bioRxiv Channel: Columbia University https://biorxiv.org This feed contains articles for bioRxiv Channel "Columbia University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast ]]> https://biorxiv.org/content/10.1101/004614v1?rss=1 Lucas D. Ward Junbai Wang Harmen J. Bussemaker 2014-04-29 doi:10.1101/004614 Cold Spring Harbor Laboratory Press 2014-04-29 <![CDATA[ Non-crossover gene conversions show strong GC bias and unexpected clustering in humans ]]> https://biorxiv.org/content/10.1101/009175v1?rss=1 Amy L. Williams Giulio Geneovese Thomas Dyer Nicolas Altemose Katherine Truax Goo Jun Nick Patterson Simon R. Myers Joanne E. Curran Ravi Duggirala John Blangero David Reich Molly Przeworski the T2D-GENES Consortium 2014-09-16 doi:10.1101/009175 Cold Spring Harbor Laboratory Press 2014-09-16 <![CDATA[ Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance ]]> https://biorxiv.org/content/10.1101/013003v1?rss=1 Stefany Moreno-Gamez Alison L Hill Daniel I.S. Rosenbloom Dmitri A. Petrov Martin A Nowak Pleuni Pennings 2014-12-19 doi:10.1101/013003 Cold Spring Harbor Laboratory Press 2014-12-19 <![CDATA[ Scaling probabilistic models of genetic variation to millions of humans ]]> https://biorxiv.org/content/10.1101/013227v1?rss=1 Prem Gopalan Wei Hao David M. Blei John D. Storey 2014-12-24 doi:10.1101/013227 Cold Spring Harbor Laboratory Press 2014-12-24 <![CDATA[ High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants ]]> https://biorxiv.org/content/10.1101/013318v1?rss=1 Kevin J Emmett Albert K Lee Hossein Khiabanian Raul Rabadan 2014-12-29 doi:10.1101/013318 Cold Spring Harbor Laboratory Press 2014-12-29 <![CDATA[ Tools and best practices for allelic expression analysis ]]> https://biorxiv.org/content/10.1101/016097v1?rss=1 Stephane E Castel Ami Levy-Moonshine Pejman Mohammadi Eric Banks Tuuli Lappalainen 2015-03-06 doi:10.1101/016097 Cold Spring Harbor Laboratory Press 2015-03-06 <![CDATA[ Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence ]]> https://biorxiv.org/content/10.1101/016949v1?rss=1 Elise R Morton Joshua Lynch Alain Froment Sophie Lafosse Evelyne Heyer Molly Przeworski Ran Blekhman Laure Segurel 2015-03-24 doi:10.1101/016949 Cold Spring Harbor Laboratory Press 2015-03-24 <![CDATA[ Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1 ]]> https://biorxiv.org/content/10.1101/018911v1?rss=1 Daniel I S Rosenbloom Oliver Elliott Alison L Hill Timothy J Henrich Janet M Siliciano Robert F Siliciano 2015-05-03 doi:10.1101/018911 Cold Spring Harbor Laboratory Press 2015-05-03 <![CDATA[ A vision for ubiquitous sequencing ]]> https://biorxiv.org/content/10.1101/019018v1?rss=1 Yaniv Erlich 2015-05-07 doi:10.1101/019018 Cold Spring Harbor Laboratory Press 2015-05-07 <![CDATA[ Approximately independent linkage disequilibrium blocks in human populations ]]> https://biorxiv.org/content/10.1101/020255v1?rss=1 Tomaz Berisa Joseph K. Pickrell 2015-06-01 doi:10.1101/020255 Cold Spring Harbor Laboratory Press 2015-06-01 <![CDATA[ Stable recombination hotspots in birds ]]> https://biorxiv.org/content/10.1101/023101v1?rss=1 Sonal Singhal Ellen Leffler Keerthi Sannareddy Isaac Turner Oliver Venn Daniel Hooper Alva Strand Qiye Li Brian Raney Christopher Balakrishnan Simon Griffith Gil McVean Molly Przeworski 2015-07-23 doi:10.1101/023101 Cold Spring Harbor Laboratory Press 2015-07-23 <![CDATA[ Dating ancient human samples using the recombination clock ]]> https://biorxiv.org/content/10.1101/023341v1?rss=1 Priya Moorjani Sriram Sankararaman Qiaomei Fu Molly Przeworski Nick J Patterson David E. Reich 2015-07-27 doi:10.1101/023341 Cold Spring Harbor Laboratory Press 2015-07-27 <![CDATA[ Impact of the X chromosome and sex on regulatory variation ]]> https://biorxiv.org/content/10.1101/024117v1?rss=1 Kimberly R Kukurba Princy Parsana Kevin S Smith Zachary Zappala David A Knowles Marie-Julie Favé Xin Li Xiaowei Zhu James B Potash Myrna M Weissman Jianxin Shi Anshul Kundaje Douglas F Levinson Philip Awadalla Sara Mostafavi Alexis Battle Stephen B Montgomery 2015-08-07 doi:10.1101/024117 Cold Spring Harbor Laboratory Press 2015-08-07 <![CDATA[ Life history effects on the molecular clock of autosomes and sex chromosomes ]]> https://biorxiv.org/content/10.1101/024281v1?rss=1 Guy Amster Guy Sella 2015-08-10 doi:10.1101/024281 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Data science identifies novel drug interactions that prolong the QT interval ]]> https://biorxiv.org/content/10.1101/024745v1?rss=1 Tal Lorberbaum Kevin J Sampson Raymond L Woosley Robert S Kass Nicholas P Tatonetti 2015-08-16 doi:10.1101/024745 Cold Spring Harbor Laboratory Press 2015-08-16 <![CDATA[ Allele-specific expression reveals interactions between genetic variation and environment ]]> https://biorxiv.org/content/10.1101/025874v1?rss=1 David A Knowles Joe R Davis Anil Raj Xiaowei Zhu James B Potash Myrna M Weissman Jianxin Shi Douglas F Levinson Sara Mostafavi Stephen B Montgomery Alexis Battle 2015-09-01 doi:10.1101/025874 Cold Spring Harbor Laboratory Press 2015-09-01 <![CDATA[ Frequency-dependent representation of reinforcement-related information in the human medial and lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/029058v1?rss=1 Elliot Smith Garrett Banks Charles Mikell Shaun Patel Sydney Cash Emad Eskandar Sameer Sheth 2015-11-21 doi:10.1101/029058 Cold Spring Harbor Laboratory Press 2015-11-21 <![CDATA[ A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer ]]> https://biorxiv.org/content/10.1101/031419v1?rss=1 Eliseos J Mucaki Natasha G Caminsky Ami M Perri Ruipeng Lu Alain Laederach Matthew Halvorsen Joan H.M. Knoll Peter K Rogan 2015-11-11 doi:10.1101/031419 Cold Spring Harbor Laboratory Press 2015-11-11 <![CDATA[ What’s past is present: Reminders of past choices bias decisions for reward in humans ]]> https://biorxiv.org/content/10.1101/033910v1?rss=1 Aaron M Bornstein Mel W Khaw Daphna Shohamy Nathaniel D Daw 2015-12-08 doi:10.1101/033910 Cold Spring Harbor Laboratory Press 2015-12-08 <![CDATA[ Integration of mobile sequencers in an academic classroom ]]> https://biorxiv.org/content/10.1101/035303v1?rss=1 Sophie Zaaijer Yaniv Erlich 2015-12-24 doi:10.1101/035303 Cold Spring Harbor Laboratory Press 2015-12-24 <![CDATA[ Variation in the molecular clock of primates ]]> https://biorxiv.org/content/10.1101/036434v1?rss=1 Priya Moorjani Carlos Eduardo G. Amorim Peter F. Arndt Molly Przeworski 2016-01-11 doi:10.1101/036434 Cold Spring Harbor Laboratory Press 2016-01-11 <![CDATA[ A Quantitative Analysis of Localized Robustness of MYCN in Neuroblastoma ]]> https://biorxiv.org/content/10.1101/037465v1?rss=1 Romeil Sandhu sarah Tannenbaum Daniel Diolaiti Alberto Ambesi-Impiombato Andrew Kung Allen Tannenbaum 2016-01-22 doi:10.1101/037465 Cold Spring Harbor Laboratory Press 2016-01-22 <![CDATA[ Real-time predictions of reservoir size and rebound time during antiretroviral therapy interruption trials for HIV ]]> https://biorxiv.org/content/10.1101/038091v1?rss=1 Alison L Hill Daniel Scholes Rosenbloom Edward Goldstein Emily Hanhauser Daniel R Kuritzkes Robert F Siliciano Timothy J Henrich 2016-01-28 doi:10.1101/038091 Cold Spring Harbor Laboratory Press 2016-01-28 <![CDATA[ Rare variant phasing and haplotypic expression from RNA-sequencing with phASER ]]> https://biorxiv.org/content/10.1101/039529v1?rss=1 Stephane E Castel Pejman Mohammadi Wendy K Chung Yufeng Shen Tuuli Lappalainen 2016-02-12 doi:10.1101/039529 Cold Spring Harbor Laboratory Press 2016-02-12 <![CDATA[ C. elegans paraoxonase-like proteins control the functional expression of DEG/ENaC mechanosensory proteins ]]> https://biorxiv.org/content/10.1101/040337v1?rss=1 Yushu Chen Shashank Bharill Zeynep Altun Robert O'Hagan Brian Coblitz Ehud I. Isacoff Martin Chalfie 2016-02-19 doi:10.1101/040337 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects ]]> https://biorxiv.org/content/10.1101/040493v1?rss=1 Christian Marshall Daniel Howrigan Daniele Merico Bhooma Thiruvahindrapuram Wenting Wu Douglas Greer Daniel Antaki Aniket Shetty Peter Holmans Dalila Pinto Madhusudan Gujral William Brandler Dheeraj Malholtra Zhouzhi Wang Karin Fuentes Fajarado Stephan Ripke Ingrid Agartz Esben Agerbo Margot Albus Madeline Alexander Farooq Amin Joshua Atkins Silviu Bacanu Richard Belliveau Sarah Bergen Marcelo Bertalan Elizabeth Bevilacqua Tim Bigdeli Donald Black Richard Bruggeman Nancy Buccola Randy Buckner Brendan Bulik-Sullivan William Byerley Wiepke Cahn Guiqing Cai Murray Cairns Dominique Campion Rita Ca 2016-02-23 doi:10.1101/040493 Cold Spring Harbor Laboratory Press 2016-02-23 <![CDATA[ Focused Ultrasound Enhances Decision-Making in Monkeys ]]> https://biorxiv.org/content/10.1101/041152v1?rss=1 Matthew Downs Amanda Buch Maria Eleni Karakatsani Tobias Teichert Carlos Sierra Shangshang Chen Elisa E Konofagou Vincent P Ferrera 2016-02-24 doi:10.1101/041152 Cold Spring Harbor Laboratory Press 2016-02-24 <![CDATA[ Learning In Spike Trains: Estimating Within-Session Changes In Firing Rate Using Weighted Interpolation ]]> https://biorxiv.org/content/10.1101/041301v1?rss=1 Greg Jensen Fabian Munoz Vincent P Ferrera 2016-02-26 doi:10.1101/041301 Cold Spring Harbor Laboratory Press 2016-02-26 <![CDATA[ Fast imaging of DNA motion reveals distinct sub-diffusion regimes at the site of DNA damage ]]> https://biorxiv.org/content/10.1101/042051v1?rss=1 Judith Mine-Hattab Vincent Recamier Ignacio Izeddin Rodney Rothstein Xavier Darzacq 2016-03-01 doi:10.1101/042051 Cold Spring Harbor Laboratory Press 2016-03-01 <![CDATA[ Mechanical signals inhibit growth of a grafted tumor in vivo: Proof of Concept ]]> https://biorxiv.org/content/10.1101/045534v1?rss=1 Remy BROSSEL Alexandre YAHI Stephane DAVID Laura MORENO VELASQUEZ Jean-Marc GUINEBRETIERE 2016-03-24 doi:10.1101/045534 Cold Spring Harbor Laboratory Press 2016-03-24 <![CDATA[ Prevalent Presence of Periodic Actin-spectrin-based Membrane Skeleton in a Broad Range of Neuronal Cell Types and Animal Species ]]> https://biorxiv.org/content/10.1101/045856v1?rss=1 Jiang He Ruobo Zhou Zhuhao Wu Monica Carrasco Peri Kurshan Jonathan Farley David Simon Guiping Wang Boran Han Junjie Hao Evan Heller Marc Freeman Kang Shen Tom Maniatis Marc Tessier-Lavigne Xiaowei Zhuang 2016-04-08 doi:10.1101/045856 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ NQO1 C609T (Pro187Ser) increases risk of carcinogenesis of Oral Submucous Fibrosis by interacting with phosphorylated p53 and cyclin D1 ]]> https://biorxiv.org/content/10.1101/046052v1?rss=1 Sanjit Mukherjee Jay Gopal Ray Atul Katarkar Keya Chaudhuri 2016-03-28 doi:10.1101/046052 Cold Spring Harbor Laboratory Press 2016-03-28 <![CDATA[ The promise of disease gene discovery in South Asia ]]> https://biorxiv.org/content/10.1101/047035v1?rss=1 Nathan Joel Nakatsuka Priya Moorjani Niraj Rai Biswanath Sarkar Arti Tandon Nick Patterson Lalji Singh David Reich Kumarasamy Thangaraj 2016-04-06 doi:10.1101/047035 Cold Spring Harbor Laboratory Press 2016-04-06 <![CDATA[ Curvature Analysis of Estrogen Receptor Positive Breast Cancer Under PI3K Inhibition ]]> https://biorxiv.org/content/10.1101/049437v1?rss=1 Romeil Sandhu Eneda Toska Maurizio Scaltriti Jose Baselga Joseph Deasy Jung Hun Oh Sarah Tannenbaum Allen Tannenbaum 2016-04-20 doi:10.1101/049437 Cold Spring Harbor Laboratory Press 2016-04-20 <![CDATA[ Imaging decision-related neural cascades in the human brain ]]> https://biorxiv.org/content/10.1101/050856v1?rss=1 Jordan Muraskin Truman Brown Jennifer Walz Bryan Conroy Robin I Goldman Paul Sajda 2016-05-04 doi:10.1101/050856 Cold Spring Harbor Laboratory Press 2016-05-04 <![CDATA[ Generating an Executable Model of the Drosophila Central Complex ]]> https://biorxiv.org/content/10.1101/051318v1?rss=1 Lev E Givon Aurel A Lazar 2016-05-02 doi:10.1101/051318 Cold Spring Harbor Laboratory Press 2016-05-02 <![CDATA[ GEFs and Rac GTPases control directional specificity of neurite extension along the anterior-posterior axis ]]> https://biorxiv.org/content/10.1101/052019v1?rss=1 Martin Chalfie Chaogu Zheng Margarete Diaz-Cuadros 2016-05-06 doi:10.1101/052019 Cold Spring Harbor Laboratory Press 2016-05-06 <![CDATA[ A cellular and regulatory map of the GABAergic nervous system of C. elegans ]]> https://biorxiv.org/content/10.1101/052431v1?rss=1 Marie Gendrel Emily G Atlas Oliver Hobert 2016-05-10 doi:10.1101/052431 Cold Spring Harbor Laboratory Press 2016-05-10 <![CDATA[ Systematic Reconstruction of Autism Biology with Multi-Level Whole Exome Analysis ]]> https://biorxiv.org/content/10.1101/052878v1?rss=1 Weijun Luo Chaolin Zhang Cory Brouwer 2016-05-11 doi:10.1101/052878 Cold Spring Harbor Laboratory Press 2016-05-11 <![CDATA[ Combining complex networks and data mining: why and how ]]> https://biorxiv.org/content/10.1101/054064v1?rss=1 Massimiliano Zanin David Papo Pedro A. Sousa Ernestina Menasalvas Andrea Nicchi Elaine Kubik Stefano Boccaletti 2016-05-21 doi:10.1101/054064 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ PackIO and EphysViewer: software tools for acquisition and analysis of neuroscience data ]]> https://biorxiv.org/content/10.1101/054080v1?rss=1 Brendon O Watson Rafael Yuste Adam M Packer 2016-05-18 doi:10.1101/054080 Cold Spring Harbor Laboratory Press 2016-05-18 <![CDATA[ Transitive inference in humans and rhesus macaques after massed training of the last two list items ]]> https://biorxiv.org/content/10.1101/055335v1?rss=1 Greg Jensen Yelda Alkan Fabian Munoz Vincent P Ferrera Herbert S Terrace 2016-05-25 doi:10.1101/055335 Cold Spring Harbor Laboratory Press 2016-05-25 <![CDATA[ Human germline mutation and the erratic evolutionary clock ]]> https://biorxiv.org/content/10.1101/058024v1?rss=1 Priya Moorjani Ziyue Gao Molly Przeworski 2016-06-09 doi:10.1101/058024 Cold Spring Harbor Laboratory Press 2016-06-09 <![CDATA[ A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes ]]> https://biorxiv.org/content/10.1101/058826v1?rss=1 Chaolin Zhang Yufeng Shen 2016-06-14 doi:10.1101/058826 Cold Spring Harbor Laboratory Press 2016-06-14 <![CDATA[ Analyzing climate variations on multiple timescales can guide Zika virus response measures ]]> https://biorxiv.org/content/10.1101/059808v1?rss=1 Angel G Munoz Madeleine C Thomson Lisa Goddard Sylvain Aldighieri 2016-06-19 doi:10.1101/059808 Cold Spring Harbor Laboratory Press 2016-06-19 <![CDATA[ Detection of statistically significant network changes in complex biological networks ]]> https://biorxiv.org/content/10.1101/061515v1?rss=1 Raghvendra Mall Luigi Cerulo Halima Bensmail Antonio Iavarone Michele Ceccarelli 2016-06-30 doi:10.1101/061515 Cold Spring Harbor Laboratory Press 2016-06-30 <![CDATA[ Effects of tDCS on motor learning and memory formation: a consensus and critical position paper ]]> https://biorxiv.org/content/10.1101/064204v1?rss=1 Ethan R Buch Emiliano Santarnecchi Andrea Antal Jan Born Pablo A Celnik Joseph Classen Christian Gerloff Mark Hallett Friedhelm C Hummel Michael A Nitsche Alvaro Pascual-Leone Walter J Paulus Janine Reis Edwin M Robertson John C Rothwell Marco Sandrini Heidi M Schambra Eric M Wassermann Ulf Ziemann Leonardo G Cohen 2016-07-18 doi:10.1101/064204 Cold Spring Harbor Laboratory Press 2016-07-18 <![CDATA[ Chaotic propagation of spatial cytoskeletal instability modulates integrity of podocyte foot processes ]]> https://biorxiv.org/content/10.1101/065839v1?rss=1 Cibele V Falkenberg Evren U Azeloglu Mark Stothers Thomas J Deerinck Yibang Chen John C He Mark H. Ellisman James C. Hone Ravi Iyengar Leslie M. Loew 2016-07-26 doi:10.1101/065839 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ Estimate of disease heritability using 4.7 million familial relationships inferred from electronic health records ]]> https://biorxiv.org/content/10.1101/066068v1?rss=1 Fernanda Polubriaginof Kayla Quinnies Rami Vanguri Alexandre Yahi Mary Simmerling Iuliana Ionita-Laza Hojjat Salmasian Suzanne Bakken George Hripcsak David Goldstein Krzysztof Kiryluk David K Vawdrey Nicholas P Tatonetti 2016-07-28 doi:10.1101/066068 Cold Spring Harbor Laboratory Press 2016-07-28 <![CDATA[ Mutations in EBF3 disturb transcriptional profiles and underlie a novel syndrome of intellectual disability, ataxia and facial dysmorphism ]]> https://biorxiv.org/content/10.1101/067454v1?rss=1 Frederike Leonie Harms Katta Mohan Girisha Andrew Alexander Hardigan Fanny Kortum Anju Shukla Malik Alawi Ashwin Dalal Lauren Brady Mark Tarnopolsky Lynne M. Bird Sophia Ceulemans Martina Bebin Kevin M. Bowling Susan M. Hiatt Edward J. Lose Michelle Primiano Wendy K. Chung Jane Juusola Zeynep C. Akdemir Matthew Bainbridge Wu-Lin Charng Margaret Drummond-Borg Mohammad K. Eldomery Ayman W. El-Hattab Mohammed A.M. Saleh Stephane Bezieau Benjamin Cogne Bertrand Isidor Sebastien Kury James R. Lupski Richard M. Myers Gregory M. Cooper Kerstin Kutsche 2016-08-03 doi:10.1101/067454 Cold Spring Harbor Laboratory Press 2016-08-03 <![CDATA[ Recombination-driven genome evolution and stability of bacterial species ]]> https://biorxiv.org/content/10.1101/067942v1?rss=1 Purushottam Dixit Tin Y Pang Sergei Maslov 2016-08-04 doi:10.1101/067942 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ Tissue-specific functional effect prediction of genetic variation and applications to complex trait genetics ]]> https://biorxiv.org/content/10.1101/069229v1?rss=1 Daniel Backenroth Krzysztof Kiryluk Bin Xu Lynn Pethukova Badri Vardarajan Ekta Khurana Angela Christiano Joseph Buxbaum Iuliana Ionita-Laza 2016-08-11 doi:10.1101/069229 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ Understanding the contributions of visual stimuli to contextual fear conditioning: a proof-of-concept study using LCD screens ]]> https://biorxiv.org/content/10.1101/069781v1?rss=1 Nathen J. Murawski Arun Asok 2016-08-16 doi:10.1101/069781 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Orientation tuning depends on spatial frequency in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/069997v1?rss=1 Inbal Ayzenshtat Jesse Jackson Rafael Yuste 2016-08-17 doi:10.1101/069997 Cold Spring Harbor Laboratory Press 2016-08-17 <![CDATA[ A novel quantile regression approach for eQTL discovery ]]> https://biorxiv.org/content/10.1101/070052v1?rss=1 Xiaoyu Song Gen Li Iuliana Ionita-Laza Ying Wei 2016-08-17 doi:10.1101/070052 Cold Spring Harbor Laboratory Press 2016-08-17 <![CDATA[ An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/070193v1?rss=1 50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue. ]]> Jinzhou Yuan Peter A. Sims 2016-08-18 doi:10.1101/070193 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ Assembly of Radically Recoded E. coli Genome Segments ]]> https://biorxiv.org/content/10.1101/070417v1?rss=1 Julie E. Norville Cameron L. Gardner Eduardo Aponte Conor K. Camplisson Alexandra Gonzales David K. Barclay Katerina A. Turner Victoria Longe Maria Mincheva Jun Teramoto Kento Tominaga Ryota Sugimoto James E. DiCarlo Marc Guell Eriona Hysolli John Aach Christopher J. Gregg Barry L. Wanner George M. Church 2016-08-19 doi:10.1101/070417 Cold Spring Harbor Laboratory Press 2016-08-19 <![CDATA[ The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives ]]> https://biorxiv.org/content/10.1101/073635v1?rss=1 Yuval B Simons Guy Sella 2016-09-06 doi:10.1101/073635 Cold Spring Harbor Laboratory Press 2016-09-06 <![CDATA[ Capacity-approaching DNA storage ]]> https://biorxiv.org/content/10.1101/074237v1?rss=1 Yaniv Erlich Dina Zielinski 2016-09-09 doi:10.1101/074237 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Directed Network Discovery with Dynamic Network Modeling ]]> https://biorxiv.org/content/10.1101/074286v1?rss=1 Stefano Anzellotti Dorit Kliemann Nir Jacoby Rebecca Saxe 2016-09-12 doi:10.1101/074286 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ Local genetic effects on gene expression across 44 human tissues ]]> https://biorxiv.org/content/10.1101/074450v1?rss=1 Francois Aguet Andrew A Brown Stephane Castel Joe R Davis Pejman Mohammadi Ayellet V Segre Zachary Zappala Nathan S Abell Laure Fresard Eric R Gamazon Ellen Gelfand Machael J Gloudemans Yuan He Farhad Hormozdiari Xiao Li Xin Li Boxiang Liu Diego Garrido-Martin Halit Ongen John J Palowitch YoSon Park Christine B Peterson Gerald Quon Stephan Ripke Andrey A Shabalin Tyler C Shimko Benjamin J Strober Timothy J Sullivan Nicole A Teran Emily K Tsang Hailei Zhang Yi-Hui Zhou Alexis Battle Carlos D Bustamonte Nancy J Cox Barbara E Engelhardt Eleazar Eskin Gad Getz Manolis Kellis Gen Li Daniel G MacArt 2016-09-09 doi:10.1101/074450 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Length control of filamentous structures in cells by the limiting pool mechanism ]]> https://biorxiv.org/content/10.1101/075655v1?rss=1 Lishibanya Mohapatra Thibaut J. Lagny David Harbage Predrag R. Jelenkovic Jane Kondev 2016-09-16 doi:10.1101/075655 Cold Spring Harbor Laboratory Press 2016-09-16 <![CDATA[ Deep-time parallel evolution of myrmecoid syndrome in rove beetle symbionts of army ants ]]> https://biorxiv.org/content/10.1101/076315v1?rss=1 Munetoshi Maruyama Joseph Parker 2016-09-20 doi:10.1101/076315 Cold Spring Harbor Laboratory Press 2016-09-20 <![CDATA[ GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway ]]> https://biorxiv.org/content/10.1101/076414v1?rss=1 Krzysztof Kiryluk Yifu Li Zina Moldoveanu Hitoshi Suzuki Colin Reily Ping Hou Jingyuan Xie Nikol Mladkova Sindhuri Prakash Clara Fischman Samantha Shapiro Robert A. LeDesma Drew Bradbury Iuliana Ionita-Laza Frank Eitner Thomas Rauen Nicolas Maillard Francois Berthoux Jurgen Floege Nan Chen Hong Zhang Francesco Scolari Robert J. Wyatt Bruce A. Julian Ali G. Gharavi Jan Novak 2016-09-21 doi:10.1101/076414 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Multidimensional stimulus-response correlation reveals supramodal neural responses to naturalistic stimuli ]]> https://biorxiv.org/content/10.1101/077230v1?rss=1 Jacek Dmochowski Jason Ki Paul De Guzman Paul Sajda Lucas C Parra 2016-09-25 doi:10.1101/077230 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ Contribution of de novo non-coding mutations to autism and identification of risk genes from whole-genome sequencing of affected families ]]> https://biorxiv.org/content/10.1101/077578v1?rss=1 Yuwen Liu A. Ercument Cicek Yanyu Liang Jinchen Li Rebecca A Muhle Nicholas Knoblauch Martina Krenzer Yue Mei Yan Wang Yi Jiang Even Geller Zhongshan Li Iuliana Ionita-Laza Jinyu Wu Kun Xia James P Noonan Zhong Sheng Sun Xin He 2016-09-26 doi:10.1101/077578 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ DNA Compass: a secure, client-side site for navigating personal genetic information ]]> https://biorxiv.org/content/10.1101/077867v1?rss=1 Charles Curnin Assaf Gordon Yaniv Erlich 2016-09-27 doi:10.1101/077867 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change ]]> https://biorxiv.org/content/10.1101/078717v1?rss=1 Pejman Mohammadi Stephane E Castel Andrew A Brown Tuuli Lappalainen 2016-09-30 doi:10.1101/078717 Cold Spring Harbor Laboratory Press 2016-09-30 <![CDATA[ Commentary: BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks. Science 348, 1241-4. ]]> https://biorxiv.org/content/10.1101/079202v1?rss=1 Spiro P. Pantazatos Xinyi Li 2016-10-04 doi:10.1101/079202 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Recovery of hand function after stroke: separable systems for finger strength and control ]]> https://biorxiv.org/content/10.1101/079269v1?rss=1 Jing Xu Naveed Ejaz Benjamin Hertler Meret Branscheidt Mario Widmer Andreia V Faria Michelle Harran Juan C Cortes Nathan Kim Pablo A Celnik Tomoko Kitago Andreas Luft John W Krakauer Jörn Diedrichsen 2016-10-04 doi:10.1101/079269 Cold Spring Harbor Laboratory Press 2016-10-04 <![CDATA[ Using Machine Learning to Parse Breast Pathology Reports ]]> https://biorxiv.org/content/10.1101/079913v1?rss=1 Adam Yala Regina Barzilay Laura Salama Molly Griffin Grace Sollender Aditya Bardia Constance Lehman Julliette M Buckley Suzanne B Coopey Fernanda Polubriaginof Judy E Garber Barbara L Smith Michele A Gadd Michelle C Specht Thomas M Gudewicz Anthony Guidi Alphonse Taghian Kevin S Hughes 2016-10-10 doi:10.1101/079913 Cold Spring Harbor Laboratory Press 2016-10-10 <![CDATA[ Sexually dimorphic differentiation of a C. elegans hub neuron is cell-autonomously controlled by a conserved transcription factor ]]> https://biorxiv.org/content/10.1101/081083v1?rss=1 Serrano Saiz, E. Oren-Suissa, M. Bayer, E. A. Hobert, O. 2016-10-14 doi:10.1101/081083 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ Scalable variational inference for super resolution microscopy ]]> https://biorxiv.org/content/10.1101/081703v1?rss=1 Sun, R. Archer, E. Paninski, L. 2016-11-19 doi:10.1101/081703 Cold Spring Harbor Laboratory Press 2016-11-19 <![CDATA[ Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions ]]> https://biorxiv.org/content/10.1101/083741v1?rss=1 Hensel, C. H. Vanzo, R. Martin, M. Dixon, S. Lambert, C. G. Levy, B. Nelson, L. Peiffer, A. Ho, K. Mowery-Rushton, P. Serrano, M. South, S. Ward, K. Wassman, E. R. 2016-10-26 doi:10.1101/083741 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Cause for pause before leaping to conclusions about stepping ]]> https://biorxiv.org/content/10.1101/085886v1?rss=1 Zylberberg, A. Shadlen, M. N. 2016-11-11 doi:10.1101/085886 Cold Spring Harbor Laboratory Press 2016-11-11 <![CDATA[ Identifying genetic variants that affect viability in large cohorts ]]> https://biorxiv.org/content/10.1101/085969v1?rss=1 Mostafavi, H. Berisa, T. Przeworski, M. Pickrell, J. K. 2016-11-07 doi:10.1101/085969 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Electrical Stimulus Artifact Cancellation and Neural Spike Detection on Large Multi-Electrode Arrays ]]> https://biorxiv.org/content/10.1101/089912v1?rss=1 Mena, G. E. Grosberg, L. E. Hottowy, P. Litke, A. Cunningham, J. Chichilnisky, E. Paninski, L. 2016-11-27 doi:10.1101/089912 Cold Spring Harbor Laboratory Press 2016-11-27 <![CDATA[ Estimation of time-varying decision thresholds from the choice and reaction times without assumptions on the shape ]]> https://biorxiv.org/content/10.1101/090217v1?rss=1 Kang, Y. H. R. 2016-11-29 doi:10.1101/090217 Cold Spring Harbor Laboratory Press 2016-11-29 <![CDATA[ Multi-scale approaches for high-speed imaging and analysis of large neural populations ]]> https://biorxiv.org/content/10.1101/091132v1?rss=1 Friedrich, J. Yang, W. Soudry, D. Mu, Y. Ahrens, M. B. Yuste, R. Peterka, D. S. Paninski, L. 2016-12-02 doi:10.1101/091132 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Mindboggling morphometry of human brains ]]> https://biorxiv.org/content/10.1101/091322v1?rss=1 Klein, A. Ghosh, S. S. Bao, F. S. Giard, J. Hame, Y. Stavsky, E. Lee, N. Rossa, B. Reuter, M. Chaibub Neto, E. Keshavan, A. 2016-12-03 doi:10.1101/091322 Cold Spring Harbor Laboratory Press 2016-12-03 <![CDATA[ The population genetics of human disease: the case of recessive, lethal mutations ]]> https://biorxiv.org/content/10.1101/091579v1?rss=1 Guerra Amorim, C. E. Gao, Z. Baker, Z. Diesel, J. F. Simons, Y. B. Haque, I. S. Pickrell, J. Przeworski, M. 2016-12-04 doi:10.1101/091579 Cold Spring Harbor Laboratory Press 2016-12-04 <![CDATA[ A new law of human perception ]]> https://biorxiv.org/content/10.1101/091918v1?rss=1 Wei, X.-X. Stocker, A. A. 2016-12-06 doi:10.1101/091918 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ The Fruit Fly Brain Observatory: from structure to function ]]> https://biorxiv.org/content/10.1101/092288v1?rss=1 Ukani, N. H. Yeh, C.-H. Tomkins, A. Zhou, Y. Florescu, D. Ortiz, C. L. Huang, Y.-C. Wang, C.-T. Richmond, P. Lo, C.-C. Coca, D. Chiang, A.-S. Lazar, A. A. 2016-12-14 doi:10.1101/092288 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ NeuroNLP: a natural language portal for aggregated fruit fly brain data ]]> https://biorxiv.org/content/10.1101/092429v1?rss=1 Ukani, N. H. Tomkins, A. Yeh, C.-H. Bruning, W. Fenichel, A. L. Zhou, Y. Huang, Y.-C. Florescu, D. Ortiz, C. L. Richmond, P. Lo, C.-C. Coca, D. Chiang, A.-S. Lazar, A. A. 2016-12-14 doi:10.1101/092429 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ NeuroGFX: a graphical functional explorer for fruit fly brain circuits ]]> https://biorxiv.org/content/10.1101/092437v1?rss=1 Yeh, C.-H. Zhou, Y. Ukani, N. H. Lazar, A. A. 2016-12-14 doi:10.1101/092437 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Evidence that the ventral stream codes the errors used in hierarchical inference and learning ]]> https://biorxiv.org/content/10.1101/092551v1?rss=1 Issa, E. B. Cadieu, C. F. DiCarlo, J. J. 2016-12-08 doi:10.1101/092551 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates ]]> https://biorxiv.org/content/10.1101/093096v1?rss=1 Baker, Z. Schumer, M. Haba, Y. Holland, C. Rosenthal, G. G. Przeworski, M. 2016-12-11 doi:10.1101/093096 Cold Spring Harbor Laboratory Press 2016-12-11 <![CDATA[ Correcting Chimeric Crosstalk in Single Cell RNA-seq Experiments ]]> https://biorxiv.org/content/10.1101/093237v1?rss=1 Dixit, A. 2016-12-12 doi:10.1101/093237 Cold Spring Harbor Laboratory Press 2016-12-12 <![CDATA[ Detection of long repeat expansions from PCR-free whole-genome sequence data ]]> https://biorxiv.org/content/10.1101/093831v1?rss=1 95% accurate. ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions. ]]> Dolzhenko, E. van Vugt, J. J. F. A. Shaw, R. J. Bekritsky, M. A. van Blitterswijk, M. Kingsbury, Z. Humphray, S. J. Schellevis, R. D. Brands, W. J. Baker, M. Rademakers, R. Kooyman, M. Tazelaar, G. H. P. van Es, M. A. McLaughlin, R. Sproviero, W. Shatunov, A. Jones, A. Al Khleifat, A. Pittman, A. Morgan, S. Hardiman, O. Al-Chalabi, A. van den Berg, L. H. Bentley, D. R. Eberle, M. A. Veldink, J. H. 2016-12-19 doi:10.1101/093831 Cold Spring Harbor Laboratory Press 2016-12-19 <![CDATA[ Benefits of siderophore release lie in mediating diffusion limitation at low iron solubility ]]> https://biorxiv.org/content/10.1101/093948v1?rss=1 Leventhal, G. Ackermann, M. Schiessl, K. 2016-12-14 doi:10.1101/093948 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Individual- versus group-optimality in the production of secreted bacterial compounds ]]> https://biorxiv.org/content/10.1101/094086v1?rss=1 Schiessl, K. Ross-Gillespie, A. Cornforth, D. M. Weigert, M. Bigosch, C. Brown, S. P. Ackermann, M. Kümmerli, R. 2016-12-14 doi:10.1101/094086 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Magnitude and mechanism of siderophore-mediated competition in bacterial interactions ]]> https://biorxiv.org/content/10.1101/094094v1?rss=1 Schiessl, K. Janssen, E. M.- L. Kraemer, S. M. McNeill, K. Ackermann, M. 2016-12-14 doi:10.1101/094094 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Stabilized supralinear network dynamics account for stimulus-induced changes of noise variability in the cortex ]]> https://biorxiv.org/content/10.1101/094334v1?rss=1 Hennequin, G. Ahmadian, Y. Rubin, D. B. Lengyel, M. Miller, K. D. 2016-12-14 doi:10.1101/094334 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Dynamic flexibility in striatal-cortical circuits supports reinforcement learning ]]> https://biorxiv.org/content/10.1101/094383v1?rss=1 Gerraty, R. T. Davidow, J. Y. Foerde, K. Galvan, A. Bassett, D. S. Shohamy, D. 2016-12-15 doi:10.1101/094383 Cold Spring Harbor Laboratory Press 2016-12-15 <![CDATA[ K-mer Motif Multinomial Mixtures ]]> https://biorxiv.org/content/10.1101/096735v1?rss=1 Trippe, B. L. Prabhakaran, S. Bussemaker, H. 2016-12-24 doi:10.1101/096735 Cold Spring Harbor Laboratory Press 2016-12-24 <![CDATA[ Creating a National Vector Surveillance System: Integrated mosquito trap data and digital epidemiology ]]> https://biorxiv.org/content/10.1101/096875v1?rss=1 1000 mosquito control agencies in the US with enormous troves of data that are hidden among many data silos. For CSVMaC, we propose the creation of a nationally-coordinated open-access database to collate mosquito data. The database would provide scientific and public health communities with highly resolved spatiotemporal data on arboviral disease vectors, empowering new interventions and insights while leveraging pre-existing human efforts, operational infrastructure, and investments already funded by taxpayers. ]]> Rund, S. S. C. Martinez, M. E. 2016-12-27 doi:10.1101/096875 Cold Spring Harbor Laboratory Press 2016-12-27 <![CDATA[ Fast Assembling of Neuron Fragments in Serial 3D Sections ]]> https://biorxiv.org/content/10.1101/097253v1?rss=1 Chen, H. Iascone, D. M. da Costa, N. M. Lein, E. Liu, T. Peng, H. 2016-12-29 doi:10.1101/097253 Cold Spring Harbor Laboratory Press 2016-12-29 <![CDATA[ Dopamine Negatively Regulates the NCA Ion Channels in C. elegans ]]> https://biorxiv.org/content/10.1101/097394v1?rss=1 Topalidou, I. Cooper, K. Ailion, M. 2016-12-30 doi:10.1101/097394 Cold Spring Harbor Laboratory Press 2016-12-30 <![CDATA[ JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data ]]> https://biorxiv.org/content/10.1101/099234v1?rss=1 Ji, J. He, D. Feng, Y. He, Y. Xue, F. Xie, L. 2017-01-09 doi:10.1101/099234 Cold Spring Harbor Laboratory Press 2017-01-09 <![CDATA[ Temporal super-resolution in single-molecule experiments ]]> https://biorxiv.org/content/10.1101/099648v1?rss=1 Kinz-Thompson, C. D. Gonzalez, R. L. 2017-01-12 doi:10.1101/099648 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Inferential Learning of Serial Order of Perceptual Categories by Rhesus Monkeys (Macaca mulatta) ]]> https://biorxiv.org/content/10.1101/102897v1?rss=1 Tanner, N. Jensen, G. Ferrera, V. P. Terrace, H. S. 2017-01-26 doi:10.1101/102897 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ The 4D Nucleome Project ]]> https://biorxiv.org/content/10.1101/103499v1?rss=1 Dekker, J. Belmont, A. S. Guttman, M. Leshyk, V. O. Lis, J. T. Lomvardas, S. Mirny, L. A. O'Shea, C. C. Park, P. J. Ren, B. Ritland, J. C. Shendure, J. Zhong, S. The 4D Nucleome Network, 2017-01-26 doi:10.1101/103499 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Health Information Needs and Health Seeking Behavior during the 2014-2016 Ebola Outbreak: A Twitter Content Analysis ]]> https://biorxiv.org/content/10.1101/103515v1?rss=1 Odlum, M. Yoon, S. 2017-01-27 doi:10.1101/103515 Cold Spring Harbor Laboratory Press 2017-01-27 <![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[ Using computational theory to constrain statistical models of neural data ]]> https://biorxiv.org/content/10.1101/104737v1?rss=1 Linderman, S. W. Gershman, S. J. 2017-01-31 doi:10.1101/104737 Cold Spring Harbor Laboratory Press 2017-01-31 <![CDATA[ Statistical Correction of the Winner’s Curse Explains Replication Variability in Quantitative Trait Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/104786v1?rss=1 Palmer, C. Pe'er, I. 2017-01-31 doi:10.1101/104786 Cold Spring Harbor Laboratory Press 2017-01-31 <![CDATA[ Quantitative analysis of population-scale family trees using millions of relatives ]]> https://biorxiv.org/content/10.1101/106427v1?rss=1 Kaplanis, J. Gordon, A. Wahl, M. Gershovits, M. Markus, B. Sheikh, M. Gymrek, M. Bhatia, G. MarArthur, D. G. Price, A. Erlich, Y. 2017-02-07 doi:10.1101/106427 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ A probabilistic approach to discovering dynamic full-brain functional connectivity patterns ]]> https://biorxiv.org/content/10.1101/106690v1?rss=1 Manning, J. Zhu, X. Willke, T. Ranganath, R. Stachenfeld, K. Hasson, U. Blei, D. M. Norman, K. A. 2017-02-07 doi:10.1101/106690 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Inferring intracellular signal transduction circuitry from molecular perturbation experiments ]]> https://biorxiv.org/content/10.1101/107730v1?rss=1 Wynn, M. L. Egber, M. Consul, N. Chang, J. Wu, Z.-F. Meravjer, S. D. Schnell, S. 2017-02-10 doi:10.1101/107730 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Recurrent inhibition in striatum enables transfer of time-flexible skills to basal ganglia ]]> https://biorxiv.org/content/10.1101/110072v1?rss=1 Murray, J. M. Escola, G. S. 2017-02-21 doi:10.1101/110072 Cold Spring Harbor Laboratory Press 2017-02-21 <![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 Statistical Model of Shared Variability in the Songbird Auditory System ]]> https://biorxiv.org/content/10.1101/113670v1?rss=1 Buesing, L. Calabrese, A. Cunningham, J. Woolley, S. Paninski, L. 2017-03-04 doi:10.1101/113670 Cold Spring Harbor Laboratory Press 2017-03-04 <![CDATA[ Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations ]]> https://biorxiv.org/content/10.1101/116376v1?rss=1 Kim-Hellmuth, S. Bechheim, M. Puetz, B. Mohammadi, P. Nedelec, Y. Giangreco, N. Becker, J. Kaiser, V. Fricker, N. Beier, E. Boor, P. Castel, S. Noethen, M. M. Barreiro, L. B. Pickrell, J. K. Mueller-Myhsok, B. Lappalainen, T. Schumacher, J. Hornung, V. 2017-03-13 doi:10.1101/116376 Cold Spring Harbor Laboratory Press 2017-03-13 <![CDATA[ Pediatric Sarcoma Data Forms a Unique Cluster Measured via the Earth Mover’s Distance ]]> https://biorxiv.org/content/10.1101/116384v1?rss=1 Chen, Y. Dela Cruz, F. Sandhu, R. Kung, A. Mundi, P. Deasy, J. Tannenbaum, A. 2017-03-13 doi:10.1101/116384 Cold Spring Harbor Laboratory Press 2017-03-13 <![CDATA[ Contrasting determinants of mutation rates in germline and soma ]]> https://biorxiv.org/content/10.1101/117325v1?rss=1 Chen, C. Qi, H. Shen, Y. Pickrell, J. Przeworski, M. 2017-03-16 doi:10.1101/117325 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ A Transformation From Latency To Ensemble Coding In A Model Of Piriform Cortex ]]> https://biorxiv.org/content/10.1101/118364v1?rss=1 Stern, M. Bolding, K. Abbott, L. Franks, K. 2017-03-20 doi:10.1101/118364 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Light Sheet Theta Microscopy for High-resolution Quantitative Imaging of Large Biological Systems ]]> https://biorxiv.org/content/10.1101/119289v1?rss=1 Migliori, B. Datta, M. S. Apak, M. C. Tomer, R. 2017-03-22 doi:10.1101/119289 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ De novo BK channel mutation causes epilepsy by regulating voltage-dependent, but not calcium-dependent, activation ]]> https://biorxiv.org/content/10.1101/120543v1?rss=1 Wang, Q. K. Willemsen, M. Li, X. Poschmann, S. Chen, Q. Oundjian, N. J. Snoeijen-Schouwenaars, F. M. Kamsteeg, E.-J. 2017-03-25 doi:10.1101/120543 Cold Spring Harbor Laboratory Press 2017-03-25 <![CDATA[ A Systematic Nomenclature for the Drosophila Ventral Nervous System ]]> https://biorxiv.org/content/10.1101/122952v1?rss=1 Court, R. C. Armstrong, J. D. Borner, J. Card, G. Costa, M. Dickinson, M. Duch, C. Korff, W. Mann, R. Merritt, D. Murphey, R. Namiki, S. Seeds, A. Shepherd, D. Shirangi, T. Simpson, J. Truman, J. Tuthill, J. Williams, D. 2017-04-26 doi:10.1101/122952 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ HadoopCNV: A Dynamic Programming Imputation Algorithm To Detect Copy Number Variants From Sequencing Data ]]> https://biorxiv.org/content/10.1101/124339v1?rss=1 Yang, H. Chen, G. Lima, L. Fang, H. Jimenez, L. Li, M. Lyon, G. J. He, M. Wang, K. 2017-04-05 doi:10.1101/124339 Cold Spring Harbor Laboratory Press 2017-04-05 <![CDATA[ Increasing Suppression Of Saccade-Related Transients Along The Human Visual Hierarchy ]]> https://biorxiv.org/content/10.1101/124867v1?rss=1 Golan, T. Davidesco, I. Meshulam, M. Groppe, D. M. Megevand, P. Yeagle, E. M. Goldfinger, M. S. Harel, M. Melloni, L. Schroeder, C. E. Deouell, L. Y. Mehta, A. D. Malach, R. 2017-04-20 doi:10.1101/124867 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ The central amygdala controls learning in the lateral amygdala ]]> https://biorxiv.org/content/10.1101/126649v1?rss=1 Yu, K. Ahrens, S. Zhang, X. Schiff, H. Ramakrishnan, C. Fenno, L. Deisseroth, K. Zhou, P. Paninski, L. Li, B. 2017-04-11 doi:10.1101/126649 Cold Spring Harbor Laboratory Press 2017-04-11 <![CDATA[ Highly sensitive detection of small variants in multi-sample ultra-deep tumor sequencing ]]> https://biorxiv.org/content/10.1101/128587v1?rss=1 Rabadan, R. Marsilio, S. Chiorazzi, N. Pasqualucci, L. Khiabanian, H. 2017-04-19 doi:10.1101/128587 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ Finger recruitment patterns during mirror movements suggest two systems for hand recovery after stroke ]]> https://biorxiv.org/content/10.1101/129510v1?rss=1 Ejaz, N. Xu, J. Branscheidt, M. Hertler, B. Schambra, H. Widmer, M. Faria, A. V. Harran, M. Cortes, J. C. Kim, N. Kitago, T. Celnik, P. A. Luft, A. Krakauer, J. W. Diedrichsen, J. 2017-04-22 doi:10.1101/129510 Cold Spring Harbor Laboratory Press 2017-04-22 <![CDATA[ Structure-based analysis of CysZ-mediated cellular uptake of sulfate ]]> https://biorxiv.org/content/10.1101/131318v1?rss=1 Liu, Q. Clarke, O. B. Leal Pinto, E. Kloss, B. Tabuso, S. Love, J. Punta, M. Banerjee, S. Rajashankar, K. R. Rost, B. Logothetis, D. Quick, M. Hendrickson, W. A. Mancia, F. Assur Sanghai, Z. 2017-04-26 doi:10.1101/131318 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/131326v1?rss=1 Zheng, C. Diaz-Cuadros, M. Jao, S. L. Nguyen, K. Hall, D. H. Chalfie, M. 2017-04-26 doi:10.1101/131326 Cold Spring Harbor Laboratory Press 2017-04-26 <![CDATA[ Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models ]]> https://biorxiv.org/content/10.1101/131367v1?rss=1 Yousefi, S. Amrollahi, F. Amgad, M. Dong, C. Lewis, J. E. Song, C. Gutman, D. A. Halani, S. H. Enrique Velazquez Vega, J. Brat, D. J. Cooper, L. A. 2017-04-27 doi:10.1101/131367 Cold Spring Harbor Laboratory Press 2017-04-27 <![CDATA[ Rapid DNA Re-Identification for Cell Line Authentication and Forensics ]]> https://biorxiv.org/content/10.1101/132381v1?rss=1 Zaaijer, S. Erlich, Y. Speyer, D. Piccone, R. Gordon, A. 2017-04-30 doi:10.1101/132381 Cold Spring Harbor Laboratory Press 2017-04-30 <![CDATA[ Three-Dimensional Two-Photon Optogenetics And Imaging Of Neural Circuits In Vivo ]]> https://biorxiv.org/content/10.1101/132506v1?rss=1 Yang, W. Carrillo-Reid, L. Bando, Y. Peterka, D. S. Yuste, R. 2017-04-30 doi:10.1101/132506 Cold Spring Harbor Laboratory Press 2017-04-30 <![CDATA[ RGBM: Regularized Gradient Boosting Machines For The Identification of Transcriptional Regulators Of Discrete Glioma Subtypes ]]> https://biorxiv.org/content/10.1101/132670v1?rss=1 Mall, R. Cerulo, L. Kunji, K. Bensmail, H. Sabedot, T. Noushmehr, H. Iavarone, A. Ceccarelli, M. 2017-05-01 doi:10.1101/132670 Cold Spring Harbor Laboratory Press 2017-05-01 <![CDATA[ Hebbian Learning in a Random Network Captures Selectivity Properties of Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/133025v1?rss=1 Lindsay, G. W. Rigotti, M. Warden, M. R. Miller, E. K. Fusi, S. 2017-05-02 doi:10.1101/133025 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Deep Neural Networks In Computational Neuroscience ]]> https://biorxiv.org/content/10.1101/133504v1?rss=1 Kietzmann, T. C. McClure, P. Kriegeskorte, N. 2017-05-04 doi:10.1101/133504 Cold Spring Harbor Laboratory Press 2017-05-04 <![CDATA[ Genetic Instrumental Variable (GIV) Regression: Explaining Socioeconomic And Health Outcomes In Non-Experimental Data ]]> https://biorxiv.org/content/10.1101/134197v1?rss=1 DiPrete, T. A. Burik, C. Koellinger, P. 2017-05-05 doi:10.1101/134197 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ DNA.Land: A Digital Biobank Using A Massive Crowdsourcing Approach ]]> https://biorxiv.org/content/10.1101/135715v1?rss=1 Yuan, J. Gordon, A. Speyer, D. Aufrichtig, R. Zielinski, D. Pickrell, J. Erlich, Y. 2017-05-09 doi:10.1101/135715 Cold Spring Harbor Laboratory Press 2017-05-09 <![CDATA[ Fetal death certificate data quality: A tale of two US counties ]]> https://biorxiv.org/content/10.1101/136432v1?rss=1 13 years, with an identifiable FDC. We identified the frequency of missing and misreported (any departure from the study value) FDC data by county, race/ethnicity, gestational age, and whether the stillbirth was antepartum or intrapartum.nnResultsData quality varied by item, and was highest in Salt Lake County. Reporting was generally not associated with maternal or delivery characteristics. Reasons for poor data quality varied by item in DeKalb County: some items were frequently missing and misreported; however, others were of poor quality due to either missing or misreported data.nnConclusionsFDC data suffer from missing and inaccurate data, with variations by item and county. Salt Lake County data illustrate that high quality reporting is attainable. The overall quality of reporting must be improved to support consequential epidemiologic analyses for stillbirth, and improvement efforts should be tailored to the needs of each jurisdiction.nnAbbreviations and Acronyms ]]> Christiansen-Lindquist, L. Silver, R. M. Parker, C. B. Dudley, D. J. Koch, M. A. Reddy, U. M. Saade, G. R. Goldenberg, R. L. Hogue, C. J. R. 2017-05-30 doi:10.1101/136432 Cold Spring Harbor Laboratory Press 2017-05-30 <![CDATA[ Maximum Entropy Framework For Inference Of Cell Population Heterogeneity In Signaling Networks ]]> https://biorxiv.org/content/10.1101/137513v1?rss=1 Dixit, P. Lyashenko, E. Niepel, M. Vitkup, D. 2017-05-12 doi:10.1101/137513 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ The Condensin Complex Is A Mechanochemical Motor That Translocates Along DNA ]]> https://biorxiv.org/content/10.1101/137711v1?rss=1 Terekawa, T. Bisht, S. Eeftens, J. Dekker, C. Haering, C. Greene, E. 2017-05-13 doi:10.1101/137711 Cold Spring Harbor Laboratory Press 2017-05-13 <![CDATA[ Cellular Adaptation Through Fitness-Directed Transcriptional Tuning ]]> https://biorxiv.org/content/10.1101/137810v1?rss=1 Freddolino, P. L. Yang, J. Tavazoie, S. 2017-05-14 doi:10.1101/137810 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ Bifunctionality Of A Biofilm Matrix Protein Controlled By Redox State ]]> https://biorxiv.org/content/10.1101/138099v1?rss=1 Arnaouteli, S. Ferreira, A. S. Schor, M. Morris, R. J. Bromley, K. M. Jo, J. K. Cortez, K. L. Sukhodub, T. Prescott, A. R. Dietrich, L. E. P. MacPhee, C. E. Stanley-Wall, N. 2017-05-15 doi:10.1101/138099 Cold Spring Harbor Laboratory Press 2017-05-15 <![CDATA[ Could The Recent Zika Epidemic Have Been Predicted? ]]> https://biorxiv.org/content/10.1101/139253v1?rss=1 Munoz, A. G. Thomson, M. C. Stewart-Ibarra, A. M. Vecchi, G. A. Chourio, X. Najera, P. Moran, Z. Yang, X. 2017-05-19 doi:10.1101/139253 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ The Cerebellum Does More Than Sensory-Prediction-Error-Based Learning In Sensorimotor Adaptation Tasks ]]> https://biorxiv.org/content/10.1101/139337v1?rss=1 Butcher, P. A. Ivry, R. Kuo, S.-H. Rydz, D. Krakauer, J. W. Taylor, J. A. 2017-05-17 doi:10.1101/139337 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Mapping The Malaria Parasite Drug-Able Genome Using In Vitro Evolution And Chemogenomics ]]> https://biorxiv.org/content/10.1101/139386v1?rss=1 Cowell, A. N. Istvan, E. S. Lukens, A. K. Gomez-Lorenzo, M. G. Vanaerschot, M. Sakata-Kato, T. Flannery, E. L. Magistrado, P. Abraham, M. Lamonte, G. M. Williams, R. M. Franco, V. Arriago, I. Linares, M. Bopp, S. Corey, V. Gnadig, N. F. Coburn-Flynn, O. Reimer, C. Gupta, P. Murithi, J. M. Fuchs, O. Sasaki, E. Kim, S. W. Teng, C. Wang, L. T. Willis, P. Siegel, D. Tanaseichuk, O. Zhong, Y. Zhou, Y. Otillie, S. Gamo, F.-J. Lee, M. C. S. Goldberg, D. E. Fidock, D. A. Wirth, D. F. Winzeler, E. A. 2017-05-22 doi:10.1101/139386 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Re-Evaluating Evolution In The HIV Reservoir ]]> https://biorxiv.org/content/10.1101/140731v1?rss=1 Rosenbloom, D. I. S. Hill, A. L. Laskey, S. B. Siliciano, R. F. 2017-05-22 doi:10.1101/140731 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Selective Inhibitory Control Of Pyramidal Neuron Ensembles And Cortical Subnetworks By Chandelier Cells ]]> https://biorxiv.org/content/10.1101/140822v1?rss=1 Lu, J. Tucciarone, J. Padilla-Coreano, N. He, M. Gordon, J. A. Huang, Z. J. 2017-05-22 doi:10.1101/140822 Cold Spring Harbor Laboratory Press 2017-05-22 <![CDATA[ Learning Fast And Slow: Deviations From The Matching Law Can Reflect An Optimal Strategy Under Uncertainty ]]> https://biorxiv.org/content/10.1101/141309v1?rss=1 IIgaya, K. Ahmadian, Y. Sugrue, L. Corrado, G. Loewenstein, Y. Newsome, W. T. Fusi, S. 2017-05-24 doi:10.1101/141309 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Swapping Of Transmembrane Domains In The Epithelial Calcium Channel TRPV6 ]]> https://biorxiv.org/content/10.1101/141523v1?rss=1 Singh, A. K. Saotome, K. Sobolevsky, A. I. 2017-05-24 doi:10.1101/141523 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ The Complete Connectome Of A Learning And Memory Center In An Insect Brain ]]> https://biorxiv.org/content/10.1101/141762v1?rss=1 Eichler, K. Litwin-Kumar, A. Li, F. Park, Y. Andrade, I. Schneider-Mizell, C. M. Saumweber, T. Huser, A. Eschbach, C. Gerber, B. Fetter, R. D. Truman, J. W. Priebe, C. E. Abbott, L. F. Thum, A. S. Zlatic, M. Cardona, A. 2017-05-24 doi:10.1101/141762 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Sequential Eviction Of Crowded Nucleoprotein Complexes By The RecBCD Molecular Motor ]]> https://biorxiv.org/content/10.1101/142224v1?rss=1 Terakawa, T. Redding, S. Silverstein, T. D. Greene, E. C. 2017-05-25 doi:10.1101/142224 Cold Spring Harbor Laboratory Press 2017-05-25 <![CDATA[ Cooperative Interactions Enable Singular Olfactory Receptor Expression ]]> https://biorxiv.org/content/10.1101/142489v1?rss=1 1000 olfactory receptor (ORs) genes requires the formation of large heterochromatic chromatin domains that sequester the OR gene clusters. Within these domains, intergenic transcriptional enhancers evade heterochromatic silencing and converge into interchromosomal hubs that assemble over the transcriptionally active OR. The significance of this nuclear organization in OR choice remains elusive. Here, we show that transcription factors Lhx2 and Ebf specify OR enhancers by binding in a functionally cooperative fashion to stereotypically spaced motifs that defy heterochromatin. Specific displacement of Lhx2 and Ebf from OR enhancers resulted in pervasive, long-range, and trans downregulation of OR transcription, whereas pre-assembly of a multi-enhancer hub increased the frequency of OR choice in cis. Our data provide genetic support for the requirement and sufficiency of interchromosomal interactions in singular OR choice and generate general regulatory principles for stochastic, mutually exclusive gene expression programs. ]]> Lomvardas, S. Schieren, I. Monahan, K. Cheung, J. Mumbey-Wafula, A. Monuki, E. 2017-05-27 doi:10.1101/142489 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. B 2017-07-13 doi:10.1101/143933 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Large Meta-Analysis Provides Evidence For An Association Of Serum Vitamin D With Pulmonary Function ]]> https://biorxiv.org/content/10.1101/144717v1?rss=1 Xu, J. Bartz, T. M. Chittoor, G. Eiriksdottir, G. Manichaikul, A. W. Sun, F. Terzikhan, N. Zhou, X. Booth, S. L. Brusselle, G. G. de Boer, I. H. Fornage, M. Frazier-Wood, A. C. Graff, M. Gudnason, V. Harris, T. B. Hofman, A. Hou, R. Houston, D. K. Jacobs, D. R. Kritchevsky, S. B. Latourelle, J. Lemaitre, R. N. Lutsey, P. L. O'Connor, G. Oelsner, E. C. Pankow, J. S. Psaty, B. M. Rohde, R. R. Rich, S. S. Rotter, J. I. Smith, L. J. Stricker, B. H. Voruganti, V. S. Wang, T. J. Zillikens, M. C. Barr, R. G. Dupuis, J. Gharib, S. A. Lahousse, L. London, S. J. 2017-06-02 doi:10.1101/144717 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ pals-22, A Member Of An Expanded C. elegans Gene Family, Controls Silencing Of Repetitive DNA ]]> https://biorxiv.org/content/10.1101/145094v1?rss=1 Leyva-Diaz, E. Stefanakis, N. Carrera, I. Glenwinkel, L. Wang, G. Driscoll, M. Hobert, O. 2017-06-02 doi:10.1101/145094 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Detecting polygenic adaptation in admixture graphs ]]> https://biorxiv.org/content/10.1101/146043v1?rss=1 Racimo, F. Berg, J. J. Pickrell, J. K. 2017-06-04 doi:10.1101/146043 Cold Spring Harbor Laboratory Press 2017-06-04 <![CDATA[ Role of inhibitory control in modulating spread of focal ictal activity ]]> https://biorxiv.org/content/10.1101/146407v1?rss=1 Liou, J.-y. Ma, H. Wenzel, M. Zhao, M. Baird-Daniel, E. Smith, E. Daniel, A. Emerson, R. G. Yuste, R. Schwartz, T. H. Schevon, C. 2017-06-05 doi:10.1101/146407 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ Diabetes and dementia incidence in Latin America; a 10/66 population-based cohort study ]]> https://biorxiv.org/content/10.1101/148155v1?rss=1 = 7mmol/L). Blood pressure, smoking, underactivity and waist circumference were assessed from questionnaires and physical examination. Incident 10/66 dementia (and subtypes), and mortality, were ascertained three to five years later.nnResults12,297 interviews were completed at baseline, with 80-95% responding by site. The at risk cohort comprised 10,945 dementia-free individuals, of whom 8,171 (75%) provided blood samples. Mean age varied from 72.0 to 75.1 years by site. Total diabetes prevalence was 43.5% in Puerto Rico, ranging from 11.5% to 27.0% in other sites. Most diabetes cases (50.2% to 68.4%) were not controlled (fasting glucose >7.0 mmol/L). 7,000 participants were followed up for 26,423 person-years with 659 incident dementia cases, and 905 dementia free deaths. Total diabetes was associated with incident 10/66 dementia (pooled meta-analysed adjusted sub-hazard ratio [pASHR] 1.25, 95% CI, 1.05-1.49, I2=48.6%), with a stronger association for uncontrolled (pASHR 1.47, 95% CI 1.19-1.81, I2=49.6%) than controlled cases (pASHR 1.29, 95% CI 0.95-1.74, I2=13.3%). Total diabetes was strongly associated with the incidence of vascular dementia (pASHR 2.25, 95% CI 1.24-4.08, I2=23.7%), but not Alzheimers Disease (pASHR 0.99, 95% CI 0.70-1.42, I2=49.0%).nnConclusionsDiabetes, particularly when poorly controlled, may increase dementia risk. There is considerable scope for improved detection and control of diabetes among older people in these settings, and hence an opportunity to carry out proof of concept prevention trials. Overlapping epidemics of these age dependent disorders will challenge poorly-resourced health systems in the future. ]]> Salas, A. Acosta, D. M. Guerra, M. Huang, Y. Jimenez-Velazquez, I. Z. Llibre Rodriguez, J. J. Sosa, A. L. Dewey, M. E. Gaona, C. Guerchet, M. M. Gonzalez, L. M. Liu, Z. Luchsinger, J. A. Lopez Medina, A. M. Salinas, R. M. Prince, M. J. 2017-07-10 doi:10.1101/148155 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ Harmonization of cortical thickness measurements across scanners and sites ]]> https://biorxiv.org/content/10.1101/148502v1?rss=1 Fortin, J.-P. Cullen, N. Sheline, Y. I. Taylor, W. D. Aselcioglu, I. Adams, P. Cooper, C. Fava, M. McGrath, P. J. McInnis, M. Parsey, R. V. Phillips, M. L. Trivedi, M. H. Weissman, M. M. Shinohara, R. T. 2017-06-10 doi:10.1101/148502 Cold Spring Harbor Laboratory Press 2017-06-10 <![CDATA[ Correlated Light-Serial Scanning Electron Microscopy (CoLSSEM) for ultrastructural visualization of single neurons in vivo ]]> https://biorxiv.org/content/10.1101/148585v1?rss=1 Hirabayashi, Y. Tapia, J. C. Polleux, F. 2017-06-10 doi:10.1101/148585 Cold Spring Harbor Laboratory Press 2017-06-10 <![CDATA[ Differing strategies used by motor neurons and glia to achieve robust development of an adult neuropil in Drosophila ]]> https://biorxiv.org/content/10.1101/149229v1?rss=1 Enriquez, J. Quintana Rio, L. Blazeski, R. Mason, C. Mann, R. S. 2017-06-13 doi:10.1101/149229 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ The Healthy Brain Network Biobank: An open resource for transdiagnostic research in pediatric mental health and learning disorders ]]> https://biorxiv.org/content/10.1101/149369v1?rss=1 Alexander, L. M. Escalera, J. Ai, L. Andreotti, C. Febre, K. Mangone, A. Vega Potler, N. Langer, N. Alexander, A. Kovacs, M. Litke, S. O'Hagan, B. Bronstein, B. Bui, A. Bushey, M. Castagna, V. Camacho, N. Chan, E. Citera, D. Clucas, J. Cohen, S. Eaves, M. Fradera, B. Grant-Villegas, N. Green, G. Gregory, C. Hart, E. Harris, S. Lord, C. Kahn, D. Kabotyanski, K. Kleinman, K. Koo, B. Kramer, E. Margolis, A. Merikangas, K. Milham, J. Minniti, G. Neuhaus, R. Nussbaum, A. Osman, Y. Parra, L. Pugh, K. R. Racanello, A. Restrepo, A. Saltzman, T. Septimus, B 2017-06-13 doi:10.1101/149369 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ YASS: Yet Another Spike Sorter ]]> https://biorxiv.org/content/10.1101/151928v1?rss=1 Lee, J. Carlson, D. Shokri, H. Yao, W. Goetz, G. Hagen, E. Batty, E. Chichilnisky, E. Einevoll, G. Paninski, L. 2017-06-19 doi:10.1101/151928 Cold Spring Harbor Laboratory Press 2017-06-19 <![CDATA[ Inferring single-trial neural population dynamics using sequential auto-encoders ]]> https://biorxiv.org/content/10.1101/152884v1?rss=1 Pandarinath, C. O'Shea, D. J. Collins, J. Jozefowicz, R. Stavisky, S. D. Kao, J. C. Trautmann, E. M. Kaufman, M. T. Ryu, S. I. Hochberg, L. R. Henderson, J. M. Shenoy, K. V. Abbott, L. F. Sussillo, D. 2017-06-20 doi:10.1101/152884 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Neural Networks for Efficient Bayesian Decoding of Natural Images from Retinal Neurons ]]> https://biorxiv.org/content/10.1101/153759v1?rss=1 Parthasarathy, N. Batty, E. Falcon, W. Rutten, T. Rajpal, M. Chichilnisky, E. J. Paninski, L. 2017-06-22 doi:10.1101/153759 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Response to Editas: Unexpected mutations after CRISPR-Cas9 editing in vivo ]]> https://biorxiv.org/content/10.1101/154450v1?rss=1 Schaefer, K. A. Wu, W.-H. Colgan, D. F. Tsang, S. H. Bassuk, A. G. Mahajan, V. B. 2017-06-23 doi:10.1101/154450 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Dopamine neuron dependent behaviors mediated by glutamate cotransmission ]]> https://biorxiv.org/content/10.1101/154864v1?rss=1 Mingote, S. Chuhma, N. Kalmbach, A. Thomsen, G. M. Wang, Y. Mihali, A. Sferrazza, C. Zucker-Scharff, I. Siena, A.-C. Welch, M. G. Lizardi-Ortiz, J. Sulzer, D. Moore, H. Gaisler-Salomon, I. Rayport, S. 2017-06-23 doi:10.1101/154864 Cold Spring Harbor Laboratory Press 2017-06-23 <![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[ Spatiotemporal organization of whole-body muscle activity during upright reaching movements in various directions: modularity or not modularity? ]]> https://biorxiv.org/content/10.1101/155085v1?rss=1 Hilt, P. M. Delis, I. Pozzo, T. Berret, B. 2017-06-24 doi:10.1101/155085 Cold Spring Harbor Laboratory Press 2017-06-24 <![CDATA[ Combined social and spatial coding in a descending projection from the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/155929v1?rss=1 Murugan, M. Park, M. Taliaferro, J. Jang, H. J. Cox, J. Parker, N. Bhave, V. Nectow, A. Pillow, J. Witten, I. 2017-06-26 doi:10.1101/155929 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Delineating the macroscale areal organization of the macaque cortex in vivo ]]> https://biorxiv.org/content/10.1101/155952v1?rss=1 Xu, T. Falchier, A. Sullivan, E. Linn, G. Ramirez, J. Ross, D. Feczko, E. Opitz, A. Bagley, J. Sturgeon, D. Earl, E. Miranda-Domingue, O. Perrone, A. Craddock, C. Schroeder, C. Colcombe, S. Fair, D. Milham, M. 2017-06-26 doi:10.1101/155952 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Distinct epigenetic shift in a subset of Glioma CpG island methylator phenotype (G-CIMP) during tumor recurrence ]]> https://biorxiv.org/content/10.1101/156646v1?rss=1 de Souza, C. F. Sabedot, T. S. Malta, T. M. Stetson, L. Morozova, O. Sokolov, A. Laird, P. W. Wiznerowicz, M. Iavarone, A. Snyder, J. deCarvalho, A. C. Sanborn, Z. McDonald, K. L. Friedman, W. A. Tirapelli, D. Poisson, L. Mikkelsen, T. Carlotti, C. G. Kalkanis, S. N. Zenklusen, J. C. Salama, S. R. Barnholtz-Sloan, J. S. Noushmehr, H. 2017-06-28 doi:10.1101/156646 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ A Genome-wide Association and Admixture Mapping Study of Bronchodilator Drug Response in African Americans with Asthma ]]> https://biorxiv.org/content/10.1101/157198v1?rss=1 Spear, M. L. Hu, D. Pino-Yanes, M. Huntsman, S. Eng, C. Levin, A. M. White, M. J. McGarry, M. E. Thakur, N. Galanter, J. M. Mak, A. C. Y. Oh, S. S. Davis, A. Kumar, R. Farber, H. J. Meade, K. Avila, P. C. Serebrisky, D. Lenoir, M. A. Brigino-Buenaventura, E. A. Rodriquez Cintron, W. Thyne, S. M. Rodriguez-Santana, J. R. Ford, J. G. Chapela, R. Moreno Estrada, A. Sandoval, K. Seibold, M. A. Williams, L. K. Winkler, C. A. Torgerson, D. G. Hernandez, R. D. Burchard, E. G. 2017-06-28 doi:10.1101/157198 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Classifiers with limited connectivity ]]> https://biorxiv.org/content/10.1101/157289v1?rss=1 Kushnir, L. Fusi, S. 2017-06-29 doi:10.1101/157289 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ GWAS of epigenetic ageing rates in blood reveals a critical role for TERT ]]> https://biorxiv.org/content/10.1101/157776v1?rss=1 Lu, A. T. Xue, L. Salfati, E. L. Chen, B. H. Ferrucci, L. Levy, D. Joehanes, R. Murabito, J. M. Kiel, D. P. Tsai, P.-C. Yet, I. Bell, J. T. Mangino, M. Tanaka, T. McRae, A. Marioni, R. E. Visscher, P. M. Wray, N. R. Deary, I. J. Levine, M. E. Quach, A. Assimes, T. L. Tsao, P. S. Absher, D. Stewart, J. D. Li, Y. Reiner, A. P. Hou, L. Baccarelli, A. A. Whitsel, E. A. Aviv, A. Cardona, A. Day, F. R. Perry, J. R. B. Ong, K. K. Raj, K. Lunetta, K. L. Horvath, S. 2017-06-30 doi:10.1101/157776 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ Receptor-Based Mechanism of Relative Sensing in Mammalian Signaling Networks ]]> https://biorxiv.org/content/10.1101/158774v1?rss=1 Lyashenko, E. Niepel, M. Dixit, P. Lim, S. K. Sorger, P. Vitkup, D. 2017-07-02 doi:10.1101/158774 Cold Spring Harbor Laboratory Press 2017-07-02 <![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[ 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[ Neurotropism of enterovirus D68 isolates is independent of sialic acid and is not a recently acquired phenotype ]]> https://biorxiv.org/content/10.1101/161778v1?rss=1 Rosenfeld, A. B. Warren, A. L. Racaniello, V. R. 2017-07-10 doi:10.1101/161778 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ A naturalistic assay for measuring behavioral responses to aversive stimuli at millisecond timescale ]]> https://biorxiv.org/content/10.1101/161885v1?rss=1 Schoonover, C. E. Fink, A. J. P. Axel, R. 2017-07-14 doi:10.1101/161885 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ 2-Way k-Means as a Model for Microbiome Samples ]]> https://biorxiv.org/content/10.1101/161935v1?rss=1 Jackson, W. J. Agarwal, I. Pe'er, I. 2017-07-11 doi:10.1101/161935 Cold Spring Harbor Laboratory Press 2017-07-11 <![CDATA[ Polioviruses that bind a chimeric Pvr-nectin-2 protein identify capsid residues involved in receptor interaction ]]> https://biorxiv.org/content/10.1101/162800v1?rss=1 Lin, Y. Racaniello, V. R. 2017-07-12 doi:10.1101/162800 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Meta-analysis of exome array data identifies six novel genetic loci for lung function ]]> https://biorxiv.org/content/10.1101/164426v1?rss=1 Jackson, V. E. Latourelle, J. C. Wain, L. V. Smith, A. V. Grove, M. L. Bartz, T. M. Obeidat, M. Province, M. A. Gao, W. Qaiser, B. Porteous, D. J. Cassano, P. A. Ahluwalia, T. S. Grarup, N. Li, J. Altmaier, E. Marten, J. Harris, S. E. Manichaikul, A. Pottinger, T. D. Li-Gao, R. Lind-Thomsen, A. Mahajan, A. Lahousse, L. Imboden, M. Teumer, A. Prins, B. Lyytikäinen, L.-P. Eiriksdottir, G. Franceschini, N. Sitlani, C. M. Brody, J. A. Bosse, Y. Timens, W. Kraja, A. Loukola, A. Tang, W. Liu, Y. Bork-Jensen, J. Justesen, J. M. Linneberg, A. Lange, L. 2017-07-17 doi:10.1101/164426 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Polygenic Risk Score of Sporadic Late Onset Alzheimer Disease Reveals a Shared Architecture with the Familial and Early Onset Forms ]]> https://biorxiv.org/content/10.1101/165209v1?rss=1 Del Aguila, J. L. Saef, B. Black, K. Fernandez, M.-V. John Budde, J. Ibanez, L. Kapoor, M. Tosto, G. Mayeux, R. P. Holtzman, D. M. Fagan, A. M. Morris, J. C. Bateman, R. J. Goate, A. M. Cruchaga, C. Harari, O. 2017-07-19 doi:10.1101/165209 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ SOD1A4V aggregation alters ubiquitin homeostasis in ALS ]]> https://biorxiv.org/content/10.1101/166165v1?rss=1 Farrawell, N. E. Lambert-Smith, I. Mitchell, K. McKenna, J. McAlary, L. Ciryam, P. Vine, K. L. Saunders, D. Yerbury, J. J. 2017-07-20 doi:10.1101/166165 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Automated analysis of internally programmed grooming behavior in Drosophila using a k-nearest neighbors classifier ]]> https://biorxiv.org/content/10.1101/166561v1?rss=1 Qiao, B. Li, C. Allen, V. Shirasu-Hiza, M. M. Syed, S. 2017-07-21 doi:10.1101/166561 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ Conformational Dynamics and Energy Landscapes of Ligand Binding in RyR1 ]]> https://biorxiv.org/content/10.1101/167080v1?rss=1 Dashti, A. Ben Hail, D. Mashayekhi, G. Schwander, P. des Georges, A. Frank, J. Ourmazd, A. 2017-07-21 doi:10.1101/167080 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ High-depth whole genome sequencing of a large population-specific reference panel: Enhancing sensitivity, accuracy, and imputation ]]> https://biorxiv.org/content/10.1101/167924v1?rss=1 Lencz, T. Yu, J. Palmer, C. Carmi, S. Ben-Avraham, D. Barzilai, N. Bressman, S. Darvasi, A. Cho, J. Clark, L. Gumus, Z. Joseph, V. Klein, R. Lipkin, S. Offit, K. Ostrer, H. Ozelius, L. Peter, I. Atzmon, G. Pe'er, I. 2017-07-24 doi:10.1101/167924 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Conjunction of Factors Triggering Waves of Seasonal Influenza ]]> https://biorxiv.org/content/10.1101/168476v1?rss=1 Chattopadhyay, I. Kiciman, E. Elliott, J. Shaman, J. Rzhetsky, A. 2017-07-27 doi:10.1101/168476 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Avoidance of toxic misfolding does not explain the sequence constrains of highly expressed proteins across organisms ]]> https://biorxiv.org/content/10.1101/168963v1?rss=1 Plata, G. Vitkup, D. 2017-07-26 doi:10.1101/168963 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Comparison of decision-related signals in sensory and motor preparatory responses of neurons in Area LIP ]]> https://biorxiv.org/content/10.1101/169219v1?rss=1 Shushruth, S. Mazurek, M. E. Shadlen, M. N. 2017-07-27 doi:10.1101/169219 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ HPCDb: an integrated database of pancreatic cancer ]]> https://biorxiv.org/content/10.1101/169771v1?rss=1 1). Further, protein-protein interactions (PPIs) were investigated through the Human Protein Reference Database. miRNA-target relationships were also identified using the online software TargetScan. Currently, HPCDb contains 3284 genes, 120 miRNAs, 589 SNPs, 10,139 PPIs, and 3904 miRNA-target pairs. The detailed information on PC-related genes (e.g., gene identifier (ID), symbol, synonyms, full name, chip sets, expression alteration, PubMed ID, and PPIs), miRNAs (e.g., accession number, chromosome location, related disease, PubMed ID, and miRNA-target interactions), and SNPs (e.g., SNP ID, allele, gene, PubMed ID, chromosome location, and disease) is presented through user-friendly query interfaces or convenient links to NCBI GEO, NCBI PubMed, NCBI Gene, NCBI dbSNP, and miRBase. Overall, HPCDb provides biologists with relevant information on human PC-related molecules at multiple levels, helping to generate new hypotheses or identify candidate markers. ]]> Tan, Y. Tan, Y. Lu, L. Zhang, H. Sun, C. Liang, Y. Zeng, J. Yang, X. Li, D. Zou, H. 2017-07-28 doi:10.1101/169771 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently ]]> https://biorxiv.org/content/10.1101/170795v1?rss=1 Yu, C. Gan, H. Zhang, Z. 2017-08-01 doi:10.1101/170795 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ Forgot what you like? Evidence for hippocampal dependence of value-based decisions ]]> https://biorxiv.org/content/10.1101/170969v1?rss=1 Enkavi, A. Z. Weber, B. Zweyer, I. Wagner, J. Elger, C. E. Weber, E. U. Johnson, E. J. 2017-07-31 doi:10.1101/170969 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulence ]]> https://biorxiv.org/content/10.1101/171538v1?rss=1 Jo, J. Cortez, K. L. Cornell, W.-C. Price-Whelan, A. Dietrich, L. E. P. 2017-08-02 doi:10.1101/171538 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ Serial representation of items during working memory maintenance at letter-selective cortical sites ]]> https://biorxiv.org/content/10.1101/171660v1?rss=1 Bahramisharif, A. Jensen, O. Jacobs, J. Lisman, J. 2017-08-02 doi:10.1101/171660 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ Domain-Specific Patterns of Activity Support Metacognition in Human Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/172445v1?rss=1 Morales, J. Lau, H. Fleming, S. M. 2017-08-04 doi:10.1101/172445 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ GTP Hydrolysis by eIF5B in the Last Step of Translation Initiation Is Activated by a Rotation of the Small Ribosomal Subunit. ]]> https://biorxiv.org/content/10.1101/172825v1?rss=1 Fernandez, I. S. Ramakrishnan, V. 2017-08-04 doi:10.1101/172825 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ A spatial memory signal shows that the parietal cortex has access to a craniotopic representation of space ]]> https://biorxiv.org/content/10.1101/173245v1?rss=1 Semework, M. Steenrod, S. C. Goldberg, M. E. 2017-08-08 doi:10.1101/173245 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease ]]> https://biorxiv.org/content/10.1101/174565v1?rss=1 Raj, T. Li, Y. Wong, G. Ramdhani, S. Wang, Y.-c. Ng, B. Wang, M. Gupta, I. Haroutunian, V. Zhang, B. Schadt, E. E. Young-Pearse, T. Mostafavi, S. Sklar, P. Bennett, D. De Jager, P. L. 2017-08-10 doi:10.1101/174565 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Comparing colours using visual models ]]> https://biorxiv.org/content/10.1101/175992v1?rss=1 Maia, R. White, T. 2017-08-18 doi:10.1101/175992 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Prestimulus Activity in the Cingulo-Opercular Network Predicts Memory for Naturalistic Episodic Experience ]]> https://biorxiv.org/content/10.1101/176057v1?rss=1 Cohen, N. Ben-Yakov, A. Weber, J. Edelson, M. Paz, R. Dudai, Y. 2017-08-14 doi:10.1101/176057 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site ]]> https://biorxiv.org/content/10.1101/176073v1?rss=1 Zhang, L. Martini, G. Rube, H. T. Kribelbauer, J. F. Rastogi, C. FitzPatrick, V. D. Houtman, J. C. Bussemaker, H. J. Pufall, M. A. 2017-08-14 doi:10.1101/176073 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ The effect of sequence mismatches on binding affinity and endonuclease activity are decoupled throughout the Cas9 binding site ]]> https://biorxiv.org/content/10.1101/176255v1?rss=1 Zhang, L. Rube, H. T. Bussemaker, H. J. Pufall, M. A. 2017-08-14 doi:10.1101/176255 Cold Spring Harbor Laboratory Press 2017-08-14 <![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[ N6-Methyladenine DNA Modification in Human Genome ]]> https://biorxiv.org/content/10.1101/176958v1?rss=1 Xiao, C.-L. Zhu, S. He, M.-H. Chen, Y. Yu, G.-L. Chen, D. Xie, S.-Q. Luo, F. Liang, Z. Gu, X.-F. Wang, K. Yan, G.-R. 2017-08-16 doi:10.1101/176958 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ Genomics of Natural Populations: Evolutionary Forces that Establish and Maintain Gene Arrangements in Drosophila pseudoosbscura ]]> https://biorxiv.org/content/10.1101/177204v1?rss=1 30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions. This study analyzes the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (1) genetic drift, (2) hitchhiking with an adaptive allele, (3) direct effects of inversions to create gene disruptions caused by breakpoints, or (4) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harboring elevated frequencies of arrangement-specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favored because they maintain linked associations among multi-locus allelic combinations among different arrangements. ]]> Fuller, Z. L. Haynes, G. Richards, S. Schaeffer, S. W. 2017-08-17 doi:10.1101/177204 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Replication of early and recent Zika virus isolates throughout mouse brain development ]]> https://biorxiv.org/content/10.1101/177816v1?rss=1 Rosenfeld, A. B. Doobin, D. J. Warren, A. L. Racaniello, V. R. Vallee, R. B. 2017-08-17 doi:10.1101/177816 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Community-based benchmarking improves spike inference from two-photon calcium imaging data ]]> https://biorxiv.org/content/10.1101/177956v1?rss=1 Berens, P. Freeman, J. Deneux, T. Chenkov, N. McColgan, T. Speiser, A. Macke, J. H. Turaga, S. Mineault, P. Rupprecht, P. Gerhard, S. Friedrich, R. W. Friedrich, J. Paninski, L. Pachitariu, M. Harris, K. D. Bolte, B. Machado, T. A. Ringach, D. Reimer, J. Froudarakis, E. Euler, T. Roman-Roson, M. Theis, L. Tolias, A. S. Bethge, M. 2017-08-18 doi:10.1101/177956 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ A unifying motif for spatial and directional surround suppression ]]> https://biorxiv.org/content/10.1101/180125v1?rss=1 Liu, L. D. Miller, K. D. Pack, C. C. 2017-08-24 doi:10.1101/180125 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Alpha activity in the ventral and dorsal visual stream controls information flow during working memory ]]> https://biorxiv.org/content/10.1101/180166v1?rss=1 Leszczynski, M. Fell, J. Jensen, O. Axmacher, N. 2017-08-24 doi:10.1101/180166 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments ]]> https://biorxiv.org/content/10.1101/180646v1?rss=1 130 PTM sites in Escherichia coli to unravel how PTMs regulate cell metabolism and fitness in response to environmental changes, such as the glucose-acetate diauxie. Using a new metabolic modeling approach, we found a significant fraction of post-translationally modified enzymes are predicted to control shifts in pathway usage following evolutionarily-important environmental changes. Genetic screens using Multiplex Automated Genome Engineering confirmed that these PTMs impact cellular fitness, especially under dynamically changing environments. Finally, mechanisms of how individual PTMs impact protein function were detailed using molecular dynamics simulations and enzyme assays for enolase, transaldolase, and serine hydroxymethyltransferase. Thus, by integrating whole-cell data and pathway modeling with detailed biochemical analysis, we unraveled how individual PTMs regulate enzymes, pathways, and phenotypes to adapt to sudden environmental changes. ]]> Brunk, E. Chang, R. L. Xia, J. Hefzi, H. Yurkovich, J. T. Kim, D. Buckmiller, E. Wang, H. Yang, C. Palsson, B. O. Church, G. Lewis, N. E. 2017-08-25 doi:10.1101/180646 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Inter-homologue repair in fertilized human eggs? ]]> https://biorxiv.org/content/10.1101/181255v1?rss=1 Egli, D. Zuccaro, M. Kosicki, M. Church, G. Bradley, A. Jasin, M. 2017-08-28 doi:10.1101/181255 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Synthesis of a eukaryotic chromosome reveals a role for N6-methyladenine in nucleosome organization ]]> https://biorxiv.org/content/10.1101/184929v1?rss=1 Beh, L. Y. Debelouchina, G. T. Lindblad, K. A. Kulej, K. Hutton, E. R. Bracht, J. R. Sebra, R. P. Garcia, B. A. Muir, T. W. Landweber, L. F. 2017-09-06 doi:10.1101/184929 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Cell size and growth rate are modulated by TORC2-dependent signals ]]> https://biorxiv.org/content/10.1101/188698v1?rss=1 Lucena, R. Alcaide-Gavilan, M. Schubert, K. He, M. Domnauer, M. Marquer, C. Kellogg, D. 2017-09-14 doi:10.1101/188698 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Conservation of preparatory neural events regardless of how movement is initiated ]]> https://biorxiv.org/content/10.1101/189035v1?rss=1 Lara, A. H. Elsayed, G. F. Cunningham, J. Churchland, M. M. 2017-09-14 doi:10.1101/189035 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ OnACID: Online Analysis of Calcium Imaging Data in Real Time ]]> https://biorxiv.org/content/10.1101/193383v1?rss=1 Giovannucci, A. Friedrich, J. Kaufman, M. Churchland, A. K. Chklovskii, D. Paninski, L. Pnevmatikakis, E. A. 2017-10-02 doi:10.1101/193383 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Force dependence of filopodia adhesion: involvement of myosin II and formins ]]> https://biorxiv.org/content/10.1101/195420v1?rss=1 Alieva, N. O. Efremov, A. K. Hu, S. Oh, D. Chen, Z. Natarajan, M. Ong, H. T. Jegou, A. Romet-Lemonne, G. Groves, J. T. Sheetz, M. P. Yan, J. Bershadsky, A. D. 2017-09-28 doi:10.1101/195420 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Multiethnic Meta-analysis Identifies New Loci for Pulmonary Function ]]> https://biorxiv.org/content/10.1101/196048v1?rss=1 Wyss, A. B. Sofer, T. Lee, M. K. Terzikhan, N. Nguyen, J. N. Lahousse, L. Latourelle, J. C. Smith, A. V. Bartz, T. M. Feitosa, M. F. Gao, W. Ahluwalia, T. S. Tang, W. Oldmeadow, C. Duan, Q. de Jong, K. Wojczynski, M. K. Wang, X.-Q. Noordam, R. Hartwig, F. P. Jackson, V. E. Wang, T. Obeidat, M. Hobbs, B. D. Huan, T. Kichaev, G. Jin, J. Graff, M. Harris, T. B. Kalhan, R. Heckbert, S. R. Paternoster, L. Burkart, K. M. Liu, Y. Holliday, E. G. Wilson, J. G. Vonk, J. M. Sanders, J. Barr, R. G. de Mutsert, R. Baptista Menezes, A. M. Adams, H. H. H. van den Be 2017-10-05 doi:10.1101/196048 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ 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[ Transcriptomic characterization of MRI contrast, focused on the T1-w/T2-w ratio in the cerebral cortex ]]> https://biorxiv.org/content/10.1101/196386v1?rss=1 Ritchie, J. Pantazatos, S. French, L. 2017-09-30 doi:10.1101/196386 Cold Spring Harbor Laboratory Press 2017-09-30 <![CDATA[ Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience ]]> https://biorxiv.org/content/10.1101/196949v1?rss=1 nView larger version (13K):norg.highwire.dtl.DTLVardef@16fff01org.highwire.dtl.DTLVardef@1ceacd4org.highwire.dtl.DTLVardef@1b49960org.highwire.dtl.DTLVardef@1c1ad13_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO The central role of data science in modern large - scale neuroscience.Topics reviewed herein are indicated in black.nnC_FIG ]]> Paninski, L. Cunningham, J. 2017-10-02 doi:10.1101/196949 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Genetic analysis of over one million people identifies 535 novel loci for blood pressure. ]]> https://biorxiv.org/content/10.1101/198234v1?rss=1 Evangelou, E. Warren, H. R. Mosen-Ansorena, D. Mifsud, B. Pazoki, R. Gao, H. Ntritsos, G. Dimou, N. Cabrera, C. P. Karaman, I. Ng, F. L. Evangelou, M. Witkowska, K. Tzanis, E. Hellwege, J. N. Giri, A. Velez Edwards, D. R. Sun, Y. V. Cho, K. Gaziano, J. M. Wilson, P. W. F. Tsao, P. S. Kovesdy, C. P. Esko, T. Magi, R. Milani, L. Almgren, P. Boutin, T. Debette, S. Ding, J. Giulianini, F. Holliday, E. G. Jackson, A. U. Li-Gao, R. Lin, W.-Y. Luan, J. Mangino, M. Oldmeadow, C. Prins, B. Qian, Y. Sargurupremraj, M. Shah, N. Surendran, P. Theriault, S. Verwe 2017-10-11 doi:10.1101/198234 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Molecular function limits divergent protein evolution on planetary timescales ]]> https://biorxiv.org/content/10.1101/198663v1?rss=1 25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site in orthologs strictly conserving their molecular function. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations. ]]> Konate, M. Plata, G. Park, J. Wang, H. H. Vitkup, D. 2017-10-05 doi:10.1101/198663 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Introducing prescribed biases in out of equilibrium Markov models ]]> https://biorxiv.org/content/10.1101/198697v1?rss=1 Dixit, P. 2017-10-04 doi:10.1101/198697 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Hox-logic of preadaptations for social insect symbiosis in rove beetles ]]> https://biorxiv.org/content/10.1101/198945v1?rss=1 Parker, J. Eldredge, K. T. Thomas, I. Coleman, R. Davis, S. 2017-10-05 doi:10.1101/198945 Cold Spring Harbor Laboratory Press 2017-10-05 <![CDATA[ Towards establishing internal validity for correlated gene expression measures in imaging genomics of functional networks: why distance corrections and external face validity alone fall short. Reply to "Distance is not everything in imaging genomics of functional networks: reply to a commentary on Correlated gene expression supports synchronous activity in brain networks" ]]> https://biorxiv.org/content/10.1101/2019.12.09.869412v1?rss=1 0.9, p<0.001), not by rsfMRI samples. Simulations using 14mm radius clusters most resembled rsfMRI networks. When thresholding at p<10-4, the SSF-FPR was 0.47. Genes that maximize SF have high global spatial autocorrelation. In conclusion, SSF is unrelated to rsfMRI networks. The main conclusion of Richiardi et. al. 2015 is based on a finding that is [~]50% likely to be a false positive, not less than 0.01% as originally reported in the article1. We discuss why distance corrections alone and external face validity are insufficient to establish a trustworthy relationship between correlated gene expression measures and rsfMRI networks, and propose more rigorous approaches to preclude common pitfalls in related studies. ]]> Pantazatos, S. Schmidt, M. 2019-12-12 doi:10.1101/2019.12.09.869412 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Population structure and clonal prevalence of scleractinian corals (Montipora capitata and Porites compressa) in Kaneohe Bay, Oahu ]]> https://biorxiv.org/content/10.1101/2019.12.11.860585v1?rss=1 Locatelli, N. S. Drew, J. 2019-12-12 doi:10.1101/2019.12.11.860585 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Reduced transfer coefficient of carbon monoxide in pulmonary arterial hypertension implicates rare protein-truncating variants in KDR ]]> https://biorxiv.org/content/10.1101/2019.12.11.871210v1?rss=1 Swietlik, E. M. Greene, D. Zhu, N. Megy, K. Cogliano, M. Rajaram, S. Pandya, D. Tilly, T. Lutz, K. A. Welch, C. C. L. Pauciulo, M. W. Southgate, L. Martin, J. M. Treacy, C. M. UK National Cohort Study of Idiopathic and Heritable PAH, NIHR Bioresource for Translational Research - Rare Diseases, US PAH Biobank Enrolling Centers' Investigators, Lawrie, A. Wilkins, M. R. Trembath, R. C. Shen, Y. Wendy, C. K. Swift, A. J. Nichols, W. C. Morrell, N. W. Gräf, S. 2019-12-12 doi:10.1101/2019.12.11.871210 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ A Holistic Analysis of the Intestinal Stem Cell Niche Network ]]> https://biorxiv.org/content/10.1101/2019.12.12.871756v1?rss=1 Hansen, D. M. Meneses Giles, P. I. He, X. C. Chen, S. Paulson, A. Dekaney, C. M. Wang, J. Hu, D. Venkatraman, A. Kim, W. Kaddis, J. Olack, B. J. Dunn, J. C. Y. Kuo, C. Henning, S. Hanash, A. M. Houchen, C. W. Lynch, J. Martin, M. G. Niland, J. C. Stelzner, M. Wong, M. Wang, T. C. Yu, J. Yan, K. Li, L. 2019-12-12 doi:10.1101/2019.12.12.871756 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish ]]> https://biorxiv.org/content/10.1101/2019.12.12.874586v1?rss=1 Powell, D. L. Garcia, M. Keegan, M. Reilly, P. Du, K. Diaz-Loyo, A. P. Banerjee, S. Blakkan, D. Reich, D. E. Andolfatto, P. Rosenthal, G. G. Schartl, M. Schumer, M. 2019-12-13 doi:10.1101/2019.12.12.874586 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ Robust neural control of virtual locomotion enabled by a novel decoding strategy ]]> https://biorxiv.org/content/10.1101/2019.12.13.862532v1?rss=1 Schroeder, K. E. Perkins, S. M. Wang, Q. Churchland, M. M. 2019-12-14 doi:10.1101/2019.12.13.862532 Cold Spring Harbor Laboratory Press 2019-12-14 <![CDATA[ A simple circuit model of visual cortex explains neural and behavioral aspects of attention ]]> https://biorxiv.org/content/10.1101/2019.12.13.875534v1?rss=1 Lindsay, G. W. Rubin, D. B. Miller, K. D. 2019-12-13 doi:10.1101/2019.12.13.875534 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ L-type voltage-gated calcium channel agonists improve hearing loss and modify ribbon synapse morphology in the zebrafish model of Usher Syndrome Type 1 ]]> https://biorxiv.org/content/10.1101/2019.12.16.878231v1?rss=1 Koleilat, A. Dugdale, J. A. Christenson, T. A. Bellah, J. L. Lambert, A. L. Masino, M. A. Ekker, S. C. Schimmenti, L. A. 2019-12-16 doi:10.1101/2019.12.16.878231 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Distinct signatures of reward value and variance on spiking activity and functional interactions in monkey fronto-parietal areas ]]> https://biorxiv.org/content/10.1101/2019.12.17.879262v1?rss=1 Taghizadeh, B. Karimimehr, S. Foley, N. C. Cohanpour, M. Semework, M. Sheth, S. A. Lashgari, R. Gottlieb, J. 2019-12-18 doi:10.1101/2019.12.17.879262 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ A model of flexible motor sequencing through thalamic control of cortical dynamics ]]> https://biorxiv.org/content/10.1101/2019.12.17.880153v1?rss=1 Logiaco, L. Abbott, L. Escola, S. 2019-12-18 doi:10.1101/2019.12.17.880153 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling ]]> https://biorxiv.org/content/10.1101/2019.12.19.882985v1?rss=1 DelGiorno, K. E. Chung, C.-Y. Maurer, H. C. Weiser Novak, S. Giraddi, R. R. Wang, D. Naeem, R. F. Fang, L. Andrade, L. R. Lytle, N. K. Ali, W. H. Tsui, C. Gubbala, V. B. Ridinger-Saison, M. Ohmoto, M. O'Connor, C. Erikson, G. Shokhirev, M. N. Urade, Y. Matsumoto, I. Vavinskaya, V. Singh, P. K. Manor, U. Olive, K. P. Wahl, G. 2019-12-20 doi:10.1101/2019.12.19.882985 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Whole-body imaging of neural and muscle activity during behavior in Hydra: bidirectional effects of osmolarity on contraction bursts ]]> https://biorxiv.org/content/10.1101/2019.12.20.883835v1?rss=1 Yamamoto, W. Yuste, R. 2019-12-20 doi:10.1101/2019.12.20.883835 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Is the rat prefrontal cortex crucial for cognitive control during spatial cognition? ]]> https://biorxiv.org/content/10.1101/2019.12.20.884262v1?rss=1 Park, E. H. O'Reilly, K. Taborga, D. Nicholas, K. Ahmed, A. Ruiz, N. Fenton, A. 2019-12-22 doi:10.1101/2019.12.20.884262 Cold Spring Harbor Laboratory Press 2019-12-22 <![CDATA[ A community-maintained standard library of population genetic models ]]> https://biorxiv.org/content/10.1101/2019.12.20.885129v1?rss=1 Adrion, J. R. Cole, C. B. Dukler, N. Galloway, J. G. Gladstein, A. L. Gower, G. Kyriazis, C. C. Ragsdale, A. P. Tsambos, G. Baumdicker, F. Carlson, J. Cartwright, R. A. Durvasula, A. Kim, B. Y. McKenzie, P. Messer, P. W. Noskova, E. Ortega-Del Vecchyo, D. Struck, T. J. Gravel, S. Gutenkunst, R. N. Ralph, P. L. Schrider, D. R. Siepel, A. Kelleher, J. Kern, A. D. 2019-12-21 doi:10.1101/2019.12.20.885129 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria ]]> https://biorxiv.org/content/10.1101/2019.12.22.885152v1?rss=1 Tan, Y. Z. Zhang, L. Rodrigues, J. Zheng, R. B. Giacometti, S. I. Rosario, A. L. Kloss, B. Dandey, V. P. Wei, H. Brunton, R. Raczkowski, A. M. Athayde, D. Catalao, M. J. Pimentel, M. Clarke, O. B. Lowary, T. L. Archer, M. Niederweis, M. Potter, C. S. Carragher, B. Mancia, F. 2019-12-23 doi:10.1101/2019.12.22.885152 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Structure of the Glutamate-Like Receptor GLR3.2 ligand-binding domain ]]> https://biorxiv.org/content/10.1101/2019.12.23.887497v1?rss=1 Gangwar, S. P. Green, M. Sobolevsky, A. 2019-12-24 doi:10.1101/2019.12.23.887497 Cold Spring Harbor Laboratory Press 2019-12-24 <![CDATA[ Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression ]]> https://biorxiv.org/content/10.1101/2019.12.24.887968v1?rss=1 Aiderus, A. Newberg, J. Y. Guzman-Rojas, L. Contreras-Sandoval, A. M. Meshey, A. L. Jones, D. J. Amaya-Manzanares, F. Rangel, R. Ward, J. M. Lee, S. C. Ban, K. H.-K. Rogers, K. Rogers, S. M. Selvanesan, L. McNoe, L. A. Copeland, N. G. Jenkins, N. A. Tsai, K. Y. Black, M. A. Mann, K. M. Mann, M. B. 2019-12-26 doi:10.1101/2019.12.24.887968 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Hox binding specificity is directed by DNA sequence preferences and differential abilities to engage inaccessible chromatin. ]]> https://biorxiv.org/content/10.1101/2019.12.29.890335v1?rss=1 Bulajic, M. Srivastava, D. Dasen, J. Wichterle, H. Mahony, S. Mazzoni, E. O. 2019-12-30 doi:10.1101/2019.12.29.890335 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ Value and choice as separable, stable representations in orbitofrontal cortex ]]> https://biorxiv.org/content/10.1101/2019.12.31.892109v1?rss=1 Kimmel, D. L. Elsayed, G. F. Cunningham, J. P. Newsome, W. T. 2020-01-02 doi:10.1101/2019.12.31.892109 Cold Spring Harbor Laboratory Press 2020-01-02 <![CDATA[ Programmable and portable CRISPR-Cas transcriptional activation in bacteria ]]> https://biorxiv.org/content/10.1101/2020.01.03.882431v1?rss=1 Ho, H.-I. Fang, J. R. Cheung, J. Wang, H. H. 2020-01-03 doi:10.1101/2020.01.03.882431 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Anti-tumor effects of an Id antagonist with no acquired resistance ]]> https://biorxiv.org/content/10.1101/2020.01.06.894840v1?rss=1 Wojnarowicz, P. M. Escalono, M. G. Huang, Y.-H. Desai, B. Chin, Y. Shah, R. Xu, S. Ouerfelli, O. Soni, R. K. Philip, J. Montrose, D. C. Healey, J. H. Rajasekhar, V. K. Garland, W. A. Norton, L. Rosen, N. Hendrickson, R. C. Zhou, X. K. Iavarone, A. Massague, J. Dannenberg, A. J. Lasorella, A. Benezra, R. 2020-01-06 doi:10.1101/2020.01.06.894840 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ A latent variable approach to decoding neural population activity ]]> https://biorxiv.org/content/10.1101/2020.01.06.896423v1?rss=1 Whiteway, M. R. Averbeck, B. Butts, D. A. 2020-01-07 doi:10.1101/2020.01.06.896423 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Identifying strategies to target the metabolic flexibility of tumours. ]]> https://biorxiv.org/content/10.1101/2020.01.06.896571v1?rss=1 Yuneva, M. Mendez-Lucas, A. Lin, W. Driscoll, P. C. Legrave, N. Novellasdemunt Vilaseca, L. Xie, C. Charles, M. Wilson, Z. Jones, N. P. Rayport, S. G. Rodriguez-Justo, M. Li, V. S. W. MacRae, J. I. Hay, N. Chen, X. 2020-01-07 doi:10.1101/2020.01.06.896571 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ Depletion of the AD risk gene SORL1 selectively impairs neuronal endosomal traffic independent of amyloidogenic APP processing ]]> https://biorxiv.org/content/10.1101/2020.01.06.896670v1?rss=1 Knupp, A. Mishra, S. Martinez, R. Braggin, J. Szabo, M. Hailey, D. W. Small, S. A. Jayadev, S. Young, J. E. 2020-01-06 doi:10.1101/2020.01.06.896670 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Novel genetic features of human and mouse Purkinje cell differentiation defined by comparative transcriptomics. ]]> https://biorxiv.org/content/10.1101/2020.01.07.897371v1?rss=1 Buchholz, D. E. Carroll, T. S. Kocabas, A. Zhu, X. Behesti, H. Faust, P. L. Stalbow, L. Fang, Y. Hatten, M. E. 2020-01-08 doi:10.1101/2020.01.07.897371 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Individual differences among deep neural network models ]]> https://biorxiv.org/content/10.1101/2020.01.08.898288v1?rss=1 Mehrer, J. Spoerer, C. J. Kriegeskorte, N. Kietzmann, T. C. 2020-01-09 doi:10.1101/2020.01.08.898288 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ ECSIT prevents Alzheimer's disease pathology by regulating neuronal mitochondrial ROS and mitophagy ]]> https://biorxiv.org/content/10.1101/2020.01.09.900407v1?rss=1 Lepelley, A. Vaughn, L. S. Staniszewski, A. Zhang, H. Du, F. Koppensteiner, P. Tomljanovic, Z. Carneiro, F. R. Teich, A. F. Ninan, I. Yan, S. S. Postler, T. S. Hayden, M. S. Arancio, O. Ghosh, S. 2020-01-10 doi:10.1101/2020.01.09.900407 Cold Spring Harbor Laboratory Press 2020-01-10 <![CDATA[ Talin Folding; the Tuning Fork of Cellular Mechanotransduction ]]> https://biorxiv.org/content/10.1101/2020.01.10.901991v1?rss=1 Tapia-Rojo, R. Fernandez, J. M. 2020-01-11 doi:10.1101/2020.01.10.901991 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Efficient and accurate inference of microbial trajectories from longitudinal count data ]]> https://biorxiv.org/content/10.1101/2020.01.10.902163v1?rss=1 Joseph, T. A. Pasarkar, A. P. Pe'er, I. 2020-01-11 doi:10.1101/2020.01.10.902163 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Scaling of information in large neural populations reveals signatures of information-limiting correlations ]]> https://biorxiv.org/content/10.1101/2020.01.10.902171v1?rss=1 Kafashan, M. Jaffe, A. Chettih, S. N. Nogueira, R. Arandia-Romero, I. Harvey, C. D. Moreno-Bote, R. Drugowitsch, J. 2020-01-11 doi:10.1101/2020.01.10.902171 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Cortical music selectivity does not require musical training ]]> https://biorxiv.org/content/10.1101/2020.01.10.902189v1?rss=1 Boebinger, D. L. Norman-Haignere, S. V. McDermott, J. H. Kanwisher, N. 2020-01-11 doi:10.1101/2020.01.10.902189 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Neuronal firing and waveform alterations through ictal recruitment in humans ]]> https://biorxiv.org/content/10.1101/2020.01.11.902817v1?rss=1 Merricks, E. M. Smith, E. H. Emerson, R. G. Bateman, L. M. McKhann, G. M. Goodman, R. R. Sheth, S. A. Greger, B. House, P. A. Trevelyan, A. J. Schevon, C. A. 2020-01-13 doi:10.1101/2020.01.11.902817 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Differential contributions of synaptic and intrinsic inhibitory currents to parsing via flexible phase-locking in neural oscillators ]]> https://biorxiv.org/content/10.1101/2020.01.11.902858v1?rss=1 Pittman-Polletta, B. R. Wang, Y. Stanley, D. A. Schroeder, C. E. Whittington, M. A. Kopell, N. J. 2020-01-13 doi:10.1101/2020.01.11.902858 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ DIP/Dpr interactions and the evolutionary design of specificity in protein families ]]> https://biorxiv.org/content/10.1101/2020.01.13.899120v1?rss=1 Sergeeva, A. P. Katsamba, P. S. Cosmanescu, F. Brewer, J. J. Ahlsen, G. Mannepalli, S. Shapiro, L. Honig, B. 2020-01-14 doi:10.1101/2020.01.13.899120 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge ]]> https://biorxiv.org/content/10.1101/2020.01.13.904722v1?rss=1 Sieberts, S. K. Schaff, J. Duda, M. Pataki, B. A. Sun, M. Snyder, P. Daneault, J.-F. Parisi, F. Costante, G. Rubin, U. Banda, P. Chae, Y. Neto, E. C. Dorsey, R. Aydın, Z. Chen, A. Elo, L. L. Espino, C. Glaab, E. Goan, E. Golabchi, F. N. Görmez, Y. Jaakkola, M. K. Jonnagaddala, J. KLEn, R. Li, D. McDaniel, C. Perrin, D. Rad, N. M. Rainaldi, E. Sapienza, S. Schwab, P. Shokhirev, N. Venäläinen, M. S. Vergara-Diaz, G. Zhang, Y. Parkinson's Disease Digital Biomarker Challenge Consortium, Wang, Y. Guan, Y. Brunner, D. Bonato, P. Mangravite, L. M. Omberg 2020-01-16 doi:10.1101/2020.01.13.904722 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Investigating the Genetic Architecture of Non-Cognitive Skills Using GWAS-by-Subtraction ]]> https://biorxiv.org/content/10.1101/2020.01.14.905794v1?rss=1 Demange, P. A. Malanchini, M. Mallard, T. T. Biroli, P. Cox, S. R. Grotzinger, A. D. Tucker-Drob, E. M. Abdellaoui, A. Arseneault, L. Caspi, A. Corcoran, D. Domingue, B. Mitchell, C. van Bergen, E. Boomsma, D. I. Harris, K. M. Ip, H. F. Moffitt, T. E. Poulton, R. Prinz, J. Sugden, K. Wertz, J. Williams, B. de Zeeuw, E. L. Belsky, D. W. Harden, K. P. Nivard, M. G. 2020-01-15 doi:10.1101/2020.01.14.905794 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Bioluminescence dynamics in single germinating bacterial spores reveal metabolic heterogeneity ]]> https://biorxiv.org/content/10.1101/2020.01.14.906875v1?rss=1 Frentz, Z. Dworkin, J. 2020-01-15 doi:10.1101/2020.01.14.906875 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Clustered γ-Protocadherins Regulate Cortical Interneuron Programmed Cell Death. ]]> https://biorxiv.org/content/10.1101/2020.01.14.906941v1?rss=1 Mancia Leon, W. R. Spatazza, J. Rakela, B. Chatterjee, A. Pande, V. Maniatis, T. Hasenstaub, A. R. Stryker, M. P. Alvarez-Buylla, A. 2020-01-15 doi:10.1101/2020.01.14.906941 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ fMRI-guided white matter connectivity in fluid and crystallized cognitive abilities in healthy adults ]]> https://biorxiv.org/content/10.1101/2020.01.15.907782v1?rss=1 Gazes, Y. Sakhardande, J. Mensing, A. Razlighi, Q. Ohkawa, A. Pleshkevich, M. Luo, L. Habeck, C. 2020-01-16 doi:10.1101/2020.01.15.907782 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network ]]> https://biorxiv.org/content/10.1101/2020.01.15.908236v1?rss=1 McKenzie, P. F. Eaton, D. A. R. 2020-01-16 doi:10.1101/2020.01.15.908236 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Relating the past with the present: Information integration and segregation during ongoing narrative processing ]]> https://biorxiv.org/content/10.1101/2020.01.16.908731v1?rss=1 Chang, C. H. C. Lazaridi, C. Yeshurun, Y. Norman, K. A. Hasson, U. 2020-01-17 doi:10.1101/2020.01.16.908731 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ A standardized and reproducible method to measure decision-making in mice ]]> https://biorxiv.org/content/10.1101/2020.01.17.909838v1?rss=1 The International Brain Laboratory Aguillon, V. Angelaki, D. Bayer, H. M. Bonacchi, N. Carandini, M. Cazettes, F. Churchland, A. K. Chapuis, G. Dan, Y. Dewitt, E. Faulkner, M. Hamish, F. Haetzel, L. Hausser, M. Hofer, S. Hu, F. Khanal, A. Krasniak, C. Laranjeira, I. Mainen, Z. Meijer, G. Miska, N. Mrsic-Flogel, T. Noel, J.-P. Pan Vazquez, A. Sanders, J. Socha, K. Terry, R. Urai, A. Vergara, H. M. Wells, M. Wilson, C. Witten, I. Wool, L. Zador, A. 2020-01-17 doi:10.1101/2020.01.17.909838 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ A role for reward sensitivity in the serotonergic modulation of impulsivity ]]> https://biorxiv.org/content/10.1101/2020.01.17.910778v1?rss=1 Desrochers, S. S. Lesko, E. K. Magalong, V. M. Balsam, P. D. Nautiyal, K. M. 2020-01-18 doi:10.1101/2020.01.17.910778 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Network Insights into Improving Drug Target Inference Algorithms ]]> https://biorxiv.org/content/10.1101/2020.01.17.910885v1?rss=1 Wang, M. Noh, H. Mochan, E. Shoemaker, J. E. 2020-01-18 doi:10.1101/2020.01.17.910885 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ A Simultaneous Methylome and Proteome Quantitative Workflow for Complex Samples ]]> https://biorxiv.org/content/10.1101/2020.01.17.910943v1?rss=1 Robinson, A. E. Binek, A. Holewinski, R. Venkatraman, V. Parker, S. J. Basisty, N. Xie, X. Lund, P. J. Saxena, G. Mato, J. M. Garcia, B. A. Schilling, B. Lu, S. C. Van Eyk, J. E. 2020-01-18 doi:10.1101/2020.01.17.910943 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ Surveying Brain Tumor Heterogeneity by Single-Cell RNA Sequencing of Multi-sector Biopsies ]]> https://biorxiv.org/content/10.1101/2020.01.19.911701v1?rss=1 Yu, K. Hu, Y. Wu, F. Guo, Q. Qian, Z. Hu, W. Chen, J. Wang, K. Fan, X. Wu, X. Rasko, J. E. Fan, X. Iavarone, A. Jiang, T. Tang, F. Su, X.-D. 2020-01-19 doi:10.1101/2020.01.19.911701 Cold Spring Harbor Laboratory Press 2020-01-19 <![CDATA[ GPCR-mediated clearance of tau in post-synaptic compartments attenuates tau pathology in vivo ]]> https://biorxiv.org/content/10.1101/2020.01.21.914135v1?rss=1 Myeku, N. Schaler, A. W. Runyan, A. M. Fowler, S. L. Figueroa, H. Y. Shioda, S. Santa Maria, I. Duff, K. E. 2020-01-23 doi:10.1101/2020.01.21.914135 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Medical data and machine learning improve power of stroke genome-wide association studies. ]]> https://biorxiv.org/content/10.1101/2020.01.22.915397v1?rss=1 Thangaraj, P. M. Tatonetti, N. 2020-01-23 doi:10.1101/2020.01.22.915397 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Differentiating between integration and non-integration strategies in perceptual decision making ]]> https://biorxiv.org/content/10.1101/2020.01.24.918169v1?rss=1 Stine, G. M. Zylberberg, A. Ditterich, J. Shadlen, M. N. 2020-01-25 doi:10.1101/2020.01.24.918169 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ From SARS-CoV to Wuhan 2019-nCoV: Will History Repeat Itself? ]]> https://biorxiv.org/content/10.1101/2020.01.24.919241v1?rss=1 Chen, Z. Zhang, W. Lu, Y. Guo, C. Guo, Z. Liao, C. Zhang, X. Zhang, Y. Han, X. Li, Q. Lipkin, W. I. Lu, J. 2020-01-25 doi:10.1101/2020.01.24.919241 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ Generation of cell-free matrices that support human NK cell migration and differentiation ]]> https://biorxiv.org/content/10.1101/2020.01.26.920116v1?rss=1 Lee, B. J. Mace, E. M. 2020-01-26 doi:10.1101/2020.01.26.920116 Cold Spring Harbor Laboratory Press 2020-01-26 <![CDATA[ High fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo ]]> https://biorxiv.org/content/10.1101/2020.01.26.920256v1?rss=1 Xie, M. Adam, Y. Fan, L. Boehm, U. L. Kinsella, I. A. Zhou, D. Paninski, L. Cohen, A. E. 2020-01-27 doi:10.1101/2020.01.26.920256 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ Rapid event-related, BOLD, NHP: choose two out of three ]]> https://biorxiv.org/content/10.1101/2020.01.27.919555v1?rss=1 Pelekanos, V. Mok, R. Joly, O. Ainsworth, M. Kyriazis, D. Kelly, M. Bell, A. Kriegeskorte, N. 2020-01-28 doi:10.1101/2020.01.27.919555 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Injectable therapeutic organoids using sacrificial hydrogels ]]> https://biorxiv.org/content/10.1101/2020.01.27.922112v1?rss=1 Rossen, N. S. Anandakumaran, P. N. zur Nieden, R. Lo, K. Luo, W. Park, C. Huyan, C. Fu, Q. Song, Z. Singh-Moon, R. P. Chung, J. Goldenberg, J. Sampat, N. Harimoto, T. Bajakian, D. Gillette, B. M. Sia, S. K. 2020-01-28 doi:10.1101/2020.01.27.922112 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Distinct Predictive Patterns of Antidepressant Response to Sertraline, Placebo and Bupropion using Pre-Treatment Reward Processing as examined through Functional MRI and Deep Learning: Key Results from the EMBARC Study ]]> https://biorxiv.org/content/10.1101/2020.01.28.923821v1?rss=1 Nguyen, K. P. Chin Fatt, C. Treacher, A. Mellema, C. Cooper, C. Jha, M. Kurian, B. Fava, M. McGrath, P. J. Adams, P. Weissman, M. Phillips, M. L. Trivedi, M. H. Montillo, A. 2020-01-29 doi:10.1101/2020.01.28.923821 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Dynamic landscape of protein occupancy across the Escherichia coli chromosome ]]> https://biorxiv.org/content/10.1101/2020.01.29.924811v1?rss=1 Freddolino, P. Goss, T. J. Amemiya, H. M. Tavazoie, S. 2020-01-30 doi:10.1101/2020.01.29.924811 Cold Spring Harbor Laboratory Press 2020-01-30 <![CDATA[ Skill-specific changes in cortical preparatory activity during motor learning ]]> https://biorxiv.org/content/10.1101/2020.01.30.919894v1?rss=1 Sun, X. O'Shea, D. J. Golub, M. D. Trautmann, E. M. Vyas, S. Ryu, S. I. Shenoy, K. V. 2020-01-31 doi:10.1101/2020.01.30.919894 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis ]]> https://biorxiv.org/content/10.1101/2020.01.30.922310v1?rss=1 Rabadan, R. Mohamedi, Y. Rubin, U. Chu, T. Elliott, O. Arnes, L. Cal, S. Obaya, A. J. Levine, A. J. Camara, P. G. 2020-01-31 doi:10.1101/2020.01.30.922310 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Nucleotide Analogues as Inhibitors of Viral Polymerases ]]> https://biorxiv.org/content/10.1101/2020.01.30.927574v1?rss=1 Ju, J. Kumar, S. Li, X. Jockusch, S. Russo, J. J. 2020-01-31 doi:10.1101/2020.01.30.927574 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ A Disinhibitory Circuit for Contextual Modulation in Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2020.01.31.929166v1?rss=1 Keller, A. J. Roth, M. M. Caudill, M. Dipoppa, M. Miller, K. D. Scanziani, M. 2020-01-31 doi:10.1101/2020.01.31.929166 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Time cells in the human hippocampus and entorhinal cortex support episodic memory ]]> https://biorxiv.org/content/10.1101/2020.02.03.932749v1?rss=1 Umbach, G. Kantak, P. Jacobs, J. Kahana, M. J. Pfeiffer, B. E. Sperling, M. Lega, B. 2020-02-04 doi:10.1101/2020.02.03.932749 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Quantification of the pace of biological aging in humans through a blood test: a DNA methylation algorithm ]]> https://biorxiv.org/content/10.1101/2020.02.05.927434v1?rss=1 Belsky, D. W. Caspi, A. Arseneault, L. Corcoran, D. L. Hannon, E. Harrington, H. L. Hartmann-Rasmussen, L. J. Houts, R. Huffman, K. Kraus, W. E. Mill, J. Pieper, C. Prinz, J. Poulton, R. Sugden, K. Williams, B. Moffitt, T. E. 2020-02-07 doi:10.1101/2020.02.05.927434 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ PKMζ traces hippocampal LTP maintenance and spatial long-term memory ]]> https://biorxiv.org/content/10.1101/2020.02.05.936146v1?rss=1 Hsieh, C. Tsokas, P. Chung, A. Garcia-Jou, C. Lesburgueres, E. Burghardt, N. S. Denny, C. A. Flores-Obando, R. E. Valencia, L. M. R. Bergold, P. Cottrell, J. E. Fenton, A. A. Sacktor, T. C. 2020-02-07 doi:10.1101/2020.02.05.936146 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Visual mental imagery engages the left fusiform gyrus, but not the early visual cortex: a meta-analysis of neuroimaging evidence ]]> https://biorxiv.org/content/10.1101/2020.02.06.937151v1?rss=1 Spagna, A. Hajhajate, D. Liu, J. Bartolomeo, P. 2020-02-07 doi:10.1101/2020.02.06.937151 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Genetic Adaptation in New York City Rats ]]> https://biorxiv.org/content/10.1101/2020.02.07.938969v1?rss=1 Harpak, A. Garud, N. Rosenberg, N. A. Petrov, D. A. Combs, M. Pennings, P. S. Munshi-South, J. 2020-02-08 doi:10.1101/2020.02.07.938969 Cold Spring Harbor Laboratory Press 2020-02-08 <![CDATA[ Vascular-Derived SPARC and SerpinE1 Regulate Interneuron Tangential Migration and Accelerate Functional Maturation of Human Stem Cell-Derived Interneurons ]]> https://biorxiv.org/content/10.1101/2020.02.07.939298v1?rss=1 Genestine, M. Ambriz, D. Crabtree, G. W. Molotkova, A. Quintero, M. Mela, A. Biswas, S. Canoll, P. Hargus, G. Agalliu, D. Gogos, J. A. Au, E. 2020-02-09 doi:10.1101/2020.02.07.939298 Cold Spring Harbor Laboratory Press 2020-02-09 <![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[ RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules ]]> https://biorxiv.org/content/10.1101/2020.02.07.939645v1?rss=1 Manivannan, P. Siddiqui, M. A. Malathi, K. 2020-02-09 doi:10.1101/2020.02.07.939645 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus ]]> https://biorxiv.org/content/10.1101/2020.02.10.942748v1?rss=1 Patino-Galindo, J. A. Filip, I. AlQuraishi, M. Rabadan, R. 2020-02-18 doi:10.1101/2020.02.10.942748 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2020.02.11.941351v1?rss=1 Lopez de Maturana, E. Rodriguez, J. Alonso, L. Lao, O. Molina-Montes, E. Martin-Antoniano, I. Gomez-Rubio, P. Lawlor, R. Carrato, A. Hidalgo, M. Iglesias, M. Molero, X. Lohr, M. Michalski, C. Perea, J. O'Rorke, M. Barbera, V. Tardon, A. Farre, A. Munoz-Bellvis, L. Crnogorac-Jurcevic, T. Dominguez-Munoz, E. Gress, T. Greenhaf, W. Sharp, L. Arnes, L. Cecchini, L. Balsells, J. Costello, E. Ilzarbe, L. Kleeff, J. Kong, B. Marquez, M. Mora, J. O'Driscoll, D. Scarpa, A. Ye, W. Yu, J. Investigators, P. Garcia-Closas, M. Kogevinas, M. Rothman, N. Silverman, D. 2020-02-12 doi:10.1101/2020.02.11.941351 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Bile acid composition regulates the manganese transporter Slc30a10 in intestine ]]> https://biorxiv.org/content/10.1101/2020.02.11.944124v1?rss=1 Ahmad, T. R. Higuchi, S. Bertaggia, E. Hung, A. Shanmugarajah, N. Guilz, N. C. Gamarra, J. R. Haeusler, R. A. 2020-02-12 doi:10.1101/2020.02.11.944124 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ F-box protein MEC-15 promotes microtubule stability and neurite growth by antagonizing the HSP90 chaperone network in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.02.13.944967v1?rss=1 Zheng, C. Atlas, E. Lee, H. M. T. Jao, S. L. J. Nguyen, K. C. Q. Hall, D. H. Chalfie, M. 2020-02-13 doi:10.1101/2020.02.13.944967 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Parallel processing of sensory cue and spatial information in the Dentate Gyrus ]]> https://biorxiv.org/content/10.1101/2020.02.13.947903v1?rss=1 Tuncdemir, S. N. Grosmark, A. D. Turi, G. Shank, A. Bowler, J. Ordek, G. Losonczy, A. Hen, R. Lacefield, C. O. 2020-02-13 doi:10.1101/2020.02.13.947903 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[ Alterations in the intrinsic properties of striatal cholinergic interneurons after dopamine lesion and chronic L-DOPA ]]> https://biorxiv.org/content/10.1101/2020.02.14.950022v1?rss=1 Choi, S. J. Ma, T. Ding, Y. Cheung, T. Joshi, N. Sulzer, D. Mosharov, E. Kang, U. J. 2020-02-15 doi:10.1101/2020.02.14.950022 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ A Bayesian nonparametric approach to super-resolution single-molecule localization ]]> https://biorxiv.org/content/10.1101/2020.02.15.950873v1?rss=1 Gabitto, M. I. Marie-Nellie, H. Pakman, A. Pataki, A. Darzacq, X. Jordan, M. 2020-02-15 doi:10.1101/2020.02.15.950873 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ MouseCircuits.org: An online repository to guide the circuit era of disordered affect ]]> https://biorxiv.org/content/10.1101/2020.02.16.951608v1?rss=1 Anderson, K. R. Dumitriu, D. 2020-02-17 doi:10.1101/2020.02.16.951608 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Efficient coding of numbers explains decision bias and noise ]]> https://biorxiv.org/content/10.1101/2020.02.18.942938v1?rss=1 Prat-Carrabin, A. Woodford, M. 2020-02-19 doi:10.1101/2020.02.18.942938 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Integrated analysis of the aging brain transcriptome and proteome in tauopathy ]]> https://biorxiv.org/content/10.1101/2020.02.19.954578v1?rss=1 Mangleburg, C. G. Wu, T. Yalamanchili, H. K. Guo, C. Hsieh, Y.-C. Duong, D. M. Dammer, E. B. De Jager, P. L. Seyfried, N. T. Liu, Z. Shulman, J. M. 2020-02-20 doi:10.1101/2020.02.19.954578 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Genetic Variants and Functional Pathways Associated with Resilience to Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2020.02.19.954651v1?rss=1 0.42) nor associated with APOE (p-values>0.13). In single variant analyses, we observed a genome-wide significant locus among participants with normal cognition on chromosome 18 upstream of ATP8B1 (index SNP rs2571244, MAF=0.08, p=2.3x10-8). The top variant at this locus (rs2571244) was significantly associated with methylation in prefrontal cortex tissue at multiple CpG sites, including one just upstream of ATPB81 (cg19596477; p=2x10-13). Overall, this comprehensive genetic analysis of resilience implicates a putative role of vascular risk, metabolism, and mental health in protection from the cognitive consequences of neuropathology, while also providing evidence for a novel resilience gene along the bile acid metabolism pathway. Furthermore, the genetic architecture of resilience appears to be distinct from that of clinical AD, suggesting that a shift in focus to molecular contributors to resilience may identify novel pathways for therapeutic targets. ]]> Dumitrescu, L. Mahoney, E. R. Mukherjee, S. Lee, M. L. Bush, W. S. Engelman, C. D. Lu, Q. Fardo, D. W. Trittschuh, E. H. Mez, J. Kaczorowski, C. Hernandez Saucedo, H. Widaman, K. F. Buckley, R. Properzi, M. Mormina, E. Yang, H.-S. Harrison, T. Hedden, T. Nho, K. Andrews, S. J. Tommet, D. Hadad, N. Sanders, R. E. Ruderfer, D. M. Gifford, K. A. Moore, A. M. Cambronero, F. Zhong, X. Raghavan, N. S. Vardarajan, B. The Alzheimer's Disease Neuroimaging Initiative (ADNI), Alzheimer's Disease Genetics Consortium (ADGC), A4 Study Team, Pericak-Vance, M. A. Farre 2020-02-21 doi:10.1101/2020.02.19.954651 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ A single gene expressed in fibroblastic reticular cells predicts response to cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.02.19.955666v1?rss=1 Biasci, D. Tavare, S. Thaventhiran, J. 2020-02-21 doi:10.1101/2020.02.19.955666 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ CK1 Delta Is an mRNA Cap-Associated Protein That Drives Translation Initiation and Tumor Growth ]]> https://biorxiv.org/content/10.1101/2020.02.20.955229v1?rss=1 Pal, I. Grilo, A. M. S. Berchowitz, L. E. DasSharma, S. Mundi, P. S. Ali, A. M. Martin, M. L. Safari, M. Scotto, L. Malkovskiy, E. Sawas, A. Mukherjee, S. O'Connor, O. A. Jovanovic, M. Deng, C. 2020-02-20 doi:10.1101/2020.02.20.955229 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Phe-Gly Motifs Drive Fibrillization of TDP-43's Prion-Like Domain Droplets ]]> https://biorxiv.org/content/10.1101/2020.02.20.957969v1?rss=1 Pantoja-Uceda, D. Stuani, C. Laurents, D. V. McDermott, A. E. Buratti, E. Mompean, M. 2020-02-21 doi:10.1101/2020.02.20.957969 Cold Spring Harbor Laboratory Press 2020-02-21 <![CDATA[ Metabolic defects cause hyperactive mitochondria and Parkinson disease-like traits ]]> https://biorxiv.org/content/10.1101/2020.02.20.958322v1?rss=1 Mor, D. E. Sohrabi, S. Kaletsky, R. Keyes, W. Kalia, V. Miller, G. W. Murphy, C. T. 2020-02-22 doi:10.1101/2020.02.20.958322 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ An autoimmune disease risk variant has a trans master regulatory effect mediated by IRF1 under immune stimulation ]]> https://biorxiv.org/content/10.1101/2020.02.21.959734v1?rss=1 Brandt, M. K. Kim-Hellmuth, S. Ziosi, M. Gokden, A. Wolman, A. Lam, N. Recinos, Y. Hornung, V. K. Schumacher, J. Lappalainen, T. 2020-02-24 doi:10.1101/2020.02.21.959734 Cold Spring Harbor Laboratory Press 2020-02-24 <![CDATA[ An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors' CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design ]]> https://biorxiv.org/content/10.1101/2020.02.25.963546v1?rss=1 Herst, C. V. Burkholz, S. Sidney, J. Sette, A. Harris, P. E. Massey, S. Brazel, T. Cunha-Neto, E. Rosa, D. S. Chao, W. C. H. Carback, R. T. Hodge, T. Wang, L. Ciotlos, S. Lloyd, P. Rubsamen, R. M. 2020-02-27 doi:10.1101/2020.02.25.963546 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ A virion-based assay for glycoprotein thermostability reveals key determinants of filovirus entry and its inhibition ]]> https://biorxiv.org/content/10.1101/2020.02.25.965772v1?rss=1 Bortz, R. H. Wong, A. C. Grodus, M. G. Recht, H. Pulanco, M. C. Lasso, G. Anthony, S. J. Mittler, E. Jangra, R. K. Chandran, K. 2020-02-26 doi:10.1101/2020.02.25.965772 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ GOT1 Inhibition Primes Pancreatic Cancer for Ferroptosis through the Autophagic Release of Labile Iron ]]> https://biorxiv.org/content/10.1101/2020.02.28.970228v1?rss=1 Kremer, D. M. Nelson, B. S. Lin, L. Yarosz, E. Halbrook, C. J. Kerk, S. A. Sajjakulnukit, P. Myers, A. Thurston, G. Hou, S. Carpenter, E. S. Andren, A. Nwosu, Z. Cusmano, N. Wisner, S. Ramos, J. Gao, T. Sastra, S. A. Palermo, C. F. Badgley, M. A. Zhang, L. Asara, J. M. Pasca di Magliano, M. Shah, Y. M. Crawford, H. C. Olive, K. P. Lyssiotis, C. A. 2020-02-29 doi:10.1101/2020.02.28.970228 Cold Spring Harbor Laboratory Press 2020-02-29 <![CDATA[ Functional modeling of NMIHBA-causing PRUNE1 variants reveals a requirement for its exopolyphosphatase activity. ]]> https://biorxiv.org/content/10.1101/2020.03.02.973909v1?rss=1 A (p.Arg128Gln), c.520G>T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment. ]]> Nistala, H. Dronzek, J. Gonzaga-Jauregui, C. Man Chim, S. Rajamani, S. Nuwayhid, S. Delgado, D. Burke, E. Karaca, E. Franklin, M. C. Sarangapani, P. Podgorski, M. Tang, Y. Dominguez, M. G. Withers, M. Deckelbaum, R. A. Scheonherr, C. J. Gahl, W. A. Malicdan, M. C. Zambrowicz, B. Gale, N. W. Gibbs, R. A. Chung, W. K. Lupski, J. R. Economides, A. N. 2020-03-04 doi:10.1101/2020.03.02.973909 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ A neural code of egocentric spatial information in human medial temporal lobe ]]> https://biorxiv.org/content/10.1101/2020.03.03.973131v1?rss=1 Kunz, L. Brandt, A. Reinacher, P. C. Staresina, B. P. Reifenstein, E. T. Weidemann, C. T. Herweg, N. A. Tsitsiklis, M. Kempter, R. Kahana, M. J. Schulze-Bonhage, A. Jacobs, J. 2020-03-05 doi:10.1101/2020.03.03.973131 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Hippocampal CA2 ripples recruit social replay and promote social memory ]]> https://biorxiv.org/content/10.1101/2020.03.03.975599v1?rss=1 Oliva, A. Fernandez-Ruiz, A. Leroy, F. Siegelbaum, S. A. 2020-03-05 doi:10.1101/2020.03.03.975599 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Effects of arousal and movement on secondary somatosensory and visual thalamus ]]> https://biorxiv.org/content/10.1101/2020.03.04.977348v1?rss=1 Petty, G. H. Kinnischtzke, A. Hong, Y. K. Bruno, R. M. 2020-03-05 doi:10.1101/2020.03.04.977348 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ An inducible CRISPR-interference library for genetic interrogation of Saccharomyces cerevisiae biology ]]> https://biorxiv.org/content/10.1101/2020.03.05.978619v1?rss=1 Momen-Roknabadi, A. Oikonomou, P. Tavazoie, S. 2020-03-05 doi:10.1101/2020.03.05.978619 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ The paradoxical effects of K+ channel gain-of-function are mediated by GABAergic neuron hypoexcitability and hyperconnectivity. ]]> https://biorxiv.org/content/10.1101/2020.03.05.978841v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@110d6e1org.highwire.dtl.DTLVardef@8b63ddorg.highwire.dtl.DTLVardef@14972a9org.highwire.dtl.DTLVardef@106be1c_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG ]]> Shore, A. N. Colombo, S. Tobin, W. F. Petri, S. Cullen, E. R. Dominguez, S. Bostick, C. Beaumont, M. Williams, D. Khodagholy, D. Yang, M. Lutz, C. M. Peng, Y. Gelinas, J. N. Goldstein, D. B. Boland, M. J. Frankel, W. N. Weston, M. C. 2020-03-06 doi:10.1101/2020.03.05.978841 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Novel Bayesian transcriptome-wide association study method leveraging both cis- and trans- eQTL information through summary statistics ]]> https://biorxiv.org/content/10.1101/2020.03.05.979187v1?rss=1 Luningham, J. M. Chen, J. Tang, S. De Jager, P. Bennett, D. A. Buchman, A. S. Yang, J. 2020-03-06 doi:10.1101/2020.03.05.979187 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Ancestry adjustment improves genome-wide estimates of regional intolerance ]]> https://biorxiv.org/content/10.1101/2020.03.05.979203v1?rss=1 hayeck, t. j. Stong, N. Baugh, E. Dhindsa, R. Turner, T. N. Malakar, A. Duan, Y. Ionita-Laza, I. Goldstein, D. Andrew Allen, A. S. 2020-03-06 doi:10.1101/2020.03.05.979203 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas ]]> https://biorxiv.org/content/10.1101/2020.03.10.985226v1?rss=1 Oldrini, B. Vaquero-Siguero, N. Mu, Q. Kroon, P. Zhang, Y. Galan-Ganga, M. Bao, Z. Wang, Z. Liu, H. Sa, J. K. Zhao, J. Kim, H. Rodriguez-Perales, S. Nam, D.-H. Verhaak, R. G. Rabadan, R. Jiang, T. Wang, J. Squatrito, M. 2020-03-11 doi:10.1101/2020.03.10.985226 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Inhibition and down regulation of the serotonin transporter contribute to the progression of degenerative mitral regurgitation ]]> https://biorxiv.org/content/10.1101/2020.03.10.985382v1?rss=1 Levy, R. J. Fitzpatrick, E. Castillero, E. Shukla,, H. J. Inamdar,, V. V. Aghali, A. E. Grau, J. B. Rioux, N. Salvati, E. Keeney, S. J. Nissim, I. Gorman, R. C. C. Rauova, L. Stachelek, S. J. Brown, C. R. Krieger, A. M. Ferrari, G. 2020-03-11 doi:10.1101/2020.03.10.985382 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Perceived ambiguity of social interactions increases coupling between frontal and temporal nodes of the social brain ]]> https://biorxiv.org/content/10.1101/2020.03.11.987792v1?rss=1 Ainsworth, M. Sallet, J. Joly, O. Kriegeskorte, N. Duncan, J. Schüffelgen, U. Rushworth, M. F. Bell, A. H. 2020-03-13 doi:10.1101/2020.03.11.987792 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase ]]> https://biorxiv.org/content/10.1101/2020.03.12.989186v1?rss=1 Ju, J. Li, X. Kumar, S. Jockusch, S. Chien, M. Tao, C. Morozova, I. Kalachikov, S. Kirchdoerfer, R. Russo, J. J. 2020-03-14 doi:10.1101/2020.03.12.989186 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[ Establishing cell-intrinsic limitations in cell cycle progression controls graft growth and promotes differentiation of pancreatic endocrine cells ]]> https://biorxiv.org/content/10.1101/2020.03.13.990812v1?rss=1 Sui, L. Egli, D. M. Xin, Y. Georgieva, D. C. Diedenhofen, G. Haataja, L. Su, Q. Wang, Y. Zuccaro, M. Kim, J. Fu, J. Xing, Y. Baum, D. Arvan, P. Barbetti, F. Kleiner, S. Oberholzer, J. Goland, R. 2020-03-14 doi:10.1101/2020.03.13.990812 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Human dorsal anterior cingulate neurons signal conflict by amplifying task-relevant information ]]> https://biorxiv.org/content/10.1101/2020.03.14.991745v1?rss=1 Ebitz, B. Smith, E. Horga, G. Schevon, C. Yates, M. McKhann, G. Botvinick, M. Sheth, S. Hayden, B. 2020-03-15 doi:10.1101/2020.03.14.991745 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Multiplex single-molecule kinetics of nanopore-coupled polymerases ]]> https://biorxiv.org/content/10.1101/2020.03.15.993071v1?rss=1 Palla, M. Punthambaker, S. Stranges, P. B. Vigneault, F. Nivala, J. Wiegand, D. J. Ayer, A. Craig, T. Gremyachinskiy, D. Franklin, H. Sun, S. Pollard, J. Trans, A. Arnold, C. Schwab, C. Mcgaw, C. Sarvabhowman, P. Dalal, D. Thai, E. Amato, E. Lederman, I. Taing, M. Kelley, S. Qwan, A. Fuller, C. W. Roever, S. Church, G. M. 2020-03-16 doi:10.1101/2020.03.15.993071 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ p53 plays a central role in lymphatic anomalies ]]> https://biorxiv.org/content/10.1101/2020.03.18.992784v1?rss=1 Mylavarapu, R. Kulikauskas, M. Dierkes, C. Finlon, J. Sobhani, N. Stevens, W. Mangette, M. Arbab, F. Box, N. F. Muley, A. Shawber, C. Lovell, M. Kiefer, F. Tamburini, B. Terzian, T. 2020-03-20 doi:10.1101/2020.03.18.992784 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase ]]> https://biorxiv.org/content/10.1101/2020.03.18.997585v1?rss=1 Chien, M. Anderson, T. K. Jockusch, S. Tao, C. Kumar, S. Li, X. Russo, J. J. Kirchdoerfer, R. Ju, J. 2020-03-20 doi:10.1101/2020.03.18.997585 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ YASS: Yet Another Spike Sorter applied to large-scale multi-electrode array recordings in primate retina ]]> https://biorxiv.org/content/10.1101/2020.03.18.997924v1?rss=1 500 electrodes; open source code can be found at https://github.com/paninski-lab/yass. ]]> Lee, J. Mitelut, C. Shokri, H. Kinsella, I. Dethe, N. Wu, S. Li, K. Reyes, E. B. Turcu, D. Batty, E. Kim, Y. J. Brackbill, N. Kling, A. Goetz, G. Chichilnisky, E. J. Carlson, D. Paninski, L. 2020-03-20 doi:10.1101/2020.03.18.997924 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance ]]> https://biorxiv.org/content/10.1101/2020.03.19.997213v1?rss=1 Barbeira, A. N. Liang, Y. Bonazzola, R. Wang, G. Wheeler, H. E. Melia, O. J. Aguet, F. The GTEx Consortium, Ardlie, K. G. Wen, X. Im, H. K. 2020-03-20 doi:10.1101/2020.03.19.997213 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ CD56 regulates human NK cell cytotoxicity through Pyk2 ]]> https://biorxiv.org/content/10.1101/2020.03.19.998427v1?rss=1 Gunesch, J. Dixon, A. L. Ebrahim, T. Berrien-Elliott, M. Tatineni, S. Kumar, T. Solloa, E. H. Fehniger, T. A. Mace, E. 2020-03-20 doi:10.1101/2020.03.19.998427 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Transcriptional mediators of treatment resistance in lethal prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.03.19.998450v1?rss=1 He, M. X. Cuoco, M. S. Crowdis, J. Bosma-Moody, A. Zhang, Z. Bi, K. Kanodia, A. Su, M.-J. Rodman, C. DelloStritto, L. Shah, P. Burke, K. P. Izar, B. Bakouny, Z. Tewari, A. K. Liu, D. Camp, S. Y. Vokes, N. I. Park, J. Vigneau, S. Fong, L. Rozenblatt-Rosen, O. Regev, A. Rotem, A. Taplin, M.-E. Van Allen, E. M. 2020-03-20 doi:10.1101/2020.03.19.998450 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ The mid-lateral cerebellum is necessary for reinforcement learning ]]> https://biorxiv.org/content/10.1101/2020.03.20.000190v1?rss=1 Sendhilnathan, N. Goldberg, M. E. 2020-03-21 doi:10.1101/2020.03.20.000190 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ Noise ceiling on the crossvalidated performance of reweighted models of representational dissimilarity: Addendum to Khaligh-Razavi & Kriegeskorte (2014) ]]> https://biorxiv.org/content/10.1101/2020.03.23.003046v1?rss=1 Storrs, K. R. Khaligh-Razavi, S.-M. Kriegeskorte, N. 2020-03-25 doi:10.1101/2020.03.23.003046 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Methylation Data Processing Protocol & Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage ]]> https://biorxiv.org/content/10.1101/2020.03.24.005264v1?rss=1 Arockiaraj, A. I. Liu, D. Shaffer, J. R. Koleck, T. A. Crago, E. A. Weeks, D. Conley, Y. P. 2020-03-25 doi:10.1101/2020.03.24.005264 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Unilateral vocal nerve resection alters neurogenesis in the avian song system in a region-specific manner ]]> https://biorxiv.org/content/10.1101/2020.03.24.005330v1?rss=1 Aronowitz, J. V. Perez, A. O'Brien, C. Aziz, S. Rodriguez, E. Wasner, K. Ribeiro, S. Green, D. Faruk, F. Pytte, C. 2020-03-24 doi:10.1101/2020.03.24.005330 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ Whole Genome De Novo Variant Identification with FreeBayes and Neural Network Approaches ]]> https://biorxiv.org/content/10.1101/2020.03.24.994160v1?rss=1 Richter, F. Morton, S. Qi, H. Kitaygorodksy, A. Wang, J. Homsy, J. DePalma, S. Patel, N. Gelb, B. D. Seidman, J. G. Seidman, C. E. Shen, Y. 2020-03-25 doi:10.1101/2020.03.24.994160 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ EASE: EM-Assisted Source Extraction from calcium imaging data ]]> https://biorxiv.org/content/10.1101/2020.03.25.007468v1?rss=1 Zhou, P. Reimer, J. Zhou, D. Pasarkar, A. Kinsella, I. A. Froudarakis, E. Yatsenko, D. Fahey, P. Bodor, A. Buchanan, J. Bumbarger, D. J. Mahalingam, G. Torres, R. Dorkenwald, S. Ih, D. Lee, K. Liu, R. Macrina, T. Silversmith, W. Wu, J. Wong, W. Macarico da Costa, N. Reid, R. C. Tolias, A. Paninski, L. 2020-03-25 doi:10.1101/2020.03.25.007468 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ POMC neurons functional heterogeneity relies on mTORC1 signaling ]]> https://biorxiv.org/content/10.1101/2020.03.25.007765v1?rss=1 Saucisse, N. Mazier, W. Simon, V. Binder, E. Catania, C. Bellocchio, L. Romanov, R. A. Matias, I. Zizzari, P. Leon, S. Quarta, C. Cannich, A. Meece, K. Gonzales, D. Clark, S. Becker, J. M. Yeo, G. S. H. Merkle, F. T. Wardlaw, S. L. Harkany, T. Massa, F. Marsicano, G. Cota, D. 2020-03-26 doi:10.1101/2020.03.25.007765 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Evidence of Presence and Activation of the two Cell Cycle Kinases Nek6 and Nek7 in the ciliated Neuroretina ]]> https://biorxiv.org/content/10.1101/2020.03.27.012724v1?rss=1 Janisch, K. M. Kasanuki, J. M. Davis, R. J. Tsang, S. H. 2020-03-29 doi:10.1101/2020.03.27.012724 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ Saccadic modulation of neural activity in the human anterior thalamus during visual active sensing ]]> https://biorxiv.org/content/10.1101/2020.03.30.015628v1?rss=1 Leszczynski, M. Staudigl, T. Chaieb, L. Enkirch, S. J. Fell, J. Schroeder, C. E. 2020-03-31 doi:10.1101/2020.03.30.015628 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons ]]> https://biorxiv.org/content/10.1101/2020.03.31.018820v1?rss=1 Berg, J. Sorensen, S. A. Ting, J. T. Miller, J. A. Chartrand, T. Buchin, A. Bakken, T. E. Budzillo, A. Dee, N. Ding, S.-L. Gouwens, N. W. Hodge, R. D. Kalmbach, B. Lee, C. Lee, B. R. Alfiler, L. Baker, K. Barkan, E. Beller, A. Berry, K. Bertagnolli, D. Bickley, K. Bomben, J. Braun, T. Brouner, K. Casper, T. Chong, P. Crichton, K. Dalley, R. de Frates, R. Desta, T. Dingman Lee, S. D'Orazi, F. Dotson, N. Egdorf, T. Enstrom, R. Farrell, C. Feng, D. Fong, O. Furdan, S. Galakhova, A. A. Gamlin, C. Gary, A. Glandon, A. Goldy, J. Gorham, M. Goriounova, N. 2020-04-02 doi:10.1101/2020.03.31.018820 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Translational neurophysiological biomarkers of N-methyl-D-aspartate receptor dysfunction in serine racemase knockout mice ]]> https://biorxiv.org/content/10.1101/2020.04.01.020438v1?rss=1 Balla, A. Ginsberg, S. Abbas, A. Sershen, H. Javitt, D. C. 2020-04-03 doi:10.1101/2020.04.01.020438 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America ]]> https://biorxiv.org/content/10.1101/2020.04.02.021659v1?rss=1 Barbour, A. G. Milovic, A. Bassam, K. Shao, H. Chatzistamou, I. Tufts, D. M. Diuk-Wasser, M. 2020-04-02 doi:10.1101/2020.04.02.021659 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Coordinated postnatal maturation of striatal cholinergic interneurons and dopamine release dynamics in mice. ]]> https://biorxiv.org/content/10.1101/2020.04.02.022152v1?rss=1 McGuirt, A. F. Lieberman, O. Post, M. R. Pigulevskiy, I. Sulzer, D. 2020-04-03 doi:10.1101/2020.04.02.022152 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ Triphosphates of the Two Components in DESCOVY and TRUVADA are Inhibitors of the SARS-CoV-2 Polymerase ]]> https://biorxiv.org/content/10.1101/2020.04.03.022939v1?rss=1 Jockusch, S. Tao, C. Li, X. Anderson, T. K. Chien, M. Kumar, S. Russo, J. J. Kirchdoerfer, R. Ju, J. 2020-04-05 doi:10.1101/2020.04.03.022939 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Role of transmembrane helix 6 in substrate recognition of the amino acid transporter MhsT ]]> https://biorxiv.org/content/10.1101/2020.04.03.022970v1?rss=1 Nissen, P. Quick, M. Blunck, R. Lyons, J. Neumann, C. M. T. Focht, D. Javitch, J. A. Eguskiza, A. Malinauskaite, L. Schwarz, I. O. 2020-04-04 doi:10.1101/2020.04.03.022970 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Molecular development of muscle spindle and Golgi tendon organ sensory afferents revealed by single proprioceptor transcriptome analysis ]]> https://biorxiv.org/content/10.1101/2020.04.03.023986v1?rss=1 Oliver, K. M. Florez-Paz, D. M. Badea, T. C. Mentis, G. Z. Menon, V. de Nooij, J. C. 2020-04-05 doi:10.1101/2020.04.03.023986 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Deep whole genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias ]]> https://biorxiv.org/content/10.1101/2020.04.03.024398v1?rss=1 Bogenschutz, E. L. Fox, Z. D. Farrell, A. Wynn, J. Moore, B. Yu, L. Aspelund, G. Yandell, M. Y. Shen, Y. Chung, W. K. Kardon, G. 2020-04-05 doi:10.1101/2020.04.03.024398 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ The evolution of red colour vision is linked to coordinated rhodopsin tuning in lycaenid butterflies ]]> https://biorxiv.org/content/10.1101/2020.04.06.027102v1?rss=1 Lienard, M. A. Bernard, G. D. Allen, A. A. Lassance, J.-M. Song, S. Rabideau Childers, R. A. Yu, N. Ye, D. Stephenson, A. Valencia Montoya, W. A. Salzman, S. Whitaker, M. R. Calonje, M. Pierce, N. E. 2020-04-06 doi:10.1101/2020.04.06.027102 Cold Spring Harbor Laboratory Press 2020-04-06 <![CDATA[ The Harsh Microenvironment in Early Breast Cancer Select for a Warburg Phenotype ]]> https://biorxiv.org/content/10.1101/2020.04.07.029975v1?rss=1 Damaghi, M. West, J. Robertson-Tessi, M. Xu, L. Ferrall-Fairbanks, M. C. Stewart, P. A. Persi, E. A. Fridley, B. L. Altrock, P. M. Gatenby, R. Sims, p. A. Anderson, A. R. Gillies, R. J. 2020-04-08 doi:10.1101/2020.04.07.029975 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Dual mechanisms of ictal high frequency oscillations in human rhythmic onset seizures ]]> https://biorxiv.org/content/10.1101/2020.04.07.030205v1?rss=1 Smith, E. H. Merricks, E. M. Liou, J.-y. Casadei, C. Melloni, L. Thesen, T. Friedman, D. Doyle, W. Emerson, R. G. Goodman, R. McKhann, G. M. Sheth, S. Rolston, J. D. Schevon, C. 2020-04-10 doi:10.1101/2020.04.07.030205 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ A novel luminescence-based β-arrestin membrane recruitment assay for unmodified GPCRs ]]> https://biorxiv.org/content/10.1101/2020.04.09.034520v1?rss=1 Hauge Pedersen, M. Pham, J. Mancebo, H. Inoue, A. Javitch, J. A. 2020-04-10 doi:10.1101/2020.04.09.034520 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Cell-Type-Specific Expression of Renin-Angiotensin-System Components in the Human Body and Its Relevance to SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2020.04.11.034603v1?rss=1 Suryawanshi, H. Morozov, P. Tuschl, T. Muthukumar, T. tenOever, B. R. Yamaji, M. Williams, Z. 2020-04-11 doi:10.1101/2020.04.11.034603 Cold Spring Harbor Laboratory Press 2020-04-11 <![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[ KIF13A mediates the activity-dependent transport of ESCRT-0 proteins in axons ]]> https://biorxiv.org/content/10.1101/2020.04.16.044818v1?rss=1 Birdsall, V. Imoto, Y. Waites, C. Watanabe, S. 2020-04-18 doi:10.1101/2020.04.16.044818 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Automatic Landmark-guided Bijective Brain Image Registration by Composing Region-based Locally Diffeomorphic Warpings ]]> https://biorxiv.org/content/10.1101/2020.04.16.045609v1?rss=1 He, H. Razlighi, Q. R. 2020-04-18 doi:10.1101/2020.04.16.045609 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Dense encoding of developmental regulatory information may constrain evolvability ]]> https://biorxiv.org/content/10.1101/2020.04.17.046052v1?rss=1 Fuqua, T. Jordan, J. van Breugel, M. E. Halavatyi, A. Tischer, C. Polidoro, P. Abe, N. Tsai, A. Mann, R. S. Stern, D. L. Crocker, J. 2020-04-18 doi:10.1101/2020.04.17.046052 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) ]]> https://biorxiv.org/content/10.1101/2020.04.20.048066v1?rss=1 18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets. ]]> Butler, D. J. Mozsary, C. Meydan, C. Danko, D. C. Foox, J. Rosiene, J. Shaiber, A. Afshinnekoo, E. MacKay, M. Sedlazeck, F. J. Ivanov, N. A. Sierra, M. A. Pohle, D. Zeitz, M. Gisladottir, U. Westover, C. D. Ryon, K. Young, B. Bhattacharya, C. Ruggiero, P. Langhorst, B. W. Tanner, N. A. Gawrys, J. Meleshko, D. Xu, D. Xiang, J. Iftner, A. Bezdan, D. Sipley, J. Cong, L. Craney, A. Velu, P. Melnick, A. Hajirasouliha, I. A. Iftner, T. Salvatore, M. Loda, M. Westblade, L. F. Levy, S. Cushing, M. Tatonetti, N. P. Imielinski, M. Rennert, H. Mason, C. 2020-04-20 doi:10.1101/2020.04.20.048066 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Antibiotics may influence gut microbiome signaling to the brain in preterm neonates ]]> https://biorxiv.org/content/10.1101/2020.04.20.052142v1?rss=1 Russell, J. T. Ruoss, J. L. de la Cruz, D. Li, N. Bazacliu, C. Patton, L. Lobean McKinley, K. Garrett, T. J. Polin, R. A. Triplett, E. W. Neu, J. 2020-04-21 doi:10.1101/2020.04.20.052142 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.04.22.055327v1?rss=1 30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs. ]]> Smithgall, M. C. Scherberkova, I. Whittier, S. Green, D. 2020-04-25 doi:10.1101/2020.04.22.055327 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2020.04.22.056341v1?rss=1 Zhao, W. Dovas, A. Spinazzi, E. F. Levitin, H. M. Upadhyayula, P. Sudhakar, T. Marie, T. Otten, M. L. Sisti, M. Bruce, J. N. Canoll, P. Sims, P. A. 2020-04-24 doi:10.1101/2020.04.22.056341 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination ]]> https://biorxiv.org/content/10.1101/2020.04.23.057877v1?rss=1 Crowe, J. J. Wang, X. Shao, Z. Lee, B. J. Estes, V. Zha, S. 2020-04-24 doi:10.1101/2020.04.23.057877 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Circuits for integrating learnt and innate valences in the fly brain ]]> https://biorxiv.org/content/10.1101/2020.04.23.058339v1?rss=1 Eschbach, C. Fushiki, A. Winding, M. Afonso, B. Andrade, I. V. Cocanougher, B. T. Eichler, K. Gepner, R. Si, G. Valdes-Aleman, J. Fetter, R. D. Gershow, M. Jefferis, G. S. X. E. Samuel, A. Truman, J. W. Cardona, A. Zlatic, M. 2020-04-24 doi:10.1101/2020.04.23.058339 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses Causing SARS and COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.04.23.058776v1?rss=1 Jockusch, S. Tao, C. Li, X. Anderson, T. K. Chien, M. Kumar, S. Russo, J. J. Kirchdoerfer, R. N. Ju, J. 2020-04-25 doi:10.1101/2020.04.23.058776 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ DIY-NAMIC behavior: A high-throughput method to measure complex phenotypes in the homecage ]]> https://biorxiv.org/content/10.1101/2020.04.24.059980v1?rss=1 Lee, J. H. Capan, S. Lacefield, C. Shea, Y. M. Nautiyal, K. M. 2020-04-25 doi:10.1101/2020.04.24.059980 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks ]]> https://biorxiv.org/content/10.1101/2020.04.25.060269v1?rss=1 Samantray, S. Schumann, W. Illig, A.-M. Paul, A. Barz, B. Strodel, B. 2020-04-27 doi:10.1101/2020.04.25.060269 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ A quantitative model for the regulation of innate immune activation ]]> https://biorxiv.org/content/10.1101/2020.04.26.061465v1?rss=1 Qin, Y. Mace, E. M. Barton, J. P. 2020-04-28 doi:10.1101/2020.04.26.061465 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Permutation-based Identification of Important Biomarkers for Complex Diseases via Black-box Models ]]> https://biorxiv.org/content/10.1101/2020.04.27.064170v1?rss=1 Mi, X. Zou, F. Zou, B. Hu, J. 2020-04-29 doi:10.1101/2020.04.27.064170 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Dopamine D2R upregulation in nucleus accumbens indirect pathway does not affect Pavlovian and Go/No-Go Learning ]]> https://biorxiv.org/content/10.1101/2020.04.28.066670v1?rss=1 Martyniuk, K. M. Dandeneau, M. Balsam, P. D. Kellendonk, C. 2020-04-30 doi:10.1101/2020.04.28.066670 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Placental microRNA Expression Associates with Birthweight through Control of Adipokines: Results from Two Independent Cohorts ]]> https://biorxiv.org/content/10.1101/2020.04.28.067025v1?rss=1 Kennedy, E. M. Hermetz, K. Burt, A. Everson, T. M. Deyssenroth, M. Hao, K. Chen, J. Karagas, M. R. Pei, D. Koestler, D. C. Marsit, C. J. 2020-04-29 doi:10.1101/2020.04.28.067025 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Lab-Based and Self-Reported Indices of Fitness Show Lowered Fitness and Insight into Fitness in Individuals at Clinical High Risk for Psychosis ]]> https://biorxiv.org/content/10.1101/2020.04.30.060244v1?rss=1 Damme, K. S. F. Sloan, R. P. Bartels, M. N. Ozsan, A. Ospina, L. H. Kimhy, D. Mittal, V. A. 2020-05-02 doi:10.1101/2020.04.30.060244 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Cell-type specific gene expression profiling in heterogeneous in vitro cultures using epitope-tagged RPL22 ]]> https://biorxiv.org/content/10.1101/2020.04.30.064709v1?rss=1 Gregory, J. A. Hoelzli, E. Abdelaal, R. Braine, C. Cuevas, M. Halpern, M. Kang, K. Barretto, N. Akbalik, G. Schrode, N. Cheng, E. Bowles, K. R. Lotz, S. Goderie, S. Karch, C. Goate, A. M. temple, S. Brennand, K. Phatnani, H. 2020-05-01 doi:10.1101/2020.04.30.064709 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Release sites are positioned to activate NMDA receptors ]]> https://biorxiv.org/content/10.1101/2020.05.01.072157v1?rss=1 Li, S. Raychaudhuri, S. Lee, S. A. Wang, J. Kusick, G. F. Prater, C. Syed, S. Falahati, H. Ramos, R. Bartol, T. M. Hosy, E. Watanabe, S. 2020-05-02 doi:10.1101/2020.05.01.072157 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Adult-born granule cells support pathological microcircuits in the chronically epileptic dentate gyrus ]]> https://biorxiv.org/content/10.1101/2020.05.01.072173v1?rss=1 Sparks, F. Liao, Z. Li, W. Soltesz, I. Losonczy, A. 2020-05-03 doi:10.1101/2020.05.01.072173 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency ]]> https://biorxiv.org/content/10.1101/2020.05.01.072512v1?rss=1 Dugger, S. A. Dhindsa, R. S. De Almeida Sampaio, G. Rafikian, E. Petri, S. Teoh, J. Ye, J. Colombo, S. Yang, M. Boland, M. Frankel, W. Goldstein, D. 2020-05-01 doi:10.1101/2020.05.01.072512 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Oral pyruvate prevents glaucomatous neurodegeneration ]]> https://biorxiv.org/content/10.1101/2020.05.02.072215v1?rss=1 Williams, P. A. Harder, J. M. Guymer, C. Wood, J. P. Daskalakis, E. Chidlow, G. Cardozo, B. H. Foxworth, N. E. Cochran, K. E. Ouellette, T. B. Wheelock, C. E. Casson, R. J. John, S. W. 2020-05-03 doi:10.1101/2020.05.02.072215 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Formation of biomolecular condensates in bacteria by tuning protein electrostatics ]]> https://biorxiv.org/content/10.1101/2020.05.02.072645v1?rss=1 Yeong, V. Werth, E. G. Brown, L. M. Obermeyer, A. C. 2020-05-02 doi:10.1101/2020.05.02.072645 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids ]]> https://biorxiv.org/content/10.1101/2020.05.02.073320v1?rss=1 Duan, X. Han, Y. Yang, L. Nilsson, B. Wang, P. Zhang, T. Wang, X. Xu, D. Xiang, J. Z. uhl, s. Huang, Y. Chen, H. Wang, H. tenOever, B. R. Schwartz, R. E. Ho, D. D. Pan, F. C. Chen, S. Evans, T. R. 2020-05-02 doi:10.1101/2020.05.02.073320 Cold Spring Harbor Laboratory Press 2020-05-02 <![CDATA[ Antagonistic Effects of Intraspecific Cooperation and Interspecific Competition on Thermal Performance ]]> https://biorxiv.org/content/10.1101/2020.05.03.075325v1?rss=1 Tsai, H.-Y. Rubenstein, D. R. Chen, B.-F. Liu, M. Chan, S.-F. Chen, D.-P. Sun, S.-J. Yuan, T.-N. Shen, S.-F. 2020-05-04 doi:10.1101/2020.05.03.075325 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ PHOSPHO1, a novel skeletal regulator of insulin resistance and obesity ]]> https://biorxiv.org/content/10.1101/2020.05.04.075895v1?rss=1 Suchacki, K. J. Morton, N. M. Vary, C. Huesa, C. Yadav, M. C. Thomas, B. J. Rajoanah, S. Bunger, L. Ball, D. Barrios-Llerena, M. Guntur, A. R. Khavandgar, Z. Cawthorn, W. P. Ferron, M. Karsenty, G. Murshed, M. Rosen, C. J. MacRae, V. E. Millan, J. L. Farquharson, C. 2020-05-05 doi:10.1101/2020.05.04.075895 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids ]]> https://biorxiv.org/content/10.1101/2020.05.05.079095v1?rss=1 Han, Y. Yang, L. Duan, X. Duan, F. Nilsson-Payant, B. E. Yaron, T. M. Wang, P. Tang, X. Zhang, T. Zhao, Z. Bram, Y. Redmond, D. Houghton, S. Nguyen, D. Xu, D. Wang, X. Uhl, S. Huang, Y. Johnson, J. L. Xiang, J. Wang, H. Pan, F. C. Cantley, L. C. tenOever, B. R. Ho, D. D. Evans, T. Schwartz, R. E. Chen, H. J. Chen, S. 2020-05-05 doi:10.1101/2020.05.05.079095 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping ]]> https://biorxiv.org/content/10.1101/2020.05.05.079426v1?rss=1 Feng, Y. Beh, L. Y. Chang, W.-J. Landweber, L. F. 2020-05-07 doi:10.1101/2020.05.05.079426 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ A mouse bio-electronic nose for sensitive and versatile chemical detection ]]> https://biorxiv.org/content/10.1101/2020.05.06.079772v1?rss=1 Shor, E. Herrero-Vidal, P. Dewan, A. Uguz, I. Curto, V. F. Malliaras, G. G. Savin, C. Bozza, T. Rinberg, D. 2020-05-08 doi:10.1101/2020.05.06.079772 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ A role for tectorial membrane mechanics in activating the cochlear amplifier ]]> https://biorxiv.org/content/10.1101/2020.05.06.080549v1?rss=1 Grosh, K. Olson, E. S. Nankali, A. Wang, Y. Strimbu, C. E. 2020-05-07 doi:10.1101/2020.05.06.080549 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Diverse deep neural networks all predict human IT well, after training and fitting ]]> https://biorxiv.org/content/10.1101/2020.05.07.082743v1?rss=1 Storrs, K. R. Kietzmann, T. C. Walther, A. Mehrer, J. Kriegeskorte, N. 2020-05-08 doi:10.1101/2020.05.07.082743 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ The Genetic Architecture of DNA Replication Timing in Human Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.05.08.085324v1?rss=1 Ding, Q. Edwards, M. M. Hulke, M. L. Bracci, A. N. Hu, Y. Tong, Y. Zhu, X. Hsiao, J. Charvet, C. J. Ghosh, S. Handsaker, R. E. Eggan, K. Merkle, F. T. Gerhardt, J. Egli, D. Clark, A. G. Koren, A. 2020-05-10 doi:10.1101/2020.05.08.085324 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Bypass of DNA Interstrand crosslinks by a Rev1-DNA polymerase ζ complex ]]> https://biorxiv.org/content/10.1101/2020.05.09.085902v1?rss=1 Buch, R. B. Cheun, Y. K. Roy, U. Schärer, O. D. Burgers, P. M. 2020-05-10 doi:10.1101/2020.05.09.085902 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Epigenetic aging of classical monocytes from healthy individuals ]]> https://biorxiv.org/content/10.1101/2020.05.10.087023v1?rss=1 Shchukina, I. Bagaitkar, J. Shpynov, O. Loginicheva, E. Porter, S. Mogilenko, D. A. Wolin, E. Collins, P. Demidov, G. Artomov, M. Zaitsev, K. Sidorov, S. Camell, C. Bambouskova, M. Arthur, L. Swain, A. Panteleeva, A. Dievskii, A. Kurbatsky, E. Tsurinov, P. Chernyatchik, R. Dixit, V. D. Jovanovic, M. Stewart, S. A. Daly, M. J. Dmitriev, S. Oltz, E. M. Artyomov, M. N. 2020-05-11 doi:10.1101/2020.05.10.087023 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Recognition memory via repetition suppression in mouse hippocampal dorsal CA2 pyramidal neurons expressing the vasopressin 1b receptor ]]> https://biorxiv.org/content/10.1101/2020.05.11.078915v1?rss=1 Cymerblit-Sabba, A. Stackmann, M. Williams Avram, S. Granovetter, M. C. Cliz, N. I. Pereira, F. Smith, A. S. Song, J. Lee, H.-J. Young, W. S. 2020-05-12 doi:10.1101/2020.05.11.078915 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Alteration of menaquinone isoprenoid chain length and antibiotic sensitivity by single amino acid substitution in HepT ]]> https://biorxiv.org/content/10.1101/2020.05.11.089490v1?rss=1 Panthee, S. Paudel, A. Hamamoto, H. Uhlemann, A.-C. Sekimizu, K. 2020-05-11 doi:10.1101/2020.05.11.089490 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Amplification lags nonlinearity in the recovery from reduced endocochlear potential ]]> https://biorxiv.org/content/10.1101/2020.05.11.089789v1?rss=1 Strimbu, C. E. Wang, Y. Olson, E. S. 2020-05-14 doi:10.1101/2020.05.11.089789 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ FFA and OFA encode distinct types of face identity information ]]> https://biorxiv.org/content/10.1101/2020.05.12.090878v1?rss=1 Tsantani, M. Kriegeskorte, N. Storrs, K. Williams, A. L. McGettigan, C. Garrido, L. 2020-05-14 doi:10.1101/2020.05.12.090878 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States ]]> https://biorxiv.org/content/10.1101/2020.05.12.091256v1?rss=1 Laise, P. Bosker, G. Sun, X. Shen, Y. Douglass, E. F. Karan, C. Realubit, R. B. Pampou, S. Califano, A. Alvarez, M. J. 2020-05-17 doi:10.1101/2020.05.12.091256 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Combined pigment and metatranscriptomic analysis reveals synchronized diel patterns of phenotypic light response across domains in the open ocean ]]> https://biorxiv.org/content/10.1101/2020.05.12.091322v1?rss=1 Becker, K. W. Harke, M. J. Mende, D. R. Muratore, D. Weitz, J. S. DeLong, E. F. Dyhrman, S. T. Van Mooy, B. A. S. 2020-05-14 doi:10.1101/2020.05.12.091322 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Fear Conditioning Potentiates the Hippocampal CA1 Commissural Pathway In vivo and Increases Awake Phase Sleep ]]> https://biorxiv.org/content/10.1101/2020.05.13.093237v1?rss=1 Subramaniyan, M. Manivannan, S. Chelur, V. Tsetsenis, T. Jiang, E. Dani, J. A. 2020-05-14 doi:10.1101/2020.05.13.093237 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Establishing a transcriptome-based drug discovery paradigm for neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2020.05.13.093468v1?rss=1 Dhindsa, R. S. Zoghbi, A. W. Krizay, D. K. Vasavda, C. Goldstein, D. B. 2020-05-15 doi:10.1101/2020.05.13.093468 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis ]]> https://biorxiv.org/content/10.1101/2020.05.14.095521v1?rss=1 O'Neill, J. Hoyle, N. P. Robertson, J. B. Edgar, R. S. Beale, A. D. Peak-Chew, S. Y. Day, J. Costa, A. S. H. Frezza, C. Causton, H. C. 2020-05-16 doi:10.1101/2020.05.14.095521 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Community-scale Synchronization and Temporal Partitioning of Gene Expression, Metabolism, and Lipid Biosynthesis in Oligotrophic Ocean Surface Waters ]]> https://biorxiv.org/content/10.1101/2020.05.15.098020v1?rss=1 Muratore, D. Boysen, A. K. Harke, M. J. Becker, K. W. Casey, J. R. Coesel, S. N. Mende, D. R. Wilson, S. T. Aylward, F. O. Eppley, J. M. Vislova, A. Peng, S. Rodriguez-Gonzalez, R. A. Beckett, S. J. Armbrust, E. V. DeLong, E. F. Karl, D. M. White, A. E. Zehr, J. P. Van Mooy, B. A. S. Dyhrman, S. T. Ingalls, A. E. Weitz, J. S. 2020-05-16 doi:10.1101/2020.05.15.098020 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex ]]> https://biorxiv.org/content/10.1101/2020.05.15.098848v1?rss=1 prakash, r. sandoval, t. Morati, F. Zagelbaum, J. A. Taylor, B. Desclos, E. C. Wang, R. Sullivan, M. R. Rein, H. L. Bernstein, K. A. Krawczyk, P. M. Gautier, J. Modesti, M. Vanoli, F. Jasin, M. 2020-05-15 doi:10.1101/2020.05.15.098848 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ The effect of boundaries on grid cell patterns ]]> https://biorxiv.org/content/10.1101/2020.05.16.099168v1?rss=1 Monsalve-Mercado, M. M. Leibold, C. 2020-05-16 doi:10.1101/2020.05.16.099168 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons ]]> https://biorxiv.org/content/10.1101/2020.05.16.100032v1?rss=1 Ford, L. Asok, A. Tripp, A. D. Parro, C. Fitzpatrick, M. de Solis, C. A. Shafiian, N. Fioriti, L. Soni, R. K. Kandel, E. 2020-05-17 doi:10.1101/2020.05.16.100032 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Lipoic acid biosynthesis is essential for Plasmodium falciparum transmission and influences redox response and carbon metabolism of parasite asexual blood stages ]]> https://biorxiv.org/content/10.1101/2020.05.17.099630v1?rss=1 Biddau, M. Kumar, S. T. R. Henrich, P. Laine, L. M. Blackburn, G. J. Chokkathukalam, A. Li, T. B. Sim, K. L. Hoffman, S. L. Barrett, M. P. Coombs, G. H. McFadden, G. I. Fidock, D. A. Muller, S. Sheiner, L. 2020-05-17 doi:10.1101/2020.05.17.099630 Cold Spring Harbor Laboratory Press 2020-05-17 <![CDATA[ Glycan processing in the Golgi - optimal information coding and constraints on cisternal number and enzyme specificity ]]> https://biorxiv.org/content/10.1101/2020.05.18.101444v1?rss=1 Yadav, A. Vagne, Q. Sens, P. Iyengar, G. Rao, M. 2020-05-19 doi:10.1101/2020.05.18.101444 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Human Hair Graying is Naturally Reversible and Linked to Stress ]]> https://biorxiv.org/content/10.1101/2020.05.18.101964v1?rss=1 Rosenberg, A. Rausser, S. Ren, J. Mosharov, E. Sturm, G. M. Ogden, R. T. Patel, P. Soni, R. K. Lacefield, C. Paus, R. Picard, M. 2020-05-19 doi:10.1101/2020.05.18.101964 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ The bear bones: mosaic ancestry of Macaca arctoides explains divergent baculum morphology ]]> https://biorxiv.org/content/10.1101/2020.05.18.102251v1?rss=1 Stevison, L. Szpiech, Z. A. Bailey, N. P. Novak, T. E. Melnick, D. J. Evans, B. J. Wall, J. D. 2020-05-20 doi:10.1101/2020.05.18.102251 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Cholinergic Modulation of Hippocampally Mediated Attention and Perception ]]> https://biorxiv.org/content/10.1101/2020.05.19.104497v1?rss=1 Ruiz, N. A. Thieu, M. Aly, M. 2020-05-22 doi:10.1101/2020.05.19.104497 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Selective role of the translin/trax RNase complex in hippocampal synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2020.05.19.105189v1?rss=1 Park, A. J. Shetty, M. S. Baraban, J. M. Abel, T. 2020-05-20 doi:10.1101/2020.05.19.105189 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus ]]> https://biorxiv.org/content/10.1101/2020.05.22.103796v1?rss=1 Aronson, B. E. Scourzic, L. Shah, V. Swanzey, E. Kloetgen, A. Polyzos, A. Sinha, A. Azziz, A. Caspi, I. Li, J. Pelham-Webb, B. Wichterle, H. Tsirigos, A. Stadtfeld, M. Apostolou, E. 2020-05-24 doi:10.1101/2020.05.22.103796 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ No fruits without color: Cross-modal priming and EEG reveal different roles for different features across semantic categories ]]> https://biorxiv.org/content/10.1101/2020.05.22.110338v1?rss=1 Argiris, G. Rumiati, R. Crepaldi, D. 2020-05-22 doi:10.1101/2020.05.22.110338 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ A Study of Secondary School Students Participation in a Novel Course on Genomic Principles and Practices. ]]> https://biorxiv.org/content/10.1101/2020.05.22.110361v1?rss=1 Stefanile, A. 2020-05-22 doi:10.1101/2020.05.22.110361 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm ]]> https://biorxiv.org/content/10.1101/2020.05.22.110577v1?rss=1 Tourigny, D. S. Goldberg, A. Karr, J. R. 2020-05-26 doi:10.1101/2020.05.22.110577 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ A transfer-learning approach for first-year developmental infant brain segmentation using deep neural networks ]]> https://biorxiv.org/content/10.1101/2020.05.22.110619v1?rss=1 Wang, Y. Haghpanah, F. S. Aw, N. Laine, A. Posner, J. 2020-05-25 doi:10.1101/2020.05.22.110619 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Supramodal executive control of attention: evidence from unimodal and crossmodal dual conflict effects ]]> https://biorxiv.org/content/10.1101/2020.05.22.110643v1?rss=1 Spagna, A. Wu, T. Kim, K. Fan, J. 2020-05-25 doi:10.1101/2020.05.22.110643 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Beyond the connectome: A map of a brain architecture derived from whole-brain volumetric reconstructions ]]> https://biorxiv.org/content/10.1101/2020.05.24.112870v1?rss=1 Brittin, C. A. Cook, S. J. Hall, D. H. Emmons, S. W. Cohen, N. 2020-05-27 doi:10.1101/2020.05.24.112870 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Scale-invariance in brain activity predicts practice effects in cognitive performance ]]> https://biorxiv.org/content/10.1101/2020.05.25.114959v1?rss=1 Kardan, O. Layden, E. A. Choe, K. W. Lyu, M. Zhang, X. Beilock, S. L. Rosenberg, M. D. Berman, M. G. 2020-05-26 doi:10.1101/2020.05.25.114959 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2020.05.26.081083v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@8f89c4org.highwire.dtl.DTLVardef@19dc813org.highwire.dtl.DTLVardef@1ba7c20org.highwire.dtl.DTLVardef@2b3daa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gerbin, K. A. Grancharova, T. Donovan-Maiye, R. Hendershott, M. C. Brown, J. Dinh, S. Q. Gehring, J. L. Hirano, M. Johnson, G. R. Nath, A. Nelson, A. Roco, C. M. Rosenberg, A. B. Sluzewski, M. F. Viana, M. P. Yan, C. Zaunbrecher, R. J. Cordes Metzler, K. R. Menon, V. Palecek, S. P. Seelig, G. Gaudreault, N. Knijnenburg, T. Rafelski, S. M. Theriot, J. A. Gunawardane, R. N. 2020-05-27 doi:10.1101/2020.05.26.081083 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ A non-linear relation between levels of adult hippocampal neurogenesis and expression of the immature neuron marker doublecortin ]]> https://biorxiv.org/content/10.1101/2020.05.26.115873v1?rss=1 Mendez-David, I. DAVID, D. J. Delomenie, C. Beaulieu, M. Gardier, A. M. Hen, R. 2020-05-28 doi:10.1101/2020.05.26.115873 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Female excellence in rock climbing likely has an evolutionary origin ]]> https://biorxiv.org/content/10.1101/2020.05.26.116244v1?rss=1 Carroll, C. 2020-05-26 doi:10.1101/2020.05.26.116244 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Powerful Variance-Component TWAS method identifies novel and known risk genes for clinical and pathologic Alzheimer's dementia phenotypes ]]> https://biorxiv.org/content/10.1101/2020.05.26.117515v1?rss=1 Tang, S. Buchman, A. De Jager, P. Bennett, D. Epstein, M. Yang, J. 2020-05-29 doi:10.1101/2020.05.26.117515 Cold Spring Harbor Laboratory Press 2020-05-29 <![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[ Tumor-free elongation of mammalian nephrogenesis by excess fetal GDNF ]]> https://biorxiv.org/content/10.1101/2020.05.28.120865v1?rss=1 Li, H. Kupari, J. Gui, Y. Siefker, E. Lu, B. Mätlik, K. Olfat, S. Montano-Rodriguez, A. R. Huh, S.-H. Costantini, F. D. Andressoo, J.-O. Kuure, S. 2020-05-30 doi:10.1101/2020.05.28.120865 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Ventral tegmental area GABA neurons mediate stress-induced anhedonia. ]]> https://biorxiv.org/content/10.1101/2020.05.28.121905v1?rss=1 Lowes, D. C. Chamberlin, L. A. Kretsge, L. N. Holt, E. S. Abbas, A. I. Park, A. J. Yusufova, L. Bretton, Z. H. Firdous, A. Gordon, J. A. Harris, A. Z. 2020-05-31 doi:10.1101/2020.05.28.121905 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ The Caribbean-Hispanic Alzheimer's Brain Transcriptome Reveals Ancestry-Specific Disease Mechanisms ]]> https://biorxiv.org/content/10.1101/2020.05.28.122234v1?rss=1 Felsky, D. Sariya, S. Santa-Maria, I. Schneider, J. A. Bennett, D. A. Mayeux, R. P. De Jager, P. L. Tosto, G. 2020-05-31 doi:10.1101/2020.05.28.122234 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure ]]> https://biorxiv.org/content/10.1101/2020.05.29.123505v1?rss=1 Wang, H. Noordam, R. Cade, B. E. Schwander, K. Winkler, T. W. Lee, J. Sung, Y. J. Bentley, A. R. Manning, A. K. Aschard, H. Kilpelainen, T. O. Ilkov, M. Brown, M. R. Horimoto, A. R. Richard, M. Bartz, T. M. Vojinovic, D. Lim, E. Nierenberg, J. L. Liu, Y. Chitrala, K. Rankinen, T. Musani, S. K. Franceschini, N. Rauramaa, R. Alver, M. Zee, P. Harris, S. E. van der Most, P. J. Nolte, I. M. Munroe, P. B. Palmer, N. D. Kuhnel, B. Weiss, S. Wen, W. Hall, K. A. Lyytikainen, L.-P. O'Connell, J. R. Eiriksdottir, G. Launer, L. J. de Vries, P. S. Arking, D. Chen, 2020-05-31 doi:10.1101/2020.05.29.123505 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors ]]> https://biorxiv.org/content/10.1101/2020.05.29.123836v1?rss=1 Crowley, L. Cambuli, F. Aparicio, L. Shibata, M. Robinson, B. D. Xuan, S. Li, W. Hibshoosh, H. Loda, M. Rabadan, R. Shen, M. M. 2020-05-31 doi:10.1101/2020.05.29.123836 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Rare variant analysis of 4,241 pulmonary arterial hypertension cases from an international consortium implicate FBLN2, PDGFD and rare de novo variants in PAH ]]> https://biorxiv.org/content/10.1101/2020.05.29.124255v1?rss=1 Zhu, N. Swietlik, E. M. Welch, C. L. Pauciulo, M. W. Hagen, J. J. Zhou, X. Guo, Y. Karten, J. Pandya, D. Tilly, T. Lutz, K. A. Rosenzweig, E. Krishnan, U. Coleman, A. W. Gonzaga-Juaregiu, C. Lawrie, A. Trembath, R. C. Wilkins, M. R. Regeneron Genetics Group, PAH Biobank Enrolling Centers' Investigators, NIHR BioResource for Translational Research - Rare Diseases, National Cohort Study of Idiopathic and Heritable PAH, Morrell, N. W. Shen, Y. Graf, S. Nichols, W. C. Chung, W. K. 2020-05-30 doi:10.1101/2020.05.29.124255 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Adaptive Efficient Coding: A Variational Auto-encoder Approach ]]> https://biorxiv.org/content/10.1101/2020.05.29.124453v1?rss=1 Aridor, G. Grechi, F. Woodford, M. 2020-05-31 doi:10.1101/2020.05.29.124453 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Epigenome dysregulation resulting from NSD1 mutation in head and neck squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2020.05.30.124057v1?rss=1 Farhangdoost, N. Horth, C. Hu, B. Bareke, E. Chen, X. Li, Y. Coradin, M. Garcia, B. A. Lu, C. Majewski, J. 2020-05-31 doi:10.1101/2020.05.30.124057 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Large ribosomal subunit, eIF5B, Met-tRNAiMet and mRNA cooperate to complete accurate initiation. ]]> https://biorxiv.org/content/10.1101/2020.05.30.125153v1?rss=1 Wang, J. Wang, J. Shin, B.-s. Dever, T. Puglisi, J. Fernandez, I. 2020-05-31 doi:10.1101/2020.05.30.125153 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ coronapp: a Web Application to Annotate and Monitor SARS-CoV-2 Mutations ]]> https://biorxiv.org/content/10.1101/2020.05.31.124966v1?rss=1 Mercatelli, D. Triboli, L. Fornasari, E. Ray, F. Giorgi, F. M. 2020-06-01 doi:10.1101/2020.05.31.124966 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Template-based prediction of protein structure with deep learning ]]> https://biorxiv.org/content/10.1101/2020.06.02.129270v1?rss=1 Zhang, H. Shen, Y. 2020-06-02 doi:10.1101/2020.06.02.129270 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Precision genetic cellular models identify therapies protective against endoplasmic reticulum stress ]]> https://biorxiv.org/content/10.1101/2020.06.03.132886v1?rss=1 300 cellular features. The image-based screen identified multiple candidate compounds able to correct aberrant morphology, and we show a subset of these are able to correct cellular and molecular defects in each of the models. These results provide new directions for the treatment of rare diseases of glycosylation and deglycosylation and a framework for new drug screening paradigms for more common neurodegenerative diseases characterized by ER stress. Summary sentenceNovel drug screening modality identifies compounds that correct aberrant molecular phenotypes in precision cellular models of glycosylation defects. ]]> Lebedeva, I. V. Wagner, M. V. Sahdeo, S. Lu, Y.-F. Anyanwu-Ofili, A. Harms, M. B. Wadia, J. S. Rajagopal, G. Boland, M. J. Goldstein, D. B. 2020-06-04 doi:10.1101/2020.06.03.132886 Cold Spring Harbor Laboratory Press 2020-06-04 <![CDATA[ Analysis of socioeconomic disadvantage and pace of aging measured in saliva DNA methylation of children and adolescents ]]> https://biorxiv.org/content/10.1101/2020.06.04.134502v1?rss=1 Raffington, L. A. S. Belsky, D. W. Malanchini, M. Tucker-Drob, E. M. Harden, K. P. 2020-06-05 doi:10.1101/2020.06.04.134502 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome ]]> https://biorxiv.org/content/10.1101/2020.06.04.134692v1?rss=1 Kennedy, A. L. Myers, K. C. Bowman, J. Gibson, C. J. Camarda, N. D. Furutani, E. M. Muscato, G. M. Klein, R. H. Ballotti, K. Liu, S. Harris, C. E. Galvin, A. Malsch, M. Dale, D. Gansner, J. M. Nakano, T. A. Bertuch, A. Vlachos, A. Lipton, J. M. Castillo, P. Connelly, J. Churpek, J. Edwards, J. R. Hijiya, N. Ho, R. H. Hofmann, I. Huang, J. N. Keel, S. Lamble, A. Lau, B. W. Norkin, M. Stieglitz, E. Stock, W. Walkovich, K. Boettcher, S. Brendel, C. Fleming, M. D. Davies, S. M. Weller, E. A. Bahl, C. Carter, S. L. Shimamura, A. Lindsley, R. C. 2020-06-05 doi:10.1101/2020.06.04.134692 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Atrophy associated with tau pathology precedes overt cell death in a mouse model of progressive tauopathy ]]> https://biorxiv.org/content/10.1101/2020.06.05.136663v1?rss=1 Fung, C. Guo, J. Figueroa, H. Konofagou, E. Duff, K. 2020-06-06 doi:10.1101/2020.06.05.136663 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited ]]> https://biorxiv.org/content/10.1101/2020.06.08.134890v1?rss=1 Li, Z. Ji, B. W. Dixit, P. D. Lien, E. C. Tchourine, K. Hosios, A. M. Abbott, K. L. Westermark, A. M. Gorodetsky, E. F. Sullivan, L. B. Vander Heiden, M. Vitkup, D. 2020-06-09 doi:10.1101/2020.06.08.134890 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm ]]> https://biorxiv.org/content/10.1101/2020.06.08.138735v1?rss=1 Joo, Y. Y. Pacheco, J. A. Thompson, W. K. Rasmussen-Torvik, L. Rasmussen, L. V. Lin, F. T. Andrade, M. d. Borthwick, K. M. Bottinger, E. Cagan, A. Carrell, D. S. Denny, J. C. Ellis, S. B. Gottesman, O. Linneman, J. G. Pathak, J. Peissig, P. L. Shang, N. S. Tromp, G. Veerappan, A. Smith, M. Chisholm, R. L. Gawron, A. J. Kho, A. N. Hayes, M. G. 2020-06-09 doi:10.1101/2020.06.08.138735 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Screening of PCRP transcription factor antibodies in biochemical assays ]]> https://biorxiv.org/content/10.1101/2020.06.08.140046v1?rss=1 Lai, W. Mariani, L. Rothschild, G. Smith, E. Venters, B. Blanda, T. Kuntala, P. Bocklund, K. Mairose, J. Dweikat, S. Mistretta, K. Rossi, M. James, D. Anderson, J. Phanor, S. Zhang, W. Shaw, A. Novitzky, K. McAnarney, E. Keogh, M.-C. Shilatifard, A. Basu, U. Bulyk, M. Pugh, B. F. 2020-06-09 doi:10.1101/2020.06.08.140046 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ A Deep Learning Semiparametric Regression for Adjusting Complex Confounding Structures ]]> https://biorxiv.org/content/10.1101/2020.06.08.140418v1?rss=1 Mi, X. Tighe, P. J. Zou, F. Zou, B. 2020-06-09 doi:10.1101/2020.06.08.140418 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Organization of cortico-hippocampal networks in the human brain ]]> https://biorxiv.org/content/10.1101/2020.06.09.142166v1?rss=1 Barnett, A. J. Reilly, W. Dimsdale-Zucker, H. Mizrak, E. Reagh, Z. Ranganath, C. 2020-06-10 doi:10.1101/2020.06.09.142166 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Real-Time Microfluidics-Magnetic Tweezers connects conformational stiffness with energy landscape by a single experiment ]]> https://biorxiv.org/content/10.1101/2020.06.09.142257v1?rss=1 chakraborty, s. Chaudhuri, D. Haldar, S. Chaudhuri, D. Singh, V. Banerjee, S. 2020-06-10 doi:10.1101/2020.06.09.142257 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Generation of Rapid Sequences by Motor Cortex ]]> https://biorxiv.org/content/10.1101/2020.06.09.143040v1?rss=1 Zimnik, A. J. Churchland, M. M. 2020-06-10 doi:10.1101/2020.06.09.143040 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Single Cell-type Integrative Network Modeling IdentifiedNovel Microglial-specific Targets for the Phagosome inAlzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.06.09.143529v1?rss=1 Patel, K. R. Zhu, K. Henrion, M. Y. Beckmann, N. Moein, S. Alamprese, M. L. Allen, M. Wang, X. Chen, G. Pertel, T. Nejad, P. Reddy, J. S. Carrasquillo, M. M. Bennett, D. A. Ertekin-Taner, N. Jager, P. D. Schadt, E. Bradshaw, E. M. Chang, R. 2020-06-10 doi:10.1101/2020.06.09.143529 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ α-Synuclein facilitates dopamine release during burst firing of substantia nigra neurons in vivo ]]> https://biorxiv.org/content/10.1101/2020.06.10.145110v1?rss=1 Somayaji, M. Cataldi, S. Edwards, R. H. Mosharov, E. V. Sulzer, D. 2020-06-12 doi:10.1101/2020.06.10.145110 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Neuroscience Cloud Analysis As a Service ]]> https://biorxiv.org/content/10.1101/2020.06.11.146746v1?rss=1 Abe, T. Kinsella, I. Saxena, S. Paninski, L. Cunningham, J. P. 2020-06-12 doi:10.1101/2020.06.11.146746 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Prelimbic-amygdala overexcitability mediates trait vulnerability in a novel mouse model of acute social defeat stress ]]> https://biorxiv.org/content/10.1101/2020.06.11.147231v1?rss=1 Grossman, Y. S. Fillinger, C. Manganaro, A. Voren, G. Waldman, R. Zou, T. Jannsen, W. Kenny, P. Dumitriu, D. 2020-06-12 doi:10.1101/2020.06.11.147231 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ SARS-CoV-2 Neutralizing Antibody Responses Are More Robust in Patients with Severe Disease ]]> https://biorxiv.org/content/10.1101/2020.06.13.150250v1?rss=1 Wang, P. Liu, L. Nair, M. S. Yin, M. T. Luo, Y. Wang, Q. Yuan, T. Mori, K. Solis, A. G. Yamashita, M. Purpura, L. J. Laracy, J. C. Yu, J. Sodroski, J. Huang, Y. Ho, D. D. 2020-06-14 doi:10.1101/2020.06.13.150250 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Neural representation of linguistic feature hierarchy reflects second-language proficiency ]]> https://biorxiv.org/content/10.1101/2020.06.15.142554v1?rss=1 Di Liberto, G. Nie, J. Yeaton, J. Khalighinejad, B. Shamma, S. Mesgarani, N. 2020-06-15 doi:10.1101/2020.06.15.142554 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Categorical judgments do not modify sensory information in working memory ]]> https://biorxiv.org/content/10.1101/2020.06.15.152223v1?rss=1 Luu, L. Stocker, A. A. 2020-06-15 doi:10.1101/2020.06.15.152223 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes ]]> https://biorxiv.org/content/10.1101/2020.06.15.152488v1?rss=1 Hobson, B. D. Kong, L. Hartwick, E. W. Gonzalez, R. L. Sims, P. A. 2020-06-16 doi:10.1101/2020.06.15.152488 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Changes in the functional connectome and behavior after exposure to chronic stress and increasing neurogenesis ]]> https://biorxiv.org/content/10.1101/2020.06.15.152553v1?rss=1 Culig, L. Steadman, P. E. Kenney, J. W. Legendre, S. Minier, F. Hen, R. Frankland, P. W. Belzung, C. 2020-06-15 doi:10.1101/2020.06.15.152553 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data ]]> https://biorxiv.org/content/10.1101/2020.06.15.153031v1?rss=1 Chen, S. Zhou, X. Byington, E. Bruce, S. L. Zhang, H. Shen, Y. 2020-06-16 doi:10.1101/2020.06.15.153031 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ The sensorimotor strategies and neuronal representations of tactile shape discrimination in mice ]]> https://biorxiv.org/content/10.1101/2020.06.16.126631v1?rss=1 Rodgers, C. C. Nogueira, R. Pil, B. C. Greeman, E. A. Fusi, S. Bruno, R. M. 2020-06-16 doi:10.1101/2020.06.16.126631 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos ]]> https://biorxiv.org/content/10.1101/2020.06.17.149237v1?rss=1 Zuccaro, M. V. Xu, J. Mitchell, C. Marin, D. Zimmerman, R. Rana, B. Weinstein, E. King, R. T. Smith, M. Tsang, S. H. Goland, R. Jasin, M. Lobo, R. Treff, N. Egli, D. 2020-06-18 doi:10.1101/2020.06.17.149237 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Potent Neutralizing Monoclonal Antibodies Directed to Multiple Epitopes on the SARS-CoV-2 Spike ]]> https://biorxiv.org/content/10.1101/2020.06.17.153486v1?rss=1 Ho, D. D. Lihong, L. Wang, P. Nair, M. S. Jian, Y. Huang, Y. Rapp, M. A. Wang, Q. Luo, Y. Sahi, V. Figueroa, A. Guo, X. V. Cerutti, G. Bimela, J. Gorman, J. Zhou, T. Kwong, P. D. G. Sodroski, J. G. Yin, M. T. Sheng, Z. Shapiro, L. 2020-06-18 doi:10.1101/2020.06.17.153486 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program ]]> https://biorxiv.org/content/10.1101/2020.06.18.146423v1?rss=1 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants from up to 17 TOPMed studies per phenotype. We discuss the challenges faced in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include (1) the code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify or extend these harmonizations to additional studies; and (2) results of labeling thousands of phenotype variables with controlled vocabulary terms. ]]> Stilp, A. M. Emery, L. S. Broome, J. G. Buth, E. J. Khan, A. T. Laurie, C. A. Wang, F. F. Wong, Q. Chen, D. D'Augustine, C. M. Heard-Costa, N. L. Hohensee, C. R. Johnson, W. C. Juarez, L. D. Liu, J. Mutalik, K. M. Raffield, L. M. Wiggins, K. L. de Vries, P. S. Kelly, T. N. Kooperberg, C. Natarajan, P. Peloso, G. M. Peyser, P. A. Reiner, A. P. Arnett, D. K. Aslibekyan, S. Barnes, K. C. Bielak, L. F. Bis, J. C. Cade, B. E. Chen, M.-H. Correa, A. Cupples, L. A. de Andrade, M. Ellinor, P. T. Fornage, M. Franceschini, N. Gan, W. Ganesh, S. K. Graffelman, J. 2020-06-20 doi:10.1101/2020.06.18.146423 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Whole genome doubling confers unique genetic vulnerabilities on tumor cells ]]> https://biorxiv.org/content/10.1101/2020.06.18.159095v1?rss=1 Quinton, R. J. Didomizio, A. Vittoria, M. A. Ticas, C. J. Patel, S. Koga, Y. Kotynkova, K. Vakhshoorzadeh, J. Hermance, N. Kuroda, T. S. Parulekar, N. Taylor, A. M. Manning, A. L. Campbell, J. D. Ganem, N. J. 2020-06-19 doi:10.1101/2020.06.18.159095 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ A sweep of earth's virome reveals host-guided viral protein structural mimicry; with implications for human disease ]]> https://biorxiv.org/content/10.1101/2020.06.18.159467v1?rss=1 70%) cannot be discerned through protein sequence. The results point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. Interrogation of proteins mimicked by human-infecting viruses points to broad diversification of cellular pathways targeted via structural mimicry, identifies biological processes that may underly autoimmune disorders, and reveals virally encoded mimics that may be leveraged to engineer synthetic metabolic circuits or may serve as targets for therapeutics. Moreover, the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type, with ssRNA viruses circumventing limitations of their small genomes by mimicking human proteins to a greater extent than their large dsDNA counterparts. Finally, we identified over 140 cellular proteins that are mimicked by CoV, providing clues about cellular processes driving the pathogenesis of the ongoing COVID-19 pandemic. ]]> Lasso, G. Honig, B. Shapira, S. 2020-06-18 doi:10.1101/2020.06.18.159467 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization ]]> https://biorxiv.org/content/10.1101/2020.06.18.160176v1?rss=1 Brown, B. C. Knowles, D. A. 2020-06-20 doi:10.1101/2020.06.18.160176 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins ]]> https://biorxiv.org/content/10.1101/2020.06.19.161299v1?rss=1 Lim, S. M. Cruz, V. E. Antoku, S. Gundersen, G. G. Schwartz, T. 2020-06-20 doi:10.1101/2020.06.19.161299 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Structural Diversity and Phylogenetic Distribution of Valyl tRNA-like Structures in Viruses ]]> https://biorxiv.org/content/10.1101/2020.06.19.162263v1?rss=1 Sherlock, M. E. Hartwick, E. W. MacFadden, A. Kieft, J. S. 2020-06-19 doi:10.1101/2020.06.19.162263 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Naturalistic coding of working memory in primate prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.06.19.162446v1?rss=1 Roussy, M. Luna, R. Duong, L. Corrigan, B. Gulli, R. A. Nogueira, R. Moreno-Bote, R. Sachs, A. J. Palaniyappan, L. Martinez-Trujillo, J. C. 2020-06-22 doi:10.1101/2020.06.19.162446 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ anti-IL-6 versus anti-IL-6R Blocking Antibodies to Treat Acute Ebola Infection in BALB/c Mice with Potential Implications for Treating Patients Presenting with COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.06.20.162826v1?rss=1 Rubsamen, R. M. Burkholz, S. Massey, S. Brasel, T. Hodge, T. Wang, L. Herst, C. Carback, R. T. Harris, P. 2020-06-21 doi:10.1101/2020.06.20.162826 Cold Spring Harbor Laboratory Press 2020-06-21 <![CDATA[ C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor ]]> https://biorxiv.org/content/10.1101/2020.06.22.164475v1?rss=1 Walhout, M. Giese, G. Walker, M. Ponomarova, O. Zhang, H. Li, X. Minevich, G. 2020-06-23 doi:10.1101/2020.06.22.164475 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age ]]> https://biorxiv.org/content/10.1101/2020.06.22.165225v1?rss=1 Lieberman, N. A. P. Peddu, V. Xie, H. Shrestha, L. Huang, M. Mears, M. C. Cajimat, M. N. Bente, D. A. Shi, P.-Y. Bovier, F. Roychoudhury, P. Jerome, K. R. Moscona, A. Porotto, M. Greninger, A. L. 2020-06-22 doi:10.1101/2020.06.22.165225 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Robust single neuron tracking of calcium imaging in behaving Hydra ]]> https://biorxiv.org/content/10.1101/2020.06.22.165696v1?rss=1 Lagache, T. Hanson, A. Fairhall, A. Yuste, R. 2020-06-23 doi:10.1101/2020.06.22.165696 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes ]]> https://biorxiv.org/content/10.1101/2020.06.22.166033v1?rss=1 5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes. ]]> Zhou, T. Teng, I.-T. Olia, A. S. Cerutti, G. Gorman, J. Nazzari, A. Shi, W. Tsybovsky, Y. Wang, L. Wang, S. Zhang, B. Zhang, Y. Katsamba, P. S. Petrova, Y. Banach, B. B. Fahad, A. S. Liu, L. Lopez Acevedo, S. N. Madan, B. Oliveira de Souza, M. Pan, X. Wang, P. Wolfe, J. R. Yin, M. Ho, D. D. Phung, E. DiPiazza, A. Chang, L. Abiona, O. Corbett, K. S. DeKosky, B. J. Graham, B. S. Mascola, J. R. Misasi, J. Ruckwardt, T. Sullivan, N. J. Shapiro, L. Kwong, P. D. 2020-06-23 doi:10.1101/2020.06.22.166033 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Prelimbic-dependent activation of amygdala somatostatin interneurons signals non-aversive cues to promote discrimination. ]]> https://biorxiv.org/content/10.1101/2020.06.23.156018v1?rss=1 Stujenske, J. M. O'Neill, P.-K. Nahmoud, I. Goldberg, S. Diaz, L. Labkovich, M. Hardin, W. Bolkan, S. S. Reardon, T. R. Spellman, T. J. Salzman, C. D. Gordon, J. A. Likhtik, E. 2020-06-24 doi:10.1101/2020.06.23.156018 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Single-cell RNA-seq analysis reveals the pan-cancer transformation of adipose-derived stromal cells into COL11A1-expressing metastasis associated fibroblasts ]]> https://biorxiv.org/content/10.1101/2020.06.23.166066v1?rss=1 Zhu, K. Cai, L. Cui, C. Anastassiou, D. 2020-06-23 doi:10.1101/2020.06.23.166066 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Opposing Wnt and JAK-STAT signaling gradients define a stem cell domain by regulating spatially patterned cell division and differentiation at two borders ]]> https://biorxiv.org/content/10.1101/2020.06.23.167536v1?rss=1 Melamed, D. Kalderon, D. 2020-06-23 doi:10.1101/2020.06.23.167536 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Drosophila Hedgehog can act as a morphogen in the absence of regulated Ci processing ]]> https://biorxiv.org/content/10.1101/2020.06.23.167585v1?rss=1 Little, J. C. Garcia-Garcia, E. Sul, A. Kalderon, D. 2020-06-23 doi:10.1101/2020.06.23.167585 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ FlyBrainLab: Accelerating the Discovery of the Functional Logic of the Fruit Fly Brain in the Connectomic/Synaptomic Era ]]> https://biorxiv.org/content/10.1101/2020.06.23.168161v1?rss=1 Lazar, A. A. Liu, T. Turkcan, M. K. Zhou, Y. 2020-06-24 doi:10.1101/2020.06.23.168161 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes ]]> https://biorxiv.org/content/10.1101/2020.06.24.169052v1?rss=1 Manley, J. L. Lieu, Y. K. Liu, Z. Wei, X. Penson, A. Zhang, J. An, X. Rabadan, R. Raza, A. Mukherjee, S. 2020-06-26 doi:10.1101/2020.06.24.169052 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Kinetics of CDK4/6 inhibition determine different temporal locations of the restriction point ]]> https://biorxiv.org/content/10.1101/2020.06.24.169409v1?rss=1 Kim, S. Leong, A. Nayar, C. Kim, M. Yang, H. W. 2020-06-24 doi:10.1101/2020.06.24.169409 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Intra-session test-retest reliability of functional connectivity in infants ]]> https://biorxiv.org/content/10.1101/2020.06.25.169524v1?rss=1 Wang, Y. Hinds, W. Duarte, C. S. Lee, S. Monk, C. Wall, M. Canino, G. Milani, A. C. C. Jackowski, A. Mamin, M. G. Foerster, B. U. Gringrich, J. Weissman, M. M. Peterson, B. Semanek, D. Perez, E. A. Labat, E. Torres, I. B. Silva, I. D. Parente, C. Abdala, N. Posner, J. 2020-06-25 doi:10.1101/2020.06.25.169524 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Gradual segregation of Adult Stem Cells and Niche cells during development from common precursors under the guidance of graded extracellular signals ]]> https://biorxiv.org/content/10.1101/2020.06.25.171447v1?rss=1 Reilein, A. Kogan, H. V. Misner, R. Park, K. S. Kalderon, D. 2020-06-26 doi:10.1101/2020.06.25.171447 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Follicle Stem Cells (FSCs) in the Drosophila ovary; a critique of published studies defining the number, location and behavior of FSCs ]]> https://biorxiv.org/content/10.1101/2020.06.25.171579v1?rss=1 Kalderon, D. Melamed, D. Reilein, A. 2020-06-27 doi:10.1101/2020.06.25.171579 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Antibiotics effects on the fecal metabolome in preterm infants ]]> https://biorxiv.org/content/10.1101/2020.06.26.159590v1?rss=1 Patton, L. Li, N. Garrett, T. J. Ruoss, J. L. Russell, J. T. de la Cruz, D. Bazacliu, C. Polin, R. A. Triplett, E. W. Neu, J. 2020-06-26 doi:10.1101/2020.06.26.159590 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Multitrait genetic-phenotype associations to connect disease variants and biological mechanisms ]]> https://biorxiv.org/content/10.1101/2020.06.26.172999v1?rss=1 Julienne, H. Laville, V. McCaw, Z. R. He, Z. Guillemot, V. Lasry, C. Ziyatdinov, A. Vaysse, A. Lechat, P. Menager, H. Le Goff, W. Dube, M.-P. Kraft, P. Ionita-Laza, I. Vilhjalmsson, B. J. Aschard, H. 2020-06-28 doi:10.1101/2020.06.26.172999 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Integrating single-cell RNA-seq and imaging with SCOPE-seq2 ]]> https://biorxiv.org/content/10.1101/2020.06.28.176404v1?rss=1 Liu, Z. Yuan, J. Lasorella, A. Iavarone, A. Bruce, J. N. Canoll, P. Sims, P. A. 2020-06-29 doi:10.1101/2020.06.28.176404 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline ]]> https://biorxiv.org/content/10.1101/2020.06.29.177238v1?rss=1 Rahman, M. S. Islam, M. R. Hoque, M. N. Alam, A. S. M. R. U. Akther, M. Puspo, J. A. Akter, S. Anwar, A. Sultana, M. Hossain, M. A. 2020-06-29 doi:10.1101/2020.06.29.177238 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Functional characterization of human Heschl's gyrus in response to natural speech ]]> https://biorxiv.org/content/10.1101/2020.06.29.178178v1?rss=1 Khalighinejad, B. Herrero, J. Bickel, S. Mehta, A. Mesgarani, N. 2020-06-30 doi:10.1101/2020.06.29.178178 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Accounting for imperfect detection reveals role of host traits in structuring viral diversity of a wild bat community ]]> https://biorxiv.org/content/10.1101/2020.06.29.178798v1?rss=1 Sjodin, A. R. Anthony, S. J. Willig, M. R. Tingley, M. W. 2020-06-30 doi:10.1101/2020.06.29.178798 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Membrane pore energetics and the pathways to membrane rupture ]]> https://biorxiv.org/content/10.1101/2020.06.29.178988v1?rss=1 An, D. Thiyagarajan, S. Antipov, E. Alcott, B. E. O'Shaughnessy, B. 2020-06-30 doi:10.1101/2020.06.29.178988 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ A chronic photocapacitor implant for noninvasive neurostimulation with deep red light ]]> https://biorxiv.org/content/10.1101/2020.07.01.182113v1?rss=1 Silvera-Ejneby, M. Jakesova, M. Ferrero, J. J. Migliaccio, L. Zhao, Z. Berggren, M. Khodagholy, D. Derek, V. Gelinas, J. Glowacki, E. D. 2020-07-02 doi:10.1101/2020.07.01.182113 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Partial inhibition of mitochondrial complex I attenuates neurodegeneration and restores energy homeostasis and synaptic function in a symptomatic Alzheimers mouse model ]]> https://biorxiv.org/content/10.1101/2020.07.01.182428v1?rss=1 Stojakovic, A. Trushin, S. Sheu, A. Khalili, L. Chang, S.-Y. Li, X. Christensen, T. Salisbury, J. L. Geroux, R. E. Gateno, B. Flannery, P. J. Dehankar, M. Funk, C. C. Wilkins, J. Stepanova, A. OHagan, T. Galkin, A. Nesbitt, J. Zhu, X. Tripathi, U. Macura, S. Tchkonia, T. Pirtskhalava, T. Kirkland, J. L. Kudgus, R. A. Schoon, R. A. Reid, J. M. Yamazaki, Y. Kanekiyo, T. Zhang, S. Nemutlu, E. Dzeja, P. Jaspersen, A. Kwon, C. Y. I. Lee, M. K. Trushina, E. 2020-07-01 doi:10.1101/2020.07.01.182428 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Association of the invasive Haemaphysalis longicornis tick with vertebrate hosts, other native tick vectors, and tick-borne pathogens in New York City ]]> https://biorxiv.org/content/10.1101/2020.07.01.182626v1?rss=1 Tufts, D. M. Goodman, L. B. Benedict, M. C. Davis, A. D. VanAcker, M. C. Diuk-Wasser, M. A. 2020-07-02 doi:10.1101/2020.07.01.182626 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Scaled Recoupling of Chemical Shift Anisotropies at High Magnetic Fields under MAS with Interspersed C-elements ]]> https://biorxiv.org/content/10.1101/2020.07.02.184770v1?rss=1 Fritzsching, K. J. Keeler, E. G. He, C. McDermott, A. E. 2020-07-06 doi:10.1101/2020.07.02.184770 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ The Primary Tumor Immune Microenviornment Status Predicts the Response to Immunotherapy and Overall Survival in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2020.07.03.186221v1?rss=1 Moorthy, A. K. Quinn, A. 2020-07-03 doi:10.1101/2020.07.03.186221 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Antagonistic epistasis of Hnf4a and FoxO1 networks through enhancer interactionsin beta-cell function ]]> https://biorxiv.org/content/10.1101/2020.07.04.187864v1?rss=1 Kuo, T. Du, W. Miyachi, Y. Dadi, P. K. Jacobson, D. A. Accili, D. 2020-07-05 doi:10.1101/2020.07.04.187864 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2020.07.04.187989v1?rss=1 Zhou, T. Tsybovsky, Y. Olia, A. S. Gorman, J. Rapp, M. A. Cerutti, G. Katsamba, P. S. Nazzari, A. Schon, A. Wang, P. D. Bimela, J. Shi, W. Teng, I.-T. Zhang, B. Boyington, J. C. Chuang, G.-Y. Sampson, J. M. Sastry, M. Stephens, T. Stuckey, J. Wang, S. Friesner, R. A. Ho, D. D. Mascola, J. R. Shapiro, L. Kwong, P. D. 2020-07-04 doi:10.1101/2020.07.04.187989 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Genetic background modifies vulnerability to glaucoma related phenotypes in Lmx1b mutant mice ]]> https://biorxiv.org/content/10.1101/2020.07.05.188516v1?rss=1 Tolman, N. Macalinao, D. G. Kearney, A. L. Macnicoll, K. H. de Vries, W. N. Jackson, I. Cross, S. H. Kizhatil, K. K. Nair, S. John, S. W. 2020-07-05 doi:10.1101/2020.07.05.188516 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits ]]> https://biorxiv.org/content/10.1101/2020.07.06.146951v1?rss=1 Pahl, M. C. Doege, C. A. Hodge, K. M. Littleton, S. H. Leonard, M. E. Lu, S. Rausch, R. Pippin, J. A. Bradfield, J. P. Hammond, R. K. Boehm, K. Berkowitz, R. I. Lasconi, C. Su, C. Chesi, A. Johnson, M. Wells, A. D. Voight, B. F. Leibel, R. L. Cousminer, D. L. Grant, S. F. A. 2020-07-06 doi:10.1101/2020.07.06.146951 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture ]]> https://biorxiv.org/content/10.1101/2020.07.06.185066v1?rss=1 Chia, R. Sabir, M. S. Bandres-Ciga, S. Saez-Atienzar, S. Reynolds, R. H. Gustavsson, E. Walton, R. L. Ahmed, S. Viollet, C. Ding, J. Makarious, M. B. Diez-Fairen, M. Portley, M. K. Shah, Z. Abramzon, Y. Hernandez, D. G. Blauwendraat, C. Stone, D. J. Eicher, J. Parkkinen, L. Ansorge, O. Clark, L. Honig, L. S. Marder, K. Lemstra, A. St. George-Hyslop, P. Londos, E. Morgan, K. Lashley, T. Warner, T. T. Jaunmuktane, Z. Galasko, D. Santana, I. Tienari, P. Myllykangas, L. Oinas, M. Cairns, N. J. Morris, J. C. Halliday, G. M. Van Deerlin, V. M. Trojanowski, J. 2020-07-06 doi:10.1101/2020.07.06.185066 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Screening predictors of weight loss: an Integromics Approach ]]> https://biorxiv.org/content/10.1101/2020.07.06.188284v1?rss=1 Joel Correa da Rosa Jose O. Aleman Jason Mohabir Yupu Liang Jan L Breslow Peter R. Holt 2020-07-10 doi:10.1101/2020.07.06.188284 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus ]]> https://biorxiv.org/content/10.1101/2020.07.07.190546v1?rss=1 Wells, H. L. Letko, M. C. Lasso, G. Ssebide, B. Nziza, J. Byarugaba, D. K. Navarrete-Macias, I. Liang, E. Cranfield, M. Han, B. A. Tingley, M. W. Diuk-Wasser, M. Goldstein, T. Kreuder Johnson, C. Mazet, J. Chandran, K. Munster, V. Gilardi, K. Anthony, S. J. 2020-07-07 doi:10.1101/2020.07.07.190546 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Extracting neural signals from semi-immobilized animals with deformable non-negative matrix factorization ]]> https://biorxiv.org/content/10.1101/2020.07.07.192120v1?rss=1 Nejatbakhsh, A. Varol, E. Yemini, E. Venkatachalam, V. Lin, A. Samuel, A. D. T. Paninski, L. 2020-07-10 doi:10.1101/2020.07.07.192120 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Survival of the salient: Emotion rescues otherwise forgettable memories via neural reactivation and post-encoding hippocampal connectivity ]]> https://biorxiv.org/content/10.1101/2020.07.07.192252v1?rss=1 Clewett, D. Dunsmoor, J. Bachman, S. Phelps, E. Davachi, L. 2020-07-10 doi:10.1101/2020.07.07.192252 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Public and private human T cell clones respond differentially to HCMV antigen when boosted by CD3 co-potentiation ]]> https://biorxiv.org/content/10.1101/2020.07.08.193805v1?rss=1 Laura R.E. Becher Wendy K. Nevala Shari S. Sutor Megan Abergel Michele M. Hoffmann Christopher A. Parks Larry R. Pease Adam G. Schrum Svetomir N. Markovic Diana Gil 2020-07-08 doi:10.1101/2020.07.08.193805 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy ]]> https://biorxiv.org/content/10.1101/2020.07.08.194332v1?rss=1 Pavan Bachireddy Elham Azizi Cassandra Burdziak Vinhkhang N Nguyen Christina Ennis Zi-Ning Choo Shuqiang Li Kenneth J Livak Donna S Neuberg Robert J Soiffer Jerome Ritz Edwin P Alyea Dana Pe'er Catherine J Wu 2020-07-10 doi:10.1101/2020.07.08.194332 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Modulation of Sensory Response at Different Time Lags after Locus Coeruleus Micro-stimulation ]]> https://biorxiv.org/content/10.1101/2020.07.09.188615v1?rss=1 Zeinab Fazlali Yadollah Ranjbar-Slamloo Ehsan Arabzadeh 2020-07-09 doi:10.1101/2020.07.09.188615 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Distributed control of motor circuits for backward walking in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.11.198663v1?rss=1 Kai Feng Rajyashree Sen Ryo Minegishi Michael Duebbert Till Bockemuehl Ansgar Bueschges Barry Dickson 2020-07-12 doi:10.1101/2020.07.11.198663 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Impact of genetic susceptibility to multiple sclerosis on the T cell epigenome: proximal and distal effects ]]> https://biorxiv.org/content/10.1101/2020.07.11.198721v1?rss=1 Tina Roostaei Hans-Ulrich Klein Daniel Felsky Pia Kivisakk Sarah M. Connor Alexandra Kroshilina Christina Yung Yiyi Ma Belinda J. Kaskow Xiaorong Shao Brooke Rhead Jia Liu Nikolaos Patsopoulos Lisa F. Barcellos Howard L. Weiner Philip L. De Jager 2020-07-12 doi:10.1101/2020.07.11.198721 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Endosomal trafficking is required for glycosylation and normal maturation of the Alzheimer's-associated protein sorLA ]]> https://biorxiv.org/content/10.1101/2020.07.12.199885v1?rss=1 Christensen, S. K. Narimatsu, Y. Simoes, S. Goth, C. K. Vaegter, C. B. Small, S. A. Clausen, H. Andersen, O. M. 2020-07-13 doi:10.1101/2020.07.12.199885 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ Causal inference in environmental sound recognition ]]> https://biorxiv.org/content/10.1101/2020.07.13.200949v1?rss=1 Traer, J. Norman-Haignere, S. V. McDermott, J. H. 2020-07-13 doi:10.1101/2020.07.13.200949 Cold Spring Harbor Laboratory Press 2020-07-13 <![CDATA[ A structural model of a Ras-Raf signalosome ]]> https://biorxiv.org/content/10.1101/2020.07.15.165266v1?rss=1 Mysore, V. P. Zhou, Z.-W. Ambrogio, C. Li, L. Kapp, J. N. Lu, C. Wang, Q. Tucker, M. R. Okoro, J. J. Nagy-Davidescu, G. Bai, X. Pluckthun, A. Janne, P. A. Westover, K. D. Shan, Y. Shaw, D. E. 2020-07-15 doi:10.1101/2020.07.15.165266 Cold Spring Harbor Laboratory Press 2020-07-15 <![CDATA[ An automated, high throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma ]]> https://biorxiv.org/content/10.1101/2020.07.16.206987v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@13ab547org.highwire.dtl.DTLVardef@1535020org.highwire.dtl.DTLVardef@b191aaorg.highwire.dtl.DTLVardef@1d23fa4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ware, S. A. Desai, N. Lopez, M. Leach, D. Zhang, Y. Giordano, L. Nouraie, M. Picard, M. Kaufman, B. 2020-07-16 doi:10.1101/2020.07.16.206987 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Does the phase of ongoing EEG oscillations predict auditory perception? ]]> https://biorxiv.org/content/10.1101/2020.07.17.209387v1?rss=1 Tal, I. Leszczynski, M. Mesgarani, N. Schroeder, C. E. 2020-07-17 doi:10.1101/2020.07.17.209387 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ CRISPR RNA-guided integrases for high-efficiency and multiplexed bacterial genome engineering ]]> https://biorxiv.org/content/10.1101/2020.07.17.209452v1?rss=1 Vo, P. L. H. Ronda, C. Klompe, S. E. Chen, E. E. Acree, C. Wang, H. H. Sternberg, S. H. 2020-07-18 doi:10.1101/2020.07.17.209452 Cold Spring Harbor Laboratory Press 2020-07-18 <![CDATA[ Delay-Induced Uncertainty in Physiological Systems ]]> https://biorxiv.org/content/10.1101/2020.07.17.209544v1?rss=1 Karamched, B. R. Albers, D. Hripcsak, G. Ott, W. 2020-07-19 doi:10.1101/2020.07.17.209544 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly ]]> https://biorxiv.org/content/10.1101/2020.07.20.209130v1?rss=1 Mascibroda, L. G. Shboul, M. Elrod, N. D. Colleaux, L. Hamamy, H. Huang, K.-L. Peart, N. J. Singh, M. K. Lee, H. Merriman, B. Jodoin, J. N. Lee, L. A. Al-Rawashdeh, B. Ababneh, O. El-Khateeb, M. Fathalla, R. Escande-Beillard, N. Nelson, S. F. Wu, Y. Tong, L. Kenney, L. J. Russell, W. K. Amiel, J. Reversade, B. Wagner, E. J. 2020-07-21 doi:10.1101/2020.07.20.209130 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Transcriptional response modules characterise IL-1 and IL-6 activity in COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.07.22.202275v1?rss=1 Bell, L. C. K. Noursadeghi, M. Pollara, G. 2020-07-23 doi:10.1101/2020.07.22.202275 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Beyond orphaned infants: novel effects of maternal death in wild primates ]]> https://biorxiv.org/content/10.1101/2020.07.22.212605v1?rss=1 Zipple, M. N. Altmann, J. Campos, F. A. Cords, M. Fedigan, L. M. Lawler, R. R. Lonsdorf, E. V. Perry, S. Pusey, A. E. Stoinski, T. S. Strier, K. Alberts, S. C. 2020-07-22 doi:10.1101/2020.07.22.212605 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ The frailty syndrome as an emergent state of parallel dysregulation in multiple physiological systems ]]> https://biorxiv.org/content/10.1101/2020.07.22.214718v1?rss=1 Ghachem, A. Fried, L. P. Legault, V. Bandeen-Roche, K. Presse, N. Cohen, A. A. 2020-07-23 doi:10.1101/2020.07.22.214718 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ The genetic architecture of the sexually selected sword ornament and its evolution in hybrid populations ]]> https://biorxiv.org/content/10.1101/2020.07.23.218164v1?rss=1 Powell, D. L. Payne, C. Keegan, M. Banerjee, S. M. Cui, R. Andolfatto, P. Schumer, M. Rosenthal, G. G. 2020-07-24 doi:10.1101/2020.07.23.218164 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ The trajectory of cortical GABA levels across thelifespan: An individual participant datameta-analysis of edited MRS studies ]]> https://biorxiv.org/content/10.1101/2020.07.23.218792v1?rss=1 Porges, E. C. Jensen, G. Foster, B. Edden, R. A. E. Puts, N. A. J. 2020-07-24 doi:10.1101/2020.07.23.218792 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Developing Small Molecules that Inhibit K-Ras/GTP Binding Based on New Affinity Measurements ]]> https://biorxiv.org/content/10.1101/2020.07.27.218248v1?rss=1 Carta, L. Hutcheson, R. Davis, S. A. Rudolph, M. J. Reynolds, C. H. Quick, M. Williams, T. M. Schmertzler, M. Hadari, Y. R. 2020-07-29 doi:10.1101/2020.07.27.218248 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Erythrocyte CD55 mediates the internalization of Plasmodium falciparum parasites ]]> https://biorxiv.org/content/10.1101/2020.07.27.223644v1?rss=1 Shakya, B. Patel, S. D. Tani, Y. Egan, E. S. 2020-07-27 doi:10.1101/2020.07.27.223644 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Intrinsic excitability mechanisms of neuronal ensemble formation ]]> https://biorxiv.org/content/10.1101/2020.07.29.223966v1?rss=1 Alejandre-Garcia, T. Kim, S. Perez-Ortega, J. E. Yuste, R. 2020-07-29 doi:10.1101/2020.07.29.223966 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments ]]> https://biorxiv.org/content/10.1101/2020.07.30.229088v1?rss=1 Yahi, A. Hoffman, P. Brandt, M. Mohammadi, P. Tatonetti, N. P. Lappalainen, T. 2020-07-30 doi:10.1101/2020.07.30.229088 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ Subcellular mRNA localization and local translation of Arhgap11a in radial glial cells regulates cortical development ]]> https://biorxiv.org/content/10.1101/2020.07.30.229724v1?rss=1 Pilaz, L.-J. Joshi, K. Liu, J. Tsunekawa, Y. Alsina, F. Sethi, S. Suzuki, I. Vanderhaeghen, P. Polleux, F. Silver, D. 2020-07-31 doi:10.1101/2020.07.30.229724 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ The cooperative assembly of shelterin bridge provides a kinetic gateway that controls telomere length homeostasis ]]> https://biorxiv.org/content/10.1101/2020.07.31.231530v1?rss=1 Liu, J. Hu, X. Bao, K. Kim, J.-K. Jia, S. Qiao, F. 2020-08-02 doi:10.1101/2020.07.31.231530 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ The Multispecies Coalescent in Space and Time ]]> https://biorxiv.org/content/10.1101/2020.08.02.233395v1?rss=1 McKenzie, P. F. Eaton, D. A. R. 2020-08-03 doi:10.1101/2020.08.02.233395 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Epigenome Prediction of Gene Expression using a Dynamical System Approach ]]> https://biorxiv.org/content/10.1101/2020.08.03.234740v1?rss=1 Brunner, J. D. Kim, J. Downing, T. L. Mjolsness, E. Kober, K. M. 2020-08-04 doi:10.1101/2020.08.03.234740 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors ]]> https://biorxiv.org/content/10.1101/2020.08.03.235291v1?rss=1 Iketani, S. Forouhar, F. Liu, H. Hong, S. J. Lin, F.-Y. Nair, M. S. Zask, A. Huang, Y. Xing, L. Stockwell, B. R. Chavez, A. Ho, D. D. 2020-08-04 doi:10.1101/2020.08.03.235291 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Concerted evolution reveals co-adapted amino acid substitutions in frogs that prey on toxic toads ]]> https://biorxiv.org/content/10.1101/2020.08.04.234435v1?rss=1 Mohammadi, S. Yang, L. Harpak, A. Herrera-Alvarez, S. Rodriguez-Ordonez, M. d. P. Peng, J. Zhang, K. Storz, J. F. Dobler, S. Crawford, A. J. Andolfatto, P. 2020-08-05 doi:10.1101/2020.08.04.234435 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Spatial tissue profiling by imaging-free molecular tomography ]]> https://biorxiv.org/content/10.1101/2020.08.04.235655v1?rss=1 Schede, H. H. Schneider, C. G. Stergiadou, J. Borm, L. E. Ranjak, A. Yamawaki, T. M. David, F. P. A. Lonnerberg, P. Laurent, G. Tosches, M. A. Codeluppi, S. La Manno, G. 2020-08-04 doi:10.1101/2020.08.04.235655 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Threshold concentration and random collision determine the growth of the phase-separated huntingtin inclusion from a stable core ]]> https://biorxiv.org/content/10.1101/2020.08.05.237073v1?rss=1 Pei, S. Swayne, T. C. Morris, J. F. Emtage, L. 2020-08-06 doi:10.1101/2020.08.05.237073 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Epistasis and physico-chemical constraints contribute to spatial clustering of amino acid substitutions in protein evolution. ]]> https://biorxiv.org/content/10.1101/2020.08.05.237594v1?rss=1 Taverner, A. M. Blaine, L. J. Andolfatto, P. 2020-08-05 doi:10.1101/2020.08.05.237594 Cold Spring Harbor Laboratory Press 2020-08-05 <![CDATA[ Sofosbuvir Terminated RNA is More Resistant to SARS-CoV-2 Proofreader than RNA Terminated by Remdesivir ]]> https://biorxiv.org/content/10.1101/2020.08.07.242156v1?rss=1 Jockusch, S. Tao, C. Li, X. Chien, M. Kumar, S. Morozova, I. Kalachikov, S. Russo, J. J. Ju, J. 2020-08-10 doi:10.1101/2020.08.07.242156 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Urinary proteome profiling for stratifying patients with familial Parkinsons disease ]]> https://biorxiv.org/content/10.1101/2020.08.09.243584v1?rss=1 Virreira Winter, S. Karayel, O. Strauss, M. T. Padmanabhan, S. Surface, M. Merchant, K. Alcalay, R. N. Mann, M. 2020-08-10 doi:10.1101/2020.08.09.243584 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ A Uropathogenic E. coli UTI89 model of prostatic inflammation and collagen accumulation for use in studying aberrant collagen production in the prostate ]]> https://biorxiv.org/content/10.1101/2020.08.10.238196v1?rss=1 RUETTEN, H. M. Sandhu, J. Mueller, B. Wang, P. Zhang, H. L. Wegner, K. A. Cadena, M. Sandhu, S. Abler, L. Zhu, J. O'Driscoll, C. A. Chelgren, B. Wang, Z. Shen, T. Barasch, J. Bjorling, D. E. Vezina, C. M. 2020-08-10 doi:10.1101/2020.08.10.238196 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons ]]> https://biorxiv.org/content/10.1101/2020.08.11.246769v1?rss=1 Ipsaro, J. J. O'Brien, P. A. Bhattacharya, S. Palmer, A. G. Joshua-Tor, L. 2020-08-11 doi:10.1101/2020.08.11.246769 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Deep and superficial layers of the primary somatosensory cortex are critical for whisker-based texture discrimination in mice ]]> https://biorxiv.org/content/10.1101/2020.08.12.245381v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@16c4d20org.highwire.dtl.DTLVardef@13b8832org.highwire.dtl.DTLVardef@16ac3aborg.highwire.dtl.DTLVardef@5426d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Park, J. M. Hong, Y. K. Rodgers, C. C. Dahan, J. B. Schmidt, E. R. Bruno, R. M. 2020-08-12 doi:10.1101/2020.08.12.245381 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Systematic evaluation of genome sequencing as a first-tier diagnostic test for prenatal and pediatric disorders ]]> https://biorxiv.org/content/10.1101/2020.08.12.248526v1?rss=1 Lowther, C. Valkanas, E. Giordano, J. L. Wang, H. Z. Currall, B. B. O'Keefe, K. Collins, R. L. Zhao, X. Austin-Tse, C. A. Evangelista, E. Aggarwal, V. Lucente, D. Gauthier, L. D. Tolonen, C. Sahakian, N. An, J.-Y. Dong, S. Norton, M. E. MacKenzie, T. Devlin, B. Gilmore, K. Powell, B. Brandt, A. Vetrini, F. DiVito, M. Goldstein, D. B. Sanders, S. J. MacArthur, D. G. Hodge, J. C. O'Donnell-Luria, A. Rehm, H. Vora, N. Levy, B. Brand, H. Wapner, R. Talkowski, M. E. 2020-08-13 doi:10.1101/2020.08.12.248526 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ Scarless engineering of the Drosophila genome near any site-specific integration site ]]> https://biorxiv.org/content/10.1101/2020.08.13.249656v1?rss=1 Feng, S. Lu, S. Grueber, W. B. Mann, R. S. 2020-08-14 doi:10.1101/2020.08.13.249656 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses ]]> https://biorxiv.org/content/10.1101/2020.08.13.249953v1?rss=1 Mishra, N. Huang, X. Joshi, S. Guo, C. Ng, J. Thakkar, R. Wu, Y. Dong, X. Li, Q. Pinapati, R. Sullivan, E. Caciula, A. Tokarz, R. Briese, T. Lu, J. Lipkin, W. I. 2020-08-14 doi:10.1101/2020.08.13.249953 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ BARcode DEmixing through Non-negative Spatial Regression (BarDensr) ]]> https://biorxiv.org/content/10.1101/2020.08.17.253666v1?rss=1 Chen, S. Loper, J. Chen, X. Zador, T. Paninski, L. 2020-08-17 doi:10.1101/2020.08.17.253666 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Brain Amyloid and the Transition to Dementia in Down Syndrome ]]> https://biorxiv.org/content/10.1101/2020.08.19.257790v1?rss=1 Keator, D. B. Doran, E. Taylor, L. A. Phelan, M. J. Hom, C. Tseung, K. van Erp, T. G. M. Potkin, S. G. Brickman, A. M. Rosas, D. H. Yassa, M. A. Silverman, W. Lott, I. T. 2020-08-20 doi:10.1101/2020.08.19.257790 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Distinct cortical systems reinstate the content and context of episodic memories ]]> https://biorxiv.org/content/10.1101/2020.08.20.248567v1?rss=1 Kragel, J. E. Ezzyat, Y. Lega, B. C. Sperlin, M. R. Worrell, G. A. Gross, R. E. Jobst, B. C. Sheth, S. A. Zaghloul, K. A. Stein, J. M. Kahana, M. J. 2020-08-24 doi:10.1101/2020.08.20.248567 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking ]]> https://biorxiv.org/content/10.1101/2020.08.20.259705v1?rss=1 Wu, A. Buchanan, E. K. Whiteway, M. R. Schartner, M. Meijer, G. T. Noel, J.-P. Rodriguez, E. Everett, C. Norovich, A. Schaffer, E. S. Mishra, N. Salzman, C. D. Angelaki, D. E. International Brain Laboratory, T. Cunningham, J. P. Paninski, L. 2020-08-22 doi:10.1101/2020.08.20.259705 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation ]]> https://biorxiv.org/content/10.1101/2020.08.20.259770v1?rss=1 Lapointe, C. P. Grosely, R. Johnson, A. G. Wang, J. Fernandez, I. S. Puglisi, J. D. 2020-08-21 doi:10.1101/2020.08.20.259770 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Offline Memory Reactivation Promotes the ConsolidationOf Spatially Unbiased Long-Term Cognitive Maps ]]> https://biorxiv.org/content/10.1101/2020.08.20.259879v1?rss=1 Grosmark, A. D. Sparks, F. T. Davis, M. J. Losonczy, A. 2020-08-22 doi:10.1101/2020.08.20.259879 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Neuroticism alters the transcriptome of the frontal cortex to contribute to the cognitive decline and onset of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.08.21.261677v1?rss=1 De Jager, C. H. White, C. C. Bennett, D. A. Ma, Y. 2020-08-22 doi:10.1101/2020.08.21.261677 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Plasmodium berghei K13 Mutations Mediate In Vivo Artemisinin Resistance That is Reversed by Proteasome Inhibition ]]> https://biorxiv.org/content/10.1101/2020.08.24.256842v1?rss=1 Simwela, N. V. Stokes, B. H. Aghabi, D. Bogyo, M. Fidock, D. A. Waters, A. P. 2020-08-24 doi:10.1101/2020.08.24.256842 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Meta-azotomics of engineered wastewater treatment processes reveals differential contributions of established and novel models of N-cycling ]]> https://biorxiv.org/content/10.1101/2020.08.25.229054v1?rss=1 Park, M.-R. Annavajhala, M. K. Chandran, K. 2020-08-25 doi:10.1101/2020.08.25.229054 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Individual bitter-sensing neurons in Drosophila exhibit both ON and OFF responses that influence synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2020.08.25.266619v1?rss=1 Devineni, A. V. Deere, J. U. Sun, B. Axel, R. 2020-08-26 doi:10.1101/2020.08.25.266619 Cold Spring Harbor Laboratory Press 2020-08-26 <![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[ Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease ]]> https://biorxiv.org/content/10.1101/2020.08.26.251611v1?rss=1 Shah, K. Bedi, R. Rogozhnikov, A. Ramkumar, P. Tong, Z. Rash, B. Stanton, M. Sorokin, J. Apaydin, C. Batarse, A. Bergamaschi, J. Blattner, R. Brown, S. Bosshardt, A. Castrillo, C. Dang, B. Drusinsky, S. Enriquez, L. Grayson, D. Hilliard, J. Hsu, P.