Heightened empathic responses led by imbalanced cortico-amygdala circuit in Shank3 autism mouse model ]]> https://biorxiv.org/content/10.1101/2025.11.14.688290v1?rss=1 Qiao, S. Jiang, Y.-h. 2025-11-14 doi:10.1101/2025.11.14.688290 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ SCAPE: An AI-Driven Platform for Comprehensive Single-Cell Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.11.15.688526v1?rss=1 Wu, M. Wu, H. Zhou, Y. CHENG, S. 2025-11-16 doi:10.1101/2025.11.15.688526 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Anopheles mosquitoes exposed to long-acting antimalarials via drug-spiked bloodmeal absorb drug but do not suffer fitness costs ]]> https://biorxiv.org/content/10.1101/2025.11.13.688204v1?rss=1 Goheen, M. M. Orfano, A. Dah, S. R. Foy, B. D. Brackney, D. E. Li, F. Ouedraogo, J. B. Da, D. F. Dabire, R. K. Some, A. F. Bei, A. K. Parikh, S. 2025-11-17 doi:10.1101/2025.11.13.688204 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Surface-by-temperature interactions shape the relationship between viral free-living survival and reproduction ]]> https://biorxiv.org/content/10.1101/2025.11.16.688743v1?rss=1 Kabengele, K. Seth, A. Johnson, T. Ogbunugafor, C. B. 2025-11-17 doi:10.1101/2025.11.16.688743 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling ]]> https://biorxiv.org/content/10.1101/2025.11.18.686377v1?rss=1 Kumar, S. Jung, H. A. Walker, G. Rana, J. K. Fu, R. Hong, M. T. Malerba, F. Kumar, J. Navratna, V. Jung, W. Miller, S. J. Kruckenhauser, L. M. Capsoni, S. Hafler, B. P. Cattaneo, A. Krishnan, Y. Mosalaganti, S. Bhattacharyya, M. 2025-11-18 doi:10.1101/2025.11.18.686377 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Absence of Sensory Cooling Activity and Cooling Agents from California's New ''Non-Menthol'' Cigarettes Marketed in 2025 ]]> https://biorxiv.org/content/10.1101/2025.11.17.688932v1?rss=1 Jabba, S. V. Erythropel, H. C. Anastas, P. T. Krishnan-Sarin, S. O'Malley, S. Zimmerman, J. B. Jordt, S. E. 2025-11-19 doi:10.1101/2025.11.17.688932 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ LRRK2 integrates Rab and GABARAP interactions to sense and respond to distinct lysosomal stresses ]]> https://biorxiv.org/content/10.1101/2025.11.19.689251v1?rss=1 Clegg, D. Bentley-DeSousa, A. Roczniak-Ferguson, A. Ferguson, S. M. 2025-11-19 doi:10.1101/2025.11.19.689251 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ ApoE lipidation, not isoform, is the key modulator of Aβ interaction, uptake, and cytotoxicity ]]> https://biorxiv.org/content/10.1101/2025.11.19.685371v1?rss=1 APOE{varepsilon}3>APOE{varepsilon}2), it remains an important open question whether these differences are due directly to isoform-specific interactions between ApoE and A{beta} or indirect effects on A{beta} clearance. This is further complicated because ApoE exists in lipidated or unlipidated states, which influence its biochemical properties. To disentangle how single ApoE mutations confer vastly different effects on A{beta} pathology, we investigated how both the ApoE isoform and lipidation modulate its interaction with inert and cytotoxic A{beta} species, and its effect on A{beta} uptake and cytotoxicity in human astrocytes. MethodsWe prepared A{beta} in distinct aggregation states (monomers, oligomers, and fibrils) and ApoE in different lipidation states to characterize their size and affinity for one another using fluorescence correlation spectroscopy and fluorescence polarization, respectively. We then utilized flow cytometry and live cell imaging to quantify the uptake of A{beta} in different aggregation states by primary and immortalized human astrocytes in the presence of different isoforms of lipidated or unlipidated ApoE. ResultsThis study revealed that ApoE lipidation, not isoform, has the biggest impact on its interaction with A{beta}, on the uptake of A{beta} by astrocytes, and on A{beta}-induced cytotoxicity. Specifically, unlipidated ApoE preferentially interacts with A{beta} oligomers and fibrils, which substantially inhibits their uptake by astrocytes. Conversely, lipidated ApoE showed no interaction with A{beta} oligomers and had a reduced ability to inhibit A{beta} uptake. ConclusionsOur observations provide important molecular details that suggest previously observed ApoE isoform-specific differences in AD risk are likely driven primarily by in vivo differences in ApoE lipidation, rather than biophysical differences between ApoE isoforms in their interaction with A{beta}. We propose that the impaired lipidation of ApoE4 in the brain increases levels of unlipidated ApoE, which then bind toxic A{beta} oligomers and reduce their clearance by astrocytes. These findings underscore the therapeutic potential of interventions aimed at increasing ApoE lipidation and decreasing interactions between toxic A{beta} oligomers and ApoE. ]]> Nurmakova, K. Gomes, G.-N. W. Levine, Z. A. 2025-11-20 doi:10.1101/2025.11.19.685371 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ A unified genetic perturbation language for human cellular programming ]]> https://biorxiv.org/content/10.1101/2025.11.20.689421v1?rss=1 Hartman, A. Takacsi-Nagy, O. Kernick, C. Theberath, N. E. Lu, J. Wu, L. Mantilla, M. Mittra, S. McClellan, A. Johnson, N. Mohamad, L. Castillo-Colin, L. Hoque, F. Eapen, A. Chen, A. Moser, L. M. Rogando, T. Hernandez, A. Santostefano, K. Satpathy, A. T. Roth, T. L. 2025-11-20 doi:10.1101/2025.11.20.689421 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ A gene expression atlas of a juvenile nervous system ]]> https://biorxiv.org/content/10.1101/2025.11.21.689793v1?rss=1 Taylor, S. R. Olson, C. Ripoll-Sanchez, L. Valperga, G. McWhirter, R. Barney, S. T. Atkinson, A. Goel, S. Weinreb, A. Hardin, A. Rolfson, A. Pattee, J. Aguilar, G. R. Merritt, D. M. Eroglu, M. Majeed, M. Grundvig, E. Child, E. Vertes, P. E. Schafer, W. Varol, E. Hammarlund, M. Hobert, O. Miller, D. M. 2025-11-22 doi:10.1101/2025.11.21.689793 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ Proteogenomic profiling of soft tissue leiomyosarcoma reveals distinct molecular subtypes with divergent outcomes and therapeutic vulnerabilities ]]> https://biorxiv.org/content/10.1101/2025.11.19.689365v1?rss=1 Tanaka, A. Ogawa, M. Otani, Y. Hendrickson, R. C. Zhuoning, L. Agaram, N. P. Klimstra, D. S. Wang, J. Y. Roehrl, M. H. A. 2025-11-24 doi:10.1101/2025.11.19.689365 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Visual perceptual learning enhances functional connectivity in retinotopic space ]]> https://biorxiv.org/content/10.1101/2025.11.21.689780v1?rss=1 Bejjanki, V. R. Turk-Browne, N. B. 2025-11-24 doi:10.1101/2025.11.21.689780 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ In vivo assessment of differential toxicity of cancer treatment drugs in Fanconi Anemia ]]> https://biorxiv.org/content/10.1101/2025.11.21.689800v1?rss=1 Grompe, M. Dorrell, C. Burtness, B. Cruz-Gomez, S. MacMillan, A. 2025-11-24 doi:10.1101/2025.11.21.689800 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ The discovery and patterns of the underlying long-standing mild-effect mutator alleles in S. cerevisiae populations ]]> https://biorxiv.org/content/10.1101/2025.11.22.689970v1?rss=1 C and A>G mutations in natural polymorphisms of the African beer population of S. cerevisiae. Remarkably, the mutation spectrum deviation in this population is greater than that observed between some Saccharomyces species. Furthermore, computational analysis suggests the introgression of mild mutator allele(s) from the African beer population into a subset of the French dairy population, motivating experimental characterization of de novo mutations in these strains. We observed a consistent but weak enrichment of A>C and A>G mutations among de novo mutations in the African beer population, likely reflecting their low overall frequency. Other mutation types showed greater variability, with one outlier strain (AFL from African beer) exhibiting an excess of C>A mutations. Comparisons across strains that have been empirically assayed for mutation spectra revealed that de novo mutations display the greatest variability, followed by rare polymorphisms. This pattern suggests that additional mutator alleles may segregate in natural populations but are often purged due to their fitness costs. We infer that the mild enrichment of A>C and A>G mutations in African beer strains reflects mutator alleles with weak effects that can persist through evolution. ]]> Jiang, P. Sudhesh, V. Phan, M. M.-N. Bansal, I. Wheeler, C. Herr, A. J. Dunham, M. J. Harris, K. 2025-11-24 doi:10.1101/2025.11.22.689970 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks ]]> https://biorxiv.org/content/10.1101/2025.11.22.689899v1?rss=1 Li, H. Shan, Z. Fu, H. Du, Y. Gao, S. Gao, P. Cooper-Knock, J. Min, Y. Xing, X. Zhang, S. 2025-11-25 doi:10.1101/2025.11.22.689899 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Kruppel-like factor 1 acts upstream of the SKN-1/Nrf transcription factors to modulate oxidative stress, lipid homeostasis and longevity ]]> https://biorxiv.org/content/10.1101/2025.11.22.689963v1?rss=1 Castillo-Quan, J. I. McCarty, A. Kurdeikaite, U. Gilmore, K. Cabral, A. Mejia, J. Barrett, J. La Terza, M. Johnson, E. Carroll, A. Schaffer, J. Moroz, N. 2025-11-25 doi:10.1101/2025.11.22.689963 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Transgenerational plasticity affects fitness and mediates local adaptation ]]> https://biorxiv.org/content/10.1101/2025.11.23.690023v1?rss=1 Branch, H. A. Moxley, D. R. Angert, A. L. 2025-11-25 doi:10.1101/2025.11.23.690023 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Endothelial cell MHC molecules are necessary and sufficient to reject 3D-printed human skin grafts in an advanced human immune system mouse ]]> https://biorxiv.org/content/10.1101/2025.11.24.689811v1?rss=1 Tobiasova, Z. Sefik, E. Qin, L. McNiff, J. Davis, G. Flavell, R. Saltzman, W. M. Pober, J. S. 2025-11-25 doi:10.1101/2025.11.24.689811 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data ]]> https://biorxiv.org/content/10.1101/2025.11.23.689932v1?rss=1 Li, R. Yang, J. Su, P.-C. Jaffe, A. Lindenbaum, O. Kluger, Y. 2025-11-26 doi:10.1101/2025.11.23.689932 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Graded Notch Signaling Functions as a Rheostat of Lineage Plasticity and Therapy Resistance in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.11.23.690056v1?rss=1 Jiang, Y. Cheng, S. Zhang, C. Y. Jin, X. Li, L. Fraidenburg, M. Wang, C. Kim, I. Y. Mu, P. 2025-11-26 doi:10.1101/2025.11.23.690056 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Mapping galectin-3 ligands in tear fluid establishes spliceoform-dependent lacritin binding ]]> https://biorxiv.org/content/10.1101/2025.11.24.690288v1?rss=1 Chang, V. Lian, I. Mahoney, K. E. Romano, J. Afshari, A. R. Chen, R. J. Chen, X. Fineide, F. Khan, A. Z. Utheim, T. P. Karlsson, N. G. Laurie, G. W. Malaker, S. A. 2025-11-26 doi:10.1101/2025.11.24.690288 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ The pos-1 3' untranslated region governs germline specification and proliferation to ensure reproductive robustness ]]> https://biorxiv.org/content/10.1101/2025.11.26.690476v1?rss=1 Varderesian, H. V. Utaegbulam, J. N. Brown, H. E. Ramirez, B. Velcani, M. Ryder, S. P. 2025-11-28 doi:10.1101/2025.11.26.690476 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Local homeostatic scaling supports stable rate propagation under noise and heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.11.25.689806v1?rss=1 Li, H. McDougal, R. A. 2025-11-29 doi:10.1101/2025.11.25.689806 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ ATHENA: A deep learning-based AI for functional prediction of genomic mutations and synergistic vulnerabilities in prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.11.26.690813v1?rss=1 CHENG, S. Jin, X. Qian, J. Jiang, Y. Kim, I. Deng, S. Mu, P. 2025-11-29 doi:10.1101/2025.11.26.690813 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ HDL-associated phosphatidylserine blunts myeloid activation and protects from atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.11.26.689708v1?rss=1 Bernal, A. Hamid, A. Grao-Roldan, C. Scarpa, A. Sanchez, I. Nicolas-Avila, J. A. Pena-Couso, L. Yaghmour, M. H. Benguria, A. Rosado, A. Sanchez, L. Torroja, C. Dopazo, A. Sanchez-Cabo, F. Hidalgo, A. Senders, M. L. van Leent, M. M. T. Seep, L. Hasenauer, J. Placek, K. Thiele, C. Netea, M. G. Mulder, W. J. M. Riksen, N. P. Perez-Medina, C. 2025-11-30 doi:10.1101/2025.11.26.689708 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ A clinical-stage oncology compound selectively targets drug-resistant cancers ]]> https://biorxiv.org/content/10.1101/2025.11.26.690878v1?rss=1 Long, K. Bhattacharjee, D. Newman-Stonebraker, S. H. Suhr, S. Mercado, B. Q. Tighe, A. Romero, L. Thompson, S. L. Sausville, E. L. John, K. M. Julian, L. Mishra, S. Klingbeil, O. Gupta, P. Bhatt, U. Gao, A. C. Ricardo, S. Vakoc, C. R. Bornhauser, B. C. Corsello, S. M. Taylor, S. S. Holland, P. L. Sheltzer, J. M. 