-K. Johnson, C. Jones, R. Lash, A. Lee, E. Li, K. McKay, A. Mount, E. Nicola, J. Oumzil, I. Paek, J. Pascoe, D. Piepho, A. Poust, S. Quang, D. Schultz, M. Sims, J. Taylor, P. Treiman, G. Wueseke, O. Young, N. Pollen, A. A. Flanzer, D. Chao, D. Skibinski, G. Kato, S. Escola, S. 2020-08-27 doi:10.1101/2020.08.26.251611 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development ]]> https://biorxiv.org/content/10.1101/2020.08.27.268730v1?rss=1 Joglekar, A. Przhibelskiy, A. D. Mahfouz, A. Collier, P. Lin, S. Schlusche, A. K. Marrocco, J. Williams, S. R. Haase, B. Hayes, A. Chew, J. G. Weisenfeld, N. I. Wong, M. Y. Stein, A. N. Hardwick, S. Hunt, T. Bent, Z. Fedrigo, O. Sloan, S. A. Risso, D. Jarvis, E. D. Flicek, P. Luo, W. Pitt, G. S. Frankish, A. Smit, A. B. Ross, M. E. Tilgner, H. U. 2020-08-27 doi:10.1101/2020.08.27.268730 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ De Novo Mutation in an Enhancer of EBF3 in simplex autism ]]> https://biorxiv.org/content/10.1101/2020.08.28.270751v1?rss=1 Padhi, E. M. Hayeck, T. J. Mannion, B. Chatterjee, S. Byrska-Bishop, M. Musunuri, R. Narzisi, G. Abhyankar, A. Cheng, Z. Hunter, R. D. Akiyama, J. Fries, L. E. Ng, J. Stong, N. Allen, A. S. Dickel, D. E. Bernier, R. A. Gorkin, D. U. Pennacchio, L. A. Zody, M. C. Turner, T. N. 2020-08-28 doi:10.1101/2020.08.28.270751 Cold Spring Harbor Laboratory Press 2020-08-28 <![CDATA[ A simplified cell-based assay to identify coronavirus 3CL protease inhibitors ]]> https://biorxiv.org/content/10.1101/2020.08.29.272864v1?rss=1 Resnick, S. J. Iketani, S. Hong, S. J. Zask, A. Liu, H. Kim, S. Melore, S. Nair, M. S. Huang, Y. Tay, N. E. S. Rovis, T. Yang, H. W. Stockwell, B. R. Ho, D. D. Chavez, A. 2020-08-29 doi:10.1101/2020.08.29.272864 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ The connectome of the adult Drosophila mushroom body: implications for function ]]> https://biorxiv.org/content/10.1101/2020.08.29.273276v1?rss=1 Li, F. Lindsey, J. Marin, E. Otto, N. Dreher, M. Dempsey, G. Stark, I. Bates, A. S. Pleijzier, M. W. Schlegel, P. Nern, A. Takemura, S. Yang, T. Francis, A. Braun, A. Parekh, R. Costa, M. Scheffer, L. Aso, Y. Jefferis, G. S. X. E. Abbott, L. F. Litwin-Kumar, A. Waddell, S. Rubin, G. M. 2020-08-29 doi:10.1101/2020.08.29.273276 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization ]]> https://biorxiv.org/content/10.1101/2020.08.30.274035v1?rss=1 1000 olfactory receptor (OR) genes is stochastic but, yet, spatially organized in stereotypic anatomical segments, or "zones", along the dorsoventral axis of the mouse olfactory epithelium. We discovered that zonal OR expression is specified by OR chromatin structure and genome architecture during olfactory neuron differentiation. Specifically, across every zone dorsally expressed ORs have higher levels of heterochromatic marks and long-range contacts than ORs expressed ventrally. However, OR heterochromatin levels and frequency of genomic contacts between ORs gradually increase towards ventral zones. Consequently, ORs from dorsal indexes accumulate high H3K9me3/H3K79me3 enrichment and become silenced in ventral zones, while ORs from ventral indexes lack activating long-range genomic interactions and, thus, cannot be chosen in dorsal segments. This process is regulated by NFIA, B, and X gradients along the dorsoventral axis, triple deletion of which causes homeotic transformations on zonal OR expression, heterochromatin formation, and genomic compartmentalization. ]]> Bashkirova, E. Monahan, K. Campbell, C. E. Osinski, J. M. Tan, L. Schieren, I. Barnea, G. Xie, S. Gronostajski, R. M. Lomvardas, S. 2020-08-30 doi:10.1101/2020.08.30.274035 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ Extreme stiffness of neuronal synapses and implications for synaptic adhesion and plasticity ]]> https://biorxiv.org/content/10.1101/2020.08.31.273466v1?rss=1 Yang, J. Mandriota, N. Harrellson, S. G. Jones-Molina, J. A. Yuste, R. Lefort, R. Sahin, O. 2020-09-01 doi:10.1101/2020.08.31.273466 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Corticospinal neurons encode complex motor signals that are broadcast to dichotomous striatal circuits ]]> https://biorxiv.org/content/10.1101/2020.08.31.275180v1?rss=1 Nelson, A. Abdelmesih, B. Costa, R. M. 2020-08-31 doi:10.1101/2020.08.31.275180 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Reduction of Glut1 in retinal neurons but not the RPE alleviates polyol accumulation and normalizes early characteristics of diabetic retinopathy. ]]> https://biorxiv.org/content/10.1101/2020.08.31.275230v1?rss=1 Holoman, N. C. Aiello, J. J. Trobenter, T. D. Tarchick, M. J. Kozlowski, M. R. Makowski, E. R. De Vivo, D. C. Singh, C. Sears, J. E. Samuels, I. S. 2020-09-01 doi:10.1101/2020.08.31.275230 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Fully Automated Detection of Paramagnetic Rims in Multiple Sclerosis Lesions on 3T Susceptibility-Based MR Imaging ]]> https://biorxiv.org/content/10.1101/2020.08.31.276238v1?rss=1 Lou, C. Sati, P. Absinta, M. Clark, K. Dworkin, J. D. Valcarcel, A. M. Schindler, M. K. Reich, D. S. Sweeney, E. M. Shinohara, R. T. 2020-09-02 doi:10.1101/2020.08.31.276238 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion ]]> https://biorxiv.org/content/10.1101/2020.09.01.267211v1?rss=1 Frangieh, C. J. Melms, J. C. Thakore, P. I. Geiger-Schuller, K. R. Ho, P. Luoma, A. M. Cleary, B. R. Malu, S. Cuoco, M. Zhao, M. Rogava, M. Hovey, L. Rotem, A. Bernatche, C. Wucherpfennig, K. W. Johnson, B. E. Rozenblatt-Rosen, O. Schadendorf, D. Regev, A. Izar, B. 2020-09-01 doi:10.1101/2020.09.01.267211 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing ]]> https://biorxiv.org/content/10.1101/2020.09.01.277525v1?rss=1 Hoffer, E. D. Hong, S. Maehigashi, T. Gonzalez, R. L. Whitford, P. Dunham, C. M. 2020-09-01 doi:10.1101/2020.09.01.277525 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Angiotensin converting enzyme 2 is a novel target of the γ-secretase complex ]]> https://biorxiv.org/content/10.1101/2020.09.01.277954v1?rss=1 Bartolome, A. Liang, J. Wang, P. Ho, D. D. Pajvani, U. B. 2020-09-03 doi:10.1101/2020.09.01.277954 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Gaze Behaviour Reveals Flexible Encoding of Competing Reach Goals Under Conditions of Target Uncertainty ]]> https://biorxiv.org/content/10.1101/2020.09.02.279414v1?rss=1 de Brouwer, A. J. Carter, M. J. Smail, L. C. Wolpert, D. M. Gallivan, J. P. Flanagan, J. R. 2020-09-03 doi:10.1101/2020.09.02.279414 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil ]]> https://biorxiv.org/content/10.1101/2020.09.03.281626v1?rss=1 Di Rienzi, S. Johnson, E. Waters, J. L. Kennedy, E. A. Jacobson, J. Lawrence, P. Wang, D. H. Worgall, T. S. Brenna, J. T. Ley, R. E. 2020-09-03 doi:10.1101/2020.09.03.281626 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Retromer Combinatorials for Gene-Therapy Across a Spectrum of Neurological Diseases ]]> https://biorxiv.org/content/10.1101/2020.09.03.282327v1?rss=1 Qureshi, Y. H. Patel, V. M. Kannan, S. Waksal, S. D. Petsko, G. A. Small, S. A. 2020-09-04 doi:10.1101/2020.09.03.282327 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Serum metabolomic biomarkers of perceptual speed in cognitively normal and mildly impaired subjects with fasting state stratification ]]> https://biorxiv.org/content/10.1101/2020.09.03.282343v1?rss=1 Borkowski, K. Taha, A. Y. Pedersen, T. L. De Jager, P. L. Bennett, D. A. Kaddurah-Daouk, R. Newman, J. W. 2020-09-04 doi:10.1101/2020.09.03.282343 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization ]]> https://biorxiv.org/content/10.1101/2020.09.04.281345v1?rss=1 60 types of central brain neurons that interconnect to generate male-typical behaviors. While the indispensable function of FruM in sex-specific behavior has been understood for decades, the molecular mechanisms underlying its activity remain unknown. Here, we take a genome-wide, brain-wide approach to identifying regulatory elements whose activity depends on the presence of FruM. We identify 436 high-confidence genomic regions differentially accessible in male fruitless neurons, validate candidate regions as bona-fide, differentially regulated enhancers, and describe the particular cell types in which these enhancers are active. We find that individual enhancers are not activated universally but are dedicated to specific fru+ cell types. Aside from fru itself, genes are not dedicated to or common across the fru circuit; rather, FruM appears to masculinize each cell type differently, by tweaking expression of the same effector genes used in other circuits. Finally, we find FruM motifs enriched among regulatory elements that are open in the female but closed in the male. Together, these results suggest that FruM acts cell-type-specifically to decommission regulatory elements in male fruitless neurons. ]]> Brovkina, M. V. Duffie, R. Burtis, A. E. Clowney, E. J. 2020-09-04 doi:10.1101/2020.09.04.281345 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Self-Supervised Natural Image Reconstruction and Rich Semantic Classification from Brain Activity ]]> https://biorxiv.org/content/10.1101/2020.09.06.284794v1?rss=1 Gaziv, G. Beliy, R. Granot, N. Hoogi, A. Strappini, F. Golan, T. Irani, M. 2020-09-08 doi:10.1101/2020.09.06.284794 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Phase precession in the human hippocampus and entorhinal cortex ]]> https://biorxiv.org/content/10.1101/2020.09.06.285320v1?rss=1 Qasim, S. E. Fried, I. Jacobs, J. 2020-09-06 doi:10.1101/2020.09.06.285320 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Early alphavirus replication dynamics in single cells reveal a passive basis for superinfection exclusion ]]> https://biorxiv.org/content/10.1101/2020.09.07.282053v1?rss=1 Singer, Z. S. Ambrose, P. Danino, T. Rice, C. 2020-09-07 doi:10.1101/2020.09.07.282053 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps ]]> https://biorxiv.org/content/10.1101/2020.09.07.283994v1?rss=1 Chak, T. C. S. Harris, S. E. Hultgren, K. M. Duffy, J. E. Rubenstein, D. R. 2020-09-09 doi:10.1101/2020.09.07.283994 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Dopamine D2 receptors modulate the cholinergic pause and inhibitory learning ]]> https://biorxiv.org/content/10.1101/2020.09.07.284612v1?rss=1 Gallo, E. F. Greenwald, J. Teboul, E. Martyniuk, K. M. Li, Y. Javitch, J. A. Balsam, P. D. Kellendonk, C. 2020-09-07 doi:10.1101/2020.09.07.284612 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Nonlinear decoding of natural images from large-scale primate retinal ganglion recordings ]]> https://biorxiv.org/content/10.1101/2020.09.07.285742v1?rss=1 1000 simultaneously recorded macaque RGC units, the decoder demonstrates the necessity of nonlinear computations for accurate decoding of the fine structures of visual stimuli. Specifically, high-pass spatial features of natural images can only be decoded using nonlinear techniques, while low-pass features can be extracted equally well by linear and nonlinear methods. Together, these results advance the state of the art in decoding natural stimuli from large populations of neurons. Author summaryNeural decoding is a fundamental problem in computational and statistical neuroscience. There is an enormous literature on this problem, applied to a wide variety of brain areas and nervous systems. Here we focus on the problem of decoding visual information from the retina. The bulk of previous work here has focused on simple linear decoders, applied to modest numbers of simultaneously recorded cells, to decode artificial stimuli. In contrast, here we develop a scalable nonlinear decoding method to decode natural images from the responses of over a thousand simultaneously recorded units, and show that this decoder significantly improves on the state of the art. ]]> Kim, Y. J. Brackbill, N. Batty, E. Lee, J. Mitelut, C. Tong, W. Chichilnisky, E. J. Paninski, L. 2020-09-07 doi:10.1101/2020.09.07.285742 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Unique Genotypic Features of HIV-1 C Gp41 Membrane Proximal External Region Variants during Pregnancy Relate to Mother-to-child Transmission via Breastfeeding ]]> https://biorxiv.org/content/10.1101/2020.09.07.286278v1?rss=1 Yin, L. Chang, K.-F. Nakamura, K. J. Kuhn, L. Aldrovandi, G. M. Goodenow, M. M. 2020-09-08 doi:10.1101/2020.09.07.286278 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[ Neural encoding of socially adjusted value during competitive and hazardous foraging ]]> https://biorxiv.org/content/10.1101/2020.09.11.294058v1?rss=1 Silston, B. Wise, T. Qi, S. Sui, X. Dayan, P. Mobbs, D. 2020-09-12 doi:10.1101/2020.09.11.294058 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ SpineS: An interactive time-series analysis software for dendritic spines ]]> https://biorxiv.org/content/10.1101/2020.09.12.294546v1?rss=1 Argunsah, A. O. Erdil, E. Ghani, M. U. Hobbiss, A. F. Cortes, Y. R. Cetin, M. Israely, I. Unay, D. Karayannis, T. 2020-09-14 doi:10.1101/2020.09.12.294546 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ A two-site flexible clamp mechanism for RET-GDNF-GFRα1 assembly reveals both conformational adaptation and strict geometric spacing ]]> https://biorxiv.org/content/10.1101/2020.09.13.286047v1?rss=1 Adams, S. Purkiss, A. G. Knowles, P. P. Nans, A. Briggs, D. C. Borg, A. Earl, C. P. Goodman, K. M. Nawrotek, A. Borg, A. J. McIntosh, P. B. Houghton, F. M. Kjaer, S. McDonald, N. Q. 2020-09-13 doi:10.1101/2020.09.13.286047 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection ]]> https://biorxiv.org/content/10.1101/2020.09.16.300244v1?rss=1 Tkatchenko, T. V. Tkatchenko, A. V. 2020-09-18 doi:10.1101/2020.09.16.300244 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ Diversity reduces extinction risk at global scales ]]> https://biorxiv.org/content/10.1101/2020.09.17.296285v1?rss=1 Weeks, B. C. Naeem, S. Lasky, J. Tobias, J. 2020-09-19 doi:10.1101/2020.09.17.296285 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Dual strategies in human confidence judgments ]]> https://biorxiv.org/content/10.1101/2020.09.17.299743v1?rss=1 Bertana, A. Chetverikov, A. van Bergen, R. S. Ling, S. Jehee, J. 2020-09-19 doi:10.1101/2020.09.17.299743 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Comprehensive characterization of protein-protein interaction network perturbations by human disease mutations ]]> https://biorxiv.org/content/10.1101/2020.09.18.302588v1?rss=1 Cheng, F. Zhao, J. Wang, Y. Lu, W. Liu, Z. Zhou, Y. Martin, W. Wang, R. Huang, J. Hao, T. Yue, H. Ma, J. Hou, Y. Castrillon, J. Fang, J. Lathia, J. D. Keri, R. A. Lightstone, F. C. Antman, E. M. Rabadan, R. Hill, D. E. Eng, C. Vidal, M. Loscalzo, J. 2020-09-21 doi:10.1101/2020.09.18.302588 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Influence of sensory modality and control dynamics on human path integration ]]> https://biorxiv.org/content/10.1101/2020.09.21.307256v1?rss=1 Stavropoulos, A. Lakshminarasimhan, K. J. Laurens, J. Pitkow, X. Angelaki, D. 2020-09-23 doi:10.1101/2020.09.21.307256 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ Microfluidic Isolation of Aptamers with Affinity towards Multiple Myeloma Monoclonal Immunoglobulins (M-Ig) ]]> https://biorxiv.org/content/10.1101/2020.09.22.308650v1?rss=1 Olsen, T. R. Tapia-Alveal, C. Stojanovic, M. N. Worgall, T. S. Lin, Q. 2020-09-22 doi:10.1101/2020.09.22.308650 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Transsynaptic mapping of Drosophila mushroom body output neurons ]]> https://biorxiv.org/content/10.1101/2020.09.22.309021v1?rss=1 Scaplen, K. M. Talay, M. Fisher, J. D. Cohn, R. Sorkac, A. Aso, Y. Barnea, G. Kaun, K. R. 2020-09-23 doi:10.1101/2020.09.22.309021 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2020.09.23.310003v1?rss=1 Lakkis, J. Wang, D. Zhang, Y. Hu, G. Wang, K. Pan, H. Ungar, L. Reilly, M. Li, X. Li, M. 2020-09-25 doi:10.1101/2020.09.23.310003 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Representational drift in primary olfactory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.24.312132v1?rss=1 Schoonover, C. E. Ohashi, S. N. Axel, R. Fink, A. J. P. 2020-09-25 doi:10.1101/2020.09.24.312132 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Virus-Like Particle Based-Vaccines Elicit Neutralizing Antibodies against the HIV-1 Fusion Peptide ]]> https://biorxiv.org/content/10.1101/2020.09.25.308957v1?rss=1 Mogus, A. T. Liu, L. Jia, M. Ajayi, D. T. Xu, K. Kong, R. Huang, J. Yu, J. Kwong, P. D. Mascola, J. R. Ho, D. D. Tsuji, M. Chackerian, B. 2020-09-25 doi:10.1101/2020.09.25.308957 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ The Impact of Psychopathology, Social Adversity and Stress-relevant DNAm on Prospective Risk for Post-traumatic Stress: A Machine Learning Approach ]]> https://biorxiv.org/content/10.1101/2020.09.25.313635v1?rss=1 88% of the prediction. The top ranked GRRN CpG site was cg05616442, in AKT1, and the top ranked social adversity feature was loneliness. ConclusionMultiple factors including prior PTSS, social adversity, and DNAm play a role in predicting prospective risk of PTSS. ML models identified factors accounting for increased PTSS risk with high accuracy, which may help to target risk factors that reduce the likelihood or course of PTSD, potentially pointing to approaches that can lead to early intervention. ]]> Wani, A. H. Aiello, A. E. Kim, G. S. Xue, F. Martin, C. L. Ratanatharathorn, A. Qu, A. Koenen, K. Galea, S. Wildman, D. E. Uddin, M. 2020-09-28 doi:10.1101/2020.09.25.313635 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome ]]> https://biorxiv.org/content/10.1101/2020.09.27.313445v1?rss=1 Masuda, K. Kornberg, A. Lin, S. Ho, P. Secener, K. Suek, N. Bacarella, A. M. Ingham, M. Rosario, V. Al-Masrou, A. M. Lee-Kong, S. A. Kiran, P. R. Yan, K. S. Stoeckius, M. Smibert, P. Oberstein, P. E. Sims, P. A. Han, A. 2020-09-28 doi:10.1101/2020.09.27.313445 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Signal separability in integrated neurophotonics ]]> https://biorxiv.org/content/10.1101/2020.09.27.315556v1?rss=1 Yatsenko, D. Moreaux, L. C. Choi, J. Tolias, A. Shepard, K. L. Roukes, M. L. 2020-09-29 doi:10.1101/2020.09.27.315556 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans ]]> https://biorxiv.org/content/10.1101/2020.09.28.317156v1?rss=1 Ma, Y. Yu, L. Olah, M. Smith, R. Oatman, S. R. Allen, M. Pishva, E. Zhang, B. Menon, V. Ertekin-Taner, N. Lunnon, K. Bennett, D. A. Klein, H.-U. De Jager, P. 2020-09-29 doi:10.1101/2020.09.28.317156 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Widely used mutants of eiger, encoding the Drosophila Tumor Necrosis factor, carry additional mutations in the NimrodC1 phagocytosis receptor ]]> https://biorxiv.org/content/10.1101/2020.09.30.316257v1?rss=1 Kodra, A. de la Cova, C. Gerhold, A. R. Johnston, L. A. 2020-10-01 doi:10.1101/2020.09.30.316257 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Hierarchical integration across multiple timescales in human auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.30.321687v1?rss=1 Norman-Haignere, S. V. Long, L. K. Devinsky, O. Doyle, W. Irobunda, I. Merricks, E. Feldstein, N. A. McKhann, G. M. V. Schevon, C. Flinker, A. Mesgarani, N. 2020-10-01 doi:10.1101/2020.09.30.321687 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Distinct higher-order representations of natural sounds in human and ferret auditory cortex ]]> https://biorxiv.org/content/10.1101/2020.09.30.321695v1?rss=1 Landemard, A. Bimbard, C. Demene, C. Shamma, S. Norman-Haignere, S. V. Boubenec, Y. 2020-10-01 doi:10.1101/2020.09.30.321695 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Neuroinflammation characterizes the earliest changes in Alzheimer's disease pathology and associated subjective cognitive impairment in adult hydrocephalus biopsies ]]> https://biorxiv.org/content/10.1101/2020.10.01.322511v1?rss=1 Huang, W. Bartosch, A. M. Xiao, H. Flowers, X. Leskinen, S. Tomljanovic, Z. Iodice, G. Boyett, D. Spinazzi, E. Menon, V. McGovern, R. A. McKhann, G. M. Teich, A. F. 2020-10-05 doi:10.1101/2020.10.01.322511 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine ]]> https://biorxiv.org/content/10.1101/2020.10.02.323238v1?rss=1 Wall, J. Sathirapongsasuti, J. F. Gupta, R. Barik, A. Rai, R. K. Rasheed, A. Radha, V. Belsare, S. Menon, R. Phalke, S. Mittal, A. Fang, J. Tanneeru, D. Robinson, J. Chaudhary, R. Fuchsberger, C. Forer, L. Schoenherr, S. Bei, Q. Bhangale, T. Tom, J. Gadde, S. G. K. V, P. B. Naik, N. K. Wang, M. Kwok, P.-Y. Khera, A. V. Lakshmi, B. R. Butterworth, A. Danesh, J. Seshagiri, S. Kathiresan, S. Ghosh, A. Mohan, V. Chowdhury, A. Saleheen, D. Stawiski, E. Peterson, A. S. 2020-10-02 doi:10.1101/2020.10.02.323238 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Genetic or toxicant induced disruption of vesicular monoamine storage and global metabolic profiling in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.10.02.324095v1?rss=1 bradner, j. Kalia, V. Lau, F. Sharma, M. Bucher, M. Johnson, M. Chen, M. Walker, D. Jones, D. Miller, G. 2020-10-02 doi:10.1101/2020.10.02.324095 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Sleeve gastrectomy promotes sustained weight loss while increasing heat production in middle aged, obese female mice ]]> https://biorxiv.org/content/10.1101/2020.10.04.325787v1?rss=1 Emiliano, A. B. He, Y. Higuchi, S. Lopatinsky, N. Nemr, R. Schwartz, G. J. 2020-10-05 doi:10.1101/2020.10.04.325787 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Metabolomic profiling identifies complex lipid species associated with response to weight loss interventions ]]> https://biorxiv.org/content/10.1101/2020.10.05.326025v1?rss=1 Bihlmeyer, N. A. Kwee, L. C. Clish, C. B. Deik, A. A. Gerszten, R. E. Pagidipati, N. J. Laferrere, B. Svetkey, L. P. Newgard, C. B. Kraus, W. E. Shah, S. H. 2020-10-05 doi:10.1101/2020.10.05.326025 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ Fat Mass Regain in Middle-Aged Mice after Sleeve Gastrectomy is divergent from plasma leptin levels ]]> https://biorxiv.org/content/10.1101/2020.10.05.326785v1?rss=1 0.05). SWM group had a significantly lower cumulative food intake throughout the study, except for week 1 (p<0.01). Glucose tolerance was only demonstrably better in the SG group compared to SH group at 8 weeks post-operatively (p<0.01). Plasma leptin was significantly lower in the SG group compared to both SWM and SH groups group by the second post-operative month (p<0.01), in spite of SGs increasing fat mass accumulation. In the second post-operative month, both FGF-21 and GDF-15 were increased in the SH group compared to the SG and SWM groups (p<0.05), while there was no difference in plasma insulin among the three groups. Heat production was surprisingly higher in the SH group compared to the other two groups (p<0.05), even though brown adipose tissue Peroxisome Proliferator-Activated Receptor Gamma (PPARg) and Cidea mRNA expression were significantly higher in SG and SWM compared to SH (p<0.01). There was no change in BAT UCP-1 mRNA expression among the groups (p>0.05). There was also no change in fecal lipid content among the groups (p>0.05). ConclusionsSG in obese, middle aged male mice leads is accompanied by fat mass regain in the second post-operative month, while plasma leptin levels continue to be significantly lower. This raises the question of whether the observed fat mass regain consists mostly of visceral adipose tissue. ]]> Emiliano, A. He, Y. Higuchi, S. Nemr, R. Lopatinsky, N. Schwartz, G. J. 2020-10-07 doi:10.1101/2020.10.05.326785 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Divergent sensory processing converges in frontal cortex for a planned motor response ]]> https://biorxiv.org/content/10.1101/2020.10.06.326678v1?rss=1 Esmaeili, V. Tamura, K. Muscinelli, S. P. Modirshanechi, A. Boscaglia, M. Lee, A. B. Oryshchuk, A. Foustoukos, G. Liu, Y. Crochet, S. Gerstner, W. Petersen, C. C. H. 2020-10-06 doi:10.1101/2020.10.06.326678 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Temporal transitions in post-mitotic neurons throughout the C. elegans nervous system ]]> https://biorxiv.org/content/10.1101/2020.10.06.328880v1?rss=1 Sun, H. Hobert, O. 2020-10-07 doi:10.1101/2020.10.06.328880 Cold Spring Harbor Laboratory Press 2020-10-07 <![CDATA[ Systemic benefits of Gc inhibition to preserve insulin sensitivity ]]> https://biorxiv.org/content/10.1101/2020.10.06.328963v1?rss=1 Kuo, T. Accili, D. 2020-10-08 doi:10.1101/2020.10.06.328963 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Transcribed germline-limited coding sequences in Oxytricha trifallax ]]> https://biorxiv.org/content/10.1101/2020.10.07.330092v1?rss=1 Landweber, L. F. Miller, R. V. Neme, R. Clay, D. Pathmanathan, J. Lu, M. W. Yerlici, V. T. Khurana, J. S. 2020-10-08 doi:10.1101/2020.10.07.330092 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Synergistic effect of deoxynucleosides and AAV gene therapy for thymidine kinase 2 deficiency ]]> https://biorxiv.org/content/10.1101/2020.10.08.330969v1?rss=1 Lopez-Gomez, C. Sanchez-Quintero, M. J. Lee, E. J. Kleiner, G. Xie, J. Akman, H. O. Gao, G. Hirano, M. 2020-10-08 doi:10.1101/2020.10.08.330969 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Loss of clustered protocadherin diversity alters the spatial distribution of cortical interneurons ]]> https://biorxiv.org/content/10.1101/2020.10.08.331488v1?rss=1 Gallerani, N. Au, E. 2020-10-08 doi:10.1101/2020.10.08.331488 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Dopamine neuron synaptic connectivity defines physiological striatal domains ]]> https://biorxiv.org/content/10.1101/2020.10.11.334961v1?rss=1 Chuhma, N. Oh, S. J. Rayport, S. 2020-10-11 doi:10.1101/2020.10.11.334961 Cold Spring Harbor Laboratory Press 2020-10-11 <![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[ The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction ]]> https://biorxiv.org/content/10.1101/2020.10.12.335711v1?rss=1 Secombe, J. Belalcazar, H. M. Hicks, E. L. Zamurrad, S. Liebl, F. L. W. 2020-10-12 doi:10.1101/2020.10.12.335711 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Racial and ethnic imbalance in neuroscience reference lists and intersections with gender ]]> https://biorxiv.org/content/10.1101/2020.10.12.336230v1?rss=1 Bertolero, M. A. Dworkin, J. D. David, S. U. Lloreda, C. L. Srivastava, P. Stiso, J. Zhou, D. 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Baldassano, C. 2020-10-14 doi:10.1101/2020.10.14.338145 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Multiscale and multimodal reconstruction of cortical structure and function ]]> https://biorxiv.org/content/10.1101/2020.10.14.338681v1?rss=1 Turner, N. L. Macrina, T. Bae, J. A. Yang, R. Wilson, A. M. Schneider-Mizell, C. Lee, K. Lu, R. Wu, J. Bodor, A. L. Bleckert, A. A. Brittain, D. Froudarakis, E. Dorkenwald, S. Collman, F. Kemnitz, N. Ih, D. Silversmith, W. M. Zung, J. Zlateski, A. Tartavull, I. Yu, S.-c. Popovych, S. Mu, S. Wong, W. Jordan, C. S. Castro, M. Buchanan, J. Bumbarger, D. J. Takeno, M. Torres, R. Mahalingam, G. Elabbady, L. Li, Y. Cobos, E. Zhou, P. Suckow, S. Becker, L. Paninski, L. Polleux, F. Reimer, J. Tolias, A. S. Reid, R. C. Macarico da Costa, N. Seung, H. S. 2020-10-14 doi:10.1101/2020.10.14.338681 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Multiple decisions about one object involve parallel sensory acquisition but time-multiplexed evidence incorporation ]]> https://biorxiv.org/content/10.1101/2020.10.15.341008v1?rss=1 Kang, Y. H. Löffler, A. Jeurissen, D. Zylberberg, A. Wolpert, D. Shadlen, M. N. 2020-10-16 doi:10.1101/2020.10.15.341008 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Androgen regulation of bowel function in mice and humans ]]> https://biorxiv.org/content/10.1101/2020.10.15.341081v1?rss=1 Rastelli, D. Robinson, A. Matthews, L. T. Perez, K. Dan, W. Yim, P. Mixer, M. Prochera, A. Hassan, R. Hall, K. Ballou, S. Nee, J. Lembo, A. Rao, M. 2020-10-15 doi:10.1101/2020.10.15.341081 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Mitochondrial profiling reveals dynamic, sex- and age-specific mitochondrial phenotypes in human immune cell subtypes ]]> https://biorxiv.org/content/10.1101/2020.10.16.342923v1?rss=1 Rausser, S. Trumpff, C. McGill, M. A. Junker, A. Wang, W. Ho, S.-H. Mitchell, A. Karan, K. R. Monk, C. Segerstrom, S. C. Reed, R. G. Picard, M. 2020-10-16 doi:10.1101/2020.10.16.342923 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[ Hierarchical Bayesian Models of Reinforcement Learning: Introduction and comparison to alternative methods ]]> https://biorxiv.org/content/10.1101/2020.10.19.345512v1?rss=1 van Geen, C. Gerraty, R. T. 2020-10-20 doi:10.1101/2020.10.19.345512 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Conserved core visual object recognition across simian primates: Marmoset image-by-image behavior mirrors that of humans and macaques ]]> https://biorxiv.org/content/10.1101/2020.10.19.345561v1?rss=1 Kell, A. J. E. Bokor, S. L. Jeon, Y.-N. Toosi, T. Issa, E. B. 2020-10-20 doi:10.1101/2020.10.19.345561 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Diet unmasks genetic variants that regulate lifespan in outbred Drosophila ]]> https://biorxiv.org/content/10.1101/2020.10.19.346312v1?rss=1 Pallares, L. F. Lea, A. J. Han, C. Filippova, E. V. Andolfatto, P. Ayroles, J. 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Bonne, G. Worman, H. J. 2020-10-20 doi:10.1101/2020.10.20.347088 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Mechanosensitive calcium signaling in filopodia ]]> https://biorxiv.org/content/10.1101/2020.10.21.346247v1?rss=1 Efremov, A. K. Yao, M. Sheetz, M. P. Bershadsky, A. D. Martinac, B. Yan, J. 2020-10-21 doi:10.1101/2020.10.21.346247 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Recurrent Switching Dynamical Systems Models for Multiple Interacting Neural Populations ]]> https://biorxiv.org/content/10.1101/2020.10.21.349282v1?rss=1 Glaser, J. I. Whiteway, M. R. Cunningham, J. P. Paninski, L. Linderman, S. W. 2020-10-22 doi:10.1101/2020.10.21.349282 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Bayesian inference: The comprehensive approach to analyzing single-molecule experiments ]]> https://biorxiv.org/content/10.1101/2020.10.23.353110v1?rss=1 Kinz-Thompson, C. D. Ray, K. K. Gonzalez, R. L. 2020-10-25 doi:10.1101/2020.10.23.353110 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Transfer learning from simulations improves the classification of OCT images of glandular epithelia ]]> https://biorxiv.org/content/10.1101/2020.10.26.355180v1?rss=1 Ostvar, S. Troung, H. Silver, E. R. Lightdale, C. J. Hur, C. Tatonetti, N. P. 2020-10-26 doi:10.1101/2020.10.26.355180 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Gamete simulation improves polygenic transmission disequilibrium analysis ]]> https://biorxiv.org/content/10.1101/2020.10.26.355602v1?rss=1 Chen, J. You, J. Zhao, Z. Ni, Z. Huang, K. Wu, Y. Fletcher, J. Lu, Q. 2020-10-27 doi:10.1101/2020.10.26.355602 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Pseudomonas aeruginosa PA14 biofilms produce R-bodies, extendable protein polymers with roles in host colonization and virulence ]]> https://biorxiv.org/content/10.1101/2020.10.26.356394v1?rss=1 Wang, B. Lin, Y.-C. Jo, J. Price-Whelan, A. Tao McDonald, S. Brown, L. M. Dietrich, L. E. 2020-10-27 doi:10.1101/2020.10.26.356394 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ TGS1 controls snRNA 3' end processing, prevents neurodegeneration and ameliorates SMN-dependent neurological phenotypes in vivo ]]> https://biorxiv.org/content/10.1101/2020.10.27.356782v1?rss=1 Chen, L. Roake, C. M. Maccallini, P. Bavasso, F. Dehghannasiri, R. Santonicola, P. Mendoza-Ferreira, N. Scatolini, L. Rizzuti, L. Esposito, A. Gallotta, I. Francia, S. Cacchione, S. Hammerschmidt, M. De Pitta, C. Sales, G. Salzman, J. Pellizzoni, L. Wirth, B. Di Schiavi, E. Gatti, M. Artandi, S. E. Raffa, G. D. 2020-10-27 doi:10.1101/2020.10.27.356782 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Pancreatic Ductal Adenocarcinoma Comprises Coexisting Regulatory States with both Common and Distinct Dependencies ]]> https://biorxiv.org/content/10.1101/2020.10.27.357269v1?rss=1 Laise, P. Turunen, M. Maurer, C. Curiel, A. Elyada, E. Schmierer, B. Tomassoni, L. Worley, J. Alvarez, M. J. Kesner, J. Tan, X. Tagore, S. Wang, A. L. E. Ge, S. Iuga, A. C. Griffin, A. Wong, W. Manji, G. Notta, F. Tuveson, D. Olive, K. P. Califano, A. 2020-10-27 doi:10.1101/2020.10.27.357269 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ The mutability of demographic noise in microbial range expansions ]]> https://biorxiv.org/content/10.1101/2020.10.27.357483v1?rss=1 Yu, Q. Gralka, M. Duvernoy, M.-C. Sousa, M. Harpak, A. Hallatschek, O. 2020-10-28 doi:10.1101/2020.10.27.357483 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Differentiation of Human induced Pluripotent Stem Cells to Authentic Macrophages using Fully Defined, Serum Free, Open Source Media ]]> https://biorxiv.org/content/10.1101/2020.10.27.357632v1?rss=1 Vaughan-Jackson, A. Stodolak, S. Ebrahimi, K. H. Browne, C. Reardon, P. K. Pires, E. Gilbert-Jaramillo, J. Cowley, S. A. James, W. S. 2020-10-27 doi:10.1101/2020.10.27.357632 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Counterfactual Hypothesis Testing of Tumor Microenvironment Scenarios Through Semantic Image Synthesis ]]> https://biorxiv.org/content/10.1101/2020.10.27.358101v1?rss=1 Li, D. Ma, Q. Chen, J. L. Liu, A. Cheung, J. Xie, Y. Gudjonson, H. Nawy, T. Pe'er, D. Pe'er, I. 2020-10-28 doi:10.1101/2020.10.27.358101 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Longitudinal ultrasonic dimensions and parametric solid models of the gravid uterus and cervix ]]> https://biorxiv.org/content/10.1101/2020.10.28.358812v1?rss=1 Louwagie, E. M. Carlson, L. Over, V. Mao, L. Fang, S. Westervelt, A. Vink, J. Hall, T. Feltovich, H. Myers, K. M. 2020-10-28 doi:10.1101/2020.10.28.358812 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Long-term stability of neuronal ensembles in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2020.10.28.359117v1?rss=1 Perez-Ortega, J. Alejandre-Garcia, T. Yuste, R. 2020-10-28 doi:10.1101/2020.10.28.359117 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ A novel family of secreted proteins linked to plant gall development ]]> https://biorxiv.org/content/10.1101/2020.10.28.359562v1?rss=1 Korgaonkar, A. Han, C. Lemire, A. L. Siwanowicz, I. Bennouna, D. Kopec, R. Andolfatto, P. Shigenobu, S. Stern, D. L. 2020-10-28 doi:10.1101/2020.10.28.359562 Cold Spring Harbor Laboratory Press 2020-10-28 <![CDATA[ Regulation of intracellular signaling and neuron function by Bardet-Biedl Syndrome proteins in patient-specific iPSC-derived neurons ]]> https://biorxiv.org/content/10.1101/2020.10.29.359851v1?rss=1 Wang, L. Liu, Y. Stratigopoulos, G. Panigrahi, S. Sui, L. Leduc, C. A. Glover, H. J. De Rosa, M. C. Burnett, L. C. Williams, D. J. Shang, L. Goland, R. Tsang, S. H. Wardlaw, S. Egli, D. Zheng, D. Doege, C. A. Leibel, R. L. 2020-10-29 doi:10.1101/2020.10.29.359851 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Novel insights from point-dendrometers in an urban setting: linking environmental variation to fluctuations in stem radius. ]]> https://biorxiv.org/content/10.1101/2020.10.29.361121v1?rss=1 Griffin, K. L. Harris, T. G. Bruner, S. McKenzie, P. F. Hise, J. 2020-10-30 doi:10.1101/2020.10.29.361121 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants ]]> https://biorxiv.org/content/10.1101/2020.11.03.365395v1?rss=1 Miller, D. E. Sulovari, A. Wang, T. Loucks, H. Hoekzema, K. Munson, K. M. Lewis, A. P. Almanza Fuerte, E. P. Paschal, C. R. Thies, J. Bennett, J. T. Glass, I. Dipple, K. M. Patterson, K. Bonkowski, E. S. Nelson, Z. Squire, A. Sikes, M. Beckman, E. Bennett, R. L. Earl, D. Lee, W. Allikmets, R. Perlman, S. J. Chow, P. Hing, A. V. Adam, M. P. Sun, A. Lam, C. Chang, I. University of Washington Center for Mendelian Genomics, Cherry, T. Chong, J. X. Bamshad, M. J. Nickerson, D. A. Mefford, H. C. Doherty, D. Eichler, E. E. 2020-11-04 doi:10.1101/2020.11.03.365395 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ ASCL1 drives induction of a transitory cell state required for repair of the injured neonatal brain ]]> https://biorxiv.org/content/10.1101/2020.11.03.366872v1?rss=1 Bayin, N. S. Mizrak, D. Stephen, D. N. Lao, Z. Sims, P. A. Joyner, A. L. 2020-11-03 doi:10.1101/2020.11.03.366872 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ A region-based method for causal mediation analysis of DNA methylation data ]]> https://biorxiv.org/content/10.1101/2020.11.03.366989v1?rss=1 Yan, Q. Forno, E. Celedon, J. Chen, W. 2020-11-04 doi:10.1101/2020.11.03.366989 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Intranasal fusion inhibitory lipopeptide prevents direct contact SARS-CoV-2 transmission in ferrets ]]> https://biorxiv.org/content/10.1101/2020.11.04.361154v1?rss=1 de Vries, R. D. Schmitz, K. S. Bovier, F. T. Noack, D. Haagmans, B. L. Biswas, S. Rockx, B. Gellman, S. H. Alabi, C. A. de Swart, R. L. MOSCONA, A. Porotto, M. 2020-11-05 doi:10.1101/2020.11.04.361154 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination ]]> https://biorxiv.org/content/10.1101/2020.11.04.367136v1?rss=1 Roy, U. Kwon, Y. Marie, L. Symington, L. Sung, P. Lisby, M. Greene, E. C. 2020-11-04 doi:10.1101/2020.11.04.367136 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations ]]> https://biorxiv.org/content/10.1101/2020.11.07.372573v1?rss=1 Wu, B. Zhu, W. Wang, Y. Wang, Q. Zhou, L. Liu, Z. W. Bi, L. Barun, M. Kreiswirth, B. N. Chen, L. Chen, S. Wang, X. Wang, W. 2020-11-08 doi:10.1101/2020.11.07.372573 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Adaptive current-flow models of ECT: Explaining individual static impedance, dynamic impedance, and brain current delivery ]]> https://biorxiv.org/content/10.1101/2020.11.08.373712v1?rss=1 Unal, G. Swami, J. K. Canela, C. Cohen, S. Khadka, N. Rad, M. Short, B. Argyelan, M. Sackeim, H. Bikson, M. 2020-11-09 doi:10.1101/2020.11.08.373712 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/2020.11.10.330183v1?rss=1 He, S. Schein, A. Sarsani, V. Flaherty, P. 2020-11-10 doi:10.1101/2020.11.10.330183 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Epigenome-wide study of brain DNA methylation among opioid users and controls ]]> https://biorxiv.org/content/10.1101/2020.11.10.377069v1?rss=1 Shu, C. Sosnowski, D. W. Tao, R. Deep-Soboslay, A. Kleinman, J. E. Hyde, T. M. Jaffe, A. E. Sabunciyan, S. Maher, B. S. 2020-11-11 doi:10.1101/2020.11.10.377069 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Structure and variability of optogenetic responses identify the operating regime of cortex ]]> https://biorxiv.org/content/10.1101/2020.11.11.378729v1?rss=1 Palmigiano, A. Fumarola, F. Mossing, D. P. Kraynyukova, N. Adesnik, H. Miller, K. 2020-11-11 doi:10.1101/2020.11.11.378729 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Cellular and immunological mechanisms mediate reservoir host specialization by genotypically variable microparasites ]]> https://biorxiv.org/content/10.1101/2020.11.13.380550v1?rss=1 Lin, Y.-P. Tufts, D. M. Dupuis, A. P. Combs, M. Marcinkiewicz, A. L. Hirsbrunner, A. D. Diaz, A. J. Stout, J. L. Blom, A. M. Strle, K. Davis, A. D. Kramer, L. D. Diuk-Wasser, M. A. 2020-11-14 doi:10.1101/2020.11.13.380550 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Upregulated functionality of mitochondria-associated ER membranes in a mouse model of traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2020.11.13.381756v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@12d0989org.highwire.dtl.DTLVardef@1cd1eb2org.highwire.dtl.DTLVardef@19a56caorg.highwire.dtl.DTLVardef@1b7f3e1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Agrawal, R. R. Larrea, D. Shi, L. Song, D. Xu, Y. Yun, T. D. Emmanuele, V. Cummins, L. G. Macaluso, F. P. Kernie, S. G. Min, W. Deckelbaum, R. J. Area-Gomez, E. 2020-11-15 doi:10.1101/2020.11.13.381756 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Decreasing pdzd8-mediated mitochondrial-ER contacts in neurons improves fitness by increasing mitophagy ]]> https://biorxiv.org/content/10.1101/2020.11.14.382861v1?rss=1 Hewitt, V. L. Miller-Fleming, L. Andreazza, S. Mattedi, F. Prudent, J. Polleux, F. Vagnoni, A. Whitworth, A. J. 2020-11-15 doi:10.1101/2020.11.14.382861 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ TCRβ Sequencing Reveals Spatial and Temporal Evolution of Clonal CD4 T cell Responses in a Breach of Tolerance Model of Inflammatory Arthritis ]]> https://biorxiv.org/content/10.1101/2020.11.15.383539v1?rss=1 Al Khabouri, S. Benson, R. A. Prendergast, C. T. Gray, J. I. Otto, T. D. Brewer, J. M. Garside, P. 2020-11-15 doi:10.1101/2020.11.15.383539 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract ]]> https://biorxiv.org/content/10.1101/2020.11.17.387522v1?rss=1 Rippe, J. P. Dixon, G. B. Fuller, Z. L. Liao, Y. Matz, M. V. 2020-11-19 doi:10.1101/2020.11.17.387522 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Contextual inference underlies the learning of sensorimotor repertoires ]]> https://biorxiv.org/content/10.1101/2020.11.23.394320v1?rss=1 Heald, J. Lengyel, M. Wolpert, D. 2020-11-23 doi:10.1101/2020.11.23.394320 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Predicting perturbation effects from resting state activity using functional causal flow ]]> https://biorxiv.org/content/10.1101/2020.11.23.394916v1?rss=1 Nejatbakhsh, A. Fumarola, F. Esteki, S. Toyoizumi, T. Kiani, R. Mazzucato, L. 2020-11-24 doi:10.1101/2020.11.23.394916 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Differential effects of amplitude-modulated transcranial focused ultrasound on excitatory and inhibitory neurons ]]> https://biorxiv.org/content/10.1101/2020.11.26.400580v1?rss=1 Nguyen, D. T. Berisha, D. Konofagou, E. Dmochowski, J. P. 2020-11-27 doi:10.1101/2020.11.26.400580 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Precise spatial representations in the hippocampus of a food-caching bird ]]> https://biorxiv.org/content/10.1101/2020.11.27.399444v1?rss=1 Payne, H. L. Lynch, G. F. Aronov, D. 2020-11-27 doi:10.1101/2020.11.27.399444 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies ]]> https://biorxiv.org/content/10.1101/2020.11.30.404087v1?rss=1 Beebe-Wang, N. Celik, S. Weinberger, E. Sturmfels, P. De Jager, P. L. Mostafavi, S. Lee, S.-I. 2020-12-01 doi:10.1101/2020.11.30.404087 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Differential integrin adhesome expression defines human natural killer cell residency and developmental stage ]]> https://biorxiv.org/content/10.1101/2020.12.01.404806v1?rss=1 Hegewisch Solloa, E. Seo, S. Mundy-Bosse, B. L. Mishra, A. Waldman, E. Maurrasse, S. Grunstein, E. Connors, T. J. Freud, A. G. Mace, E. M. 2020-12-01 doi:10.1101/2020.12.01.404806 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Biliverdin reductase bridges focal adhesion kinase to Src to modulate synaptic signaling ]]> https://biorxiv.org/content/10.1101/2020.12.01.405720v1?rss=1 Vasavda, C. Semenza, E. R. Liew, J. Kothari, R. Dhindsa, R. S. Shanmukha, S. Ricco, C. Tokhunts, R. Snowman, A. M. Albacarys, L. K. Paul, B. D. Snyder, S. H. 2020-12-02 doi:10.1101/2020.12.01.405720 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2020.12.01.406363v1?rss=1 Chan, J. M. Quintanal-Villalonga, A. Gao, V. Xie, Y. Allaj, V. Chaudhary, O. Masilionis, I. Egger, J. Chow, A. Walle, T. Mattar, M. Yarlagadda, D. V. Wang, J. L. Offin, M. Ciampricotti, M. Bhanot, U. K. Lai, W. V. Bott, M. J. Jones, D. R. Ruiz, A. Hollmann, T. Poirier, J. T. Nawy, T. Mazutis, L. Sen, T. Pe'er, D. Rudin, C. M. 2020-12-01 doi:10.1101/2020.12.01.406363 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Distinct Contributions of Nonpredictive and Predictive Peripheral Cues to Visual Conscious Perception: an MEG study ]]> https://biorxiv.org/content/10.1101/2020.12.05.413161v1?rss=1 Spagna, A. Bayle, D. J. Romeo, Z. Yahia-Cherif, L. Chica, A. B. Bartolomeo, P. 2020-12-07 doi:10.1101/2020.12.05.413161 Cold Spring Harbor Laboratory Press 2020-12-07 <![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[ Paired motor cortex and spinal cord epidural stimulation strengthens sensorimotor connections and improves forelimb function after cervical spinal cord injury in rats. ]]> https://biorxiv.org/content/10.1101/2020.12.07.398289v1?rss=1 Pal, A. Park, H. Ramamurthy, A. Asan, A. S. Bethea, T. Johnkutty, M. Carmel, J. B. 2020-12-08 doi:10.1101/2020.12.07.398289 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ No behavioral evidence for rhythmic facilitation of perceptual discrimination ]]> https://biorxiv.org/content/10.1101/2020.12.10.418947v1?rss=1 Lin, W. M. Oetringer, D. Bakker-Marshall, I. Emmerzaal, J. Wilsch, A. ElShafei, H. A. El Rassi, E. Haegens, S. 2020-12-11 doi:10.1101/2020.12.10.418947 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A broad exome study of the genetic architecture of asthma reveals novel patient subgroups ]]> https://biorxiv.org/content/10.1101/2020.12.10.419663v1?rss=1 Cameron-Christie, S. Mackay, A. Wang, Q. Olsson, H. Angermann, B. Lassi, G. Lindgren, J. Hühn, M. Cameron-Christie, Y. O. Gavala, M. Wang, J. Povysil, G. Deevi, S. V. V. Belfield, G. Dillmann, I. Muthas, D. Cohen, S. Young, S. Platt, A. Petrovski, S. 2020-12-11 doi:10.1101/2020.12.10.419663 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Hippocampal cells multiplex positive and negative engrams ]]> https://biorxiv.org/content/10.1101/2020.12.11.419887v1?rss=1 Shpokayte, M. McKissick, O. Yuan, B. Rahsepar, B. Fernandez, F. R. Ruesch, E. A. Grella, S. L. White, J. A. Liu, X. S. Ramirez, S. 2020-12-11 doi:10.1101/2020.12.11.419887 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Using publicly available data to conduct rapid assessments of extinction risk ]]> https://biorxiv.org/content/10.1101/2020.12.14.413906v1?rss=1 Levin, M. O. Meek, J. B. Boom, B. Kross, S. M. Eskew, E. A. 2020-12-15 doi:10.1101/2020.12.14.413906 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Juvenile exposure to acute traumatic stress leads to long-lasting alterations in grey matter myelination in adult female but not male rats ]]> https://biorxiv.org/content/10.1101/2020.12.14.422686v1?rss=1 Breton, J. M. Barraza, M. Hu, K. Y. Frias, S. J. Long, K. L. P. Kaufer, D. 2020-12-15 doi:10.1101/2020.12.14.422686 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Pyramidal tract neurons drive feed-forward excitation of striatum through cholinergic interneurons ]]> https://biorxiv.org/content/10.1101/2020.12.14.422716v1?rss=1 Morgenstern, N. A. Isidro, A. F. Israely, I. Costa, R. M. 2020-12-15 doi:10.1101/2020.12.14.422716 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ From neuron to muscle to movement: a complete biomechanical model of Hydra contractile behaviors ]]> https://biorxiv.org/content/10.1101/2020.12.14.422784v1?rss=1 Wang, H. Swore, J. J. Sharma, S. Szymanski, J. R. Yuste, R. Daniel, T. L. Regnier, M. Bosma, M. Fairhall, A. L. 2020-12-15 doi:10.1101/2020.12.14.422784 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel ]]> https://biorxiv.org/content/10.1101/2020.12.14.422800v1?rss=1 Perez-Conesa, S. Keeler, E. G. Zhang, D. Delemotte, L. McDermott, A. E. 2020-12-15 doi:10.1101/2020.12.14.422800 Cold Spring Harbor Laboratory Press 2020-12-15 <![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[ DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling ]]> https://biorxiv.org/content/10.1101/2020.12.15.422925v1?rss=1 Aghayeva, U. Bhattacharya, A. Sural, S. Jaeger, E. Churgin, M. Fang-Yen, C. Hobert, O. 2020-12-15 doi:10.1101/2020.12.15.422925 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data ]]> https://biorxiv.org/content/10.1101/2020.12.21.423514v1?rss=1 Douglass, E. F. Allaway, R. J. Szalai, B. Wang, W. Tian, T. Fernandez, A. Realubit, R. Karan, C. Zheng, S. Pessia, A. Tanoli, Z. Jafari, M. Wan, F. Li, S. Xiong, Y. Duran-Frigola, M. Bertoni, M. Badia-i-Mompel, P. Mateo, L. Guitart-Pla, O. Chung, V. DREAM CTD-squared Pancancer Drug Activity Challenge Consortium, Tang, J. Zeng, J. Aloy, P. Saez-Rodriguez, J. Guinney, J. Gerhard, D. S. Califano, A. 2020-12-22 doi:10.1101/2020.12.21.423514 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody ]]> https://biorxiv.org/content/10.1101/2020.12.21.423787v1?rss=1 Wang, R. T. Xu, A. F. Zhou, Q. Song, T. Xu, K. J. Xu, G. 2020-12-21 doi:10.1101/2020.12.21.423787 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Cadherin-11 dimerization multi-site kinetics: combined partial unfolding and strand-swapping ]]> https://biorxiv.org/content/10.1101/2020.12.21.423864v1?rss=1 Koss, H. Honig, B. H. Shapiro, L. S. Palmer, A. G. 2020-12-22 doi:10.1101/2020.12.21.423864 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Systematic detection of functional proteoform groups from bottom-up proteomic datasets ]]> https://biorxiv.org/content/10.1101/2020.12.22.423928v1?rss=1 Bludau, I. Frank, M. Doerig, C. Cai, Y. Heusel, M. Rosenberger, G. Picotti, P. Collins, B. C. Roest, H. Aebersold, R. 2020-12-22 doi:10.1101/2020.12.22.423928 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ A neuronal circuit for vector computation builds an allocentric traveling-direction signal in the Drosophila fan-shaped body ]]> https://biorxiv.org/content/10.1101/2020.12.22.423967v1?rss=1 Lyu, C. Abbott, L. F. Maimon, G. 2020-12-23 doi:10.1101/2020.12.22.423967 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Multi-cellular communities are perturbed in the aging human brain and with Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2020.12.22.424084v1?rss=1 Cain, A. Taga, M. McCabe, C. Hekselman, I. White, C. C. Green, G. Rozenblatt-Rosen, O. Zhang, F. Yeger-Lotem, E. Bennett, D. A. Yang, H.-S. Regev, A. Menon, V. Habib, N. De Jager, P. 2020-12-23 doi:10.1101/2020.12.22.424084 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Multi-Modal Biomarkers of Cerebral Edema in Low Resolution MRI ]]> https://biorxiv.org/content/10.1101/2020.12.23.424020v1?rss=1 Tu, D. Goyal, M. S. Dworkin, J. D. Kampondeni, S. Vidal, L. Biondo-Savin, E. Juvvadi, S. Raghavan, P. Nicholas, J. Chetcuti, K. Clark, K. Satterthwaite, T. D. Yushkevich, P. Davatzikos, C. Erus, G. Postels, D. G. Taylor, T. E. Small, D. S. Shinohara, R. T. 2020-12-25 doi:10.1101/2020.12.23.424020 Cold Spring Harbor Laboratory Press 2020-12-25 <![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[ Differential Expression of NPAS4 in the Dorsolateral Prefrontal Cortex Following Acute Opioid Intoxication ]]> https://biorxiv.org/content/10.1101/2020.12.23.424239v1?rss=1 Sosnowski, D. W. Jaffe, A. E. Tao, R. Deep-Soboslay, A. Kleinman, J. E. Hyde, T. M. Shu, C. Sabunciyan, S. Maher, B. S. 2020-12-23 doi:10.1101/2020.12.23.424239 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Reversing Transcriptome-Wide Association Studies to improve expression Quantitative Trait Loci associations ]]> https://biorxiv.org/content/10.1101/2020.12.27.424460v1?rss=1 Yuan, J. Lai, B. Pe'er, I. 2020-12-28 doi:10.1101/2020.12.27.424460 Cold Spring Harbor Laboratory Press 2020-12-28 <![CDATA[ Global cognitive performance is not influenced by diurnal rhythm ]]> https://biorxiv.org/content/10.1101/2020.12.29.424677v1?rss=1 De Jager, C. H. Burns, E. Stern, Y. 2020-12-30 doi:10.1101/2020.12.29.424677 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[ Stabilized Supralinear Network: Model of Layer 2/3 of the Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2020.12.30.424892v1?rss=1 Obeid, D. Miller, K. D. 2021-01-02 doi:10.1101/2020.12.30.424892 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ A genome wide copper-sensitized screen identifies novel regulators of mitochondrial cytochrome c oxidase activity ]]> https://biorxiv.org/content/10.1101/2020.12.31.424969v1?rss=1 Garza, N. M. Griffin, A. T. Zulkifli, M. Qiu, C. Kaplan, C. D. Gohil, V. M. 2021-01-02 doi:10.1101/2020.12.31.424969 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Insights into Genome Recoding from the Mechanism of a Classic +1-Frameshifting tRNA ]]> https://biorxiv.org/content/10.1101/2020.12.31.424971v1?rss=1 Gamper, H. Li, H. Masuda, I. Robkis, D. M. Christian, T. Conn, A. B. Blaha, g. Petersson, E. J. Gonzalez, R. L. Hou, Y.-M. 2021-01-02 doi:10.1101/2020.12.31.424971 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses ]]> https://biorxiv.org/content/10.1101/2020.12.31.424987v1?rss=1 Banach, B. B. Cerutti, G. Fahad, A. S. Shen, C.-H. Oliveira de Souza, M. Katsamba, P. S. Tsybovsky, Y. Wang, P. Nair, M. S. Huang, Y. Francino Urdaniz, I. M. Steiner, P. J. Gutierrez-Gonzalez, M. Liu, L. Lopez Acevedo, S. N. Nazzari, A. Wolfe, J. R. Luo, Y. Olia, A. S. Teng, I.-T. Yu, J. Zhou, T. Reddem, E. R. Bimela, J. Pan, X. Madan, B. Laflin, A. D. Nimrania, R. Yuen, K.-T. Whitehead, T. A. Ho, D. D. Kwong, P. D. Shapiro, L. DeKosky, B. J. 2021-01-03 doi:10.1101/2020.12.31.424987 Cold Spring Harbor Laboratory Press 2021-01-03 <![CDATA[ The gastrin-releasing peptide regulates stress-enhanced fear and dopamine signaling ]]> https://biorxiv.org/content/10.1101/2020.12.31.424996v1?rss=1 Morishita, Y. Fuentes, I. Favate, J. Zushida, K. Nishi, A. Hevi, C. Goldsmith, N. Buyske, S. Sillivan, S. E. Miller, C. A. Kandel, E. R. Uchida, S. Shah, P. Shumyatsky, G. P. 2021-01-01 doi:10.1101/2020.12.31.424996 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ YhcB (DUF1043), a novel cell division protein conserved across gamma-proteobacteria ]]> https://biorxiv.org/content/10.1101/2020.12.31.425005v1?rss=1 Mehla, J. Liechti, G. Morgenstern, R. M. Caufield, J. H. Hosseinnia, A. Gagarinova, A. Phanse, S. Brockett, M. Sakhawalkarar, N. Babu, M. Xiao, R. Montelionege, G. T. Vorobiev, S. den Blaauwen, T. Hunt, J. F. Uetz, P. 2021-01-02 doi:10.1101/2020.12.31.425005 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ LIN28 selectively modulates a subclass of let-7 microRNAs ]]> https://biorxiv.org/content/10.1101/202036v1?rss=1 Ustianenko, D. Chiu, H.-S. Weyn-Vanhentenryck, S. M. Sumazin, P. Zhang, C. 2017-10-12 doi:10.1101/202036 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ Magnetic tweezers meets AFM: ultra-stable protein dynamics across the force spectrum ]]> https://biorxiv.org/content/10.1101/2021.01.04.425265v1?rss=1 120 pN) have remained elusive with this technique and have been addressed with Atomic Force Microscopy (AFM), which can reach higher forces but displays less stability and resolution. Herein, we develop a magnetic tweezers approach that can apply AFM-like mechanical loads while maintaining its hallmark resolution and stability in a range of forces that spans from 1 to 500 pN. We demonstrate our approach by exploring the folding and unfolding dynamics of the highly mechanostable adhesive protein FimA from the Gram-positive pathogen Actinomyces oris. FimA unfolds at loads >300 pN, while its folding occurs at forces <15 pN, producing a large dissipation of energy that could be crucial for the shock absorption of mechanical challenges during host invasion. Our novel magnetic tweezers approach entails an all-in-one force spectroscopy technique for protein dynamics studies across a broad spectrum of physiologically-relevant forces and timescales. ]]> Alonso-Caballero, A. Tapia-Rojo, R. Badilla, C. L. Fernandez, J. M. 2021-01-05 doi:10.1101/2021.01.04.425265 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Large-scale quantification of human osteocyte lacunar morphological biomarkers as assessed by ultra-high-resolution desktop micro-computed tomography ]]> https://biorxiv.org/content/10.1101/2021.01.05.425223v1?rss=1 ), and local lacunar volume (), all of which demonstrate the sensitivity of the method and are possible biomarker candidates. This study provides the foundation required for future large-scale morphometric studies using ultra-high-resolution desktop micro-CT and high-throughput analysis of millions of osteocyte lacunae in human bone samples. Furthermore, the validation of this technology for imaging of human lacunar properties establishes the quality and reliability required for the accurate, precise, and sensitive assessment of osteocyte morphometry in clinical bone biopsies. ]]> Goff, E. Buccino, F. Bregoli, C. McKinley, J. P. Aeppli, B. Recker, R. R. Shane, E. Cohen, A. Kuhn, G. Müller, R. 2021-01-05 doi:10.1101/2021.01.05.425223 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Plasmodium falciparum K13 mutations in Africa and Asia present varying degrees of artemisinin resistance and an elevated fitness cost in African parasites ]]> https://biorxiv.org/content/10.1101/2021.01.05.425445v1?rss=1 Stokes, B. H. Rubiano, K. Dhingra, S. K. Mok, S. Straimer, J. Gnadig, N. F. Bath, J. R. Deni, I. Ward, K. E. Striepen, J. Yeo, T. Ross, L. S. Legrand, E. Ariey, F. Cunningham, C. H. Souleymane, I. M. Gansane, A. Nzoumbou-Boko, R. Ndayikunda, C. Kabanywanyi, A. M. Uwimana, A. Smith, S. J. Kolley, O. Ndounga, M. Warsame, M. Leang, R. Nosten, F. Anderson, T. J. C. Rosenthal, P. J. Menard, D. Fidock, D. A. 2021-01-05 doi:10.1101/2021.01.05.425445 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Brain connectivity at rest predicts individual differences in normative activity during movie watching ]]> https://biorxiv.org/content/10.1101/2021.01.06.425410v1?rss=1 Gruskin, D. C. Patel, G. H. 2021-01-08 doi:10.1101/2021.01.06.425410 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ A Multi-dimensional Integrative Scoring Framework for Predicting Functional Regions in the Human Genome ]]> https://biorxiv.org/content/10.1101/2021.01.06.425527v1?rss=1 Li, X. Yung, G. Zhou, H. Sun, R. Li, Z. Liu, Y. Ionita-Laza, I. Lin, X. 2021-01-08 doi:10.1101/2021.01.06.425527 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Resolving the molecular fingerprint of the distal carboxy tail in modulating CaV1 calcium dependent inactivation ]]> https://biorxiv.org/content/10.1101/2021.01.06.425618v1?rss=1 Sang, L. Vieira, D. C. O. Yue, D. T. Ben-Johny, M. Dick, I. E. 2021-01-06 doi:10.1101/2021.01.06.425618 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Artemisia annua L. extracts prevent in vitro replication of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.01.08.425825v1?rss=1 12 years old, yet the hot-water extract was still found to be active. The UK and South African variants, B1.1.7 and B1.351, were similarly inhibited. While all hot water extracts were effective, concentrations of artemisinin and total flavonoids varied by nearly 100-fold in the extracts. Artemisinin alone showed an estimated IC50 of about 70 M, and the clinically used artemisinin derivatives artesunate, artemether, and dihydroartemisinin were ineffective or cytotoxic at elevated micromolar concentrations. In contrast, the antimalarial drug amodiaquine had an IC50 = 5.8 M. Extracts had minimal effects on infection of Vero E6 or Calu-3 cells by a reporter virus pseudotyped by the SARS-CoV-2 spike protein. There was no cytotoxicity within an order of magnitude above the antiviral IC90 values. ConclusionsA. annua extracts inhibit SARS-CoV-2 infection, and the active component(s) in the extracts is likely something besides artemisinin or a combination of components that block virus infection at a step downstream of virus entry. Further studies will determine in vivo efficacy to assess whether A. annua might provide a cost-effective therapeutic to treat SARS-CoV-2 infections. List of compounds studiedAmodiaquine Artemisinin Artesunate Artemether Deoxyartemisinin Dihydroartemisinin HighlightsO_LIArtemisia annua is effective in stopping replication of SARS-CoV-2 including 2 new variants. C_LIO_LIThe anti-viral effect does not correlate to artemisinin, nor to the total flavonoid content. C_LIO_LIThe anti-viral mechanism does not appear to involve blockade virus entry into cell. C_LIO_LIThe plant offers two additional benefits: a decreased inflammatory response and blunting of fibrosis. C_LIO_LIA. annua may provide a safe, low-cost alternative for treating patients infected with SARS-CoV-2. C_LI ]]> Nair, M. S. Huang, Y. Fidock, D. A. Polyak, S. J. Wagoner, J. Towler, M. Weathers, P. 2021-01-08 doi:10.1101/2021.01.08.425825 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition ]]> https://biorxiv.org/content/10.1101/2021.01.10.425752v1?rss=1 Ho, C.-M. Jih, J. Lai, M. Li, X. Goldberg, D. Beck, J. R. Zhou, H. 2021-01-11 doi:10.1101/2021.01.10.425752 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite ]]> https://biorxiv.org/content/10.1101/2021.01.10.426120v1?rss=1 Cerutti, G. Guo, Y. Zhou, T. Gorman, J. Lee, M. Rapp, M. Reddem, E. R. Yu, J. Bahna, F. Bimela, J. Huang, Y. Katsamba, P. S. Lihong, L. Nair, M. S. Rawi, R. Olia, A. S. Wang, P. Chuang, G.-Y. Ho, D. D. Sheng, Z. Kwong, P. D. Shapiro, L. 2021-01-11 doi:10.1101/2021.01.10.426120 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class ]]> https://biorxiv.org/content/10.1101/2021.01.11.426218v1?rss=1 Rapp, M. Guo, Y. Reddem, E. R. Liu, L. Wang, P. Yu, J. Cerutti, G. Bimela, J. Bahna, F. Mannepalli, S. Zhang, B. Kwong, P. D. Ho, D. D. Shapiro, L. Sheng, Z. 2021-01-11 doi:10.1101/2021.01.11.426218 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Somatic Depolarization Enhances Hippocampal CA1 Dendritic Spike Propagation and Distal Input Driven Synaptic Plasticity ]]> https://biorxiv.org/content/10.1101/2021.01.12.426178v1?rss=1 Bock, T. Siegelbaum, S. A. 2021-01-13 doi:10.1101/2021.01.12.426178 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Allosteric MAPKAPK2 Inhibitors Improve Plaque Stability in Advanced Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2021.01.12.426264v1?rss=1 Ozcan, L. Kasikara, C. Yurdagul, A. Kuriakose, G. Hubbard, B. Serrano-Wu, M. H. Tabas, I. 2021-01-12 doi:10.1101/2021.01.12.426264 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ A simple explanation for declining temperature sensitivity with warming ]]> https://biorxiv.org/content/10.1101/2021.01.12.426288v1?rss=1 Wolkovich, E. M. Auerbach, J. L. Chamberlain, C. J. Buonaiuto, D. M. Ettinger, A. K. Morales-Castilla, I. Gelman, A. 2021-01-13 doi:10.1101/2021.01.12.426288 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats ]]> https://biorxiv.org/content/10.1101/2021.01.12.426369v1?rss=1 Goff, S. P. Winans, S. 2021-01-12 doi:10.1101/2021.01.12.426369 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ Astrocyte-derived ApoE is Required for the Maturation of Injury-induced Hippocampal Neurons and Regulates Cognitive Recovery After Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2021.01.13.425890v1?rss=1 Yu, T.-S. Tensaouti, Y. Stephanz, E. P. Rafikian, E. E. Yang, M. Kernie, S. G. 2021-01-14 doi:10.1101/2021.01.13.425890 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ A convergent structure-function substrate of cognitive imbalances in autism ]]> https://biorxiv.org/content/10.1101/2021.01.14.426284v1?rss=1 Hong, S.-J. Laurent, M. Park, B.-Y. Benkarim, O. Valk, S. L. Paquola, C. Lariviere, S. Vos de Wael, R. Degre-Pelletier, J. Soulieres, I. Ramphal, B. Margolis, A. Milham, M. Di Martino, A. Bernhardt, B. 2021-01-14 doi:10.1101/2021.01.14.426284 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ Reconstructing tumor trajectories during therapy through integration of multiple measurement modalities. ]]> https://biorxiv.org/content/10.1101/2021.01.14.426737v1?rss=1 Griffiths, J. I. Chen, J. O'Dea, A. Sharma, P. Winblad, O. Trivedi, M. Kalinsky, K. Wisinski, K. O'Regan, R. Makhoul, I. Spring, L. Bardia, A. Yuan, Y. Jahanzeb, M. Adler, F. Cohen, A. Bild, A. Khan, Q. 2021-01-17 doi:10.1101/2021.01.14.426737 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Ubx orchestrates tissue identity through regional and bidirectional changes to chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2021.01.15.426863v1?rss=1 Loker, R. Sanner, J. E. Mann, R. S. 2021-01-16 doi:10.1101/2021.01.15.426863 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ The Mitochondrial Calcium Uniporter of Pulmonary Type 2 Cells Determines Severity of ARDS ]]> https://biorxiv.org/content/10.1101/2021.01.18.427173v1?rss=1 Islam, M. N. Gusarova, G. A. Das, S. R. Li, L. Monma, E. Anjaneyulu, M. Owusu-Ansah, E. Bhattacharya, S. Bhattacharya, J. 2021-01-18 doi:10.1101/2021.01.18.427173 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Molecular programs of fibrotic change in aging human lung ]]> https://biorxiv.org/content/10.1101/2021.01.18.427195v1?rss=1 Lee, J. Islam, M. N. Boostanpour, K. Aran, D. Christenson, S. Matthay, M. A. Eckalbar, W. DePianto, D. J. Arron, J. R. Magee, L. Bhattacharya, S. Matsumoto, R. Kubota, M. Farber, D. L. Bhattacharya, J. Wolters, P. J. Bhattacharya, M. 2021-01-19 doi:10.1101/2021.01.18.427195 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Enhancing top-down proteomics of brain tissue with FAIMS ]]> https://biorxiv.org/content/10.1101/2021.01.18.427216v1?rss=1 Fulcher, J. M. Makaju, A. Moore, R. J. Zhou, M. Bennett, D. C. De Jager, P. L. Qian, W.-J. Pasa-Tolic, L. Petyuk, V. A. 2021-01-19 doi:10.1101/2021.01.18.427216 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine inhibitors ]]> https://biorxiv.org/content/10.1101/2021.01.19.427299v1?rss=1 Griffiths, J. I. Chen, J. Cosgrove, P. A. O'Dea, A. Sharma, P. Ma, C. Trivedi, M. Kalinsky, K. Wisinski, K. B. O'Regan, R. Makhoul, , I. Spring, L. M. Bardia, A. Adler, F. R. Cohen, A. L. Chang, J. T. Khan, Q. J. Bild, A. 2021-01-20 doi:10.1101/2021.01.19.427299 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Tianeptine, but not fluoxetine, decreases avoidant behavior in a mouse model of early developmental exposure to fluoxetine ]]> https://biorxiv.org/content/10.1101/2021.01.19.427351v1?rss=1 Pekarskaya, E. A. Holt, E. S. Gingrich, J. A. Ansorge, M. S. Javitch, J. A. Canetta, S. E. 2021-01-20 doi:10.1101/2021.01.19.427351 Cold Spring Harbor Laboratory Press 2021-01-20 <![CDATA[ Hyperoxia Inhibits the Growth of Mouse Forebrain Oligodendrocyte Progenitors ]]> https://biorxiv.org/content/10.1101/2021.01.20.427261v1?rss=1 Moore, L. M. McLane, L. E. Wahl, S. E. Ornelas, I. Wood, T. L. Canoll, P. D. Levison, S. W. 2021-01-21 doi:10.1101/2021.01.20.427261 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Actin fence therapy with exogenous V12Rac1 protects against Acute Lung Injury ]]> https://biorxiv.org/content/10.1101/2021.01.20.427469v1?rss=1 Gusarova, G. A. Das, S. Islam, M. N. Westphalen, K. Jin, G. Shmarakov, I. O. Li, L. Bhattacharya, S. Bhattacharya, J. 2021-01-21 doi:10.1101/2021.01.20.427469 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ The brain clock portal system: SCN-OVLT ]]> https://biorxiv.org/content/10.1101/2021.01.24.427962v1?rss=1 Yao, Y. Taub, A. B. LeSauter, J. Silver, R. 2021-01-26 doi:10.1101/2021.01.24.427962 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Disrupting D2-NMDA receptor heteromerization blocks the rewarding effects of cocaine but preserves natural reward processing ]]> https://biorxiv.org/content/10.1101/2021.01.25.428078v1?rss=1 Andry, A. Estefani, S.-J. Paula, P. Sebastian, F. P. Anna, P. Veronique, D. S.-P. Nicolas, H. Vanesa, O. Marie-Charlotte, A. Vincent, K. Sandrine, B. Roman, W. Ying, Z. Charlene, J. Alexis-Pierre, B. Gustavo, T. Naguib, M. Jonathan, J. Jocelyne, C. Pierre, T. Jacques, B. Peter, V. 2021-01-26 doi:10.1101/2021.01.25.428078 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Genome-wide analysis of mitochondrial DNA copy number reveals multiple loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation ]]> https://biorxiv.org/content/10.1101/2021.01.25.428086v1?rss=1 Longchamps, R. J. Yang, S. Y. Castellani, C. A. Shi, W. Lane, J. Grove, M. L. Bartz, T. M. Sarnowski, C. Burrows, K. Guyatt, A. L. Gaunt, T. R. Kacprowski, T. Yang, J. De, P. L. Yu, L. CHARGE Aging and Longevity Group, Bergman, A. Xia, R. Fornage, M. Feitosa, M. F. Wojczynski, M. K. Kraja, A. T. Province, M. A. Amin, N. Rivadeneira, F. Tiemeier, H. Uitterlinden, A. G. Broer, L. Van, J. Van, C. Raffield, L. M. Lange, L. Rich, S. S. Lemaitre, R. N. Goodarzi, M. O. Sitlani, C. M. Mak, A. C. Bennett, D. A. Rodriguez, S. Murabito, J. M. Lunetta, K. L. Soto 2021-01-28 doi:10.1101/2021.01.25.428086 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization ]]> https://biorxiv.org/content/10.1101/2021.01.25.428137v1?rss=1 Wang, P. Lihong, L. Iketani, S. Luo, Y. Guo, Y. Wang, M. Yu, J. Zhang, B. Kwong, P. D. Graham, B. S. Mascola, J. R. Chang, J. Y. Yin, M. T. Sobieszczyk, M. E. Kyratsous, C. A. Shapiro, L. Sheng, Z. Nair, M. S. Huang, Y. Ho, D. D. 2021-01-26 doi:10.1101/2021.01.25.428137 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Human stem cell model of HNF1A deficiency shows uncoupled insulin to C-peptide secretion with accumulation of abnormal insulin granules ]]> https://biorxiv.org/content/10.1101/2021.01.26.428260v1?rss=1 Gonzalez, B. J. Zhao, H. Niu, J. Williams, D. J. Lee, J. Goulbourne, C. N. Xing, Y. Wang, Y. Oberholzer, J. Chen, X. LeDuc, C. A. Chung, W. K. Colecraft, H. M. Gromada, J. Shen, Y. Goland, R. S. Leibel, R. L. Egli, D. 2021-01-26 doi:10.1101/2021.01.26.428260 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ High-order areas and auditory cortex both represent the high-level event structure of music ]]> https://biorxiv.org/content/10.1101/2021.01.26.428291v1?rss=1 Williams, J. A. Margulis, E. H. Nastase, S. A. Chen, J. Hasson, U. Norman, K. A. Baldassano, C. A. 2021-01-26 doi:10.1101/2021.01.26.428291 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Paths to annihilation: Genetic and demographic consequences of range contraction patterns ]]> https://biorxiv.org/content/10.1101/2021.01.26.428313v1?rss=1 Rogan, J. Parker, M. R. Hancock, Z. B. Earl, A. D. Buchholtz, E. K. Chyn, K. Martina, J. Fitzgerald, L. A. 2021-01-27 doi:10.1101/2021.01.26.428313 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ P. falciparum K13 mutations present varying degrees of artemisinin resistance and reduced fitness in African parasites ]]> https://biorxiv.org/content/10.1101/2021.01.27.428390v1?rss=1 Stokes, B. H. Rubiano, K. Dhingra, S. K. Mok, S. Straimer, J. Gnadig, N. F. Bath, J. R. Deni, I. Ward, K. E. Striepen, J. Yeo, T. Ross, L. S. Legrand, E. Ariey, F. Cunningham, C. H. Souleymane, I. M. Gansane, A. Nzoumbou-Boko, R. Ndayikunda, C. Kabanywanyi, A. M. Uwimana, A. Smith, S. J. Kolley, O. Ndounga, M. Warsame, M. Leang, R. Nosten, F. Anderson, T. Rosenthal, P. J. Menard, D. Fidock, D. A. 2021-01-30 doi:10.1101/2021.01.27.428390 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Sauna-like conditions or menthol treatment reduce tau phosphorylation through mild hyperthermia ]]> https://biorxiv.org/content/10.1101/2021.01.27.428475v1?rss=1 Guisle, I. Petry, S. Morin, F. Kerauden, R. Whittington, R. A. Calon, F. Hebert, S. Planel, E. 2021-01-28 doi:10.1101/2021.01.27.428475 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.01.27.428525v1?rss=1 Feng, H. Moakley, D. F. Chen, S. McKenzie, M. G. Menon, V. Zhang, C. 2021-01-28 doi:10.1101/2021.01.27.428525 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Neptune: An environment for the delivery of genomic medicine ]]> https://biorxiv.org/content/10.1101/2021.01.29.428608v1?rss=1 Venner, E. Yi, V. Murdock, D. R. Kalla, S. E. Wu, T.-J. Sabo, A. Li, S. Meng, Q. Tian, X. Murugan, M. Cohen, M. Kovar, C. Wei, W.-Q. Chung, W. Weng, C. Weisner, G. Jarvik, G. Muzny, D. M. Gibbs, R. 2021-02-01 doi:10.1101/2021.01.29.428608 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Genomic Considerations for FHIR; eMERGE Implementation Lessons ]]> https://biorxiv.org/content/10.1101/2021.01.31.429037v1?rss=1 Murugan, M. Babb, L. J. Taylor, C. O. Rasmussen, L. V. Freimuth, R. R. Venner, E. Yan, F. Yi, V. Granite, S. J. Zouk, H. Aronson, S. J. Power, K. Fedotov, A. Crosslin, D. R. Fasel, D. Jarvik, G. P. Hakonarson, H. Bangash, H. Kullo, I. J. Connolly, J. J. Nestor, J. G. Caraballo, P. J. Wei, W. Wiley, K. Rehm, H. L. Gibbs, R. A. 2021-02-01 doi:10.1101/2021.01.31.429037 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Preparatory activity links frontal eye field activity with small amplitude motor unit recruitment of neck muscles during gaze planning ]]> https://biorxiv.org/content/10.1101/2021.02.01.429125v1?rss=1 Rungta, S. P. Basu, D. Sendhilnathan, N. Murthy, A. 2021-02-02 doi:10.1101/2021.02.01.429125 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Motor cortex activity across movement speeds is predicted by network-level strategies for generating muscle activity ]]> https://biorxiv.org/content/10.1101/2021.02.01.429168v1?rss=1 Saxena, S. Russo, A. Cunningham, J. Churchland, M. M. 2021-02-02 doi:10.1101/2021.02.01.429168 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Phase Gradients and Anisotropy of the Suprachiasmatic Network ]]> https://biorxiv.org/content/10.1101/2021.02.01.429173v1?rss=1 Yoshikawa, T. Pauls, S. D. Foley, N. Taub, A. LeSauter, J. Foley, D. Honma, K.-I. Honma, S. Silver, R. 2021-02-02 doi:10.1101/2021.02.01.429173 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Variation in Placental microRNA Expression Associates with Familial Cardiovascular Disease ]]> https://biorxiv.org/content/10.1101/2021.02.01.429202v1?rss=1 Tehrani, J. M. Kennedy, E. M. Tian, F.-Y. Everson, T. M. Deyssenroth, M. Burt, A. Hermetz, K. Hao, K. Chen, J. Koestler, D. C. Marsit, C. J. 2021-02-02 doi:10.1101/2021.02.01.429202 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Accurate and robust inference of microbial growth dynamics from metagenomic sequencing ]]> https://biorxiv.org/content/10.1101/2021.02.02.429365v1?rss=1 Joseph, T. A. Chlenski, P. Korem, T. Pe'er, I. 2021-02-02 doi:10.1101/2021.02.02.429365 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Alpha oscillations shape sensory representation and perceptual accuracy ]]> https://biorxiv.org/content/10.1101/2021.02.02.429418v1?rss=1 Zhou, Y. J. Iemi, L. Schoffelen, J.-M. de Lange, F. P. Haegens, S. 2021-02-03 doi:10.1101/2021.02.02.429418 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration ]]> https://biorxiv.org/content/10.1101/2021.02.03.429622v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@d6d9e5org.highwire.dtl.DTLVardef@17b6790org.highwire.dtl.DTLVardef@cc581eorg.highwire.dtl.DTLVardef@1ad2129_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fitzgerald, A. A. Marcisak, E. F. Nasir, A. Glasgow, E. Jablonski, S. Van der Veken, P. Pearson, G. Fertig, E. J. Mace, E. M. Weiner, L. M. 2021-02-03 doi:10.1101/2021.02.03.429622 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Somatosensory innervation of healthy human oral tissues ]]> https://biorxiv.org/content/10.1101/2021.02.03.429664v1?rss=1 Moayedi, Y. Michlig, S. Park, M. Koch, A. Lumpkin, E. A. 2021-02-05 doi:10.1101/2021.02.03.429664 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Impact of Propionic Acidemia on Brain Astrocytes ]]> https://biorxiv.org/content/10.1101/2021.02.07.428966v1?rss=1 Cotrina, M. L. Sun, W. Chen, M. J. Guenzel, A. J. Zhagnay, J. Goldman, J. Barry, M. Nedergaard, M. 2021-02-08 doi:10.1101/2021.02.07.428966 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction ]]> https://biorxiv.org/content/10.1101/2021.02.08.430312v1?rss=1 Kabir, M. F. Karami, A. Cruz-Acuna, R. Klochkova, A. Saxena, R. Mu, A. Murray, M. G. Keith, K. Madzo, J. Huang, H. Jelinek, J. Karakasheva, T. Hamilton, K. E. Muir, A. B. Tetreault, M.-P. Whelan, K. A. 2021-02-09 doi:10.1101/2021.02.08.430312 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Harmful Algal Bloom-Forming Organism Responds to Nutrient Stress Distinctly From Model Phytoplankton ]]> https://biorxiv.org/content/10.1101/2021.02.08.430350v1?rss=1 McLean, C. Haley, S. T. Swarr, G. J. Kido Soule, M. C. Dyrhman, S. T. Kujawinski, E. B. 2021-02-10 doi:10.1101/2021.02.08.430350 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Disruption of nuclear architecture as a cause of COVID-19 induced anosmia ]]> https://biorxiv.org/content/10.1101/2021.02.09.430314v1?rss=1 Zazhytska, M. Kodra, A. Hoagland, D. A. Fullard, J. Shayya, H. J. Omer, A. Firestein, S. Gong, Q. Canoll, P. Goldman, J. E. Roussos, P. tenOever, B. R. Overdevest, J. B. Lomvardas, S. 2021-02-09 doi:10.1101/2021.02.09.430314 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system ]]> https://biorxiv.org/content/10.1101/2021.02.09.430532v1?rss=1 Hart, T. M. Dupuis, A. P. Tufts, D. M. Blom, A. M. Starkey, S. Rego, R. O. M. Ram, S. Kraiczy, P. Kramer, L. D. Diuk-Wasser, M. A. Kolokotronis, S.-O. Lin, Y.-P. 2021-02-10 doi:10.1101/2021.02.09.430532 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Prediction of adverse drug reactions associated with drug-drug interactions using hierarchical classification ]]> https://biorxiv.org/content/10.1101/2021.02.10.430512v1?rss=1 Kim, C. Tatonetti, N. 2021-02-11 doi:10.1101/2021.02.10.430512 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Prenatal environmental variation, alternative reproductive tactics and the formation of a mixed-kin cooperative society ]]> https://biorxiv.org/content/10.1101/2021.02.10.430612v1?rss=1 Shah, S. Rubenstein, D. R. 2021-02-10 doi:10.1101/2021.02.10.430612 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Connectivity patterns shape sensory representation in a cerebellum-like network ]]> https://biorxiv.org/content/10.1101/2021.02.10.430647v1?rss=1 Zavitz, D. Amematsro, E. Borisyuk, A. Caron, S. J. C. 2021-02-10 doi:10.1101/2021.02.10.430647 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Computational Simulation of 4-D Micro-Circular Network in Zebrafish Tail Amputation and Regeneration ]]> https://biorxiv.org/content/10.1101/2021.02.10.430654v1?rss=1 Roustaei, M. Baek, K. I. Wang, Z. Cavallero, S. Satta, S. Lai, A. O'Donnell, R. Vedula, V. Ding, Y. Marsden, A. L. Hsiai, T. 2021-02-11 doi:10.1101/2021.02.10.430654 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ A rationally designed c-di-AMP FRET biosensor to monitor nucleotide dynamics ]]> https://biorxiv.org/content/10.1101/2021.02.10.430713v1?rss=1 Pollock, A. J. Choi, P. H. Zaver, S. A. Tong, L. Woodward, J. J. 2021-02-11 doi:10.1101/2021.02.10.430713 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ The C. elegans Notch proteins LIN-12 and GLP-1 are tuned to lower force thresholds for activation than Drosophila Notch ]]> https://biorxiv.org/content/10.1101/2021.02.11.429991v1?rss=1 Langridge, P. D. Chan, J. Y. Garcia-Diaz, A. Greenwald, I. Struhl, G. 2021-02-12 doi:10.1101/2021.02.11.429991 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Learning Sparse Log-Ratios for High-Throughput Sequencing Data ]]> https://biorxiv.org/content/10.1101/2021.02.11.430695v1?rss=1 Gordon-Rodriguez, E. Quinn, T. P. Cunningham, J. P. 2021-02-12 doi:10.1101/2021.02.11.430695 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ The non-linear mixed representations in somatosensory cortex support simple and complex tasks ]]> https://biorxiv.org/content/10.1101/2021.02.11.430704v1?rss=1 Nogueira, R. Rodgers, C. C. Bruno, R. M. Fusi, S. 2021-02-11 doi:10.1101/2021.02.11.430704 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome ]]> https://biorxiv.org/content/10.1101/2021.02.11.430742v1?rss=1 Weerts, M. J. A. Lanko, K. Guzman-Vega, F. J. Jackson, A. Ramakrishnan, R. Cardona-Londono, K. J. Pena-Guerra, K. A. van Bever, Y. van Paassen, B. Kievit, A. van Slegtenhorst, M. Allen, N. M. Kehoe, C. M. Robinson, H. K. Pang, L. Banu, S. H. Zaman, M. Efthymiou, S. Houlden, H. Jarvela, I. Lauronen, L. Maatta, T. Schrauwen, I. Leal, S. M. Ruivenkamp, C. A. L. Barge-Schaapveld, D. Q. C. M. Peeters-Scholte, C. M. P. C. D. Galehdari, H. Mazaheri, N. Sisodiya, S. M. Harrison, V. Sun, A. Thies, J. Pedroza, L. A. Taranchenko, Y. L. Chinn, I. K. Lupski, J. R. Garza 2021-02-15 doi:10.1101/2021.02.11.430742 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ Evolutionary divergence of locomotion in two related vertebrate species ]]> https://biorxiv.org/content/10.1101/2021.02.11.430752v1?rss=1 Rajan, G. Lafaye, J. Carbo-Tano, M. Duroure, K. Faini, G. Tanese, D. Panier, T. Candelier, R. Henninger, J. Britz, R. Judkewitz, B. Gebhardt, C. Emiliani, V. Debregeas, G. Wyart, C. Del Bene, F. 2021-02-12 doi:10.1101/2021.02.11.430752 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Abrupt remapping in human CA3/dentate gyrus signals resolution of memory interference ]]> https://biorxiv.org/content/10.1101/2021.02.11.430826v1?rss=1 Guo, W. Favila, S. E. Kim, G. Molitor, R. J. Kuhl, B. A. 2021-02-12 doi:10.1101/2021.02.11.430826 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing ]]> https://biorxiv.org/content/10.1101/2021.02.11.430876v1?rss=1 Vo, P. L. H. Acree, C. Smith, M. L. Sternberg, S. H. 2021-02-12 doi:10.1101/2021.02.11.430876 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Region-specific maladaptive gray matter myelination is associated with differential susceptibility to stress-induced behavior in male rodents and humans ]]> https://biorxiv.org/content/10.1101/2021.02.15.431176v1?rss=1 Long, K. L. P. Chao, L. L. Kazama, Y. An, A. Hu, K. Y. Peretz, L. Muller, D. C. Y. Roan, V. D. Misra, R. Toth, C. E. Breton, J. M. Casazza, W. Mostafavi, S. M. Huber, B. R. Woodward, S. H. Neylan, T. C. Kaufer, D. 2021-02-15 doi:10.1101/2021.02.15.431176 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ A glycan gate controls opening of the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2021.02.15.431212v1?rss=1 Sztain, T. E. Ahn, S.-H. Bogetti, A. T. Casalino, L. Goldsmith, J. A. McCool, R. S. Kearns, F. L. McCammon, J. A. McLellan, J. S. Chong, L. Amaro, R. E. 2021-02-16 doi:10.1101/2021.02.15.431212 Cold Spring Harbor Laboratory Press 2021-02-16 <![CDATA[ Affinity Requirements For Control Of Synaptic Targeting And Neuronal Cell Survival By Heterophilic IgSF Cell Adhesion Molecules ]]> https://biorxiv.org/content/10.1101/2021.02.16.431482v1?rss=1 Xu, S. Sergeeva, A. P. Katsamba, P. S. Mannepalli, S. Bahna, F. Bimela, J. Zipursky, L. S. Shapiro, L. Honig, B. Zinn, K. 2021-02-17 doi:10.1101/2021.02.16.431482 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ A transient postnatal quiescent period precedes emergence of mature cortical dynamics ]]> https://biorxiv.org/content/10.1101/2021.02.17.430487v1?rss=1 Dominguez, S. Ma, L. Yu, H. Pouchelon, G. Mayer, C. Spyropoulos, G. D. Cea, C. Buzsaki, G. Fishell, G. Khodagholy, D. Gelinas, J. N. 2021-02-17 doi:10.1101/2021.02.17.430487 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Nuclear HMGB1 protects from non-alcoholic fatty liver diseases through negative regulation of liver X receptor ]]> https://biorxiv.org/content/10.1101/2021.02.17.431446v1?rss=1 Personnaz, J. Piccolo, E. Dortignac, A. Iacovoni, J. S. Mariette, J. Polizzi, A. Batut, A. Deleruyelle, S. Paccoud, R. Moreau, E. Martins, F. Clouaire, T. Benhamed, F. Montagner, A. Wahli, W. A. Schwabe, R. F. Yart, A. Castan-Laurell, I. Postic, C. Moro, C. Legube, G. Lee, C.-H. Guillou, H. Valet, P. Dray, C. Pradere, J.-P. 2021-02-17 doi:10.1101/2021.02.17.431446 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies ]]> https://biorxiv.org/content/10.1101/2021.02.18.431725v1?rss=1 Ofer, N. Berger, D. R. Kasthuri, N. Lichtman, J. W. Yuste, R. 2021-02-18 doi:10.1101/2021.02.18.431725 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Alzheimer's-like remodeling of neuronal ryanodine receptor in COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.02.18.431811v1?rss=1 Marks, A. R. Dridi, H. Reiken, S. Liu, X. Sittenfeld, L. 2021-02-18 doi:10.1101/2021.02.18.431811 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Unique functions for Notch4 in murine embryonic lymphangiogenesis ]]> https://biorxiv.org/content/10.1101/2021.02.19.431982v1?rss=1 Muley, A. Kim Uh, M. James, J. M. Murtomaki, A. McCarron, J. D. Kitajewski, C. Gnarra, M. Riitano, G. Mukouyama, Y.-s. Kitajewski, J. Shawber, C. J. 2021-02-20 doi:10.1101/2021.02.19.431982 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ Vesicular stomatitis virus chimeras expressing the Oropouche virus glycoproteins elicit protective immune responses in mice. ]]> https://biorxiv.org/content/10.1101/2021.02.19.432025v1?rss=1 Stubbs, S. H. Pontelli, M. C. MISHRA, N. Zhuo, C. Souza, J. d. P. Viana, R. M. M. Lipkin, W. I. H. Knipe, D. Arruda, E. A. Whelan, S. P. J. 2021-02-19 doi:10.1101/2021.02.19.432025 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Structural Basis for Accommodation of Emerging B.1.351 and B.1.1.7 Variants by Two Potent SARS-CoV-2 Neutralizing Antibodies ]]> https://biorxiv.org/content/10.1101/2021.02.21.432168v1?rss=1 Cerutti, G. Rapp, M. Guo, Y. Bahna, F. Bimela, J. Reddem, E. R. Yu, J. Wang, P. Liu, L. Huang, Y. Ho, D. D. Kwong, P. D. Sheng, Z. Shapiro, L. 2021-02-22 doi:10.1101/2021.02.21.432168 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ pyControl: Open source, Python based, hardware and software for controlling behavioural neuroscience experiments. ]]> https://biorxiv.org/content/10.1101/2021.02.22.432227v1?rss=1 Akam, T. Lustig, A. Rowland, J. Kapanaiah, S. K. T. Esteve-Agraz, J. Panniello, M. Marquez, C. Kohl, M. Kätzel, D. Costa, R. M. Walton, M. E. 2021-02-23 doi:10.1101/2021.02.22.432227 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Parallel processing of natural images by overlapping retinal neuronal ensembles ]]> https://biorxiv.org/content/10.1101/2021.02.22.432289v1?rss=1 Perez-Ortega, J. E. Araya, J. Ibaceta, C. Herzog, R. Escobar, M.-J. Pena-Ortega, F. Carillo-Reid, L. Palacios, A. G. 2021-02-23 doi:10.1101/2021.02.22.432289 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders ]]> https://biorxiv.org/content/10.1101/2021.02.22.432309v1?rss=1 Whiteway, M. R. Biderman, D. Friedman, Y. Dipoppa, M. Buchanan, E. K. Wu, A. Zhou, J. Noel, J.-P. R. The International Brain Lab, Cunningham, J. P. Paninski, L. 2021-02-23 doi:10.1101/2021.02.22.432309 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Engineering protease-resistant peptides to inhibit human parainfluenza viral respiratory infection ]]> https://biorxiv.org/content/10.1101/2021.02.22.432312v1?rss=1 Outlaw, V. K. Cheloha, R. W. Jurgens, E. Bovier, F. T. Zhu, Y. Kreitler, D. F. Harder, O. K. Niewiesk, S. Porotto, M. Gellman, S. H. Moscona, A. 2021-02-22 doi:10.1101/2021.02.22.432312 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Single Unit Analysis and Wide-Field Imaging Reveal Alterations in Excitatory andInhibitory Neurons in Glioma ]]> https://biorxiv.org/content/10.1101/2021.02.23.432381v1?rss=1 Gill, B. J. A. Khan, F. A. Merricks, E. M. Goldberg, A. R. Wu, X. Sosunov, A. A. Sudhakar, T. Liou, J.-y. Dovas, A. McKhann, G. M. Canoll, P. Schevon, C. 2021-02-23 doi:10.1101/2021.02.23.432381 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Genetic incompatibilities do not snowball in a demographic model of speciation ]]> https://biorxiv.org/content/10.1101/2021.02.23.432472v1?rss=1 Maya-Lastra, C. A. Eaton, D. A. R. 2021-02-23 doi:10.1101/2021.02.23.432472 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Identical Sequences, Different Behaviors: ProteinDiversity Captured at the Single-Molecule Level ]]> https://biorxiv.org/content/10.1101/2021.02.24.432730v1?rss=1 Tapia-Rojo, R. Alonso-Caballero, A. Badilla, C. L. Fernandez, J. 2021-02-25 doi:10.1101/2021.02.24.432730 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Spatiospectral brain networks reflective of improvisational experience ]]> https://biorxiv.org/content/10.1101/2021.02.25.432633v1?rss=1 Faller, J. Goldman, A. J. Lin, Y. McIntosh, J. R. Sajda, P. 2021-02-25 doi:10.1101/2021.02.25.432633 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Using optogenetics to link myosin patterns to contractile cell behaviors during convergent extension ]]> https://biorxiv.org/content/10.1101/2021.02.25.432882v1?rss=1 Herrera-Perez, R. M. Cupo, C. Allan, C. Lin, A. Kasza, K. E. 2021-02-26 doi:10.1101/2021.02.25.432882 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Ovarian Tumor Mitochondria Exhibit Abnormal Phenotypes and Blunted Associations with Biobehavioral Factors ]]> https://biorxiv.org/content/10.1101/2021.02.26.432917v1?rss=1 Bindra, S. McGill, M. A. Triplett, M. K. Tyagi, A. Thaker, P. H. Dahmoush, L. Goodheart, M. J. Ogden, T. Owusu-Ansah, E. Karan, K. Cole, S. Sood, A. K. Lutgendorf, S. K. Picard, M. 2021-02-26 doi:10.1101/2021.02.26.432917 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Sparse balance: excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights ]]> https://biorxiv.org/content/10.1101/2021.02.26.433027v1?rss=1 Khajeh, R. Fumarola, F. Abbott, L. 2021-02-26 doi:10.1101/2021.02.26.433027 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ 3D Neuronal Mitochondrial Morphology in Axons, Dendrites, and Somata of the Aging Mouse Hippocampus ]]> https://biorxiv.org/content/10.1101/2021.02.26.433056v1?rss=1 Faitg, J. Lacefield, C. Davey, T. White, K. Laws, R. Kosmidis, S. Reeve, A. K. Kandel, E. Vincent, A. E. Picard, M. 2021-02-27 doi:10.1101/2021.02.26.433056 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Improved correspondence of fMRI visual field localizer data after macroanatomical alignment ]]> https://biorxiv.org/content/10.1101/2021.02.26.433066v1?rss=1 Qubad, M. Barnes-Scheufler, C. V. Schaum, M. Raspor, E. Roesler, L. Peters, B. Goebel, R. Reif, A. Bittner, R. A. 2021-02-27 doi:10.1101/2021.02.26.433066 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Alanine cross-feeding determines Escherichia coli colony growth dynamics ]]> https://biorxiv.org/content/10.1101/2021.02.28.433255v1?rss=1 Diaz-Pascual, F. Lempp, M. Nosho, K. Jeckel, H. Jo, J. K. Neuhaus, K. Hartmann, R. Jelli, E. Hansen, M. F. Dietrich, L. E. P. Link, H. Drescher, K. 2021-02-28 doi:10.1101/2021.02.28.433255 Cold Spring Harbor Laboratory Press 2021-02-28 <![CDATA[ Transfer learning framework for cell segmentationwith incorporation of geometric features ]]> https://biorxiv.org/content/10.1101/2021.02.28.433289v1?rss=1 Jin, Y. Toberoff, A. Azizi, E. 2021-03-01 doi:10.1101/2021.02.28.433289 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Spontaneous neural oscillations influence behavior and sensory representations by suppressing neuronal excitability ]]> https://biorxiv.org/content/10.1101/2021.03.01.433450v1?rss=1 Iemi, L. Gwilliams, L. Samaha, J. Auksztulewicz, R. Cycowicz, Y. M. King, J.-R. Nikulin, V. V. Thesen, T. Doyle, W. Devinsky, O. Schroeder, C. E. Melloni, L. Haegens, S. 2021-03-02 doi:10.1101/2021.03.01.433450 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization ]]> https://biorxiv.org/content/10.1101/2021.03.01.433466v1?rss=1 Wang, P. Wang, M. Yu, J. Cerutti, G. Nair, M. S. Huang, Y. Kwong, P. D. Shapiro, L. Ho, D. D. 2021-03-02 doi:10.1101/2021.03.01.433466 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Homothorax Controls a Binary Rhodopsin Switch in Drosophila Ocelli ]]> https://biorxiv.org/content/10.1101/2021.03.04.433862v1?rss=1 Mishra, A. K. Fritsch, C. Voutev, R. Mann, R. S. Sprecher, S. G. 2021-03-04 doi:10.1101/2021.03.04.433862 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Mature parvalbumin interneuron function in prefrontal cortex requires activity during a postnatal sensitive period ]]> https://biorxiv.org/content/10.1101/2021.03.04.433943v1?rss=1 Canetta, S. E. Holt, E. S. Benoit, L. J. Teboul, E. Ogden, R. T. Harris, A. Z. Kellendonk, C. 2021-03-04 doi:10.1101/2021.03.04.433943 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ TAFKAP: An improved method for probabilistic decoding of cortical activity ]]> https://biorxiv.org/content/10.1101/2021.03.04.433946v1?rss=1 van Bergen, R. S. Jehee, J. F. M. 2021-03-05 doi:10.1101/2021.03.04.433946 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Intra-epithelial non-canonical Activin A signalling safeguards prostate progenitor quiescence ]]> https://biorxiv.org/content/10.1101/2021.03.05.433921v1?rss=1 Cambuli, F. Foletto, V. Alaimo, A. De Felice, D. Gandolfi, F. Palumbieri, M. D. Zaffagni, M. Genovesi, S. Lorenzoni, M. Celotti, M. Bertossio, E. Mazzero, G. Bertossi, A. Bisio, A. Berardinelli, F. Antoccia, A. Gaspari, M. Barbareschi, M. Fiorentino, M. Shen, M. M. Loda, M. Romanel, A. Lunardi, A. 2021-03-07 doi:10.1101/2021.03.05.433921 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology ]]> https://biorxiv.org/content/10.1101/2021.03.05.434171v1?rss=1 Bermperidis, T. Rai, R. Torres, E. B. 2021-03-09 doi:10.1101/2021.03.05.434171 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ General and cell-type-specific aspects of the motor neuron maturation transcriptional program ]]> https://biorxiv.org/content/10.1101/2021.03.05.434185v1?rss=1 Patel, T. Hammelman, J. Closser, M. Gifford, D. K. Wichterle, H. 2021-03-06 doi:10.1101/2021.03.05.434185 Cold Spring Harbor Laboratory Press 2021-03-06 <![CDATA[ Medulla glutamatergic neurons control wake-sleep transitions ]]> https://biorxiv.org/content/10.1101/2021.03.07.434263v1?rss=1 Teng, S. Zhen, F. Schalchli, J. C. Chen, X. Jin, H. Wang, L. Peng, Y. 2021-03-08 doi:10.1101/2021.03.07.434263 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe ]]> https://biorxiv.org/content/10.1101/2021.03.08.434385v1?rss=1 Demichev, V. Yu, F. Teo, G. C. Szyrwiel, L. Rosenberger, G. Decker, J. Kaspar-Schoenefeld, S. Lilley, K. S. Muelleder, M. Nesvizhskii, A. I. Ralser, M. 2021-03-09 doi:10.1101/2021.03.08.434385 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Identification of putative causal loci in whole-genome sequencing data via knockoff statistics ]]> https://biorxiv.org/content/10.1101/2021.03.08.434451v1?rss=1 He, Z. Liu, L. Wang, C. Le Guen, Y. Lee, J. Gogarten, S. Lu, F. Montgomery, S. Tang, H. Silverman, E. K. Cho, M. H. Greicius, M. Ionita-Laza, I. 2021-03-09 doi:10.1101/2021.03.08.434451 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ High resolution structure of the membrane embedded skeletal muscle ryanodine receptor ]]> https://biorxiv.org/content/10.1101/2021.03.09.434632v1?rss=1 Melville, Z. Kim, K. Clarke, O. B. Marks, A. R. 2021-03-09 doi:10.1101/2021.03.09.434632 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Transient Kinetic Proofreading ]]> https://biorxiv.org/content/10.1101/2021.03.10.434642v1?rss=1 Iyengar, G. Perry, M. 2021-03-12 doi:10.1101/2021.03.10.434642 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Variable autoinhibition among deafness-associated variants of Diaphanous 1 (DIAPH1) ]]> https://biorxiv.org/content/10.1101/2021.03.10.434847v1?rss=1 Lakha, R. Montero, A. M. Jabeen, T. Costeas, C. C. Ma, J. Vizcarra, C. L. 2021-03-10 doi:10.1101/2021.03.10.434847 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Adipocyte Tribbles1 Regulates Plasma Adiponectin and Plasma Lipids in Mice ]]> https://biorxiv.org/content/10.1101/2021.03.11.434882v1?rss=1 Ha, E. E. Quartuccia, G. I. Ling, R. Xue, C. Hernandez-Ono, A. Imam, R. Cui, J. Soni, R. K. Bauer, R. C. 2021-03-12 doi:10.1101/2021.03.11.434882 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Two distinct mechanisms underlie dosage sensitivity in Pumilio1-associated diseases ]]> https://biorxiv.org/content/10.1101/2021.03.11.435015v1?rss=1 Botta, S. de Prisco, N. Chemiakine, A. Cabaj, M. Brandt, V. L. Patel, P. Soni, R. K. Gennarino, V. A. 2021-03-12 doi:10.1101/2021.03.11.435015 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ The geometry of face memory ]]> https://biorxiv.org/content/10.1101/2021.03.12.435023v1?rss=1 She, L. Benna, M. K. Shi, Y. Fusi, S. Tsao, D. Y. 2021-03-12 doi:10.1101/2021.03.12.435023 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ 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[ An integrative transcriptional logic model of hepatic insulin resistance ]]> https://biorxiv.org/content/10.1101/2021.03.15.435438v1?rss=1 KITAMOTO, T. Kuo, T. Okabe, A. Kaneda, A. Accili, D. 2021-03-16 doi:10.1101/2021.03.15.435438 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Myosin turnover controls actomyosin contractile instability ]]> https://biorxiv.org/content/10.1101/2021.03.18.436017v1?rss=1 Thiyagarajan, S. Wang, S. Chew, T. G. Huang, J. BALASUBRAMANIAN, M. O'Shaughnessy, B. 2021-03-18 doi:10.1101/2021.03.18.436017 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Meta-learning local synaptic plasticity for continual familiarity detection ]]> https://biorxiv.org/content/10.1101/2021.03.21.436287v1?rss=1 Tyulmankov, D. Yang, G. R. Abbott, L. 2021-03-22 doi:10.1101/2021.03.21.436287 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Single dose of amphetamine induces delayed subregional attenuation of striatal cholinergic interneuron activity ]]> https://biorxiv.org/content/10.1101/2021.03.22.436417v1?rss=1 Ztaou, S. Oh, S. J. Tepler, S. Fleury, S. Matamales, M. Bertran-Gonzalez, J. Chuhma, N. Rayport, S. 2021-03-22 doi:10.1101/2021.03.22.436417 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans ]]> https://biorxiv.org/content/10.1101/2021.03.22.436458v1?rss=1 Jiang, V. Khare, S. D. Banta, S. 2021-03-22 doi:10.1101/2021.03.22.436458 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[ Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin Nanoparticle Vaccine in Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2021.03.24.436523v1?rss=1 Joyce, M. G. King, H. A. D. Elakhal Naouar, I. Ahmed, A. Peachman, K. K. Cincotta, C. M. Subra, C. Chen, R. E. Thomas, P. V. Chen, W.-H. Sankhala, R. S. Hajduczki, A. Martinez, E. J. Peterson, C. E. Chang, W. C. Choe, M. Smith, C. Lee, P. J. Headley, J. A. Taddese, M. G. Elyard, H. A. Cook, A. Anderson, A. McGuckin-Wuertz, K. Dong, M. Swafford, I. Case, J. B. Currier, J. R. Lal, K. G. O'Connell, R. J. Molnar, S. Nair, M. S. Dussupt, V. Daye, S. P. Zeng, X. Barkei, E. K. Staples, H. M. Alfson, K. Carrion, R. Krebs, S. J. Paquin-Proulx, D. Karasavva, N. 2021-03-25 doi:10.1101/2021.03.24.436523 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Transthyretin promotes axon growth via regulation of microtubule dynamics and tubulin acetylation ]]> https://biorxiv.org/content/10.1101/2021.03.24.436762v1?rss=1 Eira, J. Magalhaes, J. Macedo, N. Pero, M. E. Misgeld, T. Sousa, M. M. Bartolini, F. Liz, M. A. 2021-03-25 doi:10.1101/2021.03.24.436762 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Tracking the rates and mechanisms of canopy damage and recovery following Hurricane Maria using multitemporal lidar data ]]> https://biorxiv.org/content/10.1101/2021.03.26.436869v1?rss=1 1 m, 2018-2020), whereas 21.6% of forests with initial height losses showed little or no height gain, and 17.8% of forests exhibited no structural changes >|1| m in either period. Canopy layers <10 m accounted for most increases in canopy height and fractional cover between 2018-2020, with gains split evenly between height growth and lateral crown expansion by surviving individuals. These findings benchmark rates of gap formation, crown expansion, and canopy closure following hurricane damage. MANUSCRIPT HIGHLIGHTSO_LIHurricane Maria gave forests a haircut by toppling trees and shearing branches. C_LIO_LIRegrowth after Maria was patchy, with equal areas of height gain and no change. C_LIO_LI3-D measures of forest recovery after hurricanes can improve ecosystem models. C_LI ]]> Leitold, V. Morton, D. C. Martinuzzi, S. Paynter, I. Uriarte, M. Keller, M. Ferraz, A. Cook, B. D. Corp, L. A. Gonzalez, G. 2021-03-28 doi:10.1101/2021.03.26.436869 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Phase separation of RNA-binding protein promotes polymerase engagement and transcription ]]> https://biorxiv.org/content/10.1101/2021.03.26.436939v1?rss=1 Shao, W. Bi, X. Gao, B. Wu, J. Pan, Y. Yin, Y. Liu, Z. Zhang, W. Jiang, X. Ren, W. Xu, Y. Wu, Z. Wang, K. Zhan, G. Lu, J. Han, X. Li, T. Li, G. Wang, J. Deng, H. Li, B. Shen, X. 2021-03-29 doi:10.1101/2021.03.26.436939 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain ]]> https://biorxiv.org/content/10.1101/2021.03.29.437526v1?rss=1 Deryckere, A. Styfhals, R. Elagoz, A. M. Maes, G. E. Seuntjens, E. 2021-03-30 doi:10.1101/2021.03.29.437526 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.03.31.437939v1?rss=1 Masoudi, N. Schnabel, R. Hobert, O. 2021-03-31 doi:10.1101/2021.03.31.437939 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Antagonistic inhibitory subnetworks control cooperation and competition across cortical space ]]> https://biorxiv.org/content/10.1101/2021.03.31.437953v1?rss=1 Mossing, D. P. Veit, J. Palmigiano, A. Miller, K. D. Adesnik, H. 2021-03-31 doi:10.1101/2021.03.31.437953 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Stratification of Risk of Progression to Colectomy in Ulcerative Colitis using Measured and Predicted Gene Expression ]]> https://biorxiv.org/content/10.1101/2021.04.02.438187v1?rss=1 Mo, A. Nagpal, S. Gettler, K. Haritunians, T. Giri, M. Haberman, Y. Karns, R. Prince, J. Arafat, D. Hsu, N.-Y. Chuang, L.-S. Argmann, C. Kasarskis, A. Suarez-Farinas, M. Gotman, N. Mengesha, E. Venkateswaran, S. Rufo, P. A. Baker, S. S. Sauer, C. G. Markowitz, J. Pfefferkorn, M. D. Rosh, J. R. Boyle, B. M. Mack, D. R. Baldassano, R. N. Shah, S. LeLeiko, N. S. Heyman, M. B. Griffiths, A. M. Patel, A. S. Noe, J. D. Thomas, S. D. Aronow, B. J. Walters, T. D. McGovern, D. P. Hyams, J. S. Kugathasan, S. Cho, J. Denson, L. A. Gibson, G. 2021-04-04 doi:10.1101/2021.04.02.438187 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Decisions in an Innate Behavioral Sequence ]]> https://biorxiv.org/content/10.1101/2021.04.03.438315v1?rss=1 Cury, K. M. Axel, R. 2021-04-04 doi:10.1101/2021.04.03.438315 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Mixed selectivity coding of sensory and motor social signals in the thalamus of a weakly electric fish ]]> https://biorxiv.org/content/10.1101/2021.04.04.438391v1?rss=1 Wallach, A. Melanson, A. Longtin, A. Maler, L. 2021-04-04 doi:10.1101/2021.04.04.438391 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ Optimizing touchscreen measures of rodent cognition by eliminating image bias ]]> https://biorxiv.org/content/10.1101/2021.04.05.438342v1?rss=1 Belarde, J. A. Chen, C. W. Rafikian, E. Yang, M. Troy, C. M. 2021-04-06 doi:10.1101/2021.04.05.438342 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Large-Scale Deep Multi-Layer Analysis of Alzheimer's Disease Brain Reveals Strong Proteomic Disease-Related Changes Not Observed at the RNA Level ]]> https://biorxiv.org/content/10.1101/2021.04.05.438450v1?rss=1 2000 brains to better understand these changes, which highlighted alterations in astrocytes and microglia as likely key drivers of disease. Here, we extend this analysis by analyzing >1000 brain tissues using a tandem mass tag mass spectrometry (TMT-MS) pipeline, which allowed us to nearly triple the number of quantified proteins across cases. A consensus protein co-expression network analysis of this deeper dataset revealed new co-expression modules that were highly preserved across cohorts and brain regions, and strongly altered in AD. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism, and a module related to the matrisome. Analysis of paired genomic and proteomic data within subjects showed that expression level of the matrisome module was influenced by the APOE {varepsilon}4 allele, but was not related to the rate of cognitive decline after adjustment for neuropathology. In contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD. ]]> Johnson, E. C. B. Carter, E. K. Dammer, E. B. Duong, D. Gerasimov, E. S. Liu, Y. Liu, J. Betarbet, R. Ping, L. Yin, L. Serrano, G. E. Beach, T. G. Peng, J. De Jager, P. L. Gaiteri, C. Bennett, D. A. Gearing, M. Wingo, T. S. Wingo, A. P. Lah, J. J. Levey, A. I. Seyfried, N. T. 2021-04-06 doi:10.1101/2021.04.05.438450 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development ]]> https://biorxiv.org/content/10.1101/2021.04.05.438484v1?rss=1 Hein, R. F. C. Wu, J. H. Tsai, Y.-H. Wu, A. Miller, A. J. Holloway, E. M. Frum, T. Conchola, A. S. Szenker-Ravi, E. Reversade, B. Yan, K. S. Kuo, C. J. Spence, J. R. 2021-04-06 doi:10.1101/2021.04.05.438484 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ The TNF Egr participates in signaling during cell competition in the absence of a requirement for JNK ]]> https://biorxiv.org/content/10.1101/2021.04.06.438672v1?rss=1 Kodra, A. de la Cova, C. C. Sharma Singh, A. Johnston, L. A. 2021-04-06 doi:10.1101/2021.04.06.438672 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Pre-Stimulus Alpha-Band Phase Gates Afferent Visual Cortex Responses ]]> https://biorxiv.org/content/10.1101/2021.04.06.438680v1?rss=1 Dou, W. Morrow, A. Iemi, L. Samaha, J. 2021-04-08 doi:10.1101/2021.04.06.438680 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Visualizing the organization and differentiation of the male-specific nervous system of C. elegans ]]> https://biorxiv.org/content/10.1101/2021.04.06.438718v1?rss=1 Tekieli, T. Yemini, E. Nejatbakhsh, A. Varol, E. Fernandez, R. W. Masoudi, N. Paninski, L. Hobert, O. 2021-04-06 doi:10.1101/2021.04.06.438718 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.04.07.438882v1?rss=1 Morris, J. A. Daniloski, Z. Domingo, J. Barry, T. Ziosi, M. Glinos, D. A. Hao, S. Mimitou, E. Smibert, P. Roeder, K. Katsevich, E. Lappalainen, T. Sanjana, N. E. 2021-04-08 doi:10.1101/2021.04.07.438882 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ FRAME-tags: genetically encoded fluorescent markers for multiplexed barcoding and time-resolved tracking of live cells ]]> https://biorxiv.org/content/10.1101/2021.04.09.436507v1?rss=1 Anzalone, A. V. Jimenez, M. Cornish, V. W. 2021-04-09 doi:10.1101/2021.04.09.436507 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Face dissimilarity judgements are predicted by representational distance in deep neural networks and principal-component face space ]]> https://biorxiv.org/content/10.1101/2021.04.09.438859v1?rss=1 Jozwik, K. M. O'Keeffe, J. Storrs, K. R. Kriegeskorte, N. 2021-04-10 doi:10.1101/2021.04.09.438859 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Large fluctuations of the fusion intermediate help SARS-CoV-2 capture host cell membranes ]]> https://biorxiv.org/content/10.1101/2021.04.09.439051v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@1374b59org.highwire.dtl.DTLVardef@133d21forg.highwire.dtl.DTLVardef@127f2ddorg.highwire.dtl.DTLVardef@1b9ab8f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Su, R. Zeng, J. O'Shaughnessy, B. 2021-04-10 doi:10.1101/2021.04.09.439051 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques ]]> https://biorxiv.org/content/10.1101/2021.04.09.439166v1?rss=1 King, H. A. D. Joyce, M. G. Elakhal Naouar, I. Ahmed, A. Macedo Cincotta, C. Subra, C. Peachman, K. K. Hack, H. H. Chen, R. E. Thomas, P. V. Chen, W.-H. Sankhala, R. S. Hajduczki, A. Martinez, E. J. Peterson, C. E. Chang, W. C. Choe, M. Smith, C. Headley, J. A. Elyard, H. A. Cook, A. Anderson, A. Wuertz, K. M. Dong, M. Swafford, I. Case, J. B. Currier, J. R. Lal, K. G. Amare, M. F. Dussupt, V. Molnar, S. Daye, S. P. Zeng, X. Barkei, E. K. Alfson, K. Staples, H. M. Carrion, R. Krebs, S. J. Paquin-Proulx, D. Karasavvas, N. Polonis, V. R. Jagodzinski, L. L 2021-04-10 doi:10.1101/2021.04.09.439166 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Welch-weighted Egger regression reduces false positives due to correlated pleiotropy in Mendelian randomization ]]> https://biorxiv.org/content/10.1101/2021.04.09.439229v1?rss=1 Brown, B. C. Knowles, D. A. 2021-04-10 doi:10.1101/2021.04.09.439229 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ State dependence of neural networks on past history and stimulus presentation in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.04.09.439242v1?rss=1 Cecere, Z. T. Yemini, E. Sharpee, T. O. Chalasani, S. H. 2021-04-11 doi:10.1101/2021.04.09.439242 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Subjective confidence reflects representation of Bayesian probability in cortex ]]> https://biorxiv.org/content/10.1101/2021.04.10.439272v1?rss=1 Geurts, L. S. Cooke, J. R. H. van Bergen, R. S. Jehee, J. F. M. 2021-04-10 doi:10.1101/2021.04.10.439272 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ ALS and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy ]]> https://biorxiv.org/content/10.1101/2021.04.12.439050v1?rss=1 Harding, O. Evans, C. S. Ye, J. Cheung, J. Maniatis, T. Holzbaur, E. L. F. 2021-04-12 doi:10.1101/2021.04.12.439050 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Developmental changes in story-evoked responses in the neocortex and hippocampus ]]> https://biorxiv.org/content/10.1101/2021.04.12.439526v1?rss=1 Cohen, S. S. Baldassano, C. 2021-04-12 doi:10.1101/2021.04.12.439526 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Adipsin promotes bone marrow adiposity by priming mesenchymal stem cells ]]> https://biorxiv.org/content/10.1101/2021.04.13.439598v1?rss=1 Qiang, L. Aaron, N. Kraakman, M. J. Zhou, Q. Liu, Q. Yang, J. Liu, L. Yu, L. Wang, L. He, Y. Fan, L. Hirakawa, H. Ding, L. Lo, J. Wang, W. Zhao, B. Guo, E. Sun, L. Rosen, C. J. 2021-04-13 doi:10.1101/2021.04.13.439598 Cold Spring Harbor Laboratory Press 2021-04-13 <![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[ Evolving the Olfactory System with Machine Learning ]]> https://biorxiv.org/content/10.1101/2021.04.15.439917v1?rss=1 Wang, P. Y. Sun, Y. Axel, R. Abbott, L. Yang, G. R. 2021-04-16 doi:10.1101/2021.04.15.439917 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ A direct lateral entorhinal cortex to hippocampal CA2 circuit conveys social information required for social memory ]]> https://biorxiv.org/content/10.1101/2021.04.15.440048v1?rss=1 Lopez-Rojas, J. de Solis, C. A. Leroy, F. Kandel, E. R. Siegelbaum, S. A. 2021-04-16 doi:10.1101/2021.04.15.440048 Cold Spring Harbor Laboratory Press 2021-04-16 <![CDATA[ State and stimulus dependence reconcile motion computation and the Drosophila connectome ]]> https://biorxiv.org/content/10.1101/2021.04.17.440267v1?rss=1 Behnia, R. Kohn, J. R. Portes, J. P. Christenson, M. P. Abbott, L. 2021-04-17 doi:10.1101/2021.04.17.440267 Cold Spring Harbor Laboratory Press 2021-04-17 <![CDATA[ Multi-scale semi-supervised clustering of brain images: deriving disease subtypes ]]> https://biorxiv.org/content/10.1101/2021.04.19.440501v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@2769e9org.highwire.dtl.DTLVardef@19a691borg.highwire.dtl.DTLVardef@6a9264org.highwire.dtl.DTLVardef@b0e686_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> WEN, J. Varol, E. Sotiras, A. Yang, Z. Chand, G. B. Erus, G. Shou, H. Hwang, G. Davatzikos, C. 2021-04-20 doi:10.1101/2021.04.19.440501 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Transient dopamine neuron activity precedes and encodes the vigor of contralateral movements ]]> https://biorxiv.org/content/10.1101/2021.04.20.440527v1?rss=1 Mendonca, M. D. Alves da Silva, J. Hernandez, L. F. Castela, I. Obeso, J. Costa, R. M. 2021-04-20 doi:10.1101/2021.04.20.440527 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ FACT subunit SUPT16H associates with BRD4 and contributes to silencing of antiviral interferon signaling ]]> https://biorxiv.org/content/10.1101/2021.04.21.440833v1?rss=1 Zhou, D. Park, J.-G. Wu, Z. Huang, H. Fiches, G. N. Biswas, A. Li, T.-W. Ma, Q. Martinez-Sobrido, L. Santoso, N. Zhu, J. 2021-04-21 doi:10.1101/2021.04.21.440833 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ The role of neural flexibility in cognitive aging ]]> https://biorxiv.org/content/10.1101/2021.04.22.440855v1?rss=1 Varangis, E. Qi, W. Stern, Y. Lee, S. 2021-04-23 doi:10.1101/2021.04.22.440855 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Interleukin-15 Receptor α Chain Knockout NOD-SCID mice have reduced numbers of NK cells, develop thymic lymphomas and fail to engraft human hematopoietic cells ]]> https://biorxiv.org/content/10.1101/2021.04.22.440980v1?rss=1 Vecchione, A. Nauman, G. A. Khosravi Marharlooei, M. Danzl, N. M. Li, H. W. Chavez, E. Y. Low, B. E. Wiles, M. V. Serreze, D. Ding, L. Sykes, M. 2021-04-22 doi:10.1101/2021.04.22.440980 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Flexible use of memory by food-caching birds in a laboratory behavioral paradigm ]]> https://biorxiv.org/content/10.1101/2021.04.22.441012v1?rss=1 Applegate, M. C. Aronov, D. 2021-04-23 doi:10.1101/2021.04.22.441012 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2021.04.22.441027v1?rss=1 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. As expected, differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in differentiation population composition and cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables. ]]> Grancharova, T. Gerbin, K. A. Rosenberg, A. B. Roco, C. M. Arakaki, J. DeLizzo, C. Dinh, S. Q. Donovan-Maiye, R. Hirano, M. Nelson, A. Tang, J. Theriot, J. A. Yan, C. Menon, V. Palecek, S. P. Seelig, G. Gunawardane, R. N. 2021-04-23 doi:10.1101/2021.04.22.441027 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Predicting functional effect of missense variants using graph attention neural networks ]]> https://biorxiv.org/content/10.1101/2021.04.22.441037v1?rss=1 Zhang, H. Xu, M. S. Chung, W. K. Shen, Y. 2021-04-23 doi:10.1101/2021.04.22.441037 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2021.04.23.441024v1?rss=1 McDonald, J. T. Enguita, F. J. Taylor, D. Bowen, R. A. Griffin, R. J. Priebe, W. Emmett, M. R. McGrath, M. Sajadi, M. Harris, A. D. Clement, J. Dybas, J. M. Aykin-Burns, N. Guarnieri, J. W. Singh, L. N. Grabham, P. Baylin, S. Yousey, A. Pearson, A. N. Corry, P. M. Saravia-Butler, A. Aunins, T. R. Nagpal, P. Meydan, C. Foox, J. Mozsary, C. Cerqueira, B. Zaksas, V. Singh, U. Wurtele, E. S. Costes, S. V. Galeano, D. Paccanaro, A. Meinig, S. L. Hagan, R. S. Bowman, N. M. UNC COVID-19 Pathobiology Consortium, Wolfgang, M. C. Altinok, S. Sapoval, N. Treangen 2021-04-23 doi:10.1101/2021.04.23.441024 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ A synthetic peptide CTL vaccine targeting nucleocapsid confers protection from SARS-CoV-2 challenge in rhesus macaques ]]> https://biorxiv.org/content/10.1101/2021.04.24.441228v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@c0730aorg.highwire.dtl.DTLVardef@c0bff7org.highwire.dtl.DTLVardef@7b1ea6org.highwire.dtl.DTLVardef@11950a5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Harris, P. Brasel, T. Massey, C. Herst, C. Burkholz, S. Lloyd, P. Blankenberg, T. Bey, T. Carback, R. Hodge, T. Ciotlos, S. Wang, L. Comer, J. E. Rubsamen, R. M. 2021-04-26 doi:10.1101/2021.04.24.441228 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ A human brain vascular atlas reveals diverse cell mediators of Alzheimer's disease risk ]]> https://biorxiv.org/content/10.1101/2021.04.26.441262v1?rss=1 Yang, A. C. Vest, R. Kern, F. Lee, D. Maat, C. A. Losada, P. M. Chen, M. B. Agam, M. Schaum, N. 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Angelaki, D. 2021-04-27 doi:10.1101/2021.04.26.441532 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Real time observation of chaperone-modulated talin mechanics under single molecule resolution ]]> https://biorxiv.org/content/10.1101/2021.04.27.441571v1?rss=1 Banerjee, S. Chaudhuri, D. Chakraborty, S. Haldar, S. 2021-04-27 doi:10.1101/2021.04.27.441571 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Pparg drives luminal differentiation and luminal tumor formation in the urothelium ]]> https://biorxiv.org/content/10.1101/2021.04.27.441646v1?rss=1 Tate, T. Xiang, T. Zhou, M. Kim, W. Y. Chen, X. Kim, H. Batourina, E. Lin, C.-S. Lu, C. Wobker, S. E. Mckiernan, J. M. Mendelsohn, C. L. 2021-04-28 doi:10.1101/2021.04.27.441646 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Human interictal epileptiform discharges are traveling waves reflecting ictal self-organization ]]> https://biorxiv.org/content/10.1101/2021.04.28.440978v1?rss=1 Smith, E. H. Liou, J.-Y. Merricks, E. M. Davis, T. S. Thomson, K. Greger, B. House, P. A. Emerson, R. Goodman, R. R. McKhann, G. M. Sheth, S. A. Schevon, C. A. Rolston, J. D. 2021-04-29 doi:10.1101/2021.04.28.440978 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ scvi-tools: a library for deep probabilistic analysis of single-cell omics data ]]> https://biorxiv.org/content/10.1101/2021.04.28.441833v1?rss=1 Gayoso, A. Lopez, R. Xing, G. Boyeau, P. Wu, K. Jayasuriya, M. Mehlman, E. Langevin, M. Liu, Y. Samaran, J. Misrachi, G. Nazaret, A. Clivio, O. Xu, C. Ashuach, T. Lotfollahi, M. Svensson, V. da Veiga Beltrame, E. Talavera-Lopez, C. Pachter, L. Theis, F. J. Streets, A. Jordan, M. I. Regier, J. Yosef, N. 2021-04-29 doi:10.1101/2021.04.28.441833 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Systematic over-crediting in California's forest carbon offsets program ]]> https://biorxiv.org/content/10.1101/2021.04.28.441870v1?rss=1 Badgley, G. Freeman, J. Hamman, J. J. Haya, B. Trugman, A. T. Anderegg, W. R. L. Cullenward, D. 2021-04-29 doi:10.1101/2021.04.28.441870 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ High-Yield Monocyte, Macrophage, and Dendritic Cell Differentiation from Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2021.04.29.441947v1?rss=1 95%), CD34-CD14+ monocytes in 19-23 days and yields 13.5-fold more monocytes by day 35 when compared to previous methods. These iPSC-monocytes are analogous to human blood-derived monocytes and readily differentiate into MDM and moDC. The efficient workflow and increase in monocyte output heightens feasibility for high throughput studies and enables clinical-scale iPSC-derived manufacturing processes. ]]> Armitage, L. H. Khosravi Maharlooei, M. Meacham, A. M. Butfiloski, E. J. Viola, R. M. Egli, D. Sykes, M. Wallet, M. A. Mathews, C. E. 2021-04-29 doi:10.1101/2021.04.29.441947 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ Preserved motor memory in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2021.04.30.441882v1?rss=1 Lahlou, S. Gabitov, E. Owen, L. L. W. Shohamy, D. Sharp, M. 2021-05-01 doi:10.1101/2021.04.30.441882 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ Sequential sampling from memory underlies action selection during abstract decision making ]]> https://biorxiv.org/content/10.1101/2021.04.30.442176v1?rss=1 Shushruth, S. Shadlen, M. N. 2021-04-30 doi:10.1101/2021.04.30.442176 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ A multisensory circuit for gating intense aversive experiences ]]> https://biorxiv.org/content/10.1101/2021.05.01.441648v1?rss=1 Asok, A. Leroy, F. Parro, C. de Solis, C. A. Ford, L. Fitzpatrick, M. Kalmbach, A. Neve, R. Rayman, J. B. Kandel, E. 2021-05-02 doi:10.1101/2021.05.01.441648 Cold Spring Harbor Laboratory Press 2021-05-02 <![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[ Use of Induced Pluripotent Stem Cells to Build Isogenic Systems and Investigate Type 1 Diabetes ]]> https://biorxiv.org/content/10.1101/2021.05.03.441837v1?rss=1 Armitage, L. H. Stimpson, S. E. Santostefano, K. E. Sui, L. Ogundare, S. O. Newby, B. N. Castro-Gutierrez, R. Huber, M. K. Taylor, J. P. Sharma, P. Radichev, I. Perry, D. J. Fredette, N. Savinov, A. Terada, N. Brusko, T. M. Wallet, M. A. Russ, H. Chen, J. Egli, D. Mathews, C. E. 2021-05-03 doi:10.1101/2021.05.03.441837 Cold Spring Harbor Laboratory Press 2021-05-03 <![CDATA[ Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment ]]> https://biorxiv.org/content/10.1101/2021.05.03.442486v1?rss=1 Varn, F. S. Johnson, K. C. Wade, T. E. Malta, T. M. Sabedot, T. S. Barthel, F. P. Kim, H. Ahmed, N. Datta, I. Barnholtz-Sloan, J. S. Bakas, S. D'Angelo, F. Gan, H. K. Garofano, L. Huse, J. T. Khasraw, M. Kocakavuk, E. Migliozzi, S. Ormond, D. R. Paek, S. H. Van Meir, E. G. Walenkamp, A. M. E. Watts, C. Weller, M. Weiss, T. Wesseling, P. Stead, L. F. Poisson, L. M. Noushmehr, H. Iavarone, A. Verhaak, R. G. The GLASS Consortium, 2021-05-04 doi:10.1101/2021.05.03.442486 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Single-cell gene regulatory network inference atscale: The Inferelator 3.0 ]]> https://biorxiv.org/content/10.1101/2021.05.03.442499v1?rss=1 Skok Gibbs, C. Jackson, C. A. Saldi, G.-A. Shah, A. Tjärnberg, A. Watters, A. De Veaux, N. Tchourine, K. Yi, R. Hamamsy, T. Castro, D. M. Carriero, N. Gresham, D. Miraldi, E. R. Bonneau, R. 2021-05-04 doi:10.1101/2021.05.03.442499 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Genetic network regulating visual acuity makes limited contribution to visually guided eye emmetropization ]]> https://biorxiv.org/content/10.1101/2021.05.04.442661v1?rss=1 Tkatchenko, T. V. Tkatchenko, A. V. 2021-05-05 doi:10.1101/2021.05.04.442661 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Neural Representations of Food-Related Attributes in the Human Orbitofrontal Cortex in Health and Disease ]]> https://biorxiv.org/content/10.1101/2021.05.05.441818v1?rss=1 Xue, A. M. Foerde, K. Walsh, B. T. Steinglass, J. E. Shohamy, D. Bakkour, A. 2021-05-06 doi:10.1101/2021.05.05.441818 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Flexible neural control of motor units ]]> https://biorxiv.org/content/10.1101/2021.05.05.442653v1?rss=1 Marshall, N. J. Glaser, J. I. Trautmann, E. M. Amematsro, E. A. Perkins, S. M. Shadlen, M. N. Abbott, L. F. Cunningham, J. P. Churchland, M. M. 2021-05-05 doi:10.1101/2021.05.05.442653 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2021.05.06.442895v1?rss=1 Huemer, M. Mairpady Shambat, S. Pereira, S. Van Gestel, L. Bergada-Pijuan, J. Gomez Mejia, A. Chang, C.-C. Vulin, C. Baer, J. Dworkin, J. Zinkernagel, A. S. 2021-05-06 doi:10.1101/2021.05.06.442895 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[ Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord ]]> https://biorxiv.org/content/10.1101/2021.05.06.443008v1?rss=1 Fiederling, F. Hammond, L. A. Ng, D. Mason, C. Dodd, J. 2021-05-07 doi:10.1101/2021.05.06.443008 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Resource Profile and User Guide of the Polygenic Index Repository ]]> https://biorxiv.org/content/10.1101/2021.05.08.443158v1?rss=1 Becker, J. Burik, C. A. P. Goldman, G. Wang, N. Jayashankar, H. Bennett, M. Belsky, D. W. Linner, R. K. Ahlskog, R. Kleinman, A. Hinds, D. A. 23andMe Research Group, Caspi, A. Corcoran, D. L. Moffitt, T. E. Poulton, R. Sugden, K. Williams, B. S. Harris, K. M. Steptoe, A. Ajnakina, O. Milani, L. Esko, T. Iacono, W. G. McGue, M. Magnusson, P. K. E. Mallard, T. T. Harden, K. P. Tucker-Drob, E. M. Herd, P. Freese, J. Young, A. Beauchamp, J. P. Koellinger, P. Oskarsson, S. Johannesson, M. Visscher, P. M. Meyer, M. N. Laibson, D. Cesarini, D. Benjamin, D. J. 2021-05-10 doi:10.1101/2021.05.08.443158 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Rab35 and glucocorticoids regulate APP and BACE1 trafficking to modulate Aβ production ]]> https://biorxiv.org/content/10.1101/2021.05.10.443354v1?rss=1 Zhuravleva, V. Vaz Silva, J. Zhu, M. Gomes, P. Silva, J. M. Sousa, N. Sotiropoulos, I. Waites, C. L. 2021-05-11 doi:10.1101/2021.05.10.443354 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Absence of muricholic acid due to Cyp2c-deficiency protects against high fat diet-induced obesity in male mice but promotes liver damage ]]> https://biorxiv.org/content/10.1101/2021.05.10.443487v1?rss=1 Oteng, A.-B. Higuchi, S. Banks, A. S. Haeusler, R. A. 2021-05-10 doi:10.1101/2021.05.10.443487 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Hierarchical confounder discovery in the experiment-machine learning cycle ]]> https://biorxiv.org/content/10.1101/2021.05.11.443616v1?rss=1 Rogozhnikov, A. Ramkumar, P. Kato, S. Escola, S. 2021-05-12 doi:10.1101/2021.05.11.443616 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Delayed DNA replication in haploid human embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2021.05.11.443666v1?rss=1 Edwards, M. M. Zuccaro, M. V. Sagi, I. Ding, Q. Vershkov, D. Benvenisty, N. Egli, D. Koren, A. 2021-05-12 doi:10.1101/2021.05.11.443666 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole cell mechanics ]]> https://biorxiv.org/content/10.1101/2021.05.12.443683v1?rss=1 Vahabikashi, A. Sivagurunathan, S. Nicdao, F. A. S. Han, Y. L. Park, C. Y. Tran, J. R. Gundersen, G. G. Reddy, K. Luxton, G. G. Guo, M. Fredberg, J. J. Zheng, Y. Adam, S. A. Goldman, R. D. 2021-05-13 doi:10.1101/2021.05.12.443683 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ The Origin of Bladder Cancer from Mucosal Field Effects ]]> https://biorxiv.org/content/10.1101/2021.05.12.443785v1?rss=1 Bondaruk, J. Jaksik, R. Wang, Z. Cogdell, D. Lee, S. Chen, Y. Dinh, K. N. Majewski, T. Zhang, L. Cao, S. Yao, H. Weinstein, J. N. Navai, N. Dinney, C. Gao, J. Theodorescu, D. Logothetis, C. Guo, C. C. Wang, W. McConkey, D. J. Wei, P. Kimmel, M. Czerniak, B. 2021-05-14 doi:10.1101/2021.05.12.443785 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183 ]]> https://biorxiv.org/content/10.1101/2021.05.12.443866v1?rss=1 de Vries, L. E. Jansen, P. A. Barcelo, C. Munro, J. Verhoef, J. M. Pasaje, C. F. A. Rubiano, K. Striepen, J. Bolscher, J. M. Henderson, R. Huijs, T. Koolen, K. M. Tumwebaze, P. K. Yeo, T. Aguiar, A. C. Angulo-Barturen, I. Churchyard, A. Baum, J. Fernandez, B. C. Gamo, F.-J. Guido, R. V. Jimenez-Diaz, M. B. Pereira, D. B. Rochford, R. Sanz, L. M. Trevitt, G. Wittlin, S. Cooper, R. A. Rosenthal, P. J. Sauerwein, R. W. Schalkwijk, J. Hermkens, P. H. Bonnert, R. Campo, B. Fidock, D. A. Llinas, M. Niles, J. C. Kooij, T. W. Dechering, K. J. 2021-05-14 doi:10.1101/2021.05.12.443866 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Thrombopoietin from hepatocytes promotes hematopoietic stem cell regeneration after myeloablation ]]> https://biorxiv.org/content/10.1101/2021.05.13.443980v1?rss=1 Ding, L. Gao, L. Decker, M. Chen, H. 2021-05-13 doi:10.1101/2021.05.13.443980 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Ranking Reprogramming Factors for Directed Differentiation ]]> https://biorxiv.org/content/10.1101/2021.05.14.444080v1?rss=1 Hammelman, J. Patel, T. Closser, M. Wichterle, H. Gifford, D. K. 2021-05-17 doi:10.1101/2021.05.14.444080 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Pre-training RNNs on ecologically relevant tasks explains sub-optimal behavioral reset ]]> https://biorxiv.org/content/10.1101/2021.05.15.444287v1?rss=1 Molano-Mazon, M. Duque, D. Yang, G. R. de la Rocha, J. 2021-05-17 doi:10.1101/2021.05.15.444287 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Flexibility of Functional Neuronal Assemblies Supports Human Memory ]]> https://biorxiv.org/content/10.1101/2021.05.16.444361v1?rss=1 Umbach, G. Tan, R. J. Jacobs, J. Pfeiffer, B. E. Lega, B. 2021-05-17 doi:10.1101/2021.05.16.444361 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Impaired α-tubulin re-tyrosination leads to synaptic dysfunction and is a feature of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2021.05.17.443847v1?rss=1 Peris, L. Qu, X. Soleilhac, J.-M. Parato, J. Lante, F. Kumar, A. Pero, M. E. Martinez-Hernandez, J. Corrao, C. Falivelli, G. Payet, F. Gory-Faure, S. Bosc, C. Blanca Ramirez, M. Sproul, A. Brocard, J. Di Cara, B. Delagrange, P. Buisson, A. Goldberg, Y. Moutin, M.-J. Bartolini, F. Andrieux, A. 2021-05-17 doi:10.1101/2021.05.17.443847 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Schema representations in distinct brain networks support narrative memory during encoding and retrieval ]]> https://biorxiv.org/content/10.1101/2021.05.17.444363v1?rss=1 Masis-Obando, R. Norman, K. A. Baldassano, C. 2021-05-17 doi:10.1101/2021.05.17.444363 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Toughening mechanisms for the attachment of architectured materials: The mechanics of the tendon enthesis ]]> https://biorxiv.org/content/10.1101/2021.05.17.444505v1?rss=1 Golman, M. Abraham, A. C. Kurtaliaj, I. Marshall, B. P. Hu, Y. J. Schwartz, A. G. Guo, X. E. Birman, V. Thurner, P. J. Genin, G. M. Thomopoulos, S. 2021-05-18 doi:10.1101/2021.05.17.444505 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Impaired and Intact Aspects of Attentional Competition and Prioritization during Visual Working Memory Encoding in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.05.19.442954v1?rss=1 Barnes, C. V. Roesler, L. Schaum, M. Schiweck, C. Peters, B. Reif, A. Wibral, M. Bittner, R. A. 2021-05-19 doi:10.1101/2021.05.19.442954 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Maternal separation affects fronto-cortical activity in rat pups during dam-pup interactions and behavioral transitions ]]> https://biorxiv.org/content/10.1101/2021.05.19.444831v1?rss=1 Ranger, M. Behring, T. Kaidbey, J. H. Anwar, M. Lipshutz, A. B. Mollicone, I. Hassan, G. Fasano, K. Hinz, N. K. Ludwig, R. J. Myers, M. M. Welch, M. G. Dumitriu, D. 2021-05-21 doi:10.1101/2021.05.19.444831 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Rare copy number variants (CNVs) and breast cancer risk ]]> https://biorxiv.org/content/10.1101/2021.05.20.444828v1?rss=1 Dennis, J. Tyrer, J. P. Walker, L. C. Michailidou, K. Dorling, L. Bolla, M. K. Wang, Q. Ahearn, T. U. Andrulis, I. L. Anton-Culver, H. Antonenkova, N. N. Arndt, V. Aronson, K. J. Beane Freeman, L. E. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bogdanova, N. V. Bojesen, S. E. Brenner, H. Castelao, J. E. Chang-Claude, J. Chenevix-Trench, G. Clarke, C. L. Collaborators, N. Collee, J. M. Consortium, C. Couch, F. J. Cox, A. Cross, S. S. Czene, K. Devilee, P. Dork, T. Dossus, L. Eliassen, A. H. Eriksson, M. Evans, D. G. Fasching, P. A. Figueroa, J. 2021-05-21 doi:10.1101/2021.05.20.444828 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ PISCES: A pipeline for the Systematic, Protein Activity-based Analysis of Single Cell RNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/2021.05.20.445002v1?rss=1 Vlahos, L. J. Obradovic, A. Laise, P. Worley, J. Tan, X. Wang, A.-L. Califano, A. 2021-05-22 doi:10.1101/2021.05.20.445002 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ The proportional recovery rule redux: Arguments for its biological and predictive relevance ]]> https://biorxiv.org/content/10.1101/2021.05.20.445022v1?rss=1 Goldsmith, J. Kitago, T. Garcia de la Garza, A. Kundert, R. Luft, A. Stinear, C. M. Byblow, W. D. Kwakkel, G. Krakauer, J. W. 2021-05-21 doi:10.1101/2021.05.20.445022 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ Demuxalot: scaled up genetic demultiplexing for single-cell sequencing ]]> https://biorxiv.org/content/10.1101/2021.05.22.443646v1?rss=1 Rogozhnikov, A. Ramkumar, P. Kato, S. Escola, S. 2021-05-23 doi:10.1101/2021.05.22.443646 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ MLC Seq: De novo sequencing of full-length tRNA isoforms by mass ladder complementation ]]> https://biorxiv.org/content/10.1101/2021.05.22.445286v1?rss=1 Yuan, X. Su, Y. Zhang, X. Turkel, S. J. Shi, S. Wang, X. Choi, E.-J. Wu, W. Liu, H. Viner, R. Russo, J. J. Li, W. Bao, X. Chen, Q. Zhang, S. 2021-05-23 doi:10.1101/2021.05.22.445286 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Role of molecular polymorphism in defining tau filament structures in neurodegenerative diseases ]]> https://biorxiv.org/content/10.1101/2021.05.24.445353v1?rss=1 Xiang, X. Arakhamia, T. Carlomagno, Y. Dhingra, S. Thierry, M. DeTure, M. Cook, C. N. Dickson, D. W. Petrucelli, L. Fitzpatrick, A. 2021-05-25 doi:10.1101/2021.05.24.445353 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Mechanistic studies of non-canonical amino acid mutagenesis ]]> https://biorxiv.org/content/10.1101/2021.05.24.445427v1?rss=1 Fleisher, R. C. Michael, N. Gonzalez, R. L. 2021-06-03 doi:10.1101/2021.05.24.445427 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ SARS-CoV-2 Nsp14 activates NF-κB signaling and induces IL-8 upregulation ]]> https://biorxiv.org/content/10.1101/2021.05.26.445787v1?rss=1 Li, T.-W. Kenney, A. D. Liu, H. Fiches, G. N. Zhou, D. Biswas, A. Que, J. Santoso, N. Yount, J. S. Zhu, J. 2021-05-26 doi:10.1101/2021.05.26.445787 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures ]]> https://biorxiv.org/content/10.1101/2021.05.28.446215v1?rss=1 Dhanwani, R. Rodrigues Lima-Junior, J. Sethi, A. Pham, J. Williams, G. Frazier, A. Xu, Y. Amara, A. W. Standaert, D. G. Goldman, J. G. Litvan, I. Alcalay, R. N. Peters, B. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2021-05-29 doi:10.1101/2021.05.28.446215 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Effect sizes and test-retest reliability of the fMRI-based Neurologic Pain Signature ]]> https://biorxiv.org/content/10.1101/2021.05.29.445964v1?rss=1 Han, X. Ashar, Y. K. Kragel, P. Petre, B. Schelkun, V. Atlas, L. Chang, L. J. Jepma, M. Koban, L. Losin, E. R. Roy, M. Woo, C.-W. Wager, T. D. 2021-05-30 doi:10.1101/2021.05.29.445964 Cold Spring Harbor Laboratory Press 2021-05-30 <![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[ Influence of age on functional memory T cell diversity ]]> https://biorxiv.org/content/10.1101/2021.05.29.446296v1?rss=1 Fang, F. Cao, W. Zhu, W. Lam, N. Li, L. Gaddam, S. Wang, Y. Kim, C. Lambert, S. Zhang, H. Hu, B. Farber, D. L. Weyand, C. M. Goronzy, J. J. 2021-05-30 doi:10.1101/2021.05.29.446296 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Hematologic and systemic metabolic alterations due to Mediterranean type II G6PD deficiency in a novel murine model ]]> https://biorxiv.org/content/10.1101/2021.05.31.446353v1?rss=1 D'Alessandro, A. Howie, H. L. Hay, A. M. Dziewulska, K. H. Brown, B. Wither, M. J. Karafin, M. Stone, E. F. Spitalnik, S. L. Hod, E. A. Francis, R. O. Fu, X. Thomas, T. Zimring, J. C. 2021-05-31 doi:10.1101/2021.05.31.446353 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Subcellular proteomics of dopamine neurons in the mouse brain reveals axonal enrichment of proteins encoded by Parkinson's disease-linked genes ]]> https://biorxiv.org/content/10.1101/2021.06.01.446584v1?rss=1 Hobson, B. D. Choi, S. J. Soni, R. K. Sulzer, D. Sims, P. A. 2021-06-01 doi:10.1101/2021.06.01.446584 Cold Spring Harbor Laboratory Press 2021-06-01 <![CDATA[ Mutation saturation for fitness effects at human CpG sites ]]> https://biorxiv.org/content/10.1101/2021.06.02.446661v1?rss=1 Agarwal, I. Przeworski, M. 2021-06-02 doi:10.1101/2021.06.02.446661 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Mouse brain-wide mitochondrial connectivity anchored in gene, brain and behavior ]]> https://biorxiv.org/content/10.1101/2021.06.02.446767v1?rss=1 Rosenberg, A. Saggar, M. Rogu, P. Limonges, A. W. Sandi, C. Mosharov, E. V. Dumitriu, D. Anacker, C. Picard, M. 2021-06-02 doi:10.1101/2021.06.02.446767 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Localization of TRP channels in healthy oral mucosa from human donors ]]> https://biorxiv.org/content/10.1101/2021.06.02.446798v1?rss=1 Moayedi, Y. Michlig, S. Park, M. Koch, A. Lumpkin, E. A. 2021-06-02 doi:10.1101/2021.06.02.446798 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Preclinical evaluation of a precision medicine approach to DNA vaccination in Type 1 diabetes ]]> https://biorxiv.org/content/10.1101/2021.06.02.446808v1?rss=1 Postigo Fernandez, J. Creusot, R. J. 2021-06-02 doi:10.1101/2021.06.02.446808 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Predicting localized affinity of RNA binding proteins to transcripts with convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2021.06.02.446817v1?rss=1 Kitaygorodsky, A. Jin, E. Shen, Y. 2021-06-03 doi:10.1101/2021.06.02.446817 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ Chronic opioid treatment arrests neurodevelopment and alters synaptic activity in human midbrain organoids ]]> https://biorxiv.org/content/10.1101/2021.06.02.446827v1?rss=1 Kim, H. S. Xiao, Y. Chen, X. He, S. Im, J. Willner, M. J. Finlayson, M. O. Xu, C. Zhu, H. Choi, S. J. Mosharov, E. V. Kim, H.-W. Xu, B. Leong, K. W. 2021-06-02 doi:10.1101/2021.06.02.446827 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Nitrogen fixation in mesoscale eddies of the North Pacific Subtropical Gyre: patterns and mechanisms ]]> https://biorxiv.org/content/10.1101/2021.06.03.446955v1?rss=1 Dugenne, M. Gradoville, M. R. Church, M. J. Barone, B. Wilson, S. T. Sheyn, U. Harke, M. Björkman, K. M. Hawco, N. J. Hynes, A. M. Ribalet, F. White, A. E. Karl, D. M. DeLong, E. F. Dyhrman, S. T. Armbrust, E. V. John, S. Eppley, J. M. Harding, K. Stewart, B. Cabello, A. M. Turk-Kubo, K. A. Caffin, M. Zehr, J. 2021-06-03 doi:10.1101/2021.06.03.446955 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ A severe form of maternal separation in rat consisting of nineteen-day 6-hour daily separation at unpredictable times minimally affects behavior across lifespan and possibly confers protection against some maladaptive outcomes ]]> https://biorxiv.org/content/10.1101/2021.06.07.447289v1?rss=1 Behring, T. B. Kyle, M. H. Hussain, M. Zhang, J. Manganaro, A. Kaidbey, J. H. Ludwig, R. J. Myers, M. M. Welch, M. G. Dumitriu, D. 2021-06-07 doi:10.1101/2021.06.07.447289 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Constitutive AP2gamma deficiency reduces postnatal hippocampal neurogenesis and induces behavioral deficits in juvenile mice that persist during adulthood ]]> https://biorxiv.org/content/10.1101/2021.06.07.447328v1?rss=1 Loureiro-Campos, E. Alves, N. D. Mateus-Pinheiro, A. Patricio, P. Soares-Cunha, C. Silva, J. Sardinha, V. M. Mendes-Pinheiro, B. Silveira-Rosa, T. Rodrigues, A. J. Oliveira, J. Sousa, N. Pinto, L. 2021-06-08 doi:10.1101/2021.06.07.447328 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ Activity in the dorsomedial striatum decreases with improvement in motor coordination ]]> https://biorxiv.org/content/10.1101/2021.06.07.447452v1?rss=1 Cataldi, S. Lacefield, C. N, S. Kumar, G. Sulzer, D. 2021-06-08 doi:10.1101/2021.06.07.447452 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ PRDM9 losses in vertebrates are coupled to the loss of at least three other meiotic genes ]]> https://biorxiv.org/content/10.1101/2021.06.08.447603v1?rss=1 Cavassim, M. I. A. Baker, Z. Hoge, C. Schierup, M. Schumer, M. Przeworski, M. 2021-06-09 doi:10.1101/2021.06.08.447603 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Toward a More Accurate 3D Atlas of C. elegans Neurons ]]> https://biorxiv.org/content/10.1101/2021.06.09.447813v1?rss=1 SKUHERSKY, M. Wu, T. Yemini, E. Boyden, E. Tegmark, M. 2021-06-10 doi:10.1101/2021.06.09.447813 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Brain network dynamics codify heterogeneity in seizure propagation ]]> https://biorxiv.org/content/10.1101/2021.06.12.448205v1?rss=1 Rungratsameetaweemana, N. Lainscsek, C. Cash, S. S. Garcia, J. O. Sejnowski, T. J. Bansal, K. 2021-06-14 doi:10.1101/2021.06.12.448205 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome ]]> https://biorxiv.org/content/10.1101/2021.06.14.448190v1?rss=1 Kindschuh, W. F. Baldini, F. Liu, M. C. Gerson, K. D. Liao, J. Lee, H. H. Anton, L. Gajer, P. Ravel, J. Levy, M. Elovitz, M. Korem, T. 2021-06-14 doi:10.1101/2021.06.14.448190 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Cross-species metabolomic analysis of DDT and Alzheimer's disease-associated tau toxicity ]]> https://biorxiv.org/content/10.1101/2021.06.14.448355v1?rss=1 Kalia, V. Niedzwiecki, M. M. Bradner, J. M. Lau, F. K. Bucher, M. L. Manz, K. E. Coates Fuentes, Z. Pennell, K. D. Picard, M. Walker, D. I. Hu, W. T. Jones, D. P. Miller, G. W. 2021-06-15 doi:10.1101/2021.06.14.448355 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[ NSun2 deficiency promotes tau hyperphosphorylation and neurodegeneration through epitranscriptomic regulation of miR-125b ]]> https://biorxiv.org/content/10.1101/2021.06.16.448614v1?rss=1 Kim, Y. A. Blaze, J. Winters, T. Kumar, A. Tein, E. Sproul, A. A. Teich, A. Bartolini, F. Akbarian, S. Hargus, G. Santa-Maria, I. 2021-06-16 doi:10.1101/2021.06.16.448614 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ SARS-CoV-2 envelope-protein corruption of homeostatic signaling mechanisms in mammalian cells ]]> https://biorxiv.org/content/10.1101/2021.06.16.448640v1?rss=1 Schulze, T. Hartel, A. Hoeler, S. Hemming, C. Lehn, R. Tandl, D. Greiner, T. Bertl, A. Shepard, K. Moroni, A. Thiel, G. Rauh, O. 2021-06-16 doi:10.1101/2021.06.16.448640 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Semi-supervised sequence modeling for improved behavioral segmentation ]]> https://biorxiv.org/content/10.1101/2021.06.16.448685v1?rss=1 Whiteway, M. R. Schaffer, E. S. Wu, A. Buchanan, E. K. Onder, O. F. Mishra, N. Paninski, L. 2021-06-17 doi:10.1101/2021.06.16.448685 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Behavioral and nociceptor states of inflammatory painacross timescales in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2021.06.16.448689v1?rss=1 Bohic, M. Pattison, L. A. Jhumka, Z. A. Rossi, H. Thackray, J. K. Ricci, M. Foster, W. Arnold, J. Mossazghi, N. Yttri, E. A. Tischfield, M. A. Smith, E. S. J. Abdus-Saboor, I. Abraira, V. E. 2021-06-17 doi:10.1101/2021.06.16.448689 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Coupling of Ca2+-triggered unclamping and membrane fusion during neurotransmitter release ]]> https://biorxiv.org/content/10.1101/2021.06.16.448753v1?rss=1 McDargh, Z. A. Polley, A. Zeng, J. O'Shaughnessy, B. A. 2021-06-17 doi:10.1101/2021.06.16.448753 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[ Alzheimer's disease-associated P460L mutation in ephrin receptor type A1 (EphA1) leads to dysregulated Rho-GTPase signaling ]]> https://biorxiv.org/content/10.1101/2021.06.17.448790v1?rss=1 Kim, Y. Lasso, G. Patel, H. Vardarajan, B. Santa-Maria, I. Lefort, R. 2021-06-18 doi:10.1101/2021.06.17.448790 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Recovery of conformational continuum from single-particle cryo-EM data: Optimization of ManifoldEM informed by ground-truth studies ]]> https://biorxiv.org/content/10.1101/2021.06.18.449029v1?rss=1 Seitz, E. Schwander, P. Acosta-Reyes, F. J. Maji, S. Frank, J. 2021-06-19 doi:10.1101/2021.06.18.449029 Cold Spring Harbor Laboratory Press 2021-06-19 <![CDATA[ Measles fusion complexes from central nervous system clinical isolates: decreased interaction between hemagglutinin and fusion proteins ]]> https://biorxiv.org/content/10.1101/2021.06.18.449082v1?rss=1 Mathieu, C. Nascimento Figueira, T. Decker, A. R. Ferren, M. Bovier, F. T. Jurgens, E. M. Marcink, T. C. Moscona, A. Porotto, M. 2021-06-19 doi:10.1101/2021.06.18.449082 Cold Spring Harbor Laboratory Press 2021-06-19 <![CDATA[ Large-scale neural recordings with single-cell resolution in human cortex using high-density Neuropixels probes ]]> https://biorxiv.org/content/10.1101/2021.06.20.449152v1?rss=1 Paulk, A. C. Kfir, Y. Khanna, A. Mustroph, M. Trautmann, E. M. Soper, D. J. Stavisky, S. D. Welkenhuysen, M. Dutta, B. Shenoy, K. V. Hochberg, L. R. Richardson, M. Williams, Z. M. Cash, S. S. 2021-06-21 doi:10.1101/2021.06.20.449152 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ A hemifused complex is the hub in a network of pathways to membrane fusion ]]> https://biorxiv.org/content/10.1101/2021.06.20.449175v1?rss=1 Warner, J. An, D. Stratton, B. O'Shaughnessy, B. 2021-06-20 doi:10.1101/2021.06.20.449175 Cold Spring Harbor Laboratory Press 2021-06-20 <![CDATA[ SNAREs and Synaptotagmin cooperatively determine the Ca2+ sensitivity of neurotransmitter release in fixed stoichiometry modules ]]> https://biorxiv.org/content/10.1101/2021.06.22.449527v1?rss=1 McDargh, Z. A. O'Shaughnessy, B. A. 2021-06-23 doi:10.1101/2021.06.22.449527 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Dopamine Neurons Evaluate Natural Fluctuations in Performance Quality ]]> https://biorxiv.org/content/10.1101/2021.06.23.449657v1?rss=1 Duffy, A. Latimer, K. W. Goldberg, J. H. Fairhall, A. L. Gadagkar, V. 2021-06-24 doi:10.1101/2021.06.23.449657 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Why are SNAREpins rod-shaped? ]]> https://biorxiv.org/content/10.1101/2021.06.23.449668v1?rss=1 Zeng, J. McDargh, Z. An, D. O'Shaughnessy, B. 2021-06-24 doi:10.1101/2021.06.23.449668 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Contractile ring constriction and septation in fission yeast are integrated mutually stabilizing processes ]]> https://biorxiv.org/content/10.1101/2021.06.25.449700v1?rss=1 Thiyagarajan, S. McDargh, Z. A. Wang, S. O'Shaughnessy, B. 2021-06-25 doi:10.1101/2021.06.25.449700 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Fast 3D Clear: A Fast, Aqueous-Based, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body ]]> https://biorxiv.org/content/10.1101/2021.06.25.449994v1?rss=1 Kosmidis, S. Negrean, A. Dranovsky, A. Losonczy, A. Kandel, E. 2021-06-28 doi:10.1101/2021.06.25.449994 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Dynamical transitions of the actomyosin cortex can trigger single cell morphogenesis ]]> https://biorxiv.org/content/10.1101/2021.06.25.450008v1?rss=1 Zhu, H. Alonso-Matilla, R. McDargh, Z. A. O'Shaughnessy, B. 2021-06-26 doi:10.1101/2021.06.25.450008 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ Interrogation of genome-wide, experimentally dissected gene regulatory networks reveals mechanisms underlying dynamic cellular state control ]]> https://biorxiv.org/content/10.1101/2021.06.28.449297v1?rss=1 1,000 transcriptional regulators expressed in single colorectal adenocarcinoma cells, followed by single-cell RNA-seq profiling at two timepoints, 1 day and 4 days, allowed reverse engineering the underlying tumor context-specific, causal regulatory network. Furthermore, the availability of experimentally derived, highly multiplexed gene reporter assays for each regulator, as identified by this analysis, allowed accurate assessment of differential protein activity following silencing of each regulator, thus providing proof-of-concept for generating comprehensive, tissue-specific networks of transcriptional and post-translational interactions. Analysis of this causal network allowed elucidation of complex autoregulatory mechanisms that have eluded previous computational approaches and supported systematic elucidation of cooperative mechanisms, where one regulatory protein can modulate the activity of another regulatory protein, as well as transcriptional mimicry, where one regulatory protein can phenocopy others. ]]> Tan, X. Worley, J. Turunen, M. Wong, K. Fernandez, E. C. Paull, E. Jones, S. Wang, J. Noh, H. Salvatori, B. Chavez, A. Califano, A. 2021-06-30 doi:10.1101/2021.06.28.449297 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments ]]> https://biorxiv.org/content/10.1101/2021.06.28.450186v1?rss=1 Scott, E. R. Bruna, E. M. Uriarte, M. 2021-06-30 doi:10.1101/2021.06.28.450186 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data ]]> https://biorxiv.org/content/10.1101/2021.06.28.450265v1?rss=1 Maffei, C. Lee, C. Planich, M. Ramprasad, M. Ravi, N. Trainor, D. Urban, Z. Kim, M. Jones, R. Henin, A. Hofmann, S. Pizzagalli, D. Auerbach, R. Gabrieli, J. Whitfield-Gabrieli, S. Greve, D. Haber, S. Yendiki, A. 2021-06-30 doi:10.1101/2021.06.28.450265 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain ]]> https://biorxiv.org/content/10.1101/2021.06.29.450397v1?rss=1 Cerutti, G. Guo, Y. Wang, P. Nair, M. S. Huang, Y. Yu, J. Liu, L. Katsamba, P. S. Bahna, F. Reddem, E. R. Kwong, P. D. Ho, D. D. Sheng, Z. Shapiro, L. 2021-06-29 doi:10.1101/2021.06.29.450397 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of iron oxidation ]]> https://biorxiv.org/content/10.1101/2021.06.29.450459v1?rss=1 Inaba, Y. West, A. C. Banta, S. 2021-07-01 doi:10.1101/2021.06.29.450459 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Probing molecular specificity with deep sequencing and biophysically interpretable machine learning ]]> https://biorxiv.org/content/10.1101/2021.06.30.450414v1?rss=1 Rube, H. T. Rastogi, C. Feng, S. Kribelbauer, J. F. Li, A. Becerra, B. Melo, L. A. N. Do, B. V. Li, X. Adam, H. H. Shah, N. H. Mann, R. S. Bussemaker, H. J. 2021-07-01 doi:10.1101/2021.06.30.450414 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Long Term Study of Motivational and Cognitive Effects of Low-intensity Focused Ultrasound Neuromodulation in the Dorsal Striatum of Nonhuman Primates ]]> https://biorxiv.org/content/10.1101/2021.06.30.450605v1?rss=1 Munoz, F. Meaney, A. Gross, A. Liu, K. Pouliopoulos, A. N. Liu, D. Konofagou, E. E. Ferrera, V. P. 2021-07-01 doi:10.1101/2021.06.30.450605 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans ]]> https://biorxiv.org/content/10.1101/2021.07.02.450719v1?rss=1 Nair, S. Srivastava, C. Brown, R. V. Koli, S. Choquet, H. Kang, H. S. Kuo, Y.-M. Grimm, S. A. Sutherland, C. Badea, A. Johnson, G. A. Zhao, Y. Yin, J. Okamoto, K. Kizhatil, K. Borras, T. Zode, G. Clark, G. Chakrabarti, S. John, S. W. M. Jorgenson, E. Jetten, A. M. 2021-07-05 doi:10.1101/2021.07.02.450719 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements ]]> https://biorxiv.org/content/10.1101/2021.07.02.450762v1?rss=1 Murphy, D. Elyashiv, E. Amster, G. Sella, G. 2021-07-02 doi:10.1101/2021.07.02.450762 Cold Spring Harbor Laboratory Press 2021-07-02 <![CDATA[ Signatures of rapid synaptic learning in the hippocampus during novel experiences ]]> https://biorxiv.org/content/10.1101/2021.07.02.450956v1?rss=1 Priestley, J. B. Bowler, J. C. Rolotti, S. V. Fusi, S. Losonczy, A. 2021-07-03 doi:10.1101/2021.07.02.450956 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Network-based identification and pharmacological targeting of host cell master regulators induced by SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2021.07.03.451001v1?rss=1 80% of drugs predicted to be effective by this methodology induced significant reduction of SARS-CoV-2 infection, without affecting cell viability. ViroTreat is fully generalizable and can be extended to identify drugs targeting the host cell-based MR signatures induced by virtually any pathogen. ]]> Laise, P. Stanifer, M. L. Bosker, G. Sun, X. Triana, S. Doldan, P. La Manna, F. De Menna, M. Realubit, R. B. Pampou, S. Karan, C. Alexandrov, T. Kruithof-de Julio, M. Califano, A. Boulant, S. Alvarez, M. J. 2021-07-04 doi:10.1101/2021.07.03.451001 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms ]]> https://biorxiv.org/content/10.1101/2021.07.05.450786v1?rss=1 Pividori, M. Lu, S. Li, B. Su, C. Johnson, M. E. Wei, W.-Q. Feng, Q. Namjou, B. Kiryluk, K. Kullo, I. Luo, Y. Sullivan, B. D. Skarke, C. Ritchie, M. D. Grant, S. F. A. Greene, C. S. 2021-07-06 doi:10.1101/2021.07.05.450786 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Meta-analysis of exhausted CD8+ T cells from Homo sapiens and Mus musculus provides robust targets for immunotherapy ]]> https://biorxiv.org/content/10.1101/2021.07.05.451111v1?rss=1 Zhang, L. Guo, Y. Nishi, H. 2021-07-05 doi:10.1101/2021.07.05.451111 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Brain-like functional specialization emerges spontaneously in deep neural networks ]]> https://biorxiv.org/content/10.1101/2021.07.05.451192v1?rss=1 Dobs, K. Martinez, J. Kell, A. J. E. Kanwisher, N. 2021-07-06 doi:10.1101/2021.07.05.451192 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Re-convolving the compositional landscape of primary and recurrent glioblastoma using single nucleus RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.07.06.451295v1?rss=1 Al-Dalahmah, O. Argenziano, M. Boyett, D. Save, A. Mahajan, A. Khan, F. Tuddenham, J. goldberg, a. r. Dovas, A. Banu, M. Furnari, J. Sudhakar, T. Bush, E. Lassman, A. Bruce, J. Sims, P. Menon, V. Canoll, P. 2021-07-07 doi:10.1101/2021.07.06.451295 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ A single-cell transcriptomic atlas characterizes liver non-parenchymal cells in healthy and diseased mice ]]> https://biorxiv.org/content/10.1101/2021.07.06.451396v1?rss=1 Wang, Z. Qian, J. Lu, X. Zhang, P. Guo, R. Lou, H. Zhang, S. Yang, J. Fan, X. 2021-07-07 doi:10.1101/2021.07.06.451396 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Pre-trial predictors of conflict response efficacy in human dorsolateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.07.07.451322v1?rss=1 Herman, A. B. Smith, E. Yates, M. McKhann, G. Botvinick, M. Hayden, B. Sheth, S. 2021-07-09 doi:10.1101/2021.07.07.451322 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Intracellular phase separation of globular proteins facilitated by short cationic peptides ]]> https://biorxiv.org/content/10.1101/2021.07.08.450573v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@1dc5380org.highwire.dtl.DTLVardef@1ee01a9org.highwire.dtl.DTLVardef@af0a85org.highwire.dtl.DTLVardef@1dba73d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yeong, V. Wang, J.-w. Horn, J. M. Obermeyer, A. C. 2021-07-08 doi:10.1101/2021.07.08.450573 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Directional Gaussian Mixture Models of the gut microbiome elucidate microbial spatial structure ]]> https://biorxiv.org/content/10.1101/2021.07.09.451866v1?rss=1 Pasarkar, A. P. Joseph, T. A. Pe'er, I. 2021-07-11 doi:10.1101/2021.07.09.451866 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Dynamics of glioma-associated microglia and macrophages reveals their divergent roles in the immune response of brain ]]> https://biorxiv.org/content/10.1101/2021.07.11.451874v1?rss=1 Qian, J. Wang, C. Wang, B. Li, C. Fu, K. Wang, Y. Gao, Y. Niu, C. Zhao, C. Liu, J. Wang, L. Liu, R. Luo, F. Lu, M. Liu, Y. Chu, Y. 2021-07-12 doi:10.1101/2021.07.11.451874 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Making Strides in Doctoral-Level Career Outcomes Reporting: Surveying the Landscape of Classification and Visualization Methodologies and Creating a Crosswalk Tool ]]> https://biorxiv.org/content/10.1101/2021.07.12.451657v1?rss=1 Collins, T. Ramadoss, D. Layton, R. MacDonald, J. Wheeler, R. Bankston, A. Stayart, C. A. Hao, Y. Robinson-Hamm, J. Sinche, M. Burghart, S. Carlsen-Bryan, A. Eswara, P. Krasna, H. Xu, H. Sullivan, M. 2021-07-14 doi:10.1101/2021.07.12.451657 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ In vivo evidence that SORL1, encoding the endosomal recycling receptor SORLA, can function as a causal gene in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2021.07.13.452149v1?rss=1 Andersen, O. M. Boegh, N. Landau, A. M. Ploeen, G. G. Jensen, A. M. G. Monti, G. Ulhoei, B. P. Nyengaard, J. R. Jacobsen, K. R. Joergensen, M. M. Holm, I. E. Kristensen, M. L. Hansen, E. S. Teunissen, C. E. Breidenbach, L. Droescher, M. Liu, Y. Pedersen, H. S. Callesen, H. Luo, Y. Bolund, L. Brooks, D. J. Laustsen, C. Small, S. A. Mikkelsen, L. F. Soerensen, C. B. 2021-07-13 doi:10.1101/2021.07.13.452149 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Motor memories of object dynamics are categorically organized ]]> https://biorxiv.org/content/10.1101/2021.07.13.452183v1?rss=1 Cesanek, E. Zhang, Z. Ingram, J. N. Wolpert, D. M. Flanagan, J. R. 2021-07-14 doi:10.1101/2021.07.13.452183 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ A Floxed exon (Flexon) approach to Cre-mediated conditional gene expression ]]> https://biorxiv.org/content/10.1101/2021.07.13.452276v1?rss=1 Shaffer, J. M. Greenwald, I. 2021-07-13 doi:10.1101/2021.07.13.452276 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Ing4-deficiency enhances HSC quiescence and confers resistance to inflammatory stress ]]> https://biorxiv.org/content/10.1101/2021.07.14.452366v1?rss=1 Thompson, Z. Anderson, G. A. Rodriguez, M. Gabriel, S. Binder, V. Taylor, A. M. Kathrein, K. L. 2021-07-15 doi:10.1101/2021.07.14.452366 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis ]]> https://biorxiv.org/content/10.1101/2021.07.14.452380v1?rss=1 Bhan, N. J. Castinado, A. Glaser, J. I. Kalhor, R. K. Strutz, J. Boyden, E. Church, G. Kording, K. P. Tyo, K. 2021-07-14 doi:10.1101/2021.07.14.452380 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene ]]> https://biorxiv.org/content/10.1101/2021.07.15.452499v1?rss=1 Modamio, J. Saraiva, C. Gomez-Giro, G. Nickels, S. L. Jarazo, J. Antony, P. Barbuti, P. Halder, R. Jaeger, C. Krueger, R. Glaab, E. Schwamborn, J. C. 2021-07-15 doi:10.1101/2021.07.15.452499 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2021.07.16.452702v1?rss=1 Mor, D. E. Huertas, F. Morse, A. M. Kaletsky, R. Murphy, C. T. Kalia, V. Miller, G. W. Moskalenko, O. Conesa, A. McIntyre, L. M. 2021-07-16 doi:10.1101/2021.07.16.452702 Cold Spring Harbor Laboratory Press 2021-07-16 <![CDATA[ A Reinforcement Meta-Learning Framework of Executive Function and Information Demand ]]> https://biorxiv.org/content/10.1101/2021.07.18.452793v1?rss=1 Silvetti, M. Lasaponara, S. Horan, M. Gottlieb, J. 2021-07-19 doi:10.1101/2021.07.18.452793 Cold Spring Harbor Laboratory Press 2021-07-19 <![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[ Mitochondrial Respiratory Chain Protein Co-Regulation in the Human Brain ]]> https://biorxiv.org/content/10.1101/2021.07.19.452923v1?rss=1 2.5-times higher co-regulation than mitochondrial (mt)DNA-encoded subunits. Moreover, mtDNA copy number was unrelated to mtDNA-encoded subunits abundance, suggesting that mtDNA content is not limiting. Alzheimers disease (AD) brains exhibited reduced abundance of complex I RC subunits, an effect largely driven by a 2-4% overall lower mitochondrial protein content. These findings provide foundational knowledge to identify molecular mechanisms contributing to age- and disease-related erosion of mitochondrial function in the human brain. ]]> Trumpff, C. Owusu-Ansah, E. Klein, H.-U. Lee, A. Petyuk, V. Wingo, T. S. Wingo, A. Thambisetty, M. Ferrucci, L. Seyfried, N. Bennett, D. A. De Jager, P. L. Picard, M. 2021-07-19 doi:10.1101/2021.07.19.452923 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Transcription factor regulation of eQTL activity across individuals and tissues ]]> https://biorxiv.org/content/10.1101/2021.07.20.453075v1?rss=1 Flynn, E. Tsu, A. L. Kasela, S. Kim-Hellmuth, S. Aguet, F. Ardlie, K. G. Bussemaker, H. J. Mohammadi, P. Lappalainen, T. 2021-07-20 doi:10.1101/2021.07.20.453075 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus ]]> https://biorxiv.org/content/10.1101/2021.07.20.453090v1?rss=1 Herb, B. Glover, H. J. Bhaduri, A. Casella, A. M. Bale, T. L. Kriegstein, A. Doege, C. Ament, S. A. 2021-07-20 doi:10.1101/2021.07.20.453090 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Uncertainty modulates visual maps during non-instrumental information demand ]]> https://biorxiv.org/content/10.1101/2021.07.20.453107v1?rss=1 Li, Y. Daddaoua, N. Horan, M. Gottlieb, J. 2021-07-21 doi:10.1101/2021.07.20.453107 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases ]]> https://biorxiv.org/content/10.1101/2021.07.20.453126v1?rss=1 Hobbs, H. T. Shah, N. H. Badroos, J. M. Gee, C. L. Marqusee, S. Kuriyan, J. 2021-07-20 doi:10.1101/2021.07.20.453126 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics ]]> https://biorxiv.org/content/10.1101/2021.07.21.453274v1?rss=1 Wang, X. Sacramento, C. Q. Jockusch, S. Chaves, O. A. Tao, C. Fintelman-Rodrigues, N. Chien, M. Temerozo, J. R. Li, X. Kumar, S. Xie, W. Patel, D. J. Meyer, C. Garzia, A. Tuschl, T. Bozza, P. T. Russo, J. J. Souza, T. M. L. Ju, J. 2021-07-21 doi:10.1101/2021.07.21.453274 Cold Spring Harbor Laboratory Press 2021-07-21 <![CDATA[ How clustered protocadherin binding specificity is tuned for neuronal self/non-self-recognition ]]> https://biorxiv.org/content/10.1101/2021.07.22.453400v1?rss=1 Goodman, K. M. Katsamba, P. S. Rubinstein, R. Ahlsen, G. Bahna, F. Mannepalli, S. Dan, H. Sampogna, R. Shapiro, L. Honig, B. 2021-07-23 doi:10.1101/2021.07.22.453400 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Novel Class of Psychedelic Iboga Alkaloids Disrupts Opioid Addiction States ]]> https://biorxiv.org/content/10.1101/2021.07.22.453441v1?rss=1 Havel, V. Kruegel, A. C. Bechand, B. McIntosh, S. Stallings, L. Hodges, A. Wulf, M. G. Nelson, M. Hunkele, A. Ansonoff, M. Pintar, J. E. Hwu, C. Abi-Gerges, N. Zaidi, S. A. Katritch, V. Yang, M. Javitch, J. A. Majumdar, S. Hemby, S. E. Sames, D. 2021-07-23 doi:10.1101/2021.07.22.453441 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses ]]> https://biorxiv.org/content/10.1101/2021.07.27.453843v1?rss=1 Fukuma, N. Hulke, M. L. Brener, M. I. Golob, S. Zilinyi, R. Zhou, Z. Tzimas, C. Russo, I. McGroder, C. Pfeiffer, R. Chong, A. Zhang, G. Burkhoff, D. Leon, M. B. Maurer, M. Moses, J. W. Uhlemann, A.-C. Hibshoosh, H. Uriel, N. Szabolcs, M. J. Redfors, B. Marboe, C. C. Baldwin, M. R. Tucker, N. R. Tsai, E. J. 2021-07-27 doi:10.1101/2021.07.27.453843 Cold Spring Harbor Laboratory Press 2021-07-27 <![CDATA[ miR-17~92 exerts stage-specific effects in adult V-SVZ neural stem cell lineages ]]> https://biorxiv.org/content/10.1101/2021.07.28.454109v1?rss=1 Favaloro, F. DeLeo, A. Delgado, A. Doetsch, F. 2021-07-28 doi:10.1101/2021.07.28.454109 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[ Subcellular and regional localization of mRNA translation in midbrain dopamine neurons ]]> https://biorxiv.org/content/10.1101/2021.07.30.454065v1?rss=1 Hobson, B. D. Kong, L. Angelo, M. F. Lieberman, O. J. Mosharov, E. V. Herzog, E. Sulzer, D. Sims, P. A. 2021-08-01 doi:10.1101/2021.07.30.454065 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ Neural temporal context reinstatement of event structure during memory recall ]]> https://biorxiv.org/content/10.1101/2021.07.30.454370v1?rss=1 Lohnas, L. J. Healey, K. Davachi, L. 2021-08-01 doi:10.1101/2021.07.30.454370 Cold Spring Harbor Laboratory Press 2021-08-01 <![CDATA[ NusG links transcription and translation in Escherichia coli extracts ]]> https://biorxiv.org/content/10.1101/2021.07.31.454578v1?rss=1 Bailey, E. J. Gottesman, M. E. Gonzalez, R. L. 2021-07-31 doi:10.1101/2021.07.31.454578 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Single-sequence protein structure prediction using language models from deep learning ]]> https://biorxiv.org/content/10.1101/2021.08.02.454840v1?rss=1 Chowdhury, R. Bouatta, N. Biswas, S. Rochereau, C. Church, G. M. Sorger, P. K. AlQuraishi, M. N. 2021-08-04 doi:10.1101/2021.08.02.454840 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ A programmable probiotic encapsulation system enhances therapeutic delivery in vivo ]]> https://biorxiv.org/content/10.1101/2021.08.03.454638v1?rss=1 Harimoto, T. Hahn, J. Chen, Y.-Y. Im, J. Zhang, J. Hou, N. Li, F. Coker, C. Gray, K. Harr, N. Chowdhury, S. Pu, K. Nimura, C. Arpaia, N. Leong, K. W. Danino, T. 2021-08-03 doi:10.1101/2021.08.03.454638 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Resurrecting essential amino acid biosynthesis in a mammalian cell ]]> https://biorxiv.org/content/10.1101/2021.08.03.454854v1?rss=1 Trolle, J. McBee, R. M. Kaufman, A. Pinglay, S. Berger, H. German, S. Liu, L. Shen, M. J. Guo, X. Martin, J. A. Pacold, M. Jones, D. R. Boeke, J. D. Wang, H. H. 2021-08-03 doi:10.1101/2021.08.03.454854 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ St18 specifies globus pallidus projection neuron identity in MGE lineage ]]> https://biorxiv.org/content/10.1101/2021.08.03.454907v1?rss=1 Nunnelly, L. Campbell, M. Lee, D. Gu, G. Menon, V. Au, E. 2021-08-04 doi:10.1101/2021.08.03.454907 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[ The road not taken: disconnection of a human-unique cortical pathway in schizophrenia and its effects on naturalistic social cognition ]]> https://biorxiv.org/content/10.1101/2021.08.04.455137v1?rss=1 Patel, G. H. Gruskin, D. C. Arkin, S. C. Jamerson, E. C. Ruiz-Betancourt, D. R. Klim, C. C. Sanchez-Pena, J. P. Bartel, L. P. Lee, J. K. Grinband, J. Martinez, A. Berman, R. A. Ochsner, K. N. Leopold, D. A. Javitt, D. C. 2021-08-05 doi:10.1101/2021.08.04.455137 Cold Spring Harbor Laboratory Press 2021-08-05 <![CDATA[ Neuronal responses to focused ultrasound are gated by pre-stimulation brain rhythms ]]> https://biorxiv.org/content/10.1101/2021.08.06.455443v1?rss=1 Nguyen, D. Konofagou, E. Dmochowski, J. P. 2021-08-08 doi:10.1101/2021.08.06.455443 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia ]]> https://biorxiv.org/content/10.1101/2021.08.08.455318v1?rss=1 Thomas, L. Underwood, J. Rose, N. H. Fuller, Z. L. Dugal, L. Grimaldi, C. Richards, Z. T. Cooke, I. R. Palumbi, S. R. Gilmour, J. 2021-08-08 doi:10.1101/2021.08.08.455318 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ MiSDEED: a synthetic multi-omics engine for microbiome power analysis and study design ]]> https://biorxiv.org/content/10.1101/2021.08.09.455682v1?rss=1 Chlenski, P. Hsu, M. Pe'er, I. 2021-08-10 doi:10.1101/2021.08.09.455682 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ The epigenetic evolution of gliomas is determined by their IDH1 mutation status and treatment regimen ]]> https://biorxiv.org/content/10.1101/2021.08.09.455687v1?rss=1 Malta, T. M. Sabedot, T. S. Datta, I. Garofano, L. Vallentgoed, W. Varn, F. S. Aldape, K. D'Angelo, F. Bakas, S. Barnholtz-Sloan, J. S. Gan, H. K. Hasanain, M. Hau, A.-C. Johnson, K. C. Khasraw, M. Kocakavuk, E. Kouwenhoven, M. C. Migliozzi, S. Niclou, S. Niers, J. M. Ormond, D. R. Paek, S. H. Reifenberger, G. Smitt, P. A. S. Smits, M. Stead, L. F. van den Bent, M. J. Van Meir, E. G. Walenkamp, A. Weiss, T. Weller, M. Westerman, B. A. Ylstra, B. Wesseling, P. Lasorella, A. French, P. Poisson, L. M. The GLASS Consortium, Verhaak, R. Iavarone, A. Noushme 2021-08-11 doi:10.1101/2021.08.09.455687 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Multiple macroecological laws do characterize various aspects of microbiota dynamics ]]> https://biorxiv.org/content/10.1101/2021.08.09.455744v1?rss=1 Tchourine, K. Carballo-Pacheco, M. Vitkup, D. 2021-08-10 doi:10.1101/2021.08.09.455744 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ High Leaf Respiration Rates May Limit the Success of White Spruce Saplings growing in The Kampfzone at the Arctic Treeline ]]> https://biorxiv.org/content/10.1101/2021.08.10.455813v1?rss=1 Griffin, K. L. Schmeige, S. C. Bruner, S. G. Boelman, N. T. Vierling, L. A. Eitel, J. U. H. 2021-08-10 doi:10.1101/2021.08.10.455813 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Improved blind demixing methods for recovering dense neuronal morphology from barcode imaging data ]]> https://biorxiv.org/content/10.1101/2021.08.10.455873v1?rss=1 Chen, S. Loper, J. Zhou, P. Paninski, L. 2021-08-11 doi:10.1101/2021.08.10.455873 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ A systematic data-driven approach to analyze sensor-level EEG connectivity: Identifying robust phase-synchronized network components using surface Laplacian with spectral-spatial PCA ]]> https://biorxiv.org/content/10.1101/2021.08.10.455879v1?rss=1 Smith, E. E. Bel-Bahar, T. Kayser, J. 2021-08-10 doi:10.1101/2021.08.10.455879 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Phase transition specified by a binary code patterns the vertebrate eye cup ]]> https://biorxiv.org/content/10.1101/2021.08.12.455556v1?rss=1 Balasubramanian, R. Min, X. Quinn, P. M. J. Giudice, Q. L. Tao, C. Polanco, K. Makrides, N. Peregrin, J. Bouaziz, M. Mao, Y. Wang, Q. Costa, B. L. Buenaventura, D. Wang, F. Ma, L. Tsang, S. H. Fabre, P. J. Zhang, X. 2021-08-13 doi:10.1101/2021.08.12.455556 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Mixed selectivity in the cerebellar Purkinje-cell response during visuomotor association learning ]]> https://biorxiv.org/content/10.1101/2021.08.12.456160v1?rss=1 Sendhilnathan, N. Ipata, A. E. Goldberg, M. E. 2021-08-12 doi:10.1101/2021.08.12.456160 Cold Spring Harbor Laboratory Press 2021-08-12 <![CDATA[ Seizures, behavioral deficits and adverse drug responses in two new genetic mouse models of HCN1 epileptic encephalopathy ]]> https://biorxiv.org/content/10.1101/2021.08.16.456452v1?rss=1 Santoro, B. Merseburg, A. Kasemir, J. Buss, E. W. Leroy, F. Bock, T. Porro, A. Barnett, A. Tröder, S. E. Engeland, B. Stockebrand, M. Moroni, A. Siegelbaum, S. Isbrandt, D. 2021-08-17 doi:10.1101/2021.08.16.456452 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Variation in white spruce needle respiration across the species range ]]> https://biorxiv.org/content/10.1101/2021.08.18.456715v1?rss=1 Griffin, K. L. Griffin, Z. M. Schmiege, S. C. Bruner, S. G. Boelman, N. T. Vierling, L. A. Eitel, J. U. 2021-08-19 doi:10.1101/2021.08.18.456715 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Identifying Therapeutic Strategies in IgA Nephropathy through Comprehensive Transcriptomic Characterization ]]> https://biorxiv.org/content/10.1101/2021.08.18.456879v1?rss=1 Ofori, K. Yakubu, A. Rai, A. J. 2021-08-19 doi:10.1101/2021.08.18.456879 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Lifelong single-cell profiling of cranial neural crest diversification ]]> https://biorxiv.org/content/10.1101/2021.08.19.456710v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@1c4ca91org.highwire.dtl.DTLVardef@cf0d10org.highwire.dtl.DTLVardef@162bfe9org.highwire.dtl.DTLVardef@2565fd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fabian, P. Tseng, K.-C. Thiruppathy, M. Arata, C. Chen, H.-J. Smeeton, J. Nelson, N. Crump, J. G. 2021-08-19 doi:10.1101/2021.08.19.456710 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Oculomotor freezing tracks perception and is immune to decision bias ]]> https://biorxiv.org/content/10.1101/2021.08.19.456961v1?rss=1 White, A. L. Moreland, J. C. Rolfs, M. 2021-08-19 doi:10.1101/2021.08.19.456961 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Homologous recombination induced by a replication fork barrier requires cooperation between strand invasion and strand annealing activities ]]> https://biorxiv.org/content/10.1101/2021.08.20.456128v1?rss=1 Marie, L. Symington, L. S. 2021-08-20 doi:10.1101/2021.08.20.456128 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Different neural codes serve long and short-term memory functions in primate Hippocampus and Lateral Prefrontal Cortex during virtual navigation ]]> https://biorxiv.org/content/10.1101/2021.08.20.457136v1?rss=1 Corrigan, B. W. Gulli, R. A. Doucet, G. Roussy, M. Luna, R. Sachs, A. J. Martinez-Trujillo, J. C. 2021-08-21 doi:10.1101/2021.08.20.457136 Cold Spring Harbor Laboratory Press 2021-08-21 <![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[ Microenvironmental correlates of immune checkpoint inhibitor response in human melanoma brain metastases revealed by T cell receptor and single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.08.25.456956v1?rss=1 Alvarez-Breckenridge, C. A. Markson, S. C. Stocking, J. H. Nayyar, N. Lastrapes, M. Strickland, M. R. Kim, A. E. de Sauvage, M. Dahal, A. Larson, J. M. Mora, J. L. Navia, A. W. Kuter, B. M. Gill, C. M. Bertalan, M. S. Shaw, B. Kaplan, A. Subramanian, M. Jain, A. Danish, H. Kumar, S. White, M. Shahid, O. Pauken, K. E. Miller, B. C. Izar, B. Davies, M. Frederick, D. T. Boland, G. M. Herbert, C. Shaw, M. Martinez-Lage, M. Frosch, M. P. Wang, N. Gerstner, E. R. Nahed, B. V. Curry, W. T. Carter, B. S. Cahill, D. P. Sharpe, A. Suv?, M. L. Sullivan, R. J. Bra 2021-08-28 doi:10.1101/2021.08.25.456956 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Oxo-M and 4-PPBP Delivery via Multi-Domain Peptide Hydrogel Toward Tendon Regeneration ]]> https://biorxiv.org/content/10.1101/2021.08.25.457430v1?rss=1 Park, G. Y. Tarafder, S. Eyen, S. L. Park, S. Kim, R. Siddiqui, Z. Kumar, V. Lee, C. H. 2021-08-27 doi:10.1101/2021.08.25.457430 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency ]]> https://biorxiv.org/content/10.1101/2021.08.25.457543v1?rss=1 Huang, X. Bashkenova, N. Hong, Y. Guallar, D. Hu, Z. Malik, V. Li, D. Shen, X. Zhou, H. Wang, J. 2021-08-25 doi:10.1101/2021.08.25.457543 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ The impact of genetic modifiers on variation in germline mutation rates within and among human populations ]]> https://biorxiv.org/content/10.1101/2021.08.25.457718v1?rss=1 > 1), which evolve rapidly, contribute the most to variation between them. Moreover, a modest number of modifier sites (e.g., 10 per mutation type in the standard classification into 96 types) subject to moderate to strong selection (2Nes > 1) could account for the variation in mutation rates observed among human populations. If such modifier sites indeed underlie differences among populations, they should also cause variation in mutation rates within populations and their effects should be detectable in pedigree studies. ]]> Milligan, W. R. Amster, G. Sella, G. 2021-08-27 doi:10.1101/2021.08.25.457718 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[ PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms. ]]> https://biorxiv.org/content/10.1101/2021.08.27.457864v1?rss=1 Pandit, K. Petrescu, J. Cuevas, M. Stephenson, W. Smibert, P. Phatnani, H. Maniatis, S. 2021-08-28 doi:10.1101/2021.08.27.457864 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Tightly-coupled inhibitory and excitatory functional networks in the early visual cortex ]]> https://biorxiv.org/content/10.1101/2021.08.27.457908v1?rss=1 Mulholland, H. N. Hein, B. Kaschube, M. Smith, G. 2021-08-28 doi:10.1101/2021.08.27.457908 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ The brain uses invariant dynamics to generalize outputs across movements ]]> https://biorxiv.org/content/10.1101/2021.08.27.457931v1?rss=1 Athalye, V. R. Khanna, P. Gowda, S. Orsborn, A. L. Costa, R. M. Carmena, J. M. 2021-08-28 doi:10.1101/2021.08.27.457931 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ What do we gain when tolerating loss? The information bottleneck, lossy compression, and detecting horizontal gene transfer ]]> https://biorxiv.org/content/10.1101/2021.08.27.457981v1?rss=1 Narechania, A. DeSalle, R. Mathema, B. Kreiswirth, B. N. Planet, P. J. 2021-08-28 doi:10.1101/2021.08.27.457981 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Unique Microglial Transcriptomic Signature within the Hippocampal Neurogenic Niche ]]> https://biorxiv.org/content/10.1101/2021.08.29.457876v1?rss=1 Chintamen, S. Gaur, P. Vo, N. Bradshaw, E. Menon, V. Kernie, S. G. 2021-08-29 doi:10.1101/2021.08.29.457876 Cold Spring Harbor Laboratory Press 2021-08-29 <![CDATA[ Critical period for vision-dependent modulation of postnatal retinal neurogenesis ]]> https://biorxiv.org/content/10.1101/2021.08.30.458213v1?rss=1 Tkatchenko, T. V. Michurina, T. Tomarev, S. I. Nakaya, N. Enikolopov, G. N. Tkatchenko, A. V. 2021-08-31 doi:10.1101/2021.08.30.458213 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Neck motor unit activity displays neural signatures of temporal control during sequential saccade planning ]]> https://biorxiv.org/content/10.1101/2021.08.31.458347v1?rss=1 Basu, D. Sendhilnathan, N. Murthy, A. 2021-09-01 doi:10.1101/2021.08.31.458347 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ SMN controls neuromuscular junction integrity through U7 snRNP ]]> https://biorxiv.org/content/10.1101/2021.08.31.458410v1?rss=1 Tisdale, S. Van Alstyne, M. Simon, C. M. Mentis, G. Z. Pellizzoni, L. 2021-09-01 doi:10.1101/2021.08.31.458410 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Fluid-structure interaction simulation of tissue degradation and its effects on intra-aneurysm hemodynamics ]]> https://biorxiv.org/content/10.1101/2021.09.01.458529v1?rss=1 Wang, H. Uhlmann, K. Vedula, V. Balzani, D. Varnik, F. 2021-09-02 doi:10.1101/2021.09.01.458529 Cold Spring Harbor Laboratory Press 2021-09-02 <![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[ Coding of social odors in the hippocampal CA2 region as a substrate for social memory ]]> https://biorxiv.org/content/10.1101/2021.09.02.458744v1?rss=1 Hassan, S. I. Bigler, S. Siegelbaum, S. A. 2021-09-03 doi:10.1101/2021.09.02.458744 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Category-specific representational patterns in left inferior frontal and temporal cortex reflect similarities and differences in the sensorimotor and distributional properties of concepts. ]]> https://biorxiv.org/content/10.1101/2021.09.03.458378v1?rss=1 Carota, F. Kriegeskorte, N. nili, h. Pulvermueller, F. 2021-09-03 doi:10.1101/2021.09.03.458378 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Protein Structure Prediction Using a Maximum Likelihood Formulation of a Recurrent Geometric Network ]]> https://biorxiv.org/content/10.1101/2021.09.03.458873v1?rss=1 Qi, G. Tollefson, M. R. Gogal, R. A. Smith, R. J. H. AlQuraishi, M. Schnieders, M. J. 2021-09-04 doi:10.1101/2021.09.03.458873 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Serine Starvation Silences Estrogen Receptor Signaling through Histone Hypoacetylation ]]> https://biorxiv.org/content/10.1101/2021.09.05.459037v1?rss=1 Li, A. M. Li, Y. He, B. Ramirez, Y. Jiang, H. Zhou, M.-N. Lu, C. Gruber, J. J. Rankin, E. B. Ye, J. 2021-09-06 doi:10.1101/2021.09.05.459037 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ The 14-3-3 Proteins Bmh1 and Bmh2 Are Key Regulators of Meiotic Commitment ]]> https://biorxiv.org/content/10.1101/2021.09.06.459189v1?rss=1 Gavade, J. Puccia, C. M. Herod, S. G. Trinidad, J. Berchowitz, L. E. Lacefield, S. 2021-09-06 doi:10.1101/2021.09.06.459189 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Artemisia annua hot-water extracts show potent activity in vitro against Covid-19 variants including delta ]]> https://biorxiv.org/content/10.1101/2021.09.08.459260v1?rss=1 Nair, M. S. Huang, Y. Fidock, D. A. Towler, M. Weathers, P. 2021-09-08 doi:10.1101/2021.09.08.459260 Cold Spring Harbor Laboratory Press 2021-09-08 <![CDATA[ Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program ]]> https://biorxiv.org/content/10.1101/2021.09.08.459433v1?rss=1 Caballero, M. Ge, T. Rebelo, A. R. Seo, S. Kim, S. Brooks, K. Zuccaro, M. L. Kanagaraj, R. Vershkov, D. Kim, D. Smogorzewska, A. Smolka, M. B. Benvenisty, N. West, S. C. Egli, D. C. Mace, E. M. Koren, A. 2021-09-09 doi:10.1101/2021.09.08.459433 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Deficits in decision-making induced by parietal cortex inactivation are compensated at two time scales ]]> https://biorxiv.org/content/10.1101/2021.09.10.459856v1?rss=1 Jeurissen, D. Shushruth, S. El-Shamayleh, Y. Horwitz, G. D. Shadlen, M. 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Tong, L. 2021-09-14 doi:10.1101/2021.09.14.460315 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ "Understanding Cortical Arousals during Sleep from Leg Movements: A Pilot Study." ]]> https://biorxiv.org/content/10.1101/2021.09.14.460395v1?rss=1 Bansal, K. Garcia, J. Feltch, C. Earley, C. Robucci, R. Banerjee, N. Brooks, J. 2021-09-14 doi:10.1101/2021.09.14.460395 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ CD56 at the human NK cell lytic immunological synapse ]]> https://biorxiv.org/content/10.1101/2021.09.15.460290v1?rss=1 Martinez, A. L. Gunesch, J. T. Mace, E. M. 2021-09-15 doi:10.1101/2021.09.15.460290 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Dynamic behavior of cell-free mitochondrial DNA in human saliva ]]> https://biorxiv.org/content/10.1101/2021.09.15.460321v1?rss=1 Trumpff, C. Rausser, S. Haahr, R. Karan, K. R. Gouspillou, G. Kirschbaum, C. Picard, M. 2021-09-15 doi:10.1101/2021.09.15.460321 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ A structured evaluation of cryopreservation in generating single cell transcriptomes from cerebrospinal fluid ]]> https://biorxiv.org/content/10.1101/2021.09.15.460354v1?rss=1 Touil, H. Roostaei, T. Calini, D. Diaconu, C. Epstein, S. E. Raposo, C. Craveiro, L. Callegiri, I. Bryois, J. Riley, C. S. Menon, V. Derfuss, T. De Jager, P. Malhotra, D. 2021-09-17 doi:10.1101/2021.09.15.460354 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Source-to-Target Automatic Rotating Estimation (STARE) -- A publicly-available, blood-free quantification approach for PET tracers with irreversible kinetics: Theoretical framework and validation for FDG ]]> https://biorxiv.org/content/10.1101/2021.09.15.460504v1?rss=1 Bartlett, E. A. Ogden, R. T. Mann, J. J. Zanderigo, F. 2021-09-15 doi:10.1101/2021.09.15.460504 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Relationships between individual differences in dual process and electrophysiological signatures of familiarity and recollection during retrieval ]]> https://biorxiv.org/content/10.1101/2021.09.15.460509v1?rss=1 Dimsdale-Zucker, H. R. Maciejewska, K. Kim, K. Yonelinas, A. P. Ranganath, C. 2021-09-17 doi:10.1101/2021.09.15.460509 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Influence of Rule and Reward-based Strategies on Inferences of Serial Order by Monkeys ]]> https://biorxiv.org/content/10.1101/2021.09.16.459819v1?rss=1 Ferhat, A.-T. Jensen, G. Terrace, H. S. Ferrera, V. P. 2021-09-17 doi:10.1101/2021.09.16.459819 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Zoonotic potential of a novel bat morbillivirus ]]> https://biorxiv.org/content/10.1101/2021.09.17.460143v1?rss=1 Ikegame, S. Carmichael, J. C. Wells, H. Furler, R. L. Acklin, J. A. Chiu, H.-P. Oguntuyo, K. Y. Cox, R. M. Patel, A. R. Kowdle, S. Stevens, C. S. Eckley, M. Zhan, S. Lim, J. K. Hashiguchi, T. Durigon, E. L. Schountz, T. Epstein, J. E. Plemper, R. K. Daszak, P. Anthony, S. J. Lee, B. 2021-09-17 doi:10.1101/2021.09.17.460143 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Distinct ground state and activated state modes of spiking in forebrain neurons ]]> https://biorxiv.org/content/10.1101/2021.09.20.461152v1?rss=1 Levenstein, D. Girardeau, G. Gornet, J. Grosmark, A. Huszar, R. Peyrache, A. Senzai, Y. Watson, B. Rinzel, J. Buzsaki, G. 2021-09-21 doi:10.1101/2021.09.20.461152 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Ion currents through Kir potassium channels are gated by anionic lipids. ]]> https://biorxiv.org/content/10.1101/2021.09.21.461288v1?rss=1 Jin, R. He, S. Black, K. A. Clarke, O. B. Wu, D. Bolla, J. R. Johnson, P. Periasamy, A. Wardak, A. Czabotar, P. Colman, P. M. Robinson, C. V. Laver, D. Smith, B. J. Gulbis, J. M. 2021-09-22 doi:10.1101/2021.09.21.461288 Cold Spring Harbor Laboratory Press 2021-09-22 <![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[ Identification of touch neurons underlying dopaminergic pleasurable touch and sexual receptivity ]]> https://biorxiv.org/content/10.1101/2021.09.22.461355v1?rss=1 Middleton, L. Schaffler, M. Succi, I. Foster, W. Gradwell, M. Bohic, M. Ejoh, L. Abraira, V. Abdus-Saboor, I. 2021-09-22 doi:10.1101/2021.09.22.461355 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Signatures of visuospatial information foraging during learning of complex environments ]]> https://biorxiv.org/content/10.1101/2021.09.22.461356v1?rss=1 Barack, D. L. Bakkour, A. Shohamy, D. Salzman, C. D. 2021-09-22 doi:10.1101/2021.09.22.461356 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Microbial Biotextiles for a Circular Materials Economy ]]> https://biorxiv.org/content/10.1101/2021.09.22.461422v1?rss=1 Schiros, T. N. Antrobus, R. Farias, D. Chiu, Y.-T. Joseph, C. T. Esdaille, S. Sanchiricco, G. K. Miquelon, G. An, D. Russell, S. T. Chitu, A. Goetz, S. Chasse, A. M. V. Nuckolls, C. Kumar, S. K. Lu, H. H. 2021-09-24 doi:10.1101/2021.09.22.461422 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ A rise-to-threshold signal for a relative value deliberation ]]> https://biorxiv.org/content/10.1101/2021.09.23.461548v1?rss=1 Vijayan, V. Wang, F. Wang, K. Chakravorty, A. Adachi, A. Akhlaghpour, H. Dickson, B. J. Maimon, G. 2021-09-24 doi:10.1101/2021.09.23.461548 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Learning of biased representations in LIP through interactions between recurrent connectivity and Hebbian plasticity ]]> https://biorxiv.org/content/10.1101/2021.09.23.461557v1?rss=1 Zhang, W. Gottlieb, J. Miller, K. D. 2021-09-24 doi:10.1101/2021.09.23.461557 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Caspase-4/11 exacerbates disease severity in SARS-CoV-2 infection by promoting inflammation and thrombosis ]]> https://biorxiv.org/content/10.1101/2021.09.24.461743v1?rss=1 Eltobgy, M. Zani, A. Kenney, A. Estfanous, S. Kim, E. Badr, A. Carafice, C. Daily, K. Whitham, O. Pietrzak, M. Webb, A. Kawahara, J. Eddy, A. Denz, P. Lu, M. KC, M. Peeples, M. Li, J. Zhu, J. Que, J. Robinson, R. Rosas Mejia, O. Rayner, R. Hall-Stoodley, L. Seveau, S. Gavrilin, M. A. Tedeschi, A. Partida-Sanchez, S. Roberto, F. Hemann, E. Abdelrazik, E. Forero, A. Nimjee, S. Boyaka, P. Cormet-Boyaka, E. Yount, J. Amer, A. 2021-09-25 doi:10.1101/2021.09.24.461743 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Glycerol-driven Denitratation: Process Kinetics, Microbial Ecology, and Operational Controls ]]> https://biorxiv.org/content/10.1101/2021.09.25.461789v1?rss=1 Baideme, M. Long, C. Plante, L. Starke, J. Butkus, M. Chandran, K. 2021-09-25 doi:10.1101/2021.09.25.461789 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ Flygenvectors: The spatial and temporal structure of neural activity across the fly brain ]]> https://biorxiv.org/content/10.1101/2021.09.25.461804v1?rss=1 Schaffer, E. S. Mishra, N. Whiteway, M. R. Li, W. Vancura, M. B. Freedman, J. Patel, K. B. Voleti, V. Paninski, L. Hillman, E. M. C. Abbott, L. Axel, R. 2021-09-26 doi:10.1101/2021.09.25.461804 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Compartment-specific tuning of hippocampal dendritic feature selectivity by intracellular Ca2+ release ]]> https://biorxiv.org/content/10.1101/2021.09.27.460811v1?rss=1 O'Hare, J. K. Hirabayashi, Y. Hewitt, V. L. Blockus, H. Szoboszlay, M. Rolotti, S. V. Geiller, T. C. Negrean, A. Chelur, V. Losonczy, A. Polleux, F. 2021-09-28 doi:10.1101/2021.09.27.460811 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Fragile X syndrome patient-derived neurons developing in the mouse brain show FMR1 -dependent phenotypes ]]> https://biorxiv.org/content/10.1101/2021.09.27.461739v1?rss=1 Krzisch, M. A. Wu, H. A. Yuan, B. Whitfield, T. W. Liu, X. S. Fu, D. Shih, J. Garrett-Engele, C. M. Chang, A. N. Warren, S. Cacace, A. Andrykovich, K. A. Rietjens, R. G. J. Jain, B. Wallace, O. Sur, M. Jaenisch, R. 2021-09-28 doi:10.1101/2021.09.27.461739 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Prospective isolation of mouse and human hematopoietic stem cells using Plexin domain containing 2 ]]> https://biorxiv.org/content/10.1101/2021.09.27.461900v1?rss=1 Tanaka, Y. Kubota, Y. Lieberam, I. Barlow, J. L. Bramley, J. W. Sakuma, C. Shibata, T. Nakagawa, M. Kurosawa, Y. Maruyama, T. Okumura, C. J. Akuta, T. Kent, D. G. Jessell, T. M. Goyama, S. Kimura, S. Kitamura, T. 2021-09-27 doi:10.1101/2021.09.27.461900 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ The activities of LRRK2 and GCase are positively correlated in clinical biospecimens and experimental models of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2021.09.27.461935v1?rss=1 Kedariti, M. Frattini, E. Baden, P. Cogo, S. Civiero, L. Ziviani, E. Aureli, M. Kaganovich, A. Cookson, M. R. Stefanis, L. R. Surface, M. Deleidi, M. Di Fonzo, A. Alcalay, R. N. Rideout, H. Greggio, E. Plotegher, N. 2021-09-28 doi:10.1101/2021.09.27.461935 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ Here's the twist: How the brain updates naturalistic event memories as our understanding of the past changes ]]> https://biorxiv.org/content/10.1101/2021.09.28.462068v1?rss=1 Zadbood, A. Nastase, S. A. Chen, J. Norman, K. A. Hasson, U. 2021-09-30 doi:10.1101/2021.09.28.462068 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Structures of core eukaryotic protein complexes ]]> https://biorxiv.org/content/10.1101/2021.09.30.462231v1?rss=1 Humphreys, I. R. Pei, J. Baek, M. Krishnakumar, A. Anishchenko, I. Ovchinnikov, S. R. Zheng, J. Ness, T. Banjade, S. Bagde, S. R. Stancheva, V. Li, X. Liu, K. Zheng, Z. Barerro, D. Roy, U. Fernandez, I. S. Szakal, B. Branzei, D. Greene, E. C. Biggins, S. Keeney, S. Miller, E. A. Fromme, J. C. Hendrickson, T. Cong, Q. Baker, D. 2021-09-30 doi:10.1101/2021.09.30.462231 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ A role for cell polarity in lifespan and mitochondrial quality control in the budding yeast Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2021.09.30.462607v1?rss=1 Yang, E. J. Pernice, W. M. Pon, L. A. 2021-09-30 doi:10.1101/2021.09.30.462607 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Powassan Viruses Spread Cell to Cell During Direct Isolation from IxodesTicks and Persistently Infect Human Brain Endothelial Cells and Pericytes ]]> https://biorxiv.org/content/10.1101/2021.09.30.462684v1?rss=1 Conde, J. N. Sanchez-Vicente, S. Saladino, N. Gorbunova, E. E. Schutt, W. R. Mladinich, M. C. Himmler, G. Benach, J. L. Kim, H. K. Mackow, E. R. 2021-10-02 doi:10.1101/2021.09.30.462684 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Distinct signatures of loss of consciousness during Focal Impaired Awareness (FIA) versus Focal to Bilateral Tonic-Clonic (FBTC) seizures ]]> https://biorxiv.org/content/10.1101/2021.10.01.462586v1?rss=1 Juan, E. Gorska, U. Kozma, C. Papantonatos, C. Bugnon, T. Denis, C. Kremen, V. Worrell, G. Struck, A. Bateman, L. Merricks, E. M. Blumenfeld, H. Tononi, G. Schevon, C. Boly, M. 2021-10-03 doi:10.1101/2021.10.01.462586 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Mechanically active integrins direct cytotoxic secretion at the immune synapse ]]> https://biorxiv.org/content/10.1101/2021.10.02.462778v1?rss=1 Wang, M. S. Hu, Y. Sanchez, E. Xie, X. Roy, N. H. De Jesus, M. Jin, W. Lee, J. H. Hong, Y. Kim, M. Kam, L. C. Salaita, K. Huse, M. 2021-10-03 doi:10.1101/2021.10.02.462778 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ Identification and validation of a non-genetically encoded vulnerability to XPO1 inhibition in malignant rhabdoid tumors - expanding patient-driven discovery beyond the Nof1. ]]> https://biorxiv.org/content/10.1101/2021.10.02.462793v1?rss=1 Marks, L. J. Diolaiti, D. Mundi, P. Gaviria, E. S. Rainey, A. R. Yamashiro, D. J. Fazlollahi, L. Hosoi, H. Katsumi, Y. Kuwahara, Y. Dela Cruz, F. S. Califano, A. Kung, A. L. 2021-10-02 doi:10.1101/2021.10.02.462793 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ An Information Theoretic Framework for Protein Activity Measurement ]]> https://biorxiv.org/content/10.1101/2021.10.02.462873v1?rss=1 Griffin, A. T. Vlahos, L. J. Chiuzan, C. Califano, A. 2021-10-02 doi:10.1101/2021.10.02.462873 Cold Spring Harbor Laboratory Press 2021-10-02 <![CDATA[ Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments ]]> https://biorxiv.org/content/10.1101/2021.10.03.462951v1?rss=1 Mundi, P. S. Dela Cruz, F. S. Grunn, A. Diolaiti, D. Mauguen, A. Siddiquee, A. You, D. Realubit, R. Karan, C. Ortiz, M. V. Accordino, M. Aloni, Z. Brogan, F. Bruce, J. Caescu, C. I. Carvajal, R. Crew, K. Decastro, G. Heaney, M. Henick, B. Hershman, D. Hou, J. Iwamoto, F. Jurcic, J. Kiran, P. R. Kluger, M. Kreisl, T. Lamanna, N. Lassman, A. Lim, E. Manji, G. McKhann, G. McKiernan, J. Neugut, A. Olive, K. Rosenblat, T. Schwartz, G. K. Shu, C. Sisti, M. Tergas, A. Vattakalam, R. Welch, M. Wenske, S. Wright, J. Hibshoosh, H. Kalinsky, K. Aburi, M. Sim 2021-10-03 doi:10.1101/2021.10.03.462951 Cold Spring Harbor Laboratory Press 2021-10-03 <![CDATA[ SARS-CoV-2 hijacks neutralizing dimeric IgA for enhanced nasal infection and injury ]]> https://biorxiv.org/content/10.1101/2021.10.05.463282v1?rss=1 Zhou, B. Zhou, R. Chan, J. F.-W. Zeng, J. Zhang, Q. Yuan, S. Liu, L. Robinot, R. Shan, S. Ge, J. Kwong, H. Y.-H. Zhou, D. Xu, H. Chan, C. C.-S. Poon, V. K.-M. Chu, H. Yue, M. Kwan, K.-Y. Chan, C.-Y. Liu, N. Chan, C. C.-Y. Chik, K. K.-H. Du, Z. Au, K.-K. Huang, H. Man, H.-O. Cao, J. Li, C. Wang, Z. Zhou, J. Song, Y. Yeung, M.-L. To, K. K.-W. Ho, D. D. Chakrabarti, L. A. Wang, X. Zhang, L. Yuen, K.-Y. Chen, Z. 2021-10-06 doi:10.1101/2021.10.05.463282 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Non-invasive Imaging of Sense of Smell by Tracking the Voltage-Gated Sodium Channel NaV1.7 ]]> https://biorxiv.org/content/10.1101/2021.10.07.463532v1?rss=1 Adilbay, D. Gonzales, J. Demetrio de Souza Franca, P. Roberts, S. Patel, S. Viray, T. Chow, C. Y. King, G. F. Jain, S. K. Ordonez, A. A. Caroll, L. S. Pillarsetty, N. Reiner, T. 2021-10-08 doi:10.1101/2021.10.07.463532 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Identification of a novel modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast ]]> https://biorxiv.org/content/10.1101/2021.10.07.463535v1?rss=1 Sing, C. N. Garcia, E. J. Lipkin, T. Huckaba, T. Tsang, C. A. Coughlin, A. Yang, E. J. Boldogh, I. R. Higuchi-Sanabria, R. Pon, L. 2021-10-07 doi:10.1101/2021.10.07.463535 Cold Spring Harbor Laboratory Press 2021-10-07 <![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[ A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression ]]> https://biorxiv.org/content/10.1101/2021.10.08.463652v1?rss=1 Culbertson, B. Garcia, K. Markett, D. Asgharian, H. Chen, L. Fish, L. Navickas, A. Yu, J. Woo, B. Nanda, S. Rabinowitz, J. Goodarzi, H. 2021-10-09 doi:10.1101/2021.10.08.463652 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ Probiotic-guided CAR-T cells for universal solid tumor targeting ]]> https://biorxiv.org/content/10.1101/2021.10.10.463366v1?rss=1 Vincent, R. L. Gurbatri, C. Redenti, A. Coker, C. Arpaia, N. Danino, T. 2021-10-11 doi:10.1101/2021.10.10.463366 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ CD47 cross-dressing by extracellular vesicles expressing CD47 inhibits phagocytosis without transmitting cell death signals ]]> https://biorxiv.org/content/10.1101/2021.10.11.463903v1?rss=1 Li, Y. Wu, Y. Federzoni, E. A. Wang, X. Dharmawan, A. Hu, X. Wang, H. Hawley, R. J. Stevens, S. Sykes, M. Yang, Y.-G. 2021-10-11 doi:10.1101/2021.10.11.463903 Cold Spring Harbor Laboratory Press 2021-10-11 <![CDATA[ Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae ]]> https://biorxiv.org/content/10.1101/2021.10.12.464153v1?rss=1 Wells, H. L. Loh, E. Nava, A. Lee, M. H. Lee, J. Sukor, J. R. A. Navarrete-Macias, I. Liang, E. Firth, C. Epstein, J. Rostal, M. Zambrana-Torrelio, C. Murray, K. A. Daszak, P. Goldstein, T. Mazet, J. A. K. Lee, B. Hughes, T. Durigon, E. L. Anthony, S. J. 2021-10-13 doi:10.1101/2021.10.12.464153 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.10.13.464307v1?rss=1 Wang, P. Casner, R. G. Nair, M. S. Yu, J. Guo, Y. Wang, M. Chan, J. F. W. Cerutti, G. Iketani, S. Liu, L. Sheng, Z. Chen, Z. Yuen, K.-Y. Kwong, P. D. Huang, Y. Shapiro, L. Ho, D. D. 2021-10-14 doi:10.1101/2021.10.13.464307 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Genotype-Phenotype Correlation of T Cell Subtypes Reveals Senescent and Cytotoxic Genes in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2021.10.19.464914v1?rss=1 Dressman, D. Buttrick, T. Cimpean, M. Bennett, D. Menon, V. Bradshaw, E. M. Vardarajan, B. Elyaman, W. 2021-10-23 doi:10.1101/2021.10.19.464914 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Novel graph theoretic biological pathway network analytics methods for analyzing and discovering Alzheimer's disease related genes ]]> https://biorxiv.org/content/10.1101/2021.10.19.465019v1?rss=1 Saha, S. Soliman, A. Rajasekaran, S. 2021-10-20 doi:10.1101/2021.10.19.465019 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Social mobility and biological aging among older adults in the United States ]]> https://biorxiv.org/content/10.1101/2021.10.19.465042v1?rss=1 Graf, G. H.-J. Zhang, Y. Domingue, B. W. Harris, K. M. Kothari, M. Kwon, D. Muennig, P. A. Belsky, D. W. 2021-10-23 doi:10.1101/2021.10.19.465042 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ Limited specificity of molecular interactions incurs an environment-dependent fitness cost in bacteria ]]> https://biorxiv.org/content/10.1101/2021.10.20.465141v1?rss=1 Igler, C. Fourcade, C. Waldminghaus, T. Pauler, F. Santhanam, B. Tkacik, G. Guet, C. C. 2021-10-20 doi:10.1101/2021.10.20.465141 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Abstract representations emerge naturally in neural networks trained to perform multiple tasks ]]> https://biorxiv.org/content/10.1101/2021.10.20.465187v1?rss=1 Johnston, W. J. Fusi, S. 2021-10-21 doi:10.1101/2021.10.20.465187 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ A positively Tuned Voltage Indicator Reveals Electrical Correlates of Calcium Activity in the Brain ]]> https://biorxiv.org/content/10.1101/2021.10.21.465345v1?rss=1 Evans, S. W. Shi, D. Chavarha, M. Plitt, M. H. Taxidis, J. Madruga, B. Van Keulen, S. C. Pang, M. Su, S. Hwang, F.-J. Zhang, G. Reese, A. Pradhan, L. Fan, J. L. Lee, S. Liu, Y. Suomivuori, C.-M. Jiang, D. Negrean, A. Wang, S. Ji, N. Clandinin, T. Dror, R. Bi, G. G. Makinson, C. D. Golshani, P. Giocomo, L. M. Losonczy, A. Ding, J. B. Lin, M. Z. 2021-10-23 doi:10.1101/2021.10.21.465345 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[ 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[ The post-transcriptional regulation of TFs in immature motoneurons shapes the axon-muscle connectome ]]> https://biorxiv.org/content/10.1101/2021.10.22.465474v1?rss=1 GUAN, W. Bellemin, S. Bouchet, M. Venkatasubramanian, L. Guillermin, C. Laurencon, A. Cherif, K. Darmas, A. Godin, C. Urdy, S. S. Mann, R. Enriquez, J. 2021-10-23 doi:10.1101/2021.10.22.465474 Cold Spring Harbor Laboratory Press 2021-10-23 <![CDATA[ ARP2/3- and resection-coupled genome reorganization facilitates translocations ]]> https://biorxiv.org/content/10.1101/2021.10.22.465487v1?rss=1 Zagelbaum, J. Schooley, A. Zhao, J. Schrank, B. R. Callen, E. Zha, S. Gottesman, M. Nussenzweig, A. Rabadan, R. Dekker, J. Gautier, J. 2021-10-24 doi:10.1101/2021.10.22.465487 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ E-Cannula reveals anatomical diversity in sharp-wave ripples as a driver for the recruitment of distinct hippocampal assemblies ]]> https://biorxiv.org/content/10.1101/2021.10.22.465514v1?rss=1 Liu, X. Terada, S. Kim, J. Lu, Y. Ramezani, M. Grosmark, A. D. Losonczy, A. Kuzum, D. 2021-10-24 doi:10.1101/2021.10.22.465514 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ A transcriptomic axis predicts state modulation of cortical interneurons ]]> https://biorxiv.org/content/10.1101/2021.10.24.465600v1?rss=1 Bugeon, S. Duffield, J. Dipoppa, M. Prankerd, I. Ritoux, A. Nicoloutsopoulos, D. Orme, D. Shinn, M. Peng, H. Forrest, H. Viduolyte, A. Bai Reddy, C. Isogai, Y. Carandini, M. Harris, K. D. 2021-10-24 doi:10.1101/2021.10.24.465600 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ The number of Follicle Stem Cells in a Drosophila ovariole. ]]> https://biorxiv.org/content/10.1101/2021.10.25.465475v1?rss=1 Kalderon, D. Melamed, D. Reilein, A. 2021-10-28 doi:10.1101/2021.10.25.465475 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Deep neural networks and visuo-semantic models explain complementary components of human ventral-stream representational dynamics ]]> https://biorxiv.org/content/10.1101/2021.10.25.465583v1?rss=1 Jozwik, K. M. Kietzmann, T. C. Cichy, R. M. Kriegeskorte, N. Mur, M. 2021-10-26 doi:10.1101/2021.10.25.465583 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Eicosanoids in the pancreatic tumor microenvironment: a multicellular, multifaceted progression ]]> https://biorxiv.org/content/10.1101/2021.10.27.466097v1?rss=1 Gubbala, V. B. Jyotsana, N. Trinh, V. Q. Maurer, H. C. Naeem, R. F. Lytle, N. K. Ma, Z. Zhao, S. Lin, W. Han, H. Shi, Y. Hunter, T. singh, P. K. Olive, K. P. Tan, M. C. B. Kaech, S. M. Wahl, G. DelGiorno, K. E. 2021-10-28 doi:10.1101/2021.10.27.466097 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Diverse operant control of different motor cortex populations during learning ]]> https://biorxiv.org/content/10.1101/2021.10.29.466535v1?rss=1 Vendrell-Llopis, N. Fang, C. Qu, A. J. Costa, R. M. Carmena, J. M. 2021-11-02 doi:10.1101/2021.10.29.466535 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ A neural substrate for Bayesian integration in human parietal cortex ]]> https://biorxiv.org/content/10.1101/2021.10.30.466508v1?rss=1 Singletary, N. M. Gottlieb, J. Horga, G. 2021-10-31 doi:10.1101/2021.10.30.466508 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Temporal Pattern of Synaptic Activation Determines the Longevity of Structural Plasticity at Single Dendritic Spines ]]> https://biorxiv.org/content/10.1101/2021.10.31.466684v1?rss=1 Argunsah, A. O. Israely, I. 2021-11-03 doi:10.1101/2021.10.31.466684 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition ]]> https://biorxiv.org/content/10.1101/2021.11.01.466615v1?rss=1 Karthaus, W. Chan, J. Setty, M. Love, J. Zaidi, S. Choo, Z.-N. Persad, S. LaClair, J. Lawrence, K. Chaudhary, O. Xu, T. Masilionis, I. Mazutis, L. Chaligne, R. Pe'er, D. Sawyers, C. 2021-11-01 doi:10.1101/2021.11.01.466615 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Defining the architecture of cerebrospinal fluid cellular communities in neuroinflammatory diseases ]]> https://biorxiv.org/content/10.1101/2021.11.01.466797v1?rss=1 Roostaei, T. Diaconu, C. Touil, H. Harbison, C. Zhang, Y. Epstein, S. Tuddenham, J. Bryois, J. Wiendl, H. Meyer zu Hörste, G. Malhotra, D. Riley, C. Menon, V. De Jager, P. L. 2021-11-05 doi:10.1101/2021.11.01.466797 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Proteomic and single-cell transcriptomic dissection of human plasmacytoid dendritic cell response to influenza virus ]]> https://biorxiv.org/content/10.1101/2021.11.01.466839v1?rss=1 Ghanem, M. H. Shih, A. J. Khalili, H. Werth, E. Chakrabarty, J. K. Brown, L. M. Simpfendorfer, K. R. Gregersen, P. K. 2021-11-04 doi:10.1101/2021.11.01.466839 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ A gradient of electrophysiological novelty responses along the human hippocampal long axis. ]]> https://biorxiv.org/content/10.1101/2021.11.02.466832v1?rss=1 Yebra, M. Jensen, O. Kunz, L. Moratti, S. Axmacher, N. Strange, B. A. 2021-11-03 doi:10.1101/2021.11.02.466832 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Dynamic Flux Balance Analysis Game ]]> https://biorxiv.org/content/10.1101/2021.11.02.466952v1?rss=1 Iyengar, G. Perry, M. 2021-11-04 doi:10.1101/2021.11.02.466952 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Fine-mapping from summary data with the "Sum of Single Effects" model ]]> https://biorxiv.org/content/10.1101/2021.11.03.467167v1?rss=1 Zou, Y. Carbonetto, P. Wang, G. Stephens, M. 2021-11-04 doi:10.1101/2021.11.03.467167 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Comparisons of ribonuclease HI homologs and mutants uncover a multi-state model for substrate recognition ]]> https://biorxiv.org/content/10.1101/2021.11.04.467286v1?rss=1 Martin, J. A. Palmer, A. G. 2021-11-04 doi:10.1101/2021.11.04.467286 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[ Distinct profiles of LRRK2 activation and Rab GTPase phosphorylation in clinical samples from different PD cohorts ]]> https://biorxiv.org/content/10.1101/2021.11.05.465894v1?rss=1 Peptropoulou-Vathi, L. Simitsi, A. M. Valkimadi, P.-E. Kedariti, M. Dimitrakopoulos, L. Koros, C. Papadimitriou, D. Papadimitriou, A. Stefanis, L. Alcalay, R. N. Rideout, H. J. 2021-11-05 doi:10.1101/2021.11.05.465894 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Three-dimensional spike localization and improved motion correction for Neuropixels recordings ]]> https://biorxiv.org/content/10.1101/2021.11.05.467503v1?rss=1 Boussard, J. Varol, E. Lee, H. D. Dethe, N. Paninski, L. 2021-11-08 doi:10.1101/2021.11.05.467503 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Mushroom body input connections form independently of sensory activity in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.11.06.467552v1?rss=1 Hayashi, T. MacKenzie, A. J. Ganguly, I. Smihula, H. Jacob, M. S. Litwin-Kumar, A. Caron, S. J. C. 2021-11-07 doi:10.1101/2021.11.06.467552 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ Cohort Profile: Genetic data in the German Socio-Economic Panel Innovation Sample (Gene-SOEP) ]]> https://biorxiv.org/content/10.1101/2021.11.06.467573v1?rss=1 Koellinger, P. D. Okbay, A. Kweon, H. Schweinert, A. Karlsson Linner, R. Goebel, J. Richter, D. Reiber, L. Zweck, B. M. Belsky, D. Biroli, P. Mata, R. Tucker-Drob, E. M. Harden, K. P. Wagner, G. Hertwig, R. 2021-11-10 doi:10.1101/2021.11.06.467573 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Optogenetic dissection of the roles of actomyosin in the mechanics underlying tissue fluidity ]]> https://biorxiv.org/content/10.1101/2021.11.07.467642v1?rss=1 Herrera-Perez, R. M. Cupo, C. Allan, C. Dagle, A. B. Kasza, K. E. 2021-11-08 doi:10.1101/2021.11.07.467642 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Identifying Causal Subsequent Memory Effects ]]> https://biorxiv.org/content/10.1101/2021.11.08.467782v1?rss=1 Halpern, D. J. Tubridy, S. Davachi, L. Gureckis, T. M. 2021-11-10 doi:10.1101/2021.11.08.467782 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Individual differences in frontoparietal plasticity in humans ]]> https://biorxiv.org/content/10.1101/2021.11.08.467831v1?rss=1 Boroshok, A. L. Park, A. T. Fotiadis, P. Velasquez, G. H. Tooley, U. A. Simon, K. R. Forde, J. C. P. Delgado Reyes, L. M. Tisdall, M. D. Bassett, D. S. Cooper, E. A. Mackey, A. P. 2021-11-10 doi:10.1101/2021.11.08.467831 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Effects of tendon viscoelasticity in the distribution of forces over sutures in a model tendon-to-bone repair ]]> https://biorxiv.org/content/10.1101/2021.11.09.467963v1?rss=1 Huang, Y. hoppe, e. Kurtaliaj, I. Birman, V. Thomopoulos, S. Genin, G. M. 2021-11-11 doi:10.1101/2021.11.09.467963 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Similarities Between Somatosensory Cortical Responses Induced via Natural Touch and Microstimulation in the Ventral Posterior Lateral Thalamus in Macaques ]]> https://biorxiv.org/content/10.1101/2021.11.10.468076v1?rss=1 Francis, J. T. Rozenboym, A. von Kraus, L. Xu, S. Chhatbar, P. Semework, M. Hawley, E. Chapin, J. K. 2021-11-11 doi:10.1101/2021.11.10.468076 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Learning enhances behaviorally relevant representations in apical dendrites ]]> https://biorxiv.org/content/10.1101/2021.11.10.468144v1?rss=1 Benezra, S. E. Patel, K. B. Perez Campos, C. Hillman, E. M. C. Bruno, R. M. 2021-11-11 doi:10.1101/2021.11.10.468144 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice ]]> https://biorxiv.org/content/10.1101/2021.11.11.465186v1?rss=1 Wang, Y. Shiladardi, K. Hsu, T. Odinammadu, K. O. Maruyama, T. Wu, W. Lin, C.