2025-11-30 doi:10.1101/2025.11.26.690878 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome ]]> https://biorxiv.org/content/10.1101/2025.11.29.690828v1?rss=1 Shen, B. A. Asfahl, K. L. Lim, B. Bertolli, S. K. Minot, S. S. Radey, M. C. Penewit, K. Ngo, B. Salipante, S. J. Johnston, C. D. Peterson, S. B. Goodman, A. D. Mougous, J. D. 2025-11-30 doi:10.1101/2025.11.29.690828 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Detection of serotonin and serotonin related gene reveals unique roles in human intestinal epithelial development ]]> https://biorxiv.org/content/10.1101/2025.11.27.690965v1?rss=1 Phan, L. Smith, L. K. Milano, K. M. Gu, W. Strine, M. S. Kliman, H. J. Konnikova, L. 2025-12-01 doi:10.1101/2025.11.27.690965 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Dopamine and serotonin transients predict depressive symptom relief following deep brain stimulation of human subcallosal cingulate cortex ]]> https://biorxiv.org/content/10.64898/2025.11.28.691184v1?rss=1 Shevlin, B. R. K. R. K. Fu, Q. X. Batten, S. R. Kopell, B. H. Neal Davis, A. Heflin, M. Heisig, S. Rozell, C. J. Kato, A. Kulkarni, K. R. Choi, K. S. Song, H. N. ONeil, S. Nauvel, T. Trivedi, I. White, J. P. Lohrenz, T. Figee, M. Twomey, T. Moran, R. Bang, D. Hartle, A. E. Howe, W. M. Kishida, K. T. Barbosa, L. S. Fiore, V. G. Saez, I. Montague, P. R. Mayberg, H. S. Gu, X. 2025-12-02 doi:10.64898/2025.11.28.691184 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Antibody peptide epitope conjugates for αPD-1 therapy-resistant head and neck squamous cell carcinoma ]]> https://biorxiv.org/content/10.64898/2025.11.28.691238v1?rss=1 Shui, Y. I. Millar, D. G. Altenburger, L. M. Chrisikos, T. Kalbfleisch, M. J. Hata, A. Sadow, P. M. Faquin, W. C. Martinot, A. J. Snyder, C. M. Pittet, M. J. Pai, S. I. Cobbold, M. Mempel, T. R. 2025-12-02 doi:10.64898/2025.11.28.691238 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Flexible brain state engagement predicts cognitive control transdiagnostically ]]> https://biorxiv.org/content/10.64898/2025.11.30.691395v1?rss=1 600), including participants with anxiety disorder, schizophrenia, mood disorder, substance use disorders, post-traumatic stress disorder, obsessive-compulsive disorder, and neurodevelopmental disorder. To capture the multifaceted nature of cognitive control, we assessed two of its components, inhibition and shift, using both task-based and questionnaire data. Flexible brain state engagement predicted all cognitive control metrics in previously unseen individuals transdiagnostically, regardless of which dataset was used for model training. Connectome-based predictive modeling also revealed that shared brain networks underpinned flexible brain state engagement in a transdiagnostic manner. Leveraging brain network dynamics, we further observed that moments of more flexible brain state engagement aligned with moments of network connectivity related to better cognitive control within the same individual. This temporal alignment was replicated in all three datasets with heterogeneous samples. Altogether, this study provides robust evidence that flexible engagement of brain state may support both inter- and intra-individual differences in cognitive control across individuals with diverse mental health profiles. Funding sources F31AA032179; R01MH121095 ]]> Ye, J. Mehta, S. Khaitova, M. Arora, J. Tokoglu, F. Hahn, C. A. Lacadie, C. Greene, A. S. Constable, R. T. Scheinost, D. 2025-12-02 doi:10.64898/2025.11.30.691395 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Near-atomic in-situ architecture and membrane-coupled dynamics of the Vibrio cholerae sheathed flagellum ]]> https://biorxiv.org/content/10.64898/2025.12.02.691832v1?rss=1 Guo, W. Yue, J. Park, J. H. Mendez, D. V. Botting, J. M. Kumar, R. Yu, H. Sen, A. Yan, J. Yildiz, F. H. Liu, J. 2025-12-02 doi:10.64898/2025.12.02.691832 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ A foundation model for microbial growth dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.01.691707v1?rss=1 Holmes, Z. A. Shyti, I. Hoffman, A. L. Duncker, K. E. Ma, H. R. Zhou, Z. Lee, D. Maddamsetti, R. Kim, K. Simsek, E. Hamrick, G. S. Son, H. Villalobos, C. A. Lu, J. Ha, Y. Shende, A. R. Yao, Z. Liu, S. Shapiro, D. M. Kholina, K. Davis, H. Baig, Y. Wu, F. Wang, S. Wang, X. Chatterjee, P. Lynch, M. D. Lopatkin, A. J. David, L. A. Chory, E. You, L. 2025-12-03 doi:10.64898/2025.12.01.691707 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Cryo-electron microscopy ensemble optimization using individual particles and physical constraints ]]> https://biorxiv.org/content/10.64898/2025.12.02.691891v1?rss=1 Sanchez, D. S. Thiede, E. H. Lederman, R. Cossio, P. 2025-12-04 doi:10.64898/2025.12.02.691891 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression ]]> https://biorxiv.org/content/10.64898/2025.12.02.691870v1?rss=1 Zhou, Y. D. Wang, P. Schaffer, E. Komnick, M. R. Brown, H. Taylor, G. M. Fiske, K. Sheehan, C. Dermody, T. Muir, A. Esterhazy, D. 2025-12-05 doi:10.64898/2025.12.02.691870 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants ]]> https://biorxiv.org/content/10.64898/2025.12.02.691900v1?rss=1 3,000 CHD-risk variants for allelic binding for the cardiac TFs NKX2-5, GATA4, and TBX5 in a high-throughput manner. These binding affinity data sets were coupled with a massively parallel reporter assay (MPRA) to screen CHD-risk variant genotype-dependent regulatory activity. We identified 170 variants that exhibit allelic TF binding and 187 that modulate gene expression. Combining both approaches revealed three high-confidence variants with genotype-dependent TF binding, genotype-dependent transcriptional activity, and eQTL behavior in cardiac cells. Collectively, this study provides the first combined high-throughput biochemical and functional genomic evaluation of thousands of CHD-risk variants. HighlightsO_LIAllelic binding affinity measurements of [~]9,600 variants for NKX2-5, GATA4, and TBX5 C_LIO_LIEvaluaFon of >3,000 CHD-risk variants for genotype-dependent regulatory acFvity C_LIO_LIInteracFon networks idenFfy funcFonal variants and genes involving cardiac eQTLs C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/691900v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1f2dc96org.highwire.dtl.DTLVardef@1700929org.highwire.dtl.DTLVardef@696ec4org.highwire.dtl.DTLVardef@1e724d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pena-Martinez, E. G. Sharma, S. Medina-Feliciano, J. G. Root, E. Parks, L. G. Granitto, M. Pomales-Matos, D. A. Messon-Bird, J. L. Barreiro-Rosario, A. C. Sanabria-Alberto, L. Rivera-Madera, A. Rodriguez-Rios, J. M. Velazquez-Roig, R. Figueroa-Rosado, J. A. Noon, M. Donmez, O. A. Forney, C. Hesse, H. K. Dunn, K. A. Chen, X. Hass, M. Lawson, L. Weirauch, M. T. Kottyan, L. Reilly, S. K. Bhimsaria, D. Rodriguez-Martinez, J. A. 2025-12-05 doi:10.64898/2025.12.02.691900 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Mosaic PIK3CA-related overgrowth spectrum (PROS) mutations cause non-cell autonomous vascular overgrowth and pan-lineage dysregulation at disease onset ]]> https://biorxiv.org/content/10.64898/2025.12.03.691507v1?rss=1 Brunsdon, H. Wang, N. Raredon, M. S. B. Madsen, R. R. Semple, R. K. Patton, E. E. 2025-12-06 doi:10.64898/2025.12.03.691507 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ BrainBridge Characterizes Key Factors affecting Alzheimer's Disease and Associated Phenotypes ]]> https://biorxiv.org/content/10.64898/2025.12.03.692255v1?rss=1 Liu, T. Hao, M. Sun, E. Markov, Y. Zhang, L. Zou, J. Zhao, H. 2025-12-06 doi:10.64898/2025.12.03.692255 Cold Spring Harbor Laboratory Press 2025-12-06 <![CDATA[ Visual Semantic Encoding and Identification of Naturalistic Movies via High-Density Diffuse Optical Tomography ]]> https://biorxiv.org/content/10.64898/2025.12.03.692158v1?rss=1 Fehner, W. Fogarty, M. Tang, J. Wilhelm, D. Bajracharya, A. Markow, Z. E. Hines, A. M. Trobaugh, J. W. Huth, A. G. Culver, J. P. 2025-12-08 doi:10.64898/2025.12.03.692158 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation ]]> https://biorxiv.org/content/10.64898/2025.12.08.692954v1?rss=1 Fang, D. Babich, J. M. Stanton, R. Vock, I. W. Abdallah, K. Zhu, M. Li, R. Simon, M. D. Gilbert, W. V. Nachtergaele, S. 2025-12-08 doi:10.64898/2025.12.08.692954 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ High-resolution microCT reveals relationships between stomata and interior leaf anatomy in Sorghum ]]> https://biorxiv.org/content/10.64898/2025.12.05.692612v1?rss=1 Fischer, J. Theroux-Rancourt, G. Brodersen, C. R. Leakey, A. D. B. 2025-12-09 doi:10.64898/2025.12.05.692612 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Phenotypic and functional characterization of tumor-reactive T cells in malignant pleural effusions ]]> https://biorxiv.org/content/10.64898/2025.12.05.692662v1?rss=1 Gaiger, N. S. Coburn, J. Lee, M. Zhang, L. Chen, H.-L. Woodard, G. A. Kluger, H. M. Schoenfeld, D. A. Lu, B. Y. 2025-12-09 doi:10.64898/2025.12.05.692662 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ The protein interactome of the Neuron Specific Gene family (NSG1-3) ]]> https://biorxiv.org/content/10.64898/2025.12.07.692831v1?rss=1 Serrano Rodriguez, A. Overby, M. Srivastava, U. Chander, P. Vega, L. Wilson, S. Zychowski, K. E. Rangaraju, S. Kaastrup-Mueller, H. Weick, J. P. 2025-12-10 doi:10.64898/2025.12.07.692831 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Structural basis of stepwise G protein activation by a viral chemokine receptor ]]> https://biorxiv.org/content/10.64898/2025.12.10.692789v1?rss=1 Jude, K. M. Suomivuori, C.-M. Waghray, D. Maeda, S. Fujiyoshi, Y. Inoue, A. Garcia, K. C. Tsutsumi, N. 2025-12-10 doi:10.64898/2025.12.10.692789 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Signaling induced biophysical disruption of repressed chromatin domains drives immune cell fate ]]> https://biorxiv.org/content/10.64898/2025.12.08.692984v1?rss=1 Martinez de Paz, A. Chin, C. R. Ketavarapu, M. Sun, Y. Marunde, M. R. Chang, J. Khan, L. Cohen, J. Yang, R. Bale, M. J. Daman, A. W. Kumar, V. E. Jiang, C. Ahimovic, D. J. Owyong, M. Ravishankar, A. Wong, W. Shih, R. Graham, B. Smith, C. E. Karagianidis, I. Cerchietti, L. Flowers, C. R. Green, M. R. Mason, C. E. Sun, J. C. Martin-Trujillo, A. Niec, R. E. Long, Y. Keogh, M.-C. Liu, S. Beguelin, W. Leslie, C. S. Melnick, A. M. Josefowicz, S. Z. 2025-12-11 doi:10.64898/2025.12.08.692984 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Optical photothermal infrared imaging of fatty acid metabolism in the ER of living cells ]]> https://biorxiv.org/content/10.64898/2025.12.09.693044v1?rss=1 Castillo, H. B. Davis, C. M. 2025-12-11 doi:10.64898/2025.12.09.693044 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Perturbational single-cell profiling of patient tumors defines lineage- and context-specific programs of innate immune resistance ]]> https://biorxiv.org/content/10.64898/2025.12.09.693245v1?rss=1 Perry, C. J. Frey, A. Fei, Y. Wang, J. Costa, P. Nassar, A. H. Ghadermarzi, S. Levine, D. Tong, W. Wei, J. Koda, A. Mackie, M. He, M. Nie, Y. Clulo, K. Ouerghi, F. Dumit, T. C. Yaskolko, M. Ding, M. Caldera, A. Kyrysyuk, O. Lum, L. Allen, J. W. Guo, W. Naqash, A. R. Elliott, A. Vanderwalde, A. Capelletti, M. Adeyelu, T. Barry, S. T. Hugaboom, M. Bacchiocchi, A. Kluger, H. M. Bosenberg, M. Iwasaki, A. Braun, D. A. Clune, J. van Dijk, D. Olino, K. Ishizuka, J. 2025-12-12 doi:10.64898/2025.12.09.693245 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Lysosomal swelling triggers LRRK2 activity ]]> https://biorxiv.org/content/10.64898/2025.12.09.693280v1?rss=1 Malankhanova, T. Liu, Z. Strader, S. Wang, W. Sung, K. W. Li, Z. Ferguson, S. M. West, A. B. 2025-12-12 doi:10.64898/2025.12.09.693280 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Age-varying DNA methylation patterns associated with blood pressure across the lifespan ]]> https://biorxiv.org/content/10.64898/2025.12.09.693332v1?rss=1 Xu, G. Zhuang, X. Amei, A. Wang, Z. Oh, E. 2025-12-12 doi:10.64898/2025.12.09.693332 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Hierarchical Community Structure of the Adult Drosophila Connectome Reveals Conserved Circuit Archetypes ]]> https://biorxiv.org/content/10.64898/2025.12.10.689094v1?rss=1 Betzel, R. Del Rio, O. Labora, N. Dvali, S. Larsen, B. Lynn, C. W. Misic, B. Parkes, L. Sporns, O. Tervo-Clemmens, B. Puxeddu, M. G. Seguin, C. 2025-12-13 doi:10.64898/2025.12.10.689094 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Cellular responses to FGF1 are modulated by palmitoylation of the docking protein FRS2α ]]> https://biorxiv.org/content/10.64898/2025.12.11.693497v1?rss=1 An, S. Suzuki, Y. Mohanty, J. Tome, F. Lax, I. Schlessinger, J. 2025-12-13 doi:10.64898/2025.12.11.693497 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Optimal feedback solutions recapitulate key features of motorcortical population dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.12.694046v1?rss=1 Almani, M. N. Saxena, S. 2025-12-13 doi:10.64898/2025.12.12.694046 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Universal genomic constraints in the evolvability of thermal physiology ]]> https://biorxiv.org/content/10.64898/2025.12.12.693958v1?rss=1 Waldron, B. P. Tarimo, E. Sashittal, P. Naughton, N. Munoz, M. M. Uyeda, J. C. 2025-12-14 doi:10.64898/2025.12.12.693958 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Rehabilitation drives functional reorganization of intact corticospinal-supraspinal projections following partial spinal cord injury ]]> https://biorxiv.org/content/10.64898/2025.12.12.694014v1?rss=1 Bonanno, J. L. Trivedi, S. O'Brien, C. F. Saha, S. Cafferty, W. B. J. 2025-12-16 doi:10.64898/2025.12.12.694014 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ High-Fidelity Tuning of Olfactory Mixture Distances in the Perceptual Space of Smell Through a Community Effort ]]> https://biorxiv.org/content/10.64898/2025.12.13.694160v1?rss=1 Satarifard, V. Sisson, L. Han, Y. Ilidio, P. Hladis, M. Lalis, M. Song, X. Yin, W. Ravia, A. Zheng, C. X. Andreoletti, G. Albrecht, J. Pellegrino, R. Wang, Z. Yang, S. D'hondt, R. Ghinis, A. de Boer, J. Nakano, F. K. Gharahighehi, A. DREAM Olfactory Mixtures Prediction Consortium, Sanchez-Lengeling, B. Keller, A. Vosshall, L. B. Fiorucci, S. Tewari, A. Topin, J. Vens, C. Bjorkman, M. Kragic, D. Sobel, N. Christakis, N. A. Mainland, J. D. Meyer, P. 2025-12-16 doi:10.64898/2025.12.13.694160 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Cross-species consensus atlas of the primate basal ganglia ]]> https://biorxiv.org/content/10.64898/2025.12.15.694496v1?rss=1 Johansen, N. J. Fu, Y. Schmitz, M. Dubuc, A. Kempynck, N. Wirthlin, M. Garcia, A. D. Hewitt, M. Turner, M. A. Seeman, S. C. Long, B. Liu, X.