-S. Damoci, C. B. Spear, E. D. Shin, J.-Y. Hsu, W. Michaelis, S. Worman, H. J. 2021-11-12 doi:10.1101/2021.11.11.465186 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Inhibition of Interactions Between NDPK-B and NDPK-C in Presence of Graphene Oxide ]]> https://biorxiv.org/content/10.1101/2021.11.12.465807v1?rss=1 Zaznaev, A. Macwan, I. 2021-11-13 doi:10.1101/2021.11.12.465807 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ 'Constituent length' effects in fMRI do not provide evidence for abstract syntactic processing ]]> https://biorxiv.org/content/10.1101/2021.11.12.467812v1?rss=1 Shain, C. Kean, H. Lipkin, B. Affourtit, J. Siegelman, M. Mollica, F. Fedorenko, E. 2021-11-13 doi:10.1101/2021.11.12.467812 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Structural brain connectivity predicts acute pain after mild traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2021.11.12.468345v1?rss=1 Branco, P. Bosak, N. Bielefeld, J. Cong, O. Granovsky, Y. Kahn, I. Yarnitsky, D. Apkarian, A. V. 2021-11-13 doi:10.1101/2021.11.12.468345 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[ Insightful inference compensates for distorted perception ]]> https://biorxiv.org/content/10.1101/2021.11.13.468497v1?rss=1 Mihali, A. L. Broeker, M. D. Horga, G. 2021-11-15 doi:10.1101/2021.11.13.468497 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Predicting human decision making in psychological tasks with recurrent neural networks ]]> https://biorxiv.org/content/10.1101/2021.11.15.468588v1?rss=1 Lin, B. Bouneffouf, D. Cecchi, G. 2021-11-16 doi:10.1101/2021.11.15.468588 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Complementary population codes in the dorsal and ventral hippocampus during associative learning ]]> https://biorxiv.org/content/10.1101/2021.11.16.468862v1?rss=1 Biane, J. S. Ladow, M. A. Stefanini, F. Boddu, S. P. Fan, A. Hassan, S. Dundar, N. Apodaca-Montano, D. L. Woods, N. I. Khierbek, M. A. 2021-11-18 doi:10.1101/2021.11.16.468862 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Mapping morphological malformation to genetic dysfunction in blood vessel organoids with 22q11.2 Deletion Syndrome ]]> https://biorxiv.org/content/10.1101/2021.11.17.468969v1?rss=1 He, S. Xu, C. Lao, Y.-H. Chauhan, S. Xiao, Y. Willner, M. J. Jin, Y. McElroy, S. Rao, S. Gogos, J. Tomer, R. Azizi, E. Xu, B. Leong, K. W. 2021-11-19 doi:10.1101/2021.11.17.468969 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Robust Identification of Temporal Biomarkers in Longitudinal Omics Studies ]]> https://biorxiv.org/content/10.1101/2021.11.19.469350v1?rss=1 Metwally, A. A. Zhang, T. Wu, S. Kellogg, R. Zhou, W. Tang, H. Snyder, M. 2021-11-20 doi:10.1101/2021.11.19.469350 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data ]]> https://biorxiv.org/content/10.1101/2021.11.20.469390v1?rss=1 De Falco, A. Caruso, F. P. Su, X. D. Iavarone, A. Ceccarelli, M. 2021-11-22 doi:10.1101/2021.11.20.469390 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Crosstalk between guanosine nucleotides regulates cellular heterogeneity in protein synthesis during nutrient limitation ]]> https://biorxiv.org/content/10.1101/2021.11.22.469502v1?rss=1 Diez, S. Hydorn, M. Whalen, A. Dworkin, J. 2021-11-22 doi:10.1101/2021.11.22.469502 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Parent-offspring inference in highly inbred populations ]]> https://biorxiv.org/content/10.1101/2021.11.23.469656v1?rss=1 Runge, J.-N. König, B. Lindholm, A. K. Bendesky, A. 2021-11-23 doi:10.1101/2021.11.23.469656 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Quasi-universal scaling in mouse-brain neuronal activity stems from edge-of-instability critical dynamics ]]> https://biorxiv.org/content/10.1101/2021.11.23.469734v1?rss=1 B. Morales, G. Di Santo, S. Munoz, M. A. 2021-11-23 doi:10.1101/2021.11.23.469734 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Neuronal activity in the human amygdala and hippocampus enhances emotional memory encoding ]]> https://biorxiv.org/content/10.1101/2021.11.28.470278v1?rss=1 Qasim, S. E. Mohan, U. R. Stein, J. M. Jacobs, J. 2021-11-29 doi:10.1101/2021.11.28.470278 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ The Importance of Mentors and How to Handle More Than One Mentor ]]> https://biorxiv.org/content/10.1101/2021.11.29.469764v1?rss=1 Marshall, A. G. Brady, L. Palavicino-Maggio, C. Neikirk, K. Vue, Z. Beasley, H. Garza Lopez, E. Murray, S. Martinez, D. Shuler, H. Spencer, E. Morton, D. Hinton, A. 2021-12-01 doi:10.1101/2021.11.29.469764 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Using a Champion-Oriented Mindset to Overcome the Challenges of Graduate School ]]> https://biorxiv.org/content/10.1101/2021.11.29.469904v1?rss=1 Marshall, A. Palavicino-Maggio, C. Neikirk, K. Vue, Z. Beasley, H. Lopez, E. G. Murray, S. A. Martinez, D. Davis, J. Shuler, H. Spencer, E. Morton, D. Hinton, A. 2021-12-01 doi:10.1101/2021.11.29.469904 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ Epistasis is not a strong constraint on the recurrent evolution of toxin-resistant Na+,K+-ATPases among tetrapods ]]> https://biorxiv.org/content/10.1101/2021.11.29.470343v1?rss=1 Mohammadi, S. Yang, L. Herrera-Alvarez, S. Rodriguez-Ordonez, M. d. P. Zhang, K. Storz, J. Crawford, A. J. Andolfatto, P. 2021-11-29 doi:10.1101/2021.11.29.470343 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ 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[ Adolescent rats extend help to outgroup members, highlighting a neural network for group identity categorization. ]]> https://biorxiv.org/content/10.1101/2021.11.29.470434v1?rss=1 Breton, J. Eisner, J. S. Gandhi, V. S. Musick, N. Zhang, A. Long, K. L. P. Perloff, O. S. Hu, K. Y. Pham, C. M. Lalchandani, P. Barraza, M. K. Kantor, B. Kaufer, D. Ben-Ami Bartal, I. 2021-12-01 doi:10.1101/2021.11.29.470434 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ RNA-guided cell targeting with CRISPR/RfxCas13d collateral activity in human cells ]]> https://biorxiv.org/content/10.1101/2021.11.30.470032v1?rss=1 Shi, P. Murphy, M. R. Aparicio, A. O. Kesner, J. S. Fang, Z. Chen, Z. Trehan, A. Wu, X. 2021-11-30 doi:10.1101/2021.11.30.470032 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ The enteric nervous system of C. elegans is specified by the Sine Oculis-like homeobox gene ceh-34 ]]> https://biorxiv.org/content/10.1101/2021.11.30.470650v1?rss=1 Vidal, B. Gulez, B. Cao, W. X. Diaz, E. L. Tekieli, T. Hobert, O. 2021-12-01 doi:10.1101/2021.11.30.470650 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[ Role of oxidation of excitation-contraction coupling machinery in age-dependent loss of muscle function in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.12.05.471286v1?rss=1 dridi, H. Forrester, F. Umanskaya, A. Xie, W. Reiken, S. Lacampagne, A. Marks, A. R. 2021-12-06 doi:10.1101/2021.12.05.471286 Cold Spring Harbor Laboratory Press 2021-12-06 <![CDATA[ Imaging-Guided Bioreactor for De-Epithelialization and Long-Term Cultivation of Ex Vivo Rat Trachea ]]> https://biorxiv.org/content/10.1101/2021.12.06.470803v1?rss=1 Mir, S. M. Chen, J. Pinezich, M. O'Neill, J. Huang, S. Vunjak-Novakovic, G. Kim, J. 2021-12-07 doi:10.1101/2021.12.06.470803 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies ]]> https://biorxiv.org/content/10.1101/2021.12.06.471440v1?rss=1 He, Z. Liu, L. Belloy, M. E. Le Guen, Y. Sossin, A. Liu, X. Qi, X. Ma, S. Wyss-Coray, T. Tang, H. Sabatti, C. Candes, E. Greicius, M. D. Ionita-Laza, I. 2021-12-07 doi:10.1101/2021.12.06.471440 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ An effective workshop on How to be an Effective Mentor for Underrepresented STEM Trainees ]]> https://biorxiv.org/content/10.1101/2021.12.06.471498v1?rss=1 Marshall, A. Vue, Z. Palavicino-Maggio, C. Spencer, E. C. Beasley, H. K. Garza Lopez, E. Conley, Z. Neikirk, K. Murray, S. A. Martinez, D. Davis, J. Brady, L. Shuler, H. D. Morton, D. Hinton, A. 2021-12-08 doi:10.1101/2021.12.06.471498 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ]]> https://biorxiv.org/content/10.1101/2021.12.07.470215v1?rss=1 Ramdas, S. Judd, J. Graham, S. E. Kanoni, S. Wang, Y. Surakka, I. Wenz, B. Clarke, S. L. Chesi, A. Wells, A. Bhatti, K. F. Vedantam, S. Winkler, T. W. Locke, A. E. Marouli, E. Zajac, G. J. Wu, K.-H. H. Ntalla, I. Hui, Q. Klarin, D. Hilliard, A. T. Wang, Z. Xue, C. Thorleifsson, G. Helgadottir, A. Gudbjartsson, D. F. Holm, H. Olafsson, I. Hwang, M. Y. Han, S. Akiyama, M. Sakaue, S. Terao, C. Kanai, M. Zhou, W. Brumpton, B. M. Rasheed, H. Havulinna, A. S. Veturi, Y. Pacheco, J. A. Rosenthal, E. A. Lingren, T. Feng, Q. Kullo, I. J. Narita, A. Takayama, 2021-12-08 doi:10.1101/2021.12.07.470215 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Chemical induction of gut β-like-cells by combined FoxO1/Notch inhibition as a glucose-lowering treatment for diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.07.471572v1?rss=1 Kitamoto, T. Lee, Y.-K. McKimpson, W. M. Watanabe, H. Sultana, N. Du, W. Fan, J. Diaz, B. Lin, H. V. Leibel, R. L. Belvedere, S. Accili, D. 2021-12-07 doi:10.1101/2021.12.07.471572 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ The Spatial Reach of Neuronal Coherence and Spike-field Coupling across the Human Neocortex ]]> https://biorxiv.org/content/10.1101/2021.12.07.471617v1?rss=1 LFP > SFC). The spectral frequency of coherence also affected its magnitude. Alpha coherence (8-14 Hz) was generally higher than other frequencies for signals nearest the microelectrode arrays, whereas delta coherence (1-3 Hz) was higher for signals that were farther away. Action potentials in all brain regions were most coherent with the phase of alpha oscillations, which suggests that alpha waves could play a larger, more spatially local role in spike timing than other frequencies. These findings provide a deeper understanding of the spatial and spectral dynamics of neuronal coherence, further advancing knowledge about how activity propagates across the human brain. ]]> Myers, J. Smith, E. H. Leszczynski, M. O'Sullivan, J. McKhann, G. M. Mesgarani, N. Schroeder, C. Schevon, C. Sheth, S. 2021-12-09 doi:10.1101/2021.12.07.471617 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Intermittent brain network reconfigurations and the resistance to social media influence ]]> https://biorxiv.org/content/10.1101/2021.12.07.471625v1?rss=1 Lima Dias Pinto, I. I. Rungratsameetaweemana, N. Flaherty, K. Periyannan, A. Meghdadi, A. Richard, C. Berka, C. Bansal, K. Omar Garcia, J. 2021-12-09 doi:10.1101/2021.12.07.471625 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Reconfigurations in brain networks upon awakening from slow wave sleep: Interventions and implications in neural communication ]]> https://biorxiv.org/content/10.1101/2021.12.07.471633v1?rss=1 Hilditch, C. J. Bansal, K. Chachad, R. Wong, L. R. Bathurst, N. G. Feick, N. H. Santamaria, A. Shattuck, N. L. Garcia, J. O. Flynn-Evans, E. E. 2021-12-09 doi:10.1101/2021.12.07.471633 Cold Spring Harbor Laboratory Press 2021-12-09 <![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[ Neural Oscillatory Characteristics of Feedback Associated Activity in Globus Pallidus Interna ]]> https://biorxiv.org/content/10.1101/2021.12.07.471662v1?rss=1 Choubdar, H. Mahdavi, M. Rostami, Z. Zabeh, E. Gillies, M. J. Green, A. L. Aziz, T. Lashgari, R. 2021-12-09 doi:10.1101/2021.12.07.471662 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ The Role of Mentoring in Promoting Diversity, Equity, and Inclusion in STEM Education and Research ]]> https://biorxiv.org/content/10.1101/2021.12.08.471502v1?rss=1 Marshall, A. Vue, Z. Palavicino-maggio, C. Spencer, E. C. Beasley, H. K. Garza- Lopez, E. Conley, Z. Neikirk, K. Murray, S. A. Martinez, D. Davis, J. Brady, L. J. Shuler, H. D. Morton, D. Hinton, A. 2021-12-09 doi:10.1101/2021.12.08.471502 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ The Gulf Coast tick, Amblyomma maculatum (Ixodida: Ixodidae) and spotted fever group Rickettsia in the highly urbanized northeastern US ]]> https://biorxiv.org/content/10.1101/2021.12.08.471803v1?rss=1 Bajwa, W. I. Tsynman, L. Egizi, A. M. Tokarz, R. Maestas, L. P. Fonseca, D. M. 2021-12-10 doi:10.1101/2021.12.08.471803 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Dopamine D2Rs Coordinate Cue-Evoked Changes in Striatal Acetylcholine Levels ]]> https://biorxiv.org/content/10.1101/2021.12.08.471871v1?rss=1 Kellendonk, C. Martyniuk, K. M. Torres-Herraez, A. Rubinstein, M. Labouesse, M. A. 2021-12-11 doi:10.1101/2021.12.08.471871 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Robust regulatory architecture of pan-neuronal gene expression ]]> https://biorxiv.org/content/10.1101/2021.12.10.472091v1?rss=1 Leyva-Diaz, E. Hobert, O. 2021-12-11 doi:10.1101/2021.12.10.472091 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Molecular architecture of 40S initiation complexes on the Hepatitis C virus IRES: from ribosomal attachment to eIF5B-mediated reorientation of initiator tRNA ]]> https://biorxiv.org/content/10.1101/2021.12.10.472117v1?rss=1 Brown, Z. P. Abaeva, I. S. De, S. Hellen, C. U. T. Pestova, T. V. Frank, J. 2021-12-11 doi:10.1101/2021.12.10.472117 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Mouse models of NADK2 deficiency analyzed for metabolic and gene expression changes to elucidate pathophysiology ]]> https://biorxiv.org/content/10.1101/2021.12.10.472125v1?rss=1 Murray, G. Bais, P. Hatton, C. Tadenev, A. Morelli, K. Schroder, D. Doty, R. Fiehn, O. John, S. Bult, C. Cox, G. Burgess, R. 2021-12-11 doi:10.1101/2021.12.10.472125 Cold Spring Harbor Laboratory Press 2021-12-11 <![CDATA[ Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.12.11.472236v1?rss=1 Liu, L. Iketani, S. Guo, Y. Casner, R. Reddem, E. Nair, M. S. Yu, J. Chan, J. Wang, M. Cerutti, G. Li, Z. Castagna, C. Corredor, L. Chu, H. Yuan, S. Poon, V. Chan, C. Chen, Z. Luo, Y. Cunningham, M. Chavez, A. Yin, M. Perlin, D. Tsuji, M. Yuen, K.-Y. Kwong, P. Sheng, Z. Huang, Y. Shapiro, L. Ho, D. D. 2021-12-14 doi:10.1101/2021.12.11.472236 Cold Spring Harbor Laboratory Press 2021-12-14 <![CDATA[ A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A ]]> https://biorxiv.org/content/10.1101/2021.12.13.472381v1?rss=1 Gorbunova, V. Simon, M. Trombline, G. Yang, J. Earley, E. J. Zhang, L. Gigas, J. Zagorulya, M. Gilbert, M. Robbins, P. D. Vijg, J. Seluanov, A. Suh, Y. Garcia, B. Thomas, D. D. Yuen, S. L. Pope, A. Van Meter, M. Emmrich, S. Moody, K. Barzilai, N. Wolfe, A. Atzmon, G. Schaff, T. M. 2021-12-13 doi:10.1101/2021.12.13.472381 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Leukocyte cytokine responses in adult patients with mitochondrial DNA defects ]]> https://biorxiv.org/content/10.1101/2021.12.13.472449v1?rss=1 G mutation or single, large-scale mtDNA deletions, we examined: i) cytokine responses (IL-6, TNF-, IL-1{beta}) in response to acute lipopolysaccharide (LPS) exposure, and ii) sensitivity to the immunosuppressive effects of glucocorticoid signaling (dexamethasone) on cytokine production. In dose-response experiments to determine the half-maximal effective LPS concentration (EC50), relative to controls, leukocytes from patients with mtDNA deletions showed 74 - 79% lower responses for IL-6 and IL-1{beta} (pIL-6=0.031, pIL-1{beta}=0.009). Moreover, IL-6 response to LPS in presence of GC was also blunted in cells from patients with mtDNA deletions (pIL-6=0.006), but not in leukocytes from patients with the m.3243A>G mutation. Overall, these ex vivo data provide preliminary evidence that some systemic OxPhos defects may compromise immune cytokine responses and glucocorticoid sensitivity. Further work in larger cohorts is needed to define the nature of immune dysregulation in patients with mitochondrial disease, and their potential implications for disease phenotypes. ]]> Karan, K. R. Trumpff, C. Cross, M. Englestad, K. M. Marsland, A. L. McGuire, P. Hirano, M. Picard, M. 2021-12-16 doi:10.1101/2021.12.13.472449 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Genuine Selective Caspase-2 Inhibition with new Irreversible Small Peptidomimetics ]]> https://biorxiv.org/content/10.1101/2021.12.13.472505v1?rss=1 Bosc, E. Anastasie, J. Soualmia, F. Coric, P. Kim, J. Y. Lacin, G. Duplus, E. Tixador, P. Brugg, b. Reboud-Ravaux, M. Bouaziz, S. Karin, M. El Amri, C. Jacotot, E. D. 2021-12-15 doi:10.1101/2021.12.13.472505 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Neural Readout of a Latency Code in the Active Electrosensory System ]]> https://biorxiv.org/content/10.1101/2021.12.14.472594v1?rss=1 Sawtell, N. B. Perks, K. 2021-12-16 doi:10.1101/2021.12.14.472594 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity, and Sleep under Entrainment ]]> https://biorxiv.org/content/10.1101/2021.12.14.472617v1?rss=1 Persons, J. Abhilash, L. Lopatkin, A. J. Roelofs, A. Bell, E. V. Fernandez, M. d. l. P. Shafer, O. T. 2021-12-16 doi:10.1101/2021.12.14.472617 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Preterm birth alters the maturation of the GABAergic system in the human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.12.14.472624v1?rss=1 Lacaille, H. Vacher, C.-M. Penn, A. A. 2021-12-15 doi:10.1101/2021.12.14.472624 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Wavelength-dependent DNA photodamage in a 3-D human skin model over the far-UVC and germicidal-UVC wavelength ranges from 215 to 255 nm ]]> https://biorxiv.org/content/10.1101/2021.12.14.472653v1?rss=1 Welch, D. Aquino de Muro, M. Buonanno, M. Brenner, D. J. 2021-12-16 doi:10.1101/2021.12.14.472653 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.12.14.472719v1?rss=1 Liu, L. Iketani, S. Guo, Y. Chan, J. F.-W. Wang, M. Liu, L. Luo, Y. Chu, H. Huang, Y. Nair, M. S. Yu, J. Chik, K. K.-H. Yuen, T. T.-T. Yoon, C. To, K. K.-W. Chen, H. Yin, M. T. Sobieszczyk, M. E. Huang, Y. Wang, H. H. Sheng, Z. Yuen, K.-Y. Ho, D. D. 2021-12-15 doi:10.1101/2021.12.14.472719 Cold Spring Harbor Laboratory Press 2021-12-15 <![CDATA[ Spontaneous Neuronal Oscillations in the Human Insula are Hierarchically Organized Traveling Waves ]]> https://biorxiv.org/content/10.1101/2021.12.16.473034v1?rss=1 Das, A. Myers, J. Mathura, R. Shofty, B. Metzger, B. A. Bijanki, K. Wu, C. Jacobs, J. Sheth, S. A. 2021-12-19 doi:10.1101/2021.12.16.473034 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement ]]> https://biorxiv.org/content/10.1101/2021.12.17.473193v1?rss=1 Mitelut, C. Zhang, Y. Sekino, Y. Boyd, J. Bolanos, F. Swindale, N. V. Silasi, G. Saxena, S. Murphy, T. H. 2021-12-20 doi:10.1101/2021.12.17.473193 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders ]]> https://biorxiv.org/content/10.1101/2021.12.17.473207v1?rss=1 Baker, B. H. Zhang, S. Simon, J. M. McLarnan, S. M. Chung, W. K. Pearson, B. L. 2021-12-20 doi:10.1101/2021.12.17.473207 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Music-selective cortex is sensitive to structure in both pitch and time ]]> https://biorxiv.org/content/10.1101/2021.12.17.473232v1?rss=1 Boebinger, D. L. Norman-Haignere, S. V. McDermott, J. H. Kanwisher, N. G. 2021-12-19 doi:10.1101/2021.12.17.473232 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Platr4 is an ESC-specific lncRNA that exhibits its function downstream on meso/endoderm lineage commitment ]]> https://biorxiv.org/content/10.1101/2021.12.20.473435v1?rss=1 Hazra, R. Brine, L. Garcia, L. Benz, B. Chirathivat, N. Shen, M. M. Wilkinson, J. E. Lyons, S. Spector, D. L. 2021-12-21 doi:10.1101/2021.12.20.473435 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Neonatal enthesis healing involves non-inflammatory formation of acellular scar through ECM secretion by resident cells ]]> https://biorxiv.org/content/10.1101/2021.12.20.473454v1?rss=1 Vinestock, R. C. Felsenthal, N. Assaraf, E. Katz, E. Rubin, S. Heinemann-Yerushalmi, L. Krief, S. Dezorella, N. Levin-Zaidman, S. Tsoory, M. Thomopoulos, S. Zelzer, E. 2021-12-20 doi:10.1101/2021.12.20.473454 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Insight into the mechanism of H+-coupled nucleobase transport ]]> https://biorxiv.org/content/10.1101/2021.12.20.473561v1?rss=1 Weng, J. Zhou, X. Wiriyasermkul, P. Ren, Z. Yan, X. Chen, K. Iturbe, E. G. Zhou, M. Quick, M. 2021-12-21 doi:10.1101/2021.12.20.473561 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Structural basis for antibody resistance to SARS-CoV-2 omicron variant ]]> https://biorxiv.org/content/10.1101/2021.12.21.473620v1?rss=1 Cerutti, G. Guo, Y. Lihong, L. Zhang, Z. Liu, L. Luo, Y. Huang, Y. Wang, H. H. Ho, D. D. Sheng, Z. Shapiro, L. 2021-12-23 doi:10.1101/2021.12.21.473620 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Super-resolution vibrational imaging using expansion stimulated Raman scattering microscopy ]]> https://biorxiv.org/content/10.1101/2021.12.22.473713v1?rss=1 Shi, L. Klimas, A. Gallagher, B. Cheng, Z. Fu, F. Wijesekara, P. Miao, Y. Ren, X. Zhao, Y. Min, W. 2021-12-23 doi:10.1101/2021.12.22.473713 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Learning enhances encoding of time and temporal surprise in primary sensory cortex ]]> https://biorxiv.org/content/10.1101/2021.12.23.474000v1?rss=1 Rabinovich, R. J. Kato, D. D. Bruno, R. M. 2021-12-23 doi:10.1101/2021.12.23.474000 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency ]]> https://biorxiv.org/content/10.1101/2021.12.24.474136v1?rss=1 Li, D. Yang, J. Huang, X. Zhou, H. Wang, J. 2021-12-25 doi:10.1101/2021.12.24.474136 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ A Multimodal Approach to Investigate the Neural Mechanisms of Real World Social Vision ]]> https://biorxiv.org/content/10.1101/2021.12.26.474173v1?rss=1 Alreja, A. Ward, M. J. Ma, Q. Richardson, M. Russ, B. Bickel, S. Van Wouwe, N. Gonzalez-Martinez, J. A. Parker, L. S. Neimat, J. Schroeder, C. Morency, L.-P. Ghuman, A. S. 2021-12-28 doi:10.1101/2021.12.26.474173 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Functional properties of the spike glycoprotein of the emerging SARS-CoV-2 variant B.1.1.529 ]]> https://biorxiv.org/content/10.1101/2021.12.27.474288v1?rss=1 Wang, Q. Anang, S. Iketani, S. Guo, Y. Liu, L. Ho, D. D. Sodroski, J. G. 2021-12-29 doi:10.1101/2021.12.27.474288 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ The Functional Logic of Odor Information Processing in the Drosophila Antennal Lobe ]]> https://biorxiv.org/content/10.1101/2021.12.27.474306v1?rss=1 Lazar, A. A. Liu, T. Yeh, C.-H. 2021-12-28 doi:10.1101/2021.12.27.474306 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ A Programmable Ontology Encompassing the Functional Logic of the Drosophila Brain ]]> https://biorxiv.org/content/10.1101/2021.12.28.474399v1?rss=1 Lazar, A. A. Turkcan, M. K. Zhou, Y. 2021-12-29 doi:10.1101/2021.12.28.474399 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Natural history of nonhuman primates after conjunctival exposure to Ebola virus ]]> https://biorxiv.org/content/10.1101/2021.12.29.474476v1?rss=1 Cross, R. W. Prasad, A. N. Woolsey, C. Agans, K. N. Borisevich, V. Dobias, N. S. Comer, J. E. Deer, D. J. Geisbert, J. B. Rasmussen, A. Lipkin, W. I. Fenton, K. A. Geisbert, T. W. 2021-12-30 doi:10.1101/2021.12.29.474476 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ V1 receptive field structure contributes to neuronal response latency ]]> https://biorxiv.org/content/10.1101/2021.12.30.474591v1?rss=1 Vafaei, A. Mohammadi, M. Khadir, A. Zabeh, E. YazdaniBanafsheDaragh, F. Khorasani, M. Lashgari, R. 2022-01-01 doi:10.1101/2021.12.30.474591 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling ]]> https://biorxiv.org/content/10.1101/2022.01.04.474945v1?rss=1 Jobin, M.-L. De Smedt-Peyrusse, V. Ducrocq, F. Oummadi, A. Baccouch, R. Hauge Pedersen, M. Medel Lacruz, B. Van-Delft, P. Fouillen, L. Mongrand, S. Selent, J. Tolentino-Cortez, T. Barreda-Gomez, G. Gregoire, S. Masson, E. Durroux, T. Javitch, J. A. Guixa-Gonzalez, R. Alves, I. Trifilieff, P. 2022-01-04 doi:10.1101/2022.01.04.474945 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras ]]> https://biorxiv.org/content/10.1101/2022.01.06.475190v1?rss=1 Hidalgo, F. Nocka, L. M. Shah, N. H. Gorday, K. Latorraca, N. R. Bandaru, P. Templeton, S. Lee, D. Karandur, D. Pelton, J. G. Marqusee, S. Wemmer, D. Kuriyan, J. 2022-01-06 doi:10.1101/2022.01.06.475190 Cold Spring Harbor Laboratory Press 2022-01-06 <![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[ Seasonal variability in carbon:234thorium ratios of suspended and sinking particles in coastal Antarctic waters: Field data and modeling synthesis ]]> https://biorxiv.org/content/10.1101/2022.01.07.475468v1?rss=1 Stukel, M. R. Schofield, O. M. E. Ducklow, H. W. 2022-01-10 doi:10.1101/2022.01.07.475468 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ RNA-sequencing of human post-mortem hypothalamus and nucleus accumbens identifies expression profiles associated with obesity. ]]> https://biorxiv.org/content/10.1101/2022.01.08.473382v1?rss=1 Wake, C. Schneider, J. A. Stein, T. D. Bregu, J. Labadorf, A. McKee, A. De Jager, P. L. Bennett, D. A. Seshadri, S. Myers, R. H. DeStefano, A. L. 2022-01-11 doi:10.1101/2022.01.08.473382 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ The dorsal hippocampus' role in context-based timing in rodents ]]> https://biorxiv.org/content/10.1101/2022.01.10.475732v1?rss=1 De Corte, B. J. Farley, S. J. Heslin, K. A. Parker, K. L. Freeman, J. H. 2022-01-11 doi:10.1101/2022.01.10.475732 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Novel modification of Luminex assay for characterization of extracellular vesicle populations in biofluids. ]]> https://biorxiv.org/content/10.1101/2022.01.12.475897v1?rss=1 Volpert, O. V. Gershun, E. Elgart, K. Kalia, V. Wu, H. Baccarelli, A. A. Eren, E. Kapogiannis, D. Verma, A. Levine, A. Eitan, E. 2022-01-12 doi:10.1101/2022.01.12.475897 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Rare Genetic Variants Correlate with Better Processing Speed ]]> https://biorxiv.org/content/10.1101/2022.01.12.476030v1?rss=1 0.7. The results were replicated using genetic data imputed to the 1000 Genomes phase 3 reference panel from two Danish twin cohorts: the study of Middle Aged Danish Twins and the Longitudinal Study of Aging Danish Twins. The GWAS in LLFS discovered 20 rare genetic variants (minor allele frequency (MAF) < 1.0%) that reached genome-wide significance (p-value < 5x10-8). Among these, 18 variants had large protective effects on the processing speed, including rs7623455, rs9821776, rs9821587, rs78704059 on chromosome 3, which were replicated in the combined Danish twin cohort. These SNPs are located in/near two genes, THRB and RARB, that belonged to thyroid hormone receptors family that may influence speed of metabolism and cognitive aging. The gene-level tests in LLFS confirmed that these two genes are associated with processing speed. ]]> Song, Z. Gurinovich, A. Nygaard, M. Mengel-From, J. Andersen, S. Cosentino, S. Schupfs, N. Lee, J. Zmuda, J. Ukraintseva, S. Arbeev, K. Christensen, K. Perls, T. Sebastiani, P. 2022-01-12 doi:10.1101/2022.01.12.476030 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Dynamical Latent State Computation in the Posterior Parietal Cortex ]]> https://biorxiv.org/content/10.1101/2022.01.12.476065v1?rss=1 Lakshminarasimhan, K. J. Avila, E. Pitkow, X. Angelaki, D. E. 2022-01-12 doi:10.1101/2022.01.12.476065 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ Bulk and Single-nucleus Transcriptomics Highlight Intra-telencephalic and Somatostatin Neurons in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.01.12.476076v1?rss=1 Consens, M. E. Chen, Y. Menon, V. Wang, Y. Schneider, J. A. De Jager, P. L. Bennett, D. A. Tripathy, S. J. Felsky, D. 2022-01-13 doi:10.1101/2022.01.12.476076 Cold Spring Harbor Laboratory Press 2022-01-13 <![CDATA[ Characterizing the conformational free-energy landscape of RNA using single-molecule field-effect transistors ]]> https://biorxiv.org/content/10.1101/2022.01.13.475405v1?rss=1 Jang, S. S. Dubnik, S. Hon, J. Nuckolls, C. Gonzalez, R. L. 2022-01-14 doi:10.1101/2022.01.13.475405 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Prom1 and Notch regulate ciliary length and dynamics in multiciliated cells of the airway epithelium ]]> https://biorxiv.org/content/10.1101/2022.01.13.475833v1?rss=1 Hurtado Serra, C. F. Liu, H. Qian, J. Mori, M. Lu, J. Cardoso, W. V. 2022-01-14 doi:10.1101/2022.01.13.475833 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ A deep learning pipeline for segmentation of Proteus mirabilis colony patterns ]]> https://biorxiv.org/content/10.1101/2022.01.17.475672v1?rss=1 Doshi, A. Shaw, M. Tonea, R. Minyety, R. Moon, S. Laine, A. Guo, J. Danino, T. 2022-01-17 doi:10.1101/2022.01.17.475672 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Exploiting Color Space Geometry for Visual Stimulus Design across Animals ]]> https://biorxiv.org/content/10.1101/2022.01.17.476640v1?rss=1 Christenson, M. P. Mousavi, S. N. Heath, S. L. Behnia, R. 2022-01-20 doi:10.1101/2022.01.17.476640 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ SARS-CoV-2 infection results in lasting and systemic perturbations post recovery ]]> https://biorxiv.org/content/10.1101/2022.01.18.476786v1?rss=1 Frere, J. J. Serafini, R. A. Pryce, K. D. Zazhytska, M. Oishi, K. Golynker, I. Panis, M. Zimering, J. Horiuchi, S. Hoagland, D. A. Moller, R. Ruiz, A. Overdevest, J. B. Kodra, A. Canoll, P. D. Goldman, J. E. Borczuk, A. C. Chandar, V. Bram, Y. Schwartz, R. Lomvardas, S. Zachariou, V. tenOever, B. 2022-01-20 doi:10.1101/2022.01.18.476786 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ A local translation program regulates centriole amplification in the airway epithelium ]]> https://biorxiv.org/content/10.1101/2022.01.18.476821v1?rss=1 Liu, H. Li, H. Jiang, Z. Jin, S. Song, R. Yang, Y. Li, J. Huang, J. Zhang, X. Dong, X. Que, J. Mori, M. Fritzler, M. J. He, L. Cardoso, W. V. Lu, J. 2022-01-20 doi:10.1101/2022.01.18.476821 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Phenotypic dissection of epithelial lineages and therapeutic manipulation of differentiation programs in human Adenoid Cystic Carcinomas ]]> https://biorxiv.org/content/10.1101/2022.01.19.476843v1?rss=1 Viragova, S. Aparicio, L. Zhao, J. Valencia Salazar, L. E. Schurer, A. Dhuri, A. Sahoo, D. Moskaluk, C. A. Rabadan, R. Dalerba, P. 2022-01-21 doi:10.1101/2022.01.19.476843 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Excessive self-grooming of Shank3 mutant mice is associated with gene dysregulation and imbalance between the striosome and matrix compartments in the striatum ]]> https://biorxiv.org/content/10.1101/2022.01.19.476922v1?rss=1 Ferhat, A.-T. Biton, A. Verpy, E. Forget, B. de Chaumont, F. Mueller, F. Le Sourd, A.-M. Coqueran, S. Schmitt, J. Rochefort, C. Rondi-Reig, L. Leboucher, A. Boland, A. Fin, B. Deleuze, J.-F. Boeckers, T. Ey, E. Bourgeron, T. 2022-01-21 doi:10.1101/2022.01.19.476922 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Overestimated Polygenic Prediction due to Overlapping Subjects in Genetic Datasets ]]> https://biorxiv.org/content/10.1101/2022.01.19.476997v1?rss=1 Park, D. K. Chen, M. Kim, S. Joo, Y. Y. Loving, R. Kim, H.-S. Cha, J. Yoo, S. Kim, J. H. 2022-01-22 doi:10.1101/2022.01.19.476997 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Engineered bacterial swarm patterns as spatial records of environmental inputs ]]> https://biorxiv.org/content/10.1101/2022.01.20.477106v1?rss=1 Doshi, A. Shaw, M. Tonea, R. Moon, S. Doshi, A. Laine, A. Guo, J. Danino, T. 2022-01-21 doi:10.1101/2022.01.20.477106 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ A Genome-wide CRISPR Screen Identifies WDFY3 as a Novel Regulator of Macrophage Efferocytosis ]]> https://biorxiv.org/content/10.1101/2022.01.21.477299v1?rss=1 Shi, J. Wu, X. Wang, Z. Li, F. Meng, Y. Moore, R. M. Cui, J. Xue, C. Croce, K. R. Yurdagul, A. Doench, J. G. Li, W. Zarbalis, K. S. Tabas, I. Yamamoto, A. Zhang, H. 2022-01-22 doi:10.1101/2022.01.21.477299 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ A brain atlas of the camouflaging dwarf cuttlefish, Sepia bandensis ]]> https://biorxiv.org/content/10.1101/2022.01.23.477393v1?rss=1 Montague, T. G. Rieth, I. J. Gjerswold-Selleck, S. Garcia-Rosales, D. Aneja, S. Elkis, D. Zhu, N. Kentis, S. Rubino, F. A. Nemes, A. Wang, K. Hammond, L. A. Emiliano, R. Ober, R. A. Guo, J. Axel, R. 2022-01-24 doi:10.1101/2022.01.23.477393 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Chondroitin sulfates enhances the barrier function of basement membrane assembled by heparan sulfates ]]> https://biorxiv.org/content/10.1101/2022.01.23.477428v1?rss=1 Tao, C. Makrides, N. Wu, Y. Brooks, S. E. Esko, J. D. Zhang, X. 2022-01-24 doi:10.1101/2022.01.23.477428 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ The geometry of hippocampal CA2 representations enables abstract coding of social familiarity and identity ]]> https://biorxiv.org/content/10.1101/2022.01.24.477361v1?rss=1 Boyle, L. M. Posani, L. Irfan, S. Siegelbaum, S. A. Fusi, S. 2022-01-25 doi:10.1101/2022.01.24.477361 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Morphological analysis of human and mouse dendritic spines reveals a morphological continuum and differences across ages and species ]]> https://biorxiv.org/content/10.1101/2022.01.24.477510v1?rss=1 Ofer, N. Benavides-Piccione, R. DeFelipe, J. Yuste, R. 2022-01-25 doi:10.1101/2022.01.24.477510 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ LET-dependence of radiation-induced makers of Immunogenic Cell Death in human cancer cell lines ]]> https://biorxiv.org/content/10.1101/2022.01.25.477729v1?rss=1 Ponnaiya, B. Lomastro, A. Grabham, P. W. Garty, g. Harken, A. D. Amundson, S. A. Hillman, E. M. C. Brenner, D. J. 2022-01-26 doi:10.1101/2022.01.25.477729 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ CyclinD2-mediated regulation of neurogenic output from the retinal ciliary margin is perturbed in albinism ]]> https://biorxiv.org/content/10.1101/2022.01.27.477954v1?rss=1 Slavi, N. Balasubramanian, R. Lee, M. A. Liapin, M. Oaks-Leaf, R. Peregrin, J. Potenski, A. Troy, C. M. Ross, M. E. Herrera, E. Kosmidis, S. John, S. W. M. Mason, C. A. 2022-01-28 doi:10.1101/2022.01.27.477954 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ STK25 inhibits PKA signaling by phosphorylating PRKAR1A ]]> https://biorxiv.org/content/10.1101/2022.01.27.478084v1?rss=1 Zhang, X. Wang, B. Z. Kim, M. Nash, T. Liu, B. Rao, J. Lock, R. Tamargo, M. Soni, R. Belov, J. Li, E. Vunjak-Novakovic, G. Fine, B. 2022-01-28 doi:10.1101/2022.01.27.478084 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Mapping SARS-CoV-2 antigenic relationships and serological responses ]]> https://biorxiv.org/content/10.1101/2022.01.28.477987v1?rss=1 3 months post-2nd dose. We find changes in immunodominance of different spike regions depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine strain selection. One sentence summaryAntigenic Cartography of SARS-CoV-2 variants reveals amino acid substitutions governing immune escape and immunodominance patterns. ]]> Wilks, S. H. Muhlemann, B. Shen, X. Tureli, S. LeGresley, E. B. Netzl, A. Caniza, M. A. Chacaltana-Huarcaya, J. N. Daniell, X. Datto, M. B. Denny, T. N. Drosten, C. Fouchier, R. A. M. Garcia, P. J. Halfmann, P. J. Jassem, A. Jones, T. C. Kawaoka, Y. Krammer, F. McDanal, C. Pajon, R. Simon, V. Stockwell, M. Tang, H. van Bakel, H. Webby, R. Montefiori, D. C. Smith, D. J. 2022-01-28 doi:10.1101/2022.01.28.477987 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data ]]> https://biorxiv.org/content/10.1101/2022.01.28.478116v1?rss=1 Ehsan, N. Kotis, B. Castel, S. Song, E. Mancuso, N. Mohammadi, P. 2022-01-28 doi:10.1101/2022.01.28.478116 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ An actionable map of arm and hand muscle responses to electrical stimulation of the dorsal cervical spinal cord in humans ]]> https://biorxiv.org/content/10.1101/2022.01.29.478182v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@136b6c8org.highwire.dtl.DTLVardef@11a0c45org.highwire.dtl.DTLVardef@11baf9corg.highwire.dtl.DTLVardef@a62d62_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> McIntosh, J. R. Joiner, E. F. Goldberg, J. L. Murray, L. M. Yasin, B. Mendiratta, A. Karceski, S. C. Thuet, E. Modik, O. Shelkov, E. Mandigo, C. Riew, K. D. Harel, N. Y. Virk, M. S. Carmel, J. B. 2022-01-31 doi:10.1101/2022.01.29.478182 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Neuronal membrane proteasomes homeostatically regulate neural circuit activity in vivo and are required for learning-induced behavioral plasticity ]]> https://biorxiv.org/content/10.1101/2022.01.29.478314v1?rss=1 He, H.-y. Ramachandran, K. McLain, N. Faulkner, R. Ahsan, A. Bera, R. Margolis, S. S. Cline, H. T. 2022-01-30 doi:10.1101/2022.01.29.478314 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Spatiotemporal dissociation of brain network connectivity in salience processing: A simultaneous pupillometry-EEG-fMRI study ]]> https://biorxiv.org/content/10.1101/2022.01.29.478345v1?rss=1 He, H. Hong, L. Sajda, P. 2022-02-01 doi:10.1101/2022.01.29.478345 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Rapid Carbon Dioxide Capture and Short-Term Biocompatible Sequestration in Aquatic Environments by Monoethanolamine Scrubbing within Calcium Alginate Gel ]]> https://biorxiv.org/content/10.1101/2022.01.31.478517v1?rss=1 Ogundare, S. O. 2022-02-02 doi:10.1101/2022.01.31.478517 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Histone deacetylase inhibitor induces acetyl-CoA depletion leading to lethal metabolic stress in RAS-pathway activated cells ]]> https://biorxiv.org/content/10.1101/2022.01.31.478570v1?rss=1 Basseville, A. Violet, P.-C. Safari, M. Sourbier, C. Linehan, M. Robey, R. W. Levine, M. Sackett, D. L. Bates, S. E. 2022-02-01 doi:10.1101/2022.01.31.478570 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Transcriptomic analysis of aging mouse sciatic nerve reveals early pathways leading to sarcopenia ]]> https://biorxiv.org/content/10.1101/2022.02.01.478571v1?rss=1 2; false discovery rate [FDR] < 0.05) which we validated with qRT-PCR of the three top up- and down-regulated genes. Up-regulated genes were associated with circadian rhythm and the AMPK signaling pathway, while down-regulated genes were associated with biosynthesis and metabolic pathways and circadian rhythm. Strikingly, we detected a significant increase in Myog expression (log2 fold change = 18.93, FDR q-value = 1.54x10-12) in sciatic nerve of 18-month-old mice, before up-regulation in muscle was observed. We identified seven clusters of genes with similar expression patterns across groups. Functional enrichment analysis of these clusters revealed biological processes that may be implicated in sarcopenia initiation including extracellular matrix organization and circadian regulation of gene expression. ConclusionsGene expression changes in mouse peripheral nerve can be detected prior to overt clinical onset of sarcopenia. These early molecular changes we report shed a new light on biological processes that may be implicated in sarcopenia initiation and pathogenesis. Future studies will validate which of the key changes we reported have disease modifying and/or biomarker potential. ]]> Comfort, N. Gade, M. Strait, M. Merwin, S. J. Antoniou, D. Memou, A. Rideout, H. J. Corti, S. Kariya, S. Re, D. B. 2022-02-03 doi:10.1101/2022.02.01.478571 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Deep Mendelian Randomization: Investigating the causal knowledge of genomic deep learning models ]]> https://biorxiv.org/content/10.1101/2022.02.01.478608v1?rss=1 Malina, S. Cizin, D. Knowles, D. A. 2022-02-02 doi:10.1101/2022.02.01.478608 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Enhanced excitability of the hippocampal CA2 region and its contribution to seizure generation in a mouse model of temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/2022.02.02.478736v1?rss=1 Whitebirch, A. C. LaFrancois, J. J. Jain, S. Leary, P. Santoro, B. Siegelbaum, S. A. Scharfman, H. E. 2022-02-05 doi:10.1101/2022.02.02.478736 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ CACNB4 overexpression decreases dendritic spine density in sex-specific manner ]]> https://biorxiv.org/content/10.1101/2022.02.02.478824v1?rss=1 Parker, E. M. Kindja, N. L. DeGiosio, R. A. Salisbury, R. B. Krivinko, J. M. Cheetham, C. E. J. MacDonald, M. L. Sweet, R. 2022-02-03 doi:10.1101/2022.02.02.478824 Cold Spring Harbor Laboratory Press 2022-02-03 <![CDATA[ Superstitious learning of abstract order from random reinforcement ]]> https://biorxiv.org/content/10.1101/2022.02.02.478909v1?rss=1 Jin, Y. Jensen, G. Gottlieb, J. P. Ferrera, V. P. 2022-02-04 doi:10.1101/2022.02.02.478909 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Traveling waves in the monkey frontoparietal network predict recent reward memory ]]> https://biorxiv.org/content/10.1101/2022.02.03.478583v1?rss=1 Zabeh, E. Foley, N. C. Jacobs, J. Gottlieb, J. 2022-02-06 doi:10.1101/2022.02.03.478583 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ Interaction of an α-synuclein epitope with HLA-DRB1*15:01 initiates early enteric features of Parkinson's disease in humanized mice ]]> https://biorxiv.org/content/10.1101/2022.02.03.479014v1?rss=1 Garretti, F. Monahan, C. Sloan, N. Shariar, S. Kim, S. W. Sette, A. Cutforth, T. Kanter, E. Sulzer, D. Agalliu, D. 2022-02-05 doi:10.1101/2022.02.03.479014 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Transfer Learning for Cognitive Reserve Quantification ]]> https://biorxiv.org/content/10.1101/2022.02.03.479059v1?rss=1 Zhu, X. Liu, Y. Habeck, C. G. Stern, Y. Lee, S. 2022-02-06 doi:10.1101/2022.02.03.479059 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ Expectation for sweet taste changes peripheral glucose metabolism via basolateral amygdala ]]> https://biorxiv.org/content/10.1101/2022.02.03.479066v1?rss=1 Yamamoto, I. Yonekura, T. Ishimoto, T. Xu, S.-C. Iijima, N. Kimura, K. Diano, S. Toda, C. 2022-02-06 doi:10.1101/2022.02.03.479066 Cold Spring Harbor Laboratory Press 2022-02-06 <![CDATA[ Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age ]]> https://biorxiv.org/content/10.1101/2022.02.04.479011v1?rss=1 Rocha Moreira, L. Klicka, J. Smith, B. T. 2022-02-08 doi:10.1101/2022.02.04.479011 Cold Spring Harbor Laboratory Press 2022-02-08 <![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[ Transient oscillations of neural firing rate associated with routing of evidence in a perceptual decision ]]> https://biorxiv.org/content/10.1101/2022.02.07.478903v1?rss=1 Odean, N. N. Sanayei, M. Shadlen, M. N. 2022-02-10 doi:10.1101/2022.02.07.478903 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Antibody Evasion Properties of SARS-CoV-2 Omicron Sublineages ]]> https://biorxiv.org/content/10.1101/2022.02.07.479306v1?rss=1 Iketani, S. Liu, L. Guo, Y. Liu, L. Huang, Y. Wang, M. Luo, Y. Yu, J. Yin, M. T. Sobieszczyk, M. E. Huang, Y. Wang, H. H. Sheng, Z. Ho, D. D. 2022-02-09 doi:10.1101/2022.02.07.479306 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ A paternal bias in germline mutation is widespread across amniotes and can arise independently of cell divisions ]]> https://biorxiv.org/content/10.1101/2022.02.07.479417v1?rss=1 de Manuel, M. Wu, F. L. Przeworski, M. 2022-02-09 doi:10.1101/2022.02.07.479417 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ The direction and timing of theta and alpha traveling waves modulate human memory processing ]]> https://biorxiv.org/content/10.1101/2022.02.07.479466v1?rss=1 Mohan, U. R. Zhang, H. Jacobs, J. 2022-02-10 doi:10.1101/2022.02.07.479466 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Light/dark and temperature cycling modulate metabolic electron flow in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/2022.02.07.479496v1?rss=1 Kahl, L. J. Eckartt, K. Morales, D. K. Price-Whelan, A. Dietrich, L. E. P. 2022-02-08 doi:10.1101/2022.02.07.479496 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Principled clustering of functional signals reveals gradients in processing both within the anterior hippocampus and across its long axis ]]> https://biorxiv.org/content/10.1101/2022.02.08.479587v1?rss=1 Thorp, J. N. Gasser, C. Blessing, E. M. Davachi, L. 2022-02-10 doi:10.1101/2022.02.08.479587 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Motor cortical influence relies on task-specific activity covariation ]]> https://biorxiv.org/content/10.1101/2022.02.09.479479v1?rss=1 Warriner, C. L. Fageiry, S. Saxena, S. Costa, R. M. Miri, A. 2022-02-10 doi:10.1101/2022.02.09.479479 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Selective integration of diverse taste inputs within a single taste modality ]]> https://biorxiv.org/content/10.1101/2022.02.09.479727v1?rss=1 Deere, J. U. Uttley, H. A. Martinez Santana, N. Devineni, A. V. 2022-02-10 doi:10.1101/2022.02.09.479727 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Architecture of the human erythrocyte ankyrin-1 complex ]]> https://biorxiv.org/content/10.1101/2022.02.10.479914v1?rss=1 Vallese, F. Kim, K. Yen, L. Y. Johnston, J. D. Noble, A. J. Cali, T. Clarke, O. B. 2022-02-10 doi:10.1101/2022.02.10.479914 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Optimal routing to cerebellum-like structures ]]> https://biorxiv.org/content/10.1101/2022.02.10.480014v1?rss=1 Muscinelli, S. Wagner, M. Litwin-Kumar, A. 2022-02-11 doi:10.1101/2022.02.10.480014 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ The OncoLoop network-based precision oncology framework ]]> https://biorxiv.org/content/10.1101/2022.02.11.479456v1?rss=1 Vasciaveo, A. Zou, M. Arriaga, J. M. Geraldes de Almeida, F. Douglass, E. F. Shibata, M. Rodriguez-Calero, A. de Brot, S. Mitrofanova, A. Chua, C. W. Karan, C. Realubit, R. Pampou, S. Y. Kim, J. Y. Corey, E. Alvarez, M. Rubin, M. A. Shen, M. M. Califano, A. Abate-Shen, C. 2022-02-14 doi:10.1101/2022.02.11.479456 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Vaccine-elicitation of cross-group neutralizing protective antibodies to influenza A viruses ]]> https://biorxiv.org/content/10.1101/2022.02.11.480115v1?rss=1 Moin, S. M. Boyington, J. C. Boyoglu-Barnum, S. Gillespie, R. A. Cerutti, G. Cheung, C. S.-F. Cagigi, A. Gallagher, J. R. Brand, J. Prabhakaran, M. Tsybovsky, Y. Stephens, T. Fisher, B. E. Creanga, A. Ataca, S. Rawi, R. Corbett, K. S. Crank, M. C. Gorman, J. McDermott, A. B. Harris, A. K. Zhou, T. Kwong, P. D. Shapiro, L. Mascola, J. R. Graham, B. S. Kanekiyo, M. 2022-02-12 doi:10.1101/2022.02.11.480115 Cold Spring Harbor Laboratory Press 2022-02-12 <![CDATA[ In vivo calcium imaging identifies functionally and molecularly distinct subsets of tongue-innervating mechanosensory neurons ]]> https://biorxiv.org/content/10.1101/2022.02.11.480171v1?rss=1 Moayedi, Y. Xu, S. Obayashi, S. K. Hoffman, B. U. Gerling, G. J. Lumpkin, E. A. 2022-02-14 doi:10.1101/2022.02.11.480171 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications ]]> https://biorxiv.org/content/10.1101/2022.02.13.480272v1?rss=1 Wang, Y. Fan, J. L. Melms, J. C. Amin, A. D. Georgis, Y. Ho, P. Tagore, S. Abril-Rodriguez, G. Biermann, J. Hofree, M. Caprio, L. Berhe, S. Khan, S. A. Henick, B. S. Ribas, A. Taylor, A. M. Schwartz, G. K. Carvajal, R. D. Azizi, E. Izar, B. 2022-02-13 doi:10.1101/2022.02.13.480272 Cold Spring Harbor Laboratory Press 2022-02-13 <![CDATA[ Functional and effective connectivity between dorsolateral prefrontal and subgenual anterior cingulate cortex depends on the timing of transcranial magnetic stimulation relative to the phase of prefrontal alpha EEG ]]> https://biorxiv.org/content/10.1101/2022.02.14.480466v1?rss=1 Pantazatos, S. P. McIntosh, J. R. Saber, G. T. Sun, X. Doose, J. Faller, J. Lin, Y. Teves, J. B. Blankenship, A. Huffman, S. Goldman, R. I. George, M. S. Sajda, P. Brown, T. 2022-02-16 doi:10.1101/2022.02.14.480466 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data ]]> https://biorxiv.org/content/10.1101/2022.02.15.480548v1?rss=1 Zhou, B. Wang, C. Putzel, G. Hu, J. Liu, M. Wu, F. Chen, Y. Pironti, A. Li, H. 2022-02-19 doi:10.1101/2022.02.15.480548 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Decision formation in parietal cortex transcends a fixed frame of reference ]]> https://biorxiv.org/content/10.1101/2022.02.16.478899v1?rss=1 So, N. Shadlen, M. N. 2022-02-17 doi:10.1101/2022.02.16.478899 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ A new insight into MYC action: control of RNA polymerase II methylation and transcription termination ]]> https://biorxiv.org/content/10.1101/2022.02.17.480813v1?rss=1 Scagnoli, F. Palma, A. Favia, A. Scuoppo, C. Illi, B. Nasi, S. 2022-02-17 doi:10.1101/2022.02.17.480813 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ A unique mineralizing pool of Gli1+ stem cells builds the tendon enthesis and demonstrates therapeutic potential ]]> https://biorxiv.org/content/10.1101/2022.02.17.480929v1?rss=1 Fang, F. Xiao, Y. Zelzer, E. Leong, K. W. Thomopoulos, S. 2022-02-18 doi:10.1101/2022.02.17.480929 Cold Spring Harbor Laboratory Press 2022-02-18 <![CDATA[ An NKX-COUP-TFII genomic code for mucosal vascular addressins and organ morphogenesis ]]> https://biorxiv.org/content/10.1101/2022.02.17.480956v1?rss=1 Dinh, t. t. Xiang, M. Rajaraman, A. Wang, Y. Salazar, N. Roper, W. Rhee, S. Brulois, K. O'Hara, E. Keifel, H. Dinh, T. Gonzalez, D. Bao, E. Red-Horse, K. Balogh, P. Gabris, F. Gaszner, B. Berta, G. Pan, J. Butcher, E. 2022-02-19 doi:10.1101/2022.02.17.480956 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ A Ferroptosis-mediated regulation of the biogenesis of the oxidative phosphorylation system ]]> https://biorxiv.org/content/10.1101/2022.02.17.480976v1?rss=1 Murari, A. Rhooms, S.-k. Hossain, K. Liu, T. Li, H. Goparaju, N. S. Osei, C. Owusu-Ansah, E. 2022-02-19 doi:10.1101/2022.02.17.480976 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Mural norrin/β-catenin signaling regulates Lama2 expression to promote neurovascular unit assembly ]]> https://biorxiv.org/content/10.1101/2022.02.18.481046v1?rss=1 Biswas, S. Shahriar, S. Giangreco, N. P. Arvanitis, P. Winkler, M. Tatonetti, N. P. Brunken, W. J. Cutforth, T. Agalliu, D. 2022-02-19 doi:10.1101/2022.02.18.481046 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Reactive microglia and cytokine release entails microtubule remodeling from acentrosomal to centrosomal arrays ]]> https://biorxiv.org/content/10.1101/2022.02.21.481355v1?rss=1 Rosito, M. Sanchini, C. Gosti, G. Moreno, M. De Panfilis, S. Giubettini, M. Debellis, D. Catalano, F. Peruzzi, G. Marotta, R. Indrieri, A. De Leonibus, E. Ragozzino, D. Ruocco, G. Di Angelantonio, S. Bartolini, F. 2022-02-22 doi:10.1101/2022.02.21.481355 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Systematic Elucidation and Pharmacological Targeting of Tumor-Infiltrating Regulatory T Cell Master Regulators ]]> https://biorxiv.org/content/10.1101/2022.02.22.481404v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1cca60borg.highwire.dtl.DTLVardef@a93ce6org.highwire.dtl.DTLVardef@dd2aa2org.highwire.dtl.DTLVardef@1a2c98_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Obradovic, A. Ager, C. Turunen, M. Nirschl, T. Khosravi-Maharlooei, M. Jackson, C. Yegnasubramanian, V. DeMarzo, A. Kochel, C. Allaf, M. Bivalacqua, T. Lim, M. Karan, C. Drake, C. Califano, A. 2022-02-23 doi:10.1101/2022.02.22.481404 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Myopia alters the structural organization of the retinal astrocyte template, associated vasculature and ganglion layer thickness. ]]> https://biorxiv.org/content/10.1101/2022.02.22.481546v1?rss=1 Lin, C. R. Toychiev, A. Slavi, N. Srinivas, M. Ablordeppey, R. K. Benavente-Perez, A. 2022-02-24 doi:10.1101/2022.02.22.481546 Cold Spring Harbor Laboratory Press 2022-02-24 <![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[ Three membrane fusion pore families determine the pathways of pore dilation ]]> https://biorxiv.org/content/10.1101/2022.02.23.481713v1?rss=1 Su, R. Wang, S. McDargh, Z. A. O'Shaughnessy, B. 2022-02-24 doi:10.1101/2022.02.23.481713 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Actin turnover protects the cytokinetic contractile ring from structural instability ]]> https://biorxiv.org/content/10.1101/2022.02.23.481727v1?rss=1 McDargh, Z. A. Zhu, T. Zhu, H. O'Shaughnessy, B. 2022-02-24 doi:10.1101/2022.02.23.481727 Cold Spring Harbor Laboratory Press 2022-02-24 <![CDATA[ Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2022.02.25.481990v1?rss=1 314,000 single-cell RA synovial cell atlas with 77 cell states from T, B/plasma, natural killer, myeloid, stromal, and endothelial cells. We stratified tissue samples into six distinct cell type abundance phenotypes (CTAPs) individually enriched for specific cell states. These CTAPs demonstrate the striking diversity of RA synovial inflammation, ranging from marked enrichment of T and B cells (CTAP-TB) to a congregation of specific myeloid, fibroblast, and endothelial cells largely lacking lymphocytes (CTAP-EFM). Disease-relevant cytokines, histology, and serology metrics are associated with certain CTAPs. This comprehensive RA synovial atlas and molecular, tissue-based CTAP stratification reveal new insights into RA pathology and heterogeneity, which could lead to novel targeted-treatment approaches in RA. ]]> Zhang, F. Jonsson, A. H. Nathan, A. Wei, K. Millard, N. Xiao, Q. Gutierrez-Arcelus, M. Apruzzese, W. Watts, G. F. M. Weisenfeld, D. Kang, J. B. Rumker, L. Mears, J. Slowikowski, K. Weinand, K. Orange, D. E. Rangel-Moreno, J. Geraldino-Pardilla, L. Deane, K. D. Tabechian, D. Ceponis, A. Firestein, G. S. Maybury, M. Sahbudin, I. Ben-Artzi, A. Mandelin, A. M. Nerviani, A. Rivellese, F. Pitzalis, C. Hughes, L. B. Horowitz, D. DiCarlo, E. Gravallese, E. M. Boyce, B. F. Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus 2022-02-28 doi:10.1101/2022.02.25.481990 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors ]]> https://biorxiv.org/content/10.1101/2022.02.26.482133v1?rss=1 Feng, S. Rastogi, C. Loker, R. E. Glassford, W. J. Rube, H. T. Bussemaker, H. J. Mann, R. S. 2022-02-27 doi:10.1101/2022.02.26.482133 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Inhibition of advanced glycation end product formation and serum protein infiltration in bioprosthetic heart valve leaflets: Investigations of anti-glycation agents. ]]> https://biorxiv.org/content/10.1101/2022.02.28.482351v1?rss=1 Zakharchenko, A. Rock, C. Thomas, T. Keeney, S. Hall, E. Takano, H. Krieger, A. Ferrari, G. Levy, R. 2022-02-28 doi:10.1101/2022.02.28.482351 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ New Insights on the Evolutionary Relationships Between the Major Lineages of Amoebozoa ]]> https://biorxiv.org/content/10.1101/2022.02.28.482369v1?rss=1 Tekle, Y. I. Wang, F. Wood, F. Anderson, O. R. Smirnov, A. 2022-03-02 doi:10.1101/2022.02.28.482369 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Case Study of Single-cell Protein Activity Based Drug Prediction for Precision Treatment of Cholangiocarcinoma ]]> https://biorxiv.org/content/10.1101/2022.02.28.482410v1?rss=1 Obradovic, A. Tomassoni, L. Yu, D. Guillan, K. Souto, K. Fraser, E. Bates, S. Drake, C. G. Saenger, Y. Cruz, F. D. Kung, A. Califano, A. 2022-03-02 doi:10.1101/2022.02.28.482410 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte ]]> https://biorxiv.org/content/10.1101/2022.03.01.482163v1?rss=1 Liao, X. Kennel, P. Liu, B. Nash, T. Zuang, R. Godier-Furnemont, A. Xue, C. Lu, R. Colombo, P. Uriel, N. Reilly, M. Marx, S. Vunjak-Novakovic, G. Topkara, V. K. 2022-03-02 doi:10.1101/2022.03.01.482163 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ EMC10 reduction in human neurons and adult mouse brain rescues cellular and behavioral deficits linked to 22q11.2 deletion ]]> https://biorxiv.org/content/10.1101/2022.03.01.482495v1?rss=1 Thakur, P. Lackinger, M. Diamantopoulou, A. Rao, S. Chen, Y. Ferng, A. Mazur, C. Kordasiewicz, H. Shprintzen, R. J. Markx, S. Xu, B. Gogos, J. A. 2022-03-04 doi:10.1101/2022.03.01.482495 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ A promoter-proximal silencer modifies the activity of a shared enhancer to mediate divergent expression of nub and pdm2 paralogs in wing development ]]> https://biorxiv.org/content/10.1101/2022.03.01.482523v1?rss=1 Loker, R. Mann, R. S. 2022-03-03 doi:10.1101/2022.03.01.482523 Cold Spring Harbor Laboratory Press 2022-03-03 <![CDATA[ NAC1 Modulates Autoimmunity by Suppressing Regulatory T Cell- Mediated Tolerance ]]> https://biorxiv.org/content/10.1101/2022.03.01.482525v1?rss=1 Yang, J.-M. Ren, Y. Kumar, A. Xiong, X. das, j. Peng, H.-y. Wang, L. Ren, X. Alainz, R. C. de Figueiredo, P. Fang, D. Liu, X. Wang, J. Song, J. J. 2022-03-04 doi:10.1101/2022.03.01.482525 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Connectomic Analysis of the Drosophila Lateral Neuron Clock Cells Reveals the Synaptic Basis of Functional Pacemaker Classes. ]]> https://biorxiv.org/content/10.1101/2022.03.02.482743v1?rss=1 Shafer, O. T. Gutierrez, G. J. Li, K. Mildenhall, A. Spira, D. Marty, J. Lazar, A. A. Fernandez, M. d. l. P. 2022-03-04 doi:10.1101/2022.03.02.482743 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ The role of TGFβ signaling in Gli1+ tendon and enthesis cells ]]> https://biorxiv.org/content/10.1101/2022.03.03.482926v1?rss=1 Song, L. Golman, M. Abraham, A. C. Zelzer, E. Thomopoulos, S. 2022-03-04 doi:10.1101/2022.03.03.482926 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Emotion schema effects on associative memory differ across emotion categories at the behavioural, physiological and neural level ]]> https://biorxiv.org/content/10.1101/2022.03.04.482789v1?rss=1 Riegel, M. Wypych, M. Wierzba, M. Szczepanik, M. Jednorog, K. Vuilleumier, P. Marchewka, A. 2022-03-07 doi:10.1101/2022.03.04.482789 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ NKG2A and HLA-E define a novel alternative immune checkpoint axis in bladder cancer ]]> https://biorxiv.org/content/10.1101/2022.03.04.482960v1?rss=1 Salome, B. Sfakianos, J. P. Daza, J. Charap, A. Hammer, C. Banchereau, R. Farkas, A. M. Geanon, D. Kelly, G. de Real, R. M. Lee, B. Beaumont, K. G. Shroff, S. Wang, Y. S. A. Wang, Y.-C. Thin, T. H. Garcia-Barros, M. Hegewisch-Solloa, E. Mace, E. M. Wang, L. O'Donnell, T. Chowell, D. Fernandez-Rodriguez, R. Skobe, M. Taylor, N. Kim-Schulze, S. Sebra, R. P. Palmer, D. Clancy-Thompson, E. Hammond, S. Kamphorst, A. O. Malmberg, K.-J. Marcenaro, E. Romero, P. Brody, R. Viard, M. Yuki, Y. Martin, M. Carrington, M. Mehrazin, R. Wiklund, P. Mellman, I. Mariath 2022-03-05 doi:10.1101/2022.03.04.482960 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ LanA (Language Atlas): A probabilistic atlas for the language network based on fMRI data from >800 individuals ]]> https://biorxiv.org/content/10.1101/2022.03.06.483177v1?rss=1 Lipkin, B. Tuckute, G. Affourtit, J. Small, H. Mineroff, Z. Kean, H. Jouravlev, O. Rakocevic, L. Pritchett, B. Siegelman, M. Hoeflin, C. Pongos, A. Blank, I. Shruhl, M. K. Ivanova, A. Shannon, S. Sathe, A. Hoffmann, M. Nieto-Castanon, A. Fedorenko, E. 2022-03-07 doi:10.1101/2022.03.06.483177 800 individuals]]> Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Elevated HLA-E and NKG2A as a consequence of chronic immune activation defines resistance to M. bovis BCG immunotherapy in Non-Muscle-Invasive Bladder Cancer ]]> https://biorxiv.org/content/10.1101/2022.03.06.483198v1?rss=1 Ranti, D. Wang, Y.-S. Daza, J. Beiber, C. Salome, B. Merritt, E. Cavallo, J.-A. Hegewisch-Solloa, E. Mace, E. M. Farkas, A. M. Schroff, S. Tran, M. Qi, J. Patel, M. Geanon, D. Kelly, G. Dereal, R. Lee, B. Kim-Schulze, S. Thin, T. H. Garcia-Barros, M. Beaumont, K. G. Lee, Y. LaRoche, D. Sebra, R. Brody, R. Tocheva, A. Hopkins, B. Wiklund, P. Galsky, M. D. Bhardwaj, N. Sfakianos, J. P. Horowitz, A. 2022-03-07 doi:10.1101/2022.03.06.483198 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ The genomic landscapes of desert birds are structured by contemporary features ]]> https://biorxiv.org/content/10.1101/2022.03.07.483329v1?rss=1 Provost, K. L. Shue, S. Y. Forcellati, M. Smith, B. T. 2022-03-08 doi:10.1101/2022.03.07.483329 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ Biodiversity effects on seedling biomass growth are modulated by light environment across functional groups ]]> https://biorxiv.org/content/10.1101/2022.03.08.483461v1?rss=1 Anujan, K. Shabnam, A. Ali, I. Kumar, G. A. Sankaran, M. Krishnadas, M. Naeem, S. 2022-03-08 doi:10.1101/2022.03.08.483461 Cold Spring Harbor Laboratory Press 2022-03-08 <![CDATA[ The lateral intraparietal area preferentially supports stimulus selection in directed tasks compared to undirected free behavior ]]> https://biorxiv.org/content/10.1101/2022.03.09.483625v1?rss=1 Johnston, W. J. Tetrick, S. M. Freedman, D. J. 2022-03-11 doi:10.1101/2022.03.09.483625 Cold Spring Harbor Laboratory Press 2022-03-11 <![CDATA[ Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning ]]> https://biorxiv.org/content/10.1101/2022.03.09.483665v1?rss=1 Tan, R. Shen, Y. 2022-03-12 doi:10.1101/2022.03.09.483665 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ DNA Double Strand Breaks cause chromosome loss through sister chromatid tethering in human embryos ]]> https://biorxiv.org/content/10.1101/2022.03.10.483502v1?rss=1 Turocy, J. Marin, D. Xu, S. Xu, J. Robles, A. Treff, N. Egli, D. 2022-03-10 doi:10.1101/2022.03.10.483502 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Alterations to the broad-spectrum formin inhibitor SMIFH2 improve potency ]]> https://biorxiv.org/content/10.1101/2022.03.10.483826v1?rss=1 Orman, M. Landis, M. Oza, A. Nambiar, D. Gjeci, J. Song, K. Huang, V. Klestzick, A. Hachicho, C. Liu, S. Q. Kamm, J. M. Bartolini, F. Vadakkan, J. J. Rojas, C. M. Vizcarra, C. L. 2022-03-10 doi:10.1101/2022.03.10.483826 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Alveolar regeneration following viral infection is independent of tuft cells ]]> https://biorxiv.org/content/10.1101/2022.03.11.483948v1?rss=1 Que, J. Huang, H. Jiang, M. Zhang, Y. Biermann, J. Melms, J. C. Danielsson, J. Fang, Y. Yang, Y. Qiang, L. Liu, J. Zhou, Y. Wang, M. Hu, Z. Wang, T. Saqi, A. Sun, J. Matsumoto, I. Cardoso, W. V. Emala, C. Zhu, J. Izar, B. Mou, H. 2022-03-12 doi:10.1101/2022.03.11.483948 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ High-throughput Production of Diverse Xenobiotic Metabolites with P450-transduced Huh7 Hepatoma Cell Lines ]]> https://biorxiv.org/content/10.1101/2022.03.12.484071v1?rss=1 Lee, C.-m. Liu, K. H. Singer, G. Miller, G. W. Li, S. Jones, D. P. Morgan, E. T. 2022-03-14 doi:10.1101/2022.03.12.484071 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Regulation of Cardiomyocyte Adhesion and Mechanosignalling Through Distinct Nanoscale Behaviour of Integrin Ligands Mimicking Healthy or Fibrotic ECM ]]> https://biorxiv.org/content/10.1101/2022.03.13.483961v1?rss=1 Hawkes, W. Marhuenda, E. Reynolds, P. M. O'Neill, C. Pandey, P. Wilson, D. G. S. Freeley, M. Huang, D. Hu, J. Gondarenko, S. Hone, J. Gadegaard, N. Palma, M. Iskratsch, T. 2022-03-13 doi:10.1101/2022.03.13.483961 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum supports social novelty preference ]]> https://biorxiv.org/content/10.1101/2022.03.15.484224v1?rss=1 De Leon Reyes, N. S. Sierra Diaz, P. A. Nogueira Manas, R. Ruiz-Pino, A. Nomura, Y. de Solis, C. A. Schulkin, J. Asok, A. Leroy, F. 2022-03-16 doi:10.1101/2022.03.15.484224 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease ]]> https://biorxiv.org/content/10.1101/2022.03.16.484543v1?rss=1 Rustam, S. Hu, Y. Mahjour, S. B. Rendeiro, A. F. Ravichandran, H. Randell, S. H. Richmond, B. Polosukhin, V. Kropski, J. A. Blackwell, T. S. d'Ovidio, F. Martinez, F. J. Elemento, O. Shaykhiev, R. 2022-03-16 doi:10.1101/2022.03.16.484543 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ No evidence of induced skin cancer or other skin abnormalities after long term (66 week) chronic exposure to 222-nm far-UVC radiatio ]]> https://biorxiv.org/content/10.1101/2022.03.16.484636v1?rss=1 Welch, D. Kleiman, N. J. Arden, P. C. Kuryla, C. L. Buonanno, M. Ponnaiya, B. Wu, X. Brenner, D. J. 2022-03-18 doi:10.1101/2022.03.16.484636 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Triple Notch/Tgfβ/FoxO1 blockade converts multiple intestinal sub-lineages into β-like cells and lowers glycemia in diabetic animals ]]> https://biorxiv.org/content/10.1101/2022.03.21.484748v1?rss=1 Du, W. Wang, J. Kuo, T. Wang, L. McKimpson, W. Son, J. Watanabe, H. Kitamoto, T. Yunkyoung, L. Ratner, L. McCune, K. Chen, Y.-W. Grubbs, B. Thornton, M. Fan, J. Sultana, N. Diaz, B. Balasubramanian, I. Gao, N. Belvedere, S. Accili, D. 2022-03-21 doi:10.1101/2022.03.21.484748 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2022.03.21.485049v1?rss=1 Ho, P. Melms, J. C. Rogava, M. Frangieh, C. J. Shah, S. B. Walsh, Z. Kyrysyuk, O. Amin, A. D. Caprio, L. Fullerton, B. T. Soni, R. Ager, C. R. Biermann, J. Wang, Y. Mu, M. Fatima, H. Moore, E. K. Vasan, N. Bakhoum, S. F. Reiner, S. L. Bernatchez, C. Mace, E. M. Wucherpfennig, K. W. Schadendorf, D. Schwartz, G. K. Izar, B. 2022-03-21 doi:10.1101/2022.03.21.485049 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[ Glioblastoma states are defined by cohabitating cellular populations with progression-, imaging- and sex-distinct patterns ]]> https://biorxiv.org/content/10.1101/2022.03.23.485500v1?rss=1 Bond, K. M. Curtin, L. Hawkins-Daarud, A. Urcuyo, J. C. De Leon, G. Sereduk, C. Singleton, K. W. Langworthy, J. M. Jackson, P. R. Krishna, C. Zimmerman, R. S. Patra, D. P. Bendok, B. R. Smith, K. Nakaji, P. Donev, K. Baxter, L. C. Mrugala, M. M. Al-Dalahmah, O. Hu, L. S. Tran, N. L. Rubin, J. B. Canoll, P. Swanson, K. R. 2022-03-26 doi:10.1101/2022.03.23.485500 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Cyb5r3-based mechanism and reversal of secondary failure to sulfonylurea ]]> https://biorxiv.org/content/10.1101/2022.03.23.485508v1?rss=1 Watanabe, H. Du, W. Son, J. Sui, L. Asahara, S.-i. Kurland, I. J. Kuo, T. Kitamoto, T. Miyachi, Y. de Cabo, R. Accili, D. 2022-03-26 doi:10.1101/2022.03.23.485508 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model. ]]> https://biorxiv.org/content/10.1101/2022.03.23.485541v1?rss=1 Kemfack, A. M. Hernandez-Morato, I. Moayedi, Y. Pitman, M. 2022-03-23 doi:10.1101/2022.03.23.485541 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ Temporal coordination between chromosome mobility and homologous recombination ]]> https://biorxiv.org/content/10.1101/2022.03.24.485580v1?rss=1 Joseph, F. Lee, S. J. Bryant, E. E. Reid, R. J. D. Sunjevaric, I. Rothstein, R. 2022-03-24 doi:10.1101/2022.03.24.485580 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Improving patient survival by direct targeting of chimeric protein-protein interaction networks ]]> https://biorxiv.org/content/10.1101/2022.03.24.485646v1?rss=1 Tagore, S. Frenkel-Morgenstern, M. 2022-03-27 doi:10.1101/2022.03.24.485646 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Suboptimal foraging decisions and involvement of the ventral tegmental area in human opioid addiction ]]> https://biorxiv.org/content/10.1101/2022.03.24.485654v1?rss=1 Raio, C. M. Biernacki, K. Kapoor, A. Wengler, K. Bonagura, D. Xue, J. Constantino, S. M. Horga, G. Konova, A. B. 2022-03-27 doi:10.1101/2022.03.24.485654 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Stable working memory and perceptual representations in macaque lateral prefrontal cortex during naturalistic vision in virtual environments ]]> https://biorxiv.org/content/10.1101/2022.03.24.485710v1?rss=1 Roussy, M. Corrigan, B. W. Luna, R. Gulli, R. A. Sachs, A. J. Palaniyappan, L. Martinez-Trujillo, J. C. 2022-03-27 doi:10.1101/2022.03.24.485710 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Sex-specific effects of chronic paternal stress on offspring development are partially mediated via mothers. ]]> https://biorxiv.org/content/10.1101/2022.03.25.485798v1?rss=1 Mashoodh, R. Habrylo, I. B. Gudsnuk, K. M. Champagne, F. A. 2022-03-27 doi:10.1101/2022.03.25.485798 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Neuroimaging within the Dominantly Inherited Alzheimer's Network (DIAN): PET and MRI ]]> https://biorxiv.org/content/10.1101/2022.03.25.485799v1?rss=1 McKay, N. S. Gordon, B. A. Hornbeck, R. C. Jack, C. R. Koeppe, R. Flores, S. Keefe, S. Hobbs, D. A. Joseph-Mathurin, N. Wang, Q. Rahmani, F. Chen, C. D. McCullough, A. Koudelis, D. Chua, J. Ances, B. M. Millar, P. R. Nickels, M. L. Perrin, R. J. Allegri, R. F. Berman, S. B. Brooks, W. S. Cash, D. M. Chhatwal, J. P. Farlow, M. R. Fox, N. C. Fulham, M. Ghetti, B. Graff-Radford, N. Ikeuchi, T. Day, G. S. Klunk, W. Levin, J. Lee, J.-H. Martins, R. Masters, C. L. Mori, H. McConathy, J. Noble, J. M. Rowe, C. Salloway, S. Sanchez-Valle, R. Schofield, P. R. S 2022-03-30 doi:10.1101/2022.03.25.485799 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ The Human Motoneuron Expression Signature is Defined by ALS-Related Genes ]]> https://biorxiv.org/content/10.1101/2022.03.25.485808v1?rss=1 Yadav, A. Matson, K. J. E. Li, L. Hua, I. Gaur, P. Alkaslasi, M. R. Hasan, S. Galuta, A. Dedek, A. Ameri, S. Parnell, J. Alshardan, M. M. Ququmji, F. A. Alhamad, S. M. Wang, A. P. Poulen, G. Lonjon, N. Vachiery-Lahaye, F. Nalls, M. A. Nalls, M. A. Qi, Y. A. Hildebrand, M. E. Mery, P.-F. Bourinet, E. Bauchet, L. Tsai, E. C. Ward, M. E. Le Pichon, C. Menon, V. Levine, A. 2022-03-28 doi:10.1101/2022.03.25.485808 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues ]]> https://biorxiv.org/content/10.1101/2022.03.25.485871v1?rss=1 Feng, S. Mann, R. S. 2022-03-27 doi:10.1101/2022.03.25.485871 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Single-agent Foxo1 inhibition normalizes glycemia and induces gut β-like cells in streptozotocin-diabetic mice ]]> https://biorxiv.org/content/10.1101/2022.03.26.485929v1?rss=1 Lee, Y.-K. Nie, Y. Diaz, B. Sultana, N. Kitamoto, T. Du, W. Leibel, R. Accili, D. Belvedere, S. 2022-03-27 doi:10.1101/2022.03.26.485929 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Nonlinear EEG signatures of mind wandering during breath focus meditation ]]> https://biorxiv.org/content/10.1101/2022.03.27.485924v1?rss=1 Lu, Y. Rodriguez-Larios, J. 2022-03-27 doi:10.1101/2022.03.27.485924 Cold Spring Harbor Laboratory Press 2022-03-27 <![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[ Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution ]]> https://biorxiv.org/content/10.1101/2022.03.28.485354v1?rss=1 Woych, J. Gurrola, A. O. Deryckere, A. Jaeger, E. C. B. Gumnit, E. Merello, G. Gu, J. Araus, A. J. Leigh, N. D. Yun, M. Simon, A. Tosches, M. A. 2022-03-29 doi:10.1101/2022.03.28.485354 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Mutated Tumor Suppressors Follow Oncogenes Profile by the Gene Hypermethylation of Partners in the Protein Interaction Networks ]]> https://biorxiv.org/content/10.1101/2022.03.28.486156v1?rss=1 Tagore, S. Frenkel-Morgenstern, M. 2022-03-29 doi:10.1101/2022.03.28.486156 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Endothelial Caspase-9 Promotes Glial Changes, Inflammation, and Contrast Sensitivity Decline in Retinal Vascular Injury ]]> https://biorxiv.org/content/10.1101/2022.03.30.486450v1?rss=1 Ortiz, C. C. Neal, A. Avrutsky, M. Choi, M. Smart, J. Lawson, J. Troy, C. M. 2022-03-30 doi:10.1101/2022.03.30.486450 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.03.30.486484v1?rss=1 Yamada, D. Bushey, D. Li, F. Hibbard, K. Sammons, M. Funke, J. Litwin-Kumar, A. Hige, T. Aso, Y. 2022-03-31 doi:10.1101/2022.03.30.486484 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ GTP-bound E. coli FtsZ filaments are composed of Tense monomers: A DNP NMR study using interface detection. ]]> https://biorxiv.org/content/10.1101/2022.04.01.486622v1?rss=1 McCoy, K. M. McDermott, A. E. 2022-04-01 doi:10.1101/2022.04.01.486622 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Collagen remodeling dictates pancreatic cancer bioenergetics and outcome through DDR1 activation or degradation ]]> https://biorxiv.org/content/10.1101/2022.04.02.486837v1?rss=1 Su, H. Yang, F. Fu, R. Trinh, B. Sun, N. Liu, J. Kumar, A. Baglieri, J. Siruno, J. Dozier, S. Nair, A. Filliol, A. Rosenthal, S. B. Santini, J. Metallo, C. M. Molina, A. Schwabe, R. F. Lowy, A. M. Brenner, D. Sun, B. Karin, M. 2022-04-04 doi:10.1101/2022.04.02.486837 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Intracellular acidification is a hallmark of thymineless death in E. coli ]]> https://biorxiv.org/content/10.1101/2022.04.04.487045v1?rss=1 Ketcham, A. Freddolino, P. Tavazoie, S. 2022-04-04 doi:10.1101/2022.04.04.487045 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Unaltered T cell responses to common antigens in individuals with Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2022.04.05.487195v1?rss=1 Williams, G. P. Muskat, K. Frazier, A. Xu, Y. Mateus, J. Grifoni, A. Antunes, R. d. S. Weiskopf, D. Amara, A. W. Standaert, D. G. Goldman, J. G. Litvan, I. Alcalay, R. N. Sulzer, D. Arlehamn, C. S. L. Sette, A. 2022-04-08 doi:10.1101/2022.04.05.487195 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ 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[ 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[ Intradiscal Inflammatory Stimulation Induces Spinal Pain Behavior and Intervertebral Disc Degeneration In Vivo ]]> https://biorxiv.org/content/10.1101/2022.04.11.487751v1?rss=1 Lisiewski, L. E. Jacobsen, H. E. Viola, D. C. Kenawy, H. M. Kiridly, D. N. Chahine, N. O. 2022-04-12 doi:10.1101/2022.04.11.487751 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Conserved cell-type specific signature of resilience to Alzheimer's disease nominates role for excitatory cortical neurons ]]> https://biorxiv.org/content/10.1101/2022.04.12.487877v1?rss=1 Telpoukhovskaia, M. A. Hadad, N. Gurdon, B. Dai, M. Ouellette, A. R. Neuner, S. M. Dunn, A. R. Hansen, S. Wu, Y. Dumitrescu, L. O'Connell, K. M. S. Dammer, E. B. Seyfried, N. T. Muzumdar, S. Gillis, J. Robson, P. Zhang, J.-G. Hohman, T. J. Philip, V. Menon, V. Kaczorowski, C. C. 2022-04-13 doi:10.1101/2022.04.12.487877 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Comparative genomics in Orobanchaceae provides insight into the origin and evolution of plant parasitism ]]> https://biorxiv.org/content/10.1101/2022.04.13.488246v1?rss=1 Xu, Y. Zhang, J. Ma, C. Lei, Y. Shen, G. Jin, J.-J. Eaton, D. A. R. Wu, J. 2022-04-14 doi:10.1101/2022.04.13.488246 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Visual working memory recruits two functionally distinct alpha rhythms in posterior cortex ]]> https://biorxiv.org/content/10.1101/2022.04.15.488484v1?rss=1 Rodriguez Larios, J. ElShafei, A. Wiehe, M. Haegens, S. 2022-04-16 doi:10.1101/2022.04.15.488484 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ RET Signaling Persists in the Adult Intestine and Stimulates Motility by Limiting PYY Release from Enteroendocrine Cells ]]> https://biorxiv.org/content/10.1101/2022.04.15.488514v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@4c8e83org.highwire.dtl.DTLVardef@204d13org.highwire.dtl.DTLVardef@a429d8org.highwire.dtl.DTLVardef@1b75265_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shepherd, A. Feinstein, L. Sabel, S. Rastelli, D. Mezhibovsky, E. Matthews, L. Muppirala, A. Robinson, A. Gershon, M. D. Rao, M. 2022-04-16 doi:10.1101/2022.04.15.488514 Cold Spring Harbor Laboratory Press 2022-04-16 <![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[ C. elegans Sine oculis/SIX-type homeobox genes act as homeotic switches to define neuronal subtype identities ]]> https://biorxiv.org/content/10.1101/2022.04.19.488792v1?rss=1 Cros, C. Hobert, O. 2022-04-20 doi:10.1101/2022.04.19.488792 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Prefusion-Stabilized Lassa Virus Trimer Identifies Neutralizing Nanobodies and Reveals an Apex-Situated Site of Vulnerability ]]> https://biorxiv.org/content/10.1101/2022.04.21.488985v1?rss=1 Gorman, J. Cheung, C. S.-F. Duan, Z. Sun, Y. Wang, P. Boyington, J. C. Biju, A. Bylund, T. Cheng, C. Ou, L. Stephens, T. Tsybovsky, Y. Verardi, R. Wang, S. Yang, Y. Zhang, B. Zheng, C. Zhou, T. Mascola, J. R. Ho, D. D. Ho, M. Kwong, P. D. 2022-04-21 doi:10.1101/2022.04.21.488985 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Neuromuscular denervation and deafferentation but not motor neuron death are disease features in the Smn 2B/- mouse model of SMA ]]> https://biorxiv.org/content/10.1101/2022.04.21.489030v1?rss=1 Carlini, M. J. Triplett, M. K. Pellizzoni, L. 2022-04-21 doi:10.1101/2022.04.21.489030 Cold Spring Harbor Laboratory Press 2022-04-21 <![CDATA[ Saturation mutagenesis of a predicted ancestral Syk-family kinase ]]> https://biorxiv.org/content/10.1101/2022.04.24.489292v1?rss=1 Hobbs, H. T. Shah, N. H. Shoemaker, S. R. Amacher, J. F. Marqusee, S. Kuriyan, J. 2022-04-24 doi:10.1101/2022.04.24.489292 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ Isthmal stem cells sustain intestinal homeostasis and regeneration ]]> https://biorxiv.org/content/10.1101/2022.04.26.489611v1?rss=1 Malagola, E. Vasciaveo, A. Ochiai, Y. Kim, W. Middelhoff, M. Nienhuser, H. Belin, B. LaBella, J. Zamechek, L. Wong, M. Li, L. Guha, C. Yan, K. Califano, A. Wang, T. 2022-04-28 doi:10.1101/2022.04.26.489611 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Sensory regulation of absence seizures in a mouse model of Gnb1 encephalopathy ]]> https://biorxiv.org/content/10.1101/2022.04.28.489780v1?rss=1 Teng, S. Zhen, F. McRae, B. R. Zhu, E. Frankel, W. N. Peng, Y. 2022-04-28 doi:10.1101/2022.04.28.489780 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Molecular Characterization of the Tumor Microenvironment in Renal Medullary Carcinoma ]]> https://biorxiv.org/content/10.1101/2022.04.28.489873v1?rss=1 Tourigny, D. S. Zucker, M. Kim, M. Russo, P. Coleman, J. Lee, C.-H. Carlo, M. I. Chen, Y.-B. Hakimi, A. A. Kotecha, R. R. Reznik, E. 2022-04-28 doi:10.1101/2022.04.28.489873 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification ]]> https://biorxiv.org/content/10.1101/2022.04.29.490095v1?rss=1 Reilly, M. B. Tekieli, T. Cros, C. Aguilar, G. R. Lao, J. Toker, I. A. Vidal, B. Leyva-Diaz, E. Bhattacharya, A. Smith, J. J. Kovacevic, I. Gulez, B. Fernandez, R. Bradford, E. F. Ramadan, Y. H. Kratsios, P. Bao, Z. Hobert, O. 2022-05-02 doi:10.1101/2022.04.29.490095 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter ]]> https://biorxiv.org/content/10.1101/2022.05.01.490196v1?rss=1 Kinz-Thompson, C. D. Lopez Redondo, M. Mulligan, C. Sauer, D. B. Marden, J. J. Song, J. Tajkhorshid, E. Hunt, J. F. Stokes, D. L. Mindell, J. A. Wang, D.-N. Gonzalez, R. L. 2022-05-01 doi:10.1101/2022.05.01.490196 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Direct observation of the neural computations underlying a single decision ]]> https://biorxiv.org/content/10.1101/2022.05.02.490321v1?rss=1 Steinemann, N. A. Stine, G. M. Trautmann, E. M. Zylberberg, A. Wolpert, D. M. Shadlen, M. N. 2022-05-04 doi:10.1101/2022.05.02.490321 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ A neural mechanism for terminating decisions ]]> https://biorxiv.org/content/10.1101/2022.05.02.490327v1?rss=1 Stine, G. M. Trautmann, E. M. Jeurissen, D. Shadlen, M. N. 2022-05-04 doi:10.1101/2022.05.02.490327 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.05.02.490362v1?rss=1 Tagore, S. Wang, Y. Biermann, J. Rabadan, R. Azizi, E. Izar, B. 2022-05-04 doi:10.1101/2022.05.02.490362 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Common genetic variants in CHRNA5 alter β-amyloid neuropathology and highlight chandelier cells in human aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.05.03.490491v1?rss=1 Rybnicek, J. Chen, Y. Milic, M. McLaurin, J. De Jager, P. Schneider, J. A. Wang, Y. Bennett, D. A. Tripathy, S. Felsky, D. Lambe, E. K. 2022-05-05 doi:10.1101/2022.05.03.490491 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Within- and between-subject reproducibility and variability in multi-modal, longitudinal brain networks ]]> https://biorxiv.org/content/10.1101/2022.05.03.490544v1?rss=1 Nakuci, J. Wasylyshyn, N. Cieslak, M. Elliot, J. C. Bansal, K. Giesbrecht, B. Grafton, S. T. Vettel, J. M. Garcia, J. O. Muldoon, S. F. 2022-05-04 doi:10.1101/2022.05.03.490544 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Human papilloma virus E6 regulates therapy responses in oropharyngeal cancer by repressing the PGC-1α/ERRα axis ]]> https://biorxiv.org/content/10.1101/2022.05.04.490169v1?rss=1 Sannigrahi, M. K. Rajagopalan, P. Lai, L. Liu, X. Sahu, V. Nakagawa, H. Jalaly, J. B. Brody, R. M. Morgan, I. M. Windle, B. E. Wang, X. Gimotty, P. A. Kelly, D. P. White, E. A. Basu, D. 2022-05-05 doi:10.1101/2022.05.04.490169 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Multivariate Analysis of PET Pharmacokinetic Parameters ]]> https://biorxiv.org/content/10.1101/2022.05.04.490593v1?rss=1 Matheson, G. J. Ogden, R. T. 2022-05-04 doi:10.1101/2022.05.04.490593 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Expression of GDNF Receptors Within Nucleus Ambiguus During Rat Development ]]> https://biorxiv.org/content/10.1101/2022.05.04.490634v1?rss=1 Blount, Q. Hernandez-Morato, I. Moayedi, Y. Pitman, M. J. 2022-05-04 doi:10.1101/2022.05.04.490634 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Airway Basal Cells Show Regionally Distinct Potential to Undergo Metaplastic Differentiation ]]> https://biorxiv.org/content/10.1101/2022.05.04.490677v1?rss=1 Zhou, Y. Yang, Y. Qian, J. Ge, J. Sinner, D. I. Ding, H. Califano, A. Cardoso, W. V. 2022-05-05 doi:10.1101/2022.05.04.490677 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Novel Computational Models of Evoked Dopamine Release In Vivo Measured by Fast Scan Cyclic Voltammetry Quantify the Regulation of Presynaptic Kinetics by Synucleins ]]> https://biorxiv.org/content/10.1101/2022.05.04.490695v1?rss=1 N, S. Somayaji, M. Miotto, M. Mosharov, E. V. Knowles, D. A. Ruocco, G. Sulzer, D. L. 2022-05-05 doi:10.1101/2022.05.04.490695 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ TMEM106B is increased in Multiple Sclerosis plaques, and deletion causes accumulation of lipid after demyelination ]]> https://biorxiv.org/content/10.1101/2022.05.05.490697v1?rss=1 Shafit-Zagardo, B. Sidoli, S. Goldman, J. E. DuBois, J. C. Corboy, J. R. Strittmatter, S. M. Guzik, H. Graff, S. Nagra, R. M. 2022-05-05 doi:10.1101/2022.05.05.490697 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Vertical gradients in physiological function and resource allocation of white spruce diverge at the northern- and southern-most range extremes ]]> https://biorxiv.org/content/10.1101/2022.05.06.490824v1?rss=1 Schmiege, S. C. Griffin, K. L. Boelman, N. T. Vierling, L. A. Bruner, S. G. Min, E. Maguire, A. J. Jensen, J. Eitel, J. U. H. 2022-05-06 doi:10.1101/2022.05.06.490824 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Single-Cell RNAseq Analysis Reveals Robust Anti-PD-1-Mediated Increase of Immune Infiltrate in Metastatic Castration-Sensitive Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2022.05.06.490968v1?rss=1 Hawley, J. E. Obradovic, A. Z. Dallos, M. C. Lim, E. A. Runcie, K. Ager, C. R. McKiernan, J. M. Anderson, C. B. Decastro, G. J. Weintraub, J. L. Virk, R. K. Lowy, I. Hu, J. Chaimowitz, M. G. Guo, X. V. Zhang, Y. Worley, J. Stein, M. N. Califano, A. Drake, C. G. 2022-05-09 doi:10.1101/2022.05.06.490968 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval pigmentation in Bombyx mori ]]> https://biorxiv.org/content/10.1101/2022.05.07.490996v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@10e5708org.highwire.dtl.DTLVardef@73ec82org.highwire.dtl.DTLVardef@ac6094org.highwire.dtl.DTLVardef@f8a54e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tomihara, K. Andolfatto, P. Kiuchi, T. 2022-05-08 doi:10.1101/2022.05.07.490996 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis ]]> https://biorxiv.org/content/10.1101/2022.05.07.491015v1?rss=1 Huszar, R. Zhang, Y. Blockus, H. Buzsaki, G. 2022-05-08 doi:10.1101/2022.05.07.491015 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. ]]> https://biorxiv.org/content/10.1101/2022.05.09.490778v1?rss=1 Feng, Y. Neme, R. Beh, L. Y. Chen, X. Braun, J. Lu, M. W. Landweber, L. F. 2022-05-10 doi:10.1101/2022.05.09.490778 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Reproducibility of in-vivo electrophysiological measurements in mice ]]> https://biorxiv.org/content/10.1101/2022.05.09.491042v1?rss=1 The International Brain Laboratory, Banga, K. Benson, J. Bonacchi, N. Bruijns, S. A. Campbell, R. Chapuis, G. A. Churchland, A. K. Davatolhagh, M. F. Lee, H. D. Faulkner, M. Steinmetz, N. A. Paninski, L. Taheri, M. Roth, N. 2022-05-09 doi:10.1101/2022.05.09.491042 Cold Spring Harbor Laboratory Press 2022-05-09 <![CDATA[ Ocular and Facial Far-UVC Doses from Ceiling-Mounted 222 nm Far-UVC Fixtures ]]> https://biorxiv.org/content/10.1101/2022.05.09.491217v1?rss=1 Duncan, M. A. Welch, D. Shuryak, I. Brenner, D. J. 2022-05-10 doi:10.1101/2022.05.09.491217 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2022.05.09.491239v1?rss=1 Du, D. X. Fitzpatrick, A. 2022-05-10 doi:10.1101/2022.05.09.491239 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Identification of a novel deFADding activity in 5' to 3' exoribonucleases ]]> https://biorxiv.org/content/10.1101/2022.05.10.491372v1?rss=1 Sharma, S. Yang, J. Doamekpor, S. K. Grudizen-Nogalska, E. Tong, L. Kiledjian, M. 2022-05-10 doi:10.1101/2022.05.10.491372 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Saccade-related modulation of oscillatory activity in primary auditory cortex ]]> https://biorxiv.org/content/10.1101/2022.05.10.491383v1?rss=1 Barczak, A. O'Connell, M. N. McGinnis, T. Mackin, K. Schroeder, C. E. Lakatos, P. 2022-05-11 doi:10.1101/2022.05.10.491383 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Accelerating the clock: Interconnected speedup of energetic and molecular dynamics during aging in cultured human cells ]]> https://biorxiv.org/content/10.1101/2022.05.10.491392v1?rss=1 100-fold hypermetabolic phenotype characterized by increased maintenance costs, and associated with increased mtDNA genome density, upregulation of senescence-associated extracellular secretion, and induction of maintenance-related transcriptional programs. 3) Finally, manipulating MR with mitochondria-targeted metabolic, genetic, and pharmacological perturbations predictably altered the molecular rate of aging, providing experimental evidence for the interplay of MR and aging in a human system. These data highlight the key role that the partitioning of energetic resources between growth and maintenance/repair processes plays in cellular aging, and converge with predictions of cross-species metabolic theory indicating that energy metabolism governs how human cells age. Significance StatementHow cells age is of fundamental importance to understanding the diversity of mammalian lifespans and the wide variation in human aging trajectories. By aging primary human fibroblasts over several months in parallel with multi-omics and energetic profiling, we find that as human cells age and progressively divide more slowly, surprisingly, they progressively consume energy faster. By manipulating cellular metabolic rates, we confirm that the higher the cellular metabolic rate, the faster cells experience telomere shortening and epigenetic aging - a speedup phenotype consistent with allometric scaling theory. By modeling robust energetic and molecular aging trajectories across donors and experimental conditions, we find that independent of cell division rates, molecular aging trajectories are predicted by the partitioning of the energy budget between growth and maintenance processes. These results integrate molecular and energetic drivers of aging and therefore have important long-term implications to understand biological aging phenomena ranging from cellular senescence to human longevity. ]]> Sturm, G. Bobba-Alves, N. Tumasian, R. A. Michelson, J. Ferrucci, L. Kempes, C. P. Picard, M. 2022-05-12 doi:10.1101/2022.05.10.491392 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology ]]> https://biorxiv.org/content/10.1101/2022.05.10.491406v1?rss=1 Manubens-Gil, L. Zhou, Z. Chen, H. Ramanathan, A. Liu, X. Liu, Y. Bria, A. Gillette, T. Ruan, Z. Yang, J. Radojevic, M. Zhao, T. Cheng, L. Qu, L. Liu, S. Bouchard, K. E. Gu, L. Cai, W. Ji, S. Roysam, B. Wang, C.-W. Yu, H. Sironi, A. Iascone, D. M. Zhou, J. Bas, E. Conde-Sousa, E. Aguiar, P. Li, X. Li, Y. Nanda, S. Wang, Y. Muresan, L. Fua, P. Ye, B. He, H.-y. Staiger, J. F. Peter, M. Cox, D. N. Simonneau, M. Oberlaender, M. Jefferis, G. Ito, K. Gonzalez-Bellido, P. Kim, J. Rubel, E. Cline, H. T. Zeng, H. Nern, A. Chiang, A.-S. Yao, J. Roskams, 2022-05-11 doi:10.1101/2022.05.10.491406 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Baseline control of optimal performance in recurrent neural networks ]]> https://biorxiv.org/content/10.1101/2022.05.11.491436v1?rss=1 Ogawa, S. Fumarola, F. Mazzucato, L. 2022-05-11 doi:10.1101/2022.05.11.491436 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Context-dependent transcriptional regulation by Drosophila Polycomb Response Elements ]]> https://biorxiv.org/content/10.1101/2022.05.11.491498v1?rss=1 Coleman, R. T. Struhl, G. 2022-05-11 doi:10.1101/2022.05.11.491498 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ SPACE-GM: geometric deep learning of disease-associated microenvironments from multiplex spatial protein profiles. ]]> https://biorxiv.org/content/10.1101/2022.05.12.491707v1?rss=1 Wu, Z. Trevino, A. E. Wu, E. Swanson, K. Kim, H. J. D'Angio, H. B. Preska, R. Charville, G. W. Dalerba, P. D. Egloff, A. M. Uppaluri, R. Duvvuri, U. Mayer, A. T. Zou, J. 2022-05-13 doi:10.1101/2022.05.12.491707 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Integration of gene expression data in Bayesian association analysis of rare variants ]]> https://biorxiv.org/content/10.1101/2022.05.13.491893v1?rss=1 Zhong, G. Choi, Y. A. Shen, Y. 2022-05-15 doi:10.1101/2022.05.13.491893 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ tRNA Methylation Resolves Codon Usage Bias at the Limit of Cell Viability ]]> https://biorxiv.org/content/10.1101/2022.05.14.491930v1?rss=1 Masuda, I. Yamaki, Y. Detroja, R. Tagore, S. Moore, H. Maharjan, S. Nakano, Y. Christian, T. Matsubara, R. Lowe, T. M. Frenkel-Morgenstern, M. Hou, Y.-M. 2022-05-14 doi:10.1101/2022.05.14.491930 Cold Spring Harbor Laboratory Press 2022-05-14 <![CDATA[ Bayesian statistics improves biological interpretability of metabolomics data from human cohorts ]]> https://biorxiv.org/content/10.1101/2022.05.17.492312v1?rss=1 Brydges, C. Che, X. Lipkin, W. I. Fiehn, O. 2022-05-19 doi:10.1101/2022.05.17.492312 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Jak2V617F Reversible Activation Shows an Essential Requirement for Jak2V617F in Myeloproliferative Neoplasms ]]> https://biorxiv.org/content/10.1101/2022.05.18.492332v1?rss=1 Dunbar, A. Bowman, R. L. Park, Y. Izzo, F. Myers, R. M. Karzai, A. Jun Kim, W. Fernandez Maestre, I. Waarts, M. R. Nazir, A. Xiao, W. Brodsky, M. Farina, M. Cai, L. Cai, S. F. Wang, B. An, W. Yang, J. L. Mowla, S. Eisman, S. E. Mishra, T. Houston, R. Guzzardi, E. Martinez Benitez, A. R. Viny, A. Koche, R. Landau, D. A. Levine, R. L. 2022-05-18 doi:10.1101/2022.05.18.492332 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Sparse RNNs can support high-capacity classification ]]> https://biorxiv.org/content/10.1101/2022.05.18.492540v1?rss=1 Turcu, D. Abbott, L. 2022-05-19 doi:10.1101/2022.05.18.492540 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Neural learning rules for generating flexible predictions and computing the successor representation ]]> https://biorxiv.org/content/10.1101/2022.05.18.492543v1?rss=1 Fang, C. Aronov, D. Abbott, L. F. Mackevicius, E. 2022-05-19 doi:10.1101/2022.05.18.492543 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ The regulatory landscapes of human ovarian ageing ]]> https://biorxiv.org/content/10.1101/2022.05.18.492547v1?rss=1 Suh, Y. Jin, C. Wang, X. Hudgins, A. Gamliel, A. Pei, M. Kim, S. Contreras, D. Hoeijmakers, J. Campisi, J. Lobo, R. Williams, Z. Rosenfeld, M. G. 2022-05-19 doi:10.1101/2022.05.18.492547 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ A comparative study of structural variant calling strategies using the Alzheimer's Disease Sequencing Project's whole genome family data ]]> https://biorxiv.org/content/10.1101/2022.05.19.492472v1?rss=1 900 bp. We validated 83.0% (88/106) and 72.5% (37/51) of calls made by Scalpel and Parliament, respectively. Eleven deletions called by both Parliament and Scalpel in the 101-900 bin were tested and all were confirmed by Sanger sequencing. ConclusionsWe developed a flexible protocol to assess the quality of deletion detection across a wide range of sizes. We also generated a truth set of Sanger sequencing validated deletions with precise breakpoints covering a wide spectrum of sizes between 1 and 17,000 bp. ]]> Malamon, J. S. Farrell, J. J. Xia, L. C. Dombroski, B. A. Lee, W.-P. Das, R. G. Vardarajan, B. N. Way, J. Kuzma, A. B. Valladares, O. Leung, Y. Y. Scanlon, A. Lopez, I. A. B. Brehony, J. Worley, K. C. Zhang, N. R. Wang, L.-S. Farrer, L. A. Schellenberg, G. D. 2022-05-20 doi:10.1101/2022.05.19.492472 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Host adaptation drives genetic diversity in a vector-borne disease system ]]> https://biorxiv.org/content/10.1101/2022.05.19.492734v1?rss=1 Combs, M. A. Tufts, D. M. Adams, B. Lin, Y.-P. Kolokotronis, S.-O. Diuk-Wasser, M. A. 2022-05-19 doi:10.1101/2022.05.19.492734 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ A global atlas of substrate specificities for the human serine/threonine kinome ]]> https://biorxiv.org/content/10.1101/2022.05.22.492882v1?rss=1 Johnson, J. L. Yaron, T. M. Huntsman, E. M. Kerelsky, A. Song, J. Regev, A. Lin, T.-Y. Liberatore, K. Cizin, D. M. Cohen, B. M. Vasan, N. Ma, Y. Krismer, K. Torres Robles, J. van de Kooij, B. van Vlimmeren, A. E. Andree-Busch, N. Käufer, N. F. Dorovkov, M. V. Ryazanov, A. G. Takagi, Y. Kastenhuber, E. R. Goncalves, M. D. Elemento, O. Taatjes, D. J. Maucuer, A. Yamashita, A. Degterev, A. Blenis, J. Hornbeck, P. V. Turk, B. E. Yaffe, M. B. Cantley, L. C. 2022-05-22 doi:10.1101/2022.05.22.492882 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ High-throughput deep learning variant effect prediction with Sequence UNET ]]> https://biorxiv.org/content/10.1101/2022.05.23.493038v1?rss=1 Dunham, A. S. Beltrao, P. AlQuraishi, M. 2022-05-24 doi:10.1101/2022.05.23.493038 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ A critical role for touch neurons in a skin-brain pathway for stress resilience ]]> https://biorxiv.org/content/10.1101/2022.05.23.493062v1?rss=1 Schaffler, M. D. Johnson, M. Hing, B. Kahler, P. Hultman, I. Srivastava, S. Arnold, J. Blendy, J. N. Hultman, R. Abdus-Saboor, I. 2022-05-23 doi:10.1101/2022.05.23.493062 Cold Spring Harbor Laboratory Press 2022-05-23 <![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[ Anti-chemokine antibodies after SARS-CoV-2 infection correlate with favorable disease course ]]> https://biorxiv.org/content/10.1101/2022.05.23.493121v1?rss=1 Muri, J. Cecchinato, V. Cavalli, A. Shanbhag, A. A. Matkovic, M. Biggiogero, M. Maida, P. A. Toscano, C. Ghovehoud, E. Danelon-Sargenti, G. Gong, T. Piffaretti, P. Bianchini, F. Crivelli, V. Podesvova, L. Pedotti, M. Jarrossay, D. Sgrignani, J. Thelen, S. Uhr, M. Bernasconi, E. Rauch, A. Manzo, A. Ciurea, A. Rocchi, M. B. L. Varani, L. Moser, B. Thelen, M. Garzoni, C. Franzetti-Pellanda, A. Uguccioni, M. Robbiani, D. F. 2022-05-23 doi:10.1101/2022.05.23.493121 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Saccadic modulation of neural excitability in auditory areas of the neocortex ]]> https://biorxiv.org/content/10.1101/2022.05.24.493336v1?rss=1 Leszczynski, M. Bickel, S. Nentwich, M. Russ, B. E. Parra, L. Lakatos, P. Mehta, A. Schroeder, C. E. 2022-05-26 doi:10.1101/2022.05.24.493336 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ γ-Protocadherins control synapse formation and peripheral branching of touch sensory neurons ]]> https://biorxiv.org/content/10.1101/2022.05.25.493080v1?rss=1 Meltzer, S. Comeau, K. Chirila, A. Osei-Asante, E. DeLisle, M. Zhang, Q. Kalish, B. T. Tasnim, A. Huey, E. Fuller, L. C. Flaherty, E. K. Lefebvre, J. L. Maniatis, T. Garrett, A. M. Weiner, J. A. Ginty, D. D. 2022-05-25 doi:10.1101/2022.05.25.493080 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Phylogenomic diversity elucidates mechanistic insights into Lyme borreliae host association ]]> https://biorxiv.org/content/10.1101/2022.05.25.493352v1?rss=1 Combs, M. A. Marcinkiewicz, A. L. Dupuis, A. P. Davis, A. D. Lederman, P. Nowak, T. A. Stout, J. L. Strle, K. Fingerle, V. Margos, G. Ciota, A. T. Diuk-Wasser, M. A. Kolokotronis, S.-O. Lin, Y.-P. 2022-05-25 doi:10.1101/2022.05.25.493352 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ SARS-CoV-2 Omicron BA.2.12.1, BA.4, and BA.5 subvariants evolved to extend antibody evasion ]]> https://biorxiv.org/content/10.1101/2022.05.26.493517v1?rss=1 Wang, Q. Guo, Y. Iketani, S. Li, Z. Mohri, H. Wang, M. Yu, J. Bowen, A. D. Chan, J. Y. Shah, J. G. Nguyen, N. Meyers, K. Yin, M. T. Sobieszczyk, M. E. Sheng, Z. Huang, Y. Liu, L. Ho, D. 2022-05-26 doi:10.1101/2022.05.26.493517 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Taste cues elicit prolonged modulation of feeding behavior in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.05.27.493715v1?rss=1 Deere, J. U. Devineni, A. V. 2022-05-28 doi:10.1101/2022.05.27.493715 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Unifying model for three forms of contextual modulation including feedback input from higher visual areas ]]> https://biorxiv.org/content/10.1101/2022.05.27.493753v1?rss=1 Di santo, S. Dipoppa, M. Keller, A. Roth, M. Scanziani, M. Miller, K. D. 2022-05-28 doi:10.1101/2022.05.27.493753 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Potent and pan-neutralization of SARS-CoV-2 variants of concern by DARPins ]]> https://biorxiv.org/content/10.1101/2022.05.30.493765v1?rss=1 Chonira, V. K. Kwon, Y.-D. Gorman, J. Case, J. B. Ku, Z. Simeon, R. Casner, R. G. Harris, D. R. Olia, A. S. Stevens, T. Shapiro, L. Boyd, H. Tsybovsky, Y. Krammer, F. Diamond, M. Kwong, P. D. An, Z. Chen, Z. 2022-05-31 doi:10.1101/2022.05.30.493765 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Radiation therapy promotes unsaturated fatty acids to maintain survival of glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.06.01.494338v1?rss=1 De Martino, M. Daviaud, C. Minns, H. E. Attarwala, N. Chen, Q. Dephoure, N. Gartrell, R. D. Laiakis, E. C. Vanpouille-Box, C. 2022-06-01 doi:10.1101/2022.06.01.494338 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Connectome-based predictive modeling of cognitive reserve using task-based functional connectivity ]]> https://biorxiv.org/content/10.1101/2022.06.01.494342v1?rss=1 Boyle, R. Connaughton, M. McGlinchey, E. Knight, S. P. De Looze, C. Carey, D. Stern, Y. Robertson, I. H. Kenny, R. A. Whelan, R. 2022-06-02 doi:10.1101/2022.06.01.494342 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ Normative values of neuromelanin-sensitive MRI signal in older adults obtained using a standard protocol for acquisition and analysis ]]> https://biorxiv.org/content/10.1101/2022.06.02.493125v1?rss=1 Al Haddad, R. Chamoun, M. Tardif, C. Guimond, S. Horga, G. Rosa-Neto, P. Cassidy, C. 2022-06-05 doi:10.1101/2022.06.02.493125 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes ]]> https://biorxiv.org/content/10.1101/2022.06.02.494568v1?rss=1 Feng, H. Lu, X.-J. Liu, L. Ustianenko, D. Zhang, C. 2022-06-02 doi:10.1101/2022.06.02.494568 Cold Spring Harbor Laboratory Press 2022-06-02 <![CDATA[ 7-UP: generating in silico CODEX from a small set of immunofluorescence markers ]]> https://biorxiv.org/content/10.1101/2022.06.03.494624v1?rss=1 Wu, E. Trevino, A. E. Wu, Z. Swanson, K. Kim, H. J. D'Angio, H. B. Preska, R. Charville, G. W. Dalerba, P. D. Duvvuri, U. Levi, J. Colevas, A. D. Bedi, N. Chang, S. Sunwoo, J. B. Mayer, A. T. Zou, J. 2022-06-05 doi:10.1101/2022.06.03.494624 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Epigenome-wide association study analysis of calorie restriction in humans, CALERIE™ Trial analysis ]]> https://biorxiv.org/content/10.1101/2022.06.03.494722v1?rss=1 Ramaker, M. E. Corcoran, D. L. Apsley, A. T. Kraus, V. B. Kraus, W. E. Kobor, M. S. Lin, D. T. Orenduff, M. C. Waziry, R. Huffman, K. M. Belsky, D. W. 2022-06-05 doi:10.1101/2022.06.03.494722 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization. ]]> https://biorxiv.org/content/10.1101/2022.06.04.494709v1?rss=1 Tuddenham, J. F. Taga, M. Haage, V. Roostaei, T. White, C. Lee, A. J. Fujita, M. Khairallah, A. Green, G. Hyman, B. Frosch, M. Hopp, S. Beach, T. G. Corboy, J. Habib, N. Klein, H.-U. Soni, R. K. Teich, A. F. Hickman, R. A. Alcalay, R. N. Shneider, N. Schneider, J. Sims, P. A. Bennet, D. A. Olah, M. Menon, V. De Jager, P. L. 2022-06-05 doi:10.1101/2022.06.04.494709 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Single-cell multi-omics defines the cell-type specific impact of splicing aberrations in human hematopoietic clonal outgrowths ]]> https://biorxiv.org/content/10.1101/2022.06.08.495292v1?rss=1 Gaiti, F. Chamely, P. Hawkins, A. G. Cortes-Lopez, M. Swett, A. D. Ganesan, S. Mouhieddine, T. H. Dai, X. Kluegel, L. Chen, C. Batta, K. Beaulaurier, J. Drong, A. W. Hickey, S. Dusaj, N. Mullokandov, G. Su, J. Chaligne, R. Juul, S. Harrington, E. Knowles, D. A. Wiseman, D. H. Ghobrial, I. M. Taylor, J. Abdel-Wahab, O. Landau, D. A. 2022-06-09 doi:10.1101/2022.06.08.495292 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ An Internal Model of Sensorimotor Context in Freely Swimming Electric Fish ]]> https://biorxiv.org/content/10.1101/2022.06.08.495343v1?rss=1 Wallach, A. Sawtell, N. B. 2022-06-12 doi:10.1101/2022.06.08.495343 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ AAV-mediated neuronal expression of a scFv antibody selective for Aβ oligomers protects synapses and rescues memory in Alzheimer models ]]> https://biorxiv.org/content/10.1101/2022.06.10.495369v1?rss=1 Selles, M. C. Fortuna, J. T. S. Cercato, M. C. Santos, L. E. Domett, L. Bitencourt, A. L. B. Carraro, M. F. Souza, A. S. Janickova, H. de Souza, J. M. Alves-Leon, S. Prado, V. F. Prado, M. A. M. Epstein, A. L. Salvetti, A. Arancio, O. Klein, W. L. Sebollela, A. De Felice, F. G. Jerusalinsky, D. A. Ferreira, S. T. 2022-06-15 doi:10.1101/2022.06.10.495369 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Notch2 signaling guides B cells away from germinal centers towards marginal zone B cell and plasma cell differentiation ]]> https://biorxiv.org/content/10.1101/2022.06.13.495961v1?rss=1 Babushku, T. Rane, S. Lechner, M. Zimber-Strobl, U. Strobl, L. J. 2022-06-17 doi:10.1101/2022.06.13.495961 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ CaV1.2 channelopathic mutations evoke diverse pathophysiological mechanisms ]]> https://biorxiv.org/content/10.1101/2022.06.13.495975v1?rss=1 Bamgboye, M. A. Herold, K. G. Vieira, D. C. O. Traficante, M. K. Rogers, P. J. Ben-Johny, M. Dick, I. E. 2022-06-16 doi:10.1101/2022.06.13.495975 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Similar striatal activity exerts different control over automatic and flexible motor sequences ]]> https://biorxiv.org/content/10.1101/2022.06.13.495989v1?rss=1 Mizes, K. G. C. Lindsey, J. W. Escola, S. Olveczky, B. P. 2022-06-14 doi:10.1101/2022.06.13.495989 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction ]]> https://biorxiv.org/content/10.1101/2022.06.14.495937v1?rss=1 Salcedo, A. Tarabichi, M. Buchanan, A. Espiritu, S. M. G. Zhang, H. Zhu, K. Yang, T.-H. O. Leshchiner, I. Anastassiou, D. Guan, Y. Jang, G. H. Haase, K. Deshwar, A. G. Zou, W. Umar, I. Dentro, S. Wintersinger, J. A. Chiotti, K. Demeulemeester, J. Jolly, C. Scyza, L. Ko, M. PCAWG-11 Working Group, SMC-Het Participants, Wedge, D. C. Morris, Q. D. Ellrot, K. Van Loo, P. Boutros, P. C. 2022-06-15 doi:10.1101/2022.06.14.495937 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[ Glutamatergic neuron types in the amygdala of the urodele amphibian Pleurodeles waltl ]]> https://biorxiv.org/content/10.1101/2022.06.15.496313v1?rss=1 Deryckere, A. Woych, J. Jaeger, E. C. B. Tosches, M. A. 2022-06-17 doi:10.1101/2022.06.15.496313 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Engineered bacteria recruit and orchestrate anti-tumor immunity ]]> https://biorxiv.org/content/10.1101/2022.06.16.496462v1?rss=1 Savage, T. M. Vincent, R. L. Rae, S. S. Huang, L. H. Ahn, A. Pu, K. Li, F. Coker, C. Danino, T. Arpaia, N. 2022-06-17 doi:10.1101/2022.06.16.496462 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Mcm2 promotes stem cell differentiation via its ability to bind H3-H4 ]]> https://biorxiv.org/content/10.1101/2022.06.16.496513v1?rss=1 Xu, X. Hua, X. Brown, K. Ren, X. Zhang, Z. 2022-06-17 doi:10.1101/2022.06.16.496513 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Generating New Musical Preferences from Hierarchical Mapping of Predictions to Reward ]]> https://biorxiv.org/content/10.1101/2022.06.17.496615v1?rss=1 Kathios, N. Sachs, M. E. Zhang, E. Ou, Y. Loui, P. 2022-06-18 doi:10.1101/2022.06.17.496615 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Timing and causes of the evolution of the germline mutation spectrum in humans ]]> https://biorxiv.org/content/10.1101/2022.06.17.496622v1?rss=1 TTC mutations in Europeans and novel signals of divergence in C>G and T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa, in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations, and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects on de novo mutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors--genetic modifiers or environmental exposures--must have had a non-negligible impact on the human mutation landscape. ]]> Gao, Z. Zhang, Y. Przeworski, M. Moorjani, P. 2022-06-18 doi:10.1101/2022.06.17.496622 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Semantic novelty modulates neural responses to visual change across the human brain ]]> https://biorxiv.org/content/10.1101/2022.06.20.496467v1?rss=1 Nentwich, M. Leszczynski, M. Russ, B. E. Hirsch, L. Markowitz, N. Sapru, K. Schroeder, C. E. Mehta, A. Bickel, S. Parra, L. C. 2022-06-22 doi:10.1101/2022.06.20.496467 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Resource-Rational Account of Sequential Effects in Human Prediction ]]> https://biorxiv.org/content/10.1101/2022.06.20.496900v1?rss=1 Prat-Carrabin, A. Meyniel, F. da Silveira, R. A. 2022-06-22 doi:10.1101/2022.06.20.496900 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Spatial regulation of Drosophila ovarian Follicle Stem Cell division rates and cell cycle transitions ]]> https://biorxiv.org/content/10.1101/2022.06.22.497017v1?rss=1 Melamed, D. Choi, A. Reilein, A. Kalderon, D. 2022-06-26 doi:10.1101/2022.06.22.497017 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome ]]> https://biorxiv.org/content/10.1101/2022.06.22.497108v1?rss=1 Hassan, A. Byju, S. Freitas, F. C. Roc, C. Pender, N. Nguyen, K. Kimbrough, E. M. Mattingly, J. Gonzalez, R. L. Oliveira, R. J. d. Dunham, C. M. Whitford, P. C. 2022-06-22 doi:10.1101/2022.06.22.497108 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Targeted cortical stimulation reveals principles of cortical contextual interactions ]]> https://biorxiv.org/content/10.1101/2022.06.22.497254v1?rss=1 Wang, S. Palmigiano, A. Miller, K. D. Van Hooser, S. D. 2022-06-24 doi:10.1101/2022.06.22.497254 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ The Functional Landscape of SARS-CoV-2 3CL Protease ]]> https://biorxiv.org/content/10.1101/2022.06.23.497404v1?rss=1 Iketani, S. Hong, S. J. Sheng, J. Bahari, F. Culbertson, B. Atanaki, F. F. Aditham, A. K. Kratz, A. F. Luck, M. I. Tian, R. Goff, S. P. Montazeri, H. Sabo, Y. Ho, D. D. Chavez, A. 2022-06-24 doi:10.1101/2022.06.23.497404 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ Hepatocyte Rap1a Contributes To Obesity- and Statin-Associated Hyperglycemia ]]> https://biorxiv.org/content/10.1101/2022.06.25.497009v1?rss=1 Wang, Y. Spolitu, S. Zadroga, J. A. Sarecha, A. K. Ozcan, L. 2022-06-26 doi:10.1101/2022.06.25.497009 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Rad51 and Dmc1 have similar tolerance for mismatches in yeast meiosis ]]> https://biorxiv.org/content/10.1101/2022.06.26.497685v1?rss=1 Haber, J. E. Choi, J. Xue, L. L. Cao, Y. Kim, J. 2022-06-28 doi:10.1101/2022.06.26.497685 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Determination of expression profiles for Drosophila ovarian Follicle Stem Cells (FSCs) using single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2022.06.27.497544v1?rss=1 Dong, Z. Pang, L. Liu, Z. Sheng, Y. Thibault, X. Reilein, A. Kalderon, D. Huang, J. 2022-06-27 doi:10.1101/2022.06.27.497544 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Single nuclei RNAseq analysis of HD mouse models and human brain reveals impaired oligodendrocyte maturation and potential role for thiamine metabolism ]]> https://biorxiv.org/content/10.1101/2022.06.27.497613v1?rss=1 Lim, R. G. Al-Dalahmah, O. Wu, J. M. Gold, M. P. Reidling, J. C. Tang, G. Adam, M. Dansu, D. K. Park, H.-J. Casaccia, P. Miramontes, R. Reyes-Ortiz, A. M. Lau, A. Khan, F. Paryani, F. Tang, A. Ofori, K. N. A. Miyoshi, E. Michael, N. Geller, N. Flowers, X. E. Vonsattel, J. P. Davidson, S. Menon, V. Swarup, V. Fraenkel, E. Goldman, J. E. Thompson, L. M. 2022-06-30 doi:10.1101/2022.06.27.497613 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Use of a ubiquitous gene-editing tool in budding yeast causes off-target repression of neighboring gene protein synthesis ]]> https://biorxiv.org/content/10.1101/2022.06.27.497784v1?rss=1 Powers, E. N. Llacsahuanga Allcca, L. Doron-Mandel, E. Kim Kim, J. Jovanovic, M. Brar, G. A. 2022-06-29 doi:10.1101/2022.06.27.497784 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Hepatocytes deficient in nuclear envelope protein lamina-associated polypeptide 1 are an ideal mammalian system to study intranuclear lipid droplets ]]> https://biorxiv.org/content/10.1101/2022.06.27.497855v1?rss=1 Ostlund, C. Hernandez-Ono, A. Turk, S. J. Dauer, W. T. Ginsberg, H. N. Worman, H. J. Shin, J.-Y. 2022-06-28 doi:10.1101/2022.06.27.497855 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ High-resolution magic angle spinning NMR of KcsA in liposomes: the highly mobile C-terminus ]]> https://biorxiv.org/content/10.1101/2022.06.28.498019v1?rss=1 McDermott, A. E. Howarth, G. S. 2022-06-29 doi:10.1101/2022.06.28.498019 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ CoxMKF: A Knockoff Filter for High-Dimensional Mediation Analysis with a Survival Outcome in Epigenetic Studies ]]> https://biorxiv.org/content/10.1101/2022.06.29.498077v1?rss=1 Tian, P. Yao, M. Huang, T. Liu, Z. 2022-07-02 doi:10.1101/2022.06.29.498077 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Cell type- and state- resolved immune transcriptomic profiling identifies glucocorticoid-responsive molecular defects in multiple sclerosis T cells ]]> https://biorxiv.org/content/10.1101/2022.06.29.498195v1?rss=1 Roostaei, T. Sabrin, A. Kivisakk, P. McCabe, C. Nejad, P. Felsky, D. Touil, H. Vlachos, I. Hui, D. Fransson, J. Patsopoulos, N. A. Kuchroo, V. K. Zujovic, V. Weiner, H. L. Klein, H.-U. De Jager, P. L. 2022-07-02 doi:10.1101/2022.06.29.498195 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Nuclear architecture protein Distal antenna balances genome-binding and phase-separation properties to regulate neuroblast competence ]]> https://biorxiv.org/content/10.1101/2022.06.30.498164v1?rss=1 Benchorin, G. Li, M. J. Cho, R. J. Hu, Y. Kohwi, M. 2022-06-30 doi:10.1101/2022.06.30.498164 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Dendrite architecture determines mitochondrial distribution patterns in vivo ]]> https://biorxiv.org/content/10.1101/2022.07.01.497972v1?rss=1 Donovan, E. J. Agrawal, A. Liberman, N. Kalai, J. Chua, J. N. Koslover, E. F. Barnhart, E. L. 2022-07-03 doi:10.1101/2022.07.01.497972 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Rotating Frame Relaxation for Magic Angle Spinning Solid State NMR, A Promising Tool for Characterizing Biopolymer Motion ]]> https://biorxiv.org/content/10.1101/2022.07.02.498561v1?rss=1 McDermott, A. E. Keeler, E. G. 2022-07-03 doi:10.1101/2022.07.02.498561 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Uncertainty alters the balance between incremental learning and episodic memory ]]> https://biorxiv.org/content/10.1101/2022.07.05.498877v1?rss=1 Nicholas, J. Daw, N. D. Shohamy, D. 2022-07-06 doi:10.1101/2022.07.05.498877 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Human-specific progenitor sub-domain contributes to extended neurogenesis and increased motor neuron production ]]> https://biorxiv.org/content/10.1101/2022.07.05.498885v1?rss=1 1000-fold more neurons in the human central nervous system. Expansion of human neocortex has been in part attributed to the population of outer radial glia and amplifying progenitors that increase the output of neurogenic lineages. However, outer radial glia appear to be absent in many regions of the developing human nervous system, prompting us to search for alternative populations of progenitors that contribute to the expansion of human neurogenesis in one such region - the developing spinal cord. To this end, we performed high-temporal resolution single-cell expression analysis of human and mouse motor neuron progenitors generated from pluripotent stem cells in vitro. Alignment of human and mouse data using canonical correlation analysis identified "human-specific" progenitor clusters characterized by early co-expression of NKX2-2 and OLIG2 that lacked an orthologous murine counterpart. A matching progenitor population has been previously described in the human embryonic spinal cord1, but its function remained unknown. Our lineage tracing analysis demonstrates that these cells function as ventral motor neuron progenitors (vpMNs), but in contrast to classical pMNs, vpMNs exhibit increased Notch activity and generate motor neurons in a delayed and protracted manner. Concomitantly, vpMNs undergo more rounds of cell division before undergoing neurogenesis, leading to ~2-fold increase in total motor neuron output, and contributing preferentially to later-born, limb-innervating motor neuron subtypes. Thus, instead of relying on transit-amplifying progenitors, human spinal cord evolved a novel progenitor subdomain that extends timescales and expands output of human motor neurogenesis. ]]> Jang, S. Gunmit, E. Wichterle, H. 2022-07-05 doi:10.1101/2022.07.05.498885 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Molecular basis for the role of disulfide-linked αCTs in the activation of insulin-like growth factor 1 receptor and insulin receptor ]]> https://biorxiv.org/content/10.1101/2022.07.06.498988v1?rss=1 Li, J. Wu, J. Bai, X.-c. Choi, E. 2022-07-06 doi:10.1101/2022.07.06.498988 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Highly fucosylated N-glycans at the synaptic vesicle and neuronal plasma membrane ]]> https://biorxiv.org/content/10.1101/2022.07.06.499060v1?rss=1 Bradberry, M. M. Peters-Clarke, T. M. Chapman, E. R. Coon, J. J. 2022-07-07 doi:10.1101/2022.07.06.499060 Cold Spring Harbor Laboratory Press 2022-07-07 <![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[ Rescue of alveolar wall liquid secretion blocks fatal lung injury by influenza-staphylococcal coinfection ]]> https://biorxiv.org/content/10.1101/2022.07.07.499169v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@180caceorg.highwire.dtl.DTLVardef@82ce71org.highwire.dtl.DTLVardef@1bf9358org.highwire.dtl.DTLVardef@628fec_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tang, S. De Jesus, A. C. Chavez, D. Suthakaran, S. Moore, S. K. L. Rathnasinghe, R. Schotsaert, M. Bhattacharya, J. Hook, J. L. 2022-07-08 doi:10.1101/2022.07.07.499169 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Loss of FOXP3 function causes expansion of two pools of autoreactive T cells in patients with IPEX syndrome. ]]> https://biorxiv.org/content/10.1101/2022.07.10.499494v1?rss=1 Borna, S. Lee, E. Lakshmanan, U. Mavers, M. Narula, M. Ramachandran, A. Baker, J. Schulze, J. Olek, S. Marois, L. Gernez, Y. Bhatia, M. Bertaina, A. Roncarolo, M. G. Meffre, E. Bacchetta, R. 2022-07-11 doi:10.1101/2022.07.10.499494 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Homeostatic responses to hypoxia by the carotid body and adrenal medulla are based on mutual antagonism between HIF-1α and HIF-2α ]]> https://biorxiv.org/content/10.1101/2022.07.11.499380v1?rss=1 Yuan, G. Peng, Y.-J. Reddy, V. D. Makarenko, V. Nanduri, J. Khan, S. A. Garcia, J. A. Kumar, G. K. Semenza, G. L. Prabhakar, N. R. 2022-07-11 doi:10.1101/2022.07.11.499380 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Mechanisms underlying reshuffling of visual responses by optogenetic stimulation in mice and monkeys ]]> https://biorxiv.org/content/10.1101/2022.07.13.499597v1?rss=1 Sanzeni, A. Palmigiano, A. Nguyen, T. H. Luo, J. Nassi, J. J. Reynolds, J. H. Histed, M. H. Miller, K. D. Brunel, N. 2022-07-15 doi:10.1101/2022.07.13.499597 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ Multiset correlation and factor analysis enables exploration of multi-omic data ]]> https://biorxiv.org/content/10.1101/2022.07.18.500246v1?rss=1 Brown, B. C. Wang, C. L. Kasela, S. Aguet, F. Nachun, D. C. Taylor, K. D. Tracy, R. P. Durda, P. Lui, Y. Johnson, W. C. Van Den Berg, D. Gupta, N. Gabriel, S. Smith, J. D. Gerzten, R. Clish, C. Wong, Q. Papanicolau, G. Blackwell, T. W. Rotter, J. I. Rich, S. S. Ardlie, K. G. Knowles, D. A. Lappalainen, T. 2022-07-20 doi:10.1101/2022.07.18.500246 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Versatile Multiple Object Tracking in Sparse 2D/3D Videos Via Diffeomorphic Image Registration ]]> https://biorxiv.org/content/10.1101/2022.07.18.500485v1?rss=1 Yu, J. Nejatbakhsh, A. Torkashvand, M. Gangadharan, S. Seyedolmohadesin, M. Kim, J. Paninski, L. Venkatachalam, V. 2022-07-20 doi:10.1101/2022.07.18.500485 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Event integration and temporal pattern separation: how hierarchical knowledge emerges in hippocampal subfields through learning ]]> https://biorxiv.org/content/10.1101/2022.07.18.500527v1?rss=1 Bein, O. Davachi, L. 2022-07-20 doi:10.1101/2022.07.18.500527 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Causal feature selection using a knowledge graph combining structured knowledge from the biomedical literature and ontologies: a use case studying depression as a risk factor for Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.07.18.500549v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@1c3f417org.highwire.dtl.DTLVardef@1ce1703org.highwire.dtl.DTLVardef@148d645org.highwire.dtl.DTLVardef@eb55e7_HPS_FORMAT_FIGEXP M_FIG C_FIG Statement of SignificanceO_ST_ABSProblemC_ST_ABSExtensive knowledge is required to identify confounders for estimating total effects in observational settings. The literature is too vast for humans to process. Bias may remain from not adjusting on unknown confounders or erroneously adjusting on a collider or mediator. What is already knownStructured literature-derived knowledge is often useful but is noisy. What this papers addsWe present a biomedical knowledge graph linking literature-derived and ontology-ground knowledge of biochemical processes with definitions of clinical disease. We search the KG to distill a model for estimating the (total) effect of depression on Alzheimers disease from observational data. ]]> Malec, S. A. Taneja, S. B. Albert, S. M. Shaaban, C. E. Karim, H. T. Callahan, T. J. Munro, P. W. Levine, A. S. Boyce, R. D. 2022-07-20 doi:10.1101/2022.07.18.500549 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Epinephrine inhibits PI3K alpha via the Hippo kinases. ]]> https://biorxiv.org/content/10.1101/2022.07.19.500601v1?rss=1 Lin, T.-Y. Ramsamooj, S. Liberatore, K. Lantier, L. Vasan, N. Karukurichi, K. Hwang, S.-K. Kesicki, E. A. Kastenhuber, E. R. Wiederhold, T. Yaron, T. M. Zhu, M. Ma, Y. Paddock, M. N. Zhang, G. Hopkins, B. D. McGuinness, O. Schwartz, R. E. Cantley, L. C. Johnson, J. L. Goncalves, M. D. 2022-07-20 doi:10.1101/2022.07.19.500601 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ A unified model for the surveillance of translation in diverse noncoding sequences ]]> https://biorxiv.org/content/10.1101/2022.07.20.500724v1?rss=1 Kesner, J. S. Chen, Z. Aparicio, A. A. Wu, X. 2022-07-21 doi:10.1101/2022.07.20.500724 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Adaptive decision making depends on pupil-linked arousal in rats performing tactile discrimination tasks ]]> https://biorxiv.org/content/10.1101/2022.07.20.500875v1?rss=1 Narasimhan, S. Schriver, B. J. Wang, Q. 2022-07-22 doi:10.1101/2022.07.20.500875 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Unbiased Classification of the Human Brain Proteome Resolves Distinct Clinical and Pathophysiological Subtypes of Cognitive Impairment ]]> https://biorxiv.org/content/10.1101/2022.07.22.501017v1?rss=1 600 dorsolateral prefrontal cortex tissues from Religious Orders Study and Rush Memory and Aging Project participants with clinical diagnoses of no cognitive impairment, mild cognitive impairment (MCI), and AD dementia. Unbiased classification of MCI and AD cases based on individual proteomic profiles resolved three classes with expression differences across numerous cell types and biological ontologies. Two classes displayed molecular signatures atypical of those previously observed in AD neurodegeneration, such as elevated synaptic and decreased inflammatory markers. In one class, these atypical proteomic features were associated with clinical and pathological hallmarks of cognitive resilience. These results promise to better define disease heterogeneity within AD and meaningfully impact its diagnostic and therapeutic precision. ]]> Higginbotham, L. A. Carter, E. K. Dammer, E. B. Haque, R. U. Johnson, E. C. B. Duong, D. Yin, L. De Jager, P. L. Bennett, D. A. Lah, J. J. Levey, A. I. Seyfried, N. T. 2022-07-25 doi:10.1101/2022.07.22.501017 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ SARS-CoV-2 omicron variants succumb in vitro to Artemisia annua hot water extracts ]]> https://biorxiv.org/content/10.1101/2022.07.22.501141v1?rss=1 Nair, M. S. Huang, Y. Weathers, P. 2022-07-25 doi:10.1101/2022.07.22.501141 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Epigenome-wide meta-analysis of BMI in nine population-based cohorts: examining the utility of methylation as a biomarker of BMI ]]> https://biorxiv.org/content/10.1101/2022.07.26.498234v1?rss=1 Do, W. L. Sun, D. Meeks, K. A. Dugue, P.-A. Demerath, E. W. Guan, W. Li, S. Chen, W. Milne, R. L. Adeyemo, A. Agyemang, C. Nassir, R. Manson, J. E. Shadyab, A. H. Hou, L. Horvath, S. Assimes, T. L. Bhatti, P. Jordahl, K. M. Baccarelli, A. A. Smith, A. Staimez, L. R. Stein, A. D. Whitsel, E. A. Narayan, K. M. V. Conneely, K. N. 2022-07-27 doi:10.1101/2022.07.26.498234 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Rhesus Infant Nervous Temperament Predicts Peri-Adolescent Central Amygdala Metabolism & Behavioral Inhibition Measured by a Machine-Learning Approach ]]> https://biorxiv.org/content/10.1101/2022.07.26.501512v1?rss=1 Holley, D. Campos, L. J. Zhang, Y. Capitanio, J. P. Fox, A. S. 2022-07-27 doi:10.1101/2022.07.26.501512 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Tenotomy-induced muscle atrophy is sex-specific and independent of NFκB ]]> https://biorxiv.org/content/10.1101/2022.07.26.501541v1?rss=1 Meyer, G. A. Thomopoulos, S. Abu-Amer, Y. Shen, K. 2022-07-27 doi:10.1101/2022.07.26.501541 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Germ-cell specific eIF4E1B regulates maternal RNA translation to ensure zygotic genome activation ]]> https://biorxiv.org/content/10.1101/2022.07.27.501690v1?rss=1 Yang, G. Xin, Q. Feng, I. Dean, J. 2022-07-29 doi:10.1101/2022.07.27.501690 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Perinatal correlated retinal activity is required for the wiring of visual axons in non-image forming nuclei ]]> https://biorxiv.org/content/10.1101/2022.07.27.501692v1?rss=1 Herrera, E. Negueruela, S. Morenilla-Palao, C. Herrera, M. Coca, Y. Florez-Paz, D. M. Lopez-Cascales, M. T. Gomis, A. 2022-07-29 doi:10.1101/2022.07.27.501692 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Proton and alpha radiation-induced mutational profiles in human cells ]]> https://biorxiv.org/content/10.1101/2022.07.29.501997v1?rss=1 Delhomme, T. M. Buonanno, M. Grilj, V. Biayna, J. Supek, F. 2022-07-29 doi:10.1101/2022.07.29.501997 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.07.31.502235v1?rss=1 Wang, Q. Iketani, S. Li, Z. Guo, Y. Yeh, A. Y. Liu, M. Yu, J. Sheng, Z. Huang, Y. Liu, L. Ho, D. D. 2022-08-01 doi:10.1101/2022.07.31.502235 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Free energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity ]]> https://biorxiv.org/content/10.1101/2022.08.01.502301v1?rss=1 Sergeeva, A. P. Katsamba, P. S. Sampson, J. M. Bahna, F. Mannepalli, S. Morano, N. C. Shapiro, L. Friesner, R. A. Honig, B. 2022-08-01 doi:10.1101/2022.08.01.502301 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display ]]> https://biorxiv.org/content/10.1101/2022.08.01.502334v1?rss=1 Li, A. Voleti, R. Lee, M. Gagoski, D. Shah, N. H. 2022-08-01 doi:10.1101/2022.08.01.502334 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Profile of the somatic mutational landscape in breast tumors from Hispanic/Latina women ]]> https://biorxiv.org/content/10.1101/2022.08.01.502349v1?rss=1 Ding, Y. C. Song, H. Adamson, A. Schmolze, D. Hu, D. Huntsman, S. Steele, L. Patrick, C. Hernandez, N. Adams, C. D. Fejerman, L. Gardner, K. L. Napoles, A. M. Perez-Stable, E. J. Weitzel, J. N. Bengtsson, H. Huang, F. W. Neuhausen, S. L. Ziv, E. 2022-08-03 doi:10.1101/2022.08.01.502349 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Effects of fire regime on birds community in an Amazonian savanna ]]> https://biorxiv.org/content/10.1101/2022.08.01.502386v1?rss=1 Coelho, L. A. Ritter, C. d. Lima, A. Cintra, R. Magnusson, W. Sanaiotti, T. 2022-08-03 doi:10.1101/2022.08.01.502386 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ A high-speed, modular display system for diverse neuroscience applications ]]> https://biorxiv.org/content/10.1101/2022.08.02.502550v1?rss=1 Isaacson, M. Ferguson, L. Loesche, F. Ganguly, I. Chen, J. Chiu, A. Liu, J. Dickson, W. Reiser, M. 2022-08-03 doi:10.1101/2022.08.02.502550 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ FAK-SFK Signaling Integrates ECM Rigidity Sensing and Engagement of ERBB2 to Activate YAP and Promote Invasive Growth and Metastasis in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.08.03.502677v1?rss=1 Wang, X. Wang, S. 2022-08-05 doi:10.1101/2022.08.03.502677 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting tumor mutation burden ]]> https://biorxiv.org/content/10.1101/2022.08.04.502834v1?rss=1 Schvartzman, J. M. Forsyth, G. C. Walch, H. Chatila, W. Santella, A. Menghrajani, K. Sanchez-Vega, F. Koche, R. Thompson, C. B. 2022-08-05 doi:10.1101/2022.08.04.502834 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps ]]> https://biorxiv.org/content/10.1101/2022.08.04.502839v1?rss=1 Satler, J. D. Herre, E. A. Heath, T. A. Machado, C. A. Zuniga, A. G. Jander, K. C. Eaton, D. A. R. Nason, J. D. 2022-08-05 doi:10.1101/2022.08.04.502839 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir ]]> https://biorxiv.org/content/10.1101/2022.08.07.499047v1?rss=1 Iketani, S. Mohri, H. Culbertson, B. Hong, S. J. Duan, Y. Luck, M. I. Annavajhala, M. K. Guo, Y. Sheng, Z. Uhlemann, A.-C. Goff, S. P. Sabo, Y. Yang, H. Chavez, A. Ho, D. D. 2022-08-08 doi:10.1101/2022.08.07.499047 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Centuries of genome instability and evolution in soft-shell clam transmissible cancer ]]> https://biorxiv.org/content/10.1101/2022.08.07.503107v1?rss=1 Hart, S. F. Yonemitsu, M. A. Giersch, R. M. Beal, B. F. Arriagada, G. Davis, B. W. Ostrander, E. A. Goff, S. P. Metzger, M. J. 2022-08-11 doi:10.1101/2022.08.07.503107 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ The effects of ethnoracial-related stressors during pregnancy on the developing offspring brain. ]]> https://biorxiv.org/content/10.1101/2022.08.08.503168v1?rss=1 Spann, M. N. Alleyne, K. Holland, C. M. Davids, A. Pierre-Louis, A. Bang, C. Oyeneye, V. Kiflom, R. Shea, E. Cheng, B. Peterson, B. S. Monk, C. Scheinost, D. 2022-08-11 doi:10.1101/2022.08.08.503168 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps ]]> https://biorxiv.org/content/10.1101/2022.08.09.503400v1?rss=1 Remesh, S. G. Merz, G. E. Britol, A. F. Chio, U. S. Rizo, A. N. Pospiech, T. H. Lui, I. Laurie, M. T. Glasgow, J. Le, C. Q. Zhang, Y. Diwanji, D. Hernandez, E. Lopez, J. Pawar, K. I. Pourmal, S. Smith, A. M. Zhou, F. QBI Coronavirus Research Group Structural Biology Consortium, DeRisi, J. Kortemme, T. Rosenberg, O. S. Glasgow, A. Leung, K. K. Wells, J. A. Verba, K. A. 2022-08-10 doi:10.1101/2022.08.09.503400 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Relating pathogenic loss-of function mutations in humans to their evolutionary fitness costs ]]> https://biorxiv.org/content/10.1101/2022.08.11.503594v1?rss=1 Agarwal, I. Fuller, Z. L. Myers, S. Przeworski, M. 2022-08-12 doi:10.1101/2022.08.11.503594 Cold Spring Harbor Laboratory Press 2022-08-12 <![CDATA[ D-cycloserine, a mixed NMDAR agonist/antagonist is Not Susceptible to Self-administration, unlike S-ketamine Using an Intravenous Self-administration Model in Naive and Ketamine-habituated Sprague-Dawley Rats ]]> https://biorxiv.org/content/10.1101/2022.08.12.503713v1?rss=1 Javitt, D. C. Javitt, J. C. 2022-08-15 doi:10.1101/2022.08.12.503713 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Destabilized 3UTR ARE therapeutically degrades ERBB2 in drug-resistant ERBB2+ cancer models ]]> https://biorxiv.org/content/10.1101/2022.08.14.503914v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@139d8dborg.highwire.dtl.DTLVardef@cc1fd3org.highwire.dtl.DTLVardef@13d9086org.highwire.dtl.DTLVardef@db69bf_HPS_FORMAT_FIGEXP M_FIG A. Depiction represents multiple ERBB2 expressing cancer cells with stable 3UTR ARE and the signaling cascade known to cause chemo resistance. B. Depiction of the engineered destabilized 3UTR ARE of ERBB2 and the destabilization and degradation of the ERBB2 transcript, protein and kinases involved in mediation of drug resistance C_FIG ]]> Awah, C. Glemaud, Y. Levine, F. Yang, K. Ansary, A. Dong, F. Ash, L. Zhang, J. Weiser, D. Ogunwobi, O. O. 2022-08-15 doi:10.1101/2022.08.14.503914 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans ]]> https://biorxiv.org/content/10.1101/2022.08.15.501889v1?rss=1 Gervais, N. C. La Bella, A. A. Wensing, L. F. Acquaviva, V. Best, M. Sharma, J. Uthayakumar, D. Chavez, A. Santiago-Tirado, F. Flores-Mireles, A. L. Shapiro, R. S. 2022-08-15 doi:10.1101/2022.08.15.501889 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data ]]> https://biorxiv.org/content/10.1101/2022.08.15.503962v1?rss=1 Yang, J. Xu, Y. Liu, Z. 2022-08-15 doi:10.1101/2022.08.15.503962 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Task-dependent optimal representations for cerebellarlearning ]]> https://biorxiv.org/content/10.1101/2022.08.15.504040v1?rss=1 Xie, M. Muscinelli, S. Harris, K. D. Litwin-Kumar, A. 2022-08-15 doi:10.1101/2022.08.15.504040 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Cancer tissue of origin constrains the growth and metabolism of metastases ]]> https://biorxiv.org/content/10.1101/2022.08.17.504141v1?rss=1 Sivanand, S. Gultekin, Y. Winter, P. Vermeulen, S. Y. Do, B. T. Danai, L. V. Tchourine, K. Crowder, K. Kunchok, T. Lau, A. N. Darnell, A. M. Morita, S. Duda, D. G. Aguirre, A. Wolpin, B. M. Lewis, C. A. Vitkup, D. Shalek, A. K. Vander Heiden, M. G. 2022-08-18 doi:10.1101/2022.08.17.504141 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Neural sequences in primate prefrontal cortex encode working memory in naturalistic environments ]]> https://biorxiv.org/content/10.1101/2022.08.18.504406v1?rss=1 Roussy, M. Busch, A. Luna, R. Leavitt, M. Mofrad, M. H. Gulli, R. A. Corrigan, B. Minac, J. Sachs, A. J. Palaniyappan, L. Muller, L. W. Martinez-Trujillo, J. C. 2022-08-18 doi:10.1101/2022.08.18.504406 Cold Spring Harbor Laboratory Press 2022-08-18 <![CDATA[ Muscle-derived Cues are Required to Specify Proprioceptor Pool Identity ]]> https://biorxiv.org/content/10.1101/2022.08.18.504408v1?rss=1 Norovich, A. L. Brenner-Morton, S. Jessell, T. M. 2022-08-19 doi:10.1101/2022.08.18.504408 Cold Spring Harbor Laboratory Press 2022-08-19 <![CDATA[ A systems biology-based identification and in vivo functional screening of Alzheimer's disease risk genes reveals modulators of memory function ]]> https://biorxiv.org/content/10.1101/2022.08.19.504537v1?rss=1 Hudgins, A. D. Zhou, S. Arey, R. N. Murphy, C. T. Suh, Y. 2022-08-22 doi:10.1101/2022.08.19.504537 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent ]]> https://biorxiv.org/content/10.1101/2022.08.19.504573v1?rss=1 McKenzie, P. F. Eaton, D. A. R. 2022-08-22 doi:10.1101/2022.08.19.504573 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Neurogenic induction by Ngfr reduces reactive astrocytic Lcn2/Slc22a17 signalling, amyloid deposition and Tau phosphorylation ]]> https://biorxiv.org/content/10.1101/2022.08.20.504608v1?rss=1 Siddiqui, T. Cosacak, M. I. popova, S. Bhattarai, P. Santa-Maria, I. tosto, g. Kizil, C. 2022-08-21 doi:10.1101/2022.08.20.504608 Cold Spring Harbor Laboratory Press 2022-08-21 <![CDATA[ Imbalanced immune response and dysregulation of neural functions underline fatal opportunistic encephalitis caused by astrovirus ]]> https://biorxiv.org/content/10.1101/2022.08.20.504643v1?rss=1 Maximova, O. A. Weller, M. L. Krogmann, T. Sturdevant, D. E. Ricklefs, S. Virtaneva, K. Martens, C. Wollenberg, K. Minai, M. Moore, I. N. Sauter, C. S. Barker, J. N. Lipkin, I. Seilhean, D. Nath, A. Cohen, J. I. 2022-08-23 doi:10.1101/2022.08.20.504643 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Individual risk attitudes arise from noise in neurocognitive magnitude representations ]]> https://biorxiv.org/content/10.1101/2022.08.22.504413v1?rss=1 Barretto Garcia, M. de Hollander, G. Grueschow, M. Polania, R. Woodford, M. Ruff, C. 2022-08-22 doi:10.1101/2022.08.22.504413 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ Pupil-linked phasic arousal relates to the reduction of response inhibition: inferences from a simultaneous pupillometry and EEG-fMRI study ]]> https://biorxiv.org/content/10.1101/2022.08.22.504728v1?rss=1 Hong, L. He, H. Sajda, P. 2022-08-23 doi:10.1101/2022.08.22.504728 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Targeting default mode network connectivity with mindfulness-based fMRI neurofeedback: A pilot study among adolescents with affective disorder history ]]> https://biorxiv.org/content/10.1101/2022.08.22.504796v1?rss=1 Zhang, J. Raya, J. Morfini, F. Urban, Z. Pagliaccio, D. Yendiki, A. Auerbach, R. P. Bauer, C. C. C. Whitfield-Gabrieli, S. 2022-08-25 doi:10.1101/2022.08.22.504796 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.08.23.504974v1?rss=1 Kumpornsin, K. Kochakarn, T. Yeo, T. Luth, M. Pearson, R. D. Hoshizaki, J. Schindler, K. Mok, S. Park, H. Uhlemann, A.-C. Cubel, S. M. Franco, V. Gomez-Lorenzo, M. Gamo, F.-J. Winzeler, E. Fidock, D. A. Chookajorn, T. Lee, M. C. 2022-08-23 doi:10.1101/2022.08.23.504974 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Temporal and spatial staging of lung alveolar regeneration is determined by the grainyhead transcription factor Tfcp2l1 ]]> https://biorxiv.org/content/10.1101/2022.08.23.504977v1?rss=1 Cardenas-Diaz, F. L. Liberti, D. C. Leach, J. P. Babu, A. Barasch, J. Shen, T. Diaz-Miranda, M. A. Zhou, S. Ying, Y. Morley, M. P. Morrisey, E. E. 2022-08-24 doi:10.1101/2022.08.23.504977 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression ]]> https://biorxiv.org/content/10.1101/2022.08.24.504986v1?rss=1 DeBlasi, J. M. Falzone, A. Caldwell, S. Kang, Y. P. Prieto-Farigua, N. Prigge, J. R. Schmidt, E. E. Chio, I. I. C. Karreth, F. A. DeNicola, G. M. 2022-08-24 doi:10.1101/2022.08.24.504986 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Synergistic stabilization of microtubules by BUB-1, HCP-1 and CLS- 2 controls meiotic spindle assembly in C. elegans oocytes ]]> https://biorxiv.org/content/10.1101/2022.08.24.505151v1?rss=1 Macaisne, N. Bellutti, L. Laband, K. Edwards, F. Pitayu-Nugroho, L. Gervais, A. Ganeswaran, T. Geoffroy, H. Maton, G. Canman, J. C. Lacroix, B. Dumont, J. 2022-08-25 doi:10.1101/2022.08.24.505151 Cold Spring Harbor Laboratory Press 2022-08-25 <![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[ Target-enriched enzymatic methyl sequencing: flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation ]]> https://biorxiv.org/content/10.1101/2022.08.26.505457v1?rss=1 Rubenstein, D. R. Solomon, J. 2022-08-26 doi:10.1101/2022.08.26.505457 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Prioritizing landscapes to reconcile biodiversity conservation, ecosystem services, and human well-being in India ]]> https://biorxiv.org/content/10.1101/2022.08.27.505513v1?rss=1 Srivathsa, A. Vasudev, D. Nair, T. Chakrabarti, S. Chanchani, P. DeFries, R. Deomurari, A. Dutta, S. Ghose, D. Goswami, V. Nayak, R. Neelakantan, A. Thatte, P. Vaidyanathan, S. Verma, M. Krishnaswamy, J. Sankaran, M. Ramakrishnan, U. 2022-08-29 doi:10.1101/2022.08.27.505513 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Boosting of neural circuit chaos at the onset of collective oscillations ]]> https://biorxiv.org/content/10.1101/2022.08.28.505598v1?rss=1 Palmigiano, A. Engelken, R. Wolf, F. 2022-08-28 doi:10.1101/2022.08.28.505598 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ ALK signaling drives tumorigenicity and chemoresistance of pancreatic ductal adenocarcinoma cells ]]> https://biorxiv.org/content/10.1101/2022.08.29.505637v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@21d661org.highwire.dtl.DTLVardef@1817b5eorg.highwire.dtl.DTLVardef@1ca97aaorg.highwire.dtl.DTLVardef@1ab5443_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Parejo-Alonso, B. Royo-Garcia, A. Espiau-Romera, P. Courtois, S. Curiel-Garcia, A. Zagorac, S. Villaoslada, I. Olive, K. P. Heeschen, C. Sancho, P. 2022-08-29 doi:10.1101/2022.08.29.505637 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ SHINE: Protein Language Model based Pathogenicity Prediction for Inframe Insertion and Deletion Variants ]]> https://biorxiv.org/content/10.1101/2022.08.30.505840v1?rss=1 Fan, X. Pan, H. Tian, A. Chung, W. Shen, Y. 2022-09-02 doi:10.1101/2022.08.30.505840 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Magnetic Resonance Spectroscopy Spectral Registration Using Deep Learning ]]> https://biorxiv.org/content/10.1101/2022.08.31.506120v1?rss=1 Ma, D. J. Yang, Y. Harguindeguy, N. Tian, Y. Guo, J. 2022-09-03 doi:10.1101/2022.08.31.506120 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+,K+-ATPases ]]> https://biorxiv.org/content/10.1101/2022.09.01.506169v1?rss=1 Mohammadi, S. Özdemir, H. I. Ozbek, P. Sumbul, F. Stiller, J. Deng, Y. Crawford, A. J. Rowland, H. M. Storz, J. F. Andolfatto, P. Dobler, S. 2022-09-04 doi:10.1101/2022.09.01.506169 Cold Spring Harbor Laboratory Press 2022-09-04 <![CDATA[ Resistance of SARS-CoV-2 Omicron Subvariant BA.4.6 to Antibody Neutralization ]]> https://biorxiv.org/content/10.1101/2022.09.05.506628v1?rss=1 Wang, Q. Li, Z. Ho, J. Guo, Y. Yeh, A. Y. Liu, M. Wang, M. Yu, J. Sheng, Z. Liu, L. Ho, D. D. 2022-09-06 doi:10.1101/2022.09.05.506628 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Decomposing spatial heterogeneity of cell trajectories with Paella ]]> https://biorxiv.org/content/10.1101/2022.09.05.506682v1?rss=1 Hou, W. Ji, Z. 2022-09-06 doi:10.1101/2022.09.05.506682 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies ]]> https://biorxiv.org/content/10.1101/2022.09.06.506813v1?rss=1 Martorella, M. Kasela, S. Garcia-Flores, R. Gokden, A. Castel, S. E. Lappalainen, T. 2022-09-06 doi:10.1101/2022.09.06.506813 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Genome-wide metabolite quantitative trait loci analysis (mQTL) in red blood cells from volunteer blood donors ]]> https://biorxiv.org/content/10.1101/2022.09.07.506936v1?rss=1 Moore, A. Busch, M. P. Dziewulska, K. Francis, R. O. Hod, E. A. Zimring, J. C. D'Alessandro, A. Page, G. P. 2022-09-07 doi:10.1101/2022.09.07.506936 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ The functional impact of rare variation across the regulatory cascade ]]> https://biorxiv.org/content/10.1101/2022.09.07.507008v1?rss=1 Li, T. Ferraro, N. Strober, B. J. Aguet, F. Kasela, S. Arvanitis, M. Ni, B. van de Wiel, L. Hershberg, E. Ardlie, K. Arking, D. E. Beer, R. L. Brody, J. Blackwell, T. W. Clish, C. Gabriel, S. Gerszten, R. Guo, X. Gupta, N. Johnson, W. C. Lappalainen, T. Lin, H. J. Liu, Y. Nickerson, D. A. Papanicolaou, G. Pritchard, J. K. Qasba, P. Shojaie, A. Smith, J. Sotoodehnia, N. Taylor, K. D. Tracy, R. P. Van den Berg, D. Wheeler, M. Rich, S. S. Rotter, J. I. Battle, A. J. Montgomery, S. B. 2022-09-09 doi:10.1101/2022.09.07.507008 Cold Spring Harbor Laboratory Press 2022-09-09 <![CDATA[ Multilayer Networks of Plasmid Genetic Similarity Reveal Potential Pathways of Gene Transmission ]]> https://biorxiv.org/content/10.1101/2022.09.08.507140v1?rss=1 Shapiro, J. T. Zorea, A. Brown Kav, A. Ontiveros, V. J. Mizrahi, I. Pilosof, S. 2022-09-11 doi:10.1101/2022.09.08.507140 Cold Spring Harbor Laboratory Press 2022-09-11 <![CDATA[ An Immune Cell Recirculation-Enabled Microfluidic Array to Study Dynamic Immunotherapeutic Activity in Recapitulated Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2022.09.09.507299v1?rss=1 Chi, C.-W. Lao, Y.-H. Ahmed, A. H. R. He, S. Merghoub, T. Leong, K. W. Wang, S. 2022-09-12 doi:10.1101/2022.09.09.507299 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ A Programmable Model for Exploring the Functional Logic of the Drosophila Antennal Lobe ]]> https://biorxiv.org/content/10.1101/2022.09.10.506216v1?rss=1 Lazar, A. A. Turkcan, M. K. Zhou, Y. 2022-09-13 doi:10.1101/2022.09.10.506216 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ A Programmable Model for Exploring the Functional Logic of the Drosophila Mushroom Body ]]> https://biorxiv.org/content/10.1101/2022.09.10.506218v1?rss=1 Lazar, A. A. Turkcan, M. K. Zhou, Y. 2022-09-10 doi:10.1101/2022.09.10.506218 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Environment-wide and epigenome-wide association study of adiposity in "Children of 1997" birth cohort ]]> https://biorxiv.org/content/10.1101/2022.09.12.507623v1?rss=1 Zhao, J. Fan, B. Huang, J. Cowling, B. J. Au Yeung, S. L. R. Baccarelli, A. M. Leung, G. Schooling, C. M. 2022-09-15 doi:10.1101/2022.09.12.507623 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Divergent regulation of KCNQ1/E1 by targeted recruitment of protein kinase A to distinct sites on the channel complex ]]> https://biorxiv.org/content/10.1101/2022.09.12.507626v1?rss=1 Zou, X. Shanmugam, S. K. Kanner, S. A. Sampson, K. J. Kass, R. S. Colecraft, H. M. 2022-09-14 doi:10.1101/2022.09.12.507626 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ PLAE web app enables powerful searching and multiple visualizations across one million unified single-cell ocular transcriptomes ]]> https://biorxiv.org/content/10.1101/2022.09.12.507632v1?rss=1 Swamy, V. S. Batz, Z. McGaughey, D. M. 2022-09-14 doi:10.1101/2022.09.12.507632 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.09.13.506996v1?rss=1 Li, N. Zhu, Q. Tian, Y. Ahn, K. J. Wang, X. Cramer, Z. Folkert, I. W. Yu, P. Jou, J. Adams-Tzivelekidis, S. Sehgal, P. Mahmoud, N. N. Aarons, C. B. Roses, R. E. Thomas-Tikhonenko, A. Furth, E. E. Stanger, B. Z. Rustgi, A. K. Haldar, M. Katona, B. W. Tan, K. Lengner, C. J. 2022-09-15 doi:10.1101/2022.09.13.506996 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Association of Whole-Person Eigen-Polygenic Risk Scores with Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.09.13.507735v1?rss=1 Kharaghani, A. Tio, E. Milic, M. Bennett, D. A. De Jager, P. L. Schneider, J. A. Sun, L. Felsky, D. 2022-09-15 doi:10.1101/2022.09.13.507735 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Social dominance status and social stability in spiny mice (Acomys cahirinus) and its relation to ear-hole regeneration and glucocorticoids ]]> https://biorxiv.org/content/10.1101/2022.09.13.507818v1?rss=1 Varholick, J. A. Godinez, G. Mobin, S. Jenkins, A. Romeo, R. D. Barbazuk, W. B. Maden, M. 2022-09-16 doi:10.1101/2022.09.13.507818 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing ]]> https://biorxiv.org/content/10.1101/2022.09.14.507926v1?rss=1 Triplett, M. A. Gajowa, M. Antin, B. Sadahiro, M. Adesnik, H. Paninski, L. 2022-09-17 doi:10.1101/2022.09.14.507926 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Relative Brain Age Is Associated with Socioeconomic Status and Anxiety/Depression Problems in Youth ]]> https://biorxiv.org/content/10.1101/2022.09.15.505331v1?rss=1 Cohen, J. W. Ramphal, B. Deserisy, M. Zhao, Y. Pagliaccio, D. Colcombe, S. Milham, M. P. Margolis, A. E. 2022-09-19 doi:10.1101/2022.09.15.505331 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression ]]> https://biorxiv.org/content/10.1101/2022.09.16.508303v1?rss=1 Guet, C. C. Bruneaux, L. oikonomou, P. Aldana, M. Cluzel, P. 2022-09-17 doi:10.1101/2022.09.16.508303 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions ]]> https://biorxiv.org/content/10.1101/2022.09.16.508329v1?rss=1 WEN, J. Yang, Z. Nasrallah, I. Cui, Y. Erus, G. Srinivasan, D. Abdulkadir, A. Mamourian, E. Hwang, G. Singh, A. Bergman, M. Bao, J. Varol, E. Zhou, Z. Boquet-Pujadas, A. Chen, J. Toga, A. W. Saykin, A. J. Hohman, T. Thompson, P. Villeneuve, S. Gollub, R. Sotiras, A. Wittfeld, K. Grabe, H. Tosun, D. Bilgel, M. An, Y. Marcus, D. LaMontagne, P. J. Heckbert, S. Austin, T. Launer, L. Espeland, M. Masters, C. Maruff, P. Fripp, J. Johnson, S. C. Morris, j. Albert, M. Nick, R. Resnick, S. M. Ferrucci, L. Fan, Y. Mohamad, H. Wolk, D. Shen, L. Shou, H. Dav 2022-09-19 doi:10.1101/2022.09.16.508329 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Divisive Normalization Circuits Faithfully Represent Auditory and Visual Stimuli ]]> https://biorxiv.org/content/10.1101/2022.09.17.506431v1?rss=1 Lazar, A. A. Liu, T. Zhou, Y. 2022-09-18 doi:10.1101/2022.09.17.506431 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions ]]> https://biorxiv.org/content/10.1101/2022.09.17.508184v1?rss=1 Trudeau, S. J. Hwang, H. Mathur, D. Begum, K. Petrey, D. Murray, D. Honig, B. 2022-09-19 doi:10.1101/2022.09.17.508184 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Post-mating parental behavior trajectories differ across four species of deer mice ]]> https://biorxiv.org/content/10.1101/2022.09.18.508265v1?rss=1 Khadraoui, M. Merritt, J. R. Hoekstra, H. E. Bendesky, A. 2022-09-19 doi:10.1101/2022.09.18.508265 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ A multiplex platform to identify mechanisms and modulators of proteotoxicity in neurodegeneration ]]> https://biorxiv.org/content/10.1101/2022.09.19.508444v1?rss=1 Resnick, S. J. Qamar, S. S. Sheng, J. Huang, L. H. Nixon-Abell, J. Melore, S. Chung, C. W. Li, X. Wang, J. Zhang, N. Shneider, N. A. Kaminski, C. F. Ruggeri, F. S. Schierle, G. S. K. St George-Hyslop, P. Chavez, A. 2022-09-19 doi:10.1101/2022.09.19.508444 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Posterior white matter hyperintensities are associated with reduced medial temporal lobe subregional integrity and long-term memory in older adults ]]> https://biorxiv.org/content/10.1101/2022.09.19.508591v1?rss=1 Rizvi, B. Sathishkumar, M. Kim, S. Marquez, F. Granger, S. J. Larson, M. S. Miranda, B. A. Hollearn, M. K. McMillan, L. Nan, B. Tustison, N. J. Lao, P. J. Brickman, A. M. Greenia, D. Corrada, M. M. Kawas, C. H. Yassa, M. A. 2022-09-21 doi:10.1101/2022.09.19.508591 Cold Spring Harbor Laboratory Press 2022-09-21 <![CDATA[ Odorant Mixture Separation in Drosophila Early Olfactory System ]]> https://biorxiv.org/content/10.1101/2022.09.20.508558v1?rss=1 Lazar, A. A. Liu, T. Yeh, C.-H. Zhou, Y. 2022-09-22 doi:10.1101/2022.09.20.508558 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution ]]> https://biorxiv.org/content/10.1101/2022.09.20.508799v1?rss=1 Carmona, L. M. Tun, L. T. Kim, A. Shiao, R. Kissner, M. D. Menon, V. Costa, R. M. 2022-09-22 doi:10.1101/2022.09.20.508799 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Targeted Protein Degradation via Nanoparticles ]]> https://biorxiv.org/content/10.1101/2022.09.21.508905v1?rss=1 Liu, Y. Liu, R. Dong, J. Xia, X. Yang, H. Wei, S. Fan, L. Fang, M. Zou, Y. Zheng, M. Leong, K. W. Shi, B. 2022-09-22 doi:10.1101/2022.09.21.508905 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Dynamic refinement of behavioral structure mediates dopamine-dependent credit assignment ]]> https://biorxiv.org/content/10.1101/2022.09.22.507905v1?rss=1 Tang, J. C. Y. Paixao, V. Carvalho, F. Silva, A. Klaus, A. Alves da Silva, J. Costa, R. M. 2022-09-22 doi:10.1101/2022.09.22.507905 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ A Haptoglobin (HP) Structural Variant Alters the Effect of APOE Alleles on Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.09.22.508749v1?rss=1 Bai, H. Naj, A. C. Benchek, P. Dumitrescu, L. Hohman, T. Hamilton-Nelson, K. Kallianpur, A. R. Griswold, A. J. Vardarajan, B. Martin, E. R. Beecham, G. Below, J. E. Schellenberg, G. D. Mayeux, R. Farrer, L. Pericak-Vance, M. A. Haines, J. L. Bush, W. S. 2022-09-23 doi:10.1101/2022.09.22.508749 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Altered MAM function shifts mitochondrial metabolism in SOD1-mutant models of ALS ]]> https://biorxiv.org/content/10.1101/2022.09.22.508778v1?rss=1 Larrea, D. Tamucci, K. A. Kabra, K. Velasco, K. Yun, T. D. Pera, M. Montesinos, J. Agrawal, R. R. Smerdon, J. W. Lowry, E. R. Stepanova, A. Yoval-Sanchez, B. Galkin, A. Wichterle, H. Area-Gomez, E. 2022-09-22 doi:10.1101/2022.09.22.508778 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ The impact of Mmu17 non-Hsa21 orthologous genes in the Ts65Dn mouse model of Down syndrome: the "gold standard" revisited ]]> https://biorxiv.org/content/10.1101/2022.09.23.509067v1?rss=1 Guedj, F. Kane, E. Bishop, L. Pennings, J. L. A. Herault, Y. Bianchi, D. W. 2022-09-26 doi:10.1101/2022.09.23.509067 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Leveraging vision to understand curiosity ]]> https://biorxiv.org/content/10.1101/2022.09.23.509220v1?rss=1 Cohanpour, M. Aly, M. Gottlieb, J. 2022-09-26 doi:10.1101/2022.09.23.509220 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Enhancing Sox/Oct cooperativity induces higher-grade developmental reset ]]> https://biorxiv.org/content/10.1101/2022.09.23.509242v1?rss=1 MacCarthy, C. M. Malik, V. Wu, G. Velychko, T. Keshet, G. Jauch, R. Cojocaru, V. Scholer, H. Velychko, S. 2022-09-25 doi:10.1101/2022.09.23.509242 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ Multimodal mass spectrometry imaging reveals single-cell metabolic states in mammalian liver ]]> https://biorxiv.org/content/10.1101/2022.09.26.508878v1?rss=1 28K-GCIB-SIMS)) at 1 {micro}m single-cell resolution. This allowed us to perform multi-modal mass spectrometry imaging (MSI) to detect metabolites, lipids, and proteins in single cells within functional liver zones and diverse cell types in the native tissue state. Our workflow utilizes the desorption electrospray ionization (DESI) mass spectrometry imaging (MSI) to build a reference map of metabolic heterogeneity and zonation across liver functional units. Then cryogenic (H2O)n>28K-GCIB-SIMS and C60-SIMS integrated metabolomics, lipidomic and proteomics, - characterizing the metabolic state in single cells on the same tissue section. We found for the first time that lipids and metabolites can classify liver metabolic zones and liver cell types beyond histological and protein-marker annotation. This provides a multi-modal workflow to define single-cell states in normal physiology and disease in mammalian tissue. ]]> Tian, H. Rajbhandari, P. R. Tarolli, J. Decker, A. M. Neelakantan, T. V. Angerer, T. Zandkarimi, F. Daniels, J. Remotti, H. R. Frache, G. Winograd, N. Stockwell, B. R. 2022-09-28 doi:10.1101/2022.09.26.508878 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Context-dependent requirement of G protein coupling for Latrophilin-2 in target selection of hippocampal axons ]]> https://biorxiv.org/content/10.1101/2022.09.26.509559v1?rss=1 Pederick, D. T. Perry-Hauser, N. A. Meng, H. He, Z. Javitch, J. A. Luo, L. 2022-09-27 doi:10.1101/2022.09.26.509559 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Specific connectivity optimizes learning in thalamocortical loops ]]> https://biorxiv.org/content/10.1101/2022.09.27.509618v1?rss=1 Lakshminarasimhan, K. Xie, M. Cohen, J. D. Sauerbrei, B. Hantman, A. W. Litwin-Kumar, A. Escola, S. 2022-09-28 doi:10.1101/2022.09.27.509618 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Decoding Age-specific Changes in Brain Functional Connectivity Using a Sliding-window Based Clustering Method ]]> https://biorxiv.org/content/10.1101/2022.09.27.509677v1?rss=1 Zhang, A. Pagliaccio, D. Marsh, R. Lee, S. 2022-09-28 doi:10.1101/2022.09.27.509677 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Down the Penrose stairs: How selection for fewer recombination hotspots maintains their existence ]]> https://biorxiv.org/content/10.1101/2022.09.27.509707v1?rss=1 Baker, Z. Przeworski, M. Sella, G. 2022-09-28 doi:10.1101/2022.09.27.509707 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Endosomal Chemokine Receptor Signalosomes Regulate Central Mechanisms Underlying Cell Migration ]]> https://biorxiv.org/content/10.1101/2022.09.27.509755v1?rss=1 Hahn, H. Daly, C. Little, J. Perry-Hauser, N. A. Inoue, A. Plouffe, B. Thomsen, A. R. B. 2022-09-28 doi:10.1101/2022.09.27.509755 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts ]]> https://biorxiv.org/content/10.1101/2022.09.27.509770v1?rss=1 Kumbier, K. Roth, M. Li, Z. Lazzari-Dean, J. Waters, C. Huang, P. Korobeynikov, V. Consortium, N. Y. G. C. Phatnani, H. Schneider, N. Jacobson, M. Wu, L. Altschuler, S. 2022-09-28 doi:10.1101/2022.09.27.509770 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Beyond the metropolis: Street tree densities and resident perceptions on ecosystem services in small urban centers in India ]]> https://biorxiv.org/content/10.1101/2022.09.28.509699v1?rss=1 Anujan, K. Velho, N. Kuriakose, G. P J, E. Nagendra, H. 2022-09-30 doi:10.1101/2022.09.28.509699 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Predicting enzyme substrate chemical structure with protein language models ]]> https://biorxiv.org/content/10.1101/2022.09.28.509940v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1dab89forg.highwire.dtl.DTLVardef@8eec65org.highwire.dtl.DTLVardef@141ff13org.highwire.dtl.DTLVardef@1d16212_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jinich, A. Nazia, S. Z. Tellez, A. V. Rappoport, D. Rhee, K. Y. 2022-09-30 doi:10.1101/2022.09.28.509940 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Aberrant DNA repair is a vulnerability in histone H3.3-mutant brain tumors ]]> https://biorxiv.org/content/10.1101/2022.09.29.510093v1?rss=1 Rondinelli, B. Giacomini, G. Piquet, S. Chevallier, O. Dabin, J. Bai, S.-K. Kim, B. Siddaway, R. Raught, B. Coyaud, E. Shan, C.-M. Reid, R. J. D. Toda, T. Rothstein, R. Wilhelm, T. Barra, V. Crane, A. Dubois, F. Bandopadhayay, P. Beroukhim, R. Naim, V. Jia, S. Hawkins, C. Polo, S. E. 2022-09-30 doi:10.1101/2022.09.29.510093 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Mechanisms of insertions at a DNA double-strand break ]]> https://biorxiv.org/content/10.1101/2022.09.30.509517v1?rss=1 Min, J. Zhao, J. Zagelbaum, J. Takahashi, S. Cummings, P. Schooley, A. Dekker, J. Gottesman, M. E. Rabadan, R. Gautier, J. 2022-10-01 doi:10.1101/2022.09.30.509517 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Entropic control of the free energy landscape of an archetypal biomolecular machine ]]> https://biorxiv.org/content/10.1101/2022.10.03.510626v1?rss=1 Ray, K. K. Kinz-Thompson, C. D. Fei, J. Wang, B. Lin, Q. Gonzalez, R. L. 2022-10-05 doi:10.1101/2022.10.03.510626 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ A neural model of proximity to reward ]]> https://biorxiv.org/content/10.1101/2022.10.03.510669v1?rss=1 Botros, P. Vendrell-Llopis, N. Costa, R. Carmena, J. 2022-10-06 doi:10.1101/2022.10.03.510669 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Simple scaling laws control the genetic architectures of human complex traits ]]> https://biorxiv.org/content/10.1101/2022.10.04.509926v1?rss=1 Simons, Y. B. Mostafavi, H. Smith, C. J. Pritchard, J. K. Sella, G. 2022-10-07 doi:10.1101/2022.10.04.509926 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Nimbolide Targets RNF114 to Induce the Trapping of PARP1 and Poly-ADP-Ribosylation-Dependent DNA Repair Factors ]]> https://biorxiv.org/content/10.1101/2022.10.04.510815v1?rss=1 Li, P. Zhen, Y. Kim, C. Deng, H. Deng, H. Wang, X.-D. Qin, T. Yu, Y. 2022-10-06 doi:10.1101/2022.10.04.510815 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics ]]> https://biorxiv.org/content/10.1101/2022.10.04.510898v1?rss=1 Boyeau, P. Hong, J. Gayoso, A. Jordan, M. Azizi, E. Yosef, N. 2022-10-06 doi:10.1101/2022.10.04.510898 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Neural representational geometry correlates with behavioral differences between monkeys ]]> https://biorxiv.org/content/10.1101/2022.10.05.511024v1?rss=1 Fascianelli, V. Stefanini, F. Tsujimoto, S. Genovesio, A. Fusi, S. 2022-10-07 doi:10.1101/2022.10.05.511024 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ GLUT1 ablation in astrocytes paradoxically improves central and peripheral glucose metabolism via enhanced insulin-stimulated ATP release ]]> https://biorxiv.org/content/10.1101/2022.10.06.511112v1?rss=1 Ardanaz, C. G. De la Cruz, A. Elizalde-Horcada, M. Puerta, E. Ramirez, M. J. Ortega, J. E. Urbiola, A. Ederra, C. Ariz, M. Ortiz-de-Solorzano, C. Fernandez-Irigoyen, J. Santamaria, E. Karsenty, G. Bruning, J. C. Solas, M. 2022-10-07 doi:10.1101/2022.10.06.511112 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ The methyltransferases METTL7A and METTL7B confer resistance to thiol-based histone deacetylase inhibitors ]]> https://biorxiv.org/content/10.1101/2022.10.07.511310v1?rss=1 Robey, R. W. Fitzsimmons, C. M. Guiblet, W. M. Frye, W. J. E. Gonzalez Dalmasy, J. Wang, L. Huff, L. M. Ali-Rahmani, F. Lipsey, C. C. Wade, H. M. Mitchell, A. V. Maligireddy, S. S. Jenkins, L. M. Nikitina, T. Zhurkin, V. B. Piscopio, A. D. Bates, S. E. Arda, H. E. Gottesman, M. M. Batista, P. J. 2022-10-07 doi:10.1101/2022.10.07.511310 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Intestinal myofibroblasts regulate intestinal epithelial cell plasticity via YAP/TAZ ]]> https://biorxiv.org/content/10.1101/2022.10.07.511327v1?rss=1 Pastuła, A. Janssen, K. P. Steiger, K. Slotta-Huspenina, J. Hauck, S. M. Schmid, R. M. Quante, M. Borgmann, M. Ruiz-Fernandez, M. J. A. Wang, T. C. Friedman, R. A. Ehmer, U. Fottner, M. 2022-10-10 doi:10.1101/2022.10.07.511327 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Mechanism of dual pharmacological correction and potentiation of human CFTR ]]> https://biorxiv.org/content/10.1101/2022.10.10.510913v1?rss=1 Wang, C. Yang, Z. Loughlin, B. J. Xu, H. Veit, G. Vorobiev, S. Clarke, O. B. Jiang, F. Li, Y. Singh, S. Rich, Z. Menten, E. R. Grassucci, R. A. Wang, W. Mezzell, A. Fu, Z. Wong, K.-H. Wang, J. Wetmore, D. R. Sutton, R. B. Brouillette, C. G. Urbatsch, I. L. Kappes, J. C. Lukacs, G. L. Frank, J. Hunt, J. F. 2022-10-11 doi:10.1101/2022.10.10.510913 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Neural dynamics and geometry for transitive inference ]]> https://biorxiv.org/content/10.1101/2022.10.10.511448v1?rss=1 B and B > C, then A > C). We found NNs that (i) generalized perfectly, despite lacking overt transitive structure prior to training, (ii) generalized when the task required working memory (WM), a capacity thought essential to inference in the brain, (iii) emergently expressed behaviors long observed in living subjects, in addition to a novel order-dependent behavior, and (iv) adopted different task solutions yielding alternative behavioral and neural predictions. Further, in a large-scale experiment, we found that human subjects performing WM-based TI showed behavior inconsistent with a class of NNs expressing an intuitive task solution. These findings provide neural insights into a classical relational ability, with wider implications for how the brain realizes relational cognition. ]]> Kay, K. Wei, X.-X. Khajeh, R. Beiran, M. Cueva, C. J. Jensen, G. Ferrera, V. P. Abbott, L. F. 2022-10-11 doi:10.1101/2022.10.10.511448 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Restricted effects of the sole C. elegans Daughterless/E homolog, HLH-2, on nervous system development ]]> https://biorxiv.org/content/10.1101/2022.10.10.511552v1?rss=1 Masoudi, N. Schnabel, R. Yemini, E. Leyva-Diaz, E. Hobert, O. 2022-10-10 doi:10.1101/2022.10.10.511552 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Data Descriptor: Human whole exome genotype data for Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.10.11.511653v1?rss=1 30. Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community via https://dss.niagads.org/. ]]> Leung, Y. Y. Naj, A. C. Chou, Y.-F. Valladares, O. Wheeler, N. Lin, H. Gangadharan, P. Qu, L. Clark, K. Cantwell, L. Nicaretta, H. the Alzheimer's Disease Sequencing Project, Seshadri, S. Brkanac, Z. Cruchaga, C. Pericak-Vance, M. A. Mayeux, R. Kuzma, A. B. Lee, W.-P. Bush, W. S. DeStefano, A. L. Martin, E. Schellenberg, G. D. Wang, L.-S. 2022-10-13 doi:10.1101/2022.10.11.511653 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Complex Intracellular Mechanisms of TBK1 Kinase Activation Revealed by a Specific Small Molecule Inhibitor ]]> https://biorxiv.org/content/10.1101/2022.10.11.511671v1?rss=1 Ye, J. Dephoure, N. Maniatis, T. 2022-10-12 doi:10.1101/2022.10.11.511671 Cold Spring Harbor Laboratory Press 2022-10-12 <![CDATA[ Allee effects mediate the impact of land-use change on the thermal niche of social species ]]> https://biorxiv.org/content/10.1101/2022.10.11.511768v1?rss=1 Chan, S.-F. Rubenstein, D. R. Wang, T.-W. Chen, Y.-Y. Chen, I.-C. Ni, D.-Z. Shih, W.-K. Shen, S.-F. 2022-10-14 doi:10.1101/2022.10.11.511768 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Direct Brain Recordings Identify a Causal Subsequent-Memory Effect ]]> https://biorxiv.org/content/10.1101/2022.10.12.511606v1?rss=1 Rubinstein, D. Y. Weidemann, C. T. Sperling, M. R. Kahana, M. J. 2022-10-17 doi:10.1101/2022.10.12.511606 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease ]]> https://biorxiv.org/content/10.1101/2022.10.12.511960v1?rss=1 Schonhoff, A. M. Figge, D. A. Jurkuvenaite, A. J. Gallups, N. J. Childers, G. M. Webster, J. A. Standaert, D. G. Goldman, J. E. Harms, A. S. 2022-10-16 doi:10.1101/2022.10.12.511960 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Therapeutic modulation of the blood-brain barrier and ischemic stroke by a bioengineered FZD4-selective WNT surrogate ]]> https://biorxiv.org/content/10.1101/2022.10.13.510564v1?rss=1 Ding, J. Lee, S.-J. Vlahos, L. Yuki, K. Rada, C. van Unen, V. Vuppalapaty, M. Chen, H. Sura, A. McCormick, A. Tomaske, M. Alwahabi, S. Nguyen, H. Nowatzke, W. Kim, L. Kelly, L. Vollrath, D. Califano, A. Yeh, W.-C. Li, Y. Kuo, C. 2022-10-14 doi:10.1101/2022.10.13.510564 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2022.10.13.512056v1?rss=1 Dadonaite, B. Crawford, K. H. Radford, C. E. Farrell, A. G. Yu, T. C. Hannon, W. W. Zhou, P. Andrabi, R. Burton, D. R. Liu, L. Ho, D. D. Neher, R. A. Bloom, J. D. 2022-10-13 doi:10.1101/2022.10.13.512056 Cold Spring Harbor Laboratory Press 2022-10-13 <![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[ Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion ]]> https://biorxiv.org/content/10.1101/2022.10.13.512143v1?rss=1 Ko, K.-P. Huang, Y. Zhang, S. Zou, G. Kim, B. Zhang, J. Jun, S. Martin, C. Dunbar, K. J. Efe, G. Rustgi, A. K. Nakagawa, H. Park, J.-I. 2022-10-17 doi:10.1101/2022.10.13.512143 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ The Molecular and Evolutionary Principles of Histone Folding in Eukarya and Archaea ]]> https://biorxiv.org/content/10.1101/2022.10.15.512373v1?rss=1 Zhao, H. Wu, H. Guseman, A. Abeykoon, D. Camara, C. M. Dalal, Y. Fushman, D. Papoian, G. 2022-10-16 doi:10.1101/2022.10.15.512373 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Distinct beta frequencies reflect categorical decisions ]]> https://biorxiv.org/content/10.1101/2022.10.17.512497v1?rss=1 Rassi, E. Zhang, Y. Mendoza, G. Mendez, J. C. Merchant, H. Haegens, S. 2022-10-21 doi:10.1101/2022.10.17.512497 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ DISRUPTION OF SYMPATHETIC OUTFLOW TO INTRA-ABDOMINAL ORGANS EMULATES THE METABOLIC EFFECTS OF SLEEVE GASTRECTOMY IN OBESE MICE ]]> https://biorxiv.org/content/10.1101/2022.10.17.512615v1?rss=1 Emiliano, A. Kraljevic, M. Lopatinsky, N. R. Batista, R. Jiang, C. Schwartz, G. J. 2022-10-21 doi:10.1101/2022.10.17.512615 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Persistent Homology-based Functional Connectivity Explains Cognitive Ability: Life-span Study ]]> https://biorxiv.org/content/10.1101/2022.10.17.512619v1?rss=1 Ryu, H. Habeck, C. G. Stern, Y. Lee, S. 2022-10-21 doi:10.1101/2022.10.17.512619 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Ripple-locked coactivity of stimulus-specific neurons supports human associative memory ]]> https://biorxiv.org/content/10.1101/2022.10.17.512635v1?rss=1 Kunz, L. Staresina, B. P. Reinacher, P. C. Brandt, A. Guth, T. A. Schulze-Bonhage, A. Jacobs, J. 2022-10-21 doi:10.1101/2022.10.17.512635 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. ]]> https://biorxiv.org/content/10.1101/2022.10.18.512708v1?rss=1 Kehrer, T. Cupic, A. Ye, C. Yildiz, S. Bouhhadou, M. Crossland, N. A. Barrall, E. Cohen, P. Tseng, A. Cagatay, T. Rathnasinghe, R. Flores, D. Jangra, S. Alam, F. Mena, N. Aslam, S. Saqi, A. Marin, A. Rutkowska, M. Ummadi, M. R. Pisanelli, G. Richardson, R. B. Veit, E. C. Fabius, J. M. A. Soucheray, M. Polacco, B. J. Evans, M. J. Swaney, D. L. Gonzalez-Reiche, A. S. Sordillo, E. M. van Bakel, H. Simon, V. Zuliani-Alvarez, L. Fontoura, B. M. A. Rosenberg, B. R. Krogan, N. J. Martinez-Sobrido, L. Garcia-Sastre, A. Miorin, L. 2022-10-19 doi:10.1101/2022.10.18.512708 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ A developmental program that regulates mammalian organ size offsets evolutionary distance ]]> https://biorxiv.org/content/10.1101/2022.10.19.512107v1?rss=1 Shimamura, Y. Tanaka, J. Kakiuchi, M. Sarmah, H. Miura, A. Hwang, Y. Sawada, A. Ninish, Z. Yamada, K. Cai, J. J. Mori, M. 2022-10-21 doi:10.1101/2022.10.19.512107 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Genetic mapping reveals Pou2af2-dependent tuning of tuft cell differentiation and intestinal type 2 immunity ]]> https://biorxiv.org/content/10.1101/2022.10.19.512785v1?rss=1 Nadjsombati, M. S. Niepoth, N. Webeck, L. M. Kennedy, E. A. Jones, D. L. Baldridge, M. T. Bendesky, A. von Moltke, J. 2022-10-21 doi:10.1101/2022.10.19.512785 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Long-range DNA end resection supports homologous recombination by checkpoint activation rather than extensive homology generation ]]> https://biorxiv.org/content/10.1101/2022.10.19.512848v1?rss=1 Kimble, M. T. Johnson, M. J. Nester, M. R. Symington, L. S. 2022-10-21 doi:10.1101/2022.10.19.512848 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Novel Master Regulators of Microglial Phagocytosis and Repurposed FDA-approved Drug for Treatment of Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/2022.10.19.512953v1?rss=1 Zhu, K. He, Q. Tsai, S.-F. Mudalige, D. M. Tang, A. Henrion, M. Y. R. Liu, Y. Vijayan, R. Zaidi, S. S. A. Branden, L. Cadiz, M. P. Hodos-Nkhereanye, R. Moein, S. Alamprese, M. L. Bennett, D. A. De Jager, P. Kuo, Y.-M. Ronaldson, P. T. Chang, R. 2022-10-21 doi:10.1101/2022.10.19.512953 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Perceiving Depth from Texture and Disparity Cues: Evidence for a Non-Probabilistic Account of Cue Integration ]]> https://biorxiv.org/content/10.1101/2022.10.20.513044v1?rss=1 Kemp, J. T. Cesanek, E. Domini, F. 2022-10-21 doi:10.1101/2022.10.20.513044 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Consolidation-dependent behavioral integration of sequences related to mPFC neural overlap and hippocampal-cortical connectivity ]]> https://biorxiv.org/content/10.1101/2022.10.20.513126v1?rss=1 Tompary, A. Davachi, L. 2022-10-21 doi:10.1101/2022.10.20.513126 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity ]]> https://biorxiv.org/content/10.1101/2022.10.21.513166v1?rss=1 Li, X. Lappalainen, T. Bussemaker, H. J. 2022-10-21 doi:10.1101/2022.10.21.513166 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Neuronal birthdate reveals topography in a vestibular brainstem circuit for gaze stabilization ]]> https://biorxiv.org/content/10.1101/2022.10.21.513243v1?rss=1 Goldblatt, D. Huang, S. Greaney, M. R. Hamling, K. R. Voleti, V. Perez-Campos, C. Patel, K. B. Li, W. Hillman, E. M. C. Bagnall, M. W. Schoppik, D. 2022-10-22 doi:10.1101/2022.10.21.513243 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut ]]> https://biorxiv.org/content/10.1101/2022.10.21.513299v1?rss=1 Urtecho, G. Moody, T. M. Huang, Y. Sheth, R. U. Richardson, M. Lekan, O. Velez-Cortes, F. Ricaurte, D. Wang, H. H. 2022-10-22 doi:10.1101/2022.10.21.513299 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot ]]> https://biorxiv.org/content/10.1101/2022.10.22.513349v1?rss=1 Wang, Q. Bowen, A. Valdez, R. Gherasim, C. Gordon, A. Lihong, L. Ho, D. D. 2022-10-24 doi:10.1101/2022.10.22.513349 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Antibody avidity and multi-specificity combined to confer protection against SARS-CoV-2 and resilience against viral escape ]]> https://biorxiv.org/content/10.1101/2022.10.23.513379v1?rss=1 Burn Aschner, C. Muthuraman, K. Kucharska, I. Cui, H. Prieto, K. Nair, M. S. Wang, M. Huang, Y. Christie-Holmes, N. Poon, B. Lam, J. Sultana, A. Kozak, R. Mubareka, S. Rubinstein, J. L. Rujas, E. Treanor, B. Ho, D. D. Jetha, A. Julien, J.-P. 2022-10-24 doi:10.1101/2022.10.23.513379 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ SDRAP for annotating scrambled or rearranged genomes ]]> https://biorxiv.org/content/10.1101/2022.10.24.513505v1?rss=1 Braun, J. Neme, R. Feng, Y. Landweber, L. F. Jonoska, N. 2022-10-25 doi:10.1101/2022.10.24.513505 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Reward modulates visual responses in the superficial superior colliculus of mice ]]> https://biorxiv.org/content/10.1101/2022.10.24.513513v1?rss=1 Baruchin, L. J. Alleman, M. Schröder, S. 2022-10-25 doi:10.1101/2022.10.24.513513 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ A Unified Modular Framework to Incorporate Structural Dependency in Spatial Omics Data ]]> https://biorxiv.org/content/10.1101/2022.10.25.513785v1?rss=1 Su, J. Reynier, J.-B. Fu, X. Zhong, G. Jiang, J. Supo Escalante, R. Wang, Y. Izar, B. Knowles, D. A. Rabadan, R. 2022-10-27 doi:10.1101/2022.10.25.513785 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Effect of age and sex on gene expression-based radiation biodosimetry using mouse peripheral blood ]]> https://biorxiv.org/content/10.1101/2022.10.27.514053v1?rss=1 Broustas, C. G. Shuryak, I. Duval, A. J. Amundson, S. A. 2022-10-28 doi:10.1101/2022.10.27.514053 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients ]]> https://biorxiv.org/content/10.1101/2022.10.27.514070v1?rss=1 Pita-Juarez, Y. Karagkouni, D. Kalavros, N. Melms, J. C. Niezen, S. Delorey, T. M. Essene, A. L. Brook, O. R. Pant, D. Skelton-Badlani, D. Naderi, P. Huang, P. Pan, L. Hether, T. Andrews, T. S. Ziegler, C. G. K. Reeves, J. Myloserdnyy, A. Chen, R. Nam, A. Phelan, S. Liang, Y. Amin, A. D. Biermann, J. Hibshoosh, H. Veregge, M. Kramer, Z. Jacobs, C. Yalcin, Y. Phillips, D. Slyper, M. Subramanian, A. Ashenberg, O. Bloom-Ackermann, Z. Tran, V. M. Gomez, J. Sturm, A. Zhang, S. Fleming, S. J. Warren, S. Beechem, J. Hung, D. Babadi, M. Padera, R. F. MacParl 2022-10-28 doi:10.1101/2022.10.27.514070 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Wnt signaling regulates passive cell competition in the retina by inducing differential cell adhesion ]]> https://biorxiv.org/content/10.1101/2022.10.27.514088v1?rss=1 Min, X. Mao, Y. Wu, H. Bock, J. Tao, C. Zhang, X. 2022-10-28 doi:10.1101/2022.10.27.514088 Cold Spring Harbor Laboratory Press 2022-10-28 <![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[ A Biophysical Basis for Learning and Transmitting Sensory Predictions ]]> https://biorxiv.org/content/10.1101/2022.10.31.514538v1?rss=1 Muller, S. Z. Abbott, L. F. Sawtell, N. B. 2022-11-01 doi:10.1101/2022.10.31.514538 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Hypothesis-driven modeling of the human lung-ventilator system for Acute Respiratory Distress Syndrome research ]]> https://biorxiv.org/content/10.1101/2022.10.31.514563v1?rss=1 stroh, j. n. Albers, D. Smith, B. Sottile, P. Hripcsak, G. 2022-11-01 doi:10.1101/2022.10.31.514563 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Foxa2 lineage+ mesendoderm forms a competitive pulmonary mesenchyme niche crucial for generating the entire lungs ]]> https://biorxiv.org/content/10.1101/2022.10.31.514628v1?rss=1 Miura, A. Sarmah, H. Tanaka, J. Hwang, Y. Sawada, A. Shimamura, Y. Fang, Y. Shimizu, D. Ninish, Z. Suer, J. L. Dubois, N. Davis, J. Toyooka, S. Wu, J. Que, J. Hawkins, F. J. Lin, C.-S. Mori, M. 2022-11-02 doi:10.1101/2022.10.31.514628 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state. ]]> https://biorxiv.org/content/10.1101/2022.11.01.514701v1?rss=1 Padavannil, A. Murari, A. Rhooms, S.-K. Owusu-Ansah, E. Letts, J. A. 2022-11-01 doi:10.1101/2022.11.01.514701 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Induced Degradation of Lineage-specific Oncoproteins Drives the Selective PARP1 Inhibitor Toxicity in Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2022.11.02.514072v1?rss=1 Kim, C. Wang, X.-D. Yu, Y. 2022-11-03 doi:10.1101/2022.11.02.514072 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ An inhibitory plasticity mechanism for world structure inference by hippocampal replay ]]> https://biorxiv.org/content/10.1101/2022.11.02.514897v1?rss=1 Liao, Z. Hadjiabadi, D. H. Terada, S. Soltesz, I. Losonczy, A. 2022-11-03 doi:10.1101/2022.11.02.514897 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Beta band rhythms influence reaction times ]]> https://biorxiv.org/content/10.1101/2022.11.03.515019v1?rss=1 Rassi, E. Lin, W. M. Zhang, Y. Emmerzaal, J. Haegens, S. 2022-11-03 doi:10.1101/2022.11.03.515019 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ The role of the cerebellum in learning to predict reward: evidence from cerebellar ataxia ]]> https://biorxiv.org/content/10.1101/2022.11.04.515251v1?rss=1 Nicholas, J. Amlang, C. Lin, C.-Y. Montaser-Kouhsari, L. Desai, N. Pan, M.-K. Kuo, S.-H. Shohamy, D. 2022-11-06 doi:10.1101/2022.11.04.515251 Cold Spring Harbor Laboratory Press 2022-11-06 <![CDATA[ Peptidergic modulation of motor neuron output via CART signaling at C bouton synapses ]]> https://biorxiv.org/content/10.1101/2022.11.05.515234v1?rss=1 Eleftheriadis, P. E. Pothakos, K. Sharples, S. A. Apostolou, P. E. Mina, M. Tetringa, E. Miles, G. B. Zagoraiou, L. 2022-11-05 doi:10.1101/2022.11.05.515234 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex ]]> https://biorxiv.org/content/10.1101/2022.11.07.515446v1?rss=1 Fujita, M. Gao, Z. Zeng, L. McCabe, C. White, C. C. Ng, B. Green, G. S. Rozenblatt-Rosen, O. Phillips, D. Amir-Zilberstein, L. Lee, H. Pearse, R. V. Khan, A. Vardarajan, B. N. Kiryluk, K. Ye, C. J. Klein, H.-U. Wang, G. Regev, A. Habib, N. Schneider, J. A. Wang, Y. Young-Pearse, T. Mostafavi, S. Bennett, D. A. Menon, V. De Jager, P. L. 2022-11-08 doi:10.1101/2022.11.07.515446 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Investigation of the neural effects of memory training to reduce false memories in older adults: Univariate and multivariate analyses ]]> https://biorxiv.org/content/10.1101/2022.11.08.515495v1?rss=1 Turney, I. C. Chamberlain, J. D. Hakun, J. G. Steinkrauss, A. C. Ross, L. A. Kirchhoff, B. A. Dennis, N. A. 2022-11-09 doi:10.1101/2022.11.08.515495 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Clinical PARP inhibitors allosterically induce PARP2 retention on DNA ]]> https://biorxiv.org/content/10.1101/2022.11.08.515634v1?rss=1 Langelier, M.-F. Lin, X. Zha, S. Pascal, J. M. 2022-11-08 doi:10.1101/2022.11.08.515634 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ FLASH and Conventional Radiation Induce Differential Immune Responses in Diffuse Intrinsic Pontine Glioma, Highlighting Potential for Combination Immunotherapy ]]> https://biorxiv.org/content/10.1101/2022.11.09.515507v1?rss=1 Padilla, O. Minns, H. E. Wei, H.-J. Webster-Carrion, A. Tazhibi, M. McQuillan, N. M. Zhang, X. Yeh, R. Zhang, Z. Hei, T. K. Szalontay, L. Pavisic, J. Garty, G. Garvin, J. H. Canoll, P. D. Vanpouille-Box, C. Menon, V. Olah, M. Wu, C.-C. Rabadan, R. Gartrell, R. D. 2022-11-10 doi:10.1101/2022.11.09.515507 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Reduced cholecystokinin-expressing interneuron input contributes to disinhibition of the hippocampal CA2 region in a mouse model of temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/2022.11.09.515872v1?rss=1 Whitebirch, A. C. Barnett, A. Santoro, B. Scharfman, H. E. Siegelbaum, S. A. 2022-11-10 doi:10.1101/2022.11.09.515872 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Retinoic acid signaling modulates smooth muscle cell phenotypic switching in atherosclerosis through epigenetic regulation of gene expression ]]> https://biorxiv.org/content/10.1101/2022.11.09.515888v1?rss=1 Pan, H. Ho, S. E. Xue, C. Cui, J. Ross, L. S. Reilly, M. P. 2022-11-10 doi:10.1101/2022.11.09.515888 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Establishing the Median Infectious Dose (ID50) and Characterizing the Clinical Manifestations of Mouse, Rat, Cow, and Human Corynebacterium bovis Isolates in Select Immunocompromised Mouse Strains ]]> https://biorxiv.org/content/10.1101/2022.11.10.515978v1?rss=1 Mendoza, G. Cheleuitte-Nieves, C. Lipman, N. S. Wipf, J. R. K. Ricart Arbona, R. J. Miranda, I. C. Ricart Arbona, R. J. 2022-11-10 doi:10.1101/2022.11.10.515978 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Direct Cortical Inputs to Hippocampal Area CA1 Transmit Complementary Signals for Goal-directed Navigation ]]> https://biorxiv.org/content/10.1101/2022.11.10.516009v1?rss=1 Bowler, J. C. Losonczy, A. 2022-11-13 doi:10.1101/2022.11.10.516009 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Converting an allocentric goal into an egocentric steering signal ]]> https://biorxiv.org/content/10.1101/2022.11.10.516026v1?rss=1 Mussells Pires, P. Abbott, L. F. Maimon, G. 2022-11-13 doi:10.1101/2022.11.10.516026 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Trans-eQTL mapping in gene sets identifies network effects of genetic variants ]]> https://biorxiv.org/content/10.1101/2022.11.11.516189v1?rss=1 Wang, L. Babushkin, N. Liu, Z. Liu, X. 2022-11-11 doi:10.1101/2022.11.11.516189 Cold Spring Harbor Laboratory Press 2022-11-11 <![CDATA[ SUMO2 Protects Against Tau-induced Synaptic and Cognitive Dysfunction ]]> https://biorxiv.org/content/10.1101/2022.11.11.516192v1?rss=1 Orsini, F. Argyrousi, E. K. Restelli, E. Ford, L. K. Takamura, H. Matsuzaki, S. Zentilin, L. Pascente, R. Kanaan, N. M. Soni, R. Katayama, T. Chiesa, R. Forloni, G. Kosik, K. S. Kandel, E. R. Fraser, P. E. Arancio, O. Fioriti, L. 2022-11-13 doi:10.1101/2022.11.11.516192 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ The HCN1 hyperpolarization-activated cyclic nucleotide-gated channel enhances evoked GABA release from parvalbumin positive interneurons ]]> https://biorxiv.org/content/10.1101/2022.11.11.516205v1?rss=1 Bock, T. Buss, E. W. Lofaro, O. M. Leroy, F. W. Santoro, B. Siegelbaum, S. A. 2022-11-13 doi:10.1101/2022.11.11.516205 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Systematic characterization of brain cellular crosstalk signaling networks in Alzheimer's disease reveals a novel role for SEMA6D in TREM2-dependent microglial activation ]]> https://biorxiv.org/content/10.1101/2022.11.11.516215v1?rss=1 D'Oliveira Albanus, R. Finan, G. Brase, L. Chen, S. Guo, Q. Kannan, A. Acquarone, M. You, S.-F. Novotny, B. C. Ribeiro Pereira, P. M. Morris, J. C. Bateman, R. J. McDade, E. Cruchaga, C. Chhatwal, J. P. Dominantly Inherited Alzheimer Network (DIAN), Mace, E. E. Benitez, B. A. Piccio, L. Sutherland, G. T. Ma, Q. Fu, H. Karch, C. M. Harari, O. Kim, T.-W. 2022-11-13 doi:10.1101/2022.11.11.516215 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Using conditional Generative Adversarial Networks (GAN) to generate de novo synthetic cell nuclei for training machine learning-based image segmentation ]]> https://biorxiv.org/content/10.1101/2022.11.12.516283v1?rss=1 Cosacak, M. I. Kizil, C. 2022-11-15 doi:10.1101/2022.11.12.516283 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ The tissue-specific autophagic response to nutrient deprivation ]]> https://biorxiv.org/content/10.1101/2022.11.12.516287v1?rss=1 Yang, Y. J. Grosso Jasutkar, H. Griffey, C. J. Kim, K. Melia, T. Dephoure, N. Yamamoto, A. 2022-11-15 doi:10.1101/2022.11.12.516287 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD ]]> https://biorxiv.org/content/10.1101/2022.11.12.516293v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@11ce287org.highwire.dtl.DTLVardef@15c201aorg.highwire.dtl.DTLVardef@13f90c9org.highwire.dtl.DTLVardef@3aa3be_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Li, F. Flynn, E. Shi, J. Wu, X. Wang, Z. Xue, C. Cheng, H. Meng, Y. Cui, J. Zhu, Y. Rozenblyum, A. Chun, J. Hernandez-Ono, A. Razani, B. Westerterp, M. Bauer, R. C. Suh, Y. Hao, K. Lappalainen, T. Zhang, H. 2022-11-15 doi:10.1101/2022.11.12.516293 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Spatial mapping of posture-dependent resistance to passive displacement of the hypertonic arm post-stroke ]]> https://biorxiv.org/content/10.1101/2022.11.13.516311v1?rss=1 Kanade-Mehta, P. Bengtson, M. Stoeckmannn, T. McGuire, J. Ghez, C. Scheidt, R. A. 2022-11-16 doi:10.1101/2022.11.13.516311 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Neuronal contact predicts connectivity in the C. elegans brain ]]> https://biorxiv.org/content/10.1101/2022.11.13.516316v1?rss=1 Cook, S. J. Kalinski, C. A. Hobert, O. 2022-11-13 doi:10.1101/2022.11.13.516316 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Engineered hydrogel reveals contribution of matrix mechanics to esophageal adenocarcinoma 3D organoids and identify matrix-activated therapeutic targets ]]> https://biorxiv.org/content/10.1101/2022.11.13.516357v1?rss=1 Cruz-Acuna, R. Kariuki, S. W. Sugiura, K. Loebel, C. Karakasheva, T. Gabre, J. T. Burdick, J. A. Rustgi, A. K. 2022-11-16 doi:10.1101/2022.11.13.516357 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Single-cell RNA sequencing implicates venous endothelial cells as a source of VEGF-mediated neo-angiogenesis in neuroinflammation ]]> https://biorxiv.org/content/10.1101/2022.11.15.516660v1?rss=1 Shahriar, S. Price, M. Z. Wayne, C. R. Glendinning, M. D. Prochilo, G. Stuhlmann, H. Biswas, S. Menon, V. Agalliu, D. 2022-11-15 doi:10.1101/2022.11.15.516660 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Cas9-mediated tagging of endogenous loci using HITAG ]]> https://biorxiv.org/content/10.1101/2022.11.16.516691v1?rss=1 Kim, J. Kratz, A. Sheng, J. Zhang, L. Singh, B. K. Chavez, A. 2022-11-17 doi:10.1101/2022.11.16.516691 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Tree growth enhancement drives a persistent biomass gain in unmanaged temperate forests ]]> https://biorxiv.org/content/10.1101/2022.11.16.516717v1?rss=1 Marques, L. Weng, E. Bugmann, H. Forrester, D. I. Rohner, B. Hobi, M. L. Trotsiuk, V. Stocker, B. D. 2022-11-17 doi:10.1101/2022.11.16.516717 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Computational structure prediction methods enable the systematic identification of oncogenic mutations ]]> https://biorxiv.org/content/10.1101/2022.11.18.517015v1?rss=1 Fu, X. Reglero, C. Swamy, V. Loh, J. W. Khiabanian, H. Albero, R. Forouhar, F. Al Quraishi, M. Ferrando, A. A. Rabadan, R. 2022-11-20 doi:10.1101/2022.11.18.517015 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization ]]> https://biorxiv.org/content/10.1101/2022.11.20.517210v1?rss=1 Ahdritz, G. Bouatta, N. Kadyan, S. Xia, Q. Gerecke, W. O'Donnell, T. J. Berenberg, D. Fisk, I. Zanichelli, N. Zhang, B. Nowaczynski, A. Wang, B. Stepniewska-Dziubinska, M. M. Zhang, S. Ojewole, A. Guney, M. E. Biderman, S. Watkins, A. M. Ra, S. Lorenzo, P. R. Nivon, L. Weitzner, B. Ban, Y.-E. A. Sorger, P. K. Mostaque, E. Zhang, Z. Bonneau, R. AlQuraishi, M. 2022-11-22 doi:10.1101/2022.11.20.517210 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times ]]> https://biorxiv.org/content/10.1101/2022.11.21.517401v1?rss=1 Jiang, M. Chandran, K. Li, A. Khunjar, W. 2022-11-21 doi:10.1101/2022.11.21.517401 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Starfysh reveals heterogeneous spatial dynamics in the breast tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2022.11.21.517420v1?rss=1 He, S. Jin, Y. Nazaret, A. Shi, L. Chen, X. Rampersaud, S. Dhillon, B. S. Valdez, I. Friend, L. E. Fan, J. L. Park, C. Y. Mintz, R. Lao, Y.-H. Carrera, D. Fang, K. W. Mehdi, K. Rohde, M. McFaline-Figueroa, J. L. Blei, D. Leong, K. W. Rudensky, A. Y. Plitas, G. Azizi, E. 2022-11-24 doi:10.1101/2022.11.21.517420 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG ]]> https://biorxiv.org/content/10.1101/2022.11.21.517430v1?rss=1 50% of the time. Using antibiotics and deletion mutants, we showed that most chromosome-associated NusG is involved in rrn anti-termination and in transcriptiontranslation coupling. NusG involvement in rrn anti-termination was mediated via its participation in phase-separated transcriptional condensates. Our work illuminates the diverse activities of a central regulator while offering a guide on how to dissect the roles of multi-functional machines using in vivo imaging. ]]> el Sayyed, H. Pambos, O. J. Stracy, M. Gottesman, M. E. Kapanidis, A. N. 2022-11-22 doi:10.1101/2022.11.21.517430 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes ]]> https://biorxiv.org/content/10.1101/2022.11.22.517471v1?rss=1 Morgante, F. Carbonetto, P. Wang, G. Zou, Y. Sarkar, A. Stephens, M. 2022-11-23 doi:10.1101/2022.11.22.517471 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants ]]> https://biorxiv.org/content/10.1101/2022.11.23.517532v1?rss=1 Wang, Q. Iketani, S. Li, Z. Liu, L. Guo, Y. Huang, Y. Bowen, A. D. Liu, M. Wang, M. Yu, J. Valdez, R. Lauring, A. S. Sheng, Z. Wang, H. H. Gordon, A. Liu, L. Ho, D. D. 2022-11-28 doi:10.1101/2022.11.23.517532 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ Interactions between circuit architecture and plasticity in a closed-loop system ]]> https://biorxiv.org/content/10.1101/2022.11.23.517718v1?rss=1 Payne, H. L. Raymond, J. L. Goldman, M. S. 2022-11-24 doi:10.1101/2022.11.23.517718 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Kinetic models for PET displacement studies ]]> https://biorxiv.org/content/10.1101/2022.11.25.517914v1?rss=1 Laurell, G. L. Plaven-Sigray, P. Johansen, A. Raval, N. R. Nasser, A. Madsen, C. A. Madsen, J. Hansen, H. D. Donovan, L. L. Knudsen, G. M. Lammertsma, A. A. Ogden, R. T. Svarer, C. Schain, M. 2022-11-26 doi:10.1101/2022.11.25.517914 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Emergent perceptual biases from state-space geometry in spiking recurrent neural networks trained to discriminate time intervals ]]> https://biorxiv.org/content/10.1101/2022.11.26.518023v1?rss=1 Serrano-Fernandez, L. Beiran, M. Parga, N. 2022-11-26 doi:10.1101/2022.11.26.518023 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ DRG afferents that mediate physiologic and pathologic mechanosensation from the distal colon ]]> https://biorxiv.org/content/10.1101/2022.11.27.518103v1?rss=1 Wolfson, R. L. Abdelaziz, A. Rankin, G. Kushner, S. Qi, L. Mazor, O. Choi, S. Sharma, N. Ginty, D. D. 2022-11-28 doi:10.1101/2022.11.27.518103 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ The connectome of an insect brain ]]> https://biorxiv.org/content/10.1101/2022.11.28.516756v1?rss=1 Winding, M. Pedigo, B. D. Barnes, C. L. Patsolic, H. G. Park, Y. Kazimiers, T. Fushiki, A. Andrade, I. V. Li, F. Valdes-Aleman, J. Khandelwal, A. Randel, N. Barsotti, E. Correia, A. Fetter, R. D. Hartenstein, V. Priebe, C. E. Vogelstein, J. T. Cardona, A. Zlatic, M. 2022-11-28 doi:10.1101/2022.11.28.516756 Cold Spring Harbor Laboratory Press 2022-11-28 <![CDATA[ A Novel Localized Tracing Technique to Explore Intra-Amygdala Functional and Structural Connectivity Patterns as Mediators of Individual Variability in Stress Response ]]> https://biorxiv.org/content/10.1101/2022.11.29.517584v1?rss=1 Lipshutz, A. Saltz, V. Anderson, K. R. Manganaro, A. Dumitriu, D. 2022-12-01 doi:10.1101/2022.11.29.517584 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ ApoE isoforms differentially regulate neuronal membrane proteasomes to shift the threshold for pathological aggregation of endogenous Tau ]]> https://biorxiv.org/content/10.1101/2022.11.29.518293v1?rss=1 Paradise, V. Sabu, M. Bafia, J. Sharif, N. A. Nguyen, C. Dhanraj Mukim, R. Wang, X. Fu, J. Ndubisi, J. Maldonado, G. Strickland, M. Figueroa, H. Almeida, D. L. Hyman, B. T. Holtzman, D. M. Nuriel, T. Ramachandran, K. V. 2022-11-29 doi:10.1101/2022.11.29.518293 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Toward a Cell Culture Model of Portal Axis Lipid Handling ]]> https://biorxiv.org/content/10.1101/2022.11.30.518512v1?rss=1 Cook, J. R. Green, P. H. R. Haeusler, R. A. 2022-12-01 doi:10.1101/2022.11.30.518512 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons ]]> https://biorxiv.org/content/10.1101/2022.11.30.518560v1?rss=1 Qian, J. Guan, X. Xie, B. Xu, C. Niu, J. Xin, T. Li, C. Colecraft, H. Jaenisch, R. Liu, X. S. 2022-12-02 doi:10.1101/2022.11.30.518560 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ AUTS2 gene dosage affects synaptic AMPA receptors via a local dendritic spine AUTS2-TTC3-AKT-mTORC1 signaling dysfunction ]]> https://biorxiv.org/content/10.1101/2022.12.01.518705v1?rss=1 Bestel, A.-M. Duchon, A. Viard, J. Kvajo, M. Daudin, R. Khelfaoui, M. Haziza, S. Loe-Mie, Y. Aime, M. Suizu, F. Birling, M.-C. Bensaid, M. Jacquot, S. Koebel, P. Reverdy, C. Rain, J.-C. Noguchi, M. Marques, X. Triller, A. Humeau, Y. Herault, Y. Karayiorgou, M. Gogos, J. Simonneau, M. 2022-12-01 doi:10.1101/2022.12.01.518705 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree ]]> https://biorxiv.org/content/10.1101/2022.12.01.518706v1?rss=1 Li, X. Pura, J. Allen, A. Owzar, K. Harms, M. Xie, J. 2022-12-02 doi:10.1101/2022.12.01.518706 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ The python-derived 16α-hydroxylated bile acid, pythocholic acid decreases food intake and increases jejunal fatty acid ethanolamides in mice. ]]> https://biorxiv.org/content/10.1101/2022.12.01.518764v1?rss=1 Higuchi, S. Wood, C. DiPatrizio, N. V. Kawamura, A. Haeusler, R. A. 2022-12-03 doi:10.1101/2022.12.01.518764 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Mechanistic implications of the interaction of the soluble substrate-binding protein with a type II ABC importer ]]> https://biorxiv.org/content/10.1101/2022.12.02.518933v1?rss=1 Zhu, L. Kim, J. Leng, K. Ramos, J. E. Kinz-Thompson, C. D. Karpowich, N. K. Gonzalez, R. L. Hunt, J. F. 2022-12-03 doi:10.1101/2022.12.02.518933 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Realtime observation of ATP-driven single B12 molecule translocationthrough BtuCD-F ]]> https://biorxiv.org/content/10.1101/2022.12.02.518935v1?rss=1 Zhu, L. Kim, J. Leng, K. Ramos, J. E. Kinz-Thompson, C. D. Karpowich, N. K. Gonzalez, R. L. Hunt, J. F. 2022-12-03 doi:10.1101/2022.12.02.518935 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Robust online multiband drift estimation in electrophysiology data ]]> https://biorxiv.org/content/10.1101/2022.12.04.519043v1?rss=1 Windolf, C. Paulk, A. C. Kfir, Y. Trautmann, E. Garcia, S. Meszena, D. Munoz, W. Caprara, I. Jamali, M. Boussard, J. C. Williams, Z. M. Cash, S. S. Paninski, L. Varol, E. 2022-12-05 doi:10.1101/2022.12.04.519043 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ The impact of genetically controlled splicing on exon inclusion and protein structure ]]> https://biorxiv.org/content/10.1101/2022.12.05.518915v1?rss=1 Einson, J. Minaeva, M. Rafi, F. Lappalainen, T. 2022-12-07 doi:10.1101/2022.12.05.518915 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ RNA conformational propensities determine cellular activity ]]> https://biorxiv.org/content/10.1101/2022.12.05.519207v1?rss=1 Kelly, M. L. Roy, R. Geng, A. Ganser, L. R. Manghrani, A. Cullen, B. R. Schulze-Gahmen, U. Herschlag, D. Al-Hashimi, H. M. 2022-12-07 doi:10.1101/2022.12.05.519207 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Fractions strategy differences in those born extremely preterm ]]> https://biorxiv.org/content/10.1101/2022.12.06.519175v1?rss=1 Carr, S. Babinchak, W. M. Istrate, A. Martyn-Dow, B. Wang, G. Chen, W. Fondran, J. Zhang, J. Wein, M. Yoon, S. Y. Birnbaum, A. Roth, E. Gross, C. Minich, N. Thompson, L. Kim, W. H. Stern, Y. Nosarti, C. Taylor, H. G. Tatsuoka, C. 2022-12-06 doi:10.1101/2022.12.06.519175 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Redundant representations are required to disambiguate simultaneously presented complex stimuli ]]> https://biorxiv.org/content/10.1101/2022.12.07.519040v1?rss=1 Johnston, W. J. Freedman, D. J. 2022-12-07 doi:10.1101/2022.12.07.519040 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Structure of a reversible amyloid fibril formed by the CPEB3 prion-like domain reveals a core sequence involved in translational regulation ]]> https://biorxiv.org/content/10.1101/2022.12.07.519389v1?rss=1 Flores, M. D. Sawaya, M. R. Boyer, D. R. Zink, S. Tovmasyan, S. Saucedo, A. Zee, C.-T. Cardenas, J. Fioriti, L. Rodriguez, J. A. 2022-12-07 doi:10.1101/2022.12.07.519389 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Associations of Socioeconomic Disparities With Buccal DNA-Methylation Measures Of Biological Aging ]]> https://biorxiv.org/content/10.1101/2022.12.07.519438v1?rss=1 Raffington, L. Schwaba, T. Aikins, M. Richter, D. Wagner, G. G. Harden, K. P. Belsky, D. W. Tucker-Drob, E. M. 2022-12-07 doi:10.1101/2022.12.07.519438 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Trans-cellular control of synapse properties by a cell type-specific splicing regulator ]]> https://biorxiv.org/content/10.1101/2022.12.07.519444v1?rss=1 Traunmuller, L. Schulz, J. M. Ortiz, R. Feng, H. Furlanis, E. Gomez, A. M. Schreiner, D. Bischofberger, J. Zhang, C. Scheiffele, P. 2022-12-07 doi:10.1101/2022.12.07.519444 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Gremlin 1 is required for macrophage M2 polarization ]]> https://biorxiv.org/content/10.1101/2022.12.07.519468v1?rss=1 Mthunzi, L. Rowan, S. Knaus, U. McLoughlin, P. 2022-12-07 doi:10.1101/2022.12.07.519468 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Adult born hippocampal granule cells promote pattern separation by bidirectionally modulating the remapping of place and cue cells. ]]> https://biorxiv.org/content/10.1101/2022.12.08.519632v1?rss=1 Tuncdemir, S. N. Grosmark, A. D. Chung, H. Luna, V. M. Lacefield, C. O. Losonczy, A. Hen, R. 2022-12-08 doi:10.1101/2022.12.08.519632 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Theory of systems memory consolidation via recall-gated plasticity ]]> https://biorxiv.org/content/10.1101/2022.12.08.519638v1?rss=1 Lindsey, J. Litwin-Kumar, A. 2022-12-08 doi:10.1101/2022.12.08.519638 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Context-dependent functions of mitochondria protein quality control in lung ]]> https://biorxiv.org/content/10.1101/2022.12.08.519642v1?rss=1 Xu, L. Tan, C. Barr, J. Talaba, N. McCulley, D. Shen, Y. Chung, W. K. Sun, X. 2022-12-10 doi:10.1101/2022.12.08.519642 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models ]]> https://biorxiv.org/content/10.1101/2022.12.09.519842v1?rss=1 Watson, J. L. Juergens, D. Bennett, N. R. Trippe, B. L. Yim, J. Eisenach, H. E. Ahern, W. Borst, A. J. Ragotte, R. J. Milles, L. F. Wicky, B. I. M. Hanikel, N. Pellock, S. J. Courbet, A. Sheffler, W. Wang, J. Venkatesh, P. Sappington, I. Vazquez Torres, S. Lauko, A. De Bortoli, V. Mathieu, E. Barzilay, R. Jaakkola, T. S. DiMaio, F. Baek, M. Baker, D. 2022-12-10 doi:10.1101/2022.12.09.519842 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Focused ultrasound-mediated brain genome editing ]]> https://biorxiv.org/content/10.1101/2022.12.10.519924v1?rss=1 Lao, Y.-H. Ji, R. Zhou, J. K. Snow, K. J. Kwon, N. Saville, E. He, S. Chauhan, S. Chi, C.-W. Datta, M. S. Zhang, H. Quek, C. H. Cai, S. Li, M. Gaitan, Y. Bechtel, L. Wu, S.-Y. Lutz, C. M. Tomer, R. Murray, S. A. Chavez, A. Konofagou, E. E. Leong, K. W. 2022-12-11 doi:10.1101/2022.12.10.519924 Cold Spring Harbor Laboratory Press 2022-12-11 <![CDATA[ Biochemical network motifs can transduce and process oscillatory information ]]> https://biorxiv.org/content/10.1101/2022.12.10.519932v1?rss=1 Reja, J. Fallon, T. K. Leader, A. Azeloglu, E. U. 2022-12-13 doi:10.1101/2022.12.10.519932 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Single Cell transcriptional analysis of ex vivo models of cortical and hippocampal development identifies unique longitudinal trends ]]> https://biorxiv.org/content/10.1101/2022.12.11.519959v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@1be59a3org.highwire.dtl.DTLVardef@1ef18b9org.highwire.dtl.DTLVardef@402c1dorg.highwire.dtl.DTLVardef@1103789_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO (A) Schematic representing select gene expression progression through neuronal network maturation from human cortical organoids (3- and 6-Month Organoid), newborn mice (P0 Mouse), immature ex vivo cortex derived cultures (DIV 3 ex vivo), functionally mature ex vivo cortex derived cultures (DIV15-31 ex vivo), and adult mice (P56 Mouse). Color represents proportion of excitatory neurons with detectable expression for selected representative genes Mapk10, Igfbp2, which increase and decrease through network maturation, respectively. (B) Schematic representing divergent expression patterns between genes associated with epilepsy and ASD through network maturation between the organoids and ex vivo cultures shown in (A). Color scales represent the change in the percentile, in respect to all genes, of the proportion of excitatory neurons with detectable expression. C_FIG ]]> Krizay, D. K. Goldstein, D. B. Boland, M. J. 2022-12-12 doi:10.1101/2022.12.11.519959 Cold Spring Harbor Laboratory Press 2022-12-12 <![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[ GeneSegNet: A deep learning framework for cell segmentation by integrating gene expression and imaging ]]> https://biorxiv.org/content/10.1101/2022.12.13.520283v1?rss=1 Wang, W. Wang, Y. Liu, D. Hou, W. Zhou, T. Ji, Z. 2022-12-15 doi:10.1101/2022.12.13.520283 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain ]]> https://biorxiv.org/content/10.1101/2022.12.14.520294v1?rss=1 Sulzer, D. Hobson, B. Stanley, A. De Los Santos, M. Culbertson, B. Mosharov, E. Sims, P. 2022-12-15 doi:10.1101/2022.12.14.520294 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Repetition accelerates neural markers of memory consolidation ]]> https://biorxiv.org/content/10.1101/2022.12.14.520481v1?rss=1 Yu, W. Zadbood, A. Chanales, A. J. H. Davachi, L. 2022-12-15 doi:10.1101/2022.12.14.520481 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Direct neural perturbations reveal a dynamical mechanism for robust computation ]]> https://biorxiv.org/content/10.1101/2022.12.16.520768v1?rss=1 O'Shea, D. J. Duncker, L. Goo, W. Sun, X. Vyas, S. Trautmann, E. M. Diester, I. Ramakrishnan, C. Deisseroth, K. Sahani, M. Shenoy, K. V. 2022-12-16 doi:10.1101/2022.12.16.520768 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Single-Cell Analysis of 5-ALA Intraoperative Labeling Specificity for Glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.12.17.520870v1?rss=1 Liu, Z. Mela, A. Furnari, J. Kotidis, C. Sperring, C. Humala, N. Bruce, J. N. Canoll, P. Sims, P. A. 2022-12-19 doi:10.1101/2022.12.17.520870 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Greengenes2 enables a shared data universe for microbiome studies ]]> https://biorxiv.org/content/10.1101/2022.12.19.520774v1?rss=1 McDonald, D. Jiang, Y. Balaban, M. Cantrell, K. Zhu, Q. Gonzalez, A. Morton, J. T. Nicolaou, G. Parks, D. Karst, S. M. Albertsen, M. Hugenholtz, P. DeSantis, T. Mirarab, S. Knight, R. 2022-12-20 doi:10.1101/2022.12.19.520774 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ The hippocampus binds movements to their temporal position in a motor sequence ]]> https://biorxiv.org/content/10.1101/2022.12.20.521084v1?rss=1 Dolfen, N. Reverberi, S. Op de beeck, H. King, B. R. Albouy, G. 2022-12-20 doi:10.1101/2022.12.20.521084 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Biologically-informed deep neural networks provide quantitative assessment of intratumoral heterogeneity in post-treatment glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.12.20.521086v1?rss=1 Wang, H. Argenziano, M. G. Yoon, H. Boyett, D. Save, A. Petridis, P. Savage, W. Jackson, P. Hawkins-Daarud, A. Tran, N. Hu, L. Al-Dalahmah, O. Bruce, J. N. Grinband, J. Swanson, K. Canoll, P. Li, J. 2022-12-20 doi:10.1101/2022.12.20.521086 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Quantitative modeling of the emergence of macroscopic grid-like representations ]]> https://biorxiv.org/content/10.1101/2022.12.20.521210v1?rss=1 Bin Khalid, I. Reifenstein, E. T. Auer, N. Kunz, L. Kempter, R. 2022-12-20 doi:10.1101/2022.12.20.521210 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Switching between external and internal attention in hippocampal networks ]]> https://biorxiv.org/content/10.1101/2022.12.20.521285v1?rss=1 Poskanzer, C. Aly, M. 2022-12-20 doi:10.1101/2022.12.20.521285 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Tobacco smoke exposure results in recruitment of inflammatory airspace monocytes and accelerated growth of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.12.21.521304v1?rss=1 Corleis, B. Tzouanas, C. N. Wadsworth, M. H. Cho, J. L. Linder, A. H. Schiff, A. E. Dickey, A. K. Medoff, B. D. Shalek, A. K. Kwon, D. S. 2022-12-21 doi:10.1101/2022.12.21.521304 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Mesoscale neural effects of transcranial magnetic stimulation ]]> https://biorxiv.org/content/10.1101/2022.12.26.521973v1?rss=1 Perera, N. D. Alekseichuk, I. Shirinpour, S. Wischnewski, M. Linn, G. Masiello, K. Butler, B. Russ, B. E. Schroeder, C. E. Falchier, A. Opitz, A. 2022-12-27 doi:10.1101/2022.12.26.521973 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Glucocorticoid and adrenergic receptor distribution across human organs and tissues: a map for stress transduction ]]> https://biorxiv.org/content/10.1101/2022.12.29.520757v1?rss=1 Basarrate, S. Monzel, A. S. Smith, J. Marsland, A. L. Trumpff, C. Picard, M. 2022-12-29 doi:10.1101/2022.12.29.520757 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Why the brown ghost chirps at night ]]> https://biorxiv.org/content/10.1101/2022.12.29.522225v1?rss=1 Oboti, L. Pedraja, F. Ritter, M. Lohse, M. Klette, L. Krahe, R. 2022-12-29 doi:10.1101/2022.12.29.522225 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response ]]> https://biorxiv.org/content/10.1101/2023.01.01.522340v1?rss=1 Ager, C. R. Zhang, M. Chaimowitz, M. Bansal, S. Obradovic, A. Rogava, M. Melms, J. C. McCann, P. Spina, C. Drake, C. G. Dallos, M. C. Izar, B. 2023-01-02 doi:10.1101/2023.01.01.522340 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2023.01.02.521806v1?rss=1 Hsu, D. Gao, J. Yamaguchi, N. Pinzaru, A. Mandayam, N. Liberti, M. Heissel, S. Alwaseem, H. Tavazoie, S. Tavazoie, S. 2023-01-02 doi:10.1101/2023.01.02.521806 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2023.01.02.522483v1?rss=1 Fritschi, C. J. Anang, S. Gong, Z. Mohammadi, M. Richard, J. Bourassa, C. Severino, K. T. Richter, H. Yang, D. Chen, H.-C. Chiu, T.-J. Seaman, M. Madani, N. Abrams, C. Finzi, A. Hendrickson, W. A. Sodroski, J. Smith, A. B. 2023-01-07 doi:10.1101/2023.01.02.522483 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ The prospect of universal coronavirus immunity: a characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses ]]> https://biorxiv.org/content/10.1101/2023.01.03.519511v1?rss=1 Soni, M. K. Migliori, E. Fu, J. Assal, A. Chan, H. T. Pan, J. Khatiwada, P. Ciubotariu, R. May, M. S. Pereira, M. R. De Giorgi, V. Sykes, M. Mapara, M. Y. Muranski, P. 2023-01-04 doi:10.1101/2023.01.03.519511 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ The genetic architecture of the human skeletal form ]]> https://biorxiv.org/content/10.1101/2023.01.03.521284v1?rss=1 Kun, E. Javan, E. M. Smith, O. Gulamali, F. Fuente, J. d. l. Flynn, B. I. Vajrala, K. Trutner, Z. Jayakumar, P. Tucker-Drob, E. M. Sohail, M. Singh, T. Narasimhan, V. M. 2023-01-03 doi:10.1101/2023.01.03.521284 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Representational geometry explains puzzling error distributions in behavioral tasks ]]> https://biorxiv.org/content/10.1101/2023.01.03.522667v1?rss=1 Wei, X.-X. Woodford, M. 2023-01-04 doi:10.1101/2023.01.03.522667 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ MitoQuicLy: a high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva ]]> https://biorxiv.org/content/10.1101/2023.01.04.522744v1?rss=1 Michelson, J. Rausser, S. Peng, A. Yu, T. Sturm, G. Trumpff, C. Kaufman, B. A. Rai, A. J. Picard, M. 2023-01-04 doi:10.1101/2023.01.04.522744 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Emergence of brain-like mirror-symmetric viewpoint tuning in convolutional neural networks ]]> https://biorxiv.org/content/10.1101/2023.01.05.522909v1?rss=1 Farzmahdi, A. Zarco, W. Freiwald, W. Kriegeskorte, N. Golan, T. 2023-01-05 doi:10.1101/2023.01.05.522909 Cold Spring Harbor Laboratory Press 2023-01-05 <![CDATA[ An entorhinal-like region in food-caching birds ]]> https://biorxiv.org/content/10.1101/2023.01.05.522940v1?rss=1 Applegate, M. C. Gutnichenko, K. S. Mackevicius, E. L. Aronov, D. 2023-01-06 doi:10.1101/2023.01.05.522940 Cold Spring Harbor Laboratory Press 2023-01-06 <![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[ Magnetic Resonance Fingerprinting based Thermometry (MRFT): application to ex vivo imaging near DBS leads ]]> https://biorxiv.org/content/10.1101/2023.01.11.523421v1?rss=1 0.958) between T1 and temperature and {Delta}s and temperatures in our temperature sensitivity calibration experiment. MRFT and PRFS thermometry both accurately predict temperature (RMSE<1.55 {degrees}C) compared to probe measurements. MRFT estimated temperature near DBS lead has a similar trend as the probe temperature. Both B0 maps show inhomogeneities around the lead. ]]> Qian, E. Poojar, P. Fung, M. Jin, Z. Vaughan, J. T. Shrivastava, D. Gultekin, D. Fernandes, T. Geethanath, S. 2023-01-15 doi:10.1101/2023.01.11.523421 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Major axes of variation in tree demography across global forests ]]> https://biorxiv.org/content/10.1101/2023.01.11.523538v1?rss=1 Leite, M. d. S. McMahon, S. M. Prado, P. I. Davies, S. J. Oliveira, A. A. d. De Deurwaerder, H. P. Aguilar, S. Anderson-Teixeira, K. J. Aqilah, N. Bourg, N. A. Brockelman, W. Y. Castano, N. Chang-Yang, C.-H. Chen, Y.-Y. Chuyong, G. Clay, K. Duque, A. Ediriweera, S. Ewango, C. E. N. Gilbert, G. Gunatilleke, I. A. U. N. Gunatilleke, C. V. S. Howe, R. Huasco, W. H. Itoh, A. Johnson, D. J. Kenfack, D. Kral, K. Leong, Y. T. Lutz, J. A. Makana, J.-R. Malhi, Y. McShea, W. J. Mohamad, M. Nasardin, M. Nathalang, A. Parker, G. Parmigiani, R. P?rez, R. Phillips, R. 2023-01-13 doi:10.1101/2023.01.11.523538 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Engraftment of wild-type alveolar type II epithelial cells in surfactant protein C deficient mice ]]> https://biorxiv.org/content/10.1101/2023.01.12.523571v1?rss=1 Iezza, D. Predella, C. NI, K. Murray, J. W. Liu, H.-Y. Saqi, A. Glasser, S. W. Dorrello, N. V. 2023-01-12 doi:10.1101/2023.01.12.523571 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ SEC-TMT facilitates quantitative differential analysis of protein interaction networks ]]> https://biorxiv.org/content/10.1101/2023.01.12.523793v1?rss=1 Doron-Mandel, E. Bokor, B. J. Ma, Y. Street, L. A. Tang, L. C. Abdou, A. A. Shah, N. H. Rosenberger, G. Jovanovic, M. 2023-01-12 doi:10.1101/2023.01.12.523793 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ Growth increases but regeneration declines in response to warming and drying at Arctic treeline in white spruce (Picea glauca) ]]> https://biorxiv.org/content/10.1101/2023.01.12.523811v1?rss=1 2m tall) increased by 54% (p<0.0001, Wilcoxon test). Tree-ring width was positively correlated with May-August temperature (p<0.01, Pearson coefficient) during the 20th century. However, after circa 1950, the positive correlation between temperature and growth weakened (i.e., temperature divergence) while the positive correlation with July precipitation strengthened (p<0.01, Pearson coefficient), suggesting that continued drying may limit future growth at this section of Arctic treeline. We conclude that while warmer temperatures appear to benefit annual growth in mature trees, the warmer and drier environmental conditions in spring and summer inhibit regeneration and therefore may be inhibiting the northward advance at this Arctic treeline site. Researchers should consider the interactions between temperature, water availability, and tree age when examining the future of treeline and boreal forest in a changing climate. ]]> Jensen, J. Boelman, N. Eitel, J. Vierling, L. Maguire, A. Oelkers, R. Silva, C. Andreu-Hayles, L. D'Arrigo, R. Griffin, K. L. 2023-01-15 doi:10.1101/2023.01.12.523811 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Conserved Roles for the Dynein Intermediate Chain and Ndel1 in Assembly and Activation of Dynein ]]> https://biorxiv.org/content/10.1101/2023.01.13.523097v1?rss=1 Okada, K. Iyer, B. R. Lammers, L. G. Gutierrez, P. A. Li, W. Markus, S. M. McKenney, R. J. 2023-01-14 doi:10.1101/2023.01.13.523097 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth ]]> https://biorxiv.org/content/10.1101/2023.01.13.523991v1?rss=1 Liao, J. Shenhav, L. Serrano, M. Zhu, B. Buck, G. A. Korem, T. 2023-01-17 doi:10.1101/2023.01.13.523991 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Hippocampal area CA2 controls seizure dynamics, interictal EEG abnormalities and social comorbidity in mouse models of temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/2023.01.15.524149v1?rss=1 250Hz) rescues social memory deficits of chronic epileptic mice C_LI ]]> Lisgaras, C. P. Oliva, A. Mckenzie, S. LaFrancois, J. Siegelbaum, S. A. Scharfman, H. E. 2023-01-19 doi:10.1101/2023.01.15.524149 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Ankh : Optimized Protein Language Model Unlocks General-Purpose Modelling ]]> https://biorxiv.org/content/10.1101/2023.01.16.524265v1?rss=1 Elnaggar, A. Essam, H. Salah-Eldin, W. Moustafa, W. Elkerdawy, M. Rochereau, C. Rost, B. 2023-01-18 doi:10.1101/2023.01.16.524265 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Normative modeling of brain morphometry in Clinical High-Risk for Psychosis ]]> https://biorxiv.org/content/10.1101/2023.01.17.523348v1?rss=1 1.96) scores. ResultsCHR-P and healthy individuals overlapped in the distributions of the observed values, regional z-scores, and all ADS vales. The proportion of CHR-P individuals with infranormal or supranormal values in any metric was low (<12%) and similar to that of healthy individuals. CHR-P individuals who converted to psychosis compared to those who did not convert had a higher percentage of infranormal values in temporal regions (5-7% vs 0.9-1.4%). In the CHR-P group, only the ADSSA showed significant but weak associations (|{beta}|<0.09; PFDR<0.05) with positive symptoms and IQ. Conclusions and RelevanceThe study findings challenge the usefulness of macroscale neuromorphometric measures as diagnostic biomarkers of psychosis risk and suggest that such measures do not provide an adequate explanation for psychosis risk. Key pointsO_ST_ABSQuestionC_ST_ABSIs the risk of psychosis associated with brain morphometric changes that deviate significantly from healthy variation? FindingsIn this study of 1340 individuals high-risk for psychosis (CHR-P) and 1237 healthy participants, individual-level variation in macroscale neuromorphometric measures of the CHR-P group was largely nested within healthy variation and was not associated with the severity of positive psychotic symptoms or conversion to a psychotic disorder. MeaningThe findings suggest the macroscale neuromorphometric measures have limited utility as diagnostic biomarkers of psychosis risk. ]]> Haas, S. S. Ge, R. Agartz, I. Amminger, G. P. Andreassen, O. A. Bachman, P. Baeza, I. Choi, S. Colibazzi, T. Cropley, V. L. de la Fuente-Sandoval, C. Ebdrup, B. H. Fortea, A. Fusar-Poli, P. Glenthoj, B. Y. Glenthoj, L. B. Haut, K. M. Hayes, R. A. Heekeren, K. Hooker, C. I. Hwang, W. J. Jahanshad, N. Kaess, M. Kasai, K. Katagiri, N. Kim, M. Kindler, J. Koike, S. Kristensen, T. D. Kwon, J. S. Lawrie, S. M. Lee, J. Lemmers-Jansen, I. L. Lin, A. Ma, X. Mathalon, D. H. McGuire, P. Michel, C. Mizrahi, R. Mizuno, M. Moller, P. Mora-Duran, R. Nelson, B. Nemot 2023-01-18 doi:10.1101/2023.01.17.523348 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Extensive characterization of a Williams Syndrome murine model shows Gtf2ird1-mediated rescue of select sensorimotor tasks, but no effect on enhanced social behavior ]]> https://biorxiv.org/content/10.1101/2023.01.18.523029v1?rss=1 Dougherty, J. D. Nygaard, K. R. Maloney, S. E. Swift, R. G. McCullough, K. B. Wagner, R. E. Fass, S. B. Garbett, K. Mirnics, K. Veenstra-VanderWeele, J. 2023-01-18 doi:10.1101/2023.01.18.523029 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Transposon mutagenesis libraries reveal novel molecular requirements during CRISPR RNA-guided DNA integration ]]> https://biorxiv.org/content/10.1101/2023.01.19.524723v1?rss=1 Walker, M. W. G. Klompe, S. E. Zhang, D. J. Sternberg, S. H. 2023-01-19 doi:10.1101/2023.01.19.524723 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Dopamine D2 receptors in nucleus accumbens cholinergic interneurons increase impulsive choice ]]> https://biorxiv.org/content/10.1101/2023.01.20.524596v1?rss=1 Cavallaro, J. Yeisley, J. Akdogan, B. Floeder, J. R. Balsam, P. D. Gallo, E. F. 2023-01-20 doi:10.1101/2023.01.20.524596 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures ]]> https://biorxiv.org/content/10.1101/2023.01.24.525358v1?rss=1 Yi, X. Fritzsching, K. Rogawski, R. Xu, Y. McDermott, A. E. 2023-01-25 doi:10.1101/2023.01.24.525358 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Double-strand breaks induce inverted duplication chromosome rearrangements by a DNA polymerase delta and Rad51-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2023.01.24.525421v1?rss=1 Al-Zain, A. Nester, M. R. Symington, L. S. 2023-01-25 doi:10.1101/2023.01.24.525421 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Multi-region brain transcriptomes uncover two subtypes of aging individuals with differences in Alzheimer risk and the impact of APOEe4 ]]> https://biorxiv.org/content/10.1101/2023.01.25.524961v1?rss=1 Lee, A. J. Ma, Y. Yu, L. Dawe, R. J. McCabe, C. Arfanakis, K. Mayeux, R. Bennett, D. A. Klein, H.-U. De Jager, P. 2023-01-25 doi:10.1101/2023.01.25.524961 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Mechanism of HflX-mediated recycling of E. coli ribosome studied by time-resolved cryo-EM ]]> https://biorxiv.org/content/10.1101/2023.01.25.525430v1?rss=1 Bhattacharjee, S. Frank, J. Feng, X. 2023-01-25 doi:10.1101/2023.01.25.525430 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.25.525502v1?rss=1 Yi, X. Zhang, L. Friesner, R. McDermott, A. E. 2023-01-25 doi:10.1101/2023.01.25.525502 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Zinc Alters the Supramolecular Organization of Nucleic Acid Complexes with Full-Length TIA1 ]]> https://biorxiv.org/content/10.1101/2023.01.25.525508v1?rss=1 Yang, Y. Fritzsching, K. He, S. McDermott, A. E. 2023-01-25 doi:10.1101/2023.01.25.525508 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Reticulocytes in donor RBC units enhance RBC alloimmunization ]]> https://biorxiv.org/content/10.1101/2023.01.25.525560v1?rss=1 Thomas, T. Qiu, A. Kim, C. Y. Gordy, D. E. Miller, A. Tredicine, M. Dzieciatkowska, M. Dei Zotti, F. Hod, E. A. D'Alessandro, A. Zimring, J. C. Spitalnik, S. L. Hudson, K. E. 2023-01-25 doi:10.1101/2023.01.25.525560 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Remapping in a recurrent neural network model of navigation and context inference ]]> https://biorxiv.org/content/10.1101/2023.01.25.525596v1?rss=1 Low, I. I. Giocomo, L. M. Williams, A. H. 2023-01-26 doi:10.1101/2023.01.25.525596 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10-/- mouse model of inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/2023.01.26.525771v1?rss=1 Armstrong, H. Rahbari, M. Park, H. Sharon, D. Thiesen, A. Hotte, N. Sun, N. Syed, H. Abofayed, H. Wang, W. Madsen, K. Wine, E. Mason, A. 2023-01-27 doi:10.1101/2023.01.26.525771 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ demuxmix: Demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models ]]> https://biorxiv.org/content/10.1101/2023.01.27.525961v1?rss=1 Klein, H.-U. 2023-01-29 doi:10.1101/2023.01.27.525961 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Generation and expansion of transitional lung organoids from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2023.01.30.526265v1?rss=1 Snoeck, H.-W. Matkovic Leko, I. Schrode, N. Pezet, M. G. Thimraj, T. A. Beaumont, K. Torres, J. A. 2023-02-01 doi:10.1101/2023.01.30.526265 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Spatial uncertainty and environmental geometry in navigation ]]> https://biorxiv.org/content/10.1101/2023.01.30.526278v1?rss=1 Kang, Y. H. Wolpert, D. M. Lengyel, M. 2023-02-01 doi:10.1101/2023.01.30.526278 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA polyubiquitination ]]> https://biorxiv.org/content/10.1101/2023.01.31.526362v1?rss=1 Wang, Y.-C. Kelso, A. A. Karamafrooz, A. Chen, Y.-H. Chen, W.-K. Cheng, C.-T. Qi, Y. Gu, L. Malkas, L. Kung, H.-J. Moldovan, G.-L. Ciccia, A. Stark, J. M. Ann, D. K. 2023-02-03 doi:10.1101/2023.01.31.526362 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants ]]> https://biorxiv.org/content/10.1101/2023.01.31.526505v1?rss=1 Einson, J. Glinos, D. Boerwinkle, E. Castaldi, P. Darbar, D. de Andrade, M. Ellinor, P. Fornage, M. Gabriel, S. Germer, S. Gibbs, R. Hersh, C. Johnsen, J. Kaplan, R. Konkle, B. Kooperberg, C. Nassir, R. Loos, R. J. F. Meyers, D. A. Mitchell, B. D. Psaty, B. Vasan, R. S. Rich, S. S. Rienstra, M. Rotter, J. I. Saferali, A. Shoemaker, M. B. Silverman, E. Smith, A. V. Mohammadi, P. Castel, S. E. Iossifov, I. Lappalainen, T. 2023-01-31 doi:10.1101/2023.01.31.526505 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Large-scale brain-wide neural recording in nonhuman primates ]]> https://biorxiv.org/content/10.1101/2023.02.01.526664v1?rss=1 Trautmann, E. M. Hesse, J. K. Stine, G. Xia, R. Shude Zhu, S. O'Shea, D. J. Karsh, B. Colonell, J. Lanfranchi, F. Vyas, S. Zimnik, A. Steinemann, N. A. Wagenaar, D. A. Andrei, A. Mora Lopez, C. OCallaghan, J. M. Putzeys, J. Raducanu, B. C. Welkenhuysen, M. Churchland, M. Moore, T. Shadlen, M. N. Shenoy, K. V. Tsao, D. Dutta, B. Harris, T. 2023-02-03 doi:10.1101/2023.02.01.526664 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses ]]> https://biorxiv.org/content/10.1101/2023.02.01.526675v1?rss=1 Markovina, S. Chen, L.-Y. Shi, V. Wang, S. Freeman, R. Ruiz, F. Jayachandran, K. Zhang, J. Cosper, P. Sun, L. Luke, C. Spina, C. Grigsby, P. Schwarz, J. 2023-02-03 doi:10.1101/2023.02.01.526675 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Neuromuscular Basis of Drosophila larval escape behavior ]]> https://biorxiv.org/content/10.1101/2023.02.01.526733v1?rss=1 Cooney, P. C. Li, W. Huang, Y. Hormigo, R. Tabachnik, T. Hillman, E. M. C. Grueber, W. B. Zarin, A. A. 2023-02-03 doi:10.1101/2023.02.01.526733 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference ]]> https://biorxiv.org/content/10.1101/2023.02.02.526909v1?rss=1 Tjärnberg, A. Beheler-Amass, M. Jackson, C. A. Christiaen, L. Gresham, D. J. Bonneau, R. 2023-02-03 doi:10.1101/2023.02.02.526909 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ 5-HT4 receptor agonists treatment reduces tau pathology and behavioral deficit in the PS19 mouse model of tauopathy ]]> https://biorxiv.org/content/10.1101/2023.02.03.526871v1?rss=1 Myeku, N. Jiang, S. Sydney, E. Runyan, A. Serpe, R. Figueroa, H. Yang, M. 2023-02-04 doi:10.1101/2023.02.03.526871 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration ]]> https://biorxiv.org/content/10.1101/2023.02.03.527039v1?rss=1 Anderson, T. Mo, J. Gagarin, E. Sherwood, D. Blumenkrantz, M. Mao, E. Leon, G. Chen, H.-J. Tseng, K.-C. Fabian, P. Crump, J. G. Smeeton, J. 2023-02-04 doi:10.1101/2023.02.03.527039 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate in aging fibroblasts ]]> https://biorxiv.org/content/10.1101/2023.02.03.527065v1?rss=1 Zhou, W. Karan, K. Klein, H.-U. Sturm, G. De Jager, P. Bennett, D. A. Hirano, M. Picard, M. Mills, R. 2023-02-04 doi:10.1101/2023.02.03.527065 Cold Spring Harbor Laboratory Press 2023-02-04 <![CDATA[ Effect of Total Sphingomyelin Synthase Activity on Low Density Lipoprotein Catabolism in Mice ]]> https://biorxiv.org/content/10.1101/2023.02.03.527088v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@50757eorg.highwire.dtl.DTLVardef@51ad9dorg.highwire.dtl.DTLVardef@5d362corg.highwire.dtl.DTLVardef@18fbe63_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jiang, X.-C. Li, Z. He, M. Worgall, T. S. Chen, G. 2023-02-07 doi:10.1101/2023.02.03.527088 Cold Spring Harbor Laboratory Press 2023-02-07 <![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[ Maintenance and transformation of representational formats during working memory prioritization ]]> https://biorxiv.org/content/10.1101/2023.02.08.527513v1?rss=1 Estefan, D. P. Fellner, M. C. Kunz, L. Zhang, H. Reinacher, P. Roy, C. Brandt, A. Schulze-Bonhage, A. Yang, L. Wang, S. Liu, J. Xue, G. Axmacher, N. 2023-02-09 doi:10.1101/2023.02.08.527513 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ P53 Acetylation Exerts Critical Roles In Pressure Overload Induced Coronary Microvascular Dysfunction and Heart Failure ]]> https://biorxiv.org/content/10.1101/2023.02.08.527691v1?rss=1 He, X. Cantrell, A. C. Williams, Q. A. Gu, W. Chen, Y. Chen, J.-X. Zeng, H. 2023-02-09 doi:10.1101/2023.02.08.527691 Cold Spring Harbor Laboratory Press 2023-02-09 <![CDATA[ Neural correlates of drinking reduction during cognitive behavioral therapy for alcohol use disorder ]]> https://biorxiv.org/content/10.1101/2023.02.08.527703v1?rss=1 Naqvi, N. H. Srivastava, A. B. Lee, J. Mariani, J. J. Patel, G. H. Levin, F. R. 2023-02-10 doi:10.1101/2023.02.08.527703 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ A Non-Canonical IRAK Signaling Pathway Triggered by DNA Damage ]]> https://biorxiv.org/content/10.1101/2023.02.08.527716v1?rss=1 Li, Y. Shah, R. B. Sarti, S. Belcher, A. L. Lee, B. J. Gorbatenko, A. Nemati, F. Yu, I. Stanley, Z. Shao, Z. Silva, J. Zha, S. Sidi, S. 2023-02-08 doi:10.1101/2023.02.08.527716 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ ImmuneMirror: a Machine Learning-based Integrative Pipeline and Web Server for Neoantigen Prediction ]]> https://biorxiv.org/content/10.1101/2023.02.09.527828v1?rss=1 10 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study may identify MSI-H patients who do not benefit from this treatment. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as an actionable target in esophageal squamous cell carcinoma (ESCC). This is the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction. ]]> Chuwdhury, G. S. Guo, Y. Cheung, C.-L. Lam, K.-O. Kam, N.-W. Liu, Z. Dai, W. 2023-02-10 doi:10.1101/2023.02.09.527828 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective ]]> https://biorxiv.org/content/10.1101/2023.02.09.527935v1?rss=1 Ong, H. W. Liang, Y. Richardson, W. Lowry, E. R. Wells, C. I. Chen, X. Silvestre, M. Dempster, K. Silvaroli, J. A. Smith, J. L. Wichterle, H. Pabla, N. S. Ultanir, S. K. Bullock, A. N. Drewry, D. Axtman, A. D. 2023-02-10 doi:10.1101/2023.02.09.527935 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Scalable co-sequencing of RNA and DNA from individual nuclei ]]> https://biorxiv.org/content/10.1101/2023.02.09.527940v1?rss=1 Olsen, T. R. Talla, P. Furnari, J. Bruce, J. N. Canoll, P. Zha, S. Sims, P. A. 2023-02-10 doi:10.1101/2023.02.09.527940 Cold Spring Harbor Laboratory Press 2023-02-10 <![CDATA[ Evolution of connectivity architecture in the Drosophila mushroom body ]]> https://biorxiv.org/content/10.1101/2023.02.10.528036v1?rss=1 Caron, S. J. C. Ellis, K. E. Smihula, H. Ganguli, I. Vigato, E. Bervoets, S. Auer, T. O. Benton, R. Litwin Kumar, A. 2023-02-12 doi:10.1101/2023.02.10.528036 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Mechanical control of neural plate folding by apical domain alteration ]]> https://biorxiv.org/content/10.1101/2023.02.10.528047v1?rss=1 Sokol, S. Y. Matsuda, M. Rozman, J. Kasza, K. Ostvar, S. 2023-02-12 doi:10.1101/2023.02.10.528047 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ STAT3 protects HSCs from intrinsic interferon signaling and loss of long-term blood-forming activity ]]> https://biorxiv.org/content/10.1101/2023.02.10.528069v1?rss=1 Patel, B. Zhou, Y. Babcock, R. L. Ma, F. Zal, M. A. Kumar, D. Medik, Y. B. Kahn, L. M. Pineda, J. E. Park, E. M. Tang, X. Raso, M. G. Zal, T. Clise-Dwyer, K. Giancotti, F. G. Colla, S. Watowich, S. S. 2023-02-11 doi:10.1101/2023.02.10.528069 Cold Spring Harbor Laboratory Press 2023-02-11 <![CDATA[ Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data ]]> https://biorxiv.org/content/10.1101/2023.02.11.528088v1?rss=1 Stear, B. J. Ahooyi, T. M. Vasisht, S. Simmons, A. Beigel, K. Callahan, T. J. Silverstein, J. C. Taylor, D. M. 2023-02-13 doi:10.1101/2023.02.11.528088 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Judging the difficulty of perceptual decisions ]]> https://biorxiv.org/content/10.1101/2023.02.13.528254v1?rss=1 Löffler, A. Zylberberg, A. N. Shadlen, M. Wolpert, D. M. 2023-02-14 doi:10.1101/2023.02.13.528254 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ A non-canonical Hippo pathway represses the expression of deltaNp63 ]]> https://biorxiv.org/content/10.1101/2023.02.13.528336v1?rss=1 Low-Calle, A. M. Ghoneima, H. Ortega, N. Cuibus, A. M. Katz, C. Tong, D. Prives, C. Prywes, R. 2023-02-13 doi:10.1101/2023.02.13.528336 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster ]]> https://biorxiv.org/content/10.1101/2023.02.13.528341v1?rss=1 Wang, Q. Bowen, A. D. Tam, A. R. Valdez, R. Stoneman, E. Mellis, I. A. Gordon, A. Liu, L. Ho, D. D. 2023-02-14 doi:10.1101/2023.02.13.528341 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ BOLD response is more than just magnitude: improving detection sensitivity through capturing hemodynamic profiles ]]> https://biorxiv.org/content/10.1101/2023.02.13.528362v1?rss=1 Chen, G. Taylor, P. A. Reynolds, R. C. Leibenluft, E. Pine, D. S. Brotman, M. A. Pagliaccio, D. Haller, S. P. 2023-02-14 doi:10.1101/2023.02.13.528362 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Threshold inclusion size triggers conversion of huntingtin to prion-like state that is reversible in newly born cells ]]> https://biorxiv.org/content/10.1101/2023.02.13.528394v1?rss=1 Asgarkhani, L. Khandakar, I. Pakan, R. Swayne, T. C. Emtage, L. 2023-02-14 doi:10.1101/2023.02.13.528394 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Spatiotemporal dynamics of sensory neuron and Merkel-cell remodeling are decoupled during epidermal homeostasis ]]> https://biorxiv.org/content/10.1101/2023.02.14.528558v1?rss=1 Clary, R. C. Jenkins, B. A. Lumpkin, E. A. 2023-02-14 doi:10.1101/2023.02.14.528558 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Tumor Niche Network-Defined Subtypes Predict Immunotherapy Response of Esophageal Squamous Cell Cancer ]]> https://biorxiv.org/content/10.1101/2023.02.15.528539v1?rss=1 Ko, K.-P. Zhang, S. Huang, Y. Kim, B. Zou, G. Jun, S. Zhang, J. Martin, C. Dunbar, K. J. Efe, G. Rustgi, A. K. Zhang, H. Nakagawa, H. Park, J.-I. 2023-02-15 doi:10.1101/2023.02.15.528539 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Amygdala AVPR1A mediates susceptibility to chronic social isolation in females ]]> https://biorxiv.org/content/10.1101/2023.02.15.528679v1?rss=1 Francois, M. Delgado, I. C. Lafond, A. Lewis, E. Kuromaru, M. Hassouna, R. Deng, S. Thaker, V. V. Dolen, G. Zeltser, L. M. 2023-02-15 doi:10.1101/2023.02.15.528679 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ 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[ Spatial heterogeneity in biofilm metabolism elicited by local control of phenazinemethylation ]]> https://biorxiv.org/content/10.1101/2023.02.15.528762v1?rss=1 Evans, C. R. Smiley, M. K. Thio, S. A. Wei, M. Price-Whelan, A. M. Min, W. Dietrich, L. E. 2023-02-16 doi:10.1101/2023.02.15.528762 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Genetic manipulation of betta fish ]]> https://biorxiv.org/content/10.1101/2023.02.16.528733v1?rss=1 Palmiotti, A. Lichak, M. R. Shih, P.-Y. Bendesky, A. 2023-02-16 doi:10.1101/2023.02.16.528733 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Alteration of functional connectivity in the cortex and major brain networks of non-human primates following focused ultrasound exposure ]]> https://biorxiv.org/content/10.1101/2023.02.16.528741v1?rss=1 Liu, D. Silva, F. A. M. Sanatkhani, S. Pouliopoulos, A. Konofagou, E. Grinband, J. Ferrera, V. P. 2023-02-16 doi:10.1101/2023.02.16.528741 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Interpersonal early adversity demonstrates dissimilarity from early socioeconomic disadvantage in the course of human brain development: A meta-analysis ]]> https://biorxiv.org/content/10.1101/2023.02.16.528877v1?rss=1 Vannucci, A. Fields, A. Hansen, E. Katz, A. Kerwin, J. Tachida, A. Martin, N. Tottenham, N. 2023-02-18 doi:10.1101/2023.02.16.528877 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ mRNA interactions with disordered regions control protein activity ]]> https://biorxiv.org/content/10.1101/2023.02.18.529068v1?rss=1 Luo, Y. Pratihar, S. Horste, E. Mitschka, S. Mey, A. Al-Hashimi, H. M. Mayr, C. 2023-02-18 doi:10.1101/2023.02.18.529068 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Negative Affect homogenizes and Positive Affect diversifies Social Memory Consolidation across people ]]> https://biorxiv.org/content/10.1101/2023.02.20.528994v1?rss=1 Iyer, S. Collier, E. Finn, E. S. Meyer, M. 2023-02-21 doi:10.1101/2023.02.20.528994 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Rie1 and Sgn1 form an RNA-binding complex that enforces the meiotic entry cell fate decision ]]> https://biorxiv.org/content/10.1101/2023.02.20.529006v1?rss=1 Gaspary, A. Laureau, R. Dyatel, A. Dursuk, G. Berchowitz, L. E. 2023-02-20 doi:10.1101/2023.02.20.529006 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Phased nanopore assembly with Shasta and modular graph phasing with GFAse ]]> https://biorxiv.org/content/10.1101/2023.02.21.529152v1?rss=1 Lorig-Roach, R. Meredith, M. Monlong, J. Jain, M. Olsen, H. McNulty, B. Porubsky, D. Montague, T. G. Lucas, J. Condon, C. Eizenga, J. Juul, S. McKenzie, S. Simmonds, S. Park, J. Asri, M. Koren, S. Eichler, E. Axel, R. Martin, B. Carnevali, P. Miga, K. Paten, B. 2023-02-22 doi:10.1101/2023.02.21.529152 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Myomatrix arrays for high-definition muscle recording ]]> https://biorxiv.org/content/10.1101/2023.02.21.529200v1?rss=1 Chung, B. Zia, M. Thomas, K. Michaels, J. A. Jacob, A. Pack, A. Williams, M. Nagapudi, K. Teng, L. H. Arrambide, E. Ouellette, L. Oey, N. Gibbs, R. Anschutz, P. Lu, J. Wu, Y. Kashefi, M. Oya, T. Kersten, R. Mosberger, A. C. O`Connell, S. Wang, R. Marques, H. G. P. Mendes, A. R. Lenschow, C. Kondakath, G. Kim, J. J. Olson, W. Quinn, K. Perkins, P. Gatto, G. Thanawalla, A. R. Coltman, S. K. Kim, T. Smith, T. S. Binder-Markey, B. Zaback, M. Thompson, C. K. Giszter, S. Person, A. Goulding, M. Azim, E. Thakor, N. O`Connor, D. Trimmer, B. Q. Lima, S. Car 2023-02-22 doi:10.1101/2023.02.21.529200 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Gut microbiota promotes pain chronicity in Myosin1A deficient male mice ]]> https://biorxiv.org/content/10.1101/2023.02.21.529352v1?rss=1 Reynders, A. Jhumka, A. Gaillard, S. Hoeffel, G. Mantilleri, A. Malapert, P. Salio, C. Ugolini, S. Castets, F. Saurin, A. J. Serino, M. Moqrich, A. 2023-02-21 doi:10.1101/2023.02.21.529352 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks ]]> https://biorxiv.org/content/10.1101/2023.02.22.529437v1?rss=1 Donoghue, T. Cao, R. Han, C. Z. Holman, C. M. Brandmeir, N. J. Wang, S. Jacobs, J. 2023-02-22 doi:10.1101/2023.02.22.529437 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.02.22.529581v1?rss=1 Banu, M. A. Dovas, A. Argenziano, M. G. Zhao, W. Cuervo, H. Higgins, D. M. Sperring, C. P. Pereira, B. Ye, L. F. Mahajan, A. Humala, N. Furnari, J. L. Upadhyayula, P. S. Zandkarimi, F. Nguyen, T. T. Wu, P. B. Hai, L. Karan, C. Razavilar, A. Siegelin, M. D. Kitajewski, J. Bruce, J. N. Stockwell, B. R. Sims, P. A. Canoll, P. D. 2023-02-23 doi:10.1101/2023.02.22.529581 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Multiplex Base Editing to Protect from CD33-Directed Therapy: Implications for Immune and Gene Therapy ]]> https://biorxiv.org/content/10.1101/2023.02.23.529353v1?rss=1 70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in NHPs. In vitro, dual gene-edited cells could be enriched via treatment with the CD33 antibody-drug conjugate, gemtuzumab ozogamicin (GO). Together, our results highlight the potential of adenine base editors for improved immune and gene therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/529353v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@70c99dorg.highwire.dtl.DTLVardef@c46ef4org.highwire.dtl.DTLVardef@505fd2org.highwire.dtl.DTLVardef@c30b8c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Borot, F. Humbert, O. Newby, G. A. Fields, E. Kohli, S. Radtke, S. Laszlo, G. S. Mayuranathan, T. Ali, A. M. Weiss, M. J. Yen, J. S. Walter, R. B. Liu, D. R. Mukherjee, S. Kiem, H.-P. 2023-02-23 doi:10.1101/2023.02.23.529353 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Structural basis of histone H2A lysine 119 deubiquitination by Polycomb Repressive Deubiquitinase BAP1/ASXL1 ]]> https://biorxiv.org/content/10.1101/2023.02.23.529554v1?rss=1 50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing new insight into understanding cancer etiology. One Sentence SummaryWe reveal the molecular mechanism of nucleosomal H2AK119Ub deubiquitination by human BAP1/ASXL1. ]]> Thomas, J. F. Valencia-Sanchez, M. I. Tamburri, S. Gloor, S. L. Rustichelli, S. Godinez-Lopez, V. De Ioannes, P. Lee, R. Abini-Agbomson, S. Gretarsson, K. Burg, J. M. Hickman, A. R. Sun, L. Gopinath, S. Taylor, H. Meiners, M. J. Cheek, M. A. Rice, W. Nudler, E. Lu, C. Keogh, M. C. Pasini, D. Armache, K.-J. 2023-02-23 doi:10.1101/2023.02.23.529554 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Olfactory fear conditioning biases olfactory stem cell receptor fate ]]> https://biorxiv.org/content/10.1101/2023.02.23.529692v1?rss=1 Liff, C. W. Ayman, Y. R. Jaeger, E. C. B. Lee, H. S. Kim, A. Marlin, B. J. 2023-02-23 doi:10.1101/2023.02.23.529692 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ The pluripotency factor Tex10 finetunes Wnt signaling for PGC and male germline development ]]> https://biorxiv.org/content/10.1101/2023.02.23.529824v1?rss=1 Li, D. Yang, J. Ma, F. Malik, V. Zang, R. Shi, X. Huang, X. Zhou, H. Wang, J. 2023-02-24 doi:10.1101/2023.02.23.529824 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Traumatic brain injury-induced fear generalization in mice involves hippocampal memory trace dysfunction and is alleviated by (R,S)-ketamine ]]> https://biorxiv.org/content/10.1101/2023.02.24.529876v1?rss=1 McGowan, J. C. Ladner, L. R. Shubeck, C. X. Tapia, J. LaGamma, C. T. Anqueira-Gonzalez, A. DeFrancesco, A. Chen, B. K. Hunsberger, H. C. Sydnor, E. J. Logan, R. W. Yu, T.-S. Kernie, S. G. Denny, C. A. 2023-02-27 doi:10.1101/2023.02.24.529876 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Cell-type-specific regulation of APOE levels in human neurons by the Alzheimer's disease risk gene SORL1 ]]> https://biorxiv.org/content/10.1101/2023.02.25.530017v1?rss=1 Lee, H. Aylward, A. J. Pearse, R. V. Hsieh, Y.-C. Augur, Z. M. Benoit, C. R. Chou, V. Knupp, A. Pan, C. Goberdhan, S. Duong, D. M. Seyfried, N. T. Bennett, D. A. Klein, H.-U. De Jager, P. L. Menon, V. Young, J. E. Young-Pearse, T. L. 2023-02-25 doi:10.1101/2023.02.25.530017 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ INPP5D/SHIP1 regulates inflammasome activation in human microglia ]]> https://biorxiv.org/content/10.1101/2023.02.25.530025v1?rss=1 Chou, V. Pearse, R. V. Aylward, A. J. Fancher, S. B. Ashour, N. Lee, H. Lam, M. Benoit, C. R. Seyfried, N. T. Bennett, D. A. De Jager, P. L. Menon, V. Young-Pearse, T. L. 2023-02-26 doi:10.1101/2023.02.25.530025 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ A frontosensory circuit for visual context processing is synchronous in the theta/alpha band ]]> https://biorxiv.org/content/10.1101/2023.02.25.530044v1?rss=1 Bastos, G. Holmes, J. T. Ross, J. M. Rader, A. M. Gallimore, C. G. Peterka, D. S. Hamm, J. P. 2023-02-25 doi:10.1101/2023.02.25.530044 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ The classic psychedelic DOI induces a persistent desynchronized state in medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2023.02.26.529963v1?rss=1 Olson, R. Bartlett, L. Sonneborn, A. Bretton-Granatoor, Z. Firdous, A. Harris, A. Abbas, A. 2023-02-27 doi:10.1101/2023.02.26.529963 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ PrePPI: A structure informed proteome-wide database of protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2023.02.27.530276v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@b66c15org.highwire.dtl.DTLVardef@71d817org.highwire.dtl.DTLVardef@21d984org.highwire.dtl.DTLVardef@4f6f55_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Petrey, D. Zhao, H. Trudeau, S. J. Murray, D. Honig, B. 2023-02-28 doi:10.1101/2023.02.27.530276 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Maternal age effects on offspring lifespan and reproduction vary within a species ]]> https://biorxiv.org/content/10.1101/2023.02.27.530305v1?rss=1 Liguori, A. Korm, S. Profetto, A. Richters, E. Gribble, K. E. 2023-02-28 doi:10.1101/2023.02.27.530305 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa ]]> https://biorxiv.org/content/10.1101/2023.02.28.529447v1?rss=1 Neumayer, G. Torkelson, J. Li, S. McCarthy, K. Zhen, H. Vangipuram, M. Jackow, J. Rami, A. Hansen, C. Guo, Z. Gaddam, S. Pappalardo, A. Li, L. Cramer, A. Roy, K. Nguyen, T. M. Tanabe, K. McGrath, P. Bruckner, A. Bilousova, G. Roop, D. Bailey, I. Tang, J. Christiano, A. Steinmetz, L. Wernig, M. Oro, A. E. 2023-03-01 doi:10.1101/2023.02.28.529447 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Immature myeloid cells are indispensable for intestinal regeneration post irradiation injury ]]> https://biorxiv.org/content/10.1101/2023.02.28.530500v1?rss=1 Jiang, Z. Waterbury, Q. T. Fu, N. Kim, W. Malagola, E. T. Guha, C. Shawber, C. J. Yan, K. S. Wang, T. C. 2023-03-01 doi:10.1101/2023.02.28.530500 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Temporal single-cell transcriptomic analysis of the sox1a:eGFP transgenic line identified the lateral floor plate progenitor cells as the origin of intraspinal serotonergic neurons ]]> https://biorxiv.org/content/10.1101/2023.03.01.530240v1?rss=1 Chen, F. Kohler, M. Cucun, G. Takamiya, M. Kizil, C. Cosacak, M. I. Rastegar, S. 2023-03-02 doi:10.1101/2023.03.01.530240 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Brain state dynamics reflect emotion transitions induced by music ]]> https://biorxiv.org/content/10.1101/2023.03.01.530528v1?rss=1 Sachs, M. E. Ochsner, K. Baldassano, C. 2023-03-02 doi:10.1101/2023.03.01.530528 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Regulated alternative splicing of Dscam2 is required for somatosensory circuit wiring ]]> https://biorxiv.org/content/10.1101/2023.03.01.530539v1?rss=1 Galindo, S. E. Shin, G. J.-e. Millard, S. S. Grueber, W. B. 2023-03-01 doi:10.1101/2023.03.01.530539 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Human synaptic neoteny requires species-specific balancing of SRGAP2-SYNGAP1 cross-inhibition ]]> https://biorxiv.org/content/10.1101/2023.03.01.530630v1?rss=1 Libe-Philippot, B. Iwata, R. Recupero, A. J. Wierda, K. Ditkowska, M. Gaspariunaite, V. Vermaercke, B. Peze-Heidsieck, E. Remans, D. Charrier, C. Polleux, F. Vanderhaeghen, P. 2023-03-02 doi:10.1101/2023.03.01.530630 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression ]]> https://biorxiv.org/content/10.1101/2023.03.02.529724v1?rss=1 Hasselluhn, M. C. Decker-Farrell, A. R. Vlahos, L. Thomas, D. H. Curiel-Garcia, A. Maurer, H. C. Wasko, U. N. Tomassoni, L. Sastra, S. A. Palermo, C. F. Dalton, T. C. Ma, A. Li, F. Tolosa, E. J. Hibshoosh, H. Muir, A. Fernandez-Zapico, M. E. Califano, A. Olive, K. P. 2023-03-02 doi:10.1101/2023.03.02.529724 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Childhood adversity in mothers is associated with accelerated epigenetic aging in pregnancy and in male newborns ]]> https://biorxiv.org/content/10.1101/2023.03.02.530806v1?rss=1 Dye, C. K. Wu, H. Monk, C. Belsky, D. W. Alschuler, D. Lee, S. O'Donnel, K. J. Scorza, P. 2023-03-06 doi:10.1101/2023.03.02.530806 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ The Expression of Vesicular Glutamate Transporter 1 (VGLUT1) in the Rat Larynx and Implications for Laryngeal Proprioception ]]> https://biorxiv.org/content/10.1101/2023.03.02.530889v1?rss=1 Yu, V. Hernandez-Morato, I. Brenner-Morton, S. L. Pitman, M. J. 2023-03-02 doi:10.1101/2023.03.02.530889 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Rett Syndrome astrocytes disrupt neuronal activity and cerebral organoid development through transfer of dysfunctional mitochondria ]]> https://biorxiv.org/content/10.1101/2023.03.02.530903v1?rss=1 Tomasello, D. L. Barrasa, M. I. Mankus, D. Alarcon, K. I. Lytton-Jean, A. K. Liu, X. S. Jaenisch, R. 2023-03-02 doi:10.1101/2023.03.02.530903 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells ]]> https://biorxiv.org/content/10.1101/2023.03.03.530998v1?rss=1 View larger version (62K): org.highwire.dtl.DTLVardef@8bd384org.highwire.dtl.DTLVardef@1ebc004org.highwire.dtl.DTLVardef@8b4dbforg.highwire.dtl.DTLVardef@19d7052_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kirk, J. S. Wang, J. Tracz, A. Long, M. Rosario, S. R. Ji, Y. Kumar, R. Liu, X. Singh, P. K. Puzanov, I. Chatta, G. Cheng, Q. Huang, J. Wrana, J. L. Lovell, J. Yu, H. Liu, S. Shen, M. M. Liu, T. Tang, D. G. 2023-03-06 doi:10.1101/2023.03.03.530998 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling ]]> https://biorxiv.org/content/10.1101/2023.03.05.531201v1?rss=1 Booth, G. T. Daza, R. M. Srivatsan, S. R. McFaline-Figueroa, J. L. Green Gladden, R. Furlan, S. N. Shendure, J. Trapnell, C. 2023-03-06 doi:10.1101/2023.03.05.531201 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Atherosclerosis is a smooth muscle cell-driven tumor-like disease ]]> https://biorxiv.org/content/10.1101/2023.03.06.531330v1?rss=1 Pan, H. Ho, S. E. Xue, C. Cui, J. Ross, L. S. Li, F. Solomon, R. A. Connolly, E. S. Reilly, M. P. 2023-03-07 doi:10.1101/2023.03.06.531330 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Calorie Restriction activates a gastric Notch-FOXO1 pathway to expand Ghrelin cells ]]> https://biorxiv.org/content/10.1101/2023.03.06.531352v1?rss=1 McKimpson, W. M. Spiegel, S. Mukhanova, M. Kraakman, M. Du, W. Kitamoto, T. Yu, J. Pajvani, U. Accili, D. 2023-03-07 doi:10.1101/2023.03.06.531352 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Gene-level alignment of single cell trajectories informs the progression of in vitro T cell differentiation ]]> https://biorxiv.org/content/10.1101/2023.03.08.531713v1?rss=1 Sumanaweera, D. Suo, C. Muraro, D. Dann, E. Polanski, K. Steemers, A. Park, J.-E. Dumitrascu, B. Teichmann, S. 2023-03-10 doi:10.1101/2023.03.08.531713 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ The path to "femmes fatales": the evolution of toxin resistance in predatory fireflies. ]]> https://biorxiv.org/content/10.1101/2023.03.08.531760v1?rss=1 Yang, L. Borne, F. Aardema, M. L. Zhen, Y. Peng, J. Wu, M. Visconti, R. Betz, A. Roland, B. P. Talsma, A. D. Palladino, M. Petschenka, G. Andolfatto, P. 2023-03-10 doi:10.1101/2023.03.08.531760 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56 delta holoenzyme ]]> https://biorxiv.org/content/10.1101/2023.03.09.530109v1?rss=1 Wu, C.-G. Balakrishnan, V. K. Parihar, P. S. Konovolov, K. Chen, Y.-C. Merrill, R. A. Wei, H. Carragher, B. Sundaresan, R. Cui, Q. Wadzinski, B. E. Swingle, M. R. Musiyenko, A. Honkanen, R. Suzuki, A. Strack, S. Huang, X. Xing, Y. 2023-03-09 doi:10.1101/2023.03.09.530109 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease ]]> https://biorxiv.org/content/10.1101/2023.03.09.531820v1?rss=1 Boeynaems, S. Ma, X. R. Yeong, V. Ginell, G. M. Chen, J.-H. Blum, J. A. Nakayama, L. Sanyal, A. Briner, A. Van Haver, D. Pauwels, J. Ekman, A. Schmidt, H. B. Sundararajan, K. Porta, L. Lasker, K. Larabell, C. Hayashi, M. A. F. Kundaje, A. Impens, F. Obermeyer, A. Holehouse, A. S. Gitler, A. D. 2023-03-09 doi:10.1101/2023.03.09.531820 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Optical coherence tomography of human fetal membrane sub-layers during dynamic loading ]]> https://biorxiv.org/content/10.1101/2023.03.09.531932v1?rss=1 0.8). Intact amniochorion bilayer and separated amnion and chorion were individually loaded, and the amnion layer was identified as the load-bearing layer within intact fetal membranes for both labored and C-section samples, consistent with prior work. Additionally, the rupture pressure and thickness of the amniochorion bilayer from the near-placental region were greater than those of the near-cervical region for labored samples. This location-dependent change in fetal membrane thickness was not attributable to the load-bearing amnion layer. Finally, the initial phase of the loading curve indicates that amniochorion bilayer from the near-cervical region is strain-hardened compared to the near-placental region in labored samples. Overall, these studies fill a gap in our understanding of the structural and mechanical properties of human fetal membranes at high resolution under dynamic loading events. ]]> Samimi, K. Contreras Guzman, E. Wu, M. Carlson, L. Feltovich, H. Hall, T. J. Myers, K. M. Oyen, M. L. Skala, M. C. 2023-03-12 doi:10.1101/2023.03.09.531932 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Impaired potency of neutralizing antibodies against cell-cell fusion mediated by SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.03.09.531948v1?rss=1 Wang, Q. Yeh, A. Y. Guo, Y. Yu, J. Ho, D. D. Liu, L. 2023-03-10 doi:10.1101/2023.03.09.531948 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy ]]> https://biorxiv.org/content/10.1101/2023.03.10.531983v1?rss=1 McFaline-Figueroa, J. L. Srivatsan, S. Hill, A. J. Gasperini, M. Jackson, D. L. Saunders, L. Domcke, S. Regalado, S. G. Lazarchuck, P. Alvarez, S. Monnat, R. J. Shendure, J. Trapnell, C. 2023-03-12 doi:10.1101/2023.03.10.531983 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Efferocytosis-Induced Lactate Enables the Proliferation of Pro-Resolving Macrophages to Mediate Tissue Repair ]]> https://biorxiv.org/content/10.1101/2023.03.10.532107v1?rss=1 Ngai, D. Schilperoort, M. Tabas, I. 2023-03-12 doi:10.1101/2023.03.10.532107 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Distinct Th17 effector cytokines differentially promote microglial and blood-brain barrier inflammatory responses during post-infectious encephalitis ]]> https://biorxiv.org/content/10.1101/2023.03.10.532135v1?rss=1 Wayne, C. R. Bremner, L. I. Faust, T. E. Duran-Laforet, V. Ampatey, N. Ho, S. J. Feinberg, P. A. Arvanitis, P. Ciric, B. Delaney, S. L. Vargas-Deming, W. Swedo, S. Menon, V. Schafer, D. P. Cutforth, T. Agalliu, D. 2023-03-12 doi:10.1101/2023.03.10.532135 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Unsupervised discovery of family specific vocal usage in the Mongolian gerbil ]]> https://biorxiv.org/content/10.1101/2023.03.11.532197v1?rss=1 Peterson, R. E. Choudhri, A. MItelut, C. Tanelus, A. Capo-Battaglia, A. Williams, A. H. Schneider, D. M. Sanes, D. H. 2023-03-13 doi:10.1101/2023.03.11.532197 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ GeneTuring tests GPT models in genomics ]]> https://biorxiv.org/content/10.1101/2023.03.11.532238v1?rss=1 Hou, W. Ji, Z. 2023-03-13 doi:10.1101/2023.03.11.532238 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Organization and Plasticity of Inhibition in Hippocampal Recurrent Circuits ]]> https://biorxiv.org/content/10.1101/2023.03.13.532296v1?rss=1 Vancura, B. Geiller, T. Losonczy, A. 2023-03-13 doi:10.1101/2023.03.13.532296 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ More than a prickly morphology: plastome variation in the prickly pear cacti (Opuntieae) ]]> https://biorxiv.org/content/10.1101/2023.03.13.532486v1?rss=1 Kohler, M. Reginato, M. Jin, J.-J. Majure, L. C. 2023-03-14 doi:10.1101/2023.03.13.532486 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Topography of inputs into the hippocampal formation of a food-caching bird ]]> https://biorxiv.org/content/10.1101/2023.03.14.532572v1?rss=1 Applegate, M. C. Gutnichenko, K. S. Aronov, D. 2023-03-15 doi:10.1101/2023.03.14.532572 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Transposon-encoded nucleases use guide RNAs to selfishly bias their inheritance ]]> https://biorxiv.org/content/10.1101/2023.03.14.532601v1?rss=1 Meers, C. Le, H. Pesari, S. R. Hoffmann, F. T. Walker, M. W. G. Gezelle, J. Sternberg, S. H. 2023-03-14 doi:10.1101/2023.03.14.532601 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Rats rapidly switch between retrospective and inferential value computations ]]> https://biorxiv.org/content/10.1101/2023.03.14.532617v1?rss=1 Mah, A. Bossio, V. Constantinople, C. M. 2023-03-15 doi:10.1101/2023.03.14.532617 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Hox genes modulate physical forces to differentially shape small and large intestinal epithelia ]]> https://biorxiv.org/content/10.1101/2023.03.15.532602v1?rss=1 Gill, H. K. Yin, S. Nerurkar, N. L. Lawlor, J. C. Huycke, T. R. Mahadevan, L. Tabin, C. J. 2023-03-15 doi:10.1101/2023.03.15.532602 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice ]]> https://biorxiv.org/content/10.1101/2023.03.15.532726v1?rss=1 Bashkirova, E. Klimpert, N. Pourmorady, A. Monahan, K. Campbell, C. Osinski, J. Tan, L. Schieren, I. Stecky, R. Barnea, G. Xie, X. S. Abdus-Saboor, I. Shykind, B. Marlin, B. J. Gronostajski, R. Fleischmann, A. Lomvardas, S. 2023-03-15 doi:10.1101/2023.03.15.532726 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Complement C3 interacts with cytochrome c to influence myocardial apoptosis during heart ischemia/reperfusion ]]> https://biorxiv.org/content/10.1101/2023.03.15.532779v1?rss=1 Fang, Z. Lee, H. Liu, J. Wong, K. A. Brown, L. M. Zhang, M. 2023-03-15 doi:10.1101/2023.03.15.532779 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ MFN2-dependent recruitment of ATAT1 coordinates mitochondria motility with alpha-tubulin acetylation and is disrupted in CMT2A ]]> https://biorxiv.org/content/10.1101/2023.03.15.532838v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@3db8eorg.highwire.dtl.DTLVardef@143821corg.highwire.dtl.DTLVardef@1132b13org.highwire.dtl.DTLVardef@1710383_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMitochondria contacts with MTs are hotspots of -tubulin acetylation through the recruitment of ATAT1 by MFN2 C_LIO_LIMutations in MFN2 associated with CMT2A disease lose this activity by sequestering ATAT1 C_LIO_LIDistal axonal degeneration caused by loss of MFN2 depends on acetylated tubulin-mediated mitochondria transport C_LI eTOCRecruitment of ATAT1 to mitochondria by MFN2 is critical for axonal viability through the regulation of mitochondria transport, and is disrupted in CMT2A ]]> Kumar, A. Larrea, D. Pero, M. E. Infante, P. Conenna, M. Shin, G. J.-e. Grueber, W. B. Di Marcotullio, L. Area-Gomez, E. Bartolini, F. 2023-03-16 doi:10.1101/2023.03.15.532838 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ TorchLens: A Python package for extracting and visualizing hidden activations of PyTorch models ]]> https://biorxiv.org/content/10.1101/2023.03.16.532916v1?rss=1 Taylor, J. E. Kriegeskorte, N. 2023-03-18 doi:10.1101/2023.03.16.532916 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ How far are we from personalized gene expression prediction using sequence-to-expression deep neural networks? ]]> https://biorxiv.org/content/10.1101/2023.03.16.532969v1?rss=1 Sasse, A. Ng, B. Spiro, A. Tasaki, S. Bennett, D. Gaiteri, C. De Jager, P. L. Chikina, M. Mostafavi, S. 2023-03-20 doi:10.1101/2023.03.16.532969 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Actomyosin pulsing rescues embryonic tissue folding from disruption by myosin fluctuations ]]> https://biorxiv.org/content/10.1101/2023.03.16.533016v1?rss=1 Zhu, H. O'Shaughnessy, B. 2023-03-18 doi:10.1101/2023.03.16.533016 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Perirhinal Cortex Learns A Predictive Map of The Task Environment ]]> https://biorxiv.org/content/10.1101/2023.03.17.532214v1?rss=1 Lee, D. G. McLachlan, C. A. Nogueira, R. Kwon, O. Carey, A. House, G. Lagani, G. D. LaMay, D. Fusi, S. Chen, J. L. 2023-03-18 doi:10.1101/2023.03.17.532214 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases ]]> https://biorxiv.org/content/10.1101/2023.03.17.533036v1?rss=1 Lampe, G. D. King, R. T. Halpin-Healy, T. S. Klompe, S. E. Hogan, M. I. Vo, P. L. H. Tang, S. Chavez, A. Sternberg, S. H. 2023-03-18 doi:10.1101/2023.03.17.533036 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Leptomeningeal anti-tumor immunity follows unique signaling principles ]]> https://biorxiv.org/content/10.1101/2023.03.17.533041v1?rss=1 Remsik, J. Tong, X. Kunes, R. Z. Li, M. J. Osman, A. Chabot, K. Sener, U. Wilcox, J. A. Isakov, D. Snyder, J. Bale, T. Chaligne, R. Pe'er, D. D. Boire, A. 2023-03-20 doi:10.1101/2023.03.17.533041 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ 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[ Bacterial genome engineering using CRISPR RNA-guided transposases ]]> https://biorxiv.org/content/10.1101/2023.03.18.533263v1?rss=1 Gelsinger, D. R. Vo, P. L. H. Klompe, S. E. Ronda, C. Wang, H. H. Sternberg, S. H. 2023-03-21 doi:10.1101/2023.03.18.533263 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.03.19.533333v1?rss=1 Maurer, H. C. Curiel-Garcia, A. Holmstrom, S. Laise, P. Palermo, C. F. Sastra, S. A. Andren, A. Li, Z. LeLarge, T. Sagalovskiy, I. Ross, D. R. Rosarioo, V. Lu, K. Ferraiuolo, E. Spinosa, N. Wong, W. Shaw, K. Chabot, J. A. Genkinger, J. Hibshoosh, H. Manji, G. A. Iuga, A. Schmid, R. M. Badgley, M. A. Johnson, K. Califano, A. Lyssiotis, C. Olive, K. P. 2023-03-21 doi:10.1101/2023.03.19.533333 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.03.21.533654v1?rss=1 Bartosch, A. M. W. Youth, E. H. H. Hansen, S. Kaufman, M. E. Xiao, H. Koo, S. Y. Ashok, A. Sivakumar, S. Soni, R. K. Dumitrescu, L. C. Lam, T. G. Ropri, A. S. Lee, A. J. Klein, H.-U. Vardarajan, B. N. Bennett, D. A. J. Young-Pearse, T. De Jager, P. L. Hohman, T. J. Sproul, A. A. Teich, A. F. 2023-03-21 doi:10.1101/2023.03.21.533654 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Spatial Proteomics Reveals Novel TREM2 Interactors in ER-Mitochondria Interface in Microglia ]]> https://biorxiv.org/content/10.1101/2023.03.21.533722v1?rss=1 Kwak, C. Finan, G. M. Park, Y. R. Mun, J. Y. Rhee, H.-W. Kim, T.-W. 2023-03-24 doi:10.1101/2023.03.21.533722 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2023.03.22.533805v1?rss=1 Wang, Q. Li, Z. Guo, Y. Mellis, I. A. Iketani, S. Liu, M. Yu, J. Valdez, R. Lauring, A. S. Sheng, Z. Gordon, A. Liu, L. Ho, D. D. 2023-03-22 doi:10.1101/2023.03.22.533805 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[ ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes ]]> https://biorxiv.org/content/10.1101/2023.03.22.533832v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@16f3e10org.highwire.dtl.DTLVardef@538f39org.highwire.dtl.DTLVardef@1e00d4eorg.highwire.dtl.DTLVardef@89967d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nixon-Abell, J. Ruggeri, F. S. Qamar, S. Herling, T. W. Czekalska, M. A. Shen, Y. Wang, G. King, C. Fernandopulle, M. S. Sneideris, T. Watson, J. L. Pillai, V. V. Meadows, W. Henderson, J. Chambers, J. E. Wagstaff, J. L. Williams, S. H. Coyle, H. Lu, Y. Zhang, S. Marciniak, S. J. Freund, S. M. Derivery, E. Ward, M. E. Vendruscolo, M. Knowles, T. P. St George Hyslop, P. 2023-03-24 doi:10.1101/2023.03.22.533832 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Functional identification of language-responsive channels in individual participants in MEG investigations ]]> https://biorxiv.org/content/10.1101/2023.03.23.533424v1?rss=1 Bruffaerts, R. Pongos, A. Shain, C. Lipkin, B. Siegelman, M. Wens, V. Sjogard, M. Pantazis, D. Blank, I. Goldman, S. De Tiege, X. Fedorenko, E. 2023-03-23 doi:10.1101/2023.03.23.533424 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Environmental correlates of tree reproductive phenology in a tropical state of India - insights from a citizen science project ]]> https://biorxiv.org/content/10.1101/2023.03.24.533907v1?rss=1 Anujan, K. Mardian, J. Luo, C. Rajkumar, R. SeasonWatch Citizen Scientist Network, Tasic, H. Akseer, N. Ramaswami, G. 2023-03-25 doi:10.1101/2023.03.24.533907 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions ]]> https://biorxiv.org/content/10.1101/2023.03.24.534143v1?rss=1 Huang, X. Balmer, S. Lyu, C. Xiang, Y. Malik, V. Wang, H. Zhang, Y. Xie, W. Hadjantonakis, A.-K. Zhou, H. Wang, J. 2023-03-25 doi:10.1101/2023.03.24.534143 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut ]]> https://biorxiv.org/content/10.1101/2023.03.25.534219v1?rss=1 Fogarty, E. C. Schechter, M. S. Lolans, K. Sheahan, M. L. Veseli, I. Moore, R. Kiefl, E. Moody, T. Rice, P. A. Yu, M. K. Mimee, M. Chang, E. B. McLellan, S. L. Willis, A. D. Comstock, L. E. Eren, A. M. 2023-03-25 doi:10.1101/2023.03.25.534219 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Activity-dependent subcellular compartmentalization of dendritic mitochondria structure in CA1 pyramidal neurons ]]> https://biorxiv.org/content/10.1101/2023.03.25.534233v1?rss=1 Virga, D. M. Hamilton, S. Osei, B. Morgan, A. Zamponi, E. Park, N. J. Hewitt, V. L. Zhang, D. Gonzalez, K. C. Bloss, E. Polleux, F. Lewis, T. L. 2023-03-26 doi:10.1101/2023.03.25.534233 Cold Spring Harbor Laboratory Press 2023-03-26 <![CDATA[ Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.03.26.534192v1?rss=1 Jackson, C. Cherry, C. Bom, S. Dykema, A. Thompson, E. Zheng, M. Ji, Z. Hou, W. Li, R. Zhang, H. Choi, J. Rodriguez, F. Weingart, J. Yegnasubramanian, S. Lim, M. Bettegowda, C. Powell, J. Eliesseff, J. Ji, H. Pardoll, D. 2023-03-27 doi:10.1101/2023.03.26.534192 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Loss of Grem1-articular cartilage progenitor cells causes osteoarthritis. ]]> https://biorxiv.org/content/10.1101/2023.03.29.534651v1?rss=1 Ng, J. Q. Jafarov, T. H. Little, C. B. Wang, T. Ali, A. Ma, Y. Radford, G. Vrbanac, L. Ichinose, M. Whittle, S. Hunter, D. Lannagan, T. Suzuki, N. Goyne, J. M. Kobayashi, H. WANG, T. C. Haynes, D. Menicanin, D. Gronthos, S. Worthley, D. L. Woods, S. L. Mukherjee, S. 2023-03-30 doi:10.1101/2023.03.29.534651 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Medial Prefrontal Cortex Serotonin Input Regulates Cognitive Flexibility in Mice ]]> https://biorxiv.org/content/10.1101/2023.03.30.534775v1?rss=1 Morgan, A. A. Alves, N. D. Stevens, G. S. Yeasmin, T. Mackay, A. Power, S. K. Sargin, D. Hanna, C. Adib, A. Ziolkowski-Blake, A. Lambe, E. K. Ansorge, M. S. 2023-03-30 doi:10.1101/2023.03.30.534775 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ A high-throughput approach reveals distinct peptide charging behaviors in electrospray ionization mass spectrometry ]]> https://biorxiv.org/content/10.1101/2023.03.31.535171v1?rss=1 Xu, A. M. Tang, L. C. Jovanovic, M. Regev, O. 2023-04-03 doi:10.1101/2023.03.31.535171 Cold Spring Harbor Laboratory Press 2023-04-03 <![CDATA[ ALDH2 dysfunction accelerates ESCC pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.04.03.534985v1?rss=1 Flashner, S. Shimonosono, M. Matsuura, N. Ohashi, S. Klein-Szanto, A. J. Diehl, J. A. Chen, C.-H. Nakagawa, H. 2023-04-05 doi:10.1101/2023.04.03.534985 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Colorectal cancer detection and treatment with engineered probiotics ]]> https://biorxiv.org/content/10.1101/2023.04.03.535370v1?rss=1 Gurbatri, C. R. Radford, G. Vrbanac, L. Coker, C. Im, J. Taylor, S. R. Jang, Y. Sivan, A. Rhee, K. Saleh, A. A. Chien, T. Zandkarimi, F. Lia, I. Lannagan, T. R. Wang, T. Wright, J. A. Thomas, E. Kobayashi, H. Ng, J. Q. Lawrence, M. Sammour, T. Thomas, M. Lewis, M. Papanicolas, L. Perry, J. Fitzsimmons, T. Kaazan, P. Lim, A. Marker, J. Ostroff, C. Rogers, G. Arpaia, N. Worthley, D. L. Woods, S. L. Danino, T. 2023-04-05 doi:10.1101/2023.04.03.535370 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Potential Immunomodulatory Role of Lead in Monocyte/Macrophage Differentiation ]]> https://biorxiv.org/content/10.1101/2023.04.03.535415v1?rss=1 Nicholson, S. M. Schanne, F. A. X. 2023-04-05 doi:10.1101/2023.04.03.535415 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Lead (Pb) Inhibits-PMA Induced Microglia Multinucleation ]]> https://biorxiv.org/content/10.1101/2023.04.04.535606v1?rss=1 Nicholson, S. M. Schanne, F. A. X. Chen, K. 2023-04-06 doi:10.1101/2023.04.04.535606 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Suppression of ferroptosis by vitamin A or antioxidants is essential for neuronal development ]]> https://biorxiv.org/content/10.1101/2023.04.05.535746v1?rss=1 Tschuck, J. Padmanabhan Nair, V. Galhoz, A. Ciceri, G. Rothenaigner, I. Tchieu, J. Tai, H.-M. Stockwell, B. R. Studer, L. Menden, M. P. Vincendeau, M. Hadian, K. 2023-04-05 doi:10.1101/2023.04.05.535746 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ α-Melanocyte-Stimulating Hormone Regulates Pathological Cardiac Remodeling by Activating Melanocortin 5 Receptor in Cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2023.04.06.535956v1?rss=1 Suominen, A. M. Saldo Rubio, G. Ruohonen, S. Szabo, Z. Pohjolainen, L. Ghimire, B. Ruohonen, S. T. Saukkonen, K. Ijas, J. Skarp, S. Kaikkonen, L. Cai, M. Wardlaw, S. L. Ruskoaho, H. Talman, V. Savontaus, E. Kerkelä, R. Rinne, P. 2023-04-11 doi:10.1101/2023.04.06.535956 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking ]]> https://biorxiv.org/content/10.1101/2023.04.08.536123v1?rss=1 Liu, L. Casner, R. G. Guo, Y. Wang, Q. Iketani, S. Chan, J. F.-W. Yu, J. Dadonaite, B. Nair, M. S. Mohri, H. Reddem, E. R. Yuan, S. Poon, V. K.-M. Chan, C. C.-S. Yuen, K.-Y. Sheng, Z. Huang, Y. Bloom, J. D. Shapiro, L. Ho, D. D. 2023-04-10 doi:10.1101/2023.04.08.536123 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ A rapid and bidirectional reporter of neural activity reveals neural correlates of social behaviors in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.04.10.536242v1?rss=1 Bonheur, M. Swartz, K. J. Metcalf, M. G. Zhukovskaya, A. Mehta, A. Connors, K. E. Barasch, J. G. Wen, X. Jamieson, A. R. Martin, K. C. Axel, R. Hattori, D. 2023-04-11 doi:10.1101/2023.04.10.536242 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ A potential patient stratification biomarker for Parkinson's disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells ]]> https://biorxiv.org/content/10.1101/2023.04.11.536367v1?rss=1 Naaldijk, Y. Fernandez, B. Fasiczka, R. Fdez, E. Leghay, C. Croitoru, I. Kwok, J. B. Boulesnane, Y. Vizeneux, A. Mutez, E. Calvez, C. Destee, A. Taymans, J.-M. Vinagre Aragon, A. Bergareche Yarza, A. Padmanabhan, S. Delgado, M. Alcalay, R. N. Chatterton, Z. Dzamko, N. Halliday, G. Ruiz-Martinez, J. Chartier-Harlin, M.-C. Hilfiker, S. 2023-04-12 doi:10.1101/2023.04.11.536367 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Whole-brain mapping reveals the divergent impact of ketamine on the dopamine system ]]> https://biorxiv.org/content/10.1101/2023.04.12.536506v1?rss=1 Datta, M. S. Chen, Y. Chauhan, S. Zhang, J. De La Cruz, E. D. Gong, C. Tomer, R. 2023-04-12 doi:10.1101/2023.04.12.536506 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes ]]> https://biorxiv.org/content/10.1101/2023.04.13.536805v1?rss=1 Paudel, B. B. Tan, S.-F. Fox, T. E. Ung, J. Shaw, J. Dunton, W. Lee, I. Sharma, A. Viny, A. D. Barth, B. M. Tallman, M. S. Cabot, M. Garrett-Bakelman, F. E. Levine, R. L. Kester, M. Claxton, D. Feith, D. J. Janes, K. A. Loughran, T. P. 2023-04-17 doi:10.1101/2023.04.13.536805 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Building functional circuits in multispecies brains. ]]> https://biorxiv.org/content/10.1101/2023.04.13.536815v1?rss=1 Throesch, B. Imtiaz, M. K. Munoz-Castaneda, R. Sakurai, M. James, K. N. Rodriguez, A. Martin, G. S. Lippi, G. Kuprianov, S. Wu, Z. Osten, P. Belmonte, J. C. I. Wu, J. Baldwin, K. K. 2023-04-15 doi:10.1101/2023.04.13.536815 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model ]]> https://biorxiv.org/content/10.1101/2023.04.14.536893v1?rss=1 3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type. ]]> Zou, Y. Carbonetto, P. Xie, D. Wang, G. Stephens, M. 2023-04-14 doi:10.1101/2023.04.14.536893 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ A cell-type-specific nitric oxide-cGMP pathway regulates proprioceptor morphology ]]> https://biorxiv.org/content/10.1101/2023.04.14.536921v1?rss=1 Cohn, R. Kolba, N. Picache, J. A. Lin, N. Saleem, A. Grueber, W. 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Bartolini, F. Stefani, F. D. Caceres, A. Bisbal, M. 2023-04-17 doi:10.1101/2023.04.17.537156 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Factorized visual representations in the primate visual system and deep neural networks ]]> https://biorxiv.org/content/10.1101/2023.04.22.537916v1?rss=1 Lindsey, J. W. Issa, E. B. 2023-04-22 doi:10.1101/2023.04.22.537916 Cold Spring Harbor Laboratory Press 2023-04-22 <![CDATA[ A DRG genetic toolkit reveals molecular, morphological, and functional diversity of somatosensory neuron subtypes ]]> https://biorxiv.org/content/10.1101/2023.04.22.537932v1?rss=1 Qi, L. Iskols, M. Shi, D. Reddy, P. Walker, C. Lezgiyeva, K. Voisin, T. Pawlak, M. Kuchroo, V. K. Chiu, I. Ginty, D. D. Sharma, N. 2023-04-23 doi:10.1101/2023.04.22.537932 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ 3D structural human interactome reveals proteome-wide perturbations by disease mutations ]]> https://biorxiv.org/content/10.1101/2023.04.24.538110v1?rss=1 Xiong, D. Zhao, J. Qiu, Y. Zhou, Y. Lee, D. Gupta, S. Lu, W. Liang, S. Kang, J. J. Eng, C. Loscalzo, J. Cheng, F. Yu, H. 2023-04-25 doi:10.1101/2023.04.24.538110 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors. ]]> https://biorxiv.org/content/10.1101/2023.04.24.538118v1?rss=1 Karagiannis, D. Wu, W. Li, A. Hayashi, M. Chen, X. Yip, M. Mangipudi, V. Xu, X. Sanchez-Rivera, F. J. Soto-Feliciano, Y. M. Ye, J. Papagiannakopoulos, T. Lu, C. 2023-04-28 doi:10.1101/2023.04.24.538118 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Pathogenic Mutations in the C2A Domain of Dysferlin form Amyloid that Activates the Inflammasome. ]]> https://biorxiv.org/content/10.1101/2023.04.24.538129v1?rss=1 Scott, I. L. Dominguez, M. J. Snow, A. Harsini, F. M. Williams, J. Fuson, K. L. Thapa, R. Bhattacharjee, P. Cornwall, G. A. Keyel, P. A. Sutton, R. B. 2023-04-26 doi:10.1101/2023.04.24.538129 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ The mitochondrial Ca2+ channel MCU is critical for tumor growth by supporting cell cycle progression and proliferation ]]> https://biorxiv.org/content/10.1101/2023.04.26.538295v1?rss=1 Fernandez Garcia, E. Paudel, U. Noji, M. C. Bowman, C. E. Pitarresi, J. R. Rustgi, A. K. Wellen, K. E. Arany, Z. Weissenrieder, J. S. Foskett, J. K. 2023-04-28 doi:10.1101/2023.04.26.538295 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Visually evoked neuronal ensembles reactivate during sleep ]]> https://biorxiv.org/content/10.1101/2023.04.26.538480v1?rss=1 Lines, J. Yuste, R. 2023-04-27 doi:10.1101/2023.04.26.538480 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ A benchmark study on current GWAS models in admixed populations ]]> https://biorxiv.org/content/10.1101/2023.04.27.538299v1?rss=1 Yang, Z. Huaman, B. Reyes-Dumeyer, D. Montesinos, R. Soto-Anari, M. Custodio, N. Tosto, G. 2023-04-28 doi:10.1101/2023.04.27.538299 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools ]]> https://biorxiv.org/content/10.1101/2023.04.28.538703v1?rss=1 Biderman, D. Whiteway, M. R. Hurwitz, C. Greenspan, N. R. Lee, R. S. Vishnubhotla, A. Schartner, M. Huntenburg, J. M. Khanal, A. Meijer, G. T. Noel, J.-P. Pan-Vazquez, A. Socha, K. Z. Urai, A. E. The International Brain Laboratory, Warren, R. Noone, D. Pedraja, F. Cunningham, J. Sawtell, N. B. Paninski, L. 2023-04-28 doi:10.1101/2023.04.28.538703 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ A transposase-derived gene required for human brain development ]]> https://biorxiv.org/content/10.1101/2023.04.28.538770v1?rss=1 Jubierre Zapater, L. Rodriguez Fos, E. Planas-Felix, M. Lewis, S. Cameron, D. Demarest, P. Nabila, A. Zhao, J. Bergin, P. Reed, C. Yamada, M. Socci, N. Hayes, M. Rabadan, R. Torrents, D. Kruer, M. C. Toth, M. Kentsis, A. 2023-04-28 doi:10.1101/2023.04.28.538770 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Deep immunological imprinting due to the ancestral spike in the current bivalent COVID-19 vaccine ]]> https://biorxiv.org/content/10.1101/2023.05.03.539268v1?rss=1 Wang, Q. Guo, Y. Tam, A. R. Valdez, R. Gordon, A. Lihong, L. Ho, D. D. 2023-05-04 doi:10.1101/2023.05.03.539268 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Amyloid pathology impairs homeostatic inhibitory synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2023.05.04.539450v1?rss=1 Niraula, S. Yan, S. S. Subramanian, J. 2023-05-05 doi:10.1101/2023.05.04.539450 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Soluble antigen arrays improve the efficacy and safety of peptide-based tolerogenic immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.05.05.539161v1?rss=1 Firdessa Fite, R. Johnson, S. N. Leon, M. A. Sestak, J. O. Berkland, C. Creusot, R. J. 2023-05-07 doi:10.1101/2023.05.05.539161 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Apposed networks of interacting TCRs and BCRs exhibiting mosaicked CDR3 sequences made of fixed junctional motifs ]]> https://biorxiv.org/content/10.1101/2023.05.06.539704v1?rss=1 Ahmed, R. Majety, N. Chan, K. C. Giwa, A. Heinemann, J. Zhang, H. Margolick, J. Al-Hallaf, R. Paul, P. Bell, D. R. Song, Y. Lee, S. Zhou, R. Wolfe, R. M. Donner, T. Jie, C. Hamad, A. R. A. 2023-05-08 doi:10.1101/2023.05.06.539704 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Exploration biases how forelimb reaches to a spatial target are learned ]]> https://biorxiv.org/content/10.1101/2023.05.08.539291v1?rss=1 Mosberger, A. C. Sibener, L. J. Chen, T. X. Rodrigues, H. F. Hormigo, R. Ingram, J. N. Athalye, V. R. Tabachnik, T. Wolpert, D. M. Murray, J. M. Costa, R. M. 2023-05-08 doi:10.1101/2023.05.08.539291 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Sprouty4 is required for Mdm2 regulation of invasion, focal adhesion formation and metastasis in cells lacking p53. ]]> https://biorxiv.org/content/10.1101/2023.05.08.539890v1?rss=1 de Queiroz, R. M. Efe, G. Guzman, A. Hashimoto, N. Kawashima, Y. Tanaka, T. Rutsgi, A. K. Prives, C. 2023-05-09 doi:10.1101/2023.05.08.539890 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Transcription Coupled Repair of DNA Interstrand Crosslinks by UVSSA ]]> https://biorxiv.org/content/10.1101/2023.05.10.538304v1?rss=1 Liebau, R. C. Waters, C. Ahmed, A. Soni, R. K. Gautier, J. 2023-05-10 doi:10.1101/2023.05.10.538304 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.05.10.540158v1?rss=1 Rayamajhi, D. Ege, M. Ukhanov, K. Ringers, C. Zhang, Y. Jeong, I. D'Gama, P. P. Li, S. S. Cosacak, M. I. Kizil, C. Park, H.-C. Yaksi, E. Martens, J. R. Brody, S. L. Jurisch-Yaksi, N. Roy, S. 2023-05-10 doi:10.1101/2023.05.10.540158 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome ]]> https://biorxiv.org/content/10.1101/2023.05.10.540203v1?rss=1 Yang, X.-c. Desotell, A. Lin, M.-H. Paige, A. S. Malinowska, A. Sun, Y. Aik, W. S. Dadlez, M. Tong, L. Dominski, Z. 2023-05-10 doi:10.1101/2023.05.10.540203 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Polygenic Risk Associated with Alzheimer's Disease and Other Traits Influences Genes Involved in T Cell Signaling and Activation ]]> https://biorxiv.org/content/10.1101/2023.05.10.540219v1?rss=1 Dressman, D. Tasaki, S. Yu, L. Schneider, J. A. Bennett, D. A. Elyaman, W. Vardarajan, B. N. 2023-05-13 doi:10.1101/2023.05.10.540219 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations ]]> https://biorxiv.org/content/10.1101/2023.05.11.540442v1?rss=1 Holt, C. J. Miller, K. D. Ahmadian, Y. 2023-05-12 doi:10.1101/2023.05.11.540442 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ SEPTIN 7 INTERACTS WITH NUMB TO PRESERVE SARCOMERE STRUCTURAL ORGANIZATION AND MUSCLE CONTRACTILE FUNCTION. ]]> https://biorxiv.org/content/10.1101/2023.05.11.540467v1?rss=1 De Gasperi, R. Csernoch, L. Dienes, B. Gonczi, M. Chakrabarty, J. K. Goeta, S. Aslan, A. Toro, C. A. Karasik, D. Brown, L. M. Brotto, M. Cardozo, C. P. 2023-05-14 doi:10.1101/2023.05.11.540467 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Modulation of infraslow oscillation in the dentate gyrus during Non-REM sleep ]]> https://biorxiv.org/content/10.1101/2023.05.12.540575v1?rss=1 Turi, G. F. Chen, X. Teng, S. Lim, E. C. Dias, C. Hu, R. Zhen, F. Peng, Y. 2023-05-13 doi:10.1101/2023.05.12.540575 Cold Spring Harbor Laboratory Press 2023-05-13 <![CDATA[ Spatial Tracking Across Time (ST AT ): Tracking Neurons Across In-Vivo Imaging Sessions through Optimizing Local Neighborhood Motion Consistency ]]> https://biorxiv.org/content/10.1101/2023.05.13.540658v1?rss=1 Gu, S. Mackevicius, E. L. Fee, M. S. Zhou, P. 2023-05-14 doi:10.1101/2023.05.13.540658 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ DNA damage primes hematopoietic stem cells for direct megakaryopoiesis ]]> https://biorxiv.org/content/10.1101/2023.05.13.540665v1?rss=1 Garyn, C. M. Bover, O. Murray, J. W. Jing, M. Salas Briceno, K. J. Ross, S. R. Snoeck, H.-W. 2023-05-15 doi:10.1101/2023.05.13.540665 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Phase-tuned neuronal firing encodes human contextual representations for navigational goals ]]> https://biorxiv.org/content/10.1101/202374v1?rss=1 Watrous, A. J. Miller, J. Qasim, S. E. Fried, I. Jacobs, J. 2017-10-12 doi:10.1101/202374 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ Comprehensive single cell RNAseq analysis of the kidney reveals novel cell types and unexpected cell plasticity ]]> https://biorxiv.org/content/10.1101/203125v1?rss=1 Park, J. Shrestha, R. Qiu, C. Kondo, A. Huang, S. Werth, M. Li, M. Barasch, J. Susztak, K. 2017-10-13 doi:10.1101/203125 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ Decisions are expedited through multiple neural adjustments spanning the sensorimotor hierarchy ]]> https://biorxiv.org/content/10.1101/203141v1?rss=1 Steinemann, N. A. O'Connell, R. G. Kelly, S. P. 2017-10-14 doi:10.1101/203141 Cold Spring Harbor Laboratory Press 2017-10-14 <![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[ Adapterama III: Quadruple-indexed, triple-enzyme RADseq libraries for about $1USD per Sample (3RAD) ]]> https://biorxiv.org/content/10.1101/205799v1?rss=1 Glenn, T. C. Bayona-Vasquez, N. J. Kieran, T. J. Pierson, T. W. Hoffberg, S. L. Scott, P. A. Bentley, K. E. Finger, J. W. Watson, P. R. Louha, S. Troendle, N. Diaz-Jaimes, P. Mauricio, R. Faircloth, B. C. 2017-10-19 doi:10.1101/205799 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ A molecular network of the aging brain implicates INPPL1 and PLXNB1 in Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/205807v1?rss=1 Mostafavi, S. Gaiteri, C. Sullivan, S. White, C. Takasi, S. Xu, J. Taga, M. Klein, H. Patrick, E. Komashko, V. McCable, C. Smith, R. Bradshaw, E. Root, D. Yu, L. Regev, A. Chibnik, L. Schneider, J. Young-Pearse, T. Bennett, D. De Jager, P. 2017-10-19 doi:10.1101/205807 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Distinct Epigenomic Patterns Are Associated with Haploinsufficiency and Predict Risk Genes of Developmental Disorders ]]> https://biorxiv.org/content/10.1101/205849v1?rss=1 Han, X. Chen, S. Flynn, E. D. Wintner, D. Shen, Y. 2017-10-19 doi:10.1101/205849 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Genetic analysis of de novo variants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicates MYRF as a candidate gene ]]> https://biorxiv.org/content/10.1101/206037v1?rss=1 Qi, H. Yu, L. Zhou, X. Kitaygorodsky, A. Wynn, J. Zhu, N. Aspelund, G. Lim, F. Y. Crombleholme, T. Cusick, R. Azarow, K. Danko, M. E. Chung, D. Warner, B. W. Mychaliska, G. B. Potoka, D. Wagner, A. J. ElFiky, M. Wilson, J. M. High, F. A. Longoni, M. Donahoe, P. Chung, W. K. Shen, Y. 2017-10-19 doi:10.1101/206037 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Life history effects on neutral polymorphism levels of autosomes and sex chromosomes ]]> https://biorxiv.org/content/10.1101/206862v1?rss=1 Amster, G. Sella, G. 2017-10-20 doi:10.1101/206862 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ How Cognitive and Reactive Fear Circuits Optimize Escape Decisions in Humans ]]> https://biorxiv.org/content/10.1101/207936v1?rss=1 Qi, S. Sun, J. Guo, F. Daw, N. Hassabis, D. Mobbs, D. 2017-10-23 doi:10.1101/207936 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Division-independent differentiation mandates proliferative competition among stem cells ]]> https://biorxiv.org/content/10.1101/208983v1?rss=1 Reilein, A. Melamed, D. Tavare, S. Kalderon, D. 2017-10-25 doi:10.1101/208983 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Gene expression in patient-derived neural progenitors provide insights into neurodevelopmental aspects of schizophrenia ]]> https://biorxiv.org/content/10.1101/209197v1?rss=1 Evgrafov, O. V. Armoskus, C. Wrobel, B. B. Spitsyna, V. N. Souaiaia, T. Herstein, J. S. Walker, C. P. Nguyen, J. D. Camarena, A. Weitz, J. R. Kim, J. M. H. Lopez Duarte, E. Wang, K. Simpson, G. M. Sobell, J. L. Medeiros, H. Pato, M. T. Pato, C. N. Knowles, J. A. 2017-10-26 doi:10.1101/209197 Cold Spring Harbor Laboratory Press 2017-10-26 <![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[ Molecular basis for the recognition of the human AAUAAA polyadenylation signal ]]> https://biorxiv.org/content/10.1101/209809v1?rss=1 Sun, Y. Zhang, Y. Hamilton, K. Manley, J. L. Shi, Y. Walz, T. Tong, L. 2017-10-27 doi:10.1101/209809 Cold Spring Harbor Laboratory Press 2017-10-27 <![CDATA[ Pathogen Population Structure Can Explain Hospital Outbreaks ]]> https://biorxiv.org/content/10.1101/210534v1?rss=1 Spagnolo, F. Cristofari, P. Tattonetti, N. P. Ginzburg, L. R. Dykhuizen, D. E. 2017-10-31 doi:10.1101/210534 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ The role of chromosomal inversions in speciation ]]> https://biorxiv.org/content/10.1101/211771v1?rss=1 Fuller, Z. Leonard, C. Young, R. Schaeffer, S. Phadnis, N. 2017-10-31 doi:10.1101/211771 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes ]]> https://biorxiv.org/content/10.1101/212407v1?rss=1 Schumer, M. Xu, C. Powell, D. Durvasula, A. Skov, L. Holland, C. Sankararaman, S. Andolfatto, P. Rosenthal, G. Przeworski, M. 2017-11-01 doi:10.1101/212407 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Spatio-temporal elasticity patterns in extracellular matrix during Hydra morphogenesis ]]> https://biorxiv.org/content/10.1101/214718v1?rss=1 Veschgini, M. Petersen, H. O. Abuillan, W. Rossetti, F. F. Özbek, S. Burghammer, M. Holstein, T. W. Tanaka, M. 2017-11-06 doi:10.1101/214718 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ The medial temporal lobe organizes memory across time and space: Causal evidence from brain stimulation ]]> https://biorxiv.org/content/10.1101/215806v1?rss=1 Goyal, A. Miller, J. Watrous, A. J. Lee, S. A. Coffey, T. Sperling, M. Sharan, A. Worrell, G. Brent, B. Lega, B. Jobst, B. C. Davis, K. Gross, R. Sheth, S. Ezzyat, Y. Das, S. Stein, J. Gorniak, R. Kahana, M. Rizzuto, D. Jacobs, J. 2017-11-07 doi:10.1101/215806 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ Russian Doll Genes and Complex Chromosome Rearrangements in Oytricha trifallax ]]> https://biorxiv.org/content/10.1101/216440v1?rss=1 Braun, J. Nabergall, L. Neme, R. Landweber, L. Saito, M. Jonoska, N. 2017-11-08 doi:10.1101/216440 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Electrophysiological signatures of spatial boundaries in the human subiculum ]]> https://biorxiv.org/content/10.1101/218040v1?rss=1 Lee, S. A. Miller, J. F. Watrous, A. J. Sperling, M. Sharan, A. Worrell, G. A. Berry, B. M. Jobst, B. C. Davis, K. A. Gross, R. E. Lega, B. Sheth, S. Das, S. R. Stein, J. M. Gorniak, R. Rizzuto, D. S. Jacobs, J. 2017-11-12 doi:10.1101/218040 Cold Spring Harbor Laboratory Press 2017-11-12 <![CDATA[ Theta and alpha oscillations are traveling waves in the human neocortex ]]> https://biorxiv.org/content/10.1101/218198v1?rss=1 Zhang, H. Watrous, A. J. Patel, A. Jacobs, J. 2017-11-11 doi:10.1101/218198 Cold Spring Harbor Laboratory Press 2017-11-11 <![CDATA[ Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus ]]> https://biorxiv.org/content/10.1101/219683v1?rss=1 Quinodoz, S. A. Ollikainen, N. Tabak, B. Palla, A. Schmidt, J. M. Detmar, E. Lai, M. Shishkin, A. Bhat, P. Trinh, V. Aznauryan, E. Russell, P. Cheng, C. Jovanovic, M. Chow, A. McDonel, P. Garber, M. Guttman, M. 2017-11-18 doi:10.1101/219683 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Stopping Transformed Growth with Cytoskeletal Proteins: Turning a Devil into an Angel ]]> https://biorxiv.org/content/10.1101/221176v1?rss=1 Yang, B. Wolfenson, H. Nakazawa, N. Liu, S. Hu, J. Sheetz, M. 2017-11-17 doi:10.1101/221176 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions. ]]> https://biorxiv.org/content/10.1101/221358v1?rss=1 Suzuki, I. K. Gacquer, D. Van Heurck, R. Kumar, D. Wojno, M. Bilheu, A. Herpoel, A. Cheron, J. Polleux, F. Detours, V. Vanderhaeghen, P. 2017-11-17 doi:10.1101/221358 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/221994v1?rss=1 Azizi, E. Carr, A. J. Plitas, G. Cornish, A. E. Konopacki, C. Prabhakaran, S. Nainys, J. Wu, K. Kiseliovas, V. Setty, M. Choi, K. Dao, P. Mazutis, L. Rudensky, A. Y. Pe'er, D. 2017-11-25 doi:10.1101/221994 Cold Spring Harbor Laboratory Press 2017-11-25 <![CDATA[ An atlas of Caenorhabditis elegans chemoreceptor expression ]]> https://biorxiv.org/content/10.1101/222570v1?rss=1 Vidal, B. Aghayeva, U. Sun, H. Wang, C. Glenwinkel, L. Bayer, E. Hobert, O. 2017-11-20 doi:10.1101/222570 Cold Spring Harbor Laboratory Press 2017-11-20 <![CDATA[ Peptidomimetic blockade of MYB in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/222620v1?rss=1 Ramaswamy, K. Forbes, L. Minuesa, G. Gindin, T. Brown, F. Kharas, M. Krivtsov, A. Armstrong, S. Still, E. de Stanchina, E. Knoechel, B. Koche, R. Kentsis, A. 2017-11-20 doi:10.1101/222620 Cold Spring Harbor Laboratory Press 2017-11-20 <![CDATA[ Experimental assay of a fitness landscape on a macroevolutionary scale ]]> https://biorxiv.org/content/10.1101/222778v1?rss=1 Pokusaeva, V. Usmanova, D. Putintseva, E. Espinar, L. Sarkisyan, K. Mishin, A. Bogatyreva, N. Ivankov, D. Filion, G. Carey, L. Kondrashov, F. A. 2017-11-21 doi:10.1101/222778 Cold Spring Harbor Laboratory Press 2017-11-21 <![CDATA[ Cyclin-Dependent Kinase Activity is Required for Type I Interferon Production ]]> https://biorxiv.org/content/10.1101/224121v1?rss=1 Cingoz, O. Goff, S. 2017-11-22 doi:10.1101/224121 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Elevated polygenic burden for autism is associated with differential DNA methylation at birth. ]]> https://biorxiv.org/content/10.1101/225193v1?rss=1 Hannon, E. Schendel, D. Ladd-Acosta, C. Grove, J. iPSYCH-Broad ASD Group, Hansen, C. S. Andrews, S. V. Hougaard, D. Bresnahan, M. Mors, O. Hollegaard, M. V. Baekvad-Hansen, M. Hornig, M. Mortensen, P. B. Borglum, A. Werge, T. Pedersen, M. G. Nordentoft, M. Buxbaum, J. Fallin, D. Bybjerg-Grauholm, J. Reichenberg, A. Mill, J. 2017-11-26 doi:10.1101/225193 Cold Spring Harbor Laboratory Press 2017-11-26 <![CDATA[ Systems genetics identifies modifiers of Alzheimer’s disease risk and resilience ]]> https://biorxiv.org/content/10.1101/225714v1?rss=1 Neuner, S. M. Hohman, T. J. Richholt, R. Bennett, D. A. Schneider, J. A. De Jager, P. L. Huentelman, M. J. O'Connell, K. M. S. Kaczorowski, C. C. 2017-11-27 doi:10.1101/225714 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Identification and Targeting of Cortical Ensembles ]]> https://biorxiv.org/content/10.1101/226514v1?rss=1 Carrillo-Reid, L. Han, S. Taralova, E. Jebara, T. Yuste, R. 2017-11-29 doi:10.1101/226514 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Counterfactual reasoning underlies the learning of priors in decision making ]]> https://biorxiv.org/content/10.1101/227421v1?rss=1 Zylberberg, A. Wolpert, D. M. Shadlen, M. N. 2017-11-30 doi:10.1101/227421 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ An open resource for nonhuman primate imaging ]]> https://biorxiv.org/content/10.1101/227462v1?rss=1 Milham, M. Ai, L. Koo, B. Xu, T. Balezeau, F. Baxter, M. G. Croxson, P. L. Damatac, C. G. Harel, N. Freiwald, W. Griffiths, T. D. Everling, S. Jung, B. Kastner, S. Leopold, D. A. Mars, R. B. Menon, R. S. Messinger, A. Morrison, J. H. Nacef, J. Nagy, J. Rios, M. O. Petkov, C. I. Pinsk, M. Poirier, C. Rajimehr, R. Rushworth, M. F. Russ, B. E. Schmid, M. Schwiedrzik, C. M. Sallet, J. Seidlitz, J. Ungerleider, L. Thiele, A. Tsao, D. Yacoub, E. Ye, F. Zarco, W. Margulies, D. S. Schroeder, C. E. 2017-11-30 doi:10.1101/227462 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Accurate estimation of neural population dynamics without spike sorting ]]> https://biorxiv.org/content/10.1101/229252v1?rss=1 Trautmann, E. Stavisky, S. Lahiri, S. Ames, K. Kaufman, M. Ryu, S. Ganguli, S. Shenoy, K. 2017-12-05 doi:10.1101/229252 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Routine Single Particle CryoEM Sample and Grid Characterization by Tomography ]]> https://biorxiv.org/content/10.1101/230276v1?rss=1 Noble, A. J. Dandey, V. P. Wei, H. Brasch, J. Chase, J. Acharya, P. Tan, Y. Z. Zhang, Z. Kim, L. Y. Scapin, G. Rapp, M. Eng, E. T. Rice, W. J. Cheng, A. Negro, C. J. Shapiro, L. Kwong, P. D. Jeruzalmi, D. des Georges, A. Potter, C. S. Carragher, B. 2017-12-07 doi:10.1101/230276 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES ]]> https://biorxiv.org/content/10.1101/230615v1?rss=1 Fernandez, I. S. Pisareva, V. P. Pisarev, A. V. 2017-12-07 doi:10.1101/230615 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ Association of BDNF Val66Met Polymorphism and Brain BDNF levels with Major Depression and Suicide ]]> https://biorxiv.org/content/10.1101/233304v1?rss=1 Youssef, M. Underwood, M. Huang, Y.-Y. Hsiung, S.-c. Liu, Y. Simpson, N. Bakalian, M. Rosoklija, G. Dwork, A. J. Arango, V. Mann, J. J. 2017-12-30 doi:10.1101/233304 Cold Spring Harbor Laboratory Press 2017-12-30 <![CDATA[ Understanding Biological Visual Attention Using Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/233338v1?rss=1 Lindsay, G. W. Miller, K. D. 2017-12-13 doi:10.1101/233338 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ A cortical immune network map identifies a subset of human microglia involved in Tau pathology ]]> https://biorxiv.org/content/10.1101/234351v1?rss=1 Patrick, E. Olah, M. Taga, M. Klein, H.-U. Xu, J. White, C. C. Felsky, D. Gaiteri, C. Chibnik, L. B. Mostafavi, S. Schneider, J. A. Bennett, D. A. Bradshaw, E. M. De Jager, P. L. 2017-12-14 doi:10.1101/234351 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ The signaling lipid sphingosine 1-phosphate regulates mechanical pain ]]> https://biorxiv.org/content/10.1101/236778v1?rss=1 Hill, R. Z. Hoffman, B. Morita, T. Campos, S. M. Lumpkin, E. A. Brem, R. B. Bautista, D. M. 2017-12-19 doi:10.1101/236778 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons ]]> https://biorxiv.org/content/10.1101/237347v1?rss=1 Yuan, Y. Xie, S. Darnell, J. C. Darnell, A. J. Saito, Y. Phatnani, H. Murphy, E. Zhang, C. Maniatis, T. Darnell, R. 2018-01-07 doi:10.1101/237347 Cold Spring Harbor Laboratory Press 2018-01-07 <![CDATA[ A Parallel Processing Model of Drosophila Olfactory Sensory Neurons and Its Biological Validation ]]> https://biorxiv.org/content/10.1101/237669v1?rss=1 Lazar, A. A. A. Yeh, C.-H. 2017-12-21 doi:10.1101/237669 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Olfactory and Vomeronasal Receptor Feedback Employ Divergent Mechanisms of PERK Activation ]]> https://biorxiv.org/content/10.1101/239830v1?rss=1 Dalton, R. Karagoz, E. Kahiapo, J. Sharma, R. Bashkirova, L. Lyons, D. Matsunami, H. Walter, P. 2018-01-04 doi:10.1101/239830 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases ]]> https://biorxiv.org/content/10.1101/240408v1?rss=1 95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases. ]]> Welch, D. Buonanno, M. Grilj, V. Shuryak, I. Crickmore, C. Bigelow, A. W. Randers-Pehrson, G. Johnson, G. W. Brenner, D. J. 2017-12-28 doi:10.1101/240408 Cold Spring Harbor Laboratory Press 2017-12-28 <![CDATA[ Large-scale, high-resolution comparison of the core visual object recognition behavior of humans, monkeys, and state-of-the-art deep artificial neural networks ]]> https://biorxiv.org/content/10.1101/240614v1?rss=1 Rajalingham, R. Issa, E. B. Bashivan, P. Kar, K. Schmidt, K. DiCarlo, J. J. 2018-01-01 doi:10.1101/240614 Cold Spring Harbor Laboratory Press 2018-01-01 <![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[ meaRtools: an R package for the Comprehensive Analysis of Neuronal Networks Recorded on Multi-Electrode Arrays ]]> https://biorxiv.org/content/10.1101/242065v1?rss=1 =3) and is updated frequently on the CRAN web-server repository. The package, along with full documentation can be downloaded from: https://cran.r-project.org/web/packages/meaRtools/.nnAuthor summaryCultured neuronal networks are widely used to study and characterize neuronal network activity. Among the many uses of neuronal cultures are the capabilities to evaluate neurotoxicity and the effects of pharmacological compounds on cellular physiology. Multi-well microelectrode arrays (MEAs) can collect high-throughput data from multiple neuronal cultures simultaneously, and thereby make possible hypotheses-driven inquiries into neurobiology and neuropharmacology. The analysis of MEA-derived information presents many computational challenges. High frequency data recorded simultaneously from hundreds of electrodes can be difficult to handle. The need to compare network activity across various drug treatments or genotypes recorded on the same plate from experiments lasting several weeks presents another challenge. These challenges inspired us to develop meaRtools; an MEA data analysis package that contains new methods to characterize network activity patterns, which are illustrated here using examples from a genetic mouse model of epilepsy. Among the highlights of meaRtools are novel algorithms designed to characterize neuronal activity dynamics and network properties such as bursting and synchronization, options to combine multiple recordings and use a robust statistical framework to draw appropriate statistical inferences, and finally data visualizations and plots. In summary, meaRtools provides a platform for the analyses of singular and longitudinal MEA experiments. ]]> Gelfman, S. Wang, Q. Lu, Y.-F. Hall, D. Bostick, C. Dhindsa, R. Halvorsen, M. McSweeney, K. M. Cotterill, E. Edinburgh, T. Petrovski, S. Boland, M. J. Allen, A. S. Goldstein, D. B. Eglen, S. J. 2018-01-02 doi:10.1101/242065 Cold Spring Harbor Laboratory Press 2018-01-02 <![CDATA[ Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages ]]> https://biorxiv.org/content/10.1101/242123v1?rss=1 Bunnik, E. M. Cook, K. B. Varoquaux, N. Batugedara, G. Prudhomme, J. Shi, L. Andolina, C. Ross, L. S. Brady, D. Fidock, D. A. Nosten, F. Tewari, R. Sinnis, P. Ay, F. Vert, J.-P. Noble, W. Le Roch, K. G. 2018-01-02 doi:10.1101/242123 Cold Spring Harbor Laboratory Press 2018-01-02 <![CDATA[ Investigating the viral ecology of global bee communities with high-throughput metagenomics ]]> https://biorxiv.org/content/10.1101/243139v1?rss=1 0.1 % of the reads in a given sample. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for metagenomics analysis of viruses, and greatly expands our understanding of the diversity of viruses found in bee communities. ]]> Galbraith, D. A. Fuller, Z. Brockmann, A. Frazier, M. Gikungu, M. W. Kapheim, K. M. Kerby, J. T. Kocher, S. D. Losyev, O. Muli, E. Patch, H. M. Sakamoto, J. M. Stanley, S. Vaudo, A. D. Grozinger, C. M. 2018-01-04 doi:10.1101/243139 Cold Spring Harbor Laboratory Press 2018-01-04 <![CDATA[ Evolutionary tradeoffs and the structure of allelic polymorphisms ]]> https://biorxiv.org/content/10.1101/244210v1?rss=1 Sheftel, H. Szekely, P. Mayo, A. Sella, G. Alon, U. 2018-01-06 doi:10.1101/244210 Cold Spring Harbor Laboratory Press 2018-01-06 <![CDATA[ Precise temporal regulation of alternative splicing during neural development ]]> https://biorxiv.org/content/10.1101/247601v1?rss=1 Weyn-Vanhentenryck, S. M. Feng, H. Ustianenko, D. Duffie, R. Yan, Q. Jacko, M. Martinez, J. C. Goodwin, M. Zhang, X. Hengst, U. Lomvardas, S. Swanson, M. S. Zhang, C. 2018-01-14 doi:10.1101/247601 Cold Spring Harbor Laboratory Press 2018-01-14 <![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[ Accurate analysis of genuine CRISPR editing events with ampliCan ]]> https://biorxiv.org/content/10.1101/249474v1?rss=1 Labun, K. Guo, X. Chavez, A. Church, G. Gagnon, J. A. Valen, E. 2018-01-17 doi:10.1101/249474 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ 2-APB arrests human keratinocyte proliferation and inhibits cutaneous squamous cell carcinoma in vitro ]]> https://biorxiv.org/content/10.1101/249821v1?rss=1 Nelson, A. M. Moayedi, Y. Greenberg, S. A. Ruiz, M. E. Jensen, U. B. Owens, D. M. Lumpkin, E. A. 2018-01-23 doi:10.1101/249821 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ Single-Cell Transcriptome Analysis of Lineage Diversity and Microenvironment in High-Grade Glioma ]]> https://biorxiv.org/content/10.1101/250704v1?rss=1 Yuan, J. Levitin, H. M. Frattini, V. Bush, E. C. Samanamud, J. Ceccarelli, M. Dovas, A. Zanazzi, G. Canoll, P. Bruce, J. N. Lasorella, A. Iavarone, A. Sims, P. A. 2018-01-19 doi:10.1101/250704 Cold Spring Harbor Laboratory Press 2018-01-19 <![CDATA[ Quantitative Assessment of Protein Activity in Orphan Tissues and Single Cells Using the metaVIPER Algorithm ]]> https://biorxiv.org/content/10.1101/252072v1?rss=1 Ding, H. Douglass, E. F. Sonabend, A. M. Mela, A. Bose, S. Gonzalez, C. Canoll, P. D. Sims, P. A. Alvarez, M. J. Califano, A. 2018-01-22 doi:10.1101/252072 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Structure-guided design of a cell penetrating peptide preventing cAMP modulation of HCN channels ]]> https://biorxiv.org/content/10.1101/253096v1?rss=1 Moroni, A. Saponaro, A. Cantini, F. Porro, A. Bucchi, A. DiFrancesco, D. Maione, V. Donadoni, C. Introini, B. Mesirca, P. Mangoni, M. E. Thiel, G. Banci, L. Santoro, B. 2018-01-24 doi:10.1101/253096 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ 10 Year Epidemiologic data of Parkinson`s Disease: A Nationwide Population-based Retrospective Cohort of South Korea ]]> https://biorxiv.org/content/10.1101/253682v1?rss=1 Kim, H. S. Kwon, J.-B. Lim, H. S. Cha, j. Kim, H. W. 2018-01-26 doi:10.1101/253682 Cold Spring Harbor Laboratory Press 2018-01-26 <![CDATA[ Risk factors associated with Parkinson’s disease: An 11-year population-based South Korean study ]]> https://biorxiv.org/content/10.1101/253690v1?rss=1 Kim, H. S. Lee, H.-J. Cha, J. Kwon, J. Lim, H. 2018-01-26 doi:10.1101/253690 Cold Spring Harbor Laboratory Press 2018-01-26 <![CDATA[ Accurate Prediction of Alzheimer’s Disease Using Multi-Modal MRI and High-Throughput Brain Phenotyping ]]> https://biorxiv.org/content/10.1101/255141v1?rss=1 Wang, Y. Xu, C. Lee, S. Stern, Y. Kim, J. H. Yoo, S. Kim, H. S. Cha, J. 2018-01-30 doi:10.1101/255141 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform ]]> https://biorxiv.org/content/10.1101/257196v1?rss=1 Wei, S. Williams, Z. Weiss, Z. R. 2018-01-31 doi:10.1101/257196 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ MVP: predicting pathogenicity of missense variants by deep neural networks ]]> https://biorxiv.org/content/10.1101/259390v1?rss=1 Qi, H. Chen, C. Zhang, H. Long, J. J. Chung, W. K. Guan, Y. Shen, Y. 2018-02-02 doi:10.1101/259390 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Inference of population structure from ancient DNA ]]> https://biorxiv.org/content/10.1101/261131v1?rss=1 Joseph, T. A. Pe'er, I. 2018-02-07 doi:10.1101/261131 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Emergence of Human Amygdala Functional Networks: 3 Months to 5 Years of Age ]]> https://biorxiv.org/content/10.1101/261347v1?rss=1 Gabard-Durnam, L. J. O'Muircheartaigh, J. Dirks, H. Dean, D. Tottenham, N. Deoni, S. 2018-02-07 doi:10.1101/261347 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Generation of pulmonary neuro-endocrine cells and tumors resembling small cell lung cancers from human embryonic stem cells ]]> https://biorxiv.org/content/10.1101/261461v1?rss=1 Chen, J. Poran, A. Unni, A. Huang, S. Elemento, O. Snoeck, H.-W. Varmus, H. 2018-02-07 doi:10.1101/261461 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Diet Modifies Colonic Microbiota and CD4+ T cell Repertoire to Trigger Flares in a Novel Model of Colitis Induced by IL-23 ]]> https://biorxiv.org/content/10.1101/262634v1?rss=1 Chen, L. He, Z. Iuga, A. C. Filho, S. M. Faith, J. J. Clemente, J. C. Deshpande, M. Jayaprakash, A. Colombel, J.-F. Lafaille, J. J. Sachidanandam, R. Furtado, G. C. Lira, S. A. 2018-02-08 doi:10.1101/262634 Cold Spring Harbor Laboratory Press 2018-02-08 <![CDATA[ Haploinsufficiency of autism candidate gene NUAK1 impairs cortical development and behavior ]]> https://biorxiv.org/content/10.1101/262725v1?rss=1 Courchet, V. Roberts, A. J. Del Carmine, P. Lewis, T. L. Polleux, F. Courchet, J. 2018-02-09 doi:10.1101/262725 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ From categories to dimensions: spatio-temporal dynamics of the cerebral representations of emotion in voice ]]> https://biorxiv.org/content/10.1101/265843v1?rss=1 500ms). Our results thus show that both categorical and dimensional models account for patterns of cerebral responses to emotions in voices but with a different timeline and detail as to how these patterns evolve from discrete categories to progressively refined continuous dimensions.nnOne Sentence Summary: Emotions expressed in the voice are instantly categorized in cortical processing and their distinct qualities are refined dimensionally only later on. ]]> Giordano, B. L. Whiting, C. Kriegeskorte, N. Kotz, S. A. Belin, P. Gross, J. 2018-02-15 doi:10.1101/265843 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Spacing of Cue-approach Training Leads to Better Maintenance of Behavioral Change ]]> https://biorxiv.org/content/10.1101/268821v1?rss=1 Bakkour, A. Botvinik Nezer, R. Cohen, N. Hover, A. M. Poldrack, R. A. Schonberg, T. 2018-02-21 doi:10.1101/268821 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Value-based decisions involve sequential sampling from memory ]]> https://biorxiv.org/content/10.1101/269290v1?rss=1 Bakkour, A. Zylberberg, A. Shadlen, M. N. Shohamy, D. 2018-02-22 doi:10.1101/269290 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ Hedgehog signaling controls progenitor differentiation timing during heart development ]]> https://biorxiv.org/content/10.1101/270751v1?rss=1 Rowton, M. Hoffmann, A. D. Steimle, J. D. Yang, X. H. Guzzetta, A. Lazarevic, S. Kim, C. Deng, N. Lu, E. Jacobs-Li, J. Yu, S. Hanson, E. Perez-Cervantes, C. Chan, S. S.-K. Ikegami, K. Garry, D. J. Kyba, M. Moskowitz, I. P. 2018-02-23 doi:10.1101/270751 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Identification of changing ribosome protein compositions using cryo-EM and mass spectrometry ]]> https://biorxiv.org/content/10.1101/271833v1?rss=1 Frank, J. 2018-02-26 doi:10.1101/271833 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/272278v1?rss=1 Khan, A. Liu, Q. Chen, X. Zeng, Y. Stucky, A. Sedghizadeh, P. P. Adelpour, D. Zhang, X. Wang, K. Zhong, J. F. 2018-02-26 doi:10.1101/272278 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Dazl regulates germ cell survival through a network of polyA proximal mRNA interactions ]]> https://biorxiv.org/content/10.1101/273292v1?rss=1 Zagore, L. L. Sweet, T. J. Hannigan, M. M. Weyn-Vanhentenryck, S. M. Zhang, C. Licatalosi, D. D. 2018-02-28 doi:10.1101/273292 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Epigenome-wide study uncovers tau pathology-driven changes of chromatin organization in the aging human brain ]]> https://biorxiv.org/content/10.1101/273789v1?rss=1 Klein, H.-U. McCabe, C. Gjoneska, E. Sullivan, S. E. Kaskow, B. J. Tang, A. Smith, R. V. Xu, J. Pfenning, A. R. Bernstein, B. E. Meissner, A. Schneider, J. A. Mostafavi, S. Tsai, L.-H. Young-Pearse, T. L. Bennett, D. A. De Jager, P. L. 2018-02-28 doi:10.1101/273789 Cold Spring Harbor Laboratory Press 2018-02-28 <![CDATA[ Electrodiffusion model of synaptic potentials in dendritic spines ]]> https://biorxiv.org/content/10.1101/274373v1?rss=1 Lagache, T. Jayant, K. Yuste, R. 2018-03-01 doi:10.1101/274373 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Rapid preimplantation genetic screening (PGS) using a handheld, nanopore-based, DNA sequencer ]]> https://biorxiv.org/content/10.1101/274563v1?rss=1 3.5 hours) and sequencing (>12 hours) times. Whole-chromosome aneuploidy screening results obtained from nanopore-based sequencing were identical to those obtained using NGS.nnConclusion(s)Methods for PGS of embryos have evolved from FISH to microarrays and most recently to NGS. Here we report the first application of nanopore-based sequencing for PGS on trophecoderm biopsy samples using a rapid multiplex short-read nanopore sequencing library preparation. Aneuploidy screening could be performed on 5 samples in one nanopore flowcell with 1 to 2 hour sequencing times. Overall, nanopore sequencing is a promising tool to perform rapid PGS assay onsite with a rapid turnover time, enabling same day testing and embryo transfer thus obviating the need for complex, large and expensive DNA sequencers or frozen embryos. ]]> Wei, S. Weiss, Z. R. Gaur, P. Forman, E. Williams, Z. 2018-03-01 doi:10.1101/274563 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Immediate early gene activation throughout the brain is associated with dynamic changes in social context ]]> https://biorxiv.org/content/10.1101/275495v1?rss=1 Williamson, C. M. Klein, I. S. Lee, W. Curley, J. P. 2018-03-02 doi:10.1101/275495 Cold Spring Harbor Laboratory Press 2018-03-02 <![CDATA[ An epigenetic biomarker of aging for lifespan and healthspan ]]> https://biorxiv.org/content/10.1101/276162v1?rss=1 Levine, M. E. Lu, A. T. Quach, A. Chen, B. Assimes, T. L. Bandinelli, S. Hou, L. Baccarelli, A. A. Stewart, J. D. Li, Y. Whitsel, E. A. Wilson, J. G. Reiner, A. P. Aviv, A. Lohman, K. Liu, Y. Ferrucci, L. Horvath, S. 2018-03-05 doi:10.1101/276162 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Scalable approximate Bayesian inference for particle tracking data ]]> https://biorxiv.org/content/10.1101/276253v1?rss=1 Sun, R. Paninski, L. 2018-03-05 doi:10.1101/276253 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ MFF-dependent mitochondrial fission regulates presynaptic release and axon branching by limiting axonal mitochondria size ]]> https://biorxiv.org/content/10.1101/276691v1?rss=1 Lewis, T. L. Kwon, S.-K. Lee, A. Shaw, R. Polleux, F. 2018-03-05 doi:10.1101/276691 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data ]]> https://biorxiv.org/content/10.1101/277178v1?rss=1 Liu, Q. Georgieva, D. C. Egli, D. Wang, K. 2018-03-05 doi:10.1101/277178 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Focal optogenetic suppression in macaque area MT biases direction discrimination and choice confidence, but only transiently ]]> https://biorxiv.org/content/10.1101/277251v1?rss=1 Fetsch, C. R. Odean, N. N. Jeurissen, D. El-Shamayleh, Y. Horwitz, G. D. Shadlen, M. N. 2018-03-06 doi:10.1101/277251 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ An eQTL landscape of kidney tissue in human nephrotic syndrome ]]> https://biorxiv.org/content/10.1101/281162v1?rss=1 1 independent signal associated with its expression. 12% and 26% of eQTLs were GLOM-specific and TI-specific, respectively. GLOM eQTLs were most significantly enriched in podocyte transcripts and TI eQTLs in proximal tubules. The IGAN TWAS identified significant GLOM & TI genes, primarily at the HLA region.nnIn this study of NS patients, we discovered GLOM & TI eQTLs, identified those that were tissue-specific, deconvoluted them into cell-specific signals, and used them to characterize known GWAS alleles. These data are publicly available for browsing and download at http://nephqtl.org. ]]> Gillies, C. E. Putler, R. Menon, R. Otto, E. Yasutake, K. Nair, V. Fermin, D. Eddy, S. Vega-Warner, V. Nephrotic Syndrome Study Network, Hacohen, N. Wen, X. Kretzler, M. Sampson, M. 2018-03-14 doi:10.1101/281162 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ A direct glia-to-neuron natural transdifferentiation ensures nimble sensory-motor coordination of male mating behaviour ]]> https://biorxiv.org/content/10.1101/285320v1?rss=1 Molina-Garcia, L. Cook, S. J. Kim, B. Bonnington, R. Sammut, M. O'Shea, J. Elliott, D. Hall, D. H. Emmons, S. Barrios, A. Poole, R. J. 2018-03-21 doi:10.1101/285320 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ A novel time-stamp mechanism transforms egocentric encounters into an allocentric spatial representation ]]> https://biorxiv.org/content/10.1101/285494v1?rss=1 Wallach, A. Harvey-Girard, E. Jun, J. J. Longtin, A. Maler, L. 2018-03-23 doi:10.1101/285494 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Optical Imaging of Metabolic Dynamics in Animals ]]> https://biorxiv.org/content/10.1101/285908v1?rss=1 Shi, L. Zheng, C. Shen, Y. Chen, Z. Silveira, E. S. Zhang, L. Wei, M. Liu, C. de Sena-Tomas, C. Targoff, K. Min, W. 2018-03-22 doi:10.1101/285908 Cold Spring Harbor Laboratory Press 2018-03-22 <![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[ Perturbed functional networks in Alzheimers Disease reveal opposing roles for TGIF and EGR3 ]]> https://biorxiv.org/content/10.1101/286674v1?rss=1 Canchi, S. Raao, B. Masliah, D. Rosenthal, S. B. Sasik, R. Fisch, K. M. Jager, P. D. Bennett, D. A. Rissman, R. A. 2018-03-22 doi:10.1101/286674 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Inhibition of norepinephrine signaling during a sensitive period disrupts locus coeruleus circuitry and emotional behaviors in adulthood ]]> https://biorxiv.org/content/10.1101/287243v1?rss=1 Meng, Q. Garcia-Garcia, A. L. Dranovsky, A. Leonardo, E. D. 2018-03-23 doi:10.1101/287243 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Ldb1 mediates trans enhancement in mammals ]]> https://biorxiv.org/content/10.1101/287524v1?rss=1 Monahan, K. Horta, A. Mumbay-Wafula, A. Li, L. Zhao, Y. Love, P. Lomvardas, S. 2018-03-23 doi:10.1101/287524 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity ]]> https://biorxiv.org/content/10.1101/287532v1?rss=1 30 intergenic enhancers generate a multi-chromosomal hub that associates only with the single active OR from a pool of [~]1400 genes. Our data reveal that interchromosomal interactions can form with remarkable stereotypy between like neurons, generating a regulatory landscape for stochastic, monogenic, and monoallelic gene expression. ]]> Horta, A. Monahan, K. Bashkirova, L. Lomvardas, S. 2018-03-23 doi:10.1101/287532 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Simulations and Electrostatic Analysis Suggest an Active Role for DNA Conformational Changes During Genome Packaging by Bacteriophages ]]> https://biorxiv.org/content/10.1101/288415v1?rss=1 Sharp, K. A. Lu, X.-J. Cingolani, G. Harvey, S. C. 2018-03-30 doi:10.1101/288415 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Systematic Elucidation and Validation of OncoProtein-Centric Molecular Interaction Maps ]]> https://biorxiv.org/content/10.1101/289538v1?rss=1 Broyde, J. Simpson, D. R. Murray, D. Giorgi, F. M. Lachmann, A. Jackson, P. K. Sweet-Cordero, E. A. Honig, B. Califano, A. 2018-03-27 doi:10.1101/289538 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis ]]> https://biorxiv.org/content/10.1101/289603v1?rss=1 60% accuracy by SILAC assays, including "novel substrates of the EGFR and c-MET TKs, which play a critical oncogenic role in lung cancer. This systematic, data-driven model supported drug response prediction on an individual sample basis, including accurate prediction and validation of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either gene, thus contributing to current precision oncology efforts. ]]> Bansal, M. Peyton, M. He, J. Kaustagi, M. Iyer, A. Comb, M. White, M. Minna, J. Califano, A. 2018-03-29 doi:10.1101/289603 Cold Spring Harbor Laboratory Press 2018-03-29 <![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[ Hippocampal signature of associative memory measured by chronic ambulatory intracranial EEG ]]> https://biorxiv.org/content/10.1101/291740v1?rss=1 Henin, S. Shankar, A. Hasulak, N. Friedman, D. Dugan, P. Melloni, L. Flinker, A. Sarac, C. Fang, M. Doyle, W. Tcheng, T. Devinsky, O. Davachi, L. Liu, A. 2018-03-30 doi:10.1101/291740 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots ]]> https://biorxiv.org/content/10.1101/291922v1?rss=1 Dashti, A. Ben Hail, D. Mashayekhi, G. Schwander, P. des Georges, A. Frank, J. Ourmazd, A. 2018-03-30 doi:10.1101/291922 Cold Spring Harbor Laboratory Press 2018-03-30 <![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[ Effects of exclusive breastfeeding on infant gut microbiota: a meta-analysis across studies and populations ]]> https://biorxiv.org/content/10.1101/292755v1?rss=1 Ho, N. T. Li, F. Lee-Sarwar, K. A. Tun, H. M. Brown, B. Pannaraj, P. S. Wood, L. F. Bender, J. M. Sordillo, J. E. Azad, M. B. Thompson, A. L. Weiss, S. T. Azcarate-Peril, M. A. Litonjua, A. A. Kozyrskyj, A. L. Jaspan, H. B. Aldrovandi, G. M. Kuhn, L. 2018-03-31 doi:10.1101/292755 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ A distributed neural code in ensembles of dentate gyrus granule cells ]]> https://biorxiv.org/content/10.1101/292953v1?rss=1 Stefanini, F. Kheirbek, M. Kushnir, L. Jennings, J. H. Stuber, G. Hen, R. Fusi, S. 2018-04-03 doi:10.1101/292953 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Electrophysiological evidence for cerebellar involvement in higher-order cognitive processing ]]> https://biorxiv.org/content/10.1101/294454v1?rss=1 Sendhilnathan, N. Semework, M. Goldberg, M. E. Ipata, A. E. 2018-04-03 doi:10.1101/294454 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effect models ]]> https://biorxiv.org/content/10.1101/294678v1?rss=1 Ho, N. T. Li, F. 2018-04-04 doi:10.1101/294678 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments ]]> https://biorxiv.org/content/10.1101/295071v1?rss=1 Farek, J. Hughes, D. Mansfield, A. Krasheninina, O. Nasser, W. Sedlazeck, F. J. Khan, Z. Venner, E. Metcalf, G. Boerwinkle, E. Muzny, D. M. Gibbs, R. A. Salerno, W. 2018-04-05 doi:10.1101/295071 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ VenomKB v2.0: A knowledge repository for computational toxinology ]]> https://biorxiv.org/content/10.1101/295204v1?rss=1 Romano, J. Nwankwo, V. Tatonetti, N. 2018-04-06 doi:10.1101/295204 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Flexible coding of memory and space in the primate hippocampus during virtual navigation ]]> https://biorxiv.org/content/10.1101/295774v1?rss=1 Gulli, R. A. Duong, L. Corrigan, B. W. Doucet, G. Williams, S. Fusi, S. Martinez-Trujillo, J. C. 2018-04-06 doi:10.1101/295774 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Myosin filaments reversibly generate large forces in cells ]]> https://biorxiv.org/content/10.1101/296400v1?rss=1 Lohner, J. Rupprecht, J.-F. Hu, J. Mandriota, N. Saxena, M. Hone, J. Pitta de Araujo, D. Sahin, O. Prost, J. Sheetz, M. 2018-04-09 doi:10.1101/296400 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Prospective Motion correction improves the sensitivity of fMRI pattern decoding ]]> https://biorxiv.org/content/10.1101/296442v1?rss=1 Huang, P. Carlin, J. D. Alink, A. N. Kriegeskorte, N. M. Henson, R. N. Correia, M. M. 2018-04-09 doi:10.1101/296442 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Rational design of a compact CRISPR-Cas9 activator for AAV- mediated delivery ]]> https://biorxiv.org/content/10.1101/298620v1?rss=1 Vora, S. Cheng, J. Xiao, R. VanDusen, N. J. Quintino, L. Pu, W. T. Vandenberghe, L. H. Chavez, A. Church, G. 2018-04-15 doi:10.1101/298620 Cold Spring Harbor Laboratory Press 2018-04-15 <![CDATA[ Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase in E. coli ]]> https://biorxiv.org/content/10.1101/303594v1?rss=1 Rajagopalan, K. Dworkin, J. 2018-04-18 doi:10.1101/303594 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Spatio-temporally specific transcranial magnetic stimulation to test the locus of perceptual decision making in the human brain ]]> https://biorxiv.org/content/10.1101/304063v1?rss=1 300ms post stimulus onset) in the lateral occipital cortex (LOC) to object discrimination processes. We applied paired-pulse transcranial magnetic stimulation (ppTMS) to LOC at different temporal latencies with the specific prediction, based on these studies, that ppTMS beginning at 400ms after stimulus onset would slow reaction time (RT) performance. Thirteen healthy adults performed a two-alternative forced choice task selecting whether a car or face was present on each trial amidst visual noise pre-titrated to approximate 79% accuracy. ppTMS, with pulses separated by 50ms, was applied at one of five stimulus onset asynchronies: -200, 200, 400, 450, or 500ms, and a sixth no-stimulation condition. As predicted, TMS at 400ms resulted in significant slowing of RTs, providing causal evidence in support of LOC contribution to perceptual decision processing. In addition, TMS delivered at -200ms resulted in faster RTs, indicating early stimulation may result in performance enhancement. These findings build upon correlational EEG and fMRI observations and demonstrate the use of TMS in predictive validation of psychophysiological models. ]]> Luber, B. Jangraw, D. C. Appelbaum, L. G. Harrison, A. Hilbig, S. Beynel, L. Jones, T. Sajda, P. Lisanby, S. H. 2018-04-18 doi:10.1101/304063 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Sub-2 A Ewald Curvature Corrected Single-Particle Cryo-EM ]]> https://biorxiv.org/content/10.1101/305599v1?rss=1 Tan, Y. Z. Aiyer, S. Mietzsch, M. Hull, J. A. McKenna, R. Grieger, J. Samulski, R. J. Baker, T. S. Agbandje-McKenna, M. Lyumkis, D. 2018-04-21 doi:10.1101/305599 Cold Spring Harbor Laboratory Press 2018-04-21 <![CDATA[ Whole Exome Sequencing in 20,197 Persons for Rare Variants in Alzheimer Disease ]]> https://biorxiv.org/content/10.1101/305631v1?rss=1 Raghavan, N. S. Brickman, A. M. Andrews, H. Manly, J. J. Schupf, N. Lantigua, R. The Alzheimers Disease Sequencing Project, Wolock, C. J. Kamalakaran, S. Petrovski, S. Tosto, G. Vardarajan, B. N. Goldstein, D. B. Mayeux, R. 2018-04-20 doi:10.1101/305631 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[ A common statistical misunderstanding in Psychology and Neuroscience: Do we need normally distributed independent or dependent variables for linear regression to work? ]]> https://biorxiv.org/content/10.1101/305946v1?rss=1 Habeck, C. Brickman, A. 2018-04-24 doi:10.1101/305946 Cold Spring Harbor Laboratory Press 2018-04-24 <![CDATA[ Molecular genetic analysis of Steroid Resistant Nephrotic Syndrome: Detection of a novel mutation ]]> https://biorxiv.org/content/10.1101/305987v1?rss=1 A; Q3524K). We identified 4 pathogenic mutations, located in exon 4 and 5 of NPHS2 gene in 20% of patients (V180M, P118L, R168C and Leu156Phe). Also our study has contributed to the descriptions of previously known pathogenic mutations across WT1 (R205C) and SMARCAL1 (R764Q) and a novel polymorphism in CRB2.nnConclusion: Our study concludes that mutations of exon 4 and 5 NPHS2 gene are common in Iranian and some other ethnic groups. We suggest conducting WES after NPHS2 screening and further comprehensive studies to identify the most common genes in the development of SRNS, which might help in Clinical impact on management in patients with SRNS.nnDetection of a novel mutation in SRNS ]]> Serajpour, N. Karimi, B. Hooman, N. Hosseini, R. Khosravi, P. Milo Rasouly, H. Shojaei, A. 2018-04-22 doi:10.1101/305987 Cold Spring Harbor Laboratory Press 2018-04-22 <![CDATA[ Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1 ]]> https://biorxiv.org/content/10.1101/306282v1?rss=1 Xu, K. Acharya, P. Kong, R. Cheng, C. Chuang, G.-Y. Liu, K. Louder, M. K. O Dell, S. Rawi, R. Sastry, M. Shen, C.-H. Zhang, B. Zhou, T. Asokan, M. Bailer, R. T. Chambers, M. Chen, X. Choi, C. W. Dandey, V. P. Doria-Rose, N. A. Druz, A. Eng, E. T. Farney, S. K. Foulds, K. E. Geng, H. Georgiev, I. S. Gorman, J. Hill, K. R. Jafari, A. J. Kwon, Y. D. Lai, Y.-T. Lemmin, T. McKee, K. Ohr, T. Y. Ou, L. Peng, D. Rowshan, A. P. Sheng, Z. Todd, J.-P. Tsybovsky, Y. Viox, E. G. Wang, Y. Wei, H. Yang, Y. Zhou, A. F. Chen, R. Yang, L. Scorpio, D. G. McDermott, 2018-04-23 doi:10.1101/306282 Cold Spring Harbor Laboratory Press 2018-04-23 <![CDATA[ Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients ]]> https://biorxiv.org/content/10.1101/307835v1?rss=1 Farhan, S. M. K. Howrigan, D. P. Abbott, L. Byrnes, A. Churchhouse, C. Phatnani, H. Smith, B. Topp, S. Rampersaud, E. Wu, G. Wuu, J. Gubitz, A. Kilm, J. Mordes, D. Ghosh, S. CReATe Consortium, FALS Consortium, ALSGENS Consortium, Eggan, K. Rademakers, R. McCauley, J. Schule, R. Zuchner, S. Benatar, M. Taylor, J. P. Nalls, M. Traynor, B. Shaw, C. Goldstein, D. Harms, M. Daly, M. Neale, B. 2018-04-25 doi:10.1101/307835 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Ablation of proliferating neural stem cells during early life is sufficient to reduce adult hippocampal neurogenesis ]]> https://biorxiv.org/content/10.1101/308387v1?rss=1 Youssef, M. Krish, V. S. Kirshenbaum, G. S. Atsak, P. Lass, T. J. Lieberman, S. R. Leonardo, E. D. Dranovsky, A. 2018-04-25 doi:10.1101/308387 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ iPSC-derived neurons as a tool for probing molecular pharmacology of antipsychotic action. ]]> https://biorxiv.org/content/10.1101/308486v1?rss=1 Kim, E. S. Leonardo, E. D. Dranovsky, A. 2018-04-25 doi:10.1101/308486 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Homeostatic plasticity scales dendritic spine volumes and changes the threshold and specificity of Hebbian plasticity ]]> https://biorxiv.org/content/10.1101/308965v1?rss=1 Hobbiss, A. F. Ramiro Cortes, Y. Israely, I. 2018-04-26 doi:10.1101/308965 Cold Spring Harbor Laboratory Press 2018-04-26 <![CDATA[ A Magnetic Head Design for Manipulating Single Proteins with Force ]]> https://biorxiv.org/content/10.1101/310060v1?rss=1 Tapia-Rojo, R. Eckels, E. C. Fernandez, J. M. 2018-04-28 doi:10.1101/310060 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ A CRISPR/Cas9 based strategy to manipulate the Alzheimer’s amyloid pathway ]]> https://biorxiv.org/content/10.1101/310193v1?rss=1 Sun, J. Carlson-Stevermer, J. Das, U. Shen, M. Delenclos, M. Snead, A. Wang, L. Loi, J. Petersen, A. Stockton, M. Bhattacharyya, A. Jones, M. Sproul, A. McLean, P. Zhao, X. Saha, K. Roy, S. 2018-04-28 doi:10.1101/310193 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Isopeptide-Blocker Impairs the Mechanics of Recently Translated Pilin Proteins ]]> https://biorxiv.org/content/10.1101/310227v1?rss=1 Rivas-Pardo, J. A. Tapia-Rojo, R. Badilla, C. L. Fernandez, J. M. 2018-04-28 doi:10.1101/310227 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Creating Standards for Evaluating Tumour Subclonal Reconstruction ]]> https://biorxiv.org/content/10.1101/310425v1?rss=1 Boutros, P. C. Salcedo, A. Tarabichi, M. Espiritu, S. M. G. Deshwar, A. G. David, M. Wilson, N. M. Dentro, S. Wintersinger, J. A. Liu, L. Y. Ko, M. Sivanandan, S. Zhang, H. Zhu, K. Yang, T.-H. Chilton, J. M. Buchanan, A. Lalansingh, C. M. P'ng, C. Anghel, C. V. Umar, I. Lo, B. Simpson, J. T. Stuart, J. M. Anastassiou, D. Guan, Y. Ewing, A. Ellrott, K. Wedge, D. C. Morris, Q. D. Van Loo, P. DREAM SMC-Het Participants, 2018-04-28 doi:10.1101/310425 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Quantification of human gut microbiota variability using replicate sampling and spike-in sequencing ]]> https://biorxiv.org/content/10.1101/310649v1?rss=1 Ji, B. W. Sheth, R. U. Dixit, P. D. Wang, H. H. Vitkup, D. 2018-05-02 doi:10.1101/310649 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Adult-born neurons maintain hippocampal cholinergic inputs and support working memory during aging ]]> https://biorxiv.org/content/10.1101/311423v1?rss=1 Kirshenbaum, G. Robson, V. K. Shansky, R. M. Savage, L. M. Leonardo, E. D. Dranovsky, A. 2018-04-30 doi:10.1101/311423 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Decision-making increases episodic memory via post-encoding consolidation. ]]> https://biorxiv.org/content/10.1101/311571v1?rss=1 Murty, V. DuBrow, S. Davachi, L. 2018-04-30 doi:10.1101/311571 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ Short-term effectiveness of HIV care coordination among persons with recent HIV diagnosis or history of poor HIV outcomes ]]> https://biorxiv.org/content/10.1101/311597v1?rss=1 Nash, D. Robertson, M. Penrose, K. Chamberlin, S. Robbins, R. R. Braunstein, S. L. Myers, J. E. Abraham, B. Kulkarni, S. Waldro, L. Levin, B. Irvine, M. K. 2018-05-02 doi:10.1101/311597 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates ]]> https://biorxiv.org/content/10.1101/312579v1?rss=1 25% of HIV-1 strains have now been identified that recognize all major exposed surfaces of the prefusion-closed Env trimer. Here we analyzed all 206 broadly neutralizing antibody-HIV-1 Env complexes in the PDB with resolution suitable to define their interaction chemistries. These segregated into 20 antibody classes based on ontogeny and recognition, and into 6 epitope categories (V1V2, glycan-V3, CD4-binding site, silent face center, fusion peptide, and subunit interface) based on recognized Env residues. We measured antibody neutralization on a 208-isolate panel and analyzed features of paratope and B cell ontogeny. The number of protruding loops, CDR H3 length, and level of somatic hypermutation for broadly HIV-1 neutralizing antibodies were significantly higher than for a comparison set of non-HIV-1 antibodies. For epitope, the number of independent sequence segments was higher (P < 0.0001), as well as the glycan component surface area (P = 0.0005). Based on B cell ontogeny, paratope, and breadth, the CD4-binding site antibody IOMA appeared to be a promising candidate for lineage-based vaccine design. In terms of epitope-based vaccine design, antibody VRC34.01 had few epitope segments, low epitope-glycan content, and high epitope-conformational variability, which may explain why VRC34.01-based design is yielding promising vaccine results. ]]> Chuang, G.-Y. Zhou, J. Rawi, R. Shen, C.-H. Sheng, Z. West, A. P. Zhang, B. Zhou, T. Bailer, R. T. Doria-Rose, N. A. Louder, M. K. McKee, K. Mascola, J. R. Bjorkman, P. J. Shapiro, L. Kwong, P. D. 2018-05-02 doi:10.1101/312579 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ The Pseudomonas aeruginosa complement of lactate dehydrogenases enables use of D- and L-lactate and metabolic crossfeeding ]]> https://biorxiv.org/content/10.1101/313593v1?rss=1 Lin, Y.-C. Cornell, W. C. Price-Whelan, A. Dietrich, L. E. P. 2018-05-03 doi:10.1101/313593 Cold Spring Harbor Laboratory Press 2018-05-03 <![CDATA[ Multisite phosphorylation regulates phenotypic variability in antibiotic tolerance ]]> https://biorxiv.org/content/10.1101/315085v1?rss=1 Libby, E. Reuveni, S. Dworkin, J. 2018-05-04 doi:10.1101/315085 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Systems Analysis of the 22q11.2 Microdeletion Syndrome Converges on a Mitochondrial Interactome Necessary for Synapse Function and Behavior ]]> https://biorxiv.org/content/10.1101/315143v1?rss=1 Gokhale, A. Freeman, A. A. Hartwig, C. Bassell, J. L. Zlatic, S. A. Sapp, C. Vadlamudi, T. Abudulai, F. Crocker, A. Werner, E. Wen, Z. Repetto, G. M. Gogos, J. A. Claypool, S. M. Forsyth, J. K. Bearden, C. Gausier, J. Lewis, D. A. Seyfried, N. T. Faundez, V. 2018-05-04 doi:10.1101/315143 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Trans-ethnic polygenic analysis supports genetic overlaps of lumbar disc degeneration with height, body mass index, and bone mineral density ]]> https://biorxiv.org/content/10.1101/316737v1?rss=1 Zhou, X. Cheung, C.-L. Karasugi, T. Karppinen, J. Samartzis, D. Hsu, Y.-H. Mak, T. S. H. Song, Y.-Q. Chiba, K. Kawaguchi, Y. Li, Y. Chan, D. Cheung, K. M.-C. Ikegawa, S. Cheah, K. S.-E. Sham, P. C. 2018-05-07 doi:10.1101/316737 Cold Spring Harbor Laboratory Press 2018-05-07 <![CDATA[ Genetic determinants of risk and survival in pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/317164v1?rss=1 16 years versus 8 years), compared to patients homozygous for the alternative allele.nnInterpretationWe have found that common genetic variation at loci in HLA-DPA1/DPB1 and an enhancer near SOX17 are associated with PAH. Impairment of Sox17 function may be more common in PAH than suggested by rare mutations in SOX17. Allelic variation at HLA-DPB1 stratifies PAH patients for survival following diagnosis, with implications for future therapeutic trial design.nnFundingUK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, Inserm, Universite Paris-Sud, and French ANR. ]]> Rhodes, C. Batai, K. Bleda, M. Haimel, M. Southgate, L. Germain, M. Pauciulo, M. Hadinnapola, C. Girerd, B. Arora, A. Knight, J. Hanscombe, K. Karnes, J. Kaakinen, M. Gall, H. Ulrich, A. Harbaum, L. Aman, J. Cebola, I. Ferrer, J. NIHR BioResource Rare Diseases Consortium, UK PAH Cohort Study Consortium, US PAH Biobank Consortium, Ahmad, F. Amouyel, P. Archer, S. Argula, R. Austin, E. Badesch, D. Bakshi, S. Barnett, C. Benza, R. Bhatt, N. Bogaard, H. Burger, C. Chakinala, M. Church, C. Coghlan, J. Condliffe, R. Corris, P. Danesino, C. Debette, S. 2018-05-16 doi:10.1101/317164 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Local Contractions Test Rigidity of E-Cadherin Adhesions ]]> https://biorxiv.org/content/10.1101/318642v1?rss=1 Yang, Y. Nguyen, E. Mege, R.-M. Ladoux, B. Sheetz, M. P. 2018-05-09 doi:10.1101/318642 Cold Spring Harbor Laboratory Press 2018-05-09 <![CDATA[ Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project ]]> https://biorxiv.org/content/10.1101/318857v1?rss=1 Naj, A. C. Lin, H. Vardarajan, B. N. White, S. Lancour, D. Ma, Y. Schmidt, M. Sun, F. Butkiewicz, M. Bush, W. S. Kunkle, B. W. Malamon, J. Amin, N. Choi, S. H. Hamilton-Nelson, K. L. van der Lee, S. J. Gupta, N. Koboldt, D. C. Saad, M. Wang, B. Nato, A. Q. Sohi, H. K. Kuzma, A. Alzheimer's Disease Sequencing Project (ADSP), Wang, L.-S. Cupples, L. A. van Duijn, C. Seshadri, S. Schellenberg, G. D. Boerwinkle, E. Bis, J. C. Dupuis, J. Salerno, W. J. Wijsman, E. M. Martin, E. DeStefano, A. L. 2018-05-11 doi:10.1101/318857 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knock-Out Mice ]]> https://biorxiv.org/content/10.1101/319368v1?rss=1 Das Sharma, S. Metz, J. B. Li, H. Hobson, B. D. Hornstein, N. Sulzer, D. Tang, G. Sims, P. A. 2018-05-10 doi:10.1101/319368 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Neuronal morphologies built for reliable physiology in a rhythmic motor circuit ]]> https://biorxiv.org/content/10.1101/319582v1?rss=1 Otopalik, A. G. Marder, E. 2018-05-11 doi:10.1101/319582 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions ]]> https://biorxiv.org/content/10.1101/319707v1?rss=1 Stimson, J. Gardy, J. L. Mathema, B. Crudu, V. Cohen, T. Colijn, C. 2018-05-10 doi:10.1101/319707 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ Tumor suppressor DAPK1 catalyzes adhesion assembly on rigid but anoikis on soft matrices ]]> https://biorxiv.org/content/10.1101/320739v1?rss=1 Qin, R. Wolfenson, H. Saxena, M. Sheetz, M. 2018-05-11 doi:10.1101/320739 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ GLMdenoise improves multivariate pattern analysis of fMRI data ]]> https://biorxiv.org/content/10.1101/320838v1?rss=1 Charest, I. Kriegeskorte, N. Kay, K. 2018-05-13 doi:10.1101/320838 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ Unattended but actively stored: EEG dynamics reveal a dissociation between selective attention and storage in working memory ]]> https://biorxiv.org/content/10.1101/320952v1?rss=1 Gunseli, E. Fahrenfort, J. J. van Moorselaar, D. Daoultzis, K. C. C. Meeter, M. Olivers, C. N. L. 2018-05-13 doi:10.1101/320952 Cold Spring Harbor Laboratory Press 2018-05-13 <![CDATA[ ZAG-1/ZEB and EGL-44/TEAD form a negative feedback loop to safeguard the choice of cell fate ]]> https://biorxiv.org/content/10.1101/320978v1?rss=1 Zheng, C. Jin, F. Q. Trippe, B. L. Chalfie, M. 2018-05-12 doi:10.1101/320978 Cold Spring Harbor Laboratory Press 2018-05-12 <![CDATA[ Epigenetic selection and the DNA methylation signatures of adverse prenatal environments ]]> https://biorxiv.org/content/10.1101/321711v1?rss=1 Tobi, E. van den Heuvel, J. Zwaan, B. Lumey, L. H. Heijmans, B. T. Uller, T. 2018-05-25 doi:10.1101/321711 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Loss-of-function in IRF2BPL is associated with neurological phenotypes ]]> https://biorxiv.org/content/10.1101/322495v1?rss=1 Marcogliese, P. C. Shashi, V. Spillmann, R. C. Stong, N. Rosenfeld, J. A. Koenig, M. K. Martinez-Agosto, J. A. Herzog, M. Chen, A. H. Dickson, P. I. Lin, H. J. Vera, M. U. Salamon, N. Ortiz, D. Infante, E. Steyaert, W. Dermaut, B. Poppe, B. Chung, H.-L. Zuo, Z. Lee, P.-T. Kanca, O. Xia, F. Yang, Y. Smith, E. C. Jasien, J. Kansagra, S. Spiridigliozzi, G. El-Dairi, M. Lark, R. Riley, K. Koeberl, D. D. Golden-Grant, K. Program for Undiagnosed Diseases (UD-PrOZA), Undiagnosed Diseases Network, Yamamoto, S. Wangler, M. F. Mirzaa, G. Hemelsoet, D. Lee, B. 2018-05-15 doi:10.1101/322495 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ D-amino acid-mediated translation arrest is modulated by the identity of the incoming aminoacyl-tRNA ]]> https://biorxiv.org/content/10.1101/323295v1?rss=1 Fleisher, R. C. Cornish, V. W. Gonzalez, R. L. 2018-05-26 doi:10.1101/323295 Cold Spring Harbor Laboratory Press 2018-05-26 <![CDATA[ Complex-centric proteome profiling by SEC-SWATH-MS ]]> https://biorxiv.org/content/10.1101/323683v1?rss=1 Heusel, M. Bludau, I. Rosenberger, G. Hafen, R. Frank, M. Banaei-Esfahani, A. Collins, B. Gstaiger, M. Aebersold, R. 2018-05-21 doi:10.1101/323683 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Common Neural Code for Reward and Information Value ]]> https://biorxiv.org/content/10.1101/324665v1?rss=1 Kobayashi, K. Hsu, M. 2018-05-17 doi:10.1101/324665 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Connecting Patterns of Tumor Growth with Sex Differences in Extreme Survivorship for Primary Glioblastoma Patients ]]> https://biorxiv.org/content/10.1101/325464v1?rss=1 Whitmire, P. Rickertsen, C. R. Hawkins-Daarud, A. Carrasco, E. Lorence, J. De Leon, G. Curtin, L. Bayless, S. Clark-Swanson, K. Peeri, N. C. Corpuz, C. Lewis-de los Angeles, C. P. Bendok, B. R. Gonzalez-Cuyar, L. Vora, S. Mrugala, M. Hu, L. S. Wang, L. Porter, A. Kumthekar, P. Johnston, S. K. Egan, K. M. Gatenby, R. Canoll, P. Rubin, J. B. Swanson, K. R. 2018-05-18 doi:10.1101/325464 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ Overlooked roles of DNA damage and maternal age in generating human germline mutations ]]> https://biorxiv.org/content/10.1101/327098v1?rss=1 Gao, Z. Moorjani, P. Amster, G. Przeworski, M. 2018-05-21 doi:10.1101/327098 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Base-pair Ambiguity and the Kinetics of RNA Folding: a Hypothesis-Driven Statistical Analysis ]]> https://biorxiv.org/content/10.1101/329698v1?rss=1 Zhou, G. Loper, J. Geman, S. 2018-05-25 doi:10.1101/329698 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data ]]> https://biorxiv.org/content/10.1101/334706v1?rss=1 Buchanan, E. K. Kinsella, I. Zhou, D. Zhu, R. Zhou, P. Gerhard, F. Ferrante, J. Ma, Y. Kim, S. Shaik, M. Liang, Y. Lu, R. Reimer, J. Fahey, P. Muhammad, T. Dempsey, G. Hillman, E. Ji, N. Tolias, A. Paninski, L. 2018-05-30 doi:10.1101/334706 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ Binary transcriptional control of pattern formation in development ]]> https://biorxiv.org/content/10.1101/335919v1?rss=1 Lammers, N. C. Galstyan, V. Reimer, A. Medin, S. A. Wiggins, C. H. Garcia, H. G. 2018-05-31 doi:10.1101/335919 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Optogenetic silencing of immature and mature neurons in dentate gyrus to assess their roles in memory discriminations ]]> https://biorxiv.org/content/10.1101/335992v1?rss=1 van Dijk, M. T. Fenton, A. A. 2018-06-02 doi:10.1101/335992 Cold Spring Harbor Laboratory Press 2018-06-02 <![CDATA[ Faces and voices in the brain: a modality-general person-identity representation in superior temporal sulcus ]]> https://biorxiv.org/content/10.1101/338475v1?rss=1 Tsantani, M. Kriegeskorte, N. McGettigan, C. Garrido, L. 2018-06-04 doi:10.1101/338475 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Network Reconstruction from Perturbation Time Course Data ]]> https://biorxiv.org/content/10.1101/341008v1?rss=1 Smith, G. R. Bouhaddou, M. Stern, A. D. Anglin, C. M. Zadeh, O. M. Erskin, J. Birtwistle, M. 2018-06-07 doi:10.1101/341008 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ A single cell-based atlas of human microglial states reveals associations with neurological disorders and histopathological features of the aging brain ]]> https://biorxiv.org/content/10.1101/343780v1?rss=1 Olah, M. Menon, V. Habib, N. Taga, M. Yung, C. Cimpean, M. Khairalla, A. Dionne, D. Hopp, S. Frosch, M. P. Hyman, B. T. Beach, T. G. Sarkis, R. Cosgrove, G. R. Helgager, J. Golden, J. A. Pennell, P. B. Schneider, J. A. Bennett, D. A. Regev, A. Elyaman, W. Bradshaw, E. M. De Jager, P. L. 2018-06-11 doi:10.1101/343780 Cold Spring Harbor Laboratory Press 2018-06-11 <![CDATA[ Comparison of stimulus-evoked BOLD responses in human and monkey visual cortex ]]> https://biorxiv.org/content/10.1101/345330v1?rss=1 Patel, G. H. Cohen, A. L. Baker, J. T. Snyder, L. H. Corbetta, M. 2018-06-12 doi:10.1101/345330 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Topographic Organization of Extraoccipital Visual Processing Areas in the Macaque ]]> https://biorxiv.org/content/10.1101/345363v1?rss=1 Patel, G. H. Snyder, L. H. Corbetta, M. 2018-06-12 doi:10.1101/345363 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Attentional Modulation of Macaque Visual Processing Areas ]]> https://biorxiv.org/content/10.1101/345439v1?rss=1 Patel, G. H. Snyder, L. H. Corbetta, M. 2018-06-12 doi:10.1101/345439 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Accuracy and reliability of PBR28 specific binding estimated without the use of a reference region ]]> https://biorxiv.org/content/10.1101/345645v1?rss=1 Plaven-Sigray, P. Schain, M. Zanderigo, F. Karolinska [11C]PBR28 study group, Rabiner, I. Gunn, R. Ogden, T. Cervenka, S. 2018-06-14 doi:10.1101/345645 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Measurement of selective constraint on human gene expression ]]> https://biorxiv.org/content/10.1101/345801v1?rss=1 Glassberg, E. C. Gao, Z. Harpak, A. Lan, X. Pritchard, J. K. 2018-06-13 doi:10.1101/345801 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Dissecting the neural focus of attention reveals distinct processes for spatial attention and object-based storage in visual working memory ]]> https://biorxiv.org/content/10.1101/347518v1?rss=1 Hakim, N. Adam, K. C. S. Gunseli, E. Awh, E. Vogel, E. K. 2018-06-15 doi:10.1101/347518 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Nominally non-responsive frontal and sensory cortical cells encode task-relevant variables via ensemble consensus-building ]]> https://biorxiv.org/content/10.1101/347617v1?rss=1 Insanally, M. N. Carcea, I. Field, R. E. Rodgers, C. C. DePasquale, B. Rajan, K. DeWeese, M. R. Albanna, B. F. Froemke, R. C. 2018-06-14 doi:10.1101/347617 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Reconstructing intelligible speech from the human auditory cortex ]]> https://biorxiv.org/content/10.1101/350124v1?rss=1 Akbari, H. Khalighinejad, B. Herrero, J. Mehta, A. Mesgarani, N. 2018-06-19 doi:10.1101/350124 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Re-identification of genomic data using long range familial searches ]]> https://biorxiv.org/content/10.1101/350231v1?rss=1 Erlich, Y. Shor, T. Carmi, S. Pe'er, I. 2018-06-18 doi:10.1101/350231 Cold Spring Harbor Laboratory Press 2018-06-18 <![CDATA[ Neuropathological correlates and genetic architecture of microglial activation in elderly human brain ]]> https://biorxiv.org/content/10.1101/350389v1?rss=1 Felsky, D. Roostaei, T. Nho, K. Risacher, S. L. Bradshaw, E. M. Petyuk, V. Schneider, J. A. Saykin, A. Bennett, D. A. De Jager, P. L. 2018-06-19 doi:10.1101/350389 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli ]]> https://biorxiv.org/content/10.1101/350744v1?rss=1 Fedorec, A. J. H. Ozdemir, T. Doshi, A. Rosa, L. Velazquez, O. Danino, T. Barnes, C. P. 2018-06-19 doi:10.1101/350744 Cold Spring Harbor Laboratory Press 2018-06-19 <![CDATA[ Endo-lysosomal sorting and degradation of Tau mediates glucocorticoid-driven hippocampalmalfunction ]]> https://biorxiv.org/content/10.1101/352724v1?rss=1 Vaz-Silva, J. Zhu, M. Jin, Q. Zhuravleva, V. Gomes, P. Quintremil, S. Meira, T. Silva, J. Dioli, C. Soares-Cunha, C. Daskalakis, N. Sousa, N. Sotiropoulos, I. Waites, C. L. 2018-06-21 doi:10.1101/352724 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Inhibitory and excitatory populations in parietal cortex are equally selective for decision outcome in both novices and experts ]]> https://biorxiv.org/content/10.1101/354340v1?rss=1 Najafi, F. Elsayed, G. F. Pnevmatikakis, E. Cunningham, J. Churchland, A. K. 2018-06-22 doi:10.1101/354340 Cold Spring Harbor Laboratory Press 2018-06-22 <![CDATA[ Reduced signal for polygenic adaptation of height in UK Biobank ]]> https://biorxiv.org/content/10.1101/354951v1?rss=1 Berg, J. J. Harpak, A. Sinnott-Armstrong, N. Joergensen, A. M. Mostafavi, H. Field, Y. Boyle, E. A. Zhang, X. Racimo, F. Pritchard, J. K. Coop, G. 2018-06-25 doi:10.1101/354951 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Expanded genetic landscape of chronic obstructive pulmonary disease reveals heterogeneous cell type and phenotype associations ]]> https://biorxiv.org/content/10.1101/355644v1?rss=1 Sakornsakolpat, P. Prokopenko, D. Lamontagne, M. Reeve, N. F. Guyatt, A. L. Jackson, V. E. Shrine, N. Qiao, D. Bartz, T. M. Kim, D. K. Lee, M. K. Latourelle, J. C. Li, X. Morrow, J. D. Obeidat, M. Wyss, A. B. Zhou, X. Bakke, P. Barr, R. G. Beaty, T. H. Belinsky, S. A. Brusselle, G. G. Crapo, J. D. Jong, K. d. DeMeo, D. L. Fingerlin, T. E. Gharib, S. A. Gulsvik, A. Hall, I. P. Hokanson, J. E. Kim, W. J. Lomas, D. A. London, S. J. Meyers, D. A. O'Connor, G. T. Rennard, S. I. Schwartz, D. A. Sliwinski, P. Sparrow, D. Strachan, D. P. Tal-Singer, R. Tesfaig 2018-06-26 doi:10.1101/355644 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ An Optically Decodable Bead Array for Linking Imaging and Sequencing with Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/355677v1?rss=1 Yuan, J. Sheng, J. Sims, P. A. 2018-06-25 doi:10.1101/355677 Cold Spring Harbor Laboratory Press 2018-06-25 <![CDATA[ Genome analysis of the unicellular eukaryote Euplotes vannus provides insights into mating type determination and tolerance to environmental stresses ]]> https://biorxiv.org/content/10.1101/357715v1?rss=1 Chen, X. Jiang, Y. Gao, F. Zheng, W. Krock, T. J. Stover, N. A. Lu, C. Katz, L. A. Song, W. 2018-06-29 doi:10.1101/357715 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Reduced repertoire of cortical microstates and neuronal ensembles in medically-induced loss of consciousness ]]> https://biorxiv.org/content/10.1101/358168v1?rss=1 Wenzel, M. Han, S. Smith, E. H. Erik, H. Greger, B. House, P. A. Yuste, R. 2018-07-13 doi:10.1101/358168 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Efficient coding of subjective value ]]> https://biorxiv.org/content/10.1101/358317v1?rss=1 Polania, R. Woodford, M. Ruff, C. 2018-06-29 doi:10.1101/358317 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Seizures start as silent microseizures by neuronal ensembles ]]> https://biorxiv.org/content/10.1101/358903v1?rss=1 Wenzel, M. Hamm, J. P. Peterka, D. S. Yuste, R. 2018-06-29 doi:10.1101/358903 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Salmonella effectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways ]]> https://biorxiv.org/content/10.1101/359117v1?rss=1 Newson, J. Scott, N. Yeuk Wah Chung, I. Wong Fok Lung, T. Giogha, C. Wang, N. Strugnell, R. Brown, N. Cygler, M. Pearson, J. Hartland, E. 2018-06-29 doi:10.1101/359117 Cold Spring Harbor Laboratory Press 2018-06-29 <![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[ The return to water in ancestral Xenopus was accompanied by a novel mechanisms for producing and shaping vocal signals ]]> https://biorxiv.org/content/10.1101/360255v1?rss=1 Kwong-Brown, U. Tobias, M. L. Elias, D. O. Hall, I. C. Elemans, C. P. H. Kelley, D. B. 2018-07-03 doi:10.1101/360255 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Tracking disease resistance deployment in potato breeding by enrichment sequencing ]]> https://biorxiv.org/content/10.1101/360644v1?rss=1 Armstrong, M. R. Vossen, J. Lim, T. Y. Hutten, R. C. B. Xu, J. Strachan, S. M. Harrower, B. Champouret, N. Gilroy, E. M. Hein, I. 2018-07-02 doi:10.1101/360644 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ Why mediation analysis trumps Mendelian randomization in population epigenomics studies of the Dutch Famine ]]> https://biorxiv.org/content/10.1101/362392v1?rss=1 Tobi, E. W. van Zwet, E. W. Lumey, L. Heijmans, B. T. 2018-07-05 doi:10.1101/362392 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ Energetic substrate availability regulates synchronous activity in an excitatory neural network ]]> https://biorxiv.org/content/10.1101/363671v1?rss=1 Tourigny, D. S. Abdul Karim, M. K. Echeveste, R. Kotter, M. R. O'Neill, J. S. 2018-07-06 doi:10.1101/363671 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Functional grading of pericellular matrix surrounding chondrocytes: potential roles in signaling and fluid transport ]]> https://biorxiv.org/content/10.1101/365569v1?rss=1 Saadat, F. Lagieski, M. J. Birman, V. Thomopoulos, S. Genin, G. M. 2018-07-09 doi:10.1101/365569 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg. ]]> https://biorxiv.org/content/10.1101/366948v1?rss=1 Newcomb, S. Voutev, R. Jory, A. Delker, R. K. Slattery, M. Mann, R. S. 2018-07-10 doi:10.1101/366948 Cold Spring Harbor Laboratory Press 2018-07-10 <![CDATA[ De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization ]]> https://biorxiv.org/content/10.1101/367003v1?rss=1 Levitin, H. M. Yuan, J. Cheng, Y. L. Ruiz, F. J. R. Bush, E. C. Bruce, J. N. Canoll, P. Iavarone, A. Lasorella, A. Blei, D. M. Sims, P. A. 2018-07-11 doi:10.1101/367003 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Genetic data and cognitively-defined late-onset Alzheimer’s disease subgroups ]]> https://biorxiv.org/content/10.1101/367615v1?rss=1 1.30). There was substantial variation across studies in the proportions of people in each subgroup. In each study, higher proportions of people with isolated substantial relative memory impairment had [≥]1 APOE e4 allele than any other subgroup (overall p= 1.5 x 10-27). Across subgroups, there were 33 novel suggestive loci across the genome with p<10-5 and an extreme OR compared to controls, of which none had statistical evidence of heterogeneity and 30 had ORs in the same direction across all datasets. These data support the biological coherence of cognitively-defined subgroups and nominate novel genetic loci. ]]> Mukherjee, S. Mez, J. Trittschuh, E. Saykin, A. J. Gibbons, L. E. Fardo, D. W. Wessels, M. Bauman, J. Moore, M. Choi, S.-E. Gross, A. L. Rich, J. Louden, D. K. Sanders, R. E. Grabowski, T. J. Bird, T. D. McCurry, S. M. Snitz, B. E. Kamboh, M. I. Lopez, O. L. De Jager, P. L. Bennett, D. A. Keene, C. D. Larson, E. B. Crane, P. K. 2018-07-11 doi:10.1101/367615 Cold Spring Harbor Laboratory Press 2018-07-11 <![CDATA[ Detecting adaptive differentiation in structured populations with genomic data and common gardens ]]> https://biorxiv.org/content/10.1101/368506v1?rss=1 Josephs, E. B. Berg, J. J. Ross-Ibarra, J. Coop, G. 2018-07-13 doi:10.1101/368506 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Parameterized expertise: Evidence for gradations of musical expertise from electroencephalographic monitoring of auditory decision-making ]]> https://biorxiv.org/content/10.1101/370379v1?rss=1 Sherwin, J. Sajda, P. 2018-07-16 doi:10.1101/370379 Cold Spring Harbor Laboratory Press 2018-07-16 <![CDATA[ Macroecological relationships in the dynamics of gut microbiota ]]> https://biorxiv.org/content/10.1101/370676v1?rss=1 Ji, B. W. Sheth, R. U. Dixit, P. D. Vitkup, D. 2018-07-18 doi:10.1101/370676 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ \"DoC-feeling\": a new behavioural tool to help diagnose the Minimally Conscious State. ]]> https://biorxiv.org/content/10.1101/370775v1?rss=1 Hermann, B. Goudard, G. Courcoux, K. Valente, M. Labat, S. Despois, L. Bourmaleau, J. Richard Gillis, L. Faugeras, F. Demeret, S. Sitt, J. D. Naccache, L. Rohaut, B. 2018-07-24 doi:10.1101/370775 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature ]]> https://biorxiv.org/content/10.1101/371088v1?rss=1 Tagore, S. Gorohovski, A. Jensen, L. J. Frenkel-Morgenstern, M. 2018-07-17 doi:10.1101/371088 Cold Spring Harbor Laboratory Press 2018-07-17 <![CDATA[ RecNW: A fast pairwise aligner for targeted sequencing ]]> https://biorxiv.org/content/10.1101/371989v1?rss=1 Yahi, A. Lappalainen, T. Mohammadi, P. Tatonetti, N. 2018-07-19 doi:10.1101/371989 Cold Spring Harbor Laboratory Press 2018-07-19 <![CDATA[ Tracking Activity In A Deformable Nervous System With Motion Correction And Point-Set Registration ]]> https://biorxiv.org/content/10.1101/373035v1?rss=1 Lagache, T. Lansdell, B. Tang, J. Yuste, R. Fairhall, A. 2018-07-20 doi:10.1101/373035 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Parkinson’s disease-linked Parkin mutations impair glutamatergic synaptic transmission and plasticity ]]> https://biorxiv.org/content/10.1101/373597v1?rss=1 Zhu, M. Cortese, G. Waites, C. 2018-07-20 doi:10.1101/373597 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Regional collapsing of rare variation implicates specific genic regions in ALS ]]> https://biorxiv.org/content/10.1101/375774v1?rss=1 Gelfman, S. Dugger, S. A. Araujo Martins Moreno, C. Ren, Z. Wolock, C. J. Shneider, N. A. Phatnani, H. Cirulli, E. T. Lasseigne, B. N. Harris, T. Maniatis, T. Rouleau, G. A. Brown, R. H. Gitler, A. D. Myers, R. M. Petrovski, S. Allen, A. Harms, M. B. Goldstein, D. B. 2018-07-24 doi:10.1101/375774 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ High resolution discovery of chromatin interactions ]]> https://biorxiv.org/content/10.1101/376194v1?rss=1 Guo, Y. Krismer, K. Closser, M. Wichterle, H. Gifford, D. K. 2018-07-25 doi:10.1101/376194 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Developmental Regulation of an Organelle Tether Coordinates Mitochondrial Remodeling in Meiosis ]]> https://biorxiv.org/content/10.1101/376509v1?rss=1 Unal, E. Sawyer, E. Joshi, P. Berchowitz, L. 2018-07-24 doi:10.1101/376509 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Substantia nigra dopamine neurons evoke a delayed excitation in lateral dorsal striatal cholinergic interneurons via glutamate cotransmission ]]> https://biorxiv.org/content/10.1101/377150v1?rss=1 Chuhma, N. Mingote, S. Yetnikoff, L. Kalmbach, A. Ma, T. Ztaou, S. Sienna, A.-C. Tepler, S. Poulin, J.-F. Ansorge, M. Awatramani, R. Kang, U. J. Rayport, S. 2018-07-25 doi:10.1101/377150 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ An open source platform for analyzing and sharing worm behavior data ]]> https://biorxiv.org/content/10.1101/377960v1?rss=1 Javer, A. Currie, M. Lee, C. W. Hokanson, J. Li, K. Martineau, C. N. Yemini, E. Grundy, L. J. Li, C. Chng, Q. Schafer, W. R. Nollen, E. A. Kerr, R. Brown, A. E. 2018-07-26 doi:10.1101/377960 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay ]]> https://biorxiv.org/content/10.1101/378349v1?rss=1 Hiatt, S. Neu, M. B. Ramaker, R. C. Hardigan, A. A. Prokop, J. W. Hancarova, M. Prchalova, D. Havlovicova, M. Prchal, J. Stranecky, V. Yim, D. K. Powis, Z. Keren, B. Nava, C. Mignot, C. Rio, M. Revah-Politi, A. Hemati, P. Stong, N. Iglesias, A. D. Suchy, S. F. Willaert, R. Wentzensen, I. M. Wheeler, P. G. Brick, L. Kozenko, M. Hurst, A. C. Wheless, J. W. Lacassie, Y. Sedlacek, Z. Myers, R. M. Barsh, G. S. Cooper, G. M. 2018-07-29 doi:10.1101/378349 Cold Spring Harbor Laboratory Press 2018-07-29 <![CDATA[ Acetic acid activates distinct taste pathways in Drosophila to elicit opposing, state-dependent feeding responses ]]> https://biorxiv.org/content/10.1101/378414v1?rss=1 Devineni, A. V. Sun, B. Zhukovskaya, A. Axel, R. 2018-07-26 doi:10.1101/378414 Cold Spring Harbor Laboratory Press 2018-07-26 <![CDATA[ Predicting negative control drugs to support research in drug safety ]]> https://biorxiv.org/content/10.1101/380832v1?rss=1 Hao, Y. Tatonetti, N. P. 2018-07-30 doi:10.1101/380832 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Measuring intolerance to mutation in human genetics ]]> https://biorxiv.org/content/10.1101/382481v1?rss=1 Fuller, Z. Berg, J. J. Mostafavi, H. Sella, G. Przeworski, M. 2018-08-01 doi:10.1101/382481 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Disulfide bonds: the power switches of elastic proteins ]]> https://biorxiv.org/content/10.1101/383711v1?rss=1 Eckels, E. C. Haldar, S. Tapia-Rojo, R. Rivas Pardo, J. A. Fernandez, J. M. 2018-08-02 doi:10.1101/383711 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Conserved cell types with divergent features between human and mouse cortex ]]> https://biorxiv.org/content/10.1101/384826v1?rss=1 Hodge, R. D. Bakken, T. E. Miller, J. A. Smith, K. A. Barkan, E. R. Graybuck, L. T. Close, J. L. Long, B. Penn, O. Yao, Z. Eggermont, J. Hollt, T. Levi, B. P. Shehata, S. I. Aevermann, B. Beller, A. Bertagnolli, D. Brouner, K. Casper, T. Cobbs, C. Dalley, R. Dee, N. Ding, S.-L. Ellenbogen, R. G. Fong, O. Garren, E. Goldy, J. Gwinn, R. P. Hirschstein, D. Keene, C. D. Keshk, M. Ko, A. L. Lathia, K. Mahfouz, A. Maltzer, Z. McGraw, M. Nguyen, T. N. Nyhus, J. Ojemann, J. G. Oldre, A. Parry, S. Reynolds, S. Rimorin, C. Shapovalova, N. V. Somasundaram, S. 2018-08-05 doi:10.1101/384826 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Dynamic self-organized error-correction of grid cells by border cells ]]> https://biorxiv.org/content/10.1101/385229v1?rss=1 Pollock, E. Desai, N. Wei, X.-X. Balasubramanian, V. 2018-08-05 doi:10.1101/385229 Cold Spring Harbor Laboratory Press 2018-08-05 <![CDATA[ Camphor white oil induces tumor regression through cytotoxic T cell-dependent mechanisms ]]> https://biorxiv.org/content/10.1101/386789v1?rss=1 Moayedi, Y. Greenberg, S. A. Jenkins, B. A. Marshall, K. L. Dimitrov, L. V. Nelson, A. M. Owens, D. M. Lumpkin, E. A. 2018-08-07 doi:10.1101/386789 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ A Chemically-triggered Transition from Conflict to Cooperation in Burying Beetles ]]> https://biorxiv.org/content/10.1101/389163v1?rss=1 Chen, B.-F. Liu, M. Rubenstein, D. R. Sun, S.-J. Liu, J.-N. Lin, Y.-H. Shen, S.-F. 2018-08-09 doi:10.1101/389163 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/389270v1?rss=1 Maniatis, S. Aijo, T. Vickovic, S. Braine, C. Kang, K. Mollbrink, A. Andrusivova, Z. Saarenpaa, S. Saiz-Castro, G. Cuevas, M. Watters, A. Lundeberg, J. Bonneau, R. Phatnani, H. 2018-08-09 doi:10.1101/389270 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Real-time structural dynamics of late steps in bacterial translation initiation visualized using time-resolved cryogenic electron microscopy ]]> https://biorxiv.org/content/10.1101/390674v1?rss=1 Kaledhonkar, S. Fu, Z. Caban, K. Li, W. Chen, B. Sun, M. Gonzalez, R. L. Frank, J. 2018-08-13 doi:10.1101/390674 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Triggering visually-guided behavior by holographic activation of pattern completion neurons in cortical ensembles ]]> https://biorxiv.org/content/10.1101/394999v1?rss=1 Carrillo-Reid, L. Han, S. Yang, W. Akrouh, A. Yuste, R. 2018-08-17 doi:10.1101/394999 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Whole-neuron synaptic mapping reveals local balance between excitatory and inhibitory synapse organization ]]> https://biorxiv.org/content/10.1101/395384v1?rss=1 Iascone, D. M. Li, Y. Sumbul, U. Doron, M. Chen, H. Andreu, V. Goudy, F. Segev, I. Peng, H. Polleux, F. 2018-08-19 doi:10.1101/395384 Cold Spring Harbor Laboratory Press 2018-08-19 <![CDATA[ Human antibody cocktail deploys multiple functions to confer pan-ebolavirus protection ]]> https://biorxiv.org/content/10.1101/395525v1?rss=1 Wec, A. Z. Bornholdt, Z. A. He, S. Herbert, A. S. Goodwin, E. Wirchnianski, A. S. Gunn, B. M. Zhang, Z. Zhu, W. Liu, G. Abelson, D. M. Moyer, C. L. Jangra, R. K. James, R. M. Bakken, R. R. Bohorova, N. Bohorov, O. Kim, D. H. Pauly, M. H. Velasco, J. Bortz, R. H. Whaley, K. J. Goldstein, T. Anthony, S. J. Alter, G. Walker, L. M. Dye, J. M. Zeitlin, L. Qiu, X. Chandran, K. 2018-08-20 doi:10.1101/395525 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Large-Scale Annotation of Histopathology Images from Social Media ]]> https://biorxiv.org/content/10.1101/396663v1?rss=1 Schaumberg, A. J. Juarez, W. Choudhury, S. J. Pastrian, L. G. Pritt, B. S. Prieto Pozuelo, M. Sotillo Sanchez, R. Ho, K. Zahra, N. Sener, B. D. Yip, S. Xu, B. Annavarapu, S. R. Morini, A. Jones, K. A. Rosado-Orozco, K. Sirintrapun, S. J. Aly, M. Fuchs, T. J. 2018-08-21 doi:10.1101/396663 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Forecasting seasonal influenza in the U.S.: A collaborative multi-year, multi-model assessment of forecast performance ]]> https://biorxiv.org/content/10.1101/397190v1?rss=1 Reich, N. G. Brooks, L. Fox, S. Kandula, S. McGowan, C. Moore, E. Osthus, D. Ray, E. L. Tushar, A. Yamana, T. Biggerstaff, M. Johansson, M. A. Rosenfeld, R. Shaman, J. 2018-08-24 doi:10.1101/397190 Cold Spring Harbor Laboratory Press 2018-08-24 <![CDATA[ Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells ]]> https://biorxiv.org/content/10.1101/398107v1?rss=1 King, D. M. Maricque, B. B. Cohen, B. A. 2018-08-22 doi:10.1101/398107 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[ ENRICH: a fast method to improve the quality of flexible macromolecular reconstructions ]]> https://biorxiv.org/content/10.1101/400317v1?rss=1 Kazemi, M. Sorzano, C. O. S. Des Georges, A. Carazo, J. M. Vargas, J. 2018-08-26 doi:10.1101/400317 Cold Spring Harbor Laboratory Press 2018-08-26 <![CDATA[ Potential Bias of Doubly Labeled Water for Measuring Energy Expenditure Differences Between Diets Varying in Carbohydrate ]]> https://biorxiv.org/content/10.1101/403931v1?rss=1 Hall, K. D. Guo, J. Chen, K. Y. Leibel, R. L. Reitman, M. L. Rosenbaum, M. Smith, S. R. Ravussin, E. 2018-08-30 doi:10.1101/403931 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity ]]> https://biorxiv.org/content/10.1101/404327v1?rss=1 Hon, J. Gonzalez, R. L. 2018-08-30 doi:10.1101/404327 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Wave-like activity patterns in the neuropil of striatal cholinergic interneurons in freely moving mice represent their collective spiking dynamics ]]> https://biorxiv.org/content/10.1101/404467v1?rss=1 Rehani, R. Atamna, Y. Tiroshi, L. Chiu, W.-H. Aceves Buendia, J. d. J. Martins, G. J. Jacobson, G. A. Goldberg, J. A. 2018-08-30 doi:10.1101/404467 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Wnt/Fgf crosstalk is required for the specification of tracheal basal progenitor cells ]]> https://biorxiv.org/content/10.1101/405159v1?rss=1 Hou, Z. Wu, Q. Sun, X. Chen, H. Li, Y. Zhang, Y. Mori, M. Yang, Y. Jiang, M. Que, J. 2018-08-31 doi:10.1101/405159 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Acute Psychological Stress Triggers Circulating Cell-Free Mitochondrial DNA ]]> https://biorxiv.org/content/10.1101/405886v1?rss=1 Trumpff, C. Marsland, A. L. Basualto-Alarcon, C. Martin, J. L. Carroll, J. E. Sturm, G. Vincent, A. E. Mosharov, E. V. Gu, Z. Kaufman, B. A. Picard, M. 2018-08-31 doi:10.1101/405886 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Plasticity of the electrical connectome of C. elegans ]]> https://biorxiv.org/content/10.1101/406207v1?rss=1 Bhattacharya, A. Aghayeva, U. Berghoff, E. Hobert, O. 2018-08-31 doi:10.1101/406207 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Brain-Score: Which Artificial Neural Network for Object Recognition is most Brain-Like? ]]> https://biorxiv.org/content/10.1101/407007v1?rss=1 Schrimpf, M. Kubilius, J. Hong, H. Majaj, N. J. Rajalingham, R. Issa, E. B. Kar, K. Bashivan, P. Prescott-Roy, J. Schmidt, K. Yamins, D. L. K. DiCarlo, J. J. 2018-09-05 doi:10.1101/407007 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Diagnosis and Prognosis Using Machine Learning Trained on BrainMorphometry and White Matter Connectomes ]]> https://biorxiv.org/content/10.1101/407601v1?rss=1 Wang, Y. Xu, C. Park, J.-H. Lee, S. Stern, Y. Yoo, S. Kim, J. H. Kim, H. S. Cha, J. 2018-09-04 doi:10.1101/407601 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ Characterizing the nonlinear structure of shared variability in cortical neuron populations using neural networks ]]> https://biorxiv.org/content/10.1101/407858v1?rss=1 Whiteway, M. R. Socha, K. Bonin, V. Butts, D. A. 2018-09-04 doi:10.1101/407858 Cold Spring Harbor Laboratory Press 2018-09-04 <![CDATA[ The geometry of abstraction in hippocampus and prefrontal cortex ]]> https://biorxiv.org/content/10.1101/408633v1?rss=1 Bernardi, S. Benna, M. K. Rigotti, M. Munuera, J. Fusi, S. Salzman, D. 2018-09-06 doi:10.1101/408633 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Object-in-Place Memory Predicted by Anterolateral Entorhinal Cortex and Parahippocampal Cortex Volume in Older Adults ]]> https://biorxiv.org/content/10.1101/409607v1?rss=1 Yeung, L.-K. Olsen, R. K. Hong, B. Mihajlovic, V. D'Angelo, M. C. Kacollja, A. Ryan, J. D. Barense, M. D. 2018-09-06 doi:10.1101/409607 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity ]]> https://biorxiv.org/content/10.1101/409672v1?rss=1 Alexander, J. M. Guan, J. Huang, B. Lomvardas, S. Weiner, O. D. 2018-09-05 doi:10.1101/409672 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Glycogen Synthase Kinase 3 induces multilineage maturation of human pluripotent stem cell-derived lung progenitors in 3D culture. ]]> https://biorxiv.org/content/10.1101/410894v1?rss=1 Snoeck, H.-W. Rodrigues Toste de Carvalho, A. L. Strikoudis, A. Dantas, T. Chen, Y.-W. Liu, H.-Y. Vallee, R. B. Correia-Pinto, J. 2018-09-06 doi:10.1101/410894 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Music reveals medial prefrontal cortex sensitive period in childhood ]]> https://biorxiv.org/content/10.1101/412007v1?rss=1 Gabard-Durnam, L. J. Hensch, T. Tottenham, N. 2018-09-09 doi:10.1101/412007 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic Variation. ]]> https://biorxiv.org/content/10.1101/412361v1?rss=1 Cherry, T. J. Yang, M. G. Harmin, D. A. Tao, P. Timms, A. E. Bauwens, M. Allikmets, R. Jones, E. M. Chen, R. DeBaere, E. Greenberg, M. E. 2018-09-08 doi:10.1101/412361 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Timing mechanism of sexually dimorphic nervous system differentiation ]]> https://biorxiv.org/content/10.1101/416735v1?rss=1 Pereira, L. Aeschimann, F. Wang, C. Lawson, H. Serrano-Saiz, E. Portman, D. S. Grosshans, H. Hobert, O. 2018-09-13 doi:10.1101/416735 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Genotypic clustering does not imply recent tuberculosis transmission in a high prevalence setting: A genomic epidemiology study in Lima, Peru ]]> https://biorxiv.org/content/10.1101/418202v1?rss=1 Dixit, A. Freschi, L. Vargas, R. Calderon, R. Sacchettini, J. Drobniewski, F. Galea, J. T. Contreras, C. Yataco, R. Zhang, Z. Lecca, L. Kolokotronis, S.-O. Mathema, B. Farhat, M. R. 2018-09-16 doi:10.1101/418202 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Atlas-CNV: a validated approach to call Single-Exon CNVs in the eMERGESeq gene panel ]]> https://biorxiv.org/content/10.1101/422337v1?rss=1 Chiang, T. Liu, X. Wu, T.-J. Hu, J. Sedlazeck, F. J. White, S. Schaid, D. de Andrade, M. Jarvik, G. P. Crosslin, D. Stanaway, I. Carrell, D. S. Connolly, J. J. Hakonarson, H. Groopman, E. E. Gharavi, A. G. Fedotov, A. Bi, W. Leduc, M. S. Murdock, D. R. Jiang, Y. Meng, L. Eng, C. M. Wen, S. Yang, Y. Muzny, D. M. Boerwinkle, E. Salerno, W. Venner, E. Gibbs, R. A. 2018-09-27 doi:10.1101/422337 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Sae2 antagonizes Rad9 accumulation at DNA double-strand breaks to attenuate checkpoint signaling and facilitate end resection ]]> https://biorxiv.org/content/10.1101/424218v1?rss=1 Yu, T.-Y. Kimble, M. Symington, L. S. 2018-09-23 doi:10.1101/424218 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Effects of two centuries of global environmental variation on phenology and physiology of Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/424242v1?rss=1 DeLeo, V. L. Menge, D. N. L. Hanks, E. M. Juenger, T. E. Lasky, J. R. 2018-09-23 doi:10.1101/424242 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Xrs2 and Tel1 independently contribute to MR-mediated DNA tethering and replisome stability ]]> https://biorxiv.org/content/10.1101/425942v1?rss=1 Oh, J. Lee, S. J. Rothstein, R. Symington, L. S. 2018-09-25 doi:10.1101/425942 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ Quasi-universality in single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/426239v1?rss=1 Aparicio, L. Bordyuh, M. Blumberg, A. J. Rabadan, R. 2018-10-05 doi:10.1101/426239 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Multiplex transcriptional characterizations across diverse and hybrid bacterial cell-free expression systems ]]> https://biorxiv.org/content/10.1101/427559v1?rss=1 1,000 diverse regulatory sequences revealed functional differences in gene expression that could be predictively modeled. Finally, we constructed and examined the transcriptional capacities of dual-species "hybrid" cell lysates that can simultaneously harness gene expression properties of multiple organisms. We expect that this cell-free multiplex transcriptional measurement approach will improve genetic circuit prototyping in new bacterial chassis for synthetic biology. ]]> Yim, S. S. Johns, N. I. Park, J. Gomes, A. L. C. McBee, R. M. Richardson, M. Ronda, C. Chen, S. P. Garenne, D. Noireaux, V. Wang, H. H. 2018-09-26 doi:10.1101/427559 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ pavo 2.0: new tools for the spectral and spatial analysis of colour in R ]]> https://biorxiv.org/content/10.1101/427658v1?rss=1 Maia, R. Gruson, H. Endler, J. A. White, T. E. 2018-09-26 doi:10.1101/427658 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Redefining Nephrotic Syndrome in Molecular Terms: Outcome-associated molecular clusters and patient stratification with noninvasive surrogate biomarkers ]]> https://biorxiv.org/content/10.1101/427880v1?rss=1 Mariani, L. H. Eddy, S. Martini, S. Eichinger, F. Godfrey, B. Nair, V. Adler, S. G. Appel, G. B. Athavale, A. Barisoni, L. Brown, E. Cattran, D. C. Dell, K. M. Derebail, V. Fervenza, F. C. Fornoni, A. Gadegbeku, C. A. Gibson, K. L. Gipson, D. Greenbaum, L. A. Hingorani, S. R. Hlandunewich, M. A. Hogan, J. Holzman, L. B. Jefferson, J. A. Kaskel, F. J. Kopp, J. B. Lafayette, R. A. Lemley, K. V. Lieske, J. C. Lin, J.-J. Myers, K. E. Nachman, P. H. Nast, C. C. Neu, A. M. Reich, H. N. Sambandam, K. Sedor, J. R. Sethna, C. B. Srivastava, T. Trachtman, H. Tran 2018-09-27 doi:10.1101/427880 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites ]]> https://biorxiv.org/content/10.1101/428615v1?rss=1 Feng, H. Bao, S. Weyn-Vanhentenryck, S. M. Khan, A. Wong, J. Shah, A. Flynn, E. D. Zhang, C. 2018-09-27 doi:10.1101/428615 Cold Spring Harbor Laboratory Press 2018-09-27 <![CDATA[ Regulation of arousal via on-line neurofeedback improves human performance in a demanding sensory-motor task ]]> https://biorxiv.org/content/10.1101/428755v1?rss=1 Faller, J. Cummings, J. Saproo, S. Sajda, P. 2018-09-28 doi:10.1101/428755 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ Improved Pathogenic Variant Localization using a Hierarchical Model of Sub-regional Intolerance ]]> https://biorxiv.org/content/10.1101/431536v1?rss=1 Hayeck, T. J. Stong, N. Wolock, C. J. Copeland, B. Kamalakaran, S. Goldstein, D. Allen, A. 2018-09-30 doi:10.1101/431536 Cold Spring Harbor Laboratory Press 2018-09-30 <![CDATA[ Genetic variants influence on the placenta regulatory landscape ]]> https://biorxiv.org/content/10.1101/432211v1?rss=1 Delahaye, F. Do, C. Kong, Y. Ashkar, R. Salas, M. Tycko, B. Wapner, R. Hughes, F. 2018-10-03 doi:10.1101/432211 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Right hemisphere superiority for executive control of attention ]]> https://biorxiv.org/content/10.1101/432732v1?rss=1 Spagna, A. Kim, T. H. Wu, T. Fan, J. 2018-10-02 doi:10.1101/432732 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Genetic And Epigenetic Fine Mapping Of Complex Trait Associated Loci In The Human Liver ]]> https://biorxiv.org/content/10.1101/432823v1?rss=1 Caliskan, M. Manduchi, E. Rao, H. S. Segert, J. A. Holsbach Beltrame, M. Trizzino, M. Park, Y. Baker, S. W. Chesi, A. Johnson, M. E. Hodge, K. M. Leonard, M. E. Loza, B. Xin, D. Berrido, A. M. Hand, N. J. Bauer, R. C. Wells, A. D. Olthoff, K. M. Shaked, A. Rader, D. J. Grant, S. F. Brown, C. D. 2018-10-08 doi:10.1101/432823 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Heading direction with respect to a reference point modulates place-cell activity ]]> https://biorxiv.org/content/10.1101/433516v1?rss=1 Jercog, P. E. Ahmadian, Y. Woodruff, C. Deb-Sen, R. Abbott, L. F. Kandel, E. R. 2018-10-02 doi:10.1101/433516 Cold Spring Harbor Laboratory Press 2018-10-02 <![CDATA[ Single neurons in the human entorhinal cortex remap to distinguish individual spatial memories ]]> https://biorxiv.org/content/10.1101/433862v1?rss=1 Qasim, S. E. Miller, J. Inman, C. S. Gross, R. Willie, J. T. Lega, B. Lin, J.-J. Sharan, A. Wu, C. Sperling, M. R. Sheth, S. McKhann, G. M. Smith, E. H. Schevon, C. Stein, J. Jacobs, J. 2018-10-03 doi:10.1101/433862 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Ligand Geometry Controls Adhesion formation via Integrin Clustering ]]> https://biorxiv.org/content/10.1101/435826v1?rss=1 Changede, R. Cai, H. Wind, S. Sheetz, M. P. 2018-10-04 doi:10.1101/435826 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ High local mutual information drives the response in the human language network ]]> https://biorxiv.org/content/10.1101/436204v1?rss=1 Mollica, F. Siegelman, M. Diachek, E. Piantadosi, S. T. Mineroff, Z. Futrell, R. Fedorenko, E. 2018-10-08 doi:10.1101/436204 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Bright and photostable chemigenetic indicators for extended in vivo voltage imaging ]]> https://biorxiv.org/content/10.1101/436840v1?rss=1 Abdelfattah, A. S. Kawashima, T. Singh, A. Novak, O. Liu, H. Shuai, Y. Huang, Y.-C. Grimm, J. B. Patel, R. Friedrich, J. Mensh, B. D. Paninski, L. Macklin, J. J. Podgorski, K. Lin, B.-J. Chen, T.-W. Turner, G. C. Liu, Z. Koyama, M. Svoboda, K. Ahrens, M. B. Lavis, L. D. Schreiter, E. R. 2018-10-06 doi:10.1101/436840 Cold Spring Harbor Laboratory Press 2018-10-06 <![CDATA[ Robust Algorithms for Capturing Population Dynamics and Transport in Oceanic Variables along Drifter Trajectories using Linear Dynamical Systems with Latent Variables ]]> https://biorxiv.org/content/10.1101/438036v1?rss=1 Yan, Y. Jebara, T. Abernathey, R. Goes, J. Gomes, H. 2018-10-08 doi:10.1101/438036 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Stereotyped Terminal Axon Branching of Leg Motor Neurons Mediated by IgSF Proteins DIP-α and Dpr10 ]]> https://biorxiv.org/content/10.1101/438267v1?rss=1 Venkatasubramanian, L. Guo, Z. Xu, S. Tan, L. Xiao, Q. Nagarkar-Jaiswal, S. Mann, R. S. 2018-10-08 doi:10.1101/438267 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Deep brain stimulation of the nucleus accumbens shell does not decrease cocaine self-administration in cocaine-dependent rats but increases GluR1/GluA1 in the central nucleus of the amygdala ]]> https://biorxiv.org/content/10.1101/438507v1?rss=1 Kononoff, J. Melas, P. A. Qvist, J. S. de Guglielmo, G. Kallupi, M. Kandel, E. R. George, O. 2018-10-08 doi:10.1101/438507 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Minimal phenotyping yields GWAS hits of low specificity for major depression ]]> https://biorxiv.org/content/10.1101/440735v1?rss=1 Cai, N. Kendler, K. Flint, J. 2018-10-11 doi:10.1101/440735 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Role of RIG-I-like receptors in innate immune sensing of Coxsackievirus B3 and encephalomyocarditis virus in murine macrophages and fibroblasts ]]> https://biorxiv.org/content/10.1101/441667v1?rss=1 Francisco, E. Suthar, M. Gale, M. Rosenfeld, A. Racaniello, V. R. 2018-10-13 doi:10.1101/441667 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Deep structural brain lesions associated with consciousness impairment early after haemorrhagic stroke ]]> https://biorxiv.org/content/10.1101/441709v1?rss=1 Rohaut, B. Doyle, K. W. Reynolds, A. S. Igwe, K. Couch, C. Matory, A. Rizvi, B. Roh, D. Velasquez, A. Megjhani, M. Park, S. Agarwal, S. Mauro, C. M. Li, G. Eliseyev, A. Perlbarg, V. Connolly, S. E. Brickman, A. Claassen, J. 2018-10-15 doi:10.1101/441709 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Interfacial actin protrusions mechanically potentiate killing by cytotoxic T cells ]]> https://biorxiv.org/content/10.1101/443309v1?rss=1 Tamzalit, F. Wang, M. S. Jin, W. Boyko, V. Heddleston, J. M. Black, C. T. Kam, L. C. Huse, M. 2018-10-14 doi:10.1101/443309 Cold Spring Harbor Laboratory Press 2018-10-14 <![CDATA[ Deficient FGF signaling in the developing peripheral retina disrupts ciliary margin development and causes aniridia ]]> https://biorxiv.org/content/10.1101/443416v1?rss=1 Balasubramanian, R. Tao, C. Polanco, K. Zhong, J. Wang, F. Ma, L. Zhang, X. 2018-10-16 doi:10.1101/443416 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations ]]> https://biorxiv.org/content/10.1101/444687v1?rss=1 Nam, A. S. Kim, K.-T. Chaligne, R. Izzo, F. Ang, C. Abu-Zeinah, G. Omans, N. D. Pastore, A. Taylor, J. Alonso, A. Mariani, M. Cubillos-Ruiz, J. R. Tam, W. Hoffman, R. Scandura, J. M. Rabadan, R. Abdel-Wahab, O. Smibert, P. Landau, D. A. 2018-10-16 doi:10.1101/444687 Cold Spring Harbor Laboratory Press 2018-10-16 <![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[ Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth ]]> https://biorxiv.org/content/10.1101/447680v1?rss=1 Pizzinga, M. Bates, C. Lui, J. Forte, G. Morales-Polanco, F. Linney, E. Knotkova, B. Wilson, B. Solari, C. A. Berchowitz, L. E. Portela, P. Ashe, M. P. 2018-10-19 doi:10.1101/447680 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Predicting the future with multi-scale successor representations ]]> https://biorxiv.org/content/10.1101/449470v1?rss=1 Momennejad, I. Howard, M. W. 2018-10-22 doi:10.1101/449470 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ Cortical subnetworks encode context of a visual stimulus ]]> https://biorxiv.org/content/10.1101/452219v1?rss=1 Hamm, J. P. Shymkiv, Y. Han, S. Yang, W. Yuste, R. 2018-10-25 doi:10.1101/452219 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Building Key Populations HIV Treatment Cascades in Data-Scarce Environments: Towards a participatory stakeholder methodology for cascades construction, adoption, and utilization ]]> https://biorxiv.org/content/10.1101/452417v1?rss=1 Lane, T. Grasso, M. Scheibe, A. Liu, G. Marr, A. Murangandi, P. Aynalem, G. Slabbert, M. Malaka, L. Isdahl, Z. Osmand, T. Nadol, P. 2018-10-24 doi:10.1101/452417 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Visual cue-related activity of cells in the medial entorhinal cortex during navigation in virtual reality ]]> https://biorxiv.org/content/10.1101/453787v1?rss=1 Kinkhabwala, A. Gu, Y. Aronov, D. Tank, D. W. 2018-10-25 doi:10.1101/453787 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Early detection of impending cryostorage tank failure using a weight-based monitoring system ]]> https://biorxiv.org/content/10.1101/455311v1?rss=1 Michaelson, Z. P. Bondalapati, S. T. Amrane, S. Prosser, R. W. Hill, D. M. Gaur, P. Recio, M. Travassos, D. E. Wolfkamp, M. D. Sadowy, S. Thomas, C. Forman, E. J. Williams, Z. 2018-10-30 doi:10.1101/455311 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Neural Dynamics of Executive Function in Cognitively-able Kindergarteners with Autism Spectrum Disorders (ASD) as Predictors of Concurrent Academic Achievement: Preliminary Study ]]> https://biorxiv.org/content/10.1101/455485v1?rss=1 Kim, S. H. Buzzell, G. Faja, S. Choi, Y. B. Brito, N. Shuffrey, L. Fifer, W. Morrison, F. Lord, C. Fox, N. 2018-10-29 doi:10.1101/455485 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ Deep Learning on MRI Affirms the Prominence of the Hippocampal Formation in Alzheimer’s Disease Classification ]]> https://biorxiv.org/content/10.1101/456277v1?rss=1 Feng, X. Yang, J. Lipton, Z. C. Small, S. A. Provenzano, F. A. 2018-10-31 doi:10.1101/456277 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Complementary subnetworks of cortical somatostatin interneurons ]]> https://biorxiv.org/content/10.1101/456574v1?rss=1 Naka, A. Shababo, B. Snyder, B. Egladyous, A. Sridharan, S. Paninski, L. Adesnik, H. 2018-10-30 doi:10.1101/456574 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ On the inference speed and video-compression robustness of DeepLabCut ]]> https://biorxiv.org/content/10.1101/457242v1?rss=1 Mathis, A. Warren, R. A. 2018-10-30 doi:10.1101/457242 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ The Markov link method: a nonparametric approach to combine observations from multiple experiments ]]> https://biorxiv.org/content/10.1101/457283v1?rss=1 Loper, J. Bakken, T. Sumbul, U. Murphy, G. Zeng, H. Blei, D. Blei, D. 2018-10-30 doi:10.1101/457283 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ Biological adaptation under fluctuating selection ]]> https://biorxiv.org/content/10.1101/457762v1?rss=1 Liu, M. Rubenstein, D. Liu, W.-C. Shen, S.-F. 2018-10-31 doi:10.1101/457762 Cold Spring Harbor Laboratory Press 2018-10-31 <![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[ Local online learning in recurrent networks with random feedback ]]> https://biorxiv.org/content/10.1101/458570v1?rss=1 Murray, J. M. 2018-10-31 doi:10.1101/458570 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Enhancer redundancy predicts gene pathogenicity and informs complex disease gene discovery ]]> https://biorxiv.org/content/10.1101/459123v1?rss=1 Wang, X. Goldstein, D. B. 2018-11-01 doi:10.1101/459123 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Systematic identification of human SNPs affecting regulatory element activity ]]> https://biorxiv.org/content/10.1101/460402v1?rss=1 van Arensbergen, J. Pagie, L. FitzPatrick, V. de Haas, M. Baltissen, M. Comoglio, F. van der Weide, R. Teunissen, H. Vosa, U. Franke, L. de Wit, E. Vermeulen, M. Bussemaker, H. van Steensel, B. 2018-11-04 doi:10.1101/460402 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ ENvironmental Dynamics Underlying Responsive Extreme Survivors (ENDURES) of Glioblastoma: a Multi-disciplinary Team-based, Multifactorial Analytical Approach ]]> https://biorxiv.org/content/10.1101/461236v1?rss=1 Johnston, S. K. Whitmire, P. Massey, S. C. Kumthekar, P. Porter, A. B. Raghunand, N. Gonzalez-Cuyar, L. F. Mrugala, M. M. Hawkins-Daarud, A. Jackson, P. R. Hu, L. S. Sarkaria, J. N. Wang, L. Gatenby, R. A. Egan, K. M. Canoll, P. Swanson, K. R. 2018-11-04 doi:10.1101/461236 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Multiple mechanisms link prestimulus neural oscillations to sensory responses ]]> https://biorxiv.org/content/10.1101/461558v1?rss=1 Iemi, L. Busch, N. A. Laudini, A. Samaha, J. Villringer, A. Nikulin, V. V. 2018-11-04 doi:10.1101/461558 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Task-Related Hemodynamic Responses Are Modulated by Reward and Task-engagement ]]> https://biorxiv.org/content/10.1101/463042v1?rss=1 Cardoso, M. M. Lima, B. Sirotin, Y. B. Das, A. 2018-11-05 doi:10.1101/463042 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ A comparison of deep learning and linear-nonlinear cascade approaches to neural encoding ]]> https://biorxiv.org/content/10.1101/463422v1?rss=1 Moskovitz, T. H. Roy, N. A. Pillow, J. W. 2018-11-06 doi:10.1101/463422 Cold Spring Harbor Laboratory Press 2018-11-06 <![CDATA[ Performance Limitations in Sensorimotor Control: Tradeoffs between Neural Computing and Accuracy in Tracking Fast Movements ]]> https://biorxiv.org/content/10.1101/464230v1?rss=1 Saxena, S. Sarma, S. V. Dahleh, M. 2018-11-07 doi:10.1101/464230 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Mechanism and resistance for antimycobacterial activity of a fluoroquinophenoxazine compound ]]> https://biorxiv.org/content/10.1101/464990v1?rss=1 10 fold lower than the compound concentrations required for producing negatively supercoiled DNA during ligation of nicked circular DNA. Thus, the DNA-binding property of FP-11g may contribute to its antimycobacterial mechanism, but that alone cannot account for the observed inhibition of Mtb topoisomerase I. ]]> Tse-Dinh, Y.-C. Garcia, P. K. Annamalai, T. Wang, W. Bell, R. S. Le, D. Martin Pancorbo, P. Sikandar, S. Seddek, A. Yu, X. Sun, D. Uhlemann, A.-C. Tiwari, P. B. Leng, F. 2018-11-07 doi:10.1101/464990 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Characterization of proprioceptive system dynamics in behaving Drosophila larvae using high-speed volumetric microscopy ]]> https://biorxiv.org/content/10.1101/467274v1?rss=1 Vaadia, R. Li, W. Voleti, V. Singhania, A. Hillman, E. M. C. Grueber, W. B. 2018-11-09 doi:10.1101/467274 Cold Spring Harbor Laboratory Press 2018-11-09 <![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[ The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy ]]> https://biorxiv.org/content/10.1101/470047v1?rss=1 Fu, Z. Indrisiunaite, G. Kaledhonkar, S. Shah, B. Sun, M. Chen, B. Grassucci, R. A. Ehrenberg, M. Frank, J. 2018-11-14 doi:10.1101/470047 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Functional interrogation of a depression-related serotonergic SNP, rs6295, using a humanized mouse model ]]> https://biorxiv.org/content/10.1101/472621v1?rss=1 Cunningham, A. M. Santos, T. L. Gutzeit, V. A. Hamilton, H. Hen, R. Donaldson, Z. 2018-11-17 doi:10.1101/472621 Cold Spring Harbor Laboratory Press 2018-11-17 <![CDATA[ Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells ]]> https://biorxiv.org/content/10.1101/474478v1?rss=1 Grudzien-Nogalska, E. Wu, Y. Jiao, X. Cui, H. Hart, R. P. Tong, L. Kiledjian, M. 2018-11-20 doi:10.1101/474478 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Reconstitution of eukaryotic chromosomes and manipulation of DNA N6-methyladenine alters chromatin and gene expression ]]> https://biorxiv.org/content/10.1101/475384v1?rss=1 Beh, L. Y. Debelouchina, G. T. Clay, D. M. Thompson, R. E. Lindblad, K. A. Hutton, E. R. Bracht, J. R. Sebra, R. P. Muir, T. W. Landweber, L. F. 2018-11-20 doi:10.1101/475384 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Nuclei multiplexing with barcoded antibodies for single-nucleus genomics ]]> https://biorxiv.org/content/10.1101/476036v1?rss=1 Gaublomme, J. T. Li, B. McCabe, C. Knecht, A. Drokhlyansky, E. Van Wittenberghe, N. Waldman, J. Dionne, D. Nguyen, L. De Jager, P. Yeung, B. Zhao, X. Habib, N. Rozenblatt-Rosen, O. Regev, A. 2018-11-23 doi:10.1101/476036 Cold Spring Harbor Laboratory Press 2018-11-23 <![CDATA[ Convolutional Sparse Coded Dynamic Brain Functional Connectivity ]]> https://biorxiv.org/content/10.1101/476663v1?rss=1 Yan, J. zhu, y. 2018-11-27 doi:10.1101/476663 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ Genomic variation in educational attainment modifies Alzheimer’s disease risk ]]> https://biorxiv.org/content/10.1101/478776v1?rss=1 Raghavan, N. Vardarajan, B. Mayeux, R. 2018-11-28 doi:10.1101/478776 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ arcasHLA: high resolution HLA typing from RNA seq ]]> https://biorxiv.org/content/10.1101/479824v1?rss=1 Orenbuch, R. Filip, I. Comito, D. Shaman, J. Pe'er, I. Rabadan, R. 2018-12-03 doi:10.1101/479824 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ APOE4 is Associated with Differential Regional Vulnerability to Bioenergetic Deficits in Aged APOE Mice ]]> https://biorxiv.org/content/10.1101/482422v1?rss=1 Nuriel, T. Larrea, D. Guilfoyle, D. N. Pirhaji, L. Shannon, K. Arain, H. Ashok, A. Pera, M. Chen, Q. Dillman, A. A. Figueroa, H. Y. Cookson, M. R. Gross, S. S. Fraenkel, E. Duff, K. E. Area-Gomez, E. 2018-11-29 doi:10.1101/482422 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/content/10.1101/484113v1?rss=1 Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. Grove, J. Klei, L. Stevens, C. Reichert, J. Mulhern, M. Artomov, M. Gerges, S. Sheppard, B. Xu, X. Bhaduri, A. Norman, U. Brand, H. Schwartz, G. Nguyen, R. Guerrero, E. Dias, C. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Stress-induced phospho-ubiquitin formation causes parkin degradation ]]> https://biorxiv.org/content/10.1101/484857v1?rss=1 Kovalchuke, L. Mosharov, E. V. Levy, O. A. Greene, L. A. 2018-12-05 doi:10.1101/484857 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Topological Data Analysis of Single-cell Hi-C Contact Maps ]]> https://biorxiv.org/content/10.1101/486936v1?rss=1 Carriere, M. Rabadan, R. 2018-12-04 doi:10.1101/486936 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Attenuation of Aβ-associated hyperactivity reduces Aβ and tau pathology along the entorhinal cortex-hippocampal network ]]> https://biorxiv.org/content/10.1101/487405v1?rss=1 Rodriguez, G. A. Barrett, G. M. Duff, K. E. Hussaini, A. 2018-12-04 doi:10.1101/487405 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Using DNA from mothers and children to study parental investment in children’s educational attainment ]]> https://biorxiv.org/content/10.1101/489781v1?rss=1 Wertz, J. Moffitt, T. E. Agnew-Blais, J. Arseneault, L. Belsky, D. W. Corcoran, D. L. Houts, R. Matthews, T. Prinz, J. A. Richmond-Rakerd, L. S. Sugden, K. Williams, B. Caspi, A. 2018-12-09 doi:10.1101/489781 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Cellular multifunctionality in the muscle activity of Hydra vulgaris ]]> https://biorxiv.org/content/10.1101/489930v1?rss=1 Szymanski, J. R. Yuste, R. 2018-12-07 doi:10.1101/489930 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Inferring Processes of Coevolutionary Diversification in a Community of Panamanian Strangler Figs and Associated Pollinating Wasps ]]> https://biorxiv.org/content/10.1101/490862v1?rss=1 Satler, J. D. Herre, A. Jander, C. Eaton, D. A. R. Machado, C. A. Heath, T. A. Nason, J. D. 2018-12-09 doi:10.1101/490862 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Rapid screening of engineered microbial therapies in a 3-D multicellular model ]]> https://biorxiv.org/content/10.1101/491159v1?rss=1 Harimoto, T. Singer, Z. Velazquez, O. Zhang, J. Castro, S. Hinchliffe, T. Mather, W. Danino, T. 2018-12-10 doi:10.1101/491159 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Mechanical Stretch Kills Transformed Cancer Cells ]]> https://biorxiv.org/content/10.1101/491746v1?rss=1 Tijore, A. Yao, M. Wang, Y.-H. Nematbakhsh, Y. Hariharan, A. Lim, C. T. Sheetz, M. 2018-12-10 doi:10.1101/491746 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Clinical and Functional Characterization of Melanocortin 4 Receptor genetic variants in African American and/or Hispanic children with severe early onset obesity. ]]> https://biorxiv.org/content/10.1101/491969v1?rss=1 120% of 95th percentile of CDC 2000 growth charts at an age < 6 years, with no known pathological cause of obesity were enrolled.nnResultsEight rare MC4R mutations (2.6%) were identified in this study (R7S, F202L (n=2), M215I, G252D, V253I, I269N, F284I), three of which have not been previously reported (M215I, G252D, F284I). The pathogenicity of the variants was confirmed either by prior literature reports, or by functional testing. There was no significant difference in the BMI or height trajectories of children with or without MC4R mutations in this cohort.nnConclusionsWhile the prevalence of MC4R mutations in this cohort was similar to that reported in obese children of European ancestry, some of the variants were novel. ]]> De Rosa, M. C. Chesi, A. McCormack, S. Zhou, J. Weaver, B. McDonald, M. Christensen, S. Liimatta, K. Rosenbaum, M. Hakonarson, H. Doege, C. A. Hirschhorn, J. N. Grant, S. F. Thaker, V. V. 2018-12-10 doi:10.1101/491969 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Targeting the CaV - interaction yields a selective antagonist of the N-type CaV2.2 channel with broad antinociceptive efficacy ]]> https://biorxiv.org/content/10.1101/492181v1?rss=1 Chefdeville, A. Yu, J. Yang, X. Moutal, A. Gokhale, V. Shuja, Z. Chew, L. Bellampalli, S. S. Luo, S. Francois-Moutal, L. Ha, T. Perez-Miller, S. Park, K. D. Patwardhan, A. M. Streicher, J. M. Colecraft, H. M. Khanna, M. Khanna, R. 2018-12-10 doi:10.1101/492181 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Pan-Cancer modelling of genomic alterations through gene expression ]]> https://biorxiv.org/content/10.1101/492561v1?rss=1 Giorgi, F. M. Ray, F. 2018-12-10 doi:10.1101/492561 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Identification of three sequence motifs in the transcription termination factor Sen1 that mediate direct interactions with Nrd1 ]]> https://biorxiv.org/content/10.1101/492736v1?rss=1 Zhang, Y. Chun, Y. Buratowski, S. Tong, L. 2018-12-10 doi:10.1101/492736 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ Real-time capture of horizontal gene transfers from gut microbiota by engineered CRISPR-Cas acquisition ]]> https://biorxiv.org/content/10.1101/492751v1?rss=1 Munck, C. Sheth, R. U. Freedberg, D. E. Wang, H. H. 2018-12-10 doi:10.1101/492751 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ The loci of behavioral evolution: Fas2 and tilB underlie differences in pupation site choice behavior between Drosophila melanogaster and D. simulans ]]> https://biorxiv.org/content/10.1101/494013v1?rss=1 Pischedda, A. Shahandeh, M. P. Turner, T. L. 2018-12-11 doi:10.1101/494013 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Rare variants imputation in admixed populations: Comparison across reference panels and bioinformatics tools. ]]> https://biorxiv.org/content/10.1101/494229v1?rss=1 Sariya, S. Lee, J. Mayeux, R. Vardarajan, B. N. Reyes-Dumeyer, D. Manly, J. Brickman, A. Lantigua, R. Medrano, M. Jimenez-Velazquez, I. Z. Tosto, G. 2018-12-13 doi:10.1101/494229 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Unique properties of high-order thalamic inputs versus cortical inputs to primary somatosensory cortex ]]> https://biorxiv.org/content/10.1101/495218v1?rss=1 Zhang, E. Bruno, R. M. 2018-12-13 doi:10.1101/495218 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Analysing linear multivariate pattern transformations in neuroimaging data ]]> https://biorxiv.org/content/10.1101/497180v1?rss=1 Basti, A. Mur, M. Kriegeskorte, N. Pizzella, V. Marzetti, L. Hauk, O. 2018-12-14 doi:10.1101/497180 Cold Spring Harbor Laboratory Press 2018-12-14 <![CDATA[ Imbalanced Nucleocytoskeletal Connections Create Common Polarity Defects in Progeria and Physiological Aging ]]> https://biorxiv.org/content/10.1101/497297v1?rss=1 60 years) individuals. The mechanism underlying these defects is excessive interaction of the nucleus with microtubules. Our work identifies nuclear-based defects in cell polarization as intrinsic factors in premature and physiological aging and suggests means for correcting them. ]]> Chang, W. Wang, Y. Luxton, G. W. G. Ostlund, C. Worman, H. J. Gundersen, G. G. 2018-12-15 doi:10.1101/497297 Cold Spring Harbor Laboratory Press 2018-12-15 <![CDATA[ Serotonin regulates mitochondrial biogenesis and function in rodent cortical neurons via the 5-HT2A receptor and SIRT1-PGC-1α axis ]]> https://biorxiv.org/content/10.1101/497982v1?rss=1 Fanibunda, S. Deb, S. Maniyadath, B. Gupta, S. Weisstaub, N. Gingrich, J. Vaidya, A. Kolthur-Seetharam, U. Vaidya, V. A. 2018-12-16 doi:10.1101/497982 Cold Spring Harbor Laboratory Press 2018-12-16 <![CDATA[ Functionally distinct high and low theta oscillations in the human hippocampus ]]> https://biorxiv.org/content/10.1101/498055v1?rss=1 Goyal, A. Miller, J. Qasim, S. Watrous, A. J. Stein, J. M. Inman, C. S. Gross, R. E. Willie, J. T. Lega, B. Lin, J.-J. Sharan, A. Wu, C. Sperling, M. R. Sheth, S. A. McKhann, G. M. Smith, E. H. Schevon, C. Jacobs, J. 2018-12-17 doi:10.1101/498055 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Functional and Optogenetic Approaches to Discovering Stable Subtype-Specific Circuit Mechanisms in Depression ]]> https://biorxiv.org/content/10.1101/498964v1?rss=1 Grosenick, L. Shi, T. C. Gunning, F. Dubin, M. J. Downar, J. Liston, C. 2018-12-17 doi:10.1101/498964 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Neuronal activity in the posterior cingulate cortex signals environmental information and predicts behavioral variability during routine foraging ]]> https://biorxiv.org/content/10.1101/499814v1?rss=1 Barack, D. L. Platt, M. L. 2018-12-19 doi:10.1101/499814 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ A counterselectable sucrose sensitivity marker permits efficient and flexible mutagenesis in Streptococcus agalactiae ]]> https://biorxiv.org/content/10.1101/499822v1?rss=1 99% of colonies that emerge from our protocol had the expected knockout phenotype and that among a subset tested by sequencing, 100% had the correct genotype. We also generated barcoded nonsense mutations in the cylE gene in two GBS strains, showing that the approach can be used to make small, precise chromosomal mutations.nnImportanceThe ability to generate chromosomal mutations is fundamental to microbiology. Historically, however, GBS pathogenesis research has been made challenging by the relative genetic intractability of the organism. Generating a single knockout in GBS using traditional techniques can take many months, with highly variable success rates. Furthermore, traditional methods do not offer a straightforward way to generate single base pair polymorphisms or other subtle changes, especially to noncoding regions of the chromosome. We have developed a new sucrose counterselection-based method that permits rapid, efficient, and flexible GBS mutagenesis. Our technique requires no additional equipment beyond what is needed for traditional approaches. We believe that it will catalyze rapid advances in GBS genetics research by significantly easing the path to generating mutants. ]]> Hooven, T. A. Bonakdar, M. Chamby, A. B. Ratner, A. J. 2018-12-19 doi:10.1101/499822 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Generation of Transgenic Human Malaria Parasites With Strong Fluorescence in the Transmission Stages ]]> https://biorxiv.org/content/10.1101/500793v1?rss=1 McLean, K. J. Straimer, J. Hopp, C. S. Vega-Rodriguez, J. Tripathi, A. Mlambo, G. Doumolin, P. C. Harris, C. T. Tong, X. Shears, M. J. Ankarklev, J. Kafsack, B. Fidock, D. A. Sinnis, P. 2018-12-18 doi:10.1101/500793 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection ]]> https://biorxiv.org/content/10.1101/502443v1?rss=1 Souza, T. Rangel Vieira, Y. Delatorre, E. Barbosa-Lima, G. Leal Faria Luiz, R. Vizzoni, A. Jain, K. Mesquita, M. Bhuva, N. Gogarten, J. F. Ng, J. Thakkar, R. Surrage Calheiros, A. Teixeira Monteiro, A. P. Bozza, P. T. Bozza, F. A. Tschoeke, D. A. Leomil, L. Lima de Mendonca, M. C. Damasceno dos Santos Rodrigues, C. Torres, M. C. Bispo de Filippis, A. M. Ribeiro Nogueira, R. M. Thompson, F. L. Lemos, C. Durovni, B. Cerbino-Neto, J. Morel, C. M. Lipkin, I. Mishra, N. 2018-12-20 doi:10.1101/502443 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ The elasticity of individual protocadherin 15 molecules implicates cadherins as the gating springs for hearing ]]> https://biorxiv.org/content/10.1101/503029v1?rss=1 Bartsch, T. F. Hengel, F. E. Oswald, A. Dionne, G. Chipendo, I. V. Mangat, S. S. El Shatanofy, M. Shapiro, L. Mueller, U. Hudspeth, A. J. 2018-12-20 doi:10.1101/503029 Cold Spring Harbor Laboratory Press 2018-12-20 <![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[ Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal ]]> https://biorxiv.org/content/10.1101/503755v1?rss=1 Hamilton, K. Sun, Y. Tong, L. 2018-12-30 doi:10.1101/503755 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Extensive recombination suppression and chromosome-wide differentiation of a segregation distorter in Drosophila ]]> https://biorxiv.org/content/10.1101/504126v1?rss=1 2 million generations). Through direct recombination experiments and population genetic analyses, we infer that this high level of differentiation is maintained by a combination of suppressed recombination and epistatic selection. Finally, our data reveal a massive mutational target size for protein and expression level changes specific to SR generated by its three non-overlapping inversions. Together our results imply that the entire SR chromosome in D. pseudoobscura behaves as a single co-adapted gene complex and has been maintained through a combination of suppressed recombination and epistatic selection. This finding highlights the dramatic consequences segregation distorters can have in shaping chromosome-wide patterns of recombination, nucleotide variation, and gene expression. ]]> Fuller, Z. L. Koury, S. A. Leonard, C. J. Young, R. E. Ikegami, K. Westlake, J. Richards, S. Schaeffer, S. W. Phadnis, N. 2018-12-21 doi:10.1101/504126 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Dual-color volumetric imaging of neural activity of cortical columns ]]> https://biorxiv.org/content/10.1101/504233v1?rss=1 Han, S. Yang, W. Yuste, R. 2018-12-21 doi:10.1101/504233 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Comparison of Two-Talker Attention Decoding from EEG with Nonlinear Neural Networks and Linear Methods ]]> https://biorxiv.org/content/10.1101/504522v1?rss=1 Ciccarelli, G. Nolan, M. Perricone, J. Calamia, P. Haro, S. O'Sullivan, J. Mesgarani, N. Quatieri, T. Smalt, C. 2018-12-21 doi:10.1101/504522 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Delay activity dynamics: task dependent time encoding and low dimensional trajectories ]]> https://biorxiv.org/content/10.1101/504936v1?rss=1 Cueva, C. J. Marcos, E. Saez, A. Genovesio, A. Jazayeri, M. Romo, R. Salzman, C. D. Shadlen, M. N. Fusi, S. 2018-12-29 doi:10.1101/504936 Cold Spring Harbor Laboratory Press 2018-12-29 <![CDATA[ Synapse propensity of human memory CD8 T cells confers competitive advantage over naïve counterparts ]]> https://biorxiv.org/content/10.1101/507392v1?rss=1 Mayya, V. Judokusumo, E. Abu-Shah, E. Neiswanger, W. Kam, L. C. Dustin, M. L. 2018-12-28 doi:10.1101/507392 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ The MHC class-II HLA-DR receptor mediates bat influenza A-like H17N10 virus entry into mammalian cells ]]> https://biorxiv.org/content/10.1101/507467v1?rss=1 Giotis, E. S. Carnell, G. Young, E. F. Ghanny, S. Soteropoulos, P. Barclay, W. S. Skinner, M. A. Temperton, N. 2019-01-04 doi:10.1101/507467 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits ]]> https://biorxiv.org/content/10.1101/507525v1?rss=1 Nagpal, S. Meng, X. Epstein, M. P. Tsoi, L. C. Patrick, M. Gibson, G. De Jager, P. Bennett, D. A. Wingo, A. P. Wingo, T. S. Yang, J. 2018-12-28 doi:10.1101/507525 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ Detection of circulating extracellular mRNAs by modified small RNA-sequencing analysis ]]> https://biorxiv.org/content/10.1101/507681v1?rss=1 Akat, K. M. Lee, Y. A. Hurley, A. Morozov, P. Max, K. E. A. Brown, M. Bogardus, K. Sopeyin, A. Hildner, K. Diacovo, T. Neurath, M. F. Borggrefe, M. Tuschl, T. 2018-12-31 doi:10.1101/507681 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ An increase in spontaneous activity mediates visual habituation ]]> https://biorxiv.org/content/10.1101/507814v1?rss=1 Miller, J.-e. K. Miller, B. R. Yuste, R. 2018-12-28 doi:10.1101/507814 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach ]]> https://biorxiv.org/content/10.1101/510420v1?rss=1 Logsdon, B. Perumal, T. M. Swarup, V. Wang, M. Funk, C. Gaiteri, C. Allen, M. Wang, X. Dammer, E. Srivastava, G. Mukherjee, S. Sieberts, S. K. Omberg, L. Dang, K. D. Eddy, J. A. Snyder, P. Chae, Y. Amberkar, S. Wei, W. Hide, W. Preuss, C. Ergun, A. Ebert, P. J. Airey, D. C. Carter, G. W. Mostafavi, S. Yu, L. Klein, H.-U. Collier, D. A. Golde, T. Levey, A. Bennett, D. A. Estrada, K. Decker, M. Liu, Z. Shulman, J. M. Zhang, B. Schadt, E. De Jager, P. L. Price, N. D. Ertekin-Taner, N. Mangravite, L. M. 2019-01-03 doi:10.1101/510420 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Integrating Quality of Life and Survival Outcomes Cardiovascular Clinical Trials: Results from the PARTNER Trial ]]> https://biorxiv.org/content/10.1101/513895v1?rss=1 Spertus, J. Hatfield, L. A. Cohen, D. J. Arnold, S. V. Ho, M. Jones, P. G. Leon, M. Zuckerman, B. Spertus, J. A. 2019-01-12 doi:10.1101/513895 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Tau-mediated Disruption of the Spliceosome Triggers Cryptic RNA-splicing and Neurodegeneration in Alzheimer’s Disease ]]> https://biorxiv.org/content/10.1101/514927v1?rss=1 Hsieh, Y.-C. Guo, C. Yalamanchili, H. K. Abreha, M. Al-Ouran, R. Li, Y. Dammer, E. B. Lah, J. J. Levey, A. I. Bennett, D. A. De Jager, P. L. Seyfried, N. T. Liu, Z. Shulman, J. M. 2019-01-09 doi:10.1101/514927 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Molecular Logic of Spinocerebellar Tract Neuron Diversity and Connectivity ]]> https://biorxiv.org/content/10.1101/516435v1?rss=1 Baek, M. Menon, V. Jessell, T. Hantman, A. Dasen, J. 2019-01-09 doi:10.1101/516435 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Exome sequencing of 457 autism families recruited online provides evidence for novel ASD genes ]]> https://biorxiv.org/content/10.1101/516625v1?rss=1 Feliciano, P. Zhou, X. Astrovskaya, I. Turner, T. Wang, T. Brueggeman, L. Barnard, R. Hsieh, A. Snyder, L. G. Muzny, D. Sabo, A. The SPARK Consortium, Gibbs, R. Eichler, E. O'Roak, B. Michaelson, J. Volfovsky, N. Shen, Y. Chung, W. 2019-01-09 doi:10.1101/516625 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ White matter regions with low microstructure in young adults are associated with white matter hyperintensities in late life ]]> https://biorxiv.org/content/10.1101/517763v1?rss=1 20%) and we determined whether WMH frequency bins were different by normative FA values defined in the younger group. ResultsFractional anisotropy values were lower (p<0.001) in WMH regions compared with NAWM regions in the older sample. Areas with higher WMH frequency in older adults had lower FA values in younger adults (5-10%>10-15%>15-20%; p<0.001). DiscussionLow FA values are observed in frank WMH, but FA is also normatively low in regions with high WMH frequency prior to damage. Regions with normatively lower microstructure are more susceptible to future damage from factors such as chronic hypoperfusion or pathology. ]]> Lao, P. Vorberger, R. Narkhede, A. Gazes, Y. Igwe, K. Guzman, V. Last, B. Habeck, C. Stern, Y. Brickman, A. 2019-01-23 doi:10.1101/517763 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Signatures of replication, recombination and sex in the spectrum of rare variants on the human X chromosome and autosomes ]]> https://biorxiv.org/content/10.1101/519421v1?rss=1 G as a mutagenic signature of male meiotic double strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes. ]]> Agarwal, I. Przeworski, M. 2019-01-15 doi:10.1101/519421 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Stereotyped large amplitude cortical LFP events can be clustered and reveal precisely ordered phase-locking in neuronal populations ]]> https://biorxiv.org/content/10.1101/519454v1?rss=1 2Hz) rat auditory and barrel cortex neurons (Luczak et al., 2015) support this hypothesis. Yet it is unknown whether UP-states are homogeneous and whether neurons with firing rates <2Hz in visual cortex or other species exhibit spiking order. Using extracellular recordings during anesthetized states in cat visual cortex and mouse visual, auditory and barrel cortex, we show that UP-states can be tracked and clustered based on the shape of the LFP waveform. We show that LFP event clusters (LECs) have current-source-density profiles that are common across different recordings or animals and using simultaneous electrophysiology and widefield voltage and calcium imaging in mouse we confirm that LEC transitions are cortex-wide phenomena. Individual LEC events can be resolved in time to within 1 - 4 ms and they elicit synchronous firing of over 75% of recorded neurons with most neurons synchronizing their firing to within {+/-}5 - 15 ms relative LECs. Firing order of different neurons during LEC events was preserved over periods of ~30 minutes enabling future studies of UP-state transitions and firing order with near millisecond precision.nnSignificant StatementDuring sleep and anesthetic states mammalian cortex undergoes substantial changes from awake active states. Recent studies show that single neurons in some cortical areas in rats undergo increased spiking during sleep and anesthetic states (called UP-state transitions) with some neurons firing in an order similar to awake states. This suggests that sensory processing may be similar across all states and that firing order is important for stimulus processing. Yet UP-state transitions remain poorly understood and it is unclear whether firing order is present in other cortical areas or species. Here we describe multiple classes of UP-state transitions and show most neurons in visual cortex in cats and visual, barrel and auditory cortex in mice exhibit firing order during such transitions. ]]> Mitelut, C. Spacek, M. Chan, A. W. Murphy, T. H. Swindale, N. V. 2019-01-12 doi:10.1101/519454 Cold Spring Harbor Laboratory Press 2019-01-12 <![CDATA[ Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes ]]> https://biorxiv.org/content/10.1101/521054v1?rss=1 Fachal, L. Aschard, H. Beesley, J. Barnes, D. Allen, J. Kar, S. Pooley, K. Dennis, J. Michailidou, K. Turman, C. Soucy, P. Lemacon, A. Lush, M. Tyrer, J. Ghoussaini, M. Moradi Marjaneh, M. Jiang, X. Agata, S. Aittomaki, K. Alonso, M. R. Andrulis, I. Anton-Culver, H. Antonenkova, N. Arason, A. Arndt, V. Aronson, K. Arun, B. Auber, B. Auer, P. Azzollini, J. Balmana, J. Barkardottir, R. Barrowdale, D. Beeghly-Fadiel, A. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Blot, W. Bogdanova, N. Bojesen, S. Bolla, M. Bonanni, B. Borg, A. B 2019-01-15 doi:10.1101/521054 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Understanding the variation in wood densities of trees and its implications for carbon assessments ]]> https://biorxiv.org/content/10.1101/523480v1?rss=1 Teegalapalli, K. Pandey, C. K. Osuri, A. Ratnam, J. Sankaran, M. 2019-01-17 doi:10.1101/523480 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Single-neuron representations of spatial memory targets in humans ]]> https://biorxiv.org/content/10.1101/523753v1?rss=1 Tsitsiklis, M. Miller, J. Qasim, S. E. Inman, C. S. Gross, R. E. Willie, J. R. Smith, E. H. Sheth, S. A. Schevon, C. A. Sperling, M. R. Sharan, A. Stein, J. M. Jacobs, J. 2019-01-17 doi:10.1101/523753 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Alpha-Synuclein is a Target of Fic-mediated Adenylylation/AMPylation: Implications for Parkinson’s Disease ]]> https://biorxiv.org/content/10.1101/525659v1?rss=1 Mattoo, S. Sanyal, A. Dutta, S. Chandran, A. Koller, A. Camara, A. Watson, B. G. Sengupta, R. Ysselstein, D. Montenegro, P. Cannon, J. R. Rochet, C. 2019-01-21 doi:10.1101/525659 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[ Incorporating prior information into signal-detection analyses across biologically informed gene-sets ]]> https://biorxiv.org/content/10.1101/525840v1?rss=1 Zhang, M. Gelfman, S. McCarthy, J. Goldstein, D. B. Allen, A. S. 2019-01-23 doi:10.1101/525840 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Trophic complexity alters the diversity-multifunctionality relationship in experimental grassland mesocosms ]]> https://biorxiv.org/content/10.1101/525881v1?rss=1 Anujan, K. Heilpern, S. A. Prager, C. M. Naeem, S. 2019-01-23 doi:10.1101/525881 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Regular cycling between representations of alternatives in the hippocampus ]]> https://biorxiv.org/content/10.1101/528976v1?rss=1 Kay, K. Chung, J. E. Sosa, M. Schor, J. S. Karlsson, M. P. Larkin, M. C. Liu, D. F. Frank, L. M. 2019-01-28 doi:10.1101/528976 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Social hierarchy position in female mice is associated with plasma corticosterone levels and hypothalamic gene expression ]]> https://biorxiv.org/content/10.1101/529131v1?rss=1 Williamson, C. M. Lee, W. Decasien, A. R. Lanham, A. Romeo, R. D. Curley, J. P. 2019-01-23 doi:10.1101/529131 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a-deficient mice ]]> https://biorxiv.org/content/10.1101/529701v1?rss=1 Mukai, J. Cannavo, E. Sun, Z. Crabtree, G. Diamantopoulou, A. Thakur, P. Chang, C.