-P. Dan, S. DeBerardine, M. Kapen, I. Yanny, A. M. Avola, A. Barlow, S. T. Bertagnolli, D. Bhandiwad, A. Budzillo, A. Caballero, V. E. N. Caceres, L. Casper, T. Chakka, A. B. Chakrabarty, R. Clark, M. Daniel, S. Eggermont, J. Ferrer, R. French, L. Gloe, J. Goldy, J. Guilford, N. Guzman, J. Hirschstein, D. Ho, W. James, K. Jones, D. L. Jungert, M. Kannan, M. Kedzierska, K. Z. Kroes, T. Leytze, M. Manning, A. McCu 2025-12-16 doi:10.64898/2025.12.15.694496 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ slideimp: Efficient Imputation for DNA Methylation Data ]]> https://biorxiv.org/content/10.64898/2025.12.15.694394v1?rss=1 Pham, H. Lombroso, A. P. Cevik, E. C. Taylor, H. S. O'Donnell, K. J. 2025-12-17 doi:10.64898/2025.12.15.694394 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ UV induces common cutaneous amyloid-like melanosomal protein aggregates ]]> https://biorxiv.org/content/10.64898/2025.12.17.689083v1?rss=1 Theodosakis, N. Howland, P. B. Hejna, M. Ostrowski, S. M. Cohen-Neamie, T. A. Joseph, R. A. Ji, H. Greuel, A. E. Boozer, J. R. Demian, M. Y. Asim, A. Nguyen, K. Mu, A. M. Seifert, P. Kaminiow, K. D. Zhang, Y. Fassini, A. Germana, S. Shaw, K. C. Lin, W. M. Hoang, M. P. Wu, X. Chandra, S. S. Hacohen, N. Ballabio, A. Bakshi, R. Udeshi, N. D. Horn, T. D. Ganesan, A. K. Murphy, G. F. Carr, S. A. Hyman, B. Song, J. S. Fisher, D. E. 2025-12-18 doi:10.64898/2025.12.17.689083 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ A K27-linked Ubiquitin Checkpoint Controls NOTCH Homeostasis ]]> https://biorxiv.org/content/10.64898/2025.12.18.695023v1?rss=1 Mansoori, B. Song, Y. Zhang, T. Zheng, Z. Zhu, Q. Li, S. Reale, M. Pangilinan, C. Machhar, J. S. Liang, J. Chang, J. Hong, Y.-K. Wertheim, G. B. Murphy, M. E. Kim, Y.-M. Muschen, M. Gack, M. U. Kossenkov, A. V. Liu, Q. Auslander, N. Aifantis, I. Parekh, C. Liang, C. 2025-12-19 doi:10.64898/2025.12.18.695023 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Structural Basis of TACO1-Mediated Efficient Mitochondrial Translation ]]> https://biorxiv.org/content/10.64898/2025.12.18.695269v1?rss=1 Wang, S. Brischigliaro, M. Zhang, Y. Wu, C. Zheng, W. Barrientos, A. Xiong, Y. 2025-12-19 doi:10.64898/2025.12.18.695269 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Synaptotagmin-7 is required for synchronous but not asynchronous facilitation of glutamate release at cortical boutons ]]> https://biorxiv.org/content/10.64898/2025.12.19.695358v1?rss=1 Kotzadimitriou, D. Langley, H. McGowan, E. R.F. Mendonca, P. Tagliatti, E. Timofeeva, Y. Krishnakumar, S. S. Volynski, K. E. 2025-12-22 doi:10.64898/2025.12.19.695358 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ A standardized and reproducible behavioral protocol to elicit visual spatial attention in mice ]]> https://biorxiv.org/content/10.64898/2025.12.19.695467v1?rss=1 Peelman, K. Allen, N. Ahn, J. Del Rosario, J. Jacobson, K. C. Kim, E. Lien, A. D. Lopez-Esteva, M. Lovell, L. Worden, K. Yang, Y. Zhuang, J. Haider, B. 2025-12-22 doi:10.64898/2025.12.19.695467 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.64898/2025.12.19.695410v1?rss=1 Wirth, C. Zhang, T. Diaz-Gay, M. Steele, C. D. Hoang, P. H. Yang, Y. Khandekar, A. Zhao, W. Sang, J. Leduc, C. Baine, M. K. Travis, W. D. Sholl, L. M. Joubert, P. Homer, R. Yang, S.-R. Tran, T.-V.-T. McElderry, J. P. Hartman, C. Miraftab, M. Lee, O. W. Jones, K. M. Zhu, B. Santamaria, J. M. Schabath, M. B. Yendamuri, S. S. Manczuk, M. Lissowska, J. Swiatkowska, B. Mukeria, A. Shangina, O. Zaridze, D. Holcatova, I. Janout, V. Mates, D. Ognjanovic, S. Savic, M. Kontic, M. Bosse, Y. Rothberg, B. E. G. Christiani, D. C. Gaborieau, V. Brennan, P. Liu, G. 2025-12-23 doi:10.64898/2025.12.19.695410 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A Retinoic Acid Autoregulatory Loop Governing Prefrontal-Motor Arealization ]]> https://biorxiv.org/content/10.64898/2025.12.23.696038v1?rss=1 Yang, L. Shibata, M. Park, S. Liu, Y. Salamon, I. Liu, J. Kim, S.-K. Shibata, A. Deveau-French, A. Mato Blanco, X. Bai, S. Nottoli, T. Xing, X. Rohani, N. Sanders, S. J. Kovner, R. Pattabiraman, K. Sestan, N. 2025-12-24 doi:10.64898/2025.12.23.696038 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Mast cell extracellular granules are bioactive condensates driven by heparin and polyamine ]]> https://biorxiv.org/content/10.64898/2025.12.25.696514v1?rss=1 Xiong, Y. Tomares, D. T. Guo, J. Sato, K. Zeng, L. Tian, Y. Su, M. Albis, A. Pant, A. Pappu, R. V. Su, X. 2025-12-26 doi:10.64898/2025.12.25.696514 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Targeted metagenomic sequencing with spiked primers for enrichment of viruses in wastewater for pathogen surveillance ]]> https://biorxiv.org/content/10.64898/2025.12.26.690930v1?rss=1 Parker, M. C. Apinda, N. Uamngamsup, S. Phetra, P. Yano, T. Sangkakam, K. Eiamsam-ang, T. Muenthaisong, A. Phetra, P. Huang, A. T. Smolinski, M. Olson, S. H. Grubaugh, N. D. Phelps, M. Rosario, K. Gil, J. Susumpow, P. 2025-12-26 doi:10.64898/2025.12.26.690930 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ SuperFocus enables whole-slide cell-level spatial omics from spot-based measurements and histology across modalities ]]> https://biorxiv.org/content/10.64898/2025.12.26.696575v1?rss=1 Lu, Y. Enninful, A. Bao, S. Bai, Z. Xu, M. L. Xiao, Y. Fan, R. Ma, Z. 2025-12-27 doi:10.64898/2025.12.26.696575 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Template-based RNA structure prediction advanced through a blind code competition ]]> https://biorxiv.org/content/10.64898/2025.12.30.696949v1?rss=1 Lee, Y. He, S. Oda, T. Rao, G. J. Kim, Y. Kim, R. Kim, H. Heng, C. K. Kowerko, D. Li, H. Nguyen, H. Sampathkumar, A. Enrique Gomez, R. Chen, M. Yoshizawa, A. Kuraishi, S. Ogawa, K. Zou, S. Paullier, A. Zhao, B. Chen, H.-L. Hsu, T.-A. Hirano, T. Gezelle, J. G. Haack, D. Hong, Y. Jadhav, S. Koirala, D. Kretsch, R. C. Lewicka, A. Li, S. Marcia, M. Piccirilli, J. Rudolfs, B. Srivastava, Y. Steckelberg, A.-L. Su, Z. Toor, N. Wang, L. Yang, Z. Zhang, K. Zou, J. Baker, D. Chen, S.-J. Chiu, W. Demkin, M. Favor, A. Hummer, A. M. Joshi, C. K. Kryshtafovyc 2025-12-30 doi:10.64898/2025.12.30.696949 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Assembly and glycosylation of Helicobacter pylori sheathed flagella ]]> https://biorxiv.org/content/10.64898/2025.12.30.697013v1?rss=1 Kumar, R. Tachiyama, S. Yu, H. Heydari, S. Guo, J. Botting, J. M. Guo, W. Hoover, T. R. Liu, J. 2025-12-30 doi:10.64898/2025.12.30.697013 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ A Neyman-Pearson Framework for Modeling Cellular Decision Making Using Single-Cell TNF-NF-κB Signaling Data ]]> https://biorxiv.org/content/10.64898/2025.12.30.696266v1?rss=1 Emadi, A. Lipniacki, T. Levchenko, A. Abdi, A. 2025-12-31 doi:10.64898/2025.12.30.696266 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Lamin A/C directs nucleosome-scale chromatin remodeling to define early lineage segregation in mammals ]]> https://biorxiv.org/content/10.64898/2026.01.01.696913v1?rss=1 Sherrard, A. Zhong, L. Hoppe, C. Krishna, S. Youlten, S. Boswell, C. W. Cross, S. Sievers, F. E. Ardestani, G. Sakkas, D. Miao, L. Smith, Z. D. Sozen, B. Giraldez, A. J. 2026-01-02 doi:10.64898/2026.01.01.696913 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ CAR-T-drug conjugate against solid tumor ]]> https://biorxiv.org/content/10.64898/2026.01.02.696502v1?rss=1 Xin, S. Feng, Y. Zhang, F. Yu, J. Dong, C. Tao, B. Tang, K. Wu, Q. Chen, B. Ren, P. Verma, N. Liu, C. Suzuki, K. Ling, X. Park, D. Kluger, H. Crawford, J. Fan, R. Zhou, J. Chen, S. 2026-01-02 doi:10.64898/2026.01.02.696502 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Aging, matrix metalloproteinase imaging, and survival prospects in aortic aneurysm ]]> https://biorxiv.org/content/10.64898/2026.01.02.697375v1?rss=1 51-week-old (old) Apoe-/- mice. Aortic MMP activation was quantified by PET/CT using an MMP-targeted tracer, 64Cu-RYM2, at baseline and 1 week after Ang II infusion. MMP activity and expression were quantified by tissue zymography and quantitative reverse transcription polymerase chain reaction, and compared between different segments of the aorta in young and old animals, and before and after Ang II infusion. ResultsOld animals survival to 28 days was significantly lower than that of young Ang-II-infused Apoe-/- mice (P < 0.05). 64Cu-RYM2 PET/CT showed significantly higher aortic MMP activation before and 1 week after Ang-II infusion in old compared to young Apoe-/-mice. The 64Cu-RYM2 signal was significantly higher in animals that did not survive 28 days than those that did (P < 0.01). MMP activity significantly increased by 4 days after Ang-II infusion, when dissection was found in a subset of Apoe-/- mice; and was significantly higher in the dissected, compared to adjacent, apparently normal, segments of the aorta. MMP activity was also significantly higher in the ascending thoracic aorta of untreated young and old mice, as well as of Ang-II-treated Apoe-/-mice (which was associated with significantly higher Mmp2 gene expression), and of old wild-type mice. ConclusionAging is associated with increased MMP activity along the aorta and worse AA survival. MMP-targeted molecular imaging can inform the aneurysm survival prospects. Selective MMP inhibitors and tracers may help prevent and track aneurysm growth, dissection, and rupture. ]]> Ghim, M. Varli, O. Ahmad, A. Neishabouri, A. Kukreja, G. Zhang, Z. Zarnegar, S. Gangemi, N. Toczek, J. Zhang, J. Liu, C. Liu, Y. Gropler, R. Sadeghi, M. M. 2026-01-02 doi:10.64898/2026.01.02.697375 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Spatiotemporal Mapping of Tertiary Lymphoid Structure Heterogeneity Shapes Immune Niches and Clinical Outcomes in Intrahepatic Cholangiocarcinoma ]]> https://biorxiv.org/content/10.64898/2026.01.02.697439v1?rss=1 Gao, L. Mei, J. Hong, L. Jin, Y. Cheng, J. Sun, X. Liu, C. Li, B. Meng, X. Lin, B. Sun, Y. Zhao, P. Chen, M. Guo, R. Xin, S. Yun, J. Martinez-Reyes, I. Wei, W. Fang, W. Bao, X. 2026-01-06 doi:10.64898/2026.01.02.697439 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Bedaquiline inhibits the ATP synthase leak channel and prevents glutamate-induced neuronal death ]]> https://biorxiv.org/content/10.64898/2026.01.05.697836v1?rss=1 Kumar, A. Smith, E. Mezghani, I. Eedarapalli, S. Wu, Y. Ferdous, K. A. Amjad, E. Park, H.-A. Mnatsakanyan, N. 2026-01-06 doi:10.64898/2026.01.05.697836 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae ]]> https://biorxiv.org/content/10.64898/2026.01.06.697970v1?rss=1 Herzog, K. S. Randi, S. Osabutey, D. Paraggio, C. Bungiro, R. Owusu, I. S. O. Appiah-Tsum, F. Lamptey, A. Quaye, I. Vaughan, S. Wilson, M. D. Ghansah, A. Cappello, M. Fauver, J. R. 2026-01-07 doi:10.64898/2026.01.06.697970 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ RIG-I RNA agonist activates immunostimulatory macrophages to enhance checkpoint immunotherapy for glioblastoma ]]> https://biorxiv.org/content/10.64898/2026.01.07.698153v1?rss=1 Xu, H. Lee, S. Leser, F. Fedorova, O. Lu, P. Song, E. Touat, M. Eichmann, A. Iwasaki, A. Pyle, A. M. Thomas, J.