-Y. Cai, Y. Lomvardas, S. Takata, A. Xu, B. Gogos, J. 2019-01-26 doi:10.1101/529701 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Huntington's disease onset is determined by length of uninterrupted CAG, not encoded polyglutamine, and is modified by DNA maintenance mechanisms ]]> https://biorxiv.org/content/10.1101/529768v1?rss=1 Genetic Modifiers of Huntington's Disease (GeM-HD) Consortium, Lee, J.-M. Correia, K. Loupe, J. Kim, K.-H. Barker, D. Hong, E. P. Chao, M. J. Long, J. D. Lucente, D. Vonsattel, J.-P. Mouro Pinto, R. Abu Elneel, K. Ramos, E. M. Mysore, J. S. Gillis, T. Wheeler, V. C. MacDonald, M. E. Gusella, J. F. Massey, T. McAllister, B. Medway, C. Stone, T. C. Hall, L. Jones, L. Holmans, P. Kwak, S. Ehrhardt, A. Sampaio, C. Ciosi, M. Maxwell, A. Chatzi, A. Monckton, D. G. Orth, M. Landwehrmeyer, G. B. Paulsen, J. S. Dorsey, E. R. Shoulson, I. Myers, R. H. 2019-01-24 doi:10.1101/529768 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Analysis of genetic networks regulating refractive eye development in collaborative cross progenitor strain mice reveals new genes and pathways underlying human myopia ]]> https://biorxiv.org/content/10.1101/530766v1?rss=1 Tkatchenko, T. V. Shah, R. L. Nagasaki, T. Tkatchenko, A. V. 2019-01-25 doi:10.1101/530766 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Computed Tomography Measures of Inter-site tumor Heterogeneity for Classifying Outcomes in High-Grade Serous Ovarian Carcinoma: a Retrospective Study ]]> https://biorxiv.org/content/10.1101/531046v1?rss=1 Veeraraghavan, H. Vargas, H. A. Sanchez, A. J. Micco, M. Mema, E. Capanu, M. Zheng, J. Lakhman, Y. Crispin-Ortuzar, M. Huang, E. Levine, D. A. Deasy, J. O. Snyder, A. Miller, M. L. Brenton, J. D. Sala, E. 2019-01-26 doi:10.1101/531046 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Dissociation of broadband high-frequency activity and neuronal firing in the neocortex ]]> https://biorxiv.org/content/10.1101/531368v1?rss=1 Leszczynski, M. Barczak, A. Kajikawa, Y. Ulbert, I. Falchier, A. Tal, I. Haegens, S. Melloni, L. Knight, R. Schroeder, C. 2019-01-25 doi:10.1101/531368 Cold Spring Harbor Laboratory Press 2019-01-25 <![CDATA[ Early Life Adversity, but not suicide, is associated with less prefrontal cortex gray matter in adulthood ]]> https://biorxiv.org/content/10.1101/531871v1?rss=1 Underwood, M. D. Bakalian, M. Escobar, T. Kassir, S. Mann, J. J. Arango, V. 2019-01-27 doi:10.1101/531871 Cold Spring Harbor Laboratory Press 2019-01-27 <![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[ Prophylactic TLR9 stimulation reduces brain metastasis through microglia activation ]]> https://biorxiv.org/content/10.1101/533927v1?rss=1 Benbenishty, A. Gadrich, M. Cottarelli, A. Lubart, A. Kain, D. Amer, M. Shaashua, L. Glasner, A. Erez, N. Agalliu, D. Mayo, L. Ben-Eliyahu, S. Blinder, P. 2019-01-31 doi:10.1101/533927 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 implicated in Tau pathology ]]> https://biorxiv.org/content/10.1101/535682v1?rss=1 Taga, M. Petyuk, V. A. White, C. Marsh, G. Ma, Y. Klein, H.-U. Connor, S. M. Khairallah, A. Olah, M. Schneider, J. Ransohoff, R. Bennett, D. A. Crotti, A. Bradshaw, E. M. De Jager, P. L. 2019-01-30 doi:10.1101/535682 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ mTOR suppresses macroautophagy during postnatal development of the striatum. ]]> https://biorxiv.org/content/10.1101/536680v1?rss=1 Lieberman, O. Pigulevskiy, I. Post, M. Sulzer, D. Santini, E. 2019-01-31 doi:10.1101/536680 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Increasing Synaptic GluN2B levels within the Basal and Lateral Amygdala Enables the Modification of Strong Reconsolidation Resistant Fear Memories ]]> https://biorxiv.org/content/10.1101/537142v1?rss=1 de Solis, C. A. Gonzalez, C. U. Galdamez, M. A. Perish, J. M. Woodard, S. W. Salinas, C. E. Miller, J. N. Elahi, H. Pineda, O. H. Oad, S. Gatica de las Fuentes, S. Owen, M. S. Sandoval, A. Holehonnur, R. Ploski, J. E. 2019-01-31 doi:10.1101/537142 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Brain-derived circulating cell-free DNA defines the brain region and cell specific origins associated with neuronal atrophy ]]> https://biorxiv.org/content/10.1101/538827v1?rss=1 Chatterton, Z. Mendelev, N. Chen, S. Raj, T. Walker, R. Carr, W. Kamimori, G. Beeri, M. Ge, Y. Dwork, A. Haghighi, F. 2019-02-02 doi:10.1101/538827 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ Modeling of fibrotic lung disease using 3D organoids derived from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/538991v1?rss=1 Snoeck, H.-W. Strikoudis, A. Loffredo, L. Chen, Y.-W. 2019-02-03 doi:10.1101/538991 Cold Spring Harbor Laboratory Press 2019-02-03 <![CDATA[ Sensorimotor adaptation compensates for distortions of 3D shape information ]]> https://biorxiv.org/content/10.1101/540187v1?rss=1 Cesanek, E. Taylor, J. A. Domini, F. 2019-02-04 doi:10.1101/540187 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Intracranial EEG reveals bihemispheric parietal and extra parietal brain networks supporting mental arithmetic ]]> https://biorxiv.org/content/10.1101/542142v1?rss=1 Umbach, G. Rugg, M. Worrell, G. Sperling, M. Gross, R. Jobst, B. Jacobs, J. Zaghloul, K. Stein, J. Davis, K. Lega, B. 2019-02-06 doi:10.1101/542142 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Predictability in the evolution of Orthopteran cardenolide insensitivity ]]> https://biorxiv.org/content/10.1101/542811v1?rss=1 Yang, L. Ravikanthachari, N. Marino-Perez, R. Deshmukh, R. Wu, M. Rosenstein, A. Kunte, K. Song, H. Andolfatto, P. 2019-02-07 doi:10.1101/542811 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Weak modulation of thalamic discharge by basal ganglia output in association with a reaching task ]]> https://biorxiv.org/content/10.1101/546598v1?rss=1 Schwab, B. C. Kase, D. Zimnik, A. Rosenbaum, R. Rubin, J. E. Turner, R. S. 2019-02-11 doi:10.1101/546598 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Aversive learning strengthens episodic memory in both adolescents and adults ]]> https://biorxiv.org/content/10.1101/547331v1?rss=1 Cohen, A. O. Matese, N. G. Filimontseva, A. Shen, X. Shi, T. C. Livne, E. Hartley, C. A. 2019-02-12 doi:10.1101/547331 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing ]]> https://biorxiv.org/content/10.1101/549220v1?rss=1 Georgieva, D. Liu, Q. Wang, K. Egli, D. 2019-02-14 doi:10.1101/549220 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension ]]> https://biorxiv.org/content/10.1101/550327v1?rss=1 Zhu, N. Pauciulo, M. W. Welch, C. L. Lutz, K. A. Coleman, A. W. Gonzaga-Jauregui, C. Wang, J. Grimes, J. M. Martin, L. J. He, H. PAH Biobank, Shen, Y. Chung, W. K. Nichols, W. C. 2019-02-14 doi:10.1101/550327 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation ]]> https://biorxiv.org/content/10.1101/552117v1?rss=1 Sasani, T. A. Pedersen, B. S. Gao, Z. Baird, L. Przeworski, M. Jorde, L. B. Quinlan, A. R. 2019-02-17 doi:10.1101/552117 Cold Spring Harbor Laboratory Press 2019-02-17 <![CDATA[ Motor cortex signals corresponding to the two arms are shared across hemispheres, mixed among neurons, yet partitioned within the population response ]]> https://biorxiv.org/content/10.1101/552257v1?rss=1 Ames, K. C. Churchland, M. M. 2019-02-18 doi:10.1101/552257 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Cross-Species Alignment of Single Cell States with Biological Process Activity ]]> https://biorxiv.org/content/10.1101/555268v1?rss=1 Ding, H. Blair, A. Stuart, J. 2019-02-19 doi:10.1101/555268 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease ]]> https://biorxiv.org/content/10.1101/555557v1?rss=1 Szabo, P. A. Levitin, H. M. Miron, M. Snyder, M. E. Senda, T. Yuan, J. Cheng, Y. L. Bush, E. C. Dogra, P. Thapa, P. Farber, D. L. Sims, P. A. 2019-02-20 doi:10.1101/555557 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor ]]> https://biorxiv.org/content/10.1101/555565v1?rss=1 LeVine, M. V. Terry, D. S. Khelashvili, G. Siegel, Z. S. Quick, M. Javitch, J. A. Blanchard, S. C. Weinstein, H. 2019-02-20 doi:10.1101/555565 Cold Spring Harbor Laboratory Press 2019-02-20 <![CDATA[ Holding the arm still through subcortical mathematical integration of cortical commands ]]> https://biorxiv.org/content/10.1101/556282v1?rss=1 Albert, S. T. Hadjiosif, A. Jang, J. Krakauer, J. W. Shadmehr, R. 2019-02-24 doi:10.1101/556282 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Programmable bacteria induce durable tumor regression and systemic antitumor immunity ]]> https://biorxiv.org/content/10.1101/561159v1?rss=1 Chowdhury, S. Hinchliffe, T. E. Castro, S. Coker, C. Arpaia, N. Danino, T. 2019-03-01 doi:10.1101/561159 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Mouse Model Systems of Autism Spectrum Disorder: Replicability and Informatics Signature ]]> https://biorxiv.org/content/10.1101/561233v1?rss=1 Kabitzke, P. A. Morales, D. He, D. Cox, K. Sutphen, J. Thiede, L. Sabath, E. Hanania, T. Biemans, B. Brunner, D. 2019-02-27 doi:10.1101/561233 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ A spatial cell culture model for predicting chemotherapy dosing strategies ]]> https://biorxiv.org/content/10.1101/561746v1?rss=1 Zhu, S. Deb, D. Danino, T. 2019-02-28 doi:10.1101/561746 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies ]]> https://biorxiv.org/content/10.1101/562785v1?rss=1 Gurbatri, C. Coker, C. Hinchliffe, T. E. Lia, I. Castro, S. Treuting, P. M. Arpaia, N. Danino, T. 2019-03-01 doi:10.1101/562785 Cold Spring Harbor Laboratory Press 2019-03-01 <![CDATA[ Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program ]]> https://biorxiv.org/content/10.1101/563866v1?rss=1 400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency <1% and 46% are singletons. These rare variants provide insights into mutational processes and recent human evolutionary history. The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and extends the reach of nearly all genome-wide association studies to include variants down to ~0.01% in frequency. ]]> Taliun, D. Harris, D. N. Kessler, M. D. Carlson, J. Szpiech, Z. A. Torres, R. Gagliano Taliun, S. A. Corvelo, A. Gogarten, S. M. Min Kang, H. Pitsillides, A. N. LeFaive, J. Lee, S.-b. Tian, X. Browning, B. L. Das, S. Emde, A.-K. Clarke, W. E. Loesch, D. P. Shetty, A. C. Blackwell, T. W. Wong, Q. Aguet, F. Albert, C. Alonso, A. Ardlie, K. G. Aslibekyan, S. Auer, P. L. Barnard, J. Barr, R. G. Becker, L. C. Beer, R. L. Benjamin, E. J. Bielak, L. F. Blangero, J. Boehnke, M. Bowden, D. W. Brody, J. A. Burchard, E. G. Cade, B. E. Casella, J. F. Chalazan, B. L 2019-03-06 doi:10.1101/563866 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Comparative analysis of EHR-based stroke phenotyping methods, their applications, and interpretation ]]> https://biorxiv.org/content/10.1101/565671v1?rss=1 Thangaraj, P. M. Kummer, B. Lorberbaum, T. Elkind, M. Tatonetti, N. P. 2019-03-09 doi:10.1101/565671 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Social status in mouse social hierarchies is associated with variation in oxytocin and vasopressin 1a receptor densities ]]> https://biorxiv.org/content/10.1101/566067v1?rss=1 Lee, W. Hiura, L. Yang, E. Broekman, K. A. Ophir, A. G. Curley, J. 2019-03-03 doi:10.1101/566067 Cold Spring Harbor Laboratory Press 2019-03-03 <![CDATA[ Deconvolving the contributions of cell-type heterogeneity on cortical gene expression ]]> https://biorxiv.org/content/10.1101/566307v1?rss=1 Patrick, E. Taga, M. Ergun, A. Ng, B. Casazza, W. Cimpean, M. Yung, C. Schneider, J. A. Bennet, D. A. Gaiteri, C. De Jager, P. L. Bradshaw, E. M. Mostafavi, S. 2019-03-04 doi:10.1101/566307 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ A Collaborative Multi-Model Ensemble for Real-Time Influenza Season Forecasting in the U.S. ]]> https://biorxiv.org/content/10.1101/566604v1?rss=1 Reich, N. G. McGowan, C. J. Yamana, T. K. Tushar, A. Ray, E. L. Osthus, D. Kandula, S. Brooks, L. C. Crawford-Crudell, W. Gibson, G. C. Moore, E. Silva, R. Biggerstaff, M. Johansson, M. Rosenfeld, R. Shaman, J. 2019-03-08 doi:10.1101/566604 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ TmDOTP : An NMR- based Thermometer for Magic Angle Spinning NMR Experiments ]]> https://biorxiv.org/content/10.1101/566729v1?rss=1 Zhang, D. Itin, B. McDermott, A. 2019-03-04 doi:10.1101/566729 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Allosteric studies of an open pH gate KcsA mutant in its activated and inactivated states ]]> https://biorxiv.org/content/10.1101/567024v1?rss=1 Sun, Z. Xu, Y. Zhang, D. McDermott, A. E. 2019-03-04 doi:10.1101/567024 Cold Spring Harbor Laboratory Press 2019-03-04 <![CDATA[ Bioisosterism reveals new structure-odor relationships ]]> https://biorxiv.org/content/10.1101/567701v1?rss=1 Tahirova, N. Poivet, E. Xu, L. Peterlin, Z. Zou, D.-J. Firestein, S. 2019-03-05 doi:10.1101/567701 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank ]]> https://biorxiv.org/content/10.1101/572347v1?rss=1 10-fold increase compared to imputed sequence for the same participants. Nearly all genes (>97%) had [≥]1 predicted loss of function carrier, and most genes (>69%) had [≥]10 loss of function carriers. We illustrate the power of characterizing loss of function variation in this large population through association analyses across 1,741 phenotypes. In addition to replicating a range of established associations, we discover novel loss of function variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical significance in this population, finding that 2% of the population has a medically actionable variant. Additionally, we leverage the phenotypic data to characterize the relationship between rare BRCA1 and BRCA2 pathogenic variants and cancer risk. Exomes from the first 49,960 participants are now made accessible to the scientific community and highlight the promise offered by genomic sequencing in large-scale population-based studies. ]]> Van Hout, C. V. Tachmazidou, I. Backman, J. D. Hoffman, J. X. Yi, B. Pandey, A. Gonzaga-Jauregui, C. Khalid, S. Liu, D. Banerjee, N. Li, A. H. O'Dushlaine, C. Marcketta, A. Staples, J. Schumann, C. Hawes, A. Maxwell, E. Barnard, L. Lopez, A. Penn, J. Habegger, L. Blumenfeld, A. L. Yadav, A. Praveen, K. Jones, M. Salerno, W. J. Chung, W. K. Surakka, I. Willer, C. J. Hveem, K. Leader, J. B. Carey, D. J. Ledbetter, D. H. Cardon, L. Yancopoulos, G. D. Economides, A. Coppola, G. Shuldiner, A. R. Balasubramanian, S. Cantor, M. Nelson, M. R. Whittaker, J. C. 2019-03-09 doi:10.1101/572347 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Rapid invariant encoding of scene layout in human OPA ]]> https://biorxiv.org/content/10.1101/577064v1?rss=1 Henriksson, L. Mur, M. Kriegeskorte, N. 2019-03-14 doi:10.1101/577064 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Identifying the most influential features of neural population responses for information encoding and behavior ]]> https://biorxiv.org/content/10.1101/577379v1?rss=1 Nogueira, R. Peltier, N. E. Anzai, A. DeAngelis, G. C. Martinez-Trujillo, J. Moreno-Bote, R. 2019-03-14 doi:10.1101/577379 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ A HaloTag-TEV genetic cassette for mechanical phenotyping of native proteins ]]> https://biorxiv.org/content/10.1101/577445v1?rss=1 Rivas-Pardo, J. A. Li, Y. Martonfalvi, Z. Tapia-Rojo, R. Unger, A. Fernandez-Trasancos, A. Herrero-Galan, E. Velazquez-Carreras, D. Linke, W. A. Fernandez, J. M. Alegre-Cebollada, J. 2019-03-14 doi:10.1101/577445 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ The Fruit Fly Brain Observatory: From Structure to Function ]]> https://biorxiv.org/content/10.1101/580290v1?rss=1 Ukani, N. H. Yeh, C.-H. Tomkins, A. Zhou, Y. Florescu, D. Luna Ortiz, C. Huang, Y.-C. Wang, C.-T. Turkcan, M. K. Liu, T. Richmond, P. Lo, C.-C. Coca, D. Chiang, A.-S. Lazar, A. A. 2019-03-18 doi:10.1101/580290 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Rational use of Episodic and Working Memory: A Normative Account of Prospective Memory ]]> https://biorxiv.org/content/10.1101/580324v1?rss=1 Momennejad, I. Norman, K. A. Cohen, J. D. Singh, S. Lewis, R. L. 2019-03-17 doi:10.1101/580324 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena ]]> https://biorxiv.org/content/10.1101/582833v1?rss=1 Jiang, Y.-Y. Maier, W. Baumeister, R. Minevich, G. Joachimiak, E. Wloga, D. Ruan, Z. Kannan, N. Bocarro, S. Bahraini, A. Vasudevan, K. K. Lechtreck, K. Orias, E. Gaertig, J. 2019-03-19 doi:10.1101/582833 Cold Spring Harbor Laboratory Press 2019-03-19 <![CDATA[ Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective ]]> https://biorxiv.org/content/10.1101/583104v1?rss=1 Marcus, J. H. Posth, C. Ringbauer, H. Lai, L. Skeates, R. Sidore, C. Beckett, J. Furtwängler, A. Olivieri, A. Chiang, C. Al-Asadi, H. Dey, K. Joseph, T. A. Der Sarkissian, C. Radzeviciute, R. Gradoli, M. G. Haak, W. Reich, D. Schlessinger, D. Cucca, F. Krause, J. Novembre, J. 2019-03-21 doi:10.1101/583104 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Live-cell Imaging Analysis of Antimycin-Type Depsipeptides via Bioorthogonal Stimulated Raman Scattering Microscopy ]]> https://biorxiv.org/content/10.1101/583252v1?rss=1 Seidel, J. A. Miao, Y. Porterfield, W. Cai, W. Zhu, X. Kim, S.-J. Hu, F. Bhattarai-Kline, S. Min, W. Zhang, W. 2019-03-21 doi:10.1101/583252 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Epigenome-wide meta-analysis of PTSD across 10 military and civilian cohorts identifies novel methylation loci ]]> https://biorxiv.org/content/10.1101/585109v1?rss=1 Smith, A. K. Ratanatharathorn, A. Maihofer, A. X. Naviaux, R. K. Aiello, A. E. Amstadter, A. B. Ashley-Koch, A. E. Baker, D. G. Beckham, J. C. Boks, M. P. Bromet, E. Dennis, M. Galea, S. Garrett, M. E. Geuze, E. Guffanti, G. Hauser, M. A. Katrinli, S. Kilaru, V. Kessler, R. C. Kimbrel, N. A. Koenen, K. C. Kuan, P.-F. Li, K. Logue, M. W. Lori, A. Luft, B. J. Miller, M. W. Naviaux, J. C. Nugent, N. R. Qin, X. Ressler, K. J. Risbrough, V. B. Rutten, B. P. F. Stein, M. B. Ursano, R. J. Vermetten, E. Vinkers, C. H. Wang, L. Youssef, N. A. INTRuST Clinical Con 2019-03-21 doi:10.1101/585109 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Anchoring of actin to the plasma membrane enables tension production in the fission yeast cytokinetic ring ]]> https://biorxiv.org/content/10.1101/586792v1?rss=1 Wang, S. O'Shaughnessy, B. 2019-03-22 doi:10.1101/586792 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Stability of Nitroxide Biradical TOTAPOL in Biological Samples ]]> https://biorxiv.org/content/10.1101/592766v1?rss=1 McCoy, K. M. Rogawski, R. Stovicek, O. McDermott, A. E. 2019-03-31 doi:10.1101/592766 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Evolution of neuronal anatomy and circuitry in two highly divergent nematode species ]]> https://biorxiv.org/content/10.1101/595025v1?rss=1 Hong, R. L. Riebesell, M. Bumbarger, D. J. Cook, S. J. Carstensen, H. R. Sarpolaki, T. Cochella, L. Castrejon, J. Moreno, E. Sieriebriennikov, B. Hobert, O. Sommer, R. J. 2019-04-01 doi:10.1101/595025 Cold Spring Harbor Laboratory Press 2019-04-01 <![CDATA[ The human-specific paralogs SRGAP2B and SRGAP2C differentially modulate SRGAP2A-dependent synaptic development ]]> https://biorxiv.org/content/10.1101/596940v1?rss=1 Schmidt, E. R. Kupferman, J. Stackmann, M. Polleux, F. 2019-04-02 doi:10.1101/596940 Cold Spring Harbor Laboratory Press 2019-04-02 <![CDATA[ Genetic Associations with Mathematics Tracking and Persistence in Secondary School ]]> https://biorxiv.org/content/10.1101/598532v1?rss=1 Harden, K. P. Domingue, B. W. Belsky, D. W. Boardman, J. Crosnoe, R. Malanchini, M. Nivard, M. G. Tucker-Drob, E. M. Harris, K. M. 2019-04-05 doi:10.1101/598532 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Mid-lateral Cerebellar Purkinje Cells Provide a Cognitive Error Signal When Monkeys Learn a New Visuomotor Association ]]> https://biorxiv.org/content/10.1101/600221v1?rss=1 Sendhilnathan, N. Ipata, A. E. Goldberg, M. E. 2019-04-05 doi:10.1101/600221 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Deleterious in late life mitochondrial alleles and aging: secrets of Japanese centenarians ]]> https://biorxiv.org/content/10.1101/603282v1?rss=1 Mikhailova, A. Shamansky, V. Bazykin, G. A. Mazunin, I. Gunbin, K. Kunz, W. Reymond, A. Tanaka, M. Khrapko, K. Popadin, K. 2019-04-15 doi:10.1101/603282 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ Human Aging DNA Methylation Signatures are Conserved but Accelerated in Cultured Fibroblasts ]]> https://biorxiv.org/content/10.1101/605295v1?rss=1 nView larger version (60K):norg.highwire.dtl.DTLVardef@101e4f2org.highwire.dtl.DTLVardef@15df049org.highwire.dtl.DTLVardef@4a704dorg.highwire.dtl.DTLVardef@112f970_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractnnC_FIG ]]> Sturm, G. Cardenas, A. Bind, M.-A. Horvath, S. Wang, S. Wang, Y. Hagg, S. Hirano, M. Picard, M. 2019-04-10 doi:10.1101/605295 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging ]]> https://biorxiv.org/content/10.1101/605493v1?rss=1 Chakraborty, T. Driscoll, M. Murphy, M. M. Roudot, P. Chang, B.-J. Vora, S. Wong, W. M. Nielson, C. Zhang, H. Zhemkov, V. Hiremath, C. De La Cruz, E. D. Bezprozvanny, I. Zhao, H. Tomer, R. Heintzmann, R. Meeks, J. Marciano, D. Morrison, S. Danuser, G. Dean, K. Fiolka, R. 2019-04-11 doi:10.1101/605493 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ The Israeli Acute Paralysis Virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. ]]> https://biorxiv.org/content/10.1101/606236v1?rss=1 Fernandez, I. Frank, J. Acosta-Reyes, F. Neupane, R. 2019-04-11 doi:10.1101/606236 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ MiR-219 deficiency in Alzheimer’s disease contributes to neurodegeneration and memory dysfunction through post-transcriptional regulation of tau-kinase network ]]> https://biorxiv.org/content/10.1101/607176v1?rss=1 Arnes, M. Kim, Y. A. Lannes, J. Alaniz, M. E. Cho, J. D. McCabe, B. D. Santa-Maria, I. 2019-04-12 doi:10.1101/607176 Cold Spring Harbor Laboratory Press 2019-04-12 <![CDATA[ Stasimon contributes to the loss of sensory synapses and motor neuron death in a mouse model of spinal muscular atrophy ]]> https://biorxiv.org/content/10.1101/608513v1?rss=1 Simon, C. M. Van Alstyne, M. Lotti, F. Bianchetti, E. Tisdale, S. Mentis, G. Z. Pellizzoni, L. 2019-04-15 doi:10.1101/608513 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ Combined behavioral and electrophysiological evidence for a direct cortical effect of prefrontal tDCS on disorders of consciousness ]]> https://biorxiv.org/content/10.1101/612309v1?rss=1 Hermann, B. Raimondo, F. Hirsch, L. A. Huang, Y. Denis-Valente, M. Perez, P. Engemann, D.-A. Faugeras, F. Weiss, N. Demeret, S. Rohaut, B. Parra, L. C. Sitt, J. D. Naccache, L. 2019-04-18 doi:10.1101/612309 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Hippocampal network reorganization underlies the formation of a temporal association memory ]]> https://biorxiv.org/content/10.1101/613638v1?rss=1 Ahmed, M. S. Priestley, J. B. Castro, A. Stefanini, F. Balough, E. M. Lavoie, E. Mazzucato, L. Fusi, S. Losonczy, A. 2019-04-18 doi:10.1101/613638 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Sex-dependent polygenic effects on the clinical progressions of Alzheimer’s disease ]]> https://biorxiv.org/content/10.1101/613893v1?rss=1 Fan, C. C. Banks, S. J. Thompson, W. K. Chen, C.-H. McEvoy, L. K. Tan, C. H. Kukull, W. Bennett, D. A. Farrer, L. A. Mayeux, R. Schellenberg, G. D. Andreassen, O. A. Desikan, R. Dale, A. M. 2019-04-18 doi:10.1101/613893 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Interaction between DNA damage response, translation and apoptosome determines cancer susceptibility to TOP2 poisons ]]> https://biorxiv.org/content/10.1101/614024v1?rss=1 nView larger version (14K):norg.highwire.dtl.DTLVardef@310f7org.highwire.dtl.DTLVardef@14ed578org.highwire.dtl.DTLVardef@a0d9c0org.highwire.dtl.DTLVardef@37f59a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Awah, C. U. Chen, L. Bansal, M. Mahajan, A. Winter, J. Lad, M. Warnke, L. Gonzalez-Buendia, E. Park, C. Zhang, D. Feldstein, E. Yu, D. Zannikou, M. Balyasnikova, I. Martuscello, R. Konermann, S. Gyorffy, B. Burdett, K. Scholtens, D. Stupp, R. Ahmed, A. Hsu, P. Sonabend, A. M. 2019-04-25 doi:10.1101/614024 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ Neurostructural Heterogeneity in Youth with Internalizing Symptoms ]]> https://biorxiv.org/content/10.1101/614438v1?rss=1 Kaczkurkin, A. N. Sotiras, A. Baller, E. B. Calkins, M. E. Chand, G. B. Cui, Z. Erus, G. Fan, Y. Gur, R. E. Gur, R. C. Moore, T. M. Roalf, D. R. Rosen, A. F. G. Ruparel, K. Shinohara, R. T. Varol, E. Wolf, D. H. Davatzikos, C. Satterthwaite, T. D. 2019-04-23 doi:10.1101/614438 Cold Spring Harbor Laboratory Press 2019-04-23 <![CDATA[ Myeloid Tribbles 1 induces early atherosclerosis via enhanced foam cell expansion ]]> https://biorxiv.org/content/10.1101/615872v1?rss=1 Johnston, J. Angyal, A. Bauer, R. Hamby, S. Suvarna, K. Baidzajevas, K. Hegedus, Z. Dear, N. Turner, M. The Cardiogenics Consortium, Wilson, H. Goodall, A. Rader, D. J. Shoulders, C. C. Francis, S. Kiss-Toth, E. 2019-05-05 doi:10.1101/615872 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ A single wave of monocytes is sufficient to replenish the long-term Langerhans cell network after immune injury ]]> https://biorxiv.org/content/10.1101/617514v1?rss=1 nView larger version (32K):norg.highwire.dtl.DTLVardef@1c08563org.highwire.dtl.DTLVardef@753e0corg.highwire.dtl.DTLVardef@13ca3cforg.highwire.dtl.DTLVardef@269ffc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ferrer, I. R. West, H. C. Henderson, S. L. Ushakov, D. S. Santos e Sousa, P. L. Strid, J. Chakraverty, R. Yates, A. J. Bennett, C. L. 2019-04-24 doi:10.1101/617514 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ The role of lineage, hemilineage and temporal identity in establishing neuronal targeting and connectivity in the Drosophila embryo ]]> https://biorxiv.org/content/10.1101/617936v1?rss=1 Mark, B. Lai, S.-L. Arzan Zarin, A. Manning, L. Cardona, A. Truman, J. W. Doe, C. Q. 2019-04-24 doi:10.1101/617936 Cold Spring Harbor Laboratory Press 2019-04-24 <![CDATA[ Retromer repletion with AAV9-VPS35 restores endosomal function in the mouse hippocampus ]]> https://biorxiv.org/content/10.1101/618496v1?rss=1 Qureshi, Y. Berman, D. E. Klein, R. L. Patel, V. M. Simoes, S. Kannan, S. Cox, R. Waksal, S. Stevens, B. Petsko, G. A. Small, S. A. 2019-04-26 doi:10.1101/618496 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Dopamine modulates learning-related changes in dynamic striatal-cortical connectivity in Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/619478v1?rss=1 Gerraty, R. T. Sharp, M. E. Buch, A. Bassett, D. S. Shohamy, D. 2019-04-26 doi:10.1101/619478 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Adapterama II: Universal amplicon sequencing on Illumina platforms (TaggiMatrix) ]]> https://biorxiv.org/content/10.1101/619544v1?rss=1 Glenn, T. C. Pierson, T. W. Bayona-Vasquez, N. J. Kieran, T. J. Hoffberg, S. L. Thomas, J. C. Lefever, D. E. Finger, J. W. Gao, B. Bian, X. Louha, S. Kolli, R. T. Bentley, K. Rushmore, J. Wong, K. Shaw, T. I. Rothrock, M. J. McKee, A. M. Guo, T. L. Mauricio, R. Molina, M. Cummings, B. S. Lash, L. H. Lu, K. Gilbert, G. S. Hubbell, S. P. Faircloth, B. C. 2019-04-26 doi:10.1101/619544 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Isoform specificity of PKMs during long-term facilitation in Aplysia is mediated through stabilization by KIBRA ]]> https://biorxiv.org/content/10.1101/620633v1?rss=1 Ferguson, L. Hu, J. Cai, D. Chen, S. Dunn, T. W. Glanzman, D. L. Schacher, S. Sossin, W. S. 2019-04-26 doi:10.1101/620633 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures ]]> https://biorxiv.org/content/10.1101/620948v1?rss=1 Richardson, M. Gottel, N. Gilbert, J. A. Lax, S. 2019-04-28 doi:10.1101/620948 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ A new approach to automated CBMN scoring following high doses ]]> https://biorxiv.org/content/10.1101/620971v1?rss=1 Repin, M. Brenner, D. J. Garty, G. 2019-04-27 doi:10.1101/620971 Cold Spring Harbor Laboratory Press 2019-04-27 <![CDATA[ Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo. ]]> https://biorxiv.org/content/10.1101/621185v1?rss=1 Taverner, A. M. Yang, L. Barile, Z. J. Becky, L. Peng, J. Pinharanda, A. Rao, A. Roland, B. P. Talsma, A. D. Wei, D. Petschenka, G. Palladino, M. J. Andolfatto, P. 2019-04-28 doi:10.1101/621185 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ Psychotic symptoms in 16p11.2 copy number variant carriers ]]> https://biorxiv.org/content/10.1101/621250v1?rss=1 Jutla, A. Turner, J. B. Green Snyder, L. Chung, W. K. Veenstra-VanderWeele, J. 2019-05-05 doi:10.1101/621250 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Memory for Individual Items is Related to Non-Reinforced Preference Change ]]> https://biorxiv.org/content/10.1101/621292v1?rss=1 Botvinik-Nezer, R. Bakkour, A. Salomon, T. Shohamy, D. Schonberg, T. 2019-04-29 doi:10.1101/621292 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Hierarchical recurrent state space models reveal discrete and continuous dynamics of neural activity in C. elegans ]]> https://biorxiv.org/content/10.1101/621540v1?rss=1 Linderman, S. W. Nichols, A. L. A. Blei, D. M. Zimmer, M. Paninski, L. 2019-04-29 doi:10.1101/621540 Cold Spring Harbor Laboratory Press 2019-04-29 <![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[ The Role of Sevenless in Drosophila R7 Photoreceptor Specification ]]> https://biorxiv.org/content/10.1101/624155v1?rss=1 Tomlinson, A. Mavromatakis, Y. E. Arias, R. 2019-04-30 doi:10.1101/624155 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Are place cells just memory cells? Memory compression leads to spatial tuning and history dependence ]]> https://biorxiv.org/content/10.1101/624239v1?rss=1 Benna, M. K. Fusi, S. 2019-04-30 doi:10.1101/624239 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Electronic Health Records Based Prediction of Future Incidence of Alzheimers Disease Using Machine Learning ]]> https://biorxiv.org/content/10.1101/625582v1?rss=1 Park, J. H. Cho, H. E. Kim, J. H. Wall, M. Stern, Y. Lim, H. Yoo, S. Kim, H.-S. CHA, J. 2019-05-02 doi:10.1101/625582 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ cohorts: A Python package for clinical ‘omics data management ]]> https://biorxiv.org/content/10.1101/626051v1?rss=1 Giangreco, N. P. Fine, B. M. Tatonetti, N. P. 2019-05-02 doi:10.1101/626051 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Human Trypanosoma cruzi infection risk is driven by eco-social interactions in rural communities of the Argentine Chaco ]]> https://biorxiv.org/content/10.1101/627141v1?rss=1 Fernandez, M. d. P. Gaspe, M. S. Sartor, P. Gürtler, R. E. 2019-05-03 doi:10.1101/627141 Cold Spring Harbor Laboratory Press 2019-05-03 <![CDATA[ The use of a centrifuge-free RABiT-II system for high-throughput micronucleus analysis ]]> https://biorxiv.org/content/10.1101/627596v1?rss=1 Repin, M. Pampou, S. Y. Brenner, D. J. Garty, G. 2019-05-04 doi:10.1101/627596 Cold Spring Harbor Laboratory Press 2019-05-04 <![CDATA[ Identification of Pathogenic Structural Variants in Rare Disease Patients through Genome Sequencing ]]> https://biorxiv.org/content/10.1101/627661v1?rss=1 Holt, J. M. Birch, C. L. Brown, D. M. Gajapathy, M. Sosonkina, N. Wilk, B. Wilk, M. Spillmann, R. C. Stong, N. Lee, H. Huang, A. Y. Bonner, D. Kohler, J. N. Macnamara, E. F. Diseases Network, U. Nelson, S. F. Shashi, V. Worthey, E. A. 2019-05-15 doi:10.1101/627661 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons ]]> https://biorxiv.org/content/10.1101/629295v1?rss=1 An, D. Fujiki, R. Iannitelli, D. Smerdon, J. Maity, S. Rose, M. Gelber, A. Wanaselja, E. Yagudayeva, I. Lee, J. Vogel, C. Wichterle, H. Engle, E. Mazzoni, E. 2019-05-07 doi:10.1101/629295 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Variable prediction accuracy of polygenic scores within an ancestry group ]]> https://biorxiv.org/content/10.1101/629949v1?rss=1 Mostafavi, H. Harpak, A. Conley, D. Pritchard, J. K. Przeworski, M. 2019-05-07 doi:10.1101/629949 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Predicting neurodevelopmental outcomes in children with perinatal HIV using a novel machine learning algorithm ]]> https://biorxiv.org/content/10.1101/632273v1?rss=1 90%). Dynamic change indices and interactions between mental health and biological indices emerged as key predictors.nnConclusionMachine learning-based regression defined a unique explanatory model of neurocognitive outcomes among children with pHIV. The predictive algorithm included a combination of HIV, physical health, and mental health indices extracted from readily available clinical measures. Studies are needed to explore the clinical relevance of the data-driven explanatory model, including potential to inform targeted interventions aimed at modifiable risk factors. ]]> Paul, R. Mellins, C. Robbins, R. Kerr, S. Malee, K. Sophonphan, J. Jahanshad, N. Auripibul, L. Thongpibul, K. Kosalaraksa, P. Kanjanavanit, S. Ngampiyaskul, C. Luesomboon, W. Wongsawat, J. Vonthanak, S. Chettra, K. Suwanlerk, T. Valcour, V. Balla, L. Salminen, L. Preston, R. Garcia, P. Ananworanich, J. Puthanakit, T. 2019-05-09 doi:10.1101/632273 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4+ T cell memory ]]> https://biorxiv.org/content/10.1101/632281v1?rss=1 Hogan, T. Nowicka, M. Cownden, D. Pearson, C. Yates, A. Seddon, B. 2019-05-09 doi:10.1101/632281 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions ]]> https://biorxiv.org/content/10.1101/632554v1?rss=1 Park, C. Ponath, G. Levine-Ritterman, M. Bull, E. Swanson, E. Segal, B. M. Pitt, D. 2019-05-09 doi:10.1101/632554 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Quantifying genetic regulatory variation in human populations improves transcriptome analysis in rare disease patients ]]> https://biorxiv.org/content/10.1101/632794v1?rss=1 Mohammadi, P. Castel, S. E. Cummings, B. B. Einson, J. Sousa, C. Hoffman, P. Donkervoort, S. Mohassel, P. Foley, R. Wheeler, H. E. Im, H. K. Bonnemann, C. G. MacArthur, D. G. Lappalainen, T. 2019-05-09 doi:10.1101/632794 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ 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[ POLARIS: path of least action analysis on energy landscapes ]]> https://biorxiv.org/content/10.1101/633628v1?rss=1 Seitz, E. E. Frank, J. 2019-05-17 doi:10.1101/633628 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Decrease in within-trial variability contributes to a decrease in across-trial variability of neural firing in the primate cortex during neural computations ]]> https://biorxiv.org/content/10.1101/635532v1?rss=1 Sendhilnathan, N. Basu, D. Murthy, A. 2019-05-12 doi:10.1101/635532 Cold Spring Harbor Laboratory Press 2019-05-12 <![CDATA[ Cell Generation Dynamics Underlying Naïve T Cell Homeostasis in Adult Humans ]]> https://biorxiv.org/content/10.1101/635995v1?rss=1 Mold, J. Reu, P. Olin, A. Bernard, S. Michaëlsson, J. Rane, S. Yates, A. Khosravi, A. Salehpour, M. Possnert, G. Brodin, P. Frisen, J. 2019-05-13 doi:10.1101/635995 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Genome-wide association study of susceptibility to idiopathic pulmonary fibrosis ]]> https://biorxiv.org/content/10.1101/636761v1?rss=1 Allen, R. J. Guillen-Guio, B. Oldham, J. M. Ma, S.-F. Dressen, A. Paynton, M. L. Kraven, L. M. Obeidat, M. Li, X. Ng, M. Braybrooke, R. Molina-Molina, M. Hobbs, B. D. Putman, R. K. Sakornsakolpat, P. Booth, H. L. Fahy, W. A. Hart, S. P. Hill, M. R. Hirani, N. Hubbard, R. B. McAnulty, R. J. Millar, A. B. Navaratnam, V. Oballa, E. Parfrey, H. Saini, G. Whyte, M. K. Gudmundsson, G. Gudnason, V. Hatabu, H. Lederer, D. J. Manichaikul, A. Newell, J. D. O'Connor, G. T. Ortega, V. E. Xu, H. Fingerlin, T. E. Bosse, Y. Hao, K. Joubert, P. Nickle, D. C. Sin, D. 2019-05-14 doi:10.1101/636761 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy ]]> https://biorxiv.org/content/10.1101/637199v1?rss=1 Lee, A. Kondapalli, C. Virga, D. M. Lewis, T. L. Koo, S. Y. Ashok, A. Mairet-Coello, G. Herzig, S. Shaw, R. Sproul, A. Polleux, F. 2019-05-14 doi:10.1101/637199 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Clinically-relevant cell type cross-talk identified from a human lung tumor microenvironment interactome ]]> https://biorxiv.org/content/10.1101/637306v1?rss=1 Gentles, A. J. Hui, A. Feng, W. Azizi, A. Nair, R. Knowles, D. Yu, A. Jeong, Y. Bejnood, A. Forgo, E. Varma, S. Xu, Y. Kuong, A. Nair, V. West, R. Van de Rijn, M. Hoang, C. Diehn, M. Plevritis, S. 2019-05-30 doi:10.1101/637306 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Development of a high-throughput γ-H2AX assay based on imaging flow cytometry ]]> https://biorxiv.org/content/10.1101/637371v1?rss=1 Lee, Y. Wang, Q. Shuryak, I. Brenner, D. J. Turner, H. C. 2019-05-15 doi:10.1101/637371 Cold Spring Harbor Laboratory Press 2019-05-15 <![CDATA[ A zero-inflated gamma model for post-deconvolved calcium imaging traces ]]> https://biorxiv.org/content/10.1101/637652v1?rss=1 Wei, X.-X. Zhou, D. Grosmark, A. Ajabi, Z. Sparks, F. Zhou, P. Brandon, M. Losonczy, A. Paninski, L. 2019-05-14 doi:10.1101/637652 Cold Spring Harbor Laboratory Press 2019-05-14 <![CDATA[ Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions ]]> https://biorxiv.org/content/10.1101/638544v1?rss=1 4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes), and provide the results as a community resource. We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. In addition, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a common resource for use across the community in research programs. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975). ]]> Sieberts, S. K. Perumal, T. M. Carrasquillo, M. M. Allen, M. Reddy, J. S. Hoffman, G. E. Dang, K. K. Calley, J. Ebert, P. J. Eddy, J. Wang, X. Greenwood, A. K. Mostafavi, S. the AMP-AD Consortium, the CommonMind Consortium (CMC), Omberg, L. Peters, M. Logsdon, B. A. De Jager, P. L. Ertekin-Taner, N. Mangravite, L. M. 2019-05-17 doi:10.1101/638544 Cold Spring Harbor Laboratory Press 2019-05-17 <![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[ Genetic overlap between psychiatric disorders and neuropsychiatric symptoms in HD ]]> https://biorxiv.org/content/10.1101/639658v1?rss=1 Ellis, N. Tee, A. McAllister, B. Massey, T. McLauchlan, D. Stone, T. Correia, K. Loupe, J. Kim, K.-H. Barker, D. Hong, E. P. Chao, M. J. Long, J. D. Lucente, D. Vonsattel, J. P. G. Mouro Pinto, R. Elneel, K. A. Ramos, E. M. Mysore, J. S. Gillis, T. Wheeler, V. C. Medway, C. Hall, L. Kwak, S. Ehrhardt, A. G. Sampaio, C. Ciosi, M. Maxwell, A. Chatzi, A. Monckton, D. Orth, M. Landwehrmeyer, G. B. Paulsen, J. S. Shoulson, I. Myers, R. Duijn, E. v. Rickards, H. MacDonald, M. Lee, J.-M. Gusella, J. F. Jones, L. Holmans, P. 2019-05-17 doi:10.1101/639658 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Dissection of central clock function in Drosophila through cell-specific CRISPR-mediated clock gene disruption ]]> https://biorxiv.org/content/10.1101/640011v1?rss=1 Shirasu-Hiza, M. Delventhal, R. Pantalia, M. M. O'Connor, R. M. Ulgherait, M. Kim, H. X. Basturk, M. K. Canman, J. C. 2019-05-17 doi:10.1101/640011 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ New Approaches for Quantitative Reconstruction of Radiation Dose in Human Blood Cells ]]> https://biorxiv.org/content/10.1101/640052v1?rss=1 Ghandhi, S. A. Shuryak, I. Morton, S. R. Amundson, S. A. Brenner, D. J. 2019-05-17 doi:10.1101/640052 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Distinct antagonist-bound inactive states underlie the divergence in the structures of the dopamine D2 and D3 receptors ]]> https://biorxiv.org/content/10.1101/640870v1?rss=1 Lane, J. R. Abramyan, A. M. Verma, R. K. Lim, H. D. Javitch, J. A. Shi, L. 2019-05-17 doi:10.1101/640870 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ A general LC/MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures ]]> https://biorxiv.org/content/10.1101/643387v1?rss=1 Zhang, N. Shi, S. Jia, T. Z. Ziegler, A. Yoo, B. Yuan, X. Li, W. Zhang, S. 2019-05-20 doi:10.1101/643387 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Scalable and cost-effective ribonuclease-based rRNA depletion for bacterial transcriptomics ]]> https://biorxiv.org/content/10.1101/645895v1?rss=1 5,000 common microbes from RefSeq, and an online tool to generate custom probe libraries. This approach lays the groundwork for large-scale and cost-effective bacterial transcriptomics studies. ]]> Huang, Y. Sheth, R. Kaufman, A. Wang, H. 2019-05-24 doi:10.1101/645895 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ New High Throughput Approaches to Detect Partial-body and Neutron Exposures on an Individual Basis ]]> https://biorxiv.org/content/10.1101/646711v1?rss=1 Shuryak, I. Turner, H. C. Perrier, J. R. Cunha, L. Pujol Canadell, M. Durrani, M. H. Harken, A. Bertucci, A. Taveras, M. Garty, G. Brenner, D. J. 2019-05-23 doi:10.1101/646711 Cold Spring Harbor Laboratory Press 2019-05-23 <![CDATA[ Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed ]]> https://biorxiv.org/content/10.1101/647164v1?rss=1 Van Etten, M. Lee, K. M. Chang, S.-M. Baucom, R. S. 2019-05-24 doi:10.1101/647164 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Cytogenetically-based biodosimetry after high doses of radiation ]]> https://biorxiv.org/content/10.1101/647362v1?rss=1 Pujol Canadell, M. Perrier, J. R. Cunha, L. Shuryak, I. Harken, A. Garty, G. Brenner, D. 2019-05-22 doi:10.1101/647362 Cold Spring Harbor Laboratory Press 2019-05-22 <![CDATA[ DNA damage response in peripheral mouse blood leukocytes in vivo after variable, low-dose rate exposure ]]> https://biorxiv.org/content/10.1101/648568v1?rss=1 Wang, Q. Pujol, M. C. Taveras, M. Perrier, J. Bueno-Beti, C. Shuryak, I. Brenner, D. J. Turner, H. C. 2019-05-24 doi:10.1101/648568 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ PI3K activation prevents Aβ42-induced synapse loss and favors insoluble amyloid deposits formation ]]> https://biorxiv.org/content/10.1101/649087v1?rss=1 Arnes, M. Romero, N. Casas-Tinto, S. Acebes, A. Ferrus, A. 2019-05-24 doi:10.1101/649087 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Multilevel feedback architecture for adaptive regulation of learning in the insect brain ]]> https://biorxiv.org/content/10.1101/649731v1?rss=1 Eschbach, C. Fushiki, A. Winding, M. Schneider-Mizell, C. Shao, M. Arruda, R. Eichler, K. Valdes-Aleman, J. Ohyama, T. Thum, A. S. Gerber, B. Fetter, R. D. Truman, J. W. Litwin-Kumar, A. Cardona, A. Zlatic, M. 2019-05-27 doi:10.1101/649731 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Neural trajectories in the supplementary motor area and primary motor cortex exhibit distinct geometries, compatible with different classes of computation ]]> https://biorxiv.org/content/10.1101/650002v1?rss=1 Russo, A. Khajeh, R. Bittner, S. R. Perkins, S. M. Cunningham, J. P. Abbott, L. F. Churchland, M. M. 2019-05-24 doi:10.1101/650002 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data ]]> https://biorxiv.org/content/10.1101/650093v1?rss=1 Saxena, S. Kinsella, I. Musall, S. Kim, S. H. Meszaros, J. Thibodeaux, D. N. Kim, C. Cunningham, J. Hillman, E. Churchland, A. Paninski, L. 2019-05-25 doi:10.1101/650093 Cold Spring Harbor Laboratory Press 2019-05-25 <![CDATA[ From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response ]]> https://biorxiv.org/content/10.1101/650150v1?rss=1 Gallaher, J. A. Massey, S. C. Hawkins-Daarud, A. C. Noticewala, S. S. Rockne, R. C. Johnston, S. K. Gonzalez-Cuyar, L. Juliano, J. Gil, O. Swanson, K. R. Canoll, P. Anderson, A. R. A. 2019-05-26 doi:10.1101/650150 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ A Universal Nonparametric Event Detection Framework for Neuropixels Data ]]> https://biorxiv.org/content/10.1101/650671v1?rss=1 Chen, H. Chen, S. Deng, X. 2019-05-27 doi:10.1101/650671 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Castration-mediated IL-8 Promotes Myeloid Infiltration and Prostate Cancer Progression ]]> https://biorxiv.org/content/10.1101/651083v1?rss=1 Lopez-Bujanda, Z. A. Haffner, M. C. Chaimowitz, M. G. Chowdhury, N. Venturini, N. J. Obradovic, A. Hansen, C. S. Jackow, J. Sfanos, K. S. Bieberich, C. J. Hurley, P. J. Selby, M. J. Korman, A. J. Christiano, A. M. De Marzo, A. M. Drake, C. G. 2019-05-27 doi:10.1101/651083 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models ]]> https://biorxiv.org/content/10.1101/652537v1?rss=1 Facompre, N. D. Rajagopalan, P. Sahu, V. Pearson, A. T. Montone, K. T. James, C. D. Gleber-Netto, F. O. Weinstein, G. S. Jalaly, J. Lin, A. Rustgi, A. K. Nakagawa, H. Califano, J. A. Pickering, C. R. White, E. A. Windle, B. A. Morgan, I. M. Cohen, R. B. Gimotty, P. A. Basu, D. 2019-05-30 doi:10.1101/652537 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Community driven dynamics of oscillatory network responses to threat ]]> https://biorxiv.org/content/10.1101/652834v1?rss=1 Muthuraman, M. Chirumamilla, V. C. Koirala, N. Anwar, A. R. Tuescher, O. Vogt, J. Horstmann, P. Meyer, B. George, B. Gonazalez-Escamilla, G. Groppa, S. 2019-05-30 doi:10.1101/652834 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Brain-predicted age difference score is related to specific cognitive functions: A multi-site replication analysis ]]> https://biorxiv.org/content/10.1101/652867v1?rss=1 Boyle, R. Jollans, L. Rueda-Delgado, L. M. Rizzo, R. Yener, G. G. McMorrow, J. P. Knight, S. P. Carey, D. Robertson, I. H. Emek-Savas, D. D. Stern, Y. Kenny, R. A. Whelan, R. 2019-05-30 doi:10.1101/652867 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ An Engineered Cas-Transposon System for Programmable and Precise DNA Transpositions ]]> https://biorxiv.org/content/10.1101/654996v1?rss=1 300-fold compared to an untargeted transposase, and that site-specific transposition is dependent on target choice while robust to log-fold variations in protein and DNA concentrations. We then showed that Himar-dCas9 mediates site-specific transposition into a target plasmid in E. coli. This work provides CasTn as a new method for host-independent, programmable, targeted DNA insertions to expand the genomic engineering toolbox. ]]> Chen, S. P. Wang, H. H. 2019-06-03 doi:10.1101/654996 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering ]]> https://biorxiv.org/content/10.1101/655043v1?rss=1 Wei, M. Fan, X. Ding, M. Li, R. Shao, S. Hou, Y. Meng, S. Tang, F. Li, C. Sun, Y. 2019-05-30 doi:10.1101/655043 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Understanding Cognitive Impairment in Mood Disorders: Mediation Analyses in the UK Biobank Cohort ]]> https://biorxiv.org/content/10.1101/655290v1?rss=1 Cullen, B. Smith, D. J. Deary, I. J. Pell, J. P. Keyes, K. M. Evans, J. J. 2019-05-31 doi:10.1101/655290 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Modeling missing cases and transmission links in networks of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa ]]> https://biorxiv.org/content/10.1101/655969v1?rss=1 Nelson, K. N. Gandhi, N. R. Mathema, B. Lopman, B. Brust, J. C. Auld, S. C. Ismail, N. Omar, S. V. Brown, T. S. Allana, S. Campbell, A. Moodley, P. Mlisana, K. Shah, N. S. Jenness, S. M. 2019-06-07 doi:10.1101/655969 Cold Spring Harbor Laboratory Press 2019-06-07 <![CDATA[ Demultiplexing overlapping signaling scaffold functions to probe lipid messenger coupling to cytoskeletal dynamics. ]]> https://biorxiv.org/content/10.1101/657049v1?rss=1 Trenton, N. J. McLaughlin, R. T. Bellamkonda, S. Tsao, D. Mace, E. orange, j. Schweikhard, V. Diehl, M. R. 2019-06-14 doi:10.1101/657049 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Benefits of commitment in hierarchical inference ]]> https://biorxiv.org/content/10.1101/658914v1?rss=1 Qiu, C. Luu, L. Stocker, A. A. 2019-06-03 doi:10.1101/658914 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ A Novel Tmem119-tdTomato Reporter Mouse Model for Studying Microglia in the Central Nervous System ]]> https://biorxiv.org/content/10.1101/665893v1?rss=1 Ruan, C. Sun, L. Kroshilina, A. Beckers, L. De Jager, P. L. Bradshaw, E. M. Hasson, S. Wang, G. Elyaman, W. 2019-06-10 doi:10.1101/665893 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Reliability and Reproducibility of T1-weighted images: comparing MPRAGE and Prospective Motion Correction with Volumetric Navigators ]]> https://biorxiv.org/content/10.1101/666289v1?rss=1 Ai, L. Craddock, R. C. Tottenham, N. Colcombe, S. Milham, M. Franco, A. R. 2019-06-10 doi:10.1101/666289 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Spectral Hallmark of Auditory-Tactile Interactions in Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/668319v1?rss=1 Zhang, M. Kwon, S. E. Ben-Johny, M. O'Connor, D. H. Issa, J. B. 2019-06-13 doi:10.1101/668319 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Tetrodotoxin-sensitive sodium channels mediate action potential firing and excitability in menthol-sensitive Vglut3-lineage sensory neurons ]]> https://biorxiv.org/content/10.1101/670620v1?rss=1 Griffith, T. N. Docter, T. A. Lumpkin, E. A. 2019-06-13 doi:10.1101/670620 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Probabilistic Models of Larval Zebrafish Behavior: Structure on Many Scales ]]> https://biorxiv.org/content/10.1101/672246v1?rss=1 Johnson, R. E. Linderman, S. Panier, T. Wee, C. L. Song, E. Herrera, K. J. Miller, A. Engert, F. 2019-06-15 doi:10.1101/672246 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ Development and Validation of Phenotype Classifiers across Multiple Sites in the Observational Health Sciences and Informatics (OHDSI) Network ]]> https://biorxiv.org/content/10.1101/673418v1?rss=1 Kashyap, M. Seneviratne, M. G. Banda, J. M. Falconer, T. Ryu, B. Yoo, S. Hripcsak, G. Shah, N. H. 2019-06-24 doi:10.1101/673418 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Biofilm inhibitor taurolithocholic acid alters colony morphology, specialized metabolism, and virulence of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/675405v1?rss=1 Condren, A. R. Kahl, L. J. Kritikos, G. Banzhaf, M. Dietrich, L. E. P. Sanchez, L. M. 2019-06-20 doi:10.1101/675405 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity ]]> https://biorxiv.org/content/10.1101/675439v1?rss=1 6,000 regulatory and signaling proteins, thus providing a previously unattainable single-cell characterization level. This helped identify four novel, molecularly distinct subtypes that successfully harmonize across multiple GBM datasets, including previously published bulk and single-cell profiles and single cell profiles from seven orthotopic PDX models, representative of prior subtype diversity. GBM is thus characterized by the plastic coexistence of single cells in two mutually-exclusive developmental lineages, with additional stratification provided by their proliferative potential. Consistently, all previous subtypes could be recapitulated by single-cell mixtures drawn from newly identified states. Critically, drug sensitivity was predicted and validated as highly state-dependent, both in single-cell assays from patient-derived explants and in PDX models, suggesting that successful treatment requires combinations of multiple drugs targeting these distinct tumor states.nnSignificanceWe propose a new, 4-subtype GBM classification, which harmonizes across bulk and single-cell datasets. Single-cell mixtures from these subtypes effectively recapitulate all prior classifications, suggesting that the latter are a byproduct of GBM heterogeneity. Finally, we predict single-cell level activity of three clinically-relevant drugs, and validate them in patient-derived explant. ]]> Ding, H. Burgenske, D. M. Zhao, W. Subramaniam, P. S. Bakken, K. K. He, L. Alvarez, M. J. Laise, P. Paull, E. O. Spinazzi, E. F. Dovas, A. Marie, T. Upadhyayula, P. Dela Cruz, F. Diolaiti, D. Kung, A. Bruce, J. N. Canoll, P. Sims, P. A. Sarkaria, J. N. Califano, A. 2019-06-19 doi:10.1101/675439 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ A neuronal signature for monogamous reunion ]]> https://biorxiv.org/content/10.1101/675959v1?rss=1 Scribner, J. L. Vance, E. Protter, D. S. W. Saslow, E. Cameron, R. Klein, E. Jimenez, J. C. Kheirbek, M. A. Donaldson, Z. 2019-06-19 doi:10.1101/675959 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans ]]> https://biorxiv.org/content/10.1101/676312v1?rss=1 Yemini, E. Lin, A. Nejatbakhsh, A. Varol, E. Sun, R. Mena, G. E. Samuel, A. D. Paninski, L. Venkatachalam, V. Hobert, O. 2019-06-20 doi:10.1101/676312 Cold Spring Harbor Laboratory Press 2019-06-20 <![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[ Recurrent networks can recycle neural resources to flexibly trade speed for accuracy in visual recognition ]]> https://biorxiv.org/content/10.1101/677237v1?rss=1 Spoerer, C. J. Kietzmann, T. C. Kriegeskorte, N. 2019-06-20 doi:10.1101/677237 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Unbiased Assessment of H-STS cells as high-fidelity models for gastro-enteropancreatic neuroendocrine tumor drug mechanism of action analysis ]]> https://biorxiv.org/content/10.1101/677435v1?rss=1 Alvarez, M. J. Yan, P. Alpaugh, M. L. Bowden, M. Sicinska, E. Zhou, C. W. Karan, C. Realubit, R. B. Mundi, P. S. Grunn, A. Jäger, D. Chabot, J. A. Fojo, A. T. Oberstein, P. E. Hibshoosh, H. Milsom, J. W. Kulke, M. H. Loda, M. Chiosis, G. Reidy-Lagunes, D. L. Califano, A. 2019-06-23 doi:10.1101/677435 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ A Comparison of Comorbidities and their Contribution to Medical Resource Utilization for Matched HIV-Infected and Uninfected Individuals: A Cross-Sectional Analysis ]]> https://biorxiv.org/content/10.1101/678136v1?rss=1 Odlum, M. Yoon, S. 2019-06-20 doi:10.1101/678136 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Intensity Warping for multisite MRI Harmonization ]]> https://biorxiv.org/content/10.1101/679357v1?rss=1 Wrobel, J. Martin, M. L. Shinohara, R. T. Goldsmith, J. 2019-06-21 doi:10.1101/679357 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Activity-dependent nucleation of dynamic microtubules at presynaptic boutons is required for neurotransmission ]]> https://biorxiv.org/content/10.1101/679464v1?rss=1 Qu, X. Kumar, A. Blockus, H. Waites, C. Bartolini, F. 2019-06-21 doi:10.1101/679464 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Understanding the functional and structural differences across excitatory and inhibitory neurons ]]> https://biorxiv.org/content/10.1101/680439v1?rss=1 Minni, S. Ji-An, L. Moskovitz, T. Lindsay, G. Miller, K. Dipoppa, M. Yang, G. R. 2019-06-25 doi:10.1101/680439 Cold Spring Harbor Laboratory Press 2019-06-25 <![CDATA[ Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics ]]> https://biorxiv.org/content/10.1101/682815v1?rss=1 Aso, Y. Ray, R. Long, X. Cichewicz, K. Ngo, T.-T. B. Christoforou, C. Sharp, B. Lemire, A. L. Hirsh, J. Litwin Kumar, A. Rubin, G. M. 2019-06-26 doi:10.1101/682815 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Human condensin I and II drive extensive ATP-dependent compaction of nucleosome-bound DNA ]]> https://biorxiv.org/content/10.1101/683540v1?rss=1 Kong, M. Cutts, E. Pan, D. Beuron, F. Kaliyappan, T. Xue, C. Morris, E. Musacchio, A. Vannini, A. Greene, E. 2019-06-27 doi:10.1101/683540 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinsons disease ]]> https://biorxiv.org/content/10.1101/686550v1?rss=1 Brown, E. E. Blauwendraat, C. Trinh, J. Rizig, M. Nalls, M. Leveille, E. Ruskey, J. Jonvik, H. Tan, M. Bandres-Ciga, S. Hassin-Baer, S. Brockmann, K. Hardy, J. Singleton, A. Alcalay, R. Gasser, T. Grosset, D. Williams, N. Pittman, A. Gan-Or, Z. Fernandez-Santiago, R. Brice, A. Lesage, S. Farrer, M. Wood, N. Morris, H. R. 2019-06-28 doi:10.1101/686550 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Molecular estimation of neurodegeneration pseudotime in older brains ]]> https://biorxiv.org/content/10.1101/686824v1?rss=1 Mukherjee, S. Preuss, C. Jayadev, S. Garden, G. A. Greenwood, A. K. Sieberts, S. K. De Jager, P. L. Ertekin-Taner, N. Carter, G. W. Mangravite, L. M. Logsdon, B. 2019-06-28 doi:10.1101/686824 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Detecting GPCR Complexes in Postmortem Human Brain with Proximity Ligation Assay and a Bayesian Classifier ]]> https://biorxiv.org/content/10.1101/687780v1?rss=1 Zhu, Y. Meszaros, J. Walle, R. Fan, R. Sun, Z. Dwork, A. J. Trifilieff, P. Javitch, J. A. 2019-07-02 doi:10.1101/687780 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Natural selection shapes codon usage in the human genome ]]> https://biorxiv.org/content/10.1101/688051v1?rss=1 Dhindsa, R. S. Copeland, B. R. Mustoe, A. M. Goldstein, D. B. 2019-07-01 doi:10.1101/688051 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Risk of Seizures Induced by Intracranial Research Stimulation: Analysis of 770 Stimulation Sessions ]]> https://biorxiv.org/content/10.1101/688119v1?rss=1 Goldstein, H. Smith, E. Gross, R. E. Jobst, B. C. Lega, B. C. Sperling, M. R. Worrell, G. A. Zaghloul, K. A. Wanda, P. A. Kahana, M. J. Rizzuto, D. S. Schevon, C. A. McKhann, G. M. Sheth, S. A. 2019-07-02 doi:10.1101/688119 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Population subspaces reflect movement intention for arm and brain-machine interface control ]]> https://biorxiv.org/content/10.1101/688259v1?rss=1 Lalazar, H. Murray, J. M. Abbott, L. F. Vaadia, E. 2019-07-02 doi:10.1101/688259 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Neuronal responses in posterior parietal cortex during learning of implied serial order ]]> https://biorxiv.org/content/10.1101/689133v1?rss=1 Munoz, F. Jensen, G. Kennedy, B. C. Alkan, Y. Terrace, H. S. Ferrera, V. P. 2019-07-02 doi:10.1101/689133 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Tracking the mind’s eye: Primate gaze behavior during virtual visuomotor navigation reflects belief dynamics ]]> https://biorxiv.org/content/10.1101/689786v1?rss=1 Lakshminarasimhan, K. J. Avila, E. Neyhart, E. DeAngelis, G. C. Pitkow, X. Angelaki, D. E. 2019-07-02 doi:10.1101/689786 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Genetic immunodeficiency and autoimmune disease reveal distinct roles of Hem1 in the WAVE2 and mTORC2 complexes ]]> https://biorxiv.org/content/10.1101/692004v1?rss=1 Comrie, W. A. Poli, M. C. Cook, S. A. Similuk, M. Oler, A. Faruqi, A. J. Kuhns, D. B. Yang, S. Carisey, A. F. Fournier, B. Anderson, D. E. Price, S. Chahla, W. A. Vargas-Hernandez, A. Forbes, L. R. Mace, E. M. Cao, T. N. Coban-Akdemir, Z. H. Jhangiani, S. N. Muzny, D. M. Gibbs, R. A. Lupski, J. R. Orange, J. S. Cuvelier, G. D. E. Al Hassani, M. AL Kaabi, N. Al Yafei, Z. Jyonouchi, S. Raje, N. Caldwell, J. W. Huang, Y. Burkhardt, J. K. Latour, S. Chen, B. ElGhazali, G. Rao, V. K. Chinn, I. K. Lenardo, M. J. 2019-07-04 doi:10.1101/692004 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Compound stimuli reveal the structure of visual motion selectivity in macaque MT neurons ]]> https://biorxiv.org/content/10.1101/692533v1?rss=1 Zaharia, A. D. Goris, R. L. T. Movshon, J. A. Simoncelli, E. 2019-07-04 doi:10.1101/692533 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Variants in the degron of AFF3 cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy ]]> https://biorxiv.org/content/10.1101/693937v1?rss=1 Voisin, N. Schnur, R. E. Douzgou, S. Hiatt, S. M. Rustad, C. F. Brown, N. J. Earl, D. L. Keren, B. Levchenko, O. Geuer, S. Amor, D. Brusco, A. Bebin, E. M. Cappuccio, G. Charrow, J. Chatron, N. Cooper, G. M. Dadali, E. Delafontaine, J. Del Giudice, E. Douglas, G. Funari, T. Giannuzzi, G. Guex, N. Heron, D. Holla, O. L. Hurst, A. C. E. Juusola, J. Kronn, D. Lavrov, A. Lee, C. Merckoll, E. Mikhaleva, A. Norman, J. Pradervand, S. Sanders, V. Sirchia, F. Takenouchi, T. Tanaka, A. J. Taska-Tench, H. Tonne, E. Tveten, K. Vitiello, G. Uehara, T. Nava, C. Y 2019-07-17 doi:10.1101/693937 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Analysis of task-based functional MRI data preprocessed with fMRIPrep ]]> https://biorxiv.org/content/10.1101/694364v1?rss=1 Esteban, O. Ciric, R. Finc, K. Blair, R. W. Markiewicz, C. J. Moodie, C. A. Kent, J. D. Goncalves, M. DuPre, E. Gomez, D. E. Ye, Z. Salo, T. Valabregue, R. Amlien, I. K. Liem, F. Jacoby, N. Stojic, H. Cieslak, M. Urchs, S. Halchenko, Y. O. Ghosh, S. S. de la Vega, A. Yarkoni, T. Wright, J. A. Thompson, W. H. Poldrack, R. A. Gorgolewski, K. J. 2019-07-08 doi:10.1101/694364 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Intracranial recordings from human auditory cortex reveal a neural population selective for musical song ]]> https://biorxiv.org/content/10.1101/696161v1?rss=1 Norman-Haignere, S. Feather, J. Brunner, P. Ritaccio, A. McDermott, J. H. Schalk, G. Kanwisher, N. 2019-07-09 doi:10.1101/696161 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ G protein-coupled potassium channels implicated in mouse and cellular models of GNB1 Encephalopathy ]]> https://biorxiv.org/content/10.1101/697235v1?rss=1 Colombo, S. Petri, S. Shalomov, B. Reddy, H. P. Tabak, G. Dhindsa, R. S. Gelfman, S. Teng, S. Krizay, D. Rafikian, E. E. Bera, A. K. Yang, M. Boland, M. J. Peng, Y. Frankel, W. N. Dascal, N. Goldstein, D. B. 2019-07-09 doi:10.1101/697235 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Perifornical Area Urocortin-3 Neurons Promote Infant-directed Neglect and Aggression ]]> https://biorxiv.org/content/10.1101/697334v1?rss=1 Autry, A. E. Wu, Z. Kohl, J. Bambah-Mukku, D. Rubinstein, N. D. Marin-Rodriguez, B. Carta, I. Sedwick, V. Dulac, C. 2019-07-09 doi:10.1101/697334 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ Human induced pluripotent stem cell-derived neuroectodermal epithelial cells mistaken for blood-brain barrier-forming endothelial cells ]]> https://biorxiv.org/content/10.1101/699173v1?rss=1 Lu, T. M. Redmond, D. Magdeldin, T. Nguyen, D. T. Snead, A. Sproul, A. Xiang, J. Fine, H. A. Shido, K. Rosenwaks, Z. Rafii, S. Agalliu, D. Lis, R. 2019-07-11 doi:10.1101/699173 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Discovering therapeutic activities from venoms using differential gene expression ]]> https://biorxiv.org/content/10.1101/699280v1?rss=1 Romano, J. D. Li, H. Realubit, R. Karan, C. Tatonetti, N. 2019-07-15 doi:10.1101/699280 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ Ins2 gene bursting activity defines a mature beta-cell state ]]> https://biorxiv.org/content/10.1101/702589v1?rss=1 Modi, H. Skovso, S. Ellis, C. Krentz, N. A. J. Zhao, Y. B. Cen, H. Noursadeghi, N. Panzhinskiy, E. Hu, X. Dionne, D. A. Xuan, S. Huisind, M. O. Kieffer, T. J. Lynn, F. C. Johnson, J. 2019-07-14 doi:10.1101/702589 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ A custom genotyping array reveals population-level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa ]]> https://biorxiv.org/content/10.1101/702910v1?rss=1 Harlemon, M. Ajayi, O. Kachambwa, P. Kim, M. S. Simonti, C. N. Quiver, M. H. Petersen, D. C. Mittal, A. Fernandez, P. Hsing, A. W. Baichoo, S. Agalliu, I. Jalloh, M. Gueye, S. M. Snyper, N. Y. Adusei, B. Mensah, J. E. Abrahams, A. O. D. Adebiyi, A. O. Orunmuyi, A. Aisuodionoe-Shadrach, O. I. Nwegbu, M. M. Joffe, M. Chen, W. C. Irusen, H. Neugut, A. I. Quintana, Y. Seutloali, M. Fadipe, M. Warren, C. Woehrmann, M. H. Zhang, P. Ongaco, C. Mawhinney, M. McBride, J. Andrews, C. Adams, M. Pugh, E. Rebbeck, T. R. Petersen, L. Lachance, J. 2019-07-15 doi:10.1101/702910 Cold Spring Harbor Laboratory Press 2019-07-15 <![CDATA[ CD8+ T-cell-mediated immunoediting influences genomic evolution and immune evasion in murine gliomas ]]> https://biorxiv.org/content/10.1101/705152v1?rss=1 Kane, J. R. Zhao, J. Tsujiuchi, T. Laffleur, B. Mahajan, A. Rao, G. Mela, A. Dmello, C. Arrieta, V. A. Chen, L. Zhang, D. Y. Gonzalez-Buendia, E. Lee-Chang, C. Xiao, T. Rothschild, G. Basu, U. Horbinski, C. Lesniak, M. S. Heimberger, A. B. Rabadan, R. Canoll, P. D. Sonabend, A. M. 2019-07-16 doi:10.1101/705152 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Analysis of common and rare VPS13C variants in late onset Parkinson disease ]]> https://biorxiv.org/content/10.1101/705533v1?rss=1 Rudakou, U. Ruskey, J. A. Krohn, L. Laurent, S. B. Spiegelman, D. Greenbaum, L. Yahalom, G. Desautels, A. Montplaisir, J. Y. Y. Fahn, S. Waters, C. H. Levy, O. Kehoe, C. M. Narayan, S. Dauvilliers, Y. Dupre, N. Hassin-Baer, S. Alcalay, R. N. Rouleau, G. A. Fon, E. A. Gan-Or, Z. 2019-07-20 doi:10.1101/705533 Cold Spring Harbor Laboratory Press 2019-07-20 <![CDATA[ Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system ]]> https://biorxiv.org/content/10.1101/706143v1?rss=1 Halpin-Healy, T. Klompe, S. Sternberg, S. Fernandez, I. 2019-07-18 doi:10.1101/706143 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Context-dependent gene regulation by transcription factor complexes ]]> https://biorxiv.org/content/10.1101/706473v1?rss=1 Kribelbauer, J. F. Loker, R. E. Feng, S. Rastogi, C. Abe, N. Rube, H. T. T. Bussemaker, H. J. Mann, R. S. 2019-07-18 doi:10.1101/706473 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Sex Differences in Predictors of Seizure in Contrast-Enhancing Gliomas at Clinical Presentation: A Network Approach ]]> https://biorxiv.org/content/10.1101/708032v1?rss=1 Johnston, S. K. Khurana, A. Whitmire, P. Ranjbar, S. Sharma, A. Hawkins-Daarud, A. Rubin, J. B. Porter, A. B. Canoll, P. D. Egan, K. Hu, L. S. Mrugala, M. M. Kumthekar, P. Swanson, K. R. 2019-07-22 doi:10.1101/708032 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Mutations in CalDAG-GEFI Lead to Striatal Signaling Deficits and Psychomotor Symptoms in Multiple Species Including Human ]]> https://biorxiv.org/content/10.1101/709246v1?rss=1 Crittenden, J. R. Sauvage, M. Kitsukawa, T. Burguiere, E. Cepeda, C. Andre, V. M. Canault, M. Thomsen, M. Zhang, H. Costa, C. Martella, G. Ghiglieri, V. Pescatore, K. A. Unterwald, E. M. Jackson, W. Housman, D. E. Caine, S. B. Sulzer, D. Calabresi, P. Levine, M. S. Brefel-Courbon, C. Smith, A. C. Alessi, M.-C. Azulay, J.-P. Graybiel, A. M. 2019-07-22 doi:10.1101/709246 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Centrioles control the capacity, but not the specificity, of cytotoxic T cell killing ]]> https://biorxiv.org/content/10.1101/710053v1?rss=1 Tamzalit, F. Tran, D. Jin, W. Boyko, V. Bazzi, H. Kepecs, A. Kam, L. C. Anderson, K. V. Huse, M. 2019-07-22 doi:10.1101/710053 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Temporal microstructure of dyadic social behavior during relationship formation in mice ]]> https://biorxiv.org/content/10.1101/711036v1?rss=1 Lee, W. Fu, J. Bouwman, N. Farago, P. Curley, J. 2019-07-22 doi:10.1101/711036 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Ovarian hormones mediate the prophylactic efficacy of (R,S)-ketamine and (2R,6R)-hydroxynorketamine in female mice ]]> https://biorxiv.org/content/10.1101/712752v1?rss=1 Chen, B. K. LaGamma, C. T. Xu, X. Deng, S.-X. Brachman, R. A. Suckow, R. F. Cooper, T. B. Landry, D. W. Denny, C. A. 2019-07-24 doi:10.1101/712752 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Prophylactic efficacy of 5-HT4R agonists against stress ]]> https://biorxiv.org/content/10.1101/712786v1?rss=1 Chen, B. K. Mendez-David, I. Faye, C. Gardier, A. M. David, D. J. Denny, C. A. 2019-07-24 doi:10.1101/712786 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Brain-age in midlife is associated with accelerated biological aging and cognitive decline in a longitudinal birth-cohort ]]> https://biorxiv.org/content/10.1101/712851v1?rss=1 Elliott, M. L. Belsky, D. W. Knodt, A. R. Ireland, D. Melzer, T. R. Poulton, R. Ramrakha, S. Caspi, A. Moffitt, T. E. Hariri, A. R. 2019-07-26 doi:10.1101/712851 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ A polygenic and phenotypic risk prediction for Polycystic Ovary Syndrome evaluated by Phenome-wide association studies ]]> https://biorxiv.org/content/10.1101/714113v1?rss=1 Joo, Y. Y. Actkins, K. Pacheco, J. A. Basile, A. O. Carroll, R. Crosslin, D. R. Day, F. Denny, J. C. Velez Edwards, D. R. Hakonarson, H. Harley, J. B. Hebbring, S. J. Ho, K. Jarvik, G. P. Jones, M. Karderi, T. Mentch, F. D. Meun, C. Namjou, B. Pendergrass, S. Ritchie, M. D. Stanaway, I. B. Urbanek, M. Walunas, T. L. Smith, M. Chisholm, R. L. International PCOS Consortium, Kho, A. N. Davis, L. Hayes, M. G. 2019-07-24 doi:10.1101/714113 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ Attenuation of Motion Artifacts in fMRI using Discrete Reconstruction of Irregular fMRI Trajectories (DRIFT) ]]> https://biorxiv.org/content/10.1101/714436v1?rss=1 Parker, D. Razlighi, Q. 2019-07-25 doi:10.1101/714436 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Cortical encoding of melodic expectations in human temporal cortex ]]> https://biorxiv.org/content/10.1101/714634v1?rss=1 Di Liberto, G. M. Pelofi, C. Bianco, R. Patel, P. Mehta, A. Herrero, J. de Cheveigne, A. Shamma, S. Mesgarani, N. 2019-07-25 doi:10.1101/714634 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Alpha-1 Antitrypsin Antisense Oligonucleotide Modulates Protease-Antiprotease Imbalance without Further Aggravating Smoke-induced Lung Injury ]]> https://biorxiv.org/content/10.1101/719682v1?rss=1 Xiao, R. Stearns, K. Zelonina, T. Goldklang, M. P. Blomenkamp, K. Teckman, J. D'Armiento, J. M. 2019-07-30 doi:10.1101/719682 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Human inference in changing environments ]]> https://biorxiv.org/content/10.1101/720516v1?rss=1 Prat-Carrabin, A. Wilson, R. C. Cohen, J. D. Azeredo da Silveira, R. 2019-07-31 doi:10.1101/720516 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Pathogenic Role of Delta 2 Tubulin in Bortezomib Induced Peripheral Neuropathy ]]> https://biorxiv.org/content/10.1101/721852v1?rss=1 Pero, M. E. Meregalli, C. Qu, X. Kumar, A. Shorey, M. Rolls, M. Tanji, K. Brannagan, T. Alberti, P. Fumagalli, G. Monza, L. Cavaletti, G. Bartolini, F. 2019-08-02 doi:10.1101/721852 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Statistical inference for the evolutionary history of cancer genomes ]]> https://biorxiv.org/content/10.1101/722033v1?rss=1 Đinh, K. N. Jaksik, R. Kimmel, M. Lambert, A. Tavare, S. 2019-08-01 doi:10.1101/722033 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ A theoretical model for focal seizure initiation, propagation, termination, and progression ]]> https://biorxiv.org/content/10.1101/724088v1?rss=1 Liou, J.-y. Smith, E. H. Bateman, L. M. Bruce, S. L. McKhann, G. M. Goodman, R. R. Emerson, R. G. Schevon, C. A. Abbott, L. F. 2019-08-03 doi:10.1101/724088 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Anxiety, avoidance, and sequential evaluation ]]> https://biorxiv.org/content/10.1101/724492v1?rss=1 Zorowitz, S. Momennejad, I. Daw, N. D. 2019-08-05 doi:10.1101/724492 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ A size principle for leg motor control in Drosophila ]]> https://biorxiv.org/content/10.1101/730218v1?rss=1 Azevedo, A. W. Gurung, P. Venkatasubramanian, L. Mann, R. Tuthill, J. C. 2019-08-08 doi:10.1101/730218 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Multiplexed, bioorthogonal labeling of multicomponent, biomolecular complexes using genomically encoded, non-canonical amino acids ]]> https://biorxiv.org/content/10.1101/730465v1?rss=1 Desai, B. J. Gonzalez, R. L. 2019-08-09 doi:10.1101/730465 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Familial relationships in electronic health records (EHR) v2 ]]> https://biorxiv.org/content/10.1101/731976v1?rss=1 Liu, Z. Tatonetti, N. 2019-08-20 doi:10.1101/731976 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2 ]]> https://biorxiv.org/content/10.1101/732537v1?rss=1 60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbed Nephroparvovirus, which is consistent with nomenclature for the genus Erythroparvovirus. ]]> Jolly, C. J. Lee, Q. Padula, M. P. Pinello, N. Williams, S. H. O'Rourke, M. B. Fumagalli, M. J. Orkin, J. D. Shaban, B. Brenner, O. Weninger, W. Souza, W. M. d. Melin, A. D. Wong, J. J.- L. Crim, M. J. Monette, S. Roediger, B. 2019-08-15 doi:10.1101/732537 Cold Spring Harbor Laboratory Press 2019-08-15 <![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[ Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference ]]> https://biorxiv.org/content/10.1101/733642v1?rss=1 Walter, K. S. Colijn, C. Cohen, T. Mathema, B. Liu, Q. Bowers, J. R. Engelthaler, D. M. Narechania, A. Croda, J. Andrews, J. R. 2019-08-24 doi:10.1101/733642 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway ]]> https://biorxiv.org/content/10.1101/735894v1?rss=1 LaMonte, G. M. Marapana, D. S. Gnadig, N. Ottilie, S. Luth, M. R. Worgall, T. S. Rocamora, F. Goldgof, G. M. Mohunlal, R. Kumar, T. R. S. Thompson, J. K. Vigil, E. Yang, J. Hutson, D. Johnson, T. Huang, J. Williams, R. M. Zou, B. Y. Cheung, A. L. Kumar, P. Egan, T. J. Lee, M. C. S. Siegel, D. Cowman, A. F. Fidock, D. A. Winzeler, E. A. 2019-08-15 doi:10.1101/735894 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Ability of the misfolding avoidance hypothesis to explain protein evolutionary rates in the light of empirical evidence ]]> https://biorxiv.org/content/10.1101/736280v1?rss=1 Plata, G. Usmanova, D. R. Vitkup, D. 2019-09-10 doi:10.1101/736280 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Models of heterogeneous dopamine signaling in an insect learning and memory center ]]> https://biorxiv.org/content/10.1101/737064v1?rss=1 Jiang, L. Litwin-Kumar, A. 2019-08-15 doi:10.1101/737064 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Targeting MEK5 impairs non-homologous end-joining repair and sensitizes prostate cancer to DNA damaging agents ]]> https://biorxiv.org/content/10.1101/737080v1?rss=1 Broustas, C. G. Duval, A. J. Chaudhary, K. R. Friedman, R. A. Virk, R. K. Lieberman, H. B. 2019-08-15 doi:10.1101/737080 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Modeling and treating GRIN2A developmental and epileptic encephalopathy in mice ]]> https://biorxiv.org/content/10.1101/737239v1?rss=1 G), was identified in a child with DEE, and Grin2a knockin mice were generated to model and extend understanding of this intractable childhood disease. Homozygous and heterozygous mutant mice exhibit altered hippocampal morphology at two weeks of age, and homozygotes exhibit lethal tonic-clonic seizures in the third week. Heterozygous adult mice display a variety of distinct features, including resistance to electrically induced partial seizures, as well as hyperactivity and repetitive and reduced anxiety behaviors. Multielectrode recordings of mutant neuronal networks reveal hyperexcitability and altered bursting and synchronicity. When expressed in heterologous cells, mutant receptors exhibit enhanced NMDAR agonist potency and slow deactivation following rapid removal of glutamate, as occurs at synapses. Consistent with these observations, NMDAR-mediated synaptic currents in hippocampal slices from mutant mice show a prolonged deactivation time course. Standard antiepileptic drug monotherapy was ineffective in the patient, but combined treatment of NMDAR antagonists with antiepileptic drugs substantially reduced the seizure burden albeit without appreciable developmental improvement. Chronic treatment of homozygous mutant mouse pups with NMDAR antagonists delayed the onset of lethal seizures but did not prevent them. These studies illustrate the power of modeling severe neurodevelopmental seizure disorders using multiple experimental modalities and suggest their extended utility in identifying and evaluating new therapies. ]]> Amador, A. Bostick, C. D. Olson, H. Peters, J. Camp, C. R. Krizay, D. Chen, W. Han, W. Tang, W. Kanber, A. Kim, S. Teoh, J. J. Petri, S. Paek, H. Kim, H.-O. A. Lutz, C. M. Yang, M. Myers, S. J. Bhattacharya, S. Yuan, H. Goldstein, D. B. Poduri, A. Boland, M. J. Traynelis, S. F. Frankel, W. 2019-08-16 doi:10.1101/737239 Cold Spring Harbor Laboratory Press 2019-08-16 <![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[ Release of stem cells from quiescence reveals multiple gliogenic domains in the adult brain ]]> https://biorxiv.org/content/10.1101/738013v1?rss=1 Delgado, A. Maldonado-Soto, A. Silva-Vargas, V. Mizrak, D. von Kaenel, T. Paul, A. Madar, A. Cuervo, H. Kitajewski, J. Lin, C.-S. Doetsch, F. 2019-08-16 doi:10.1101/738013 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Acute and Chronic Molecular Signatures and Associated Symptoms of Blast Exposure in Military Breachers ]]> https://biorxiv.org/content/10.1101/738054v1?rss=1 Wang, Z. Wilson, C. Mendelev, N. Ge, Y. Galfalvy, H. Elder, G. Ahlers, S. Yarnell, A. M. LoPreseti, M. L. Kamimori, G. Carr, W. Haghighi, F. 2019-08-28 doi:10.1101/738054 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Genetic modifiers of risk and age at onset in GBA associated Parkinson disease and Lewy body dementia ]]> https://biorxiv.org/content/10.1101/738351v1?rss=1 10-fold. An outstanding question in the field is what other genetic factors that influence GBA-associated risk for disease, and whether these overlap with known PD risk variants.nnUsing multiple, large case-control datasets, totalling 217,165 individuals (22,757 PD cases, 13,431 PD proxy cases, 622 LBD cases and 180,355 controls), we identified 1,772 PD cases, 711 proxy cases and 7,624 controls with a GBA variant (p.E326K, p.T369M or p.N370S). We performed a genome-wide association study and analysed the most recent PD-associated genetic risk score to detect genetic influences on GBA risk and age at onset. We attempted to replicate our findings in two independent datasets, including the personal genetics company 23andMe, Inc. and whole-genome sequencing data. Our analysis showed that the overall PD genetic risk score modifies risk for disease and decreases age at onset in carriers of GBA variants. Notably, this effect was consistent across all tested GBA risk variants. Dissecting this signal demonstrated that variants in close proximity to SNCA and CTSB (encoding cathepsin B) are the most significant contributors. Risk variants in the CTSB locus were identified to decrease mRNA expression of CTSB. Additional analyses suggest a possible genetic interaction between GBA and CTSB and GBA p.N370S neurons were shown to have decreased Cathepsin B expression compared to controls. These data provide a genetic basis for modification of GBA-associated PD risk and age at onset and demonstrate that variability at genes implicated in lysosomal function exerts the largest effect on GBA associated risk for disease. Further, these results have important implications for selection of GBA carriers for therapeutic interventions. ]]> Blauwendraat, C. Reed, X. Krohn, L. Heilbron, K. Bandres-Ciga, S. Tan, M. Gibbs, J. R. Hernandez, D. G. Kumaran, R. Langston, R. Bonet Ponce, L. Alcalay, R. Hassin-Baer, S. Greenbaum, L. Iwaki, H. Leonard, H. Grenn, F. P. Ruskey, J. A. Sabir, M. Ahmed, S. Makarious, M. B. Pihlstrom, L. Toft, M. van Hilten, J. J. Marinus, J. Schulte, C. Sharma, M. Brockmann, K. Siitonen, A. Majamaa, K. Eerola-Rautio, J. Tienari, P. The 23andMe Research Team, Pantelyat, A. Hillis-Trupe, A. Dawson, T. Rosenthal, L. Albert, M. Resnick, S. M. Ferrucci, L. Morris, C. M. Ple 2019-08-18 doi:10.1101/738351 Cold Spring Harbor Laboratory Press 2019-08-18 <![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[ Cortical Overgrowth in a Preclinical Forebrain Organoid Model of CNTNAP2-Associated Autism Spectrum Disorder ]]> https://biorxiv.org/content/10.1101/739391v1?rss=1 de Jong, J. O. Llapashtica, C. Strauss, K. Provenzano, F. Sun, Y. Cortese, G. P. Brigatti, K. W. Corneo, B. Migliori, B. Kushner, S. A. Kellendonk, C. Javitch, J. A. Xu, B. Markx, S. 2019-08-19 doi:10.1101/739391 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Mnemonic prediction errors bias hippocampal states ]]> https://biorxiv.org/content/10.1101/740563v1?rss=1 Bein, O. Duncan, K. Davachi, L. 2019-08-20 doi:10.1101/740563 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ THE C99 FRAGMENT OF APP REGULATES CHOLESTEROL TRAFFICKING ]]> https://biorxiv.org/content/10.1101/740670v1?rss=1 Area-Gomez, E. Pera, M. Larrea, D. Montesinos, J. Guardia-Laguarta, C. Agrawal, R. R. Velasco, K. R. Xu, Y. Koo, S. Y. Snead, A. M. Sproul, A. A. 2019-08-21 doi:10.1101/740670 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Identification of immunoreactive linear epitopes of Borrelia miyamotoi ]]> https://biorxiv.org/content/10.1101/741009v1?rss=1 Tokarz, R. Tagliafierro, T. Caciula, A. Mishra, N. Thakkar, R. Chauhan, L. V. Sameroff, S. Delaney, S. Wormser, G. Marques, A. R. Lipkin, W. I. 2019-08-20 doi:10.1101/741009 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Direct Observation of a Coil-to-Helix Contraction Triggered by Vinculin Binding to Talin ]]> https://biorxiv.org/content/10.1101/741884v1?rss=1 Tapia-Rojo, R. Alonso-Caballero, A. Fernandez, J. M. 2019-08-21 doi:10.1101/741884 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Tri-4C: efficient identification of cis-regulatory loops at hundred base pair resolution ]]> https://biorxiv.org/content/10.1101/743005v1?rss=1 20-fold more enhancer:promoter (E:P) loops than in situ HiC. In addition to vasly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease. ]]> Zhu, Y. Suh, Y. 2019-08-22 doi:10.1101/743005 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Protein folding modulates the adhesion strategy of Gram positive pathogens ]]> https://biorxiv.org/content/10.1101/743393v1?rss=1 Alonso-Caballero, A. Echelman, D. J. Tapia-Rojo, R. Haldar, S. Eckels, E. C. Fernandez, J. M. 2019-08-21 doi:10.1101/743393 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Paclitaxel-induced peripheral neuropathy is caused by epidermal ROS and mitochondrial damage through conserved MMP-13 activation ]]> https://biorxiv.org/content/10.1101/743419v1?rss=1 Cirrincione, A. M. Rieger, S. Pellegrini, A. D. Dominy, J. Benjamin, M. E. Utkina-Sosunova, I. Lotti, F. Jergova, S. Sagen, J. 2019-08-21 doi:10.1101/743419 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors ]]> https://biorxiv.org/content/10.1101/743625v1?rss=1 Teoh, J. J. Subramanian, N. Pero, M. E. Bartolini, F. Amador, A. Kanber, A. Williams, D. Petri, S. Yang, M. Allen, A. S. Beal, J. Haut, S. R. Frankel, W. 2019-09-08 doi:10.1101/743625 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ The domain-general multiple demand (MD) network does not support core aspects of language comprehension: a large-scale fMRI investigation ]]> https://biorxiv.org/content/10.1101/744094v1?rss=1 Diachek, E. Blank, I. A. Siegelman, M. Fedorenko, E. 2019-08-22 doi:10.1101/744094 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Low Affinity Binding Sites in an Activating CRM Mediate Negative Autoregulation of the Drosophila Hox Gene Ultrabithorax ]]> https://biorxiv.org/content/10.1101/744631v1?rss=1 Delker, R. K. Ranade, V. Loker, R. Voutev, R. Mann, R. S. 2019-08-22 doi:10.1101/744631 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ The effects of direct brain stimulation in humans depend on frequency, amplitude, and white-matter proximity. ]]> https://biorxiv.org/content/10.1101/746834v1?rss=1 Mohan, U. R. Watrous, A. J. Miller, J. F. Lega, B. C. Sperling, M. R. Worrell, G. A. Gross, R. E. Zaghloul, K. A. Jobst, B. C. Davis, K. A. Sheth, S. A. Stein, J. M. Das, S. R. Gorniak, R. Wanda, P. A. Kahana, M. J. Jacobs, J. 2019-08-28 doi:10.1101/746834 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Genetic screens reveal a central role for heme biosynthesis in artemisinin susceptibility ]]> https://biorxiv.org/content/10.1101/746974v1?rss=1 Harding, C. Sidik, S. M. Petrova, B. Gnädig, N. F. Okombo, J. Ward, K. E. Markus, B. M. Fidock, D. A. Lourido, S. 2019-08-28 doi:10.1101/746974 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Identifying a task-invariant cognitive reserve network using task potency ]]> https://biorxiv.org/content/10.1101/747311v1?rss=1 van Loenhoud, A. C. Habeck, C. van der Flier, W. M. Ossenkoppele, R. Stern, Y. 2019-08-28 doi:10.1101/747311 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Hyperactive MEK1 signaling in cortical GABAergic interneurons causes embryonic parvalbumin-neuron death and deficits in behavioral inhibition ]]> https://biorxiv.org/content/10.1101/748087v1?rss=1 Holter, M. C. Hewitt, L. T. Nishimura, K. J. Bjorklund, G. R. Shah, S. Fry, N. R. Rees, K. P. Gupta, T. A. Daniels, C. W. Li, G. Marsh, S. Treiman, D. M. Olive, M. F. Anderson, T. R. Sanabria, F. Snider, W. D. Newbern, J. M. 2019-08-27 doi:10.1101/748087 Cold Spring Harbor Laboratory Press 2019-08-27 <![CDATA[ From intent to implementation: Factors affecting public involvement in life science research ]]> https://biorxiv.org/content/10.1101/748889v1?rss=1 Burns, J. A. Korzec, K. Dorris, E. R. 2019-08-28 doi:10.1101/748889 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ An assessment of LRRK2 serine 935 phosphorylation in human peripheral blood mononuclear cells in idiopathic Parkinson’s disease and G2019S LRRK2 cohorts ]]> https://biorxiv.org/content/10.1101/749226v1?rss=1 Padmanabhan, S. Lanz, T. A. Gorman, D. Wolfe, M. Levers, N. Joshi, N. Liong, C. Narayan, S. Alcalay, R. N. Hutten, S. J. Baptista, M. A. S. Merchant, K. 2019-08-29 doi:10.1101/749226 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Antibiotic Resistance Increases Evolvability and Maximizes Opportunities Across Fitness Landscapes ]]> https://biorxiv.org/content/10.1101/750729v1?rss=1 Spagnolo, F. Dykhuizen, D. E. 2019-08-29 doi:10.1101/750729 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Identification of MCM8IP, an interactor of MCM8-9 and RPA1 that promotes homologous recombination and DNA synthesis in response to DNA damage ]]> https://biorxiv.org/content/10.1101/751974v1?rss=1 Huang, J.-W. Taglialatela, A. Acharya, A. Leuzzi, G. Nambiar, T. S. Cuella-Martin, R. Hayward, S. B. Brunette, G. J. Anand, R. Soni, R. K. Clark, N. L. Bernstein, K. A. Cejka, P. Ciccia, A. 2019-09-03 doi:10.1101/751974 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/752295v1?rss=1 Venkat, S. Tisdale, A. A. Schwarz, J. R. Alahmari, A. A. Maurer, H. C. Olive, K. P. Eng, K. H. Feigin, M. E. 2019-08-30 doi:10.1101/752295 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Olfactory Landmarks and Path Integration Converge to Form a Cognitive Spatial Map ]]> https://biorxiv.org/content/10.1101/752360v1?rss=1 Fischler, W. M. Joshi, N. Devi-Chou, V. Kitch, L. Schnitzer, M. Abbott, L. F. Axel, R. 2019-08-30 doi:10.1101/752360 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Optogenetic reactivation of prefrontal social memory trace mimics social buffering of fear ]]> https://biorxiv.org/content/10.1101/752386v1?rss=1 Gutzeit, V. A. Ahuna, K. Santos, T. L. Cunningham, A. M. Sadsad Rooney, M. Denny, C. A. Donaldson, Z. R. 2019-08-30 doi:10.1101/752386 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ The Imposition of Value on Odor: Transient and Persistent Representations of Odor Value in Prefrontal Cortex ]]> https://biorxiv.org/content/10.1101/753426v1?rss=1 Wang, P. Y. Boboila, C. Shamash, P. Wu, Z. Stein, N. P. Abbott, L. F. Axel, R. 2019-08-30 doi:10.1101/753426 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Serotonergic modulation of walking in Drosophila ]]> https://biorxiv.org/content/10.1101/753624v1?rss=1 Howard, C. E. Chen, C.-L. Tabachnik, T. Hormigo, R. Ramdya, P. Mann, R. S. 2019-09-05 doi:10.1101/753624 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Task sharing clubfoot treatment in Latin America: a cross-sectional survey of expert opinions ]]> https://biorxiv.org/content/10.1101/755298v1?rss=1 Martinez, R. Smythe, T. Pettitt-Schieber, C. Everhart, J. Hyman, J. 2019-09-02 doi:10.1101/755298 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Loss of a novel striated muscle-enriched mitochondrial protein Coq10a enhances postnatal cardiac hypertrophic growth ]]> https://biorxiv.org/content/10.1101/755793v1?rss=1 Hirose, K. Chang, S. Yu, H. Wang, J. Barca, E. Chen, X. Khyeam, S. Tajima, K. Yoneshiro, T. Kajimura, S. Quinzii, C. M. Hu, G. Huang, G. N. 2019-09-03 doi:10.1101/755793 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Membrane composition influences the conformation and function of the dopamine transporter in vivo ]]> https://biorxiv.org/content/10.1101/755819v1?rss=1 Fong, W. M. Erreger, K. Choi, S. J. Reddy, I. Johnson, C. W. Mosharov, E. V. Javitch, J. A. Galli, A. Yamamoto, A. 2019-09-05 doi:10.1101/755819 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Context-dependent decision making in a premotor circuit ]]> https://biorxiv.org/content/10.1101/757104v1?rss=1 Wu, Z. Litwin-Kumar, A. Shamash, P. Taylor, A. Axel, R. Shadlen, M. N. 2019-09-03 doi:10.1101/757104 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ A Modular Master Regulator Landscape Determines the Impact of Genetic Alterations on the Transcriptional Identity of Cancer Cells ]]> https://biorxiv.org/content/10.1101/758268v1?rss=1 50% of the somatic alterations identified in individual samples were in proteins affecting Master-Regulator activity, thus yielding novel insight into mechanisms linking tumor genetics and transcriptional identity and establishing novel non-oncogene dependencies. Experimental validation of functional mutations upstream of the most conserved MR-Block confirmed their ability to affect MR-protein activity, suggesting that the proposed methodology may effectively complement and extend current pan-cancer knowledge. ]]> Paull, E. O. Aytes, A. Subramaniam, P. Giorgi, F. M. Douglass, E. F. Chu, B. Jones, S. J. Zheng, S. Verhaak, R. Abate-Shen, C. T. Alvarez, M. Califano, A. 2019-09-05 doi:10.1101/758268 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Widespread Receptor Driven Modulation in Peripheral Olfactory Coding ]]> https://biorxiv.org/content/10.1101/760330v1?rss=1 10,000) olfactory sensory neurons distributed over large areas of intact mouse olfactory epithelium. This approach allowed us to investigate the responses to mixtures or blends of odors and their components, a more realistic stimulus than monomolecular odors. In up to 38% of responding cells, responses to a mixture of odors were different - absent, smaller or larger - than what would be expected from the sum of the individual components. Further investigation revealed instances of both antagonism and allosteric enhancement in the primary olfactory sensory neurons. All 10 of the odor compounds tested were found to act as both agonists and antagonists at different receptors. We present a hypothetical scheme for how modulation at the peripheral receptors increases the capability of the olfactory system to recognize patterns of complex odor mixtures. The widespread modulation of primary sensory receptors argues against a simple combinatorial code and should motivate a search for alternative coding strategies. ]]> Xu, L. Li, W. Voleti, V. Hillman, E. M. C. Firestein, S. 2019-09-08 doi:10.1101/760330 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Interdependency of respiratory metabolism and phenazine-associated physiology in Pseudomonas aeruginosa PA14 ]]> https://biorxiv.org/content/10.1101/760454v1?rss=1 Jo, J. Price-Whelan, A. Cornell, W. C. Dietrich, L. E. P. 2019-09-06 doi:10.1101/760454 Cold Spring Harbor Laboratory Press 2019-09-06 <![CDATA[ Unsupervised Clusterless Decoding using a Switching Poisson Hidden Markov Model ]]> https://biorxiv.org/content/10.1101/760470v1?rss=1 Ackermann, E. R. Kemere, C. T. Cunningham, J. P. 2019-09-08 doi:10.1101/760470 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Escalating protein supersaturation underlies inclusion formation in muscle proteinopathies ]]> https://biorxiv.org/content/10.1101/762245v1?rss=1 Ciryam, P. Antalek, M. Samper, F. C. Tartaglia, G. Dobson, C. M. Guettsches, A.-K. Eggers, B. Vorgerd, M. Marcus, K. Kley, R. Morimoto, R. Vendruscolo, M. Weihl, C. C. 2019-09-12 doi:10.1101/762245 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types ]]> https://biorxiv.org/content/10.1101/762500v1?rss=1 Van Driesche, S. J. Sawicka, K. Zhang, C. Hung, S. K. Y. Park, C. Y. Fak, J. J. Yang, C. Darnell, R. B. Darnell, J. C. 2019-09-09 doi:10.1101/762500 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations ]]> https://biorxiv.org/content/10.1101/763524v1?rss=1 Amster, G. Murphy, D. A. Milligan, W. M. Sella, G. 2019-09-09 doi:10.1101/763524 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Glioma-induced alterations in neuronal activity and neurovascular coupling during disease progression ]]> https://biorxiv.org/content/10.1101/763805v1?rss=1 Montgomery, M. K. Kim, S. H. Dovas, A. Patel, K. Mela, A. Humala, N. Zhao, H. T. Thibodeaux, D. N. Shaik, M. Ma, Y. Grinband, J. Chow, D. S. Schevon, C. Hillman, E. M. C. Canoll, P. 2019-09-10 doi:10.1101/763805 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Protein Tyrosine Phosphatase 1B Regulates MicroRNA-208b-Argonaute 2 Association and Thyroid Hormone Responsiveness in Cardiac Hypertrophy ]]> https://biorxiv.org/content/10.1101/763953v1?rss=1 Coulis, G. Shi, Y. Labbe, D. P. Bergeron, A. Sahmi, F. Vinette, V. Karsenty, G. Allen, B. G. Tremblay, M. Tardif, J.-C. Boivin, B. 2019-09-10 doi:10.1101/763953 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration ]]> https://biorxiv.org/content/10.1101/764100v1?rss=1 Wert, K. Velez, G. Vijayalakshmi, K. Shankar, V. Sengillo, J. Zare, R. N. Bassuk, A. G. Tsang, S. H. Mahajan, V. B. 2019-09-10 doi:10.1101/764100 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ cAb-Rep: A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence ]]> https://biorxiv.org/content/10.1101/765099v1?rss=1 Guo, Y. Chen, K. Kwong, P. D. Shapiro, L. Sheng, Z. 2019-09-11 doi:10.1101/765099 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Dynamic arousal signals construct memories of time and events ]]> https://biorxiv.org/content/10.1101/765214v1?rss=1 Clewett, D. Gasser, C. Davachi, L. 2019-09-11 doi:10.1101/765214 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ The hippocampus is critical for spatial relational attention ]]> https://biorxiv.org/content/10.1101/765222v1?rss=1 Ruiz, N. A. Meager, M. R. Agarwal, S. Aly, M. 2019-09-11 doi:10.1101/765222 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ Hippocampal subfields integrate information about past temporal and cognitive contexts ]]> https://biorxiv.org/content/10.1101/766311v1?rss=1 Dimsdale-Zucker, H. R. Montchal, M. E. Reagh, Z. M. Wang, S.-F. Libby, L. A. Ranganath, C. R. 2019-09-12 doi:10.1101/766311 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ 2D-HELS-AA MS Seq: Direct sequencing of tRNA reveals its different isoforms and multiple dynamic base modifications ]]> https://biorxiv.org/content/10.1101/767129v1?rss=1 Zhang, N. Shi, S. Wang, X. Ni, W. Yuan, X. Duan, J. Jia, T. Z. Yoo, B. Ziegler, A. Russo, J. J. Li, W. Zhang, S. 2019-09-12 doi:10.1101/767129 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ AFF3 and BACH2 are master regulators of metabolic inflexibility, β/α-cell transition, and dedifferentiation in type 2 diabetes ]]> https://biorxiv.org/content/10.1101/768135v1?rss=1 Son, J. Ding, H. Accili, D. Califano, A. 2019-09-12 doi:10.1101/768135 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Predicting the genetic ancestry of 2.6 million New York City patients using clinical data ]]> https://biorxiv.org/content/10.1101/768440v1?rss=1 Ramlall, V. Quinnies, K. M. Vanguri, R. Lorberbaum, T. Goldstein, D. B. Tatonetti, N. P. 2019-09-14 doi:10.1101/768440 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Trypsin treatment unlocks barrier for zoonotic coronaviruses infection ]]> https://biorxiv.org/content/10.1101/768663v1?rss=1 Menachery, V. D. Dinnon, K. Yount, B. McAnarney, E. T. Gralinski, L. Hale, A. E. Graham, R. Scobey, T. D. Anthony, S. J. Wang, L. Graham, B. S. Randell, S. H. Lipkin, W. I. Baric, R. S. 2019-09-16 doi:10.1101/768663 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ A Bayesian approach to accurate and robust signature detection on LINCS L1000 data ]]> https://biorxiv.org/content/10.1101/769620v1?rss=1 Qiu, Y. Lu, T. Lim, H. Xie, L. 2019-09-16 doi:10.1101/769620 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ MetroNome - a visual data exploration platform for integrating human genotypic and phenotypic data across diseases ]]> https://biorxiv.org/content/10.1101/769646v1?rss=1 Stolte, C. Shi, K. Lapchyk, N. Novod, N. Abhyankar, A. Ostrow, L. W. Phatnani, H. Bloom, T. 2019-09-14 doi:10.1101/769646 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Frontal and parietal neurons encode reward prediction errors in multiple reference frames ]]> https://biorxiv.org/content/10.1101/769869v1?rss=1 Foley, N. C. Cohanpour, M. Semework, M. Sheth, S. A. Gottlieb, J. 2019-09-15 doi:10.1101/769869 Cold Spring Harbor Laboratory Press 2019-09-15 <![CDATA[ Single-cell profiling and SCOPE-seq reveal the lineage dynamics of adult neurogenesis and NOTUM as a key V-SVZ regulator ]]> https://biorxiv.org/content/10.1101/770610v1?rss=1 56,000 V-SVZ and olfactory bulb (OB) cells by single-cell RNA-sequencing (scRNA-seq). Our analyses revealed the diversity of V-SVZ-derived OB neurons, the temporal dynamics of lineage progression, and a key intermediate NSC population enriched for expression of Notum, which encodes a secreted WNT antagonist. Single Cell Optical Phenotyping and Expression (SCOPE-seq), a technology linking live cell imaging with scRNA-seq, uncovered dynamic control of cell size concomitant with NSC differentiation with Notum+ NSCs at a critical size poised for cell division, and a preference of NOTUM surface binding to neuronal precursors with active WNT signaling. Finally, in vivo pharmacological inhibition of NOTUM significantly expanded neuronal precursor pools in the V-SVZ. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, a secreted enzyme that ensures efficient neurogenesis by preventing WNT signaling activation in NSC progeny. ]]> Mizrak, D. Bayin, N. S. Yuan, J. Liu, Z. Suciu, R. Niphakis, M. J. Ngo, N. Lum, K. M. Cravatt, B. F. Joyner, A. L. Sims, P. A. 2019-09-16 doi:10.1101/770610 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Cyb5r3 links FoxO1-dependent mitochondrial dysfunction with β-cell failure ]]> https://biorxiv.org/content/10.1101/774364v1?rss=1 Fan, J. Du, W. Kim-Muller, J.-Y. Kuo, T. Son, J. Larrea, D. Garcia, C. J. Kitamoto, T. Kraakman, M. J. Owusu-Ansah, E. Cirulli, V. Accili, D. 2019-09-19 doi:10.1101/774364 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Computational Justice: Simulating Structural Bias and Interventions ]]> https://biorxiv.org/content/10.1101/776211v1?rss=1 Momennejad, I. Sinclair, S. Cikara, M. 2019-09-25 doi:10.1101/776211 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Studying Spatial Memory in Augmented and Virtual reality ]]> https://biorxiv.org/content/10.1101/777946v1?rss=1 Maidenbaum, S. Patel, A. Garlin, I. C. Jacobs, J. 2019-09-23 doi:10.1101/777946 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ SAMPL: The Spreading Activation and Memory PLasticity Model ]]> https://biorxiv.org/content/10.1101/778563v1?rss=1 Sievers, B. Momennejad, I. 2019-09-23 doi:10.1101/778563 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses ]]> https://biorxiv.org/content/10.1101/778605v1?rss=1 Zhang, H. Ahearn, T. Lecarpentier, J. Barnes, D. Beesley, J. Qi, G. Jiang, X. O'Mara, T. A. Zhao, N. Bolla, M. K. Dunning, A. M. Dennis, J. Wang, Q. Abu Ful, Z. Aittomaki, K. Andrulis, I. L. Anton-Culver, H. Arndt, V. Aronson, K. J. Arun, B. K. Auer, P. L. Azzollini, J. Barrowdale, D. Becher, H. Beckmann, M. W. Behrens, S. Benitez, J. Bermisheva, M. Bialkowska, K. Blanco, A. Blomqvist, C. Bogdanova, N. V. Bojesen, S. E. Bonanni, B. Bondavalli, D. Borg, A. Brauch, H. Brenner, H. Briceno, I. Broeks, A. Brucker, S. Y. Bruning, T. Burwinkel, B. Buys, S. 2019-09-24 doi:10.1101/778605 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ A novel terpene synthase produces an anti-aphrodisiac pheromone in the butterfly Heliconius melpomene ]]> https://biorxiv.org/content/10.1101/779678v1?rss=1 Darragh, K. Orteu, A. Byers, K. J. R. P. Szczerbowski, D. Warren, I. A. Rastas, P. Pinharanda, A. L. Davey, J. Garza, S. F. Abondano Almeida, D. Merrill, R. M. McMillan, W. O. Schulz, S. Jiggins, C. D. 2019-09-23 doi:10.1101/779678 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Anisotropy links cell shapes to a solid-to-fluid transition during convergent extension ]]> https://biorxiv.org/content/10.1101/781492v1?rss=1 Wang, X. Merkel, M. Sutter, L. B. Erdemci-Tandogan, G. Manning, M. L. Kasza, K. E. 2019-09-25 doi:10.1101/781492 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Reproducibility Assessment of Neuromelanin-Sensitive Magnetic Resonance Imaging Protocols for Region-of-Interest and Voxelwise Analyses ]]> https://biorxiv.org/content/10.1101/781815v1?rss=1 Wengler, K. He, X. Abi-Dargham, A. Horga, G. 2019-09-25 doi:10.1101/781815 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Clickable methionine as a universal probe for labelling intracellular bacteria ]]> https://biorxiv.org/content/10.1101/784371v1?rss=1 Atwal, S. Giengkam, S. Jaiyen, Y. Feaga, h. Dworkin, J. Salje, J. 2019-09-26 doi:10.1101/784371 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Diverse transcriptomic signatures across human tissues identify functional rare genetic variation ]]> https://biorxiv.org/content/10.1101/786053v1?rss=1 Ferraro, N. M. Strober, B. J. Einson, J. Li, X. Aguet, F. Barbeira, A. N. Castel, S. E. Davis, J. R. Hilliard, A. T. Kotis, B. Park, Y. Scott, A. J. Smail, C. Tsang, E. K. Ardlie, K. G. Assimes, T. L. Hall, I. Im, H. K. GTEx Consortium, Lappalainen, T. Mohammadi, P. Montgomery, S. B. Battle, A. 2019-10-03 doi:10.1101/786053 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Predictive Representations in Hippocampal and Prefrontal Hierarchies ]]> https://biorxiv.org/content/10.1101/786434v1?rss=1 Brunec, I. K. Momennejad, I. 2019-09-30 doi:10.1101/786434 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ The GTEx Consortium atlas of genetic regulatory effects across human tissues ]]> https://biorxiv.org/content/10.1101/787903v1?rss=1 Aguet, F. Barbeira, A. N. Bonazzola, R. Brown, A. Castel, S. E. Jo, B. Kasela, S. Kim-Hellmuth, S. Liang, Y. Oliva, M. Parsana, P. E. Flynn, E. Fresard, L. Gaamzon, E. R. Hamel, A. R. He, Y. Hormozdiari, F. Mohammadi, P. Munoz-Aguirre, M. Park, Y. Saha, A. Segrc, A. V. Strober, B. J. Wen, X. Wucher, V. Das, S. Garrido-Martin, D. Gay, N. R. Handsaker, R. E. Hoffman, P. J. Kashin, S. Kwong, A. Li, X. MacArthur, D. Rouhana, J. M. Stephens, M. Todres, E. Vinuela, A. Wang, G. Zou, Y. The GTEx Consortium, Brown, C. D. Cox, N. Dermitzakis, E. Engelhardt, 2019-10-03 doi:10.1101/787903 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Predicting Minimal Residual Disease in Acute Myeloid Leukemia through Stochastic Modeling of Clonality ]]> https://biorxiv.org/content/10.1101/790261v1?rss=1 Dinh, K. N. Jaksik, R. Corey, S. Kimmel, M. 2019-10-02 doi:10.1101/790261 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Circuit mechanisms underlying chromatic encoding in Drosophila photoreceptors ]]> https://biorxiv.org/content/10.1101/790295v1?rss=1 Heath, S. L. Christenson, M. P. Oriol, E. Saavedra-Weisenhaus, M. Kohn, J. R. Behnia, R. 2019-10-04 doi:10.1101/790295 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Polygenic adaptation after a sudden change in environment ]]> https://biorxiv.org/content/10.1101/792952v1?rss=1 Hayward, L. K. Sella, G. 2019-10-03 doi:10.1101/792952 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Long non-coding RNA gene regulation and trait associations across human tissues ]]> https://biorxiv.org/content/10.1101/793091v1?rss=1 de Goede, O. M. Ferraro, N. M. Nachun, D. C. Rao, A. Aguet, F. Barbeira, A. N. Castel, S. E. Kim-Hellmuth, S. Park, Y. Scott, A. J. Strober, B. J. GTEx Consortium, Brown, C. D. Wen, X. Hall, I. M. Battle, A. Lappalainen, T. Im, H. K. Ardlie, K. G. Quertermous, T. Kirkegaard, K. Montgomery, S. B. 2019-10-04 doi:10.1101/793091 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Sites of Circadian Clock Neuron Plasticity Mediate Sensory Integration and Entrainment. ]]> https://biorxiv.org/content/10.1101/794537v1?rss=1 Fernandez, M. d. l. P. Pettibone, H. L. Roell, C. J. Huynh, K. V. Davey, C. E. Lennox, S. M. Kostadinov, B. S. Shafer, O. T. 2019-10-07 doi:10.1101/794537 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ An amygdala circuit mediates experience-dependent momentary exploratory arrests ]]> https://biorxiv.org/content/10.1101/797001v1?rss=1 Botta, P. Fushiki, A. Vicente, A. M. Hammond, L. A. Mosberger, A. C. Gerfen, C. R. Peterka, D. S. Costa, R. M. 2019-10-08 doi:10.1101/797001 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Light-mediated decreases in cyclic di-GMP levels are potentiated by pyocyanin and inhibit structure formation in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/797357v1?rss=1 Kahl, L. J. Price-Whelan, A. Dietrich, L. E. P. 2019-10-08 doi:10.1101/797357 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Remembrance of things practiced: A two-pathway circuit for sequential learning ]]> https://biorxiv.org/content/10.1101/797548v1?rss=1 Murray, J. M. Escola, S. 2019-10-08 doi:10.1101/797548 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Leukocyte-derived High-mobility group box 1 controls innate immune responses against Listeria monocytogenes. ]]> https://biorxiv.org/content/10.1101/797902v1?rss=1 Volmari, A. Foelsch, K. Yan, K. Qi, M. Bartels, K. Kondratowicz, S. Boettcher, M. Nishibori, M. Liu, K. Schwabe, R. F. Lohse, A. W. Huber, S. Mittruecker, H.-W. Huebener, P. 2019-10-08 doi:10.1101/797902 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ ASEP: gene-based detection of allele-specific expression in a population by RNA-seq ]]> https://biorxiv.org/content/10.1101/798124v1?rss=1 Fan, J. Hu, J. Xue, C. Zhang, H. Reilly, M. P. Xiao, R. Li, M. 2019-10-08 doi:10.1101/798124 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Efficient sampling and noisy decisions ]]> https://biorxiv.org/content/10.1101/799064v1?rss=1 Heng, J. A. Woodford, M. Polania, R. 2019-10-09 doi:10.1101/799064 Cold Spring Harbor Laboratory Press 2019-10-09 <![CDATA[ Single-nucleus RNA-seq identifies Huntington disease astrocyte states ]]> https://biorxiv.org/content/10.1101/799973v1?rss=1 Al-Dalahmah, O. Sosunov, A. A. Shaik, A. Ofori, K. Liu, Y. Vonsattel, J. P. G. Adorjan, I. Menon, V. Goldman, J. E. 2019-10-10 doi:10.1101/799973 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Neurodevelopmental shifts in learned value transfer on cognitive control during adolescence ]]> https://biorxiv.org/content/10.1101/801126v1?rss=1 Insel, C. Charifson, M. Somerville, L. H. 2019-10-10 doi:10.1101/801126 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Hippocampal spike-time correlations and place-field overlaps during open field foraging ]]> https://biorxiv.org/content/10.1101/801209v1?rss=1 Monsalve-Mercado, M. M. Roudi, Y. 2019-10-16 doi:10.1101/801209 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ A Consensus Proteomic Analysis of Alzheimer’s Disease Brain and Cerebrospinal Fluid Reveals Early Changes in Energy Metabolism Associated with Microglia and Astrocyte Activation ]]> https://biorxiv.org/content/10.1101/802959v1?rss=1 2000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brain that may serve as therapeutic targets and fluid biomarkers for the disease. ]]> Johnson, E. Dammer, E. B. Duong, D. M. Ping, L. Zhou, M. Yin, L. Higginbotham, L. A. Guajardo, A. White, B. Troncoso, J. C. Thambisetty, M. Montine, T. J. Lee, E. B. Trojanowski, J. Q. Beach, T. G. Reiman, E. M. Haroutunian, V. Wang, M. Schadt, E. Zhang, B. Dickson, D. W. Ertekin-Taner, N. Golde, T. E. Petyuk, V. A. De Jager, P. L. Bennett, D. A. Wingo, T. S. Rangaraju, S. Hajjar, I. Shulman, J. M. Lah, J. J. Levey, A. I. Seyfried, N. T. 2019-10-13 doi:10.1101/802959 Cold Spring Harbor Laboratory Press 2019-10-13 <![CDATA[ Net effects of field and landscape scale habitat on insect and bird damage to sunflowers ]]> https://biorxiv.org/content/10.1101/804328v1?rss=1 Kross, S. Martinico, B. Bourbour, R. P. Townsend, J. M. McColl, C. Kelsey, R. 2019-10-15 doi:10.1101/804328 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Hepatic FoxOs induce apolipoprotein M and are required for sphingosine-1-phosphate to bind high density lipoproteins ]]> https://biorxiv.org/content/10.1101/804336v1?rss=1 Izquierdo, M. C. Shanmugarajah, N. Lee, S. X. Haeusler, R. 2019-10-15 doi:10.1101/804336 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Persistent DNA Hyper-methylation Dampens Host Anti-Mycobacterial Immunity ]]> https://biorxiv.org/content/10.1101/805457v1?rss=1 DiNardo, A. R. Rajapakshe, K. Nishiguchi, T. Mtetwa, G. Dlamini, Q. Kahari, J. Mahapatra, S. Kay, A. Maphalala, G. Mace, E. Grimm, S. L. Makedonas, G. Cirillo, J. D. Netea, M. G. van Crevel, R. Coarfa, C. Mandalakas, A. M. 2019-10-16 doi:10.1101/805457 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence ]]> https://biorxiv.org/content/10.1101/806711v1?rss=1 Feaga, H. Kopylov, M. Kim, J. K. Jovanovic, M. Dworkin, J. 2019-10-16 doi:10.1101/806711 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Transcriptional and Biochemical Function ]]> https://biorxiv.org/content/10.1101/807669v1?rss=1 Gruber, C. N. Calis, J. Buta, S. Evrony, G. Martin, J. C. Uhl, S. Caron, R. Jarchin, L. Dunkin, D. Phelps, R. Webb, B. D. Saland, J. Merad, M. Orange, J. Mace, E. M. Rosenberg, B. R. Gelb, B. Bogunovic, D. 2019-10-17 doi:10.1101/807669 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ (p)ppGpp directly regulates translation initiation during entry into quiescence ]]> https://biorxiv.org/content/10.1101/807917v1?rss=1 Diez, S. Ryu, J. Caban, K. Gonzalez, R. L. Dworkin, J. 2019-10-17 doi:10.1101/807917 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Flexible recruitment of memory-based choice representations by human medial-frontal cortex ]]> https://biorxiv.org/content/10.1101/809673v1?rss=1 Minxha, J. Adolphs, R. Fusi, S. Mamelak, A. Rutishauser, U. 2019-10-18 doi:10.1101/809673 Cold Spring Harbor Laboratory Press 2019-10-18 <![CDATA[ Decomposing Simon task BOLD activation using a drift-diffusion model framework ]]> https://biorxiv.org/content/10.1101/809947v1?rss=1 McIntosh, J. R. Sajda, P. 2019-10-21 doi:10.1101/809947 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[ Flexible reset and entrainment of delta oscillations in primate primary auditory cortex: modeling and experiment ]]> https://biorxiv.org/content/10.1101/812024v1?rss=1 Stanley, D. A. Falchier, A. Y. Pittman-Polletta, B. R. Lakatos, P. Whittington, M. A. Schroeder, C. E. Kopell, N. J. 2019-10-22 doi:10.1101/812024 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Detecting prodromal Alzheimer’s disease with MRI through deep learning ]]> https://biorxiv.org/content/10.1101/813899v1?rss=1 Feng, X. Provenzano, F. A. Small, S. A. Alzheimer's Disease Neuroimaging Initiative, 2019-10-22 doi:10.1101/813899 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs ]]> https://biorxiv.org/content/10.1101/815605v1?rss=1 Do, C. Dumont, E. Salas, M. Castano, A. Mujahed, H. Maldonado, L. Singh, A. Bhagat, G. Lehman, S. Christiano, A. M. Madhavan, S. Nagy, P. L. Green, P. H. R. Feinman, R. Trimble, C. Marder, K. Honig, L. Monk, C. Goy, A. Chow, K. Goldlust, S. Kaptain, G. Siegel, D. Tycko, B. 2019-11-01 doi:10.1101/815605 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Genetic control of the human brain proteome ]]> https://biorxiv.org/content/10.1101/816652v1?rss=1 Robins, C. Wingo, A. P. Fan, W. Doung, D. M. Meigs, J. Gerasimov, E. S. Dammer, E. B. Cutler, D. J. De Jager, P. Bennett, D. A. Lah, J. J. Levey, A. I. Seyfried, N. T. Wingo, T. S. 2019-10-24 doi:10.1101/816652 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Thermal versus Mechanical Unfolding in a Model Protein ]]> https://biorxiv.org/content/10.1101/816801v1?rss=1 Tapia-Rojo, R. Mazo, J. J. Falo, F. 2019-10-24 doi:10.1101/816801 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ High-Throughput Translational Profiling with riboPLATE-seq ]]> https://biorxiv.org/content/10.1101/819094v1?rss=1 Metz, J. B. Hornstein, N. J. Das Sharma, S. Worley, J. Sims, P. A. 2019-10-25 doi:10.1101/819094 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[ Identification and biochemical characterization of a novel eukaryotic-like Ser/Thr kinase in E. coli ]]> https://biorxiv.org/content/10.1101/819920v1?rss=1 Rajagopalan, K. Dworkin, J. 2019-10-25 doi:10.1101/819920 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ SUSTAINED DOPAMINERGIC PLATEAUS AND NORADRENERGIC DEPRESSIONS BIAS TRANSITIONS INTO EXPLOITATIVE BEHAVIORAL STATES ]]> https://biorxiv.org/content/10.1101/822650v1?rss=1 Koralek, A. C. Costa, R. M. 2019-10-29 doi:10.1101/822650 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Genomic features of BRDT binding sites in gene units suggest transcriptional partners and specific epigenetic landscapes to regulate transcriptional activity during spermatogenesis ]]> https://biorxiv.org/content/10.1101/822874v1?rss=1 Wang, L. Chepelev, I. Her, Y. R. Manterola, M. Berkovits, B. Cui, K. Zhao, K. Wolgemuth, D. J. 2019-10-30 doi:10.1101/822874 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Hypoxia inducible factor-2α increases sensitivity of colon cancer cells towards oxidative cell death ]]> https://biorxiv.org/content/10.1101/823997v1?rss=1 Singhal, R. Olive, K. P. Lyssiotis, C. A. Shah, Y. M. 2019-10-30 doi:10.1101/823997 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Preparation for upcoming attentional states in the hippocampus and medial prefrontal cortex ]]> https://biorxiv.org/content/10.1101/825349v1?rss=1 Günseli, E. Aly, M. 2019-10-31 doi:10.1101/825349 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Human NK cell deficiency as a result of biallelic mutations in MCM10 ]]> https://biorxiv.org/content/10.1101/825554v1?rss=1 Mace, E. Paust, S. Conte, M. I. Baxley, R. M. Schmit, M. Mukherjee, M. Pezzi, A. E. Chmielowiec, J. Tatineni, S. Chinn, I. Akdemir, Z. C. Jhangiani, S. N. Muzny, D. M. Stray-Pedersen, A. Bradley, R. E. Moody, M. Connor, P. P. Heaps, A. Steward, C. Banerjee, P. P. Gibbs, R. A. Borowiak, M. Lupski, J. R. Jolles, S. R. Bielinsky, A. Orange, J. 2019-11-02 doi:10.1101/825554 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Dissociable brain mechanisms for long-term memory of disgust- and fear- related associations ]]> https://biorxiv.org/content/10.1101/825844v1?rss=1 Riegel, M. Wierzba, M. Wypych, M. Ritchey, M. Jednorog, K. Grabowska, A. Vuilleumier, P. Marchewka, A. 2019-10-31 doi:10.1101/825844 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Aversion of the invasive Asian longhorned tick to the white-footed mouse, the dominant reservoir of tick-borne pathogens in the United States ]]> https://biorxiv.org/content/10.1101/826289v1?rss=1 Ronai, I. Tufts, D. M. Diuk-Wasser, M. A. 2019-10-31 doi:10.1101/826289 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ PKM2 ablation enhanced retinal function and survival in a preclinical model of retinitis pigmentosa ]]> https://biorxiv.org/content/10.1101/826651v1?rss=1 Zhang, E. Ryu, J. Levi, S. R. Oh, J. K. Hsu, C. W. Lima de Carvalho, J. R. Cui, X. Yang, T. Tsang, S. H. 2019-10-31 doi:10.1101/826651 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Leveraging correlations between polygenic risk score predictors to detect heterogeneity in GWAS cohorts ]]> https://biorxiv.org/content/10.1101/827162v1?rss=1 50, 000 cases and controls collected by the Psychiatric Genomics Consortium. We observe significant heterogeneity in mega-analysis of the combined PGC data (p-value 8.54e-4), as well as in individual cohorts meta-analyzed using Fishers method (p-value 0.03), based on significantly associated variants. ]]> Yuan, J. Xing, H. Lamy, A. L. The Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lencz, T. Pe'er, I. 2019-11-01 doi:10.1101/827162 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ The antimalarial natural product salinipostin A identifies essential α/β serine hydrolases involved in lipid metabolism in P. falciparum parasites ]]> https://biorxiv.org/content/10.1101/827287v1?rss=1 Yoo, E. Schulze, C. J. Stokes, B. H. Onguka, O. Yeo, T. Mok, S. Gnadig, N. F. Zhou, Y. Kurita, K. Foe, I. T. Terrell, S. M. Boucher, M. J. Cieplak, P. Linington, R. G. Long, J. Z. Uhlemann, A.-C. Weerapana, E. Fidock, D. A. Bogyo, M. 2019-11-01 doi:10.1101/827287 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ A MAP of tumor-host interactions in glioma at single cell resolution ]]> https://biorxiv.org/content/10.1101/827758v1?rss=1 Caruso, F. Garofano, L. D'Angelo, F. Yu, K. Tang, F. Yuan, J. Zhang, J. Cerulo, L. Bedognetti, D. Sims, P. Suva, M. Su, X.-D. Lasorella, A. Iavarone, A. Ceccarelli, M. 2019-11-01 doi:10.1101/827758 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Induction of pancreatic tumor-selective ferroptosis through modulation of cystine import ]]> https://biorxiv.org/content/10.1101/827972v1?rss=1 Badgley, M. A. Kremer, D. Maurer, H. C. DelGiorno, K. E. Lee, H.-J. Purohit, V. Sagalovskiy, I. Ma, A. Kapillian, J. Firl, C. E. M. Decker, A. R. Sastra, S. A. Palermo, C. F. Andrade, L. R. Sajjakulnukit, P. Zhang, L. Tolstyka, Z. P. Hirschhorn, T. Lamb, C. Liu, T. Gu, W. Seeley, E. S. Stone, E. Georgiou, G. Manor, U. Iuga, A. Wahl, G. M. Stockwell, B. R. Lyssiotis, C. A. Olive, K. P. 2019-11-01 doi:10.1101/827972 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Failure to engage the TPJ-pSTS during naturalistic scene processing in schizophrenia ]]> https://biorxiv.org/content/10.1101/828988v1?rss=1 Patel, G. H. Arkin, S. C. Ruiz-Betancourt, D. Plaza, F. I. Mirza, S. A. Vieira, D. J. Strauss, N. E. Klim, C. C. Sanchez-Pena, J. P. Bartel, L. P. Grinband, J. Martinez, A. Berman, R. A. Ochsner, K. N. Leopold, D. A. Javitt, D. C. 2019-11-02 doi:10.1101/828988 Cold Spring Harbor Laboratory Press 2019-11-02 <![CDATA[ Integrins protect nociceptive neurons in models of paclitaxel-mediated peripheral sensory neuropathy ]]> https://biorxiv.org/content/10.1101/829655v1?rss=1 Shin, G. J.-e. Pero, M. E. Hammond, L. A. Burgos, A. Galindo, S. E. Bartolini, F. Grueber, W. B. 2019-11-04 doi:10.1101/829655 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Genome-wide association study identifies 49 common genetic variants associated with handedness. ]]> https://biorxiv.org/content/10.1101/831321v1?rss=1 Cuellar Partida, G. Tung, J. Y. Eriksson, N. Albrecht, E. Aliev, F. Andreassen, O. A. Barroso, I. Beckmann, J. S. Boks, M. P. Boomsma, D. I. Boyd, H. A. Breteler, M. M. Campbell, H. Chasman, D. I. Cherkas, L. F. Davies, G. de Geus, E. J. Deary, I. J. Deloukas, P. Dick, D. M. Duffy, D. L. Eriksson, J. G. Esko, T. Feenstra, B. Geller, F. Gieger, C. Giegling, I. Gordon, S. D. Han, J. Hansen, T. F. Hartmann, A. M. Heikkila, K. Hicks, A. A. Hayward, C. Hirschhorn, J. N. Hottenga, J.-J. Huffman, J. E. Hwang, L.-D. Ikram, M. A. Kaprio, J. Kemp, J. P. Khaw, K.- 2019-11-07 doi:10.1101/831321 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Estimating and interpreting nonlinear receptive fields of sensory responses with deep neural network models ]]> https://biorxiv.org/content/10.1101/832212v1?rss=1 Keshishian, M. Akbari, H. Khalighinejad, B. Herrero, J. Mehta, A. Mesgarani, N. 2019-11-07 doi:10.1101/832212 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Predictive whisker kinematics reveal context-dependent sensorimotor strategies ]]> https://biorxiv.org/content/10.1101/833103v1?rss=1 Wallach, A. Deutsch, D. Oram, T. Ahissar, E. 2019-11-06 doi:10.1101/833103 Cold Spring Harbor Laboratory Press 2019-11-06 <![CDATA[ Coding of social novelty in the hippocampal CA2 region and its disruption and rescue in a mouse model of schizophrenia ]]> https://biorxiv.org/content/10.1101/833723v1?rss=1 Donegan, M. L. Stefanini, F. Meira, T. Gordon, J. A. Fusi, S. Siegelbaum, S. A. 2019-11-07 doi:10.1101/833723 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Unravelling the genetic architecture of musical rhythm ]]> https://biorxiv.org/content/10.1101/836197v1?rss=1 Niarchou, M. Sathirapongsasuti, J. F. Jacoby, N. Bell, E. McArthur, E. Straub, P. The 23andMe Research Team, McAuley, J. D. Capra, J. A. Ullen, F. Creanza, N. Mosing, M. A. Hinds, D. Davis, L. K. Gordon, R. L. 2019-11-09 doi:10.1101/836197 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis ]]> https://biorxiv.org/content/10.1101/836668v1?rss=1 Chen, J. Liao, A. Powers, E. N. Liao, H. Kohlstaedt, L. A. Evans, R. Holly, R. M. Kim Kim, J. Jovanovic, M. Unal, E. 2019-11-09 doi:10.1101/836668 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Origin and microenvironment contribute to the sexually dimorphic phenotype and function of peritoneal macrophages. ]]> https://biorxiv.org/content/10.1101/837336v1?rss=1 Bain, C. C. Gibson, D. A. Steers, N. J. Boufea, K. Louwe, P. A. Doherty, C. Huici, V. Gentek, R. Magalhaes-Pinto, M. Bajenoff, M. Benezech, C. Dockrell, D. Saunders, P. T. Batadar, N. Jenkins, S. J. 2019-11-14 doi:10.1101/837336 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Interrogating theoretical models of neural computation with deep inference ]]> https://biorxiv.org/content/10.1101/837567v1?rss=1 Bittner, S. R. Palmigiano, A. Piet, A. T. Duan, C. A. Brody, C. D. Miller, K. D. Cunningham, J. P. 2019-11-11 doi:10.1101/837567 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Positive valence bias is associated with inverse frontoamygdalar connectivity and less depressive symptoms in developmentally mature children ]]> https://biorxiv.org/content/10.1101/839761v1?rss=1 Petro, N. Tottenham, N. Neta, M. 2019-11-15 doi:10.1101/839761 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Synaptogenic activity of the axon guidance molecule Robo2 is critical for hippocampal circuit function ]]> https://biorxiv.org/content/10.1101/840710v1?rss=1 Blockus, H. Rolotti, S. Szoboszlay, M. Ming, T. Schroeder, A. Vennekens, K. M. Katsamba, P. Bahna, F. Mannepalli, S. Ahlsen, G. Honig, B. Shapiro, L. de Wit, J. Losonczy, A. Polleux, F. 2019-11-13 doi:10.1101/840710 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Complex spikes encode reward expectation signals during visuomotor association learning ]]> https://biorxiv.org/content/10.1101/841858v1?rss=1 Sendhilnathan, N. Ipata, A. E. Goldberg, M. E. 2019-11-14 doi:10.1101/841858 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Two Ways to Change Your Mind: Effects of Intentional Strength and Motor Costs on Changes of Intention. ]]> https://biorxiv.org/content/10.1101/841882v1?rss=1 Loffler, A. Sylaidi, A. Fountas, Z. Haggard, P. 2019-11-15 doi:10.1101/841882 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Neural correlates of goal-directed and non-goal-directed movements ]]> https://biorxiv.org/content/10.1101/843011v1?rss=1 Sendhilnathan, N. Basu, D. Goldberg, M. E. Schall, J. D. Murthy, A. 2019-11-15 doi:10.1101/843011 Cold Spring Harbor Laboratory Press 2019-11-15 <![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[ Chronic Mcm10 deficiency causes defects in telomere maintenance in human cells ]]> https://biorxiv.org/content/10.1101/844498v1?rss=1 Baxley, R. M. Leung, W. Matson, J. P. Oram, M. K. Schmit, M. M. Wang, L. Hedberg, J. Rogers, C. B. Harvey, A. J. Basu, D. Hendrickson, E. A. Mace, E. M. Orange, J. Cook, J. G. Bielinsky, A.-K. 2019-11-16 doi:10.1101/844498 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ A comparison of humans and baboons suggests germline mutation rates do not track cell divisions ]]> https://biorxiv.org/content/10.1101/844910v1?rss=1 Wu, F. L. Strand, A. Ober, C. Wall, J. D. Moorjani, P. Przeworski, M. 2019-11-16 doi:10.1101/844910 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies ]]> https://biorxiv.org/content/10.1101/846915v1?rss=1 Diaz, J. E. L. Ahsen, M. E. Schaffter, T. Chen, X. Realubit, R. B. Karan, C. Califano, A. Losic, B. Stolovitzky, G. 2019-11-18 doi:10.1101/846915 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Multiplexed biosensors for precision bacteria tropism in vivo ]]> https://biorxiv.org/content/10.1101/851311v1?rss=1 Chien, T. Harimoto, T. Kepecs, B. Gray, K. Coker, C. Pu, K. Azad, T. Danino, T. 2019-11-21 doi:10.1101/851311 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Humanization of SRGAP2C expression increases cortico-cortical connectivity and reliability of sensory-evoked responses in the mouse brain ]]> https://biorxiv.org/content/10.1101/852970v1?rss=1 Schmidt, E. R. E. Zhao, H. T. Hillman, E. M. C. Polleux, F. 2019-11-24 doi:10.1101/852970 Cold Spring Harbor Laboratory Press 2019-11-24 <![CDATA[ Face familiarity detection with complex synapses ]]> https://biorxiv.org/content/10.1101/854059v1?rss=1 Ji-An, L. Stefanini, F. Benna, M. K. Fusi, S. 2019-11-25 doi:10.1101/854059 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis. ]]> https://biorxiv.org/content/10.1101/854182v1?rss=1 Cheng, H. K. Tan, S. K. Sweeney, T. E. Jeganathan, P. Briese, T. Khadka, V. Strouts, F. Thair, S. Dalai, S. Hitchcock, M. Multani, A. Aronson, J. Andermann, T. Yu, A. Yang, S. Holmes, S. Lipkin, W. I. Khatri, P. Relman, D. A. 2019-11-25 doi:10.1101/854182 Cold Spring Harbor Laboratory Press 2019-11-25 <![CDATA[ The Oscillatory ReConstruction Algorithm (ORCA) adaptively identifies frequency bands to improve spectral decomposition in human and rodent neural recordings ]]> https://biorxiv.org/content/10.1101/855288v1?rss=1 Watrous, A. J. Buchanan, R. 2019-11-25 doi:10.1101/855288 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[ Suppression of homeostatic gene expression and increased expression of metabolism-related genes are early features of glaucoma in optic nerve head microglia ]]> https://biorxiv.org/content/10.1101/856427v1?rss=1 Tribble, J. R. Harder, J. M. Williams, P. A. John, S. W. 2019-11-26 doi:10.1101/856427 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Quantitative delineation of herpesviruses in bats for use in ecological studies ]]> https://biorxiv.org/content/10.1101/856518v1?rss=1 Sjodin, A. R. Willig, M. R. Anthony, S. J. 2019-11-26 doi:10.1101/856518 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Cascading Epigenomic Model for GWAS ]]> https://biorxiv.org/content/10.1101/859512v1?rss=1 Ng, B. Casazza, W. Mostafavi, S. 2019-11-29 doi:10.1101/859512 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Digital polymerase chain reaction in an array of microfluidic printed droplets ]]> https://biorxiv.org/content/10.1101/860411v1?rss=1 Men, Y. Li, J. Ao, T. Li, Z. Wu, B. Li, W. Ding, Y. Tseng, K.-H. Tan, W. Pan, T. Li, B. Chen, Y. 2019-12-03 doi:10.1101/860411 Cold Spring Harbor Laboratory Press 2019-12-03 <![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[ Prolonged anesthesia alters brain synaptic architecture ]]> https://biorxiv.org/content/10.1101/862334v1?rss=1 Wenzel, M. Leunig, A. Han, S. Peterka, D. S. Yuste, R. 2019-12-02 doi:10.1101/862334 Cold Spring Harbor Laboratory Press 2019-12-02 <![CDATA[ A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate. ]]> https://biorxiv.org/content/10.1101/863761v1?rss=1 Neupane, R. Pisareva, V. Rodriguez, C. Pisarev, A. Fernandez, I. 2019-12-04 doi:10.1101/863761 Cold Spring Harbor Laboratory Press 2019-12-04 <![CDATA[ Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations ]]> https://biorxiv.org/content/10.1101/864116v1?rss=1 Seitz, E. Acosta-Reyes, F. Schwander, P. Frank, J. 2019-12-03 doi:10.1101/864116 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Increased yields of duplex sequencing data by a series of quality control tools ]]> https://biorxiv.org/content/10.1101/864835v1?rss=1 Povysil, G. Heinzl, M. Salazar, R. Stoler, N. Nekrutenko, A. Tiemann-Boege, I. 2019-12-05 doi:10.1101/864835 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Mitral valve leaflet response to ischemic mitral regurgitation: From gene expression to tissue remodeling ]]> https://biorxiv.org/content/10.1101/864876v1?rss=1 Howsmon, D. P. Rego, B. V. Castillero, E. Ayoub, S. Khalighi, A. H. Gorman, R. C. Gorman, J. H. Ferrari, G. Sacks, M. S. 2019-12-06 doi:10.1101/864876 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing ]]> https://biorxiv.org/content/10.1101/866244v1?rss=1 200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities. ]]> Blattman, S. B. Jiang, W. Oikonomou, P. Tavazoie, S. 2019-12-06 doi:10.1101/866244 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching ]]> https://biorxiv.org/content/10.1101/867754v1?rss=1 Fuller, Z. L. Mocellin, V. J. L. Morris, L. Cantin, N. Shepherd, J. Sarre, L. Peng, J. Liao, Y. Pickrell, J. Andolfatto, P. L. Matz, M. V. Bay, L. K. Przeworski, M. 2019-12-06 doi:10.1101/867754 Cold Spring Harbor Laboratory Press 2019-12-06 <![CDATA[ The connectome of the Caenorhabditis elegans pharynx ]]> https://biorxiv.org/content/10.1101/868513v1?rss=1 Cook, S. J. Crouse, C. M. Yemini, E. Hall, D. H. Emmons, S. W. Hobert, O. 2019-12-08 doi:10.1101/868513 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Brain computation by assemblies of neurons ]]> https://biorxiv.org/content/10.1101/869156v1?rss=1 Vempala, S. Papadimitriou, C. Mitropolsky, D. Collins, M. Maass, W. 2019-12-08 doi:10.1101/869156 Cold Spring Harbor Laboratory Press 2019-12-08 <![CDATA[ Adverse caregiving in infancy blunts neural processing of the mother: Translating across species ]]> https://biorxiv.org/content/10.1101/870261v1?rss=1 Opendak, M. M. Theisen, E. Blomkvist, A. Hollis, K. Lind, T. Sarro, E. Lundstrom, J. N. Tottenham, N. Dozier, M. Wilson, D. Sullivan, R. 2019-12-10 doi:10.1101/870261 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases ]]> https://biorxiv.org/content/10.1101/870527v1?rss=1 Zhao, M. Havrilla, J. M. Fang, L. Chen, Y. Peng, J. Liu, C. Wu, C. Sarmady, M. Botas, P. Isla, J. Lyon, G. Weng, C. Wang, K. 2019-12-10 doi:10.1101/870527 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Fate mapping quantifies the dynamics of B cell development and activation throughout life ]]> https://biorxiv.org/content/10.1101/871624v1?rss=1 Verheijen, M. Rane, S. Yates, A. J. Seddon, B. 2019-12-11 doi:10.1101/871624 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Escherichia coli NusG links the lead ribosome with the transcription elongation complex ]]> https://biorxiv.org/content/10.1101/871962v1?rss=1 Washburn, R. Zuber, P. K. Sun, M. Hashem, Y. Shen, B. Li, W. Harvey, S. Knauer, S. H. Frank, J. Gottesman, M. E. 2019-12-11 doi:10.1101/871962 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Embodied cognition, embodied regulation, and the Data Rate Theorem ]]> https://biorxiv.org/content/10.1101/001586v1?rss=1 Rodrick Wallace 2013-12-23 doi:10.1101/001586 Cold Spring Harbor Laboratory Press 2013-12-23 <![CDATA[ Biochemical ‘Cambrian’ explosion-implosions: the generation and pruning of genetic codes ]]> https://biorxiv.org/content/10.1101/002436v1?rss=1 Rodrick Wallace 2014-02-06 doi:10.1101/002436 Cold Spring Harbor Laboratory Press 2014-02-06 <![CDATA[ Does ‘information control the living state’? ]]> https://biorxiv.org/content/10.1101/003186v1?rss=1 Rodrick Wallace 2014-03-04 doi:10.1101/003186 Cold Spring Harbor Laboratory Press 2014-03-04 <![CDATA[ Metabolic free energy and deterministic-but-for-error biological codes: a ‘Data Rate Theorem’ aging model ]]> https://biorxiv.org/content/10.1101/003384v1?rss=1 Rodrick Wallace 2014-03-17 doi:10.1101/003384 Cold Spring Harbor Laboratory Press 2014-03-17 <![CDATA[ Retrieval-extinction within the memory reconsolidation window does not influence appetitive choice ]]> https://biorxiv.org/content/10.1101/014316v1?rss=1 Akram Bakkour Tom Schonberg Ashleigh Hover Russell Poldrack 2015-01-24 doi:10.1101/014316 Cold Spring Harbor Laboratory Press 2015-01-24 <![CDATA[ Abundant contribution of short tandem repeats to gene expression variation in humans ]]> https://biorxiv.org/content/10.1101/017459v1?rss=1 Melissa Gymrek Thomas Willems Haoyang Zeng Barak Markus Mark J Daly Alkes L Price Jonathan Pritchard Yaniv Erlich 2015-04-02 doi:10.1101/017459 Cold Spring Harbor Laboratory Press 2015-04-02 <![CDATA[ Reactivation of reward-related patterns from single past episodes supports memory-based decision making ]]> https://biorxiv.org/content/10.1101/035196v1?rss=1 G. Elliott Wimmer Christian Buechel 2015-12-24 doi:10.1101/035196 Cold Spring Harbor Laboratory Press 2015-12-24 <![CDATA[ Pain to remember: a single incidental association with pain leads to increased memory for neutral items one year later ]]> https://biorxiv.org/content/10.1101/035212v1?rss=1 G. Elliott Wimmer Christian Buechel 2015-12-24 doi:10.1101/035212 Cold Spring Harbor Laboratory Press 2015-12-24 <![CDATA[ Biological screens from linear codes: theory and tools ]]> https://biorxiv.org/content/10.1101/035352v1?rss=1 Yaniv Erlich Anna Gilbert Hung Ngo Atri Rudra Nicolas Thierry-Mieg Mary Wootters Dina Zielinski Or Zuk 2015-12-25 doi:10.1101/035352 Cold Spring Harbor Laboratory Press 2015-12-25 <![CDATA[ Population-Scale Sequencing Data Enables Precise Estimates of Y-STR Mutation Rates ]]> https://biorxiv.org/content/10.1101/036590v1?rss=1 Thomas Willems Melissa Gymrek G. David Poznik Chris Tyler-Smith The 1000 Genomes Project Chromosome Y Group Yaniv Erlich 2016-01-15 doi:10.1101/036590 Cold Spring Harbor Laboratory Press 2016-01-15 <![CDATA[ Deep mutational scanning reveals tail anchor characteristics important for mitochondrial targeting ]]> https://biorxiv.org/content/10.1101/045351v1?rss=1 Abdurrahman Keskin Emel Akdogan Cory D. Dunn 2016-03-23 doi:10.1101/045351 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets ]]> https://biorxiv.org/content/10.1101/045773v1?rss=1 Apurva Narechania Richard H Baker Rob DeSalle Barun Mathema Barry Kreiswirth Sergios-Orestis Kolokotronis Paul J Planet 2016-03-25 doi:10.1101/045773 Cold Spring Harbor Laboratory Press 2016-03-25 <![CDATA[ Democratizing DNA Fingerprinting ]]> https://biorxiv.org/content/10.1101/061556v1?rss=1 Sophie Zaaijer Assaf Gordon Robert Piccone Daniel Speyer Yaniv Erlich 2016-06-30 doi:10.1101/061556 Cold Spring Harbor Laboratory Press 2016-06-30 <![CDATA[ The Real-time fMRI Neurofeedback Based Stratification of Default Network Regulation Neuroimaging Data Repository. ]]> https://biorxiv.org/content/10.1101/075275v1?rss=1 Amalia McDonald Jordan Muraskin Nicholas Thomas Van Dam Caroline Froehlich Benjamin Puccio John Pellman Clemens CC Bauer Alexis Akeyson Melissa Breland Vince Calhoun Steven Carter Tiffany Chang Chelsea Gessner Alyssa Giannone Steven Giavasis Jamie Glass Steven Homann Margaret King Melissa Kramer Drew Landis Alexis Lieval Jonathan Lisinski Anna MacKay-Brandt Brittny Miller Laura Panek Hayley Reed Christine Santiago Eszter Schoell Richard Sinning Melissa Sital Elise Taverna Russell Tobe Kristin Trautmann Betty Varghese Lauren Walden Runtang Wang Abigail B Waters Dylan C Wood F. Xavier Castellano 2016-09-15 doi:10.1101/075275 Cold Spring Harbor Laboratory Press 2016-09-15 <![CDATA[ Human anterolateral entorhinal cortex volumes are associated with preclinical cognitive decline ]]> https://biorxiv.org/content/10.1101/080374v1?rss=1 Rosanna K Olsen Lok-Kin Yeung Alix Noly-Gandon Maria C D'Angelo Arber Kacollja Victoria Smith Jennifer D Ryan Morgan D Barense 2016-10-12 doi:10.1101/080374 Cold Spring Harbor Laboratory Press 2016-10-12 <![CDATA[ A framework to interpret short tandem repeat variation in humans ]]> https://biorxiv.org/content/10.1101/092734v1?rss=1 Gymrek, M. Willems, T. Erlich, Y. Reich, D. E. 2016-12-09 doi:10.1101/092734 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ VIRUS-HOST INFECTION DYNAMICS OF MARINE SINGLE-CELLED EUKARYOTES RESOLVED FROM METATRANSCRIPTOMICS ]]> https://biorxiv.org/content/10.1101/093716v1?rss=1 Moniruzzaman, M. Wurch, L. L. Alexander, H. Dyhrman, S. T. Gobler, C. J. Wilhelm, S. W. 2016-12-13 doi:10.1101/093716 Cold Spring Harbor Laboratory Press 2016-12-13 <![CDATA[ Bacterial tail anchors can target to the mitochondrial outer membrane ]]> https://biorxiv.org/content/10.1101/111716v1?rss=1 Bal, G. L. Keskin, A. Seferoglu, A. B. Dunn, C. D. 2017-02-25 doi:10.1101/111716 Cold Spring Harbor Laboratory Press 2017-02-25 <![CDATA[ H3K27me3-mediated silencing of Wilms Tumor 1 supports the proliferation of brain tumor cells harboring the H3.3K27M mutation ]]> https://biorxiv.org/content/10.1101/114082v1?rss=1 Fang, D. Gan, H. Cheng, L. Lee, J.-H. Zhou, H. Sarkaria, J. N. Daniels, D. J. Zhang, Z. 2017-03-06 doi:10.1101/114082 Cold Spring Harbor Laboratory Press 2017-03-06 <![CDATA[ Reinforcement learning over time: spaced versus massed training establishes stronger value associations ]]> https://biorxiv.org/content/10.1101/158964v1?rss=1 Wimmer, G. E. Poldrack, R. A. 2017-07-03 doi:10.1101/158964 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Skin photoreceptors in the leopard frog ]]> https://biorxiv.org/content/10.1101/161364v1?rss=1 Wald, G. Rayport, S. 2017-07-09 doi:10.1101/161364 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ Major flaws in "Identification of individuals by trait prediction using whole-genome" ]]> https://biorxiv.org/content/10.1101/185330v1?rss=1 Erlich, Y. 2017-09-06 doi:10.1101/185330 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Effects of mechanical loading on cortical defect repair using a novel mechanobiological model of bone healing ]]> https://biorxiv.org/content/10.1101/190819v1?rss=1 Liu, C. Carrera, R. Flamini, V. Kenny, L. Cabahug-Zuckerman, P. George, B. Hunter, D. Liu, B. Singh, G. Leucht, P. Mann, K. A. Helms, J. A. Castillo, A. B. 2017-09-19 doi:10.1101/190819 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9 ]]> https://biorxiv.org/content/10.1101/195776v1?rss=1 Guo, X. Chavez, A. Tung, A. Chan, Y. Cecchi, R. Lopez Garnier, S. Kaas, C. Kelsic, E. Schubert, M. DiCarlo, J. Collins, J. Church, G. 2017-09-29 doi:10.1101/195776 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis ]]> https://biorxiv.org/content/10.1101/2019.12.14.850305v1?rss=1 Han, W. Ma, X. Balibar, C. J. Baxter Rath, C. M. Benton, B. Bermingham, A. Casey, F. Chi-Leon, B. Cho, M.-K. Frank, A. O. Frommlet, A. Ho, C.-M. Lee, P. S. Li, M. Lingel, A. Ma, S. Merritt, H. Ornelas, E. de Pascale, G. Prathapam, R. Prosen, K. R. Rasper, D. Ruzin, A. Sawyer, W. Shaul, J. Shen, X. Shia, S. Steffek, M. Subramanian, S. Vo, J. Wang, F. Wartchow, C. Uehara, T. 2019-12-15 doi:10.1101/2019.12.14.850305 Cold Spring Harbor Laboratory Press 2019-12-15 <![CDATA[ Loss of Tsc1 from striatal direct pathway neurons impairs endocannabinoid-LTD and enhances motor routine learning ]]> https://biorxiv.org/content/10.1101/2019.12.15.877126v1?rss=1 Benthall, K. N. Cording, K. R. Agopyan-Miu, A. H. C. W. Chen, E. Y. Bateup, H. S. 2019-12-16 doi:10.1101/2019.12.15.877126 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Phenotypic delay: mechanistic models and their implications for the evolution of resistance to antibiotics ]]> https://biorxiv.org/content/10.1101/2019.12.19.883132v1?rss=1 Carballo-Pacheco, M. Nicholson, M. D. Lilja, E. E. Allen, R. J. Waclaw, B. 2019-12-20 doi:10.1101/2019.12.19.883132 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Online analysis of microendoscopic 1-photon calcium imaging data streams ]]> https://biorxiv.org/content/10.1101/2020.01.31.929141v1?rss=1 Friedrich, J. Giovannucci, A. Pnevmatikakis, E. A. 2020-01-31 doi:10.1101/2020.01.31.929141 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Both DNA binding domains of p53 are required for its ultra rapid recruitment to sites of UV damage ]]> https://biorxiv.org/content/10.1101/2020.02.09.938993v1?rss=1 Wang, Y.-H. Ho, T. Hariharan, A. Goh, H. C. Sheetz, M. Lane, D. 2020-02-10 doi:10.1101/2020.02.09.938993 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Hippocampal and cortical mechanisms at retrieval explain variability in episodic remembering in older adults ]]> https://biorxiv.org/content/10.1101/2020.02.11.940668v1?rss=1 Trelle, A. N. Carr, V. A. Guerin, S. A. Thieu, M. K. Jayakumar, M. Guo, W. Nadiadwala, A. Corso, N. K. Hunt, M. P. Litovsky, C. P. Tanner, N. J. Deutsch, G. K. Bernstein, J. D. Harrison, M. B. Khazenzon, A. M. Jiang, J. Sha, S. J. Fredericks, C. A. Rutt, B. K. Mormino, E. C. Kerchner, G. A. Wagner, A. D. 2020-02-12 doi:10.1101/2020.02.11.940668 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Allosteric action of nucleotides on Hsp90 across several time- and length scales ]]> https://biorxiv.org/content/10.1101/2020.02.15.950725v1?rss=1 Wolf, S. Sohmen, B. Hellenkamp, B. Thurn, J. Stock, G. Hugel, T. 2020-02-16 doi:10.1101/2020.02.15.950725 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ Accelerated single cell seeding in relapsed multiple myeloma ]]> https://biorxiv.org/content/10.1101/2020.02.25.963272v1?rss=1 Landau, H. J. Yellapantula, V. Diamond, B. J. Rustad, E. H. Maclachlan, K. Gundem, G. Medina-Martinez, J. Arango Ossa, J. E. Levine, M. Zhou, Y. Rajya, K. L. Baez, P. Attiyeh, M. Makohon-Moore, A. Zhang, L. Boyle, E. E. Ashby, C. Blaney, P. Patel, M. Zhang, Y. Dogan, A. Chung, D. Giralt, S. Lahoud, O. B. Peled, J. Scordo, M. Shah, G. Hassoun, H. Korde, N. S. Lesokhin, A. M. Lu, S. Mailankody, S. Shah, U. A. Smith, E. Hultcrantz, M. L. Ulaner, G. van Rhee, F. Morgan, G. Landgren, O. Papaemmanuil, E. Iacobuzio-Donahue, C. A. Maura, F. 2020-02-26 doi:10.1101/2020.02.25.963272 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Phosphorylation barcode-dependent signal bias of the dopamine D1 receptor ]]> https://biorxiv.org/content/10.1101/2020.03.03.971846v1?rss=1 Kaya, A. I. Perry Hauser, N. Gurevich, V. V. Iverson, T. 2020-03-04 doi:10.1101/2020.03.03.971846 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Force-dependent Piezo1 recruitment to focal adhesions regulates adhesion maturation and turnover specifically in non-transformed cells ]]> https://biorxiv.org/content/10.1101/2020.03.09.972307v1?rss=1 Yao, M. Tijore, A. S. Cox, C. D. Hariharan, A. Tran Van Nhieu, G. Martinac, B. Sheetz, M. 2020-03-09 doi:10.1101/2020.03.09.972307 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ A surface metric and software toolbox for EEG electrode grids in the macaque ]]> https://biorxiv.org/content/10.1101/2020.03.10.986588v1?rss=1 Li, F. Teichert, T. 2020-03-12 doi:10.1101/2020.03.10.986588 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Reward learning and working memory: effects of massed versus spaced training and post-learning delay period ]]> https://biorxiv.org/content/10.1101/2020.03.19.997098v1?rss=1 Wimmer, G. E. Poldrack, R. A. 2020-03-20 doi:10.1101/2020.03.19.997098 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Recollection-related hippocampal fMRI effects predict longitudinal memory change in healthy older adults ]]> https://biorxiv.org/content/10.1101/2020.03.19.999060v1?rss=1 Hou, M. de Chastelaine, M. Jayakumar, M. Donley, B. E. Rugg, M. D. 2020-03-20 doi:10.1101/2020.03.19.999060 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Genetic architecture of a mutation's expressivity and penetrance ]]> https://biorxiv.org/content/10.1101/2020.04.03.024547v1?rss=1 Schell, R. Mullis, M. N. Matsui, T. Foree, R. Ehrenreich, I. M. 2020-04-05 doi:10.1101/2020.04.03.024547 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Concerted action of kinesin-1 KIF5B and kinesin-3 KIF13B promotes efficient transport of exocytotic vesicles to microtubule plus ends ]]> https://biorxiv.org/content/10.1101/2020.04.06.027862v1?rss=1 Serra-Marques, A. Martin, M. Katrukha, E. A. Grigoriev, I. Peeters, C. A. E. Liu, Q. Hooikaas, P. J. Yao, Y. Smal, I. Pedersen, L. B. Meijering, E. A. Kapitein, L. C. Akhmanova, A. 2020-04-07 doi:10.1101/2020.04.06.027862 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ RNA matchmaking remodels lncRNA structure and promotes PRC2 activity ]]> https://biorxiv.org/content/10.1101/2020.04.13.040071v1?rss=1 Balas, M. M. Hartwick, E. W. Barrington, C. Roberts, J. T. Wu, S. K. Bettcher, R. Griffin, A. M. Kieft, J. S. Johnson, A. M. 2020-04-14 doi:10.1101/2020.04.13.040071 Cold Spring Harbor Laboratory Press 2020-04-14 <![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[ Breakage of the Oligomeric CaMKII Hub by the Regulatory Segment of the Kinase ]]> https://biorxiv.org/content/10.1101/2020.04.15.043067v1?rss=1 Karandur, D. Bhattacharyya, M. Xia, Z. Lee, Y. K. Muratcioglu, S. McAffee, D. McSpadden, E. Qiu, B. Groves, J. T. Williams, E. R. Kuriyan, J. 2020-04-16 doi:10.1101/2020.04.15.043067 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Predicting the Viability of Beta-Lactamase: How Folding and Binding Free Energies Correlate with Beta-Lactamase Fitness ]]> https://biorxiv.org/content/10.1101/2020.04.15.043661v1?rss=1 Yang, J. Naik, N. Patel, J. S. Wylie, C. S. Gu, W. Huang, J. Ytreberg, F. M. Naik, M. T. Weinreich, D. M. Rubenstein, B. M. 2020-04-16 doi:10.1101/2020.04.15.043661 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Astrocytes and neurons share brain region-specific transcriptional signatures ]]> https://biorxiv.org/content/10.1101/2020.04.21.038737v1?rss=1 Herrero-Navarro, A. Puche-Aroca, L. Moreno-Juan, V. Sempere-Ferrandez, A. Espinosa, A. Susin, R. Torres-Masjoan, L. Leyva-Diaz, E. Karow, M. Figueres-Onate, M. Lopez-Mascaraque, L. Lopez-Atalaya, J. P. Berninger, B. Lopez-Bendito, G. 2020-04-22 doi:10.1101/2020.04.21.038737 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Latrophilin 2 controls vascular morphogenesis and function by inhibiting endothelial cell adhesion and YAP/TAZ mechanosignaling ]]> https://biorxiv.org/content/10.1101/2020.04.28.065979v1?rss=1 Camillo, C. Facchinello, N. Villari, G. Gays, D. Gioelli, N. Sandri, C. Arese, M. Tamagnone, L. Valdembri, D. Santoro, M. M. Serini, G. G. 2020-04-28 doi:10.1101/2020.04.28.065979 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Therapeutic remodeling of CBP transcription factor complex controls oncogenic gene expression in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2020.05.05.077156v1?rss=1 Forbes, L. Cifani, P. Minuesa, G. Chen, C. Takao, S. Kharas, M. G. Koche, R. P. Kentsis, A. 2020-05-05 doi:10.1101/2020.05.05.077156 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Tolerance induction in memory CD4 T cells is partial and reversible ]]> https://biorxiv.org/content/10.1101/2020.05.25.114785v1?rss=1 Gray, J. I. Al Khabouri, S. Morton, F. Clambey, E. Gapin, L. Matsuda, J. L. Kappler, J. W. Marrack, P. Garside, P. Otto, T. D. MacLeod, M. K. 2020-05-27 doi:10.1101/2020.05.25.114785 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Reactivation of pain-related patterns in the hippocampus from single past episodes relates to successful memory-based decision making ]]> https://biorxiv.org/content/10.1101/2020.05.29.123893v1?rss=1 Wimmer, G. E. Buechel, C. 2020-05-31 doi:10.1101/2020.05.29.123893 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ ATAV - a comprehensive platform for population-scale genomic analyses ]]> https://biorxiv.org/content/10.1101/2020.06.08.136507v1?rss=1 Ren, Z. Povysil, G. Goldstein, D. B. 2020-06-09 doi:10.1101/2020.06.08.136507 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Membrane Insertion of MoS2 Nanosheets: Fresh vs. Aged ]]> https://biorxiv.org/content/10.1101/2020.06.17.158378v1?rss=1 Ye, R. Song, W. Gu, Z. Zhou, R. 2020-06-18 doi:10.1101/2020.06.17.158378 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Structural Consequences of the Villin Headpiece Interaction with a Carbon Nitride Polyaniline (C3N) Nanosheet ]]> https://biorxiv.org/content/10.1101/2020.06.17.158402v1?rss=1 Gu, Z. Perez-Aguilar, J. M. Zhou, R. 2020-06-19 doi:10.1101/2020.06.17.158402 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Dynamic extrinsic pacing of the HOX clock in human axial progenitors controls motor neuron subtype specification ]]> https://biorxiv.org/content/10.1101/2020.06.27.175646v1?rss=1 Mouilleau, V. Vaslin, C. Gribaudo, S. Robert, R. Nicolas, N. Jarrige, M. Terray, A. Lesueur, L. Mathis, M. W. Croft, G. Daynac, M. ROUILLER-FABRE, V. Wichterle, H. Ribes, V. Martinat, C. Nedelec, S. 2020-06-27 doi:10.1101/2020.06.27.175646 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Interplay between UNG and AID governs intratumoral heterogeneity in mature B cell lymphoma ]]> https://biorxiv.org/content/10.1101/2020.06.29.177303v1?rss=1 Ramiro, A. R. Delgado, P. Alvarez-Prado, A. Marina-Zarate, E. Sernandez, I. Mur, S. M. de la Barrera, J. Sanchez-Cabo, F. Canamero, M. de Molina, A. Belver, L. de Yebenes, V. G. 2020-06-29 doi:10.1101/2020.06.29.177303 Cold Spring Harbor Laboratory Press 2020-06-29 <![CDATA[ Stabilization of β-catenin promotes melanocyte specification at the expense of the Schwann cell lineage ]]> https://biorxiv.org/content/10.1101/2020.06.29.179291v1?rss=1 Colombo, S. Petit, V. Wagner, R. Y. Champeval, D. Yajima, I. Gesbert, F. Davidson, I. Delmas, V. Larue, L. 2020-06-30 doi:10.1101/2020.06.29.179291 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ Lateral Hypothalamic GABAergic neurons encode and potentiate sucrose palatability ]]> https://biorxiv.org/content/10.1101/2020.06.30.180646v1?rss=1 Garcia, A. Coss, A. Luis-Islas, J. Puron-Sierra, L. Luna, M. Villavicencio, M. Gutierrez, R. 2020-07-02 doi:10.1101/2020.06.30.180646 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ Microbiome Dynamics of Bovine Mastitis Progression and Genomic Determinants ]]> https://biorxiv.org/content/10.1101/2020.07.13.200808v1?rss=1 H>RCM>SCM). PS analysis identified 385, 65, 80 and 144 bacterial strains in CM, RCM, SCM, and H milk, respectively, with an inclusion of 67.19% previously unreported opportunistic strains in mastitis metagenomes. Moreover, MR detected 56, 13, 9 and 46 archaeal, and 40, 24, 11 and 37 viral genera in CM, RCM, SCM and H-milk metagenomes, respectively. The CM-microbiomes had closest association with RCM-microbiomes followed by SCM, and H-microbiomes. Furthermore, we identified 333, 304, 183 and 50 virulence factors-associated genes (VFGs), and 48, 31, 11 and 6 antibiotic resistance genes (AGRs) in CM, RCM, SCM, and H-microbiomes, respectively, showing a significant correlation between the relative abundances of VFGs (p = 0.001), ARGs (p = 0.0001), and associated bacterial taxa. We also detected correlated variations in the presence and abundance of several metabolic functional genes related to bacterial colonization, proliferation, chemotaxis, motility and invasion, oxidative stress, virulence and pathogenicity, phage integration and excision, biofilm-formation, and quorum-sensing to be associated with different episodes of mastitis. Therefore, profiling the dynamics of microbiome in different states of mastitis, concurrent VFGs, ARGs, and genomic functional correlations will contribute to developing microbiome-based diagnostics and therapeutics for bovine mastitis, and carries significant implications on curtailing the economic fallout from this disease. ]]> Hoque, M. N. Istiaq, A. Rahman, M. S. Islam, M. R. Anwar, A. Siddiki, A. Z. Sultana, M. Crandall, K. A. Hossain, M. A. 2020-07-13 doi:10.1101/2020.07.13.200808 Cold Spring Harbor Laboratory Press 2020-07-13 <![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[ Single-cell identity definition using random forests and recursive feature elimination (scRFE) ]]> https://biorxiv.org/content/10.1101/2020.08.03.233650v1?rss=1 Park, M. Vorperian, S. Wang, S. Pisco, A. O. 2020-08-04 doi:10.1101/2020.08.03.233650 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Methods for detecting PER2::LUCIFERASE bioluminescence rhythms in freely moving mice ]]> https://biorxiv.org/content/10.1101/2020.08.24.264531v1?rss=1 Martin-Burgos, B. Wang, W. William, I. Tir, S. Mohammad, I. Javed, R. Smith, S. Cui, Y. Smith, C. van der Vinne, V. Molyneux, P. C. Miller, S. C. Weaver, D. R. Leise, T. L. Harrington, M. 2020-08-24 doi:10.1101/2020.08.24.264531 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis ]]> https://biorxiv.org/content/10.1101/2020.09.14.295923v1?rss=1 Lucilla, P. Lasser, M. Yusuff, T. Jensen, M. Ingraham, P. Huber, E. Singh, M. D. Monahan, C. Iyer, J. Desai, I. Karthikeyan, S. Gould, D. J. Yennawar, S. Weiner, A. T. Krishnan, A. Rolls, M. Lowery, L. A. Girirajan, S. 2020-09-14 doi:10.1101/2020.09.14.295923 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ SSMD: A semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data ]]> https://biorxiv.org/content/10.1101/2020.09.22.309278v1?rss=1 Lu, X. Tu, S.-W. Chang, W. Wan, C. Wang, J. Zang, Y. Ramdas, B. Kapur, R. Lu, X. Cao, S. Zhang, C. 2020-09-23 doi:10.1101/2020.09.22.309278 Cold Spring Harbor Laboratory Press 2020-09-23 <![CDATA[ scFEA: A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2020.09.23.310656v1?rss=1 Alghamdi, N. Chang, W. Dang, P. Lu, X. Wan, C. Huang, Z. Wang, J. Fishel, M. L. Cao, S. Zhang, C. 2020-09-24 doi:10.1101/2020.09.23.310656 Cold Spring Harbor Laboratory Press 2020-09-24 <![CDATA[ ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins ]]> https://biorxiv.org/content/10.1101/2020.09.24.298851v1?rss=1 Ayyappan, V. Wat, R. Barber, C. Vivelo, C. Gauch, K. Visanpattanasin, P. Cook, G. Sazeides, C. Leung, A. K. L. 2020-09-25 doi:10.1101/2020.09.24.298851 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Ultrasound-mediated mechanical forces selectively kill tumor cells ]]> https://biorxiv.org/content/10.1101/2020.10.09.332726v1?rss=1 Tijore, A. Margadant, F. Yao, M. Hariharan, A. Chew, C. A. Z. Powell, S. Bonney, G. K. Sheetz, M. 2020-10-09 doi:10.1101/2020.10.09.332726 Cold Spring Harbor Laboratory Press 2020-10-09 <![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[ Isoform-specific roles of the Drosophila filamin-type protein Jitterbug (Jbug) during development ]]> https://biorxiv.org/content/10.1101/2020.10.13.337626v1?rss=1 Chung, S. Le, T. P. Vishwakarma, V. Cheng, Y. L. Andrew, D. J. 2020-10-14 doi:10.1101/2020.10.13.337626 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ A multimodal cell census and atlas of the mammalian primary motor cortex ]]> https://biorxiv.org/content/10.1101/2020.10.19.343129v1?rss=1 BRAIN Initiative Cell Census Network (BICCN), Adkins, R. S. Aldridge, A. I. Allen, S. Ament, S. A. An, X. Armand, E. Ascoli, G. A. Bakken, T. E. Bandrowski, A. Banerjee, S. Barkas, N. Bartlett, A. Bateup, H. S. Behrens, M. M. Berens, P. Berg, J. Bernabucci, M. Bernaerts, Y. Bertagnolli, D. Biancalani, T. Boggeman, L. Booeshaghi, A. S. Bowman, I. Bravo, H. C. Cadwell, C. R. Callaway, E. M. Carlin, B. O'Connor, C. Carter, R. Casper, T. Castanon, R. G. Castro, J. R. Chance, R. K. Chatterjee, A. Chen, H. Chun, J. Colantuoni, C. Crabtree, J. Creasy, H. Cric 2020-10-21 doi:10.1101/2020.10.19.343129 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ The Histone Chaperone CAF-1 Sustains Myeloid Lineage Identity ]]> https://biorxiv.org/content/10.1101/2020.10.22.350447v1?rss=1 Guo, Y. Ji, F. Murn, J. Frankhouser, D. Blanco, A. Chiem, C. Jang, M. Sadreyev, R. Rockne, R. Sykes, D. Hochedlinger, K. Cheloufi, S. 2020-10-22 doi:10.1101/2020.10.22.350447 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Single-cell RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates and humans ]]> https://biorxiv.org/content/10.1101/2020.11.05.367482v1?rss=1 Bakken, T. E. van Velthoven, C. T. J. Menon, V. Hodge, R. D. Yao, Z. Nguyen, T. N. Graybuck, L. T. Horwitz, G. D. Bertagnolli, D. Goldy, J. Garren, E. Parry, S. Casper, T. Shehata, S. I. Barkan, E. R. Szafer, A. Levi, B. P. Dee, N. Smith, K. A. Sunkin, S. M. Bernard, A. Phillips, J. W. Hawrylycz, M. Koch, C. Murphy, G. Lein, E. Zeng, H. Tasic, B. 2020-11-06 doi:10.1101/2020.11.05.367482 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ Mutations in the juxtamembrane segment of the cholesterol-binding site of APP alter its processing and promotes production of shorter, less toxic Aβ peptides. ]]> https://biorxiv.org/content/10.1101/2020.11.16.384891v1?rss=1 Hanbouch, L. Schaack, B. Kasri, A. Fontaine, G. Gkanatsiou, E. Brinkmalm, G. Portelius, E. Blennow, K. Mourier, G. Gilles, N. Millan, M. J. Marquer, C. Zetterberg, H. Boussicault, L. Potier, M.-C. 2020-11-16 doi:10.1101/2020.11.16.384891 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Precise spatiotemporal control of voltage-gated sodium channels by photocaged saxitoxin ]]> https://biorxiv.org/content/10.1101/2020.11.18.389130v1?rss=1 Elleman, A. V. Devienne, G. Makinson, C. D. Haynes, A. L. Huguenard, J. R. Du Bois, J. 2020-11-20 doi:10.1101/2020.11.18.389130 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ A human stem cell-derived neurosensory-epithelial circuitry on-a-chip to model herpes simplex virus reactivation ]]> https://biorxiv.org/content/10.1101/2020.11.19.390260v1?rss=1 Mazzara, P. G. Criscuolo, E. Rasponi, M. Massimino, L. Muggeo, S. Palma, C. Castelli, M. Clementi, M. Burioni, R. Mancini, N. Broccoli, V. Clementi, N. 2020-11-19 doi:10.1101/2020.11.19.390260 Cold Spring Harbor Laboratory Press 2020-11-19 <![CDATA[ Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures ]]> https://biorxiv.org/content/10.1101/2020.11.30.404947v1?rss=1 DING, H. Anastopoulos, I. Bailey, A. D. Paten, B. Stuart, J. 2020-12-02 doi:10.1101/2020.11.30.404947 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Early cis-regulatory events in the formation of retinal horizontal cells ]]> https://biorxiv.org/content/10.1101/2020.12.02.409003v1?rss=1 Schick, E. Gonzalez, K. C. Dutta, P. Hossain, K. Ghinia Tegla, M. G. Emerson, M. M. 2020-12-03 doi:10.1101/2020.12.02.409003 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Cell type-specific isolation and transcriptomic profiling informs glial pathology in human temporal lobe epilepsy ]]> https://biorxiv.org/content/10.1101/2020.12.11.421370v1?rss=1 Tome-Garcia, J. Nudelman, G. Mussa, Z. Caballero, E. Jiang, Y. Beaumont, K. G. Wang, Y.-C. Sebra, R. G. Akbarian, S. Pinto, D. Zaslavsky, E. Tsankova, N. M. 2020-12-12 doi:10.1101/2020.12.11.421370 Cold Spring Harbor Laboratory Press 2020-12-12 <![CDATA[ Total recall: episodic memory retrieval,choice, and memory confidence in the rat ]]> https://biorxiv.org/content/10.1101/2020.12.14.420174v1?rss=1 Joo, H. R. Liang, H. Chung, J. E. Geaghan-Breiner, C. Fan, J. L. Nachman, B. Kepecs, A. Frank, L. M. 2020-12-15 doi:10.1101/2020.12.14.420174 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure ]]> https://biorxiv.org/content/10.1101/2021.01.13.426578v1?rss=1 Li, H. Wang, S. Lee, F.-H. Roark, R. S. Murphy, A. I. Smith, J. Zhao, C. Rando, J. Chohan, N. Ding, Y. Kim, E. Lindemuth, E. Bar, K. J. Pandrea, I. Apetrei, C. Keele, B. F. Lifson, J. D. Lewis, M. G. Denny, T. N. Haynes, B. F. Hahn, B. H. Shaw, G. M. 2021-01-13 doi:10.1101/2021.01.13.426578 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Implant- and anesthesia-related factors affecting threshold intensities for vagus nerve stimulation ]]> https://biorxiv.org/content/10.1101/2021.01.22.427329v1?rss=1 Ahmed, U. Chang, Y.-C. Lopez, M. Wong, J. Datta-Chaudhuri, T. Rieth, L. Al-Abed, Y. Zanos, S. 2021-01-26 doi:10.1101/2021.01.22.427329 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Transcriptome variation in human tissues revealed by long-read sequencing ]]> https://biorxiv.org/content/10.1101/2021.01.22.427687v1?rss=1 Glinos, D. A. Garborcauskas, G. Hoffman, P. Ehsan, N. Jiang, L. Gokden, A. Dai, X. Aguet, F. Brown, K. L. Garimella, K. Bowers, T. Costello, M. Ardlie, K. Jian, R. Tucker, N. R. Ellinor, P. T. Harrington, E. D. Tang, H. Snyder, M. Juul, S. Mohammadi, P. MacArthur, D. G. Lappalainen, T. Cummings, B. 2021-01-23 doi:10.1101/2021.01.22.427687 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ Adenosine metabolized from extracellular ATP promotes type 2 immunity through triggering A2BAR signaling on intestinal epithelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.24.428000v1?rss=1 El-Naccache, d. w. chen, f. palma, m. lemenze, a. Wu, w. mishra, p. eltzshig, h. robson, s. c. Di Virgilio, f. Hasko, G. gause, w. 2021-01-26 doi:10.1101/2021.01.24.428000 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Notch-Jagged signaling complex defined by an interaction mosaic ]]> https://biorxiv.org/content/10.1101/2021.02.19.432005v1?rss=1 Zeronian, M. R. Klykov, O. Portell i de Montserrat, J. Konijnenberg, M. J. Gaur, A. Scheltema, R. A. Janssen, B. J. C. 2021-02-19 doi:10.1101/2021.02.19.432005 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Transgenic mice for in vivo epigenome editing with CRISPR-based systems ]]> https://biorxiv.org/content/10.1101/2021.03.08.434430v1?rss=1 Gemberling, M. Siklenka, K. Rodriguez, E. Eisinger, K. Barrera, A. Liu, F. Kantor, A. Li, L. Cigliola, V. Hazlett, M. Williams, C. Bartelt, L. Bodle, J. Daniels, H. Rouse, C. Hilton, I. Madigan, V. Asokan, A. Ciofani, M. Poss, K. Reddy, T. E. West, A. Gersbach, C. 2021-03-08 doi:10.1101/2021.03.08.434430 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Stromal inflammation is a targetable driver of hematopoietic aging ]]> https://biorxiv.org/content/10.1101/2021.03.08.434485v1?rss=1 Verovskaya, E. V. Mitchell, C. A. Calero-Nieto, F. J. Herault, A. Dellorusso, P. D. Wang, X. Zhang, S. Y. Flohr Svendsen, A. Pietras, E. M. Bakker, S. T. Ho, T. T. Gottgens, B. Passegue, E. 2021-03-09 doi:10.1101/2021.03.08.434485 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ Divergent epigenetic profiles from two differentially impacted wild populationsof estuarine cordgrass (Sporobolus alterniflorus) ]]> https://biorxiv.org/content/10.1101/2021.03.22.436412v1?rss=1 DeCarlo, L. Meckler, F. Hans, M. Kelemen, S. Magun, H. Noah, M. Pappajohn, L. Anderson, N. Berger, R. Berkel, J. Brooke, N. Chen, L. Chijioke, O. Dewees, N. Faulkner, P. Frank, J. Holzman, W. Marino, V. Ravaschiere, A. Wang, Y. Williams, A. Williams, Z. Gentile, D. Cox, R. 2021-03-22 doi:10.1101/2021.03.22.436412 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.03.23.436694v1?rss=1 Jimenez, D. S. Kim, J. Ragipani, B. Zhang, B. Street, L. A. Kramer, M. Albritton, S. E. Winterkorn, L. Ercan, S. 2021-03-24 doi:10.1101/2021.03.23.436694 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ The lysine-rich intracellular loop and cell type-specific co-factors are required for IFITM3 antiviral immunity in hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2021.04.06.438585v1?rss=1 Unali, G. Giordano, A. M. S. Cuccovillo, I. Abou Alezz, M. Apolonia, L. Merelli, I. Malim, M. M. Petrillo, C. Kajaste-Rudnitski, A. 2021-04-07 doi:10.1101/2021.04.06.438585 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ A general approach for stabilizing nanobodies for intracellular expression ]]> https://biorxiv.org/content/10.1101/2021.04.06.438746v1?rss=1 Dingus, J. G. Tang, J. C. Y. Cepko, C. L. 2021-04-08 doi:10.1101/2021.04.06.438746 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Intrinsic Timescales Across the Basal Ganglia ]]> https://biorxiv.org/content/10.1101/2021.04.07.438040v1?rss=1 Nougaret, S. Fascianelli, V. Ravel, S. Genovesio, A. 2021-04-07 doi:10.1101/2021.04.07.438040 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding ]]> https://biorxiv.org/content/10.1101/2021.04.11.438056v1?rss=1 Breimann, L. Morao, A. K. Kim, J. Jimenez, D. Maryn, N. Bikkasani, K. Carrozza, M. J. Albritton, S. E. Kramer, M. Street, L. A. Cerimi, K. Schumann, V.-F. Bahry, E. Preibisch, S. Woehler, A. Ercan, S. 2021-04-12 doi:10.1101/2021.04.11.438056 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Integrative Clinical and Molecular Characterization of Translocation Renal Cell Carcinoma ]]> https://biorxiv.org/content/10.1101/2021.04.14.439908v1?rss=1 Bakouny, Z. Sadagopan, A. Ravi, P. Metaferia, N. Y. Li, J. AbuHammad, S. Tang, S. Denize, T. Garner, E. R. Gao, X. Braun, D. A. Hirsch, L. Steinharter, J. A. Bouchard, G. Walton, E. West, D. Labaki, C. Dudani, S. Gan, C.-L. Sethunath, V. Carvalho, F. L. Imamovic, A. Ricker, C. Vokes, N. I. Nyman, J. Park, J. Hirsch, M. S. Haq, R. Lee, G.-S. M. McGregor, B. A. Chang, S. L. Feldman, A. S. Wu, C. J. McDermott, D. F. Heng, D. Y. C. Signoretti, S. Van Allen, E. M. Choueiri, T. K. Viswanathan, S. R. 2021-04-15 doi:10.1101/2021.04.14.439908 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Regulation of Vg1 biogenesis during mesendoderm induction ]]> https://biorxiv.org/content/10.1101/2021.04.25.441333v1?rss=1 Dingal, P. C. D. P. Carte, A. N. Montague, T. G. Schier, A. F. 2021-04-26 doi:10.1101/2021.04.25.441333 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ EOMES is responsible for WNT memory and can substitute for WNT in mesendoderm specification ]]> https://biorxiv.org/content/10.1101/2021.05.01.442278v1?rss=1 Yoney, A. Bai, L. Brivanlou, A. H. Siggia, E. D. 2021-05-01 doi:10.1101/2021.05.01.442278 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ High-Stability Polyimide-based Flexible Electrodes with IrOx to Interface the Mouse Vagus Nerve ]]> https://biorxiv.org/content/10.1101/2021.05.10.442867v1?rss=1 7x. PI encapsulation had stable impedance spectra for at least 336 days for interdigitated electrodes. Stim-Stab testing using an aggressive paradigm and rigorous optical and electrical characterization, revealed that half of electrodes showed less than minor damage at the endpoints. A trend of decreasing respiratory rate with stimulation current reached statistical significance at 500 {micro}A, demonstrating efficacy for Flex electrodes. SignificanceFlex electrodes offer demonstrated efficacy, low impedance (443 {+/-} 32 {Omega} at 103 Hz), excellent bench test stability, and cost-effective fabrication. Acute devices are easy to integrate, and mechanically robust chronic devices will be investigated in vivo in future studies. These characteristics make the electrodes well-positioned to advance bioelectronics medicine research by 1) enabling reliable studies with statistically relevant populations of acute mouse models, and 2) offering the potential for a technology that can be used in chronic studies, which scales to very small nerves. ]]> Sun, T. Falcone, J. D. Crosfield, C. Lopez, M. F. Peragine, J. Modi, R. Sharma, R. Baker, B. Anderson, G. Savani, S. Li, C. Chang, E. H. Sohal, H. Rieth, L. 2021-05-11 doi:10.1101/2021.05.10.442867 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Slow Cortical Waves via Cyclicity ]]> https://biorxiv.org/content/10.1101/2021.05.16.444387v1?rss=1 Abraham, I. Shahsavarani, B. Zimmerman, B. Husain, F. baryshnikov, y. 2021-05-17 doi:10.1101/2021.05.16.444387 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ The Telomere Length Landscape of Localized Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2021.05.22.445239v1?rss=1 Livingstone, J. Shiah, Y.-J. Yamaguchi, T. N. Heisler, L. E. Huang, V. Lesurf, R. Drysdale, E. Green, J. van der Kwast, T. Bristow, R. G. Fraser, M. Boutros, P. C. 2021-05-25 doi:10.1101/2021.05.22.445239 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Measuring the metabolic evolution of glioblastoma throughout tumor development, regression, and recurrence with hyperpolarized magnetic resonance ]]> https://biorxiv.org/content/10.1101/2021.06.10.447987v1?rss=1 Salzillo, T. C. Mawoneke, V. Weygand, J. Shetty, A. Gumin, J. Zacharias Millward, N. M. Gammon, S. T. Piwnica-Worms, D. Fuller, G. N. Logothetis, C. J. Lang, F. F. Bhattacharya, P. K. 2021-06-11 doi:10.1101/2021.06.10.447987 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota ]]> https://biorxiv.org/content/10.1101/2021.06.12.448098v1?rss=1 Bloom, S. M. Mafunda, N. A. Woolston, B. M. Hayward, M. R. Frempong, J. F. Abai, A. B. Xu, J. Mitchell, A. J. Westergaard, X. Hussain, F. A. Xulu, N. Dong, M. Dong, K. L. Gumbi, T. Ceasar, X. Rice, J. K. Choksi, N. Ismail, N. Ndung'u, T. Ghebremichael, M. S. Balskus, E. P. Mitchell, C. M. Kwon, D. S. 2021-06-12 doi:10.1101/2021.06.12.448098 Cold Spring Harbor Laboratory Press 2021-06-12 <![CDATA[ Raman Needle Arthroscopy for In Vivo Molecular Assessment of Cartilage ]]> https://biorxiv.org/content/10.1101/2021.06.15.448529v1?rss=1 Kroupa, K. Wu, M. I. Zhang, J. Jensen, M. Wong, W. Engiles, J. B. Grinstaff, M. W. Snyder, B. D. Bergholt, M. S. Albro, M. B. 2021-06-16 doi:10.1101/2021.06.15.448529 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Probing Neuro-Endocrine Interactions Through Wireless Magnetothermal Stimulation of Peripheral Organs ]]> https://biorxiv.org/content/10.1101/2021.06.24.449506v1?rss=1 Maeng, L. Y. Rosenfeld, D. Simandl, G. J. Koehler, F. Senko, A. Moon, J. Varnavides, G. Murillo, M. F. Reimer, A. E. Wald, A. Anikeeva, P. Widge, A. S. 2021-06-25 doi:10.1101/2021.06.24.449506 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Identification and characterization of hPSC-derived FOXA2+ progenitor cells with ventricular cardiac differentiation potential ]]> https://biorxiv.org/content/10.1101/2021.07.18.452860v1?rss=1 Dubois, N. Calderon, D. Wickramasinghe, N. Sarrafha, L. Schaniel, C. Chen, S. Tomishima, M. 2021-07-19 doi:10.1101/2021.07.18.452860 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of Tcf4 expression ]]> https://biorxiv.org/content/10.1101/2021.08.02.454783v1?rss=1 Kim, H. Gao, E. B. Draper, A. Berens, N. C. Vihma, H. Zhang, X. Higashi-Howard, A. Ritola, K. Simon, J. Kennedy, A. J. Philpot, B. 2021-08-04 doi:10.1101/2021.08.02.454783 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ TSC2-extracellular matrix crosstalk controls pulmonary vascular proliferation and pulmonary hypertension ]]> https://biorxiv.org/content/10.1101/2021.08.10.455847v1?rss=1 Shen, Y. Goncharov, D. A. Pena, A. Baust, J. Barragan, A. C. Ray, A. Rode, A. Bachman, T. N. Chang, B. Rojas, M. DeLisser, H. Mora, A. L. Kudryashova, T. V. Goncharova, E. A. 2021-08-10 doi:10.1101/2021.08.10.455847 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Distinct neural circuits establish the same chemosensory behavior in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.08.17.456617v1?rss=1 Banerjee, N. Shih, P.-Y. Rojas Palato, E. J. Sternberg, P. W. Hallem, E. 2021-08-17 doi:10.1101/2021.08.17.456617 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Electrical activity recorded from the spinal cord in freely moving rats using a subdural bioelectronic implant ]]> https://biorxiv.org/content/10.1101/2021.08.21.457239v1?rss=1 Harland, B. C. Aqrawe, Z. Vomero, M. Boehler, C. Raos, B. Asplund, M. O'Carroll, S. Svirskis, D. 2021-08-23 doi:10.1101/2021.08.21.457239 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2 ]]> https://biorxiv.org/content/10.1101/2021.08.31.458351v1?rss=1 Fukudome, A. Singh, J. Mishra, V. Reddem, E. Martinez-Marquez, F. Wenzel, S. Yan, R. Shiozaki, M. Yu, Z. Wang, J. C.-Y. Takagi, Y. Pikaard, C. 2021-08-31 doi:10.1101/2021.08.31.458351 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Reovirus sensitizes microsatellite stable colorectal cancer to anti-PD-1 treatment via cross-talk in innate and adaptive immune systems ]]> https://biorxiv.org/content/10.1101/2021.09.03.458915v1?rss=1 Augustine, T. John, P. Friedman, T. Jiffry, J. Guzik, H. Mannan, R. Gupta, R. Delano, C. Mariadason, J. Zang, X. Maitra, R. Goel, S. 2021-09-04 doi:10.1101/2021.09.03.458915 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Structural origins of Escherichia coli RNA polymerase open promoter complex stability ]]> https://biorxiv.org/content/10.1101/2021.09.08.459427v1?rss=1 Saecker, R. M. Chen, J. Chiu, C. E. Malone, B. Sortiris, J. Ebrahim, M. Yen, L. Y. Eng, E. T. Darst, S. A. 2021-09-09 doi:10.1101/2021.09.08.459427 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Astrocytic cell adhesion genes linked to schizophrenia promote synaptic programs in neurons ]]> https://biorxiv.org/content/10.1101/2021.09.11.459765v1?rss=1 Pietilainen, O. Nehme, R. Trehan, A. Eggan, K. 2021-09-12 doi:10.1101/2021.09.11.459765 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ c-Kit mediates cutaneous sensory axon innervation and multi-kinase inhibitor-induced neurotoxicity ]]> https://biorxiv.org/content/10.1101/2021.09.13.460106v1?rss=1 Tuttle, A. M. Pomaville, M. B. Delgado, K. C. Wright, K. M. Nechiporuk, A. V. 2021-09-15 doi:10.1101/2021.09.13.460106 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Integrated gene analyses of de novo mutations from 46,612 trios with autism and developmental disorders ]]> https://biorxiv.org/content/10.1101/2021.09.15.460398v1?rss=1 Wang, T. Kim, C. Bakken, T. E. Gillentine, M. A. Henning, B. Mao, Y. Gilissen, C. Consortium, S. Nowakowski, T. J. Eichler, E. E. 2021-09-16 doi:10.1101/2021.09.15.460398 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia ]]> https://biorxiv.org/content/10.1101/2021.09.22.461360v1?rss=1 Nehme, R. Pietilainen, O. Artomov, M. Tegtmeyer, M. Bell, C. Ganna, A. Singh, T. Trehan, A. Valakh, V. Sherwood, J. Manning, D. Peirent, E. Malik, R. Guss, E. J. Hawes, D. Beccard, A. Bara, A. M. Hazelbaker, D. Z. Zuccaro, E. Genovese, G. Loboda, A. A. Neumann, A. Lilliehook, C. Kuismin, O. Hamalainen, E. Kurki, M. Hultman, C. M. Kahler, A. K. Paulo, J. A. Madison, J. Cohen, B. McPhie, D. Adolfsson, R. Perlis, R. Dolmetsch, R. Farhi, S. McCarroll, S. Hyman, S. Neale, B. Barrett, L. E. Harper, W. Palotie, A. Daly, M. Eggan, K. 2021-09-22 doi:10.1101/2021.09.22.461360 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Large-scale exploration of whole-brain structural connectivity in anorexia nervosa: alterations in the connectivity of frontal and subcortical networks ]]> https://biorxiv.org/content/10.1101/2021.10.05.463197v1?rss=1 Lloyd, E. C. Foerde, K. E. Muratore, A. F. Aw, N. Semanek, D. Steinglass, J. E. Posner, J. 2021-10-08 doi:10.1101/2021.10.05.463197 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ Examining opioid withdrawal scoring and adaptation of global scoring systems to male and female C57BL/6J mice ]]> https://biorxiv.org/content/10.1101/2021.10.11.463944v1?rss=1 Bravo, I. M. Bluitt, M. McElligott, Z. A. 2021-10-12 doi:10.1101/2021.10.11.463944 Cold Spring Harbor Laboratory Press 2021-10-12 <![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[ KTD1 is a yeast defense factor against K28 killer toxin ]]> https://biorxiv.org/content/10.1101/2021.10.25.465803v1?rss=1 Andreev, I. Giovanetti, S. M. Urtecho, G. Shriner, D. Bloom, J. S. Sadhu, M. J. 2021-10-25 doi:10.1101/2021.10.25.465803 Cold Spring Harbor Laboratory Press 2021-10-25 <![CDATA[ A lineage-specific epigenetic memory of inflammation potentiates Kras-driven pancreatic tumorigenesis ]]> https://biorxiv.org/content/10.1101/2021.11.01.466807v1?rss=1 Falvo, D. J. Grimont, A. Zumbo, P. Yang, J. L. Osterhoudt, A. Breves, S. L. Pan, G. Rendeiro, A. F. Wilkinson, J. E. Dündar, F. Elemento, O. Yantiss, R. K. Betel, D. Koche, R. Chandwani, R. 2021-11-04 doi:10.1101/2021.11.01.466807 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Distinct replay signatures for planning and memory maintenance ]]> https://biorxiv.org/content/10.1101/2021.11.08.467745v1?rss=1 Wimmer, G. E. Liu, Y. McNamee, D. Dolan, R. 2021-11-10 doi:10.1101/2021.11.08.467745 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation ]]> https://biorxiv.org/content/10.1101/2021.11.15.468656v1?rss=1 Drozdz, M. M. Doane, A. S. Alkallas, R. Desman, G. Bareja, R. Reilly, M. Bang, J. Yusupova, M. You, J. Wang, J. Z. Verma, A. Aguirre, K. Kane, E. Watson, I. R. Elemento, O. Piskounova, E. Merghoub, T. Zippin, J. H. 2021-11-16 doi:10.1101/2021.11.15.468656 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice ]]> https://biorxiv.org/content/10.1101/2021.11.24.469878v1?rss=1 Brenneman, K. V. Li, X. Kumar, S. Delgado, E. Checkley, L. A. Shoue, D. A. Reyes, A. Abatiyow, B. Haile, M. Tripura, R. Peto, T. Lek, D. Button-Simons, K. A. Kappe, S. H. I. Dhorda, M. Nosten, F. Nkhoma, S. C. Cheeseman, I. H. Vaughan, A. M. Ferdig, M. T. Anderson, T. J. 2021-11-24 doi:10.1101/2021.11.24.469878 Cold Spring Harbor Laboratory Press 2021-11-24 <![CDATA[ Genomic architecture controls spatial structuring in Amazonian birds ]]> https://biorxiv.org/content/10.1101/2021.12.01.470789v1?rss=1 Thom, G. Moreira, L. R. Batista, R. Gehara, M. Aleixo, A. Smith, B. T. 2021-12-02 doi:10.1101/2021.12.01.470789 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Allometric tissue-scale forces activate mechanoresponsive immune cells to drive pathological foreign body response to biomedical implants ]]> https://biorxiv.org/content/10.1101/2022.01.14.476395v1?rss=1 Padmanabhan, J. Chen, K. Sivaraj, D. Kuehlmann, B. A. Bonham, C. A. Dohi, T. Henn, D. Stern-Buchbinder, Z. A. Than, P. A. Hosseini, H. S. Barrera, J. A. Kussie, H. C. Magbual, N. J. Borrelli, M. R. Trotsyuk, A. A. Kwon, S. H. Dunn, J. C. Y. Maan, Z. N. Januszyk, M. Prantl, L. Gurtner, G. C. 2022-01-15 doi:10.1101/2022.01.14.476395 Cold Spring Harbor Laboratory Press 2022-01-15 <![CDATA[ Wireless closed-loop smart bandage for chronic wound management and accelerated tissue regeneration ]]> https://biorxiv.org/content/10.1101/2022.01.16.476432v1?rss=1 Jiang, Y. Trotsyuk, A. Niu, S. Henn, D. Chen, K. Shih, C.-C. Larson, M. Mermin-Bunnell, A. Mittal, S. Lai, J.-C. Saberi, A. Beard, E. Jing, S. Zhong, D. Steele, S. Sun, K. Jain, T. Zhao, E. Neimeth, C. Viana, W. Tang, J. Sivaraj, D. Padmanabhan, J. Rodrigues, M. Perrault, D. Chattopadhyay, A. Maan, Z. Leeolou, M. Bonham, C. Kwon, S. H. Kussie, H. Fischer, K. Gurusankar, G. Liang, K. Zhang, K. Nag, R. Snyder, M. Januszyk, M. Gurtner, G. Bao, Z. 2022-01-18 doi:10.1101/2022.01.16.476432 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Light activation of Orange Carotenoid Protein reveals initial C8'-C7' double bond trans/cis photoisomerization ]]> https://biorxiv.org/content/10.1101/2022.01.17.475858v1?rss=1 Chukhutsina, V. Baxter, J. Fadini, A. Morgan, R. M. Pope, M. Maghlaoui, K. Orr, C. Wagner, A. van Thor, J. 2022-01-18 doi:10.1101/2022.01.17.475858 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Human neural progenitors establish a diffusion barrier in the ER membrane during cell division ]]> https://biorxiv.org/content/10.1101/2022.02.02.478772v1?rss=1 Bin Imtiaz, K. Royall, L. N. Jessberger, S. 2022-02-02 doi:10.1101/2022.02.02.478772 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Spatially Resolved Transcriptomics for Evaluation of Intracranial Vessels in a Rabbit Model: Proof of Concept ]]> https://biorxiv.org/content/10.1101/2022.02.09.479726v1?rss=1 Zabriskie, M. S. Cooke, D. L. Wang, C. Alexander, M. D. 2022-02-10 doi:10.1101/2022.02.09.479726 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ A Single Multipurpose FSH-Blocking Therapeutic for Osteoporosis and Obesity ]]> https://biorxiv.org/content/10.1101/2022.02.28.482279v1?rss=1 Gera, S. Kuo, T.-C. Korkmaz, F. Sant, D. DeMambro, V. Gumerova, A. A. Sudha, K. Padilla, A. Prevot, G. Munitz, J. Teunissen, A. van Leent, M. M. T. Post, T. G. J. M. Fernandes, J. C. Netto, J. Sultana, F. Shelly, E. Kumar, P. Cullen, L. Chatterjee, J. Miyashita, S. Kannangara, H. Bhongade, M. Ievleva, K. Muradova, V. Batista, R. Robinson, C. Macdonald, A. Babunovic, S. Saxena, M. Meseck, M. Caminis, J. Iqbal, J. New, M. I. Ryu, V. Kim, S.-M. Cao, J. Zaidi, N. Fayad, Z. A. Lizneva, D. J. Rosen, C. Yuen, T. Zaidi, M. 2022-03-02 doi:10.1101/2022.02.28.482279 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Isolation of a potently neutralizing and protective human monoclonal antibody targeting yellow fever virus ]]> https://biorxiv.org/content/10.1101/2022.02.28.482437v1?rss=1 Crowe, J. E. Doyle, M. Genualdi, J. R. Bailey, A. Kose, N. Gainza, C. Rodriguez, J. Reeder, K. M. Nelson, C. A. Jethva, P. N. Sutton, R. E. Bombardi, R. G. Gross, M. Julander, J. G. Fremont, D. H. Diamond, M. 2022-03-01 doi:10.1101/2022.02.28.482437 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modeling ]]> https://biorxiv.org/content/10.1101/2022.03.20.485056v1?rss=1 Novak, R. Lin, T. Kaushal, S. Sperry, M. M. Vigneault, F. Gardner, E. Loomba, S. Shcherbina, K. Keshari, V. Dinis, A. Vasan, A. Chandrasekhar, V. Takeda, T. Turner, J. R. Levin, M. Ingber, D. E. 2022-03-21 doi:10.1101/2022.03.20.485056 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ XY sex determination in a cnidarian ]]> https://biorxiv.org/content/10.1101/2022.03.22.485406v1?rss=1 600 million years ago. In this study, we show that the cnidarian Hydractinia symbiolongicarpus has XY sex determination, establishing this species as a model system for sex determination in an understudied group of animals. ]]> Chen, R. Sanders, S. M. Ma, Z. Paschall, J. Chang, E. S. Riscoe, B. M. Schnitzler, C. E. Baxevanis, A. D. Nicotra, M. L. 2022-03-23 doi:10.1101/2022.03.22.485406 Cold Spring Harbor Laboratory Press 2022-03-23 <![CDATA[ A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes ]]> https://biorxiv.org/content/10.1101/2022.03.23.485495v1?rss=1 Song, D.-A. Alber, S. Doron-Mandel, E. Schmid, V. Albus, C. A. Leitner, O. Hamawi, H. Oses-Prieto, J. A. Burlingame, A. Fainzilber, M. Rishal, I. 2022-03-26 doi:10.1101/2022.03.23.485495 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process in C57BL/6J Mice ]]> https://biorxiv.org/content/10.1101/2022.03.25.485824v1?rss=1 Xie, K. Fuchs, H. Scifo, E. Liu, D. Aziz, A. Aguilar- Pimentel, J. A. Amarie, O. V. Becker, L. da Silva-Buttkus, P. Calzada-Wack, J. Cho, Y.-L. Deng, Y. Edwards, A. C. Garrett, L. Georgopoulou, C. Gerlini, R. Hoelter, S. M. Klein-Rodewald, T. Kramer, M. Leuchtenberger, S. Lountzi, D. Mayer-Kuckuk, P. Nover, L. L. Oestereicher, M. A. Overkott, C. Pearson, B. L. Rathkolb, B. Rozman, J. Russ, J. Schaaf, K. Spielmann, N. Sanz-Moreno, A. Stoeger, C. Treise, I. Bano, D. Busch, D. H. Graw, J. Klingenspor, M. Klopstock, T. Mock, B. A. Salomoni, P. Schmidt-Weber 2022-03-27 doi:10.1101/2022.03.25.485824 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Variable Selection via Grace-AKO with Applications in Genomics ]]> https://biorxiv.org/content/10.1101/2022.03.30.486361v1?rss=1 Tian, P. Hu, Y. Liu, Z. Zhang, Y. D. 2022-03-31 doi:10.1101/2022.03.30.486361 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data ]]> https://biorxiv.org/content/10.1101/2022.04.02.486748v1?rss=1 Persad, S. Choo, Z.-N. Dien, C. Masilionis, I. Chaligne, R. Nawy, T. Brown, C. C. Pe'er, I. Setty, M. Pe'er, D. 2022-04-03 doi:10.1101/2022.04.02.486748 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Talin-drug interaction reveals a key molecular determinant for biphasic mechanical effect: studied under single-molecule resolution ]]> https://biorxiv.org/content/10.1101/2022.04.04.486950v1?rss=1 Chakraborty, S. Bhatt, M. Chowdhury, D. Chaudhuri, D. Haldar, S. 2022-04-05 doi:10.1101/2022.04.04.486950 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Probing different paradigms of morphine withdrawal on sleep behavior in male and female C57BL/6J mice ]]> https://biorxiv.org/content/10.1101/2022.04.06.487380v1?rss=1 Bedard, M. L. Lord, J. S. Perez, P. J. Bravo, I. M. Teklezghi, A. T. Tarantino, L. M. Diering, G. H. McElligott, Z. A. 2022-04-07 doi:10.1101/2022.04.06.487380 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Restricting α-Synuclein Transport into Mitochondria by Inhibition of α-Synuclein-VDAC Complexation as a Potential Therapeutic Target for Parkinson's Disease Treatment ]]> https://biorxiv.org/content/10.1101/2022.04.07.487541v1?rss=1 Rajendran, M. Queralt-Martin, M. Gurnev, P. A. Rosencrans, W. M. Rovini, A. Jacobs, D. Abrantes, K. Hoogerheide, D. P. Bezrukov, S. M. Rostovtseva, T. K. 2022-04-08 doi:10.1101/2022.04.07.487541 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ The Interplay of Attention and Conscious Perception: Evidence from Human Intracerebral Recordings and Computational Modeling ]]> https://biorxiv.org/content/10.1101/2022.04.10.487690v1?rss=1 Liu, J. Bayle, D. J. Spagna, A. Sitt, J. D. Bourgeois, A. Lehongre, K. Fernandez-Vidal, S. Navarro, V. Adam, C. Lambrecq, V. Malkinson, T. S. Bartolomeo, P. 2022-04-11 doi:10.1101/2022.04.10.487690 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Synaptic vesicle-bound molecular bridges organize sequential vesicle states along parallel pathways ]]> https://biorxiv.org/content/10.1101/2022.04.10.487799v1?rss=1 Papantoniou, C. Laugks, U. Betzin, J. Capitanio, C. Ferrero, J. J. Sanchez-Prieto, J. Schoch, S. Brose, N. Baumeister, W. Cooper, B. H. Imig, C. Lucic, V. 2022-04-10 doi:10.1101/2022.04.10.487799 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ The E3/E4 ubiquitin ligase UFD-2 mediates negative feedback on Raf protein stability ]]> https://biorxiv.org/content/10.1101/2022.04.14.488377v1?rss=1 Townley, R. Deniaud, A. Stacy, K. S. Rodriguez Torres, C. S. Cheraghi, F. de la Cova, C. C. 2022-04-15 doi:10.1101/2022.04.14.488377 Cold Spring Harbor Laboratory Press 2022-04-15 <![CDATA[ Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers ]]> https://biorxiv.org/content/10.1101/2022.04.26.489563v1?rss=1 Chaudhuri, D. Chowdhury, D. Chakraborty, S. Dutta, A. Mistry, A. Haldar, S. 2022-04-26 doi:10.1101/2022.04.26.489563 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer's disease vulnerable neurons ]]> https://biorxiv.org/content/10.1101/2022.05.14.491965v1?rss=1 Rodriguez-Rodriguez, P. Arroyo-Garcia, L. E. Li, L. Tsagkogianni, C. Wang, W. Salas-Allende, I. Plautz, Z. Cedazo-Minguez, A. Sinha, S. Troyanskaya, O. G. Flajolet, M. Yao, V. Roussarie, J.-P. 2022-05-15 doi:10.1101/2022.05.14.491965 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Incubation of palatable food craving is associated with brain-wide neuronal activation in mice ]]> https://biorxiv.org/content/10.1101/2022.05.31.494210v1?rss=1 Madangopal, R. Szelenyi, E. Nguyen, J. Brenner, M. Drake, O. Pham, D. Shekara, A. Jin, M. Choong, J. J. Heins, C. Komer, L. Weber, S. Hope, B. T. Shaham, Y. Golden, S. A. 2022-06-01 doi:10.1101/2022.05.31.494210 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Candesartan treatment preserves learning and working memory in female TgF344-AD rats ]]> https://biorxiv.org/content/10.1101/2022.06.14.496112v1?rss=1 Sinon, C. G. Carter, K. Ma, J. Bagchi, P. Zhang, X. Williams, P.-J. C. Dammer, E. B. Seyfried, N. T. Garcia, P. S. Sutliff, R. L. Hajjar, I. 2022-06-17 doi:10.1101/2022.06.14.496112 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ ztf-16 is a novel heterochronic modulator that opposes adult cell fate in dauer and continuous life histories in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.06.20.496913v1?rss=1 Hansen, M. A. Dahal, A. Bernstein, T. A. Kohtz, C. Ali, S. Daul, A. L. Montoye, E. A. Panzade, G. P. Alessi, A. F. Flibotte, S. Vargas, M. L. Bourgeois, J. Brown, C. J. Kim, J. K. Rougvie, A. E. Zinovyeva, A. Karp, X. 2022-06-22 doi:10.1101/2022.06.20.496913 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ RAPID, TIME-RESOLVED PROXIMITY LABELING BY SBP1 IDENTIFIES A PORIN DOMAIN PROTEIN AT THE MALARIA PARASITE PERIPHERY ]]> https://biorxiv.org/content/10.1101/2022.06.30.498261v1?rss=1 Anaguano, D. Brooks, C. F. Cobb, D. W. Muralidharan, V. 2022-07-01 doi:10.1101/2022.06.30.498261 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ A manually curated annotation characterises genomic features of P. falciparum lncRNAs ]]> https://biorxiv.org/content/10.1101/2022.07.08.499349v1?rss=1 Hoshizaki, J. Adjalley, S. Thathy, V. Judge, K. Berriman, M. Reid, A. J. Lee, M. C. S. 2022-07-09 doi:10.1101/2022.07.08.499349 Cold Spring Harbor Laboratory Press 2022-07-09 <![CDATA[ Genetic architecture of creativity and extensive genetic overlap with psychiatric disorders revealed from genome-wide association analyses of 241,736 individuals ]]> https://biorxiv.org/content/10.1101/2022.07.25.501322v1?rss=1 Kim, H. Ahn, Y. Yoon, J. Jung, K. Kim, S. Shim, I. Park, T. H. Ko, H. Jung, S.-H. Kim, J. Park, S. Lee, D. J. Choi, S. Cha, S. Kim, B. Cho, M. Y. Cho, H. Kim, D. S. Ihm, H. K. Park, W.-Y. Bakhshi, H. O'Connell, K. Andreassen, O. Flint, J. Kendler, K. S. Myung, W. Won, H.-H. 2022-07-25 doi:10.1101/2022.07.25.501322 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas ]]> https://biorxiv.org/content/10.1101/2022.07.26.501417v1?rss=1 Burdziak, C. Alonso-Curbelo, D. Walle, T. Barriga, F. M. Reyes, J. Xie, Y. Zhao, Z. Zhao, C. J. Chen, H.-A. Chaudhary, O. Masilionis, I. Choo, Z.-N. Gao, V. Luan, W. Wuest, A. Ho, Y.-J. Wei, Y. Quail, D. Koche, R. Mazutis, L. Nawy, T. Chaligne, R. Lowe, S. W. Pe'er, D. 2022-07-27 doi:10.1101/2022.07.26.501417 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ ENGRAILED-1 transcription factor exerts a paracrine neurotrophic activity on adult spinal cord α-motoneurons. ]]> https://biorxiv.org/content/10.1101/2022.08.16.504081v1?rss=1 Leboeuf, M. Vargas-Abonce, S. E. Peze-Hedsieck, E. Dupont, E. Jimenez-Alonso, L. MOYA, K. L. Prochiantz, A. 2022-08-16 doi:10.1101/2022.08.16.504081 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Cardiovascular Hemodynamics in Mice with Tumor Necrosis Factor Receptor - Associated Factor 2 Mediated Cytoprotection in the Heart ]]> https://biorxiv.org/content/10.1101/2022.09.03.506447v1?rss=1 Marshall, A. G. Neikirk, K. Vue, Z. Beasley, H. K. Garza-Lopez, E. Vang, L. Barongan, T. Evans, Z. Anudokem, J. Pham, T. T. Gomez, J. A. Exil, V. Dai, D.-F. Entman, M. L. Taffet, G. E. Hinton, A. Reddy, A. K. 2022-09-06 doi:10.1101/2022.09.03.506447 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ A continental scale analysis reveals widespread root bimodality ]]> https://biorxiv.org/content/10.1101/2022.09.14.507823v1?rss=1 Lu, M. Wang, S. Malhotra, A. Tumber-Davila, S. J. Weintraub-Leff, S. McCormack, L. Wang, X. T. Jackson, R. B. 2022-09-17 doi:10.1101/2022.09.14.507823 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells ]]> https://biorxiv.org/content/10.1101/2022.09.19.507319v1?rss=1 Liu, H. Xu, C. Diplas, B. H. Brown, A. Strickland, L. M. Ling, J. McLendon, R. E. Keir, S. T. Ashley, D. M. He, Y. Waitkus, M. S. 2022-09-19 doi:10.1101/2022.09.19.507319 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Ultrastructure of synaptic connectivity within sub-regions of the SCN revealed by genetically encoded EM tag and SBEM ]]> https://biorxiv.org/content/10.1101/2022.09.26.509467v1?rss=1 Calligaro, H. Shoghi, A. Chen, X. Kim, K.-Y. Liu, Y. H. Khov, B. Finander, B. Le, H. Ellisman, M. H. Panda, S. 2022-09-26 doi:10.1101/2022.09.26.509467 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Lineage-specific oncogenes drive growth of major forms of human cancer using common downstream mechanisms ]]> https://biorxiv.org/content/10.1101/2022.09.27.509636v1?rss=1 Kauko, O. Turunen, M. Pihlajamaa, P. Hakkinen, A. Queiroz, R. M. Paakkonen, M. Ventela, S. Gaetani, M. Lundstrom, S. Murgia, A. Sahu, B. Routila, J. Irjala, H. Griffin, J. L. Lilley, K. S. Kivioja, T. Hautaniemi, S. Taipale, J. 2022-09-28 doi:10.1101/2022.09.27.509636 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Raman microspectroscopy reveals unsaturation heterogeneity at the lipid droplet level and validates an in vitro model of bone marrow adipocyte subtypes ]]> https://biorxiv.org/content/10.1101/2022.10.03.510634v1?rss=1 Tratwal, J. Falgayrac, G. Berthaume, N. Bataclan, C. Tavakol, D. N. Campos, V. Duponchel, L. Daley, G. Q. Penel, G. Chauveau, C. Naveiras, O. 2022-10-04 doi:10.1101/2022.10.03.510634 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Flexible IrOx Neural Electrode for Mouse Vagus Nerve Stimulation ]]> https://biorxiv.org/content/10.1101/2022.10.12.511950v1?rss=1 Sun, T. Tsaava, T. Peragine, J. Crosfield, C. Lopez, M. F. Modi, R. Sharma, R. Li, C. Sohal, H. Chang, E. H. Rieth, L. 2022-10-16 doi:10.1101/2022.10.12.511950 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Multi-omic profiling of the developing human cerebral cortex at the single cell level ]]> https://biorxiv.org/content/10.1101/2022.10.14.512250v1?rss=1 Zhu, K. Bendl, J. Rahman, S. Vicari, J. M. Coleman, C. Clarence, T. Latouche, O. Tsankova, N. M. Li, A. Brennand, K. J. Lee, D. Yuan, G. Fullard, J. F. Roussos, P. 2022-10-17 doi:10.1101/2022.10.14.512250 Cold Spring Harbor Laboratory Press 2022-10-17 <![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[ Elevated estradiol during a hormone simulated pseudopregnancy decreases sleep and increases hypothalamic activation in female Syrian hamsters ]]> https://biorxiv.org/content/10.1101/2022.10.27.514063v1?rss=1 Irvine, A. Gaffney, M. I. Haughee, E. K. Horton, M. A. Morris, H. C. Harris, K. C. Corbin, J. E. Merrill, C. Perlis, M. L. Been, L. E. 2022-10-28 doi:10.1101/2022.10.27.514063 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Phencyclidine disrupts neural coordination and cognitive control by dysregulating translation ]]> https://biorxiv.org/content/10.1101/2022.11.18.517075v1?rss=1 Park, E. Kao, H.-Y. Jourdi, H. van Dijk, M. Carrillo-Segura, S. Tunnell, K. W. Gutierrez, J. Wallace, E. J. Troy-Regier, M. Radwan, B. Lesburgueres, E. Alarcon, J. M. Fenton, A. A. 2022-11-18 doi:10.1101/2022.11.18.517075 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Anti-integrin αvβ6 autoantibodies are a novel predictive biomarker in ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2022.11.21.517399v1?rss=1 Livanos, A. E. Dunn, A. Fischer, J. Ungaro, R. C. Turpin, W. Lee, S.-H. Rui, S. Del Valle, D. M. Julia, J. J. Martinez-Delgado, G. Riddle, M. S. Murray, J. A. Laird, R. M. Torres, J. Agrawal, M. Magee, J. S. Dervieux, T. Gnjatic, S. Sheppard, D. Sands, B. E. Porter, C. K. Croitoru, K. Petralia, F. Colombel, J.-F. Mehandru, S. 2022-11-24 doi:10.1101/2022.11.21.517399 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Characterization of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoprotein Conformational States on Infectious Virus Particles ]]> https://biorxiv.org/content/10.1101/2022.12.01.518799v1?rss=1 Nguyen, H. T. Wang, Q. Anang, S. Sodroski, J. G. 2022-12-02 doi:10.1101/2022.12.01.518799 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Pleiotropy of autism-associated chromatin regulators ]]> https://biorxiv.org/content/10.1101/2022.12.07.519375v1?rss=1 Lasser, M. Sun, N. Xu, Y. Law, K. Gonzalez, S. Wang, B. Drury, V. Drake, S. Zaltsman, Y. Dea, J. Bader, E. McCluskey, K. E. State, M. W. Willsey, A. J. Willsey, H. R. 2022-12-07 doi:10.1101/2022.12.07.519375 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response ]]> https://biorxiv.org/content/10.1101/2022.12.13.520329v1?rss=1 73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment naive non-small cell lung cancers (NSCLC) with single cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Notably, one subset selectively expresses high levels of OX40 and GITR, whose engangement by cognate ligand mediated proliferative programs and NF-kB activation, as well as multiple genes involved in Treg suppression, in particular LAG3. Functionally, the OX40hiGITRhi subset in the most highly suppressive ex vivo and Treg expression of OX40, GITR and LAG3, correlated with resistance to PD-1 blockade. Surprisingly, in the murine tumor model, we found that virtually all TIL-Treg expressing T cell receptors that are specific for TAA fully develop a distinct Th1-like signature over a two-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFN{gamma} and certain pro-inflammatory granzymes. Application of a gene score from the murine TAA-specific Th1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1 responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally-defined subsets with potentially opposing effects on ICB-induced anti-tumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to anti-tumor responses. One-Sentence SummaryWe define 10 subsets of lung cancer-infiltrating regulatory T cells, one of which is highly suppressive and enriched in anti-PD-1 non-responders and the other is Th1-like and is enriched in PD-1 responders. ]]> Dykema, A. G. Zhang, J. Zhang, B. Cheung, L. S. Zeng, Z. Cherry, C. M. Li, T. Caushi, J. X. Nishimoto, M. Connor, S. Ji, Z. Munoz, A. J. Hou, W. Zhan, W. Singh, D. Rashid, R. Mitchell-Flack, M. Bom, S. Tam, A. Wang, Y. Sawosik, C. A. Tirado, L. E. Tomasovic, L. M. VanDyke, D. Spangler, J. B. Anagnostou, V. Yang, S. Spicer, J. Rayes, R. Taube, J. M. Brahmer, J. R. Forde, P. M. Yegnasubramanian, S. Ji, H. Pardoll, D. M. Smith, K. N. 2022-12-15 doi:10.1101/2022.12.13.520329 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Supervised discovery of interpretable gene programs from single-cell data ]]> https://biorxiv.org/content/10.1101/2022.12.20.521311v1?rss=1 Kunes, R. Z. Walle, T. Nawy, T. Pe'er, D. 2022-12-21 doi:10.1101/2022.12.20.521311 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ Context-dependence of T-loop mediated long-range RNA tertiary interactions ]]> https://biorxiv.org/content/10.1101/2022.12.26.521914v1?rss=1 Hansen, L. Kletzien, O. A. Urquijo, M. Schwanz, L. T. Batey, R. T. 2022-12-27 doi:10.1101/2022.12.26.521914 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors ]]> https://biorxiv.org/content/10.1101/2022.12.27.521482v1?rss=1 Iyer, S. R. Nusser, K. Jones, K. Shinde, P. Beach, C. Z. Keddy, C. Aguero, E. Force, J. Shinde, U. Davare, M. A. 2022-12-27 doi:10.1101/2022.12.27.521482 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Paternal morphine exposure enhances morphine self-administration and induces region-specific neural adaptations in reward-related brain regions of male offspring ]]> https://biorxiv.org/content/10.1101/2023.01.03.522600v1?rss=1 Toussaint, A. B. Ellis, A. S. Bongiovanni, A. R. Peterson, D. R. Bavley, C. C. Karbalaei, R. Mayberry, H. L. Bhakta, S. Dressler, C. C. Imperio, C. G. Maurer, J. J. Schmidt, H. D. Chen, C. Bland, K. Liu-Chen, L.-Y. Wimmer, M. E. 2023-01-04 doi:10.1101/2023.01.03.522600 Cold Spring Harbor Laboratory Press 2023-01-04 <![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[ C. elegans SMOC-1 interacts with both BMP and glypican to regulate BMP signaling ]]> https://biorxiv.org/content/10.1101/2023.01.06.523017v1?rss=1 DeGroot, M. S. Williams, B. Chang, T. Y. Maas Gamboa, M. L. Larus, I. M. Fromme, J. C. Liu, J. 2023-01-08 doi:10.1101/2023.01.06.523017 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2023.01.19.524731v1?rss=1 Canales-Herrerias, P. Uzzan, M. Seki, A. Czepielewski, R. S. Verstockt, B. Livanos, A. Raso, F. Dunn, A. Dai, D. Wang, A. Al-taie, Z. Martin, J. Ko, H. M. Tokuyama, M. Tankelevich, M. Meringer, H. Cossarini, F. Jha, D. Krek, A. Paulsen, J. D. Zuber Nakadar, M. Wong, J. Erlich, E. C. Onufer, E. J. Helmink, B. A. Sharma, K. Rosenstein, A. Chung, G. Dawson, T. Juarez, J. Yajnik, V. Cerutti, A. Faith, J. Suarez-Farinas, M. Argmann, C. Petralia, F. Randolph, G. J. Polydorides, A. D. Reboldi, A. Colombel, J. F. Mehandru, S. 2023-01-20 doi:10.1101/2023.01.19.524731 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial metabolic reprogramming ]]> https://biorxiv.org/content/10.1101/2023.01.19.524841v1?rss=1 Wang, Y. Kulkarni, V. V. Pantaleon Garcia, J. Leiva-Juarez, M. M. Goldblatt, D. L. Gulraiz, F. Chen, J. Donepudi, S. R. Lorenzi, P. L. Wang, H. Wong, L.-J. Tuvim, M. J. Evans, S. E. 2023-01-21 doi:10.1101/2023.01.19.524841 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Conformationally Adaptive Dyes Enable Protein-Adaptive Differential Scanning Fluorometry ]]> https://biorxiv.org/content/10.1101/2023.01.23.525251v1?rss=1 Wu, T. S. Yu, J. C. Suresh, A. Gale-Day, Z. J. Alteen, M. G. Woo, A. S. Millbern, Z. Johnson, O. T. Carroll, E. C. Partch, C. L. Fourches, D. Vilnueza, N. R. Vocadlo, D. J. Gestwicki, J. E. 2023-01-24 doi:10.1101/2023.01.23.525251 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Antagonistic regulation of salt and sugar chemotaxis plasticity by a single chemosensory neuron in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2023.01.25.525622v1?rss=1 Tomioka, M. Umemura, Y. Ueoka, Y. Chin, R. Katae, K. Uchiyama, C. Ike, Y. Iino, Y. 2023-01-27 doi:10.1101/2023.01.25.525622 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense ]]> https://biorxiv.org/content/10.1101/2023.01.26.525578v1?rss=1 Leibel, S. L. McVicar, R. N. Murad, R. Kwong, E. M. Clark, A. E. Alvarado, A. Grimmig, B. A. Nuryyev, R. Young, R. E. Lee, J. C. Peng, W. Zhu, Y. P. Griffis, E. Nowell, C. J. James, B. Alarcon, S. Malhotra, A. Gearing, L. J. Hertzog, P. J. Galapate, C. M. Galenkamp, K. M. O. Commisso, C. Smith, D. M. Sun, X. Carlin, A. F. Croker, B. A. Snyder, E. Y. 2023-01-27 doi:10.1101/2023.01.26.525578 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis ]]> https://biorxiv.org/content/10.1101/2023.01.27.525950v1?rss=1 Bayer, L. V. Milano, S. N. Formel, S. K. Kaur, H. Ravichandran, R. Cambeiro, J. A. Slinko, L. Catrina, I. E. Bratu, D. P. 2023-01-28 doi:10.1101/2023.01.27.525950 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Aberrant accumulation of age- and disease-associated factors following neural probe implantation in a mouse model of Alzheimers disease ]]> https://biorxiv.org/content/10.1101/2023.02.11.528131v1?rss=1 Wellman, S. M. Coyne, O. A. Douglas, M. M. Kozai, T. D. Y. 2023-02-12 doi:10.1101/2023.02.11.528131 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Physiological reprogramming in vivo mediated by Sox4 pioneer factor activity ]]> https://biorxiv.org/content/10.1101/2023.02.14.528556v1?rss=1 Katsuda, T. Sussman, J. Ito, K. Katznelson, A. Yuan, S. Li, J. Merrell, A. J. Takenaka, N. Cure, H. Li, Q. Rasool, R. U. Asangani, I. A. Zaret, K. S. Stanger, B. 2023-02-14 doi:10.1101/2023.02.14.528556 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Augmentation of Histone Deacetylase 6 Activity Impairs Mitochondrial Respiratory Complex I in Ischemic/Reperfused Diabetic Hearts ]]> https://biorxiv.org/content/10.1101/2023.02.21.529462v1?rss=1 Ge, Z.-D. Baumgardt, S. L. Fang, J. Fu, X. Liu, Y. Xia, Z. Zhao, M. Chen, L. Mishra, R. Gunasekaran, M. Saha, P. Forbess, J. M. Bosnjak, Z. J. Camara, A. K. S. Kersten, J. Thorp, E. B. Kaushal, S. 2023-02-22 doi:10.1101/2023.02.21.529462 Cold Spring Harbor Laboratory Press 2023-02-22 <![CDATA[ Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior ]]> https://biorxiv.org/content/10.1101/2023.02.27.530077v1?rss=1 Pennington, Z. T. LaBanca, A. R. Sompolpong, P. Christenson Wick, Z. Feng, Y. Shuman, T. Cai, D. J. 2023-02-27 doi:10.1101/2023.02.27.530077 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Aversive experience drives offline ensemble reactivation to link memories across days ]]> https://biorxiv.org/content/10.1101/2023.03.13.532469v1?rss=1 Zaki, Y. Pennington, Z. T. Morales-Rodriguez, D. Francisco, T. R. LaBanca, A. R. Dong, Z. Segura, S. C. Silva, A. J. Shuman, T. Fenton, A. Rajan, K. Cai, D. J. 2023-03-14 doi:10.1101/2023.03.13.532469 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen Cryptococcus neoformans: a target for novel antifungals ]]> https://biorxiv.org/content/10.1101/2023.03.14.530545v1?rss=1 Washington, E. J. Zhou, Y. Hsu, A. L. Petrovich, M. Borgnia, M. J. Bartesaghi, A. Brennan, R. G. 2023-03-14 doi:10.1101/2023.03.14.530545 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Taxonomic distribution of metabolic functions underpin nutrient cycling in Trichodesmium consortia ]]> https://biorxiv.org/content/10.1101/2023.03.15.532517v1?rss=1 Koedooder, C. Zhang, F. Wang, S. Haley, S. T. Tolic, N. Nicora, C. D. Basu, S. Gledhill, M. Boiteau, R. Dyhrman, S. Rubin-Blum, M. Shaked, Y. 2023-03-16 doi:10.1101/2023.03.15.532517 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Visuomotor experience induces functional and structural plasticity of chandelier cells ]]> https://biorxiv.org/content/10.1101/2023.04.21.537780v1?rss=1 Seignette, K. Jamann, N. Papale, P. Terra, H. Porneso, R. P. O. de Kraker, L. van der Togt, C. van der Aa, M. Neering, P. Ruimschotel, E. Roelfsema, P. R. Montijn, J. S. Self, M. W. Kole, M. H. P. Levelt, C. N. 2023-04-21 doi:10.1101/2023.04.21.537780 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ On the dynamic contact angle of capillary-driven microflows in open channels ]]> https://biorxiv.org/content/10.1101/2023.04.24.537941v1?rss=1 Tokihiro, J. C. Berthier, J. McManamen, A. M. Phan, D. N. Thongpang, S. Theberge, A. B. 2023-04-27 doi:10.1101/2023.04.24.537941 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Organization of orbitofrontal-auditory pathways in the Mongolian gerbil ]]> https://biorxiv.org/content/10.1101/2023.04.25.538296v1?rss=1 Ying, R. Hamlette, L. Nikoobakht, L. Balaji, R. Miko, N. Caras, M. L. 2023-04-28 doi:10.1101/2023.04.25.538296 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Ventral hippocampal CCK interneurons gate context-reward memory ]]> https://biorxiv.org/content/10.1101/2023.04.27.538595v1?rss=1 Nguyen, R. Sivakumaran, S. Lambe, E. K. Kim, J. 2023-04-27 doi:10.1101/2023.04.27.538595 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining ]]> https://biorxiv.org/content/10.1101/2023.04.27.538600v1?rss=1 Cullati, S. N. Zhang, E. Shan, Y. Guillen, R. X. Chen, J.