-L. 2026-01-08 doi:10.64898/2026.01.07.698153 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1 ]]> https://biorxiv.org/content/10.64898/2026.01.07.698282v1?rss=1 Hu, B. Alvarez, D. Rocha-Roa, C. Guyard, V. Li, D. Wang, X. De Camilli, P. Vanni, S. Reinisch, K. 2026-01-08 doi:10.64898/2026.01.07.698282 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Evaluating Acridones as Novel Therapeutics for Human Babesiosis ]]> https://biorxiv.org/content/10.64898/2026.01.07.698299v1?rss=1 Vydyam, P. Zhang, E. Chattopadhyay Pal, A. Dodean, R. Kancharla, P. Kelly, J. X. Ben Mamoun, C. 2026-01-08 doi:10.64898/2026.01.07.698299 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Diagnostic Value of Antibody Responses to Mycobacterium avium subsp. paratuberculosis-Derived Proteins PtpA and PtpB in Rheumatoid Arthritis ]]> https://biorxiv.org/content/10.64898/2026.01.08.698458v1?rss=1 Hernandez-Bello, J. Cerpa-Cruz, S. Sanchez-Zuno, G. A. Nicoletti, F. Munoz-Valle, J. F. Bach, H. 2026-01-08 doi:10.64898/2026.01.08.698458 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Stack: In-Context Learning of Single-Cell Biology ]]> https://biorxiv.org/content/10.64898/2026.01.09.698608v1?rss=1 Dong, M. Adduri, A. Gautam, D. Carpenter, C. Shah, R. Ricci-Tam, C. Kluger, Y. Burke, D. P. Roohani, Y. H. 2026-01-09 doi:10.64898/2026.01.09.698608 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ A Hybrid Gag Lattice as a Structural Intermediate in HIV-1 Maturation ]]> https://biorxiv.org/content/10.64898/2026.01.10.698794v1?rss=1 Meuser, M. E. Wu, C. Macke, A. C. Shi, J. Cheng, J. Yang, R. R. Freniere, C. Lin, J. Aiken, C. Perilla, J. R. Xiong, Y. 2026-01-11 doi:10.64898/2026.01.10.698794 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling. ]]> https://biorxiv.org/content/10.64898/2026.01.11.698831v1?rss=1 Plucinska, K. Wayne, C. R. Sanford, H. Mathew, B. Ropek, N. Adaniya, S. M. Model, C. Gomez-Banoy, N. Morozova, K. Cao, X. Friedman, J. M. Loh, K. H. Cohen, P. Vinogradova, E. V. 2026-01-12 doi:10.64898/2026.01.11.698831 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ MIF-mediated reprogramming of myeloid lineage within the glioma tumor microenvironment impacts the efficacy of immune stimulatory gene therapy ]]> https://biorxiv.org/content/10.64898/2026.01.13.699283v1?rss=1 Zhu, Z. Kanis, N. C. George, A. E. Albdewi, M. Li, Y. Mujeeb, A. A. McClellan, B. L. Singh, G. Liu, J. Al-Holou, W. N. Heth, J. A. Welch, J. D. Lathia, J. D. Lowenstein, P. R. Bucala, R. Castro, M. G. 2026-01-14 doi:10.64898/2026.01.13.699283 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Evaluating Synergy of Clinically Utilized Phage OMKO1 with Five Antibiotics from Different Classes against Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.64898/2026.01.13.699299v1?rss=1 Kane, E. L. Chan, B. K. Mould, D. L. Kortright, K. E. Koff, J. Turner, P. E. 2026-01-14 doi:10.64898/2026.01.13.699299 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Type IV Secretion System Drives Lipid Mixing ]]> https://biorxiv.org/content/10.64898/2026.01.14.699567v1?rss=1 Chetrit, D. Roy, C. Karatekin, E. 2026-01-15 doi:10.64898/2026.01.14.699567 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing ]]> https://biorxiv.org/content/10.64898/2026.01.16.699998v1?rss=1 Hartweger, H. Ruprecht, C. Yao, K.-H. Laffont, P. Lima dos Reis, G. Zhou, P. Hägglöf, T. Binet, L. Loewe, M. Hong, J. P. Xiao, T. Sefik, E. Hernandez, B. Gazumyan, A. Jankovic, M. Seaman, M. S. Costa, G. Nelson, S. A. Clark, J. Kanatani, S. Wilson, P. C. Krammer, F. Levashina, E. A. Julien, J.-P. Wardemann, H. Sinnis, P. Stamatatos, L. Flavell, R. A. Nussenzweig, M. C. 2026-01-18 doi:10.64898/2026.01.16.699998 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Cortical astrocytes control stress resilience ]]> https://biorxiv.org/content/10.64898/2026.01.17.700119v1?rss=1 Kondev, V. J. Holt, L. Kipp, B. Gyles, T. Racine, I. McKernan, W. Ahmed, S. Kahn, E. S. Minier-Toribio, A. Blaschke, C. Naguib, S. Futamura, R. Rojas, G. Labanca, A. Nestler, E. J. 2026-01-18 doi:10.64898/2026.01.17.700119 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ 5'Untranslated regions provide a versatile toolkit for tunable exogenous protein expression ]]> https://biorxiv.org/content/10.64898/2026.01.19.700389v1?rss=1 Garcia, C. Poch, D. Alemayhu, A. M. Paulsen, C. E. 2026-01-19 doi:10.64898/2026.01.19.700389 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Molecular Imaging of Collagen Turnover in Myocardial Infarction ]]> https://biorxiv.org/content/10.64898/2026.01.16.699986v1?rss=1 Neishabouri, A. Ghim, M. Varli, O. Ahmad, A. Kukreja, G. Zhang, Z. Li, J. Toczek, J. Salarian, M. Zhang, J. Ein Alshaeba, D. Akar, F. G. Liu, C. Yu, S. M. Sadeghi, M. M. 2026-01-20 doi:10.64898/2026.01.16.699986 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Establishing the molecular basis for MDA5 mutation-linked autoimmunity ]]> https://biorxiv.org/content/10.64898/2026.01.20.700587v1?rss=1 Xu, L. Chung, K. Guo, R. Pan, A. Pyle, A. 2026-01-20 doi:10.64898/2026.01.20.700587 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Memory erasure by dopamine-gated retrospective learning ]]> https://biorxiv.org/content/10.64898/2026.01.17.700100v1?rss=1 Jeong, H. Zsembik, L. Farouq, F. Chakraborty, R. Belur, N. Zhou, M. Sanders, A. D. Wang, S. X. Srinivasan, A. Cox, S. M. L. Garr, E. Brooke, S. Janak, P. H. Leyton, M. Chen, R. Namboodiri, V. M. K. 2026-01-21 doi:10.64898/2026.01.17.700100 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Afterimages drive a shared visual motion reversal illusion in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.01.19.700413v1?rss=1 Wu, H. Gou, T. Clark, D. 2026-01-21 doi:10.64898/2026.01.19.700413 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ A synaptic locus of song learning ]]> https://biorxiv.org/content/10.64898/2026.01.20.699515v1?rss=1 Schreiner, D. C. Brudner, S. Li, A. Pearson, J. Mooney, R. 2026-01-21 doi:10.64898/2026.01.20.699515 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Genome-wide divergence in a desert plant in the Baja California Peninsula driven by glacial cycles and adaptation to different climatic conditions ]]> https://biorxiv.org/content/10.64898/2026.01.19.699825v1?rss=1 Andreev, V. Araya-Donoso, R. Baty, S. M. Wilder, B. T. Lira-Noriega, A. Moore, D. G. Culver, M. Dolby, G. A. Munguia-Vega, A. 2026-01-22 doi:10.64898/2026.01.19.699825 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Neuronal microscale biophysical instability mediates macroscale network dynamics shaping pathological manifestations ]]> https://biorxiv.org/content/10.64898/2026.01.20.697254v1?rss=1 Kumar, V. Sanchez Franco, V. M. Ferry, F. S. Xie, Y. Hutson, A. N. Zhang, Y. J. Daniels, S. D. Nguyen, D. L. Spera, L. K. Snyder, E. M. Knauss, A. Sudhakar, S. L. Duan, G. Y. Paul, E. M. Tabuchi, M. 2026-01-22 doi:10.64898/2026.01.20.697254 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ PRISME: A MATLAB Toolbox For Large Data-Driven Multimodal Power Benchmarking ]]> https://biorxiv.org/content/10.64898/2026.01.21.700878v1?rss=1 Cravo, F. Fischbach, A. Shearer, H. Rosenblatt, M. Scheinost, D. Noble, S. 2026-01-22 doi:10.64898/2026.01.21.700878 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Identification of Lupus Immune Complex-Driven Pathogenic Pro-inflammatory Monocytes and Macrophages in Systemic Lupus Erythematosus ]]> https://biorxiv.org/content/10.64898/2026.01.21.700902v1?rss=1 Osmani, L. Shin, M. Lee, S. J. Cai, H. Seong, W. J. Kim, H. Yoo, J. Kim, M. Bracamonte, W. Felix, M. Ahn, J. G. Park, H.-J. Shin, J. J. Unlu, S. Par-Young, J. Doherty, E. Chen, J. Dong, M. X. Koumpouras, F. Gomez, J. L. Kaminski, N. Bucala, R. You, S. Kang, I. 2026-01-22 doi:10.64898/2026.01.21.700902 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Conserved assembly architecture of the essential herpesvirus packaging accessory factor ]]> https://biorxiv.org/content/10.64898/2026.01.22.701024v1?rss=1 Bailey, E. J. Devarkar, S. C. Szczepaniak, R. Meissner, L. M. Chen, X. Wu, C. Weller, S. K. Xiong, Y. Didychuk, A. L. 2026-01-22 doi:10.64898/2026.01.22.701024 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.64898/2026.01.21.699487v1?rss=1 Houpt, N. S. Hernandez, C. A. Turner, P. E. 2026-01-23 doi:10.64898/2026.01.21.699487 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Identification of germline chromatin modifying factors that influence zygotic transcription activation in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.01.21.700918v1?rss=1 Mazzetto, M. Adekplor, P. Reinke, V. 2026-01-23 doi:10.64898/2026.01.21.700918 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A ]]> https://biorxiv.org/content/10.64898/2026.01.22.701120v1?rss=1 Kravitz, C. J. Patel, K. Wingrove, E. Zhao, D. Tang, T. Chande, S. Zhao, M. Huo, Y. Westbrook, T. F. Yan, Q. Nguyen, D. X. 2026-01-23 doi:10.64898/2026.01.22.701120 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Benchmarking generative scaffold design methods for peptide engineering in TCR-MHC complexes ]]> https://biorxiv.org/content/10.64898/2026.01.22.701133v1?rss=1 Xie, L. Dam, G.-B. Patel, Y. Denzler, L. Shao, Y. Wang, R. Caron, E. Yasumizu, Y. Hafler, D. A. Rodriguez Martinez, M. 2026-01-23 doi:10.64898/2026.01.22.701133 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ Uncovering Dynamic Neural Information Flow with Continuous-Time Weighted Dynamic Bayesian Networks ]]> https://biorxiv.org/content/10.64898/2026.01.22.701045v1?rss=1 Sheffield, A. G. Denagamage, S. Morton, M. P. Nandy, A. S. Jadi, M. P. 2026-01-24 doi:10.64898/2026.01.22.701045 Cold Spring Harbor Laboratory Press 2026-01-24 <![CDATA[ Structural and Evolutionary Divergence of the RAG1/1L N-Terminal Zinc-Finger Domain ]]> https://biorxiv.org/content/10.64898/2026.01.24.700457v1?rss=1 Hong, J. Liu, Z. Martin, E. Wei, K. Schatz, D. G. Zhang, Y. 2026-01-25 doi:10.64898/2026.01.24.700457 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Epithelial Reprogramming and Transition during Pulmonary Bioengineering ]]> https://biorxiv.org/content/10.64898/2026.01.24.701406v1?rss=1 View larger version (68K): org.highwire.dtl.DTLVardef@1d456f3org.highwire.dtl.DTLVardef@1989ba5org.highwire.dtl.DTLVardef@127dd7org.highwire.dtl.DTLVardef@3dd7a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mizoguchi, S. Lee, V. Kim, H. Edelstein, S. E. Wang, N. Tomas Gracia, M. Danelski, C. Haynes, C. Rivero, R. Stitelman, D. Obata, T. Greaney, A. M. Tsuchiya, T. Kyriakides, T. Kaminski, N. Raredon, M. S. B. 2026-01-26 doi:10.64898/2026.01.24.701406 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Activating Ras-MAPK pathway variants drive hippocampal clonal competition in human epilepsy ]]> https://biorxiv.org/content/10.64898/2026.01.26.701822v1?rss=1 40% of MTLE specimens harboring activating Ras-MAPK variants in PTPN11, NF1, BRAF, KRAS, and twelve genes not previously associated with focal epilepsy. Eight Ras-MAPK genes showed positive clonal selection in MTLE. Increased somatic variant burden predicted worse surgical outcome. Somatic Ras-MAPK variants at ultra-low (<0.5%) variant allele fractions were associated with older seizure onset and HS pathology, supporting a late prenatal or postnatal origin. Ras-MAPK variants in MTLE were enriched in cells derived from hippocampal progenitors--neurons, astrocytes, oligodendrocytes--in line with the known neuronal hyperexcitability and seizures induced by Ras-MAPK overactivation9,10; in contrast, Alzheimer disease hippocampi exhibited microglial enrichment of Ras-MAPK variants, consistent with prior reports11. Single-nucleus RNA sequencing showed increased expression of Ras-MAPK genes in neurons and upregulation of pathways mediating neurogenesis and neural development in MTLE. Functional validation of novel, recurrent PTPN11 variants confirmed gain-of-function, while cellular modeling in induced pluripotent stem cells demonstrated proliferative/survival advantages for mutant cells in mosaic culture. Overall, our data suggest that somatic Ras-MAPK variants and acquired risk factors may converge on clonal competition in the hippocampus to modulate epilepsy risk. ]]> Khoshkhoo, S. Bae, M. Wang, Y. Tillett, A. Ramirez, R. B. Finander, B. Egan, E. D. Marx, L. Patel, D. Zhou, Z. Chahine, Y. Chhouk, B. Zoullas, S. M. Lai, A. Coras, R. Bielle, F. Navarro, V. Mathon, B. Valiante, T. A. Chameh, H. M. Gao, A. Krings, T. Gooley, S. Hildebrand, M. S. Bulluss, K. Clark, J. Morokoff, A. P. King, J. A. Todaro, M. Kwan, P. O'Brien, T. J. Berkovic, S. F. Scheffer, I. E. Perucca, P. Lapinskas, E. Rolston, J. D. Cosgrove, G. R. Sarkis, R. A. D'Gama, A. M. Alexadrescu, S. Yang, E. Poduri, A. Richardson, R. M. Erson-Omay, E. Z. DeL 2026-01-27 doi:10.64898/2026.01.26.701822 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ MacroH2A-Mediated Gene Repression through Nucleosome Compaction and Remodeling Inhibition ]]> https://biorxiv.org/content/10.64898/2026.01.26.701634v1?rss=1 Tan, D. Sokolova, V. Jiang, R. Mullins, A. Lee, G. Pan, B. H. 2026-01-28 doi:10.64898/2026.01.26.701634 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Lunar gravity predicts sleep timing ]]> https://biorxiv.org/content/10.64898/2026.01.27.701907v1?rss=1 Rodriguez Ferrante, G. Casiraghi, L. Spiousas, I. Trebucq, L. Klei, V. Kahn, J. W. Rice, A. Wood, D. Fernandez-Duque, E. Bales, K. L. Gallep, C. M. Golombek, D. A. de la Iglesia, H. O. 2026-01-29 doi:10.64898/2026.01.27.701907 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Distinct control of T cell proliferation and effector function by partitioning of intracellular sulfur from cysteine ]]> https://biorxiv.org/content/10.64898/2026.01.27.702014v1?rss=1 Kelly, B. Cha, M. Gremelspacher, T. Martin, J. L. Andreis, M. Carrizo, G. E. Gidley, M. Stanczak, M. A. Apostolova, P. Sanin, D. E. Majumdar, A. Pearce, E. L. 2026-01-29 doi:10.64898/2026.01.27.702014 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A dramatic protein fold switch powers a bactericidal nanomachine ]]> https://biorxiv.org/content/10.64898/2026.01.28.702463v1?rss=1 He, Y. Li, A. S. C. Cai, X. Tachiyama, S. Kumar, R. Chakravarty, D. Porter, L. Liu, J. Davidson, A. R. Zhou, Z. H. 2026-01-29 doi:10.64898/2026.01.28.702463 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Volumetric mechanoplasticity couples melanoma drug tolerance to susceptibility to CD8+ T cell killing ]]> https://biorxiv.org/content/10.64898/2026.01.27.701903v1?rss=1 Zhang, X. Zhang, D. Gong, X. Yu, A. P. Jain, R. K. Munn, L. L. Mak, M. 2026-01-30 doi:10.64898/2026.01.27.701903 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Nanobody MET CAR T cells show efficacy in solid tumors ]]> https://biorxiv.org/content/10.64898/2026.01.27.702111v1?rss=1 Chen, P.