-S. Navarrete-Perea, J. Elmore, Z. C. Ren, L. Gygi, S. P. Gould, K. L. 2023-04-28 doi:10.1101/2023.04.27.538600 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Hippocampal contextualization of social rewards ]]> https://biorxiv.org/content/10.1101/2023.05.12.540475v1?rss=1 Mendes Duarte, J. Li, K. Nguyen, R. Ciocchi, S. 2023-05-12 doi:10.1101/2023.05.12.540475 Cold Spring Harbor Laboratory Press 2023-05-12 <![CDATA[ Estradiol and luteinizing hormone reverse memory loss in phencyclidine model of schizophrenia: Evidence for hippocampal GABA action ]]> https://biorxiv.org/content/10.1101/207159v1?rss=1 Riordan, A. J. Schaler, A. W. Fried, J. B. Paine, T. A. Thornton, J. E. 2017-10-21 doi:10.1101/207159 Cold Spring Harbor Laboratory Press 2017-10-21 <![CDATA[ Acto-myosin driven functional nanoclusters of GPI-anchored proteins are generated by integrin receptor signaling ]]> https://biorxiv.org/content/10.1101/232223v1?rss=1 Kalappurakkal, J. M. Anilkumar, A. A. Patra, C. van Zanten, T. S. Sheetz, M. Mayor, S. 2017-12-11 doi:10.1101/232223 Cold Spring Harbor Laboratory Press 2017-12-11 <![CDATA[ A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research ]]> https://biorxiv.org/content/10.1101/251967v1?rss=1 3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals. ]]> De Jager, P. Ma, Y. McCabe, C. Xu, J. Vardarajan, B. N. Felsky, D. Klein, H.-U. White, C. C. Peters, M. A. Lodgson, B. Nejad, P. Tang, A. Mangravite, L. M. Yu, L. Gaiteri, C. Mostafavi, S. Schneider, J. A. Bennett, D. A. 2018-01-23 doi:10.1101/251967 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ SciLMM: Computing heritability with millions of individuals ]]> https://biorxiv.org/content/10.1101/256396v1?rss=1 Shor, T. Geiger, D. Erlich, Y. Weissbrod, O. 2018-01-30 doi:10.1101/256396 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Transcriptional deconvolution reveals consistent functional subtypes of pancreatic cancer epithelium and stroma ]]> https://biorxiv.org/content/10.1101/288779v1?rss=1 He, J. Maurer, H. C. Holmstrom, S. R. Su, T. Ahmed, A. Hibshoosh, H. Chabot, J. A. Oberstein, P. E. Sepulveda, A. R. Genkinger, J. M. Zhang, J. Iuga, A. C. Califano, A. Bansal, M. Olive, K. P. 2018-03-26 doi:10.1101/288779 Cold Spring Harbor Laboratory Press 2018-03-26 <![CDATA[ Predictive control of electrophysiological network architecture using direct, single-node neurostimulation in humans ]]> https://biorxiv.org/content/10.1101/292748v1?rss=1 Khambhati, A. N. Kahn, A. E. Costantini, J. Ezzyat, Y. Solomon, E. A. Gross, R. E. Jobst, B. C. Sheth, S. A. Zaghloul, K. A. Worrell, G. Seger, S. Lega, B. C. Weiss, S. Sperling, M. R. Gorniak, R. Das, S. R. Stein, J. M. Rizzuto, D. S. Kahana, M. J. Lucas, T. H. Davis, K. A. Tracy, J. I. Bassett, D. S. 2018-03-31 doi:10.1101/292748 Cold Spring Harbor Laboratory Press 2018-03-31 <![CDATA[ Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci ]]> https://biorxiv.org/content/10.1101/309559v1?rss=1 Liu, B. Pjanic, M. Wang, T. Nguyen, T. Gloudemans, M. Rao, A. Castano, V. G. Nurnberg, S. T. Rader, D. J. Elwyn, S. Ingelsson, E. Montgomery, S. B. Miller, C. L. Quertermous, T. 2018-04-30 doi:10.1101/309559 Cold Spring Harbor Laboratory Press 2018-04-30 <![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[ Two Sides of the Same Coin: The Hippocampus as a Common Neural Substrate for Model-Based Planning and Spatial Memory ]]> https://biorxiv.org/content/10.1101/359232v1?rss=1 Vikbladh, O. M. Meager, M. R. King, J. Blackmon, K. Devinsky, O. Shohamy, D. Burgess, N. Daw, N. D. 2018-07-13 doi:10.1101/359232 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Epigenomic landscape of the human pathogen Clostridium difficile ]]> https://biorxiv.org/content/10.1101/398891v1?rss=1 Oliveira, P. H. Kim, A. Sekulovic, O. Garrett, E. M. Trzilova, D. Mead, E. A. Pak, T. Zhu, S. Deikus, G. Touchon, M. Beckford, C. Zeitouni, N. E. Altman, D. Webster, E. Oussenko, I. Aggarwal, A. K. Bashir, A. Patel, G. Hamula, C. Huprikar, S. Roberts, R. J. Schadt, E. E. Sebra, R. Bakel, H. v. Kasarskis, A. Tamayo, R. Shen, A. Fang, G. 2018-08-23 doi:10.1101/398891 Cold Spring Harbor Laboratory Press 2018-08-23 <![CDATA[ Engineered transfer RNAs for suppression of premature termination codons ]]> https://biorxiv.org/content/10.1101/400127v1?rss=1 Lueck, J. D. Yoon, J. S. Perales-Puchalt, A. Mackey, A. L. Infield, D. T. Behlke, M. A. Pope, M. R. Weiner, D. B. Skach, W. R. McCray, P. B. Ahern, C. A. 2018-08-27 doi:10.1101/400127 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening ]]> https://biorxiv.org/content/10.1101/418830v1?rss=1 Zhang, L. Bell, D. R. Luan, B. Zhou, R. 2018-09-16 doi:10.1101/418830 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ Probing variability in a cognitive map using manifold inference from neural dynamics ]]> https://biorxiv.org/content/10.1101/418939v1?rss=1 Low, R. J. Lewallen, S. Aronov, D. Nevers, R. Tank, D. W. 2018-09-16 doi:10.1101/418939 Cold Spring Harbor Laboratory Press 2018-09-16 <![CDATA[ A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells ]]> https://biorxiv.org/content/10.1101/437855v1?rss=1 Lutfullahoglu-Bal, G. Seferoglu, A. B. Keskin, A. Akdogan, E. Dunn, C. D. 2018-10-08 doi:10.1101/437855 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Learning of distant state predictions by the orbitofrontal cortex in humans ]]> https://biorxiv.org/content/10.1101/450999v1?rss=1 Wimmer, G. E. Buechel, C. 2018-10-24 doi:10.1101/450999 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Repression of an activity-dependent autocrine insulin signal is required for sensory neuron development in C. elegans. ]]> https://biorxiv.org/content/10.1101/481010v1?rss=1 Bayer Horowitz, L. Brandt, J. P. Ringstad, N. 2018-11-28 doi:10.1101/481010 Cold Spring Harbor Laboratory Press 2018-11-28 <![CDATA[ Robust Antibacterial Activity of Tungsten Oxide (WO3-X) Nanodots ]]> https://biorxiv.org/content/10.1101/494260v1?rss=1 Duan, G. Chen, L. Jing, Z. De Luna, P. Wen, L. Zhang, L. Zhao, L. Xu, J. Li, Z. Yang, Z. Zhou, R. 2018-12-13 doi:10.1101/494260 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Nanoporous Boron Nitride for High Efficient Water Desalination ]]> https://biorxiv.org/content/10.1101/500876v1?rss=1 Gu, Z. Liu, S. Dai, X. Chen, S. Yang, Z. Zhou, R. 2018-12-18 doi:10.1101/500876 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Phototrophic lactate utilization by Rhodopseudomonas palustris is stimulated by co-utilization with additional substrates ]]> https://biorxiv.org/content/10.1101/502963v1?rss=1 Govindaraju, A. McKinlay, J. B. LaSarre, B. 2018-12-21 doi:10.1101/502963 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Rapid memory reactivation at movie event boundaries promotes episodic encoding ]]> https://biorxiv.org/content/10.1101/511782v1?rss=1 Silva, M. Baldassano, C. Fuentemilla, L. 2019-01-04 doi:10.1101/511782 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Epidemiology of Staphylococcus aureus in Neonates on Admission to a Chinese Neonatal Intensive Care Unit ]]> https://biorxiv.org/content/10.1101/529941v1?rss=1 Geng, W. Qi, Y. Li, W. McConvillle, T. H. Ricciuti, A. H. Grohs, E. Saiman, L. Uhlemann, A.-C. 2019-01-24 doi:10.1101/529941 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Single cell profiling of CRISPR/Cas9-induced OTX2 deficient retinas reveals fate switch from restricted progenitors ]]> https://biorxiv.org/content/10.1101/538710v1?rss=1 Ghinia Tegla, M. G. Buenaventura, D. F. Kim, D. Y. Thakurdin, C. Gonzalez, K. C. Emerson, M. M. 2019-02-02 doi:10.1101/538710 Cold Spring Harbor Laboratory Press 2019-02-02 <![CDATA[ Discordant gene responses to radiation in humans and mice: hematopoietically humanized mice may save the day for radiation biomarker identification. ]]> https://biorxiv.org/content/10.1101/558882v1?rss=1 Ghandhi, S. Smilenov, L. Pujol-Canadell, M. Amundson, S. A. 2019-02-24 doi:10.1101/558882 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Development of a Comprehensive Antibody Staining Database using a Standardized Analytics Pipeline ]]> https://biorxiv.org/content/10.1101/563742v1?rss=1 Amir, E.-a. D. Lee, B. Badoual, P. Gordon, M. Guo, X. V. Merad, M. Rahman, A. H. 2019-02-28 doi:10.1101/563742 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Brain Age Prediction: Cortical and Subcortical Shape Covariation in the Developing Human Brain ]]> https://biorxiv.org/content/10.1101/570333v1?rss=1 Zhao, Y. Klein, A. Castellanos, F. Milham, M. P. 2019-03-07 doi:10.1101/570333 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control ]]> https://biorxiv.org/content/10.1101/581868v1?rss=1 Viny, A. D. Bowman, R. L. Liu, Y. Lavallee, V.-P. Redlich, S. E. Xiao, W. Durham, B. H. Navitski, A. Park, J. Braunstein, S. Azizi, E. Witkin, M. Baslan, T. Ott, C. J. Pe'er, D. Dekker, J. Koche, R. Levine, R. L. 2019-03-18 doi:10.1101/581868 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ SICaRiO: Short Indel Call filteRing with bOosting ]]> https://biorxiv.org/content/10.1101/601450v1?rss=1 Bhuyan, M. S. I. Pe'er, I. Rahman, M. S. 2019-04-07 doi:10.1101/601450 Cold Spring Harbor Laboratory Press 2019-04-07 <![CDATA[ Machine Source Localization of Tursiops Truncatus Whistle-like Sounds in a Reverberant Aquatic Environment ]]> https://biorxiv.org/content/10.1101/606673v1?rss=1 Woodward, S. F. Reiss, D. Magnasco, M. 2019-04-11 doi:10.1101/606673 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ A microfabricated, 3D-sharpened silicon shuttle for insertion of flexible electrode arrays through dura mater into brain ]]> https://biorxiv.org/content/10.1101/614685v1?rss=1 Joo, H. R. Fan, J. L. Chen, S. Pebbles, J. A. Liang, H. Chung, J. E. Yorita, A. M. Tooker, A. C. Tolosa, V. M. Geaghan-Breiner, C. Roumis, D. K. Liu, D. F. Haque, R. Frank, L. M. 2019-04-26 doi:10.1101/614685 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Adaptive and Innate Immune Cell Responses in Tendons and Lymph Nodes After Tendon Injury and Repair ]]> https://biorxiv.org/content/10.1101/658310v1?rss=1 Noah, A. C. Li, T. M. Martinez, L. M. Wada, S. Swanson, J. B. Disser, N. P. Sugg, K. B. Rodeo, S. A. Lu, T. T. Mendias, C. L. 2019-06-03 doi:10.1101/658310 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ NMDA receptor in vasopressin 1b neurons is not required for short-term social memory, object memory or aggression. ]]> https://biorxiv.org/content/10.1101/670893v1?rss=1 Williams Avram, S. Fastman, J. Cymerblit-Sabba, A. Smith, A. Vincent, M. Song, J. Lee, H.-J. Granovetter, M. Lee, S. H. Cilz, N. Stackmann, M. Chaturvedi, R. Young, W. S. 2019-06-13 doi:10.1101/670893 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia ]]> https://biorxiv.org/content/10.1101/677260v1?rss=1 Vincent, B. J. Rice, G. R. Wong, G. M. Glassford, W. J. Downs, K. I. Shastay, J. L. Charles-Obi, K. Natarajan, M. Gogol, M. M. Zeitlinger, J. Rebeiz, M. 2019-06-26 doi:10.1101/677260 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation ]]> https://biorxiv.org/content/10.1101/683516v1?rss=1 Wasik, B. R. Voorhees, I. E. H. Barnard, K. N. Lawrence, B. K. Weichert, W. Hood, G. Nogales, A. Martinez-Sobrido, L. Holmes, E. C. Parrish, C. R. 2019-06-27 doi:10.1101/683516 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ SMART: An open source extension of WholeBrain for iDISCO+ LSFM intact mouse brain registration and segmentation ]]> https://biorxiv.org/content/10.1101/727529v1?rss=1 Jin, M. Nguyen, J. D. Weber, S. J. Mejias-Aponte, C. A. Madangopal, R. Golden, S. A. 2019-08-06 doi:10.1101/727529 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Receptor-Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G-Protein Gα - Subunit AtGPA1 ]]> https://biorxiv.org/content/10.1101/752337v1?rss=1 Jia, H. Song, G. Werth, E. G. Walley, J. W. Hicks, L. M. Jones, A. M. 2019-08-31 doi:10.1101/752337 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Episodic memory retrieval is supported by rapid replay of episode content ]]> https://biorxiv.org/content/10.1101/758185v1?rss=1 Wimmer, G. E. Liu, Y. Vehar, N. Behrens, T. E. Dolan, R. J. 2019-09-08 doi:10.1101/758185 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ A two-stage approach to identifying and validating modifiable factors for the prevention of depression ]]> https://biorxiv.org/content/10.1101/759753v1?rss=1 90th percentile) for clinically significant depression at follow-up based on their (i) polygenic risk, or (ii) reported traumatic life events. Using a factors-wide design corrected for multiple testing and adjusted for potential confounders, we identified modifiable factors associated with follow-up depression in the full sample and among at-risk individuals. Using a two-sample Mendelian randomization (MR) design, we then examined which significant factors showed potential causal influences on depression risk, or vice versa.nnResultsA range of baseline modifiable factors were prospectively associated with follow-up depression, including factors related to social engagement, physical activity, media use, and diet. MR follow-up analyses provided further support for the effects of social support-seeking, TV use, and other factors on depression risk.nnConclusionAs the field increasingly quantifies the role of genetic factors in complex conditions such as depression, knowledge of modifiable factors that could offset ones genetic risk has become highly relevant. Here, we present an approach to screening for potentially modifiable factors that may offset the risk of depression in general and among at-risk individuals. In light of the burden of disease associated with depression and the urgent need for actionable preventive strategies, this approach could help prioritize candidates for follow-up studies including clinical trials for depression prevention. ]]> Choi, K. W. Stein, M. B. Nishimi, K. Ge, T. Coleman, J. R. Chen, C.-Y. Ratanatharathorn, A. Zheutlin, A. B. Dunn, E. C. 23andMe Research Team, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Breen, G. Koenen, K. C. Smoller, J. W. 2019-09-08 doi:10.1101/759753 Cold Spring Harbor Laboratory Press 2019-09-08 <![CDATA[ Methylome-Wide Association Study Of Central Adiposity Implicates Genes Involved In Immune And Endocrine Systems ]]> https://biorxiv.org/content/10.1101/766832v1?rss=1 Justice, A. E. Chittoor, G. Gondalia, R. Melton, P. E. Lim, E. Grove, M. L. Whitsel, E. A. Liu, C.-T. Cupples, L. A. Fernandez-Rhodes, L. Guan, W. Bressler, J. Fornage, M. Boerwinkle, E. Li, Y. Demerath, E. Heard-Costa, N. Levy, D. Stewart, J. D. Baccarelli, A. Hou, L. Conneely, K. Mori, T. Beilin, L. J. Huang, R.-C. Gordon-Larsen, P. Howard, A. G. North, K. E. 2019-09-12 doi:10.1101/766832 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ DeltaNeTS+: Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks ]]> https://biorxiv.org/content/10.1101/788968v1?rss=1 Noh, H. Hua, Z. Chrysinas, P. Shoemaker, J. E. Gunawan, R. 2019-10-02 doi:10.1101/788968 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Evolutionary Origins of Recurrent Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/811133v1?rss=1 Sakamoto, H. Attiyeh, M. Gerold, J. Makohon-Moore, A. P. Hayashi, A. Hong, J. Kappagantula, R. Zhang, L. Melchor, J. Reiter, J. Heyde, A. Bielski, C. Penson, A. Chakravarty, D. O'Reilly, E. Wood, L. Hruban, R. H. Nowak, M. A. Socci, N. Taylor, B. S. Iacobuzio-Donahue, C. A. 2019-10-31 doi:10.1101/811133 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ An enhancer:involucrin regulatory module impacts human skin barrier adaptation out-of-Africa and modifies atopic dermatitis risk ]]> https://biorxiv.org/content/10.1101/816520v1?rss=1 Mathyer, M. E. Brettmann, E. A. Schmidt, A. D. Goodwin, Z. A. Quiggle, A. M. Oh, I. Y. Tycksen, E. Zhou, L. Estrada, Y. D. Wong, X. F. C. C. Denil, S. L. Matkovich, S. A. Shemer, A. Common, J. E. Guttman-Yassky, E. de Guzman Strong, C. 2019-11-05 doi:10.1101/816520 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ A Synthetic Biology Approach to Sequential Stripe Patterning and Somitogenesis ]]> https://biorxiv.org/content/10.1101/825406v1?rss=1 Wu, F. He, C. Fang, X. Baez, J. Ohnmacht, T. Zhang, Q. Chen, X. Allison, K. R. Kuang, Y. Wang, X. 2019-10-31 doi:10.1101/825406 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Predictive Coding Models for Pain Perception ]]> https://biorxiv.org/content/10.1101/843284v1?rss=1 Song, Y. Yao, M. Kemprecos, H. byrne, a. Xiao, Z. Zhang, Q. Singh, A. Wang, J. Chen, Z. S. 2019-11-18 doi:10.1101/843284 Cold Spring Harbor Laboratory Press 2019-11-18 <![CDATA[ Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation ]]> https://biorxiv.org/content/10.1101/848044v1?rss=1 Bhattacharyya, M. Lee, Y. K. Muratcioglu, S. Qiu, B. Nyayapati, P. Schulman, H. Groves, J. T. Kuriyan, J. 2019-11-20 doi:10.1101/848044 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis ]]> https://biorxiv.org/content/10.1101/850305v1?rss=1 Han, W. Ma, X. Balibar, C. J. Baxter Rath, C. M. Benton, B. Bermingham, A. Casey, F. Chie-Leon, B. Cho, M.-K. Frank, A. O. Frommlet, A. Ho, C.-M. Lee, P. S. Li, M. Lingel, A. Ma, S. Merritt, H. Ornelas, E. de Pascale, G. Prathapam, R. Prosen, K. R. Rasper, D. Ruzin, A. Sawyer, W. Shaul, J. Shen, X. Shia, S. Steffek, M. Subramanian, S. Vo, J. Wang, F. Wartchow, C. Uehara, T. 2019-12-17 doi:10.1101/850305 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline ]]> https://biorxiv.org/content/10.1101/857953v1?rss=1 Huels, A. Robins, C. Conneely, K. Edgar, R. D. De Jager, P. Bennett, D. A. Wingo, A. Wingo, T. S. 2019-11-29 doi:10.1101/857953 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ RNA- and ATAC-sequencing Reveals a Unique CD83+ Microglial Population Focally Depleted in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2023.05.17.540842v1?rss=1 Chatila, Z. K. Yadav, A. Mares, J. Flowers, X. E. Yun, T. D. Rashid, M. Talcoff, R. Pelly, Z. Zhang, Y. De Jager, P. L. Teich, A. F. Costa, R. M. Gomez, E. A. Martins, G. J. Alcalay, R. N. Vonsattel, J. P. Menon, V. Bradshaw, E. M. Przedborski, S. 2023-05-17 doi:10.1101/2023.05.17.540842 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Longevity-associated SMAD3 non-coding centenarian variant impairs a cell-type specific enhancer to reduce inflammation ]]> https://biorxiv.org/content/10.1101/2023.05.17.540984v1?rss=1 Yang, J. Tare, A. Zhang, L. Kim, S. Ryu, S. Guo, Q. Zhu, Y. Wang, X. Wang, X. Hudgins, A. D. Guan, D. Jin, C. Chang, H.-K. Atzmon, G. Milman, S. Barzilai, N. Vijg, J. Niedernhofer, L. Robbins, P. D. Suh, Y. 2023-05-18 doi:10.1101/2023.05.17.540984 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut ]]> https://biorxiv.org/content/10.1101/2023.05.18.541363v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@abb6fborg.highwire.dtl.DTLVardef@17a297eorg.highwire.dtl.DTLVardef@13a454borg.highwire.dtl.DTLVardef@9b699d_HPS_FORMAT_FIGEXP M_FIG C_FIG Summary statementThis study employs a mathematical model to investigate the interplay between morphogen gradients and tissue mechanics in regulating the collective cell movements that drive hindgut morphogenesis in the chick embryo. ]]> Nerurkar, N. Oikonomou, P. Cirne, H. C. 2023-05-18 doi:10.1101/2023.05.18.541363 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ Ordinary differential equations to construct invertible generative models of cell type and tissue-specific regulatory networks ]]> https://biorxiv.org/content/10.1101/2023.05.18.540731v1?rss=1 Niktab, E. Atkinson, P. H. Walterfang, M. Winship, I. Sturley, S. L. Munkacsi, A. B. 2023-05-19 doi:10.1101/2023.05.18.540731 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ A Hypothalamic Circuit Underlying the Dynamic Control of Social Homeostasis ]]> https://biorxiv.org/content/10.1101/2023.05.19.540391v1?rss=1 Liu, D. Rahman, M. Johnson, A. Tsutsui-Kimura, I. Pena, N. Talay, M. Logeman, B. L. Finkbeiner, S. Choi, S. Capo-Battaglia, A. Abdus-Saboor, I. Ginty, D. D. Uchida, N. Watabe-Uchida, M. Dulac, C. 2023-05-19 doi:10.1101/2023.05.19.540391 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ The regulation of Insulin/IGF-1 signaling by miR-142-3p associated with human longevity ]]> https://biorxiv.org/content/10.1101/2023.05.19.541542v1?rss=1 Wang, X. Jung, H. J. Milholland, B. Cui, J. Tazearslan, C. Atzmon, G. Wang, X. Yang, J. Guo, Q. Barzilai, N. Robbins, P. D. Suh, Y. 2023-05-20 doi:10.1101/2023.05.19.541542 Cold Spring Harbor Laboratory Press 2023-05-20 <![CDATA[ Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a ]]> https://biorxiv.org/content/10.1101/2023.05.18.541339v1?rss=1 Zhu, Y. Tazearslan, C. Rosenfeld, M. G. Fiser, A. Suh, Y. 2023-05-22 doi:10.1101/2023.05.18.541339 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Meta-omics analysis revealed structural and metabolic shifts of acidification communities after feeding with thermal hydrolysis pretreated food waste ]]> https://biorxiv.org/content/10.1101/2023.05.23.541846v1?rss=1 Jiang, M. Chandran, K. Khunjar, W. O. Gilmore, K. 2023-05-24 doi:10.1101/2023.05.23.541846 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Ouvrai: Opening access to remote VR studies of human behavioral neuroscience ]]> https://biorxiv.org/content/10.1101/2023.05.23.542017v1?rss=1 Cesanek, E. Shivkumar, S. Ingram, J. N. Wolpert, D. M. 2023-05-24 doi:10.1101/2023.05.23.542017 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner. ]]> https://biorxiv.org/content/10.1101/2023.05.23.542022v1?rss=1 Shao, Z. Lee, B. J. Zhang, H. Lin, X. Li, C. Jiang, W. Chirathivat, N. Gershik, S. Shen, M. M. Baer, R. Zha, S. 2023-05-24 doi:10.1101/2023.05.23.542022 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ A pancreatic cancer mouse model with human immunity ]]> https://biorxiv.org/content/10.1101/2023.05.24.542127v1?rss=1 Miyamura, N. Suzuki, K. Friedman, R. A. Floratos, A. Kunisada, Y. Masuda, K. Lowy, A. M. Tsuji, M. Sugahara, K. N. 2023-05-24 doi:10.1101/2023.05.24.542127 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Tumor-resident regulatory T cells in pancreatic cancer express the αvβ5 integrin as a targetable activation marker ]]> https://biorxiv.org/content/10.1101/2023.05.24.542137v1?rss=1 Suzuki, K. Kunisada, Y. Miyamura, N. Eikawa, S. Hurtado de Mendoza, T. Mose, E. S. Lu, C. Kuroda, Y. Ruoslahti, E. Lowy, A. M. Sugahara, K. N. 2023-05-24 doi:10.1101/2023.05.24.542137 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Sessile alveolar macrophage connexin-43 determines mechano-immunity in the lung ]]> https://biorxiv.org/content/10.1101/2023.05.24.541735v1?rss=1 Mthunzi, L. Gusarova, G. A. Islam, M. N. Bhattacharya, S. Bhattacharya, J. 2023-05-25 doi:10.1101/2023.05.24.541735 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ The hippocampus of the common marmoset is a GPS, but G is for gaze ]]> https://biorxiv.org/content/10.1101/2023.05.24.542209v1?rss=1 Piza, D. B. Corrigan, B. W. Gulli, R. A. Do Carmo, S. Cuello, A. C. Muller, L. Martinez-Trujillo, J. C. 2023-05-25 doi:10.1101/2023.05.24.542209 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Characterizing physical interactions between male and female mosquitoes (Aedes aegypti) in relation to female receptivity and insemination outcomes using a hydrophobic fluorescent dye ]]> https://biorxiv.org/content/10.1101/2023.05.25.542180v1?rss=1 Cramer, M. M. Gabel, T. M. Duvall, L. 2023-05-25 doi:10.1101/2023.05.25.542180 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Bayesian target optimisation for high-precision holographic optogenetics ]]> https://biorxiv.org/content/10.1101/2023.05.25.542307v1?rss=1 Triplett, M. A. Gajowa, M. Adesnik, H. Paninski, L. 2023-05-25 doi:10.1101/2023.05.25.542307 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ ZIPPI: proteome-scale sequence-based evaluation of protein-protein interaction models ]]> https://biorxiv.org/content/10.1101/2023.05.25.542344v1?rss=1 Zhao, H. Petrey, D. S. Murray, D. Honig, B. 2023-05-25 doi:10.1101/2023.05.25.542344 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Genuine beta bursts in human working memory: controlling for the influence of lower-frequency rhythms ]]> https://biorxiv.org/content/10.1101/2023.05.26.542448v1?rss=1 Rodriguez-Larios, J. Haegens, S. 2023-05-26 doi:10.1101/2023.05.26.542448 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. ]]> https://biorxiv.org/content/10.1101/2023.05.26.542515v1?rss=1 Menolfi, D. Lee, B. J. Zhang, H. Jiang, W. Brown, N. E. Wang, Y. Zhao, J. Holmes, A. Gershik, S. Rabadan, R. Kim, B. Zha, S. 2023-05-27 doi:10.1101/2023.05.26.542515 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Convergent evolution of noxious heat sensing by TRPA5, a novel class of heat sensor in Rhodnius prolixus ]]> https://biorxiv.org/content/10.1101/2023.05.26.542450v1?rss=1 Lienard, M. A. Baez-Nieto, D. Tsai, C.-C. Valencia-Montoya, W. A. Werin, B. Johanson, U. Lassance, J.-M. Pan, J. Q. Yu, N. Pierce, N. E. 2023-05-28 doi:10.1101/2023.05.26.542450 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ Barcoding of episodic memories in the hippocampus of a food-caching bird ]]> https://biorxiv.org/content/10.1101/2023.05.27.542597v1?rss=1 Chettih, S. N. Mackevicius, E. L. Hale, S. Aronov, D. 2023-05-28 doi:10.1101/2023.05.27.542597 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ A marker chromosome in psychosis identifies glycine decarboxylase (GLDC) as a novel regulator of neuronal and synaptic function in the hippocampus ]]> https://biorxiv.org/content/10.1101/2023.05.29.542745v1?rss=1 Kambali, M. Li, Y. Unichenko, P. Pliego, J. F. Yadav, R. Liu, J. McGuinness, P. Cobb, J. G. Wang, M. Nagarajan, R. Lyu, J. Vongsouthi, V. Jackson, C. J. Engin, E. Coyle, J. Shin, J. Talkowski, M. E. Homanics, G. E. Bolshakov, V. Henneberger, C. Rudolph, U. 2023-05-29 doi:10.1101/2023.05.29.542745 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in meso-carnivores in the northeastern United States ]]> https://biorxiv.org/content/10.1101/2023.05.31.541188v1?rss=1 Olarte-Castillo, X. A. Plimpton, L. D. McQueary, H. C. Sun, Y. Yu, Y. T. Cover, S. C. Richardson, A. N. Grenier, J. K. Cummings, K. J. Bunting, E. M. Diuk-Wasser, M. Needle, D. Schuler, K. Stanhope, M. J. Whittaker, G. Goodman, L. B. 2023-06-01 doi:10.1101/2023.05.31.541188 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.05.31.542897v1?rss=1 Ehrhardt, E. Whitehead, S. C. Namiki, S. Minegishi, R. Siwanowicz, I. Feng, K. Otsuna, H. FlyLight Project Team, Meissner, G. W. Stern, D. Truman, J. Shepherd, D. Dickinson, M. H. Dickson, B. J. Cohen, I. Card, G. M. Korff, W. 2023-06-01 doi:10.1101/2023.05.31.542897 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Cyanide-dependent control of terminal oxidase hybridization by Pseudomonas aeruginosa MpaR ]]> https://biorxiv.org/content/10.1101/2023.05.31.543164v1?rss=1 Smiley, M. K. Sekaran, D. C. Price-Whelan, A. Dietrich, L. E. P. 2023-06-01 doi:10.1101/2023.05.31.543164 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness ]]> https://biorxiv.org/content/10.1101/2023.06.02.543338v1?rss=1 Mok, S. Yeo, T. Hong, D. Shears, M. J. Ross, L. S. Ward, K. E. Dhingra, S. K. Kanai, M. Bridgford, J. L. Tripathi, A. K. Mlambo, G. Burkhard, A. Y. Fairhurst, K. J. Gil-Iturbe, E. Park, H. Rozenberg, F. D. Kim, J. Mancia, F. Quick, M. Uhlemann, A.-C. Sinnis, P. Fidock, D. A. 2023-06-03 doi:10.1101/2023.06.02.543338 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Deep-learning Based Pathological Assessment of Frozen Procurement Kidney Biopsies Predicts Graft Loss and Guides Organ Utilization: A Large-scale Retrospective Study ]]> https://biorxiv.org/content/10.1101/2023.05.31.543098v1?rss=1 Yi, Z. Xi, C. Menon, M. C. Cravedi, P. Tedla, F. Soto, A. Sun, Z. Liu, K. Zhang, J. Wei, C. Chen, M. Wang, W. Veremis, B. Garcia-barros, M. Kumar, A. Haakinson, D. Brody, R. Gallon, L. O'Connell, P. Naesens, M. Shapiro, R. Colvin, R. Ward, S. Salem, F. Zhang, W. 2023-06-04 doi:10.1101/2023.05.31.543098 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Behavioral control through the direct, focal silencing of neuronal activity ]]> https://biorxiv.org/content/10.1101/2023.05.31.543113v1?rss=1 Elleman, A. V. Milicic, N. Williams, D. J. Liu, C. J. Haynes, A. L. Simko, J. Ehrlich, D. E. Makinson, C. D. Du Bois, J. 2023-06-04 doi:10.1101/2023.05.31.543113 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Scalable projected Light Sheet Microscopy for high-resolution imaging of large samples ]]> https://biorxiv.org/content/10.1101/2023.05.31.543173v1?rss=1 Chen, Y. Gong, C. Chauhan, S. De La Cruz, E. D. Datta, M. S. Tomer, R. 2023-06-05 doi:10.1101/2023.05.31.543173 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. ]]> https://biorxiv.org/content/10.1101/2023.06.02.542863v1?rss=1 Jha, D. Al-Taie, Z. Krek, A. Eshghi, S. T. Fantou, A. Laurent, T. Tankelevich, M. Cao, X. Meringer, H. Livanos, A. Tokuyama, M. Cossarini, F. Bourreille, A. Josien, R. Hou, R. Canales-Herrerias, P. Ungaro, R. C. Kayal, M. Marion, J. Polydorides, A. D. Ko, H. M. D'souza, D. Merand, R. Kim-Schulze, S. Hackney, J. A. Nguyen, A. McBride, J. M. Yuan, G.-C. Colombel, J.-F. Martin, J. C. Argmann, C. Suarez-Farinas, M. Petralia, F. Mehandru, S. 2023-06-05 doi:10.1101/2023.06.02.542863 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution ]]> https://biorxiv.org/content/10.1101/2023.06.03.543563v1?rss=1 Banayan, N. E. Loughlin, B. J. Singh, S. Forouhar, F. Lu, G. Wong, K.-H. Neky, M. Hunt, H. S. Bateman, L. B. Tamez, A. Handelman, S. K. Price, W. N. Hunt, J. F. 2023-06-06 doi:10.1101/2023.06.03.543563 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation ]]> https://biorxiv.org/content/10.1101/2023.06.05.543407v1?rss=1 Marin, E. C. Morris, B. J. Stuerner, T. Champion, A. S. Krzeminski, D. Badalamente, G. Gkantia, M. Dunne, C. R. Eichler, K. Takemura, S.-y. Tamimi, I. F. M. Fang, S. Moon, S. S. Cheong, H. S. J. Li, F. Schlegel, P. Berg, S. FlyEM Project Team, Card, G. M. Costa, M. Shepherd, D. Jefferis, G. S. X. E. 2023-06-06 doi:10.1101/2023.06.05.543407 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ A Connectome of the Male Drosophila Ventral Nerve Cord ]]> https://biorxiv.org/content/10.1101/2023.06.05.543757v1?rss=1 Takemura, S.-y. Hayworth, K. J. Huang, G. B. Januszewski, M. Lu, Z. Marin, E. C. Preibisch, S. Xu, C. S. Bogovic, J. Champion, A. S. Cheong, H. S. J. Costa, M. Eichler, K. Katz, W. Knecht, C. Li, F. Morris, B. J. Ordish, C. Rivlin, P. K. Schlegel, P. Shinomiya, K. Sturner, T. Zhao, T. Badalamente, G. Bailey, D. Brooks, P. Canino, B. S. Clements, J. Cook, M. Duclos, O. Dunne, C. R. Fairbanks, K. Fang, S. Finley-May, S. Francis, A. George, R. Gkantia, M. Harrington, K. Hopkins, G. P. Hsu, J. Hubbard, P. M. Javier, A. Kainmueller, D. Korff, W. Kovalyak, 2023-06-06 doi:10.1101/2023.06.05.543757 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress ]]> https://biorxiv.org/content/10.1101/2023.06.05.543769v1?rss=1 Wolin, E. Guo, J. K. Blanco, M. R. Perez, A. A. Goronzy, I. N. Abdou, A. A. Gorhe, D. Guttman, M. Jovanovic, M. 2023-06-07 doi:10.1101/2023.06.05.543769 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1 ]]> https://biorxiv.org/content/10.1101/2023.06.07.544141v1?rss=1 Maurina, S. F. O'Sullivan, J. P. Sharma, G. Pineda Rodriguez, D. C. MacFadden, A. Cendali, F. Henen, M. A. Kieft, J. S. Glasgow, A. Steckelberg, A.-L. 2023-06-08 doi:10.1101/2023.06.07.544141 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Whole body cell map tracks tissue-specific immune cell accumulation and plasticity loss through ageing ]]> https://biorxiv.org/content/10.1101/2023.06.08.542671v1?rss=1 Mangiola, S. Milton, M. Ranathunga, N. LiWaiSuen, C. Yang, E. Hutchison, W. Garnham, A. Iskander, J. Pal, B. Yadav, V. J. Carey, V. Kallies, A. Bedoui, S. Morgan, M. Papenfuss, A. T. 2023-06-08 doi:10.1101/2023.06.08.542671 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Large-scale map of RNA binding protein interactomes across the mRNA life-cycle ]]> https://biorxiv.org/content/10.1101/2023.06.08.544225v1?rss=1 Rothamel, K. Street, L. Brannan, K. Jin, W. Rhine, K. Al-Azzam, N. Wolin, E. Bokor, B. Abdou, A. Doron-Mandel, E. W. Kim, J. Ma, Y. Ahdout, J. Dong, K. Madrigel, A. Mujumba, M. Jovanovic, M. Yeo, G. W. 2023-06-08 doi:10.1101/2023.06.08.544225 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Acvr1b loss promotes formation of precancerous lesions from acinar and ductal cells of origin ]]> https://biorxiv.org/content/10.1101/2023.06.08.544226v1?rss=1 Saeki, K. Patil, S. Sun, Y. Su, G. H. Kopp, J. L. 2023-06-08 doi:10.1101/2023.06.08.544226 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ A Deep Neural Network Two-part Model and Feature Importance Test for Semi-continuous Data ]]> https://biorxiv.org/content/10.1101/2023.06.07.544106v1?rss=1 0), others experience none (i.e., POP score = 0), indicating the existence of two distinct data processes at play. Existing parametric or semi-parametric two-part modeling methods for this type of semicontinuous data can fail to appropriately model these two underlying data processes as such methods rely heavily on (generalized) linear additive assumptions. However, many factors may interact to jointly influence the experience of POP non-additively and non-linearly. Motivated by this challenge and inspired by the flexibility of deep neural networks (DNN) to accurately approximate complex functions universally, we derive a DNN-based two-part model by adapting the conventional DNN methods by adding two additional components: a bootstrapping procedure along with a filtering algorithm to boost the stability of the conventional DNN, an approach we denote as sDNN. To improve the interpretability and transparency of sDNN, we further derive a feature importance testing procedure to identify important features contributing to the outcome measurements of the two data processes, denoting this approach fsDNN. We show that fsDNN not only offers a valid feature importance test but also that using the identified features can further improve the predictive performance of sDNN. The proposed sDNN- and fsDNN-based twopart models are applied to the analysis of real data from a POP study, in which application they clearly demonstrate advantages over the existing parametric and semi-parametric two-part models. Further, we conduct extensive numerical studies to demonstrate that sDNN and fsDNN consistently outperform the existing two-part models regardless of the data complexity. An R package implementing the proposed methods has been developed and deposited on GitHub (https://github.com/SkadiEye/fsDNN). ]]> Zou, B. Mi, X. Xenakis, J. Wu, D. Hu, J. Zou, F. 2023-06-09 doi:10.1101/2023.06.07.544106 Cold Spring Harbor Laboratory Press 2023-06-09 <![CDATA[ The chromatin landscape of healthy and injured cell types in the human kidney ]]> https://biorxiv.org/content/10.1101/2023.06.07.543965v1?rss=1 Gisch, D. L. Brennan, M. Lake, B. B. Basta, J. Keller, M. Melo Ferreira, R. Akilesh, S. Ghag, R. Lu, C. Cheng, Y.-H. Collins, K. S. Parikh, S. V. Rovin, B. H. Robbins, L. Conklin, K. Y. Diep, D. Zhang, B. Knoten, A. Barwinska, D. Asghari, M. Sabo, A. R. Ferkowicz, M. J. Sutton, T. A. Kelly, K. J. De Boer, I. H. Rosas, S. E. Kiryluk, K. Hodgin, J. B. Alakwaa, F. Jefferson, N. Gaut, J. P. Gehlenborg, N. Phillips, C. L. El-Achkar, T. M. Dagher, P. C. Hato, T. Zhang, K. Himmelfarb, J. Kretzler, M. Mollah, S. Kidney Precision Medicine Project, Jain, S. Ra 2023-06-10 doi:10.1101/2023.06.07.543965 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Glucocorticoid stress hormones stimulate vesicle-free Tau secretion and spreading in the brain ]]> https://biorxiv.org/content/10.1101/2023.06.07.544054v1?rss=1 Yu, Q. Du, F. Belli, I. Gomes, P. A. Sotiropoulos, I. Waites, C. L. 2023-06-10 doi:10.1101/2023.06.07.544054 Cold Spring Harbor Laboratory Press 2023-06-10 <![CDATA[ Transforming descending input into behavior: The organization of premotor circuits in the Drosophila Male Adult Nerve Cord connectome ]]> https://biorxiv.org/content/10.1101/2023.06.07.543976v1?rss=1 Cheong, H. S. J. Eichler, K. Stuerner, T. Asinof, S. K. Champion, A. S. Marin, E. C. Oram, T. B. Sumathipala, M. Venkatasubramanian, L. Namiki, S. Siwanowicz, I. Costa, M. Berg, S. Janelia FlyEM Project Team, Jefferis, G. S. X. E. Card, G. M. 2023-06-12 doi:10.1101/2023.06.07.543976 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation ]]> https://biorxiv.org/content/10.1101/2023.06.11.543863v1?rss=1 Ousalem, F. Singh, S. Bailey, N. A. Wong, K.-H. Zhu, L. Neky, M. J. Sibindi, C. Fei, J. Gonzalez, R. L. Boël, G. Hunt, J. F. 2023-06-12 doi:10.1101/2023.06.11.543863 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Resting-state EEG signatures of Alzheimer's disease are driven by periodic but not aperiodic changes ]]> https://biorxiv.org/content/10.1101/2023.06.11.544491v1?rss=1 Kopcanova, M. Tait, L. Donoghue, T. Stothart, G. Smith, L. Flores Sandoval, A. A. Davila-Perez, P. Buss, S. Shafi, M. M. Pascual-Leone, A. Fried, P. J. Benwell, C. S. Y. 2023-06-12 doi:10.1101/2023.06.11.544491 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB ]]> https://biorxiv.org/content/10.1101/2023.06.12.544631v1?rss=1 Acharya, A. Bret, H. Huang, J.-W. Muetze, M. Goese, M. Kissling, V. Seidel, R. Ciccia, A. Guerois, R. Cejka, P. 2023-06-12 doi:10.1101/2023.06.12.544631 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2023.06.12.544654v1?rss=1 Edwards, M. M. Wang, N. Massey, D. Egli, D. Koren, A. 2023-06-12 doi:10.1101/2023.06.12.544654 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Organization of an Ascending Circuit that Conveys Flight Motor State ]]> https://biorxiv.org/content/10.1101/2023.06.07.544074v1?rss=1 Cheong, H. S. J. Boone, K. N. Bennett, M. M. Salman, F. Ralston, J. D. Hatch, K. Allen, R. F. Phelps, A. M. Cook, A. P. Phelps, J. S. Erginkaya, M. Lee, W.-C. A. Card, G. M. Daly, K. C. Dacks, A. M. 2023-06-13 doi:10.1101/2023.06.07.544074 Cold Spring Harbor Laboratory Press 2023-06-13 <![CDATA[ Ultra-high field fMRI of visual mental imagery in typical imagers and aphantasic individuals ]]> https://biorxiv.org/content/10.1101/2023.06.14.544909v1?rss=1 Liu, J. Zhan, M. Hajhajate, D. Spagna, A. Dehaene, S. Cohen, L. Bartolomeo, P. 2023-06-14 doi:10.1101/2023.06.14.544909 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Common molecular signatures between coronavirus infection and Alzheimer's disease reveal targets for drug development ]]> https://biorxiv.org/content/10.1101/2023.06.14.544970v1?rss=1 Abyadeh, M. Yadav, V. Kaya, A. 2023-06-15 doi:10.1101/2023.06.14.544970 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome ]]> https://biorxiv.org/content/10.1101/2023.06.15.543498v1?rss=1 Singh, S. Gentry, R. C. Fu, Z. Bailey, N. A. Altomare, C. G. Wong, K.-H. Neky, M. J. Wang, C. Ray, K. K. Chi, Y.-C. Zhang, Z. Grassucci, R. A. Frank, J. Boël, G. Gonzalez, R. L. Hunt, J. F. 2023-06-17 doi:10.1101/2023.06.15.543498 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Unbiased single-cell morphology with self-supervised vision transformers ]]> https://biorxiv.org/content/10.1101/2023.06.16.545359v1?rss=1 Doron, M. Moutakanni, T. Chen, Z. S. Moshkov, N. Caron, M. Touvron, H. Bojanowski, P. Pernice, W. M. Caicedo, J. C. 2023-06-18 doi:10.1101/2023.06.16.545359 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Regional pulmonary perfusion, blood volume, and their relationship change during early ARDS in an experimental study ]]> https://biorxiv.org/content/10.1101/2023.06.19.545593v1?rss=1 Santos, A. Motta-Ribeiro, G. C. De Prost, N. Tucci, M. R. Wellman, T. J. Vidal Melo, M. F. Winkler, T. 2023-06-19 doi:10.1101/2023.06.19.545593 Cold Spring Harbor Laboratory Press 2023-06-19 <![CDATA[ Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms ]]> https://biorxiv.org/content/10.1101/2023.06.20.545666v1?rss=1 Dayton, H. Kiss, J. Wei, M. Chauhan, S. LaMarre, E. Cornell, W. C. Janakiraman, A. Min, W. Tomer, R. Price-Whelan, A. Nirody, J. A. Dietrich, L. E. 2023-06-20 doi:10.1101/2023.06.20.545666 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Jointly efficient encoding and decoding in neural populations ]]> https://biorxiv.org/content/10.1101/2023.06.21.545848v1?rss=1 Blanco Malerba, S. Micheli, A. Woodford, M. Azeredo da Silveira, R. 2023-06-21 doi:10.1101/2023.06.21.545848 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport ]]> https://biorxiv.org/content/10.1101/2023.06.19.545594v1?rss=1 Liu, Y. Jin, Y. Azizi, E. Blumberg, A. J. 2023-06-22 doi:10.1101/2023.06.19.545594 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Functional interaction of torsinA and its activators in liver lipid metabolism ]]> https://biorxiv.org/content/10.1101/2023.06.21.545957v1?rss=1 Hernandez-Ono, A. Zhao, Y. P. Murray, J. M. Ostlund, C. A. Lee, M. J. Ginsberg, H. N. Worman, H. J. Shin, J.-Y. 2023-06-22 doi:10.1101/2023.06.21.545957 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Small-field visual projection neurons detect translational optic flow and support walking control ]]> https://biorxiv.org/content/10.1101/2023.06.21.546024v1?rss=1 Isaacson, M. D. Eliason, J. L. Nern, A. Rogers, E. M. Lott, G. K. Tabachnik, T. Rowell, W. J. Edwards, A. W. Korff, W. L. Rubin, G. M. Branson, K. Reiser, M. B. 2023-06-22 doi:10.1101/2023.06.21.546024 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Blood flow directionality establishes the SCN as source and OVLT as target within a new vascular portal pathway ]]> https://biorxiv.org/content/10.1101/2023.06.20.545729v1?rss=1 Roy, R. K. Yao, Y. Green, I. K. Silver, R. Stern, J. E. 2023-06-24 doi:10.1101/2023.06.20.545729 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus MT:10398A>G ]]> https://biorxiv.org/content/10.1101/2023.06.22.546129v1?rss=1 G (rs2853826) was significantly associated with overall MT-heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT-heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci. ]]> Smullen, M. Olson, M. N. Murray, L. F. Suresh, M. Yan, G. Dawes, P. Barton, N. J. Mason, J. N. Zhang, Y. Fernandez-Fontaine, A. A. Church, G. M. Mastroeni, D. Wang, Q. Lim, E. T. Chan, Y. Readhead, B. 2023-06-25 doi:10.1101/2023.06.22.546129 G]]> Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Single neuron analysis of aging associated changes in learning reveals progressive impairmentsin transcriptional plasticity ]]> https://biorxiv.org/content/10.1101/2023.06.23.546336v1?rss=1 Badal, K. K. Sadhu, A. McCracken, C. Raveendra, B. L. Lozano-Villada, S. Shetty, A. C. Gillette, P. Zhao, Y. Stommes, D. Fieber, L. A. Schmale, M. C. Mahurkar, A. Hawkins, R. D. Puthanveettil, S. V. 2023-06-25 doi:10.1101/2023.06.23.546336 Cold Spring Harbor Laboratory Press 2023-06-25 <![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[ Present: flexible neuroscience- and technology-driven frameworks for the study of classroom engagement ]]> https://biorxiv.org/content/10.1101/2023.06.23.544732v1?rss=1 Shatto, C. L. Thorpe, J. N. Friedman, J. S. Rosario, I. E. Gu, Z. Shi, J. Zhuo, M. Brown, A. He, X. Spagna, A. 2023-06-26 doi:10.1101/2023.06.23.544732 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Synaptic vesicle glycoprotein 2C enhances vesicular storage of dopamine and counters dopaminergic toxicity ]]> https://biorxiv.org/content/10.1101/2023.06.26.546143v1?rss=1 Bucher, M. L. Dunn, A. R. Bradner, J. M. Egerton, K. S. Burkett, J. P. Johnson, M. A. Miller, G. W. 2023-06-26 doi:10.1101/2023.06.26.546143 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects ]]> https://biorxiv.org/content/10.1101/2023.06.26.546528v1?rss=1 Kasela, S. Aguet, F. Kim-Hellmuth, S. Brown, B. C. Nachun, D. C. Tracy, R. P. Durda, P. Liu, Y. Taylor, K. D. Johnson, W. C. Van Den Berg, D. Gabriel, S. Gupta, N. Smith, J. D. Blackwell, T. W. Rotter, J. I. Ardlie, K. G. Manichaikul, A. Rich, S. E. Barr, R. G. Lappalainen, T. 2023-06-27 doi:10.1101/2023.06.26.546528 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ The Salivary Microbiome and Predicted Metabolite Production are Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.06.27.546733v1?rss=1 Solfisburg, Q. S. Baldini, F. Baldwin-Hunter, B. L. Lee, H. H. Park, H. Freedberg, D. E. Lightdale, C. J. Korem, T. Abrams, J. A. 2023-06-28 doi:10.1101/2023.06.27.546733 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ A shared linguistic space for transmitting our thoughts from brain to brain in natural conversations ]]> https://biorxiv.org/content/10.1101/2023.06.27.546708v1?rss=1 Zada, Z. Goldstein, A. Y. Michelmann, S. Simony, E. Price, A. Hasenfratz, L. Barham, E. Zadbood, A. Doyle, W. Friedman, D. Dugan, P. Melloni, L. Devore, S. Flinker, A. Devinsky, O. Nastase, S. A. Hasson, U. 2023-06-29 doi:10.1101/2023.06.27.546708 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ A modular approach to handle in-vivo drift correction for high-density extracellular recordings ]]> https://biorxiv.org/content/10.1101/2023.06.29.546882v1?rss=1 Garcia, S. Windolf, C. Boussard, J. Dichter, B. Buccino, A. P. Yger, P. 2023-06-29 doi:10.1101/2023.06.29.546882 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Sex peptide receptor is not required for refractoriness to remating or induction of egg laying in Aedes aegypti ]]> https://biorxiv.org/content/10.1101/2023.06.28.546954v1?rss=1 Amaro, I. A. Wohl, M. P. Pitcher, S. Alfonso-Parra, C. Avila, F. W. Paige, A. S. Helinski, M. Duvall, L. B. Harrington, L. C. Wolfner, M. F. McMeniman, C. J. 2023-06-30 doi:10.1101/2023.06.28.546954 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ A frame and a hotspot in cochlear mechanics ]]> https://biorxiv.org/content/10.1101/2023.06.29.547111v1?rss=1 Strimbu, C. E. Chiriboga, L. A. Frost, B. L. Fallah, E. Olson, E. S. 2023-06-30 doi:10.1101/2023.06.29.547111 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ The subacromial bursa is a key regulator of the rotator cuff and a new therapeutic target for improving repair ]]> https://biorxiv.org/content/10.1101/2023.07.01.547347v1?rss=1 Marshall, B. P. Ferrer, X. E. Kunes, J. A. Innis, A. C. Luzzi, A. J. Forrester, L. A. Burt, K. G. Lee, A. J. Song, L. Hung, C. T. Levine, W. N. Kovacevic, D. Thomopoulos, S. 2023-07-02 doi:10.1101/2023.07.01.547347 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ BRD4 directs mitotic cell division by inhibiting DNA damage ]]> https://biorxiv.org/content/10.1101/2023.07.02.547436v1?rss=1 Ozato, K. Wu, T. Hou, H. Dey, A. Bachu, M. Chen, X. Wisniewski, J. Kudoh, F. Chen, C. Chauhan, S. Xiao, H. Pan, R. 2023-07-02 doi:10.1101/2023.07.02.547436 Cold Spring Harbor Laboratory Press 2023-07-02 <![CDATA[ Efficient numerosity estimation under limited time ]]> https://biorxiv.org/content/10.1101/2023.07.03.547493v1?rss=1 Heng, J. A. Woodford, M. Polania, R. 2023-07-03 doi:10.1101/2023.07.03.547493 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Serotonergic modulation of the BNST-CeA circuit promotes sex differences in fear learning ]]> https://biorxiv.org/content/10.1101/2023.07.03.547577v1?rss=1 Ravenelle, R. Fernandes-Henriques, C. Lee, J. Liu, J. Likhtik, E. Burghardt, N. S. 2023-07-03 doi:10.1101/2023.07.03.547577 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Covalent macrocyclic proteasome inhibitors mitigate resistance in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2023.07.03.547579v1?rss=1 Bennett, J. M. Ward, K. E. Muir, R. Kabeche, S. Yoo, E. Yeo, T. Lam, G. Berger, G. Faucher, F. F. Lin, G. Gerwick, W. H. Yeh, E. Fidock, D. A. Bogyo, M. 2023-07-03 doi:10.1101/2023.07.03.547579 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis ]]> https://biorxiv.org/content/10.1101/2023.07.03.547507v1?rss=1 Inamo, J. Keegan, J. Griffith, A. Ghosh, T. Horisberger, A. Howard, K. Pulford, J. Murzin, E. Hancock, B. Jonsson, A. H. Seifert, J. Feser, M. L. Norris, J. M. Cao, Y. Apruzzese, W. Bridges, S. L. Bykerk, V. Goodman, S. Donlin, L. Firestein, G. S. Perlman, H. Bathon, J. M. Hughes, L. B. Tabechian, D. Filer, A. Pitzalis, C. H. Anolik, J. Moreland, L. Guthridge, J. M. James, J. A. Brenner, M. B. Raychaudhuri, S. Sparks, J. A. The Accelerating Medicines Partnership RA/SLE Network, Holers, V. M. Deane, K. D. Lederer, J. A. Rao, D. A. Zhang, F. 2023-07-04 doi:10.1101/2023.07.03.547507 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Neuron-dependent tuft cell expansion initiates sinonasal allergic Type 2 inflammation ]]> https://biorxiv.org/content/10.1101/2023.07.04.547596v1?rss=1 Ortiz-Carpena, J. F. Inclan-Rico, J. M. Weiner, M. B. Pastore, C. F. Hung, L.-Y. Wilkerson, W. B. Lin, C. Gentile, M. E. Cohen, N. A. Abdus-Saboor, I. Vaughan, A. E. Rossi, H. L. Herbert, D. R. 2023-07-04 doi:10.1101/2023.07.04.547596 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ A Brain-Wide Map of Neural Activity during Complex Behaviour ]]> https://biorxiv.org/content/10.1101/2023.07.04.547681v1?rss=1 International Brain Lab, Benson, B. Benson, J. Birman, D. Bonacchi, N. Carandini, M. Catarino, J. A. Chapuis, G. A. Churchland, A. K. Dan, Y. Dayan, P. DeWitt, E. E. Engel, T. A. Fabbri, M. Faulkner, M. Fiete, I. R. Findling, C. Freitas-Silva, L. Gercek, B. Harris, K. D. Hausser, M. Hofer, S. B. Hu, F. Hubert, F. Huntenburg, J. M. Khanal, A. Krasniak, C. Langdon, C. Lau, P. Y. P. Mainen, Z. F. Meijer, G. T. Miska, N. J. Mrsic-Flogel, T. D. Noel, J.-P. Nylund, K. Pan-Vazquez, A. Pouget, A. Rossant, C. Roth, N. Schaeffer, R. Schartner, M. Shi, Y. Socha 2023-07-04 doi:10.1101/2023.07.04.547681 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Brain-wide representations of prior information in mouse decision-making ]]> https://biorxiv.org/content/10.1101/2023.07.04.547684v1?rss=1 Findling, C. Hubert, F. International Brain Laboratory, Acerbi, L. Benson, B. Benson, J. Birman, D. Bonacchi, N. Carandini, M. Catarino, J. A. Chapuis, G. A. Churchland, A. K. Dan, Y. DeWitt, E. E. Engel, T. A. Fabbri, M. Faulkner, M. Fiete, I. R. Freitas-Silva, L. Gercek, B. Harris, K. D. Hausser, M. Hofer, S. B. Hu, F. Huntenburg, J. M. Khanal, A. Krasniak, C. Langdon, C. Latham, P. E. Lau, P. Y. P. Meijer, G. T. Miska, N. J. Mrsic-Flogel, T. D. Noel, J.-P. Nylund, K. Paninski, L. Pan-Vazquez, A. Pillow, J. Rossant, C. Roth, N. Schaeffer, R. Schartn 2023-07-04 doi:10.1101/2023.07.04.547684 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ A neural mechanism for discriminating threatening from safe social experiences ]]> https://biorxiv.org/content/10.1101/2023.07.04.547723v1?rss=1 Kassraian, P. Bigler, S. Gilly, D. M. Shrotri, N. Siegelbaum, S. A. 2023-07-04 doi:10.1101/2023.07.04.547723 Cold Spring Harbor Laboratory Press 2023-07-04 <![CDATA[ Immune-Epithelial Dynamics and Tissue Remodeling in Chronically Inflamed Nasal Epithelium via Multi-scaled Transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.07.01.547352v1?rss=1 Liao, G. Nakayama, T. Lee, I. T. Zhu, B. Overdevest, J. B. Yan, C. H. Zarabanda, D. Gall, P. A. Dholakia, S. S. Borchard, N. A. Yang, A. Kim, D. Bravo, D. T. Patel, Z. M. Hwang, P. H. Wagh, D. Coller, J. Philips, K. Chang, M. T. Lechner, M. Ma, Q. Li, Z. Nolan, G. Barouch, D. Nayak, J. V. Jiang, S. 2023-07-05 doi:10.1101/2023.07.01.547352 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues ]]> https://biorxiv.org/content/10.1101/2023.07.06.547944v1?rss=1 Caron, D. P. Specht, W. L. Chen, D. Wells, S. B. Szabo, P. A. Jensen, I. J. Farber, D. L. Sims, P. A. 2023-07-07 doi:10.1101/2023.07.06.547944 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f ]]> https://biorxiv.org/content/10.1101/2023.07.07.547762v1?rss=1 Gusach, A. Lee, Y. Khoshgrudi, A. N. Mukhaleva, E. Ma, N. Koers, E. J. Chen, Q. Edwards, P. Huang, F. Kim, J. Mancia, F. Veprintsev, D. J. Vaidehi, N. Weyand, S. Tate, C. G. 2023-07-07 doi:10.1101/2023.07.07.547762 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Deep FASTQ and BAM co-compression in Genozip 15 ]]> https://biorxiv.org/content/10.1101/2023.07.07.548069v1?rss=1 Lan, D. M. Hughes, D. S. T. Llamas, B. 2023-07-07 doi:10.1101/2023.07.07.548069 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ Sex-Specific Effects of Anxiety on Cognition and Activity-Dependent Neural Networks: Insights from (Female) Mice and (Wo)Men ]]> https://biorxiv.org/content/10.1101/2023.07.07.548180v1?rss=1 Hunsberger, H. Lee, S. Jin, M. Lanio, M. Whye, A. Cha, J. Scarlata, M. Jayaseelan, K. Denny, C. A. 2023-07-10 doi:10.1101/2023.07.07.548180 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Cholesterol-associated Locus EHBP1 Protects against NASH Fibrosis ]]> https://biorxiv.org/content/10.1101/2023.07.08.548218v1?rss=1 C variant in NASH patients is associated with decreased hepatic EHBP1 expression and augmented NASH fibrosis. Congruent with the human data, EHBP1 loss- and gain-of-function increases and decreases NASH fibrosis in mice, respectively. Mechanistic studies reveal that EHBP1 promotes sortilin (SORT1)-mediated PCSK9 secretion, leading to LDLR degradation, decreased LDL uptake, and reduced TAZ, a fibrogenic effector. Moreover, we show that the TNF/PPAR pathway suppresses EHBP1 in NASH. These data not only provide new mechanistic insight into the role of EHBP1 in cholesterol metabolism and NASH fibrosis by uncovering the interaction between EHBP1 and other cholesterol-related loci, including SORT1, PCSK9, and LDLR, but also elucidate a novel interplay between inflammation and EHBP1-mediated cholesterol metabolism. HighlightsHepatic EHBP1 is reduced in human and mouse fibrotic NASH EHBP1 rs10496099 T>C is associated with decreased hepatic EHBP1 and augmented NASH EHBP1 reduces LDLR, cholesterol uptake, and TAZ in hepatocytes EHBP1 promotes sortilin-mediated PCSK9 secretion in hepatocytes TNF suppresses EHBP1 expression in hepatocytes ]]> Ma, F. Longo, M. Huang, X. Meroni, M. Prakash, S. Paolini, E. Bhattacharya, D. Wang, S. Wang, X. Mughal, S. Hussain, S. Anand, S. Yurdagul, A. Rom, O. Dongiovanni, P. Friedman, S. Cai, B. 2023-07-10 doi:10.1101/2023.07.08.548218 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling ]]> https://biorxiv.org/content/10.1101/2023.07.10.548257v1?rss=1 van Vlimmeren, A. E. Voleti, R. Chartier, C. A. Jiang, Z. Karandur, D. Shah, N. H. 2023-07-10 doi:10.1101/2023.07.10.548257 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Signatures of Jamming in the Cellular Potts Model ]]> https://biorxiv.org/content/10.1101/2023.07.10.548321v1?rss=1 Devanny, A. J. Lee, D. J. Kampman, L. Kaufman, L. J. 2023-07-11 doi:10.1101/2023.07.10.548321 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Glutamatergic neuronal activity regulates angiogenesis and blood-retinal barrier maturation via Norrin/β-catenin signaling ]]> https://biorxiv.org/content/10.1101/2023.07.10.548410v1?rss=1 Biswas, S. Shahriar, S. Bachay, G. Arvanitis, P. Brunken, W. J. Agalliu, D. 2023-07-11 doi:10.1101/2023.07.10.548410 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features ]]> https://biorxiv.org/content/10.1101/2023.07.11.548536v1?rss=1 Hoge, C. R. de Manuel, M. Mahgoub, M. Okami, N. Fuller, Z. L. Banerjee, S. Baker, Z. Mcnulty, M. Andolfatto, P. Macfarlan, T. S. Schumer, M. Tzika, A. C. Przeworski, M. 2023-07-11 doi:10.1101/2023.07.11.548536 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Beyond Correlation: Optimal Transport Metrics For Characterizing Representational Stability and Remapping in Neurons Encoding Spatial Memory ]]> https://biorxiv.org/content/10.1101/2023.07.11.548592v1?rss=1 Aoun, A. Shetler, O. Hussaini, S. A. 2023-07-13 doi:10.1101/2023.07.11.548592 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Hue selectivity from recurrent circuitry in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.07.12.548573v1?rss=1 Christenson, M. P. Sanz Diez, A. Heath, S. L. Saavedra-Weisenhaus, M. Adashi, A. Abbott, L. Behnia, R. 2023-07-13 doi:10.1101/2023.07.12.548573 Cold Spring Harbor Laboratory Press 2023-07-13 <![CDATA[ Clonal CD8 T cells in the leptomeninges are locally controlled and influence microglia in human neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.07.13.548931v1?rss=1 Hobson, R. Levy, S. H. S. Flaherty, D. Xiao, H. Ciener, B. Reddy, H. Singal, C. Teich, A. F. Shneider, N. A. Bradshaw, E. M. Elyaman, W. 2023-07-14 doi:10.1101/2023.07.13.548931 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Mechanism of target site selection by type V-K CRISPR-associated transposases ]]> https://biorxiv.org/content/10.1101/2023.07.14.548620v1?rss=1 George, J. T. Acree, C. Park, J.-U. Kong, M. Wiegand, T. Pignot, Y. L. Kellogg, E. H. Greene, E. C. Sternberg, S. H. 2023-07-14 doi:10.1101/2023.07.14.548620 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Regression and Alignment for Functional Data and Network Topology ]]> https://biorxiv.org/content/10.1101/2023.07.13.548836v1?rss=1 Tu, D. Wrobel, J. Satterthwaite, T. D. Goldsmith, J. Gur, R. C. Gur, R. E. Gertheiss, J. Bassett, D. S. Shinohara, R. T. 2023-07-15 doi:10.1101/2023.07.13.548836 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization ]]> https://biorxiv.org/content/10.1101/2023.07.13.548849v1?rss=1 Antin, B. Sadahiro, M. Gajowa, M. Triplett, M. A. Adesnik, H. Paninski, L. 2023-07-15 doi:10.1101/2023.07.13.548849 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition. ]]> https://biorxiv.org/content/10.1101/2023.07.17.547998v1?rss=1 Wei, J. Wood, T. W. P. Flaherty, K. Enny, A. Andrescavage, A. Brazer, D. Navon, D. Stewart, T. A. Cohen, H. Shanabag, A. Kuroda, S. Braasch, I. Nakamura, T. 2023-07-17 doi:10.1101/2023.07.17.547998 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Optical Control of G-Actin with a Photoswitchable Latrunculin ]]> https://biorxiv.org/content/10.1101/2023.07.17.549222v1?rss=1 Veprek, N. A. Cooper, M. H. Laprell, L. Yang, E. J.-N. Folkerts, S. Bao, R. Oertner, T. G. Pon, L. A. Zuchero, J. B. Trauner, D. H. 2023-07-19 doi:10.1101/2023.07.17.549222 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Generating object-based attention through reconstruction ]]> https://biorxiv.org/content/10.1101/2023.07.17.549340v1?rss=1 Ahn, S. Adeli, H. Zelinsky, G. 2023-07-19 doi:10.1101/2023.07.17.549340 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Elastic fibers define embryonic tissue stiffness to enable buckling morphogenesis of the small intestine ]]> https://biorxiv.org/content/10.1101/2023.07.18.549562v1?rss=1 Loffet, E. A. Durel, J. F. Kam, R. Lim, H. Nerurkar, N. L. 2023-07-19 doi:10.1101/2023.07.18.549562 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ A spatial threshold for astrocyte calcium surge ]]> https://biorxiv.org/content/10.1101/2023.07.18.549563v1?rss=1 23% of the arborization being activated was surpassed. Using transgenic IP3R2-/- mice, we found that type-2 IP3 receptors were necessary for the generation of the astrocyte calcium surge. We finally show using in situ electrophysiological recordings that the spatial threshold of the astrocyte calcium signal consequently determined the gliotransmitter release. Present results reveal a fundamental property of astrocyte calcium physiology, i.e., a spatial threshold for the astrocyte intracellular calcium signal propagation, which depends on astrocyte intrinsic properties and governs the astrocyte integration of local synaptic activity and the subsequent neuromodulation. One-Sentence SummaryThere is a spatial threshold for the astrocyte intracellular calcium signal propagation that is determined by astrocyte intrinsic properties and controls gliotransmission. ]]> Lines, J. Baraibar, A. M. Nanclares, C. Martin, E. Aguilar, J. d. l. R. Kofuji, P. Navarrete, M. Araque, A. 2023-07-19 doi:10.1101/2023.07.18.549563 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.07.18.549585v1?rss=1 Li, J. J. Vasciaveo, A. Karagiannis, D. Sun, Z. Chen, X. Socciarelli, F. Frankenstein, Z. Zou, M. Pannellini, T. Chen, Y. Gardner, K. Robinson, B. D. de Bono, J. Abate-Shen, C. Rubin, M. A. Loda, M. Sawyers, C. L. Califano, A. Lu, C. Shen, M. M. 2023-07-19 doi:10.1101/2023.07.18.549585 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation ]]> https://biorxiv.org/content/10.1101/2023.07.18.549587v1?rss=1 Smith, T. M. Arora, M. Austin, C. Avila, J. N. Duval, M. Lim, T. T. Piper, P. Vaiglova, P. Vos, J. d. Williams, I. S. Zhao, J.-x. Green, D. R. 2023-07-19 doi:10.1101/2023.07.18.549587 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ Early life adversity reduces affiliative behavior towards a distressed cagemate and leads to sex-specific alterations in corticosterone responses ]]> https://biorxiv.org/content/10.1101/2023.07.20.549876v1?rss=1 Breton, J. M. Cort, Z. Demaestri, C. Critz, M. Nevins, S. Downend, K. Ofray, D. Romeo, R. D. Bath, K. G. 2023-07-23 doi:10.1101/2023.07.20.549876 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Detection and localization of conspecifics in ghost knifefish are influenced by the relationship between the spatial organization of receptors and signals. ]]> https://biorxiv.org/content/10.1101/2023.07.20.549925v1?rss=1 Ramachandra, K. L. Milam, O. E. Pedraja, F. Cornett, J. D. Marsat, G. 2023-07-23 doi:10.1101/2023.07.20.549925 Cold Spring Harbor Laboratory Press 2023-07-23 <![CDATA[ Structure and symmetries of the genetic codes for vertebrate, ascidian and yeast mitochondria ]]> https://biorxiv.org/content/10.1101/2023.07.23.548166v1?rss=1 Kohli, R. 2023-07-24 doi:10.1101/2023.07.23.548166 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ The brain hierarchically represents the past and future during multistep anticipation ]]> https://biorxiv.org/content/10.1101/2023.07.24.550399v1?rss=1 Tarder-Stoll, H. Baldassano, C. Aly, M. 2023-07-26 doi:10.1101/2023.07.24.550399 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements ]]> https://biorxiv.org/content/10.1101/2023.07.24.549988v1?rss=1 Trauernicht, M. Rastogi, C. Manzo, S. G. Bussemaker, H. J. van Steensel, B. 2023-07-27 doi:10.1101/2023.07.24.549988 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ The Nucleoporin Nup153 Is the Anchor for Kif1a during Basal Nuclear migration in Brain Progenitor Cells ]]> https://biorxiv.org/content/10.1101/2023.07.25.550108v1?rss=1 Falnikar, A. Quintremil, S. Helmer, P. Vallee, R. B. 2023-07-28 doi:10.1101/2023.07.25.550108 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ The reach of reactivation: Effects of consciously-triggered versus unconsciously-triggered reactivation of associative memory ]]> https://biorxiv.org/content/10.1101/2023.07.26.546400v1?rss=1 Tal, A. Schechtman, E. Caughran, B. Paller, K. Davachi, L. 2023-07-28 doi:10.1101/2023.07.26.546400 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Neural mechanisms of transitive inference and fast knowledge reassembly in learning neural networks ]]> https://biorxiv.org/content/10.1101/2023.07.27.550739v1?rss=1 B and B>C, infer A>C), which can be quickly and globally reorganized upon learning a new item (learn A>B>C and D>E>F, then C>D, and infer B>E). Despite considerable study, neural mechanisms of transitive inference and fast reassembly of existing knowledge remain elusive. Here we adopt a meta-learning ("learning-to-learn") approach. We train artificial neural networks, endowed with synaptic plasticity and neuromodulation, to be able to learn novel orderings of arbitrary stimuli from repeated presentation of stimulus pairs. We then obtain a complete mechanistic understanding of this discovered neural learning algorithm. Remarkably, this learning involves active cognition: items from previous trials are selectively reinstated in working memory, enabling delayed, self-generated learning and knowledge reassembly. These findings identify a new mechanism for relational learning and insight, suggest new interpretations of neural activity in cognitive tasks, and highlight a novel approach to discovering neural mechanisms capable of supporting cognitive behaviors. ]]> Miconi, T. Kay, K. 2023-07-28 doi:10.1101/2023.07.27.550739 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Prefrontal Cortex Neural Correlates of the Contraction Bias in Frequency Discrimination ]]> https://biorxiv.org/content/10.1101/2023.07.27.550794v1?rss=1 Serrano-Fernandez, L. Beiran, M. Romo, R. Parga, N. 2023-07-28 doi:10.1101/2023.07.27.550794 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ ChromaFold predicts the 3D contact map from single-cell chromatin accessibility ]]> https://biorxiv.org/content/10.1101/2023.07.27.550836v1?rss=1 Gao, V. R. Yang, R. Das, A. Luo, R. Luo, H. McNally, D. R. Karagiannidis, I. Rivas, M. A. Wang, Z.-m. Barisic, D. Karbalayghareh, A. Wong, W. Zhan, Y. Chin, C. R. Noble, W. S. Bilmes, J. A. Apostolou, E. Kharas, M. Beguelin, W. Viny, A. D. Huangfu, D. Rudensky, A. Melnick, A. Leslie, C. S. 2023-07-28 doi:10.1101/2023.07.27.550836 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Universal length fluctuations of actin structures found in cells ]]> https://biorxiv.org/content/10.1101/2023.07.27.550898v1?rss=1 Rosario, A. A. A. McInally, S. G. Jelenkovic, P. R. Goode, B. L. Kondev, J. 2023-07-28 doi:10.1101/2023.07.27.550898 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Functional and anatomical connectivity predict brain stimulation's mnemonic effects ]]> https://biorxiv.org/content/10.1101/2023.07.27.550851v1?rss=1 Ezzyat, Y. Kragel, J. E. Solomon, E. A. Lega, B. C. Aronson, J. P. Jobst, B. C. Gross, R. E. Sperling, M. R. Worrell, G. A. Sheth, S. A. Wanda, P. A. Rizzuto, D. S. Kahana, M. J. 2023-07-29 doi:10.1101/2023.07.27.550851 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2023.07.29.551032v1?rss=1 Sun, C. Zhou, C. Daneshvar, K. Kratkiewicz, A. J. Ben Saad, A. Hess, A. Chen, J. Y. Pondick, J. V. York, S. R. Li, W. Moran, S. P. Gentile, S. Ur Rahman, R. Li, Z. Sparks, R. Habboub, T. Kim, B.-M. Choi, M. Affo, S. Schwabe, R. F. Popov, Y. V. Mullen, A. C. 2023-07-30 doi:10.1101/2023.07.29.551032 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Extrachromosomal Telomeres Derived from Excessive Strand Displacements ]]> https://biorxiv.org/content/10.1101/2023.07.31.551186v1?rss=1 Lee, J. Lee, J. Sohn, E. J. Taglialatela, A. O'Sullivan, R. J. Ciccia, A. Min, J. 2023-07-31 doi:10.1101/2023.07.31.551186 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria ]]> https://biorxiv.org/content/10.1101/2023.08.01.551457v1?rss=1 Liao, J. Yeong, V. Obermeyer, A. C. 2023-08-01 doi:10.1101/2023.08.01.551457 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ EZH2 inhibition sensitizes IDH1R132H mutant gliomas to histone deacetylase inhibitor. ]]> https://biorxiv.org/content/10.1101/2023.07.31.551045v1?rss=1 Sprinzen, L. Garcia, F. G. Mela, A. Lei, L. Upadhyayula, P. Mahajan, A. Humala, N. Manier, L. Caprioli, R. M. Quinones-Hinojosa, A. Casaccia, P. Canoll, P. 2023-08-02 doi:10.1101/2023.07.31.551045 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[ Stimulation of mRNA translation rescues hippocampal synaptic plasticity and memory in mouse models of Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.08.03.551808v1?rss=1 Ribeiro, F. C. Cozachenco, D. Argyrousi, E. K. Staniszewski, A. Wiebe, S. Calixtro, J. D. Soares-Neto, R. Al-Chami, A. El Sayegh, F. Bermudez, S. Arsenault, E. Cossenza, M. Lacaille, J.-C. Nader, K. Sun, H. De Felice, F. G. Lourenco, M. V. Arancio, O. Aguilar-Valles, A. Sonenberg, N. Ferreira, S. T. 2023-08-03 doi:10.1101/2023.08.03.551808 Cold Spring Harbor Laboratory Press 2023-08-03 <![CDATA[ Predicting brain activity using Transformers ]]> https://biorxiv.org/content/10.1101/2023.08.02.551743v1?rss=1 Adeli, H. Minni, S. Kriegeskorte, N. 2023-08-05 doi:10.1101/2023.08.02.551743 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ A computational pipeline for spatial mechano-transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.08.03.551894v1?rss=1 Hallou, A. He, R. Simons, B. D. Dumitrascu, B. 2023-08-05 doi:10.1101/2023.08.03.551894 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Material Properties of Nonpregnant and Pregnant Human Uterine Layers ]]> https://biorxiv.org/content/10.1101/2023.08.07.551726v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@2d347eorg.highwire.dtl.DTLVardef@1d14584org.highwire.dtl.DTLVardef@2b0920org.highwire.dtl.DTLVardef@1642359_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fodera, D. M. Russell, S. R. Lund-Jackson, J. L. Fang, S. Vink, J.-S. Y. Oyen, M. L. Myers, K. M. 2023-08-08 doi:10.1101/2023.08.07.551726 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Nuclear Factor Kappa B Over-Activation in the Intervertebral Disc Leads to Macrophage Recruitment and Severe Disc Degeneration ]]> https://biorxiv.org/content/10.1101/2023.08.07.552274v1?rss=1 Burt, K. G. Kim, M. K. M. Viola, D. C. Abraham, A. C. Chahine, N. O. 2023-08-08 doi:10.1101/2023.08.07.552274 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Top-down attention shifts behavioral and neural event boundaries in narratives with overlapping event scripts ]]> https://biorxiv.org/content/10.1101/2023.08.08.552465v1?rss=1 De Soares, A. Kim, T. Mugisho, F. Zhu, E. Lin, A. Zheng, C. Baldassano, C. 2023-08-09 doi:10.1101/2023.08.08.552465 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Non-invasive vagus nerve stimulation improves sensory performance in humans ]]> https://biorxiv.org/content/10.1101/2023.08.08.552508v1?rss=1 Jigo, M. Carmel, J. B. Wang, Q. Rodenkirch, C. 2023-08-12 doi:10.1101/2023.08.08.552508 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ The Influence of Multivalent Charge and PEGylation on Shape Transitions in Fluid Lipid Assemblies: From Vesicles to Discs, Rods, and Spheres ]]> https://biorxiv.org/content/10.1101/2023.08.09.552538v1?rss=1 Steffes, V. M. Zhang, Z. Ewert, K. K. Safinya, C. R. 2023-08-13 doi:10.1101/2023.08.09.552538 Cold Spring Harbor Laboratory Press 2023-08-13 <![CDATA[ Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring ]]> https://biorxiv.org/content/10.1101/2023.08.11.552969v1?rss=1 Correa Pinto, D. Canal Delgado, I. Yang, H. Clemenceau, A. Corvelo, A. Narzisi, G. Musunuri, R. Berger, J. Hendricks, L. Tokumura, K. Luo, N. Li, H. Oury, F. Ducy, P. Yadav, V. K. Li, X. Karsenty, G. 2023-08-14 doi:10.1101/2023.08.11.552969 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ DARTsort: A modular drift tracking spike sorter for high-density multi-electrode probes ]]> https://biorxiv.org/content/10.1101/2023.08.11.553023v1?rss=1 Boussard, J. Windolf, C. Hurwitz, C. Lee, H. D. Yu, H. Winter, O. Paninski, L. 2023-08-14 doi:10.1101/2023.08.11.553023 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types ]]> https://biorxiv.org/content/10.1101/2023.08.13.553130v1?rss=1 Zeppilli, S. Gurrola, A. O. Demetci, P. Brann, D. Attey, R. Zilkha, N. Kimchi, T. Datta, S. R. Singh, R. Tosches, M. A. Crombach, A. Fleischmann, A. 2023-08-14 doi:10.1101/2023.08.13.553130 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ SARS-CoV-2 Neutralizing Antibodies Following a Second BA.5 Bivalent Booster ]]> https://biorxiv.org/content/10.1101/2023.08.13.553148v1?rss=1 Wang, Q. Bowen, A. Ho, J. Zhang, R. Valdez, R. Stoneman, E. Gordon, A. Lihong, L. Ho, D. D. 2023-08-14 doi:10.1101/2023.08.13.553148 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells ]]> https://biorxiv.org/content/10.1101/2023.08.14.553318v1?rss=1 Mellis, I. A. Bodkin, N. Goyal, Y. 2023-08-15 doi:10.1101/2023.08.14.553318 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Increasing the accuracy of single-molecule data analysis using tMAVEN ]]> https://biorxiv.org/content/10.1101/2023.08.15.553409v1?rss=1 Verma, A. R. Ray, K. K. Bodick, M. E. Kinz-Thompson, C. D. Gonzalez, R. L. 2023-08-17 doi:10.1101/2023.08.15.553409 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ A Computational Approach for the Identification of Novel L1 Transcriptional Regulators ]]> https://biorxiv.org/content/10.1101/2023.08.15.553416v1?rss=1 Bravo, J. I. Mizrahi, C. R. Kim, S. Zhang, L. Suh, Y. Benayoun, B. A. 2023-08-17 doi:10.1101/2023.08.15.553416 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells ]]> https://biorxiv.org/content/10.1101/2023.08.18.553799v1?rss=1 Rangan, R. Khavnekar, S. Lerer, A. Johnston, J. Kelley, R. Obr, M. Kotecha, A. Zhong, E. D. 2023-08-18 doi:10.1101/2023.08.18.553799 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2023.08.17.553736v1?rss=1 Dellorusso, P. V. Proven, M. A. Calero-Nieto, F. J. Wang, X. Mitchell, C. A. Hartmann, F. Amouzgar, M. Favaro, P. DeVilbiss, A. W. Swann, J. W. Ho, T. T. Zhao, Z. W. Bendall, S. C. Morrison, S. J. Gottgens, B. Passegue, E. 2023-08-19 doi:10.1101/2023.08.17.553736 Cold Spring Harbor Laboratory Press 2023-08-19 <![CDATA[ Noncoding genetic variation in ISPD distinguishes gamecocks from nongame chickens ]]> https://biorxiv.org/content/10.1101/2023.08.16.553562v1?rss=1 4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance. ]]> Bendesky, A. Brew, J. Francis, K. X. Tello Corbetto, E. F. Gonzalez Ariza, A. Nogales Baena, S. Shimmura, T. 2023-08-21 doi:10.1101/2023.08.16.553562 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Combined Mek inhibition and Pparg activation Eradicates Muscle Invasive Bladder cancer in a Mouse Model of BBN-induced Carcinogenesis ]]> https://biorxiv.org/content/10.1101/2023.08.19.553961v1?rss=1 Tate, T. Plumber, S. A. Al-Ahmadie, H. Chen, X. Choi, W. Lu, C. Viny, A. D. Batourina, E. Gretarsson, K. Alija, B. Molotkov, A. Wiessner, G. Mckiernan, J. M. McConkey, D. J. Dinney, C. Czerniak, B. Mendelsohn, C. L. 2023-08-21 doi:10.1101/2023.08.19.553961 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Deep screening of proximal and distal splicing-regulatory elements in a native sequence context ]]> https://biorxiv.org/content/10.1101/2023.08.21.554109v1?rss=1 Recinos, Y. Ustianenko, D. Yeh, Y.-T. Wang, X. Jacko, M. Yesantharao, L. V. Wu, Q. Zhang, C. 2023-08-21 doi:10.1101/2023.08.21.554109 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Belief embodiment through eye movements facilitates memory-guided navigation ]]> https://biorxiv.org/content/10.1101/2023.08.21.554107v1?rss=1 Stavropoulos, A. Lakshminarasimhan, K. J. Angelaki, D. E. 2023-08-22 doi:10.1101/2023.08.21.554107 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ Mitochondrial protein FKBP8 captures PDZD8 to form mitochondria-ER contacts ]]> https://biorxiv.org/content/10.1101/2023.08.22.554218v1?rss=1 Nakamura, K. Aoyama-Ishiwatari, S. Nagao, T. Paaran, M. Obara, C. J. Sakurai-Saito, Y. Johnston, J. Du, Y. Suga, S. Tsuboi, M. Nakakido, M. Tsumoto, K. Kishi, Y. Gotoh, Y. Kwak, C. Rhee, H.-W. Seo, J. K. Kosako, H. Potter, C. Carragher, B. Lippincott-Schwartz, J. Polleux, F. Hirabayashi, Y. 2023-08-22 doi:10.1101/2023.08.22.554218 Cold Spring Harbor Laboratory Press 2023-08-22 <![CDATA[ A mathematical theory of relational generalization in transitive inference ]]> https://biorxiv.org/content/10.1101/2023.08.22.554287v1?rss=1 B and B > C) and generalize it to new combinations of items (A > C). Through mathematical analysis, we found that a broad range of biologically relevant learning models (e.g. gradient flow or ridge regression) perform TI successfully and recapitulate signature behavioral patterns long observed in living subjects. First, we found that models with item-wise additive representations automatically encode transitive relations. Second, for more general representations, a single scalar "conjunctivity factor" determines model behavior on TI and, further, the principle of norm minimization (a standard statistical inductive bias) enables models with fixed, partly conjunctive representations to generalize transitively. Finally, neural networks in the "rich regime," which enables representation learning and has been found to improve generalization, unexpectedly show poor generalization and anomalous behavior. We find that such networks implement a form of norm minimization (over hidden weights) that yields a local encoding mechanism lacking transitivity. Our findings show how minimal statistical learning principles give rise to a classical relational inductive bias (transitivity), explain empirically observed behaviors, and establish a formal approach to understanding the neural basis of relational abstraction. ]]> Lippl, S. Kay, K. Jensen, G. Ferrera, V. P. Abbott, L. F. 2023-08-23 doi:10.1101/2023.08.22.554287 Cold Spring Harbor Laboratory Press 2023-08-23 <![CDATA[ Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings ]]> https://biorxiv.org/content/10.1101/2023.08.23.554527v1?rss=1 Ye, Z. Shelton, A. M. Shaker, J. R. Boussard, J. M. Colonell, J. Minavi, S. Chen, S. Windolf, C. Hurwitz, C. Namima, T. Pedraja, F. Weiss, S. Raducanu, B. Ness, T. Einevoll, G. T. Laurent, G. Sawtell, N. B. Bair, W. Pasupathy, A. Mora-Lopez, C. Dutta, B. Paninski, L. Siegle, J. H. Koch, C. Olsen, S. r. Harris, T. D. Steinmetz, N. A. 2023-08-24 doi:10.1101/2023.08.23.554527 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Antibody Neutralization of Emerging SARS-CoV-2: EG.5.1 and XBC.1.6 ]]> https://biorxiv.org/content/10.1101/2023.08.21.553968v1?rss=1 Wang, Q. Guo, Y. Zhang, R. M. Ho, J. Mohri, H. Valdez, R. Manthei, D. M. Gordon, A. Liu, L. Ho, D. D. 2023-08-25 doi:10.1101/2023.08.21.553968 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Transcriptome analysis of left-right intrinsic laryngeal muscles shows divergent expression of genes associated with innervation ]]> https://biorxiv.org/content/10.1101/2023.08.25.554869v1?rss=1 Kemfack, A. M. Hernandez-Morato, I. Moayedi, Y. Pitman, M. J. 2023-08-27 doi:10.1101/2023.08.25.554869 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Dopaminergic D2 receptor modulation of striatal cholinergic interneurons governs sequence learning ]]> https://biorxiv.org/content/10.1101/2023.08.28.554807v1?rss=1 Chancey, J. H. Kellendonk, C. M. Javitch, J. A. Lovinger, D. M. 2023-08-29 doi:10.1101/2023.08.28.554807 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Developmental pyrethroid exposure disrupts molecular pathways for circadian rhythms and synaptic plasticity in mouse brain. ]]> https://biorxiv.org/content/10.1101/2023.08.28.555113v1?rss=1 Nguyen, J. H. Curtis, M. A. Imami, A. S. Ryan, W. G. Alganem, K. Neifer, K. L. Nawor, C. N. Kistler, B. P. Miller, G. W. Shukla, R. McCullumsmith, R. E. Burkett, J. P. 2023-08-29 doi:10.1101/2023.08.28.555113 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Rab7a activation promotes degradation of select tight junction proteins at the blood-brain barrier after ischemic stroke ]]> https://biorxiv.org/content/10.1101/2023.08.29.555373v1?rss=1 Cottarelli, A. Shahriar, S. Arac, A. Glendinning, M. Tuohy, M. C. Prochilo, G. Neal, J. B. Edinger, A. Agalliu, D. 2023-08-30 doi:10.1101/2023.08.29.555373 Cold Spring Harbor Laboratory Press 2023-08-30 <![CDATA[ Middle-schoolers' reading and processing depth in response to digital and print media: An N400 study ]]> https://biorxiv.org/content/10.1101/2023.08.30.553693v1?rss=1 Froud, K. Levinson, L. Maddox, C. Smith, P. 2023-09-01 doi:10.1101/2023.08.30.553693 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Myostatin is a major endocrine driver of follicle-stimulating hormone synthesis ]]> https://biorxiv.org/content/10.1101/2023.08.30.555595v1?rss=1 Ongaro, L. Zhou, X. Wang, Y. Zhou, Z. Schultz, H. Buddle, E. R. S. Brule, E. Lin, Y.-F. Schang, G. Castonguay, R. Liu, Y. Su, G. H. Seidah, N. Ray, K. C. Karp, S. J. Boehm, U. Lee, S.-J. Bernard, D. J. 2023-09-01 doi:10.1101/2023.08.30.555595 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Mitosis exit followed by death in interphase prevents the development of polyploid giant cancer cells. ]]> https://biorxiv.org/content/10.1101/2023.08.31.555795v1?rss=1 Vicente, J. J. Khan, K. Tillinghast, G. McFaline-Figueroa, J. L. Sancak, Y. Stella, N. 2023-09-01 doi:10.1101/2023.08.31.555795 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Cryo-EM studies of the interplay between uS2 ribosomal protein and leaderless mRNA during bacterial translation initiation ]]> https://biorxiv.org/content/10.1101/2023.09.02.556006v1?rss=1 Acosta-Reyes, F. J. BHATTACHARJEE, S. Gottesman, M. E. Frank, J. 2023-09-02 doi:10.1101/2023.09.02.556006 Cold Spring Harbor Laboratory Press 2023-09-02 <![CDATA[ Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states ]]> https://biorxiv.org/content/10.1101/2023.08.31.555823v1?rss=1 Balasubramanian, R. Kizhatil, K. Li, T. Tolman, N. Bhandari, A. Clark, G. Bupp-Chickering, V. Zhou, S. Peregrin, J. Simon, M. Montgomery, C. Qian, J. John, S. 2023-09-03 doi:10.1101/2023.08.31.555823 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Permanent Neonatal Diabetes-causing Insulin Mutations have Dominant Effects on Proinsulin Processing and Beta Cell Identity ]]> https://biorxiv.org/content/10.1101/2023.09.01.555839v1?rss=1 Zhang, Y. Sui, L. Du, Q. Haataja, L. Yin, Y. Viola, R. Xu, S. Nielsson, C. U. Leibel, R. L. Barbetti, F. Arvan, P. Egli, D. 2023-09-05 doi:10.1101/2023.09.01.555839 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Galvanic vs. Pulsatile Effects on Decision-Making Networks: Reshaping the Neural Activation Landscape ]]> https://biorxiv.org/content/10.1101/2023.09.01.555903v1?rss=1 1s), has re-emerged as an alternative to pulsatile stimulation. In this paper, we use a winner-take-all decision-making cortical network model to investigate differences between pulsatile and galvanic stimulation in the context of a perceptual decision-making task. Based on previous work, we hypothesized that galvanic stimulation would produce more spatiotemporally distributed, network-sensitive neural responses, while pulsatile stimulation would produce highly synchronized activation of a limited group of neurons. Our results in-silico support these hypotheses for low-amplitude galvanic stimulation but deviate when galvanic amplitudes are large enough to directly activate or block nearby neurons. We conclude that with careful parametrization, galvanic stimulation could overcome some limitations of pulsatile stimulation to deliver more naturalistic firing patterns in the group of targeted neurons. ]]> Adkisson, P. W. Steinhardt, C. R. Fridman, G. Y. 2023-09-05 doi:10.1101/2023.09.01.555903 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Motor cortex is required for flexible but not automatic motor sequences ]]> https://biorxiv.org/content/10.1101/2023.09.05.556348v1?rss=1 Mizes, K. G. C. Lindsey, J. Escola, G. S. Olveczky, B. P. 2023-09-05 doi:10.1101/2023.09.05.556348 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ In situ cryoET reveals inhibitor-induced perturbations in Pf80S GTPase interactions ]]> https://biorxiv.org/content/10.1101/2023.09.03.556115v1?rss=1 Anton, L. Cheng, W. Haile, M. Cobb, D. W. Zhu, X. Han, L. Li, E. Nair, A. Lee, C. L. Ke, H. Zhang, G. Doud, E. H. Ho, C.-M. 2023-09-06 doi:10.1101/2023.09.03.556115 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Abca4 inhibition in a cone-rich rodent leads to Stargardt Disease type 1-like retinal degeneration ]]> https://biorxiv.org/content/10.1101/2023.09.04.556201v1?rss=1 30% cones. Sanger sequencing of the CRISPR-targeted sequence showed clear edition of the Abca4 gene. At 2 months post- injection, non-invasive fundus imaging showed widespread photoreceptor loss, confirmed by optical coherence tomography. Functional recording by scotopic and photopic single flash, and photopic flicker electroretinography, showed significant decline in photopic (cone) but not scotopic (rod) light responses. Post-mortem real-time PCR, immunohistochemistry and western blotting showed significant decrease of cone-specific (MW cone opsin) but not rod- specific (rhodopsin) markers. Transmission electron microscopy showed large numbers of lipid inclusions in treated but not control retinal pigmented epithelium. Finally, ultrahigh performance liquid chromatographic analysis of whole P. obesus eyes showed the presence of all-trans retinal-dimer, also seen in Abca4-/- mice but not normal rod-rich mouse or rat eyes. In conclusion, this animal model of STGD1 more accurately reflects human STGD1 and should be valuable for characterizing pathogenic pathways and exploring treatment options. ]]> Sassone, F. Ciocca, D. Roux, M. J. Rossolillo, P. Birling, M.-C. Sparrow, J. R. Hicks, D. 2023-09-06 doi:10.1101/2023.09.04.556201 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ FYN regulates aqueous humor outflow and IOP through the phosphorylation of VE-cadherin ]]> https://biorxiv.org/content/10.1101/2023.09.04.556253v1?rss=1 Kizhatil, K. Clark, G. Sunderland, D. Bhandari, A. Horbal, L. Balasubramanian, R. John, S. 2023-09-06 doi:10.1101/2023.09.04.556253 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ MAGPIE: an interactive tool for visualizing and analyzing many simultaneous protein interactions with a binding partner ]]> https://biorxiv.org/content/10.1101/2023.09.04.556273v1?rss=1 Rodriguez, D. C. P. Weber, K. C. Glasgow, A. 2023-09-06 doi:10.1101/2023.09.04.556273 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry & high-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2023.09.05.556371v1?rss=1 Hegewisch-Solloa, E. Melsen, J. E. Ravichandran, H. Rendeiro, A. Mundy-Bosse, B. Freud, A. G. Melms, J. C. Eisman, S. E. Izar, B. Grunstein, E. Connors, T. J. Elemento, O. Horowitz, A. Mace, E. M. 2023-09-06 doi:10.1101/2023.09.05.556371 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Replication stress in activated human NK cells induces sensitivity to apoptosis ]]> https://biorxiv.org/content/10.1101/2023.09.07.556586v1?rss=1 Guilz, N. C. Ahn, Y.-O. Seo, S. Fatima, H. Pedroza, L. A. SONI, R. Wang, N. Egli, D. Mace, E. 2023-09-07 doi:10.1101/2023.09.07.556586 Cold Spring Harbor Laboratory Press 2023-09-07 <![CDATA[ Cohesin still drives homologous recombination repair of DNA double-strand breaks in late mitosis. ]]> https://biorxiv.org/content/10.1101/2023.09.08.556828v1?rss=1 Ayra Plasencia, J. Symington, L. S. Machin, F. 2023-09-08 doi:10.1101/2023.09.08.556828 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells ]]> https://biorxiv.org/content/10.1101/2023.09.08.556927v1?rss=1 Wang, Q. Zhang, S. Nguyen, H. T. Sodroski, J. G. 2023-09-09 doi:10.1101/2023.09.08.556927 Cold Spring Harbor Laboratory Press 2023-09-09 <![CDATA[ Accelerated physiology and increased energy expenditure in animals and humans with mitochondrial defects: A meta-analysis ]]> https://biorxiv.org/content/10.1101/2023.09.09.556754v1?rss=1 10% elevation in EE relative to control animals, compared to 11% reporting <10% reduction in EE (p<0.0001, Chi-square). Of the experimental conditions where locomotor activity was also quantified, 39% showed that OxPhos-deficient animals had elevated EE despite reduced locomotor activity, which would be expected to decrease EE. To extend this finding in humans, we re-analyzed a high-quality clinical and multi-omics dataset (Sharma et al. 2021) of mitochondrial disease patients with the m.3243A>G mutation. This analysis similarly indicates an upregulation of energetically costly physiological, immune, and metabolic parameters in people with OxPhos deficiency. These results suggest that animals and humans with mitochondrial defects must expend more energy to sustain life, a state clinically called hypermetabolism. High-quality human energetics studies are needed to understand the magnitude, mechanisms, and modifiability of hypermetabolism in mitochondrial disorders. ]]> Sercel, A. J. Sturm, G. Shaulson, E. D. Gallagher, D. St-Onge, M.-P. Kempes, C. P. Pontzer, H. Hirano, M. Picard, M. 2023-09-10 doi:10.1101/2023.09.09.556754 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy ]]> https://biorxiv.org/content/10.1101/2023.09.09.556982v1?rss=1 Zhang, Y. Karagiannis, D. Liu, H. Lin, M. Fang, Y. Jiang, M. Chen, X. Suresh, S. Huang, H. She, J. Shi, F. Yang, P. El-Rifai, W. Zaika, A. Oro, A. E. Rustgi, A. K. Wang, T. C. Lu, C. Que, J. 2023-09-11 doi:10.1101/2023.09.09.556982 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Biological and Genetic Determinants of Red Blood Cell Glycolysis ]]> https://biorxiv.org/content/10.1101/2023.09.11.557250v1?rss=1 View larger version (87K): org.highwire.dtl.DTLVardef@1a556b7org.highwire.dtl.DTLVardef@1e02b13org.highwire.dtl.DTLVardef@2bfab1org.highwire.dtl.DTLVardef@15787e3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBlood donor age and sex affect glycolysis in stored RBCs from 13,029 volunteers; C_LIO_LIAncestry, genetic polymorphisms in PFKP, HK1, CD38/BST1 influence RBC glycolysis; C_LIO_LIModeled PFKP effects relate to preventing loss of the total AXP pool in stored RBCs; C_LIO_LIATP and hypoxanthine are biomarkers of hemolysis in vitro and in vivo. C_LI ]]> Nemkov, T. Stephenson, D. Earley, E. J. Keele, G. R. Hay, A. Erickson, C. Dzieciatkowska, M. Key, A. M. Moore, A. Stone, M. Deng, X. Kleinman, S. Spitalnik, S. L. Hod, E. A. Hansen, K. Churchill, G. A. Roubinian, N. Norris, P. J. Busch, M. P. Zimring, J. C. Page, G. P. D'Alessandro, A. 2023-09-11 doi:10.1101/2023.09.11.557250 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Disentangling sources of clock-like mutations in germline and soma ]]> https://biorxiv.org/content/10.1101/2023.09.07.556720v1?rss=1 Spisak, N. de Manuel, M. Milligan, W. R. Sella, G. Przeworski, M. 2023-09-12 doi:10.1101/2023.09.07.556720 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state ]]> https://biorxiv.org/content/10.1101/2023.09.08.556867v1?rss=1 Paryani, F. Kwon, J.-S. Ng, C. W. Madden, N. Ofori, K. Tang, A. Lu, H. Li, J. Mahajan, A. Davidson, S. M. Basile, A. McHugh, C. Vonsattel, J. P. Hickman, R. Zody, M. Houseman, D. E. Goldman, J. E. Yoo, A. E. Menon, V. Al-Dalahmah, O. 2023-09-12 doi:10.1101/2023.09.08.556867 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma ]]> https://biorxiv.org/content/10.1101/2023.09.09.557001v1?rss=1 Cheng, Y. L. Banu, M. A. Zhao, W. Rosenfeld, S. S. Canoll, P. Sims, P. A. 2023-09-12 doi:10.1101/2023.09.09.557001 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Categorization dynamically alters representations in human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.11.557257v1?rss=1 Henderson, M. M. Serences, J. T. Rungratsameetaweemana, N. 2023-09-13 doi:10.1101/2023.09.11.557257 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Plasma membrane abundance dictates phagocytic capacity and functional crosstalk in myeloid cells ]]> https://biorxiv.org/content/10.1101/2023.09.12.556572v1?rss=1 Winer, B. Y. Settle, A. H. Yakimov, A. M. Jeronimo, C. Lazarovt, T. Tipping, M. Saoi, M. Sawh, A. Sepp, A.-L. L. Galiano, M. Perry, J. S. A. Wong, Y. Y. Geissmann, F. Cross, J. Zhou, T. Kam, L. C. Pasoli, H. A. Hohl, T. Cyster, J. G. Weiner, O. Huse, M. 2023-09-13 doi:10.1101/2023.09.12.556572 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Toolkits for detailed and high-throughput interrogation of synapses in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.09.12.557402v1?rss=1 Majeed, M. Han, H. Zhang, K. Liao, C.-P. Hobert, O. Lu, H. 2023-09-13 doi:10.1101/2023.09.12.557402 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox ]]> https://biorxiv.org/content/10.1101/2023.09.12.557474v1?rss=1 Schertzer, M. D. Stirn, A. Isaev, K. Pereira, L. Das, A. Harbison, C. Park, S. H. Wessels, H.-H. Sanjana, N. E. Knowles, D. A. 2023-09-13 doi:10.1101/2023.09.12.557474 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Maternal IL-10 restricts fetal emergency myelopoiesis ]]> https://biorxiv.org/content/10.1101/2023.09.13.557548v1?rss=1 Collins, A. Swann, J. W. Proven, M. A. Patel, C. Mitchell, C. A. Kasbekar, M. Dellorusso, P. V. Passegue, E. 2023-09-13 doi:10.1101/2023.09.13.557548 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Probing learning through the lens of changes in circuit dynamics ]]> https://biorxiv.org/content/10.1101/2023.09.13.557585v1?rss=1 Marschall, O. Savin, C. 2023-09-13 doi:10.1101/2023.09.13.557585 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Explaining Deep Learning-Based Representations of Resting State Functional Connectivity Data: Focusing on Interpreting Nonlinear Patterns in Autism Spectrum Disorder ]]> https://biorxiv.org/content/10.1101/2023.09.13.557591v1?rss=1 Kim, Y.-g. Ravid, O. Zhang, X. Kim, Y. Neria, Y. Lee, S. Zhu, X. 2023-09-13 doi:10.1101/2023.09.13.557591 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Collective Sensing in Electric Fish ]]> https://biorxiv.org/content/10.1101/2023.09.13.557613v1?rss=1 Pedraja, F. Sawtell, N. B. 2023-09-13 doi:10.1101/2023.09.13.557613 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Temporal Generative Models for Learning Heterogeneous Group Dynamics of Ecological Momentary Data ]]> https://biorxiv.org/content/10.1101/2023.09.13.557652v1?rss=1 Kim, S. Kim, Y.-g. Wang, Y. 2023-09-14 doi:10.1101/2023.09.13.557652 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ maskNMF: A denoise-sparsen-detect approach for extracting neural signals from dense imaging data ]]> https://biorxiv.org/content/10.1101/2023.09.14.557777v1?rss=1 Pasarkar, A. P. Kinsella, I. Zhou, P. Wu, M. M. Pan, D. Fan, J. L. Wang, Z. Abdeladim, L. Peterka, D. S. Adesnik, H. Ji, N. Paninski, L. 2023-09-15 doi:10.1101/2023.09.14.557777 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ HILAMA: High-dimensional multi-omic mediation analysis with latent confounding ]]> https://biorxiv.org/content/10.1101/2023.09.15.557839v1?rss=1 Wang, X. Liu, J. Hu, S. S. Liu, Z. Lu, H. Liu, L. 2023-09-15 doi:10.1101/2023.09.15.557839 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ A Novel Aberrantly Spliced Gain-of-Function NT5C2 Isoform Contributes to Thiopurine Resistance in Acute Lymphoblastic Leukemia ]]> https://biorxiv.org/content/10.1101/2023.09.14.557413v1?rss=1 Diz, M. T. Reglero, C. Falkenstein, C. D. Castro, A. Hayer, K. E. Radens, C. Quesnel-Vallieres, M. Ang, Z. Sehgal, P. Li, M. M. Barash, Y. Tasian, S. K. Ferrando, A. Thomas-Tikhonenko, A. 2023-09-16 doi:10.1101/2023.09.14.557413 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Poly-basic peptides and polymers as new drug candidate against Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2023.09.16.558069v1?rss=1 Sivakumar, R. Floyd, K. Jessey, E. Kim Kim, J. Bayguinov, P. Fitzpatrick, J. A. J. Goldfarb, D. Jovanovic, M. Tripathi, A. Djuranovic, S. Pavlovic Djuranovic, S. 2023-09-16 doi:10.1101/2023.09.16.558069 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ CCAR1 promotes DNA repair via an unanticipated role in alternative splicing ]]> https://biorxiv.org/content/10.1101/2023.09.18.557780v1?rss=1 Karasu, M. E. Joseph, B. Mironov, A. Schroeder, M. S. Gvozdenovic, A. Zavolan, M. Corn, J. E. 2023-09-18 doi:10.1101/2023.09.18.557780 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Uncovering Invariant Representations in Functional Neuroimaging with Deep Metric Learning ]]> https://biorxiv.org/content/10.1101/2023.09.17.558181v1?rss=1 Mittal, A. Sun, X. Paisley, J. Sajda, P. 2023-09-19 doi:10.1101/2023.09.17.558181 Cold Spring Harbor Laboratory Press 2023-09-19 <![CDATA[ Lung influenza virus specific memory CD4 T cell location and optimal cytokine production are dependent on interactions with lung antigen-presenting cells ]]> https://biorxiv.org/content/10.1101/2023.09.19.558387v1?rss=1 Hargrave, K. E. Worrell, J. C. Pirillo, C. Brennan, E. Masdefiol Garriga, A. Gray, J. I. Purnell, T. Roberts, E. W. MacLeod, M. K. 2023-09-21 doi:10.1101/2023.09.19.558387 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Dissociable roles of thalamic nuclei in the refinement of reaches to spatial targets ]]> https://biorxiv.org/content/10.1101/2023.09.20.558560v1?rss=1 Sibener, L. J. Mosberger, A. C. Chen, T. X. Athalye, V. R. Murray, J. M. Costa, R. M. 2023-09-21 doi:10.1101/2023.09.20.558560 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Age-related STAT3 signaling regulates severity of respiratory syncytial viral infection in human bronchial epithelial cells ]]> https://biorxiv.org/content/10.1101/2023.09.20.558606v1?rss=1 Zhao, C. Wang, W. Bai, Y. Amonkar, G. Mou, H. Olejnik, J. Hume, A. J. Muhlberger, E. Fang, Y. Que, J. Fearns, R. Ai, X. Lerou, P. H. 2023-09-21 doi:10.1101/2023.09.20.558606 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ Postnatal maternal care moderates the effects of prenatal bisphenol exposure on offspring neurodevelopmental, behavioral, and transcriptomic outcomes ]]> https://biorxiv.org/content/10.1101/2023.09.19.558481v1?rss=1 Lauby, S. C. Lapp, H. E. Salazar, M. Semyrenko, S. Chauhan, D. Margolis, A. E. Champagne, F. A. 2023-09-22 doi:10.1101/2023.09.19.558481 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ The Silene latifolia genome and its giant Y chromosome ]]> https://biorxiv.org/content/10.1101/2023.09.21.558754v1?rss=1 Moraga, C. Branco, C. Rougemont, Q. Veltsos, P. Jedlicka, P. Muyle, A. Hanique, M. Tannier, E. Liu, X. Mendoza-Galindo, E. Lemaitre, C. Fields, P. D. Cruaud, C. Labadie, K. Belser, C. Briolay, J. Santoni, S. Cegan, R. Linheiro, R. Rodriguez de la Vega, R. Adam, G. El Filali, A. Mossion, V. Boualem, A. Tavares, R. Chebbi, A. Cordaux, R. Fruchard, C. Prentout, D. Velt, A. Spataro, B. Delmotte, S. Weingartner, L. Toegelova, H. Tulpova, Z. Capal, P. Simkova, H. Storchova, H. Kruger, M. Abeyawardana, O. A. Taylor, D. Olson, M. Sloan, D. B. Karrenberg, S. 2023-09-22 doi:10.1101/2023.09.21.558754 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes ]]> https://biorxiv.org/content/10.1101/2023.09.21.558869v1?rss=1 Zhang, Y. He, T. Boussard, J. Windolf, C. Winter, O. Trautmann, E. Roth, N. Barrell, H. Churchland, M. M. Steinmetz, N. A. The International Brain Laboratory, Varol, E. Hurwitz, C. Paninski, L. 2023-09-22 doi:10.1101/2023.09.21.558869 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Sensory experience steers representational drift in mouse visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.22.558966v1?rss=1 Bauer, J. Lewin, U. Herbert, E. Gjorgjieva, J. Schoonover, C. E. Fink, A. J. P. Rose, T. Bonhoeffer, T. Hübener, M. 2023-09-22 doi:10.1101/2023.09.22.558966 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model ]]> https://biorxiv.org/content/10.1101/2023.09.21.558743v1?rss=1 View larger version (57K): org.highwire.dtl.DTLVardef@17673c8org.highwire.dtl.DTLVardef@1ab61a8org.highwire.dtl.DTLVardef@98781forg.highwire.dtl.DTLVardef@1f63e9b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Musharrafieh, R. Safonova, Y. Song, G. Roark, R. S. Lee, F.-H. Zhang, S. Hurtado, J. Yong, P. Wang, S. Russell, R. M. Ding, W. Li, Y. Rando, J. Murphy, A. I. Lindemuth, E. Zhao, C. Connell, A. J. Lee, W.-H. Mishra, N. Avillion, G. He, W. Callaghan, S. Dueker, K. Vo, A. L. Li, X. Capozzola, T. Joyce, C. Zhao, F. Anzanello, F. Liu, W. Bibollet-Ruche, F. Ramos, A. Li, H. Lewis, M. G. Ozorowski, G. Landais, E. Foley, B. T. Wagh, K. Sok, D. Briney, B. Ward, A. B. Hahn, B. H. Burton, D. R. Shaw, G. M. Andrabi, R. 2023-09-23 doi:10.1101/2023.09.21.558743 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Asymmetric Contribution of a Selectivity Filter Gate in Triggering Inactivation of CaV1.3 Channels ]]> https://biorxiv.org/content/10.1101/2023.09.21.558864v1?rss=1 del Rivero Morfin, P. J. Kochiss, A. L. Liedl, K. R. Flucher, B. E. Fernandez-Quintero, M. L. I. Ben-Johny, M. 2023-09-23 doi:10.1101/2023.09.21.558864 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A Genetically Encoded Actuator Selectively Boosts L-type Calcium Channels in Diverse Physiological Settings ]]> https://biorxiv.org/content/10.1101/2023.09.22.558856v1?rss=1 del Rivero Morfin, P. J. Scala Chavez, D. Jayaraman, S. Yang, L. Kochiss, A. Colecraft, H. M. Liu, X. S. Marx, S. O. Rajadhyaksha, A. M. Ben-Johny, M. 2023-09-23 doi:10.1101/2023.09.22.558856 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Neutron Scattering Analysis of the Cryptococcus neoformans Polysaccharide Reveals Solution Rigidity and Repeating Fractal-like Structural Patterns ]]> https://biorxiv.org/content/10.1101/2023.09.22.559017v1?rss=1 Wang, Z. Teixeira, S. C. M. Strother, C. Bowen, A. Casadevall, A. Cordero, R. J. 2023-09-23 doi:10.1101/2023.09.22.559017 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Automatic monitoring of whole-body neural activity in behaving Hydra ]]> https://biorxiv.org/content/10.1101/2023.09.22.559063v1?rss=1 Hanson, A. Reme, R. Telerman, N. Yamamoto, W. Olivo-Marin, J.-C. Lagache, T. Yuste, R. 2023-09-23 doi:10.1101/2023.09.22.559063 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ The representational geometry of emotional states in basolateral amygdala ]]> https://biorxiv.org/content/10.1101/2023.09.23.558668v1?rss=1 O'Neill, P.-K. Posani, L. Meszaros, J. Warren, P. Schoonover, C. E. Fink, A. J. P. Fusi, S. Salzman, C. D. 2023-09-23 doi:10.1101/2023.09.23.558668 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Perisaccadic and Attentional Remapping of Receptive Fields in Lateral Intraparietal Area and Frontal Eye Fields ]]> https://biorxiv.org/content/10.1101/2023.09.23.558993v1?rss=1 Wang, X. Zhang, C. Yang, L. Jin, M. Goldberg, M. E. Zhang, M. Qian, N. 2023-09-23 doi:10.1101/2023.09.23.558993 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ Activity-dependent development of the body's touch receptors ]]> https://biorxiv.org/content/10.1101/2023.09.23.559109v1?rss=1 Santiago, C. Sharma, N. Africawala, N. Siegrist, J. Handler, A. Tasnim, A. Anjum, R. Turecek, J. Lehnert, B. P. Renauld, S. Nolan-Tamariz, M. Iskols, M. Magee, A. R. Paradis, S. Ginty, D. D. 2023-09-24 doi:10.1101/2023.09.23.559109 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ GET: a foundation model of transcription across human cell types ]]> https://biorxiv.org/content/10.1101/2023.09.24.559168v1?rss=1 1Mbp) regulatory regions that were missed by previous models. In B cells, we identified a lymphocyte-specific transcription factor-transcription factor interaction that explains the functional significance of a leukemia-risk predisposing germline mutation. In sum, we provide a generalizable and accurate model for transcription together with catalogs of gene regulation and transcription factor interactions, all with cell type specificity. ]]> Fu, X. Mo, S. Shao, A. Laurent, A. Buendia, A. Ferrando, A. A. Ciccia, A. Lan, Y. Palomero, T. Owens, D. M. Xing, E. P. Rabadan, R. 2023-09-24 doi:10.1101/2023.09.24.559168 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike ]]> https://biorxiv.org/content/10.1101/2023.09.24.559214v1?rss=1 Wang, Q. Guo, Y. Liu, L. Schwanz, L. T. Li, Z. Ho, J. Zhang, R. M. Iketani, S. Yu, J. Huang, Y. Qu, Y. Valdez, R. Lauring, A. S. Gordon, A. Wang, H. H. Liu, L. Ho, D. D. 2023-09-25 doi:10.1101/2023.09.24.559214 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ iPSC-based modeling of helicase deficiency reveals impaired cell proliferation and increased apoptosis after NK cell lineage commitment ]]> https://biorxiv.org/content/10.1101/2023.09.25.559149v1?rss=1 Seo, S. Patil, S. L. Ahn, Y.-O. Armetta, J. Hegewisch-Solloa, E. Castillo, M. Guilz, N. C. Patel, A. Corneo, B. Borowiak, M. Gunaratne, P. Mace, E. M. 2023-09-25 doi:10.1101/2023.09.25.559149 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Minimal epistatic networks from integrated sequence and mutational protein data. ]]> https://biorxiv.org/content/10.1101/2023.09.25.559251v1?rss=1 Cocco, S. Monasson, R. Posani, L. 2023-09-25 doi:10.1101/2023.09.25.559251 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Ventral CA1 Population Codes for Anxiety ]]> https://biorxiv.org/content/10.1101/2023.09.25.559358v1?rss=1 Lim, S. C.-H. Fusi, S. Hen, R. 2023-09-26 doi:10.1101/2023.09.25.559358 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Altered hierarchical gradients of intrinsic neural timescales in mild cognitive impairment and Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.09.26.559549v1?rss=1 ZHANG, A. Wengler, K. Zhu, X. Horga, G. Goldberg, T. lee, s. For Alzheimer's Disease Neuroimaging Initiative, 2023-09-27 doi:10.1101/2023.09.26.559549 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ A tale of two receptors: simultaneous targeting of NMDARs and 5-HT4Rs exerts additive effects against stress ]]> https://biorxiv.org/content/10.1101/2023.09.27.559065v1?rss=1 Chen, B. K. Luna, V. M. Jin, M. Shah, A. Shannon, M. E. Pauers, M. M. Williams, B. L. Pham, V. Hunsberger, H. C. Gardier, A. M. Mendez-David, I. David, D. J. Denny, C. A. 2023-09-27 doi:10.1101/2023.09.27.559065 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation ]]> https://biorxiv.org/content/10.1101/2023.09.27.559313v1?rss=1 NSD2>NSD3>ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements. ]]> Shipman, G. Padilla, R. Horth, C. Hu, B. Bareke, E. Vitorino, F. Gongora, J. Garcia, B. Lu, C. Majewski, J. 2023-09-27 doi:10.1101/2023.09.27.559313 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Neocortico-hippocampal ripple-based coordination during naturalistic encoding ]]> https://biorxiv.org/content/10.1101/2023.09.27.559739v1?rss=1 Silva, M. Wu, X. Sabio, M. Conde-Blanco, E. Roldan, P. Donaire, A. Carreno, M. Axmacher, N. Baldassano, C. Fuentemilla, L. 2023-09-27 doi:10.1101/2023.09.27.559739 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Evolution of gene expression across brain regions in behaviorally divergent deer mice ]]> https://biorxiv.org/content/10.1101/2023.09.28.559844v1?rss=1 Kautt, A. Chen, J. Lewarch, C. L. Hu, C. Turner, K. Lassance, J.-M. Baier, F. Bedford, N. L. Bendesky, A. Hoekstra, H. E. 2023-09-28 doi:10.1101/2023.09.28.559844 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Engineered bacteria launch and control an oncolytic virus ]]> https://biorxiv.org/content/10.1101/2023.09.28.559873v1?rss=1 Singer, Z. S. Pabon, J. Huang, H. Rice, C. M. Danino, T. 2023-09-28 doi:10.1101/2023.09.28.559873 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ GENERATION OF FUNCTIONAL NEURONS FROM ADULT HUMAN MUCOSAL OLFACTORY ENSHEATHING GLIA BY DIRECT LINEAGE CONVERSION ]]> https://biorxiv.org/content/10.1101/2023.09.28.559940v1?rss=1 Portela-Lomba, M. Simon, D. Callejo-Mostoles, M. de la Fuente, G. Fernandez de Sevilla, D. Garcia-Escudero, V. Moreno-Flores, M. T. Sierra, J. 2023-09-29 doi:10.1101/2023.09.28.559940 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Single-cell multimodal profiling of atherosclerosis identifies CD200 as a lineage marker of vascular smooth muscle cells and their derived cells ]]> https://biorxiv.org/content/10.1101/2023.09.29.557779v1?rss=1 Bashore, A. C. Chung, A. Ibikunle, C. Yan, H. Xue, C. Li, M. Bauer, R. C. Reilly, M. P. 2023-09-29 doi:10.1101/2023.09.29.557779 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ A conserved class of viral RNA structures regulate translation reinitiation through dynamic ribosome interactions ]]> https://biorxiv.org/content/10.1101/2023.09.29.560040v1?rss=1 Sherlock, M. Langeberg, C. Segar, K. Kieft, J. S. 2023-09-29 doi:10.1101/2023.09.29.560040 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Probiotic neoantigen delivery vectors for precision cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.09.29.560228v1?rss=1 Redenti, A. Im, J. Redenti, B. Li, F. Rouanne, M. Sheng, Z. Sun, W. Gurbatri, C. R. Huang, S. Komaranchath, M. Jang, Y. Hahn, J. Ballister, E. R. Vincent, R. L. Vardoshivilli, A. Danino, T. Arpaia, N. 2023-09-30 doi:10.1101/2023.09.29.560228 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration ]]> https://biorxiv.org/content/10.1101/2023.09.29.560217v1?rss=1 Bramer, L. Dixon, H. M. Degnan, D. J. Rohlman, D. Herbstman, J. B. Waters, K. M. Anderson, K. A. 2023-10-02 doi:10.1101/2023.09.29.560217 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Overlap and divergence of neural circuits mediating distinct behavioral responses to sugar ]]> https://biorxiv.org/content/10.1101/2023.10.01.560401v1?rss=1 Jacobs, R. V. Wang, C. X. Lozada-Perdomo, F. V. Nguyen, L. Deere, J. U. Uttley, H. A. Devineni, A. V. 2023-10-02 doi:10.1101/2023.10.01.560401 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Predation-resistant Pseudomonas bacteria engage in symbiont-like behavior with the social amoeba Dictyostelium discoideum ]]> https://biorxiv.org/content/10.1101/2023.10.02.560472v1?rss=1 Steele, M. I. Peiser, J. M. Shreenidhi, P. M. Strassmann, J. E. Queller, D. C. 2023-10-02 doi:10.1101/2023.10.02.560472 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutieres syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.10.02.560505v1?rss=1 Kundnani, D. L. Yang, T. Gombolay, A. Mukherjee, K. Newnam, G. Meers, C. Mehta, Z. H. Mouawad, C. Storici, F. 2023-10-02 doi:10.1101/2023.10.02.560505 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus ]]> https://biorxiv.org/content/10.1101/2023.10.02.560480v1?rss=1 Prentout, D. Muyle, A. Zemp, N. El Filali, A. Boussau, B. Touzet, P. Widmer, A. Kafer, J. Marais, G. A. 2023-10-03 doi:10.1101/2023.10.02.560480 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ SABRE: Self-Attention Based model for predicting T-cell Receptor Epitope Specificity ]]> https://biorxiv.org/content/10.1101/2023.10.02.560555v1?rss=1 Wang, Z. Shen, Y. 2023-10-03 doi:10.1101/2023.10.02.560555 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.10.02.560584v1?rss=1 Buck, S. A. Rubin, S. A. Kunkhyen, T. Treiber, C. D. Xue, X. Fenno, L. E. Mabry, S. J. Sundar, V. R. Yang, Z. Shah, D. Ketchesin, K. D. Becker-Krail, D. D. Vasylieva, I. Smith, M. C. Weisel, F. J. Wang, W. Erickson-Oberg, M. Q. O'Leary, E. I. Aravind, E. Ramakrishnan, C. Kim, Y. S. Wu, Y. Quick, M. Coleman, J. A. MacDonald, W. A. Elbakri, R. De Miranda, B. R. Palladino, M. J. McCabe, B. D. Fish, K. N. Seney, M. L. Rayport, S. Mingote, S. Deisseroth, K. Hnasko, T. S. Awatramani, R. Watson, A. M. Waddell, S. Cheetham, C. E. Logan, R. W. Freyberg, Z. 2023-10-03 doi:10.1101/2023.10.02.560584 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Mice require proprioception to establish long-term visuospatial memory. ]]> https://biorxiv.org/content/10.1101/2023.10.03.560558v1?rss=1 Goldberg, M. E. Rutler, O. Bruno, R. M. Park, J. M. Persaud, S. Kosmidis, S. Hirano, N. 2023-10-05 doi:10.1101/2023.10.03.560558 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia ]]> https://biorxiv.org/content/10.1101/2023.10.04.557612v1?rss=1 Sneha, R. B. Brundu, F. Chen, Y. Sun, Y. Zhu, H. Shprintzen, R. J. Tomer, R. Rabadan, R. Leong, K. W. Markx, S. Xu, B. Gogos, J. A. 2023-10-05 doi:10.1101/2023.10.04.557612 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Synaptic Basis of Behavioral Timescale Plasticity ]]> https://biorxiv.org/content/10.1101/2023.10.04.560848v1?rss=1 Gonzalez, K. C. Negrean, A. Liao, Z. Polleux, F. Losonczy, A. 2023-10-05 doi:10.1101/2023.10.04.560848 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Structural and molecular basis of choline uptake into the brain by FLVCR2 ]]> https://biorxiv.org/content/10.1101/2023.10.05.561059v1?rss=1 Cater, R. J. Mukherjee, D. Gil Iturbe, E. Erramilli, S. K. Chen, T. Koo, K. Santander, N. G. Reckers, A. R. Kloss, B. Gawda, T. Choy, B. C. Zhang, Z. Clarke, O. B. Yee, S. W. Kossiakoff, A. K. Quick, M. Arnold, T. Mancia, F. 2023-10-05 doi:10.1101/2023.10.05.561059 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Psychosocial experiences are associated with human brain mitochondrial biology ]]> https://biorxiv.org/content/10.1101/2023.10.06.559575v1?rss=1 Trumpff, C. Monzel, A. Sandi, C. Menon, V. Klein, H.-U. Fujita, M. Lee, A. J. Petyuk, V. A. Hurst, C. Duong, D. A. Seyfried, N. Wingo, A. Wingo, T. S. Wang, Y. Thambisetty, M. Ferrucci, L. Bennett, D. A. De Jager, P. Picard, M. 2023-10-06 doi:10.1101/2023.10.06.559575 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES ]]> https://biorxiv.org/content/10.1101/2023.10.08.561395v1?rss=1 Guarnieri, J. W. Topper, M. Beigel, K. Haltoom, J. A. Chadburn, A. Frere, J. An, J. Cope, H. Borczuk, A. Sinha, S. Lim, C. Kim, J. Park, J. Meydan, C. Foox, J. Mozsary, C. Bram, Y. Richard, S. Epsi, N. Agan, B. Chenoweth, J. Simons, M. Tribble, D. Burgess, T. Dalgard, C. L. Heise, M. T. Moorman, N. Baxter, V. Madden, E. A. Taft-Benz, S. Anderson, E. Sanders, W. A. Dickmander, R. J. Widjaja, G. A. Janssen, K. Lie, T. Murdock, D. G. Angelin, A. Albrecht, Y. E. S. Olali, A. Dybas, J. M. Priebe, W. Emmett, M. R. Best, S. Johnson, M. K. Trovao, N. S. Cl 2023-10-09 doi:10.1101/2023.10.08.561395 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Effect of altered production and storage of dopamine on development and behavior in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.10.07.561350v1?rss=1 Lee, I. Knickerbocker, A. Depew, C. Martin, E. Dicent, J. Miller, G. W. Bucher, M. L. 2023-10-10 doi:10.1101/2023.10.07.561350 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium ]]> https://biorxiv.org/content/10.1101/2023.10.08.561457v1?rss=1 700 oncology drugs in cell lines representing high-fidelity models of 23 aggressive tumor subtypes and developed an integrative computational framework for the proteome-wide assessment of drug-mediated, tissue-specific differential protein activity. This allows systematic, mechanism-based elucidation of tissue context-specific compound MoA and polypharmacology, including discovery and experimental validation of post-translationally-mediated inhibition of undruggable oncoproteins--such as MYC, CTNNB1, CENPF and UHRF1--as well as previously unknown inhibitors of MAPK, PI3K, and folate pathways, among others, as further suggested by protein structure analysis. This framework can help characterize the MoA of discovery compound libraries, thus supporting more systematic and quantitative approaches to precision oncology. ]]> Hu, L. Z. Douglass, E. Turunen, M. Pampou, S. Grunn, A. Realubit, R. Antolin, A. A. Wang, A. L. E. Li, H. Subramaniam, P. Karan, C. Alvarez, M. Califano, A. 2023-10-10 doi:10.1101/2023.10.08.561457 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Hippocampal differentiation of competing memories predicts the precision of preparatory coding in visual cortex ]]> https://biorxiv.org/content/10.1101/2023.10.09.561548v1?rss=1 Favila, S. E. Aly, M. 2023-10-10 doi:10.1101/2023.10.09.561548 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ The neural basis of swap errors in working memory ]]> https://biorxiv.org/content/10.1101/2023.10.09.561584v1?rss=1 Alleman, M. Panichello, M. Buschman, T. J. Johnston, W. J. 2023-10-10 doi:10.1101/2023.10.09.561584 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Interplay of RAP2 GTPase and the cytoskeleton in Hippo pathway regulation ]]> https://biorxiv.org/content/10.1101/2023.10.10.561687v1?rss=1 Wu, C. Cai, X. Wang, Y. Rodriguez, C. D. Herrmann, L. Zoaldi, G. Huang, C.-Y. Wang, X. Sanghvi, V. R. Lu, R. O. Meng, Z. 2023-10-10 doi:10.1101/2023.10.10.561687 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Disrupted endosomal trafficking of the Vangl-Celsr polarity complex causes congenital anomalies in trachea-esophageal separation ]]> https://biorxiv.org/content/10.1101/2023.10.11.561909v1?rss=1 Edwards, N. A. Kashyap, A. Warren, A. Agricola, Z. Kenny, A. P. Shen, Y. Chung, W. K. Zorn, A. M. 2023-10-11 doi:10.1101/2023.10.11.561909 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Heterozygous expression of a Kcnt1 gain-of-function variant has differential effects on SST- and PV-expressing cortical GABAergic neurons ]]> https://biorxiv.org/content/10.1101/2023.10.11.561953v1?rss=1 Shore, A. N. Qunies, A. M. Spitznagel, B. D. Weaver, C. D. Emmitte, K. Frankel, W. Weston, M. C. 2023-10-11 doi:10.1101/2023.10.11.561953 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Tricyclic and tetracyclic antidepressants upregulate VMAT2 activity and rescue disease-causing VMAT2 variants ]]> https://biorxiv.org/content/10.1101/2023.10.09.561601v1?rss=1 Wang, X. Marmouzi, I. Finnie, P. S. Stove, S. I. Butcher, M. L. Lipina, T. V. Ramsey, A. J. Miller, G. W. Salahpour, A. 2023-10-12 doi:10.1101/2023.10.09.561601 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Ultrahigh throughput evolution of tryptophan synthase in droplets via an aptamer-biosensor ]]> https://biorxiv.org/content/10.1101/2023.10.11.561886v1?rss=1 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic read-outs which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a biosensor to quantitatively report on tryptophan production in droplets. The utility of the biosensor was validated by identifying 5-fold improved tryptophan synthases from [~]100,000 protein variants. More generally this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution. ]]> Scheele, R. Weber, Y. Nintzel, F. Herger, M. Kaminski, T. S. Hollfelder, F. 2023-10-12 doi:10.1101/2023.10.11.561886 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Cognitive Reserve Against Alzheimer's Pathology Is Linked to Brain Activity During Memory Formation ]]> https://biorxiv.org/content/10.1101/2023.10.10.561675v1?rss=1 Vockert, N. Machts, J. Kleineidam, L. Nemali, A. Schutze, H. Yakupov, R. Peters, O. Gref, D. Schneider, L. S. Preis, L. Priller, J. Spruth, E. J. Altenstein, S. Schneider, A. Fliessbach, K. Wiltfang, J. Rostamzadeh, A. Glanz, W. Incesoy, E. Teipel, S. Kilimann, I. Goerss, D. Laske, C. Munk, M. H. Spottke, A. Roy, N. Heneka, M. T. Brosseron, F. Wagner, M. Wolfsgruber, S. Dobisch, L. Dechent, P. Hetzer, S. Scheffler, K. Zeidman, P. Stern, Y. Schott, B. H. Jessen, F. Duzel, E. Maass, A. Ziegler, G. the DELCODE study group, 2023-10-13 doi:10.1101/2023.10.10.561675 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body ]]> https://biorxiv.org/content/10.1101/2023.10.12.561793v1?rss=1 Ganguly, I. Heckman, E. L. Litwin-Kumar, A. Clowney, E. J. Behnia, R. 2023-10-14 doi:10.1101/2023.10.12.561793 Cold Spring Harbor Laboratory Press 2023-10-14 <![CDATA[ Rho GTPase signaling and mDia facilitate endocytosis via presynaptic actin ]]> https://biorxiv.org/content/10.1101/2023.10.12.561997v1?rss=1 Oevel, K. Hohensee, S. Kumar, A. Rosas-Brugada, I. Bartolini, F. Soykan, T. Haucke, V. 2023-10-16 doi:10.1101/2023.10.12.561997 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Iterative convergent computation may not be a useful inductive bias for residual neural networks ]]> https://biorxiv.org/content/10.1101/2023.10.13.562196v1?rss=1 Lippl, S. Peters, B. Kriegeskorte, N. 2023-10-17 doi:10.1101/2023.10.13.562196 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Developmental pyrethroid exposure disrupts folate metabolism in mouse brain ]]> https://biorxiv.org/content/10.1101/2023.10.13.562226v1?rss=1 Curtis, M. A. Saferin, N. Nguyen, J. H. Imami, A. S. Neifer, K. L. Miller, G. W. Burkett, J. P. 2023-10-17 doi:10.1101/2023.10.13.562226 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Methylphenidate modulates motor cortical dynamics and behavior ]]> https://biorxiv.org/content/10.1101/2023.10.15.562405v1?rss=1 Verhein, J. R. Vyas, S. Shenoy, K. V. 2023-10-17 doi:10.1101/2023.10.15.562405 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Insulin sensitization by hepatic FoxO deletion is insufficient to lower atherosclerosis in mice ]]> https://biorxiv.org/content/10.1101/2023.10.14.562366v1?rss=1 Izquierdo, M. C. Harris, M. Shanmugarajah, N. Zhong, K. Ozcan, L. Fredman, G. Haeusler, R. A. 2023-10-18 doi:10.1101/2023.10.14.562366 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Predicting functional consequences of recent natural selection in Britain ]]> https://biorxiv.org/content/10.1101/2023.10.16.562549v1?rss=1 Poyraz, L. Colbran, L. L. Mathieson, I. 2023-10-19 doi:10.1101/2023.10.16.562549 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Cell age, not chronological age, governs the dynamics and longevity of circulating CD4+ memory T cells ]]> https://biorxiv.org/content/10.1101/2023.10.16.562650v1?rss=1 Bullock, M. E. Hogan, T. Morris, S. Nowicka, M. van Dorp, C. Yates, A. J. Seddon, B. 2023-10-19 doi:10.1101/2023.10.16.562650 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness ]]> https://biorxiv.org/content/10.1101/2023.10.17.562578v1?rss=1 Kusoglu, A. Ornek, D. Dansik, A. Uzun, C. Ozkan, S. N. Sarica, S. Yangin, K. Ozdinc, S. Turan Sorhun, D. Solcan, N. Doganalp, E. C. Arlov, O. Cunningham, K. Karaoglu, I. C. Kizilel, S. Solaroglu, I. Bulutay, P. Firat, P. Erus, S. Tanju, S. Dilege, S. Vunjak-Novakovic, G. Tuncbag, N. Ozturk, E. 2023-10-20 doi:10.1101/2023.10.17.562578 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Investigating RNA splicing as a source of cellular diversity using a binomial mixture model ]]> https://biorxiv.org/content/10.1101/2023.10.17.562774v1?rss=1 Isaev, K. Knowles, D. A. 2023-10-20 doi:10.1101/2023.10.17.562774 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling ]]> https://biorxiv.org/content/10.1101/2023.10.17.562783v1?rss=1 Zhou, J. Zhou, S. Chen, B. Sangsoy, K. Luengwilai, K. Albornoz, K. Beckles, D. M. 2023-10-20 doi:10.1101/2023.10.17.562783 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Top-down signaling dynamically mediates information processing in biologically inspired RNNs ]]> https://biorxiv.org/content/10.1101/2023.10.17.562828v1?rss=1 Aquino, T. G. Kim, R. Rungratsameetaweemana, N. 2023-10-20 doi:10.1101/2023.10.17.562828 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Detection of Blood Volume Reduction and Vasoconstriction Following Focused Ultrasound Blood-Brain Barrier Opening Using Ultrasound Flow Imaging ]]> https://biorxiv.org/content/10.1101/2023.10.19.563176v1?rss=1 Bae, S. Lee, S. A. Konofagou, E. E. 2023-10-22 doi:10.1101/2023.10.19.563176 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ Comparison of Tug-of-War Models Assuming Moran versus Branching Process Population Dynamics ]]> https://biorxiv.org/content/10.1101/2023.10.20.563302v1?rss=1 Dinh, K. N. Kurpas, M. K. Kimmel, M. 2023-10-23 doi:10.1101/2023.10.20.563302 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.10.20.563319v1?rss=1 Wang, Q. Antone, J. Alsop, E. Reiman, R. Funk, C. Bendl, J. Dudley, J. T. Liang, W. S. Karr, T. L. Roussos, P. Bennett, D. A. De Jager, P. L. Serrano, G. Beach, T. Van Keuren-Jensen, K. Mastroeni, D. Reiman, E. M. Readhead, B. P. 2023-10-23 doi:10.1101/2023.10.20.563319 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Geranylgeranyl Isoprenoids and Hepatic Rap1a Regulate Basal and Statin-Induced Expression of PCSK9 ]]> https://biorxiv.org/content/10.1101/2023.10.23.563509v1?rss=1 Wang, Y. Tinsley, B. Spolitu, S. Zadroga, J. A. Agarwal, H. Sarecha, A. K. Ozcan, L. 2023-10-23 doi:10.1101/2023.10.23.563509 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Neural signatures of stress susceptibility and resilience in the amygdala-hippocampal network ]]> https://biorxiv.org/content/10.1101/2023.10.23.563652v1?rss=1 Xia, F. Fascianelli, V. Vishwakarma, N. Ghinger, F. G. Fusi, S. Kheirbek, M. 2023-10-24 doi:10.1101/2023.10.23.563652 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Rap1 Activation Protects Against Fatty Liver and Non-Alcoholic Steatohepatitis Development ]]> https://biorxiv.org/content/10.1101/2023.10.24.563728v1?rss=1 Agarwal, H. Wang, Y. Ozcan, L. 2023-10-24 doi:10.1101/2023.10.24.563728 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Increased spontaneous Ca2+ activity in Cardiac Purkinje cells after myocardial infarction; A consequence of a dramatic shift of SERCA isoforms as potential adaptation to acute ischemia? ]]> https://biorxiv.org/content/10.1101/2023.10.23.563678v1?rss=1 Stuyvers, B. D. Boyden, P. A. Amin, R. Wiede, L. L. Dore, J. ter Keurs, H. E. Dun, W. Guo, Y. Haissaguerre, M. Hocini, M. Brette, F. Bernus, O. Chaigne, S. Loyer, V. Naulin, J. Quesson, B. Alafiatayo, A. Benoukraf, T. 2023-10-26 doi:10.1101/2023.10.23.563678 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ A Spatiotemporal and Machine-Learning Platform Accelerates the Manufacturing of hPSC-derived Esophageal Mucosa ]]> https://biorxiv.org/content/10.1101/2023.10.24.563664v1?rss=1 Yang, Y. McCullough, C. G. Seninge, L. Guo, L. Kwon, W.-J. Zhang, Y. Z. Li, N. Y. Gaddam, S. Pan, C. Zhen, H. Torkelson, J. Glass, I. Charville, G. Que, J. Stuart, J. Ding, H. Oro, A. E. 2023-10-26 doi:10.1101/2023.10.24.563664 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS ]]> https://biorxiv.org/content/10.1101/2023.10.24.563701v1?rss=1 View larger version (42K): org.highwire.dtl.DTLVardef@1e49c3forg.highwire.dtl.DTLVardef@1ce05b0org.highwire.dtl.DTLVardef@d77205org.highwire.dtl.DTLVardef@7ed2cd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Spence, H. Waldron, F. M. Saleeb, R. S. Brown, A.-L. Rifai, O. M. Gilodi, M. Read, F. Roberts, K. Milne, G. Wilkinson, D. O'Shaughnessy, J. Pastore, A. Fratta, P. Shneider, N. Tartaglia, G. G. Zacco, E. Horrocks, M. H. Gregory, J. 2023-10-27 doi:10.1101/2023.10.24.563701 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Aberrant Local Synchrony in Distinct Mouse Models of Epileptic Encephalopathy ]]> https://biorxiv.org/content/10.1101/2023.10.24.563817v1?rss=1 Ressler, A. Dugger, S. Colombo, S. Petri, S. Krizay, D. Frankel, W. Goldstein, D. Boland, M. J. 2023-10-27 doi:10.1101/2023.10.24.563817 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway ]]> https://biorxiv.org/content/10.1101/2023.10.24.563880v1?rss=1 Chen, H. Ferguson, C. J. Mitchell, D. C. Titus, A. Paulo, J. A. Hwang, A. Lin, T.-H. Yano, H. Gu, W. Song, S.-K. Yuede, C. M. Gygi, S. P. Bonni, A. Kim, A. H. 2023-10-27 doi:10.1101/2023.10.24.563880 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ DREDge: robust motion correction for high-density extracellular recordings across species ]]> https://biorxiv.org/content/10.1101/2023.10.24.563768v1?rss=1 Windolf, C. Yu, H. Paulk, A. C. Meszena, D. Munoz, W. Boussard, J. Hardstone, R. Caprara, I. Jamali, M. Kfir, Y. Xu, D. Chung, J. E. Sellers, K. K. Ye, Z. Shaker, J. Lebedeva, A. Raghavan, M. Trautmann, E. Melin, M. D. Couto, J. Garcia, S. Coughlin, B. Horvath, C. Fiath, R. Ulbert, I. Movshon, J. A. Shadlen, M. N. Churchland, M. M. Churchland, A. K. Steinmetz, N. A. Chang, E. F. Schweitzer, J. S. Williams, Z. M. Cash, S. S. Paninski, L. Varol, E. 2023-10-29 doi:10.1101/2023.10.24.563768 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Multimodal fusion of brain signals for robust prediction of psychosis transition ]]> https://biorxiv.org/content/10.1101/2023.10.25.563602v1?rss=1 Reinen, J. M. Polosecki, P. Castro, E. Corcoran, C. M. Cecchi, G. Colibazzi, T. 2023-10-29 doi:10.1101/2023.10.25.563602 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Modulation of NK cell migration by IL-15 defined using a new tool for data-driven clustering of heterogeneous cell behaviour trajectories ]]> https://biorxiv.org/content/10.1101/2023.10.28.564355v1?rss=1 Shannon, M. J. Eisman, S. E. Lowe, A. R. Sloan, T. Mace, E. M. 2023-10-29 doi:10.1101/2023.10.28.564355 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ The Drosophila Circadian Clock Gene Cycle Controls Development of Clock Neurons ]]> https://biorxiv.org/content/10.1101/2023.10.29.564626v1?rss=1 Biondi, G. McCormick, G. M. Fernandez, M. P. 2023-10-29 doi:10.1101/2023.10.29.564626 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Hepatocyte-Targeted siTAZ Therapy Lowers Liver Fibrosis in NASH Diet-Fed Chimeric Mice with Hepatocyte-Humanized Livers ]]> https://biorxiv.org/content/10.1101/2023.10.27.564478v1?rss=1 Wang, X. Moore, M. P. Shi, H. Miyata, Y. Donnelly, S. K. Radiloff, D. R. Tabas, I. 2023-11-01 doi:10.1101/2023.10.27.564478 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies ]]> https://biorxiv.org/content/10.1101/2023.10.30.564764v1?rss=1 Li, X. Chen, H. Selvaraj, M. S. Van Buren, E. Zhou, H. Wang, Y. Sun, R. McCaw, Z. R. Yu, Z. Arnett, D. K. Bis, J. C. Blangero, J. Boerwinkle, E. Bowden, D. W. Brody, J. A. Cade, B. E. Carson, A. P. Carlson, J. C. Chami, N. Chen, Y.-D. I. Curran, J. E. de Vries, P. S. Fornage, M. Franceschini, N. Freedman, B. I. Gu, C. Heard-Costa, N. L. He, J. Hou, L. Hung, Y.-J. Irvin, M. R. Kaplan, R. C. Kardia, S. L. R. Kelly, T. Konigsberg, I. Kooperberg, C. Kral, B. G. Li, C. Loos, R. J. F. Mahaney, M. C. Martin, L. W. Mathias, R. A. Minster, R. L. Mitchell, B. D 2023-11-02 doi:10.1101/2023.10.30.564764 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Towards robust and generalizable representations of extracellular data using contrastive learning ]]> https://biorxiv.org/content/10.1101/2023.10.30.564831v1?rss=1 Vishnubhotla, A. Loh, C. Paninski, L. Srivastava, A. Hurwitz, C. L. 2023-11-02 doi:10.1101/2023.10.30.564831 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ ERas-Null Mice Generated Directly from Embryonic Stem Cells in a Lipid-rich Medium Enable the Discovery of A Novel Role in Craniofacial Development ]]> https://biorxiv.org/content/10.1101/2023.11.01.565209v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@c2dd48org.highwire.dtl.DTLVardef@14dbd07org.highwire.dtl.DTLVardef@b54a86org.highwire.dtl.DTLVardef@2fcdd5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Qin, Y. Tian, Q. Chung, H. Geng, F. James, D. J. Wang, J. Wen, D. 2023-11-03 doi:10.1101/2023.11.01.565209 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Biomechanical Modeling of Cesarean Section Scars and Scar Defects ]]> https://biorxiv.org/content/10.1101/2023.11.03.565565v1?rss=1 Scott, A. K. Louwagie, E. M. Myers, K. M. Oyen, M. L. 2023-11-05 doi:10.1101/2023.11.03.565565 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ The circulating immune cell landscape stratifies metastatic burden in breast cancer patients ]]> https://biorxiv.org/content/10.1101/2023.11.01.565223v1?rss=1 109,591 peripheral blood mononuclear cells from healthy individuals and breast cancer patients, we tested whether molecular traits of the circulating immune cells, probed with single-cell transcriptomics, can be used to segregate metastatic profiles. Our analyses revealed significant compositional and transcriptional differences in PBMCs of patients with restricted or high metastatic burden versus healthy subjects. The abundance of T cell and monocyte subtypes segregated cancer patients from healthy individuals, while memory and unconventional T cells were enriched in low metastatic burden disease. The cell communication axes were also found to be tightly associated with the extent of metastatic burden. Additionally, we identified a PBMC-derived metastatic gene signature capable of discerning metastatic condition from a healthy state. Our study provides unique molecular insights into the peripheral immune system operating in metastatic breast cancer, revealing potential new biomarkers of the extent of the metastatic state. Tracking such immune traits associated with metastatic spread could complement existing diagnostic tools. ]]> Mangiola, S. Brown, R. Berthelet, J. Guleria, S. Liyanage, C. Ostrouska, S. Wilcox, J. Merdas, M. Larsen, P. F. Bell, C. Schroder, J. Mielke, L. Mariadason, J. Chang-Hao Tsao, S. Chen, Y. Yadav, V. K. Anderson, R. L. Vodala, S. Merino, D. Behren, A. Yeo, B. Papenfuss, T. A. Pal, B. 2023-11-06 doi:10.1101/2023.11.01.565223 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Evidence for impaired hippocampal circuitry in schizophrenia and its link to memory dysfunction ]]> https://biorxiv.org/content/10.1101/2023.11.05.565219v1?rss=1 Zadbood, A. Tang, Y. Su, W. Hu, H. Capichioni, G. Yang, S. Wang, J. Gasser, C. Bein, O. Hui, L. Jia, Q. Zhang, T. Hong, Y. Wang, J. Goff, D. Davachi, L. 2023-11-06 doi:10.1101/2023.11.05.565219 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons ]]> https://biorxiv.org/content/10.1101/2023.11.07.566059v1?rss=1 Raudales, R. Kim, G. Kelly, S. M. Hatfield, J. Guan, W. Zhao, S. Paul, A. Qian, Y. Li, B. Huang, Z. J. 2023-11-08 doi:10.1101/2023.11.07.566059 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ C3 and CD47 dependent mechanisms in the refinement of sensory-motor circuits during spinal cord development ]]> https://biorxiv.org/content/10.1101/2023.11.08.566259v1?rss=1 Florez-Paz, D. M. Mentis, G. Z. 2023-11-08 doi:10.1101/2023.11.08.566259 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Signals of microbial growth learned from single amplicon samples ]]> https://biorxiv.org/content/10.1101/2023.11.07.565791v1?rss=1 Chlenski, P. A. Ricaurte, D. Pe'er, I. 2023-11-09 doi:10.1101/2023.11.07.565791 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum ]]> https://biorxiv.org/content/10.1101/2023.11.07.566113v1?rss=1 Schwartz, H. T. T. Tan, C.-H. Peraza, J. Raymundo, K. L. T. Sternberg, P. W. 2023-11-10 doi:10.1101/2023.11.07.566113 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy ]]> https://biorxiv.org/content/10.1101/2023.11.08.562798v1?rss=1 Worley, J. Noh, H. You, D. Turunen, M. Ding, H. Paull, E. O. Griffen, A. Grunn, A. Zhang, M. Guillan, K. Bush, E. Brosius, S. Hibshoosh, H. Mundi, P. S. Sims, P. Dalerba, P. Dela Cruz, F. S. Kung, A. L. Califano, A. 2023-11-10 doi:10.1101/2023.11.08.562798 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ A Proximal Sox2 Enhancer Cluster is Required for the Anterior Regional Identity of Neural Progenitors ]]> https://biorxiv.org/content/10.1101/2023.11.09.566464v1?rss=1 Tobias, I. C. Moorthy, S. D. Shchuka, V. M. Langroudi, L. Gillespie, Z. E. Duncan, A. G. Tian, R. Cherednychenko, M. Gajewska, N. A. Di Roberto, R. B. Mitchell, J. A. 2023-11-10 doi:10.1101/2023.11.09.566464 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adenoviral expression of Ca2+ indicators ]]> https://biorxiv.org/content/10.1101/2023.11.08.566169v1?rss=1 Masala, N. Mittag, M. Ambrad Giovannetti, E. O'Neil, D. A. Distler, F. J. Rupprecht, P. Helmchen, F. Yuste, R. Fuhrmann, M. Beck, H. Wenzel, M. Kelly, T. 2023-11-11 doi:10.1101/2023.11.08.566169 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Abstract representations emerge in human hippocampal neurons during inference behavior ]]> https://biorxiv.org/content/10.1101/2023.11.10.566490v1?rss=1 Courellis, H. S. Minxha, J. Ramirez Cardenas, A. Kimmel, D. L. Reed, C. M. Valiante, T. A. Salzman, C. D. Mamelak, A. N. Adolphs, R. Fusi, S. Rutishauser, U. 2023-11-11 doi:10.1101/2023.11.10.566490 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury ]]> https://biorxiv.org/content/10.1101/2023.11.10.566497v1?rss=1 Ghag, R. Kaushal, M. Nwanne, G. Knoten, A. Kiryluk, K. Rosenberg, A. Menez, S. Bagnasco, S. M. Sperati, C. J. Atta, M. G. Gaut, J. P. Williams, J. C. El-Achkar, T. M. Arend, L. J. Parikh, C. R. Jain, S. 2023-11-12 doi:10.1101/2023.11.10.566497 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ GENTANGLE: integrated computational design of gene entanglements ]]> https://biorxiv.org/content/10.1101/2023.11.09.565696v1?rss=1 Marti, J. M. Hsu, C. Rochereau, C. Blazejewski, T. Nisonoff, H. Leonard, S. P. Kang-Yun, C. S. Chlebek, J. L. Ricci, D. P. Park, D. M. Wang, H. H. Listgarten, J. Jiao, Y. Allen, J. E. 2023-11-13 doi:10.1101/2023.11.09.565696 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Characterization of a Novel Mouse Platelet Transfusion Model ]]> https://biorxiv.org/content/10.1101/2023.11.10.566577v1?rss=1 Gordy, D. Swayne, T. Berry, G. J. Thomas, T. A. Hudson, K. E. Stone, E. F. 2023-11-14 doi:10.1101/2023.11.10.566577 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ SHIELD: Skull-shaped hemispheric implants enabling large-scale-electrophysiology datasets in the mouse brain ]]> https://biorxiv.org/content/10.1101/2023.11.12.566771v1?rss=1 Bennett, C. Ouellette, B. Ramirez, T. K. Cahoon, A. Cabasco, H. Belski, H. Gillis, R. Grasso, C. Howard, R. Johnson, T. Loeffler, H. Smith, H. Sullivan, D. Williford, A. Caldejon, S. Durand, S. Gale, S. D. Guthrie, A. Ha, V. Han, W. Hardcastle, B. McBride, E. Mochizuki, C. Sridhar, A. Suarez, L. Swapp, J. Wilkes, J. Farrell, C. Groblewski, P. Olsen, S. 2023-11-14 doi:10.1101/2023.11.12.566771 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl- Channel ]]> https://biorxiv.org/content/10.1101/2023.11.14.567055v1?rss=1 Phan, L. X. Owji, A. P. Yang, T. Crain, J. Sansom, M. Tucker, S. J. 2023-11-14 doi:10.1101/2023.11.14.567055 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ The in vitro functional profiles of fentanyl and nitazene analogs at the μ-opioid receptor - high efficacy is dangerous regardless of signaling bias ]]> https://biorxiv.org/content/10.1101/2023.11.10.566672v1?rss=1 Tsai, M.-H. M. Chen, L. Baumann, M. H. Canals, M. Javitch, J. A. Lane, J. R. Shi, L. 2023-11-15 doi:10.1101/2023.11.10.566672 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ The Parkinson's disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2023.11.11.566693v1?rss=1 Jones-Tabah, J. He, K. Senkevich, K. Karpilovsky, N. Deyab, G. Cousineau, Y. Nikanorova, D. Goldsmith, T. del Cid Pellitero, E. Chen, C. X.-Q. Luo, W. You, Z. Abdian, N. Pietrantonio, I. Goiran, T. Ahmad, J. Ruskey, J. A. Asayesh, F. Spiegelman, D. Fahn, S. Waters, C. Monchi, O. Dauvilliers, Y. Dupre, N. Miliukhina, I. Timofeeva, A. Emelyanov, A. Pchelina, S. Greenbaum, L. Hassin-Baer, S. Alcalay, R. N. Milnerwood, A. Durcan, T. M. Gan-Or, Z. Fon, E. A. 2023-11-15 doi:10.1101/2023.11.11.566693 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Deep generative model deciphers derailed trajectories in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2023.11.11.566719v1?rss=1 Nazaret, A. Fan, J. L. Lavallee, V.-P. Cornish, A. E. Kiseliovas, V. Masilionis, I. Chun, J. Bowman, R. L. Eisman, S. E. Wang, J. Shi, L. Levine, R. L. Mazutis, L. Blei, D. Pe'er, D. Azizi, E. 2023-11-15 doi:10.1101/2023.11.11.566719 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Generation of salivary glands derived from pluripotent stem cells via conditional blastocyst complementation ]]> https://biorxiv.org/content/10.1101/2023.11.13.566845v1?rss=1 Tanaka, J. Miura, A. Shimamura, Y. Hwang, Y. Shimizu, D. Kondo, Y. Sawada, A. SARMAH, H. Ninish, Z. Mishima, K. Mori, M. 2023-11-15 doi:10.1101/2023.11.13.566845 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ The mechanism of mRNA activation ]]> https://biorxiv.org/content/10.1101/2023.11.15.567265v1?rss=1 Gentry, R. C. Ide, N. A. Comunale, V. M. Hartwick, E. W. Kinz-Thompson, C. D. Gonzalez, R. L. 2023-11-15 doi:10.1101/2023.11.15.567265 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Evaluation of gelatin bloom strength on gelatin methacryloyl hydrogel properties ]]> https://biorxiv.org/content/10.1101/2023.11.13.566924v1?rss=1 Zambuto, S. G. Kolluru, S. S. Ferchichi, E. Rudewick, H. Fodera, D. G. Myers, K. M. Zustiak, S. P. Oyen, M. L. 2023-11-16 doi:10.1101/2023.11.13.566924 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Causal interpretations of family GWAS in the presence of heterogeneous effects ]]> https://biorxiv.org/content/10.1101/2023.11.13.566950v1?rss=1 Veller, C. Przeworski, M. Coop, G. 2023-11-16 doi:10.1101/2023.11.13.566950 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data ]]> https://biorxiv.org/content/10.1101/2023.11.14.566956v1?rss=1 Park, C. Mani, S. Beltran-Velez, N. Maurer, K. Gohil, S. Li, S. Huang, T. Knowles, D. A. Wu, C. J. Azizi, E. 2023-11-16 doi:10.1101/2023.11.14.566956 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Fecal microbiota transplantation (FMT) from healthy and bipolar donors elicits distinct emotional behaviors and gut-brain metabolite profiles in mice ]]> https://biorxiv.org/content/10.1101/2023.11.16.566698v1?rss=1 Bukowski-Thall, G. Fellendorf, F. Gorkiewicz, S. Ip, K. C. K. Schmidt, L. Durdevic, M. Fabisch, H. Mörkl, S. Wagner-Skacel, J. Bengesser, S. Lenger, M. Dalkner, N. Gorkiewicz, G. Högenauer, C. Madl, T. Moissl-Eichinger, C. Farzi, A. Reininghaus, E. 2023-11-16 doi:10.1101/2023.11.16.566698 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Chronic activation of a negative engram induces behavioral and cellular abnormalities ]]> https://biorxiv.org/content/10.1101/2023.11.15.567268v1?rss=1 Jellinger, A. L. Suthard, R. L. Yuan, B. Surets, M. Ruesch, E. A. Caban, A. J. Liu, X. S. Shpokayte, M. Ramirez, S. 2023-11-17 doi:10.1101/2023.11.15.567268 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ PD-1 signaling uncovers a pathogenic subset of T cells in inflammatory arthritis ]]> https://biorxiv.org/content/10.1101/2023.11.16.566893v1?rss=1 Staube, J. Bukhari, S. Lerrer, S. Winchester, R. Henick, B. Dragovich, M. Mor, A. 2023-11-17 doi:10.1101/2023.11.16.566893 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ SAP expressing T peripheral helper cells identify systemic lupus erythematosus patients with lupus nephritis ]]> https://biorxiv.org/content/10.1101/2023.11.16.566902v1?rss=1 Gartshteyn, Y. Gartshteyn, Y. Geraldino-Pardilla, L. Bukhari, S. Lerrer, S. Askanase, A. D. Mor, A. 2023-11-17 doi:10.1101/2023.11.16.566902 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Exclusion of PD-1 from the immune synapse: a novel strategy to modulate T cell function ]]> https://biorxiv.org/content/10.1101/2023.11.16.566907v1?rss=1 Hao, L. Y. Lerrer, S. Song, R. Goeckeritz, M. Hu, X. Mor, A. 2023-11-17 doi:10.1101/2023.11.16.566907 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ The meditative brain: State and trait changes in harmonic complexity for long-term mindfulness meditators ]]> https://biorxiv.org/content/10.1101/2023.11.16.567347v1?rss=1 Atasoy, S. Escrich, A. Stark, E. Terry, K. G. M. Camara, E. Sanjuan, A. Chandaria, S. Deco, G. Kringelbach, M. 2023-11-17 doi:10.1101/2023.11.16.567347 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Germ fate determinants protect germ precursor cell division by restricting septin and anillin levels at the division plane ]]> https://biorxiv.org/content/10.1101/2023.11.17.566773v1?rss=1 Connors, C. Q. Mauro, M. S. Wiles, J. T. Countryman, A. D. Martin, S. L. Lacroix, B. Shirasu-Hiza, M. Dumont, J. Kasza, K. E. Davies, T. R. Canman, J. C. 2023-11-17 doi:10.1101/2023.11.17.566773 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ High prevalence of Prdm9-independentrecombination hotspots in placental mammals ]]> https://biorxiv.org/content/10.1101/2023.11.17.567540v1?rss=1 Joseph, J. Prentout, D. Laverre, A. Tricou, T. Duret, L. 2023-11-17 doi:10.1101/2023.11.17.567540 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Topographical and cell type-specific connectivity of rostral and caudal forelimb corticospinal neuron populations ]]> https://biorxiv.org/content/10.1101/2023.11.17.567623v1?rss=1 Carmona, L. M. Thomas, E. Smith, K. Tasic, B. Costa, R. M. Nelson, A. 2023-11-17 doi:10.1101/2023.11.17.567623 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Hierarchical motion perception as causal inference ]]> https://biorxiv.org/content/10.1101/2023.11.18.567582v1?rss=1 Shivkumar, S. DeAngelis, G. C. Haefner, R. M. 2023-11-18 doi:10.1101/2023.11.18.567582 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ Noncanonical Activity of Med4 as a Gatekeeper of Metastasis through Epigenetic Control of Integrin Signaling ]]> https://biorxiv.org/content/10.1101/2023.11.18.566087v1?rss=1 Bae, S.-Y. Chen, Y. Chen, H. Kumar, D. Karaiskos, S. Xu, J. J. Lu, C. Viny, A. D. Giancotti, F. G. 2023-11-19 doi:10.1101/2023.11.18.566087 Cold Spring Harbor Laboratory Press 2023-11-19 <![CDATA[ Antagonistic conflict between transposon-encoded introns and guide RNAs ]]> https://biorxiv.org/content/10.1101/2023.11.20.567912v1?rss=1 Zedaveinyte, R. Meers, C. Le, H. C. Mortman, E. E. Tang, S. Lampe, G. D. Pesari, S. R. Gelsinger, D. R. Wiegand, T. Sternberg, S. H. 2023-11-20 doi:10.1101/2023.11.20.567912 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ CD56/NCAM mediates cell migration of human NK cells by promoting integrin-mediated adhesion turnover ]]> https://biorxiv.org/content/10.1101/2023.11.21.567714v1?rss=1 Dixon, A. Shannon, M. Sloan, T. Mace, E. 2023-11-22 doi:10.1101/2023.11.21.567714 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ Adolescent Thalamocortical Inhibition Alters Prefrontal Excitation-Inhibition Balance. ]]> https://biorxiv.org/content/10.1101/2023.11.22.568048v1?rss=1 Petersen, D. C. K. Kellendonk, C. Canetta, S. 2023-11-22 doi:10.1101/2023.11.22.568048 Cold Spring Harbor Laboratory Press 2023-11-22 <![CDATA[ A Novel Role for Phospholamban in the Thalamic Reticular Nucleus ]]> https://biorxiv.org/content/10.1101/2023.11.22.568306v1?rss=1 Klocke, B. Britzolaki, A. Saurine, J. Ott, H. Krone, K. Bahamonde, K. Thelen, C. Tzimas, C. Sanoudou, D. Kranias, E. G. Pitychoutis, P. M. 2023-11-23 doi:10.1101/2023.11.22.568306 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Neuronal calcium spikes enable vector inversion in the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2023.11.24.568537v1?rss=1 Ishida, I. G. Sethi, S. Mohren, T. L. Abbott, L. Maimon, G. 2023-11-24 doi:10.1101/2023.11.24.568537 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against emerging SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2023.11.26.568730v1?rss=1 Wang, Q. Guo, Y. Bowen, A. Mellis, I. A. Valdez, R. Gherasim, C. Gordon, A. Liu, L. Ho, D. D. 2023-11-27 doi:10.1101/2023.11.26.568730 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ A Distinct Neural Code Supports Prospection of Future Probabilities During Instrumental Information-Seeking ]]> https://biorxiv.org/content/10.1101/2023.11.27.568849v1?rss=1 Singletary, N. M. Horga, G. Gottlieb, J. 2023-11-27 doi:10.1101/2023.11.27.568849 Cold Spring Harbor Laboratory Press 2023-11-27 <![CDATA[ (R,S)-ketamine's rapid-acting antidepressant effects are modulated by NR2B- containing NMDA receptors on adult-born hippocampal neurons ]]> https://biorxiv.org/content/10.1101/2023.11.28.569043v1?rss=1 Bulthuis, N. E. McGowan, J. C. Ladner, L. R. LaGamma, C. T. Lim, S. C. Shubeck, C. X. Brachman, R. A. Sydnor, E. Pavlova, I. P. Seo, D.-o. Drew, M. R. Denny, C. A. 2023-11-29 doi:10.1101/2023.11.28.569043 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Biomineralization and biomechanical trade-offs under heterogeneous environments in the eastern oyster Crassostrea virginica ]]> https://biorxiv.org/content/10.1101/2023.11.28.569049v1?rss=1 Telesca, L. Linsley, B. K. Witek, L. Hönisch, B. 2023-11-29 doi:10.1101/2023.11.28.569049 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Engraftment and injury repair in regionally conditioned rat lung in vivo by lung progenitors derived from human pluripotent stem cells. ]]> https://biorxiv.org/content/10.1101/2023.11.28.569060v1?rss=1 Liu, H.-Y. Predella, C. Chen, Y.-W. Wang, J. Fare, S. Pezet, M. G. Liang, S. Saqi, A. Murray, J. W. Vunjak-Novakovic, G. Snoeck, H.-W. Dorrello, N. V. 2023-11-29 doi:10.1101/2023.11.28.569060 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Length control emerges from cytoskeletal network geometry ]]> https://biorxiv.org/content/10.1101/2023.11.28.569063v1?rss=1 McInally, S. G. Reading, A. J. B. Rosario, A. Jelenkovic, P. R. Goode, B. Kondev, J. 2023-11-29 doi:10.1101/2023.11.28.569063 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases ]]> https://biorxiv.org/content/10.1101/2023.11.30.569447v1?rss=1 Wiegand, T. Hoffmann, F. T. Walker, M. W. G. Tang, S. Richard, E. Le, H. C. Meers, C. Sternberg, S. H. 2023-11-30 doi:10.1101/2023.11.30.569447 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ Bidirectional Energy Flow in the Photosystem II Supercomplex ]]> https://biorxiv.org/content/10.1101/2023.11.30.569278v1?rss=1 Leonardo, C. Yang, S.-J. Orcutt, K. Iwai, M. Arsenault, E. A. Fleming, G. R. 2023-12-01 doi:10.1101/2023.11.30.569278 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Temporal Tracking of Plasma Cells in vivo Using J-chain CreERT2 Reporter System. ]]> https://biorxiv.org/content/10.1101/2023.12.02.569736v1?rss=1 Borbet, T. C. Zaldana, K. Zavitsanou, A.-M. Hines, M. J. Bajwa, S. Morrison, T. Boehringer, T. Hallisey, V. M. Cadwell, K. Koralov, S. B. 2023-12-04 doi:10.1101/2023.12.02.569736 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Tumor-selective effects of active RAS inhibition in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2023.12.03.569791v1?rss=1 90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS, we assessed the therapeutic potential of RMC-7977 in a comprehensive range of PDAC models, including human and murine cell lines, human patient-derived organoids, human PDAC explants, subcutaneous and orthotopic cell-line or patient derived xenografts, syngeneic allografts, and genetically engineered mouse models. We observed broad and pronounced anti-tumor activity across these models following direct RAS inhibition at doses and concentrations that were well-tolerated in vivo. Pharmacological analyses revealed divergent responses to RMC-7977 in tumor versus normal tissues. Treated tumors exhibited waves of apoptosis along with sustained proliferative arrest whereas normal tissues underwent only transient decreases in proliferation, with no evidence of apoptosis. Together, these data establish a strong preclinical rationale for the use of broad-spectrum RAS inhibition in the setting of PDAC. ]]> Wasko, U. N. Jiang, J. Garcia, A. C. Wang, Y. Lee, B. Orlen, M. Drizyte-Miller, K. Menard, M. Dilly, J. Sastra, S. A. Palermo, C. F. Dalton, T. Hasselluhn, M. C. Decker-Farrell, A. R. Chang, S. Jiang, L. Wei, X. Yang, Y.-c. Helland, C. Courtney, H. Gindin, Y. Zhao, R. Kemp, S. B. Clendenin, C. Sor, R. Vostrejs, W. Amparo, A. A. Hibshman, P. S. Rees, M. G. Ronan, M. M. Roth, J. A. Bakir, B. Badgley, M. A. Chabot, J. A. Kluger, M. D. Manji, G. A. Quintana, E. Wang, Z. Smith, J. A. M. Holderfield, M. Wildes, D. Aguirre, A. J. Der, C. J. Vonderheide, R. H 2023-12-04 doi:10.1101/2023.12.03.569791 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ behaviorMate: An Intranet of Things Approach for Adaptable Control of Behavioral and Navigation-Based Experiments ]]> https://biorxiv.org/content/10.1101/2023.12.04.569989v1?rss=1 Bowler, J. C. Zakka, G. Yong, H. C. Li, W. Rao, B. Liao, Z. Priestley, J. B. Losonczy, A. 2023-12-06 doi:10.1101/2023.12.04.569989 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Microsomal triglyceride transfer protein is necessary to maintain lipid homeostasis and retinal function ]]> https://biorxiv.org/content/10.1101/2023.12.06.570418v1?rss=1 Grubaugh, C. R. Dhingra, A. Prakash, B. Montenegro, D. Sparrow, J. R. Daniele, L. L. Curcio, C. A. Bell, B. A. Hussain, M. M. Boesze-Battaglia, K. 2023-12-06 doi:10.1101/2023.12.06.570418 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Glial swip-10 expression controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis ]]> https://biorxiv.org/content/10.1101/2023.12.06.570462v1?rss=1 Rodriguez, P. Kalia, V. Gibson, C. L. Gichi, Z. Rajoo, A. Matier, C. D. Pezacki, A. T. Xiao, T. Carvelli, L. Chang, C. J. Miller, G. W. Khamoui, A. V. Boerner, J. Blakely, R. D. 2023-12-08 doi:10.1101/2023.12.06.570462 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Benchmarking DNA binding affinity models using allele-specific transcription factor binding data ]]> https://biorxiv.org/content/10.1101/2023.12.15.571887v1?rss=1 Li, X. Melo, L. A. Bussemaker, H. J. 2023-12-15 doi:10.1101/2023.12.15.571887 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2023.12.15.571700v1?rss=1 Henderson, R. Anasti, K. Manne, K. Stalls, V. Saunders, C. Bililign, Y. Williams, A. Bubphamala, J. Montani, M. Kachhap, S. Li, J. Jaing, C. Newman, A. Cain, D. Lu, X. Venkatayogi, S. Berry, M. Wagh, K. Korber, B. Saunders, K. O. Tian, M. Alt, F. Wiehe, K. Acharya, P. Alam, S. M. Haynes, B. F. 2023-12-16 doi:10.1101/2023.12.15.571700 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Powdery mildew infection induces a non-canonical route to storage lipid formation at the expense of host thylakoid lipids to fuel its spore production ]]> https://biorxiv.org/content/10.1101/2023.12.15.571944v1?rss=1 Jaenisch, J. Xue, H. Schlapfer, J. McGarrigle, E. R. Louie, K. B. Northen, T. Wildermuth, M. C. 2023-12-16 doi:10.1101/2023.12.15.571944 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Preclinical studies with ground germinated barley (GGB) for oral enzyme replacement therapy (Oral-ERT) in Pompe disease knockout mice ]]> https://biorxiv.org/content/10.1101/2023.12.27.573457v1?rss=1 Martiniuk, F. Mack, A. Martiniuk, J. Meinke, P. Schoser, B. Hu, G. Tchou-Wong, K.-M. 2023-12-28 doi:10.1101/2023.12.27.573457 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Fine-tuning Large Language Models for Rare Disease Concept Normalization ]]> https://biorxiv.org/content/10.1101/2023.12.28.573586v1?rss=1 Wang, A. Liu, C. Yang, J. Weng, C. 2023-12-29 doi:10.1101/2023.12.28.573586 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Identification of a Musashi2 translocation as a novel oncogene in myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2023.12.29.573601v1?rss=1 Spinler, K. Hamilton, M. Bajaj, J. Shima, Y. Diaz, E. Kritzik, M. Reya, T. 2023-12-29 doi:10.1101/2023.12.29.573601 Cold Spring Harbor Laboratory Press 2023-12-29 <![CDATA[ Concerted neuron-astrocyte gene expression declines in aging and schizophrenia ]]> https://biorxiv.org/content/10.1101/2024.01.07.574148v1?rss=1 Ling, E. Nemesh, J. Goldman, M. Kamitaki, N. Reed, N. Handsaker, R. E. Genovese, G. Vogelgsang, J. S. Gerges, S. Kashin, S. Ghosh, S. Esposito, J. M. French, K. Meyer, D. Lutservitz, A. Mullally, C. D. Wysoker, A. Spina, L. Neumann, A. Hogan, M. Ichihara, K. Berretta, S. McCarroll, S. A. 2024-01-08 doi:10.1101/2024.01.07.574148 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response ]]> https://biorxiv.org/content/10.1101/2024.01.12.575095v1?rss=1 Powers, E. N. Reynaud, K. Sousa, C. Kuwayama, N. Jovanovic, M. Ingolia, N. Brar, G. A. 2024-01-14 doi:10.1101/2024.01.12.575095 Cold Spring Harbor Laboratory Press 2024-01-14 <![CDATA[ Resilience to Early Life Adversity Effects on Stress Reactivity by Postnatal Knockdown of 5-HT1A Autoreceptors ]]> https://biorxiv.org/content/10.1101/2024.01.22.576344v1?rss=1 Dixon, R. Malave, L. Thompson, R. Wu, S. Sadik, N. Anacker, C. 2024-01-22 doi:10.1101/2024.01.22.576344 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ The Temporal Dynamics of Aperiodic Neural Activity Track Changes in Sleep Architecture ]]> https://biorxiv.org/content/10.1101/2024.01.25.577204v1?rss=1 Ameen, M. S. Jacobs, J. Schabus, M. Hoedlmoser, K. Donoghue, T. 2024-01-26 doi:10.1101/2024.01.25.577204 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Human vascular organoids with a mosaic AKT1 mutation recapitulate Proteus syndrome ]]> https://biorxiv.org/content/10.1101/2024.01.26.577324v1?rss=1 He, S. Zhu, Y. Chauhan, S. Tavakol, D. N. Lee, J. H. Berris, R. B.-L. Xu, C. Lee, J. Lee, C. Cai, S. McElroy, S. Vunjak-Novakovic, G. Tomer, R. Azizi, E. Xu, B. Lao, Y.-H. Leong, K. W. 2024-01-27 doi:10.1101/2024.01.26.577324 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians ]]> https://biorxiv.org/content/10.1101/2024.02.15.580289v1?rss=1 Jaeger, E. C. B. Vijatovic, D. Deryckere, A. Zorin, N. Nguyen, A. L. Ivanian, G. Woych, J. Arnold, R. C. Ortega Gurrola, A. Shvartsman, A. Barbieri, F. Toma, F. A. Gorbsky, G. J. Horb, M. E. Cline, H. T. Shay, T. F. Kelley, D. B. Yamaguchi, A. Shein-Idelson, M. Tosches, M. A. Sweeney, L. B. 2024-02-16 doi:10.1101/2024.02.15.580289 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ The Dorsal Column Nuclei Scales Mechanical Allodynia During Neuropathic Pain ]]> https://biorxiv.org/content/10.1101/2024.02.20.581208v1?rss=1 Upadhyay, A. Gradwell, M. A. Vajtay, T. J. Conner, J. Sayal, A. A. Azadegan, C. Patel, K. R. Thackray, J. K. Bohic, M. Imai, F. Ogundare, S. O. Yoshida, Y. Abdus-Saboor, I. Azim, E. Abraira, V. E. G. 2024-02-23 doi:10.1101/2024.02.20.581208 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ MU-BRAIN: MUltiethnic Brain Rna-seq for Alzheimer INitiative ]]> https://biorxiv.org/content/10.1101/2024.02.20.581250v1?rss=1 Yang, Z. Cieza, B. Reyes-Dumeyer, D. Lee, A. Ma, Y. Yilmaz, E. Lantigua, R. Miller, G. Brown, L. Honig, L. Ciener, B. Leskinin, S. Sivakumar, S. Vardarajan, B. Dugger, B. Jin, L.-W. Murray, M. Dickson, D. Rissman, R. Hiniker, A. Pericak-Vance, M. Vance, J. Foroud, T. Kizil, C. Teich, A. Mayeux, R. Tosto, G. 2024-02-23 doi:10.1101/2024.02.20.581250 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ PreMode predicts mode of action of missense variants by deep graph representation learning of protein sequence and structural context ]]> https://biorxiv.org/content/10.1101/2024.02.20.581321v1?rss=1 Zhong, G. Zhao, Y. Zhuang, D. Chung, W. K. Shen, Y. 2024-02-23 doi:10.1101/2024.02.20.581321 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ A specific phosphorylation-dependent conformational switch of SARS-CoV-2 nucleoprotein inhibits RNA binding ]]> https://biorxiv.org/content/10.1101/2024.02.22.579423v1?rss=1 Botova, M. Camacho-Zarco, A. R. Tognetti, J. Bessa, L. M. Guseva, S. Mikkola, E. Salvi, N. Maurin, D. Herrmann, T. Blackledge, M. 2024-02-23 doi:10.1101/2024.02.22.579423 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Dynamic representation of appetitive and aversive stimuli in nucleus accumbens shell D1- and D2-medium spiny neurons ]]> https://biorxiv.org/content/10.1101/2024.02.22.581563v1?rss=1 Domingues, A. V. Carvalho, T. T. A. Martins, G. J. Correia, R. Coimbra, B. Goncalves, R. Wezik, M. Gaspar, R. Pinto, L. Sousa, N. Costa, R. M. Soares-Cunha, C. Rodrigues, A. J. 2024-02-23 doi:10.1101/2024.02.22.581563 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Emergence of a synergistic scaffold in the brains of human infants ]]> https://biorxiv.org/content/10.1101/2024.02.23.581375v1?rss=1 Varley, T. F. Sporns, O. Stevenson, N. J. Welch, M. G. Myers, M. M. Vanhatalo, S. Tokariev, A. 2024-02-23 doi:10.1101/2024.02.23.581375 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Next Generation Neuropeptide Y Receptor Small Molecule Agonists Inhibit Mosquito Biting Behavior ]]> https://biorxiv.org/content/10.1101/2024.02.28.582529v1?rss=1 Zeledon, E. V. Baxt, L. A. Khan, T. A. Michino, M. Miller, M. Huggins, D. J. Jiang, C. S. Vosshall, L. B. Duvall, L. B. 2024-03-02 doi:10.1101/2024.02.28.582529 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors ]]> https://biorxiv.org/content/10.1101/2024.03.03.583211v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@193cfe1org.highwire.dtl.DTLVardef@134edccorg.highwire.dtl.DTLVardef@1e81deforg.highwire.dtl.DTLVardef@56406_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Suazo, K. Mishra, V. Maity, S. Auger, S. Justyna, K. Petre, A. Ottoboni, L. Ongaro, J. Corti, S. Lotti, F. Przedborski, S. Distefano, M. D. 2024-03-06 doi:10.1101/2024.03.03.583211 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Cis inhibition of co-expressed DIPs and Dprs shapes neural development ]]> https://biorxiv.org/content/10.1101/2024.03.04.583391v1?rss=1 Morano, N. C. Lopez, D. S. Meltzer, H. Sergeeva, A. P. Katsamba, P. S. Gupta, H. P. Becker, J. E. Bornstein, B. Cosmanescu, F. Schuldiner, O. Mann, R. S. Honig, B. Shapiro, L. 2024-03-06 doi:10.1101/2024.03.04.583391 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ High-Throughput Phenotyping of Seed Quality Traits Using Imaging and Deep Learning in Dry Pea ]]> https://biorxiv.org/content/10.1101/2024.03.05.583564v1?rss=1 Morales, M. Worral, H. Piche, L. Atanda, S. A. Dariva, F. Ramos, C. Hoang, K. Yan, C. Flores, P. Bandillo, N. 2024-03-06 doi:10.1101/2024.03.05.583564 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Integrated stress response associated with dark microglia promotes microglial lipogenesis and contributes to neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.03.04.582965v1?rss=1 Flury, A. Aljayousi, L. Aziz, S. Park, H.-J. Khakpour, M. Sandberg, C. Ibanez, F. G. Braniff, O. Deme, P. McGrath, J. D. Ngo, T. Mechler, J. Ramirez, D. M. Avnon-Klein, D. Murray, J. W. Liu, J. Haughey, N. J. Werneburg, S. Tremblay, M.-E. Ayata, P. 2024-03-08 doi:10.1101/2024.03.04.582965 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Robust Methods For Quantifying Neuronal Morphology And Molecular Signaling Reveal That Psychedelics Do Not Induce Neuroplasticity ]]> https://biorxiv.org/content/10.1101/2024.03.04.583022v1?rss=1 Boltaev, U. Park, H. W. Brown, K. R. Delgado, M. Wu, J. Diaz-Pacheco, B. N. Botero Pinzon, M. He, K. Ahern, E. Goldshmid, N. Simpson, E. H. Sames, D. 2024-03-08 doi:10.1101/2024.03.04.583022 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ Nociceptive neurons interact directly with gastric cancer cells via a CGRP/Ramp1 axis to promote tumor progression ]]> https://biorxiv.org/content/10.1101/2024.03.04.583209v1?rss=1 Zhi, X. Wu, F. Qian, J. Ochiai, Y. Lian, G. Malagola, E. Chen, D. Ryeom, S. W. WANG, T. C. 2024-03-08 doi:10.1101/2024.03.04.583209 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity ]]> https://biorxiv.org/content/10.1101/2024.03.05.583623v1?rss=1 50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities11, thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders. ]]> Mosharov, E. Rosenberg, A. M. Monzel, A. S. Osto, C. A. Stiles, L. Rosoklija, G. B. Dwork, A. J. Bindra, S. Zhang, Y. Fujita, M. Mariani, M. B. Bakalian, M. Sulzer, D. De Jager, P. Menon, V. Shirihai, O. S. Mann, J. Underwood, M. Boldrini, M. Thiebaut de Schotten, M. S. Picard, M. 2024-03-07 doi:10.1101/2024.03.05.583623 Cold Spring Harbor Laboratory Press 2024-03-07 <![CDATA[ Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer ]]> https://biorxiv.org/content/10.1101/2024.03.06.583256v1?rss=1 De Felice, D. Alaimo, A. Bressan, D. Genovesi, S. Marmocchi, E. Annesi, N. Beccaceci, G. Dalfovo, D. Cutrupi, F. Foletto, V. Lorenzoni, M. Gandolfi, F. Kannan, S. Verma, C. S. Vasciaveo, A. Shen, M. M. Romanel, A. Chiacchiera, F. Cambuli, F. Lunardi, A. 2024-03-10 doi:10.1101/2024.03.06.583256 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury ]]> https://biorxiv.org/content/10.1101/2024.03.07.583787v1?rss=1 Fleischer, S. Nash, T. R. Tamargo, M. A. Lock, R. I. Venturini, G. Morsink, M. Li, V. Lamberti, M. J. Graney, P. L. Liberman, M. Kim, Y. Zhuang, R. Z. Whitehead, J. Friedman, R. A. SONI, R. Seidman, J. G. Seidman, C. E. Geraldino-Pardilla, L. Winchester, R. Vunjak-Novakovic, G. 2024-03-12 doi:10.1101/2024.03.07.583787 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Transcranial Functional Ultrasound Imaging Detects Focused Ultrasound Neuromodulation Induced Hemodynamic Changes in Mouse and Nonhuman Primate Brains In Vivo ]]> https://biorxiv.org/content/10.1101/2024.03.08.583971v1?rss=1 Christian, A. Bendig, J. Blackman, S. G. McCune, E. P. Bae, S. Jimenez-Gambin, S. Ji, R. Konofagou, E. E. 2024-03-12 doi:10.1101/2024.03.08.583971 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Automated Identification of Germline de novo Mutations in Family Trios: A Consensus-Based Informatic Approach ]]> https://biorxiv.org/content/10.1101/2024.03.08.584100v1?rss=1 Shadrina, M. Kalay, O. Demirkaya-Budak, S. LeDuc, C. A. Chung, W. K. Turgut, D. Budak, G. Arslan, E. Semenyuk, V. Davis-Dusenbery, B. Seidman, C. E. Yost, H. J. Jain, A. Gelb, B. D. 2024-03-13 doi:10.1101/2024.03.08.584100 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Structure-based probe reveals the presence of large transthyretin aggregates in plasma of ATTR amyloidosis patients ]]> https://biorxiv.org/content/10.1101/2024.03.09.584228v1?rss=1 Pedretti, R. Wang, L. Yakubovska, A. Zhang, Q. S. Nguyen, B. Grodin, J. L. Masri, A. Saelices, L. 2024-03-10 doi:10.1101/2024.03.09.584228 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ SARS-CoV-2 Omicron BA.2.87.1 Exhibits Higher Susceptibility to Serum Neutralization Than EG.5.1 and JN.1 ]]> https://biorxiv.org/content/10.1101/2024.03.10.584306v1?rss=1 Wang, Q. Guo, Y. Schwanz, L. T. Mellis, I. A. Sun, Y. Qu, Y. Urtecho, G. Valdez, R. Stoneman, E. Gordon, A. Wang, H. H. Liu, L. Ho, D. D. 2024-03-11 doi:10.1101/2024.03.10.584306 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ La Crosse virus reassortants highlight genomic determinants of infection and pathogenesis ]]> https://biorxiv.org/content/10.1101/2024.03.11.584386v1?rss=1 Rondeau, N. C. Spector, S. N. Thannickal, S. A. Stapleford, K. A. 2024-03-11 doi:10.1101/2024.03.11.584386 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning ]]> https://biorxiv.org/content/10.1101/2024.03.11.584515v1?rss=1 Vaxenburg, R. Siwanowicz, I. Merel, J. Robie, A. A. Morrow, C. Novati, G. Stefanidi, Z. Card, G. M. Reiser, M. B. Botvinick, M. M. Branson, K. M. Tassa, Y. Turaga, S. C. 2024-03-14 doi:10.1101/2024.03.11.584515 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ PET Imaging of the Serotonin 1A Receptor in Major Depressive Disorder: Hierarchical Multivariate Analysis of 11CWAY100635 Overcomes Outcome Measure Discrepancies ]]> https://biorxiv.org/content/10.1101/2024.03.12.584569v1?rss=1 Matheson, G. J. Zanderigo, F. Miller, J. M. Bartlett, E. A. Mann, J. J. Ogden, R. T. 2024-03-12 doi:10.1101/2024.03.12.584569 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts ]]> https://biorxiv.org/content/10.1101/2024.03.12.584665v1?rss=1 Lin, X. Gupta, D. Vaitsiankova, A. Bhandari, S. K. Leung, K. S. K. Menolfi, D. Lee, B. J. Russell, H. R. Gershik, S. Gu, W. McKinnon, P. J. DANTZER, F. Rothenberg, E. Tomkinson, A. E. Zha, S. 2024-03-14 doi:10.1101/2024.03.12.584665 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms ]]> https://biorxiv.org/content/10.1101/2024.03.12.584681v1?rss=1 Lambourne, L. Mattioli, K. Santoso, C. Sheynkman, G. Inukai, S. Kaundal, B. Berenson, A. Spirohn-Fitzgerald, K. Bhattacharjee, A. Rothman, E. Shrestha, S. Laval, F. Yang, Z. Bisht, D. Sewell, J. A. Li, G. Prasad, A. Phanor, S. Lane, R. Campbell, D. M. Hunt, T. Balcha, D. Gebbia, M. Twizere, J.-C. Hao, T. Frankish, A. Riback, J. Salomonis, N. Calderwood, M. A. Hill, D. E. Sahni, N. Vidal, M. Bulyk, M. L. Fuxman Bass, J. I. 2024-03-14 doi:10.1101/2024.03.12.584681 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy ]]> https://biorxiv.org/content/10.1101/2024.03.13.584744v1?rss=1 Saecker, R. M. Mueller, A. U. Malone, B. Chen, J. Budell, W. C. Dandey, V. P. Maruthi, K. Mendez, J. H. Molina, N. Eng, E. T. Yen, L. Y. Potter, C. S. Carragher, B. Darst, S. A. 2024-03-14 doi:10.1101/2024.03.13.584744 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Open-Source Tools to Analyze Temporal and Spatial Properties of Local Field Potentials ]]> https://biorxiv.org/content/10.1101/2024.03.14.584529v1?rss=1 Barrett, G. M. Vajram, S. A. Shetler, O. Aoun, A. Hussaini, S. A. 2024-03-14 doi:10.1101/2024.03.14.584529 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Early-life stress alters chromatin modifications in VTA to prime stress sensitivity ]]> https://biorxiv.org/content/10.1101/2024.03.14.584631v1?rss=1 Geiger, L. T. Balouek, J.-A. R. Farrelly, L. A. Chen, A. S. Tang, M. Bennett, S. N. Nestler, E. J. Garcia, B. A. Maze, I. Pena, C. J. 2024-03-14 doi:10.1101/2024.03.14.584631 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ 5-HT1B receptors mediate dopaminergic inhibition of vesicular fusion and GABA release from striatonigral synapses. ]]> https://biorxiv.org/content/10.1101/2024.03.14.584991v1?rss=1 Molinari, M. Lieberman, O. J. Sulzer, D. Santini, E. Borgkvist, A. 2024-03-14 doi:10.1101/2024.03.14.584991 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Endogenous Precision of the Number Sense ]]> https://biorxiv.org/content/10.1101/2024.03.14.585091v1?rss=1 Prat-Carrabin, A. Woodford, M. 2024-03-18 doi:10.1101/2024.03.14.585091 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[ Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations ]]> https://biorxiv.org/content/10.1101/2024.03.17.585370v1?rss=1 Fernandez, E. C. Tomassoni, L. Zhang, X. Wang, J. Obradovic, A. Laise, P. Griffin, A. T. Vlahos, L. Minns, H. E. Morales, D. V. Simmons, C. Gallitto, M. Wei, H.-J. Martins, T. J. Becker, P. S. Crawford, J. R. Tzaridis, T. Wechsler-Reya, R. J. Garvin, J. Gartrell, R. D. Szalontay, L. Zacharoulis, S. Wu, C.-C. Zhang, Z. Califano, A. Pavisic, J. 2024-03-17 doi:10.1101/2024.03.17.585370 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Variational inference for microbiome survey data with application to global ocean data ]]> https://biorxiv.org/content/10.1101/2024.03.18.585474v1?rss=1 Mishra, A. K. McNichol, J. Fuhrman, J. Blei, D. Muller, C. L. 2024-03-19 doi:10.1101/2024.03.18.585474 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch ]]> https://biorxiv.org/content/10.1101/2024.03.18.585588v1?rss=1 Gretarsson, K. H. Abini-Agbomson, S. Gloor, S. Weinberg, D. N. McCuiston, J. L. Kumary, V. U. N. S. Hickman, A. Sahu, V. Lee, R. Xu, X. Lipieta, N. Flashner, S. Adeleke, O. A. Popova, I. K. Taylor, H. Noll, K. Windham, C. L. Maryanski, D. Venters, B. J. Nakagawa, H. Keogh, M. Armache, K.-J. Lu, C. 2024-03-20 doi:10.1101/2024.03.18.585588 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ MED1 IDR acetylation reorganizes the transcription preinitiation complex, rewires 3D chromatin interactions and reprograms gene expression ]]> https://biorxiv.org/content/10.1101/2024.03.18.585606v1?rss=1 Lin, R. Roeder, R. G. Barrows, D. Mo, Y. Onikubo, T. Zhang, Z. 2024-03-18 doi:10.1101/2024.03.18.585606 Cold Spring Harbor Laboratory Press 2024-03-18 <![CDATA[ Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties. ]]> https://biorxiv.org/content/10.1101/2024.03.19.585766v1?rss=1 Prakash, P. Khodke, P. Balasubramaniam, M. Davids, B.-O. Hollis, T. Davis, J. Pandhare, J. Kumbhar, B. Dash, C. 2024-03-19 doi:10.1101/2024.03.19.585766 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Illuminating the Dark Cancer Phosphoproteome Through a Machine-Learned Co-Regulation Map of 26,280 Phosphosites ]]> https://biorxiv.org/content/10.1101/2024.03.19.585786v1?rss=1 Jiang, W. Jaehnig, E. J. Liao, Y. Yaron-Barir, T. M. Johnson, J. L. Cantley, L. C. Zhang, B. 2024-03-21 doi:10.1101/2024.03.19.585786 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ Development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2024.03.20.585981v1?rss=1 Du, D. X. Bartnik, A. C. Duncan, C. J. R. Choudhry, U. Tabachnik, T. Sallah, C. Najafi, E. Yang, D.-S. Maxson, J. M. Fitzpatrick, A. W. P. 2024-03-25 doi:10.1101/2024.03.20.585981 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults ]]> https://biorxiv.org/content/10.1101/2024.03.21.585983v1?rss=1 Harris, K. M. Levitt, B. E. Gaydosh, L. Martin, C. Meyer, J. M. Mishra, A. A. Kelly, A. L. Aiello, A. E. 2024-03-27 doi:10.1101/2024.03.21.585983 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli . ]]> https://biorxiv.org/content/10.1101/2024.03.21.586065v1?rss=1 Liponska, A. Monlezun, L. Wilkins, I. Ngo, S. Oïffer, T. Bouchachi, C. Hunt, J. F. Aalberts, D. P. Boël, G. 2024-03-21 doi:10.1101/2024.03.21.586065 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons ]]> https://biorxiv.org/content/10.1101/2024.03.21.586118v1?rss=1 Shi, J. Nutkovich, B. Kushinsky, D. Rao, B. Y. Herrlinger, S. A. Mihaila, T. S. Malina, K. C.-K. OToole, C. K. Conde Paredes, M. E. Yong, H. C. Varol, E. Losonczy, A. Spiegel, I. 2024-03-26 doi:10.1101/2024.03.21.586118 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection ]]> https://biorxiv.org/content/10.1101/2024.03.21.586142v1?rss=1 Florek, L. C. Lin, X. Lin, Y.-C. Chakraborty, A. Lin, M.-H. Price-Whelan, A. Tong, L. Rahme, L. Dietrich, L. E. P. 2024-03-22 doi:10.1101/2024.03.21.586142 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Attentional modulation of secondary somatosensory and visual thalamus of mice ]]> https://biorxiv.org/content/10.1101/2024.03.22.586242v1?rss=1 Petty, G. Bruno, R. M. 2024-03-25 doi:10.1101/2024.03.22.586242 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Multidimensional analysis of cortical interneuron synaptic features reveals underlying synaptic heterogeneity ]]> https://biorxiv.org/content/10.1101/2024.03.22.586340v1?rss=1 Dummer, P. Lee, D. Hossain, S. Wang, R. Evard, A. Schneider-Mizell, C. M. Menon, V. Au, E. 2024-03-27 doi:10.1101/2024.03.22.586340 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences ]]> https://biorxiv.org/content/10.1101/2024.03.22.586363v1?rss=1 Xu, C. Bao, S. Chen, H. Jiang, T. Zhang, C. 2024-03-25 doi:10.1101/2024.03.22.586363 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Roles for RERE in lymphatic endothelial cell proliferation and survival, and human cystic lymphatic malformations ]]> https://biorxiv.org/content/10.1101/2024.03.24.586490v1?rss=1 Rogerson, D. M. Muley, A. Vogel, Z. Giordano, J. Wapner, R. Shawber, C. 2024-03-27 doi:10.1101/2024.03.24.586490 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ The regulatory architecture of the primed pluripotent cell state ]]> https://biorxiv.org/content/10.1101/2024.03.25.586622v1?rss=1 Li, B. I. Alvarez, M. J. Zhao, H. Chirathivat, N. Califano, A. Shen, M. M. 2024-03-27 doi:10.1101/2024.03.25.586622 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response. ]]> https://biorxiv.org/content/10.1101/2024.03.25.586632v1?rss=1 Elvira-Blazquez, D. Fernandez-Justel, J. Arcas, A. Statello, L. Goni, E. Gonzalez, J. Ricci, B. Zaccara, S. Raimondi, I. Huarte, M. 2024-03-28 doi:10.1101/2024.03.25.586632 Cold Spring Harbor Laboratory Press 2024-03-28 <![CDATA[ Global variation in prior exposure shapes antibody neutralization profiles of SARS-CoV-2 variants up to BA.2.86 ]]> https://biorxiv.org/content/10.1101/2024.03.27.586820v1?rss=1 Turner, S. Amirthalingam, G. Bailey, D. Barouch, D. H. Bewley, K. R. Brown, K. Cao, Y. R. Chan, Y.-W. Charlton, S. DOVE consortium, Coombes, N. S. Hallis, B. Ho, D. D. Jian, F. Lasrado, N. Lassauniere, R. Lihong, L. Montefiori, D. C. Moss, P. Newman, J. Parry, H. Polacek Strandh, C. Rasmussen, M. Shao, F. Shen, X. Thakur, N. Thomson, E. C. Wang, J. Wang, P. Wang, Q. C. Willett, B. J. Yisimayi, A. Smith, D. J. 2024-03-27 doi:10.1101/2024.03.27.586820 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Genome-wide association study of glucocerebrosidase activity modifiers. ]]> https://biorxiv.org/content/10.1101/2024.03.27.586821v1?rss=1 Somerville, E. N. Krohn, L. Senkevich, K. Yu, E. Ahmad, J. Asayesh, F. Ruskey, J. A. Spiegelman, D. Fahn, S. Waters, C. Sardi, S. P. Alcalay, R. N. Gan-Or, Z. 2024-04-02 doi:10.1101/2024.03.27.586821 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Inhibition of striatal indirect pathway during second postnatal week leads to long lasting deficits in motivated behavior ]]> https://biorxiv.org/content/10.1101/2024.03.29.586960v1?rss=1 Olivetti, P. R. Torres-Herraez, A. Raudales, R. Sumerau, M. E. Moyles, S. Balsam, P. Kellendonk, C. 2024-03-31 doi:10.1101/2024.03.29.586960 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Functional ultrasound (fUS) imaging of displacement-guided focused ultrasound (FUS) neuromodulation in mice ]]> https://biorxiv.org/content/10.1101/2024.03.29.587355v1?rss=1 Kim, S. Kwon, N. Hossain, M. M. Bendig, J. Konofagou, E. 2024-04-01 doi:10.1101/2024.03.29.587355 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections ]]> https://biorxiv.org/content/10.1101/2024.03.30.587445v1?rss=1 Yip, M. C. Gonzalez, M. M. Lewallen, C. F. Landry, C. R. Kolb, I. Yang, B. Stoy, W. M. Fong, M.-f. J Rowan, M. Boyden, E. S. Forest, C. R. 2024-04-01 doi:10.1101/2024.03.30.587445 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Conditional deletion of CEACAM1 causes hepatic stellate cell activation ]]> https://biorxiv.org/content/10.1101/2024.04.02.586238v1?rss=1 Muturi, H. T. Ghadieh, H. E. Asalla, S. Lester, S. G. Verhulst, S. Stankus, H. L. Zaidi, S. Abdolahipour, R. Belew, G. D. Grunsven, L. A. v. Friedman, S. L. Schwabe, R. F. Hinds, T. D. Najjar, S. M. 2024-04-03 doi:10.1101/2024.04.02.586238 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Selectivity of Complex Coacervation in Multi-Protein Mixtures ]]> https://biorxiv.org/content/10.1101/2024.04.02.587643v1?rss=1 Ahn, S. Y. Obermeyer, A. C. 2024-04-03 doi:10.1101/2024.04.02.587643 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Ketamine metabolism via hepatic CYP450 isoforms contributes to its sustained antidepressant actions. ]]> https://biorxiv.org/content/10.1101/2024.04.03.587904v1?rss=1 Nguyen, T. M. L. Guilloux, J.-P. Defaix, C. Mendez-David, I. Etting, I. Alvarez, J.-C. McGowan, J. C. Highland, J. N. Zanos, P. Lovett, J. Moaddel, R. Corruble, E. David, D. J. Gould, T. D. Denny, C. A. Gardier, A. 2024-04-05 doi:10.1101/2024.04.03.587904 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.04.03.587939v1?rss=1 Dinh, K. N. Vazquez-Garcia, I. Chan, A. Malhotra, R. Weiner, A. Mcpherson, A. Tavare, S. 2024-04-03 doi:10.1101/2024.04.03.587939 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Embryonic motor neuron programming factors reactivate immature gene expression and suppress ALS pathologies in postnatal motor neurons ]]> https://biorxiv.org/content/10.1101/2024.04.03.587963v1?rss=1 Lowry, E. R. Patel, T. Costa, J. A. Chang, E. Tariq, S. Melikyan, H. Davis, I. M. Aziz, S. Dermentzaki, G. Lotti, F. Wichterle, H. 2024-04-05 doi:10.1101/2024.04.03.587963 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Generation of hiPSC-derived brain microvascular endothelial cells using a combination of directed differentiation and transcriptional reprogramming strategies ]]> https://biorxiv.org/content/10.1101/2024.04.03.588012v1?rss=1 Patel, R. Cui, A. Bosco, P. Ackcan, U. Richters, E. Barrilero Delgado, P. Agalliu, D. Sproul, A. A. 2024-04-05 doi:10.1101/2024.04.03.588012 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Extracellular Matrix Instability and Chronic Inflammation Underlie Maladaptive Right Ventricular Pressure Overload Remodeling and Failure in Male Mice ]]> https://biorxiv.org/content/10.1101/2024.04.03.588013v1?rss=1 Russo, I. Dun, W. Mehta, S. Amed, S. Tzimas, C. Fukuma, N. Tsai, E. J. 2024-04-05 doi:10.1101/2024.04.03.588013 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Application of tissue-scale tension to avian epithelia in vivo to study multiscale mechanical properties and inter-germ layer coupling ]]> https://biorxiv.org/content/10.1101/2024.04.04.588089v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@7f0d90org.highwire.dtl.DTLVardef@153a4b0org.highwire.dtl.DTLVardef@614051org.highwire.dtl.DTLVardef@c5b432_HPS_FORMAT_FIGEXP M_FIG C_FIG A simple approach is devised to quantitatively apply tension to epithelia in vivo, and used to study endoderm mechanics in the deeloping chick embryo. ]]> Oikonomou, P. Calvary, L. Cirne, H. C. Welch, A. E. Durel, J. F. Powell, O. Nerurkar, N. L. 2024-04-06 doi:10.1101/2024.04.04.588089 Cold Spring Harbor Laboratory Press 2024-04-06 <![CDATA[ WENDY: Gene Regulatory Network Inference with Covariance Dynamics ]]> https://biorxiv.org/content/10.1101/2024.04.04.588131v1?rss=1 Wang, Y. Zheng, P. Cheng, Y.-c. Wang, Z. Aravkin, A. 2024-04-09 doi:10.1101/2024.04.04.588131 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data ]]> https://biorxiv.org/content/10.1101/2024.04.05.588351v1?rss=1 Xiang, Z. Liu, Z. Dinh, K. N. 2024-04-10 doi:10.1101/2024.04.05.588351 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Alternating Access of a Neurotransmitter:Sodium Symporter Bacterial Homolog Determined from AlphaFold2 Ensembles and DEER Spectroscopy ]]> https://biorxiv.org/content/10.1101/2024.04.08.587957v1?rss=1 Schwartz, A. C. Stein, R. A. Gil-Itrube, E. Quick, M. Mchaourab, H. S. 2024-04-11 doi:10.1101/2024.04.08.587957 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ A heterogenous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase ]]> https://biorxiv.org/content/10.1101/2024.04.08.587960v1?rss=1 Giglio, R. M. Hou, N. Wyatt, A. Hong, J. Shi, L. Vaikunthan, M. Fuchs, H. Nima, J. P. Malinowski, S. W. Ligon, K. L. McFaline-Figueroa, J. R. Yosef, N. Azizi, E. McFaline-Figueroa, J. L. 2024-04-09 doi:10.1101/2024.04.08.587960 Cold Spring Harbor Laboratory Press 2024-04-09 <![CDATA[ IL-1RA Disrupts ATP Activation of P2RX7 in Human Monocyte-Derived Microglia-like Cells ]]> https://biorxiv.org/content/10.1101/2024.04.08.588607v1?rss=1 Heavener, K. S. Kabra, K. Yidenk, M. Bradshaw, E. 2024-04-12 doi:10.1101/2024.04.08.588607 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies ]]> https://biorxiv.org/content/10.1101/2024.04.09.588340v1?rss=1 Zaidi, S. Park, J. Chan, J. M. Roudier, M. Zhao, J. L. Gopalan, A. Wadosky, K. M. Patel, R. A. Sayar, E. Karthaus, W. R. Kates, D. H. Chaudhary, O. Xu, T. Masilionis, I. Mazutis, L. Chaligne, R. Obradovic, A. Linkov, I. Barlas, A. Jungbluth, A. Rekhtman, N. Silber, J. Manova-Todorova, K. Watson, P. A. True, L. D. Morrissey, C. M. Scher, H. I. Rathkopf, D. Morris, M. J. Goodrich, D. W. Choi, J. Nelson, P. S. Haffner, M. Sawyers, C. 2024-04-12 doi:10.1101/2024.04.09.588340 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Drug resistant Mycobacterium tuberculosis strains have altered cell envelope hydrophobicity that influences infection outcomes in human macrophages ]]> https://biorxiv.org/content/10.1101/2024.04.10.588986v1?rss=1 Schami, A. Islam, M. N. Wall, M. Hicks, A. Meredith, R. Kreiswirth, B. Mathema, B. Belisle, J. T. Torrelles, J. B. 2024-04-11 doi:10.1101/2024.04.10.588986 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Impact of redox fluctuations on the spatial distribution of the microbial community in a forest soil: A lysimeter experiment ]]> https://biorxiv.org/content/10.1101/2024.04.11.588997v1?rss=1 Wang, S. Miele, F. Benettin, P. Asadollahi, M. Pasqualini, J. Frutschi, M. Rossi, P. Jacquemin, N. Rinaldo, A. Bernier-Latmani, R. 2024-04-11 doi:10.1101/2024.04.11.588997 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Regulation of lung cancer initiation and progression by the stem cell determinant Musashi ]]> https://biorxiv.org/content/10.1101/2024.04.11.589053v1?rss=1 Barber, A. G. Quintero, C. M. Hamilton, M. Rajbhandari, N. Sasik, R. Zhang, Y. Kim, C. Husain, H. Sun, X. Reya, T. 2024-04-15 doi:10.1101/2024.04.11.589053 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Association of 10 VEGF Family Genes with Alzheimer's Disease Pathology at Single Cell Resolution ]]> https://biorxiv.org/content/10.1101/2024.04.12.589221v1?rss=1 Wu, Y. Libby, J. B. Dumitrescu, L. De Jager, P. L. Menon, V. Schneider, J. A. Bennett, D. A. Hohman, T. J. 2024-04-15 doi:10.1101/2024.04.12.589221 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Human adherent cortical organoids in a multiwell format ]]> https://biorxiv.org/content/10.1101/2024.04.15.589507v1?rss=1 van der Kroeg, M. Bansal, S. Unkel, M. A. Smeenk, H. Kushner, S. A. de Vrij, F. M. 2024-04-16 doi:10.1101/2024.04.15.589507 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Enteric glia regulate Paneth cell secretion and intestinal microbial ecology ]]> https://biorxiv.org/content/10.1101/2024.04.15.589545v1?rss=1 Prochera, A. Muppirala, A. N. Kuziel, G. A. Soualhi, S. Shepherd, A. Sun, L. Issac, B. Rosenberg, H. J. Karim, F. Perez, K. Smith, K. H. Archibald, T. H. Rakoff-Nahoum, S. Hagen, S. J. Rao, M. 2024-04-19 doi:10.1101/2024.04.15.589545 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Lateral Entorhinal Cortex Dysfunction in Alzheimers Disease Mice ]]> https://biorxiv.org/content/10.1101/2024.04.15.589589v1?rss=1 Raghuraman, R. Aoun, A. Herman, M. Shetler, C. O. Nahmani, E. Hussaini, S. A. 2024-04-17 doi:10.1101/2024.04.15.589589 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations ]]> https://biorxiv.org/content/10.1101/2024.04.16.589592v1?rss=1 Reddy, J. S. Heath, L. Linden, A. V. Allen, M. Lopes, K. d. P. Seifar, F. Wang, E. Ma, Y. Poehlman, W. Quicksall, Z. S. Runnels, A. Wang, Y. Duong, D. M. Yin, L. Xu, K. Modeste, E. S. Shantaraman, A. Dammer, E. B. Ping, L. Oatman, S. R. Scanlan, J. Ho, C. Carrasquillo, M. M. Atik, M. Yepez, G. Mitchell, A. O. Nguyen, T. T. Chen, X. Marquez, D. X. Reddy, H. Xiao, H. Seshadri, S. Mayeux, R. Prokop, S. Lee, E. B. Serrano, G. E. Beach, T. G. Teich, A. F. Haroutunian, V. Fox, E. J. Gearing, M. Wingo, A. Wingo, T. Lah, J. J. Levey, A. I. Dickson, D. W. B 2024-04-20 doi:10.1101/2024.04.16.589592 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Ultra-secure storage and analysis of genetic data for the advancement of precision medicine ]]> https://biorxiv.org/content/10.1101/2024.04.16.589793v1?rss=1 Blindenbach, J. Kang, J. Hong, S. Karam, C. Lehner, T. Gürsoy, G. 2024-04-20 doi:10.1101/2024.04.16.589793 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Lifting the curse from high dimensional data: Automated projection pursuit clustering for the variety of biological data modalities ]]> https://biorxiv.org/content/10.1101/2024.04.18.589981v1?rss=1 Simpson, C. Tabatsky, E. Rahil, Z. Eddins, D. J. Tkachev, S. Georgescauld, F. Papalegis, D. Culka, M. Levy, T. Gregoretti, I. Chernyshev, A. Koeppen, H. Walther, G. Ghosn, E. E. B. Orlova, D. 2024-04-22 doi:10.1101/2024.04.18.589981 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Redefining FLASH RT: the impact of mean dose rate and dose per pulse in the gastrointestinal tract ]]> https://biorxiv.org/content/10.1101/2024.04.19.590158v1?rss=1 100 Gy/s), increasing DPP led to better sparing of regenerating crypts, with a more prominent effect seen at 12 and 14 Gy TAI. However, at fixed DPPs >4 Gy, similar sparing of crypts was demonstrated irrespective of MDR (from 0.3 to 1440 Gy/s). At a fixed high DPP of 4.7 Gy, survival was equivalently improved relative to CONV for all MDRs from 0.3 Gy/s to 104 Gy/s, but at a lower DPP of 0.93 Gy, increasing MDR produced a greater survival effect. We also confirmed that high DPP, regardless of MDR, produced the same magnitude of tumor growth delay relative to CONV using a clinically relevant melanoma mouse model. ConclusionsThis study demonstrates the strong influence that the beam parameter settings have on the magnitude of the FLASH effect. Both high DPP and UHDR appeared independently sufficient to produce FLASH sparing of GI toxicity, while isoeffective tumor response was maintained across all conditions. ]]> Liu, K. Waldrop, T. Aguilar, E. Mims, N. Neill, D. Delahoussaye, A. Li, Z. Swanson, D. Lin, S. H. Koong, A. C. Taniguchi, C. M. Loo, B. W. Mitra, D. Schueler, E. 2024-04-23 doi:10.1101/2024.04.19.590158 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Temperature and photoperiod differentially impact maternal phenotypes in diapause egg-laying Aedes albopictus mosquitoes ]]> https://biorxiv.org/content/10.1101/2024.04.19.590231v1?rss=1 Lee, I. H. Lee, A. S. Kogan, H. V. Dong, L. Duvall, L. B. 2024-04-24 doi:10.1101/2024.04.19.590231 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Psychobiological regulation of plasma and saliva GDF15 dynamics in health and mitochondrial diseases ]]> https://biorxiv.org/content/10.1101/2024.04.19.590241v1?rss=1 Huang, Q. Trumpff, C. Monzel, A. S. Rausser, S. Haahr, R. Devine, J. Liu, C. C. Kelly, C. Thompson, E. Kurade, M. S. Shaulson, E. D. Li, S. Engelstad, K. Tanji, K. Lauriola, V. Wang, T. Wang, S. Zuraikat, F. M. St-Onge, M.-P. Kaufman, B. A. Sloan, R. Juster, R.-P. Marsland, A. L. Gouspillou, G. Hirano, M. Picard, M. 2024-04-21 doi:10.1101/2024.04.19.590241 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Defining the cellular origin of seminoma by transcriptional and epigenetic mapping to the normal human germline ]]> https://biorxiv.org/content/10.1101/2024.04.20.590406v1?rss=1 Cheng, K. Seita, Y. Whelan, E. C. Yokomizo, R. Hwang, Y. S. Rotolo, A. Krantz, I. D. Kaur, M. Ginsberg, J. P. Lal, P. Luo, X. Pierorazio, P. M. Linn, R. L. Ryeom, S. Sasaki, K. 2024-04-25 doi:10.1101/2024.04.20.590406 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations ]]> https://biorxiv.org/content/10.1101/2024.04.22.590325v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1c5e607org.highwire.dtl.DTLVardef@1810ee5org.highwire.dtl.DTLVardef@1f8f1acorg.highwire.dtl.DTLVardef@c28053_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIReliable calculation of relative binding free energy changes for most protein mutations to within [~]1 kcal/mol. C_LIO_LIAutomated Protein FEP+ Groups treatment of alternate protonation states for titratable residues. C_LIO_LIApplication of FEP+ methodology to "real-world" protein design projects. C_LI ]]> Sampson, J. M. Cannon, D. A. Duan, J. Sergeeva, A. P. Epstein, J. C. K. Katsamba, P. S. Mannepalli, S. M. Bahna, F. A. Adihou, H. Gueret, S. M. Gopalakrishnan, R. Geschwindner, S. Rees, D. G. Sigurdardottir, A. Wilkinson, T. Dodd, R. B. De Maria, L. Mobarec, J. C. Shapiro, L. Honig, B. Buchanan, A. Friesner, R. A. Wang, L. 2024-04-24 doi:10.1101/2024.04.22.590325 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Large- Scale Deep Proteomic Analysis in Alzheimer's Disease Brain Regions Across Race and Ethnicity ]]> https://biorxiv.org/content/10.1101/2024.04.22.590547v1?rss=1 Seifar, F. Fox, E. J. Shantaraman, A. Liu, Y. Dammer, E. B. Modeste, E. Duong, D. M. Yin, L. Trautwig, A. N. Guo, Q. Xu, K. Ping, L. Reddy, J. S. Allen, M. Quicksall, Z. Heath, L. Scanlan, J. Wang, E. Wang, M. Vander Linden, A. Poehlman, W. Chen, X. Baheti, S. Ho, C. Nguyen, T. Yepez, G. Mitchell, A. O. Oatman, S. R. Wang, X. Carrasquillo, M. M. Runnels, A. Beach, T. Serrano, G. E. Dickson, D. W. Lee, E. B. Golde, T. E. Prokop, S. Barnes, L. L. Zhang, B. Haroutunian, V. Gearing, M. Lah, J. J. De Jager, P. Bennett, D. A. Greenwood, A. Ertekin-Taner, 2024-04-26 doi:10.1101/2024.04.22.590547 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Therapeutic Activity of Resolvin D1 (RvD1) in Murine MASH ]]> https://biorxiv.org/content/10.1101/2024.04.22.590633v1?rss=1 Navarro-Corcuera, A. Zhu, Y. Ma, F. Gupta, N. Asplund, H. Yuan, F. Friedman, S. Sansbury, B. E. Huang, X. Cai, B. 2024-04-26 doi:10.1101/2024.04.22.590633 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[ Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology ]]> https://biorxiv.org/content/10.1101/2024.04.23.590816v1?rss=1 Gaur, P. Bryois, J. Calini, D. Foo, L. Hoozemans, J. J. M. Malhotra, D. Menon, V. 2024-04-27 doi:10.1101/2024.04.23.590816 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Quinoxaline-Based Anti-Schistosomal Compounds Have Potent Anti-Malarial Activity ]]> https://biorxiv.org/content/10.1101/2024.04.23.590861v1?rss=1 Rawat, M. Padalino, G. Yeo, T. Brancale, A. Fidock, D. Hoffmann, K. Lee, M. 2024-04-24 doi:10.1101/2024.04.23.590861 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ A dynamic compositional equilibrium governs mRNA recognition by eIF3 ]]> https://biorxiv.org/content/10.1101/2024.04.25.581977v1?rss=1 Ide, N. A. Gentry, R. C. Rudbach, M. A. Yoo, K. Velez, P. K. Communale, V. M. Hartwick, E. W. Kinz-Thompson, C. D. Gonzalez, R. L. Aitken, C. E. 2024-04-26 doi:10.1101/2024.04.25.581977 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Common neural mechanisms supporting time judgements in humans and monkeys ]]> https://biorxiv.org/content/10.1101/2024.04.25.591075v1?rss=1 Rodriguez Larios, J. Rassi, E. Mendoza, G. Merchant, H. Haegens, S. 2024-04-28 doi:10.1101/2024.04.25.591075 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Heparan sulfate regulates amphiregulin signaling towards reparative lung mesenchymal cells during influenza A infection ]]> https://biorxiv.org/content/10.1101/2024.04.25.591175v1?rss=1 Loffredo, L. F. Surpur, A. Ringham, O. R. Li, F. de los Santos-Alexis, K. Arpaia, N. 2024-04-28 doi:10.1101/2024.04.25.591175 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Equilibrium Tension and Compression Mechanical Properties of the Human Uterus ]]> https://biorxiv.org/content/10.1101/2024.04.25.591208v1?rss=1 Fang, S. Duarte-Cordon, C. A. Fodera, D. M. Shi, L. Chen, X. Advincula, A. P. Vink, J. Hendon, C. P. Myers, K. M. 2024-04-28 doi:10.1101/2024.04.25.591208 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Advancing cooperative breeding research with a peer-reviewed and "live" Cooperative-Breeding Database (Co-BreeD) ]]> https://biorxiv.org/content/10.1101/2024.04.26.591342v1?rss=1 Ben Mocha, Y. Woith, M. Drobniak, S. M. Markman, S. Frisoni, F. Baglione, V. Boersma, J. Cousseau, L. Covas, R. Braga de Miranda, G. H. Dey, C. J. Doutrelant, C. Gula, R. Heinsohn, R. Kingma, S. A. Li, J. Middleton, K.-M. Radford, A. Restrepo, C. Rubenstein, D. R. Schradin, C. Theuerkauf, J. Warrington, M. H. Williams, D. A. Woxvold, I. A. Griesser, M. 2024-04-29 doi:10.1101/2024.04.26.591342 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ MT-125 Inhibits Non-Muscle Myosin IIA and IIB, Synergizes with Oncogenic Kinase Inhibitors, and Prolongs Survival in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2024.04.27.591399v1?rss=1 Kenchappa, R. Radnai, L. Young, E. J. Zarco, N. Lin, L. Dovas, A. Meyer, C. T. Haddock, A. Hall, A. Canoll, P. T. Cameron, M. Nagaiah, N. K. Rumbaugh, G. Griffin, P. R. Kamenecka, T. M. Miller, C. A. Rosenfeld, S. S. 2024-04-29 doi:10.1101/2024.04.27.591399 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Potent neutralization by a receptor binding domain monoclonal antibody with broad specificity for SARS-CoV-2 JN.1 and other variants ]]> https://biorxiv.org/content/10.1101/2024.04.27.591446v1?rss=1 Piepenbrink, M. S. Khalil, A. M. Chang, A. Mostafa, A. Basu, M. Sarkar, S. Panjwani, S. Ha, Y. H. Ma, Y. Ye, C. Wang, Q. Green, T. J. Kizziah, J. L. Erdmann, N. B. Goepfert, P. A. Lihong, L. Ho, D. D. Martinez-Sobrido, L. Walter, M. R. Kobie, J. J. 2024-04-29 doi:10.1101/2024.04.27.591446 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Disorganized Inhibitory Dynamics and Functional Connectivity in Hippocampal area CA1 of 22q11.2 Deletion Mutant Mice ]]> https://biorxiv.org/content/10.1101/2024.04.28.591464v1?rss=1 Herrlinger, S. A. Rao, B. Paredes, M. E. C. Tuttman, A. L. Arain, H. Varol, E. Gogos, J. A. Losonczy, A. 2024-04-30 doi:10.1101/2024.04.28.591464 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Functional Localization of the Human Auditory and Visual Thalamus Using a Thalamic Localizer Functional Magnetic Resonance Imaging Task ]]> https://biorxiv.org/content/10.1101/2024.04.28.591516v1?rss=1 Williams, J. C. Tubiolo, P. N. Zheng, Z. J. Silver-Frankel, E. B. Pham, D. T. Haubold, N. K. Abeykoon, S. K. Abi-Dargham, A. Horga, G. Van Snellenberg, J. X. 2024-04-30 doi:10.1101/2024.04.28.591516 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Coordination and persistence of aggressive visual communication in Siamese fighting fish ]]> https://biorxiv.org/content/10.1101/2024.04.29.591330v1?rss=1 Everett, C. P. Norovich, A. L. Burke, J. E. Whiteway, M. R. Shih, P.-Y. Zhu, Y. Paninski, L. Bendesky, A. 2024-05-01 doi:10.1101/2024.04.29.591330 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Cell rearrangement progression along the apical-basal axis is linked with 3D epithelial tissue structure ]]> https://biorxiv.org/content/10.1101/2024.04.29.591620v1?rss=1 Kusaka, E. M. Ostvar, S. Wang, X. Liu, X. Kasza, K. E. 2024-04-30 doi:10.1101/2024.04.29.591620 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Distinct anatomical and functional corticospinal inputs innervate different spinal neuron types ]]> https://biorxiv.org/content/10.1101/2024.04.29.591683v1?rss=1 Fageiry, S. Warriner, C. L. Loper, J. Paninski, L. Reardon, T. Jessell, T. M. Costa, R. M. Miri, A. 2024-05-01 doi:10.1101/2024.04.29.591683 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Strategies for motion- and respiration-robust estimation of fMRI intrinsic neural timescales ]]> https://biorxiv.org/content/10.1101/2024.04.30.590832v1?rss=1 Goldberg, A. Rosario, I. Power, J. Horga, G. Wengler, K. 2024-05-01 doi:10.1101/2024.04.30.590832 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ A survival-critical role for Drosophila giant interneurons during predation ]]> https://biorxiv.org/content/10.1101/2024.04.30.591368v1?rss=1 Chai, C. M. Morrow, C. Parikh, D. D. von Reyn, C. R. Leonardo, A. Card, G. M. 2024-05-01 doi:10.1101/2024.04.30.591368 Cold Spring Harbor Laboratory Press 2024-05-01 <![CDATA[ Trazodone, dibenzoylmethane and tauroursodeoxycholic acid do not prevent motor dysfunction and neurodegeneration in Marinesco-Sjögren syndrome mice ]]> https://biorxiv.org/content/10.1101/2024.04.30.591862v1?rss=1 Lavigna, G. Grasso, A. Pasini, C. Grande, V. Mignogna, L. Restelli, E. Masone, A. Fracasso, C. Lucchetti, J. Gobbi, M. Chiesa, R. 2024-05-03 doi:10.1101/2024.04.30.591862 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Uterus and cervix anatomical changes and cervix stiffness evolution throughout pregnancy ]]> https://biorxiv.org/content/10.1101/2024.05.01.592023v1?rss=1 Louwagie, E. M. Russell, S. R. Hairston, J. C. Nottman, C. Nhan-Chang, C.-L. Fuchs, K. Gyamfi-Bannerman, C. Booker, W. Andrikopoulou, M. Friedman, A. Zork, N. Wapner, R. Vink, J. Mourad, M. Feltovich, H. House, M. Myers, K. 2024-05-03 doi:10.1101/2024.05.01.592023 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Follicular helper- and peripheral helper-like T cells drive autoimmune disease in human immune system mice ]]> https://biorxiv.org/content/10.1101/2024.05.02.591692v1?rss=1 Vecchione, A. Khosravi-Maharlooei, M. Danzl, N. Li, H. W. Nauman, G. Madley, R. Waffarn, E. Winchester, R. Ruiz, A. Ding, X. Fousteri, G. Sykes, M. 2024-05-05 doi:10.1101/2024.05.02.591692 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Tumor-selective treatment of metastatic pancreatic cancer with an engineered, probiotic living drug ]]> https://biorxiv.org/content/10.1101/2024.05.02.592216v1?rss=1 Decker-Farrell, A. R. Sastra, S. A. Harimoto, T. Hasselluhn, M. C. Palermo, C. F. Ballister, E. R. Badgley, M. A. Danino, T. Olive, K. P. 2024-05-05 doi:10.1101/2024.05.02.592216 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Differential control of intestine function by genetically defined enteric neurons ]]> https://biorxiv.org/content/10.1101/2024.05.02.592229v1?rss=1 Shi, D. Reddy, P. Walker, C. Marrin, M. Siu, C. Sharma, N. 2024-05-05 doi:10.1101/2024.05.02.592229 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ In vitro heterochronic parabiosis identifies pigment epithelium-derived factor as a systemic mediator of rejuvenation by young blood ]]> https://biorxiv.org/content/10.1101/2024.05.02.592258v1?rss=1 Wang, X. Tazearslan, C. Kim, S. Guo, Q. Contreras, D. Yang, J. Hudgins, A. D. Suh, Y. 2024-05-05 doi:10.1101/2024.05.02.592258 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ The Ccm3-GckIII signaling axis regulates Rab11-dependent recycling to the apical compartment ]]> https://biorxiv.org/content/10.1101/2024.05.03.592387v1?rss=1 Burguete, A. S. Song, Y. Ghabrial, A. S. 2024-05-05 doi:10.1101/2024.05.03.592387 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Modulation of aggression by social novelty recognition memory in the hippocampal CA2 region ]]> https://biorxiv.org/content/10.1101/2024.05.03.592403v1?rss=1 Villegas, A. Siegelbaum, S. A. 2024-05-04 doi:10.1101/2024.05.03.592403 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Two routes to value-based decisions in Parkinsons disease: differentiating incremental reinforcement learning from episodic memory ]]> https://biorxiv.org/content/10.1101/2024.05.03.592414v1?rss=1 Montaser-Kouhsari, L. Nicholas, J. Gerraty, R. Shohamy, D. 2024-05-03 doi:10.1101/2024.05.03.592414 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas ]]> https://biorxiv.org/content/10.1101/2024.05.03.592420v1?rss=1 Kazansky, Y. Mueller, H. S. Cameron, D. Demarest, P. Zaffaroni, N. Arrighetti, N. Zuco, V. Mundi, P. S. Kuwahara, Y. Somwar, R. Qu, R. Califano, A. De Stanchina, E. Dela Cruz, F. S. Kung, A. L. Gounder, M. Kentsis, A. 2024-05-06 doi:10.1101/2024.05.03.592420 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ The tricellular junction protein ILDR2 in glomerulopathies: insights and implications ]]> https://biorxiv.org/content/10.1101/2024.05.03.592456v1?rss=1 Siegerist, F. Kliewe, F. Hammer, E. Schakau, P. Soh, J. E. C. Weber, C. Puelles, V. Lindenmeyer, M. Reichelt-Wurm, S. Drenic, V. Chatziantoniou, C. Chadjichristos, C. Zhang, Y. Nauck, M. Völker, U. Endlich, N. 2024-05-06 doi:10.1101/2024.05.03.592456 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice ]]> https://biorxiv.org/content/10.1101/2024.05.06.592101v1?rss=1 Burdge, J. Jhumka, A. Ogundare, S. Baer, N. Fulton, S. Bistis, B. Foster, W. Toussaint, A. Li, M. Morizawa, Y. M. Yadessa, L. Khan, A. Delinois, A. Mayiseni, W. Loran, N. Yang, G. Abdus-Saboor, I. 2024-05-07 doi:10.1101/2024.05.06.592101 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Episodic memory supports the acquisition of structured task representations ]]> https://biorxiv.org/content/10.1101/2024.05.06.592749v1?rss=1 Lu, Q. Hummos, A. Norman, K. A. 2024-05-07 doi:10.1101/2024.05.06.592749 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ E-cadherin tunes tissue mechanical behavior before and during morphogenetic tissue flows ]]> https://biorxiv.org/content/10.1101/2024.05.07.592778v1?rss=1 Wang, X. Cupo, C. M. Ostvar, S. Countryman, A. D. Kasza, K. E. 2024-05-08 doi:10.1101/2024.05.07.592778 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ KRas, in addition to Tp53 is a driver for early carcinogenesis and a molecular target in a mouse model of invasive gastro-esophageal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.05.07.592904v1?rss=1 Anand, A. Schoemig, L. Lange, S. Tran, L. Flisikowski, K. Oellinger, R. Rad, R. Vieth, M. Steiger, K. Baumeister, T. Strangmann, J. Alguel, H. Ciecielski, K. Boettcher, K. Fang, H.-Y. Carvalho, M. Mohammad-Shahi, D. Gerland, S. Proano-Vasco, A. Schnieke, A. Thimme, R. Schmid, R. Wang, T. C. Quante, M. 2024-05-10 doi:10.1101/2024.05.07.592904 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Effect of interhemispheric zero-phase entrainment of the intrinsic mu-rhythm on behavioral and neural markers of predictive coding ]]> https://biorxiv.org/content/10.1101/2024.05.07.592996v1?rss=1 Heise, K.-F. Albouy, G. Dolfen, N. Peeters, R. Mantini, D. Swinnen, S. P. 2024-05-08 doi:10.1101/2024.05.07.592996 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ De novo gene synthesis by an antiviral reverse transcriptase ]]> https://biorxiv.org/content/10.1101/2024.05.08.593200v1?rss=1 Tang, S. Conte, V. Zhang, D. J. Zedaveinyte, R. Lampe, G. D. Wiegand, T. Tang, L. C. Wang, M. Walker, M. W. G. George, J. T. Berchowitz, L. E. Jovanovic, M. Sternberg, S. H. 2024-05-08 doi:10.1101/2024.05.08.593200 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Experience-dependent, sexually dimorphic synaptic connectivity defined by sex-specific cadherin expression ]]> https://biorxiv.org/content/10.1101/2024.05.08.593207v1?rss=1 Liao, C.-P. Majeed, M. Hobert, O. 2024-05-08 doi:10.1101/2024.05.08.593207 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Drosophila glue evolved different adhesive and mechanical properties across 50 million years ]]> https://biorxiv.org/content/10.1101/2024.05.08.593221v1?rss=1 Monier, M. Lorenzi, J.-N. Narasimha, S. Borne, F. Contremoulins, V. Mevel, L. Petit, R. Graner, F. Courtier-Orgogozo, V. 2024-05-10 doi:10.1101/2024.05.08.593221 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Specialized Pericyte Subtypes in the Pulmonary Capillary ]]> https://biorxiv.org/content/10.1101/2024.05.09.593174v1?rss=1 Klouda, T. Kim, Y. Baek, S.