-H. Li, Q. Devereaux, S. Sohai, D. Cha, P.-C. Raghunandan, R. Chen, N. Li, Y. Nguyen, M. Stankewich, M. C. Morrow, J. S. Augert, A. Yan, Q. C. Katz, S. G. 2026-01-30 doi:10.64898/2026.01.27.702111 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ ProMeta: A meta-learning framework for robust disease diagnosis and prediction from plasma proteomics ]]> https://biorxiv.org/content/10.64898/2026.01.28.702242v1?rss=1 Li, H. Gu, H. Hu, L. Zhang, Z. Lv, Y. Gao, P. Cooper-Knock, J. Min, Y. Zeng, J. Zhang, S. 2026-01-30 doi:10.64898/2026.01.28.702242 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ mPFC Synaptosome Proteomics Reveals Novel Pathways and Muscarinic Receptor Changes in a Learned Helplessness Mouse Model ]]> https://biorxiv.org/content/10.64898/2026.01.29.701137v1?rss=1 Abdulla, Z. I. Garcia-Milian, R. Giahyue, E. Fertuzinhos, S. Collin, F. Wang, W. Lam, T. Nairn, A. Picciotto, M. R. 2026-01-30 doi:10.64898/2026.01.29.701137 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Contrasting controls on tree methane emissions in upland and wetland forests ]]> https://biorxiv.org/content/10.64898/2026.01.29.702553v1?rss=1 Gewirtzman, J. Hegwood, N. Burrows, H. Lutz, M. Thompson, G. Duncan, B. Yang, M. Jurado, S. Marra, R. Matthes, J. H. 2026-01-30 doi:10.64898/2026.01.29.702553 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Two tiers of piRNA clusters balance diversification of piRNAs with limitation of off-target effects ]]> https://biorxiv.org/content/10.64898/2026.01.28.702291v1?rss=1 Poulet, A. Witmer, M. Li, D. Cathelin, R. van Wolfswinkel, J. C. 2026-01-31 doi:10.64898/2026.01.28.702291 Cold Spring Harbor Laboratory Press 2026-01-31 <![CDATA[ Borrelia Burgdorferi binds Serum Amyloid A and Modulates Subcutaneous Adipose Tissue Immune Signaling ]]> https://biorxiv.org/content/10.64898/2026.01.29.702514v1?rss=1 Esterly, A. T. Du, S. Lee, B. Johnson, E. E. Odell, A. V. Sefik, E. Yu, Q. Cui, Y. Ayyala, H. Haykal, S. Odell, I. D. Flavell, R. A. Fikrig, E. Zapata, H. 2026-02-02 doi:10.64898/2026.01.29.702514 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Granulocyte colony-stimulating factor acts through calcium-permeable AMPA receptors to potentiate cocaine reward ]]> https://biorxiv.org/content/10.64898/2026.01.30.702629v1?rss=1 Hofford, R. S. Wilson, R. McArdle, C. Euston, T. Sens, J. P. Mastrantoni, A. McCabe, T. Meckel, K. R. Wang, W. Lucerne, K. E. Osman, A. Raab-Graham, K. F. Lam, T. T. Kiraly, D. D. 2026-02-02 doi:10.64898/2026.01.30.702629 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Core-sheath coupling controls flagellar curvature and motility in Leptospira ]]> https://biorxiv.org/content/10.64898/2026.02.02.703089v1?rss=1 San Martin, F. Brady, M. R. Fule, L. Rodriguez, A. Mondino, S. Larrieux, N. Wunder, E. A. Ko, A. I. Rey, M. Chamot-Rooke, J. Duran, R. Trajtenberg, F. Picardeau, M. Sindelar, C. V. Buschiazzo, A. 2026-02-02 doi:10.64898/2026.02.02.703089 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis ]]> https://biorxiv.org/content/10.64898/2026.02.01.703113v1?rss=1 Birsoy, K. Liu, S. Gad, M. Li, C. Cho, K. Liu, Y. Wangdu, k. Belay, V. Millet, A. Kojima, H. Sanford, H. Wolk, M. Urnavicius, L. Fedorova, M. Patti, G. J. J. Vinogradova, E. V. Hite, R. K. 2026-02-03 doi:10.64898/2026.02.01.703113 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Components of an ESCRT-independent nuclear envelope assembly pathway ]]> https://biorxiv.org/content/10.64898/2026.02.01.703137v1?rss=1 Sydir, E. M. Farra, M. H. Whitford, A. L. Hinojosa, S. Kao, P.-Y. Paulo, J. A. Swarup, S. Lusk, C. P. Harper, J. W. Lee, I.-J. Pellman, D. 2026-02-03 doi:10.64898/2026.02.01.703137 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Ctenophore mesoglea: building a mucus-like body ]]> https://biorxiv.org/content/10.64898/2026.02.02.702917v1?rss=1 Siwiecki, S. Black, I. M. Archer-hartmann, S. A. Vlach, J. Heiss, C. Dunn, C. Azadi, P. Sweeney, A. 2026-02-04 doi:10.64898/2026.02.02.702917 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Film Recall Reveals Intact Event Memory but Impaired Sequence Memory in Temporal Lobe Epilepsy Patients ]]> https://biorxiv.org/content/10.64898/2026.02.03.702007v1?rss=1 Zhang, H. Farahani, F. Tefera, E. Botnick, B. Thapaliya, B. Lee, H. Borges, H. Zhang, W. Barr, W. Henin, S. Shi, Y. Chen, J. Liu, A. 2026-02-05 doi:10.64898/2026.02.03.702007 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Prenatal stress interacts with embryonic loss of Fgfr2 to increase locomotor hyperactivity in mice ]]> https://biorxiv.org/content/10.64898/2026.02.04.703738v1?rss=1 Chen, M. X. Jager, P. Sawyer, A. Stevens, H. E. 2026-02-05 doi:10.64898/2026.02.04.703738 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ A transcriptional code controlling fluid shear stress-induced gene expression ]]> https://biorxiv.org/content/10.64898/2026.02.04.703710v1?rss=1 Fleisinger, L. Bruche, S. Lim, H. Rataj, A. Rodriquez-Caro, H. Genovese, A. Vinayachandran, V. Nornes, S. Szumska, D. Gupta, D. S. Ratnayaka, I. Chouliaras, K. Giers, M. Conway, S. J. Neal, A. Payne, S. Schwartz, M. A. Jain, M. K. Coon, B. G. De Val, S. 2026-02-06 doi:10.64898/2026.02.04.703710 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Deconstructing empirical fitness seascapes across scales of granularity ]]> https://biorxiv.org/content/10.64898/2026.02.04.703871v1?rss=1 Manivannan, S. N. Ogbunugafor, C. B. 2026-02-06 doi:10.64898/2026.02.04.703871 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Dynamic emotional updating as a computational marker of well-being ]]> https://biorxiv.org/content/10.64898/2026.02.05.703205v1?rss=1 Nagar, N. Vasilchenko, K. Jangraw, D. C. Rutledge, R. B. Keren, H. 2026-02-09 doi:10.64898/2026.02.05.703205 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ New records of signature spiders (Araneidae: Argiope spp.) from India with the resurrection of A. undulata Thorell, 1887 ]]> https://biorxiv.org/content/10.64898/2026.02.06.704477v1?rss=1 Kerr, A. M. Papeschi, S. 2026-02-09 doi:10.64898/2026.02.06.704477 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Cell-specific roles for the conserved Galpha chaperone RIC-8 in cilia biology ]]> https://biorxiv.org/content/10.64898/2026.02.07.704597v1?rss=1 Campagna, C. Descoteaux, A. E. Poole, A. Peet, E. Malaiwong, N. O'Donnell, M. P. Nechipurenko, I. 2026-02-09 doi:10.64898/2026.02.07.704597 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ SenNet Portal: Build, Optimization and Usage ]]> https://biorxiv.org/content/10.64898/2026.02.06.704469v1?rss=1 Borner, K. Blood, P. D. Silverstein, J. C. Ruffalo, M. Satija, R. Gehlenborg, N. Honick, B. Bueckle, A. Jain, Y. Qaurooni, D. Shirey, B. Sibilla, M. Metis, K. Bisciotti, J. Morgan, R. S. Betancur, D. Sablosky, G. R. Turner, M. L. Kim, S.-J. Lee, P. J. Bartz, J. Domanskyi, S. Peters, S. T. Enninful, A. Farzad, N. Fan, R. SenNet Team, Herr, B. W. 2026-02-10 doi:10.64898/2026.02.06.704469 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ CoPrimeEEG: CRT-Guided Dual-Branch Reconstruction from Co-Prime Sub-Nyquist EEG ]]> https://biorxiv.org/content/10.64898/2026.02.08.704713v1?rss=1 Yu, Y. Liu, D. Wu, Y. N. 2026-02-10 doi:10.64898/2026.02.08.704713 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics ]]> https://biorxiv.org/content/10.64898/2026.02.10.705077v1?rss=1 Lu, C. Kluger, Y. Ma, R. 2026-02-12 doi:10.64898/2026.02.10.705077 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation ]]> https://biorxiv.org/content/10.64898/2026.02.11.705401v1?rss=1 Xiao, W. Hann, T. Perry, Z. Pandey, V. Cheng, J. Wohlschlegel, J. Pyle, A. M. Black, D. L. 2026-02-12 doi:10.64898/2026.02.11.705401 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Computational modeling of neurotransmitter cycling predicts human brain glutamate and GABA dynamics in response to administration of exogenous ketones ]]> https://biorxiv.org/content/10.64898/2026.02.11.700015v1?rss=1 Antal, B. B. Mujica-Parodi, L. R. Strey, H. H. Ratai, E.-M. Mangia, S. Rothman, D. 2026-02-14 doi:10.64898/2026.02.11.700015 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Cell phenotypes in the biomedical literature: a systematic analysis and text mining corpus ]]> https://biorxiv.org/content/10.64898/2026.02.11.705457v1?rss=1 Rotenberg, N. H. Leaman, R. Islamaj, R. Kuivaniemi, H. Tromp, G. Fluharty, B. Richardson, S. Eastwood, C. Diller, M. Xu, B. Pankajam, A. V. Osumi-Sutherland, D. Lu, Z. Scheuermann, R. H. 2026-02-14 doi:10.64898/2026.02.11.705457 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Phylogenomics and the origins of sharks ]]> https://biorxiv.org/content/10.64898/2026.02.13.705779v1?rss=1 Brownstein, C. Near, T. J. 2026-02-15 doi:10.64898/2026.02.13.705779 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ scAmp analyzes focal gene amplifications at single-cell resolution ]]> https://biorxiv.org/content/10.64898/2026.02.14.705928v1?rss=1 Jones, M. G. Weiser, N. E. Hung, K. L. Yan, X. Agarwal, S. Luebeck, J. Gnanasekar, A. Howitt, B. E. Curtis, E. J. Yu, K. Rose, J. C. Kraft, K. Amiri, V. V. P. Satpathy, L. Bafna, V. Mischel, P. S. Chang, H. Y. 2026-02-15 doi:10.64898/2026.02.14.705928 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Visual experience drives functional reorganization of cortical GABAergic circuits ]]> https://biorxiv.org/content/10.64898/2026.02.12.705412v1?rss=1 Sun, S. Yue, Y. Li, Z. Perrenoud, Q. Cardin, J. A. 2026-02-16 doi:10.64898/2026.02.12.705412 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Growth-dependent sensory bet-hedging enhances collective navigation ]]> https://biorxiv.org/content/10.64898/2026.02.13.705748v1?rss=1 Avgidis, F. Jurgelyte, R. Emonet, T. Shimizu, T. S. 2026-02-16 doi:10.64898/2026.02.13.705748 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Differences in dynamic motor selection in stuttering ]]> https://biorxiv.org/content/10.64898/2026.02.14.705922v1?rss=1 Echeverria-Altuna, I. Demirel, B. Boettcher, S. E. P. Watkins, K. E. Nobre, A. C. 2026-02-16 doi:10.64898/2026.02.14.705922 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Spatial Rewiring of Enterocyte Identity in Celiac Disease ]]> https://biorxiv.org/content/10.64898/2026.02.14.705877v1?rss=1 Barkai, T. Frieman-Sharabi, R. Bahar Halpern, K. Novoselsky, R. Korem Kohanim, Y. Shir, S. Golani, O. Goliand, I. Addadi, Y. Kedmi, M. Keren-Shaul, H. Prichislov, L. Guz-Mark, A. Nissim, H. Shamir, R. Shouval, D. Itzkovitz, S. 2026-02-17 doi:10.64898/2026.02.14.705877 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Modified RNA Extraction Methods to Eliminate Agarose Impurities in Precision-Cut Lung Slices ]]> https://biorxiv.org/content/10.64898/2026.02.16.705835v1?rss=1 Rangel, R. Anderson, S. DeIuliis, G. Manning, E. E. Ahangari, F. Pandit, A. Kaminski, N. Marti-Munoz, J. 2026-02-17 doi:10.64898/2026.02.16.705835 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Value-Based Evidence Accumulation as a Transdiagnostic Marker of General Distress ]]> https://biorxiv.org/content/10.64898/2026.02.16.706202v1?rss=1 Pushkarskaya, H. Russell, C. M. Cheng, K. Chen, J. Pittenger, C. 2026-02-18 doi:10.64898/2026.02.16.706202 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Thrombo-inflammatory endothelial signatures in JAK2-mutated myeloproliferative neoplasms ]]> https://biorxiv.org/content/10.64898/2026.02.16.706250v1?rss=1 Abosabie, S. A. S. Boye-Doe, A. Ali, M. Podoltsev, N. Stegner, D. Mendez, L. M. Sharda, A. V. 2026-02-18 doi:10.64898/2026.02.16.706250 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Chemical interactions in polyethylene glycol-induced condensates lead to an anomalous FRET response from a flexible linker-fluorescent protein crowding sensor ]]> https://biorxiv.org/content/10.64898/2026.02.16.706251v1?rss=1 Mohapatra, A. Antarasen, J. Latham, D. R. Barilla, M. A. Davis, C. M. Kisley, L. 2026-02-18 doi:10.64898/2026.02.16.706251 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Structural evolution of the MTCH family of mitochondrial insertases ]]> https://biorxiv.org/content/10.64898/2026.02.17.705849v1?rss=1 Stevens, T. A. Luo, Z. Lee, C. Hazu, M. Galatis, E. G. Inglis, A. J. Guna, A. Voorhees, R. M. 2026-02-18 doi:10.64898/2026.02.17.705849 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Glycolytic Specialization Shapes Neuronal Physiology and Function in vivo ]]> https://biorxiv.org/content/10.64898/2026.02.17.706437v1?rss=1 Wolfe, A. D. Niu, L. Yilmaz, L. S. Ravikumar, S. Thomas, M. J. Walhout, A. J. M. Wang, Z.