-H. Bhaumik, M. Liu, Y. Liu, T. Que, J. Wu, J. C. Raby, B. A. de Jesus Perez, V. Yuan, K. 2024-05-14 doi:10.1101/2024.05.09.593174 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Metagenomic coverage bias at transcription start sites is correlated with gene expression ]]> https://biorxiv.org/content/10.1101/2024.05.09.593333v1?rss=1 Qian, G. Coleman, I. Korem, T. Ho, J. W. K. 2024-05-13 doi:10.1101/2024.05.09.593333 Cold Spring Harbor Laboratory Press 2024-05-13 <![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[ Task-specific topographical maps of neural activity in the primate lateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2024.05.10.591729v1?rss=1 Xiang, J. D. Roussy, M. Corrigan, B. Gulli, R. A. Luna, R. Mofrad, M. H. Muller, L. Diedrichsen, J. Schmitz, T. W. Martinez-Trujillo, J. Mur, M. 2024-05-10 doi:10.1101/2024.05.10.591729 Cold Spring Harbor Laboratory Press 2024-05-10 <![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[ Targeting LxCxE cleft pocket of retinoblastoma protein in M2 macrophages inhibits ovarian cancer progression ]]> https://biorxiv.org/content/10.1101/2024.05.10.593562v1?rss=1 Tcyganov, E. N. Kwak, T. Yang, X. Poli, A. N. R. Hart, C. Bhuniya, A. Cassel, J. Kossenkov, A. Auslander, N. Lu, L. Sharma, P. Mendoza, M. D. G. C. Zhigarev, D. Cadungog, M. G. Jean, S. Chatterjee-Paer, S. Weiner, D. B. Donthireddy, L. Bristow, B. Zhang, R. Tyurin, V. A. Tyurina, Y. Y. Bayir, H. Kagan, V. E. Salvino, J. M. Montaner, L. J. 2024-05-14 doi:10.1101/2024.05.10.593562 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ L-Dopa induced dyskinesias require Cholinergic Interneuron expression of Dopamine 2 receptor. ]]> https://biorxiv.org/content/10.1101/2024.05.10.593604v1?rss=1 Uribe-Cano, S. Malave, L. Kottmann, A. H. 2024-05-12 doi:10.1101/2024.05.10.593604 Cold Spring Harbor Laboratory Press 2024-05-12 <![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[ ILC2s navigate tissue redistribution during infection using stage-specific S1P receptors ]]> https://biorxiv.org/content/10.1101/2024.05.12.592576v1?rss=1 Ito, T. Ishida, Y. Zhang, Y. Guichard, V. Zhang, W. Han, R. P. Guckian, K. Chun, J. Que, J. Smith, A. Urban, J. F. Huang, Y. 2024-05-14 doi:10.1101/2024.05.12.592576 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Endogenous OptoRhoGEFs reveal biophysical principles of epithelial tissue furrowing ]]> https://biorxiv.org/content/10.1101/2024.05.12.593711v1?rss=1 Countryman, A. D. Doherty, C. A. Herrera-Perez, R. M. Kasza, K. E. 2024-05-12 doi:10.1101/2024.05.12.593711 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Joint population coding and temporal coherence link an attended talker's voice and location features in naturalistic multi-talker scenes. ]]> https://biorxiv.org/content/10.1101/2024.05.13.593814v1?rss=1 van der Heijden, K. Patel, P. Bickel, S. Herrero, J. L. Mehta, A. Mesgarani, N. 2024-05-14 doi:10.1101/2024.05.13.593814 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Revealing the principles of inter- and intra-domain regulation in a signaling enzyme via scanning mutagenesis ]]> https://biorxiv.org/content/10.1101/2024.05.13.593907v1?rss=1 Jiang, Z. van Vlimmeren, A. E. Karandur, D. Semmelman, A. Shah, N. H. 2024-05-13 doi:10.1101/2024.05.13.593907 Cold Spring Harbor Laboratory Press 2024-05-13 <![CDATA[ Patterning, regulation, and role of FoxO/DAF-16 in the early embryo ]]> https://biorxiv.org/content/10.1101/2024.05.13.594029v1?rss=1 Mauro, M. S. Martin, S. L. Dumont, J. Shirasu-Hiza, M. Canman, J. C. 2024-05-14 doi:10.1101/2024.05.13.594029 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ PDGF-BB overexpression in p53 null oligodendrocyte progenitors increases H3K27me3 and induces transcriptional changes which favor proliferation ]]> https://biorxiv.org/content/10.1101/2024.05.14.594214v1?rss=1 Huang, D. Mela, A. Natarajan, B. V. Garcia, B. Canoll, P. Casaccia, P. 2024-05-14 doi:10.1101/2024.05.14.594214 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ The main duct of von Ebner's glands is a source of Sox10+ taste bud progenitors and susceptible to pathogen infections ]]> https://biorxiv.org/content/10.1101/2024.05.14.594215v1?rss=1 Kastriti, M. E. Ishan, M. Choudhary, S. K. KRAMER, N. E. Rashid, M. M. Do, H. G. T. Wang, Z. Xu, T. Schwabe, R. F. Ye, K. Adameyko, I. Liu, H.-X. 2024-05-16 doi:10.1101/2024.05.14.594215 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites ]]> https://biorxiv.org/content/10.1101/2024.05.14.594230v1?rss=1 Lin, X. Leung, K. S. K. Wolfe, K. F. Lee, B. J. Zha, S. 2024-05-17 doi:10.1101/2024.05.14.594230 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations ]]> https://biorxiv.org/content/10.1101/2024.05.15.594372v1?rss=1 Ghandian, S. Albarghouthi, L. Nava, K. Sharma, S. R. R. Minaud, L. Beckett, L. Saito, N. DeCarli, C. Rissman, R. A. Teich, A. F. Jin, L.-W. Dugger, B. N. Keiser, M. J. 2024-05-17 doi:10.1101/2024.05.15.594372 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos ]]> https://biorxiv.org/content/10.1101/2024.05.15.594414v1?rss=1 Breimann, L. Bahry, E. Zouinkhi, M. Kolyvanov, K. Street, L. A. Preibisch, S. Ercan, S. 2024-05-16 doi:10.1101/2024.05.15.594414 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix ]]> https://biorxiv.org/content/10.1101/2024.05.15.594415v1?rss=1 Manghrani, A. Rangadurai, A. K. Szekely, O. Liu, B. Guseva, S. Al-Hashimi, H. 2024-05-15 doi:10.1101/2024.05.15.594415 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ A Novel Gene ARHGAP44 for Longitudinal Changes in Glycated Hemoglobin (HbA1c) in Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Offspring Study (FOS) ]]> https://biorxiv.org/content/10.1101/2024.05.16.594575v1?rss=1 Wang, S. Lenzini, P. Thygarajan, B. Lee, J. H. Vardarajan, B. N. Yashin, A. Miljkovic, I. Daw, E. W. Lin, S. J. Patti, G. Brent, M. Zmuda, J. M. Perls, T. T. Christensen, K. Province, M. A. An, P. 2024-05-21 doi:10.1101/2024.05.16.594575 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Stable, chronic in-vivo recordings from a fully wireless subdural-contained 65,536-electrode brain-computer interface device ]]> https://biorxiv.org/content/10.1101/2024.05.17.594333v1?rss=1 Jung, T. Zeng, N. Fabbri, J. D. Eichler, G. Li, Z. Willeke, K. Wingel, K. E. Dubey, A. Huq, R. Sharma, M. Hu, Y. Ramakrishnan, G. Tien, K. Mantovani, P. Parihar, A. Yin, H. Oswalt, D. Misdorp, A. Uguz, I. Shinn, T. Rodriguez, G. J. Nealley, C. Gonzales, I. Roukes, M. Knecht, J. Yoshor, D. Canoll, P. Spinazzi, E. Carloni, L. P. Pesaran, B. Patel, S. Youngerman, B. Cotton, R. J. Tolias, A. Shepard, K. L. 2024-05-17 doi:10.1101/2024.05.17.594333 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Phase synchrony between prefrontal noradrenergic and cholinergic signals indexes inhibitory control ]]> https://biorxiv.org/content/10.1101/2024.05.17.594562v1?rss=1 Liu, Y. Nong, Y. Feng, J. Li, G. Sajda, P. Li, Y. Wang, Q. 2024-05-17 doi:10.1101/2024.05.17.594562 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Accelerating Genome- and Phenome-Wide Association Studies using GPUs - A case study using data from the Million Veteran Program ]]> https://biorxiv.org/content/10.1101/2024.05.17.594583v1?rss=1 Rodriguez, A. A. Kim, Y. Nandi, T. N. Keat, K. Bhukar, R. Conery, M. Liu, M. Hessington, J. Begoli, E. Tourassi, G. Muralidhar, S. Natarajan, P. Voight, B. F. Cho, K. Gaziano, M. J. Damrauer, S. Liao, K. P. Zhou, W. Huffman, J. E. Verma, A. Madduri, R. K. 2024-05-21 doi:10.1101/2024.05.17.594583 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription ]]> https://biorxiv.org/content/10.1101/2024.05.17.594600v1?rss=1 Wagner, T. Priyanka, P. Micheletti, R. Friedman, M. J. Nair, S. J. Gamliel, A. Taylor, H. Song, X. Cho, M. Oh, S. Li, W. Han, J. Ohgi, K. A. Abrass, M. D'Antonio-Chronowska, A. D'Antonio, M. Hazuda, H. Duggirala, R. Blangero, J. Ding, S. Guzmann, C. Frazer, K. Aggarwal, A. K. Zemljic-Harpf, A. E. Rosenfeld, M. G. Suh, Y. 2024-05-19 doi:10.1101/2024.05.17.594600 Cold Spring Harbor Laboratory Press 2024-05-19 <![CDATA[ The CALERIE™ Genomic Data Resource ]]> https://biorxiv.org/content/10.1101/2024.05.17.594714v1?rss=1 Ryan, C. P. Corcoran, D. L. Banskota, N. Eckstein Indik, C. Floratos, A. Friedman, R. A. Kobor, M. S. Kraus, V. B. Kraus, W. MacIsaac, J. Orenduff, M. Pieper, C. F. White, J. Ferrucci, L. Horvath, S. Huffman, K. M. Belsky, D. W. 2024-05-21 doi:10.1101/2024.05.17.594714 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Modeling epithelial homeostasis and perturbation in three-dimensional human esophageal organoids ]]> https://biorxiv.org/content/10.1101/2024.05.20.595023v1?rss=1 Shimonosono, M. Morimoto, M. Hirose, W. Tomita, Y. Matsuura, N. Flashner, S. Ebadi, M. S. Okayasu, E. H. Lee, C. Y. Britton, W. R. Martin, C. Wuertz, B. R. Parikh, A. S. Sachdeva, U. M. Ondrey, F. G. Atigadda, V. R. Elmets, C. A. Abrams, J. Muir, A. B. Klein-Szanto, A. J. Weinberg, K. I. Momen-Heravi, F. Nakagawa, H. 2024-05-21 doi:10.1101/2024.05.20.595023 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Regulation of dopamine release by tonic activity patterns in the striatal brain slice ]]> https://biorxiv.org/content/10.1101/2024.05.22.595411v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@e9412corg.highwire.dtl.DTLVardef@1b5cce4org.highwire.dtl.DTLVardef@9ebabforg.highwire.dtl.DTLVardef@f66982_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Boumhaouad, S. Makowicz, E. A. Choi, S. Bouhaddou, N. Balla, J. Taghzouti, K. Sulzer, D. Mosharov, E. 2024-05-23 doi:10.1101/2024.05.22.595411 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ A microglia-containing cerebral organoid model to study early life immune challenges ]]> https://biorxiv.org/content/10.1101/2024.05.24.595814v1?rss=1 Buonfiglioli, A. Kübler, R. Missall, R. De Jong, R. Chan, S. Haage, V. Wendt, S. Lin, A. J. Mattei, D. Graziani, M. Latour, B. Gigase, F. Nygaard, H. B. De Jager, P. L. De Witte, L. D. 2024-05-26 doi:10.1101/2024.05.24.595814 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Lineage-specific proteome remodeling of diverse lung cancer cells by targeted epigenetic inhibitors ]]> https://biorxiv.org/content/10.1101/2024.05.23.592075v1?rss=1 Lin, C. Sniezek, C. M. Giglio, R. M. Karki, R. McGann, C. D. Garcia, B. A. McFaline-Figueroa, J. L. Schweppe, D. K. 2024-05-28 doi:10.1101/2024.05.23.592075 Cold Spring Harbor Laboratory Press 2024-05-28 <![CDATA[ micronuclAI: Automated quantification of micronuclei for assessment of chromosomal instability. ]]> https://biorxiv.org/content/10.1101/2024.05.24.595722v1?rss=1 Ibarra-Arellano, M. A. Caprio, L. A. Hada, A. Stotzem, N. Cai, L. Shah, S. Melms, J. C. Wuennemann, F. Izar, B. Schapiro, D. 2024-05-29 doi:10.1101/2024.05.24.595722 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Developmental maturation of millimeter-scale functional networks across brain areas ]]> https://biorxiv.org/content/10.1101/2024.05.28.595371v1?rss=1 Powell, N. J. Hein, B. Kong, D. Elpelt, J. Mulholland, H. N. Kaschube, M. Smith, G. B. 2024-05-29 doi:10.1101/2024.05.28.595371 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Multiwell-based G0-PCC assay for radiation biodosimetry ]]> https://biorxiv.org/content/10.1101/2024.05.27.596074v1?rss=1 Royba, E. Shuryak, I. Ponnaiya, B. Repin, M. Pampou, S. Karan, C. Turner, H. Garty, G. Brenner, D. J. 2024-05-30 doi:10.1101/2024.05.27.596074 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Amygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis. ]]> https://biorxiv.org/content/10.1101/2024.06.01.596819v1?rss=1 Rifai, O. M. Waldron, F. M. O'Shaughnessy, J. Read, F. L. Gilodi, M. Pastore, A. Shneider, N. Tartaglia, G. G. Zacco, E. Spence, H. Gregory, J. 2024-06-01 doi:10.1101/2024.06.01.596819 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs ]]> https://biorxiv.org/content/10.1101/2024.05.28.596103v1?rss=1 Shin, J. H. Cuevas, L. M. Roy, R. Bonilla, S. L. Al-Hashimi, H. Greenleaf, W. Herschlag, D. 2024-06-02 doi:10.1101/2024.05.28.596103 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Revealing biomolecular structure and motion with neural ab initio cryo-EM reconstruction ]]> https://biorxiv.org/content/10.1101/2024.05.30.596729v1?rss=1 Levy, A. Grzadkowski, M. Poitevin, F. Vallese, F. Clarke, O. B. Wetzstein, G. Zhong, E. D. 2024-06-02 doi:10.1101/2024.05.30.596729 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Tendon Inversion Improves Tendon-to-Bone Healing in a Rat Bicep Tenodesis Model ]]> https://biorxiv.org/content/10.1101/2024.05.31.596842v1?rss=1 Cong, T. Li, T. M. Buller, D. C. Arvind, V. Nasser, P. Laudier, D. M. Ferlauto, H. R. Hall, A. J. Li, D. M. Huang, A. H. Cagle, P. J. Galatz, L. M. Hausman, M. R. 2024-06-03 doi:10.1101/2024.05.31.596842 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells ]]> https://biorxiv.org/content/10.1101/2024.06.02.597057v1?rss=1 Tanaka, J. Kondo, Y. Sakurai, M. Sawada, A. Hwang, Y. Miura, A. Shimamura, Y. Shimizu, D. Hu, Y. Sarmah, H. Ninish, Z. Cai, J. J. Wu, J. Mori, M. 2024-06-03 doi:10.1101/2024.06.02.597057 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Endogenously produced hydrogen cyanide serves as a novel mammalian gasotransmitter ]]> https://biorxiv.org/content/10.1101/2024.06.03.597146v1?rss=1 Zuhra, K. Petrosino, M. Janickova, L. Vignane, T. Petric, J. Khalaf, M. Philipp, T. Ravani, S. Anand, A. Martins, V. Santos, S. Kieronska-Rudek, A. Majtan, T. Filgueira, L. Maric, D. Hoogewijs, D. Erdemir, S. Malkondu, S. Sitek, B. Chlopicki, S. Kelestemur, T. Hasko, G. Papapetropoulos, A. Logue, B. Boss, G. Filipovic, M. Szabo, C. 2024-06-03 doi:10.1101/2024.06.03.597146 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism ]]> https://biorxiv.org/content/10.1101/2024.06.04.596633v1?rss=1 Stuerner, T. Brooks, P. Serratosa Capdevila, L. Morris, B. J. Javier, A. Fang, S. Gkantia, M. Cachero, S. Beckett, I. R. Champion, A. S. Moitra, I. Richards, A. Klemm, F. Kugel, L. Namiki, S. Cheong, H. S. Kovalyak, J. Tenshaw, E. Parekh, R. Schlegel, P. Phelps, J. S. Mark, B. Dorkenwald, S. Bates, A. S. Matsliah, A. Yu, S.-c. McKellar, C. E. Sterling, A. Seung, S. Murthy, M. Tuthill, J. Lee, W.-C. A. Card, G. M. Costa, M. Jefferis, G. S. X. E. Eichler, K. 2024-06-06 doi:10.1101/2024.06.04.596633 Cold Spring Harbor Laboratory Press 2024-06-06 <![CDATA[ Parkinson's LRRK2-G2019S risk gene mutation drives sex-specific behavioral and cellular adaptations to chronic variable stress ]]> https://biorxiv.org/content/10.1101/2024.06.05.597647v1?rss=1 Guevara, C. A. Alloo, K. Gupta, S. Thomas, R. Del Valle, P. Magee, A. R. Benson, D. L. Huntley, G. W. 2024-06-08 doi:10.1101/2024.06.05.597647 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ RESPAN: an accurate, unbiased and automated pipeline for analysis of dendritic morphology and dendritic spine mapping ]]> https://biorxiv.org/content/10.1101/2024.06.06.597812v1?rss=1 Garcia, S. B. Schlotter, A. P. Pereira, D. Polleux, F. Hammond, L. 2024-06-08 doi:10.1101/2024.06.06.597812 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ TLR4 deficiency does not alter glaucomatous progression in a mouse model of chronic glaucoma ]]> https://biorxiv.org/content/10.1101/2024.06.07.597951v1?rss=1 Zhang, C. Simon, M. Harder, J. M. Lim, H. Montgomery, C. Wang, Q. John, S. W. M. 2024-06-08 doi:10.1101/2024.06.07.597951 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ The ventral CA2 region of the hippocampus and its differential contributions to social memory and social aggression ]]> https://biorxiv.org/content/10.1101/2024.06.07.597964v1?rss=1 Boyle, L. M. Sheng, W. Leroy, F. Sahai, R. Irfan, S. Lee, H.-J. Villegas, A. Young, W. S. Siegelbaum, S. A. 2024-06-08 doi:10.1101/2024.06.07.597964 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Resistance to Spindle Inhibitors in Glioblastoma Depends on STAT3 and Therapy Induced Senescence ]]> https://biorxiv.org/content/10.1101/2024.06.09.598115v1?rss=1 Rosenfeld, S. S. Zarco, N. Dovas, A. Farias, V. Nagaiah, N. Haddock, A. Sims, P. Hambardzumyan, D. Meyer, C. T. Canoll, P. Kenchappa, R. 2024-06-09 doi:10.1101/2024.06.09.598115 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging ]]> https://biorxiv.org/content/10.1101/2024.06.11.598452v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@1bc4664org.highwire.dtl.DTLVardef@1b1750dorg.highwire.dtl.DTLVardef@17bddaaorg.highwire.dtl.DTLVardef@115de4e_HPS_FORMAT_FIGEXP M_FIG C_FIG Lay summaryX-ray tomography was used to examine the African clawed frog (Xenopus laevis). An extensive data set of specimens from tadpoles to adult frogs provides novel insights into the changes and developmental dynamics of selected structures, which opens avenues to an improved understanding of this crucial animal model. ]]> Laznovsky, J. Kavkova, M. Reis, A. Robovska-Havelkova, P. Krivanek, J. Zikmund, T. Kaiser, J. Buchtova, M. Harnos, J. 2024-06-11 doi:10.1101/2024.06.11.598452 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Ferroptosis regulates hemolysis in stored murine and human red blood cells ]]> https://biorxiv.org/content/10.1101/2024.06.11.598512v1?rss=1 View larger version (117K): org.highwire.dtl.DTLVardef@150fec2org.highwire.dtl.DTLVardef@859c43org.highwire.dtl.DTLVardef@1d60156org.highwire.dtl.DTLVardef@f1b91e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> D'Alessandro, A. Keele, G. R. Hay, A. Nemkov, T. Earley, E. J. Stephenson, D. Vincent, M. Deng, X. Stone, M. Dzieciatkowska, M. Hansen, K. Kleinman, S. Spitalnik, S. L. Roubinian, N. Norris, P. J. Busch, M. P. Page, G. P. Stockwell, B. R. Churchill, G. A. Zimring, J. C. 2024-06-11 doi:10.1101/2024.06.11.598512 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene ]]> https://biorxiv.org/content/10.1101/2024.06.11.598384v1?rss=1 Roark, R. S. Habib, R. Gorman, J. Li, H. Connell, A. J. Bonsignori, M. Guo, Y. Hogarty, M. P. Olia, A. S. Sowers, K. Zhang, B. Bibollet-Ruche, F. Callaghan, S. Carey, J. W. Cerutti, G. Harris, D. R. He, W. Lewis, E. Liu, T. Mason, R. D. Park, Y. Rando, J. M. Singh, A. Wolff, J. Lei, Q. P. Louder, M. K. Doria-Rose, N. A. Andrabi, R. Saunders, K. O. Seaman, M. S. Haynes, B. F. Kulp, D. W. Mascola, J. R. Roederer, M. Sheng, Z. Hahn, B. H. Shaw, G. M. Kwong, P. D. Shapiro, L. 2024-06-12 doi:10.1101/2024.06.11.598384 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition ]]> https://biorxiv.org/content/10.1101/2024.06.11.598405v1?rss=1 Baumeister, T. Proano Vasco, A. I. Metwaly, A. Kleigrewe, K. Kuznetsov, A. Schoemig, L. Borgmann, M. Khiat, M. Anand, A. Boettcher, K. Haller, D. Dunkel, A. Somoza, V. Reiter, S. Meng, C. Thimme, R. Schmid, R. Patil, D. Burgermeister, E. Huang, Y. Sun, Y. Wang, H. Wang, T. C. Abrams, J. Quante, M. 2024-06-12 doi:10.1101/2024.06.11.598405 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Dynamic changes in structure and function of brain mural cells around chronically implanted microelectrodes ]]> https://biorxiv.org/content/10.1101/2024.06.11.598494v1?rss=1 wellman, s. Forrest, A. M. Douglas, M. M. Subbaraman, A. Zhang, G. Kozai, T. D. Y. 2024-06-13 doi:10.1101/2024.06.11.598494 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Comparative analysis of new, mScarlet-based red fluorescent tags in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.06.11.598534v1?rss=1 Cao, W. X. Merritt, D. Pe, K. Cesar, M. Hobert, O. 2024-06-13 doi:10.1101/2024.06.11.598534 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Optimized phenotype definitions boost GWAS power ]]> https://biorxiv.org/content/10.1101/2024.06.11.598562v1?rss=1 Zietz, M. Brown, K. L. Gisladottir, U. Tatonetti, N. 2024-06-13 doi:10.1101/2024.06.11.598562 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution ]]> https://biorxiv.org/content/10.1101/2024.06.13.598904v1?rss=1 Cook, S. J. Kalinski, C. A. Loer, C. M. Memar, N. Majeed, M. Stephen, S. R. Bumbarger, D. J. Riebesell, M. Schnabel, R. Sommer, R. J. Hobert, O. 2024-06-13 doi:10.1101/2024.06.13.598904 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis ]]> https://biorxiv.org/content/10.1101/2024.06.12.598609v1?rss=1 Singh, D. Robin, T. Urbakh, M. Reuveni, S. 2024-06-14 doi:10.1101/2024.06.12.598609 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes ]]> https://biorxiv.org/content/10.1101/2024.06.13.597128v1?rss=1 Moakley, D. F. Campbell, M. Anglada-Girotto, M. Feng, H. Califano, A. Au, E. Zhang, C. 2024-06-16 doi:10.1101/2024.06.13.597128 Cold Spring Harbor Laboratory Press 2024-06-16 <![CDATA[ The DNA Damage Checkpoint Targets the Kinetochore for Relocation of Collapsed Forks to the Periphery ]]> https://biorxiv.org/content/10.1101/2024.06.17.599319v1?rss=1 Maclay, T. M. Whalen, J. Johnson, M. Freudenreich, C. H. 2024-06-17 doi:10.1101/2024.06.17.599319 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ The Role of Alpha Synuclein in Synucleinopathy: Impact on Lipid Regulation at Mitochondria ER Membranes ]]> https://biorxiv.org/content/10.1101/2024.06.17.599406v1?rss=1 Barbuti, P. A. Guardia-Laguarta, C. Yun, T. Chatila, Z. K. Flowers, X. Santos, B. F. Larsen, S. B. Hattori, N. Bradshaw, E. Dettmer, U. Fanning, S. Vilas, M. Reddy, H. Teich, A. Krueger, R. Area-Gomez, E. Przedborski, S. 2024-06-17 doi:10.1101/2024.06.17.599406 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Strand asymmetry in the repair of replication dependent double-strand breaks ]]> https://biorxiv.org/content/10.1101/2024.06.17.598707v1?rss=1 Kimble, M. T. Sane, A. Reid, R. J. D. S. Johnson, M. J. Rothstein, R. Symington, L. S. 2024-06-19 doi:10.1101/2024.06.17.598707 Cold Spring Harbor Laboratory Press 2024-06-19 <![CDATA[ Amygdala-predominant α-synuclein pathology exacerbates hippocampal neuron loss in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.06.21.599515v1?rss=1 Gawor, K. Tome, S. Vandenberghe, R. Van Damme, P. Vandenbulcke, M. Otto, M. von Arnim, C. A. F. Ghebremedhin, E. Ronisz, A. Ospitalieri, S. Blaschko, M. Thal, D. R. 2024-06-27 doi:10.1101/2024.06.21.599515 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Disentangling the splicing factor programs underlying complex molecular phenotypes ]]> https://biorxiv.org/content/10.1101/2024.06.21.600051v1?rss=1 Anglada-Girotto, M. Moakley, D. F. Zhang, C. Miravet-Verde, S. Califano, A. Serrano, L. 2024-06-27 doi:10.1101/2024.06.21.600051 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Cell type-specific regulation by different cytokinetic pathways in the early embryo ]]> https://biorxiv.org/content/10.1101/2024.06.27.601054v1?rss=1 Connors, C. Q. Martin, S. L. Dumont, J. Shirasu-Hiza, M. Canman, J. C. 2024-06-29 doi:10.1101/2024.06.27.601054 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Crk mediates Csk-Hippo signaling independently of Yap tyrosine phosphorylation to induce cell extrusion ]]> https://biorxiv.org/content/10.1101/2024.06.27.601065v1?rss=1 Hannan, A. Wang, Q. Wu, Y. Makrides, N. Qu, X. Mao, J. Que, J. Cardoso, W. V. Zhang, X. 2024-07-01 doi:10.1101/2024.06.27.601065 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ Scalable Hypothalamic Arcuate Neuron Differentiation from Human Pluripotent Stem Cells Suitable for Modeling Metabolic and Reproductive Disorders ]]> https://biorxiv.org/content/10.1101/2024.06.27.601062v1?rss=1 Jovanovic, V. M. Narisu, N. Bonnycastle, L. L. Tharakan, R. Mesch, K. T. Glover, H. J. Yan, T. Sinha, N. Sen, C. Castellano, D. Yang, S. Blivis, D. Ryu, S. Bennett, D. F. Rosales-Soto, G. Inman, J. Ormanoglu, P. LeClair, C. A. Xia, M. Schneider, M. Hernandez-Ochoa, E. O. Erdos, M. R. Simeonov, A. Chen, S. Singec, I. Collins, F. S. Doege, C. S. Tristan, C. A. 2024-07-02 doi:10.1101/2024.06.27.601062 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Phospholipase Cgamma regulates lacrimal gland branching by competing with PI3K in phosphoinositide metabolism ]]> https://biorxiv.org/content/10.1101/2024.06.28.601066v1?rss=1 Wang, Q. Tao, C. Wu, Y. Anderson, K. E. Hannan, A. Lin, C.-s. Hawkins, P. T. Stephens, L. Zhang, X. 2024-07-02 doi:10.1101/2024.06.28.601066 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Anatomical and functional analysis of the corticospinal tract in an FRDA mouse model ]]> https://biorxiv.org/content/10.1101/2024.06.28.601178v1?rss=1 Nishiyama, M. Kalambogias, J. Imai, F. Yang, E. Lang, S. de Nooij, J. C. Yoshida, Y. 2024-07-02 doi:10.1101/2024.06.28.601178 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Tracking spatial patterns and nocturnal arousal in an undisturbed natural population of the pulse-type weakly electric fish Gymnotus omarorum ]]> https://biorxiv.org/content/10.1101/2024.06.29.600875v1?rss=1 Migliaro, A. Pedraja, F. Mucha, S. Benda, J. Silva, A. 2024-07-02 doi:10.1101/2024.06.29.600875 Cold Spring Harbor Laboratory Press 2024-07-02 <![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[ Combined HDAC and eIF4A inhibition: A novel epigenetic therapy for pancreatic adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.06.30.600495v1?rss=1 Safari, M. Scotto, L. Basseville, A. Litman, T. Xue, H. Petrukhin, L. Zhou, P. Morales, D. V. Damoci, C. Zhu, M. Hull, K. Olive, K. P. Fojo, T. Romo, D. Bates, S. E. 2024-07-02 doi:10.1101/2024.06.30.600495 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Comparison of Infinium MethylationEPIC v2.0 to v1.0 for human population epigenetics: considerations for addressing EPIC version differences in DNA methylation-based tools ]]> https://biorxiv.org/content/10.1101/2024.07.02.600461v1?rss=1 Zhuang, B. C. Jude, M. S. Konwar, C. Ryan, C. P. Whitehead, J. Engelbrecht, H.-R. MacIsaac, J. L. Dever, K. Toan, T. K. Korinek, K. Zimmer, Z. Huffman, K. M. Lee, N. R. McDade, T. W. Kuzawa, C. W. Belsky, D. W. Kobor, M. S. 2024-07-03 doi:10.1101/2024.07.02.600461 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Polyamines regulate cell fate by altering the activity of histone-modifying enzymes ]]> https://biorxiv.org/content/10.1101/2024.07.02.600738v1?rss=1 Emmons-Bell, M. Forsyth, G. Sundquist, A. Oldeman, S. Gardikioti, A. de Souza, R. Coene, J. Kamel, M. Ayyappan, S. Fuchs, H. A. Verhelst, S. Smeeton, J. Musselman, C. A. Schvartzman, J. M. 2024-07-03 doi:10.1101/2024.07.02.600738 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[ Biomolecular condensates can function as inherent catalysts ]]> https://biorxiv.org/content/10.1101/2024.07.06.602359v1?rss=1 Guo, X. Farag, M. Qian, N. Yu, X. Ni, A. Ma, Y. Yu, W. King, M. Liu, V. Lee, J. Min, W. Zare, R. N. Pappu, R. V. Dai, Y. 2024-07-10 doi:10.1101/2024.07.06.602359 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Oncogenic NOVA1 expression dysregulates alternative splicing in breast cancer ]]> https://biorxiv.org/content/10.1101/2024.07.08.602566v1?rss=1 Moakley, D. F. Zhang, C. 2024-07-10 doi:10.1101/2024.07.08.602566 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Spectral-switching analysis reveals real-time neuronal network representations of concurrent spontaneous naturalistic behaviors in human brain ]]> https://biorxiv.org/content/10.1101/2024.07.08.600416v1?rss=1 Zhu, H. Michalak, A. J. Merricks, E. M. Agopyan-Miu, A. H. C. W. Jacobs, J. Hamberger, M. J. Sheth, S. McKhann, G. M. Feldstein, N. Schevon, C. Hillman, E. M. C. 2024-07-11 doi:10.1101/2024.07.08.600416 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ A variational deep-learning approach to modeling memory T cell dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.08.602409v1?rss=1 van Dorp, C. H. Gray, J. I. Paik, D. H. Farber, D. L. Yates, A. J. 2024-07-11 doi:10.1101/2024.07.08.602409 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Integrative deep immune profiling of the elderly reveals systems-level signatures of aging, sex, smoking, and clinical traits ]]> https://biorxiv.org/content/10.1101/2024.07.10.602828v1?rss=1 Riemann, L. Gutierrez, R. Odak, I. Barros-Martins, J. Roesner, L. M. Leon Lara, X. Falk, C. Schulz, T. F. Hansen, G. Werfel, T. Foerster, R. 2024-07-14 doi:10.1101/2024.07.10.602828 Cold Spring Harbor Laboratory Press 2024-07-14 <![CDATA[ A linear ontogeny accounts for the development of naive, memory and tumour-infiltrating regulatory T cells in mice ]]> https://biorxiv.org/content/10.1101/2024.07.10.602914v1?rss=1 Pathak, S. Hogan, T. rane, S. Huang, Y. Sinclair, C. Barry, S. Carnevalli, L. Yates, A. Seddon, B. 2024-07-16 doi:10.1101/2024.07.10.602914 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Platelet integrin αIIbβ3 plays a key role in venous thrombogenesis in a mouse model ]]> https://biorxiv.org/content/10.1101/2024.07.11.602533v1?rss=1 Adair, B. D. Field, C. O. Alonso, J. L. Xiong, J.-P. Deng, S.-X. Ahn, H. S. Mashin, E. Clish, C. B. van Agthoven, J. Yeager, M. Guo, Y. Tess, D. A. Landry, D. W. Poncz, M. Arnaout, M. A. 2024-07-16 doi:10.1101/2024.07.11.602533 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Functional analysis of conserved C. elegans bHLH family members uncovers lifespan control by a peptidergic hub neuron ]]> https://biorxiv.org/content/10.1101/2024.07.12.603289v1?rss=1 Aguilar, G. R. Vidal, B. Ji, H. Evenblij, J. Ji, H. Valperga, G. Liao, C.-P. Fang-Yen, C. Hobert, O. 2024-07-16 doi:10.1101/2024.07.12.603289 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ A SMARTR workflow for multi-ensemble atlas mapping and brain-wide network analysis ]]> https://biorxiv.org/content/10.1101/2024.07.12.603299v1?rss=1 Jin, M. Ogundare, S. Lanio, M. Sorid, S. Whye, A. R. Leal Santos, S. Franceschini, A. Denny, C. A. 2024-07-16 doi:10.1101/2024.07.12.603299 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Lineage-specific genomic imprinting in the ZNF791 locus ]]> https://biorxiv.org/content/10.1101/2024.07.13.603355v1?rss=1 Ahn, J. Hwang, I.-S. Park, M.-R. Rosa-Velazquez, M. Cho, I.-C. Relling, A. E. Hwang, S. Lee, K. 2024-07-16 doi:10.1101/2024.07.13.603355 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction ]]> https://biorxiv.org/content/10.1101/2024.07.16.603632v1?rss=1 Chartier, C. A. Woods, V. A. Xu, Y. van Vlimmeren, A. E. Jovanovic, M. McDermott, A. E. Keedy, D. A. Shah, N. H. 2024-07-16 doi:10.1101/2024.07.16.603632 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Alternative splicing controls pan-neuronal homeobox gene expression ]]> https://biorxiv.org/content/10.1101/2024.07.16.603806v1?rss=1 Leyva-Diaz, E. Cesar, M. Pe, K. Jorda-Llorens, J. I. Valdivia, J. Hobert, O. 2024-07-19 doi:10.1101/2024.07.16.603806 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Oxygen Microenvironments in E. coli Biofilm Nutrient Transport Channels: Insights from Complementary Sensing Approaches ]]> https://biorxiv.org/content/10.1101/2024.07.20.603676v1?rss=1 Bottura, B. McConnell, G. Florek, L. C. Smiley, M. K. Martin, R. Eana, A. Dayton, H. T. Eckartt, K. N. Price-Whelan, A. Hoskisson, P. A. Dietrich, L. E. P. Rooney, L. M. 2024-07-20 doi:10.1101/2024.07.20.603676 Cold Spring Harbor Laboratory Press 2024-07-20 <![CDATA[ Engineering Candida boidinii formate dehydrogenase for activity with NMN(H) ]]> https://biorxiv.org/content/10.1101/2024.07.17.604001v1?rss=1 Vainstein, S. Banta, S. 2024-07-22 doi:10.1101/2024.07.17.604001 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration. ]]> https://biorxiv.org/content/10.1101/2024.07.18.604174v1?rss=1 Lv, G. Sayles, N. M. Huang, Y. Mancinelli, C. D. McAvoy, K. Shneider, N. A. Manfredi, G. Kawamata, H. Eliezer, D. 2024-07-22 doi:10.1101/2024.07.18.604174 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Extending the Acute Skin Response Spectrum to Include the Far-UVC ]]> https://biorxiv.org/content/10.1101/2024.07.19.604306v1?rss=1 Gutierrez-Bayona, N. E. Petersen, C. Hashmi, R. H. Buonanno, M. Shuryak, I. Ponnaiya, B. Kleiman, N. J. Brenner, D. J. Welch, D. 2024-07-23 doi:10.1101/2024.07.19.604306 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Long-lived adult-born hippocampal neurons promote successful cognitive aging ]]> https://biorxiv.org/content/10.1101/2024.07.19.604332v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@524afforg.highwire.dtl.DTLVardef@b9b2b1org.highwire.dtl.DTLVardef@182a19corg.highwire.dtl.DTLVardef@1402b64_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Blin, N. Charrier, V. Farrugia, F. Cartier, E. Pacary, E. Koehl, M. Lois, C. Lie, D. C. Masachs, N. Abrous, N. 2024-07-23 doi:10.1101/2024.07.19.604332 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization ]]> https://biorxiv.org/content/10.1101/2024.07.22.604482v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@8b0f55org.highwire.dtl.DTLVardef@19bd139org.highwire.dtl.DTLVardef@c52117org.highwire.dtl.DTLVardef@1ffa2bd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Hanif, S. Z. Au, C. C. Torregroza, I. Jannath, S. Fabiha, T. Bhinder, B. Washburn, M. Devost, D. Liu, S. Bhardwaj, P. Evans, T. Anand, P. K. Tarran, R. Palikhe, S. Elemento, O. Dow, L. E. Blenis, J. Hebert, T. Brown, K. A. 2024-07-23 doi:10.1101/2024.07.22.604482 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Dietary iron deficiency impairs effector function of memory T cells following influenza infection ]]> https://biorxiv.org/content/10.1101/2024.07.22.604599v1?rss=1 Bradley, M. C. Gray, J. La Carpia, F. Idzikowski, E. Guyer, R. Pethe, K. Hod, E. Connors, T. J. 2024-07-23 doi:10.1101/2024.07.22.604599 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Functional optimization in distinct tissues and conditions constrains the rate of protein evolution ]]> https://biorxiv.org/content/10.1101/2024.07.22.604632v1?rss=1 Usmanova, D. R. Plata, G. Vitkup, D. 2024-07-23 doi:10.1101/2024.07.22.604632 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo ]]> https://biorxiv.org/content/10.1101/2024.07.22.604682v1?rss=1 Tilley, L. Xie, S. C. Tai, C.-W. Morton, C. J. Ma, L. Huang, S.-C. Wittlin, S. Du, Y. Hu, Y. Dogovski, C. Salimimarand, M. Griffin, R. England, D. de la Curz, E. Deni, I. Yeo, T. Burkhard, A. Y. Striepen, J. Schindler, K. A. Crespo, B. Gamo, F. J. Khandokar, Y. Hutton, C. A. Rabie, T. Birkholtz, L.-M. Famodimu, M. T. Delves, M. J. Bolsher, J. Koolen, K. M. J. van der Laak, R. Aguiar, A. C. C. Pereira, D. B. Creek, D. J. Fidock, D. A. Dick, L. R. Brand, S. L. Gould, A. E. Langston, S. Griffin, M. D. W. 2024-07-23 doi:10.1101/2024.07.22.604682 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Entorhinal cortex represents task-relevant remote locations independent of CA1 ]]> https://biorxiv.org/content/10.1101/2024.07.23.604815v1?rss=1 Aery Jones, E. A. Low, I. I. C. Cho, F. S. Giocomo, L. M. 2024-07-24 doi:10.1101/2024.07.23.604815 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ In vivo quantification of anterior and posterior chamber volumes in mice: implications for aqueous humor dynamics ]]> https://biorxiv.org/content/10.1101/2024.07.24.604989v1?rss=1 Kim, D. Fang, R. Zhang, P. Sun, C. Li, G. Montgomery, C. John, S. W. M. Stamer, W. D. Zhang, H. F. Ethier, C. R. 2024-07-25 doi:10.1101/2024.07.24.604989 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ How to reward animals based on their subjective percepts: A Bayesian approach to online estimation of perceptual biases. ]]> https://biorxiv.org/content/10.1101/2024.07.25.605047v1?rss=1 Dong, Y. Lengyel, G. Shivkumar, S. Anzai, A. DiRisio, G. F. Haefner, R. M. DeAngelis, G. C. 2024-07-25 doi:10.1101/2024.07.25.605047 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ FZD2 inhibits YAP and prevents cell cycle reentry in adult murine cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2024.07.26.605158v1?rss=1 Bisson, J. A. Quijada, P. J. Wang, Y. T. Lighthouse, J. K. Helt, J. C. Kim, E. Morrisey, E. E. Brookes, P. S. Small, E. M. Cohen, E. D. 2024-07-26 doi:10.1101/2024.07.26.605158 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Optimized reporters for multiplexed detection of transcription factor activity ]]> https://biorxiv.org/content/10.1101/2024.07.26.605239v1?rss=1 Trauernicht, M. Filipovska, T. Rastogi, C. van Steensel, B. 2024-07-26 doi:10.1101/2024.07.26.605239 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Characterizing microglial signaling dynamics during inflammation using single-cell mass cytometry ]]> https://biorxiv.org/content/10.1101/2024.07.27.605444v1?rss=1 Kumar, S. Kahle, A. D. Keeler, A. B. Zunder, E. R. Deppmann, C. D. 2024-07-29 doi:10.1101/2024.07.27.605444 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Low-side and multitone suppression in the base of the gerbil cochlea ]]> https://biorxiv.org/content/10.1101/2024.07.29.605696v1?rss=1 Strimbu, C. E. Olson, E. S. E. 2024-07-30 doi:10.1101/2024.07.29.605696 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Capillary connections between sensory circumventricular organs and adjacent parenchyma enable local volume transmission ]]> https://biorxiv.org/content/10.1101/2024.07.30.605849v1?rss=1 Yao, Y. Chen, Y. Tomer, R. Silver, R. 2024-07-31 doi:10.1101/2024.07.30.605849 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ SMURF1/2 are novel regulators of WNK1 stability ]]> https://biorxiv.org/content/10.1101/2024.07.31.606092v1?rss=1 Jaykumar, A. B. Plumber, S. Binns, D. Wichaidit, C. Luby-Phelps, K. Cobb, M. H. 2024-08-01 doi:10.1101/2024.07.31.606092 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Local Synthesis of Reticulon-1C Lessens the Outgrowth of Injured Axons by Controlling Spastin Activity ]]> https://biorxiv.org/content/10.1101/2024.08.11.607514v1?rss=1 Luarte, A. Gallardo, J. Corvalan, D. Chakraborty, A. Gouveia-Roque, C. Bertin, F. Contreras, C. Ramirez, J. P. Weber, A. Acevedo, W. Zuschratter, W. Herrera, R. Wyneken, U. Paula Lima, A. Adasme, T. Figueroa, A. Gonzalez, C. Gonzalez-Billault, C. Hengst, U. Couve, A. 2024-08-12 doi:10.1101/2024.08.11.607514 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design ]]> https://biorxiv.org/content/10.1101/2024.08.12.606135v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@8f9769org.highwire.dtl.DTLVardef@11da734org.highwire.dtl.DTLVardef@1cc51c0org.highwire.dtl.DTLVardef@10b3c27_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Armer, C. Kane, H. Cortade, D. L. Redestig, H. Estell, D. A. Yusuf, A. Rollins, N. J. Spinner, H. Marks, D. Brunette, T. Kelly, P. J. DeBenedictis, E. 2024-08-12 doi:10.1101/2024.08.12.606135 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Pemivibart is less active against recent SARS-CoV-2 JN.1 sublineages ]]> https://biorxiv.org/content/10.1101/2024.08.12.607496v1?rss=1 Wang, Q. Guo, Y. Ho, J. Ho, D. D. 2024-08-13 doi:10.1101/2024.08.12.607496 Cold Spring Harbor Laboratory Press 2024-08-13 <![CDATA[ Spatially organized striatal neuromodulator release encodes trajectory errors ]]> https://biorxiv.org/content/10.1101/2024.08.13.607797v1?rss=1 Brown, E. H. Zi, Y. Vu, M.-A. T. Bouabid, S. Lindsey, J. Godfrey-Nwachukwu, C. Attarwala, A. Litwin-Kumar, A. DePasquale, B. Howe, M. 2024-08-14 doi:10.1101/2024.08.13.607797 Cold Spring Harbor Laboratory Press 2024-08-14 <![CDATA[ Transcriptomic signatures of mouse ovarian aging and estropausal transition at single cell resolution ]]> https://biorxiv.org/content/10.1101/2024.08.12.607592v1?rss=1 Wang, X. Yang, J. Jin, C. Wang, X. Contreras, D. Devos, M. Suh, Y. 2024-08-15 doi:10.1101/2024.08.12.607592 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Spatial mapping of immunosuppressive cancer-associated fibroblast gene signatures in H&E-stained images using additive multiple instance learning ]]> https://biorxiv.org/content/10.1101/2024.08.12.607604v1?rss=1 Markey, M. Kim, J. Goldstein, Z. Gerardin, Y. Brosnan-Cashman, J. Javed, S. A. Juyal, D. Padigela, H. Yu, L. Rahsepar, B. Abel, J. Hennek, S. Khosla, A. Taylor-Weiner, A. Parmar, C. 2024-08-15 doi:10.1101/2024.08.12.607604 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Statistical estimation of sparsity and efficiency for molecular codes ]]> https://biorxiv.org/content/10.1101/2024.08.13.607773v1?rss=1 Fung, J. H. Carriere, M. Blumberg, A. J. 2024-08-15 doi:10.1101/2024.08.13.607773 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Multi-strategies embedded framework for neoantigen vaccine maturation ]]> https://biorxiv.org/content/10.1101/2024.08.14.607669v1?rss=1 Zhang, G. Fu, Y. Chan, K. C. Jin, R. Yang, Y. Zhou, R. 2024-08-15 doi:10.1101/2024.08.14.607669 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development ]]> https://biorxiv.org/content/10.1101/2024.08.14.608000v1?rss=1 Yim, K. M. Baumgartner, M. Krenzer, M. Larios, M. F. R. Hill-Teran, G. Nottoli, T. Muhle, R. A. Noonan, J. P. 2024-08-15 doi:10.1101/2024.08.14.608000 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ The genetic landscape of antibiotic sensitivity in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2024.08.15.608136v1?rss=1 Li, W. Liu, M. Oikonomou, P. Blattman, S. B. Hettleman, J. Gonzalez, J. Chen, H. Tavazoie, S. Jiang, W. 2024-08-17 doi:10.1101/2024.08.15.608136 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Relationships of hematocrit concentration with dementia from a multiethnic population-based study ]]> https://biorxiv.org/content/10.1101/2024.08.15.608190v1?rss=1 50 years) from the Northern Manhattan Study (NOMAS) enrolled between 2003-2008. Participants received baseline hematocrit testing, MRI neuroimaging, and cognitive assessments at baseline and long-term follow-up. Associations of baseline hematocrit as a categorical variable (low, normal [reference], and high based on laboratory reference levels) with incident dementia were assessed using Cox models adjusting for relevant covariates. Separate analyses investigated whether MRI CSVD mediated these relationships. ResultsWe studied 1207 NOMAS participants (mean age 71{+/-}9 years, 60% female, 66% Hispanic). Mean hematocrit was 41.2% ({+/-}3.8) with 16% of participants developing incident dementia. Lower hematocrit associated with increased dementia risk (adjusted hazard ratio 1.81 [1.01-3.23]) after adjusting for age, sex, race/ethnicity, education, APOE status, and comorbidities. High hematocrit was not associated with dementia risk. No interactions by sex or race/ethnicity were seen and baseline CSVD did not mediate relationships between hematocrit and dementia. ConclusionsLow hematocrit associated with dementia risk in our diverse population cohort. Further work is needed to assess mechanisms behind anemias relationship with dementia to assess whether this can serve as a trackable, preventable/treatable risk factor for dementia. ]]> Roh, D. J. Liu, M. Strobino, K. Assuras, S. Guzman, V. A. Levin, B. Spitalnik, S. Rundek, T. Wright, C. B. Elkind, M. S. V. Gutierrez, J. 2024-08-17 doi:10.1101/2024.08.15.608190 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ ClearScope: a fully integrated light sheet theta microscope for sub-cellular resolution imaging without lateral size constraints ]]> https://biorxiv.org/content/10.1101/2024.08.15.608141v1?rss=1 Fay, M. G. Lang, P. J. Denu, D. S. O'Connor, N. J. Haydock, B. W. Blaisdell, J. O. Roussel, N. Wilson, A. L. Aronson, S. R. Angstman, P. J. Gong, C. Butola, T. Devinsky, O. Basu, J. Tomer, R. Glaser, J. R. 2024-08-19 doi:10.1101/2024.08.15.608141 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Low hemoglobin causes hematoma expansion and poor intracerebral hemorrhage outcomes ]]> https://biorxiv.org/content/10.1101/2024.08.15.608155v1?rss=1 Cottarelli, A. Momoon, R. Ji, R. Mao, E. Boehme, A. K. Kumar, A. Song, S. Allegra, V. Sharma, S. V. Konofagou, E. Spektor, V. Guo, J. Connolly, E. S. Sekar, P. Woo, D. Roh, D. J. 2024-08-19 doi:10.1101/2024.08.15.608155 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Population Representation of the Confidence in a Decision in the Lateral Intraparietal Area of the Macaque ]]> https://biorxiv.org/content/10.1101/2024.08.15.608159v1?rss=1 Zylberberg, A. Shadlen, M. N. 2024-08-19 doi:10.1101/2024.08.15.608159 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Macrophage WDFY3, a protector against autoimmunity ]]> https://biorxiv.org/content/10.1101/2024.08.17.608411v1?rss=1 Wu, X. Wang, Z. Croce, K. R. Li, F. Cui, J. D'Agati, V. C. Soni, R. Khalid, S. Saleheen, D. Tabas, I. Yamamoto, A. Zhang, H. 2024-08-19 doi:10.1101/2024.08.17.608411 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ Three Open Questions in Polygenic Score Portability ]]> https://biorxiv.org/content/10.1101/2024.08.20.608703v1?rss=1 Wang, J. Y. Lin, N. Zietz, M. Mares, J. Narasimhan, V. M. Rathouz, P. J. Harpak, A. 2024-08-21 doi:10.1101/2024.08.20.608703 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Olfactory receptor coexpression and co-option in the dengue mosquito ]]> https://biorxiv.org/content/10.1101/2024.08.21.608847v1?rss=1 Adavi, E. D. dos Anjos, V. L. Kotb, S. Metz, H. C. Tian, D. Zhao, Z. Zung, J. L. Rose, N. H. McBride, C. S. 2024-08-22 doi:10.1101/2024.08.21.608847 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Pemphigus vulgaris autoantibodies induce an ER stress response ]]> https://biorxiv.org/content/10.1101/2024.08.22.608849v1?rss=1 Hoffman, C. L. Bharathan, N. K. Shibata, Y. Giang, W. Gudjonsson, J. E. Seykora, J. T. Prouty, S. M. Payne, A. S. Kowalczyk, A. P. 2024-08-23 doi:10.1101/2024.08.22.608849 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2024.08.24.609538v1?rss=1 Nunes de Almeida, F. Vasciaveo, A. Antao, A. M. Zou, M. Di Bernardo, M. de Brot, S. Rodriguez-Calero, A. Chui, A. Wang, A. L. E. Floch, N. Kim, J. Y. Afari, S. N. Mukhammadov, T. Arriaga, J. M. Lu, J. Shen, M. M. Rubin, M. Califano, A. Abate-Shen, C. 2024-08-26 doi:10.1101/2024.08.24.609538 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Flanker task parameters are related to the strength of association between the ERN and anxiety: a meta-analysis ]]> https://biorxiv.org/content/10.1101/2024.08.27.609944v1?rss=1 Buzzell, G. A. Niu, Y. Machado, E. Dickinson, R. Moser, J. S. Morales, S. Troller-Renfree, S. V. 2024-08-28 doi:10.1101/2024.08.27.609944 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Cell type-specific impact of aging and Alzheimer disease on hippocampal CA1 perforant path input ]]> https://biorxiv.org/content/10.1101/2024.08.27.609952v1?rss=1 Santoro, B. Srinivas, K. V. Reyes, I. Tian, C. Masurkar, A. V. 2024-08-28 doi:10.1101/2024.08.27.609952 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses ]]> https://biorxiv.org/content/10.1101/2024.08.28.610136v1?rss=1 Mendelsohn, A. Nikoobakht, L. Bikoff, J. Costa, R. 2024-08-29 doi:10.1101/2024.08.28.610136 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Brain Charts for the Rhesus Macaque Lifespan ]]> https://biorxiv.org/content/10.1101/2024.08.28.610193v1?rss=1 Alldritt, S. Ramirez, J. S. B. Vos de Wael, R. Bethlehem, R. Seidlitz, J. Wang, Z. Nenning, K.-H. Esper, N. B. Smallwood, J. Franco, A. R. Byeon, K. Alexander-Bloch, A. Messinger, A. Chen, A. Thiele, A. Weiss, A. R. Shmuel, A. Fox, A. Tusche, A. Brambrink, A. M. Falchier, A. Hiba, B. Jarraya, B. Jung, B. Butler, B. Russ, B. E. Howell, B. R. Drzewiecki, C. M. Guedj, C. Schwiedrzik, C. M. Amiez, C. Wilson, C. R. E. Klink, C. Kroenke, C. Constantinidis, C. Garin, C. M. Poirier, C. Gale, D. J. Leopold, D. A. Rudko, D. A. Amaral, D. G. Tsao, D. Cook, D. J. 2024-08-30 doi:10.1101/2024.08.28.610193 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Movement-related activity in the internal globus pallidus of the parkinsonian macaque ]]> https://biorxiv.org/content/10.1101/2024.08.29.610310v1?rss=1 Kase, D. Zimnik, A. J. Han, Y. Harsch, D. R. Bacha, S. Cox, K. M. Bostan, A. C. Richardson, R. M. Turner, R. S. 2024-08-30 doi:10.1101/2024.08.29.610310 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts ]]> https://biorxiv.org/content/10.1101/2024.08.29.610342v1?rss=1 DING, H. Wang, Z. Liu, Z. Fang, Y. Zhang, H. H. Sun, X. Hao, N. Que, J. 2024-08-30 doi:10.1101/2024.08.29.610342 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression ]]> https://biorxiv.org/content/10.1101/2024.08.30.610508v1?rss=1 Wang, T. C. Laise, P. 2024-08-30 doi:10.1101/2024.08.30.610508 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Evolution of lateralized gustation in nematodes ]]> https://biorxiv.org/content/10.1101/2024.08.31.610597v1?rss=1 Mackie, M. Le, V. V. Carstensen, H. R. Kushnir, N. R. Castro, D. L. Dimov, I. M. Quach, K. T. Cook, S. J. Hobert, O. Chalasani, S. H. Hong, R. L. 2024-09-02 doi:10.1101/2024.08.31.610597 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ HLA-E and NKG2A Mediate Resistance to M. bovis BCG Immunotherapy in Non-Muscle-Invasive Bladder Cancer ]]> https://biorxiv.org/content/10.1101/2024.09.02.610816v1?rss=1 Ranti, D. Yu, H. Wang, Y. Bieber, C. Strandgaard, T. Salome, B. Houghton, S. Kim, J. Ravichandran, H. Okulate, I. Merritt, E. Bang, S. Demetriou, A. Li, Z. Lindskrog, S. V. Ruan, D. F. Daza, J. Rai, R. Hegewisch-Solloa, E. Mace, E. Fernandez-Rodriguez, R. Izadmehr, S. Doherty, G. Farkas, A. Cruz-Encarnacion, P. Shroff, S. Patel, F. Tran, M. Park, J. Qi, J. Patel, M. Geanon, D. Kelly, G. de Real, R. Lee, B. Nie, K. Miake-Lye, S. Angeliadis, K. Radkevich, E. Thin, T. H. Garcia-Barros, M. Brown, H. Martin, B. Mateo, A. Soto, A. Sussman, R. Shiwlani, S 2024-09-03 doi:10.1101/2024.09.02.610816 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Spike frequency adaptation in primate lateral prefrontal cortex neurons results from interplay between intrinsic properties and circuit dynamics ]]> https://biorxiv.org/content/10.1101/2024.09.03.610998v1?rss=1 Koch, N. A. Corrigan, B. W. Feyerabend, M. Gulli, R. A. Jimenez-Sosa, M. S. Abbass, M. Sunstrum, J. K. Matovic, S. Roussy, M. Luna, R. Mestern, S. A. Mahmoudian, B. Vijayraghavan, S. Igarashi, H. Pradeepan, K. S. Assis, W. J. Pruszynski, J. A. Tripathy, S. Staiger, J. F. Gonzalez-Burgos, G. Neef, A. Treue, S. Everling, S. Inoue, W. Khadra, A. Martinez-Trujillo, J. C. 2024-09-05 doi:10.1101/2024.09.03.610998 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ A conserved cell-type gradient across the human mediodorsal and paraventricular thalamus ]]> https://biorxiv.org/content/10.1101/2024.09.03.611112v1?rss=1 Schulmann, A. Feng, N. Auluck, P. K. Mukherjee, A. Komal, R. Leng, Y. Gao, C. Williams Avram, S. K. Roy, S. Usdin, T. B. Xu, Q. Imamovic, V. Patel, Y. Akula, N. Raznahan, A. Menon, V. Roussos, P. Duncan, L. Elkahloun, A. Singh, J. Kelly, M. C. Halassa, M. M. Hattar, S. Penzo, M. A. Marenco, S. McMahon, F. 2024-09-05 doi:10.1101/2024.09.03.611112 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Interhemispheric CA1 projections support spatial cognition and are affected in a mouse model of the 22q11.2 deletion syndrome ]]> https://biorxiv.org/content/10.1101/2024.09.05.611389v1?rss=1 De Leon Reyes, N. S. Bortolozzo-Gleich, M. H. Nomura, Y. Garcia Frigola, C. Nieto, M. Gogos, J. Leroy, F. 2024-09-06 doi:10.1101/2024.09.05.611389 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Time spent in conversation over meals predicts default network function: Evidence from a passive mobile-sensing and fMRI study. ]]> https://biorxiv.org/content/10.1101/2024.09.04.611232v1?rss=1 Bhatt, D. Huckins, J. F. Nepal, S. Campbell, A. T. Meyer, M. 2024-09-08 doi:10.1101/2024.09.04.611232 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Discordance in acute gastrointestinal toxicity between synchrotron-based proton and linac-based electron ultra-high dose rate irradiation ]]> https://biorxiv.org/content/10.1101/2024.09.04.611307v1?rss=1 Liu, K. Titt, U. Esplen, N. M. Connell, L. Konradsson, E. K. Yang, M. Wang, X. Takaoka, T. Li, Z. Koong, A. C. Mitra, D. Mohan, R. Loo, B. W. Lin, S. H. Schueler, E. 2024-09-08 doi:10.1101/2024.09.04.611307 Cold Spring Harbor Laboratory Press 2024-09-08 <![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[ Cancer Interception During Treatment: Using Growth Kinetics to Create a Continuous Variable for Assessing Disease Response ]]> https://biorxiv.org/content/10.1101/2024.09.10.612311v1?rss=1 Zhou, M. Fojo, T. Schwartz, L. Bates, S. E. Blagoev, K. B. 2024-09-11 doi:10.1101/2024.09.10.612311 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Proteostasis and metabolic dysfunction in a distinct subset of storage-induced senescent erythrocytes targeted for clearance ]]> https://biorxiv.org/content/10.1101/2024.09.11.612195v1?rss=1 Peltier, S. Marin, M. Dzieciatkowska, M. Dussiot, M. Roy, M. Bruce, J. Leblanc, L. Hadjou, Y. Georgeault, S. Fricot, A. Roussel, C. Stephenson, D. Casimir, M. Sissoko, A. Paye, F. Dokmak, S. Ndour, P. A. Roingeard, P. Gautier, E.-F. Spitalnik, S. Hermine, O. Buffet, P. A. D'Alessandro, A. Amireault, P. 2024-09-12 doi:10.1101/2024.09.11.612195 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding ]]> https://biorxiv.org/content/10.1101/2024.09.09.612073v1?rss=1 Fang, C. Lindsey, J. Aronov, D. Abbott, L. Chettih, S. N. 2024-09-13 doi:10.1101/2024.09.09.612073 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Inflammation perturbs hematopoiesis by remodeling specific compartments of the bone marrow niche ]]> https://biorxiv.org/content/10.1101/2024.09.12.612751v1?rss=1 Swann, J. W. Zhang, R. Verovskaya, E. V. Calero-Nieto, F. J. Wang, X. Proven, M. A. Shyu, P. T. Guo, E. Gottgens, B. Passegue, E. 2024-09-13 doi:10.1101/2024.09.12.612751 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Nanomedicines targeting signaling of protease-activated receptor 2 in organelles provide sustained analgesia ]]> https://biorxiv.org/content/10.1101/2024.09.10.612022v1?rss=1 Teng, S. L. Latorre, R. Bhansali, D. Lewis, P. K. Pollard, R. E. Peach, C. J. Sokrat, B. Thanigai, G. S. A. Chiu, T. Jensen, D. D. Jimenez-Vargas, N. N. Mocherniak, A. Parreiras-E-Silva, L. T. Bouvier, M. Bogyo, M. Gaspari, M. M. Vanner, S. J. Pinkerton, N. M. Leong, K. W. Schmidt, B. L. Bunnett, N. W. 2024-09-14 doi:10.1101/2024.09.10.612022 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ High fidelity genetic markers for sexing Cannabis sativa seedlings ]]> https://biorxiv.org/content/10.1101/2024.09.10.612257v1?rss=1 Prentout, D. El Aoudati, S. Mathis, F. Marais, G. Henri, H. 2024-09-14 doi:10.1101/2024.09.10.612257 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Focused ultrasound enhanced antibody delivery for the treatment of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.09.13.611071v1?rss=1 Kwon, N. Batts, A. J. Zhang, H. Lewis-Jackson, V. Konofagou, E. Przedborski, S. 2024-09-14 doi:10.1101/2024.09.13.611071 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Cross-sectional brain age assessments are limited in predicting future brain change ]]> https://biorxiv.org/content/10.1101/2024.09.11.612523v1?rss=1 Korbmacher, M. Vidal-Pineiro, D. Wang, M.-Y. van der Meer, D. Wolfers, T. Nakua, H. Eikefjord, E. Andreassen, O. Westlye, L. T. Maximov, I. I. 2024-09-15 doi:10.1101/2024.09.11.612523 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Mindfulness-based Neurofeedback: A Systematic Review of EEG and fMRI studies ]]> https://biorxiv.org/content/10.1101/2024.09.12.612669v1?rss=1 Treves, I. N. Greene, K. D. Bajwa, Z. Wool, E. Kim, N. Bauer, C. C. Bloom, P. A. Pagliaccio, D. Zhang, J. Whitfield-Gabrieli, S. Auerbach, R. P. 2024-09-15 doi:10.1101/2024.09.12.612669 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Purkinje cells in Crus I and II encode the visual stimulus and the impending choice as monkeys learn a reinforcement based visuomotor association task ]]> https://biorxiv.org/content/10.1101/2024.09.13.612926v1?rss=1 Ipata, A. Fascianelli, V. De Zeeuw, C. I. Sendhilnathan, N. Fusi, S. Goldberg, M. E. 2024-09-15 doi:10.1101/2024.09.13.612926 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Neural and verbal responses to attachment-schema narratives differ based on past and current caregiving experiences ]]> https://biorxiv.org/content/10.1101/2024.09.13.612953v1?rss=1 Lee, C. S. Cohen, S. S. Hutchinson, S. Tottenham, N. Baldassano, C. 2024-09-15 doi:10.1101/2024.09.13.612953 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Exploiting correlations across trials and behavioral sessions to improve neural decoding ]]> https://biorxiv.org/content/10.1101/2024.09.14.613047v1?rss=1 Zhang, Y. Lyu, H. Hurwitz, C. Wang, S. Findling, C. L. Hubert, F. Pouget, A. International Brain Laboratory, Varol, E. Paninski, L. 2024-09-15 doi:10.1101/2024.09.14.613047 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening ]]> https://biorxiv.org/content/10.1101/2024.09.14.613076v1?rss=1 Thakur, B. Katte, R. H. Xu, W. Janowska, K. Sammour, S. Henderson, R. Lu, M. Kwong, P. D. Acharya, P. 2024-09-15 doi:10.1101/2024.09.14.613076 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Heritability of movie-evoked brain activity and connectivity ]]> https://biorxiv.org/content/10.1101/2024.09.16.612469v1?rss=1 Gruskin, D. C. Vieira, D. J. Lee, J. K. Patel, G. H. 2024-09-16 doi:10.1101/2024.09.16.612469 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. ]]> https://biorxiv.org/content/10.1101/2024.09.16.613181v1?rss=1 Schoot Uiterkamp, F. E. Maes, M. E. Alamalhoda, M. Firoozi, A. Colombo, G. Siegert, S. 2024-09-16 doi:10.1101/2024.09.16.613181 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ An Iterative Approach to Polish the Nanopore Sequencing Basecalling for Therapeutic RNA Quality Control ]]> https://biorxiv.org/content/10.1101/2024.09.12.612711v1?rss=1 Wang, Z. Tu, M.-J. Liu, Z. Wang, K. K. Fang, Y. Hao, N. Zhang, H. H. Que, J. Sun, X. Yu, A.-M. DING, H. 2024-09-18 doi:10.1101/2024.09.12.612711 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Structural insights into terminal arabinosylation biosynthesis of the mycobacterial cell wall arabinan ]]> https://biorxiv.org/content/10.1101/2024.09.17.613533v1?rss=1 Liu, Y. Brown, C. M. Erramilli, S. Su, Y.-C. Tseng, P.-S. Wang, Y.-J. Duong, N. H. Tokarz, P. Kloss, B. Han, C.-R. Chen, H.-Y. Rodrigues, J. Archer, M. Lowary, T. L. Kossiakoff, A. A. Stansfeld, P. J. Nygaard, R. Mancia, F. 2024-09-18 doi:10.1101/2024.09.17.613533 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE ]]> https://biorxiv.org/content/10.1101/2024.09.17.613550v1?rss=1 Liu, Y. Brown, C. M. Borges, N. Nobre, R. N. Erramilli, S. Dufrisne, M. B. Kloss, B. Giacometti, S. Esteves, A. M. Timoteo, C. G. Tokarz, P. Cater, R. Morita, Y. S. Kossiakoff, A. A. Santos, H. Stansfeld, P. J. Nygaard, R. Mancia, F. 2024-09-18 doi:10.1101/2024.09.17.613550 Cold Spring Harbor Laboratory Press 2024-09-18 <![CDATA[ Manufacturing-Aware Generative Model Architectures Enable Biological Sequence Design and Synthesis at Petascale ]]> https://biorxiv.org/content/10.1101/2024.09.13.612900v1?rss=1 Weinstein, E. N. Gollub, M. G. Slabodkin, A. Gardner, C. L. Dobbs, K. Cui, X.-B. Amin, A. N. Church, G. M. Wood, E. B. 2024-09-19 doi:10.1101/2024.09.13.612900 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity ]]> https://biorxiv.org/content/10.1101/2024.09.14.613024v1?rss=1 Zhuang, H. Gai, X. Zhang, A. R. Hou, W. Ji, Z. Shi, P. 2024-09-19 doi:10.1101/2024.09.14.613024 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output ]]> https://biorxiv.org/content/10.1101/2024.09.18.613279v1?rss=1 Trevisan, A. J. Han, K. Chapman, P. Kulkarni, A. S. Hinton, J. M. Ramirez, C. Klein, I. Gatto, G. Gabitto, M. I. Menon, V. Bikoff, J. B. 2024-09-19 doi:10.1101/2024.09.18.613279 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Is there a ubiquitous spectrolaminar motif of local field potential power across primate neocortex? ]]> https://biorxiv.org/content/10.1101/2024.09.18.613490v1?rss=1 Mackey, C. A. Duecker, K. Neymotin, S. A. Dura-Bernal, S. Haegens, S. Barczak, A. O'Connell, M. N. Jones, S. Ding, M. Ghuman, A. S. Schroeder, C. E. 2024-09-19 doi:10.1101/2024.09.18.613490 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Cortico-hippocampal interactions underlie schema-supported memory encoding in older adults ]]> https://biorxiv.org/content/10.1101/2024.09.18.613755v1?rss=1 Huang, S. Bogdan, P. C. Howard, C. M. Gillette, K. Deng, L. Welch, E. McAllister, M. L. Giovanello, K. S. Davis, S. W. Cabeza, R. 2024-09-19 doi:10.1101/2024.09.18.613755 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Circadian modulation of mosquito host-seeking persistence by Pigment-Dispersing Factor impacts daily biting patterns ]]> https://biorxiv.org/content/10.1101/2024.09.19.613886v1?rss=1 Dong, L. Hormigo, R. Barnett, J. M. Greppi, C. Duvall, L. B. 2024-09-19 doi:10.1101/2024.09.19.613886 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Structure-guided engineering of type I-F CASTs for targeted gene insertion in human cells ]]> https://biorxiv.org/content/10.1101/2024.09.19.613948v1?rss=1 Lampe, G. D. Liang, A. R. Zhang, D. J. Fernandez, I. S. Sternberg, S. H. 2024-09-19 doi:10.1101/2024.09.19.613948 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Morphological profiling in human dopaminergic neurons identifies mitochondrial uncoupling as a neuroprotective effect ]]> https://biorxiv.org/content/10.1101/2024.09.19.613945v1?rss=1 Gorgogietas, V. Weiss, A. Cousin, L. Hoffmann, D. Schmitt, K. Ogier, A. Barbuti, P. A. Santos, B. F. R. Boussaad, I. Wittich, A. Zaliani, A. Pless, O. Krueger, R. Sommer, P. Wilbertz, J. H. 2024-09-20 doi:10.1101/2024.09.19.613945 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation ]]> https://biorxiv.org/content/10.1101/2024.09.19.613951v1?rss=1 Stewart, A. F. Fulton, S. L. Durand-de Cuttoli, R. Thompson, R. E. Chen, P.-J. Brindley, E. Cetin, B. Farrelly, L. A. Futamura, R. Claypool, S. Bastle, R. M. Di Salvo, G. Peralta, C. Molina, H. Baljinnyam, E. Marro, S. G. Russo, S. J. Devita, R. J. Muir, T. W. Maze, I. 2024-09-20 doi:10.1101/2024.09.19.613951 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Clonal dynamics and somatic evolution of haematopoiesis in mouse ]]> https://biorxiv.org/content/10.1101/2024.09.17.613129v1?rss=1 Kapadia, C. D. Williams, N. Dawson, K. J. Watson, C. Yousefzadeh, M. J. Le, D. Nyamondo, K. Cagan, A. Waldvogel, S. De La Fuente, J. Leongamornlert, D. Mitchell, E. Florez, M. A. Aguilar, R. Martell, A. Guzman, A. Harrison, D. Niedernhofer, L. J. King, K. Y. Campbell, P. J. Blundell, J. Goodell, M. A. Nangalia, J. 2024-09-21 doi:10.1101/2024.09.17.613129 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Vocal Call Locator Benchmark (VCL) for localizing rodent vocalizations from multi-channel audio ]]> https://biorxiv.org/content/10.1101/2024.09.20.613758v1?rss=1 Peterson, R. E. Tanelus, A. Ick, C. Mimica, B. Francis, N. Ivan, V. J. Choudhri, A. Falkner, A. Murthy, M. Schneider, D. M. Sanes, D. H. 2024-09-21 doi:10.1101/2024.09.20.613758 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis ]]> https://biorxiv.org/content/10.1101/2024.09.20.614050v1?rss=1 Vijatovic, D. Toma, F. A. Harrington, Z. P. M. Sommer, C. Hauschild, R. Trevisan, A. J. Chapman, P. Julseth, M. J. Brenner-Morton, S. Gabitto, M. I. Dasen, J. S. Bikoff, J. B. Sweeney, L. B. 2024-09-21 doi:10.1101/2024.09.20.614050 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Role of Forkhead box F1 in the Pathobiology of Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/2024.09.18.611448v1?rss=1 Gomez-Arroyo, J. Houweling, A. C. Bogaard, H. J. Aman, J. Kitzmiller, J. A. Porollo, A. Dooijes, D. Meijboom, L. J. Hale, P. Pauciulo, M. W. Hong, J. Zhu, N. Welch, C. Shen, Y. Zacharias, W. J. McCormack, F. X. Aldred, M. A. Weirauch, M. T. Graf, S. T. Rhodes, C. J. Chung, W. K. Whitsett, J. A. Martin, L. J. Kalinichenko, V. K. Nichols, W. A. 2024-09-22 doi:10.1101/2024.09.18.611448 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics ]]> https://biorxiv.org/content/10.1101/2024.09.18.613276v1?rss=1 Matentzoglu, N. Bello, S. M. Stefancsik, R. Alghamdi, S. M. Anagnostopoulos, A. V. Balhoff, J. P. Balk, M. A. Bradford, Y. M. Bridges, Y. Callahan, T. J. Caufield, H. Cuzick, A. Carmody, L. C. Caron, A. R. de Souza, V. Engel, S. R. Fey, P. Fisher, M. Gehrke, S. Grove, C. Hansen, P. Harris, N. L. Harris, M. A. Harris, L. Ibrahim, A. Jacobsen, J. O. B. Köhler, S. McMurry, J. A. Munoz-Fuentes, V. Munoz-Torres, M. C. Parkinson, H. Pendlington, Z. M. Pilgrim, C. Robb, S. M. C. Robinson, P. N. Seager, J. Segerdell, E. Smedley, D. Sollis, E. Toro, S. Vasilevsk 2024-09-22 doi:10.1101/2024.09.18.613276 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Brain-body mitochondrial distribution patterns lack coherence and point to tissue-specific and individualized regulatory mechanisms ]]> https://biorxiv.org/content/10.1101/2024.09.20.614152v1?rss=1 Devine, J. Monzel, A. S. Shire, D. Rosenberg, A. M. Junker, A. Cohen, A. A. Picard, M. 2024-09-22 doi:10.1101/2024.09.20.614152 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Widespread brain activity increases in frontal lobe seizures with impaired consciousness ]]> https://biorxiv.org/content/10.1101/2024.09.20.614207v1?rss=1 Salardini, E. Vaddiparti, A. Kumar, A. Martin, R. A. Gebere, R. Z. Arencibia, C. A. Dhakar, M. B. Grover, E. H. Quraishi, I. H. Sternberg, E. J. George, I. C. Sivaraju, A. Bonito, J. Zaveri, H. P. Gober, L. M. Ahmed, S. Ghoshal, S. Wu, K. Farooque, P. Hirsch, L. J. Damisah, E. Gerrard, J. L. Spencer, D. D. Yoo, J. Y. Young, J. J. Friedman, D. Shum, J. Blumenfeld, H. 2024-09-23 doi:10.1101/2024.09.20.614207 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ The exit of naïve pluripotency contains a lipid metabolism-induced checkpoint for genome integrity. ]]> https://biorxiv.org/content/10.1101/2024.09.22.613751v1?rss=1 de Souza, R. A. Barneda, D. Karimlou, D. Bovee, N. G. P. Zheng, Y. Kahlman, E. J. E. M. Lopes Novo, C. Ellis, J. K. Leeke, B. J. Prakash Bangalore, M. Liu, Z. Sousa, B. C. Lopez-Clavijo, A. F. Jansen, J. H. Barahona, M. Percharde, M. Keun, H. C. Christian, M. Marks, H. Azuara, V. 2024-09-23 doi:10.1101/2024.09.22.613751 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Temporal integration in human auditory cortex is predominantly yoked to absolute time, not structure duration ]]> https://biorxiv.org/content/10.1101/2024.09.23.614358v1?rss=1 Norman-Haignere, S. V. Keshishian, M. K. Devinsky, O. Doyle, W. McKhann, G. M. Schevon, C. A. Flinker, A. Mesgarani, N. 2024-09-24 doi:10.1101/2024.09.23.614358 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Auditory decision-making deficits after permanent noise-induced hearing loss ]]> https://biorxiv.org/content/10.1101/2024.09.23.614535v1?rss=1 Berns, M. P. Nunez, G. M. Zhang, X. Chavan, A. Zemlianova, K. Mowery, T. M. Yao, J. D. 2024-09-24 doi:10.1101/2024.09.23.614535 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ The capacity of the medial temporal lobe to represent memory items in their ordinal position in a sequence is domain-general ]]> https://biorxiv.org/content/10.1101/2024.09.25.614993v1?rss=1 Temudo, A. Dolfen, N. King, B. R. Albouy, G. 2024-09-26 doi:10.1101/2024.09.25.614993 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Tissue resident memory CD4+ T cells are sustained by site-specific levels of self-renewal and replacement from precursors ]]> https://biorxiv.org/content/10.1101/2024.09.26.615039v1?rss=1 Chandler, J. Bullock, M. E. Swain, A. Williams, C. van Dorp, C. Seddon, B. Yates, A. J. 2024-09-28 doi:10.1101/2024.09.26.615039 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Nuclear Type I Myosins are Essential for Life and Genome Organization ]]> https://biorxiv.org/content/10.1101/2024.09.26.615191v1?rss=1 Peng, A. Y. T. Li, J. Freeman, B. C. 2024-09-28 doi:10.1101/2024.09.26.615191 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Potentiation of active locomotor state by spinal-projecting serotonergic neurons ]]> https://biorxiv.org/content/10.1101/2024.09.26.615260v1?rss=1 Dasen, J. Fenstermacher, S. Dymecki, S. Chaimowitz, C. Vonasek, A. Gattuso, H. Jessell, T. 2024-09-28 doi:10.1101/2024.09.26.615260 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ MKK4 and MKK7 control degeneration of retinal ganglion cell somas and axons after glaucoma-relevant injury. ]]> https://biorxiv.org/content/10.1101/2024.09.27.614559v1?rss=1 Marola, O. J. Syc-Mazurek, S. B. Yablonski, S. E. R. Shrager, P. G. John, S. W. M. Libby, R. T. 2024-09-28 doi:10.1101/2024.09.27.614559 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ HEXIM1 is correlated with Alzheimer's disease pathology and regulates immediate early gene dynamics in neurons ]]> https://biorxiv.org/content/10.1101/2024.09.27.615234v1?rss=1 Htet, M. Estay-Olmos, C. Hu, L. Wu, Y. Powers, B. E. Campbell, C. Ahmed, M. R. Hohman, T. J. Schneider, J. A. Bennett, D. A. Menon, V. De Jager, P. Kaas, G. A. Colbran, R. J. Greer, C. B. 2024-09-28 doi:10.1101/2024.09.27.615234 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Imprecise counting of observations in averaging tasks predicts primacy and recency effects ]]> https://biorxiv.org/content/10.1101/2024.09.29.615676v1?rss=1 Prat-Carrabin, A. Woodford, M. 2024-10-01 doi:10.1101/2024.09.29.615676 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Modular representations emerge in neural networks trained to perform context-dependent tasks ]]> https://biorxiv.org/content/10.1101/2024.09.30.615925v1?rss=1 Johnston, W. J. Fusi, S. 2024-10-01 doi:10.1101/2024.09.30.615925 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis ]]> https://biorxiv.org/content/10.1101/2024.09.30.615801v1?rss=1 Zagare, A. Balaur, I. Rougny, A. Saraiva, C. Gobin, M. Monzel, A. S. Ghosh, S. Satagopam, V. P. Schwamborn, J. C. 2024-10-02 doi:10.1101/2024.09.30.615801 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Remote activation of place codes by gaze in a highly visual animal ]]> https://biorxiv.org/content/10.1101/2024.09.30.615982v1?rss=1 Payne, H. L. Aronov, D. 2024-10-02 doi:10.1101/2024.09.30.615982 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia ]]> https://biorxiv.org/content/10.1101/2024.10.01.614851v1?rss=1 Memel, M. Staffaroni, A. Ilan-Gala, I. Garcia Castro, J. Kornak, J. Tartaglia, C. Saloner, R. VandeBunte, A. Paolillo, E. Cadwallader, C. Chen, C. Gorno-Tempini, M. L. Mandelli, M. Apostolova, L. Graff-Radford, N. Litvan, I. Bayram, E. Pressman, P. Miyagawa, T. Mackenzie, I. Goldman, J. Darby, R. Appleby, B. Petrucelli, L. Gendron, T. Heuer, H. Forseberg, L. Rojas, J. Boeve, B. Brushaber, N. Domoto-Reilly, K. Ghoshal, N. Lapid, M. Pascual, B. Lee, S. Ramos, E. Ramanan, V. Rademakers, R. Rascovsky, K. Pantelyat, A. Masdeu, J. Snyder, A. Boxer, A. Rosen 2024-10-03 doi:10.1101/2024.10.01.614851 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations ]]> https://biorxiv.org/content/10.1101/2024.10.02.616147v1?rss=1 Feczko, E. J. Stoyell, S. M. Moore, L. A. Alexopoulos, D. Bagonis, M. Barrett, K. Bower, B. Cavender, A. Chamberlain, T. A. Conan, G. Day, T. K. Goradia, D. Graham, A. Heisler-Roman, L. Hendrickson, T. J. Houghton, A. Kardan, O. Kiffmeyer, E. A. Lee, E. G. Lundquist, J. T. Lucena, C. Martin, T. Mummaneni, A. Myricks, M. Narnur, P. Perrone, A. J. Reiners, P. Rueter, A. R. Saw, H. Styner, M. Sung, S. Tiklasky, B. Wisnowski, J. L. Yacoub, E. Zimmermann, B. Smyser, C. D. Rosenberg, M. D. Fair, D. A. Elison, J. T. 2024-10-03 doi:10.1101/2024.10.02.616147 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Automated Tumor and FUS Lesion Quantification on Multi-frequency Harmonic Motion and B-mode Imaging Using a Multi-modality Neural Network ]]> https://biorxiv.org/content/10.1101/2024.10.02.616303v1?rss=1 Hu, S. Liu, Y. Li, X. Konofagou, E. 2024-10-03 doi:10.1101/2024.10.02.616303 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Aperiodic neural excitation of the prefrontal cortex offsets age-related decrease in hippocampal theta activity for spatial memory maintenance ]]> https://biorxiv.org/content/10.1101/2024.10.03.616418v1?rss=1 Park, S.-E. Donoghue, T. Jacobs, J. Lee, S. A. 2024-10-04 doi:10.1101/2024.10.03.616418 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Parallel neuroinflammatory pathways to cerebrovascular injury and amyloid-beta in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2024.10.03.616579v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@2d3c39org.highwire.dtl.DTLVardef@1ccc453org.highwire.dtl.DTLVardef@6d40bdorg.highwire.dtl.DTLVardef@b543cb_HPS_FORMAT_FIGEXP M_FIG C_FIG Credit: BioRender was used to help create this graphical abstract. ]]> Rizvi, B. Adams, J. N. Bamford, A. Kim, S. Sathishkumar, M. Tustison, N. J. Taylor, L. Tuteja, N. McMillan, L. Nan, B. Cai, H. Escalante, Y. Y. Meza, N. Harris, A. L. Malhas, R. Brickman, A. M. Mapstone, M. Thomas, E. A. Yassa, M. A. 2024-10-04 doi:10.1101/2024.10.03.616579 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Splicing dysregulation in glioblastoma alters the function of cell migration-related genes ]]> https://biorxiv.org/content/10.1101/2024.10.05.616792v1?rss=1 Seong, M. Bak-Gordon, P. Liu, Z. Canoll, P. Manley, J. 2024-10-06 doi:10.1101/2024.10.05.616792 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Single-Cell RNA-Seq Reveals Adventitial Fibroblast Alterations during Mouse Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2024.10.05.616802v1?rss=1 Fries, L. E. Chung, A. Chang, H.-K. Yuan, T. Bauer, R. C. 2024-10-06 doi:10.1101/2024.10.05.616802 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ Genetic variation in male mate choice for large females in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2024.10.05.616829v1?rss=1 Freed, G. S. Martinez, I. G. Lev, A. Anthony Cuadrado, A.-M. Pischedda, A. 2024-10-06 doi:10.1101/2024.10.05.616829 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ EPHA2 Regulates SOX2 during Esophageal Development ]]> https://biorxiv.org/content/10.1101/2024.10.08.617209v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@16b8a8aorg.highwire.dtl.DTLVardef@1548672org.highwire.dtl.DTLVardef@46e28corg.highwire.dtl.DTLVardef@1c35578_HPS_FORMAT_FIGEXP M_FIG SFD: Serum-Free Differentiation media; EPC: esophageal progenitor cells; HEO: human esophageal organoids Created with BioRender.com C_FIG HighlightsO_LISOX2 is crucial for proper esophageal development. C_LIO_LIEPHA2 is a receptor tyrosine kinase involved in various developmental processes. C_LIO_LIEPHA2 activates SOX2. C_LIO_LIInhibition of EPHA2 decreased SOX2 expression and human esophageal organoid formation. C_LI ]]> Li, T. Mitani, Y. Cruz-Acuna, R. Karaksheva, T. A. Sahu, V. Martin, C. Nakagawa, H. Gabre, J. 2024-10-10 doi:10.1101/2024.10.08.617209 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Relation of CMV and brain atrophy to trajectories of immunosenescence in diverse populations ]]> https://biorxiv.org/content/10.1101/2024.10.07.614568v1?rss=1 Touil, H. Luquez, T. Comandante-Lou, N. Lee, A. J. Fujita, M. Habeck, C. Kroshilina, A. Hegewisch-Solloa, E. McInvale, J. Zuroff, L. Isnard, S. Walker, E. Zhang, L. Routy, J.-P. Zhang, Y. Mace, E. M. Klotz, L. Wiendl, H. Xia, Z. Bar-Or, A. Menon, V. Stern, Y. De Jager, P. L. 2024-10-11 doi:10.1101/2024.10.07.614568 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Tuning Insulin Receptor Signaling Using De Novo Designed Agonists ]]> https://biorxiv.org/content/10.1101/2024.10.07.617068v1?rss=1 Wang, X. Cardoso, S. Cai, K. Venkatesh, P. Hung, A. Ng, M. Hall, C. Coventry, B. Lee, D. Chowhan, R. Gerben, S. Li, J. An, W. Hon, M. Accili, D. Bai, X. Choi, E. Baker, D. 2024-10-11 doi:10.1101/2024.10.07.617068 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ A CXCR4 partial agonist improves immunotherapy by targeting polymorphonuclear myeloid-derived suppressor cells and cancer-driven granulopoiesis ]]> https://biorxiv.org/content/10.1101/2024.10.09.617228v1?rss=1 Qian, J. Ma, C. Waterbury, Q. T. Zhi, X. Moon, C. S. Tu, R. Kobayashi, H. Wu, F. Zheng, B. Zeng, Y. Zheng, H. Ochiai, Y. White, R. A. Harle, D. W. LaBella, J. S. Zamechek, L. B. Hu, L. Z. Moy, R. H. Han, A. S. Daugherty, B. Lederman, S. WANG, T. C. 2024-10-11 doi:10.1101/2024.10.09.617228 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Migration strategies of a high-latitude breeding songbird (Setophaga coronata coronata) revealed using multi-sensor geolocators and stable isotopes ]]> https://biorxiv.org/content/10.1101/2024.10.09.617415v1?rss=1 Szarmach, S. J. Beam, J. K. Moore, M. Van Doren, B. M. Brelsford, A. Toews, D. P. L. 2024-10-11 doi:10.1101/2024.10.09.617415 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome ]]> https://biorxiv.org/content/10.1101/2024.10.08.617108v1?rss=1 Richardson, M. Zhao, S. Sheth, R. U. Lin, L. Qu, Y. Lee, J. Moody, T. Ricaurte, D. Huang, Y. Velez-Cortes, F. Urtecho, G. Wang, H. H. 2024-10-12 doi:10.1101/2024.10.08.617108 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Distinct roles of SNR, speech Intelligibility, and attentional effort on neural speech tracking in noise ]]> https://biorxiv.org/content/10.1101/2024.10.10.616515v1?rss=1 He, X. Raghavan, V. S. Mesgarani, N. 2024-10-12 doi:10.1101/2024.10.10.616515 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Decoding the Unintelligible: Neural Speech Tracking in Low Signal-to-Noise Ratios ]]> https://biorxiv.org/content/10.1101/2024.10.10.616521v1?rss=1 He, X. Raghavan, V. S. Mesgarani, N. 2024-10-12 doi:10.1101/2024.10.10.616521 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Microscopic deconstruction of cortical circuit stimulation by transcranial ultrasound ]]> https://biorxiv.org/content/10.1101/2024.10.10.617091v1?rss=1 Lemaire, T. Yuan, Y. Gellman, C. LeMessurier, A. M. Haiken Dray, S. R. Little, J. P. Froemke, R. C. Shoham, S. 2024-10-12 doi:10.1101/2024.10.10.617091 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Prefrontal representations of retrospective spatial working memory in a rodent radial maze task ]]> https://biorxiv.org/content/10.1101/2024.10.10.617655v1?rss=1 Taliaferro, J. P. Posani, L. Greenwald, J. Lim, S. McGowan, J. C. Pekarskaya, E. Lacefield, C. Fusi, S. Kellendonk, C. 2024-10-12 doi:10.1101/2024.10.10.617655 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Orthrus: Towards Evolutionary and Functional RNA Foundation Models ]]> https://biorxiv.org/content/10.1101/2024.10.10.617658v1?rss=1 Fradkin, P. Shi, R. Isaev, K. Frey, B. J. Morris, Q. Lee, L. J. Wang, B. 2024-10-12 doi:10.1101/2024.10.10.617658 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ HDAC Inhibitors recapitulate Human Disease-Associated Microglia Signatures in vitro ]]> https://biorxiv.org/content/10.1101/2024.10.11.617544v1?rss=1 Haage, V. C. Tuddenham, J. F. Bautista, A. White, C. C. Garcia, F. Patel, R. Comandante-Lou, N. Marshe, V. Soni, R. K. Sims, P. A. Menon, V. Sproul, A. A. De Jager, P. L. 2024-10-12 doi:10.1101/2024.10.11.617544 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering ]]> https://biorxiv.org/content/10.1101/2024.10.11.617640v1?rss=1 De, S. Zhou, M. Brown, Z. P. Burton-Smith, R. N. Hashem, Y. Pestova, T. Hellen, C. U. T. Frank, J. 2024-10-12 doi:10.1101/2024.10.11.617640 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ A computational principle of habit formation ]]> https://biorxiv.org/content/10.1101/2024.10.12.618033v1?rss=1 Lakshminarasimhan, K. J. 2024-10-13 doi:10.1101/2024.10.12.618033 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Mechanical properties are tuned during development with the fibrous network nature of the Arabidopsis cell wall ]]> https://biorxiv.org/content/10.1101/2024.10.09.617478v1?rss=1 Chen, S. Burda, I. Jani, P. Pendrak, B. Silberstein, M. N. Roeder, A. H. K. 2024-10-14 doi:10.1101/2024.10.09.617478 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium. ]]> https://biorxiv.org/content/10.1101/2024.10.11.617898v1?rss=1 Dirvin, B. G. Noh, H. Tomassoni, L. Cao, D. Zhou, Y. Ke, X. Qian, J. Schotsaert, M. Garcia-Sastre, A. Karan, C. Califano, A. Cardoso, W. V. 2024-10-14 doi:10.1101/2024.10.11.617898 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ Essential tremor with tau pathology features seeds indistinguishable in conformation from Alzheimer's disease and primary age-related tauopathy ]]> https://biorxiv.org/content/10.1101/2024.10.12.617973v1?rss=1 Saez-Calveras, N. Vaquer-Alicea, J. White, C. L. Tak, Y. Cosentino, S. Faust, P. L. Louis, E. D. Diamond, M. I. 2024-10-14 doi:10.1101/2024.10.12.617973 Cold Spring Harbor Laboratory Press 2024-10-14 <![CDATA[ SeqDance: A Protein Language Model for Representing Protein Dynamic Properties ]]> https://biorxiv.org/content/10.1101/2024.10.11.617911v1?rss=1 Hou, C. Shen, Y. 2024-10-15 doi:10.1101/2024.10.11.617911 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Mutant p53 regulates cancer cell invasion in complex three-dimensional environments through mevalonate pathway-dependent Rho/ROCK signaling. ]]> https://biorxiv.org/content/10.1101/2024.10.13.618100v1?rss=1 Guzman, A. Kawase, T. Devanny, A. J. Efe, G. Navaridas, R. Yu, K. Regunath, K. Mercer, I. G. Avard, R. C. Muniz de Queiroz, R. Rustgi, A. K. Kaufman, L. J. Prives, C. 2024-10-15 doi:10.1101/2024.10.13.618100 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis ]]> https://biorxiv.org/content/10.1101/2024.10.15.618357v1?rss=1 Wang, Z. Elbanna, Y. Godet, I. Peters, L. Lampe, G. Chen, Y. Xavier, J. Huse, M. Massague, J. 2024-10-15 doi:10.1101/2024.10.15.618357 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ TRENDY: Gene Regulatory Network Inference Enhanced by Transformer ]]> https://biorxiv.org/content/10.1101/2024.10.14.618189v1?rss=1 Tian, X. Patel, Y. Wang, Y. 2024-10-16 doi:10.1101/2024.10.14.618189 Cold Spring Harbor Laboratory Press 2024-10-16 <![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[ Associations between prenatal distress, mitochondrial health, and gestational age: findings from two pregnancy studies in the USA and Turkey ]]> https://biorxiv.org/content/10.1101/2024.10.16.618719v1?rss=1 Huang, Q. Shire, D. Hollis, F. Abuaish, S. Picard, M. Monk, C. Duman, E. A. Trumpff, C. 2024-10-16 doi:10.1101/2024.10.16.618719 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ An analysis of RNA quality metrics in human brain tissue ]]> https://biorxiv.org/content/10.1101/2024.10.14.618253v1?rss=1 Tian, J. Lam, T. Ross, S. Ciener, B. Leskinen, S. Sivakumar, S. Bennett, D. A. Menon, V. McKhann, G. M. Runnels, A. Teich, A. 2024-10-17 doi:10.1101/2024.10.14.618253 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1) ]]> https://biorxiv.org/content/10.1101/2024.10.15.616105v1?rss=1 Chen, T. Vallese, F. Gil-Iturbe, E. Kim, K. Quick, M. Clarke, O. Tajkhorshid, E. 2024-10-17 doi:10.1101/2024.10.15.616105 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ A First-in-Class Dual Degrader of Bcl-2/Bcl-xL Reverses HIV Latency and Eliminates Ex Vivo Reservoirs ]]> https://biorxiv.org/content/10.1101/2024.10.16.618723v1?rss=1 Chang, L.-C. Yin, M. T. Laird, G. M. Ritter, K. D. Shah, J. Debnath, A. K. 2024-10-17 doi:10.1101/2024.10.16.618723 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ IOP-induced blood-retinal barrier compromise contributes to RGC death in glaucoma ]]> https://biorxiv.org/content/10.1101/2024.10.15.618539v1?rss=1 Zhang, C. Simon, M. Lim, H. Tolman, N. G. Horbal, L. Juarez, F. A. Bhandari, A. Montgomery, C. John, S. W. M. 2024-10-18 doi:10.1101/2024.10.15.618539 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Intratumoral CXCL12 Gradients Contextualize Tumor Cell Invasion, Migration and Immune Suppression in Breast Cancer ]]> https://biorxiv.org/content/10.1101/2024.10.15.618571v1?rss=1 Anastasiadou, D. P. Couturier, N. Goel, S. Argyris, D. G. Vodopyanov, S. Rivera-Sanchez, L. Gonzalez, E. Kreger, J. Griffen, A. Kazakov, A. Burt, J. Recoder, N. Duran, C. L. Harney, A. S. Quesnel, A. Filippou, P. S. Lenis, V. P. Shukla, S. Entenberg, D. Zintiridou, A. Chen, X. Eddy, R. J. Oktay, M. H. Condeelis, J. S. Karagiannis, N. S. Briceno, A. Guzik, H. Alon, R. DesMarais, V. Ioannou, G. Gnjatic, S. Raynolds, D. M. Macedo, R. Reshef, R. Gil-Henn, H. MacLean, A. L. Roussos Torres, E. LaFave, L. M. Lauvau, G. Karagiannis, G. S. 2024-10-18 doi:10.1101/2024.10.15.618571 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics ]]> https://biorxiv.org/content/10.1101/2024.10.16.618766v1?rss=1 Zhao, L. Xu, K. Talyzina, I. Shi, J. Li, S. Yang, Y. Zhang, S. Zheng, j. Sobolevsky, A. Chen, H. Cui, J. 2024-10-18 doi:10.1101/2024.10.16.618766 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ ACSS2 regulates ferroptosis in an E2F1-dependent manner in breast cancer brain metastatic cells ]]> https://biorxiv.org/content/10.1101/2024.10.18.619082v1?rss=1 Esquea, E. Young, R. Ciraku, L. Merzy, J. Ahmed, N. Talarico, A. Karuppiah, M. Gocal, W. Simone, N. Dick, A. Reginato, M. 2024-10-21 doi:10.1101/2024.10.18.619082 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Neural and behavioral reinstatement jointly reflect retrieval of narrative events ]]> https://biorxiv.org/content/10.1101/2024.10.19.619187v1?rss=1 Nau, M. Greene, A. Tarder-Stoll, H. Lossio-Ventura, J. A. Pereira, F. Chen, J. Baldassano, C. Baker, C. 2024-10-21 doi:10.1101/2024.10.19.619187 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ An interkinetic envelope surrounds chromosomes between meiosis I and II in C. elegans oocytes ]]> https://biorxiv.org/content/10.1101/2024.10.19.619195v1?rss=1 El Mossadeq, L. Bellutti, L. Le Borgne, R. Canman, J. C. PINTARD, L. Verbavatz, J.-M. Askjaer, P. Dumont, J. 2024-10-21 doi:10.1101/2024.10.19.619195 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Shc1 cooperates with Frs2 and Shp2 to recruit Grb2 in FGF-induced lens development ]]> https://biorxiv.org/content/10.1101/2024.10.20.619055v1?rss=1 Wang, Q. Li, H. Mao, Y. Garg, A. Park, E. S. Wu, Y. Chow, A. Peregrin, J. Zhang, X. 2024-10-22 doi:10.1101/2024.10.20.619055 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+ sensor proteins ]]> https://biorxiv.org/content/10.1101/2024.10.20.619163v1?rss=1 Horne, C. Dite, T. A. Young, S. N. Mather, L. J. Dagley, L. F. Johnson, J. L. Yaron-Barir, T. M. Huntsman, E. M. Daly, L. A. Byrne, D. P. A. Cadell, A. L. Ng, B. H. Yousef, J. Multari, D. H. Shen, L. McAloon, L. M. Manning, G. Febbraio, M. A. Means, A. R. Cantley, L. C. Tanzer, M. C. Croucher, D. R. Eyers, C. E. Eyers, P. A. Scott, J. W. Murphy, J. M. 2024-10-22 doi:10.1101/2024.10.20.619163 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ A rapid, facile, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies ]]> https://biorxiv.org/content/10.1101/2024.10.21.619433v1?rss=1 Erath, J. Kemper, D. Mugo, E. Jacoby, A. Valenzuela, E. Jungers, C. F. Beatty, W. L. Hashem, Y. Jovanovic, M. Djuranovic, S. Djuranovic, S. P. 2024-10-22 doi:10.1101/2024.10.21.619433 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Humans are resource-rational predictors in a sequence learning task ]]> https://biorxiv.org/content/10.1101/2024.10.21.619537v1?rss=1 Ferdinand, V. Yu, A. Marzen, S. 2024-10-22 doi:10.1101/2024.10.21.619537 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ A Transcriptional Signature of Induced Neurons Differentiates Virologically Suppressed People Living With HIV from People Without HIV ]]> https://biorxiv.org/content/10.1101/2024.10.22.619617v1?rss=1 Ostermann, P. N. Wu, Y. Bowler, S. A. Siddiqui, M. A. Herrera, A. Sidharta, M. Ramnarine, K. Martinez-Meza, S. St. Bernard, L. A. Nixon, D. F. Jones, R. B. Yamashita, M. Ndhlovu, L. C. Zhou, T. Evering, T. H. 2024-10-22 doi:10.1101/2024.10.22.619617 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Dysregulated balance of D- and L-amino acids modulating glutamatergic neurotransmission in severe spinal muscular atrophy. ]]> https://biorxiv.org/content/10.1101/2024.10.22.619645v1?rss=1 Hassan, A. di Vito, R. Nuzzo, T. Vidali, M. Carlini, M. J. Yadav, S. Yang, H. D'Amico, A. Kolici, X. Valsecchi, V. Panicucci, C. Pignataro, G. Bruno, C. Bertini, E. Errico, F. Pellizzoni, L. Usiello, A. 2024-10-22 doi:10.1101/2024.10.22.619645 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ MIIST305 mitigates gastrointestinal acute radiation syndrome injury and ameliorates radiation-induced gut microbiome dysbiosis ]]> https://biorxiv.org/content/10.1101/2024.10.22.619652v1?rss=1 Mitra, D. Armijo, G. K. Ober, E. H. Baker, S. M. Turner, H. C. Broustas, C. G. 2024-10-22 doi:10.1101/2024.10.22.619652 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ An end-to-end model of active electrosensation ]]> https://biorxiv.org/content/10.1101/2024.10.22.619741v1?rss=1 Turcu, D. Zadina, A. N. Abbott, L. Sawtell, N. B. 2024-10-22 doi:10.1101/2024.10.22.619741 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ The YTHDF Proteins Shape the Brain Gene Signatures of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.10.23.619425v1?rss=1 Tasaki, S. Avey, D. R. Kearns, N. A. Iatrou, A. Yu, C. De Tissera, S. Vyas, H. Xu, J. Flood, D. J. Rothamel, K. Wingo, A. P. Wingo, T. S. Seyfried, N. T. De Jager, P. L. Yeo, G. Gaiteri, C. Bennett, D. A. Wang, Y. 2024-10-23 doi:10.1101/2024.10.23.619425 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ 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[ Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene ]]> https://biorxiv.org/content/10.1101/2024.10.21.619409v1?rss=1 Kim, K. Li, H. Yuan, Q. Melville, Z. Zalk, R. Des Georges, A. Frank, J. Hendrickson, W. A. Marks, A. R. Clarke, O. B. 2024-10-24 doi:10.1101/2024.10.21.619409 Cold Spring Harbor Laboratory Press 2024-10-24 <![CDATA[ Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis ]]> https://biorxiv.org/content/10.1101/2024.10.21.619529v1?rss=1 Jones, M. G. Sun, D. Min, K. H. Colgan, W. N. Tian, L. Weir, J. A. Chen, V. Z. Koblan, L. W. Yost, K. E. Mathey-Andrews, N. Russell, A. J. C. Stickels, R. R. Balderrama, K. S. Rideout, W. M. Chang, H. Y. Jacks, T. Chen, F. Weissman, J. S. Yosef, N. Yang, D. 2024-10-24 doi:10.1101/2024.10.21.619529 Cold Spring Harbor Laboratory Press 2024-10-24 <![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[ A Novel Cyanine-Based Fluorescent Dye for Targeted Mitochondrial Imaging in Neurotoxic Conditions and In Vivo Brain Studies ]]> https://biorxiv.org/content/10.1101/2024.10.24.619902v1?rss=1 Bi, L. Yan, X. Chen, X. Hou, S. Li, X. Ju, J. Shan, Z. 2024-10-26 doi:10.1101/2024.10.24.619902 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ The Oviposition Inhibitory Neuron is a potential hub of multi-circuit integration in the Drosophila brain ]]> https://biorxiv.org/content/10.1101/2024.10.25.620362v1?rss=1 Weber Langstaff, R. Srivastava, P. Kunin, A. Gutierrez, G. J. 2024-10-26 doi:10.1101/2024.10.25.620362 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Stoichiometry of HIV-1 Envelope Glycoprotein Protomers with Changes That Stabilize or Destabilize the Pretriggered Conformation ]]> https://biorxiv.org/content/10.1101/2024.10.25.620268v1?rss=1 Zhang, Z. Anang, S. Wang, Q. Nguyen, H. T. Chen, H.-C. Chiu, T.-J. Yang, D. Smith, A. B. Sodroski, J. G. 2024-10-27 doi:10.1101/2024.10.25.620268 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Tricked by Edge Cases: Can Current Approaches Lead to Accurate Prediction of T-Cell Specificity with Machine Learning? ]]> https://biorxiv.org/content/10.1101/2024.10.23.619492v1?rss=1 Culka, M. Orlova, D. 2024-10-28 doi:10.1101/2024.10.23.619492 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ A circuit model for transsaccadic space updating and mislocalization ]]> https://biorxiv.org/content/10.1101/2024.10.27.620527v1?rss=1 Wang, X. Tsien, S. Goldberg, M. E. Zhang, M. Qian, N. 2024-10-28 doi:10.1101/2024.10.27.620527 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Spatial Expression of Long Non-Coding RNAs in Human Brains of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.10.27.620550v1?rss=1 Ng, B. Avey, D. R. Lopes, K. d. P. Fujita, M. Tasaki, S. Vialle, R. A. Iatrou, A. Tissera, S. D. Chang, T.-H. Xu, J. Vyas, H. Kearns, N. A. Menon, V. Gaiteri, C. De Jager, P. L. Bennett, D. A. Wang, Y. 2024-10-28 doi:10.1101/2024.10.27.620550 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Tumor-specific antibodies elicited by engineered bacteria promote bladder cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2024.10.24.620122v1?rss=1 Rouanne, M. Chen, N. Mariuzza, D. L. Li, F. de los Santos-Alexis, K. Savage, T. M. Vincent, R. L. Mendelsohn, C. L. Danino, T. Arpaia, N. 2024-10-29 doi:10.1101/2024.10.24.620122 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Sensitivity to photoperiod is a complex trait in Camelina sativa ]]> https://biorxiv.org/content/10.1101/2024.10.25.620367v1?rss=1 Ramirez-Corona, B. Seagren, E. Sherman, C. Imaizumi, T. Queitsch, C. Cuperus, J. 2024-10-29 doi:10.1101/2024.10.25.620367 Cold Spring Harbor Laboratory Press 2024-10-29 <![CDATA[ Elongation of the nascent avian foregut requires coordination of intrinsic and extrinsic cell behaviors ]]> https://biorxiv.org/content/10.1101/2024.10.31.621372v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@374c2corg.highwire.dtl.DTLVardef@69ed3aorg.highwire.dtl.DTLVardef@55823aorg.highwire.dtl.DTLVardef@1d8d4fd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Powell, O. Garcia, E. Sriram, V. Qu, Y. Nerurkar, N. L. 2024-11-01 doi:10.1101/2024.10.31.621372 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment ]]> https://biorxiv.org/content/10.1101/2024.11.01.621152v1?rss=1 Tolman, N. Li, T. Balasubramanian, R. Li, G. Bupp-Chickering, V. Kelly, R. A. Simon, M. Peregrin, J. Montgomery, C. Stamer, W. D. Qian, J. John, S. W. M. 2024-11-01 doi:10.1101/2024.11.01.621152 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ HMGB1 mediates macrophage recruitment and regional intervertebral disc tissue functional and mechanical property changes following injury. ]]> https://biorxiv.org/content/10.1101/2024.10.30.621107v1?rss=1 Burt, K. G. Kim, M. K. M. Viola, D. C. Genualdi, J. R. Marciano, G. F. Chahine, N. O. 2024-11-03 doi:10.1101/2024.10.30.621107 Cold Spring Harbor Laboratory Press 2024-11-03 <![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[ A Multi-Modal Deep Learning Framework with Both Sequence and Structure for Tumor Antigens Prediction ]]> https://biorxiv.org/content/10.1101/2024.11.06.622193v1?rss=1 Jin, R. Ge, J. Zhang, G. Deng, Z. Hsieh, K. Hou, T. Zhou, R. 2024-11-08 doi:10.1101/2024.11.06.622193 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ SIMPL: Scalable and hassle-free optimization of neural representations from behaviour ]]> https://biorxiv.org/content/10.1101/2024.11.11.623030v1?rss=1 George, T. M. Glaser, P. Stachenfeld, K. Barry, C. Clopath, C. 2024-11-12 doi:10.1101/2024.11.11.623030 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Therapeutic benefits of maintaining CDK4/6 inhibitors and incorporating CDK2 inhibitors beyond progression in breast cancer ]]> https://biorxiv.org/content/10.1101/2024.11.11.623139v1?rss=1 Armand, J. Kim, S. Kim, K. Son, E. Kim, M. Yang, H. W. 2024-11-15 doi:10.1101/2024.11.11.623139 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Urban greenspace connectivity drive shifts in host assemblages and tick-borne pathogen infection ]]> https://biorxiv.org/content/10.1101/2024.11.12.623035v1?rss=1 VanAcker, M. C. Hofmeester, T. R. Zhang-Sun, J. Goethert, H. C. Diuk-Wasser, M. A. 2024-11-15 doi:10.1101/2024.11.12.623035 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ A Robust Computational Framework for the Optimization of CDK7 Inhibitors as Promising Cancer Therapy ]]> https://biorxiv.org/content/10.1101/2024.11.13.623385v1?rss=1 Shi, Z. Gao, X. Buratto, D. Zhou, R. 2024-11-15 doi:10.1101/2024.11.13.623385 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Impact of a Cancer-Associated Mutation on Poly(ADP-ribose) Polymerase1 Inhibition ]]> https://biorxiv.org/content/10.1101/2024.11.13.623412v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@4d4562org.highwire.dtl.DTLVardef@10643dborg.highwire.dtl.DTLVardef@511ae2org.highwire.dtl.DTLVardef@bc2403_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure.C_FLOATNO Impact of V762A mutation on inhibition of PARP1. C_FIG ]]> Shanmugam, N. Chatterjee, S. Cisneros, G. A. 2024-11-15 doi:10.1101/2024.11.13.623412 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ ATF4 regulates mitochondrial dysfunction, mitophagy, and autophagy, contributing to corneal endothelial apoptosis under chronic ER stress in Fuchs dystrophy ]]> https://biorxiv.org/content/10.1101/2024.11.14.623646v1?rss=1 Qureshi, S. Lee, S. Ritzer, L. Kim, S. Y. Steidl, W. Krest, G. J. Kasi, A. Kumar, V. 2024-11-15 doi:10.1101/2024.11.14.623646 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ AI-assisted imaging screening reveals mechano-molecular tissue organizers and network of signaling hubs. ]]> https://biorxiv.org/content/10.1101/2024.11.14.623670v1?rss=1 Bertocchi, C. Alegria, J. J. Vasquez-Sepulveda, S. Ibanez-Prat, R. Srinivasan, A. Arrano-Valenzuela, I. Castro-Pereira, B. Soto-Montandon, C. Trujillo-Espergel, A. Owen, G. I. Kanchanawong, P. Cerda, M. Motta, G. Zaidel-Bar, R. Ravasio, A. 2024-11-15 doi:10.1101/2024.11.14.623670 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Rarely categorical, always high-dimensional: how the neural code changes along the cortical hierarchy ]]> https://biorxiv.org/content/10.1101/2024.11.15.623878v1?rss=1 Posani, L. Wang, S. Muscinelli, S. Paninski, L. Fusi, S. 2024-11-17 doi:10.1101/2024.11.15.623878 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Topoisomerase 3A (TOP3A) Dependent Alternative Lengthening of Telomeres (ALT) ]]> https://biorxiv.org/content/10.1101/2024.11.18.624152v1?rss=1 KHANDAGALE, P. R. Sun, Y. Saha, S. Saha, L. K. Pommier, Y. R. 2024-11-19 doi:10.1101/2024.11.18.624152 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Humans and marmosets share similar face recognition signatures in shape-based visual face discrimination behavior ]]> https://biorxiv.org/content/10.1101/2024.11.19.624374v1?rss=1 Jeon, Y.-N. Cho, H. Y. Green, A. C. Issa, E. B. 2024-11-19 doi:10.1101/2024.11.19.624374 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Fisetin extends lifespan in a murine model of recessive dystrophic epidermolysis bullosa ]]> https://biorxiv.org/content/10.1101/2024.11.23.625023v1?rss=1 Miller, W. C. Strege, C. L. Popp, C. M. Tito, S. M. I. Eide, C. Ebens, C. L. Riddle, M. Lees, C. Seelig, D. Bui, K. Yousefzadeh, M. J. McGrath, J. Tolar, J. 2024-11-24 doi:10.1101/2024.11.23.625023 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ Molecular patterns of evolutionary changes throughout the whole nervous system of multiple nematode species ]]> https://biorxiv.org/content/10.1101/2024.11.23.624988v1?rss=1 Toker, I. A. Ripoll-Sanchez, L. Geiger, L. T. Saini, K. S. Beets, I. Vertes, P. E. Schafer, W. R. Ben-David, E. Hobert, O. 2024-11-25 doi:10.1101/2024.11.23.624988 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Cell-type specific responses to single-pulse electrical stimulation of the human brain ]]> https://biorxiv.org/content/10.1101/2024.11.24.625077v1?rss=1 Cowan, R. L. Davis, T. S. Merricks, E. M. Kundu, B. Shofty, B. Rahimpour, S. Schevon, C. A. Rolston, J. D. Smith, E. H. 2024-11-26 doi:10.1101/2024.11.24.625077 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ CD47 predominates over CD24 as a macrophage immune checkpoint in cancer. ]]> https://biorxiv.org/content/10.1101/2024.11.25.625185v1?rss=1 Allen, J. Meglan, A. Vaccaro, K. Velarde, J. Chen, V. Ribeiro, J. Blandin, J. Gupta, S. Mishra, R. Ho, R. Love, J. Reinhardt, F. Bell, G. W. Chen, J. Weinberg, R. Yang, D. Weissman, J. Weiskopf, K. 2024-11-26 doi:10.1101/2024.11.25.625185 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Cortical assembloids support the development of fast-spiking human PVALB+ cortical interneurons and uncover schizophrenia-associated defects ]]> https://biorxiv.org/content/10.1101/2024.11.26.624368v1?rss=1 Walsh, R. M. Crabtree, G. W. Kalpana, K. Jubierre, L. Koo, S. Y. Ciceri, G. Gogos, J. Kruglikov, I. Studer, L. 2024-11-26 doi:10.1101/2024.11.26.624368 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Impaired spatial coding and neuronal hyperactivity in the medial entorhinal cortex of APP NL-G-F mice ]]> https://biorxiv.org/content/10.1101/2024.11.26.624990v1?rss=1 Rodriguez, G. A. Rothenberg, E. F. Shetler, C. O. Aoun, A. Posani, L. Vajram, S. V. Tedesco, T. Fusi, S. Hussaini, S. A. 2024-11-26 doi:10.1101/2024.11.26.624990 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ How sturdy is your memory palace? Reliable room representations predict subsequent reinstatement of placed objects ]]> https://biorxiv.org/content/10.1101/2024.11.26.625465v1?rss=1 Masis-Obando, R. Norman, K. A. Baldassano, C. 2024-11-26 doi:10.1101/2024.11.26.625465 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Paired CRISPR screens to map gene regulation in cis and trans ]]> https://biorxiv.org/content/10.1101/2024.11.27.625752v1?rss=1 Xue, X. Gajic, Z. Z. Caragine, C. M. Legut, M. Walker, C. Kim, J. Y. S. Wang, X. Yan, R. E. Wessels, H.-H. Lu, C. Bapodra, N. Gürsoy, G. Sanjana, N. E. 2024-11-27 doi:10.1101/2024.11.27.625752 Cold Spring Harbor Laboratory Press 2024-11-27 <![CDATA[ Ecological Scaling of Temporal Fluctuations with Bacterial Abundance in Gut Microbiota Depends on Functional Properties of Individual Microbial Species and Bacterial Communities ]]> https://biorxiv.org/content/10.1101/2024.11.28.625948v1?rss=1 Su, P. Tchourine, K. Vitkup, D. 2024-11-29 doi:10.1101/2024.11.28.625948 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Circadian Activity Predicts Breeding Phenology in the Asian Burying Beetle Nicrophorus nepalensis ]]> https://biorxiv.org/content/10.1101/2024.11.30.626159v1?rss=1 Chen, H. Rubenstein, D. R. Mai, G.-S. Chang, C.-F. Shen, S.-F. 2024-12-01 doi:10.1101/2024.11.30.626159 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Gene mobility elements mediate cell type specific genome organization and radial gene movement in vivo ]]> https://biorxiv.org/content/10.1101/2024.11.30.626181v1?rss=1 Lucas, T. Wang, L.-I. Glass-Klaiber, J. Quiroz, E. Patra, S. Molotkova, N. Kohwi, M. 2024-12-01 doi:10.1101/2024.11.30.626181 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Internal states emerge early during learning of a perceptual decision-making task ]]> https://biorxiv.org/content/10.1101/2024.11.30.626182v1?rss=1 Cuturela, L. I. The International Brain Laboratory, Pillow, J. W. 2024-12-01 doi:10.1101/2024.11.30.626182 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Impact of Temporal Uncertainty on Sign-tracking Behavior ]]> https://biorxiv.org/content/10.1101/2024.11.30.626192v1?rss=1 Kaneko, R. Simpson, E. H. Balsam, P. D. 2024-12-01 doi:10.1101/2024.11.30.626192 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Integration of spatial multiplexed protein imaging and transcriptomics in the human kidney tracks the regenerative potential timeline of proximal tubules ]]> https://biorxiv.org/content/10.1101/2024.11.26.625544v1?rss=1 Asghari, M. Sabo, A. R. Barwinska, D. Melo Ferreira, R. Ferkowicz, M. Bowen, W. Cheng, Y. Gisch, D. Gulbronson, C. Phillips, C. L. Kelly, K. J. Sutton, T. A. Williams, J. Vazquez, M. O'Toole, J. Palevsky, P. Rosas, S. Waikar, S. S. Kiryluk, K. Parikh, C. Hodgins, J. Sarder, P. De Boer, I. Himmelfarb, J. Kretzler, M. Kidney Precision Medicine Project, Jain, S. Eadon, M. Winfree, S. El-Achkar, T. M. Dagher, P. C. 2024-12-02 doi:10.1101/2024.11.26.625544 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ PAG orchestrates T cell immune synapse function by binding to actin ]]> https://biorxiv.org/content/10.1101/2024.11.29.625440v1?rss=1 Moore, E. K. Strazza, M. Hu, X. Tymm, C. Paiola, M. Shannon, M. J. Xie, X. Bukhari, S.-S. Lerrer, S. Mace, E. M. Winchester, R. Mor, A. 2024-12-03 doi:10.1101/2024.11.29.625440 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ KP.2-based monovalent mRNA vaccines robustly boost antibody responses to SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2024.12.02.626472v1?rss=1 Wang, Q. Mellis, I. A. Wu, M. Bowen, A. Gherasim, C. Valdez, R. Shah, J. G. Purpura, L. J. Yin, M. T. Gordon, A. Guo, Y. Ho, D. D. 2024-12-03 doi:10.1101/2024.12.02.626472 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection ]]> https://biorxiv.org/content/10.1101/2024.11.29.624972v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Perugino, C. Liu, H. Feldman, J. Marbourg, J. Guy, T. Hui, A. Ingram, N. Liebaert, J. Chaudhary, N. Tao, W. Jacob-Dolan, C. Hauser, B. M. Mian, Z. Nathan, A. Zhao, Z. Kaseke, C. Tano-Menka, R. Getz, M. Senjobe, F. Berrios, C. Ofoman, O. Manickas-Hill, Z. Wesemann, D. Lemieux, J. Goldberg, M. B. Nundel, K. Moormann, A. M. Marshak-Rothstein, A. Larocque, R. Ryan, E. Iafrate, A. J. Lingwood, D. Gaiha, G. Charles, R. Balazs, A. B. Pandit, A. Naranbhai, V. Schmidt, A. Pillai, S. 2024-12-04 doi:10.1101/2024.11.29.624972 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Passage through micro-sprayer increases functional activity-implications for activity assays in time-resolved cryo-EM ]]> https://biorxiv.org/content/10.1101/2024.12.01.624867v1?rss=1 Garg, P. Feng, X. De, S. Frank, J. 2024-12-04 doi:10.1101/2024.12.01.624867 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases ]]> https://biorxiv.org/content/10.1101/2024.12.03.626531v1?rss=1 Petassi, M. Shin, Y. Jessop, A. Morse, K. Kim, S. Matei, R. Raina, V. Greene, E. 2024-12-04 doi:10.1101/2024.12.03.626531 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures ]]> https://biorxiv.org/content/10.1101/2024.12.03.626649v1?rss=1 Converse, A. Perry, M. J. Dipali, S. S. Isola, J. V. Kelley, E. B. Varberg, J. M. Zelinkski, M. B. Gerton, J. L. Stout, M. Pritchard, M. T. Duncan, F. 2024-12-04 doi:10.1101/2024.12.03.626649 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2024.12.03.626676v1?rss=1 Randolph, H. E. Aguirre-Gamboa, R. Brunet-Ratnasingham, E. Nakanishi, T. Locher, V. Ketter, E. Brandolino, C. Larochelle, C. Prat, A. Arbour, N. Dumaine, A. Finzi, A. Durand, M. Richards, J. B. Kaufmann, D. E. Barreiro, L. B. 2024-12-04 doi:10.1101/2024.12.03.626676 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Automated Cell Type Annotation with Reference Cluster Mapping ]]> https://biorxiv.org/content/10.1101/2024.11.30.626130v1?rss=1 Galanti, V. Shi, L. Azizi, E. Liu, Y. Blumberg, A. J. 2024-12-05 doi:10.1101/2024.11.30.626130 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Investigating the consequences of chronic short sleep for metabolism and survival of oxidative stress ]]> https://biorxiv.org/content/10.1101/2024.12.01.626207v1?rss=1 Tener, S. J. Kim, C. E. Lee, J. Oraedu, K. Gatto, J. A. Chang, T. Y. Lam, C. Schanta, R. Jankowski, M. S. Park, S. Hurley, J. M. Ulgherait, M. Canman, J. C. Ja, W. Collins, D. B. Shirasu-Hiza, M. 2024-12-05 doi:10.1101/2024.12.01.626207 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ CellSexID: Sex-Based Computational Tracking of Cellular Origins in Chimeric Models ]]> https://biorxiv.org/content/10.1101/2024.12.02.626449v1?rss=1 Tai, H. Li, Q. Wang, J. Tan, J. Lang, R. Petrof, B. J. Ding, J. 2024-12-05 doi:10.1101/2024.12.02.626449 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Voltage Gated Calcium Channel Dysregulation May Contribute to Neurological Symptoms in Calmodulinopathies ]]> https://biorxiv.org/content/10.1101/2024.12.02.626503v1?rss=1 Hussey, J. W. DeMarco, E. DiSilvestre, D. Brohus, M. Busuioc, A.-O. Iversen, E. D. Jensen, H. H. Nyegaard, M. Overgaard, M. T. Ben-Johny, M. Dick, I. E. 2024-12-05 doi:10.1101/2024.12.02.626503 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Optimizing a Human Monoclonal Antibody for Better Neutralization of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2024.12.04.626800v1?rss=1 Wang, Q. Guo, Y. Casner, R. G. Yu, J. Nair, M. S. Ho, J. Reddem, E. R. Tzang, C. C. Huang, Y. Shapiro, L. Liu, L. Ho, D. D. 2024-12-05 doi:10.1101/2024.12.04.626800 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Phantom epistasis through the lens of genealogies ]]> https://biorxiv.org/content/10.1101/2024.12.03.626630v1?rss=1 Ignatieva, A. Ferreira, L. A. F. 2024-12-07 doi:10.1101/2024.12.03.626630 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ A Reference Tissue Implementation of Simultaneous Multifactor Bayesian Analysis (SiMBA) of PET Time Activity Curve Data ]]> https://biorxiv.org/content/10.1101/2024.12.04.626559v1?rss=1 Matheson, G. J. Lundberg, J. Garde, M. Veldman, E. R. Tateno, A. Okubo, Y. Tiger, M. Ogden, R. T. 2024-12-07 doi:10.1101/2024.12.04.626559 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ The kinesin KIF3AC recycles endocytosed integrin to polarize adhesion formation towards the leading edge ]]> https://biorxiv.org/content/10.1101/2024.12.09.627580v1?rss=1 Rockenbach, J. A. Nader, G. P. Antoku, S. Gundersen, G. G. 2024-12-12 doi:10.1101/2024.12.09.627580 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Cervical transcutaneous vagus nerve stimulation enhances speech recognition in noise: A crossover, placebo-controlled study ]]> https://biorxiv.org/content/10.1101/2024.12.10.627804v1?rss=1 Jigo, M. Carmel, J. B. Wang, Q. Rodenkirch, C. 2024-12-16 doi:10.1101/2024.12.10.627804 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Adaptation shapes the representational geometry in mouse V1 to efficiently encode the environment ]]> https://biorxiv.org/content/10.1101/2024.12.11.628035v1?rss=1 Dipoppa, M. Nogueira, R. Bugeon, S. Friedman, Y. Reddy, C. B. Harris, K. D. Ringach, D. L. Miller, K. D. Carandini, M. Fusi, S. 2024-12-16 doi:10.1101/2024.12.11.628035 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Specificity, length, and luck: How genes are prioritized by rare and common variant association studies ]]> https://biorxiv.org/content/10.1101/2024.12.12.628073v1?rss=1 Spence, J. P. Mostafavi, H. Ota, M. Milind, N. Gjorgjieva, T. Smith, C. J. Simons, Y. B. Sella, G. Pritchard, J. K. 2024-12-16 doi:10.1101/2024.12.12.628073 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Eye movements organize excitability state, information coding and network connectivity in the human hippocampus ]]> https://biorxiv.org/content/10.1101/2024.12.12.628236v1?rss=1 Leszczynski, M. Espinal, E. Smith, E. Schevon, C. Sheth, S. Schroeder, C. E. 2024-12-16 doi:10.1101/2024.12.12.628236 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Fitness drivers of division of labor in vertebrates ]]> https://biorxiv.org/content/10.1101/2024.12.10.627807v1?rss=1 Garcia-Ruiz, I. Rubenstein, D. R. 2024-12-17 doi:10.1101/2024.12.10.627807 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence ]]> https://biorxiv.org/content/10.1101/2024.12.13.628425v1?rss=1 View larger version (112K): org.highwire.dtl.DTLVardef@5d2a9borg.highwire.dtl.DTLVardef@982c74org.highwire.dtl.DTLVardef@8e90b3org.highwire.dtl.DTLVardef@1bddf3c_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Livraghi, L. Hanly, J. J. Loh, L. S. Henry, A. Keck, C. M. T. Shirey, V. M. Tsai, C.-C. Yu, N. Van Belleghem, S. M. Roberts, W. M. Boggs, C. L. Martin, A. 2024-12-17 doi:10.1101/2024.12.13.628425 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Metformin inhibits nuclear egress of chromatin fragments in senescence and aging ]]> https://biorxiv.org/content/10.1101/2024.12.16.628669v1?rss=1 Kumazawa, T. Xu, Y. O'Brien, T. Lee, J.-W. Wang, Y. Cetinbas, M. Sadreyev, R. Bardeesy, N. Cheng, C.-W. He, B. Dou, Z. 2024-12-17 doi:10.1101/2024.12.16.628669 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance ]]> https://biorxiv.org/content/10.1101/2024.12.17.628992v1?rss=1 Gezelle, J. G. Korn, S. M. McDonald, J. T. Gong, Z. Erickson, A. Huang, C.-H. Yang, F. Cronin, M. Kuo, Y.-W. Wimberly, B. T. Steckelberg, A.-L. 2024-12-20 doi:10.1101/2024.12.17.628992 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Response of Serum-isolated Extracellular Vesicles to Focused Ultrasound Blood-Brain Barrier Opening ]]> https://biorxiv.org/content/10.1101/2024.12.17.629012v1?rss=1 Kline-Schoder, A. R. Tsitsos, F. N. Batts, A. J. DiBenedetto, M. R. Liu, K. Bae, S. Konofagou, E. E. 2024-12-20 doi:10.1101/2024.12.17.629012 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS ]]> https://biorxiv.org/content/10.1101/2024.12.19.629196v1?rss=1 Kiewisz, R. Fabig, G. Conway, W. Johnston, J. Kostyuchenko, V. Barinka, C. Clarke, O. B. Magaj, M. Yazdkhasti, H. Vallese, F. Lok, S.-m. Redemann, S. Muller-Reichert, T. Bepler, T. 2024-12-20 doi:10.1101/2024.12.19.629196 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Binding items to contexts through conjunctive neural representations with the Method of Loci ]]> https://biorxiv.org/content/10.1101/2024.12.19.629352v1?rss=1 Huang, J. Manglik, A. Dutra, N. Tarder-Stoll, H. Chamberlain, T. A. Ajemian, R. Zhang, Q. Norman, K. A. Baldassano, C. 2024-12-20 doi:10.1101/2024.12.19.629352 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria ]]> https://biorxiv.org/content/10.1101/2024.12.18.628924v1?rss=1 5%). Increases in the models interrupted feeding rate slowly increase the number of recombination events occurring from interrupted feeds. A comparison of drug-resistance management strategies with this new model shows that, over a 15-year timeframe, triple artemisinin-combination therapies (ACT) strategies show the largest reductions in treatment failures and the longest delays until artemisinin resistance reaches a critical 1% threshold. Multiple first-line therapies (MFT) are second best under these criteria, and ACT cycling approaches are third best. MFT strategies generate a greater diversity of recombinant genotypes but fewer recombination events generating MDR and slower emergence of these recombinant MDR genotypes. ]]> Tran, K. T. Nguyen, T. D. Weissman, D. B. Li, E. Z. Mok, S. Small-Saunders, J. L. Bousema, T. Zupko, R. J. Tran, T. N.-A. Boni, M. F. 2024-12-21 doi:10.1101/2024.12.18.628924 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model ]]> https://biorxiv.org/content/10.1101/2024.12.18.629251v1?rss=1 Morais, L. H. Stiles, L. Freeman, M. Oguienko, A. D. Hoang, J. D. Jones, J. Quan, B. Devine, J. Bois, J. S. Chou, T.-F. Trinh, J. Picard, M. Gradinaru, V. Mazmanian, S. K. 2024-12-21 doi:10.1101/2024.12.18.629251 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ An A-T Hoogsteen base pair in a naked DNA hairpin motif: A Protein-Recognized Conformation ]]> https://biorxiv.org/content/10.1101/2024.12.22.630000v1?rss=1 Guseva, S. Szekely, O. Geng, A. Smith, K. Pratihar, S. Gu, S. Al-Hashimi, H. M. 2024-12-23 doi:10.1101/2024.12.22.630000 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Gametocyte production and transmission fitness of African and Asian Plasmodium falciparum isolates with differential susceptibility to artemisinins ]]> https://biorxiv.org/content/10.1101/2024.12.23.630038v1?rss=1 Proellochs, N. I. Andolina, C. Ramjith, J. Stoter, R. van Gemert, G.-J. Graumans, W. Campino, S. Vanheer, L. N. Okitwi, M. Tumwebaze, P. K. Conrad, M. D. Clark, T. G. Fidock, D. A. Menard, D. Mok, S. Bousema, T. 2024-12-23 doi:10.1101/2024.12.23.630038 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression ]]> https://biorxiv.org/content/10.1101/2024.12.23.630085v1?rss=1 Gagoski, D. Rube, H. T. Rastogi, C. Melo, L. A. N. Li, X. Voleti, R. Shah, N. H. Bussemaker, H. J. 2024-12-23 doi:10.1101/2024.12.23.630085 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Patches: A Representation Learning framework for Decoding Shared and Condition-Specific Transcriptional Programs in Wound Healing ]]> https://biorxiv.org/content/10.1101/2024.12.23.630186v1?rss=1 Beker, O. Amador, D. Nima, J. P. Deursen, S. V. Woappi, Y. Dumitrascu, B. 2024-12-24 doi:10.1101/2024.12.23.630186 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Aggression experience and observation promote shared behavioral and neural changes ]]> https://biorxiv.org/content/10.1101/2024.12.26.630396v1?rss=1 Falkner, A. L. Iravedra Garcia, J. M. Guthman, E. M. Cuturela, L. I. Ocasio-Arce, E. J. Pillow, J. W. 2024-12-26 doi:10.1101/2024.12.26.630396 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ Exact linear theory of perturbation response in a space- and feature-dependent cortical circuitmodel ]]> https://biorxiv.org/content/10.1101/2024.12.27.630558v1?rss=1 Chau, H. Y. Miller, K. D. Palmigiano, A. 2024-12-28 doi:10.1101/2024.12.27.630558 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Convergent representations and spatiotemporal dynamics of speech and language in brain and deep neural networks ]]> https://biorxiv.org/content/10.1101/2024.12.28.630582v1?rss=1 Chen, P. Xiang, S. He, L. Chang, E. F. Li, Y. 2024-12-28 doi:10.1101/2024.12.28.630582 Cold Spring Harbor Laboratory Press 2024-12-28 <![CDATA[ Astrocyte-derived extracellular matrix proteins regulate synapse remodeling in stress-induced depression ]]> https://biorxiv.org/content/10.1101/2024.12.30.630684v1?rss=1 Zhang, R. Rodriguez-Rodriguez, P. Medrihan, L. Chang, J. C. Ferraro, T. Del Cioppo Vasques, P. McCabe, K. Wang, W. Menard, C. Cathomas, F. Chan, K. L. Parise, L. F. Shaham, S. Roussarie, J.-P. Troyanskaya, O. G. Russo, S. Milosevic, A. 2024-12-30 doi:10.1101/2024.12.30.630684 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ When do measured representational distances reflect the neural representational geometry? ]]> https://biorxiv.org/content/10.1101/2024.12.30.630743v1?rss=1 Bossio Botero, V. Kriegeskorte, N. 2024-12-30 doi:10.1101/2024.12.30.630743 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Transient glycan-shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques ]]> https://biorxiv.org/content/10.1101/2024.12.30.630768v1?rss=1 Morris, D. J. Gorman, J. Zhou, T. Lora, J. Connell, A. J. Li, H. Liu, W. Roark, R. S. Campion, M. S. Carey, J. W. Habib, R. Li, Y. Martella, C. L. Park, Y. Singh, A. Sowers, K. J. Teng, I.-T. Wang, S. Chohan, N. Ding, W. Lauer, C. Lewis, E. Mason, R. D. Rando, J. M. Peyton, L. Schramm, C. A. Wagh, K. Korber, B. Seaman, M. S. Douek, D. C. Haynes, B. F. Kulp, D. W. Roederer, M. Hahn, B. H. Kwong, P. D. Shaw, G. M. 2024-12-31 doi:10.1101/2024.12.30.630768 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax ]]> https://biorxiv.org/content/10.1101/2024.12.31.630814v1?rss=1 Villano, D. J. Prahlad, M. Singhal, A. Sanbonmatsu, K. Y. Landweber, L. F. 2025-01-02 doi:10.1101/2024.12.31.630814 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Structure of an LGR dimer - an evolutionary predecessor of glycoprotein hormone receptors ]]> https://biorxiv.org/content/10.1101/2024.12.31.630923v1?rss=1 Gong, Z. Chen, S. Fu, Z. Kloss, B. Wang, C. Clarke, O. B. Fan, Q. R. Hendrickson, W. A. 2025-01-02 doi:10.1101/2024.12.31.630923 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ The mechanosensory DEG/ENaC channel DEGT-1 is a proprioceptor of C. elegans foregut movement ]]> https://biorxiv.org/content/10.1101/2025.01.01.631014v1?rss=1 Bayer, E. A. Mango, S. E. Hobert, O. Schier, A. F. 2025-01-02 doi:10.1101/2025.01.01.631014 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Brain-Guided Convolutional Neural Networks Reveal Task-Specific Representations in Scene Processing ]]> https://biorxiv.org/content/10.1101/2025.01.02.631092v1?rss=1 Hansen, B. C. Greene, M. R. Lewinsohn, H. A. S. Kris, A. E. Smyth, S. Tang, B. 2025-01-02 doi:10.1101/2025.01.02.631092 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance ]]> https://biorxiv.org/content/10.1101/2025.01.02.631098v1?rss=1 Seto, M. Clifton, M. Gomez, M. L. Coughlan, G. Gifford, K. A. Jefferson, A. L. De Jager, P. Bennett, D. A. Wang, Y. Barnes, L. L. Schneider, J. A. Hohman, T. J. Buckley, R. F. Dumitrescu, L. 2025-01-02 doi:10.1101/2025.01.02.631098 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Recessive but damaging alleles of muscle-specific ribosomal protein gene RPL3L drive neonatal dilated cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2025.01.02.630345v1?rss=1 Murphy, M. R. Ganapathi, M. Lee, T. M. Fisher, J. M. Patel, M. V. Jayakar, P. Buchanan, A. Soni, R. K. Yin, Y. Yang, F. Reilly, M. P. Chung, W. K. Wu, X. 2025-01-03 doi:10.1101/2025.01.02.630345 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Antidepressants promote developmental-like plasticity through remodeling of extracellular matrix ]]> https://biorxiv.org/content/10.1101/2025.01.03.631260v1?rss=1 Nguyen, P. T. Tamura, S. Sun, E. Shi, Y. Xiao, Y. Lacefield, C. Turi, G. Hen, R. 2025-01-04 doi:10.1101/2025.01.03.631260 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Enhanced yield and subtype identity of hPSC-derived midbrain dopamine neuron by modulation of WNT and FGF18 signaling ]]> https://biorxiv.org/content/10.1101/2025.01.06.631400v1?rss=1 Kim, T. W. Piao, J. Bocchi, V. D. Koo, S. Y. Choi, S. J. Chaudhry, F. Yang, D. Cho, H. S. Hergenreder, E. Perera, L. R. Joshi, S. Mrad, Z. A. Claros, N. Donohue, S. A. Frank, A. K. Walsh, R. Mosharov, E. V. Betel, D. Tabar, V. Studer, L. 2025-01-06 doi:10.1101/2025.01.06.631400 Cold Spring Harbor Laboratory Press 2025-01-06 <![CDATA[ Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord ]]> https://biorxiv.org/content/10.1101/2025.01.10.632483v1?rss=1 Kandror, E. K. Wang, A. Carriere, M. Peterson, A. Liao, W. Tjarnberg, A. Fung, J. H. Mahbubani, K. T. Loper, J. Pangburn, W. Xu, Y. Saeb-Parsy, K. Rabadan, R. Maniatis, T. Rizvi, A. H. 2025-01-11 doi:10.1101/2025.01.10.632483 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ Ptpn14 Knockout Mice Reveal Critical Female-Specific Roles for the Hippo Pathway ]]> https://biorxiv.org/content/10.1101/2025.01.13.632464v1?rss=1 McCrea, E. M. Makrides, N. Tabata, T. Vogel, H. Howitt, B. Reineking, W. Vilches-Moure, J. G. Wang, M. Zhang, X. Attardi, L. D. 2025-01-13 doi:10.1101/2025.01.13.632464 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Percolation and lifestyle transition in microbial metabolism ]]> https://biorxiv.org/content/10.1101/2025.01.12.632617v1?rss=1 Supo-Escalante, R. Plata, G. Usmanova, D. R. Vitkup, D. 2025-01-15 doi:10.1101/2025.01.12.632617 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Integrated model of the protein molecular clock across mammalian species ]]> https://biorxiv.org/content/10.1101/2025.01.14.633008v1?rss=1 Saini, A. Usmanova, D. R. Vitkup, D. 2025-01-15 doi:10.1101/2025.01.14.633008 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Elevated SUN1 promotes aging-related polarity defects through mechanical coupling microtubules to the nuclear lamina ]]> https://biorxiv.org/content/10.1101/2025.01.15.633301v1?rss=1 Li, Y. Chen, M. Antoku, S. Ding, J. Huang, K. Gundersen, G. G. Chang, W. 2025-01-18 doi:10.1101/2025.01.15.633301 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[ Transient pH changes drive vacuole formation in enzyme-polymer condensates ]]> https://biorxiv.org/content/10.1101/2025.01.16.633379v1?rss=1 Modi, N. Nimiwal, R. Liao, J. Li, Y. Bishop, K. J. Obermeyer, A. C. 2025-01-21 doi:10.1101/2025.01.16.633379 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Characterization of Microbubble Cavitation in Theranostic Ultrasound-mediated Blood-Brain Barrier Opening and Gene Delivery ]]> https://biorxiv.org/content/10.1101/2025.01.17.633644v1?rss=1 Tsitsos, F. N. Batts, A. J. Jimenez, D. A. Li, C. Ji, R. Bae, S. Theodorou, A. Gorman, S. L. Konofagou, E. E. 2025-01-22 doi:10.1101/2025.01.17.633644 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Immune cell mitochondrial phenotypes are largely preserved in mitochondrial diseases and do not reflect disease severity ]]> https://biorxiv.org/content/10.1101/2025.01.18.633635v1?rss=1 G, n=23; single, large-scale mitochondrial DNA (mtDNA) deletions, n=14) and 68 healthy women and men from the MiSBIE study. ResultsWe first confirm and quantify robust cell type differences in mitochondrial content, activities of OxPhos complexes I, II, and IV, and the mitochondrial respiratory capacity (MRC) index. In relation to MitoD, neither mitochondrial content nor OxPhos capacity were consistently affected, other than a mild monocyte-specific reduction in complex I (partially mtDNA encoded) relative to complex II (entirely nDNA encoded), consistent with the mtDNA defects examined. Relative to the large differences in cell type-specific mitochondrial phenotypes, differences in MitoD relative to controls were generally small (<25%) across mitochondrial measures. The MitoD biomarkers GDF15 and FGF21, as well as clinical disease severity measures, were most strongly related to mitochondrial abnormalities in platelets, and most weakly related to mitochondrial OxPhos capacity in lymphocytes, which are known to eliminate mtDNA defects. Finally, comparing PBMCs collected in the morning/fasted state to the afternoon/fed state following a stressful experience, we report significant time-dependent changes in mitochondrial biology over the time scale of hours. ConclusionsOverall, these results demonstrate that the dynamic and cell-type specific mitochondrial phenotypes are preserved in mitochondrial diseases and are generally unrelated to the severity of MitoD symptoms. ]]> Liu, C. C. Kurade, M. Monzel, A. S. Kelly, C. Trumpff, C. Hirano, M. Picard, M. 2025-01-22 doi:10.1101/2025.01.18.633635 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Pyruvate and Related Energetic Metabolites Modulate Resilience Against High Genetic Risk for Glaucoma ]]> https://biorxiv.org/content/10.1101/2025.01.18.633745v1?rss=1 Li, K. Tolman, N. V. Segre, A. Stuart, K. Zeleznik, O. A. Vallabh, N. A. Hu, K. Zebardast, N. Hanyuda, A. Raita, Y. Montgomery, C. Zhang, C. Hysi, P. G. Do, R. Khawaja, A. Wiggs, J. Kang, J. John, S. Pasquale, L. 2025-01-22 doi:10.1101/2025.01.18.633745 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ DNA Methylation-Based Cell Type Deconvolution Reveals the Distinct Cell Composition in Brain Tumor Microenvironment ]]> https://biorxiv.org/content/10.1101/2025.01.19.633794v1?rss=1 Liu, F. Qian, J. Ma, C. 2025-01-22 doi:10.1101/2025.01.19.633794 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Family matters! The influence of family, peers, mentors, and professors on STEM college students motivational beliefs and career decision making ]]> https://biorxiv.org/content/10.1101/2025.01.22.633242v1?rss=1 Tuma, T. T. Rosenzweig, E. Q. Chen, X.-Y. Lemons, P. P. 2025-01-23 doi:10.1101/2025.01.22.633242 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Convergent flow-mediated mesenchymal force drives embryonic foregut constriction and splitting ]]> https://biorxiv.org/content/10.1101/2025.01.22.634318v1?rss=1 Yan, R. Hoffmann, L. A. Oikonomou, P. Li, D. Lee, C. Gill, H. K. Mongera, A. Nerurkar, N. Mahadevan, L. Tabin, C. J. 2025-01-23 doi:10.1101/2025.01.22.634318 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Maturation of Hippocampus-Medial Prefrontal Cortex Projections Defines a Pathway-Specific Sensitive Period for Cognitive Flexibility ]]> https://biorxiv.org/content/10.1101/2025.01.23.634573v1?rss=1 Cruz-Sanchez, A. Abdusalom, A. Chasiotis, H. Gugustea, R. Mumtaz, U. Hasantash, M. Anacker, C. Arruda-Carvalho, M. 2025-01-23 doi:10.1101/2025.01.23.634573 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Early Proteasome Gene Downregulation And Impaired Proteasomes Function Underlie Proteostasis Failure In Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.01.21.634128v1?rss=1 Myeku, N. Jiang, S. Srikanth, M. Sherpe, R. Yavari, S. Gaur, P. Collins, G. A. SONI, R. Menon, V. 2025-01-24 doi:10.1101/2025.01.21.634128 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Physiological analysis of the mechanism of Ci transcription factor activation through multiple Fused phosphorylation sites in Hedgehog signal transduction ]]> https://biorxiv.org/content/10.1101/2025.01.24.634727v1?rss=1 Kim, H. Little, J. Li, J. Patel, B. Kalderon, D. 2025-01-25 doi:10.1101/2025.01.24.634727 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ The geometry of the neural state space of decisions ]]> https://biorxiv.org/content/10.1101/2025.01.24.634806v1?rss=1 Monsalve-Mercado, M. M. Miller, K. D. 2025-01-25 doi:10.1101/2025.01.24.634806 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Symmetries and continuous attractors in disordered neural circuits ]]> https://biorxiv.org/content/10.1101/2025.01.26.634933v1?rss=1 Clark, D. G. Abbott, L. F. Sompolinsky, H. 2025-01-26 doi:10.1101/2025.01.26.634933 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[ HMG box-containing protein 1 (HBP1) prevents pancreatic injury in experimental pancreatitis but accelerates pancreatic neoplasia progression ]]> https://biorxiv.org/content/10.1101/2025.01.24.634817v1?rss=1 lee, S.-W. Ekstrom, T. Manalo, E. Ye, S. Berry, M. Grygoryev, D. Szczepaniak, M. Marmolejo, C. O. Haverlack, S. Lee, J. Shah, V. M. Keith, D. Muschler, J. L. Chin, K. Sears, R. C. Weisberg, S. P. Morgan, T. K. kim, j. 2025-01-27 doi:10.1101/2025.01.24.634817 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ NCBP2-AS2 is a mitochondrial microprotein, regulates energy metabolism and neurogenesis, and is downregulated in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.01.25.634884v1?rss=1 Popova, S. Bhattarai, P. Yilmaz, E. Lascu, D. Kuo, J.-H. Erdem, G. Coban, B. Michling, J. Cosacak, M. I. Tayran, H. Kurth, T. Schambony, A. Buchholz, F. Gentzel, M. Kizil, C. 2025-01-27 doi:10.1101/2025.01.25.634884 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Resident Tissue Macrophages Govern Intraocular Pressure Homeostasis ]]> https://biorxiv.org/content/10.1101/2025.01.25.634888v1?rss=1 Liu, K. C. Grimsrud, A. O. Suarez, M. F. Schuman, D. De Ieso, M. L. Kuhn, M. Kelly, R. A. Mathew, R. Kalnitsky, J. Mack, M. Ginhoux, F. Bupp-Chickering, V. Balasubramanian, R. John, S. W. M. Stamer, W. D. Saban, D. R. 2025-01-27 doi:10.1101/2025.01.25.634888 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[ Axonal pathology differentially affects human Purkinje cell subtypes in the essential tremor cerebellum ]]> https://biorxiv.org/content/10.1101/2025.01.26.633063v1?rss=1 Widner, J. Faust, P. L. Louis, E. D. Fujita, H. 2025-01-28 doi:10.1101/2025.01.26.633063 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Single-Cell Multimodal Profiling Reveals a Novel CD26+ Fibroblast Subpopulation in Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.01.27.635067v1?rss=1 Bashore, A. C. Coronel, J. Xue, C. Zhu, L. Y. Reilly, M. 2025-01-28 doi:10.1101/2025.01.27.635067 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Distinctive associations between plasma p-tau181 levels and hippocampal subfield volume across the Alzheimer's disease continuum ]]> https://biorxiv.org/content/10.1101/2025.01.27.635113v1?rss=1 Rich, A. Oh, H. 2025-01-28 doi:10.1101/2025.01.27.635113 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Roles Played by Enhancer of Split Transcription Factors in Drosophila R7 Photoreceptor Specification ]]> https://biorxiv.org/content/10.1101/2025.01.30.635716v1?rss=1 Arias, R. A. Mavromatakis, Y. E. Tomlinson, A. 2025-01-30 doi:10.1101/2025.01.30.635716 Cold Spring Harbor Laboratory Press 2025-01-30 <![CDATA[ Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions ]]> https://biorxiv.org/content/10.1101/2025.01.28.635258v1?rss=1 Noel, R. L. Kugelman, T. Karakatsani, M. E. Shahriar, S. Willner, M. J. Choi, C. S. Nimi, Y. Ji, R. Agalliu, D. Konofagou, E. E. 2025-01-31 doi:10.1101/2025.01.28.635258 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Blood mitochondrial health markers cf-mtDNA and GDF15 in human aging ]]> https://biorxiv.org/content/10.1101/2025.01.28.635306v1?rss=1 Trumpff, C. Huang, Q. Michelson, J. Liu, C. C. Shire, D. Habeck, C. G. Stern, Y. Picard, M. 2025-01-31 doi:10.1101/2025.01.28.635306 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Impact of sucrose sinks on phloem transport ]]> https://biorxiv.org/content/10.1101/2025.01.28.635320v1?rss=1 Nakad, M. Weng, E. Gentine, P. 2025-01-31 doi:10.1101/2025.01.28.635320 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids ]]> https://biorxiv.org/content/10.1101/2025.01.30.635158v1?rss=1 Robles, N. V. Moran, B. M. Rodriguez Barrera, M. J. Jofre, G. I. Gunn, T. Iverson, E. N. K. Beskid, S. Baczenas, J. Sedghifar, A. Andolfatto, P. Brandvain, Y. Havird, J. C. Rosenthal, G. G. Schumer, M. 2025-01-31 doi:10.1101/2025.01.30.635158 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Parallel hierarchical encoding of linguistic representations in the human auditory cortex and recurrent automatic speech recognition systems ]]> https://biorxiv.org/content/10.1101/2025.01.30.635775v1?rss=1 Keshishian, M. Mischler, G. Thomas, S. Kingsbury, B. Bickel, S. Mehta, A. D. Mesgarani, N. 2025-02-01 doi:10.1101/2025.01.30.635775 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion. ]]> https://biorxiv.org/content/10.1101/2025.01.31.633084v1?rss=1 Zhu, Y. LI, A. Maji, S. Lee, B. J. Korn, S. M. Gertie, J. A. Dorrity, T. J. Wang, J. Wang, K. J. Pelletier, A. Moakley, D. F. Kelly, R. D. Holmes, A. B. Rabadan, R. Edgell, D. R. Schild-Poulter, C. Modesti, M. Steckelberg, A.-L. Hendrickson, E. A. Chung, H. Zhang, C. Zha, S. 2025-02-01 doi:10.1101/2025.01.31.633084 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ FETCH enables fluorescent labeling of membrane proteins in vivo with spatiotemporal control in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.01.31.635819v1?rss=1 Rostam, K. D. Morano, N. C. Menon, K. P. Lopez, D. H. Shapiro, L. Zinn, K. Feng, S. Mann, R. S. 2025-02-01 doi:10.1101/2025.01.31.635819 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and -independent mitophagy ]]> https://biorxiv.org/content/10.1101/2025.01.31.635900v1?rss=1 Levi-DAncona, E. Walker, E. M. Zhu, J. Deng, Y. Sidarala, V. Stendahl, A. M. Reck, E. C. Henry-Kanarek, B. A. Lietzke, A. C. Pasmooij, M. B. Hubers, D. L. Basrur, V. Ghosh, S. Stiles, L. Nesvizhskii, A. I. Shirihai, O. S. Soleimanpour, S. A. 2025-02-01 doi:10.1101/2025.01.31.635900 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Mapping the GDF15 Arm of the Integrated Stress Response in Human Cells and Tissues ]]> https://biorxiv.org/content/10.1101/2025.01.31.635929v1?rss=1 Smith, J. L. M. Tanner, K. Devine, J. Monzel, A. S. Cohen, A. A. Picard, M. 2025-02-01 doi:10.1101/2025.01.31.635929 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ The distribution of highly deleterious variants across human ancestry groups ]]> https://biorxiv.org/content/10.1101/2025.01.31.635988v1?rss=1 Stolyarova, A. Coop, G. Przeworski, M. 2025-02-01 doi:10.1101/2025.01.31.635988 Cold Spring Harbor Laboratory Press 2025-02-01 <![CDATA[ Novel Pipelines to Extract Differences in Proteome Dynamics Based on Health Status ]]> https://biorxiv.org/content/10.1101/2025.02.01.636015v1?rss=1 Xu, B. Zhao, J. Huang, T. Honfo, S. H. Trumpff, C. Picard, M. Cohen, A. Liu, M. 2025-02-04 doi:10.1101/2025.02.01.636015 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity ]]> https://biorxiv.org/content/10.1101/2025.02.03.635951v1?rss=1 Monzel, A. S. Devine, J. Kapri, D. Enriquez, J. A. Trumpff, C. Picard, M. 2025-02-04 doi:10.1101/2025.02.03.635951 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ APOE4 exacerbates glucocorticoid stress hormone-induced tau pathology via mitochondrial dysfunction ]]> https://biorxiv.org/content/10.1101/2025.02.03.636364v1?rss=1 Yu, Q. Du, F. Goodman, J. Waites, C. 2025-02-05 doi:10.1101/2025.02.03.636364 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Genetic basis of partner choice ]]> https://biorxiv.org/content/10.1101/2025.02.03.636375v1?rss=1 Zheng, Q. van Alten, S. Lyngstad, T. H. Ciscato, E. Sun, Z. Miao, J. Wu, Y. Dorn, S. Zheng, B. Havdahl, A. Corfield, E. C. Nivard, M. Galama, T. J. Turley, P. Chiappori, P.-A. Fletcher, J. M. Lu, Q. 2025-02-05 doi:10.1101/2025.02.03.636375 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ Fatty Acid Transport Protein-2 (FATP2) Inhibition Enhances Glucose Tolerance through α-Cell-mediated GLP-1 Secretion ]]> https://biorxiv.org/content/10.1101/2025.01.31.635976v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@190c799org.highwire.dtl.DTLVardef@203076org.highwire.dtl.DTLVardef@14dbf26org.highwire.dtl.DTLVardef@140869e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khan, S. Gaivin, R. J. Liu, Z. Li, V. Samuels, I. Son, J. Osei-Owusu, P. Garvin, J. L. Accili, D. Schelling, J. R. 2025-02-06 doi:10.1101/2025.01.31.635976 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Transcriptional control of T cell tissue adaptation and effector function in infants and adults ]]> https://biorxiv.org/content/10.1101/2025.02.01.636039v1?rss=1 Szabo, P. A. Levitin, H. M. Connors, T. J. Chen, D. Jin, J. Thapa, P. Guyer, R. Caron, D. P. Gray, J. I. Matsumoto, R. Kubota, M. Brusko, M. Brusko, T. M. Farber, D. L. Sims, P. A. 2025-02-06 doi:10.1101/2025.02.01.636039 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Discovering Symbolic Cognitive Models from Human and Animal Behavior ]]> https://biorxiv.org/content/10.1101/2025.02.05.636732v1?rss=1 Castro, P. S. Tomasev, N. Anand, A. Sharma, N. Mohanta, R. Dev, A. Perlin, K. Jain, S. Levin, K. Elteto, N. Dabney, W. Novikov, A. Turner, G. C. Eckstein, M. K. Daw, N. D. Miller, K. J. Stachenfeld, K. L. 2025-02-06 doi:10.1101/2025.02.05.636732 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ EpiFoundation: A Foundation Model for Single-Cell ATAC-seq via Peak-to-Gene Alignment ]]> https://biorxiv.org/content/10.1101/2025.02.05.636688v1?rss=1 Wu, J. Wan, C. Ji, Z. Zhou, Y. Hou, W. 2025-02-08 doi:10.1101/2025.02.05.636688 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ MethylProphet: A Generalized Gene-Contextual Model for Inferring Whole-Genome DNA Methylation Landscape ]]> https://biorxiv.org/content/10.1101/2025.02.05.636730v1?rss=1 Huang, X. Liu, Q. Zhao, Y. Tang, X. Zhou, Y. Hou, W. 2025-02-08 doi:10.1101/2025.02.05.636730 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models ]]> https://biorxiv.org/content/10.1101/2025.02.06.636901v1?rss=1 Adams, E. Bai, L. Lee, M. Yu, Y. AlQuraishi, M. 2025-02-08 doi:10.1101/2025.02.06.636901 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Niche-driven phenotypic plasticity and cis-regulatory dynamics of a revised model for intestinal secretory differentiation ]]> https://biorxiv.org/content/10.1101/2025.02.07.636917v1?rss=1 Bhattacharya, S. Tei, G. Singh, P. N. P. Malagola, E. Eskiocak, O. He, R. Kraiczy, J. Gu, W. Perlov, Y. Beyaz, S. WANG, T. C. Zhou, Q. Shivdasani, R. A. 2025-02-08 doi:10.1101/2025.02.07.636917 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy ]]> https://biorxiv.org/content/10.1101/2025.02.09.636592v1?rss=1 Drago, D. Giri, S. Chattaerjee, R. Simoni Nieves, A. Abedrabbo, M. Genna, A. Uribe Rios, M. L. Lindzen, M. Sekar, A. Gupta, N. Aharoni, N. Bhandari, T. Mayalagu, A. Schwarzmuller, L. Tarade, N. Zhu, R. Mohan-Raju, H.-R. Karatekin, F. Roncato, F. Eyal-Lubling, Y. Keidar, T. Nof, Y. Belugali Nataraj, N. Bernshtein, K. S. Wagner, B. Ulhas Nair, N. Sanghvi, N. Alon, R. Seger, R. Pikarsky, E. Donzelli, S. Blandino, G. Wiemann, S. Lev, S. Prywes, R. Barkan, D. Rueda, O. Caldas, C. Ruppin, E. Shiloh, Y. Dahlhoff, M. Yarden, Y. 2025-02-10 doi:10.1101/2025.02.09.636592 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Learning decouples accuracy and reaction time for rapid decisions in a transitive inference task ]]> https://biorxiv.org/content/10.1101/2025.02.11.636952v1?rss=1 Silva, F. A. M. Jensen, G. Shinn, M. Murray, J. Terrace, H. Ferrera, V. P. 2025-02-12 doi:10.1101/2025.02.11.636952 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.02.11.637559v1?rss=1 Miller, J. A. Travaglini, K. J. Luquez, T. Hostetler, R. E. Oster, A. Daniel, S. Tasic, B. Menon, V. 2025-02-12 doi:10.1101/2025.02.11.637559 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.02.11.637768v1?rss=1 20 {micro}m) are irregularly and randomly organized, while neuron pairs that are extremely close (< 20 {micro}m) have strongly correlated orientation tuning, indicating a narrow yet strong spatially clustered organization of orientation preference, which we term micro-clustered organization. Exploring a circuit-based model of recurrently coupled mouse V1 we derived two key predictions for the micro-cluster: spatially localized recurrent connections over a comparable narrow spatial scale, and common relative spatial spreads of balanced excitation and inhibition in the network over broad spatial scales. These predictions are validated by both anatomical and optogenetic-based physiological circuit mapping experiments. Altogether, our work takes an important step in building a circuit-based theory of visual processing in mouse V1 over spatial scales that are often ignored, yet contain powerful synaptic interactions. ]]> Yu, P. Yang, Y. Gozel, O. Oldenburg, I. Dipoppa, M. Rossi, F. Miller, K. Adesnik, H. Ji, N. Doiron, B. 2025-02-13 doi:10.1101/2025.02.11.637768 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ SA55 broadly neutralizes SARS-CoV-2 and robustly prevents viral escape by JN.1 sublineages ]]> https://biorxiv.org/content/10.1101/2025.02.12.638008v1?rss=1 Shi, L. Bowen, A. Han, J. Zheng, X. Luo, H. Yao, T. Guo, M. Yu, Y. Jian, F. Cao, Y. R. ke, l. Guo, Y. Liu, L. 2025-02-14 doi:10.1101/2025.02.12.638008 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ MYRF is Essential in Mesothelial Cells to Promote Lung Development and Maturation ]]> https://biorxiv.org/content/10.1101/2025.02.13.635155v1?rss=1 Luna, G. Verheyden, J. Tan, C. Kim, E. Hwa, M. Sahi, J. Shen, Y. Chung, W. McCulley, D. Sun, X. 2025-02-14 doi:10.1101/2025.02.13.635155 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ A vector-based strategy for olfactory navigation in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.02.15.638426v1?rss=1 Siliciano, A. F. Minni, S. Morton, C. Dowell, C. K. Eghbali, N. B. Rhee, J. Y. Abbott, L. F. Ruta, V. 2025-02-16 doi:10.1101/2025.02.15.638426 Cold Spring Harbor Laboratory Press 2025-02-16 <![CDATA[ Improved Graph-based Antibody-aware Epitope Prediction with Protein Language Model-based Embeddings ]]> https://biorxiv.org/content/10.1101/2025.02.12.637989v1?rss=1 Ahmed, M. Ali, S. Jan, A. Khan, I. U. Patterson, M. 2025-02-17 doi:10.1101/2025.02.12.637989 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ On inputs to deep learning for RNA 3D structure prediction ]]> https://biorxiv.org/content/10.1101/2025.02.14.638364v1?rss=1 Szikszai, M. Magnus, M. Kadyan, S. Rivas, E. 2025-02-17 doi:10.1101/2025.02.14.638364 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ SUGP1 loss is the sole driver of SF3B1 hotspot mutant missplicing in cancer ]]> https://biorxiv.org/content/10.1101/2025.02.17.638713v1?rss=1 Xing, P. Bak-Gordon, P. Xie, J. Zhang, J. Liu, Z. Manley, J. L. 2025-02-17 doi:10.1101/2025.02.17.638713 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ SUMO2 Promotes Histone Pre-mRNA Processing by Stabilizing Histone Locus Body Interactions and Facilitating U7 snRNP Assembly ]]> https://biorxiv.org/content/10.1101/2025.02.15.638447v1?rss=1 He, S. Lyu, P. Skinner, M. W. Desotell, A. Foley, B. McCaig, C. M. Wang, W. Qian, J. Tong, L. Marzluff, W. F. Matunis, M. J. 2025-02-18 doi:10.1101/2025.02.15.638447 Cold Spring Harbor Laboratory Press 2025-02-18 <![CDATA[ The forkhead transcription factor FKH-7/FOXP acts in chemosensory neurons to regulate developmental decision-making ]]> https://biorxiv.org/content/10.1101/2025.02.17.638733v1?rss=1 Chai, C. M. Taylor, S. R. Tischbirek, C. H. Wong, W.-R. Cai, L. Miller, D. M. Sternberg, P. W. 2025-02-21 doi:10.1101/2025.02.17.638733 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network ]]> https://biorxiv.org/content/10.1101/2025.02.18.638828v1?rss=1 Fadini, A. Li, M. McCoy, A. J. Terwilliger, T. C. Read, R. J. Hekstra, D. R. AlQuraishi, M. 2025-02-21 doi:10.1101/2025.02.18.638828 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Genome modeling and design across all domains of life with Evo 2 ]]> https://biorxiv.org/content/10.1101/2025.02.18.638918v1?rss=1 Brixi, G. Durrant, M. G. Ku, J. Poli, M. Brockman, G. Chang, D. Gonzalez, G. A. King, S. H. Li, D. B. Merchant, A. T. Naghipourfar, M. Nguyen, E. Ricci-Tam, C. Romero, D. W. Sun, G. Taghibakshi, A. Vorontsov, A. Yang, B. Deng, M. Gorton, L. Nguyen, N. Wang, N. K. Adams, E. Baccus, S. A. Dillmann, S. Ermon, S. Guo, D. Ilango, R. Janik, K. Lu, A. X. Mehta, R. Mofrad, M. R. K. Ng, M. Y. Pannu, J. Re, C. Schmok, J. C. St. John, J. Sullivan, J. Zhu, K. Zynda, G. Balsam, D. Collison, P. Costa, A. B. Hernandez-Boussard, T. Ho, E. Liu, M.-Y. McGrath, T. P 2025-02-21 doi:10.1101/2025.02.18.638918 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads ]]> https://biorxiv.org/content/10.1101/2025.02.15.638440v1?rss=1 Al-Abri, R. Gursoy, G. 2025-02-23 doi:10.1101/2025.02.15.638440 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ PRDM16 controls smooth muscle cell fate in atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.02.19.639186v1?rss=1 Tan, J. Cheng, L. Calhoun, R. P. Weller, A. Drareni, K. Fong, S. Barbara, E. Lim, H. W. Xue, C. Winter, H. Auguste, G. Miller, C. L. Reilly, M. Maegdefessel, L. Lutgens, E. Seale, P. 2025-02-23 doi:10.1101/2025.02.19.639186 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ An updated catalogue of split-GAL4 driver lines for descending neurons in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2025.02.22.639679v1?rss=1 Zung, J. L. Namiki, S. Meissner, G. W. Costa, M. Eichler, K. Stürner, T. Jefferis, G. S. X. E. Managan, C. FlyLight Project Team, Korff, W. Card, G. M. 2025-02-24 doi:10.1101/2025.02.22.639679 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Multi-omic subtypes of Alzheimer's dementia are differentially associated with psychological traits ]]> https://biorxiv.org/content/10.1101/2025.02.21.639584v1?rss=1 Zammit, A. R. Yu, L. Poole, V. N. Arfanakis, K. Schneider, J. A. Petyuk, V. A. De Jager, P. Kaddurah-Daouk, R. Iturria-Medina, Y. Bennett, D. A. 2025-02-26 doi:10.1101/2025.02.21.639584 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health ]]> https://biorxiv.org/content/10.1101/2025.02.24.639850v1?rss=1 Shafiei, G. Esper, N. B. Hoffmann, M. S. Ai, L. Chen, A. A. Cluce, J. Covitz, S. Giavasis, S. Lane, C. Mehta, K. Moore, T. M. Salo, T. Tapera, T. M. Calkins, M. E. Colcombe, S. Davatzikos, C. Gur, R. E. Gur, R. C. Pan, P. M. Jackowski, A. P. Rokem, A. Rohde, L. A. Shinohara, R. T. Tottenham, N. Zuo, X.-N. Cieslak, M. Franco, A. R. Kiar, G. Salum, G. A. Milham, M. P. Satterthwaite, T. D. 2025-02-26 doi:10.1101/2025.02.24.639850 Cold Spring Harbor Laboratory Press 2025-02-26 <![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[ Derivation and analysis of human somatic sensory neuron subtypes facilitated through fluorescent hPSC reporters ]]> https://biorxiv.org/content/10.1101/2025.02.25.640131v1?rss=1 Malka-Gibor, E. Oliver, K. M. Chen, S. Garcia-Diaz, A. Williams, D. Corneo, B. de Nooij, J. C. 2025-02-26 doi:10.1101/2025.02.25.640131 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ A skeletal muscle-sympathetic nerve-intestine network underlies muscle inflammation and atrophy induced by immobilization ]]> https://biorxiv.org/content/10.1101/2025.02.25.640219v1?rss=1 Hirata, Y. Nomura, K. Hozumi, K. Sugawara, K. Hosokawa, Y. Uchiyama, K. Inoue, T. Nishigaki, T. Liyuan, A. Niikura, T. Fukui, T. Oe, K. Kuroda, R. Hamakita, S. Kumagai, S. Hirata, J. Karsenty, G. Ohbayashi, K. Yada, T. Iwasaki, Y. Ogawa, W. 2025-03-01 doi:10.1101/2025.02.25.640219 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants ]]> https://biorxiv.org/content/10.1101/2025.02.26.640373v1?rss=1 van Vlimmeren, A. E. Tang, L. C. Jiang, Z. Iyer, A. Voleti, R. Krismer, K. Gaublomme, J. T. Jovanovic, M. Shah, N. H. 2025-03-01 doi:10.1101/2025.02.26.640373 Cold Spring Harbor Laboratory Press 2025-03-01 <![CDATA[ Dynamically rich states in balanced networks induced by single-neuron dynamics ]]> https://biorxiv.org/content/10.1101/2025.02.28.640576v1?rss=1 Drangmeister, M. Engelken, R. Schleimer, J.-H. Schreiber, S. 2025-03-02 doi:10.1101/2025.02.28.640576 Cold Spring Harbor Laboratory Press 2025-03-02 <![CDATA[ Portable transcranial therapeutic ultrasound enhances targeted gene delivery for Parkinson's disease: from rodent models to non-human primates ]]> https://biorxiv.org/content/10.1101/2025.03.02.639893v1?rss=1 Batts, A. J. Ji, R. Bae, S. Tsitsos, F. N. Jimenez-Gambin, S. Kwon, N. Gorman, S. L. Tsakri, D. Noel, R. L. Bendig, J. Jimenez, D. A. DiBenedetto, M. Del Castillo, S. A. Keleta, F. B. Caicedo, J. Romanov, A. Curley, C. T. Dzhashiashvili, Y. Walton-Gibbs, G. D. Hollidge, B. S. Przedborski, S. Ramsburg, E. Danos, O. Ferrera, V. P. Engel, E. A. Smith, J. B. Konofagou, E. E. 2025-03-03 doi:10.1101/2025.03.02.639893 Cold Spring Harbor Laboratory Press 2025-03-03 <![CDATA[ Biopsychosocial Correlates of Resting and Stress-Reactive Salivary GDF15: Preliminary Findings ]]> https://biorxiv.org/content/10.1101/2025.02.27.640377v1?rss=1 Liu, C. C. Trumpff, C. Huang, Q. Juster, R.-P. Picard, M. 2025-03-04 doi:10.1101/2025.02.27.640377 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Decoding neuronal wiring by joint inference of cell identity and synaptic connectivity ]]> https://biorxiv.org/content/10.1101/2025.03.04.640006v1?rss=1 Gupta, H. P. Azevedo, A. Chen, Y.-C. D. Xing, K. Sims, P. A. Varol, E. Mann, R. 2025-03-04 doi:10.1101/2025.03.04.640006 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.02.28.640922v1?rss=1 Jimenez-Sanchez, A. Persad, S. Hayashi, A. Umeda, S. Sharma, R. Xie, Y. Mehta, A. Park, W. Masilionis, I. Chu, T. Zhu, F. Hong, J. Chaligne, R. O'Reilly, E. M. Mazutis, L. Nawy, T. Pe'er, I. Iacobuzio-Donahue, C. A. Pe'er, D. 2025-03-06 doi:10.1101/2025.02.28.640922 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Assigning Targetable Molecular Pathways to Transdiagnostic Subgroups Across Autism and Related Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.04.641443v1?rss=1 Ellegood, J. Beauchamp, A. Yee, Y. Devenyi, G. Ziolkowski, J. Qiu, L. Askalan, R. Ayub, M. Suetterlin, P. Donovan, A. Basson, M. A. Quesnel, K. M. Berube, N. G. Woo, T. Beversdorf, D. Bjornsson, H. Blakely, R. Crawley, J. Crosbie, J. Orr, B. O. Davis, G. W. Genestine, M. DiCicco-Bloom, E. Egan, S. Fink, K. D. Asbury, S. Lai, J. Rilett, K. Foster, J. A. Vincent, J. B. Frankland, P. Georgiades, S. Penagarikano, O. Geschwind, D. Giger, R. J. Markx, S. Gogos, J. Golzio, C. Pagani, M. Gozzi, A. Pacey, L. K. Hampson, D. Huang, T.-N. Yen, T.-L. Hsueh, Y.-P. 2025-03-10 doi:10.1101/2025.03.04.641443 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Independent Continuous Tracking of Multiple Agents in the Human Hippocampus ]]> https://biorxiv.org/content/10.1101/2025.03.06.641914v1?rss=1 Chericoni, A. Fine, J. M. Chavez, A. G. Franch, M. Mickiewicz, E. Mathura, R. Adkinson, J. Bartoli, E. Jacobs, J. Provenza, N. Watrous, A. Yoo, S. B. M. Sheth, S. Hayden, B. Y. 2025-03-10 doi:10.1101/2025.03.06.641914 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ A chemical screen identifies p38 MAPK inhibition as a candidate neuroprotective strategy for combinatorial SMA therapy ]]> https://biorxiv.org/content/10.1101/2025.03.06.641938v1?rss=1 Carlini, M. J. Espinoza-Derout, J. Van Alstyne, M. Tisdale, S. Workman, E. Triplett, M. Tattoli, I. Yadav, S. Henderson, C. Watterson, M. D. Pellizzoni, L. 2025-03-10 doi:10.1101/2025.03.06.641938 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Two-timepoint assays of neural responses increase the sensitivity and specificity of single-cell whole-brain activity screens ]]> https://biorxiv.org/content/10.1101/2025.03.07.641687v1?rss=1 Ramirez, A. Rogerson, L. Kyzar, E. J. Berland, C. Rodriguez, E. Guerrero, J. Hammond, L. Ferrante, A. W. Salzman, C. D. 2025-03-10 doi:10.1101/2025.03.07.641687 Cold Spring Harbor Laboratory Press 2025-03-10 <![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[ Alpha modulation of spiking activity across multiple brain regions in mice performing a tactile selective detection task ]]> https://biorxiv.org/content/10.1101/2025.03.07.642074v1?rss=1 Kelley, C. Slater, C. Sorrentino, M. Noone, D. Hung, J. Sajda, P. Wang, Q. 2025-03-10 doi:10.1101/2025.03.07.642074 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ High throughput identification of genetic regulators of microglial inflammatory processes in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.03.09.642133v1?rss=1 Cardona, C. L. Wei, L. Kim, J. Angeles, E. Singh, G. Chen, S. Ifediora, N. Canoll, P. Teich, A. F. Hargus, G. Chavez, A. Sproul, A. A. 2025-03-11 doi:10.1101/2025.03.09.642133 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Direct cerebellar control over motor production in a species with extreme cerebellar enlargement ]]> https://biorxiv.org/content/10.1101/2025.03.10.642493v1?rss=1 Pedraja, F. Genecin, M. Noone, D. Biderman, D. Cho, P. Ehrlich, D. E. Sawtell, N. B. 2025-03-11 doi:10.1101/2025.03.10.642493 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Deciphering Ibogaines Matrix Pharmacology: Multiple Transporter Modulation at Serotonin Synapses ]]> https://biorxiv.org/content/10.1101/2025.03.04.641351v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@a1cacaorg.highwire.dtl.DTLVardef@8be27org.highwire.dtl.DTLVardef@1fc320forg.highwire.dtl.DTLVardef@3a8837_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hwu, C. Havel, V. Westergaard, X. Mendieta, A. M. Serrano, I. C. Hwu, J. Walther, D. Lankri, D. Selinger, T. L. He, K. Liu, R. Shern, T. P. Sun, S. Ma, B. Gonzalez, B. Goodman, H. J. Sonders, M. S. Baumann, M. H. Carrera, I. Sulzer, D. Sames, D. 2025-03-12 doi:10.1101/2025.03.04.641351 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ A cascade of structural rearrangements positions peptide release factor II for polypeptide hydrolysis on the ribosome ]]> https://biorxiv.org/content/10.1101/2025.03.09.642146v1?rss=1 Michael, N. Huang, B. Ray, K. K. Kinz-Thompson, C. D. Gonzalez, R. L. 2025-03-13 doi:10.1101/2025.03.09.642146 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Preventing neuropathy and improving anti-cancer chemotherapy with a carbazole-based compound ]]> https://biorxiv.org/content/10.1101/2025.03.10.642317v1?rss=1 Bosc, L. Pero, M. E. Balayssac, D. Jacquemot, N. Allard, J. Suzanne, P. Vollaire, J. Cottet-Rousselle, C. Michallet, S. Villaret, J. Torch, S. Marais, S. Elena-Herrmann, B. Schlattner, U. Mercier, A. Josserand, V. Thibert, C. Dallemagne, P. Bartolini, F. Lafanechere, L. 2025-03-13 doi:10.1101/2025.03.10.642317 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Rational redesign of antigen binding domain improves in vivo efficacy of CD22-CAR T cells ]]> https://biorxiv.org/content/10.1101/2025.03.13.643183v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@1d543e3org.highwire.dtl.DTLVardef@5bf226org.highwire.dtl.DTLVardef@76cd2forg.highwire.dtl.DTLVardef@198fd37_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> DeGolier, K. R. Walsh, Z. H. Leach, L. Brzezinski, C. Novak, A. Dimitrov, D. Kohler, M. E. Fry, T. J. 2025-03-15 doi:10.1101/2025.03.13.643183 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Ontogeny of the spinal cord dorsal horn ]]> https://biorxiv.org/content/10.1101/2025.03.14.643370v1?rss=1 Roome, R. B. Yadav, A. Flores, L. Puarr, A. Nardini, D. Richardson, A. Waclaw, R. R. Arkell, R. M. Menon, V. Johnson, J. E. Levine, A. 2025-03-15 doi:10.1101/2025.03.14.643370 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Targeting Monoallelic CREBBP/EP300 Mutations in Germinal Center-Derived B-Cell Lymphoma with a First-in-Class Histone Acetyltransferase Activator ]]> https://biorxiv.org/content/10.1101/2025.03.13.642871v1?rss=1 Liu, Y. Piorczynski, T. B. Estrella, B. Ricker, E. C. Pazos, M. Gonzalez, Y. Tolu, S. S. Ryu Tiger, Y. K. Karan, C. Cremers, S. Nandakumar, R. Honig, B. Hwang, H. Kelleher, N. L. Camarillo, J. M. Abshiru, N. A. Amengual, J. E. 2025-03-17 doi:10.1101/2025.03.13.642871 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ HazardPyMatch: A Tool for identifying reproductive and other hazards in scientific laboratories ]]> https://biorxiv.org/content/10.1101/2025.03.14.643365v1?rss=1 Parker, E. M. Zavitsanou, A.-M. Liff, C. Jeurissen, D. El Houda MIMOUNI, N. Succi, I. Rogers, E. Liistro, M. 2025-03-17 doi:10.1101/2025.03.14.643365 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Quantile-specific confounding: correction for subtle population stratification via quantile regression ]]> https://biorxiv.org/content/10.1101/2025.03.18.638253v1?rss=1 Wang, C. Masala, M. Fiorillo, E. Devoto, M. Cucca, F. Ionita-Laza, I. 2025-03-19 doi:10.1101/2025.03.18.638253 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ The carnosinase dipeptidase CNDP1 is a novel metabolic vulnerability in brain metastasis ]]> https://biorxiv.org/content/10.1101/2025.03.18.644053v1?rss=1 Gomez-Munoz, M. A. Karz, A. Navarro, M. Osorio-Vasquez, V. M. Katsara, O. Walker, A. Berico, P. Medellin, A. P. Eskow, N. M. Wan, Y. Ibrahim, M. Tagore, S. DSouza, E. K. Izar, B. Vega-Saenz de Miera, E. Osman, I. Pacold, M. Kong, X. Levesque, M. Possemato, R. Holmen, S. Schneider, R. Vincent, T. Ruggles, K. Biancur, D. Hernando, E. 2025-03-19 doi:10.1101/2025.03.18.644053 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ The Na V1.5 auxiliary subunit FGF13 modulates channels by regulating membrane cholesterol independent of channel binding ]]> https://biorxiv.org/content/10.1101/2025.03.19.644183v1?rss=1 Gade, A. Malvezzi, M. Das, L. T. Matsui, M. Ma, C.-I. J. Mazdisnian, K. Marx, S. O. Maxfield, F. R. Pitt, G. S. 2025-03-19 doi:10.1101/2025.03.19.644183 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ ATP hydrolysis-driven structural transitions within the S. cerevisiae Rad51 and Dmc1 nucleoprotein filaments ]]> https://biorxiv.org/content/10.1101/2025.03.19.644215v1?rss=1 Shin, Y. Kim, S. Greene, E. C. 2025-03-19 doi:10.1101/2025.03.19.644215 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Two Axes of White Matter Development ]]> https://biorxiv.org/content/10.1101/2025.03.19.644049v1?rss=1 Luo, A. C. Meisler, S. L. Sydnor, V. J. Alexander-Bloch, A. Bagautdinova, J. Barch, D. M. Bassett, D. S. Davatzikos, C. Franco, A. R. Goldsmith, J. Gur, R. E. Gur, R. C. Hu, F. Jaskir, M. Kiar, G. Keller, A. S. Larsen, B. Mackey, A. P. Milham, M. P. Roalf, D. R. Shafiei, G. Shinohara, R. T. Somerville, L. H. Weinstein, S. M. Yeatman, J. D. Cieslak, M. Rokem, A. Satterthwaite, T. D. 2025-03-20 doi:10.1101/2025.03.19.644049 Cold Spring Harbor Laboratory Press 2025-03-20 <![CDATA[ Translating the Post-Mortem Brain Multi-Omics Molecular Taxonomy of Alzheimer's Dementia to Living Humans ]]> https://biorxiv.org/content/10.1101/2025.03.20.644323v1?rss=1 Iturria-Medina, Y. Poole, V. N. Zammit, A. R. de Paiva Lopes, K. Vialle, R. A. Yu, L. Tasaki, S. Batalha, C. Hong, J. H. Sanchez-Rodriguez, L. Geddes, M. R. Abadir, P. Ortlund, E. A. De Jager, P. Menon, V. Schnaider Beeri, M. Buchman, A. S. Levin, Y. Morgenstern, D. Schneider, J. A. Kaddurah-Daouk, R. Wyss-Coray, T. Seyfried, N. Poulakis, K. Rosa-Neto, P. Wang, Y. Bennett, D. A. 2025-03-24 doi:10.1101/2025.03.20.644323 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ BAND: Behavior-Aligned Neural Dynamics is all you need to capture motor corrections ]]> https://biorxiv.org/content/10.1101/2025.03.21.644350v1?rss=1 Kudryashova, N. Hurwitz, C. Perich, M. G. Hennig, M. H. 2025-03-24 doi:10.1101/2025.03.21.644350 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Theory of multiscale epithelial mechanics under stretch: from active gels to vertex models ]]> https://biorxiv.org/content/10.1101/2025.03.23.644792v1?rss=1 Ouzeri, A. Kale, S. Chahare, N. Torres-Sanchez, A. Santos, D. Trepat, X. Arroyo, M. 2025-03-25 doi:10.1101/2025.03.23.644792 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Right-hemisphere frontoparietal oscillations precede conscious report of visual targets. ]]> https://biorxiv.org/content/10.1101/2025.03.24.644800v1?rss=1 Spagna, A. Liu, J. Bartolomeo, P. 2025-03-25 doi:10.1101/2025.03.24.644800 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase ]]> https://biorxiv.org/content/10.1101/2025.03.24.645077v1?rss=1 Tang, S. Zedaveinyte, R. Burman, N. Pandey, S. Ramirez, J. L. Kulber, L. M. Wiegand, T. Wilkinson, R. A. Ma, Y. Zhang, D. J. Lampe, G. D. Berisa, M. Jovanovic, M. Wiedenheft, B. Sternberg, S. H. 2025-03-25 doi:10.1101/2025.03.24.645077 Cold Spring Harbor Laboratory Press 2025-03-25 <![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[ Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination ]]> https://biorxiv.org/content/10.1101/2025.03.26.645561v1?rss=1 Shin, Y. Petassi, M. Jessop, A. Kim, S. Matei, R. Morse, K. Raina, V. Roy, U. Greene, E. C. 2025-03-26 doi:10.1101/2025.03.26.645561 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ A large-scale method to measure the absolute stoichiometries of protein Poly-ADP-Ribosylation ]]> https://biorxiv.org/content/10.1101/2025.03.27.645734v1?rss=1 1%) predominantly targets proteins involved in transcription regulation and chromatin remodeling. Thus, our study provides a systems-scale, quantitative view of PARylation stoichiometries under genotoxic conditions, which serves as invaluable resources for future functional studies of this important protein posttranslational modification. ]]> Li, P. Zhang, Y. Yu, Y. 2025-03-27 doi:10.1101/2025.03.27.645734 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ Structural Studies of an Anti-necroptosis Viral:Human Functional Hetero-amyloid M45:RIPK3 using SSNMR ]]> https://biorxiv.org/content/10.1101/2025.03.26.644761v1?rss=1 He, C. Varghese, N. R. Keeler, E. G. Pham, C. L. L. Williams, B. Tetter, S. Semaan, C. Wilde, K. L. Brown, S. H. J. Bouwer, J. C. Gambin, Y. Sierecki, E. Steain, M. Sunde, M. McDermott, A. E. 2025-03-29 doi:10.1101/2025.03.26.644761 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Genomic and Transcriptomic Signatures of SETD1A Disruption in Human Excitatory Neuron Development and Psychiatric Disease Risk ]]> https://biorxiv.org/content/10.1101/2025.03.26.645419v1?rss=1 Sun, Z. Zhu, H. He, X. Lendemeijer, B. Wang, Z. Fan, J. Sun, Y. Zhang, Z. Markx, S. Kushner, S. A. Xu, B. Gogos, J. A. 2025-03-29 doi:10.1101/2025.03.26.645419 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Computational Mechanisms of Temporal Anticipation in Perception and Action ]]> https://biorxiv.org/content/10.1101/2025.03.28.646008v1?rss=1 Vishne, G. Deouell, L. Y. Landau, A. N. 2025-03-30 doi:10.1101/2025.03.28.646008 Cold Spring Harbor Laboratory Press 2025-03-30 <![CDATA[ Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders ]]> https://biorxiv.org/content/10.1101/2025.03.28.645799v1?rss=1 Herrlinger, S. A. Wang, J. Rao, B. Y. Chang, J. Gogos, J. Losonczy, A. Vitkup, D. 2025-03-31 doi:10.1101/2025.03.28.645799 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ Bidirectional Modulation of Somatostatin-expressing Interneurons in the Basolateral Amygdala Reduces Neuropathic Pain Perception in Mice ]]> https://biorxiv.org/content/10.1101/2025.03.28.645947v1?rss=1 Apte, A. Fernald, J. Slater, C. Sorrentino, M. Youngerman, B. Wang, Q. 2025-04-02 doi:10.1101/2025.03.28.645947 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery ]]> https://biorxiv.org/content/10.1101/2025.04.02.646746v1?rss=1 Haudiquet, M. Chakravarti, A. Zhiying, Z. Ramirez, J. L. Herrero del Valle, A. Olinares, P. D. B. Lavenir, R. Aït Ahmed, M. de la Cruz, M. J. Chait, B. Sternberg, S. H. Bernheim, A. Patel, D. 2025-04-02 doi:10.1101/2025.04.02.646746 Cold Spring Harbor Laboratory Press 2025-04-02 <![CDATA[ Brainwide genetic capture for conscious state transitions ]]> https://biorxiv.org/content/10.1101/2025.03.28.646066v1?rss=1 Lazaro, H. Schneider, K. N. Jin, M. Beck, A. Rijsketic, D. R. Murry, A. D. Navarrete, J. Shin, C. C. Barrow, A. C. Campuzano, I. Nota, M. H. Ressler, N. Apley, E. Zhang, J. Gutierrez, G. Szelenyi, E. R. Nilsson, S. R. Denny, C. A. Bruchas, M. R. Heifets, B. D. de la Iglesia, H. O. Golden, S. A. Heshmati, M. 2025-04-03 doi:10.1101/2025.03.28.646066 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Cationic amino acid identity and net charge influence condensate properties in E. coli ]]> https://biorxiv.org/content/10.1101/2025.03.29.646054v1?rss=1 Kidane, A. K. Rosenfeld, J. R. Johnston, J. D. Dubbeldam, C. Paraan, M. Obermeyer, A. C. 2025-04-03 doi:10.1101/2025.03.29.646054 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Enhanced FLI1 accessibility mediates STAG2-mutant leukemogenesis ]]> https://biorxiv.org/content/10.1101/2025.04.01.646632v1?rss=1 Xu, J. Scoca, V. Chen, Y. Zhan, Y. A. Fisher, A. Udoh, E.-o. Fernando, S. Alija, B. Pantazi, J. Sudunagunta, V. Stewart, E. Galang, A. M. D. Williams, M. Bhagat, G. Gebhard, C. Visconte, V. Ondrejka, S. Delwel, R. Hu, M. Koche, R. P. Viny, A. D. 2025-04-03 doi:10.1101/2025.04.01.646632 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ A proteogenomic tool uncovers protein markers for human microglial states ]]> https://biorxiv.org/content/10.1101/2025.03.31.646212v1?rss=1 Haage, V. Bautista, A. R. Tuddenham, J. F. Marshe, V. Chiu, R. Liu, Y. Lama, T. Kelly, S. S. Parghi, N. A. Park, J. Buonfiglioli, A. Furnari, J. L. Haq, I. Pearse, R. Patel, R. Terzioglu, G. Touil, H. Zeng, L. Noble, J. Sarkis, R. A. Shneider, N. A. de Witte, L. Schneider, J. A. Teich, A. Young-Pearse, T. L. Riley, C. Bennett, D. A. Canoll, P. Bruce, J. N. Howden, A. J. Lloyd, A. F. De Strooper, B. F. Sher, F. Sproul, A. A. Olah, M. Taga, M. Zhang, Y. Caisheng, L. Fujita, M. Petyuk, V. A. De Jager, P. A. 2025-04-04 doi:10.1101/2025.03.31.646212 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ A transgene harboring the human Glucose Transporter1 (GLUT1) gene locus ameliorates disease in GLUT1 deficiency syndrome model mice. ]]> https://biorxiv.org/content/10.1101/2025.04.05.647372v1?rss=1 Tang, M. Teng, S. Kim, A. Y. Peng, Y. Monani, U. R. 2025-04-06 doi:10.1101/2025.04.05.647372 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ Conserved energetic changes drive function in an ancient protein fold ]]> https://biorxiv.org/content/10.1101/2025.04.02.646877v1?rss=1 Wells, M. L. Lu, C. Sultanov, D. Weber, K. C. Gong, Z. Glasgow, A. 2025-04-07 doi:10.1101/2025.04.02.646877 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Predicting specificity of TCR-pMHC interactions using machine learning and biophysical models ]]> https://biorxiv.org/content/10.1101/2025.04.04.647165v1?rss=1 Culka, M. Lounsbury, N. W. Thrift, W. Nerli, S. Wallace, A. Nikolenyi, G. Orlova, D. Mukhyala, K. AlQuraishi, M. 2025-04-07 doi:10.1101/2025.04.04.647165 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Endometrial cancer progression driven by PTEN-deficiency requires miR-424(322)~503. ]]> https://biorxiv.org/content/10.1101/2025.04.07.647575v1?rss=1 Vidal-Sabanes, M. Bonifaci, N. Navaridas, R. Egea, J. Encinas, M. Rodriguez-Barrueco, R. Silva, J. M. Matias-Guiu, X. Llobet-Navas, D. Dolcet, X. 2025-04-10 doi:10.1101/2025.04.07.647575 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Tff2 marks gastric corpus progenitors that give rise to pyloric metaplasia/SPEM following injury ]]> https://biorxiv.org/content/10.1101/2025.04.09.647847v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@48a2d1org.highwire.dtl.DTLVardef@b96642org.highwire.dtl.DTLVardef@1e89a4dorg.highwire.dtl.DTLVardef@1ea6a86_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG Pyloric metaplasia, also known as spasmolytic polypeptide-expressing metaplasia (SPEM), arises in the corpus in response to oxyntic atrophy, but its origin and role in gastric cancer remain poorly understood. Using Tff2-CreERT knockin mice, we identified highly proliferative Tff2+ progenitors in the corpus isthmus that give rise to multiple secretory lineages, including chief cells. While lacking long-term self-renewal ability, Tff2+ corpus progenitors rapidly expand to form short-term SPEM following acute injury or loss of chief cells. Genetic ablation of Tff2+ progenitors abrogated SPEM formation, while genetic ablation of GIF+ chief cells enhanced SPEM formation from Tff2+ progenitors. In response to H. pylori infection, Tff2+ progenitors progressed first to metaplasia and then later to dysplasia. Interestingly, induction of KrasG12D mutations in Tff2+ progenitors facilitated direct progression to dysplasia in part through the acquisition of stem cell-like properties. In contrast, Kras-mutated SPEM and chief cells were not able to progress to dysplasia. Tff2 mRNA was downregulated in isthmus cells during progression to dysplasia. Single-cell RNA sequencing and spatial transcriptomics of human tissues revealed distinct differentiation trajectories for SPEM and gastric cancer. These findings challenge the conventional interpretation of the stepwise progression through metaplasia and instead identify Tff2+ progenitor cells as potential cells of origin for SPEM and possibly for gastric cancer. ]]> Tu, R. Zheng, H. Zheng, B. Zhong, Q. Qian, J. Wu, F. Shiokawa, T. Ochiai, Y. Kobayashi, H. Waterbury, Q. T. Zamechek, L. B. Takahashi, S. Mizuno, S. Huang, C. Li, P. Hayakawa, Y. Wang, T. C. 2025-04-10 doi:10.1101/2025.04.09.647847 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Regulation of airway fumarate by host and pathogen promotes S. aureus pneumonia ]]> https://biorxiv.org/content/10.1101/2025.04.10.647998v1?rss=1 Chen, Y.-T. Liu, Z. Fucich, D. Giulieri, S. G. Liu, Z. Wadhwa, R. Rios, G. Henschel, H. Tyagi, N. Olivier, F. A. B. Monk, I. R. Shah, S. S. Sridhar, S. H. Drikic, M. Bianco, C. Lohia, G. K. Beg, A. Z. Planet, P. J. Lewis, I. A. Sebra, R. Traven, A. Hachani, A. Stinear, T. P. Howden, B. Boyd, J. Riquelme, S. A. Wang, C. Prince, A. S. Wong, T. 2025-04-10 doi:10.1101/2025.04.10.647998 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Spatial Transcriptomics Using Archived Formalin-Fixed Paraffin-Embedded Core Needle Biopsy Tissues Revealed Unique Transcriptomic Signatures in Kidney Transplant Rejections ]]> https://biorxiv.org/content/10.1101/2025.04.08.647600v1?rss=1 Wongworawat, Y. C. Nepal, C. Duhon, M. Chen, W. Nguyen, M.-T. Godzik, A. Qiu, X. Li, V. W. Yu, G. Villicana, R. Zuppan, C. De Vera, M. Haas, M. Wang, C. 2025-04-15 doi:10.1101/2025.04.08.647600 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis ]]> https://biorxiv.org/content/10.1101/2025.04.09.647907v1?rss=1 Vuille, J. A. Tanriover, C. Micalizzi, D. S. Ebright, R. Y. Animesh, S. Morris, R. Hajizadeh, S. Nicholson, Z. J. Russell, H. C. Zaniewski, E. F. Wittner, B. S. Wesley, B. K. Grunewald, J. Szalay, R. N. Antmen, E. Fox, D. B. Yang, M. Joung, J. K. Gulhan, D. C. Elia, A. E. H. Haas, W. Oh, E. Maheswaran, S. Haber, D. A. 2025-04-15 doi:10.1101/2025.04.09.647907 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Brain Signal Variability During Rest as a Neural Mechanism Underlying Cognitive Reserve ]]> https://biorxiv.org/content/10.1101/2025.04.09.648011v1?rss=1 Coors, A. Stern, Y. Habeck, C. 2025-04-15 doi:10.1101/2025.04.09.648011 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Deconvoluting single-cell transcriptomics reveals cellular programs regulated by cell-cell communication in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.04.09.648030v1?rss=1 Zhang, H. Lu, B. Cooper, G. F. Saeed, A. Paisley, J. W. Lu, X. Chen, L. 2025-04-15 doi:10.1101/2025.04.09.648030 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Item recognition is associated with gut microbiota composition in healthy humans ]]> https://biorxiv.org/content/10.1101/2025.04.10.648258v1?rss=1 Oyarzun, J. P. Kuntz, T. M. Morgan, X. C. Davachi, L. Huttenhower, C. LeDoux, J. E. Phelps, E. A. 2025-04-16 doi:10.1101/2025.04.10.648258 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Muc6-expressing gastric isthmus progenitors contribute to regeneration and metaplasia supported by myeloid-mesenchymal interactions ]]> https://biorxiv.org/content/10.1101/2025.04.15.648856v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@10fc2eaorg.highwire.dtl.DTLVardef@1c5b82corg.highwire.dtl.DTLVardef@1be747dorg.highwire.dtl.DTLVardef@d1d722_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Arai, J. Iwata, Y. Tsubosaka, A. Kinoshita, H. Shinohara, S. Abe, S. Shiokawa, T. Oura, K. Suzuki, N. Hata, M. Kurokawa, K. Oya, Y. Tsuboi, M. Ihara, S. Murakami, K. Shiomi, C. Uekura, C. Fujiwara, H. Tateno, H. Mizuno, S. Takahashi, S. Kanai, A. Suzuki, Y. Ushiku, T. Ijichi, H. Hirata, Y. Kasuga, M. O'Brien, V. P. Salama, N. Kakiuchi, M. Ishikawa, S. WANG, T. C. Hayakawa, Y. Fujishiro, M. 2025-04-16 doi:10.1101/2025.04.15.648856 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries ]]> https://biorxiv.org/content/10.1101/2025.04.16.649077v1?rss=1 Pauli, J. Garger, D. Peymani, F. Wettich, J. Sachs, N. Wirth, J. Zhang, H. Tabas, I. Tall, A. Li, M. Reilly, M. Branzan, D. Prokisch, H. Menden, M. P. Maegdefessel, L. 2025-04-16 doi:10.1101/2025.04.16.649077 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Alzheimer's disease and its co-pathologies: implications for hippocampal degeneration, cognitive decline, and the role of APOE ϵ4 ]]> https://biorxiv.org/content/10.1101/2025.04.11.648343v1?rss=1 Gawor, K. Verrept, S. Arekatla, G. Wouters, D. Ronisz, A. Hecht, M. Laureyssen, C. Ver Donck, H. Lahaije, B. Ospitalieri, S. Vandenbulcke, M. Otto, M. von Arnim, C. A. F. Ghebremedhin, E. Hanseeuw, B. Vandenberghe, R. Blaschko, M. Sifrim, A. Sleegers, K. Thal, D. R. Tome, S. O. 2025-04-17 doi:10.1101/2025.04.11.648343 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Switches from tonic to burst firing enable memory consolidation through late-phase synaptic plasticity ]]> https://biorxiv.org/content/10.1101/2025.04.12.648539v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@7a8922org.highwire.dtl.DTLVardef@c13425org.highwire.dtl.DTLVardef@46a505org.highwire.dtl.DTLVardef@1fc0820_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jacquerie, K. Tyulmankov, D. Sacre, P. Drion, G. 2025-04-18 doi:10.1101/2025.04.12.648539 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ A polymeric, PDMS-based large-scale skull replacement suitable for optical and mechanical access for long-term neuronal imaging, electrophysiology, and optogenetics ]]> https://biorxiv.org/content/10.1101/2025.04.15.648966v1?rss=1 View larger version (71K): org.highwire.dtl.DTLVardef@1900a2dorg.highwire.dtl.DTLVardef@18c436corg.highwire.dtl.DTLVardef@19e6a4corg.highwire.dtl.DTLVardef@154c228_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG ]]> Takahashi, K. Huis in 't Veld, G. J. Benedetti, D. Wang, J.-Y. Pontes Quero, S. Yuste, R. Pennartz, C. M. A. Olcese, U. 2025-04-20 doi:10.1101/2025.04.15.648966 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Genome-wide mapping of mesoscale neuronal RNA organization and condensation ]]> https://biorxiv.org/content/10.1101/2025.04.19.649570v1?rss=1 Becker, L. A. Quinodoz, S. A. Comi, T. J. Kimchi, O. Knowles, D. A. Brangwynne, C. P. 2025-04-20 doi:10.1101/2025.04.19.649570 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Multiple human enhancer RNAs contain long translated open reading frames ]]> https://biorxiv.org/content/10.1101/2025.04.18.649583v1?rss=1 300 nts), many of which can be actively translated, as determined by ribosome profiling, and produce proteins that accumulate in cells, as shown by mass spectrometry (MS) data. Focusing on the largest of the encoded proteins, which we designate as eORFs, and which can be up to [~]45 KDa, we found remarkably that most are highly basic, with pIs >11.5. This unusual chemistry reflects a striking overabundance of arginine residues, and occurs despite a relative paucity of lysines. Exogenous expression of the ten largest eORFs revealed that they accumulate stably in cells as full-length proteins, and most localize to the nucleus and associate with chromatin. Identification of interacting proteins by MS suggested possible roles for these proteins in several nuclear processes. The eORFs studied are well-conserved among primates, although they are largely absent from other mammals. Notably, several contain human-specific C-terminal extensions and display properties suggestive of de novo gene birth. In summary, we have discovered that a fraction of human eRNAs can function as mRNAs, revealing a new and unexpected role for these transcripts. ]]> Vlasov, P. A. Ogami, K. Valenzuela, E. Kawaguchi, R. K. Jovanovic, M. Manley, J. L. 2025-04-21 doi:10.1101/2025.04.18.649583 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Single Cell Landscape of Sex-specific Drivers of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2025.04.18.647076v1?rss=1 Wu, Y. Travaglini, K. J. Gabitto, M. Keene, D. Dunn, A. Kaczorowski, C. Harari, O. De Jager, P. Menon, V. Schneider, J. A. Bennett, D. A. Dumitrescu, L. Hohman, T. J. 2025-04-22 doi:10.1101/2025.04.18.647076 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Mechanistic Insights into Proteomic Mutation-Phenotype Linkages from Tiling Mutagenesis Screens ]]> https://biorxiv.org/content/10.1101/2025.04.17.649336v1?rss=1 He, W. Huang, J.-W. Wang, Y. Hayward, S. B. Leuzzi, G. Fu, R. Wang, S. Vaitsiankova, A. Bedford, M. T. Guerois, R. Ciccia, A. Xu, H. 2025-04-23 doi:10.1101/2025.04.17.649336 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ The Effects of Antidepressants on the Hippocampus: A Meta-Analysis of Public Transcriptional Profiling Data ]]> https://biorxiv.org/content/10.1101/2025.04.21.648805v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@8b41b1org.highwire.dtl.DTLVardef@85d600org.highwire.dtl.DTLVardef@a4bc1eorg.highwire.dtl.DTLVardef@13a8723_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Geoghegan, E. M. Hagenauer, M. H. Hernandez, E. Espinoza, S. Flandreau, E. I. Nguyen, P. T. Bhuiyan, M. R. Mensch, S. Watson, S. J. Akil, H. 2025-04-23 doi:10.1101/2025.04.21.648805 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Ontology-aware DNA methylation classification with a curated atlas ofhuman tissues and cell types ]]> https://biorxiv.org/content/10.1101/2025.04.18.649618v1?rss=1 Kim, M. Dannenfelser, R. Cui, Y. Allen, G. Yao, V. 2025-04-24 doi:10.1101/2025.04.18.649618 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ BRCA2 reversion mutation-independent resistance to PARP inhibition in prostate cancer through loss of function perturbations in the DNA pre-replication complex ]]> https://biorxiv.org/content/10.1101/2025.04.20.649668v1?rss=1 Pappas, K. J. Ferrari, M. Smith, P. Nandakumar, S. Khan, Z. Young, S. B. LaClair, J. Russo, M. V. Huang-Hobbs, E. Schultz, N. Abida, W. Karthaus, W. Jasin, M. Sawyers, C. 2025-04-24 doi:10.1101/2025.04.20.649668 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to α-synuclein ]]> https://biorxiv.org/content/10.1101/2025.04.21.649867v1?rss=1 Freuchet, A. Johansson, E. Frazier, A. Litvan, I. Goldman, J. G. Alcalay, R. N. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2025-04-24 doi:10.1101/2025.04.21.649867 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ T cell responses towards PINK1 and α-synuclein are elevated in prodromal Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.04.21.649871v1?rss=1 Johansson, E. Freuchet, A. Williams, G. P. Michealis, T. Frazier, A. Litvan, I. Goldman, J. G. Alcalay, R. N. Standaert, D. G. Amara, A. W. Stover, N. Fon, E. A. Postuma, R. B. Sidney, J. Sulzer, D. Lindestam Arlehamn, C. S. Sette, A. 2025-04-24 doi:10.1101/2025.04.21.649871 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs ]]> https://biorxiv.org/content/10.1101/2025.04.23.650082v1?rss=1 Gattoni, G. Lin, C.-Y. York, J. R. Keitley, D. LaBonne, C. Yu, J.-K. Gillis, A. Benito-Gutierrez, E. 2025-04-24 doi:10.1101/2025.04.23.650082 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Understanding Protein Language Model Scaling on Mutation Effect Prediction ]]> https://biorxiv.org/content/10.1101/2025.04.25.650688v1?rss=1 Hou, C. Liu, D. Zafar, A. Shen, Y. 2025-04-29 doi:10.1101/2025.04.25.650688 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment ]]> https://biorxiv.org/content/10.1101/2025.04.25.650693v1?rss=1 Calderon, R. I. Sah, N. Huang, M. Kittle, R. H. Shaik, W. Chousal, J. N. Kallol, S. Bui, T. Morey, R. Mitre, A. Fogarty, N. M. E. Gerri, C. Zheng, C. DeHoff, P. M. Home, P. Niakan, K. Cook-Andersen, H. Fisch, K. M. Paul, S. Soncin, F. 2025-04-29 doi:10.1101/2025.04.25.650693 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Safety learning induces postsynaptic potentiation of direct pathway spiny projection neurons in the tail of the striatum ]]> https://biorxiv.org/content/10.1101/2025.04.29.651089v1?rss=1 Stanley, A. T. Choi, S. J. Frank, A. Makowicz, E. Cataldi, S. Shashaank, N. Mosharov, E. V. Lacefield, C. Miniaci, M. Sulzer, D. 2025-04-30 doi:10.1101/2025.04.29.651089 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Personalized Multiscale Modeling of Left Atrial Mechanics and Blood Flow ]]> https://biorxiv.org/content/10.1101/2025.04.26.650771v1?rss=1 Shi, L. Chen, I. Y. Vedula, V. 2025-05-01 doi:10.1101/2025.04.26.650771 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ An open, fully-processed data resource for studying mood and sleep variability in the developing brain ]]> https://biorxiv.org/content/10.1101/2025.05.01.651544v1?rss=1 Brook, J. B. H. Salo, T. Luo, A. C. Bagautdinova, J. Rush, S. Alexander-Bloch, A. F. Baller, E. B. Calkins, M. E. Cieslak, M. Cooper, E. C. Detre, J. A. Elliot, M. A. Fair, D. A. Freedman, P. Gehrman, P. R. Gur, R. C. Gur, R. E. Klein, A. Laney, N. Laumann, T. O. Mehta, K. Merikangas, K. Milham, M. P. Mitchell, J. A. Moore, T. M. Nelson, S. M. Ruparel, K. Sevchik, B. L. Shanmugan, S. Shou, H. Taso, M. White, L. K. Wolf, D. H. Tisdall, D. Roalf, D. R. Satterthwaite, T. D. 2025-05-02 doi:10.1101/2025.05.01.651544 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ G2VTCR: predicting antigen binding specificity by Weisfeiler-Lehman graph embedding of T cell receptor sequences ]]> https://biorxiv.org/content/10.1101/2025.04.29.651344v1?rss=1 Wang, Z. Shen, Y. 2025-05-04 doi:10.1101/2025.04.29.651344 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ CircRNA hypomethylation in the human amygdala implicates FKBP5 in alcohol use disorder ]]> https://biorxiv.org/content/10.1101/2025.05.04.652083v1?rss=1 Ghandour, T. Glausier, J. R. Asok, A. Doyle, M. R. Campo, P. Colnaghi, L. Lewis, D. A. Kandel, D. B. Kandel, E. R. de Guglielmo, G. Huang, S.-s. C. Melas, P. A. 2025-05-04 doi:10.1101/2025.05.04.652083 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development ]]> https://biorxiv.org/content/10.1101/2025.05.03.652068v1?rss=1 Habib, R. Roark, R. S. Li, H. Connell, A. J. Hogarty, M. P. Wagh, K. Wang, S. Marchitto, L. Skelly, A. N. Carey, J. W. Sowers, K. J. Ayyanathan, K. Plante, S. J. Bibollet-Ruche, F. Park, Y. Agostino, C. J. Singh, A. Martella, C. L. Lewis, E. Lora, J. Ding, W. Campion, M. S. Zhao, C. Liu, W. Li, Y. Li, X. Liang, B. Chowdhury, R. R. Amereh, K. Van Itallie, E. Sheng, Z. Ghosh, A. R. Bar, K. J. Williams, W. B. Wiehe, K. Saunders, K. O. Edwards, R. J. Cain, D. W. Lewis, M. Batista, F. D. Burton, D. R. Andrabi, R. Kulp, D. W. Haynes, B. F. Korber, B. Shap 2025-05-06 doi:10.1101/2025.05.03.652068 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Disrupted priming within draining lymph nodes drives immune quiescence in gastric cancer ]]> https://biorxiv.org/content/10.1101/2025.05.05.651897v1?rss=1 150,000 cells). From single cell analysis, we identified two distinct sources of impaired tumor surveillance within tumor draining lymph nodes. First, we observed that a significant fraction of tumor draining lymph nodes had undergone cytokine-driven reprogramming, leading to reduced dendritic cell homing and limited T cell priming. Second, T cells undergoing successful activation exhibited limited expansion and constrained differentiation, marked by expression of the quiescence-associated transcription factor Kruppel-like Factor 2 (KLF2). Overexpression of KLF2 in primary T cells limited both their differentiation and cytotoxic capacity. These findings implicate both impaired T cell priming and KLF2-dependent T cell quiescence in limiting T cell immunity in gastric adenocarcinoma. We suggest these findings represent an emerging model for immune silencing in tumors developing from tissues with chronic inflammation. ]]> Salehi, S. Stroobant, E. E. Lees, H. Lin, Y.-H. Shimada, S. Abate, M. Zatzman, M. J. Ceglia, N. Freeman, S. Laszkowska, M. Maron, S. B. McPherson, A. Rusk, N. Havasov, E. Drebin, H. Gu, P. Tang, L. H. Janjigian, Y. Y. Soldatov, R. Chaligne, R. Shah, S. P. Strong, V. E. Vardhana, S. A. 2025-05-06 doi:10.1101/2025.05.05.651897 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Regenie.QRS: computationally efficient whole-genome quantile regression at biobank scale ]]> https://biorxiv.org/content/10.1101/2025.05.02.651730v1?rss=1 Wang, F. Wang, C. Wang, T. Masala, M. Fiorillo, E. Devoto, M. Cucca, F. Ionita-Laza, I. 2025-05-07 doi:10.1101/2025.05.02.651730 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain ]]> https://biorxiv.org/content/10.1101/2025.05.02.651738v1?rss=1 Brann, D. H. Tsukahara, T. Tau, C. Kalloor, D. Lubash, R. Thamarai Kannan, L. Klimpert, N. Kollo, M. Escamilla-Del-Arenal, M. Bintu, B. Bozza, T. Datta, S. R. 2025-05-08 doi:10.1101/2025.05.02.651738 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.05.02.651907v1?rss=1 Su, J. Qu, Y. Schertzer, M. D. Yang, H. Jiang, J. Lhakhang, T. Nelson, T. M. Park, S. Lai, Q. Fu, X. Choi, S.-W. Knowles, D. A. Rabadan, R. 2025-05-08 doi:10.1101/2025.05.02.651907 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ No Evidence of Direct Activation of Human Neutrophil Responses by Multivalent Prefusion Trimeric SARS-CoV-2 Spike Protein ex vivo ]]> https://biorxiv.org/content/10.1101/2025.05.08.652856v1?rss=1 Fortin, A. Huot, S. Caron, E. Laflamme, C. Pagliuzza, A. Chomont, N. Gilbert, C. Zhang, B. Kwong, P. D. Pouliot, M. Grandvaux, N. 2025-05-08 doi:10.1101/2025.05.08.652856 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Th9-endothelial cell crosstalk promotes inflammatory atherosclerotic cardiovascular disease ]]> https://biorxiv.org/content/10.1101/2025.05.05.652112v1?rss=1 Baral, I. Baumer, Y. Burma, A. Sylvester, M. Jones, K. Kitakule, M. M. Dey, A. Rodante, J. Gutierrez-Huerta, C. A. Taramangalam, B. Perez, J. D. Guo, L. Grogan, A. Shiraki, T. Finn, A. Son, A. Cho, K. Khillian, J. Chen, M. Mehta, N. N. Frischmeyer-Guerrerio, P. A. Milner, J. D. Powell-Wiley, T. M. Falduto, G. H. Schwartz, D. M. 2025-05-09 doi:10.1101/2025.05.05.652112 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS-chemokine-myeloid axis ]]> https://biorxiv.org/content/10.1101/2025.05.06.652454v1?rss=1 Beernaert, B. Jady-Clark, R. L. Shah, P. Ramon-Gil, E. Lawson, N. M. Brodtman, Z. D. Tagore, S. Stihler, F. Carter, A. S. Clarke, S. Liu, T. Zhu, W. Erdal, E. Easton, A. Campo, L. Browne, M. Ash, S. Waddell, N. Crosby, T. Lord, S. R. Mann, D. A. Melero, I. de Andrea, C. E. Tijhuis, A. E. Foijer, F. Hammond, E. M. Akdemir, K. C. Leslie, J. Izar, B. Parkes, E. E. 2025-05-10 doi:10.1101/2025.05.06.652454 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Adaptation by stochastic tuning of gene expression in mammalian cells ]]> https://biorxiv.org/content/10.1101/2025.05.07.651953v1?rss=1 Momen-Roknabadi, A. Oikonomou, P. Tavazoie, S. 2025-05-10 doi:10.1101/2025.05.07.651953 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ APOE genotype confers context dependent neurovascular vulnerability in immune-vascularized human forebrain organoids ]]> https://biorxiv.org/content/10.1101/2025.05.08.652864v1?rss=1 Fang, H. Liao, X. Bullen, C. K. Pu, R. Wang, H. Condoleo, J. Cheat, S. Chen, X. Zhang, Y. Zhang, S. Huo, D. Lissit, K. Yang, A. Jarvis, K. Neifert, S. Huang, Y. Bishai, W. Jain, S. K. Dawson, T. Dawson, V. L. Xu, J. 2025-05-10 doi:10.1101/2025.05.08.652864 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Brain-wide cell-type-specific noradrenergic modulation of the transcriptome ]]> https://biorxiv.org/content/10.1101/2025.05.09.653136v1?rss=1 Slater, C. Lantin, T. Wellman, S. Jia, L. Gonzalez, G. McFaline-Figueroa, J. L. Wang, Q. 2025-05-10 doi:10.1101/2025.05.09.653136 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks ]]> https://biorxiv.org/content/10.1101/2025.05.07.652715v1?rss=1 Zhao, H. Velez, C. Naravane, A. C. Saha, A. Feldman, J. Skolnick, J. Murray, D. Honig, B. 2025-05-12 doi:10.1101/2025.05.07.652715 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Distribution and structural diversity of Type IV internal ribosome entry sites ]]> https://biorxiv.org/content/10.1101/2025.05.12.653553v1?rss=1 Segar, K. E. Sherlock, M. E. Kieft, J. S. 2025-05-12 doi:10.1101/2025.05.12.653553 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ The contribution of the locus coeruleus-norepinephrine system to the coupling between pupil-linked arousal and cortical state ]]> https://biorxiv.org/content/10.1101/2025.05.07.652771v1?rss=1 Weiss, E. Liu, Y. A. Wang, Q. 2025-05-13 doi:10.1101/2025.05.07.652771 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Probing the CaV1.2 interactome in heart failure identifies a positive modulator of inotropy and lusitropy ]]> https://biorxiv.org/content/10.1101/2025.05.08.652977v1?rss=1 Rodriques, A. Liu, G. Katchman, A. N. Zakharov, S. I. Wan, E. Y. Kalocsay, M. Eisert, R. Bradshaw, G. A. Chen, B. Yang, L. Reiken, S. Liao, X. Ji, R. Saadallah, N. Fanourakis, S. Topkara, V. K. Yuan, Q. Kushner, J. 2025-05-13 doi:10.1101/2025.05.08.652977 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Cholinergic blockade reveals role for human hippocampal theta in encoding but not retrieval ]]> https://biorxiv.org/content/10.1101/2025.05.12.653487v1?rss=1 Gedankien, T. Kriegel, J. Zabeh, E. McDonagh, D. Lega, B. Jacobs, J. 2025-05-13 doi:10.1101/2025.05.12.653487 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Cell-type-specific synaptic scaling mechanisms differentially contribute to associative learning ]]> https://biorxiv.org/content/10.1101/2025.05.14.654005v1?rss=1 Veneto, F. Kepce, A. Wu, Y. K. Gjorgjieva, J. 2025-05-14 doi:10.1101/2025.05.14.654005 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Pleasure in groove is associated with neuromelanin levels in the substantia nigra of younger healthy individuals: A neuromelanin-sensitive MRI study ]]> https://biorxiv.org/content/10.1101/2025.05.10.653047v1?rss=1 Etani, T. Nakajima, S. Honda, S. Homma, S. Kaneko, Y. Kondoh, S. Tarumi, R. Tsugawa, S. Moriyama, S. Tobari, Y. Samma, T. Horga, G. Cassidy, C. Uchida, H. Fujii, S. 2025-05-15 doi:10.1101/2025.05.10.653047 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients ]]> https://biorxiv.org/content/10.1101/2025.05.15.653154v1?rss=1 Cohen, D. A. Obradovic, A. Jovanovic, L. Mitani, Y. Li, T. Lee, S. De, D. Bethancourt, C.-N. Shin, A. Dunbar, K. Cambuli, F. Lengner, C. Li, N. Rogers, C. Ho, J. Jakubikova, V. Blystone, E. Pumpalova, Y. Dionigi, B. Vickovic, S. Cheng, C.-W. Gabre, J. 2025-05-16 doi:10.1101/2025.05.15.653154 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Oxytocin receptor absence reduces selectivity in peer relationships and alters neurochemical release dynamics in prairie voles ]]> https://biorxiv.org/content/10.1101/2025.05.15.654128v1?rss=1 Black, A. M. Komatsu, N. Zhao, J. Taskey, S. R. Serrano, N. S. Sharma, R. Manoli, D. S. Landry, M. P. Beery, A. 2025-05-16 doi:10.1101/2025.05.15.654128 Cold Spring Harbor Laboratory Press 2025-05-16 <![CDATA[ Pervasive homeobox gene function in the male-specific nervous system of Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.05.13.653874v1?rss=1 Fernandez, R. W. Digirolamo, A. J. Valperga, G. Aguilar, G. R. Molina-Garcia, L. Kersh, R. M. Wang, C. Pe, K. Ramadan, Y. H. Loer, C. Barrios, A. Hobert, O. 2025-05-17 doi:10.1101/2025.05.13.653874 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ When should adaptation arise from a polygenic response versus few large effect changes? ]]> https://biorxiv.org/content/10.1101/2025.05.15.654234v1?rss=1 Milligan, W. R. Hayward, L. K. Sella, G. 2025-05-17 doi:10.1101/2025.05.15.654234 Cold Spring Harbor Laboratory Press 2025-05-17 <![CDATA[ fMRIPrep Lifespan: Extending A Robust Pipeline for Functional MRI Preprocessing to Developmental Neuroimaging ]]> https://biorxiv.org/content/10.1101/2025.05.14.654069v1?rss=1 Goncalves, M. Moser, J. Madison, T. J. McCollum, r. Lundquist, J. T. Fayzullobekova, B. Hadera, L. Pham, H. H. N. Moore, L. A. Houghton, A. M. Conan, G. Styner, M. A. Alexopoulos, D. Smyser, C. D. Stoyell, S. M. Koirala, S. Nelson, S. M. Weldon, K. B. Lee, E. Hermosillo, R. J. M. Vizioli, L. Yacoub, E. Patel, G. H. Sanchez, J. Wengler, K. Salo, T. Satterthwaite, T. D. Elison, J. T. Markiewicz, C. J. Poldrack, R. A. Feczko, E. Esteban, O. Fair, D. A. 2025-05-18 doi:10.1101/2025.05.14.654069 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ An Anisotropic Reactive Viscoelastic Model of the Rhesus Macaque Cervix for Studying Cervical Remodeling ]]> https://biorxiv.org/content/10.1101/2025.05.14.654071v1?rss=1 Cordon, C. A. D. Fang, S. Rosado-Mendez, I. M. Ateshian, G. Hall, T. J. Feltovich, H. Myers, K. M. 2025-05-18 doi:10.1101/2025.05.14.654071 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ The thermal benefits of a mound-burrow system in a semi-desert Australian landscape: will this pebble fortress provide refuge from climate change? ]]> https://biorxiv.org/content/10.1101/2025.05.14.654155v1?rss=1 Firman, R. C. Rubenstein, D. R. 2025-05-18 doi:10.1101/2025.05.14.654155 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Mutation-selection-drift balance models of complex diseases ]]> https://biorxiv.org/content/10.1101/2025.05.18.654722v1?rss=1 Berg, J. J. Li, X. Riall, K. Hayward, L. Sella, G. 2025-05-18 doi:10.1101/2025.05.18.654722 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Whole-brain chemosensory responses of both C. elegans sexes ]]> https://biorxiv.org/content/10.1101/2025.05.15.654129v1?rss=1 Seyedolmohadesin, M. Fu, X. Torkashvand, M. Rasouli, S. Lang, S. Li, L. Kalinski, C. Cook, S. J. Schroeder, F. C. Yemini, E. Venkatachalam, V. 2025-05-19 doi:10.1101/2025.05.15.654129 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ The antibacterial factor APOL3 couples lysosomal damage to mitochondrial DNA efflux and type I IFN induction ]]> https://biorxiv.org/content/10.1101/2025.05.16.654477v1?rss=1 Ritacco, D. A. Shahnawaz, H. Oduguwa, A. Hawk, J. S. Vizcaino, B. Farber, D. L. Gaudet, R. G. 2025-05-19 doi:10.1101/2025.05.16.654477 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Identification of α-azacyclic acetamide-based inhibitors of P. falciparum Na+ pump (PfATP4) with fast-killing asexual blood-stage antimalarial activity by phenotypic screening ]]> https://biorxiv.org/content/10.1101/2025.05.20.655166v1?rss=1 Casas, A. Imlay, L. S. Thathy, V. Deni, I. Lehane, A. M. Lawong, A. K. Fairhurst, K. J. Striepen, J. Lee, S. Kumar, A. Xing, C. Niederstrasser, H. Posner, B. A. Laleu, B. Charman, S. A. Fidock, D. A. Ready, J. M. Phillips, M. A. 2025-05-20 doi:10.1101/2025.05.20.655166 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Accounting for uncertainty in residual variances improves calibration of the Sum of Single Effects model for small sample sizes ]]> https://biorxiv.org/content/10.1101/2025.05.16.654543v1?rss=1 Denault, W. R. P. Carbonetto, P. Li, R. Consortium, T. A. s. D. F. G. Wang, G. Stephens, M. 2025-05-21 doi:10.1101/2025.05.16.654543 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Brain Multi-Omic Subtypes of Neuroticism Reveal Molecular Signatures linked to Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.05.19.654904v1?rss=1 Zammit, A. R. Lopes, K. d. P. Batalha, C. M. P. F. Yu, L. Poole, V. N. Tasaki, S. Kapasi, A. Wang, Y. De Jager, P. L. Menon, V. Seyfried, N. Kaddurah-Daouk, R. Iturria-Medina, Y. Bennett, D. A. 2025-05-21 doi:10.1101/2025.05.19.654904 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation ]]> https://biorxiv.org/content/10.1101/2025.05.20.655228v1?rss=1 Ibikunle, C. O. Xue, C. Kim, E. Yan, H. Coronel, J. Zhu, L. Y. Cui, J. Chung, A. Bauer, R. C. Sachs, N. Maegdefessel, L. Li, M. Tall, A. R. Bashore, A. C. Reilly, M. 2025-05-23 doi:10.1101/2025.05.20.655228 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Early Indirect Neurogenesis transitions to late Direct Neurogenesis in mouse cerebral cortex development ]]> https://biorxiv.org/content/10.1101/2025.05.22.655488v1?rss=1 Cardenas, A. Celik, I. Espinos, A. Streicher, C. Lopez-Gonzalez, L. Del Valle Anton, L. Fernandez, V. Amin, S. Negri, E. Fernandez Ortuno, E. Hippenmeyer, S. Borrell, V. 2025-05-23 doi:10.1101/2025.05.22.655488 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Physics-Informed Digital Twin Can Predict Cerebral Blood Flow and Cerebral Vascular Regulation Mechanisms in Neurocritical Care Patients ]]> https://biorxiv.org/content/10.1101/2025.05.22.655581v1?rss=1 Briggs, J. K. stroh, j. n. Park, S. Foreman, B. Tymko, M. Carr, J. Sirlanci, M. Ainslie, P. Benninger, R. K. Bennett, T. D. Albers, D. J. 2025-05-23 doi:10.1101/2025.05.22.655581 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ A Python Toolbox for Representational Similarity Analysis ]]> https://biorxiv.org/content/10.1101/2025.05.22.655542v1?rss=1 van den Bosch, J. J. Golan, T. Peters, B. Taylor, J. Shahbazi, M. Lin, B. Charest, I. Diedrichsen, J. Kriegeskorte, N. Mur, M. Schuett, H. 2025-05-27 doi:10.1101/2025.05.22.655542 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Tissue signatures of human macrophages during homeostasis and activation ]]> https://biorxiv.org/content/10.1101/2025.05.23.655632v1?rss=1 Caron, D. P. Specht, W. L. Chen, D. Wells, S. B. Szabo, P. A. Sims, P. A. Farber, D. L. 2025-05-28 doi:10.1101/2025.05.23.655632 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[ Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation ]]> https://biorxiv.org/content/10.1101/2025.05.28.656712v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@ffcd62org.highwire.dtl.DTLVardef@50eaeorg.highwire.dtl.DTLVardef@6df44org.highwire.dtl.DTLVardef@12bfacf_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Swann, J. W. Fung, J. H. Chen, Z. Olson, O. C. Collins, A. Lhakang, T. Proven, M. A. Zhang, R. Rabadan, R. Passegue, E. 2025-05-29 doi:10.1101/2025.05.28.656712 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Converging pathways: shared brain circuitry engaged by monoaminergic antidepressants, ketamine and psilocybin ]]> https://biorxiv.org/content/10.1101/2025.05.26.655791v1?rss=1 Joseph, K. Collins, J. Genovese, T. Maxwell, M. Lieberman, J. A. Osten, P. 2025-05-30 doi:10.1101/2025.05.26.655791 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Context-Dependent Variability Of HIF Heterodimers Influences Interactions With Macromolecular And Small Molecule Partners ]]> https://biorxiv.org/content/10.1101/2025.05.29.656908v1?rss=1 Closson, J. D. Xu, X. Zhang, M. Tiyani, T. T. Marcelino, L. P. Isiorho, E. A. Nagati, J. S. Garcia, J. A. Gardner, K. H. 2025-05-30 doi:10.1101/2025.05.29.656908 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.05.28.656689v1?rss=1 Grimont, A. Falvo, D. J. Sisso, W. J. Zumbo, P. Chan, C. W. Santos, F. Pan, G. Cleveland, M. Yaron, T. Osterhoudt, A. S. Meng, Y. Zafra, M. P. Fall, W. B. Rendeiro, A. F. Hissong, E. Yantiss, R. K. Betel, D. Magnuson, M. A. Leach, S. D. Rustgi, A. K. Dow, L. E. Chandwani, R. 2025-06-01 doi:10.1101/2025.05.28.656689 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ From Morphology to Computation: How Synaptic Organization Shapes Place Fields in CA1 Pyramidal Neurons ]]> https://biorxiv.org/content/10.1101/2025.05.30.657022v1?rss=1 Tasciotti, S. Iascone, D. M. Chavlis, S. Hammond, L. Katz, Y. Losonczy, A. Polleaux, F. Poirazi, P. 2025-06-01 doi:10.1101/2025.05.30.657022 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Social experience alters behaviors by reprogramming the Fruitless pathway and circadian state in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.05.30.657129v1?rss=1 Du, C. Okuwa, S. Jia, L. Rozados Barreiro, M. Scott, S. Sotelo Fonseca, J. E. Mabuchi, Y. Appadoo, S. Garcia, L. Rohrbach, S. Koruk, S. Balkanli, E. Lin, J. Yapici, N. Jones, C. Volkan, P. 2025-06-03 doi:10.1101/2025.05.30.657129 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Deciphering the combinatorial expression pattern and genetic regulatory mechanisms of Beats and Sides in the olfactory circuits of Drosophila ]]> https://biorxiv.org/content/10.1101/2025.05.31.657193v1?rss=1 Duan, Q. Okuwa, S. Estrella, R. Yeung, C. Chen, Y.-C. D. Rio, L. Q. Vien, K. M. Volkan, P. C. 2025-06-03 doi:10.1101/2025.05.31.657193 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Global Landscape of Human Kinase Motifs in Viral Proteomes ]]> https://biorxiv.org/content/10.1101/2025.06.02.657064v1?rss=1 Alba, K. Winters, D. M. Makanani, S. K. Kaushal, P. Delgado, Y. Ashley, I. A. Sharma, S. Blanc, S. F. Kim, E. Yaron, T. Johnson, J. L. Selby, J. Hur, M. Ni, J. Nguyen, J. Brent, M. H. Yip, E. Kassem, A. Wohlschlegel, J. Fregoso, O. I. Wu, T.-T. Li, M. M. Bouhaddou, M. 2025-06-03 doi:10.1101/2025.06.02.657064 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Cytokine expression profile in the human brain of older adults ]]> https://biorxiv.org/content/10.1101/2025.06.02.657444v1?rss=1 Godoy, J. B. Vialle, R. A. dos Santos, L. Raittz, R. T. Wang, Y. Menon, V. De Jager, P. Schneider, J. A. Tasaki, S. Bennett, D. A. Guizelini, D. Lopes, K. 2025-06-04 doi:10.1101/2025.06.02.657444 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Implantable CMOS Deep-Brain Fluorescence Imager with Single-Neuron Resolution ]]> https://biorxiv.org/content/10.1101/2025.06.03.657675v1?rss=1 Yilmaz, S. Choi, J. Uguz, I. Kim, J. Akrouh, A. Taal, A. J. Andino-Pavlovsky, V. Yin, H. Fabbri, J. D. Moreaux, L. Roukes, M. L. Shepard, K. L. 2025-06-06 doi:10.1101/2025.06.03.657675 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ IL-18 inhibition enlarges lesions, necrotic cores and thickens fibrous caps in Jak2V617F clonal hematopoiesis-driven atherosclerosis. ]]> https://biorxiv.org/content/10.1101/2025.06.03.657754v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@a93b2forg.highwire.dtl.DTLVardef@6cc057org.highwire.dtl.DTLVardef@1c7afc5org.highwire.dtl.DTLVardef@e4da82_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIInflammasome activation produces active IL-1 and IL-18 and worsens atherosclerosis in clonal hematopoiesis (CH) however the contribution of IL-18 is unknown. C_LIO_LIAntibody inhibition of IL-18 increased plaque collagen but also increased early lesion area and late lesions with large necrotic cores in Jak2VF CH mice. C_LIO_LIThere was a reversal of AIM2 inflammasome activation but a switch to apoptosis which along with reduced efferocytosis increased necrosis C_LIO_LIThese events appeared to be coordinated by reduced IFN-{gamma} which increased collagen but also decreased expression of efferocytotic genes. Our studies call into question whether inhibition of IL-18 would stabilize plaques in CH. C_LI ]]> Tavallaie, M. Hsu, C.-C. Hardaway, B. Dou, H. Fidler, T. Kim, E. Wang, N. Westerterp, M. Tall, A. R. 2025-06-06 doi:10.1101/2025.06.03.657754 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Early neuronal reprogramming and cell cycle reentry shape Alzheimer's disease progression ]]> https://biorxiv.org/content/10.1101/2025.06.04.653670v1?rss=1 Meir, R. Schwartz, G. Adam, M. Avni Lapidot, A. Cain, A. Green, G. S. Menon, V. Bennett, D. A. De Jager, P. Habib, N. 2025-06-06 doi:10.1101/2025.06.04.653670 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ PP2A METHYLESTERASE, PME-1, AND PP2A METHYLTRANSFERASE, LCMT-1, CONTROL SENSITIVITY TO IMPAIRMENTS CAUSED BY INJURY-RELATED OLIGOMERIC TAU ]]> https://biorxiv.org/content/10.1101/2025.06.05.657660v1?rss=1 Sundaresh, S. N. Vogel, E. W. Hue, C. D. Zhang, H. Staniszewski, A. Berman, H. L. Gill, Z. Asam, K. Liang, S. Shen, L. Gnanaprakash, M. Acquarone, E. Fa, M. Kanaan, N. M. Morrison, B. Arancio, O. Nicholls, R. E. 2025-06-06 doi:10.1101/2025.06.05.657660 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Simultaneous cortical responses to multiple written words ]]> https://biorxiv.org/content/10.1101/2025.06.05.658099v1?rss=1 Chauhan, V. S. McCook, K. Latif, M. White, A. L. 2025-06-06 doi:10.1101/2025.06.05.658099 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ LIMD1 Loss Confers a GPX4-Dependent Cell State in Lung Cancer ]]> https://biorxiv.org/content/10.1101/2025.06.06.658274v1?rss=1 Saha, A. Grevitt, P. Marques, J. G. Von Kriegsheim, A. Shah, K. M. Gao, Z. Stockwell, B. R. Finch, A. J. Peck, B. Sharp, T. V. 2025-06-07 doi:10.1101/2025.06.06.658274 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ TICKHUNTER: A Targeted Hybridization-Capture Sequencing Approach for the Detection and Characterization of Tick-borne Pathogens and Blood Meals ]]> https://biorxiv.org/content/10.1101/2025.06.06.658355v1?rss=1 Wang, X. Brown, J. J. Lilly, M. V. Plimpton, L. Murrell, C. M. Llanos-Soto, S. G. Zehr, J. D. Sun, Y. Reboul, G. Sams, K. Sabaawy, A. Singh, L. Tallmadge, R. L. Mitchell, P. K. Anderson, R. R. Ladd-Wilson, S. G. Bourgikos, E. Vogels, C. B. Olarte-Castillo, X. A. Diuk-Wasser, M. Goodman, L. B. 2025-06-07 doi:10.1101/2025.06.06.658355 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[ Uncovering Heterogeneous Effects via Localized Feature Selection ]]> https://biorxiv.org/content/10.1101/2025.06.03.657761v1?rss=1 Liu, X. Gu, J. Chen, Z. Chu, B. Liu, L. Morrison, T. Butler, R. R. Edelson, J. Li, J. Longo, F. M. Tang, H. Ionita-laza, I. Sabatti, C. Candes, E. He, Z. 2025-06-09 doi:10.1101/2025.06.03.657761 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ A Radiomic Approach to Clinical MRI Refines the Thalamus-Cognition Link in Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2025.06.05.657698v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@6f1dd8org.highwire.dtl.DTLVardef@11069c6org.highwire.dtl.DTLVardef@905512org.highwire.dtl.DTLVardef@1c12171_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Overview of the involvement of different cohorts in the study, specific study objectives and the statistical analysis approaches employed. Abbreviations: SDMT: Symbol Digit Modalities Test, PASAT: Paced Auditory Serial Addition Test, DSST: Digit Symbol Substitution Test, LASSO: Least Absolute Shrinkage and Selection Operator. C_FIG ResultsTwenty-eight RF-ROI pairs were associated with SDMT in the replication set (FDR<0.05). Of these, 24 were also associated with PASAT (FDR[≤]0.03), and 2 with DSST. Only ventral nuclei volume showed replicated associations among volumetrics. Only 4 putamen-derived pairs were associated with SDMT (FDR=0.04). LASSO results confirmed RF outperformed volumes. DiscussionRF extracted from the thalamus are strongly associated with cognitive performance in PwMS, outperforming volumetric measures and supporting their potential as sensitive imaging biomarkers. ]]> Buyukturkoglu, K. Lu, L. Davis, L. Orellana, R. E. White, C. C. Sun, R. Ozcelik, S. Isenstein, N. M. Onomichi, K. B. Iqbal, R. Zhao, B. Stern, Y. Zeydan, B. Kantarci, O. H. Riley, C. S. De Jager, P. L. 2025-06-09 doi:10.1101/2025.06.05.657698 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[ The vault particle is enclosed by a C13-symmetric cap with a positively charged exterior ]]> https://biorxiv.org/content/10.1101/2025.06.06.658390v1?rss=1 Li, H. Vallese, F. Clarke, O. B. 2025-06-10 doi:10.1101/2025.06.06.658390 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Exapted CRISPR-Cas12f homologs drive RNA-guided transcription ]]> https://biorxiv.org/content/10.1101/2025.06.10.658865v1?rss=1 Hoffmann, F. T. Wiegand, T. Palmieri, A. I. Glass-Klaiber, J. Xiao, R. Tang, S. Le, H. Meers, C. Lampe, G. D. Chang, L. Sternberg, S. H. 2025-06-10 doi:10.1101/2025.06.10.658865 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ Structural basis of RNA-guided transcription by a dCas12f-σE-RNAP complex ]]> https://biorxiv.org/content/10.1101/2025.06.10.658880v1?rss=1 Xiao, R. Hoffmann, F. T. Xie, D. Wiegand, T. Palmieri, A. I. Sternberg, S. H. Chang, L. 2025-06-10 doi:10.1101/2025.06.10.658880 Cold Spring Harbor Laboratory Press 2025-06-10 <![CDATA[ KRT6A and KRT17 mark distinct stem cell populations in the adult palpebral conjunctiva and Meibomian gland ]]> https://biorxiv.org/content/10.1101/2025.06.10.658923v1?rss=1 Zhu, X. Xu, M. Owens, D. M. Millar, S. E. 2025-06-11 doi:10.1101/2025.06.10.658923 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Conformational dynamics of the active state of β-arrestin 1 ]]> https://biorxiv.org/content/10.1101/2025.06.10.658911v1?rss=1 Ngo, V. Asher, W. B. Javitch, J. A. Shi, L. 2025-06-14 doi:10.1101/2025.06.10.658911 Cold Spring Harbor Laboratory Press 2025-06-14 <![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[ The nucleus forms a dynamic contact with the plasma membrane to maintain the glandular epithelial architecture ]]> https://biorxiv.org/content/10.1101/2025.06.13.659552v1?rss=1 Rayer, M. S. Mui, K. Pendyala, K. Rockenbach Zenzen, J. A. Antoku, S. Lele, T. Gundersen, G. G. 2025-06-15 doi:10.1101/2025.06.13.659552 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ The nucleus activates mechano-responsiveness via FHOD-associated LINC complexes ]]> https://biorxiv.org/content/10.1101/2025.06.13.659598v1?rss=1 Antoku, S. Gundersen, G. G. Worman, H. J. Morrow, J. P. Joseph, L. C. Fine, B. M. Zhang, X. Kushner, J. Lin, C.-S. Schwartz, T. Dabhade, P. 2025-06-15 doi:10.1101/2025.06.13.659598 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer ]]> https://biorxiv.org/content/10.1101/2025.06.15.659774v1?rss=1 Koblan, L. W. Yost, K. E. Zheng, P. Colgan, W. N. Jones, M. G. Yang, D. Kumar, A. Sandhu, J. Schnell, A. Sun, D. Ergen, C. Saunders, R. A. Zhuang, X. Allen, W. E. Yosef, N. Weissman, J. S. 2025-06-15 doi:10.1101/2025.06.15.659774 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Generation of knock-in Cre and FlpO mouse lines for precise targeting of striatal projection neurons and dopaminergic neurons ]]> https://biorxiv.org/content/10.1101/2025.06.15.659794v1?rss=1 Albarran, E. Fushiki, A. Nelson, A. Ng, D. Chaimowitz, C. Nikoobakht, L. Sippy, T. Peterka, D. S. Costa, R. M. 2025-06-15 doi:10.1101/2025.06.15.659794 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ A Hotspot Phosphorylation Site on SHP2 Drives Oncoprotein Activation and Drug Resistance ]]> https://biorxiv.org/content/10.1101/2025.06.11.659120v1?rss=1 Karunaraj, P. Scheele, R. Wells, M. L. Rathod, R. Abrahamson, S. Taylor, L. C. Gokulu, I. S. Chowdhury, L. Kazmi, A. Song, W. Hornbeck, P. Li, J. Glasgow, A. Vasan, N. 2025-06-16 doi:10.1101/2025.06.11.659120 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data ]]> https://biorxiv.org/content/10.1101/2025.06.11.658931v1?rss=1 Zhang, Z. Glatt-Deeley, H. Zou, L. Song, D. Miura, P. 2025-06-17 doi:10.1101/2025.06.11.658931 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Seahorse Metabolic Analysis for Human and Mouse Cardiac Organotypic Slices ]]> https://biorxiv.org/content/10.1101/2025.06.11.659150v1?rss=1 Trampel, K. A. Li, B. Melisova, A. Madrid, M. K. George, S. A. Efimov, I. R. 2025-06-17 doi:10.1101/2025.06.11.659150 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Rapid acquisition of HIV-1 neutralization breadth in a rhesus V2 apex germline antibody mouse model after a single bolus immunization ]]> https://biorxiv.org/content/10.1101/2025.06.12.659380v1?rss=1 Ghosh, A. R. Habib, R. Mishra, N. Roark, R. S. Akauliya, M. Albowaidey, A. A. Allen, J. D. Amereh, K. Avillion, G. Bottermann, M. Liang, B. Chaudhary, N. Callaghan, S. Dye, J. Li, X. Ellis-Pugh, J. R. Chowdhury, R. R. James, N. E. Liu, X. Maiorino, L. Villavicencio, P. M. Nedellec, R. Oberoi, P. Sowers, K. J. Park, Y. Prum, T. Rodriguez, L. Ssozi, M. Torres, J. Walsh, A. A. Warner, J. E. Weldon, S. R. Xu, L. Wiehe, K. Crispin, M. Ward, A. B. Nair, U. Hahn, B. H. Burton, D. R. Shapiro, L. Kwong, P. D. Irvine, D. J. Andrabi, R. Shaw, G. M. Batista, F. 2025-06-17 doi:10.1101/2025.06.12.659380 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Pulsed-laser lensing for phase modulation in electron microscopy ]]> https://biorxiv.org/content/10.1101/2025.06.12.659428v1?rss=1 Du, D. X. Bartnik, A. C. Duncan, C. J. R. Choudhry, U. Tabachnik, T. Sallah, C. Ogawa, Y. Najafi, E. Yang, D.-S. Maxson, J. M. Fitzpatrick, A. W. P. 2025-06-17 doi:10.1101/2025.06.12.659428 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[ The contribution of native protein complexes to targeted protein degradation ]]> https://biorxiv.org/content/10.1101/2025.06.17.660125v1?rss=1 Glennie, L. Curnutt, N. Cartwright, T. Dunbar, K. J. Chatelier, B. L. Wood, N. Macartney, T. J. Woo, C. M. Sapkota, G. P. 2025-06-17 doi:10.1101/2025.06.17.660125 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Sex bias determines MERS-CoV infection outcomes in a mouse model of differential pathogenicity ]]> https://biorxiv.org/content/10.1101/2025.06.19.660369v1?rss=1 Habbick, M. R. Bushmaker, T. Singh, R. Sharma, P. Munster, V. J. van Doremalen, N. Rasmussen, A. L. 2025-06-19 doi:10.1101/2025.06.19.660369 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity ]]> https://biorxiv.org/content/10.1101/2025.06.20.659510v1?rss=1 Ward, A. O. Schonrock, N. McCann, A. J. Phanor, S. K. Kock, K. H. Kurland, J. V. Wu, F. Murray, N. J. Walshe, J. Alankarage, D. Dunwoodie, S. L. Meunier, F. A. Francois, M. Bulyk, M. L. Ramialison, M. Harvey, R. P. 2025-06-20 doi:10.1101/2025.06.20.659510 Cold Spring Harbor Laboratory Press 2025-06-20 <![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[ HMMR/RHAMM recruits SACK1D/FAM83D-CK1α complex at the mitotic spindle to control spindle alignment ]]> https://biorxiv.org/content/10.1101/2025.06.23.661043v1?rss=1 Sapkota, G. P. Cartwright, T. N. Nakarakanti, N. K. Dunbar, K. Fulcher, L. Bader, S. Wood, N. Macartney, T. 2025-06-24 doi:10.1101/2025.06.23.661043 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Disrupted Energy Landscape in Individuals with Mild Cognitive Impairment: Insights from Network Control Theory ]]> https://biorxiv.org/content/10.1101/2025.06.19.660545v1?rss=1 Neumann, D. L. Razlighi, Q. Stern, Y. Devanand, D. P. Jamison, K. Kuceyeski, A. Tozlu, C. 2025-06-25 doi:10.1101/2025.06.19.660545 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Mitochondrial Energy Transformation Capacity Influences Brain Activation During Sensory, Affective, and Cognitive Tasks ]]> https://biorxiv.org/content/10.1101/2025.06.25.661482v1?rss=1 Bo, K. Kelly, C. Trumpff, C. Hirano, M. Wager, T. Picard, M. 2025-06-25 doi:10.1101/2025.06.25.661482 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Behavioral heterogeneity in host-seeking and post-feedingsuppression among disease vector mosquitoes ]]> https://biorxiv.org/content/10.1101/2025.06.18.660345v1?rss=1 Uehara, T. Dong, L. Duvall, L. B. 2025-06-26 doi:10.1101/2025.06.18.660345 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ US6 hijacks the peptide-loading complex by trapping transporter-chaperone dynamics ]]> https://biorxiv.org/content/10.1101/2025.06.25.661491v1?rss=1 Stolz, M. Susac, L. Fahim, A. Keller, R. Saggau, L. Mancia, F. Trowitzsch, S. Tampe, R. 2025-06-27 doi:10.1101/2025.06.25.661491 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Long Noncoding RNAs Enforce Pancreatic Cancer Identity and Block Reprogramming ]]> https://biorxiv.org/content/10.1101/2025.06.25.661419v1?rss=1 Grygoryev, D. Lee, S.-W. Frankston, C. M. Rakshe, S. Berry, M. Hirano, A. Ekstrom, T. Manalo, E. Tessier, J. Chow-Castro, M. Link, J. Keith, D. Sheppard, B. C. Fei, S. Morgan, T. Remotti, H. E. Yang, W. Furth, E. Thakurela, S. Sears, R. C. Kim, J. 2025-06-28 doi:10.1101/2025.06.25.661419 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma ]]> https://biorxiv.org/content/10.1101/2025.06.25.661622v1?rss=1 Wang, Y. Cai, Z. Zeng, Q. Gao, Y. Ouyang, J. Xu, Y. Yang, S. He, S. Nie, Y. Cai, Y. Zhou, F. Jin, C. Wang, X. Xie, Z. Zhu, D. Xie, T. Cheng, K.-T. Yang, C. Fu, X. Wang, J. Zhang, K. Yao, J. Rabadan, R. Chen, H. 2025-06-30 doi:10.1101/2025.06.25.661622 Cold Spring Harbor Laboratory Press 2025-06-30 <![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[ Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants ]]> https://biorxiv.org/content/10.1101/2025.06.30.662374v1?rss=1 van Vlimmeren, A. E. Giglio, R. M. Jiang, Z. Lee, M. McFaline-Figueroa, J. L. Shah, N. H. 2025-07-02 doi:10.1101/2025.06.30.662374 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Perplexity as a Metric for Isoform Diversity in the Human Transcriptome ]]> https://biorxiv.org/content/10.1101/2025.07.02.662769v1?rss=1 Schertzer, M. D. Park, S. H. Su, J. Sheynkman, G. M. Knowles, D. A. 2025-07-02 doi:10.1101/2025.07.02.662769 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Multiscale wrinkling dynamics in epithelial shells ]]> https://biorxiv.org/content/10.1101/2025.06.30.662426v1?rss=1 Chahare, N. Ouzeri, A. Wilson, T. Bal, P. K. Golde, T. Vilanova, G. Pujol-Vives, P. Roca-Cusachs, P. Trepat, X. Arroyo, M. 2025-07-03 doi:10.1101/2025.06.30.662426 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Why are so many fusogens rod-shaped? ]]> https://biorxiv.org/content/10.1101/2025.06.30.662463v1?rss=1 Butu, I. C. Zeng, J. An, D. McDargh, Z. A. Duan, K. O'Shaughnessy, B. 2025-07-03 doi:10.1101/2025.06.30.662463 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Two parallel lineage-committed progenitors contribute to the developing brain ]]> https://biorxiv.org/content/10.1101/2025.07.02.662771v1?rss=1 Dundes, C. E. Jokhai, R. T. Ahsan, H. Kang, R. S. Salomon-Shulman, R. E. A. Rajan, A. Kim, Y. S. Stanton, L. J. Xu, C. Do, S. McDonald, B. D. Lopez, J. M. A. Urrutia, H. A. Greenfeld, H. Wong, A. Qu, Y. Petkovic, A. S. Miao, Y. Garcia, K. C. Monje, M. Wagner, D. E. Bronner, M. E. Lowe, C. J. Loh, K. M. 2025-07-03 doi:10.1101/2025.07.02.662771 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Connectome analysis of a cerebellum-like circuit for sensory prediction ]]> https://biorxiv.org/content/10.1101/2025.07.03.662989v1?rss=1 Perks, K. E. Petkova, M. D. Muller, S. Z. Genecin, M. Ghatare, A. Schalek, R. Wu, Y. Januszewski, M. Jain, V. Lichtman, J. W. Abbott, L. Sawtell, N. B. 2025-07-03 doi:10.1101/2025.07.03.662989 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ The pathogenic E139D mutation stabilizes a non-canonical active state of the multi-domain phosphatase SHP2 ]]> https://biorxiv.org/content/10.1101/2025.07.02.662799v1?rss=1 van Vlimmeren, A. E. Jiang, Z. Karandur, D. Applebaum Licht, A. T. Shah, N. H. 2025-07-04 doi:10.1101/2025.07.02.662799 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ CloneCoordinate: Open-source software for collaborative DNA construction ]]> https://biorxiv.org/content/10.1101/2025.07.04.663221v1?rss=1 Jeon, E. Shen, Z. Christ, S. Qi, E. Fan, I. Lee, N. Morgan, O. Ohl, M. Millson, D. Laker, M. Pierson, A. Villegas Garcia, E. Zhang, Y. Choi, A. Iyengar, A. Kim, R. Lee, J. Niedeck, L. Oeien, V. Rashid, M. Seetharaman, N. Singh, A. Soble, D. Yu, J. Yu, K. Berdy, S. Chang, E. Kitazono, R. Ortiz, S. Taylor, D. Thuronyi, B. W. 2025-07-06 doi:10.1101/2025.07.04.663221 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Music-evoked reactivation during continuous perception is associated with enhanced subsequent recall of naturalistic events ]]> https://biorxiv.org/content/10.1101/2025.07.05.663273v1?rss=1 Williams, J. A. Margulis, E. H. Baldassano, C. Hasson, U. Chen, J. Norman, K. A. 2025-07-06 doi:10.1101/2025.07.05.663273 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ A New Computational Inverse Modeling Approach for Cellular Traction Force Microscopy that Accounts for Hydrogel Compressibility ]]> https://biorxiv.org/content/10.1101/2025.07.03.663064v1?rss=1 Peery, G. West, T. M. Chemuturi, S. S. Pham, J. H. Ferrari, G. Sacks, M. S. 2025-07-07 doi:10.1101/2025.07.03.663064 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Hydration free energy is a significant predictor of globular protein incorporation into condensates ]]> https://biorxiv.org/content/10.1101/2025.07.03.663089v1?rss=1 Anderson, S. Harrison, M. Dignon, G. L. 2025-07-07 doi:10.1101/2025.07.03.663089 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Tendon fibroblast inflammatory responses depend on NF-κβ and JAK/STAT signaling and alter mechanotransduction pathways ]]> https://biorxiv.org/content/10.1101/2025.07.04.663209v1?rss=1 Sup, M. Kim, M. M. Song, L. Genin, G. M. Thomopoulos, S. 2025-07-08 doi:10.1101/2025.07.04.663209 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Musculoskeletal architecture of the shoulder: A comparative anatomy study in bats and mice informing human rotator cuff function ]]> https://biorxiv.org/content/10.1101/2025.07.04.663211v1?rss=1 Kurtaliaj, I. Kunes, J. Li, S. Rowley, M. Forrester, L. A. Golman, M. Swartz, S. M. Levine, W. N. Genin, G. M. Thomopoulos, S. 2025-07-08 doi:10.1101/2025.07.04.663211 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ GREmLN: A Cellular Regulatory Network-Aware Transcriptomics Foundation Model ]]> https://biorxiv.org/content/10.1101/2025.07.03.663009v1?rss=1 Zhang, M. Swamy, V. Cassius, R. Dupire, L. Kanatsoulis, C. Paull, E. AlQuraishi, M. Karaletsos, T. Califano, A. 2025-07-09 doi:10.1101/2025.07.03.663009 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ Avoidance engages dopaminergic punishment in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.07.07.663268v1?rss=1 Amin, F. Stone, J. T. Koenig, C. Mancini, N. Murakami, K. Bidaye, S. S. Heim, M.-M. Owald, D. Majumder, U. Grunwald Kadow, I. C. Pierzchlinska, A. Litwin-Kumar, A. Barnstedt, O. Gerber, B. 2025-07-10 doi:10.1101/2025.07.07.663268 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Identification of novel protective loci for executive function using the trail making test part B in the Long Life Family Study ]]> https://biorxiv.org/content/10.1101/2025.07.08.663708v1?rss=1 3.0). Statistical fine-mapping nominated five variants including three SNPs (NTRK3-rs74031103, protective CEMIP-rs2271159, and protective AGBL1-rs4134376) and two INDELs (protective KLHL25-15:85882445:IND, and protective CEMIP-15:80893381:IND) contributing to the linkage peak. Four out of these five variants are protective for TMT-B. The rs2271159 SNP influences CEMIP expression in cerebellum and hippocampus, while the 15:80893381:IND modulates CEMIP expression in blood. Additionally, the variant rs4134376 is a basal ganglia-specific eQTL for AGBL1. In conclusion, we utilized GWLS, leveraged multi-omics data (whole genome sequence genomic data, transcriptomic data, and lipidomic data), and identified novel protective variants and genes for TMT-B performance. ]]> Wang, L. Tanner, K. Andersen, S. L. Cosentino, S. Moghaddam, V. A. Daw, E. W. Anema, J. A. Lin, S. J. Acharya, S. Province, M. Wojczynski, M. K. 2025-07-12 doi:10.1101/2025.07.08.663708 Cold Spring Harbor Laboratory Press 2025-07-12 <![CDATA[ Fragment-Guided New Therapeutic Molecule Discovery and Mapping of Clinically Relevant Interactomes ]]> https://biorxiv.org/content/10.1101/2025.07.09.663848v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1db97a4org.highwire.dtl.DTLVardef@1c0a159org.highwire.dtl.DTLVardef@1a10711org.highwire.dtl.DTLVardef@d7016a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kanapeckaite, A. Okuyan, S. Wagg, D. J. Koster, J. Jancoriene, L. Sakalauskaite, I. Brasiuniene, B. Townsend-Nicholson, A. 2025-07-14 doi:10.1101/2025.07.09.663848 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Principled measures and estimates of trait polygenicity ]]> https://biorxiv.org/content/10.1101/2025.07.10.664154v1?rss=1 O'Connor, L. J. Sella, G. 2025-07-15 doi:10.1101/2025.07.10.664154 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Framed RSA: Representational comparisons that honor bothgeometry and population-mean response preferences ]]> https://biorxiv.org/content/10.1101/2025.07.10.664257v1?rss=1 Taylor, J. E. Kriegeskorte, N. 2025-07-16 doi:10.1101/2025.07.10.664257 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Metabolic imprinting drives epithelial memory during mucosal fungal infection ]]> https://biorxiv.org/content/10.1101/2025.07.11.664387v1?rss=1 Sekar, J. Solis, N. V. Miao, J. Millet, N. Tom, B. Quintanilla, D. Pellon, A. Moyes, D. L. Gogos, J. Rossiter, H. Filler, S. G. Netea, M. Yee, J. K. Swidergall, M. 2025-07-17 doi:10.1101/2025.07.11.664387 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Dynamic remodeling of the pancreas immune landscape in obesity. ]]> https://biorxiv.org/content/10.1101/2025.07.14.664803v1?rss=1 Weisberg, S. P. Koshkin, A. Tanagala, K. K. K. Eichinger, A. Chait, M. Shakil, S. Young, A. Yoshikawa, J. Sakamoto, Y. Wells, S. B. Chen, X. Reizis, B. Farber, D. L. 2025-07-18 doi:10.1101/2025.07.14.664803 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Benchmarking the Impact of Anatomical Segmentation on In Vivo Magnetic Resonance Spectroscopy ]]> https://biorxiv.org/content/10.1101/2025.07.15.664931v1?rss=1 Archibald, J. Igwe, K. C. Kaiser, A. Landheer, K. Lee, J. Kramer, J. L. K. Zolch, N. Gudmundson, A. Zollner, H. J. Fleischer, C. C. Oeltzschner, G. Near, J. Mikkelsen, M. 2025-07-18 doi:10.1101/2025.07.15.664931 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ An Iron-regulated Signalling Pathway Controls Adipose Browning and Cancer Cachexia ]]> https://biorxiv.org/content/10.1101/2025.07.16.664180v1?rss=1 Nam, J. S. Dixon, M. S. Ahmadi, P. Schilling, K. Pan, S. Chen, Y. Yoon, N. A. Sun, Y. Lu, J. Ichimiya, S. Genkinger, J. M. Caffrey, T. C. Klute, K. A. Swanson, B. J. Grandgenett, P. Hollingsworth, M. A. Suguhara, K. Kluger, M. D. Ferrante, A. Diano, S. Chio, I. I. C. 2025-07-18 doi:10.1101/2025.07.16.664180 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Advantages of outcrossing in Plasmodium falciparum: insights from genetic crosses using fluorescent labelled parasites ]]> https://biorxiv.org/content/10.1101/2025.07.18.665596v1?rss=1 Li, X. Jutzeler, K. S. Abatiyow, B. A. Rezakhani, N. Haile, M. T. Leeb, A. S. Patel, H. Kappe, S. H. I. Nosten, F. Cheeseman, I. H. Ferdig, M. T. Anderson, T. J. Vaughan, A. M. Kumar, S. 2025-07-19 doi:10.1101/2025.07.18.665596 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ SOX9 is part of a combinatorial marker that reveals early development and embryological origins of the mouse brown adipose tissue depots ]]> https://biorxiv.org/content/10.1101/2025.07.16.665135v1?rss=1 Brent, A. E. Chan, R. Sirkay, V. Morton, B. R. Mansfield, J. H. 2025-07-21 doi:10.1101/2025.07.16.665135 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ CAKUT variants in PRPF8, DYRK2, and CEP78: implications for splicing and ciliogenesis ]]> https://biorxiv.org/content/10.1101/2025.07.16.665151v1?rss=1 Merz, L. M. Shril, S. Carrocci, T. J. Rezi, C. K. Zeps, N. J. Jimenez-Izquierdo, R. Bergmann, F. Petriman, N. A. Kolvenbach, C. M. Mertens, N. D. Johansen, S. L. Halbritter, J. Hilger, A. C. Hentges, K. E. Rasouly, H. M. Gharavi, A. G. Lorentzen, E. Calzado, M. Kispert, A. Yoshida, S. Pedersen, L. B. Hoskins, A. A. Buerger, F. Hildebrandt, F. 2025-07-21 doi:10.1101/2025.07.16.665151 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Ras-Responsive Element Binding Protein 1 regulates survival of Group 3 medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.07.16.665230v1?rss=1 Beigi Masihi, M. Chambers, K. Friedman, R. Pampou, S. Gudenas, B. L. Torrejon, J. Lee, C. Furnari, G. Chau, L. Q. GC, S. Lin, Y. Chapman, O. S. Skowron, P. Garzia, L. Taylor, M. D. Chavez, L. Ayrault, O. Northcott, P. A. Karan, C. Wechsler-Reya, R. J. 2025-07-21 doi:10.1101/2025.07.16.665230 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Antibody evasion and receptor binding of SARS-CoV-2 LP.8.1.1, NB.1.8.1, XFG, and related subvariants ]]> https://biorxiv.org/content/10.1101/2025.07.18.662329v1?rss=1 Mellis, I. A. Wu, M. Hong, H. Tzang, C.-C. Bowen, A. Wang, Q. Gherasim, C. Pierce, V. M. Shah, J. G. Purpura, L. J. Yin, M. T. Gordon, A. Guo, Y. Ho, D. D. 2025-07-21 doi:10.1101/2025.07.18.662329 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ The Calcium Pump ATP2B1/PMCA1 Regulates CNS Vascular Development by Facilitating Norrin- and WNT7A/B-induced Frizzled4 signaling ]]> https://biorxiv.org/content/10.1101/2025.07.17.664964v1?rss=1 Jo, H.-N. Kiffmeyer, E. Zhang, C. Zhang, L. Odame, E. Dinh, Q. C. Levey, J. Howe, M. Roux, K. J. Fischer, K.-D. Chen, Z. Junge, H. J. 2025-07-22 doi:10.1101/2025.07.17.664964 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Dopamine release effects on striatal blood oxygenation and whole brain plasticity underlying associative learning ]]> https://biorxiv.org/content/10.1101/2025.07.20.665732v1?rss=1 Lawen, A. Succi, I. K. Lichtman, D. Peterka, D. S. Abdus-Saboor, I. J. Kahn, I. 2025-07-24 doi:10.1101/2025.07.20.665732 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Hippocampal input-driven plasticity of prefrontal interneurons reveals a circuit basis for impaired spatial working memory. ]]> https://biorxiv.org/content/10.1101/2025.07.21.665987v1?rss=1 View larger version (61K): org.highwire.dtl.DTLVardef@29a326org.highwire.dtl.DTLVardef@1964208org.highwire.dtl.DTLVardef@1c94e4corg.highwire.dtl.DTLVardef@1336edb_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFSilverstein et al. investigated how ventral hippocampus (vHPC) inputs to medial prefrontal cortex (mPFC) interact with mPFC interneuron populations to support spatial working memory (SWM) in mice. They show that repeated vHPC input stimulation that reduces vHPC drive onto vasoactive intestinal peptide (VIP) interneurons also elevates delay-related VIP interneuron activity in early SWM task training, and this enhanced activity correlates with poorer training performance. Mice modelling the 22q11.2 deletion syndrome--known to have SWM learning deficits--recapitulate this altered VIP interneuron activity and show reduced vHPC input targeting of VIP interneurons. HIGHLIGHTSO_LIRepeated stimulation of vHPC inputs to mPFC persistently depresses VIP interneuron activity and enhances SST interneuron activity in mice C_LIO_LIBlunted monosynaptic drive onto mPFC VIP interneurons by repeated vHPC input stimulation plausibly reproduces in vivo activity changes C_LIO_LIStimulated mice show heightened VIP interneuron activity during the delay epoch in early SWM task training that correlates with poorer training performance C_LIO_LIMice modeling the 22q11.2 deletion syndrome with known SWM task learning deficits mirror this aberrant VIP interneuron activity profile and show reduced vHPC input targeting of VIP interneurons C_LI ]]> Silverstein, S. E. Clarity, T. T. Deshpande, M. S. Vaughan, E. Novik, S. Yarur, H. E. Zhang, S. Tsai, V. S. Ye, R. Mikofsky, R. M. Hsiang, M. Bauman, A. Loewinger, G. Pereira, F. Morales, M. Sohal, V. S. Tejeda, H. Gordon, J. A. Kupferschmidt, D. A. 2025-07-24 doi:10.1101/2025.07.21.665987 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ The multiplier benefits of integrating non-sewered and sewered wastewater treatment and sanitation processes ]]> https://biorxiv.org/content/10.1101/2025.07.22.666153v1?rss=1 Kone, D. Friedman, L. Chandran, K. 2025-07-24 doi:10.1101/2025.07.22.666153 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Diet-responsive proteogenomic effects following short-term restriction of animal products in humans ]]> https://biorxiv.org/content/10.1101/2025.07.21.665884v1?rss=1 Simistiras, A. Bocher, O. Emmanouil, C. Skoulakis, A. Glentis, S. Scarmeas, N. Zeggini, E. Rouskas, K. Dimas, A. S. 2025-07-25 doi:10.1101/2025.07.21.665884 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[ Depot-Specific Roles for C/EBPα in White Adipose Tissue Development and Metabolism ]]> https://biorxiv.org/content/10.1101/2025.07.22.666007v1?rss=1 Hu, K. Y. Dodge, E. A. Maguire, O. A. Ma, K. Y. Matias, C. V. Himede, H. S. Gomez Pardo, J. Cepeda, M. Bauer, R. C. 2025-07-26 doi:10.1101/2025.07.22.666007 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1. ]]> https://biorxiv.org/content/10.1101/2025.07.22.666009v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@ca611corg.highwire.dtl.DTLVardef@ad9264org.highwire.dtl.DTLVardef@1661c00org.highwire.dtl.DTLVardef@b86798_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ochiai, Y. Kobayashi, H. Sunagawa, M. Baba, T. Malagola, E. Wu, F. Tanaka, T. Hata, M. Arai, J. Jiang, Z. White, R. A. Zhi, X. Qian, J. Waterbury, Q. T. Tu, R. Zheng, B. Zeng, Y. Zheng, H. Zhang, P. Li, S. Zamechek, L. B. LaBella, J. S. Sugie, T. Iida, T. Enomoto, A. Eltzschig, H. K. Palermo, C. F. Chio, I. I. C. Olive, K. P. Wang, T. C. 2025-07-26 doi:10.1101/2025.07.22.666009 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Aggressive Cholesterol Lowering Normalizes Atherosclerosis Regression in Jak2V617F Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2025.07.23.666334v1?rss=1 Hardaway, B. D. Fidler, T. P. Tavallaie, M. Avrampou, K. Hsu, C.-C. Schiavone, S. Xiao, T. Wang, N. Tall, A. R. 2025-07-27 doi:10.1101/2025.07.23.666334 Cold Spring Harbor Laboratory Press 2025-07-27 <![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[ A multimodal approach for visualization and identification of electrophysiological cell types in vivo ]]> https://biorxiv.org/content/10.1101/2025.07.24.666654v1?rss=1 Lee, E. K. Gul, A. E. Heller, G. Lakunina, A. Yu, H. Shelton, A. Olsen, S. Steinmetz, N. A. Hurwitz, C. L. Jaramillo, S. Przytycki, P. Chandrasekaran, C. 2025-07-31 doi:10.1101/2025.07.24.666654 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ CD33-CD45 Interaction Reveals a Mechanistic Link to Alzheimer's Disease Susceptibility ]]> https://biorxiv.org/content/10.1101/2025.07.28.667311v1?rss=1 Vo, N. Rillahan, C. D. Chatila, Z. K. Virga, D. M. Hall, J. L. Tamucci, K. A. Rashid, M. Connor, S. M. Chintamen, S. Guzman, G. Taga, M. Liu, M. De Jager, P. L. St George-Hyslop, P. Lee, A. J. Vardarajan, B. N. Bennett, D. A. Kohler, J. J. Schenone, M. Elyaman, W. Carr, S. A. Bradshaw, E. M. 2025-07-31 doi:10.1101/2025.07.28.667311 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ CD33 and Clusterin Interact Biophysically and Genetically to Modulate Alzheimer Risk ]]> https://biorxiv.org/content/10.1101/2025.07.29.667318v1?rss=1 Dodd, R. B. Enomoto, M. Zhou, Y. Sato, K. Zhang, Y. Chen, F. Acheson, B. Ghaffari, D. Sayn-Wittgenstein, E. Manning, J. J. Dukas, G. V. Patel, R. Schweizer Burguete, A. Kralovec, M. J. Rashid, M. Hall, J. L. Tamucci, K. A. Chatila, Z. K. Liu, M. Lee, A. J. Vardarajan, B. N. Taga, M. Pollari, S. Rabinovitch, A. Rillahan, C. D. Bobkov, A. A. Sergienko, E. Meadows, W. Qamar, S. S. Randle, S. J. Johnson, C. M. Sevalle, J. Griffen, J. Bohm, C. Ikura, M. Xian, X. Herz, J. Kelly, M. A. West, J. Satapathy, S. Wilson, M. R. Javitch, J. A. Fraser, P. Bennett, D 2025-07-31 doi:10.1101/2025.07.29.667318 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Alteration of Water Exchange Rates Following Focused Ultrasound-Mediated BBB Opening in the Dorsal Striatum of Non-Human Primates: A Diffusion-Prepared pCASL Study ]]> https://biorxiv.org/content/10.1101/2025.07.29.667530v1?rss=1 0.05). Region-of-interest analysis within the sonicated caudate demonstrated a significant localized decrease in Kw, with median (IQR) values of 45.0 (40.6 - 55.6) min-1 at the BBBO site versus 61.6 (58.3 - 70.4) min-1 in the contralateral control region (p < 0.05), confirming spatially specific suppression of transendothelial water flux. In contrast, whole-brain Kw increased significantly following BBBO, with median (IQR) values of 49.8 (46.3 - 55.9) min-1 in non-BBBO sessions versus 59.4 (56.6 - 66.3) min-1 in BBBO sessions (p < 0.01), indicating a diffuse enhancement of water exchange across the brain. These findings establish DP-pCASL-derived Kw as a sensitive, non-contrast biomarker for both local and global BBB permeability changes induced by focused ultrasound, supporting its potential for longitudinal monitoring in preclinical and clinical neurotherapeutic applications. ]]> Liu, D. Shao, X. Munoz Silva, F. A. Sanatkhani, S. Lee, R. Konofagou, E. Wang, D. J. Ferrera, V. P. 2025-08-01 doi:10.1101/2025.07.29.667530 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Altered striatal dopamine regulation in ADGRL3 knockout mice ]]> https://biorxiv.org/content/10.1101/2025.07.31.667389v1?rss=1 Perry-Hauser, N. A. Torres-Herraez, A. Boumhaouad, S. Makowicz, E. A. Lowes, D. C. Jin, M. Denny, C. A. Sulzer, D. Mosharov, E. V. Kellendonk, C. Javitch, J. A. 2025-08-01 doi:10.1101/2025.07.31.667389 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Fast photostimulus optimization for holographic control of neural ensemble activity in vivo ]]> https://biorxiv.org/content/10.1101/2025.07.31.667911v1?rss=1 Triplett, M. A. Bäumler, E. Prodan, A. Stonis, R. Peterka, D. S. Häusser, M. Paninski, L. 2025-08-01 doi:10.1101/2025.07.31.667911 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ STAT3 regulates basal cell identity and morphogenesis during early esophageal development ]]> https://biorxiv.org/content/10.1101/2025.08.01.668154v1?rss=1 Kariuki, S. W. Mitani, Y. Bailey, D. D. Efe, G. Tripathi, V. V. Tekin, H. Suzuki, K. Que, J. Gabre, J. Cruz-Acuna, R. 2025-08-01 doi:10.1101/2025.08.01.668154 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Rapid remodeling of the human gut microbiome in response to short-term animal product restriction ]]> https://biorxiv.org/content/10.1101/2025.07.30.667695v1?rss=1 Emmanouil, C. Anezaki, M. Simistiras, A. Glentis, S. Scarmeas, N. Hatzis, P. Rouskas, K. Dimas, A. S. 2025-08-02 doi:10.1101/2025.07.30.667695 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Structures of Naked Mole-Rat, Tuco-Tuco, and Guinea Pig Ribosomes: Is rRNA Fragmentation Linked to Translational Fidelity? ]]> https://biorxiv.org/content/10.1101/2025.08.01.667930v1?rss=1 Gutierrez-Vargas, C. De, S. Maji, S. Liu, Z. Ke, Z. Nieb, M. Seluanov, A. Gorbunova, V. Frank, J. 2025-08-02 doi:10.1101/2025.08.01.667930 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Habenular μ-opioid receptor knockout and chronic systemic receptor blockade promote negative affect and heighten nociceptive sensitivity ]]> https://biorxiv.org/content/10.1101/2025.08.02.668171v1?rss=1 Pekarskaya, E. A. Galiza Soares, J. A. Hough, F. G. Langreck, C. B. Tucciarone, J. M. Javitch, J. A. 2025-08-03 doi:10.1101/2025.08.02.668171 Cold Spring Harbor Laboratory Press 2025-08-03 <![CDATA[ Reengineering the antigen optimization process for superior neoantigen vaccine design ]]> https://biorxiv.org/content/10.1101/2025.08.03.668363v1?rss=1 109 possible peptides) and limited accuracy of existing immunogenicity predictors hinder efficient vaccine design for patient-specific human leukocyte antigens (HLAs). We present AlphaVacc, a deep reinforcement learning framework that integrates Monte Carlo Tree Search with a Transformer-based network to optimize antigenic peptides. AlphaVacc outperforms previous generative models in binding-affinity prediction. Experimental validation of 12 AlphaVacc-generated variants of the BING-4 peptide confirmed that 11 showed increased HLA-A*02:01 binding and 7 elicited significant T cell responses. Further testing of 16 single-mutation peptides confirmed computational predictions for 15 candidates, exhibiting a remarkable success rate. AlphaVacc thus provides a powerful tool for designing neoantigen-based cancer vaccines and may accelerate personalized immunotherapies. ]]> Zhang, G. Fu, Y. Buratto, D. Chan, K. C. Wang, H. Huang, Y. Huang, L. Zhou, R. 2025-08-04 doi:10.1101/2025.08.03.668363 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ Noise-driven morphogenesis independent of transcriptional regulatory programs ]]> https://biorxiv.org/content/10.1101/2025.08.04.662975v1?rss=1 Toppen, J. Tavazoie, S. 2025-08-06 doi:10.1101/2025.08.04.662975 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Miniaturized widefield microscope for high speed voltage imaging ]]> https://biorxiv.org/content/10.1101/2025.08.04.668551v1?rss=1 3 at a framerate of 530 Hz. ]]> Saladrigas, C. A. Speed, F. Teel, A. Zohrabi, M. Miscles, E. J. Futia, G. L. Baker, L. V. Zhang, Y. Kymissis, I. Bright, V. Welle, C. G. Restrepo, D. Gopinath, J. T. Gibson, E. A. 2025-08-06 doi:10.1101/2025.08.04.668551 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Stenberg cells reveals escape from NK cell recognition and an unfolded protein response ]]> https://biorxiv.org/content/10.1101/2025.08.05.667241v1?rss=1 Roshal, M. Kong, I. Y. Dinalankara, W. Reichel, J. B. Teater, M. R. Bhinder, B. Zairis, S. Brody, J. D. Park, S. I. Kovach, A. E. Oberley, M. J. Lim, M. Barth, M. J. Elemento, O. Melnick, A. Rabadan, R. Chadburn, A. Marchionni, L. Giulino-Roth, L. Cesarman, E. 2025-08-07 doi:10.1101/2025.08.05.667241 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ TPClust: Temporal Profile-Guided Subtyping Using High-Dimensional Omics Data ]]> https://biorxiv.org/content/10.1101/2025.08.05.668514v1?rss=1 Hu, B. De Jager, P. L. Bennett, D. A. Vardarajan, B. N. Wang, Y. Lee, A. J. 2025-08-07 doi:10.1101/2025.08.05.668514 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Comparative analysis of plasma and bone marrow nutrient levels in pediatric B-ALL patients ]]> https://biorxiv.org/content/10.1101/2025.08.05.668707v1?rss=1 Abbott, K. L. Ali, A. Munim, M. B. Bagchi, D. P. Kunchok, T. Waite, M. Wiggers, C. R. M. Dimitrov, B. Harris, M. H. Knoechel, B. Silverman, L. B. Vander Heiden, M. G. Pikman, Y. 2025-08-07 doi:10.1101/2025.08.05.668707 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Dual pathway regulation of castration response and ferroptosis in the prostate epithelium ]]> https://biorxiv.org/content/10.1101/2025.08.06.668974v1?rss=1 Li, W. Zhou, J.-B. Wang, Z. Zandkarimi, F. Milner, T. A. Xuan, S. Christin, J. R. Laplaca, C. J. Greenberg, A. S. Chute, J. P. Hibshoosh, H. Stockwell, B. R. Shen, M. M. 2025-08-09 doi:10.1101/2025.08.06.668974 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Cell-type-selective synaptogenesis during the development of excitatory connectivity in the mammalian neocortex ]]> https://biorxiv.org/content/10.1101/2025.08.08.669371v1?rss=1 Gutman-Wei, A. Y. Sudarsanam, S. Cabalinan, A. G. Shahid, N. Shi, A. Guzman Clavel, L. E. Spindler-Krage, S. M. Agarwal, A. Kolodkin, A. L. Brown, S. P. 2025-08-09 doi:10.1101/2025.08.08.669371 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Cis-regulatory evolution of Wnt-family genes contributes to a morphological difference between silkworm species. ]]> https://biorxiv.org/content/10.1101/2025.08.10.669386v1?rss=1 Tomihara, K. Pinharanda, A. Kwon, Y. M. Taverner, A. M. Kors, L. Aardema, M. L. Holder, J. C. Poyraz, L. Reilly, P. F. Kiuchi, T. Andolfatto, P. 2025-08-12 doi:10.1101/2025.08.10.669386 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Regulatory network topology and the genetic architecture of gene expression ]]> https://biorxiv.org/content/10.1101/2025.08.12.669924v1?rss=1 Aguirre, M. Spence, J. P. Sella, G. Pritchard, J. K. 2025-08-13 doi:10.1101/2025.08.12.669924 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules ]]> https://biorxiv.org/content/10.1101/2025.08.11.669689v1?rss=1 Cheng, A. P. Rusinek, I. Sossin, A. Widman, A. J. Meiri, E. Krieger, G. Hirschberg, O. Tov, D. S. Gilad, S. Jaimovich, A. Barad, O. Avaylon, S. Rajagopalan, S. Potenski, C. Prieto, T. Yuan, D. J. Furatero, R. Runnels, A. Costa, B. M. Shoag, J. E. Al Assaad, M. Sigouros, M. Manohar, J. King, A. Wilkes, D. Otilano, J. Malbari, M. S. Elemento, O. Mosquera, J. M. Altorki, N. K. Saxena, A. Callahan, M. K. Robine, N. Germer, S. Evrony, G. Faltas, B. M. Landau, D. A. 2025-08-14 doi:10.1101/2025.08.11.669689 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Recombinant proteasome provides new avenues for anti-malarial drug development. ]]> https://biorxiv.org/content/10.1101/2025.08.13.670186v1?rss=1 Fajtova, P. Zhang, H. Urich, L. da Silva, E. B. da Silva, C. H. Almaliti, J. Al-Hindy, M. Boura, E. Fidock, D. A. Kirkman, L. Lin, G. Bogyo, M. Gerwick, W. H. Zhao, J. O'Donoghue, A. J. 2025-08-14 doi:10.1101/2025.08.13.670186 Cold Spring Harbor Laboratory Press 2025-08-14 <![CDATA[ Epigenetic Shifts Reveal Alzheimer's Origins after Sustained Picomolar Aβ Exposure ]]> https://biorxiv.org/content/10.1101/2025.08.12.668749v1?rss=1 Paquola, A. Acquarone, E. Staniszewski, A. Teich, A. F. Arancio, O. 2025-08-15 doi:10.1101/2025.08.12.668749 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Inverse expression of Ten3 and Lphn2 across the developing mouse brain reveals a global strategy for circuit assembly ]]> https://biorxiv.org/content/10.1101/2025.08.13.670004v1?rss=1 Chon, U. Pederick, D. T. Song, J. H. Zhang, Y. Rana, I. Luo, L. 2025-08-15 doi:10.1101/2025.08.13.670004 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ The Consequences of Statistical Tests on Using Proxy Measurements in Place of Gold Standard Measurements: An Application to Magnetic Resonance Spectroscopy ]]> https://biorxiv.org/content/10.1101/2025.08.13.670023v1?rss=1 Treacy, M. Juchem, C. Landheer, K. 2025-08-16 doi:10.1101/2025.08.13.670023 Cold Spring Harbor Laboratory Press 2025-08-16 <![CDATA[ Characterizing Post-Mortem Brain Molecular Taxonomy of Cognitive Resilience and Translating it to Living Humans ]]> https://biorxiv.org/content/10.1101/2025.08.13.670106v1?rss=1 Batalha, C. M. P. F. Yu, L. Zammit, A. R. Poole, V. N. Buchman, A. S. Lopes, K. d. P. Vialle, R. Abadir, P. Nidadavolu, L. Wyss-Coray, T. Seyfried, N. T. Wang, Y. Tasaki, S. De Jager, P. L. Iturria-Medina, Y. Bennett, D. A. 2025-08-18 doi:10.1101/2025.08.13.670106 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ MDS-associated SF3B1 mutations promote aberrant fate choice of hematopoietic stem cell via mis-splicing of mediator kinase module component CDK8 ]]> https://biorxiv.org/content/10.1101/2025.08.14.670174v1?rss=1 Bonner, E. A. Hsueh, T.-Y. Song, A. Arriaga-Gomez, E. A. Venkataraman, R. Sinha, S. Nguyen, E. Ferrell, P. B. Welner, R. S. Lu, R. Stirewalt, D. L. Doulatov, S. Lee, S. C. 2025-08-19 doi:10.1101/2025.08.14.670174 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[ Revisiting alpha-theta cross-frequency dynamics during working memory ]]> https://biorxiv.org/content/10.1101/2025.08.18.670850v1?rss=1 Rodriguez Larios, J. Roberts, M. J. Haegens, S. 2025-08-19 doi:10.1101/2025.08.18.670850 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ The TRP-channel painless mediates substrate stiffness sensing in the legs during Drosophila oviposition ]]> https://biorxiv.org/content/10.1101/2025.08.18.670869v1?rss=1 Ray, V. Braecker, L. Kourtidis, A. Rosher, C. Dinges, G. Pierzchlinska, A. Bueschges, A. M. Feng, K. Cury, K. M. Gompel, N. 2025-08-19 doi:10.1101/2025.08.18.670869 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal ]]> https://biorxiv.org/content/10.1101/2025.08.15.670438v1?rss=1 Balasubramanian, R. Tolman, N. Li, T. Hannan, A. Bupp-Chickering, V. Polanco, K. Bhandari, A. Zhou, S. Simon, M. Peregrin, J. Montgomery, C. Kizhatil, K. Qian, J. John, S. 2025-08-21 doi:10.1101/2025.08.15.670438 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Synaptic high-frequency jumping synchronises vision to high-speed behaviour ]]> https://biorxiv.org/content/10.1101/2025.08.20.671248v1?rss=1 Mansour, N. Takalo, J. Kemppainen, J. Bridges, A. D. MaBouDi, H. Bohra, A. A. Anielska, K. Vasas, V. Robert, T. Yi, B. Shukla, S. Zhou, Y. Kittelmann, M. Ouwendijk, J. Mantell, J. Lawson, M. Duke, E. Lazar, A. A. Verkade, P. Chittka, L. Juusola, M. 2025-08-22 doi:10.1101/2025.08.20.671248 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ MiR-23b Neutralization In Brain Endothelium Promotes Blood-Brain Barrier Repair Through Wnt/Beta-catenin Dependent And Independent Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.08.20.671398v1?rss=1 Pedersen, I. M. Martinez, V. A. Nakanishi, S. Krog, J. D. Krog, I. D. Jury, D. Lawson, B. Körbelin, J. Agalliu, D. 2025-08-25 doi:10.1101/2025.08.20.671398 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ HP1B and H3K9me3 Regulate Olfactory Receptor Choice and Transcriptional Identity ]]> https://biorxiv.org/content/10.1101/2025.08.21.671605v1?rss=1 Escamilla-del-Arenal, M. Duffie, R. Shayya, H. Loconte, V. Ekman, A. Street, L. A. Horta, A. Canzio, D. Monahan, K. Larabell, C. A. Jovanovic, M. Lomvardas, S. 2025-08-25 doi:10.1101/2025.08.21.671605 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9 ]]> https://biorxiv.org/content/10.1101/2025.08.25.672025v1?rss=1 Ahsan, M. Saha, A. Ramos, D. Strohkendl, I. Skeens, E. Lisi, G. P. Taylor, D. W. Palermo, G. 2025-08-26 doi:10.1101/2025.08.25.672025 Cold Spring Harbor Laboratory Press 2025-08-26 <![CDATA[ Genetics-to-structure multiscale analysis identifies disrupted calcium homeostasis as a mechanism of psychiatric disease ]]> https://biorxiv.org/content/10.1101/2025.08.25.672202v1?rss=1 Gerges, S. Straarup, N. C. El-Brolosy, M. A. Satterstrom, F. K. Kamitaki, N. Yuan, J. Ling, E. Lin, R. Goldman, M. Singh, T. Weissman, J. S. Berretta, S. Pan, J. Q. Finucane, H. Stock, C. Nissen, P. McCarroll, S. A. Daly, M. J. 2025-08-27 doi:10.1101/2025.08.25.672202 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain ]]> https://biorxiv.org/content/10.1101/2025.08.23.671843v1?rss=1 Chen, P. Chai, J. Soundararajan, A. Hepfer, R. G. Kheyfets, B. Hu, J. Alshanqiti, I. Raman, S. Tosa, I. Huh, J. T. Yee, M. Damon, B. J. Wang, S. Kim, Y. S. Chung, M.-K. Embree, M. C. Lee, J. S. Ye, T. Yao, H. 2025-08-28 doi:10.1101/2025.08.23.671843 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A keratin bundling transition uncages the nucleus in stretchedepithelia ]]> https://biorxiv.org/content/10.1101/2025.08.25.672104v1?rss=1 Golde, T. Pensalfini, M. Chahare, N. Roca-Cusachs, P. Wiche, G. Charras, G. Arroyo, M. Trepat, X. 2025-08-29 doi:10.1101/2025.08.25.672104 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ A Signaling Hub in the Mosquito Rectum Coordinates Reproductive Investment After Blood Feeding ]]> https://biorxiv.org/content/10.1101/2025.08.25.672111v1?rss=1 Greppi, C. Frank, K. Saltz, V. Duvall, L. B. 2025-08-29 doi:10.1101/2025.08.25.672111 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ SAGA (Simplified Association Genomewide Analyses): a user-friendly Pipeline to Democratize Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/2025.08.25.672146v1?rss=1 Cieza, B. Pandey, N. Ruhela, V. Ali, S. tosto, g. 2025-08-29 doi:10.1101/2025.08.25.672146 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Automated image segmentation uncovers the role of CD74high human microglia in cognitive decline ]]> https://biorxiv.org/content/10.1101/2025.08.25.672200v1?rss=1 Taga, M. Fujita, M. Parghi, N. Haage, V. Teich, A. Schneider, J. A. Bennett, D. A. Zhang, Y. De Jager, P. L. 2025-08-30 doi:10.1101/2025.08.25.672200 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Asymmetric Social Representations in the Prefrontal Cortex for Cooperative Behavior ]]> https://biorxiv.org/content/10.1101/2025.08.27.672249v1?rss=1 Cheng, Y. Chen, Y. Kwak, M. Kempner, R. P. Singha, R. Winslow, J. Liu, R. Khan, U. Spangler, T. Khan, A. Pereira, T. D. Whiteway, M. R. Schaffer, E. S. Rungratsameetaweemana, N. Yang, N. Wu, H. Z. 2025-08-31 doi:10.1101/2025.08.27.672249 Cold Spring Harbor Laboratory Press 2025-08-31 <![CDATA[ Repeated Viewing of a Narrative Movie Changes Event Timescales in The Brain ]]> https://biorxiv.org/content/10.1101/2025.08.27.672403v1?rss=1 Al-Zahli, N. Aly, M. Baldassano, C. 2025-09-01 doi:10.1101/2025.08.27.672403 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Low nucleus to cytoplasmic ratio compromises cytokinesis, genome stability and development in haploid embryonic cells ]]> https://biorxiv.org/content/10.1101/2025.08.30.673237v1?rss=1 Zuccaro, M. V. Georgieva, D. Xu, S. Du, Q. Chia, G. Amrane, S. Grossman, L. C. De Los Angeles, A. Prosser, R. Lobo, R. Egli, D. 2025-09-02 doi:10.1101/2025.08.30.673237 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment ]]> https://biorxiv.org/content/10.1101/2025.09.02.673664v1?rss=1 Hernandez-Romero, I. A. Peralta-Alvarez, C. A. Roman-Figueroa, A. Cano-Dominguez, N. Soto-Nava, M. Zhou, H. Huang, X. Recillas-Targa, F. Poot-Hernandez, A. C. Furlan-Magaril, M. Avila-Rios, S. Wang, J. Valle-Garcia, D. Valdes, J. 2025-09-02 doi:10.1101/2025.09.02.673664 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ Evaluating Place Cell Detection Methods in Ratsand Humans: Implications for Cross-Species Spatial Coding ]]> https://biorxiv.org/content/10.1101/2025.08.29.672705v1?rss=1 Zhang, W. Donoghue, T. Qasim, S. E. Jacobs, J. 2025-09-03 doi:10.1101/2025.08.29.672705 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Neurovascular Large artery dilatation increases the risk for Alzheimer's disease pathology ]]> https://biorxiv.org/content/10.1101/2025.08.29.672901v1?rss=1 Simpson, D. Morrone, C. D. Wear, D. Khani, A. Liu, F. Gutierrez, J. Yu, W. H. 2025-09-03 doi:10.1101/2025.08.29.672901 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Limited generalizability of dynamic fMRI correlates of adolescent rumination ]]> https://biorxiv.org/content/10.1101/2025.08.29.673124v1?rss=1 Treves, I. N. Park, M. S. Spence, J. Jaffe, N. Pidvirny, K. Tierney, A. O. Kucyi, A. Gabrieli, J. D. E. Auerbach, R. P. Webb, C. A. 2025-09-03 doi:10.1101/2025.08.29.673124 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Characterizing representational shaping of individual motor and object representations after sequence learning ]]> https://biorxiv.org/content/10.1101/2025.09.02.673680v1?rss=1 Dolfen, N. Tal, A. Fias, W. Davachi, L. 2025-09-03 doi:10.1101/2025.09.02.673680 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Extracellular activity of a bacterial protease associated with reduced phage infectivity ]]> https://biorxiv.org/content/10.1101/2025.09.03.674096v1?rss=1 Herbst, E. Rosen Blechman, G. Fedorenko, T. Melamed, S. Amitai, G. Sorek, R. 2025-09-03 doi:10.1101/2025.09.03.674096 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Unraveling operational drivers of nitrous oxide emissions in biological wastewater treatment systems through machine learning analysis of multi-decadal datasets ]]> https://biorxiv.org/content/10.1101/2025.08.31.673305v1?rss=1 Augustine, G. Chandran, K. 2025-09-04 doi:10.1101/2025.08.31.673305 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Structural Compression and Entorhinal Vulnerability: Linking Tentorial Adjacency to Tau Burden and Dementia Progression ]]> https://biorxiv.org/content/10.1101/2025.09.02.670249v1?rss=1 Zhang, L. Franceschi, A. M. Crary, J. F. Provenzano, F. A. 2025-09-04 doi:10.1101/2025.09.02.670249 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Early postpartum development of pup urine preference in mothers ]]> https://biorxiv.org/content/10.1101/2025.09.01.673527v1?rss=1 Andreu, V. Sen, R. Mimouni, N. E. H. Lee, E. J. Ferguson, D.-L. Stutzman, A. Marlin, B. J. 2025-09-05 doi:10.1101/2025.09.01.673527 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ A neural network with episodic memory learns causal relationships between narrative events ]]> https://biorxiv.org/content/10.1101/2025.09.01.673596v1?rss=1 Song, H. Lu, Q. Nguyen, T. T. Chen, J. Leong, Y. C. Rosenberg, M. D. Ching, S. Zacks, J. M. 2025-09-05 doi:10.1101/2025.09.01.673596 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ 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[ Complementary regulation of memory flexibility and stabilization by dentate gyrus granule cells and mossy cells ]]> https://biorxiv.org/content/10.1101/2025.09.05.674488v1?rss=1 GoodSmith, D. Carson, W. H. Sheffield, M. E. 2025-09-06 doi:10.1101/2025.09.05.674488 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Sensory Compression as a Unifying Principle for Action Chunking and Time Coding in the Brain ]]> https://biorxiv.org/content/10.1101/2025.09.05.674585v1?rss=1 Kumar, S. Le Cauchois, M. B. Mathis, A. Duncker, L. Howlett, J. R. Mattar, M. G. 2025-09-06 doi:10.1101/2025.09.05.674585 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ Disrupted Lipid Homeostasis as a Pathogenic Mechanism in ABCA7-Associated Alzheimers Disease Risk ]]> https://biorxiv.org/content/10.1101/2025.09.03.673792v1?rss=1 Pericak-Vance, M. A. Nam, Y. DeRosa, B. A. Ramirez, A. M. Ayele, B. A. Whitehead, P. G. Adams, L. D. Golightly, C. G. Starks, T. D. Laverde-Paz, J. Cukier, H. N. Akinyemi, R. Sarfo, F. Akpalu, A. Cuccaro, M. L. Williams, S. Caban-Holt, A. Reitz, C. Haines, J. L. Goldie, B. S. Rajabli, F. Dykxhoorn, D. M. Young, J. I. Vance, J. M. 2025-09-07 doi:10.1101/2025.09.03.673792 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ Protective immunity against malaria by a nanoparticle CIS43-based junctional vaccine alone or in combination with R21 ]]> https://biorxiv.org/content/10.1101/2025.09.05.665822v1?rss=1 Tripathi, P. Koo, J.-H. Chen, X. Da Silva Pereira, L. Dillon, M. Zhang, B. Lofgren, M. Nguyen, K. T. Teng, I.-T. Bonilla, B. Kerscher, S. Kong, W.-P. Ransier, A. Stephens, T. Tsybovsky, Y. Weldon, S. R. Douek, D. C. Pierson, T. C. Batista, F. D. Idris, A. H. Seder, R. A. Kwong, P. D. Zhou, T. 2025-09-08 doi:10.1101/2025.09.05.665822 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Motor cortex flexibly deploys a high-dimensional repertoire of subskills ]]> https://biorxiv.org/content/10.1101/2025.09.07.674717v1?rss=1 Amematsro, E. A. Trautmann, E. M. Marshall, N. J. Abbott, L. Shadlen, M. N. Wolpert, D. M. Churchland, M. M. 2025-09-08 doi:10.1101/2025.09.07.674717 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Electrode position, size, and orientation determine efficacy of cervical epidural stimulation to recruit forelimb muscles in rats ]]> https://biorxiv.org/content/10.1101/2025.09.05.674051v1?rss=1 Pascual-Leone, A. Tyagi, V. Asan, A. S. Rocha-Flores, P. E. Rodriguez-Lopez, O. Voit, W. E. McIntosh, J. R. Carmel, J. B. 2025-09-11 doi:10.1101/2025.09.05.674051 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles ]]> https://biorxiv.org/content/10.1101/2025.09.07.674724v1?rss=1 Urban, J. Kav, A. B. Kindschuh, W. F. Park, H. Khan, R. R. Watters, E. Pe'er, I. Uhlemann, A.-C. Korem, T. 2025-09-12 doi:10.1101/2025.09.07.674724 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Epigenome-wide association study meta-analysis of wellbeing ]]> https://biorxiv.org/content/10.1101/2025.09.08.674802v1?rss=1 Bartels, M. van de Weijer, M. P. Azcona Granada, N. Baselmans, B. M. L. Suderman, M. Soerensen, M. Buchwald, J. Mulder, R. H. Rawal, R. Luciano, M. Bonder, M. J. Choudhary, P. Lowry, E. Lind, P. Schwartz, J. Debrabant, B. Ollikainen, M. Felix, J. Bakermans-Kranenburg, M. Tiemeier, H. Gieger, C. Waldenberger, M. Martin, N. G. Vokonas, P. Baccarelli, A. Christensen, K. Kaprio, J. van Ijzendoorn, M. Emeny, R. Deary, I. Franke, L. Sebert, S. McRae, A. Spiro, A. van Dongen, J. 2025-09-12 doi:10.1101/2025.09.08.674802 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[ High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles ]]> https://biorxiv.org/content/10.1101/2025.09.08.674935v1?rss=1 Kim, K. Li, H. Clarke, O. B. 2025-09-12 doi:10.1101/2025.09.08.674935 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Sequential sampling from memory underlies perceptual decisions unyoked from actions ]]> https://biorxiv.org/content/10.1101/2025.09.10.675475v1?rss=1 Sharma, P. Shadlen, M. Shushruth, S. 2025-09-13 doi:10.1101/2025.09.10.675475 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ A comparison of movement-related neuronal activities in cerebellar- and basal ganglia-recipient regions of the macaque thalamus ]]> https://biorxiv.org/content/10.1101/2025.09.12.675921v1?rss=1 Kase, D. Zimnik, A. J. Pearce, T. M. Turner, R. S. 2025-09-13 doi:10.1101/2025.09.12.675921 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Uncovering the features of Measles-targeting human antibodies elicited by the MMR vaccine ]]> https://biorxiv.org/content/10.1101/2025.09.09.675230v1?rss=1 Acciani, M. D. Zyla, D. S. Niemeyer, G. Harkins, S. S. Parekh, D. Pawlack, E. Lacarbonara, D. Niewiesk, S. POROTTO, M. Hastie, K. Saphire, E. O. 2025-09-15 doi:10.1101/2025.09.09.675230 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ VesiclePy: A Machine Learning Vesicle Analysis Toolbox for Volume Electron Microscopy ]]> https://biorxiv.org/content/10.1101/2025.09.08.674799v1?rss=1 Adhinarta, J. K. Fan, Y. Gohain, A. Lin, M. Nurkin, P. Ren, R. Roth, M. Zhang, S. Yakobe, A. Yuste, R. Wei, D. 2025-09-16 doi:10.1101/2025.09.08.674799 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ ALM enables contextual decision-making via dynamic reconfiguration of local circuits ]]> https://biorxiv.org/content/10.1101/2025.09.11.675319v1?rss=1 Shen, J. Rungratsameetaweemana, N. Sharma, P. Peterka, D. S. Wu, H. Z. Shadlen, M. N. 2025-09-16 doi:10.1101/2025.09.11.675319 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Design principles of a membrane-spanning ubiquitin ligase ]]> https://biorxiv.org/content/10.1101/2025.09.11.675358v1?rss=1 Williams, C. Nocka, L. M. Hedger, G. Parashara, P. Pardon, E. Latorraca, N. R. Pusapati, G. V. Lartey, D. Gao, L. Milenkovic, L. Chalk, R. Steyaert, J. Marqusee, S. Carrique, L. Bazan, J. F. Rouse, S. L. Kong, J. H. Siebold, C. Rohatgi, R. 2025-09-16 doi:10.1101/2025.09.11.675358 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Structural and Mechanistic Basis for Antibody Neutralization of the Measles Fusion Protein ]]> https://biorxiv.org/content/10.1101/2025.09.11.675466v1?rss=1 Zyla, D. S. Della Marca, R. Lacarbonara, D. Niemeyer, G. Zipursky, G. Di Clemente, L. Jonathan-Trakht, G. Kalantarov, G. Acciani, M. Laterza, G. Vyshenska, D. Hastie, K. Horvat, B. Greninger, A. L. Niewiesk, S. Saphire, E. O. POROTTO, M. 2025-09-16 doi:10.1101/2025.09.11.675466 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo Randomization System to Model Cell Growth Behavior and Infer the Optimal Library Design for Growth-Based Double Knockout Screens ]]> https://biorxiv.org/content/10.1101/2025.09.11.675497v1?rss=1 Gu, Y. Hart, T. Novelo, L. Shen, J. P. 2025-09-16 doi:10.1101/2025.09.11.675497 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ The Hippocampus Rapidly Integrates Sequence Representations During Novel Multistep Predictions ]]> https://biorxiv.org/content/10.1101/2025.09.15.676324v1?rss=1 Tarder-Stoll, H. Baldassano, C. Aly, M. 2025-09-16 doi:10.1101/2025.09.15.676324 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Spontaneous reinstatement of episodic memories in the developing human brain ]]> https://biorxiv.org/content/10.1101/2025.09.15.676365v1?rss=1 Yates, T. S. Callaghan, B. L. Silvers, J. A. VanTieghem, M. Choy, T. O'Sullivan, K. Davachi, L. Tottenham, N. 2025-09-16 doi:10.1101/2025.09.15.676365 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Endothelial Type I Interferon signaling modulates the vascular response to ischemic brain injury ]]> https://biorxiv.org/content/10.1101/2025.09.09.675258v1?rss=1 Tuohy, M. C. Kuo, P.-C. Chelminski, A. Muharremi, E. DeSantis, C. Cui, A. Russo, A. Jamoul, D. Hillman, E. Crary, J. F. Yen, J.-H. J. Agalliu, D. 2025-09-17 doi:10.1101/2025.09.09.675258 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Insular Traveling Waves Link Distributed Neural Dynamics to Human Memory Performance ]]> https://biorxiv.org/content/10.1101/2025.09.15.676376v1?rss=1 Das, A. Wu, C. Sheth, S. Jacobs, J. 2025-09-17 doi:10.1101/2025.09.15.676376 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Bayesian causal inference unifies perceptual and neuronal processing of center-surround motion in area MT ]]> https://biorxiv.org/content/10.1101/2025.09.17.676722v1?rss=1 Lengyel, G. Shivkumar, S. DeAngelis, G. Haefner, R. M. 2025-09-17 doi:10.1101/2025.09.17.676722 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation. ]]> https://biorxiv.org/content/10.1101/2025.09.17.676780v1?rss=1 Tolonen, M. Xu, Z. Beker, O. Kapoor, V. Dumitrascu, B. Sedzinski, J. 2025-09-17 doi:10.1101/2025.09.17.676780 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Loss of Nuclear TDP-43 Impairs Lipid Metabolism in Microglia-Like Cells ]]> https://biorxiv.org/content/10.1101/2025.09.17.676815v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@f10b2dorg.highwire.dtl.DTLVardef@114d48forg.highwire.dtl.DTLVardef@8f25f9org.highwire.dtl.DTLVardef@63309_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITDP-43 nuclear depletion causes increased LD, driven by triglyceride accumulation. C_LIO_LITDP-43 nuclear depletion causes increased phagocytosis and pro-inflammatory cytokine expression. C_LIO_LIInhibiting triglyceride synthesis using DGAT inhibitors rescues LD and pro-inflammatory phenotype in TDP-43 depleted MDMi C_LIO_LIALS patient-derived MDMi display increased LD and IL1B expression, rescued by DGAT inhibitors C_LI ]]> Kabra, K. Dressman, D. Talcoff, R. Yidenk, M. Rifai, O. M. Hoover, B. N. Shneider, N. A. Elyaman, W. Area-Gomez, E. Bradshaw, E. M. 2025-09-17 doi:10.1101/2025.09.17.676815 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Prelamin A Does Not Promote Atherosclerosis or Vascular Smooth Muscle Loss ]]> https://biorxiv.org/content/10.1101/2025.09.15.676432v1?rss=1 Wang, Y. Joseph, L. C. Östlund, C. Kuriakose, G. Hsu, W. Michaelis, S. Worman, H. 2025-09-18 doi:10.1101/2025.09.15.676432 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Synaptic and neural pathway redundancy enables the robustness of a sensory-motor reflex and promotes predation escape in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.09.18.677212v1?rss=1 He, H. Fong, E. K. H. Kumar, S. Lee, H. M. T. Leifer, A. M. Chalfie, M. Zheng, C. 2025-09-19 doi:10.1101/2025.09.18.677212 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Characterization of the hemodynamic response function in default mode network subregions for task-evoked negative BOLD responses ]]> https://biorxiv.org/content/10.1101/2025.09.19.677202v1?rss=1 He, H. Yazdi, B. G. Sedaghat, A. Hojjati, S. H. Ozoria, S. Chernek, P. Calimag, J. Feiz, F. Razlighi, Q. R. 2025-09-19 doi:10.1101/2025.09.19.677202 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ RESTRICT-seq enables time-gated CRISPR screens and uncovers novel epigenetic dependencies of SCC resistance ]]> https://biorxiv.org/content/10.1101/2025.09.17.676440v1?rss=1 Ozcan, S. C. Amador, D. G. Powers, J. Njiru, A. Ansari, Z. Woappi, Y. 2025-09-20 doi:10.1101/2025.09.17.676440 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Sex differences in transcription-associated mutagenesis in the human germline ]]> https://biorxiv.org/content/10.1101/2025.09.18.677082v1?rss=1 Wyman, M. AGARWAL, I. de Manuel, M. Spisak, N. Przeworski, M. 2025-09-20 doi:10.1101/2025.09.18.677082 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ Phytoplankton community structure and photophysiological strategies in the oligotrophic Indian Ocean spawning ground of Southern Bluefin Tuna ]]> https://biorxiv.org/content/10.1101/2025.09.18.677227v1?rss=1 Goes, J. Gomes, H. Wu, X. Kranz, S. Swalethorp, R. Wu, J. Tirkey, A. Landry, M. 2025-09-21 doi:10.1101/2025.09.18.677227 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Metadomain and metaloop genome interactions in mammalian T cells ]]> https://biorxiv.org/content/10.1101/2025.09.19.677419v1?rss=1 2 Mb) chromatin interactions linked to gene regulation in T cells - A new algorithm identifies distal and interchromosomal meta-TADs and metaloops - An interchromosomal T cell-specific active hub emerges from metadomain clustering - Epigenomic compendium implicates TFs associated with long-range interactions ]]> Dolsten, G. Wang, Z.-M. Huang, X. Song, S. Wilson, M. J. Bing, X. Y. Ke, W. Cafiero, T. R. Nelson, A. N. Fernando, S. Ploss, A. Schedl, P. Levine, M. S. Viny, A. D. Rudensky, A. Y. Pritykin, Y. 2025-09-21 doi:10.1101/2025.09.19.677419 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Glucose promotes neuron morphology abnormalities and egg-laying defects dependentofthe serotonin signaling pathway in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.09.20.677429v1?rss=1 Ruiz, M. A. Dumesnil, D. R. Shah, A. Ladage, M. L. Song, L. Padilla, P. A. 2025-09-21 doi:10.1101/2025.09.20.677429 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ BAG3 coordinates astrocytic proteostasis of Alzheimer's disease-linked proteins via proteasome, autophagy, and retromer complex interactions ]]> https://biorxiv.org/content/10.1101/2025.09.20.677505v1?rss=1 Augur, Z. M. Fogo, G. M. Benoit, C. R. Terzioglu, G. Murphy, Z. R. Arbery, M. R. Comandante-Lou, N. Duong, D. M. Seyfried, N. T. De Jager, P. L. Young-Pearse, T. L. 2025-09-21 doi:10.1101/2025.09.20.677505 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ The Highly Selective 5-HT2B Receptor Antagonist MW073 Mitigates Aggressive Behavior in an Alzheimer Disease Mouse Model. ]]> https://biorxiv.org/content/10.1101/2025.09.21.677617v1?rss=1 Acquarone, E. Roy, S. M. Staniszewski, A. Watterson, D. M. Arancio, O. 2025-09-21 doi:10.1101/2025.09.21.677617 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Foxh1 is a locus-specific PRC2 recruiter governing germ layer silencing ]]> https://biorxiv.org/content/10.1101/2025.09.21.677640v1?rss=1 Cho, J. Hendrickson, C. Mar, N. Y.-J. Blitz, I. L. Fish, M. Wang, W. Cho, K. W. Y. 2025-09-22 doi:10.1101/2025.09.21.677640 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Impact of Task Similarity and Training Regimes on Cognitive Transfer and Interference ]]> https://biorxiv.org/content/10.1101/2025.09.22.677779v1?rss=1 Menghi, N. Vigano', S. Johnston, W. J. Elnagar, S. Fusi, S. Doeller, C. F. 2025-09-22 doi:10.1101/2025.09.22.677779 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Establishing a continuum of cell types in the visual cortex ]]> https://biorxiv.org/content/10.1101/2025.09.22.677893v1?rss=1 Yoo, J. Xie, F. Butrus, S. Xu, R. Tan, Z. Gorzek, R. Mirshahidi, P. Tring, E. Suresh, S. Kim, J. Fleishman, G. Tan, L. Ringach, D. Trachtenberg, J. Xu, X. Zipursky, S. L. Shekhar, K. Jain, S. 2025-09-22 doi:10.1101/2025.09.22.677893 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT ]]> https://biorxiv.org/content/10.1101/2025.09.21.677669v1?rss=1 Chen, Z. Zhang, B. Tang, L. Gong, F. Wan, L. Ma, L. 2025-09-23 doi:10.1101/2025.09.21.677669 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ A Dual Assay to Compare Protein Levels and Toxicity of Alpha-Synuclein Variants: Acute Expression of Wild-Type versus S129A ]]> https://biorxiv.org/content/10.1101/2025.09.23.678012v1?rss=1 Li, B. Levy, O. A. Ramalingam, N. Dettmer, U. 2025-09-23 doi:10.1101/2025.09.23.678012 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity ]]> https://biorxiv.org/content/10.1101/2025.09.23.678110v1?rss=1 Scheidemantel, L. P. de Paiva Lopes, K. Gaiteri, C. Menon, V. De Jager, P. L. Schneider, J. A. Buchman, A. S. Wang, Y. Tasaki, S. Raittz, R. T. Bennett, D. A. Vialle, R. A. 2025-09-23 doi:10.1101/2025.09.23.678110 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Role of tankyrase scaffolding in the β-catenin destruction complex and WNT signaling ]]> https://biorxiv.org/content/10.1101/2025.09.22.677768v1?rss=1 Wang, Q. Li, L. You, L. Wang, S. Han, L. Wang, B. Yao, L. Lu, Y. Mender, I. Flusche, A. M. Kim, C. Yarravarapu, N. Lemoff, A. Lum, L. Shay, J. W. Yu, Y. Chen, C. 2025-09-24 doi:10.1101/2025.09.22.677768 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ AMICI: Attention Mechanism Interpretation of Cell-cell Interactions ]]> https://biorxiv.org/content/10.1101/2025.09.22.677860v1?rss=1 Hong, J. Desai, K. Nguyen, T. D. Nazaret, A. Levy, N. Ergen, C. Plitas, G. Azizi, E. 2025-09-24 doi:10.1101/2025.09.22.677860 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ Associations between reproduction-focused life strategy, sex and Borderline Personality Disorder symptom expression: Evidence from the NESARC national study. ]]> https://biorxiv.org/content/10.1101/2025.09.19.676842v1?rss=1 Baptista, A. Farkas, B. C. Hoertel, N. Olfson, M. Speranza, M. Jacquet, P. O. 2025-09-25 doi:10.1101/2025.09.19.676842 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data ]]> https://biorxiv.org/content/10.1101/2025.09.22.677881v1?rss=1 Perez, M. Hong, J. Zweig, A. Azizi, E. 2025-09-25 doi:10.1101/2025.09.22.677881 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Predictive gaze orienting during navigation in virtual reality ]]> https://biorxiv.org/content/10.1101/2025.09.24.678200v1?rss=1 KONDYLI, V. Leszczynski, M. 2025-09-25 doi:10.1101/2025.09.24.678200 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Mapping disease critical spatially variable gene programs by integrating spatial transcriptomics with human genetics ]]> https://biorxiv.org/content/10.1101/2025.09.24.678397v1?rss=1 Lee, H. Sun, H. Cao, X. Karaahmet, B. Li, Z. Ulrich-Klein, H. Taga, M. Wang, G. De Jager, P. L. Bennett, D. A. Pinello, L. Jin, X. Mazumder, R. Dey, K. K. 2025-09-25 doi:10.1101/2025.09.24.678397 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ A neural network model of free recall learns multiple memory strategies ]]> https://biorxiv.org/content/10.1101/2025.09.25.678592v1?rss=1 Li, M. Jensen, K. T. Zhang, Q. Lu, Q. Mattar, M. G. 2025-09-25 doi:10.1101/2025.09.25.678592 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Integration of Multiomic and Multi-phenotypic Data Identifies Biological Pathways Associated with Physical Fitness ]]> https://biorxiv.org/content/10.1101/2025.09.24.677381v1?rss=1 Alizadeh, A. Graf, J. Misner, M. J. Burns, A. A. Ginty, F. O'Donovan, K. J. Wickiser, J. K. Barringer, N. Freisinger, G. Hermansen, N. McDonough, J. E. Davis, B. M. Loghin, E. R. Surrette, C. Tu, P. Welch, J. Boomhower, O. Lenigk, R. Sorell, R. Hammond, T. Peterson, S. Caron, A. Safa, L. Chadwick, C. Stacey, S. Jobin, J. Evans, S. C. Xue, R. Khinda, G. S. Williams, E. D. Chhabra, S. Huynh, N. Fraenkel, E. Marinelli, L. 2025-09-26 doi:10.1101/2025.09.24.677381 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Convection-enhanced delivery of dexamethasone in glioma suppresses myeloid inflammation while avoiding systemic toxicities ]]> https://biorxiv.org/content/10.1101/2025.09.24.677899v1?rss=1 Rolfe, N. W. Dadario, N. B. Lei, L. Teasley, D. E. Amini, M. Chabot, P. J. Ifediora, N. Winans, N. J. Yoh, N. Tang, A. Khoury, N. Furnari, J. Kotidis, C. Stucke, C. H. Urena, N. M. Sun, Y. Upadhyayula, P. Argenziano, M. G. Sperring, C. P. Brand, A. Viswanathan, A. Humala, N. Sims, P. A. Gill, B. J. Canoll, P. Bruce, J. N. 2025-09-26 doi:10.1101/2025.09.24.677899 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[ A Low-dimensional Manifold Representation of the Human Brain Aging Continuum ]]> https://biorxiv.org/content/10.1101/2025.09.24.678174v1?rss=1 Liang, Z. Szczepanski, C. J. Li, C. Li, J. Rusinek, H. Ge, Y. Zhang, J. 2025-09-27 doi:10.1101/2025.09.24.678174 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Mutation bias in driver genes reveals the distribution of effects of oncogenic mutations ]]> https://biorxiv.org/content/10.1101/2025.09.25.678277v1?rss=1 Stolyarova, A. Bazykin, G. 2025-09-28 doi:10.1101/2025.09.25.678277 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Local thalamic interneurons drive spindle termination and enable sleep-dependent learning ]]> https://biorxiv.org/content/10.1101/2025.09.26.678870v1?rss=1 Simko, J. Ramirez, T. K. Martin, C. Leung, S. Sung, E. A. Makinson, C. D. 2025-09-28 doi:10.1101/2025.09.26.678870 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ ONC206 demonstrates potent anti-tumorigenic activity and is a potential novel therapeutic strategy for high-risk medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.09.25.678693v1?rss=1 Tzaridis, T. D. Liu, J. Chien, F. L. Malhotra, A. Zhu, D. Gershon, I. Zhang, H. Velazquez Vega, J. E. Schniederjan, M. Sposito, T. Adams, P. D. Allen, J. E. Prabhu, V. V. Wechsler-Reya, R. MacDonald, T. J. 2025-09-29 doi:10.1101/2025.09.25.678693 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Structural Studies of Nedicistrovirus IRES-Driven, Initiation Factor-independent Translation Shed Light on Key Steps of Eukaryotic Translation Elongation ]]> https://biorxiv.org/content/10.1101/2025.09.29.679340v1?rss=1 De, S. Altomare, C. G. Abaeva, I. S. Dadhwal, P. Garg, P. Acosta-Reyes, F. Brown, Z. P. Pestova, T. V. Hellen, C. U. T. Frank, J. 2025-09-29 doi:10.1101/2025.09.29.679340 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.09.29.678849v1?rss=1 Wang, W. Berube, P. Yang, B. Castanon, R. Bartlett, A. Komandur, K. Nery, J. R. Barragan, C. Kenworthy, M. Valadon, C. Altshul, J. Petrella, A. Chan, D. Chen, C. Acerbo, A. S. Luo, J. Jain, M. Soma, E. Chen, H. Liem, M. Marrin, M. O'Connor, C. Zemke, N. Oakley, D. H. Ren, B. Hyman, B. T. Ecker, J. R. 2025-09-30 doi:10.1101/2025.09.29.678849 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Rare centenarian SIRT6 coding variants elevate SIRT6 protein levels and resist cellular senescence ]]> https://biorxiv.org/content/10.1101/2025.09.29.679208v1?rss=1 Yang, J. Han, H. Wang, X. Zhu, Y. Chen, H. Suh, Y. 2025-09-30 doi:10.1101/2025.09.29.679208 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Epigenetic CRISPR Screening of 9p21.3 Non-Coding Regions identifies Cis-Regulatory Elements of P16INK4a and P15INK4b Controlling Cellular Senescence ]]> https://biorxiv.org/content/10.1101/2025.09.29.679215v1?rss=1 Yang, J. Han, H. Wang, X. Suh, Y. 2025-09-30 doi:10.1101/2025.09.29.679215 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Single-Neuron Encoding of Learnability in the Dorsal Anterior Cingulate Cortex ]]> https://biorxiv.org/content/10.1101/2025.09.29.679390v1?rss=1 Jin, Y. Jensen, G. Ferrera, V. Gottlieb, J. 2025-09-30 doi:10.1101/2025.09.29.679390 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Benchmarking generative AI tools for literature retrieval and summarization in genomic variant interpretation. ]]> https://biorxiv.org/content/10.1101/2025.09.29.679212v1?rss=1 Gazzo, A. M. Berardelli, S. Biancospino, M. Cuollo, L. Dei Zotti, F. Ferraro, E. Marra, A. Tartarotti, E. Magni, P. 2025-10-01 doi:10.1101/2025.09.29.679212 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Vaccine Elicitation of HIV-1 Neutralizing Antibodies Against Both V2 Apex and Fusion Peptide in Rhesus Macaques ]]> https://biorxiv.org/content/10.1101/2025.09.29.679292v1?rss=1 1000-fold higher autologous tier 2-neutralization titers than the wildtype Env trimer and enhanced heterologous NAb breadth. Both FP and V2-apex monoclonal antibodies (mAb) were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures that were similar to well-characterized FP and V2 apex bNAbs, although the V2 apex mAbs showed incomplete maturation. These results demonstrate proof-of-concept for simultaneous vaccine elicitation of NAbs against multiple sites of Env vulnerability, which will likely be critical for an effective HIV-1 vaccine. HIGHLIGHTSO_LIDesigned a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex C_LIO_LIV2-SET Env trimer conferred higher binding of V2 apex bNAbs, longer retention in draining lymph nodes, and >1000-fold higher induction of autologous neutralization titers compared with wildtype Env trimer C_LIO_LIDual-epitope vaccine enhanced serum tier 2 neutralization breadth C_LIO_LIDual-epitope vaccine elicited FP- and V2 apex-specific neutralizing mAbs with genetic signatures similar to well-characterized FP and V2 apex bNAbs C_LI ]]> Duan, H. Nkolola, J. P. Wang, S. Chaudhari, J. Teng, I.-T. Lavine, C. Parchment, D. K. Sellers, G. S. McKee, K. O'Dell, S. Choe, M. Du, H. Zhang, B. Perez, A. A. E. Rossler, A. Lasrado, N. Biju, A. Becker, J. E. Carroll, R. Carson, A. S. Henry, A. R. Morano, N. C. Mughal, M. Rawi, R. Roark, R. S. Schramm, C. A. Shen, C.-H. Smith, S. C. Stephens, T. Tsybovsky, Y. Van Wazer, D. J. Wang, H. Yang, Y. Rutten, L. Langedijk, J. P. M. Cheng, C. Wang, L. Douek, D. C. Koup, R. A. Mascola, J. R. Shapiro, L. Zhou, T. Doria-Rose, N. A. Korber, B. Seaman, M. S. P 2025-10-01 doi:10.1101/2025.09.29.679292 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing ]]> https://biorxiv.org/content/10.1101/2025.09.30.679624v1?rss=1 Eisemann, T. Masihi, M. B. Tzaridis, T. Pister, V. Youm, I. Chambers, K. R. Dutta, A. Wenzel, A. T. Chin, K. Pomeroy, S. L. Mesirov, J. P. Fraenkel, E. Bagchi, A. Chavez, L. Wechsler-Reya, R. J. 2025-10-02 doi:10.1101/2025.09.30.679624 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Transfer of graded information through gated receptivity to widely broadcast signals ]]> https://biorxiv.org/content/10.1101/2025.09.30.679638v1?rss=1 Brown, L. S. So, N. Abbott, L. F. Shadlen, M. N. Goldman, M. S. 2025-10-02 doi:10.1101/2025.09.30.679638 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Age-Related Decline in NCKX4-Mediated Calcium Clearance Accelerates Aortic Remodeling and Drives Early Vascular Aging ]]> https://biorxiv.org/content/10.1101/2025.10.01.679848v1?rss=1 Bomfim, G. H. S. Asam, K. Patel, N. Rosenberg, K. Mitaishvili, E. Aguiar, T. Zorn, E. Ramasamy, R. Aouizerat, B. Lacruz, R. 2025-10-03 doi:10.1101/2025.10.01.679848 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ A conserved logic for the development of cortical layering in tetrapods ]]> https://biorxiv.org/content/10.1101/2025.10.01.679862v1?rss=1 Deryckere, A. Choudhary, S. Lynch, C. Limperis, L. K. V. P. Affatato, P. Woych, J. Gumnit, E. Ortega Gurrola, A. Satija, R. Mayer, C. Tosches, M. A. 2025-10-03 doi:10.1101/2025.10.01.679862 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Suppressing cortical glutamatergic neurons produces paradoxical interictal discharges and seizures ]]> https://biorxiv.org/content/10.1101/2025.10.02.676593v1?rss=1 3 h and sometimes evolved into seizures. By contrast, CNO activation of excitatory neurons via CaMKII-hM3Dq DREADDs desynchronized activity without epileptiform discharges. The same process duplicated in wild-type animals provoked similar epileptiform discharges. ConclusionSelective suppression of excitation can paradoxically drive cortical networks into hypersynchronous, epileptic states, challenging the simple excess-excitation model of ictogenesis. These findings highlight that seizures may result from relative inhibitory dominance, and that considering this excess inhibition mechanism could inspire new therapeutic approaches. ]]> Wu, S. Zhou, Q. Ryu, J. Li, G. Iyer, A. Gill, B. Ma, H. Fang, H. Schevon, C. Schwartz, T. H. Liou, J.-y. 2025-10-03 doi:10.1101/2025.10.02.676593 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Retinoic acid production via the ray-finned fish gene beta-carotene oxygenase 1-like is essential for juvenile development ]]> https://biorxiv.org/content/10.1101/2025.09.30.679646v1?rss=1 Krupa, L. S. Villamayor, P. R. Bandara, S. Zhang, Y. Palmiotti, A. von Lintig, J. Bendesky, A. 2025-10-04 doi:10.1101/2025.09.30.679646 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation ]]> https://biorxiv.org/content/10.1101/2025.10.02.680008v1?rss=1 Dias Maia Henriques, A. M. Davies, T. R. Dmitrieff, S. Minc, N. Canman, J. C. Dumont, J. Maton, G. 2025-10-04 doi:10.1101/2025.10.02.680008 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Single-cell nanodroplet processing proteomics pipeline for analysis of human-derived microglia ]]> https://biorxiv.org/content/10.1101/2025.10.02.680067v1?rss=1 Ives, A. Fulcher, J. M. Bautista, A. Kitata, R. Williams, S. Bennett, D. A. De Jager, P. Petyuk, V. A. 2025-10-04 doi:10.1101/2025.10.02.680067 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Design of TCR-mimicking binders for pHLA with high potency ]]> https://biorxiv.org/content/10.1101/2025.10.03.680404v1?rss=1 10-fold selectivity over wild type. Motivated by the challenge of KRAS G12V-HLA-A*03:01, which lacks electrostatic cues, we implemented message-passing neural network (MPNN)-based optimization strategies to broaden binder design beyond charge-dependent interfaces. When reapplied to p53 R175H, these strategies improved success rates from 2/5 to 5/5, with most candidates exhibiting minimal or no binding to the wild-type complex. Chimera-based and residue-retention approaches within the MPNN optimization further expanded the sequence-structure search space while preserving critical hotspot interactions. This integrated framework thus enables the design of nanomolar, mutation-selective binders to pHLA complexes, advancing next-generation personalized cancer immunotherapies. ]]> Xie, T. Fu, Y. Gong, S.-M. Buratto, D. Zhou, R. 2025-10-04 doi:10.1101/2025.10.03.680404 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Statistical and Evolutionary Analysis of Sequenced DNA from Breast Cancer FFPE Specimens ]]> https://biorxiv.org/content/10.1101/2025.10.04.680485v1?rss=1 Kurpas, M. K. Kus, P. Jaksik, R. Dinh, K. N. Adamczyk, A. Majchrzyk, K. Kimmel, M. 2025-10-05 doi:10.1101/2025.10.04.680485 Cold Spring Harbor Laboratory Press 2025-10-05 <![CDATA[ Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy. ]]> https://biorxiv.org/content/10.1101/2025.10.04.680473v1?rss=1 Chen, B. Millett-Sikking, A. Galecki, S. Daetwyler, S. Jiou, J. Monistrol, J. Shen, Q. Zhou, F. Y. Lin, H.-Y. Jenkins, E. Stein, M. Marlar-Pavey, M. Sturm, G. Y. Li, A. Tang, Q. Feng, B. Diaz, U. Chen, Y. Shalizi, A. Gillich, A. Friedman, J. R. Tomer, R. R. Chang, B.-J. Marshall, W. Shahmoradian, S. Dean, K. M. Fiolka, R. P. 2025-10-06 doi:10.1101/2025.10.04.680473 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.05.680583v1?rss=1 Tchourine, K. Carballo-Pacheco, M. Vitkup, D. 2025-10-06 doi:10.1101/2025.10.05.680583 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ A parietal grid-like code rotates with cognitive maps but lags rapid behavioral transfer ]]> https://biorxiv.org/content/10.1101/2025.10.06.680746v1?rss=1 Yu, L. Q. Vaidya, A. R. Akhmetzhanova, A. Bruinsma, S. Nassar, M. R. 2025-10-07 doi:10.1101/2025.10.06.680746 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding. ]]> https://biorxiv.org/content/10.1101/2025.10.07.681056v1?rss=1 Saia-Cereda, V. M. Sharma, A. Flanagan, K. Elmsaouri, S. Steiner, S. Benassi, S. Reis-de-Oliveira, G. Whiteley, J. T. Chandrabhatta, A. Mendes, A. P. Randolph-Moore, L. Xenitopoulos, D. Jetzer, M. Oefner, R. Benner, C. Santos, R. Yeo, G. W. Marchetto, M. C. 2025-10-08 doi:10.1101/2025.10.07.681056 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ 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[ Novel, small molecules targeting the 5-HT4R receptor protect against stress-induced maladapative behavior with efficacy across age ]]> https://biorxiv.org/content/10.1101/2025.10.08.680712v1?rss=1 Ravenelle, R. Deng, S.-X. Nelson, M. Pedersen, M. H. Mendez-David, I. David, D. J. Luna, V. M. Turi, G. Abramson, M. Javitch, J. A. Landry, D. W. Chen, B. K. Denny, C. A. 2025-10-08 doi:10.1101/2025.10.08.680712 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ A scalable proteogenomic framework for dissecting phospho-signaling pathways in primary immune cells ]]> https://biorxiv.org/content/10.1101/2025.10.08.681012v1?rss=1 Beusch, C. M. Morningstar, C. Semaan, M. Monaco, C. M. Welbourn, S. Swaldi, H. Ko, J.-K. Kenney, D. Sousa, A. Sakai, H. Liu, D. Akiyama, H. Saeed, M. Gordon, D. E. 2025-10-08 doi:10.1101/2025.10.08.681012 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Nanobody-Driven Stabilization Synergistically Rescues F508del-CFTR and Reveals an Alternative Active State of the Channel ]]> https://biorxiv.org/content/10.1101/2025.10.08.681081v1?rss=1 Overtus, M. Rubil, T. Charlick, J. N. Paige, A. S. Loughlin, B. J. Rich, Z. Rodrat, M. Yang, Z. Balazs, A. Kappes, J. C. Mall, M. A. Sheppard, D. N. Hunt, J. F. Govaerts, C. 2025-10-08 doi:10.1101/2025.10.08.681081 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Stabilized Full-Length Measles Fusion Protein Elicits Potent Immunity and Protection In Vivo ]]> https://biorxiv.org/content/10.1101/2025.10.07.681039v1?rss=1 Zyla, D. S. Zipursky, G. Marca, R. D. Lacarbonara, D. Niemeyer, G. Peng, W. Predella, C. Stearns, K. Leedale, C. Miller, J. Tay, D. Kao, J. Acciani, M. Clemente, L. D. Das, A. Parekh, D. Avalos, R. D. McGill, G. Dorrello, N. V. Hastie, K. M. Alabi, C. A. Snijder, J. Moscona, A. Greninger, A. L. Niewiesk, S. Saphire, E. O. Porotto, M. 2025-10-09 doi:10.1101/2025.10.07.681039 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[ A novel post-translational modification of fimbriae drives pathogenicity in Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/2025.10.03.680091v1?rss=1 Dobihal, G. S. Lewis, K. Yu, L. Herrera, C. Trent, M. S. Flores Kim, J. Uhlemann, A.-C. 2025-10-10 doi:10.1101/2025.10.03.680091 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ The neural computations underlying context dependent attribute-based valuation of complex stimuli. ]]> https://biorxiv.org/content/10.1101/2025.10.10.681681v1?rss=1 Fransen, A. Man, V. Iigaya, K. O`Doherty, J. P. 2025-10-12 doi:10.1101/2025.10.10.681681 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus ]]> https://biorxiv.org/content/10.1101/2025.10.11.681805v1?rss=1 2,700 cells with accompanying transcriptomic information, reconstructing >70 years of somatic evolution. T cell expansions identified from T cell receptor (TCR) sequences validated the clonal structure of the single-nucleotide variant (SNV)-based phylogenies and phylogenetic cross-correlation analysis showed that epithelial cells had higher degrees of shared ancestry by spatial location compared to immune cells. Mapping mutation signatures to the phylogenetic tree revealed the emergence of tobacco/alcohol exposure-related signatures later in life, consistent with the donors exposure histories. We identified variants in driver genes that were previously reported in the phenotypically normal esophagus, detecting clonal expansions harboring mutations in genes including TP53 and FAT1. We mapped the evolution of clones with both monoallelic as well as biallelic TP53 loss, including a clone associated with high expression of cell cycling genes and higher chromosome instability. Leveraging the matched transcriptome data, we uncovered cell type biases in mutant clones, with a higher proportion of TP53 or FAT1-mutant cells in an earlier basal epithelial cell state compared to wild-type cells. We further observed copy-neutral loss of heterozygosity (CNLOH) events on chromosome 9q that spanned the NOTCH1 locus in up to [~]35% of epithelial cells. Mapping CNLOH events to the phylogenetic tree revealed a striking pattern in which CNLOH was separately acquired many times, reflecting convergent evolution. Cells with CNLOH events were biased towards the earlier basal epithelial state, suggestive of a selective advantage that leads to prevalent recurrence of chr9q CNLOH. Together, we demonstrate that SMART-PTA is an efficient, scalable approach for single-cell whole-genome and whole-transcriptome profiling to build phenotypically annotated single-cell phylogenies with enough throughput and power for application to normal tissue somatic evolution. Moreover, we reconstruct the evolutionary history of the esophageal epithelium at high scale and resolution, providing a window into the dynamics and processes that shape clonal expansions in phenotypically normal tissues throughout a lifespan. ]]> Prieto, T. Yuan, D. J. Zinno, J. Hughes, C. Midler, N. Kao, S. Huuhtanen, J. Raviram, R. Fotopoulou, F. Ruthen, N. Rajagopalan, S. Schiffman, J. S. D Avino, A. R. Yoon, S.-H. Sotelo, J. Omans, N. D. Wheeler, N. Garces, A. Pradhan, B. Cheng, A. P. Robine, N. Potenski, C. Godfrey, K. Kakiuchi, N. Yokoyama, A. Ogawa, S. Abrams, J. Raimondi, I. Landau, D. A. 2025-10-13 doi:10.1101/2025.10.11.681805 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies ]]> https://biorxiv.org/content/10.1101/2025.10.11.681836v1?rss=1 Yao, M. Tian, P. Li, X. Bian, S. Wang, G. Gu, Y. Navas-Acien, A. Vardarajan, B. N. Belsky, D. W. Miller, G. W. Baccarelli, A. A. Liu, Z. 2025-10-13 doi:10.1101/2025.10.11.681836 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Transcriptional regulation of disease-relevant microglial activation programs ]]> https://biorxiv.org/content/10.1101/2025.10.12.681832v1?rss=1 McQuade, A. Mishra, R. Hagan, V. Liang, W. Colias, P. Castillo, V. C. Lubin, J. Haage, V. Marshe, V. Fujita, M. Gomes, L. Ta, T. Teter, O. Chasins, S. E. De Jager, P. L. Nunez, J. K. Kampmann, M. 2025-10-13 doi:10.1101/2025.10.12.681832 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Resolving Cellular Morphology in the Human Brain with Multiparametric Diffusion MR Spectroscopy ]]> https://biorxiv.org/content/10.1101/2025.10.12.681859v1?rss=1 Doering, A. Roeseler, F. Simsek, K. Afzali, M. Kreis, R. Landheer, K. Jones, D. K. Valette, J. Palombo, M. 2025-10-13 doi:10.1101/2025.10.12.681859 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Systematic elucidation and pharmacologic targeting on non-oncogene dependencies in imatinib-resistant gastrointestinal stromal tumor ]]> https://biorxiv.org/content/10.1101/2025.10.12.681609v1?rss=1 Mundi, P. S. Grunn, A. Kojadinovic, A. Karan, C. Realubit, R. Caescu, I. C. Hibshoosh, H. Aburi, M. Alvarez, M. J. Ingham, M. Evans, D. Rothschild, S. Schwartz, G. K. Califano, A. 2025-10-14 doi:10.1101/2025.10.12.681609 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Quantifying Uncertainty in Polygenic Risk Scores Using Conformalized Quantile Regression ]]> https://biorxiv.org/content/10.1101/2025.10.13.682102v1?rss=1 Wang, C. Wang, F. Bogdan, M. Masala, M. Fiorillo, E. Devoto, M. Cucca, F. Belsky, D. Ionita-Laza, I. 2025-10-14 doi:10.1101/2025.10.13.682102 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[ Structural and dynamic studies uncover a distinct allosteric modulatory site at the mu-opioid receptor ]]> https://biorxiv.org/content/10.1101/2025.10.14.682454v1?rss=1 Zhang, H. Konovalov, K. Parpounas, A. K. Provasi, D. Yang, S. Abraham, A. Warren, A. L. Zilberg, G. Wang, S. Filizola, M. Wacker, D. 2025-10-15 doi:10.1101/2025.10.14.682454 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ HXMS: a standardized file format for HX/MS data ]]> https://biorxiv.org/content/10.1101/2025.10.14.682397v1?rss=1 Weber, K. C. Lu, C. Alvarez, R. V. Pascal, B. D. Glasgow, A. 2025-10-16 doi:10.1101/2025.10.14.682397 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Antiviral reverse transcriptases reveal the evolutionary origin of telomerase ]]> https://biorxiv.org/content/10.1101/2025.10.16.682844v1?rss=1 Tang, S. Ramirez, J. L. Mestre, M. R. Zhang, D. J. Wang, M. Wiegand, T. Ma, Y. Jovanovic, M. Pinilla-Redondo, R. Sternberg, S. H. 2025-10-16 doi:10.1101/2025.10.16.682844 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Identity and functions of monoaminergic neurons in the predatory nematode Pristionchus pacificus reveal nervous system conservation and divergence ]]> https://biorxiv.org/content/10.1101/2025.10.16.682888v1?rss=1 Loer, C. M. Yim, H. Geiger, L. T. Ramadan, Y. H. Hampton, M. F. Bernal, D. V. Carstensen, H. R. Morgan, J. Rivard, L. Medina, T. Cook, S. J. Okumura, M. Lightfoot, J. W. Hobert, O. Hong, R. L. 2025-10-16 doi:10.1101/2025.10.16.682888 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Evidence for an energetic trade-off model linking inflammaging and immunosenescence in the US Health and Retirement Study and UK Biobank ]]> https://biorxiv.org/content/10.1101/2025.10.17.682903v1?rss=1 Aronoff, J. E. Franck, M. Cohen, A. A. Trumble, B. C. 2025-10-17 doi:10.1101/2025.10.17.682903 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Modeling Alzheimer's Disease with APOE4 Neuron-Glial Brain Assembloids Reveals IGFBPs as Therapeutic Targets ]]> https://biorxiv.org/content/10.1101/2025.10.17.683162v1?rss=1 View larger version (51K): org.highwire.dtl.DTLVardef@f91740org.highwire.dtl.DTLVardef@165726eorg.highwire.dtl.DTLVardef@13b957forg.highwire.dtl.DTLVardef@d40307_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sherman, E. Qiu, K. Roberts, R. Shichman, L. Li, S. Sun, H. Ide, L. Tucker, A. lee, s. Gniadzik, W. Shin, J.-B. Sol-Church, K. Kapur, J. Zhang, A. Erisir, A. Jiang, L. Alzheimer's Disease Neuroimaging Initiative, 2025-10-19 doi:10.1101/2025.10.17.683162 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Map of spiking activity underlying change detection in the mouse visual system ]]> https://biorxiv.org/content/10.1101/2025.10.17.683190v1?rss=1 75,000 high-quality units in 54 mice, mapping area-, cortical layer-, and cell type-specific coding of sensory and motor information. Modulation by task-engagement increased across the thalamocortical hierarchy but was strongest in the midbrain. Novel images modulated cortical (but not thalamic) responses through delayed recurrent activity. Population decoding and optogenetics identified a critical decision window for change detection and revealed that mice use an adaptation-based rather than image-comparison strategy. This comprehensive resource provides a valuable substrate for understanding sensorimotor computations in neural networks. ]]> Bennett, C. Gale, S. D. Heller, G. Ramirez, T. K. Belski, H. Piet, A. Zobeiri, O. Amster, A. Arkhipov, A. Cahoon, A. Caldejon, S. Carlson, M. Casal, L. Daniel, S. Farrell, C. Garrett, M. Gillis, R. Grasso, C. Hardcastle, B. Hytnen, R. Johnson, T. Ledochowitsch, P. L'Heureux, Q. Mastrovito, D. McBride, E. Mihalas, S. Mochizuki, C. Morrison, C. Nayan, C. Ngo, K. North, K. Ollerenshaw, D. Ouellette, B. Rhoads, P. Ronellenfitch, K. Schroedter, M. Siegle, J. H. Slaughterbeck, C. Sullivan, D. Swapp, J. Taormina, M. Wakeman, W. Waughman, X. Williford, A. Ph 2025-10-19 doi:10.1101/2025.10.17.683190 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells ]]> https://biorxiv.org/content/10.1101/2025.10.19.682634v1?rss=1 Liu, J. Xia, Y. Mog, B. Gliech, C. Shaw, E. Ferris, D. Moritz, B. Awosika, T. DiNapoli, S. Glavaris, S. Kaeo, K. J. Li, Y. Marcou, N. Pearlman, A. H. Ahmedna, T. Bugrovsky, R. Sanz, I. Bettegowda, C. Paul, S. Duarte-Alvarado, V. Wirtz, D. Goldman, D. W. Petri, M. A. Kinzler, K. W. Zhou, S. Andrade, F. Vogelstein, B. Konig, M. F. 2025-10-19 doi:10.1101/2025.10.19.682634 Cold Spring Harbor Laboratory Press 2025-10-19 <![CDATA[ 3D Contractile and Remodeling Behaviors of Functionally Normal and Prolapsed Human Mitral Valve Interstitial Cells ]]> https://biorxiv.org/content/10.1101/2025.10.20.683556v1?rss=1 West, T. M. Peery, G. Chemuturi, S. S. Pham, J. H. Ferrari, G. Sacks, M. S. 2025-10-21 doi:10.1101/2025.10.20.683556 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Generative inference unifies feedback processing for learning and perception in natural and artificial vision ]]> https://biorxiv.org/content/10.1101/2025.10.21.683535v1?rss=1 Toosi, T. Miller, K. D. 2025-10-22 doi:10.1101/2025.10.21.683535 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ FLASH Radiotherapy Mitigates Radiation-Induced Lymphopenia and Prevents Immunosuppression via Chk1-STAT3 Axis Modulation in a Preclinical Thoracic Irradiation Model ]]> https://biorxiv.org/content/10.1101/2025.10.21.683770v1?rss=1 Liu, K. Tao, R. Aguilar, E. Wang, M. Aggarwal, S. Neill, D. Velasquez, B. Beddar, S. Koong, A. C. Mohan, R. Schueler, E. Lin, S. H. 2025-10-23 doi:10.1101/2025.10.21.683770 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ A machine learning method for calculating highly localized protein stabilities ]]> https://biorxiv.org/content/10.1101/2025.10.21.683809v1?rss=1 Lu, C. Weber, K. C. McBride, S. K. Reckers, A. Glasgow, A. 2025-10-23 doi:10.1101/2025.10.21.683809 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques ]]> https://biorxiv.org/content/10.1101/2025.10.22.684023v1?rss=1 Mishra, N. Liang, B. Roark, R. S. Ghosh, A. Callaghan, S. Lee, W.-H. Li, X. Vo, A. L. Avillion, G. Habib, R. H. Bibollet-Ruche, F. Giese, G. Somanathan, A. Chowdhury, R. R. Oberoi, P. Amereh, K. Zhu, Y. Zhang, Y. Kassab, M. Tjio, L. Andrabi, S. Reyes, R. A. Allen, J. D. James, N. E. Randall, K. N. van der Maas, L. Ben-Akiva, E. Kaczmarek-Michaels, K. plante, S. Martella, C. L. Skelly, A. N. Singh, A. Hurtado, J. Dueker, K. Capozzola, T. Nedellec, R. Ozorowski, G. Lewis, M. Falcone, S. Carfi, A. Himansu, S. Shapiro, L. Crispin, M. Hahn, B. H. Briney, 2025-10-23 doi:10.1101/2025.10.22.684023 Cold Spring Harbor Laboratory Press 2025-10-23 <![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[ Modular Noncovalent Functionalization of Electrospun Piezoelectric Scaffolds with Bioactive Nanocarriers ]]> https://biorxiv.org/content/10.1101/2025.10.25.684210v1?rss=1 Bortel, S. P. Chowdhury, S. S. J. Cheng, J. Uvaldo, D. Wright, M. Arinzeh, T. L. Correa, S. 2025-10-26 doi:10.1101/2025.10.25.684210 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Brendo: an open resource for uniquely transcribed genes in brain endothelial cells ]]> https://biorxiv.org/content/10.1101/2025.10.25.684508v1?rss=1 Beker, O. Ramezani Khorsand, F. Adebali, O. Mustafaoglu, N. 2025-10-26 doi:10.1101/2025.10.25.684508 Cold Spring Harbor Laboratory Press 2025-10-26 <![CDATA[ Inhibitory control and error processing in Obsessive-Compulsive Disorder: A mega-analysis of task-based fMRI data by the ENIGMA-OCD consortium ]]> https://biorxiv.org/content/10.1101/2025.10.22.683868v1?rss=1 Dzinalija, N. van den Heuvel, O. A. Simpson, H. B. Ivanov, I. Araujo, A. Balachander, S. Beucke, J. Brandeis, D. Brem, S. Bruin, W. Buitelaar, J. Castelo-Branco, M. Choi, S. Eng, G. K. Fitzsimmons, S. M. D. D. Fortea, L. Fullana, M. A. Grutzmann, R. Hansen, B. Huijser, C. de Joode, N. T. Kathmann, N. Kaufmann, C. Kim, M. Koch, K. Kwon, J. S. Lim, J. X. Martinez-Zalacain, I. Menchon, J. M. van de Mortel, L. A. Narayanaswamy, J. C. Ousdal, O. T. Postma, T. S. Rodriguez-Manrique, D. van Rooij, D. Shivakumar, V. Soriano-Mas, C. Stern, E. R. Thomopoulos, S. I. 2025-10-27 doi:10.1101/2025.10.22.683868 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ A workflow using diaPASEF global quantitative proteomic analysis reveals extracellular vesicle biomarker candidates for non-invasive diagnostics in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2025.10.26.684684v1?rss=1 Vij, M. Kurnia, P. Dimapanat, L. Soni, R. Rai, A. J. 2025-10-27 doi:10.1101/2025.10.26.684684 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Mitofusin agonists enhances long-term engraftment and potency of cultured hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2025.10.27.684807v1?rss=1 Biondo, A. Candelaria, G. Jin, D. K. Lin, E. McLaughlin, D. Liang, Z. Leong, K. Hillyer, C. D. Snoeck, H.-W. Luchsinger, L. L. 2025-10-27 doi:10.1101/2025.10.27.684807 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.10.27.684958v1?rss=1 Cai, B. Ma, F. Liu, Y. Xu, Y. Liu, W. Gupta, N. Zhu, Y. Xiao, L. Traylor, J. Rom, O. Kovacic, J. Fidler, T. Yurdagul, A. Orr, A. W. Huang, X. 2025-10-28 doi:10.1101/2025.10.27.684958 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ A non-invasive method to genotype cephalopod sex by quantitative PCR ]]> https://biorxiv.org/content/10.1101/2025.10.28.685099v1?rss=1 Rubino, F. A. Coffing, G. C. Gibbons, C. J. Small, S. T. Desvignes, T. Pessutti, J. Petersen, A. M. Arkhipkin, A. Shcherbich, Z. Postlethwait, J. H. Kern, A. D. Montague, T. G. 2025-10-29 doi:10.1101/2025.10.28.685099 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Nuclear Packing Sets Fluidity Along the Epithelial to Mesenchymal Spectrum ]]> https://biorxiv.org/content/10.1101/2025.10.29.684532v1?rss=1 Yu, K. Devanny, A. J. Kaufman, L. J. 2025-10-30 doi:10.1101/2025.10.29.684532 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Crosstalk between the Methyl-Cytosine Dioxygenase TET3 and the Methyl-CpG-binding protein MECP2 Controls Neuronal Maturation ]]> https://biorxiv.org/content/10.1101/2025.10.29.685266v1?rss=1 Traube, F. R. Gasparoni, G. Winkler, A. Geserich, A. S. Sepulveda, H. Angel, J. C. Yue, X. Habibey, R. Splith, V. Gokce, G. I. Giorgio, G. Bernardini, C. Sachsse, R. Scheel, C. Bickerstaff-Westbrook, M. Biel, M. Carell, T. Busskamp, V. Rao, A. Walter, J. Michalakis, S. 2025-10-30 doi:10.1101/2025.10.29.685266 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Cross-species connectome comparisons reveal the network attributes of memory capacity and time series prediction ]]> https://biorxiv.org/content/10.1101/2025.10.29.685101v1?rss=1 Qian, Y. Yan, Y. Wu, G. She, Q. Yu, H. 2025-10-31 doi:10.1101/2025.10.29.685101 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Pharmacological reduction of neutrophil infiltration reduces Clostridioides difficile infection severity ]]> https://biorxiv.org/content/10.1101/2025.10.30.685526v1?rss=1 Keenan, O. Soto Ocana, J. Semon, A. Zhou, T. H. Furth, E. E. Bee, G. C. W. Aldridge, D. L. Diamantino, J. Hunter, C. A. Cadwell, K. Aronoff, D. M. Zackular, J. P. 2025-10-31 doi:10.1101/2025.10.30.685526 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Pan-cancer 3D genomic analysis revealed extremely long Polycomb loops as the biomarker for sensitivity to Polycomb inhibition ]]> https://biorxiv.org/content/10.1101/2025.10.30.685561v1?rss=1 Moran, S. Fan, Z. Zanovello, M. Feng, F. Wang, X. Q. D. Lu, C. Liu, J. Zhang, X. 2025-10-31 doi:10.1101/2025.10.30.685561 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Sensory receptor expansion and neural accommodation in butterfly color vision ]]> https://biorxiv.org/content/10.1101/2025.10.30.685642v1?rss=1 Gao, K. Ainsworth, J. Donati, A. Zhao, Y. Ragsac, M. F. Genduso, C. Andre, Z. Tomlinson, A. Perry, M. W. 2025-10-31 doi:10.1101/2025.10.30.685642 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Shared Binding Site but Divergent Resistance Profiles Uncover Novel Resistance Mechanisms in Plasmodium HSP90 Inhibitors ]]> https://biorxiv.org/content/10.1101/2025.10.30.684657v1?rss=1 Ko, F.-H. Lukens, A. de Souza, M. L. Foy, A. Hsiao, J. Ndiaye, T. Okombo, J. Yeo, T. Park, H. Uhlemann, A.-C. Boonyalai, N. Kumpornsin, K. Girling, G. Pasaje, C. Godoy, L. Ottilie, S. Durst, G. L. Chatterjee, A. Niles, J. Lee, M. Fidock, D. A. Wirth, D. F. Winzeler, E. 2025-11-01 doi:10.1101/2025.10.30.684657 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Neural heterogeneity shapes the temporal structure of human working memory ]]> https://biorxiv.org/content/10.1101/2025.10.31.684900v1?rss=1 Kussovska, D. Kim, R. Rungratsameetaweemana, N. 2025-11-01 doi:10.1101/2025.10.31.684900 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS ]]> https://biorxiv.org/content/10.1101/2025.10.31.685813v1?rss=1 Le, P. Lal, N. Xu, S. Mumford, S. Huang, M. Yang, D. Mizrahi, O. Hoover, B. Mei, Y. Rothamel, K. Her, H.-L. Blue, S. Shneider, N. Yeo, G. W. 2025-11-02 doi:10.1101/2025.10.31.685813 Cold Spring Harbor Laboratory Press 2025-11-02 <![CDATA[ Genetic background and transient prenatal disruption of vitamin A signaling determine susceptibility to airway hyperresponsiveness in mice ]]> https://biorxiv.org/content/10.1101/2025.10.31.685835v1?rss=1 Otoshi, T. Kameshwar, A. K. S. Kotton, B. D. Seki, Y. Cardell, Z. Xiangyi, K. Matsuno, Y. Rajaram, P. Kim, Y.-K. Sharpton, S. M. Quadro, L. Cardoso, W. V. Suzuki, M. 2025-11-03 doi:10.1101/2025.10.31.685835 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ SNNs Are Not Transformers (Yet): The Architectural Problems for SNNs in Modeling Long-Range Dependencies ]]> https://biorxiv.org/content/10.1101/2025.10.31.685901v1?rss=1 Fishell, W. Honnuraiah, S. 2025-11-03 doi:10.1101/2025.10.31.685901 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Long-term Locus Coeruleus Stimulation Exacerbates Tau Pathology in PS19 Mice ]]> https://biorxiv.org/content/10.1101/2025.11.01.686018v1?rss=1 Nong, Y. Wellman, S. Zhang, H. Liu, Y. A. Argyrousi, E. K. Arancio, O. Wang, Q. 2025-11-03 doi:10.1101/2025.11.01.686018 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy ]]> https://biorxiv.org/content/10.1101/2025.11.02.685475v1?rss=1 30 mm working distances. Integration with a low-cost LSM platform yielded a compact, scalable system demonstrated for multi-immersion, multi-color, subcellular-resolution mapping of cleared or expanded mouse, salamander, and cavefish brains, human iPSC-derived organoids, and 3D histopathology of breast tissue. HySIL and SCOPE establish an accessible foundation for scalable, high-resolution volumetric imaging, advancing data-driven biological discovery. ]]> Gong, C. Affatato, P. Fay, M. Guttikonda, S. R. O'Connor, N. J. Noble, E. Heal, M. Haydock, B. Mapa, R. De La Cruz, E. D. Kowalko, J. E. Tosches, M. A. Gerfen, C. R. Hen, R. Makinson, C. D. Hibshoosh, H. Glaser, J. Tomer, R. 2025-11-04 doi:10.1101/2025.11.02.685475 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Alzheimer's Disease Risk Variants Interact with Amyloid-beta to Modulate Monocyte Function ]]> https://biorxiv.org/content/10.1101/2025.11.02.686117v1?rss=1 Chatila, Z. K. Bradshaw, E. M. 2025-11-04 doi:10.1101/2025.11.02.686117 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart ]]> https://biorxiv.org/content/10.1101/2025.11.02.686137v1?rss=1 1,800 genes and at whole-organ 3D imaging scale C_LIO_LICombines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics C_LIO_LIGenerates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution C_LIO_LIIntroduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets C_LI ]]> Kern, C. Zhang, Q. Lu, Y. Eschbach, J. Zeng, Z. Farah, E. N. Tai, C.-Y. Yang, K. Jenie, I. Yao, F. Zhao, Z. Ma, Q. Padilla, C. G. Monell, A. Moghadami, S. Zhu, F. Li, B. Hou, A. Tucker, G. Ellison, D. Chi, N. C. Qiu, X. Zhu, Q. Bintu, B. 2025-11-04 doi:10.1101/2025.11.02.686137 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Hidden Spirals Reveal Neurocomputational Mechanisms of Traveling Waves in Human Memory ]]> https://biorxiv.org/content/10.1101/2025.11.03.686225v1?rss=1 Das, A. Zhang, J. Zabeh, E. Ermentrout, B. Jacobs, J. 2025-11-04 doi:10.1101/2025.11.03.686225 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.11.03.686160v1?rss=1 0.8), including established AD loci (BIN1, PTK2B, DMPK) with consistent effects across populations. Importantly, at BIN1 we fine-mapped regulatory variants associated with gene expression and AD risk beyond the GWAS index SNP--most notably rs11682128, which is only in modest LD with rs6733839 (r^2{approx}0.34)--demonstrating that multi-population TWAS can implicate additional functional variants not captured by single-SNP GWAS signals. We also discovered a novel association between COG4 expression and AD in NHW, implicating Golgi apparatus function. Using independent SuShiE-derived models from TOPMed MESA (PBMC), several associations replicated directionally across ancestries, with statistical significance most evident in NHW. Our results show that multi-population fine-mapping improves eQTL resolution and TWAS interpretability, reveals regulatory variants beyond GWAS index SNPs, and underscores the need to expand non-European AD cohorts to resolve shared and population-specific mechanisms. ]]> Sun, X. Mews, M. Wheeler, N. R. Benchek, P. Gu, T. Gomez, L. Ray, N. Reitz, C. Naj, A. C. Below, J. E. Tosto, G. Cornejo-Olivas, M. Byrd, G. S. Feliciano-Astacio, B. E. Celis, K. Rajabli, F. Kunkle, B. W. Pericak-Vance, M. A. Haines, J. L. Griswold, A. J. Bush, W. S. 2025-11-05 doi:10.1101/2025.11.03.686160 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ MotifAE Reveals Functional Motifs from Protein Language Model: Unsupervised Discovery and Interpretability Analysis ]]> https://biorxiv.org/content/10.1101/2025.11.04.686576v1?rss=1 Hou, C. Liu, D. Shen, Y. 2025-11-05 doi:10.1101/2025.11.04.686576 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Characterization of Phytoplankton-Excreted Metabolites Mediating Carbon Flux through the Surface Ocean ]]> https://biorxiv.org/content/10.1101/2025.11.04.686593v1?rss=1 Zhu, Y. Anderson, H. S. Salcedo, E. Miller, S. E. Longnecker, K. Soule, M. C. K. Haley, S. T. Swarr, G. J. Braakman, R. Dyhrman, S. T. Kujawinski, E. B. 2025-11-05 doi:10.1101/2025.11.04.686593 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Phospho 394Y LCK flow-cytometry readout predicts dasatinib sensitivity in paediatric T-cell acute lymphoblastic leukaemia ]]> https://biorxiv.org/content/10.1101/2025.11.04.684929v1?rss=1 POLL, A. A. Shi, Y. Rauwolf, K. K. Bornhauser, B. Kulozik, A. Bourquin, J.-P. Irving, J. A. van Delft, F. 2025-11-06 doi:10.1101/2025.11.04.684929 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[ Mapping unsolved lipidomes accelerates lipid discovery in major bacterial pathogens ]]> https://biorxiv.org/content/10.1101/2025.11.06.685907v1?rss=1 Nair, Y. M. Menon, A. R. Lin, Z. Vossenberg, M. R. L. Munsamy-Govender, V. Young, D. C. Xet-Mull, A. M. Babunovic, G. H. Cheng, T.-Y. Raman, S. Rhee, K. Y. Rock, J. M. de Jong, A. Minnaard, A. J. Mayfield, J. A. Tobin, D. M. Moody, D. B. 2025-11-07 doi:10.1101/2025.11.06.685907 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Histone H1 Promotes Silencing of Unintegrated HIV-1 DNA ]]> https://biorxiv.org/content/10.1101/2025.11.07.687224v1?rss=1 Zhu, J. Wang, G. Z. Pinto, H. D. Hilton, S. E. Skoultchi, A. I. Goff, S. P. 2025-11-07 doi:10.1101/2025.11.07.687224 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics ]]> https://biorxiv.org/content/10.1101/2025.11.07.687201v1?rss=1 Wang, H. Q. Fortson, D. G. Burton, E. D. Whitbeck, H. S. Robles, B. M. Bortey, L. Adler, A. J. Kalai, J. I. Napoleone, G. Barnhart, E. L. 2025-11-09 doi:10.1101/2025.11.07.687201 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Neuropathological Correlates of Apathy Progression in Alzheimer's Disease and Related Dementias: A Longitudinal NACC Cohort Study ]]> https://biorxiv.org/content/10.1101/2025.11.06.686966v1?rss=1 Qi, Y. Goldberg, T. E. Kim, H. Devanand, D. P. Lee, S. 2025-11-10 doi:10.1101/2025.11.06.686966 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Lightweight open-source fine-tuning of SAM2 enables domain-specific microscopy segmentation ]]> https://biorxiv.org/content/10.1101/2025.11.08.687405v1?rss=1 Bhat, E. Selvan, S. Okekenwa, S. Dechkounian, Z. Lin, V. Nakano, M. Saha, M. Song, Y. 2025-11-10 doi:10.1101/2025.11.08.687405 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Colibactin-producing E. coli promote carcinogenesis of gastroesophageal adenocarcinoma and simultaneously induce autophagy and differentiation ]]> https://biorxiv.org/content/10.1101/2025.11.10.687579v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1281a14org.highwire.dtl.DTLVardef@1c83c91org.highwire.dtl.DTLVardef@10088d2org.highwire.dtl.DTLVardef@1698a2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Proano Vasco, A. I. Obwegs, D. Bruder, K. Ritzkowski, C. Eichner, S. Houle, L. Sun, Y. Tanes, C. Klaas, L. Schoemig, L. R. Mohammad-Shahi, D. S. Bittinger, K. Wang, K. K. Rustgi, A. K. Falk, G. W. Thimme, R. Wang, T. C. Wang, H. H. Stecher, B. Dobrindt, U. Abrams, J. A. Sagar, S. Quante, M. 2025-11-11 doi:10.1101/2025.11.10.687579 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Revisiting the evidence for long-lived balancing selection in humans. ]]> https://biorxiv.org/content/10.1101/2025.11.10.687682v1?rss=1 Munby, H. Przeworski, M. 2025-11-11 doi:10.1101/2025.11.10.687682 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ An Open, Fully-processed, Longitudinal Data Resource to Study Brain Development and Transdiagnostic Executive Function ]]> https://biorxiv.org/content/10.1101/2025.11.10.687633v1?rss=1 Sevchik, B. L. Shafiei, G. Murtha, K. Linguiti, S. Brodrick, L. Brook, J. B. H. Cieslak, M. Flook, E. Mehta, K. Meisler, S. L. Ruparel, K. Rush, S. Salo, T. Singleton, S. P. Tong, T. T. Salunke, M. Bassett, D. S. Calkins, M. E. Elliott, M. A. Gur, R. E. Gur, R. C. Moore, T. M. Scott, J. C. Shinohara, R. T. Tisdall, M. D. Wolf, D. H. Roalf, D. R. Satterthwaite, T. D. 2025-11-12 doi:10.1101/2025.11.10.687633 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Fosl2 regulates the transition from parietal epithelial cells to myofibroblasts in the kidney ]]> https://biorxiv.org/content/10.1101/2025.11.10.687667v1?rss=1 Bronstein, R. Estrada, C. C. Revelo, M. P. Sheikh, F. Haley, J. D. D'Agati, V. Salant, D. J. He, J. C. Guo, Y. Mallipattu, S. K. 2025-11-12 doi:10.1101/2025.11.10.687667 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Fast-conducting mechanonociceptors uniquely engage reflexive and affective pain circuitry to drive protective responses ]]> https://biorxiv.org/content/10.1101/2025.11.11.687663v1?rss=1 Lezgiyeva, K. Liu, J. Nguyen, K. DeLisle, M. M. Ko, F. C. Fullam, S. Obeidat, A. M. Turecek, J. Alkislar, I. Lehnert, B. P. Martinez-Garcia, R. I. Sivakumar, R. Choi, J. Mazor, O. Garibyan, L. Sharma, N. Emanuel, A. J. Malfait, A.-M. Miller, R. E. Ginty, D. D. 2025-11-12 doi:10.1101/2025.11.11.687663 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Multiple patterns of selectivity in superior colliculus control visual search ]]> https://biorxiv.org/content/10.1101/2025.11.11.687826v1?rss=1 Leite, A. Adeli, H. McPeek, R. M. Zelinsky, G. J. 2025-11-12 doi:10.1101/2025.11.11.687826 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Investigating the Effects of APOE Genotype on Intracellular Cholesterol and the Endolysosomal System in the Aging Mouse Brain ]]> https://biorxiv.org/content/10.1101/2025.11.11.687891v1?rss=1 de Leeuw, S. Nuriel, T. 2025-11-13 doi:10.1101/2025.11.11.687891 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Stress resilience is associated with transcriptional remodeling in the VTA ]]> https://biorxiv.org/content/10.1101/2025.11.13.687606v1?rss=1 Minerva, A. R. McMannon, B. Lin, R. Zhukovskaya, A. Witten, I. B. Pena, C. J. 2025-11-13 doi:10.1101/2025.11.13.687606 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ The phenotypic landscape of the mycobacterial cell ]]> https://biorxiv.org/content/10.1101/2025.11.14.688347v1?rss=1 35 antibiotics, detergents, and other anti-microbials predominantly targeting the cell envelope of Mycobacterium smegmatis, a saprophytic model Mycobacterium. We highlight new information derived from this screen, including the identification of novel functions for previously uncharacterized conserved and essential genes (in mycolic acid and arabinogalactan synthesis), the discovery of a new drug scaffold/protein target pair, and insights into the mechanism of action of two commonly used antibiotics. These data are also a valuable resource for the mycobacterial research community, as they provide thousands of novel phenotypes for uncharacterized genes and meaningful phenotypic correlations between annotated and uncharacterized genes. ]]> Herrera, N. Todor, H. Kim, L. M. Burkhart, H. N. Billings, E. Warner, T. C. Lee, S. Y. Sayegh, N. Y. Bosch, B. Kiessling, L. L. Mancia, F. Rock, J. M. Gross, C. A. 2025-11-15 doi:10.1101/2025.11.14.688347 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ Spatially Mapping the Mechanical and Structural Properties of the Seedling Uterine Fibroid-Myometrium Interface ]]> https://biorxiv.org/content/10.1101/2025.11.14.687752v1?rss=1 Fodera, D. M. Sutcu, A. Joasil, A. S. Therien, A. M. Jackson, J. Advincula, A. P. Chen, X. Hendon, C. P. Oyen, M. L. Korem, T. Myers, K. M. 2025-11-16 doi:10.1101/2025.11.14.687752 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Reconstructing the emergence of the human chorion via HIPPO-mediated trophoblast induction ]]> https://biorxiv.org/content/10.1101/2025.11.18.688276v1?rss=1 Zhang, M. Lim, R. L. Reis, A. H. Piszker, W. Boyd, W. W. Pagon, A. Mahajan, A. Wu, L. Zhao, C. Petropoulos, S. Ronda, C. Simunovic, M. 2025-11-18 doi:10.1101/2025.11.18.688276 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ CANVAS causing AAGGG repeat expansions cause tissue-specific reduction in RFC1 expression and increase sensitivity to DNA damage ]]> https://biorxiv.org/content/10.1101/2025.11.18.688292v1?rss=1 Curro, R. Dominik, N. Facchini, S. Schnekenberg, R. P. Perini, C. Ronco, R. Rugginini, B. Ghia, A. Bione, S. Tagliaferri, N. Grupelli, G. P. Lowe, S. A. Hicks, A. R. Vegezzi, E. Simone, R. Bertini, A. Abati, E. Velasco, R. Sereno, M. Gutierrez-Gutierrez, G. Thomas, S. Alberti, P. Khurana, V. Attems, J. Troakes, C. Gustavsson, E. K. Lignani, G. Qiu, Y. Sleigh, J. N. Tucci, A. Fratta, P. Isaacs, A. Lim, Y. M. Jaunmuktane, Z. Brandner, S. Bennett, D. L. Przedborski, S. Opal, P. Hoke, A. Kuo, S.-H. Reilly, M. M. Houlden, H. Ryten, M. Cavaletti, G. Argyri 2025-11-18 doi:10.1101/2025.11.18.688292 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ A Reversible Mitochondrial ROS Probe for Monitoring Mitophagy Dynamics: Development and Application of MitoFlare ]]> https://biorxiv.org/content/10.1101/2025.11.18.689025v1?rss=1 95% basal quenching and rapid, fully reversible fluorescence activation in response to mitochondrial superoxide, hydroxyl radicals, lipid-derived peroxyl species, and peroxynitrite. When combined with LysoTracker Green, MitoFlare forms a dual-probe imaging platform that resolves the entire mitophagy cascade with high spatial and temporal fidelity in intact PC12 neuronal cells. Using this platform, we established a quantitative framework comprising three mechanistically distinct metrics: (i) a proximity index that reports early mitochondrial engagement with lysosomes, (ii) Manders M1 coefficient that captures mid-stage mitochondria-lysosome fusion and mitophagosome formation, and (iii) a quenching/swelling index that resolves terminal lysosomal degradation. Nutrient deprivation induced a complete, temporally ordered mitophagy program, including mtROS priming, Parkin-OPTN-associated fusion, and efficient acidification-dependent cargo degradation. In contrast, inhibition of v-ATPase with bafilomycin A1 arrested mitophagy at the fusion stage, resulting in persistent redox-active mitochondrial cargo that failed to undergo lysosomal digestion. Importantly, MitoFlares reversible redox chemistry uniquely revealed accumulation of undegraded, oxidatively active mitochondrial remnants within non-acidified vesicles--pathological intermediates that are undetectable using irreversible ROS dyes or genetically encoded reporters. These findings demonstrate that mitophagy proceeds through discrete, redox-regulated and lysosome-dependent phases that can be quantitatively mapped in real time. By enabling synchronized measurement of oxidative activation, organelle trafficking, fusion, and degradation, the MitoFlare-LysoTracker system establishes a new benchmark for dynamic mitophagy analysis in physiologically relevant models. This platform provides a powerful foundation for mechanistic interrogation of mitochondrial quality control and for accelerating the discovery of therapeutic strategies aimed at restoring mitophagic fidelity in neurodegenerative, cardiovascular, and metabolic diseases. ]]> Hou, S. Yan, X. Li, X. Ju, J. Shan, Z. Bi, L. 2025-11-18 doi:10.1101/2025.11.18.689025 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Molecular mechanism by which SARS-CoV-2 Orf9b suppresses the Tom70-Hsp90 interaction to evade innate immunity ]]> https://biorxiv.org/content/10.1101/2025.11.18.689095v1?rss=1 Sherer, N. Bastiray, A. Chen, X.-R. Molugu, T. Yadav, G. P. Igumenova, T. I. Cho, J.-H. 2025-11-18 doi:10.1101/2025.11.18.689095 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ Copper-Free Click Chemistry Enables High-Fidelity Engineering of Mitochondria Targeted Brain-Derived Exosomes ]]> https://biorxiv.org/content/10.1101/2025.11.19.689327v1?rss=1 75 % mitochondrial colocalization, and intact organelle architecture. In vivo neuroinflammation and biodistribution analyses demonstrated immunological neutrality, strong central nervous system retention, and minimal peripheral dispersion following intracerebroventricular administration. Proteomic profiling of unlabeled Sprague-Dawley (SD) and hypertensive Dahl salt-sensitive (DSS) BR-EVs uncovered hypertension-driven enrichment of oxidative and complement pathways correlating with mitochondrial fragmentation and reactive oxygen species generation in neuronal cultures. These findings establish SPAAC-mediated ligand conjugation as a biocompatible and chemically precise approach for generating mitochondria-targeted exosomes that preserve exosomal identity, biodistribution, and signaling fidelity--advancing a foundational platform for organelle-specific delivery and mechanistic imaging in the central nervous system. ]]> Yan, X. Chen, X. Hou, S. Li, X. Ju, J. Shan, Z. Bi, L. 2025-11-19 doi:10.1101/2025.11.19.689327 Cold Spring Harbor Laboratory Press 2025-11-19 <![CDATA[ A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants ]]> https://biorxiv.org/content/10.1101/2025.11.20.689508v1?rss=1 Cohen, R. O. Chomentowska, A. Cai, L. Eaton, D. A. R. 2025-11-21 doi:10.1101/2025.11.20.689508 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ ARCADIA Reveals Spatially Dependent Transcriptional Programs through Integration of scRNA-seq and Spatial Proteomics ]]> https://biorxiv.org/content/10.1101/2025.11.20.689521v1?rss=1 Rozenman, B. Hoffer-Hawlik, K. Djedjos, N. Azizi, E. 2025-11-21 doi:10.1101/2025.11.20.689521 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery. ]]> https://biorxiv.org/content/10.1101/2025.11.21.689547v1?rss=1 Street, L. A. Majumdar, M. Rothamel, K. L. Gogus, E. Brar, G. A. Yeo, G. W. Rube, T. Jovanovic, M. 2025-11-21 doi:10.1101/2025.11.21.689547 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy ]]> https://biorxiv.org/content/10.1101/2025.11.21.689741v1?rss=1 View larger version (76K): org.highwire.dtl.DTLVardef@1897489org.highwire.dtl.DTLVardef@1420587org.highwire.dtl.DTLVardef@178e8ddorg.highwire.dtl.DTLVardef@1003b44_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Karafin, M. S. Issaian, A. V. Bevers, S. Reisz, J. A. Hay, A. Keele, G. R. Dzieciatkowska, M. Cendali, F. I. Haiman, Z. B. Key, A. M. Nemkov, T. Stephenson, D. Marsh, E. Moore, A. Palha, M. S. Legenzov, E. A. Lamb, D. R. Deng, X. Stone, M. Hansen, K. Kleinman, S. Norris, P. J. Busch, M. P. Vallese, F. Palsson, B. O. Spitalnik, S. Kao, J. P. Roubinian, N. H. Janetzko, J. Page, G. P. Eisenmesser, E. Z. Zimring, J. C. Buehler, P. W. D'Alessandro, A. 2025-11-22 doi:10.1101/2025.11.21.689741 Cold Spring Harbor Laboratory Press 2025-11-22 <![CDATA[ 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[ A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome ]]> https://biorxiv.org/content/10.1101/2025.11.23.690048v1?rss=1 ElNaggar, S. Chen, W. C. Prodehl, L. M. Marumo, T. K. Khan, M. U. Mathew, C. G. Ruff, P. Jin, Z. Neugut, A. I. Rustgi, A. K. Uhlemann, A.-C. Korem, T. Abrams, J. A. 2025-11-24 doi:10.1101/2025.11.23.690048 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Distinct NIR Reflectance Spectra Associated with Foliar Symptoms of Beech Leaf Disease ]]> https://biorxiv.org/content/10.1101/2025.11.22.689946v1?rss=1 Moore, E. G. Dabydeen, L. C. Salha, R. Bichler, J. Borsuk, A. M. 2025-11-25 doi:10.1101/2025.11.22.689946 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Comparative metagenomics using pan-metagenomics graphs ]]> https://biorxiv.org/content/10.1101/2025.11.24.690211v1?rss=1 Coleman, I. Mametyarova, N. Zaznaev, A. Cai, P. Yu, L. Meydan, Y. Litman, A. Sharma, A. He, L. Simkhovich, A. Seeram, D. Park, H. Nobel, Y. R. Kav, A. B. Pe'er, I. Uhlemann, A.-C. Korem, T. 2025-11-26 doi:10.1101/2025.11.24.690211 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Synaptopodin KO rat for assessing the dendritic spine apparatus and axonal cisternal organelle in synaptic plasticity, development, and behavior ]]> https://biorxiv.org/content/10.1101/2025.11.25.690444v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@e588c0org.highwire.dtl.DTLVardef@175302eorg.highwire.dtl.DTLVardef@ae3a81org.highwire.dtl.DTLVardef@82f0a1_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kuwajima, M. Ostrovskaya, O. I. Kirk, L. M. Alario, A. Yin, W. Singh, S. Xaymongkhol, A. Li, A. Prasad, E. Harris, K. M. 2025-11-27 doi:10.1101/2025.11.25.690444 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain. ]]> https://biorxiv.org/content/10.1101/2025.11.25.690439v1?rss=1 Liu, A. De Jager, P. L. Bennett, D. The Alzheimer's Disease Functional Genomics Consortium, Wang, G. Denault, W. R. P. 2025-11-28 doi:10.1101/2025.11.25.690439 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction ]]> https://biorxiv.org/content/10.1101/2025.11.25.690514v1?rss=1 McCreight, A. Cho, Y. Li, R. Nachun, D. Gan, H.-Y. Carbonetto, P. Stephens, M. Denault, W. R. Wang, G. 2025-11-28 doi:10.1101/2025.11.25.690514 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Upregulation of MAM by C99 disrupts ACSL4 activity and phospholipid homeostasis in Alzheimer disease. ]]> https://biorxiv.org/content/10.1101/2025.11.25.690197v1?rss=1 Montesinos, J. Yun, T. Salomon-Cruz, I. D. Agudelo-castrillon, S. Uceda, M. Ferrer, A. C. Anton-Barros, C. Gomez-lopez, N. Agrawal, R. R. Larrea, D. Velasco, K. R. Fernandez-Bernal, A. Benitez, E. Zhu, X. Schon, E. A. Cardona-Gomez, G. P. Area-Gomez, E. 2025-11-29 doi:10.1101/2025.11.25.690197 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Deep Red Blood Cell Proteome Defines the Band 3 N-Terminus Interactome as a Regulator of Hypoxic Adaptation via BLVRB-Dependent S-Nitroso Transfer ]]> https://biorxiv.org/content/10.1101/2025.11.29.691178v1?rss=1 View larger version (89K): org.highwire.dtl.DTLVardef@122468org.highwire.dtl.DTLVardef@114428dorg.highwire.dtl.DTLVardef@11d40c4org.highwire.dtl.DTLVardef@1870fb7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDeep proteomics defines a complete, contamination-free RBC proteome (3,775 proteins) C_LIO_LICross-linking proteomics maps an oxygen-sensitive Band 3-centered interactome C_LIO_LIO2-dependent BLVRB-Band 3 binding regulates metabolism via S-nitrosation of GAPDH C_LIO_LIBand 3 N-terminus is required for hypoxic remodeling and exercise tolerance in vivo C_LI ]]> Issaian, A. V. Dzieciatkowska, M. Bevers, S. Zohreh, S. Hay, A. Saviola, A. Redzic, J. S. Reisz, J. A. Keele, G. R. Cendali, F. I. Haiman, Z. B. Nemkov, T. Stephenson, D. Lisk, C. Vallese, F. Palsson, B. O. King, S. B. Page, G. P. Doctor, A. Hudson, K. E. Hansen, K. C. Irwin, D. C. Mohandas, N. Zimring, J. C. Eisenmesser, E. Z. D'Alessandro, A. 2025-11-30 doi:10.1101/2025.11.29.691178 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Robust Integration of Sparse Single-Cell Alternative Splicing and Gene Expression Data with SpliceVI ]]> https://biorxiv.org/content/10.1101/2025.11.26.690853v1?rss=1 Vaidyanathan, S. Isaev, K. Zweig, A. Knowles, D. A. 2025-12-01 doi:10.1101/2025.11.26.690853 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ GPTAnno: Ontology-tree-guided hierarchical cell type annotation based on GPT models for single-cell data ]]> https://biorxiv.org/content/10.1101/2025.11.27.690951v1?rss=1 Song, Y. Tang, M. Liu, Q. Wang, H. Qian, L. Zou, F. Hou, W. 2025-12-01 doi:10.1101/2025.11.27.690951 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ miR-424(322)~503 impairs colon cancer progression driven by PTEN deficiency. ]]> https://biorxiv.org/content/10.64898/2025.11.28.691183v1?rss=1 Vidal-Sabanes, M. Bonifaci, N. Navaridas, R. Egea, J. Encinas, M. Rodriguez-Barrueco, R. Silva, J. M. Matias-Guiu, X. Llobet-Navas, D. Llobet-Navas, D. Dolcet, X. 2025-12-02 doi:10.64898/2025.11.28.691183 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ DENDRO: Recovery and denoising of whole-tree dendritic voltagefrom 2D voltage movies ]]> https://biorxiv.org/content/10.64898/2025.12.01.691576v1?rss=1 Antin, B. Park, P. Pasarkar, A. P. Ferah, U. King, C. Cohen, A. E. Paninski, L. 2025-12-03 doi:10.64898/2025.12.01.691576 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Attention modulates hippocampal sharp-wave ripples in humans ]]> https://biorxiv.org/content/10.64898/2025.12.02.691881v1?rss=1 Domagala, M. Chaieb, L. Schroeder, C. Surges, R. Mormann, F. Fell, J. Leszczynski, M. 2025-12-05 doi:10.64898/2025.12.02.691881 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Striatal ensembles specify and control granular forelimb actions ]]> https://biorxiv.org/content/10.64898/2025.12.03.692128v1?rss=1 Rodrigues-Vaz, I. Athalye, V. R. Peterka, D. S. Costa, R. M. 2025-12-08 doi:10.64898/2025.12.03.692128 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Microbiome-behavior coupling shapes infant adaptation to early maternal unpredictability ]]> https://biorxiv.org/content/10.64898/2025.12.03.692149v1?rss=1 Amso, D. Bottino, G. F. Forest, T. A. Bonham, K. S. Zieff, M. Patel, F. Miles, M. Herr, D. Espinoza-Heredia, C. D'Amato, C. Ren, J. Goldstone, M. Mbale, E. Alexander, D. C. Jones, D. K. Williams, S. C. Fifer, W. P. Gabard-Durnam, L. Klepac-Ceraj, V. Donald, K. A. 2025-12-08 doi:10.64898/2025.12.03.692149 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Behavioral Opportunism and Altered Dopamine Dynamics in Mice Exposed to Early Life Adversity ]]> https://biorxiv.org/content/10.64898/2025.12.03.692237v1?rss=1 Gallo, M. E. Hamid, A. A. Jaskir, A. Pan, T. Ofray, D. Demaestri, C. Breton, J. More, A. I. Frank, M. J. Moore, C. I. Bath, K. G. 2025-12-08 doi:10.64898/2025.12.03.692237 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ In vivo imaging of reactive oxygen species after myocardial ischemia-reperfusion injury: a large animal multimodal imaging and transcriptomic study ]]> https://biorxiv.org/content/10.64898/2025.12.04.691257v1?rss=1 Swago, S. Camillo, C. Awad, M. Gallagher, E. Thompson, E. W. Castillero, E. Peng, T. Pei, L. Cheng, Z. Tsourkas, A. Gorman, R. Ferrari, V. A. McManus, M. Mach, R. H. Karp, J. S. Tschabrunn, C. Ferrari, G. Witschey, W. R. Bravo, P. E. 2025-12-08 doi:10.64898/2025.12.04.691257 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Rare longevity-associated variants, including a reduced-function mutation in cGAS, identified in multigenerational long-lived families ]]> https://biorxiv.org/content/10.64898/2025.12.04.689698v1?rss=1 Putter, P. C. Guan, D. Gehrmann, T. Kolbe, D. Yang, J. Han, H. Kim, S. Lakenberg, N. Suchiman, H. E. D. Trompet, S. Liu, G. C. Ballhysa, E. Antebi, A. van den Berg, N. M. A. Nebel, A. Beekman, M. Suh, Y. Slagboom, P. E. Deelen, J. 2025-12-09 doi:10.64898/2025.12.04.689698 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Tether-mediated extraction of myelinoid bodies by microglia and astrocytes can maintain myelin integrity ]]> https://biorxiv.org/content/10.64898/2025.12.05.692364v1?rss=1 Spaete, E. Higgins, K. P. Kim, Y. Mangana, C. Komarek, L. Teymouri, M. Gerwig, U. C. Melzer, S. Sadowski, B. Ruhwedel, T. Janjic, P. A. Lodder, S. Dwork, A. J. Kole, M. H. P. Steyer, A. M. Moebius, W. Nave, K.-A. Goebbels, S. 2025-12-09 doi:10.64898/2025.12.05.692364 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Electroconvulsive Therapy Induces Dopaminergic Axon Regeneration, Corticostriatal Remodeling, and Restoration of Motor Function in Parkinsonian Mice ]]> https://biorxiv.org/content/10.64898/2025.12.05.692581v1?rss=1 Frank, A. Choi, S. J. Bendig, J. Monzel, A. S. Ferguson, A. C. Boumhaouad, S. Picard, M. Mosharov, E. V. Sulzer, D. 2025-12-09 doi:10.64898/2025.12.05.692581 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Graph embeddings for identifying symmetries in connectomes ]]> https://biorxiv.org/content/10.64898/2025.12.06.692615v1?rss=1 Shan, H. Litwin-Kumar, A. 2025-12-10 doi:10.64898/2025.12.06.692615 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Proteasome activator Blm10 maintains cellular proteostatic balance and gamete quality in budding yeast ]]> https://biorxiv.org/content/10.64898/2025.12.08.693079v1?rss=1 Reyes, M. C. Ramos-Ortiz, D. R. Cheng, J. A. Spiri, S. Doron-Mandel, E. Kim Kim, J. Ma, Y. Jovanovic, M. Martin, A. Brar, G. A. 2025-12-11 doi:10.64898/2025.12.08.693079 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[ VIP-OT: Dissecting Single-Cell Biochemical State Dynamics under Perturbation via Vibrational Painting and Optimal Transport ]]> https://biorxiv.org/content/10.64898/2025.12.09.693255v1?rss=1 Li, X. Stark, S. G. Liu, X. Wei, M. Zhao, Z. Qi, J. Chen, X. Dang, T. N. S. Wu, Y. Zhang, K. Min, W. Shu, J. 2025-12-12 doi:10.64898/2025.12.09.693255 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Speaker Identity is Robustly Encoded in Spatial Patterns of Intracranial EEG for Attention Decoding ]]> https://biorxiv.org/content/10.64898/2025.12.10.693470v1?rss=1 Dindar, S. S. Jiang, X. Choudhari, V. Bickel, S. Mehta, A. Schevon, C. McKhann, G. M. Friedman, D. Flinker, A. Mesgarani, N. 2025-12-12 doi:10.64898/2025.12.10.693470 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ A theory of multi-task computation and task selection ]]> https://biorxiv.org/content/10.64898/2025.12.12.693832v1?rss=1 Marschall, O. Clark, D. G. Litwin-Kumar, A. 2025-12-12 doi:10.64898/2025.12.12.693832 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Over-Reliance on Prior Expectations in Relapsing-Remitting Multiple Sclerosis ]]> https://biorxiv.org/content/10.64898/2025.12.10.693435v1?rss=1 Pourmohammadi, A. Rezaei, H. Adibi, A. Dehghani, M. Gorji, A. Sima, S. Adibi, I. Sanayei, M. 2025-12-13 doi:10.64898/2025.12.10.693435 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Transcranial Focused Ultrasound of the Human Subgenual Anterior Cingulate Reconfigures Resting State Connectivity: A Sham-Controlled fMRI Study ]]> https://biorxiv.org/content/10.64898/2025.12.10.693481v1?rss=1 Malave, A. Valera, E. Birnbaum, A. Konofagou, E. Dmochowski, J. P. 2025-12-13 doi:10.64898/2025.12.10.693481 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Conserved Landscape of Chemokine Receptor Co-expression Defines the Functional States of CD8+ T Cells in Melanoma ]]> https://biorxiv.org/content/10.64898/2025.12.10.693486v1?rss=1 View larger version (29K): org.highwire.dtl.DTLVardef@19b0f44org.highwire.dtl.DTLVardef@1076129org.highwire.dtl.DTLVardef@17c0be6org.highwire.dtl.DTLVardef@f14893_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI{middle dot} CXCR6, CXCR3 and CCR5 co-expression signature stratifies patient survival in human melanoma C_LIO_LI{middle dot} CD8+ T cells co-expressing CXCR6, CXCR3 and CCR5 are critical effectors with high proliferative, cytotoxic, and activation profile in human and mice melanoma C_LIO_LI{middle dot} CD8+ T cells co-expressing CXCR6, CXCR3 and CCR5 drive anti-tumoral responses during checkpoint blockade in both human and mice C_LI ]]> Macedo, R. Harle, D. W. Hoffer-Hawlik, K. Wang, X. K. McMahon-Skates, T. Matschiner, A. Belay, K. Saenger, Y. M. Izar, B. Azizi, E. Reshef, R. 2025-12-13 doi:10.64898/2025.12.10.693486 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability ]]> https://biorxiv.org/content/10.64898/2025.12.12.693948v1?rss=1 Alam, S. Dermentzaki, G. Garcia, D. C. Li, M. Wang, R. Campbell, M. Balbo, I. Phillips, B. L. Li, M. Estrada, J. Zazhytska, M. Yeh, Y.-T. Min, L. Rafikian, E. Valenzuela, E. Joseph, B. Patel, T. Ustienenko, D. Lovett, H. Feng, H. Wang, X. Morton, S. B. Lin, C. S. Waites, C. L. Wichterle, H. Chen, L. Yang, M. Au, E. Jovanovic, M. Lomvardas, S. Jenkins, P. M. Yang, R. Kuo, S. H. Peng, Y. Yang, G. Harrison, N. L. Zhang, C. 2025-12-13 doi:10.64898/2025.12.12.693948 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Personalized biventricular mechanics and sensitivity to model morphology ]]> https://biorxiv.org/content/10.64898/2025.12.11.693778v1?rss=1 Brown, A. Shi, L. Salvador, M. Kong, F. Ennis, D. B. Chen, I. Y. Vedula, V. Marsden, A. L. 2025-12-15 doi:10.64898/2025.12.11.693778 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Parallel neuronal ensembles control behavior across sensorimotor levels in Drosophila ]]> https://biorxiv.org/content/10.64898/2025.12.13.693955v1?rss=1 Liessem, S. Asinof, S. K. Nern, A. Sumathipala, M. Rogers, E. Erginkaya, M. Dallmann, C. J. Card, G. M. Ache, J. M. 2025-12-16 doi:10.64898/2025.12.13.693955 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ From labels to latents: revealing state-dependent hippocampal computations with Jump Latent Variable Model ]]> https://biorxiv.org/content/10.64898/2025.12.14.694183v1?rss=1 Zheng, Z. Zutshi, I. Huszar, R. Zhang, Y. Karadas, M. Buzsaki, G. Williams, A. H. 2025-12-16 doi:10.64898/2025.12.14.694183 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing ]]> https://biorxiv.org/content/10.64898/2025.12.17.694518v1?rss=1 Yu, T. Yoon, J. Zhu, Y. Li, A. Lee, B. J. Moakley, D. F. Duan, J. Deng, Q. Hou, F. Yan, M. Gennarino, V. A. Zhang, K. Chen, L. Zha, S. Zhang, C. 2025-12-18 doi:10.64898/2025.12.17.694518 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling ]]> https://biorxiv.org/content/10.64898/2025.12.18.693686v1?rss=1 Wesley, B. K. Wos, F. Germer, S. Carter, J. E. Maniatis, S. Dinh, K. N. Chu, T. Robine, N. Fitzgerald, R. Zhuang, L. Tavare, S. Nowicki-Osuch, K. 2025-12-22 doi:10.64898/2025.12.18.693686 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ One More Lap: Environmental Modulation of Small-Scale Exploration in Weakly Electric Fish ]]> https://biorxiv.org/content/10.64898/2025.12.18.694964v1?rss=1 Vazquez, J. Gascue, V. Quintana, L. A. Pedraja, F. Migliaro, A. 2025-12-22 doi:10.64898/2025.12.18.694964 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Visual input drives diverse ER calcium signals in neurons in vivo ]]> https://biorxiv.org/content/10.64898/2025.12.18.695086v1?rss=1 Delgado, K. C. Wass, K. Lefebvre, L. Kotla, K. R. Barnhart, E. L. 2025-12-22 doi:10.64898/2025.12.18.695086 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Spatial proteomic mapping of the human and mouse retina using IBEX ]]> https://biorxiv.org/content/10.64898/2025.12.19.695231v1?rss=1 Meng, Y. Kubiak, J. Dzieniak, Z. Fowler, L. Avient, R. Hopley, J. Li, L. Li, C. Tian, Y. Charbit, B. Chu, C. J. 2025-12-22 doi:10.64898/2025.12.19.695231 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Correlative Ultrastructural Mapping of Lewy Pathology Reveals Regional Diversity in Parkinsons and Dementia with Lewy bodies ]]> https://biorxiv.org/content/10.64898/2025.12.19.695426v1?rss=1 10,000 mitochondria revealed disease- and region-specific signatures of altered mitochondrial homeostasis. Specifically, the density of mitochondria increased in both PD and DLB, but mitochondrial swelling occurred exclusively in PD and was confined to the SN. These findings indicate that LB ultrastructure alone does not distinguish PD from DLB; instead, mitochondrial morphology provides a more sensitive readout of disease identity and regional susceptibility. Overall, we provide a high-resolution framework for human Lewy pathology in PD and DLB, revealing that ultrastructural responses to -Syn pathology are driven primarily by neuronal identity and regional vulnerability. Our results highlight the need for disease- and region-specific models that capture human phenotypes to advance mechanistic understanding and therapeutic targeting of synucleinopathies. ]]> Shafiei, N. Proniakova, D. Simjanoska, M. Sjodal, A. M. R. Stähli, D. Aaron, E. Kasas, S. Krause, M. S. Wittwer, M. Radecke, J. Stahlberg, H. van de Berg, W. D. Lewis, A. J. 2025-12-22 doi:10.64898/2025.12.19.695426 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ What sets the mutation rate of a cell type in an animal species? ]]> https://biorxiv.org/content/10.64898/2025.12.19.695482v1?rss=1 de Manuel, M. Przeworski, M. Spisak, N. Stolyarova, A. 2025-12-22 doi:10.64898/2025.12.19.695482 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Longitudinal Neurocognitive Trajectories in a Large Cohort of Youth Who Use Cannabis: Combining Self-Report and Toxicology ]]> https://biorxiv.org/content/10.64898/2025.12.20.695698v1?rss=1 Wade, N. E. Sullivan, R. M. Wallace, A. L. Visontay, R. Szpak, V. Lisdahl, K. M. Huestis, M. A. Goncalves, P. D. Byrne, H. Mewton, L. Jacobus, J. Tapert, S. F. 2025-12-23 doi:10.64898/2025.12.20.695698 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions ]]> https://biorxiv.org/content/10.64898/2025.12.22.695505v1?rss=1 Hart, A. Merolle, M. Howard, C. Haskins, B. E. Cohn, I. Bobba, S. Xiao, R. Yang, Y. Cadwell, K. Ma, J. Yano, H. Hou, X. Wallbank, B. A. Cutillo, D. The MIST Consortium, Ivanov, I. I. Striepen, B. Shin, S. Brodsky, I. E. Artis, D. Hunter, C. Beiting, D. P. 2025-12-23 doi:10.64898/2025.12.22.695505 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons ]]> https://biorxiv.org/content/10.64898/2025.12.26.696633v1?rss=1 Escamilla-del-Arenal, M. Tang, L. C. Kodra, A. Shayya, H. J. Ugurbil, A. C. Stathi, O. Keskin, A. Horta, A. Pulupa, J. M. Ye, J. Jovanovic, M. Lomvardas, S. Duffie, R. 2025-12-27 doi:10.64898/2025.12.26.696633 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ TMPO promotes cellular dissemination and metastasis in circulating tumor cells ]]> https://biorxiv.org/content/10.64898/2025.12.27.696673v1?rss=1 Giacobbe, A. Obradovic, A. Z. Lu, J. Park, S. Pedraz-Valdunciel, C. Fanelli, G. N. Zheng, A. Kim, J. Y. Dixon, M. S. Nam, J. S. Picech, F. Laplaca, C. Virk, R. K. Di Bernardo, M. Chui, A. Arriaga, J. M. Afari, S. Nunes de Almeida, F. Zou, M. Garcia, H. Robinson, B. D. Guo, H. Maheswaran, S. Harber, D. A. Miyamoto, D. T. Nanus, D. M. Tagawa, S. T. Zheng, T. Loda, M. Chio, C. I. I. Shen, M. Giannakakou, P. Califano, A. Sims, P. A. Abate-Shen, C. 2025-12-27 doi:10.64898/2025.12.27.696673 Cold Spring Harbor Laboratory Press 2025-12-27 <![CDATA[ Profiling tyrosine kinase substrate recognition using bacterial peptide display and deep sequencing ]]> https://biorxiv.org/content/10.64898/2025.12.28.696772v1?rss=1 Lee, M. Shah, N. H. 2025-12-30 doi:10.64898/2025.12.28.696772 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Template-based RNA structure prediction advanced through a blind code competition ]]> https://biorxiv.org/content/10.64898/2025.12.30.696949v1?rss=1 Lee, Y. He, S. Oda, T. Rao, G. J. Kim, Y. Kim, R. Kim, H. Heng, C. K. Kowerko, D. Li, H. Nguyen, H. Sampathkumar, A. Enrique Gomez, R. Chen, M. Yoshizawa, A. Kuraishi, S. Ogawa, K. Zou, S. Paullier, A. Zhao, B. Chen, H.-L. Hsu, T.-A. Hirano, T. Gezelle, J. G. Haack, D. Hong, Y. Jadhav, S. Koirala, D. Kretsch, R. C. Lewicka, A. Li, S. Marcia, M. Piccirilli, J. Rudolfs, B. Srivastava, Y. Steckelberg, A.-L. Su, Z. Toor, N. Wang, L. Yang, Z. Zhang, K. Zou, J. Baker, D. Chen, S.-J. Chiu, W. Demkin, M. Favor, A. Hummer, A. M. Joshi, C. K. Kryshtafovyc 2025-12-30 doi:10.64898/2025.12.30.696949 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ A Novel Therapeutic Approach: Notch Inhibition Enhances Radiotherapy and Checkpoint Blockade Therapy via Reprogramming of the Tumor Microenvironment ]]> https://biorxiv.org/content/10.64898/2025.12.30.696685v1?rss=1 Wang, Q. Banerjee, D. Connolly, E. Vanpouille-Box, C. Shawber, C. J. Vanguri, R. Yamashiro, D. Connolly, E. 2025-12-31 doi:10.64898/2025.12.30.696685 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Expression of the human immunomodulatory protein, human B7-1 (CD80), accelerates neuroinflammation, synaptic loss, microvascular instability and lethality in a murine model of Alzheimers Disease ]]> https://biorxiv.org/content/10.64898/2025.12.30.697078v1?rss=1 Danelon, V. Garrett-Thomson, S. Morano, N. Constanza, R. Kermani, P. Smith, R. Almo, S. C. Lee, F. S. Hempstead, B. L. 2025-12-31 doi:10.64898/2025.12.30.697078 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Aging-associated alternative splicing programs conserved between human and mouse tissues ]]> https://biorxiv.org/content/10.64898/2025.12.30.697080v1?rss=1 Isaev, K. Knowles, D. A. 2025-12-31 doi:10.64898/2025.12.30.697080 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Lab-on-a-3D-Printer for Democratized Reconfigurable Digital Microfluidics ]]> https://biorxiv.org/content/10.64898/2026.01.01.697313v1?rss=1 Ye, S. Schremmer, B. R. Guan, Z. Goncharov, A. Han, G.-R. Rajasenan, V. Zou, Y. Li, X. McDonough, C. R. Ozcan, A. Di Carlo, D. 2026-01-02 doi:10.64898/2026.01.01.697313 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Conformational changes upon pore blocker removal reveal conductive states of TMEM16A ]]> https://biorxiv.org/content/10.64898/2026.01.02.697443v1?rss=1 60 Cl- permeation events and a single-channel conductance matching experiments. Additional electrostatic and kinetic modeling indicated that TMEM16As transition from outward-rectification to Ohmic conductance with increasing Ca2+ results from a weak voltage dependence of Ca2+ binding, which act cooperatively to open the pore. HIGHLIGHTSO_LIRemoval of the inhibitor 1PBC from TMEM16A induces spontaneous transitions to ion conductive and non-conductive states via bending in TM4 at two different locations. C_LIO_LISimulations suggest that the open state is stabilized by a small hydrophobic network between TM3 and 4 and disrupting this network biases channel closure in electrophysiological recordings. C_LIO_LIA kinetic model of conduction based on energetics from the all-atom MD simulations coupled to continuum calculations gives a linear current-voltage curve consistent with the fully open conformation and removal of 1 Ca2+ switches to an outwardly rectifying state via electrostatic influence on the Cl- energy profile. However, the rectification is too weak to match experiment, but a cooperative model of Ca2+ binding with weak voltage-dependence does match experiment. C_LI ]]> Stephens, C. A. Marcoline, F. V. Peters, C. J. Grabe, M. 2026-01-03 doi:10.64898/2026.01.02.697443 Cold Spring Harbor Laboratory Press 2026-01-03 <![CDATA[ A panoramic view of the expression and function of the Doublesex/DMRT gene family in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.01.01.697290v1?rss=1 Wang, C. Salzberg, Y. Oren-Suissa, M. Hobert, O. 2026-01-05 doi:10.64898/2026.01.01.697290 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ LP.8.1-directed COVID-19 mRNA vaccines boost neutralizing antibodies and mitigate ancestral immune imprinting ]]> https://biorxiv.org/content/10.64898/2026.01.03.697434v1?rss=1 Mellis, I. A. Wu, M. Hong, H. Bowen, A. Gherasim, C. Pierce, V. M. Yin, M. T. Gordon, A. Guo, Y. Ho, D. D. 2026-01-05 doi:10.64898/2026.01.03.697434 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Elements of Olfactory Intelligence in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.01.05.697602v1?rss=1 Lazar, A. A. Zhou, Y. 2026-01-05 doi:10.64898/2026.01.05.697602 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ A PIWI protein-dependent DNA N6-adenine methylation pathway in Oxytricha protects genomic sequences from deletion ]]> https://biorxiv.org/content/10.64898/2026.01.06.698049v1?rss=1 Angelova, M. T. Feng, Y. Villano, D. J. Aslan, E. Lu, M. W. Esteve, P.-O. Sen, S. Jack, W. E. Pradhan, S. Landweber, L. F. 2026-01-07 doi:10.64898/2026.01.06.698049 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ Neural representations supporting generalization under continual learning ]]> https://biorxiv.org/content/10.64898/2026.01.07.698044v1?rss=1 Kimmel, D. L. Stachenfeld, K. L. Kriegeskorte, N. Fusi, S. Salzman, C. D. Shohamy, D. 2026-01-08 doi:10.64898/2026.01.07.698044 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Global context rapidly shapes sensory responses in V1 ]]> https://biorxiv.org/content/10.64898/2026.01.07.698143v1?rss=1 Peterka, D. S. Imai, F. Ross, J. M. Bastos, G. Hornick, M. Rachmany, L. Gallimore, C. G. Hockley, A. Hamm, J. P. 2026-01-08 doi:10.64898/2026.01.07.698143 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Electrostatic Self-Assembly of Protein Nanoparticles from Intrinsically Disordered Polypeptide and Globular Protein Pairs ]]> https://biorxiv.org/content/10.64898/2026.01.07.698192v1?rss=1 Ahn, S. Y. Jen, M. S. K. Lee, D. G. Johnston, J. D. Liao, J. Kim, E. S. Yue, Y. T. Elbaum, S. Gang, O. Obermeyer, A. C. 2026-01-08 doi:10.64898/2026.01.07.698192 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ CD2AP's structure and oligomerization are compromised by the K301M mutation: implications for Nephrotic syndrome ]]> https://biorxiv.org/content/10.64898/2026.01.08.698362v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@1f49f1dorg.highwire.dtl.DTLVardef@fa2e06org.highwire.dtl.DTLVardef@e399c0org.highwire.dtl.DTLVardef@831c17_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Qadri, A. H. Trapathi, R. M. Faheem, I. Meshram, S. Reddem,, E. R. Ramachandran, R. Pasupulati, A. k. 2026-01-09 doi:10.64898/2026.01.08.698362 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Mapping kinase-dependent tumor immune adaptation with multiplexed single-cell CRISPR screens ]]> https://biorxiv.org/content/10.64898/2026.01.08.698516v1?rss=1 Shi, L. Giglio, R. M. Cai, Q. Vaikunthan, M. Hong, J. Naqvi, A. Milea, M. Khanshali, H. Schoonen, A. Hou, N. Guo, J. Fraidenburg, M. Shen, X. Malinowski, S. W. Ligon, K. L. Rabadan, R. Azizi, E. McFaline-Figueroa, J. L. 2026-01-09 doi:10.64898/2026.01.08.698516 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ A novel imprinting cluster at the porcine CRSP complex locus defines a species-specific imprinted domain ]]> https://biorxiv.org/content/10.64898/2026.01.09.698515v1?rss=1 Ahn, J. Hwang, I.-S. Park, M.-R. Cho, I.-C. Hwang, S. Lee, K. 2026-01-09 doi:10.64898/2026.01.09.698515 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ Chronic ER Stress Disrupts Mitochondrial-Associated ER Membrane Integrity in Corneal Endothelial Cells. ]]> https://biorxiv.org/content/10.64898/2026.01.09.698664v1?rss=1 Lee, S. Kim, S. Y. Akram, O. Qureshi, S. Kashi, A. Steidl, W. Ritzer, L. Price, M. Price, F. W. Schon, E. Kumar, V. 2026-01-11 doi:10.64898/2026.01.09.698664 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Behavioral Signatures of Post-Decisional Attention in Preferential Choice ]]> https://biorxiv.org/content/10.64898/2026.01.10.698805v1?rss=1 Zylberberg, A. Krajbich, I. Shadlen, M. N. 2026-01-12 doi:10.64898/2026.01.10.698805 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells ]]> https://biorxiv.org/content/10.64898/2026.01.10.698835v1?rss=1 Candeli, N. den Hartigh, L. Hou, N. Marco, A. Sanchez-Villacana, J. A. Garcia-Gonzales, A. Gandhi, S. L. Sgualdino, F. Miller, A. J. Spence, J. de Sousa Lopes, S. C. McFaline-Figueroa, J. L. Clevers, H. Dayton, T. L. 2026-01-12 doi:10.64898/2026.01.10.698835 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ MTFP1 preserves β-cell cristae structure and bioenergetics to ensure insulin release and glucose homeostasis ]]> https://biorxiv.org/content/10.64898/2026.01.12.697845v1?rss=1 Sarwat, S. Alen, R. Wu, Z. Zhang, C. Paszek, M. Yang, M. Ostinelli, G. Mihalovits, A. Baker, B. Wai, T. Rutter, G. A. Rodriguez, T. A. Martinez-Sanchez, A. 2026-01-12 doi:10.64898/2026.01.12.697845 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ A conserved C. elegans zinc finger-homeodomain protein, ZFH-2, continuously required for structural integrity and function of alimentary tract and gonad ]]> https://biorxiv.org/content/10.64898/2026.01.13.699069v1?rss=1 Sussfeld, A. Vidal, B. Sural, S. Merritt, D. M. Aguilar, G. R. Ramadan, Y. Hobert, O. 2026-01-14 doi:10.64898/2026.01.13.699069 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Dose-dependent power and connectivity modulation of low frequency oscillations through transcranial magnetic stimulation in non-human primates. ]]> https://biorxiv.org/content/10.64898/2026.01.13.699238v1?rss=1 Güth, M. R. Perera, N. D. Linn, G. Masiello, K. Butler, B. Russ, B. E. Schroeder, C. E. Falchier, A. Opitz, A. 2026-01-14 doi:10.64898/2026.01.13.699238 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ The geometry of context-dependent biased decisions during learning ]]> https://biorxiv.org/content/10.64898/2026.01.14.699497v1?rss=1 Nogueira, R. Esteki, S. Fusi, S. Kiani, R. 2026-01-15 doi:10.64898/2026.01.14.699497 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ 4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions ]]> https://biorxiv.org/content/10.64898/2026.01.15.699736v1?rss=1 Woappi, Y. Chin Cheong, J. Van Deursen, S. L. Amador, D. Hiner, S. 2026-01-16 doi:10.64898/2026.01.15.699736 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ A Preoptic Neurocircuit That Modulates Metabolic Flexibility ]]> https://biorxiv.org/content/10.64898/2026.01.15.699760v1?rss=1 Roessler, J. M. Alkire, M. Nigrin, N. Wang, H. Reid, C. M. Cortopassi, M. D. Waite, M. Linnehan, B. Griffith, E. C. Madigan, M. Kunchok, T. Banks, A. S. Schulte, F. Kim, B. Kim, B.-Y. Kim, J. K. Hrvatin, S. 2026-01-16 doi:10.64898/2026.01.15.699760 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ Phosphorylation of Cyclophilin-D is Not Required for Regulation of The Mitochondrial Permeability Transition Pore by GSK3β ]]> https://biorxiv.org/content/10.64898/2026.01.15.699680v1?rss=1 Alex, L. Klutho, P. Song, L. Gutierrez-Aguilar, M. Baines, C. 2026-01-19 doi:10.64898/2026.01.15.699680 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ Behavioral state-dependent norepinephrine dynamics in the primary somatosensory and prefrontal cortices during tactile detection tasks ]]> https://biorxiv.org/content/10.64898/2026.01.16.699887v1?rss=1 Kelley, C. Lantin, T. Slater, C. Sorrentino, M. Yu, K. Yuan, B. Kann, M. Liu, Y. A. Kim, J. S. Wang, Q. 2026-01-20 doi:10.64898/2026.01.16.699887 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Dysregulated TGFb-ERK Signaling Drives Aberrant Extracellular Matrix Production in Noonan Syndrome-Associated Pulmonary Valve Stenosis ]]> https://biorxiv.org/content/10.64898/2026.01.16.700032v1?rss=1 Liu, C. Z. Patel, S. Sidoli, S. Prasad, A. Charytonowicz, D. Mazine, A. Mikryukov, A. A. Abdul-Ghafar, J. Kahn, E. S. Young, D. Porter, G. A. Katzman, P. J. Sanders, S. P. Carreon, C. K. Hubmacher, D. Lincoln, J. Keller, G. Chung, W. K. Sebra, R. Gelb, B. D. 2026-01-20 doi:10.64898/2026.01.16.700032 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart ]]> https://biorxiv.org/content/10.64898/2026.01.16.700033v1?rss=1 Pozo, M. R. Pressler, M. P. Horvath, A. Entcheva, E. 2026-01-20 doi:10.64898/2026.01.16.700033 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Cancer drives atherosclerotic plaque vulnerability by inducing pathological angiogenesis ]]> https://biorxiv.org/content/10.64898/2026.01.18.700232v1?rss=1 Luo, L. Fu, C. Jarr, K.-U. Baylis, R. Sun, V. H. Heemelaar, J. von Scheidt, M. Ramirez, D. Krefting, J. Sachs, N. Wettich, J. L. Winter, H. Gao, H. Wang, F. Adkar, S. Haas, A. Gonzalez, M. Nead, K. T. Maegdefessel, L. Schunkert, H. Neilan, T. G. Leeper, N. J. 2026-01-20 doi:10.64898/2026.01.18.700232 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ sf-pediatric: A robust and age-adaptable end-to-end pipeline for pediatric diffusion MRI ]]> https://biorxiv.org/content/10.64898/2026.01.19.700454v1?rss=1 Gagnon, A. Bore, A. Valcourt Caron, A. Edde, M. Thoumyre, S. Lepage, J.-F. Talati, A. Posner, J. Ouellet, A. Brunet, M. A. Takser, L. Rheault, F. Descoteaux, M. 2026-01-20 doi:10.64898/2026.01.19.700454 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[ Opposite Effects of Alpha Oscillations on Mind-Wandering With Eyes Open and Closed ]]> https://biorxiv.org/content/10.64898/2026.01.20.700111v1?rss=1 Thielking, E. M. Ramsey, H. Samaha, J. Andrillon, T. Iemi, L. 2026-01-22 doi:10.64898/2026.01.20.700111 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Harnessing Biological Variability for Mechanistic Inference: A Practical Stochastic Framework ]]> https://biorxiv.org/content/10.64898/2026.01.22.701043v1?rss=1 Wang, R.-Y. Danciu, D.-P. Klawe, F. Z. Marciniak-Czochra, A. 2026-01-22 doi:10.64898/2026.01.22.701043 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Validation of differentiated sinoatrial-like hiPSCs as a model of native sinus node myocytes ]]> https://biorxiv.org/content/10.64898/2026.01.21.700785v1?rss=1 Torre, E. Sleiman, Y. Dridi, H. Charrabi, A. Mekrane, N. Angelini, G. Talssi, L. Soni, R. K. Di Biase, V. Faure- Gautron, H. Seyer, P. de Tombe, P. Marks, A. R. Pasquie, J.-L. Lacampagne, A. Mangoni, M. E. Mesirca, P. Meli, A. C. 2026-01-23 doi:10.64898/2026.01.21.700785 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[ Opening the black box: a modular approach to spike sorting ]]> https://biorxiv.org/content/10.64898/2026.01.23.701239v1?rss=1 Garcia, S. Halcrow, C. Windolf, C. McKenzie, Z. M. Adkisson-Floro, P. Mayorquin, H. R. Dichter, B. K. Buccino, A. P. Yger, P. 2026-01-26 doi:10.64898/2026.01.23.701239 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Stress adaptation pathways and HA-CD44 signaling maintain the survival of pancreatic cancer cells with centrosome amplification ]]> https://biorxiv.org/content/10.64898/2026.01.24.701523v1?rss=1 Ozcan, S. C. Goksel, E. Kalkan, B. M. Cicek, E. Kanevetci, B. Acilan, C. 2026-01-26 doi:10.64898/2026.01.24.701523 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Proximity labeling reveals cell cycle-specific NEK2 interactions and a regulatory axis controlling NUSAP1 stability ]]> https://biorxiv.org/content/10.64898/2026.01.25.701545v1?rss=1 Cicek, E. Ozcan, S. C. Kanevetci, B. Kalkan, B. Ozkan, N. E. Ozlu, N. Acilan, C. 2026-01-27 doi:10.64898/2026.01.25.701545 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Mapping SARS-CoV-2 Nucleocapsid Function with Nanobodies ]]> https://biorxiv.org/content/10.64898/2026.01.26.701894v1?rss=1 Weinstein, J. B. Bates, T. A. Anastas, A. Alfahdli, A. Trank-Green, M. McBride, S. K. Garcia, M. Parson, M. A. Jenkins, M. L. Burke, J. E. Barklis, E. Tafesse, F. G. 2026-01-27 doi:10.64898/2026.01.26.701894 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ EZH2 Inhibition Reshapes 3D Chromatin Architecture to Induce Immunogenic Phenotype in Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.64898/2026.01.26.701784v1?rss=1 Parveen, S. Adhinaveni, R. Fang, K. Choppavarapu, L. Du, M. Leone, G. de Sarkar, N. Jin, V. X. Chen, H.-Z. 2026-01-28 doi:10.64898/2026.01.26.701784 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Interferon Beta Drives Therapy Resistance in a Patient Derived Model of High Grade Serous Ovarian Cancer ]]> https://biorxiv.org/content/10.64898/2026.01.27.699126v1?rss=1 Conant, A. Suzuki, T. McGivney, K. Ayyadevara, V. S. S. A. Asariah, S. Deng, J. Nyein, E. Coats, J. Yu, G. Ioffe, Y. J. Hurtz, C. Unternaehrer, J. J. 2026-01-28 doi:10.64898/2026.01.27.699126 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Distinct allosteric remodeling of HIV-1 Env dynamics on virions by gp41-directed antibodies reveals two modes of neutralization ]]> https://biorxiv.org/content/10.64898/2026.01.27.702099v1?rss=1 Xu, W. Gonepudi, N. K. Liu, J. He, Y. Katte, R. Wang, R. Awuah, H. B. Han, Y. Yu, J. Zhang, B. Hu, B. Ho, D. D. Acharya, P. Kwong, P. D. Lu, M. 2026-01-28 doi:10.64898/2026.01.27.702099 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice ]]> https://biorxiv.org/content/10.64898/2026.01.22.701181v1?rss=1 Casaletto, J. A. Scott, R. T. Rathod, A. Jain, A. Chandar, A. Adapala, A. Prajapati, A. Nautiyal, A. Jayaraman, A. Boddu, A. Kelam, A. Jain, A. Pham, B. Shastry, D. Narayanan, D. Kosaraju, E. Paley, E. Uribe, F. P. Shahid, I. Ye, I. Wu, J. Lin, J. Srinivas, K. Della Monica, M. P. Hitt, M. Lin, M. Volkan, M. Kharya, M. Kaul, M. Jaffer, M. A. Ali, M. Chang, N. Z. Ashri, N. Couderc, N. B. Paladugu, P. Hiremath, R. Pathak, R. Dogra, S. Srinivas, S. Samaddar, S. Gopinath, S. Sawant, S. Cai, S. Pala, V. Nair, V. Shi, Z. Narayanan, S. Mundackal Thomas, D 2026-01-29 doi:10.64898/2026.01.22.701181 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Hemodynamic Analysis of a Repaired Ascending Aorta with Preserved Aortic Root ]]> https://biorxiv.org/content/10.64898/2026.01.28.702307v1?rss=1 Zhai, H. Chen, Y. Kitada, Y. Takayama, H. Vedula, V. 2026-01-29 doi:10.64898/2026.01.28.702307 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Development and field test of an intervention to reduce conflict in faculty-doctoral student mentoring relationships ]]> https://biorxiv.org/content/10.64898/2026.01.29.702507v1?rss=1 Tuma, T. T. Rosenzweig, E. Q. Lavner, J. A. Zhang, Y. Dolan, E. L. 2026-01-29 doi:10.64898/2026.01.29.702507 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ Active strains in the basal organ of Corti in gerbil ]]> https://biorxiv.org/content/10.64898/2026.01.27.702095v1?rss=1 Wong, K. H. Strimbu, C. E. Olson, E. S. 2026-01-30 doi:10.64898/2026.01.27.702095 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Decoding the MYC locus reveals a druggable ultraconserved RNA element ]]> https://biorxiv.org/content/10.64898/2026.01.29.702547v1?rss=1 Shi, P. Yang, F. FNU, T. Huang, W. Aparicio, A. O. Kalicki, C. H. Trehan, A. Murphy, M. R. Rotlevi, E. R. Xing, L. Reilly, M. P. Que, J. Wu, X. 2026-01-30 doi:10.64898/2026.01.29.702547 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[ Predicting neutron radiation exposure characteristics from an in vitro human skin model using RNA-seq ]]> https://biorxiv.org/content/10.64898/2026.01.29.702673v1?rss=1 0.99), and regression models achieved high accuracy for estimating both absorbed dose (R2 = 0.97) and days post-exposure (R2 = 0.99). The latter, while highly predictive, may partially reflect transcriptional shifts associated with progressive degradation of the in vitro tissue model over time. Collectively, these findings demonstrate that RNA-based molecular signatures from human skin tissue provide a robust framework for quantitative estimation of neutron radiation exposure and temporal response dynamics. ]]> Gardner, M. W. LeSassier, D. S. Gil, J. C. Werth, J. C. Pont, M. N. Garty, G. Scheuermann, E. A. Turner, H. C. Cocola, P. J. Grice, C. June, V. M. Vaccaro, C. A. Tashner, B. E. Hewitt, F. C. 2026-01-30 doi:10.64898/2026.01.29.702673 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Dissociable Effects of Early and Adolescent Adversity on Emotional Contagion ]]> https://biorxiv.org/content/10.64898/2026.01.29.702530v1?rss=1 Maldonado, P. P. Berretta, E. Canicatti, V. Feng, X. Soyman, E. Cuturela, L. I. Rajendran, R. Sadeghi, M. Babiczky, A. Goebel, G. Krugers, H. J. Keysers, C. Gazzola, V. 2026-02-02 doi:10.64898/2026.01.29.702530 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ IDH-mutant inhibitors enhance the sensitivity of IDH1-mutant gliomas to cysteine-methionine deprivation and ferroptosis ]]> https://biorxiv.org/content/10.64898/2026.01.30.702627v1?rss=1 Canoll, P. Mela, A. Brand, A. Mahajan, A. Dovas, A. Humala, N. Kanangat, S. Kleinstein, A. Leskinen, S. Nguyen, T. Gao, Q. Upadhyayula, P. Guo, J. Gill, B. Siegelin, M. Sims, P. Stockwell, B. Bruce, J. 2026-02-02 doi:10.64898/2026.01.30.702627 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Efficient task generalization and humanlike face perception in models that learn to discriminate face geometry ]]> https://biorxiv.org/content/10.64898/2026.01.31.703048v1?rss=1 Lee, S. Ying, Z. Dey, A. Jeon, Y.-N. Issa, E. B. 2026-02-03 doi:10.64898/2026.01.31.703048 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain ]]> https://biorxiv.org/content/10.64898/2026.02.02.703166v1?rss=1 750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. C_LI ]]> Xie, Y. Chang, L. Zhong, G. Rink, J. A. Baez-Becerra, T. Armand, E. Ding, W. Li, K. Boone, E. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Huang, B. Wang, Z. Barcoma, A. S. Willier, J. K. Knutson, K. W. Liu, J. Cho, S. Cao, S. Russo, K. G. Young, C. K. Arzavala, J. Sanchez, Y. Bikkina, A. Schenker-Ahmed, N. Kern, C. Zhao, Z. Klein, A. Flores, J. Tai, C.-Y. Olness, J. Monell, A. Moghadami, S. Barragan, C. Chen, C. Owens, W. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Emerson, N. Osteen, J. Lucero, J. Li, D. Hodge, R. D. Wang, T. Keene, 2026-02-03 doi:10.64898/2026.02.02.703166 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia ]]> https://biorxiv.org/content/10.64898/2026.02.03.703645v1?rss=1 Chang, L. Li, K. Xie, Y. Zhong, G. Rink, J. A. Baez-Becerra, C. T. Lie, A. Indralingam, H. S. Dong, K. Loe, T. Wang, Z. Zu, S. Kern, J. C. Zhao, Z. Boone, E. Flores, J. Monell, A. Olness, J. Barragan, C. Osgood, E. Owens, W. Schenker-Ahmed, N. Zhang, W. Liu, D. Barcoma, A. S. Willier, J. K. Knutson, K. W. Russo, K. G. Liu, J. Cho, S. Arzavala, J. Young, C. K. Sundaram, G. V. Manning, A. C. Sanchez, Y. Bikkina, A. Berry, J. Gao, X. OConnor, C. Liem, M. Marrin, M. V. Rose, C. Alt, S. N. Zhu, C. Zemke, N. R. Ding, W. Klein, A. Fu, Y. Johansen, N. B 2026-02-04 doi:10.64898/2026.02.03.703645 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ ACE-2-like Enzymatic Activity in Anti-SARS-CoV-2 Spike Protein Monoclonal Antibodies ]]> https://biorxiv.org/content/10.64898/2026.02.02.703244v1?rss=1 Song, Y. Mehl, F. No, T. Livingston, L. Quintero Barbosa, J. S. Hayashi, J. Serrero, G. Bortz, P. S. Wilson, J. Crowe, J. E. Ho, D. D. Yin, M. T. Tan, J. Zeichner, S. L. 2026-02-05 doi:10.64898/2026.02.02.703244 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Gum Odina, a novel prebiotic, promotes the expression of sealing tight junction proteins in colon organoids developed from the C57BL/6 mice model ]]> https://biorxiv.org/content/10.64898/2026.02.03.703214v1?rss=1 Sikdar, S. Dutta, P. Mitra, D. Samanta, A. 2026-02-05 doi:10.64898/2026.02.03.703214 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in post-streptococcal encephalitis ]]> https://biorxiv.org/content/10.64898/2026.02.04.703836v1?rss=1 Wayne, C. R. Akcan, U. Faust, T. E. Duran-Laforet, V. Jamoul, D. Bremner, L. Ampatey, N. Akcan, B. Ho, S. J. Ciric, B. Delaney, S. Vargas, W. S. Swedo, S. Menon, V. Schafer, D. P. Cutforth, T. Agalliu, D. 2026-02-07 doi:10.64898/2026.02.04.703836 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Engineered probiotics for tumor-targeted combination chemoimmunotherapy ]]> https://biorxiv.org/content/10.64898/2026.02.04.703875v1?rss=1 Yang, Z. Im, J. Chen, N. Mariuzza, D. L. de los Santos-Alexis, K. Li, F. Danino, T. Arpaia, N. 2026-02-07 doi:10.64898/2026.02.04.703875 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Bidirectional allosteric ligand regulation in a central glycolytic enzyme ]]> https://biorxiv.org/content/10.64898/2026.02.05.704047v1?rss=1 Sundberg, B. Lu, C. Wells, M. L. Weber, K. C. Gong, Z. Glasgow, A. 2026-02-08 doi:10.64898/2026.02.05.704047 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ Results of a large scale study of the binding of 50 type IIinhibitors to 348 kinases: The role of protein reorganization ]]> https://biorxiv.org/content/10.64898/2026.02.05.704068v1?rss=1 Vardanyan, V. H. Haldane, A. Hwang, H. Coskun, D. Lihan, M. Miller, E. B. Friesner, R. A. Levy, R. M. 2026-02-08 doi:10.64898/2026.02.05.704068 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ When attention falters: brain, breathing, and behavioral signals of lapses in interoceptive attention ]]> https://biorxiv.org/content/10.64898/2026.02.07.704566v1?rss=1 0.75). Breathing variability and breathing-behavior coupling showed smaller but generalizable predictive value (AUCs < 0.65). Whole-brain connectivity models also predicted lapses (AUC {approx} 0.65) and incorporated regions within the DMN, dorsal, and ventral attention networks--overlapping with systems implicated in exteroceptive attention-- as well as the somatomotor network. Further, models that included brain connectivity marginally outperformed behavior-only models. Together, these findings suggest that interoceptive lapses reflect both shared mechanisms with exteroceptive attention failures and additional contributions from brain systems involved in bodily representation and sensory pathways. Although generalizability is limited by the clinical sample and absence of an exteroceptive comparison task, these results highlight candidate brain-body markers of interoceptive attention that may inform real-time monitoring during mind-body interventions and improve understanding of interoceptive disturbance in affective disorders. ]]> Treves, I. N. Shaffer, C. Decker, A. Jaffe, N. Tierney, A. O. Auerbach, R. P. Webb, C. A. 2026-02-10 doi:10.64898/2026.02.07.704566 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ LineageSim: A Single-Cell Lineage Simulator with Fate-Aware Gene Expression ]]> https://biorxiv.org/content/10.64898/2026.02.08.704635v1?rss=1 Lai, H. Sadria, M. 2026-02-10 doi:10.64898/2026.02.08.704635 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[ A pilot study for whole proteome tagging in C. elegans ]]> https://biorxiv.org/content/10.64898/2026.02.09.704846v1?rss=1 Eroglu, M. Hobert, O. 2026-02-10 doi:10.64898/2026.02.09.704846 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ 3D Visualization and Proteomic Analysis of Human Cardiac Transthyretin Amyloidosis Tissue Reveals Microangiopathy and Capillary Occlusion ]]> https://biorxiv.org/content/10.64898/2026.02.09.704431v1?rss=1 Donnelly, J. P. Schaefer, J.-H. Yoon, L. Massey, L. Ash, C. Gao, Z. Nugroho, K. Jaeger, M. Pang, Z. O'Neill, R. T. Maurer, M. S. Powers, E. Lander, G. C. Ye, L. Kelly, J. W. 2026-02-11 doi:10.64898/2026.02.09.704431 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ miR-940 suppresses ferroptosis by controlling expression of key regulatory genes ]]> https://biorxiv.org/content/10.64898/2026.02.09.704912v1?rss=1 Kolak, A. Tschuck, J. Weiss, S. A. Kaemena, D. Klimm, K. Galhoz, A. Ringelstetter, L. Fennell, M. Merl-Pham, J. Artati, A. Strasser, S. Garippa, R. Witting, M. Zischka, H. Schick, J. A. Hauck, S. M. Menden, M. P. Vincendeau, M. Stockwell, B. R. Hadian, K. 2026-02-11 doi:10.64898/2026.02.09.704912 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ External validation and time-stability analysis of STARE, a blood-free quantification tool for irreversible PET tracers ]]> https://biorxiv.org/content/10.64898/2026.02.09.704936v1?rss=1 Laurell, G. L. Bartlett, E. A. Schmidt, M. Anishenko, S. Shkolnik, I. Ogden, R. T. Mann, J. J. Beylin, D. Miller, J. M. Zanderigo, F. 2026-02-11 doi:10.64898/2026.02.09.704936 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Grasping at the organization of object knowledge: testing different object-related dimensions as organizational principles of ventral temporal cortex. ]]> https://biorxiv.org/content/10.64898/2026.02.10.705013v1?rss=1 Serriere, L. Argiris, G. Gomes, J. Giorjiani, G. Bergstrom, F. Walbrin, J. Almeida, J. 2026-02-11 doi:10.64898/2026.02.10.705013 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Chromosomal instability and chromosome 17p loss drive convergentNDE1 synthetic lethality in metastatic cancer cells ]]> https://biorxiv.org/content/10.64898/2026.02.10.704921v1?rss=1 Teddy, C. M. Hoj, J. P. Caci, J. Lu, M. Killarney, S. T. Ben-Yishay, T. Ben-David, U. M. Wood, K. C. 2026-02-12 doi:10.64898/2026.02.10.704921 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ 4,5-dihydroxyhexanoic acid is a robust circulating and urine marker of mitochondrial disease and its severity ]]> https://biorxiv.org/content/10.64898/2026.02.10.705117v1?rss=1 90% of detected features in modern metabolomics experiments and hold immense untapped promise for new basic and biomedical research. We recently used mass spectrometry-based metabolomics to identify and validate 19 circulating blood-based biomarkers for patients with the mitochondrial DNA (mtDNA) m.3243A>G pathogenic variant, which is the most frequent cause of the mitochondrial disorder MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). However, the most significantly changing biomarker corresponded to an "unknown" metabolite. Here, we combine cheminformatics with analytical chemistry and identify that feature as 4,5-dihydroxyhexanoic acid (4,5-DHHA), a metabolite previously associated with inherited defects of gamma-aminobutyric acid (GABA) catabolism, but with no prior links to mitochondrial respiratory chain disorders. We validate this finding in an independent MELAS cohort and further show that 4,5-DHHA levels correlate with disease severity and are elevated in patients with other forms of mitochondrial disease and sepsis. Furthermore, brain 4,5-DHHA levels were elevated in two genetic mouse models of mitochondrial disease. In vitro and tissue culture experiments indicate that 4,5-DHHA is generated when the GABA catabolite succinic semialdehyde reacts with an intermediate of the pyruvate dehydrogenase reaction and is sensitive to mitochondrial complex I function. Our work identifies 4,5-DHHA as a robust plasma and urine marker of mitochondrial dysfunction in humans and reveals new connections between the respiratory chain and GABA metabolism. Significance StatementInborn errors of the mitochondrial respiratory chain cause severe, progressive diseases, yet effective treatments and biomarkers remain limited. Modern metabolomics detects thousands of molecules in biofluids, but the vast majority are unidentified. In this study, we investigate the most significantly altered blood metabolite in patients with the most common mitochondrial disease - MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) - and identify it as an 4,5-dihydroxyhexanoic acid (4,5-DHHA). We show that 4,5-DHHA is reproducibly elevated and correlates with severity. Levels are increased across multiple mitochondrial disorders as well as in sepsis and rise when respiratory chain function is impaired. These findings establish 4,5-DHHA as a promising biomarker of mitochondrial dysfunction and reveal a link to dysregulated GABA metabolism. ]]> Skinner, O. S. Miranda, M. Dong, F. Struhl, T. Walker, M. A. Schleifer, G. Henke, M. T. Clardy, J. Hirano, M. De Vivo, D. C. Schon, E. A. Engelstad, K. Siegmund, S. E. Laprise, C. Des Rosiers, C. Sharma, R. Mootha, V. K. 2026-02-12 doi:10.64898/2026.02.10.705117 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ SMARCAL1 is a candidate therapeutic target for ALT-positive tumors ]]> https://biorxiv.org/content/10.64898/2026.02.15.704070v1?rss=1 Taglialatela, A. Lee, J. Azeroglu, B. Chen, X. Dello Stritto, M. R. Gouge, A. Lama-Diaz, T. Vaitsiankova, A. Leuzzi, G. Dela Cruz, F. Khan, Z. F. Kung, A. L. Cejka, P. Denchi, E. L. Min, J. Ciccia, A. 2026-02-16 doi:10.64898/2026.02.15.704070 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Privacy-Preserving Pangenome Graphs ]]> https://biorxiv.org/content/10.64898/2026.02.16.706152v1?rss=1 Blindenbach, J. Soni, S. Gursoy, G. 2026-02-18 doi:10.64898/2026.02.16.706152 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Private Information Leakage from Polygenic Risk Scores ]]> https://biorxiv.org/content/10.64898/2026.02.16.706191v1?rss=1 Nikitin, K. Gursoy, G. 2026-02-18 doi:10.64898/2026.02.16.706191 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Wayfarer: A multiscale framework for spatial analysis of tumor progression ]]> https://biorxiv.org/content/10.64898/2026.02.16.706245v1?rss=1 Moses, L. Herault, A. Cabon, L. Dumitrascu, B. 2026-02-18 doi:10.64898/2026.02.16.706245 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ NanoHIVSeq: A Long-Read Bioinformatics Pipeline for High-Throughput Processing of HIV Env Sequences ]]> https://biorxiv.org/content/10.64898/2026.02.17.706429v1?rss=1 99.9% or >Q30) comparable to UMI approaches. Our findings indicated that NanoHIVSeq allows flexible and simplified ONT library preparation for reproducible and efficient Env sequencing especially for large cohorts. ]]> Sheng, Z. Xiao, Q. Qiao, Y. Lu, H. McWhirter, J. Sagar, M. Wu, X. 2026-02-19 doi:10.64898/2026.02.17.706429 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Isogenic cortical organoids enable precision targeting of APP variant-specific pathways in Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2026.02.19.706886v1?rss=1 Grass, T. Cosacak, I. M. Ordureau, A. Price, F. Kavali, S. Caldarelli, A. Qiao, M. N. Vardarajan, B. N. Paulo, J. A. Marass, M. Rubin, L. L. Kizil, C. Rodriguez-Muela, N. 2026-02-20 doi:10.64898/2026.02.19.706886 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Chemical activation of mitophagy via the N-degron pathway alleviates mitochondrial neuropathies ]]> https://biorxiv.org/content/10.64898/2026.02.19.706908v1?rss=1 Kwon, S. C. Kim, B.-S. Kim, H. Kang, D. E. Lee, G. E. Jung, E. J. Lee, M. J. Son, Y. S. Park, D.-h. Park, D. Y. Lee, J. Cho, E. H. Kim, S. B. Heo, A. J. Suh, Y. H. Jang, W.-D. Han, D. Ji, C. H. Ahn, J.-Y. Kwon, Y. T. 2026-02-20 doi:10.64898/2026.02.19.706908 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A universal platform for simultaneous TCRα/β removal enables safer and more potent TCR therapies and autoimmune modeling ]]> https://biorxiv.org/content/10.64898/2026.02.19.706929v1?rss=1 90% deletion efficiency in Jurkat and primary human T cells, markedly enhancing the expression, pairing fidelity, and functional potency of transgenic receptors. Using a clinically relevant HLA-A*02:01-restricted DMF5 TCR, we show that dual TCR ablation boosts antigen-specific activation and cytotoxicity in vitro and significantly enhances tumor clearance in vivo in human immune system (HIS) mice, while preventing graft-versus-host disease (GVHD). Targeted locus amplification revealed that CRISPR-induced double-strand breaks did not alter lentiviral integration profiles, confirming genomic safety. Extending this approach to four insulin-reactive TCRs demonstrated that removal of endogenous receptors increased transduction efficiency and functional activity, with one (1E6) showing selective activation and infiltration of stem cell-derived islet grafts (SC-islets) in vivo. This study establishes a universal, safe, and scalable genome-editing platform for generating functionally precise human T cells. By integrating cancer immunotherapy and autoimmune disease modelling within a single framework, it provides a strong preclinical rationale for dual endogenous TCR removal as a route to improved specificity, safety, and therapeutic efficacy in TCR-based cell therapies. ]]> Zanetti, G. Legut, M. Chen, A. Fathi, F. Suek, N. Teteloshvili, N. Li, H. W. Ding, X. Traum, D. Kaestner, K. Hoang, R. E. Bremer, E. Sewell, A. K. Parent, A. V. Creusot, R. J. Sykes, M. Khosravi Maharlooei, M. 2026-02-20 doi:10.64898/2026.02.19.706929 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ A Scalable Design for Proximity-Inducing Molecules ]]> https://biorxiv.org/content/10.64898/2026.02.20.706349v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@132f70dorg.highwire.dtl.DTLVardef@f9aa62org.highwire.dtl.DTLVardef@12143edorg.highwire.dtl.DTLVardef@f296d4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Karaj, E. Venkatarangan, V. Sindi, S. H. Siriwongsup, S. Lee, C. Pergu, R. Vedagopuram, S. Kailass, K. Tran, K. Singh, P. Singh, S. Kawai, J. Fung, J. E. Tefera, M. Dhaliwal, R. Chaudhary, S. K. Keyes, A. Sadagopan, A. Boatner, L. Shah, N. H. Fehl, C. Backus, K. M. Choudhary, A. 2026-02-21 doi:10.64898/2026.02.20.706349 Cold Spring Harbor Laboratory Press 2026-02-21 <![CDATA[ CLADES - Contrastive Learning Augmented DifferEntial Splicing with Orthologous Positive Pairs ]]> https://biorxiv.org/content/10.64898/2026.02.20.707118v1?rss=1 Talukder, A. Keung, N. Pe'er, I. Knowles, D. A. 2026-02-21 doi:10.64898/2026.02.20.707118 Cold Spring Harbor Laboratory Press 2026-02-21 <![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[ Protein-stabilizing and neurotransmission-potentiating activities of a synaptic chaperone modify spinal muscular atrophy in model mice ]]> https://biorxiv.org/content/10.64898/2026.02.23.707472v1?rss=1 Her, Y.-R. Fuentes-Moliz, A. Kothary, R. Tabares, L. Monani, U. R. 2026-02-24 doi:10.64898/2026.02.23.707472 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Modeling patient variants of Cnot1 and Cdc42bpb results in distinct forms of congenital diaphragmatic hernia in mice ]]> https://biorxiv.org/content/10.64898/2026.02.24.707527v1?rss=1 T (p.R623W), develop dorsal diaphragmatic hernias with low (<50%) penetrance, and mutants showed alterations in mRNA isoform expression consistent with the molecular role of Cnot1 in RNA splicing. These results underscore the power of in vivo functional modeling to validate genes and patient-specific variants uncovered by patient sequencing, reveal two previously unrecognized genetic causes of CDH, and highlight the heterogeneity of different patient anatomic presentations. ]]> Bogenschutz, E. L. Carpenter, C. Wong, A. Palmer, K. Mehta, A. Ledermann, Y. Heffner, C. Snow, K. J. Bult, C. Shen, Y. Donahoe, P. K. Rowbotham, S. P. High, F. A. Chung, W. K. Murray, S. A. 2026-02-26 doi:10.64898/2026.02.24.707527 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ cGAS inhibition delays TDP-43-driven ALS Pathogenesis ]]> https://biorxiv.org/content/10.64898/2026.02.24.707791v1?rss=1 Liu, Y. Feng, W. Aikedan, A. A. Lee, S.-I. Bhagwat, M. Nagiri, R. K. Wong, M. Y. Amin, S. Qu, W. Zhu, J. Wang, S.-Y. Ye, P. Norman, K. Coronas-Samano, G. B. Olah, M. Tilgner, H. U. Sinha, S. Gan, L. 2026-02-26 doi:10.64898/2026.02.24.707791 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Sex-specific Genetic Regulatory Effects in Chickens ]]> https://biorxiv.org/content/10.64898/2026.02.26.708179v1?rss=1 Zhang, H. Lin, B. Xi, Y. Zhu, D. Peng, C. Tu, J. Liu, H. GUAN, D. Ouyang, Q. Liu, B. Fan, C. Song, Z. Meng, X. Li, H. Zheng, W. Zhu, X. An, B. Li, Z. Wang, Y. Lu, J. Wang, M. Teng, J. Lu, X. Cui, L. Li, B. Guo, S. Song, Z. Xie, K. Li, Y. Madsen, O. Ionita-Laza, I. Wright, D. Godia, M. Xiang, R. Wang, X. Hao, D. Zhang, Q. Yin, Y. Yi, G. Wang, Z. Zhou, C. Wang, Y. Sun, C. Hu, X. Yang, N. Darrington, C. Hsu, S.-H. Zhao, X. Zhou, H. van der Wijst, M. Zeng, J. Liu, L. Shi, S. Hou, Y. Zhao, G. Zhao, P. Fang, L. He, X. 2026-02-28 doi:10.64898/2026.02.26.708179 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Local GPCR density tips the balance of μ-opioid receptor trafficking ]]> https://biorxiv.org/content/10.64898/2026.02.26.708286v1?rss=1 Holsey, M. D. Bondar, A. Geggier, P. Dukas, G. V. Webb, C. M. Govindaraju, A. Mathiasen, S. Canals, M. Lambert, N. A. Asher, W. B. Javitch, J. A. 2026-02-28 doi:10.64898/2026.02.26.708286 Cold Spring Harbor Laboratory Press 2026-02-28 <![CDATA[ Direct tensile force activates Adgrl3 in a tethered agonist-dependent manner ]]> https://biorxiv.org/content/10.64898/2026.02.27.706744v1?rss=1 Mathiasen, S. Holmkvist, J. F. L. Hamel, L. Barooji, Y. F. Chung, Y. K. Regmi, R. Vejre, P. C. Rosell-Teixido, J. Martinez, K. L. Rosenkilde, M. Bendix, P. M. M. Javitch, J. A. 2026-03-01 doi:10.64898/2026.02.27.706744 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2026.02.26.708370v1?rss=1 Chen Wu, L. Hu, X. Zhan, F. Sun, C. Gonzales, J. Ofer, R. Tran, T. Verzi, M. P. Liu, L. Yang, J. 2026-03-02 doi:10.64898/2026.02.26.708370 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Therapeutic targeting inflammation linking periodontitis and atherosclerotic comorbidities using cell-free DNA-capturing nanomaterials ]]> https://biorxiv.org/content/10.64898/2026.03.01.708715v1?rss=1 Huang, H. Zhu, X. Chen, X. Chen, F. Cheng, S. Ding, S. Xiao, Y. Xie, X. Cheng, C. Yang, R. Chen, J. Liu, J. Yang, X. Yang, C. Shi, B. Shao, D. Zhao, L. Leong, K. W. 2026-03-03 doi:10.64898/2026.03.01.708715 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Disrupted O-GalNAc glycosylation as a mechanism and biomarker of SLC35A2-associated epilepsy ]]> https://biorxiv.org/content/10.64898/2026.03.02.708854v1?rss=1 Mealer, R. G. Anderson, J. J. Smith, S. L. Masters, B. M. Barth, S. H. Huizar, K. D. Sran, S. Yoon, H. Ringland, A. Muron, S. J. Bowyer, M. E. DGama, A. M. Poduri, A. P. Lidov, H. G. Yang, E. Furnari, J. Canoll, P. D. Ostendorf, A. P. Koboldt, D. C. Pierson, C. R. Thomas, D. L. Philpot, B. D. Noel, M. Cummings, R. D. Heinzen, E. L. Bedrosian, T. A. 2026-03-04 doi:10.64898/2026.03.02.708854 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Adaptive integration of model-based and model-free strategies in human reinforcement learning of reachable space ]]> https://biorxiv.org/content/10.64898/2026.03.02.709046v1?rss=1 Zhu, T. Syan, R. Vejandla, S. Gallivan, J. P. Wolpert, D. M. Flanagan, J. R. 2026-03-04 doi:10.64898/2026.03.02.709046 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ CNS-resident B cells develop locally into a pro-inflammatory age-associated phenotype during aging and after stroke ]]> https://biorxiv.org/content/10.64898/2026.03.02.709112v1?rss=1 McAtee, A. Kenwood, M. Ujas, T. Colson, M. K. Watkins, J. Winford, E. Cotter, K. Britsch, D. Betz, D. Turchan-Cholewo, J. Lutshumba, J. Stuart, C. Shah, G. Runice, L. Ebbert, M. Cherra, S. J. Nelson, P. Sturgill, J. L. Monson, N. Goldberg, M. P. Stowe, A. M. 2026-03-04 doi:10.64898/2026.03.02.709112 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Defining the Antigenic Topology and Prospective Binding Breadth of Vaccination-induced SARS-CoV-2 Neutralizing Antibodies ]]> https://biorxiv.org/content/10.64898/2026.03.03.709398v1?rss=1 Jaiswal, D. Altomare, C. G. Adelsberg, D. C. Sapse, I. A. Krammer, F. Simon, V. Ellebedy, A. H. Bajic, G. 2026-03-04 doi:10.64898/2026.03.03.709398 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Toward Computationally Complete Spatial Omics ]]> https://biorxiv.org/content/10.64898/2026.03.03.709303v1?rss=1 Li, W. Mao, L. Liu, Y. Peng, F. Sachs, N. Wu, W. Yiu, S. P. T. Yan, H. Schroeder, A. Yu, X. Jin, K. Jiang, S. Chen, Z. Loth, M. Gomez, L. Lubo, I. Blank, N. Samarah, L. Basak, A. Cho, Y. W. Chen, C.-Y. Kim, D. M. Shalek, A. K. Solis Soto, L. M. Rabinowitz, J. Reilly, M. Qian, X. Thaiss, C. Maegdefessel, L. Wang, L. Kadara, H. Jiang, S. Deng, Y. Li, M. 2026-03-05 doi:10.64898/2026.03.03.709303 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma ]]> https://biorxiv.org/content/10.64898/2026.03.05.709911v1?rss=1 Taylor, B. Dong, W. Keal, T. Wang, Z. Saravanan, B. Gibbs, Z. A. Miyake, Y. Kawauchi, D. Vadla, R. Banerjee, A. Elkassih, O. Kashyap, S. Jones, B. M. Malukhina, K. Nafisi, M. Loe, T. H. Bendik, J. McAllister, T. Xie, Y. Chang, L. Chen, C. Ren, B. Furnari, F. Bintu, B. 2026-03-07 doi:10.64898/2026.03.05.709911 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Community assembly explains invasion differences between two contrasting forest types ]]> https://biorxiv.org/content/10.64898/2026.03.05.709929v1?rss=1 Poddar, U. Dong, T. Lam, K. Lee, V. Wilson, P. Gurevitch, J. D'Andrea, R. 2026-03-07 doi:10.64898/2026.03.05.709929 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ A population-scale red blood cell proteome reveals genetically encoded aging clocks predictive of hemolysis and blood donor activity ]]> https://biorxiv.org/content/10.64898/2026.03.07.710284v1?rss=1 View larger version (96K): org.highwire.dtl.DTLVardef@15bd46eorg.highwire.dtl.DTLVardef@1d7c107org.highwire.dtl.DTLVardef@1c1d870org.highwire.dtl.DTLVardef@168dc6f_HPS_FORMAT_FIGEXP M_FIG Dzieciatkowska et al. generate the first population-scale atlas of the RBC proteome across 13,000 donors and develop proteomic and metabolomic aging clocks that quantify biological age. Molecular {Delta}Age is reproducible across donations, genetically encoded and accelerated in G6PD deficiency, sickle cell trait/disease, and iron deficiency - yet reset by iron repletion, tracking with cognitive function and brain iron/myelin. RBC aging clocks predict hemolytic fragility, transfusion efficacy, and donor activity 12 years later. C_FIG HighlightsO_LIRBC proteome atlas of 13,091 donors reveals demographic and genetic programs C_LIO_LIGenetically encoded RBC aging clocks identify regulators of molecular {Delta}age C_LIO_LIMolecular aging features predict hemolysis and transfusion response across cohorts C_LIO_LIRBC molecular age forecasts long-term donor activity over a 12-year follow-up C_LI ]]> Dzieciatkowska, M. Issaian, A. V. Keele, G. R. Saviola, A. Stephenson, D. Bevers, S. Reisz, J. A. Haiman, Z. B. Nemkov, T. Fang, F. Moore, A. Deng, X. Stone, M. Kleinman, S. Norris, P. J. Wang, X. Thein, S.-L. Hod, E. A. Busch, M. P. Roubinian, N. H. Page, G. P. Hansen, K. D'Alessandro, A. 2026-03-08 doi:10.64898/2026.03.07.710284 Cold Spring Harbor Laboratory Press 2026-03-08 <![CDATA[ RhoGEF12 regulates endosomal SORL1-retromer and its inhibition is therapeutic in human neuronal models of Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2026.03.06.709427v1?rss=1 Qureshi, Y. H. Williams, C. A. Hajdu, I. Kannan, S. Govindarajan, A. Vegh, B. Petsko, G. A. Young, J. E. Zavodszky, P. Small, S. A. 2026-03-09 doi:10.64898/2026.03.06.709427 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Electrophysiologically Targeted Biopsies Reveal the Transcriptional Landscape of Focal Epilepsy ]]> https://biorxiv.org/content/10.64898/2026.03.06.708552v1?rss=1 Viswanathan, A. Murch, M. Brand, A. Furnari, J. L. Rolfe, N. W. Yadav, A. Stucke, C. H. Mahajan, A. Li, J. Kahle, A. Amini, M. Sands, T. T. Al-Dalahmah, O. Bruce, J. N. Gill, B. J. A. Feldstein, N. A. Youngerman, B. E. McKhann, G. M. Menon, V. Canoll, P. Winawer, M. Schevon, C. A. 2026-03-10 doi:10.64898/2026.03.06.708552 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Hierarchical Gating of Cortical Population Dynamics Drives Pain ]]> https://biorxiv.org/content/10.64898/2026.03.06.710170v1?rss=1 Hu, E. Sun, G. Zhu, E. Tian, C. Reyes, I. Chen, Z. S. Masurkar, A. V. Zhang, Q. wang, j. 2026-03-10 doi:10.64898/2026.03.06.710170 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Introduction to Single-cell Physiologically-Based Pharmacokinetic (scPBPK) Models ]]> https://biorxiv.org/content/10.64898/2026.03.09.710595v1?rss=1 Saini, A. Gallo, J. 2026-03-11 doi:10.64898/2026.03.09.710595 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Integrated Gait and Pose Analysis Utilizing Computer Vision for Parkinsonian Behavioral Phenotyping in Mice ]]> https://biorxiv.org/content/10.64898/2026.03.10.706230v1?rss=1 Jennings, M. J. Anigbo, A. Przedborski, S. 2026-03-11 doi:10.64898/2026.03.10.706230 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Drosophila germ band extension: a two-state reshaping mechanism ]]> https://biorxiv.org/content/10.64898/2026.03.09.710653v1?rss=1 Zhu, T. Zhu, H. O'Shaughnessy, B. 2026-03-12 doi:10.64898/2026.03.09.710653 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Context-dependent genetic regulation of gene expression in pigs ]]> https://biorxiv.org/content/10.64898/2026.03.11.710275v1?rss=1 Wang, F. Wang, C. Teng, J. Fang, L. Ionita-Laza, I. 2026-03-13 doi:10.64898/2026.03.11.710275 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals ]]> https://biorxiv.org/content/10.64898/2026.03.11.710917v1?rss=1 Lobo, M. Johansson, E. Kumari, S. Schoultz, E. Ahlinder, I. Liang, S. Carlsson, T. Johansson, B. R. Marotta, P. De Felice, M. Dahlberg, J. Guibentif, C. Fagman, H. Maehr, R. Nilsson, M. 2026-03-13 doi:10.64898/2026.03.11.710917 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ T6SS mutants exploit itaconate to support infection of phagocytes ]]> https://biorxiv.org/content/10.64898/2026.03.11.711069v1?rss=1 Prince, A. S. Beg, A. Z. Fields, B. L. Chen, Y. T. Wong Fok Lung, T. Gowdy, G. Talat, A. Khan, A. U. Shah, S. S. Lewis, I. Riquelme, S. 2026-03-13 doi:10.64898/2026.03.11.711069 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ PHGDH is a targetable driver of PDAC progression ]]> https://biorxiv.org/content/10.64898/2026.03.11.711147v1?rss=1 Kim, Y. Sun, L. J. Long, M. Caldwell, S. Maurer, H. C. Olive, K. P. Karreth, F. A. DeNicola, G. M. 2026-03-14 doi:10.64898/2026.03.11.711147 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[ CXCR4 coordinates adhesion, migration, and development of human NK cells ]]> https://biorxiv.org/content/10.64898/2026.03.12.711152v1?rss=1 Eisman, S. Grossberg, F. Koenigsberg, B. McDermott, D. van den Haak, F. Pedroza, L. Murphy, P. Mace, E. 2026-03-15 doi:10.64898/2026.03.12.711152 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction ]]> https://biorxiv.org/content/10.64898/2026.03.12.711379v1?rss=1 Su, Y. Liu, D. Menon, V. Song, B. Boccara, S. Zhang, N. Zhao, H. Zhao, J. H. Wang, L. Hu, N. Nzima, M. Katz, A. Swargam, B. K. Ament, S. A. Diao, Y. Zhang, H. Chao, L. Hon, G. Huangfu, D. Li, W. 2026-03-16 doi:10.64898/2026.03.12.711379 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ IgG Propels Atherosclerosis by Noncanonically Activating Macrophages ]]> https://biorxiv.org/content/10.64898/2026.03.13.711718v1?rss=1 Zahr, T. Zhang, K. Huang, S. Xue, C. Yu, L. Yu, Z. Li, B. Liang, D. Wang, Q. Shadrina, M. Wan, Q. Li, X. You, F. Kontorovich, A. R. Reilly, M. Hu, Z. Feng, W. Wang, L. Qiang, L. 2026-03-17 doi:10.64898/2026.03.13.711718 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Age determines NK cell fate and tissue compartmentalization to CMV infection ]]> https://biorxiv.org/content/10.64898/2026.03.16.712099v1?rss=1 Jensen, I. Redenti, B. Wells, S. Gray, J. Caron, D. Farber, D. L. 2026-03-17 doi:10.64898/2026.03.16.712099 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Age-related sleep changes in the human brain: insights from a large-scale thalamocortical model ]]> https://biorxiv.org/content/10.64898/2026.03.16.712170v1?rss=1 Navas Zuloaga, M. G. Purcell, S. M. Bazhenov, M. 2026-03-18 doi:10.64898/2026.03.16.712170 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Multi-omics characterization of vascular, neurodegenerative, and mixed neuropathology in the aging human brain ]]> https://biorxiv.org/content/10.64898/2026.03.17.712511v1?rss=1 Lee, A. J. Liu, M. Yilmaz, E. Kizil, C. Oveisgharan, S. Schneider, J. A. Bennett, D. A. Mayeux, R. Vardarajan, B. N. 2026-03-18 doi:10.64898/2026.03.17.712511 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ How attention saves energy in vision ]]> https://biorxiv.org/content/10.64898/2026.03.18.710397v1?rss=1 Butkus, E. Ying, Z. Kriegeskorte, N. 2026-03-19 doi:10.64898/2026.03.18.710397 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ RNAGAN: Train One and Get Four, Multipurpose Human RNA-Seq Analysis Tool with Enhanced Interpretability and Small Data Size Capability ]]> https://biorxiv.org/content/10.64898/2026.03.17.712527v1?rss=1 HOU, Z. Lee, V. H.-F. Kwong, D. L.-W. Guan, X. Liu, Z. Dai, W. 2026-03-20 doi:10.64898/2026.03.17.712527 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ PARG inhibition sequesters nuclear PAR-binding proteins, including XRCC1 and its partners, into nuclear condensates to elicit cytotoxicity ]]> https://biorxiv.org/content/10.64898/2026.03.18.712393v1?rss=1 Dumoulin, I. Lee, B. Zhang, C. Lin, X. Wang, Y. zha, S. 2026-03-20 doi:10.64898/2026.03.18.712393 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ The enhanced multi-tissue atlas of regulatory effects in cattle ]]> https://biorxiv.org/content/10.64898/2026.03.18.712441v1?rss=1 Li, H. Zhang, H. Zhu, D. Zhao, P. Wei, Z. Lu, J. Gong, M. Zhang, Q. Zheng, W. Liu, X. GUAN, D. Teng, J. Lin, Q. Tang, Y. Gao, Y. Zhao, S. Zhang, Z. Du, J. Fang, C. An, B. Lin, B. Zhang, H. Tian, M. Tian, J. Chen, S. Liu, W. Wang, Y. Wang, M.-S. Ibeagha-Awemu, E. M. Crooijmans, R. Derks, M. Godia, M. Madsen, O. Pausch, H. Leonard, A. S. Frantz, L. MacHugh, D. E. Grady, J. F. O. Ionita-Laza, I. Zhao, X. Guan, L. Zhou, H. Marmol-Sanchez, E. van der Wijst, M. Lu, X. Jiang, H. Yang, Z. Yang, Q. Liu, Q. Xu, C. Li, M. Hou, Y. Pan, Z. Chen, Y. Xian 2026-03-20 doi:10.64898/2026.03.18.712441 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Comprehensive classification of HCN1 variants linked to neurodevelopmental disorders with and without epilepsy ]]> https://biorxiv.org/content/10.64898/2026.03.18.712601v1?rss=1 Castelli, R. Marini, C. Porro, A. Castellini, A. Fontana, G. Saponaro, A. Cavalleri, G. Rizzi, S. Fusco, C. Parida, A. Caswell, R. Sherlaw, C. Pruna, D. Read, C. Bleakley, L. E. Howell, K. B. Scheffer, I. Cuddapah, V. A. Zeidler, S. Pavlidis, E. Pal, D. Szczaluba, K. Mirzaa, G. Couque, N. Capri, Y. Faivre, L. Tran Mau Them, F. Sirchia, F. Korff, C. M. DiFrancesco, D. Thiel, G. Depienne, C. Santoro, B. Moroni, A. 2026-03-20 doi:10.64898/2026.03.18.712601 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ During natural vision, semantic novelty modulates fixation-related processing in primate cortex ]]> https://biorxiv.org/content/10.64898/2026.03.18.712708v1?rss=1 Raghavan, V. S. Madsen, J. Nentwich, M. Leszczynski, M. Falchier, A. Bickel, S. Russ, B. E. Parra, L. C. 2026-03-20 doi:10.64898/2026.03.18.712708 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Focal adhesion kinase promotes metastasis in BRAF-mutant melanoma ]]> https://biorxiv.org/content/10.64898/2026.03.19.712212v1?rss=1 Stanley, K. A. Field, M. N. Pavek, A. M. Pettey, S. N. Medellin, A. P. Parkman, G. L. Randhahn, M. Turapov, T. Kircher, D. A. Izar, B. Young, A. VanBrocklin, M. W. Holmen, S. L. 2026-03-21 doi:10.64898/2026.03.19.712212 Cold Spring Harbor Laboratory Press 2026-03-21 <![CDATA[ Spatial polarization of endothelial ICAM-1 governs T-cell exclusion in melanoma ]]> https://biorxiv.org/content/10.64898/2026.03.19.712709v1?rss=1 Park, H.-R. Kim, S. J. Kozlov, N. Tagore, S. Wu, L. Izar, B. Kim, M. 2026-03-23 doi:10.64898/2026.03.19.712709 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Loss of Lamp2a-dependent chaperone-mediated autophagy drives dry AMD-like retinal pathology in mice and is rescued by BK channel activation ]]> https://biorxiv.org/content/10.64898/2026.03.19.712761v1?rss=1 Mir, H. A. Mahesh, G. Palanimuthu, A. Cioffi, C. L. Petrukhin, K. 2026-03-23 doi:10.64898/2026.03.19.712761 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ HOW FIVE DECADES OF LAND-COVER CHANGE RESHAPED SUITABLE HABITAT FOR PUERTO RICAN TREE SPECIES ]]> https://biorxiv.org/content/10.64898/2026.03.21.710527v1?rss=1 Moro, L. Milesi, P. Helmer, E. Uriarte, M. Muscarella, R. 2026-03-24 doi:10.64898/2026.03.21.710527 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ A comparative dataset on population genetics, traits, and distributions for nineteen Caribbean tree species ]]> https://biorxiv.org/content/10.64898/2026.03.21.713382v1?rss=1 Moro, L. Milesi, P. Cabrera Garcia, B. Clase, T. Borras Sayas, F. Gibney, E. Pina, Y. Uriarte, M. Muscarella, R. 2026-03-24 doi:10.64898/2026.03.21.713382 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ dreampy: Pseudobulk mixed-model differential expression for single-cell RNA-seq in Python ]]> https://biorxiv.org/content/10.64898/2026.03.21.713408v1?rss=1 Wells, S. B. Shahnawaz, H. Jones, J. L. 2026-03-24 doi:10.64898/2026.03.21.713408 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Coacervate droplet sequestration of heterogenous nanoplastics with elastin-like polypeptides ]]> https://biorxiv.org/content/10.64898/2026.03.21.713410v1?rss=1 Ling, N. R. Kotecha, A. Obermeyer, A. C. 2026-03-24 doi:10.64898/2026.03.21.713410 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Genetic architectures of brain-related traits are shaped by strong selective constraints ]]> https://biorxiv.org/content/10.64898/2026.03.22.713538v1?rss=1 Zhu, H. Simons, Y. B. Spence, J. P. Sella, G. Pritchard, J. K. 2026-03-25 doi:10.64898/2026.03.22.713538 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Single-cell Transcriptomic Variance Analysis Reveals Intercellular Circadian Desynchrony in the Alzheimer's Affected Human Brain ]]> https://biorxiv.org/content/10.64898/2026.03.23.713759v1?rss=1 Hollis, H. C. Veltri, A. Korac, K. Menon, V. Bennett, D. A. Ronnekleiv-Kelly, S. Kim, J. Anafi, R. C. 2026-03-25 doi:10.64898/2026.03.23.713759 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Tabula Sapiens reveals the non-coding RNA landscape across 22 human organs and tissues ]]> https://biorxiv.org/content/10.64898/2026.03.23.713770v1?rss=1 Lee, J. Mantri, M. Murthy, K. Seeker, L. A. Crowley, G. Jones, R. C. Tabula Sapiens Consortium, Quake, S. R. 2026-03-25 doi:10.64898/2026.03.23.713770 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[ Epigenetic control of S100A8/A9-driven monocytic inflammation licenses anti-leukemic functionality of immature NK cells during hematopoietic stem cell differentiation. ]]> https://biorxiv.org/content/10.64898/2026.03.25.714180v1?rss=1 Schirrmann, R. L. Stowitschek, D. Sutter, M. Lee, J.-H. Zhao, B. Lee, S.-H. Neyazi, A. Broesamle, B. F. Ginsberg, F. Krammer, P. Kuebler, A. Vogl, T. Wittkowski, H. Ahmad, S. Kraemer, B. Peter, N. Klimiankou, M. Ritter, M. Skokowa, J. Atar, D. Mace, E. Barroso Oquendo, M. Casadei, N. Guengoermues, N. Handgretinger, R. Jones, F. Holzer, U. Andre, M. C. 2026-03-27 doi:10.64898/2026.03.25.714180 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Contrasting Probabilistic and Intentional Accounts of Confidence in Perceptual Decisions ]]> https://biorxiv.org/content/10.64898/2026.03.24.714055v1?rss=1 Zylberberg, A. 2026-03-30 doi:10.64898/2026.03.24.714055 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Glutamine addiction is a therapeutic target to block emergency myelopoiesis ]]> https://biorxiv.org/content/10.64898/2026.03.26.714544v1?rss=1 Olson, O. C. Zhang, R. Proven, M. A. Swann, J. C. Huang, K. Lowry, W. E. Passegue, E. 2026-03-30 doi:10.64898/2026.03.26.714544 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Condition-matched in silico prediction of drug transcriptional responses enables mechanism-guided screening and combination discovery ]]> https://biorxiv.org/content/10.64898/2026.03.27.714886v1?rss=1 Xiao, M. He, Y. Hu, J. Zou, F. Zou, B. 2026-03-31 doi:10.64898/2026.03.27.714886 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Branch-specific axon pruning induced by Dpr4/DIP-{Theta} transneuronal interactions ]]> https://biorxiv.org/content/10.64898/2026.03.29.715068v1?rss=1 Meltzer, H. Shachar, S. Sergeeva, A. Bornstein, B. Shapira, G. Katsamba, P. S. Mannepalli, S. M. Bahna, F. Moreno, N. Alyagor, I. Berkun, V. Currier, T. A. Shapiro, L. Honig, B. Schuldiner, O. 2026-03-31 doi:10.64898/2026.03.29.715068 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ VYD2311 is a promising candidate for passive immunization against COVID-19 in immunocompromised individuals ]]> https://biorxiv.org/content/10.64898/2026.03.31.715419v1?rss=1 Mellis, I. A. Wu, M. Daniel, K. Hong, H. Guo, Y. Ho, D. D. 2026-04-01 doi:10.64898/2026.03.31.715419 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Efficient Generation of Functional TCRαβ+ Cytotoxic T Cells from hiPSCs via Small-Molecule Modulation ]]> https://biorxiv.org/content/10.64898/2026.03.31.715684v1?rss=1 Kubaczka, C. Kambli, N. K. Windisch, R. Yu, K. Zhao, Y. Wu, S. Frenis, K. Walcheck, M. Falchetti, M. Najia, M. LeBlanc, Z. C. North, T. E. Rowe, R. G. Daley, G. Q. SCHLAEGER, T. M. 2026-04-01 doi:10.64898/2026.03.31.715684 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Nanoparticle encapsulation enhances spatial distribution of Panobinostat to treat metastatic medulloblastoma via the intrathecal route ]]> https://biorxiv.org/content/10.64898/2026.03.31.715392v1?rss=1 Babayemi, O. Larson, J. D. Chaudhuri, S. Valesquez, F. Morton, J. Kuo, C.-F. Sablatura, L. K. Baquer, G. Reagan, M. S. Stopka, S. Sandberg, D. I. Agar, N. R. Sevick-Muraca, E. Wechsler-Reya, R. J. Sirianni, R. W. 2026-04-02 doi:10.64898/2026.03.31.715392 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ A neural mechanism for online discovery of latent contexts ]]> https://biorxiv.org/content/10.64898/2026.03.31.715618v1?rss=1 Hummos, A. Wang, M. B. Lu, Q. Norman, K. A. Jazayeri, M. 2026-04-02 doi:10.64898/2026.03.31.715618 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ sRQA: AN INTEGRATIVE PIPELINE FOR SYMBOLIC RECURRENCE QUANTIFICATION ANALYSIS ]]> https://biorxiv.org/content/10.64898/2026.03.31.715624v1?rss=1 Curtin, A. Merriman, E. Curtin, P. 2026-04-02 doi:10.64898/2026.03.31.715624 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Protocol for genotyping cephalopod sex using a skin swab and quantitative PCR ]]> https://biorxiv.org/content/10.64898/2026.03.31.715692v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@10797f5org.highwire.dtl.DTLVardef@18961a2org.highwire.dtl.DTLVardef@690df0org.highwire.dtl.DTLVardef@1122899_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Montague, T. G. Rubino, F. A. Gibbons, C. J. Mungioli, T. J. Small, S. T. Coffing, G. C. Kern, A. D. 2026-04-02 doi:10.64898/2026.03.31.715692 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Double Mutations in Plasmodium falciparum Kelch13 drive resistance to next-generation artemisinin derivatives in malaria parasites ]]> https://biorxiv.org/content/10.64898/2026.04.02.716214v1?rss=1 Bower-Lepts, C. Ward, K. E. Wittlin, S. Stokes, B. H. Yeo, T. Qahash, T. Small-Saunders, J. L. Park, H. Uhlemann, A.-C. Llinas, M. Fidock, D. A. Mok, S. 2026-04-03 doi:10.64898/2026.04.02.716214 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Harnessing within-cultivar variation to identify hidden genetic resistance using single plant-omics ]]> https://biorxiv.org/content/10.64898/2026.04.02.710456v1?rss=1 Redmond, E. J. Li, M. Holden, S. Awan, M. J. A. Zhang, Y. Gill, J. S. Virhia, J. Hargreaves, J. Danks, P. Sleath, B. Subramaniam, R. Hicks, C. Overy, D. P. Brar, G. S. Ezer, D. 2026-04-06 doi:10.64898/2026.04.02.710456 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ PRISM: A High-Throughput Simulation Infrastructure for CADD Agents ]]> https://biorxiv.org/content/10.64898/2026.04.02.716083v1?rss=1 Shi, Z. Gao, X. Xu, M. Zhu, X. Wang, P. Yang, Y. Yang, Z. Zhou, R. 2026-04-06 doi:10.64898/2026.04.02.716083 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Comparative single cell analysis of wound and cancer identifies the metabolic dialogues between tumor initiating stem cells and macrophages ]]> https://biorxiv.org/content/10.64898/2026.04.02.716187v1?rss=1 Guo, W. Leon, D. Nicholson, B. Que, J. Miao, Y. P. 2026-04-06 doi:10.64898/2026.04.02.716187 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Regulation of Nucleus Pulposus Cell Phenotype Through RhoA Signaling and Microenvironment ]]> https://biorxiv.org/content/10.64898/2026.04.05.716233v1?rss=1 Bond, G. Kim, M. K. M. Lisiewski, L. Jacobsen, T. Chahine, N. 2026-04-07 doi:10.64898/2026.04.05.716233 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Hierarchical decoding of targeting tripeptide motif by the cytosolic iron-sulfur cluster assembly targeting complex ]]> https://biorxiv.org/content/10.64898/2026.04.06.716496v1?rss=1 Buzuk, A. Khan, O. Kang, S. Yim, L. Vajda, S. Perlstein, D. 2026-04-08 doi:10.64898/2026.04.06.716496 Cold Spring Harbor Laboratory Press 2026-04-08 <![CDATA[ High-Low training is safe and effective in improving outcomes in a rodent model of chronic cervical spinal cord injury. ]]> https://biorxiv.org/content/10.64898/2026.04.06.716770v1?rss=1 Britsch, D. R. S. Cotter, K. M. Stuart, C. M. J. Turchan-Cholewo, J. Colson, M. K. Winford, E. D. Ujas, T. A. Lutshumba, J. Calulot, C. Gensel, J. C. Alilain, W. Stowe, A. 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