-W. Goodman, R. H. Colon-Ramos, D. A. 2026-02-18 doi:10.64898/2026.02.17.706437 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ VDJdive and ECLIPSE enhance single-cell TCR sequencing analysis through the probabilistic resolution of ambiguous clonotypes ]]> https://biorxiv.org/content/10.64898/2026.02.18.706444v1?rss=1 Burns, E. C. Movassagh, M. Lundell, J. F. Ye, M. Ye, Z. Oliveira, G. Rout, R. Hugaboom, M. B. Street, K. Braun, D. A. 2026-02-20 doi:10.64898/2026.02.18.706444 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A ventral tegmental area GABAergic projection to the ventral pallidum regulates value-based decision making in mice ]]> https://biorxiv.org/content/10.64898/2026.02.19.706858v1?rss=1 Zhou, W. Yousuf, H. Mineur, Y. S. Picciotto, M. 2026-02-20 doi:10.64898/2026.02.19.706858 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Mechanisms of HIV Latency in Hematopoietic Progenitors: GFI1 as a Key Regulator ]]> https://biorxiv.org/content/10.64898/2026.02.19.706859v1?rss=1 Onyango, J. A. Li, C. Chen, C. Disbennett, W. M. Virgilio, M. C. Painter, M. M. Terry, V. H. Ramnani, B. Welch, J. D. Collins, K. L. 2026-02-20 doi:10.64898/2026.02.19.706859 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Differential analysis of image-based chromatin tracing data with Dory ]]> https://biorxiv.org/content/10.64898/2026.02.19.706897v1?rss=1 Ma, Z. Liu, M. Wang, S. Wang, S. Zang, C. 2026-02-20 doi:10.64898/2026.02.19.706897 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Hijacking of inflammasome responses by the complement system during Pseudomonas aeruginosa-Aspergillus fumigatus sur-infection ]]> https://biorxiv.org/content/10.64898/2026.02.20.707105v1?rss=1 Khau, S. Treps, L. Ilango, G. Riteau, N. Couillin, I. Togbe, D. Bigot, J. Balloy, V. David, C. Charrier Le Blan, M. Fouquenet, D. Vasseur, V. Fontaine, T. Pappworth, I. Marchbank, K. Paget, C. Baranek, T. Biquand, E. Britto, C. J. Guillot, L. Si-Tahar, M. Briard, B. 2026-02-22 doi:10.64898/2026.02.20.707105 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Simplifying principles that underlie the highly complex peptide motif of the promiscuous chicken class I molecule, BF2*21:01 ]]> https://biorxiv.org/content/10.64898/2026.02.20.707067v1?rss=1 Harrison, M. Chappell, P. E. Halabi, S. Danysz, M. Mararo, E. M. Magiera, L. Hermann, C. Deery, M. J. Lilley, K. S. Wallny, H.-J. Avila, D. W. Mwangi, W. Nair, V. Lea, S. M. Ternette, N. Kaufman, J. 2026-02-23 doi:10.64898/2026.02.20.707067 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Reverse electron transfer at mitochondrial complex I restrains dopaminergic neuron activity to promote early-life sleep in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.02.22.707308v1?rss=1 Rosa, J. B. Kim, H. H. Luong, J. Yang, J. Yee, P. Yan, A. Rodriguez, A. Kayser, M. S. 2026-02-23 doi:10.64898/2026.02.22.707308 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ The Kaposi's sarcoma-associated herpesvirus viral genome packaging accessory factor ORF68 forms cytoplasmic puncta dependent on the viral tyrosine kinase ]]> https://biorxiv.org/content/10.64898/2026.02.23.707506v1?rss=1 Gelles-Watnick, S. Liu, D. Cerezo-Matias, M. A. Liu, J. Ospina, G. Schafer, A. Kabeche, L. Cristea, I. M. Didychuk, A. L. 2026-02-23 doi:10.64898/2026.02.23.707506 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Exploring the Influence of Chemical Exposures in Breast Cancer Disparities: High-Throughput Transcriptomic Analysis in Normal Breast Cells from Diverse Donors ]]> https://biorxiv.org/content/10.64898/2026.02.23.707203v1?rss=1 Zhao, N. Zhao, P. Tapaswi, A. Polemi, K. M. Thong, T. Sexton, J. Z. Charles, S. Wicha, M. S. Svoboda, L. Zhou, X. Colacino, J. 2026-02-24 doi:10.64898/2026.02.23.707203 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Peripheral Metabolic Reprogramming Links TDP-43 Proteinopathy to Sleep Disruption ]]> https://biorxiv.org/content/10.64898/2026.02.23.707321v1?rss=1 Rodriguez, A. Belfer, S. J. Luong, J. Shcherbakova, O. Kain, P. Sengupta, A. Perlegos, A. Jin, Z. Weljie, A. Bonini, N. M. Kayser, M. S. 2026-02-24 doi:10.64898/2026.02.23.707321 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ IL-35 produced by dendritic cells via TIM-3-STAT3 signaling contributes to the development of visceral leishmaniasis ]]> https://biorxiv.org/content/10.64898/2026.02.23.707416v1?rss=1 Kumar, S. Shubham, S. Mishra, M. Kumar, R. Sen, P. 2026-02-24 doi:10.64898/2026.02.23.707416 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ 3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes ]]> https://biorxiv.org/content/10.64898/2026.02.23.707469v1?rss=1 LHote, L. Sacristan, L. Ferguson, R. Siekmann, A. Rogers, L. Richter, B. Weissenbock, H. Lorke, J. Artemis, L. LEveque, E. Hark, R. Engel, P. Webber, M. T. J. Bennett, M. Rose-Beers, K. Nichols, E. Alegre, M. M. Ramsoe, M. Fiddyment, S. Vinas-Caron, L. C. Papin, D. V. Light-Maka, I. C. Key, F. M. Albarnaz, J. Downing, T. Pekar, J. Lemey, P. Bradley, D. Vnoucek, J. Makarewicz, C. A. Story, J. Collins, M. Teasdale, M. D. Binois-Roman, A. Calvignac-Spencer, S. Daly, K. G. 2026-02-24 doi:10.64898/2026.02.23.707469 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Leveraging DNA and RNA oscillatory dynamics to investigate the ecology and physiology of a freshwater microbial community ]]> https://biorxiv.org/content/10.64898/2026.02.24.707719v1?rss=1 Shoemaker, W. R. Dal Bello, M. Grilli, J. 2026-02-24 doi:10.64898/2026.02.24.707719 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Liver Disease Reveals KIF12 as a Critical Regulator of Mitochondria, Lysosome and Cilia Localization ]]> https://biorxiv.org/content/10.64898/2026.02.24.707575v1?rss=1 Seth, A. Brancale, J. Dashti-Gibson, N. Florentino, R. M. Faccioli, L. A. P. Liu, Z. Konkwo, C. Hong, H. Soto-Gutierrez, A. Vilarinho, S. 2026-02-25 doi:10.64898/2026.02.24.707575 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Development of a recombinant adeno-associated virus vector for human T lymphocyte- and natural killer cell-targeted gene therapy ]]> https://biorxiv.org/content/10.64898/2026.02.26.707014v1?rss=1 Jahnz, H. Hamann, M. V. Kim, H. Sun, Y. Quiroz, N. S. Zhu, L. Swaiba, U. E. Foth, D. Beschorner, N. Kumar, P. Lange, U. C. 2026-02-27 doi:10.64898/2026.02.26.707014 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ A single-nucleus multiome analysis of transcriptome and chromatin accessibility reveals cell-type-specific immune modulation for chronic cannabis use among people with HIV infection ]]> https://biorxiv.org/content/10.64898/2026.02.26.708082v1?rss=1 Li, M. Asam, K. Duan, X. Page, G. P. Hu, Y. Martinez, C. Cohen, M. H. Archin, N. Valizadeh, A. Hancock, D. B. Johnson, E. O. Aouizerat, B. Xu, K. 2026-02-27 doi:10.64898/2026.02.26.708082 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA ]]> https://biorxiv.org/content/10.64898/2026.02.26.708114v1?rss=1 Fu, L. Chen, J. Lian, D. Du, S. Wu, D. Yang, C. Wang, Z. Ma, H. Li, Z. Lake, N. J. APG Consortium, Yang, X. Shi, Y. Zhang, G. Ma, K. Mao, Y. 2026-02-27 doi:10.64898/2026.02.26.708114 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ The pod components of the Shigella T3SS sorting platform accommodate multiple copies of Spa33 (SctQ) ]]> https://biorxiv.org/content/10.64898/2026.02.26.708312v1?rss=1 Whittier, S. K. Tachiyama, S. Heydari, S. Picking, W. L. Liu, J. Picking, W. D. 2026-02-27 doi:10.64898/2026.02.26.708312 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Identifying genetic regulations on immune cell type proportions and their impacts on autoimmune diseases ]]> https://biorxiv.org/content/10.64898/2026.02.26.708418v1?rss=1 Lin, C. Shen, J. Sun, J. Xie, Y. Xu, L. Lin, Y. Hu, J. Zhao, H. 2026-03-01 doi:10.64898/2026.02.26.708418 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ Hierarchical membrane-chromatin tethering buffers nuclear envelope assembly against alterations in lipid flux ]]> https://biorxiv.org/content/10.64898/2026.02.27.708386v1?rss=1 Barger, S. Sepulveda, S. Yang, H. Goudge, M. Lee, S. Ridgway, N. Bahmanyar, S. 2026-03-02 doi:10.64898/2026.02.27.708386 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Continuous In Vitro Propagation of the Human Pathogen Babesia microti in Human Erythrocytes ]]> https://biorxiv.org/content/10.64898/2026.03.01.708882v1?rss=1 Kumari, G. Chattopadhyay Pal, A. Singh, P. Ben Mamoun, C. 2026-03-02 doi:10.64898/2026.03.01.708882 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ The orbitofrontal cortex constructs allocentric schemas by integrating dynamic mobile agents with static environmental anchors ]]> https://biorxiv.org/content/10.64898/2026.03.01.708836v1?rss=1 Zhu, Z. Zhang, B. Zhang, X. Naya, Y. 2026-03-03 doi:10.64898/2026.03.01.708836 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Multisensory coding of audiovisual movies in the human hippocampus ]]> https://biorxiv.org/content/10.64898/2026.03.01.708855v1?rss=1 Raccah, O. Agarwal, A. Zhu, Y. Turk-Browne, N. B. 2026-03-03 doi:10.64898/2026.03.01.708855 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Large-scale Perturbation of Systems Biology-Derived Genes Reveals Modifiers of HD-associated Transcriptomic Networks and Pathology ]]> https://biorxiv.org/content/10.64898/2026.03.02.709091v1?rss=1 Langfelder, P. Wang, N. Ramanathan, L. Oh, Y. M. Lee, S. Gao, F. Gu, X. Stricos, M. Plascencia, M. Vaca, R. Richman, J. Vogt, T. F. Horvath, S. Yoo, A. S. Aaronson, J. Rosinski, J. Yang, X. W. 2026-03-04 doi:10.64898/2026.03.02.709091 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Systemic RNAi in planarians depends on spread of RNPs from active stem cells ]]> https://biorxiv.org/content/10.64898/2026.03.03.709314v1?rss=1 Allikka Parambil, S. Ascunce Gonzalez, K. Poulet, A. Cruz, L. Lee, H.-L. Witmer, M. van Wolfswinkel, J. C. 2026-03-04 doi:10.64898/2026.03.03.709314 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Structure basis for single-strand nucleic acid targeting by IscB and variants ]]> https://biorxiv.org/content/10.64898/2026.03.03.709405v1?rss=1 Xu, C. Yang, Q. Niu, X. ke, a. 2026-03-04 doi:10.64898/2026.03.03.709405 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Enhancing cGMP signaling with psilocybin reduces head twitch and restructures the synaptic proteome while maintaining antidepressant response ]]> https://biorxiv.org/content/10.64898/2026.03.06.710108v1?rss=1 Floris, G. Jefferson, S. J. Rondeau, J. Menniti, F. S. Kwan, A. C. De Aquino, J. P. Krystal, J. H. Pittenger, C. Kaye, A. P. 2026-03-10 doi:10.64898/2026.03.06.710108 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Neuronal overexpression of mouse potassium channel subunit Kcnn1 in A53T α-synuclein mice more than doubles median survival time, associated with suppression of phospho-S129 α-synuclein formation ]]> https://biorxiv.org/content/10.64898/2026.03.09.709927v1?rss=1 Nagy, M. Fenton, W. A. Horwich, A. L. 2026-03-11 doi:10.64898/2026.03.09.709927 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Cognitive reappraisal of food and emotion cues involves common and unique neural contributions ]]> https://biorxiv.org/content/10.64898/2026.03.09.710570v1?rss=1 Laing-Young, J. M. Savage, C. R. Tomaso, C. Neta, M. Nelson, T. D. Schultz, D. H. 2026-03-11 doi:10.64898/2026.03.09.710570 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ The Nuclear-Cytoskeletal Interface Is a Vulnerability in Aging Endothelium ]]> https://biorxiv.org/content/10.64898/2026.03.09.710624v1?rss=1 Francis, C. Eichmann, A. Leser, F. Lopez, R. 2026-03-11 doi:10.64898/2026.03.09.710624 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Acute Degradation of Pumilio Proteins Uncovers a Biphasic Post-transcriptional Regulatory Hierarchy Controlling Embryonic Stem Cell Fate Decisions ]]> https://biorxiv.org/content/10.64898/2026.03.10.710821v1?rss=1 Huang, Y. Li, W. Richman, H. E. Liu, Y. Lin, H. 2026-03-11 doi:10.64898/2026.03.10.710821 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Interdependent RNA structural motifs at the 3'-terminus of the West Nile virus genome regulate viral growth ]]> https://biorxiv.org/content/10.64898/2026.03.11.711107v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@14b10a5org.highwire.dtl.DTLVardef@131e63aorg.highwire.dtl.DTLVardef@1021aa9org.highwire.dtl.DTLVardef@12470a4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tsao, L. H. Brackney, D. E. Pyle, A. M. 2026-03-11 doi:10.64898/2026.03.11.711107 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Baseline cellular state dictates the molecular impact of KRAS mutant variants in pancreatic cancer cells ]]> https://biorxiv.org/content/10.64898/2026.03.10.710185v1?rss=1 Quinones-Aviles, Y. Salovska, B. Markham, C. S. Di, Y. Turk, B. E. Liu, Y. Muzumdar, M. D. 2026-03-12 doi:10.64898/2026.03.10.710185 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ 3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis ]]> https://biorxiv.org/content/10.64898/2026.03.10.710708v1?rss=1 Rabbani, M. Apell, Z. Parnell, T. J. Moritz, L. Kim, S. Srinivasan, S. Agrawal, R. Vargo, A. Orchard, P. Xie, W. Freddolino, L. Boyle, A. P. Li, J. Z. Lesch, B. J. Cairns, B. Kim, M. Wilson, T. E. Hammoud, S. S. 2026-03-12 doi:10.64898/2026.03.10.710708 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ ATF4 and EcR interact to mediate both transcriptional activation and repression in the Drosophila fat body ]]> https://biorxiv.org/content/10.64898/2026.03.10.710866v1?rss=1 Michaca, M. H. Grmai, L. Vasudevan, D. 2026-03-12 doi:10.64898/2026.03.10.710866 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Image Analysis Tools for Electron Microscopy ]]> https://biorxiv.org/content/10.64898/2026.03.11.711125v1?rss=1 Shtengel, D. Shtengel, G. Xu, C. S. Hess, H. F. 2026-03-14 doi:10.64898/2026.03.11.711125 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ NeuroMark-SZ: A Holistic Resting-State-fMRI-Based Model for Divergent Functional Circuitry in Schizophrenia ]]> https://biorxiv.org/content/10.64898/2026.03.12.710902v1?rss=1 Jensen, K. M. Ballem, R. Kinsey, S. Andres-Camazon, P. Fu, Z. Chen, J. Haas, S. S. Diaz-Caneja, C. M. Bustillo, J. R. Preda, A. van Erp, T. G. M. Pearlson, G. Sui, J. Kochunov, P. Turner, J. A. Calhoun, V. D. Iraji, A. 2026-03-14 doi:10.64898/2026.03.12.710902 Cold Spring Harbor Laboratory Press 2026-03-14 <![CDATA[ A strong start for sustained success: inclusivity through a national group mentorship program for first-year graduate students ]]> https://biorxiv.org/content/10.64898/2026.03.12.710679v1?rss=1 Labra, S. R. Tornini, V. A. Rodriguez Salazar, M. P. Cossio, D. M. Gelpi, R. A. Rubio Perez, B. E. Rodriguez, Y. M. Leana-Sandoval, G. Hernandez, K. Goldman, O. V. Fernandez, R. W. 2026-03-15 doi:10.64898/2026.03.12.710679 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Human claustrum neurons encode uncertainty and prediction errors during aversive learning ]]> https://biorxiv.org/content/10.64898/2026.03.13.711590v1?rss=1 damisah, e. c. Hu, M. Dalvit, R. Medina, M. dougherty, m. Zhou, Y. barretonieves, j. obaid, s. Afrasiyabi, A. Krishnaswamy, S. Kaye, A. P. Gunel, M. krystal, j. Sheth, K. N. Gu, X. Pittenger, C. wise, t. 2026-03-15 doi:10.64898/2026.03.13.711590 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid ]]> https://biorxiv.org/content/10.64898/2026.03.12.711294v1?rss=1 Korem Kohanim, Y. Barkai, T. Novoselsky, R. Shir, S. Bahar Halpern, K. Reich-Zeliger, S. Elkahal, J. Tessler, I. Shivatzki, S. Schwartz, I. Remer, E. Avior, G. Hoefllin, R. Kedmi, M. Keren-Shaul, H. Goliand, I. Addadi, Y. Golani, O. Alon, E. Itzkovitz, S. Medzhitov, R. 2026-03-16 doi:10.64898/2026.03.12.711294 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Task-based functional connectivity in striato-motor-cortical system in autism: Associations with sex and executive function ]]> https://biorxiv.org/content/10.64898/2026.03.13.711578v1?rss=1 Jack, A. Gupta, A. R. GENDAAR Consortium, 2026-03-16 doi:10.64898/2026.03.13.711578 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ A Deep Quantitative Proteome Turnover Platform for Human iPSC-derived Neurons ]]> https://biorxiv.org/content/10.64898/2026.03.14.711828v1?rss=1 Hao, L. Frankenfield, A. M. Shih, J. Zhang, T. Ni, J. Mazli, W. N. A. b. Lo, E. Liu, Y. Wang, J. 2026-03-16 doi:10.64898/2026.03.14.711828 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Specialists drive biodiversity scaling in symbiotic relationships ]]> https://biorxiv.org/content/10.64898/2026.03.13.711632v1?rss=1 Carlson, C. J. Yoder, J. B. Poisot, T. 2026-03-17 doi:10.64898/2026.03.13.711632 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ PNPLA3I148M is a novel regulator of bone mass independent of MASLD ]]> https://biorxiv.org/content/10.64898/2026.03.13.711662v1?rss=1 Goldscheitter, G. M. Seneshaw, M. Mirshahi, F. Summerlin, M. Ip, A. Coelho, A. Genetos, D. Sanyal, A. Donahue, H. 2026-03-17 doi:10.64898/2026.03.13.711662 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Tonsillar expression quantitative trait loci verify and expand genetic contributors to childhood atopic diseases ]]> https://biorxiv.org/content/10.64898/2026.03.13.711667v1?rss=1 Lorenz, K. Yoon, S. Le Coz, C. Zur, K. Wells, A. Romberg, N. Voight, B. F. 2026-03-17 doi:10.64898/2026.03.13.711667 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Impaired motor activity in a CRISPR SCA5 L253P knock-in mouse is associated with selective beta-III-spectrin subcellular redistribution in the cerebellum ]]> https://biorxiv.org/content/10.64898/2026.03.14.711824v1?rss=1 Avery, A. W. O'Callaghan, B. L. Thiel, M. T. Denha, S. A. O'Callaghan, D. G. Cismas, E. M. Lamp, J. Orr, H. T. Hays, T. S. 2026-03-17 doi:10.64898/2026.03.14.711824 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Optogenetic Analysis of Behavior in the Mosquito Aedes aegypti ]]> https://biorxiv.org/content/10.64898/2026.03.15.711871v1?rss=1 Rami, S. So, M. Travis, C. Jiao, Y. Shamble, P. Sorrells, T. R. 2026-03-18 doi:10.64898/2026.03.15.711871 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Cell wall charge gates iron availability in plant roots ]]> https://biorxiv.org/content/10.64898/2026.03.15.711884v1?rss=1 Liu, C. Dobrogojski, J. Miranda, P. R. Wölki, D. Marconi, M. Ulbrich, N. Gonzalez-Delgado, A. Kang, H. S. Kubalova, M. Fendrych, M. Ebert, B. Wabnik, K. Barbez, E. 2026-03-18 doi:10.64898/2026.03.15.711884 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Hippocampal patterns and associative memory: Distinct intracranial EEG temporal encoding patterns support memory ]]> https://biorxiv.org/content/10.64898/2026.03.18.712716v1?rss=1 Xue, A. M. Hsu, S. LaRocque, K. F. Raccah, O. M. Gonzalez, A. Parvizi, J. Wagner, A. D. 2026-03-20 doi:10.64898/2026.03.18.712716 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Loss of Sun2 ablates nuclear mechanosensing-driven extracellular matrix production and mitigates lung fibrosis ]]> https://biorxiv.org/content/10.64898/2026.03.18.712778v1?rss=1 Carley, E. Sandria, S. Peng, X. Y. Davidson, K. Nassereddine, A. Ryu, C. Rivera, R. McGovern, J. Ghincea, A. Lusk, C. P. Herzog, E. L. Horsley, V. King, M. C. 2026-03-20 doi:10.64898/2026.03.18.712778 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ SUN2 mediates epigenetic remodeling to drive mechanotransduction during skin fibrosis ]]> https://biorxiv.org/content/10.64898/2026.03.19.712957v1?rss=1 Nassereddine, A. Davidson, K. Sandria, S. Das, S. Rivera, R. Tran, V. A. Antani, J. D. Hinchcliff, M. D. King, M. C. Horsley, V. 2026-03-20 doi:10.64898/2026.03.19.712957 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads ]]> https://biorxiv.org/content/10.64898/2026.03.20.713111v1?rss=1 Gao, Y. Liao, W.-W. Qin, Q. Hall, I. M. Li, H. 2026-03-22 doi:10.64898/2026.03.20.713111 Cold Spring Harbor Laboratory Press 2026-03-22 <![CDATA[ Nav1.5 expressed in TrkB+ sensory neurons mediates paclitaxel-induced mechanical pain hypersensitivity ]]> https://biorxiv.org/content/10.64898/2026.03.19.713015v1?rss=1 Gomes, F. I. Adjafre, B. L. Lee, S. Prudente, A. da Silva, G. Silva, E. A. Kanada, L. Roman-Campos, D. Alves-Filho, J. C. Cunha, F. Waxman, S. Dib-Hajj, S. Berta, T. Cunha, T. M. 2026-03-23 doi:10.64898/2026.03.19.713015 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ A mosaic of climate vulnerability: local warming rates meet intraspecific divergence in heat tolerance ]]> https://biorxiv.org/content/10.64898/2026.03.20.713229v1?rss=1 Jawad, W. A. Salgado, A. L. Cheng, B. S. Gignoux-Wolfsohn, S. A. Hays, C. Munoz, M. M. Sasaki, M. C. Kelly, M. W. 2026-03-23 doi:10.64898/2026.03.20.713229 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Metaplastic sleep regulation in Drosophila determined by microscale circadian neural dynamics ]]> https://biorxiv.org/content/10.64898/2026.03.21.713346v1?rss=1 Hutson, A. N. Zarjetskiy, A. N. Zhang, Y. J. Pokaleva, N. Paul, E. M. Xie, Y. Chong, B. Sanchez Franco, V. M. Zukowski, L. H. Faulk, E. E. Walker, J. A. Brown, A. M. Nguyen, D. L. Ferry, F. S. Snyder, E. M. Tabuchi, M. 2026-03-24 doi:10.64898/2026.03.21.713346 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Temperature-dependent performance scales with maximum heat tolerance across ectotherms ]]> https://biorxiv.org/content/10.64898/2026.03.21.713427v1?rss=1 100 ectotherms, we tested how heat tolerance (CTmax) relates to key TPC traits: thermal optima, thermal maxima, and the supra-optimal range of temperatures where performance is positive. Across taxa, TPC traits were positively related to CTmax, demonstrating a link between heat tolerance and temperature-dependent performance at sub-critical temperatures. While acute locomotor performance scaled proportionally with CTmax, metabolic processes and sustained locomotion scaled sub-proportionally, suggesting decoupling of CTmax and performance among high-CTmax species. This suggests that using CTmax as a comparative metric may overestimate thermal safety margins for metabolic processes critical to growth. Our results indicate that while CTmax and TPCs reflect shared underlying constraints--particularly in acute neuro-muscular traits--their relationship is dependent on timescale and the TPC response trait. Our findings connect our understanding of the processes that maintain performance over thermal gradients with those that cause performance to fail, improving our ability to project species persistence in a warming world. SignificanceClimate warming is increasingly reshaping the thermal environments that govern species persistence worldwide. Predicting vulnerability requires integrating multiple aspects of thermal biology, yet relationships among widely used thermal traits remain poorly understood. By synthesizing data from more than 100 ectotherm species, we quantify links between acute heat tolerance and traits describing sustained biological function across temperatures. We show that performance at relatively benign temperatures and performance at thermal extremes are coupled, but this coupling is strongly process and timescale dependent, with close correspondence for short term locomotion but weaker coupling for metabolic processes. Our results link the processes that maintain performance across temperatures with those that cause failure, fundamentally advancing our projections of species performance in a warming world. ]]> Cicchino, A. S. Collier, J. Bieg, C. Davis, K. Ghalambor, C. K. Robey, A. J. Sunday, J. M. Vasseur, D. Bernhardt, J. R. 2026-03-24 doi:10.64898/2026.03.21.713427 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Somatic evolution of a cross-reactive germline antibody that expands its breadth to neutralize new SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.64898/2026.03.20.713312v1?rss=1 Lv, H. Feng, Z. Teo, Q. W. Chen, C. Gopal, A. B. Choi, D. Tan, T. J. C. Tang, Y. S. Siu, L. Nourmohammad, A. Bruzzone, R. Wilson, I. A. Yuan, M. Wu, N. C. Mok, C. K.-P. 2026-03-25 doi:10.64898/2026.03.20.713312 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Fluorogenic speed-optimized DNA-PAINT probes enable super-resolution imaging of whole cells ]]> https://biorxiv.org/content/10.64898/2026.03.23.710523v1?rss=1 Stoller, S. Jha, A. Bewersdorf, J. Schueder, F. 2026-03-25 doi:10.64898/2026.03.23.710523 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Cross-Species Multi-Omics Profiling Identifies Conserved Activated Valvular Interstitial Cell Population Driving Myxomatous Mitral Valve Degeneration ]]> https://biorxiv.org/content/10.64898/2026.03.23.713796v1?rss=1 Gao, F. Mason, I. Dong, M. Lu, Y. Zhang, D. Lou, X. Hameed, I. Yang, M. Zhong, M. Krane, M. Ferrari, G. Tellides, G. Liu, Y. Fan, R. Geirsson, A. 2026-03-25 doi:10.64898/2026.03.23.713796 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Epizootic tipping points: Environmental viral feedbacks predict amphibian die-offs ]]> https://biorxiv.org/content/10.64898/2026.03.24.714032v1?rss=1 Billet, L. S. Hoverman, J. T. Sauer, E. L. Bermudez, J.-G. Skelly, D. K. 2026-03-27 doi:10.64898/2026.03.24.714032 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Neurodegeneration risk variants promote lysosomal TMEM106B fibrilaccumulation ]]> https://biorxiv.org/content/10.64898/2026.03.26.714634v1?rss=1 Replogle, J. M. Marks, J. D. Fernandez, M. G. Yuan, H. Yu, B. Winters, E. Jawahar, V. M. Deshmukh, R. Sutanto, R. Kowal, I. Frankenfield, A. Shi, R. Carlomagno, Y. Jansen-West, K. Todd, T. Kopach, A. Ndayambaje, I. S. Qi, Y. A. Shantaraman, A. Pozo-Cabanell, I. Sheth, U. Yue, M. Duong, D. Ferguson, S. M. Bennett, D. A. Damme, M. Boeve, B. F. Day, G. S. Kellman, B. Skarnes, W. C. Petersen, R. C. Josephs, K. A. Graff-Radford, N. McDonough, J. A. Prudencio, M. Barmada, S. J. Zhang, Y. Hao, L. DeTure, M. Rawlinson, B. Cook, E. E. Casey, M. C. Perez, N. Di 2026-03-28 doi:10.64898/2026.03.26.714634 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Representational Dynamics in the Hippocampus and Medial Prefrontal Cortex during Learning and Task Mastery ]]> https://biorxiv.org/content/10.64898/2026.03.27.714523v1?rss=1 Barayeu, U. Cumpelick, A. Kaefer, K. Csicsvari, J. 2026-03-28 doi:10.64898/2026.03.27.714523 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Cryo-EM structures of photosystem I with alternative quinones reveals new insight into cofactor selectivity ]]> https://biorxiv.org/content/10.64898/2026.03.27.714801v1?rss=1 Brininger, C. M. Wang, J. Kurashov, V. Russell, B. P. Magdaong, N. C. M. Iwig, D. F. Est, A. v. d. Golbeck, J. H. Vinyard, D. J. Lakshmi, K. V. Gisriel, C. J. 2026-03-28 doi:10.64898/2026.03.27.714801 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ ClumPyCells resolves spatial aggregation in complex tissues overcoming size biases ]]> https://biorxiv.org/content/10.64898/2026.03.26.714529v1?rss=1 Zhao, Z. Cui, L. Aguilar-Navarro, A. G. Monajemzadeh, M. Chang, Q. Chen, Z. Tsui, H. Flores-Figueroa, E. Schwartz, G. W. 2026-03-30 doi:10.64898/2026.03.26.714529 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Complementary constraints in germ and immune cells shape evolution of gene regulation and phenotype ]]> https://biorxiv.org/content/10.64898/2026.03.27.714809v1?rss=1 Griffin, K. N. Marshall, K. L. Russell, G. A. Attanasio, J. Farris, D. B. Yu, H. Fagerberg, E. Iyer, N. R. Lee, R. Sumigray, K. D. Joshi, N. S. Wang, A. Lesch, B. J. 2026-03-30 doi:10.64898/2026.03.27.714809 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model ]]> https://biorxiv.org/content/10.64898/2026.03.27.714913v1?rss=1 Pan, X. Shrawat, A. Raghavan, S. Dong, C. Yang, Y. Li, Z. Zheng, W. J. Eckhardt, S. G. Wu, E. Fuxman Bass, J. I. Jarosz, D. F. Chen, S. McGrail, D. J. Sheynkman, G. M. Huang, J. H. Sahni, N. Yi, S. S. 2026-03-31 doi:10.64898/2026.03.27.714913 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Channel Capacity for Time-Resolved Effective Connectivity in Functional Neuroimaging ]]> https://biorxiv.org/content/10.64898/2026.03.28.714906v1?rss=1 Jian, J. Li, B. Multezem, N. Mandino, F. Lake, E. M. Xu, N. 2026-03-31 doi:10.64898/2026.03.28.714906 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ B7-H3 Modulates Cell Adhesion and Immune Evasion to Promote Tumor Progression and Natural Killer Cell Resistance in Hepatocellular Carcinoma ]]> https://biorxiv.org/content/10.64898/2026.03.28.714951v1?rss=1 Han, S. H. Cheon, Y. J. Lee, H. M. Seo, H. Lee, J. Y. Kim, M. J. Yoon, S. R. Choi, D. Ryu, C. J. 2026-03-31 doi:10.64898/2026.03.28.714951 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Residue burial encodes a protein's fold ]]> https://biorxiv.org/content/10.64898/2026.03.28.714986v1?rss=1 Grigas, A. T. Sumner, J. O'Hern, C. S. 2026-03-31 doi:10.64898/2026.03.28.714986 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ The OS-Prey (Omnibus Study of Prey) database: A compilation of diet records for birds of prey. ]]> https://biorxiv.org/content/10.64898/2026.03.28.714998v1?rss=1 Uiterwaal, S. F. La Sorte, F. A. Coblentz, K. E. DeLong, J. P. 2026-03-31 doi:10.64898/2026.03.28.714998 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Deletion of endothelial KLF4 as a model for preeclampsia ]]> https://biorxiv.org/content/10.64898/2026.03.30.715448v1?rss=1 Meredith, E. Meredith, A. T. Mani, A. Schwartz, M. A. 2026-03-31 doi:10.64898/2026.03.30.715448 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Disrupting miR-466l-3p and HuR Cooperation with Target Site Blockers Reveals a Therapeutic Strategy to Destabilize mRNA Transcripts ]]> https://biorxiv.org/content/10.64898/2026.03.30.709388v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1a87bceorg.highwire.dtl.DTLVardef@5824b2org.highwire.dtl.DTLVardef@d14f6eorg.highwire.dtl.DTLVardef@1b5c033_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TEXTBOXMechanism of TSB-mediated disruption of cooperative miRNA-HuR-dependent mRNA stabilizationA: In the canonical model, destabilizing miRNAs (e.g., miR-16) bind to their target sites within the 3'UTR, recruiting the RNA-induced silencing complex (miRISC) to promote mRNA decay or translational repression. B: In contrast, a newly identified class of miRNAs--stabilizing miRNAs (E-miRNAs), such as miR-466l-3p--bind to specific target sequences within AU-rich elements (AREs) in the 3'UTR. This binding facilitates cooperative recruitment of the RNA-binding protein HuR (ELAVL1), resulting in enhanced mRNA stability and/or translation. C: Target site blockers (TSBs) designed to occlude miRNA-binding sites competitively inhibit miRISC loading, thereby disrupting HuR engagement and reversing stabilization. This selective disruption leads to transcript-specific mRNA destabilization without affecting global miRNA function. C_TEXTBOX ]]> Ramgolam, V. Yarovinsky, T. O. Huntenburg, S. Bergman, C. Ruddle, N. Bender, J. 2026-04-01 doi:10.64898/2026.03.30.709388 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Signal, noise, and bias in phylogenetic inference:potential and limits to the resolution of phylogenetic trees in the phylogenomic era ]]> https://biorxiv.org/content/10.64898/2026.03.30.714540v1?rss=1 Dornburg, A. Su, Z. T. Jin, Y. Fisk, N. Townsend, J. P. 2026-04-01 doi:10.64898/2026.03.30.714540 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ The cytoplasmic lattice in mammalian eggs sequesters ubiquitination machinery and tubulin in reserve ]]> https://biorxiv.org/content/10.64898/2026.03.30.715190v1?rss=1 Li, Y. Zheng, W. Leem, J. Wu, C. Tang, S. Mogessie, B. Xiong, Y. 2026-04-01 doi:10.64898/2026.03.30.715190 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ IMMREP25: Unseen Peptides ]]> https://biorxiv.org/content/10.64898/2026.03.30.715276v1?rss=1 Richardson, E. Aarts, Y. J. M. Altin, J. A. Baakman, C. A. B. Bradley, P. Chen, B. Clifford, J. Dhar, M. Diepenbroek, D. Fast, E. Gowthaman, R. He, J. Karnaukhov, V. Marzella, D. F. Meysman, P. Nielsen, M. Nilsson, J. B. Deleuran, S. N. Parizi, F. M. Pelissier, A. Pierce, B. G. Rodriguez Martinez, M. Roran A R, D. Saravanakumar, S. Shao, Y. Smit, N. Van Houcke, M. Visani, G. M. Wan, Y.-T. R. Wang, X. Woods, L. Wuyts, S. Xiao, C. Xue, L. C. IMMREP25 Participant Consortium, Barton, J. Noakes, M. May, D. H. Peters, B. 2026-04-01 doi:10.64898/2026.03.30.715276 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Extending island biogeography theory to biotic islands: Microbial communities in epiphytic bird's nest fern Asplenium nidus ]]> https://biorxiv.org/content/10.64898/2026.03.30.715435v1?rss=1 Tseng, Y.-P. Wei, S. Ke, P.-J. 2026-04-01 doi:10.64898/2026.03.30.715435 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ DNAM-1 immunoreceptor integrates innate and adaptive immune programs to drive intestinal inflammation ]]> https://biorxiv.org/content/10.64898/2026.03.30.715436v1?rss=1 Ide, N. Sato, k. Hayashi, K. Almeida, M. S. Abe, F. Kim, T. Nakahashi-Oda, C. Shibuya, K. Shibuya, A. 2026-04-01 doi:10.64898/2026.03.30.715436 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Site-specific O-glycans influence lacritin structure and multimerization in tears ]]> https://biorxiv.org/content/10.64898/2026.03.30.715376v1?rss=1 Chang, V. Chen, R. Lian, I. Mahoney, K. E. Romano, J. Laurie, G. Malaker, S. A. 2026-04-02 doi:10.64898/2026.03.30.715376 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Endocytosis shapes extracellular chemical gradients in autonomous cell-cell attraction ]]> https://biorxiv.org/content/10.64898/2026.03.31.715676v1?rss=1 Barrios, J. Goetz, A. Leggett, S. E. Dixit, P. D. 2026-04-02 doi:10.64898/2026.03.31.715676 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Top-down regulation of ingestive behavior fragmentation ]]> https://biorxiv.org/content/10.64898/2026.03.31.715709v1?rss=1 Qi, T. Krull, C. Leung, V. H. Mardare, V. Yang, D. Lal, N. Ma, J. Wang, S. Shen, H. Zhang, A. Zhao, B. Heydari Seradj, S. Korotkova, T. Kennedy, A. Ye, L. 2026-04-03 doi:10.64898/2026.03.31.715709 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ nELAVL phosphorylation by CDKL5 regulates inter-condensates composition and communication to promote experience-dependent maturation of the visual cortex ]]> https://biorxiv.org/content/10.64898/2026.04.03.716270v1?rss=1 Yuan, S. Zhu, Y. Zheng, Z. Yip, H. M. Chan, M. S. W. Zhang, Z. Chai, Y. Jenks, K. R. Tsimring, K. Heller, G. R. Zepeda, J. C. Celotto, M. Hung, H. K. Duan, Y. Lau, S.-F. Ho, C. W. Y. Tsang, H. W. S. Fu, A. K. Y. Lai, H. M. Kwok, A. J. Ko, H. Gu, C. Ng, B. W.-L. Liao, J. Fung, S. H. Cao, Q. Tsui, S. K.-W. Ku, T. Tan, L. Colarusso, A. Lasker, K. Wan, Y. Zhu, J. Ip, J. P. K. 2026-04-04 doi:10.64898/2026.04.03.716270 Cold Spring Harbor Laboratory Press 2026-04-04 <![CDATA[ Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches ]]> https://biorxiv.org/content/10.64898/2026.04.02.716161v1?rss=1 Farzad, N. Enninful, A. Lu, Y. Parisi, F. Fung, A. Kwon, Y. Li, Y. Labrosse, M. Yang, M. Strino, F. Chen, L. Yang, J. Zhong, M. Gao, F. Tao, B. Cunningham, J. Bai, Z. Li, H. Wang, F. Stankewich, M. Kim, D. Dong, M. Bramer, L. M. Bhat, M. R. Loe, E. Craft, J. Pasa-Tolic, L. Halene, S. Shi, L. Kluger, Y. Xu, M. L. Fan, R. 2026-04-06 doi:10.64898/2026.04.02.716161 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics ]]> https://biorxiv.org/content/10.64898/2026.04.03.716370v1?rss=1 Lewis, W. R. Aizenbud, Y. Strino, F. Kluger, Y. Parisi, F. 2026-04-07 doi:10.64898/2026.04.03.716370 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Whole-brain cellular-resolution functional network properties of seizure susceptibility ]]> https://biorxiv.org/content/10.64898/2026.04.04.715761v1?rss=1 Qin, W. Beevis, J. Wilde, M. Stednitz, S. Arnold, J. Ma, M. Favre-Bulle, I. A. Peterson, A. Hoffman, E. J. Scott, E. 2026-04-07 doi:10.64898/2026.04.04.715761 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery ]]> https://biorxiv.org/content/10.64898/2026.04.04.716470v1?rss=1 Liu, T. Jiang, S. Zhang, F. Sun, K. Head-Gordon, T. Zhao, H. 2026-04-07 doi:10.64898/2026.04.04.716470 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ HIV-1 Reverse Transcriptase interactions with Long-acting NNRTI, Depulfavirine (VM1500A) ]]> https://biorxiv.org/content/10.64898/2026.04.06.715899v1?rss=1 Snyder, A. A. Kaufman, I. L. Risener, C. J. Kirby, K. A. Sarafianos, S. G. 2026-04-07 doi:10.64898/2026.04.06.715899 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Context-Dependent Reactive Antipredator Behavior of Chacma Baboons (Papio ursinus) Amidst Predator Recovery ]]> https://biorxiv.org/content/10.64898/2026.04.05.716544v1?rss=1 Van Cuylenborg, S. M. Wright, N. S. Palmer, M. S. Carvalho, S. Gaynor, K. M. 2026-04-08 doi:10.64898/2026.04.05.716544 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ Intranasal Anti-CD3 Antibody Treatment Attenuates Post-COVID Neuroinflammation and Enhances Hippocampal Neurogenesis and Cognitive Function in Mice ]]> https://biorxiv.org/content/10.64898/2026.04.07.716934v1?rss=1 Lu, P. Izzy, S. Da Silva, P. Imkamp, H. T. Christenson, J. R. Yahya, T. Mansi, M. H. A. Alawi, A. Moreira, T. G. Monje, M. Weiner, H. L. Iwasaki, A. 2026-04-08 doi:10.64898/2026.04.07.716934 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ A MinD-like ATPase couples flagellation and cell division in spirochetes ]]> https://biorxiv.org/content/10.64898/2026.04.08.717139v1?rss=1 Li, C. Zhang, K. Guo, W. Lynch, M. J. Crane, B. Liu, J. 2026-04-08 doi:10.64898/2026.04.08.717139 Cold Spring Harbor Laboratory Press 2026-04-08